Multiple sequence alignment - TraesCS2D01G312600

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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 TraesCS2D01G312600 chr2D 100.000 4063 0 0 1 4063 402259313 402263375 0.000000e+00 7504.0
1 TraesCS2D01G312600 chr2B 89.240 1394 98 20 688 2045 476416576 476415199 0.000000e+00 1696.0
2 TraesCS2D01G312600 chr2B 85.171 1342 126 33 2034 3325 476411991 476410673 0.000000e+00 1308.0
3 TraesCS2D01G312600 chr2B 87.252 706 69 8 1 689 476417325 476416624 0.000000e+00 785.0
4 TraesCS2D01G312600 chr2B 83.654 520 57 20 3551 4063 476408489 476407991 7.950000e-127 464.0
5 TraesCS2D01G312600 chr2B 96.078 51 1 1 3506 3555 476408638 476408588 9.360000e-12 82.4
6 TraesCS2D01G312600 chr2A 92.086 1112 64 9 782 1879 539324480 539325581 0.000000e+00 1544.0
7 TraesCS2D01G312600 chr2A 87.488 1079 88 20 1877 2926 539325662 539326722 0.000000e+00 1201.0
8 TraesCS2D01G312600 chr2A 83.840 526 42 20 3551 4047 539327444 539327955 1.030000e-125 460.0
9 TraesCS2D01G312600 chr2A 85.158 411 30 16 2922 3324 539326764 539327151 3.810000e-105 392.0
10 TraesCS2D01G312600 chr2A 88.848 269 27 3 1 269 539019055 539019320 1.090000e-85 327.0
11 TraesCS2D01G312600 chr2A 100.000 35 0 0 739 773 539019326 539019360 9.430000e-07 65.8
12 TraesCS2D01G312600 chr4B 79.937 633 104 18 64 692 416211505 416212118 1.040000e-120 444.0
13 TraesCS2D01G312600 chr3D 77.635 778 129 29 1 759 388522650 388521899 8.070000e-117 431.0
14 TraesCS2D01G312600 chr5B 77.760 625 126 13 10 628 234292067 234291450 4.960000e-99 372.0
15 TraesCS2D01G312600 chr7B 76.602 718 139 18 4 711 717168315 717169013 6.420000e-98 368.0
16 TraesCS2D01G312600 chr3B 76.643 715 137 22 1 707 416511969 416511277 6.420000e-98 368.0
17 TraesCS2D01G312600 chr5D 77.338 631 123 17 1 621 9288004 9288624 4.990000e-94 355.0
18 TraesCS2D01G312600 chr5D 76.609 637 122 21 1 622 247750881 247751505 3.920000e-85 326.0
19 TraesCS2D01G312600 chr7A 82.308 390 57 10 311 693 375898471 375898855 1.090000e-85 327.0
20 TraesCS2D01G312600 chr5A 76.108 632 123 25 1 622 7479899 7480512 5.100000e-79 305.0
21 TraesCS2D01G312600 chr5A 78.175 504 92 15 1 495 456743189 456743683 5.100000e-79 305.0


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 TraesCS2D01G312600 chr2D 402259313 402263375 4062 False 7504.00 7504 100.000 1 4063 1 chr2D.!!$F1 4062
1 TraesCS2D01G312600 chr2B 476407991 476417325 9334 True 867.08 1696 88.279 1 4063 5 chr2B.!!$R1 4062
2 TraesCS2D01G312600 chr2A 539324480 539327955 3475 False 899.25 1544 87.143 782 4047 4 chr2A.!!$F2 3265
3 TraesCS2D01G312600 chr4B 416211505 416212118 613 False 444.00 444 79.937 64 692 1 chr4B.!!$F1 628
4 TraesCS2D01G312600 chr3D 388521899 388522650 751 True 431.00 431 77.635 1 759 1 chr3D.!!$R1 758
5 TraesCS2D01G312600 chr5B 234291450 234292067 617 True 372.00 372 77.760 10 628 1 chr5B.!!$R1 618
6 TraesCS2D01G312600 chr7B 717168315 717169013 698 False 368.00 368 76.602 4 711 1 chr7B.!!$F1 707
7 TraesCS2D01G312600 chr3B 416511277 416511969 692 True 368.00 368 76.643 1 707 1 chr3B.!!$R1 706
8 TraesCS2D01G312600 chr5D 9288004 9288624 620 False 355.00 355 77.338 1 621 1 chr5D.!!$F1 620
9 TraesCS2D01G312600 chr5D 247750881 247751505 624 False 326.00 326 76.609 1 622 1 chr5D.!!$F2 621
10 TraesCS2D01G312600 chr5A 7479899 7480512 613 False 305.00 305 76.108 1 622 1 chr5A.!!$F1 621

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
454 478 0.551131 AGGACAAGGATGAAGGGGCT 60.551 55.0 0.0 0.0 0.0 5.19 F
1224 1359 0.180406 CCCGTAGATTTGTCCCCCAG 59.820 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1701 0.395312 GGAACTTCCACTTCCGGTCA 59.605 55.0 0.0 0.0 36.28 4.02 R
3096 6627 0.107897 TGCTTCGCCGACCATAACAT 60.108 50.0 0.0 0.0 0.00 2.71 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
37 38 9.230122 TCATACTCAAAGCAGTGATATCAAAAA 57.770 29.630 7.07 0.00 0.00 1.94
174 179 2.356553 TACACTGTCAACGGGCGC 60.357 61.111 0.00 0.00 0.00 6.53
181 186 1.153628 GTCAACGGGCGCTGACTAT 60.154 57.895 17.47 0.00 37.98 2.12
182 187 1.153647 TCAACGGGCGCTGACTATG 60.154 57.895 7.64 0.00 0.00 2.23
220 239 9.301153 CCCTTGCAAACAATATTTATACTCAAC 57.699 33.333 0.00 0.00 34.61 3.18
226 245 7.859325 AACAATATTTATACTCAACAGGCGT 57.141 32.000 0.00 0.00 0.00 5.68
227 246 7.859325 ACAATATTTATACTCAACAGGCGTT 57.141 32.000 0.00 0.00 35.01 4.84
277 296 3.640967 TGCCAACAAATAGAGCCACTTTT 59.359 39.130 0.00 0.00 0.00 2.27
278 297 3.989817 GCCAACAAATAGAGCCACTTTTG 59.010 43.478 0.00 0.00 35.21 2.44
279 298 3.989817 CCAACAAATAGAGCCACTTTTGC 59.010 43.478 0.00 0.00 33.88 3.68
283 303 2.134789 ATAGAGCCACTTTTGCAGGG 57.865 50.000 0.00 0.00 0.00 4.45
379 403 0.734889 CTGCAATGACGTGGGAATCC 59.265 55.000 0.00 0.00 0.00 3.01
454 478 0.551131 AGGACAAGGATGAAGGGGCT 60.551 55.000 0.00 0.00 0.00 5.19
455 479 1.213296 GGACAAGGATGAAGGGGCTA 58.787 55.000 0.00 0.00 0.00 3.93
456 480 1.777272 GGACAAGGATGAAGGGGCTAT 59.223 52.381 0.00 0.00 0.00 2.97
632 685 5.770162 CCACAGTGAAAACCTAGGAGAAAAT 59.230 40.000 17.98 0.00 0.00 1.82
654 722 8.538409 AAATCAAGGAGTTTAATGTTTGCATC 57.462 30.769 0.00 0.00 33.50 3.91
655 723 6.647334 TCAAGGAGTTTAATGTTTGCATCA 57.353 33.333 0.00 0.00 33.50 3.07
807 938 2.037367 GGGGAAGGCAAAGGGGAC 59.963 66.667 0.00 0.00 0.00 4.46
815 947 1.217942 AGGCAAAGGGGACAAAAGACT 59.782 47.619 0.00 0.00 0.00 3.24
1068 1203 2.278013 GATGGACCGACGACGCTC 60.278 66.667 0.64 0.00 38.29 5.03
1224 1359 0.180406 CCCGTAGATTTGTCCCCCAG 59.820 60.000 0.00 0.00 0.00 4.45
1232 1367 4.270008 AGATTTGTCCCCCAGTTATTTCG 58.730 43.478 0.00 0.00 0.00 3.46
1292 1427 1.858372 AAACGTTGGTGGTATGCGCC 61.858 55.000 4.18 0.00 0.00 6.53
1362 1507 2.189521 GTATCCACCCGCCCACAG 59.810 66.667 0.00 0.00 0.00 3.66
1368 1513 3.168528 ACCCGCCCACAGTCTTGT 61.169 61.111 0.00 0.00 38.31 3.16
1371 1516 1.669115 CCGCCCACAGTCTTGTCAG 60.669 63.158 0.00 0.00 34.62 3.51
1374 1519 0.947244 GCCCACAGTCTTGTCAGTTG 59.053 55.000 0.00 0.00 34.62 3.16
1375 1520 1.597742 CCCACAGTCTTGTCAGTTGG 58.402 55.000 0.00 0.00 34.62 3.77
1391 1538 5.758784 GTCAGTTGGAGTTATAGGGTTATGC 59.241 44.000 0.00 0.00 0.00 3.14
1403 1550 1.655484 GGTTATGCTGCCAATTTGCC 58.345 50.000 0.00 0.00 0.00 4.52
1405 1552 2.001872 GTTATGCTGCCAATTTGCCAC 58.998 47.619 0.00 0.00 0.00 5.01
1476 1632 8.256605 GTGATCTGAGTGTCTAATGCCATATAT 58.743 37.037 0.00 0.00 0.00 0.86
1545 1701 1.149101 TTCTGAAGCCCCTGGACTTT 58.851 50.000 0.00 0.00 0.00 2.66
1599 1755 1.349026 AGTGGTGACATACAGCTGCTT 59.651 47.619 15.27 0.00 46.14 3.91
1719 1875 3.951037 TGATTACATATTTGGCACGGCTT 59.049 39.130 0.00 0.00 0.00 4.35
1721 1877 2.652941 ACATATTTGGCACGGCTTTG 57.347 45.000 0.00 0.00 0.00 2.77
1766 1922 3.871006 TCCGCACTACTTCTTGCAATATG 59.129 43.478 0.00 0.00 38.76 1.78
1767 1923 3.002656 CCGCACTACTTCTTGCAATATGG 59.997 47.826 0.00 0.00 38.76 2.74
1802 1958 7.753580 GGCGCAATTAGATATGTTAAATTACCC 59.246 37.037 10.83 0.00 0.00 3.69
1803 1959 8.293867 GCGCAATTAGATATGTTAAATTACCCA 58.706 33.333 0.30 0.00 0.00 4.51
1854 2012 9.527157 TGATTGGTATTAGTTTTTCTCATGGAA 57.473 29.630 0.00 0.00 0.00 3.53
1857 2015 8.561738 TGGTATTAGTTTTTCTCATGGAAGAC 57.438 34.615 0.00 0.00 35.16 3.01
1899 2140 2.295885 AGGTATCTGCTTGCTTGATGC 58.704 47.619 10.20 9.05 43.25 3.91
1914 2155 5.127356 TGCTTGATGCATGGAATGAATGTAA 59.873 36.000 2.46 0.00 44.65 2.41
1941 2182 8.891720 GCAGAATTGAGAAATGAGAATAGAAGT 58.108 33.333 0.00 0.00 0.00 3.01
2123 5583 7.588512 ACTGCTTTGATCTGAGTATTTTTCAC 58.411 34.615 0.00 0.00 0.00 3.18
2175 5647 2.307098 AGAAGTGCTATGTTGCCCTCTT 59.693 45.455 0.00 0.00 0.00 2.85
2200 5672 7.437713 TTGTGATATAGAGATGTTCTTGGGT 57.562 36.000 0.00 0.00 37.36 4.51
2201 5673 6.820335 TGTGATATAGAGATGTTCTTGGGTG 58.180 40.000 0.00 0.00 37.36 4.61
2202 5674 6.384015 TGTGATATAGAGATGTTCTTGGGTGT 59.616 38.462 0.00 0.00 37.36 4.16
2204 5676 7.225538 GTGATATAGAGATGTTCTTGGGTGTTG 59.774 40.741 0.00 0.00 37.36 3.33
2212 5691 3.139397 TGTTCTTGGGTGTTGGTAAGGAT 59.861 43.478 0.00 0.00 0.00 3.24
2216 5695 4.351407 TCTTGGGTGTTGGTAAGGATACAA 59.649 41.667 0.00 0.00 41.41 2.41
2221 5700 5.126545 GGGTGTTGGTAAGGATACAATTTCC 59.873 44.000 0.00 0.00 41.41 3.13
2226 5705 4.229582 TGGTAAGGATACAATTTCCCTGCT 59.770 41.667 0.00 0.00 41.41 4.24
2227 5706 4.822350 GGTAAGGATACAATTTCCCTGCTC 59.178 45.833 0.00 0.00 41.41 4.26
2233 5712 2.292267 ACAATTTCCCTGCTCTATGCG 58.708 47.619 0.00 0.00 46.63 4.73
2242 5721 3.262420 CCTGCTCTATGCGTTAGTTTGT 58.738 45.455 0.00 0.00 46.63 2.83
2247 5726 5.872617 TGCTCTATGCGTTAGTTTGTAACAT 59.127 36.000 0.00 0.00 46.63 2.71
2254 5733 4.438200 GCGTTAGTTTGTAACATCCATGGG 60.438 45.833 13.02 0.00 0.00 4.00
2271 5750 1.493022 TGGGGAAATATGGCGCTTAGT 59.507 47.619 7.64 0.00 0.00 2.24
2306 5785 8.222984 CAAATTTTGGGTCACTAAAACGATAC 57.777 34.615 0.97 0.00 39.41 2.24
2307 5786 7.754851 AATTTTGGGTCACTAAAACGATACT 57.245 32.000 0.00 0.00 39.41 2.12
2320 5799 4.895668 AACGATACTGTTTCTGGGGTTA 57.104 40.909 0.00 0.00 0.00 2.85
2330 5809 7.787725 CTGTTTCTGGGGTTATAACAGTATC 57.212 40.000 17.16 0.00 40.29 2.24
2333 5812 6.742559 TTCTGGGGTTATAACAGTATCCTC 57.257 41.667 17.16 0.00 34.02 3.71
2343 5822 9.694137 GTTATAACAGTATCCTCTGGTGATTAC 57.306 37.037 10.81 0.00 39.48 1.89
2358 5837 6.371809 GGTGATTACCGATTGCTATTTTCA 57.628 37.500 0.00 0.00 37.19 2.69
2374 5853 7.814107 TGCTATTTTCATCAGTTTTCAATCACC 59.186 33.333 0.00 0.00 0.00 4.02
2377 5856 2.159430 TCATCAGTTTTCAATCACCGCG 59.841 45.455 0.00 0.00 0.00 6.46
2389 5868 3.370231 ACCGCGGCAAATTGGTCC 61.370 61.111 28.58 0.00 0.00 4.46
2429 5908 4.859304 AGATTGTGCTGCATTTCTTCAA 57.141 36.364 5.27 4.50 0.00 2.69
2446 5929 9.865321 ATTTCTTCAAATGTAAACATCAGGATG 57.135 29.630 7.70 7.70 36.57 3.51
2464 5948 5.939883 CAGGATGAGACTTTACACCATTTGA 59.060 40.000 0.00 0.00 39.69 2.69
2497 5981 3.395639 TGTCAGCTTTACCGTTACTTGG 58.604 45.455 0.00 0.00 0.00 3.61
2500 5984 3.810941 TCAGCTTTACCGTTACTTGGTTG 59.189 43.478 0.00 0.00 40.96 3.77
2509 5993 3.004315 CCGTTACTTGGTTGCAAATGACT 59.996 43.478 0.00 0.00 0.00 3.41
2528 6012 2.708861 ACTTGTAATCCCCATCCGCATA 59.291 45.455 0.00 0.00 0.00 3.14
2531 6015 4.753516 TGTAATCCCCATCCGCATATAG 57.246 45.455 0.00 0.00 0.00 1.31
2540 6024 5.702670 CCCCATCCGCATATAGCAAATATAG 59.297 44.000 0.00 0.00 46.13 1.31
2541 6025 6.464322 CCCCATCCGCATATAGCAAATATAGA 60.464 42.308 0.00 0.00 46.13 1.98
2544 6028 5.041287 TCCGCATATAGCAAATATAGACGC 58.959 41.667 0.00 0.00 46.13 5.19
2547 6031 6.036083 CCGCATATAGCAAATATAGACGCTTT 59.964 38.462 0.00 0.00 46.13 3.51
2593 6077 2.049248 CGCACCACATGGCCAAAC 60.049 61.111 10.96 0.00 39.32 2.93
2598 6082 0.752054 ACCACATGGCCAAACTTGTG 59.248 50.000 24.36 24.36 42.71 3.33
2601 6085 2.546373 CCACATGGCCAAACTTGTGAAG 60.546 50.000 30.20 15.83 44.61 3.02
2606 6090 0.463620 GCCAAACTTGTGAAGGCCAA 59.536 50.000 5.01 0.00 39.42 4.52
2607 6091 1.134551 GCCAAACTTGTGAAGGCCAAA 60.135 47.619 5.01 0.00 39.42 3.28
2608 6092 2.825205 CCAAACTTGTGAAGGCCAAAG 58.175 47.619 5.01 2.99 0.00 2.77
2611 6095 3.525268 AACTTGTGAAGGCCAAAGTTG 57.475 42.857 5.01 0.00 0.00 3.16
2617 6101 3.214328 GTGAAGGCCAAAGTTGAAGAGA 58.786 45.455 5.01 0.00 0.00 3.10
2794 6282 9.450807 AGATAAGAAACAAATCAAAACTCAACG 57.549 29.630 0.00 0.00 0.00 4.10
2823 6311 0.250513 GGTTTGATCTGAGGCTCGGT 59.749 55.000 22.18 10.32 0.00 4.69
2862 6350 3.523157 TGCTTCCTGAGATTCATGGGTAA 59.477 43.478 0.00 0.00 0.00 2.85
2867 6355 5.032846 TCCTGAGATTCATGGGTAAGTCTT 58.967 41.667 0.00 0.00 0.00 3.01
2868 6356 5.104776 TCCTGAGATTCATGGGTAAGTCTTG 60.105 44.000 0.00 0.00 0.00 3.02
2898 6386 6.597672 ACACCAAAATATTCTTGCGAGACATA 59.402 34.615 2.11 5.83 0.00 2.29
2899 6387 6.907212 CACCAAAATATTCTTGCGAGACATAC 59.093 38.462 2.11 0.00 0.00 2.39
2937 6465 8.486210 AGCAGGATATCACTACAATTCAACTTA 58.514 33.333 4.83 0.00 0.00 2.24
3026 6554 0.179048 TGCAAGCATCCATAGACCGG 60.179 55.000 0.00 0.00 0.00 5.28
3057 6585 0.107703 TGTGACCCAATCAGATCGGC 60.108 55.000 0.00 0.00 38.28 5.54
3058 6586 0.107703 GTGACCCAATCAGATCGGCA 60.108 55.000 0.00 0.00 38.28 5.69
3080 6611 2.364970 CTGAACCTCCTAGGATGAGCAG 59.635 54.545 19.79 18.95 37.67 4.24
3084 6615 1.412217 CCTCCTAGGATGAGCAGACCA 60.412 57.143 13.12 0.00 37.67 4.02
3089 6620 1.142748 GGATGAGCAGACCAGGACG 59.857 63.158 0.00 0.00 0.00 4.79
3090 6621 1.608717 GGATGAGCAGACCAGGACGT 61.609 60.000 0.00 0.00 0.00 4.34
3096 6627 0.037326 GCAGACCAGGACGTTGATGA 60.037 55.000 0.00 0.00 0.00 2.92
3108 6639 3.194861 ACGTTGATGATGTTATGGTCGG 58.805 45.455 0.00 0.00 0.00 4.79
3128 6659 2.977405 CGAAGCAAGGGAGTTCTTTG 57.023 50.000 0.00 0.00 0.00 2.77
3129 6660 1.537202 CGAAGCAAGGGAGTTCTTTGG 59.463 52.381 0.00 0.00 0.00 3.28
3132 6663 1.705186 AGCAAGGGAGTTCTTTGGCTA 59.295 47.619 0.00 0.00 28.38 3.93
3136 6667 4.082125 CAAGGGAGTTCTTTGGCTACAAT 58.918 43.478 0.00 0.00 36.29 2.71
3138 6669 4.740902 AGGGAGTTCTTTGGCTACAATTT 58.259 39.130 0.00 0.00 36.29 1.82
3139 6670 4.767409 AGGGAGTTCTTTGGCTACAATTTC 59.233 41.667 0.00 0.00 36.29 2.17
3143 6674 5.635120 AGTTCTTTGGCTACAATTTCCTCT 58.365 37.500 0.00 0.00 36.29 3.69
3153 6684 4.178545 ACAATTTCCTCTGCAAAATCCG 57.821 40.909 0.00 0.00 0.00 4.18
3212 6746 7.085746 TGATGTACAGAAATGAGCAAACATTG 58.914 34.615 0.33 0.00 39.88 2.82
3218 6752 8.130307 ACAGAAATGAGCAAACATTGTTTTAC 57.870 30.769 12.02 7.81 39.88 2.01
3259 6796 4.634199 TCGAGTTTATCTGGACCGTTTTT 58.366 39.130 0.00 0.00 0.00 1.94
3261 6798 4.433805 CGAGTTTATCTGGACCGTTTTTCG 60.434 45.833 0.00 0.00 39.52 3.46
3262 6799 4.383173 AGTTTATCTGGACCGTTTTTCGT 58.617 39.130 0.00 0.00 37.94 3.85
3264 6801 1.425412 ATCTGGACCGTTTTTCGTCG 58.575 50.000 0.00 0.00 37.94 5.12
3265 6802 1.203313 CTGGACCGTTTTTCGTCGC 59.797 57.895 0.00 0.00 37.94 5.19
3289 6827 7.062605 CGCTTTGTTTTGAAGAGCATAATGAAT 59.937 33.333 0.00 0.00 33.07 2.57
3290 6828 9.357652 GCTTTGTTTTGAAGAGCATAATGAATA 57.642 29.630 0.00 0.00 33.68 1.75
3308 6847 4.943093 TGAATAATGCTCTTGCTGCTTGTA 59.057 37.500 0.00 0.00 40.48 2.41
3325 6864 5.765677 TGCTTGTAGTTGGCACATAAAACTA 59.234 36.000 0.00 0.00 39.30 2.24
3326 6865 6.072728 TGCTTGTAGTTGGCACATAAAACTAG 60.073 38.462 0.00 0.00 39.30 2.57
3327 6866 6.072673 GCTTGTAGTTGGCACATAAAACTAGT 60.073 38.462 0.00 0.00 39.30 2.57
3329 6868 7.429636 TGTAGTTGGCACATAAAACTAGTTC 57.570 36.000 8.95 0.00 39.30 3.01
3330 6869 5.607119 AGTTGGCACATAAAACTAGTTCG 57.393 39.130 8.95 0.90 39.30 3.95
3331 6870 4.454504 AGTTGGCACATAAAACTAGTTCGG 59.545 41.667 8.95 1.69 39.30 4.30
3332 6871 3.340034 TGGCACATAAAACTAGTTCGGG 58.660 45.455 8.95 0.54 0.00 5.14
3333 6872 2.096980 GGCACATAAAACTAGTTCGGGC 59.903 50.000 8.95 10.34 0.00 6.13
3334 6873 3.007635 GCACATAAAACTAGTTCGGGCT 58.992 45.455 8.95 0.00 0.00 5.19
3335 6874 3.063588 GCACATAAAACTAGTTCGGGCTC 59.936 47.826 8.95 0.00 0.00 4.70
3336 6875 4.504858 CACATAAAACTAGTTCGGGCTCT 58.495 43.478 8.95 0.00 0.00 4.09
3337 6876 4.330074 CACATAAAACTAGTTCGGGCTCTG 59.670 45.833 8.95 3.19 0.00 3.35
3338 6877 4.222145 ACATAAAACTAGTTCGGGCTCTGA 59.778 41.667 8.95 0.00 0.00 3.27
3339 6878 3.764237 AAAACTAGTTCGGGCTCTGAA 57.236 42.857 8.95 0.00 0.00 3.02
3340 6879 3.983044 AAACTAGTTCGGGCTCTGAAT 57.017 42.857 8.95 0.00 0.00 2.57
3341 6880 3.528597 AACTAGTTCGGGCTCTGAATC 57.471 47.619 1.12 0.00 0.00 2.52
3342 6881 2.741145 ACTAGTTCGGGCTCTGAATCT 58.259 47.619 0.00 3.34 0.00 2.40
3343 6882 2.691011 ACTAGTTCGGGCTCTGAATCTC 59.309 50.000 0.00 0.00 0.00 2.75
3344 6883 1.561643 AGTTCGGGCTCTGAATCTCA 58.438 50.000 0.62 0.00 0.00 3.27
3345 6884 2.114616 AGTTCGGGCTCTGAATCTCAT 58.885 47.619 0.62 0.00 0.00 2.90
3346 6885 3.300388 AGTTCGGGCTCTGAATCTCATA 58.700 45.455 0.62 0.00 0.00 2.15
3347 6886 3.900601 AGTTCGGGCTCTGAATCTCATAT 59.099 43.478 0.62 0.00 0.00 1.78
3348 6887 4.346418 AGTTCGGGCTCTGAATCTCATATT 59.654 41.667 0.62 0.00 0.00 1.28
3349 6888 4.263018 TCGGGCTCTGAATCTCATATTG 57.737 45.455 0.00 0.00 0.00 1.90
3350 6889 2.740981 CGGGCTCTGAATCTCATATTGC 59.259 50.000 0.00 0.00 0.00 3.56
3351 6890 3.556633 CGGGCTCTGAATCTCATATTGCT 60.557 47.826 0.00 0.00 0.00 3.91
3352 6891 4.322273 CGGGCTCTGAATCTCATATTGCTA 60.322 45.833 0.00 0.00 0.00 3.49
3353 6892 5.177326 GGGCTCTGAATCTCATATTGCTAG 58.823 45.833 0.00 0.00 0.00 3.42
3354 6893 4.630940 GGCTCTGAATCTCATATTGCTAGC 59.369 45.833 8.10 8.10 0.00 3.42
3355 6894 4.630940 GCTCTGAATCTCATATTGCTAGCC 59.369 45.833 13.29 0.00 0.00 3.93
3356 6895 5.791666 CTCTGAATCTCATATTGCTAGCCA 58.208 41.667 13.29 0.19 0.00 4.75
3357 6896 5.545588 TCTGAATCTCATATTGCTAGCCAC 58.454 41.667 13.29 0.00 0.00 5.01
3358 6897 5.306419 TCTGAATCTCATATTGCTAGCCACT 59.694 40.000 13.29 0.00 0.00 4.00
3359 6898 6.494835 TCTGAATCTCATATTGCTAGCCACTA 59.505 38.462 13.29 1.22 0.00 2.74
3360 6899 6.459066 TGAATCTCATATTGCTAGCCACTAC 58.541 40.000 13.29 0.00 0.00 2.73
3370 6909 2.159170 GCTAGCCACTACCAGAGTTCAG 60.159 54.545 2.29 0.00 35.64 3.02
3404 6943 4.631377 TCACCTTGCTCATTAGATTTCACG 59.369 41.667 0.00 0.00 0.00 4.35
3405 6944 3.941483 ACCTTGCTCATTAGATTTCACGG 59.059 43.478 0.00 0.00 0.00 4.94
3406 6945 3.242870 CCTTGCTCATTAGATTTCACGGC 60.243 47.826 0.00 0.00 0.00 5.68
3408 6947 1.261619 GCTCATTAGATTTCACGGCCG 59.738 52.381 26.86 26.86 0.00 6.13
3411 6950 1.400142 CATTAGATTTCACGGCCGCAA 59.600 47.619 28.58 16.31 0.00 4.85
3413 6952 1.355796 TAGATTTCACGGCCGCAACG 61.356 55.000 28.58 11.92 37.36 4.10
3421 6961 2.047560 GGCCGCAACGACCTAACT 60.048 61.111 0.00 0.00 0.00 2.24
3423 6963 1.495951 GCCGCAACGACCTAACTTG 59.504 57.895 0.00 0.00 0.00 3.16
3426 6966 1.604693 CCGCAACGACCTAACTTGACT 60.605 52.381 0.00 0.00 0.00 3.41
3427 6967 2.352030 CCGCAACGACCTAACTTGACTA 60.352 50.000 0.00 0.00 0.00 2.59
3428 6968 2.660236 CGCAACGACCTAACTTGACTAC 59.340 50.000 0.00 0.00 0.00 2.73
3440 6980 6.590292 CCTAACTTGACTACCAACATACACTG 59.410 42.308 0.00 0.00 0.00 3.66
3441 6981 4.894784 ACTTGACTACCAACATACACTGG 58.105 43.478 0.00 0.00 38.77 4.00
3442 6982 3.328382 TGACTACCAACATACACTGGC 57.672 47.619 0.00 0.00 36.03 4.85
3443 6983 2.635427 TGACTACCAACATACACTGGCA 59.365 45.455 0.00 0.00 36.03 4.92
3444 6984 3.262420 GACTACCAACATACACTGGCAG 58.738 50.000 14.16 14.16 36.03 4.85
3445 6985 2.637872 ACTACCAACATACACTGGCAGT 59.362 45.455 15.88 15.88 34.95 4.40
3446 6986 3.835978 ACTACCAACATACACTGGCAGTA 59.164 43.478 21.59 6.14 37.52 2.74
3447 6987 3.053831 ACCAACATACACTGGCAGTAC 57.946 47.619 21.59 0.00 36.03 2.73
3448 6988 2.370519 ACCAACATACACTGGCAGTACA 59.629 45.455 21.59 11.36 36.03 2.90
3449 6989 3.009033 ACCAACATACACTGGCAGTACAT 59.991 43.478 21.59 13.25 36.03 2.29
3450 6990 3.623060 CCAACATACACTGGCAGTACATC 59.377 47.826 21.59 0.00 0.00 3.06
3451 6991 4.507710 CAACATACACTGGCAGTACATCT 58.492 43.478 21.59 1.21 0.00 2.90
3452 6992 5.395214 CCAACATACACTGGCAGTACATCTA 60.395 44.000 21.59 5.34 0.00 1.98
3453 6993 5.932619 ACATACACTGGCAGTACATCTAA 57.067 39.130 21.59 1.17 0.00 2.10
3454 6994 6.294361 ACATACACTGGCAGTACATCTAAA 57.706 37.500 21.59 0.08 0.00 1.85
3455 6995 6.707290 ACATACACTGGCAGTACATCTAAAA 58.293 36.000 21.59 0.00 0.00 1.52
3456 6996 7.165485 ACATACACTGGCAGTACATCTAAAAA 58.835 34.615 21.59 0.00 0.00 1.94
3488 8586 1.905215 CCTAGGCTACATCTGATGGGG 59.095 57.143 20.83 13.50 33.60 4.96
3489 8587 2.614259 CTAGGCTACATCTGATGGGGT 58.386 52.381 20.83 3.76 33.60 4.95
3493 8591 1.133976 GCTACATCTGATGGGGTGCTT 60.134 52.381 20.83 1.67 33.60 3.91
3498 8596 1.357137 TCTGATGGGGTGCTTGTACA 58.643 50.000 0.00 0.00 0.00 2.90
3499 8597 1.915489 TCTGATGGGGTGCTTGTACAT 59.085 47.619 0.00 0.00 0.00 2.29
3503 8601 1.614996 TGGGGTGCTTGTACATGTTG 58.385 50.000 2.30 0.00 0.00 3.33
3504 8602 1.133637 TGGGGTGCTTGTACATGTTGT 60.134 47.619 2.30 0.00 0.00 3.32
3505 8603 2.106684 TGGGGTGCTTGTACATGTTGTA 59.893 45.455 2.30 0.00 0.00 2.41
3538 8980 6.661805 ACATTACCATTCCAAAATAACCGACT 59.338 34.615 0.00 0.00 0.00 4.18
3546 8988 4.000988 CCAAAATAACCGACTACACAGCT 58.999 43.478 0.00 0.00 0.00 4.24
3547 8989 4.092968 CCAAAATAACCGACTACACAGCTC 59.907 45.833 0.00 0.00 0.00 4.09
3548 8990 2.846039 ATAACCGACTACACAGCTCG 57.154 50.000 0.00 0.00 0.00 5.03
3549 8991 0.169672 TAACCGACTACACAGCTCGC 59.830 55.000 0.00 0.00 0.00 5.03
3572 9118 6.404844 CGCATAGATAGACCTGTATACCAAGG 60.405 46.154 7.54 7.54 0.00 3.61
3573 9119 6.127310 GCATAGATAGACCTGTATACCAAGGG 60.127 46.154 12.58 6.89 0.00 3.95
3622 9168 3.621268 TCTTAACAATCCTTCATTCGCCG 59.379 43.478 0.00 0.00 0.00 6.46
3633 9179 0.591170 CATTCGCCGGTTCAAACAGT 59.409 50.000 1.90 0.00 0.00 3.55
3634 9180 1.801771 CATTCGCCGGTTCAAACAGTA 59.198 47.619 1.90 0.00 0.00 2.74
3699 9247 5.370584 TCATCCTGATAATGATGACAAGGGT 59.629 40.000 0.00 0.00 41.72 4.34
3725 9273 1.237533 TTCATTTGCTCTTGCGCTCA 58.762 45.000 9.73 0.00 43.34 4.26
3794 9342 3.142174 CTCCACAAGAACACCTTCCTTC 58.858 50.000 0.00 0.00 31.42 3.46
3807 9355 0.766131 TTCCTTCGTAAACCTGCCCA 59.234 50.000 0.00 0.00 0.00 5.36
3808 9356 0.766131 TCCTTCGTAAACCTGCCCAA 59.234 50.000 0.00 0.00 0.00 4.12
3809 9357 1.165270 CCTTCGTAAACCTGCCCAAG 58.835 55.000 0.00 0.00 0.00 3.61
3810 9358 1.271163 CCTTCGTAAACCTGCCCAAGA 60.271 52.381 0.00 0.00 0.00 3.02
3811 9359 2.500229 CTTCGTAAACCTGCCCAAGAA 58.500 47.619 0.00 0.00 0.00 2.52
3812 9360 2.178912 TCGTAAACCTGCCCAAGAAG 57.821 50.000 0.00 0.00 0.00 2.85
3813 9361 1.165270 CGTAAACCTGCCCAAGAAGG 58.835 55.000 0.00 0.00 39.65 3.46
3823 9371 1.986882 CCCAAGAAGGCAAGAACACT 58.013 50.000 0.00 0.00 35.39 3.55
3824 9372 1.610522 CCCAAGAAGGCAAGAACACTG 59.389 52.381 0.00 0.00 35.39 3.66
3825 9373 2.301346 CCAAGAAGGCAAGAACACTGT 58.699 47.619 0.00 0.00 0.00 3.55
3879 9472 6.226787 TGACACCAACAAAAGACAAACATTT 58.773 32.000 0.00 0.00 0.00 2.32
3880 9473 6.367422 TGACACCAACAAAAGACAAACATTTC 59.633 34.615 0.00 0.00 0.00 2.17
3926 9520 3.617540 TGTGTATTTTGCCAAGTCACG 57.382 42.857 0.00 0.00 0.00 4.35
3933 9527 0.030504 TTGCCAAGTCACGTGCAATG 59.969 50.000 11.67 8.88 38.68 2.82
3934 9528 0.817229 TGCCAAGTCACGTGCAATGA 60.817 50.000 11.67 0.00 0.00 2.57
3950 9544 2.919859 CAATGAGCATCTAGTATCGGCG 59.080 50.000 0.00 0.00 34.92 6.46
3951 9545 1.605753 TGAGCATCTAGTATCGGCGT 58.394 50.000 6.85 0.00 34.92 5.68
3967 9561 2.651701 GGCGTACTGTGTGATATCGAG 58.348 52.381 0.00 0.00 0.00 4.04
3969 9563 3.058155 GGCGTACTGTGTGATATCGAGAT 60.058 47.826 0.00 0.00 0.00 2.75
3973 9567 6.620949 GCGTACTGTGTGATATCGAGATGTAT 60.621 42.308 0.00 0.00 0.00 2.29
3974 9568 7.412672 GCGTACTGTGTGATATCGAGATGTATA 60.413 40.741 0.00 0.00 0.00 1.47
3975 9569 8.111224 CGTACTGTGTGATATCGAGATGTATAG 58.889 40.741 0.00 0.00 0.00 1.31
3976 9570 7.987750 ACTGTGTGATATCGAGATGTATAGT 57.012 36.000 0.00 0.00 0.00 2.12
3988 9582 6.930164 TCGAGATGTATAGTCAGAGGTTCTAC 59.070 42.308 0.00 0.00 0.00 2.59
3992 9586 5.506708 TGTATAGTCAGAGGTTCTACTGCA 58.493 41.667 0.00 0.00 34.57 4.41
4012 9608 3.181511 GCACGCAATGAAGCTTGTATGTA 60.182 43.478 2.10 0.00 36.29 2.29
4018 9614 6.746822 CGCAATGAAGCTTGTATGTATTTCAA 59.253 34.615 2.10 0.00 0.00 2.69
4024 9620 7.611467 TGAAGCTTGTATGTATTTCAAGGACAT 59.389 33.333 2.10 0.00 38.93 3.06
4028 9624 6.925610 TGTATGTATTTCAAGGACATCTGC 57.074 37.500 0.00 0.00 35.48 4.26
4029 9625 5.822519 TGTATGTATTTCAAGGACATCTGCC 59.177 40.000 0.00 0.00 35.48 4.85
4057 9653 7.671302 AGTGTTTCTAGTGTATATATGCCAGG 58.329 38.462 0.00 0.00 0.00 4.45
4058 9654 7.290248 AGTGTTTCTAGTGTATATATGCCAGGT 59.710 37.037 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.547372 GCATGCCAAATCCACAAGTCT 59.453 47.619 6.36 0.00 0.00 3.24
220 239 1.268539 GGTCTTCACAAACAACGCCTG 60.269 52.381 0.00 0.00 0.00 4.85
226 245 6.599244 GGATCAGATATGGTCTTCACAAACAA 59.401 38.462 0.00 0.00 34.00 2.83
227 246 6.115446 GGATCAGATATGGTCTTCACAAACA 58.885 40.000 0.00 0.00 34.00 2.83
279 298 3.313526 CCTATCTCGTTTTTGCATCCCTG 59.686 47.826 0.00 0.00 0.00 4.45
283 303 4.876107 TCCTTCCTATCTCGTTTTTGCATC 59.124 41.667 0.00 0.00 0.00 3.91
293 313 0.244994 CCCGCATCCTTCCTATCTCG 59.755 60.000 0.00 0.00 0.00 4.04
379 403 3.189080 TCATCAATTGCCACAAAGTCTCG 59.811 43.478 0.00 0.00 0.00 4.04
454 478 7.013846 GGTTTATCAAAATCATGGGTTCGGATA 59.986 37.037 0.00 0.00 0.00 2.59
455 479 6.183360 GGTTTATCAAAATCATGGGTTCGGAT 60.183 38.462 0.00 0.00 0.00 4.18
456 480 5.126384 GGTTTATCAAAATCATGGGTTCGGA 59.874 40.000 0.00 0.00 0.00 4.55
632 685 6.647334 TGATGCAAACATTAAACTCCTTGA 57.353 33.333 0.00 0.00 36.35 3.02
654 722 7.811236 ACAGAAAATGTATTTGAGAAGTGCATG 59.189 33.333 0.00 0.00 41.60 4.06
655 723 7.889469 ACAGAAAATGTATTTGAGAAGTGCAT 58.111 30.769 0.00 0.00 41.60 3.96
983 1118 1.451567 ATCGGACGCGAGAGAGGAA 60.452 57.895 15.93 0.00 34.13 3.36
984 1119 2.180862 CATCGGACGCGAGAGAGGA 61.181 63.158 15.93 0.89 34.13 3.71
985 1120 2.329690 CATCGGACGCGAGAGAGG 59.670 66.667 15.93 6.41 34.13 3.69
1046 1181 2.441532 TCGTCGGTCCATCCCCTC 60.442 66.667 0.00 0.00 0.00 4.30
1047 1182 2.758737 GTCGTCGGTCCATCCCCT 60.759 66.667 0.00 0.00 0.00 4.79
1068 1203 0.170339 TGATGTGGTACAGCTCGTCG 59.830 55.000 0.00 0.00 41.80 5.12
1165 1300 5.791303 ATTAGGGTTTAAGCAGGGTTACT 57.209 39.130 0.00 0.00 0.00 2.24
1224 1359 4.119442 TGGACTACTGGAGCGAAATAAC 57.881 45.455 0.00 0.00 0.00 1.89
1232 1367 4.557695 CGAGATACATTGGACTACTGGAGC 60.558 50.000 0.00 0.00 0.00 4.70
1292 1427 4.565962 CAGCAACATCAGCAGAGTAAGTAG 59.434 45.833 0.00 0.00 0.00 2.57
1349 1494 3.953775 AAGACTGTGGGCGGGTGG 61.954 66.667 0.00 0.00 0.00 4.61
1351 1496 3.168528 ACAAGACTGTGGGCGGGT 61.169 61.111 0.00 0.00 33.30 5.28
1354 1499 0.532862 AACTGACAAGACTGTGGGCG 60.533 55.000 0.00 0.00 35.30 6.13
1357 1502 2.158900 ACTCCAACTGACAAGACTGTGG 60.159 50.000 0.00 0.00 35.30 4.17
1362 1507 5.046520 ACCCTATAACTCCAACTGACAAGAC 60.047 44.000 0.00 0.00 0.00 3.01
1368 1513 5.665812 AGCATAACCCTATAACTCCAACTGA 59.334 40.000 0.00 0.00 0.00 3.41
1371 1516 4.515567 GCAGCATAACCCTATAACTCCAAC 59.484 45.833 0.00 0.00 0.00 3.77
1374 1519 3.072476 TGGCAGCATAACCCTATAACTCC 59.928 47.826 0.00 0.00 0.00 3.85
1375 1520 4.351874 TGGCAGCATAACCCTATAACTC 57.648 45.455 0.00 0.00 0.00 3.01
1403 1550 0.877071 GAGTGACAATGGCCACTGTG 59.123 55.000 27.07 17.60 43.02 3.66
1405 1552 1.002888 AGAGAGTGACAATGGCCACTG 59.997 52.381 13.78 13.78 43.02 3.66
1429 1584 3.476552 CAGGTGAACTGGTTACACACAT 58.523 45.455 0.00 0.00 43.70 3.21
1476 1632 7.386851 CCTCTAGGTTGTAGAACTGAAAATGA 58.613 38.462 2.43 0.00 32.15 2.57
1545 1701 0.395312 GGAACTTCCACTTCCGGTCA 59.605 55.000 0.00 0.00 36.28 4.02
1599 1755 5.560722 TTGTGACTGGTATCTTCTTGGAA 57.439 39.130 0.00 0.00 0.00 3.53
1669 1825 7.712797 TCTTGCTCTCACATAAACGATATACA 58.287 34.615 0.00 0.00 0.00 2.29
1674 1830 5.349817 CACTTCTTGCTCTCACATAAACGAT 59.650 40.000 0.00 0.00 0.00 3.73
1675 1831 4.686091 CACTTCTTGCTCTCACATAAACGA 59.314 41.667 0.00 0.00 0.00 3.85
1719 1875 3.840437 GCAGTTGCCTCACCACAA 58.160 55.556 0.00 0.00 34.31 3.33
1736 1892 0.818296 AAGTAGTGCGGACTAGCTGG 59.182 55.000 17.84 0.00 35.24 4.85
1766 1922 2.293122 TCTAATTGCGCCATAACATGCC 59.707 45.455 4.18 0.00 0.00 4.40
1767 1923 3.624326 TCTAATTGCGCCATAACATGC 57.376 42.857 4.18 0.00 0.00 4.06
1850 2007 2.754552 GCATAAACTGGCATGTCTTCCA 59.245 45.455 0.00 0.00 0.00 3.53
1875 2116 4.128925 TCAAGCAAGCAGATACCTAGTG 57.871 45.455 0.00 0.00 0.00 2.74
1899 2140 7.485810 TCAATTCTGCTTACATTCATTCCATG 58.514 34.615 0.00 0.00 0.00 3.66
1900 2141 7.558807 TCTCAATTCTGCTTACATTCATTCCAT 59.441 33.333 0.00 0.00 0.00 3.41
1901 2142 6.885918 TCTCAATTCTGCTTACATTCATTCCA 59.114 34.615 0.00 0.00 0.00 3.53
1902 2143 7.325660 TCTCAATTCTGCTTACATTCATTCC 57.674 36.000 0.00 0.00 0.00 3.01
1903 2144 9.798994 ATTTCTCAATTCTGCTTACATTCATTC 57.201 29.630 0.00 0.00 0.00 2.67
1904 2145 9.582431 CATTTCTCAATTCTGCTTACATTCATT 57.418 29.630 0.00 0.00 0.00 2.57
1905 2146 8.963725 TCATTTCTCAATTCTGCTTACATTCAT 58.036 29.630 0.00 0.00 0.00 2.57
1914 2155 9.111613 CTTCTATTCTCATTTCTCAATTCTGCT 57.888 33.333 0.00 0.00 0.00 4.24
1923 2164 8.954950 TGATCCAACTTCTATTCTCATTTCTC 57.045 34.615 0.00 0.00 0.00 2.87
1941 2182 9.123902 CCAAAACTGATATATGAACTGATCCAA 57.876 33.333 0.00 0.00 0.00 3.53
2084 5544 8.152898 AGATCAAAGCAGTCACATATATAAGCA 58.847 33.333 0.00 0.00 0.00 3.91
2089 5549 7.733969 ACTCAGATCAAAGCAGTCACATATAT 58.266 34.615 0.00 0.00 0.00 0.86
2093 5553 4.283363 ACTCAGATCAAAGCAGTCACAT 57.717 40.909 0.00 0.00 0.00 3.21
2094 5554 3.758755 ACTCAGATCAAAGCAGTCACA 57.241 42.857 0.00 0.00 0.00 3.58
2175 5647 7.770433 CACCCAAGAACATCTCTATATCACAAA 59.230 37.037 0.00 0.00 32.46 2.83
2200 5672 5.949354 CAGGGAAATTGTATCCTTACCAACA 59.051 40.000 0.00 0.00 37.14 3.33
2201 5673 5.163550 GCAGGGAAATTGTATCCTTACCAAC 60.164 44.000 0.00 0.00 37.14 3.77
2202 5674 4.953579 GCAGGGAAATTGTATCCTTACCAA 59.046 41.667 0.00 0.00 37.14 3.67
2204 5676 4.793201 AGCAGGGAAATTGTATCCTTACC 58.207 43.478 0.00 0.00 37.14 2.85
2212 5691 3.118408 ACGCATAGAGCAGGGAAATTGTA 60.118 43.478 0.00 0.00 46.13 2.41
2216 5695 2.717639 AACGCATAGAGCAGGGAAAT 57.282 45.000 0.00 0.00 46.13 2.17
2221 5700 3.262420 ACAAACTAACGCATAGAGCAGG 58.738 45.455 3.09 0.00 46.13 4.85
2226 5705 6.399743 TGGATGTTACAAACTAACGCATAGA 58.600 36.000 3.09 0.00 35.47 1.98
2227 5706 6.656314 TGGATGTTACAAACTAACGCATAG 57.344 37.500 0.00 0.00 37.66 2.23
2233 5712 5.258051 TCCCCATGGATGTTACAAACTAAC 58.742 41.667 15.22 0.00 35.03 2.34
2242 5721 4.415596 GCCATATTTCCCCATGGATGTTA 58.584 43.478 15.22 0.00 43.80 2.41
2247 5726 0.539438 GCGCCATATTTCCCCATGGA 60.539 55.000 15.22 0.00 43.80 3.41
2254 5733 3.002348 GTGTGACTAAGCGCCATATTTCC 59.998 47.826 2.29 0.00 0.00 3.13
2263 5742 1.298157 TGGCATGTGTGACTAAGCGC 61.298 55.000 0.00 0.00 33.19 5.92
2292 5771 5.929992 CCCAGAAACAGTATCGTTTTAGTGA 59.070 40.000 0.00 0.00 39.17 3.41
2301 5780 6.342906 TGTTATAACCCCAGAAACAGTATCG 58.657 40.000 13.01 0.00 0.00 2.92
2307 5786 6.655930 GGATACTGTTATAACCCCAGAAACA 58.344 40.000 13.01 0.00 0.00 2.83
2330 5809 2.158900 AGCAATCGGTAATCACCAGAGG 60.159 50.000 0.00 0.00 46.14 3.69
2333 5812 6.038161 TGAAAATAGCAATCGGTAATCACCAG 59.962 38.462 0.00 0.00 46.14 4.00
2343 5822 7.028962 TGAAAACTGATGAAAATAGCAATCGG 58.971 34.615 0.00 0.00 0.00 4.18
2344 5823 8.451687 TTGAAAACTGATGAAAATAGCAATCG 57.548 30.769 0.00 0.00 0.00 3.34
2356 5835 2.159430 CGCGGTGATTGAAAACTGATGA 59.841 45.455 0.00 0.00 0.00 2.92
2357 5836 2.508867 CGCGGTGATTGAAAACTGATG 58.491 47.619 0.00 0.00 0.00 3.07
2358 5837 1.468520 CCGCGGTGATTGAAAACTGAT 59.531 47.619 19.50 0.00 0.00 2.90
2374 5853 1.154035 GAAGGACCAATTTGCCGCG 60.154 57.895 0.00 0.00 0.00 6.46
2377 5856 3.752747 CCATTTTGAAGGACCAATTTGCC 59.247 43.478 0.00 0.00 0.00 4.52
2389 5868 7.113404 CACAATCTTTCGTGTACCATTTTGAAG 59.887 37.037 0.00 0.00 0.00 3.02
2406 5885 5.204409 TGAAGAAATGCAGCACAATCTTT 57.796 34.783 16.31 5.78 38.14 2.52
2429 5908 9.167311 GTAAAGTCTCATCCTGATGTTTACATT 57.833 33.333 17.45 11.66 36.98 2.71
2435 5918 5.013079 TGGTGTAAAGTCTCATCCTGATGTT 59.987 40.000 7.00 0.00 39.72 2.71
2446 5929 5.562890 GCCAAGTCAAATGGTGTAAAGTCTC 60.563 44.000 0.00 0.00 40.23 3.36
2464 5948 2.283145 AGCTGACATTCTTGCCAAGT 57.717 45.000 4.04 0.00 0.00 3.16
2497 5981 4.021544 TGGGGATTACAAGTCATTTGCAAC 60.022 41.667 0.00 0.00 40.59 4.17
2500 5984 4.202151 GGATGGGGATTACAAGTCATTTGC 60.202 45.833 0.00 0.00 40.59 3.68
2509 5993 4.625324 GCTATATGCGGATGGGGATTACAA 60.625 45.833 0.00 0.00 0.00 2.41
2540 6024 0.392461 TACCAGGGATGCAAAGCGTC 60.392 55.000 2.68 2.68 43.13 5.19
2541 6025 0.676782 GTACCAGGGATGCAAAGCGT 60.677 55.000 0.00 0.00 0.00 5.07
2544 6028 1.271871 TGGTGTACCAGGGATGCAAAG 60.272 52.381 0.00 0.00 42.01 2.77
2547 6031 4.241769 TGGTGTACCAGGGATGCA 57.758 55.556 0.00 0.00 42.01 3.96
2588 6072 2.168313 ACTTTGGCCTTCACAAGTTTGG 59.832 45.455 3.32 0.00 0.00 3.28
2593 6077 3.381272 TCTTCAACTTTGGCCTTCACAAG 59.619 43.478 3.32 0.96 0.00 3.16
2598 6082 3.214328 TGTCTCTTCAACTTTGGCCTTC 58.786 45.455 3.32 0.00 0.00 3.46
2601 6085 4.385358 TTTTGTCTCTTCAACTTTGGCC 57.615 40.909 0.00 0.00 0.00 5.36
2604 6088 4.746611 GGGCATTTTGTCTCTTCAACTTTG 59.253 41.667 0.00 0.00 0.00 2.77
2606 6090 4.218312 AGGGCATTTTGTCTCTTCAACTT 58.782 39.130 0.00 0.00 0.00 2.66
2607 6091 3.837355 AGGGCATTTTGTCTCTTCAACT 58.163 40.909 0.00 0.00 0.00 3.16
2608 6092 4.590850 AAGGGCATTTTGTCTCTTCAAC 57.409 40.909 0.00 0.00 0.00 3.18
2633 6117 6.151144 TCTCATGTAATCGAAGTGAACTCTGA 59.849 38.462 0.00 0.00 0.00 3.27
2634 6118 6.325596 TCTCATGTAATCGAAGTGAACTCTG 58.674 40.000 0.00 0.00 0.00 3.35
2794 6282 3.486383 TCAGATCAAACCCTGGAAACAC 58.514 45.455 0.00 0.00 35.60 3.32
2868 6356 4.621034 CGCAAGAATATTTTGGTGTTGACC 59.379 41.667 10.41 0.00 41.27 4.02
2906 6394 4.486125 TGTAGTGATATCCTGCTTGCAA 57.514 40.909 0.00 0.00 0.00 4.08
2907 6395 4.486125 TTGTAGTGATATCCTGCTTGCA 57.514 40.909 0.00 0.00 0.00 4.08
2908 6396 5.528690 TGAATTGTAGTGATATCCTGCTTGC 59.471 40.000 0.00 0.00 0.00 4.01
2909 6397 7.281774 AGTTGAATTGTAGTGATATCCTGCTTG 59.718 37.037 0.00 0.00 0.00 4.01
2910 6398 7.341805 AGTTGAATTGTAGTGATATCCTGCTT 58.658 34.615 0.00 0.00 0.00 3.91
2912 6400 7.559590 AAGTTGAATTGTAGTGATATCCTGC 57.440 36.000 0.00 1.73 0.00 4.85
3026 6554 1.004277 TGGGTCACAATAGCCTCAACC 59.996 52.381 0.00 0.00 37.91 3.77
3057 6585 2.102252 GCTCATCCTAGGAGGTTCAGTG 59.898 54.545 22.23 11.24 36.53 3.66
3058 6586 2.292521 TGCTCATCCTAGGAGGTTCAGT 60.293 50.000 22.23 0.00 36.53 3.41
3080 6611 2.386661 ACATCATCAACGTCCTGGTC 57.613 50.000 0.00 0.00 0.00 4.02
3084 6615 4.442706 GACCATAACATCATCAACGTCCT 58.557 43.478 0.00 0.00 0.00 3.85
3089 6620 2.032894 CGCCGACCATAACATCATCAAC 60.033 50.000 0.00 0.00 0.00 3.18
3090 6621 2.159028 TCGCCGACCATAACATCATCAA 60.159 45.455 0.00 0.00 0.00 2.57
3096 6627 0.107897 TGCTTCGCCGACCATAACAT 60.108 50.000 0.00 0.00 0.00 2.71
3108 6639 1.068954 CAAAGAACTCCCTTGCTTCGC 60.069 52.381 0.00 0.00 0.00 4.70
3124 6655 3.507233 TGCAGAGGAAATTGTAGCCAAAG 59.493 43.478 0.00 0.00 33.44 2.77
3127 6658 2.877097 TGCAGAGGAAATTGTAGCCA 57.123 45.000 0.00 0.00 0.00 4.75
3128 6659 4.519540 TTTTGCAGAGGAAATTGTAGCC 57.480 40.909 0.00 0.00 0.00 3.93
3129 6660 5.105063 GGATTTTGCAGAGGAAATTGTAGC 58.895 41.667 0.00 0.00 0.00 3.58
3132 6663 3.826157 TCGGATTTTGCAGAGGAAATTGT 59.174 39.130 0.00 0.00 0.00 2.71
3136 6667 2.754552 CCATCGGATTTTGCAGAGGAAA 59.245 45.455 0.00 0.00 0.00 3.13
3138 6669 1.281867 ACCATCGGATTTTGCAGAGGA 59.718 47.619 0.00 0.00 0.00 3.71
3139 6670 1.755179 ACCATCGGATTTTGCAGAGG 58.245 50.000 0.00 0.00 0.00 3.69
3143 6674 4.075682 TGAGTAAACCATCGGATTTTGCA 58.924 39.130 6.18 0.00 0.00 4.08
3153 6684 6.623767 GCCTCAAAAGACATGAGTAAACCATC 60.624 42.308 0.00 0.00 42.19 3.51
3218 6752 7.611213 ACTCGAAAATACTCCTTTATGTTGG 57.389 36.000 0.00 0.00 0.00 3.77
3238 6772 4.433805 CGAAAAACGGTCCAGATAAACTCG 60.434 45.833 0.00 0.00 38.46 4.18
3259 6796 2.286184 GCTCTTCAAAACAAAGCGACGA 60.286 45.455 0.00 0.00 0.00 4.20
3261 6798 3.065019 TGCTCTTCAAAACAAAGCGAC 57.935 42.857 0.00 0.00 35.74 5.19
3262 6799 3.988379 ATGCTCTTCAAAACAAAGCGA 57.012 38.095 0.00 0.00 35.74 4.93
3264 6801 7.642071 TTCATTATGCTCTTCAAAACAAAGC 57.358 32.000 0.00 0.00 0.00 3.51
3289 6827 3.942829 ACTACAAGCAGCAAGAGCATTA 58.057 40.909 0.00 0.00 45.49 1.90
3290 6828 2.787994 ACTACAAGCAGCAAGAGCATT 58.212 42.857 0.00 0.00 45.49 3.56
3291 6829 2.486472 ACTACAAGCAGCAAGAGCAT 57.514 45.000 0.00 0.00 45.49 3.79
3308 6847 4.454504 CCGAACTAGTTTTATGTGCCAACT 59.545 41.667 10.02 0.00 35.00 3.16
3325 6864 1.561643 TGAGATTCAGAGCCCGAACT 58.438 50.000 0.00 0.00 0.00 3.01
3326 6865 2.611225 ATGAGATTCAGAGCCCGAAC 57.389 50.000 0.00 0.00 0.00 3.95
3327 6866 4.635223 CAATATGAGATTCAGAGCCCGAA 58.365 43.478 0.00 0.00 0.00 4.30
3329 6868 2.740981 GCAATATGAGATTCAGAGCCCG 59.259 50.000 0.00 0.00 0.00 6.13
3330 6869 4.018484 AGCAATATGAGATTCAGAGCCC 57.982 45.455 0.00 0.00 0.00 5.19
3331 6870 4.630940 GCTAGCAATATGAGATTCAGAGCC 59.369 45.833 10.63 0.00 0.00 4.70
3332 6871 4.630940 GGCTAGCAATATGAGATTCAGAGC 59.369 45.833 18.24 0.00 0.00 4.09
3333 6872 5.638657 GTGGCTAGCAATATGAGATTCAGAG 59.361 44.000 18.24 0.00 0.00 3.35
3334 6873 5.306419 AGTGGCTAGCAATATGAGATTCAGA 59.694 40.000 18.24 0.00 0.00 3.27
3335 6874 5.549347 AGTGGCTAGCAATATGAGATTCAG 58.451 41.667 18.24 0.00 0.00 3.02
3336 6875 5.557576 AGTGGCTAGCAATATGAGATTCA 57.442 39.130 18.24 0.00 0.00 2.57
3337 6876 5.872070 GGTAGTGGCTAGCAATATGAGATTC 59.128 44.000 18.24 0.00 34.93 2.52
3338 6877 5.307976 TGGTAGTGGCTAGCAATATGAGATT 59.692 40.000 18.24 0.00 40.74 2.40
3339 6878 4.840680 TGGTAGTGGCTAGCAATATGAGAT 59.159 41.667 18.24 0.00 40.74 2.75
3340 6879 4.223144 TGGTAGTGGCTAGCAATATGAGA 58.777 43.478 18.24 0.00 40.74 3.27
3341 6880 4.281941 TCTGGTAGTGGCTAGCAATATGAG 59.718 45.833 18.24 3.89 42.61 2.90
3342 6881 4.223144 TCTGGTAGTGGCTAGCAATATGA 58.777 43.478 18.24 1.18 42.61 2.15
3343 6882 4.039730 ACTCTGGTAGTGGCTAGCAATATG 59.960 45.833 18.24 0.00 42.61 1.78
3344 6883 4.227197 ACTCTGGTAGTGGCTAGCAATAT 58.773 43.478 18.24 0.65 42.61 1.28
3345 6884 3.643237 ACTCTGGTAGTGGCTAGCAATA 58.357 45.455 18.24 3.71 42.61 1.90
3346 6885 2.472029 ACTCTGGTAGTGGCTAGCAAT 58.528 47.619 18.24 4.73 42.61 3.56
3347 6886 1.938585 ACTCTGGTAGTGGCTAGCAA 58.061 50.000 18.24 0.85 42.61 3.91
3348 6887 1.825474 GAACTCTGGTAGTGGCTAGCA 59.175 52.381 18.24 7.65 41.30 3.49
3349 6888 1.825474 TGAACTCTGGTAGTGGCTAGC 59.175 52.381 6.04 6.04 38.88 3.42
3350 6889 2.428890 CCTGAACTCTGGTAGTGGCTAG 59.571 54.545 0.00 0.00 38.88 3.42
3351 6890 2.457598 CCTGAACTCTGGTAGTGGCTA 58.542 52.381 0.00 0.00 38.88 3.93
3352 6891 1.270907 CCTGAACTCTGGTAGTGGCT 58.729 55.000 0.00 0.00 38.88 4.75
3353 6892 0.391793 GCCTGAACTCTGGTAGTGGC 60.392 60.000 4.75 0.00 38.88 5.01
3354 6893 1.205893 GAGCCTGAACTCTGGTAGTGG 59.794 57.143 4.75 0.00 38.88 4.00
3355 6894 2.175202 AGAGCCTGAACTCTGGTAGTG 58.825 52.381 4.75 0.00 45.36 2.74
3356 6895 2.614134 AGAGCCTGAACTCTGGTAGT 57.386 50.000 4.75 0.00 45.36 2.73
3370 6909 1.065564 AGCAAGGTGAGATTCAGAGCC 60.066 52.381 0.00 0.00 0.00 4.70
3379 6918 5.877012 GTGAAATCTAATGAGCAAGGTGAGA 59.123 40.000 0.00 0.00 0.00 3.27
3384 6923 3.242870 GCCGTGAAATCTAATGAGCAAGG 60.243 47.826 0.00 0.00 0.00 3.61
3405 6944 0.947180 TCAAGTTAGGTCGTTGCGGC 60.947 55.000 0.00 0.00 0.00 6.53
3406 6945 0.788391 GTCAAGTTAGGTCGTTGCGG 59.212 55.000 0.00 0.00 0.00 5.69
3408 6947 2.991866 GGTAGTCAAGTTAGGTCGTTGC 59.008 50.000 0.00 0.00 0.00 4.17
3411 6950 3.638160 TGTTGGTAGTCAAGTTAGGTCGT 59.362 43.478 0.00 0.00 35.80 4.34
3413 6952 6.589139 GTGTATGTTGGTAGTCAAGTTAGGTC 59.411 42.308 0.00 0.00 35.80 3.85
3421 6961 3.071747 TGCCAGTGTATGTTGGTAGTCAA 59.928 43.478 0.00 0.00 36.81 3.18
3423 6963 3.262420 CTGCCAGTGTATGTTGGTAGTC 58.738 50.000 1.12 0.00 40.85 2.59
3426 6966 3.579151 TGTACTGCCAGTGTATGTTGGTA 59.421 43.478 7.83 0.00 36.81 3.25
3427 6967 2.370519 TGTACTGCCAGTGTATGTTGGT 59.629 45.455 7.83 0.00 36.81 3.67
3428 6968 3.052455 TGTACTGCCAGTGTATGTTGG 57.948 47.619 7.83 0.00 37.53 3.77
3454 6994 3.427573 AGCCTAGGTTATTGCCGTTTTT 58.572 40.909 11.31 0.00 0.00 1.94
3455 6995 3.081710 AGCCTAGGTTATTGCCGTTTT 57.918 42.857 11.31 0.00 0.00 2.43
3456 6996 2.801077 AGCCTAGGTTATTGCCGTTT 57.199 45.000 11.31 0.00 0.00 3.60
3457 6997 2.502538 TGTAGCCTAGGTTATTGCCGTT 59.497 45.455 11.31 0.00 0.00 4.44
3458 6998 2.112998 TGTAGCCTAGGTTATTGCCGT 58.887 47.619 11.31 0.00 0.00 5.68
3459 6999 2.902705 TGTAGCCTAGGTTATTGCCG 57.097 50.000 11.31 0.00 0.00 5.69
3464 7004 4.780021 CCCATCAGATGTAGCCTAGGTTAT 59.220 45.833 11.31 0.00 0.00 1.89
3471 7011 1.135094 CACCCCATCAGATGTAGCCT 58.865 55.000 9.64 0.00 0.00 4.58
3488 8586 7.744715 GTGTTAGAATACAACATGTACAAGCAC 59.255 37.037 0.00 0.00 38.13 4.40
3489 8587 7.442666 TGTGTTAGAATACAACATGTACAAGCA 59.557 33.333 0.00 0.00 38.13 3.91
3499 8597 8.952278 GGAATGGTAATGTGTTAGAATACAACA 58.048 33.333 0.00 0.00 33.70 3.33
3538 8980 3.502595 GGTCTATCTATGCGAGCTGTGTA 59.497 47.826 0.00 0.00 0.00 2.90
3546 8988 5.812286 TGGTATACAGGTCTATCTATGCGA 58.188 41.667 5.01 0.00 0.00 5.10
3547 8989 6.404844 CCTTGGTATACAGGTCTATCTATGCG 60.405 46.154 5.01 0.00 0.00 4.73
3548 8990 6.127310 CCCTTGGTATACAGGTCTATCTATGC 60.127 46.154 5.01 0.00 0.00 3.14
3549 8991 7.182760 TCCCTTGGTATACAGGTCTATCTATG 58.817 42.308 5.01 0.00 0.00 2.23
3596 9142 7.307989 CGGCGAATGAAGGATTGTTAAGATAAT 60.308 37.037 0.00 0.00 0.00 1.28
3597 9143 6.018262 CGGCGAATGAAGGATTGTTAAGATAA 60.018 38.462 0.00 0.00 0.00 1.75
3607 9153 1.339631 TGAACCGGCGAATGAAGGATT 60.340 47.619 9.30 0.00 0.00 3.01
3608 9154 0.251916 TGAACCGGCGAATGAAGGAT 59.748 50.000 9.30 0.00 0.00 3.24
3610 9156 0.878416 TTTGAACCGGCGAATGAAGG 59.122 50.000 9.30 0.00 0.00 3.46
3619 9165 2.095372 GCAGTATACTGTTTGAACCGGC 59.905 50.000 28.95 10.95 45.45 6.13
3699 9247 4.672542 GCGCAAGAGCAAATGAATTACTGA 60.673 41.667 0.30 0.00 42.27 3.41
3725 9273 7.619050 AGAGACTGATTGATGACTACAACAAT 58.381 34.615 0.00 0.00 46.71 2.71
3794 9342 1.165270 CCTTCTTGGGCAGGTTTACG 58.835 55.000 0.00 0.00 0.00 3.18
3807 9355 4.781934 ACTTACAGTGTTCTTGCCTTCTT 58.218 39.130 0.00 0.00 0.00 2.52
3808 9356 4.423625 ACTTACAGTGTTCTTGCCTTCT 57.576 40.909 0.00 0.00 0.00 2.85
3809 9357 6.348540 CCATTACTTACAGTGTTCTTGCCTTC 60.349 42.308 0.00 0.00 0.00 3.46
3810 9358 5.473504 CCATTACTTACAGTGTTCTTGCCTT 59.526 40.000 0.00 0.00 0.00 4.35
3811 9359 5.003804 CCATTACTTACAGTGTTCTTGCCT 58.996 41.667 0.00 0.00 0.00 4.75
3812 9360 5.001232 TCCATTACTTACAGTGTTCTTGCC 58.999 41.667 0.00 0.00 0.00 4.52
3813 9361 5.932303 TCTCCATTACTTACAGTGTTCTTGC 59.068 40.000 0.00 0.00 0.00 4.01
3814 9362 9.653287 TTATCTCCATTACTTACAGTGTTCTTG 57.347 33.333 0.00 0.00 0.00 3.02
3851 9418 7.551585 TGTTTGTCTTTTGTTGGTGTCATAAT 58.448 30.769 0.00 0.00 0.00 1.28
3858 9425 6.146837 TGTGAAATGTTTGTCTTTTGTTGGTG 59.853 34.615 0.00 0.00 0.00 4.17
3861 9428 7.795859 AGTTGTGAAATGTTTGTCTTTTGTTG 58.204 30.769 0.00 0.00 0.00 3.33
3863 9430 9.086336 CATAGTTGTGAAATGTTTGTCTTTTGT 57.914 29.630 0.00 0.00 0.00 2.83
3879 9472 4.967084 AAGGGTGTGTACATAGTTGTGA 57.033 40.909 0.00 0.00 36.53 3.58
3880 9473 5.121768 GCTTAAGGGTGTGTACATAGTTGTG 59.878 44.000 4.29 0.00 36.53 3.33
3933 9527 2.743126 AGTACGCCGATACTAGATGCTC 59.257 50.000 0.00 0.00 33.50 4.26
3934 9528 2.484651 CAGTACGCCGATACTAGATGCT 59.515 50.000 0.00 0.00 33.50 3.79
3947 9541 2.289820 TCTCGATATCACACAGTACGCC 59.710 50.000 3.12 0.00 0.00 5.68
3950 9544 8.937884 ACTATACATCTCGATATCACACAGTAC 58.062 37.037 3.12 0.00 0.00 2.73
3951 9545 9.152595 GACTATACATCTCGATATCACACAGTA 57.847 37.037 3.12 0.72 0.00 2.74
3967 9561 6.263392 TGCAGTAGAACCTCTGACTATACATC 59.737 42.308 0.00 0.00 34.02 3.06
3969 9563 5.357314 GTGCAGTAGAACCTCTGACTATACA 59.643 44.000 0.00 0.00 34.02 2.29
3973 9567 2.747989 CGTGCAGTAGAACCTCTGACTA 59.252 50.000 0.00 0.00 34.02 2.59
3974 9568 1.542030 CGTGCAGTAGAACCTCTGACT 59.458 52.381 0.00 0.00 34.02 3.41
3975 9569 1.983972 CGTGCAGTAGAACCTCTGAC 58.016 55.000 0.00 0.00 34.02 3.51
3976 9570 0.243907 GCGTGCAGTAGAACCTCTGA 59.756 55.000 0.00 0.00 34.02 3.27
3988 9582 0.039798 ACAAGCTTCATTGCGTGCAG 60.040 50.000 0.00 0.00 44.13 4.41
3992 9586 5.818136 AATACATACAAGCTTCATTGCGT 57.182 34.783 0.00 0.00 38.13 5.24
4012 9608 4.946157 CACTTAGGCAGATGTCCTTGAAAT 59.054 41.667 1.96 0.00 35.21 2.17
4018 9614 3.584848 AGAAACACTTAGGCAGATGTCCT 59.415 43.478 0.00 2.22 37.72 3.85
4024 9620 6.852420 ATACACTAGAAACACTTAGGCAGA 57.148 37.500 0.00 0.00 0.00 4.26
4028 9624 9.640963 GGCATATATACACTAGAAACACTTAGG 57.359 37.037 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.