Multiple sequence alignment - TraesCS7B01G123500

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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 TraesCS7B01G123500 chr7B 100.000 6491 0 0 1 6491 144709397 144702907 0.000000e+00 11987.0
1 TraesCS7B01G123500 chr7B 87.685 406 34 8 908 1300 145057585 145057183 5.930000e-125 459.0
2 TraesCS7B01G123500 chr7B 87.063 286 28 6 582 865 144815748 144815470 1.360000e-81 315.0
3 TraesCS7B01G123500 chr7B 84.321 287 33 6 1011 1297 144738595 144738321 2.980000e-68 270.0
4 TraesCS7B01G123500 chr7B 77.410 332 68 5 2120 2446 145029871 145029542 2.390000e-44 191.0
5 TraesCS7B01G123500 chr7B 98.837 86 1 0 5902 5987 222329690 222329775 3.130000e-33 154.0
6 TraesCS7B01G123500 chr7B 87.705 122 7 7 5872 5991 666664400 666664285 1.140000e-27 135.0
7 TraesCS7B01G123500 chr7B 78.846 208 21 11 187 380 145058349 145058151 1.140000e-22 119.0
8 TraesCS7B01G123500 chr7B 93.443 61 2 2 318 377 145033424 145033365 8.960000e-14 89.8
9 TraesCS7B01G123500 chr7B 91.803 61 5 0 3557 3617 144705778 144705718 1.160000e-12 86.1
10 TraesCS7B01G123500 chr7B 91.803 61 5 0 3620 3680 144705841 144705781 1.160000e-12 86.1
11 TraesCS7B01G123500 chr7D 93.403 3077 149 22 382 3439 178703841 178700800 0.000000e+00 4508.0
12 TraesCS7B01G123500 chr7D 96.664 2458 63 6 3455 5907 178700817 178698374 0.000000e+00 4067.0
13 TraesCS7B01G123500 chr7D 93.548 310 13 4 72 380 178704233 178703930 7.670000e-124 455.0
14 TraesCS7B01G123500 chr7D 87.160 405 39 8 908 1300 179125701 179125298 1.280000e-121 448.0
15 TraesCS7B01G123500 chr7D 82.591 494 26 24 6028 6486 178698349 178697881 1.320000e-101 381.0
16 TraesCS7B01G123500 chr7D 85.714 287 30 7 582 865 178943054 178942776 6.370000e-75 292.0
17 TraesCS7B01G123500 chr7D 88.614 202 12 8 187 380 178994930 178994732 1.090000e-57 235.0
18 TraesCS7B01G123500 chr7D 84.146 246 26 6 1056 1300 178863945 178863712 6.550000e-55 226.0
19 TraesCS7B01G123500 chr7D 76.970 330 73 2 2120 2446 178991275 178990946 1.110000e-42 185.0
20 TraesCS7B01G123500 chr7D 80.288 208 18 10 187 380 179126426 179126228 1.140000e-27 135.0
21 TraesCS7B01G123500 chr7D 91.803 61 5 0 3557 3617 178700652 178700592 1.160000e-12 86.1
22 TraesCS7B01G123500 chr7D 90.164 61 6 0 3620 3680 178700715 178700655 5.400000e-11 80.5
23 TraesCS7B01G123500 chr7D 85.333 75 7 2 487 557 179126119 179126045 2.510000e-09 75.0
24 TraesCS7B01G123500 chr7A 96.854 2098 54 5 3455 5548 182719563 182717474 0.000000e+00 3498.0
25 TraesCS7B01G123500 chr7A 95.165 1944 82 6 912 2852 182722139 182720205 0.000000e+00 3059.0
26 TraesCS7B01G123500 chr7A 94.612 798 43 0 2642 3439 182720343 182719546 0.000000e+00 1236.0
27 TraesCS7B01G123500 chr7A 88.152 844 63 19 30 845 182723340 182722506 0.000000e+00 970.0
28 TraesCS7B01G123500 chr7A 80.757 977 104 50 382 1296 183485816 183484862 0.000000e+00 686.0
29 TraesCS7B01G123500 chr7A 87.230 509 30 18 5989 6486 182717181 182716697 1.230000e-151 547.0
30 TraesCS7B01G123500 chr7A 90.850 306 24 4 997 1300 183657947 183657644 2.180000e-109 407.0
31 TraesCS7B01G123500 chr7A 93.382 272 12 4 5639 5907 182717448 182717180 1.310000e-106 398.0
32 TraesCS7B01G123500 chr7A 84.406 404 38 9 905 1297 182860097 182859708 2.210000e-99 374.0
33 TraesCS7B01G123500 chr7A 84.828 290 31 6 1012 1300 183310991 183310714 4.960000e-71 279.0
34 TraesCS7B01G123500 chr7A 76.970 330 73 2 2120 2446 183643498 183643169 1.110000e-42 185.0
35 TraesCS7B01G123500 chr7A 80.460 261 31 15 125 380 183649139 183648894 1.440000e-41 182.0
36 TraesCS7B01G123500 chr7A 100.000 85 0 0 5906 5990 646081408 646081324 2.420000e-34 158.0
37 TraesCS7B01G123500 chr7A 76.791 349 35 25 38 380 182860822 182860514 3.130000e-33 154.0
38 TraesCS7B01G123500 chr7A 92.857 56 4 0 3564 3619 182719391 182719336 1.500000e-11 82.4
39 TraesCS7B01G123500 chrUn 94.949 99 4 1 5896 5993 84437828 84437926 3.130000e-33 154.0
40 TraesCS7B01G123500 chr2D 97.753 89 2 0 5902 5990 577800148 577800060 3.130000e-33 154.0
41 TraesCS7B01G123500 chr1B 96.739 92 2 1 5903 5993 280164119 280164210 1.130000e-32 152.0
42 TraesCS7B01G123500 chr5A 96.703 91 2 1 5902 5991 684312646 684312736 4.050000e-32 150.0
43 TraesCS7B01G123500 chr5A 93.069 101 5 2 5892 5991 371028683 371028584 5.240000e-31 147.0
44 TraesCS7B01G123500 chr6B 94.000 100 2 4 5898 5993 335100561 335100462 1.460000e-31 148.0


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 TraesCS7B01G123500 chr7B 144702907 144709397 6490 True 4053.066667 11987 94.535333 1 6491 3 chr7B.!!$R4 6490
1 TraesCS7B01G123500 chr7B 145057183 145058349 1166 True 289.000000 459 83.265500 187 1300 2 chr7B.!!$R6 1113
2 TraesCS7B01G123500 chr7D 178697881 178704233 6352 True 1596.266667 4508 91.362167 72 6486 6 chr7D.!!$R3 6414
3 TraesCS7B01G123500 chr7D 179125298 179126426 1128 True 219.333333 448 84.260333 187 1300 3 chr7D.!!$R5 1113
4 TraesCS7B01G123500 chr7D 178990946 178994930 3984 True 210.000000 235 82.792000 187 2446 2 chr7D.!!$R4 2259
5 TraesCS7B01G123500 chr7A 182716697 182723340 6643 True 1398.628571 3498 92.607429 30 6486 7 chr7A.!!$R7 6456
6 TraesCS7B01G123500 chr7A 183484862 183485816 954 True 686.000000 686 80.757000 382 1296 1 chr7A.!!$R2 914
7 TraesCS7B01G123500 chr7A 182859708 182860822 1114 True 264.000000 374 80.598500 38 1297 2 chr7A.!!$R8 1259

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
897 1188 0.250209 CCCCTCAATCTGGATGCGAG 60.250 60.0 0.00 4.32 0.00 5.03 F
898 1189 0.467384 CCCTCAATCTGGATGCGAGT 59.533 55.0 0.00 0.00 0.00 4.18 F
2391 4664 0.877649 CTCAAGCGCTGTCTGTGTGT 60.878 55.0 12.58 0.00 0.00 3.72 F
2558 4831 0.417841 ACAGAGTGGGTGGATAGGGT 59.582 55.0 0.00 0.00 0.00 4.34 F
3450 5795 0.614415 ATGATGCTCCCCCGCAAAAA 60.614 50.0 0.00 0.00 44.06 1.94 F
4011 6356 0.106708 TTGCACCACCTCAGACAGAC 59.893 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2541 4814 0.983378 GCACCCTATCCACCCACTCT 60.983 60.000 0.00 0.0 0.00 3.24 R
2558 4831 1.024271 GTCAAGTGTTGGCTTCAGCA 58.976 50.000 0.30 0.0 44.36 4.41 R
3284 5629 0.109153 ATGCTGTTCTGTGCTGTCCA 59.891 50.000 0.00 0.0 0.00 4.02 R
3851 6196 0.607489 CTCCCTGCAACTCCCAACAG 60.607 60.000 0.00 0.0 0.00 3.16 R
5444 7794 1.305219 GCATGCGCCACTTGGACTTA 61.305 55.000 4.18 0.0 37.39 2.24 R
5621 7971 1.350351 AGAGACACTGAAGCCAGCAAT 59.650 47.619 0.00 0.0 44.16 3.56 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
25 26 7.999679 CAATAAAATTGCAGGTAGAAGGATGA 58.000 34.615 0.00 0.00 0.00 2.92
26 27 8.636213 CAATAAAATTGCAGGTAGAAGGATGAT 58.364 33.333 0.00 0.00 0.00 2.45
27 28 6.705863 AAAATTGCAGGTAGAAGGATGATC 57.294 37.500 0.00 0.00 0.00 2.92
28 29 3.459232 TTGCAGGTAGAAGGATGATCG 57.541 47.619 0.00 0.00 0.00 3.69
29 30 2.666317 TGCAGGTAGAAGGATGATCGA 58.334 47.619 0.00 0.00 0.00 3.59
30 31 2.625314 TGCAGGTAGAAGGATGATCGAG 59.375 50.000 0.00 0.00 0.00 4.04
31 32 2.887783 GCAGGTAGAAGGATGATCGAGA 59.112 50.000 0.00 0.00 0.00 4.04
32 33 3.509575 GCAGGTAGAAGGATGATCGAGAT 59.490 47.826 0.00 0.00 0.00 2.75
33 34 4.617995 GCAGGTAGAAGGATGATCGAGATG 60.618 50.000 0.00 0.00 0.00 2.90
34 35 3.509575 AGGTAGAAGGATGATCGAGATGC 59.490 47.826 0.00 0.00 0.00 3.91
35 36 3.367910 GGTAGAAGGATGATCGAGATGCC 60.368 52.174 0.00 0.00 0.00 4.40
36 37 2.323599 AGAAGGATGATCGAGATGCCA 58.676 47.619 0.00 0.00 0.00 4.92
67 68 1.427809 TGGTGGATGGAGCCTATGAG 58.572 55.000 0.00 0.00 0.00 2.90
102 104 5.445939 CGTGACGTCATTCCCTAATTTTCTG 60.446 44.000 23.12 0.00 0.00 3.02
111 113 3.581332 TCCCTAATTTTCTGGTGACGTCT 59.419 43.478 17.92 0.00 0.00 4.18
131 133 5.501413 CGTCTGCTAGCATACAAAATGACTG 60.501 44.000 26.90 15.85 0.00 3.51
138 140 3.485877 GCATACAAAATGACTGGTCGAGC 60.486 47.826 7.89 7.89 0.00 5.03
283 311 2.969238 CTGGCAGGATAAGGCGCG 60.969 66.667 6.61 0.00 0.00 6.86
479 633 1.963747 CCGGAGCGAAAATGTCAAAC 58.036 50.000 0.00 0.00 0.00 2.93
540 703 4.227134 CCGGAGCCGAGTGGATGG 62.227 72.222 11.05 0.00 42.83 3.51
648 893 2.348888 ACACCCTCTCCGCTTACCG 61.349 63.158 0.00 0.00 0.00 4.02
730 998 4.458989 TCCTGCTTATTCATGTGTTCCAAC 59.541 41.667 0.00 0.00 0.00 3.77
847 1138 3.971305 TCTAACTCCAAAGTGGTCCTGAA 59.029 43.478 0.00 0.00 39.03 3.02
866 1157 8.694540 GTCCTGAAGAGATCATATATGCATACT 58.305 37.037 8.99 0.00 37.44 2.12
867 1158 8.911965 TCCTGAAGAGATCATATATGCATACTC 58.088 37.037 8.99 9.83 37.44 2.59
897 1188 0.250209 CCCCTCAATCTGGATGCGAG 60.250 60.000 0.00 4.32 0.00 5.03
898 1189 0.467384 CCCTCAATCTGGATGCGAGT 59.533 55.000 0.00 0.00 0.00 4.18
899 1190 1.688735 CCCTCAATCTGGATGCGAGTA 59.311 52.381 0.00 0.00 0.00 2.59
900 1191 2.301296 CCCTCAATCTGGATGCGAGTAT 59.699 50.000 0.00 0.00 0.00 2.12
902 1193 3.006217 CCTCAATCTGGATGCGAGTATCA 59.994 47.826 3.76 0.00 33.17 2.15
910 1595 8.697507 ATCTGGATGCGAGTATCATATACATA 57.302 34.615 3.76 0.00 33.17 2.29
920 1606 3.981071 TCATATACATAGCTGTGGGGC 57.019 47.619 15.46 0.00 36.79 5.80
985 1682 2.597455 CCCCCATCTTTTGTTCACTGT 58.403 47.619 0.00 0.00 0.00 3.55
986 1683 2.965147 CCCCCATCTTTTGTTCACTGTT 59.035 45.455 0.00 0.00 0.00 3.16
987 1684 3.005791 CCCCCATCTTTTGTTCACTGTTC 59.994 47.826 0.00 0.00 0.00 3.18
988 1685 3.636300 CCCCATCTTTTGTTCACTGTTCA 59.364 43.478 0.00 0.00 0.00 3.18
1023 1734 2.614057 CCATTATTGAACTCGGCTGTCC 59.386 50.000 0.00 0.00 0.00 4.02
1031 1742 2.048222 TCGGCTGTCCTTGAAGCG 60.048 61.111 0.00 0.00 40.46 4.68
1041 1752 2.320215 CTTGAAGCGCACAAGGTGA 58.680 52.632 27.66 7.36 40.39 4.02
1096 1807 0.955428 TACAAGCTCAAGGCCGCAAG 60.955 55.000 0.00 0.00 43.05 4.01
1119 2026 2.822399 CTAGGCTAACGGGGCAGG 59.178 66.667 0.00 0.00 0.00 4.85
1389 3626 3.479203 CCTGAGCCGGCCACCATA 61.479 66.667 26.15 1.97 0.00 2.74
1453 3690 3.570638 CAGATGAAGCAGCCGCCG 61.571 66.667 0.00 0.00 39.83 6.46
1522 3759 3.357079 CGCCCAACAGGTCAGCAC 61.357 66.667 0.00 0.00 38.26 4.40
1529 3766 3.129502 CAGGTCAGCACGCCATGG 61.130 66.667 7.63 7.63 0.00 3.66
1767 4037 4.815533 TGCTGCTTCTCTAGTCTTGATT 57.184 40.909 0.00 0.00 0.00 2.57
1818 4088 2.467826 GCATGTCTGGCTTCGCTCC 61.468 63.158 0.00 0.00 0.00 4.70
1977 4247 2.107950 TGTTTATGAGGGCAGTTCCG 57.892 50.000 0.00 0.00 34.94 4.30
2115 4385 0.899720 ACCGAGATTACGCAAGGGAA 59.100 50.000 0.00 0.00 46.39 3.97
2391 4664 0.877649 CTCAAGCGCTGTCTGTGTGT 60.878 55.000 12.58 0.00 0.00 3.72
2541 4814 3.552684 GCCTTCATTGCAAAGCTGTAACA 60.553 43.478 1.71 0.00 29.27 2.41
2543 4816 4.022935 CCTTCATTGCAAAGCTGTAACAGA 60.023 41.667 1.71 0.00 32.44 3.41
2554 4827 2.500098 GCTGTAACAGAGTGGGTGGATA 59.500 50.000 0.00 0.00 32.44 2.59
2558 4831 0.417841 ACAGAGTGGGTGGATAGGGT 59.582 55.000 0.00 0.00 0.00 4.34
2584 4857 4.159321 TGAAGCCAACACTTGACAAAATGA 59.841 37.500 6.19 0.00 0.00 2.57
2592 4865 7.416817 CAACACTTGACAAAATGATGAGTACA 58.583 34.615 6.19 0.00 0.00 2.90
2654 4927 5.641209 AGCAATGTACAGATTGTCAGAGAAC 59.359 40.000 10.16 0.00 35.98 3.01
2773 5118 1.530293 CTCAGACAAGTCAGCAGCAAC 59.470 52.381 2.72 0.00 0.00 4.17
2793 5138 6.712095 AGCAACATACAGAACTTGATTCTCAA 59.288 34.615 0.00 0.00 44.99 3.02
2801 5146 5.048434 CAGAACTTGATTCTCAAAGGGTTCC 60.048 44.000 12.85 0.00 44.99 3.62
2892 5237 4.835615 ACAGAAGTAGAAGGTGTCATGTCT 59.164 41.667 0.00 0.00 0.00 3.41
2901 5246 5.769662 AGAAGGTGTCATGTCTAATTTGCAA 59.230 36.000 0.00 0.00 0.00 4.08
2937 5282 4.012374 ACAGCAATCTTGTATCAACTGGG 58.988 43.478 0.00 0.00 0.00 4.45
2972 5317 6.000246 TGTATCAGCCAGTGATTTGGATAA 58.000 37.500 0.00 0.00 44.05 1.75
3090 5435 2.108970 ACTACCGAGGAAGTTCCATCC 58.891 52.381 23.87 11.12 39.61 3.51
3115 5460 5.381757 ACAACTTGGAAATACAACCTGCTA 58.618 37.500 0.00 0.00 0.00 3.49
3157 5502 3.072915 CCCCATGGCACTATCATCAAGTA 59.927 47.826 6.09 0.00 0.00 2.24
3172 5517 5.411361 TCATCAAGTAACGGTGGAAATTCTG 59.589 40.000 0.00 0.00 0.00 3.02
3234 5579 2.637382 TGCAACATCTGGTAACCTGAGA 59.363 45.455 0.00 0.00 35.07 3.27
3251 5596 5.781306 ACCTGAGAATAGATGCTGATGATCT 59.219 40.000 0.00 0.00 34.47 2.75
3260 5605 1.213430 TGCTGATGATCTGGCAATGGA 59.787 47.619 10.17 0.00 0.00 3.41
3284 5629 1.280710 TGAATTACCCGACAGCCATGT 59.719 47.619 0.00 0.00 44.31 3.21
3331 5676 4.949856 AGCAAATGTCCAATAACCCTACTG 59.050 41.667 0.00 0.00 0.00 2.74
3343 5688 2.251409 CCCTACTGGTGCAGATGATG 57.749 55.000 0.00 0.00 35.18 3.07
3348 5693 1.065636 ACTGGTGCAGATGATGGTGAG 60.066 52.381 0.00 0.00 35.18 3.51
3358 5703 5.698545 GCAGATGATGGTGAGGTTAGATTAC 59.301 44.000 0.00 0.00 0.00 1.89
3359 5704 6.226787 CAGATGATGGTGAGGTTAGATTACC 58.773 44.000 0.00 0.00 38.53 2.85
3373 5718 7.776969 AGGTTAGATTACCTATCGACAACACTA 59.223 37.037 0.00 0.00 46.65 2.74
3378 5723 4.184079 ACCTATCGACAACACTACCAAC 57.816 45.455 0.00 0.00 0.00 3.77
3419 5764 7.118825 GCATCAGAGATGTATTAAATGCAGCTA 59.881 37.037 8.60 0.00 41.61 3.32
3421 5766 8.768957 TCAGAGATGTATTAAATGCAGCTATC 57.231 34.615 0.00 0.00 41.61 2.08
3422 5767 7.543520 TCAGAGATGTATTAAATGCAGCTATCG 59.456 37.037 0.00 0.00 41.61 2.92
3423 5768 7.543520 CAGAGATGTATTAAATGCAGCTATCGA 59.456 37.037 0.00 0.00 41.61 3.59
3424 5769 8.090831 AGAGATGTATTAAATGCAGCTATCGAA 58.909 33.333 0.00 0.00 41.61 3.71
3425 5770 8.607441 AGATGTATTAAATGCAGCTATCGAAA 57.393 30.769 0.00 0.00 39.80 3.46
3426 5771 9.224267 AGATGTATTAAATGCAGCTATCGAAAT 57.776 29.630 0.00 0.00 39.80 2.17
3427 5772 9.483062 GATGTATTAAATGCAGCTATCGAAATC 57.517 33.333 0.00 0.00 0.00 2.17
3428 5773 7.806690 TGTATTAAATGCAGCTATCGAAATCC 58.193 34.615 0.00 0.00 0.00 3.01
3429 5774 6.882610 ATTAAATGCAGCTATCGAAATCCA 57.117 33.333 0.00 0.00 0.00 3.41
3430 5775 4.825546 AAATGCAGCTATCGAAATCCAG 57.174 40.909 0.00 0.00 0.00 3.86
3431 5776 3.758755 ATGCAGCTATCGAAATCCAGA 57.241 42.857 0.00 0.00 0.00 3.86
3432 5777 3.758755 TGCAGCTATCGAAATCCAGAT 57.241 42.857 0.00 0.00 0.00 2.90
3433 5778 3.396560 TGCAGCTATCGAAATCCAGATG 58.603 45.455 0.00 0.00 0.00 2.90
3434 5779 3.070015 TGCAGCTATCGAAATCCAGATGA 59.930 43.478 0.00 0.00 0.00 2.92
3435 5780 4.252073 GCAGCTATCGAAATCCAGATGAT 58.748 43.478 0.00 0.00 34.22 2.45
3436 5781 4.093115 GCAGCTATCGAAATCCAGATGATG 59.907 45.833 0.00 0.00 32.68 3.07
3437 5782 4.093115 CAGCTATCGAAATCCAGATGATGC 59.907 45.833 0.00 0.00 32.68 3.91
3438 5783 4.020396 AGCTATCGAAATCCAGATGATGCT 60.020 41.667 0.00 0.00 32.68 3.79
3439 5784 4.329528 GCTATCGAAATCCAGATGATGCTC 59.670 45.833 0.00 0.00 32.68 4.26
3440 5785 3.117491 TCGAAATCCAGATGATGCTCC 57.883 47.619 0.00 0.00 32.68 4.70
3441 5786 2.149578 CGAAATCCAGATGATGCTCCC 58.850 52.381 0.00 0.00 32.68 4.30
3442 5787 2.512705 GAAATCCAGATGATGCTCCCC 58.487 52.381 0.00 0.00 32.68 4.81
3443 5788 0.776176 AATCCAGATGATGCTCCCCC 59.224 55.000 0.00 0.00 32.68 5.40
3444 5789 1.486997 ATCCAGATGATGCTCCCCCG 61.487 60.000 0.00 0.00 30.54 5.73
3445 5790 2.281345 CAGATGATGCTCCCCCGC 60.281 66.667 0.00 0.00 0.00 6.13
3446 5791 2.769621 AGATGATGCTCCCCCGCA 60.770 61.111 0.00 0.00 45.10 5.69
3447 5792 2.192979 GATGATGCTCCCCCGCAA 59.807 61.111 0.00 0.00 44.06 4.85
3448 5793 1.453745 GATGATGCTCCCCCGCAAA 60.454 57.895 0.00 0.00 44.06 3.68
3449 5794 1.000233 ATGATGCTCCCCCGCAAAA 60.000 52.632 0.00 0.00 44.06 2.44
3450 5795 0.614415 ATGATGCTCCCCCGCAAAAA 60.614 50.000 0.00 0.00 44.06 1.94
3795 6140 6.128117 GGATGAGCAACAAGGTTATAAAACGA 60.128 38.462 0.00 0.00 36.39 3.85
3804 6149 3.195396 AGGTTATAAAACGACGGGCACTA 59.805 43.478 0.00 0.00 36.39 2.74
3851 6196 1.395045 GCTCTAATGGGGGCCTTTGC 61.395 60.000 0.84 0.00 0.00 3.68
3882 6227 2.795329 TGCAGGGAGAAGACAAAATCC 58.205 47.619 0.00 0.00 0.00 3.01
3978 6323 4.523813 GATGGTTGAAAGTGTGTGTTACG 58.476 43.478 0.00 0.00 0.00 3.18
4011 6356 0.106708 TTGCACCACCTCAGACAGAC 59.893 55.000 0.00 0.00 0.00 3.51
4228 6573 3.004629 TGTTTTCTACTACTCGAACGCCA 59.995 43.478 0.00 0.00 0.00 5.69
4491 6836 0.322546 CACTGACCAGGTTAAGGGGC 60.323 60.000 0.00 0.00 0.00 5.80
4602 6947 2.171448 GTCAGGCACCCTTATCAGTGAT 59.829 50.000 11.12 11.12 36.01 3.06
4821 7166 6.072618 CCATCTCTTTCATGTCATCTATTGCC 60.073 42.308 0.00 0.00 0.00 4.52
5429 7779 6.498304 TGAAGAAAGTTTGCAACTCTGATTC 58.502 36.000 0.00 7.16 41.91 2.52
5444 7794 4.965814 TCTGATTCTCTTGTGCTTCAGTT 58.034 39.130 0.00 0.00 33.88 3.16
5470 7820 1.980951 AAGTGGCGCATGCATGTACG 61.981 55.000 26.79 22.41 45.35 3.67
5471 7821 2.435762 TGGCGCATGCATGTACGT 60.436 55.556 26.79 0.00 45.35 3.57
5472 7822 1.153549 TGGCGCATGCATGTACGTA 60.154 52.632 26.79 13.33 45.35 3.57
5473 7823 1.275657 GGCGCATGCATGTACGTAC 59.724 57.895 26.79 18.90 45.35 3.67
5490 7840 2.859538 CGTACATGCAAATGAATTGGCC 59.140 45.455 0.00 0.00 39.54 5.36
5509 7859 4.067192 GGCCTTTTTGCATGATCAGTTTT 58.933 39.130 0.09 0.00 0.00 2.43
5516 7866 7.467557 TTTTGCATGATCAGTTTTGAAGAAC 57.532 32.000 0.09 0.00 36.78 3.01
5600 7950 4.467082 TGTCTGCATCAAATAAGGGCAAAT 59.533 37.500 0.00 0.00 33.58 2.32
5621 7971 7.537306 GCAAATAGCTGAATTTCGTTTGAGTAA 59.463 33.333 0.00 0.00 41.15 2.24
5628 7978 6.148948 TGAATTTCGTTTGAGTAATTGCTGG 58.851 36.000 0.00 0.00 0.00 4.85
5643 7993 1.270518 TGCTGGCTTCAGTGTCTCTTC 60.271 52.381 0.00 0.00 40.51 2.87
5695 8045 7.815840 TTTTATATGTTGCATTAGCCTGCTA 57.184 32.000 0.00 0.00 42.75 3.49
5706 8056 5.448360 GCATTAGCCTGCTAAGACAGAAAAG 60.448 44.000 15.97 1.20 41.18 2.27
5714 8064 4.141482 TGCTAAGACAGAAAAGGTTGAGGT 60.141 41.667 0.00 0.00 0.00 3.85
5866 8220 4.883585 ACATGATACATTGCCAGGTACAAG 59.116 41.667 0.00 0.00 0.00 3.16
5905 8259 5.892348 ACTTTAGGGGTGTCATTCTCAATT 58.108 37.500 0.00 0.00 0.00 2.32
5906 8260 7.027874 ACTTTAGGGGTGTCATTCTCAATTA 57.972 36.000 0.00 0.00 0.00 1.40
5907 8261 6.884836 ACTTTAGGGGTGTCATTCTCAATTAC 59.115 38.462 0.00 0.00 0.00 1.89
5908 8262 6.636454 TTAGGGGTGTCATTCTCAATTACT 57.364 37.500 0.00 0.00 0.00 2.24
5909 8263 5.104259 AGGGGTGTCATTCTCAATTACTC 57.896 43.478 0.00 0.00 0.00 2.59
5910 8264 4.080299 AGGGGTGTCATTCTCAATTACTCC 60.080 45.833 0.00 0.00 31.23 3.85
5911 8265 4.200092 GGGTGTCATTCTCAATTACTCCC 58.800 47.826 5.39 5.39 39.94 4.30
5912 8266 4.080299 GGGTGTCATTCTCAATTACTCCCT 60.080 45.833 11.17 0.00 41.93 4.20
5913 8267 5.119694 GGTGTCATTCTCAATTACTCCCTC 58.880 45.833 0.00 0.00 0.00 4.30
5914 8268 5.119694 GTGTCATTCTCAATTACTCCCTCC 58.880 45.833 0.00 0.00 0.00 4.30
5915 8269 4.141937 TGTCATTCTCAATTACTCCCTCCG 60.142 45.833 0.00 0.00 0.00 4.63
5916 8270 4.030913 TCATTCTCAATTACTCCCTCCGT 58.969 43.478 0.00 0.00 0.00 4.69
5917 8271 4.469945 TCATTCTCAATTACTCCCTCCGTT 59.530 41.667 0.00 0.00 0.00 4.44
5918 8272 4.467198 TTCTCAATTACTCCCTCCGTTC 57.533 45.455 0.00 0.00 0.00 3.95
5919 8273 2.764572 TCTCAATTACTCCCTCCGTTCC 59.235 50.000 0.00 0.00 0.00 3.62
5920 8274 2.500098 CTCAATTACTCCCTCCGTTCCA 59.500 50.000 0.00 0.00 0.00 3.53
5921 8275 2.907696 TCAATTACTCCCTCCGTTCCAA 59.092 45.455 0.00 0.00 0.00 3.53
5922 8276 3.328343 TCAATTACTCCCTCCGTTCCAAA 59.672 43.478 0.00 0.00 0.00 3.28
5923 8277 4.076394 CAATTACTCCCTCCGTTCCAAAA 58.924 43.478 0.00 0.00 0.00 2.44
5924 8278 4.586306 ATTACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
5925 8279 5.703730 ATTACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
5926 8280 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5927 8281 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5928 8282 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5929 8283 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5930 8284 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5931 8285 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5932 8286 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
5933 8287 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
5934 8288 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
5935 8289 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
5936 8290 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
5937 8291 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
5938 8292 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
5939 8293 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
5940 8294 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
5941 8295 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
5942 8296 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
5943 8297 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
5944 8298 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
5951 8305 9.915629 AGATGACTCAACTTTGTACTAACTTAG 57.084 33.333 0.00 0.00 0.00 2.18
5952 8306 9.694137 GATGACTCAACTTTGTACTAACTTAGT 57.306 33.333 6.68 6.68 42.68 2.24
5980 8334 8.970691 AAAATTGAGTCATCTATTTTGGAACG 57.029 30.769 11.47 0.00 44.08 3.95
5981 8335 6.683974 ATTGAGTCATCTATTTTGGAACGG 57.316 37.500 0.00 0.00 0.00 4.44
5982 8336 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
5983 8337 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
5984 8338 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
5985 8339 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5986 8340 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5987 8341 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
6026 8380 6.371548 TGTGCCTTTATTTAGCAGTAGTTCTG 59.628 38.462 0.00 0.00 46.12 3.02
6125 8480 2.805099 CTCTCCTCTGTTGTTGTTCAGC 59.195 50.000 0.00 0.00 0.00 4.26
6126 8481 2.170397 TCTCCTCTGTTGTTGTTCAGCA 59.830 45.455 0.00 0.00 36.00 4.41
6195 8551 3.525800 ACCTTTTGAGGGCTAACACAT 57.474 42.857 0.00 0.00 0.00 3.21
6196 8552 3.844640 ACCTTTTGAGGGCTAACACATT 58.155 40.909 0.00 0.00 0.00 2.71
6197 8553 4.993028 ACCTTTTGAGGGCTAACACATTA 58.007 39.130 0.00 0.00 0.00 1.90
6198 8554 4.765339 ACCTTTTGAGGGCTAACACATTAC 59.235 41.667 0.00 0.00 0.00 1.89
6199 8555 4.764823 CCTTTTGAGGGCTAACACATTACA 59.235 41.667 0.00 0.00 0.00 2.41
6200 8556 5.335661 CCTTTTGAGGGCTAACACATTACAC 60.336 44.000 0.00 0.00 0.00 2.90
6201 8557 4.359434 TTGAGGGCTAACACATTACACA 57.641 40.909 0.00 0.00 0.00 3.72
6202 8558 3.670625 TGAGGGCTAACACATTACACAC 58.329 45.455 0.00 0.00 0.00 3.82
6203 8559 3.071747 TGAGGGCTAACACATTACACACA 59.928 43.478 0.00 0.00 0.00 3.72
6204 8560 3.408634 AGGGCTAACACATTACACACAC 58.591 45.455 0.00 0.00 0.00 3.82
6205 8561 3.142951 GGGCTAACACATTACACACACA 58.857 45.455 0.00 0.00 0.00 3.72
6207 8563 4.036971 GGGCTAACACATTACACACACAAA 59.963 41.667 0.00 0.00 0.00 2.83
6275 8657 1.219522 AAAACGGCGGTCTTCAGTCG 61.220 55.000 13.24 0.00 42.00 4.18
6290 8672 6.688813 GTCTTCAGTCGCCAAATAATTTCATC 59.311 38.462 0.00 0.00 0.00 2.92
6305 8687 4.794278 TTTCATCACTAAGGTGCGTCTA 57.206 40.909 0.00 0.00 42.72 2.59
6325 8707 7.097834 CGTCTACTTTTAAATTCCCTCACTCT 58.902 38.462 0.00 0.00 0.00 3.24
6326 8708 7.063544 CGTCTACTTTTAAATTCCCTCACTCTG 59.936 40.741 0.00 0.00 0.00 3.35
6329 8711 9.454859 CTACTTTTAAATTCCCTCACTCTGATT 57.545 33.333 0.00 0.00 0.00 2.57
6330 8712 8.712228 ACTTTTAAATTCCCTCACTCTGATTT 57.288 30.769 0.00 0.00 0.00 2.17
6354 8738 1.477105 GTTGTTGCTTTCTGGTTCGC 58.523 50.000 0.00 0.00 0.00 4.70
6357 8741 1.150536 TTGCTTTCTGGTTCGCCCT 59.849 52.632 0.00 0.00 36.08 5.19
6378 8762 5.464389 CCCTTTTTCAACATTCTCTTTGCTG 59.536 40.000 0.00 0.00 0.00 4.41
6379 8763 6.044682 CCTTTTTCAACATTCTCTTTGCTGT 58.955 36.000 0.00 0.00 0.00 4.40
6380 8764 6.019318 CCTTTTTCAACATTCTCTTTGCTGTG 60.019 38.462 0.00 0.00 0.00 3.66
6381 8765 5.581126 TTTCAACATTCTCTTTGCTGTGT 57.419 34.783 0.00 0.00 0.00 3.72
6382 8766 4.556942 TCAACATTCTCTTTGCTGTGTG 57.443 40.909 0.00 0.00 0.00 3.82
6383 8767 3.047796 CAACATTCTCTTTGCTGTGTGC 58.952 45.455 0.00 0.00 43.25 4.57
6384 8768 2.579873 ACATTCTCTTTGCTGTGTGCT 58.420 42.857 0.00 0.00 43.37 4.40
6385 8769 2.954318 ACATTCTCTTTGCTGTGTGCTT 59.046 40.909 0.00 0.00 43.37 3.91
6386 8770 3.382546 ACATTCTCTTTGCTGTGTGCTTT 59.617 39.130 0.00 0.00 43.37 3.51
6387 8771 4.580167 ACATTCTCTTTGCTGTGTGCTTTA 59.420 37.500 0.00 0.00 43.37 1.85
6388 8772 4.818534 TTCTCTTTGCTGTGTGCTTTAG 57.181 40.909 0.00 0.00 43.37 1.85
6389 8773 2.549754 TCTCTTTGCTGTGTGCTTTAGC 59.450 45.455 0.00 0.00 43.37 3.09
6409 8794 3.260884 AGCATTTGAAAGTCCGTCCTAGA 59.739 43.478 0.00 0.00 0.00 2.43
6458 8845 1.080093 CTTGTTCCGCTGGACGCTA 60.080 57.895 0.00 0.00 41.76 4.26
6470 8857 4.091220 CGCTGGACGCTAGTAGTAGTATAC 59.909 50.000 6.47 0.00 38.07 1.47
6471 8858 4.391523 GCTGGACGCTAGTAGTAGTATACC 59.608 50.000 6.47 6.05 37.80 2.73
6486 8878 5.099042 AGTATACCTTGGTGTGTTCCATC 57.901 43.478 2.03 0.00 37.33 3.51
6487 8879 4.783227 AGTATACCTTGGTGTGTTCCATCT 59.217 41.667 2.03 0.00 37.33 2.90
6488 8880 4.657814 ATACCTTGGTGTGTTCCATCTT 57.342 40.909 2.03 0.00 37.33 2.40
6489 8881 2.863809 ACCTTGGTGTGTTCCATCTTC 58.136 47.619 0.00 0.00 37.33 2.87
6490 8882 2.162681 CCTTGGTGTGTTCCATCTTCC 58.837 52.381 0.00 0.00 37.33 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.999679 TCATCCTTCTACCTGCAATTTTATTG 58.000 34.615 0.00 0.00 0.00 1.90
1 2 8.773033 ATCATCCTTCTACCTGCAATTTTATT 57.227 30.769 0.00 0.00 0.00 1.40
4 5 5.297776 CGATCATCCTTCTACCTGCAATTTT 59.702 40.000 0.00 0.00 0.00 1.82
6 7 4.101585 TCGATCATCCTTCTACCTGCAATT 59.898 41.667 0.00 0.00 0.00 2.32
7 8 3.643320 TCGATCATCCTTCTACCTGCAAT 59.357 43.478 0.00 0.00 0.00 3.56
9 10 2.625314 CTCGATCATCCTTCTACCTGCA 59.375 50.000 0.00 0.00 0.00 4.41
10 11 2.887783 TCTCGATCATCCTTCTACCTGC 59.112 50.000 0.00 0.00 0.00 4.85
11 12 4.617995 GCATCTCGATCATCCTTCTACCTG 60.618 50.000 0.00 0.00 0.00 4.00
12 13 3.509575 GCATCTCGATCATCCTTCTACCT 59.490 47.826 0.00 0.00 0.00 3.08
13 14 3.367910 GGCATCTCGATCATCCTTCTACC 60.368 52.174 0.00 0.00 0.00 3.18
14 15 3.256879 TGGCATCTCGATCATCCTTCTAC 59.743 47.826 0.00 0.00 0.00 2.59
15 16 3.500343 TGGCATCTCGATCATCCTTCTA 58.500 45.455 0.00 0.00 0.00 2.10
16 17 2.323599 TGGCATCTCGATCATCCTTCT 58.676 47.619 0.00 0.00 0.00 2.85
17 18 2.827800 TGGCATCTCGATCATCCTTC 57.172 50.000 0.00 0.00 0.00 3.46
18 19 2.702478 TCTTGGCATCTCGATCATCCTT 59.298 45.455 0.00 0.00 0.00 3.36
19 20 2.299582 CTCTTGGCATCTCGATCATCCT 59.700 50.000 0.00 0.00 0.00 3.24
20 21 2.036992 ACTCTTGGCATCTCGATCATCC 59.963 50.000 0.00 0.00 0.00 3.51
21 22 3.383620 ACTCTTGGCATCTCGATCATC 57.616 47.619 0.00 0.00 0.00 2.92
22 23 3.834489 AACTCTTGGCATCTCGATCAT 57.166 42.857 0.00 0.00 0.00 2.45
23 24 4.736126 TTAACTCTTGGCATCTCGATCA 57.264 40.909 0.00 0.00 0.00 2.92
24 25 5.112686 AGTTTAACTCTTGGCATCTCGATC 58.887 41.667 0.00 0.00 0.00 3.69
25 26 5.091261 AGTTTAACTCTTGGCATCTCGAT 57.909 39.130 0.00 0.00 0.00 3.59
26 27 4.537135 AGTTTAACTCTTGGCATCTCGA 57.463 40.909 0.00 0.00 0.00 4.04
27 28 4.962693 CAAGTTTAACTCTTGGCATCTCG 58.037 43.478 0.00 0.00 38.70 4.04
35 36 5.070001 TCCATCCACCAAGTTTAACTCTTG 58.930 41.667 0.00 10.77 41.06 3.02
36 37 5.316987 CTCCATCCACCAAGTTTAACTCTT 58.683 41.667 0.00 0.00 0.00 2.85
67 68 2.462889 TGACGTCACGTAAACAGGTTC 58.537 47.619 15.76 0.00 41.37 3.62
102 104 1.134367 TGTATGCTAGCAGACGTCACC 59.866 52.381 31.06 12.29 40.64 4.02
111 113 4.588899 ACCAGTCATTTTGTATGCTAGCA 58.411 39.130 21.85 21.85 0.00 3.49
153 155 4.275508 CTGGCCATCCATCCCCCG 62.276 72.222 5.51 0.00 42.51 5.73
218 221 1.518352 TGCATTGATCCCGTCGACG 60.518 57.895 30.33 30.33 39.44 5.12
256 276 2.080654 ATCCTGCCAGACCTAGAGAC 57.919 55.000 0.00 0.00 0.00 3.36
283 311 0.837940 AGGGCCTATTTCCTCGTTCC 59.162 55.000 2.82 0.00 0.00 3.62
293 322 4.195334 CCGCAGCCAGGGCCTATT 62.195 66.667 5.28 0.00 43.17 1.73
648 893 2.941453 TGGAATCTGTAGACAGCGAC 57.059 50.000 4.72 0.00 43.46 5.19
730 998 0.901827 GGGTTGCTGGGTAATTTGGG 59.098 55.000 0.00 0.00 0.00 4.12
866 1157 5.723405 CCAGATTGAGGGGATGTGATATAGA 59.277 44.000 0.00 0.00 0.00 1.98
867 1158 5.723405 TCCAGATTGAGGGGATGTGATATAG 59.277 44.000 0.00 0.00 0.00 1.31
897 1188 5.360591 GCCCCACAGCTATGTATATGATAC 58.639 45.833 0.00 0.00 37.65 2.24
898 1189 4.408921 GGCCCCACAGCTATGTATATGATA 59.591 45.833 0.00 0.00 37.65 2.15
899 1190 3.200825 GGCCCCACAGCTATGTATATGAT 59.799 47.826 0.00 0.00 37.65 2.45
900 1191 2.571653 GGCCCCACAGCTATGTATATGA 59.428 50.000 0.00 0.00 37.65 2.15
902 1193 2.921221 AGGCCCCACAGCTATGTATAT 58.079 47.619 0.00 0.00 37.65 0.86
910 1595 1.852626 AAGGTAAGGCCCCACAGCT 60.853 57.895 0.00 0.00 38.26 4.24
920 1606 6.465439 ACAAAGGAAAGAAACAAGGTAAGG 57.535 37.500 0.00 0.00 0.00 2.69
977 1674 1.365699 ACGGTGTGTGAACAGTGAAC 58.634 50.000 0.00 0.00 0.00 3.18
979 1676 1.066787 TGAACGGTGTGTGAACAGTGA 60.067 47.619 0.00 0.00 0.00 3.41
980 1677 1.062002 GTGAACGGTGTGTGAACAGTG 59.938 52.381 0.00 0.00 0.00 3.66
981 1678 1.338294 TGTGAACGGTGTGTGAACAGT 60.338 47.619 0.00 0.00 0.00 3.55
983 1680 1.080298 GTGTGAACGGTGTGTGAACA 58.920 50.000 0.00 0.00 0.00 3.18
984 1681 0.375803 GGTGTGAACGGTGTGTGAAC 59.624 55.000 0.00 0.00 0.00 3.18
985 1682 0.036294 TGGTGTGAACGGTGTGTGAA 60.036 50.000 0.00 0.00 0.00 3.18
986 1683 0.179234 ATGGTGTGAACGGTGTGTGA 59.821 50.000 0.00 0.00 0.00 3.58
987 1684 1.021202 AATGGTGTGAACGGTGTGTG 58.979 50.000 0.00 0.00 0.00 3.82
988 1685 2.623878 TAATGGTGTGAACGGTGTGT 57.376 45.000 0.00 0.00 0.00 3.72
1023 1734 0.040958 GTCACCTTGTGCGCTTCAAG 60.041 55.000 26.64 26.64 41.06 3.02
1041 1752 1.846007 CTGCTCAGACTAGTGAGGGT 58.154 55.000 0.00 0.00 43.71 4.34
1088 1799 2.894387 CTAGCTGAGCTTGCGGCC 60.894 66.667 14.14 0.00 41.08 6.13
1096 1807 1.068250 CCCGTTAGCCTAGCTGAGC 59.932 63.158 0.00 0.00 40.10 4.26
1119 2026 0.110056 CAGTTGCTCACACGGAATGC 60.110 55.000 0.00 0.00 0.00 3.56
1163 2082 7.296150 AGGAAGAGAGAGTAAGGATCATACCTA 59.704 40.741 0.00 0.00 39.62 3.08
1226 3072 2.925563 GAGAAATGGCAGAAAATTGGCG 59.074 45.455 0.00 0.00 45.80 5.69
1453 3690 1.179814 ATATCCTCCGTCACTCCGCC 61.180 60.000 0.00 0.00 0.00 6.13
1486 3723 0.603065 GGACCTTGCCCATTGTTGTC 59.397 55.000 0.00 0.00 0.00 3.18
1522 3759 0.820482 TTGATGCTGGATCCATGGCG 60.820 55.000 16.63 4.42 0.00 5.69
1529 3766 4.083431 CGAAATCATCCTTGATGCTGGATC 60.083 45.833 1.79 1.79 41.83 3.36
1767 4037 2.518407 TCCCCTACTCAGGAGCAAGATA 59.482 50.000 0.00 0.00 45.91 1.98
1818 4088 5.125356 TCCAGTATCATGGTAAACTGCATG 58.875 41.667 3.67 0.00 41.43 4.06
1977 4247 2.084546 ACCTGATCTTTTAACGGCTGC 58.915 47.619 0.00 0.00 0.00 5.25
2163 4433 2.079158 CCAGCTTGGTATGTGACAGTG 58.921 52.381 0.00 0.00 31.35 3.66
2167 4437 2.717639 ATCCCAGCTTGGTATGTGAC 57.282 50.000 3.35 0.00 35.17 3.67
2391 4664 1.595109 CAGCAGAACAGCCACGACA 60.595 57.895 0.00 0.00 34.23 4.35
2541 4814 0.983378 GCACCCTATCCACCCACTCT 60.983 60.000 0.00 0.00 0.00 3.24
2543 4816 1.082954 AGCACCCTATCCACCCACT 59.917 57.895 0.00 0.00 0.00 4.00
2554 4827 1.529244 GTGTTGGCTTCAGCACCCT 60.529 57.895 0.30 0.00 43.74 4.34
2558 4831 1.024271 GTCAAGTGTTGGCTTCAGCA 58.976 50.000 0.30 0.00 44.36 4.41
2569 4842 6.767902 AGTGTACTCATCATTTTGTCAAGTGT 59.232 34.615 0.00 0.00 0.00 3.55
2584 4857 2.356125 GCCCCAATGACAGTGTACTCAT 60.356 50.000 0.00 0.00 0.00 2.90
2592 4865 1.355381 TCATCTTGCCCCAATGACAGT 59.645 47.619 0.00 0.00 0.00 3.55
2654 4927 1.863454 GCTCTGTATCTTGATGGTGCG 59.137 52.381 0.00 0.00 0.00 5.34
2759 5104 3.069289 TCTGTATGTTGCTGCTGACTTG 58.931 45.455 0.00 0.00 0.00 3.16
2801 5146 2.093288 TCAAGCTCTGTATCTTGCTGGG 60.093 50.000 0.00 0.00 39.47 4.45
2861 5206 5.354792 ACACCTTCTACTTCTGTATCTCGAC 59.645 44.000 0.00 0.00 0.00 4.20
2892 5237 4.943093 TCAGCAGAGTAGCATTGCAAATTA 59.057 37.500 11.91 0.00 40.22 1.40
2901 5246 3.756739 GCTGTCAGCAGAGTAGCAT 57.243 52.632 20.16 0.00 45.28 3.79
2937 5282 3.323115 TGGCTGATACAGATCTCACATCC 59.677 47.826 0.00 0.00 32.44 3.51
2972 5317 0.921166 TGGCATGATGTCCTCCATGT 59.079 50.000 0.00 0.00 41.49 3.21
3090 5435 4.783242 CAGGTTGTATTTCCAAGTTGTCG 58.217 43.478 1.45 0.00 0.00 4.35
3115 5460 3.772853 TTGCAACCTGCTGACCGCT 62.773 57.895 0.00 0.00 45.31 5.52
3157 5502 2.649531 TGGACAGAATTTCCACCGTT 57.350 45.000 0.00 0.00 38.28 4.44
3172 5517 3.502979 TGCAACGGTAAAATACCTTGGAC 59.497 43.478 14.71 5.77 46.81 4.02
3211 5556 3.609853 TCAGGTTACCAGATGTTGCATC 58.390 45.455 3.51 1.18 0.00 3.91
3234 5579 4.635699 TGCCAGATCATCAGCATCTATT 57.364 40.909 0.00 0.00 0.00 1.73
3251 5596 3.450457 GGGTAATTCACATTCCATTGCCA 59.550 43.478 0.00 0.00 35.09 4.92
3260 5605 2.290641 TGGCTGTCGGGTAATTCACATT 60.291 45.455 0.00 0.00 0.00 2.71
3284 5629 0.109153 ATGCTGTTCTGTGCTGTCCA 59.891 50.000 0.00 0.00 0.00 4.02
3331 5676 0.254178 ACCTCACCATCATCTGCACC 59.746 55.000 0.00 0.00 0.00 5.01
3348 5693 6.803642 AGTGTTGTCGATAGGTAATCTAACC 58.196 40.000 0.00 0.00 40.06 2.85
3358 5703 3.119743 TCGTTGGTAGTGTTGTCGATAGG 60.120 47.826 0.00 0.00 0.00 2.57
3359 5704 4.087510 TCGTTGGTAGTGTTGTCGATAG 57.912 45.455 0.00 0.00 0.00 2.08
3360 5705 4.156373 TGATCGTTGGTAGTGTTGTCGATA 59.844 41.667 0.00 0.00 36.84 2.92
3373 5718 1.303317 GTGGGGCTTGATCGTTGGT 60.303 57.895 0.00 0.00 0.00 3.67
3378 5723 1.442526 GATGCTGTGGGGCTTGATCG 61.443 60.000 0.00 0.00 0.00 3.69
3419 5764 3.558746 GGGAGCATCATCTGGATTTCGAT 60.559 47.826 0.00 0.00 36.25 3.59
3421 5766 2.149578 GGGAGCATCATCTGGATTTCG 58.850 52.381 0.00 0.00 36.25 3.46
3422 5767 2.512705 GGGGAGCATCATCTGGATTTC 58.487 52.381 0.00 0.00 36.25 2.17
3423 5768 1.146566 GGGGGAGCATCATCTGGATTT 59.853 52.381 0.00 0.00 36.25 2.17
3424 5769 0.776176 GGGGGAGCATCATCTGGATT 59.224 55.000 0.00 0.00 36.25 3.01
3425 5770 1.486997 CGGGGGAGCATCATCTGGAT 61.487 60.000 0.00 0.00 36.25 3.41
3426 5771 2.142761 CGGGGGAGCATCATCTGGA 61.143 63.158 0.00 0.00 36.25 3.86
3427 5772 2.429058 CGGGGGAGCATCATCTGG 59.571 66.667 0.00 0.00 36.25 3.86
3428 5773 2.281345 GCGGGGGAGCATCATCTG 60.281 66.667 0.00 0.00 36.25 2.90
3429 5774 2.769621 TGCGGGGGAGCATCATCT 60.770 61.111 0.00 0.00 42.92 2.90
3450 5795 8.373220 AGAAAAGCATCATCTGGATTTCTTTTT 58.627 29.630 11.79 0.00 41.45 1.94
3451 5796 7.817962 CAGAAAAGCATCATCTGGATTTCTTTT 59.182 33.333 10.95 10.95 42.65 2.27
3452 5797 7.177921 TCAGAAAAGCATCATCTGGATTTCTTT 59.822 33.333 8.37 0.00 40.71 2.52
3453 5798 6.662234 TCAGAAAAGCATCATCTGGATTTCTT 59.338 34.615 8.37 0.00 40.71 2.52
3519 5864 4.940046 CCAGCTTGATATGTCAAAGACACT 59.060 41.667 6.35 0.00 45.65 3.55
3770 6115 6.027749 CGTTTTATAACCTTGTTGCTCATCC 58.972 40.000 0.00 0.00 0.00 3.51
3795 6140 1.754380 TTGCTGTCTGTAGTGCCCGT 61.754 55.000 0.00 0.00 0.00 5.28
3804 6149 3.610040 TCGGTTATCATTGCTGTCTGT 57.390 42.857 0.00 0.00 0.00 3.41
3851 6196 0.607489 CTCCCTGCAACTCCCAACAG 60.607 60.000 0.00 0.00 0.00 3.16
3978 6323 1.200948 GGTGCAAACTTCATCCTCTGC 59.799 52.381 0.00 0.00 0.00 4.26
4011 6356 5.668471 TCCTTAGCATCTCTTGACTCATTG 58.332 41.667 0.00 0.00 0.00 2.82
4228 6573 2.941064 CCACAGATGACGCAAATGAGAT 59.059 45.455 0.00 0.00 0.00 2.75
4491 6836 5.076484 GATGAAGAATCTTCCGCAACCGG 62.076 52.174 19.16 0.00 42.98 5.28
4602 6947 6.040616 ACTTCTGTCTCTTCTTTTCCGTCTTA 59.959 38.462 0.00 0.00 0.00 2.10
4607 6952 5.774630 AGTACTTCTGTCTCTTCTTTTCCG 58.225 41.667 0.00 0.00 0.00 4.30
4821 7166 2.191802 CTCAGCAGAAGCATGACTACG 58.808 52.381 0.00 0.00 45.49 3.51
5026 7371 1.683943 TTCAGCCATCTTGCTATGCC 58.316 50.000 0.00 0.00 40.32 4.40
5058 7403 1.871126 GCAGCAAGGAAGCCACCTTC 61.871 60.000 8.77 5.39 46.94 3.46
5267 7612 1.654317 GCAGCCTGAAGATCTCTGTG 58.346 55.000 0.00 0.00 0.00 3.66
5429 7779 4.380531 TGGACTTAACTGAAGCACAAGAG 58.619 43.478 0.00 0.00 38.92 2.85
5444 7794 1.305219 GCATGCGCCACTTGGACTTA 61.305 55.000 4.18 0.00 37.39 2.24
5470 7820 4.127566 AGGCCAATTCATTTGCATGTAC 57.872 40.909 5.01 0.00 33.73 2.90
5471 7821 4.822685 AAGGCCAATTCATTTGCATGTA 57.177 36.364 5.01 0.00 33.73 2.29
5472 7822 3.706600 AAGGCCAATTCATTTGCATGT 57.293 38.095 5.01 0.00 33.73 3.21
5473 7823 5.157781 CAAAAAGGCCAATTCATTTGCATG 58.842 37.500 5.01 0.00 33.73 4.06
5490 7840 7.703298 TCTTCAAAACTGATCATGCAAAAAG 57.297 32.000 0.00 0.00 0.00 2.27
5509 7859 7.175104 AGGGCAAATAATAAGACAGTTCTTCA 58.825 34.615 0.00 0.00 41.48 3.02
5516 7866 9.533253 CCAAAATAAGGGCAAATAATAAGACAG 57.467 33.333 0.00 0.00 0.00 3.51
5531 7881 4.824479 ACTCCAAATGCCAAAATAAGGG 57.176 40.909 0.00 0.00 0.00 3.95
5600 7950 7.021196 GCAATTACTCAAACGAAATTCAGCTA 58.979 34.615 0.00 0.00 0.00 3.32
5621 7971 1.350351 AGAGACACTGAAGCCAGCAAT 59.650 47.619 0.00 0.00 44.16 3.56
5628 7978 2.838736 TGGTTGAAGAGACACTGAAGC 58.161 47.619 0.00 0.00 0.00 3.86
5643 7993 8.063630 GCAACAGTTCAAATCTAAAATTGGTTG 58.936 33.333 0.00 0.00 32.74 3.77
5695 8045 3.947834 CACACCTCAACCTTTTCTGTCTT 59.052 43.478 0.00 0.00 0.00 3.01
5706 8056 2.484889 GAGACAGAACACACCTCAACC 58.515 52.381 0.00 0.00 0.00 3.77
5714 8064 2.705658 ACCAGATTGGAGACAGAACACA 59.294 45.455 1.40 0.00 40.96 3.72
5749 8099 4.034048 CGATGGTCGGAACTTTTAATGGAG 59.966 45.833 0.00 0.00 36.00 3.86
5888 8242 4.200092 GGAGTAATTGAGAATGACACCCC 58.800 47.826 0.00 0.00 29.36 4.95
5893 8247 4.141914 ACGGAGGGAGTAATTGAGAATGAC 60.142 45.833 0.00 0.00 0.00 3.06
5905 8259 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
5906 8260 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
5907 8261 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
5908 8262 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5909 8263 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5910 8264 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
5911 8265 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
5912 8266 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
5913 8267 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
5914 8268 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
5915 8269 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
5916 8270 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
5917 8271 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
5918 8272 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
5925 8279 9.915629 CTAAGTTAGTACAAAGTTGAGTCATCT 57.084 33.333 1.40 0.00 0.00 2.90
5926 8280 9.694137 ACTAAGTTAGTACAAAGTTGAGTCATC 57.306 33.333 14.00 0.00 37.23 2.92
5955 8309 8.028938 CCGTTCCAAAATAGATGACTCAATTTT 58.971 33.333 0.00 0.00 33.07 1.82
5956 8310 7.393234 TCCGTTCCAAAATAGATGACTCAATTT 59.607 33.333 0.00 0.00 0.00 1.82
5957 8311 6.884295 TCCGTTCCAAAATAGATGACTCAATT 59.116 34.615 0.00 0.00 0.00 2.32
5958 8312 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
5959 8313 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
5960 8314 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
5961 8315 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
5962 8316 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
5963 8317 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5964 8318 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5965 8319 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5966 8320 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5967 8321 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5968 8322 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5969 8323 6.785963 AGATATACTCCCTCCGTTCCAAAATA 59.214 38.462 0.00 0.00 0.00 1.40
5970 8324 5.607171 AGATATACTCCCTCCGTTCCAAAAT 59.393 40.000 0.00 0.00 0.00 1.82
5971 8325 4.966805 AGATATACTCCCTCCGTTCCAAAA 59.033 41.667 0.00 0.00 0.00 2.44
5972 8326 4.553678 AGATATACTCCCTCCGTTCCAAA 58.446 43.478 0.00 0.00 0.00 3.28
5973 8327 4.150359 GAGATATACTCCCTCCGTTCCAA 58.850 47.826 0.00 0.00 39.53 3.53
5974 8328 3.139584 TGAGATATACTCCCTCCGTTCCA 59.860 47.826 0.00 0.00 44.34 3.53
5975 8329 3.764218 TGAGATATACTCCCTCCGTTCC 58.236 50.000 0.00 0.00 44.34 3.62
5976 8330 4.022155 GGTTGAGATATACTCCCTCCGTTC 60.022 50.000 0.00 0.00 44.34 3.95
5977 8331 3.896272 GGTTGAGATATACTCCCTCCGTT 59.104 47.826 0.00 0.00 44.34 4.44
5978 8332 3.498334 GGTTGAGATATACTCCCTCCGT 58.502 50.000 0.00 0.00 44.34 4.69
5979 8333 2.488545 CGGTTGAGATATACTCCCTCCG 59.511 54.545 0.00 0.00 44.34 4.63
5980 8334 3.256136 CACGGTTGAGATATACTCCCTCC 59.744 52.174 0.00 0.00 44.34 4.30
5981 8335 3.890147 ACACGGTTGAGATATACTCCCTC 59.110 47.826 0.00 0.00 44.34 4.30
5982 8336 3.637229 CACACGGTTGAGATATACTCCCT 59.363 47.826 0.00 0.00 44.34 4.20
5983 8337 3.799232 GCACACGGTTGAGATATACTCCC 60.799 52.174 0.00 0.00 44.34 4.30
5984 8338 3.381949 GCACACGGTTGAGATATACTCC 58.618 50.000 0.00 0.00 44.34 3.85
5985 8339 3.068307 AGGCACACGGTTGAGATATACTC 59.932 47.826 0.00 0.00 45.11 2.59
5986 8340 3.031736 AGGCACACGGTTGAGATATACT 58.968 45.455 0.00 0.00 0.00 2.12
5987 8341 3.454371 AGGCACACGGTTGAGATATAC 57.546 47.619 0.00 0.00 0.00 1.47
6026 8380 8.884726 GTGATCCTTTACTTTCCTAATCTGAAC 58.115 37.037 0.00 0.00 0.00 3.18
6081 8436 6.132658 AGATCTCAGAATAAGTAGTGCTGGA 58.867 40.000 0.00 0.00 0.00 3.86
6125 8480 2.359900 GGCATACCTTCACTGAACCTG 58.640 52.381 0.00 0.00 0.00 4.00
6126 8481 2.789409 GGCATACCTTCACTGAACCT 57.211 50.000 0.00 0.00 0.00 3.50
6172 8528 4.139038 TGTGTTAGCCCTCAAAAGGTAAC 58.861 43.478 5.42 5.42 41.59 2.50
6173 8529 4.440826 TGTGTTAGCCCTCAAAAGGTAA 57.559 40.909 0.00 0.00 41.59 2.85
6207 8563 5.931724 CCGCCATTTAATTGTTCTCCTTTTT 59.068 36.000 0.00 0.00 0.00 1.94
6305 8687 8.712228 AAATCAGAGTGAGGGAATTTAAAAGT 57.288 30.769 0.00 0.00 0.00 2.66
6325 8707 5.291178 CAGAAAGCAACAACCATGAAATCA 58.709 37.500 0.00 0.00 0.00 2.57
6326 8708 4.687483 CCAGAAAGCAACAACCATGAAATC 59.313 41.667 0.00 0.00 0.00 2.17
6329 8711 3.030291 ACCAGAAAGCAACAACCATGAA 58.970 40.909 0.00 0.00 0.00 2.57
6330 8712 2.665165 ACCAGAAAGCAACAACCATGA 58.335 42.857 0.00 0.00 0.00 3.07
6354 8738 5.464389 CAGCAAAGAGAATGTTGAAAAAGGG 59.536 40.000 0.00 0.00 31.48 3.95
6357 8741 6.310956 CACACAGCAAAGAGAATGTTGAAAAA 59.689 34.615 0.00 0.00 33.76 1.94
6382 8766 4.159120 GACGGACTTTCAAATGCTAAAGC 58.841 43.478 0.00 0.00 36.39 3.51
6383 8767 4.455877 AGGACGGACTTTCAAATGCTAAAG 59.544 41.667 0.00 0.00 38.41 1.85
6384 8768 4.394729 AGGACGGACTTTCAAATGCTAAA 58.605 39.130 0.00 0.00 0.00 1.85
6385 8769 4.015872 AGGACGGACTTTCAAATGCTAA 57.984 40.909 0.00 0.00 0.00 3.09
6386 8770 3.695830 AGGACGGACTTTCAAATGCTA 57.304 42.857 0.00 0.00 0.00 3.49
6387 8771 2.568623 AGGACGGACTTTCAAATGCT 57.431 45.000 0.00 0.00 0.00 3.79
6388 8772 3.371285 GTCTAGGACGGACTTTCAAATGC 59.629 47.826 0.00 0.00 0.00 3.56
6389 8773 4.822026 AGTCTAGGACGGACTTTCAAATG 58.178 43.478 0.00 0.00 40.65 2.32
6409 8794 8.720562 GCCATAATTTTTGACAAATGCTAAAGT 58.279 29.630 0.50 0.00 0.00 2.66
6458 8845 6.379417 GGAACACACCAAGGTATACTACTACT 59.621 42.308 2.25 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.