Multiple sequence alignment - TraesCS5D01G068900

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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 TraesCS5D01G068900 chr5D 100.000 5711 0 0 1 5711 65908384 65902674 0.000000e+00 10547
1 TraesCS5D01G068900 chr5D 78.166 687 124 20 3591 4265 534006464 534005792 1.140000e-111 414
2 TraesCS5D01G068900 chr5D 86.061 165 23 0 4356 4520 534005318 534005154 1.640000e-40 178
3 TraesCS5D01G068900 chr5A 91.337 3567 201 43 1523 5052 55164756 55161261 0.000000e+00 4776
4 TraesCS5D01G068900 chr5A 97.639 720 16 1 1 720 55172224 55171506 0.000000e+00 1234
5 TraesCS5D01G068900 chr5A 98.289 409 7 0 1116 1524 55165582 55165174 0.000000e+00 717
6 TraesCS5D01G068900 chr5A 98.000 400 7 1 783 1181 55165970 55165571 0.000000e+00 693
7 TraesCS5D01G068900 chr5A 85.602 382 28 9 5085 5439 55161259 55160878 5.400000e-100 375
8 TraesCS5D01G068900 chr5A 89.723 253 10 12 5461 5711 55160890 55160652 5.560000e-80 309
9 TraesCS5D01G068900 chr5B 94.945 2018 76 12 2262 4269 65187339 65189340 0.000000e+00 3138
10 TraesCS5D01G068900 chr5B 91.743 763 45 3 4271 5031 65189467 65190213 0.000000e+00 1044
11 TraesCS5D01G068900 chr5B 88.840 681 42 9 1525 2181 65186644 65187314 0.000000e+00 806
12 TraesCS5D01G068900 chr5B 94.211 380 19 1 917 1296 65185626 65186002 1.380000e-160 577
13 TraesCS5D01G068900 chr5B 77.826 690 122 26 3591 4265 674269596 674268923 1.150000e-106 398
14 TraesCS5D01G068900 chr5B 84.906 371 23 13 5096 5439 65190209 65190573 1.520000e-90 344
15 TraesCS5D01G068900 chr5B 89.695 262 15 5 5459 5709 65190559 65190819 1.980000e-84 324
16 TraesCS5D01G068900 chr5B 86.061 165 23 0 4356 4520 674268494 674268330 1.640000e-40 178
17 TraesCS5D01G068900 chr5B 88.321 137 16 0 1131 1267 674271007 674270871 1.270000e-36 165
18 TraesCS5D01G068900 chr2A 86.209 2712 290 53 1924 4581 75659891 75657210 0.000000e+00 2859
19 TraesCS5D01G068900 chr2A 88.158 152 18 0 2 153 579725264 579725415 1.260000e-41 182
20 TraesCS5D01G068900 chr2A 87.755 147 18 0 9 155 53079867 53080013 7.610000e-39 172
21 TraesCS5D01G068900 chr2B 86.496 2029 212 37 2935 4948 116850664 116848683 0.000000e+00 2172
22 TraesCS5D01G068900 chr2B 80.620 1290 166 34 1656 2914 116851999 116850763 0.000000e+00 920
23 TraesCS5D01G068900 chr2D 83.141 1299 174 29 1656 2919 75763969 75762681 0.000000e+00 1144
24 TraesCS5D01G068900 chr2D 89.333 600 62 2 3985 4583 75762137 75761539 0.000000e+00 752
25 TraesCS5D01G068900 chr2D 87.282 574 52 9 3383 3952 75762686 75762130 2.240000e-178 636
26 TraesCS5D01G068900 chr2D 86.275 153 17 4 2 153 367243181 367243032 4.580000e-36 163
27 TraesCS5D01G068900 chr4A 78.624 683 125 19 3591 4265 637922679 637923348 3.160000e-117 433
28 TraesCS5D01G068900 chr4A 80.672 238 37 6 4357 4591 637923804 637924035 5.880000e-40 176
29 TraesCS5D01G068900 chr6B 80.000 330 37 12 5139 5439 657942313 657941984 3.470000e-52 217
30 TraesCS5D01G068900 chr6D 79.808 312 35 11 5156 5439 434511952 434511641 9.700000e-48 202
31 TraesCS5D01G068900 chr6A 79.100 311 38 18 5156 5439 581889361 581889051 7.550000e-44 189
32 TraesCS5D01G068900 chr7B 88.235 153 15 3 4 156 218755773 218755624 4.550000e-41 180
33 TraesCS5D01G068900 chr7B 85.806 155 21 1 2 156 284859260 284859107 4.580000e-36 163
34 TraesCS5D01G068900 chr3B 86.364 154 17 4 2 154 302317645 302317495 1.270000e-36 165
35 TraesCS5D01G068900 chr1A 85.897 156 19 2 1 156 116234988 116235140 4.580000e-36 163
36 TraesCS5D01G068900 chr7D 85.093 161 19 5 1 159 379847817 379847974 5.920000e-35 159


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 TraesCS5D01G068900 chr5D 65902674 65908384 5710 True 10547.000000 10547 100.000000 1 5711 1 chr5D.!!$R1 5710
1 TraesCS5D01G068900 chr5D 534005154 534006464 1310 True 296.000000 414 82.113500 3591 4520 2 chr5D.!!$R2 929
2 TraesCS5D01G068900 chr5A 55160652 55165970 5318 True 1374.000000 4776 92.590200 783 5711 5 chr5A.!!$R2 4928
3 TraesCS5D01G068900 chr5A 55171506 55172224 718 True 1234.000000 1234 97.639000 1 720 1 chr5A.!!$R1 719
4 TraesCS5D01G068900 chr5B 65185626 65190819 5193 False 1038.833333 3138 90.723333 917 5709 6 chr5B.!!$F1 4792
5 TraesCS5D01G068900 chr5B 674268330 674271007 2677 True 247.000000 398 84.069333 1131 4520 3 chr5B.!!$R1 3389
6 TraesCS5D01G068900 chr2A 75657210 75659891 2681 True 2859.000000 2859 86.209000 1924 4581 1 chr2A.!!$R1 2657
7 TraesCS5D01G068900 chr2B 116848683 116851999 3316 True 1546.000000 2172 83.558000 1656 4948 2 chr2B.!!$R1 3292
8 TraesCS5D01G068900 chr2D 75761539 75763969 2430 True 844.000000 1144 86.585333 1656 4583 3 chr2D.!!$R2 2927
9 TraesCS5D01G068900 chr4A 637922679 637924035 1356 False 304.500000 433 79.648000 3591 4591 2 chr4A.!!$F1 1000

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
764 765 0.026803 GTCCGCGCTGCATTTAGAAG 59.973 55.000 5.56 0.0 0.0 2.85 F
765 766 0.391130 TCCGCGCTGCATTTAGAAGT 60.391 50.000 5.56 0.0 0.0 3.01 F
2112 2623 0.392998 GGTGTTGTCGGAGCCATCAT 60.393 55.000 0.00 0.0 0.0 2.45 F
2124 2635 1.069596 CCATCATGATCGGTGGCGA 59.930 57.895 4.86 0.0 0.0 5.54 F
3608 4349 0.805322 GACAGACAGCAGAGATGCCG 60.805 60.000 0.00 0.0 34.9 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2668 0.306533 GTTGGCTTCTTTCGTTCGCA 59.693 50.000 0.00 0.0 0.00 5.10 R
2255 2772 0.673333 CCTGTACTTGCACATCGGCA 60.673 55.000 0.00 0.0 43.19 5.69 R
3608 4349 1.065709 TCACCTTCCGCATAGAAACCC 60.066 52.381 0.00 0.0 0.00 4.11 R
3681 4422 4.080975 TCCCTCCACGATATTTTTACCGTT 60.081 41.667 0.00 0.0 32.50 4.44 R
5079 6493 0.458889 GGAGTGTGCGTATGCCGTAA 60.459 55.000 4.05 0.0 41.78 3.18 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
50 51 5.514279 ACTATGCGCTTTTCTATCAATTGC 58.486 37.500 9.73 0.00 0.00 3.56
73 74 4.201970 CCGAACAACAATTTGTGTACCAGT 60.202 41.667 2.13 0.00 45.69 4.00
75 76 6.133392 CGAACAACAATTTGTGTACCAGTAG 58.867 40.000 2.13 0.00 45.69 2.57
80 81 7.094118 ACAACAATTTGTGTACCAGTAGTTTGT 60.094 33.333 2.13 0.00 44.66 2.83
96 97 5.907197 AGTTTGTTATGTTCGTGAGTGAG 57.093 39.130 0.00 0.00 0.00 3.51
188 189 2.455032 GAAGTCGTGAGGATGATGTCG 58.545 52.381 0.00 0.00 0.00 4.35
238 239 3.450904 GGCTAGGGTATATGTGGGATCA 58.549 50.000 0.00 0.00 0.00 2.92
279 280 3.738281 CGGTCTAACATCGCCTGAATTCT 60.738 47.826 7.05 0.00 0.00 2.40
317 318 4.199002 TGACATCTTAGGATCAGCCCTA 57.801 45.455 0.00 0.00 37.74 3.53
383 384 2.291741 CACAAAAGGTCTCTTCAGGCAC 59.708 50.000 0.00 0.00 31.82 5.01
520 521 6.227298 ACATGAGATGGTAGGAGTTTACAG 57.773 41.667 0.00 0.00 33.60 2.74
722 723 9.992910 TGTACTTGTACTTCATGTTAGTATACG 57.007 33.333 11.53 9.84 36.20 3.06
723 724 7.982371 ACTTGTACTTCATGTTAGTATACGC 57.018 36.000 11.67 0.00 31.71 4.42
724 725 7.769220 ACTTGTACTTCATGTTAGTATACGCT 58.231 34.615 11.67 0.00 31.71 5.07
725 726 7.914346 ACTTGTACTTCATGTTAGTATACGCTC 59.086 37.037 11.67 0.00 31.71 5.03
726 727 6.424683 TGTACTTCATGTTAGTATACGCTCG 58.575 40.000 11.67 0.00 31.31 5.03
727 728 5.496133 ACTTCATGTTAGTATACGCTCGT 57.504 39.130 0.00 0.00 0.00 4.18
728 729 5.271625 ACTTCATGTTAGTATACGCTCGTG 58.728 41.667 5.05 4.12 0.00 4.35
729 730 5.065602 ACTTCATGTTAGTATACGCTCGTGA 59.934 40.000 5.05 11.90 0.00 4.35
730 731 5.488645 TCATGTTAGTATACGCTCGTGAA 57.511 39.130 5.05 0.00 0.00 3.18
731 732 6.068473 TCATGTTAGTATACGCTCGTGAAT 57.932 37.500 5.05 0.00 0.00 2.57
732 733 6.140786 TCATGTTAGTATACGCTCGTGAATC 58.859 40.000 5.05 0.00 0.00 2.52
733 734 5.488645 TGTTAGTATACGCTCGTGAATCA 57.511 39.130 5.05 0.00 0.00 2.57
734 735 6.068473 TGTTAGTATACGCTCGTGAATCAT 57.932 37.500 5.05 0.00 0.00 2.45
735 736 6.500910 TGTTAGTATACGCTCGTGAATCATT 58.499 36.000 5.05 0.00 0.00 2.57
736 737 6.976349 TGTTAGTATACGCTCGTGAATCATTT 59.024 34.615 5.05 0.00 0.00 2.32
737 738 8.130469 TGTTAGTATACGCTCGTGAATCATTTA 58.870 33.333 5.05 0.00 0.00 1.40
738 739 8.628279 GTTAGTATACGCTCGTGAATCATTTAG 58.372 37.037 5.05 0.00 0.00 1.85
739 740 6.967135 AGTATACGCTCGTGAATCATTTAGA 58.033 36.000 5.05 0.00 0.00 2.10
740 741 7.423199 AGTATACGCTCGTGAATCATTTAGAA 58.577 34.615 5.05 0.00 0.00 2.10
741 742 6.755461 ATACGCTCGTGAATCATTTAGAAG 57.245 37.500 5.05 0.00 0.00 2.85
742 743 4.495422 ACGCTCGTGAATCATTTAGAAGT 58.505 39.130 0.00 0.00 0.00 3.01
743 744 5.647589 ACGCTCGTGAATCATTTAGAAGTA 58.352 37.500 0.00 0.00 0.00 2.24
744 745 6.273825 ACGCTCGTGAATCATTTAGAAGTAT 58.726 36.000 0.00 0.00 0.00 2.12
745 746 6.199154 ACGCTCGTGAATCATTTAGAAGTATG 59.801 38.462 0.00 0.00 0.00 2.39
746 747 6.199154 CGCTCGTGAATCATTTAGAAGTATGT 59.801 38.462 0.00 0.00 0.00 2.29
747 748 7.559845 GCTCGTGAATCATTTAGAAGTATGTC 58.440 38.462 0.00 0.00 0.00 3.06
748 749 7.306866 GCTCGTGAATCATTTAGAAGTATGTCC 60.307 40.741 0.00 0.00 0.00 4.02
749 750 6.695713 TCGTGAATCATTTAGAAGTATGTCCG 59.304 38.462 0.00 0.00 0.00 4.79
750 751 6.562270 CGTGAATCATTTAGAAGTATGTCCGC 60.562 42.308 0.00 0.00 0.00 5.54
751 752 5.462068 TGAATCATTTAGAAGTATGTCCGCG 59.538 40.000 0.00 0.00 0.00 6.46
752 753 3.120792 TCATTTAGAAGTATGTCCGCGC 58.879 45.455 0.00 0.00 0.00 6.86
753 754 2.953466 TTTAGAAGTATGTCCGCGCT 57.047 45.000 5.56 0.00 0.00 5.92
754 755 2.203800 TTAGAAGTATGTCCGCGCTG 57.796 50.000 5.56 0.00 0.00 5.18
755 756 0.248907 TAGAAGTATGTCCGCGCTGC 60.249 55.000 5.56 0.00 0.00 5.25
756 757 1.809619 GAAGTATGTCCGCGCTGCA 60.810 57.895 5.56 1.79 0.00 4.41
757 758 1.153369 AAGTATGTCCGCGCTGCAT 60.153 52.632 5.56 9.68 0.00 3.96
758 759 0.744414 AAGTATGTCCGCGCTGCATT 60.744 50.000 5.56 0.00 0.00 3.56
759 760 0.744414 AGTATGTCCGCGCTGCATTT 60.744 50.000 5.56 0.00 0.00 2.32
760 761 0.934496 GTATGTCCGCGCTGCATTTA 59.066 50.000 5.56 0.00 0.00 1.40
761 762 1.070577 GTATGTCCGCGCTGCATTTAG 60.071 52.381 5.56 0.00 0.00 1.85
762 763 0.461870 ATGTCCGCGCTGCATTTAGA 60.462 50.000 5.56 0.00 0.00 2.10
763 764 0.672091 TGTCCGCGCTGCATTTAGAA 60.672 50.000 5.56 0.00 0.00 2.10
764 765 0.026803 GTCCGCGCTGCATTTAGAAG 59.973 55.000 5.56 0.00 0.00 2.85
765 766 0.391130 TCCGCGCTGCATTTAGAAGT 60.391 50.000 5.56 0.00 0.00 3.01
766 767 1.134936 TCCGCGCTGCATTTAGAAGTA 60.135 47.619 5.56 0.00 0.00 2.24
767 768 1.004927 CCGCGCTGCATTTAGAAGTAC 60.005 52.381 5.56 0.00 0.00 2.73
768 769 1.658596 CGCGCTGCATTTAGAAGTACA 59.341 47.619 5.56 0.00 0.00 2.90
769 770 2.534939 CGCGCTGCATTTAGAAGTACAC 60.535 50.000 5.56 0.00 0.00 2.90
770 771 2.534939 GCGCTGCATTTAGAAGTACACG 60.535 50.000 0.00 0.00 0.00 4.49
771 772 2.534939 CGCTGCATTTAGAAGTACACGC 60.535 50.000 0.00 0.00 0.00 5.34
772 773 2.534939 GCTGCATTTAGAAGTACACGCG 60.535 50.000 3.53 3.53 0.00 6.01
773 774 2.666508 CTGCATTTAGAAGTACACGCGT 59.333 45.455 5.58 5.58 0.00 6.01
774 775 2.410392 TGCATTTAGAAGTACACGCGTG 59.590 45.455 35.99 35.99 0.00 5.34
775 776 2.664568 GCATTTAGAAGTACACGCGTGA 59.335 45.455 42.94 24.54 0.00 4.35
776 777 3.122278 GCATTTAGAAGTACACGCGTGAA 59.878 43.478 42.94 24.87 0.00 3.18
777 778 4.721226 GCATTTAGAAGTACACGCGTGAAG 60.721 45.833 42.94 20.00 0.00 3.02
778 779 3.902261 TTAGAAGTACACGCGTGAAGA 57.098 42.857 42.94 24.98 0.00 2.87
779 780 2.333389 AGAAGTACACGCGTGAAGAG 57.667 50.000 42.94 19.19 0.00 2.85
780 781 1.607628 AGAAGTACACGCGTGAAGAGT 59.392 47.619 42.94 26.14 0.00 3.24
781 782 2.810274 AGAAGTACACGCGTGAAGAGTA 59.190 45.455 42.94 22.95 0.00 2.59
802 803 2.099062 CGGCGCTGCATTTGAGAC 59.901 61.111 7.64 0.00 0.00 3.36
862 863 1.888018 CACATTCTGGCTGCTTGGG 59.112 57.895 0.00 0.00 0.00 4.12
1404 1460 5.585047 CCAGTAGCTTGGGTAAGTAAATGAC 59.415 44.000 0.00 0.00 36.27 3.06
1409 1465 5.815740 AGCTTGGGTAAGTAAATGACGTATG 59.184 40.000 0.00 0.00 36.27 2.39
1570 2048 5.358725 TGATACCAGCGATGAAGTTGTAGTA 59.641 40.000 0.06 0.00 0.00 1.82
1579 2057 5.569441 CGATGAAGTTGTAGTACACACAGAG 59.431 44.000 1.43 0.00 36.69 3.35
1586 2064 2.795175 AGTACACACAGAGGAACGTG 57.205 50.000 0.00 0.00 39.10 4.49
1607 2091 0.893727 AGCGGAACCAACAACATCCC 60.894 55.000 0.00 0.00 0.00 3.85
1652 2136 1.303236 AAGCATGCCGGCTGTACAA 60.303 52.632 29.70 6.08 45.07 2.41
1661 2145 1.641577 CGGCTGTACAAGAAGTAGGC 58.358 55.000 0.00 0.00 32.19 3.93
1665 2149 2.163815 GCTGTACAAGAAGTAGGCGAGA 59.836 50.000 0.00 0.00 32.19 4.04
1672 2156 4.039366 ACAAGAAGTAGGCGAGAAAGAACT 59.961 41.667 0.00 0.00 0.00 3.01
1702 2188 3.550842 CCGACAGCGTGATGAAGATCATA 60.551 47.826 0.00 0.00 40.78 2.15
1794 2281 4.161333 GAGAACAAAGATGACCGCATTTG 58.839 43.478 0.00 0.00 34.11 2.32
1830 2323 1.681327 GGGAGCGACCTAGGTCACA 60.681 63.158 35.32 0.00 44.77 3.58
1881 2374 1.452025 CGACGTATGCGCCTAGAAATG 59.548 52.381 4.18 0.00 42.83 2.32
1892 2385 3.425359 CGCCTAGAAATGCACTTTGACAG 60.425 47.826 0.00 0.00 0.00 3.51
1913 2407 2.228480 GGTACCAGGACCAAGGCCA 61.228 63.158 7.15 0.00 39.51 5.36
1929 2423 1.213537 CCATCAAAGTTGCAGCCCG 59.786 57.895 0.00 0.00 0.00 6.13
1939 2433 4.759205 GCAGCCCGGGGGAAACAT 62.759 66.667 25.28 0.00 37.50 2.71
1943 2437 0.697854 AGCCCGGGGGAAACATATCT 60.698 55.000 25.28 2.90 37.50 1.98
2108 2619 1.003839 GATGGTGTTGTCGGAGCCA 60.004 57.895 0.00 0.00 0.00 4.75
2112 2623 0.392998 GGTGTTGTCGGAGCCATCAT 60.393 55.000 0.00 0.00 0.00 2.45
2124 2635 1.069596 CCATCATGATCGGTGGCGA 59.930 57.895 4.86 0.00 0.00 5.54
2151 2668 1.672356 GACCAGCGATGCACAAGGT 60.672 57.895 0.00 0.00 0.00 3.50
2194 2711 2.496899 ACGCATGAAGACATCCCTTT 57.503 45.000 0.00 0.00 34.15 3.11
2202 2719 4.728772 TGAAGACATCCCTTTTGTGACAT 58.271 39.130 0.00 0.00 0.00 3.06
2329 2846 3.437741 ACCGTTTTATGTTCGATGAACCC 59.562 43.478 7.18 0.00 41.35 4.11
2363 2882 1.697432 AGTCAAATGACCCACGGAGAA 59.303 47.619 9.84 0.00 45.85 2.87
2427 2958 3.688086 GAGATCGATCTCCCCGGG 58.312 66.667 35.46 15.80 45.88 5.73
2489 3020 7.503521 GGATACTGCGATATCATGATAGAGA 57.496 40.000 19.73 0.00 33.83 3.10
2544 3075 2.712057 TGAACCTTTCGGACGAGTAC 57.288 50.000 0.00 0.00 0.00 2.73
2799 3410 1.747355 CTCAGGTTGGGCACATGAATC 59.253 52.381 0.00 0.00 45.40 2.52
2815 3426 8.680001 GCACATGAATCTAATGCCATATTCATA 58.320 33.333 11.82 0.00 43.65 2.15
3119 3824 3.178539 GCTACGGGCAAGCTTGAC 58.821 61.111 30.39 27.74 41.35 3.18
3152 3857 4.619863 GCAGAGAAGGTAATGTCGGTGTTA 60.620 45.833 0.00 0.00 0.00 2.41
3163 3868 4.804608 TGTCGGTGTTATTGTTCACTTG 57.195 40.909 0.00 0.00 35.26 3.16
3165 3870 5.060506 TGTCGGTGTTATTGTTCACTTGAT 58.939 37.500 0.00 0.00 35.26 2.57
3353 4080 4.822350 TCTCCATAATGATCTCGTCGAGTT 59.178 41.667 21.15 13.64 0.00 3.01
3608 4349 0.805322 GACAGACAGCAGAGATGCCG 60.805 60.000 0.00 0.00 34.90 5.69
3681 4422 3.519107 TGTGGACAAGGATAAGCTCATCA 59.481 43.478 0.00 0.00 0.00 3.07
4457 5835 2.402305 CAGCTGACAGGATTATCGAGC 58.598 52.381 8.42 0.00 0.00 5.03
4537 5922 4.333926 GTCTGATGCCTTCGATAAGCTTTT 59.666 41.667 3.20 0.00 0.00 2.27
4606 5997 3.821033 AGCAGCCGAATTTTTGTAACTCT 59.179 39.130 0.00 0.00 0.00 3.24
4633 6042 0.170561 TAGGCGAGCTTCGAGTGTTC 59.829 55.000 9.32 0.00 43.74 3.18
4634 6043 1.372997 GGCGAGCTTCGAGTGTTCA 60.373 57.895 9.32 0.00 43.74 3.18
4635 6044 1.347817 GGCGAGCTTCGAGTGTTCAG 61.348 60.000 9.32 0.00 43.74 3.02
4636 6045 0.664767 GCGAGCTTCGAGTGTTCAGT 60.665 55.000 9.32 0.00 43.74 3.41
4637 6046 1.772182 CGAGCTTCGAGTGTTCAGTT 58.228 50.000 0.00 0.00 43.74 3.16
4638 6047 1.453524 CGAGCTTCGAGTGTTCAGTTG 59.546 52.381 0.00 0.00 43.74 3.16
4639 6048 2.743938 GAGCTTCGAGTGTTCAGTTGA 58.256 47.619 0.00 0.00 0.00 3.18
4640 6049 3.123804 GAGCTTCGAGTGTTCAGTTGAA 58.876 45.455 9.20 9.20 0.00 2.69
4641 6050 6.337569 CGAGCTTCGAGTGTTCAGTTGAAC 62.338 50.000 16.14 16.14 46.99 3.18
4747 6156 1.486310 AGACCTTGTCTGCTTGTCACA 59.514 47.619 0.00 0.00 41.76 3.58
4772 6181 8.889717 CAGTTTTAGGTCTGTTCTTTTCAAGTA 58.110 33.333 0.00 0.00 0.00 2.24
4859 6268 7.031226 TGAATGAAAGACCTCAAAGAACAAG 57.969 36.000 0.00 0.00 0.00 3.16
4891 6301 4.878397 CAGGACTCAAACTGAAACTGTTCT 59.122 41.667 0.00 0.00 36.86 3.01
4966 6380 8.136165 AGACTGTTATAAGACATAAACTAGGCG 58.864 37.037 0.00 0.00 0.00 5.52
5001 6415 6.383763 TGGGGATCACCATCATGAAAATAAT 58.616 36.000 14.36 0.00 42.91 1.28
5004 6418 8.212995 GGGGATCACCATCATGAAAATAATTTT 58.787 33.333 9.87 0.00 42.91 1.82
5006 6420 8.971321 GGATCACCATCATGAAAATAATTTTCG 58.029 33.333 0.00 0.00 42.58 3.46
5042 6456 1.077212 CCCTCCAAGTGCATCAGGG 60.077 63.158 0.00 0.00 38.07 4.45
5064 6478 6.625873 GGCATTCCCTAAATCTCAACTAAG 57.374 41.667 0.00 0.00 0.00 2.18
5065 6479 6.357367 GGCATTCCCTAAATCTCAACTAAGA 58.643 40.000 0.00 0.00 0.00 2.10
5066 6480 6.828785 GGCATTCCCTAAATCTCAACTAAGAA 59.171 38.462 0.00 0.00 0.00 2.52
5067 6481 7.503902 GGCATTCCCTAAATCTCAACTAAGAAT 59.496 37.037 0.00 0.00 0.00 2.40
5068 6482 8.907885 GCATTCCCTAAATCTCAACTAAGAATT 58.092 33.333 0.00 0.00 0.00 2.17
5071 6485 9.807921 TTCCCTAAATCTCAACTAAGAATTTGT 57.192 29.630 0.00 0.00 35.01 2.83
5072 6486 9.449719 TCCCTAAATCTCAACTAAGAATTTGTC 57.550 33.333 0.00 0.00 31.54 3.18
5073 6487 8.678199 CCCTAAATCTCAACTAAGAATTTGTCC 58.322 37.037 0.00 0.00 31.54 4.02
5074 6488 9.231297 CCTAAATCTCAACTAAGAATTTGTCCA 57.769 33.333 0.00 0.00 31.54 4.02
5077 6491 8.924511 AATCTCAACTAAGAATTTGTCCAAGA 57.075 30.769 0.00 0.00 31.54 3.02
5078 6492 9.525826 AATCTCAACTAAGAATTTGTCCAAGAT 57.474 29.630 0.00 0.00 31.54 2.40
5079 6493 8.924511 TCTCAACTAAGAATTTGTCCAAGATT 57.075 30.769 0.00 0.00 31.54 2.40
5080 6494 9.354673 TCTCAACTAAGAATTTGTCCAAGATTT 57.645 29.630 0.00 0.00 31.54 2.17
5083 6497 9.329913 CAACTAAGAATTTGTCCAAGATTTACG 57.670 33.333 0.00 0.00 31.54 3.18
5114 6528 1.063806 CTCCAGTCAAAGAAGCGTCG 58.936 55.000 0.00 0.00 0.00 5.12
5133 6547 2.299013 TCGTGTGGTTAAGCAGTCAGAT 59.701 45.455 7.79 0.00 0.00 2.90
5138 6552 4.756642 TGTGGTTAAGCAGTCAGATTGAAG 59.243 41.667 7.79 0.00 0.00 3.02
5167 6581 5.186198 GCTAAATCTGACTTCAGGCCTTTA 58.814 41.667 0.00 0.00 43.91 1.85
5168 6582 5.825151 GCTAAATCTGACTTCAGGCCTTTAT 59.175 40.000 0.00 0.00 43.91 1.40
5197 6613 6.373774 ACTTGTTCATCACAGGAATGATCTTC 59.626 38.462 0.00 0.00 37.20 2.87
5201 6617 4.102210 TCATCACAGGAATGATCTTCTCCC 59.898 45.833 0.00 0.00 37.20 4.30
5203 6619 2.776536 CACAGGAATGATCTTCTCCCCT 59.223 50.000 0.00 0.00 0.00 4.79
5208 6624 3.397282 GGAATGATCTTCTCCCCTTGGAT 59.603 47.826 0.00 0.00 40.80 3.41
5241 6657 3.865745 GGATCAATCTTGTAGGTGTCGTG 59.134 47.826 0.00 0.00 0.00 4.35
5285 6722 3.810373 CAAACGAGTGCAAGTGGATTAC 58.190 45.455 0.00 0.00 0.00 1.89
5286 6723 1.710013 ACGAGTGCAAGTGGATTACG 58.290 50.000 0.00 0.00 0.00 3.18
5288 6725 1.920574 CGAGTGCAAGTGGATTACGAG 59.079 52.381 0.00 0.00 0.00 4.18
5289 6726 2.415491 CGAGTGCAAGTGGATTACGAGA 60.415 50.000 0.00 0.00 0.00 4.04
5292 6729 3.064207 GTGCAAGTGGATTACGAGAACA 58.936 45.455 0.00 0.00 0.00 3.18
5293 6730 3.123621 GTGCAAGTGGATTACGAGAACAG 59.876 47.826 0.00 0.00 0.00 3.16
5294 6731 3.006430 TGCAAGTGGATTACGAGAACAGA 59.994 43.478 0.00 0.00 0.00 3.41
5295 6732 3.368236 GCAAGTGGATTACGAGAACAGAC 59.632 47.826 0.00 0.00 0.00 3.51
5296 6733 3.870633 AGTGGATTACGAGAACAGACC 57.129 47.619 0.00 0.00 0.00 3.85
5409 6850 5.685841 TCTTTAAGAACGCTTGCAATGTAC 58.314 37.500 0.00 0.00 35.56 2.90
5438 6879 4.098960 GGCCAATGCAATCATATATGGAGG 59.901 45.833 12.78 3.89 40.13 4.30
5439 6880 4.098960 GCCAATGCAATCATATATGGAGGG 59.901 45.833 12.78 5.18 32.39 4.30
5440 6881 5.266788 CCAATGCAATCATATATGGAGGGT 58.733 41.667 12.78 0.00 32.39 4.34
5441 6882 5.718130 CCAATGCAATCATATATGGAGGGTT 59.282 40.000 12.78 0.00 32.39 4.11
5442 6883 6.211986 CCAATGCAATCATATATGGAGGGTTT 59.788 38.462 12.78 0.00 32.39 3.27
5443 6884 7.256404 CCAATGCAATCATATATGGAGGGTTTT 60.256 37.037 12.78 0.00 32.39 2.43
5444 6885 7.860649 ATGCAATCATATATGGAGGGTTTTT 57.139 32.000 12.78 0.00 0.00 1.94
5530 6972 3.329520 TGACAAGGCCCTGTAAGTAACAT 59.670 43.478 7.07 0.00 37.50 2.71
5557 6999 7.836183 TGTCTAATCAGCATAGAGATATAGCCA 59.164 37.037 0.00 0.00 30.33 4.75
5558 7000 8.859090 GTCTAATCAGCATAGAGATATAGCCAT 58.141 37.037 0.00 0.00 30.33 4.40
5563 7005 8.876303 TCAGCATAGAGATATAGCCATATAGG 57.124 38.462 0.00 0.00 41.84 2.57
5564 7006 8.452056 TCAGCATAGAGATATAGCCATATAGGT 58.548 37.037 0.00 0.00 40.61 3.08
5565 7007 8.739039 CAGCATAGAGATATAGCCATATAGGTC 58.261 40.741 0.00 0.00 40.61 3.85
5566 7008 8.677871 AGCATAGAGATATAGCCATATAGGTCT 58.322 37.037 0.00 0.00 40.61 3.85
5669 7134 9.775539 ATACCCATCTCATCATATTGTACTAGT 57.224 33.333 0.00 0.00 0.00 2.57
5671 7136 9.775539 ACCCATCTCATCATATTGTACTAGTAT 57.224 33.333 5.75 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.201970 ACTGGTACACAAATTGTTGTTCGG 60.202 41.667 0.00 3.40 46.01 4.30
73 74 6.741109 TCTCACTCACGAACATAACAAACTA 58.259 36.000 0.00 0.00 0.00 2.24
75 76 5.900339 TCTCACTCACGAACATAACAAAC 57.100 39.130 0.00 0.00 0.00 2.93
80 81 3.195610 AGGCATCTCACTCACGAACATAA 59.804 43.478 0.00 0.00 0.00 1.90
158 159 6.549736 TCATCCTCACGACTTCCTATGATTTA 59.450 38.462 0.00 0.00 0.00 1.40
163 164 4.038522 ACATCATCCTCACGACTTCCTATG 59.961 45.833 0.00 0.00 0.00 2.23
188 189 0.902531 TCTCGACCAAACCTCATCCC 59.097 55.000 0.00 0.00 0.00 3.85
279 280 2.233676 TGTCAAAGCCGAGATGAAGCTA 59.766 45.455 0.00 0.00 35.30 3.32
383 384 1.482593 ACACTTAGAATGAGGGGAGCG 59.517 52.381 0.00 0.00 0.00 5.03
571 572 4.870426 TGAGAGAAACACAACTGTCTGAAC 59.130 41.667 0.00 0.00 0.00 3.18
616 617 8.446489 TGTTGTTCAAAATCTATTAACATGCG 57.554 30.769 0.00 0.00 30.76 4.73
654 655 6.261381 ACAAAGTAGAACCGTGCTAATTTTGA 59.739 34.615 21.13 0.00 34.91 2.69
720 721 4.495422 ACTTCTAAATGATTCACGAGCGT 58.505 39.130 0.00 0.00 0.00 5.07
721 722 6.199154 ACATACTTCTAAATGATTCACGAGCG 59.801 38.462 0.00 0.00 0.00 5.03
722 723 7.306866 GGACATACTTCTAAATGATTCACGAGC 60.307 40.741 0.00 0.00 0.00 5.03
723 724 7.096436 CGGACATACTTCTAAATGATTCACGAG 60.096 40.741 0.00 0.00 0.00 4.18
724 725 6.695713 CGGACATACTTCTAAATGATTCACGA 59.304 38.462 0.00 0.00 0.00 4.35
725 726 6.562270 GCGGACATACTTCTAAATGATTCACG 60.562 42.308 0.00 0.00 0.00 4.35
726 727 6.562270 CGCGGACATACTTCTAAATGATTCAC 60.562 42.308 0.00 0.00 0.00 3.18
727 728 5.462068 CGCGGACATACTTCTAAATGATTCA 59.538 40.000 0.00 0.00 0.00 2.57
728 729 5.612709 GCGCGGACATACTTCTAAATGATTC 60.613 44.000 8.83 0.00 0.00 2.52
729 730 4.211374 GCGCGGACATACTTCTAAATGATT 59.789 41.667 8.83 0.00 0.00 2.57
730 731 3.741344 GCGCGGACATACTTCTAAATGAT 59.259 43.478 8.83 0.00 0.00 2.45
731 732 3.120792 GCGCGGACATACTTCTAAATGA 58.879 45.455 8.83 0.00 0.00 2.57
732 733 3.060272 CAGCGCGGACATACTTCTAAATG 60.060 47.826 8.83 0.00 0.00 2.32
733 734 3.123804 CAGCGCGGACATACTTCTAAAT 58.876 45.455 8.83 0.00 0.00 1.40
734 735 2.536365 CAGCGCGGACATACTTCTAAA 58.464 47.619 8.83 0.00 0.00 1.85
735 736 1.801395 GCAGCGCGGACATACTTCTAA 60.801 52.381 13.03 0.00 0.00 2.10
736 737 0.248907 GCAGCGCGGACATACTTCTA 60.249 55.000 13.03 0.00 0.00 2.10
737 738 1.519455 GCAGCGCGGACATACTTCT 60.519 57.895 13.03 0.00 0.00 2.85
738 739 1.154205 ATGCAGCGCGGACATACTTC 61.154 55.000 13.03 0.00 0.00 3.01
739 740 0.744414 AATGCAGCGCGGACATACTT 60.744 50.000 13.03 0.00 0.00 2.24
740 741 0.744414 AAATGCAGCGCGGACATACT 60.744 50.000 13.03 3.15 0.00 2.12
741 742 0.934496 TAAATGCAGCGCGGACATAC 59.066 50.000 13.03 0.00 0.00 2.39
742 743 1.202475 TCTAAATGCAGCGCGGACATA 60.202 47.619 13.03 0.01 0.00 2.29
743 744 0.461870 TCTAAATGCAGCGCGGACAT 60.462 50.000 13.03 11.49 0.00 3.06
744 745 0.672091 TTCTAAATGCAGCGCGGACA 60.672 50.000 13.03 9.47 0.00 4.02
745 746 0.026803 CTTCTAAATGCAGCGCGGAC 59.973 55.000 13.03 3.17 0.00 4.79
746 747 0.391130 ACTTCTAAATGCAGCGCGGA 60.391 50.000 13.03 3.45 0.00 5.54
747 748 1.004927 GTACTTCTAAATGCAGCGCGG 60.005 52.381 8.83 2.11 0.00 6.46
748 749 1.658596 TGTACTTCTAAATGCAGCGCG 59.341 47.619 0.00 0.00 0.00 6.86
749 750 2.534939 CGTGTACTTCTAAATGCAGCGC 60.535 50.000 0.00 0.00 0.00 5.92
750 751 2.534939 GCGTGTACTTCTAAATGCAGCG 60.535 50.000 0.00 0.00 0.00 5.18
751 752 2.534939 CGCGTGTACTTCTAAATGCAGC 60.535 50.000 0.00 0.00 0.00 5.25
752 753 2.666508 ACGCGTGTACTTCTAAATGCAG 59.333 45.455 12.93 0.00 0.00 4.41
753 754 2.410392 CACGCGTGTACTTCTAAATGCA 59.590 45.455 30.50 0.00 0.00 3.96
754 755 2.664568 TCACGCGTGTACTTCTAAATGC 59.335 45.455 35.74 0.00 0.00 3.56
755 756 4.619760 TCTTCACGCGTGTACTTCTAAATG 59.380 41.667 35.74 16.67 0.00 2.32
756 757 4.801891 TCTTCACGCGTGTACTTCTAAAT 58.198 39.130 35.74 0.00 0.00 1.40
757 758 4.224433 CTCTTCACGCGTGTACTTCTAAA 58.776 43.478 35.74 20.13 0.00 1.85
758 759 3.251729 ACTCTTCACGCGTGTACTTCTAA 59.748 43.478 35.74 20.82 0.00 2.10
759 760 2.810274 ACTCTTCACGCGTGTACTTCTA 59.190 45.455 35.74 14.71 0.00 2.10
760 761 1.607628 ACTCTTCACGCGTGTACTTCT 59.392 47.619 35.74 14.49 0.00 2.85
761 762 2.047679 ACTCTTCACGCGTGTACTTC 57.952 50.000 35.74 0.00 0.00 3.01
762 763 2.663879 CGTACTCTTCACGCGTGTACTT 60.664 50.000 35.74 20.42 33.47 2.24
763 764 1.136141 CGTACTCTTCACGCGTGTACT 60.136 52.381 35.74 18.24 33.47 2.73
764 765 1.136252 TCGTACTCTTCACGCGTGTAC 60.136 52.381 35.74 27.32 39.23 2.90
765 766 1.136252 GTCGTACTCTTCACGCGTGTA 60.136 52.381 35.74 27.02 39.23 2.90
766 767 0.385223 GTCGTACTCTTCACGCGTGT 60.385 55.000 35.74 20.59 39.23 4.49
767 768 1.386293 CGTCGTACTCTTCACGCGTG 61.386 60.000 32.76 32.76 39.23 5.34
768 769 1.154525 CGTCGTACTCTTCACGCGT 60.155 57.895 5.58 5.58 39.23 6.01
769 770 1.862147 CCGTCGTACTCTTCACGCG 60.862 63.158 3.53 3.53 39.23 6.01
770 771 2.150837 GCCGTCGTACTCTTCACGC 61.151 63.158 0.00 0.00 39.23 5.34
771 772 1.862147 CGCCGTCGTACTCTTCACG 60.862 63.158 0.00 0.00 40.72 4.35
772 773 2.150837 GCGCCGTCGTACTCTTCAC 61.151 63.158 0.00 0.00 38.14 3.18
773 774 2.177531 GCGCCGTCGTACTCTTCA 59.822 61.111 0.00 0.00 38.14 3.02
774 775 1.868251 CAGCGCCGTCGTACTCTTC 60.868 63.158 2.29 0.00 38.14 2.87
775 776 2.178521 CAGCGCCGTCGTACTCTT 59.821 61.111 2.29 0.00 38.14 2.85
776 777 4.477975 GCAGCGCCGTCGTACTCT 62.478 66.667 2.29 0.00 38.14 3.24
777 778 4.771356 TGCAGCGCCGTCGTACTC 62.771 66.667 2.29 0.00 38.14 2.59
778 779 3.642778 AATGCAGCGCCGTCGTACT 62.643 57.895 2.29 0.00 38.14 2.73
779 780 2.736682 AAATGCAGCGCCGTCGTAC 61.737 57.895 2.29 0.00 38.14 3.67
780 781 2.433491 AAATGCAGCGCCGTCGTA 60.433 55.556 2.29 0.00 38.14 3.43
781 782 4.088762 CAAATGCAGCGCCGTCGT 62.089 61.111 2.29 0.00 38.14 4.34
862 863 0.808060 GAAAGAGTAGGCTGCGAGGC 60.808 60.000 0.00 2.19 41.73 4.70
917 919 8.522542 AGAGAATATAAACTGGACGACTTACT 57.477 34.615 0.00 0.00 0.00 2.24
1152 1208 1.376609 CGCCCTTGTAAGTCATGCCC 61.377 60.000 0.00 0.00 0.00 5.36
1409 1465 0.108019 AGGACCAAAAGGACGTGACC 59.892 55.000 0.00 0.00 0.00 4.02
1579 2057 0.600782 TTGGTTCCGCTACACGTTCC 60.601 55.000 0.00 0.00 41.42 3.62
1586 2064 1.467342 GGATGTTGTTGGTTCCGCTAC 59.533 52.381 0.00 0.00 0.00 3.58
1652 2136 4.281182 TCAAGTTCTTTCTCGCCTACTTCT 59.719 41.667 0.00 0.00 0.00 2.85
1661 2145 2.726760 CGGAGTGTCAAGTTCTTTCTCG 59.273 50.000 0.00 0.00 0.00 4.04
1665 2149 3.458189 CTGTCGGAGTGTCAAGTTCTTT 58.542 45.455 0.00 0.00 0.00 2.52
1672 2156 1.299850 CACGCTGTCGGAGTGTCAA 60.300 57.895 7.34 0.00 43.93 3.18
1702 2188 1.301716 GTGTCCACACCATCTGCGT 60.302 57.895 0.00 0.00 40.85 5.24
1794 2281 2.373169 TCCCTCAGGCCATAATGTCATC 59.627 50.000 5.01 0.00 0.00 2.92
1830 2323 0.400213 TCCTTCCATTGCACCGACTT 59.600 50.000 0.00 0.00 0.00 3.01
1881 2374 0.875059 GGTACCAGCTGTCAAAGTGC 59.125 55.000 13.81 6.29 0.00 4.40
1913 2407 1.978617 CCCGGGCTGCAACTTTGAT 60.979 57.895 8.08 0.00 0.00 2.57
1929 2423 1.322442 GCTGCAGATATGTTTCCCCC 58.678 55.000 20.43 0.00 0.00 5.40
2108 2619 1.300156 CGTCGCCACCGATCATGAT 60.300 57.895 8.25 8.25 46.38 2.45
2112 2623 4.470170 CGTCGTCGCCACCGATCA 62.470 66.667 0.00 0.00 46.38 2.92
2122 2633 2.579787 GCTGGTCCATCGTCGTCG 60.580 66.667 0.00 0.00 38.55 5.12
2124 2635 2.415608 ATCGCTGGTCCATCGTCGT 61.416 57.895 14.42 0.61 0.00 4.34
2151 2668 0.306533 GTTGGCTTCTTTCGTTCGCA 59.693 50.000 0.00 0.00 0.00 5.10
2194 2711 1.414550 TCAAGTCCGGACATGTCACAA 59.585 47.619 35.00 15.09 32.42 3.33
2202 2719 2.244695 ACTATGTGTCAAGTCCGGACA 58.755 47.619 35.00 14.85 42.62 4.02
2255 2772 0.673333 CCTGTACTTGCACATCGGCA 60.673 55.000 0.00 0.00 43.19 5.69
2341 2860 0.762418 TCCGTGGGTCATTTGACTGT 59.238 50.000 10.32 0.00 44.20 3.55
2363 2882 2.331194 CTATCGTTTCGTCGGTGGTTT 58.669 47.619 0.00 0.00 0.00 3.27
2373 2892 6.884187 TGAAAGTCTTTTTCCTATCGTTTCG 58.116 36.000 0.00 0.00 0.00 3.46
2489 3020 7.876068 ACAAATTGCATTGTCTCAATTCTCATT 59.124 29.630 0.00 0.00 39.23 2.57
2544 3075 7.013846 CCTCTTAGTCTTAAGGACCTCTACATG 59.986 44.444 1.85 0.00 45.54 3.21
2749 3354 1.276622 ATACAAGGTCCGACCAAGCT 58.723 50.000 19.95 0.00 41.95 3.74
2815 3426 6.553100 TCCAACCACAGGAAACAGAAATATTT 59.447 34.615 0.00 0.00 30.71 1.40
3119 3824 1.135257 ACCTTCTCTGCAAGATCGACG 60.135 52.381 0.00 0.00 45.62 5.12
3152 3857 6.050432 ACAAATGTTGCATCAAGTGAACAAT 58.950 32.000 14.61 0.00 34.16 2.71
3412 4144 8.538701 TGTCCATGCACCAAAGATAAAAATTAT 58.461 29.630 0.00 0.00 0.00 1.28
3588 4329 2.663358 GCATCTCTGCTGTCTGTCG 58.337 57.895 0.00 0.00 45.32 4.35
3608 4349 1.065709 TCACCTTCCGCATAGAAACCC 60.066 52.381 0.00 0.00 0.00 4.11
3681 4422 4.080975 TCCCTCCACGATATTTTTACCGTT 60.081 41.667 0.00 0.00 32.50 4.44
4478 5856 0.543749 CCCTGGATCACCTCTCCAAC 59.456 60.000 0.00 0.00 42.12 3.77
4606 5997 4.142227 ACTCGAAGCTCGCCTAAGATAAAA 60.142 41.667 0.00 0.00 40.21 1.52
4642 6051 9.745018 ATATTCTCAACTTCTCCATTGAAAGAA 57.255 29.630 0.00 0.00 34.52 2.52
4643 6052 9.745018 AATATTCTCAACTTCTCCATTGAAAGA 57.255 29.630 0.00 0.00 34.52 2.52
4719 6128 4.035612 AGCAGACAAGGTCTCTAGTACA 57.964 45.455 0.00 0.00 41.37 2.90
4772 6181 1.353022 TGGAAATTTACCAGGCGGAGT 59.647 47.619 0.00 0.00 35.59 3.85
4859 6268 2.945668 AGTTTGAGTCCTGCTTGTTGAC 59.054 45.455 0.00 0.00 0.00 3.18
4891 6301 3.074675 TCTTAAAATACCCAAGCCGCA 57.925 42.857 0.00 0.00 0.00 5.69
5001 6415 4.094887 GCATTGACTCAAGATAGGCGAAAA 59.905 41.667 0.00 0.00 0.00 2.29
5004 6418 2.483714 GGCATTGACTCAAGATAGGCGA 60.484 50.000 0.00 0.00 0.00 5.54
5006 6420 2.158696 AGGGCATTGACTCAAGATAGGC 60.159 50.000 0.00 0.58 0.00 3.93
5042 6456 7.865706 TTCTTAGTTGAGATTTAGGGAATGC 57.134 36.000 0.00 0.00 0.00 3.56
5052 6466 8.924511 TCTTGGACAAATTCTTAGTTGAGATT 57.075 30.769 0.00 0.00 33.72 2.40
5053 6467 9.525826 AATCTTGGACAAATTCTTAGTTGAGAT 57.474 29.630 0.00 0.00 33.72 2.75
5054 6468 8.924511 AATCTTGGACAAATTCTTAGTTGAGA 57.075 30.769 0.00 0.00 33.72 3.27
5057 6471 9.329913 CGTAAATCTTGGACAAATTCTTAGTTG 57.670 33.333 0.00 0.00 35.55 3.16
5058 6472 8.512138 CCGTAAATCTTGGACAAATTCTTAGTT 58.488 33.333 0.00 0.00 0.00 2.24
5059 6473 7.361799 GCCGTAAATCTTGGACAAATTCTTAGT 60.362 37.037 0.00 0.00 0.00 2.24
5060 6474 6.967199 GCCGTAAATCTTGGACAAATTCTTAG 59.033 38.462 0.00 0.00 0.00 2.18
5061 6475 6.431543 TGCCGTAAATCTTGGACAAATTCTTA 59.568 34.615 0.00 0.00 0.00 2.10
5062 6476 5.242838 TGCCGTAAATCTTGGACAAATTCTT 59.757 36.000 0.00 0.00 0.00 2.52
5063 6477 4.764823 TGCCGTAAATCTTGGACAAATTCT 59.235 37.500 0.00 0.00 0.00 2.40
5064 6478 5.054390 TGCCGTAAATCTTGGACAAATTC 57.946 39.130 0.00 0.00 0.00 2.17
5065 6479 5.659440 ATGCCGTAAATCTTGGACAAATT 57.341 34.783 0.00 0.00 0.00 1.82
5066 6480 5.220777 CGTATGCCGTAAATCTTGGACAAAT 60.221 40.000 0.00 0.00 0.00 2.32
5067 6481 4.093703 CGTATGCCGTAAATCTTGGACAAA 59.906 41.667 0.00 0.00 0.00 2.83
5068 6482 3.619483 CGTATGCCGTAAATCTTGGACAA 59.381 43.478 0.00 0.00 0.00 3.18
5069 6483 3.191669 CGTATGCCGTAAATCTTGGACA 58.808 45.455 0.00 0.00 0.00 4.02
5070 6484 2.033151 GCGTATGCCGTAAATCTTGGAC 60.033 50.000 0.00 0.00 39.32 4.02
5071 6485 2.206750 GCGTATGCCGTAAATCTTGGA 58.793 47.619 0.00 0.00 39.32 3.53
5072 6486 1.937223 TGCGTATGCCGTAAATCTTGG 59.063 47.619 4.05 0.00 41.78 3.61
5073 6487 2.350192 TGTGCGTATGCCGTAAATCTTG 59.650 45.455 4.05 0.00 41.78 3.02
5074 6488 2.350498 GTGTGCGTATGCCGTAAATCTT 59.650 45.455 4.05 0.00 41.78 2.40
5075 6489 1.931172 GTGTGCGTATGCCGTAAATCT 59.069 47.619 4.05 0.00 41.78 2.40
5076 6490 1.931172 AGTGTGCGTATGCCGTAAATC 59.069 47.619 4.05 0.00 41.78 2.17
5077 6491 1.931172 GAGTGTGCGTATGCCGTAAAT 59.069 47.619 4.05 0.00 41.78 1.40
5078 6492 1.352114 GAGTGTGCGTATGCCGTAAA 58.648 50.000 4.05 0.00 41.78 2.01
5079 6493 0.458889 GGAGTGTGCGTATGCCGTAA 60.459 55.000 4.05 0.00 41.78 3.18
5080 6494 1.140161 GGAGTGTGCGTATGCCGTA 59.860 57.895 4.05 0.00 41.78 4.02
5081 6495 2.125673 GGAGTGTGCGTATGCCGT 60.126 61.111 4.05 0.00 41.78 5.68
5082 6496 2.125713 TGGAGTGTGCGTATGCCG 60.126 61.111 4.05 0.00 41.78 5.69
5083 6497 1.079127 ACTGGAGTGTGCGTATGCC 60.079 57.895 4.05 0.00 41.78 4.40
5090 6504 1.265365 GCTTCTTTGACTGGAGTGTGC 59.735 52.381 0.00 0.00 0.00 4.57
5098 6512 1.071239 CACACGACGCTTCTTTGACTG 60.071 52.381 0.00 0.00 0.00 3.51
5114 6528 4.065088 TCAATCTGACTGCTTAACCACAC 58.935 43.478 0.00 0.00 0.00 3.82
5133 6547 3.994392 GTCAGATTTAGCACCGACTTCAA 59.006 43.478 0.00 0.00 0.00 2.69
5138 6552 3.585862 TGAAGTCAGATTTAGCACCGAC 58.414 45.455 0.00 0.00 0.00 4.79
5167 6581 3.489355 TCCTGTGATGAACAAGTTGCAT 58.511 40.909 1.81 0.00 38.67 3.96
5168 6582 2.929641 TCCTGTGATGAACAAGTTGCA 58.070 42.857 1.81 0.00 38.67 4.08
5201 6617 2.348472 TCCTAATAGGGGCATCCAAGG 58.652 52.381 6.46 0.00 35.59 3.61
5203 6619 3.608067 TGATCCTAATAGGGGCATCCAA 58.392 45.455 6.46 0.00 35.59 3.53
5208 6624 4.665009 ACAAGATTGATCCTAATAGGGGCA 59.335 41.667 6.46 2.37 35.59 5.36
5241 6657 4.379918 GCAATTCTCAGGTTAAGGACTTGC 60.380 45.833 0.00 0.00 37.26 4.01
5285 6722 5.352293 TCATTGATGATTTGGTCTGTTCTCG 59.648 40.000 0.00 0.00 0.00 4.04
5286 6723 6.748333 TCATTGATGATTTGGTCTGTTCTC 57.252 37.500 0.00 0.00 0.00 2.87
5447 6888 9.513906 TCCTCCATATATGATTAAATCGCAAAA 57.486 29.630 14.54 0.00 0.00 2.44
5448 6889 9.685276 ATCCTCCATATATGATTAAATCGCAAA 57.315 29.630 14.54 0.00 0.00 3.68
5466 6907 9.964408 TGGATCTTATTCTCATATATCCTCCAT 57.036 33.333 0.00 0.00 33.06 3.41
5467 6908 9.964408 ATGGATCTTATTCTCATATATCCTCCA 57.036 33.333 0.00 0.00 33.06 3.86
5507 6948 3.244422 TGTTACTTACAGGGCCTTGTCAG 60.244 47.826 25.65 24.45 32.56 3.51
5530 6972 8.690884 GGCTATATCTCTATGCTGATTAGACAA 58.309 37.037 0.00 0.00 0.00 3.18
5557 6999 9.664777 TTTATGGGTGTACAACTAGACCTATAT 57.335 33.333 11.44 0.72 38.67 0.86
5558 7000 9.664777 ATTTATGGGTGTACAACTAGACCTATA 57.335 33.333 11.44 5.47 38.20 1.31
5559 7001 7.983166 TTTATGGGTGTACAACTAGACCTAT 57.017 36.000 11.44 6.46 39.82 2.57
5560 7002 7.620491 TGATTTATGGGTGTACAACTAGACCTA 59.380 37.037 11.44 0.00 36.66 3.08
5561 7003 6.442564 TGATTTATGGGTGTACAACTAGACCT 59.557 38.462 11.44 0.00 36.66 3.85
5562 7004 6.646267 TGATTTATGGGTGTACAACTAGACC 58.354 40.000 11.44 0.00 35.84 3.85
5563 7005 8.204836 AGATGATTTATGGGTGTACAACTAGAC 58.795 37.037 11.44 0.00 0.00 2.59
5564 7006 8.319057 AGATGATTTATGGGTGTACAACTAGA 57.681 34.615 11.44 0.00 0.00 2.43
5601 7062 2.884012 ACATGGACGACAAATTTGAGCA 59.116 40.909 24.64 11.68 0.00 4.26
5670 7135 9.847224 TTGACTTTTCCTTCTCACTTTAGTAAT 57.153 29.630 0.00 0.00 0.00 1.89
5671 7136 9.847224 ATTGACTTTTCCTTCTCACTTTAGTAA 57.153 29.630 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.