Multiple sequence alignment - TraesCS2B01G089100

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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 TraesCS2B01G089100 chr2B 100.000 5774 0 0 1 5774 50345189 50350962 0.000000e+00 10663
1 TraesCS2B01G089100 chr2B 100.000 1868 0 0 6061 7928 50351249 50353116 0.000000e+00 3450
2 TraesCS2B01G089100 chr2B 97.604 1461 28 3 4315 5774 83943609 83945063 0.000000e+00 2497
3 TraesCS2B01G089100 chr2B 90.924 606 27 8 1147 1752 736599974 736599397 0.000000e+00 789
4 TraesCS2B01G089100 chr2B 90.594 606 29 8 1147 1752 736604248 736603671 0.000000e+00 778
5 TraesCS2B01G089100 chr2B 96.712 365 11 1 6061 6424 83945100 83945464 2.450000e-169 606
6 TraesCS2B01G089100 chr2B 76.987 956 169 39 2343 3272 50288720 50289650 4.270000e-137 499
7 TraesCS2B01G089100 chr2B 78.986 690 112 24 2387 3060 39369135 39369807 2.630000e-119 440
8 TraesCS2B01G089100 chr2B 80.042 476 79 10 3798 4261 39371180 39371651 9.850000e-89 339
9 TraesCS2B01G089100 chr2B 79.029 453 79 14 3788 4228 50290478 50290926 6.020000e-76 296
10 TraesCS2B01G089100 chr2B 91.979 187 12 2 1 184 37777141 37776955 7.890000e-65 259
11 TraesCS2B01G089100 chr2B 90.306 196 14 4 1 193 215842589 215842396 1.320000e-62 252
12 TraesCS2B01G089100 chr2B 89.848 197 17 3 1 194 17154869 17155065 4.750000e-62 250
13 TraesCS2B01G089100 chr2B 96.800 125 4 0 976 1100 736600100 736599976 8.060000e-50 209
14 TraesCS2B01G089100 chr2B 96.800 125 4 0 976 1100 736604374 736604250 8.060000e-50 209
15 TraesCS2B01G089100 chr2B 91.743 109 9 0 266 374 50626105 50626213 1.380000e-32 152
16 TraesCS2B01G089100 chr2B 89.189 111 12 0 264 374 43799832 43799942 1.070000e-28 139
17 TraesCS2B01G089100 chr2D 96.365 3274 86 12 1046 4315 30585195 30588439 0.000000e+00 5356
18 TraesCS2B01G089100 chr2D 95.627 1532 47 4 6415 7928 30588434 30589963 0.000000e+00 2440
19 TraesCS2B01G089100 chr2D 91.950 559 36 7 182 737 30584205 30584757 0.000000e+00 774
20 TraesCS2B01G089100 chr2D 77.533 908 162 31 2386 3272 30549140 30550026 7.100000e-140 508
21 TraesCS2B01G089100 chr2D 77.727 880 149 34 2343 3195 22466097 22466956 5.530000e-136 496
22 TraesCS2B01G089100 chr2D 93.617 329 20 1 800 1127 30584761 30585089 2.570000e-134 490
23 TraesCS2B01G089100 chr2D 77.010 883 158 33 2343 3199 22431608 22430745 1.560000e-126 464
24 TraesCS2B01G089100 chr2D 80.972 494 78 12 3827 4306 22429531 22429040 2.090000e-100 377
25 TraesCS2B01G089100 chr2D 82.005 439 67 8 3798 4228 22468138 22468572 5.850000e-96 363
26 TraesCS2B01G089100 chr2D 78.475 446 81 13 3794 4228 30550401 30550842 2.180000e-70 278
27 TraesCS2B01G089100 chr2D 95.122 82 4 0 266 347 30655886 30655967 6.460000e-26 130
28 TraesCS2B01G089100 chr4B 97.682 1467 30 4 4309 5773 580802410 580803874 0.000000e+00 2518
29 TraesCS2B01G089100 chr4B 90.954 608 25 11 1147 1752 658571895 658572474 0.000000e+00 791
30 TraesCS2B01G089100 chr4B 82.603 776 86 31 5007 5767 31815207 31815948 2.410000e-179 640
31 TraesCS2B01G089100 chr4B 95.798 238 9 1 6061 6297 580804106 580804343 4.490000e-102 383
32 TraesCS2B01G089100 chr4B 97.656 128 3 0 6294 6421 580810965 580811092 3.720000e-53 220
33 TraesCS2B01G089100 chr4B 96.800 125 4 0 976 1100 658571769 658571893 8.060000e-50 209
34 TraesCS2B01G089100 chr2A 95.112 1289 38 10 2187 3468 32542844 32544114 0.000000e+00 2008
35 TraesCS2B01G089100 chr2A 95.213 1149 43 5 1046 2193 32540961 32542098 0.000000e+00 1807
36 TraesCS2B01G089100 chr2A 90.070 1138 55 20 179 1311 32539878 32540962 0.000000e+00 1423
37 TraesCS2B01G089100 chr2A 97.059 680 19 1 6415 7093 32544876 32545555 0.000000e+00 1144
38 TraesCS2B01G089100 chr2A 95.664 715 13 2 3616 4315 32544170 32544881 0.000000e+00 1133
39 TraesCS2B01G089100 chr2A 77.754 953 166 36 2343 3272 32529897 32530826 1.950000e-150 544
40 TraesCS2B01G089100 chr2A 92.090 354 26 2 7408 7761 32545956 32546307 1.540000e-136 497
41 TraesCS2B01G089100 chr2A 91.395 337 27 2 7592 7928 32546305 32546639 2.020000e-125 460
42 TraesCS2B01G089100 chr2A 77.224 843 143 32 2386 3199 24163683 24162861 1.570000e-121 448
43 TraesCS2B01G089100 chr2A 79.764 509 80 19 3815 4306 24161306 24160804 1.640000e-91 348
44 TraesCS2B01G089100 chr2A 79.427 384 71 7 3817 4195 32531706 32532086 1.700000e-66 265
45 TraesCS2B01G089100 chr2A 87.029 239 10 7 7155 7376 32545729 32545963 4.750000e-62 250
46 TraesCS2B01G089100 chr2A 95.763 118 4 1 7088 7205 32545618 32545734 1.050000e-43 189
47 TraesCS2B01G089100 chr2A 100.000 63 0 0 3496 3558 32544111 32544173 5.030000e-22 117
48 TraesCS2B01G089100 chr6B 93.951 1091 53 6 957 2044 18915585 18916665 0.000000e+00 1637
49 TraesCS2B01G089100 chrUn 93.809 953 39 8 957 1908 40797654 40798587 0.000000e+00 1415
50 TraesCS2B01G089100 chrUn 96.296 81 2 1 847 927 40797577 40797656 1.800000e-26 132
51 TraesCS2B01G089100 chr3B 84.807 1323 137 29 4318 5621 250281415 250282692 0.000000e+00 1271
52 TraesCS2B01G089100 chr3B 90.625 608 28 10 1145 1752 11381646 11382224 0.000000e+00 780
53 TraesCS2B01G089100 chr3B 83.443 610 73 15 5041 5636 670999493 671000088 7.000000e-150 542
54 TraesCS2B01G089100 chr3B 92.350 183 13 1 1 182 756284654 756284472 7.890000e-65 259
55 TraesCS2B01G089100 chr3B 97.656 128 3 0 976 1103 11381522 11381649 3.720000e-53 220
56 TraesCS2B01G089100 chr3B 96.800 125 4 0 976 1100 123784959 123784835 8.060000e-50 209
57 TraesCS2B01G089100 chr3D 86.796 1136 122 10 4315 5434 171351683 171352806 0.000000e+00 1242
58 TraesCS2B01G089100 chr3D 84.014 294 34 5 6124 6415 171572751 171573033 3.650000e-68 270
59 TraesCS2B01G089100 chr3A 85.923 1094 123 13 4361 5437 208835353 208836432 0.000000e+00 1138
60 TraesCS2B01G089100 chr3A 80.894 649 74 29 5140 5772 1798976 1798362 4.330000e-127 466
61 TraesCS2B01G089100 chr4A 82.444 974 117 33 4819 5774 587253489 587252552 0.000000e+00 802
62 TraesCS2B01G089100 chr4A 91.892 185 12 2 1 182 71082477 71082661 1.020000e-63 255
63 TraesCS2B01G089100 chr7B 92.915 494 24 5 1259 1752 625272389 625272871 0.000000e+00 708
64 TraesCS2B01G089100 chr7B 90.845 284 22 4 1626 1908 398322741 398322461 2.090000e-100 377
65 TraesCS2B01G089100 chr7B 90.722 194 15 2 1 191 377817304 377817497 1.020000e-63 255
66 TraesCS2B01G089100 chr5D 83.220 733 103 15 4315 5036 483880457 483881180 0.000000e+00 654
67 TraesCS2B01G089100 chr5D 92.473 186 11 2 1 183 128585892 128585707 6.100000e-66 263
68 TraesCS2B01G089100 chr5A 83.051 708 102 14 4336 5036 605662692 605661996 1.880000e-175 627
69 TraesCS2B01G089100 chr1B 83.013 624 78 15 5027 5636 532068372 532068981 2.520000e-149 540
70 TraesCS2B01G089100 chr1B 87.879 66 4 3 674 739 685657383 685657322 3.070000e-09 75
71 TraesCS2B01G089100 chr6A 80.102 784 97 30 4882 5620 26483536 26482767 5.450000e-146 529
72 TraesCS2B01G089100 chr6A 90.256 195 15 3 2 193 6808044 6808237 1.320000e-62 252
73 TraesCS2B01G089100 chr5B 90.625 224 19 2 1822 2044 700120522 700120744 6.020000e-76 296
74 TraesCS2B01G089100 chr1A 91.099 191 13 3 1 188 482775967 482775778 1.020000e-63 255
75 TraesCS2B01G089100 chr4D 87.500 136 8 6 3157 3291 281291328 281291455 1.780000e-31 148


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 TraesCS2B01G089100 chr2B 50345189 50353116 7927 False 7056.50 10663 100.00000 1 7928 2 chr2B.!!$F6 7927
1 TraesCS2B01G089100 chr2B 83943609 83945464 1855 False 1551.50 2497 97.15800 4315 6424 2 chr2B.!!$F7 2109
2 TraesCS2B01G089100 chr2B 736599397 736604374 4977 True 496.25 789 93.77950 976 1752 4 chr2B.!!$R3 776
3 TraesCS2B01G089100 chr2B 50288720 50290926 2206 False 397.50 499 78.00800 2343 4228 2 chr2B.!!$F5 1885
4 TraesCS2B01G089100 chr2B 39369135 39371651 2516 False 389.50 440 79.51400 2387 4261 2 chr2B.!!$F4 1874
5 TraesCS2B01G089100 chr2D 30584205 30589963 5758 False 2265.00 5356 94.38975 182 7928 4 chr2D.!!$F4 7746
6 TraesCS2B01G089100 chr2D 22466097 22468572 2475 False 429.50 496 79.86600 2343 4228 2 chr2D.!!$F2 1885
7 TraesCS2B01G089100 chr2D 22429040 22431608 2568 True 420.50 464 78.99100 2343 4306 2 chr2D.!!$R1 1963
8 TraesCS2B01G089100 chr2D 30549140 30550842 1702 False 393.00 508 78.00400 2386 4228 2 chr2D.!!$F3 1842
9 TraesCS2B01G089100 chr4B 580802410 580804343 1933 False 1450.50 2518 96.74000 4309 6297 2 chr4B.!!$F3 1988
10 TraesCS2B01G089100 chr4B 31815207 31815948 741 False 640.00 640 82.60300 5007 5767 1 chr4B.!!$F1 760
11 TraesCS2B01G089100 chr4B 658571769 658572474 705 False 500.00 791 93.87700 976 1752 2 chr4B.!!$F4 776
12 TraesCS2B01G089100 chr2A 32539878 32546639 6761 False 902.80 2008 93.93950 179 7928 10 chr2A.!!$F2 7749
13 TraesCS2B01G089100 chr2A 32529897 32532086 2189 False 404.50 544 78.59050 2343 4195 2 chr2A.!!$F1 1852
14 TraesCS2B01G089100 chr2A 24160804 24163683 2879 True 398.00 448 78.49400 2386 4306 2 chr2A.!!$R1 1920
15 TraesCS2B01G089100 chr6B 18915585 18916665 1080 False 1637.00 1637 93.95100 957 2044 1 chr6B.!!$F1 1087
16 TraesCS2B01G089100 chrUn 40797577 40798587 1010 False 773.50 1415 95.05250 847 1908 2 chrUn.!!$F1 1061
17 TraesCS2B01G089100 chr3B 250281415 250282692 1277 False 1271.00 1271 84.80700 4318 5621 1 chr3B.!!$F1 1303
18 TraesCS2B01G089100 chr3B 670999493 671000088 595 False 542.00 542 83.44300 5041 5636 1 chr3B.!!$F2 595
19 TraesCS2B01G089100 chr3B 11381522 11382224 702 False 500.00 780 94.14050 976 1752 2 chr3B.!!$F3 776
20 TraesCS2B01G089100 chr3D 171351683 171352806 1123 False 1242.00 1242 86.79600 4315 5434 1 chr3D.!!$F1 1119
21 TraesCS2B01G089100 chr3A 208835353 208836432 1079 False 1138.00 1138 85.92300 4361 5437 1 chr3A.!!$F1 1076
22 TraesCS2B01G089100 chr3A 1798362 1798976 614 True 466.00 466 80.89400 5140 5772 1 chr3A.!!$R1 632
23 TraesCS2B01G089100 chr4A 587252552 587253489 937 True 802.00 802 82.44400 4819 5774 1 chr4A.!!$R1 955
24 TraesCS2B01G089100 chr5D 483880457 483881180 723 False 654.00 654 83.22000 4315 5036 1 chr5D.!!$F1 721
25 TraesCS2B01G089100 chr5A 605661996 605662692 696 True 627.00 627 83.05100 4336 5036 1 chr5A.!!$R1 700
26 TraesCS2B01G089100 chr1B 532068372 532068981 609 False 540.00 540 83.01300 5027 5636 1 chr1B.!!$F1 609
27 TraesCS2B01G089100 chr6A 26482767 26483536 769 True 529.00 529 80.10200 4882 5620 1 chr6A.!!$R1 738

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
135 136 0.179100 ACTGGACGATGATTGAGGCG 60.179 55.000 0.00 0.00 0.00 5.52 F
136 137 0.179100 CTGGACGATGATTGAGGCGT 60.179 55.000 0.00 0.00 39.99 5.68 F
264 265 0.331278 CCCTGGGGACAATACAGCAA 59.669 55.000 4.27 0.00 42.06 3.91 F
351 356 0.623723 TAGCGGGAAAATCCAAGGCT 59.376 50.000 11.71 11.71 40.51 4.58 F
840 857 0.672711 GGACTGGTTTGGTACTCGCC 60.673 60.000 0.00 0.00 0.00 5.54 F
953 970 1.446272 GGACCCTTCTGCGAGTTCG 60.446 63.158 0.00 0.00 43.27 3.95 F
966 984 1.670087 CGAGTTCGTCTGCCTCATGTT 60.670 52.381 0.00 0.00 34.11 2.71 F
2108 6813 2.492484 GCTATACCATCTGGGGTAGACG 59.508 54.545 11.91 0.00 46.07 4.18 F
3331 9601 1.694150 TGAACTACAGTGAGCCTTGCT 59.306 47.619 0.00 0.00 43.88 3.91 F
4250 10983 1.680338 AGAAATGGATGCCCTTACGC 58.320 50.000 0.00 0.00 0.00 4.42 F
6102 12932 1.269621 GGTGCAGTATAATCTCGCCGT 60.270 52.381 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 5987 2.079925 GAACTAGCAGCAAGGGAACAG 58.920 52.381 0.00 0.0 0.00 3.16 R
1676 6378 2.339712 CCAGTTTTTGCGCTGGGG 59.660 61.111 9.73 0.0 46.27 4.96 R
1774 6476 5.302059 TCCTAATGCAGCTTTACGAGTATCT 59.698 40.000 0.00 0.0 0.00 1.98 R
2338 7795 4.418013 TCAATCATAACGTGCAAACAGG 57.582 40.909 0.00 0.0 37.69 4.00 R
2462 7922 3.673809 GCATAGAATCGGTAAGCCTAACG 59.326 47.826 0.00 0.0 39.72 3.18 R
2859 8333 5.360649 AGCCTCCTGGTATTAAACTTCTC 57.639 43.478 0.00 0.0 35.27 2.87 R
3167 8668 4.927267 ATTCAGGACACATAAGGGACAA 57.073 40.909 0.00 0.0 0.00 3.18 R
3885 10589 2.851263 ACCCATTCGCAACTGAGTTA 57.149 45.000 0.00 0.0 0.00 2.24 R
4313 11052 3.723835 CGCGCGCTTTTTATGTTCTAGTT 60.724 43.478 30.48 0.0 0.00 2.24 R
6339 13170 0.109919 TCGGATCACTGTCACGAACG 60.110 55.000 0.00 0.0 0.00 3.95 R
7589 14549 0.169009 GCGAGCAAAATGGTGACTCC 59.831 55.000 0.00 0.0 0.00 3.85 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
21 22 1.373748 CTGGCAAACAGCATGGTGC 60.374 57.895 24.31 10.50 46.59 5.01
30 31 4.450122 GCATGGTGCGAGCGTGTG 62.450 66.667 0.00 0.00 35.22 3.82
31 32 3.792047 CATGGTGCGAGCGTGTGG 61.792 66.667 0.00 0.00 0.00 4.17
37 38 4.683334 GCGAGCGTGTGGGCAAAC 62.683 66.667 0.00 0.00 34.64 2.93
38 39 2.972505 CGAGCGTGTGGGCAAACT 60.973 61.111 0.00 0.00 34.64 2.66
39 40 2.946762 GAGCGTGTGGGCAAACTC 59.053 61.111 0.00 0.00 34.64 3.01
40 41 1.598130 GAGCGTGTGGGCAAACTCT 60.598 57.895 0.00 0.00 34.64 3.24
41 42 1.569479 GAGCGTGTGGGCAAACTCTC 61.569 60.000 0.00 0.00 34.64 3.20
42 43 2.617274 GCGTGTGGGCAAACTCTCC 61.617 63.158 0.00 0.00 0.00 3.71
43 44 1.227823 CGTGTGGGCAAACTCTCCA 60.228 57.895 0.00 0.00 0.00 3.86
44 45 0.817634 CGTGTGGGCAAACTCTCCAA 60.818 55.000 0.00 0.00 31.73 3.53
45 46 1.620822 GTGTGGGCAAACTCTCCAAT 58.379 50.000 0.00 0.00 31.73 3.16
46 47 1.270550 GTGTGGGCAAACTCTCCAATG 59.729 52.381 0.00 0.00 31.73 2.82
47 48 0.244721 GTGGGCAAACTCTCCAATGC 59.755 55.000 0.00 0.00 38.06 3.56
50 51 2.657297 GCAAACTCTCCAATGCCCA 58.343 52.632 0.00 0.00 32.73 5.36
51 52 0.244721 GCAAACTCTCCAATGCCCAC 59.755 55.000 0.00 0.00 32.73 4.61
52 53 1.619654 CAAACTCTCCAATGCCCACA 58.380 50.000 0.00 0.00 0.00 4.17
53 54 1.270550 CAAACTCTCCAATGCCCACAC 59.729 52.381 0.00 0.00 0.00 3.82
54 55 0.478072 AACTCTCCAATGCCCACACA 59.522 50.000 0.00 0.00 0.00 3.72
55 56 0.250901 ACTCTCCAATGCCCACACAC 60.251 55.000 0.00 0.00 0.00 3.82
56 57 0.962356 CTCTCCAATGCCCACACACC 60.962 60.000 0.00 0.00 0.00 4.16
57 58 1.228521 CTCCAATGCCCACACACCA 60.229 57.895 0.00 0.00 0.00 4.17
58 59 1.228521 TCCAATGCCCACACACCAG 60.229 57.895 0.00 0.00 0.00 4.00
59 60 2.652530 CAATGCCCACACACCAGC 59.347 61.111 0.00 0.00 0.00 4.85
60 61 2.601367 AATGCCCACACACCAGCC 60.601 61.111 0.00 0.00 0.00 4.85
61 62 4.684134 ATGCCCACACACCAGCCC 62.684 66.667 0.00 0.00 0.00 5.19
68 69 3.000819 CACACCAGCCCCGTCCTA 61.001 66.667 0.00 0.00 0.00 2.94
69 70 3.001406 ACACCAGCCCCGTCCTAC 61.001 66.667 0.00 0.00 0.00 3.18
70 71 4.143333 CACCAGCCCCGTCCTACG 62.143 72.222 0.00 0.00 42.11 3.51
71 72 4.691359 ACCAGCCCCGTCCTACGT 62.691 66.667 0.00 0.00 40.58 3.57
72 73 4.143333 CCAGCCCCGTCCTACGTG 62.143 72.222 0.00 0.00 40.58 4.49
73 74 4.143333 CAGCCCCGTCCTACGTGG 62.143 72.222 0.00 0.00 42.14 4.94
76 77 4.446413 CCCCGTCCTACGTGGCAC 62.446 72.222 7.79 7.79 40.58 5.01
77 78 3.687102 CCCGTCCTACGTGGCACA 61.687 66.667 19.09 0.00 40.58 4.57
93 94 5.987777 TGGCACACAAAATCAATCTTTTG 57.012 34.783 7.53 7.53 46.63 2.44
105 106 8.511465 AAATCAATCTTTTGTGTCAAGATTCG 57.489 30.769 5.16 3.07 44.30 3.34
106 107 6.618287 TCAATCTTTTGTGTCAAGATTCGT 57.382 33.333 5.16 0.00 44.30 3.85
107 108 6.429624 TCAATCTTTTGTGTCAAGATTCGTG 58.570 36.000 5.16 0.00 44.30 4.35
108 109 4.209452 TCTTTTGTGTCAAGATTCGTGC 57.791 40.909 0.00 0.00 0.00 5.34
109 110 3.625313 TCTTTTGTGTCAAGATTCGTGCA 59.375 39.130 0.00 0.00 0.00 4.57
110 111 4.095632 TCTTTTGTGTCAAGATTCGTGCAA 59.904 37.500 0.00 0.00 0.00 4.08
111 112 4.362932 TTTGTGTCAAGATTCGTGCAAA 57.637 36.364 0.00 0.00 0.00 3.68
112 113 4.362932 TTGTGTCAAGATTCGTGCAAAA 57.637 36.364 0.00 0.00 0.00 2.44
113 114 3.951306 TGTGTCAAGATTCGTGCAAAAG 58.049 40.909 0.00 0.00 0.00 2.27
114 115 3.625313 TGTGTCAAGATTCGTGCAAAAGA 59.375 39.130 0.00 0.00 0.00 2.52
115 116 3.968724 GTGTCAAGATTCGTGCAAAAGAC 59.031 43.478 0.00 0.00 0.00 3.01
116 117 3.625313 TGTCAAGATTCGTGCAAAAGACA 59.375 39.130 0.00 0.00 0.00 3.41
117 118 3.968724 GTCAAGATTCGTGCAAAAGACAC 59.031 43.478 0.00 0.00 34.62 3.67
118 119 3.876914 TCAAGATTCGTGCAAAAGACACT 59.123 39.130 0.00 0.00 35.84 3.55
119 120 3.885484 AGATTCGTGCAAAAGACACTG 57.115 42.857 0.00 0.00 35.84 3.66
120 121 2.549754 AGATTCGTGCAAAAGACACTGG 59.450 45.455 0.00 0.00 35.84 4.00
121 122 2.031258 TTCGTGCAAAAGACACTGGA 57.969 45.000 0.00 0.00 35.84 3.86
122 123 1.295792 TCGTGCAAAAGACACTGGAC 58.704 50.000 0.00 0.00 35.84 4.02
123 124 3.825812 GTGCAAAAGACACTGGACG 57.174 52.632 0.00 0.00 35.12 4.79
124 125 1.295792 GTGCAAAAGACACTGGACGA 58.704 50.000 0.00 0.00 35.12 4.20
125 126 1.873591 GTGCAAAAGACACTGGACGAT 59.126 47.619 0.00 0.00 35.12 3.73
126 127 1.872952 TGCAAAAGACACTGGACGATG 59.127 47.619 0.00 0.00 0.00 3.84
127 128 2.143122 GCAAAAGACACTGGACGATGA 58.857 47.619 0.00 0.00 0.00 2.92
128 129 2.744202 GCAAAAGACACTGGACGATGAT 59.256 45.455 0.00 0.00 0.00 2.45
129 130 3.189287 GCAAAAGACACTGGACGATGATT 59.811 43.478 0.00 0.00 0.00 2.57
130 131 4.715896 CAAAAGACACTGGACGATGATTG 58.284 43.478 0.00 0.00 0.00 2.67
131 132 3.961480 AAGACACTGGACGATGATTGA 57.039 42.857 0.00 0.00 0.00 2.57
132 133 3.516981 AGACACTGGACGATGATTGAG 57.483 47.619 0.00 0.00 0.00 3.02
133 134 2.167281 AGACACTGGACGATGATTGAGG 59.833 50.000 0.00 0.00 0.00 3.86
134 135 1.293924 CACTGGACGATGATTGAGGC 58.706 55.000 0.00 0.00 0.00 4.70
135 136 0.179100 ACTGGACGATGATTGAGGCG 60.179 55.000 0.00 0.00 0.00 5.52
136 137 0.179100 CTGGACGATGATTGAGGCGT 60.179 55.000 0.00 0.00 39.99 5.68
137 138 0.460109 TGGACGATGATTGAGGCGTG 60.460 55.000 0.00 0.00 37.07 5.34
138 139 0.460284 GGACGATGATTGAGGCGTGT 60.460 55.000 0.00 0.00 37.07 4.49
139 140 0.647410 GACGATGATTGAGGCGTGTG 59.353 55.000 0.00 0.00 37.07 3.82
140 141 0.740868 ACGATGATTGAGGCGTGTGG 60.741 55.000 0.00 0.00 35.44 4.17
141 142 1.431488 CGATGATTGAGGCGTGTGGG 61.431 60.000 0.00 0.00 0.00 4.61
142 143 1.718757 GATGATTGAGGCGTGTGGGC 61.719 60.000 0.00 0.00 42.69 5.36
151 152 4.619227 CGTGTGGGCGAGTTGGGT 62.619 66.667 0.00 0.00 0.00 4.51
152 153 2.745037 GTGTGGGCGAGTTGGGTA 59.255 61.111 0.00 0.00 0.00 3.69
153 154 1.071814 GTGTGGGCGAGTTGGGTAA 59.928 57.895 0.00 0.00 0.00 2.85
154 155 1.071814 TGTGGGCGAGTTGGGTAAC 59.928 57.895 0.00 0.00 37.06 2.50
155 156 2.030958 GTGGGCGAGTTGGGTAACG 61.031 63.158 0.00 0.00 41.71 3.18
175 176 3.773630 CACGTGCGGGCGTTAGTG 61.774 66.667 0.82 0.00 43.83 2.74
176 177 4.289245 ACGTGCGGGCGTTAGTGT 62.289 61.111 0.00 0.00 43.04 3.55
177 178 2.126385 CGTGCGGGCGTTAGTGTA 60.126 61.111 0.00 0.00 0.00 2.90
180 181 1.142314 TGCGGGCGTTAGTGTATCC 59.858 57.895 0.00 0.00 0.00 2.59
226 227 4.379499 GGGTAAAAATGTCTCCAGCTTTCG 60.379 45.833 0.00 0.00 0.00 3.46
237 238 0.875059 CAGCTTTCGGTGACTTTCCC 59.125 55.000 0.00 0.00 41.05 3.97
249 250 0.625849 ACTTTCCCCAGCATACCCTG 59.374 55.000 0.00 0.00 0.00 4.45
264 265 0.331278 CCCTGGGGACAATACAGCAA 59.669 55.000 4.27 0.00 42.06 3.91
281 286 5.706916 ACAGCAATATAAATATGCAGCAGC 58.293 37.500 0.00 0.00 42.57 5.25
332 337 1.972223 CACACGAGACGAGGGGAGT 60.972 63.158 0.00 0.00 0.00 3.85
337 342 2.124236 AGACGAGGGGAGTAGCGG 60.124 66.667 0.00 0.00 0.00 5.52
350 355 0.738975 GTAGCGGGAAAATCCAAGGC 59.261 55.000 0.00 0.00 38.64 4.35
351 356 0.623723 TAGCGGGAAAATCCAAGGCT 59.376 50.000 11.71 11.71 40.51 4.58
352 357 0.681243 AGCGGGAAAATCCAAGGCTC 60.681 55.000 0.00 0.00 38.64 4.70
353 358 1.993369 GCGGGAAAATCCAAGGCTCG 61.993 60.000 0.00 0.00 38.64 5.03
354 359 1.376609 CGGGAAAATCCAAGGCTCGG 61.377 60.000 0.00 0.00 38.64 4.63
419 424 8.367911 GGGTTCAAGATAAAATTCAAGAACCTT 58.632 33.333 17.35 0.00 43.73 3.50
428 433 3.414700 AAGAACCTTCTGCGCGCG 61.415 61.111 28.44 28.44 37.65 6.86
533 550 2.507452 CCAGCATCGCCCATCTCA 59.493 61.111 0.00 0.00 0.00 3.27
630 647 1.601663 CCGAGATCTCATTCGTCTGGC 60.602 57.143 22.31 0.00 35.14 4.85
672 689 3.810941 TGTTCTTTATGTTTCCGCGTCTT 59.189 39.130 4.92 0.00 0.00 3.01
733 750 4.891727 ATGTCGGATCGGGCGTGC 62.892 66.667 0.00 0.00 0.00 5.34
754 771 1.079336 GGTGCTAGTTCGTGGGGAC 60.079 63.158 0.00 0.00 0.00 4.46
756 773 1.604308 TGCTAGTTCGTGGGGACGA 60.604 57.895 0.00 0.00 40.66 4.20
761 778 0.974383 AGTTCGTGGGGACGATTTCT 59.026 50.000 0.00 0.00 42.02 2.52
840 857 0.672711 GGACTGGTTTGGTACTCGCC 60.673 60.000 0.00 0.00 0.00 5.54
953 970 1.446272 GGACCCTTCTGCGAGTTCG 60.446 63.158 0.00 0.00 43.27 3.95
966 984 1.670087 CGAGTTCGTCTGCCTCATGTT 60.670 52.381 0.00 0.00 34.11 2.71
1202 1639 5.830912 TGTGCTGGAAAGAACATTTTACAG 58.169 37.500 6.39 6.39 46.97 2.74
1288 5987 3.003482 GCAGATGATGAGGTGCAAATCTC 59.997 47.826 0.00 0.00 33.88 2.75
1370 6069 4.997565 ACACTTGAGTTGTTTGTCCAATG 58.002 39.130 0.00 0.00 0.00 2.82
1411 6110 3.360867 AGAAGGATGTCTCGTCAGTCAT 58.639 45.455 0.00 0.00 31.81 3.06
1412 6111 4.527944 AGAAGGATGTCTCGTCAGTCATA 58.472 43.478 0.00 0.00 29.57 2.15
1413 6112 4.950475 AGAAGGATGTCTCGTCAGTCATAA 59.050 41.667 0.00 0.00 29.57 1.90
1541 6242 8.025445 GCCTTATTTGTGCTAGAATAATGGATG 58.975 37.037 0.00 0.00 30.01 3.51
1774 6476 4.335315 GTCAGTGATGTTTTCAAGTGTCCA 59.665 41.667 0.00 0.00 35.70 4.02
1866 6570 4.558470 GTCATAAATTGCATGTTCACCACG 59.442 41.667 0.00 0.00 0.00 4.94
2108 6813 2.492484 GCTATACCATCTGGGGTAGACG 59.508 54.545 11.91 0.00 46.07 4.18
2131 6836 8.391075 ACGTTGGATTCTTTCTGAAATTCTTA 57.609 30.769 2.88 0.00 38.29 2.10
2338 7795 6.882656 TCCAGGCATATTTCATCTATCTAGC 58.117 40.000 0.00 0.00 0.00 3.42
2357 7814 2.819608 AGCCTGTTTGCACGTTATGATT 59.180 40.909 0.00 0.00 0.00 2.57
2669 8138 3.523547 TGCATGCAACTAATTTCATGGC 58.476 40.909 20.30 0.00 37.40 4.40
2859 8333 3.281341 TGTCGCTGTTTTATTTGGCAG 57.719 42.857 0.00 0.00 0.00 4.85
3141 8637 4.392047 ACAGACAAATGAACTCTGCATGA 58.608 39.130 0.00 0.00 35.75 3.07
3259 8867 5.066893 TGCTGCATCACCAGAAAATATCTTC 59.933 40.000 0.00 0.00 35.73 2.87
3331 9601 1.694150 TGAACTACAGTGAGCCTTGCT 59.306 47.619 0.00 0.00 43.88 3.91
3468 9995 5.080337 TGCTACTAGAATAGCTGCCATAGT 58.920 41.667 12.21 2.66 46.54 2.12
3621 10184 9.492973 CATCATTTTCCATTTGACTTAAACCTT 57.507 29.630 0.00 0.00 0.00 3.50
3637 10200 3.223674 ACCTTCACTTTCCGGAATGTT 57.776 42.857 27.96 14.11 0.00 2.71
3638 10201 3.562182 ACCTTCACTTTCCGGAATGTTT 58.438 40.909 27.96 9.73 0.00 2.83
3639 10202 3.958147 ACCTTCACTTTCCGGAATGTTTT 59.042 39.130 27.96 9.06 0.00 2.43
3885 10589 4.437682 TCAGGAGTTCAGTCATTTGGTT 57.562 40.909 0.00 0.00 0.00 3.67
3906 10610 2.094762 ACTCAGTTGCGAATGGGTAC 57.905 50.000 4.77 0.00 0.00 3.34
3988 10697 8.614469 TTCAAAATCCTGTTGTTTCTTTGTTT 57.386 26.923 0.00 0.00 0.00 2.83
4250 10983 1.680338 AGAAATGGATGCCCTTACGC 58.320 50.000 0.00 0.00 0.00 4.42
4586 11329 4.619437 TCGTGGTGTTTACAAAGTTTCC 57.381 40.909 0.00 0.00 0.00 3.13
5449 12262 5.118729 TCCCTTCTAAACACCAAAACTGA 57.881 39.130 0.00 0.00 0.00 3.41
5452 12265 7.466804 TCCCTTCTAAACACCAAAACTGATAT 58.533 34.615 0.00 0.00 0.00 1.63
5453 12266 7.947890 TCCCTTCTAAACACCAAAACTGATATT 59.052 33.333 0.00 0.00 0.00 1.28
5454 12267 8.585018 CCCTTCTAAACACCAAAACTGATATTT 58.415 33.333 0.00 0.00 0.00 1.40
5669 12490 7.554835 TCAGTAATGAACAAACAGTACCAAAGT 59.445 33.333 0.00 0.00 40.62 2.66
5680 12501 2.850568 AGTACCAAAGTAATGGAGGGGG 59.149 50.000 0.00 0.00 43.54 5.40
6102 12932 1.269621 GGTGCAGTATAATCTCGCCGT 60.270 52.381 0.00 0.00 0.00 5.68
6136 12966 2.672996 GCAAAGGGCTGGCGAGAA 60.673 61.111 0.00 0.00 40.25 2.87
6144 12974 1.668151 GCTGGCGAGAAACGAAGGT 60.668 57.895 0.00 0.00 45.77 3.50
6145 12975 1.901650 GCTGGCGAGAAACGAAGGTG 61.902 60.000 0.00 0.00 45.77 4.00
6302 13133 7.773690 ACTGTTGAAGGGATTATTAATTAGCGT 59.226 33.333 0.00 0.00 0.00 5.07
6339 13170 2.003301 GACCGAGCTCAAATCTTGGAC 58.997 52.381 15.40 1.44 38.28 4.02
6341 13172 1.673033 CCGAGCTCAAATCTTGGACGT 60.673 52.381 15.40 0.00 37.30 4.34
6362 13193 0.793478 CGTGACAGTGATCCGACGAC 60.793 60.000 0.00 0.00 0.00 4.34
6464 13295 8.941977 ACGTTGAGTATTTTCTATGCATAAACA 58.058 29.630 8.00 0.00 0.00 2.83
6980 13812 5.393461 CCTGGCAAGAAAAATACTGGATGAC 60.393 44.000 0.00 0.00 0.00 3.06
7004 13836 8.152309 ACGGTGTAGAAATCTAGTGATACTAC 57.848 38.462 0.00 0.00 39.80 2.73
7100 14000 2.226330 TGGCTTGTACATGGTGTGTTC 58.774 47.619 10.47 0.00 42.29 3.18
7226 14169 9.958180 TGATATTAATTTACATCATCCGACCAT 57.042 29.630 0.00 0.00 0.00 3.55
7239 14182 7.606135 TCATCCGACCATAAGGAAAACTATA 57.394 36.000 0.00 0.00 40.32 1.31
7429 14389 4.094830 AGTATTGAACCTTTTGGGACGT 57.905 40.909 0.00 0.00 46.08 4.34
7452 14412 9.042008 ACGTACTGTTAATGAATCATGAATACC 57.958 33.333 0.00 0.00 0.00 2.73
7553 14513 7.446319 TCTCGAAGAACTATAATGTCCCGATAA 59.554 37.037 0.00 0.00 34.09 1.75
7589 14549 9.534565 CTATTCCTTGGTATATGAATGGTATCG 57.465 37.037 0.00 0.00 0.00 2.92
7661 14621 6.271488 TGCTTGTCTTTTCTTCAATATGGG 57.729 37.500 0.00 0.00 0.00 4.00
7677 14637 8.830201 TCAATATGGGAATTTGTTGTCTTTTG 57.170 30.769 0.00 0.00 0.00 2.44
7742 14702 3.624861 CCCTGAGATTTGACCATTCTTCG 59.375 47.826 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.373748 GCACCATGCTGTTTGCCAG 60.374 57.895 0.00 0.00 44.53 4.85
4 5 2.735883 GCACCATGCTGTTTGCCA 59.264 55.556 0.00 0.00 40.96 4.92
5 6 2.431260 CGCACCATGCTGTTTGCC 60.431 61.111 0.00 0.00 42.25 4.52
6 7 1.443194 CTCGCACCATGCTGTTTGC 60.443 57.895 0.00 0.00 42.25 3.68
7 8 1.443194 GCTCGCACCATGCTGTTTG 60.443 57.895 0.00 0.00 42.25 2.93
8 9 2.956987 GCTCGCACCATGCTGTTT 59.043 55.556 0.00 0.00 42.25 2.83
9 10 3.425713 CGCTCGCACCATGCTGTT 61.426 61.111 0.00 0.00 42.25 3.16
10 11 4.687215 ACGCTCGCACCATGCTGT 62.687 61.111 0.00 0.00 42.25 4.40
11 12 4.156622 CACGCTCGCACCATGCTG 62.157 66.667 0.00 0.00 42.25 4.41
12 13 4.687215 ACACGCTCGCACCATGCT 62.687 61.111 0.00 0.00 42.25 3.79
13 14 4.450122 CACACGCTCGCACCATGC 62.450 66.667 0.00 0.00 40.69 4.06
14 15 3.792047 CCACACGCTCGCACCATG 61.792 66.667 0.00 0.00 0.00 3.66
20 21 4.683334 GTTTGCCCACACGCTCGC 62.683 66.667 0.00 0.00 0.00 5.03
21 22 2.954753 GAGTTTGCCCACACGCTCG 61.955 63.158 0.00 0.00 0.00 5.03
22 23 1.569479 GAGAGTTTGCCCACACGCTC 61.569 60.000 3.27 3.27 33.49 5.03
23 24 1.598130 GAGAGTTTGCCCACACGCT 60.598 57.895 0.00 0.00 0.00 5.07
24 25 2.617274 GGAGAGTTTGCCCACACGC 61.617 63.158 0.00 0.00 0.00 5.34
25 26 0.817634 TTGGAGAGTTTGCCCACACG 60.818 55.000 0.00 0.00 0.00 4.49
26 27 1.270550 CATTGGAGAGTTTGCCCACAC 59.729 52.381 0.00 0.00 0.00 3.82
27 28 1.619654 CATTGGAGAGTTTGCCCACA 58.380 50.000 0.00 0.00 0.00 4.17
28 29 0.244721 GCATTGGAGAGTTTGCCCAC 59.755 55.000 0.00 0.00 0.00 4.61
29 30 2.657297 GCATTGGAGAGTTTGCCCA 58.343 52.632 0.00 0.00 0.00 5.36
32 33 0.244721 GTGGGCATTGGAGAGTTTGC 59.755 55.000 0.00 0.00 0.00 3.68
33 34 1.270550 GTGTGGGCATTGGAGAGTTTG 59.729 52.381 0.00 0.00 0.00 2.93
34 35 1.133513 TGTGTGGGCATTGGAGAGTTT 60.134 47.619 0.00 0.00 0.00 2.66
35 36 0.478072 TGTGTGGGCATTGGAGAGTT 59.522 50.000 0.00 0.00 0.00 3.01
36 37 0.250901 GTGTGTGGGCATTGGAGAGT 60.251 55.000 0.00 0.00 0.00 3.24
37 38 0.962356 GGTGTGTGGGCATTGGAGAG 60.962 60.000 0.00 0.00 0.00 3.20
38 39 1.074775 GGTGTGTGGGCATTGGAGA 59.925 57.895 0.00 0.00 0.00 3.71
39 40 1.228521 TGGTGTGTGGGCATTGGAG 60.229 57.895 0.00 0.00 0.00 3.86
40 41 1.228521 CTGGTGTGTGGGCATTGGA 60.229 57.895 0.00 0.00 0.00 3.53
41 42 2.934570 GCTGGTGTGTGGGCATTGG 61.935 63.158 0.00 0.00 0.00 3.16
42 43 2.652530 GCTGGTGTGTGGGCATTG 59.347 61.111 0.00 0.00 0.00 2.82
43 44 2.601367 GGCTGGTGTGTGGGCATT 60.601 61.111 0.00 0.00 0.00 3.56
44 45 4.684134 GGGCTGGTGTGTGGGCAT 62.684 66.667 0.00 0.00 0.00 4.40
50 51 3.839046 TAGGACGGGGCTGGTGTGT 62.839 63.158 0.00 0.00 0.00 3.72
51 52 3.000819 TAGGACGGGGCTGGTGTG 61.001 66.667 0.00 0.00 0.00 3.82
52 53 3.001406 GTAGGACGGGGCTGGTGT 61.001 66.667 0.00 0.00 0.00 4.16
53 54 4.143333 CGTAGGACGGGGCTGGTG 62.143 72.222 0.00 0.00 38.08 4.17
63 64 1.301423 TTTTGTGTGCCACGTAGGAC 58.699 50.000 0.00 0.00 41.22 3.85
64 65 2.147958 GATTTTGTGTGCCACGTAGGA 58.852 47.619 8.04 0.00 41.22 2.94
65 66 1.876799 TGATTTTGTGTGCCACGTAGG 59.123 47.619 0.00 0.00 37.14 3.18
66 67 3.617540 TTGATTTTGTGTGCCACGTAG 57.382 42.857 0.00 0.00 37.14 3.51
67 68 3.818210 AGATTGATTTTGTGTGCCACGTA 59.182 39.130 0.00 0.00 37.14 3.57
68 69 2.622942 AGATTGATTTTGTGTGCCACGT 59.377 40.909 0.00 0.00 37.14 4.49
69 70 3.287312 AGATTGATTTTGTGTGCCACG 57.713 42.857 0.00 0.00 37.14 4.94
70 71 5.740406 CAAAAGATTGATTTTGTGTGCCAC 58.260 37.500 4.22 0.00 42.55 5.01
71 72 5.987777 CAAAAGATTGATTTTGTGTGCCA 57.012 34.783 4.22 0.00 42.55 4.92
86 87 4.275689 TGCACGAATCTTGACACAAAAGAT 59.724 37.500 0.00 0.00 44.40 2.40
87 88 3.625313 TGCACGAATCTTGACACAAAAGA 59.375 39.130 0.00 0.00 38.01 2.52
88 89 3.951306 TGCACGAATCTTGACACAAAAG 58.049 40.909 0.00 0.00 0.00 2.27
89 90 4.362932 TTGCACGAATCTTGACACAAAA 57.637 36.364 0.00 0.00 0.00 2.44
90 91 4.362932 TTTGCACGAATCTTGACACAAA 57.637 36.364 0.00 0.00 0.00 2.83
91 92 4.095632 TCTTTTGCACGAATCTTGACACAA 59.904 37.500 0.00 0.00 0.00 3.33
92 93 3.625313 TCTTTTGCACGAATCTTGACACA 59.375 39.130 0.00 0.00 0.00 3.72
93 94 3.968724 GTCTTTTGCACGAATCTTGACAC 59.031 43.478 0.00 0.00 0.00 3.67
94 95 3.625313 TGTCTTTTGCACGAATCTTGACA 59.375 39.130 0.00 0.00 0.00 3.58
95 96 3.968724 GTGTCTTTTGCACGAATCTTGAC 59.031 43.478 0.00 0.00 0.00 3.18
96 97 3.876914 AGTGTCTTTTGCACGAATCTTGA 59.123 39.130 0.00 0.00 41.36 3.02
97 98 3.970610 CAGTGTCTTTTGCACGAATCTTG 59.029 43.478 0.00 0.00 41.36 3.02
98 99 3.003689 CCAGTGTCTTTTGCACGAATCTT 59.996 43.478 0.00 0.00 41.36 2.40
99 100 2.549754 CCAGTGTCTTTTGCACGAATCT 59.450 45.455 0.00 0.00 41.36 2.40
100 101 2.548057 TCCAGTGTCTTTTGCACGAATC 59.452 45.455 0.00 0.00 41.36 2.52
101 102 2.290641 GTCCAGTGTCTTTTGCACGAAT 59.709 45.455 0.00 0.00 41.36 3.34
102 103 1.668751 GTCCAGTGTCTTTTGCACGAA 59.331 47.619 0.00 0.00 41.36 3.85
103 104 1.295792 GTCCAGTGTCTTTTGCACGA 58.704 50.000 0.00 0.00 41.36 4.35
104 105 0.042188 CGTCCAGTGTCTTTTGCACG 60.042 55.000 0.00 0.00 41.36 5.34
105 106 1.295792 TCGTCCAGTGTCTTTTGCAC 58.704 50.000 0.00 0.00 37.13 4.57
106 107 1.872952 CATCGTCCAGTGTCTTTTGCA 59.127 47.619 0.00 0.00 0.00 4.08
107 108 2.143122 TCATCGTCCAGTGTCTTTTGC 58.857 47.619 0.00 0.00 0.00 3.68
108 109 4.452114 TCAATCATCGTCCAGTGTCTTTTG 59.548 41.667 0.00 0.00 0.00 2.44
109 110 4.641396 TCAATCATCGTCCAGTGTCTTTT 58.359 39.130 0.00 0.00 0.00 2.27
110 111 4.248859 CTCAATCATCGTCCAGTGTCTTT 58.751 43.478 0.00 0.00 0.00 2.52
111 112 3.368843 CCTCAATCATCGTCCAGTGTCTT 60.369 47.826 0.00 0.00 0.00 3.01
112 113 2.167281 CCTCAATCATCGTCCAGTGTCT 59.833 50.000 0.00 0.00 0.00 3.41
113 114 2.544685 CCTCAATCATCGTCCAGTGTC 58.455 52.381 0.00 0.00 0.00 3.67
114 115 1.406069 GCCTCAATCATCGTCCAGTGT 60.406 52.381 0.00 0.00 0.00 3.55
115 116 1.293924 GCCTCAATCATCGTCCAGTG 58.706 55.000 0.00 0.00 0.00 3.66
116 117 0.179100 CGCCTCAATCATCGTCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
117 118 0.179100 ACGCCTCAATCATCGTCCAG 60.179 55.000 0.00 0.00 0.00 3.86
118 119 0.460109 CACGCCTCAATCATCGTCCA 60.460 55.000 0.00 0.00 32.38 4.02
119 120 0.460284 ACACGCCTCAATCATCGTCC 60.460 55.000 0.00 0.00 32.38 4.79
120 121 0.647410 CACACGCCTCAATCATCGTC 59.353 55.000 0.00 0.00 32.38 4.20
121 122 0.740868 CCACACGCCTCAATCATCGT 60.741 55.000 0.00 0.00 35.35 3.73
122 123 1.431488 CCCACACGCCTCAATCATCG 61.431 60.000 0.00 0.00 0.00 3.84
123 124 1.718757 GCCCACACGCCTCAATCATC 61.719 60.000 0.00 0.00 0.00 2.92
124 125 1.750399 GCCCACACGCCTCAATCAT 60.750 57.895 0.00 0.00 0.00 2.45
125 126 2.359850 GCCCACACGCCTCAATCA 60.360 61.111 0.00 0.00 0.00 2.57
126 127 3.499737 CGCCCACACGCCTCAATC 61.500 66.667 0.00 0.00 0.00 2.67
127 128 3.958147 CTCGCCCACACGCCTCAAT 62.958 63.158 0.00 0.00 0.00 2.57
128 129 4.680237 CTCGCCCACACGCCTCAA 62.680 66.667 0.00 0.00 0.00 3.02
130 131 4.681978 AACTCGCCCACACGCCTC 62.682 66.667 0.00 0.00 0.00 4.70
131 132 4.988598 CAACTCGCCCACACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
134 135 2.718747 TTACCCAACTCGCCCACACG 62.719 60.000 0.00 0.00 0.00 4.49
135 136 1.071814 TTACCCAACTCGCCCACAC 59.928 57.895 0.00 0.00 0.00 3.82
136 137 1.071814 GTTACCCAACTCGCCCACA 59.928 57.895 0.00 0.00 0.00 4.17
137 138 2.030958 CGTTACCCAACTCGCCCAC 61.031 63.158 0.00 0.00 32.09 4.61
138 139 2.344500 CGTTACCCAACTCGCCCA 59.656 61.111 0.00 0.00 32.09 5.36
139 140 3.122971 GCGTTACCCAACTCGCCC 61.123 66.667 0.00 0.00 42.33 6.13
160 161 1.477030 GATACACTAACGCCCGCACG 61.477 60.000 0.00 0.00 39.50 5.34
161 162 1.149964 GGATACACTAACGCCCGCAC 61.150 60.000 0.00 0.00 0.00 5.34
162 163 1.142314 GGATACACTAACGCCCGCA 59.858 57.895 0.00 0.00 0.00 5.69
163 164 1.947642 CGGATACACTAACGCCCGC 60.948 63.158 0.00 0.00 0.00 6.13
164 165 0.101040 TTCGGATACACTAACGCCCG 59.899 55.000 0.00 0.00 38.41 6.13
165 166 1.135024 TGTTCGGATACACTAACGCCC 60.135 52.381 0.00 0.00 0.00 6.13
166 167 2.282701 TGTTCGGATACACTAACGCC 57.717 50.000 0.00 0.00 0.00 5.68
167 168 4.852609 ATTTGTTCGGATACACTAACGC 57.147 40.909 0.00 0.00 0.00 4.84
168 169 7.844169 CACAATATTTGTTCGGATACACTAACG 59.156 37.037 0.00 0.00 43.23 3.18
169 170 8.662141 ACACAATATTTGTTCGGATACACTAAC 58.338 33.333 0.00 0.00 43.23 2.34
170 171 8.780846 ACACAATATTTGTTCGGATACACTAA 57.219 30.769 0.00 0.00 43.23 2.24
171 172 7.493320 GGACACAATATTTGTTCGGATACACTA 59.507 37.037 5.23 0.00 43.23 2.74
172 173 6.315393 GGACACAATATTTGTTCGGATACACT 59.685 38.462 5.23 0.00 43.23 3.55
173 174 6.315393 AGGACACAATATTTGTTCGGATACAC 59.685 38.462 5.23 0.00 43.23 2.90
174 175 6.411376 AGGACACAATATTTGTTCGGATACA 58.589 36.000 5.23 0.00 43.23 2.29
175 176 6.920569 AGGACACAATATTTGTTCGGATAC 57.079 37.500 5.23 0.00 43.23 2.24
176 177 6.256975 CGAAGGACACAATATTTGTTCGGATA 59.743 38.462 11.42 0.00 43.23 2.59
177 178 5.064707 CGAAGGACACAATATTTGTTCGGAT 59.935 40.000 11.42 2.79 43.23 4.18
180 181 5.445939 CCTCGAAGGACACAATATTTGTTCG 60.446 44.000 12.28 12.28 38.82 3.95
226 227 1.682087 GGTATGCTGGGGAAAGTCACC 60.682 57.143 0.00 0.00 41.45 4.02
237 238 1.570857 TTGTCCCCAGGGTATGCTGG 61.571 60.000 4.22 0.00 40.28 4.85
249 250 8.190784 GCATATTTATATTGCTGTATTGTCCCC 58.809 37.037 0.00 0.00 0.00 4.81
264 265 4.927049 ACCCAGCTGCTGCATATTTATAT 58.073 39.130 23.86 0.00 42.74 0.86
281 286 1.382420 CTCCTCTCCAGGGACCCAG 60.382 68.421 14.60 4.17 40.80 4.45
332 337 0.623723 AGCCTTGGATTTTCCCGCTA 59.376 50.000 0.00 0.00 35.03 4.26
337 342 1.809869 GCCGAGCCTTGGATTTTCC 59.190 57.895 0.80 0.00 36.96 3.13
352 357 4.715523 TTTTCTGCCCCTCCGCCG 62.716 66.667 0.00 0.00 0.00 6.46
353 358 2.751837 CTTTTCTGCCCCTCCGCC 60.752 66.667 0.00 0.00 0.00 6.13
354 359 2.751837 CCTTTTCTGCCCCTCCGC 60.752 66.667 0.00 0.00 0.00 5.54
518 535 2.507944 GGTGAGATGGGCGATGCT 59.492 61.111 0.00 0.00 0.00 3.79
630 647 3.057315 ACATCCAGAAGCACCAAATTTCG 60.057 43.478 0.00 0.00 0.00 3.46
672 689 1.641140 CGCGAACTGTGCACAAGAA 59.359 52.632 21.98 0.00 0.00 2.52
733 750 1.736645 CCCACGAACTAGCACCACG 60.737 63.158 0.00 0.00 0.00 4.94
734 751 1.375523 CCCCACGAACTAGCACCAC 60.376 63.158 0.00 0.00 0.00 4.16
735 752 1.534476 TCCCCACGAACTAGCACCA 60.534 57.895 0.00 0.00 0.00 4.17
736 753 1.079336 GTCCCCACGAACTAGCACC 60.079 63.158 0.00 0.00 0.00 5.01
737 754 4.592426 GTCCCCACGAACTAGCAC 57.408 61.111 0.00 0.00 0.00 4.40
754 771 3.544834 CGATGCTACAGCCAAAGAAATCG 60.545 47.826 0.00 1.58 41.18 3.34
756 773 2.684881 CCGATGCTACAGCCAAAGAAAT 59.315 45.455 0.00 0.00 41.18 2.17
761 778 1.748879 GGCCGATGCTACAGCCAAA 60.749 57.895 0.00 0.00 45.07 3.28
824 841 1.740296 CCGGCGAGTACCAAACCAG 60.740 63.158 9.30 0.00 0.00 4.00
840 857 3.298958 TGACTAGCAGAAGGGCCG 58.701 61.111 0.00 0.00 0.00 6.13
947 964 1.728971 CAACATGAGGCAGACGAACTC 59.271 52.381 0.00 0.00 0.00 3.01
953 970 3.141398 TCAGAAACAACATGAGGCAGAC 58.859 45.455 0.00 0.00 0.00 3.51
966 984 4.358851 CAACGGCAAGAAATTCAGAAACA 58.641 39.130 0.00 0.00 0.00 2.83
1114 1550 2.278596 CATGCCGTCCGGACTACG 60.279 66.667 30.92 19.31 43.80 3.51
1202 1639 2.113860 TGGCAGAGCATTACTTCACC 57.886 50.000 0.00 0.00 0.00 4.02
1288 5987 2.079925 GAACTAGCAGCAAGGGAACAG 58.920 52.381 0.00 0.00 0.00 3.16
1411 6110 6.163476 AGAAATCGCACACTGTTATGAGTTA 58.837 36.000 0.00 0.00 0.00 2.24
1412 6111 4.997395 AGAAATCGCACACTGTTATGAGTT 59.003 37.500 0.00 0.00 0.00 3.01
1413 6112 4.569943 AGAAATCGCACACTGTTATGAGT 58.430 39.130 0.00 0.00 0.00 3.41
1541 6242 8.220755 TGGTACTTCATCCTAAATAATTGCAC 57.779 34.615 0.00 0.00 0.00 4.57
1676 6378 2.339712 CCAGTTTTTGCGCTGGGG 59.660 61.111 9.73 0.00 46.27 4.96
1774 6476 5.302059 TCCTAATGCAGCTTTACGAGTATCT 59.698 40.000 0.00 0.00 0.00 1.98
1866 6570 5.517770 GCACAATAAAAGAATCCACTGCATC 59.482 40.000 0.00 0.00 0.00 3.91
2076 6781 6.876257 CCCAGATGGTATAGCAGAATAAACTC 59.124 42.308 10.82 0.67 0.00 3.01
2131 6836 8.314751 TGGAAGAAGAAGAAGAAACGAATATCT 58.685 33.333 0.00 0.00 0.00 1.98
2153 6858 8.410141 ACGTCTAACAAAATGATTTTTCTGGAA 58.590 29.630 0.00 0.00 32.72 3.53
2154 6859 7.936584 ACGTCTAACAAAATGATTTTTCTGGA 58.063 30.769 0.00 0.00 32.72 3.86
2155 6860 8.574196 AACGTCTAACAAAATGATTTTTCTGG 57.426 30.769 0.00 0.00 32.72 3.86
2185 6890 9.801873 GTTTCCATTGTAATTGCACAGTATAAT 57.198 29.630 0.00 0.00 0.00 1.28
2338 7795 4.418013 TCAATCATAACGTGCAAACAGG 57.582 40.909 0.00 0.00 37.69 4.00
2357 7814 3.805066 TCCAACATTCAAGGGTCATCA 57.195 42.857 0.00 0.00 0.00 3.07
2406 7865 5.012561 CCACTAAATTGGGTGGGAAAATGAA 59.987 40.000 17.47 0.00 46.47 2.57
2462 7922 3.673809 GCATAGAATCGGTAAGCCTAACG 59.326 47.826 0.00 0.00 39.72 3.18
2859 8333 5.360649 AGCCTCCTGGTATTAAACTTCTC 57.639 43.478 0.00 0.00 35.27 2.87
3167 8668 4.927267 ATTCAGGACACATAAGGGACAA 57.073 40.909 0.00 0.00 0.00 3.18
3259 8867 3.562141 TGTGGTGGTGTTGTTCTTTATCG 59.438 43.478 0.00 0.00 0.00 2.92
3375 9879 9.900112 AAGTATTGTTTCCTCTATACCCTCTAT 57.100 33.333 0.00 0.00 30.51 1.98
3377 9881 9.900112 ATAAGTATTGTTTCCTCTATACCCTCT 57.100 33.333 0.00 0.00 30.51 3.69
3378 9882 9.930693 CATAAGTATTGTTTCCTCTATACCCTC 57.069 37.037 0.00 0.00 30.51 4.30
3379 9883 9.670442 TCATAAGTATTGTTTCCTCTATACCCT 57.330 33.333 0.00 0.00 30.51 4.34
3380 9884 9.930693 CTCATAAGTATTGTTTCCTCTATACCC 57.069 37.037 0.00 0.00 30.51 3.69
3614 10177 4.721132 ACATTCCGGAAAGTGAAGGTTTA 58.279 39.130 23.40 0.00 32.11 2.01
3885 10589 2.851263 ACCCATTCGCAACTGAGTTA 57.149 45.000 0.00 0.00 0.00 2.24
3906 10610 9.408069 ACTACAGAACATTAAGTTAAGAACTCG 57.592 33.333 1.21 0.00 41.91 4.18
3988 10697 9.660180 AGCACTTGTTTTAAAACCAAATCTAAA 57.340 25.926 24.55 11.05 38.11 1.85
4312 11051 4.491280 CGCGCGCTTTTTATGTTCTAGTTA 60.491 41.667 30.48 0.00 0.00 2.24
4313 11052 3.723835 CGCGCGCTTTTTATGTTCTAGTT 60.724 43.478 30.48 0.00 0.00 2.24
4586 11329 3.845775 CACGGTATGCTCAATTTTGAACG 59.154 43.478 0.00 0.00 36.64 3.95
4966 11730 8.357290 TGTAAGGTATGTCTCTAGCAACTTTA 57.643 34.615 0.00 0.00 0.00 1.85
5039 11803 4.279420 GGAATGGAAATAGATGCTTCCCAC 59.721 45.833 0.00 0.00 40.45 4.61
5155 11921 3.845781 AGCCTTATATGAGGGTGTGTG 57.154 47.619 16.79 0.00 45.39 3.82
5449 12262 8.857098 AGTTCTGATGCATGCTTTATGAAATAT 58.143 29.630 20.33 0.00 39.21 1.28
5452 12265 6.327154 CAGTTCTGATGCATGCTTTATGAAA 58.673 36.000 20.33 2.05 39.21 2.69
5453 12266 5.163591 CCAGTTCTGATGCATGCTTTATGAA 60.164 40.000 20.33 14.10 39.21 2.57
5454 12267 4.337274 CCAGTTCTGATGCATGCTTTATGA 59.663 41.667 20.33 9.22 39.21 2.15
5669 12490 2.041430 TGGCGTCCCCCTCCATTA 59.959 61.111 0.00 0.00 0.00 1.90
5680 12501 2.125753 CTGTCCTCTGCTGGCGTC 60.126 66.667 0.00 0.00 0.00 5.19
5689 12510 2.926779 TGCTGGCTGCTGTCCTCT 60.927 61.111 17.45 0.00 43.37 3.69
6102 12932 1.682684 GCTCCTCTGTTCCTCCCGA 60.683 63.158 0.00 0.00 0.00 5.14
6136 12966 1.057851 TCCCACCTTCCACCTTCGTT 61.058 55.000 0.00 0.00 0.00 3.85
6144 12974 0.178964 CAAAGCCTTCCCACCTTCCA 60.179 55.000 0.00 0.00 0.00 3.53
6145 12975 1.536073 GCAAAGCCTTCCCACCTTCC 61.536 60.000 0.00 0.00 0.00 3.46
6268 13099 1.550524 TCCCTTCAACAGTCTGATCCG 59.449 52.381 6.91 0.00 0.00 4.18
6302 13133 2.027561 CGGTCATCCCACAGGTTTCTTA 60.028 50.000 0.00 0.00 0.00 2.10
6339 13170 0.109919 TCGGATCACTGTCACGAACG 60.110 55.000 0.00 0.00 0.00 3.95
6341 13172 0.109919 CGTCGGATCACTGTCACGAA 60.110 55.000 0.00 0.00 35.17 3.85
6362 13193 2.897350 GCGATTTGGAGCTCCCCG 60.897 66.667 29.95 25.06 34.29 5.73
6454 13285 8.752005 ATACTGAGGTTTACATGTTTATGCAT 57.248 30.769 2.30 3.79 37.85 3.96
6464 13295 9.855021 GCACAATTTTAATACTGAGGTTTACAT 57.145 29.630 0.00 0.00 0.00 2.29
6535 13366 9.314321 CGTAATCTGTATTGGTTGACTTATTCT 57.686 33.333 0.00 0.00 0.00 2.40
6709 13541 2.352960 GCTCCACTTGAATTCCACGATC 59.647 50.000 2.27 0.00 0.00 3.69
6980 13812 7.289395 CGTAGTATCACTAGATTTCTACACCG 58.711 42.308 0.00 0.00 38.67 4.94
7004 13836 3.131046 AGATGCCAATAAAAGAAAGCCCG 59.869 43.478 0.00 0.00 0.00 6.13
7078 13910 1.953686 ACACACCATGTACAAGCCAAC 59.046 47.619 0.00 0.00 40.88 3.77
7239 14182 3.189287 GTGCTGGATCGACAGAATTGTTT 59.811 43.478 7.19 0.00 40.97 2.83
7392 14352 7.362662 GTTCAATACTTGCAGATTCAGTTTCA 58.637 34.615 0.00 0.00 0.00 2.69
7429 14389 7.931407 AGCGGTATTCATGATTCATTAACAGTA 59.069 33.333 0.00 0.00 0.00 2.74
7452 14412 0.244994 ACACTCTACAGGCTTCAGCG 59.755 55.000 0.00 0.00 43.26 5.18
7535 14495 8.795842 TTTGTTGTTATCGGGACATTATAGTT 57.204 30.769 0.00 0.00 0.00 2.24
7589 14549 0.169009 GCGAGCAAAATGGTGACTCC 59.831 55.000 0.00 0.00 0.00 3.85
7640 14600 9.933723 AAATTCCCATATTGAAGAAAAGACAAG 57.066 29.630 0.00 0.00 0.00 3.16
7661 14621 9.476761 CAAAAAGCTACAAAAGACAACAAATTC 57.523 29.630 0.00 0.00 0.00 2.17
7677 14637 7.698836 ACAATTGTGTCATTCAAAAAGCTAC 57.301 32.000 11.07 0.00 29.49 3.58
7742 14702 6.311690 GCAGAGTACTTCTCCACATTTTCTAC 59.688 42.308 0.00 0.00 43.71 2.59
7771 14896 9.758651 ACATATGTATTGCTCATAACGACTAAA 57.241 29.630 6.56 0.00 32.62 1.85
7816 14941 3.382546 CCAGCTTCCATTTTATCACCCAG 59.617 47.826 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.