Multiple sequence alignment - TraesCS7B01G384300

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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 TraesCS7B01G384300 chr7B 100.000 3921 0 0 1 3921 650131058 650127138 0.000000e+00 7241.0
1 TraesCS7B01G384300 chr7B 84.444 945 127 13 1018 1958 32330516 32331444 0.000000e+00 913.0
2 TraesCS7B01G384300 chr7B 84.468 940 128 14 1018 1954 32408355 32409279 0.000000e+00 911.0
3 TraesCS7B01G384300 chr7B 88.281 640 75 0 1320 1959 169433377 169434016 0.000000e+00 767.0
4 TraesCS7B01G384300 chr7B 87.888 644 78 0 1316 1959 32344792 32345435 0.000000e+00 758.0
5 TraesCS7B01G384300 chr7B 87.143 280 32 3 999 1275 169433032 169433310 8.180000e-82 315.0
6 TraesCS7B01G384300 chr7B 83.448 145 21 2 2789 2933 32332693 32332834 8.840000e-27 132.0
7 TraesCS7B01G384300 chr7B 97.561 41 1 0 498 538 552542460 552542500 1.950000e-08 71.3
8 TraesCS7B01G384300 chr7D 88.945 2786 214 53 850 3567 582304159 582301400 0.000000e+00 3352.0
9 TraesCS7B01G384300 chr7D 84.514 988 125 13 999 1959 205131724 205132710 0.000000e+00 952.0
10 TraesCS7B01G384300 chr7D 85.111 947 114 18 1018 1959 82899030 82899954 0.000000e+00 942.0
11 TraesCS7B01G384300 chr7D 87.925 588 42 8 50 625 582305276 582304706 0.000000e+00 665.0
12 TraesCS7B01G384300 chr7D 87.889 289 16 7 3635 3921 582301383 582301112 4.890000e-84 322.0
13 TraesCS7B01G384300 chr7D 85.211 142 18 2 2789 2930 82902843 82902981 4.080000e-30 143.0
14 TraesCS7B01G384300 chr7D 100.000 43 0 0 1 43 37926104 37926146 3.250000e-11 80.5
15 TraesCS7B01G384300 chr7D 100.000 28 0 0 510 537 576175396 576175423 7.000000e-03 52.8
16 TraesCS7B01G384300 chr7A 89.952 2269 141 43 789 3012 674275403 674273177 0.000000e+00 2846.0
17 TraesCS7B01G384300 chr7A 85.729 974 119 16 999 1953 217202644 217203616 0.000000e+00 1011.0
18 TraesCS7B01G384300 chr7A 86.716 813 44 12 3129 3921 674273175 674272407 0.000000e+00 845.0
19 TraesCS7B01G384300 chr7A 88.080 646 76 1 1313 1958 85031185 85031829 0.000000e+00 765.0
20 TraesCS7B01G384300 chr7A 88.170 541 45 11 65 588 674277272 674276734 9.250000e-176 627.0
21 TraesCS7B01G384300 chr7A 77.778 675 123 21 2079 2739 84855875 84856536 1.320000e-104 390.0
22 TraesCS7B01G384300 chr7A 91.244 217 19 0 1018 1234 84854670 84854886 2.960000e-76 296.0
23 TraesCS7B01G384300 chr2B 88.050 636 76 0 1318 1953 792124367 792123732 0.000000e+00 754.0
24 TraesCS7B01G384300 chr2B 97.674 43 1 0 1 43 592806981 592806939 1.510000e-09 75.0
25 TraesCS7B01G384300 chr6D 77.474 293 60 6 2025 2314 462635119 462634830 1.870000e-38 171.0
26 TraesCS7B01G384300 chr6D 76.768 297 53 14 2025 2313 462690725 462691013 6.790000e-33 152.0
27 TraesCS7B01G384300 chr6A 76.689 296 57 11 2025 2314 609479857 609479568 1.890000e-33 154.0
28 TraesCS7B01G384300 chr6A 75.850 294 61 10 2025 2313 609552505 609552793 1.470000e-29 141.0
29 TraesCS7B01G384300 chr6A 87.629 97 12 0 448 544 396573817 396573721 3.200000e-21 113.0
30 TraesCS7B01G384300 chr6A 97.561 41 1 0 498 538 30596810 30596850 1.950000e-08 71.3
31 TraesCS7B01G384300 chr6B 76.014 296 57 13 2025 2313 705491859 705492147 1.470000e-29 141.0
32 TraesCS7B01G384300 chr6B 75.170 294 65 7 2025 2314 705474384 705474673 8.840000e-27 132.0
33 TraesCS7B01G384300 chr5B 100.000 43 0 0 1 43 532315124 532315082 3.250000e-11 80.5
34 TraesCS7B01G384300 chr3B 100.000 43 0 0 1 43 436512491 436512533 3.250000e-11 80.5
35 TraesCS7B01G384300 chr3B 100.000 43 0 0 1 43 661542539 661542581 3.250000e-11 80.5
36 TraesCS7B01G384300 chr3B 92.453 53 4 0 485 537 734993570 734993622 4.200000e-10 76.8
37 TraesCS7B01G384300 chr3B 97.561 41 1 0 498 538 789021572 789021612 1.950000e-08 71.3
38 TraesCS7B01G384300 chr1B 100.000 43 0 0 1 43 468111117 468111159 3.250000e-11 80.5
39 TraesCS7B01G384300 chrUn 97.674 43 1 0 1 43 334625054 334625096 1.510000e-09 75.0
40 TraesCS7B01G384300 chrUn 97.674 43 1 0 1 43 339946480 339946522 1.510000e-09 75.0
41 TraesCS7B01G384300 chrUn 97.674 43 1 0 1 43 457029205 457029163 1.510000e-09 75.0


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 TraesCS7B01G384300 chr7B 650127138 650131058 3920 True 7241.000000 7241 100.000000 1 3921 1 chr7B.!!$R1 3920
1 TraesCS7B01G384300 chr7B 32408355 32409279 924 False 911.000000 911 84.468000 1018 1954 1 chr7B.!!$F2 936
2 TraesCS7B01G384300 chr7B 32344792 32345435 643 False 758.000000 758 87.888000 1316 1959 1 chr7B.!!$F1 643
3 TraesCS7B01G384300 chr7B 169433032 169434016 984 False 541.000000 767 87.712000 999 1959 2 chr7B.!!$F5 960
4 TraesCS7B01G384300 chr7B 32330516 32332834 2318 False 522.500000 913 83.946000 1018 2933 2 chr7B.!!$F4 1915
5 TraesCS7B01G384300 chr7D 582301112 582305276 4164 True 1446.333333 3352 88.253000 50 3921 3 chr7D.!!$R1 3871
6 TraesCS7B01G384300 chr7D 205131724 205132710 986 False 952.000000 952 84.514000 999 1959 1 chr7D.!!$F2 960
7 TraesCS7B01G384300 chr7D 82899030 82902981 3951 False 542.500000 942 85.161000 1018 2930 2 chr7D.!!$F4 1912
8 TraesCS7B01G384300 chr7A 674272407 674277272 4865 True 1439.333333 2846 88.279333 65 3921 3 chr7A.!!$R1 3856
9 TraesCS7B01G384300 chr7A 217202644 217203616 972 False 1011.000000 1011 85.729000 999 1953 1 chr7A.!!$F2 954
10 TraesCS7B01G384300 chr7A 85031185 85031829 644 False 765.000000 765 88.080000 1313 1958 1 chr7A.!!$F1 645
11 TraesCS7B01G384300 chr7A 84854670 84856536 1866 False 343.000000 390 84.511000 1018 2739 2 chr7A.!!$F3 1721
12 TraesCS7B01G384300 chr2B 792123732 792124367 635 True 754.000000 754 88.050000 1318 1953 1 chr2B.!!$R2 635

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
728 1105 1.012998 CACGTGCTGCATCGATTCG 60.013 57.895 23.94 16.23 0.0 3.34 F
1276 2736 0.178935 CATCTCCTCTCCTCCTCCCC 60.179 65.000 0.00 0.00 0.0 4.81 F
1277 2737 0.330431 ATCTCCTCTCCTCCTCCCCT 60.330 60.000 0.00 0.00 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 6039 0.032017 AGCCGAGAAGATACCCCAGT 60.032 55.0 0.0 0.0 0.00 4.00 R
2583 6265 0.596082 CGTGGAATCACACCCCAAAC 59.404 55.0 0.0 0.0 43.79 2.93 R
2976 6797 0.818040 CGCCACAAGGTAATAGGGGC 60.818 60.0 0.0 0.0 37.19 5.80 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
21 22 3.683802 CTTTGGAGGAGATCAAGCAAGT 58.316 45.455 0.00 0.00 0.00 3.16
22 23 4.836825 CTTTGGAGGAGATCAAGCAAGTA 58.163 43.478 0.00 0.00 0.00 2.24
23 24 5.435291 CTTTGGAGGAGATCAAGCAAGTAT 58.565 41.667 0.00 0.00 0.00 2.12
24 25 5.441718 TTGGAGGAGATCAAGCAAGTATT 57.558 39.130 0.00 0.00 0.00 1.89
25 26 5.028549 TGGAGGAGATCAAGCAAGTATTC 57.971 43.478 0.00 0.00 0.00 1.75
26 27 4.141620 TGGAGGAGATCAAGCAAGTATTCC 60.142 45.833 0.00 0.00 0.00 3.01
27 28 4.384940 GAGGAGATCAAGCAAGTATTCCC 58.615 47.826 0.00 0.00 0.00 3.97
28 29 3.782523 AGGAGATCAAGCAAGTATTCCCA 59.217 43.478 0.00 0.00 0.00 4.37
29 30 3.879892 GGAGATCAAGCAAGTATTCCCAC 59.120 47.826 0.00 0.00 0.00 4.61
30 31 4.384647 GGAGATCAAGCAAGTATTCCCACT 60.385 45.833 0.00 0.00 0.00 4.00
31 32 5.184892 AGATCAAGCAAGTATTCCCACTT 57.815 39.130 0.00 0.00 39.34 3.16
32 33 6.313519 AGATCAAGCAAGTATTCCCACTTA 57.686 37.500 0.00 0.00 36.61 2.24
33 34 6.721318 AGATCAAGCAAGTATTCCCACTTAA 58.279 36.000 0.00 0.00 36.61 1.85
34 35 6.599638 AGATCAAGCAAGTATTCCCACTTAAC 59.400 38.462 0.00 0.00 36.61 2.01
35 36 4.693566 TCAAGCAAGTATTCCCACTTAACG 59.306 41.667 0.00 0.00 36.61 3.18
36 37 3.606687 AGCAAGTATTCCCACTTAACGG 58.393 45.455 0.00 0.00 36.61 4.44
37 38 3.262405 AGCAAGTATTCCCACTTAACGGA 59.738 43.478 0.00 0.00 36.61 4.69
38 39 3.621715 GCAAGTATTCCCACTTAACGGAG 59.378 47.826 0.00 0.00 36.61 4.63
39 40 4.828829 CAAGTATTCCCACTTAACGGAGT 58.171 43.478 0.00 0.00 38.69 3.85
40 41 4.732672 AGTATTCCCACTTAACGGAGTC 57.267 45.455 0.00 0.00 45.00 3.36
41 42 2.667473 ATTCCCACTTAACGGAGTCG 57.333 50.000 0.00 0.00 45.00 4.18
42 43 1.619654 TTCCCACTTAACGGAGTCGA 58.380 50.000 0.00 0.00 45.00 4.20
43 44 1.843368 TCCCACTTAACGGAGTCGAT 58.157 50.000 0.00 0.00 45.00 3.59
44 45 3.003394 TCCCACTTAACGGAGTCGATA 57.997 47.619 0.00 0.00 45.00 2.92
45 46 2.684881 TCCCACTTAACGGAGTCGATAC 59.315 50.000 0.00 0.00 45.00 2.24
46 47 2.424601 CCCACTTAACGGAGTCGATACA 59.575 50.000 0.00 0.00 45.00 2.29
47 48 3.119388 CCCACTTAACGGAGTCGATACAA 60.119 47.826 0.00 0.00 45.00 2.41
48 49 4.487948 CCACTTAACGGAGTCGATACAAA 58.512 43.478 0.00 0.00 45.00 2.83
59 60 4.127171 AGTCGATACAAAACAAGCACTGT 58.873 39.130 0.00 0.00 41.27 3.55
69 70 4.357918 AACAAGCACTGTAGGACTTGAT 57.642 40.909 17.53 7.67 41.59 2.57
77 78 5.468746 GCACTGTAGGACTTGATACAAAACA 59.531 40.000 0.00 0.00 31.81 2.83
106 108 9.462174 CACATTCTGTGTAAATTGTGTAATGTT 57.538 29.630 0.00 0.00 43.08 2.71
126 128 8.863872 AATGTTACTAACCAGTATTGCTTCTT 57.136 30.769 0.00 0.00 37.12 2.52
135 149 4.520492 CCAGTATTGCTTCTTTTGACCTGT 59.480 41.667 0.00 0.00 0.00 4.00
136 150 5.335191 CCAGTATTGCTTCTTTTGACCTGTC 60.335 44.000 0.00 0.00 0.00 3.51
137 151 5.471456 CAGTATTGCTTCTTTTGACCTGTCT 59.529 40.000 0.00 0.00 0.00 3.41
138 152 4.843220 ATTGCTTCTTTTGACCTGTCTG 57.157 40.909 0.00 0.00 0.00 3.51
139 153 2.575532 TGCTTCTTTTGACCTGTCTGG 58.424 47.619 0.00 0.00 42.93 3.86
140 154 2.172505 TGCTTCTTTTGACCTGTCTGGA 59.827 45.455 2.23 0.00 39.71 3.86
141 155 3.181440 TGCTTCTTTTGACCTGTCTGGAT 60.181 43.478 2.23 0.00 39.71 3.41
142 156 3.190118 GCTTCTTTTGACCTGTCTGGATG 59.810 47.826 2.23 0.00 39.71 3.51
143 157 4.645535 CTTCTTTTGACCTGTCTGGATGA 58.354 43.478 2.23 0.00 39.71 2.92
144 158 4.277515 TCTTTTGACCTGTCTGGATGAG 57.722 45.455 2.23 0.00 39.71 2.90
145 159 3.903714 TCTTTTGACCTGTCTGGATGAGA 59.096 43.478 2.23 0.00 39.71 3.27
146 160 3.969287 TTTGACCTGTCTGGATGAGAG 57.031 47.619 2.23 0.00 39.71 3.20
156 170 3.034635 TCTGGATGAGAGCCTTCTTACC 58.965 50.000 0.00 0.00 32.53 2.85
158 172 1.757699 GGATGAGAGCCTTCTTACCGT 59.242 52.381 0.00 0.00 32.53 4.83
160 174 2.743636 TGAGAGCCTTCTTACCGTTG 57.256 50.000 0.00 0.00 32.53 4.10
165 179 4.313282 AGAGCCTTCTTACCGTTGTAAAC 58.687 43.478 0.00 0.00 45.31 2.01
261 275 2.093921 TGTTTCCGAACTCGATATGGCA 60.094 45.455 0.00 0.00 43.02 4.92
264 278 4.801330 TTCCGAACTCGATATGGCATAT 57.199 40.909 19.57 19.57 43.02 1.78
265 279 4.110036 TCCGAACTCGATATGGCATATG 57.890 45.455 24.02 15.47 43.02 1.78
336 350 3.641434 ACATGAGATTGCCAGTAGCTT 57.359 42.857 0.00 0.00 44.23 3.74
356 370 4.699637 CTTTAGACCACCTGTGTGTGTAA 58.300 43.478 0.00 1.61 41.09 2.41
359 373 3.476552 AGACCACCTGTGTGTGTAAATG 58.523 45.455 0.00 0.00 41.09 2.32
366 380 6.198687 CACCTGTGTGTGTAAATGTTAACAG 58.801 40.000 14.65 0.00 37.72 3.16
394 421 7.647715 CGGATCTATGTTCTTTTGTTTGTTGTT 59.352 33.333 0.00 0.00 0.00 2.83
421 450 3.647824 GCATACAGCAGCCGATCC 58.352 61.111 0.00 0.00 44.79 3.36
433 462 1.072331 AGCCGATCCTTGTTGTTGAGT 59.928 47.619 0.00 0.00 0.00 3.41
434 463 2.301870 AGCCGATCCTTGTTGTTGAGTA 59.698 45.455 0.00 0.00 0.00 2.59
435 464 2.415512 GCCGATCCTTGTTGTTGAGTAC 59.584 50.000 0.00 0.00 0.00 2.73
467 499 7.255836 CGGATTGTATTACTACCTCTGATCCAA 60.256 40.741 0.00 0.00 0.00 3.53
492 524 6.969993 ATAAGGGTTGCAGTTTTGAACTAA 57.030 33.333 0.00 0.00 40.46 2.24
493 525 4.649088 AGGGTTGCAGTTTTGAACTAAC 57.351 40.909 0.00 0.00 40.46 2.34
501 533 4.142026 GCAGTTTTGAACTAACCCCAGTTT 60.142 41.667 0.00 0.00 40.46 2.66
502 534 5.068067 GCAGTTTTGAACTAACCCCAGTTTA 59.932 40.000 0.00 0.00 40.46 2.01
503 535 6.734871 GCAGTTTTGAACTAACCCCAGTTTAG 60.735 42.308 0.00 0.00 40.46 1.85
529 561 2.031683 GCGACACTTATTTTGGATCGGG 59.968 50.000 0.00 0.00 0.00 5.14
580 618 9.802039 GGTATGGATTTATTAACCATCCTGTAA 57.198 33.333 0.00 0.00 42.44 2.41
589 627 6.952773 TTAACCATCCTGTAATGTAATGGC 57.047 37.500 0.00 0.00 40.45 4.40
592 630 4.889409 ACCATCCTGTAATGTAATGGCTTG 59.111 41.667 0.00 0.00 40.45 4.01
603 641 5.702065 TGTAATGGCTTGTTGACCCTATA 57.298 39.130 0.00 0.00 0.00 1.31
604 642 6.260700 TGTAATGGCTTGTTGACCCTATAT 57.739 37.500 0.00 0.00 0.00 0.86
607 645 4.422073 TGGCTTGTTGACCCTATATGAG 57.578 45.455 0.00 0.00 0.00 2.90
608 646 4.037222 TGGCTTGTTGACCCTATATGAGA 58.963 43.478 0.00 0.00 0.00 3.27
609 647 4.660303 TGGCTTGTTGACCCTATATGAGAT 59.340 41.667 0.00 0.00 0.00 2.75
610 648 5.132648 TGGCTTGTTGACCCTATATGAGATT 59.867 40.000 0.00 0.00 0.00 2.40
611 649 5.703130 GGCTTGTTGACCCTATATGAGATTC 59.297 44.000 0.00 0.00 0.00 2.52
614 652 6.332735 TGTTGACCCTATATGAGATTCGAG 57.667 41.667 0.00 0.00 0.00 4.04
616 654 6.016192 TGTTGACCCTATATGAGATTCGAGAC 60.016 42.308 0.00 0.00 0.00 3.36
629 670 2.034879 CGAGACCGTGCATGCCTTT 61.035 57.895 16.68 0.00 0.00 3.11
632 673 2.990967 ACCGTGCATGCCTTTGGG 60.991 61.111 16.68 11.27 0.00 4.12
694 765 6.658188 ATTTCTTTCGGGGTAACAATGAAA 57.342 33.333 0.00 0.00 39.74 2.69
695 766 5.699097 TTCTTTCGGGGTAACAATGAAAG 57.301 39.130 10.64 10.64 44.83 2.62
696 767 4.721132 TCTTTCGGGGTAACAATGAAAGT 58.279 39.130 14.45 0.00 44.31 2.66
697 768 5.867330 TCTTTCGGGGTAACAATGAAAGTA 58.133 37.500 14.45 4.00 44.31 2.24
698 769 5.702209 TCTTTCGGGGTAACAATGAAAGTAC 59.298 40.000 14.45 0.00 44.31 2.73
699 770 4.895668 TCGGGGTAACAATGAAAGTACT 57.104 40.909 0.00 0.00 39.74 2.73
700 771 5.999205 TCGGGGTAACAATGAAAGTACTA 57.001 39.130 0.00 0.00 39.74 1.82
705 1082 7.363268 CGGGGTAACAATGAAAGTACTACTAGT 60.363 40.741 0.00 0.00 39.74 2.57
728 1105 1.012998 CACGTGCTGCATCGATTCG 60.013 57.895 23.94 16.23 0.00 3.34
741 1118 2.972625 TCGATTCGGTTTTCAGCAGAT 58.027 42.857 6.18 0.00 0.00 2.90
743 1120 3.370978 TCGATTCGGTTTTCAGCAGATTC 59.629 43.478 6.18 0.00 0.00 2.52
744 1121 3.125146 CGATTCGGTTTTCAGCAGATTCA 59.875 43.478 0.00 0.00 0.00 2.57
824 2256 4.659874 CGACAAACGCCCGTGCAC 62.660 66.667 6.82 6.82 37.32 4.57
848 2280 4.799824 GCGCGCAACGGGTAGGTA 62.800 66.667 29.10 0.00 43.93 3.08
898 2334 3.010413 GCTGTTACCTACCGGCGGT 62.010 63.158 35.91 35.91 40.16 5.68
976 2412 2.807045 GACGCAGACCGCTGACAG 60.807 66.667 0.00 0.00 45.17 3.51
1245 2694 1.588139 CGGATTCCTCGTACGTGCC 60.588 63.158 16.05 8.25 0.00 5.01
1247 2696 1.514087 GATTCCTCGTACGTGCCCA 59.486 57.895 16.05 0.00 0.00 5.36
1276 2736 0.178935 CATCTCCTCTCCTCCTCCCC 60.179 65.000 0.00 0.00 0.00 4.81
1277 2737 0.330431 ATCTCCTCTCCTCCTCCCCT 60.330 60.000 0.00 0.00 0.00 4.79
1278 2738 0.996762 TCTCCTCTCCTCCTCCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
1279 2739 0.998945 CTCCTCTCCTCCTCCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1281 2741 0.998945 CCTCTCCTCCTCCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1288 2752 1.074850 CCTCCCCTCTCTTCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
1289 2753 1.456705 CTCCCCTCTCTTCTCCCCG 60.457 68.421 0.00 0.00 0.00 5.73
1310 2790 3.443045 CCATTGCTGACCGGCACC 61.443 66.667 0.00 0.00 42.27 5.01
1979 3496 1.528161 GACACTCGTTACCAAAACCCG 59.472 52.381 0.00 0.00 0.00 5.28
1986 3503 4.133078 TCGTTACCAAAACCCGTTACATT 58.867 39.130 0.00 0.00 0.00 2.71
1989 3506 5.399006 CGTTACCAAAACCCGTTACATTTTC 59.601 40.000 0.00 0.00 0.00 2.29
1991 3508 5.538849 ACCAAAACCCGTTACATTTTCAT 57.461 34.783 0.00 0.00 0.00 2.57
1992 3509 5.293560 ACCAAAACCCGTTACATTTTCATG 58.706 37.500 0.00 0.00 36.34 3.07
1995 3512 2.802719 ACCCGTTACATTTTCATGGCT 58.197 42.857 0.00 0.00 34.27 4.75
1996 3513 2.491693 ACCCGTTACATTTTCATGGCTG 59.508 45.455 0.00 0.00 34.27 4.85
1999 3516 3.427503 CCGTTACATTTTCATGGCTGTCC 60.428 47.826 0.00 0.00 34.27 4.02
2073 5452 2.435938 TTCATCGGCCTCAACGCC 60.436 61.111 0.00 0.00 46.13 5.68
2091 5599 3.499737 GCCATCAGCGTTCGGGTG 61.500 66.667 0.00 0.00 45.52 4.61
2205 5713 1.153939 CCTCGTGCTCGTCTTCAGG 60.154 63.158 8.17 3.36 38.33 3.86
2326 5838 1.973281 CCCGTGCTTTCAGGCATGT 60.973 57.895 0.00 0.00 44.86 3.21
2332 5844 3.721035 GTGCTTTCAGGCATGTTTCTTT 58.279 40.909 0.00 0.00 44.34 2.52
2333 5845 4.122046 GTGCTTTCAGGCATGTTTCTTTT 58.878 39.130 0.00 0.00 44.34 2.27
2337 5849 6.183360 TGCTTTCAGGCATGTTTCTTTTCTTA 60.183 34.615 0.00 0.00 37.29 2.10
2367 5888 7.013750 TCACACCATTGCTAGTTTCATTTTGTA 59.986 33.333 0.00 0.00 0.00 2.41
2368 5889 7.651304 CACACCATTGCTAGTTTCATTTTGTAA 59.349 33.333 0.00 0.00 0.00 2.41
2369 5890 8.367156 ACACCATTGCTAGTTTCATTTTGTAAT 58.633 29.630 0.00 0.00 0.00 1.89
2370 5891 9.206870 CACCATTGCTAGTTTCATTTTGTAATT 57.793 29.630 0.00 0.00 0.00 1.40
2371 5892 9.777297 ACCATTGCTAGTTTCATTTTGTAATTT 57.223 25.926 0.00 0.00 0.00 1.82
2397 5919 3.262660 TCATGTCTGCTCAACCTCATCTT 59.737 43.478 0.00 0.00 0.00 2.40
2453 6012 2.352651 CCTTGTCGCATACATCAACCTG 59.647 50.000 0.00 0.00 38.10 4.00
2459 6018 1.683011 GCATACATCAACCTGGGCTGT 60.683 52.381 0.00 0.00 0.00 4.40
2480 6039 1.264749 ACTACATCTTCGGGCTGCCA 61.265 55.000 22.05 0.00 0.00 4.92
2509 6068 3.577649 TCTTCTCGGCTACAAGTTCAG 57.422 47.619 0.00 0.00 0.00 3.02
2513 6072 2.163815 TCTCGGCTACAAGTTCAGCTAC 59.836 50.000 6.07 0.00 37.91 3.58
2533 6211 2.158430 ACGGAGTTGGGGTAATTGGTTT 60.158 45.455 0.00 0.00 37.78 3.27
2537 6215 4.262292 GGAGTTGGGGTAATTGGTTTTGTC 60.262 45.833 0.00 0.00 0.00 3.18
2547 6225 8.984764 GGGTAATTGGTTTTGTCATTTAAACTC 58.015 33.333 0.00 0.00 35.22 3.01
2592 6274 5.535753 AAAGAAGAAGAATGTTTGGGGTG 57.464 39.130 0.00 0.00 0.00 4.61
2599 6281 3.165071 AGAATGTTTGGGGTGTGATTCC 58.835 45.455 0.00 0.00 0.00 3.01
2600 6282 2.692709 ATGTTTGGGGTGTGATTCCA 57.307 45.000 0.00 0.00 0.00 3.53
2606 6288 1.909986 TGGGGTGTGATTCCACGATAA 59.090 47.619 0.00 0.00 46.06 1.75
2610 6292 4.401202 GGGGTGTGATTCCACGATAATTTT 59.599 41.667 0.00 0.00 46.06 1.82
2625 6329 9.687717 CACGATAATTTTGGTTATGAATTTTGC 57.312 29.630 0.00 0.00 0.00 3.68
2643 6347 3.724508 TGCGACATTGGTTGTGATTTT 57.275 38.095 0.00 0.00 39.18 1.82
2669 6373 4.992740 TGGGCCGGCATGCTTTGT 62.993 61.111 30.85 0.00 0.00 2.83
2696 6400 4.556942 TGCACTTCAGACACTGATTTTG 57.443 40.909 2.30 2.43 40.39 2.44
2741 6445 4.746535 TTGGAACGCAGAGGTATGAATA 57.253 40.909 0.00 0.00 0.00 1.75
2742 6446 4.746535 TGGAACGCAGAGGTATGAATAA 57.253 40.909 0.00 0.00 0.00 1.40
2743 6447 5.092554 TGGAACGCAGAGGTATGAATAAA 57.907 39.130 0.00 0.00 0.00 1.40
2744 6448 5.492895 TGGAACGCAGAGGTATGAATAAAA 58.507 37.500 0.00 0.00 0.00 1.52
2752 6469 7.520614 CGCAGAGGTATGAATAAAATTCCTTCC 60.521 40.741 0.00 0.00 0.00 3.46
2847 6667 2.092968 TCATGTCTCATGCCCTACAACC 60.093 50.000 5.03 0.00 0.00 3.77
2938 6759 6.266330 TGGAGTAGAACTAGATCACCATGATG 59.734 42.308 0.00 0.00 37.20 3.07
2976 6797 2.935201 CCCGAAGAAAGAGAGAAGCATG 59.065 50.000 0.00 0.00 0.00 4.06
3012 6833 4.457603 TGTGGCGCTGATGTAAAATTTAGT 59.542 37.500 7.64 0.00 0.00 2.24
3013 6834 5.048364 TGTGGCGCTGATGTAAAATTTAGTT 60.048 36.000 7.64 0.00 0.00 2.24
3014 6835 5.861787 GTGGCGCTGATGTAAAATTTAGTTT 59.138 36.000 7.64 0.00 0.00 2.66
3016 6837 6.584563 TGGCGCTGATGTAAAATTTAGTTTTC 59.415 34.615 7.64 0.00 40.40 2.29
3017 6838 6.806739 GGCGCTGATGTAAAATTTAGTTTTCT 59.193 34.615 7.64 0.00 40.40 2.52
3018 6839 7.966204 GGCGCTGATGTAAAATTTAGTTTTCTA 59.034 33.333 7.64 0.00 40.40 2.10
3019 6840 9.000018 GCGCTGATGTAAAATTTAGTTTTCTAG 58.000 33.333 0.00 0.00 40.40 2.43
3044 6869 7.335422 AGTCACATTTGTAAGATGGTCATTCTC 59.665 37.037 0.00 0.00 0.00 2.87
3134 6962 3.751175 GGCATCTGTGTGCTTTAGTTGTA 59.249 43.478 7.48 0.00 44.45 2.41
3137 6965 6.093495 GGCATCTGTGTGCTTTAGTTGTATAA 59.907 38.462 7.48 0.00 44.45 0.98
3223 7051 8.696410 TTTTTCCTTTGACATTTGTTGTAGTC 57.304 30.769 0.00 0.00 39.18 2.59
3224 7052 7.639113 TTTCCTTTGACATTTGTTGTAGTCT 57.361 32.000 0.00 0.00 39.18 3.24
3225 7053 6.618287 TCCTTTGACATTTGTTGTAGTCTG 57.382 37.500 0.00 0.00 39.18 3.51
3226 7054 6.119536 TCCTTTGACATTTGTTGTAGTCTGT 58.880 36.000 0.00 0.00 39.18 3.41
3227 7055 6.260050 TCCTTTGACATTTGTTGTAGTCTGTC 59.740 38.462 0.00 0.00 39.18 3.51
3291 7137 6.297582 TGGAAATTTCAAAAGGAATGCACAT 58.702 32.000 19.49 0.00 34.91 3.21
3303 7149 4.340097 AGGAATGCACATTACACATCCATG 59.660 41.667 8.27 0.00 34.05 3.66
3338 7184 6.101332 TGCCACAATAGATTTTCTGAAATGC 58.899 36.000 3.31 0.00 35.65 3.56
3365 7211 2.119495 AGGCGGAGAATACTTGGACAT 58.881 47.619 0.00 0.00 0.00 3.06
3407 7253 9.354673 CATACCAAATACTCAACATATTTCCCT 57.645 33.333 0.00 0.00 31.33 4.20
3408 7254 9.936329 ATACCAAATACTCAACATATTTCCCTT 57.064 29.630 0.00 0.00 31.33 3.95
3519 7365 1.302511 TCAAGGCGCCTTTCCAGTC 60.303 57.895 38.60 2.04 33.42 3.51
3567 7413 3.496870 AAGACACTGAAGGTGCCTTTAGG 60.497 47.826 21.62 14.67 44.21 2.69
3589 7435 4.898370 GCTTTAGCCAATCTTTACTCACG 58.102 43.478 0.00 0.00 34.31 4.35
3598 7444 6.312918 GCCAATCTTTACTCACGAAACTATCA 59.687 38.462 0.00 0.00 0.00 2.15
3616 7462 4.047125 CCGGATGGTGCCCTGGTT 62.047 66.667 0.00 0.00 0.00 3.67
3670 7516 1.871126 GAGCAACCAGAGGGCTTTGC 61.871 60.000 0.00 0.00 43.16 3.68
3693 7539 0.681733 CACTCTGCCCACACAGTAGT 59.318 55.000 0.00 0.00 38.84 2.73
3694 7540 1.070758 CACTCTGCCCACACAGTAGTT 59.929 52.381 0.00 0.00 38.84 2.24
3695 7541 1.070758 ACTCTGCCCACACAGTAGTTG 59.929 52.381 0.00 0.00 38.84 3.16
3696 7542 0.250295 TCTGCCCACACAGTAGTTGC 60.250 55.000 0.00 0.00 38.84 4.17
3697 7543 0.534877 CTGCCCACACAGTAGTTGCA 60.535 55.000 0.00 0.00 32.78 4.08
3698 7544 0.106967 TGCCCACACAGTAGTTGCAA 60.107 50.000 0.00 0.00 0.00 4.08
3699 7545 1.028905 GCCCACACAGTAGTTGCAAA 58.971 50.000 0.00 0.00 0.00 3.68
3700 7546 1.407258 GCCCACACAGTAGTTGCAAAA 59.593 47.619 0.00 0.00 0.00 2.44
3701 7547 2.543653 GCCCACACAGTAGTTGCAAAAG 60.544 50.000 0.00 0.00 0.00 2.27
3702 7548 2.948979 CCCACACAGTAGTTGCAAAAGA 59.051 45.455 0.00 0.00 0.00 2.52
3703 7549 3.569701 CCCACACAGTAGTTGCAAAAGAT 59.430 43.478 0.00 0.00 0.00 2.40
3704 7550 4.037923 CCCACACAGTAGTTGCAAAAGATT 59.962 41.667 0.00 0.00 0.00 2.40
3705 7551 5.240623 CCCACACAGTAGTTGCAAAAGATTA 59.759 40.000 0.00 0.00 0.00 1.75
3706 7552 6.071952 CCCACACAGTAGTTGCAAAAGATTAT 60.072 38.462 0.00 0.00 0.00 1.28
3707 7553 7.120579 CCCACACAGTAGTTGCAAAAGATTATA 59.879 37.037 0.00 0.00 0.00 0.98
3708 7554 8.677300 CCACACAGTAGTTGCAAAAGATTATAT 58.323 33.333 0.00 0.00 0.00 0.86
3709 7555 9.494479 CACACAGTAGTTGCAAAAGATTATATG 57.506 33.333 0.00 0.00 0.00 1.78
3724 7570 6.408035 AGATTATATGGCTTCTGCTGAGATG 58.592 40.000 0.00 0.00 39.59 2.90
3725 7571 2.251409 TATGGCTTCTGCTGAGATGC 57.749 50.000 3.97 3.97 44.83 3.91
3730 7576 1.817357 CTTCTGCTGAGATGCCACAA 58.183 50.000 0.00 0.00 0.00 3.33
3773 7619 1.308998 CCCCAACATCGCAATCCTAC 58.691 55.000 0.00 0.00 0.00 3.18
3788 7634 0.249322 CCTACCAACCTCATACGCGG 60.249 60.000 12.47 0.00 0.00 6.46
3802 7648 0.108377 ACGCGGTGCAGAATCATGTA 60.108 50.000 12.47 0.00 0.00 2.29
3857 7703 7.912250 AGAATTATTCGTCATTGCAAGATGTTC 59.088 33.333 4.94 7.50 34.02 3.18
3895 7742 0.953727 TTGCCACATTCAGCAGTCAC 59.046 50.000 0.00 0.00 40.73 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.683802 ACTTGCTTGATCTCCTCCAAAG 58.316 45.455 0.00 0.00 0.00 2.77
1 2 3.795688 ACTTGCTTGATCTCCTCCAAA 57.204 42.857 0.00 0.00 0.00 3.28
2 3 5.431765 GAATACTTGCTTGATCTCCTCCAA 58.568 41.667 0.00 0.00 0.00 3.53
3 4 4.141620 GGAATACTTGCTTGATCTCCTCCA 60.142 45.833 0.00 0.00 0.00 3.86
4 5 4.384940 GGAATACTTGCTTGATCTCCTCC 58.615 47.826 0.00 0.00 0.00 4.30
5 6 4.141620 TGGGAATACTTGCTTGATCTCCTC 60.142 45.833 0.00 0.00 0.00 3.71
6 7 3.782523 TGGGAATACTTGCTTGATCTCCT 59.217 43.478 0.00 0.00 0.00 3.69
7 8 3.879892 GTGGGAATACTTGCTTGATCTCC 59.120 47.826 0.00 0.00 0.00 3.71
8 9 4.775236 AGTGGGAATACTTGCTTGATCTC 58.225 43.478 0.00 0.00 0.00 2.75
9 10 4.851639 AGTGGGAATACTTGCTTGATCT 57.148 40.909 0.00 0.00 0.00 2.75
10 11 6.456988 CGTTAAGTGGGAATACTTGCTTGATC 60.457 42.308 0.00 0.00 40.85 2.92
11 12 5.354234 CGTTAAGTGGGAATACTTGCTTGAT 59.646 40.000 0.00 0.00 40.85 2.57
12 13 4.693566 CGTTAAGTGGGAATACTTGCTTGA 59.306 41.667 0.00 0.00 40.85 3.02
13 14 4.142687 CCGTTAAGTGGGAATACTTGCTTG 60.143 45.833 0.00 0.00 40.85 4.01
14 15 4.007659 CCGTTAAGTGGGAATACTTGCTT 58.992 43.478 0.00 0.00 40.85 3.91
15 16 3.262405 TCCGTTAAGTGGGAATACTTGCT 59.738 43.478 0.00 0.00 40.85 3.91
16 17 3.602483 TCCGTTAAGTGGGAATACTTGC 58.398 45.455 0.00 0.00 40.85 4.01
17 18 4.828829 ACTCCGTTAAGTGGGAATACTTG 58.171 43.478 0.00 0.00 40.85 3.16
18 19 4.381292 CGACTCCGTTAAGTGGGAATACTT 60.381 45.833 0.00 0.00 43.03 2.24
19 20 3.129988 CGACTCCGTTAAGTGGGAATACT 59.870 47.826 0.00 0.00 0.00 2.12
20 21 3.129287 TCGACTCCGTTAAGTGGGAATAC 59.871 47.826 0.00 0.00 37.05 1.89
21 22 3.355378 TCGACTCCGTTAAGTGGGAATA 58.645 45.455 0.00 0.00 37.05 1.75
22 23 2.173519 TCGACTCCGTTAAGTGGGAAT 58.826 47.619 0.00 0.00 37.05 3.01
23 24 1.619654 TCGACTCCGTTAAGTGGGAA 58.380 50.000 0.00 0.00 37.05 3.97
24 25 1.843368 ATCGACTCCGTTAAGTGGGA 58.157 50.000 0.00 0.00 37.05 4.37
25 26 2.424601 TGTATCGACTCCGTTAAGTGGG 59.575 50.000 0.00 0.00 37.05 4.61
26 27 3.770263 TGTATCGACTCCGTTAAGTGG 57.230 47.619 0.00 0.00 37.05 4.00
27 28 5.403166 TGTTTTGTATCGACTCCGTTAAGTG 59.597 40.000 0.00 0.00 37.05 3.16
28 29 5.531634 TGTTTTGTATCGACTCCGTTAAGT 58.468 37.500 0.00 0.00 37.05 2.24
29 30 6.456447 TTGTTTTGTATCGACTCCGTTAAG 57.544 37.500 0.00 0.00 37.05 1.85
30 31 5.107375 GCTTGTTTTGTATCGACTCCGTTAA 60.107 40.000 0.00 0.00 37.05 2.01
31 32 4.386652 GCTTGTTTTGTATCGACTCCGTTA 59.613 41.667 0.00 0.00 37.05 3.18
32 33 3.185797 GCTTGTTTTGTATCGACTCCGTT 59.814 43.478 0.00 0.00 37.05 4.44
33 34 2.735134 GCTTGTTTTGTATCGACTCCGT 59.265 45.455 0.00 0.00 37.05 4.69
34 35 2.734606 TGCTTGTTTTGTATCGACTCCG 59.265 45.455 0.00 0.00 37.07 4.63
35 36 3.746492 AGTGCTTGTTTTGTATCGACTCC 59.254 43.478 0.00 0.00 0.00 3.85
36 37 4.211374 ACAGTGCTTGTTTTGTATCGACTC 59.789 41.667 0.00 0.00 36.31 3.36
37 38 4.127171 ACAGTGCTTGTTTTGTATCGACT 58.873 39.130 0.00 0.00 36.31 4.18
38 39 4.468095 ACAGTGCTTGTTTTGTATCGAC 57.532 40.909 0.00 0.00 36.31 4.20
39 40 4.688879 CCTACAGTGCTTGTTTTGTATCGA 59.311 41.667 0.00 0.00 41.29 3.59
40 41 4.688879 TCCTACAGTGCTTGTTTTGTATCG 59.311 41.667 0.00 0.00 41.29 2.92
41 42 5.701290 AGTCCTACAGTGCTTGTTTTGTATC 59.299 40.000 0.00 0.00 41.29 2.24
42 43 5.621193 AGTCCTACAGTGCTTGTTTTGTAT 58.379 37.500 0.00 0.00 41.29 2.29
43 44 5.031066 AGTCCTACAGTGCTTGTTTTGTA 57.969 39.130 0.00 0.00 41.29 2.41
44 45 3.886123 AGTCCTACAGTGCTTGTTTTGT 58.114 40.909 0.00 0.00 41.29 2.83
45 46 4.335315 TCAAGTCCTACAGTGCTTGTTTTG 59.665 41.667 7.15 0.00 41.29 2.44
46 47 4.523083 TCAAGTCCTACAGTGCTTGTTTT 58.477 39.130 7.15 0.00 41.29 2.43
47 48 4.150897 TCAAGTCCTACAGTGCTTGTTT 57.849 40.909 7.15 0.00 41.29 2.83
48 49 3.838244 TCAAGTCCTACAGTGCTTGTT 57.162 42.857 7.15 0.00 41.29 2.83
59 60 6.358178 TGTGGTTGTTTTGTATCAAGTCCTA 58.642 36.000 0.00 0.00 0.00 2.94
106 108 7.389607 GGTCAAAAGAAGCAATACTGGTTAGTA 59.610 37.037 0.00 0.00 43.24 1.82
126 128 2.027745 GCTCTCATCCAGACAGGTCAAA 60.028 50.000 1.84 0.00 39.02 2.69
135 149 3.034635 GGTAAGAAGGCTCTCATCCAGA 58.965 50.000 0.00 0.00 0.00 3.86
136 150 2.223923 CGGTAAGAAGGCTCTCATCCAG 60.224 54.545 0.00 0.00 0.00 3.86
137 151 1.757118 CGGTAAGAAGGCTCTCATCCA 59.243 52.381 0.00 0.00 0.00 3.41
138 152 1.757699 ACGGTAAGAAGGCTCTCATCC 59.242 52.381 0.00 0.00 0.00 3.51
139 153 3.190874 CAACGGTAAGAAGGCTCTCATC 58.809 50.000 0.00 0.00 0.00 2.92
140 154 2.567615 ACAACGGTAAGAAGGCTCTCAT 59.432 45.455 0.00 0.00 0.00 2.90
141 155 1.968493 ACAACGGTAAGAAGGCTCTCA 59.032 47.619 0.00 0.00 0.00 3.27
142 156 2.745515 ACAACGGTAAGAAGGCTCTC 57.254 50.000 0.00 0.00 0.00 3.20
143 157 4.040095 AGTTTACAACGGTAAGAAGGCTCT 59.960 41.667 0.00 0.00 40.40 4.09
144 158 4.313282 AGTTTACAACGGTAAGAAGGCTC 58.687 43.478 0.00 0.00 40.40 4.70
145 159 4.347360 AGTTTACAACGGTAAGAAGGCT 57.653 40.909 0.00 0.00 40.40 4.58
146 160 5.064325 CCATAGTTTACAACGGTAAGAAGGC 59.936 44.000 0.00 0.00 40.40 4.35
156 170 4.384547 GCAAAAAGGCCATAGTTTACAACG 59.615 41.667 5.01 0.00 36.23 4.10
158 172 5.510520 CCTGCAAAAAGGCCATAGTTTACAA 60.511 40.000 5.01 0.00 0.00 2.41
160 174 4.219725 TCCTGCAAAAAGGCCATAGTTTAC 59.780 41.667 5.01 0.00 37.24 2.01
165 179 3.259123 AGTTTCCTGCAAAAAGGCCATAG 59.741 43.478 5.01 0.00 37.24 2.23
261 275 1.676916 CGAGGCGGGCATCAATCATAT 60.677 52.381 3.78 0.00 0.00 1.78
264 278 2.203056 CGAGGCGGGCATCAATCA 60.203 61.111 3.78 0.00 0.00 2.57
265 279 2.108976 TCGAGGCGGGCATCAATC 59.891 61.111 3.78 0.00 0.00 2.67
318 332 5.363939 GTCTAAAGCTACTGGCAATCTCAT 58.636 41.667 0.00 0.00 44.79 2.90
356 370 7.556844 AGAACATAGATCCGTCTGTTAACATT 58.443 34.615 9.13 0.00 35.87 2.71
359 373 7.829378 AAAGAACATAGATCCGTCTGTTAAC 57.171 36.000 0.00 0.00 35.87 2.01
366 380 6.899114 ACAAACAAAAGAACATAGATCCGTC 58.101 36.000 0.00 0.00 0.00 4.79
394 421 3.402186 GCTGTATGCATGCCCTACA 57.598 52.632 21.92 21.92 42.31 2.74
421 450 6.005583 TCCGTAGTAGTACTCAACAACAAG 57.994 41.667 5.96 0.00 0.00 3.16
433 462 9.712305 GAGGTAGTAATACAATCCGTAGTAGTA 57.288 37.037 2.37 0.00 36.14 1.82
434 463 8.435982 AGAGGTAGTAATACAATCCGTAGTAGT 58.564 37.037 2.37 0.00 37.84 2.73
435 464 8.719648 CAGAGGTAGTAATACAATCCGTAGTAG 58.280 40.741 2.37 0.00 31.60 2.57
467 499 6.233905 AGTTCAAAACTGCAACCCTTATTT 57.766 33.333 0.00 0.00 41.01 1.40
474 506 3.491964 GGGGTTAGTTCAAAACTGCAACC 60.492 47.826 12.87 12.87 44.16 3.77
501 533 5.543714 TCCAAAATAAGTGTCGCAGTTCTA 58.456 37.500 3.66 0.00 0.00 2.10
502 534 4.385825 TCCAAAATAAGTGTCGCAGTTCT 58.614 39.130 3.66 0.00 0.00 3.01
503 535 4.742438 TCCAAAATAAGTGTCGCAGTTC 57.258 40.909 3.66 0.00 0.00 3.01
529 561 7.148069 CCACAAAATGAGAAACTTATACTCCCC 60.148 40.741 0.00 0.00 0.00 4.81
551 584 7.723616 CAGGATGGTTAATAAATCCATACCACA 59.276 37.037 13.46 0.00 41.94 4.17
587 625 4.689612 TCTCATATAGGGTCAACAAGCC 57.310 45.455 0.00 0.00 46.55 4.35
589 627 6.749139 TCGAATCTCATATAGGGTCAACAAG 58.251 40.000 0.00 0.00 0.00 3.16
592 630 6.383415 GTCTCGAATCTCATATAGGGTCAAC 58.617 44.000 0.00 0.00 0.00 3.18
603 641 0.817654 TGCACGGTCTCGAATCTCAT 59.182 50.000 0.00 0.00 40.11 2.90
604 642 0.817654 ATGCACGGTCTCGAATCTCA 59.182 50.000 0.00 0.00 40.11 3.27
607 645 1.638467 GCATGCACGGTCTCGAATC 59.362 57.895 14.21 0.00 40.11 2.52
608 646 1.815421 GGCATGCACGGTCTCGAAT 60.815 57.895 21.36 0.00 40.11 3.34
609 647 2.434185 GGCATGCACGGTCTCGAA 60.434 61.111 21.36 0.00 40.11 3.71
610 648 2.449031 AAAGGCATGCACGGTCTCGA 62.449 55.000 21.36 0.00 40.11 4.04
611 649 2.034879 AAAGGCATGCACGGTCTCG 61.035 57.895 21.36 0.00 43.02 4.04
614 652 2.568090 CCAAAGGCATGCACGGTC 59.432 61.111 21.36 0.72 0.00 4.79
642 683 5.575957 CAAATCTGCTGCACTTATTACCAG 58.424 41.667 0.00 0.00 0.00 4.00
643 684 4.142403 GCAAATCTGCTGCACTTATTACCA 60.142 41.667 0.00 0.00 45.74 3.25
644 685 4.354587 GCAAATCTGCTGCACTTATTACC 58.645 43.478 0.00 0.00 45.74 2.85
672 743 5.595133 ACTTTCATTGTTACCCCGAAAGAAA 59.405 36.000 17.96 4.73 43.27 2.52
694 765 5.002516 AGCACGTGAAGAACTAGTAGTACT 58.997 41.667 22.23 8.14 0.00 2.73
695 766 5.087397 CAGCACGTGAAGAACTAGTAGTAC 58.913 45.833 22.23 0.00 0.00 2.73
696 767 4.379186 GCAGCACGTGAAGAACTAGTAGTA 60.379 45.833 22.23 0.00 0.00 1.82
697 768 3.612004 GCAGCACGTGAAGAACTAGTAGT 60.612 47.826 22.23 0.00 0.00 2.73
698 769 2.917971 GCAGCACGTGAAGAACTAGTAG 59.082 50.000 22.23 0.00 0.00 2.57
699 770 2.295070 TGCAGCACGTGAAGAACTAGTA 59.705 45.455 22.23 0.00 0.00 1.82
700 771 1.068588 TGCAGCACGTGAAGAACTAGT 59.931 47.619 22.23 0.00 0.00 2.57
705 1082 0.319469 TCGATGCAGCACGTGAAGAA 60.319 50.000 22.23 5.10 0.00 2.52
728 1105 4.730657 CATCTGTGAATCTGCTGAAAACC 58.269 43.478 0.00 0.00 0.00 3.27
741 1118 0.321346 TCTTGAGCGGCATCTGTGAA 59.679 50.000 1.45 0.00 0.00 3.18
743 1120 0.108472 TCTCTTGAGCGGCATCTGTG 60.108 55.000 1.45 0.00 0.00 3.66
744 1121 0.829333 ATCTCTTGAGCGGCATCTGT 59.171 50.000 1.45 0.00 0.00 3.41
842 2274 4.306600 GAGCGAGAGTACCTACTACCTAC 58.693 52.174 0.00 0.00 36.50 3.18
843 2275 3.005261 CGAGCGAGAGTACCTACTACCTA 59.995 52.174 0.00 0.00 36.50 3.08
844 2276 2.224018 CGAGCGAGAGTACCTACTACCT 60.224 54.545 0.00 0.00 36.50 3.08
845 2277 2.134346 CGAGCGAGAGTACCTACTACC 58.866 57.143 0.00 0.00 36.50 3.18
846 2278 1.526464 GCGAGCGAGAGTACCTACTAC 59.474 57.143 0.00 0.00 36.50 2.73
847 2279 1.863267 GCGAGCGAGAGTACCTACTA 58.137 55.000 0.00 0.00 36.50 1.82
848 2280 1.152989 CGCGAGCGAGAGTACCTACT 61.153 60.000 12.58 0.00 42.83 2.57
884 2316 3.825611 GCGACCGCCGGTAGGTAA 61.826 66.667 21.00 0.00 43.01 2.85
987 2423 2.511600 CCCATCGTCGGCAGGTTC 60.512 66.667 0.00 0.00 0.00 3.62
988 2424 4.096003 CCCCATCGTCGGCAGGTT 62.096 66.667 0.00 0.00 0.00 3.50
990 2426 4.530857 GTCCCCATCGTCGGCAGG 62.531 72.222 0.00 0.00 0.00 4.85
991 2427 4.530857 GGTCCCCATCGTCGGCAG 62.531 72.222 0.00 0.00 0.00 4.85
1151 2600 4.796231 CGAGGTGGCCGACGAAGG 62.796 72.222 0.00 0.00 32.43 3.46
1197 2646 1.380650 GGAGAAGACGGAGAGGCCT 60.381 63.158 3.86 3.86 0.00 5.19
1252 2701 0.762461 GGAGGAGAGGAGATGGGTGG 60.762 65.000 0.00 0.00 0.00 4.61
1276 2736 4.214327 GCGCCGGGGAGAAGAGAG 62.214 72.222 24.68 0.00 0.00 3.20
1281 2741 4.794648 CAATGGCGCCGGGGAGAA 62.795 66.667 24.68 6.69 0.00 2.87
1979 3496 4.782019 TGGACAGCCATGAAAATGTAAC 57.218 40.909 0.00 0.00 39.92 2.50
1999 3516 3.928727 AAGCCACAAATGTGTCAGATG 57.071 42.857 12.21 0.00 44.21 2.90
2000 3517 3.553508 GCAAAGCCACAAATGTGTCAGAT 60.554 43.478 12.21 0.00 44.21 2.90
2002 3519 2.129607 GCAAAGCCACAAATGTGTCAG 58.870 47.619 12.21 0.00 44.21 3.51
2003 3520 1.479730 TGCAAAGCCACAAATGTGTCA 59.520 42.857 12.21 0.00 44.21 3.58
2004 3521 2.129607 CTGCAAAGCCACAAATGTGTC 58.870 47.619 12.21 0.00 44.21 3.67
2006 3523 0.863144 GCTGCAAAGCCACAAATGTG 59.137 50.000 6.57 6.57 45.23 3.21
2091 5599 2.435059 GAGCCCAGCTCGTTGGAC 60.435 66.667 0.06 0.00 45.85 4.02
2197 5705 1.066502 GGAGAAGCTGTCCCTGAAGAC 60.067 57.143 4.27 0.00 37.28 3.01
2326 5838 5.118729 TGGTGTGAGGGTAAGAAAAGAAA 57.881 39.130 0.00 0.00 0.00 2.52
2332 5844 2.375174 AGCAATGGTGTGAGGGTAAGAA 59.625 45.455 0.00 0.00 0.00 2.52
2333 5845 1.985159 AGCAATGGTGTGAGGGTAAGA 59.015 47.619 0.00 0.00 0.00 2.10
2337 5849 1.362224 ACTAGCAATGGTGTGAGGGT 58.638 50.000 0.00 0.00 0.00 4.34
2367 5888 5.069516 AGGTTGAGCAGACATGAACAAAATT 59.930 36.000 0.00 0.00 0.00 1.82
2368 5889 4.586001 AGGTTGAGCAGACATGAACAAAAT 59.414 37.500 0.00 0.00 0.00 1.82
2369 5890 3.953612 AGGTTGAGCAGACATGAACAAAA 59.046 39.130 0.00 0.00 0.00 2.44
2370 5891 3.554934 AGGTTGAGCAGACATGAACAAA 58.445 40.909 0.00 0.00 0.00 2.83
2371 5892 3.141398 GAGGTTGAGCAGACATGAACAA 58.859 45.455 0.00 0.00 0.00 2.83
2372 5893 2.104622 TGAGGTTGAGCAGACATGAACA 59.895 45.455 0.00 0.00 0.00 3.18
2373 5894 2.771089 TGAGGTTGAGCAGACATGAAC 58.229 47.619 0.00 0.00 0.00 3.18
2374 5895 3.262660 AGATGAGGTTGAGCAGACATGAA 59.737 43.478 0.00 0.00 0.00 2.57
2382 5903 4.384537 CCCTGAATAAGATGAGGTTGAGCA 60.385 45.833 0.00 0.00 0.00 4.26
2383 5904 4.133078 CCCTGAATAAGATGAGGTTGAGC 58.867 47.826 0.00 0.00 0.00 4.26
2397 5919 0.182537 CCAATGGCGACCCCTGAATA 59.817 55.000 0.00 0.00 0.00 1.75
2453 6012 2.483188 CCCGAAGATGTAGTAACAGCCC 60.483 54.545 0.00 0.00 43.16 5.19
2459 6018 1.138266 GGCAGCCCGAAGATGTAGTAA 59.862 52.381 0.00 0.00 0.00 2.24
2480 6039 0.032017 AGCCGAGAAGATACCCCAGT 60.032 55.000 0.00 0.00 0.00 4.00
2486 6045 4.995124 TGAACTTGTAGCCGAGAAGATAC 58.005 43.478 0.63 0.00 32.68 2.24
2509 6068 2.285977 CAATTACCCCAACTCCGTAGC 58.714 52.381 0.00 0.00 0.00 3.58
2513 6072 2.209690 AACCAATTACCCCAACTCCG 57.790 50.000 0.00 0.00 0.00 4.63
2533 6211 9.462174 CAATTTGCAGTAGAGTTTAAATGACAA 57.538 29.630 0.00 0.00 0.00 3.18
2577 6259 3.578282 GGAATCACACCCCAAACATTCTT 59.422 43.478 0.00 0.00 0.00 2.52
2580 6262 2.632512 GTGGAATCACACCCCAAACATT 59.367 45.455 0.00 0.00 43.13 2.71
2581 6263 2.247358 GTGGAATCACACCCCAAACAT 58.753 47.619 0.00 0.00 43.13 2.71
2583 6265 0.596082 CGTGGAATCACACCCCAAAC 59.404 55.000 0.00 0.00 43.79 2.93
2588 6270 5.339990 CAAAATTATCGTGGAATCACACCC 58.660 41.667 0.00 0.00 43.79 4.61
2592 6274 8.402472 TCATAACCAAAATTATCGTGGAATCAC 58.598 33.333 1.72 0.00 40.36 3.06
2599 6281 9.687717 GCAAAATTCATAACCAAAATTATCGTG 57.312 29.630 0.00 0.00 0.00 4.35
2600 6282 8.591312 CGCAAAATTCATAACCAAAATTATCGT 58.409 29.630 0.00 0.00 0.00 3.73
2606 6288 7.903995 ATGTCGCAAAATTCATAACCAAAAT 57.096 28.000 0.00 0.00 0.00 1.82
2610 6292 5.167121 CCAATGTCGCAAAATTCATAACCA 58.833 37.500 0.00 0.00 0.00 3.67
2625 6329 4.380444 CCCCTAAAATCACAACCAATGTCG 60.380 45.833 0.00 0.00 41.46 4.35
2643 6347 3.816090 GCCGGCCCAAATCCCCTA 61.816 66.667 18.11 0.00 0.00 3.53
2669 6373 1.421268 AGTGTCTGAAGTGCAATCCCA 59.579 47.619 0.00 0.00 0.00 4.37
2696 6400 4.098044 TCCGTTCTCCACACTATGAAGATC 59.902 45.833 0.00 0.00 0.00 2.75
2741 6445 4.202212 CGAACAAAGGTGGGAAGGAATTTT 60.202 41.667 0.00 0.00 0.00 1.82
2742 6446 3.320826 CGAACAAAGGTGGGAAGGAATTT 59.679 43.478 0.00 0.00 0.00 1.82
2743 6447 2.890945 CGAACAAAGGTGGGAAGGAATT 59.109 45.455 0.00 0.00 0.00 2.17
2744 6448 2.107552 TCGAACAAAGGTGGGAAGGAAT 59.892 45.455 0.00 0.00 0.00 3.01
2787 6601 7.172868 TCAGCATTTTCCATATGAACAACAT 57.827 32.000 3.65 0.00 42.39 2.71
2789 6603 5.517770 GCTCAGCATTTTCCATATGAACAAC 59.482 40.000 3.65 0.00 31.05 3.32
2792 6606 5.511234 AGCTCAGCATTTTCCATATGAAC 57.489 39.130 3.65 0.00 31.05 3.18
2794 6608 6.153170 TGAAAAGCTCAGCATTTTCCATATGA 59.847 34.615 21.60 7.97 42.23 2.15
2795 6609 6.255020 GTGAAAAGCTCAGCATTTTCCATATG 59.745 38.462 21.60 0.00 42.23 1.78
2796 6610 6.335777 GTGAAAAGCTCAGCATTTTCCATAT 58.664 36.000 21.60 0.00 42.23 1.78
2830 6650 1.090052 GCGGTTGTAGGGCATGAGAC 61.090 60.000 0.00 0.00 0.00 3.36
2938 6759 5.704053 TCTTCGGGGAAACAGAGTTTTATTC 59.296 40.000 0.00 0.00 0.00 1.75
2976 6797 0.818040 CGCCACAAGGTAATAGGGGC 60.818 60.000 0.00 0.00 37.19 5.80
3012 6833 8.918202 ACCATCTTACAAATGTGACTAGAAAA 57.082 30.769 0.00 0.00 0.00 2.29
3013 6834 8.154203 TGACCATCTTACAAATGTGACTAGAAA 58.846 33.333 0.00 0.00 0.00 2.52
3014 6835 7.676004 TGACCATCTTACAAATGTGACTAGAA 58.324 34.615 0.00 0.00 0.00 2.10
3016 6837 8.498054 AATGACCATCTTACAAATGTGACTAG 57.502 34.615 0.00 0.00 0.00 2.57
3017 6838 8.321353 AGAATGACCATCTTACAAATGTGACTA 58.679 33.333 0.00 0.00 0.00 2.59
3018 6839 7.170965 AGAATGACCATCTTACAAATGTGACT 58.829 34.615 0.00 0.00 0.00 3.41
3019 6840 7.119699 TGAGAATGACCATCTTACAAATGTGAC 59.880 37.037 0.00 0.00 0.00 3.67
3021 6842 7.381766 TGAGAATGACCATCTTACAAATGTG 57.618 36.000 0.00 0.00 0.00 3.21
3022 6843 7.415989 GCATGAGAATGACCATCTTACAAATGT 60.416 37.037 0.00 0.00 0.00 2.71
3078 6906 8.377799 AGCATGGTCTAAGAAAATTTGGAAAAT 58.622 29.630 0.00 0.00 0.00 1.82
3115 6943 9.284968 AGTTTTATACAACTAAAGCACACAGAT 57.715 29.630 2.37 0.00 35.10 2.90
3116 6944 8.671384 AGTTTTATACAACTAAAGCACACAGA 57.329 30.769 2.37 0.00 35.10 3.41
3134 6962 5.163652 GGCGCACATTTCCTTCTAGTTTTAT 60.164 40.000 10.83 0.00 0.00 1.40
3137 6965 2.488153 GGCGCACATTTCCTTCTAGTTT 59.512 45.455 10.83 0.00 0.00 2.66
3202 7030 6.119536 ACAGACTACAACAAATGTCAAAGGA 58.880 36.000 0.00 0.00 42.70 3.36
3203 7031 6.260936 AGACAGACTACAACAAATGTCAAAGG 59.739 38.462 5.98 0.00 42.70 3.11
3210 7038 6.377327 AAACCAGACAGACTACAACAAATG 57.623 37.500 0.00 0.00 0.00 2.32
3217 7045 6.353323 TGAAATGAAAACCAGACAGACTACA 58.647 36.000 0.00 0.00 0.00 2.74
3276 7122 5.577945 GGATGTGTAATGTGCATTCCTTTTG 59.422 40.000 0.18 0.00 32.50 2.44
3291 7137 4.847198 AGATTGACTGCATGGATGTGTAA 58.153 39.130 0.00 0.00 0.00 2.41
3303 7149 3.691118 TCTATTGTGGCAAGATTGACTGC 59.309 43.478 0.00 0.00 37.03 4.40
3338 7184 2.618053 AGTATTCTCCGCCTTTCGTTG 58.382 47.619 0.00 0.00 36.19 4.10
3519 7365 0.460109 TGTCAATCACCTCGCCATCG 60.460 55.000 0.00 0.00 0.00 3.84
3567 7413 4.630069 TCGTGAGTAAAGATTGGCTAAAGC 59.370 41.667 0.00 0.00 41.14 3.51
3568 7414 6.721571 TTCGTGAGTAAAGATTGGCTAAAG 57.278 37.500 0.00 0.00 0.00 1.85
3569 7415 6.708949 AGTTTCGTGAGTAAAGATTGGCTAAA 59.291 34.615 0.00 0.00 0.00 1.85
3570 7416 6.228258 AGTTTCGTGAGTAAAGATTGGCTAA 58.772 36.000 0.00 0.00 0.00 3.09
3571 7417 5.790593 AGTTTCGTGAGTAAAGATTGGCTA 58.209 37.500 0.00 0.00 0.00 3.93
3572 7418 4.642429 AGTTTCGTGAGTAAAGATTGGCT 58.358 39.130 0.00 0.00 0.00 4.75
3573 7419 6.312918 TGATAGTTTCGTGAGTAAAGATTGGC 59.687 38.462 0.00 0.00 0.00 4.52
3607 7453 2.113774 CTGTCAGCAACCAGGGCA 59.886 61.111 0.00 0.00 0.00 5.36
3616 7462 1.640593 TTTGGGTCCCACTGTCAGCA 61.641 55.000 11.24 0.00 30.78 4.41
3670 7516 2.281761 GTGTGGGCAGAGTGGGTG 60.282 66.667 0.00 0.00 0.00 4.61
3678 7524 0.534877 TGCAACTACTGTGTGGGCAG 60.535 55.000 0.00 0.00 41.92 4.85
3693 7539 6.097270 AGCAGAAGCCATATAATCTTTTGCAA 59.903 34.615 19.67 0.00 45.00 4.08
3694 7540 5.595542 AGCAGAAGCCATATAATCTTTTGCA 59.404 36.000 19.67 0.00 45.00 4.08
3695 7541 5.919141 CAGCAGAAGCCATATAATCTTTTGC 59.081 40.000 14.26 14.26 43.78 3.68
3696 7542 7.228108 TCTCAGCAGAAGCCATATAATCTTTTG 59.772 37.037 0.00 0.00 43.56 2.44
3697 7543 7.285566 TCTCAGCAGAAGCCATATAATCTTTT 58.714 34.615 0.00 0.00 43.56 2.27
3698 7544 6.835174 TCTCAGCAGAAGCCATATAATCTTT 58.165 36.000 0.00 0.00 43.56 2.52
3699 7545 6.430962 TCTCAGCAGAAGCCATATAATCTT 57.569 37.500 0.00 0.00 43.56 2.40
3700 7546 6.408035 CATCTCAGCAGAAGCCATATAATCT 58.592 40.000 0.00 0.00 43.56 2.40
3701 7547 5.064962 GCATCTCAGCAGAAGCCATATAATC 59.935 44.000 0.00 0.00 43.56 1.75
3702 7548 4.942483 GCATCTCAGCAGAAGCCATATAAT 59.058 41.667 0.00 0.00 43.56 1.28
3703 7549 4.321718 GCATCTCAGCAGAAGCCATATAA 58.678 43.478 0.00 0.00 43.56 0.98
3704 7550 3.935315 GCATCTCAGCAGAAGCCATATA 58.065 45.455 0.00 0.00 43.56 0.86
3705 7551 2.780714 GCATCTCAGCAGAAGCCATAT 58.219 47.619 0.00 0.00 43.56 1.78
3706 7552 2.251409 GCATCTCAGCAGAAGCCATA 57.749 50.000 0.00 0.00 43.56 2.74
3707 7553 3.097461 GCATCTCAGCAGAAGCCAT 57.903 52.632 0.00 0.00 43.56 4.40
3708 7554 4.631773 GCATCTCAGCAGAAGCCA 57.368 55.556 0.00 0.00 43.56 4.75
3724 7570 2.134789 ACTCCCAAGATGATTGTGGC 57.865 50.000 0.00 0.00 0.00 5.01
3725 7571 4.081406 TGAAACTCCCAAGATGATTGTGG 58.919 43.478 0.00 0.00 0.00 4.17
3730 7576 6.381133 GGGTATTTTGAAACTCCCAAGATGAT 59.619 38.462 10.81 0.00 35.53 2.45
3788 7634 7.315142 TGGAGAAATTTTACATGATTCTGCAC 58.685 34.615 0.00 0.00 41.49 4.57
3802 7648 8.034215 TCATGTTTCGCATAATGGAGAAATTTT 58.966 29.630 0.00 0.00 38.51 1.82
3857 7703 2.809174 TGATTCAGCCGTGCGACG 60.809 61.111 0.00 0.00 42.11 5.12
3895 7742 2.954684 TAGGCTTCCGGTGCTGTGG 61.955 63.158 18.34 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.