Multiple sequence alignment - TraesCS7A01G162000

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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 TraesCS7A01G162000 chr7A 100.000 4877 0 0 1 4877 118330837 118325961 0.000000e+00 9007.0
1 TraesCS7A01G162000 chr7A 97.279 147 4 0 4731 4877 118319957 118319811 2.910000e-62 250.0
2 TraesCS7A01G162000 chr7A 94.667 150 7 1 4728 4877 141014598 141014746 1.060000e-56 231.0
3 TraesCS7A01G162000 chr7A 94.667 150 7 1 4728 4877 141621900 141622048 1.060000e-56 231.0
4 TraesCS7A01G162000 chr7A 94.000 150 8 1 4728 4877 140743473 140743621 4.910000e-55 226.0
5 TraesCS7A01G162000 chr7A 93.333 150 9 1 4728 4877 141291942 141292090 2.290000e-53 220.0
6 TraesCS7A01G162000 chr7A 93.333 150 9 1 4728 4877 141882657 141882805 2.290000e-53 220.0
7 TraesCS7A01G162000 chr7D 93.688 2741 118 17 387 3086 113224311 113221585 0.000000e+00 4052.0
8 TraesCS7A01G162000 chr7D 94.844 1377 48 12 3079 4443 113221547 113220182 0.000000e+00 2128.0
9 TraesCS7A01G162000 chr7D 83.175 422 32 14 30 424 113224719 113224310 2.790000e-92 350.0
10 TraesCS7A01G162000 chr7D 96.089 179 4 3 4502 4679 113220162 113219986 6.180000e-74 289.0
11 TraesCS7A01G162000 chr7D 100.000 45 0 0 4680 4724 113219511 113219467 3.130000e-12 84.2
12 TraesCS7A01G162000 chr7B 93.963 2054 94 13 396 2445 72615523 72613496 0.000000e+00 3079.0
13 TraesCS7A01G162000 chr7B 89.532 1433 57 25 3082 4492 72612811 72611450 0.000000e+00 1729.0
14 TraesCS7A01G162000 chr7B 90.018 561 33 9 2539 3086 72613403 72612853 0.000000e+00 704.0
15 TraesCS7A01G162000 chr7B 89.735 302 16 3 137 424 72615829 72615529 5.960000e-99 372.0
16 TraesCS7A01G162000 chr7B 95.588 68 3 0 2475 2542 72613494 72613427 5.160000e-20 110.0
17 TraesCS7A01G162000 chr3A 95.918 147 6 0 4731 4877 64745619 64745473 6.310000e-59 239.0
18 TraesCS7A01G162000 chr6A 94.000 150 8 1 4728 4877 579159785 579159933 4.910000e-55 226.0
19 TraesCS7A01G162000 chr1B 94.558 147 7 1 4731 4877 487410838 487410693 4.910000e-55 226.0


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 TraesCS7A01G162000 chr7A 118325961 118330837 4876 True 9007.00 9007 100.0000 1 4877 1 chr7A.!!$R2 4876
1 TraesCS7A01G162000 chr7D 113219467 113224719 5252 True 1380.64 4052 93.5592 30 4724 5 chr7D.!!$R1 4694
2 TraesCS7A01G162000 chr7B 72611450 72615829 4379 True 1198.80 3079 91.7672 137 4492 5 chr7B.!!$R1 4355

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
49 50 0.104671 GCTTCTGCTAGAGCTGGAGG 59.895 60.0 16.03 9.69 43.39 4.30 F
336 363 0.109132 CAAGAAAGGGCACGCCATTC 60.109 55.0 8.62 12.25 39.36 2.67 F
1582 1660 0.244450 TACCACGGGCTTTACTGACG 59.756 55.0 0.00 0.00 0.00 4.35 F
2405 2483 0.108585 ATGGCTTGATACCGGCGATT 59.891 50.0 9.30 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 1398 2.225467 GATAATCCAGCAAGGGACAGC 58.775 52.381 0.00 0.0 40.44 4.40 R
2275 2353 1.202830 ACGGTAGAAACACCATTGCCA 60.203 47.619 0.00 0.0 38.61 4.92 R
2695 2804 0.171231 GGGCAAAATCACGAGCTTCC 59.829 55.000 0.00 0.0 0.00 3.46 R
4159 4344 0.179108 CGAGATCTCCCACGTTTCCC 60.179 60.000 17.13 0.0 0.00 3.97 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
17 18 4.010224 TGCTCCTTTGCGGGCGTA 62.010 61.111 0.00 0.00 33.27 4.42
18 19 2.513897 GCTCCTTTGCGGGCGTAT 60.514 61.111 0.00 0.00 0.00 3.06
19 20 2.823829 GCTCCTTTGCGGGCGTATG 61.824 63.158 0.00 0.00 0.00 2.39
20 21 1.153449 CTCCTTTGCGGGCGTATGA 60.153 57.895 0.00 0.00 0.00 2.15
21 22 0.532862 CTCCTTTGCGGGCGTATGAT 60.533 55.000 0.00 0.00 0.00 2.45
22 23 0.107410 TCCTTTGCGGGCGTATGATT 60.107 50.000 0.00 0.00 0.00 2.57
23 24 0.307760 CCTTTGCGGGCGTATGATTC 59.692 55.000 0.00 0.00 0.00 2.52
24 25 1.299541 CTTTGCGGGCGTATGATTCT 58.700 50.000 0.00 0.00 0.00 2.40
25 26 1.261619 CTTTGCGGGCGTATGATTCTC 59.738 52.381 0.00 0.00 0.00 2.87
26 27 0.531974 TTGCGGGCGTATGATTCTCC 60.532 55.000 0.00 0.00 0.00 3.71
27 28 1.668151 GCGGGCGTATGATTCTCCC 60.668 63.158 0.00 0.00 0.00 4.30
28 29 4.675404 GGGCGTATGATTCTCCCG 57.325 61.111 0.00 0.00 0.00 5.14
49 50 0.104671 GCTTCTGCTAGAGCTGGAGG 59.895 60.000 16.03 9.69 43.39 4.30
50 51 0.104671 CTTCTGCTAGAGCTGGAGGC 59.895 60.000 8.47 0.00 40.61 4.70
61 62 1.160329 GCTGGAGGCGCGTATGATTT 61.160 55.000 8.43 0.00 0.00 2.17
65 72 0.317020 GAGGCGCGTATGATTTTGGC 60.317 55.000 8.43 0.00 0.00 4.52
66 73 1.299089 GGCGCGTATGATTTTGGCC 60.299 57.895 8.43 0.00 0.00 5.36
73 80 1.671845 GTATGATTTTGGCCGGCGTAA 59.328 47.619 22.54 15.73 0.00 3.18
75 82 0.889638 TGATTTTGGCCGGCGTAACA 60.890 50.000 22.54 10.07 0.00 2.41
82 89 1.447314 GCCGGCGTAACACTAAGCT 60.447 57.895 12.58 0.00 33.51 3.74
85 92 2.817901 CCGGCGTAACACTAAGCTTAT 58.182 47.619 6.64 0.00 33.51 1.73
86 93 3.192466 CCGGCGTAACACTAAGCTTATT 58.808 45.455 6.64 0.00 33.51 1.40
98 105 9.639601 AACACTAAGCTTATTTTCCTTATTTGC 57.360 29.630 6.64 0.00 0.00 3.68
104 119 6.322456 AGCTTATTTTCCTTATTTGCTCCCTC 59.678 38.462 0.00 0.00 0.00 4.30
114 129 2.479566 TTGCTCCCTCTTTACTGCTG 57.520 50.000 0.00 0.00 0.00 4.41
124 139 3.125316 TCTTTACTGCTGCGTTACGTTT 58.875 40.909 6.63 0.00 0.00 3.60
129 144 2.498887 CTGCGTTACGTTTGCCGC 60.499 61.111 6.63 12.04 45.92 6.53
158 173 4.515432 GAATTTACTGATTTAGCGGCGAC 58.485 43.478 12.98 1.23 0.00 5.19
221 247 5.553952 CGAAGCGTTAGATATTTCAACGTCC 60.554 44.000 14.74 4.32 45.08 4.79
255 282 3.260475 TGGCGTATAGAAACTGCATGT 57.740 42.857 0.00 0.00 0.00 3.21
296 323 1.880819 CGGGCGGTTGTGGTAGTAGT 61.881 60.000 0.00 0.00 0.00 2.73
336 363 0.109132 CAAGAAAGGGCACGCCATTC 60.109 55.000 8.62 12.25 39.36 2.67
390 430 5.688814 AAGATACTTACCGGCTTTTAGGT 57.311 39.130 0.00 0.00 44.08 3.08
393 433 3.329929 ACTTACCGGCTTTTAGGTCTG 57.670 47.619 0.00 0.00 41.63 3.51
451 527 4.641541 TGATAATTGTGTTGCCATCTCTGG 59.358 41.667 0.00 0.00 46.17 3.86
529 607 6.148811 CCGACTAGTTTGGCAATTCTAAGAAA 59.851 38.462 0.00 0.00 0.00 2.52
554 632 8.733857 AAACTTTTCTAGCTGAATTGATTTCG 57.266 30.769 0.00 0.00 37.13 3.46
689 767 6.652900 TGGATTAGTTTTTATTTGCCTTTGCC 59.347 34.615 0.00 0.00 36.33 4.52
695 773 5.411083 TTTTATTTGCCTTTGCCGTTTTC 57.589 34.783 0.00 0.00 36.33 2.29
718 796 8.809159 TTCGATAAGCATGAAATTGTTTTTCA 57.191 26.923 0.00 3.50 41.91 2.69
766 844 8.584157 TGGTAGCCTGGCATAAATTTATTATTG 58.416 33.333 22.65 0.39 0.00 1.90
787 865 9.547753 TTATTGATAGCTACCTCACAGAAAATC 57.452 33.333 0.00 0.00 0.00 2.17
803 881 8.680903 CACAGAAAATCATGGAAGTAGCTAAAT 58.319 33.333 0.00 0.00 0.00 1.40
832 910 9.751542 TTCTACAGATTAGCAAATACTAGCTTC 57.248 33.333 0.00 0.00 42.05 3.86
833 911 9.137459 TCTACAGATTAGCAAATACTAGCTTCT 57.863 33.333 0.00 0.00 42.05 2.85
834 912 9.757227 CTACAGATTAGCAAATACTAGCTTCTT 57.243 33.333 0.00 0.00 42.05 2.52
835 913 8.430801 ACAGATTAGCAAATACTAGCTTCTTG 57.569 34.615 0.00 0.00 42.05 3.02
836 914 7.011857 ACAGATTAGCAAATACTAGCTTCTTGC 59.988 37.037 0.00 10.03 42.05 4.01
850 928 4.177026 GCTTCTTGCTAACGAAGAGATGA 58.823 43.478 3.43 0.00 39.10 2.92
899 977 7.704899 AGGAAATATACTTTTTGTAAATGCGCC 59.295 33.333 4.18 0.00 34.45 6.53
920 998 5.233225 GCCGAACCATACTAATACTAACCC 58.767 45.833 0.00 0.00 0.00 4.11
922 1000 6.463472 GCCGAACCATACTAATACTAACCCTT 60.463 42.308 0.00 0.00 0.00 3.95
923 1001 6.927381 CCGAACCATACTAATACTAACCCTTG 59.073 42.308 0.00 0.00 0.00 3.61
924 1002 7.201938 CCGAACCATACTAATACTAACCCTTGA 60.202 40.741 0.00 0.00 0.00 3.02
925 1003 8.365647 CGAACCATACTAATACTAACCCTTGAT 58.634 37.037 0.00 0.00 0.00 2.57
958 1036 5.047306 CCTTTTCAGGGTTTGGGTAAATCTC 60.047 44.000 0.00 0.00 36.36 2.75
973 1051 7.508977 TGGGTAAATCTCATTGGAAGAGTTTTT 59.491 33.333 0.00 0.00 36.75 1.94
1063 1141 7.675062 TGCAAGGTCAATGTTACCAAATAAAT 58.325 30.769 0.00 0.00 39.64 1.40
1320 1398 5.931441 AAATCGAACAAGAACCTGAAGAG 57.069 39.130 0.00 0.00 0.00 2.85
1494 1572 4.526650 ACCTTTTCAACTGTTGGTTCAAGT 59.473 37.500 19.55 8.51 35.74 3.16
1521 1599 2.752903 GGAGCAAAATTACGTGGGTGAT 59.247 45.455 0.00 0.00 0.00 3.06
1582 1660 0.244450 TACCACGGGCTTTACTGACG 59.756 55.000 0.00 0.00 0.00 4.35
1620 1698 0.750546 TTGCAGCATCAGATGGCCTC 60.751 55.000 12.54 0.00 0.00 4.70
1775 1853 9.442047 CTCTTCCTATCTGTAATTTTCACACTT 57.558 33.333 0.00 0.00 0.00 3.16
1803 1881 2.423892 TCTAGACGTCCAATCAGAGCAC 59.576 50.000 13.01 0.00 0.00 4.40
2122 2200 4.184079 GCCAACAGCAGAAGATCAAAAT 57.816 40.909 0.00 0.00 42.97 1.82
2250 2328 0.674581 TCGCAGAATTCTGGCCACAG 60.675 55.000 31.41 13.97 46.30 3.66
2266 2344 2.204237 CACAGCAAGTTCAAAAAGGGC 58.796 47.619 0.00 0.00 0.00 5.19
2267 2345 2.110578 ACAGCAAGTTCAAAAAGGGCT 58.889 42.857 0.00 0.00 0.00 5.19
2275 2353 6.573094 GCAAGTTCAAAAAGGGCTCTGATTAT 60.573 38.462 0.00 0.00 0.00 1.28
2398 2476 1.678101 GCAACTCCATGGCTTGATACC 59.322 52.381 20.56 4.62 0.00 2.73
2405 2483 0.108585 ATGGCTTGATACCGGCGATT 59.891 50.000 9.30 0.00 0.00 3.34
2430 2508 8.637196 TCAGTCGGTAATACTCATCTGAATAT 57.363 34.615 0.00 0.00 0.00 1.28
2610 2719 5.536161 AGCATATTGGTGTATTTCCATGTCC 59.464 40.000 0.00 0.00 34.75 4.02
2611 2720 5.536161 GCATATTGGTGTATTTCCATGTCCT 59.464 40.000 0.00 0.00 34.75 3.85
2612 2721 6.294176 GCATATTGGTGTATTTCCATGTCCTC 60.294 42.308 0.00 0.00 34.75 3.71
2613 2722 4.649267 TTGGTGTATTTCCATGTCCTCA 57.351 40.909 0.00 0.00 34.75 3.86
2695 2804 5.207110 ACATGTATTCAGAATCGAGGGAG 57.793 43.478 0.00 0.00 0.00 4.30
2769 2878 5.675575 GCAGCTTAATTGTTGTCTCCAGATG 60.676 44.000 0.00 0.00 0.00 2.90
2821 2930 9.554724 CTAAACCAATGTACATGTTACATGTTC 57.445 33.333 31.75 26.73 38.10 3.18
2822 2931 7.517614 AACCAATGTACATGTTACATGTTCA 57.482 32.000 31.75 30.66 38.10 3.18
2831 2940 6.279123 ACATGTTACATGTTCACATTTGCAA 58.721 32.000 23.48 0.00 33.61 4.08
2834 2943 7.783090 TGTTACATGTTCACATTTGCAATTT 57.217 28.000 2.30 0.00 33.61 1.82
2909 3019 7.947890 TCATAGTAGGAATTTGTTGAGGGTTTT 59.052 33.333 0.00 0.00 0.00 2.43
2915 3025 5.279960 GGAATTTGTTGAGGGTTTTGCCTAT 60.280 40.000 0.00 0.00 37.43 2.57
2917 3027 2.524306 TGTTGAGGGTTTTGCCTATGG 58.476 47.619 0.00 0.00 37.43 2.74
2997 3108 5.116180 TGTTGCCTACTTGCTGTATGTATC 58.884 41.667 0.00 0.00 0.00 2.24
2999 3110 3.383505 TGCCTACTTGCTGTATGTATCGT 59.616 43.478 0.00 0.00 0.00 3.73
3036 3157 2.068519 TCATGTGCTTAACTGCAGTCG 58.931 47.619 21.95 12.77 44.20 4.18
3069 3192 9.927081 ATCATAATGTCTCCCATTTTAACTTCT 57.073 29.630 0.00 0.00 41.01 2.85
3257 3427 1.068121 AATCTGGCCCCATAGCTACC 58.932 55.000 0.00 0.00 0.00 3.18
3307 3477 1.438651 TCATTTGCTACGTCCTGCAC 58.561 50.000 9.76 0.00 39.05 4.57
3314 3484 2.009774 GCTACGTCCTGCACATTTGAT 58.990 47.619 0.00 0.00 0.00 2.57
3505 3675 2.163509 GAGGTTGCTTTCTCCCCTTTC 58.836 52.381 0.00 0.00 0.00 2.62
3513 3683 3.625969 GCTTTCTCCCCTTTCCAAGCTAT 60.626 47.826 0.00 0.00 34.94 2.97
3514 3684 3.652057 TTCTCCCCTTTCCAAGCTATG 57.348 47.619 0.00 0.00 0.00 2.23
3518 3688 5.473273 TCTCCCCTTTCCAAGCTATGTATA 58.527 41.667 0.00 0.00 0.00 1.47
3537 3713 2.936919 ACTGCTTCTGTGGAATGTCA 57.063 45.000 0.00 0.00 0.00 3.58
3564 3740 6.955963 CGACATATTTACAAGCACTTCTGTTC 59.044 38.462 0.00 0.00 0.00 3.18
3571 3747 3.327757 ACAAGCACTTCTGTTCCATCCTA 59.672 43.478 0.00 0.00 0.00 2.94
3575 3751 5.385198 AGCACTTCTGTTCCATCCTAAAAA 58.615 37.500 0.00 0.00 0.00 1.94
3581 3758 8.923270 ACTTCTGTTCCATCCTAAAAATTTTGA 58.077 29.630 3.73 0.00 0.00 2.69
3688 3865 2.437085 TATCCTCAAGGTCGAGCTCA 57.563 50.000 18.90 6.82 36.34 4.26
3880 4057 1.257936 GCATCGCCGTGTACTAACATG 59.742 52.381 0.00 0.00 41.51 3.21
3892 4069 6.913132 CGTGTACTAACATGATCTCTTAGGTG 59.087 42.308 0.00 0.00 44.09 4.00
4091 4269 4.280819 TCAATTCACATTCCATTCCCCTC 58.719 43.478 0.00 0.00 0.00 4.30
4107 4285 1.154205 CCTCCTGCCGTGCTTATTCG 61.154 60.000 0.00 0.00 0.00 3.34
4119 4297 4.084537 CGTGCTTATTCGTGATATGGTTCC 60.085 45.833 0.00 0.00 0.00 3.62
4159 4344 3.353114 CTGCGGCGAATGTCACACG 62.353 63.158 12.98 0.00 0.00 4.49
4160 4345 4.147322 GCGGCGAATGTCACACGG 62.147 66.667 12.98 0.00 0.00 4.94
4165 4350 0.110373 GCGAATGTCACACGGGAAAC 60.110 55.000 0.00 0.00 0.00 2.78
4182 4371 0.974383 AACGTGGGAGATCTCGGTTT 59.026 50.000 16.46 2.72 0.00 3.27
4280 4473 7.566709 CATGCTTTCACCTGTTTGTTTTATTC 58.433 34.615 0.00 0.00 0.00 1.75
4310 4503 2.576615 AGTTGCCAGGAAGTTCTGTTC 58.423 47.619 2.25 0.00 33.14 3.18
4318 4511 4.932200 CCAGGAAGTTCTGTTCTGTACATC 59.068 45.833 2.25 0.00 35.85 3.06
4407 4600 7.745717 TGAGAGAAGAAAAATCCCTTTCACTA 58.254 34.615 0.00 0.00 37.70 2.74
4408 4601 8.217799 TGAGAGAAGAAAAATCCCTTTCACTAA 58.782 33.333 0.00 0.00 37.70 2.24
4409 4602 8.996651 AGAGAAGAAAAATCCCTTTCACTAAA 57.003 30.769 0.00 0.00 37.70 1.85
4485 4678 6.159988 GCTTAGCTTTCTCACGGATATACAT 58.840 40.000 0.00 0.00 0.00 2.29
4486 4679 6.090088 GCTTAGCTTTCTCACGGATATACATG 59.910 42.308 0.00 0.00 0.00 3.21
4487 4680 4.887748 AGCTTTCTCACGGATATACATGG 58.112 43.478 0.00 0.00 0.00 3.66
4489 4682 5.070446 AGCTTTCTCACGGATATACATGGAA 59.930 40.000 0.00 0.00 0.00 3.53
4490 4683 5.758296 GCTTTCTCACGGATATACATGGAAA 59.242 40.000 0.00 0.03 0.00 3.13
4491 4684 6.428159 GCTTTCTCACGGATATACATGGAAAT 59.572 38.462 0.00 0.00 0.00 2.17
4492 4685 7.571983 GCTTTCTCACGGATATACATGGAAATG 60.572 40.741 0.00 0.00 0.00 2.32
4493 4686 6.419484 TCTCACGGATATACATGGAAATGT 57.581 37.500 0.00 0.00 38.49 2.71
4494 4687 7.533289 TCTCACGGATATACATGGAAATGTA 57.467 36.000 0.00 1.33 40.79 2.29
4495 4688 8.134202 TCTCACGGATATACATGGAAATGTAT 57.866 34.615 14.05 14.05 46.20 2.29
4496 4689 8.034804 TCTCACGGATATACATGGAAATGTATG 58.965 37.037 17.54 6.89 44.70 2.39
4497 4690 7.902087 TCACGGATATACATGGAAATGTATGA 58.098 34.615 17.54 7.30 44.70 2.15
4498 4691 8.539544 TCACGGATATACATGGAAATGTATGAT 58.460 33.333 17.54 9.55 44.70 2.45
4499 4692 8.820933 CACGGATATACATGGAAATGTATGATC 58.179 37.037 17.54 14.98 44.70 2.92
4500 4693 7.987458 ACGGATATACATGGAAATGTATGATCC 59.013 37.037 17.54 19.49 44.70 3.36
4534 4727 7.225784 ACTGACATCATCTTGTATAGGCTAG 57.774 40.000 0.00 0.00 0.00 3.42
4671 4864 6.057533 TCCATCTTGTGTATTGACATCATCC 58.942 40.000 0.00 0.00 38.04 3.51
4724 5390 0.036306 ACGGGGACAACCAGATCAAC 59.964 55.000 0.00 0.00 42.91 3.18
4725 5391 0.676782 CGGGGACAACCAGATCAACC 60.677 60.000 0.00 0.00 42.91 3.77
4726 5392 0.404040 GGGGACAACCAGATCAACCA 59.596 55.000 0.00 0.00 42.91 3.67
4727 5393 1.614317 GGGGACAACCAGATCAACCAG 60.614 57.143 0.00 0.00 42.91 4.00
4728 5394 1.351017 GGGACAACCAGATCAACCAGA 59.649 52.381 0.00 0.00 39.85 3.86
4729 5395 2.025887 GGGACAACCAGATCAACCAGAT 60.026 50.000 0.00 0.00 38.41 2.90
4730 5396 3.562176 GGGACAACCAGATCAACCAGATT 60.562 47.826 0.00 0.00 36.68 2.40
4731 5397 3.441572 GGACAACCAGATCAACCAGATTG 59.558 47.826 0.00 0.00 34.88 2.67
4732 5398 4.074970 GACAACCAGATCAACCAGATTGT 58.925 43.478 0.00 0.00 39.54 2.71
4733 5399 4.473444 ACAACCAGATCAACCAGATTGTT 58.527 39.130 0.00 0.00 39.54 2.83
4734 5400 5.630121 ACAACCAGATCAACCAGATTGTTA 58.370 37.500 0.00 0.00 39.54 2.41
4735 5401 6.068010 ACAACCAGATCAACCAGATTGTTAA 58.932 36.000 0.00 0.00 39.54 2.01
4736 5402 6.549364 ACAACCAGATCAACCAGATTGTTAAA 59.451 34.615 0.00 0.00 39.54 1.52
4737 5403 6.824305 ACCAGATCAACCAGATTGTTAAAG 57.176 37.500 0.00 0.00 39.54 1.85
4738 5404 5.183904 ACCAGATCAACCAGATTGTTAAAGC 59.816 40.000 0.00 0.00 39.54 3.51
4739 5405 5.416952 CCAGATCAACCAGATTGTTAAAGCT 59.583 40.000 0.00 0.00 39.54 3.74
4740 5406 6.404074 CCAGATCAACCAGATTGTTAAAGCTC 60.404 42.308 0.00 0.00 39.54 4.09
4741 5407 6.149973 CAGATCAACCAGATTGTTAAAGCTCA 59.850 38.462 0.00 0.00 39.54 4.26
4742 5408 6.716628 AGATCAACCAGATTGTTAAAGCTCAA 59.283 34.615 0.00 0.00 39.54 3.02
4743 5409 6.899393 TCAACCAGATTGTTAAAGCTCAAT 57.101 33.333 0.00 0.00 39.54 2.57
4744 5410 7.288810 TCAACCAGATTGTTAAAGCTCAATT 57.711 32.000 0.42 0.00 39.54 2.32
4745 5411 8.402798 TCAACCAGATTGTTAAAGCTCAATTA 57.597 30.769 0.42 0.00 39.54 1.40
4746 5412 8.855110 TCAACCAGATTGTTAAAGCTCAATTAA 58.145 29.630 0.42 0.00 39.54 1.40
4747 5413 9.474920 CAACCAGATTGTTAAAGCTCAATTAAA 57.525 29.630 0.42 0.00 34.92 1.52
4748 5414 9.476202 AACCAGATTGTTAAAGCTCAATTAAAC 57.524 29.630 0.42 0.00 34.92 2.01
4749 5415 8.860088 ACCAGATTGTTAAAGCTCAATTAAACT 58.140 29.630 0.42 0.00 34.92 2.66
4750 5416 9.696917 CCAGATTGTTAAAGCTCAATTAAACTT 57.303 29.630 0.42 0.00 34.92 2.66
4754 5420 9.816354 ATTGTTAAAGCTCAATTAAACTTGTGT 57.184 25.926 0.00 0.00 31.35 3.72
4755 5421 9.646427 TTGTTAAAGCTCAATTAAACTTGTGTT 57.354 25.926 0.00 0.00 38.16 3.32
4766 5432 9.377312 CAATTAAACTTGTGTTAATTATGGGGG 57.623 33.333 2.72 0.00 34.96 5.40
4767 5433 8.903059 ATTAAACTTGTGTTAATTATGGGGGA 57.097 30.769 0.00 0.00 34.96 4.81
4768 5434 8.722622 TTAAACTTGTGTTAATTATGGGGGAA 57.277 30.769 0.00 0.00 34.96 3.97
4769 5435 7.806680 AAACTTGTGTTAATTATGGGGGAAT 57.193 32.000 0.00 0.00 34.96 3.01
4770 5436 7.418337 AACTTGTGTTAATTATGGGGGAATC 57.582 36.000 0.00 0.00 34.15 2.52
4771 5437 6.741724 ACTTGTGTTAATTATGGGGGAATCT 58.258 36.000 0.00 0.00 0.00 2.40
4772 5438 6.833933 ACTTGTGTTAATTATGGGGGAATCTC 59.166 38.462 0.00 0.00 0.00 2.75
4773 5439 5.701224 TGTGTTAATTATGGGGGAATCTCC 58.299 41.667 0.00 0.00 35.23 3.71
4785 5451 3.000684 GGAATCTCCCCTTGTACCAAC 57.999 52.381 0.00 0.00 0.00 3.77
4786 5452 2.356844 GGAATCTCCCCTTGTACCAACC 60.357 54.545 0.00 0.00 0.00 3.77
4787 5453 0.909623 ATCTCCCCTTGTACCAACCG 59.090 55.000 0.00 0.00 0.00 4.44
4788 5454 1.376812 CTCCCCTTGTACCAACCGC 60.377 63.158 0.00 0.00 0.00 5.68
4789 5455 2.119484 CTCCCCTTGTACCAACCGCA 62.119 60.000 0.00 0.00 0.00 5.69
4790 5456 1.674322 CCCCTTGTACCAACCGCAG 60.674 63.158 0.00 0.00 0.00 5.18
4791 5457 2.332654 CCCTTGTACCAACCGCAGC 61.333 63.158 0.00 0.00 0.00 5.25
4792 5458 2.332654 CCTTGTACCAACCGCAGCC 61.333 63.158 0.00 0.00 0.00 4.85
4793 5459 1.599518 CTTGTACCAACCGCAGCCA 60.600 57.895 0.00 0.00 0.00 4.75
4794 5460 1.577328 CTTGTACCAACCGCAGCCAG 61.577 60.000 0.00 0.00 0.00 4.85
4795 5461 2.032071 GTACCAACCGCAGCCAGT 59.968 61.111 0.00 0.00 0.00 4.00
4796 5462 1.599797 GTACCAACCGCAGCCAGTT 60.600 57.895 0.00 0.00 0.00 3.16
4797 5463 1.149627 TACCAACCGCAGCCAGTTT 59.850 52.632 0.00 0.00 0.00 2.66
4798 5464 1.169661 TACCAACCGCAGCCAGTTTG 61.170 55.000 0.00 0.00 0.00 2.93
4799 5465 2.355009 CAACCGCAGCCAGTTTGC 60.355 61.111 0.00 0.00 38.18 3.68
4804 5470 2.355009 GCAGCCAGTTTGCGTTGG 60.355 61.111 0.00 0.00 37.53 3.77
4815 5481 3.977244 GCGTTGGCAACTGTGGGG 61.977 66.667 26.26 11.90 39.62 4.96
4816 5482 2.518349 CGTTGGCAACTGTGGGGT 60.518 61.111 26.26 0.00 37.61 4.95
4817 5483 2.551912 CGTTGGCAACTGTGGGGTC 61.552 63.158 26.26 0.00 37.61 4.46
4818 5484 2.203280 TTGGCAACTGTGGGGTCG 60.203 61.111 0.00 0.00 37.61 4.79
4819 5485 3.783362 TTGGCAACTGTGGGGTCGG 62.783 63.158 0.00 0.00 37.61 4.79
4820 5486 4.265056 GGCAACTGTGGGGTCGGT 62.265 66.667 0.00 0.00 0.00 4.69
4821 5487 2.203294 GCAACTGTGGGGTCGGTT 60.203 61.111 0.00 0.00 37.39 4.44
4822 5488 2.258726 GCAACTGTGGGGTCGGTTC 61.259 63.158 0.00 0.00 35.10 3.62
4823 5489 1.599797 CAACTGTGGGGTCGGTTCC 60.600 63.158 0.00 0.00 35.10 3.62
4824 5490 1.768888 AACTGTGGGGTCGGTTCCT 60.769 57.895 0.00 0.00 32.24 3.36
4825 5491 2.052047 AACTGTGGGGTCGGTTCCTG 62.052 60.000 0.00 0.00 32.24 3.86
4826 5492 2.122769 TGTGGGGTCGGTTCCTGA 60.123 61.111 0.00 0.00 0.00 3.86
4827 5493 2.346365 GTGGGGTCGGTTCCTGAC 59.654 66.667 0.00 0.00 35.60 3.51
4828 5494 2.122769 TGGGGTCGGTTCCTGACA 60.123 61.111 5.63 0.00 38.10 3.58
4829 5495 1.537889 TGGGGTCGGTTCCTGACAT 60.538 57.895 5.63 0.00 38.10 3.06
4830 5496 1.221021 GGGGTCGGTTCCTGACATC 59.779 63.158 5.63 0.00 38.10 3.06
4831 5497 1.265454 GGGGTCGGTTCCTGACATCT 61.265 60.000 5.63 0.00 38.10 2.90
4832 5498 0.175989 GGGTCGGTTCCTGACATCTC 59.824 60.000 5.63 0.00 38.10 2.75
4833 5499 1.187087 GGTCGGTTCCTGACATCTCT 58.813 55.000 5.63 0.00 38.10 3.10
4834 5500 1.135333 GGTCGGTTCCTGACATCTCTC 59.865 57.143 5.63 0.00 38.10 3.20
4835 5501 1.135333 GTCGGTTCCTGACATCTCTCC 59.865 57.143 0.00 0.00 36.37 3.71
4836 5502 1.186200 CGGTTCCTGACATCTCTCCA 58.814 55.000 0.00 0.00 0.00 3.86
4837 5503 1.135915 CGGTTCCTGACATCTCTCCAG 59.864 57.143 0.00 0.00 0.00 3.86
4838 5504 2.461695 GGTTCCTGACATCTCTCCAGA 58.538 52.381 0.00 0.00 0.00 3.86
4839 5505 2.834549 GGTTCCTGACATCTCTCCAGAA 59.165 50.000 0.00 0.00 30.24 3.02
4840 5506 3.368948 GGTTCCTGACATCTCTCCAGAAC 60.369 52.174 0.00 0.00 30.24 3.01
4841 5507 2.095461 TCCTGACATCTCTCCAGAACG 58.905 52.381 0.00 0.00 30.24 3.95
4842 5508 1.135915 CCTGACATCTCTCCAGAACGG 59.864 57.143 0.00 0.00 30.24 4.44
4843 5509 2.095461 CTGACATCTCTCCAGAACGGA 58.905 52.381 0.00 0.00 43.61 4.69
4844 5510 2.692557 CTGACATCTCTCCAGAACGGAT 59.307 50.000 0.00 0.00 45.19 4.18
4845 5511 2.428530 TGACATCTCTCCAGAACGGATG 59.571 50.000 0.00 0.00 45.19 3.51
4846 5512 1.137872 ACATCTCTCCAGAACGGATGC 59.862 52.381 0.00 0.00 45.19 3.91
4847 5513 0.755686 ATCTCTCCAGAACGGATGCC 59.244 55.000 0.00 0.00 45.19 4.40
4848 5514 0.324738 TCTCTCCAGAACGGATGCCT 60.325 55.000 0.00 0.00 45.19 4.75
4849 5515 0.103937 CTCTCCAGAACGGATGCCTC 59.896 60.000 0.00 0.00 45.19 4.70
4850 5516 0.324738 TCTCCAGAACGGATGCCTCT 60.325 55.000 0.00 0.00 45.19 3.69
4851 5517 0.539051 CTCCAGAACGGATGCCTCTT 59.461 55.000 0.00 0.00 45.19 2.85
4852 5518 0.984230 TCCAGAACGGATGCCTCTTT 59.016 50.000 0.00 0.00 39.64 2.52
4853 5519 1.089920 CCAGAACGGATGCCTCTTTG 58.910 55.000 0.00 0.00 36.56 2.77
4854 5520 1.339055 CCAGAACGGATGCCTCTTTGA 60.339 52.381 0.00 0.00 36.56 2.69
4855 5521 2.636830 CAGAACGGATGCCTCTTTGAT 58.363 47.619 0.00 0.00 0.00 2.57
4856 5522 2.353889 CAGAACGGATGCCTCTTTGATG 59.646 50.000 0.00 0.00 0.00 3.07
4857 5523 1.064654 GAACGGATGCCTCTTTGATGC 59.935 52.381 0.00 0.00 0.00 3.91
4858 5524 0.035152 ACGGATGCCTCTTTGATGCA 60.035 50.000 0.00 0.00 37.56 3.96
4859 5525 1.315690 CGGATGCCTCTTTGATGCAT 58.684 50.000 0.00 0.00 44.16 3.96
4862 5528 1.612463 GATGCCTCTTTGATGCATCCC 59.388 52.381 23.67 0.87 46.93 3.85
4863 5529 0.627451 TGCCTCTTTGATGCATCCCT 59.373 50.000 23.67 0.00 29.00 4.20
4864 5530 1.006281 TGCCTCTTTGATGCATCCCTT 59.994 47.619 23.67 0.00 29.00 3.95
4865 5531 1.680207 GCCTCTTTGATGCATCCCTTC 59.320 52.381 23.67 0.14 0.00 3.46
4866 5532 2.686118 GCCTCTTTGATGCATCCCTTCT 60.686 50.000 23.67 0.00 0.00 2.85
4867 5533 2.950309 CCTCTTTGATGCATCCCTTCTG 59.050 50.000 23.67 9.47 0.00 3.02
4868 5534 2.358267 CTCTTTGATGCATCCCTTCTGC 59.642 50.000 23.67 0.00 40.10 4.26
4869 5535 1.407979 CTTTGATGCATCCCTTCTGCC 59.592 52.381 23.67 0.00 38.89 4.85
4870 5536 0.627451 TTGATGCATCCCTTCTGCCT 59.373 50.000 23.67 0.00 38.89 4.75
4871 5537 0.106868 TGATGCATCCCTTCTGCCTG 60.107 55.000 23.67 0.00 38.89 4.85
4872 5538 0.106819 GATGCATCCCTTCTGCCTGT 60.107 55.000 16.23 0.00 38.89 4.00
4873 5539 1.141657 GATGCATCCCTTCTGCCTGTA 59.858 52.381 16.23 0.00 38.89 2.74
4874 5540 1.216064 TGCATCCCTTCTGCCTGTAT 58.784 50.000 0.00 0.00 38.89 2.29
4875 5541 2.407562 TGCATCCCTTCTGCCTGTATA 58.592 47.619 0.00 0.00 38.89 1.47
4876 5542 2.777114 TGCATCCCTTCTGCCTGTATAA 59.223 45.455 0.00 0.00 38.89 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.323758 ATACGCCCGCAAAGGAGCA 62.324 57.895 0.00 0.00 45.00 4.26
1 2 2.513897 ATACGCCCGCAAAGGAGC 60.514 61.111 0.00 0.00 45.00 4.70
2 3 0.532862 ATCATACGCCCGCAAAGGAG 60.533 55.000 0.00 0.00 45.00 3.69
3 4 0.107410 AATCATACGCCCGCAAAGGA 60.107 50.000 0.00 0.00 45.00 3.36
4 5 0.307760 GAATCATACGCCCGCAAAGG 59.692 55.000 0.00 0.00 40.63 3.11
5 6 1.261619 GAGAATCATACGCCCGCAAAG 59.738 52.381 0.00 0.00 33.17 2.77
6 7 1.295792 GAGAATCATACGCCCGCAAA 58.704 50.000 0.00 0.00 33.17 3.68
7 8 0.531974 GGAGAATCATACGCCCGCAA 60.532 55.000 0.00 0.00 36.25 4.85
8 9 1.069090 GGAGAATCATACGCCCGCA 59.931 57.895 0.00 0.00 36.25 5.69
9 10 1.668151 GGGAGAATCATACGCCCGC 60.668 63.158 0.00 0.00 37.59 6.13
10 11 4.675404 GGGAGAATCATACGCCCG 57.325 61.111 0.00 0.00 37.59 6.13
11 12 0.038159 CTCGGGAGAATCATACGCCC 60.038 60.000 0.00 0.00 42.52 6.13
12 13 0.667792 GCTCGGGAGAATCATACGCC 60.668 60.000 0.00 0.00 39.18 5.68
13 14 0.315568 AGCTCGGGAGAATCATACGC 59.684 55.000 0.00 0.00 39.18 4.42
14 15 2.294791 AGAAGCTCGGGAGAATCATACG 59.705 50.000 0.00 0.00 39.18 3.06
15 16 3.648009 CAGAAGCTCGGGAGAATCATAC 58.352 50.000 0.00 0.00 39.18 2.39
16 17 2.036475 GCAGAAGCTCGGGAGAATCATA 59.964 50.000 0.00 0.00 39.18 2.15
17 18 1.202627 GCAGAAGCTCGGGAGAATCAT 60.203 52.381 0.00 0.00 39.18 2.45
18 19 0.176680 GCAGAAGCTCGGGAGAATCA 59.823 55.000 0.00 0.00 39.18 2.57
19 20 2.984871 GCAGAAGCTCGGGAGAATC 58.015 57.895 0.00 0.00 39.18 2.52
49 50 1.654137 CGGCCAAAATCATACGCGC 60.654 57.895 5.73 0.00 0.00 6.86
50 51 1.010125 CCGGCCAAAATCATACGCG 60.010 57.895 3.53 3.53 0.00 6.01
52 53 1.010125 CGCCGGCCAAAATCATACG 60.010 57.895 23.46 0.00 0.00 3.06
61 62 0.671163 CTTAGTGTTACGCCGGCCAA 60.671 55.000 23.46 12.89 0.00 4.52
65 72 2.282701 TAAGCTTAGTGTTACGCCGG 57.717 50.000 0.86 0.00 0.00 6.13
66 73 4.852609 AAATAAGCTTAGTGTTACGCCG 57.147 40.909 12.54 0.00 0.00 6.46
73 80 9.025041 AGCAAATAAGGAAAATAAGCTTAGTGT 57.975 29.630 12.54 4.03 0.00 3.55
75 82 8.687242 GGAGCAAATAAGGAAAATAAGCTTAGT 58.313 33.333 12.54 6.45 0.00 2.24
82 89 8.664669 AAAGAGGGAGCAAATAAGGAAAATAA 57.335 30.769 0.00 0.00 0.00 1.40
85 92 7.176690 CAGTAAAGAGGGAGCAAATAAGGAAAA 59.823 37.037 0.00 0.00 0.00 2.29
86 93 6.659242 CAGTAAAGAGGGAGCAAATAAGGAAA 59.341 38.462 0.00 0.00 0.00 3.13
96 103 0.036010 GCAGCAGTAAAGAGGGAGCA 60.036 55.000 0.00 0.00 0.00 4.26
97 104 1.086634 CGCAGCAGTAAAGAGGGAGC 61.087 60.000 0.00 0.00 0.00 4.70
98 105 0.247736 ACGCAGCAGTAAAGAGGGAG 59.752 55.000 0.00 0.00 0.00 4.30
104 119 3.215244 CAAACGTAACGCAGCAGTAAAG 58.785 45.455 0.00 0.00 0.00 1.85
124 139 1.064758 AGTAAATTCCCATGAGCGGCA 60.065 47.619 1.45 0.00 0.00 5.69
129 144 6.293626 CCGCTAAATCAGTAAATTCCCATGAG 60.294 42.308 0.00 0.00 0.00 2.90
171 186 1.153647 GCATTGGCCCTTTTACGGC 60.154 57.895 0.00 0.00 46.29 5.68
172 187 1.138671 CGCATTGGCCCTTTTACGG 59.861 57.895 0.00 0.00 36.38 4.02
173 188 1.088306 TACGCATTGGCCCTTTTACG 58.912 50.000 0.00 0.00 36.38 3.18
174 189 1.202098 CGTACGCATTGGCCCTTTTAC 60.202 52.381 0.52 0.00 36.38 2.01
175 190 1.088306 CGTACGCATTGGCCCTTTTA 58.912 50.000 0.52 0.00 36.38 1.52
176 191 0.606944 TCGTACGCATTGGCCCTTTT 60.607 50.000 11.24 0.00 36.38 2.27
177 192 1.003112 TCGTACGCATTGGCCCTTT 60.003 52.632 11.24 0.00 36.38 3.11
178 193 1.449601 CTCGTACGCATTGGCCCTT 60.450 57.895 11.24 0.00 36.38 3.95
179 194 2.186903 CTCGTACGCATTGGCCCT 59.813 61.111 11.24 0.00 36.38 5.19
180 195 3.573491 GCTCGTACGCATTGGCCC 61.573 66.667 11.24 0.00 36.38 5.80
221 247 1.024579 ACGCCAAATTCACCGGCTAG 61.025 55.000 0.00 0.00 43.95 3.42
255 282 2.290367 CGTCACAAAAACTGCATCTCCA 59.710 45.455 0.00 0.00 0.00 3.86
266 293 3.955101 CCGCCCGCGTCACAAAAA 61.955 61.111 4.92 0.00 37.81 1.94
296 323 3.711190 TGGCTCAGATATAACTGCCTGAA 59.289 43.478 11.22 0.00 40.82 3.02
336 363 0.040157 CGTCACCCATTTGCACACAG 60.040 55.000 0.00 0.00 0.00 3.66
375 415 1.980036 ACCAGACCTAAAAGCCGGTAA 59.020 47.619 1.90 0.00 32.62 2.85
390 430 8.934023 ATAGAAGTTTCCAAATTTACACCAGA 57.066 30.769 0.00 0.00 0.00 3.86
529 607 7.809806 CCGAAATCAATTCAGCTAGAAAAGTTT 59.190 33.333 0.00 0.00 40.22 2.66
554 632 9.896645 ACATGACATATATGGATGAACTAATCC 57.103 33.333 23.68 0.00 45.57 3.01
685 763 2.744741 TCATGCTTATCGAAAACGGCAA 59.255 40.909 0.00 0.00 33.44 4.52
689 767 6.853279 ACAATTTCATGCTTATCGAAAACG 57.147 33.333 0.00 0.00 32.76 3.60
695 773 8.231304 AGTGAAAAACAATTTCATGCTTATCG 57.769 30.769 6.86 0.00 40.12 2.92
734 812 2.834638 ATGCCAGGCTACCAAGAATT 57.165 45.000 14.15 0.00 0.00 2.17
740 818 8.584157 CAATAATAAATTTATGCCAGGCTACCA 58.416 33.333 14.15 0.00 0.00 3.25
741 819 8.802267 TCAATAATAAATTTATGCCAGGCTACC 58.198 33.333 14.15 0.00 0.00 3.18
745 823 9.305925 GCTATCAATAATAAATTTATGCCAGGC 57.694 33.333 11.42 3.66 0.00 4.85
766 844 6.426328 CCATGATTTTCTGTGAGGTAGCTATC 59.574 42.308 0.00 0.00 0.00 2.08
787 865 9.469807 CTGTAGAACTATTTAGCTACTTCCATG 57.530 37.037 0.00 0.00 35.45 3.66
808 886 9.757227 AAGAAGCTAGTATTTGCTAATCTGTAG 57.243 33.333 0.00 0.00 38.75 2.74
810 888 7.011857 GCAAGAAGCTAGTATTTGCTAATCTGT 59.988 37.037 12.82 0.00 40.58 3.41
828 906 4.032331 GTCATCTCTTCGTTAGCAAGAAGC 59.968 45.833 0.76 0.00 42.48 3.86
832 910 6.367422 AGAAAAGTCATCTCTTCGTTAGCAAG 59.633 38.462 0.00 0.00 0.00 4.01
833 911 6.223852 AGAAAAGTCATCTCTTCGTTAGCAA 58.776 36.000 0.00 0.00 0.00 3.91
834 912 5.784177 AGAAAAGTCATCTCTTCGTTAGCA 58.216 37.500 0.00 0.00 0.00 3.49
835 913 7.995463 ATAGAAAAGTCATCTCTTCGTTAGC 57.005 36.000 0.00 0.00 0.00 3.09
839 917 7.661847 ACCAAAATAGAAAAGTCATCTCTTCGT 59.338 33.333 0.00 0.00 0.00 3.85
840 918 8.034058 ACCAAAATAGAAAAGTCATCTCTTCG 57.966 34.615 0.00 0.00 0.00 3.79
880 958 4.688511 TCGGCGCATTTACAAAAAGTAT 57.311 36.364 10.83 0.00 31.53 2.12
883 961 2.407026 GGTTCGGCGCATTTACAAAAAG 59.593 45.455 10.83 0.00 0.00 2.27
886 964 0.952280 TGGTTCGGCGCATTTACAAA 59.048 45.000 10.83 0.00 0.00 2.83
896 974 4.919754 GGTTAGTATTAGTATGGTTCGGCG 59.080 45.833 0.00 0.00 0.00 6.46
899 977 7.719483 TCAAGGGTTAGTATTAGTATGGTTCG 58.281 38.462 0.00 0.00 0.00 3.95
920 998 8.525290 ACCCTGAAAAGGTGATAAATATCAAG 57.475 34.615 4.75 0.00 43.65 3.02
922 1000 8.748412 CAAACCCTGAAAAGGTGATAAATATCA 58.252 33.333 0.00 0.00 40.19 2.15
923 1001 8.197439 CCAAACCCTGAAAAGGTGATAAATATC 58.803 37.037 0.00 0.00 37.78 1.63
924 1002 7.125659 CCCAAACCCTGAAAAGGTGATAAATAT 59.874 37.037 0.00 0.00 37.78 1.28
925 1003 6.439058 CCCAAACCCTGAAAAGGTGATAAATA 59.561 38.462 0.00 0.00 37.78 1.40
926 1004 5.248248 CCCAAACCCTGAAAAGGTGATAAAT 59.752 40.000 0.00 0.00 37.78 1.40
1320 1398 2.225467 GATAATCCAGCAAGGGACAGC 58.775 52.381 0.00 0.00 40.44 4.40
1494 1572 4.158764 CCCACGTAATTTTGCTCCCAATTA 59.841 41.667 0.00 0.00 0.00 1.40
1521 1599 6.151648 CCTGATTTTCATTAGCAAAGTGGAGA 59.848 38.462 0.00 0.00 0.00 3.71
1582 1660 3.363673 GCAACGTACTCACTAGCAAAACC 60.364 47.826 0.00 0.00 0.00 3.27
1620 1698 5.612351 GCTAAATACTCTAGGGGGTCAAAG 58.388 45.833 0.00 0.00 0.00 2.77
1775 1853 4.851843 TGATTGGACGTCTAGAGGAGTTA 58.148 43.478 18.93 2.62 0.00 2.24
1803 1881 5.659463 AGAAGAGACAGCTATGTTAAGCAG 58.341 41.667 0.00 0.00 45.30 4.24
1819 1897 4.887655 TCAGCCATATACGTCAAGAAGAGA 59.112 41.667 0.00 0.00 0.00 3.10
2250 2328 2.362077 TCAGAGCCCTTTTTGAACTTGC 59.638 45.455 0.00 0.00 0.00 4.01
2266 2344 5.359009 AGAAACACCATTGCCATAATCAGAG 59.641 40.000 0.00 0.00 0.00 3.35
2267 2345 5.263599 AGAAACACCATTGCCATAATCAGA 58.736 37.500 0.00 0.00 0.00 3.27
2275 2353 1.202830 ACGGTAGAAACACCATTGCCA 60.203 47.619 0.00 0.00 38.61 4.92
2405 2483 6.961360 ATTCAGATGAGTATTACCGACTGA 57.039 37.500 0.00 0.00 0.00 3.41
2430 2508 7.970061 GCAATCTGCATCAGAAATAACTTGTAA 59.030 33.333 0.27 0.00 44.04 2.41
2433 2511 6.807708 GCAATCTGCATCAGAAATAACTTG 57.192 37.500 0.27 1.81 44.04 3.16
2451 2529 5.148568 GCAAAACCATCAAATTGTGCAATC 58.851 37.500 0.00 0.00 0.00 2.67
2603 2708 6.070938 TGCATCTATCTAGAATGAGGACATGG 60.071 42.308 12.22 0.00 36.79 3.66
2650 2759 0.591170 CTGTTGGGCCACGTACAAAG 59.409 55.000 5.23 0.00 0.00 2.77
2695 2804 0.171231 GGGCAAAATCACGAGCTTCC 59.829 55.000 0.00 0.00 0.00 3.46
2883 2993 6.636454 ACCCTCAACAAATTCCTACTATGA 57.364 37.500 0.00 0.00 0.00 2.15
2915 3025 6.534436 CGATTAACAATGCCAAATTCAATCCA 59.466 34.615 0.00 0.00 0.00 3.41
2917 3027 6.534793 ACCGATTAACAATGCCAAATTCAATC 59.465 34.615 0.00 0.00 0.00 2.67
2965 3076 5.982516 CAGCAAGTAGGCAACAAACAATTTA 59.017 36.000 0.00 0.00 41.41 1.40
2972 3083 4.141287 ACATACAGCAAGTAGGCAACAAA 58.859 39.130 1.60 0.00 38.01 2.83
2981 3092 6.095860 ACACCTAACGATACATACAGCAAGTA 59.904 38.462 0.00 0.00 37.06 2.24
2982 3093 5.105473 ACACCTAACGATACATACAGCAAGT 60.105 40.000 0.00 0.00 0.00 3.16
2997 3108 5.580691 ACATGACAATGATACACACCTAACG 59.419 40.000 0.00 0.00 37.24 3.18
2999 3110 5.353956 GCACATGACAATGATACACACCTAA 59.646 40.000 0.00 0.00 37.24 2.69
3198 3368 5.138125 AGTCGCACAAATCCATCATTTTT 57.862 34.783 0.00 0.00 31.79 1.94
3273 3443 5.888901 AGCAAATGATGATATCCTGGATGT 58.111 37.500 19.42 12.83 0.00 3.06
3289 3459 1.155889 TGTGCAGGACGTAGCAAATG 58.844 50.000 10.83 0.00 43.20 2.32
3291 3461 1.890876 AATGTGCAGGACGTAGCAAA 58.109 45.000 10.83 6.88 43.20 3.68
3505 3675 5.464722 CACAGAAGCAGTATACATAGCTTGG 59.535 44.000 25.20 20.13 46.35 3.61
3513 3683 5.046663 TGACATTCCACAGAAGCAGTATACA 60.047 40.000 5.50 0.00 34.86 2.29
3514 3684 5.419542 TGACATTCCACAGAAGCAGTATAC 58.580 41.667 0.00 0.00 34.86 1.47
3518 3688 2.775890 CTGACATTCCACAGAAGCAGT 58.224 47.619 0.00 0.00 34.86 4.40
3537 3713 5.063944 CAGAAGTGCTTGTAAATATGTCGCT 59.936 40.000 0.00 0.00 0.00 4.93
3571 3747 8.839343 GTTCCTGGACAATGAATCAAAATTTTT 58.161 29.630 0.00 0.00 0.00 1.94
3575 3751 5.046376 GGGTTCCTGGACAATGAATCAAAAT 60.046 40.000 0.00 0.00 0.00 1.82
3675 3852 4.492955 GAGCTGAGCTCGACCTTG 57.507 61.111 19.71 0.00 45.85 3.61
3825 4002 1.338674 TGAGGTTGCGTGTAATGGAGG 60.339 52.381 0.00 0.00 0.00 4.30
3862 4039 3.318275 AGATCATGTTAGTACACGGCGAT 59.682 43.478 16.62 3.31 37.03 4.58
3892 4069 1.597742 TGCTTTTCTCTGTGGTGCTC 58.402 50.000 0.00 0.00 0.00 4.26
3925 4102 3.448934 TCCTGCATCTCTTTCTCCTCTT 58.551 45.455 0.00 0.00 0.00 2.85
3926 4103 3.033184 CTCCTGCATCTCTTTCTCCTCT 58.967 50.000 0.00 0.00 0.00 3.69
4091 4269 0.739462 TCACGAATAAGCACGGCAGG 60.739 55.000 0.00 0.00 0.00 4.85
4119 4297 1.145598 ATCTCGCATGCACTCCAGG 59.854 57.895 19.57 0.00 0.00 4.45
4159 4344 0.179108 CGAGATCTCCCACGTTTCCC 60.179 60.000 17.13 0.00 0.00 3.97
4160 4345 0.179108 CCGAGATCTCCCACGTTTCC 60.179 60.000 17.13 0.00 0.00 3.13
4165 4350 0.530744 TGAAACCGAGATCTCCCACG 59.469 55.000 17.13 5.86 0.00 4.94
4166 4351 2.347731 GTTGAAACCGAGATCTCCCAC 58.652 52.381 17.13 1.22 0.00 4.61
4167 4352 1.278127 GGTTGAAACCGAGATCTCCCA 59.722 52.381 17.13 4.97 39.66 4.37
4168 4353 2.025589 GGTTGAAACCGAGATCTCCC 57.974 55.000 17.13 5.93 39.66 4.30
4280 4473 2.575532 TCCTGGCAACTTGAGAAACAG 58.424 47.619 0.00 0.00 37.61 3.16
4408 4601 8.768501 AGGTTCTTAATTCCACTCTTCTTTTT 57.231 30.769 0.00 0.00 0.00 1.94
4409 4602 9.508642 CTAGGTTCTTAATTCCACTCTTCTTTT 57.491 33.333 0.00 0.00 0.00 2.27
4448 4641 9.394767 TGAGAAAGCTAAGCATGATAAATGTTA 57.605 29.630 0.00 0.00 0.00 2.41
4485 4678 6.425735 ACACAAGATGGATCATACATTTCCA 58.574 36.000 0.00 0.00 43.37 3.53
4486 4679 6.949352 ACACAAGATGGATCATACATTTCC 57.051 37.500 0.00 0.00 0.00 3.13
4487 4680 8.554528 CAGTACACAAGATGGATCATACATTTC 58.445 37.037 0.00 0.00 0.00 2.17
4489 4682 7.712639 GTCAGTACACAAGATGGATCATACATT 59.287 37.037 0.00 0.00 0.00 2.71
4490 4683 7.147672 TGTCAGTACACAAGATGGATCATACAT 60.148 37.037 0.00 0.00 0.00 2.29
4491 4684 6.154363 TGTCAGTACACAAGATGGATCATACA 59.846 38.462 0.00 0.00 0.00 2.29
4492 4685 6.573434 TGTCAGTACACAAGATGGATCATAC 58.427 40.000 0.00 0.00 0.00 2.39
4493 4686 6.790232 TGTCAGTACACAAGATGGATCATA 57.210 37.500 0.00 0.00 0.00 2.15
4494 4687 5.682234 TGTCAGTACACAAGATGGATCAT 57.318 39.130 0.00 0.00 0.00 2.45
4495 4688 5.187576 TGATGTCAGTACACAAGATGGATCA 59.812 40.000 0.00 0.00 38.78 2.92
4496 4689 5.664457 TGATGTCAGTACACAAGATGGATC 58.336 41.667 0.00 0.00 38.78 3.36
4497 4690 5.682234 TGATGTCAGTACACAAGATGGAT 57.318 39.130 0.00 0.00 38.78 3.41
4498 4691 5.423290 AGATGATGTCAGTACACAAGATGGA 59.577 40.000 0.00 0.00 38.78 3.41
4499 4692 5.668471 AGATGATGTCAGTACACAAGATGG 58.332 41.667 0.00 0.00 38.78 3.51
4500 4693 6.592994 ACAAGATGATGTCAGTACACAAGATG 59.407 38.462 0.00 0.00 38.78 2.90
4577 4770 7.875327 ATTTAGTTGTGTTGTAAAGTGGAGT 57.125 32.000 0.00 0.00 0.00 3.85
4614 4807 5.651387 TCATGAATAATTGTTTGCGGGAA 57.349 34.783 0.00 0.00 0.00 3.97
4678 4871 4.820897 CTGACAGAGCAGTATGTGGTAAA 58.179 43.478 0.00 0.00 36.87 2.01
4724 5390 9.696917 AAGTTTAATTGAGCTTTAACAATCTGG 57.303 29.630 0.00 0.00 35.99 3.86
4728 5394 9.816354 ACACAAGTTTAATTGAGCTTTAACAAT 57.184 25.926 0.00 0.00 38.18 2.71
4729 5395 9.646427 AACACAAGTTTAATTGAGCTTTAACAA 57.354 25.926 0.00 0.00 33.11 2.83
4740 5406 9.377312 CCCCCATAATTAACACAAGTTTAATTG 57.623 33.333 9.35 0.00 39.15 2.32
4741 5407 9.327731 TCCCCCATAATTAACACAAGTTTAATT 57.672 29.630 5.63 5.63 39.15 1.40
4742 5408 8.903059 TCCCCCATAATTAACACAAGTTTAAT 57.097 30.769 0.00 0.00 39.15 1.40
4743 5409 8.722622 TTCCCCCATAATTAACACAAGTTTAA 57.277 30.769 0.00 0.00 39.15 1.52
4744 5410 8.903059 ATTCCCCCATAATTAACACAAGTTTA 57.097 30.769 0.00 0.00 39.15 2.01
4745 5411 7.678171 AGATTCCCCCATAATTAACACAAGTTT 59.322 33.333 0.00 0.00 39.15 2.66
4746 5412 7.189087 AGATTCCCCCATAATTAACACAAGTT 58.811 34.615 0.00 0.00 41.74 2.66
4747 5413 6.741724 AGATTCCCCCATAATTAACACAAGT 58.258 36.000 0.00 0.00 0.00 3.16
4748 5414 6.265422 GGAGATTCCCCCATAATTAACACAAG 59.735 42.308 0.00 0.00 0.00 3.16
4749 5415 6.133356 GGAGATTCCCCCATAATTAACACAA 58.867 40.000 0.00 0.00 0.00 3.33
4750 5416 5.701224 GGAGATTCCCCCATAATTAACACA 58.299 41.667 0.00 0.00 0.00 3.72
4777 5443 2.031919 CTGGCTGCGGTTGGTACA 59.968 61.111 0.00 0.00 0.00 2.90
4778 5444 1.170290 AAACTGGCTGCGGTTGGTAC 61.170 55.000 9.64 0.00 0.00 3.34
4779 5445 1.149627 AAACTGGCTGCGGTTGGTA 59.850 52.632 9.64 0.00 0.00 3.25
4780 5446 2.123897 AAACTGGCTGCGGTTGGT 60.124 55.556 9.64 0.00 0.00 3.67
4781 5447 2.336088 CAAACTGGCTGCGGTTGG 59.664 61.111 9.64 4.29 0.00 3.77
4782 5448 2.355009 GCAAACTGGCTGCGGTTG 60.355 61.111 9.64 5.82 0.00 3.77
4787 5453 2.355009 CCAACGCAAACTGGCTGC 60.355 61.111 0.00 0.00 36.41 5.25
4797 5463 3.215568 CCCACAGTTGCCAACGCA 61.216 61.111 1.20 0.00 45.49 5.24
4798 5464 3.977244 CCCCACAGTTGCCAACGC 61.977 66.667 1.20 0.00 36.23 4.84
4799 5465 2.518349 ACCCCACAGTTGCCAACG 60.518 61.111 1.20 0.05 36.23 4.10
4800 5466 2.551912 CGACCCCACAGTTGCCAAC 61.552 63.158 0.00 0.00 0.00 3.77
4801 5467 2.203280 CGACCCCACAGTTGCCAA 60.203 61.111 0.00 0.00 0.00 4.52
4802 5468 4.263572 CCGACCCCACAGTTGCCA 62.264 66.667 0.00 0.00 0.00 4.92
4803 5469 3.785122 AACCGACCCCACAGTTGCC 62.785 63.158 0.00 0.00 0.00 4.52
4804 5470 2.203294 AACCGACCCCACAGTTGC 60.203 61.111 0.00 0.00 0.00 4.17
4805 5471 1.599797 GGAACCGACCCCACAGTTG 60.600 63.158 0.00 0.00 0.00 3.16
4806 5472 1.768888 AGGAACCGACCCCACAGTT 60.769 57.895 0.00 0.00 0.00 3.16
4807 5473 2.122547 AGGAACCGACCCCACAGT 60.123 61.111 0.00 0.00 0.00 3.55
4808 5474 2.214216 TCAGGAACCGACCCCACAG 61.214 63.158 0.00 0.00 0.00 3.66
4809 5475 2.122769 TCAGGAACCGACCCCACA 60.123 61.111 0.00 0.00 0.00 4.17
4810 5476 1.838073 ATGTCAGGAACCGACCCCAC 61.838 60.000 11.09 0.00 32.15 4.61
4811 5477 1.537889 ATGTCAGGAACCGACCCCA 60.538 57.895 11.09 0.00 32.15 4.96
4812 5478 1.221021 GATGTCAGGAACCGACCCC 59.779 63.158 11.09 0.00 32.15 4.95
4813 5479 0.175989 GAGATGTCAGGAACCGACCC 59.824 60.000 11.09 0.00 32.15 4.46
4814 5480 1.135333 GAGAGATGTCAGGAACCGACC 59.865 57.143 11.09 0.00 32.15 4.79
4815 5481 1.135333 GGAGAGATGTCAGGAACCGAC 59.865 57.143 0.00 0.00 0.00 4.79
4816 5482 1.272480 TGGAGAGATGTCAGGAACCGA 60.272 52.381 0.00 0.00 0.00 4.69
4817 5483 1.135915 CTGGAGAGATGTCAGGAACCG 59.864 57.143 0.00 0.00 0.00 4.44
4818 5484 2.461695 TCTGGAGAGATGTCAGGAACC 58.538 52.381 0.00 0.00 0.00 3.62
4819 5485 3.674682 CGTTCTGGAGAGATGTCAGGAAC 60.675 52.174 0.00 0.00 0.00 3.62
4820 5486 2.493675 CGTTCTGGAGAGATGTCAGGAA 59.506 50.000 0.00 0.00 0.00 3.36
4821 5487 2.095461 CGTTCTGGAGAGATGTCAGGA 58.905 52.381 0.00 0.00 0.00 3.86
4822 5488 1.135915 CCGTTCTGGAGAGATGTCAGG 59.864 57.143 0.00 0.00 42.00 3.86
4823 5489 2.095461 TCCGTTCTGGAGAGATGTCAG 58.905 52.381 0.00 0.00 43.74 3.51
4824 5490 2.215942 TCCGTTCTGGAGAGATGTCA 57.784 50.000 0.00 0.00 43.74 3.58
4834 5500 1.089920 CAAAGAGGCATCCGTTCTGG 58.910 55.000 0.00 0.00 40.09 3.86
4835 5501 2.099141 TCAAAGAGGCATCCGTTCTG 57.901 50.000 0.00 0.00 0.00 3.02
4836 5502 2.636830 CATCAAAGAGGCATCCGTTCT 58.363 47.619 0.00 0.00 0.00 3.01
4837 5503 1.064654 GCATCAAAGAGGCATCCGTTC 59.935 52.381 0.00 0.00 39.28 3.95
4838 5504 1.098050 GCATCAAAGAGGCATCCGTT 58.902 50.000 0.00 0.00 39.28 4.44
4839 5505 0.035152 TGCATCAAAGAGGCATCCGT 60.035 50.000 1.88 0.00 44.36 4.69
4840 5506 2.784547 TGCATCAAAGAGGCATCCG 58.215 52.632 1.88 0.00 44.36 4.18
4845 5511 1.680207 GAAGGGATGCATCAAAGAGGC 59.320 52.381 27.25 8.54 39.95 4.70
4846 5512 2.950309 CAGAAGGGATGCATCAAAGAGG 59.050 50.000 27.25 9.29 0.00 3.69
4847 5513 2.358267 GCAGAAGGGATGCATCAAAGAG 59.642 50.000 27.25 13.21 43.31 2.85
4848 5514 2.372264 GCAGAAGGGATGCATCAAAGA 58.628 47.619 27.25 0.00 43.31 2.52
4849 5515 1.407979 GGCAGAAGGGATGCATCAAAG 59.592 52.381 27.25 11.73 45.68 2.77
4850 5516 1.006281 AGGCAGAAGGGATGCATCAAA 59.994 47.619 27.25 0.00 45.68 2.69
4851 5517 0.627451 AGGCAGAAGGGATGCATCAA 59.373 50.000 27.25 0.00 45.68 2.57
4852 5518 0.106868 CAGGCAGAAGGGATGCATCA 60.107 55.000 27.25 0.00 45.68 3.07
4853 5519 0.106819 ACAGGCAGAAGGGATGCATC 60.107 55.000 18.81 18.81 45.68 3.91
4854 5520 1.216064 TACAGGCAGAAGGGATGCAT 58.784 50.000 0.00 0.00 45.68 3.96
4855 5521 1.216064 ATACAGGCAGAAGGGATGCA 58.784 50.000 0.00 0.00 45.68 3.96
4856 5522 3.492102 TTATACAGGCAGAAGGGATGC 57.508 47.619 0.00 0.00 43.09 3.91


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

AutoCloner maintained by Alex Coulton.