Multiple sequence alignment - TraesCS4D01G060200

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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 TraesCS4D01G060200 chr4D 100.000 3723 0 0 1 3723 36418323 36422045 0.000000e+00 6876.0
1 TraesCS4D01G060200 chr4D 92.857 56 4 0 437 492 478674582 478674637 8.570000e-12 82.4
2 TraesCS4D01G060200 chr4A 87.607 2098 149 62 775 2830 565843559 565841531 0.000000e+00 2331.0
3 TraesCS4D01G060200 chr4A 94.247 956 52 3 1755 2707 566290467 566291422 0.000000e+00 1458.0
4 TraesCS4D01G060200 chr4A 89.596 817 46 21 674 1464 566289642 566290445 0.000000e+00 1002.0
5 TraesCS4D01G060200 chr4A 78.836 378 69 7 144 520 714936348 714935981 1.030000e-60 244.0
6 TraesCS4D01G060200 chr4B 88.134 1458 116 13 1 1449 52396511 52397920 0.000000e+00 1681.0
7 TraesCS4D01G060200 chr4B 94.527 1078 50 6 1756 2830 52397959 52399030 0.000000e+00 1655.0
8 TraesCS4D01G060200 chr4B 92.841 894 63 1 1833 2725 52412402 52413295 0.000000e+00 1295.0
9 TraesCS4D01G060200 chr4B 90.658 760 46 13 2082 2830 53044715 53043970 0.000000e+00 987.0
10 TraesCS4D01G060200 chr4B 89.207 593 43 13 2239 2830 52817855 52818427 0.000000e+00 721.0
11 TraesCS4D01G060200 chr4B 86.728 648 60 15 2193 2830 52828424 52829055 0.000000e+00 697.0
12 TraesCS4D01G060200 chr4B 88.293 410 45 2 1820 2226 52829687 52830096 4.320000e-134 488.0
13 TraesCS4D01G060200 chr4B 92.163 319 23 1 2082 2398 52895473 52895791 2.040000e-122 449.0
14 TraesCS4D01G060200 chr4B 93.950 281 14 2 2432 2712 52895789 52896066 4.450000e-114 422.0
15 TraesCS4D01G060200 chr4B 89.375 320 34 0 1881 2200 52819838 52820157 1.610000e-108 403.0
16 TraesCS4D01G060200 chr4B 85.845 219 13 6 2848 3048 52399015 52399233 2.250000e-52 217.0
17 TraesCS4D01G060200 chr4B 90.909 66 6 0 1820 1885 52819049 52819114 5.120000e-14 89.8
18 TraesCS4D01G060200 chr4B 88.525 61 2 3 2771 2830 52928091 52928147 6.670000e-08 69.4
19 TraesCS4D01G060200 chr3D 95.870 678 26 2 3047 3723 45558666 45559342 0.000000e+00 1096.0
20 TraesCS4D01G060200 chr7B 94.535 677 37 0 3047 3723 505332260 505332936 0.000000e+00 1046.0
21 TraesCS4D01G060200 chr7D 86.404 684 84 7 3044 3723 559266848 559266170 0.000000e+00 739.0
22 TraesCS4D01G060200 chr7D 96.135 414 15 1 3311 3723 560587595 560588008 0.000000e+00 675.0
23 TraesCS4D01G060200 chr7D 93.204 309 19 2 3055 3363 560587289 560587595 1.580000e-123 453.0
24 TraesCS4D01G060200 chr7D 78.517 391 73 6 134 520 130404486 130404103 2.870000e-61 246.0
25 TraesCS4D01G060200 chr7D 81.533 287 39 10 1468 1746 587122700 587122980 1.350000e-54 224.0
26 TraesCS4D01G060200 chr2A 93.235 340 21 1 3047 3384 601805294 601805633 2.000000e-137 499.0
27 TraesCS4D01G060200 chr2A 97.872 141 3 0 3376 3516 601806054 601806194 1.030000e-60 244.0
28 TraesCS4D01G060200 chr6B 82.415 381 60 3 138 517 279006363 279005989 3.590000e-85 326.0
29 TraesCS4D01G060200 chr7A 78.481 395 77 5 124 517 613173854 613174241 6.170000e-63 252.0
30 TraesCS4D01G060200 chr7A 88.268 179 17 3 1482 1658 215680270 215680446 1.050000e-50 211.0
31 TraesCS4D01G060200 chr7A 76.894 264 54 7 193 452 646552932 646553192 3.880000e-30 143.0
32 TraesCS4D01G060200 chr7A 77.049 244 50 5 255 496 516150561 516150322 6.490000e-28 135.0
33 TraesCS4D01G060200 chr7A 85.714 91 13 0 255 345 516150721 516150631 3.060000e-16 97.1
34 TraesCS4D01G060200 chr7A 86.301 73 10 0 428 500 436786200 436786272 3.080000e-11 80.5
35 TraesCS4D01G060200 chr3B 82.867 286 39 6 1468 1746 663084095 663084377 7.980000e-62 248.0
36 TraesCS4D01G060200 chr3B 82.625 259 33 8 1480 1730 166126265 166126011 6.260000e-53 219.0
37 TraesCS4D01G060200 chr1D 81.752 274 40 5 1468 1734 198740079 198740349 1.740000e-53 220.0
38 TraesCS4D01G060200 chr1D 71.163 430 92 28 1850 2263 63429216 63428803 1.110000e-10 78.7
39 TraesCS4D01G060200 chr2D 80.887 293 40 11 1468 1751 602735811 602736096 2.250000e-52 217.0
40 TraesCS4D01G060200 chr1B 79.381 291 47 7 1470 1751 533982520 533982234 3.790000e-45 193.0
41 TraesCS4D01G060200 chr1B 71.795 429 91 24 1850 2263 101527952 101527539 1.100000e-15 95.3
42 TraesCS4D01G060200 chr1B 70.901 433 88 29 1850 2263 101271281 101270868 2.400000e-07 67.6
43 TraesCS4D01G060200 chr6A 81.385 231 40 3 224 452 154048839 154048610 6.350000e-43 185.0
44 TraesCS4D01G060200 chr1A 82.266 203 30 3 1536 1733 343414690 343414489 1.780000e-38 171.0
45 TraesCS4D01G060200 chr1A 79.435 248 36 10 1499 1732 469498421 469498175 1.070000e-35 161.0
46 TraesCS4D01G060200 chr5B 74.932 367 77 12 134 498 406547431 406547078 1.790000e-33 154.0
47 TraesCS4D01G060200 chr2B 88.288 111 12 1 1468 1577 158429268 158429158 8.390000e-27 132.0
48 TraesCS4D01G060200 chr5A 80.220 182 29 4 124 305 210840640 210840466 3.020000e-26 130.0
49 TraesCS4D01G060200 chr5A 79.231 130 25 2 3105 3233 138443557 138443685 5.120000e-14 89.8
50 TraesCS4D01G060200 chr5D 80.392 102 18 2 3097 3197 124425354 124425454 3.990000e-10 76.8
51 TraesCS4D01G060200 chr5D 81.250 80 13 2 3097 3175 124414749 124414827 3.100000e-06 63.9


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 TraesCS4D01G060200 chr4D 36418323 36422045 3722 False 6876.000000 6876 100.000000 1 3723 1 chr4D.!!$F1 3722
1 TraesCS4D01G060200 chr4A 565841531 565843559 2028 True 2331.000000 2331 87.607000 775 2830 1 chr4A.!!$R1 2055
2 TraesCS4D01G060200 chr4A 566289642 566291422 1780 False 1230.000000 1458 91.921500 674 2707 2 chr4A.!!$F1 2033
3 TraesCS4D01G060200 chr4B 52412402 52413295 893 False 1295.000000 1295 92.841000 1833 2725 1 chr4B.!!$F1 892
4 TraesCS4D01G060200 chr4B 52396511 52399233 2722 False 1184.333333 1681 89.502000 1 3048 3 chr4B.!!$F3 3047
5 TraesCS4D01G060200 chr4B 53043970 53044715 745 True 987.000000 987 90.658000 2082 2830 1 chr4B.!!$R1 748
6 TraesCS4D01G060200 chr4B 52828424 52830096 1672 False 592.500000 697 87.510500 1820 2830 2 chr4B.!!$F5 1010
7 TraesCS4D01G060200 chr4B 52895473 52896066 593 False 435.500000 449 93.056500 2082 2712 2 chr4B.!!$F6 630
8 TraesCS4D01G060200 chr4B 52817855 52820157 2302 False 404.600000 721 89.830333 1820 2830 3 chr4B.!!$F4 1010
9 TraesCS4D01G060200 chr3D 45558666 45559342 676 False 1096.000000 1096 95.870000 3047 3723 1 chr3D.!!$F1 676
10 TraesCS4D01G060200 chr7B 505332260 505332936 676 False 1046.000000 1046 94.535000 3047 3723 1 chr7B.!!$F1 676
11 TraesCS4D01G060200 chr7D 559266170 559266848 678 True 739.000000 739 86.404000 3044 3723 1 chr7D.!!$R2 679
12 TraesCS4D01G060200 chr7D 560587289 560588008 719 False 564.000000 675 94.669500 3055 3723 2 chr7D.!!$F2 668
13 TraesCS4D01G060200 chr2A 601805294 601806194 900 False 371.500000 499 95.553500 3047 3516 2 chr2A.!!$F1 469

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
154 155 0.030369 CGGGTGGTGCGTCTAGTATC 59.970 60.0 0.00 0.0 0.00 2.24 F
920 945 0.032678 CCATCCGATCCCAAGAGACG 59.967 60.0 0.00 0.0 0.00 4.18 F
955 980 0.179004 AACAGCGACCACCAAATCCA 60.179 50.0 0.00 0.0 0.00 3.41 F
1810 1879 0.321653 AATTGACGTGCAGGGTCCTC 60.322 55.0 11.67 0.0 33.46 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1412 0.896940 AGGTGGAGCCGAAGTCGTAA 60.897 55.000 0.00 0.00 43.70 3.18 R
1810 1879 1.153706 GACGTCCATGTACCCCGTG 60.154 63.158 3.51 0.00 0.00 4.94 R
2587 2658 1.304547 CTCCACCACCTCGAGGACT 60.305 63.158 37.69 14.23 38.94 3.85 R
3544 4309 1.122019 AGTTCCACTTGGACTCCGCT 61.122 55.000 0.00 0.00 45.39 5.52 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
23 24 2.733227 CGGGATTTCATGCTTGTCTTGC 60.733 50.000 0.00 0.00 0.00 4.01
37 38 0.911769 TCTTGCTGGGTCTGTATGGG 59.088 55.000 0.00 0.00 0.00 4.00
38 39 0.749454 CTTGCTGGGTCTGTATGGGC 60.749 60.000 0.00 0.00 0.00 5.36
39 40 1.496444 TTGCTGGGTCTGTATGGGCA 61.496 55.000 0.00 0.00 0.00 5.36
40 41 1.452108 GCTGGGTCTGTATGGGCAC 60.452 63.158 0.00 0.00 0.00 5.01
41 42 1.915078 GCTGGGTCTGTATGGGCACT 61.915 60.000 0.00 0.00 0.00 4.40
61 62 2.584835 TTTGGTTGCCTGCATCTAGT 57.415 45.000 0.00 0.00 0.00 2.57
70 71 2.810852 GCCTGCATCTAGTCCAAATAGC 59.189 50.000 0.00 0.00 0.00 2.97
97 98 2.288579 TGGATGCAAGAAAAGCTGCTTG 60.289 45.455 16.73 15.92 43.26 4.01
131 132 6.425417 CACAAGGTTCTCTTTTTCTAGTCCTC 59.575 42.308 0.00 0.00 32.41 3.71
136 137 5.584253 TCTCTTTTTCTAGTCCTCATCCG 57.416 43.478 0.00 0.00 0.00 4.18
154 155 0.030369 CGGGTGGTGCGTCTAGTATC 59.970 60.000 0.00 0.00 0.00 2.24
182 183 2.920645 CGTGTGGAGGCGTGTCTCT 61.921 63.158 1.01 0.00 34.39 3.10
189 190 2.048127 GGCGTGTCTCTGGTGGAC 60.048 66.667 0.00 0.00 0.00 4.02
205 206 2.033424 GTGGACCTGTCTTTGTCTTTGC 59.967 50.000 0.00 0.00 0.00 3.68
207 208 3.135712 TGGACCTGTCTTTGTCTTTGCTA 59.864 43.478 0.00 0.00 0.00 3.49
211 212 5.241662 ACCTGTCTTTGTCTTTGCTAGATC 58.758 41.667 0.00 0.00 34.79 2.75
214 215 5.858381 TGTCTTTGTCTTTGCTAGATCTGT 58.142 37.500 5.18 0.00 34.79 3.41
217 218 5.635280 TCTTTGTCTTTGCTAGATCTGTTCG 59.365 40.000 5.18 0.00 34.79 3.95
233 234 2.110226 GTTCGGATCTGATCGTCGTTC 58.890 52.381 4.74 0.00 0.00 3.95
234 235 1.375551 TCGGATCTGATCGTCGTTCA 58.624 50.000 11.28 5.90 0.00 3.18
238 239 3.304257 GGATCTGATCGTCGTTCATCTG 58.696 50.000 11.28 0.61 0.00 2.90
245 246 1.334992 CGTCGTTCATCTGCGTTCGT 61.335 55.000 0.00 0.00 0.00 3.85
250 251 1.344226 TTCATCTGCGTTCGTGAGCG 61.344 55.000 1.52 1.52 38.09 5.03
252 253 1.801913 ATCTGCGTTCGTGAGCGTC 60.802 57.895 7.89 1.64 37.36 5.19
272 273 2.774234 TCCAGGTTGGATCCTTCTGATC 59.226 50.000 22.36 0.00 42.67 2.92
287 288 6.322456 TCCTTCTGATCAACGATACTCTTCAT 59.678 38.462 0.00 0.00 0.00 2.57
288 289 6.640499 CCTTCTGATCAACGATACTCTTCATC 59.360 42.308 0.00 0.00 0.00 2.92
297 298 1.028330 TACTCTTCATCGACGGCGGT 61.028 55.000 12.58 0.00 38.28 5.68
300 301 1.736645 CTTCATCGACGGCGGTTGT 60.737 57.895 12.58 0.00 38.28 3.32
302 303 0.038435 TTCATCGACGGCGGTTGTTA 60.038 50.000 12.58 0.00 38.28 2.41
308 309 1.717194 GACGGCGGTTGTTATTCTGA 58.283 50.000 13.24 0.00 0.00 3.27
310 311 2.006888 ACGGCGGTTGTTATTCTGATG 58.993 47.619 13.24 0.00 0.00 3.07
315 316 2.537529 CGGTTGTTATTCTGATGCGCTG 60.538 50.000 9.73 0.00 0.00 5.18
318 319 2.279741 TGTTATTCTGATGCGCTGGTC 58.720 47.619 9.73 4.94 0.00 4.02
322 323 2.988010 TTCTGATGCGCTGGTCTTAT 57.012 45.000 9.73 0.00 0.00 1.73
334 335 2.771943 CTGGTCTTATGGGGTCTTAGCA 59.228 50.000 0.00 0.00 0.00 3.49
380 381 1.286880 CAAGTTTTGCTGGCTCCGG 59.713 57.895 0.00 0.00 0.00 5.14
400 401 0.684479 TGAGGGAGGAGTGATGACGG 60.684 60.000 0.00 0.00 0.00 4.79
401 402 0.395862 GAGGGAGGAGTGATGACGGA 60.396 60.000 0.00 0.00 0.00 4.69
413 414 4.415332 GACGGAGGCGCGTCTTCA 62.415 66.667 27.24 0.00 32.94 3.02
424 425 0.436531 GCGTCTTCAGCTCGTTTCAG 59.563 55.000 0.00 0.00 0.00 3.02
425 426 1.772182 CGTCTTCAGCTCGTTTCAGT 58.228 50.000 0.00 0.00 0.00 3.41
427 428 2.474816 GTCTTCAGCTCGTTTCAGTGT 58.525 47.619 0.00 0.00 0.00 3.55
440 441 4.201647 CGTTTCAGTGTTTGTAGTTGTCGT 60.202 41.667 0.00 0.00 0.00 4.34
443 444 6.578020 TTCAGTGTTTGTAGTTGTCGTTAG 57.422 37.500 0.00 0.00 0.00 2.34
444 445 5.893687 TCAGTGTTTGTAGTTGTCGTTAGA 58.106 37.500 0.00 0.00 0.00 2.10
459 460 8.350722 GTTGTCGTTAGATGGTCTATGAATCTA 58.649 37.037 0.00 0.00 32.92 1.98
516 517 7.017645 GCACTGCCACGATTAAATATGAATAG 58.982 38.462 0.00 0.00 0.00 1.73
524 525 9.180678 CACGATTAAATATGAATAGTTTTGGGC 57.819 33.333 0.00 0.00 0.00 5.36
530 531 3.074675 TGAATAGTTTTGGGCCGCTAA 57.925 42.857 0.00 0.00 0.00 3.09
556 557 3.134574 TGCGGAAAAGCTTAGAAAGGA 57.865 42.857 0.00 0.00 38.13 3.36
582 583 3.673902 AGCTCTGAAGAAAGGAAGAAGC 58.326 45.455 0.00 0.00 0.00 3.86
584 585 4.530161 AGCTCTGAAGAAAGGAAGAAGCTA 59.470 41.667 0.00 0.00 0.00 3.32
609 610 1.365633 GCGAGGGGTAGAGATGCTG 59.634 63.158 0.00 0.00 0.00 4.41
654 655 0.742505 AATCGATTGCAGGGCACATG 59.257 50.000 10.50 0.00 38.71 3.21
692 696 1.227764 CAGCCTGTGCAGTGAGTGT 60.228 57.895 0.00 0.00 41.13 3.55
708 712 1.841556 TGTCTGGTCACTGTCCCCC 60.842 63.158 0.00 0.00 0.00 5.40
825 833 2.691252 CCCCAGAGTACCCACCCC 60.691 72.222 0.00 0.00 0.00 4.95
826 834 2.454941 CCCAGAGTACCCACCCCT 59.545 66.667 0.00 0.00 0.00 4.79
827 835 1.689582 CCCAGAGTACCCACCCCTC 60.690 68.421 0.00 0.00 0.00 4.30
828 836 1.689582 CCAGAGTACCCACCCCTCC 60.690 68.421 0.00 0.00 0.00 4.30
829 837 1.080354 CAGAGTACCCACCCCTCCA 59.920 63.158 0.00 0.00 0.00 3.86
830 838 0.546747 CAGAGTACCCACCCCTCCAA 60.547 60.000 0.00 0.00 0.00 3.53
895 904 1.068541 GCCTTTTTAGCCACTCCAACG 60.069 52.381 0.00 0.00 0.00 4.10
899 910 0.605319 TTTAGCCACTCCAACGCCAG 60.605 55.000 0.00 0.00 0.00 4.85
920 945 0.032678 CCATCCGATCCCAAGAGACG 59.967 60.000 0.00 0.00 0.00 4.18
955 980 0.179004 AACAGCGACCACCAAATCCA 60.179 50.000 0.00 0.00 0.00 3.41
972 1012 7.040132 ACCAAATCCAAAAACAAGCAAGAAAAA 60.040 29.630 0.00 0.00 0.00 1.94
991 1032 8.970691 AGAAAAACAAAATCCGATCATACAAG 57.029 30.769 0.00 0.00 0.00 3.16
996 1037 5.163723 ACAAAATCCGATCATACAAGCACTG 60.164 40.000 0.00 0.00 0.00 3.66
1003 1044 4.986659 CGATCATACAAGCACTGATCATGA 59.013 41.667 0.00 0.00 43.46 3.07
1269 1310 4.351938 TGGTTCGAGCCGTCCGTG 62.352 66.667 14.03 0.00 0.00 4.94
1371 1412 4.265056 GGCGTCCACACCAGGGTT 62.265 66.667 0.00 0.00 0.00 4.11
1428 1469 2.629051 GACCCAACCCTCAAGTAATCG 58.371 52.381 0.00 0.00 0.00 3.34
1434 1475 1.749634 ACCCTCAAGTAATCGACCGAG 59.250 52.381 0.00 0.00 0.00 4.63
1468 1511 9.230122 TCTTCTATCTGTTTATGTCAATTGCAA 57.770 29.630 0.00 0.00 0.00 4.08
1469 1512 9.282247 CTTCTATCTGTTTATGTCAATTGCAAC 57.718 33.333 0.00 0.00 0.00 4.17
1470 1513 8.334263 TCTATCTGTTTATGTCAATTGCAACA 57.666 30.769 0.00 1.11 0.00 3.33
1472 1515 9.577110 CTATCTGTTTATGTCAATTGCAACAAT 57.423 29.630 0.00 0.00 0.00 2.71
1473 1516 7.640616 TCTGTTTATGTCAATTGCAACAATG 57.359 32.000 0.00 1.40 0.00 2.82
1483 1526 3.920738 CAACAATGCTTGCGCGTT 58.079 50.000 8.43 0.00 45.90 4.84
1581 1626 8.955061 AAATGTTTATCAAATTCTGACGTGAG 57.045 30.769 0.00 0.00 36.69 3.51
1632 1682 8.764524 TGGTAATTAAAATGAAATTGGTTCGG 57.235 30.769 0.00 0.00 39.30 4.30
1645 1695 6.564709 AATTGGTTCGGAAGGTAAGTAAAC 57.435 37.500 0.00 0.00 0.00 2.01
1646 1696 4.961438 TGGTTCGGAAGGTAAGTAAACT 57.039 40.909 0.00 0.00 0.00 2.66
1647 1697 6.418057 TTGGTTCGGAAGGTAAGTAAACTA 57.582 37.500 0.00 0.00 0.00 2.24
1648 1698 6.418057 TGGTTCGGAAGGTAAGTAAACTAA 57.582 37.500 0.00 0.00 0.00 2.24
1649 1699 6.458210 TGGTTCGGAAGGTAAGTAAACTAAG 58.542 40.000 0.00 0.00 0.00 2.18
1650 1700 5.871524 GGTTCGGAAGGTAAGTAAACTAAGG 59.128 44.000 0.00 0.00 0.00 2.69
1651 1701 6.459066 GTTCGGAAGGTAAGTAAACTAAGGT 58.541 40.000 0.00 0.00 0.00 3.50
1652 1702 6.029346 TCGGAAGGTAAGTAAACTAAGGTG 57.971 41.667 0.00 0.00 0.00 4.00
1653 1703 5.774690 TCGGAAGGTAAGTAAACTAAGGTGA 59.225 40.000 0.00 0.00 0.00 4.02
1654 1704 6.438425 TCGGAAGGTAAGTAAACTAAGGTGAT 59.562 38.462 0.00 0.00 0.00 3.06
1655 1705 7.038799 TCGGAAGGTAAGTAAACTAAGGTGATT 60.039 37.037 0.00 0.00 0.00 2.57
1656 1706 7.064253 CGGAAGGTAAGTAAACTAAGGTGATTG 59.936 40.741 0.00 0.00 0.00 2.67
1657 1707 8.098912 GGAAGGTAAGTAAACTAAGGTGATTGA 58.901 37.037 0.00 0.00 0.00 2.57
1658 1708 9.668497 GAAGGTAAGTAAACTAAGGTGATTGAT 57.332 33.333 0.00 0.00 0.00 2.57
1682 1732 9.846248 GATTATTATATGCATCAAAGGTTGGAC 57.154 33.333 0.19 0.00 0.00 4.02
1683 1733 8.759481 TTATTATATGCATCAAAGGTTGGACA 57.241 30.769 0.19 0.00 0.00 4.02
1687 1737 3.295093 TGCATCAAAGGTTGGACAAAGA 58.705 40.909 0.00 0.00 0.00 2.52
1689 1739 3.569701 GCATCAAAGGTTGGACAAAGAGA 59.430 43.478 0.00 0.00 0.00 3.10
1692 1742 4.144297 TCAAAGGTTGGACAAAGAGATGG 58.856 43.478 0.00 0.00 0.00 3.51
1695 1745 2.711009 AGGTTGGACAAAGAGATGGTGA 59.289 45.455 0.00 0.00 0.00 4.02
1696 1746 3.138283 AGGTTGGACAAAGAGATGGTGAA 59.862 43.478 0.00 0.00 0.00 3.18
1697 1747 3.888930 GGTTGGACAAAGAGATGGTGAAA 59.111 43.478 0.00 0.00 0.00 2.69
1775 1841 3.673173 GCAATGGGCTAATGGCAAG 57.327 52.632 0.00 0.00 44.01 4.01
1810 1879 0.321653 AATTGACGTGCAGGGTCCTC 60.322 55.000 11.67 0.00 33.46 3.71
1962 2031 2.359169 CCTACCTGGAGCGCCTCAA 61.359 63.158 8.34 0.00 38.35 3.02
1972 2041 3.123620 CGCCTCAAGCTGCTGGTC 61.124 66.667 1.35 0.00 40.39 4.02
2101 2170 4.077188 GCACACGTGAAGCGGCTC 62.077 66.667 25.01 0.00 46.52 4.70
2279 2350 2.661866 GCAACACCACGCTCGTCT 60.662 61.111 0.00 0.00 0.00 4.18
2718 2789 1.066858 CAGCACCACGACCTATCAGTT 60.067 52.381 0.00 0.00 0.00 3.16
2775 2855 2.067013 GAGTCTTTTTCGTCCGGGAAG 58.933 52.381 0.00 0.00 0.00 3.46
2777 2857 2.103601 AGTCTTTTTCGTCCGGGAAGAA 59.896 45.455 19.46 19.46 0.00 2.52
2778 2858 3.072211 GTCTTTTTCGTCCGGGAAGAAT 58.928 45.455 22.98 0.00 31.11 2.40
2779 2859 3.071479 TCTTTTTCGTCCGGGAAGAATG 58.929 45.455 22.98 16.41 31.11 2.67
2781 2861 2.554370 TTTCGTCCGGGAAGAATGTT 57.446 45.000 22.98 0.00 31.11 2.71
2797 2877 6.830873 AGAATGTTTTGAGATTTGCTAGCT 57.169 33.333 17.23 0.00 0.00 3.32
2798 2878 7.928307 AGAATGTTTTGAGATTTGCTAGCTA 57.072 32.000 17.23 5.31 0.00 3.32
2799 2879 8.517062 AGAATGTTTTGAGATTTGCTAGCTAT 57.483 30.769 17.23 9.41 0.00 2.97
2830 2910 3.051940 TGCCAGATGGGAGTAGAGATT 57.948 47.619 0.12 0.00 40.01 2.40
2831 2911 2.968574 TGCCAGATGGGAGTAGAGATTC 59.031 50.000 0.12 0.00 40.01 2.52
2832 2912 3.238597 GCCAGATGGGAGTAGAGATTCT 58.761 50.000 0.12 0.00 40.01 2.40
2833 2913 3.258123 GCCAGATGGGAGTAGAGATTCTC 59.742 52.174 5.49 5.49 40.01 2.87
2834 2914 4.739793 CCAGATGGGAGTAGAGATTCTCT 58.260 47.826 19.64 19.64 41.01 3.10
2835 2915 4.766891 CCAGATGGGAGTAGAGATTCTCTC 59.233 50.000 19.32 11.26 40.73 3.20
2836 2916 5.384336 CAGATGGGAGTAGAGATTCTCTCA 58.616 45.833 19.32 11.32 45.73 3.27
2837 2917 5.832595 CAGATGGGAGTAGAGATTCTCTCAA 59.167 44.000 19.32 0.60 45.73 3.02
2838 2918 6.323482 CAGATGGGAGTAGAGATTCTCTCAAA 59.677 42.308 19.32 0.00 45.73 2.69
2839 2919 6.900186 AGATGGGAGTAGAGATTCTCTCAAAA 59.100 38.462 19.32 0.00 45.73 2.44
2840 2920 6.935240 TGGGAGTAGAGATTCTCTCAAAAA 57.065 37.500 19.32 0.00 45.73 1.94
2870 2950 4.592351 AGATGGGAGTAGAGATCAACCATG 59.408 45.833 0.00 0.00 37.36 3.66
2889 2969 7.206981 ACCATGTTCTTATTGACTTCAACAG 57.793 36.000 0.00 0.00 38.86 3.16
2917 3008 5.751028 GGCATCTAGTGTTGAGTCAGAATAC 59.249 44.000 0.00 0.00 0.00 1.89
2918 3009 6.333416 GCATCTAGTGTTGAGTCAGAATACA 58.667 40.000 0.00 0.00 0.00 2.29
2920 3011 8.138074 GCATCTAGTGTTGAGTCAGAATACATA 58.862 37.037 0.00 0.00 0.00 2.29
2949 3047 4.652679 AGAAAAGAAGGATTACCCCGTT 57.347 40.909 0.00 0.00 36.73 4.44
2952 3050 4.652679 AAAGAAGGATTACCCCGTTCTT 57.347 40.909 0.00 0.00 36.33 2.52
2967 3065 7.001674 ACCCCGTTCTTTGCATTATAATGATA 58.998 34.615 26.22 12.87 38.70 2.15
2979 3077 6.916387 GCATTATAATGATACATGCAGCCATC 59.084 38.462 26.22 2.00 40.06 3.51
2983 3081 5.954296 AATGATACATGCAGCCATCTTAC 57.046 39.130 0.00 0.00 0.00 2.34
2997 3095 6.712095 CAGCCATCTTACTAAGCAAATATCCA 59.288 38.462 0.00 0.00 0.00 3.41
3011 3109 8.579850 AGCAAATATCCAAAAAGTCTGTGATA 57.420 30.769 0.00 0.00 0.00 2.15
3080 3179 2.930040 ACGTCGGCTTTATTGATCACAG 59.070 45.455 0.00 0.00 0.00 3.66
3095 3285 6.358118 TGATCACAGAACAAAGTTACACAC 57.642 37.500 0.00 0.00 0.00 3.82
3113 3303 1.825474 CACAGTCTCCCGGATACAACT 59.175 52.381 0.73 0.00 0.00 3.16
3114 3304 3.021695 CACAGTCTCCCGGATACAACTA 58.978 50.000 0.73 0.00 0.00 2.24
3187 3457 7.203910 AGCTAACATATGAGCCGCTATATTAC 58.796 38.462 10.38 0.00 39.65 1.89
3197 3467 2.387185 CGCTATATTACGTTGCCGACA 58.613 47.619 0.00 0.00 37.88 4.35
3263 3533 8.062065 AGTTTGATTTCTTTAACAACTGACCA 57.938 30.769 0.00 0.00 0.00 4.02
3283 3553 4.217550 ACCAAATGACCGAACGATCAATTT 59.782 37.500 0.00 0.00 0.00 1.82
3340 3662 4.287067 AGTCAGAGGCAAAGATAACCTTGA 59.713 41.667 0.00 0.00 34.79 3.02
3544 4309 0.250124 AACAATCGAACCTGACGGCA 60.250 50.000 0.00 0.00 0.00 5.69
3625 4390 4.877823 TGTAGAGGTGCTGCATAATCAAAG 59.122 41.667 5.27 0.00 34.08 2.77
3626 4391 4.226427 AGAGGTGCTGCATAATCAAAGA 57.774 40.909 5.27 0.00 0.00 2.52
3673 4493 0.324368 ATGACGAGGGTGTGGAGCTA 60.324 55.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.278985 CCATACAGACCCAGCAAGACA 59.721 52.381 0.00 0.00 0.00 3.41
23 24 0.620556 AAGTGCCCATACAGACCCAG 59.379 55.000 0.00 0.00 0.00 4.45
37 38 0.249996 ATGCAGGCAACCAAAAGTGC 60.250 50.000 0.00 0.00 37.17 4.40
38 39 1.342174 AGATGCAGGCAACCAAAAGTG 59.658 47.619 0.00 0.00 37.17 3.16
39 40 1.708341 AGATGCAGGCAACCAAAAGT 58.292 45.000 0.00 0.00 37.17 2.66
40 41 2.821969 ACTAGATGCAGGCAACCAAAAG 59.178 45.455 0.00 0.00 37.17 2.27
41 42 2.819608 GACTAGATGCAGGCAACCAAAA 59.180 45.455 0.00 0.00 37.17 2.44
61 62 2.389042 TCCAACGGGGCTATTTGGA 58.611 52.632 9.30 9.30 45.27 3.53
70 71 0.965439 TTTTCTTGCATCCAACGGGG 59.035 50.000 0.00 0.00 38.37 5.73
97 98 3.805207 AGAGAACCTTGTGTACACAACC 58.195 45.455 32.37 21.56 45.42 3.77
112 113 5.808030 CGGATGAGGACTAGAAAAAGAGAAC 59.192 44.000 0.00 0.00 0.00 3.01
119 120 2.500098 CACCCGGATGAGGACTAGAAAA 59.500 50.000 0.73 0.00 0.00 2.29
120 121 2.108168 CACCCGGATGAGGACTAGAAA 58.892 52.381 0.73 0.00 0.00 2.52
131 132 2.629050 CTAGACGCACCACCCGGATG 62.629 65.000 0.73 0.00 35.59 3.51
136 137 0.030369 CGATACTAGACGCACCACCC 59.970 60.000 0.00 0.00 0.00 4.61
173 174 2.048127 GGTCCACCAGAGACACGC 60.048 66.667 0.00 0.00 35.89 5.34
174 175 1.290324 CAGGTCCACCAGAGACACG 59.710 63.158 0.00 0.00 38.89 4.49
182 183 1.507140 AGACAAAGACAGGTCCACCA 58.493 50.000 0.00 0.00 38.89 4.17
189 190 5.350914 CAGATCTAGCAAAGACAAAGACAGG 59.649 44.000 0.00 0.00 36.93 4.00
211 212 1.064208 ACGACGATCAGATCCGAACAG 59.936 52.381 14.00 0.00 0.00 3.16
214 215 1.741145 TGAACGACGATCAGATCCGAA 59.259 47.619 14.00 0.14 0.00 4.30
217 218 3.304257 CAGATGAACGACGATCAGATCC 58.696 50.000 13.40 3.42 0.00 3.36
223 224 1.253034 GAACGCAGATGAACGACGATC 59.747 52.381 0.00 0.00 0.00 3.69
233 234 2.002963 GACGCTCACGAACGCAGATG 62.003 60.000 0.00 0.00 43.93 2.90
234 235 1.801913 GACGCTCACGAACGCAGAT 60.802 57.895 0.00 0.00 43.93 2.90
238 239 3.470567 CTGGACGCTCACGAACGC 61.471 66.667 0.00 0.00 43.93 4.84
252 253 3.205784 GATCAGAAGGATCCAACCTGG 57.794 52.381 15.82 0.00 45.58 4.45
267 268 5.623264 GTCGATGAAGAGTATCGTTGATCAG 59.377 44.000 7.18 0.00 45.55 2.90
272 273 3.036633 CCGTCGATGAAGAGTATCGTTG 58.963 50.000 6.11 2.21 45.55 4.10
273 274 2.541178 GCCGTCGATGAAGAGTATCGTT 60.541 50.000 6.11 0.00 45.55 3.85
274 275 1.002684 GCCGTCGATGAAGAGTATCGT 60.003 52.381 6.11 0.00 45.55 3.73
275 276 1.676057 GCCGTCGATGAAGAGTATCG 58.324 55.000 6.11 0.00 46.45 2.92
282 283 1.289109 AACAACCGCCGTCGATGAAG 61.289 55.000 6.11 0.00 38.10 3.02
287 288 0.244450 AGAATAACAACCGCCGTCGA 59.756 50.000 0.00 0.00 38.10 4.20
288 289 0.368907 CAGAATAACAACCGCCGTCG 59.631 55.000 0.00 0.00 0.00 5.12
297 298 2.677836 GACCAGCGCATCAGAATAACAA 59.322 45.455 11.47 0.00 0.00 2.83
300 301 2.988010 AGACCAGCGCATCAGAATAA 57.012 45.000 11.47 0.00 0.00 1.40
302 303 2.988010 TAAGACCAGCGCATCAGAAT 57.012 45.000 11.47 0.00 0.00 2.40
308 309 1.149174 CCCCATAAGACCAGCGCAT 59.851 57.895 11.47 0.00 0.00 4.73
310 311 1.523938 GACCCCATAAGACCAGCGC 60.524 63.158 0.00 0.00 0.00 5.92
315 316 3.454812 TCTTGCTAAGACCCCATAAGACC 59.545 47.826 0.00 0.00 31.20 3.85
334 335 8.239314 TGTAATATACAGTCGAAAAGTCGTCTT 58.761 33.333 0.00 0.00 41.89 3.01
380 381 0.457851 CGTCATCACTCCTCCCTCAC 59.542 60.000 0.00 0.00 0.00 3.51
390 391 4.498520 CGCGCCTCCGTCATCACT 62.499 66.667 0.00 0.00 36.67 3.41
400 401 2.883253 GAGCTGAAGACGCGCCTC 60.883 66.667 5.73 0.00 0.00 4.70
401 402 4.785512 CGAGCTGAAGACGCGCCT 62.786 66.667 5.73 0.00 0.00 5.52
413 414 3.793559 ACTACAAACACTGAAACGAGCT 58.206 40.909 0.00 0.00 0.00 4.09
424 425 5.464389 ACCATCTAACGACAACTACAAACAC 59.536 40.000 0.00 0.00 0.00 3.32
425 426 5.603596 ACCATCTAACGACAACTACAAACA 58.396 37.500 0.00 0.00 0.00 2.83
427 428 6.092955 AGACCATCTAACGACAACTACAAA 57.907 37.500 0.00 0.00 0.00 2.83
478 479 1.009675 CAGTGCAACGAACACCAGC 60.010 57.895 0.00 0.00 45.86 4.85
505 506 4.649218 AGCGGCCCAAAACTATTCATATTT 59.351 37.500 0.00 0.00 0.00 1.40
537 538 3.075148 ACTCCTTTCTAAGCTTTTCCGC 58.925 45.455 3.20 0.00 0.00 5.54
539 540 6.613233 GCTTAACTCCTTTCTAAGCTTTTCC 58.387 40.000 3.20 0.00 42.69 3.13
556 557 6.426646 TCTTCCTTTCTTCAGAGCTTAACT 57.573 37.500 0.00 0.00 0.00 2.24
582 583 4.142790 TCTCTACCCCTCGCACTAAATAG 58.857 47.826 0.00 0.00 0.00 1.73
584 585 3.028094 TCTCTACCCCTCGCACTAAAT 57.972 47.619 0.00 0.00 0.00 1.40
609 610 0.459585 TTCATACGCACCGAGCTTCC 60.460 55.000 0.00 0.00 42.61 3.46
646 647 1.743394 GCTACTTGTTACCATGTGCCC 59.257 52.381 0.00 0.00 31.92 5.36
650 651 1.002659 TGCCGCTACTTGTTACCATGT 59.997 47.619 0.00 0.00 33.85 3.21
654 655 0.441145 CGTTGCCGCTACTTGTTACC 59.559 55.000 3.48 0.00 0.00 2.85
678 682 0.105593 ACCAGACACTCACTGCACAG 59.894 55.000 0.00 0.00 34.47 3.66
692 696 1.841556 GTGGGGGACAGTGACCAGA 60.842 63.158 13.71 0.00 32.84 3.86
708 712 2.604046 AGCCTACCTGCGATTAAGTG 57.396 50.000 0.00 0.00 36.02 3.16
825 833 0.388649 CGTCGTCCTTGGAGTTGGAG 60.389 60.000 0.00 0.00 32.36 3.86
826 834 1.111116 ACGTCGTCCTTGGAGTTGGA 61.111 55.000 0.00 0.00 0.00 3.53
827 835 0.599558 TACGTCGTCCTTGGAGTTGG 59.400 55.000 0.00 0.00 0.00 3.77
828 836 2.056577 GTTACGTCGTCCTTGGAGTTG 58.943 52.381 0.00 0.00 0.00 3.16
829 837 1.959282 AGTTACGTCGTCCTTGGAGTT 59.041 47.619 0.00 0.00 0.00 3.01
830 838 1.613836 AGTTACGTCGTCCTTGGAGT 58.386 50.000 0.00 0.00 0.00 3.85
895 904 4.650377 GGGATCGGATGGCCTGGC 62.650 72.222 11.05 11.05 0.00 4.85
899 910 1.072159 CTCTTGGGATCGGATGGCC 59.928 63.158 0.00 0.00 0.00 5.36
920 945 0.310543 TGTTTTGTGTGGCGATGCTC 59.689 50.000 0.00 0.00 0.00 4.26
955 980 7.536964 CGGATTTTGTTTTTCTTGCTTGTTTTT 59.463 29.630 0.00 0.00 0.00 1.94
972 1012 4.943705 AGTGCTTGTATGATCGGATTTTGT 59.056 37.500 0.00 0.00 0.00 2.83
991 1032 3.317430 GGATTTCCCTTCATGATCAGTGC 59.683 47.826 0.09 0.00 0.00 4.40
996 1037 2.856222 AGCGGATTTCCCTTCATGATC 58.144 47.619 0.00 0.00 0.00 2.92
1003 1044 2.224209 CCATACGTAGCGGATTTCCCTT 60.224 50.000 7.87 0.00 0.00 3.95
1170 1211 1.303799 GCCTGTAGTCGTCCGTCAGA 61.304 60.000 0.00 0.00 0.00 3.27
1371 1412 0.896940 AGGTGGAGCCGAAGTCGTAA 60.897 55.000 0.00 0.00 43.70 3.18
1428 1469 4.578928 AGATAGAAGAAGAAGAGCTCGGTC 59.421 45.833 8.37 10.14 0.00 4.79
1434 1475 8.940768 ACATAAACAGATAGAAGAAGAAGAGC 57.059 34.615 0.00 0.00 0.00 4.09
1618 1668 5.321927 ACTTACCTTCCGAACCAATTTCAT 58.678 37.500 0.00 0.00 33.24 2.57
1621 1671 6.774170 AGTTTACTTACCTTCCGAACCAATTT 59.226 34.615 0.00 0.00 0.00 1.82
1631 1681 8.098912 TCAATCACCTTAGTTTACTTACCTTCC 58.901 37.037 0.00 0.00 0.00 3.46
1632 1682 9.668497 ATCAATCACCTTAGTTTACTTACCTTC 57.332 33.333 0.00 0.00 0.00 3.46
1655 1705 9.585369 TCCAACCTTTGATGCATATAATAATCA 57.415 29.630 0.00 0.00 0.00 2.57
1656 1706 9.846248 GTCCAACCTTTGATGCATATAATAATC 57.154 33.333 0.00 0.00 0.00 1.75
1657 1707 9.365906 TGTCCAACCTTTGATGCATATAATAAT 57.634 29.630 0.00 0.00 0.00 1.28
1658 1708 8.759481 TGTCCAACCTTTGATGCATATAATAA 57.241 30.769 0.00 0.00 0.00 1.40
1659 1709 8.759481 TTGTCCAACCTTTGATGCATATAATA 57.241 30.769 0.00 0.00 0.00 0.98
1660 1710 7.658525 TTGTCCAACCTTTGATGCATATAAT 57.341 32.000 0.00 0.00 0.00 1.28
1661 1711 7.395772 TCTTTGTCCAACCTTTGATGCATATAA 59.604 33.333 0.00 0.00 0.00 0.98
1662 1712 6.889177 TCTTTGTCCAACCTTTGATGCATATA 59.111 34.615 0.00 0.00 0.00 0.86
1663 1713 5.716228 TCTTTGTCCAACCTTTGATGCATAT 59.284 36.000 0.00 0.00 0.00 1.78
1671 1721 3.891366 ACCATCTCTTTGTCCAACCTTTG 59.109 43.478 0.00 0.00 0.00 2.77
1672 1722 3.891366 CACCATCTCTTTGTCCAACCTTT 59.109 43.478 0.00 0.00 0.00 3.11
1675 1725 3.140325 TCACCATCTCTTTGTCCAACC 57.860 47.619 0.00 0.00 0.00 3.77
1734 1784 5.123186 GCTGCGTCATCTCTATCTGTACTAT 59.877 44.000 0.00 0.00 0.00 2.12
1735 1785 4.452795 GCTGCGTCATCTCTATCTGTACTA 59.547 45.833 0.00 0.00 0.00 1.82
1740 1790 2.789491 TGCTGCGTCATCTCTATCTG 57.211 50.000 0.00 0.00 0.00 2.90
1744 1794 1.202568 CCCATTGCTGCGTCATCTCTA 60.203 52.381 0.00 0.00 0.00 2.43
1746 1796 2.020131 CCCATTGCTGCGTCATCTC 58.980 57.895 0.00 0.00 0.00 2.75
1748 1798 2.410469 GCCCATTGCTGCGTCATC 59.590 61.111 0.00 0.00 36.87 2.92
1766 1832 2.033372 CATGCCATGTCCTTGCCATTA 58.967 47.619 0.00 0.00 0.00 1.90
1775 1841 2.011222 CAATTTTGGCATGCCATGTCC 58.989 47.619 38.78 11.48 46.64 4.02
1810 1879 1.153706 GACGTCCATGTACCCCGTG 60.154 63.158 3.51 0.00 0.00 4.94
1962 2031 3.753434 CGGACTCGACCAGCAGCT 61.753 66.667 0.00 0.00 39.00 4.24
2086 2155 4.280494 ACGAGCCGCTTCACGTGT 62.280 61.111 16.51 0.00 41.42 4.49
2221 2290 1.675801 CAGCCAGAGGTTGCTCTCA 59.324 57.895 0.00 0.00 35.12 3.27
2279 2350 2.281484 GTTGTGGCGCTGGGAGAA 60.281 61.111 7.64 0.00 0.00 2.87
2587 2658 1.304547 CTCCACCACCTCGAGGACT 60.305 63.158 37.69 14.23 38.94 3.85
2764 2837 2.147958 CAAAACATTCTTCCCGGACGA 58.852 47.619 0.73 0.00 0.00 4.20
2766 2839 3.408634 TCTCAAAACATTCTTCCCGGAC 58.591 45.455 0.73 0.00 0.00 4.79
2769 2842 4.622740 GCAAATCTCAAAACATTCTTCCCG 59.377 41.667 0.00 0.00 0.00 5.14
2777 2857 9.401058 ACTAATAGCTAGCAAATCTCAAAACAT 57.599 29.630 18.83 0.00 0.00 2.71
2778 2858 8.668353 CACTAATAGCTAGCAAATCTCAAAACA 58.332 33.333 18.83 0.00 0.00 2.83
2779 2859 8.125448 CCACTAATAGCTAGCAAATCTCAAAAC 58.875 37.037 18.83 0.00 0.00 2.43
2781 2861 6.260936 GCCACTAATAGCTAGCAAATCTCAAA 59.739 38.462 18.83 0.00 0.00 2.69
2841 2921 7.334858 GTTGATCTCTACTCCCATCTCTTTTT 58.665 38.462 0.00 0.00 0.00 1.94
2842 2922 6.126911 GGTTGATCTCTACTCCCATCTCTTTT 60.127 42.308 0.00 0.00 0.00 2.27
2843 2923 5.365314 GGTTGATCTCTACTCCCATCTCTTT 59.635 44.000 0.00 0.00 0.00 2.52
2844 2924 4.898861 GGTTGATCTCTACTCCCATCTCTT 59.101 45.833 0.00 0.00 0.00 2.85
2845 2925 4.078922 TGGTTGATCTCTACTCCCATCTCT 60.079 45.833 0.00 0.00 0.00 3.10
2846 2926 4.219115 TGGTTGATCTCTACTCCCATCTC 58.781 47.826 0.00 0.00 0.00 2.75
2847 2927 4.271807 TGGTTGATCTCTACTCCCATCT 57.728 45.455 0.00 0.00 0.00 2.90
2848 2928 4.346418 ACATGGTTGATCTCTACTCCCATC 59.654 45.833 0.00 0.00 0.00 3.51
2849 2929 4.302067 ACATGGTTGATCTCTACTCCCAT 58.698 43.478 0.00 0.00 0.00 4.00
2850 2930 3.724478 ACATGGTTGATCTCTACTCCCA 58.276 45.455 0.00 0.00 0.00 4.37
2851 2931 4.407296 AGAACATGGTTGATCTCTACTCCC 59.593 45.833 0.00 0.00 29.70 4.30
2852 2932 5.606348 AGAACATGGTTGATCTCTACTCC 57.394 43.478 0.00 0.00 29.70 3.85
2853 2933 9.039870 CAATAAGAACATGGTTGATCTCTACTC 57.960 37.037 0.00 0.00 34.21 2.59
2854 2934 8.762645 TCAATAAGAACATGGTTGATCTCTACT 58.237 33.333 0.00 0.00 34.21 2.57
2855 2935 8.821894 GTCAATAAGAACATGGTTGATCTCTAC 58.178 37.037 0.00 0.00 34.21 2.59
2856 2936 8.762645 AGTCAATAAGAACATGGTTGATCTCTA 58.237 33.333 0.00 0.00 34.21 2.43
2857 2937 7.628234 AGTCAATAAGAACATGGTTGATCTCT 58.372 34.615 0.00 0.00 34.21 3.10
2858 2938 7.856145 AGTCAATAAGAACATGGTTGATCTC 57.144 36.000 0.00 0.00 34.21 2.75
2859 2939 7.884877 TGAAGTCAATAAGAACATGGTTGATCT 59.115 33.333 0.00 0.00 36.63 2.75
2860 2940 8.044060 TGAAGTCAATAAGAACATGGTTGATC 57.956 34.615 0.00 0.00 32.19 2.92
2861 2941 8.299570 GTTGAAGTCAATAAGAACATGGTTGAT 58.700 33.333 0.00 0.00 38.24 2.57
2862 2942 7.284261 TGTTGAAGTCAATAAGAACATGGTTGA 59.716 33.333 0.00 0.00 38.24 3.18
2870 2950 6.128418 GCCTCTCTGTTGAAGTCAATAAGAAC 60.128 42.308 0.00 0.00 38.24 3.01
2889 2969 3.445450 TGACTCAACACTAGATGCCTCTC 59.555 47.826 0.00 0.00 32.66 3.20
2920 3011 9.256228 GGGGTAATCCTTCTTTTCTAAAAAGAT 57.744 33.333 13.85 3.90 36.30 2.40
2921 3012 7.392393 CGGGGTAATCCTTCTTTTCTAAAAAGA 59.608 37.037 10.08 10.08 34.73 2.52
2922 3013 7.176165 ACGGGGTAATCCTTCTTTTCTAAAAAG 59.824 37.037 5.94 5.94 35.33 2.27
2949 3047 8.024865 GCTGCATGTATCATTATAATGCAAAGA 58.975 33.333 18.89 3.71 42.01 2.52
2952 3050 6.208994 TGGCTGCATGTATCATTATAATGCAA 59.791 34.615 18.89 7.80 42.01 4.08
2967 3065 3.209410 GCTTAGTAAGATGGCTGCATGT 58.791 45.455 14.27 0.00 0.00 3.21
2974 3072 7.510549 TTGGATATTTGCTTAGTAAGATGGC 57.489 36.000 14.27 0.00 0.00 4.40
2983 3081 8.514594 TCACAGACTTTTTGGATATTTGCTTAG 58.485 33.333 0.00 0.00 0.00 2.18
2997 3095 6.942576 AGCTTGTACCATATCACAGACTTTTT 59.057 34.615 0.00 0.00 0.00 1.94
3011 3109 1.141881 CCGAGCGAGCTTGTACCAT 59.858 57.895 11.03 0.00 0.00 3.55
3080 3179 4.272748 GGGAGACTGTGTGTAACTTTGTTC 59.727 45.833 0.00 0.00 38.04 3.18
3095 3285 2.623889 CCTAGTTGTATCCGGGAGACTG 59.376 54.545 21.35 7.58 0.00 3.51
3113 3303 9.924650 GTCTAGTTGTTTTTCATTCTACTCCTA 57.075 33.333 0.00 0.00 0.00 2.94
3114 3304 8.652290 AGTCTAGTTGTTTTTCATTCTACTCCT 58.348 33.333 0.00 0.00 0.00 3.69
3197 3467 3.472652 TCGGTAGTGTTCAAGCATGTTT 58.527 40.909 0.00 0.00 0.00 2.83
3263 3533 4.647964 CGAAATTGATCGTTCGGTCATTT 58.352 39.130 8.95 8.95 42.21 2.32
3283 3553 3.318275 GTGCATAGGATCAACTACTCCGA 59.682 47.826 0.00 0.00 36.62 4.55
3340 3662 2.376518 TGGCCAGAGATGAAGGTTTCTT 59.623 45.455 0.00 0.00 35.62 2.52
3508 4273 8.437360 TCGATTGTTATCAATTTAGATGCTGT 57.563 30.769 0.67 0.00 43.33 4.40
3544 4309 1.122019 AGTTCCACTTGGACTCCGCT 61.122 55.000 0.00 0.00 45.39 5.52
3625 4390 7.274250 GGTCAACAAAATCAAAGCATACTCATC 59.726 37.037 0.00 0.00 0.00 2.92
3626 4391 7.092716 GGTCAACAAAATCAAAGCATACTCAT 58.907 34.615 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.