Multiple sequence alignment - TraesCS3B01G342800

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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 TraesCS3B01G342800 chr3B 100.000 3633 0 0 1 3633 550663913 550667545 0.000000e+00 6709.0
1 TraesCS3B01G342800 chr3B 90.000 90 9 0 2375 2464 239293834 239293923 2.290000e-22 117.0
2 TraesCS3B01G342800 chr3B 91.111 45 4 0 69 113 521707170 521707214 1.090000e-05 62.1
3 TraesCS3B01G342800 chr3B 97.143 35 0 1 576 609 137329031 137328997 1.410000e-04 58.4
4 TraesCS3B01G342800 chr3D 94.345 3537 120 28 1 3508 422550256 422553741 0.000000e+00 5350.0
5 TraesCS3B01G342800 chr3D 97.222 36 1 0 582 617 585924717 585924752 1.090000e-05 62.1
6 TraesCS3B01G342800 chr3A 95.173 1989 68 15 410 2389 566334156 566332187 0.000000e+00 3116.0
7 TraesCS3B01G342800 chr3A 95.286 700 26 6 2451 3146 566332103 566331407 0.000000e+00 1103.0
8 TraesCS3B01G342800 chr6D 80.987 689 94 23 1613 2287 431083266 431083931 2.500000e-141 512.0
9 TraesCS3B01G342800 chr6D 88.333 60 5 2 55 113 455310186 455310128 1.810000e-08 71.3
10 TraesCS3B01G342800 chr6B 89.820 334 29 4 2440 2772 439390485 439390814 1.210000e-114 424.0
11 TraesCS3B01G342800 chr6B 93.023 86 6 0 2374 2459 188673610 188673695 3.810000e-25 126.0
12 TraesCS3B01G342800 chr6B 90.805 87 8 0 2378 2464 123500598 123500512 2.290000e-22 117.0
13 TraesCS3B01G342800 chr6B 84.058 69 9 2 46 113 692488752 692488685 8.420000e-07 65.8
14 TraesCS3B01G342800 chr2D 86.889 389 37 7 2000 2379 210345788 210346171 1.210000e-114 424.0
15 TraesCS3B01G342800 chr2D 89.905 317 26 3 2461 2777 210346170 210346480 1.570000e-108 403.0
16 TraesCS3B01G342800 chr2D 84.483 348 32 9 2051 2379 218299057 218299401 1.260000e-84 324.0
17 TraesCS3B01G342800 chr2D 77.559 254 35 11 29 267 322128651 322128405 2.280000e-27 134.0
18 TraesCS3B01G342800 chr2D 79.167 192 32 4 80 268 423604159 423604345 3.810000e-25 126.0
19 TraesCS3B01G342800 chr2D 82.105 95 13 4 183 276 412635728 412635637 1.080000e-10 78.7
20 TraesCS3B01G342800 chr6A 88.889 333 34 2 2440 2772 397523190 397522861 1.210000e-109 407.0
21 TraesCS3B01G342800 chr6A 85.233 386 42 8 2003 2379 457448980 457448601 2.050000e-102 383.0
22 TraesCS3B01G342800 chr2B 88.218 331 35 4 2448 2777 47631986 47632313 3.400000e-105 392.0
23 TraesCS3B01G342800 chr2B 95.294 85 4 0 2378 2462 547862205 547862121 6.330000e-28 135.0
24 TraesCS3B01G342800 chr2B 94.253 87 5 0 2376 2462 517154300 517154386 2.280000e-27 134.0
25 TraesCS3B01G342800 chr2B 96.250 80 1 2 3505 3584 735234103 735234180 2.940000e-26 130.0
26 TraesCS3B01G342800 chr2B 88.372 86 8 2 579 664 571140967 571141050 6.420000e-18 102.0
27 TraesCS3B01G342800 chr2B 75.978 179 34 7 69 244 644523108 644523280 2.320000e-12 84.2
28 TraesCS3B01G342800 chr1B 89.274 317 27 3 2461 2777 660739653 660739962 1.220000e-104 390.0
29 TraesCS3B01G342800 chr1B 84.833 389 41 9 2000 2379 660739275 660739654 3.420000e-100 375.0
30 TraesCS3B01G342800 chr4B 85.233 386 39 9 2003 2379 625349863 625349487 7.360000e-102 381.0
31 TraesCS3B01G342800 chr4B 92.222 90 6 1 2375 2463 191659427 191659338 3.810000e-25 126.0
32 TraesCS3B01G342800 chr5B 88.782 312 30 2 2461 2772 142543289 142543595 9.520000e-101 377.0
33 TraesCS3B01G342800 chr5B 76.735 245 44 9 29 270 268288482 268288248 1.370000e-24 124.0
34 TraesCS3B01G342800 chr5B 86.458 96 6 4 2286 2377 184274101 184274009 8.300000e-17 99.0
35 TraesCS3B01G342800 chr5B 76.119 201 36 8 80 276 595618889 595619081 1.070000e-15 95.3
36 TraesCS3B01G342800 chr5A 87.658 316 33 3 2461 2776 230918476 230918167 2.670000e-96 363.0
37 TraesCS3B01G342800 chr5A 87.119 295 32 5 2087 2379 230918765 230918475 2.700000e-86 329.0
38 TraesCS3B01G342800 chr5A 73.778 225 35 16 30 238 43265029 43264813 2.340000e-07 67.6
39 TraesCS3B01G342800 chr5A 100.000 29 0 0 2003 2031 230918809 230918781 2.000000e-03 54.7
40 TraesCS3B01G342800 chr1D 96.250 80 1 2 3506 3584 37958039 37958117 2.940000e-26 130.0
41 TraesCS3B01G342800 chr4D 88.119 101 10 2 2370 2468 253767551 253767451 6.370000e-23 119.0
42 TraesCS3B01G342800 chr7D 86.792 106 12 2 2367 2470 382119471 382119366 2.290000e-22 117.0
43 TraesCS3B01G342800 chr5D 76.829 246 34 15 30 269 377173649 377173421 2.290000e-22 117.0
44 TraesCS3B01G342800 chr2A 86.813 91 6 3 579 664 631657279 631657368 2.990000e-16 97.1
45 TraesCS3B01G342800 chr1A 74.872 195 39 5 79 269 28377434 28377246 3.010000e-11 80.5


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 TraesCS3B01G342800 chr3B 550663913 550667545 3632 False 6709.0 6709 100.000000 1 3633 1 chr3B.!!$F3 3632
1 TraesCS3B01G342800 chr3D 422550256 422553741 3485 False 5350.0 5350 94.345000 1 3508 1 chr3D.!!$F1 3507
2 TraesCS3B01G342800 chr3A 566331407 566334156 2749 True 2109.5 3116 95.229500 410 3146 2 chr3A.!!$R1 2736
3 TraesCS3B01G342800 chr6D 431083266 431083931 665 False 512.0 512 80.987000 1613 2287 1 chr6D.!!$F1 674
4 TraesCS3B01G342800 chr2D 210345788 210346480 692 False 413.5 424 88.397000 2000 2777 2 chr2D.!!$F3 777
5 TraesCS3B01G342800 chr1B 660739275 660739962 687 False 382.5 390 87.053500 2000 2777 2 chr1B.!!$F1 777
6 TraesCS3B01G342800 chr5A 230918167 230918809 642 True 248.9 363 91.592333 2003 2776 3 chr5A.!!$R2 773

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
101 102 0.170561 ATCCGGTCTTCGTTCGTCTG 59.829 55.0 0.00 0.0 37.11 3.51 F
169 172 0.250467 ATCGCAGTTGCTGTTCTGGT 60.250 50.0 2.29 0.0 39.32 4.00 F
1365 1382 0.238289 CATGTTGACACTCGGTTGGC 59.762 55.0 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1367 0.107410 ACAAGCCAACCGAGTGTCAA 60.107 50.0 0.0 0.0 0.0 3.18 R
1987 2021 0.255890 GCTGCTTTGGTAGGGATGGA 59.744 55.0 0.0 0.0 0.0 3.41 R
3353 3440 1.125633 ACTACGGTGTCCCAGTTTGT 58.874 50.0 0.0 0.0 0.0 2.83 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
26 27 2.167861 GCGCCTAGCCTTGTCTTCG 61.168 63.158 0.00 0.00 40.81 3.79
27 28 1.511305 CGCCTAGCCTTGTCTTCGA 59.489 57.895 0.00 0.00 0.00 3.71
44 45 1.527433 CGAGAGGTGTGTCTCCAGCA 61.527 60.000 0.00 0.00 40.04 4.41
62 63 0.747255 CAGATCTCGTGGGATCGGTT 59.253 55.000 4.16 0.00 44.71 4.44
65 66 0.976073 ATCTCGTGGGATCGGTTGGT 60.976 55.000 0.00 0.00 0.00 3.67
74 75 2.227194 GGATCGGTTGGTGTTTTGTCT 58.773 47.619 0.00 0.00 0.00 3.41
77 78 1.666700 TCGGTTGGTGTTTTGTCTTCG 59.333 47.619 0.00 0.00 0.00 3.79
98 99 1.246056 TGGATCCGGTCTTCGTTCGT 61.246 55.000 7.39 0.00 37.11 3.85
100 101 0.450983 GATCCGGTCTTCGTTCGTCT 59.549 55.000 0.00 0.00 37.11 4.18
101 102 0.170561 ATCCGGTCTTCGTTCGTCTG 59.829 55.000 0.00 0.00 37.11 3.51
102 103 1.168407 TCCGGTCTTCGTTCGTCTGT 61.168 55.000 0.00 0.00 37.11 3.41
103 104 1.002250 CCGGTCTTCGTTCGTCTGTG 61.002 60.000 0.00 0.00 37.11 3.66
104 105 0.317603 CGGTCTTCGTTCGTCTGTGT 60.318 55.000 0.00 0.00 0.00 3.72
105 106 1.406447 GGTCTTCGTTCGTCTGTGTC 58.594 55.000 0.00 0.00 0.00 3.67
106 107 1.001597 GGTCTTCGTTCGTCTGTGTCT 60.002 52.381 0.00 0.00 0.00 3.41
107 108 2.044860 GTCTTCGTTCGTCTGTGTCTG 58.955 52.381 0.00 0.00 0.00 3.51
126 127 8.314021 TGTGTCTGTGTGTCTGAATATTAGATT 58.686 33.333 0.00 0.00 0.00 2.40
127 128 9.155975 GTGTCTGTGTGTCTGAATATTAGATTT 57.844 33.333 0.00 0.00 0.00 2.17
165 168 1.733912 TCATCATCGCAGTTGCTGTTC 59.266 47.619 2.29 0.00 39.32 3.18
166 169 1.736126 CATCATCGCAGTTGCTGTTCT 59.264 47.619 2.29 0.00 39.32 3.01
167 170 1.150827 TCATCGCAGTTGCTGTTCTG 58.849 50.000 2.29 0.00 39.32 3.02
169 172 0.250467 ATCGCAGTTGCTGTTCTGGT 60.250 50.000 2.29 0.00 39.32 4.00
170 173 1.159713 TCGCAGTTGCTGTTCTGGTG 61.160 55.000 2.29 0.00 39.32 4.17
171 174 1.008079 GCAGTTGCTGTTCTGGTGC 60.008 57.895 0.00 0.00 38.21 5.01
172 175 1.280746 CAGTTGCTGTTCTGGTGCG 59.719 57.895 0.00 0.00 0.00 5.34
173 176 2.050985 GTTGCTGTTCTGGTGCGC 60.051 61.111 0.00 0.00 0.00 6.09
174 177 2.203195 TTGCTGTTCTGGTGCGCT 60.203 55.556 9.73 0.00 0.00 5.92
175 178 1.070615 TTGCTGTTCTGGTGCGCTA 59.929 52.632 9.73 0.00 0.00 4.26
176 179 0.533978 TTGCTGTTCTGGTGCGCTAA 60.534 50.000 9.73 0.00 0.00 3.09
177 180 0.321564 TGCTGTTCTGGTGCGCTAAT 60.322 50.000 9.73 0.00 0.00 1.73
181 184 3.521560 CTGTTCTGGTGCGCTAATCTAA 58.478 45.455 9.73 0.00 0.00 2.10
189 192 4.283467 TGGTGCGCTAATCTAATCCTATGT 59.717 41.667 9.73 0.00 0.00 2.29
200 203 2.938956 ATCCTATGTGGCCTTAGCAC 57.061 50.000 3.32 0.00 42.56 4.40
212 215 2.415090 GCCTTAGCACGACGACTTTCTA 60.415 50.000 0.00 0.00 39.53 2.10
215 218 2.061740 AGCACGACGACTTTCTAACC 57.938 50.000 0.00 0.00 0.00 2.85
226 229 4.787598 GACTTTCTAACCGTCGACTACAA 58.212 43.478 14.70 0.00 0.00 2.41
230 233 4.566545 TCTAACCGTCGACTACAACAAA 57.433 40.909 14.70 0.00 0.00 2.83
238 241 4.266976 CGTCGACTACAACAAAGTTTGTCT 59.733 41.667 21.10 11.95 44.59 3.41
251 254 2.107204 AGTTTGTCTGGCTCCAATGAGT 59.893 45.455 0.00 0.00 40.95 3.41
258 261 3.102090 GCTCCAATGAGTAAGGGGC 57.898 57.895 0.00 0.00 42.49 5.80
282 285 4.509737 GGCGAGGCGTGGTCTACC 62.510 72.222 0.00 0.00 0.00 3.18
283 286 3.755628 GCGAGGCGTGGTCTACCA 61.756 66.667 0.00 0.00 45.30 3.25
380 386 2.280524 TTCGTGGTCCCTTGCACG 60.281 61.111 0.00 0.00 41.74 5.34
395 401 0.521735 GCACGGCGATTTTTCCTCTT 59.478 50.000 16.62 0.00 0.00 2.85
425 431 1.299468 CCCTTCGATCTTCCTCGCG 60.299 63.158 0.00 0.00 38.52 5.87
470 476 1.591183 CTTCAACCGGGCCAATTGG 59.409 57.895 20.81 20.81 38.53 3.16
471 477 0.897863 CTTCAACCGGGCCAATTGGA 60.898 55.000 29.02 0.86 37.39 3.53
472 478 0.252012 TTCAACCGGGCCAATTGGAT 60.252 50.000 29.02 4.29 37.39 3.41
473 479 0.969917 TCAACCGGGCCAATTGGATG 60.970 55.000 29.02 15.41 37.39 3.51
504 510 1.353022 ACCACCCTAAAATCTTCCGCA 59.647 47.619 0.00 0.00 0.00 5.69
585 597 3.406595 CTCGCCCACCCAATCCCTC 62.407 68.421 0.00 0.00 0.00 4.30
586 598 4.506255 CGCCCACCCAATCCCTCC 62.506 72.222 0.00 0.00 0.00 4.30
587 599 4.506255 GCCCACCCAATCCCTCCG 62.506 72.222 0.00 0.00 0.00 4.63
624 639 4.067016 CCGTCGCCGTTTCCGTTG 62.067 66.667 0.00 0.00 0.00 4.10
677 692 2.278206 CGCAGTCCTCGACATCCG 60.278 66.667 0.00 0.00 34.60 4.18
682 697 1.993370 CAGTCCTCGACATCCGTTTTC 59.007 52.381 0.00 0.00 39.75 2.29
728 743 2.162208 CCACCCAGTGATCAATTGAACG 59.838 50.000 13.09 4.10 35.23 3.95
796 811 4.440880 CCTGTCAACAGAGGATGAGATTC 58.559 47.826 11.70 0.00 46.59 2.52
860 875 8.863872 ATAAGTAGTTAACATTTTCCTGTGCT 57.136 30.769 8.61 0.00 0.00 4.40
912 929 7.649057 AGAAGCTTTTAGGAATTACACACAAC 58.351 34.615 0.00 0.00 0.00 3.32
913 930 6.327279 AGCTTTTAGGAATTACACACAACC 57.673 37.500 0.00 0.00 0.00 3.77
940 957 3.438360 CGCATTCCTTTGTTATTGAGGC 58.562 45.455 0.00 0.00 0.00 4.70
955 972 8.465999 TGTTATTGAGGCTGTTTAATTATGTGG 58.534 33.333 0.00 0.00 0.00 4.17
961 978 6.805713 AGGCTGTTTAATTATGTGGTTATGC 58.194 36.000 0.00 0.00 0.00 3.14
1110 1127 7.408756 TTTGTCTTATTTGATCATGGAAGGG 57.591 36.000 0.00 0.00 0.00 3.95
1177 1194 4.885325 TGGTAGACTTATACACAGCATCGA 59.115 41.667 0.00 0.00 0.00 3.59
1252 1269 0.873312 CGTCGAGGCAGATGGTGATG 60.873 60.000 0.00 0.00 0.00 3.07
1351 1368 9.520515 AACTACTCATATTTTGGTTCTCATGTT 57.479 29.630 0.00 0.00 0.00 2.71
1352 1369 8.950210 ACTACTCATATTTTGGTTCTCATGTTG 58.050 33.333 0.00 0.00 0.00 3.33
1353 1370 9.166173 CTACTCATATTTTGGTTCTCATGTTGA 57.834 33.333 0.00 0.00 0.00 3.18
1354 1371 7.820648 ACTCATATTTTGGTTCTCATGTTGAC 58.179 34.615 0.00 0.00 0.00 3.18
1355 1372 7.448161 ACTCATATTTTGGTTCTCATGTTGACA 59.552 33.333 0.00 0.00 0.00 3.58
1356 1373 7.592938 TCATATTTTGGTTCTCATGTTGACAC 58.407 34.615 0.00 0.00 0.00 3.67
1357 1374 7.448161 TCATATTTTGGTTCTCATGTTGACACT 59.552 33.333 0.00 0.00 0.00 3.55
1358 1375 5.499139 TTTTGGTTCTCATGTTGACACTC 57.501 39.130 0.00 0.00 0.00 3.51
1359 1376 2.754472 TGGTTCTCATGTTGACACTCG 58.246 47.619 0.00 0.00 0.00 4.18
1360 1377 2.069273 GGTTCTCATGTTGACACTCGG 58.931 52.381 0.00 0.00 0.00 4.63
1361 1378 2.548067 GGTTCTCATGTTGACACTCGGT 60.548 50.000 0.00 0.00 0.00 4.69
1362 1379 3.131396 GTTCTCATGTTGACACTCGGTT 58.869 45.455 0.00 0.00 0.00 4.44
1363 1380 2.754472 TCTCATGTTGACACTCGGTTG 58.246 47.619 0.00 0.00 0.00 3.77
1364 1381 1.800586 CTCATGTTGACACTCGGTTGG 59.199 52.381 0.00 0.00 0.00 3.77
1365 1382 0.238289 CATGTTGACACTCGGTTGGC 59.762 55.000 0.00 0.00 0.00 4.52
1843 1875 9.668497 GGTAAGTTAATCTGAGGTTCAAGTATT 57.332 33.333 0.00 0.00 0.00 1.89
1977 2011 4.038402 CCCTGCTGATTTTTGTTCTCTTGT 59.962 41.667 0.00 0.00 0.00 3.16
1987 2021 2.344592 TGTTCTCTTGTGGTACCCCAT 58.655 47.619 10.07 0.00 44.35 4.00
2125 2172 4.874966 AGATGTAGTTCTTCATGCAGCTTC 59.125 41.667 0.00 0.00 0.00 3.86
2165 2212 9.520515 TCACTCTCAGTATATTGTGCTATCATA 57.479 33.333 0.00 0.00 0.00 2.15
2403 2454 3.583086 CCCTCCGTCCCACAATATAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
2807 2880 0.251386 TTTTTGAGCGTATGGGGGCA 60.251 50.000 0.00 0.00 0.00 5.36
2902 2981 9.840427 GATGCTTTTATTTTTCACAGCTAGTAA 57.160 29.630 0.00 0.00 0.00 2.24
2959 3038 6.923508 TCAGTGTCTATTCATAATACTTGGCG 59.076 38.462 0.00 0.00 0.00 5.69
3091 3170 2.046507 CTGGTCTGACTGGCCTGC 60.047 66.667 9.95 3.40 42.07 4.85
3226 3305 9.559958 CAATTTGACCAATAATGTAAGAGTCAC 57.440 33.333 0.00 0.00 32.87 3.67
3331 3418 6.484977 GGCCAAATTGATGGTCAAACTTAAAA 59.515 34.615 0.00 0.00 44.70 1.52
3332 3419 7.351981 GCCAAATTGATGGTCAAACTTAAAAC 58.648 34.615 0.00 0.00 40.12 2.43
3334 3421 9.108284 CCAAATTGATGGTCAAACTTAAAACTT 57.892 29.630 0.00 0.00 40.12 2.66
3335 3422 9.919348 CAAATTGATGGTCAAACTTAAAACTTG 57.081 29.630 0.00 0.00 40.12 3.16
3338 3425 9.883142 ATTGATGGTCAAACTTAAAACTTGAAA 57.117 25.926 0.00 0.00 40.12 2.69
3340 3427 9.311916 TGATGGTCAAACTTAAAACTTGAAATG 57.688 29.630 0.00 0.00 31.21 2.32
3353 3440 3.387374 ACTTGAAATGCATTGGTTCCACA 59.613 39.130 13.82 2.75 0.00 4.17
3380 3467 1.138266 GGGACACCGTAGTACATGCAT 59.862 52.381 0.00 0.00 0.00 3.96
3382 3469 3.181473 GGGACACCGTAGTACATGCATAA 60.181 47.826 0.00 0.00 0.00 1.90
3385 3472 5.862323 GGACACCGTAGTACATGCATAATAG 59.138 44.000 0.00 0.00 0.00 1.73
3442 3529 3.382832 CTTGTCGGCGTCCTCCCT 61.383 66.667 6.85 0.00 0.00 4.20
3447 3534 4.394712 CGGCGTCCTCCCTTTGCT 62.395 66.667 0.00 0.00 0.00 3.91
3451 3538 1.743252 CGTCCTCCCTTTGCTGCTC 60.743 63.158 0.00 0.00 0.00 4.26
3458 3545 4.729918 CTTTGCTGCTCCGGCCCT 62.730 66.667 0.00 0.00 37.74 5.19
3459 3546 3.326578 TTTGCTGCTCCGGCCCTA 61.327 61.111 0.00 0.00 37.74 3.53
3467 3554 1.152735 CTCCGGCCCTAGTGCTCTA 60.153 63.158 0.00 0.00 0.00 2.43
3483 3570 0.676782 TCTAAAAGCTGCGCCCTTCC 60.677 55.000 4.18 0.00 0.00 3.46
3497 3584 1.746991 CTTCCGGCTTCCTTGGCTC 60.747 63.158 0.00 0.00 0.00 4.70
3498 3585 2.190488 CTTCCGGCTTCCTTGGCTCT 62.190 60.000 0.00 0.00 0.00 4.09
3508 3595 2.358247 TTGGCTCTCCGGCGTTTC 60.358 61.111 6.01 0.00 42.02 2.78
3509 3596 2.788191 CTTGGCTCTCCGGCGTTTCT 62.788 60.000 6.01 0.00 42.02 2.52
3510 3597 2.047179 GGCTCTCCGGCGTTTCTT 60.047 61.111 6.01 0.00 0.00 2.52
3511 3598 1.671379 GGCTCTCCGGCGTTTCTTT 60.671 57.895 6.01 0.00 0.00 2.52
3512 3599 1.235281 GGCTCTCCGGCGTTTCTTTT 61.235 55.000 6.01 0.00 0.00 2.27
3513 3600 0.591659 GCTCTCCGGCGTTTCTTTTT 59.408 50.000 6.01 0.00 0.00 1.94
3530 3617 2.202295 TTTTGAACAACAGAAGGCGC 57.798 45.000 0.00 0.00 0.00 6.53
3531 3618 1.098869 TTTGAACAACAGAAGGCGCA 58.901 45.000 10.83 0.00 0.00 6.09
3532 3619 0.380378 TTGAACAACAGAAGGCGCAC 59.620 50.000 10.83 0.00 0.00 5.34
3533 3620 1.282875 GAACAACAGAAGGCGCACC 59.717 57.895 10.83 0.00 0.00 5.01
3534 3621 1.444119 GAACAACAGAAGGCGCACCA 61.444 55.000 10.83 0.00 39.06 4.17
3535 3622 1.034838 AACAACAGAAGGCGCACCAA 61.035 50.000 10.83 0.00 39.06 3.67
3536 3623 1.283793 CAACAGAAGGCGCACCAAG 59.716 57.895 10.83 0.00 39.06 3.61
3537 3624 2.555547 AACAGAAGGCGCACCAAGC 61.556 57.895 10.83 0.00 39.06 4.01
3546 3633 2.417097 GCACCAAGCGCCAAACTT 59.583 55.556 2.29 0.00 0.00 2.66
3547 3634 1.227234 GCACCAAGCGCCAAACTTT 60.227 52.632 2.29 0.00 0.00 2.66
3548 3635 0.809636 GCACCAAGCGCCAAACTTTT 60.810 50.000 2.29 0.00 0.00 2.27
3549 3636 1.208259 CACCAAGCGCCAAACTTTTC 58.792 50.000 2.29 0.00 0.00 2.29
3550 3637 0.820871 ACCAAGCGCCAAACTTTTCA 59.179 45.000 2.29 0.00 0.00 2.69
3551 3638 1.205893 ACCAAGCGCCAAACTTTTCAA 59.794 42.857 2.29 0.00 0.00 2.69
3552 3639 2.158971 ACCAAGCGCCAAACTTTTCAAT 60.159 40.909 2.29 0.00 0.00 2.57
3553 3640 2.476241 CCAAGCGCCAAACTTTTCAATC 59.524 45.455 2.29 0.00 0.00 2.67
3554 3641 3.122297 CAAGCGCCAAACTTTTCAATCA 58.878 40.909 2.29 0.00 0.00 2.57
3555 3642 3.017265 AGCGCCAAACTTTTCAATCAG 57.983 42.857 2.29 0.00 0.00 2.90
3556 3643 1.456923 GCGCCAAACTTTTCAATCAGC 59.543 47.619 0.00 0.00 0.00 4.26
3557 3644 2.863704 GCGCCAAACTTTTCAATCAGCT 60.864 45.455 0.00 0.00 0.00 4.24
3558 3645 2.982470 CGCCAAACTTTTCAATCAGCTC 59.018 45.455 0.00 0.00 0.00 4.09
3559 3646 3.550639 CGCCAAACTTTTCAATCAGCTCA 60.551 43.478 0.00 0.00 0.00 4.26
3560 3647 3.985925 GCCAAACTTTTCAATCAGCTCAG 59.014 43.478 0.00 0.00 0.00 3.35
3561 3648 4.500375 GCCAAACTTTTCAATCAGCTCAGT 60.500 41.667 0.00 0.00 0.00 3.41
3562 3649 5.278463 GCCAAACTTTTCAATCAGCTCAGTA 60.278 40.000 0.00 0.00 0.00 2.74
3563 3650 6.735694 GCCAAACTTTTCAATCAGCTCAGTAA 60.736 38.462 0.00 0.00 0.00 2.24
3564 3651 6.638468 CCAAACTTTTCAATCAGCTCAGTAAC 59.362 38.462 0.00 0.00 0.00 2.50
3565 3652 6.942532 AACTTTTCAATCAGCTCAGTAACA 57.057 33.333 0.00 0.00 0.00 2.41
3566 3653 6.942532 ACTTTTCAATCAGCTCAGTAACAA 57.057 33.333 0.00 0.00 0.00 2.83
3567 3654 6.729187 ACTTTTCAATCAGCTCAGTAACAAC 58.271 36.000 0.00 0.00 0.00 3.32
3568 3655 4.990543 TTCAATCAGCTCAGTAACAACG 57.009 40.909 0.00 0.00 0.00 4.10
3569 3656 3.990092 TCAATCAGCTCAGTAACAACGT 58.010 40.909 0.00 0.00 0.00 3.99
3570 3657 5.128992 TCAATCAGCTCAGTAACAACGTA 57.871 39.130 0.00 0.00 0.00 3.57
3571 3658 4.921515 TCAATCAGCTCAGTAACAACGTAC 59.078 41.667 0.00 0.00 0.00 3.67
3572 3659 3.994204 TCAGCTCAGTAACAACGTACA 57.006 42.857 0.00 0.00 0.00 2.90
3573 3660 4.310357 TCAGCTCAGTAACAACGTACAA 57.690 40.909 0.00 0.00 0.00 2.41
3574 3661 4.046462 TCAGCTCAGTAACAACGTACAAC 58.954 43.478 0.00 0.00 0.00 3.32
3575 3662 3.799963 CAGCTCAGTAACAACGTACAACA 59.200 43.478 0.00 0.00 0.00 3.33
3576 3663 4.447724 CAGCTCAGTAACAACGTACAACAT 59.552 41.667 0.00 0.00 0.00 2.71
3577 3664 4.447724 AGCTCAGTAACAACGTACAACATG 59.552 41.667 0.00 0.00 0.00 3.21
3578 3665 4.377022 GCTCAGTAACAACGTACAACATGG 60.377 45.833 0.00 0.00 0.00 3.66
3579 3666 4.946445 TCAGTAACAACGTACAACATGGA 58.054 39.130 0.00 0.00 0.00 3.41
3580 3667 5.543714 TCAGTAACAACGTACAACATGGAT 58.456 37.500 0.00 0.00 0.00 3.41
3581 3668 5.992829 TCAGTAACAACGTACAACATGGATT 59.007 36.000 0.00 0.00 0.00 3.01
3582 3669 7.153315 TCAGTAACAACGTACAACATGGATTA 58.847 34.615 0.00 0.00 0.00 1.75
3583 3670 7.116662 TCAGTAACAACGTACAACATGGATTAC 59.883 37.037 0.00 0.00 0.00 1.89
3584 3671 5.616488 AACAACGTACAACATGGATTACC 57.384 39.130 0.00 0.00 0.00 2.85
3585 3672 4.901868 ACAACGTACAACATGGATTACCT 58.098 39.130 0.00 0.00 37.04 3.08
3586 3673 4.693566 ACAACGTACAACATGGATTACCTG 59.306 41.667 0.00 0.00 37.04 4.00
3587 3674 4.811969 ACGTACAACATGGATTACCTGA 57.188 40.909 0.00 0.00 37.04 3.86
3588 3675 5.155278 ACGTACAACATGGATTACCTGAA 57.845 39.130 0.00 0.00 37.04 3.02
3589 3676 5.553123 ACGTACAACATGGATTACCTGAAA 58.447 37.500 0.00 0.00 37.04 2.69
3590 3677 5.998981 ACGTACAACATGGATTACCTGAAAA 59.001 36.000 0.00 0.00 37.04 2.29
3591 3678 6.148811 ACGTACAACATGGATTACCTGAAAAG 59.851 38.462 0.00 0.00 37.04 2.27
3592 3679 5.982890 ACAACATGGATTACCTGAAAAGG 57.017 39.130 0.00 0.00 37.04 3.11
3593 3680 4.220602 ACAACATGGATTACCTGAAAAGGC 59.779 41.667 0.00 0.00 37.04 4.35
3594 3681 4.322057 ACATGGATTACCTGAAAAGGCT 57.678 40.909 0.00 0.00 37.04 4.58
3595 3682 4.677182 ACATGGATTACCTGAAAAGGCTT 58.323 39.130 0.00 0.00 37.04 4.35
3596 3683 5.086621 ACATGGATTACCTGAAAAGGCTTT 58.913 37.500 6.68 6.68 37.04 3.51
3597 3684 5.185828 ACATGGATTACCTGAAAAGGCTTTC 59.814 40.000 13.76 7.62 41.25 2.62
3598 3685 3.756434 TGGATTACCTGAAAAGGCTTTCG 59.244 43.478 13.76 5.04 43.40 3.46
3599 3686 3.756963 GGATTACCTGAAAAGGCTTTCGT 59.243 43.478 13.76 9.60 43.40 3.85
3600 3687 4.142665 GGATTACCTGAAAAGGCTTTCGTC 60.143 45.833 13.76 8.78 43.40 4.20
3601 3688 1.605753 ACCTGAAAAGGCTTTCGTCC 58.394 50.000 13.76 4.07 43.40 4.79
3602 3689 0.881796 CCTGAAAAGGCTTTCGTCCC 59.118 55.000 13.76 1.69 43.40 4.46
3603 3690 0.517316 CTGAAAAGGCTTTCGTCCCG 59.483 55.000 13.76 0.00 43.40 5.14
3604 3691 1.209383 GAAAAGGCTTTCGTCCCGC 59.791 57.895 13.76 0.00 32.06 6.13
3605 3692 1.228154 AAAAGGCTTTCGTCCCGCT 60.228 52.632 13.76 0.00 0.00 5.52
3606 3693 0.822121 AAAAGGCTTTCGTCCCGCTT 60.822 50.000 13.76 0.00 0.00 4.68
3607 3694 0.822121 AAAGGCTTTCGTCCCGCTTT 60.822 50.000 6.68 0.00 0.00 3.51
3608 3695 0.035739 AAGGCTTTCGTCCCGCTTTA 59.964 50.000 0.00 0.00 0.00 1.85
3609 3696 0.252197 AGGCTTTCGTCCCGCTTTAT 59.748 50.000 0.00 0.00 0.00 1.40
3610 3697 0.377203 GGCTTTCGTCCCGCTTTATG 59.623 55.000 0.00 0.00 0.00 1.90
3611 3698 1.365699 GCTTTCGTCCCGCTTTATGA 58.634 50.000 0.00 0.00 0.00 2.15
3612 3699 1.735571 GCTTTCGTCCCGCTTTATGAA 59.264 47.619 0.00 0.00 0.00 2.57
3613 3700 2.354821 GCTTTCGTCCCGCTTTATGAAT 59.645 45.455 0.00 0.00 0.00 2.57
3614 3701 3.558418 GCTTTCGTCCCGCTTTATGAATA 59.442 43.478 0.00 0.00 0.00 1.75
3615 3702 4.034742 GCTTTCGTCCCGCTTTATGAATAA 59.965 41.667 0.00 0.00 0.00 1.40
3616 3703 5.448089 GCTTTCGTCCCGCTTTATGAATAAA 60.448 40.000 0.00 0.00 0.00 1.40
3628 3715 7.887996 CTTTATGAATAAAGCAAACTGCCAA 57.112 32.000 9.29 0.00 46.52 4.52
3629 3716 8.309163 CTTTATGAATAAAGCAAACTGCCAAA 57.691 30.769 9.29 0.00 46.52 3.28
3630 3717 7.887996 TTATGAATAAAGCAAACTGCCAAAG 57.112 32.000 0.00 0.00 46.52 2.77
3631 3718 5.528043 TGAATAAAGCAAACTGCCAAAGA 57.472 34.783 0.00 0.00 46.52 2.52
3632 3719 5.531634 TGAATAAAGCAAACTGCCAAAGAG 58.468 37.500 0.00 0.00 46.52 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.246086 CTGCTGGAGACACACCTCTC 59.754 60.000 0.00 0.00 36.67 3.20
27 28 0.178950 TCTGCTGGAGACACACCTCT 60.179 55.000 0.00 0.00 35.60 3.69
44 45 0.747255 CAACCGATCCCACGAGATCT 59.253 55.000 0.00 0.00 40.50 2.75
62 63 1.065345 TCCACCGAAGACAAAACACCA 60.065 47.619 0.00 0.00 0.00 4.17
65 66 2.500229 GGATCCACCGAAGACAAAACA 58.500 47.619 6.95 0.00 0.00 2.83
77 78 0.459759 GAACGAAGACCGGATCCACC 60.460 60.000 9.46 0.00 43.93 4.61
92 93 0.846401 CACACAGACACAGACGAACG 59.154 55.000 0.00 0.00 0.00 3.95
98 99 5.728637 ATATTCAGACACACAGACACAGA 57.271 39.130 0.00 0.00 0.00 3.41
100 101 7.227049 TCTAATATTCAGACACACAGACACA 57.773 36.000 0.00 0.00 0.00 3.72
101 102 8.709386 AATCTAATATTCAGACACACAGACAC 57.291 34.615 0.00 0.00 0.00 3.67
102 103 9.725019 AAAATCTAATATTCAGACACACAGACA 57.275 29.630 0.00 0.00 0.00 3.41
126 127 9.988350 GATGATGAAAAGAAGCGTAGATAAAAA 57.012 29.630 0.00 0.00 0.00 1.94
127 128 8.328146 CGATGATGAAAAGAAGCGTAGATAAAA 58.672 33.333 0.00 0.00 0.00 1.52
165 168 3.393089 AGGATTAGATTAGCGCACCAG 57.607 47.619 11.47 0.00 0.00 4.00
166 169 4.283467 ACATAGGATTAGATTAGCGCACCA 59.717 41.667 11.47 0.00 0.00 4.17
167 170 4.627467 CACATAGGATTAGATTAGCGCACC 59.373 45.833 11.47 0.00 0.00 5.01
169 172 4.820897 CCACATAGGATTAGATTAGCGCA 58.179 43.478 11.47 0.00 41.22 6.09
170 173 3.619038 GCCACATAGGATTAGATTAGCGC 59.381 47.826 0.00 0.00 41.22 5.92
171 174 4.081420 AGGCCACATAGGATTAGATTAGCG 60.081 45.833 5.01 0.00 41.22 4.26
172 175 5.428184 AGGCCACATAGGATTAGATTAGC 57.572 43.478 5.01 0.00 41.22 3.09
173 176 7.044798 GCTAAGGCCACATAGGATTAGATTAG 58.955 42.308 5.01 0.00 39.07 1.73
174 177 6.500400 TGCTAAGGCCACATAGGATTAGATTA 59.500 38.462 5.01 0.00 39.07 1.75
175 178 5.310594 TGCTAAGGCCACATAGGATTAGATT 59.689 40.000 5.01 0.00 39.07 2.40
176 179 4.846367 TGCTAAGGCCACATAGGATTAGAT 59.154 41.667 5.01 0.00 39.07 1.98
177 180 4.040461 GTGCTAAGGCCACATAGGATTAGA 59.960 45.833 5.01 0.00 39.07 2.10
181 184 1.070758 CGTGCTAAGGCCACATAGGAT 59.929 52.381 5.01 0.00 41.22 3.24
189 192 1.812686 AAGTCGTCGTGCTAAGGCCA 61.813 55.000 5.01 0.00 37.74 5.36
212 215 3.169355 ACTTTGTTGTAGTCGACGGTT 57.831 42.857 10.46 0.00 0.00 4.44
215 218 4.266976 AGACAAACTTTGTTGTAGTCGACG 59.733 41.667 10.46 0.00 45.52 5.12
226 229 6.952143 CTCATTGGAGCCAGACAAACTTTGT 61.952 44.000 6.87 6.87 39.58 2.83
230 233 2.107204 ACTCATTGGAGCCAGACAAACT 59.893 45.455 0.00 0.00 45.42 2.66
238 241 0.918983 CCCCTTACTCATTGGAGCCA 59.081 55.000 0.00 0.00 45.42 4.75
251 254 4.215742 CGCCGTCATCGCCCCTTA 62.216 66.667 0.00 0.00 35.54 2.69
360 365 3.047877 GCAAGGGACCACGAACCG 61.048 66.667 0.00 0.00 0.00 4.44
380 386 3.074412 TGAGTCAAGAGGAAAAATCGCC 58.926 45.455 0.00 0.00 0.00 5.54
395 401 0.539669 TCGAAGGGCTGAGTGAGTCA 60.540 55.000 0.00 0.00 0.00 3.41
425 431 4.092968 CGTTAGGTCAAAGCATTAGGTCAC 59.907 45.833 0.00 0.00 0.00 3.67
470 476 1.404035 GGGTGGTTTTACATCCGCATC 59.596 52.381 0.00 0.00 36.11 3.91
471 477 1.005450 AGGGTGGTTTTACATCCGCAT 59.995 47.619 0.00 0.00 46.46 4.73
472 478 0.402504 AGGGTGGTTTTACATCCGCA 59.597 50.000 0.00 0.00 46.46 5.69
473 479 2.406596 TAGGGTGGTTTTACATCCGC 57.593 50.000 0.00 0.00 46.46 5.54
677 692 1.712018 GGCGGCCATACCTCGAAAAC 61.712 60.000 15.62 0.00 35.61 2.43
796 811 7.069331 CCTTAAGGGGCACTATATATCTCTCAG 59.931 44.444 14.25 0.00 0.00 3.35
853 868 1.394917 GATGTAGCACGAAAGCACAGG 59.605 52.381 0.00 0.00 36.85 4.00
860 875 1.001974 AGCCAGTGATGTAGCACGAAA 59.998 47.619 0.00 0.00 43.42 3.46
912 929 0.394352 ACAAAGGAATGCGGCTAGGG 60.394 55.000 0.00 0.00 0.00 3.53
913 930 1.463674 AACAAAGGAATGCGGCTAGG 58.536 50.000 0.00 0.00 0.00 3.02
955 972 4.503910 GGAAAAGGGTGAAATGGCATAAC 58.496 43.478 0.00 0.00 0.00 1.89
961 978 2.325661 AGGGGAAAAGGGTGAAATGG 57.674 50.000 0.00 0.00 0.00 3.16
1110 1127 5.674052 AGGAGTCATATATGTGATGAGCC 57.326 43.478 12.42 5.38 34.02 4.70
1252 1269 4.082354 AGCATCTTTCCAAGAATCTGCAAC 60.082 41.667 11.31 0.00 41.31 4.17
1333 1350 7.361201 CGAGTGTCAACATGAGAACCAAAATAT 60.361 37.037 0.00 0.00 0.00 1.28
1350 1367 0.107410 ACAAGCCAACCGAGTGTCAA 60.107 50.000 0.00 0.00 0.00 3.18
1351 1368 0.107410 AACAAGCCAACCGAGTGTCA 60.107 50.000 0.00 0.00 0.00 3.58
1352 1369 1.021968 AAACAAGCCAACCGAGTGTC 58.978 50.000 0.00 0.00 0.00 3.67
1353 1370 0.738389 CAAACAAGCCAACCGAGTGT 59.262 50.000 0.00 0.00 0.00 3.55
1354 1371 0.738389 ACAAACAAGCCAACCGAGTG 59.262 50.000 0.00 0.00 0.00 3.51
1355 1372 1.470051 AACAAACAAGCCAACCGAGT 58.530 45.000 0.00 0.00 0.00 4.18
1356 1373 2.577449 AAACAAACAAGCCAACCGAG 57.423 45.000 0.00 0.00 0.00 4.63
1357 1374 2.996621 CAAAAACAAACAAGCCAACCGA 59.003 40.909 0.00 0.00 0.00 4.69
1358 1375 2.739379 ACAAAAACAAACAAGCCAACCG 59.261 40.909 0.00 0.00 0.00 4.44
1359 1376 4.757799 AACAAAAACAAACAAGCCAACC 57.242 36.364 0.00 0.00 0.00 3.77
1360 1377 5.672570 GCCTAACAAAAACAAACAAGCCAAC 60.673 40.000 0.00 0.00 0.00 3.77
1361 1378 4.393371 GCCTAACAAAAACAAACAAGCCAA 59.607 37.500 0.00 0.00 0.00 4.52
1362 1379 3.935828 GCCTAACAAAAACAAACAAGCCA 59.064 39.130 0.00 0.00 0.00 4.75
1363 1380 3.311322 GGCCTAACAAAAACAAACAAGCC 59.689 43.478 0.00 0.00 0.00 4.35
1364 1381 3.935828 TGGCCTAACAAAAACAAACAAGC 59.064 39.130 3.32 0.00 0.00 4.01
1365 1382 6.676237 AATGGCCTAACAAAAACAAACAAG 57.324 33.333 3.32 0.00 0.00 3.16
1444 1476 4.281435 TCCCGACAGTAAATACAGTCACAA 59.719 41.667 14.07 0.00 41.17 3.33
1931 1965 8.166726 AGGGAATTCTTCAAGAAATAACTCAGT 58.833 33.333 3.35 0.00 37.82 3.41
1987 2021 0.255890 GCTGCTTTGGTAGGGATGGA 59.744 55.000 0.00 0.00 0.00 3.41
2092 2138 7.397892 TGAAGAACTACATCTAGTCCTTGAG 57.602 40.000 0.00 0.00 28.13 3.02
2125 2172 1.912043 AGAGTGAGGGGAGTCCAAATG 59.088 52.381 12.30 0.00 38.24 2.32
2371 2422 1.550409 GGGACGGAGGGAGTATATGCT 60.550 57.143 0.00 0.00 0.00 3.79
2807 2880 4.451900 ACTCGATTTCAACAACCAGAAGT 58.548 39.130 0.00 0.00 0.00 3.01
2959 3038 4.779987 CACGTAGGGCTTAAAACAAAGAC 58.220 43.478 0.00 0.00 33.39 3.01
3091 3170 6.884280 ACCAGAAAATGAAAACACTCTAGG 57.116 37.500 0.00 0.00 0.00 3.02
3151 3230 5.092554 TGGCATGTAAATTAGGACGAAGA 57.907 39.130 0.00 0.00 0.00 2.87
3259 3338 3.197983 ACCATTGAATTCCTACTCCCCA 58.802 45.455 2.27 0.00 0.00 4.96
3308 3395 8.661352 AGTTTTAAGTTTGACCATCAATTTGG 57.339 30.769 0.00 0.00 42.82 3.28
3331 3418 3.387374 TGTGGAACCAATGCATTTCAAGT 59.613 39.130 9.83 2.26 34.36 3.16
3332 3419 3.742369 GTGTGGAACCAATGCATTTCAAG 59.258 43.478 9.83 1.60 34.36 3.02
3334 3421 2.697229 TGTGTGGAACCAATGCATTTCA 59.303 40.909 9.83 0.93 34.36 2.69
3335 3422 3.383620 TGTGTGGAACCAATGCATTTC 57.616 42.857 9.83 5.07 34.36 2.17
3338 3425 2.699846 AGTTTGTGTGGAACCAATGCAT 59.300 40.909 0.00 0.00 34.36 3.96
3340 3427 2.472816 CAGTTTGTGTGGAACCAATGC 58.527 47.619 0.00 0.00 34.36 3.56
3353 3440 1.125633 ACTACGGTGTCCCAGTTTGT 58.874 50.000 0.00 0.00 0.00 2.83
3442 3529 3.326578 TAGGGCCGGAGCAGCAAA 61.327 61.111 5.05 0.00 42.56 3.68
3451 3538 0.539986 TTTTAGAGCACTAGGGCCGG 59.460 55.000 14.92 0.00 0.00 6.13
3483 3570 2.124942 GGAGAGCCAAGGAAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
3510 3597 2.094494 TGCGCCTTCTGTTGTTCAAAAA 60.094 40.909 4.18 0.00 0.00 1.94
3511 3598 1.474478 TGCGCCTTCTGTTGTTCAAAA 59.526 42.857 4.18 0.00 0.00 2.44
3512 3599 1.098869 TGCGCCTTCTGTTGTTCAAA 58.901 45.000 4.18 0.00 0.00 2.69
3513 3600 0.380378 GTGCGCCTTCTGTTGTTCAA 59.620 50.000 4.18 0.00 0.00 2.69
3514 3601 1.444119 GGTGCGCCTTCTGTTGTTCA 61.444 55.000 9.68 0.00 0.00 3.18
3515 3602 1.282875 GGTGCGCCTTCTGTTGTTC 59.717 57.895 9.68 0.00 0.00 3.18
3516 3603 1.034838 TTGGTGCGCCTTCTGTTGTT 61.035 50.000 18.96 0.00 35.27 2.83
3517 3604 1.447317 CTTGGTGCGCCTTCTGTTGT 61.447 55.000 18.96 0.00 35.27 3.32
3518 3605 1.283793 CTTGGTGCGCCTTCTGTTG 59.716 57.895 18.96 0.00 35.27 3.33
3519 3606 2.555547 GCTTGGTGCGCCTTCTGTT 61.556 57.895 18.96 0.00 35.27 3.16
3520 3607 2.980233 GCTTGGTGCGCCTTCTGT 60.980 61.111 18.96 0.00 35.27 3.41
3529 3616 0.809636 AAAAGTTTGGCGCTTGGTGC 60.810 50.000 7.64 0.00 38.45 5.01
3530 3617 1.208259 GAAAAGTTTGGCGCTTGGTG 58.792 50.000 7.64 0.00 0.00 4.17
3531 3618 0.820871 TGAAAAGTTTGGCGCTTGGT 59.179 45.000 7.64 0.00 0.00 3.67
3532 3619 1.933247 TTGAAAAGTTTGGCGCTTGG 58.067 45.000 7.64 0.00 0.00 3.61
3533 3620 3.122297 TGATTGAAAAGTTTGGCGCTTG 58.878 40.909 7.64 0.00 0.00 4.01
3534 3621 3.383761 CTGATTGAAAAGTTTGGCGCTT 58.616 40.909 7.64 0.00 0.00 4.68
3535 3622 2.863704 GCTGATTGAAAAGTTTGGCGCT 60.864 45.455 7.64 0.00 0.00 5.92
3536 3623 1.456923 GCTGATTGAAAAGTTTGGCGC 59.543 47.619 0.00 0.00 0.00 6.53
3537 3624 2.982470 GAGCTGATTGAAAAGTTTGGCG 59.018 45.455 0.00 0.00 0.00 5.69
3538 3625 3.981211 TGAGCTGATTGAAAAGTTTGGC 58.019 40.909 0.00 0.00 0.00 4.52
3539 3626 5.192327 ACTGAGCTGATTGAAAAGTTTGG 57.808 39.130 0.00 0.00 0.00 3.28
3540 3627 7.195646 TGTTACTGAGCTGATTGAAAAGTTTG 58.804 34.615 0.00 0.00 0.00 2.93
3541 3628 7.333528 TGTTACTGAGCTGATTGAAAAGTTT 57.666 32.000 0.00 0.00 0.00 2.66
3542 3629 6.942532 TGTTACTGAGCTGATTGAAAAGTT 57.057 33.333 0.00 0.00 0.00 2.66
3543 3630 6.511767 CGTTGTTACTGAGCTGATTGAAAAGT 60.512 38.462 0.00 0.00 0.00 2.66
3544 3631 5.848036 CGTTGTTACTGAGCTGATTGAAAAG 59.152 40.000 0.00 0.00 0.00 2.27
3545 3632 5.295787 ACGTTGTTACTGAGCTGATTGAAAA 59.704 36.000 0.00 0.00 0.00 2.29
3546 3633 4.814234 ACGTTGTTACTGAGCTGATTGAAA 59.186 37.500 0.00 0.00 0.00 2.69
3547 3634 4.377021 ACGTTGTTACTGAGCTGATTGAA 58.623 39.130 0.00 0.00 0.00 2.69
3548 3635 3.990092 ACGTTGTTACTGAGCTGATTGA 58.010 40.909 0.00 0.00 0.00 2.57
3549 3636 4.684242 TGTACGTTGTTACTGAGCTGATTG 59.316 41.667 0.00 0.00 0.00 2.67
3550 3637 4.878439 TGTACGTTGTTACTGAGCTGATT 58.122 39.130 0.00 0.00 0.00 2.57
3551 3638 4.514781 TGTACGTTGTTACTGAGCTGAT 57.485 40.909 0.00 0.00 0.00 2.90
3552 3639 3.994204 TGTACGTTGTTACTGAGCTGA 57.006 42.857 0.00 0.00 0.00 4.26
3553 3640 3.799963 TGTTGTACGTTGTTACTGAGCTG 59.200 43.478 0.00 0.00 0.00 4.24
3554 3641 4.049546 TGTTGTACGTTGTTACTGAGCT 57.950 40.909 0.00 0.00 0.00 4.09
3555 3642 4.377022 CCATGTTGTACGTTGTTACTGAGC 60.377 45.833 0.00 0.00 0.00 4.26
3556 3643 4.986034 TCCATGTTGTACGTTGTTACTGAG 59.014 41.667 0.00 0.00 0.00 3.35
3557 3644 4.946445 TCCATGTTGTACGTTGTTACTGA 58.054 39.130 0.00 0.00 0.00 3.41
3558 3645 5.856126 ATCCATGTTGTACGTTGTTACTG 57.144 39.130 0.00 0.00 0.00 2.74
3559 3646 6.369615 GGTAATCCATGTTGTACGTTGTTACT 59.630 38.462 0.00 0.00 0.00 2.24
3560 3647 6.369615 AGGTAATCCATGTTGTACGTTGTTAC 59.630 38.462 0.00 0.00 35.89 2.50
3561 3648 6.369340 CAGGTAATCCATGTTGTACGTTGTTA 59.631 38.462 0.00 0.00 35.89 2.41
3562 3649 5.180492 CAGGTAATCCATGTTGTACGTTGTT 59.820 40.000 0.00 0.00 35.89 2.83
3563 3650 4.693566 CAGGTAATCCATGTTGTACGTTGT 59.306 41.667 0.00 0.00 35.89 3.32
3564 3651 4.932799 TCAGGTAATCCATGTTGTACGTTG 59.067 41.667 0.00 0.00 35.89 4.10
3565 3652 5.155278 TCAGGTAATCCATGTTGTACGTT 57.845 39.130 0.00 0.00 35.89 3.99
3566 3653 4.811969 TCAGGTAATCCATGTTGTACGT 57.188 40.909 0.00 0.00 35.89 3.57
3567 3654 6.403200 CCTTTTCAGGTAATCCATGTTGTACG 60.403 42.308 0.00 0.00 35.06 3.67
3568 3655 6.625081 GCCTTTTCAGGTAATCCATGTTGTAC 60.625 42.308 0.00 0.00 43.18 2.90
3569 3656 5.417580 GCCTTTTCAGGTAATCCATGTTGTA 59.582 40.000 0.00 0.00 43.18 2.41
3570 3657 4.220602 GCCTTTTCAGGTAATCCATGTTGT 59.779 41.667 0.00 0.00 43.18 3.32
3571 3658 4.463891 AGCCTTTTCAGGTAATCCATGTTG 59.536 41.667 0.00 0.00 43.18 3.33
3572 3659 4.677182 AGCCTTTTCAGGTAATCCATGTT 58.323 39.130 0.00 0.00 43.18 2.71
3573 3660 4.322057 AGCCTTTTCAGGTAATCCATGT 57.678 40.909 0.00 0.00 43.18 3.21
3574 3661 5.654497 GAAAGCCTTTTCAGGTAATCCATG 58.346 41.667 0.00 0.00 43.18 3.66
3575 3662 4.399303 CGAAAGCCTTTTCAGGTAATCCAT 59.601 41.667 0.00 0.00 43.18 3.41
3576 3663 3.756434 CGAAAGCCTTTTCAGGTAATCCA 59.244 43.478 0.00 0.00 43.18 3.41
3577 3664 3.756963 ACGAAAGCCTTTTCAGGTAATCC 59.243 43.478 0.00 0.00 43.18 3.01
3578 3665 4.142665 GGACGAAAGCCTTTTCAGGTAATC 60.143 45.833 0.00 0.00 43.18 1.75
3579 3666 3.756963 GGACGAAAGCCTTTTCAGGTAAT 59.243 43.478 0.00 0.00 43.18 1.89
3580 3667 3.143728 GGACGAAAGCCTTTTCAGGTAA 58.856 45.455 0.00 0.00 43.18 2.85
3581 3668 2.551504 GGGACGAAAGCCTTTTCAGGTA 60.552 50.000 0.00 0.00 43.18 3.08
3582 3669 1.605753 GGACGAAAGCCTTTTCAGGT 58.394 50.000 0.00 0.00 43.18 4.00
3583 3670 0.881796 GGGACGAAAGCCTTTTCAGG 59.118 55.000 0.00 0.00 42.27 3.86
3605 3692 8.147058 TCTTTGGCAGTTTGCTTTATTCATAAA 58.853 29.630 0.67 0.00 44.28 1.40
3606 3693 7.665690 TCTTTGGCAGTTTGCTTTATTCATAA 58.334 30.769 0.67 0.00 44.28 1.90
3607 3694 7.225784 TCTTTGGCAGTTTGCTTTATTCATA 57.774 32.000 0.67 0.00 44.28 2.15
3608 3695 6.100404 TCTTTGGCAGTTTGCTTTATTCAT 57.900 33.333 0.67 0.00 44.28 2.57
3609 3696 5.528043 TCTTTGGCAGTTTGCTTTATTCA 57.472 34.783 0.67 0.00 44.28 2.57


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

AutoCloner maintained by Alex Coulton.