Multiple sequence alignment - TraesCS1B01G051900

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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 TraesCS1B01G051900 chr1B 100.000 5055 0 0 1 5055 32057956 32063010 0.000000e+00 9335.0
1 TraesCS1B01G051900 chr1B 94.911 4716 195 29 358 5055 31966627 31971315 0.000000e+00 7337.0
2 TraesCS1B01G051900 chr1B 90.309 1197 74 16 3129 4311 31908313 31909481 0.000000e+00 1530.0
3 TraesCS1B01G051900 chr1B 88.775 1265 92 20 3802 5055 31911122 31912347 0.000000e+00 1504.0
4 TraesCS1B01G051900 chr1B 92.449 490 28 3 2313 2794 31907672 31908160 0.000000e+00 691.0
5 TraesCS1B01G051900 chr1B 94.458 397 18 2 1304 1697 31906728 31907123 4.330000e-170 608.0
6 TraesCS1B01G051900 chr1B 79.888 716 100 29 3825 4516 32085864 32086559 7.610000e-133 484.0
7 TraesCS1B01G051900 chr1B 82.927 451 44 15 659 1105 31905722 31906143 4.780000e-100 375.0
8 TraesCS1B01G051900 chr1B 94.931 217 11 0 363 579 31905504 31905720 1.740000e-89 340.0
9 TraesCS1B01G051900 chr1B 89.020 255 20 4 3465 3711 32065322 32065576 4.920000e-80 309.0
10 TraesCS1B01G051900 chr1B 88.672 256 21 4 3464 3711 31972376 31972631 6.360000e-79 305.0
11 TraesCS1B01G051900 chr1B 88.372 258 20 5 3464 3711 31913591 31913848 8.220000e-78 302.0
12 TraesCS1B01G051900 chr1B 86.434 258 25 5 3464 3711 32085613 32085870 1.790000e-69 274.0
13 TraesCS1B01G051900 chr1B 87.879 231 21 2 70 300 31966393 31966616 1.080000e-66 265.0
14 TraesCS1B01G051900 chr1B 88.614 202 15 3 99 300 31905291 31905484 6.540000e-59 239.0
15 TraesCS1B01G051900 chr1B 90.909 77 7 0 1018 1094 31967355 31967431 2.490000e-18 104.0
16 TraesCS1B01G051900 chr1B 90.789 76 7 0 1021 1096 31906354 31906429 8.950000e-18 102.0
17 TraesCS1B01G051900 chr1B 96.667 60 1 1 590 648 31966916 31966857 1.160000e-16 99.0
18 TraesCS1B01G051900 chr1B 94.340 53 1 2 822 873 32058732 32058783 4.200000e-11 80.5
19 TraesCS1B01G051900 chr1B 94.340 53 1 2 777 828 32058777 32058828 4.200000e-11 80.5
20 TraesCS1B01G051900 chr1B 93.617 47 2 1 790 836 31905890 31905935 9.080000e-08 69.4
21 TraesCS1B01G051900 chr1D 91.726 1837 117 21 2841 4657 19901145 19902966 0.000000e+00 2518.0
22 TraesCS1B01G051900 chr1D 93.734 1548 79 10 1304 2843 19899580 19901117 0.000000e+00 2305.0
23 TraesCS1B01G051900 chr1D 88.387 930 76 19 378 1305 19898507 19899406 0.000000e+00 1090.0
24 TraesCS1B01G051900 chr1D 90.244 123 12 0 70 192 19898282 19898404 1.460000e-35 161.0
25 TraesCS1B01G051900 chr1D 88.608 79 9 0 1018 1096 19899202 19899280 4.170000e-16 97.1
26 TraesCS1B01G051900 chr1A 90.119 1761 132 18 2912 4641 21338587 21340336 0.000000e+00 2250.0
27 TraesCS1B01G051900 chr1A 89.492 1418 83 22 1304 2718 21336491 21337845 0.000000e+00 1733.0
28 TraesCS1B01G051900 chr1A 91.525 295 19 4 359 648 21335550 21335843 7.880000e-108 401.0
29 TraesCS1B01G051900 chr1A 83.040 454 46 15 643 1096 21335800 21336222 2.860000e-102 383.0
30 TraesCS1B01G051900 chr1A 87.342 79 7 3 572 648 21335860 21335783 2.510000e-13 87.9
31 TraesCS1B01G051900 chr6D 90.679 987 74 14 1743 2722 50777517 50776542 0.000000e+00 1297.0
32 TraesCS1B01G051900 chr6D 86.458 384 45 4 2850 3228 50776084 50775703 1.010000e-111 414.0
33 TraesCS1B01G051900 chr6D 81.386 505 57 19 3214 3695 50775191 50774701 1.330000e-100 377.0
34 TraesCS1B01G051900 chr6D 90.000 90 9 0 1109 1198 50779797 50779708 3.200000e-22 117.0
35 TraesCS1B01G051900 chr6D 92.424 66 5 0 1031 1096 50779797 50779732 1.500000e-15 95.3
36 TraesCS1B01G051900 chr6B 90.112 981 77 13 1743 2717 120646175 120647141 0.000000e+00 1256.0
37 TraesCS1B01G051900 chr6B 83.669 447 43 15 3273 3695 120649122 120649562 1.320000e-105 394.0
38 TraesCS1B01G051900 chr6B 86.452 310 33 4 2912 3213 120647842 120648150 1.050000e-86 331.0
39 TraesCS1B01G051900 chr6B 89.773 88 9 0 1106 1193 120644787 120644874 4.140000e-21 113.0
40 TraesCS1B01G051900 chr6B 91.304 69 6 0 1028 1096 120644787 120644855 1.500000e-15 95.3
41 TraesCS1B01G051900 chr6B 87.838 74 7 2 576 648 708113701 708113773 9.020000e-13 86.1
42 TraesCS1B01G051900 chr6A 89.929 983 76 12 1743 2722 64258295 64259257 0.000000e+00 1245.0
43 TraesCS1B01G051900 chr6A 86.260 393 46 7 2841 3228 64259711 64260100 2.180000e-113 420.0
44 TraesCS1B01G051900 chr6A 83.257 436 52 14 3267 3695 64260925 64261346 1.030000e-101 381.0
45 TraesCS1B01G051900 chr6A 77.311 714 77 41 3746 4396 64261300 64261991 4.850000e-90 342.0
46 TraesCS1B01G051900 chr6A 89.247 93 10 0 1106 1198 64255499 64255591 3.200000e-22 117.0
47 TraesCS1B01G051900 chr6A 91.304 69 6 0 1028 1096 64255499 64255567 1.500000e-15 95.3
48 TraesCS1B01G051900 chr7D 89.146 995 81 14 1743 2722 66826381 66825399 0.000000e+00 1214.0
49 TraesCS1B01G051900 chr7D 85.942 377 34 7 2850 3224 66824485 66824126 7.940000e-103 385.0
50 TraesCS1B01G051900 chr7D 80.271 517 62 25 3749 4245 66823154 66822658 2.240000e-93 353.0
51 TraesCS1B01G051900 chr7D 86.000 300 21 9 3214 3498 66823720 66823427 8.220000e-78 302.0
52 TraesCS1B01G051900 chr7A 89.895 574 48 8 2154 2722 73807268 73807836 0.000000e+00 730.0
53 TraesCS1B01G051900 chr7A 86.811 417 44 6 1743 2156 73806767 73807175 5.970000e-124 455.0
54 TraesCS1B01G051900 chr7A 86.598 388 42 8 2841 3224 73808292 73808673 2.180000e-113 420.0
55 TraesCS1B01G051900 chr7A 79.208 505 64 24 3746 4231 73846895 73847377 3.800000e-81 313.0
56 TraesCS1B01G051900 chr7A 83.275 287 29 8 3225 3498 73809090 73809370 3.910000e-61 246.0
57 TraesCS1B01G051900 chr7A 82.464 211 24 7 3523 3725 73846769 73846974 6.730000e-39 172.0
58 TraesCS1B01G051900 chr7A 97.368 38 1 0 1304 1341 73805790 73805827 1.170000e-06 65.8
59 TraesCS1B01G051900 chr4D 89.706 68 6 1 582 648 26251197 26251130 9.020000e-13 86.1
60 TraesCS1B01G051900 chr4D 87.931 58 7 0 566 623 307814156 307814213 9.080000e-08 69.4
61 TraesCS1B01G051900 chr5A 89.474 57 2 4 563 617 519894564 519894618 9.080000e-08 69.4


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 TraesCS1B01G051900 chr1B 32057956 32063010 5054 False 9335.000000 9335 100.00000 1 5055 1 chr1B.!!$F2 5054
1 TraesCS1B01G051900 chr1B 31966393 31971315 4922 False 2568.666667 7337 91.23300 70 5055 3 chr1B.!!$F5 4985
2 TraesCS1B01G051900 chr1B 31905291 31913848 8557 False 576.040000 1530 90.52410 99 5055 10 chr1B.!!$F4 4956
3 TraesCS1B01G051900 chr1B 32085613 32086559 946 False 379.000000 484 83.16100 3464 4516 2 chr1B.!!$F7 1052
4 TraesCS1B01G051900 chr1D 19898282 19902966 4684 False 1234.220000 2518 90.53980 70 4657 5 chr1D.!!$F1 4587
5 TraesCS1B01G051900 chr1A 21335550 21340336 4786 False 1191.750000 2250 88.54400 359 4641 4 chr1A.!!$F1 4282
6 TraesCS1B01G051900 chr6D 50774701 50779797 5096 True 460.060000 1297 88.18940 1031 3695 5 chr6D.!!$R1 2664
7 TraesCS1B01G051900 chr6B 120644787 120649562 4775 False 437.860000 1256 88.26200 1028 3695 5 chr6B.!!$F2 2667
8 TraesCS1B01G051900 chr6A 64255499 64261991 6492 False 433.383333 1245 86.21800 1028 4396 6 chr6A.!!$F1 3368
9 TraesCS1B01G051900 chr7D 66822658 66826381 3723 True 563.500000 1214 85.33975 1743 4245 4 chr7D.!!$R1 2502
10 TraesCS1B01G051900 chr7A 73805790 73809370 3580 False 383.360000 730 88.78940 1304 3498 5 chr7A.!!$F1 2194
11 TraesCS1B01G051900 chr7A 73846769 73847377 608 False 242.500000 313 80.83600 3523 4231 2 chr7A.!!$F2 708

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
351 352 0.031585 CTCGGTGAACAACTCGGTGA 59.968 55.0 0.00 0.00 0.00 4.02 F
817 900 0.331278 TAATGAGTGCCCTGGGGTTG 59.669 55.0 16.03 0.00 37.65 3.77 F
2690 6848 0.393537 CTAGCTGCAGGTTGAAGGGG 60.394 60.0 25.47 2.54 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 5576 1.555967 GCCAATGGAAAAGGCTACCA 58.444 50.000 2.05 9.71 44.92 3.25 R
2737 7195 2.343387 GCAAGGCGGTGGCAAAAT 59.657 55.556 0.00 0.00 42.47 1.82 R
4635 13578 1.659098 CAAATTCCGTCCGCTCTACAC 59.341 52.381 0.00 0.00 0.00 2.90 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
24 25 7.229581 GACTATTGGGGGATAACTACTAGTG 57.770 44.000 5.39 0.00 0.00 2.74
25 26 6.082707 ACTATTGGGGGATAACTACTAGTGG 58.917 44.000 5.39 4.89 0.00 4.00
26 27 4.630382 TTGGGGGATAACTACTAGTGGA 57.370 45.455 13.86 0.00 0.00 4.02
27 28 4.630382 TGGGGGATAACTACTAGTGGAA 57.370 45.455 13.86 0.89 0.00 3.53
28 29 4.292643 TGGGGGATAACTACTAGTGGAAC 58.707 47.826 13.86 1.41 0.00 3.62
29 30 4.264941 TGGGGGATAACTACTAGTGGAACA 60.265 45.833 13.86 0.00 41.43 3.18
30 31 4.906060 GGGGGATAACTACTAGTGGAACAT 59.094 45.833 13.86 2.76 44.52 2.71
31 32 5.368816 GGGGGATAACTACTAGTGGAACATT 59.631 44.000 13.86 0.00 44.52 2.71
32 33 6.289064 GGGGATAACTACTAGTGGAACATTG 58.711 44.000 13.86 0.00 44.52 2.82
33 34 6.126854 GGGGATAACTACTAGTGGAACATTGT 60.127 42.308 13.86 0.00 44.52 2.71
34 35 6.985059 GGGATAACTACTAGTGGAACATTGTC 59.015 42.308 13.86 4.63 44.52 3.18
35 36 7.147707 GGGATAACTACTAGTGGAACATTGTCT 60.148 40.741 13.86 0.00 44.52 3.41
36 37 7.707035 GGATAACTACTAGTGGAACATTGTCTG 59.293 40.741 13.86 0.00 44.52 3.51
37 38 6.420913 AACTACTAGTGGAACATTGTCTGT 57.579 37.500 13.86 0.00 44.52 3.41
38 39 5.784177 ACTACTAGTGGAACATTGTCTGTG 58.216 41.667 13.86 0.00 44.52 3.66
39 40 4.689612 ACTAGTGGAACATTGTCTGTGT 57.310 40.909 0.00 0.00 44.52 3.72
40 41 4.380531 ACTAGTGGAACATTGTCTGTGTG 58.619 43.478 0.00 0.00 44.52 3.82
41 42 3.281727 AGTGGAACATTGTCTGTGTGT 57.718 42.857 0.00 0.00 44.52 3.72
42 43 2.945008 AGTGGAACATTGTCTGTGTGTG 59.055 45.455 0.00 0.00 44.52 3.82
43 44 2.682856 GTGGAACATTGTCTGTGTGTGT 59.317 45.455 0.00 0.00 44.52 3.72
44 45 2.682352 TGGAACATTGTCTGTGTGTGTG 59.318 45.455 0.00 0.00 38.39 3.82
45 46 2.682856 GGAACATTGTCTGTGTGTGTGT 59.317 45.455 0.00 0.00 38.39 3.72
46 47 3.487376 GGAACATTGTCTGTGTGTGTGTG 60.487 47.826 0.00 0.00 38.39 3.82
47 48 2.710377 ACATTGTCTGTGTGTGTGTGT 58.290 42.857 0.00 0.00 36.48 3.72
48 49 2.419673 ACATTGTCTGTGTGTGTGTGTG 59.580 45.455 0.00 0.00 36.48 3.82
49 50 2.177394 TTGTCTGTGTGTGTGTGTGT 57.823 45.000 0.00 0.00 0.00 3.72
50 51 1.437625 TGTCTGTGTGTGTGTGTGTG 58.562 50.000 0.00 0.00 0.00 3.82
51 52 1.270571 TGTCTGTGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
52 53 1.128507 GTCTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
53 54 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
54 55 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
55 56 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
56 57 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
57 58 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
58 59 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
59 60 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
60 61 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
61 62 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
62 63 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
63 64 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
64 65 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
65 66 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
66 67 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
67 68 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
68 69 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
84 85 3.789224 GTGTGTGTTGGTTGTCGAAAATC 59.211 43.478 0.00 0.00 0.00 2.17
85 86 3.033185 GTGTGTTGGTTGTCGAAAATCG 58.967 45.455 0.00 0.00 42.10 3.34
174 175 1.148273 GTGGCACAACACCAGAGGA 59.852 57.895 13.86 0.00 44.16 3.71
175 176 0.886490 GTGGCACAACACCAGAGGAG 60.886 60.000 13.86 0.00 44.16 3.69
176 177 1.302832 GGCACAACACCAGAGGAGG 60.303 63.158 0.00 0.00 0.00 4.30
185 186 0.545548 ACCAGAGGAGGTGGGAAGTC 60.546 60.000 0.00 0.00 41.30 3.01
188 189 0.191064 AGAGGAGGTGGGAAGTCACA 59.809 55.000 0.00 0.00 39.27 3.58
209 210 6.206634 TCACATTTGCAAAGAGTAACCCTTAG 59.793 38.462 18.19 4.85 0.00 2.18
225 226 5.876357 ACCCTTAGCTAGTGATTTTGAACA 58.124 37.500 0.00 0.00 0.00 3.18
226 227 6.303839 ACCCTTAGCTAGTGATTTTGAACAA 58.696 36.000 0.00 0.00 0.00 2.83
227 228 6.948309 ACCCTTAGCTAGTGATTTTGAACAAT 59.052 34.615 0.00 0.00 0.00 2.71
228 229 7.451566 ACCCTTAGCTAGTGATTTTGAACAATT 59.548 33.333 0.00 0.00 0.00 2.32
273 274 1.677633 GGCCGGTGCACCATAAACT 60.678 57.895 34.16 0.00 40.13 2.66
278 279 1.468520 CGGTGCACCATAAACTGAAGG 59.531 52.381 34.16 10.51 35.14 3.46
302 303 4.675404 GGTGAACGACTCCAGTGG 57.325 61.111 1.40 1.40 32.94 4.00
303 304 1.746517 GGTGAACGACTCCAGTGGT 59.253 57.895 9.54 0.00 38.65 4.16
304 305 0.963962 GGTGAACGACTCCAGTGGTA 59.036 55.000 9.54 0.00 35.94 3.25
306 307 1.067776 GTGAACGACTCCAGTGGTAGG 60.068 57.143 9.54 3.64 35.94 3.18
307 308 0.531200 GAACGACTCCAGTGGTAGGG 59.469 60.000 9.54 5.03 35.94 3.53
309 310 0.178941 ACGACTCCAGTGGTAGGGTT 60.179 55.000 9.54 0.00 35.21 4.11
310 311 0.246635 CGACTCCAGTGGTAGGGTTG 59.753 60.000 9.54 4.88 0.00 3.77
311 312 1.640917 GACTCCAGTGGTAGGGTTGA 58.359 55.000 9.54 0.00 0.00 3.18
312 313 1.275573 GACTCCAGTGGTAGGGTTGAC 59.724 57.143 9.54 0.00 0.00 3.18
313 314 0.246635 CTCCAGTGGTAGGGTTGACG 59.753 60.000 9.54 0.00 0.00 4.35
314 315 1.375523 CCAGTGGTAGGGTTGACGC 60.376 63.158 0.00 0.00 0.00 5.19
315 316 1.671742 CAGTGGTAGGGTTGACGCT 59.328 57.895 5.99 5.99 42.15 5.07
316 317 0.034896 CAGTGGTAGGGTTGACGCTT 59.965 55.000 6.01 0.00 39.91 4.68
317 318 1.274167 CAGTGGTAGGGTTGACGCTTA 59.726 52.381 6.01 0.00 39.91 3.09
318 319 1.972795 AGTGGTAGGGTTGACGCTTAA 59.027 47.619 6.01 0.00 39.91 1.85
319 320 2.071540 GTGGTAGGGTTGACGCTTAAC 58.928 52.381 6.01 0.00 39.91 2.01
320 321 1.972795 TGGTAGGGTTGACGCTTAACT 59.027 47.619 6.01 0.00 39.91 2.24
321 322 3.056607 GTGGTAGGGTTGACGCTTAACTA 60.057 47.826 6.01 0.00 39.91 2.24
322 323 3.194116 TGGTAGGGTTGACGCTTAACTAG 59.806 47.826 6.01 0.00 39.91 2.57
323 324 3.194329 GGTAGGGTTGACGCTTAACTAGT 59.806 47.826 6.01 0.00 39.91 2.57
324 325 3.314541 AGGGTTGACGCTTAACTAGTG 57.685 47.619 0.00 0.00 40.32 2.74
325 326 2.895404 AGGGTTGACGCTTAACTAGTGA 59.105 45.455 0.00 0.00 37.80 3.41
326 327 3.322828 AGGGTTGACGCTTAACTAGTGAA 59.677 43.478 0.00 0.00 37.80 3.18
327 328 3.678548 GGGTTGACGCTTAACTAGTGAAG 59.321 47.826 14.93 14.93 37.80 3.02
328 329 3.678548 GGTTGACGCTTAACTAGTGAAGG 59.321 47.826 19.78 12.76 37.80 3.46
329 330 2.955614 TGACGCTTAACTAGTGAAGGC 58.044 47.619 19.78 11.35 37.80 4.35
330 331 2.297880 TGACGCTTAACTAGTGAAGGCA 59.702 45.455 19.78 3.08 37.80 4.75
331 332 3.243941 TGACGCTTAACTAGTGAAGGCAA 60.244 43.478 19.78 2.14 37.80 4.52
332 333 3.064931 ACGCTTAACTAGTGAAGGCAAC 58.935 45.455 19.78 4.10 37.80 4.17
333 334 3.244112 ACGCTTAACTAGTGAAGGCAACT 60.244 43.478 19.78 0.00 43.49 3.16
334 335 5.091828 ACGCTTAACTAGTGAAGGCAACTC 61.092 45.833 19.78 3.13 41.71 3.01
345 346 2.702847 GGCAACTCGGTGAACAACT 58.297 52.632 0.00 0.00 0.00 3.16
346 347 0.586802 GGCAACTCGGTGAACAACTC 59.413 55.000 0.00 0.00 0.00 3.01
347 348 0.232303 GCAACTCGGTGAACAACTCG 59.768 55.000 0.00 0.00 0.00 4.18
348 349 0.859232 CAACTCGGTGAACAACTCGG 59.141 55.000 0.00 0.00 0.00 4.63
349 350 0.462789 AACTCGGTGAACAACTCGGT 59.537 50.000 0.00 0.00 0.00 4.69
350 351 0.249322 ACTCGGTGAACAACTCGGTG 60.249 55.000 0.00 0.00 0.00 4.94
351 352 0.031585 CTCGGTGAACAACTCGGTGA 59.968 55.000 0.00 0.00 0.00 4.02
352 353 0.460722 TCGGTGAACAACTCGGTGAA 59.539 50.000 0.00 0.00 0.00 3.18
353 354 0.580104 CGGTGAACAACTCGGTGAAC 59.420 55.000 0.00 0.00 0.00 3.18
354 355 1.805120 CGGTGAACAACTCGGTGAACT 60.805 52.381 0.00 0.00 0.00 3.01
355 356 2.544277 CGGTGAACAACTCGGTGAACTA 60.544 50.000 0.00 0.00 0.00 2.24
356 357 3.057734 GGTGAACAACTCGGTGAACTAG 58.942 50.000 0.00 0.00 0.00 2.57
368 373 3.113043 GGTGAACTAGGGTGGATACCTT 58.887 50.000 0.00 0.00 46.66 3.50
439 447 5.734720 TCTTGATCCATTCCTGTCTGTTAC 58.265 41.667 0.00 0.00 0.00 2.50
453 461 2.805295 TCTGTTACAGGGTTGACGCAAG 60.805 50.000 12.79 0.00 36.09 4.01
659 700 9.762381 AGACTTATATTTGGAGACTCTATAGGG 57.238 37.037 0.00 0.00 0.00 3.53
660 701 9.756571 GACTTATATTTGGAGACTCTATAGGGA 57.243 37.037 6.63 0.00 0.00 4.20
665 706 7.790782 ATTTGGAGACTCTATAGGGATTCTC 57.209 40.000 6.63 9.03 39.64 2.87
666 707 6.538209 TTGGAGACTCTATAGGGATTCTCT 57.462 41.667 16.06 5.44 39.99 3.10
667 708 7.649702 TTGGAGACTCTATAGGGATTCTCTA 57.350 40.000 16.06 10.03 39.99 2.43
668 709 7.649702 TGGAGACTCTATAGGGATTCTCTAA 57.350 40.000 16.06 6.29 39.99 2.10
669 710 7.695055 TGGAGACTCTATAGGGATTCTCTAAG 58.305 42.308 16.06 0.00 39.99 2.18
670 711 7.517953 TGGAGACTCTATAGGGATTCTCTAAGA 59.482 40.741 16.06 2.18 39.99 2.10
671 712 8.387813 GGAGACTCTATAGGGATTCTCTAAGAA 58.612 40.741 16.06 0.00 39.99 2.52
672 713 9.449719 GAGACTCTATAGGGATTCTCTAAGAAG 57.550 40.741 6.63 0.00 37.69 2.85
673 714 9.177927 AGACTCTATAGGGATTCTCTAAGAAGA 57.822 37.037 6.63 1.28 37.69 2.87
674 715 9.227777 GACTCTATAGGGATTCTCTAAGAAGAC 57.772 40.741 6.63 0.00 37.69 3.01
675 716 8.955794 ACTCTATAGGGATTCTCTAAGAAGACT 58.044 37.037 6.63 0.00 37.69 3.24
676 717 9.807921 CTCTATAGGGATTCTCTAAGAAGACTT 57.192 37.037 0.00 0.00 37.69 3.01
753 836 5.503031 GCACACATGATCTGTATACTTGCAC 60.503 44.000 0.00 0.00 35.91 4.57
768 851 3.569701 ACTTGCACACCTAATCAAACCAG 59.430 43.478 0.00 0.00 0.00 4.00
782 865 5.178096 TCAAACCAGAGATGGCAATTAGA 57.822 39.130 0.00 0.00 0.00 2.10
794 877 2.091830 GGCAATTAGAGCCCTAGGGTTT 60.092 50.000 28.96 17.62 46.50 3.27
802 885 5.568620 AGAGCCCTAGGGTTTGTATAATG 57.431 43.478 28.96 0.00 37.65 1.90
807 890 5.063880 CCCTAGGGTTTGTATAATGAGTGC 58.936 45.833 20.88 0.00 0.00 4.40
808 891 5.063880 CCTAGGGTTTGTATAATGAGTGCC 58.936 45.833 0.00 0.00 0.00 5.01
811 894 3.632145 GGGTTTGTATAATGAGTGCCCTG 59.368 47.826 0.00 0.00 0.00 4.45
812 895 3.632145 GGTTTGTATAATGAGTGCCCTGG 59.368 47.826 0.00 0.00 0.00 4.45
813 896 3.576078 TTGTATAATGAGTGCCCTGGG 57.424 47.619 8.86 8.86 0.00 4.45
814 897 1.774254 TGTATAATGAGTGCCCTGGGG 59.226 52.381 16.03 4.75 38.57 4.96
815 898 1.774856 GTATAATGAGTGCCCTGGGGT 59.225 52.381 16.03 0.00 37.65 4.95
816 899 1.308877 ATAATGAGTGCCCTGGGGTT 58.691 50.000 16.03 0.00 37.65 4.11
817 900 0.331278 TAATGAGTGCCCTGGGGTTG 59.669 55.000 16.03 0.00 37.65 3.77
818 901 1.729267 AATGAGTGCCCTGGGGTTGT 61.729 55.000 16.03 0.00 37.65 3.32
819 902 0.844661 ATGAGTGCCCTGGGGTTGTA 60.845 55.000 16.03 0.00 37.65 2.41
820 903 0.844661 TGAGTGCCCTGGGGTTGTAT 60.845 55.000 16.03 0.00 37.65 2.29
823 906 2.174854 GAGTGCCCTGGGGTTGTATAAT 59.825 50.000 16.03 0.00 37.65 1.28
826 909 4.141251 AGTGCCCTGGGGTTGTATAATTAG 60.141 45.833 16.03 0.00 37.65 1.73
828 911 4.976442 TGCCCTGGGGTTGTATAATTAGTA 59.024 41.667 16.03 0.00 37.65 1.82
876 959 4.141251 CCTGGGGTTGTATAATTAGTGCCT 60.141 45.833 0.00 0.00 0.00 4.75
880 963 5.442391 GGGTTGTATAATTAGTGCCTTGGA 58.558 41.667 0.00 0.00 0.00 3.53
892 975 3.006247 GTGCCTTGGAGCTCTCTAAAAG 58.994 50.000 14.64 9.59 29.67 2.27
895 981 4.075682 GCCTTGGAGCTCTCTAAAAGTTT 58.924 43.478 14.64 0.00 29.67 2.66
896 982 5.221843 TGCCTTGGAGCTCTCTAAAAGTTTA 60.222 40.000 14.64 0.00 29.67 2.01
897 983 5.352846 GCCTTGGAGCTCTCTAAAAGTTTAG 59.647 44.000 14.64 4.70 41.10 1.85
961 1047 1.675310 CAAAGCAGCCACCCGATCA 60.675 57.895 0.00 0.00 0.00 2.92
965 1051 1.153086 GCAGCCACCCGATCATTCT 60.153 57.895 0.00 0.00 0.00 2.40
1029 1115 4.320456 CACACCAGTGCCGCCTCT 62.320 66.667 0.00 0.00 39.21 3.69
1058 1144 2.825836 GCTGCGGCATTACTGGCT 60.826 61.111 14.08 0.00 45.42 4.75
1121 1207 2.202987 CTCTGCCTCCGATGTGCC 60.203 66.667 0.00 0.00 0.00 5.01
1150 1531 3.391382 GGCGGTGCTACTGGGAGT 61.391 66.667 0.00 0.00 0.00 3.85
1400 2550 3.499338 TGTTTCTTGCTTCACCATCCAT 58.501 40.909 0.00 0.00 0.00 3.41
1539 3274 4.261447 GGTTGGTTCACCTTGACAATGTAC 60.261 45.833 0.00 0.00 36.82 2.90
2094 5670 3.431912 TGAAATCCTTGTGTTCATCGTCG 59.568 43.478 0.00 0.00 0.00 5.12
2112 5688 2.034507 GTCGCGCAATCTCATACTTCAC 60.035 50.000 8.75 0.00 0.00 3.18
2115 5691 3.180584 CGCGCAATCTCATACTTCACTAC 59.819 47.826 8.75 0.00 0.00 2.73
2116 5692 4.112634 GCGCAATCTCATACTTCACTACA 58.887 43.478 0.30 0.00 0.00 2.74
2249 5932 3.139077 ACATCCTTTTCAGGTGTTCGAC 58.861 45.455 0.00 0.00 41.69 4.20
2399 6546 1.329599 GTTCGACTCTTTGCCGTTTGT 59.670 47.619 0.00 0.00 0.00 2.83
2408 6555 3.942748 TCTTTGCCGTTTGTCTGTACTTT 59.057 39.130 0.00 0.00 0.00 2.66
2453 6600 4.523943 TGTACGGTCACTGTAGTTGGTATT 59.476 41.667 0.00 0.00 0.00 1.89
2479 6636 5.703592 TGCTGTTATTGGAACTAAACATCGT 59.296 36.000 0.00 0.00 31.88 3.73
2638 6796 0.830648 CATTCCGCCACTTCTAGGGA 59.169 55.000 0.00 0.00 0.00 4.20
2645 6803 3.458189 CGCCACTTCTAGGGAATGTTAG 58.542 50.000 0.00 0.00 0.00 2.34
2675 6833 3.866651 ACACATGTCTGGATTGTCTAGC 58.133 45.455 0.00 0.00 0.00 3.42
2690 6848 0.393537 CTAGCTGCAGGTTGAAGGGG 60.394 60.000 25.47 2.54 0.00 4.79
2737 7195 4.985538 AGCAAGTCCTTCCTAATTGTGAA 58.014 39.130 0.00 0.00 0.00 3.18
2941 8107 7.614192 TGAATTACTCCTTTTCATACCTTTCCC 59.386 37.037 0.00 0.00 0.00 3.97
3338 9911 3.939740 ATCATGATACAAGTGGGCAGT 57.060 42.857 6.36 0.00 0.00 4.40
3403 9976 5.772521 CTGCTTTGTACTTTTGGCAGTTAT 58.227 37.500 14.06 0.00 41.21 1.89
3589 10284 7.175104 TCTTTTGCTGATCCTAGTGGTAAAAT 58.825 34.615 0.00 0.00 34.23 1.82
3604 10299 6.895204 AGTGGTAAAATAACTGCATGGGTATT 59.105 34.615 0.00 0.00 0.00 1.89
3936 10646 1.205460 ACGGGCCTTACCATTGGAGT 61.205 55.000 10.37 0.00 42.05 3.85
3955 10669 7.681939 TGGAGTTTTATCATTTGTACTGGAC 57.318 36.000 0.00 0.00 0.00 4.02
4060 12954 3.198872 GCTGCCTAACCAATGAGACTAC 58.801 50.000 0.00 0.00 0.00 2.73
4347 13282 9.120538 GGAGATCCACTTTGTATTGCTAAAATA 57.879 33.333 0.00 0.00 35.64 1.40
4586 13529 5.283294 TGAACGATATGGTTACGGTATGTG 58.717 41.667 2.80 0.00 0.00 3.21
4600 13543 3.553511 CGGTATGTGTCTCTTGATCTTGC 59.446 47.826 0.00 0.00 0.00 4.01
4625 13568 5.523588 AGTCTTGTCCAGATTCTATCCTGA 58.476 41.667 0.00 0.00 32.60 3.86
4635 13578 5.976534 CAGATTCTATCCTGACTTCGTCTTG 59.023 44.000 0.00 0.00 33.15 3.02
4643 13586 3.238441 CTGACTTCGTCTTGTGTAGAGC 58.762 50.000 0.00 0.00 32.23 4.09
4749 13694 4.631377 CCATGTGTGACGTGTTGATTATCT 59.369 41.667 0.00 0.00 33.37 1.98
4769 13714 1.543358 TGTTGATGGCGCAATTTGCTA 59.457 42.857 18.57 6.13 42.25 3.49
4831 13778 6.529125 GGTTTTGATTTCACATGATAGTGCAG 59.471 38.462 0.00 0.00 39.35 4.41
4864 13811 5.292589 CCAAGATGGCTATTGCAACATTTTC 59.707 40.000 0.00 0.00 41.91 2.29
4943 13890 2.357569 GCCAAGGATGAGGGAGATTGTT 60.358 50.000 0.00 0.00 0.00 2.83
5009 13956 2.224378 CCGAGATGGTGTCCAAGCATAT 60.224 50.000 0.00 0.00 46.95 1.78
5035 13982 3.031736 GTCATACACAAGCTCCCTCCTA 58.968 50.000 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.210984 CCACTAGTAGTTATCCCCCAATAGTC 59.789 46.154 0.00 0.00 0.00 2.59
1 2 6.082707 CCACTAGTAGTTATCCCCCAATAGT 58.917 44.000 0.00 0.00 0.00 2.12
2 3 6.320518 TCCACTAGTAGTTATCCCCCAATAG 58.679 44.000 0.00 0.00 0.00 1.73
3 4 6.297830 TCCACTAGTAGTTATCCCCCAATA 57.702 41.667 0.00 0.00 0.00 1.90
5 6 4.630382 TCCACTAGTAGTTATCCCCCAA 57.370 45.455 0.00 0.00 0.00 4.12
6 7 4.264941 TGTTCCACTAGTAGTTATCCCCCA 60.265 45.833 0.00 0.00 0.00 4.96
7 8 4.292643 TGTTCCACTAGTAGTTATCCCCC 58.707 47.826 0.00 0.00 0.00 5.40
8 9 6.126854 ACAATGTTCCACTAGTAGTTATCCCC 60.127 42.308 0.00 0.00 0.00 4.81
9 10 6.885922 ACAATGTTCCACTAGTAGTTATCCC 58.114 40.000 0.00 0.00 0.00 3.85
10 11 7.707035 CAGACAATGTTCCACTAGTAGTTATCC 59.293 40.741 0.00 0.00 0.00 2.59
11 12 8.251721 ACAGACAATGTTCCACTAGTAGTTATC 58.748 37.037 0.00 0.00 39.96 1.75
12 13 8.035394 CACAGACAATGTTCCACTAGTAGTTAT 58.965 37.037 0.00 0.00 41.41 1.89
13 14 7.014905 ACACAGACAATGTTCCACTAGTAGTTA 59.985 37.037 0.00 0.00 41.41 2.24
14 15 6.183360 ACACAGACAATGTTCCACTAGTAGTT 60.183 38.462 0.00 0.00 41.41 2.24
15 16 5.304614 ACACAGACAATGTTCCACTAGTAGT 59.695 40.000 0.00 0.00 41.41 2.73
16 17 5.635280 CACACAGACAATGTTCCACTAGTAG 59.365 44.000 0.00 0.00 41.41 2.57
17 18 5.069914 ACACACAGACAATGTTCCACTAGTA 59.930 40.000 0.00 0.00 41.41 1.82
18 19 4.141711 ACACACAGACAATGTTCCACTAGT 60.142 41.667 0.00 0.00 41.41 2.57
19 20 4.212004 CACACACAGACAATGTTCCACTAG 59.788 45.833 0.00 0.00 41.41 2.57
20 21 4.126437 CACACACAGACAATGTTCCACTA 58.874 43.478 0.00 0.00 41.41 2.74
21 22 2.945008 CACACACAGACAATGTTCCACT 59.055 45.455 0.00 0.00 41.41 4.00
22 23 2.682856 ACACACACAGACAATGTTCCAC 59.317 45.455 0.00 0.00 41.41 4.02
23 24 2.682352 CACACACACAGACAATGTTCCA 59.318 45.455 0.00 0.00 41.41 3.53
24 25 2.682856 ACACACACACAGACAATGTTCC 59.317 45.455 0.00 0.00 41.41 3.62
25 26 3.126858 ACACACACACACAGACAATGTTC 59.873 43.478 0.00 0.00 41.41 3.18
26 27 3.081061 ACACACACACACAGACAATGTT 58.919 40.909 0.00 0.00 41.41 2.71
27 28 2.419673 CACACACACACACAGACAATGT 59.580 45.455 0.00 0.00 45.43 2.71
28 29 2.419673 ACACACACACACACAGACAATG 59.580 45.455 0.00 0.00 0.00 2.82
29 30 2.419673 CACACACACACACACAGACAAT 59.580 45.455 0.00 0.00 0.00 2.71
30 31 1.803555 CACACACACACACACAGACAA 59.196 47.619 0.00 0.00 0.00 3.18
31 32 1.270571 ACACACACACACACACAGACA 60.271 47.619 0.00 0.00 0.00 3.41
32 33 1.128507 CACACACACACACACACAGAC 59.871 52.381 0.00 0.00 0.00 3.51
33 34 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
34 35 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
35 36 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
36 37 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
37 38 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
38 39 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
39 40 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
40 41 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
41 42 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
42 43 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
43 44 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
44 45 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
45 46 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
46 47 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
47 48 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
48 49 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
49 50 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
50 51 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
51 52 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
52 53 1.400888 CCAACACACACACACACACAC 60.401 52.381 0.00 0.00 0.00 3.82
53 54 0.877743 CCAACACACACACACACACA 59.122 50.000 0.00 0.00 0.00 3.72
54 55 0.878416 ACCAACACACACACACACAC 59.122 50.000 0.00 0.00 0.00 3.82
55 56 1.268079 CAACCAACACACACACACACA 59.732 47.619 0.00 0.00 0.00 3.72
56 57 1.268352 ACAACCAACACACACACACAC 59.732 47.619 0.00 0.00 0.00 3.82
57 58 1.537638 GACAACCAACACACACACACA 59.462 47.619 0.00 0.00 0.00 3.72
58 59 1.465020 CGACAACCAACACACACACAC 60.465 52.381 0.00 0.00 0.00 3.82
59 60 0.799393 CGACAACCAACACACACACA 59.201 50.000 0.00 0.00 0.00 3.72
60 61 1.080298 TCGACAACCAACACACACAC 58.920 50.000 0.00 0.00 0.00 3.82
61 62 1.809684 TTCGACAACCAACACACACA 58.190 45.000 0.00 0.00 0.00 3.72
62 63 2.904011 TTTCGACAACCAACACACAC 57.096 45.000 0.00 0.00 0.00 3.82
63 64 3.486043 CGATTTTCGACAACCAACACACA 60.486 43.478 0.00 0.00 43.74 3.72
64 65 3.033185 CGATTTTCGACAACCAACACAC 58.967 45.455 0.00 0.00 43.74 3.82
65 66 2.937149 TCGATTTTCGACAACCAACACA 59.063 40.909 0.00 0.00 44.82 3.72
66 67 3.595709 TCGATTTTCGACAACCAACAC 57.404 42.857 0.00 0.00 44.82 3.32
84 85 4.562789 TGCATCTCATCTCGTTTTACTTCG 59.437 41.667 0.00 0.00 0.00 3.79
85 86 6.408858 TTGCATCTCATCTCGTTTTACTTC 57.591 37.500 0.00 0.00 0.00 3.01
91 92 4.758674 CCCATATTGCATCTCATCTCGTTT 59.241 41.667 0.00 0.00 0.00 3.60
133 134 8.197439 CCACTTGTCACTTACACATGATATAGA 58.803 37.037 0.00 0.00 38.00 1.98
174 175 1.133513 TGCAAATGTGACTTCCCACCT 60.134 47.619 0.00 0.00 36.26 4.00
175 176 1.327303 TGCAAATGTGACTTCCCACC 58.673 50.000 0.00 0.00 36.26 4.61
176 177 3.068024 TCTTTGCAAATGTGACTTCCCAC 59.932 43.478 13.23 0.00 37.55 4.61
185 186 4.853924 AGGGTTACTCTTTGCAAATGTG 57.146 40.909 13.23 10.08 0.00 3.21
188 189 5.325239 AGCTAAGGGTTACTCTTTGCAAAT 58.675 37.500 27.18 9.40 42.43 2.32
267 268 3.074412 CACCGAGTTGCCTTCAGTTTAT 58.926 45.455 0.00 0.00 0.00 1.40
273 274 0.878523 CGTTCACCGAGTTGCCTTCA 60.879 55.000 0.00 0.00 39.56 3.02
278 279 4.338327 AGTCGTTCACCGAGTTGC 57.662 55.556 0.00 0.00 46.96 4.17
283 284 1.658114 CACTGGAGTCGTTCACCGA 59.342 57.895 0.00 0.00 45.00 4.69
300 301 1.972795 AGTTAAGCGTCAACCCTACCA 59.027 47.619 0.00 0.00 0.00 3.25
301 302 2.756840 AGTTAAGCGTCAACCCTACC 57.243 50.000 0.00 0.00 0.00 3.18
302 303 4.082571 TCACTAGTTAAGCGTCAACCCTAC 60.083 45.833 0.00 0.00 0.00 3.18
303 304 4.081406 TCACTAGTTAAGCGTCAACCCTA 58.919 43.478 0.00 0.00 0.00 3.53
304 305 2.895404 TCACTAGTTAAGCGTCAACCCT 59.105 45.455 0.00 0.00 0.00 4.34
306 307 3.678548 CCTTCACTAGTTAAGCGTCAACC 59.321 47.826 10.76 0.00 0.00 3.77
307 308 3.123116 GCCTTCACTAGTTAAGCGTCAAC 59.877 47.826 10.76 0.00 0.00 3.18
309 310 2.297880 TGCCTTCACTAGTTAAGCGTCA 59.702 45.455 10.76 6.08 0.00 4.35
310 311 2.955614 TGCCTTCACTAGTTAAGCGTC 58.044 47.619 10.76 3.93 0.00 5.19
311 312 3.064931 GTTGCCTTCACTAGTTAAGCGT 58.935 45.455 10.76 0.00 0.00 5.07
312 313 3.326747 AGTTGCCTTCACTAGTTAAGCG 58.673 45.455 10.76 6.21 0.00 4.68
313 314 3.368236 CGAGTTGCCTTCACTAGTTAAGC 59.632 47.826 10.76 7.52 0.00 3.09
314 315 3.927142 CCGAGTTGCCTTCACTAGTTAAG 59.073 47.826 9.47 9.47 0.00 1.85
315 316 3.322828 ACCGAGTTGCCTTCACTAGTTAA 59.677 43.478 0.00 0.00 0.00 2.01
316 317 2.895404 ACCGAGTTGCCTTCACTAGTTA 59.105 45.455 0.00 0.00 0.00 2.24
317 318 1.692519 ACCGAGTTGCCTTCACTAGTT 59.307 47.619 0.00 0.00 0.00 2.24
318 319 1.000955 CACCGAGTTGCCTTCACTAGT 59.999 52.381 0.00 0.00 0.00 2.57
319 320 1.272490 TCACCGAGTTGCCTTCACTAG 59.728 52.381 0.00 0.00 0.00 2.57
320 321 1.334160 TCACCGAGTTGCCTTCACTA 58.666 50.000 0.00 0.00 0.00 2.74
321 322 0.468226 TTCACCGAGTTGCCTTCACT 59.532 50.000 0.00 0.00 0.00 3.41
322 323 0.586802 GTTCACCGAGTTGCCTTCAC 59.413 55.000 0.00 0.00 0.00 3.18
323 324 0.179234 TGTTCACCGAGTTGCCTTCA 59.821 50.000 0.00 0.00 0.00 3.02
324 325 1.002792 GTTGTTCACCGAGTTGCCTTC 60.003 52.381 0.00 0.00 0.00 3.46
325 326 1.021968 GTTGTTCACCGAGTTGCCTT 58.978 50.000 0.00 0.00 0.00 4.35
326 327 0.180406 AGTTGTTCACCGAGTTGCCT 59.820 50.000 0.00 0.00 0.00 4.75
327 328 0.586802 GAGTTGTTCACCGAGTTGCC 59.413 55.000 0.00 0.00 0.00 4.52
328 329 0.232303 CGAGTTGTTCACCGAGTTGC 59.768 55.000 0.00 0.00 0.00 4.17
329 330 0.859232 CCGAGTTGTTCACCGAGTTG 59.141 55.000 0.00 0.00 0.00 3.16
330 331 0.462789 ACCGAGTTGTTCACCGAGTT 59.537 50.000 0.00 0.00 0.00 3.01
331 332 0.249322 CACCGAGTTGTTCACCGAGT 60.249 55.000 0.00 0.00 0.00 4.18
332 333 0.031585 TCACCGAGTTGTTCACCGAG 59.968 55.000 0.00 0.00 0.00 4.63
333 334 0.460722 TTCACCGAGTTGTTCACCGA 59.539 50.000 0.00 0.00 0.00 4.69
334 335 0.580104 GTTCACCGAGTTGTTCACCG 59.420 55.000 0.00 0.00 0.00 4.94
335 336 1.949465 AGTTCACCGAGTTGTTCACC 58.051 50.000 0.00 0.00 0.00 4.02
336 337 3.057734 CCTAGTTCACCGAGTTGTTCAC 58.942 50.000 0.00 0.00 0.00 3.18
337 338 2.036733 CCCTAGTTCACCGAGTTGTTCA 59.963 50.000 0.00 0.00 0.00 3.18
338 339 2.036862 ACCCTAGTTCACCGAGTTGTTC 59.963 50.000 0.00 0.00 0.00 3.18
339 340 2.044758 ACCCTAGTTCACCGAGTTGTT 58.955 47.619 0.00 0.00 0.00 2.83
340 341 1.343465 CACCCTAGTTCACCGAGTTGT 59.657 52.381 0.00 0.00 0.00 3.32
341 342 1.337823 CCACCCTAGTTCACCGAGTTG 60.338 57.143 0.00 0.00 0.00 3.16
342 343 0.974383 CCACCCTAGTTCACCGAGTT 59.026 55.000 0.00 0.00 0.00 3.01
343 344 0.113776 TCCACCCTAGTTCACCGAGT 59.886 55.000 0.00 0.00 0.00 4.18
344 345 1.486211 ATCCACCCTAGTTCACCGAG 58.514 55.000 0.00 0.00 0.00 4.63
345 346 2.381911 GTATCCACCCTAGTTCACCGA 58.618 52.381 0.00 0.00 0.00 4.69
346 347 1.411612 GGTATCCACCCTAGTTCACCG 59.588 57.143 0.00 0.00 39.11 4.94
439 447 2.002586 CATCTACTTGCGTCAACCCTG 58.997 52.381 0.00 0.00 0.00 4.45
479 487 6.959639 AGAACACATGACCAAAAGTACAAT 57.040 33.333 0.00 0.00 0.00 2.71
614 623 5.422214 GTCTTTTTAGAGACTCCATGGGA 57.578 43.478 13.02 0.00 42.18 4.37
647 688 9.177927 TCTTCTTAGAGAATCCCTATAGAGTCT 57.822 37.037 0.00 0.00 43.49 3.24
648 689 9.227777 GTCTTCTTAGAGAATCCCTATAGAGTC 57.772 40.741 0.00 0.00 33.13 3.36
649 690 8.955794 AGTCTTCTTAGAGAATCCCTATAGAGT 58.044 37.037 0.00 0.00 33.13 3.24
650 691 9.807921 AAGTCTTCTTAGAGAATCCCTATAGAG 57.192 37.037 0.00 0.00 33.13 2.43
665 706 9.680315 CCGTTCCTACATATAAAGTCTTCTTAG 57.320 37.037 0.00 0.00 33.09 2.18
666 707 9.412460 TCCGTTCCTACATATAAAGTCTTCTTA 57.588 33.333 0.00 0.00 33.09 2.10
667 708 8.302515 TCCGTTCCTACATATAAAGTCTTCTT 57.697 34.615 0.00 0.00 35.14 2.52
668 709 7.014422 CCTCCGTTCCTACATATAAAGTCTTCT 59.986 40.741 0.00 0.00 0.00 2.85
669 710 7.146648 CCTCCGTTCCTACATATAAAGTCTTC 58.853 42.308 0.00 0.00 0.00 2.87
670 711 6.041751 CCCTCCGTTCCTACATATAAAGTCTT 59.958 42.308 0.00 0.00 0.00 3.01
671 712 5.539193 CCCTCCGTTCCTACATATAAAGTCT 59.461 44.000 0.00 0.00 0.00 3.24
672 713 5.537674 TCCCTCCGTTCCTACATATAAAGTC 59.462 44.000 0.00 0.00 0.00 3.01
673 714 5.461327 TCCCTCCGTTCCTACATATAAAGT 58.539 41.667 0.00 0.00 0.00 2.66
674 715 5.539193 ACTCCCTCCGTTCCTACATATAAAG 59.461 44.000 0.00 0.00 0.00 1.85
675 716 5.461327 ACTCCCTCCGTTCCTACATATAAA 58.539 41.667 0.00 0.00 0.00 1.40
676 717 5.070823 ACTCCCTCCGTTCCTACATATAA 57.929 43.478 0.00 0.00 0.00 0.98
677 718 4.736611 ACTCCCTCCGTTCCTACATATA 57.263 45.455 0.00 0.00 0.00 0.86
678 719 3.614568 ACTCCCTCCGTTCCTACATAT 57.385 47.619 0.00 0.00 0.00 1.78
679 720 4.524802 TTACTCCCTCCGTTCCTACATA 57.475 45.455 0.00 0.00 0.00 2.29
680 721 3.393426 TTACTCCCTCCGTTCCTACAT 57.607 47.619 0.00 0.00 0.00 2.29
681 722 2.905415 TTACTCCCTCCGTTCCTACA 57.095 50.000 0.00 0.00 0.00 2.74
682 723 6.416631 AATTATTACTCCCTCCGTTCCTAC 57.583 41.667 0.00 0.00 0.00 3.18
753 836 3.629398 GCCATCTCTGGTTTGATTAGGTG 59.371 47.826 0.00 0.00 45.10 4.00
782 865 4.975794 ACTCATTATACAAACCCTAGGGCT 59.024 41.667 28.88 13.94 39.32 5.19
794 877 1.774254 CCCCAGGGCACTCATTATACA 59.226 52.381 0.00 0.00 0.00 2.29
802 885 1.209621 TATACAACCCCAGGGCACTC 58.790 55.000 0.00 0.00 39.32 3.51
807 890 5.309806 AGCTACTAATTATACAACCCCAGGG 59.690 44.000 0.00 0.00 42.03 4.45
808 891 6.270231 AGAGCTACTAATTATACAACCCCAGG 59.730 42.308 0.00 0.00 0.00 4.45
811 894 6.465084 CCAGAGCTACTAATTATACAACCCC 58.535 44.000 0.00 0.00 0.00 4.95
812 895 6.042897 ACCCAGAGCTACTAATTATACAACCC 59.957 42.308 0.00 0.00 0.00 4.11
813 896 7.063934 ACCCAGAGCTACTAATTATACAACC 57.936 40.000 0.00 0.00 0.00 3.77
814 897 8.827677 CAAACCCAGAGCTACTAATTATACAAC 58.172 37.037 0.00 0.00 0.00 3.32
815 898 8.545472 ACAAACCCAGAGCTACTAATTATACAA 58.455 33.333 0.00 0.00 0.00 2.41
816 899 8.086143 ACAAACCCAGAGCTACTAATTATACA 57.914 34.615 0.00 0.00 0.00 2.29
823 906 8.313944 TCATTATACAAACCCAGAGCTACTAA 57.686 34.615 0.00 0.00 0.00 2.24
826 909 6.480320 CACTCATTATACAAACCCAGAGCTAC 59.520 42.308 0.00 0.00 0.00 3.58
828 911 5.431765 CACTCATTATACAAACCCAGAGCT 58.568 41.667 0.00 0.00 0.00 4.09
876 959 7.506114 TGAACTAAACTTTTAGAGAGCTCCAA 58.494 34.615 10.93 0.00 42.05 3.53
880 963 9.732130 ATGAATGAACTAAACTTTTAGAGAGCT 57.268 29.630 14.36 0.00 42.05 4.09
892 975 9.458374 TTCTTTTTCGGAATGAATGAACTAAAC 57.542 29.630 0.00 0.00 36.22 2.01
896 982 8.940768 TTTTTCTTTTTCGGAATGAATGAACT 57.059 26.923 0.00 0.00 36.22 3.01
924 1010 0.038890 GGCCCAAAGAGCTTCTCCTT 59.961 55.000 0.00 0.00 0.00 3.36
925 1011 1.136329 TGGCCCAAAGAGCTTCTCCT 61.136 55.000 0.00 0.00 0.00 3.69
950 1036 2.189499 GCCAGAATGATCGGGTGGC 61.189 63.158 11.16 11.16 46.49 5.01
961 1047 1.258445 AACGACGAGGAGGCCAGAAT 61.258 55.000 5.01 0.00 0.00 2.40
965 1051 3.744719 CGAACGACGAGGAGGCCA 61.745 66.667 5.01 0.00 45.77 5.36
1012 1098 4.320456 AGAGGCGGCACTGGTGTG 62.320 66.667 13.08 0.00 46.37 3.82
1013 1099 4.320456 CAGAGGCGGCACTGGTGT 62.320 66.667 25.34 0.00 0.00 4.16
1050 1136 0.613260 CCCAGTAGCACAGCCAGTAA 59.387 55.000 0.00 0.00 0.00 2.24
1054 1140 2.959484 GCTCCCAGTAGCACAGCCA 61.959 63.158 0.00 0.00 42.30 4.75
1058 1144 0.972983 GGAGAGCTCCCAGTAGCACA 60.973 60.000 10.93 0.00 45.30 4.57
1131 1217 4.715130 TCCCAGTAGCACCGCCCT 62.715 66.667 0.00 0.00 0.00 5.19
1150 1531 2.351276 GAGGCGGGCTTTGGAGAA 59.649 61.111 5.24 0.00 0.00 2.87
1229 1631 4.397417 GCCACAAGAACTGAAGAGCATATT 59.603 41.667 0.00 0.00 0.00 1.28
1287 2090 9.739276 TCTACATCATATAATTCCCAAATCACC 57.261 33.333 0.00 0.00 0.00 4.02
1400 2550 3.753797 GGGTCCAAAAAGCACAACAAAAA 59.246 39.130 0.00 0.00 0.00 1.94
1539 3274 2.223735 ACCACTAATCGACCACTATGCG 60.224 50.000 0.00 0.00 0.00 4.73
2011 5576 1.555967 GCCAATGGAAAAGGCTACCA 58.444 50.000 2.05 9.71 44.92 3.25
2094 5670 4.112634 TGTAGTGAAGTATGAGATTGCGC 58.887 43.478 0.00 0.00 0.00 6.09
2399 6546 8.255206 TGAAACAAAGTGTAGAGAAAGTACAGA 58.745 33.333 0.00 0.00 31.00 3.41
2408 6555 7.624360 ACACAATTGAAACAAAGTGTAGAGA 57.376 32.000 13.59 0.00 36.29 3.10
2453 6600 7.551262 ACGATGTTTAGTTCCAATAACAGCATA 59.449 33.333 0.00 0.00 36.88 3.14
2638 6796 5.005740 ACATGTGTCATCAGCACTAACATT 58.994 37.500 0.00 0.00 37.70 2.71
2705 6863 3.561725 GGAAGGACTTGCTCCAATATTCG 59.438 47.826 0.00 0.00 42.46 3.34
2718 6878 7.154656 GCAAAATTCACAATTAGGAAGGACTT 58.845 34.615 0.00 0.00 0.00 3.01
2737 7195 2.343387 GCAAGGCGGTGGCAAAAT 59.657 55.556 0.00 0.00 42.47 1.82
3256 9807 7.147846 ACAGCTCCATTCAATAAATAAACAGGG 60.148 37.037 0.00 0.00 0.00 4.45
3329 9902 1.222936 GATGCTGCTACTGCCCACT 59.777 57.895 0.00 0.00 38.71 4.00
3338 9911 2.564504 AGTGACACTTCTGATGCTGCTA 59.435 45.455 1.07 0.00 0.00 3.49
3403 9976 0.896923 GCAAGGGCCATGAAATGTGA 59.103 50.000 13.93 0.00 44.81 3.58
3589 10284 4.966168 TCCTGAGTAATACCCATGCAGTTA 59.034 41.667 0.00 0.00 0.00 2.24
3936 10646 7.924541 AGTAGGGTCCAGTACAAATGATAAAA 58.075 34.615 0.00 0.00 0.00 1.52
4060 12954 2.376808 AAGAACCACAGCGATCTCAG 57.623 50.000 0.00 0.00 0.00 3.35
4401 13339 2.342279 CGAAACCCCTGCGACAGA 59.658 61.111 8.20 0.00 32.44 3.41
4586 13529 4.754114 ACAAGACTTGCAAGATCAAGAGAC 59.246 41.667 32.50 11.09 44.61 3.36
4600 13543 6.047870 CAGGATAGAATCTGGACAAGACTTG 58.952 44.000 13.77 13.77 37.88 3.16
4635 13578 1.659098 CAAATTCCGTCCGCTCTACAC 59.341 52.381 0.00 0.00 0.00 2.90
4721 13664 4.130857 TCAACACGTCACACATGGTAATT 58.869 39.130 0.00 0.00 0.00 1.40
4749 13694 2.824952 GCAAATTGCGCCATCAACA 58.175 47.368 4.18 0.00 31.71 3.33
4831 13778 3.190878 CCATCTTGGCCTCGCAAC 58.809 61.111 3.32 0.00 0.00 4.17
4887 13834 8.801913 CAAATTAGAAGAAAATCATCGCCTTTC 58.198 33.333 0.00 0.00 0.00 2.62
4943 13890 5.304686 AGGTTTCACTGTCTCATTGGTAA 57.695 39.130 0.00 0.00 0.00 2.85
5009 13956 2.028112 GGGAGCTTGTGTATGACTGACA 60.028 50.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.