Multiple sequence alignment - TraesCS5A01G013200

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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 TraesCS5A01G013200 chr5A 100.000 2682 0 0 1 2682 8919081 8916400 0.000000e+00 4953.0
1 TraesCS5A01G013200 chr5A 86.084 309 33 10 1784 2086 588559423 588559727 9.260000e-85 324.0
2 TraesCS5A01G013200 chr3D 91.158 950 72 10 1 943 597882634 597883578 0.000000e+00 1279.0
3 TraesCS5A01G013200 chr6B 91.121 946 74 8 1 941 137522450 137523390 0.000000e+00 1273.0
4 TraesCS5A01G013200 chr6B 100.000 29 0 0 2653 2681 694538075 694538047 1.000000e-03 54.7
5 TraesCS5A01G013200 chr3B 90.938 949 73 9 1 943 639558297 639557356 0.000000e+00 1264.0
6 TraesCS5A01G013200 chr3B 88.912 947 99 5 1 945 168678538 168679480 0.000000e+00 1162.0
7 TraesCS5A01G013200 chr3B 96.774 31 1 0 2651 2681 538074127 538074157 5.000000e-03 52.8
8 TraesCS5A01G013200 chrUn 90.756 952 72 9 1 946 277341895 277340954 0.000000e+00 1256.0
9 TraesCS5A01G013200 chrUn 82.857 350 50 7 1086 1431 262807926 262808269 3.350000e-79 305.0
10 TraesCS5A01G013200 chrUn 81.766 351 51 9 1086 1431 262807203 262807545 5.650000e-72 281.0
11 TraesCS5A01G013200 chr4A 90.737 950 76 9 1 943 680409228 680408284 0.000000e+00 1256.0
12 TraesCS5A01G013200 chr4A 87.658 316 37 2 1784 2098 620065269 620064955 1.520000e-97 366.0
13 TraesCS5A01G013200 chr4A 86.076 316 34 3 1784 2098 619723417 619723723 5.530000e-87 331.0
14 TraesCS5A01G013200 chr4A 100.000 29 0 0 2653 2681 575399432 575399460 1.000000e-03 54.7
15 TraesCS5A01G013200 chr7B 89.546 947 89 8 1 943 645345941 645345001 0.000000e+00 1192.0
16 TraesCS5A01G013200 chr7B 92.105 38 2 1 2644 2681 558923798 558923762 5.000000e-03 52.8
17 TraesCS5A01G013200 chr3A 89.820 943 77 13 1 937 65462973 65463902 0.000000e+00 1192.0
18 TraesCS5A01G013200 chr1D 89.263 950 78 15 1 943 389481487 389482419 0.000000e+00 1168.0
19 TraesCS5A01G013200 chr5D 83.239 1056 118 29 1637 2653 10753198 10754233 0.000000e+00 915.0
20 TraesCS5A01G013200 chr5D 87.171 304 36 3 1784 2086 548688517 548688818 2.560000e-90 342.0
21 TraesCS5A01G013200 chr5D 80.879 455 62 14 1666 2098 548841224 548840773 4.280000e-88 335.0
22 TraesCS5A01G013200 chr5D 95.238 105 5 0 1359 1463 10752895 10752999 1.650000e-37 167.0
23 TraesCS5A01G013200 chr2A 83.403 476 71 6 980 1455 71447532 71447065 4.100000e-118 435.0
24 TraesCS5A01G013200 chr2B 83.125 480 73 6 980 1459 110140398 110139927 5.300000e-117 431.0
25 TraesCS5A01G013200 chr2B 85.714 273 33 5 1782 2052 502785895 502785627 1.570000e-72 283.0
26 TraesCS5A01G013200 chr2B 100.000 30 0 0 2652 2681 104014040 104014069 3.730000e-04 56.5
27 TraesCS5A01G013200 chr2B 94.444 36 1 1 2647 2681 418663698 418663733 1.000000e-03 54.7
28 TraesCS5A01G013200 chr2D 82.917 480 74 6 980 1459 72965937 72965466 2.470000e-115 425.0
29 TraesCS5A01G013200 chr5B 87.948 307 34 3 1784 2089 692905422 692905118 2.540000e-95 359.0
30 TraesCS5A01G013200 chr5B 84.765 361 48 5 2304 2661 11331138 11330782 3.280000e-94 355.0
31 TraesCS5A01G013200 chr5B 87.025 316 39 2 1784 2098 692917592 692917278 3.280000e-94 355.0
32 TraesCS5A01G013200 chr5B 100.000 28 0 0 2654 2681 35757808 35757781 5.000000e-03 52.8
33 TraesCS5A01G013200 chr7D 82.464 422 48 11 1666 2064 480439050 480439468 1.980000e-91 346.0
34 TraesCS5A01G013200 chr1B 100.000 32 0 0 2650 2681 111669146 111669115 2.880000e-05 60.2
35 TraesCS5A01G013200 chr4B 100.000 30 0 0 2652 2681 41535725 41535754 3.730000e-04 56.5


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 TraesCS5A01G013200 chr5A 8916400 8919081 2681 True 4953 4953 100.0000 1 2682 1 chr5A.!!$R1 2681
1 TraesCS5A01G013200 chr3D 597882634 597883578 944 False 1279 1279 91.1580 1 943 1 chr3D.!!$F1 942
2 TraesCS5A01G013200 chr6B 137522450 137523390 940 False 1273 1273 91.1210 1 941 1 chr6B.!!$F1 940
3 TraesCS5A01G013200 chr3B 639557356 639558297 941 True 1264 1264 90.9380 1 943 1 chr3B.!!$R1 942
4 TraesCS5A01G013200 chr3B 168678538 168679480 942 False 1162 1162 88.9120 1 945 1 chr3B.!!$F1 944
5 TraesCS5A01G013200 chrUn 277340954 277341895 941 True 1256 1256 90.7560 1 946 1 chrUn.!!$R1 945
6 TraesCS5A01G013200 chrUn 262807203 262808269 1066 False 293 305 82.3115 1086 1431 2 chrUn.!!$F1 345
7 TraesCS5A01G013200 chr4A 680408284 680409228 944 True 1256 1256 90.7370 1 943 1 chr4A.!!$R2 942
8 TraesCS5A01G013200 chr7B 645345001 645345941 940 True 1192 1192 89.5460 1 943 1 chr7B.!!$R2 942
9 TraesCS5A01G013200 chr3A 65462973 65463902 929 False 1192 1192 89.8200 1 937 1 chr3A.!!$F1 936
10 TraesCS5A01G013200 chr1D 389481487 389482419 932 False 1168 1168 89.2630 1 943 1 chr1D.!!$F1 942
11 TraesCS5A01G013200 chr5D 10752895 10754233 1338 False 541 915 89.2385 1359 2653 2 chr5D.!!$F2 1294

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
466 467 0.259938 GTTGGGGATCAAGGCTCCAT 59.740 55.0 0.0 0.0 35.8 3.41 F
1253 1268 0.035439 AACGTGGTGCTTATGGAGGG 60.035 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1488 0.107945 AATCAACTCTCGAGGCTGGC 60.108 55.0 13.56 0.0 0.00 4.85 R
2656 2771 0.032813 TCCGGACGGAGGGAGTATTT 60.033 55.0 9.76 0.0 39.76 1.40 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
31 32 6.712547 AGTTGAAGAAGGTGAATTACTTGGAG 59.287 38.462 0.00 0.00 0.00 3.86
265 266 4.399004 AGTGCATACTCAGATTCTGACC 57.601 45.455 12.38 0.61 35.39 4.02
335 336 3.593442 TCTGGGATCAAACCTTGTGTT 57.407 42.857 0.00 0.00 39.43 3.32
339 340 4.991776 TGGGATCAAACCTTGTGTTATGA 58.008 39.130 0.00 0.00 35.67 2.15
372 373 3.515630 ACATGCTACTGTGTCAAGATCG 58.484 45.455 0.00 0.00 0.00 3.69
466 467 0.259938 GTTGGGGATCAAGGCTCCAT 59.740 55.000 0.00 0.00 35.80 3.41
591 592 6.509656 TGTAAGAGAAAGAGTAGCACGAAAA 58.490 36.000 0.00 0.00 0.00 2.29
627 628 5.365021 AGTTTATTCCCACAGGAGATCAG 57.635 43.478 0.00 0.00 45.19 2.90
638 639 0.945813 GGAGATCAGCTTGCTGATGC 59.054 55.000 33.97 25.49 43.38 3.91
684 685 8.478877 ACGAGGAGAATAAATGAGTTCAAGTAT 58.521 33.333 0.00 0.00 0.00 2.12
714 715 6.652205 AACCTGGAGAAAATTCCATAGGTA 57.348 37.500 0.00 0.00 45.80 3.08
759 760 3.143211 AGGATACGTAGAGGTAGCAGG 57.857 52.381 0.08 0.00 46.39 4.85
760 761 2.709934 AGGATACGTAGAGGTAGCAGGA 59.290 50.000 0.08 0.00 46.39 3.86
761 762 3.331294 AGGATACGTAGAGGTAGCAGGAT 59.669 47.826 0.08 0.00 46.39 3.24
800 807 6.529829 CCGTTTCTATCTCTTCTTCTGTTCTG 59.470 42.308 0.00 0.00 0.00 3.02
801 808 7.087639 CGTTTCTATCTCTTCTTCTGTTCTGT 58.912 38.462 0.00 0.00 0.00 3.41
827 840 4.282496 TCTCCTCCAAGTTGTATCTCTCC 58.718 47.826 1.45 0.00 0.00 3.71
885 900 1.302993 TTAAGCCACGGCAACCCTC 60.303 57.895 11.35 0.00 44.88 4.30
943 958 5.390567 CCAACGCTTCCTATCAAACTTACAC 60.391 44.000 0.00 0.00 0.00 2.90
944 959 5.148651 ACGCTTCCTATCAAACTTACACT 57.851 39.130 0.00 0.00 0.00 3.55
945 960 5.169295 ACGCTTCCTATCAAACTTACACTC 58.831 41.667 0.00 0.00 0.00 3.51
946 961 5.047235 ACGCTTCCTATCAAACTTACACTCT 60.047 40.000 0.00 0.00 0.00 3.24
947 962 5.289675 CGCTTCCTATCAAACTTACACTCTG 59.710 44.000 0.00 0.00 0.00 3.35
948 963 5.064071 GCTTCCTATCAAACTTACACTCTGC 59.936 44.000 0.00 0.00 0.00 4.26
949 964 4.744570 TCCTATCAAACTTACACTCTGCG 58.255 43.478 0.00 0.00 0.00 5.18
950 965 4.219944 TCCTATCAAACTTACACTCTGCGT 59.780 41.667 0.00 0.00 0.00 5.24
951 966 4.563184 CCTATCAAACTTACACTCTGCGTC 59.437 45.833 0.00 0.00 0.00 5.19
952 967 3.446310 TCAAACTTACACTCTGCGTCA 57.554 42.857 0.00 0.00 0.00 4.35
953 968 3.990092 TCAAACTTACACTCTGCGTCAT 58.010 40.909 0.00 0.00 0.00 3.06
954 969 3.740832 TCAAACTTACACTCTGCGTCATG 59.259 43.478 0.00 0.00 0.00 3.07
955 970 3.660501 AACTTACACTCTGCGTCATGA 57.339 42.857 0.00 0.00 0.00 3.07
956 971 2.947852 ACTTACACTCTGCGTCATGAC 58.052 47.619 16.21 16.21 0.00 3.06
957 972 2.296190 ACTTACACTCTGCGTCATGACA 59.704 45.455 24.93 6.25 0.00 3.58
958 973 3.056536 ACTTACACTCTGCGTCATGACAT 60.057 43.478 24.93 0.70 0.00 3.06
959 974 2.462456 ACACTCTGCGTCATGACATT 57.538 45.000 24.93 0.00 0.00 2.71
960 975 2.341257 ACACTCTGCGTCATGACATTC 58.659 47.619 24.93 13.52 0.00 2.67
961 976 2.028658 ACACTCTGCGTCATGACATTCT 60.029 45.455 24.93 0.00 0.00 2.40
962 977 2.602211 CACTCTGCGTCATGACATTCTC 59.398 50.000 24.93 8.93 0.00 2.87
963 978 2.495270 ACTCTGCGTCATGACATTCTCT 59.505 45.455 24.93 0.70 0.00 3.10
964 979 3.114809 CTCTGCGTCATGACATTCTCTC 58.885 50.000 24.93 5.74 0.00 3.20
965 980 2.159184 TCTGCGTCATGACATTCTCTCC 60.159 50.000 24.93 3.80 0.00 3.71
966 981 1.134699 TGCGTCATGACATTCTCTCCC 60.135 52.381 24.93 2.85 0.00 4.30
967 982 1.845266 CGTCATGACATTCTCTCCCG 58.155 55.000 24.93 3.73 0.00 5.14
968 983 1.536922 CGTCATGACATTCTCTCCCGG 60.537 57.143 24.93 0.00 0.00 5.73
969 984 1.123077 TCATGACATTCTCTCCCGGG 58.877 55.000 16.85 16.85 0.00 5.73
970 985 1.123077 CATGACATTCTCTCCCGGGA 58.877 55.000 25.06 25.06 0.00 5.14
971 986 1.069823 CATGACATTCTCTCCCGGGAG 59.930 57.143 40.33 40.33 43.21 4.30
1003 1018 4.166011 GTCCGCATGCGCCTGTTC 62.166 66.667 34.00 15.04 38.24 3.18
1004 1019 4.695993 TCCGCATGCGCCTGTTCA 62.696 61.111 34.00 8.24 38.24 3.18
1005 1020 3.511595 CCGCATGCGCCTGTTCAT 61.512 61.111 34.00 0.00 38.24 2.57
1006 1021 2.277692 CGCATGCGCCTGTTCATG 60.278 61.111 29.09 6.66 42.08 3.07
1008 1023 2.879168 CATGCGCCTGTTCATGCA 59.121 55.556 4.18 0.00 42.22 3.96
1009 1024 1.515519 CATGCGCCTGTTCATGCAC 60.516 57.895 4.18 0.00 40.61 4.57
1010 1025 3.042842 ATGCGCCTGTTCATGCACG 62.043 57.895 4.18 0.00 40.61 5.34
1011 1026 3.422303 GCGCCTGTTCATGCACGA 61.422 61.111 0.00 0.00 0.00 4.35
1012 1027 2.780643 CGCCTGTTCATGCACGAG 59.219 61.111 0.00 0.00 0.00 4.18
1013 1028 2.743752 CGCCTGTTCATGCACGAGG 61.744 63.158 8.76 8.76 0.00 4.63
1014 1029 1.672356 GCCTGTTCATGCACGAGGT 60.672 57.895 12.73 0.00 0.00 3.85
1015 1030 1.915614 GCCTGTTCATGCACGAGGTG 61.916 60.000 12.73 0.00 36.51 4.00
1040 1055 4.408821 GCCCAGGTGCCACGATGA 62.409 66.667 0.00 0.00 0.00 2.92
1041 1056 2.591753 CCCAGGTGCCACGATGAT 59.408 61.111 0.00 0.00 0.00 2.45
1042 1057 1.820906 CCCAGGTGCCACGATGATG 60.821 63.158 0.00 0.00 0.00 3.07
1043 1058 1.820906 CCAGGTGCCACGATGATGG 60.821 63.158 0.00 0.00 43.26 3.51
1044 1059 1.820906 CAGGTGCCACGATGATGGG 60.821 63.158 0.00 0.00 40.43 4.00
1045 1060 2.516930 GGTGCCACGATGATGGGG 60.517 66.667 0.00 0.00 40.43 4.96
1046 1061 2.516930 GTGCCACGATGATGGGGG 60.517 66.667 0.00 0.00 40.43 5.40
1047 1062 3.014538 TGCCACGATGATGGGGGT 61.015 61.111 0.00 0.00 40.43 4.95
1048 1063 2.203209 GCCACGATGATGGGGGTC 60.203 66.667 0.00 0.00 40.43 4.46
1049 1064 2.108976 CCACGATGATGGGGGTCG 59.891 66.667 0.00 0.00 40.91 4.79
1051 1066 1.227263 CACGATGATGGGGGTCGTC 60.227 63.158 0.00 0.00 45.72 4.20
1052 1067 1.684391 ACGATGATGGGGGTCGTCA 60.684 57.895 0.00 0.00 44.39 4.35
1053 1068 1.261938 ACGATGATGGGGGTCGTCAA 61.262 55.000 0.00 0.00 44.39 3.18
1054 1069 0.810031 CGATGATGGGGGTCGTCAAC 60.810 60.000 0.00 0.00 43.80 3.18
1055 1070 0.810031 GATGATGGGGGTCGTCAACG 60.810 60.000 0.00 0.00 43.80 4.10
1056 1071 2.125269 GATGGGGGTCGTCAACGG 60.125 66.667 2.31 0.00 40.29 4.44
1057 1072 4.404098 ATGGGGGTCGTCAACGGC 62.404 66.667 2.31 0.00 44.28 5.68
1063 1078 4.104143 GTCGTCAACGGCATAGGG 57.896 61.111 1.69 0.00 44.43 3.53
1064 1079 2.171725 GTCGTCAACGGCATAGGGC 61.172 63.158 1.69 0.00 44.43 5.19
1073 1088 4.489771 GCATAGGGCGGTGGTGCT 62.490 66.667 0.00 0.00 33.25 4.40
1074 1089 2.514592 CATAGGGCGGTGGTGCTG 60.515 66.667 0.00 0.00 34.52 4.41
1125 1140 2.747460 CGGCAGGTGGTGGTGATG 60.747 66.667 0.00 0.00 0.00 3.07
1192 1207 1.136565 CGCATGCAGGGGTTTTACG 59.863 57.895 19.57 0.00 0.00 3.18
1198 1213 1.134037 TGCAGGGGTTTTACGTGTTCT 60.134 47.619 0.00 0.00 0.00 3.01
1201 1216 1.413812 AGGGGTTTTACGTGTTCTCGT 59.586 47.619 0.00 5.36 45.97 4.18
1204 1219 2.546584 GGGTTTTACGTGTTCTCGTCCT 60.547 50.000 0.00 0.00 43.12 3.85
1208 1223 0.386352 TACGTGTTCTCGTCCTTGCG 60.386 55.000 0.00 0.00 43.12 4.85
1229 1244 4.816990 GCCGGTGCTACTCTTCTC 57.183 61.111 1.90 0.00 33.53 2.87
1236 1251 3.526534 GGTGCTACTCTTCTCCATGAAC 58.473 50.000 0.00 0.00 0.00 3.18
1243 1258 0.798776 CTTCTCCATGAACGTGGTGC 59.201 55.000 12.02 0.00 40.27 5.01
1245 1260 0.396435 TCTCCATGAACGTGGTGCTT 59.604 50.000 12.02 0.00 40.27 3.91
1247 1262 2.236146 TCTCCATGAACGTGGTGCTTAT 59.764 45.455 12.02 0.00 40.27 1.73
1250 1265 2.355197 CATGAACGTGGTGCTTATGGA 58.645 47.619 0.00 0.00 0.00 3.41
1251 1266 2.093306 TGAACGTGGTGCTTATGGAG 57.907 50.000 0.00 0.00 0.00 3.86
1252 1267 1.338674 TGAACGTGGTGCTTATGGAGG 60.339 52.381 0.00 0.00 0.00 4.30
1253 1268 0.035439 AACGTGGTGCTTATGGAGGG 60.035 55.000 0.00 0.00 0.00 4.30
1255 1270 1.453928 GTGGTGCTTATGGAGGGGC 60.454 63.158 0.00 0.00 0.00 5.80
1256 1271 2.195956 GGTGCTTATGGAGGGGCC 59.804 66.667 0.00 0.00 37.10 5.80
1257 1272 2.203209 GTGCTTATGGAGGGGCCG 60.203 66.667 0.00 0.00 40.66 6.13
1258 1273 4.189580 TGCTTATGGAGGGGCCGC 62.190 66.667 12.88 12.88 40.66 6.53
1278 1293 3.316573 CTCCGGGAGCACCTTCACC 62.317 68.421 11.83 0.00 36.97 4.02
1283 1298 3.112709 GAGCACCTTCACCGTCGC 61.113 66.667 0.00 0.00 0.00 5.19
1308 1323 1.302431 TGACAACATGGTGGAGCCG 60.302 57.895 16.70 0.00 41.21 5.52
1311 1326 2.360350 AACATGGTGGAGCCGCTG 60.360 61.111 0.00 0.00 41.21 5.18
1399 1414 1.812922 GTGAGCTGGGAGATGCACG 60.813 63.158 0.00 0.00 0.00 5.34
1425 1440 3.982213 CGTCATCGAGTTGGACGTA 57.018 52.632 17.93 0.00 46.68 3.57
1443 1458 2.547826 GTATTTGTCTACCTCCACGCC 58.452 52.381 0.00 0.00 0.00 5.68
1463 1478 3.646976 CTCCCATGCATGAGCGCG 61.647 66.667 28.31 10.47 46.23 6.86
1488 1503 3.764466 CGGCCAGCCTCGAGAGTT 61.764 66.667 15.71 0.00 0.00 3.01
1489 1504 2.125350 GGCCAGCCTCGAGAGTTG 60.125 66.667 15.71 11.92 0.00 3.16
1490 1505 2.650116 GGCCAGCCTCGAGAGTTGA 61.650 63.158 15.71 0.00 0.00 3.18
1491 1506 1.519719 GCCAGCCTCGAGAGTTGAT 59.480 57.895 15.71 0.00 0.00 2.57
1492 1507 0.107945 GCCAGCCTCGAGAGTTGATT 60.108 55.000 15.71 0.00 0.00 2.57
1493 1508 1.677217 GCCAGCCTCGAGAGTTGATTT 60.677 52.381 15.71 0.00 0.00 2.17
1494 1509 2.704572 CCAGCCTCGAGAGTTGATTTT 58.295 47.619 15.71 0.00 0.00 1.82
1495 1510 2.675348 CCAGCCTCGAGAGTTGATTTTC 59.325 50.000 15.71 0.00 0.00 2.29
1496 1511 3.594134 CAGCCTCGAGAGTTGATTTTCT 58.406 45.455 15.71 0.00 0.00 2.52
1497 1512 4.382040 CCAGCCTCGAGAGTTGATTTTCTA 60.382 45.833 15.71 0.00 0.00 2.10
1498 1513 5.355596 CAGCCTCGAGAGTTGATTTTCTAT 58.644 41.667 15.71 0.00 0.00 1.98
1499 1514 5.461737 CAGCCTCGAGAGTTGATTTTCTATC 59.538 44.000 15.71 0.00 0.00 2.08
1500 1515 5.127845 AGCCTCGAGAGTTGATTTTCTATCA 59.872 40.000 15.71 0.00 0.00 2.15
1501 1516 5.812642 GCCTCGAGAGTTGATTTTCTATCAA 59.187 40.000 15.71 0.00 35.86 2.57
1502 1517 6.019156 GCCTCGAGAGTTGATTTTCTATCAAG 60.019 42.308 15.71 0.00 38.54 3.02
1503 1518 7.038659 CCTCGAGAGTTGATTTTCTATCAAGT 58.961 38.462 15.71 7.38 42.49 3.16
1504 1519 7.547370 CCTCGAGAGTTGATTTTCTATCAAGTT 59.453 37.037 15.71 0.00 40.59 2.66
1505 1520 8.467402 TCGAGAGTTGATTTTCTATCAAGTTC 57.533 34.615 8.70 6.57 40.59 3.01
1506 1521 8.088365 TCGAGAGTTGATTTTCTATCAAGTTCA 58.912 33.333 8.70 0.00 40.59 3.18
1507 1522 8.877779 CGAGAGTTGATTTTCTATCAAGTTCAT 58.122 33.333 8.70 0.92 40.59 2.57
1512 1527 9.774742 GTTGATTTTCTATCAAGTTCATACACC 57.225 33.333 0.71 0.00 38.54 4.16
1535 1555 0.381801 GCTACCGTTGCATGGAATGG 59.618 55.000 30.43 30.43 46.86 3.16
1538 1558 1.392589 ACCGTTGCATGGAATGGATC 58.607 50.000 36.42 9.53 46.71 3.36
1549 1569 2.575805 GAATGGATCCATCCCTCCAC 57.424 55.000 27.45 9.42 46.59 4.02
1551 1571 3.251484 GAATGGATCCATCCCTCCACTA 58.749 50.000 27.45 0.00 46.59 2.74
1552 1572 2.103153 TGGATCCATCCCTCCACTAC 57.897 55.000 11.44 0.00 46.59 2.73
1553 1573 1.293763 TGGATCCATCCCTCCACTACA 59.706 52.381 11.44 0.00 46.59 2.74
1554 1574 1.694696 GGATCCATCCCTCCACTACAC 59.305 57.143 6.95 0.00 41.20 2.90
1555 1575 1.694696 GATCCATCCCTCCACTACACC 59.305 57.143 0.00 0.00 0.00 4.16
1570 1611 5.163205 CCACTACACCTCATGGGATATCAAA 60.163 44.000 4.83 0.00 38.76 2.69
1572 1613 5.905331 ACTACACCTCATGGGATATCAAAGA 59.095 40.000 4.83 0.00 38.76 2.52
1573 1614 5.715439 ACACCTCATGGGATATCAAAGAA 57.285 39.130 4.83 0.00 38.76 2.52
1574 1615 6.271585 ACACCTCATGGGATATCAAAGAAT 57.728 37.500 4.83 0.00 38.76 2.40
1575 1616 6.066690 ACACCTCATGGGATATCAAAGAATG 58.933 40.000 4.83 1.25 38.76 2.67
1579 1620 6.548622 CCTCATGGGATATCAAAGAATGTGTT 59.451 38.462 4.83 0.00 37.23 3.32
1582 1623 8.469200 TCATGGGATATCAAAGAATGTGTTTTC 58.531 33.333 4.83 0.00 0.00 2.29
1583 1624 6.851609 TGGGATATCAAAGAATGTGTTTTCG 58.148 36.000 4.83 0.00 0.00 3.46
1584 1625 6.127758 TGGGATATCAAAGAATGTGTTTTCGG 60.128 38.462 4.83 0.00 0.00 4.30
1585 1626 6.265577 GGATATCAAAGAATGTGTTTTCGGG 58.734 40.000 4.83 0.00 0.00 5.14
1597 1640 4.202377 TGTGTTTTCGGGTTCTCCTCAATA 60.202 41.667 0.00 0.00 0.00 1.90
1622 1665 8.324163 ACATTTCTTACAGTTATGAACACTCC 57.676 34.615 0.00 0.00 0.00 3.85
1645 1688 4.260985 TGTTCGGAACTAATCATGCATGT 58.739 39.130 25.43 10.70 0.00 3.21
1648 1716 5.276461 TCGGAACTAATCATGCATGTAGT 57.724 39.130 25.43 21.91 0.00 2.73
1672 1740 9.060347 AGTATTGTGCAGGATGAGTAAATATTG 57.940 33.333 0.00 0.00 39.69 1.90
1704 1772 0.602638 TCATGGAGGTTGACACGCAC 60.603 55.000 0.00 0.00 0.00 5.34
1705 1773 0.884259 CATGGAGGTTGACACGCACA 60.884 55.000 0.00 0.00 0.00 4.57
1711 1779 3.057018 GTTGACACGCACATCAACG 57.943 52.632 7.86 0.00 43.72 4.10
1713 1781 1.194547 GTTGACACGCACATCAACGAT 59.805 47.619 7.86 0.00 43.72 3.73
1719 1787 4.463209 ACACGCACATCAACGATTAAAAG 58.537 39.130 0.00 0.00 0.00 2.27
1726 1794 7.408290 CGCACATCAACGATTAAAAGAAAAGAC 60.408 37.037 0.00 0.00 0.00 3.01
1730 1798 9.450807 CATCAACGATTAAAAGAAAAGACAACT 57.549 29.630 0.00 0.00 0.00 3.16
1744 1812 3.041211 AGACAACTATATGGCTCCAGCA 58.959 45.455 0.03 0.00 44.36 4.41
1751 1819 3.520691 ATATGGCTCCAGCAATCATGT 57.479 42.857 0.03 0.00 44.36 3.21
1755 1823 1.473257 GGCTCCAGCAATCATGTCGTA 60.473 52.381 0.03 0.00 44.36 3.43
1756 1824 1.594862 GCTCCAGCAATCATGTCGTAC 59.405 52.381 0.00 0.00 41.59 3.67
1757 1825 2.205074 CTCCAGCAATCATGTCGTACC 58.795 52.381 0.00 0.00 0.00 3.34
1766 1834 3.685836 TCATGTCGTACCATGACGTAG 57.314 47.619 9.86 0.20 44.70 3.51
1767 1835 3.272581 TCATGTCGTACCATGACGTAGA 58.727 45.455 9.86 2.05 44.70 2.59
1768 1836 3.690628 TCATGTCGTACCATGACGTAGAA 59.309 43.478 9.86 0.00 44.70 2.10
1809 1899 8.947055 ACAACAGATTGAATAAACAAAAGCTT 57.053 26.923 0.00 0.00 39.30 3.74
1832 1922 2.318908 ACCACATCACATGCAAACCTT 58.681 42.857 0.00 0.00 0.00 3.50
1837 1927 0.961019 TCACATGCAAACCTTCTGCC 59.039 50.000 0.00 0.00 39.13 4.85
1843 1933 1.208259 GCAAACCTTCTGCCAAAACG 58.792 50.000 0.00 0.00 33.51 3.60
1853 1943 0.863144 TGCCAAAACGAGTTAGACGC 59.137 50.000 0.00 0.00 0.00 5.19
1861 1951 4.715527 AACGAGTTAGACGCCTCTAATT 57.284 40.909 8.19 4.65 40.43 1.40
1862 1952 4.030134 ACGAGTTAGACGCCTCTAATTG 57.970 45.455 8.19 4.87 40.43 2.32
1877 1967 6.430451 CCTCTAATTGCTTTGCTAATTACCG 58.570 40.000 0.00 0.00 0.00 4.02
1883 1973 2.477863 GCTTTGCTAATTACCGTGGCTG 60.478 50.000 0.00 0.00 0.00 4.85
1897 1987 2.095853 CGTGGCTGCTATGGTTAAGTTG 59.904 50.000 0.00 0.00 0.00 3.16
1898 1988 2.423538 GTGGCTGCTATGGTTAAGTTGG 59.576 50.000 0.00 0.00 0.00 3.77
1904 1994 5.723295 CTGCTATGGTTAAGTTGGCAAAAT 58.277 37.500 0.00 0.00 0.00 1.82
1908 1998 8.150945 TGCTATGGTTAAGTTGGCAAAATTTTA 58.849 29.630 0.00 0.00 0.00 1.52
1910 2000 9.705290 CTATGGTTAAGTTGGCAAAATTTTACT 57.295 29.630 0.00 0.63 0.00 2.24
1915 2005 9.710979 GTTAAGTTGGCAAAATTTTACTTTTCC 57.289 29.630 17.54 7.80 0.00 3.13
1919 2009 7.436970 AGTTGGCAAAATTTTACTTTTCCTACG 59.563 33.333 0.00 0.00 32.87 3.51
1941 2031 4.333649 CGAACCATAAGCATGACACTTCAT 59.666 41.667 0.00 0.00 43.80 2.57
1966 2056 2.335316 TGGTTTAACTTGCGAGGTGT 57.665 45.000 0.21 0.00 0.00 4.16
2015 2105 6.605471 TCTCAAGCCTCATACTAAACTTCA 57.395 37.500 0.00 0.00 0.00 3.02
2022 2112 8.894768 AGCCTCATACTAAACTTCATCATTAC 57.105 34.615 0.00 0.00 0.00 1.89
2024 2114 7.438459 GCCTCATACTAAACTTCATCATTACGT 59.562 37.037 0.00 0.00 0.00 3.57
2033 2123 3.520290 TCATCATTACGTGTGACCCTC 57.480 47.619 0.00 0.00 0.00 4.30
2048 2140 5.009710 TGTGACCCTCGTGTAGATCATTATC 59.990 44.000 0.00 0.00 0.00 1.75
2064 2156 8.424918 AGATCATTATCTACATTGTCTTTCCGT 58.575 33.333 0.00 0.00 40.82 4.69
2082 2175 8.244802 TCTTTCCGTTTTTCACAAAGTTTATCA 58.755 29.630 0.00 0.00 0.00 2.15
2085 2178 8.934507 TCCGTTTTTCACAAAGTTTATCATTT 57.065 26.923 0.00 0.00 0.00 2.32
2121 2225 2.494870 AGATTTGCTTCAATCTGTGCCC 59.505 45.455 5.79 0.00 0.00 5.36
2135 2239 2.928801 GTGCCCCCACAAAAAGAAAT 57.071 45.000 0.00 0.00 41.67 2.17
2154 2258 7.251704 AGAAATATTGTGCTTATCGTGGAAG 57.748 36.000 0.00 0.00 0.00 3.46
2220 2333 5.208463 TCCAAAACCTAAGAAAACCATGC 57.792 39.130 0.00 0.00 0.00 4.06
2224 2337 6.317391 CCAAAACCTAAGAAAACCATGCAAAA 59.683 34.615 0.00 0.00 0.00 2.44
2226 2339 6.918892 AACCTAAGAAAACCATGCAAAAAC 57.081 33.333 0.00 0.00 0.00 2.43
2227 2340 5.983540 ACCTAAGAAAACCATGCAAAAACA 58.016 33.333 0.00 0.00 0.00 2.83
2262 2375 2.350964 GCATCTAAAACCCGAAAACGCA 60.351 45.455 0.00 0.00 0.00 5.24
2287 2400 4.757149 CCTTATAATCTGGGCTTTTCCTCG 59.243 45.833 0.00 0.00 34.39 4.63
2289 2402 1.026718 AATCTGGGCTTTTCCTCGCG 61.027 55.000 0.00 0.00 34.39 5.87
2290 2403 2.185310 ATCTGGGCTTTTCCTCGCGT 62.185 55.000 5.77 0.00 34.39 6.01
2291 2404 2.358247 TGGGCTTTTCCTCGCGTC 60.358 61.111 5.77 0.00 34.39 5.19
2292 2405 2.358247 GGGCTTTTCCTCGCGTCA 60.358 61.111 5.77 0.00 34.39 4.35
2293 2406 1.964373 GGGCTTTTCCTCGCGTCAA 60.964 57.895 5.77 0.00 34.39 3.18
2294 2407 1.497722 GGCTTTTCCTCGCGTCAAG 59.502 57.895 5.77 3.69 0.00 3.02
2295 2408 1.154395 GCTTTTCCTCGCGTCAAGC 60.154 57.895 5.77 10.06 43.95 4.01
2346 2459 7.561556 AGTTATGTGTTAGTTTCTTTCGTTCG 58.438 34.615 0.00 0.00 0.00 3.95
2350 2463 6.925600 TGTGTTAGTTTCTTTCGTTCGTTAG 58.074 36.000 0.00 0.00 0.00 2.34
2351 2464 6.531240 TGTGTTAGTTTCTTTCGTTCGTTAGT 59.469 34.615 0.00 0.00 0.00 2.24
2352 2465 7.063308 TGTGTTAGTTTCTTTCGTTCGTTAGTT 59.937 33.333 0.00 0.00 0.00 2.24
2426 2539 2.254546 TTTCACAAGCGTCCATCACT 57.745 45.000 0.00 0.00 0.00 3.41
2429 2542 1.276138 TCACAAGCGTCCATCACTCAT 59.724 47.619 0.00 0.00 0.00 2.90
2437 2551 6.325919 AGCGTCCATCACTCATTTTAAAAA 57.674 33.333 4.44 0.00 0.00 1.94
2599 2714 8.579682 AAGTTCACATAACTTGAGAAAAATGC 57.420 30.769 2.49 0.00 38.88 3.56
2603 2718 8.169977 TCACATAACTTGAGAAAAATGCTTCT 57.830 30.769 0.00 0.00 38.39 2.85
2610 2725 7.955918 ACTTGAGAAAAATGCTTCTTACCATT 58.044 30.769 0.00 0.00 35.76 3.16
2615 2730 6.991531 AGAAAAATGCTTCTTACCATTTGCAA 59.008 30.769 0.00 0.00 39.88 4.08
2622 2737 5.928264 GCTTCTTACCATTTGCAAGATGTTT 59.072 36.000 15.67 8.42 0.00 2.83
2673 2788 2.685850 AAAAATACTCCCTCCGTCCG 57.314 50.000 0.00 0.00 0.00 4.79
2674 2789 0.828677 AAAATACTCCCTCCGTCCGG 59.171 55.000 0.00 0.00 0.00 5.14
2675 2790 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
2676 2791 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2677 2792 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2678 2793 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2679 2794 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2680 2795 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2681 2796 1.044790 TCCCTCCGTCCGGAAATACC 61.045 60.000 5.23 0.00 44.66 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.774690 TCATTTGCTCCAAGTAATTCACCTT 59.225 36.000 0.00 0.00 0.00 3.50
31 32 7.629222 ACTCCTATAGTTTGTTGCATCATTTGC 60.629 37.037 0.00 0.00 43.64 3.68
335 336 4.081406 AGCATGTTTCCTTGCACTTCATA 58.919 39.130 0.00 0.00 42.56 2.15
339 340 3.254166 CAGTAGCATGTTTCCTTGCACTT 59.746 43.478 0.00 0.00 42.56 3.16
372 373 3.373439 CCTTGTATTCTGCTTCAGTGCTC 59.627 47.826 0.00 0.00 32.61 4.26
466 467 6.526526 TGTCACAACATAACCTTGTAGCTTA 58.473 36.000 0.00 0.00 30.48 3.09
570 571 5.602628 AGTTTTCGTGCTACTCTTTCTCTT 58.397 37.500 0.00 0.00 0.00 2.85
627 628 1.742761 TAGTGAAGGCATCAGCAAGC 58.257 50.000 0.00 0.00 44.61 4.01
638 639 3.744426 CGTGGTAAGTGGTTTAGTGAAGG 59.256 47.826 0.00 0.00 0.00 3.46
714 715 7.654287 ATTCTAACATCCTCCCTTAATCCAT 57.346 36.000 0.00 0.00 0.00 3.41
721 722 6.437793 CGTATCCTATTCTAACATCCTCCCTT 59.562 42.308 0.00 0.00 0.00 3.95
800 807 6.043854 AGATACAACTTGGAGGAGAAGAAC 57.956 41.667 0.00 0.00 0.00 3.01
801 808 6.019748 AGAGATACAACTTGGAGGAGAAGAA 58.980 40.000 0.00 0.00 0.00 2.52
827 840 3.070018 GGATGCTTCCAGATTACATCGG 58.930 50.000 13.60 0.00 42.12 4.18
844 857 5.308825 AGGTTTTGGAATATCGCTAGGATG 58.691 41.667 0.00 0.00 36.55 3.51
885 900 5.984725 TCGGGCCACATGTATATTTATAGG 58.015 41.667 4.39 0.00 0.00 2.57
919 934 4.693566 TGTAAGTTTGATAGGAAGCGTTGG 59.306 41.667 0.00 0.00 0.00 3.77
943 958 3.114809 GAGAGAATGTCATGACGCAGAG 58.885 50.000 20.54 0.00 0.00 3.35
944 959 2.159184 GGAGAGAATGTCATGACGCAGA 60.159 50.000 20.54 3.64 0.00 4.26
945 960 2.200067 GGAGAGAATGTCATGACGCAG 58.800 52.381 20.54 0.00 0.00 5.18
946 961 1.134699 GGGAGAGAATGTCATGACGCA 60.135 52.381 20.54 4.87 0.00 5.24
947 962 1.576356 GGGAGAGAATGTCATGACGC 58.424 55.000 20.54 12.38 0.00 5.19
948 963 1.536922 CCGGGAGAGAATGTCATGACG 60.537 57.143 20.54 4.82 0.00 4.35
949 964 1.202580 CCCGGGAGAGAATGTCATGAC 60.203 57.143 18.48 19.27 0.00 3.06
950 965 1.123077 CCCGGGAGAGAATGTCATGA 58.877 55.000 18.48 0.00 0.00 3.07
951 966 1.069823 CTCCCGGGAGAGAATGTCATG 59.930 57.143 42.70 14.26 44.53 3.07
952 967 1.418334 CTCCCGGGAGAGAATGTCAT 58.582 55.000 42.70 0.00 44.53 3.06
953 968 0.687757 CCTCCCGGGAGAGAATGTCA 60.688 60.000 45.77 11.75 44.53 3.58
954 969 2.034048 GCCTCCCGGGAGAGAATGTC 62.034 65.000 45.77 22.47 44.53 3.06
955 970 2.066999 GCCTCCCGGGAGAGAATGT 61.067 63.158 45.77 0.00 44.53 2.71
956 971 1.753368 GAGCCTCCCGGGAGAGAATG 61.753 65.000 45.77 30.89 44.53 2.67
957 972 1.458588 GAGCCTCCCGGGAGAGAAT 60.459 63.158 45.77 29.21 44.53 2.40
958 973 2.042843 GAGCCTCCCGGGAGAGAA 60.043 66.667 45.77 15.85 44.53 2.87
959 974 4.507916 CGAGCCTCCCGGGAGAGA 62.508 72.222 45.77 16.28 44.53 3.10
960 975 4.507916 TCGAGCCTCCCGGGAGAG 62.508 72.222 45.77 35.04 44.53 3.20
961 976 4.507916 CTCGAGCCTCCCGGGAGA 62.508 72.222 45.77 27.68 44.53 3.71
986 1001 4.166011 GAACAGGCGCATGCGGAC 62.166 66.667 38.22 23.83 44.10 4.79
987 1002 3.974835 ATGAACAGGCGCATGCGGA 62.975 57.895 38.22 5.91 44.10 5.54
988 1003 3.511595 ATGAACAGGCGCATGCGG 61.512 61.111 38.22 25.20 44.10 5.69
989 1004 2.277692 CATGAACAGGCGCATGCG 60.278 61.111 34.83 34.83 44.10 4.73
991 1006 1.515519 GTGCATGAACAGGCGCATG 60.516 57.895 22.13 22.13 46.44 4.06
992 1007 2.879907 GTGCATGAACAGGCGCAT 59.120 55.556 17.66 0.00 46.44 4.73
994 1009 3.372676 CTCGTGCATGAACAGGCGC 62.373 63.158 10.41 13.63 44.12 6.53
995 1010 2.743752 CCTCGTGCATGAACAGGCG 61.744 63.158 10.41 0.00 41.64 5.52
996 1011 1.672356 ACCTCGTGCATGAACAGGC 60.672 57.895 17.59 4.48 38.80 4.85
997 1012 2.165380 CACCTCGTGCATGAACAGG 58.835 57.895 16.57 16.57 0.00 4.00
1023 1038 3.704231 ATCATCGTGGCACCTGGGC 62.704 63.158 12.86 0.00 43.73 5.36
1024 1039 1.820906 CATCATCGTGGCACCTGGG 60.821 63.158 12.86 0.00 0.00 4.45
1025 1040 1.820906 CCATCATCGTGGCACCTGG 60.821 63.158 12.86 7.64 31.43 4.45
1026 1041 1.820906 CCCATCATCGTGGCACCTG 60.821 63.158 12.86 10.16 37.96 4.00
1027 1042 2.591753 CCCATCATCGTGGCACCT 59.408 61.111 12.86 0.00 37.96 4.00
1028 1043 2.516930 CCCCATCATCGTGGCACC 60.517 66.667 12.86 0.00 37.96 5.01
1029 1044 2.516930 CCCCCATCATCGTGGCAC 60.517 66.667 7.79 7.79 37.96 5.01
1030 1045 3.014538 ACCCCCATCATCGTGGCA 61.015 61.111 0.00 0.00 37.96 4.92
1031 1046 2.203209 GACCCCCATCATCGTGGC 60.203 66.667 0.00 0.00 37.96 5.01
1032 1047 2.108976 CGACCCCCATCATCGTGG 59.891 66.667 0.00 0.00 39.05 4.94
1033 1048 2.900273 ACGACCCCCATCATCGTG 59.100 61.111 0.00 0.00 46.68 4.35
1035 1050 0.810031 GTTGACGACCCCCATCATCG 60.810 60.000 0.00 0.00 41.60 3.84
1036 1051 0.810031 CGTTGACGACCCCCATCATC 60.810 60.000 0.00 0.00 43.02 2.92
1037 1052 1.220749 CGTTGACGACCCCCATCAT 59.779 57.895 0.00 0.00 43.02 2.45
1038 1053 2.660206 CGTTGACGACCCCCATCA 59.340 61.111 0.00 0.00 43.02 3.07
1039 1054 2.125269 CCGTTGACGACCCCCATC 60.125 66.667 4.91 0.00 43.02 3.51
1040 1055 4.404098 GCCGTTGACGACCCCCAT 62.404 66.667 4.91 0.00 43.02 4.00
1042 1057 2.918230 CTATGCCGTTGACGACCCCC 62.918 65.000 4.91 0.00 43.02 5.40
1043 1058 1.520787 CTATGCCGTTGACGACCCC 60.521 63.158 4.91 0.00 43.02 4.95
1044 1059 1.520787 CCTATGCCGTTGACGACCC 60.521 63.158 4.91 0.00 43.02 4.46
1045 1060 1.520787 CCCTATGCCGTTGACGACC 60.521 63.158 4.91 0.00 43.02 4.79
1046 1061 2.171725 GCCCTATGCCGTTGACGAC 61.172 63.158 4.91 0.00 43.02 4.34
1047 1062 2.185867 GCCCTATGCCGTTGACGA 59.814 61.111 4.91 0.00 43.02 4.20
1048 1063 3.261951 CGCCCTATGCCGTTGACG 61.262 66.667 0.00 0.00 36.24 4.35
1049 1064 2.895372 CCGCCCTATGCCGTTGAC 60.895 66.667 0.00 0.00 36.24 3.18
1050 1065 3.395702 ACCGCCCTATGCCGTTGA 61.396 61.111 0.00 0.00 36.24 3.18
1051 1066 3.202001 CACCGCCCTATGCCGTTG 61.202 66.667 0.00 0.00 36.24 4.10
1052 1067 4.483243 CCACCGCCCTATGCCGTT 62.483 66.667 0.00 0.00 36.24 4.44
1056 1071 4.489771 AGCACCACCGCCCTATGC 62.490 66.667 0.00 0.00 36.52 3.14
1057 1072 2.514592 CAGCACCACCGCCCTATG 60.515 66.667 0.00 0.00 0.00 2.23
1058 1073 4.489771 GCAGCACCACCGCCCTAT 62.490 66.667 0.00 0.00 0.00 2.57
1108 1123 2.747460 CATCACCACCACCTGCCG 60.747 66.667 0.00 0.00 0.00 5.69
1113 1128 1.375523 GTCGTCCATCACCACCACC 60.376 63.158 0.00 0.00 0.00 4.61
1115 1130 2.654289 CGTCGTCCATCACCACCA 59.346 61.111 0.00 0.00 0.00 4.17
1176 1191 1.243902 ACACGTAAAACCCCTGCATG 58.756 50.000 0.00 0.00 0.00 4.06
1177 1192 1.883926 GAACACGTAAAACCCCTGCAT 59.116 47.619 0.00 0.00 0.00 3.96
1178 1193 1.134037 AGAACACGTAAAACCCCTGCA 60.134 47.619 0.00 0.00 0.00 4.41
1186 1201 2.540931 GCAAGGACGAGAACACGTAAAA 59.459 45.455 0.00 0.00 46.52 1.52
1188 1203 1.774639 GCAAGGACGAGAACACGTAA 58.225 50.000 0.00 0.00 46.52 3.18
1192 1207 2.853914 GCGCAAGGACGAGAACAC 59.146 61.111 0.30 0.00 38.28 3.32
1212 1227 1.142097 GGAGAAGAGTAGCACCGGC 59.858 63.158 0.00 0.00 41.61 6.13
1214 1229 1.751351 TCATGGAGAAGAGTAGCACCG 59.249 52.381 0.00 0.00 0.00 4.94
1219 1234 3.193691 ACCACGTTCATGGAGAAGAGTAG 59.806 47.826 0.00 0.00 43.02 2.57
1221 1236 1.971357 ACCACGTTCATGGAGAAGAGT 59.029 47.619 0.00 0.00 43.02 3.24
1227 1242 2.093306 TAAGCACCACGTTCATGGAG 57.907 50.000 0.00 0.00 43.02 3.86
1229 1244 1.401552 CCATAAGCACCACGTTCATGG 59.598 52.381 0.00 0.00 46.10 3.66
1236 1251 1.153168 CCCCTCCATAAGCACCACG 60.153 63.158 0.00 0.00 0.00 4.94
1243 1258 2.203209 GTGCGGCCCCTCCATAAG 60.203 66.667 0.00 0.00 34.01 1.73
1245 1260 3.161450 GAGTGCGGCCCCTCCATA 61.161 66.667 0.00 0.00 34.01 2.74
1257 1272 3.959991 GAAGGTGCTCCCGGAGTGC 62.960 68.421 16.09 6.53 38.74 4.40
1258 1273 2.266055 GAAGGTGCTCCCGGAGTG 59.734 66.667 16.09 0.00 38.74 3.51
1283 1298 3.430862 CCATGTTGTCACGGCCGG 61.431 66.667 31.76 18.67 0.00 6.13
1290 1305 1.302431 CGGCTCCACCATGTTGTCA 60.302 57.895 0.00 0.00 39.03 3.58
1312 1327 4.742201 CACCACCGACAGCTCCCG 62.742 72.222 0.00 0.00 0.00 5.14
1347 1362 3.151710 TACCCCGTCGCCATCCTG 61.152 66.667 0.00 0.00 0.00 3.86
1399 1414 0.173708 AACTCGATGACGGCCTTCTC 59.826 55.000 11.01 4.92 40.21 2.87
1425 1440 0.981183 TGGCGTGGAGGTAGACAAAT 59.019 50.000 0.00 0.00 0.00 2.32
1443 1458 1.725665 CGCTCATGCATGGGAGTTG 59.274 57.895 30.87 12.05 39.64 3.16
1473 1488 0.107945 AATCAACTCTCGAGGCTGGC 60.108 55.000 13.56 0.00 0.00 4.85
1477 1492 5.352284 TGATAGAAAATCAACTCTCGAGGC 58.648 41.667 13.56 0.00 0.00 4.70
1479 1494 8.472683 AACTTGATAGAAAATCAACTCTCGAG 57.527 34.615 5.93 5.93 34.66 4.04
1481 1496 8.244494 TGAACTTGATAGAAAATCAACTCTCG 57.756 34.615 0.00 0.00 34.66 4.04
1486 1501 9.774742 GGTGTATGAACTTGATAGAAAATCAAC 57.225 33.333 0.00 0.00 34.66 3.18
1488 1503 8.328758 AGGGTGTATGAACTTGATAGAAAATCA 58.671 33.333 0.00 0.00 0.00 2.57
1489 1504 8.738645 AGGGTGTATGAACTTGATAGAAAATC 57.261 34.615 0.00 0.00 0.00 2.17
1490 1505 9.838339 CTAGGGTGTATGAACTTGATAGAAAAT 57.162 33.333 0.00 0.00 0.00 1.82
1491 1506 7.769044 GCTAGGGTGTATGAACTTGATAGAAAA 59.231 37.037 0.00 0.00 0.00 2.29
1492 1507 7.125811 AGCTAGGGTGTATGAACTTGATAGAAA 59.874 37.037 0.00 0.00 0.00 2.52
1493 1508 6.611642 AGCTAGGGTGTATGAACTTGATAGAA 59.388 38.462 0.00 0.00 0.00 2.10
1494 1509 6.136857 AGCTAGGGTGTATGAACTTGATAGA 58.863 40.000 0.00 0.00 0.00 1.98
1495 1510 6.412362 AGCTAGGGTGTATGAACTTGATAG 57.588 41.667 0.00 0.00 0.00 2.08
1496 1511 6.267014 GGTAGCTAGGGTGTATGAACTTGATA 59.733 42.308 0.00 0.00 0.00 2.15
1497 1512 5.070580 GGTAGCTAGGGTGTATGAACTTGAT 59.929 44.000 0.00 0.00 0.00 2.57
1498 1513 4.404715 GGTAGCTAGGGTGTATGAACTTGA 59.595 45.833 0.00 0.00 0.00 3.02
1499 1514 4.694339 GGTAGCTAGGGTGTATGAACTTG 58.306 47.826 0.00 0.00 0.00 3.16
1500 1515 3.383825 CGGTAGCTAGGGTGTATGAACTT 59.616 47.826 0.00 0.00 0.00 2.66
1501 1516 2.957006 CGGTAGCTAGGGTGTATGAACT 59.043 50.000 0.00 0.00 0.00 3.01
1502 1517 2.692041 ACGGTAGCTAGGGTGTATGAAC 59.308 50.000 0.00 0.00 0.00 3.18
1503 1518 3.022557 ACGGTAGCTAGGGTGTATGAA 57.977 47.619 0.00 0.00 0.00 2.57
1504 1519 2.691526 CAACGGTAGCTAGGGTGTATGA 59.308 50.000 0.00 0.00 0.00 2.15
1505 1520 2.802057 GCAACGGTAGCTAGGGTGTATG 60.802 54.545 10.54 2.15 0.00 2.39
1506 1521 1.411612 GCAACGGTAGCTAGGGTGTAT 59.588 52.381 10.54 0.00 0.00 2.29
1507 1522 0.819582 GCAACGGTAGCTAGGGTGTA 59.180 55.000 10.54 0.00 0.00 2.90
1508 1523 1.189524 TGCAACGGTAGCTAGGGTGT 61.190 55.000 10.54 0.00 0.00 4.16
1509 1524 0.178068 ATGCAACGGTAGCTAGGGTG 59.822 55.000 5.58 5.58 0.00 4.61
1512 1527 0.464036 TCCATGCAACGGTAGCTAGG 59.536 55.000 0.00 0.00 0.00 3.02
1535 1555 1.694696 GGTGTAGTGGAGGGATGGATC 59.305 57.143 0.00 0.00 0.00 3.36
1538 1558 1.123928 GAGGTGTAGTGGAGGGATGG 58.876 60.000 0.00 0.00 0.00 3.51
1541 1561 1.622449 CCATGAGGTGTAGTGGAGGGA 60.622 57.143 0.00 0.00 33.53 4.20
1549 1569 6.425210 TCTTTGATATCCCATGAGGTGTAG 57.575 41.667 0.00 0.00 36.75 2.74
1551 1571 5.715439 TTCTTTGATATCCCATGAGGTGT 57.285 39.130 0.00 0.00 36.75 4.16
1552 1572 6.016527 CACATTCTTTGATATCCCATGAGGTG 60.017 42.308 0.00 0.00 36.75 4.00
1553 1573 6.066690 CACATTCTTTGATATCCCATGAGGT 58.933 40.000 0.00 0.00 36.75 3.85
1554 1574 6.066690 ACACATTCTTTGATATCCCATGAGG 58.933 40.000 0.00 0.00 0.00 3.86
1555 1575 7.578310 AACACATTCTTTGATATCCCATGAG 57.422 36.000 0.00 0.00 0.00 2.90
1570 1611 3.146847 GGAGAACCCGAAAACACATTCT 58.853 45.455 0.00 0.00 0.00 2.40
1572 1613 3.146847 GAGGAGAACCCGAAAACACATT 58.853 45.455 0.00 0.00 40.87 2.71
1573 1614 2.105821 TGAGGAGAACCCGAAAACACAT 59.894 45.455 0.00 0.00 40.87 3.21
1574 1615 1.487142 TGAGGAGAACCCGAAAACACA 59.513 47.619 0.00 0.00 40.87 3.72
1575 1616 2.249844 TGAGGAGAACCCGAAAACAC 57.750 50.000 0.00 0.00 40.87 3.32
1579 1620 4.837093 ATGTATTGAGGAGAACCCGAAA 57.163 40.909 0.00 0.00 40.87 3.46
1582 1623 4.770795 AGAAATGTATTGAGGAGAACCCG 58.229 43.478 0.00 0.00 40.87 5.28
1583 1624 7.110155 TGTAAGAAATGTATTGAGGAGAACCC 58.890 38.462 0.00 0.00 36.73 4.11
1584 1625 7.824779 ACTGTAAGAAATGTATTGAGGAGAACC 59.175 37.037 0.00 0.00 37.43 3.62
1585 1626 8.779354 ACTGTAAGAAATGTATTGAGGAGAAC 57.221 34.615 0.00 0.00 37.43 3.01
1597 1640 8.157476 AGGAGTGTTCATAACTGTAAGAAATGT 58.843 33.333 0.00 0.00 37.43 2.71
1621 1664 3.270027 TGCATGATTAGTTCCGAACAGG 58.730 45.455 13.69 0.00 42.97 4.00
1622 1665 4.333649 ACATGCATGATTAGTTCCGAACAG 59.666 41.667 32.75 0.18 0.00 3.16
1632 1675 7.193377 TGCACAATACTACATGCATGATTAG 57.807 36.000 32.75 24.38 42.92 1.73
1648 1716 8.978874 ACAATATTTACTCATCCTGCACAATA 57.021 30.769 0.00 0.00 0.00 1.90
1682 1750 1.432514 CGTGTCAACCTCCATGACTG 58.567 55.000 8.01 0.00 45.81 3.51
1684 1752 0.602638 TGCGTGTCAACCTCCATGAC 60.603 55.000 0.00 0.00 45.82 3.06
1689 1757 0.602638 TGATGTGCGTGTCAACCTCC 60.603 55.000 0.00 0.00 0.00 4.30
1704 1772 9.450807 AGTTGTCTTTTCTTTTAATCGTTGATG 57.549 29.630 0.00 0.00 0.00 3.07
1719 1787 5.008118 GCTGGAGCCATATAGTTGTCTTTTC 59.992 44.000 0.00 0.00 34.31 2.29
1726 1794 4.392047 TGATTGCTGGAGCCATATAGTTG 58.608 43.478 0.00 0.00 41.18 3.16
1730 1798 4.582869 GACATGATTGCTGGAGCCATATA 58.417 43.478 0.00 0.00 41.18 0.86
1732 1800 2.807837 CGACATGATTGCTGGAGCCATA 60.808 50.000 0.00 0.00 41.18 2.74
1736 1804 1.594862 GTACGACATGATTGCTGGAGC 59.405 52.381 0.00 0.00 42.50 4.70
1739 1807 2.022764 TGGTACGACATGATTGCTGG 57.977 50.000 0.00 0.00 0.00 4.85
1751 1819 3.752747 TCTTGTTCTACGTCATGGTACGA 59.247 43.478 13.28 0.00 45.68 3.43
1755 1823 8.561738 AATTTTATCTTGTTCTACGTCATGGT 57.438 30.769 0.00 0.00 0.00 3.55
1801 1891 5.745294 GCATGTGATGTGGTATAAGCTTTTG 59.255 40.000 3.20 0.00 0.00 2.44
1802 1892 5.418524 TGCATGTGATGTGGTATAAGCTTTT 59.581 36.000 3.20 0.00 0.00 2.27
1805 1895 4.155063 TGCATGTGATGTGGTATAAGCT 57.845 40.909 0.00 0.00 0.00 3.74
1806 1896 4.898829 TTGCATGTGATGTGGTATAAGC 57.101 40.909 0.00 0.00 0.00 3.09
1808 1898 5.260424 AGGTTTGCATGTGATGTGGTATAA 58.740 37.500 0.00 0.00 0.00 0.98
1809 1899 4.854173 AGGTTTGCATGTGATGTGGTATA 58.146 39.130 0.00 0.00 0.00 1.47
1810 1900 3.700538 AGGTTTGCATGTGATGTGGTAT 58.299 40.909 0.00 0.00 0.00 2.73
1811 1901 3.153369 AGGTTTGCATGTGATGTGGTA 57.847 42.857 0.00 0.00 0.00 3.25
1812 1902 1.999648 AGGTTTGCATGTGATGTGGT 58.000 45.000 0.00 0.00 0.00 4.16
1813 1903 2.559668 AGAAGGTTTGCATGTGATGTGG 59.440 45.455 0.00 0.00 0.00 4.17
1814 1904 3.571571 CAGAAGGTTTGCATGTGATGTG 58.428 45.455 0.00 0.00 0.00 3.21
1815 1905 2.029649 GCAGAAGGTTTGCATGTGATGT 60.030 45.455 0.00 0.00 41.17 3.06
1816 1906 2.602878 GCAGAAGGTTTGCATGTGATG 58.397 47.619 0.00 0.00 41.17 3.07
1817 1907 1.547372 GGCAGAAGGTTTGCATGTGAT 59.453 47.619 0.00 0.00 43.28 3.06
1832 1922 2.400399 CGTCTAACTCGTTTTGGCAGA 58.600 47.619 0.00 0.00 0.00 4.26
1837 1927 2.673833 AGAGGCGTCTAACTCGTTTTG 58.326 47.619 7.25 0.00 38.72 2.44
1843 1933 4.048241 AGCAATTAGAGGCGTCTAACTC 57.952 45.455 26.45 18.52 45.99 3.01
1853 1943 6.038271 ACGGTAATTAGCAAAGCAATTAGAGG 59.962 38.462 14.62 0.00 29.60 3.69
1861 1951 1.470890 GCCACGGTAATTAGCAAAGCA 59.529 47.619 14.62 0.00 0.00 3.91
1862 1952 1.743394 AGCCACGGTAATTAGCAAAGC 59.257 47.619 14.62 12.19 0.00 3.51
1877 1967 2.423538 CCAACTTAACCATAGCAGCCAC 59.576 50.000 0.00 0.00 0.00 5.01
1883 1973 7.433708 AAAATTTTGCCAACTTAACCATAGC 57.566 32.000 1.75 0.00 0.00 2.97
1897 1987 7.095940 GGTTCGTAGGAAAAGTAAAATTTTGCC 60.096 37.037 13.76 4.21 40.25 4.52
1898 1988 7.435784 TGGTTCGTAGGAAAAGTAAAATTTTGC 59.564 33.333 13.76 12.17 39.84 3.68
1904 1994 7.444792 TGCTTATGGTTCGTAGGAAAAGTAAAA 59.555 33.333 0.00 0.00 33.05 1.52
1908 1998 4.901868 TGCTTATGGTTCGTAGGAAAAGT 58.098 39.130 0.00 0.00 33.05 2.66
1910 2000 5.353123 GTCATGCTTATGGTTCGTAGGAAAA 59.647 40.000 0.00 0.00 33.05 2.29
1915 2005 4.433615 AGTGTCATGCTTATGGTTCGTAG 58.566 43.478 0.00 0.00 0.00 3.51
1919 2009 5.824904 ATGAAGTGTCATGCTTATGGTTC 57.175 39.130 0.00 0.00 43.13 3.62
1941 2031 3.181495 CCTCGCAAGTTAAACCAACAACA 60.181 43.478 0.00 0.00 39.81 3.33
2001 2091 9.083080 CACACGTAATGATGAAGTTTAGTATGA 57.917 33.333 0.00 0.00 0.00 2.15
2015 2105 1.822990 ACGAGGGTCACACGTAATGAT 59.177 47.619 0.00 0.00 38.47 2.45
2022 2112 0.809385 ATCTACACGAGGGTCACACG 59.191 55.000 0.00 0.00 0.00 4.49
2024 2114 2.209690 TGATCTACACGAGGGTCACA 57.790 50.000 0.00 0.00 0.00 3.58
2048 2140 6.491394 TGTGAAAAACGGAAAGACAATGTAG 58.509 36.000 0.00 0.00 0.00 2.74
2056 2148 8.244802 TGATAAACTTTGTGAAAAACGGAAAGA 58.755 29.630 0.00 0.00 0.00 2.52
2085 2178 7.439955 TGAAGCAAATCTGAGTTCGTAGTAAAA 59.560 33.333 0.00 0.00 0.00 1.52
2088 2181 6.020971 TGAAGCAAATCTGAGTTCGTAGTA 57.979 37.500 0.00 0.00 0.00 1.82
2100 2193 2.494870 GGGCACAGATTGAAGCAAATCT 59.505 45.455 4.08 4.08 45.69 2.40
2121 2225 8.776376 ATAAGCACAATATTTCTTTTTGTGGG 57.224 30.769 14.64 0.00 46.44 4.61
2130 2234 6.238484 GCTTCCACGATAAGCACAATATTTCT 60.238 38.462 13.55 0.00 46.85 2.52
2132 2236 5.821204 GCTTCCACGATAAGCACAATATTT 58.179 37.500 13.55 0.00 46.85 1.40
2179 2283 9.885934 GTTTTGGAAATAAAACCGCAAATTATT 57.114 25.926 0.00 0.00 42.07 1.40
2234 2347 1.476488 CGGGTTTTAGATGCTTTGGGG 59.524 52.381 0.00 0.00 0.00 4.96
2237 2350 4.381566 CGTTTTCGGGTTTTAGATGCTTTG 59.618 41.667 0.00 0.00 39.94 2.77
2241 2354 2.247637 GCGTTTTCGGGTTTTAGATGC 58.752 47.619 0.00 0.00 44.29 3.91
2242 2355 3.546002 TGCGTTTTCGGGTTTTAGATG 57.454 42.857 0.00 0.00 44.29 2.90
2262 2375 6.536684 AGGAAAAGCCCAGATTATAAGGAT 57.463 37.500 0.00 0.00 37.37 3.24
2287 2400 3.181520 CCACTAACTATTGTGCTTGACGC 60.182 47.826 0.00 0.00 39.77 5.19
2289 2402 4.324267 ACCCACTAACTATTGTGCTTGAC 58.676 43.478 0.00 0.00 33.26 3.18
2290 2403 4.575885 GACCCACTAACTATTGTGCTTGA 58.424 43.478 0.00 0.00 33.26 3.02
2291 2404 3.370978 CGACCCACTAACTATTGTGCTTG 59.629 47.826 0.00 0.00 33.26 4.01
2292 2405 3.259876 TCGACCCACTAACTATTGTGCTT 59.740 43.478 0.00 0.00 33.26 3.91
2293 2406 2.829720 TCGACCCACTAACTATTGTGCT 59.170 45.455 0.00 0.00 33.26 4.40
2294 2407 2.928116 GTCGACCCACTAACTATTGTGC 59.072 50.000 3.51 0.00 33.26 4.57
2295 2408 3.518590 GGTCGACCCACTAACTATTGTG 58.481 50.000 24.75 0.00 0.00 3.33
2296 2409 3.881937 GGTCGACCCACTAACTATTGT 57.118 47.619 24.75 0.00 0.00 2.71
2410 2523 1.730501 ATGAGTGATGGACGCTTGTG 58.269 50.000 0.00 0.00 39.64 3.33
2412 2525 3.837213 AAAATGAGTGATGGACGCTTG 57.163 42.857 0.00 0.00 39.64 4.01
2497 2612 9.322773 TGCATGATCAGTTTTTAAATGTCAAAA 57.677 25.926 0.09 0.00 0.00 2.44
2498 2613 8.883954 TGCATGATCAGTTTTTAAATGTCAAA 57.116 26.923 0.09 0.00 0.00 2.69
2575 2690 7.945134 AGCATTTTTCTCAAGTTATGTGAACT 58.055 30.769 0.00 0.00 40.28 3.01
2582 2697 9.077885 TGGTAAGAAGCATTTTTCTCAAGTTAT 57.922 29.630 0.00 0.00 36.42 1.89
2603 2718 6.154203 TCACAAACATCTTGCAAATGGTAA 57.846 33.333 19.12 4.44 0.00 2.85
2610 2725 9.376075 TCTAAAAATTTCACAAACATCTTGCAA 57.624 25.926 0.00 0.00 0.00 4.08
2654 2769 1.208776 CCGGACGGAGGGAGTATTTTT 59.791 52.381 4.40 0.00 37.50 1.94
2655 2770 0.828677 CCGGACGGAGGGAGTATTTT 59.171 55.000 4.40 0.00 37.50 1.82
2656 2771 0.032813 TCCGGACGGAGGGAGTATTT 60.033 55.000 9.76 0.00 39.76 1.40
2657 2772 0.032813 TTCCGGACGGAGGGAGTATT 60.033 55.000 13.64 0.00 46.06 1.89
2658 2773 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
2659 2774 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2660 2775 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2661 2776 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2662 2777 1.044790 GGTATTTCCGGACGGAGGGA 61.045 60.000 13.64 4.95 46.06 4.20
2663 2778 1.444672 GGTATTTCCGGACGGAGGG 59.555 63.158 13.64 0.00 46.06 4.30


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

AutoCloner maintained by Alex Coulton.