Multiple sequence alignment - TraesCS7A01G402000

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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 TraesCS7A01G402000 chr7A 100.000 9214 0 0 1 9214 581358386 581349173 0.000000e+00 17016.0
1 TraesCS7A01G402000 chr7D 95.266 7203 178 45 1 7110 510463821 510456689 0.000000e+00 11261.0
2 TraesCS7A01G402000 chr7D 93.502 1816 92 12 7177 8975 510456704 510454898 0.000000e+00 2676.0
3 TraesCS7A01G402000 chr7D 90.756 119 9 2 9098 9214 510454694 510454576 3.440000e-34 158.0
4 TraesCS7A01G402000 chr7B 96.175 6379 162 25 717 7036 538878422 538872067 0.000000e+00 10353.0
5 TraesCS7A01G402000 chr7B 92.434 1771 102 16 7323 9069 538870785 538869023 0.000000e+00 2499.0
6 TraesCS7A01G402000 chr7B 97.647 85 2 0 7028 7112 538870884 538870800 7.460000e-31 147.0
7 TraesCS7A01G402000 chr7B 94.595 74 3 1 7113 7186 107167556 107167628 7.560000e-21 113.0
8 TraesCS7A01G402000 chr7B 92.405 79 4 2 7113 7191 410845864 410845788 2.720000e-20 111.0
9 TraesCS7A01G402000 chr7B 90.323 62 4 2 1 60 538879015 538878954 7.670000e-11 80.5
10 TraesCS7A01G402000 chr3D 92.448 1258 73 14 5140 6386 156259233 156257987 0.000000e+00 1777.0
11 TraesCS7A01G402000 chr3D 87.724 1173 96 19 2628 3773 156286333 156285182 0.000000e+00 1325.0
12 TraesCS7A01G402000 chr3D 89.517 849 59 10 4306 5145 156260101 156259274 0.000000e+00 1048.0
13 TraesCS7A01G402000 chr3D 91.533 437 27 6 1926 2355 153511726 153512159 2.220000e-165 593.0
14 TraesCS7A01G402000 chr3D 91.168 351 19 3 3920 4259 156260463 156260114 5.040000e-127 466.0
15 TraesCS7A01G402000 chr3D 93.885 278 14 2 7743 8017 156257977 156257700 5.150000e-112 416.0
16 TraesCS7A01G402000 chr3D 80.909 440 50 14 8015 8421 156257277 156256839 5.370000e-82 316.0
17 TraesCS7A01G402000 chr3D 86.250 240 18 8 2393 2632 153512402 153512626 7.150000e-61 246.0
18 TraesCS7A01G402000 chr3D 88.961 154 17 0 3775 3928 156265411 156265258 3.400000e-44 191.0
19 TraesCS7A01G402000 chr3A 86.432 1334 127 22 2628 3928 176045454 176044142 0.000000e+00 1411.0
20 TraesCS7A01G402000 chr3A 87.771 785 65 12 4370 5145 176018372 176017610 0.000000e+00 889.0
21 TraesCS7A01G402000 chr3A 94.963 536 23 4 5341 5872 175959487 175958952 0.000000e+00 837.0
22 TraesCS7A01G402000 chr3A 83.721 559 62 14 8540 9082 175956965 175956420 1.380000e-137 501.0
23 TraesCS7A01G402000 chr3A 91.168 351 19 3 3920 4259 176023064 176022715 5.040000e-127 466.0
24 TraesCS7A01G402000 chr3A 91.667 336 24 4 6053 6386 175958544 175958211 6.520000e-126 462.0
25 TraesCS7A01G402000 chr3A 92.446 278 18 2 7743 8017 175958201 175957924 2.410000e-105 394.0
26 TraesCS7A01G402000 chr3A 81.818 440 46 13 8015 8421 175957488 175957050 1.150000e-88 339.0
27 TraesCS7A01G402000 chr3A 92.760 221 15 1 2135 2355 176118182 176117963 1.490000e-82 318.0
28 TraesCS7A01G402000 chr3A 92.233 206 16 0 5140 5345 176017569 176017364 9.050000e-75 292.0
29 TraesCS7A01G402000 chr3A 86.667 240 17 9 2393 2632 176117721 176117497 1.540000e-62 252.0
30 TraesCS7A01G402000 chr3A 88.542 192 13 2 5867 6058 175958751 175958569 3.350000e-54 224.0
31 TraesCS7A01G402000 chr3A 95.833 72 3 0 7113 7184 67314541 67314470 5.850000e-22 117.0
32 TraesCS7A01G402000 chr3A 91.463 82 5 2 7113 7193 107736082 107736002 2.720000e-20 111.0
33 TraesCS7A01G402000 chr3B 81.000 300 27 7 8887 9160 225184162 225184457 2.610000e-50 211.0
34 TraesCS7A01G402000 chr6D 98.485 66 1 0 7113 7178 128903181 128903246 5.850000e-22 117.0
35 TraesCS7A01G402000 chr2B 95.833 72 2 1 7113 7184 656000981 656000911 2.100000e-21 115.0
36 TraesCS7A01G402000 chr2A 93.421 76 5 0 7113 7188 116436962 116437037 7.560000e-21 113.0
37 TraesCS7A01G402000 chr5B 92.500 80 3 1 7113 7192 180040223 180040147 2.720000e-20 111.0
38 TraesCS7A01G402000 chr6A 92.308 78 2 1 7113 7190 582814325 582814252 3.520000e-19 108.0


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 TraesCS7A01G402000 chr7A 581349173 581358386 9213 True 17016.000000 17016 100.000000 1 9214 1 chr7A.!!$R1 9213
1 TraesCS7A01G402000 chr7D 510454576 510463821 9245 True 4698.333333 11261 93.174667 1 9214 3 chr7D.!!$R1 9213
2 TraesCS7A01G402000 chr7B 538869023 538879015 9992 True 3269.875000 10353 94.144750 1 9069 4 chr7B.!!$R2 9068
3 TraesCS7A01G402000 chr3D 156285182 156286333 1151 True 1325.000000 1325 87.724000 2628 3773 1 chr3D.!!$R2 1145
4 TraesCS7A01G402000 chr3D 156256839 156260463 3624 True 804.600000 1777 89.585400 3920 8421 5 chr3D.!!$R3 4501
5 TraesCS7A01G402000 chr3D 153511726 153512626 900 False 419.500000 593 88.891500 1926 2632 2 chr3D.!!$F1 706
6 TraesCS7A01G402000 chr3A 176044142 176045454 1312 True 1411.000000 1411 86.432000 2628 3928 1 chr3A.!!$R4 1300
7 TraesCS7A01G402000 chr3A 176017364 176018372 1008 True 590.500000 889 90.002000 4370 5345 2 chr3A.!!$R6 975
8 TraesCS7A01G402000 chr3A 175956420 175959487 3067 True 459.500000 837 88.859500 5341 9082 6 chr3A.!!$R5 3741
9 TraesCS7A01G402000 chr3A 176117497 176118182 685 True 285.000000 318 89.713500 2135 2632 2 chr3A.!!$R7 497

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
529 609 0.031043 GCATCGCCATTTATGCAGCA 59.969 50.000 0.00 0.0 46.19 4.41 F
890 1011 0.108138 GAATCTCCAGGTGGACCGTG 60.108 60.000 0.00 0.0 39.78 4.94 F
1226 1350 1.593787 CAGCGTCAGGTGGAGTCAT 59.406 57.895 0.00 0.0 41.81 3.06 F
1503 1627 1.740718 GCTTCGGGGCAAACAAAAACA 60.741 47.619 0.00 0.0 0.00 2.83 F
2655 3186 1.805428 GCAAAATGGGGTGTCGCAGT 61.805 55.000 0.00 0.0 39.23 4.40 F
3378 3926 1.408702 TGTTTCCCAGAAAAGCAGCAC 59.591 47.619 0.00 0.0 0.00 4.40 F
3864 4434 1.422024 TCAATTCCAGTTTCACCGGGA 59.578 47.619 6.32 0.0 0.00 5.14 F
4918 5507 2.158696 GGATTCTATCTGCCTTGGTGCT 60.159 50.000 0.00 0.0 0.00 4.40 F
6260 7186 2.917713 TGCCATTCCAAAGTACCCAT 57.082 45.000 0.00 0.0 0.00 4.00 F
6732 7658 0.603569 TCACGCTCCTCTTTGAGACC 59.396 55.000 0.00 0.0 34.11 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2482 0.176910 GGAGAGGCTCCTACTGCAAC 59.823 60.000 11.71 0.0 46.41 4.17 R
2818 3352 1.285078 GGTCCTCATGCCCTAAAACCT 59.715 52.381 0.00 0.0 0.00 3.50 R
2819 3353 1.285078 AGGTCCTCATGCCCTAAAACC 59.715 52.381 0.00 0.0 0.00 3.27 R
2946 3480 4.759693 AGACATGTAAAAGAATTGTCGGCA 59.240 37.500 0.00 0.0 41.15 5.69 R
3911 4481 4.212150 GTTGAAAAGAGAAAGCTACACGC 58.788 43.478 0.00 0.0 39.57 5.34 R
5280 5964 0.109781 CAACGTCATCTTTTGGGCGG 60.110 55.000 0.00 0.0 0.00 6.13 R
5690 6377 5.357596 GTCTTTTACCTCTAGACATCTCCGT 59.642 44.000 0.00 0.0 38.49 4.69 R
6491 7417 0.737715 GCTCCAGCTACAGTGAACCG 60.738 60.000 0.00 0.0 38.21 4.44 R
7110 9228 0.906282 GGGAAGGGTCCGACCACTAA 60.906 60.000 19.43 0.0 46.04 2.24 R
8596 11188 0.453390 GATAGCAGCAACTTGTGGGC 59.547 55.000 0.00 0.0 0.00 5.36 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
143 146 1.988982 GAGAACCCAGCCCAGATCCC 61.989 65.000 0.00 0.00 0.00 3.85
220 264 2.975489 TGGATTTGCTCCCTCTATCTCC 59.025 50.000 0.00 0.00 44.23 3.71
221 265 3.247162 GGATTTGCTCCCTCTATCTCCT 58.753 50.000 0.00 0.00 38.19 3.69
224 268 5.104982 GGATTTGCTCCCTCTATCTCCTATG 60.105 48.000 0.00 0.00 38.19 2.23
226 270 4.040936 TGCTCCCTCTATCTCCTATGTC 57.959 50.000 0.00 0.00 0.00 3.06
229 273 4.258543 CTCCCTCTATCTCCTATGTCGTC 58.741 52.174 0.00 0.00 0.00 4.20
236 280 4.698201 ATCTCCTATGTCGTCTCTCTCA 57.302 45.455 0.00 0.00 0.00 3.27
240 284 2.644676 CTATGTCGTCTCTCTCACCCA 58.355 52.381 0.00 0.00 0.00 4.51
283 327 2.644992 CCGTTTCCAAGGCAGCAC 59.355 61.111 0.00 0.00 0.00 4.40
284 328 2.192861 CCGTTTCCAAGGCAGCACA 61.193 57.895 0.00 0.00 0.00 4.57
285 329 1.283793 CGTTTCCAAGGCAGCACAG 59.716 57.895 0.00 0.00 0.00 3.66
286 330 1.006922 GTTTCCAAGGCAGCACAGC 60.007 57.895 0.00 0.00 0.00 4.40
287 331 1.455402 TTTCCAAGGCAGCACAGCA 60.455 52.632 0.00 0.00 35.83 4.41
379 449 1.269998 GGTAGATAGATTCGCGTGCCT 59.730 52.381 5.77 4.01 0.00 4.75
392 462 1.657751 CGTGCCTGTCTCTGGATCGA 61.658 60.000 0.00 0.00 0.00 3.59
416 486 1.538512 TGAGATGCTGCTTTGAGTTGC 59.461 47.619 0.00 0.00 0.00 4.17
515 595 4.047822 GTCTAGTCAGGATCTTTGCATCG 58.952 47.826 0.00 0.00 0.00 3.84
516 596 1.661341 AGTCAGGATCTTTGCATCGC 58.339 50.000 0.00 0.00 0.00 4.58
517 597 0.659957 GTCAGGATCTTTGCATCGCC 59.340 55.000 0.00 0.00 0.00 5.54
518 598 0.252761 TCAGGATCTTTGCATCGCCA 59.747 50.000 0.00 0.00 0.00 5.69
519 599 1.134007 TCAGGATCTTTGCATCGCCAT 60.134 47.619 0.00 0.00 0.00 4.40
520 600 1.679680 CAGGATCTTTGCATCGCCATT 59.320 47.619 0.00 0.00 0.00 3.16
521 601 2.100252 CAGGATCTTTGCATCGCCATTT 59.900 45.455 0.00 0.00 0.00 2.32
522 602 3.316029 CAGGATCTTTGCATCGCCATTTA 59.684 43.478 0.00 0.00 0.00 1.40
523 603 4.022589 CAGGATCTTTGCATCGCCATTTAT 60.023 41.667 0.00 0.00 0.00 1.40
524 604 4.022589 AGGATCTTTGCATCGCCATTTATG 60.023 41.667 0.00 0.00 0.00 1.90
525 605 3.082698 TCTTTGCATCGCCATTTATGC 57.917 42.857 0.00 0.00 46.92 3.14
528 608 2.805277 GCATCGCCATTTATGCAGC 58.195 52.632 0.00 0.00 46.19 5.25
529 609 0.031043 GCATCGCCATTTATGCAGCA 59.969 50.000 0.00 0.00 46.19 4.41
530 610 1.336517 GCATCGCCATTTATGCAGCAT 60.337 47.619 13.73 13.73 46.19 3.79
531 611 2.095110 GCATCGCCATTTATGCAGCATA 60.095 45.455 11.33 11.33 46.19 3.14
532 612 3.612241 GCATCGCCATTTATGCAGCATAA 60.612 43.478 21.83 21.83 46.19 1.90
533 613 3.902261 TCGCCATTTATGCAGCATAAG 57.098 42.857 23.79 15.63 37.57 1.73
534 614 2.553602 TCGCCATTTATGCAGCATAAGG 59.446 45.455 23.79 22.56 37.57 2.69
565 665 9.872757 CTTACTCGATTAGTTATCTTCACTCTC 57.127 37.037 0.00 0.00 39.80 3.20
577 677 0.191064 TCACTCTCAAGTCCTGGGGT 59.809 55.000 0.00 0.00 31.71 4.95
578 678 0.610687 CACTCTCAAGTCCTGGGGTC 59.389 60.000 0.00 0.00 31.71 4.46
579 679 0.900647 ACTCTCAAGTCCTGGGGTCG 60.901 60.000 0.00 0.00 0.00 4.79
581 681 2.203788 TCAAGTCCTGGGGTCGCT 60.204 61.111 0.00 0.00 0.00 4.93
582 682 0.970937 CTCAAGTCCTGGGGTCGCTA 60.971 60.000 0.00 0.00 0.00 4.26
680 791 4.570930 ACTAGTAGTGCCAAAAAGCTCTC 58.429 43.478 0.85 0.00 37.70 3.20
706 817 5.236478 AGGGCAAACTTACAATCGATAATCG 59.764 40.000 0.00 0.00 42.10 3.34
721 832 1.156736 AATCGACTTCAGGGCAAACG 58.843 50.000 0.00 0.00 0.00 3.60
758 869 5.710099 TCAACCTGGAAAATTACTAGGCTTG 59.290 40.000 0.00 14.06 39.16 4.01
863 984 8.562892 GCTGCAGTTTGATGTACATAGATTTAT 58.437 33.333 16.64 0.00 0.00 1.40
890 1011 0.108138 GAATCTCCAGGTGGACCGTG 60.108 60.000 0.00 0.00 39.78 4.94
955 1076 3.225940 GGGCTTATTCTTTCTCCATGGG 58.774 50.000 13.02 2.57 0.00 4.00
1168 1289 2.857592 TTCAGTTACCGCGACTATCC 57.142 50.000 8.23 0.00 0.00 2.59
1226 1350 1.593787 CAGCGTCAGGTGGAGTCAT 59.406 57.895 0.00 0.00 41.81 3.06
1503 1627 1.740718 GCTTCGGGGCAAACAAAAACA 60.741 47.619 0.00 0.00 0.00 2.83
1649 1773 7.821595 TTTCCTAGTATTGTACGACATGTTG 57.178 36.000 11.78 11.78 0.00 3.33
1848 1972 7.553044 GTGAATACAGTTTTGGCTATACCTCTT 59.447 37.037 0.00 0.00 40.22 2.85
1924 2048 4.329528 TGCTTGCATGTTTTTCAAACACTC 59.670 37.500 4.21 1.08 32.37 3.51
2020 2145 6.818644 TCACTTAACTAAATCCTCTGCATCAC 59.181 38.462 0.00 0.00 0.00 3.06
2205 2336 5.439721 TGATTGACTTGGGTAATGAGGATG 58.560 41.667 0.00 0.00 0.00 3.51
2329 2460 9.533831 AAATCAAATTGACCCTAGTCTTGTAAT 57.466 29.630 0.00 0.00 43.91 1.89
2491 3022 9.979578 TTGTGAAATATTTCTAGTGCATGTTTT 57.020 25.926 24.77 0.00 38.02 2.43
2492 3023 9.624697 TGTGAAATATTTCTAGTGCATGTTTTC 57.375 29.630 24.77 0.00 38.02 2.29
2493 3024 9.846248 GTGAAATATTTCTAGTGCATGTTTTCT 57.154 29.630 24.77 0.00 38.02 2.52
2655 3186 1.805428 GCAAAATGGGGTGTCGCAGT 61.805 55.000 0.00 0.00 39.23 4.40
2818 3352 4.391405 ACTCATAATCGCACATGTCTGA 57.609 40.909 0.00 0.00 0.00 3.27
2819 3353 4.366586 ACTCATAATCGCACATGTCTGAG 58.633 43.478 0.00 2.98 35.99 3.35
2921 3455 4.458989 TGACTGATATTGGTTCTTGGTTGC 59.541 41.667 0.00 0.00 0.00 4.17
2946 3480 7.364585 GCCTATCCTGTAGCATCAGAAGAATAT 60.365 40.741 9.26 0.00 37.61 1.28
2957 3491 5.991328 TCAGAAGAATATGCCGACAATTC 57.009 39.130 0.00 0.00 0.00 2.17
2962 3496 8.397906 CAGAAGAATATGCCGACAATTCTTTTA 58.602 33.333 16.55 0.00 45.39 1.52
3053 3600 8.049117 GCATTATATGGTCCATCTATTTCCTCA 58.951 37.037 7.92 0.00 0.00 3.86
3184 3731 9.762933 TTCTTTGAAAATTCTCTTAACCATTGG 57.237 29.630 0.00 0.00 0.00 3.16
3378 3926 1.408702 TGTTTCCCAGAAAAGCAGCAC 59.591 47.619 0.00 0.00 0.00 4.40
3534 4098 2.032680 TGCGGGCTTACTTATTCACC 57.967 50.000 0.00 0.00 0.00 4.02
3864 4434 1.422024 TCAATTCCAGTTTCACCGGGA 59.578 47.619 6.32 0.00 0.00 5.14
4210 4791 6.443849 TCAGAATGGGTGAGTCCTTATTTAGT 59.556 38.462 0.00 0.00 36.16 2.24
4524 5113 2.361757 TGTTGTTTCAACCCATGCTGAG 59.638 45.455 9.60 0.00 0.00 3.35
4918 5507 2.158696 GGATTCTATCTGCCTTGGTGCT 60.159 50.000 0.00 0.00 0.00 4.40
4938 5527 7.615365 TGGTGCTTCCTAATGATTAATTCTGTT 59.385 33.333 0.00 0.00 37.07 3.16
5070 5660 3.637229 TGACTAGGCTTATTCCTCTTCCG 59.363 47.826 0.00 0.00 37.66 4.30
5280 5964 7.254286 GGCGAAAGATTTTCTCTAGATTCTGAC 60.254 40.741 0.00 0.00 32.41 3.51
6137 7062 9.431887 TCATGAAACTAGTACAAGGTTATGTTC 57.568 33.333 0.00 0.00 34.75 3.18
6153 7078 6.482308 GGTTATGTTCGATGGTTTAGCTACAT 59.518 38.462 0.00 0.00 0.00 2.29
6159 7084 4.056050 CGATGGTTTAGCTACATGGGTAC 58.944 47.826 0.00 0.00 0.00 3.34
6205 7131 7.992608 TGTGCATGTAGTTTGATTAGGATGTAT 59.007 33.333 0.00 0.00 0.00 2.29
6225 7151 7.938563 TGTATACTTGATTTTGTTTGTTGGC 57.061 32.000 4.17 0.00 0.00 4.52
6260 7186 2.917713 TGCCATTCCAAAGTACCCAT 57.082 45.000 0.00 0.00 0.00 4.00
6335 7261 3.880490 TCACCGTATTCACAAAACTTGCT 59.120 39.130 0.00 0.00 0.00 3.91
6352 7278 7.761038 AACTTGCTAGTAGCCTTTGTATTTT 57.239 32.000 19.41 0.00 41.51 1.82
6365 7291 7.120726 AGCCTTTGTATTTTACATGTACTGGAC 59.879 37.037 4.68 2.92 38.68 4.02
6408 7334 5.604758 TGTCTCTAGATCCTTCACAATGG 57.395 43.478 0.00 0.00 0.00 3.16
6426 7352 5.303333 ACAATGGCTGCAATGATGATGATTA 59.697 36.000 0.50 0.00 0.00 1.75
6491 7417 2.785868 GGGTGATGGCACTCATGTC 58.214 57.895 0.00 0.00 45.12 3.06
6510 7436 0.737715 CGGTTCACTGTAGCTGGAGC 60.738 60.000 0.00 0.00 42.49 4.70
6563 7489 5.519927 GCATAGCACACAAATCATTAAACCC 59.480 40.000 0.00 0.00 0.00 4.11
6569 7495 6.690530 CACACAAATCATTAAACCCATGACT 58.309 36.000 0.00 0.00 33.42 3.41
6732 7658 0.603569 TCACGCTCCTCTTTGAGACC 59.396 55.000 0.00 0.00 34.11 3.85
6755 7681 2.664081 GCCTGCTGAGGTGGCTAGT 61.664 63.158 0.00 0.00 42.15 2.57
6900 7827 4.383552 GGTCAGAGATGTGAGGTTGCTATT 60.384 45.833 0.00 0.00 0.00 1.73
6995 7922 2.511600 GCATGACCCTCCGTTCCG 60.512 66.667 0.00 0.00 0.00 4.30
7122 9240 9.871238 ATATATATTTGATGTTAGTGGTCGGAC 57.129 33.333 0.00 0.00 0.00 4.79
7123 9241 2.754946 TTGATGTTAGTGGTCGGACC 57.245 50.000 20.36 20.36 39.22 4.46
7124 9242 0.899720 TGATGTTAGTGGTCGGACCC 59.100 55.000 23.81 14.91 37.50 4.46
7125 9243 1.192428 GATGTTAGTGGTCGGACCCT 58.808 55.000 23.81 20.55 37.50 4.34
7126 9244 1.553704 GATGTTAGTGGTCGGACCCTT 59.446 52.381 23.81 14.17 37.50 3.95
7127 9245 0.971386 TGTTAGTGGTCGGACCCTTC 59.029 55.000 23.81 13.97 37.50 3.46
7128 9246 0.248565 GTTAGTGGTCGGACCCTTCC 59.751 60.000 23.81 9.51 37.50 3.46
7129 9247 0.906282 TTAGTGGTCGGACCCTTCCC 60.906 60.000 23.81 7.17 38.99 3.97
7130 9248 2.810488 TAGTGGTCGGACCCTTCCCC 62.810 65.000 23.81 5.51 38.99 4.81
7131 9249 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
7132 9250 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
7133 9251 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
7134 9252 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
7135 9253 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
7136 9254 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
7137 9255 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
7138 9256 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
7139 9257 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
7140 9258 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
7141 9259 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
7162 9280 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
7163 9281 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
7164 9282 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
7165 9283 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
7166 9284 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
7167 9285 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
7168 9286 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
7169 9287 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
7170 9288 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
7181 9299 3.500635 GGCTGCCCTGGCCTATAT 58.499 61.111 7.66 0.00 45.57 0.86
7182 9300 2.696864 GGCTGCCCTGGCCTATATA 58.303 57.895 7.66 0.00 45.57 0.86
7183 9301 1.216990 GGCTGCCCTGGCCTATATAT 58.783 55.000 7.66 0.00 45.57 0.86
7184 9302 2.408565 GGCTGCCCTGGCCTATATATA 58.591 52.381 7.66 0.00 45.57 0.86
7185 9303 2.982488 GGCTGCCCTGGCCTATATATAT 59.018 50.000 7.66 0.00 45.57 0.86
7186 9304 3.395941 GGCTGCCCTGGCCTATATATATT 59.604 47.826 7.66 0.00 45.57 1.28
7187 9305 4.141158 GGCTGCCCTGGCCTATATATATTT 60.141 45.833 7.66 0.00 45.57 1.40
7188 9306 4.823989 GCTGCCCTGGCCTATATATATTTG 59.176 45.833 3.32 0.00 41.09 2.32
7189 9307 5.397899 GCTGCCCTGGCCTATATATATTTGA 60.398 44.000 3.32 0.00 41.09 2.69
7190 9308 6.692526 GCTGCCCTGGCCTATATATATTTGAT 60.693 42.308 3.32 0.00 41.09 2.57
7191 9309 6.604171 TGCCCTGGCCTATATATATTTGATG 58.396 40.000 3.32 0.00 41.09 3.07
7194 9312 7.229506 GCCCTGGCCTATATATATTTGATGTTC 59.770 40.741 3.32 0.00 34.56 3.18
7389 9507 9.800433 TTGCAATTACATATCTAAACAACCATG 57.200 29.630 0.00 0.00 0.00 3.66
7449 9567 3.565307 TGCCCTCAAATATTCCCATGAC 58.435 45.455 0.00 0.00 0.00 3.06
7540 9658 8.837788 TGACAATAATAGACATATTCCAGCAG 57.162 34.615 0.00 0.00 33.58 4.24
7651 9769 6.375174 ACTGATGCTTATTTGTATTGCACAGA 59.625 34.615 16.28 0.00 38.72 3.41
7751 9869 7.467403 GCCTAAGCTATGTTGGTCTATTTGAAC 60.467 40.741 0.00 0.00 35.50 3.18
7981 10101 1.673168 GGCAGGAATGGACTCATCAC 58.327 55.000 0.00 0.00 32.24 3.06
7991 10111 1.971357 GGACTCATCACGGTATGGGAT 59.029 52.381 6.17 0.00 31.40 3.85
8000 10120 3.390967 TCACGGTATGGGATGTGATGATT 59.609 43.478 0.00 0.00 36.50 2.57
8010 10130 5.829391 TGGGATGTGATGATTTTATGGAGTG 59.171 40.000 0.00 0.00 0.00 3.51
8037 10596 1.932511 CTAGTTTGCTGCTGCTAGCTC 59.067 52.381 17.56 8.40 42.97 4.09
8060 10619 4.416516 TGAGTGGTCAATTCTGGTCTCTA 58.583 43.478 0.00 0.00 0.00 2.43
8115 10674 0.793617 AAGAGAGAAGGGGGACTGGA 59.206 55.000 0.00 0.00 0.00 3.86
8186 10745 4.736126 TGGAAGAAACGATAGATCTGCA 57.264 40.909 5.18 0.00 36.31 4.41
8206 10765 4.219070 TGCATTGGTTGGAAATCTTCTCAG 59.781 41.667 0.00 0.00 0.00 3.35
8223 10782 2.935201 CTCAGCTCTTGAAGGTATGCAC 59.065 50.000 0.00 0.00 34.81 4.57
8236 10795 3.131933 AGGTATGCACTCTGTCTGTCATC 59.868 47.826 0.00 0.00 0.00 2.92
8294 10880 4.313282 ACTTAGTGAAGCCGGAAAAGTAC 58.687 43.478 5.05 0.00 35.97 2.73
8327 10919 6.036735 TGTCAAAGTAGTTGTTAACTGTGAGC 59.963 38.462 7.22 0.00 39.94 4.26
8436 11028 6.966021 TCTAGGTTAATTGAACAACTTGTGC 58.034 36.000 0.00 0.00 40.09 4.57
8461 11053 7.413328 GCTTATTCCATTTGGTTTCTTTGCATC 60.413 37.037 0.00 0.00 36.34 3.91
8504 11096 9.698309 CGGTTACATCATCTCTGTTATTATCTT 57.302 33.333 0.00 0.00 0.00 2.40
8596 11188 3.070302 GCCCTCTTGTATCTTACCTCAGG 59.930 52.174 0.00 0.00 0.00 3.86
8598 11190 3.070302 CCTCTTGTATCTTACCTCAGGCC 59.930 52.174 0.00 0.00 0.00 5.19
8631 11226 6.710295 TGCTGCTATCATTTGTAAATCGGTAT 59.290 34.615 0.00 0.00 0.00 2.73
8662 11262 4.202030 CCTTCGGTGAACTATCTGTAGTCC 60.202 50.000 0.00 0.00 40.24 3.85
8747 11351 0.698818 AGGGGAAACTTGGGCTACAG 59.301 55.000 0.00 0.00 0.00 2.74
8775 11379 6.389830 AGTCTGCTTCTGTCTGATGTATAG 57.610 41.667 0.00 0.00 0.00 1.31
8776 11380 5.890985 AGTCTGCTTCTGTCTGATGTATAGT 59.109 40.000 0.00 0.00 0.00 2.12
8777 11381 6.039270 AGTCTGCTTCTGTCTGATGTATAGTC 59.961 42.308 0.00 0.00 0.00 2.59
8787 11398 6.327365 TGTCTGATGTATAGTCCATCACCATT 59.673 38.462 0.00 0.00 42.73 3.16
8795 11406 3.947868 AGTCCATCACCATTGAACAGAG 58.052 45.455 0.00 0.00 34.61 3.35
8845 11456 1.354337 CGGACATCAGTCGTGCAAGG 61.354 60.000 0.00 0.00 45.92 3.61
8873 11484 1.226773 ATACCGACCGTTAGCGCAC 60.227 57.895 11.47 0.00 36.67 5.34
8884 11495 3.064207 CGTTAGCGCACCCAATGTATAT 58.936 45.455 11.47 0.00 0.00 0.86
8886 11497 2.638480 AGCGCACCCAATGTATATGT 57.362 45.000 11.47 0.00 0.00 2.29
8891 11502 5.358442 AGCGCACCCAATGTATATGTTTTTA 59.642 36.000 11.47 0.00 0.00 1.52
8967 11580 7.827729 GGTTGGTTACATATACTTGGGATATCC 59.172 40.741 13.87 13.87 0.00 2.59
8977 11615 5.632034 ACTTGGGATATCCTCCTTGTAAC 57.368 43.478 21.18 2.02 44.28 2.50
9004 11647 5.581126 TTCTGGAAACCATACATGATTGC 57.419 39.130 0.00 0.00 30.82 3.56
9029 11676 0.031043 TGTTGTCCGGACTACACACG 59.969 55.000 37.19 0.00 40.91 4.49
9101 11776 3.254166 TGGATGCTTCTTCAGTTCAAAGC 59.746 43.478 0.00 0.00 43.41 3.51
9121 11824 4.899502 AGCTGTATACTTGCTTGTTCAGT 58.100 39.130 15.00 0.00 32.61 3.41
9130 11833 1.330521 TGCTTGTTCAGTCGCAGAAAC 59.669 47.619 0.00 0.00 39.69 2.78
9132 11835 2.213499 CTTGTTCAGTCGCAGAAACCT 58.787 47.619 0.00 0.00 39.69 3.50
9140 11845 2.367567 AGTCGCAGAAACCTTAAGTCCA 59.632 45.455 0.97 0.00 39.69 4.02
9167 11872 3.050619 GACTCTGTCGACGAACAATGTT 58.949 45.455 11.62 0.00 0.00 2.71
9204 11909 1.219393 GCCGGTCTCTTCTTCTGGG 59.781 63.158 1.90 0.00 0.00 4.45
9207 11912 1.618888 CCGGTCTCTTCTTCTGGGGTA 60.619 57.143 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 205 5.410602 ACATAGGAGATAGAGGGAGCAAAT 58.589 41.667 0.00 0.00 0.00 2.32
220 264 2.356382 GTGGGTGAGAGAGACGACATAG 59.644 54.545 0.00 0.00 0.00 2.23
221 265 2.366533 GTGGGTGAGAGAGACGACATA 58.633 52.381 0.00 0.00 0.00 2.29
224 268 1.596895 GGGTGGGTGAGAGAGACGAC 61.597 65.000 0.00 0.00 0.00 4.34
226 270 2.701780 CGGGTGGGTGAGAGAGACG 61.702 68.421 0.00 0.00 0.00 4.18
229 273 3.775654 GCCGGGTGGGTGAGAGAG 61.776 72.222 2.18 0.00 38.44 3.20
248 292 2.603580 GATGGGGAAAGGGGGCTC 59.396 66.667 0.00 0.00 0.00 4.70
249 293 3.029981 GGATGGGGAAAGGGGGCT 61.030 66.667 0.00 0.00 0.00 5.19
325 373 2.588314 GGATCTGGCAGCAGCTCG 60.588 66.667 10.34 0.00 41.70 5.03
392 462 3.952931 ACTCAAAGCAGCATCTCAATCT 58.047 40.909 0.00 0.00 0.00 2.40
416 486 7.859613 TCGATTTTAGAGATAGAATGCGAAG 57.140 36.000 0.00 0.00 0.00 3.79
515 595 3.571401 AGTCCTTATGCTGCATAAATGGC 59.429 43.478 28.88 24.11 36.14 4.40
516 596 6.000219 AGTAGTCCTTATGCTGCATAAATGG 59.000 40.000 28.88 26.36 36.14 3.16
517 597 7.502120 AAGTAGTCCTTATGCTGCATAAATG 57.498 36.000 28.88 23.23 36.14 2.32
518 598 8.432805 AGTAAGTAGTCCTTATGCTGCATAAAT 58.567 33.333 28.88 19.32 37.93 1.40
519 599 7.792032 AGTAAGTAGTCCTTATGCTGCATAAA 58.208 34.615 28.88 16.86 37.93 1.40
520 600 7.361457 AGTAAGTAGTCCTTATGCTGCATAA 57.639 36.000 27.82 27.82 37.93 1.90
521 601 6.294010 CGAGTAAGTAGTCCTTATGCTGCATA 60.294 42.308 17.90 17.90 37.93 3.14
522 602 5.508153 CGAGTAAGTAGTCCTTATGCTGCAT 60.508 44.000 20.18 20.18 37.93 3.96
523 603 4.202020 CGAGTAAGTAGTCCTTATGCTGCA 60.202 45.833 4.13 4.13 37.93 4.41
524 604 4.036498 TCGAGTAAGTAGTCCTTATGCTGC 59.964 45.833 0.00 0.00 37.93 5.25
525 605 5.752892 TCGAGTAAGTAGTCCTTATGCTG 57.247 43.478 0.00 0.00 37.93 4.41
526 606 6.963083 AATCGAGTAAGTAGTCCTTATGCT 57.037 37.500 0.00 0.00 37.93 3.79
527 607 7.873910 ACTAATCGAGTAAGTAGTCCTTATGC 58.126 38.462 0.00 0.00 37.93 3.14
531 611 9.850198 AGATAACTAATCGAGTAAGTAGTCCTT 57.150 33.333 0.00 0.00 37.44 3.36
532 612 9.850198 AAGATAACTAATCGAGTAAGTAGTCCT 57.150 33.333 0.00 0.00 37.44 3.85
565 665 1.218316 GTAGCGACCCCAGGACTTG 59.782 63.158 0.00 0.00 0.00 3.16
577 677 2.662596 CTGCCAACCAGGTAGCGA 59.337 61.111 9.45 0.12 43.43 4.93
617 727 2.551459 CCAAACCAGCACAGAGAAGAAG 59.449 50.000 0.00 0.00 0.00 2.85
680 791 7.359264 CGATTATCGATTGTAAGTTTGCCCTAG 60.359 40.741 9.20 0.00 43.74 3.02
706 817 1.801178 CTCTTCGTTTGCCCTGAAGTC 59.199 52.381 1.64 0.00 39.97 3.01
710 821 1.878102 GCTTCTCTTCGTTTGCCCTGA 60.878 52.381 0.00 0.00 0.00 3.86
779 900 9.438291 CAAAACAACTTCAGTACAAATCTACAG 57.562 33.333 0.00 0.00 0.00 2.74
836 957 3.865164 TCTATGTACATCAAACTGCAGCG 59.135 43.478 15.27 2.42 0.00 5.18
863 984 3.781965 TCCACCTGGAGATTCATCATGAA 59.218 43.478 1.59 1.59 38.97 2.57
955 1076 2.126110 CAACAAATTCCCGCCGGC 60.126 61.111 19.07 19.07 0.00 6.13
963 1084 9.185192 CAGTAACTCTTCCAATTCAACAAATTC 57.815 33.333 0.00 0.00 35.32 2.17
1168 1289 3.802948 ACTAGCGGGACTACAGATTTG 57.197 47.619 0.00 0.00 0.00 2.32
1226 1350 4.477536 AGCCCATCTACCAAGAGAGATA 57.522 45.455 0.00 0.00 34.49 1.98
1503 1627 8.383175 TCCTCCAAAACAAGAGATAACTTACAT 58.617 33.333 0.00 0.00 31.43 2.29
1562 1686 6.668541 TCAAGCAATCTAGAAATGTAGCAC 57.331 37.500 0.00 0.00 0.00 4.40
1649 1773 9.855021 AGCAAATTCAAATTACTGTATTACACC 57.145 29.630 0.00 0.00 0.00 4.16
1848 1972 6.312141 TCATGAGTCATGACCTTCCATAAA 57.688 37.500 28.18 5.31 44.60 1.40
1924 2048 4.818314 AGGAACTGGCCCTCCTAG 57.182 61.111 14.87 0.93 40.42 3.02
2051 2176 3.391506 AAAGAGCTGGGTTGCAATTTC 57.608 42.857 0.59 0.00 34.99 2.17
2052 2177 3.843893 AAAAGAGCTGGGTTGCAATTT 57.156 38.095 0.59 0.00 34.99 1.82
2205 2336 7.218204 CGCACTATTTACATTGCCTTTAGTTTC 59.782 37.037 0.00 0.00 0.00 2.78
2351 2482 0.176910 GGAGAGGCTCCTACTGCAAC 59.823 60.000 11.71 0.00 46.41 4.17
2440 2971 3.256879 CACAGGCTAGAGAACTCAGTTCA 59.743 47.826 19.89 0.00 44.11 3.18
2441 2972 3.508012 TCACAGGCTAGAGAACTCAGTTC 59.492 47.826 9.78 9.78 42.25 3.01
2807 3341 2.749621 CCCTAAAACCTCAGACATGTGC 59.250 50.000 1.15 0.00 0.00 4.57
2818 3352 1.285078 GGTCCTCATGCCCTAAAACCT 59.715 52.381 0.00 0.00 0.00 3.50
2819 3353 1.285078 AGGTCCTCATGCCCTAAAACC 59.715 52.381 0.00 0.00 0.00 3.27
2921 3455 5.798125 TTCTTCTGATGCTACAGGATAGG 57.202 43.478 9.92 0.00 38.31 2.57
2946 3480 4.759693 AGACATGTAAAAGAATTGTCGGCA 59.240 37.500 0.00 0.00 41.15 5.69
3184 3731 7.951530 AAATGGAATCATGTTGTTTTCAGTC 57.048 32.000 0.00 0.00 33.18 3.51
3378 3926 7.386851 TCACTGACCTTCTTCATTTAGTAAGG 58.613 38.462 0.00 0.00 42.01 2.69
3864 4434 7.072263 CTGGAATTCAGTCACCTATAGGAAT 57.928 40.000 26.01 10.26 38.64 3.01
3911 4481 4.212150 GTTGAAAAGAGAAAGCTACACGC 58.788 43.478 0.00 0.00 39.57 5.34
4085 4666 7.912250 CAGTTTAGCATTGATGAGGATTAACAC 59.088 37.037 0.00 0.00 0.00 3.32
4210 4791 4.837093 AATCTCGGAGATGGGTTACAAA 57.163 40.909 20.57 0.00 34.65 2.83
4458 5046 6.209361 TCACTGATTAGCATGATTAGTCGAC 58.791 40.000 7.70 7.70 0.00 4.20
5038 5628 8.907885 AGGAATAAGCCTAGTCAATTTGAATTC 58.092 33.333 4.51 6.23 36.22 2.17
5053 5643 3.263425 TGAAACGGAAGAGGAATAAGCCT 59.737 43.478 0.00 0.00 42.17 4.58
5280 5964 0.109781 CAACGTCATCTTTTGGGCGG 60.110 55.000 0.00 0.00 0.00 6.13
5690 6377 5.357596 GTCTTTTACCTCTAGACATCTCCGT 59.642 44.000 0.00 0.00 38.49 4.69
6137 7062 3.194005 ACCCATGTAGCTAAACCATCG 57.806 47.619 0.00 0.00 0.00 3.84
6159 7084 2.299013 CAAATGGCATCTGATCATGGGG 59.701 50.000 0.00 0.00 0.00 4.96
6205 7131 8.200792 AGTAATGCCAACAAACAAAATCAAGTA 58.799 29.630 0.00 0.00 0.00 2.24
6225 7151 6.154445 GGAATGGCATGCATCTAAAGTAATG 58.846 40.000 21.36 0.00 0.00 1.90
6352 7278 3.930229 GACATTTGCGTCCAGTACATGTA 59.070 43.478 0.08 0.08 0.00 2.29
6365 7291 1.021390 AGAAGGCGAGGACATTTGCG 61.021 55.000 0.00 0.00 0.00 4.85
6408 7334 5.769367 ACACATAATCATCATCATTGCAGC 58.231 37.500 0.00 0.00 0.00 5.25
6426 7352 2.224597 TGTCTCACATCAGCCAACACAT 60.225 45.455 0.00 0.00 0.00 3.21
6491 7417 0.737715 GCTCCAGCTACAGTGAACCG 60.738 60.000 0.00 0.00 38.21 4.44
6569 7495 1.144716 GAGATGGCGACTGCATCCA 59.855 57.895 0.00 0.00 45.35 3.41
6732 7658 2.433838 CACCTCAGCAGGCAGTCG 60.434 66.667 0.00 0.00 45.05 4.18
6755 7681 1.748493 GAACACAACAACCTGCTCCAA 59.252 47.619 0.00 0.00 0.00 3.53
6900 7827 3.706594 CCTTGTCTGGTTAGCCTCTATCA 59.293 47.826 0.00 0.00 35.27 2.15
7041 9159 9.820725 CAATAATACAAAATTGATGTGGTGGAT 57.179 29.630 7.26 0.00 35.53 3.41
7110 9228 0.906282 GGGAAGGGTCCGACCACTAA 60.906 60.000 19.43 0.00 46.04 2.24
7111 9229 1.305549 GGGAAGGGTCCGACCACTA 60.306 63.158 19.43 0.00 46.04 2.74
7112 9230 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
7113 9231 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
7114 9232 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
7115 9233 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
7116 9234 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
7117 9235 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
7118 9236 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
7119 9237 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
7120 9238 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
7121 9239 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
7122 9240 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
7123 9241 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
7124 9242 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
7136 9254 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
7139 9257 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
7140 9258 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
7141 9259 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
7142 9260 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
7144 9262 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
7145 9263 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
7146 9264 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
7147 9265 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
7148 9266 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
7149 9267 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
7150 9268 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
7151 9269 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
7152 9270 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
7165 9283 4.713792 AATATATATAGGCCAGGGCAGC 57.286 45.455 16.94 0.00 44.11 5.25
7166 9284 6.252599 TCAAATATATATAGGCCAGGGCAG 57.747 41.667 16.94 0.00 44.11 4.85
7167 9285 6.160282 ACATCAAATATATATAGGCCAGGGCA 59.840 38.462 16.94 1.34 44.11 5.36
7168 9286 6.605119 ACATCAAATATATATAGGCCAGGGC 58.395 40.000 5.01 4.33 41.06 5.19
7169 9287 8.497745 AGAACATCAAATATATATAGGCCAGGG 58.502 37.037 5.01 0.00 0.00 4.45
7301 9419 5.878406 ATTAGGAAAGATGTCATCGGACT 57.122 39.130 7.18 7.24 44.61 3.85
7401 9519 6.019318 CAGCACATTTCCTTTTCTGTTTTCTG 60.019 38.462 0.00 0.00 0.00 3.02
7449 9567 2.028523 GCGATCACGAGTTCATGACTTG 59.971 50.000 0.00 3.05 44.16 3.16
7526 9644 6.462500 ACATCTGATACTGCTGGAATATGTC 58.538 40.000 0.00 0.00 0.00 3.06
7540 9658 4.640789 AAGGACTCGTGACATCTGATAC 57.359 45.455 0.00 0.00 0.00 2.24
7628 9746 6.554419 GTCTGTGCAATACAAATAAGCATCA 58.446 36.000 0.00 0.00 39.20 3.07
7651 9769 2.266055 GCAGAGGTGCCTAAGCGT 59.734 61.111 0.00 0.00 44.72 5.07
7887 10007 2.424601 AGCAAATGACATTGGTCCATCG 59.575 45.455 0.34 0.00 43.65 3.84
7981 10101 6.127925 CCATAAAATCATCACATCCCATACCG 60.128 42.308 0.00 0.00 0.00 4.02
7991 10111 9.859427 GAAAATTCACTCCATAAAATCATCACA 57.141 29.630 0.00 0.00 0.00 3.58
8000 10120 9.077885 AGCAAACTAGAAAATTCACTCCATAAA 57.922 29.630 0.00 0.00 0.00 1.40
8010 10130 4.802999 AGCAGCAGCAAACTAGAAAATTC 58.197 39.130 3.17 0.00 45.49 2.17
8037 10596 3.260380 AGAGACCAGAATTGACCACTCAG 59.740 47.826 0.00 0.00 0.00 3.35
8060 10619 1.686115 GGGTGCTCATACCTGCCAAAT 60.686 52.381 0.00 0.00 40.66 2.32
8115 10674 5.594317 GTGCATAAACTGTTATTGGGAGGAT 59.406 40.000 0.00 0.00 0.00 3.24
8186 10745 4.670765 AGCTGAGAAGATTTCCAACCAAT 58.329 39.130 0.00 0.00 0.00 3.16
8206 10765 2.935201 CAGAGTGCATACCTTCAAGAGC 59.065 50.000 0.00 0.00 0.00 4.09
8223 10782 4.111198 CAAGAATCCGATGACAGACAGAG 58.889 47.826 0.00 0.00 0.00 3.35
8236 10795 1.424493 GCGAGACAGGCAAGAATCCG 61.424 60.000 0.00 0.00 0.00 4.18
8294 10880 4.597079 ACAACTACTTTGACATTGTTGCG 58.403 39.130 0.00 0.00 38.73 4.85
8378 10970 1.470494 CAGAAGCTAGACTGCGACTCA 59.530 52.381 0.00 0.00 38.13 3.41
8436 11028 7.820872 AGATGCAAAGAAACCAAATGGAATAAG 59.179 33.333 6.42 0.00 38.94 1.73
8461 11053 2.015587 ACCGCTAGAACTAGGACGAAG 58.984 52.381 10.30 0.00 33.87 3.79
8504 11096 9.173021 ACATCAATCGTTTCAATATAGTTGGAA 57.827 29.630 0.00 0.00 0.00 3.53
8596 11188 0.453390 GATAGCAGCAACTTGTGGGC 59.547 55.000 0.00 0.00 0.00 5.36
8598 11190 4.171005 CAAATGATAGCAGCAACTTGTGG 58.829 43.478 0.00 0.00 0.00 4.17
8662 11262 4.424566 GCCCAGTTGTGCATGCCG 62.425 66.667 16.68 0.00 0.00 5.69
8747 11351 6.105333 ACATCAGACAGAAGCAGACTATTTC 58.895 40.000 0.00 0.00 0.00 2.17
8775 11379 2.421424 GCTCTGTTCAATGGTGATGGAC 59.579 50.000 0.00 0.00 32.48 4.02
8776 11380 2.040145 TGCTCTGTTCAATGGTGATGGA 59.960 45.455 0.00 0.00 32.48 3.41
8777 11381 2.422479 CTGCTCTGTTCAATGGTGATGG 59.578 50.000 0.00 0.00 32.48 3.51
8787 11398 0.249868 CACGGTTCCTGCTCTGTTCA 60.250 55.000 0.00 0.00 0.00 3.18
8795 11406 0.534203 TCAAGTTCCACGGTTCCTGC 60.534 55.000 0.00 0.00 0.00 4.85
8845 11456 1.956477 ACGGTCGGTATGGTATGGTAC 59.044 52.381 0.00 0.00 0.00 3.34
8873 11484 8.700051 TCCATTGGTAAAAACATATACATTGGG 58.300 33.333 1.86 0.00 0.00 4.12
8884 11495 6.969993 AAAGCTAGTCCATTGGTAAAAACA 57.030 33.333 1.86 0.00 0.00 2.83
8886 11497 7.213678 CCAAAAAGCTAGTCCATTGGTAAAAA 58.786 34.615 1.86 0.00 34.12 1.94
8891 11502 3.165071 CCCAAAAAGCTAGTCCATTGGT 58.835 45.455 1.86 0.00 36.44 3.67
8967 11580 6.495706 GTTTCCAGAAAACAGTTACAAGGAG 58.504 40.000 0.00 0.00 45.49 3.69
9004 11647 0.319211 TAGTCCGGACAACAAGCGTG 60.319 55.000 35.00 0.00 0.00 5.34
9029 11676 1.666189 GCAGCCTCGAGGAAACAATAC 59.334 52.381 35.69 14.33 37.39 1.89
9101 11776 4.201628 GCGACTGAACAAGCAAGTATACAG 60.202 45.833 5.50 0.00 0.00 2.74
9121 11824 2.289444 CCTGGACTTAAGGTTTCTGCGA 60.289 50.000 7.53 0.00 0.00 5.10
9130 11833 1.135333 GAGTCGAGCCTGGACTTAAGG 59.865 57.143 10.87 0.00 44.41 2.69
9132 11835 1.819288 CAGAGTCGAGCCTGGACTTAA 59.181 52.381 10.87 0.00 44.41 1.85
9155 11860 5.053286 CGTTCACAAAGAAACATTGTTCGTC 60.053 40.000 1.83 0.00 38.90 4.20
9163 11868 4.630894 TGCTTCGTTCACAAAGAAACAT 57.369 36.364 0.00 0.00 38.13 2.71
9167 11872 2.287547 GGCATGCTTCGTTCACAAAGAA 60.288 45.455 18.92 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.