Multiple sequence alignment - TraesCS6A01G058100

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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 TraesCS6A01G058100 chr6A 100.000 3000 0 0 773 3772 30715766 30718765 0.000000e+00 5541.0
1 TraesCS6A01G058100 chr6A 84.319 778 73 18 2133 2877 30653265 30654026 0.000000e+00 715.0
2 TraesCS6A01G058100 chr6A 100.000 336 0 0 1 336 30714994 30715329 4.140000e-174 621.0
3 TraesCS6A01G058100 chr6A 87.879 363 43 1 1043 1405 30612435 30612796 3.480000e-115 425.0
4 TraesCS6A01G058100 chr6A 86.777 363 48 0 1765 2127 30652542 30652904 4.540000e-109 405.0
5 TraesCS6A01G058100 chr6A 76.438 539 93 24 998 1522 40543305 40542787 1.040000e-65 261.0
6 TraesCS6A01G058100 chr6A 80.168 358 53 11 1401 1749 30628173 30628521 6.250000e-63 252.0
7 TraesCS6A01G058100 chr6D 93.626 1365 46 24 2133 3475 27505302 27503957 0.000000e+00 2001.0
8 TraesCS6A01G058100 chr6D 92.412 1252 65 15 904 2127 27507151 27505902 0.000000e+00 1759.0
9 TraesCS6A01G058100 chr6D 87.746 710 76 6 904 1612 27513177 27512478 0.000000e+00 819.0
10 TraesCS6A01G058100 chr6D 84.987 766 68 25 2133 2877 27512048 27511309 0.000000e+00 734.0
11 TraesCS6A01G058100 chr6D 77.884 945 154 36 997 1906 27546781 27545857 1.540000e-148 536.0
12 TraesCS6A01G058100 chr6D 91.916 334 27 0 1 334 27508237 27507904 5.700000e-128 468.0
13 TraesCS6A01G058100 chr6D 72.645 1104 251 38 1044 2121 27329061 27327983 6.080000e-83 318.0
14 TraesCS6A01G058100 chr6D 90.717 237 20 2 17 252 27507560 27507325 7.870000e-82 315.0
15 TraesCS6A01G058100 chr6D 95.699 93 3 1 3625 3717 27503979 27503888 8.440000e-32 148.0
16 TraesCS6A01G058100 chr6D 87.387 111 7 5 121 224 6997524 6997414 1.840000e-23 121.0
17 TraesCS6A01G058100 chr6D 78.095 105 23 0 1785 1889 454012772 454012668 2.430000e-07 67.6
18 TraesCS6A01G058100 chr6B 91.431 1307 65 29 2199 3475 51096737 51095448 0.000000e+00 1749.0
19 TraesCS6A01G058100 chr6B 93.043 1193 72 4 944 2127 51098634 51097444 0.000000e+00 1733.0
20 TraesCS6A01G058100 chr6B 86.591 1238 133 20 904 2127 51140383 51139165 0.000000e+00 1336.0
21 TraesCS6A01G058100 chr6B 84.805 770 63 30 2133 2877 51138803 51138063 0.000000e+00 725.0
22 TraesCS6A01G058100 chr6B 92.216 334 26 0 1 334 51136270 51135937 1.230000e-129 473.0
23 TraesCS6A01G058100 chr6B 76.993 552 98 19 986 1522 82004599 82005136 4.770000e-74 289.0
24 TraesCS6A01G058100 chr6B 97.297 148 3 1 3625 3772 51095470 51095324 2.250000e-62 250.0
25 TraesCS6A01G058100 chr6B 75.375 467 83 19 1027 1488 76153345 76152906 2.970000e-46 196.0
26 TraesCS6A01G058100 chr6B 92.857 84 6 0 2133 2216 51096844 51096761 5.120000e-24 122.0
27 TraesCS6A01G058100 chrUn 79.167 456 80 9 1044 1491 76751769 76751321 6.120000e-78 302.0
28 TraesCS6A01G058100 chrUn 77.399 469 89 13 986 1449 27073079 27073535 2.890000e-66 263.0
29 TraesCS6A01G058100 chrUn 81.667 240 38 5 988 1225 477421754 477421989 1.070000e-45 195.0
30 TraesCS6A01G058100 chr4D 95.570 158 3 1 3472 3629 447293660 447293813 2.250000e-62 250.0
31 TraesCS6A01G058100 chr4D 93.252 163 5 3 3471 3632 351463798 351463641 6.300000e-58 235.0
32 TraesCS6A01G058100 chr5D 95.000 160 2 3 3470 3629 380078927 380078774 2.910000e-61 246.0
33 TraesCS6A01G058100 chr5D 93.711 159 5 2 3470 3628 76972472 76972625 2.270000e-57 233.0
34 TraesCS6A01G058100 chr3D 94.904 157 3 2 3472 3628 488863428 488863579 1.350000e-59 241.0
35 TraesCS6A01G058100 chr3D 94.231 156 4 2 3473 3628 529127311 529127161 2.270000e-57 233.0
36 TraesCS6A01G058100 chr2D 93.671 158 7 3 3472 3628 296710112 296709957 2.270000e-57 233.0
37 TraesCS6A01G058100 chr1D 93.671 158 5 2 3472 3629 463344454 463344302 8.150000e-57 231.0
38 TraesCS6A01G058100 chr1D 85.217 115 12 4 113 224 145009827 145009939 3.080000e-21 113.0
39 TraesCS6A01G058100 chr1A 93.125 160 5 3 3469 3628 378253251 378253098 2.930000e-56 230.0
40 TraesCS6A01G058100 chr1B 87.719 114 10 3 113 224 322963741 322963852 3.060000e-26 130.0
41 TraesCS6A01G058100 chr2B 82.550 149 14 9 113 252 573051997 573051852 1.840000e-23 121.0
42 TraesCS6A01G058100 chr3A 84.874 119 11 5 113 224 735101026 735100908 3.080000e-21 113.0
43 TraesCS6A01G058100 chr3A 83.333 108 10 6 125 224 735069286 735069179 4.010000e-15 93.5


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 TraesCS6A01G058100 chr6A 30714994 30718765 3771 False 3081.000000 5541 100.000000 1 3772 2 chr6A.!!$F4 3771
1 TraesCS6A01G058100 chr6A 30652542 30654026 1484 False 560.000000 715 85.548000 1765 2877 2 chr6A.!!$F3 1112
2 TraesCS6A01G058100 chr6A 40542787 40543305 518 True 261.000000 261 76.438000 998 1522 1 chr6A.!!$R1 524
3 TraesCS6A01G058100 chr6D 27503888 27513177 9289 True 892.000000 2001 91.014714 1 3717 7 chr6D.!!$R5 3716
4 TraesCS6A01G058100 chr6D 27545857 27546781 924 True 536.000000 536 77.884000 997 1906 1 chr6D.!!$R3 909
5 TraesCS6A01G058100 chr6D 27327983 27329061 1078 True 318.000000 318 72.645000 1044 2121 1 chr6D.!!$R2 1077
6 TraesCS6A01G058100 chr6B 51095324 51098634 3310 True 963.500000 1749 93.657000 944 3772 4 chr6B.!!$R2 2828
7 TraesCS6A01G058100 chr6B 51135937 51140383 4446 True 844.666667 1336 87.870667 1 2877 3 chr6B.!!$R3 2876
8 TraesCS6A01G058100 chr6B 82004599 82005136 537 False 289.000000 289 76.993000 986 1522 1 chr6B.!!$F1 536

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
953 6483 0.105964 TTTGGGCCAACCTGCAGTTA 60.106 50.0 20.79 0.0 41.11 2.24 F
963 6493 0.976641 CCTGCAGTTAGAGTCCACCA 59.023 55.0 13.81 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2641 8921 0.254747 TACGGGAAGGCATCAAAGGG 59.745 55.000 0.00 0.0 0.00 3.95 R
2920 9269 1.211457 AGCTGAGCTAAGGTTCATGGG 59.789 52.381 4.49 0.0 36.99 4.00 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
26 4967 5.122396 GTCATGTGTGGTTCAATAAGAGGTC 59.878 44.000 0.00 0.00 0.00 3.85
27 4968 4.698201 TGTGTGGTTCAATAAGAGGTCA 57.302 40.909 0.00 0.00 0.00 4.02
42 4983 1.376609 GGTCAGGTAATGGCAAGGCG 61.377 60.000 0.00 0.00 34.12 5.52
50 4991 0.825010 AATGGCAAGGCGGATGGATC 60.825 55.000 0.00 0.00 0.00 3.36
51 4992 1.998444 ATGGCAAGGCGGATGGATCA 61.998 55.000 0.00 0.00 0.00 2.92
69 5010 1.136305 TCAGGGTAGCATAGTTCGCAC 59.864 52.381 0.00 0.00 0.00 5.34
84 5025 2.047274 CACCGGTGGCCACTACAG 60.047 66.667 33.91 21.52 0.00 2.74
110 5051 1.523758 AGGTCGGCAAGAACACAATC 58.476 50.000 0.00 0.00 39.61 2.67
117 5058 2.991190 GGCAAGAACACAATCTGCAATG 59.009 45.455 0.00 0.00 0.00 2.82
190 5131 5.797457 TGATGGAGATATATTGATTGGGGGT 59.203 40.000 0.00 0.00 0.00 4.95
224 5165 0.477597 TGGGTGGAAGGTGGAGGAAT 60.478 55.000 0.00 0.00 0.00 3.01
226 5167 0.681243 GGTGGAAGGTGGAGGAATGC 60.681 60.000 0.00 0.00 0.00 3.56
236 5177 3.084039 GTGGAGGAATGCATGAAAGACA 58.916 45.455 0.00 0.00 0.00 3.41
240 5181 4.161333 GAGGAATGCATGAAAGACAAACG 58.839 43.478 0.00 0.00 0.00 3.60
259 5200 1.343069 GGGCGGAATAGATGAGGAGT 58.657 55.000 0.00 0.00 0.00 3.85
265 5206 4.728534 CGGAATAGATGAGGAGTCGATTC 58.271 47.826 0.00 0.00 37.14 2.52
266 5207 4.457603 CGGAATAGATGAGGAGTCGATTCT 59.542 45.833 7.92 0.00 37.64 2.40
285 5226 6.347402 CGATTCTTTGTTGTTTCGTGAGGTAT 60.347 38.462 0.00 0.00 0.00 2.73
289 5230 2.081462 GTTGTTTCGTGAGGTATGGGG 58.919 52.381 0.00 0.00 0.00 4.96
297 5238 3.458118 TCGTGAGGTATGGGGAAATTGAT 59.542 43.478 0.00 0.00 0.00 2.57
316 5257 1.987213 TGGATTTCCACCGCAGCTA 59.013 52.632 0.00 0.00 42.01 3.32
334 5275 4.651045 CAGCTATAGGCAAGGGGAATTTTT 59.349 41.667 1.04 0.00 44.79 1.94
793 5734 0.470080 TAGAGAGAGGGGGCCGATTG 60.470 60.000 0.00 0.00 0.00 2.67
794 5735 1.762460 GAGAGAGGGGGCCGATTGA 60.762 63.158 0.00 0.00 0.00 2.57
798 5739 1.227383 GAGGGGGCCGATTGATTGT 59.773 57.895 0.00 0.00 0.00 2.71
802 5743 1.603236 GGGGCCGATTGATTGTTGCA 61.603 55.000 0.00 0.00 0.00 4.08
804 5745 1.680735 GGGCCGATTGATTGTTGCATA 59.319 47.619 0.00 0.00 0.00 3.14
805 5746 2.100584 GGGCCGATTGATTGTTGCATAA 59.899 45.455 0.00 0.00 0.00 1.90
813 5754 7.410728 CCGATTGATTGTTGCATAAAAACTGAC 60.411 37.037 0.00 0.00 0.00 3.51
822 5763 4.091424 GCATAAAAACTGACGCTGACATC 58.909 43.478 0.00 0.00 0.00 3.06
824 5765 3.885484 AAAAACTGACGCTGACATCAG 57.115 42.857 4.43 4.43 46.49 2.90
825 5766 1.800805 AAACTGACGCTGACATCAGG 58.199 50.000 10.81 3.86 45.55 3.86
831 5772 3.403624 GCTGACATCAGGGGTGGA 58.596 61.111 10.81 0.00 43.94 4.02
832 5773 1.078143 GCTGACATCAGGGGTGGAC 60.078 63.158 10.81 0.00 43.94 4.02
833 5774 1.604378 CTGACATCAGGGGTGGACC 59.396 63.158 0.58 0.00 40.20 4.46
834 5775 0.911525 CTGACATCAGGGGTGGACCT 60.912 60.000 0.58 0.00 43.08 3.85
835 5776 0.415830 TGACATCAGGGGTGGACCTA 59.584 55.000 0.00 0.00 39.34 3.08
836 5777 1.123928 GACATCAGGGGTGGACCTAG 58.876 60.000 0.00 0.00 39.34 3.02
840 5781 0.722676 TCAGGGGTGGACCTAGGATT 59.277 55.000 17.98 0.00 39.34 3.01
841 5782 0.839946 CAGGGGTGGACCTAGGATTG 59.160 60.000 17.98 0.00 39.34 2.67
844 5785 1.532238 GGTGGACCTAGGATTGGGC 59.468 63.158 17.98 0.06 0.00 5.36
845 5786 0.988678 GGTGGACCTAGGATTGGGCT 60.989 60.000 17.98 0.00 31.96 5.19
848 5789 2.711547 GTGGACCTAGGATTGGGCTAAT 59.288 50.000 17.98 0.00 31.96 1.73
849 5790 2.979678 TGGACCTAGGATTGGGCTAATC 59.020 50.000 17.98 14.56 43.64 1.75
859 5800 2.778717 GGCTAATCCCCAGGCCCT 60.779 66.667 0.00 0.00 38.77 5.19
860 5801 1.463410 GGCTAATCCCCAGGCCCTA 60.463 63.158 0.00 0.00 38.77 3.53
861 5802 1.492993 GGCTAATCCCCAGGCCCTAG 61.493 65.000 0.00 0.00 38.77 3.02
873 5814 3.757836 GCCCTAGGCTAGCTAGAGT 57.242 57.895 25.15 12.30 46.69 3.24
875 5816 1.253100 CCCTAGGCTAGCTAGAGTGC 58.747 60.000 25.15 9.57 0.00 4.40
876 5817 1.253100 CCTAGGCTAGCTAGAGTGCC 58.747 60.000 25.15 18.41 45.21 5.01
877 5818 1.253100 CTAGGCTAGCTAGAGTGCCC 58.747 60.000 25.15 14.85 45.94 5.36
878 5819 0.178958 TAGGCTAGCTAGAGTGCCCC 60.179 60.000 25.15 14.13 45.94 5.80
879 5820 1.458588 GGCTAGCTAGAGTGCCCCT 60.459 63.158 25.15 0.00 39.49 4.79
880 5821 0.178958 GGCTAGCTAGAGTGCCCCTA 60.179 60.000 25.15 0.00 39.49 3.53
881 5822 0.963225 GCTAGCTAGAGTGCCCCTAC 59.037 60.000 25.15 0.00 0.00 3.18
882 5823 1.754555 GCTAGCTAGAGTGCCCCTACA 60.755 57.143 25.15 0.00 0.00 2.74
884 5825 1.045911 AGCTAGAGTGCCCCTACAGC 61.046 60.000 0.00 0.00 32.64 4.40
886 5827 1.195115 CTAGAGTGCCCCTACAGCAA 58.805 55.000 0.00 0.00 43.02 3.91
888 5829 0.545309 AGAGTGCCCCTACAGCAAGA 60.545 55.000 0.00 0.00 43.02 3.02
890 5831 0.254178 AGTGCCCCTACAGCAAGATG 59.746 55.000 0.00 0.00 43.02 2.90
892 5833 1.825622 GCCCCTACAGCAAGATGCC 60.826 63.158 0.00 0.00 46.52 4.40
893 5834 1.152881 CCCCTACAGCAAGATGCCC 60.153 63.158 0.00 0.00 46.52 5.36
894 5835 1.609239 CCCTACAGCAAGATGCCCA 59.391 57.895 0.00 0.00 46.52 5.36
895 5836 0.465097 CCCTACAGCAAGATGCCCAG 60.465 60.000 0.00 0.00 46.52 4.45
896 5837 0.465097 CCTACAGCAAGATGCCCAGG 60.465 60.000 0.00 0.00 46.52 4.45
897 5838 0.465097 CTACAGCAAGATGCCCAGGG 60.465 60.000 0.00 0.00 46.52 4.45
928 6458 2.903135 CCTCACTTTTCTCCTCTCCAGT 59.097 50.000 0.00 0.00 0.00 4.00
930 6460 2.037772 TCACTTTTCTCCTCTCCAGTGC 59.962 50.000 0.00 0.00 33.17 4.40
931 6461 1.349357 ACTTTTCTCCTCTCCAGTGCC 59.651 52.381 0.00 0.00 0.00 5.01
953 6483 0.105964 TTTGGGCCAACCTGCAGTTA 60.106 50.000 20.79 0.00 41.11 2.24
963 6493 0.976641 CCTGCAGTTAGAGTCCACCA 59.023 55.000 13.81 0.00 0.00 4.17
1078 6641 3.384014 GACGACCTGCTCGACGAGG 62.384 68.421 25.31 13.10 46.14 4.63
1284 6847 4.209866 ATGGAGGCCCCCAATCGC 62.210 66.667 11.33 0.00 40.04 4.58
1316 6879 2.748843 GCTTCTCCTTGCAGCTCGC 61.749 63.158 0.00 1.70 42.89 5.03
1623 7213 1.542915 CTTCCAAATGAGGTGCCAGTG 59.457 52.381 0.00 0.00 0.00 3.66
1687 7280 4.563993 CCCTTCACTGTTTGATTACGGGTA 60.564 45.833 0.00 0.00 32.84 3.69
1696 7289 3.520290 TGATTACGGGTAGCTGTTCTG 57.480 47.619 12.40 0.00 0.00 3.02
1721 7320 9.258629 TGGAATCCTTGAGTTTGATTTGAATAT 57.741 29.630 0.00 0.00 0.00 1.28
1723 7322 9.525409 GAATCCTTGAGTTTGATTTGAATATGG 57.475 33.333 0.00 0.00 0.00 2.74
1761 7360 2.034124 CCAGGGCCTGTGGATATTTTG 58.966 52.381 30.68 8.67 37.23 2.44
1766 7365 2.036346 GGCCTGTGGATATTTTGGATGC 59.964 50.000 0.00 0.00 0.00 3.91
1890 7489 4.115199 GGCGAGGCCTCATGGGTT 62.115 66.667 31.67 0.00 46.69 4.11
1896 7495 2.276740 GCCTCATGGGTTCTGGGG 59.723 66.667 0.00 0.00 37.31 4.96
1920 7519 2.408050 ACTTTTGAGCTAGACACGCTG 58.592 47.619 0.00 0.00 37.96 5.18
1941 7540 3.013219 GCTTTCCCTGAATTCAGAGGAC 58.987 50.000 32.49 20.47 46.59 3.85
2028 7627 3.165606 CCACTTCATGGTCCAGCTC 57.834 57.895 0.00 0.00 44.46 4.09
2063 7662 4.286297 TCAAGAAGATGTCCGAAACCAT 57.714 40.909 0.00 0.00 0.00 3.55
2088 7687 4.704540 AGTTCGCATTTCCATCAACCATTA 59.295 37.500 0.00 0.00 0.00 1.90
2123 7722 3.074538 ACTGGAGGTAACAGAATGCCTTT 59.925 43.478 0.00 0.00 42.53 3.11
2127 7726 5.007682 GGAGGTAACAGAATGCCTTTACAA 58.992 41.667 0.00 0.00 42.53 2.41
2128 7727 5.652452 GGAGGTAACAGAATGCCTTTACAAT 59.348 40.000 0.00 0.00 42.53 2.71
2130 7729 5.102313 GGTAACAGAATGCCTTTACAATGC 58.898 41.667 0.00 0.00 42.53 3.56
2140 8333 3.499918 GCCTTTACAATGCGCATATCTCT 59.500 43.478 25.61 4.11 0.00 3.10
2170 8366 9.573133 ACACTTTTGACTCAAAATTAGAACTTG 57.427 29.630 15.72 5.44 41.53 3.16
2287 8524 5.679734 AGCGAATTATGCTTCTACCATTG 57.320 39.130 0.00 0.00 40.48 2.82
2310 8547 8.894409 TTGAACATTTTTATCTGTGCTAATCG 57.106 30.769 0.00 0.00 0.00 3.34
2345 8582 7.936847 ACCTGTAAATCTGTAACAATGACTTGA 59.063 33.333 0.00 0.00 36.20 3.02
2467 8727 4.883083 TCACTTAATTATAGGAGCTGCGG 58.117 43.478 0.00 0.00 0.00 5.69
2644 8924 9.927081 ACATTTGAGTTCATCTAAATATTCCCT 57.073 29.630 0.00 0.00 0.00 4.20
2670 8950 1.674441 GCCTTCCCGTATTTAGTTGGC 59.326 52.381 0.00 0.00 0.00 4.52
2741 9021 0.323725 GCATTGGTGGTGGAGGACAT 60.324 55.000 0.00 0.00 0.00 3.06
2766 9046 2.463876 GAGCTGAACTTTTGCACAACC 58.536 47.619 0.00 0.00 0.00 3.77
2789 9069 5.338708 CCCTTAAGATGACTGTCTGGTTCAT 60.339 44.000 9.51 0.00 0.00 2.57
2835 9115 4.177783 GAGTAGGTAAGCTTGTCTTCTGC 58.822 47.826 9.86 3.18 36.25 4.26
2849 9129 4.202357 TGTCTTCTGCATGTAAGTTGAGGT 60.202 41.667 0.00 0.00 0.00 3.85
2850 9130 5.011635 TGTCTTCTGCATGTAAGTTGAGGTA 59.988 40.000 0.00 0.00 0.00 3.08
2920 9269 2.303175 AGCGAGGACTCAAGATACTCC 58.697 52.381 0.00 0.00 0.00 3.85
2942 9291 2.200067 CATGAACCTTAGCTCAGCTCG 58.800 52.381 0.00 0.00 40.44 5.03
2944 9293 1.142778 GAACCTTAGCTCAGCTCGCG 61.143 60.000 0.00 0.00 40.44 5.87
2979 9328 1.354031 TCCCACTGCTCTTTATTGGCA 59.646 47.619 0.00 0.00 34.66 4.92
3004 9353 0.105778 GATCTTTCCTCCAGGCCTCG 59.894 60.000 0.00 0.00 34.44 4.63
3016 9365 2.735772 GGCCTCGCTTCCTCATCCA 61.736 63.158 0.00 0.00 0.00 3.41
3033 9382 0.677731 CCATTCCTCAGCCGCTTTCA 60.678 55.000 0.00 0.00 0.00 2.69
3140 9489 8.584157 TGCCAAAAATGTGAGATTGTATAACTT 58.416 29.630 0.00 0.00 0.00 2.66
3259 9609 3.055819 GGACTTGGATTCTGTGCTGTAGA 60.056 47.826 0.00 0.00 0.00 2.59
3260 9610 3.929610 GACTTGGATTCTGTGCTGTAGAC 59.070 47.826 0.00 0.00 0.00 2.59
3266 9616 4.158764 GGATTCTGTGCTGTAGACTGTAGT 59.841 45.833 0.00 0.00 0.00 2.73
3267 9617 5.357314 GGATTCTGTGCTGTAGACTGTAGTA 59.643 44.000 0.00 0.00 0.00 1.82
3268 9618 6.039941 GGATTCTGTGCTGTAGACTGTAGTAT 59.960 42.308 0.00 0.00 0.00 2.12
3269 9619 5.819825 TCTGTGCTGTAGACTGTAGTATG 57.180 43.478 0.00 0.00 0.00 2.39
3270 9620 5.254115 TCTGTGCTGTAGACTGTAGTATGT 58.746 41.667 0.00 0.00 0.00 2.29
3271 9621 6.412214 TCTGTGCTGTAGACTGTAGTATGTA 58.588 40.000 0.00 0.00 0.00 2.29
3272 9622 6.539103 TCTGTGCTGTAGACTGTAGTATGTAG 59.461 42.308 0.00 0.00 0.00 2.74
3273 9623 6.412214 TGTGCTGTAGACTGTAGTATGTAGA 58.588 40.000 0.00 0.00 0.00 2.59
3398 9749 5.596836 TTTGTTTTGAAGCTGAGGATGTT 57.403 34.783 0.00 0.00 0.00 2.71
3400 9751 4.935702 TGTTTTGAAGCTGAGGATGTTTG 58.064 39.130 0.00 0.00 0.00 2.93
3468 9821 0.390866 CTGCCTACTCCTGTGTGCTG 60.391 60.000 0.00 0.00 0.00 4.41
3469 9822 1.121407 TGCCTACTCCTGTGTGCTGT 61.121 55.000 0.00 0.00 0.00 4.40
3470 9823 0.035458 GCCTACTCCTGTGTGCTGTT 59.965 55.000 0.00 0.00 0.00 3.16
3471 9824 1.275291 GCCTACTCCTGTGTGCTGTTA 59.725 52.381 0.00 0.00 0.00 2.41
3472 9825 2.289444 GCCTACTCCTGTGTGCTGTTAA 60.289 50.000 0.00 0.00 0.00 2.01
3473 9826 3.805807 GCCTACTCCTGTGTGCTGTTAAA 60.806 47.826 0.00 0.00 0.00 1.52
3474 9827 4.385825 CCTACTCCTGTGTGCTGTTAAAA 58.614 43.478 0.00 0.00 0.00 1.52
3475 9828 4.819630 CCTACTCCTGTGTGCTGTTAAAAA 59.180 41.667 0.00 0.00 0.00 1.94
3495 9848 2.309136 AAATGAGACCAACCCAAGGG 57.691 50.000 2.91 2.91 42.03 3.95
3496 9849 0.251787 AATGAGACCAACCCAAGGGC 60.252 55.000 4.70 0.00 39.32 5.19
3498 9851 4.681624 AGACCAACCCAAGGGCTA 57.318 55.556 4.70 0.00 44.68 3.93
3499 9852 2.877150 AGACCAACCCAAGGGCTAA 58.123 52.632 4.70 0.00 44.68 3.09
3500 9853 0.404426 AGACCAACCCAAGGGCTAAC 59.596 55.000 4.70 0.00 44.68 2.34
3501 9854 0.611062 GACCAACCCAAGGGCTAACC 60.611 60.000 4.70 0.00 39.32 2.85
3540 9893 3.606886 GGAGAAAACTCCGTGAGCA 57.393 52.632 0.00 0.00 33.39 4.26
3541 9894 1.149148 GGAGAAAACTCCGTGAGCAC 58.851 55.000 0.00 0.00 33.39 4.40
3542 9895 1.149148 GAGAAAACTCCGTGAGCACC 58.851 55.000 1.36 0.00 32.04 5.01
3543 9896 0.600255 AGAAAACTCCGTGAGCACCG 60.600 55.000 1.36 0.00 32.04 4.94
3544 9897 2.171489 GAAAACTCCGTGAGCACCGC 62.171 60.000 1.36 0.00 32.04 5.68
3571 9924 4.069869 TCGGGACTCGAACGAACT 57.930 55.556 0.00 0.00 45.86 3.01
3572 9925 1.871772 TCGGGACTCGAACGAACTC 59.128 57.895 0.00 0.00 45.86 3.01
3573 9926 1.511464 CGGGACTCGAACGAACTCG 60.511 63.158 0.00 0.00 42.96 4.18
3574 9927 1.154073 GGGACTCGAACGAACTCGG 60.154 63.158 3.88 0.00 44.95 4.63
3575 9928 1.154073 GGACTCGAACGAACTCGGG 60.154 63.158 3.88 4.98 45.12 5.14
3577 9930 4.148230 CTCGAACGAACTCGGGTG 57.852 61.111 3.88 0.00 44.95 4.61
3578 9931 1.443872 CTCGAACGAACTCGGGTGG 60.444 63.158 3.88 0.00 44.95 4.61
3579 9932 2.431942 CGAACGAACTCGGGTGGG 60.432 66.667 3.88 0.00 44.95 4.61
3580 9933 2.741211 GAACGAACTCGGGTGGGC 60.741 66.667 3.88 0.00 44.95 5.36
3581 9934 3.236003 GAACGAACTCGGGTGGGCT 62.236 63.158 3.88 0.00 44.95 5.19
3582 9935 3.530910 AACGAACTCGGGTGGGCTG 62.531 63.158 3.88 0.00 44.95 4.85
3583 9936 4.760047 CGAACTCGGGTGGGCTGG 62.760 72.222 0.00 0.00 35.37 4.85
3592 9945 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
3593 9946 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
3594 9947 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
3595 9948 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
3596 9949 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
3597 9950 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
3602 9955 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
3603 9956 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
3634 9987 3.775654 GCCCCGTCCTCACTCCTG 61.776 72.222 0.00 0.00 0.00 3.86
3635 9988 2.283966 CCCCGTCCTCACTCCTGT 60.284 66.667 0.00 0.00 0.00 4.00
3636 9989 2.650116 CCCCGTCCTCACTCCTGTG 61.650 68.421 0.00 0.00 45.07 3.66
3637 9990 1.908793 CCCGTCCTCACTCCTGTGT 60.909 63.158 0.00 0.00 44.14 3.72
3638 9991 1.290324 CCGTCCTCACTCCTGTGTG 59.710 63.158 0.00 0.00 44.14 3.82
3639 9992 1.373497 CGTCCTCACTCCTGTGTGC 60.373 63.158 0.00 0.00 44.14 4.57
3640 9993 1.810606 CGTCCTCACTCCTGTGTGCT 61.811 60.000 0.00 0.00 44.14 4.40
3697 10050 4.759205 GCGGAAATGGGGCCTGGT 62.759 66.667 0.84 0.00 0.00 4.00
3704 10057 3.625632 ATGGGGCCTGGTCGAGAGT 62.626 63.158 0.84 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.003160 CCTCTTATTGAACCACACATGACA 58.997 41.667 0.00 0.00 0.00 3.58
8 4949 3.650942 ACCTGACCTCTTATTGAACCACA 59.349 43.478 0.00 0.00 0.00 4.17
26 4967 0.466189 ATCCGCCTTGCCATTACCTG 60.466 55.000 0.00 0.00 0.00 4.00
27 4968 0.466189 CATCCGCCTTGCCATTACCT 60.466 55.000 0.00 0.00 0.00 3.08
42 4983 3.177228 ACTATGCTACCCTGATCCATCC 58.823 50.000 0.00 0.00 0.00 3.51
50 4991 1.571919 GTGCGAACTATGCTACCCTG 58.428 55.000 0.00 0.00 0.00 4.45
51 4992 0.464452 GGTGCGAACTATGCTACCCT 59.536 55.000 0.00 0.00 31.54 4.34
69 5010 3.000819 TCCTGTAGTGGCCACCGG 61.001 66.667 32.29 24.89 0.00 5.28
79 5020 1.310904 GCCGACCTAGAGTCCTGTAG 58.689 60.000 0.00 0.00 43.08 2.74
84 5025 1.135053 GTTCTTGCCGACCTAGAGTCC 60.135 57.143 0.00 0.00 43.08 3.85
110 5051 1.746470 TGCATCTCTCCACATTGCAG 58.254 50.000 0.00 0.00 38.32 4.41
117 5058 5.247110 TCCCTCTATTTATGCATCTCTCCAC 59.753 44.000 0.19 0.00 0.00 4.02
190 5131 2.024464 CCACCCATGGTTCCCTTTATCA 60.024 50.000 11.73 0.00 41.64 2.15
224 5165 0.313672 GCCCGTTTGTCTTTCATGCA 59.686 50.000 0.00 0.00 0.00 3.96
226 5167 0.109781 CCGCCCGTTTGTCTTTCATG 60.110 55.000 0.00 0.00 0.00 3.07
236 5177 1.202651 CCTCATCTATTCCGCCCGTTT 60.203 52.381 0.00 0.00 0.00 3.60
240 5181 1.273886 GACTCCTCATCTATTCCGCCC 59.726 57.143 0.00 0.00 0.00 6.13
259 5200 4.025229 CCTCACGAAACAACAAAGAATCGA 60.025 41.667 0.00 0.00 34.62 3.59
265 5206 4.320202 CCCATACCTCACGAAACAACAAAG 60.320 45.833 0.00 0.00 0.00 2.77
266 5207 3.566322 CCCATACCTCACGAAACAACAAA 59.434 43.478 0.00 0.00 0.00 2.83
308 5249 1.302033 CCCTTGCCTATAGCTGCGG 60.302 63.158 0.00 0.00 44.23 5.69
310 5251 0.474184 TTCCCCTTGCCTATAGCTGC 59.526 55.000 0.00 0.00 44.23 5.25
313 5254 4.948847 CAAAAATTCCCCTTGCCTATAGC 58.051 43.478 0.00 0.00 44.14 2.97
772 5713 0.489567 ATCGGCCCCCTCTCTCTAAT 59.510 55.000 0.00 0.00 0.00 1.73
773 5714 0.264955 AATCGGCCCCCTCTCTCTAA 59.735 55.000 0.00 0.00 0.00 2.10
774 5715 0.470080 CAATCGGCCCCCTCTCTCTA 60.470 60.000 0.00 0.00 0.00 2.43
775 5716 1.764054 CAATCGGCCCCCTCTCTCT 60.764 63.158 0.00 0.00 0.00 3.10
776 5717 1.124477 ATCAATCGGCCCCCTCTCTC 61.124 60.000 0.00 0.00 0.00 3.20
777 5718 0.695803 AATCAATCGGCCCCCTCTCT 60.696 55.000 0.00 0.00 0.00 3.10
778 5719 0.536006 CAATCAATCGGCCCCCTCTC 60.536 60.000 0.00 0.00 0.00 3.20
779 5720 1.281925 ACAATCAATCGGCCCCCTCT 61.282 55.000 0.00 0.00 0.00 3.69
780 5721 0.395724 AACAATCAATCGGCCCCCTC 60.396 55.000 0.00 0.00 0.00 4.30
781 5722 0.684153 CAACAATCAATCGGCCCCCT 60.684 55.000 0.00 0.00 0.00 4.79
784 5725 0.461135 ATGCAACAATCAATCGGCCC 59.539 50.000 0.00 0.00 0.00 5.80
786 5727 5.348451 AGTTTTTATGCAACAATCAATCGGC 59.652 36.000 0.00 0.00 0.00 5.54
788 5729 7.439490 GTCAGTTTTTATGCAACAATCAATCG 58.561 34.615 0.00 0.00 0.00 3.34
793 5734 4.917415 AGCGTCAGTTTTTATGCAACAATC 59.083 37.500 0.00 0.00 0.00 2.67
794 5735 4.681025 CAGCGTCAGTTTTTATGCAACAAT 59.319 37.500 0.00 0.00 0.00 2.71
798 5739 3.313803 TGTCAGCGTCAGTTTTTATGCAA 59.686 39.130 0.00 0.00 0.00 4.08
813 5754 2.124983 CCACCCCTGATGTCAGCG 60.125 66.667 4.48 0.00 42.47 5.18
822 5763 0.839946 CAATCCTAGGTCCACCCCTG 59.160 60.000 9.08 0.00 35.97 4.45
824 5765 1.353394 CCCAATCCTAGGTCCACCCC 61.353 65.000 9.08 0.00 36.42 4.95
825 5766 1.996070 GCCCAATCCTAGGTCCACCC 61.996 65.000 9.08 0.00 36.42 4.61
827 5768 1.802553 TAGCCCAATCCTAGGTCCAC 58.197 55.000 9.08 0.00 0.00 4.02
828 5769 2.579624 TTAGCCCAATCCTAGGTCCA 57.420 50.000 9.08 0.00 0.00 4.02
829 5770 3.704800 GATTAGCCCAATCCTAGGTCC 57.295 52.381 9.08 0.00 37.64 4.46
844 5785 1.492993 GCCTAGGGCCTGGGGATTAG 61.493 65.000 34.03 13.81 44.06 1.73
845 5786 1.463410 GCCTAGGGCCTGGGGATTA 60.463 63.158 34.03 3.71 44.06 1.75
857 5798 1.253100 GGCACTCTAGCTAGCCTAGG 58.747 60.000 16.35 3.67 43.14 3.02
858 5799 1.253100 GGGCACTCTAGCTAGCCTAG 58.747 60.000 16.35 10.83 46.23 3.02
859 5800 0.178958 GGGGCACTCTAGCTAGCCTA 60.179 60.000 16.35 2.44 46.23 3.93
860 5801 1.458588 GGGGCACTCTAGCTAGCCT 60.459 63.158 16.35 1.20 46.23 4.58
861 5802 0.178958 TAGGGGCACTCTAGCTAGCC 60.179 60.000 16.35 14.09 46.28 3.93
863 5804 2.235016 CTGTAGGGGCACTCTAGCTAG 58.765 57.143 15.01 15.01 34.17 3.42
864 5805 1.754555 GCTGTAGGGGCACTCTAGCTA 60.755 57.143 15.55 0.00 36.14 3.32
865 5806 1.045911 GCTGTAGGGGCACTCTAGCT 61.046 60.000 15.55 0.00 36.14 3.32
866 5807 1.330655 TGCTGTAGGGGCACTCTAGC 61.331 60.000 15.86 15.86 38.23 3.42
867 5808 1.137872 CTTGCTGTAGGGGCACTCTAG 59.862 57.143 0.00 0.00 39.55 2.43
869 5810 0.545309 TCTTGCTGTAGGGGCACTCT 60.545 55.000 0.00 0.00 39.55 3.24
870 5811 0.543749 ATCTTGCTGTAGGGGCACTC 59.456 55.000 0.00 0.00 39.55 3.51
871 5812 0.254178 CATCTTGCTGTAGGGGCACT 59.746 55.000 0.00 0.00 39.55 4.40
872 5813 1.379642 GCATCTTGCTGTAGGGGCAC 61.380 60.000 0.00 0.00 40.96 5.01
873 5814 1.077501 GCATCTTGCTGTAGGGGCA 60.078 57.895 0.00 0.00 40.96 5.36
875 5816 1.152881 GGGCATCTTGCTGTAGGGG 60.153 63.158 0.00 0.00 44.28 4.79
876 5817 0.465097 CTGGGCATCTTGCTGTAGGG 60.465 60.000 0.00 0.00 44.28 3.53
877 5818 0.465097 CCTGGGCATCTTGCTGTAGG 60.465 60.000 0.00 1.97 44.28 3.18
878 5819 0.465097 CCCTGGGCATCTTGCTGTAG 60.465 60.000 0.00 0.00 44.28 2.74
879 5820 1.609239 CCCTGGGCATCTTGCTGTA 59.391 57.895 0.00 0.00 44.28 2.74
880 5821 2.357836 CCCTGGGCATCTTGCTGT 59.642 61.111 0.00 0.00 44.28 4.40
897 5838 1.466851 AAAAGTGAGGCTGCTTGGGC 61.467 55.000 0.00 0.00 39.26 5.36
899 5840 1.538950 GAGAAAAGTGAGGCTGCTTGG 59.461 52.381 0.00 0.00 0.00 3.61
900 5841 1.538950 GGAGAAAAGTGAGGCTGCTTG 59.461 52.381 0.00 0.00 0.00 4.01
901 5842 1.423161 AGGAGAAAAGTGAGGCTGCTT 59.577 47.619 0.00 0.00 0.00 3.91
902 5843 1.003003 GAGGAGAAAAGTGAGGCTGCT 59.997 52.381 0.00 0.00 0.00 4.24
912 6442 1.339535 GGGCACTGGAGAGGAGAAAAG 60.340 57.143 0.00 0.00 0.00 2.27
953 6483 2.147387 GTGGGGTGTGGTGGACTCT 61.147 63.158 0.00 0.00 0.00 3.24
1078 6641 2.835895 GGAGAGGCGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1687 7280 2.641815 ACTCAAGGATTCCAGAACAGCT 59.358 45.455 5.29 0.00 0.00 4.24
1696 7289 9.525409 CATATTCAAATCAAACTCAAGGATTCC 57.475 33.333 0.00 0.00 31.26 3.01
1721 7320 2.322658 GTATCACGGTTAGGATCCCCA 58.677 52.381 8.55 0.00 33.88 4.96
1723 7322 2.299297 CTGGTATCACGGTTAGGATCCC 59.701 54.545 8.55 0.00 0.00 3.85
1890 7489 2.057922 AGCTCAAAAGTTCTCCCCAGA 58.942 47.619 0.00 0.00 0.00 3.86
1896 7495 3.122111 GCGTGTCTAGCTCAAAAGTTCTC 59.878 47.826 0.00 0.00 0.00 2.87
1941 7540 2.151202 AGCATCACCGTGTACCTTTTG 58.849 47.619 0.00 0.00 0.00 2.44
1971 7570 4.046462 CCACCACCGTATTATTGTACTCG 58.954 47.826 0.00 0.00 0.00 4.18
2028 7627 3.742882 TCTTCTTGAACTGCAATGACTCG 59.257 43.478 0.00 0.00 35.59 4.18
2063 7662 2.487762 GGTTGATGGAAATGCGAACTGA 59.512 45.455 0.00 0.00 0.00 3.41
2088 7687 6.952358 TGTTACCTCCAGTATAGACACTTTCT 59.048 38.462 0.00 0.00 38.51 2.52
2123 7722 6.206829 AGTGTACTAGAGATATGCGCATTGTA 59.793 38.462 30.42 11.57 0.00 2.41
2127 7726 5.713792 AAGTGTACTAGAGATATGCGCAT 57.286 39.130 28.23 28.23 0.00 4.73
2128 7727 5.515797 AAAGTGTACTAGAGATATGCGCA 57.484 39.130 14.96 14.96 0.00 6.09
2130 7729 7.197017 AGTCAAAAGTGTACTAGAGATATGCG 58.803 38.462 0.00 0.00 0.00 4.73
2170 8366 5.049818 CAGTCATCTTCAACTTCCAACTGTC 60.050 44.000 0.00 0.00 0.00 3.51
2287 8524 7.044706 GCACGATTAGCACAGATAAAAATGTTC 60.045 37.037 0.00 0.00 0.00 3.18
2310 8547 8.347035 TGTTACAGATTTACAGGTTTTTAGCAC 58.653 33.333 0.00 0.00 0.00 4.40
2449 8702 3.244422 CCACCCGCAGCTCCTATAATTAA 60.244 47.826 0.00 0.00 0.00 1.40
2450 8703 2.301870 CCACCCGCAGCTCCTATAATTA 59.698 50.000 0.00 0.00 0.00 1.40
2451 8704 1.072331 CCACCCGCAGCTCCTATAATT 59.928 52.381 0.00 0.00 0.00 1.40
2452 8705 0.687354 CCACCCGCAGCTCCTATAAT 59.313 55.000 0.00 0.00 0.00 1.28
2641 8921 0.254747 TACGGGAAGGCATCAAAGGG 59.745 55.000 0.00 0.00 0.00 3.95
2644 8924 4.850680 ACTAAATACGGGAAGGCATCAAA 58.149 39.130 0.00 0.00 0.00 2.69
2670 8950 7.558604 ACAACCAATGATATTCCAATGGAAAG 58.441 34.615 19.57 3.48 45.41 2.62
2741 9021 3.888323 TGTGCAAAAGTTCAGCTCCATTA 59.112 39.130 0.00 0.00 0.00 1.90
2766 9046 5.152623 TGAACCAGACAGTCATCTTAAGG 57.847 43.478 2.66 0.00 0.00 2.69
2870 9150 6.856895 ACAGAAGGCAAGCTTATGTTTATTC 58.143 36.000 0.00 0.00 33.16 1.75
2877 9157 6.512415 GCTTACATACAGAAGGCAAGCTTATG 60.512 42.308 0.00 0.00 35.27 1.90
2879 9159 4.876107 GCTTACATACAGAAGGCAAGCTTA 59.124 41.667 0.00 0.00 35.27 3.09
2880 9160 3.691609 GCTTACATACAGAAGGCAAGCTT 59.308 43.478 0.00 0.00 35.27 3.74
2881 9161 3.274288 GCTTACATACAGAAGGCAAGCT 58.726 45.455 0.00 0.00 35.27 3.74
2886 9166 2.100916 TCCTCGCTTACATACAGAAGGC 59.899 50.000 0.00 0.00 0.00 4.35
2920 9269 1.211457 AGCTGAGCTAAGGTTCATGGG 59.789 52.381 4.49 0.00 36.99 4.00
2965 9314 3.429492 TCCAACATGCCAATAAAGAGCA 58.571 40.909 0.00 0.00 41.50 4.26
3004 9353 2.848691 CTGAGGAATGGATGAGGAAGC 58.151 52.381 0.00 0.00 0.00 3.86
3016 9365 0.326264 ACTGAAAGCGGCTGAGGAAT 59.674 50.000 1.81 0.00 37.60 3.01
3125 9474 9.817809 AGAAGCGATTAAAGTTATACAATCTCA 57.182 29.630 0.00 0.00 0.00 3.27
3140 9489 6.016860 CCATTCATTCATGGAGAAGCGATTAA 60.017 38.462 0.00 0.00 46.18 1.40
3268 9618 9.547753 GAAGCATACTAAATGGAAGAATCTACA 57.452 33.333 0.00 0.00 0.00 2.74
3269 9619 9.547753 TGAAGCATACTAAATGGAAGAATCTAC 57.452 33.333 0.00 0.00 0.00 2.59
3270 9620 9.547753 GTGAAGCATACTAAATGGAAGAATCTA 57.452 33.333 0.00 0.00 0.00 1.98
3271 9621 7.225538 CGTGAAGCATACTAAATGGAAGAATCT 59.774 37.037 0.00 0.00 0.00 2.40
3272 9622 7.011482 ACGTGAAGCATACTAAATGGAAGAATC 59.989 37.037 0.00 0.00 0.00 2.52
3273 9623 6.823689 ACGTGAAGCATACTAAATGGAAGAAT 59.176 34.615 0.00 0.00 0.00 2.40
3398 9749 6.099269 ACAGAAACTAGAACTACCAGAACCAA 59.901 38.462 0.00 0.00 0.00 3.67
3400 9751 6.099159 ACAGAAACTAGAACTACCAGAACC 57.901 41.667 0.00 0.00 0.00 3.62
3474 9827 2.972021 CCCTTGGGTTGGTCTCATTTTT 59.028 45.455 0.00 0.00 0.00 1.94
3475 9828 2.608623 CCCTTGGGTTGGTCTCATTTT 58.391 47.619 0.00 0.00 0.00 1.82
3476 9829 1.827245 GCCCTTGGGTTGGTCTCATTT 60.827 52.381 7.61 0.00 0.00 2.32
3477 9830 0.251787 GCCCTTGGGTTGGTCTCATT 60.252 55.000 7.61 0.00 0.00 2.57
3478 9831 1.142688 AGCCCTTGGGTTGGTCTCAT 61.143 55.000 7.61 0.00 0.00 2.90
3479 9832 0.474854 TAGCCCTTGGGTTGGTCTCA 60.475 55.000 7.61 0.00 34.28 3.27
3480 9833 0.696501 TTAGCCCTTGGGTTGGTCTC 59.303 55.000 7.61 0.00 34.28 3.36
3481 9834 0.404426 GTTAGCCCTTGGGTTGGTCT 59.596 55.000 7.61 0.00 34.28 3.85
3482 9835 0.611062 GGTTAGCCCTTGGGTTGGTC 60.611 60.000 7.61 0.00 34.28 4.02
3483 9836 1.463375 GGTTAGCCCTTGGGTTGGT 59.537 57.895 7.61 0.00 34.28 3.67
3484 9837 4.434483 GGTTAGCCCTTGGGTTGG 57.566 61.111 7.61 0.00 34.28 3.77
3523 9876 1.149148 GGTGCTCACGGAGTTTTCTC 58.851 55.000 3.38 0.00 41.61 2.87
3524 9877 0.600255 CGGTGCTCACGGAGTTTTCT 60.600 55.000 1.90 0.00 41.61 2.52
3525 9878 1.860078 CGGTGCTCACGGAGTTTTC 59.140 57.895 1.90 0.00 41.61 2.29
3526 9879 2.251642 GCGGTGCTCACGGAGTTTT 61.252 57.895 11.07 0.00 41.61 2.43
3527 9880 2.665185 GCGGTGCTCACGGAGTTT 60.665 61.111 11.07 0.00 41.61 2.66
3554 9907 1.871772 GAGTTCGTTCGAGTCCCGA 59.128 57.895 0.00 0.00 46.94 5.14
3555 9908 1.511464 CGAGTTCGTTCGAGTCCCG 60.511 63.158 1.56 0.00 43.03 5.14
3556 9909 1.154073 CCGAGTTCGTTCGAGTCCC 60.154 63.158 7.98 0.00 43.03 4.46
3557 9910 1.154073 CCCGAGTTCGTTCGAGTCC 60.154 63.158 7.98 0.00 43.03 3.85
3558 9911 0.728466 CACCCGAGTTCGTTCGAGTC 60.728 60.000 7.98 0.00 43.03 3.36
3559 9912 1.285023 CACCCGAGTTCGTTCGAGT 59.715 57.895 7.98 0.00 43.03 4.18
3560 9913 1.443872 CCACCCGAGTTCGTTCGAG 60.444 63.158 7.98 0.00 43.03 4.04
3561 9914 2.646719 CCACCCGAGTTCGTTCGA 59.353 61.111 7.98 0.00 43.03 3.71
3562 9915 2.431942 CCCACCCGAGTTCGTTCG 60.432 66.667 0.48 0.93 40.18 3.95
3563 9916 2.741211 GCCCACCCGAGTTCGTTC 60.741 66.667 0.48 0.00 37.74 3.95
3564 9917 3.239253 AGCCCACCCGAGTTCGTT 61.239 61.111 0.48 0.00 37.74 3.85
3565 9918 4.003788 CAGCCCACCCGAGTTCGT 62.004 66.667 0.48 0.00 37.74 3.85
3566 9919 4.760047 CCAGCCCACCCGAGTTCG 62.760 72.222 0.00 0.00 39.44 3.95
3575 9928 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
3576 9929 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
3577 9930 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
3578 9931 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
3579 9932 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
3580 9933 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
3585 9938 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
3586 9939 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
3617 9970 3.775654 CAGGAGTGAGGACGGGGC 61.776 72.222 0.00 0.00 0.00 5.80
3618 9971 2.283966 ACAGGAGTGAGGACGGGG 60.284 66.667 0.00 0.00 0.00 5.73
3628 9981 3.886123 ACTTTAAACAGCACACAGGAGT 58.114 40.909 0.00 0.00 0.00 3.85
3629 9982 6.874134 AGTATACTTTAAACAGCACACAGGAG 59.126 38.462 0.00 0.00 0.00 3.69
3630 9983 6.765403 AGTATACTTTAAACAGCACACAGGA 58.235 36.000 0.00 0.00 0.00 3.86
3631 9984 7.435068 AAGTATACTTTAAACAGCACACAGG 57.565 36.000 12.50 0.00 30.82 4.00
3632 9985 8.342634 ACAAAGTATACTTTAAACAGCACACAG 58.657 33.333 26.38 13.89 43.72 3.66
3633 9986 8.215926 ACAAAGTATACTTTAAACAGCACACA 57.784 30.769 26.38 0.00 43.72 3.72
3636 9989 9.603298 GGTAACAAAGTATACTTTAAACAGCAC 57.397 33.333 26.38 17.04 43.72 4.40
3637 9990 9.563748 AGGTAACAAAGTATACTTTAAACAGCA 57.436 29.630 26.38 8.57 43.72 4.41
3638 9991 9.821662 CAGGTAACAAAGTATACTTTAAACAGC 57.178 33.333 26.38 20.00 43.72 4.40
3640 9993 9.850198 ACCAGGTAACAAAGTATACTTTAAACA 57.150 29.630 26.38 12.10 43.72 2.83


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

AutoCloner maintained by Alex Coulton.