Multiple sequence alignment - TraesCS3B01G158600

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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 TraesCS3B01G158600 chr3B 100.000 7815 0 0 1 7815 153965221 153957407 0.000000e+00 14432
1 TraesCS3B01G158600 chr3B 93.985 133 7 1 4774 4906 153960316 153960185 4.780000e-47 200
2 TraesCS3B01G158600 chr3B 93.985 133 7 1 4906 5037 153960448 153960316 4.780000e-47 200
3 TraesCS3B01G158600 chr3D 95.242 4645 144 29 1 4604 103361660 103357052 0.000000e+00 7282
4 TraesCS3B01G158600 chr3D 91.664 3251 162 60 4608 7815 103357015 103353831 0.000000e+00 4401
5 TraesCS3B01G158600 chr3D 95.489 133 5 1 4774 4906 103356717 103356586 2.210000e-50 211
6 TraesCS3B01G158600 chr3D 95.489 133 5 1 4906 5037 103356849 103356717 2.210000e-50 211
7 TraesCS3B01G158600 chr3A 92.057 1322 87 15 2301 3615 552782689 552783999 0.000000e+00 1844
8 TraesCS3B01G158600 chr3A 89.156 1457 113 21 708 2122 552781126 552782579 0.000000e+00 1773
9 TraesCS3B01G158600 chr3A 86.846 1452 112 45 4914 6302 552785633 552787068 0.000000e+00 1550
10 TraesCS3B01G158600 chr3A 86.028 866 71 25 3888 4712 552784117 552784973 0.000000e+00 883
11 TraesCS3B01G158600 chr3A 83.388 608 51 21 6302 6864 552787107 552787709 1.160000e-142 518
12 TraesCS3B01G158600 chr3A 81.281 203 20 5 7143 7327 552787857 552788059 1.760000e-31 148
13 TraesCS3B01G158600 chr3A 82.857 140 14 6 7661 7792 552788211 552788348 4.950000e-22 117
14 TraesCS3B01G158600 chr4A 76.074 326 74 4 2867 3190 535430654 535430331 4.850000e-37 167


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 TraesCS3B01G158600 chr3B 153957407 153965221 7814 True 14432.000000 14432 100.000000 1 7815 1 chr3B.!!$R1 7814
1 TraesCS3B01G158600 chr3D 103353831 103361660 7829 True 3026.250000 7282 94.471000 1 7815 4 chr3D.!!$R1 7814
2 TraesCS3B01G158600 chr3A 552781126 552788348 7222 False 976.142857 1844 85.944714 708 7792 7 chr3A.!!$F1 7084

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
944 976 0.105709 CCCCTCTCCCTCTTCCTCTC 60.106 65.000 0.00 0.0 0.00 3.20 F
2287 2372 0.036306 TCGGGCAGAAGTCCCTTTTC 59.964 55.000 0.00 0.0 41.69 2.29 F
3045 3132 1.911057 AAAGGCACCCTTTGACTAGC 58.089 50.000 8.37 0.0 46.34 3.42 F
4553 4671 1.705186 ACCTGCAACCAGATAACCACT 59.295 47.619 0.00 0.0 41.77 4.00 F
6034 6684 0.326264 AGAAAGATGACAAGGGCGCT 59.674 50.000 7.64 0.0 0.00 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2749 2836 0.967380 GCACTAAGCACCCCTGCATT 60.967 55.000 0.00 0.0 46.97 3.56 R
3836 3933 2.233922 GGAAATGGTGACTCTCGGAGAA 59.766 50.000 9.32 0.0 34.09 2.87 R
4860 5100 1.003580 TGAAGAAGATCCCAGTGTGGC 59.996 52.381 0.00 0.0 35.79 5.01 R
6544 7266 0.104672 TGGAAGGGAAGACTGGGACA 60.105 55.000 0.00 0.0 0.00 4.02 R
7385 8222 0.044702 AGATCCAGATGACCCACCCA 59.955 55.000 0.00 0.0 0.00 4.51 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
95 96 2.355756 ACACGCAATATGCTGGAATGAC 59.644 45.455 0.43 0.00 42.25 3.06
96 97 1.949525 ACGCAATATGCTGGAATGACC 59.050 47.619 0.43 0.00 42.25 4.02
178 179 6.100279 TGTGGCTAGAGATCATAAAGGAATGT 59.900 38.462 0.00 0.00 0.00 2.71
209 210 1.621107 TCGTGCGTTTCCGTCTAATC 58.379 50.000 0.00 0.00 36.15 1.75
217 218 4.259850 GCGTTTCCGTCTAATCTGTTCATC 60.260 45.833 0.00 0.00 36.15 2.92
220 221 5.661056 TTCCGTCTAATCTGTTCATCTGT 57.339 39.130 0.00 0.00 0.00 3.41
224 231 4.672862 CGTCTAATCTGTTCATCTGTAGCG 59.327 45.833 0.00 0.00 0.00 4.26
281 288 7.043565 GGCCATGCATAATCCTATTATTTTGG 58.956 38.462 0.00 0.00 0.00 3.28
341 348 6.377429 TGATGTTTTAGACAGGTCGATACTCT 59.623 38.462 0.00 0.00 42.62 3.24
357 364 9.522804 GTCGATACTCTTTGAGTTGAAGATAAT 57.477 33.333 5.52 0.00 40.28 1.28
362 369 8.023050 ACTCTTTGAGTTGAAGATAATCGTTG 57.977 34.615 0.00 0.00 40.28 4.10
425 432 6.098695 ACATTAATTTGGATGCCAACATAGCT 59.901 34.615 0.00 0.00 43.82 3.32
483 490 2.158726 TCGGATGGGTTATTGGTTAGGC 60.159 50.000 0.00 0.00 0.00 3.93
494 501 4.568152 ATTGGTTAGGCGACAATTATGC 57.432 40.909 0.00 0.00 31.21 3.14
505 512 5.291614 GGCGACAATTATGCAACAATGATTT 59.708 36.000 0.00 0.00 0.00 2.17
508 515 8.379161 GCGACAATTATGCAACAATGATTTTTA 58.621 29.630 0.00 0.00 0.00 1.52
509 516 9.674208 CGACAATTATGCAACAATGATTTTTAC 57.326 29.630 0.00 0.00 0.00 2.01
511 518 9.723601 ACAATTATGCAACAATGATTTTTACCT 57.276 25.926 0.00 0.00 0.00 3.08
607 616 8.907222 ATGAAGAAAATAACCAACATTGCTTT 57.093 26.923 0.00 0.00 0.00 3.51
645 654 4.142687 CCATTGTCGACAAATTGACCTACC 60.143 45.833 32.69 0.00 38.35 3.18
646 655 3.755112 TGTCGACAAATTGACCTACCA 57.245 42.857 17.62 0.00 38.35 3.25
654 663 6.293955 CGACAAATTGACCTACCAATTGACTT 60.294 38.462 7.12 0.00 43.61 3.01
658 667 8.550376 CAAATTGACCTACCAATTGACTTTTTG 58.450 33.333 7.12 1.56 43.61 2.44
667 676 7.388460 ACCAATTGACTTTTTGCATGAAAAA 57.612 28.000 7.56 7.56 40.52 1.94
672 681 9.724839 AATTGACTTTTTGCATGAAAAATCAAG 57.275 25.926 23.08 16.18 41.62 3.02
692 701 8.688747 ATCAAGATCATAAATCCAAACTCCTC 57.311 34.615 0.00 0.00 0.00 3.71
710 719 2.701951 CCTCCTATACGGCCAACCTTTA 59.298 50.000 2.24 0.00 0.00 1.85
711 720 3.135167 CCTCCTATACGGCCAACCTTTAA 59.865 47.826 2.24 0.00 0.00 1.52
712 721 4.384427 CCTCCTATACGGCCAACCTTTAAA 60.384 45.833 2.24 0.00 0.00 1.52
713 722 5.176741 TCCTATACGGCCAACCTTTAAAA 57.823 39.130 2.24 0.00 0.00 1.52
714 723 5.568392 TCCTATACGGCCAACCTTTAAAAA 58.432 37.500 2.24 0.00 0.00 1.94
715 724 5.415389 TCCTATACGGCCAACCTTTAAAAAC 59.585 40.000 2.24 0.00 0.00 2.43
716 725 5.183522 CCTATACGGCCAACCTTTAAAAACA 59.816 40.000 2.24 0.00 0.00 2.83
717 726 3.167921 ACGGCCAACCTTTAAAAACAC 57.832 42.857 2.24 0.00 0.00 3.32
718 727 2.496470 ACGGCCAACCTTTAAAAACACA 59.504 40.909 2.24 0.00 0.00 3.72
752 761 1.407979 ACAATCTTAGAGGCGTACCCG 59.592 52.381 0.00 0.00 39.21 5.28
762 771 0.514255 GGCGTACCCGTGAAAAACTC 59.486 55.000 0.00 0.00 36.15 3.01
784 804 4.840115 TCCCAAAGAAGCAATCAAAGGATT 59.160 37.500 0.00 0.00 44.51 3.01
785 805 5.307716 TCCCAAAGAAGCAATCAAAGGATTT 59.692 36.000 0.00 0.00 41.78 2.17
786 806 5.999600 CCCAAAGAAGCAATCAAAGGATTTT 59.000 36.000 0.00 0.00 41.78 1.82
787 807 7.016072 TCCCAAAGAAGCAATCAAAGGATTTTA 59.984 33.333 0.00 0.00 41.78 1.52
821 841 0.771127 CCACTCTCAGGGAAAACCCA 59.229 55.000 8.05 0.00 41.63 4.51
923 943 2.365635 ACTCCCAGGGTCCATCCG 60.366 66.667 5.01 0.00 37.00 4.18
935 967 4.888325 CATCCGCCCCCTCTCCCT 62.888 72.222 0.00 0.00 0.00 4.20
936 968 4.565850 ATCCGCCCCCTCTCCCTC 62.566 72.222 0.00 0.00 0.00 4.30
938 970 4.806339 CCGCCCCCTCTCCCTCTT 62.806 72.222 0.00 0.00 0.00 2.85
939 971 3.157949 CGCCCCCTCTCCCTCTTC 61.158 72.222 0.00 0.00 0.00 2.87
940 972 2.770475 GCCCCCTCTCCCTCTTCC 60.770 72.222 0.00 0.00 0.00 3.46
941 973 3.124088 CCCCCTCTCCCTCTTCCT 58.876 66.667 0.00 0.00 0.00 3.36
942 974 1.074850 CCCCCTCTCCCTCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
943 975 1.598856 CCCCCTCTCCCTCTTCCTCT 61.599 65.000 0.00 0.00 0.00 3.69
944 976 0.105709 CCCCTCTCCCTCTTCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
945 977 0.105709 CCCTCTCCCTCTTCCTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
946 978 0.105709 CCTCTCCCTCTTCCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
947 979 0.467290 CTCTCCCTCTTCCTCTCCCG 60.467 65.000 0.00 0.00 0.00 5.14
1052 1084 4.400251 AGGCCGGCCCTAGTGACT 62.400 66.667 41.72 18.69 44.08 3.41
1433 1470 0.803117 CTCGACAAGGTCACGCTCTA 59.197 55.000 0.00 0.00 32.09 2.43
1449 1486 1.855360 CTCTATTCGTTTCTCCGCTGC 59.145 52.381 0.00 0.00 0.00 5.25
1450 1487 0.572590 CTATTCGTTTCTCCGCTGCG 59.427 55.000 16.34 16.34 0.00 5.18
1451 1488 0.108992 TATTCGTTTCTCCGCTGCGT 60.109 50.000 21.59 0.24 0.00 5.24
1467 1504 2.458951 TGCGTGTTTCACATTTTGCTC 58.541 42.857 1.00 0.00 33.40 4.26
1685 1742 0.923358 TGGTAATTGGTAGCTGGGGG 59.077 55.000 0.00 0.00 0.00 5.40
1778 1838 6.030228 GTCTTTTCTTTCTGTTGGACTTGTG 58.970 40.000 0.00 0.00 0.00 3.33
1822 1882 6.823286 TGGAACCTGGAAATATCAGACATA 57.177 37.500 0.00 0.00 34.36 2.29
1890 1954 4.424626 GCTAGTTTGGATAGGCAAAAAGC 58.575 43.478 0.00 0.00 44.65 3.51
2017 2081 2.228343 ACGACAAGGTTCGAGAGTAAGG 59.772 50.000 0.00 0.00 41.78 2.69
2092 2156 5.696724 AGTGCTAATAATGGCATCGTACTTC 59.303 40.000 0.00 0.00 45.35 3.01
2101 2165 2.030946 GGCATCGTACTTCTCACATTGC 59.969 50.000 0.00 0.00 0.00 3.56
2133 2206 5.496556 TCATTAGATGGTCGAATTTGGTGT 58.503 37.500 0.00 0.00 0.00 4.16
2134 2207 5.943416 TCATTAGATGGTCGAATTTGGTGTT 59.057 36.000 0.00 0.00 0.00 3.32
2191 2276 5.889289 TGCTTTCAAAGGTTAGTAACAGGTT 59.111 36.000 14.81 2.56 0.00 3.50
2192 2277 6.183360 TGCTTTCAAAGGTTAGTAACAGGTTG 60.183 38.462 14.81 13.60 0.00 3.77
2196 2281 7.324354 TCAAAGGTTAGTAACAGGTTGAAAC 57.676 36.000 14.81 0.00 29.67 2.78
2252 2337 6.021596 GCTGTAATGAACGAACCTGTAAATG 58.978 40.000 0.00 0.00 0.00 2.32
2287 2372 0.036306 TCGGGCAGAAGTCCCTTTTC 59.964 55.000 0.00 0.00 41.69 2.29
2290 2375 2.290071 CGGGCAGAAGTCCCTTTTCTTA 60.290 50.000 0.00 0.00 41.69 2.10
2291 2376 3.763057 GGGCAGAAGTCCCTTTTCTTAA 58.237 45.455 0.00 0.00 40.66 1.85
2292 2377 4.149598 GGGCAGAAGTCCCTTTTCTTAAA 58.850 43.478 0.00 0.00 40.66 1.52
2293 2378 4.587262 GGGCAGAAGTCCCTTTTCTTAAAA 59.413 41.667 0.00 0.00 40.66 1.52
2294 2379 5.069914 GGGCAGAAGTCCCTTTTCTTAAAAA 59.930 40.000 0.00 0.00 40.66 1.94
2330 2415 2.938451 TGTGTACATAGATGCTTGCTGC 59.062 45.455 0.00 0.00 43.25 5.25
2479 2566 7.202011 GGTCAGGGAACATACAGTAATGTCTAT 60.202 40.741 0.00 0.00 39.16 1.98
2492 2579 7.020602 CAGTAATGTCTATAGAGCTCGTGATG 58.979 42.308 8.37 0.00 0.00 3.07
2725 2812 6.554334 TCTTTTCCTGGACTAAAATTGACG 57.446 37.500 0.00 0.00 0.00 4.35
2925 3012 4.391405 TGAGCATTGTCATAGTCGTCAT 57.609 40.909 0.00 0.00 0.00 3.06
3045 3132 1.911057 AAAGGCACCCTTTGACTAGC 58.089 50.000 8.37 0.00 46.34 3.42
3236 3323 4.672409 GAAGCAAGTGCAACAAGTTAGTT 58.328 39.130 6.00 0.00 45.16 2.24
3295 3383 2.346766 TCTTTCTGCAGGTTGAGCAA 57.653 45.000 15.13 0.00 42.17 3.91
3656 3746 9.934190 TTTTTCACCGTAAAGTATTTTAGTGAC 57.066 29.630 10.46 0.00 40.09 3.67
3833 3930 7.787424 AGTAATGAAGAGCTCCTCCTACTTATT 59.213 37.037 10.93 4.50 0.00 1.40
3836 3933 7.259088 TGAAGAGCTCCTCCTACTTATTTTT 57.741 36.000 10.93 0.00 0.00 1.94
3856 3953 3.594603 TTCTCCGAGAGTCACCATTTC 57.405 47.619 0.00 0.00 0.00 2.17
3883 3980 6.998802 ACTTAGTTGCACTGTCTAGATTTCT 58.001 36.000 0.00 0.00 0.00 2.52
3903 4000 4.954875 TCTTTTTAGTTGGGTGCAATTGG 58.045 39.130 7.72 0.00 0.00 3.16
3998 4095 5.537188 TGTTGGAAAATGATGTAGTTTGCC 58.463 37.500 0.00 0.00 34.37 4.52
4280 4379 7.721286 TTCTCTTGAACTGAGAACATTCTTC 57.279 36.000 2.51 0.00 43.19 2.87
4288 4387 6.207691 ACTGAGAACATTCTTCTAGAGCTC 57.792 41.667 5.27 5.27 37.73 4.09
4418 4518 4.371786 CGCTAGCATCTTCATTACCTCAA 58.628 43.478 16.45 0.00 0.00 3.02
4419 4519 4.447054 CGCTAGCATCTTCATTACCTCAAG 59.553 45.833 16.45 0.00 0.00 3.02
4420 4520 5.363939 GCTAGCATCTTCATTACCTCAAGT 58.636 41.667 10.63 0.00 0.00 3.16
4421 4521 5.819901 GCTAGCATCTTCATTACCTCAAGTT 59.180 40.000 10.63 0.00 0.00 2.66
4462 4577 6.782000 AGCCCATATATTTGCTTTGGTTATGA 59.218 34.615 0.80 0.00 0.00 2.15
4475 4590 8.584157 TGCTTTGGTTATGAAACATGAACTTAT 58.416 29.630 0.00 0.00 37.34 1.73
4553 4671 1.705186 ACCTGCAACCAGATAACCACT 59.295 47.619 0.00 0.00 41.77 4.00
4591 4709 4.766891 CCACATTTTCTTTCCTCTAAGCCA 59.233 41.667 0.00 0.00 0.00 4.75
4727 4967 9.271921 TGATAGTTATTATGTGGGAGCATATCT 57.728 33.333 0.00 0.00 32.16 1.98
4842 5082 4.759693 TGTATTCTGTTGCCGTCATTCTTT 59.240 37.500 0.00 0.00 0.00 2.52
4886 5126 3.772025 CACTGGGATCTTCTTCACCTACT 59.228 47.826 0.00 0.00 0.00 2.57
5007 5626 6.636454 TCTAAATACCACACTGGGATCTTT 57.364 37.500 0.00 0.00 41.20 2.52
5051 5673 4.827284 AGGTATAGTGCCCATTTTGTATGC 59.173 41.667 0.00 0.00 0.00 3.14
5070 5692 8.896320 TGTATGCACTCTTTTAGACTTTTACA 57.104 30.769 0.00 0.00 0.00 2.41
5182 5808 6.417930 GTGAAAAAGAAATAGGCTTGTGTCAC 59.582 38.462 0.00 0.00 30.80 3.67
5348 5984 8.644374 TTGCAGGTATAACCAACTCTTTTATT 57.356 30.769 0.00 0.00 41.95 1.40
5385 6031 1.680338 AGTCTTGTGGTTGTTGAGGC 58.320 50.000 0.00 0.00 0.00 4.70
5386 6032 1.212935 AGTCTTGTGGTTGTTGAGGCT 59.787 47.619 0.00 0.00 0.00 4.58
5407 6053 8.494016 AGGCTTATTCACTGTTATTAGTGTTC 57.506 34.615 5.89 0.00 46.32 3.18
5599 6248 8.940768 TTTAGTTTGGAATGCCTAAATTATGC 57.059 30.769 0.00 0.00 30.35 3.14
5607 6257 6.264067 GGAATGCCTAAATTATGCTGTCTTCT 59.736 38.462 2.26 0.00 0.00 2.85
5732 6382 6.089016 CAGTTCAACTCACATCATTGAATTGC 59.911 38.462 8.03 0.00 42.56 3.56
5734 6384 4.768448 TCAACTCACATCATTGAATTGCCT 59.232 37.500 0.00 0.00 29.56 4.75
5838 6488 1.337354 TGGCGAACATCATGTACGTGT 60.337 47.619 14.63 1.44 0.00 4.49
5913 6563 2.802816 GTCCGGATGATAGCAATGTGAC 59.197 50.000 7.81 0.00 0.00 3.67
6029 6679 3.423539 TCCACCAGAAAGATGACAAGG 57.576 47.619 0.00 0.00 0.00 3.61
6034 6684 0.326264 AGAAAGATGACAAGGGCGCT 59.674 50.000 7.64 0.00 0.00 5.92
6055 6705 2.367512 AGGGTGGATGGAGGAGCC 60.368 66.667 0.00 0.00 37.10 4.70
6067 6717 4.216411 TGGAGGAGCCATTGTAAGTTAC 57.784 45.455 6.06 6.06 43.33 2.50
6136 6786 3.554934 TCATGTCTATTGCATGGTTCCC 58.445 45.455 0.00 0.00 42.72 3.97
6153 6803 8.863086 CATGGTTCCCTCAAATATCATATGTTT 58.137 33.333 1.90 0.00 0.00 2.83
6185 6859 6.809630 TGAAATCAAAATACCGTCACATGA 57.190 33.333 0.00 0.00 0.00 3.07
6201 6875 8.092068 CCGTCACATGATAGGGTATAATTTGTA 58.908 37.037 0.00 0.00 0.00 2.41
6285 6960 3.844211 AGTAGGGTGACATTTTAGGAGCA 59.156 43.478 0.00 0.00 0.00 4.26
6361 7077 4.647615 CGGCAGGGCTACGGATCG 62.648 72.222 0.00 0.00 0.00 3.69
6541 7263 1.228894 TGGCCTGAGAGACTTCGGT 60.229 57.895 3.32 0.00 0.00 4.69
6544 7266 1.882989 GCCTGAGAGACTTCGGTGCT 61.883 60.000 0.00 0.00 0.00 4.40
6550 7272 1.816863 GAGACTTCGGTGCTGTCCCA 61.817 60.000 0.00 0.00 0.00 4.37
6600 7325 2.718073 CCGCGCCCCAGTAGTAAGT 61.718 63.158 0.00 0.00 0.00 2.24
6653 7385 8.405531 GTTCATATAGCTTAGTGGCAAAAATCA 58.594 33.333 0.00 0.00 34.17 2.57
6678 7421 3.498082 CGTTTTATTGCTTCTTTCCCCG 58.502 45.455 0.00 0.00 0.00 5.73
6781 7538 2.122954 GGTGTGAGGGGAGGAGGT 59.877 66.667 0.00 0.00 0.00 3.85
6859 7624 0.105224 TCCCGCGTTTCAGTTTCTGA 59.895 50.000 4.92 0.00 38.87 3.27
6866 7631 3.423206 GCGTTTCAGTTTCTGATTTGCTG 59.577 43.478 0.24 0.00 40.39 4.41
6867 7632 3.423206 CGTTTCAGTTTCTGATTTGCTGC 59.577 43.478 0.24 0.00 40.39 5.25
6870 7635 4.233123 TCAGTTTCTGATTTGCTGCTTG 57.767 40.909 0.00 0.00 35.39 4.01
6871 7636 2.729882 CAGTTTCTGATTTGCTGCTTGC 59.270 45.455 0.00 0.00 36.45 4.01
6872 7637 2.626743 AGTTTCTGATTTGCTGCTTGCT 59.373 40.909 0.00 0.00 43.37 3.91
6874 7639 0.885879 TCTGATTTGCTGCTTGCTGG 59.114 50.000 0.00 0.00 43.37 4.85
6875 7640 0.601558 CTGATTTGCTGCTTGCTGGT 59.398 50.000 0.00 0.00 43.37 4.00
6876 7641 0.315886 TGATTTGCTGCTTGCTGGTG 59.684 50.000 0.00 0.00 43.37 4.17
6877 7642 0.599558 GATTTGCTGCTTGCTGGTGA 59.400 50.000 0.00 0.00 43.37 4.02
6878 7643 0.601558 ATTTGCTGCTTGCTGGTGAG 59.398 50.000 0.00 0.00 43.37 3.51
6879 7644 2.079020 TTTGCTGCTTGCTGGTGAGC 62.079 55.000 0.00 0.00 46.44 4.26
6880 7645 2.672307 GCTGCTTGCTGGTGAGCT 60.672 61.111 0.00 0.00 46.39 4.09
6889 7654 1.233285 GCTGGTGAGCTTGGAGTGTG 61.233 60.000 0.00 0.00 42.52 3.82
6901 7666 4.758692 AGTGTGCCACTCGTTCAG 57.241 55.556 0.00 0.00 41.21 3.02
6912 7677 4.293729 CACTCGTTCAGTGTTAATGACG 57.706 45.455 0.00 0.00 46.81 4.35
6930 7695 1.471684 ACGCTAGAAACCGACCTGTAG 59.528 52.381 0.00 0.00 0.00 2.74
6942 7707 1.200760 ACCTGTAGCTGTGATGGGCA 61.201 55.000 0.00 0.00 0.00 5.36
6970 7741 2.960688 GCCTCGGGTCAGCTTCCTT 61.961 63.158 4.92 0.00 0.00 3.36
6991 7762 2.573009 TCTGGATCACTTTGGCTGATGA 59.427 45.455 0.00 0.00 0.00 2.92
6992 7763 3.201487 TCTGGATCACTTTGGCTGATGAT 59.799 43.478 0.00 0.00 34.50 2.45
6993 7764 3.284617 TGGATCACTTTGGCTGATGATG 58.715 45.455 0.00 0.00 31.96 3.07
6994 7765 2.034305 GGATCACTTTGGCTGATGATGC 59.966 50.000 0.00 0.00 33.60 3.91
6995 7766 1.089112 TCACTTTGGCTGATGATGCG 58.911 50.000 0.00 0.00 0.00 4.73
6996 7767 0.099968 CACTTTGGCTGATGATGCGG 59.900 55.000 0.00 0.00 0.00 5.69
6997 7768 0.322816 ACTTTGGCTGATGATGCGGT 60.323 50.000 0.00 0.00 0.00 5.68
6998 7769 0.379669 CTTTGGCTGATGATGCGGTC 59.620 55.000 0.00 0.00 0.00 4.79
6999 7770 0.322366 TTTGGCTGATGATGCGGTCA 60.322 50.000 0.00 0.00 42.06 4.02
7001 7772 1.026182 TGGCTGATGATGCGGTCAAC 61.026 55.000 0.00 0.00 40.97 3.18
7002 7773 1.026182 GGCTGATGATGCGGTCAACA 61.026 55.000 2.70 2.70 40.97 3.33
7003 7774 1.019673 GCTGATGATGCGGTCAACAT 58.980 50.000 3.04 0.00 38.70 2.71
7004 7775 1.268386 GCTGATGATGCGGTCAACATG 60.268 52.381 3.04 0.00 38.70 3.21
7005 7776 2.282407 CTGATGATGCGGTCAACATGA 58.718 47.619 0.00 0.00 38.70 3.07
7006 7777 2.009051 TGATGATGCGGTCAACATGAC 58.991 47.619 0.00 1.88 46.23 3.06
7007 7778 2.283298 GATGATGCGGTCAACATGACT 58.717 47.619 0.00 0.00 46.19 3.41
7008 7779 2.183478 TGATGCGGTCAACATGACTT 57.817 45.000 0.00 0.00 46.19 3.01
7009 7780 2.503331 TGATGCGGTCAACATGACTTT 58.497 42.857 0.00 0.00 46.19 2.66
7010 7781 3.669536 TGATGCGGTCAACATGACTTTA 58.330 40.909 0.00 0.00 46.19 1.85
7011 7782 3.435327 TGATGCGGTCAACATGACTTTAC 59.565 43.478 0.00 0.00 46.19 2.01
7012 7783 2.147958 TGCGGTCAACATGACTTTACC 58.852 47.619 0.00 0.00 46.19 2.85
7013 7784 2.224426 TGCGGTCAACATGACTTTACCT 60.224 45.455 0.00 0.00 46.19 3.08
7014 7785 2.812011 GCGGTCAACATGACTTTACCTT 59.188 45.455 0.00 0.00 46.19 3.50
7015 7786 3.364964 GCGGTCAACATGACTTTACCTTG 60.365 47.826 0.00 0.00 46.19 3.61
7016 7787 3.813166 CGGTCAACATGACTTTACCTTGT 59.187 43.478 0.00 0.00 46.19 3.16
7017 7788 4.992319 CGGTCAACATGACTTTACCTTGTA 59.008 41.667 0.00 0.00 46.19 2.41
7018 7789 5.642063 CGGTCAACATGACTTTACCTTGTAT 59.358 40.000 0.00 0.00 46.19 2.29
7019 7790 6.814644 CGGTCAACATGACTTTACCTTGTATA 59.185 38.462 0.00 0.00 46.19 1.47
7020 7791 7.494625 CGGTCAACATGACTTTACCTTGTATAT 59.505 37.037 0.00 0.00 46.19 0.86
7021 7792 9.826574 GGTCAACATGACTTTACCTTGTATATA 57.173 33.333 0.00 0.00 46.19 0.86
7107 7926 2.241880 AGACACGTCCGCAAAACCG 61.242 57.895 0.00 0.00 0.00 4.44
7128 7947 0.522626 CATCACGGAACATTGCAGCA 59.477 50.000 0.00 0.00 0.00 4.41
7129 7948 0.806868 ATCACGGAACATTGCAGCAG 59.193 50.000 0.00 0.00 0.00 4.24
7130 7949 1.443194 CACGGAACATTGCAGCAGC 60.443 57.895 0.00 0.00 42.57 5.25
7131 7950 2.202388 CGGAACATTGCAGCAGCG 60.202 61.111 0.00 0.00 46.23 5.18
7132 7951 2.956987 GGAACATTGCAGCAGCGT 59.043 55.556 0.00 0.00 46.23 5.07
7133 7952 1.634757 CGGAACATTGCAGCAGCGTA 61.635 55.000 0.00 0.00 46.23 4.42
7134 7953 0.734889 GGAACATTGCAGCAGCGTAT 59.265 50.000 0.00 0.00 46.23 3.06
7135 7954 1.939934 GGAACATTGCAGCAGCGTATA 59.060 47.619 0.00 0.00 46.23 1.47
7136 7955 2.032549 GGAACATTGCAGCAGCGTATAG 60.033 50.000 0.00 0.00 46.23 1.31
7137 7956 1.586422 ACATTGCAGCAGCGTATAGG 58.414 50.000 0.00 0.00 46.23 2.57
7138 7957 0.870393 CATTGCAGCAGCGTATAGGG 59.130 55.000 0.00 0.00 46.23 3.53
7139 7958 0.886490 ATTGCAGCAGCGTATAGGGC 60.886 55.000 0.00 0.00 46.23 5.19
7140 7959 2.108976 GCAGCAGCGTATAGGGCA 59.891 61.111 0.00 0.00 0.00 5.36
7141 7960 2.247437 GCAGCAGCGTATAGGGCAC 61.247 63.158 0.00 0.00 0.00 5.01
7208 8037 0.534412 AGAAGAGAGCACCGGTCATG 59.466 55.000 2.59 0.00 31.89 3.07
7388 8225 2.338620 TCGCAGAGACGTGTTGGG 59.661 61.111 0.00 0.00 0.00 4.12
7404 8241 0.044702 TGGGTGGGTCATCTGGATCT 59.955 55.000 0.00 0.00 0.00 2.75
7414 8251 3.387374 GTCATCTGGATCTCAGGACACAT 59.613 47.826 10.23 0.00 43.53 3.21
7415 8252 3.387050 TCATCTGGATCTCAGGACACATG 59.613 47.826 10.23 0.00 43.53 3.21
7416 8253 1.483827 TCTGGATCTCAGGACACATGC 59.516 52.381 10.23 0.00 43.53 4.06
7434 8271 2.970324 GGCGTTGCGTGTCCTCAA 60.970 61.111 0.00 0.00 0.00 3.02
7439 8276 0.232303 GTTGCGTGTCCTCAAAGACG 59.768 55.000 0.00 0.00 39.77 4.18
7459 8300 2.570135 GAAGGGGATAGCAAGCAAGAG 58.430 52.381 0.00 0.00 0.00 2.85
7465 8306 3.181446 GGGATAGCAAGCAAGAGGAGAAT 60.181 47.826 0.00 0.00 0.00 2.40
7469 8310 1.132643 GCAAGCAAGAGGAGAATGCAG 59.867 52.381 0.00 0.00 42.45 4.41
7475 8316 1.522580 GAGGAGAATGCAGGTCCGC 60.523 63.158 6.21 3.53 35.33 5.54
7506 8347 3.416119 GTGTATGACGATCCGAGACAA 57.584 47.619 0.00 0.00 0.00 3.18
7507 8348 3.966154 GTGTATGACGATCCGAGACAAT 58.034 45.455 0.00 0.00 0.00 2.71
7508 8349 3.731216 GTGTATGACGATCCGAGACAATG 59.269 47.826 0.00 0.00 0.00 2.82
7509 8350 3.380320 TGTATGACGATCCGAGACAATGT 59.620 43.478 0.00 0.00 0.00 2.71
7510 8351 3.526931 ATGACGATCCGAGACAATGTT 57.473 42.857 0.00 0.00 0.00 2.71
7512 8353 3.659786 TGACGATCCGAGACAATGTTTT 58.340 40.909 0.00 0.00 0.00 2.43
7533 8374 3.773418 TTTTGGGTGTAATCCGAGACA 57.227 42.857 0.00 0.00 0.00 3.41
7534 8375 3.773418 TTTGGGTGTAATCCGAGACAA 57.227 42.857 0.00 0.00 0.00 3.18
7535 8376 3.992943 TTGGGTGTAATCCGAGACAAT 57.007 42.857 0.00 0.00 0.00 2.71
7536 8377 5.423704 TTTGGGTGTAATCCGAGACAATA 57.576 39.130 0.00 0.00 0.00 1.90
7537 8378 5.623956 TTGGGTGTAATCCGAGACAATAT 57.376 39.130 0.00 0.00 0.00 1.28
7540 8381 8.425237 TTGGGTGTAATCCGAGACAATATATA 57.575 34.615 0.00 0.00 0.00 0.86
7544 8385 9.517609 GGTGTAATCCGAGACAATATATATGTC 57.482 37.037 14.90 14.90 45.94 3.06
7546 8387 9.250246 TGTAATCCGAGACAATATATATGTCCA 57.750 33.333 17.28 8.49 46.60 4.02
7547 8388 9.517609 GTAATCCGAGACAATATATATGTCCAC 57.482 37.037 17.28 13.20 46.60 4.02
7549 8390 5.708697 TCCGAGACAATATATATGTCCACGT 59.291 40.000 22.95 0.00 46.60 4.49
7558 8399 0.597072 TATGTCCACGTGTGTGCGTA 59.403 50.000 15.65 4.52 45.04 4.42
7559 8400 0.249531 ATGTCCACGTGTGTGCGTAA 60.250 50.000 15.65 0.00 45.04 3.18
7562 8403 0.876777 TCCACGTGTGTGCGTAAAGG 60.877 55.000 15.65 0.00 45.04 3.11
7581 8424 1.228644 TGCTTCTGGCCTTGTGCAT 60.229 52.632 3.32 0.00 43.89 3.96
7586 8429 0.983467 TCTGGCCTTGTGCATAGTCA 59.017 50.000 3.32 0.00 43.89 3.41
7609 8452 1.396996 CGGCCCGTGATCAACTTTTAG 59.603 52.381 0.00 0.00 0.00 1.85
7612 8455 1.743394 CCCGTGATCAACTTTTAGCCC 59.257 52.381 0.00 0.00 0.00 5.19
7616 8459 2.492088 GTGATCAACTTTTAGCCCACCC 59.508 50.000 0.00 0.00 0.00 4.61
7623 8485 2.916934 ACTTTTAGCCCACCCACTGATA 59.083 45.455 0.00 0.00 0.00 2.15
7625 8487 0.837272 TTAGCCCACCCACTGATAGC 59.163 55.000 0.00 0.00 0.00 2.97
7626 8488 1.399744 TAGCCCACCCACTGATAGCG 61.400 60.000 0.00 0.00 0.00 4.26
7632 8494 1.227380 CCCACTGATAGCGTCCTGC 60.227 63.158 0.00 0.00 46.98 4.85
7642 8504 3.152703 CGTCCTGCACGTAAACCG 58.847 61.111 0.00 0.00 44.07 4.44
7649 8511 2.267426 CTGCACGTAAACCGATGATCA 58.733 47.619 0.00 0.00 40.70 2.92
7651 8513 2.863740 TGCACGTAAACCGATGATCATC 59.136 45.455 23.42 23.42 40.70 2.92
7652 8514 2.221055 GCACGTAAACCGATGATCATCC 59.779 50.000 26.30 12.47 40.70 3.51
7653 8515 3.453424 CACGTAAACCGATGATCATCCA 58.547 45.455 26.30 7.19 40.70 3.41
7654 8516 3.490896 CACGTAAACCGATGATCATCCAG 59.509 47.826 26.30 20.54 40.70 3.86
7655 8517 3.132289 ACGTAAACCGATGATCATCCAGT 59.868 43.478 26.30 21.12 40.70 4.00
7656 8518 3.490896 CGTAAACCGATGATCATCCAGTG 59.509 47.826 26.30 15.97 39.56 3.66
7657 8519 2.627515 AACCGATGATCATCCAGTGG 57.372 50.000 26.30 22.81 34.40 4.00
7658 8520 1.793414 ACCGATGATCATCCAGTGGA 58.207 50.000 26.30 15.88 34.40 4.02
7659 8521 1.414181 ACCGATGATCATCCAGTGGAC 59.586 52.381 26.30 1.75 32.98 4.02
7665 8527 4.628963 TGATCATCCAGTGGACATATGG 57.371 45.455 15.86 0.25 32.98 2.74
7709 8583 0.250553 CAACCGGAAAGTGCTACCCA 60.251 55.000 9.46 0.00 0.00 4.51
7712 8586 0.879090 CCGGAAAGTGCTACCCAAAC 59.121 55.000 0.00 0.00 0.00 2.93
7713 8587 0.515564 CGGAAAGTGCTACCCAAACG 59.484 55.000 0.00 0.00 0.00 3.60
7714 8588 1.874739 CGGAAAGTGCTACCCAAACGA 60.875 52.381 0.00 0.00 0.00 3.85
7718 8592 2.457366 AGTGCTACCCAAACGAAGAG 57.543 50.000 0.00 0.00 0.00 2.85
7720 8594 1.001633 GTGCTACCCAAACGAAGAGGA 59.998 52.381 0.00 0.00 0.00 3.71
7723 8597 2.494870 GCTACCCAAACGAAGAGGACTA 59.505 50.000 0.00 0.00 0.00 2.59
7728 8602 3.179830 CCAAACGAAGAGGACTATCACG 58.820 50.000 0.00 0.00 0.00 4.35
7735 8609 0.249238 GAGGACTATCACGCTGCTGG 60.249 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.245732 AACTCGCCTAGTCAACGACT 58.754 50.000 1.75 1.75 45.54 4.18
95 96 3.363378 GCTCGCATCGACATTAATCTTGG 60.363 47.826 0.00 0.00 0.00 3.61
96 97 3.492383 AGCTCGCATCGACATTAATCTTG 59.508 43.478 0.00 0.00 0.00 3.02
209 210 4.489810 AGAGTTTCGCTACAGATGAACAG 58.510 43.478 0.00 0.00 0.00 3.16
217 218 3.060895 CCGCTAAAAGAGTTTCGCTACAG 59.939 47.826 0.00 0.00 34.19 2.74
220 221 2.028748 ACCCGCTAAAAGAGTTTCGCTA 60.029 45.455 0.00 0.00 34.19 4.26
224 231 6.985059 ACATATAGACCCGCTAAAAGAGTTTC 59.015 38.462 0.00 0.00 31.66 2.78
341 348 5.414454 CCCCAACGATTATCTTCAACTCAAA 59.586 40.000 0.00 0.00 0.00 2.69
357 364 2.434331 CTGAAAGGCCCCCAACGA 59.566 61.111 0.00 0.00 0.00 3.85
362 369 1.341976 TGAATAAGCTGAAAGGCCCCC 60.342 52.381 0.00 0.00 0.00 5.40
425 432 4.703379 AAATTTTGCAATCTCCCCAACA 57.297 36.364 0.00 0.00 0.00 3.33
430 437 6.616774 TTGAACAAAATTTTGCAATCTCCC 57.383 33.333 26.94 10.33 41.79 4.30
431 438 7.696755 AGTTTGAACAAAATTTTGCAATCTCC 58.303 30.769 26.94 12.16 41.79 3.71
483 490 9.674208 GTAAAAATCATTGTTGCATAATTGTCG 57.326 29.630 0.00 0.00 0.00 4.35
583 592 9.474920 CTAAAGCAATGTTGGTTATTTTCTTCA 57.525 29.630 10.22 0.00 46.98 3.02
607 616 5.416639 TCGACAATGGTTAGTTAGAGTGCTA 59.583 40.000 0.00 0.00 0.00 3.49
617 626 5.048991 GGTCAATTTGTCGACAATGGTTAGT 60.049 40.000 30.10 12.59 35.55 2.24
645 654 9.504710 TTGATTTTTCATGCAAAAAGTCAATTG 57.495 25.926 21.27 0.00 45.20 2.32
646 655 9.724839 CTTGATTTTTCATGCAAAAAGTCAATT 57.275 25.926 23.51 2.14 45.54 2.32
658 667 9.537192 TGGATTTATGATCTTGATTTTTCATGC 57.463 29.630 0.00 0.00 31.59 4.06
667 676 7.723172 GGAGGAGTTTGGATTTATGATCTTGAT 59.277 37.037 0.00 0.00 0.00 2.57
672 681 9.660180 GTATAGGAGGAGTTTGGATTTATGATC 57.340 37.037 0.00 0.00 0.00 2.92
692 701 5.183522 TGTTTTTAAAGGTTGGCCGTATAGG 59.816 40.000 0.00 0.00 44.97 2.57
712 721 9.515226 AGATTGTGTATTTACTGGTATGTGTTT 57.485 29.630 0.00 0.00 0.00 2.83
713 722 9.515226 AAGATTGTGTATTTACTGGTATGTGTT 57.485 29.630 0.00 0.00 0.00 3.32
752 761 4.385358 TGCTTCTTTGGGAGTTTTTCAC 57.615 40.909 0.00 0.00 0.00 3.18
762 771 4.813750 ATCCTTTGATTGCTTCTTTGGG 57.186 40.909 0.00 0.00 0.00 4.12
821 841 6.605594 TGAGTGAGGGACTTGTTTGTAATTTT 59.394 34.615 0.00 0.00 41.55 1.82
923 943 2.770475 GGAAGAGGGAGAGGGGGC 60.770 72.222 0.00 0.00 0.00 5.80
935 967 0.544357 TTTGGAGCGGGAGAGGAAGA 60.544 55.000 0.00 0.00 0.00 2.87
936 968 0.391793 GTTTGGAGCGGGAGAGGAAG 60.392 60.000 0.00 0.00 0.00 3.46
937 969 1.677552 GTTTGGAGCGGGAGAGGAA 59.322 57.895 0.00 0.00 0.00 3.36
938 970 2.291043 GGTTTGGAGCGGGAGAGGA 61.291 63.158 0.00 0.00 0.00 3.71
939 971 2.269241 GGTTTGGAGCGGGAGAGG 59.731 66.667 0.00 0.00 0.00 3.69
940 972 0.976073 TAGGGTTTGGAGCGGGAGAG 60.976 60.000 0.00 0.00 0.00 3.20
941 973 0.545787 TTAGGGTTTGGAGCGGGAGA 60.546 55.000 0.00 0.00 0.00 3.71
942 974 0.392595 GTTAGGGTTTGGAGCGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
943 975 1.681076 GTTAGGGTTTGGAGCGGGA 59.319 57.895 0.00 0.00 0.00 5.14
944 976 1.378119 GGTTAGGGTTTGGAGCGGG 60.378 63.158 0.00 0.00 0.00 6.13
945 977 1.743995 CGGTTAGGGTTTGGAGCGG 60.744 63.158 0.00 0.00 0.00 5.52
946 978 2.396157 GCGGTTAGGGTTTGGAGCG 61.396 63.158 0.00 0.00 36.23 5.03
947 979 1.302993 TGCGGTTAGGGTTTGGAGC 60.303 57.895 0.00 0.00 0.00 4.70
1042 1074 2.202623 GTGCGCGAGTCACTAGGG 60.203 66.667 12.10 0.00 35.96 3.53
1045 1077 3.755628 GGGGTGCGCGAGTCACTA 61.756 66.667 12.10 0.00 37.94 2.74
1190 1227 3.015332 GCCTCCTCCTCCCTCCTCA 62.015 68.421 0.00 0.00 0.00 3.86
1433 1470 1.374252 ACGCAGCGGAGAAACGAAT 60.374 52.632 21.15 0.00 35.47 3.34
1449 1486 5.638721 GCTACGAGCAAAATGTGAAACACG 61.639 45.833 0.00 0.00 46.71 4.49
1450 1487 3.664025 GCTACGAGCAAAATGTGAAACAC 59.336 43.478 0.00 0.00 46.71 3.32
1467 1504 1.996191 GAAGCAGAGACCAAAGCTACG 59.004 52.381 0.00 0.00 36.07 3.51
1665 1718 1.409661 CCCCCAGCTACCAATTACCAC 60.410 57.143 0.00 0.00 0.00 4.16
1666 1719 0.923358 CCCCCAGCTACCAATTACCA 59.077 55.000 0.00 0.00 0.00 3.25
1667 1720 0.467474 GCCCCCAGCTACCAATTACC 60.467 60.000 0.00 0.00 38.99 2.85
1672 1729 3.712907 GTCGCCCCCAGCTACCAA 61.713 66.667 0.00 0.00 40.39 3.67
1778 1838 3.746045 TGGTCCACTGAGACTAACAAC 57.254 47.619 0.00 0.00 36.95 3.32
2017 2081 7.278868 AGCAATATGTAGCTGAAAAGTAGACAC 59.721 37.037 0.00 0.00 40.13 3.67
2092 2156 4.611310 ATGAAGTTCGATGCAATGTGAG 57.389 40.909 0.00 0.00 0.00 3.51
2101 2165 5.281727 TCGACCATCTAATGAAGTTCGATG 58.718 41.667 10.06 10.06 38.86 3.84
2133 2206 1.819928 ACGTATCAACAGCATGGCAA 58.180 45.000 0.00 0.00 43.62 4.52
2134 2207 1.819928 AACGTATCAACAGCATGGCA 58.180 45.000 0.00 0.00 43.62 4.92
2173 2258 6.500910 GGTTTCAACCTGTTACTAACCTTTG 58.499 40.000 1.08 0.00 45.75 2.77
2191 2276 9.770097 TGTTAGAAAAATAATGCATTGGTTTCA 57.230 25.926 27.81 17.22 0.00 2.69
2242 2327 7.537596 TTCATTGATGAAACCATTTACAGGT 57.462 32.000 4.02 0.00 43.26 4.00
2295 2380 4.448537 TGTACACAAGTTGCAGCTTTTT 57.551 36.364 13.69 0.53 0.00 1.94
2296 2381 4.654091 ATGTACACAAGTTGCAGCTTTT 57.346 36.364 13.69 4.40 0.00 2.27
2297 2382 5.063204 TCTATGTACACAAGTTGCAGCTTT 58.937 37.500 13.69 2.05 0.00 3.51
2298 2383 4.641396 TCTATGTACACAAGTTGCAGCTT 58.359 39.130 10.35 10.35 0.00 3.74
2299 2384 4.271696 TCTATGTACACAAGTTGCAGCT 57.728 40.909 1.81 0.00 0.00 4.24
2304 2389 5.122869 AGCAAGCATCTATGTACACAAGTTG 59.877 40.000 0.00 0.00 0.00 3.16
2330 2415 7.715265 ATATGCGGAAACTGATAACTTAGTG 57.285 36.000 0.00 0.00 0.00 2.74
2339 2424 8.103305 AGGTGATATTTATATGCGGAAACTGAT 58.897 33.333 0.00 0.00 0.00 2.90
2382 2468 8.922058 AAGAGCAATGATTGAACACAATATTC 57.078 30.769 9.76 0.00 34.86 1.75
2479 2566 5.053811 TGTTTTTCAACATCACGAGCTCTA 58.946 37.500 12.85 0.00 38.03 2.43
2492 2579 6.753744 AGAGCAACAATCTTCTGTTTTTCAAC 59.246 34.615 0.00 0.00 37.43 3.18
2540 2627 1.536073 TTCACACTCTCGGGCTCCAG 61.536 60.000 0.00 0.00 0.00 3.86
2725 2812 1.789523 TACCATGTACCTGAGGCTCC 58.210 55.000 12.86 0.00 0.00 4.70
2749 2836 0.967380 GCACTAAGCACCCCTGCATT 60.967 55.000 0.00 0.00 46.97 3.56
2925 3012 5.071250 ACCCTTAATATCACGGTGCAGAATA 59.929 40.000 2.51 0.00 0.00 1.75
3617 3707 4.096833 ACGGTGAAAAAGTAAGTTGGGAAC 59.903 41.667 0.00 0.00 0.00 3.62
3656 3746 3.997021 ACGGTTCAAGCTTCAATCACTAG 59.003 43.478 0.00 0.00 0.00 2.57
3833 3930 4.351874 AATGGTGACTCTCGGAGAAAAA 57.648 40.909 9.32 0.00 34.09 1.94
3836 3933 2.233922 GGAAATGGTGACTCTCGGAGAA 59.766 50.000 9.32 0.00 34.09 2.87
3841 3938 4.457834 AAGTAGGAAATGGTGACTCTCG 57.542 45.455 0.00 0.00 0.00 4.04
3883 3980 4.762289 ACCAATTGCACCCAACTAAAAA 57.238 36.364 0.00 0.00 32.95 1.94
3903 4000 8.762426 GTTTATAACTATCGTCCTTGATCCAAC 58.238 37.037 0.00 0.00 0.00 3.77
4046 4145 7.092891 TGGATGGTATCATAGGGTAGCATTTAG 60.093 40.741 13.09 0.00 38.66 1.85
4280 4379 2.955660 AGAACCTTCATCCGAGCTCTAG 59.044 50.000 12.85 3.01 0.00 2.43
4288 4387 1.363744 GTCAGCAGAACCTTCATCCG 58.636 55.000 0.00 0.00 0.00 4.18
4418 4518 4.367042 GGCTACAGCAAGTTAGGCAAACT 61.367 47.826 3.24 0.00 43.40 2.66
4419 4519 2.095212 GGCTACAGCAAGTTAGGCAAAC 60.095 50.000 3.24 0.00 44.36 2.93
4420 4520 2.159382 GGCTACAGCAAGTTAGGCAAA 58.841 47.619 3.24 0.00 44.36 3.68
4421 4521 1.613255 GGGCTACAGCAAGTTAGGCAA 60.613 52.381 3.24 0.00 44.36 4.52
4433 4534 5.536161 ACCAAAGCAAATATATGGGCTACAG 59.464 40.000 10.75 6.26 35.11 2.74
4434 4535 5.454062 ACCAAAGCAAATATATGGGCTACA 58.546 37.500 10.75 0.00 35.11 2.74
4462 4577 9.120538 ACAAACTGTACAGATAAGTTCATGTTT 57.879 29.630 29.30 11.99 33.09 2.83
4475 4590 4.764050 TCTTCCCAACAAACTGTACAGA 57.236 40.909 29.30 0.36 0.00 3.41
4553 4671 5.843019 AAATGTGGGTCTAGAAGGAGAAA 57.157 39.130 0.00 0.00 0.00 2.52
4727 4967 5.468746 GGAACATAATAACTATCCGCTGCAA 59.531 40.000 0.00 0.00 0.00 4.08
4816 5056 2.412870 TGACGGCAACAGAATACACAG 58.587 47.619 0.00 0.00 0.00 3.66
4842 5082 8.081633 CAGTGTGGCATTTAGAAAAGTGAATAA 58.918 33.333 0.00 0.00 0.00 1.40
4860 5100 1.003580 TGAAGAAGATCCCAGTGTGGC 59.996 52.381 0.00 0.00 35.79 5.01
4886 5126 9.016438 CCAGCCAACTATACCTACTTTTTAAAA 57.984 33.333 0.00 0.00 0.00 1.52
4936 5554 8.891928 CAACAGAATACACACTTTGTTTAATCG 58.108 33.333 0.00 0.00 39.91 3.34
5051 5673 8.433421 TGAAGGTGTAAAAGTCTAAAAGAGTG 57.567 34.615 0.00 0.00 0.00 3.51
5069 5691 7.563888 ACATATGAAATGAGTCATGAAGGTG 57.436 36.000 10.38 4.98 38.69 4.00
5070 5692 8.464404 CAAACATATGAAATGAGTCATGAAGGT 58.536 33.333 10.38 0.00 38.69 3.50
5155 5781 6.507023 ACACAAGCCTATTTCTTTTTCACTG 58.493 36.000 0.00 0.00 0.00 3.66
5356 5992 8.590204 TCAACAACCACAAGACTATATTCAGTA 58.410 33.333 0.00 0.00 0.00 2.74
5407 6053 9.840427 ATTACGAGTGGAAACATAATTTCAAAG 57.160 29.630 0.00 0.00 46.14 2.77
5578 6227 6.340522 ACAGCATAATTTAGGCATTCCAAAC 58.659 36.000 14.75 0.00 38.06 2.93
5607 6257 1.963515 GGGCTTGCCTCTTCTGAAAAA 59.036 47.619 11.71 0.00 0.00 1.94
5734 6384 1.410004 AGACGTGTTTGGAGTCTCCA 58.590 50.000 18.15 18.15 46.61 3.86
5913 6563 2.076863 CTTCAGCTTGAGTAAACCCGG 58.923 52.381 0.00 0.00 0.00 5.73
5956 6606 3.126831 GTGCCCGTTGATAGATTCAGAG 58.873 50.000 0.00 0.00 35.27 3.35
6034 6684 3.016971 CCTCCATCCACCCTGCCA 61.017 66.667 0.00 0.00 0.00 4.92
6055 6705 5.303333 ACAAGTTTGGGGGTAACTTACAATG 59.697 40.000 0.00 0.00 42.32 2.82
6065 6715 1.154221 GGGCACAAGTTTGGGGGTA 59.846 57.895 0.00 0.00 30.51 3.69
6067 6717 1.764054 TTGGGCACAAGTTTGGGGG 60.764 57.895 0.00 0.00 31.73 5.40
6153 6803 7.484975 ACGGTATTTTGATTTCAAACAAGTGA 58.515 30.769 5.26 0.00 44.56 3.41
6185 6859 8.255905 GCTGGATACGTACAAATTATACCCTAT 58.744 37.037 0.00 0.00 42.51 2.57
6201 6875 3.067106 CAGAACAACTTGCTGGATACGT 58.933 45.455 0.00 0.00 42.51 3.57
6361 7077 2.238521 TGGTGGATCTTGTTGCCTTTC 58.761 47.619 0.00 0.00 0.00 2.62
6418 7134 1.839424 TCTCCTTGAGCATCTCGTCA 58.161 50.000 0.00 0.00 34.92 4.35
6475 7191 0.112606 TCACCCTCGACTTCTCCACT 59.887 55.000 0.00 0.00 0.00 4.00
6523 7245 1.228894 ACCGAAGTCTCTCAGGCCA 60.229 57.895 5.01 0.00 0.00 5.36
6544 7266 0.104672 TGGAAGGGAAGACTGGGACA 60.105 55.000 0.00 0.00 0.00 4.02
6550 7272 2.960688 GCGGCTGGAAGGGAAGACT 61.961 63.158 0.00 0.00 0.00 3.24
6596 7321 2.277591 CCCACACGTCCCCGACTTA 61.278 63.158 0.00 0.00 37.88 2.24
6781 7538 4.111255 TCACCTCCCAATCAACAAATCA 57.889 40.909 0.00 0.00 0.00 2.57
6871 7636 1.233285 GCACACTCCAAGCTCACCAG 61.233 60.000 0.00 0.00 0.00 4.00
6872 7637 1.227943 GCACACTCCAAGCTCACCA 60.228 57.895 0.00 0.00 0.00 4.17
6874 7639 1.227943 TGGCACACTCCAAGCTCAC 60.228 57.895 0.00 0.00 32.18 3.51
6875 7640 3.239464 TGGCACACTCCAAGCTCA 58.761 55.556 0.00 0.00 32.18 4.26
6901 7666 3.922240 TCGGTTTCTAGCGTCATTAACAC 59.078 43.478 0.00 0.00 45.09 3.32
6906 7671 1.549170 AGGTCGGTTTCTAGCGTCATT 59.451 47.619 0.00 0.00 45.09 2.57
6912 7677 1.477295 AGCTACAGGTCGGTTTCTAGC 59.523 52.381 0.00 0.00 0.00 3.42
6930 7695 3.503363 GCTCGTGCCCATCACAGC 61.503 66.667 0.00 0.00 45.92 4.40
6970 7741 2.573009 TCATCAGCCAAAGTGATCCAGA 59.427 45.455 0.00 0.00 32.06 3.86
6999 7770 9.847224 CCCTTATATACAAGGTAAAGTCATGTT 57.153 33.333 8.96 0.00 43.14 2.71
7001 7772 8.157476 AGCCCTTATATACAAGGTAAAGTCATG 58.843 37.037 8.96 0.00 43.14 3.07
7002 7773 8.276453 AGCCCTTATATACAAGGTAAAGTCAT 57.724 34.615 8.96 0.00 43.14 3.06
7003 7774 7.685849 AGCCCTTATATACAAGGTAAAGTCA 57.314 36.000 8.96 0.00 43.14 3.41
7004 7775 8.868103 AGTAGCCCTTATATACAAGGTAAAGTC 58.132 37.037 8.96 0.00 43.14 3.01
7005 7776 8.794364 AGTAGCCCTTATATACAAGGTAAAGT 57.206 34.615 8.96 0.00 43.14 2.66
7006 7777 9.490379 CAAGTAGCCCTTATATACAAGGTAAAG 57.510 37.037 8.96 0.00 43.14 1.85
7007 7778 8.995577 ACAAGTAGCCCTTATATACAAGGTAAA 58.004 33.333 8.96 0.00 43.14 2.01
7008 7779 8.557304 ACAAGTAGCCCTTATATACAAGGTAA 57.443 34.615 8.96 0.00 43.14 2.85
7009 7780 8.557304 AACAAGTAGCCCTTATATACAAGGTA 57.443 34.615 8.96 0.00 43.14 3.08
7010 7781 7.447510 AACAAGTAGCCCTTATATACAAGGT 57.552 36.000 8.96 0.00 43.14 3.50
7011 7782 8.747538 AAAACAAGTAGCCCTTATATACAAGG 57.252 34.615 2.51 2.51 44.11 3.61
7064 7835 6.423302 TGCGTCAGGTTTTTCGTAAGTTTATA 59.577 34.615 0.00 0.00 39.48 0.98
7065 7836 5.236911 TGCGTCAGGTTTTTCGTAAGTTTAT 59.763 36.000 0.00 0.00 39.48 1.40
7107 7926 0.179156 CTGCAATGTTCCGTGATGCC 60.179 55.000 0.00 0.00 36.20 4.40
7108 7927 0.799534 GCTGCAATGTTCCGTGATGC 60.800 55.000 0.00 0.00 37.52 3.91
7128 7947 2.808206 GCCCTGTGCCCTATACGCT 61.808 63.158 0.00 0.00 0.00 5.07
7129 7948 2.280865 GCCCTGTGCCCTATACGC 60.281 66.667 0.00 0.00 0.00 4.42
7130 7949 1.227556 GTGCCCTGTGCCCTATACG 60.228 63.158 0.00 0.00 40.16 3.06
7131 7950 0.179045 CTGTGCCCTGTGCCCTATAC 60.179 60.000 0.00 0.00 40.16 1.47
7132 7951 1.344953 CCTGTGCCCTGTGCCCTATA 61.345 60.000 0.00 0.00 40.16 1.31
7133 7952 2.683465 CCTGTGCCCTGTGCCCTAT 61.683 63.158 0.00 0.00 40.16 2.57
7134 7953 3.329889 CCTGTGCCCTGTGCCCTA 61.330 66.667 0.00 0.00 40.16 3.53
7208 8037 0.464036 TAGTGCGATGGGTGATGACC 59.536 55.000 0.00 0.00 42.27 4.02
7367 8204 3.195591 AACACGTCTCTGCGAGCGT 62.196 57.895 15.78 15.78 40.67 5.07
7385 8222 0.044702 AGATCCAGATGACCCACCCA 59.955 55.000 0.00 0.00 0.00 4.51
7386 8223 0.761802 GAGATCCAGATGACCCACCC 59.238 60.000 0.00 0.00 0.00 4.61
7387 8224 1.415659 CTGAGATCCAGATGACCCACC 59.584 57.143 5.53 0.00 45.78 4.61
7388 8225 1.415659 CCTGAGATCCAGATGACCCAC 59.584 57.143 11.48 0.00 45.78 4.61
7404 8241 3.529341 AACGCCGCATGTGTCCTGA 62.529 57.895 5.38 0.00 36.45 3.86
7434 8271 1.134371 GCTTGCTATCCCCTTCGTCTT 60.134 52.381 0.00 0.00 0.00 3.01
7439 8276 2.570135 CTCTTGCTTGCTATCCCCTTC 58.430 52.381 0.00 0.00 0.00 3.46
7459 8300 1.078143 AAGCGGACCTGCATTCTCC 60.078 57.895 10.28 0.00 37.31 3.71
7465 8306 2.747460 GCATGAAGCGGACCTGCA 60.747 61.111 0.00 0.00 37.31 4.41
7475 8316 2.979006 GTCATACACGACGCATGAAG 57.021 50.000 0.00 0.00 30.85 3.02
7489 8330 4.649088 AACATTGTCTCGGATCGTCATA 57.351 40.909 0.00 0.00 0.00 2.15
7512 8353 4.088056 TGTCTCGGATTACACCCAAAAA 57.912 40.909 0.00 0.00 0.00 1.94
7514 8355 3.773418 TTGTCTCGGATTACACCCAAA 57.227 42.857 0.00 0.00 0.00 3.28
7515 8356 3.992943 ATTGTCTCGGATTACACCCAA 57.007 42.857 0.00 0.00 0.00 4.12
7516 8357 6.928348 ATATATTGTCTCGGATTACACCCA 57.072 37.500 0.00 0.00 0.00 4.51
7517 8358 8.475639 ACATATATATTGTCTCGGATTACACCC 58.524 37.037 0.00 0.00 0.00 4.61
7519 8360 9.517609 GGACATATATATTGTCTCGGATTACAC 57.482 37.037 18.89 4.43 42.48 2.90
7520 8361 9.250246 TGGACATATATATTGTCTCGGATTACA 57.750 33.333 18.89 9.47 42.48 2.41
7521 8362 9.517609 GTGGACATATATATTGTCTCGGATTAC 57.482 37.037 18.89 7.90 42.48 1.89
7522 8363 8.403236 CGTGGACATATATATTGTCTCGGATTA 58.597 37.037 18.89 4.55 42.48 1.75
7523 8364 7.093902 ACGTGGACATATATATTGTCTCGGATT 60.094 37.037 24.88 15.26 42.48 3.01
7524 8365 6.377429 ACGTGGACATATATATTGTCTCGGAT 59.623 38.462 24.88 15.60 42.48 4.18
7525 8366 5.708697 ACGTGGACATATATATTGTCTCGGA 59.291 40.000 24.88 12.16 42.48 4.55
7526 8367 5.800438 CACGTGGACATATATATTGTCTCGG 59.200 44.000 24.88 17.60 42.48 4.63
7527 8368 6.305638 CACACGTGGACATATATATTGTCTCG 59.694 42.308 21.57 22.84 42.48 4.04
7528 8369 7.114953 CACACACGTGGACATATATATTGTCTC 59.885 40.741 21.57 13.26 42.48 3.36
7529 8370 6.923508 CACACACGTGGACATATATATTGTCT 59.076 38.462 21.57 0.00 42.48 3.41
7530 8371 6.346598 GCACACACGTGGACATATATATTGTC 60.347 42.308 21.57 14.59 43.81 3.18
7531 8372 5.465390 GCACACACGTGGACATATATATTGT 59.535 40.000 21.57 7.34 43.81 2.71
7532 8373 5.388371 CGCACACACGTGGACATATATATTG 60.388 44.000 21.57 6.67 43.81 1.90
7533 8374 4.684242 CGCACACACGTGGACATATATATT 59.316 41.667 21.57 0.00 43.81 1.28
7534 8375 4.234574 CGCACACACGTGGACATATATAT 58.765 43.478 21.57 0.00 43.81 0.86
7535 8376 3.067040 ACGCACACACGTGGACATATATA 59.933 43.478 21.57 0.00 46.28 0.86
7536 8377 2.159156 ACGCACACACGTGGACATATAT 60.159 45.455 21.57 0.00 46.28 0.86
7537 8378 1.202817 ACGCACACACGTGGACATATA 59.797 47.619 21.57 0.00 46.28 0.86
7540 8381 2.108157 ACGCACACACGTGGACAT 59.892 55.556 21.57 0.00 46.28 3.06
7547 8388 1.083015 GCACCTTTACGCACACACG 60.083 57.895 0.00 0.00 39.50 4.49
7549 8390 0.941542 GAAGCACCTTTACGCACACA 59.058 50.000 0.00 0.00 0.00 3.72
7558 8399 0.106015 ACAAGGCCAGAAGCACCTTT 60.106 50.000 5.01 0.00 46.50 3.11
7559 8400 0.825010 CACAAGGCCAGAAGCACCTT 60.825 55.000 5.01 0.00 46.50 3.50
7562 8403 1.530013 ATGCACAAGGCCAGAAGCAC 61.530 55.000 13.93 0.00 46.50 4.40
7609 8452 2.203070 CGCTATCAGTGGGTGGGC 60.203 66.667 0.00 0.00 0.00 5.36
7612 8455 0.179100 CAGGACGCTATCAGTGGGTG 60.179 60.000 0.00 0.00 0.00 4.61
7616 8459 1.142185 CGTGCAGGACGCTATCAGTG 61.142 60.000 0.00 0.00 42.21 3.66
7626 8488 0.719465 CATCGGTTTACGTGCAGGAC 59.281 55.000 14.38 0.46 44.69 3.85
7632 8494 3.453424 TGGATGATCATCGGTTTACGTG 58.547 45.455 25.60 0.00 44.69 4.49
7634 8496 3.490896 CACTGGATGATCATCGGTTTACG 59.509 47.826 25.60 12.83 46.11 3.18
7639 8501 1.414181 GTCCACTGGATGATCATCGGT 59.586 52.381 25.60 22.62 38.69 4.69
7642 8504 5.046087 TCCATATGTCCACTGGATGATCATC 60.046 44.000 24.90 24.90 34.17 2.92
7649 8511 2.103094 CGTGTCCATATGTCCACTGGAT 59.897 50.000 15.80 0.00 40.96 3.41
7651 8513 1.480545 TCGTGTCCATATGTCCACTGG 59.519 52.381 15.80 0.00 0.00 4.00
7652 8514 2.166459 ACTCGTGTCCATATGTCCACTG 59.834 50.000 15.80 11.99 0.00 3.66
7653 8515 2.166459 CACTCGTGTCCATATGTCCACT 59.834 50.000 15.80 0.66 0.00 4.00
7654 8516 2.540515 CACTCGTGTCCATATGTCCAC 58.459 52.381 1.24 6.91 0.00 4.02
7655 8517 1.480545 CCACTCGTGTCCATATGTCCA 59.519 52.381 1.24 0.00 0.00 4.02
7656 8518 1.806623 GCCACTCGTGTCCATATGTCC 60.807 57.143 1.24 0.00 0.00 4.02
7657 8519 1.571919 GCCACTCGTGTCCATATGTC 58.428 55.000 1.24 0.00 0.00 3.06
7658 8520 0.178068 GGCCACTCGTGTCCATATGT 59.822 55.000 0.00 0.00 0.00 2.29
7659 8521 0.177836 TGGCCACTCGTGTCCATATG 59.822 55.000 0.00 0.00 0.00 1.78
7677 8544 3.047877 GGTTGGTTCCGGCGAGTG 61.048 66.667 9.30 0.00 0.00 3.51
7709 8583 2.492484 AGCGTGATAGTCCTCTTCGTTT 59.508 45.455 0.00 0.00 0.00 3.60
7712 8586 1.862008 GCAGCGTGATAGTCCTCTTCG 60.862 57.143 0.00 0.00 0.00 3.79
7713 8587 1.407258 AGCAGCGTGATAGTCCTCTTC 59.593 52.381 0.00 0.00 0.00 2.87
7714 8588 1.135915 CAGCAGCGTGATAGTCCTCTT 59.864 52.381 0.00 0.00 0.00 2.85
7718 8592 1.227380 CCCAGCAGCGTGATAGTCC 60.227 63.158 0.00 0.00 0.00 3.85
7720 8594 1.191535 TAACCCAGCAGCGTGATAGT 58.808 50.000 0.00 0.00 0.00 2.12
7723 8597 1.019278 CGTTAACCCAGCAGCGTGAT 61.019 55.000 0.00 0.00 0.00 3.06
7728 8602 2.124122 CAAAAACGTTAACCCAGCAGC 58.876 47.619 0.00 0.00 0.00 5.25
7735 8609 1.267982 ACGGCGACAAAAACGTTAACC 60.268 47.619 16.62 0.00 35.90 2.85


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

AutoCloner maintained by Alex Coulton.