Multiple sequence alignment - TraesCS7A01G240800

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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 TraesCS7A01G240800 chr7A 100.000 4733 0 0 1 4733 216353870 216349138 0.000000e+00 8741.0
1 TraesCS7A01G240800 chr7A 86.007 293 33 8 190 479 25338067 25337780 1.650000e-79 307.0
2 TraesCS7A01G240800 chr7D 95.519 4753 177 23 1 4733 204256510 204251774 0.000000e+00 7564.0
3 TraesCS7A01G240800 chr7B 92.799 2597 144 17 331 2900 168324604 168322024 0.000000e+00 3720.0
4 TraesCS7A01G240800 chr7B 92.966 1507 66 20 3236 4733 168321792 168320317 0.000000e+00 2159.0
5 TraesCS7A01G240800 chr7B 93.548 186 12 0 3020 3205 168321975 168321790 1.300000e-70 278.0
6 TraesCS7A01G240800 chr7B 96.970 33 1 0 1 33 168324635 168324603 6.620000e-04 56.5
7 TraesCS7A01G240800 chr6B 87.338 308 31 7 192 494 192354085 192353781 3.510000e-91 346.0
8 TraesCS7A01G240800 chr6B 90.476 63 4 2 2908 2969 563489349 563489410 1.090000e-11 82.4
9 TraesCS7A01G240800 chr6B 84.146 82 7 6 2908 2987 477220433 477220510 1.830000e-09 75.0
10 TraesCS7A01G240800 chr6D 86.601 306 33 7 192 492 105823586 105823284 9.820000e-87 331.0
11 TraesCS7A01G240800 chr6D 89.394 66 3 4 2908 2970 423681291 423681355 3.930000e-11 80.5
12 TraesCS7A01G240800 chr6D 89.231 65 4 3 2908 2970 193682526 193682589 1.410000e-10 78.7
13 TraesCS7A01G240800 chr3A 84.756 328 38 10 171 491 57231369 57231047 7.640000e-83 318.0
14 TraesCS7A01G240800 chr3A 88.362 232 24 3 246 476 57231402 57231631 4.670000e-70 276.0
15 TraesCS7A01G240800 chr2B 88.293 205 18 5 175 377 786215516 786215716 1.700000e-59 241.0
16 TraesCS7A01G240800 chr2B 84.577 201 19 4 252 451 25810143 25810332 6.250000e-44 189.0
17 TraesCS7A01G240800 chr2B 85.075 134 19 1 192 324 25690822 25690955 8.260000e-28 135.0
18 TraesCS7A01G240800 chr4A 82.079 279 41 9 226 498 485510868 485511143 3.680000e-56 230.0
19 TraesCS7A01G240800 chr5A 82.836 134 23 0 3026 3159 473021561 473021428 2.310000e-23 121.0
20 TraesCS7A01G240800 chr2D 88.406 69 5 3 2908 2973 357697983 357698051 3.930000e-11 80.5
21 TraesCS7A01G240800 chr1D 90.323 62 5 1 2910 2970 7692188 7692249 3.930000e-11 80.5
22 TraesCS7A01G240800 chr2A 84.810 79 8 4 2902 2977 144653497 144653574 5.080000e-10 76.8
23 TraesCS7A01G240800 chr1A 88.060 67 5 3 2907 2971 202090556 202090621 5.080000e-10 76.8


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 TraesCS7A01G240800 chr7A 216349138 216353870 4732 True 8741.000 8741 100.00000 1 4733 1 chr7A.!!$R2 4732
1 TraesCS7A01G240800 chr7D 204251774 204256510 4736 True 7564.000 7564 95.51900 1 4733 1 chr7D.!!$R1 4732
2 TraesCS7A01G240800 chr7B 168320317 168324635 4318 True 1553.375 3720 94.07075 1 4733 4 chr7B.!!$R1 4732

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
203 207 0.389296 CACGCTACACCCACAATCGA 60.389 55.000 0.00 0.00 0.00 3.59 F
302 306 1.265236 TTGGTGGCCAAATGACATCC 58.735 50.000 7.24 1.47 40.92 3.51 F
1688 1701 1.672145 GCACAACCTTCTCCTACGACC 60.672 57.143 0.00 0.00 0.00 4.79 F
2112 2130 0.096976 CAACGATCATTGTCCGTGCC 59.903 55.000 0.00 0.00 36.58 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1909 0.110823 CAAGAACGAGAAAACCGGCG 60.111 55.0 0.00 0.0 0.00 6.46 R
1971 1989 0.474184 CACTGGGACCCTGAACAGTT 59.526 55.0 23.36 0.0 41.85 3.16 R
3276 3306 1.647545 GCGCAAGTGAGCCATAAGCA 61.648 55.0 0.30 0.0 42.64 3.91 R
3767 3804 1.379527 CAACGAAGGTAATGCCCTCC 58.620 55.0 0.00 0.0 38.26 4.30 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
50 51 5.220662 CGGACTTCTAAAACTGCACCATATG 60.221 44.000 0.00 0.00 0.00 1.78
99 100 1.515521 GGCCTTTCGGAAGTGTGTGG 61.516 60.000 2.03 0.00 0.00 4.17
144 145 7.656137 GGATTACTAGGAATTCGTAATCTGCAA 59.344 37.037 26.52 10.30 44.27 4.08
200 204 1.002624 CCCACGCTACACCCACAAT 60.003 57.895 0.00 0.00 0.00 2.71
203 207 0.389296 CACGCTACACCCACAATCGA 60.389 55.000 0.00 0.00 0.00 3.59
221 225 8.274939 CACAATCGAAAACATAGCAAAACAAAT 58.725 29.630 0.00 0.00 0.00 2.32
222 226 8.825745 ACAATCGAAAACATAGCAAAACAAATT 58.174 25.926 0.00 0.00 0.00 1.82
263 267 9.573133 CTTTTTAGCTTCGATTATGACCAAATT 57.427 29.630 0.00 0.00 0.00 1.82
302 306 1.265236 TTGGTGGCCAAATGACATCC 58.735 50.000 7.24 1.47 40.92 3.51
351 355 4.581077 TTTGTGCTCAAATGTATGTGCA 57.419 36.364 9.78 0.42 44.74 4.57
446 451 9.777297 AAGCACCTAAAACATTTGTTCATAATT 57.223 25.926 0.00 0.00 37.25 1.40
690 702 5.230516 ACACGAAACCGAATTTTAAAACTGC 59.769 36.000 1.97 0.00 0.00 4.40
718 730 9.471084 CTATTGTTCATTTTAAACGGAGGTTTT 57.529 29.630 0.00 0.00 43.69 2.43
904 916 2.765122 ACTGCTCTTTCTGCTCTTCAC 58.235 47.619 0.00 0.00 0.00 3.18
982 994 5.172205 CCTGTTTCAGTCTAAGCCTCTAAC 58.828 45.833 0.00 0.00 0.00 2.34
1323 1335 2.158449 CGGTTTCTGTGCACTCAAGATC 59.842 50.000 19.41 8.67 0.00 2.75
1383 1395 3.583086 CTCCTATCATAATTCCACCCGGT 59.417 47.826 0.00 0.00 0.00 5.28
1456 1468 3.366070 CGTATGTTACTATCCCTGCCTCG 60.366 52.174 0.00 0.00 0.00 4.63
1457 1469 2.447408 TGTTACTATCCCTGCCTCGA 57.553 50.000 0.00 0.00 0.00 4.04
1463 1475 2.975489 ACTATCCCTGCCTCGATCAATT 59.025 45.455 0.00 0.00 0.00 2.32
1486 1499 4.847198 TCAGTTATGTGCAATGATCACCT 58.153 39.130 0.00 0.00 33.71 4.00
1492 1505 2.233271 GTGCAATGATCACCTATGGGG 58.767 52.381 0.00 0.00 41.89 4.96
1534 1547 8.420222 ACATGATCAAACTATTCTCTGACTAGG 58.580 37.037 0.00 0.00 0.00 3.02
1541 1554 7.996098 AACTATTCTCTGACTAGGATAGCTC 57.004 40.000 0.00 0.00 44.39 4.09
1542 1555 6.481643 ACTATTCTCTGACTAGGATAGCTCC 58.518 44.000 0.00 0.00 44.39 4.70
1548 1561 6.613271 TCTCTGACTAGGATAGCTCCATTTTT 59.387 38.462 0.00 0.00 44.39 1.94
1554 1567 9.343539 GACTAGGATAGCTCCATTTTTATTTGT 57.656 33.333 0.00 0.00 44.39 2.83
1577 1590 7.584108 TGTATTGTACAATCTGCAGTTTCTTG 58.416 34.615 24.00 14.77 35.38 3.02
1585 1598 4.836125 TCTGCAGTTTCTTGGAATTGTC 57.164 40.909 14.67 0.00 0.00 3.18
1599 1612 8.559536 TCTTGGAATTGTCGATTATTATTGCTC 58.440 33.333 0.00 0.00 0.00 4.26
1608 1621 9.154847 TGTCGATTATTATTGCTCTTGGATATG 57.845 33.333 0.00 0.00 0.00 1.78
1634 1647 4.510340 GCTCCCAGTATAATGTTTACGGTG 59.490 45.833 0.00 0.00 0.00 4.94
1657 1670 9.320352 GGTGTCAAACTTTTGTAAATGGTTATT 57.680 29.630 1.75 0.00 39.18 1.40
1688 1701 1.672145 GCACAACCTTCTCCTACGACC 60.672 57.143 0.00 0.00 0.00 4.79
1724 1737 7.095060 CCATTTCTGATGCGTACTAATGCTAAT 60.095 37.037 0.00 0.00 38.53 1.73
1829 1842 8.487313 GGTCTAAACCAACTTTTTCATTTGTT 57.513 30.769 0.00 0.00 45.68 2.83
1832 1845 9.145865 TCTAAACCAACTTTTTCATTTGTTGAC 57.854 29.630 0.00 0.00 41.35 3.18
1851 1864 6.831353 TGTTGACAAGGTAATTTTCTCCAAGA 59.169 34.615 0.00 0.00 0.00 3.02
1870 1886 8.824756 TCCAAGATTACTATCTTATCGCCTAT 57.175 34.615 0.46 0.00 46.83 2.57
1884 1900 4.585955 TCGCCTATTTCCTGTCACTATC 57.414 45.455 0.00 0.00 0.00 2.08
1916 1934 3.854809 CGGTTTTCTCGTTCTTGCAAAAA 59.145 39.130 0.00 0.00 0.00 1.94
1940 1958 3.638160 TGCAAGCAAAGTCAAATCCTCTT 59.362 39.130 0.00 0.00 0.00 2.85
1947 1965 6.927381 AGCAAAGTCAAATCCTCTTTTCAATG 59.073 34.615 0.00 0.00 30.41 2.82
1967 1985 2.230992 TGATGCATTGACCCGAAAAAGG 59.769 45.455 0.00 0.00 0.00 3.11
1971 1989 3.637229 TGCATTGACCCGAAAAAGGTTTA 59.363 39.130 0.00 0.00 37.88 2.01
1982 2000 5.278604 CGAAAAAGGTTTAACTGTTCAGGG 58.721 41.667 0.00 0.00 0.00 4.45
2001 2019 2.354805 GGGTCCCAGTGTTACTCATCAC 60.355 54.545 1.78 0.00 35.13 3.06
2012 2030 0.773644 ACTCATCACAACCAGCCCTT 59.226 50.000 0.00 0.00 0.00 3.95
2040 2058 2.100916 CGAGAACAATCACCGTATCCCT 59.899 50.000 0.00 0.00 0.00 4.20
2043 2061 2.981859 ACAATCACCGTATCCCTGAC 57.018 50.000 0.00 0.00 0.00 3.51
2076 2094 4.773323 AGATAGCAAGGCAAACAGAAAC 57.227 40.909 0.00 0.00 0.00 2.78
2082 2100 1.594331 AGGCAAACAGAAACGGAGAC 58.406 50.000 0.00 0.00 0.00 3.36
2098 2116 0.888619 AGACGATTCTCCAGCAACGA 59.111 50.000 0.00 0.00 0.00 3.85
2106 2124 2.621338 TCTCCAGCAACGATCATTGTC 58.379 47.619 3.15 0.00 31.83 3.18
2112 2130 0.096976 CAACGATCATTGTCCGTGCC 59.903 55.000 0.00 0.00 36.58 5.01
2121 2139 3.458163 GTCCGTGCCGAGGATGGA 61.458 66.667 2.90 2.90 40.30 3.41
2160 2178 3.214328 TGGGAAGAAGCAAGTGAAGAAC 58.786 45.455 0.00 0.00 0.00 3.01
2166 2184 4.517285 AGAAGCAAGTGAAGAACAGTGAA 58.483 39.130 0.00 0.00 31.89 3.18
2175 2193 4.335315 GTGAAGAACAGTGAACATCCAACA 59.665 41.667 0.00 0.00 0.00 3.33
2208 2226 0.320683 GCAGTCACCAAAATTGCCCC 60.321 55.000 0.00 0.00 0.00 5.80
2244 2262 0.391661 AGCGTTGTCAAGATGGCGAT 60.392 50.000 0.00 0.00 0.00 4.58
2250 2268 4.506288 CGTTGTCAAGATGGCGATATAACA 59.494 41.667 0.00 0.00 0.00 2.41
2292 2310 0.323087 ACAATCACCCTTTACCGCCC 60.323 55.000 0.00 0.00 0.00 6.13
2362 2380 1.293924 CGATGGCGAAGAGAATGCTT 58.706 50.000 0.00 0.00 40.82 3.91
2363 2381 1.667724 CGATGGCGAAGAGAATGCTTT 59.332 47.619 0.00 0.00 40.82 3.51
2385 2403 2.161855 GATGACCACTTCCAACATGCA 58.838 47.619 0.00 0.00 0.00 3.96
2388 2406 1.888512 GACCACTTCCAACATGCACAT 59.111 47.619 0.00 0.00 0.00 3.21
2456 2474 4.102838 AGGATTTGCAGACAGATCAGCTAT 59.897 41.667 0.00 0.00 38.78 2.97
2551 2569 2.438434 CGGGCATTGACAGGGACC 60.438 66.667 0.00 0.00 0.00 4.46
2585 2603 6.489361 ACTGAGTCGAAGAGAAGGTTAGTTAA 59.511 38.462 0.00 0.00 36.95 2.01
2912 2941 5.476614 CCTTGGTAGGACACAAAGTAGTAC 58.523 45.833 0.00 0.00 45.05 2.73
2914 2943 5.972107 TGGTAGGACACAAAGTAGTACTC 57.028 43.478 2.58 0.00 30.05 2.59
2951 2980 8.579863 CAAATCTAAGACAAGAATTTTGGGACT 58.420 33.333 5.68 0.00 28.49 3.85
2956 2985 3.813166 GACAAGAATTTTGGGACTGACGA 59.187 43.478 0.00 0.00 0.00 4.20
3187 3217 0.393537 CCCAAGCTCAGGTCATGGTC 60.394 60.000 4.63 0.00 0.00 4.02
3200 3230 1.303561 ATGGTCATGTTGCGCCACT 60.304 52.632 13.27 0.00 33.42 4.00
3211 3241 2.358615 CGCCACTGCCACAAGCTA 60.359 61.111 0.00 0.00 44.23 3.32
3339 3369 3.360956 CTTTGGAATGCTGCCCCGC 62.361 63.158 0.00 0.00 0.00 6.13
3404 3434 1.302033 CATCGGCTATGCAGGGGAC 60.302 63.158 0.00 0.00 0.00 4.46
3450 3480 2.674754 GTGAAGGGGAATCCGGCA 59.325 61.111 0.00 0.00 41.52 5.69
3567 3599 6.989169 GGTCTCTTGTAAGATAAGACATGCAT 59.011 38.462 0.00 0.00 32.45 3.96
3626 3659 4.015872 TGTACCCTTGTTCTTCCATGTC 57.984 45.455 0.00 0.00 0.00 3.06
3665 3700 3.193691 ACTTCATGGTTACAGAGGACTCG 59.806 47.826 0.00 0.00 34.09 4.18
3697 3734 6.607198 AGAAAAAGGGAACACAGAGAATTCAA 59.393 34.615 8.44 0.00 0.00 2.69
3767 3804 1.756538 GTTGCCATATGGTTTCTGGGG 59.243 52.381 22.79 0.00 37.57 4.96
3782 3819 1.286305 TGGGGGAGGGCATTACCTTC 61.286 60.000 0.00 0.00 43.88 3.46
3825 3862 6.552859 TTCAAGCGAACATTGAATCAACTA 57.447 33.333 0.00 0.00 40.72 2.24
3826 3863 6.741992 TCAAGCGAACATTGAATCAACTAT 57.258 33.333 0.00 0.00 33.85 2.12
3980 4017 5.220434 GCAAATCATCATTGCGCAACATAAA 60.220 36.000 27.64 11.87 43.14 1.40
3991 4028 3.306166 GCGCAACATAAAGATACGACACT 59.694 43.478 0.30 0.00 0.00 3.55
4032 4070 8.478877 TCCACAATAACCAACTTACATTTGTTT 58.521 29.630 0.00 0.00 0.00 2.83
4554 4594 1.623811 TCCACCTCTGCTTCAGTTACC 59.376 52.381 0.00 0.00 32.61 2.85
4588 4628 8.506168 AACCGCCATTATATTGTAAGATATGG 57.494 34.615 0.00 0.00 0.00 2.74
4603 4643 7.880713 TGTAAGATATGGCTGTCAACAAGTTAA 59.119 33.333 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.686916 AGACCACTTTCCAGAACTAGC 57.313 47.619 0.00 0.00 0.00 3.42
52 53 4.703897 CACAAGACCACTTTCCAGAACTA 58.296 43.478 0.00 0.00 33.70 2.24
60 61 1.197721 CGGATGCACAAGACCACTTTC 59.802 52.381 0.00 0.00 33.70 2.62
175 179 3.238497 TGTAGCGTGGGTGCACCT 61.238 61.111 33.91 17.44 41.11 4.00
200 204 9.737427 TTCTAATTTGTTTTGCTATGTTTTCGA 57.263 25.926 0.00 0.00 0.00 3.71
223 227 9.237846 CGAAGCTAAAAAGTTTCAGATTTTTCT 57.762 29.630 0.00 0.00 38.94 2.52
224 228 9.233232 TCGAAGCTAAAAAGTTTCAGATTTTTC 57.767 29.630 0.00 1.18 38.94 2.29
229 233 9.994432 CATAATCGAAGCTAAAAAGTTTCAGAT 57.006 29.630 0.00 4.17 30.67 2.90
263 267 5.649831 ACCAAATTTTGCAAGCACCTAAAAA 59.350 32.000 0.00 0.00 0.00 1.94
351 355 5.106555 CGGAATACAAATCTGCTCAAACAGT 60.107 40.000 0.00 0.00 38.84 3.55
551 562 9.734620 GCTATTATGTCATGTTAAGAAAATGCA 57.265 29.630 0.00 0.00 0.00 3.96
642 654 6.414408 TTTGGGCATTTAAAAATATGTGCG 57.586 33.333 0.00 0.00 0.00 5.34
690 702 8.040716 ACCTCCGTTTAAAATGAACAATAGAG 57.959 34.615 0.00 0.00 0.00 2.43
891 903 7.450074 TCTGGTAATAAAGTGAAGAGCAGAAA 58.550 34.615 0.00 0.00 38.19 2.52
982 994 3.375299 GCCATTGAGCTAACAACTGTAGG 59.625 47.826 0.00 0.00 32.50 3.18
1093 1105 1.408822 GGGACCGGAGCTGAAATCATT 60.409 52.381 9.46 0.00 0.00 2.57
1383 1395 2.408565 AGAAGTTCCCTTGGACTCACA 58.591 47.619 0.00 0.00 0.00 3.58
1410 1422 1.026584 CGTTGGGAAGAAAAACCGGT 58.973 50.000 0.00 0.00 0.00 5.28
1445 1457 2.173356 TGAAATTGATCGAGGCAGGGAT 59.827 45.455 0.00 0.00 0.00 3.85
1456 1468 8.867112 ATCATTGCACATAACTGAAATTGATC 57.133 30.769 0.00 0.00 0.00 2.92
1457 1469 8.471609 TGATCATTGCACATAACTGAAATTGAT 58.528 29.630 0.00 0.00 0.00 2.57
1463 1475 5.255687 AGGTGATCATTGCACATAACTGAA 58.744 37.500 0.00 0.00 37.99 3.02
1486 1499 6.905736 TGTACTGATAAAAATGCTCCCCATA 58.094 36.000 0.00 0.00 32.67 2.74
1554 1567 6.939730 TCCAAGAAACTGCAGATTGTACAATA 59.060 34.615 23.35 4.91 0.00 1.90
1559 1572 6.265196 ACAATTCCAAGAAACTGCAGATTGTA 59.735 34.615 23.35 9.67 0.00 2.41
1577 1590 7.805071 CCAAGAGCAATAATAATCGACAATTCC 59.195 37.037 0.00 0.00 0.00 3.01
1599 1612 3.784511 ACTGGGAGCATCATATCCAAG 57.215 47.619 0.00 0.00 41.75 3.61
1608 1621 5.408604 CCGTAAACATTATACTGGGAGCATC 59.591 44.000 0.00 0.00 0.00 3.91
1611 1624 4.510340 CACCGTAAACATTATACTGGGAGC 59.490 45.833 0.00 0.00 0.00 4.70
1688 1701 3.798337 GCATCAGAAATGGCAATTTACCG 59.202 43.478 0.00 0.00 36.10 4.02
1724 1737 4.764050 ATGGACCGATGGTATTGTTGTA 57.236 40.909 0.00 0.00 35.25 2.41
1763 1776 7.160049 AGGAGATTGTATGATCATCATGTGAC 58.840 38.462 12.53 4.23 40.28 3.67
1824 1837 7.411486 TGGAGAAAATTACCTTGTCAACAAA 57.589 32.000 0.00 0.00 35.15 2.83
1829 1842 9.010029 GTAATCTTGGAGAAAATTACCTTGTCA 57.990 33.333 0.00 0.00 31.44 3.58
1851 1864 9.036980 ACAGGAAATAGGCGATAAGATAGTAAT 57.963 33.333 0.00 0.00 0.00 1.89
1870 1886 2.355108 GCTGCCAGATAGTGACAGGAAA 60.355 50.000 0.00 0.00 0.00 3.13
1890 1908 1.838568 AAGAACGAGAAAACCGGCGC 61.839 55.000 0.00 0.00 0.00 6.53
1891 1909 0.110823 CAAGAACGAGAAAACCGGCG 60.111 55.000 0.00 0.00 0.00 6.46
1895 1913 5.966636 ATTTTTGCAAGAACGAGAAAACC 57.033 34.783 4.29 0.00 0.00 3.27
1916 1934 4.282703 AGAGGATTTGACTTTGCTTGCAAT 59.717 37.500 8.93 0.00 0.00 3.56
1947 1965 2.231235 ACCTTTTTCGGGTCAATGCATC 59.769 45.455 0.00 0.00 30.15 3.91
1959 1977 5.163591 ACCCTGAACAGTTAAACCTTTTTCG 60.164 40.000 1.18 0.00 0.00 3.46
1967 1985 3.146847 CTGGGACCCTGAACAGTTAAAC 58.853 50.000 13.00 0.00 0.00 2.01
1971 1989 0.474184 CACTGGGACCCTGAACAGTT 59.526 55.000 23.36 0.00 41.85 3.16
1982 2000 3.678056 TGTGATGAGTAACACTGGGAC 57.322 47.619 0.00 0.00 37.81 4.46
2001 2019 1.885871 GCTTGCTAAGGGCTGGTTG 59.114 57.895 0.00 0.00 42.39 3.77
2012 2030 2.346803 GGTGATTGTTCTCGCTTGCTA 58.653 47.619 0.00 0.00 0.00 3.49
2040 2058 4.627058 TGCTATCTTCTTGTTCGTTGTCA 58.373 39.130 0.00 0.00 0.00 3.58
2043 2061 4.670221 GCCTTGCTATCTTCTTGTTCGTTG 60.670 45.833 0.00 0.00 0.00 4.10
2082 2100 1.926561 TGATCGTTGCTGGAGAATCG 58.073 50.000 0.00 0.00 34.37 3.34
2087 2105 1.667724 GGACAATGATCGTTGCTGGAG 59.332 52.381 24.48 3.52 32.32 3.86
2094 2112 2.466867 GGCACGGACAATGATCGTT 58.533 52.632 0.00 0.00 34.73 3.85
2112 2130 5.939764 TCCTCCAATTATATCCATCCTCG 57.060 43.478 0.00 0.00 0.00 4.63
2160 2178 4.067896 AGTAGCTTGTTGGATGTTCACTG 58.932 43.478 0.00 0.00 0.00 3.66
2166 2184 5.106157 GCATTTGTAGTAGCTTGTTGGATGT 60.106 40.000 0.00 0.00 0.00 3.06
2175 2193 4.003648 GGTGACTGCATTTGTAGTAGCTT 58.996 43.478 1.11 0.00 41.05 3.74
2208 2226 1.069906 CGCTCCACCTTTTTCTTGACG 60.070 52.381 0.00 0.00 0.00 4.35
2250 2268 6.948886 TGTGAGAACCTTTGTAGACTATCTCT 59.051 38.462 7.97 0.00 34.58 3.10
2308 2326 1.534235 AGTGTGAGAAGGGGACGCT 60.534 57.895 0.00 0.00 0.00 5.07
2310 2328 1.185618 TGGAGTGTGAGAAGGGGACG 61.186 60.000 0.00 0.00 0.00 4.79
2363 2381 2.794103 CATGTTGGAAGTGGTCATCCA 58.206 47.619 0.00 0.00 43.84 3.41
2385 2403 0.396435 TCGCAGGAACTTCACCATGT 59.604 50.000 0.00 0.00 34.60 3.21
2388 2406 0.179234 TTGTCGCAGGAACTTCACCA 59.821 50.000 0.00 0.00 34.60 4.17
2456 2474 4.576216 GAGACATCAATAGCTTCTCGGA 57.424 45.455 0.00 0.00 0.00 4.55
2551 2569 4.083057 TCTCTTCGACTCAGTCACATCTTG 60.083 45.833 5.45 0.00 32.09 3.02
2585 2603 7.514721 TGTGTTAGGGAATTAGTGAAGAAGTT 58.485 34.615 0.00 0.00 0.00 2.66
2912 2941 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
2914 2943 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
2951 2980 7.320399 TCTGAAGCTAACAATCTATTTCGTCA 58.680 34.615 0.00 0.00 0.00 4.35
2956 2985 9.289782 AGTGTTTCTGAAGCTAACAATCTATTT 57.710 29.630 5.84 0.00 33.96 1.40
3187 3217 3.672447 TGGCAGTGGCGCAACATG 61.672 61.111 19.06 13.30 42.47 3.21
3276 3306 1.647545 GCGCAAGTGAGCCATAAGCA 61.648 55.000 0.30 0.00 42.64 3.91
3393 3423 2.006415 CCTTGGGGTCCCCTGCATA 61.006 63.158 28.11 3.85 45.70 3.14
3404 3434 3.688159 GCAGCACAAGCCTTGGGG 61.688 66.667 9.10 1.34 43.56 4.96
3644 3679 3.193691 ACGAGTCCTCTGTAACCATGAAG 59.806 47.826 0.00 0.00 0.00 3.02
3697 3734 9.743581 AATCCATTTTTCCTGCTTAAAATCATT 57.256 25.926 0.00 0.00 33.04 2.57
3747 3784 1.756538 CCCCAGAAACCATATGGCAAC 59.243 52.381 22.18 12.38 39.32 4.17
3767 3804 1.379527 CAACGAAGGTAATGCCCTCC 58.620 55.000 0.00 0.00 38.26 4.30
3971 4008 7.521509 ACTTAGTGTCGTATCTTTATGTTGC 57.478 36.000 0.00 0.00 0.00 4.17
4032 4070 3.876320 GCCTTTTGCAACTCAATCCAAAA 59.124 39.130 0.00 0.00 40.77 2.44
4192 4230 6.742559 ACACCTCAGTTAAAAGAGTCCTTA 57.257 37.500 5.11 0.00 31.15 2.69
4588 4628 6.744537 CAGATAGCAATTAACTTGTTGACAGC 59.255 38.462 0.00 0.00 37.18 4.40
4623 4663 5.982516 GGCCATTCGTTAAATTGCATTGATA 59.017 36.000 0.00 0.00 37.67 2.15


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

AutoCloner maintained by Alex Coulton.