Multiple sequence alignment - TraesCS7B01G111100

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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 TraesCS7B01G111100 chr7B 100.000 5099 0 0 1 5099 127027039 127021941 0.000000e+00 9417
1 TraesCS7B01G111100 chr7A 90.732 3755 166 62 1 3673 166336207 166332553 0.000000e+00 4839
2 TraesCS7B01G111100 chr7A 90.314 733 36 23 3737 4449 166332540 166331823 0.000000e+00 928
3 TraesCS7B01G111100 chr7A 84.249 273 17 12 4814 5086 166331593 166331347 5.100000e-60 243
4 TraesCS7B01G111100 chr7D 93.617 2256 68 19 477 2679 164647081 164644849 0.000000e+00 3299
5 TraesCS7B01G111100 chr7D 91.157 1063 39 21 2707 3731 164644782 164643737 0.000000e+00 1391
6 TraesCS7B01G111100 chr7D 91.847 785 46 7 3734 4510 164643698 164642924 0.000000e+00 1079
7 TraesCS7B01G111100 chr7D 93.015 272 17 2 175 445 164647353 164647083 3.700000e-106 396
8 TraesCS7B01G111100 chr7D 93.919 148 8 1 4865 5012 164641584 164641438 6.640000e-54 222
9 TraesCS7B01G111100 chr7D 94.776 134 6 1 1 134 164647990 164647858 1.860000e-49 207
10 TraesCS7B01G111100 chr7D 96.078 102 3 1 4707 4808 164642385 164642285 1.140000e-36 165
11 TraesCS7B01G111100 chr5D 89.286 140 5 4 2540 2679 399614659 399614530 3.160000e-37 167
12 TraesCS7B01G111100 chr5D 94.949 99 4 1 2581 2679 123085699 123085796 2.460000e-33 154
13 TraesCS7B01G111100 chr5B 89.286 140 5 4 2540 2679 479726972 479726843 3.160000e-37 167
14 TraesCS7B01G111100 chr5B 94.949 99 4 1 2581 2679 136047707 136047804 2.460000e-33 154
15 TraesCS7B01G111100 chr3D 87.943 141 7 2 2539 2679 540569229 540569099 1.900000e-34 158
16 TraesCS7B01G111100 chr6A 87.943 141 6 5 2539 2679 47466927 47466798 6.840000e-34 156
17 TraesCS7B01G111100 chr5A 93.939 99 5 1 2581 2679 135537519 135537616 1.140000e-31 148
18 TraesCS7B01G111100 chr1B 93.939 99 5 1 2581 2679 264358169 264358072 1.140000e-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 TraesCS7B01G111100 chr7B 127021941 127027039 5098 True 9417.000000 9417 100.000000 1 5099 1 chr7B.!!$R1 5098
1 TraesCS7B01G111100 chr7A 166331347 166336207 4860 True 2003.333333 4839 88.431667 1 5086 3 chr7A.!!$R1 5085
2 TraesCS7B01G111100 chr7D 164641438 164647990 6552 True 965.571429 3299 93.487000 1 5012 7 chr7D.!!$R1 5011

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
522 991 0.035439 GGTGGTGACCATGGTGTAGG 60.035 60.0 25.52 0.00 42.59 3.18 F
764 1261 0.815095 TGTATGTGTCGGACGAGCAT 59.185 50.0 14.04 14.04 0.00 3.79 F
2574 3106 0.178990 GCCTGAAGGTCCTGTGGTTT 60.179 55.0 0.00 0.00 37.57 3.27 F
3745 4462 0.102844 TTTTTCAGCCTGTGCACAGC 59.897 50.0 36.38 29.90 42.47 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 2961 0.392193 CAGTGAAGAGCTTGGCGGAT 60.392 55.0 0.00 0.0 0.0 4.18 R
2577 3109 0.853530 AGGAGGCTGGGTTCAAAGTT 59.146 50.0 0.00 0.0 0.0 2.66 R
4008 4743 0.038166 ACCCCTTCCGTACGTAGACA 59.962 55.0 15.21 0.0 0.0 3.41 R
4680 5491 0.107703 ATCATGTGGTGTGGGTAGCG 60.108 55.0 0.00 0.0 0.0 4.26 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
150 154 3.691342 CGCCGTCCAAGACCCAGA 61.691 66.667 0.00 0.00 0.00 3.86
307 775 1.933853 GGAACTACGCTAGCATTGGTG 59.066 52.381 16.45 0.00 0.00 4.17
315 783 2.673893 CGCTAGCATTGGTGTCAGTACA 60.674 50.000 16.45 0.00 0.00 2.90
322 790 7.792374 AGCATTGGTGTCAGTACAAATATAG 57.208 36.000 0.00 0.00 37.36 1.31
415 883 3.945346 ACCGAGGTGCATGTTTATGTTA 58.055 40.909 0.00 0.00 36.65 2.41
418 886 4.318760 CCGAGGTGCATGTTTATGTTATCG 60.319 45.833 0.00 0.00 36.65 2.92
461 929 0.588252 CTTCCAGTTCGGTGCTGTTG 59.412 55.000 0.00 0.00 35.57 3.33
522 991 0.035439 GGTGGTGACCATGGTGTAGG 60.035 60.000 25.52 0.00 42.59 3.18
661 1158 2.100846 CATTCGGATGCCTGGTGTG 58.899 57.895 0.00 0.00 0.00 3.82
682 1179 5.118990 GTGCCTGATAAGCTGATTGTTAGA 58.881 41.667 0.00 0.00 0.00 2.10
698 1195 1.847328 TAGAGTCATCCTGAACGGCA 58.153 50.000 0.00 0.00 0.00 5.69
764 1261 0.815095 TGTATGTGTCGGACGAGCAT 59.185 50.000 14.04 14.04 0.00 3.79
775 1272 1.332178 GACGAGCATGATAGTAGCGC 58.668 55.000 0.00 0.00 0.00 5.92
777 1274 1.067060 ACGAGCATGATAGTAGCGCAA 59.933 47.619 11.47 0.00 0.00 4.85
791 1288 4.631813 AGTAGCGCAATAGGAAGTTTGAAG 59.368 41.667 11.47 0.00 0.00 3.02
812 1309 2.342179 GAGTTGCTGCTTCTGGAGTAC 58.658 52.381 0.00 0.00 33.91 2.73
823 1321 4.452795 GCTTCTGGAGTACTGTTCCTTTTC 59.547 45.833 0.00 0.00 35.67 2.29
827 1325 5.480772 TCTGGAGTACTGTTCCTTTTCCTAG 59.519 44.000 0.00 0.00 35.67 3.02
841 1339 9.779951 TTCCTTTTCCTAGTAGTATAGAAACCT 57.220 33.333 0.00 0.00 0.00 3.50
857 1355 8.934023 ATAGAAACCTGTGACCTTAATTTTGA 57.066 30.769 0.00 0.00 0.00 2.69
915 1413 2.816087 CTCTGCTTGCTTACACCACATT 59.184 45.455 0.00 0.00 0.00 2.71
1080 1578 0.845102 GAGGAAGGGGAAGGGGACAA 60.845 60.000 0.00 0.00 0.00 3.18
1400 1898 8.598041 AGACCATATCTTCCATACTTATGAACC 58.402 37.037 0.00 0.00 31.62 3.62
1447 1945 7.059202 AGAGGTTTCTCAATTTGAAAATGCT 57.941 32.000 0.01 2.38 42.34 3.79
1530 2028 8.203485 TCTGGTTAATGCTTCAAACTGAAAAAT 58.797 29.630 0.00 0.00 35.73 1.82
1881 2379 4.172807 TGGGATAGAAACTGGTACCAAGT 58.827 43.478 17.11 13.07 0.00 3.16
1889 2387 5.763204 AGAAACTGGTACCAAGTTGTATGTG 59.237 40.000 22.42 9.03 0.00 3.21
2228 2743 4.502171 TCATGTGCATGGTTGTTTGTAG 57.498 40.909 11.68 0.00 39.24 2.74
2233 2748 4.340666 TGTGCATGGTTGTTTGTAGTGAAT 59.659 37.500 0.00 0.00 0.00 2.57
2291 2806 4.451435 CAGCACAGCCTGATAATATGACAG 59.549 45.833 0.00 0.00 34.77 3.51
2433 2957 6.861065 TGCTAGTTTAGACCTTTGAACTTG 57.139 37.500 0.00 0.00 34.46 3.16
2434 2958 6.354130 TGCTAGTTTAGACCTTTGAACTTGT 58.646 36.000 0.00 0.00 34.46 3.16
2436 2960 8.154856 TGCTAGTTTAGACCTTTGAACTTGTAT 58.845 33.333 0.00 0.00 34.46 2.29
2437 2961 9.649167 GCTAGTTTAGACCTTTGAACTTGTATA 57.351 33.333 0.00 0.00 34.46 1.47
2440 2964 9.668497 AGTTTAGACCTTTGAACTTGTATATCC 57.332 33.333 0.00 0.00 0.00 2.59
2441 2965 8.601476 GTTTAGACCTTTGAACTTGTATATCCG 58.399 37.037 0.00 0.00 0.00 4.18
2459 2988 1.303155 GCCAAGCTCTTCACTGCCT 60.303 57.895 0.00 0.00 0.00 4.75
2497 3027 4.151335 CAGTATGACACACACAGAAGCTTC 59.849 45.833 19.11 19.11 39.69 3.86
2572 3104 2.529744 GGCCTGAAGGTCCTGTGGT 61.530 63.158 0.00 0.00 37.57 4.16
2573 3105 1.456287 GCCTGAAGGTCCTGTGGTT 59.544 57.895 0.00 0.00 37.57 3.67
2574 3106 0.178990 GCCTGAAGGTCCTGTGGTTT 60.179 55.000 0.00 0.00 37.57 3.27
2575 3107 1.609208 CCTGAAGGTCCTGTGGTTTG 58.391 55.000 0.00 0.00 0.00 2.93
2576 3108 1.142870 CCTGAAGGTCCTGTGGTTTGA 59.857 52.381 0.00 0.00 0.00 2.69
2577 3109 2.422803 CCTGAAGGTCCTGTGGTTTGAA 60.423 50.000 0.00 0.00 0.00 2.69
2578 3110 3.287222 CTGAAGGTCCTGTGGTTTGAAA 58.713 45.455 0.00 0.00 0.00 2.69
2579 3111 3.020984 TGAAGGTCCTGTGGTTTGAAAC 58.979 45.455 0.00 0.00 0.00 2.78
2644 3176 4.447290 GCTGTCTAGAAATTCCCTTCCTC 58.553 47.826 0.00 0.00 0.00 3.71
2648 3180 5.187967 TGTCTAGAAATTCCCTTCCTCAGAC 59.812 44.000 0.00 0.00 33.72 3.51
2653 3185 0.121197 TTCCCTTCCTCAGACCCCAT 59.879 55.000 0.00 0.00 0.00 4.00
2659 3191 2.044793 TCCTCAGACCCCATCTTGTT 57.955 50.000 0.00 0.00 34.41 2.83
2679 3211 2.338785 GGGAGCTTTCAGCACTGGC 61.339 63.158 0.00 0.00 45.56 4.85
2680 3212 2.338785 GGAGCTTTCAGCACTGGCC 61.339 63.158 0.00 0.00 45.56 5.36
2681 3213 1.303155 GAGCTTTCAGCACTGGCCT 60.303 57.895 3.32 0.00 45.56 5.19
2683 3215 2.960170 CTTTCAGCACTGGCCTGC 59.040 61.111 9.95 9.41 42.56 4.85
2685 3217 3.474486 TTTCAGCACTGGCCTGCGA 62.474 57.895 9.95 8.27 42.42 5.10
2690 3222 3.506096 CACTGGCCTGCGAGCATG 61.506 66.667 9.95 0.00 0.00 4.06
2691 3223 4.025858 ACTGGCCTGCGAGCATGT 62.026 61.111 9.95 0.00 0.00 3.21
2752 3323 9.241317 GCATTATTTGTTTACCTCATTCATCTG 57.759 33.333 0.00 0.00 0.00 2.90
2857 3428 9.554053 AAATAGAGCATATTCTGGTAGTCCTAT 57.446 33.333 0.00 0.00 35.19 2.57
2872 3443 5.428184 AGTCCTATTCTACAGCTTTGCTT 57.572 39.130 0.00 0.00 36.40 3.91
2979 3577 2.452505 ACTAGGAGGAGTGAAGCTGTC 58.547 52.381 0.00 0.00 0.00 3.51
3192 3791 7.173907 AGAGATCCATGCTCATTAAATTTACCG 59.826 37.037 0.00 0.00 34.85 4.02
3239 3838 4.887748 TCTGCCTTTCTGTTTCTGACTAG 58.112 43.478 0.00 0.00 0.00 2.57
3240 3839 4.345257 TCTGCCTTTCTGTTTCTGACTAGT 59.655 41.667 0.00 0.00 0.00 2.57
3241 3840 4.380531 TGCCTTTCTGTTTCTGACTAGTG 58.619 43.478 0.00 0.00 0.00 2.74
3242 3841 4.100963 TGCCTTTCTGTTTCTGACTAGTGA 59.899 41.667 0.00 0.00 0.00 3.41
3243 3842 4.449405 GCCTTTCTGTTTCTGACTAGTGAC 59.551 45.833 0.00 0.00 0.00 3.67
3244 3843 5.740513 GCCTTTCTGTTTCTGACTAGTGACT 60.741 44.000 0.00 0.00 0.00 3.41
3245 3844 6.516860 GCCTTTCTGTTTCTGACTAGTGACTA 60.517 42.308 0.00 0.00 0.00 2.59
3289 3888 0.476771 AATGGGTTTGGTCGAGGTGT 59.523 50.000 0.00 0.00 0.00 4.16
3299 3898 0.952280 GTCGAGGTGTGACTGACTCA 59.048 55.000 0.00 0.00 33.54 3.41
3308 3907 5.305644 AGGTGTGACTGACTCATCTAGTTTT 59.694 40.000 0.00 0.00 39.07 2.43
3399 3998 3.034635 CAGCTTACCTCCTATGACCAGT 58.965 50.000 0.00 0.00 0.00 4.00
3429 4028 4.348656 CTTGACTCAAATGGCAATCGATG 58.651 43.478 0.00 0.00 0.00 3.84
3435 4034 5.047802 ACTCAAATGGCAATCGATGAAAGTT 60.048 36.000 0.00 0.00 0.00 2.66
3504 4103 4.142049 TGTGAAATTTTGTTCCCTGGTGTC 60.142 41.667 0.00 0.00 0.00 3.67
3505 4104 4.026744 TGAAATTTTGTTCCCTGGTGTCA 58.973 39.130 0.00 0.00 0.00 3.58
3506 4105 4.653341 TGAAATTTTGTTCCCTGGTGTCAT 59.347 37.500 0.00 0.00 0.00 3.06
3507 4106 4.605640 AATTTTGTTCCCTGGTGTCATG 57.394 40.909 0.00 0.00 0.00 3.07
3508 4107 1.993956 TTTGTTCCCTGGTGTCATGG 58.006 50.000 0.00 0.00 0.00 3.66
3509 4108 0.112218 TTGTTCCCTGGTGTCATGGG 59.888 55.000 0.00 0.00 42.20 4.00
3510 4109 1.678970 GTTCCCTGGTGTCATGGGC 60.679 63.158 0.00 0.00 40.69 5.36
3511 4110 1.852157 TTCCCTGGTGTCATGGGCT 60.852 57.895 0.00 0.00 40.69 5.19
3512 4111 0.548926 TTCCCTGGTGTCATGGGCTA 60.549 55.000 0.00 0.00 40.69 3.93
3513 4112 0.327480 TCCCTGGTGTCATGGGCTAT 60.327 55.000 0.00 0.00 40.69 2.97
3514 4113 0.179009 CCCTGGTGTCATGGGCTATG 60.179 60.000 4.19 4.19 38.17 2.23
3515 4114 0.179009 CCTGGTGTCATGGGCTATGG 60.179 60.000 11.16 0.00 37.39 2.74
3516 4115 0.548031 CTGGTGTCATGGGCTATGGT 59.452 55.000 11.16 0.00 37.39 3.55
3517 4116 0.255604 TGGTGTCATGGGCTATGGTG 59.744 55.000 11.16 0.00 37.39 4.17
3518 4117 0.466189 GGTGTCATGGGCTATGGTGG 60.466 60.000 11.16 0.00 37.39 4.61
3519 4118 1.103398 GTGTCATGGGCTATGGTGGC 61.103 60.000 11.16 0.65 37.39 5.01
3520 4119 1.227102 GTCATGGGCTATGGTGGCA 59.773 57.895 11.16 0.00 37.39 4.92
3521 4120 0.820891 GTCATGGGCTATGGTGGCAG 60.821 60.000 11.16 0.00 37.39 4.85
3522 4121 2.196776 ATGGGCTATGGTGGCAGC 59.803 61.111 10.30 10.30 37.05 5.25
3523 4122 2.389449 ATGGGCTATGGTGGCAGCT 61.389 57.895 18.53 6.09 37.91 4.24
3524 4123 1.941403 ATGGGCTATGGTGGCAGCTT 61.941 55.000 18.53 14.09 37.91 3.74
3525 4124 1.380380 GGGCTATGGTGGCAGCTTT 60.380 57.895 18.53 8.01 37.91 3.51
3526 4125 0.972471 GGGCTATGGTGGCAGCTTTT 60.972 55.000 18.53 5.50 37.91 2.27
3527 4126 0.174162 GGCTATGGTGGCAGCTTTTG 59.826 55.000 18.53 9.10 37.91 2.44
3557 4188 3.316308 GCACATCTTTCTGAACCTTGTGT 59.684 43.478 18.85 7.17 36.32 3.72
3668 4385 4.419522 TCGAACTAAAAAGCTGATTGCC 57.580 40.909 0.00 0.00 44.23 4.52
3669 4386 3.818210 TCGAACTAAAAAGCTGATTGCCA 59.182 39.130 0.00 0.00 44.23 4.92
3670 4387 4.458989 TCGAACTAAAAAGCTGATTGCCAT 59.541 37.500 0.00 0.00 44.23 4.40
3671 4388 5.645929 TCGAACTAAAAAGCTGATTGCCATA 59.354 36.000 0.00 0.00 44.23 2.74
3672 4389 6.318648 TCGAACTAAAAAGCTGATTGCCATAT 59.681 34.615 0.00 0.00 44.23 1.78
3673 4390 6.415867 CGAACTAAAAAGCTGATTGCCATATG 59.584 38.462 0.00 0.00 44.23 1.78
3674 4391 7.408756 AACTAAAAAGCTGATTGCCATATGA 57.591 32.000 3.65 0.00 44.23 2.15
3675 4392 7.592885 ACTAAAAAGCTGATTGCCATATGAT 57.407 32.000 3.65 0.00 44.23 2.45
3676 4393 7.431249 ACTAAAAAGCTGATTGCCATATGATG 58.569 34.615 3.65 0.00 44.23 3.07
3677 4394 5.864418 AAAAGCTGATTGCCATATGATGT 57.136 34.783 3.65 0.00 44.23 3.06
3678 4395 4.848562 AAGCTGATTGCCATATGATGTG 57.151 40.909 3.65 0.00 44.23 3.21
3679 4396 2.557056 AGCTGATTGCCATATGATGTGC 59.443 45.455 3.65 0.00 44.23 4.57
3680 4397 2.352421 GCTGATTGCCATATGATGTGCC 60.352 50.000 3.65 0.00 35.15 5.01
3681 4398 3.154710 CTGATTGCCATATGATGTGCCT 58.845 45.455 3.65 0.00 0.00 4.75
3682 4399 4.329392 CTGATTGCCATATGATGTGCCTA 58.671 43.478 3.65 0.00 0.00 3.93
3683 4400 4.074259 TGATTGCCATATGATGTGCCTAC 58.926 43.478 3.65 0.00 0.00 3.18
3684 4401 3.574354 TTGCCATATGATGTGCCTACA 57.426 42.857 3.65 0.00 41.89 2.74
3685 4402 3.130280 TGCCATATGATGTGCCTACAG 57.870 47.619 3.65 0.00 40.79 2.74
3686 4403 2.439135 TGCCATATGATGTGCCTACAGT 59.561 45.455 3.65 0.00 40.79 3.55
3702 4419 8.458843 GTGCCTACAGTACATATTTGATTGTTT 58.541 33.333 0.00 0.00 0.00 2.83
3704 4421 8.673711 GCCTACAGTACATATTTGATTGTTTCA 58.326 33.333 0.00 0.00 0.00 2.69
3717 4434 3.853831 TTGTTTCATGTGCATAGCAGG 57.146 42.857 0.00 0.00 40.08 4.85
3725 4442 0.103572 GTGCATAGCAGGGCCAAATG 59.896 55.000 6.18 4.66 40.08 2.32
3727 4444 0.826062 GCATAGCAGGGCCAAATGTT 59.174 50.000 6.18 0.14 0.00 2.71
3728 4445 1.207811 GCATAGCAGGGCCAAATGTTT 59.792 47.619 6.18 0.00 0.00 2.83
3729 4446 2.355007 GCATAGCAGGGCCAAATGTTTT 60.355 45.455 6.18 0.00 0.00 2.43
3730 4447 3.869526 GCATAGCAGGGCCAAATGTTTTT 60.870 43.478 6.18 0.00 0.00 1.94
3731 4448 2.549064 AGCAGGGCCAAATGTTTTTC 57.451 45.000 6.18 0.00 0.00 2.29
3732 4449 1.767681 AGCAGGGCCAAATGTTTTTCA 59.232 42.857 6.18 0.00 0.00 2.69
3733 4450 2.145536 GCAGGGCCAAATGTTTTTCAG 58.854 47.619 6.18 0.00 0.00 3.02
3734 4451 2.145536 CAGGGCCAAATGTTTTTCAGC 58.854 47.619 6.18 0.00 0.00 4.26
3735 4452 1.072173 AGGGCCAAATGTTTTTCAGCC 59.928 47.619 6.18 0.00 39.21 4.85
3736 4453 1.072173 GGGCCAAATGTTTTTCAGCCT 59.928 47.619 4.39 0.00 39.59 4.58
3737 4454 2.145536 GGCCAAATGTTTTTCAGCCTG 58.854 47.619 0.00 0.00 37.90 4.85
3738 4455 2.485302 GGCCAAATGTTTTTCAGCCTGT 60.485 45.455 0.00 0.00 37.90 4.00
3739 4456 2.545106 GCCAAATGTTTTTCAGCCTGTG 59.455 45.455 0.00 0.00 0.00 3.66
3740 4457 2.545106 CCAAATGTTTTTCAGCCTGTGC 59.455 45.455 0.00 0.00 37.95 4.57
3741 4458 3.196463 CAAATGTTTTTCAGCCTGTGCA 58.804 40.909 0.00 0.00 41.13 4.57
3742 4459 2.514205 ATGTTTTTCAGCCTGTGCAC 57.486 45.000 10.75 10.75 41.13 4.57
3743 4460 1.180907 TGTTTTTCAGCCTGTGCACA 58.819 45.000 20.37 20.37 41.13 4.57
3744 4461 1.134753 TGTTTTTCAGCCTGTGCACAG 59.865 47.619 35.15 35.15 43.40 3.66
3745 4462 0.102844 TTTTTCAGCCTGTGCACAGC 59.897 50.000 36.38 29.90 42.47 4.40
3746 4463 1.036481 TTTTCAGCCTGTGCACAGCA 61.036 50.000 36.38 19.09 42.47 4.41
3747 4464 1.449726 TTTCAGCCTGTGCACAGCAG 61.450 55.000 36.38 27.03 40.08 4.24
3748 4465 2.281276 CAGCCTGTGCACAGCAGA 60.281 61.111 36.38 7.52 40.08 4.26
3750 4467 3.735029 GCCTGTGCACAGCAGAGC 61.735 66.667 36.38 29.60 46.51 4.09
3751 4468 3.054503 CCTGTGCACAGCAGAGCC 61.055 66.667 36.38 0.00 46.51 4.70
3752 4469 2.281276 CTGTGCACAGCAGAGCCA 60.281 61.111 32.39 0.33 42.61 4.75
3753 4470 1.895231 CTGTGCACAGCAGAGCCAA 60.895 57.895 32.39 0.00 42.61 4.52
3754 4471 1.449726 CTGTGCACAGCAGAGCCAAA 61.450 55.000 32.39 0.00 42.61 3.28
3755 4472 0.824595 TGTGCACAGCAGAGCCAAAT 60.825 50.000 17.42 0.00 40.08 2.32
3756 4473 1.167851 GTGCACAGCAGAGCCAAATA 58.832 50.000 13.17 0.00 40.08 1.40
3757 4474 1.747355 GTGCACAGCAGAGCCAAATAT 59.253 47.619 13.17 0.00 40.08 1.28
3758 4475 2.165030 GTGCACAGCAGAGCCAAATATT 59.835 45.455 13.17 0.00 40.08 1.28
3792 4509 4.151798 GTCGTGTGAGCTATTTTTCTTGC 58.848 43.478 0.00 0.00 0.00 4.01
3795 4512 4.391830 CGTGTGAGCTATTTTTCTTGCCTA 59.608 41.667 0.00 0.00 0.00 3.93
3796 4513 5.106712 CGTGTGAGCTATTTTTCTTGCCTAA 60.107 40.000 0.00 0.00 0.00 2.69
3936 4671 1.199624 GCAACAACGGTTTTGCTCAG 58.800 50.000 16.84 3.13 43.96 3.35
4008 4743 3.667282 CGAGGTCGTGGACGTGGT 61.667 66.667 0.00 0.00 40.80 4.16
4038 4773 0.326927 GGAAGGGGTCGGTGAAATCA 59.673 55.000 0.00 0.00 0.00 2.57
4136 4871 0.613012 ATTGAACCTGGAGCTTGGCC 60.613 55.000 0.00 0.00 0.00 5.36
4138 4873 4.351054 AACCTGGAGCTTGGCCGG 62.351 66.667 0.00 0.00 0.00 6.13
4178 4913 2.414058 TTTATGTGTGGTTTGCTGCG 57.586 45.000 0.00 0.00 0.00 5.18
4215 4950 0.594602 CTCCCAGTTGTGTGCACATG 59.405 55.000 24.69 16.74 41.52 3.21
4306 5041 5.183140 AGCAGTAACATTGTAATTGGTGGTC 59.817 40.000 0.00 0.00 0.00 4.02
4480 5223 1.135527 TCCAGCGTAGGGTTTGTATCG 59.864 52.381 0.00 0.00 0.00 2.92
4484 5227 2.358267 AGCGTAGGGTTTGTATCGAGAG 59.642 50.000 0.00 0.00 0.00 3.20
4486 5229 2.947652 CGTAGGGTTTGTATCGAGAGGA 59.052 50.000 0.00 0.00 0.00 3.71
4510 5253 7.591426 GGAGTTTGTGAGACAACATTTATTCAC 59.409 37.037 0.00 0.00 37.90 3.18
4526 5326 2.920724 TCACTCCATTCACGTTTCCA 57.079 45.000 0.00 0.00 0.00 3.53
4533 5333 5.029807 TCCATTCACGTTTCCATAGCATA 57.970 39.130 0.00 0.00 0.00 3.14
4546 5346 3.008813 CCATAGCATAGCCTGACCTTCAT 59.991 47.826 0.00 0.00 0.00 2.57
4548 5348 0.950116 GCATAGCCTGACCTTCATGC 59.050 55.000 0.00 0.00 38.13 4.06
4550 5350 2.219458 CATAGCCTGACCTTCATGCTG 58.781 52.381 14.11 0.00 45.62 4.41
4551 5351 0.543277 TAGCCTGACCTTCATGCTGG 59.457 55.000 14.11 2.82 45.62 4.85
4552 5352 1.203441 AGCCTGACCTTCATGCTGGA 61.203 55.000 10.18 0.00 44.66 3.86
4553 5353 0.106819 GCCTGACCTTCATGCTGGAT 60.107 55.000 10.18 0.00 35.54 3.41
4570 5370 4.789075 TTACTGCTCGCCGGCGAC 62.789 66.667 45.37 37.03 44.01 5.19
4592 5403 4.135153 CCACTGCTCCGTCCCTCG 62.135 72.222 0.00 0.00 39.52 4.63
4593 5404 3.062466 CACTGCTCCGTCCCTCGA 61.062 66.667 0.00 0.00 42.86 4.04
4621 5432 4.069232 CTCGCTTCCACGCCTCCA 62.069 66.667 0.00 0.00 0.00 3.86
4622 5433 3.376935 CTCGCTTCCACGCCTCCAT 62.377 63.158 0.00 0.00 0.00 3.41
4623 5434 2.892425 CGCTTCCACGCCTCCATC 60.892 66.667 0.00 0.00 0.00 3.51
4625 5436 2.109126 GCTTCCACGCCTCCATCAC 61.109 63.158 0.00 0.00 0.00 3.06
4627 5438 2.876368 CTTCCACGCCTCCATCACCC 62.876 65.000 0.00 0.00 0.00 4.61
4628 5439 3.716195 CCACGCCTCCATCACCCA 61.716 66.667 0.00 0.00 0.00 4.51
4630 5441 2.284625 ACGCCTCCATCACCCAGA 60.285 61.111 0.00 0.00 0.00 3.86
4633 5444 1.222936 GCCTCCATCACCCAGACAG 59.777 63.158 0.00 0.00 0.00 3.51
4634 5445 1.557269 GCCTCCATCACCCAGACAGT 61.557 60.000 0.00 0.00 0.00 3.55
4635 5446 0.251354 CCTCCATCACCCAGACAGTG 59.749 60.000 0.00 0.00 36.54 3.66
4636 5447 0.392193 CTCCATCACCCAGACAGTGC 60.392 60.000 0.00 0.00 35.14 4.40
4637 5448 0.837691 TCCATCACCCAGACAGTGCT 60.838 55.000 0.00 0.00 35.14 4.40
4638 5449 0.675837 CCATCACCCAGACAGTGCTG 60.676 60.000 7.38 7.38 35.14 4.41
4639 5450 1.002868 ATCACCCAGACAGTGCTGC 60.003 57.895 8.53 0.00 35.14 5.25
4640 5451 2.475371 ATCACCCAGACAGTGCTGCC 62.475 60.000 0.00 0.00 35.14 4.85
4641 5452 3.170672 ACCCAGACAGTGCTGCCA 61.171 61.111 0.00 0.00 34.56 4.92
4642 5453 2.670934 CCCAGACAGTGCTGCCAC 60.671 66.667 0.00 0.00 42.39 5.01
4651 5462 4.383861 TGCTGCCACTCGCCTCTG 62.384 66.667 0.00 0.00 36.24 3.35
4652 5463 4.385405 GCTGCCACTCGCCTCTGT 62.385 66.667 0.00 0.00 36.24 3.41
4653 5464 3.006756 GCTGCCACTCGCCTCTGTA 62.007 63.158 0.00 0.00 36.24 2.74
4654 5465 1.591703 CTGCCACTCGCCTCTGTAA 59.408 57.895 0.00 0.00 36.24 2.41
4655 5466 0.737715 CTGCCACTCGCCTCTGTAAC 60.738 60.000 0.00 0.00 36.24 2.50
4656 5467 1.448013 GCCACTCGCCTCTGTAACC 60.448 63.158 0.00 0.00 0.00 2.85
4657 5468 1.218316 CCACTCGCCTCTGTAACCC 59.782 63.158 0.00 0.00 0.00 4.11
4658 5469 1.541310 CCACTCGCCTCTGTAACCCA 61.541 60.000 0.00 0.00 0.00 4.51
4659 5470 0.389948 CACTCGCCTCTGTAACCCAC 60.390 60.000 0.00 0.00 0.00 4.61
4660 5471 0.830444 ACTCGCCTCTGTAACCCACA 60.830 55.000 0.00 0.00 35.30 4.17
4661 5472 0.389948 CTCGCCTCTGTAACCCACAC 60.390 60.000 0.00 0.00 32.33 3.82
4662 5473 1.375523 CGCCTCTGTAACCCACACC 60.376 63.158 0.00 0.00 32.33 4.16
4691 5502 3.248446 TTGCCTCCGCTACCCACAC 62.248 63.158 0.00 0.00 35.36 3.82
4699 5510 0.107703 CGCTACCCACACCACATGAT 60.108 55.000 0.00 0.00 0.00 2.45
4750 5835 3.186909 CATTTGTCATTGAGCATGCAGG 58.813 45.455 21.98 0.36 32.13 4.85
4764 5849 3.431207 GCATGCAGGAATTATTGGCAGTT 60.431 43.478 14.21 0.00 37.96 3.16
4807 5892 3.837578 GCATGATGCCACCCAGAG 58.162 61.111 6.04 0.00 37.42 3.35
4808 5893 2.487532 GCATGATGCCACCCAGAGC 61.488 63.158 6.04 0.00 37.42 4.09
4809 5894 1.226542 CATGATGCCACCCAGAGCT 59.773 57.895 0.00 0.00 0.00 4.09
4810 5895 0.471191 CATGATGCCACCCAGAGCTA 59.529 55.000 0.00 0.00 0.00 3.32
4811 5896 1.134007 CATGATGCCACCCAGAGCTAA 60.134 52.381 0.00 0.00 0.00 3.09
4812 5897 1.216064 TGATGCCACCCAGAGCTAAT 58.784 50.000 0.00 0.00 0.00 1.73
4813 5898 1.565759 TGATGCCACCCAGAGCTAATT 59.434 47.619 0.00 0.00 0.00 1.40
4814 5899 2.025037 TGATGCCACCCAGAGCTAATTT 60.025 45.455 0.00 0.00 0.00 1.82
4815 5900 2.603075 TGCCACCCAGAGCTAATTTT 57.397 45.000 0.00 0.00 0.00 1.82
4816 5901 2.888212 TGCCACCCAGAGCTAATTTTT 58.112 42.857 0.00 0.00 0.00 1.94
4817 5902 2.562298 TGCCACCCAGAGCTAATTTTTG 59.438 45.455 0.00 0.00 0.00 2.44
4818 5903 2.094026 GCCACCCAGAGCTAATTTTTGG 60.094 50.000 0.00 0.00 0.00 3.28
4819 5904 3.430453 CCACCCAGAGCTAATTTTTGGA 58.570 45.455 0.00 0.00 0.00 3.53
4820 5905 3.445096 CCACCCAGAGCTAATTTTTGGAG 59.555 47.826 0.00 0.00 0.00 3.86
4821 5906 3.445096 CACCCAGAGCTAATTTTTGGAGG 59.555 47.826 0.00 0.00 0.00 4.30
4822 5907 3.076032 ACCCAGAGCTAATTTTTGGAGGT 59.924 43.478 0.00 0.00 0.00 3.85
4823 5908 3.445096 CCCAGAGCTAATTTTTGGAGGTG 59.555 47.826 0.00 0.00 0.00 4.00
4824 5909 3.445096 CCAGAGCTAATTTTTGGAGGTGG 59.555 47.826 0.00 0.00 0.00 4.61
4825 5910 3.445096 CAGAGCTAATTTTTGGAGGTGGG 59.555 47.826 0.00 0.00 0.00 4.61
4826 5911 3.076032 AGAGCTAATTTTTGGAGGTGGGT 59.924 43.478 0.00 0.00 0.00 4.51
4827 5912 3.832490 GAGCTAATTTTTGGAGGTGGGTT 59.168 43.478 0.00 0.00 0.00 4.11
4828 5913 4.231273 AGCTAATTTTTGGAGGTGGGTTT 58.769 39.130 0.00 0.00 0.00 3.27
4829 5914 4.658435 AGCTAATTTTTGGAGGTGGGTTTT 59.342 37.500 0.00 0.00 0.00 2.43
4830 5915 5.131977 AGCTAATTTTTGGAGGTGGGTTTTT 59.868 36.000 0.00 0.00 0.00 1.94
4831 5916 5.238432 GCTAATTTTTGGAGGTGGGTTTTTG 59.762 40.000 0.00 0.00 0.00 2.44
4832 5917 5.443230 AATTTTTGGAGGTGGGTTTTTGA 57.557 34.783 0.00 0.00 0.00 2.69
4842 5927 2.946990 GTGGGTTTTTGAGAGTTCGGAA 59.053 45.455 0.00 0.00 0.00 4.30
4900 6657 4.082787 TGCTAGAAGGCAAAATTACAGTGC 60.083 41.667 0.00 0.00 39.43 4.40
4955 6712 4.475135 GGAGGCCCGGAGCTGTTC 62.475 72.222 0.73 4.75 43.05 3.18
4964 6721 1.227999 CGGAGCTGTTCGGAAGCAAA 61.228 55.000 0.00 0.00 43.37 3.68
4965 6722 1.168714 GGAGCTGTTCGGAAGCAAAT 58.831 50.000 0.00 0.00 43.37 2.32
4966 6723 2.356135 GGAGCTGTTCGGAAGCAAATA 58.644 47.619 0.00 0.00 43.37 1.40
4967 6724 2.747446 GGAGCTGTTCGGAAGCAAATAA 59.253 45.455 0.00 0.00 43.37 1.40
4968 6725 3.378427 GGAGCTGTTCGGAAGCAAATAAT 59.622 43.478 0.00 0.00 43.37 1.28
4969 6726 4.346129 GAGCTGTTCGGAAGCAAATAATG 58.654 43.478 0.00 0.00 43.37 1.90
4970 6727 3.758554 AGCTGTTCGGAAGCAAATAATGT 59.241 39.130 4.64 0.00 43.37 2.71
4976 6733 6.016192 TGTTCGGAAGCAAATAATGTGGTAAA 60.016 34.615 0.00 0.00 0.00 2.01
5024 6781 3.266686 TTGGATGACTGCCCGTGGG 62.267 63.158 0.00 0.00 38.57 4.61
5043 6800 4.273235 GTGGGCTTTTGGTTGAAATTTCTG 59.727 41.667 18.64 1.56 0.00 3.02
5049 6806 7.173735 GGCTTTTGGTTGAAATTTCTGAATGAT 59.826 33.333 18.64 0.00 0.00 2.45
5068 6825 9.529325 TGAATGATTATAAGGTTGAGTAGTTCG 57.471 33.333 0.00 0.00 0.00 3.95
5083 6840 9.531942 TTGAGTAGTTCGTGTCAAACTTTATTA 57.468 29.630 0.00 0.00 38.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 111 2.430921 GTGGTCGGTCTGCGTCTG 60.431 66.667 0.00 0.00 0.00 3.51
144 148 2.066999 GGGCTCGGATCTTCTGGGT 61.067 63.158 0.00 0.00 0.00 4.51
168 172 3.637273 GTCGTTGGCAGGGAGGGT 61.637 66.667 0.00 0.00 0.00 4.34
322 790 6.380190 AGTGACTGAATCAACGAAGTACTAC 58.620 40.000 0.00 0.00 45.00 2.73
339 807 0.798159 TTTGCGCATGCTAGTGACTG 59.202 50.000 12.75 0.00 43.34 3.51
398 866 5.182487 TCACGATAACATAAACATGCACCT 58.818 37.500 0.00 0.00 0.00 4.00
415 883 4.143333 CCGGCTCCCGTTCACGAT 62.143 66.667 0.00 0.00 46.80 3.73
418 886 0.108041 TAAATCCGGCTCCCGTTCAC 60.108 55.000 0.00 0.00 46.80 3.18
474 943 1.133809 AAGCTACCCAGGCTCACCAA 61.134 55.000 0.00 0.00 39.30 3.67
522 991 1.593196 TCCACTAACAACACAGCAGC 58.407 50.000 0.00 0.00 0.00 5.25
628 1117 2.420129 CCGAATGCAAGTAGCCCTTACT 60.420 50.000 0.00 0.00 44.55 2.24
661 1158 5.363939 ACTCTAACAATCAGCTTATCAGGC 58.636 41.667 0.00 0.00 0.00 4.85
764 1261 5.531122 AACTTCCTATTGCGCTACTATCA 57.469 39.130 9.73 0.00 0.00 2.15
775 1272 5.474876 AGCAACTCCTTCAAACTTCCTATTG 59.525 40.000 0.00 0.00 0.00 1.90
777 1274 5.006386 CAGCAACTCCTTCAAACTTCCTAT 58.994 41.667 0.00 0.00 0.00 2.57
791 1288 0.036022 ACTCCAGAAGCAGCAACTCC 59.964 55.000 0.00 0.00 0.00 3.85
823 1321 7.061688 AGGTCACAGGTTTCTATACTACTAGG 58.938 42.308 0.00 0.00 0.00 3.02
1080 1578 4.016706 CGGCCTCGACCAACCCTT 62.017 66.667 0.00 0.00 39.00 3.95
1325 1823 6.429692 TGTCCCATTTATTATGTTCATAGCCG 59.570 38.462 0.00 0.00 0.00 5.52
1400 1898 2.275318 GATCCTCTTTGAAGCTCCACG 58.725 52.381 0.00 0.00 0.00 4.94
1447 1945 0.905357 GCTAAGGGGCAGTTCTCAGA 59.095 55.000 0.00 0.00 0.00 3.27
1530 2028 5.625426 GCTGACCATGAGAAGAGACAATGTA 60.625 44.000 0.00 0.00 0.00 2.29
1565 2063 8.904099 AAGTATCCAACAGGTTAATACATAGC 57.096 34.615 14.30 0.00 0.00 2.97
1881 2379 5.277106 CGTAGTGCAAGTTTGACACATACAA 60.277 40.000 16.15 0.00 37.53 2.41
1889 2387 2.221055 CACTCCGTAGTGCAAGTTTGAC 59.779 50.000 0.00 0.00 46.28 3.18
2264 2779 1.851065 TTATCAGGCTGTGCTGGGCA 61.851 55.000 15.27 0.00 35.60 5.36
2304 2828 7.452880 AATGATACCCGGTTATCATTTCATG 57.547 36.000 30.96 3.00 45.73 3.07
2318 2842 2.917933 TGCAGGAGAAAATGATACCCG 58.082 47.619 0.00 0.00 0.00 5.28
2326 2850 9.590451 CATACAAAACATATTGCAGGAGAAAAT 57.410 29.630 0.00 0.00 33.52 1.82
2429 2953 2.700897 AGAGCTTGGCGGATATACAAGT 59.299 45.455 0.00 0.00 42.60 3.16
2433 2957 3.060602 GTGAAGAGCTTGGCGGATATAC 58.939 50.000 0.00 0.00 0.00 1.47
2434 2958 2.965831 AGTGAAGAGCTTGGCGGATATA 59.034 45.455 0.00 0.00 0.00 0.86
2436 2960 1.134699 CAGTGAAGAGCTTGGCGGATA 60.135 52.381 0.00 0.00 0.00 2.59
2437 2961 0.392193 CAGTGAAGAGCTTGGCGGAT 60.392 55.000 0.00 0.00 0.00 4.18
2439 2963 2.684843 GCAGTGAAGAGCTTGGCGG 61.685 63.158 0.00 0.00 0.00 6.13
2440 2964 2.684843 GGCAGTGAAGAGCTTGGCG 61.685 63.158 0.00 0.00 0.00 5.69
2441 2965 1.303155 AGGCAGTGAAGAGCTTGGC 60.303 57.895 0.00 0.00 0.00 4.52
2459 2988 7.659390 TGTGTCATACTGTCATGTATGTTTTGA 59.341 33.333 15.84 0.00 45.82 2.69
2482 3012 1.290203 ACACGAAGCTTCTGTGTGTG 58.710 50.000 34.82 29.06 41.81 3.82
2483 3013 1.290203 CACACGAAGCTTCTGTGTGT 58.710 50.000 39.88 33.47 45.84 3.72
2524 3056 9.427821 AGTGGAGAGACTATTGATAGTACAATT 57.572 33.333 3.75 0.00 43.27 2.32
2525 3057 9.427821 AAGTGGAGAGACTATTGATAGTACAAT 57.572 33.333 3.75 0.00 43.27 2.71
2527 3059 7.834681 ACAAGTGGAGAGACTATTGATAGTACA 59.165 37.037 3.75 0.00 43.27 2.90
2528 3060 8.132362 CACAAGTGGAGAGACTATTGATAGTAC 58.868 40.741 3.75 2.68 43.27 2.73
2572 3104 3.103742 AGGCTGGGTTCAAAGTTTCAAA 58.896 40.909 0.00 0.00 0.00 2.69
2573 3105 2.693074 GAGGCTGGGTTCAAAGTTTCAA 59.307 45.455 0.00 0.00 0.00 2.69
2574 3106 2.306847 GAGGCTGGGTTCAAAGTTTCA 58.693 47.619 0.00 0.00 0.00 2.69
2575 3107 1.613925 GGAGGCTGGGTTCAAAGTTTC 59.386 52.381 0.00 0.00 0.00 2.78
2576 3108 1.217942 AGGAGGCTGGGTTCAAAGTTT 59.782 47.619 0.00 0.00 0.00 2.66
2577 3109 0.853530 AGGAGGCTGGGTTCAAAGTT 59.146 50.000 0.00 0.00 0.00 2.66
2578 3110 0.853530 AAGGAGGCTGGGTTCAAAGT 59.146 50.000 0.00 0.00 0.00 2.66
2579 3111 1.251251 CAAGGAGGCTGGGTTCAAAG 58.749 55.000 0.00 0.00 0.00 2.77
2702 3236 8.904834 TGCTACTACTTAAGATTGGAGTAAGAG 58.095 37.037 10.09 1.21 0.00 2.85
2775 3346 2.335316 TTCACTAACGTTTGGCAGGT 57.665 45.000 5.91 0.00 0.00 4.00
2857 3428 5.127031 ACTTTTTCCAAGCAAAGCTGTAGAA 59.873 36.000 0.00 0.00 39.62 2.10
2872 3443 3.193267 GGCATGCAGTATGACTTTTTCCA 59.807 43.478 21.36 0.00 41.89 3.53
2919 3517 7.335422 GCTGAACCCTACTCAATAATATCCATG 59.665 40.741 0.00 0.00 0.00 3.66
2929 3527 2.503356 CCTCAGCTGAACCCTACTCAAT 59.497 50.000 18.85 0.00 0.00 2.57
2935 3533 2.254152 ATCACCTCAGCTGAACCCTA 57.746 50.000 18.85 2.92 0.00 3.53
2979 3577 9.897744 ACATTATTATATCGTTTCAATGCTTGG 57.102 29.630 0.00 0.00 0.00 3.61
3239 3838 5.122396 GGACCTGAAAACATCATGTAGTCAC 59.878 44.000 0.00 0.00 37.08 3.67
3240 3839 5.245531 GGACCTGAAAACATCATGTAGTCA 58.754 41.667 0.00 0.00 37.08 3.41
3241 3840 4.636206 GGGACCTGAAAACATCATGTAGTC 59.364 45.833 0.00 0.00 37.08 2.59
3242 3841 4.589908 GGGACCTGAAAACATCATGTAGT 58.410 43.478 0.00 0.00 37.08 2.73
3243 3842 3.623060 CGGGACCTGAAAACATCATGTAG 59.377 47.826 0.00 0.00 37.08 2.74
3244 3843 3.008594 ACGGGACCTGAAAACATCATGTA 59.991 43.478 7.51 0.00 37.08 2.29
3245 3844 2.224769 ACGGGACCTGAAAACATCATGT 60.225 45.455 7.51 0.00 39.29 3.21
3289 3888 6.495181 AGGAAGAAAACTAGATGAGTCAGTCA 59.505 38.462 0.00 0.00 37.44 3.41
3299 3898 5.351405 ACCTACCCAGGAAGAAAACTAGAT 58.649 41.667 0.00 0.00 45.91 1.98
3308 3907 3.338824 TCCTAAGAACCTACCCAGGAAGA 59.661 47.826 0.00 0.00 45.91 2.87
3370 3969 2.541466 AGGAGGTAAGCTGCACTACTT 58.459 47.619 1.02 0.00 0.00 2.24
3399 3998 3.568007 GCCATTTGAGTCAAGGTTGTGTA 59.432 43.478 5.56 0.00 0.00 2.90
3429 4028 2.223537 CCACCTGTTGGCAAACTTTC 57.776 50.000 0.00 0.00 39.07 2.62
3458 4057 1.686355 TGTACAGGCACACAAAAGGG 58.314 50.000 0.00 0.00 0.00 3.95
3504 4103 2.198287 GCTGCCACCATAGCCCATG 61.198 63.158 0.00 0.00 33.89 3.66
3505 4104 1.941403 AAGCTGCCACCATAGCCCAT 61.941 55.000 0.00 0.00 40.76 4.00
3506 4105 2.153898 AAAGCTGCCACCATAGCCCA 62.154 55.000 0.00 0.00 40.76 5.36
3507 4106 0.972471 AAAAGCTGCCACCATAGCCC 60.972 55.000 0.00 0.00 40.76 5.19
3508 4107 0.174162 CAAAAGCTGCCACCATAGCC 59.826 55.000 0.00 0.00 40.76 3.93
3509 4108 0.890683 ACAAAAGCTGCCACCATAGC 59.109 50.000 0.00 0.00 40.18 2.97
3510 4109 1.888512 ACACAAAAGCTGCCACCATAG 59.111 47.619 0.00 0.00 0.00 2.23
3511 4110 1.612950 CACACAAAAGCTGCCACCATA 59.387 47.619 0.00 0.00 0.00 2.74
3512 4111 0.390124 CACACAAAAGCTGCCACCAT 59.610 50.000 0.00 0.00 0.00 3.55
3513 4112 0.969917 ACACACAAAAGCTGCCACCA 60.970 50.000 0.00 0.00 0.00 4.17
3514 4113 0.249031 GACACACAAAAGCTGCCACC 60.249 55.000 0.00 0.00 0.00 4.61
3515 4114 0.740737 AGACACACAAAAGCTGCCAC 59.259 50.000 0.00 0.00 0.00 5.01
3516 4115 0.740149 CAGACACACAAAAGCTGCCA 59.260 50.000 0.00 0.00 0.00 4.92
3517 4116 0.595825 GCAGACACACAAAAGCTGCC 60.596 55.000 0.00 0.00 44.50 4.85
3518 4117 2.877396 GCAGACACACAAAAGCTGC 58.123 52.632 0.00 0.00 44.11 5.25
3519 4118 1.831343 GTGCAGACACACAAAAGCTG 58.169 50.000 0.00 0.00 46.61 4.24
3668 4385 9.440773 AAATATGTACTGTAGGCACATCATATG 57.559 33.333 0.00 0.00 35.71 1.78
3669 4386 9.440773 CAAATATGTACTGTAGGCACATCATAT 57.559 33.333 0.00 0.00 36.29 1.78
3670 4387 8.646900 TCAAATATGTACTGTAGGCACATCATA 58.353 33.333 0.00 0.00 34.78 2.15
3671 4388 7.508687 TCAAATATGTACTGTAGGCACATCAT 58.491 34.615 0.00 0.00 34.78 2.45
3672 4389 6.883744 TCAAATATGTACTGTAGGCACATCA 58.116 36.000 0.00 0.00 34.78 3.07
3673 4390 7.969536 ATCAAATATGTACTGTAGGCACATC 57.030 36.000 0.00 0.00 34.78 3.06
3674 4391 7.775093 ACAATCAAATATGTACTGTAGGCACAT 59.225 33.333 0.00 0.23 36.82 3.21
3675 4392 7.109501 ACAATCAAATATGTACTGTAGGCACA 58.890 34.615 0.00 0.00 0.00 4.57
3676 4393 7.553881 ACAATCAAATATGTACTGTAGGCAC 57.446 36.000 0.00 0.00 0.00 5.01
3677 4394 8.574251 AAACAATCAAATATGTACTGTAGGCA 57.426 30.769 0.00 0.00 0.00 4.75
3678 4395 8.673711 TGAAACAATCAAATATGTACTGTAGGC 58.326 33.333 0.00 0.00 34.30 3.93
3682 4399 9.844790 CACATGAAACAATCAAATATGTACTGT 57.155 29.630 0.00 0.00 42.54 3.55
3683 4400 8.800972 GCACATGAAACAATCAAATATGTACTG 58.199 33.333 0.00 0.00 42.54 2.74
3684 4401 8.522003 TGCACATGAAACAATCAAATATGTACT 58.478 29.630 0.00 0.00 42.54 2.73
3685 4402 8.686397 TGCACATGAAACAATCAAATATGTAC 57.314 30.769 0.00 0.00 42.54 2.90
3702 4419 1.152902 GGCCCTGCTATGCACATGA 60.153 57.895 0.00 0.00 33.79 3.07
3704 4421 0.324552 TTTGGCCCTGCTATGCACAT 60.325 50.000 0.00 0.00 33.79 3.21
3717 4434 2.145536 CAGGCTGAAAAACATTTGGCC 58.854 47.619 9.42 0.00 38.50 5.36
3725 4442 1.843992 CTGTGCACAGGCTGAAAAAC 58.156 50.000 34.65 13.56 41.91 2.43
3727 4444 1.036481 TGCTGTGCACAGGCTGAAAA 61.036 50.000 39.92 17.98 43.94 2.29
3728 4445 1.449726 CTGCTGTGCACAGGCTGAAA 61.450 55.000 39.92 19.25 43.94 2.69
3729 4446 1.895231 CTGCTGTGCACAGGCTGAA 60.895 57.895 39.92 19.54 43.94 3.02
3730 4447 2.281276 CTGCTGTGCACAGGCTGA 60.281 61.111 39.92 20.12 43.94 4.26
3731 4448 2.281276 TCTGCTGTGCACAGGCTG 60.281 61.111 39.92 32.32 43.94 4.85
3732 4449 2.032223 CTCTGCTGTGCACAGGCT 59.968 61.111 39.92 0.00 43.94 4.58
3733 4450 3.735029 GCTCTGCTGTGCACAGGC 61.735 66.667 39.92 31.58 43.94 4.85
3734 4451 3.054503 GGCTCTGCTGTGCACAGG 61.055 66.667 39.92 27.56 43.94 4.00
3735 4452 1.449726 TTTGGCTCTGCTGTGCACAG 61.450 55.000 37.09 37.09 46.40 3.66
3736 4453 0.824595 ATTTGGCTCTGCTGTGCACA 60.825 50.000 20.37 20.37 33.79 4.57
3737 4454 1.167851 TATTTGGCTCTGCTGTGCAC 58.832 50.000 10.75 10.75 33.79 4.57
3738 4455 2.133281 ATATTTGGCTCTGCTGTGCA 57.867 45.000 17.64 3.51 36.92 4.57
3739 4456 3.515330 AAATATTTGGCTCTGCTGTGC 57.485 42.857 8.93 8.93 0.00 4.57
3758 4475 3.064271 GCTCACACGACCAACAGTAAAAA 59.936 43.478 0.00 0.00 0.00 1.94
3792 4509 3.756117 ACAGAAACTTTGCCTCCTTAGG 58.244 45.455 0.00 0.00 46.76 2.69
3795 4512 4.985538 TGATACAGAAACTTTGCCTCCTT 58.014 39.130 0.00 0.00 0.00 3.36
3796 4513 4.640771 TGATACAGAAACTTTGCCTCCT 57.359 40.909 0.00 0.00 0.00 3.69
3905 4639 0.594796 GTTGTTGCGCTTCCACCTTG 60.595 55.000 9.73 0.00 0.00 3.61
3936 4671 1.152922 ACGGACCGATCCTCCTCTC 60.153 63.158 23.38 0.00 43.73 3.20
4008 4743 0.038166 ACCCCTTCCGTACGTAGACA 59.962 55.000 15.21 0.00 0.00 3.41
4014 4749 3.064324 ACCGACCCCTTCCGTACG 61.064 66.667 8.69 8.69 0.00 3.67
4038 4773 1.425066 TCCTTGTCCAATTGGTCAGCT 59.575 47.619 23.76 0.00 34.88 4.24
4136 4871 0.890683 AGCTCAAATTCAAAGCCCCG 59.109 50.000 3.75 0.00 36.69 5.73
4138 4873 3.391506 ACAAGCTCAAATTCAAAGCCC 57.608 42.857 0.00 0.00 36.69 5.19
4178 4913 0.321653 AGATGACCAACGGCAACTCC 60.322 55.000 0.00 0.00 0.00 3.85
4227 4962 5.278604 ACGGTTTTCAAGCTTGATGTAAAC 58.721 37.500 30.17 30.17 35.91 2.01
4306 5041 2.798283 CAAATGGTTGCTCAAGCTGTTG 59.202 45.455 12.24 11.48 42.66 3.33
4412 5149 8.442384 TCTTTCAGAAGCAAACAAATTTTTGTC 58.558 29.630 8.98 0.00 40.23 3.18
4414 5151 9.609950 TTTCTTTCAGAAGCAAACAAATTTTTG 57.390 25.926 1.56 1.56 38.56 2.44
4427 5164 5.473931 GGATTTCCCTTTTCTTTCAGAAGC 58.526 41.667 0.00 0.00 35.37 3.86
4453 5190 1.360551 CCCTACGCTGGATCGAGTG 59.639 63.158 15.80 15.80 0.00 3.51
4454 5191 0.683504 AACCCTACGCTGGATCGAGT 60.684 55.000 6.60 0.00 0.00 4.18
4455 5192 0.460311 AAACCCTACGCTGGATCGAG 59.540 55.000 0.00 0.00 0.00 4.04
4458 5195 2.973694 TACAAACCCTACGCTGGATC 57.026 50.000 0.00 0.00 0.00 3.36
4480 5223 4.060038 TGTTGTCTCACAAACTCCTCTC 57.940 45.455 0.00 0.00 40.15 3.20
4484 5227 7.591426 GTGAATAAATGTTGTCTCACAAACTCC 59.409 37.037 0.00 0.00 40.15 3.85
4486 5229 8.225603 AGTGAATAAATGTTGTCTCACAAACT 57.774 30.769 0.00 0.00 40.15 2.66
4510 5253 3.270027 TGCTATGGAAACGTGAATGGAG 58.730 45.455 0.00 0.00 0.00 3.86
4526 5326 4.283363 CATGAAGGTCAGGCTATGCTAT 57.717 45.455 0.00 0.00 0.00 2.97
4546 5346 1.153369 GGCGAGCAGTAATCCAGCA 60.153 57.895 0.00 0.00 0.00 4.41
4548 5348 1.592669 CCGGCGAGCAGTAATCCAG 60.593 63.158 9.30 0.00 0.00 3.86
4549 5349 2.499205 CCGGCGAGCAGTAATCCA 59.501 61.111 9.30 0.00 0.00 3.41
4550 5350 2.967615 GCCGGCGAGCAGTAATCC 60.968 66.667 12.58 0.00 0.00 3.01
4551 5351 3.330853 CGCCGGCGAGCAGTAATC 61.331 66.667 44.86 0.00 42.83 1.75
4552 5352 3.833645 TCGCCGGCGAGCAGTAAT 61.834 61.111 45.37 0.00 44.01 1.89
4602 5413 2.811317 GAGGCGTGGAAGCGAGTG 60.811 66.667 0.00 0.00 38.18 3.51
4603 5414 4.070552 GGAGGCGTGGAAGCGAGT 62.071 66.667 0.00 0.00 38.18 4.18
4604 5415 3.376935 ATGGAGGCGTGGAAGCGAG 62.377 63.158 0.00 0.00 38.18 5.03
4605 5416 3.371097 GATGGAGGCGTGGAAGCGA 62.371 63.158 0.00 0.00 38.18 4.93
4607 5418 2.109126 GTGATGGAGGCGTGGAAGC 61.109 63.158 0.00 0.00 0.00 3.86
4609 5420 2.668632 GGTGATGGAGGCGTGGAA 59.331 61.111 0.00 0.00 0.00 3.53
4611 5422 3.687321 CTGGGTGATGGAGGCGTGG 62.687 68.421 0.00 0.00 0.00 4.94
4616 5427 0.251354 CACTGTCTGGGTGATGGAGG 59.749 60.000 0.00 0.00 36.89 4.30
4621 5432 1.002868 GCAGCACTGTCTGGGTGAT 60.003 57.895 0.00 0.00 36.89 3.06
4622 5433 2.427320 GCAGCACTGTCTGGGTGA 59.573 61.111 0.00 0.00 36.89 4.02
4623 5434 2.670934 GGCAGCACTGTCTGGGTG 60.671 66.667 0.00 0.00 37.70 4.61
4625 5436 2.670934 GTGGCAGCACTGTCTGGG 60.671 66.667 3.62 0.00 35.92 4.45
4627 5438 2.025969 CGAGTGGCAGCACTGTCTG 61.026 63.158 3.62 3.77 35.92 3.51
4628 5439 2.341543 CGAGTGGCAGCACTGTCT 59.658 61.111 3.62 0.00 35.92 3.41
4630 5441 4.996434 GGCGAGTGGCAGCACTGT 62.996 66.667 0.00 0.00 46.16 3.55
4633 5444 4.385405 AGAGGCGAGTGGCAGCAC 62.385 66.667 0.00 0.00 46.16 4.40
4634 5445 4.383861 CAGAGGCGAGTGGCAGCA 62.384 66.667 0.00 0.00 46.16 4.41
4635 5446 2.507110 TTACAGAGGCGAGTGGCAGC 62.507 60.000 0.00 0.00 46.16 5.25
4636 5447 0.737715 GTTACAGAGGCGAGTGGCAG 60.738 60.000 0.00 0.00 46.16 4.85
4637 5448 1.292223 GTTACAGAGGCGAGTGGCA 59.708 57.895 0.00 0.00 46.16 4.92
4638 5449 1.448013 GGTTACAGAGGCGAGTGGC 60.448 63.158 0.00 0.00 42.51 5.01
4639 5450 1.218316 GGGTTACAGAGGCGAGTGG 59.782 63.158 0.00 0.00 0.00 4.00
4640 5451 0.389948 GTGGGTTACAGAGGCGAGTG 60.390 60.000 0.00 0.00 0.00 3.51
4641 5452 0.830444 TGTGGGTTACAGAGGCGAGT 60.830 55.000 0.00 0.00 33.42 4.18
4642 5453 0.389948 GTGTGGGTTACAGAGGCGAG 60.390 60.000 0.00 0.00 40.69 5.03
4644 5455 1.375523 GGTGTGGGTTACAGAGGCG 60.376 63.158 0.00 0.00 40.69 5.52
4645 5456 1.375523 CGGTGTGGGTTACAGAGGC 60.376 63.158 0.00 0.00 40.69 4.70
4646 5457 1.375523 GCGGTGTGGGTTACAGAGG 60.376 63.158 0.00 0.00 40.69 3.69
4647 5458 1.736645 CGCGGTGTGGGTTACAGAG 60.737 63.158 0.00 0.00 40.69 3.35
4648 5459 2.340809 CGCGGTGTGGGTTACAGA 59.659 61.111 0.00 0.00 40.69 3.41
4649 5460 3.419759 GCGCGGTGTGGGTTACAG 61.420 66.667 8.83 0.00 40.69 2.74
4674 5485 3.702048 GTGTGGGTAGCGGAGGCA 61.702 66.667 0.00 0.00 43.41 4.75
4680 5491 0.107703 ATCATGTGGTGTGGGTAGCG 60.108 55.000 0.00 0.00 0.00 4.26
4681 5492 1.745087 CAATCATGTGGTGTGGGTAGC 59.255 52.381 0.00 0.00 0.00 3.58
4683 5494 2.026356 CCTCAATCATGTGGTGTGGGTA 60.026 50.000 0.00 0.00 35.83 3.69
4691 5502 7.067859 ACATTTCTCAATACCTCAATCATGTGG 59.932 37.037 0.00 0.00 44.17 4.17
4699 5510 6.414732 CACCCTACATTTCTCAATACCTCAA 58.585 40.000 0.00 0.00 0.00 3.02
4731 5816 2.516906 TCCTGCATGCTCAATGACAAA 58.483 42.857 20.33 0.00 38.72 2.83
4750 5835 6.447162 GCCAATACCTAACTGCCAATAATTC 58.553 40.000 0.00 0.00 0.00 2.17
4764 5849 2.673258 TCTGACCATCGCCAATACCTA 58.327 47.619 0.00 0.00 0.00 3.08
4805 5890 3.431415 ACCCACCTCCAAAAATTAGCTC 58.569 45.455 0.00 0.00 0.00 4.09
4806 5891 3.542969 ACCCACCTCCAAAAATTAGCT 57.457 42.857 0.00 0.00 0.00 3.32
4807 5892 4.617253 AAACCCACCTCCAAAAATTAGC 57.383 40.909 0.00 0.00 0.00 3.09
4808 5893 6.587273 TCAAAAACCCACCTCCAAAAATTAG 58.413 36.000 0.00 0.00 0.00 1.73
4809 5894 6.384305 TCTCAAAAACCCACCTCCAAAAATTA 59.616 34.615 0.00 0.00 0.00 1.40
4810 5895 5.190726 TCTCAAAAACCCACCTCCAAAAATT 59.809 36.000 0.00 0.00 0.00 1.82
4811 5896 4.719273 TCTCAAAAACCCACCTCCAAAAAT 59.281 37.500 0.00 0.00 0.00 1.82
4812 5897 4.097418 TCTCAAAAACCCACCTCCAAAAA 58.903 39.130 0.00 0.00 0.00 1.94
4813 5898 3.704061 CTCTCAAAAACCCACCTCCAAAA 59.296 43.478 0.00 0.00 0.00 2.44
4814 5899 3.295973 CTCTCAAAAACCCACCTCCAAA 58.704 45.455 0.00 0.00 0.00 3.28
4815 5900 2.243736 ACTCTCAAAAACCCACCTCCAA 59.756 45.455 0.00 0.00 0.00 3.53
4816 5901 1.850345 ACTCTCAAAAACCCACCTCCA 59.150 47.619 0.00 0.00 0.00 3.86
4817 5902 2.658807 ACTCTCAAAAACCCACCTCC 57.341 50.000 0.00 0.00 0.00 4.30
4818 5903 2.548480 CGAACTCTCAAAAACCCACCTC 59.452 50.000 0.00 0.00 0.00 3.85
4819 5904 2.572290 CGAACTCTCAAAAACCCACCT 58.428 47.619 0.00 0.00 0.00 4.00
4820 5905 1.607148 CCGAACTCTCAAAAACCCACC 59.393 52.381 0.00 0.00 0.00 4.61
4821 5906 2.567985 TCCGAACTCTCAAAAACCCAC 58.432 47.619 0.00 0.00 0.00 4.61
4822 5907 2.946990 GTTCCGAACTCTCAAAAACCCA 59.053 45.455 3.88 0.00 0.00 4.51
4823 5908 2.292569 GGTTCCGAACTCTCAAAAACCC 59.707 50.000 11.03 0.00 0.00 4.11
4824 5909 2.032290 CGGTTCCGAACTCTCAAAAACC 60.032 50.000 11.03 0.00 0.00 3.27
4825 5910 2.867975 TCGGTTCCGAACTCTCAAAAAC 59.132 45.455 11.66 0.00 35.41 2.43
4826 5911 3.182341 TCGGTTCCGAACTCTCAAAAA 57.818 42.857 11.66 0.00 35.41 1.94
4827 5912 2.894763 TCGGTTCCGAACTCTCAAAA 57.105 45.000 11.66 0.00 35.41 2.44
4828 5913 2.894763 TTCGGTTCCGAACTCTCAAA 57.105 45.000 20.52 0.00 42.44 2.69
4829 5914 2.894763 TTTCGGTTCCGAACTCTCAA 57.105 45.000 23.44 7.77 46.12 3.02
4830 5915 3.396260 AATTTCGGTTCCGAACTCTCA 57.604 42.857 23.44 11.17 46.12 3.27
4831 5916 4.240096 TGTAATTTCGGTTCCGAACTCTC 58.760 43.478 23.44 15.28 46.12 3.20
4832 5917 4.261578 TGTAATTTCGGTTCCGAACTCT 57.738 40.909 23.44 14.09 46.12 3.24
4842 5927 8.786826 TCAAAGTTGATCTATGTAATTTCGGT 57.213 30.769 0.00 0.00 31.01 4.69
4851 5936 7.400599 AATGTGCATCAAAGTTGATCTATGT 57.599 32.000 3.51 0.00 45.62 2.29
4900 6657 1.293924 CACGCCTCCAAATGCTCTAG 58.706 55.000 0.00 0.00 0.00 2.43
4955 6712 5.288472 GCTTTTACCACATTATTTGCTTCCG 59.712 40.000 0.00 0.00 0.00 4.30
4964 6721 7.466746 AACATGTCAGCTTTTACCACATTAT 57.533 32.000 0.00 0.00 0.00 1.28
4965 6722 6.892658 AACATGTCAGCTTTTACCACATTA 57.107 33.333 0.00 0.00 0.00 1.90
4966 6723 5.789643 AACATGTCAGCTTTTACCACATT 57.210 34.783 0.00 0.00 0.00 2.71
4967 6724 5.789643 AAACATGTCAGCTTTTACCACAT 57.210 34.783 0.00 0.00 0.00 3.21
4968 6725 6.294453 CCATAAACATGTCAGCTTTTACCACA 60.294 38.462 0.00 0.00 0.00 4.17
4969 6726 6.092748 CCATAAACATGTCAGCTTTTACCAC 58.907 40.000 0.00 0.00 0.00 4.16
4970 6727 5.336372 GCCATAAACATGTCAGCTTTTACCA 60.336 40.000 0.00 0.00 0.00 3.25
4976 6733 3.091633 AGGCCATAAACATGTCAGCTT 57.908 42.857 5.01 0.00 0.00 3.74
5024 6781 7.481275 TCATTCAGAAATTTCAACCAAAAGC 57.519 32.000 19.99 0.00 0.00 3.51
5043 6800 9.530633 ACGAACTACTCAACCTTATAATCATTC 57.469 33.333 0.00 0.00 0.00 2.67
5049 6806 7.218228 TGACACGAACTACTCAACCTTATAA 57.782 36.000 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.