Multiple sequence alignment - TraesCS2D01G394500

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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 TraesCS2D01G394500 chr2D 100.000 4967 0 0 1 4967 506138461 506143427 0.000000e+00 9173.0
1 TraesCS2D01G394500 chr2D 90.826 109 8 2 3504 3611 506141868 506141975 1.440000e-30 145.0
2 TraesCS2D01G394500 chr2D 90.826 109 8 2 3408 3515 506141964 506142071 1.440000e-30 145.0
3 TraesCS2D01G394500 chr2B 94.043 940 51 4 529 1467 593639550 593640485 0.000000e+00 1421.0
4 TraesCS2D01G394500 chr2B 91.263 950 49 19 2571 3513 593647340 593648262 0.000000e+00 1264.0
5 TraesCS2D01G394500 chr2B 88.553 760 62 15 3504 4251 593648159 593648905 0.000000e+00 898.0
6 TraesCS2D01G394500 chr2B 90.379 686 36 9 4284 4967 593653616 593654273 0.000000e+00 874.0
7 TraesCS2D01G394500 chr2B 88.060 402 31 8 1900 2289 593640833 593641229 1.260000e-125 460.0
8 TraesCS2D01G394500 chr2B 93.130 262 15 2 34 294 593638600 593638859 1.010000e-101 381.0
9 TraesCS2D01G394500 chr2B 90.498 221 13 5 313 533 593639227 593639439 8.140000e-73 285.0
10 TraesCS2D01G394500 chr2B 95.376 173 8 0 2402 2574 593646387 593646559 4.900000e-70 276.0
11 TraesCS2D01G394500 chr2A 89.097 963 59 15 3322 4259 650624411 650625352 0.000000e+00 1155.0
12 TraesCS2D01G394500 chr2A 95.238 630 25 3 842 1471 650621730 650622354 0.000000e+00 992.0
13 TraesCS2D01G394500 chr2A 88.777 597 42 15 1609 2192 650622431 650623015 0.000000e+00 708.0
14 TraesCS2D01G394500 chr2A 88.996 518 41 11 322 837 650618816 650619319 1.170000e-175 627.0
15 TraesCS2D01G394500 chr2A 90.625 448 20 7 2172 2614 650623026 650623456 4.310000e-160 575.0
16 TraesCS2D01G394500 chr2A 93.496 369 18 4 2659 3026 650623449 650623812 1.220000e-150 544.0
17 TraesCS2D01G394500 chr2A 88.525 427 38 8 4530 4952 650626018 650626437 1.600000e-139 507.0
18 TraesCS2D01G394500 chr2A 90.441 272 21 4 3053 3322 650624063 650624331 2.200000e-93 353.0
19 TraesCS2D01G394500 chr2A 87.770 278 19 4 4261 4532 650625435 650625703 1.340000e-80 311.0
20 TraesCS2D01G394500 chr2A 93.333 150 9 1 1 150 650618669 650618817 2.330000e-53 220.0
21 TraesCS2D01G394500 chr2A 93.939 99 5 1 3416 3513 650624587 650624685 1.110000e-31 148.0
22 TraesCS2D01G394500 chr2A 85.345 116 15 2 1507 1620 327477451 327477566 8.730000e-23 119.0
23 TraesCS2D01G394500 chr2A 76.224 143 26 8 1923 2062 475806774 475806911 8.920000e-08 69.4
24 TraesCS2D01G394500 chr3B 87.611 113 9 3 1509 1620 637088493 637088601 5.220000e-25 126.0
25 TraesCS2D01G394500 chr3B 86.239 109 13 2 1514 1620 761883177 761883069 3.140000e-22 117.0
26 TraesCS2D01G394500 chr3B 100.000 34 0 0 2285 2318 111680834 111680801 4.150000e-06 63.9
27 TraesCS2D01G394500 chr5B 84.615 117 11 7 1509 1620 123753554 123753440 5.260000e-20 110.0
28 TraesCS2D01G394500 chr5B 81.897 116 15 6 1509 1620 230882378 230882265 5.290000e-15 93.5
29 TraesCS2D01G394500 chr5B 92.857 56 2 1 4202 4255 448126301 448126356 4.120000e-11 80.5
30 TraesCS2D01G394500 chr4B 83.333 120 16 4 1488 1607 609113512 609113397 1.890000e-19 108.0
31 TraesCS2D01G394500 chr4B 94.340 53 1 1 4205 4255 526266734 526266682 4.120000e-11 80.5
32 TraesCS2D01G394500 chr1D 83.761 117 12 3 1502 1618 105352527 105352418 2.450000e-18 104.0
33 TraesCS2D01G394500 chr1D 93.023 43 3 0 2276 2318 343353202 343353160 4.150000e-06 63.9
34 TraesCS2D01G394500 chr4A 87.640 89 8 3 1519 1607 278325877 278325792 3.160000e-17 100.0
35 TraesCS2D01G394500 chr4A 100.000 34 0 0 2285 2318 132999999 133000032 4.150000e-06 63.9
36 TraesCS2D01G394500 chr6A 83.036 112 14 2 1509 1620 115318963 115318857 4.090000e-16 97.1
37 TraesCS2D01G394500 chr7D 94.643 56 1 1 4202 4255 1744375 1744430 8.860000e-13 86.1
38 TraesCS2D01G394500 chr6D 94.231 52 3 0 4205 4256 69269888 69269837 4.120000e-11 80.5
39 TraesCS2D01G394500 chr6B 94.340 53 1 1 4205 4255 541949884 541949832 4.120000e-11 80.5
40 TraesCS2D01G394500 chr7A 86.765 68 6 2 4195 4260 96559145 96559211 6.900000e-09 73.1
41 TraesCS2D01G394500 chr7A 100.000 33 0 0 2287 2319 730456744 730456776 1.490000e-05 62.1
42 TraesCS2D01G394500 chrUn 76.812 138 25 7 1928 2062 449512751 449512618 2.480000e-08 71.3
43 TraesCS2D01G394500 chr5D 88.333 60 5 1 4195 4252 346639798 346639857 2.480000e-08 71.3
44 TraesCS2D01G394500 chr3D 97.436 39 1 0 2280 2318 558261137 558261175 3.210000e-07 67.6
45 TraesCS2D01G394500 chr1A 83.562 73 11 1 1990 2062 208685478 208685549 3.210000e-07 67.6
46 TraesCS2D01G394500 chr1A 93.023 43 3 0 2276 2318 443129942 443129900 4.150000e-06 63.9
47 TraesCS2D01G394500 chr4D 100.000 34 0 0 2285 2318 339060447 339060414 4.150000e-06 63.9
48 TraesCS2D01G394500 chr1B 100.000 34 0 0 2285 2318 594014760 594014727 4.150000e-06 63.9
49 TraesCS2D01G394500 chr1B 95.000 40 0 2 2280 2317 389222135 389222174 1.490000e-05 62.1


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 TraesCS2D01G394500 chr2D 506138461 506143427 4966 False 3154.333333 9173 93.884000 1 4967 3 chr2D.!!$F1 4966
1 TraesCS2D01G394500 chr2B 593653616 593654273 657 False 874.000000 874 90.379000 4284 4967 1 chr2B.!!$F1 683
2 TraesCS2D01G394500 chr2B 593646387 593648905 2518 False 812.666667 1264 91.730667 2402 4251 3 chr2B.!!$F3 1849
3 TraesCS2D01G394500 chr2B 593638600 593641229 2629 False 636.750000 1421 91.432750 34 2289 4 chr2B.!!$F2 2255
4 TraesCS2D01G394500 chr2A 650618669 650626437 7768 False 558.181818 1155 90.930636 1 4952 11 chr2A.!!$F3 4951

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
309 311 1.191489 ACTTTTCCAATTGGGGCGGG 61.191 55.000 24.29 12.87 37.22 6.13 F
1314 4190 0.846015 CCTCCACCCATGGCAAGATA 59.154 55.000 6.09 0.00 46.80 1.98 F
1474 4350 0.178903 TGTTGGAGAGGTAGGCTGGT 60.179 55.000 0.00 0.00 0.00 4.00 F
1475 4351 0.250513 GTTGGAGAGGTAGGCTGGTG 59.749 60.000 0.00 0.00 0.00 4.17 F
1478 4354 0.614979 GGAGAGGTAGGCTGGTGTCA 60.615 60.000 0.00 0.00 0.00 3.58 F
2976 6769 1.073284 TGTCTGGTTTCCTTACAGGCC 59.927 52.381 0.00 0.00 36.06 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 4206 0.729116 CATAAGAAGCAGTGCACCGG 59.271 55.000 19.20 7.56 0.00 5.28 R
3033 6829 0.625849 AACATGCCTAACCTCAGGGG 59.374 55.000 0.00 0.00 41.89 4.79 R
3218 7236 1.066587 CTGAGAGGTCGAATCGCCC 59.933 63.158 11.36 3.46 0.00 6.13 R
3352 7450 2.283145 AGCAAGGAACTCATGCAACT 57.717 45.000 0.00 0.00 42.45 3.16 R
3359 7457 3.176924 AGAGAGGTAGCAAGGAACTCA 57.823 47.619 0.00 0.00 38.49 3.41 R
4602 9133 0.320508 GACGGGTTCCACTTCCACTC 60.321 60.000 0.00 0.00 0.00 3.51 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
125 126 5.709594 TCTGATGGATGAATGAGGAGACTA 58.290 41.667 0.00 0.00 44.43 2.59
129 130 6.328410 TGATGGATGAATGAGGAGACTACATT 59.672 38.462 0.00 0.00 44.43 2.71
162 163 4.152402 CGTTCCATGACACGATTCTTCTTT 59.848 41.667 10.21 0.00 38.76 2.52
183 184 5.957910 TTGCGGTTAAATTGAAACACAAG 57.042 34.783 6.34 0.00 42.02 3.16
218 219 4.993029 AGTGGTCACAGCTAGAATCTAC 57.007 45.455 3.82 0.00 0.00 2.59
220 221 4.959210 AGTGGTCACAGCTAGAATCTACAT 59.041 41.667 3.82 0.00 0.00 2.29
257 259 7.391833 AGAATGAAAACCTGGTGAGTATTTCTC 59.608 37.037 17.29 10.35 43.03 2.87
281 283 5.167303 ACCACCTTCCAATCTTCTTAGTC 57.833 43.478 0.00 0.00 0.00 2.59
297 299 8.985805 TCTTCTTAGTCGATTGTTTACTTTTCC 58.014 33.333 0.00 0.00 0.00 3.13
298 300 8.665643 TTCTTAGTCGATTGTTTACTTTTCCA 57.334 30.769 0.00 0.00 0.00 3.53
299 301 8.665643 TCTTAGTCGATTGTTTACTTTTCCAA 57.334 30.769 0.00 0.00 0.00 3.53
300 302 9.280174 TCTTAGTCGATTGTTTACTTTTCCAAT 57.720 29.630 0.00 0.00 0.00 3.16
301 303 9.893305 CTTAGTCGATTGTTTACTTTTCCAATT 57.107 29.630 0.00 0.00 0.00 2.32
302 304 9.672086 TTAGTCGATTGTTTACTTTTCCAATTG 57.328 29.630 0.00 0.00 32.38 2.32
303 305 7.145323 AGTCGATTGTTTACTTTTCCAATTGG 58.855 34.615 19.08 19.08 32.13 3.16
304 306 6.364976 GTCGATTGTTTACTTTTCCAATTGGG 59.635 38.462 24.29 10.60 32.13 4.12
305 307 5.637387 CGATTGTTTACTTTTCCAATTGGGG 59.363 40.000 24.29 13.83 37.22 4.96
306 308 4.344359 TGTTTACTTTTCCAATTGGGGC 57.656 40.909 24.29 5.21 37.22 5.80
307 309 3.243907 TGTTTACTTTTCCAATTGGGGCG 60.244 43.478 24.29 12.48 37.22 6.13
308 310 1.551452 TACTTTTCCAATTGGGGCGG 58.449 50.000 24.29 14.15 37.22 6.13
309 311 1.191489 ACTTTTCCAATTGGGGCGGG 61.191 55.000 24.29 12.87 37.22 6.13
310 312 1.898330 CTTTTCCAATTGGGGCGGGG 61.898 60.000 24.29 6.66 37.22 5.73
311 313 3.914551 TTTCCAATTGGGGCGGGGG 62.915 63.158 24.29 0.00 37.22 5.40
345 696 5.612725 TGGAATCCAGGGCATAATTTTTC 57.387 39.130 0.00 0.00 0.00 2.29
347 698 4.099419 GGAATCCAGGGCATAATTTTTCGT 59.901 41.667 0.00 0.00 0.00 3.85
613 1081 6.179756 ACATGCACATGGTTCTTCTAATACA 58.820 36.000 14.73 0.00 42.91 2.29
699 1167 8.618702 ATGCATACATTTTCCAATTTGAAACA 57.381 26.923 0.00 0.00 34.13 2.83
779 1248 9.614269 AAATATATGTTAATTAATGGTGGGCCT 57.386 29.630 4.53 0.00 35.27 5.19
983 3859 2.434359 CGGCCACGGAAGTTCTCC 60.434 66.667 2.24 0.00 46.40 3.71
986 3862 2.669240 CCACGGAAGTTCTCCCCC 59.331 66.667 2.25 0.00 46.40 5.40
987 3863 2.221299 CCACGGAAGTTCTCCCCCA 61.221 63.158 2.25 0.00 46.40 4.96
1314 4190 0.846015 CCTCCACCCATGGCAAGATA 59.154 55.000 6.09 0.00 46.80 1.98
1316 4192 1.492176 CTCCACCCATGGCAAGATACT 59.508 52.381 6.09 0.00 46.80 2.12
1317 4193 1.490490 TCCACCCATGGCAAGATACTC 59.510 52.381 6.09 0.00 46.80 2.59
1322 4198 1.142465 CCATGGCAAGATACTCTGGCT 59.858 52.381 0.00 0.00 43.02 4.75
1330 4206 2.038659 AGATACTCTGGCTGCTTCTCC 58.961 52.381 0.00 0.00 0.00 3.71
1343 4219 2.738213 CTTCTCCCGGTGCACTGCTT 62.738 60.000 20.76 0.00 0.00 3.91
1352 4228 1.131883 GGTGCACTGCTTCTTATGCTG 59.868 52.381 17.98 0.00 38.90 4.41
1379 4255 5.992217 TGGATTTTAAAACCGTGAATTTGGG 59.008 36.000 1.97 0.00 0.00 4.12
1467 4343 2.656069 GGCGGCTGTTGGAGAGGTA 61.656 63.158 0.00 0.00 0.00 3.08
1474 4350 0.178903 TGTTGGAGAGGTAGGCTGGT 60.179 55.000 0.00 0.00 0.00 4.00
1475 4351 0.250513 GTTGGAGAGGTAGGCTGGTG 59.749 60.000 0.00 0.00 0.00 4.17
1478 4354 0.614979 GGAGAGGTAGGCTGGTGTCA 60.615 60.000 0.00 0.00 0.00 3.58
1480 4356 1.834263 GAGAGGTAGGCTGGTGTCAAT 59.166 52.381 0.00 0.00 0.00 2.57
1481 4357 1.834263 AGAGGTAGGCTGGTGTCAATC 59.166 52.381 0.00 0.00 0.00 2.67
1502 4391 8.958506 TCAATCTGTACTCTTCTAGGTTACTTC 58.041 37.037 0.00 0.00 0.00 3.01
1503 4392 8.962679 CAATCTGTACTCTTCTAGGTTACTTCT 58.037 37.037 0.00 0.00 0.00 2.85
1504 4393 8.741603 ATCTGTACTCTTCTAGGTTACTTCTC 57.258 38.462 0.00 0.00 0.00 2.87
1505 4394 7.687388 TCTGTACTCTTCTAGGTTACTTCTCA 58.313 38.462 0.00 0.00 0.00 3.27
1506 4395 8.162085 TCTGTACTCTTCTAGGTTACTTCTCAA 58.838 37.037 0.00 0.00 0.00 3.02
1507 4396 8.338072 TGTACTCTTCTAGGTTACTTCTCAAG 57.662 38.462 0.00 0.00 0.00 3.02
1508 4397 7.943447 TGTACTCTTCTAGGTTACTTCTCAAGT 59.057 37.037 0.00 0.00 45.40 3.16
1511 4400 9.536510 ACTCTTCTAGGTTACTTCTCAAGTATT 57.463 33.333 0.00 0.00 43.09 1.89
1516 4405 9.406113 TCTAGGTTACTTCTCAAGTATTACCTC 57.594 37.037 17.47 0.00 45.50 3.85
1518 4407 8.068892 AGGTTACTTCTCAAGTATTACCTCAG 57.931 38.462 11.61 0.00 45.50 3.35
1519 4408 7.674772 AGGTTACTTCTCAAGTATTACCTCAGT 59.325 37.037 11.61 0.00 45.50 3.41
1521 4410 6.532988 ACTTCTCAAGTATTACCTCAGTCC 57.467 41.667 0.00 0.00 40.69 3.85
1523 4412 4.942944 TCTCAAGTATTACCTCAGTCCCA 58.057 43.478 0.00 0.00 0.00 4.37
1524 4413 5.338632 TCTCAAGTATTACCTCAGTCCCAA 58.661 41.667 0.00 0.00 0.00 4.12
1525 4414 5.783360 TCTCAAGTATTACCTCAGTCCCAAA 59.217 40.000 0.00 0.00 0.00 3.28
1526 4415 6.271391 TCTCAAGTATTACCTCAGTCCCAAAA 59.729 38.462 0.00 0.00 0.00 2.44
1528 4417 6.940298 TCAAGTATTACCTCAGTCCCAAAAAG 59.060 38.462 0.00 0.00 0.00 2.27
1529 4418 5.254115 AGTATTACCTCAGTCCCAAAAAGC 58.746 41.667 0.00 0.00 0.00 3.51
1532 4421 2.310538 ACCTCAGTCCCAAAAAGCTTG 58.689 47.619 0.00 0.00 0.00 4.01
1534 4423 2.294512 CCTCAGTCCCAAAAAGCTTGTC 59.705 50.000 0.00 0.00 0.00 3.18
1535 4424 3.217626 CTCAGTCCCAAAAAGCTTGTCT 58.782 45.455 0.00 0.00 0.00 3.41
1536 4425 3.631250 TCAGTCCCAAAAAGCTTGTCTT 58.369 40.909 0.00 0.00 36.34 3.01
1539 4428 4.338118 CAGTCCCAAAAAGCTTGTCTTACA 59.662 41.667 0.00 0.00 33.88 2.41
1540 4429 5.010012 CAGTCCCAAAAAGCTTGTCTTACAT 59.990 40.000 0.00 0.00 33.88 2.29
1541 4430 5.598417 AGTCCCAAAAAGCTTGTCTTACATT 59.402 36.000 0.00 0.00 33.88 2.71
1542 4431 6.098266 AGTCCCAAAAAGCTTGTCTTACATTT 59.902 34.615 0.00 0.00 33.88 2.32
1543 4432 6.200854 GTCCCAAAAAGCTTGTCTTACATTTG 59.799 38.462 0.00 4.37 33.21 2.32
1544 4433 6.048509 CCCAAAAAGCTTGTCTTACATTTGT 58.951 36.000 0.00 0.00 32.28 2.83
1545 4434 6.200854 CCCAAAAAGCTTGTCTTACATTTGTC 59.799 38.462 0.00 0.00 32.28 3.18
1546 4435 6.980397 CCAAAAAGCTTGTCTTACATTTGTCT 59.020 34.615 0.00 0.00 32.28 3.41
1547 4436 8.134895 CCAAAAAGCTTGTCTTACATTTGTCTA 58.865 33.333 0.00 0.00 32.28 2.59
1548 4437 9.173939 CAAAAAGCTTGTCTTACATTTGTCTAG 57.826 33.333 0.00 0.00 33.88 2.43
1549 4438 8.677148 AAAAGCTTGTCTTACATTTGTCTAGA 57.323 30.769 0.00 0.00 33.88 2.43
1550 4439 8.854614 AAAGCTTGTCTTACATTTGTCTAGAT 57.145 30.769 0.00 0.00 33.88 1.98
1551 4440 9.944376 AAAGCTTGTCTTACATTTGTCTAGATA 57.056 29.630 0.00 0.00 33.88 1.98
1552 4441 8.934507 AGCTTGTCTTACATTTGTCTAGATAC 57.065 34.615 0.00 0.00 0.00 2.24
1553 4442 7.702772 AGCTTGTCTTACATTTGTCTAGATACG 59.297 37.037 0.00 0.00 0.00 3.06
1554 4443 7.043325 GCTTGTCTTACATTTGTCTAGATACGG 60.043 40.741 0.00 0.00 0.00 4.02
1555 4444 7.634671 TGTCTTACATTTGTCTAGATACGGA 57.365 36.000 0.00 0.00 0.00 4.69
1556 4445 8.234136 TGTCTTACATTTGTCTAGATACGGAT 57.766 34.615 0.00 0.00 0.00 4.18
1557 4446 8.135529 TGTCTTACATTTGTCTAGATACGGATG 58.864 37.037 0.00 0.85 0.00 3.51
1558 4447 8.136165 GTCTTACATTTGTCTAGATACGGATGT 58.864 37.037 13.29 13.29 34.19 3.06
1559 4448 9.346005 TCTTACATTTGTCTAGATACGGATGTA 57.654 33.333 11.94 11.94 32.86 2.29
1576 4465 8.699283 ACGGATGTATCTAACACTAAAACTTC 57.301 34.615 0.00 0.00 42.09 3.01
1577 4466 7.763071 ACGGATGTATCTAACACTAAAACTTCC 59.237 37.037 0.00 0.00 42.09 3.46
1578 4467 7.043590 CGGATGTATCTAACACTAAAACTTCCG 60.044 40.741 10.97 10.97 42.09 4.30
1579 4468 7.763071 GGATGTATCTAACACTAAAACTTCCGT 59.237 37.037 0.00 0.00 42.09 4.69
1580 4469 9.793252 GATGTATCTAACACTAAAACTTCCGTA 57.207 33.333 0.00 0.00 42.09 4.02
1582 4471 9.793252 TGTATCTAACACTAAAACTTCCGTATC 57.207 33.333 0.00 0.00 31.43 2.24
1586 4475 9.453572 TCTAACACTAAAACTTCCGTATCTAGA 57.546 33.333 0.00 0.00 0.00 2.43
1587 4476 9.500864 CTAACACTAAAACTTCCGTATCTAGAC 57.499 37.037 0.00 0.00 0.00 2.59
1588 4477 7.458409 ACACTAAAACTTCCGTATCTAGACA 57.542 36.000 0.00 0.00 0.00 3.41
1589 4478 7.889469 ACACTAAAACTTCCGTATCTAGACAA 58.111 34.615 0.00 0.00 0.00 3.18
1590 4479 8.362639 ACACTAAAACTTCCGTATCTAGACAAA 58.637 33.333 0.00 0.00 0.00 2.83
1591 4480 9.367444 CACTAAAACTTCCGTATCTAGACAAAT 57.633 33.333 0.00 0.00 0.00 2.32
1592 4481 9.583765 ACTAAAACTTCCGTATCTAGACAAATC 57.416 33.333 0.00 0.00 0.00 2.17
1593 4482 9.804758 CTAAAACTTCCGTATCTAGACAAATCT 57.195 33.333 0.00 0.00 39.15 2.40
1609 4498 8.480643 AGACAAATCTAGAACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
1610 4499 7.549488 AGACAAATCTAGAACAAGTAATTCGGG 59.451 37.037 0.00 0.00 31.46 5.14
1611 4500 7.391620 ACAAATCTAGAACAAGTAATTCGGGA 58.608 34.615 0.00 0.00 0.00 5.14
1612 4501 7.333672 ACAAATCTAGAACAAGTAATTCGGGAC 59.666 37.037 0.00 0.00 0.00 4.46
1657 4546 1.981254 CCAGCAATAAAACTGCGGTG 58.019 50.000 0.00 0.00 44.75 4.94
1662 4551 4.006989 AGCAATAAAACTGCGGTGATACA 58.993 39.130 0.00 0.00 44.75 2.29
1673 4567 5.535030 ACTGCGGTGATACATAATAGACTGA 59.465 40.000 0.00 0.00 0.00 3.41
1679 4573 6.647067 GGTGATACATAATAGACTGAACTGCC 59.353 42.308 0.00 0.00 0.00 4.85
1775 4672 7.692460 TTGCAACTCATTGAATTCTATCAGT 57.308 32.000 7.05 3.70 38.15 3.41
1876 4781 5.278061 ACCTAATAGACTGCCCTAGTTTGA 58.722 41.667 0.00 0.00 40.53 2.69
1885 4790 2.092968 TGCCCTAGTTTGACAGCATAGG 60.093 50.000 0.00 0.00 34.08 2.57
1915 4877 3.391506 ACCGTAGTTCTAAACACCACC 57.608 47.619 0.00 0.00 0.00 4.61
1930 4892 2.680841 CACCACCGTTTTTCTCACTTCA 59.319 45.455 0.00 0.00 0.00 3.02
1936 4898 6.238648 CCACCGTTTTTCTCACTTCAGTTTAT 60.239 38.462 0.00 0.00 0.00 1.40
2008 4970 9.151471 CCATGTTTGGGATACTACGATTTATAG 57.849 37.037 0.00 0.00 39.56 1.31
2060 5022 6.883756 ACATCAAAGTTTTCAAAACCATGGTT 59.116 30.769 24.86 24.86 40.45 3.67
2111 5083 2.208326 AAAAACTGAGCTGCCAAACG 57.792 45.000 0.00 0.00 0.00 3.60
2112 5084 1.102978 AAAACTGAGCTGCCAAACGT 58.897 45.000 0.00 0.00 0.00 3.99
2159 5131 2.300433 TGGCATGTGCAATATGAGACC 58.700 47.619 14.51 7.93 44.36 3.85
2255 5258 2.801111 GACTTCGGAGAACAGGTTTGTC 59.199 50.000 0.00 0.00 45.90 3.18
2289 5292 5.416952 CCCTCTGCACTTCTTGTTGAATATT 59.583 40.000 0.00 0.00 33.71 1.28
2291 5294 7.414540 CCCTCTGCACTTCTTGTTGAATATTAC 60.415 40.741 0.00 0.00 33.71 1.89
2292 5295 7.377766 TCTGCACTTCTTGTTGAATATTACC 57.622 36.000 0.00 0.00 33.71 2.85
2294 5297 7.334421 TCTGCACTTCTTGTTGAATATTACCTC 59.666 37.037 0.00 0.00 33.71 3.85
2295 5298 6.374333 TGCACTTCTTGTTGAATATTACCTCC 59.626 38.462 0.00 0.00 33.71 4.30
2296 5299 6.456988 GCACTTCTTGTTGAATATTACCTCCG 60.457 42.308 0.00 0.00 33.71 4.63
2298 5301 6.817140 ACTTCTTGTTGAATATTACCTCCGTC 59.183 38.462 0.00 0.00 33.71 4.79
2299 5302 5.667466 TCTTGTTGAATATTACCTCCGTCC 58.333 41.667 0.00 0.00 0.00 4.79
2301 5304 3.775866 TGTTGAATATTACCTCCGTCCCA 59.224 43.478 0.00 0.00 0.00 4.37
2305 5308 6.008696 TGAATATTACCTCCGTCCCAAATT 57.991 37.500 0.00 0.00 0.00 1.82
2306 5309 7.139287 TGAATATTACCTCCGTCCCAAATTA 57.861 36.000 0.00 0.00 0.00 1.40
2307 5310 7.221450 TGAATATTACCTCCGTCCCAAATTAG 58.779 38.462 0.00 0.00 0.00 1.73
2308 5311 6.758806 ATATTACCTCCGTCCCAAATTAGT 57.241 37.500 0.00 0.00 0.00 2.24
2309 5312 4.914177 TTACCTCCGTCCCAAATTAGTT 57.086 40.909 0.00 0.00 0.00 2.24
2310 5313 3.067684 ACCTCCGTCCCAAATTAGTTG 57.932 47.619 0.00 0.00 36.94 3.16
2311 5314 2.374170 ACCTCCGTCCCAAATTAGTTGT 59.626 45.455 0.00 0.00 35.23 3.32
2312 5315 3.007635 CCTCCGTCCCAAATTAGTTGTC 58.992 50.000 0.00 0.00 35.23 3.18
2313 5316 3.307480 CCTCCGTCCCAAATTAGTTGTCT 60.307 47.826 0.00 0.00 35.23 3.41
2314 5317 4.324267 CTCCGTCCCAAATTAGTTGTCTT 58.676 43.478 0.00 0.00 35.23 3.01
2315 5318 5.484715 CTCCGTCCCAAATTAGTTGTCTTA 58.515 41.667 0.00 0.00 35.23 2.10
2316 5319 5.484715 TCCGTCCCAAATTAGTTGTCTTAG 58.515 41.667 0.00 0.00 35.23 2.18
2317 5320 5.246656 TCCGTCCCAAATTAGTTGTCTTAGA 59.753 40.000 0.00 0.00 35.23 2.10
2318 5321 5.350640 CCGTCCCAAATTAGTTGTCTTAGAC 59.649 44.000 5.27 5.27 35.23 2.59
2319 5322 5.929992 CGTCCCAAATTAGTTGTCTTAGACA 59.070 40.000 11.42 11.42 41.09 3.41
2336 5339 4.756084 AGACAAGTTTTCAGCTACATGC 57.244 40.909 0.00 0.00 43.29 4.06
2372 5379 6.554334 TTAGCTTTGTTACTGTGGCTTTAG 57.446 37.500 0.00 0.00 0.00 1.85
2526 5533 8.966069 ATCTTCTGGAAATACTAAAGTAAGGC 57.034 34.615 0.00 0.00 33.76 4.35
2529 5536 8.927675 TTCTGGAAATACTAAAGTAAGGCAAA 57.072 30.769 0.00 0.00 33.76 3.68
2541 5548 7.775053 AAAGTAAGGCAAAGATATTTGGTCA 57.225 32.000 14.29 0.00 32.78 4.02
2686 6479 7.390718 AGGTTCTTAGTAGGTTTGCAATTAGTG 59.609 37.037 0.00 0.00 0.00 2.74
2687 6480 7.174426 GGTTCTTAGTAGGTTTGCAATTAGTGT 59.826 37.037 0.00 0.00 0.00 3.55
2688 6481 8.565416 GTTCTTAGTAGGTTTGCAATTAGTGTT 58.435 33.333 0.00 0.00 0.00 3.32
2766 6559 1.115467 ATACTGGAGAGCAGGTTCCG 58.885 55.000 0.00 0.00 36.22 4.30
2778 6571 2.159268 GCAGGTTCCGTACTTCTAGTCC 60.159 54.545 0.00 0.00 0.00 3.85
2807 6600 4.384647 GGATGCCCTGTAGTTTCTCATCTT 60.385 45.833 0.00 0.00 32.03 2.40
2855 6648 2.961741 TGTTAACATTTTGGCTGCCTGA 59.038 40.909 21.03 5.69 0.00 3.86
2954 6747 9.092876 CTTGCAAATTTAGGTTGTTACTTTTCA 57.907 29.630 0.00 0.00 0.00 2.69
2976 6769 1.073284 TGTCTGGTTTCCTTACAGGCC 59.927 52.381 0.00 0.00 36.06 5.19
2984 6777 3.366052 TTCCTTACAGGCCTGAAATCC 57.634 47.619 39.19 0.00 34.61 3.01
3047 6843 2.597578 TTTTTCCCCTGAGGTTAGGC 57.402 50.000 0.00 0.00 36.47 3.93
3096 7114 7.360269 CCAGTGAAATGCATTTGTATTTGTTCC 60.360 37.037 28.67 10.77 39.76 3.62
3211 7229 7.013083 GGACACTTCAGATGCAGATATTGAAAT 59.987 37.037 0.00 0.00 0.00 2.17
3218 7236 7.012989 TCAGATGCAGATATTGAAATGTTCCAG 59.987 37.037 0.00 0.00 0.00 3.86
3338 7436 6.371548 TGGCTGATAGTAGTTTTGTTAGCAAG 59.628 38.462 0.00 0.00 35.82 4.01
3352 7450 6.544197 TTTGTTAGCAAGTCTTCATGGTACAA 59.456 34.615 0.00 0.00 37.72 2.41
3359 7457 8.444930 GCAAGTCTTCATGGTACAAGTTGCAT 62.445 42.308 1.81 0.00 44.87 3.96
3394 7492 9.216117 TGCTACCTCTCTTATTTTAAACAGTTC 57.784 33.333 0.00 0.00 0.00 3.01
3429 7527 7.334421 TGAAAATATTCTTGTCCTGACTAGCAC 59.666 37.037 4.20 0.00 36.48 4.40
3486 7584 9.703892 CTAGGGATAGACACAATATTTTCTCTG 57.296 37.037 0.00 0.00 0.00 3.35
3496 7594 9.167311 ACACAATATTTTCTCTGAATACTCCAC 57.833 33.333 0.00 0.00 0.00 4.02
3505 7603 9.436957 TTTCTCTGAATACTCCACTATTTCAAC 57.563 33.333 0.00 0.00 0.00 3.18
3506 7604 8.134202 TCTCTGAATACTCCACTATTTCAACA 57.866 34.615 0.00 0.00 0.00 3.33
3507 7605 8.762645 TCTCTGAATACTCCACTATTTCAACAT 58.237 33.333 0.00 0.00 0.00 2.71
3508 7606 9.388506 CTCTGAATACTCCACTATTTCAACATT 57.611 33.333 0.00 0.00 0.00 2.71
3545 7643 5.107453 GCATACTGCGATGTATACAAAGACC 60.107 44.000 10.14 0.00 31.71 3.85
3617 7715 6.627395 TTTCAACATTACTGTACCCTGTTG 57.373 37.500 20.32 20.32 44.96 3.33
3664 7785 3.689347 TGTTTTCAGACCATCCATCTGG 58.311 45.455 2.37 0.00 43.25 3.86
3722 7843 1.825474 CGGGTGTCACTACTCCATCTT 59.175 52.381 2.35 0.00 40.41 2.40
3731 7852 4.532126 TCACTACTCCATCTTGTCCAACAT 59.468 41.667 0.00 0.00 0.00 2.71
3771 7892 2.159435 AGTTGTTGTTCTCGCACAAACC 60.159 45.455 0.00 0.00 38.40 3.27
3800 7921 9.312904 TGATGGATTAAGGAAATCATTATTCCC 57.687 33.333 18.55 9.97 46.17 3.97
3801 7922 8.670521 ATGGATTAAGGAAATCATTATTCCCC 57.329 34.615 18.55 7.07 46.17 4.81
3802 7923 6.719370 TGGATTAAGGAAATCATTATTCCCCG 59.281 38.462 18.55 0.00 46.17 5.73
3858 7980 3.440173 AGGTTTTGAAGTATGTGGCATCG 59.560 43.478 0.00 0.00 0.00 3.84
3945 8067 2.586648 ACCCTGGATCCAAAGTTCAC 57.413 50.000 17.00 0.00 0.00 3.18
3949 8071 1.075374 CTGGATCCAAAGTTCACCCCA 59.925 52.381 17.00 0.00 0.00 4.96
3981 8103 4.358841 TGAATGGGGTGGTGCGGG 62.359 66.667 0.00 0.00 0.00 6.13
4105 8229 3.555966 GGCCTATGACAAGGTAGCAATT 58.444 45.455 0.00 0.00 39.02 2.32
4150 8274 2.676471 GCTGCCCGTCCCATGTTT 60.676 61.111 0.00 0.00 0.00 2.83
4186 8310 4.523173 CGCAATATTACTCTACTCCCTCCA 59.477 45.833 0.00 0.00 0.00 3.86
4197 8321 7.007723 ACTCTACTCCCTCCATTCACTATTAG 58.992 42.308 0.00 0.00 0.00 1.73
4254 8380 8.903570 TGAGTAAACAAACACACTAAAACATG 57.096 30.769 0.00 0.00 0.00 3.21
4259 8385 4.400884 ACAAACACACTAAAACATGCTCCA 59.599 37.500 0.00 0.00 0.00 3.86
4323 8530 6.961360 TGAACTATGTACTGTCCTATCAGG 57.039 41.667 0.00 0.00 39.48 3.86
4335 8542 2.792370 TCCTATCAGGAACTAGGCTCCT 59.208 50.000 9.34 9.34 42.51 3.69
4358 8565 3.329889 ATCCGCCTGCCCTGTCAA 61.330 61.111 0.00 0.00 0.00 3.18
4359 8566 3.335356 ATCCGCCTGCCCTGTCAAG 62.335 63.158 0.00 0.00 0.00 3.02
4360 8567 4.335647 CCGCCTGCCCTGTCAAGT 62.336 66.667 0.00 0.00 0.00 3.16
4361 8568 2.662596 CGCCTGCCCTGTCAAGTA 59.337 61.111 0.00 0.00 0.00 2.24
4362 8569 1.448540 CGCCTGCCCTGTCAAGTAG 60.449 63.158 0.00 0.00 0.00 2.57
4363 8570 1.078143 GCCTGCCCTGTCAAGTAGG 60.078 63.158 3.12 3.12 35.01 3.18
4364 8571 1.553690 GCCTGCCCTGTCAAGTAGGA 61.554 60.000 9.95 0.00 37.52 2.94
4365 8572 0.539051 CCTGCCCTGTCAAGTAGGAG 59.461 60.000 1.58 0.00 37.52 3.69
4366 8573 1.270907 CTGCCCTGTCAAGTAGGAGT 58.729 55.000 0.00 0.00 37.52 3.85
4433 8640 1.524863 CGGTGACTGGACTCGAACCT 61.525 60.000 9.25 0.00 0.00 3.50
4468 8678 8.777865 TCTTGTTAAACTAGGATGACAAGATG 57.222 34.615 22.38 8.54 44.51 2.90
4553 9083 4.992381 AAATCCTTATCGCTAATCGCAC 57.008 40.909 0.00 0.00 39.08 5.34
4640 9171 1.459539 CCTATCCGGCAAGAGGGGA 60.460 63.158 0.00 0.00 0.00 4.81
4762 9293 2.715532 ATTCGGCACACGCACACTCT 62.716 55.000 0.00 0.00 43.86 3.24
4771 9302 4.427661 GCACACTCTCGCTCGCCT 62.428 66.667 0.00 0.00 0.00 5.52
4831 9362 1.792057 GTTTGCGCGTGAACGGATG 60.792 57.895 8.43 0.00 40.23 3.51
4881 9412 2.434359 GGGAAGAACGTCTGCGGG 60.434 66.667 0.00 0.00 43.45 6.13
4891 9422 1.070786 GTCTGCGGGGTGAACAAGA 59.929 57.895 0.00 0.00 0.00 3.02
4892 9423 0.951040 GTCTGCGGGGTGAACAAGAG 60.951 60.000 0.00 0.00 0.00 2.85
4893 9424 2.281484 TGCGGGGTGAACAAGAGC 60.281 61.111 0.00 0.00 0.00 4.09
4895 9426 1.896660 GCGGGGTGAACAAGAGCAA 60.897 57.895 0.00 0.00 0.00 3.91
4896 9427 1.856265 GCGGGGTGAACAAGAGCAAG 61.856 60.000 0.00 0.00 0.00 4.01
4897 9428 1.237285 CGGGGTGAACAAGAGCAAGG 61.237 60.000 0.00 0.00 0.00 3.61
4928 9459 3.001939 ACTGCAAAGTAACGAAGAAACCG 59.998 43.478 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 5.354234 GTCATGGAACGGAAATACTCAATGT 59.646 40.000 0.00 0.00 0.00 2.71
129 130 4.250464 GTGTCATGGAACGGAAATACTCA 58.750 43.478 0.00 0.00 0.00 3.41
162 163 5.000012 ACTTGTGTTTCAATTTAACCGCA 58.000 34.783 0.00 0.00 35.35 5.69
183 184 4.142271 TGTGACCACTTTTGAATCACCAAC 60.142 41.667 1.62 0.00 37.64 3.77
218 219 9.459640 CAGGTTTTCATTCTAGCATTGATAATG 57.540 33.333 0.00 0.00 41.85 1.90
220 221 7.615365 ACCAGGTTTTCATTCTAGCATTGATAA 59.385 33.333 0.00 0.00 0.00 1.75
257 259 6.301169 ACTAAGAAGATTGGAAGGTGGTAG 57.699 41.667 0.00 0.00 0.00 3.18
281 283 5.637387 CCCCAATTGGAAAAGTAAACAATCG 59.363 40.000 26.60 2.75 37.39 3.34
294 296 4.390556 CCCCCGCCCCAATTGGAA 62.391 66.667 26.60 0.00 37.39 3.53
308 310 3.421844 GATTCCAGTAACATATGCCCCC 58.578 50.000 1.58 0.00 0.00 5.40
309 311 3.181434 TGGATTCCAGTAACATATGCCCC 60.181 47.826 0.00 0.00 0.00 5.80
310 312 4.074970 CTGGATTCCAGTAACATATGCCC 58.925 47.826 22.45 0.00 45.82 5.36
575 1043 8.192774 ACCATGTGCATGTATGAGAAAAATAAG 58.807 33.333 10.76 0.00 37.11 1.73
779 1248 4.522114 TCTTCATGGACCGCAATTAATGA 58.478 39.130 0.00 0.00 0.00 2.57
983 3859 2.625460 ATGGTGATGGTGGGTGGGG 61.625 63.158 0.00 0.00 0.00 4.96
986 3862 4.342427 CCATGGTGATGGTGGGTG 57.658 61.111 2.57 0.00 43.98 4.61
1278 4154 2.512896 GCCGAAGCAGGGGATGAT 59.487 61.111 0.00 0.00 39.53 2.45
1314 4190 2.654079 CGGGAGAAGCAGCCAGAGT 61.654 63.158 0.00 0.00 0.00 3.24
1316 4192 3.393970 CCGGGAGAAGCAGCCAGA 61.394 66.667 0.00 0.00 0.00 3.86
1317 4193 3.710722 ACCGGGAGAAGCAGCCAG 61.711 66.667 6.32 0.00 0.00 4.85
1322 4198 3.241530 AGTGCACCGGGAGAAGCA 61.242 61.111 14.63 4.95 37.16 3.91
1330 4206 0.729116 CATAAGAAGCAGTGCACCGG 59.271 55.000 19.20 7.56 0.00 5.28
1343 4219 7.375053 GGTTTTAAAATCCACACAGCATAAGA 58.625 34.615 3.52 0.00 0.00 2.10
1352 4228 7.341446 CAAATTCACGGTTTTAAAATCCACAC 58.659 34.615 3.52 0.00 0.00 3.82
1354 4230 6.073494 CCCAAATTCACGGTTTTAAAATCCAC 60.073 38.462 3.52 0.00 0.00 4.02
1379 4255 2.682494 TCTCCGGCACCCACCTAC 60.682 66.667 0.00 0.00 0.00 3.18
1467 4343 2.234908 GAGTACAGATTGACACCAGCCT 59.765 50.000 0.00 0.00 0.00 4.58
1474 4350 7.889073 AGTAACCTAGAAGAGTACAGATTGACA 59.111 37.037 0.00 0.00 0.00 3.58
1475 4351 8.283699 AGTAACCTAGAAGAGTACAGATTGAC 57.716 38.462 0.00 0.00 0.00 3.18
1478 4354 9.181061 GAGAAGTAACCTAGAAGAGTACAGATT 57.819 37.037 0.00 0.00 0.00 2.40
1480 4356 7.687388 TGAGAAGTAACCTAGAAGAGTACAGA 58.313 38.462 0.00 0.00 0.00 3.41
1481 4357 7.925043 TGAGAAGTAACCTAGAAGAGTACAG 57.075 40.000 0.00 0.00 0.00 2.74
1502 4391 5.677319 TTGGGACTGAGGTAATACTTGAG 57.323 43.478 0.00 0.00 0.00 3.02
1503 4392 6.442541 TTTTGGGACTGAGGTAATACTTGA 57.557 37.500 0.00 0.00 0.00 3.02
1504 4393 6.349363 GCTTTTTGGGACTGAGGTAATACTTG 60.349 42.308 0.00 0.00 0.00 3.16
1505 4394 5.710567 GCTTTTTGGGACTGAGGTAATACTT 59.289 40.000 0.00 0.00 0.00 2.24
1506 4395 5.014228 AGCTTTTTGGGACTGAGGTAATACT 59.986 40.000 0.00 0.00 0.00 2.12
1507 4396 5.254115 AGCTTTTTGGGACTGAGGTAATAC 58.746 41.667 0.00 0.00 0.00 1.89
1508 4397 5.514500 AGCTTTTTGGGACTGAGGTAATA 57.486 39.130 0.00 0.00 0.00 0.98
1510 4399 3.876309 AGCTTTTTGGGACTGAGGTAA 57.124 42.857 0.00 0.00 0.00 2.85
1511 4400 3.117663 ACAAGCTTTTTGGGACTGAGGTA 60.118 43.478 0.00 0.00 0.00 3.08
1512 4401 2.310538 CAAGCTTTTTGGGACTGAGGT 58.689 47.619 0.00 0.00 0.00 3.85
1513 4402 2.294512 GACAAGCTTTTTGGGACTGAGG 59.705 50.000 0.00 0.00 0.00 3.86
1515 4404 3.297134 AGACAAGCTTTTTGGGACTGA 57.703 42.857 0.00 0.00 0.00 3.41
1516 4405 4.338118 TGTAAGACAAGCTTTTTGGGACTG 59.662 41.667 0.00 0.00 38.05 3.51
1518 4407 4.911514 TGTAAGACAAGCTTTTTGGGAC 57.088 40.909 0.00 0.00 38.05 4.46
1519 4408 6.127196 ACAAATGTAAGACAAGCTTTTTGGGA 60.127 34.615 16.28 0.00 36.69 4.37
1521 4410 6.980397 AGACAAATGTAAGACAAGCTTTTTGG 59.020 34.615 16.28 1.30 36.69 3.28
1523 4412 9.120538 TCTAGACAAATGTAAGACAAGCTTTTT 57.879 29.630 0.00 0.00 38.05 1.94
1524 4413 8.677148 TCTAGACAAATGTAAGACAAGCTTTT 57.323 30.769 0.00 0.00 38.05 2.27
1525 4414 8.854614 ATCTAGACAAATGTAAGACAAGCTTT 57.145 30.769 0.00 0.00 38.05 3.51
1526 4415 9.372369 GTATCTAGACAAATGTAAGACAAGCTT 57.628 33.333 0.00 0.00 40.68 3.74
1528 4417 7.043325 CCGTATCTAGACAAATGTAAGACAAGC 60.043 40.741 0.00 0.00 0.00 4.01
1529 4418 8.188799 TCCGTATCTAGACAAATGTAAGACAAG 58.811 37.037 0.00 0.00 0.00 3.16
1532 4421 8.136165 ACATCCGTATCTAGACAAATGTAAGAC 58.864 37.037 0.00 0.00 0.00 3.01
1550 4439 9.793252 GAAGTTTTAGTGTTAGATACATCCGTA 57.207 33.333 0.00 0.00 39.39 4.02
1551 4440 7.763071 GGAAGTTTTAGTGTTAGATACATCCGT 59.237 37.037 0.00 0.00 39.39 4.69
1552 4441 7.043590 CGGAAGTTTTAGTGTTAGATACATCCG 60.044 40.741 0.00 0.00 39.26 4.18
1553 4442 7.763071 ACGGAAGTTTTAGTGTTAGATACATCC 59.237 37.037 0.00 0.00 46.40 3.51
1554 4443 8.699283 ACGGAAGTTTTAGTGTTAGATACATC 57.301 34.615 0.00 0.00 46.40 3.06
1556 4445 9.793252 GATACGGAAGTTTTAGTGTTAGATACA 57.207 33.333 0.00 0.00 46.40 2.29
1560 4449 9.453572 TCTAGATACGGAAGTTTTAGTGTTAGA 57.546 33.333 0.00 0.00 46.40 2.10
1561 4450 9.500864 GTCTAGATACGGAAGTTTTAGTGTTAG 57.499 37.037 0.00 0.00 46.40 2.34
1562 4451 9.013229 TGTCTAGATACGGAAGTTTTAGTGTTA 57.987 33.333 0.00 0.00 46.40 2.41
1563 4452 7.889469 TGTCTAGATACGGAAGTTTTAGTGTT 58.111 34.615 0.00 0.00 46.40 3.32
1564 4453 7.458409 TGTCTAGATACGGAAGTTTTAGTGT 57.542 36.000 0.00 0.00 46.40 3.55
1565 4454 8.752766 TTTGTCTAGATACGGAAGTTTTAGTG 57.247 34.615 0.00 0.00 46.40 2.74
1566 4455 9.583765 GATTTGTCTAGATACGGAAGTTTTAGT 57.416 33.333 0.00 0.00 46.40 2.24
1567 4456 9.804758 AGATTTGTCTAGATACGGAAGTTTTAG 57.195 33.333 0.00 0.00 46.40 1.85
1569 4458 9.804758 CTAGATTTGTCTAGATACGGAAGTTTT 57.195 33.333 6.63 0.00 41.16 2.43
1570 4459 9.186837 TCTAGATTTGTCTAGATACGGAAGTTT 57.813 33.333 10.30 0.00 41.91 2.66
1571 4460 8.749026 TCTAGATTTGTCTAGATACGGAAGTT 57.251 34.615 10.30 0.00 41.91 2.66
1572 4461 8.623030 GTTCTAGATTTGTCTAGATACGGAAGT 58.377 37.037 14.05 0.00 45.47 3.01
1573 4462 8.622157 TGTTCTAGATTTGTCTAGATACGGAAG 58.378 37.037 14.05 0.00 45.47 3.46
1574 4463 8.515695 TGTTCTAGATTTGTCTAGATACGGAA 57.484 34.615 14.05 0.00 45.47 4.30
1575 4464 8.515695 TTGTTCTAGATTTGTCTAGATACGGA 57.484 34.615 14.05 0.00 45.47 4.69
1576 4465 8.407064 ACTTGTTCTAGATTTGTCTAGATACGG 58.593 37.037 14.05 12.83 45.47 4.02
1583 4472 9.582431 CCGAATTACTTGTTCTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
1584 4473 7.549488 CCCGAATTACTTGTTCTAGATTTGTCT 59.451 37.037 0.00 0.00 0.00 3.41
1585 4474 7.548075 TCCCGAATTACTTGTTCTAGATTTGTC 59.452 37.037 0.00 0.00 0.00 3.18
1586 4475 7.333672 GTCCCGAATTACTTGTTCTAGATTTGT 59.666 37.037 0.00 0.00 0.00 2.83
1587 4476 7.464178 CGTCCCGAATTACTTGTTCTAGATTTG 60.464 40.741 0.00 0.00 0.00 2.32
1588 4477 6.534079 CGTCCCGAATTACTTGTTCTAGATTT 59.466 38.462 0.00 0.00 0.00 2.17
1589 4478 6.040878 CGTCCCGAATTACTTGTTCTAGATT 58.959 40.000 0.00 0.00 0.00 2.40
1590 4479 5.126707 ACGTCCCGAATTACTTGTTCTAGAT 59.873 40.000 0.00 0.00 0.00 1.98
1591 4480 4.460382 ACGTCCCGAATTACTTGTTCTAGA 59.540 41.667 0.00 0.00 0.00 2.43
1592 4481 4.561606 CACGTCCCGAATTACTTGTTCTAG 59.438 45.833 0.00 0.00 0.00 2.43
1593 4482 4.487948 CACGTCCCGAATTACTTGTTCTA 58.512 43.478 0.00 0.00 0.00 2.10
1594 4483 3.323243 CACGTCCCGAATTACTTGTTCT 58.677 45.455 0.00 0.00 0.00 3.01
1595 4484 2.414138 CCACGTCCCGAATTACTTGTTC 59.586 50.000 0.00 0.00 0.00 3.18
1596 4485 2.419667 CCACGTCCCGAATTACTTGTT 58.580 47.619 0.00 0.00 0.00 2.83
1597 4486 1.338389 CCCACGTCCCGAATTACTTGT 60.338 52.381 0.00 0.00 0.00 3.16
1598 4487 1.066716 TCCCACGTCCCGAATTACTTG 60.067 52.381 0.00 0.00 0.00 3.16
1599 4488 1.206371 CTCCCACGTCCCGAATTACTT 59.794 52.381 0.00 0.00 0.00 2.24
1600 4489 0.822164 CTCCCACGTCCCGAATTACT 59.178 55.000 0.00 0.00 0.00 2.24
1601 4490 0.808847 GCTCCCACGTCCCGAATTAC 60.809 60.000 0.00 0.00 0.00 1.89
1602 4491 1.259142 TGCTCCCACGTCCCGAATTA 61.259 55.000 0.00 0.00 0.00 1.40
1603 4492 2.267961 GCTCCCACGTCCCGAATT 59.732 61.111 0.00 0.00 0.00 2.17
1604 4493 3.000819 TGCTCCCACGTCCCGAAT 61.001 61.111 0.00 0.00 0.00 3.34
1605 4494 3.998672 GTGCTCCCACGTCCCGAA 61.999 66.667 0.00 0.00 31.34 4.30
1619 4508 1.207593 CTACTTTGCCAGCACGTGC 59.792 57.895 32.79 32.79 42.49 5.34
1620 4509 1.207593 GCTACTTTGCCAGCACGTG 59.792 57.895 12.28 12.28 37.73 4.49
1621 4510 3.655481 GCTACTTTGCCAGCACGT 58.345 55.556 0.00 0.00 37.73 4.49
1657 4546 7.210174 TGTGGCAGTTCAGTCTATTATGTATC 58.790 38.462 0.00 0.00 0.00 2.24
1662 4551 6.372659 CACTTTGTGGCAGTTCAGTCTATTAT 59.627 38.462 0.00 0.00 0.00 1.28
1673 4567 1.405391 GGTTTGCACTTTGTGGCAGTT 60.405 47.619 0.00 0.00 41.68 3.16
1679 4573 1.134729 AGCCTTGGTTTGCACTTTGTG 60.135 47.619 0.00 0.00 36.51 3.33
1731 4628 8.938906 GTTGCAAAACCAGATGATCATAATTTT 58.061 29.630 8.54 9.88 0.00 1.82
1885 4790 7.218773 GTGTTTAGAACTACGGTTTTGGAAAAC 59.781 37.037 6.46 6.46 45.70 2.43
1978 4940 3.869246 CGTAGTATCCCAAACATGGTGTC 59.131 47.826 0.00 0.00 0.00 3.67
1989 4951 8.573885 CACAGTTCTATAAATCGTAGTATCCCA 58.426 37.037 0.00 0.00 0.00 4.37
2008 4970 6.449635 TGGCATTGATAAATACCACAGTTC 57.550 37.500 0.00 0.00 0.00 3.01
2031 4993 7.736447 TGGTTTTGAAAACTTTGATGTGTTT 57.264 28.000 18.95 0.00 37.92 2.83
2060 5022 8.684386 TTTGACTATTTGGTGAATACTGTGAA 57.316 30.769 0.00 0.00 0.00 3.18
2255 5258 4.767255 GCAGAGGGGTCCGTGCTG 62.767 72.222 6.96 0.00 36.10 4.41
2289 5292 3.583966 ACAACTAATTTGGGACGGAGGTA 59.416 43.478 0.00 0.00 39.84 3.08
2291 5294 3.007635 GACAACTAATTTGGGACGGAGG 58.992 50.000 0.00 0.00 39.84 4.30
2292 5295 3.939066 AGACAACTAATTTGGGACGGAG 58.061 45.455 0.00 0.00 39.84 4.63
2294 5297 5.350640 GTCTAAGACAACTAATTTGGGACGG 59.649 44.000 0.00 0.00 39.84 4.79
2295 5298 5.929992 TGTCTAAGACAACTAATTTGGGACG 59.070 40.000 0.00 0.00 39.78 4.79
2296 5299 7.444487 ACTTGTCTAAGACAACTAATTTGGGAC 59.556 37.037 1.13 0.00 45.88 4.46
2298 5301 7.745620 ACTTGTCTAAGACAACTAATTTGGG 57.254 36.000 1.13 0.00 45.88 4.12
2305 5308 7.272978 AGCTGAAAACTTGTCTAAGACAACTA 58.727 34.615 1.13 0.00 45.88 2.24
2306 5309 6.116126 AGCTGAAAACTTGTCTAAGACAACT 58.884 36.000 1.13 0.00 45.88 3.16
2307 5310 6.364945 AGCTGAAAACTTGTCTAAGACAAC 57.635 37.500 1.13 0.00 45.88 3.32
2309 5312 6.578944 TGTAGCTGAAAACTTGTCTAAGACA 58.421 36.000 0.00 0.00 41.09 3.41
2310 5313 7.513968 CATGTAGCTGAAAACTTGTCTAAGAC 58.486 38.462 0.00 0.00 37.36 3.01
2311 5314 6.147821 GCATGTAGCTGAAAACTTGTCTAAGA 59.852 38.462 0.00 0.00 41.15 2.10
2312 5315 6.310197 GCATGTAGCTGAAAACTTGTCTAAG 58.690 40.000 0.00 0.00 41.15 2.18
2313 5316 6.241207 GCATGTAGCTGAAAACTTGTCTAA 57.759 37.500 0.00 0.00 41.15 2.10
2314 5317 5.862924 GCATGTAGCTGAAAACTTGTCTA 57.137 39.130 0.00 0.00 41.15 2.59
2315 5318 4.756084 GCATGTAGCTGAAAACTTGTCT 57.244 40.909 0.00 0.00 41.15 3.41
2359 5366 3.008266 GGGGTACAACTAAAGCCACAGTA 59.992 47.826 0.00 0.00 34.88 2.74
2365 5372 4.012374 GGTAAAGGGGTACAACTAAAGCC 58.988 47.826 0.00 0.00 0.00 4.35
2372 5379 5.384336 TGGTAAAAGGTAAAGGGGTACAAC 58.616 41.667 0.00 0.00 0.00 3.32
2431 5438 3.675467 AGCAAGTTCAAGTTGTCGTTC 57.325 42.857 6.82 0.00 31.33 3.95
2650 6443 4.161565 CCTACTAAGAACCTGGTGTATGCA 59.838 45.833 0.00 0.00 0.00 3.96
2753 6546 1.819903 AGAAGTACGGAACCTGCTCTC 59.180 52.381 0.00 0.00 0.00 3.20
2778 6571 3.845781 AACTACAGGGCATCCATACTG 57.154 47.619 0.00 0.00 37.01 2.74
2789 6582 6.712547 AGACAAAAAGATGAGAAACTACAGGG 59.287 38.462 0.00 0.00 0.00 4.45
2976 6769 5.964958 TTCTTTGCCTTAGTGGATTTCAG 57.035 39.130 0.00 0.00 38.35 3.02
2984 6777 5.125100 TGAGCATTTTCTTTGCCTTAGTG 57.875 39.130 0.00 0.00 41.06 2.74
3033 6829 0.625849 AACATGCCTAACCTCAGGGG 59.374 55.000 0.00 0.00 41.89 4.79
3039 6835 7.229506 GCAGAATAGATTTAACATGCCTAACCT 59.770 37.037 0.00 0.00 0.00 3.50
3041 6837 7.857885 GTGCAGAATAGATTTAACATGCCTAAC 59.142 37.037 0.00 0.00 0.00 2.34
3042 6838 7.013274 GGTGCAGAATAGATTTAACATGCCTAA 59.987 37.037 0.00 0.00 0.00 2.69
3046 6842 5.973565 GTGGTGCAGAATAGATTTAACATGC 59.026 40.000 0.00 0.00 0.00 4.06
3047 6843 6.095300 TGGTGGTGCAGAATAGATTTAACATG 59.905 38.462 0.00 0.00 0.00 3.21
3096 7114 5.121811 CAGAATTCTGTCCAAGGGTATCTG 58.878 45.833 24.65 0.00 39.09 2.90
3151 7169 6.708949 TGTAACTAGAGAAACATTGTCCAACC 59.291 38.462 0.00 0.00 0.00 3.77
3211 7229 1.079405 GTCGAATCGCCCTGGAACA 60.079 57.895 0.00 0.00 0.00 3.18
3218 7236 1.066587 CTGAGAGGTCGAATCGCCC 59.933 63.158 11.36 3.46 0.00 6.13
3338 7436 4.455533 TCATGCAACTTGTACCATGAAGAC 59.544 41.667 7.50 0.00 40.56 3.01
3352 7450 2.283145 AGCAAGGAACTCATGCAACT 57.717 45.000 0.00 0.00 42.45 3.16
3359 7457 3.176924 AGAGAGGTAGCAAGGAACTCA 57.823 47.619 0.00 0.00 38.49 3.41
3363 7461 9.227777 GTTTAAAATAAGAGAGGTAGCAAGGAA 57.772 33.333 0.00 0.00 0.00 3.36
3422 7520 5.052481 TCGTATACATCGTAGTGTGCTAGT 58.948 41.667 3.32 0.00 33.62 2.57
3429 7527 3.252701 AGGCCTTCGTATACATCGTAGTG 59.747 47.826 0.00 0.00 0.00 2.74
3558 7656 9.911788 ATTCAGAGAAAATATTGTGTGTATCCT 57.088 29.630 0.00 0.00 0.00 3.24
3609 7707 2.244695 TGACATCGTACTCAACAGGGT 58.755 47.619 0.00 0.00 0.00 4.34
3617 7715 2.281762 GCACGGAAATGACATCGTACTC 59.718 50.000 0.88 0.00 34.31 2.59
3651 7749 4.696479 ACAATACTCCAGATGGATGGTC 57.304 45.455 1.15 0.00 44.46 4.02
3664 7785 7.556275 TGGGAGTGGATCAATTAAACAATACTC 59.444 37.037 0.00 0.00 0.00 2.59
3704 7825 3.368531 GGACAAGATGGAGTAGTGACACC 60.369 52.174 0.84 0.00 36.88 4.16
3752 7873 1.202087 CGGTTTGTGCGAGAACAACAA 60.202 47.619 0.00 0.00 39.70 2.83
3754 7875 0.653636 TCGGTTTGTGCGAGAACAAC 59.346 50.000 0.00 0.00 39.70 3.32
3756 7877 0.865111 CATCGGTTTGTGCGAGAACA 59.135 50.000 0.00 0.00 0.00 3.18
3799 7920 1.274167 TGAGGCACAGTTTACTACGGG 59.726 52.381 0.00 0.00 0.00 5.28
3800 7921 2.736144 TGAGGCACAGTTTACTACGG 57.264 50.000 0.00 0.00 0.00 4.02
3801 7922 4.092968 GGAAATGAGGCACAGTTTACTACG 59.907 45.833 0.00 0.00 36.92 3.51
3802 7923 5.001232 TGGAAATGAGGCACAGTTTACTAC 58.999 41.667 0.00 0.00 36.92 2.73
3858 7980 0.457337 CTTCCGGCATTTCAAGCAGC 60.457 55.000 0.00 0.00 0.00 5.25
3945 8067 1.286880 CGCAGTTTCAGCTTTGGGG 59.713 57.895 0.00 0.00 0.00 4.96
3949 8071 2.287788 CCATTCACGCAGTTTCAGCTTT 60.288 45.455 0.00 0.00 41.61 3.51
3981 8103 1.021968 GGTTCGTATTGGATGGCCAC 58.978 55.000 8.16 1.35 45.94 5.01
4081 8205 1.538419 GCTACCTTGTCATAGGCCGAC 60.538 57.143 0.00 0.00 38.99 4.79
4090 8214 6.605471 TCTTCTCTAATTGCTACCTTGTCA 57.395 37.500 0.00 0.00 0.00 3.58
4105 8229 7.497595 TGAGCCGCTTTATTATTTCTTCTCTA 58.502 34.615 0.00 0.00 0.00 2.43
4137 8261 1.555967 ATTTGGAAACATGGGACGGG 58.444 50.000 0.00 0.00 42.32 5.28
4142 8266 2.501316 GAGGGGAATTTGGAAACATGGG 59.499 50.000 0.00 0.00 42.32 4.00
4150 8274 3.593442 ATATTGCGAGGGGAATTTGGA 57.407 42.857 0.00 0.00 35.64 3.53
4234 8360 5.810074 GGAGCATGTTTTAGTGTGTTTGTTT 59.190 36.000 0.00 0.00 0.00 2.83
4254 8380 7.334421 TGAATTACAAGATGTTCTACTTGGAGC 59.666 37.037 0.00 0.00 45.03 4.70
4323 8530 3.224884 GATGCGATAGGAGCCTAGTTC 57.775 52.381 2.33 0.00 42.54 3.01
4358 8565 4.961440 TTCCCAGGTTACTACTCCTACT 57.039 45.455 0.00 0.00 32.26 2.57
4359 8566 5.456779 AGATTCCCAGGTTACTACTCCTAC 58.543 45.833 0.00 0.00 32.26 3.18
4360 8567 5.435707 AGAGATTCCCAGGTTACTACTCCTA 59.564 44.000 0.00 0.00 32.26 2.94
4361 8568 4.233287 AGAGATTCCCAGGTTACTACTCCT 59.767 45.833 0.00 0.00 33.96 3.69
4362 8569 4.548669 AGAGATTCCCAGGTTACTACTCC 58.451 47.826 0.00 0.00 0.00 3.85
4363 8570 5.202004 TGAGAGATTCCCAGGTTACTACTC 58.798 45.833 0.00 0.00 0.00 2.59
4364 8571 5.208294 TGAGAGATTCCCAGGTTACTACT 57.792 43.478 0.00 0.00 0.00 2.57
4365 8572 5.598830 TGATGAGAGATTCCCAGGTTACTAC 59.401 44.000 0.00 0.00 0.00 2.73
4366 8573 5.598830 GTGATGAGAGATTCCCAGGTTACTA 59.401 44.000 0.00 0.00 0.00 1.82
4433 8640 5.745294 CCTAGTTTAACAAGATAGCGCGTTA 59.255 40.000 8.43 6.54 0.00 3.18
4468 8678 7.511959 AAGAGGATCCAAGTAAACTTTTGTC 57.488 36.000 15.82 0.00 33.66 3.18
4553 9083 3.069158 CGGGTGTTATCTTAGGTAGGTGG 59.931 52.174 0.00 0.00 0.00 4.61
4585 9115 3.264897 CGGGCAGCGATCTTTCGG 61.265 66.667 0.00 0.00 45.59 4.30
4595 9126 2.743928 CACTTCCACTCGGGCAGC 60.744 66.667 0.00 0.00 36.21 5.25
4596 9127 2.046892 CCACTTCCACTCGGGCAG 60.047 66.667 0.00 0.00 36.21 4.85
4598 9129 1.671379 GTTCCACTTCCACTCGGGC 60.671 63.158 0.00 0.00 36.21 6.13
4599 9130 1.003718 GGTTCCACTTCCACTCGGG 60.004 63.158 0.00 0.00 38.37 5.14
4600 9131 1.003718 GGGTTCCACTTCCACTCGG 60.004 63.158 0.00 0.00 0.00 4.63
4601 9132 1.374252 CGGGTTCCACTTCCACTCG 60.374 63.158 0.00 0.00 0.00 4.18
4602 9133 0.320508 GACGGGTTCCACTTCCACTC 60.321 60.000 0.00 0.00 0.00 3.51
4603 9134 1.752833 GACGGGTTCCACTTCCACT 59.247 57.895 0.00 0.00 0.00 4.00
4604 9135 1.302271 GGACGGGTTCCACTTCCAC 60.302 63.158 0.00 0.00 45.10 4.02
4605 9136 3.153825 GGACGGGTTCCACTTCCA 58.846 61.111 0.00 0.00 45.10 3.53
4640 9171 3.801997 CCCCAGGGAATGCTCGCT 61.802 66.667 7.25 0.00 45.27 4.93
4770 9301 0.721718 CGAAAGTCTAAAGCGGGCAG 59.278 55.000 0.00 0.00 0.00 4.85
4771 9302 0.672401 CCGAAAGTCTAAAGCGGGCA 60.672 55.000 0.00 0.00 38.40 5.36
4774 9305 1.708027 CGCCGAAAGTCTAAAGCGG 59.292 57.895 0.00 0.00 44.47 5.52
4831 9362 2.160417 CCGATCAAGTGCCAACTTTCTC 59.840 50.000 0.00 0.00 44.47 2.87
4881 9412 0.823356 TGCCCTTGCTCTTGTTCACC 60.823 55.000 0.00 0.00 38.71 4.02
4891 9422 1.458639 GCAGTGTTCTTGCCCTTGCT 61.459 55.000 0.00 0.00 38.71 3.91
4892 9423 1.006922 GCAGTGTTCTTGCCCTTGC 60.007 57.895 0.00 0.00 38.26 4.01
4893 9424 0.746063 TTGCAGTGTTCTTGCCCTTG 59.254 50.000 0.00 0.00 0.00 3.61
4895 9426 1.035139 CTTTGCAGTGTTCTTGCCCT 58.965 50.000 0.00 0.00 0.00 5.19
4896 9427 0.746659 ACTTTGCAGTGTTCTTGCCC 59.253 50.000 0.00 0.00 0.00 5.36
4897 9428 3.372060 GTTACTTTGCAGTGTTCTTGCC 58.628 45.455 0.00 0.00 34.06 4.52
4928 9459 2.548875 CAGGATCACTACTGCTGCTTC 58.451 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.