Multiple sequence alignment - TraesCS4D01G105600

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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 TraesCS4D01G105600 chr4D 100.000 4543 0 0 1 4543 84275822 84280364 0.000000e+00 8390.0
1 TraesCS4D01G105600 chr4D 95.349 86 4 0 243 328 134953846 134953931 2.200000e-28 137.0
2 TraesCS4D01G105600 chr4A 93.617 3384 127 40 764 4102 497010359 497013698 0.000000e+00 4970.0
3 TraesCS4D01G105600 chr4A 86.019 422 40 8 1193 1600 661867029 661866613 6.980000e-118 435.0
4 TraesCS4D01G105600 chr4A 89.716 282 24 3 4262 4540 497013747 497014026 5.590000e-94 355.0
5 TraesCS4D01G105600 chr4A 89.496 238 19 4 328 564 497007657 497007889 3.440000e-76 296.0
6 TraesCS4D01G105600 chr4A 86.638 232 16 6 49 273 497004554 497004777 4.540000e-60 243.0
7 TraesCS4D01G105600 chr4A 95.745 47 1 1 732 778 497009114 497009159 1.750000e-09 75.0
8 TraesCS4D01G105600 chr4B 90.808 1523 86 18 1869 3360 119274714 119276213 0.000000e+00 1988.0
9 TraesCS4D01G105600 chr4B 85.453 1203 77 37 732 1880 119273483 119274641 0.000000e+00 1162.0
10 TraesCS4D01G105600 chr4B 87.941 680 49 21 3391 4054 119276198 119276860 0.000000e+00 771.0
11 TraesCS4D01G105600 chr4B 91.200 500 31 9 104 593 119272157 119272653 0.000000e+00 667.0
12 TraesCS4D01G105600 chr4B 100.000 42 0 0 1 42 119272070 119272111 1.360000e-10 78.7
13 TraesCS4D01G105600 chr4B 85.455 55 4 1 612 666 119273064 119273114 2.000000e-03 54.7
14 TraesCS4D01G105600 chr1A 86.047 516 70 2 2291 2805 114545530 114546044 1.850000e-153 553.0
15 TraesCS4D01G105600 chr1B 85.853 516 71 2 2291 2805 167713497 167714011 8.590000e-152 547.0
16 TraesCS4D01G105600 chr1D 85.659 516 72 2 2291 2805 110335417 110335931 4.000000e-150 542.0
17 TraesCS4D01G105600 chr2D 85.915 213 27 3 4282 4493 196966301 196966511 1.640000e-54 224.0
18 TraesCS4D01G105600 chr7B 84.651 215 26 6 4282 4493 90402925 90403135 1.660000e-49 207.0
19 TraesCS4D01G105600 chr6B 93.023 86 5 1 243 328 85137436 85137352 1.720000e-24 124.0


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 TraesCS4D01G105600 chr4D 84275822 84280364 4542 False 8390.0 8390 100.000000 1 4543 1 chr4D.!!$F1 4542
1 TraesCS4D01G105600 chr4A 497004554 497014026 9472 False 1187.8 4970 91.042400 49 4540 5 chr4A.!!$F1 4491
2 TraesCS4D01G105600 chr4B 119272070 119276860 4790 False 786.9 1988 90.142833 1 4054 6 chr4B.!!$F1 4053
3 TraesCS4D01G105600 chr1A 114545530 114546044 514 False 553.0 553 86.047000 2291 2805 1 chr1A.!!$F1 514
4 TraesCS4D01G105600 chr1B 167713497 167714011 514 False 547.0 547 85.853000 2291 2805 1 chr1B.!!$F1 514
5 TraesCS4D01G105600 chr1D 110335417 110335931 514 False 542.0 542 85.659000 2291 2805 1 chr1D.!!$F1 514

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
99 123 0.179073 AAACCAGATCGCGGGATGAG 60.179 55.0 20.80 11.30 31.51 2.90 F
715 5363 0.306533 GGCGACACGTGTCATGTTTT 59.693 50.0 39.14 10.09 44.99 2.43 F
1189 7083 0.172578 ATGTCGATGCGAGTTCCGAA 59.827 50.0 0.00 0.00 41.76 4.30 F
2691 8725 1.039856 GTGTGGACATTGGCCAAGTT 58.960 50.0 24.94 13.02 37.12 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1074 6963 0.389296 ACATCGCACGGATCGAAACA 60.389 50.000 0.00 0.0 39.54 2.83 R
2694 8728 0.742281 CCTTGCAGCGCACAGATAGT 60.742 55.000 11.47 0.0 38.71 2.12 R
2769 8803 2.009774 CGAATGATCTTTTGACGGCCT 58.990 47.619 0.00 0.0 0.00 5.19 R
4080 10142 0.036164 AACACAGGCACGGCTTCATA 59.964 50.000 0.00 0.0 0.00 2.15 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
42 43 0.758734 CCAGTAATGGCATCGAGGGA 59.241 55.000 0.00 0.00 0.00 4.20
43 44 1.270518 CCAGTAATGGCATCGAGGGAG 60.271 57.143 0.00 0.00 0.00 4.30
44 45 1.414181 CAGTAATGGCATCGAGGGAGT 59.586 52.381 0.00 0.00 0.00 3.85
45 46 2.628178 CAGTAATGGCATCGAGGGAGTA 59.372 50.000 0.00 0.00 0.00 2.59
46 47 2.628657 AGTAATGGCATCGAGGGAGTAC 59.371 50.000 0.00 0.00 0.00 2.73
47 48 0.759346 AATGGCATCGAGGGAGTACC 59.241 55.000 0.00 0.00 40.67 3.34
77 101 4.292178 CCCTGCTCGAGATCCCGC 62.292 72.222 18.75 0.00 0.00 6.13
78 102 4.637489 CCTGCTCGAGATCCCGCG 62.637 72.222 18.75 0.00 36.92 6.46
79 103 3.586961 CTGCTCGAGATCCCGCGA 61.587 66.667 18.75 0.00 42.09 5.87
80 104 3.126074 CTGCTCGAGATCCCGCGAA 62.126 63.158 18.75 0.00 43.56 4.70
81 105 2.104331 GCTCGAGATCCCGCGAAA 59.896 61.111 18.75 0.00 43.56 3.46
82 106 1.518572 GCTCGAGATCCCGCGAAAA 60.519 57.895 18.75 0.00 43.56 2.29
83 107 1.753468 GCTCGAGATCCCGCGAAAAC 61.753 60.000 18.75 0.00 43.56 2.43
84 108 1.146358 CTCGAGATCCCGCGAAAACC 61.146 60.000 8.23 0.00 43.56 3.27
85 109 1.447140 CGAGATCCCGCGAAAACCA 60.447 57.895 8.23 0.00 37.82 3.67
99 123 0.179073 AAACCAGATCGCGGGATGAG 60.179 55.000 20.80 11.30 31.51 2.90
104 128 1.666234 GATCGCGGGATGAGAAGGC 60.666 63.158 20.80 0.00 31.51 4.35
130 155 5.482878 AGAATCCTCTGCATTTGGTTCAAAT 59.517 36.000 0.54 0.54 43.71 2.32
230 260 4.825085 ACTCGCACCTCCTTTTCAAATTAA 59.175 37.500 0.00 0.00 0.00 1.40
237 267 7.010460 GCACCTCCTTTTCAAATTAATATGCAC 59.990 37.037 0.00 0.00 0.00 4.57
241 271 9.352784 CTCCTTTTCAAATTAATATGCACGAAA 57.647 29.630 0.00 0.00 0.00 3.46
333 3188 6.262496 ACATAAATAGACGAATGAGACTCGGA 59.738 38.462 0.00 0.00 40.64 4.55
344 3199 6.183360 CGAATGAGACTCGGAAATTCATTGAA 60.183 38.462 0.75 0.75 38.28 2.69
347 3202 5.106555 TGAGACTCGGAAATTCATTGAAAGC 60.107 40.000 2.68 0.00 0.00 3.51
395 3250 3.552068 GGGGTTTGACTTTGATTTGACCG 60.552 47.826 0.00 0.00 0.00 4.79
403 3258 7.129109 TGACTTTGATTTGACCGTCTTTATC 57.871 36.000 0.00 1.48 0.00 1.75
534 3393 3.868077 GGTCTCAATGTTGATTCTCCTCG 59.132 47.826 0.00 0.00 36.46 4.63
555 3414 2.027837 GTGCCATCCTTGGAAGCAAATT 60.028 45.455 16.03 0.00 46.92 1.82
556 3415 2.234414 TGCCATCCTTGGAAGCAAATTC 59.766 45.455 13.17 0.00 46.92 2.17
557 3416 2.234414 GCCATCCTTGGAAGCAAATTCA 59.766 45.455 9.33 0.00 46.92 2.57
678 5326 2.161855 TCAGCCGAACTTGATGCAAAT 58.838 42.857 0.00 0.00 0.00 2.32
714 5362 0.531974 AGGCGACACGTGTCATGTTT 60.532 50.000 39.14 21.38 44.99 2.83
715 5363 0.306533 GGCGACACGTGTCATGTTTT 59.693 50.000 39.14 10.09 44.99 2.43
716 5364 1.268335 GGCGACACGTGTCATGTTTTT 60.268 47.619 39.14 9.33 44.99 1.94
717 5365 2.032722 GGCGACACGTGTCATGTTTTTA 60.033 45.455 39.14 0.00 44.99 1.52
718 5366 3.364565 GGCGACACGTGTCATGTTTTTAT 60.365 43.478 39.14 8.03 44.99 1.40
719 5367 4.215965 GCGACACGTGTCATGTTTTTATT 58.784 39.130 39.14 7.82 44.99 1.40
720 5368 4.673311 GCGACACGTGTCATGTTTTTATTT 59.327 37.500 39.14 7.36 44.99 1.40
721 5369 5.385918 GCGACACGTGTCATGTTTTTATTTG 60.386 40.000 39.14 22.99 44.99 2.32
722 5370 5.904630 CGACACGTGTCATGTTTTTATTTGA 59.095 36.000 39.14 0.00 44.99 2.69
723 5371 6.084939 CGACACGTGTCATGTTTTTATTTGAG 59.915 38.462 39.14 18.83 44.99 3.02
724 5372 6.791303 ACACGTGTCATGTTTTTATTTGAGT 58.209 32.000 17.22 0.00 0.00 3.41
725 5373 7.254852 ACACGTGTCATGTTTTTATTTGAGTT 58.745 30.769 17.22 0.00 0.00 3.01
726 5374 8.399425 ACACGTGTCATGTTTTTATTTGAGTTA 58.601 29.630 17.22 0.00 0.00 2.24
727 5375 9.393249 CACGTGTCATGTTTTTATTTGAGTTAT 57.607 29.630 7.58 0.00 0.00 1.89
728 5376 9.959749 ACGTGTCATGTTTTTATTTGAGTTATT 57.040 25.926 0.00 0.00 0.00 1.40
738 5386 8.868744 TTTTATTTGAGTTATTAAGCGACACG 57.131 30.769 0.00 0.00 0.00 4.49
739 5387 7.585286 TTATTTGAGTTATTAAGCGACACGT 57.415 32.000 0.00 0.00 0.00 4.49
740 5388 4.896562 TTGAGTTATTAAGCGACACGTG 57.103 40.909 15.48 15.48 0.00 4.49
741 5389 3.904571 TGAGTTATTAAGCGACACGTGT 58.095 40.909 23.64 23.64 0.00 4.49
742 5390 3.916172 TGAGTTATTAAGCGACACGTGTC 59.084 43.478 33.76 33.76 41.47 3.67
743 5391 3.904571 AGTTATTAAGCGACACGTGTCA 58.095 40.909 39.14 24.81 44.99 3.58
744 5392 4.491676 AGTTATTAAGCGACACGTGTCAT 58.508 39.130 39.14 28.63 44.99 3.06
745 5393 4.326278 AGTTATTAAGCGACACGTGTCATG 59.674 41.667 39.14 27.96 44.99 3.07
746 5394 2.143008 TTAAGCGACACGTGTCATGT 57.857 45.000 39.14 27.38 44.99 3.21
747 5395 2.143008 TAAGCGACACGTGTCATGTT 57.857 45.000 39.14 30.36 44.99 2.71
748 5396 1.295792 AAGCGACACGTGTCATGTTT 58.704 45.000 39.14 27.26 44.99 2.83
896 6770 2.998480 ACGCCACCCACGTCCATA 60.998 61.111 0.00 0.00 40.28 2.74
898 6772 2.666207 GCCACCCACGTCCATACA 59.334 61.111 0.00 0.00 0.00 2.29
911 6785 5.047590 CACGTCCATACACATATAAGCCCTA 60.048 44.000 0.00 0.00 0.00 3.53
970 6859 2.124487 CGTCGCCTCCTCTCCTCT 60.124 66.667 0.00 0.00 0.00 3.69
982 6871 3.114647 CTCCTCTTCCTCCGTCGCG 62.115 68.421 0.00 0.00 0.00 5.87
1039 6928 2.340443 GATCCGTCCCATCTCCGC 59.660 66.667 0.00 0.00 0.00 5.54
1074 6963 6.072286 CCCTTTTCATGCAATAATCTCGCTAT 60.072 38.462 0.00 0.00 0.00 2.97
1131 7020 2.299867 GGTAGGGTTTTGTCTCCGTACA 59.700 50.000 13.40 0.00 42.94 2.90
1177 7071 1.153568 CCCTGTGTGCGATGTCGAT 60.154 57.895 6.60 0.00 43.02 3.59
1189 7083 0.172578 ATGTCGATGCGAGTTCCGAA 59.827 50.000 0.00 0.00 41.76 4.30
1202 7096 1.066143 GTTCCGAAGAGCTGGGATCAA 60.066 52.381 0.00 0.00 0.00 2.57
1218 7112 5.014755 TGGGATCAAGTTAGGGTTATGTGTT 59.985 40.000 0.00 0.00 0.00 3.32
1295 7189 4.818447 AGGATAAAATTGGATGGATGCCA 58.182 39.130 0.00 0.00 38.19 4.92
1350 7245 4.808558 TCTATTTGCAATTGACACCTTGC 58.191 39.130 10.34 12.80 46.19 4.01
1386 7281 4.164413 GCTATGGTCCTAGAGTTTTTCCCT 59.836 45.833 0.00 0.00 0.00 4.20
1476 7383 8.716646 TCATCAATATCGTGTTAATGTTGAGT 57.283 30.769 0.00 0.00 37.56 3.41
1507 7414 3.955650 TCAGAACTAGGGCAACAGTAC 57.044 47.619 0.00 0.00 39.74 2.73
1513 7420 2.563179 ACTAGGGCAACAGTACTGTCTG 59.437 50.000 28.04 24.93 44.13 3.51
1604 7511 3.906998 TGTGATTGCCAATTTGTAACCG 58.093 40.909 0.00 0.00 0.00 4.44
1611 7518 1.269448 CCAATTTGTAACCGTGCTGCT 59.731 47.619 0.00 0.00 0.00 4.24
1612 7519 2.584791 CAATTTGTAACCGTGCTGCTC 58.415 47.619 0.00 0.00 0.00 4.26
1705 7616 3.061295 CAGATGTGACGTATGCTGTTGTC 59.939 47.826 0.00 0.00 0.00 3.18
1777 7704 6.497785 TTTTCTGTGGACTTCGTTAAAACA 57.502 33.333 0.00 0.00 0.00 2.83
2059 8072 4.568072 TTCTATTTCTGCTGCCACCTTA 57.432 40.909 0.00 0.00 0.00 2.69
2104 8134 9.339492 CTGATTTTCTGAGAAGTTTTGATTAGC 57.661 33.333 0.00 0.00 0.00 3.09
2566 8600 3.635099 CTGAGGGTCAGGGTCCATA 57.365 57.895 0.00 0.00 40.71 2.74
2583 8617 3.067106 CCATACATACCATGTCCTTCGC 58.933 50.000 0.00 0.00 43.67 4.70
2691 8725 1.039856 GTGTGGACATTGGCCAAGTT 58.960 50.000 24.94 13.02 37.12 2.66
2694 8728 2.107378 TGTGGACATTGGCCAAGTTCTA 59.893 45.455 24.94 16.66 37.12 2.10
2769 8803 1.398692 GTGCCAAGTTCAAGTTCCCA 58.601 50.000 0.00 0.00 0.00 4.37
2807 8841 0.108186 CGCAGCAGGAAGTGGTATGA 60.108 55.000 0.00 0.00 34.15 2.15
2867 8901 6.072728 TGTGTTATGGAAAGTCGGAAATTCTG 60.073 38.462 0.00 0.00 0.00 3.02
3058 9092 6.090129 GCTTCAGTTCTGTTCTACTAGACTG 58.910 44.000 0.00 0.00 0.00 3.51
3059 9093 5.630661 TCAGTTCTGTTCTACTAGACTGC 57.369 43.478 0.00 0.00 0.00 4.40
3200 9240 9.935241 TTCTGATTCCTAATAATCTATCAGTGC 57.065 33.333 0.00 0.00 39.76 4.40
3259 9303 8.681486 TGATGCTTACAAGTGCTAATATCAAT 57.319 30.769 0.00 0.00 0.00 2.57
3483 9543 3.118261 TCTTCTTCCAACTCTTGTGCAGT 60.118 43.478 0.00 0.00 0.00 4.40
3515 9575 0.324275 ATGGCCCCATTGCTAAACGT 60.324 50.000 0.00 0.00 31.82 3.99
3575 9635 2.655090 TGCACAGACCATTTCCTTCA 57.345 45.000 0.00 0.00 0.00 3.02
3799 9859 4.277921 GCTGGAGAATTTTCTGGATCATCC 59.722 45.833 0.00 0.00 37.73 3.51
3817 9877 8.890718 GGATCATCCATGAATGATGTATAACTG 58.109 37.037 12.68 0.00 44.47 3.16
3837 9897 2.025981 TGTTGCCTATGCTCAATCACCT 60.026 45.455 0.00 0.00 38.71 4.00
3838 9898 3.199727 TGTTGCCTATGCTCAATCACCTA 59.800 43.478 0.00 0.00 38.71 3.08
3839 9899 3.758755 TGCCTATGCTCAATCACCTAG 57.241 47.619 0.00 0.00 38.71 3.02
3844 9904 2.768253 TGCTCAATCACCTAGTGTGG 57.232 50.000 10.33 0.00 45.48 4.17
3873 9933 5.744171 TCATTGATGTGTGGCTAGTTATGT 58.256 37.500 0.00 0.00 0.00 2.29
3883 9943 7.067129 TGTGTGGCTAGTTATGTTTGTTTGTTA 59.933 33.333 0.00 0.00 0.00 2.41
3922 9984 9.249053 TGAGGCATTCAAGTAAATATTGGTAAA 57.751 29.630 0.00 0.00 31.34 2.01
3944 10006 3.512724 AGCTGCTCAAATTGCACCTAATT 59.487 39.130 0.00 0.00 36.37 1.40
3955 10017 7.588488 CAAATTGCACCTAATTTGCTTGAAAAG 59.412 33.333 8.27 0.00 45.49 2.27
3956 10018 7.282901 AAATTGCACCTAATTTGCTTGAAAAGT 59.717 29.630 2.52 0.00 38.20 2.66
4054 10116 6.231951 TGTATTTCCACAATGTTCTCCGTTA 58.768 36.000 0.00 0.00 0.00 3.18
4055 10117 5.880054 ATTTCCACAATGTTCTCCGTTAG 57.120 39.130 0.00 0.00 0.00 2.34
4057 10119 2.037902 TCCACAATGTTCTCCGTTAGCA 59.962 45.455 0.00 0.00 0.00 3.49
4058 10120 3.009723 CCACAATGTTCTCCGTTAGCAT 58.990 45.455 0.00 0.00 0.00 3.79
4077 10139 3.865446 CATCCAATTTTCCTTGGCCTTC 58.135 45.455 3.32 0.00 44.48 3.46
4080 10142 2.634453 CCAATTTTCCTTGGCCTTCACT 59.366 45.455 3.32 0.00 39.32 3.41
4083 10145 5.413499 CAATTTTCCTTGGCCTTCACTATG 58.587 41.667 3.32 0.00 0.00 2.23
4095 10157 0.108186 TCACTATGAAGCCGTGCCTG 60.108 55.000 0.00 0.00 0.00 4.85
4096 10158 0.391661 CACTATGAAGCCGTGCCTGT 60.392 55.000 0.00 0.00 0.00 4.00
4097 10159 0.391661 ACTATGAAGCCGTGCCTGTG 60.392 55.000 0.00 0.00 0.00 3.66
4098 10160 0.391661 CTATGAAGCCGTGCCTGTGT 60.392 55.000 0.00 0.00 0.00 3.72
4099 10161 0.036164 TATGAAGCCGTGCCTGTGTT 59.964 50.000 0.00 0.00 0.00 3.32
4100 10162 1.518056 ATGAAGCCGTGCCTGTGTTG 61.518 55.000 0.00 0.00 0.00 3.33
4101 10163 2.906897 AAGCCGTGCCTGTGTTGG 60.907 61.111 0.00 0.00 0.00 3.77
4102 10164 3.714487 AAGCCGTGCCTGTGTTGGT 62.714 57.895 0.00 0.00 0.00 3.67
4103 10165 3.964875 GCCGTGCCTGTGTTGGTG 61.965 66.667 0.00 0.00 0.00 4.17
4104 10166 3.286751 CCGTGCCTGTGTTGGTGG 61.287 66.667 0.00 0.00 0.00 4.61
4105 10167 2.515991 CGTGCCTGTGTTGGTGGT 60.516 61.111 0.00 0.00 0.00 4.16
4106 10168 2.833533 CGTGCCTGTGTTGGTGGTG 61.834 63.158 0.00 0.00 0.00 4.17
4107 10169 2.123939 TGCCTGTGTTGGTGGTGG 60.124 61.111 0.00 0.00 0.00 4.61
4108 10170 2.123897 GCCTGTGTTGGTGGTGGT 60.124 61.111 0.00 0.00 0.00 4.16
4109 10171 2.489275 GCCTGTGTTGGTGGTGGTG 61.489 63.158 0.00 0.00 0.00 4.17
4110 10172 1.827789 CCTGTGTTGGTGGTGGTGG 60.828 63.158 0.00 0.00 0.00 4.61
4111 10173 1.827789 CTGTGTTGGTGGTGGTGGG 60.828 63.158 0.00 0.00 0.00 4.61
4112 10174 2.520741 GTGTTGGTGGTGGTGGGG 60.521 66.667 0.00 0.00 0.00 4.96
4113 10175 4.531426 TGTTGGTGGTGGTGGGGC 62.531 66.667 0.00 0.00 0.00 5.80
4130 10192 4.662961 CGCTGGTGCCGACAGTCA 62.663 66.667 0.41 0.00 38.22 3.41
4131 10193 2.280797 GCTGGTGCCGACAGTCAA 60.281 61.111 0.41 0.00 38.22 3.18
4132 10194 2.320587 GCTGGTGCCGACAGTCAAG 61.321 63.158 0.41 0.00 38.22 3.02
4133 10195 1.669115 CTGGTGCCGACAGTCAAGG 60.669 63.158 0.41 0.00 0.00 3.61
4138 10200 4.779475 CCGACAGTCAAGGCAGTT 57.221 55.556 0.41 0.00 0.00 3.16
4139 10201 3.906660 CCGACAGTCAAGGCAGTTA 57.093 52.632 0.41 0.00 0.00 2.24
4140 10202 2.163818 CCGACAGTCAAGGCAGTTAA 57.836 50.000 0.41 0.00 0.00 2.01
4141 10203 2.699954 CCGACAGTCAAGGCAGTTAAT 58.300 47.619 0.41 0.00 0.00 1.40
4142 10204 3.074412 CCGACAGTCAAGGCAGTTAATT 58.926 45.455 0.41 0.00 0.00 1.40
4143 10205 3.502211 CCGACAGTCAAGGCAGTTAATTT 59.498 43.478 0.41 0.00 0.00 1.82
4144 10206 4.023193 CCGACAGTCAAGGCAGTTAATTTT 60.023 41.667 0.41 0.00 0.00 1.82
4145 10207 5.147162 CGACAGTCAAGGCAGTTAATTTTC 58.853 41.667 0.41 0.00 0.00 2.29
4146 10208 5.453567 ACAGTCAAGGCAGTTAATTTTCC 57.546 39.130 0.00 0.00 0.00 3.13
4147 10209 5.140454 ACAGTCAAGGCAGTTAATTTTCCT 58.860 37.500 0.00 0.00 0.00 3.36
4148 10210 5.598417 ACAGTCAAGGCAGTTAATTTTCCTT 59.402 36.000 0.00 0.00 37.61 3.36
4151 10213 3.961480 AGGCAGTTAATTTTCCTTGGC 57.039 42.857 0.00 0.00 0.00 4.52
4152 10214 2.567169 AGGCAGTTAATTTTCCTTGGCC 59.433 45.455 0.00 0.00 39.14 5.36
4153 10215 2.567169 GGCAGTTAATTTTCCTTGGCCT 59.433 45.455 3.32 0.00 36.04 5.19
4154 10216 3.007940 GGCAGTTAATTTTCCTTGGCCTT 59.992 43.478 3.32 0.00 36.04 4.35
4155 10217 4.245660 GCAGTTAATTTTCCTTGGCCTTC 58.754 43.478 3.32 0.00 0.00 3.46
4156 10218 4.485163 CAGTTAATTTTCCTTGGCCTTCG 58.515 43.478 3.32 0.00 0.00 3.79
4157 10219 3.056821 AGTTAATTTTCCTTGGCCTTCGC 60.057 43.478 3.32 0.00 0.00 4.70
4158 10220 1.632589 AATTTTCCTTGGCCTTCGCT 58.367 45.000 3.32 0.00 34.44 4.93
4159 10221 2.507407 ATTTTCCTTGGCCTTCGCTA 57.493 45.000 3.32 0.00 34.44 4.26
4160 10222 2.507407 TTTTCCTTGGCCTTCGCTAT 57.493 45.000 3.32 0.00 34.44 2.97
4161 10223 2.038387 TTTCCTTGGCCTTCGCTATC 57.962 50.000 3.32 0.00 34.44 2.08
4162 10224 0.908910 TTCCTTGGCCTTCGCTATCA 59.091 50.000 3.32 0.00 34.44 2.15
4163 10225 0.908910 TCCTTGGCCTTCGCTATCAA 59.091 50.000 3.32 0.00 34.44 2.57
4164 10226 1.134401 TCCTTGGCCTTCGCTATCAAG 60.134 52.381 3.32 0.00 33.82 3.02
4165 10227 0.659957 CTTGGCCTTCGCTATCAAGC 59.340 55.000 3.32 0.00 45.86 4.01
4166 10228 0.748005 TTGGCCTTCGCTATCAAGCC 60.748 55.000 3.32 0.00 46.68 4.35
4167 10229 2.247437 GGCCTTCGCTATCAAGCCG 61.247 63.158 0.00 0.00 46.68 5.52
4168 10230 1.521681 GCCTTCGCTATCAAGCCGT 60.522 57.895 0.00 0.00 46.68 5.68
4169 10231 1.766143 GCCTTCGCTATCAAGCCGTG 61.766 60.000 0.00 0.00 46.68 4.94
4170 10232 1.638467 CTTCGCTATCAAGCCGTGC 59.362 57.895 0.00 0.00 46.68 5.34
4171 10233 1.766143 CTTCGCTATCAAGCCGTGCC 61.766 60.000 0.00 0.00 46.68 5.01
4172 10234 2.202932 CGCTATCAAGCCGTGCCT 60.203 61.111 0.00 0.00 46.68 4.75
4173 10235 2.528743 CGCTATCAAGCCGTGCCTG 61.529 63.158 0.00 0.00 46.68 4.85
4174 10236 1.450312 GCTATCAAGCCGTGCCTGT 60.450 57.895 0.00 0.00 43.40 4.00
4175 10237 1.709147 GCTATCAAGCCGTGCCTGTG 61.709 60.000 0.00 0.00 43.40 3.66
4176 10238 0.391661 CTATCAAGCCGTGCCTGTGT 60.392 55.000 0.00 0.00 0.00 3.72
4177 10239 0.036164 TATCAAGCCGTGCCTGTGTT 59.964 50.000 0.00 0.00 0.00 3.32
4178 10240 1.518056 ATCAAGCCGTGCCTGTGTTG 61.518 55.000 0.00 0.00 0.00 3.33
4179 10241 2.906897 AAGCCGTGCCTGTGTTGG 60.907 61.111 0.00 0.00 0.00 3.77
4180 10242 3.714487 AAGCCGTGCCTGTGTTGGT 62.714 57.895 0.00 0.00 0.00 3.67
4181 10243 3.964875 GCCGTGCCTGTGTTGGTG 61.965 66.667 0.00 0.00 0.00 4.17
4182 10244 3.286751 CCGTGCCTGTGTTGGTGG 61.287 66.667 0.00 0.00 0.00 4.61
4209 10271 2.280797 GCTGGTGCCGACAGTCAA 60.281 61.111 0.41 0.00 38.22 3.18
4217 10279 2.238353 CCGACAGTCAAGGCAGTTG 58.762 57.895 0.41 0.00 37.52 3.16
4220 10282 0.947244 GACAGTCAAGGCAGTTGTGG 59.053 55.000 0.00 0.00 37.43 4.17
4237 10299 2.639327 GGGCACTTGCGGCAATCTT 61.639 57.895 16.80 0.70 43.26 2.40
4238 10300 1.312371 GGGCACTTGCGGCAATCTTA 61.312 55.000 16.80 0.00 43.26 2.10
4239 10301 0.740737 GGCACTTGCGGCAATCTTAT 59.259 50.000 16.80 0.00 43.26 1.73
4240 10302 1.134946 GGCACTTGCGGCAATCTTATT 59.865 47.619 16.80 0.00 43.26 1.40
4241 10303 2.187707 GCACTTGCGGCAATCTTATTG 58.812 47.619 16.80 5.11 0.00 1.90
4242 10304 2.415893 GCACTTGCGGCAATCTTATTGT 60.416 45.455 16.80 5.78 0.00 2.71
4243 10305 3.836949 CACTTGCGGCAATCTTATTGTT 58.163 40.909 16.80 0.00 0.00 2.83
4244 10306 4.674101 GCACTTGCGGCAATCTTATTGTTA 60.674 41.667 16.80 0.00 0.00 2.41
4245 10307 4.793216 CACTTGCGGCAATCTTATTGTTAC 59.207 41.667 16.80 0.00 0.00 2.50
4246 10308 4.700213 ACTTGCGGCAATCTTATTGTTACT 59.300 37.500 16.80 0.00 0.00 2.24
4247 10309 5.183140 ACTTGCGGCAATCTTATTGTTACTT 59.817 36.000 16.80 0.00 0.00 2.24
4248 10310 5.229921 TGCGGCAATCTTATTGTTACTTC 57.770 39.130 0.00 0.00 0.00 3.01
4249 10311 4.095782 TGCGGCAATCTTATTGTTACTTCC 59.904 41.667 0.00 0.00 0.00 3.46
4250 10312 4.335594 GCGGCAATCTTATTGTTACTTCCT 59.664 41.667 0.00 0.00 0.00 3.36
4251 10313 5.504173 GCGGCAATCTTATTGTTACTTCCTC 60.504 44.000 0.00 0.00 0.00 3.71
4252 10314 5.276868 CGGCAATCTTATTGTTACTTCCTCG 60.277 44.000 1.94 0.00 0.00 4.63
4253 10315 5.007724 GGCAATCTTATTGTTACTTCCTCGG 59.992 44.000 1.94 0.00 0.00 4.63
4254 10316 5.007724 GCAATCTTATTGTTACTTCCTCGGG 59.992 44.000 1.94 0.00 0.00 5.14
4255 10317 5.952347 ATCTTATTGTTACTTCCTCGGGT 57.048 39.130 0.00 0.00 0.00 5.28
4256 10318 5.750352 TCTTATTGTTACTTCCTCGGGTT 57.250 39.130 0.00 0.00 0.00 4.11
4257 10319 5.727434 TCTTATTGTTACTTCCTCGGGTTC 58.273 41.667 0.00 0.00 0.00 3.62
4258 10320 2.443887 TTGTTACTTCCTCGGGTTCG 57.556 50.000 0.00 0.00 37.82 3.95
4259 10321 0.604578 TGTTACTTCCTCGGGTTCGG 59.395 55.000 0.00 0.00 36.95 4.30
4260 10322 0.890683 GTTACTTCCTCGGGTTCGGA 59.109 55.000 0.00 0.00 36.95 4.55
4279 10341 2.671619 CGGCGGTTCCATGTGGTT 60.672 61.111 0.00 0.00 36.34 3.67
4290 10352 1.542915 CCATGTGGTTGGCTTCTTCTG 59.457 52.381 0.00 0.00 0.00 3.02
4301 10363 6.294508 GGTTGGCTTCTTCTGCACTAATAAAA 60.295 38.462 0.00 0.00 0.00 1.52
4304 10366 7.895759 TGGCTTCTTCTGCACTAATAAAATTT 58.104 30.769 0.00 0.00 0.00 1.82
4305 10367 9.019656 TGGCTTCTTCTGCACTAATAAAATTTA 57.980 29.630 0.00 0.00 0.00 1.40
4306 10368 9.290483 GGCTTCTTCTGCACTAATAAAATTTAC 57.710 33.333 0.00 0.00 0.00 2.01
4310 10372 8.879759 TCTTCTGCACTAATAAAATTTACTCGG 58.120 33.333 0.00 0.00 0.00 4.63
4311 10373 8.556213 TTCTGCACTAATAAAATTTACTCGGT 57.444 30.769 0.00 0.00 0.00 4.69
4312 10374 8.193250 TCTGCACTAATAAAATTTACTCGGTC 57.807 34.615 0.00 0.00 0.00 4.79
4314 10376 8.325421 TGCACTAATAAAATTTACTCGGTCAA 57.675 30.769 0.00 0.00 0.00 3.18
4316 10378 9.434559 GCACTAATAAAATTTACTCGGTCAATC 57.565 33.333 0.00 0.00 0.00 2.67
4320 10382 8.911247 AATAAAATTTACTCGGTCAATCTTGC 57.089 30.769 0.00 0.00 0.00 4.01
4323 10385 3.678056 TTACTCGGTCAATCTTGCTGT 57.322 42.857 0.00 0.00 0.00 4.40
4324 10386 4.794278 TTACTCGGTCAATCTTGCTGTA 57.206 40.909 0.00 0.00 0.00 2.74
4371 10433 4.705337 TGTTAATATTCAACAACCCCGC 57.295 40.909 0.00 0.00 33.11 6.13
4415 10477 8.608844 AATCTAAACACTTAACCTTCTGTCTG 57.391 34.615 0.00 0.00 0.00 3.51
4429 10491 4.737855 TCTGTCTGTAAGGTAGATTGGC 57.262 45.455 0.00 0.00 0.00 4.52
4442 10504 2.701163 GATTGGCGGCTACTCCTCCG 62.701 65.000 11.43 0.00 42.83 4.63
4452 10514 2.864489 GCTACTCCTCCGATGCTAAAGC 60.864 54.545 0.00 0.00 42.50 3.51
4478 10543 3.825585 TGTGCACCATTCACATACATGTT 59.174 39.130 15.69 0.00 39.29 2.71
4523 10588 6.783708 TTGTTTACCCACTTTGAATTGAGT 57.216 33.333 0.00 0.00 0.00 3.41
4536 10601 5.174037 TGAATTGAGTATCCGTTTCCCTT 57.826 39.130 0.00 0.00 0.00 3.95
4540 10605 4.360951 TGAGTATCCGTTTCCCTTGTTT 57.639 40.909 0.00 0.00 0.00 2.83
4541 10606 4.721132 TGAGTATCCGTTTCCCTTGTTTT 58.279 39.130 0.00 0.00 0.00 2.43
4542 10607 5.134661 TGAGTATCCGTTTCCCTTGTTTTT 58.865 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.201424 GGATCCAAACTCCCGGTACT 58.799 55.000 6.95 0.00 0.00 2.73
43 44 0.179702 GGGATCCAAACTCCCGGTAC 59.820 60.000 15.23 0.00 42.94 3.34
44 45 2.611520 GGGATCCAAACTCCCGGTA 58.388 57.895 15.23 0.00 42.94 4.02
45 46 3.411700 GGGATCCAAACTCCCGGT 58.588 61.111 15.23 0.00 42.94 5.28
77 101 0.810031 ATCCCGCGATCTGGTTTTCG 60.810 55.000 8.23 0.00 38.37 3.46
78 102 0.657840 CATCCCGCGATCTGGTTTTC 59.342 55.000 8.23 0.00 0.00 2.29
79 103 0.251916 TCATCCCGCGATCTGGTTTT 59.748 50.000 8.23 0.00 0.00 2.43
80 104 0.179073 CTCATCCCGCGATCTGGTTT 60.179 55.000 8.23 0.00 0.00 3.27
81 105 1.043116 TCTCATCCCGCGATCTGGTT 61.043 55.000 8.23 0.00 0.00 3.67
82 106 1.043116 TTCTCATCCCGCGATCTGGT 61.043 55.000 8.23 0.00 0.00 4.00
83 107 0.319383 CTTCTCATCCCGCGATCTGG 60.319 60.000 8.23 0.00 0.00 3.86
84 108 0.319383 CCTTCTCATCCCGCGATCTG 60.319 60.000 8.23 0.88 0.00 2.90
85 109 2.045280 CCTTCTCATCCCGCGATCT 58.955 57.895 8.23 0.00 0.00 2.75
99 123 3.767902 ATGCAGAGGATTCTAGCCTTC 57.232 47.619 0.00 0.00 35.44 3.46
104 128 5.188434 TGAACCAAATGCAGAGGATTCTAG 58.812 41.667 8.66 0.00 30.73 2.43
130 155 7.944554 ACTTCATCTTTCCTTCTGTTCCATTTA 59.055 33.333 0.00 0.00 0.00 1.40
196 226 3.689649 GGAGGTGCGAGTGAATTGTAAAT 59.310 43.478 0.00 0.00 0.00 1.40
230 260 9.433317 CGTAAATCAATAACTTTTCGTGCATAT 57.567 29.630 0.00 0.00 0.00 1.78
237 267 7.480229 TGTGATGCGTAAATCAATAACTTTTCG 59.520 33.333 0.12 0.00 38.28 3.46
241 271 7.139896 TGTGTGATGCGTAAATCAATAACTT 57.860 32.000 0.12 0.00 38.28 2.66
333 3188 7.492344 AGTTCAAAAGTCGCTTTCAATGAATTT 59.508 29.630 14.87 0.00 33.38 1.82
344 3199 2.618709 CCCTGAAGTTCAAAAGTCGCTT 59.381 45.455 7.06 0.00 0.00 4.68
347 3202 4.275936 ACATTCCCTGAAGTTCAAAAGTCG 59.724 41.667 7.06 0.00 0.00 4.18
395 3250 6.496338 AAACACAGGAATTCCGATAAAGAC 57.504 37.500 18.82 0.00 42.08 3.01
403 3258 5.897377 ATAGGAAAAACACAGGAATTCCG 57.103 39.130 18.82 15.41 43.38 4.30
555 3414 2.027192 GCCTCCATGAAAGGTACTGTGA 60.027 50.000 13.65 0.00 40.86 3.58
556 3415 2.290260 TGCCTCCATGAAAGGTACTGTG 60.290 50.000 13.65 0.00 40.86 3.66
557 3416 1.985159 TGCCTCCATGAAAGGTACTGT 59.015 47.619 13.65 0.00 40.86 3.55
654 4303 1.742761 CATCAAGTTCGGCTGATGGT 58.257 50.000 0.00 0.00 35.73 3.55
655 4304 0.379669 GCATCAAGTTCGGCTGATGG 59.620 55.000 13.50 0.00 38.72 3.51
656 4305 1.089112 TGCATCAAGTTCGGCTGATG 58.911 50.000 8.79 8.79 40.58 3.07
657 4306 1.825090 TTGCATCAAGTTCGGCTGAT 58.175 45.000 0.00 0.00 0.00 2.90
658 4307 1.603456 TTTGCATCAAGTTCGGCTGA 58.397 45.000 0.00 0.00 0.00 4.26
659 4308 2.256174 CATTTGCATCAAGTTCGGCTG 58.744 47.619 0.00 0.00 0.00 4.85
660 4309 1.403249 GCATTTGCATCAAGTTCGGCT 60.403 47.619 0.00 0.00 41.59 5.52
661 4310 0.994263 GCATTTGCATCAAGTTCGGC 59.006 50.000 0.00 0.00 41.59 5.54
663 4312 2.350899 TGGCATTTGCATCAAGTTCG 57.649 45.000 4.74 0.00 44.36 3.95
714 5362 7.953173 CACGTGTCGCTTAATAACTCAAATAAA 59.047 33.333 7.58 0.00 0.00 1.40
715 5363 7.116662 ACACGTGTCGCTTAATAACTCAAATAA 59.883 33.333 17.22 0.00 0.00 1.40
716 5364 6.587226 ACACGTGTCGCTTAATAACTCAAATA 59.413 34.615 17.22 0.00 0.00 1.40
717 5365 5.407387 ACACGTGTCGCTTAATAACTCAAAT 59.593 36.000 17.22 0.00 0.00 2.32
718 5366 4.746115 ACACGTGTCGCTTAATAACTCAAA 59.254 37.500 17.22 0.00 0.00 2.69
719 5367 4.300803 ACACGTGTCGCTTAATAACTCAA 58.699 39.130 17.22 0.00 0.00 3.02
720 5368 3.904571 ACACGTGTCGCTTAATAACTCA 58.095 40.909 17.22 0.00 0.00 3.41
721 5369 4.480958 GACACGTGTCGCTTAATAACTC 57.519 45.455 31.03 6.19 35.12 3.01
733 5381 5.985781 ACAGAATTAAACATGACACGTGTC 58.014 37.500 36.01 36.01 44.97 3.67
734 5382 6.198687 CAACAGAATTAAACATGACACGTGT 58.801 36.000 23.64 23.64 0.00 4.49
735 5383 5.624900 CCAACAGAATTAAACATGACACGTG 59.375 40.000 15.48 15.48 0.00 4.49
736 5384 5.278266 CCCAACAGAATTAAACATGACACGT 60.278 40.000 0.00 0.00 0.00 4.49
737 5385 5.153513 CCCAACAGAATTAAACATGACACG 58.846 41.667 0.00 0.00 0.00 4.49
738 5386 6.084326 ACCCAACAGAATTAAACATGACAC 57.916 37.500 0.00 0.00 0.00 3.67
739 5387 6.723298 AACCCAACAGAATTAAACATGACA 57.277 33.333 0.00 0.00 0.00 3.58
740 5388 7.494298 ACAAAACCCAACAGAATTAAACATGAC 59.506 33.333 0.00 0.00 0.00 3.06
741 5389 7.560368 ACAAAACCCAACAGAATTAAACATGA 58.440 30.769 0.00 0.00 0.00 3.07
742 5390 7.042119 GGACAAAACCCAACAGAATTAAACATG 60.042 37.037 0.00 0.00 0.00 3.21
743 5391 6.989759 GGACAAAACCCAACAGAATTAAACAT 59.010 34.615 0.00 0.00 0.00 2.71
744 5392 6.155393 AGGACAAAACCCAACAGAATTAAACA 59.845 34.615 0.00 0.00 0.00 2.83
745 5393 6.478673 CAGGACAAAACCCAACAGAATTAAAC 59.521 38.462 0.00 0.00 0.00 2.01
746 5394 6.407525 CCAGGACAAAACCCAACAGAATTAAA 60.408 38.462 0.00 0.00 0.00 1.52
747 5395 5.069781 CCAGGACAAAACCCAACAGAATTAA 59.930 40.000 0.00 0.00 0.00 1.40
748 5396 4.586841 CCAGGACAAAACCCAACAGAATTA 59.413 41.667 0.00 0.00 0.00 1.40
879 6743 2.998480 TATGGACGTGGGTGGCGT 60.998 61.111 0.00 0.00 45.86 5.68
882 6746 0.251916 ATGTGTATGGACGTGGGTGG 59.748 55.000 0.00 0.00 0.00 4.61
883 6747 2.971660 TATGTGTATGGACGTGGGTG 57.028 50.000 0.00 0.00 0.00 4.61
896 6770 3.248888 GGAGGGTAGGGCTTATATGTGT 58.751 50.000 0.00 0.00 0.00 3.72
898 6772 3.648683 TGGAGGGTAGGGCTTATATGT 57.351 47.619 0.00 0.00 0.00 2.29
911 6785 0.910088 GAGCAGTAGGGTTGGAGGGT 60.910 60.000 0.00 0.00 0.00 4.34
960 6842 0.256464 GACGGAGGAAGAGGAGAGGA 59.744 60.000 0.00 0.00 0.00 3.71
961 6843 1.098712 CGACGGAGGAAGAGGAGAGG 61.099 65.000 0.00 0.00 0.00 3.69
963 6845 1.749638 GCGACGGAGGAAGAGGAGA 60.750 63.158 0.00 0.00 0.00 3.71
967 6856 2.100603 GACGCGACGGAGGAAGAG 59.899 66.667 15.93 0.00 0.00 2.85
1039 6928 2.422093 GCATGAAAAGGGAGGTAGGGAG 60.422 54.545 0.00 0.00 0.00 4.30
1074 6963 0.389296 ACATCGCACGGATCGAAACA 60.389 50.000 0.00 0.00 39.54 2.83
1131 7020 3.006323 CCGCTAGATCAGGCAAGAACTAT 59.994 47.826 9.87 0.00 0.00 2.12
1177 7071 1.080501 CAGCTCTTCGGAACTCGCA 60.081 57.895 0.00 0.00 39.05 5.10
1189 7083 2.122768 CCCTAACTTGATCCCAGCTCT 58.877 52.381 0.00 0.00 0.00 4.09
1202 7096 4.332828 GGCAGAAACACATAACCCTAACT 58.667 43.478 0.00 0.00 0.00 2.24
1276 7170 6.945636 ATCATGGCATCCATCCAATTTTAT 57.054 33.333 0.00 0.00 43.15 1.40
1295 7189 6.672593 TGCCAAGTCTAAAGGGAATAATCAT 58.327 36.000 0.00 0.00 0.00 2.45
1350 7245 5.431765 AGGACCATAGCATCAACTTACTTG 58.568 41.667 0.00 0.00 0.00 3.16
1352 7247 6.136857 TCTAGGACCATAGCATCAACTTACT 58.863 40.000 0.00 0.00 0.00 2.24
1386 7281 6.371271 CCACACAATCTACATCATACAACACA 59.629 38.462 0.00 0.00 0.00 3.72
1476 7383 4.466726 GCCCTAGTTCTGAAGAGGTTAGAA 59.533 45.833 14.22 0.00 0.00 2.10
1507 7414 2.240493 ACCGAACACCTTTCAGACAG 57.760 50.000 0.00 0.00 0.00 3.51
1513 7420 0.958822 ATGCCAACCGAACACCTTTC 59.041 50.000 0.00 0.00 0.00 2.62
1604 7511 2.159462 GGTATTGCAGAAAGAGCAGCAC 60.159 50.000 0.00 0.00 43.75 4.40
1611 7518 7.765695 AAAAATCAGAGGTATTGCAGAAAGA 57.234 32.000 0.00 0.00 0.00 2.52
1667 7578 7.064609 CGTCACATCTGAAACCTATAAACACAT 59.935 37.037 0.00 0.00 0.00 3.21
2104 8134 2.807967 TGACACCTCAGAAATGCTTTCG 59.192 45.455 3.89 0.00 44.29 3.46
2229 8263 3.471680 GAGGGGTCTCAATTATCAGCAC 58.528 50.000 0.00 0.00 39.74 4.40
2691 8725 1.102978 TGCAGCGCACAGATAGTAGA 58.897 50.000 11.47 0.00 31.71 2.59
2694 8728 0.742281 CCTTGCAGCGCACAGATAGT 60.742 55.000 11.47 0.00 38.71 2.12
2769 8803 2.009774 CGAATGATCTTTTGACGGCCT 58.990 47.619 0.00 0.00 0.00 5.19
2807 8841 7.724061 ACCAGTATAATTTGAAAAGACAGGTGT 59.276 33.333 0.00 0.00 0.00 4.16
2867 8901 6.541086 CAATGCTTCAAACTAGTCATCTCAC 58.459 40.000 0.00 0.00 0.00 3.51
3058 9092 7.258022 ACATTTTAAGTTTTGGGAATTGTGC 57.742 32.000 0.00 0.00 0.00 4.57
3200 9240 7.936584 TGGAACAAATTTGACCAACTTAGTAG 58.063 34.615 26.39 1.48 36.16 2.57
3317 9364 3.660501 TGCGACAGAACTATGACAAGT 57.339 42.857 0.00 0.00 0.00 3.16
3483 9543 1.907807 GGCCATGGACACCAAGCAA 60.908 57.895 18.40 0.00 38.22 3.91
3619 9679 1.004745 ACTCGTTCAAGCATGGGGAAT 59.995 47.619 0.00 0.00 0.00 3.01
3799 9859 7.268199 AGGCAACAGTTATACATCATTCATG 57.732 36.000 0.00 0.00 37.56 3.07
3817 9877 2.648059 AGGTGATTGAGCATAGGCAAC 58.352 47.619 0.67 0.00 44.61 4.17
3837 9897 4.218200 CACATCAATGAAAAGGCCACACTA 59.782 41.667 5.01 0.00 0.00 2.74
3838 9898 3.006110 CACATCAATGAAAAGGCCACACT 59.994 43.478 5.01 0.00 0.00 3.55
3839 9899 3.243839 ACACATCAATGAAAAGGCCACAC 60.244 43.478 5.01 0.00 0.00 3.82
3844 9904 2.028748 AGCCACACATCAATGAAAAGGC 60.029 45.455 7.24 7.24 36.25 4.35
3873 9933 8.740123 TCAAGTAGGAGAACATAACAAACAAA 57.260 30.769 0.00 0.00 0.00 2.83
3971 10033 8.515414 AGCAACATTCCTTTGAATACTAAACTC 58.485 33.333 0.00 0.00 39.20 3.01
3986 10048 3.081061 TGAACGCAATAGCAACATTCCT 58.919 40.909 0.00 0.00 42.27 3.36
3999 10061 2.606795 GGCTAAATGCAACTGAACGCAA 60.607 45.455 0.00 0.00 45.15 4.85
4077 10139 0.391661 ACAGGCACGGCTTCATAGTG 60.392 55.000 0.00 0.00 38.77 2.74
4080 10142 0.036164 AACACAGGCACGGCTTCATA 59.964 50.000 0.00 0.00 0.00 2.15
4083 10145 2.639286 CAACACAGGCACGGCTTC 59.361 61.111 0.00 0.00 0.00 3.86
4087 10149 3.286751 CCACCAACACAGGCACGG 61.287 66.667 0.00 0.00 0.00 4.94
4095 10157 2.520741 CCCCACCACCACCAACAC 60.521 66.667 0.00 0.00 0.00 3.32
4096 10158 4.531426 GCCCCACCACCACCAACA 62.531 66.667 0.00 0.00 0.00 3.33
4113 10175 4.662961 TGACTGTCGGCACCAGCG 62.663 66.667 2.98 0.00 43.41 5.18
4114 10176 2.280797 TTGACTGTCGGCACCAGC 60.281 61.111 2.98 0.00 41.10 4.85
4115 10177 1.669115 CCTTGACTGTCGGCACCAG 60.669 63.158 2.98 0.00 36.01 4.00
4116 10178 2.425592 CCTTGACTGTCGGCACCA 59.574 61.111 2.98 0.00 0.00 4.17
4117 10179 3.050275 GCCTTGACTGTCGGCACC 61.050 66.667 18.20 0.00 43.25 5.01
4120 10182 0.320421 TAACTGCCTTGACTGTCGGC 60.320 55.000 16.80 16.80 44.02 5.54
4121 10183 2.163818 TTAACTGCCTTGACTGTCGG 57.836 50.000 2.98 0.31 0.00 4.79
4122 10184 4.749245 AAATTAACTGCCTTGACTGTCG 57.251 40.909 2.98 0.00 0.00 4.35
4123 10185 5.241728 AGGAAAATTAACTGCCTTGACTGTC 59.758 40.000 0.00 0.00 0.00 3.51
4124 10186 5.140454 AGGAAAATTAACTGCCTTGACTGT 58.860 37.500 0.00 0.00 0.00 3.55
4125 10187 5.712152 AGGAAAATTAACTGCCTTGACTG 57.288 39.130 0.00 0.00 0.00 3.51
4130 10192 3.007940 GGCCAAGGAAAATTAACTGCCTT 59.992 43.478 0.00 0.00 39.42 4.35
4131 10193 2.567169 GGCCAAGGAAAATTAACTGCCT 59.433 45.455 0.00 0.00 33.64 4.75
4132 10194 2.567169 AGGCCAAGGAAAATTAACTGCC 59.433 45.455 5.01 0.00 36.62 4.85
4133 10195 3.961480 AGGCCAAGGAAAATTAACTGC 57.039 42.857 5.01 0.00 0.00 4.40
4134 10196 4.485163 CGAAGGCCAAGGAAAATTAACTG 58.515 43.478 5.01 0.00 0.00 3.16
4135 10197 3.056821 GCGAAGGCCAAGGAAAATTAACT 60.057 43.478 5.01 0.00 0.00 2.24
4136 10198 3.056821 AGCGAAGGCCAAGGAAAATTAAC 60.057 43.478 5.01 0.00 41.24 2.01
4137 10199 3.161866 AGCGAAGGCCAAGGAAAATTAA 58.838 40.909 5.01 0.00 41.24 1.40
4138 10200 2.802719 AGCGAAGGCCAAGGAAAATTA 58.197 42.857 5.01 0.00 41.24 1.40
4139 10201 1.632589 AGCGAAGGCCAAGGAAAATT 58.367 45.000 5.01 0.00 41.24 1.82
4140 10202 2.507407 TAGCGAAGGCCAAGGAAAAT 57.493 45.000 5.01 0.00 41.24 1.82
4141 10203 2.290641 TGATAGCGAAGGCCAAGGAAAA 60.291 45.455 5.01 0.00 41.24 2.29
4142 10204 1.280710 TGATAGCGAAGGCCAAGGAAA 59.719 47.619 5.01 0.00 41.24 3.13
4143 10205 0.908910 TGATAGCGAAGGCCAAGGAA 59.091 50.000 5.01 0.00 41.24 3.36
4144 10206 0.908910 TTGATAGCGAAGGCCAAGGA 59.091 50.000 5.01 0.00 41.24 3.36
4145 10207 1.303309 CTTGATAGCGAAGGCCAAGG 58.697 55.000 5.01 0.00 41.24 3.61
4146 10208 0.659957 GCTTGATAGCGAAGGCCAAG 59.340 55.000 5.01 0.00 41.24 3.61
4147 10209 2.780595 GCTTGATAGCGAAGGCCAA 58.219 52.632 5.01 0.00 41.24 4.52
4148 10210 4.540153 GCTTGATAGCGAAGGCCA 57.460 55.556 5.01 0.00 41.24 5.36
4157 10219 0.391661 ACACAGGCACGGCTTGATAG 60.392 55.000 13.42 6.64 37.87 2.08
4158 10220 0.036164 AACACAGGCACGGCTTGATA 59.964 50.000 13.42 0.00 37.87 2.15
4159 10221 1.228245 AACACAGGCACGGCTTGAT 60.228 52.632 13.42 0.93 37.87 2.57
4160 10222 2.186160 CAACACAGGCACGGCTTGA 61.186 57.895 13.42 0.00 37.87 3.02
4161 10223 2.332514 CAACACAGGCACGGCTTG 59.667 61.111 6.48 6.48 41.47 4.01
4162 10224 2.906897 CCAACACAGGCACGGCTT 60.907 61.111 0.00 0.00 0.00 4.35
4163 10225 4.189580 ACCAACACAGGCACGGCT 62.190 61.111 0.00 0.00 0.00 5.52
4164 10226 3.964875 CACCAACACAGGCACGGC 61.965 66.667 0.00 0.00 0.00 5.68
4165 10227 3.286751 CCACCAACACAGGCACGG 61.287 66.667 0.00 0.00 0.00 4.94
4166 10228 2.515991 ACCACCAACACAGGCACG 60.516 61.111 0.00 0.00 0.00 5.34
4167 10229 2.489275 CCACCACCAACACAGGCAC 61.489 63.158 0.00 0.00 0.00 5.01
4168 10230 2.123939 CCACCACCAACACAGGCA 60.124 61.111 0.00 0.00 0.00 4.75
4169 10231 2.123897 ACCACCACCAACACAGGC 60.124 61.111 0.00 0.00 0.00 4.85
4170 10232 1.827789 CCACCACCACCAACACAGG 60.828 63.158 0.00 0.00 0.00 4.00
4171 10233 0.819259 CTCCACCACCACCAACACAG 60.819 60.000 0.00 0.00 0.00 3.66
4172 10234 1.225983 CTCCACCACCACCAACACA 59.774 57.895 0.00 0.00 0.00 3.72
4173 10235 2.193536 GCTCCACCACCACCAACAC 61.194 63.158 0.00 0.00 0.00 3.32
4174 10236 2.194597 GCTCCACCACCACCAACA 59.805 61.111 0.00 0.00 0.00 3.33
4175 10237 2.978010 CGCTCCACCACCACCAAC 60.978 66.667 0.00 0.00 0.00 3.77
4176 10238 4.947147 GCGCTCCACCACCACCAA 62.947 66.667 0.00 0.00 0.00 3.67
4200 10262 0.583438 CACAACTGCCTTGACTGTCG 59.417 55.000 2.98 0.00 33.59 4.35
4209 10271 1.829533 CAAGTGCCCACAACTGCCT 60.830 57.895 0.82 0.00 0.00 4.75
4213 10275 2.906897 CCGCAAGTGCCCACAACT 60.907 61.111 0.82 0.00 37.91 3.16
4217 10279 3.631487 GATTGCCGCAAGTGCCCAC 62.631 63.158 12.16 0.00 37.91 4.61
4220 10282 0.740737 ATAAGATTGCCGCAAGTGCC 59.259 50.000 12.16 1.25 37.91 5.01
4237 10299 3.119029 CCGAACCCGAGGAAGTAACAATA 60.119 47.826 0.00 0.00 38.22 1.90
4238 10300 2.354403 CCGAACCCGAGGAAGTAACAAT 60.354 50.000 0.00 0.00 38.22 2.71
4239 10301 1.001181 CCGAACCCGAGGAAGTAACAA 59.999 52.381 0.00 0.00 38.22 2.83
4240 10302 0.604578 CCGAACCCGAGGAAGTAACA 59.395 55.000 0.00 0.00 38.22 2.41
4241 10303 0.890683 TCCGAACCCGAGGAAGTAAC 59.109 55.000 0.00 0.00 38.22 2.50
4242 10304 1.273327 GTTCCGAACCCGAGGAAGTAA 59.727 52.381 0.00 0.00 46.03 2.24
4243 10305 0.890683 GTTCCGAACCCGAGGAAGTA 59.109 55.000 0.00 0.00 46.03 2.24
4244 10306 1.670015 GTTCCGAACCCGAGGAAGT 59.330 57.895 0.00 0.00 46.03 3.01
4245 10307 1.445582 CGTTCCGAACCCGAGGAAG 60.446 63.158 5.67 0.00 46.03 3.46
4246 10308 2.652530 CGTTCCGAACCCGAGGAA 59.347 61.111 5.67 0.00 43.57 3.36
4247 10309 3.376078 CCGTTCCGAACCCGAGGA 61.376 66.667 5.67 0.00 38.22 3.71
4252 10314 4.994471 AACCGCCGTTCCGAACCC 62.994 66.667 5.67 0.00 0.00 4.11
4253 10315 3.417224 GAACCGCCGTTCCGAACC 61.417 66.667 6.66 0.00 42.26 3.62
4259 10321 2.686816 CCACATGGAACCGCCGTTC 61.687 63.158 9.16 9.16 46.52 3.95
4260 10322 2.671619 CCACATGGAACCGCCGTT 60.672 61.111 0.00 0.00 40.66 4.44
4266 10328 0.603065 GAAGCCAACCACATGGAACC 59.397 55.000 4.53 0.00 43.54 3.62
4268 10330 2.158475 AGAAGAAGCCAACCACATGGAA 60.158 45.455 4.53 0.00 43.54 3.53
4279 10341 7.466746 AATTTTATTAGTGCAGAAGAAGCCA 57.533 32.000 0.00 0.00 0.00 4.75
4290 10352 9.434559 GATTGACCGAGTAAATTTTATTAGTGC 57.565 33.333 0.00 0.00 0.00 4.40
4301 10363 4.579869 ACAGCAAGATTGACCGAGTAAAT 58.420 39.130 0.00 0.00 0.00 1.40
4304 10366 4.794278 TTACAGCAAGATTGACCGAGTA 57.206 40.909 0.00 0.00 0.00 2.59
4305 10367 3.678056 TTACAGCAAGATTGACCGAGT 57.322 42.857 0.00 0.00 0.00 4.18
4306 10368 5.356882 TTTTTACAGCAAGATTGACCGAG 57.643 39.130 0.00 0.00 0.00 4.63
4410 10472 2.167693 CCGCCAATCTACCTTACAGACA 59.832 50.000 0.00 0.00 0.00 3.41
4411 10473 2.822764 CCGCCAATCTACCTTACAGAC 58.177 52.381 0.00 0.00 0.00 3.51
4415 10477 2.364647 AGTAGCCGCCAATCTACCTTAC 59.635 50.000 0.00 0.00 36.67 2.34
4478 10543 4.085357 AGTTCCATATATTGAAGCCGCA 57.915 40.909 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.