Multiple sequence alignment - TraesCS5B01G199000

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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 TraesCS5B01G199000 chr5B 100.000 9637 0 0 1 9637 358639273 358629637 0.000000e+00 17797.0
1 TraesCS5B01G199000 chr5B 97.079 5581 116 11 2398 7952 225539880 225534321 0.000000e+00 9359.0
2 TraesCS5B01G199000 chr5B 94.746 5558 260 6 2410 7954 493652405 493657943 0.000000e+00 8617.0
3 TraesCS5B01G199000 chr5B 95.488 5009 195 12 2971 7952 566068028 566063024 0.000000e+00 7969.0
4 TraesCS5B01G199000 chr5B 76.623 616 120 18 7962 8562 358385325 358384719 1.560000e-82 318.0
5 TraesCS5B01G199000 chr5B 76.232 568 118 17 1403 1960 358381649 358381089 1.580000e-72 285.0
6 TraesCS5B01G199000 chr7B 96.688 5556 169 6 2410 7952 681234920 681229367 0.000000e+00 9226.0
7 TraesCS5B01G199000 chr7B 96.212 4805 135 9 3197 7954 52689762 52684958 0.000000e+00 7821.0
8 TraesCS5B01G199000 chr7B 95.783 3960 154 3 4006 7952 648053904 648049945 0.000000e+00 6375.0
9 TraesCS5B01G199000 chr7B 94.898 1960 77 2 6002 7952 82561243 82559298 0.000000e+00 3044.0
10 TraesCS5B01G199000 chr7B 88.889 333 4 4 7634 7952 52690384 52690071 7.060000e-101 379.0
11 TraesCS5B01G199000 chr7B 84.615 117 18 0 9519 9635 146556804 146556688 6.110000e-22 117.0
12 TraesCS5B01G199000 chr4B 95.866 5491 212 6 2409 7886 200811210 200805722 0.000000e+00 8868.0
13 TraesCS5B01G199000 chr4B 92.793 333 10 2 7634 7952 200811209 200810877 4.070000e-128 470.0
14 TraesCS5B01G199000 chr1D 93.997 5564 291 16 2410 7952 224482759 224488300 0.000000e+00 8384.0
15 TraesCS5B01G199000 chr1D 92.262 1512 106 3 6450 7952 291496764 291495255 0.000000e+00 2134.0
16 TraesCS5B01G199000 chr1D 83.621 116 19 0 9520 9635 154453272 154453157 1.020000e-19 110.0
17 TraesCS5B01G199000 chr7D 93.744 5579 310 13 2410 7952 26398879 26393304 0.000000e+00 8333.0
18 TraesCS5B01G199000 chr2D 93.546 5578 320 11 2410 7952 455988090 455982518 0.000000e+00 8270.0
19 TraesCS5B01G199000 chr2D 93.567 5565 318 13 2410 7953 602410796 602405251 0.000000e+00 8257.0
20 TraesCS5B01G199000 chr4D 93.600 5578 297 16 2410 7952 235440155 235445707 0.000000e+00 8268.0
21 TraesCS5B01G199000 chr3D 93.496 5581 321 12 2409 7953 548603952 548598378 0.000000e+00 8257.0
22 TraesCS5B01G199000 chr3D 93.440 5564 307 24 2410 7952 590763332 590757806 0.000000e+00 8200.0
23 TraesCS5B01G199000 chr3D 76.987 239 43 10 8280 8509 389191444 389191209 1.020000e-24 126.0
24 TraesCS5B01G199000 chr5A 94.083 1690 74 11 7956 9637 406482371 406480700 0.000000e+00 2543.0
25 TraesCS5B01G199000 chr5A 94.809 1098 57 0 1312 2409 406483467 406482370 0.000000e+00 1712.0
26 TraesCS5B01G199000 chr5A 86.200 529 38 13 823 1316 406484060 406483532 3.060000e-149 540.0
27 TraesCS5B01G199000 chr5A 86.686 353 29 10 88 437 406485310 406484973 9.140000e-100 375.0
28 TraesCS5B01G199000 chr5A 75.702 605 130 17 1403 1997 405018681 405018084 4.400000e-73 287.0
29 TraesCS5B01G199000 chr5A 76.132 574 115 17 7962 8523 405039702 405039139 2.050000e-71 281.0
30 TraesCS5B01G199000 chr5A 81.457 151 8 6 494 644 406484659 406484529 1.320000e-18 106.0
31 TraesCS5B01G199000 chr5A 100.000 40 0 0 1629 1668 406484137 406484098 3.730000e-09 75.0
32 TraesCS5B01G199000 chr5D 95.473 1215 52 3 7956 9168 312368957 312367744 0.000000e+00 1936.0
33 TraesCS5B01G199000 chr5D 94.627 1098 59 0 1312 2409 312370053 312368956 0.000000e+00 1701.0
34 TraesCS5B01G199000 chr5D 94.781 479 20 3 9160 9637 312363018 312362544 0.000000e+00 741.0
35 TraesCS5B01G199000 chr5D 91.268 355 31 0 962 1316 312370472 312370118 1.460000e-132 484.0
36 TraesCS5B01G199000 chr5D 75.399 626 133 15 7962 8575 312068168 312067552 5.700000e-72 283.0
37 TraesCS5B01G199000 chr5D 81.370 365 44 10 285 644 312371252 312370907 9.530000e-70 276.0
38 TraesCS5B01G199000 chr5D 83.700 227 27 5 15 239 312371635 312371417 1.270000e-48 206.0
39 TraesCS5B01G199000 chr5D 80.000 250 41 8 8267 8510 312061209 312060963 9.950000e-40 176.0
40 TraesCS5B01G199000 chr5D 82.787 122 21 0 9514 9635 450788692 450788813 1.020000e-19 110.0
41 TraesCS5B01G199000 chr5D 86.364 66 7 2 9435 9499 227591259 227591323 4.830000e-08 71.3
42 TraesCS5B01G199000 chr5D 93.617 47 2 1 823 869 312370595 312370550 1.740000e-07 69.4
43 TraesCS5B01G199000 chr6B 98.230 113 2 0 7840 7952 660245359 660245471 2.120000e-46 198.0
44 TraesCS5B01G199000 chr6B 93.333 45 3 0 9435 9479 355423253 355423297 6.250000e-07 67.6
45 TraesCS5B01G199000 chr2B 79.891 184 30 5 8331 8509 30240002 30240183 2.820000e-25 128.0
46 TraesCS5B01G199000 chr1A 83.898 118 14 5 9520 9635 141778024 141777910 3.680000e-19 108.0
47 TraesCS5B01G199000 chr6A 83.929 112 17 1 9514 9625 103191950 103191840 1.320000e-18 106.0
48 TraesCS5B01G199000 chr7A 82.759 116 20 0 9520 9635 79328260 79328145 4.760000e-18 104.0
49 TraesCS5B01G199000 chr6D 81.967 122 22 0 9514 9635 458773454 458773575 4.760000e-18 104.0
50 TraesCS5B01G199000 chr2A 75.207 242 45 12 8280 8509 19404329 19404567 6.160000e-17 100.0
51 TraesCS5B01G199000 chr2A 86.842 76 8 2 9434 9508 697074589 697074663 6.200000e-12 84.2
52 TraesCS5B01G199000 chrUn 87.500 72 9 0 9435 9506 91455930 91455859 6.200000e-12 84.2
53 TraesCS5B01G199000 chrUn 86.667 75 9 1 9433 9506 49874638 49874564 2.230000e-11 82.4
54 TraesCS5B01G199000 chr1B 87.143 70 6 3 9434 9501 543516174 543516242 1.040000e-09 76.8
55 TraesCS5B01G199000 chr3A 93.878 49 3 0 9430 9478 119632739 119632787 3.730000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G199000 chr5B 358629637 358639273 9636 True 17797.000000 17797 100.000000 1 9637 1 chr5B.!!$R2 9636
1 TraesCS5B01G199000 chr5B 225534321 225539880 5559 True 9359.000000 9359 97.079000 2398 7952 1 chr5B.!!$R1 5554
2 TraesCS5B01G199000 chr5B 493652405 493657943 5538 False 8617.000000 8617 94.746000 2410 7954 1 chr5B.!!$F1 5544
3 TraesCS5B01G199000 chr5B 566063024 566068028 5004 True 7969.000000 7969 95.488000 2971 7952 1 chr5B.!!$R3 4981
4 TraesCS5B01G199000 chr5B 358381089 358385325 4236 True 301.500000 318 76.427500 1403 8562 2 chr5B.!!$R4 7159
5 TraesCS5B01G199000 chr7B 681229367 681234920 5553 True 9226.000000 9226 96.688000 2410 7952 1 chr7B.!!$R4 5542
6 TraesCS5B01G199000 chr7B 648049945 648053904 3959 True 6375.000000 6375 95.783000 4006 7952 1 chr7B.!!$R3 3946
7 TraesCS5B01G199000 chr7B 52684958 52690384 5426 True 4100.000000 7821 92.550500 3197 7954 2 chr7B.!!$R5 4757
8 TraesCS5B01G199000 chr7B 82559298 82561243 1945 True 3044.000000 3044 94.898000 6002 7952 1 chr7B.!!$R1 1950
9 TraesCS5B01G199000 chr4B 200805722 200811210 5488 True 4669.000000 8868 94.329500 2409 7952 2 chr4B.!!$R1 5543
10 TraesCS5B01G199000 chr1D 224482759 224488300 5541 False 8384.000000 8384 93.997000 2410 7952 1 chr1D.!!$F1 5542
11 TraesCS5B01G199000 chr1D 291495255 291496764 1509 True 2134.000000 2134 92.262000 6450 7952 1 chr1D.!!$R2 1502
12 TraesCS5B01G199000 chr7D 26393304 26398879 5575 True 8333.000000 8333 93.744000 2410 7952 1 chr7D.!!$R1 5542
13 TraesCS5B01G199000 chr2D 455982518 455988090 5572 True 8270.000000 8270 93.546000 2410 7952 1 chr2D.!!$R1 5542
14 TraesCS5B01G199000 chr2D 602405251 602410796 5545 True 8257.000000 8257 93.567000 2410 7953 1 chr2D.!!$R2 5543
15 TraesCS5B01G199000 chr4D 235440155 235445707 5552 False 8268.000000 8268 93.600000 2410 7952 1 chr4D.!!$F1 5542
16 TraesCS5B01G199000 chr3D 548598378 548603952 5574 True 8257.000000 8257 93.496000 2409 7953 1 chr3D.!!$R2 5544
17 TraesCS5B01G199000 chr3D 590757806 590763332 5526 True 8200.000000 8200 93.440000 2410 7952 1 chr3D.!!$R3 5542
18 TraesCS5B01G199000 chr5A 406480700 406485310 4610 True 891.833333 2543 90.539167 88 9637 6 chr5A.!!$R3 9549
19 TraesCS5B01G199000 chr5A 405018084 405018681 597 True 287.000000 287 75.702000 1403 1997 1 chr5A.!!$R1 594
20 TraesCS5B01G199000 chr5A 405039139 405039702 563 True 281.000000 281 76.132000 7962 8523 1 chr5A.!!$R2 561
21 TraesCS5B01G199000 chr5D 312367744 312371635 3891 True 778.733333 1936 90.009167 15 9168 6 chr5D.!!$R4 9153
22 TraesCS5B01G199000 chr5D 312067552 312068168 616 True 283.000000 283 75.399000 7962 8575 1 chr5D.!!$R2 613

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
565 945 0.179111 GACCGGACAATCTGCGATGA 60.179 55.000 9.46 0.00 35.25 2.92 F
874 1394 0.247185 CCGCATTTGGTTTGATGCCT 59.753 50.000 3.06 0.00 44.38 4.75 F
889 1409 0.597568 TGCCTTGTTCCATGCTTTCG 59.402 50.000 0.00 0.00 0.00 3.46 F
2063 4341 0.179004 TTTGTGGCACGGTCTCCAAT 60.179 50.000 13.77 0.00 33.57 3.16 F
3265 5544 1.271054 ACGAACCTCAGCAAGCATCTT 60.271 47.619 0.00 0.00 0.00 2.40 F
3757 6037 1.344438 TGTGAGAATGACCGACTTGCT 59.656 47.619 0.00 0.00 0.00 3.91 F
4591 6875 0.655733 GTCACAGTCCACCACAAACG 59.344 55.000 0.00 0.00 0.00 3.60 F
5003 7288 1.070758 CCAGGTGGCGCTGTAGATAAT 59.929 52.381 7.64 0.00 0.00 1.28 F
5078 7364 1.075601 TCATCAGGGCCTGGAAAGTT 58.924 50.000 32.23 8.71 31.51 2.66 F
6735 9033 0.878416 GAGATGATAGGACGCGAGCT 59.122 55.000 15.93 0.00 0.00 4.09 F
7954 10412 1.002773 ACCTGTCCGGTCATAACAACC 59.997 52.381 0.00 0.00 44.93 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 4010 0.905357 AAGCATAGGAACGCTGAGGT 59.095 50.000 0.00 0.0 38.82 3.85 R
1733 4011 1.134699 TCAAGCATAGGAACGCTGAGG 60.135 52.381 0.00 0.0 38.82 3.86 R
2143 4421 1.535204 GGGATGTGGCCCTTTGTGTG 61.535 60.000 0.00 0.0 45.12 3.82 R
3922 6202 0.460311 CGCCGACTTCTACATCCCTT 59.540 55.000 0.00 0.0 0.00 3.95 R
4111 6392 0.108615 CGATGCCGTCCTTCTTCAGT 60.109 55.000 0.00 0.0 0.00 3.41 R
5369 7656 0.395173 TCATCCGGATCTCCACGTCA 60.395 55.000 15.88 0.0 35.14 4.35 R
5951 8238 1.117994 CTCTGCTGGATACTGGCTCA 58.882 55.000 0.00 0.0 37.04 4.26 R
6735 9033 2.060004 CTCGCTTCGGATCGCACCTA 62.060 60.000 1.62 0.0 0.00 3.08 R
7035 9343 1.308998 CAGGTGCAGTTTTCGTCCTT 58.691 50.000 0.00 0.0 0.00 3.36 R
8319 10780 0.863144 TTGTAGAACGGTTTGCTCGC 59.137 50.000 0.00 0.0 0.00 5.03 R
9571 12039 0.532862 AGTGCACAGTGTCGGAAAGG 60.533 55.000 21.04 0.0 0.00 3.11 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
48 49 6.950545 TCCTTTTGTGATTTGTGTACTTACG 58.049 36.000 0.00 0.00 0.00 3.18
50 51 7.442969 TCCTTTTGTGATTTGTGTACTTACGAT 59.557 33.333 0.00 0.00 0.00 3.73
55 56 6.311935 TGTGATTTGTGTACTTACGATAAGGC 59.688 38.462 0.00 0.00 0.00 4.35
82 83 0.606604 GTCTGGCCCGAACTGAACTA 59.393 55.000 0.00 0.00 0.00 2.24
83 84 1.001633 GTCTGGCCCGAACTGAACTAA 59.998 52.381 0.00 0.00 0.00 2.24
92 93 3.600388 CGAACTGAACTAATGGGCTTCT 58.400 45.455 0.00 0.00 0.00 2.85
147 149 2.827921 GGAATTTGAGCCCAGAATGTGT 59.172 45.455 0.00 0.00 0.00 3.72
148 150 3.259123 GGAATTTGAGCCCAGAATGTGTT 59.741 43.478 0.00 0.00 0.00 3.32
191 194 4.398598 GGCCGCGCGAATGTTGTT 62.399 61.111 34.63 0.00 0.00 2.83
252 255 1.670811 GCACACCCAAATCGATCGATT 59.329 47.619 32.29 32.29 45.67 3.34
254 257 2.935849 CACACCCAAATCGATCGATTCA 59.064 45.455 36.05 10.25 43.26 2.57
256 259 4.006989 ACACCCAAATCGATCGATTCAAA 58.993 39.130 36.05 9.09 43.26 2.69
264 267 7.735586 CCAAATCGATCGATTCAAAAACAAAAC 59.264 33.333 36.05 0.00 43.26 2.43
269 272 8.123575 TCGATCGATTCAAAAACAAAACAAGTA 58.876 29.630 15.15 0.00 0.00 2.24
273 276 7.913297 TCGATTCAAAAACAAAACAAGTAGGAG 59.087 33.333 0.00 0.00 0.00 3.69
285 402 9.543018 CAAAACAAGTAGGAGTAAAATCGATTC 57.457 33.333 11.83 0.00 0.00 2.52
409 532 2.124151 GTGCCCTGGGATTGCGAT 60.124 61.111 19.27 0.00 0.00 4.58
444 567 6.334102 TCTTCTCGAGCTCTTCTTAGTTTT 57.666 37.500 12.85 0.00 0.00 2.43
477 600 3.710326 AGATAATGCGTCGCTACTTCA 57.290 42.857 19.50 0.00 0.00 3.02
479 602 5.372547 AGATAATGCGTCGCTACTTCATA 57.627 39.130 19.50 0.00 0.00 2.15
480 603 5.154932 AGATAATGCGTCGCTACTTCATAC 58.845 41.667 19.50 1.60 0.00 2.39
483 606 2.793933 TGCGTCGCTACTTCATACTTC 58.206 47.619 19.50 0.00 0.00 3.01
484 607 2.117910 GCGTCGCTACTTCATACTTCC 58.882 52.381 10.68 0.00 0.00 3.46
553 933 2.871427 GAATGCGATGCGACCGGAC 61.871 63.158 9.46 0.00 0.00 4.79
556 936 2.890474 GCGATGCGACCGGACAAT 60.890 61.111 9.46 0.00 0.00 2.71
557 937 2.871427 GCGATGCGACCGGACAATC 61.871 63.158 9.46 7.51 0.00 2.67
558 938 1.226974 CGATGCGACCGGACAATCT 60.227 57.895 9.46 0.00 0.00 2.40
559 939 1.482621 CGATGCGACCGGACAATCTG 61.483 60.000 9.46 1.75 0.00 2.90
560 940 1.766143 GATGCGACCGGACAATCTGC 61.766 60.000 9.46 0.21 0.00 4.26
563 943 1.226974 CGACCGGACAATCTGCGAT 60.227 57.895 9.46 0.00 35.25 4.58
564 944 1.482621 CGACCGGACAATCTGCGATG 61.483 60.000 9.46 0.00 35.25 3.84
565 945 0.179111 GACCGGACAATCTGCGATGA 60.179 55.000 9.46 0.00 35.25 2.92
567 947 1.143305 CCGGACAATCTGCGATGATC 58.857 55.000 0.00 0.00 35.25 2.92
568 948 1.143305 CGGACAATCTGCGATGATCC 58.857 55.000 0.00 9.42 35.25 3.36
569 949 1.143305 GGACAATCTGCGATGATCCG 58.857 55.000 0.00 0.00 0.00 4.18
570 950 1.539065 GGACAATCTGCGATGATCCGT 60.539 52.381 0.00 0.00 0.00 4.69
571 951 2.205074 GACAATCTGCGATGATCCGTT 58.795 47.619 0.00 0.00 0.00 4.44
573 953 2.352651 ACAATCTGCGATGATCCGTTTG 59.647 45.455 0.00 0.00 0.00 2.93
577 957 3.270027 TCTGCGATGATCCGTTTGATTT 58.730 40.909 0.00 0.00 32.41 2.17
580 960 2.629022 CGATGATCCGTTTGATTTCGC 58.371 47.619 0.00 0.00 34.66 4.70
586 966 1.265635 TCCGTTTGATTTCGCTTGGTG 59.734 47.619 0.00 0.00 0.00 4.17
596 976 1.746615 CGCTTGGTGTGGATCAGGG 60.747 63.158 0.00 0.00 0.00 4.45
641 1027 1.983224 CCGGCAAGGAAGAGGAGAA 59.017 57.895 0.00 0.00 45.00 2.87
645 1116 3.181450 CCGGCAAGGAAGAGGAGAAATAT 60.181 47.826 0.00 0.00 45.00 1.28
658 1129 3.701040 GGAGAAATATGGGCTGAAGCAAA 59.299 43.478 4.43 0.00 44.36 3.68
660 1131 3.131755 AGAAATATGGGCTGAAGCAAAGC 59.868 43.478 4.43 0.00 44.36 3.51
661 1132 1.027357 ATATGGGCTGAAGCAAAGCG 58.973 50.000 4.43 0.00 44.36 4.68
673 1152 4.035558 TGAAGCAAAGCGGATATCATGTTC 59.964 41.667 4.83 3.75 0.00 3.18
685 1164 3.957671 ATCATGTTCTTGTAGCATGCG 57.042 42.857 13.01 0.00 44.16 4.73
702 1181 5.356751 AGCATGCGTTCTCCAAATATGTTTA 59.643 36.000 13.01 0.00 0.00 2.01
719 1205 8.980481 ATATGTTTATTTCCGTCTCCTTGAAT 57.020 30.769 0.00 0.00 0.00 2.57
733 1219 3.585289 TCCTTGAATGGTGTTGGTAGCTA 59.415 43.478 0.00 0.00 0.00 3.32
749 1235 4.339814 GGTAGCTACTGTGCTCTGTAAGAT 59.660 45.833 22.74 3.76 45.62 2.40
755 1241 6.758886 GCTACTGTGCTCTGTAAGATTGTAAT 59.241 38.462 6.91 0.00 45.62 1.89
761 1247 8.094548 TGTGCTCTGTAAGATTGTAATTAGTGT 58.905 33.333 0.00 0.00 45.62 3.55
787 1273 1.021390 CCCTGCGGTTCTGCTGTTAG 61.021 60.000 5.23 0.00 35.36 2.34
813 1299 5.127845 TGTCTACTTCCCTCATGAATCTGAC 59.872 44.000 0.00 0.00 0.00 3.51
814 1300 3.533606 ACTTCCCTCATGAATCTGACG 57.466 47.619 0.00 0.00 0.00 4.35
819 1305 2.674852 CCCTCATGAATCTGACGTGTTG 59.325 50.000 0.00 0.00 0.00 3.33
820 1306 3.588955 CCTCATGAATCTGACGTGTTGA 58.411 45.455 0.00 0.00 0.00 3.18
821 1307 4.186926 CCTCATGAATCTGACGTGTTGAT 58.813 43.478 0.00 0.00 0.00 2.57
869 1389 2.049618 GCGCCGCATTTGGTTTGA 60.050 55.556 3.15 0.00 0.00 2.69
870 1390 1.445926 GCGCCGCATTTGGTTTGAT 60.446 52.632 3.15 0.00 0.00 2.57
871 1391 1.685640 GCGCCGCATTTGGTTTGATG 61.686 55.000 3.15 0.00 0.00 3.07
873 1393 1.360931 GCCGCATTTGGTTTGATGCC 61.361 55.000 3.06 0.00 44.38 4.40
874 1394 0.247185 CCGCATTTGGTTTGATGCCT 59.753 50.000 3.06 0.00 44.38 4.75
875 1395 1.338011 CCGCATTTGGTTTGATGCCTT 60.338 47.619 3.06 0.00 44.38 4.35
876 1396 1.727880 CGCATTTGGTTTGATGCCTTG 59.272 47.619 3.06 0.00 44.38 3.61
877 1397 2.769893 GCATTTGGTTTGATGCCTTGT 58.230 42.857 0.00 0.00 42.09 3.16
878 1398 3.140623 GCATTTGGTTTGATGCCTTGTT 58.859 40.909 0.00 0.00 42.09 2.83
879 1399 3.187022 GCATTTGGTTTGATGCCTTGTTC 59.813 43.478 0.00 0.00 42.09 3.18
880 1400 3.467374 TTTGGTTTGATGCCTTGTTCC 57.533 42.857 0.00 0.00 0.00 3.62
882 1402 2.607499 TGGTTTGATGCCTTGTTCCAT 58.393 42.857 0.00 0.00 0.00 3.41
885 1405 1.927487 TTGATGCCTTGTTCCATGCT 58.073 45.000 0.00 0.00 0.00 3.79
886 1406 1.927487 TGATGCCTTGTTCCATGCTT 58.073 45.000 0.00 0.00 0.00 3.91
888 1408 2.231964 TGATGCCTTGTTCCATGCTTTC 59.768 45.455 0.00 0.00 0.00 2.62
889 1409 0.597568 TGCCTTGTTCCATGCTTTCG 59.402 50.000 0.00 0.00 0.00 3.46
890 1410 0.733909 GCCTTGTTCCATGCTTTCGC 60.734 55.000 0.00 0.00 0.00 4.70
891 1411 0.883833 CCTTGTTCCATGCTTTCGCT 59.116 50.000 0.00 0.00 36.97 4.93
892 1412 2.083774 CCTTGTTCCATGCTTTCGCTA 58.916 47.619 0.00 0.00 36.97 4.26
893 1413 2.096496 CCTTGTTCCATGCTTTCGCTAG 59.904 50.000 0.00 0.00 36.97 3.42
894 1414 2.760634 TGTTCCATGCTTTCGCTAGA 57.239 45.000 0.00 0.00 36.97 2.43
895 1415 2.346803 TGTTCCATGCTTTCGCTAGAC 58.653 47.619 0.00 0.00 36.97 2.59
896 1416 2.289382 TGTTCCATGCTTTCGCTAGACA 60.289 45.455 0.00 0.00 36.97 3.41
897 1417 2.939103 GTTCCATGCTTTCGCTAGACAT 59.061 45.455 0.00 0.00 36.97 3.06
899 1419 2.093500 TCCATGCTTTCGCTAGACATGT 60.093 45.455 0.00 0.00 37.10 3.21
900 1420 2.031314 CCATGCTTTCGCTAGACATGTG 59.969 50.000 1.15 0.00 37.10 3.21
916 1436 4.060900 ACATGTGATGTGTCTGTTCAGTC 58.939 43.478 0.00 0.00 43.01 3.51
917 1437 2.742774 TGTGATGTGTCTGTTCAGTCG 58.257 47.619 0.00 0.00 0.00 4.18
936 1460 4.455533 AGTCGCATTCTCTTTGCAACATTA 59.544 37.500 0.00 0.00 40.14 1.90
941 1465 5.570589 GCATTCTCTTTGCAACATTACTGTC 59.429 40.000 0.00 0.00 39.90 3.51
986 1810 5.047802 CCATTACTCATGTGTTCTGCCTTTT 60.048 40.000 5.63 0.00 0.00 2.27
1015 1839 1.522580 GGCATGGAAGACGAGCCTC 60.523 63.158 0.00 0.00 42.01 4.70
1091 1915 1.005394 TGTTCTCGGGTCGAAAGCC 60.005 57.895 0.00 0.00 39.82 4.35
1107 1931 4.194720 CCGAAGAGGCTCCGGTCG 62.195 72.222 20.04 20.03 38.55 4.79
1119 1943 2.656069 CCGGTCGAAGGTGTGGGAT 61.656 63.158 0.00 0.00 0.00 3.85
1128 1952 0.693049 AGGTGTGGGATGACTTCACC 59.307 55.000 0.00 0.00 45.94 4.02
1143 1967 2.398754 TCACCCCCATCTACATCGAT 57.601 50.000 0.00 0.00 0.00 3.59
1197 2021 2.659016 CAGGTCTTCAGCAGCGGA 59.341 61.111 0.00 0.00 0.00 5.54
1576 3854 7.451255 TCCATGATGGATTCAGTAAGTTTGTTT 59.549 33.333 10.75 0.00 42.67 2.83
1656 3934 4.703093 AGGGAACTGTTCGACAAAGAAAAA 59.297 37.500 13.89 0.00 41.13 1.94
1687 3965 1.143684 AGGAGAAGTTGGCAGCTTTGA 59.856 47.619 17.86 0.00 0.00 2.69
1714 3992 2.159517 CGGGTTTGCTTGAGTGCTTATC 60.160 50.000 0.00 0.00 0.00 1.75
1722 4000 3.276857 CTTGAGTGCTTATCTGTGGCAT 58.723 45.455 0.00 0.00 38.27 4.40
1732 4010 5.936372 GCTTATCTGTGGCATTATGATCTGA 59.064 40.000 0.00 0.00 0.00 3.27
1733 4011 6.128336 GCTTATCTGTGGCATTATGATCTGAC 60.128 42.308 0.00 0.00 0.00 3.51
1836 4114 2.159142 GGATCCTTCCTGCAATGCAAAG 60.159 50.000 9.92 10.90 38.41 2.77
1859 4137 4.798924 GCAACTGAGCCAGGATATACTGAG 60.799 50.000 17.12 8.09 40.97 3.35
1916 4194 2.233676 TCAGCATTACACTGGACGATGT 59.766 45.455 0.00 0.00 35.78 3.06
1917 4195 2.349580 CAGCATTACACTGGACGATGTG 59.650 50.000 0.00 0.00 39.80 3.21
1923 4201 5.456548 TTACACTGGACGATGTGTTTCTA 57.543 39.130 4.10 0.00 43.88 2.10
2022 4300 4.650734 TGTCTGCAAAACATACCTCATCA 58.349 39.130 0.00 0.00 0.00 3.07
2063 4341 0.179004 TTTGTGGCACGGTCTCCAAT 60.179 50.000 13.77 0.00 33.57 3.16
2077 4355 7.169982 CACGGTCTCCAATTCATCTAGTTAATC 59.830 40.741 0.00 0.00 0.00 1.75
2095 4373 2.262266 TCAGGTCATACATGTGGGGA 57.738 50.000 9.11 0.00 30.95 4.81
2097 4375 2.705658 TCAGGTCATACATGTGGGGATC 59.294 50.000 9.11 3.53 30.95 3.36
2106 4384 2.239654 ACATGTGGGGATCGATGAACTT 59.760 45.455 0.54 0.00 0.00 2.66
2115 4393 4.142816 GGGATCGATGAACTTCACAAAGTG 60.143 45.833 0.54 0.00 45.07 3.16
2143 4421 3.782889 AGTCAACAAAGTGTTCCAAGC 57.217 42.857 0.00 0.00 38.77 4.01
2280 4558 9.322773 CATATATACATGGATGAGATGAACACC 57.677 37.037 0.00 0.00 0.00 4.16
2282 4560 4.581309 ACATGGATGAGATGAACACCTT 57.419 40.909 0.00 0.00 0.00 3.50
2334 4612 1.576421 GGGTGCAAAACGAGCTCTG 59.424 57.895 12.85 8.06 0.00 3.35
2394 4672 4.867047 TCGAAAGAGCTAAAGAAGATGCAG 59.133 41.667 0.00 0.00 34.84 4.41
2400 4678 3.940221 AGCTAAAGAAGATGCAGCAGAAG 59.060 43.478 4.07 0.00 34.65 2.85
2406 4684 4.904241 AGAAGATGCAGCAGAAGTTTACT 58.096 39.130 4.07 0.00 0.00 2.24
2407 4685 4.694509 AGAAGATGCAGCAGAAGTTTACTG 59.305 41.667 4.07 0.00 38.27 2.74
2747 5026 3.133003 CCTGTCCGGTCATAACATCTCTT 59.867 47.826 0.00 0.00 0.00 2.85
2774 5053 1.664649 CGCAAACAGCTCGTCCTCA 60.665 57.895 0.00 0.00 42.61 3.86
3044 5323 1.470979 GCCGGAAGCTGAAGACGATAA 60.471 52.381 5.05 0.00 38.99 1.75
3265 5544 1.271054 ACGAACCTCAGCAAGCATCTT 60.271 47.619 0.00 0.00 0.00 2.40
3270 5549 2.290768 ACCTCAGCAAGCATCTTGTCAT 60.291 45.455 8.18 0.00 0.00 3.06
3532 5812 1.447838 TCTGAGGATGAAACGCCGC 60.448 57.895 0.00 0.00 0.00 6.53
3757 6037 1.344438 TGTGAGAATGACCGACTTGCT 59.656 47.619 0.00 0.00 0.00 3.91
4047 6328 2.399611 GAACAAAGATCCGGCGCG 59.600 61.111 0.00 0.00 0.00 6.86
4111 6392 3.524606 GCCGGCCGTGAGCTACTA 61.525 66.667 26.12 0.00 43.05 1.82
4286 6568 1.518774 GATGTTAAGACGGCCCGGA 59.481 57.895 8.57 0.00 0.00 5.14
4299 6581 1.512996 GCCCGGATGATACTCGACGA 61.513 60.000 0.73 0.00 0.00 4.20
4476 6760 2.835431 AGCTCCCGCTCGTATGCT 60.835 61.111 0.00 0.00 45.15 3.79
4591 6875 0.655733 GTCACAGTCCACCACAAACG 59.344 55.000 0.00 0.00 0.00 3.60
4873 7158 2.058001 TCGGCCGAGATGACATGGT 61.058 57.895 27.28 0.00 0.00 3.55
5003 7288 1.070758 CCAGGTGGCGCTGTAGATAAT 59.929 52.381 7.64 0.00 0.00 1.28
5016 7301 8.282592 GCGCTGTAGATAATAATGTCATCAAAA 58.717 33.333 0.00 0.00 0.00 2.44
5078 7364 1.075601 TCATCAGGGCCTGGAAAGTT 58.924 50.000 32.23 8.71 31.51 2.66
5083 7369 2.282180 GGCCTGGAAAGTTGCCGA 60.282 61.111 0.00 0.00 33.59 5.54
5259 7545 1.901948 AAGAGCTCGTCGACCACCA 60.902 57.895 10.58 0.00 0.00 4.17
5578 7865 1.304282 GCTGCAGAAGGGGATCCAA 59.696 57.895 20.43 0.00 34.83 3.53
5919 8206 1.433879 GTCGGCAGTGCTAGTCGAT 59.566 57.895 16.11 0.00 32.46 3.59
5951 8238 2.747135 CGCGGGTAGGAAATTATGGGTT 60.747 50.000 0.00 0.00 0.00 4.11
5969 8256 1.208052 GTTGAGCCAGTATCCAGCAGA 59.792 52.381 0.00 0.00 0.00 4.26
5992 8279 4.923942 CAGCCGCTCGCCATGGAT 62.924 66.667 18.40 0.00 38.78 3.41
6735 9033 0.878416 GAGATGATAGGACGCGAGCT 59.122 55.000 15.93 0.00 0.00 4.09
6759 9057 2.409651 GATCCGAAGCGAGCGTCT 59.590 61.111 9.12 0.00 0.00 4.18
6963 9271 1.415659 CAAATCGGAGAGAGGGCATCT 59.584 52.381 0.00 0.00 43.63 2.90
7439 9777 2.359169 GGTGCCCGACATCTCCTCA 61.359 63.158 0.00 0.00 0.00 3.86
7954 10412 1.002773 ACCTGTCCGGTCATAACAACC 59.997 52.381 0.00 0.00 44.93 3.77
8012 10470 5.041191 ACCTGTAATCATGGATCCTTCAC 57.959 43.478 14.23 3.23 0.00 3.18
8041 10499 4.401022 TGGAATGCATCAAGTCTTGTCTT 58.599 39.130 12.30 1.10 0.00 3.01
8093 10554 3.496884 GCGCGAATTGGACAAGGATATAA 59.503 43.478 12.10 0.00 0.00 0.98
8098 10559 7.466725 CGCGAATTGGACAAGGATATAAAAGAA 60.467 37.037 0.00 0.00 0.00 2.52
8160 10621 7.250032 TCTATGAATATTCTGATCAGGTGGG 57.750 40.000 22.42 0.00 0.00 4.61
8190 10651 2.819608 GCTGCACATCTGGACCTAAAAA 59.180 45.455 0.00 0.00 0.00 1.94
8192 10653 4.676196 GCTGCACATCTGGACCTAAAAATG 60.676 45.833 0.00 0.00 0.00 2.32
8195 10656 3.131046 CACATCTGGACCTAAAAATGGCC 59.869 47.826 0.00 0.00 0.00 5.36
8215 10676 1.812571 CGGAACATTCTTGTGAAGGGG 59.187 52.381 0.00 0.00 38.19 4.79
8276 10737 1.003545 CATTTAGCAAGCGTCCGATGG 60.004 52.381 0.00 0.00 0.00 3.51
8306 10767 2.169832 TCAGTACTTGCAAGAGCCAC 57.830 50.000 32.50 21.24 41.13 5.01
8314 10775 2.743928 CAAGAGCCACGTCCCTGC 60.744 66.667 0.00 0.00 0.00 4.85
8562 11024 5.777850 TCCGATTGTTATCCGATTACAGA 57.222 39.130 0.86 0.00 0.00 3.41
8578 11040 2.047061 ACAGACCTGCACTAACCTCAA 58.953 47.619 0.00 0.00 0.00 3.02
8673 11135 5.056480 CCGAATGTTCCATGTAAGCTGATA 58.944 41.667 0.00 0.00 0.00 2.15
8684 11146 6.873076 CCATGTAAGCTGATATCCTTCTCTTC 59.127 42.308 0.00 0.00 0.00 2.87
8698 11160 7.477945 TCCTTCTCTTCTTCCTAATTTACGT 57.522 36.000 0.00 0.00 0.00 3.57
9026 11494 0.924090 CGTATCCTCTTCAAGCGCAC 59.076 55.000 11.47 0.00 0.00 5.34
9043 11511 2.730090 CGCACTGCATTCACTCCATTTC 60.730 50.000 1.11 0.00 0.00 2.17
9120 11588 2.858344 CAGTTTGACTTGTTCGTCGAGT 59.142 45.455 0.00 3.67 42.92 4.18
9121 11589 2.858344 AGTTTGACTTGTTCGTCGAGTG 59.142 45.455 7.70 0.00 40.56 3.51
9168 11636 4.626081 ACCACCGTGCCTGCTCAC 62.626 66.667 0.00 0.00 0.00 3.51
9194 11662 5.858381 TGCTCTCTGGTTTATATCATGTCC 58.142 41.667 0.00 0.00 0.00 4.02
9213 11681 4.117685 GTCCGGTGTTTCTGGTATATGTC 58.882 47.826 0.00 0.00 42.90 3.06
9214 11682 4.028131 TCCGGTGTTTCTGGTATATGTCT 58.972 43.478 0.00 0.00 42.90 3.41
9215 11683 4.119862 CCGGTGTTTCTGGTATATGTCTG 58.880 47.826 0.00 0.00 37.78 3.51
9216 11684 3.555956 CGGTGTTTCTGGTATATGTCTGC 59.444 47.826 0.00 0.00 0.00 4.26
9217 11685 4.680708 CGGTGTTTCTGGTATATGTCTGCT 60.681 45.833 0.00 0.00 0.00 4.24
9218 11686 4.572389 GGTGTTTCTGGTATATGTCTGCTG 59.428 45.833 0.00 0.00 0.00 4.41
9219 11687 5.178797 GTGTTTCTGGTATATGTCTGCTGT 58.821 41.667 0.00 0.00 0.00 4.40
9220 11688 6.338146 GTGTTTCTGGTATATGTCTGCTGTA 58.662 40.000 0.00 0.00 0.00 2.74
9221 11689 6.986817 GTGTTTCTGGTATATGTCTGCTGTAT 59.013 38.462 0.00 0.00 0.00 2.29
9222 11690 6.986231 TGTTTCTGGTATATGTCTGCTGTATG 59.014 38.462 0.00 0.00 0.00 2.39
9223 11691 6.731292 TTCTGGTATATGTCTGCTGTATGT 57.269 37.500 0.00 0.00 0.00 2.29
9224 11692 6.332735 TCTGGTATATGTCTGCTGTATGTC 57.667 41.667 0.00 0.00 0.00 3.06
9263 11731 1.773410 TGTTGTACCACATGTCGTCG 58.227 50.000 0.00 0.00 0.00 5.12
9352 11820 2.288030 GCTTGTTTCTCTGTGCATTGCT 60.288 45.455 10.49 0.00 0.00 3.91
9502 11970 1.003839 GGTGAAGCCACGTCATCCA 60.004 57.895 0.00 0.00 44.09 3.41
9505 11973 1.067142 GTGAAGCCACGTCATCCACTA 60.067 52.381 0.00 0.00 33.10 2.74
9564 12032 5.107220 GGCTGTGATTCTTTTTCAAGCAATG 60.107 40.000 0.00 0.00 33.12 2.82
9571 12039 8.767085 TGATTCTTTTTCAAGCAATGACAATTC 58.233 29.630 0.00 0.00 37.92 2.17
9577 12045 5.138125 TCAAGCAATGACAATTCCTTTCC 57.862 39.130 0.00 0.00 31.50 3.13
9583 12051 3.485463 TGACAATTCCTTTCCGACACT 57.515 42.857 0.00 0.00 0.00 3.55
9584 12052 3.138304 TGACAATTCCTTTCCGACACTG 58.862 45.455 0.00 0.00 0.00 3.66
9608 12076 6.767902 TGTGCACTCTCAACTTATTTTCTTCT 59.232 34.615 19.41 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.121105 GGGCCTTATCGTAAGTACACAAAT 58.879 41.667 0.84 0.00 39.48 2.32
36 37 3.514706 TGGGCCTTATCGTAAGTACACAA 59.485 43.478 4.53 0.00 39.48 3.33
43 44 3.307379 GGCTGGGCCTTATCGTAAG 57.693 57.895 4.53 0.00 46.69 2.34
66 67 1.339631 CCATTAGTTCAGTTCGGGCCA 60.340 52.381 4.39 0.00 0.00 5.36
74 75 5.248380 AGAAAGAAGCCCATTAGTTCAGT 57.752 39.130 0.00 0.00 0.00 3.41
76 77 5.880901 AGAAGAAAGAAGCCCATTAGTTCA 58.119 37.500 0.00 0.00 0.00 3.18
82 83 4.525874 CCTTGAAGAAGAAAGAAGCCCATT 59.474 41.667 0.00 0.00 0.00 3.16
83 84 4.085009 CCTTGAAGAAGAAAGAAGCCCAT 58.915 43.478 0.00 0.00 0.00 4.00
92 93 4.519906 ACCTCCAACCTTGAAGAAGAAA 57.480 40.909 0.00 0.00 0.00 2.52
189 192 0.250338 AACTGAGGGAGTGGCGAAAC 60.250 55.000 0.00 0.00 34.02 2.78
190 193 0.472471 AAACTGAGGGAGTGGCGAAA 59.528 50.000 0.00 0.00 34.02 3.46
191 194 0.034896 GAAACTGAGGGAGTGGCGAA 59.965 55.000 0.00 0.00 34.02 4.70
239 242 8.265315 TGTTTTGTTTTTGAATCGATCGATTTG 58.735 29.630 36.28 1.34 43.98 2.32
256 259 8.895737 TCGATTTTACTCCTACTTGTTTTGTTT 58.104 29.630 0.00 0.00 0.00 2.83
264 267 5.758784 GGGGAATCGATTTTACTCCTACTTG 59.241 44.000 12.81 0.00 0.00 3.16
269 272 4.299485 AGAGGGGAATCGATTTTACTCCT 58.701 43.478 14.87 14.87 0.00 3.69
273 276 3.496337 GGGGAGAGGGGAATCGATTTTAC 60.496 52.174 12.81 6.03 0.00 2.01
409 532 0.656259 CGAGAAGAGCGTACCGATGA 59.344 55.000 0.00 0.00 0.00 2.92
437 560 9.886132 ATTATCTAGCGAGAAAAGGAAAACTAA 57.114 29.630 0.00 0.00 34.61 2.24
466 589 2.223994 GGGGGAAGTATGAAGTAGCGAC 60.224 54.545 0.00 0.00 0.00 5.19
548 928 1.143305 GATCATCGCAGATTGTCCGG 58.857 55.000 0.00 0.00 45.12 5.14
549 929 1.143305 GGATCATCGCAGATTGTCCG 58.857 55.000 0.00 0.00 45.12 4.79
553 933 2.609002 TCAAACGGATCATCGCAGATTG 59.391 45.455 0.00 0.00 45.12 2.67
556 936 2.602257 ATCAAACGGATCATCGCAGA 57.398 45.000 0.00 0.00 45.75 4.26
557 937 3.611517 GAAATCAAACGGATCATCGCAG 58.388 45.455 0.00 0.00 34.28 5.18
558 938 2.030335 CGAAATCAAACGGATCATCGCA 59.970 45.455 0.00 0.00 37.97 5.10
559 939 2.629022 CGAAATCAAACGGATCATCGC 58.371 47.619 0.00 0.00 37.97 4.58
560 940 2.285220 AGCGAAATCAAACGGATCATCG 59.715 45.455 0.00 0.00 43.02 3.84
563 943 2.161410 CCAAGCGAAATCAAACGGATCA 59.839 45.455 0.00 0.00 34.28 2.92
564 944 2.161609 ACCAAGCGAAATCAAACGGATC 59.838 45.455 0.00 0.00 34.28 3.36
565 945 2.095263 CACCAAGCGAAATCAAACGGAT 60.095 45.455 0.00 0.00 38.05 4.18
567 947 1.001815 ACACCAAGCGAAATCAAACGG 60.002 47.619 0.00 0.00 0.00 4.44
568 948 2.043411 CACACCAAGCGAAATCAAACG 58.957 47.619 0.00 0.00 0.00 3.60
569 949 2.034053 TCCACACCAAGCGAAATCAAAC 59.966 45.455 0.00 0.00 0.00 2.93
570 950 2.302260 TCCACACCAAGCGAAATCAAA 58.698 42.857 0.00 0.00 0.00 2.69
571 951 1.974265 TCCACACCAAGCGAAATCAA 58.026 45.000 0.00 0.00 0.00 2.57
573 953 2.083774 TGATCCACACCAAGCGAAATC 58.916 47.619 0.00 0.00 0.00 2.17
577 957 1.296392 CCTGATCCACACCAAGCGA 59.704 57.895 0.00 0.00 0.00 4.93
580 960 0.322816 CACCCCTGATCCACACCAAG 60.323 60.000 0.00 0.00 0.00 3.61
586 966 0.107017 CCATCACACCCCTGATCCAC 60.107 60.000 0.00 0.00 0.00 4.02
596 976 1.299976 GGACCAGGACCATCACACC 59.700 63.158 2.58 0.00 0.00 4.16
635 1021 2.511218 TGCTTCAGCCCATATTTCTCCT 59.489 45.455 0.00 0.00 41.18 3.69
641 1027 1.406539 CGCTTTGCTTCAGCCCATATT 59.593 47.619 0.00 0.00 41.18 1.28
645 1116 2.769652 ATCCGCTTTGCTTCAGCCCA 62.770 55.000 0.00 0.00 41.18 5.36
658 1129 4.202253 TGCTACAAGAACATGATATCCGCT 60.202 41.667 0.00 0.00 0.00 5.52
660 1131 5.390251 GCATGCTACAAGAACATGATATCCG 60.390 44.000 11.37 0.00 43.04 4.18
661 1132 5.390251 CGCATGCTACAAGAACATGATATCC 60.390 44.000 17.13 0.00 43.04 2.59
673 1152 1.725641 TGGAGAACGCATGCTACAAG 58.274 50.000 17.13 1.61 0.00 3.16
685 1164 8.674607 AGACGGAAATAAACATATTTGGAGAAC 58.325 33.333 0.00 0.00 30.51 3.01
702 1181 3.244911 ACACCATTCAAGGAGACGGAAAT 60.245 43.478 0.00 0.00 33.37 2.17
719 1205 1.270625 GCACAGTAGCTACCAACACCA 60.271 52.381 20.31 0.00 0.00 4.17
733 1219 8.314751 ACTAATTACAATCTTACAGAGCACAGT 58.685 33.333 0.00 0.00 0.00 3.55
749 1235 3.259876 AGGGCGACAGACACTAATTACAA 59.740 43.478 0.00 0.00 0.00 2.41
755 1241 1.292223 GCAGGGCGACAGACACTAA 59.708 57.895 0.00 0.00 0.00 2.24
787 1273 3.895232 TTCATGAGGGAAGTAGACAGC 57.105 47.619 0.00 0.00 0.00 4.40
813 1299 1.725625 GGCGCAACACATCAACACG 60.726 57.895 10.83 0.00 0.00 4.49
814 1300 1.725625 CGGCGCAACACATCAACAC 60.726 57.895 10.83 0.00 0.00 3.32
819 1305 4.505217 CGAGCGGCGCAACACATC 62.505 66.667 35.02 19.99 0.00 3.06
885 1405 3.925379 ACACATCACATGTCTAGCGAAA 58.075 40.909 0.00 0.00 42.70 3.46
886 1406 3.511699 GACACATCACATGTCTAGCGAA 58.488 45.455 0.00 0.00 42.70 4.70
893 1413 4.060900 ACTGAACAGACACATCACATGTC 58.939 43.478 8.87 0.00 45.70 3.06
894 1414 4.060900 GACTGAACAGACACATCACATGT 58.939 43.478 8.87 0.00 46.22 3.21
895 1415 3.122445 CGACTGAACAGACACATCACATG 59.878 47.826 8.87 0.00 0.00 3.21
896 1416 3.320626 CGACTGAACAGACACATCACAT 58.679 45.455 8.87 0.00 0.00 3.21
897 1417 2.742774 CGACTGAACAGACACATCACA 58.257 47.619 8.87 0.00 0.00 3.58
899 1419 1.068434 TGCGACTGAACAGACACATCA 59.932 47.619 8.87 0.00 0.00 3.07
900 1420 1.783284 TGCGACTGAACAGACACATC 58.217 50.000 8.87 0.00 0.00 3.06
916 1436 4.556135 CAGTAATGTTGCAAAGAGAATGCG 59.444 41.667 0.00 0.00 46.76 4.73
917 1437 5.464168 ACAGTAATGTTGCAAAGAGAATGC 58.536 37.500 0.00 0.00 44.08 3.56
958 1482 4.697352 GCAGAACACATGAGTAATGGAACT 59.303 41.667 0.00 0.00 40.94 3.01
959 1483 4.142600 GGCAGAACACATGAGTAATGGAAC 60.143 45.833 0.00 0.00 40.94 3.62
1015 1839 3.004171 CAACCATGGCATTGGAATTGTG 58.996 45.455 13.04 0.00 39.25 3.33
1091 1915 2.600122 CTTCGACCGGAGCCTCTTCG 62.600 65.000 9.46 5.00 31.34 3.79
1095 1919 3.069318 ACCTTCGACCGGAGCCTC 61.069 66.667 9.46 0.00 0.00 4.70
1107 1931 2.427506 GTGAAGTCATCCCACACCTTC 58.572 52.381 0.00 0.00 33.74 3.46
1119 1943 2.335681 TGTAGATGGGGGTGAAGTCA 57.664 50.000 0.00 0.00 0.00 3.41
1197 2021 2.517402 TTTCGCAGGTTGCCGGTT 60.517 55.556 1.90 0.00 41.12 4.44
1252 2076 1.668793 GGGGCTTGTGTTGCATTGC 60.669 57.895 0.46 0.46 0.00 3.56
1466 3744 3.703001 TCTGACCAACCTTCAGATTCC 57.297 47.619 0.00 0.00 43.69 3.01
1576 3854 5.899547 TCTTCACCATAGGATTCAAGCTAGA 59.100 40.000 0.00 0.00 0.00 2.43
1623 3901 4.225942 TCGAACAGTTCCCTAGAGTACCTA 59.774 45.833 7.76 0.00 0.00 3.08
1656 3934 3.217626 CAACTTCTCCTTCAGCTTGGTT 58.782 45.455 0.00 0.00 0.00 3.67
1714 3992 4.063689 GAGGTCAGATCATAATGCCACAG 58.936 47.826 0.00 0.00 0.00 3.66
1722 4000 3.181475 GGAACGCTGAGGTCAGATCATAA 60.181 47.826 11.29 0.00 46.59 1.90
1732 4010 0.905357 AAGCATAGGAACGCTGAGGT 59.095 50.000 0.00 0.00 38.82 3.85
1733 4011 1.134699 TCAAGCATAGGAACGCTGAGG 60.135 52.381 0.00 0.00 38.82 3.86
1836 4114 3.070159 TCAGTATATCCTGGCTCAGTTGC 59.930 47.826 0.00 0.00 33.14 4.17
1859 4137 2.173569 AGACCCCAATCTCCAATAGCAC 59.826 50.000 0.00 0.00 0.00 4.40
1916 4194 6.936335 TGAAGCAACTGAATCATCTAGAAACA 59.064 34.615 0.00 0.00 0.00 2.83
1917 4195 7.332926 TCTGAAGCAACTGAATCATCTAGAAAC 59.667 37.037 0.00 0.00 0.00 2.78
1923 4201 5.991861 AGATCTGAAGCAACTGAATCATCT 58.008 37.500 0.00 0.00 0.00 2.90
2022 4300 2.185004 AGCTACGGTTTGCAGACATT 57.815 45.000 9.87 0.00 0.00 2.71
2063 4341 9.987272 CATGTATGACCTGATTAACTAGATGAA 57.013 33.333 0.00 0.00 0.00 2.57
2077 4355 2.548707 CGATCCCCACATGTATGACCTG 60.549 54.545 0.00 0.00 0.00 4.00
2095 4373 5.122869 CCATCACTTTGTGAAGTTCATCGAT 59.877 40.000 9.18 0.00 45.96 3.59
2097 4375 4.452114 TCCATCACTTTGTGAAGTTCATCG 59.548 41.667 9.18 0.96 45.96 3.84
2106 4384 4.687901 TGACTTCTCCATCACTTTGTGA 57.312 40.909 2.77 2.77 46.90 3.58
2115 4393 5.278022 GGAACACTTTGTTGACTTCTCCATC 60.278 44.000 0.00 0.00 41.28 3.51
2143 4421 1.535204 GGGATGTGGCCCTTTGTGTG 61.535 60.000 0.00 0.00 45.12 3.82
2251 4529 8.824781 GTTCATCTCATCCATGTATATATGCAC 58.175 37.037 5.58 0.00 0.00 4.57
2334 4612 4.511826 CCGTAAAAACTATCCTCTGGATGC 59.488 45.833 9.17 0.00 43.06 3.91
2394 4672 4.870991 GTCCTACCATCAGTAAACTTCTGC 59.129 45.833 0.00 0.00 33.48 4.26
2400 4678 4.961099 ACCCTAGTCCTACCATCAGTAAAC 59.039 45.833 0.00 0.00 0.00 2.01
2406 4684 2.590611 AGGAACCCTAGTCCTACCATCA 59.409 50.000 0.00 0.00 31.06 3.07
2407 4685 3.331718 AGGAACCCTAGTCCTACCATC 57.668 52.381 0.00 0.00 31.06 3.51
2507 4785 3.861797 CCCAACCCTAGCCGCGAT 61.862 66.667 8.23 0.00 0.00 4.58
2774 5053 4.899352 ACACTATCCAGACTTTCAGCTT 57.101 40.909 0.00 0.00 0.00 3.74
3044 5323 2.361610 CGCATTGGGAAGGTGGCT 60.362 61.111 0.00 0.00 0.00 4.75
3265 5544 1.831106 ACCTTATCCGCAGTCATGACA 59.169 47.619 27.02 6.95 0.00 3.58
3270 5549 1.557099 AGTGACCTTATCCGCAGTCA 58.443 50.000 0.00 0.00 36.92 3.41
3532 5812 1.739562 GTCCAGCTTCGCCTGAGTG 60.740 63.158 0.00 0.00 34.77 3.51
3922 6202 0.460311 CGCCGACTTCTACATCCCTT 59.540 55.000 0.00 0.00 0.00 3.95
4047 6328 1.078848 ACGGACTGCTTCTCCATGC 60.079 57.895 0.00 0.00 0.00 4.06
4108 6389 1.629043 TGCCGTCCTTCTTCAGTAGT 58.371 50.000 0.00 0.00 0.00 2.73
4111 6392 0.108615 CGATGCCGTCCTTCTTCAGT 60.109 55.000 0.00 0.00 0.00 3.41
4299 6581 1.670380 GCTCTTCGGCTTCGACTTCTT 60.670 52.381 0.00 0.00 43.17 2.52
4853 7138 1.592669 CATGTCATCTCGGCCGACC 60.593 63.158 27.28 10.29 0.00 4.79
4873 7158 1.522355 CTACCGTCGCCTACCTCGA 60.522 63.158 0.00 0.00 0.00 4.04
4938 7223 2.502213 TTGTCTTCAACGAGCTTCGA 57.498 45.000 11.64 0.00 43.74 3.71
5016 7301 0.995728 CGGCGTTTGTGCTTGTTTTT 59.004 45.000 0.00 0.00 34.52 1.94
5369 7656 0.395173 TCATCCGGATCTCCACGTCA 60.395 55.000 15.88 0.00 35.14 4.35
5679 7966 2.008543 GCTCACGATGATGTTCTGGCA 61.009 52.381 0.00 0.00 0.00 4.92
5951 8238 1.117994 CTCTGCTGGATACTGGCTCA 58.882 55.000 0.00 0.00 37.04 4.26
6270 8558 2.671070 CACCTCTTCGGCCACCAT 59.329 61.111 2.24 0.00 35.61 3.55
6633 8931 2.125269 GCGCTTCCGGGAGCTTTA 60.125 61.111 31.76 0.00 40.52 1.85
6735 9033 2.060004 CTCGCTTCGGATCGCACCTA 62.060 60.000 1.62 0.00 0.00 3.08
6779 9077 2.429930 CCCCTCAACCAGTGCGAA 59.570 61.111 0.00 0.00 0.00 4.70
7035 9343 1.308998 CAGGTGCAGTTTTCGTCCTT 58.691 50.000 0.00 0.00 0.00 3.36
7493 9831 4.608774 TCCGGGACCGTCACCACT 62.609 66.667 10.17 0.00 37.81 4.00
7867 10255 3.013921 CCCGCAAGTTATCTTAGGCAAA 58.986 45.455 0.00 0.00 32.81 3.68
7896 10354 2.635915 CCCACCGGGCATTAGTATTAGA 59.364 50.000 6.32 0.00 35.35 2.10
7954 10412 8.818141 TTAAGCAATAGAGATTCCAGTATTCG 57.182 34.615 0.00 0.00 0.00 3.34
7996 10454 2.239654 ACGGTGTGAAGGATCCATGATT 59.760 45.455 15.82 0.00 0.00 2.57
8012 10470 1.399440 CTTGATGCATTCCAGACGGTG 59.601 52.381 0.00 0.00 0.00 4.94
8041 10499 8.836268 AACAATAATTGTACAACTTAGGACGA 57.164 30.769 11.22 0.00 44.59 4.20
8093 10554 8.031277 GTCATGCACTTCCTGAAAATATTCTTT 58.969 33.333 0.00 0.00 36.48 2.52
8098 10559 6.379133 ACATGTCATGCACTTCCTGAAAATAT 59.621 34.615 12.91 0.00 0.00 1.28
8160 10621 2.538437 CAGATGTGCAGCTAGTGTCTC 58.462 52.381 0.00 0.00 0.00 3.36
8190 10651 1.176527 CACAAGAATGTTCCGGCCAT 58.823 50.000 2.24 0.00 37.82 4.40
8192 10653 1.200020 CTTCACAAGAATGTTCCGGCC 59.800 52.381 0.00 0.00 37.82 6.13
8195 10656 1.812571 CCCCTTCACAAGAATGTTCCG 59.187 52.381 0.00 0.00 37.82 4.30
8215 10676 5.808042 AATATTGCATCAGCGTATCATCC 57.192 39.130 0.00 0.00 46.23 3.51
8276 10737 3.748048 TGCAAGTACTGATCAAGTTCTGC 59.252 43.478 0.00 4.45 40.56 4.26
8314 10775 2.443957 GAACGGTTTGCTCGCCTGTG 62.444 60.000 0.00 0.00 0.00 3.66
8319 10780 0.863144 TTGTAGAACGGTTTGCTCGC 59.137 50.000 0.00 0.00 0.00 5.03
8320 10781 2.159707 CCATTGTAGAACGGTTTGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
8562 11024 1.435256 AGGTTGAGGTTAGTGCAGGT 58.565 50.000 0.00 0.00 0.00 4.00
8605 11067 1.007849 GCACCGTTTGGCATTTCGT 60.008 52.632 0.00 0.00 39.70 3.85
8673 11135 8.080363 ACGTAAATTAGGAAGAAGAGAAGGAT 57.920 34.615 0.00 0.00 0.00 3.24
8696 11158 5.807730 GCTAGTAGCACATGTTACATACG 57.192 43.478 17.47 0.00 41.89 3.06
8979 11447 3.740764 GCATCCAAACAAAACAGCCAAGA 60.741 43.478 0.00 0.00 0.00 3.02
9026 11494 2.686915 GGAGGAAATGGAGTGAATGCAG 59.313 50.000 0.00 0.00 30.11 4.41
9035 11503 1.511613 TAGGGCTGGAGGAAATGGAG 58.488 55.000 0.00 0.00 0.00 3.86
9043 11511 6.936968 AGTAAACTAATATAGGGCTGGAGG 57.063 41.667 0.00 0.00 0.00 4.30
9168 11636 3.982475 TGATATAAACCAGAGAGCAGCG 58.018 45.455 0.00 0.00 0.00 5.18
9173 11641 5.011125 ACCGGACATGATATAAACCAGAGAG 59.989 44.000 9.46 0.00 0.00 3.20
9194 11662 3.555956 GCAGACATATACCAGAAACACCG 59.444 47.826 0.00 0.00 0.00 4.94
9263 11731 9.379791 AGTTACTTAGTAAACCATGCAATAGAC 57.620 33.333 6.38 0.00 29.42 2.59
9319 11787 6.074005 CAGAGAAACAAGCAGTCGAAAATAC 58.926 40.000 0.00 0.00 0.00 1.89
9329 11797 3.305964 CAATGCACAGAGAAACAAGCAG 58.694 45.455 0.00 0.00 35.26 4.24
9502 11970 7.498900 TCGGCTTATCAAATTGATGACATTAGT 59.501 33.333 17.93 0.00 37.70 2.24
9505 11973 6.319658 ACTCGGCTTATCAAATTGATGACATT 59.680 34.615 17.93 0.00 37.70 2.71
9541 12009 5.693104 TCATTGCTTGAAAAAGAATCACAGC 59.307 36.000 0.00 0.00 34.46 4.40
9564 12032 3.058914 CACAGTGTCGGAAAGGAATTGTC 60.059 47.826 0.00 0.00 0.00 3.18
9571 12039 0.532862 AGTGCACAGTGTCGGAAAGG 60.533 55.000 21.04 0.00 0.00 3.11
9577 12045 0.855349 GTTGAGAGTGCACAGTGTCG 59.145 55.000 21.04 0.00 0.00 4.35
9583 12051 6.767902 AGAAGAAAATAAGTTGAGAGTGCACA 59.232 34.615 21.04 0.00 0.00 4.57
9584 12052 7.074502 CAGAAGAAAATAAGTTGAGAGTGCAC 58.925 38.462 9.40 9.40 0.00 4.57
9608 12076 4.933505 TGAACATCAAGATGCCAAAACA 57.066 36.364 9.85 0.20 42.39 2.83


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

AutoCloner maintained by Alex Coulton.