Multiple sequence alignment - TraesCS7A01G233700

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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 TraesCS7A01G233700 chr7A 100.000 6072 0 0 1 6072 205470977 205464906 0.000000e+00 11213.0
1 TraesCS7A01G233700 chr7A 96.154 52 2 0 1 52 407020215 407020266 1.080000e-12 86.1
2 TraesCS7A01G233700 chr7B 95.818 4495 134 21 804 5262 159520908 159516432 0.000000e+00 7210.0
3 TraesCS7A01G233700 chr7B 95.528 492 18 3 5354 5842 159516432 159515942 0.000000e+00 784.0
4 TraesCS7A01G233700 chr7B 97.854 233 4 1 5840 6072 159515858 159515627 9.480000e-108 401.0
5 TraesCS7A01G233700 chr7B 92.424 66 4 1 1 66 389447960 389447896 6.480000e-15 93.5
6 TraesCS7A01G233700 chr7B 89.041 73 4 3 1 73 304792392 304792324 3.010000e-13 87.9
7 TraesCS7A01G233700 chr7D 95.501 1778 56 9 1467 3236 195633548 195631787 0.000000e+00 2819.0
8 TraesCS7A01G233700 chr7D 94.399 1357 42 15 3939 5262 195631102 195629747 0.000000e+00 2054.0
9 TraesCS7A01G233700 chr7D 95.101 694 21 5 3214 3907 195631778 195631098 0.000000e+00 1081.0
10 TraesCS7A01G233700 chr7D 97.039 608 16 2 860 1466 195634296 195633690 0.000000e+00 1022.0
11 TraesCS7A01G233700 chr7D 93.137 408 20 5 5354 5756 195629747 195629343 5.240000e-165 592.0
12 TraesCS7A01G233700 chr7D 85.507 552 60 8 333 867 195635747 195635199 5.320000e-155 558.0
13 TraesCS7A01G233700 chr7D 96.687 332 11 0 5741 6072 195629328 195628997 2.470000e-153 553.0
14 TraesCS7A01G233700 chr7D 89.510 286 24 3 52 337 195644076 195643797 2.080000e-94 357.0
15 TraesCS7A01G233700 chr7D 93.333 105 7 0 5252 5356 489010680 489010784 8.150000e-34 156.0
16 TraesCS7A01G233700 chr7D 93.269 104 7 0 5255 5358 182833454 182833557 2.930000e-33 154.0
17 TraesCS7A01G233700 chr7D 94.059 101 6 0 5256 5356 592857513 592857613 2.930000e-33 154.0
18 TraesCS7A01G233700 chr5D 76.910 589 113 19 56 631 390262547 390263125 4.570000e-81 313.0
19 TraesCS7A01G233700 chr5D 94.118 102 6 0 5256 5357 513514562 513514663 8.150000e-34 156.0
20 TraesCS7A01G233700 chr6D 95.050 101 4 1 5259 5359 428262137 428262038 2.270000e-34 158.0
21 TraesCS7A01G233700 chr6A 94.059 101 6 0 5256 5356 23355177 23355077 2.930000e-33 154.0
22 TraesCS7A01G233700 chr3D 91.743 109 7 2 5255 5362 48071012 48070905 3.790000e-32 150.0
23 TraesCS7A01G233700 chr2B 91.589 107 9 0 5259 5365 575876622 575876516 1.360000e-31 148.0
24 TraesCS7A01G233700 chr4B 88.525 122 13 1 5234 5355 555242101 555241981 4.900000e-31 147.0
25 TraesCS7A01G233700 chr2A 95.082 61 3 0 1 61 449346654 449346594 5.010000e-16 97.1
26 TraesCS7A01G233700 chr4A 92.537 67 4 1 1 67 137710815 137710750 1.800000e-15 95.3
27 TraesCS7A01G233700 chr5B 92.424 66 3 2 1 65 430025962 430026026 6.480000e-15 93.5
28 TraesCS7A01G233700 chr5A 91.304 69 5 1 1 69 288488663 288488596 6.480000e-15 93.5
29 TraesCS7A01G233700 chr5A 91.045 67 6 0 1 67 486226205 486226271 2.330000e-14 91.6
30 TraesCS7A01G233700 chr1A 85.057 87 10 3 1 86 321632484 321632400 1.080000e-12 86.1


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 TraesCS7A01G233700 chr7A 205464906 205470977 6071 True 11213.000000 11213 100.000000 1 6072 1 chr7A.!!$R1 6071
1 TraesCS7A01G233700 chr7B 159515627 159520908 5281 True 2798.333333 7210 96.400000 804 6072 3 chr7B.!!$R3 5268
2 TraesCS7A01G233700 chr7D 195628997 195635747 6750 True 1239.857143 2819 93.910143 333 6072 7 chr7D.!!$R2 5739
3 TraesCS7A01G233700 chr5D 390262547 390263125 578 False 313.000000 313 76.910000 56 631 1 chr5D.!!$F1 575

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
61 62 0.040425 AACGCCGACAAGATTGTTGC 60.040 50.000 7.34 8.68 42.43 4.17 F
488 496 0.108662 ACGCATGCTGACGAGAATGA 60.109 50.000 17.13 0.00 37.42 2.57 F
489 497 1.001624 CGCATGCTGACGAGAATGAA 58.998 50.000 17.13 0.00 37.42 2.57 F
645 655 1.175983 CGCTTTGGGGCAACTGGTAA 61.176 55.000 0.00 0.00 0.00 2.85 F
704 714 1.632409 ACCTGCCATGTCAGAATCTGT 59.368 47.619 5.06 0.00 36.19 3.41 F
1759 2837 1.882912 TGGCTAGCACTTTGACTGTG 58.117 50.000 18.24 0.00 38.36 3.66 F
2616 3701 0.713883 ATACGCTGCGAACTTGAACG 59.286 50.000 30.47 0.00 0.00 3.95 F
3132 4227 0.742505 AGACAATTCCGCATGCCATG 59.257 50.000 13.15 0.00 0.00 3.66 F
4457 5591 1.142870 CCACAAGTGGTCTCCAAGGAA 59.857 52.381 11.08 0.00 45.53 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 3054 0.659427 CAGCATCATGGTTGGCTACG 59.341 55.000 0.00 0.00 34.25 3.51 R
2185 3264 2.166459 TCCACTCGCATCACCTTTCTAG 59.834 50.000 0.00 0.00 0.00 2.43 R
2335 3414 3.152341 CCAATCTTGCTCTGACCAAAGT 58.848 45.455 0.00 0.00 0.00 2.66 R
2495 3574 1.065854 GTGGGCAGATGAGCAGTACTT 60.066 52.381 0.00 0.00 35.83 2.24 R
2616 3701 4.975502 TGACGAAACAGAAATGAACATTGC 59.024 37.500 0.69 0.00 0.00 3.56 R
2997 4086 2.125391 TGCATCACTGAGGCGAGC 60.125 61.111 10.89 0.00 42.60 5.03 R
4610 5744 0.109781 CAGCAACCGAATTTCCACCG 60.110 55.000 0.00 0.00 0.00 4.94 R
4830 5967 2.642982 TCCCATGGGAAGGAGAGAAAA 58.357 47.619 32.09 3.29 42.05 2.29 R
5348 6522 0.249489 CCATGCTACGTGCTACTCCC 60.249 60.000 0.00 0.00 43.37 4.30 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
23 24 2.652530 CCGCATGCAGGCAAGTTT 59.347 55.556 24.53 0.00 0.00 2.66
24 25 1.735198 CCGCATGCAGGCAAGTTTG 60.735 57.895 24.53 5.38 0.00 2.93
25 26 1.735198 CGCATGCAGGCAAGTTTGG 60.735 57.895 24.53 0.41 0.00 3.28
26 27 1.375013 GCATGCAGGCAAGTTTGGG 60.375 57.895 20.11 0.00 0.00 4.12
27 28 1.294138 CATGCAGGCAAGTTTGGGG 59.706 57.895 0.00 0.00 0.00 4.96
28 29 1.155859 ATGCAGGCAAGTTTGGGGA 59.844 52.632 0.00 0.00 0.00 4.81
29 30 1.187567 ATGCAGGCAAGTTTGGGGAC 61.188 55.000 0.00 0.00 0.00 4.46
43 44 2.931649 GGACCCCCGTTCCCAGAA 60.932 66.667 0.00 0.00 0.00 3.02
44 45 2.350134 GACCCCCGTTCCCAGAAC 59.650 66.667 0.00 0.00 0.00 3.01
45 46 3.600898 GACCCCCGTTCCCAGAACG 62.601 68.421 19.99 19.99 42.74 3.95
49 50 4.367023 CCGTTCCCAGAACGCCGA 62.367 66.667 21.18 0.00 41.85 5.54
50 51 3.110178 CGTTCCCAGAACGCCGAC 61.110 66.667 15.91 0.00 36.82 4.79
51 52 2.029964 GTTCCCAGAACGCCGACA 59.970 61.111 0.00 0.00 0.00 4.35
52 53 1.595929 GTTCCCAGAACGCCGACAA 60.596 57.895 0.00 0.00 0.00 3.18
53 54 1.301401 TTCCCAGAACGCCGACAAG 60.301 57.895 0.00 0.00 0.00 3.16
54 55 1.750341 TTCCCAGAACGCCGACAAGA 61.750 55.000 0.00 0.00 0.00 3.02
57 58 0.443869 CCAGAACGCCGACAAGATTG 59.556 55.000 0.00 0.00 0.00 2.67
61 62 0.040425 AACGCCGACAAGATTGTTGC 60.040 50.000 7.34 8.68 42.43 4.17
88 89 3.611766 AGTGGATACTCGTTTGAAGGG 57.388 47.619 0.00 0.00 28.79 3.95
104 105 5.304686 TGAAGGGTTTTTCTGCTAGAGAA 57.695 39.130 0.00 0.00 39.05 2.87
107 108 7.633789 TGAAGGGTTTTTCTGCTAGAGAATAT 58.366 34.615 0.00 0.00 40.53 1.28
108 109 8.109634 TGAAGGGTTTTTCTGCTAGAGAATATT 58.890 33.333 0.00 0.00 40.53 1.28
113 114 9.047371 GGTTTTTCTGCTAGAGAATATTAGTCC 57.953 37.037 0.00 0.00 40.53 3.85
114 115 9.601217 GTTTTTCTGCTAGAGAATATTAGTCCA 57.399 33.333 0.00 0.00 40.53 4.02
118 119 8.172352 TCTGCTAGAGAATATTAGTCCAACTC 57.828 38.462 0.00 0.00 0.00 3.01
119 120 7.780271 TCTGCTAGAGAATATTAGTCCAACTCA 59.220 37.037 0.00 0.00 0.00 3.41
120 121 8.306313 TGCTAGAGAATATTAGTCCAACTCAA 57.694 34.615 0.00 0.00 0.00 3.02
139 141 3.699067 CAAAGTGCTTTGTGACTGGAAG 58.301 45.455 14.55 0.00 43.52 3.46
143 145 4.973168 AGTGCTTTGTGACTGGAAGAATA 58.027 39.130 0.00 0.00 37.43 1.75
148 150 7.750903 GTGCTTTGTGACTGGAAGAATAATTAC 59.249 37.037 0.00 0.00 37.43 1.89
150 152 8.296713 GCTTTGTGACTGGAAGAATAATTACAA 58.703 33.333 0.00 0.00 37.43 2.41
157 159 8.986477 ACTGGAAGAATAATTACAAACAATGC 57.014 30.769 0.00 0.00 37.43 3.56
158 160 8.806146 ACTGGAAGAATAATTACAAACAATGCT 58.194 29.630 0.00 0.00 37.43 3.79
179 181 4.156739 GCTTTACTGGCTTATGAGTGCTTT 59.843 41.667 0.00 0.00 0.00 3.51
182 184 3.960571 ACTGGCTTATGAGTGCTTTCAT 58.039 40.909 8.28 8.28 40.70 2.57
188 190 6.377996 TGGCTTATGAGTGCTTTCATACAATT 59.622 34.615 9.36 0.00 39.19 2.32
209 211 7.922811 ACAATTAAAAACAAGAGAGAAGGCAAG 59.077 33.333 0.00 0.00 0.00 4.01
216 218 0.988063 GAGAGAAGGCAAGGAGGGTT 59.012 55.000 0.00 0.00 0.00 4.11
218 220 1.074566 AGAGAAGGCAAGGAGGGTTTG 59.925 52.381 0.00 0.00 0.00 2.93
220 222 2.039879 GAGAAGGCAAGGAGGGTTTGTA 59.960 50.000 0.00 0.00 0.00 2.41
223 225 3.646736 AGGCAAGGAGGGTTTGTATAC 57.353 47.619 0.00 0.00 0.00 1.47
227 229 5.071923 AGGCAAGGAGGGTTTGTATACTATC 59.928 44.000 4.17 0.00 0.00 2.08
235 237 7.282450 GGAGGGTTTGTATACTATCAAACTTGG 59.718 40.741 16.44 0.00 46.88 3.61
236 238 7.696017 AGGGTTTGTATACTATCAAACTTGGT 58.304 34.615 16.44 0.00 46.88 3.67
243 245 9.845740 TGTATACTATCAAACTTGGTATGCATT 57.154 29.630 3.54 0.00 33.21 3.56
245 247 8.752005 ATACTATCAAACTTGGTATGCATTGT 57.248 30.769 3.54 0.00 0.00 2.71
246 248 7.466746 ACTATCAAACTTGGTATGCATTGTT 57.533 32.000 3.54 0.36 0.00 2.83
247 249 7.315142 ACTATCAAACTTGGTATGCATTGTTG 58.685 34.615 3.54 0.00 0.00 3.33
248 250 5.781210 TCAAACTTGGTATGCATTGTTGA 57.219 34.783 3.54 2.23 0.00 3.18
262 269 4.158394 GCATTGTTGATATGGTTGAGTGGT 59.842 41.667 0.00 0.00 0.00 4.16
270 277 7.252612 TGATATGGTTGAGTGGTCTTTCTTA 57.747 36.000 0.00 0.00 0.00 2.10
275 282 4.519350 GGTTGAGTGGTCTTTCTTAAAGGG 59.481 45.833 0.00 0.00 39.01 3.95
305 312 3.897239 TGAAACTTGGCTTCCAGAAGAA 58.103 40.909 11.57 0.00 40.79 2.52
309 316 4.104383 ACTTGGCTTCCAGAAGAATTGA 57.896 40.909 11.57 0.00 40.79 2.57
316 323 5.184671 GGCTTCCAGAAGAATTGAGTCAATT 59.815 40.000 27.23 27.23 45.25 2.32
321 328 9.965824 TTCCAGAAGAATTGAGTCAATTTTTAC 57.034 29.630 27.48 20.39 43.05 2.01
381 388 5.843673 TTTAACATGCAACAAAGTGAGGA 57.156 34.783 0.00 0.00 0.00 3.71
396 403 7.123547 ACAAAGTGAGGATTTCAAACCTACAAA 59.876 33.333 0.00 0.00 37.61 2.83
464 471 0.964358 CACGGAGGGTCGGACTACTT 60.964 60.000 8.23 0.00 0.00 2.24
477 485 3.522553 GGACTACTTTCTTACGCATGCT 58.477 45.455 17.13 5.50 0.00 3.79
480 488 3.927142 ACTACTTTCTTACGCATGCTGAC 59.073 43.478 17.13 0.00 0.00 3.51
488 496 0.108662 ACGCATGCTGACGAGAATGA 60.109 50.000 17.13 0.00 37.42 2.57
489 497 1.001624 CGCATGCTGACGAGAATGAA 58.998 50.000 17.13 0.00 37.42 2.57
515 523 5.627499 ATTTCTAGAGCGAATGTTTGCAA 57.373 34.783 7.65 0.00 40.10 4.08
521 529 3.254166 AGAGCGAATGTTTGCAAAGATGT 59.746 39.130 21.21 11.93 40.10 3.06
539 547 2.481441 TGTCCCTGCTATCACCAATCT 58.519 47.619 0.00 0.00 0.00 2.40
541 549 3.118261 TGTCCCTGCTATCACCAATCTTC 60.118 47.826 0.00 0.00 0.00 2.87
542 550 3.114606 TCCCTGCTATCACCAATCTTCA 58.885 45.455 0.00 0.00 0.00 3.02
543 551 3.118261 TCCCTGCTATCACCAATCTTCAC 60.118 47.826 0.00 0.00 0.00 3.18
544 552 3.118112 CCCTGCTATCACCAATCTTCACT 60.118 47.826 0.00 0.00 0.00 3.41
545 553 4.125703 CCTGCTATCACCAATCTTCACTC 58.874 47.826 0.00 0.00 0.00 3.51
548 556 5.423015 TGCTATCACCAATCTTCACTCTTC 58.577 41.667 0.00 0.00 0.00 2.87
550 558 6.381133 TGCTATCACCAATCTTCACTCTTCTA 59.619 38.462 0.00 0.00 0.00 2.10
551 559 7.093333 TGCTATCACCAATCTTCACTCTTCTAA 60.093 37.037 0.00 0.00 0.00 2.10
552 560 7.437862 GCTATCACCAATCTTCACTCTTCTAAG 59.562 40.741 0.00 0.00 0.00 2.18
557 566 6.071051 ACCAATCTTCACTCTTCTAAGGACTC 60.071 42.308 0.00 0.00 0.00 3.36
570 580 3.460857 AAGGACTCGTTATCCTCATGC 57.539 47.619 5.54 0.00 46.36 4.06
571 581 1.689273 AGGACTCGTTATCCTCATGCC 59.311 52.381 0.00 0.00 43.49 4.40
579 589 4.067896 CGTTATCCTCATGCCAGCTAATT 58.932 43.478 0.00 0.00 0.00 1.40
583 593 7.255104 CGTTATCCTCATGCCAGCTAATTTTTA 60.255 37.037 0.00 0.00 0.00 1.52
591 601 3.181491 GCCAGCTAATTTTTACGATGCCA 60.181 43.478 0.00 0.00 0.00 4.92
602 612 5.759506 TTTACGATGCCAAGTCTTTGAAA 57.240 34.783 0.00 0.00 36.36 2.69
609 619 4.935702 TGCCAAGTCTTTGAAATCAGTTG 58.064 39.130 0.00 0.02 36.36 3.16
631 641 2.084546 GGATTCTTACTGTGCCGCTTT 58.915 47.619 0.00 0.00 0.00 3.51
645 655 1.175983 CGCTTTGGGGCAACTGGTAA 61.176 55.000 0.00 0.00 0.00 2.85
675 685 8.463930 TGATAAGTCCAACATCTTTTTCAGTT 57.536 30.769 0.00 0.00 0.00 3.16
676 686 8.912988 TGATAAGTCCAACATCTTTTTCAGTTT 58.087 29.630 0.00 0.00 0.00 2.66
694 704 3.584848 AGTTTCTAGAGAACCTGCCATGT 59.415 43.478 11.70 0.00 33.13 3.21
701 711 2.941720 GAGAACCTGCCATGTCAGAATC 59.058 50.000 5.06 3.14 36.19 2.52
704 714 1.632409 ACCTGCCATGTCAGAATCTGT 59.368 47.619 5.06 0.00 36.19 3.41
714 724 3.109619 GTCAGAATCTGTACTAGCGTGC 58.890 50.000 10.36 0.00 32.61 5.34
734 758 6.478588 CGTGCTGAAGGACTTTGTATTATTC 58.521 40.000 0.37 0.00 33.97 1.75
736 760 6.374333 GTGCTGAAGGACTTTGTATTATTCCA 59.626 38.462 0.00 0.00 33.32 3.53
780 804 8.397575 ACTTGTTTTCTTAAAAAGGCCAAAAA 57.602 26.923 5.01 0.00 35.10 1.94
794 818 7.801716 AAGGCCAAAAATTTCTCTAAAAACC 57.198 32.000 5.01 0.00 0.00 3.27
851 875 6.633634 CACATTGTGCAATTTTCATTTGGTTC 59.366 34.615 3.43 0.00 0.00 3.62
889 1825 2.473378 CTGCTGAGAACGCAAGCG 59.527 61.111 13.50 13.50 46.03 4.68
928 1864 2.817258 TCACCATTCAACACCGAATTCC 59.183 45.455 0.00 0.00 33.27 3.01
1399 2336 3.961182 AGCATGTTTGATGATCGCATTC 58.039 40.909 0.00 0.00 34.11 2.67
1473 2551 5.705609 TTTCTGCTGAATTAGTTGGTTCC 57.294 39.130 6.88 0.00 31.56 3.62
1506 2584 7.001674 TCTGCTCTTAATTGGTTTGGTTCTAA 58.998 34.615 0.00 0.00 0.00 2.10
1632 2710 1.941999 GCACCCAGCATTGCTCTTCC 61.942 60.000 8.54 0.00 44.79 3.46
1658 2736 5.355071 TGTGTTGGTGCTCTGATATTGATTC 59.645 40.000 0.00 0.00 0.00 2.52
1755 2833 3.181491 TGTTTGTTGGCTAGCACTTTGAC 60.181 43.478 18.24 8.60 0.00 3.18
1759 2837 1.882912 TGGCTAGCACTTTGACTGTG 58.117 50.000 18.24 0.00 38.36 3.66
1867 2945 3.094572 AGAACTGATTGATGCCCCAAAG 58.905 45.455 0.00 0.00 0.00 2.77
1959 3038 6.088085 CGTTTTCCTCAATTATTGCTGTTCAC 59.912 38.462 0.00 0.00 0.00 3.18
1975 3054 7.904094 TGCTGTTCACATTTGTTTATTTTGTC 58.096 30.769 0.00 0.00 0.00 3.18
2049 3128 9.136468 CATATTTTCGTATAATTGCATCGATCG 57.864 33.333 9.36 9.36 0.00 3.69
2185 3264 8.196771 TGGAAATAATGAATTACTCCACAATGC 58.803 33.333 9.92 0.00 34.85 3.56
2297 3376 2.233676 TCATGTCACCGAACTGCTACAT 59.766 45.455 0.00 0.00 0.00 2.29
2356 3435 3.152341 ACTTTGGTCAGAGCAAGATTGG 58.848 45.455 14.53 7.26 36.89 3.16
2374 3453 6.694447 AGATTGGTATTCATTGCATTATGGC 58.306 36.000 0.00 0.00 0.00 4.40
2495 3574 7.922278 GGTATTGACGTATTGTGTTCATACCTA 59.078 37.037 0.00 0.00 34.71 3.08
2534 3614 4.019174 CCACAAATTCTCCCACTGCTATT 58.981 43.478 0.00 0.00 0.00 1.73
2535 3615 4.463891 CCACAAATTCTCCCACTGCTATTT 59.536 41.667 0.00 0.00 0.00 1.40
2616 3701 0.713883 ATACGCTGCGAACTTGAACG 59.286 50.000 30.47 0.00 0.00 3.95
2903 3989 1.931172 GCAAATTGCTCACATGGATGC 59.069 47.619 11.19 0.00 40.96 3.91
2997 4086 3.531982 CAGAAGTTTGCTGTACGTTTCG 58.468 45.455 0.00 0.00 0.00 3.46
3048 4143 6.012658 TGAATAGTGTGAAGGTGCAATTTC 57.987 37.500 0.00 0.00 0.00 2.17
3059 4154 4.786425 AGGTGCAATTTCCTATCCTTCTC 58.214 43.478 0.00 0.00 31.66 2.87
3104 4199 3.055167 TGTGGCTCAGCACAGTTATGTAT 60.055 43.478 0.00 0.00 37.65 2.29
3132 4227 0.742505 AGACAATTCCGCATGCCATG 59.257 50.000 13.15 0.00 0.00 3.66
3282 4407 6.308766 GCTTATTTTGCATGTGAACTTACTGG 59.691 38.462 0.00 0.00 0.00 4.00
3403 4537 3.837213 AAATGCTCACGACCATTTCTG 57.163 42.857 0.00 0.00 37.12 3.02
3407 4541 2.224281 TGCTCACGACCATTTCTGAAGT 60.224 45.455 0.00 0.00 0.00 3.01
3408 4542 3.006430 TGCTCACGACCATTTCTGAAGTA 59.994 43.478 0.00 0.00 0.00 2.24
3409 4543 3.368236 GCTCACGACCATTTCTGAAGTAC 59.632 47.826 0.00 0.00 0.00 2.73
3481 4615 2.599645 ATACAGCGCCTCCCTGCTTG 62.600 60.000 2.29 0.00 40.03 4.01
3540 4674 7.100409 GGACTGGATAAGACTATTTAGGATGC 58.900 42.308 0.00 0.00 0.00 3.91
3587 4721 6.810182 ACTACGTGTTACTGAATTTCGCTTAT 59.190 34.615 0.00 0.00 0.00 1.73
3631 4765 7.045416 TGTGTGGTACTTTACTTATGCCATAG 58.955 38.462 0.00 0.00 0.00 2.23
3700 4834 3.788227 AGTTTGCTTACATGGGAGTCA 57.212 42.857 0.00 0.00 0.00 3.41
3739 4873 8.989653 ACTACTGTGTTAGCTTAGATTTTCTC 57.010 34.615 0.00 0.00 0.00 2.87
3828 4962 9.953825 GTAAAGTATTATGTTCTCTCAAACACG 57.046 33.333 0.00 0.00 41.65 4.49
3880 5014 1.808945 CTCTCAAGCAACACCATGGAC 59.191 52.381 21.47 1.94 0.00 4.02
3915 5049 3.490933 GGAAGCGACTATATGTGTGAGCA 60.491 47.826 0.00 0.00 0.00 4.26
4174 5308 9.556030 CATTGCTACAAATATCAATAGCATCTG 57.444 33.333 12.84 10.59 46.91 2.90
4187 5321 1.831580 GCATCTGCTCTGGTTTTCCT 58.168 50.000 0.00 0.00 38.32 3.36
4214 5348 2.538760 TCTGGCTTCCCTGAGGGT 59.461 61.111 18.83 0.00 44.74 4.34
4333 5467 5.990996 TCTTCATTTTGAATTTTGCTGGTCC 59.009 36.000 0.00 0.00 35.59 4.46
4343 5477 7.042950 TGAATTTTGCTGGTCCATTATCAATG 58.957 34.615 0.00 0.00 38.63 2.82
4457 5591 1.142870 CCACAAGTGGTCTCCAAGGAA 59.857 52.381 11.08 0.00 45.53 3.36
4578 5712 6.550854 TGGTTTCATTCCATCTTTTTCTGACT 59.449 34.615 0.00 0.00 0.00 3.41
4811 5948 2.639839 GCTGTAGACATATGTGGGGGAT 59.360 50.000 14.43 0.00 0.00 3.85
4830 5967 5.440610 GGGATGACTCTTTTCATGGTATGT 58.559 41.667 0.00 0.00 36.30 2.29
4985 6158 6.293407 CCTCGTTTCACACACTTGTATTGATT 60.293 38.462 0.00 0.00 33.30 2.57
4993 6166 9.203421 TCACACACTTGTATTGATTAAGTACTG 57.797 33.333 0.00 0.00 33.63 2.74
4994 6167 7.957484 CACACACTTGTATTGATTAAGTACTGC 59.043 37.037 0.00 0.00 33.63 4.40
5000 6173 7.921786 TGTATTGATTAAGTACTGCTGCTTT 57.078 32.000 0.00 0.00 0.00 3.51
5081 6254 3.121030 CCTCTTGAACGCCGCTGG 61.121 66.667 0.00 0.00 0.00 4.85
5106 6279 2.421424 GCCTTACTTGCCTCTGACAATG 59.579 50.000 0.00 0.00 0.00 2.82
5131 6304 4.593597 ACAAATGTAATGGTAGTTCGCG 57.406 40.909 0.00 0.00 0.00 5.87
5167 6341 0.888619 CGTGTCAGGTCTGCTCCTAA 59.111 55.000 0.00 0.00 35.87 2.69
5254 6428 2.423446 TATGCTGCATGCTTTCTCCA 57.577 45.000 24.59 7.06 43.37 3.86
5261 6435 3.689347 TGCATGCTTTCTCCAATGTACT 58.311 40.909 20.33 0.00 0.00 2.73
5262 6436 3.691118 TGCATGCTTTCTCCAATGTACTC 59.309 43.478 20.33 0.00 0.00 2.59
5263 6437 3.065925 GCATGCTTTCTCCAATGTACTCC 59.934 47.826 11.37 0.00 0.00 3.85
5264 6438 3.350219 TGCTTTCTCCAATGTACTCCC 57.650 47.619 0.00 0.00 0.00 4.30
5265 6439 2.912956 TGCTTTCTCCAATGTACTCCCT 59.087 45.455 0.00 0.00 0.00 4.20
5266 6440 3.055094 TGCTTTCTCCAATGTACTCCCTC 60.055 47.826 0.00 0.00 0.00 4.30
5267 6441 3.682999 GCTTTCTCCAATGTACTCCCTCC 60.683 52.174 0.00 0.00 0.00 4.30
5268 6442 1.776662 TCTCCAATGTACTCCCTCCG 58.223 55.000 0.00 0.00 0.00 4.63
5269 6443 1.006758 TCTCCAATGTACTCCCTCCGT 59.993 52.381 0.00 0.00 0.00 4.69
5270 6444 1.831736 CTCCAATGTACTCCCTCCGTT 59.168 52.381 0.00 0.00 0.00 4.44
5271 6445 1.829222 TCCAATGTACTCCCTCCGTTC 59.171 52.381 0.00 0.00 0.00 3.95
5272 6446 1.134491 CCAATGTACTCCCTCCGTTCC 60.134 57.143 0.00 0.00 0.00 3.62
5273 6447 1.553248 CAATGTACTCCCTCCGTTCCA 59.447 52.381 0.00 0.00 0.00 3.53
5274 6448 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
5275 6449 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
5276 6450 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
5277 6451 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
5278 6452 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
5279 6453 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5280 6454 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5281 6455 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5282 6456 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5283 6457 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5284 6458 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
5285 6459 5.104109 TCCCTCCGTTCCAAAATAGATGATT 60.104 40.000 0.00 0.00 0.00 2.57
5286 6460 5.239525 CCCTCCGTTCCAAAATAGATGATTC 59.760 44.000 0.00 0.00 0.00 2.52
5287 6461 5.822519 CCTCCGTTCCAAAATAGATGATTCA 59.177 40.000 0.00 0.00 0.00 2.57
5288 6462 6.318648 CCTCCGTTCCAAAATAGATGATTCAA 59.681 38.462 0.00 0.00 0.00 2.69
5289 6463 7.083875 TCCGTTCCAAAATAGATGATTCAAC 57.916 36.000 0.00 0.00 0.00 3.18
5290 6464 6.884295 TCCGTTCCAAAATAGATGATTCAACT 59.116 34.615 1.83 1.83 0.00 3.16
5291 6465 7.393234 TCCGTTCCAAAATAGATGATTCAACTT 59.607 33.333 1.47 0.00 0.00 2.66
5292 6466 8.028938 CCGTTCCAAAATAGATGATTCAACTTT 58.971 33.333 1.47 0.00 0.00 2.66
5293 6467 8.853345 CGTTCCAAAATAGATGATTCAACTTTG 58.147 33.333 1.47 1.65 0.00 2.77
5294 6468 9.696917 GTTCCAAAATAGATGATTCAACTTTGT 57.303 29.630 1.47 0.00 0.00 2.83
5345 6519 8.574196 AAAGTTGAGTCATTTATTTTGGAACG 57.426 30.769 0.00 0.00 0.00 3.95
5346 6520 6.677913 AGTTGAGTCATTTATTTTGGAACGG 58.322 36.000 0.00 0.00 0.00 4.44
5347 6521 6.488683 AGTTGAGTCATTTATTTTGGAACGGA 59.511 34.615 0.00 0.00 0.00 4.69
5348 6522 6.494893 TGAGTCATTTATTTTGGAACGGAG 57.505 37.500 0.00 0.00 0.00 4.63
5349 6523 5.414454 TGAGTCATTTATTTTGGAACGGAGG 59.586 40.000 0.00 0.00 0.00 4.30
5350 6524 4.705023 AGTCATTTATTTTGGAACGGAGGG 59.295 41.667 0.00 0.00 0.00 4.30
5351 6525 4.703093 GTCATTTATTTTGGAACGGAGGGA 59.297 41.667 0.00 0.00 0.00 4.20
5352 6526 4.947388 TCATTTATTTTGGAACGGAGGGAG 59.053 41.667 0.00 0.00 0.00 4.30
5411 6586 9.057089 ACGAATTATTAATCCAGAAGCTTTAGG 57.943 33.333 0.00 6.07 0.00 2.69
5516 6696 2.305928 TGCTGTTGCCTTTATGTGTGT 58.694 42.857 0.00 0.00 38.71 3.72
5531 6711 4.330944 TGTGTGTCTGAGTACGGAATTT 57.669 40.909 0.00 0.00 32.84 1.82
5554 6734 1.692762 GGACTTATGGGGAGCCTCTCA 60.693 57.143 0.00 0.00 31.08 3.27
5564 6744 7.588866 ATGGGGAGCCTCTCATATTTTTATA 57.411 36.000 0.00 0.00 31.08 0.98
5653 6834 4.873187 ATGAAACACATGGGCTCATTAGCT 60.873 41.667 0.00 0.00 42.14 3.32
5714 6895 3.302365 AGTGAAAAACATTGATGGGCG 57.698 42.857 0.00 0.00 0.00 6.13
5742 6923 2.107950 TGTATGACCGCCTGGAAAAG 57.892 50.000 0.00 0.00 39.21 2.27
5797 7006 2.432628 CGCCTGGACCAACGAGAC 60.433 66.667 10.35 0.00 0.00 3.36
5832 7041 2.165030 ACACACCCTATAGTTTCGTCGG 59.835 50.000 0.00 0.00 0.00 4.79
5895 7189 8.341903 TCAGTAACAATTTACATGTGACAACAG 58.658 33.333 9.11 0.00 40.25 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.735198 CAAACTTGCCTGCATGCGG 60.735 57.895 20.13 20.13 0.00 5.69
7 8 1.735198 CCAAACTTGCCTGCATGCG 60.735 57.895 14.09 7.87 0.00 4.73
8 9 1.375013 CCCAAACTTGCCTGCATGC 60.375 57.895 11.82 11.82 0.00 4.06
9 10 1.186917 TCCCCAAACTTGCCTGCATG 61.187 55.000 3.71 3.71 0.00 4.06
10 11 1.155859 TCCCCAAACTTGCCTGCAT 59.844 52.632 0.00 0.00 0.00 3.96
11 12 1.832167 GTCCCCAAACTTGCCTGCA 60.832 57.895 0.00 0.00 0.00 4.41
12 13 2.574018 GGTCCCCAAACTTGCCTGC 61.574 63.158 0.00 0.00 0.00 4.85
13 14 1.908299 GGGTCCCCAAACTTGCCTG 60.908 63.158 0.00 0.00 35.81 4.85
14 15 2.526110 GGGTCCCCAAACTTGCCT 59.474 61.111 0.00 0.00 35.81 4.75
15 16 2.603473 GGGGTCCCCAAACTTGCC 60.603 66.667 23.53 0.00 44.65 4.52
26 27 2.931649 TTCTGGGAACGGGGGTCC 60.932 66.667 0.00 0.00 37.31 4.46
27 28 2.350134 GTTCTGGGAACGGGGGTC 59.650 66.667 0.00 0.00 37.31 4.46
28 29 3.633116 CGTTCTGGGAACGGGGGT 61.633 66.667 20.56 0.00 39.73 4.95
32 33 4.367023 TCGGCGTTCTGGGAACGG 62.367 66.667 26.41 15.26 43.25 4.44
33 34 3.110178 GTCGGCGTTCTGGGAACG 61.110 66.667 22.95 22.95 45.56 3.95
34 35 1.566018 CTTGTCGGCGTTCTGGGAAC 61.566 60.000 6.85 0.00 0.00 3.62
35 36 1.301401 CTTGTCGGCGTTCTGGGAA 60.301 57.895 6.85 0.00 0.00 3.97
36 37 1.541310 ATCTTGTCGGCGTTCTGGGA 61.541 55.000 6.85 0.00 0.00 4.37
37 38 0.673644 AATCTTGTCGGCGTTCTGGG 60.674 55.000 6.85 0.00 0.00 4.45
38 39 0.443869 CAATCTTGTCGGCGTTCTGG 59.556 55.000 6.85 0.00 0.00 3.86
39 40 1.148310 ACAATCTTGTCGGCGTTCTG 58.852 50.000 6.85 0.00 36.50 3.02
40 41 1.531149 CAACAATCTTGTCGGCGTTCT 59.469 47.619 6.85 0.00 41.31 3.01
41 42 1.950472 CAACAATCTTGTCGGCGTTC 58.050 50.000 6.85 2.07 41.31 3.95
42 43 0.040425 GCAACAATCTTGTCGGCGTT 60.040 50.000 6.85 0.00 41.31 4.84
43 44 1.163420 TGCAACAATCTTGTCGGCGT 61.163 50.000 6.85 0.00 41.31 5.68
44 45 0.040514 TTGCAACAATCTTGTCGGCG 60.041 50.000 0.00 0.00 41.31 6.46
45 46 2.132740 TTTGCAACAATCTTGTCGGC 57.867 45.000 0.00 10.85 41.31 5.54
67 68 3.326880 ACCCTTCAAACGAGTATCCACTT 59.673 43.478 0.00 0.00 34.21 3.16
68 69 2.904434 ACCCTTCAAACGAGTATCCACT 59.096 45.455 0.00 0.00 37.87 4.00
73 74 5.278315 GCAGAAAAACCCTTCAAACGAGTAT 60.278 40.000 0.00 0.00 0.00 2.12
74 75 4.035909 GCAGAAAAACCCTTCAAACGAGTA 59.964 41.667 0.00 0.00 0.00 2.59
88 89 9.601217 TGGACTAATATTCTCTAGCAGAAAAAC 57.399 33.333 8.18 0.00 44.66 2.43
119 120 3.620488 TCTTCCAGTCACAAAGCACTTT 58.380 40.909 0.00 0.00 0.00 2.66
120 121 3.281727 TCTTCCAGTCACAAAGCACTT 57.718 42.857 0.00 0.00 0.00 3.16
132 134 8.806146 AGCATTGTTTGTAATTATTCTTCCAGT 58.194 29.630 0.00 0.00 0.00 4.00
143 145 6.758254 AGCCAGTAAAGCATTGTTTGTAATT 58.242 32.000 0.00 0.00 0.00 1.40
148 150 6.389091 TCATAAGCCAGTAAAGCATTGTTTG 58.611 36.000 0.00 0.00 0.00 2.93
150 152 5.711976 ACTCATAAGCCAGTAAAGCATTGTT 59.288 36.000 0.00 0.00 0.00 2.83
157 159 5.412594 TGAAAGCACTCATAAGCCAGTAAAG 59.587 40.000 0.00 0.00 0.00 1.85
158 160 5.312895 TGAAAGCACTCATAAGCCAGTAAA 58.687 37.500 0.00 0.00 0.00 2.01
162 164 4.877823 TGTATGAAAGCACTCATAAGCCAG 59.122 41.667 8.79 0.00 39.43 4.85
182 184 8.458573 TGCCTTCTCTCTTGTTTTTAATTGTA 57.541 30.769 0.00 0.00 0.00 2.41
188 190 5.690865 TCCTTGCCTTCTCTCTTGTTTTTA 58.309 37.500 0.00 0.00 0.00 1.52
194 196 1.065564 CCCTCCTTGCCTTCTCTCTTG 60.066 57.143 0.00 0.00 0.00 3.02
198 200 1.074566 CAAACCCTCCTTGCCTTCTCT 59.925 52.381 0.00 0.00 0.00 3.10
216 218 9.845740 ATGCATACCAAGTTTGATAGTATACAA 57.154 29.630 5.50 0.00 0.00 2.41
220 222 8.752005 ACAATGCATACCAAGTTTGATAGTAT 57.248 30.769 0.00 0.00 0.00 2.12
223 225 7.537715 TCAACAATGCATACCAAGTTTGATAG 58.462 34.615 0.00 0.00 0.00 2.08
227 229 7.223193 CCATATCAACAATGCATACCAAGTTTG 59.777 37.037 0.00 0.00 0.00 2.93
235 237 6.914215 CACTCAACCATATCAACAATGCATAC 59.086 38.462 0.00 0.00 0.00 2.39
236 238 6.039605 CCACTCAACCATATCAACAATGCATA 59.960 38.462 0.00 0.00 0.00 3.14
243 245 4.908601 AGACCACTCAACCATATCAACA 57.091 40.909 0.00 0.00 0.00 3.33
244 246 5.940470 AGAAAGACCACTCAACCATATCAAC 59.060 40.000 0.00 0.00 0.00 3.18
245 247 6.126863 AGAAAGACCACTCAACCATATCAA 57.873 37.500 0.00 0.00 0.00 2.57
246 248 5.762179 AGAAAGACCACTCAACCATATCA 57.238 39.130 0.00 0.00 0.00 2.15
247 249 8.561738 TTTAAGAAAGACCACTCAACCATATC 57.438 34.615 0.00 0.00 0.00 1.63
248 250 7.611855 CCTTTAAGAAAGACCACTCAACCATAT 59.388 37.037 0.47 0.00 41.02 1.78
262 269 9.594936 TTTCAACATAATCCCCTTTAAGAAAGA 57.405 29.630 0.47 0.00 41.02 2.52
270 277 5.279960 GCCAAGTTTCAACATAATCCCCTTT 60.280 40.000 0.00 0.00 0.00 3.11
275 282 5.047377 TGGAAGCCAAGTTTCAACATAATCC 60.047 40.000 0.00 0.00 0.00 3.01
396 403 6.625532 AAGGATTTCCATGCATTAAACCTT 57.374 33.333 19.40 19.40 38.89 3.50
434 441 3.537580 GACCCTCCGTGCATAACAAATA 58.462 45.455 0.00 0.00 0.00 1.40
445 452 0.964358 AAGTAGTCCGACCCTCCGTG 60.964 60.000 0.00 0.00 0.00 4.94
464 471 1.201414 TCTCGTCAGCATGCGTAAGAA 59.799 47.619 13.01 0.00 37.04 2.52
477 485 9.035607 GCTCTAGAAATATTTTCATTCTCGTCA 57.964 33.333 1.43 0.00 35.22 4.35
480 488 8.286996 TCGCTCTAGAAATATTTTCATTCTCG 57.713 34.615 1.43 2.48 35.22 4.04
488 496 8.243426 TGCAAACATTCGCTCTAGAAATATTTT 58.757 29.630 1.43 0.00 33.43 1.82
489 497 7.761409 TGCAAACATTCGCTCTAGAAATATTT 58.239 30.769 0.00 0.00 33.43 1.40
515 523 2.481441 TGGTGATAGCAGGGACATCTT 58.519 47.619 0.00 0.00 0.00 2.40
521 529 3.114606 TGAAGATTGGTGATAGCAGGGA 58.885 45.455 0.00 0.00 0.00 4.20
539 547 6.095160 GGATAACGAGTCCTTAGAAGAGTGAA 59.905 42.308 0.00 0.00 32.85 3.18
541 549 5.591067 AGGATAACGAGTCCTTAGAAGAGTG 59.409 44.000 0.00 0.00 43.52 3.51
542 550 5.757988 AGGATAACGAGTCCTTAGAAGAGT 58.242 41.667 0.00 0.00 43.52 3.24
543 551 5.823570 TGAGGATAACGAGTCCTTAGAAGAG 59.176 44.000 8.86 0.00 45.93 2.85
544 552 5.752650 TGAGGATAACGAGTCCTTAGAAGA 58.247 41.667 8.86 0.00 45.93 2.87
545 553 6.442952 CATGAGGATAACGAGTCCTTAGAAG 58.557 44.000 8.86 0.00 45.93 2.85
548 556 4.551388 GCATGAGGATAACGAGTCCTTAG 58.449 47.826 0.00 4.78 45.93 2.18
550 558 2.103263 GGCATGAGGATAACGAGTCCTT 59.897 50.000 0.00 0.00 45.93 3.36
552 560 1.412710 TGGCATGAGGATAACGAGTCC 59.587 52.381 0.00 0.00 35.94 3.85
557 566 2.820059 TAGCTGGCATGAGGATAACG 57.180 50.000 0.00 0.00 0.00 3.18
570 580 4.630894 TGGCATCGTAAAAATTAGCTGG 57.369 40.909 0.00 0.00 0.00 4.85
571 581 5.640732 ACTTGGCATCGTAAAAATTAGCTG 58.359 37.500 0.00 0.00 0.00 4.24
579 589 5.759506 TTCAAAGACTTGGCATCGTAAAA 57.240 34.783 0.00 0.00 33.01 1.52
583 593 3.820467 TGATTTCAAAGACTTGGCATCGT 59.180 39.130 0.00 0.00 33.01 3.73
591 601 6.966534 ATCCACAACTGATTTCAAAGACTT 57.033 33.333 0.00 0.00 0.00 3.01
602 612 4.697352 GCACAGTAAGAATCCACAACTGAT 59.303 41.667 7.70 0.00 39.93 2.90
609 619 0.727398 GCGGCACAGTAAGAATCCAC 59.273 55.000 0.00 0.00 0.00 4.02
631 641 1.967066 CAACATTTACCAGTTGCCCCA 59.033 47.619 0.00 0.00 38.69 4.96
639 649 7.447374 TGTTGGACTTATCAACATTTACCAG 57.553 36.000 5.66 0.00 46.29 4.00
675 685 3.173151 TGACATGGCAGGTTCTCTAGAA 58.827 45.455 6.14 0.00 0.00 2.10
676 686 2.762887 CTGACATGGCAGGTTCTCTAGA 59.237 50.000 21.76 0.00 32.26 2.43
694 704 3.017442 AGCACGCTAGTACAGATTCTGA 58.983 45.455 20.33 1.49 35.18 3.27
701 711 1.472878 TCCTTCAGCACGCTAGTACAG 59.527 52.381 0.00 0.00 0.00 2.74
704 714 1.835494 AGTCCTTCAGCACGCTAGTA 58.165 50.000 0.00 0.00 0.00 1.82
714 724 8.737168 TCATGGAATAATACAAAGTCCTTCAG 57.263 34.615 0.00 0.00 0.00 3.02
734 758 8.469200 ACAAGTATGTTTGTATCCAAATCATGG 58.531 33.333 0.00 0.00 43.82 3.66
754 778 9.503399 TTTTTGGCCTTTTTAAGAAAACAAGTA 57.497 25.926 3.32 0.00 31.72 2.24
773 797 7.786178 ACTGGTTTTTAGAGAAATTTTTGGC 57.214 32.000 0.00 0.00 0.00 4.52
774 798 8.826710 GGAACTGGTTTTTAGAGAAATTTTTGG 58.173 33.333 0.00 0.00 0.00 3.28
780 804 6.041637 GGGTTGGAACTGGTTTTTAGAGAAAT 59.958 38.462 0.00 0.00 0.00 2.17
794 818 5.765182 GGATATGAACATAGGGTTGGAACTG 59.235 44.000 1.20 0.00 40.63 3.16
835 859 6.752168 AGAGTCCTGAACCAAATGAAAATTG 58.248 36.000 0.00 0.00 0.00 2.32
868 1804 0.882042 CTTGCGTTCTCAGCAGGTGT 60.882 55.000 0.00 0.00 46.01 4.16
889 1825 3.378427 GGTGAAGGTGGATGTAGCAATTC 59.622 47.826 0.00 0.00 0.00 2.17
928 1864 1.574428 CGTTGGGGTTTTGAGAGCG 59.426 57.895 0.00 0.00 0.00 5.03
1399 2336 3.670055 CCAGCAGTAACAAGCATTTTTCG 59.330 43.478 0.00 0.00 0.00 3.46
1445 2382 5.393461 CCAACTAATTCAGCAGAAATGGGTC 60.393 44.000 0.00 0.00 37.29 4.46
1491 2569 6.265422 CCTCTGAGTTTTAGAACCAAACCAAT 59.735 38.462 3.66 0.00 36.39 3.16
1495 2573 6.568653 GCATCCTCTGAGTTTTAGAACCAAAC 60.569 42.308 3.66 0.00 36.39 2.93
1506 2584 2.290577 GGAACCAGCATCCTCTGAGTTT 60.291 50.000 3.66 0.00 36.19 2.66
1632 2710 4.637091 TCAATATCAGAGCACCAACACATG 59.363 41.667 0.00 0.00 0.00 3.21
1658 2736 4.092821 TCCATATCGCAAACTCTTGAAACG 59.907 41.667 0.00 0.00 34.14 3.60
1755 2833 3.434641 CCTGTCTAGCAATGTTGTCACAG 59.565 47.826 0.00 0.00 35.94 3.66
1759 2837 4.507710 TGATCCTGTCTAGCAATGTTGTC 58.492 43.478 0.00 0.00 0.00 3.18
1839 2917 3.303593 GGCATCAATCAGTTCTACATGCG 60.304 47.826 0.00 0.00 36.78 4.73
1959 3038 7.358848 GGTTGGCTACGACAAAATAAACAAATG 60.359 37.037 0.00 0.00 29.78 2.32
1975 3054 0.659427 CAGCATCATGGTTGGCTACG 59.341 55.000 0.00 0.00 34.25 3.51
2038 3117 4.375908 CGCATAATACAACGATCGATGCAA 60.376 41.667 25.59 16.29 38.45 4.08
2049 3128 8.874745 ACGAATATAATTGCGCATAATACAAC 57.125 30.769 12.75 0.00 0.00 3.32
2118 3197 2.920647 GCACATTTGTAGGTTTCCGTGC 60.921 50.000 0.00 0.00 41.32 5.34
2165 3244 9.679661 TTTCTAGCATTGTGGAGTAATTCATTA 57.320 29.630 0.00 0.00 0.00 1.90
2185 3264 2.166459 TCCACTCGCATCACCTTTCTAG 59.834 50.000 0.00 0.00 0.00 2.43
2297 3376 6.134535 AGGTATTATGTGTTTTCCTCCACA 57.865 37.500 0.00 0.00 44.91 4.17
2335 3414 3.152341 CCAATCTTGCTCTGACCAAAGT 58.848 45.455 0.00 0.00 0.00 2.66
2356 3435 3.834231 AGGGGCCATAATGCAATGAATAC 59.166 43.478 4.39 0.00 0.00 1.89
2495 3574 1.065854 GTGGGCAGATGAGCAGTACTT 60.066 52.381 0.00 0.00 35.83 2.24
2616 3701 4.975502 TGACGAAACAGAAATGAACATTGC 59.024 37.500 0.69 0.00 0.00 3.56
2903 3989 8.492748 TGTTCTAAGTAATTTTGCGTGTAGAAG 58.507 33.333 0.00 0.00 29.50 2.85
2997 4086 2.125391 TGCATCACTGAGGCGAGC 60.125 61.111 10.89 0.00 42.60 5.03
3048 4143 7.178983 AGCATCTGAAGATAAGAGAAGGATAGG 59.821 40.741 0.00 0.00 32.63 2.57
3059 4154 8.496751 CACATATGAACAGCATCTGAAGATAAG 58.503 37.037 10.38 0.00 38.44 1.73
3132 4227 9.463443 ACAAATACAAGAAAGAAGTTTGTATGC 57.537 29.630 9.16 0.00 43.49 3.14
3318 4443 8.846943 TGTGAATCTAAAACTGCTTCAGATTA 57.153 30.769 0.29 0.17 36.38 1.75
3463 4597 3.003173 AAGCAGGGAGGCGCTGTA 61.003 61.111 7.64 0.00 44.58 2.74
3481 4615 3.568538 CTGTTCACACATTAAAGCAGGC 58.431 45.455 0.00 0.00 30.39 4.85
3587 4721 6.146837 CCACACAACAAAGTGATCAACAAAAA 59.853 34.615 0.00 0.00 42.05 1.94
3631 4765 4.339814 AGAGATAGTAACTAGCACCACTGC 59.660 45.833 0.00 0.00 44.63 4.40
3718 4852 8.539770 TCTTGAGAAAATCTAAGCTAACACAG 57.460 34.615 0.00 0.00 0.00 3.66
3828 4962 6.790285 AAGTCCATCAAACAAATGCATTTC 57.210 33.333 21.70 6.86 0.00 2.17
3880 5014 0.591659 CGCTTCCAGATGGCATGATG 59.408 55.000 3.81 3.25 34.44 3.07
4174 5308 0.402121 ACCCTCAGGAAAACCAGAGC 59.598 55.000 0.00 0.00 36.73 4.09
4187 5321 1.276622 GGAAGCCAGAGTAACCCTCA 58.723 55.000 0.00 0.00 43.12 3.86
4321 5455 6.381994 AGTCATTGATAATGGACCAGCAAAAT 59.618 34.615 0.00 0.00 39.38 1.82
4333 5467 7.532571 ACATGTGTGAACAGTCATTGATAATG 58.467 34.615 0.00 0.00 40.28 1.90
4343 5477 4.808895 TCTGTGTTACATGTGTGAACAGTC 59.191 41.667 21.79 10.86 36.41 3.51
4610 5744 0.109781 CAGCAACCGAATTTCCACCG 60.110 55.000 0.00 0.00 0.00 4.94
4811 5948 7.939039 AGAGAAAACATACCATGAAAAGAGTCA 59.061 33.333 0.00 0.00 0.00 3.41
4830 5967 2.642982 TCCCATGGGAAGGAGAGAAAA 58.357 47.619 32.09 3.29 42.05 2.29
4985 6158 4.350245 TCTAGGGAAAGCAGCAGTACTTA 58.650 43.478 0.00 0.00 0.00 2.24
4993 6166 3.072944 CAGCATATCTAGGGAAAGCAGC 58.927 50.000 0.00 0.00 0.00 5.25
4994 6167 4.314121 GACAGCATATCTAGGGAAAGCAG 58.686 47.826 0.00 0.00 0.00 4.24
5106 6279 6.245724 GCGAACTACCATTACATTTGTACAC 58.754 40.000 0.00 0.00 0.00 2.90
5131 6304 4.758674 TGACACGGATACTAGGCATACTAC 59.241 45.833 0.00 0.00 0.00 2.73
5242 6416 3.629398 GGGAGTACATTGGAGAAAGCATG 59.371 47.826 0.00 0.00 0.00 4.06
5254 6428 1.946984 TGGAACGGAGGGAGTACATT 58.053 50.000 0.00 0.00 0.00 2.71
5261 6435 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5262 6436 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
5263 6437 5.822519 TGAATCATCTATTTTGGAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
5264 6438 6.925610 TGAATCATCTATTTTGGAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
5265 6439 6.884295 AGTTGAATCATCTATTTTGGAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
5266 6440 7.088589 AGTTGAATCATCTATTTTGGAACGG 57.911 36.000 0.00 0.00 0.00 4.44
5267 6441 8.853345 CAAAGTTGAATCATCTATTTTGGAACG 58.147 33.333 0.00 0.00 35.74 3.95
5268 6442 9.696917 ACAAAGTTGAATCATCTATTTTGGAAC 57.303 29.630 10.86 0.00 40.04 3.62
5319 6493 9.672086 CGTTCCAAAATAAATGACTCAACTTTA 57.328 29.630 0.00 0.00 0.00 1.85
5320 6494 7.651704 CCGTTCCAAAATAAATGACTCAACTTT 59.348 33.333 0.00 0.00 0.00 2.66
5321 6495 7.013846 TCCGTTCCAAAATAAATGACTCAACTT 59.986 33.333 0.00 0.00 0.00 2.66
5322 6496 6.488683 TCCGTTCCAAAATAAATGACTCAACT 59.511 34.615 0.00 0.00 0.00 3.16
5323 6497 6.674066 TCCGTTCCAAAATAAATGACTCAAC 58.326 36.000 0.00 0.00 0.00 3.18
5324 6498 6.072175 CCTCCGTTCCAAAATAAATGACTCAA 60.072 38.462 0.00 0.00 0.00 3.02
5325 6499 5.414454 CCTCCGTTCCAAAATAAATGACTCA 59.586 40.000 0.00 0.00 0.00 3.41
5326 6500 5.163652 CCCTCCGTTCCAAAATAAATGACTC 60.164 44.000 0.00 0.00 0.00 3.36
5327 6501 4.705023 CCCTCCGTTCCAAAATAAATGACT 59.295 41.667 0.00 0.00 0.00 3.41
5328 6502 4.703093 TCCCTCCGTTCCAAAATAAATGAC 59.297 41.667 0.00 0.00 0.00 3.06
5329 6503 4.924625 TCCCTCCGTTCCAAAATAAATGA 58.075 39.130 0.00 0.00 0.00 2.57
5330 6504 4.705023 ACTCCCTCCGTTCCAAAATAAATG 59.295 41.667 0.00 0.00 0.00 2.32
5331 6505 4.930696 ACTCCCTCCGTTCCAAAATAAAT 58.069 39.130 0.00 0.00 0.00 1.40
5332 6506 4.376225 ACTCCCTCCGTTCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
5333 6507 4.624604 GCTACTCCCTCCGTTCCAAAATAA 60.625 45.833 0.00 0.00 0.00 1.40
5334 6508 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
5335 6509 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
5336 6510 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
5337 6511 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
5338 6512 0.543410 TGCTACTCCCTCCGTTCCAA 60.543 55.000 0.00 0.00 0.00 3.53
5339 6513 1.077805 TGCTACTCCCTCCGTTCCA 59.922 57.895 0.00 0.00 0.00 3.53
5340 6514 1.516423 GTGCTACTCCCTCCGTTCC 59.484 63.158 0.00 0.00 0.00 3.62
5341 6515 1.139095 CGTGCTACTCCCTCCGTTC 59.861 63.158 0.00 0.00 0.00 3.95
5342 6516 0.322816 TACGTGCTACTCCCTCCGTT 60.323 55.000 0.00 0.00 0.00 4.44
5343 6517 0.747283 CTACGTGCTACTCCCTCCGT 60.747 60.000 0.00 0.00 0.00 4.69
5344 6518 2.023318 CTACGTGCTACTCCCTCCG 58.977 63.158 0.00 0.00 0.00 4.63
5345 6519 1.035932 TGCTACGTGCTACTCCCTCC 61.036 60.000 0.00 0.00 43.37 4.30
5346 6520 1.033574 ATGCTACGTGCTACTCCCTC 58.966 55.000 0.00 0.00 43.37 4.30
5347 6521 0.747255 CATGCTACGTGCTACTCCCT 59.253 55.000 0.00 0.00 43.37 4.20
5348 6522 0.249489 CCATGCTACGTGCTACTCCC 60.249 60.000 0.00 0.00 43.37 4.30
5349 6523 0.460311 ACCATGCTACGTGCTACTCC 59.540 55.000 0.00 0.00 43.37 3.85
5350 6524 1.134367 TGACCATGCTACGTGCTACTC 59.866 52.381 0.00 0.00 43.37 2.59
5351 6525 1.182667 TGACCATGCTACGTGCTACT 58.817 50.000 0.00 0.00 43.37 2.57
5352 6526 2.225068 ATGACCATGCTACGTGCTAC 57.775 50.000 0.00 0.00 43.37 3.58
5411 6586 2.125106 CAGTAAGGACGCCCAGGC 60.125 66.667 0.00 0.00 37.85 4.85
5516 6696 4.087182 AGTCCAGAAATTCCGTACTCAGA 58.913 43.478 0.00 0.00 0.00 3.27
5531 6711 0.343372 AGGCTCCCCATAAGTCCAGA 59.657 55.000 0.00 0.00 0.00 3.86
5653 6834 2.225017 CCTTTTGCCCTTCCTTAGACCA 60.225 50.000 0.00 0.00 0.00 4.02
5714 6895 2.102588 AGGCGGTCATACATTACAGGAC 59.897 50.000 0.00 0.00 0.00 3.85
5742 6923 5.531659 GGATGCCCATCAATGAGATATGATC 59.468 44.000 10.17 0.00 39.54 2.92
5797 7006 4.088762 GTGTGACGTGGCATGCCG 62.089 66.667 30.87 21.99 39.42 5.69
5808 7017 4.171754 GACGAAACTATAGGGTGTGTGAC 58.828 47.826 4.43 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.