Multiple sequence alignment - TraesCS4B01G135400

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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 TraesCS4B01G135400 chr4B 100.000 7235 0 0 1 7235 177853731 177860965 0.000000e+00 13361.0
1 TraesCS4B01G135400 chr4B 84.149 429 44 18 388 803 670839757 670840174 1.890000e-105 394.0
2 TraesCS4B01G135400 chr4B 92.593 81 5 1 4770 4850 285601291 285601370 1.650000e-21 115.0
3 TraesCS4B01G135400 chr4D 93.875 2955 111 23 4335 7235 116149854 116152792 0.000000e+00 4390.0
4 TraesCS4B01G135400 chr4D 94.002 1734 55 12 939 2639 116147806 116149523 0.000000e+00 2580.0
5 TraesCS4B01G135400 chr4D 97.361 341 9 0 2753 3093 116149530 116149870 1.350000e-161 580.0
6 TraesCS4B01G135400 chr4D 92.593 81 6 0 4770 4850 281196238 281196158 4.590000e-22 117.0
7 TraesCS4B01G135400 chr4A 94.726 2408 83 21 4335 6718 460452888 460450501 0.000000e+00 3703.0
8 TraesCS4B01G135400 chr4A 94.511 2186 64 17 939 3093 460455032 460452872 0.000000e+00 3321.0
9 TraesCS4B01G135400 chr4A 92.887 239 15 2 6998 7235 460450074 460449837 5.370000e-91 346.0
10 TraesCS4B01G135400 chr4A 94.444 90 5 0 25 114 460455320 460455231 9.790000e-29 139.0
11 TraesCS4B01G135400 chr4A 97.222 72 2 0 804 875 460455242 460455171 9.860000e-24 122.0
12 TraesCS4B01G135400 chr7D 88.694 1256 122 8 3093 4336 113888866 113887619 0.000000e+00 1515.0
13 TraesCS4B01G135400 chr7D 88.528 1264 121 10 3088 4336 180752817 180754071 0.000000e+00 1509.0
14 TraesCS4B01G135400 chr7D 88.231 1266 129 10 3089 4336 63488640 63489903 0.000000e+00 1495.0
15 TraesCS4B01G135400 chr7D 82.005 439 56 20 116 538 104619133 104619564 1.150000e-92 351.0
16 TraesCS4B01G135400 chr5D 88.389 1266 125 11 3090 4336 205591801 205593063 0.000000e+00 1504.0
17 TraesCS4B01G135400 chr5D 87.401 1262 138 11 3093 4336 100858980 100857722 0.000000e+00 1430.0
18 TraesCS4B01G135400 chr5D 94.231 52 3 0 6 57 440743419 440743368 6.020000e-11 80.5
19 TraesCS4B01G135400 chr2D 88.440 1263 125 11 3093 4336 37224394 37223134 0.000000e+00 1504.0
20 TraesCS4B01G135400 chr2D 85.686 510 56 12 3091 3586 612890404 612889898 8.320000e-144 521.0
21 TraesCS4B01G135400 chr2D 83.686 472 34 24 116 554 548262024 548262485 8.740000e-109 405.0
22 TraesCS4B01G135400 chr2D 92.529 174 13 0 3093 3266 517262662 517262489 4.330000e-62 250.0
23 TraesCS4B01G135400 chr3D 88.526 1255 124 8 3094 4336 586930657 586931903 0.000000e+00 1502.0
24 TraesCS4B01G135400 chr3D 89.130 46 5 0 2264 2309 585981266 585981221 2.820000e-04 58.4
25 TraesCS4B01G135400 chr1D 87.956 1262 131 11 3093 4336 52734776 52733518 0.000000e+00 1469.0
26 TraesCS4B01G135400 chr2A 90.825 1079 81 10 3093 4163 176559618 176560686 0.000000e+00 1428.0
27 TraesCS4B01G135400 chr2A 86.765 68 7 2 6900 6965 715944004 715944071 2.800000e-09 75.0
28 TraesCS4B01G135400 chr2A 92.308 52 3 1 6900 6950 195072236 195072287 1.010000e-08 73.1
29 TraesCS4B01G135400 chr2A 91.837 49 4 0 6900 6948 615347634 615347682 1.300000e-07 69.4
30 TraesCS4B01G135400 chr5A 87.937 1086 116 8 3170 4248 580397085 580396008 0.000000e+00 1266.0
31 TraesCS4B01G135400 chr5A 93.478 46 3 0 6903 6948 55159064 55159019 1.300000e-07 69.4
32 TraesCS4B01G135400 chr5A 92.000 50 2 2 6901 6949 421833771 421833723 1.300000e-07 69.4
33 TraesCS4B01G135400 chr5A 100.000 28 0 0 7013 7040 102479544 102479571 1.300000e-02 52.8
34 TraesCS4B01G135400 chr3B 90.629 715 37 16 116 806 118535171 118535879 0.000000e+00 922.0
35 TraesCS4B01G135400 chr3B 82.449 245 37 5 2551 2792 764843478 764843237 7.350000e-50 209.0
36 TraesCS4B01G135400 chr3B 89.167 120 12 1 2551 2670 794977198 794977316 1.630000e-31 148.0
37 TraesCS4B01G135400 chr3B 74.411 297 58 14 1793 2085 589545497 589545215 2.130000e-20 111.0
38 TraesCS4B01G135400 chr5B 89.986 709 43 18 106 805 360409918 360410607 0.000000e+00 891.0
39 TraesCS4B01G135400 chr5B 82.041 245 38 5 2551 2792 456671787 456672028 3.420000e-48 204.0
40 TraesCS4B01G135400 chr5B 80.087 231 39 6 2567 2794 505563549 505563775 1.610000e-36 165.0
41 TraesCS4B01G135400 chrUn 89.755 693 43 18 106 789 323474534 323475207 0.000000e+00 861.0
42 TraesCS4B01G135400 chrUn 89.796 49 5 0 1794 1842 31808633 31808585 6.060000e-06 63.9
43 TraesCS4B01G135400 chr7A 84.382 429 48 13 388 806 625068640 625068221 3.140000e-108 403.0
44 TraesCS4B01G135400 chr7A 83.568 426 50 16 391 806 37939820 37940235 1.470000e-101 381.0
45 TraesCS4B01G135400 chr7A 100.000 28 0 0 7013 7040 463395583 463395610 1.300000e-02 52.8
46 TraesCS4B01G135400 chr6B 84.346 428 47 12 390 806 650981738 650982156 1.130000e-107 401.0
47 TraesCS4B01G135400 chr6B 79.245 159 30 3 4701 4858 477223832 477223676 2.760000e-19 108.0
48 TraesCS4B01G135400 chr6B 78.767 146 28 3 2213 2356 314512678 314512534 2.150000e-15 95.3
49 TraesCS4B01G135400 chr6B 90.196 51 5 0 6898 6948 700090383 700090433 4.680000e-07 67.6
50 TraesCS4B01G135400 chr1B 84.507 426 44 15 390 804 16131803 16132217 1.130000e-107 401.0
51 TraesCS4B01G135400 chr1B 81.507 438 54 20 116 538 319469760 319470185 1.160000e-87 335.0
52 TraesCS4B01G135400 chr2B 83.295 437 49 20 390 813 749045843 749046268 1.470000e-101 381.0
53 TraesCS4B01G135400 chr2B 83.135 421 39 18 116 525 549510291 549510690 8.930000e-94 355.0
54 TraesCS4B01G135400 chr2B 93.878 49 3 0 6900 6948 106758102 106758054 2.800000e-09 75.0
55 TraesCS4B01G135400 chr7B 81.542 428 50 19 116 525 522082395 522081979 7.000000e-85 326.0
56 TraesCS4B01G135400 chr7B 93.750 48 1 2 6901 6947 426971378 426971424 3.620000e-08 71.3
57 TraesCS4B01G135400 chr3A 79.326 445 61 24 116 549 44314707 44314283 4.270000e-72 283.0
58 TraesCS4B01G135400 chr3A 80.460 87 11 5 2003 2085 650185975 650185891 2.180000e-05 62.1
59 TraesCS4B01G135400 chr6D 77.167 473 72 28 116 575 423546414 423546863 7.250000e-60 243.0
60 TraesCS4B01G135400 chr6D 79.874 159 27 4 4701 4858 309586303 309586149 2.130000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G135400 chr4B 177853731 177860965 7234 False 13361.000000 13361 100.000000 1 7235 1 chr4B.!!$F1 7234
1 TraesCS4B01G135400 chr4D 116147806 116152792 4986 False 2516.666667 4390 95.079333 939 7235 3 chr4D.!!$F1 6296
2 TraesCS4B01G135400 chr4A 460449837 460455320 5483 True 1526.200000 3703 94.758000 25 7235 5 chr4A.!!$R1 7210
3 TraesCS4B01G135400 chr7D 113887619 113888866 1247 True 1515.000000 1515 88.694000 3093 4336 1 chr7D.!!$R1 1243
4 TraesCS4B01G135400 chr7D 180752817 180754071 1254 False 1509.000000 1509 88.528000 3088 4336 1 chr7D.!!$F3 1248
5 TraesCS4B01G135400 chr7D 63488640 63489903 1263 False 1495.000000 1495 88.231000 3089 4336 1 chr7D.!!$F1 1247
6 TraesCS4B01G135400 chr5D 205591801 205593063 1262 False 1504.000000 1504 88.389000 3090 4336 1 chr5D.!!$F1 1246
7 TraesCS4B01G135400 chr5D 100857722 100858980 1258 True 1430.000000 1430 87.401000 3093 4336 1 chr5D.!!$R1 1243
8 TraesCS4B01G135400 chr2D 37223134 37224394 1260 True 1504.000000 1504 88.440000 3093 4336 1 chr2D.!!$R1 1243
9 TraesCS4B01G135400 chr2D 612889898 612890404 506 True 521.000000 521 85.686000 3091 3586 1 chr2D.!!$R3 495
10 TraesCS4B01G135400 chr3D 586930657 586931903 1246 False 1502.000000 1502 88.526000 3094 4336 1 chr3D.!!$F1 1242
11 TraesCS4B01G135400 chr1D 52733518 52734776 1258 True 1469.000000 1469 87.956000 3093 4336 1 chr1D.!!$R1 1243
12 TraesCS4B01G135400 chr2A 176559618 176560686 1068 False 1428.000000 1428 90.825000 3093 4163 1 chr2A.!!$F1 1070
13 TraesCS4B01G135400 chr5A 580396008 580397085 1077 True 1266.000000 1266 87.937000 3170 4248 1 chr5A.!!$R3 1078
14 TraesCS4B01G135400 chr3B 118535171 118535879 708 False 922.000000 922 90.629000 116 806 1 chr3B.!!$F1 690
15 TraesCS4B01G135400 chr5B 360409918 360410607 689 False 891.000000 891 89.986000 106 805 1 chr5B.!!$F1 699
16 TraesCS4B01G135400 chrUn 323474534 323475207 673 False 861.000000 861 89.755000 106 789 1 chrUn.!!$F1 683

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
153 154 0.038892 GCAGGCGCCCATTAATGATG 60.039 55.0 26.15 12.84 35.42 3.07 F
1812 1946 0.259647 CTCAAGATGGGAATGGGCCA 59.740 55.0 9.61 9.61 0.00 5.36 F
3407 3556 0.247460 TCAGATCGGCAACCTCAGTG 59.753 55.0 0.00 0.00 0.00 3.66 F
3419 3568 0.749649 CCTCAGTGAGAATCCTCCCG 59.250 60.0 22.09 0.00 38.66 5.14 F
3797 3953 0.750182 CCCAAATGTAACGGGCCGAT 60.750 55.0 35.78 25.18 31.89 4.18 F
4633 4800 0.764369 AGAGGAGGTCAGCACAACCA 60.764 55.0 5.16 0.00 39.39 3.67 F
6084 6257 0.177141 AGTAGCGGCGGCAGAAAATA 59.823 50.0 19.21 0.00 43.41 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2040 0.543410 ACCGATGGGACTGTGGTGTA 60.543 55.000 0.0 0.0 36.97 2.90 R
3716 3871 0.038744 CCCTCAAGGACAGGCACAAT 59.961 55.000 0.0 0.0 38.24 2.71 R
4313 4480 1.445582 CTTGGGCGTACGTGACCTC 60.446 63.158 17.9 0.0 0.00 3.85 R
4633 4800 2.352805 CCGCCTTTCTCCTTGGCT 59.647 61.111 0.0 0.0 44.09 4.75 R
5771 5944 1.293924 CATCCTCATCGTCCACTTGC 58.706 55.000 0.0 0.0 0.00 4.01 R
6088 6261 0.045008 TACACCCAGGCCCCATCTAA 59.955 55.000 0.0 0.0 0.00 2.10 R
7021 7513 2.497675 CCTAGAGGCTAGAGTTTGTGCA 59.502 50.000 0.0 0.0 0.00 4.57 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
75 76 2.241176 TCCCCTGCGTAATCTTTTGGAT 59.759 45.455 0.00 0.00 35.97 3.41
76 77 3.023832 CCCCTGCGTAATCTTTTGGATT 58.976 45.455 0.00 0.00 45.53 3.01
80 81 4.342772 CTGCGTAATCTTTTGGATTTCCG 58.657 43.478 0.00 0.00 41.42 4.30
85 86 5.220605 CGTAATCTTTTGGATTTCCGGAGAC 60.221 44.000 3.34 0.00 41.42 3.36
95 96 0.690192 TTCCGGAGACAAGGCATCAA 59.310 50.000 3.34 0.00 0.00 2.57
102 103 2.871080 CAAGGCATCAAACGCGCG 60.871 61.111 30.96 30.96 0.00 6.86
103 104 4.759096 AAGGCATCAAACGCGCGC 62.759 61.111 32.58 23.91 0.00 6.86
107 108 4.851114 CATCAAACGCGCGCCTCG 62.851 66.667 32.58 16.36 42.12 4.63
132 133 3.831651 AGGAGCTCCTATACAGCGT 57.168 52.632 34.40 6.50 46.48 5.07
149 150 1.815866 GTTGCAGGCGCCCATTAAT 59.184 52.632 26.15 0.00 37.32 1.40
153 154 0.038892 GCAGGCGCCCATTAATGATG 60.039 55.000 26.15 12.84 35.42 3.07
184 185 4.552365 GCTGCTAGCATGGGCCGA 62.552 66.667 19.72 0.00 41.89 5.54
206 207 2.311854 ACTAGCTTGCTGCCCCCAT 61.312 57.895 5.26 0.00 44.23 4.00
826 855 2.679342 GCTGGTGCCCTCCATACCA 61.679 63.158 0.00 0.00 41.90 3.25
833 862 2.343758 CCTCCATACCATCGCCGG 59.656 66.667 0.00 0.00 0.00 6.13
880 926 1.063417 CCAATTCCCCTGGCTCTCAAT 60.063 52.381 0.00 0.00 0.00 2.57
889 935 1.149401 GGCTCTCAATACTGGGCCC 59.851 63.158 17.59 17.59 34.19 5.80
892 938 0.988145 CTCTCAATACTGGGCCCCCA 60.988 60.000 22.27 5.81 45.02 4.96
927 973 1.030457 GGCCCATGATCTGCTTTCTG 58.970 55.000 0.00 0.00 0.00 3.02
928 974 1.030457 GCCCATGATCTGCTTTCTGG 58.970 55.000 0.00 0.00 0.00 3.86
929 975 1.409241 GCCCATGATCTGCTTTCTGGA 60.409 52.381 0.00 0.00 0.00 3.86
930 976 2.573369 CCCATGATCTGCTTTCTGGAG 58.427 52.381 0.00 0.00 35.26 3.86
931 977 2.092538 CCCATGATCTGCTTTCTGGAGT 60.093 50.000 0.00 0.00 35.48 3.85
932 978 3.135348 CCCATGATCTGCTTTCTGGAGTA 59.865 47.826 0.00 0.00 35.48 2.59
933 979 4.378774 CCATGATCTGCTTTCTGGAGTAG 58.621 47.826 0.00 0.00 35.48 2.57
934 980 4.141756 CCATGATCTGCTTTCTGGAGTAGT 60.142 45.833 0.00 0.00 35.48 2.73
937 983 5.482908 TGATCTGCTTTCTGGAGTAGTTTC 58.517 41.667 0.00 0.00 35.48 2.78
971 1075 3.764160 CTGCGGCTTCTCCATCCCC 62.764 68.421 0.00 0.00 34.01 4.81
972 1076 4.570874 GCGGCTTCTCCATCCCCC 62.571 72.222 0.00 0.00 34.01 5.40
973 1077 2.770048 CGGCTTCTCCATCCCCCT 60.770 66.667 0.00 0.00 34.01 4.79
974 1078 2.378634 CGGCTTCTCCATCCCCCTT 61.379 63.158 0.00 0.00 34.01 3.95
987 1091 1.608336 CCCCTTTTCCCGAAACCCC 60.608 63.158 0.00 0.00 0.00 4.95
1012 1116 3.964875 CGGCAGCGCAACAACCTT 61.965 61.111 11.47 0.00 0.00 3.50
1013 1117 2.417097 GGCAGCGCAACAACCTTT 59.583 55.556 11.47 0.00 0.00 3.11
1017 1121 1.758783 CAGCGCAACAACCTTTCTTC 58.241 50.000 11.47 0.00 0.00 2.87
1020 1129 2.427095 AGCGCAACAACCTTTCTTCTTT 59.573 40.909 11.47 0.00 0.00 2.52
1288 1398 5.648092 CCCTCTCCGTTTCATCAATTTTACT 59.352 40.000 0.00 0.00 0.00 2.24
1384 1496 2.906268 GCCCATGAAGAAGGCCATT 58.094 52.632 5.01 0.00 41.00 3.16
1558 1670 2.283145 AGCTTCTTGTCCAGCATGTT 57.717 45.000 0.00 0.00 38.61 2.71
1781 1915 1.532523 TGCGGTTGCTCAATGATCAA 58.467 45.000 0.00 0.00 43.34 2.57
1812 1946 0.259647 CTCAAGATGGGAATGGGCCA 59.740 55.000 9.61 9.61 0.00 5.36
1933 2068 2.131709 GTCCCATCGGTCATCGGGA 61.132 63.158 0.00 0.00 45.66 5.14
1944 2079 1.272490 GTCATCGGGACAAGTGAGTCA 59.728 52.381 0.00 0.00 46.19 3.41
1946 2081 2.069273 CATCGGGACAAGTGAGTCAAC 58.931 52.381 0.00 0.00 40.29 3.18
1997 2132 2.231964 CCTTTACAGTGGCATGTGCATT 59.768 45.455 7.36 0.00 44.36 3.56
2088 2223 4.814771 AGAGTTACAAATATGCTAACGGCC 59.185 41.667 0.00 0.00 40.92 6.13
2089 2224 4.519213 AGTTACAAATATGCTAACGGCCA 58.481 39.130 2.24 0.00 40.92 5.36
2093 2228 5.627499 ACAAATATGCTAACGGCCATATG 57.373 39.130 2.24 0.00 40.92 1.78
2099 2234 1.425412 CTAACGGCCATATGTACGCC 58.575 55.000 2.24 12.32 39.41 5.68
2113 2248 4.035278 TGTACGCCTTGTTTTTCTTTGG 57.965 40.909 0.00 0.00 0.00 3.28
2114 2249 3.695060 TGTACGCCTTGTTTTTCTTTGGA 59.305 39.130 0.00 0.00 0.00 3.53
2225 2362 9.703892 CTATTTTGTGTCAATTAAAATGGGTCA 57.296 29.630 0.00 0.00 36.02 4.02
2276 2413 0.614415 TCACCATTGGACCATTGGGC 60.614 55.000 30.11 3.14 38.67 5.36
2547 2684 1.488705 ATTGTGCTCGTCCCCCTGAA 61.489 55.000 0.00 0.00 0.00 3.02
2625 2762 2.693069 GCAGATAGCTGGCGATATTGT 58.307 47.619 10.52 0.00 42.53 2.71
2652 2789 4.917887 CTATGTCCGCATAGCAGATTTC 57.082 45.455 2.25 0.00 45.35 2.17
2654 2791 2.554142 TGTCCGCATAGCAGATTTCTG 58.446 47.619 3.13 3.13 46.40 3.02
2728 2865 6.273071 ACATTTAATTTCAGAAATAGCGGCC 58.727 36.000 8.88 0.00 0.00 6.13
2729 2866 4.545823 TTAATTTCAGAAATAGCGGCCG 57.454 40.909 24.05 24.05 0.00 6.13
2730 2867 0.663153 ATTTCAGAAATAGCGGCCGC 59.337 50.000 42.34 42.34 42.33 6.53
2858 2995 2.744202 GAGCGTTTGAATGATCCACTGT 59.256 45.455 0.00 0.00 0.00 3.55
3168 3312 1.722034 AGCCTGAGAGACCAAAGTCA 58.278 50.000 0.00 0.00 46.15 3.41
3174 3318 5.123027 GCCTGAGAGACCAAAGTCATTTTAG 59.877 44.000 0.00 0.00 46.15 1.85
3251 3395 5.542251 TGGGAAATAAAACAAGGAAAGGGAG 59.458 40.000 0.00 0.00 0.00 4.30
3260 3404 2.110011 CAAGGAAAGGGAGGGAAGGAAA 59.890 50.000 0.00 0.00 0.00 3.13
3263 3407 2.291024 GGAAAGGGAGGGAAGGAAAGAC 60.291 54.545 0.00 0.00 0.00 3.01
3266 3410 0.621082 GGGAGGGAAGGAAAGACAGG 59.379 60.000 0.00 0.00 0.00 4.00
3270 3414 0.621082 GGGAAGGAAAGACAGGAGGG 59.379 60.000 0.00 0.00 0.00 4.30
3272 3416 1.557371 GGAAGGAAAGACAGGAGGGAG 59.443 57.143 0.00 0.00 0.00 4.30
3273 3417 2.541466 GAAGGAAAGACAGGAGGGAGA 58.459 52.381 0.00 0.00 0.00 3.71
3274 3418 2.246091 AGGAAAGACAGGAGGGAGAG 57.754 55.000 0.00 0.00 0.00 3.20
3275 3420 1.199615 GGAAAGACAGGAGGGAGAGG 58.800 60.000 0.00 0.00 0.00 3.69
3281 3426 1.394151 CAGGAGGGAGAGGGGAAGT 59.606 63.158 0.00 0.00 0.00 3.01
3282 3427 0.980231 CAGGAGGGAGAGGGGAAGTG 60.980 65.000 0.00 0.00 0.00 3.16
3283 3428 1.690985 GGAGGGAGAGGGGAAGTGG 60.691 68.421 0.00 0.00 0.00 4.00
3284 3429 1.392534 GAGGGAGAGGGGAAGTGGA 59.607 63.158 0.00 0.00 0.00 4.02
3285 3430 0.689412 GAGGGAGAGGGGAAGTGGAG 60.689 65.000 0.00 0.00 0.00 3.86
3286 3431 1.690985 GGGAGAGGGGAAGTGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
3289 3434 0.336737 GAGAGGGGAAGTGGAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
3292 3437 1.985895 GAGGGGAAGTGGAGGAGAAAA 59.014 52.381 0.00 0.00 0.00 2.29
3375 3524 4.803426 CCTCGGGTGCTCGCAGTC 62.803 72.222 3.65 0.00 0.00 3.51
3392 3541 3.069300 GCAGTCTCCATAGCTTGATCAGA 59.931 47.826 0.00 0.00 0.00 3.27
3398 3547 2.289257 CCATAGCTTGATCAGATCGGCA 60.289 50.000 22.27 13.02 34.57 5.69
3407 3556 0.247460 TCAGATCGGCAACCTCAGTG 59.753 55.000 0.00 0.00 0.00 3.66
3419 3568 0.749649 CCTCAGTGAGAATCCTCCCG 59.250 60.000 22.09 0.00 38.66 5.14
3437 3586 1.588674 CGGCTGTCCAACACTTGTTA 58.411 50.000 0.00 0.00 36.32 2.41
3457 3606 7.288810 TGTTATGAAAAACTTGCTCATTCCT 57.711 32.000 0.00 0.00 32.22 3.36
3470 3619 3.285484 CTCATTCCTAGCATGCCAAAGT 58.715 45.455 15.66 0.00 0.00 2.66
3476 3625 4.771684 GCATGCCAAAGTGCTACG 57.228 55.556 6.36 0.00 38.30 3.51
3503 3652 1.000060 GCTGCAAAGAAGACATGCCAA 60.000 47.619 0.00 0.00 39.31 4.52
3509 3658 0.890542 AGAAGACATGCCAAAGCGCA 60.891 50.000 11.47 0.00 44.31 6.09
3527 3679 1.382522 CACCATGTGCCTTCGCTATT 58.617 50.000 0.00 0.00 35.36 1.73
3569 3724 2.008329 GCAGATTCAGCTGAGACCAAG 58.992 52.381 17.43 7.47 38.14 3.61
3623 3778 2.631418 CAAGTTTGCATCTGAGCAGG 57.369 50.000 0.00 0.00 46.54 4.85
3655 3810 1.451927 TTTCGGCTGCTGGGCATAG 60.452 57.895 8.89 0.00 38.13 2.23
3713 3868 4.336889 CTTCCTTAGCATGTTATCCCGA 57.663 45.455 0.00 0.00 0.00 5.14
3716 3871 4.476297 TCCTTAGCATGTTATCCCGAGTA 58.524 43.478 0.00 0.00 0.00 2.59
3795 3951 1.377463 TCCCAAATGTAACGGGCCG 60.377 57.895 27.06 27.06 40.05 6.13
3797 3953 0.750182 CCCAAATGTAACGGGCCGAT 60.750 55.000 35.78 25.18 31.89 4.18
3826 3982 1.386533 CTGCCCCTGAATGTAAGCAG 58.613 55.000 0.00 0.00 41.43 4.24
3850 4008 7.429340 CAGCTTGTAAAAATATGCCGTAGAAAG 59.571 37.037 0.00 0.00 0.00 2.62
3860 4018 1.523095 GCCGTAGAAAGCTTGCTATCG 59.477 52.381 17.41 19.41 0.00 2.92
3863 4021 4.051922 CCGTAGAAAGCTTGCTATCGAAT 58.948 43.478 25.50 2.56 0.00 3.34
3920 4078 4.128925 TGGTGAGATGCAGCTTAGTAAG 57.871 45.455 5.67 5.47 45.14 2.34
3922 4080 4.116238 GGTGAGATGCAGCTTAGTAAGTC 58.884 47.826 5.67 4.32 41.71 3.01
3930 4088 5.470368 TGCAGCTTAGTAAGTCAGTTAGTG 58.530 41.667 11.51 0.04 0.00 2.74
3935 4093 6.151480 AGCTTAGTAAGTCAGTTAGTGTCTCC 59.849 42.308 11.51 0.00 0.00 3.71
4013 4174 0.887836 AGACGTACTGTGAGGCGACA 60.888 55.000 0.00 0.00 0.00 4.35
4085 4246 1.528824 CCGGCCATTCTCTGTCCAT 59.471 57.895 2.24 0.00 0.00 3.41
4106 4267 9.814899 GTCCATAGATCATACCAGAAAGATATG 57.185 37.037 0.00 0.00 0.00 1.78
4150 4311 3.748048 CACCTTGTGGACTGTATGACAAG 59.252 47.826 14.54 14.54 43.22 3.16
4152 4313 2.078849 TGTGGACTGTATGACAAGCG 57.921 50.000 0.00 0.00 0.00 4.68
4154 4315 0.973632 TGGACTGTATGACAAGCGGT 59.026 50.000 0.00 0.00 0.00 5.68
4156 4317 2.165641 TGGACTGTATGACAAGCGGTAG 59.834 50.000 0.00 0.00 0.00 3.18
4178 4339 0.889994 AAGATTTGATGCAGCGCCAA 59.110 45.000 2.29 0.00 0.00 4.52
4250 4411 4.517952 TGTTGATGCAAACCATTGGTAG 57.482 40.909 9.20 6.31 37.02 3.18
4311 4478 3.883631 TGCTTATCATGTTATGCGCAG 57.116 42.857 18.32 0.00 0.00 5.18
4331 4498 1.445582 GAGGTCACGTACGCCCAAG 60.446 63.158 16.72 0.40 0.00 3.61
4336 4503 3.307906 ACGTACGCCCAAGCCTCA 61.308 61.111 16.72 0.00 34.57 3.86
4337 4504 2.047655 CGTACGCCCAAGCCTCAA 60.048 61.111 0.52 0.00 34.57 3.02
4338 4505 2.100631 CGTACGCCCAAGCCTCAAG 61.101 63.158 0.52 0.00 34.57 3.02
4339 4506 2.046314 TACGCCCAAGCCTCAAGC 60.046 61.111 0.00 0.00 44.25 4.01
4350 4517 2.514205 GCCTCAAGCAAATGTGTTGT 57.486 45.000 0.00 0.00 42.97 3.32
4351 4518 3.641437 GCCTCAAGCAAATGTGTTGTA 57.359 42.857 0.00 0.00 42.97 2.41
4352 4519 4.178545 GCCTCAAGCAAATGTGTTGTAT 57.821 40.909 0.00 0.00 42.97 2.29
4353 4520 5.309323 GCCTCAAGCAAATGTGTTGTATA 57.691 39.130 0.00 0.00 42.97 1.47
4354 4521 5.095490 GCCTCAAGCAAATGTGTTGTATAC 58.905 41.667 0.00 0.00 42.97 1.47
4355 4522 5.335583 GCCTCAAGCAAATGTGTTGTATACA 60.336 40.000 0.08 0.08 42.97 2.29
4356 4523 6.676950 CCTCAAGCAAATGTGTTGTATACAA 58.323 36.000 14.35 14.35 38.80 2.41
4633 4800 0.764369 AGAGGAGGTCAGCACAACCA 60.764 55.000 5.16 0.00 39.39 3.67
4726 4894 2.594592 GGGCCCATGATACCGTGC 60.595 66.667 19.95 0.00 0.00 5.34
4732 4900 2.099141 CCATGATACCGTGCTATGGG 57.901 55.000 0.00 0.00 35.71 4.00
4800 4968 2.162681 CAAGGCTTGGGGTACAAAGAG 58.837 52.381 19.55 0.00 38.91 2.85
4978 5147 2.225255 GCTTTCTTGACAGCAGGACTTC 59.775 50.000 4.14 0.00 35.95 3.01
4992 5163 4.114794 CAGGACTTCTTTTTGCCAAGTTG 58.885 43.478 0.00 0.00 30.32 3.16
5015 5186 7.099266 TGTTATTTTCTTCGCATCCATCAAT 57.901 32.000 0.00 0.00 0.00 2.57
5033 5204 3.266513 TCAATGACAGGGGATGATGTTGA 59.733 43.478 0.00 0.00 0.00 3.18
5172 5343 7.453393 AGGTTGATGAAACACTGAGAGAAATA 58.547 34.615 0.00 0.00 40.86 1.40
5234 5405 3.181367 GCATCCAGCAGAACCACG 58.819 61.111 0.00 0.00 44.79 4.94
5343 5514 4.191243 TCTGTCGAAGAGGGTGCA 57.809 55.556 0.00 0.00 36.95 4.57
5502 5673 7.882179 AGTTTTAACAGTGTGTGAAAGAGTTT 58.118 30.769 0.00 0.00 32.65 2.66
5518 5689 8.359642 TGAAAGAGTTTAGATCATTGGTTTTGG 58.640 33.333 0.00 0.00 0.00 3.28
5520 5691 7.219484 AGAGTTTAGATCATTGGTTTTGGTG 57.781 36.000 0.00 0.00 0.00 4.17
5771 5944 7.339721 TCTGACCAGTCTTCTTATACTAGGTTG 59.660 40.741 0.00 0.00 31.56 3.77
5792 5965 1.208052 CAAGTGGACGATGAGGATGGT 59.792 52.381 0.00 0.00 0.00 3.55
5810 5983 5.050091 GGATGGTGAATGTTACGATGATGAC 60.050 44.000 0.00 0.00 0.00 3.06
5846 6019 4.253685 ACACGGATGACTCAAATGGTAAG 58.746 43.478 0.00 0.00 0.00 2.34
6063 6236 4.796606 AGGTGGAAAAATCCGATGATGAT 58.203 39.130 0.00 0.00 0.00 2.45
6079 6252 3.138930 GATGAGTAGCGGCGGCAGA 62.139 63.158 19.21 2.75 43.41 4.26
6083 6256 1.078426 AGTAGCGGCGGCAGAAAAT 60.078 52.632 19.21 0.00 43.41 1.82
6084 6257 0.177141 AGTAGCGGCGGCAGAAAATA 59.823 50.000 19.21 0.00 43.41 1.40
6086 6259 1.602377 GTAGCGGCGGCAGAAAATAAT 59.398 47.619 19.21 0.00 43.41 1.28
6087 6260 0.381801 AGCGGCGGCAGAAAATAATG 59.618 50.000 19.21 0.00 43.41 1.90
6088 6261 0.100503 GCGGCGGCAGAAAATAATGT 59.899 50.000 9.78 0.00 39.62 2.71
6090 6263 2.223386 GCGGCGGCAGAAAATAATGTTA 60.223 45.455 9.78 0.00 39.62 2.41
6091 6264 3.617669 CGGCGGCAGAAAATAATGTTAG 58.382 45.455 10.53 0.00 0.00 2.34
6092 6265 3.311322 CGGCGGCAGAAAATAATGTTAGA 59.689 43.478 10.53 0.00 0.00 2.10
6093 6266 4.024048 CGGCGGCAGAAAATAATGTTAGAT 60.024 41.667 10.53 0.00 0.00 1.98
6095 6268 5.215160 GCGGCAGAAAATAATGTTAGATGG 58.785 41.667 0.00 0.00 0.00 3.51
6096 6269 5.762045 CGGCAGAAAATAATGTTAGATGGG 58.238 41.667 0.00 0.00 0.00 4.00
6097 6270 5.278463 CGGCAGAAAATAATGTTAGATGGGG 60.278 44.000 0.00 0.00 0.00 4.96
6098 6271 5.509670 GGCAGAAAATAATGTTAGATGGGGC 60.510 44.000 0.00 0.00 0.00 5.80
6133 6306 6.283694 TCTTTGACGATGAAATAGGATGAGG 58.716 40.000 0.00 0.00 0.00 3.86
6185 6368 1.221840 CATCGCTAGCCCCACTGTT 59.778 57.895 9.66 0.00 0.00 3.16
6262 6445 0.934496 TGTTTCTTGTTCGGTCAGCG 59.066 50.000 0.00 0.00 0.00 5.18
6274 6457 1.674441 CGGTCAGCGGTGATCTAGTTA 59.326 52.381 24.15 0.00 34.36 2.24
6338 6521 1.364626 GCGTGTCTGCCTCTGGATTG 61.365 60.000 0.00 0.00 0.00 2.67
6366 6549 3.456277 AGTGTTGAAGAAGAGTGGGTTCT 59.544 43.478 0.00 0.00 35.71 3.01
6386 6571 7.875554 GGGTTCTTGGAATCTTAGTGATATCTC 59.124 40.741 3.98 0.00 34.45 2.75
6424 6609 3.529533 CTTCACATACCCTCTGCTTCTG 58.470 50.000 0.00 0.00 0.00 3.02
6426 6611 2.497675 TCACATACCCTCTGCTTCTGTC 59.502 50.000 0.00 0.00 0.00 3.51
6433 6618 2.165437 CCCTCTGCTTCTGTCTGAGTAC 59.835 54.545 0.00 0.00 0.00 2.73
6537 6748 7.446625 ACAGCTTTGTTCAGAACTTCTAATGAT 59.553 33.333 14.51 0.00 0.00 2.45
6565 6776 0.110644 GAAACGAGCAAGCGTGAAGG 60.111 55.000 2.99 0.00 44.86 3.46
6598 6809 9.246670 TCCAGAACAACATCAATCAATATCTTT 57.753 29.630 0.00 0.00 0.00 2.52
6603 6814 8.044060 ACAACATCAATCAATATCTTTCGTGT 57.956 30.769 0.00 0.00 0.00 4.49
6624 6835 4.221703 TGTTGTTCACATCAAAACCTTGGT 59.778 37.500 0.00 0.00 33.01 3.67
6698 6909 3.446873 TCACATTTCACAGGCACAAAAGT 59.553 39.130 0.00 0.00 0.00 2.66
6720 6931 1.271543 TGAGGTTGTCTGAGCAATGGG 60.272 52.381 0.00 0.00 0.00 4.00
6752 6963 5.985530 AGAAAAATAAGCAGAGCCAACAAAC 59.014 36.000 0.00 0.00 0.00 2.93
6754 6965 2.356665 TAAGCAGAGCCAACAAACCA 57.643 45.000 0.00 0.00 0.00 3.67
6757 6968 2.041701 AGCAGAGCCAACAAACCAAAT 58.958 42.857 0.00 0.00 0.00 2.32
6759 6970 3.640967 AGCAGAGCCAACAAACCAAATTA 59.359 39.130 0.00 0.00 0.00 1.40
6760 6971 3.740832 GCAGAGCCAACAAACCAAATTAC 59.259 43.478 0.00 0.00 0.00 1.89
6761 6972 4.306600 CAGAGCCAACAAACCAAATTACC 58.693 43.478 0.00 0.00 0.00 2.85
6762 6973 3.005367 AGAGCCAACAAACCAAATTACCG 59.995 43.478 0.00 0.00 0.00 4.02
6763 6974 1.795872 GCCAACAAACCAAATTACCGC 59.204 47.619 0.00 0.00 0.00 5.68
6774 6986 2.983136 CAAATTACCGCGCATTTTGTCA 59.017 40.909 8.75 0.00 0.00 3.58
6778 6990 1.927895 ACCGCGCATTTTGTCAAAAA 58.072 40.000 14.47 0.34 39.53 1.94
6839 7051 3.871074 CTGAAATCAGCTGACCCATGTCA 60.871 47.826 20.97 12.92 42.05 3.58
6886 7098 5.061721 ACTGAACAAACCTAACCTCCATT 57.938 39.130 0.00 0.00 0.00 3.16
6915 7127 8.645814 AAAGAATTTTAATACTCCCTCCGTTT 57.354 30.769 0.00 0.00 31.62 3.60
6975 7270 6.318900 CACTTATTTTGGGACAGAGGGAATAC 59.681 42.308 0.00 0.00 42.39 1.89
6976 7271 3.732048 TTTTGGGACAGAGGGAATACC 57.268 47.619 0.00 0.00 42.39 2.73
7021 7513 8.823220 AAATTATCCTGCCAGTTAGTTACATT 57.177 30.769 0.00 0.00 0.00 2.71
7045 7537 4.159879 GCACAAACTCTAGCCTCTAGGTTA 59.840 45.833 0.00 0.00 37.57 2.85
7083 7575 0.030638 CTTGTGGTTTTGCGACAGGG 59.969 55.000 0.00 0.00 37.14 4.45
7085 7577 1.358759 GTGGTTTTGCGACAGGGTG 59.641 57.895 0.00 0.00 0.00 4.61
7136 7628 9.606631 AGATCAATAGACAGGTCACTAAAATTC 57.393 33.333 1.84 0.00 0.00 2.17
7145 7637 8.029642 ACAGGTCACTAAAATTCATCTAAACG 57.970 34.615 0.00 0.00 0.00 3.60
7203 7696 8.643324 AGATTGATAGCTAAAGTTCGGTCTTAT 58.357 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.510691 AACGCCGATTACCAGCCG 60.511 61.111 0.00 0.00 0.00 5.52
9 10 0.937304 CCATCAACGCCGATTACCAG 59.063 55.000 0.00 0.00 0.00 4.00
10 11 0.250793 ACCATCAACGCCGATTACCA 59.749 50.000 0.00 0.00 0.00 3.25
11 12 0.935196 GACCATCAACGCCGATTACC 59.065 55.000 0.00 0.00 0.00 2.85
12 13 0.935196 GGACCATCAACGCCGATTAC 59.065 55.000 0.00 0.00 0.00 1.89
13 14 0.537653 TGGACCATCAACGCCGATTA 59.462 50.000 0.00 0.00 0.00 1.75
14 15 0.322098 TTGGACCATCAACGCCGATT 60.322 50.000 0.00 0.00 0.00 3.34
15 16 0.322098 TTTGGACCATCAACGCCGAT 60.322 50.000 0.00 0.00 0.00 4.18
16 17 0.322098 ATTTGGACCATCAACGCCGA 60.322 50.000 0.00 0.00 0.00 5.54
17 18 0.098728 GATTTGGACCATCAACGCCG 59.901 55.000 0.00 0.00 0.00 6.46
18 19 0.455815 GGATTTGGACCATCAACGCC 59.544 55.000 0.00 0.00 0.00 5.68
19 20 0.455815 GGGATTTGGACCATCAACGC 59.544 55.000 0.00 0.00 0.00 4.84
20 21 1.832883 TGGGATTTGGACCATCAACG 58.167 50.000 0.00 0.00 0.00 4.10
21 22 2.159057 GCATGGGATTTGGACCATCAAC 60.159 50.000 0.00 0.00 45.37 3.18
22 23 2.109774 GCATGGGATTTGGACCATCAA 58.890 47.619 0.00 0.00 45.37 2.57
23 24 1.688942 GGCATGGGATTTGGACCATCA 60.689 52.381 0.00 0.00 45.37 3.07
75 76 0.690192 TGATGCCTTGTCTCCGGAAA 59.310 50.000 5.23 0.00 0.00 3.13
76 77 0.690192 TTGATGCCTTGTCTCCGGAA 59.310 50.000 5.23 0.00 0.00 4.30
80 81 0.169009 GCGTTTGATGCCTTGTCTCC 59.831 55.000 0.00 0.00 0.00 3.71
85 86 2.871080 CGCGCGTTTGATGCCTTG 60.871 61.111 24.19 0.00 0.00 3.61
104 105 2.493973 GAGCTCCTCACCAGCGAG 59.506 66.667 0.87 0.00 42.14 5.03
105 106 2.211468 TAGGAGCTCCTCACCAGCGA 62.211 60.000 38.44 16.22 44.77 4.93
106 107 1.112315 ATAGGAGCTCCTCACCAGCG 61.112 60.000 38.44 0.00 44.77 5.18
107 108 1.616374 GTATAGGAGCTCCTCACCAGC 59.384 57.143 38.44 18.92 44.77 4.85
108 109 2.890311 CTGTATAGGAGCTCCTCACCAG 59.110 54.545 38.44 31.68 44.77 4.00
109 110 2.950781 CTGTATAGGAGCTCCTCACCA 58.049 52.381 38.44 27.79 44.77 4.17
110 111 1.616374 GCTGTATAGGAGCTCCTCACC 59.384 57.143 38.44 25.00 44.77 4.02
111 112 1.268352 CGCTGTATAGGAGCTCCTCAC 59.732 57.143 38.44 32.53 44.77 3.51
112 113 1.133761 ACGCTGTATAGGAGCTCCTCA 60.134 52.381 38.44 27.36 44.77 3.86
113 114 1.611519 ACGCTGTATAGGAGCTCCTC 58.388 55.000 38.44 24.26 44.77 3.71
132 133 0.682532 TCATTAATGGGCGCCTGCAA 60.683 50.000 28.56 15.50 45.35 4.08
144 145 1.951510 CAGGCGCCGCATCATTAAT 59.048 52.632 23.20 0.00 0.00 1.40
184 185 2.352805 GGCAGCAAGCTAGTGGGT 59.647 61.111 0.00 0.00 44.79 4.51
889 935 1.705337 CGATTAGCAGCACGGTTGGG 61.705 60.000 0.00 0.00 0.00 4.12
892 938 2.106683 GCCGATTAGCAGCACGGTT 61.107 57.895 17.09 0.00 45.91 4.44
901 947 1.446907 CAGATCATGGGCCGATTAGC 58.553 55.000 0.00 0.00 0.00 3.09
927 973 2.746362 TCCGAGACGAAGAAACTACTCC 59.254 50.000 0.00 0.00 0.00 3.85
928 974 3.436359 AGTCCGAGACGAAGAAACTACTC 59.564 47.826 0.00 0.00 37.67 2.59
929 975 3.410508 AGTCCGAGACGAAGAAACTACT 58.589 45.455 0.00 0.00 37.67 2.57
930 976 3.724422 CGAGTCCGAGACGAAGAAACTAC 60.724 52.174 0.00 0.00 37.67 2.73
931 977 2.414481 CGAGTCCGAGACGAAGAAACTA 59.586 50.000 0.00 0.00 37.67 2.24
932 978 1.197264 CGAGTCCGAGACGAAGAAACT 59.803 52.381 0.00 0.00 37.67 2.66
933 979 1.604396 CGAGTCCGAGACGAAGAAAC 58.396 55.000 0.00 0.00 37.67 2.78
934 980 0.109873 GCGAGTCCGAGACGAAGAAA 60.110 55.000 0.00 0.00 37.67 2.52
937 983 1.226156 CAGCGAGTCCGAGACGAAG 60.226 63.158 0.00 0.00 37.67 3.79
971 1075 0.611062 GAGGGGGTTTCGGGAAAAGG 60.611 60.000 0.00 0.00 31.33 3.11
972 1076 0.404426 AGAGGGGGTTTCGGGAAAAG 59.596 55.000 0.00 0.00 31.33 2.27
973 1077 0.111639 CAGAGGGGGTTTCGGGAAAA 59.888 55.000 0.00 0.00 31.33 2.29
974 1078 1.765074 CAGAGGGGGTTTCGGGAAA 59.235 57.895 0.00 0.00 0.00 3.13
1004 1108 2.434336 GCCCCAAAGAAGAAAGGTTGTT 59.566 45.455 0.00 0.00 0.00 2.83
1012 1116 2.289694 CGAAGAGAGCCCCAAAGAAGAA 60.290 50.000 0.00 0.00 0.00 2.52
1013 1117 1.276421 CGAAGAGAGCCCCAAAGAAGA 59.724 52.381 0.00 0.00 0.00 2.87
1017 1121 1.301677 GCACGAAGAGAGCCCCAAAG 61.302 60.000 0.00 0.00 0.00 2.77
1020 1129 2.922503 TGCACGAAGAGAGCCCCA 60.923 61.111 0.00 0.00 0.00 4.96
1324 1435 5.163457 CCCTAACAAAGCAAGGAAAAAGACA 60.163 40.000 0.00 0.00 31.64 3.41
1558 1670 2.502947 CCCAGAATGATGGACTGTCTCA 59.497 50.000 7.85 5.02 43.57 3.27
1812 1946 6.545202 GACCAACGTCTCAATGGGTAACATT 61.545 44.000 8.05 0.00 41.97 2.71
1906 2040 0.543410 ACCGATGGGACTGTGGTGTA 60.543 55.000 0.00 0.00 36.97 2.90
1933 2068 4.141959 CCAAATTTGGGTTGACTCACTTGT 60.142 41.667 26.87 0.00 44.70 3.16
1991 2126 5.770162 AGGCTAATAACCCTCATAAATGCAC 59.230 40.000 0.00 0.00 0.00 4.57
2042 2177 8.263940 TCTAGAACAAAGGTAATTTTGGATCG 57.736 34.615 0.00 0.00 41.29 3.69
2088 2223 6.307800 CCAAAGAAAAACAAGGCGTACATATG 59.692 38.462 0.00 0.00 0.00 1.78
2089 2224 6.207810 TCCAAAGAAAAACAAGGCGTACATAT 59.792 34.615 0.00 0.00 0.00 1.78
2093 2228 4.295857 TCCAAAGAAAAACAAGGCGTAC 57.704 40.909 0.00 0.00 0.00 3.67
2164 2301 7.538575 ACACAACATCTTTACAAATAGCATCC 58.461 34.615 0.00 0.00 0.00 3.51
2225 2362 0.991920 CCCACTGGGTAACATGGTCT 59.008 55.000 5.85 0.00 38.25 3.85
2276 2413 0.393537 GTTCAGGGACATGGAGCCAG 60.394 60.000 0.00 0.00 0.00 4.85
2340 2477 8.122481 AGAATAACTTAAGAATGGGAATGGGTT 58.878 33.333 10.09 0.00 0.00 4.11
2404 2541 6.309737 CAGAATGCTAAAAAGAAACAGATGGC 59.690 38.462 0.00 0.00 0.00 4.40
2547 2684 4.095334 CGCTACCCGCTATTTAAAACCTTT 59.905 41.667 0.00 0.00 36.13 3.11
2625 2762 0.526211 CTATGCGGACATAGCGCCTA 59.474 55.000 2.29 0.00 46.91 3.93
2729 2866 1.207593 CTATTGCGGCCGCTATTGC 59.792 57.895 42.94 20.70 42.51 3.56
2730 2867 1.207593 GCTATTGCGGCCGCTATTG 59.792 57.895 42.94 39.42 42.51 1.90
2731 2868 3.655481 GCTATTGCGGCCGCTATT 58.345 55.556 42.94 31.41 42.51 1.73
2767 2904 8.947115 GGCATAGTTTTAAATAGCGGAGATAAT 58.053 33.333 0.00 0.00 0.00 1.28
2858 2995 5.961272 TCTGCTTATGACATCGTAGTTCAA 58.039 37.500 0.00 0.00 0.00 2.69
2940 3077 4.075682 TGGTCTTGTTTCTGTTGACACAA 58.924 39.130 0.00 0.00 39.62 3.33
2941 3078 3.680490 TGGTCTTGTTTCTGTTGACACA 58.320 40.909 0.00 0.00 31.81 3.72
2942 3079 3.487544 GCTGGTCTTGTTTCTGTTGACAC 60.488 47.826 0.00 0.00 0.00 3.67
2943 3080 2.682856 GCTGGTCTTGTTTCTGTTGACA 59.317 45.455 0.00 0.00 0.00 3.58
2944 3081 2.945668 AGCTGGTCTTGTTTCTGTTGAC 59.054 45.455 0.00 0.00 0.00 3.18
3068 3210 1.546923 CACATTTGCTTGATCCCAGCA 59.453 47.619 11.70 11.70 36.72 4.41
3157 3299 6.151817 GCCTTCATCTAAAATGACTTTGGTCT 59.848 38.462 0.00 0.00 42.54 3.85
3168 3312 4.142600 GCTCACAACGCCTTCATCTAAAAT 60.143 41.667 0.00 0.00 0.00 1.82
3174 3318 1.421485 CGCTCACAACGCCTTCATC 59.579 57.895 0.00 0.00 0.00 2.92
3251 3395 0.621082 CCCTCCTGTCTTTCCTTCCC 59.379 60.000 0.00 0.00 0.00 3.97
3260 3404 1.156322 TTCCCCTCTCCCTCCTGTCT 61.156 60.000 0.00 0.00 0.00 3.41
3263 3407 0.980231 CACTTCCCCTCTCCCTCCTG 60.980 65.000 0.00 0.00 0.00 3.86
3266 3410 0.689412 CTCCACTTCCCCTCTCCCTC 60.689 65.000 0.00 0.00 0.00 4.30
3270 3414 0.336737 TCTCCTCCACTTCCCCTCTC 59.663 60.000 0.00 0.00 0.00 3.20
3272 3416 1.657804 TTTCTCCTCCACTTCCCCTC 58.342 55.000 0.00 0.00 0.00 4.30
3273 3417 2.133858 TTTTCTCCTCCACTTCCCCT 57.866 50.000 0.00 0.00 0.00 4.79
3274 3418 2.971901 TTTTTCTCCTCCACTTCCCC 57.028 50.000 0.00 0.00 0.00 4.81
3292 3437 5.458779 GTGCGAGAATAACTGCAAAGTTTTT 59.541 36.000 0.00 0.00 35.63 1.94
3375 3524 3.847542 CCGATCTGATCAAGCTATGGAG 58.152 50.000 17.19 0.00 0.00 3.86
3392 3541 0.976641 TTCTCACTGAGGTTGCCGAT 59.023 50.000 6.20 0.00 0.00 4.18
3398 3547 2.192263 GGGAGGATTCTCACTGAGGTT 58.808 52.381 2.72 0.00 40.23 3.50
3419 3568 3.146066 TCATAACAAGTGTTGGACAGCC 58.854 45.455 6.94 0.00 38.90 4.85
3437 3586 5.477984 TGCTAGGAATGAGCAAGTTTTTCAT 59.522 36.000 0.00 0.00 46.71 2.57
3509 3658 2.017049 GAAATAGCGAAGGCACATGGT 58.983 47.619 0.00 0.00 43.41 3.55
3520 3669 1.831106 TCTTGGCCTCTGAAATAGCGA 59.169 47.619 3.32 0.00 0.00 4.93
3527 3679 2.040813 AGCAGATTTCTTGGCCTCTGAA 59.959 45.455 18.83 10.71 37.85 3.02
3554 3706 1.345741 CTGGACTTGGTCTCAGCTGAA 59.654 52.381 18.85 6.19 32.47 3.02
3558 3710 0.248843 CTCCTGGACTTGGTCTCAGC 59.751 60.000 0.00 0.00 33.07 4.26
3559 3711 0.901124 CCTCCTGGACTTGGTCTCAG 59.099 60.000 0.00 0.00 33.69 3.35
3617 3772 5.063186 CGAAACTATGCATCATATCCTGCTC 59.937 44.000 0.19 0.00 39.16 4.26
3623 3778 4.436584 GCAGCCGAAACTATGCATCATATC 60.437 45.833 0.19 0.00 38.54 1.63
3679 3834 1.140312 AAGGAAGCACTGGACAAGGA 58.860 50.000 0.00 0.00 0.00 3.36
3713 3868 2.026822 CCTCAAGGACAGGCACAATACT 60.027 50.000 0.00 0.00 37.39 2.12
3716 3871 0.038744 CCCTCAAGGACAGGCACAAT 59.961 55.000 0.00 0.00 38.24 2.71
3760 3915 2.309162 TGGGACCGAATCATACCCAAAA 59.691 45.455 0.00 0.00 46.06 2.44
3826 3982 6.196538 GCTTTCTACGGCATATTTTTACAAGC 59.803 38.462 0.00 0.00 0.00 4.01
3860 4018 1.596477 CAGGAGGCCGCTAGCATTC 60.596 63.158 16.45 5.92 46.50 2.67
3863 4021 2.444706 ATCAGGAGGCCGCTAGCA 60.445 61.111 16.45 0.00 46.50 3.49
3896 4054 2.012673 CTAAGCTGCATCTCACCAACC 58.987 52.381 1.02 0.00 0.00 3.77
3920 4078 2.094442 GGAGCTGGAGACACTAACTGAC 60.094 54.545 0.00 0.00 35.60 3.51
3922 4080 1.205893 GGGAGCTGGAGACACTAACTG 59.794 57.143 0.00 0.00 35.60 3.16
4085 4246 7.734865 ACCACCATATCTTTCTGGTATGATCTA 59.265 37.037 0.00 0.00 43.91 1.98
4106 4267 2.048603 GCTTGGAGATGGCACCACC 61.049 63.158 0.00 0.00 34.33 4.61
4150 4311 3.198068 TGCATCAAATCTTCTCTACCGC 58.802 45.455 0.00 0.00 0.00 5.68
4152 4313 3.247173 CGCTGCATCAAATCTTCTCTACC 59.753 47.826 0.00 0.00 0.00 3.18
4154 4315 2.868583 GCGCTGCATCAAATCTTCTCTA 59.131 45.455 0.00 0.00 0.00 2.43
4156 4317 1.268437 GGCGCTGCATCAAATCTTCTC 60.268 52.381 7.64 0.00 0.00 2.87
4190 4351 0.388134 CACTTACGGTGCGCAGTACT 60.388 55.000 12.22 0.00 44.37 2.73
4220 4381 3.435327 GGTTTGCATCAACATACTGTCGA 59.565 43.478 3.80 0.00 0.00 4.20
4250 4411 2.903855 CCCAGCGATGTCCCATGC 60.904 66.667 0.00 0.00 0.00 4.06
4313 4480 1.445582 CTTGGGCGTACGTGACCTC 60.446 63.158 17.90 0.00 0.00 3.85
4331 4498 2.514205 ACAACACATTTGCTTGAGGC 57.486 45.000 2.55 0.00 42.22 4.70
4359 4526 9.320295 ACCCTTTTCACCTAAAATAATTGATCA 57.680 29.630 0.00 0.00 36.49 2.92
4362 4529 9.771534 CAAACCCTTTTCACCTAAAATAATTGA 57.228 29.630 0.00 0.00 36.49 2.57
4363 4530 8.998377 CCAAACCCTTTTCACCTAAAATAATTG 58.002 33.333 0.00 0.00 36.49 2.32
4633 4800 2.352805 CCGCCTTTCTCCTTGGCT 59.647 61.111 0.00 0.00 44.09 4.75
4726 4894 9.220767 GGCAATAGAGATAAGTTAAACCCATAG 57.779 37.037 0.00 0.00 0.00 2.23
4732 4900 7.388224 GGGCTAGGCAATAGAGATAAGTTAAAC 59.612 40.741 19.14 0.00 32.76 2.01
4800 4968 6.189036 AGTCCTTATTAGGCTATGTTTCCC 57.811 41.667 0.00 0.00 41.69 3.97
4978 5147 7.845622 CGAAGAAAATAACAACTTGGCAAAAAG 59.154 33.333 0.00 0.00 0.00 2.27
4992 5163 7.166473 GTCATTGATGGATGCGAAGAAAATAAC 59.834 37.037 0.00 0.00 0.00 1.89
5015 5186 3.524789 AGAATCAACATCATCCCCTGTCA 59.475 43.478 0.00 0.00 0.00 3.58
5033 5204 6.784031 ACTAACAATGAGGGAAACAGAGAAT 58.216 36.000 0.00 0.00 0.00 2.40
5262 5433 7.725251 TGTTCACCATTTTGCTTTAGAAGAAT 58.275 30.769 0.00 0.00 0.00 2.40
5273 5444 4.152759 CCACATGATTGTTCACCATTTTGC 59.847 41.667 0.00 0.00 33.85 3.68
5343 5514 5.783111 AGCGGAAGAAAGTTGCATAAAATT 58.217 33.333 0.00 0.00 0.00 1.82
5502 5673 3.772387 TGCCACCAAAACCAATGATCTA 58.228 40.909 0.00 0.00 0.00 1.98
5518 5689 6.589523 TGAAATGCATTATTACACTTTGCCAC 59.410 34.615 13.39 0.00 32.39 5.01
5520 5691 7.775397 ATGAAATGCATTATTACACTTTGCC 57.225 32.000 13.39 0.00 31.73 4.52
5596 5767 8.710551 CATAAACATCTGAATCTACTCATCAGC 58.289 37.037 0.00 0.00 40.26 4.26
5771 5944 1.293924 CATCCTCATCGTCCACTTGC 58.706 55.000 0.00 0.00 0.00 4.01
5792 5965 4.993905 ACTCGTCATCATCGTAACATTCA 58.006 39.130 0.00 0.00 0.00 2.57
5905 6078 2.502510 GGCTGCATGTTCAACGCG 60.503 61.111 3.53 3.53 0.00 6.01
6063 6236 2.443260 TTTTCTGCCGCCGCTACTCA 62.443 55.000 0.00 0.00 35.36 3.41
6079 6252 4.901250 CCAGGCCCCATCTAACATTATTTT 59.099 41.667 0.00 0.00 0.00 1.82
6083 6256 1.780309 CCCAGGCCCCATCTAACATTA 59.220 52.381 0.00 0.00 0.00 1.90
6084 6257 0.557729 CCCAGGCCCCATCTAACATT 59.442 55.000 0.00 0.00 0.00 2.71
6086 6259 1.230149 ACCCAGGCCCCATCTAACA 60.230 57.895 0.00 0.00 0.00 2.41
6087 6260 1.227383 CACCCAGGCCCCATCTAAC 59.773 63.158 0.00 0.00 0.00 2.34
6088 6261 0.045008 TACACCCAGGCCCCATCTAA 59.955 55.000 0.00 0.00 0.00 2.10
6090 6263 0.627469 ATTACACCCAGGCCCCATCT 60.627 55.000 0.00 0.00 0.00 2.90
6091 6264 0.178990 GATTACACCCAGGCCCCATC 60.179 60.000 0.00 0.00 0.00 3.51
6092 6265 0.627469 AGATTACACCCAGGCCCCAT 60.627 55.000 0.00 0.00 0.00 4.00
6093 6266 0.849094 AAGATTACACCCAGGCCCCA 60.849 55.000 0.00 0.00 0.00 4.96
6095 6268 1.005450 TCAAAGATTACACCCAGGCCC 59.995 52.381 0.00 0.00 0.00 5.80
6096 6269 2.092323 GTCAAAGATTACACCCAGGCC 58.908 52.381 0.00 0.00 0.00 5.19
6097 6270 1.737793 CGTCAAAGATTACACCCAGGC 59.262 52.381 0.00 0.00 0.00 4.85
6098 6271 3.328382 TCGTCAAAGATTACACCCAGG 57.672 47.619 0.00 0.00 0.00 4.45
6185 6368 2.288948 ACGCCAGTACAATGTTTCGGTA 60.289 45.455 0.00 0.00 0.00 4.02
6262 6445 3.197983 AGCACCAACCTAACTAGATCACC 59.802 47.826 0.00 0.00 0.00 4.02
6274 6457 1.002868 CTAGCAGCAGCACCAACCT 60.003 57.895 3.17 0.00 45.49 3.50
6334 6517 6.931840 ACTCTTCTTCAACACTAACCTCAATC 59.068 38.462 0.00 0.00 0.00 2.67
6338 6521 4.991687 CCACTCTTCTTCAACACTAACCTC 59.008 45.833 0.00 0.00 0.00 3.85
6386 6571 1.772819 AAGCGGGGCCCATCAGATAG 61.773 60.000 26.86 4.17 0.00 2.08
6391 6576 4.424711 GTGAAGCGGGGCCCATCA 62.425 66.667 26.86 20.08 0.00 3.07
6424 6609 1.921230 GCTAAGCAAGCGTACTCAGAC 59.079 52.381 0.00 0.00 42.53 3.51
6537 6748 3.667695 CGCTTGCTCGTTTCATTGATTCA 60.668 43.478 0.00 0.00 0.00 2.57
6565 6776 2.622942 TGATGTTGTTCTGGAAGTTGGC 59.377 45.455 0.00 0.00 33.76 4.52
6598 6809 5.901667 CAAGGTTTTGATGTGAACAACACGA 60.902 40.000 0.00 0.00 43.06 4.35
6603 6814 5.413309 AACCAAGGTTTTGATGTGAACAA 57.587 34.783 0.00 0.00 36.36 2.83
6624 6835 1.825090 ATCAGCTGTGCAATTCCGAA 58.175 45.000 14.67 0.00 0.00 4.30
6698 6909 2.886523 CCATTGCTCAGACAACCTCAAA 59.113 45.455 0.00 0.00 31.03 2.69
6720 6931 4.870363 TCTGCTTATTTTTCTTGTGGCAC 58.130 39.130 11.55 11.55 0.00 5.01
6730 6941 5.056480 GGTTTGTTGGCTCTGCTTATTTTT 58.944 37.500 0.00 0.00 0.00 1.94
6752 6963 2.333014 ACAAAATGCGCGGTAATTTGG 58.667 42.857 8.83 13.17 35.77 3.28
6754 6965 3.290308 TGACAAAATGCGCGGTAATTT 57.710 38.095 8.83 0.00 0.00 1.82
6757 6968 2.776312 TTTGACAAAATGCGCGGTAA 57.224 40.000 8.83 0.00 0.00 2.85
6759 6970 1.857837 CTTTTTGACAAAATGCGCGGT 59.142 42.857 13.90 0.00 31.28 5.68
6760 6971 1.857837 ACTTTTTGACAAAATGCGCGG 59.142 42.857 20.60 8.60 31.28 6.46
6761 6972 3.971871 TCTACTTTTTGACAAAATGCGCG 59.028 39.130 20.60 0.00 31.28 6.86
6762 6973 5.881637 TTCTACTTTTTGACAAAATGCGC 57.118 34.783 20.60 0.00 31.28 6.09
6763 6974 6.840789 GCTTTTCTACTTTTTGACAAAATGCG 59.159 34.615 20.60 14.30 31.28 4.73
6774 6986 9.651913 TTCTTGTGAATTGCTTTTCTACTTTTT 57.348 25.926 0.00 0.00 0.00 1.94
6804 7016 6.817641 CAGCTGATTTCAGTAGTTCTTCTGAT 59.182 38.462 8.42 0.00 45.45 2.90
6808 7020 5.350091 GGTCAGCTGATTTCAGTAGTTCTTC 59.650 44.000 21.47 0.19 45.45 2.87
6816 7028 2.040813 ACATGGGTCAGCTGATTTCAGT 59.959 45.455 21.47 13.35 45.45 3.41
6839 7051 0.341961 TCCATAGTGGCCCAGGTACT 59.658 55.000 0.00 0.00 37.47 2.73
6947 7242 5.311121 TCCCTCTGTCCCAAAATAAGTGTTA 59.689 40.000 0.00 0.00 0.00 2.41
6975 7270 7.678947 ATTTACAAGAACAAGAGATGTCTGG 57.321 36.000 0.00 0.00 42.99 3.86
7004 7305 3.501828 TGTGCAATGTAACTAACTGGCAG 59.498 43.478 14.16 14.16 0.00 4.85
7021 7513 2.497675 CCTAGAGGCTAGAGTTTGTGCA 59.502 50.000 0.00 0.00 0.00 4.57
7045 7537 7.342026 ACCACAAGTTACCTTTGAAAAAGAGAT 59.658 33.333 1.31 0.00 0.00 2.75
7083 7575 3.399440 TGGATTGTTGAATTTGCCCAC 57.601 42.857 0.00 0.00 0.00 4.61
7085 7577 3.244526 ACCTTGGATTGTTGAATTTGCCC 60.245 43.478 0.00 0.00 0.00 5.36
7196 7689 5.453587 CGCTAGTGTTGTAACGTATAAGACC 59.546 44.000 0.00 0.00 0.00 3.85
7203 7696 4.090354 GCAATTCGCTAGTGTTGTAACGTA 59.910 41.667 2.66 0.00 37.77 3.57


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

AutoCloner maintained by Alex Coulton.