Multiple sequence alignment - TraesCS7B01G054600

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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 TraesCS7B01G054600 chr7B 100.000 5122 0 0 1 5122 57682520 57677399 0.000000e+00 9459.0
1 TraesCS7B01G054600 chr7B 96.667 210 7 0 4913 5122 347660378 347660169 2.930000e-92 350.0
2 TraesCS7B01G054600 chr7B 93.333 60 4 0 3750 3809 589961651 589961710 7.060000e-14 89.8
3 TraesCS7B01G054600 chr7B 95.349 43 2 0 3414 3456 642282477 642282435 9.200000e-08 69.4
4 TraesCS7B01G054600 chr7A 93.802 3469 175 22 720 4170 103401583 103398137 0.000000e+00 5179.0
5 TraesCS7B01G054600 chr7A 87.252 706 62 20 1 693 103402266 103401576 0.000000e+00 780.0
6 TraesCS7B01G054600 chr7A 93.443 61 4 0 3750 3810 628664398 628664458 1.960000e-14 91.6
7 TraesCS7B01G054600 chr7D 92.837 3588 167 33 614 4171 101140454 101136927 0.000000e+00 5120.0
8 TraesCS7B01G054600 chr7D 92.077 732 55 3 4187 4916 133425735 133426465 0.000000e+00 1027.0
9 TraesCS7B01G054600 chr7D 91.929 731 57 2 4187 4916 133512886 133513615 0.000000e+00 1022.0
10 TraesCS7B01G054600 chr7D 81.798 456 41 20 529 974 101250262 101249839 1.370000e-90 344.0
11 TraesCS7B01G054600 chr7D 93.443 61 4 0 3750 3810 545696999 545697059 1.960000e-14 91.6
12 TraesCS7B01G054600 chr1A 90.312 1218 117 1 1142 2359 86126452 86127668 0.000000e+00 1594.0
13 TraesCS7B01G054600 chr1A 90.901 1143 104 0 1215 2357 498071802 498072944 0.000000e+00 1535.0
14 TraesCS7B01G054600 chr1A 90.984 732 62 4 4188 4916 554973349 554974079 0.000000e+00 983.0
15 TraesCS7B01G054600 chr1A 89.660 735 71 4 4187 4916 440418121 440418855 0.000000e+00 931.0
16 TraesCS7B01G054600 chr4A 89.021 1093 98 7 1266 2358 678817699 678818769 0.000000e+00 1334.0
17 TraesCS7B01G054600 chr4A 87.879 66 7 1 8 73 29055926 29055990 5.500000e-10 76.8
18 TraesCS7B01G054600 chr4A 96.875 32 1 0 2111 2142 681918953 681918922 3.000000e-03 54.7
19 TraesCS7B01G054600 chr6D 91.096 730 62 3 4189 4916 306879977 306880705 0.000000e+00 985.0
20 TraesCS7B01G054600 chr6D 92.308 39 3 0 2540 2578 24831959 24831921 7.160000e-04 56.5
21 TraesCS7B01G054600 chr2D 90.587 733 61 4 4188 4916 435330295 435329567 0.000000e+00 965.0
22 TraesCS7B01G054600 chr2D 89.754 732 70 3 4189 4916 646636166 646636896 0.000000e+00 931.0
23 TraesCS7B01G054600 chr2D 86.060 868 105 3 1142 2008 536602727 536601875 0.000000e+00 918.0
24 TraesCS7B01G054600 chr2B 90.327 734 65 5 4186 4916 624275449 624276179 0.000000e+00 957.0
25 TraesCS7B01G054600 chr2B 90.595 723 64 3 4197 4916 87746878 87747599 0.000000e+00 955.0
26 TraesCS7B01G054600 chr2B 97.585 207 5 0 4916 5122 13882354 13882148 6.310000e-94 355.0
27 TraesCS7B01G054600 chr2B 96.714 213 6 1 4911 5122 782553576 782553364 2.270000e-93 353.0
28 TraesCS7B01G054600 chr2B 88.679 53 6 0 8 60 173757695 173757643 1.190000e-06 65.8
29 TraesCS7B01G054600 chr2A 90.042 472 39 4 3206 3677 398418413 398418876 5.670000e-169 604.0
30 TraesCS7B01G054600 chr2A 86.653 472 34 9 3206 3677 398887652 398887210 3.560000e-136 496.0
31 TraesCS7B01G054600 chr2A 97.115 208 6 0 4915 5122 402717281 402717074 8.160000e-93 351.0
32 TraesCS7B01G054600 chr5B 90.291 309 20 7 3370 3677 695755489 695755788 3.720000e-106 396.0
33 TraesCS7B01G054600 chr5B 98.058 206 4 0 4917 5122 565626298 565626503 4.880000e-95 359.0
34 TraesCS7B01G054600 chr5B 97.156 211 6 0 4912 5122 68623960 68623750 1.750000e-94 357.0
35 TraesCS7B01G054600 chr5B 96.729 214 6 1 4910 5122 30640895 30640682 6.310000e-94 355.0
36 TraesCS7B01G054600 chr5B 97.573 206 5 0 4917 5122 532557521 532557726 2.270000e-93 353.0
37 TraesCS7B01G054600 chr5B 92.308 104 7 1 3206 3308 695755386 695755489 4.130000e-31 147.0
38 TraesCS7B01G054600 chr5B 88.462 52 4 2 2528 2578 51977123 51977173 1.540000e-05 62.1
39 TraesCS7B01G054600 chr3B 97.573 206 5 0 4917 5122 631729536 631729331 2.270000e-93 353.0
40 TraesCS7B01G054600 chr1B 92.424 66 3 2 13 78 317361763 317361700 5.460000e-15 93.5
41 TraesCS7B01G054600 chr6B 84.286 70 5 5 2512 2578 40450182 40450248 4.280000e-06 63.9
42 TraesCS7B01G054600 chr6A 94.872 39 2 0 2540 2578 23366064 23366026 1.540000e-05 62.1
43 TraesCS7B01G054600 chr5A 100.000 31 0 0 10 40 454687021 454687051 1.990000e-04 58.4
44 TraesCS7B01G054600 chr4B 96.875 32 1 0 2111 2142 599885481 599885450 3.000000e-03 54.7


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 TraesCS7B01G054600 chr7B 57677399 57682520 5121 True 9459.0 9459 100.000 1 5122 1 chr7B.!!$R1 5121
1 TraesCS7B01G054600 chr7A 103398137 103402266 4129 True 2979.5 5179 90.527 1 4170 2 chr7A.!!$R1 4169
2 TraesCS7B01G054600 chr7D 101136927 101140454 3527 True 5120.0 5120 92.837 614 4171 1 chr7D.!!$R1 3557
3 TraesCS7B01G054600 chr7D 133425735 133426465 730 False 1027.0 1027 92.077 4187 4916 1 chr7D.!!$F1 729
4 TraesCS7B01G054600 chr7D 133512886 133513615 729 False 1022.0 1022 91.929 4187 4916 1 chr7D.!!$F2 729
5 TraesCS7B01G054600 chr1A 86126452 86127668 1216 False 1594.0 1594 90.312 1142 2359 1 chr1A.!!$F1 1217
6 TraesCS7B01G054600 chr1A 498071802 498072944 1142 False 1535.0 1535 90.901 1215 2357 1 chr1A.!!$F3 1142
7 TraesCS7B01G054600 chr1A 554973349 554974079 730 False 983.0 983 90.984 4188 4916 1 chr1A.!!$F4 728
8 TraesCS7B01G054600 chr1A 440418121 440418855 734 False 931.0 931 89.660 4187 4916 1 chr1A.!!$F2 729
9 TraesCS7B01G054600 chr4A 678817699 678818769 1070 False 1334.0 1334 89.021 1266 2358 1 chr4A.!!$F2 1092
10 TraesCS7B01G054600 chr6D 306879977 306880705 728 False 985.0 985 91.096 4189 4916 1 chr6D.!!$F1 727
11 TraesCS7B01G054600 chr2D 435329567 435330295 728 True 965.0 965 90.587 4188 4916 1 chr2D.!!$R1 728
12 TraesCS7B01G054600 chr2D 646636166 646636896 730 False 931.0 931 89.754 4189 4916 1 chr2D.!!$F1 727
13 TraesCS7B01G054600 chr2D 536601875 536602727 852 True 918.0 918 86.060 1142 2008 1 chr2D.!!$R2 866
14 TraesCS7B01G054600 chr2B 624275449 624276179 730 False 957.0 957 90.327 4186 4916 1 chr2B.!!$F2 730
15 TraesCS7B01G054600 chr2B 87746878 87747599 721 False 955.0 955 90.595 4197 4916 1 chr2B.!!$F1 719

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
123 128 0.107456 CAGCAATAGGAGGCACCGAT 59.893 55.000 0.00 0.00 44.74 4.18 F
1371 1389 0.037697 ATCTGTCCAGCAACGCGTTA 60.038 50.000 26.11 5.60 0.00 3.18 F
1845 1868 1.147376 CAACACCAACCTCGACCCA 59.853 57.895 0.00 0.00 0.00 4.51 F
2473 2496 0.950836 CATGATCCTCGCTCTCGACT 59.049 55.000 0.00 0.00 40.21 4.18 F
3620 3652 0.669318 ATTGCACCTGGTACGTGACG 60.669 55.000 2.24 2.24 32.77 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1779 0.818040 GGCAACCTGTCGAACACCTT 60.818 55.000 0.00 0.0 0.00 3.50 R
2403 2426 0.537371 CCTCCAGGTGGTTGTTGGAC 60.537 60.000 0.00 0.0 36.13 4.02 R
3105 3128 1.302192 GAGCACCTTTACGGCCACA 60.302 57.895 2.24 0.0 35.61 4.17 R
4089 4145 1.135228 GGAGAAGAGCGAGTCCTTGAC 60.135 57.143 0.00 0.0 0.00 3.18 R
4949 5010 0.107831 TTTTGACCCACGCTACTGCT 59.892 50.000 0.00 0.0 36.97 4.24 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
29 30 6.070366 TGCTACCTCTAGTGTTCTCTGTACTA 60.070 42.308 0.00 0.00 0.00 1.82
34 35 6.038825 CCTCTAGTGTTCTCTGTACTACCATG 59.961 46.154 0.00 0.00 0.00 3.66
40 41 6.754209 GTGTTCTCTGTACTACCATGATTGAG 59.246 42.308 0.00 0.00 0.00 3.02
46 47 8.727100 TCTGTACTACCATGATTGAGGAATAT 57.273 34.615 0.00 0.00 0.00 1.28
113 118 2.111878 CGGGGGAGCAGCAATAGG 59.888 66.667 0.00 0.00 0.00 2.57
119 124 0.817229 GGAGCAGCAATAGGAGGCAC 60.817 60.000 0.00 0.00 0.00 5.01
120 125 0.817229 GAGCAGCAATAGGAGGCACC 60.817 60.000 0.00 0.00 39.35 5.01
123 128 0.107456 CAGCAATAGGAGGCACCGAT 59.893 55.000 0.00 0.00 44.74 4.18
124 129 0.107456 AGCAATAGGAGGCACCGATG 59.893 55.000 0.00 0.00 44.74 3.84
148 153 1.061131 GTCATCTTGTGTCGCCATTCG 59.939 52.381 0.00 0.00 40.15 3.34
162 167 3.899981 ATTCGCCGCTTCCTGTGCA 62.900 57.895 0.00 0.00 0.00 4.57
170 175 1.298859 GCTTCCTGTGCAACCTACCG 61.299 60.000 0.00 0.00 34.36 4.02
183 188 4.393680 GCAACCTACCGACAATTTGTATCA 59.606 41.667 1.15 0.00 0.00 2.15
185 190 5.155278 ACCTACCGACAATTTGTATCACA 57.845 39.130 1.15 0.00 0.00 3.58
186 191 5.741011 ACCTACCGACAATTTGTATCACAT 58.259 37.500 1.15 0.00 0.00 3.21
222 227 8.664798 TCAGATAATTTGTATCACCTTTGTTCG 58.335 33.333 0.00 0.00 0.00 3.95
223 228 7.910162 CAGATAATTTGTATCACCTTTGTTCGG 59.090 37.037 0.00 0.00 0.00 4.30
228 233 7.931578 TTTGTATCACCTTTGTTCGGAATAT 57.068 32.000 0.00 0.00 0.00 1.28
240 245 9.289303 CTTTGTTCGGAATATAAGACATTTTGG 57.711 33.333 0.00 0.00 0.00 3.28
294 299 8.947304 AAAATGAATGAACAAACACAACAAAC 57.053 26.923 0.00 0.00 0.00 2.93
297 302 5.985530 TGAATGAACAAACACAACAAACACA 59.014 32.000 0.00 0.00 0.00 3.72
311 316 5.984233 ACAAACACACGGCTATATACATG 57.016 39.130 0.00 0.00 0.00 3.21
312 317 4.272504 ACAAACACACGGCTATATACATGC 59.727 41.667 0.00 0.00 0.00 4.06
315 320 4.641396 ACACACGGCTATATACATGCAAT 58.359 39.130 0.00 0.00 0.00 3.56
366 371 7.928706 ACATCTTATAATTCAGAACGAAGGGAG 59.071 37.037 0.00 0.00 36.95 4.30
368 373 8.529424 TCTTATAATTCAGAACGAAGGGAGTA 57.471 34.615 0.00 0.00 36.95 2.59
369 374 8.630917 TCTTATAATTCAGAACGAAGGGAGTAG 58.369 37.037 0.00 0.00 36.95 2.57
485 492 5.301805 AGGTGTTGCTATAGTGCTTTTTGTT 59.698 36.000 0.84 0.00 0.00 2.83
486 493 5.629435 GGTGTTGCTATAGTGCTTTTTGTTC 59.371 40.000 0.84 0.00 0.00 3.18
488 495 6.695278 GTGTTGCTATAGTGCTTTTTGTTCAA 59.305 34.615 0.84 0.00 0.00 2.69
489 496 6.917477 TGTTGCTATAGTGCTTTTTGTTCAAG 59.083 34.615 0.84 0.00 0.00 3.02
540 547 5.747197 CGTGTTCTCAACTAGTACAACTTGT 59.253 40.000 0.00 0.00 37.26 3.16
568 577 7.122715 TGGATAACCACTTAATTAACCAGCAT 58.877 34.615 0.00 0.00 41.77 3.79
636 646 4.128554 ACAATTTGACGCGTACTTTGAG 57.871 40.909 13.97 2.24 0.00 3.02
637 647 3.805422 ACAATTTGACGCGTACTTTGAGA 59.195 39.130 13.97 0.00 0.00 3.27
648 658 6.038603 ACGCGTACTTTGAGACTAATACCATA 59.961 38.462 11.67 0.00 0.00 2.74
649 659 6.359087 CGCGTACTTTGAGACTAATACCATAC 59.641 42.308 0.00 0.00 0.00 2.39
652 662 9.448294 CGTACTTTGAGACTAATACCATACTTC 57.552 37.037 0.00 0.00 0.00 3.01
667 680 5.354234 ACCATACTTCGGATAAACAAAGCTG 59.646 40.000 0.00 0.00 0.00 4.24
994 1012 3.299977 CCACCCACGTCCTGTCGA 61.300 66.667 0.00 0.00 34.70 4.20
1016 1034 1.526575 CCAATGGCCAAGTTGCTCGT 61.527 55.000 10.96 0.00 0.00 4.18
1048 1066 1.522092 GTCATCCTCCATGTCGGCA 59.478 57.895 0.00 0.00 33.66 5.69
1066 1084 0.387239 CATCATCGTGCCGATCGCTA 60.387 55.000 10.32 0.00 45.19 4.26
1309 1327 4.540735 GGGGGATACACGGCGTGG 62.541 72.222 39.03 23.28 46.14 4.94
1338 1356 2.282462 CTGGGGCGGCTGTCTTTT 60.282 61.111 9.56 0.00 0.00 2.27
1371 1389 0.037697 ATCTGTCCAGCAACGCGTTA 60.038 50.000 26.11 5.60 0.00 3.18
1506 1525 1.451567 CTACCTCGACCTCAGCGGA 60.452 63.158 0.00 0.00 36.31 5.54
1509 1528 1.258445 ACCTCGACCTCAGCGGAAAT 61.258 55.000 0.00 0.00 36.31 2.17
1560 1580 4.704833 TGCAACTGCTCCGCCCTC 62.705 66.667 2.95 0.00 42.66 4.30
1825 1848 1.837051 AACCTCTCCAGCCACGACA 60.837 57.895 0.00 0.00 0.00 4.35
1845 1868 1.147376 CAACACCAACCTCGACCCA 59.853 57.895 0.00 0.00 0.00 4.51
1902 1925 2.105128 CTCGAGCTCGCCGGAAAT 59.895 61.111 30.97 0.00 39.60 2.17
1905 1928 2.186903 GAGCTCGCCGGAAATGGA 59.813 61.111 5.05 0.00 0.00 3.41
1911 1934 2.267961 GCCGGAAATGGACTCGGT 59.732 61.111 5.05 0.00 43.87 4.69
1914 1937 1.449601 CGGAAATGGACTCGGTGGG 60.450 63.158 0.00 0.00 0.00 4.61
2053 2076 3.430929 CCTCAACCTCTCCAATAACCTCG 60.431 52.174 0.00 0.00 0.00 4.63
2122 2145 3.118592 GCAGCTATACCTCTCCAACAACT 60.119 47.826 0.00 0.00 0.00 3.16
2266 2289 1.521450 GCTGATGCTGCACCACAACT 61.521 55.000 3.57 0.00 36.03 3.16
2403 2426 2.613977 CCTCAAGCTGTACCTGAACCTG 60.614 54.545 0.00 0.00 0.00 4.00
2473 2496 0.950836 CATGATCCTCGCTCTCGACT 59.049 55.000 0.00 0.00 40.21 4.18
2609 2632 3.706373 GCTGCCGTTCCTGGAGGA 61.706 66.667 6.18 0.00 43.73 3.71
2775 2798 2.852075 TTCCGAGGCAACCCCAGT 60.852 61.111 0.00 0.00 35.39 4.00
2974 2997 3.069980 GACATCGAGGAGCAGGCGT 62.070 63.158 3.06 0.00 0.00 5.68
3045 3068 1.315981 ATGGCTTCGCAGAGTCTCGA 61.316 55.000 9.65 9.65 38.43 4.04
3533 3565 3.789858 CAGCAGCAGCAGCACGAG 61.790 66.667 12.92 0.00 45.49 4.18
3603 3635 2.795329 CAGGGTTCAGTTGGCTACATT 58.205 47.619 1.24 0.00 0.00 2.71
3620 3652 0.669318 ATTGCACCTGGTACGTGACG 60.669 55.000 2.24 2.24 32.77 4.35
3621 3653 2.018727 TTGCACCTGGTACGTGACGT 62.019 55.000 17.03 17.03 44.35 4.34
3622 3654 2.019951 GCACCTGGTACGTGACGTG 61.020 63.158 22.16 5.82 41.39 4.49
3709 3753 3.128349 TCCTGCGATTAACGGCTAATTC 58.872 45.455 0.00 0.00 42.83 2.17
3836 3880 1.066587 GATCTTCGACGAGGGGCTG 59.933 63.158 7.16 0.00 0.00 4.85
3845 3889 4.479993 GAGGGGCTGACGCTGCAT 62.480 66.667 4.18 0.00 43.22 3.96
3950 4006 2.583593 GCGGTCGTGGAGCTGATC 60.584 66.667 0.00 0.00 0.00 2.92
4031 4087 1.484240 TGCCACGACATCACCATGATA 59.516 47.619 0.00 0.00 34.28 2.15
4141 4197 4.871933 AATCAACACCCAGAAACCAATC 57.128 40.909 0.00 0.00 0.00 2.67
4159 4215 5.525378 ACCAATCGAGATGACAAGAATTAGC 59.475 40.000 2.74 0.00 0.00 3.09
4171 4227 5.368145 ACAAGAATTAGCGCATCTCCAATA 58.632 37.500 11.47 0.00 0.00 1.90
4172 4228 5.237344 ACAAGAATTAGCGCATCTCCAATAC 59.763 40.000 11.47 0.00 0.00 1.89
4173 4229 4.960938 AGAATTAGCGCATCTCCAATACA 58.039 39.130 11.47 0.00 0.00 2.29
4174 4230 5.555017 AGAATTAGCGCATCTCCAATACAT 58.445 37.500 11.47 0.00 0.00 2.29
4175 4231 5.410746 AGAATTAGCGCATCTCCAATACATG 59.589 40.000 11.47 0.00 0.00 3.21
4176 4232 1.233019 AGCGCATCTCCAATACATGC 58.767 50.000 11.47 0.00 39.70 4.06
4177 4233 0.946528 GCGCATCTCCAATACATGCA 59.053 50.000 0.30 0.00 42.65 3.96
4178 4234 1.538512 GCGCATCTCCAATACATGCAT 59.461 47.619 0.30 0.00 42.65 3.96
4179 4235 2.743664 GCGCATCTCCAATACATGCATA 59.256 45.455 0.30 0.00 42.65 3.14
4180 4236 3.189080 GCGCATCTCCAATACATGCATAA 59.811 43.478 0.30 0.00 42.65 1.90
4181 4237 4.320421 GCGCATCTCCAATACATGCATAAA 60.320 41.667 0.30 0.00 42.65 1.40
4182 4238 5.761003 CGCATCTCCAATACATGCATAAAA 58.239 37.500 0.00 0.00 42.65 1.52
4183 4239 6.207928 CGCATCTCCAATACATGCATAAAAA 58.792 36.000 0.00 0.00 42.65 1.94
4184 4240 6.864685 CGCATCTCCAATACATGCATAAAAAT 59.135 34.615 0.00 0.00 42.65 1.82
4185 4241 8.022550 CGCATCTCCAATACATGCATAAAAATA 58.977 33.333 0.00 0.00 42.65 1.40
4186 4242 9.695526 GCATCTCCAATACATGCATAAAAATAA 57.304 29.630 0.00 0.00 42.18 1.40
4246 4302 3.814504 AAGAGGAAGAGAATTGGCCAA 57.185 42.857 23.00 23.00 0.00 4.52
4270 4326 8.432359 CAATTTATAAGAAAAACTGGCCGAAAC 58.568 33.333 0.00 0.00 0.00 2.78
4338 4396 1.971695 CTTCCCTGTCGCCCAAACC 60.972 63.158 0.00 0.00 0.00 3.27
4350 4408 0.468029 CCCAAACCACCAGAGTTGCT 60.468 55.000 0.00 0.00 0.00 3.91
4405 4463 4.155280 GCCGTACAAACCACATAAACTCAT 59.845 41.667 0.00 0.00 0.00 2.90
4410 4468 7.117236 CGTACAAACCACATAAACTCATACACT 59.883 37.037 0.00 0.00 0.00 3.55
4480 4538 1.876416 CGACCAAAACCGACACTCCAT 60.876 52.381 0.00 0.00 0.00 3.41
4560 4618 2.645567 CACCTGAGCTGACGACGT 59.354 61.111 0.00 0.00 0.00 4.34
4566 4624 3.891586 GAGCTGACGACGTTGCCGA 62.892 63.158 18.69 0.00 37.88 5.54
4576 4634 3.698463 GTTGCCGACCACACGACG 61.698 66.667 0.00 0.00 35.09 5.12
4607 4665 3.066064 CACTCCACAACATTGTTTTCCGA 59.934 43.478 0.00 0.00 39.91 4.55
4699 4757 2.642254 CCCGAGCCACCGTGAACTA 61.642 63.158 0.00 0.00 0.00 2.24
4711 4769 2.546373 CCGTGAACTAACGAAGGACCAA 60.546 50.000 0.00 0.00 46.49 3.67
4748 4808 1.270839 CCTCAAGAGGGAAGCGACAAA 60.271 52.381 8.28 0.00 44.87 2.83
4815 4876 2.363018 CTGGAGAGCCCGAGACCA 60.363 66.667 0.00 0.00 37.93 4.02
4836 4897 1.039856 GGCAACAATGGTGGTGAAGT 58.960 50.000 0.00 0.00 46.17 3.01
4875 4936 1.407437 CCAAGGAGGGAATGAAGTCCG 60.407 57.143 0.00 0.00 38.72 4.79
4906 4967 2.180769 CGCCGACAATGACCGAGA 59.819 61.111 0.00 0.00 0.00 4.04
4916 4977 0.878416 ATGACCGAGATCGAGCTAGC 59.122 55.000 1.61 6.62 43.02 3.42
4917 4978 0.463833 TGACCGAGATCGAGCTAGCA 60.464 55.000 18.83 0.00 43.02 3.49
4918 4979 0.040781 GACCGAGATCGAGCTAGCAC 60.041 60.000 18.83 10.18 43.02 4.40
4919 4980 0.464735 ACCGAGATCGAGCTAGCACT 60.465 55.000 18.83 7.72 43.02 4.40
4920 4981 1.202663 ACCGAGATCGAGCTAGCACTA 60.203 52.381 18.83 2.65 43.02 2.74
4921 4982 1.195900 CCGAGATCGAGCTAGCACTAC 59.804 57.143 18.83 4.42 43.02 2.73
4922 4983 2.139917 CGAGATCGAGCTAGCACTACT 58.860 52.381 18.83 9.17 43.02 2.57
4923 4984 3.318886 CGAGATCGAGCTAGCACTACTA 58.681 50.000 18.83 0.00 43.02 1.82
4924 4985 3.366724 CGAGATCGAGCTAGCACTACTAG 59.633 52.174 18.83 6.15 45.71 2.57
4925 4986 5.669481 CGAGATCGAGCTAGCACTACTAGG 61.669 54.167 18.83 0.00 44.35 3.02
4948 5009 7.520451 GGGAAAACCTTATACACAGAACTTT 57.480 36.000 0.00 0.00 35.85 2.66
4949 5010 8.625786 GGGAAAACCTTATACACAGAACTTTA 57.374 34.615 0.00 0.00 35.85 1.85
4950 5011 8.727910 GGGAAAACCTTATACACAGAACTTTAG 58.272 37.037 0.00 0.00 35.85 1.85
4951 5012 8.235226 GGAAAACCTTATACACAGAACTTTAGC 58.765 37.037 0.00 0.00 0.00 3.09
4952 5013 8.685838 AAAACCTTATACACAGAACTTTAGCA 57.314 30.769 0.00 0.00 0.00 3.49
4953 5014 7.907214 AACCTTATACACAGAACTTTAGCAG 57.093 36.000 0.00 0.00 0.00 4.24
4954 5015 7.005709 ACCTTATACACAGAACTTTAGCAGT 57.994 36.000 0.00 0.00 37.30 4.40
4955 5016 8.130671 ACCTTATACACAGAACTTTAGCAGTA 57.869 34.615 0.00 0.00 32.94 2.74
4956 5017 8.251721 ACCTTATACACAGAACTTTAGCAGTAG 58.748 37.037 0.00 0.00 32.94 2.57
4957 5018 7.222999 CCTTATACACAGAACTTTAGCAGTAGC 59.777 40.741 0.00 0.00 42.56 3.58
4967 5028 4.371975 GCAGTAGCGTGGGTCAAA 57.628 55.556 0.00 0.00 0.00 2.69
4968 5029 2.624169 GCAGTAGCGTGGGTCAAAA 58.376 52.632 0.00 0.00 0.00 2.44
4969 5030 0.948678 GCAGTAGCGTGGGTCAAAAA 59.051 50.000 0.00 0.00 0.00 1.94
4987 5048 4.584327 AAAAAGAACGCTGGTGCTAATT 57.416 36.364 0.00 0.00 36.97 1.40
4988 5049 5.699097 AAAAAGAACGCTGGTGCTAATTA 57.301 34.783 0.00 0.00 36.97 1.40
4989 5050 4.946784 AAAGAACGCTGGTGCTAATTAG 57.053 40.909 8.20 8.20 36.97 1.73
5007 5068 3.826754 CAGTAGCGCGCCTGAGGA 61.827 66.667 30.33 3.07 0.00 3.71
5008 5069 3.068691 AGTAGCGCGCCTGAGGAA 61.069 61.111 30.33 1.30 0.00 3.36
5009 5070 2.125673 GTAGCGCGCCTGAGGAAA 60.126 61.111 30.33 0.00 0.00 3.13
5010 5071 2.125673 TAGCGCGCCTGAGGAAAC 60.126 61.111 30.33 0.00 0.00 2.78
5011 5072 3.659089 TAGCGCGCCTGAGGAAACC 62.659 63.158 30.33 0.00 0.00 3.27
5017 5078 3.121030 CCTGAGGAAACCGCGCTG 61.121 66.667 5.56 0.00 0.00 5.18
5018 5079 3.793144 CTGAGGAAACCGCGCTGC 61.793 66.667 5.56 0.00 0.00 5.25
5019 5080 4.617520 TGAGGAAACCGCGCTGCA 62.618 61.111 5.56 0.00 0.00 4.41
5020 5081 3.793144 GAGGAAACCGCGCTGCAG 61.793 66.667 10.11 10.11 0.00 4.41
5021 5082 4.314440 AGGAAACCGCGCTGCAGA 62.314 61.111 20.43 0.00 0.00 4.26
5022 5083 3.127533 GGAAACCGCGCTGCAGAT 61.128 61.111 20.43 0.00 0.00 2.90
5023 5084 1.813753 GGAAACCGCGCTGCAGATA 60.814 57.895 20.43 0.00 0.00 1.98
5024 5085 1.366111 GGAAACCGCGCTGCAGATAA 61.366 55.000 20.43 0.00 0.00 1.75
5025 5086 0.446222 GAAACCGCGCTGCAGATAAA 59.554 50.000 20.43 0.00 0.00 1.40
5026 5087 0.447801 AAACCGCGCTGCAGATAAAG 59.552 50.000 20.43 3.65 0.00 1.85
5027 5088 0.391130 AACCGCGCTGCAGATAAAGA 60.391 50.000 20.43 0.00 0.00 2.52
5028 5089 0.179073 ACCGCGCTGCAGATAAAGAT 60.179 50.000 20.43 0.00 0.00 2.40
5029 5090 0.510359 CCGCGCTGCAGATAAAGATC 59.490 55.000 20.43 0.00 0.00 2.75
5030 5091 1.495878 CGCGCTGCAGATAAAGATCT 58.504 50.000 20.43 0.00 43.63 2.75
5031 5092 2.608016 CCGCGCTGCAGATAAAGATCTA 60.608 50.000 20.43 0.00 40.68 1.98
5032 5093 2.660715 CGCGCTGCAGATAAAGATCTAG 59.339 50.000 20.43 0.00 40.68 2.43
5033 5094 2.411409 GCGCTGCAGATAAAGATCTAGC 59.589 50.000 20.43 0.00 40.68 3.42
5034 5095 3.646946 CGCTGCAGATAAAGATCTAGCA 58.353 45.455 20.43 9.61 41.21 3.49
5039 5100 5.777802 TGCAGATAAAGATCTAGCAGTAGC 58.222 41.667 0.00 0.00 40.68 3.58
5040 5101 4.856487 GCAGATAAAGATCTAGCAGTAGCG 59.144 45.833 0.00 0.00 42.63 4.26
5041 5102 4.856487 CAGATAAAGATCTAGCAGTAGCGC 59.144 45.833 0.00 0.00 42.63 5.92
5042 5103 4.378978 AGATAAAGATCTAGCAGTAGCGCG 60.379 45.833 0.00 0.00 40.85 6.86
5043 5104 7.820960 AGATAAAGATCTAGCAGTAGCGCGC 62.821 48.000 26.66 26.66 40.85 6.86
5050 5111 3.121030 CAGTAGCGCGCCTTGCTT 61.121 61.111 30.33 11.01 43.71 3.91
5051 5112 2.358737 AGTAGCGCGCCTTGCTTT 60.359 55.556 30.33 10.14 43.71 3.51
5052 5113 1.079405 AGTAGCGCGCCTTGCTTTA 60.079 52.632 30.33 8.92 43.71 1.85
5053 5114 0.672401 AGTAGCGCGCCTTGCTTTAA 60.672 50.000 30.33 0.00 43.71 1.52
5054 5115 0.167251 GTAGCGCGCCTTGCTTTAAA 59.833 50.000 30.33 0.00 43.71 1.52
5055 5116 0.167251 TAGCGCGCCTTGCTTTAAAC 59.833 50.000 30.33 0.00 43.71 2.01
5056 5117 1.371145 GCGCGCCTTGCTTTAAACA 60.371 52.632 23.24 0.00 43.27 2.83
5057 5118 1.605481 GCGCGCCTTGCTTTAAACAC 61.605 55.000 23.24 0.00 43.27 3.32
5058 5119 1.327292 CGCGCCTTGCTTTAAACACG 61.327 55.000 0.00 0.00 43.27 4.49
5059 5120 0.317519 GCGCCTTGCTTTAAACACGT 60.318 50.000 0.00 0.00 41.73 4.49
5060 5121 1.862411 GCGCCTTGCTTTAAACACGTT 60.862 47.619 0.00 0.00 41.73 3.99
5061 5122 2.602694 GCGCCTTGCTTTAAACACGTTA 60.603 45.455 0.00 0.00 41.73 3.18
5062 5123 2.968655 CGCCTTGCTTTAAACACGTTAC 59.031 45.455 0.00 0.00 0.00 2.50
5063 5124 3.303526 CGCCTTGCTTTAAACACGTTACT 60.304 43.478 0.00 0.00 0.00 2.24
5064 5125 4.084433 CGCCTTGCTTTAAACACGTTACTA 60.084 41.667 0.00 0.00 0.00 1.82
5065 5126 5.142265 GCCTTGCTTTAAACACGTTACTAC 58.858 41.667 0.00 0.00 0.00 2.73
5066 5127 5.049886 GCCTTGCTTTAAACACGTTACTACT 60.050 40.000 0.00 0.00 0.00 2.57
5067 5128 6.146021 GCCTTGCTTTAAACACGTTACTACTA 59.854 38.462 0.00 0.00 0.00 1.82
5068 5129 7.307337 GCCTTGCTTTAAACACGTTACTACTAA 60.307 37.037 0.00 0.00 0.00 2.24
5069 5130 8.550376 CCTTGCTTTAAACACGTTACTACTAAA 58.450 33.333 0.00 0.00 0.00 1.85
5070 5131 9.919348 CTTGCTTTAAACACGTTACTACTAAAA 57.081 29.630 0.00 0.00 0.00 1.52
5076 5137 9.553064 TTAAACACGTTACTACTAAAATTCCCA 57.447 29.630 0.00 0.00 0.00 4.37
5077 5138 7.425577 AACACGTTACTACTAAAATTCCCAC 57.574 36.000 0.00 0.00 0.00 4.61
5078 5139 5.634859 ACACGTTACTACTAAAATTCCCACG 59.365 40.000 0.00 0.00 0.00 4.94
5079 5140 5.062558 CACGTTACTACTAAAATTCCCACGG 59.937 44.000 0.00 0.00 0.00 4.94
5080 5141 4.033243 CGTTACTACTAAAATTCCCACGGC 59.967 45.833 0.00 0.00 0.00 5.68
5081 5142 3.994931 ACTACTAAAATTCCCACGGCT 57.005 42.857 0.00 0.00 0.00 5.52
5082 5143 4.296621 ACTACTAAAATTCCCACGGCTT 57.703 40.909 0.00 0.00 0.00 4.35
5083 5144 5.425196 ACTACTAAAATTCCCACGGCTTA 57.575 39.130 0.00 0.00 0.00 3.09
5084 5145 5.425630 ACTACTAAAATTCCCACGGCTTAG 58.574 41.667 0.00 0.00 0.00 2.18
5085 5146 3.014623 ACTAAAATTCCCACGGCTTAGC 58.985 45.455 0.00 0.00 0.00 3.09
5086 5147 1.182667 AAAATTCCCACGGCTTAGCC 58.817 50.000 14.22 14.22 46.75 3.93
5118 5179 8.705048 CTACACATAGTAGTAGCGATCTATGA 57.295 38.462 12.44 0.00 44.24 2.15
5119 5180 7.367159 ACACATAGTAGTAGCGATCTATGAC 57.633 40.000 12.44 0.00 40.93 3.06
5120 5181 6.091034 ACACATAGTAGTAGCGATCTATGACG 59.909 42.308 12.44 6.83 40.93 4.35
5121 5182 6.310711 CACATAGTAGTAGCGATCTATGACGA 59.689 42.308 12.44 0.00 40.93 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.762661 GGTAGTACAGAGAACACTAGAGGTAG 59.237 46.154 2.06 0.00 0.00 3.18
69 70 7.396055 CACCCAGAGAATCCCAGTTTTATTTTA 59.604 37.037 0.00 0.00 33.66 1.52
70 71 6.211384 CACCCAGAGAATCCCAGTTTTATTTT 59.789 38.462 0.00 0.00 33.66 1.82
79 80 1.153289 CGCACCCAGAGAATCCCAG 60.153 63.158 0.00 0.00 33.66 4.45
84 85 3.411517 CCCCCGCACCCAGAGAAT 61.412 66.667 0.00 0.00 0.00 2.40
85 86 4.649705 TCCCCCGCACCCAGAGAA 62.650 66.667 0.00 0.00 0.00 2.87
123 128 1.374125 CGACACAAGATGACCGGCA 60.374 57.895 0.00 0.00 0.00 5.69
124 129 2.740714 GCGACACAAGATGACCGGC 61.741 63.158 0.00 0.00 0.00 6.13
148 153 4.043200 GGTTGCACAGGAAGCGGC 62.043 66.667 0.00 0.00 33.85 6.53
156 161 1.808411 ATTGTCGGTAGGTTGCACAG 58.192 50.000 0.00 0.00 0.00 3.66
162 167 5.553123 TGTGATACAAATTGTCGGTAGGTT 58.447 37.500 0.22 0.00 0.00 3.50
275 280 5.107683 CGTGTGTTTGTTGTGTTTGTTCATT 60.108 36.000 0.00 0.00 0.00 2.57
282 287 1.271102 AGCCGTGTGTTTGTTGTGTTT 59.729 42.857 0.00 0.00 0.00 2.83
289 294 4.272504 GCATGTATATAGCCGTGTGTTTGT 59.727 41.667 0.00 0.00 0.00 2.83
290 295 4.272261 TGCATGTATATAGCCGTGTGTTTG 59.728 41.667 0.00 0.00 0.00 2.93
291 296 4.447290 TGCATGTATATAGCCGTGTGTTT 58.553 39.130 0.00 0.00 0.00 2.83
294 299 5.179182 TGAATTGCATGTATATAGCCGTGTG 59.821 40.000 0.00 0.00 0.00 3.82
297 302 6.875948 TTTGAATTGCATGTATATAGCCGT 57.124 33.333 0.00 0.00 0.00 5.68
341 346 7.928706 ACTCCCTTCGTTCTGAATTATAAGATG 59.071 37.037 0.00 0.00 35.63 2.90
349 354 6.183360 GGATACTACTCCCTTCGTTCTGAATT 60.183 42.308 0.00 0.00 35.63 2.17
424 431 8.705594 TGGTTCTATTGTTATTTTGTTTTGGGA 58.294 29.630 0.00 0.00 0.00 4.37
456 463 4.848357 AGCACTATAGCAACACCTGAAAT 58.152 39.130 0.00 0.00 36.85 2.17
485 492 6.120220 TGTCGTCAGGTCTAGATTATCTTGA 58.880 40.000 0.00 0.57 0.00 3.02
486 493 6.378710 TGTCGTCAGGTCTAGATTATCTTG 57.621 41.667 0.00 0.00 0.00 3.02
488 495 5.886474 TGTTGTCGTCAGGTCTAGATTATCT 59.114 40.000 0.00 0.00 0.00 1.98
489 496 6.132791 TGTTGTCGTCAGGTCTAGATTATC 57.867 41.667 0.00 0.00 0.00 1.75
494 501 4.142752 CGTATTGTTGTCGTCAGGTCTAGA 60.143 45.833 0.00 0.00 0.00 2.43
497 504 2.295349 ACGTATTGTTGTCGTCAGGTCT 59.705 45.455 0.00 0.00 32.26 3.85
531 538 6.121776 AGTGGTTATCCATGACAAGTTGTA 57.878 37.500 8.88 0.00 46.20 2.41
540 547 7.284489 GCTGGTTAATTAAGTGGTTATCCATGA 59.716 37.037 0.00 0.00 46.20 3.07
559 568 5.109210 CGAGACTAAACATCATGCTGGTTA 58.891 41.667 6.85 6.85 0.00 2.85
564 573 3.928992 CACACGAGACTAAACATCATGCT 59.071 43.478 0.00 0.00 0.00 3.79
568 577 4.330944 AACCACACGAGACTAAACATCA 57.669 40.909 0.00 0.00 0.00 3.07
636 646 9.754382 TTGTTTATCCGAAGTATGGTATTAGTC 57.246 33.333 0.00 0.00 0.00 2.59
648 658 2.488153 GCCAGCTTTGTTTATCCGAAGT 59.512 45.455 0.00 0.00 0.00 3.01
649 659 2.487762 TGCCAGCTTTGTTTATCCGAAG 59.512 45.455 0.00 0.00 0.00 3.79
652 662 2.480073 CCATGCCAGCTTTGTTTATCCG 60.480 50.000 0.00 0.00 0.00 4.18
664 677 0.037975 CAAGTCAAACCCATGCCAGC 60.038 55.000 0.00 0.00 0.00 4.85
667 680 0.681175 AAGCAAGTCAAACCCATGCC 59.319 50.000 0.00 0.00 37.73 4.40
818 836 2.237392 AGAAGGTGGCTGCCTAACTTAG 59.763 50.000 21.03 0.00 38.03 2.18
885 903 1.455032 GGTTTTATGGGGAGCGGGG 60.455 63.158 0.00 0.00 0.00 5.73
994 1012 2.216331 GCAACTTGGCCATTGGGGT 61.216 57.895 18.49 5.77 39.65 4.95
1016 1034 2.974794 AGGATGACGATGATTGGGATGA 59.025 45.455 0.00 0.00 0.00 2.92
1090 1108 4.648626 TGCTCCTGGTGCCTGTGC 62.649 66.667 17.31 2.00 38.26 4.57
1114 1132 2.506438 GTCGTCGGCCAGTACTGC 60.506 66.667 17.86 12.43 0.00 4.40
1293 1311 3.728279 GACCACGCCGTGTATCCCC 62.728 68.421 16.99 0.00 0.00 4.81
1338 1356 0.969149 ACAGATCAAGCACCGTGAGA 59.031 50.000 1.65 0.00 0.00 3.27
1572 1592 1.372997 GAGCGAGTTGTTGGCGAGA 60.373 57.895 0.00 0.00 35.41 4.04
1756 1779 0.818040 GGCAACCTGTCGAACACCTT 60.818 55.000 0.00 0.00 0.00 3.50
1825 1848 1.227853 GGTCGAGGTTGGTGTTGCT 60.228 57.895 0.00 0.00 0.00 3.91
1845 1868 1.661463 TGCTCAGGGAGTGGAAGAAT 58.339 50.000 0.00 0.00 31.39 2.40
1899 1922 1.991230 CCTCCCACCGAGTCCATTT 59.009 57.895 0.00 0.00 36.82 2.32
1902 1925 4.316823 AGCCTCCCACCGAGTCCA 62.317 66.667 0.00 0.00 36.82 4.02
1924 1947 1.012841 GAGAGCTCGCCAATGAAAGG 58.987 55.000 8.37 0.00 0.00 3.11
1926 1949 2.754648 CGAGAGCTCGCCAATGAAA 58.245 52.632 12.15 0.00 46.50 2.69
2053 2076 2.511600 CGGGATGGAGCCGTTGAC 60.512 66.667 0.00 0.00 0.00 3.18
2106 2129 4.430441 AGAGGAAGTTGTTGGAGAGGTAT 58.570 43.478 0.00 0.00 0.00 2.73
2266 2289 4.992740 AATGGCACCGGCAAGGCA 62.993 61.111 18.31 18.31 46.52 4.75
2403 2426 0.537371 CCTCCAGGTGGTTGTTGGAC 60.537 60.000 0.00 0.00 36.13 4.02
2473 2496 1.495584 GCAAGCTCGTTGGACGACAA 61.496 55.000 0.00 0.00 46.73 3.18
2623 2646 2.600769 ACCCGAGAGCACGTTCCT 60.601 61.111 0.00 0.00 0.00 3.36
3105 3128 1.302192 GAGCACCTTTACGGCCACA 60.302 57.895 2.24 0.00 35.61 4.17
3114 3137 4.699522 GGGTCCGCGAGCACCTTT 62.700 66.667 8.23 0.00 32.69 3.11
3150 3173 2.734673 GCGCTTGAAGCTGACGGAG 61.735 63.158 15.92 0.00 39.60 4.63
3516 3548 3.789858 CTCGTGCTGCTGCTGCTG 61.790 66.667 27.67 20.72 40.48 4.41
3528 3560 2.872001 GAGTCGTCGCTGCTCGTG 60.872 66.667 12.13 0.00 39.67 4.35
3529 3561 4.104417 GGAGTCGTCGCTGCTCGT 62.104 66.667 12.13 0.00 39.67 4.18
3603 3635 2.337170 CGTCACGTACCAGGTGCA 59.663 61.111 8.59 0.00 34.28 4.57
3693 3737 5.816919 ACCAAATGAATTAGCCGTTAATCG 58.183 37.500 0.00 0.00 39.52 3.34
3709 3753 5.523916 CCTAATCCGTACTCTGAACCAAATG 59.476 44.000 0.00 0.00 0.00 2.32
3836 3880 2.046892 ACCCAGTCATGCAGCGTC 60.047 61.111 0.00 0.00 0.00 5.19
4019 4075 2.549754 GCCGTCCTTTATCATGGTGATG 59.450 50.000 2.82 0.00 37.70 3.07
4089 4145 1.135228 GGAGAAGAGCGAGTCCTTGAC 60.135 57.143 0.00 0.00 0.00 3.18
4141 4197 2.860136 TGCGCTAATTCTTGTCATCTCG 59.140 45.455 9.73 0.00 0.00 4.04
4246 4302 7.094631 GGTTTCGGCCAGTTTTTCTTATAAAT 58.905 34.615 2.24 0.00 0.00 1.40
4270 4326 4.058124 CTGGTGTGTATCAATGTATCGGG 58.942 47.826 0.00 0.00 0.00 5.14
4350 4408 2.270257 CGGGTCGTGTGGTGGAGTA 61.270 63.158 0.00 0.00 0.00 2.59
4370 4428 4.382320 TACGGCGGAGTGTTGGCC 62.382 66.667 13.24 0.00 43.42 5.36
4375 4433 1.301165 GGTTTGTACGGCGGAGTGT 60.301 57.895 13.24 0.00 0.00 3.55
4383 4441 5.873179 ATGAGTTTATGTGGTTTGTACGG 57.127 39.130 0.00 0.00 0.00 4.02
4385 4443 8.319143 AGTGTATGAGTTTATGTGGTTTGTAC 57.681 34.615 0.00 0.00 0.00 2.90
4534 4592 4.008933 GCTCAGGTGGAGTGCGGT 62.009 66.667 0.00 0.00 45.88 5.68
4539 4597 1.228583 TCGTCAGCTCAGGTGGAGT 60.229 57.895 3.49 0.00 45.88 3.85
4560 4618 3.834447 CTCGTCGTGTGGTCGGCAA 62.834 63.158 0.00 0.00 35.00 4.52
4566 4624 1.673337 TCGGATCTCGTCGTGTGGT 60.673 57.895 0.00 0.00 40.32 4.16
4576 4634 1.272490 TGTTGTGGAGTGTCGGATCTC 59.728 52.381 0.00 5.12 0.00 2.75
4662 4720 1.976474 TGGCTTTGCGGGTTCATCC 60.976 57.895 0.00 0.00 0.00 3.51
4699 4757 0.841289 TGGAGGTTTGGTCCTTCGTT 59.159 50.000 0.00 0.00 38.02 3.85
4711 4769 4.699522 GGCGACGCCTTGGAGGTT 62.700 66.667 31.30 0.00 46.69 3.50
4730 4788 2.859165 ATTTGTCGCTTCCCTCTTGA 57.141 45.000 0.00 0.00 0.00 3.02
4815 4876 1.688197 CTTCACCACCATTGTTGCCTT 59.312 47.619 0.00 0.00 0.00 4.35
4846 4907 4.821589 CCTCCTTGGAGGCGTCGC 62.822 72.222 21.32 9.22 38.35 5.19
4867 4928 3.744719 CGGCGTCCTCGGACTTCA 61.745 66.667 13.74 0.00 42.54 3.02
4894 4955 1.107114 AGCTCGATCTCGGTCATTGT 58.893 50.000 0.00 0.00 40.29 2.71
4898 4959 0.463833 TGCTAGCTCGATCTCGGTCA 60.464 55.000 17.23 0.00 40.29 4.02
4906 4967 2.372504 TCCCTAGTAGTGCTAGCTCGAT 59.627 50.000 17.23 6.49 44.47 3.59
4916 4977 7.844009 TGTGTATAAGGTTTTCCCTAGTAGTG 58.156 38.462 0.00 0.00 45.47 2.74
4917 4978 7.897565 TCTGTGTATAAGGTTTTCCCTAGTAGT 59.102 37.037 0.00 0.00 45.47 2.73
4918 4979 8.302515 TCTGTGTATAAGGTTTTCCCTAGTAG 57.697 38.462 0.00 0.00 45.47 2.57
4919 4980 8.534496 GTTCTGTGTATAAGGTTTTCCCTAGTA 58.466 37.037 0.00 0.00 45.47 1.82
4920 4981 7.237055 AGTTCTGTGTATAAGGTTTTCCCTAGT 59.763 37.037 0.00 0.00 45.47 2.57
4921 4982 7.621796 AGTTCTGTGTATAAGGTTTTCCCTAG 58.378 38.462 0.00 0.00 45.47 3.02
4922 4983 7.563724 AGTTCTGTGTATAAGGTTTTCCCTA 57.436 36.000 0.00 0.00 45.47 3.53
4924 4985 7.520451 AAAGTTCTGTGTATAAGGTTTTCCC 57.480 36.000 0.00 0.00 41.86 3.97
4925 4986 8.235226 GCTAAAGTTCTGTGTATAAGGTTTTCC 58.765 37.037 0.00 0.00 41.05 3.13
4926 4987 8.780249 TGCTAAAGTTCTGTGTATAAGGTTTTC 58.220 33.333 0.00 0.00 0.00 2.29
4927 4988 8.685838 TGCTAAAGTTCTGTGTATAAGGTTTT 57.314 30.769 0.00 0.00 0.00 2.43
4928 4989 7.937394 ACTGCTAAAGTTCTGTGTATAAGGTTT 59.063 33.333 0.00 0.00 34.57 3.27
4929 4990 7.450903 ACTGCTAAAGTTCTGTGTATAAGGTT 58.549 34.615 0.00 0.00 34.57 3.50
4930 4991 7.005709 ACTGCTAAAGTTCTGTGTATAAGGT 57.994 36.000 0.00 0.00 34.57 3.50
4931 4992 7.222999 GCTACTGCTAAAGTTCTGTGTATAAGG 59.777 40.741 0.00 0.00 40.56 2.69
4932 4993 7.043986 CGCTACTGCTAAAGTTCTGTGTATAAG 60.044 40.741 0.00 0.00 40.56 1.73
4933 4994 6.750501 CGCTACTGCTAAAGTTCTGTGTATAA 59.249 38.462 0.00 0.00 40.56 0.98
4934 4995 6.127814 ACGCTACTGCTAAAGTTCTGTGTATA 60.128 38.462 0.00 0.00 40.56 1.47
4935 4996 5.103000 CGCTACTGCTAAAGTTCTGTGTAT 58.897 41.667 0.00 0.00 40.56 2.29
4936 4997 4.022589 ACGCTACTGCTAAAGTTCTGTGTA 60.023 41.667 0.00 0.00 40.56 2.90
4937 4998 3.243771 ACGCTACTGCTAAAGTTCTGTGT 60.244 43.478 0.00 0.00 40.56 3.72
4938 4999 3.121944 CACGCTACTGCTAAAGTTCTGTG 59.878 47.826 0.00 0.00 40.56 3.66
4939 5000 3.318017 CACGCTACTGCTAAAGTTCTGT 58.682 45.455 0.00 0.00 40.56 3.41
4940 5001 2.668457 CCACGCTACTGCTAAAGTTCTG 59.332 50.000 0.00 0.00 40.56 3.02
4941 5002 2.353803 CCCACGCTACTGCTAAAGTTCT 60.354 50.000 0.00 0.00 40.56 3.01
4942 5003 2.000447 CCCACGCTACTGCTAAAGTTC 59.000 52.381 0.00 0.00 40.56 3.01
4943 5004 1.346722 ACCCACGCTACTGCTAAAGTT 59.653 47.619 0.00 0.00 40.56 2.66
4944 5005 0.974383 ACCCACGCTACTGCTAAAGT 59.026 50.000 0.00 0.00 43.40 2.66
4945 5006 1.067142 TGACCCACGCTACTGCTAAAG 60.067 52.381 0.00 0.00 36.97 1.85
4946 5007 0.970640 TGACCCACGCTACTGCTAAA 59.029 50.000 0.00 0.00 36.97 1.85
4947 5008 0.970640 TTGACCCACGCTACTGCTAA 59.029 50.000 0.00 0.00 36.97 3.09
4948 5009 0.970640 TTTGACCCACGCTACTGCTA 59.029 50.000 0.00 0.00 36.97 3.49
4949 5010 0.107831 TTTTGACCCACGCTACTGCT 59.892 50.000 0.00 0.00 36.97 4.24
4950 5011 0.948678 TTTTTGACCCACGCTACTGC 59.051 50.000 0.00 0.00 0.00 4.40
4982 5043 0.784778 GGCGCGCTACTGCTAATTAG 59.215 55.000 32.29 8.20 36.97 1.73
4983 5044 0.387929 AGGCGCGCTACTGCTAATTA 59.612 50.000 32.29 0.00 36.97 1.40
4984 5045 1.144057 AGGCGCGCTACTGCTAATT 59.856 52.632 32.29 0.93 36.97 1.40
4985 5046 1.592669 CAGGCGCGCTACTGCTAAT 60.593 57.895 32.29 2.84 36.97 1.73
4986 5047 2.202743 CAGGCGCGCTACTGCTAA 60.203 61.111 32.29 0.00 36.97 3.09
4987 5048 3.126074 CTCAGGCGCGCTACTGCTA 62.126 63.158 32.29 13.97 36.97 3.49
4988 5049 4.504916 CTCAGGCGCGCTACTGCT 62.505 66.667 32.29 16.49 36.97 4.24
4990 5051 2.835701 TTTCCTCAGGCGCGCTACTG 62.836 60.000 32.29 28.39 36.07 2.74
4991 5052 2.646175 TTTCCTCAGGCGCGCTACT 61.646 57.895 32.29 18.16 0.00 2.57
4992 5053 2.125673 TTTCCTCAGGCGCGCTAC 60.126 61.111 32.29 15.82 0.00 3.58
4993 5054 2.125673 GTTTCCTCAGGCGCGCTA 60.126 61.111 32.29 15.80 0.00 4.26
5000 5061 3.121030 CAGCGCGGTTTCCTCAGG 61.121 66.667 8.73 0.00 0.00 3.86
5001 5062 3.793144 GCAGCGCGGTTTCCTCAG 61.793 66.667 8.73 0.00 0.00 3.35
5002 5063 4.617520 TGCAGCGCGGTTTCCTCA 62.618 61.111 8.73 0.00 0.00 3.86
5003 5064 3.793144 CTGCAGCGCGGTTTCCTC 61.793 66.667 8.73 0.00 0.00 3.71
5004 5065 2.238847 TATCTGCAGCGCGGTTTCCT 62.239 55.000 8.73 0.00 36.18 3.36
5005 5066 1.366111 TTATCTGCAGCGCGGTTTCC 61.366 55.000 8.73 0.00 36.18 3.13
5006 5067 0.446222 TTTATCTGCAGCGCGGTTTC 59.554 50.000 8.73 3.92 36.18 2.78
5007 5068 0.447801 CTTTATCTGCAGCGCGGTTT 59.552 50.000 8.73 0.00 36.18 3.27
5008 5069 0.391130 TCTTTATCTGCAGCGCGGTT 60.391 50.000 8.73 0.00 36.18 4.44
5009 5070 0.179073 ATCTTTATCTGCAGCGCGGT 60.179 50.000 9.47 4.23 36.18 5.68
5010 5071 0.510359 GATCTTTATCTGCAGCGCGG 59.490 55.000 9.47 2.11 36.06 6.46
5011 5072 1.495878 AGATCTTTATCTGCAGCGCG 58.504 50.000 9.47 0.00 41.08 6.86
5012 5073 2.411409 GCTAGATCTTTATCTGCAGCGC 59.589 50.000 9.47 0.00 42.60 5.92
5013 5074 3.646946 TGCTAGATCTTTATCTGCAGCG 58.353 45.455 9.47 0.00 42.86 5.18
5016 5077 5.563671 CGCTACTGCTAGATCTTTATCTGCA 60.564 44.000 0.00 2.15 42.60 4.41
5017 5078 4.856487 CGCTACTGCTAGATCTTTATCTGC 59.144 45.833 0.00 0.00 42.60 4.26
5018 5079 4.856487 GCGCTACTGCTAGATCTTTATCTG 59.144 45.833 0.00 0.00 42.60 2.90
5019 5080 4.378978 CGCGCTACTGCTAGATCTTTATCT 60.379 45.833 5.56 0.00 44.80 1.98
5020 5081 3.849145 CGCGCTACTGCTAGATCTTTATC 59.151 47.826 5.56 0.00 36.97 1.75
5021 5082 3.827625 CGCGCTACTGCTAGATCTTTAT 58.172 45.455 5.56 0.00 36.97 1.40
5022 5083 2.604855 GCGCGCTACTGCTAGATCTTTA 60.605 50.000 26.67 0.00 36.97 1.85
5023 5084 1.866063 GCGCGCTACTGCTAGATCTTT 60.866 52.381 26.67 0.00 36.97 2.52
5024 5085 0.318275 GCGCGCTACTGCTAGATCTT 60.318 55.000 26.67 0.00 36.97 2.40
5025 5086 1.284408 GCGCGCTACTGCTAGATCT 59.716 57.895 26.67 0.00 36.97 2.75
5026 5087 1.731257 GGCGCGCTACTGCTAGATC 60.731 63.158 32.29 5.31 36.97 2.75
5027 5088 1.739338 AAGGCGCGCTACTGCTAGAT 61.739 55.000 32.29 0.75 36.97 1.98
5028 5089 2.415608 AAGGCGCGCTACTGCTAGA 61.416 57.895 32.29 0.00 36.97 2.43
5029 5090 2.105128 AAGGCGCGCTACTGCTAG 59.895 61.111 32.29 0.00 36.97 3.42
5030 5091 2.202743 CAAGGCGCGCTACTGCTA 60.203 61.111 32.29 0.00 36.97 3.49
5040 5101 0.317519 ACGTGTTTAAAGCAAGGCGC 60.318 50.000 0.00 0.00 42.91 6.53
5041 5102 2.113910 AACGTGTTTAAAGCAAGGCG 57.886 45.000 0.00 0.00 0.00 5.52
5042 5103 4.219143 AGTAACGTGTTTAAAGCAAGGC 57.781 40.909 0.00 0.00 0.00 4.35
5043 5104 6.535274 AGTAGTAACGTGTTTAAAGCAAGG 57.465 37.500 0.00 0.00 0.00 3.61
5044 5105 9.919348 TTTTAGTAGTAACGTGTTTAAAGCAAG 57.081 29.630 0.00 0.00 0.00 4.01
5050 5111 9.553064 TGGGAATTTTAGTAGTAACGTGTTTAA 57.447 29.630 0.00 0.00 0.00 1.52
5051 5112 8.987890 GTGGGAATTTTAGTAGTAACGTGTTTA 58.012 33.333 0.00 0.00 0.00 2.01
5052 5113 7.307337 CGTGGGAATTTTAGTAGTAACGTGTTT 60.307 37.037 0.00 0.00 0.00 2.83
5053 5114 6.146021 CGTGGGAATTTTAGTAGTAACGTGTT 59.854 38.462 0.00 0.00 0.00 3.32
5054 5115 5.634859 CGTGGGAATTTTAGTAGTAACGTGT 59.365 40.000 0.00 0.00 0.00 4.49
5055 5116 5.062558 CCGTGGGAATTTTAGTAGTAACGTG 59.937 44.000 0.00 0.00 0.00 4.49
5056 5117 5.170748 CCGTGGGAATTTTAGTAGTAACGT 58.829 41.667 0.00 0.00 0.00 3.99
5057 5118 4.033243 GCCGTGGGAATTTTAGTAGTAACG 59.967 45.833 0.00 0.00 0.00 3.18
5058 5119 5.181009 AGCCGTGGGAATTTTAGTAGTAAC 58.819 41.667 0.00 0.00 0.00 2.50
5059 5120 5.425196 AGCCGTGGGAATTTTAGTAGTAA 57.575 39.130 0.00 0.00 0.00 2.24
5060 5121 5.425196 AAGCCGTGGGAATTTTAGTAGTA 57.575 39.130 0.00 0.00 0.00 1.82
5061 5122 3.994931 AGCCGTGGGAATTTTAGTAGT 57.005 42.857 0.00 0.00 0.00 2.73
5062 5123 4.272748 GCTAAGCCGTGGGAATTTTAGTAG 59.727 45.833 0.00 0.00 0.00 2.57
5063 5124 4.193865 GCTAAGCCGTGGGAATTTTAGTA 58.806 43.478 0.00 0.00 0.00 1.82
5064 5125 3.014623 GCTAAGCCGTGGGAATTTTAGT 58.985 45.455 0.00 0.00 0.00 2.24
5065 5126 2.357952 GGCTAAGCCGTGGGAATTTTAG 59.642 50.000 0.00 0.00 39.62 1.85
5066 5127 2.371306 GGCTAAGCCGTGGGAATTTTA 58.629 47.619 0.00 0.00 39.62 1.52
5067 5128 1.182667 GGCTAAGCCGTGGGAATTTT 58.817 50.000 0.00 0.00 39.62 1.82
5068 5129 2.882170 GGCTAAGCCGTGGGAATTT 58.118 52.632 0.00 0.00 39.62 1.82
5069 5130 4.657952 GGCTAAGCCGTGGGAATT 57.342 55.556 0.00 0.00 39.62 2.17
5094 5155 7.275123 CGTCATAGATCGCTACTACTATGTGTA 59.725 40.741 0.00 0.00 41.33 2.90
5095 5156 6.091034 CGTCATAGATCGCTACTACTATGTGT 59.909 42.308 0.00 0.00 41.33 3.72
5096 5157 6.310711 TCGTCATAGATCGCTACTACTATGTG 59.689 42.308 0.00 0.00 41.33 3.21
5097 5158 6.396450 TCGTCATAGATCGCTACTACTATGT 58.604 40.000 0.00 0.00 41.33 2.29
5098 5159 6.889019 TCGTCATAGATCGCTACTACTATG 57.111 41.667 0.00 0.00 41.68 2.23


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

AutoCloner maintained by Alex Coulton.