Multiple sequence alignment - TraesCS1A01G374300

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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 TraesCS1A01G374300 chr1A 100.000 2291 0 0 1 2291 549665495 549667785 0.000000e+00 4231
1 TraesCS1A01G374300 chr1A 83.271 538 54 22 869 1391 549637847 549638363 1.600000e-126 462
2 TraesCS1A01G374300 chr1B 90.047 1487 87 27 3 1443 626599983 626601454 0.000000e+00 1869
3 TraesCS1A01G374300 chr1B 82.625 541 53 26 869 1391 626594966 626595483 7.510000e-120 440
4 TraesCS1A01G374300 chr1B 81.939 526 58 22 869 1378 626507404 626506900 5.890000e-111 411
5 TraesCS1A01G374300 chr1B 90.157 254 23 2 1736 1989 626603986 626604237 1.700000e-86 329
6 TraesCS1A01G374300 chr1B 87.279 283 28 4 1442 1720 626601499 626601777 1.320000e-82 316
7 TraesCS1A01G374300 chr1B 90.722 194 18 0 2098 2291 626606948 626607141 2.260000e-65 259
8 TraesCS1A01G374300 chr1B 78.750 240 48 3 1046 1282 626649163 626649402 8.470000e-35 158
9 TraesCS1A01G374300 chr1D 90.121 1073 64 24 389 1443 456199173 456200221 0.000000e+00 1356
10 TraesCS1A01G374300 chr1D 85.343 423 47 8 869 1290 456132344 456132752 7.570000e-115 424
11 TraesCS1A01G374300 chr1D 91.732 254 20 1 1736 1989 456200960 456201212 3.620000e-93 351
12 TraesCS1A01G374300 chr1D 86.799 303 25 8 1442 1735 456200254 456200550 7.890000e-85 324
13 TraesCS1A01G374300 chr1D 80.879 387 54 11 1889 2272 456222324 456222693 1.040000e-73 287
14 TraesCS1A01G374300 chr1D 84.663 163 14 8 246 406 456199008 456199161 3.940000e-33 152
15 TraesCS1A01G374300 chr1D 77.872 235 49 3 1051 1282 456203187 456203421 2.370000e-30 143
16 TraesCS1A01G374300 chr1D 78.125 224 44 5 1063 1282 457044202 457044424 1.100000e-28 137


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 TraesCS1A01G374300 chr1A 549665495 549667785 2290 False 4231.00 4231 100.00000 1 2291 1 chr1A.!!$F2 2290
1 TraesCS1A01G374300 chr1A 549637847 549638363 516 False 462.00 462 83.27100 869 1391 1 chr1A.!!$F1 522
2 TraesCS1A01G374300 chr1B 626599983 626607141 7158 False 693.25 1869 89.55125 3 2291 4 chr1B.!!$F3 2288
3 TraesCS1A01G374300 chr1B 626594966 626595483 517 False 440.00 440 82.62500 869 1391 1 chr1B.!!$F1 522
4 TraesCS1A01G374300 chr1B 626506900 626507404 504 True 411.00 411 81.93900 869 1378 1 chr1B.!!$R1 509
5 TraesCS1A01G374300 chr1D 456199008 456203421 4413 False 465.20 1356 86.23740 246 1989 5 chr1D.!!$F4 1743

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
908 979 0.11714 TGATCTCACCCCCAGACACT 59.883 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 7812 0.039798 GAAGACGGTCGTAGCACACA 60.04 55.0 1.89 0.0 0.0 3.72 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
36 37 0.819582 CATTGCCTGGCTTAAGGTGG 59.180 55.000 21.03 0.00 39.75 4.61
90 91 0.804989 GAACCGAGGAAGTGCCATTG 59.195 55.000 0.00 0.00 40.02 2.82
120 121 2.159572 CGAAAGGTCGTTGGCTAAATGG 60.160 50.000 0.00 0.00 42.53 3.16
134 135 4.099881 GGCTAAATGGAATGGAGCAATTGA 59.900 41.667 10.34 0.00 36.77 2.57
139 140 6.645790 AATGGAATGGAGCAATTGATCTAC 57.354 37.500 22.04 8.18 0.00 2.59
182 183 8.515414 TCTCTCTATTATCACATATGAACACGG 58.485 37.037 10.38 0.00 38.69 4.94
189 216 0.732571 CATATGAACACGGTGGGCAC 59.267 55.000 13.48 1.61 0.00 5.01
190 217 0.618458 ATATGAACACGGTGGGCACT 59.382 50.000 13.48 3.67 0.00 4.40
204 231 3.077519 GCACTAGCCCGTCGGTGAT 62.078 63.158 11.06 3.08 33.58 3.06
257 284 7.994334 TCTTAAAGGTGGCATAATACCGTAAAT 59.006 33.333 0.00 0.00 41.85 1.40
261 289 5.007682 GGTGGCATAATACCGTAAATGGAT 58.992 41.667 0.00 0.00 0.00 3.41
266 294 5.566469 CATAATACCGTAAATGGATGGGGT 58.434 41.667 0.00 0.00 0.00 4.95
267 295 3.502123 ATACCGTAAATGGATGGGGTG 57.498 47.619 0.00 0.00 0.00 4.61
268 296 0.996583 ACCGTAAATGGATGGGGTGT 59.003 50.000 0.00 0.00 0.00 4.16
269 297 1.340600 ACCGTAAATGGATGGGGTGTG 60.341 52.381 0.00 0.00 0.00 3.82
270 298 1.340600 CCGTAAATGGATGGGGTGTGT 60.341 52.381 0.00 0.00 0.00 3.72
320 351 1.157585 GAAAAGGGTCGAAGGTCTGC 58.842 55.000 0.00 0.00 0.00 4.26
333 364 2.264455 AGGTCTGCTTTCAGGTCTGAT 58.736 47.619 1.16 0.00 40.69 2.90
380 411 5.184479 TGAACTAGACATACAGGTGTACCAC 59.816 44.000 3.56 0.00 38.89 4.16
385 416 2.832129 ACATACAGGTGTACCACTCCAG 59.168 50.000 3.56 0.00 38.89 3.86
408 465 8.417884 CCAGTCAAAACCTGAATACCTTTTAAA 58.582 33.333 0.00 0.00 35.22 1.52
453 510 8.003784 CGAAATGTTTTATGTTTCTTTGGCTTC 58.996 33.333 0.00 0.00 31.42 3.86
456 513 5.974751 TGTTTTATGTTTCTTTGGCTTCGTC 59.025 36.000 0.00 0.00 0.00 4.20
459 516 4.853924 ATGTTTCTTTGGCTTCGTCAAT 57.146 36.364 0.00 0.00 0.00 2.57
465 522 7.168972 TGTTTCTTTGGCTTCGTCAATAAAATG 59.831 33.333 0.00 0.00 0.00 2.32
466 523 5.708948 TCTTTGGCTTCGTCAATAAAATGG 58.291 37.500 0.00 0.00 0.00 3.16
487 545 8.409358 AATGGAAAAACTAGTTATGCTCAACT 57.591 30.769 8.92 8.30 41.56 3.16
553 611 6.324819 CACAGCTTAACAAACCTTATCATGG 58.675 40.000 0.00 0.00 0.00 3.66
554 612 5.105756 ACAGCTTAACAAACCTTATCATGGC 60.106 40.000 0.00 0.00 0.00 4.40
555 613 4.402474 AGCTTAACAAACCTTATCATGGCC 59.598 41.667 0.00 0.00 0.00 5.36
556 614 4.733523 GCTTAACAAACCTTATCATGGCCG 60.734 45.833 0.00 0.00 0.00 6.13
617 675 3.495001 GTGACACTTGTAGTTTCAGAGGC 59.505 47.826 0.00 0.00 35.79 4.70
658 716 6.633500 TGTGCTAGTAATTGAGTTGCTTTT 57.367 33.333 0.00 0.00 34.42 2.27
670 728 3.093449 GCTTTTCAGTGCGTGCGC 61.093 61.111 9.85 9.85 42.35 6.09
691 749 3.869065 CCGACTAAACTTGCCAATCCTA 58.131 45.455 0.00 0.00 0.00 2.94
743 802 3.119495 GCGTGGACCATTAATTTCTGCTT 60.119 43.478 0.00 0.00 0.00 3.91
748 807 5.066375 TGGACCATTAATTTCTGCTTCATCG 59.934 40.000 0.00 0.00 0.00 3.84
903 974 0.911525 ACCACTGATCTCACCCCCAG 60.912 60.000 0.00 0.00 0.00 4.45
908 979 0.117140 TGATCTCACCCCCAGACACT 59.883 55.000 0.00 0.00 0.00 3.55
955 1027 3.928343 GCCACTAGCTCACTACTCG 57.072 57.895 0.00 0.00 38.99 4.18
998 1070 2.690173 CGTCAGAGTTTCAGAGACGT 57.310 50.000 0.00 0.00 44.87 4.34
1116 1188 4.694233 CTGCAGCTGAGCCCGTGT 62.694 66.667 20.43 0.00 0.00 4.49
1212 1284 4.415332 CAGTACGCGCACGACCCT 62.415 66.667 5.73 0.00 43.93 4.34
1309 1388 4.259650 GCTAGATCGACGTCTATGATCGAG 60.260 50.000 24.32 24.32 46.99 4.04
1310 1389 3.915536 AGATCGACGTCTATGATCGAGA 58.084 45.455 19.60 6.42 46.99 4.04
1346 1425 1.600638 CCAGTGGCATCTCTCTGCA 59.399 57.895 0.00 0.00 44.12 4.41
1395 1481 2.004017 GTGAGTGTTTGGTTGTCGTGA 58.996 47.619 0.00 0.00 0.00 4.35
1401 1487 2.206750 GTTTGGTTGTCGTGAGTAGCA 58.793 47.619 0.00 0.00 0.00 3.49
1472 1604 4.647399 GTGAGCTCCACTAGGTAAGAGATT 59.353 45.833 12.15 0.00 42.44 2.40
1522 1658 1.264020 CAAACGGCCGGTCATCATATG 59.736 52.381 31.76 12.82 0.00 1.78
1554 1690 0.249120 TTCTCGAACGGGCATGTGAT 59.751 50.000 0.00 0.00 0.00 3.06
1555 1691 0.460109 TCTCGAACGGGCATGTGATG 60.460 55.000 0.00 0.00 0.00 3.07
1556 1692 0.460109 CTCGAACGGGCATGTGATGA 60.460 55.000 0.00 0.00 0.00 2.92
1557 1693 0.460109 TCGAACGGGCATGTGATGAG 60.460 55.000 0.00 0.00 0.00 2.90
1558 1694 1.723870 GAACGGGCATGTGATGAGC 59.276 57.895 0.00 0.00 0.00 4.26
1559 1695 0.745845 GAACGGGCATGTGATGAGCT 60.746 55.000 0.00 0.00 0.00 4.09
1560 1696 0.745845 AACGGGCATGTGATGAGCTC 60.746 55.000 6.82 6.82 0.00 4.09
1564 1700 2.029623 GGGCATGTGATGAGCTCATTT 58.970 47.619 29.26 10.39 36.57 2.32
1688 1824 5.227238 AGTAGATACTACCACAAACGACG 57.773 43.478 0.00 0.00 34.13 5.12
1729 1865 6.262193 TCTACACGCATATTCCATAATCGA 57.738 37.500 0.00 0.00 0.00 3.59
1815 4168 6.641169 TGCATGAACCACACTAAAATGTTA 57.359 33.333 0.00 0.00 0.00 2.41
1902 4255 6.263842 TGAGGTCCGTATACATCGATTTAACT 59.736 38.462 3.32 0.00 32.95 2.24
1903 4256 7.445096 TGAGGTCCGTATACATCGATTTAACTA 59.555 37.037 3.32 0.00 32.95 2.24
1928 4281 2.881111 AACCCTAGAAAAGGTCAGCC 57.119 50.000 0.00 0.00 44.90 4.85
1964 4317 8.463456 AGAATCTTGTTCGCTAGTTAAACTAC 57.537 34.615 0.00 0.00 0.00 2.73
1965 4318 7.544915 AGAATCTTGTTCGCTAGTTAAACTACC 59.455 37.037 0.00 0.00 0.00 3.18
1974 4327 5.692204 CGCTAGTTAAACTACCCATCATCAG 59.308 44.000 0.00 0.00 0.00 2.90
1985 4338 1.341209 CCATCATCAGCCTACGCACTA 59.659 52.381 0.00 0.00 37.52 2.74
1986 4339 2.224042 CCATCATCAGCCTACGCACTAA 60.224 50.000 0.00 0.00 37.52 2.24
1987 4340 3.457234 CATCATCAGCCTACGCACTAAA 58.543 45.455 0.00 0.00 37.52 1.85
1988 4341 3.819564 TCATCAGCCTACGCACTAAAT 57.180 42.857 0.00 0.00 37.52 1.40
1989 4342 4.137116 TCATCAGCCTACGCACTAAATT 57.863 40.909 0.00 0.00 37.52 1.82
1990 4343 4.513442 TCATCAGCCTACGCACTAAATTT 58.487 39.130 0.00 0.00 37.52 1.82
1991 4344 5.666462 TCATCAGCCTACGCACTAAATTTA 58.334 37.500 0.00 0.00 37.52 1.40
1992 4345 5.522460 TCATCAGCCTACGCACTAAATTTAC 59.478 40.000 0.00 0.00 37.52 2.01
1993 4346 4.186159 TCAGCCTACGCACTAAATTTACC 58.814 43.478 0.00 0.00 37.52 2.85
1994 4347 3.000925 CAGCCTACGCACTAAATTTACCG 59.999 47.826 0.00 0.84 37.52 4.02
1995 4348 2.286025 GCCTACGCACTAAATTTACCGG 59.714 50.000 0.00 0.00 34.03 5.28
1996 4349 2.867975 CCTACGCACTAAATTTACCGGG 59.132 50.000 6.32 0.00 0.00 5.73
1997 4350 1.089112 ACGCACTAAATTTACCGGGC 58.911 50.000 6.32 2.37 0.00 6.13
1998 4351 1.088306 CGCACTAAATTTACCGGGCA 58.912 50.000 6.32 0.00 0.00 5.36
1999 4352 1.469308 CGCACTAAATTTACCGGGCAA 59.531 47.619 6.32 0.00 0.00 4.52
2000 4353 2.095161 CGCACTAAATTTACCGGGCAAA 60.095 45.455 6.32 6.14 0.00 3.68
2001 4354 3.612004 CGCACTAAATTTACCGGGCAAAA 60.612 43.478 6.32 3.64 0.00 2.44
2002 4355 4.308265 GCACTAAATTTACCGGGCAAAAA 58.692 39.130 6.32 0.80 0.00 1.94
2059 4465 5.253330 GTGTGAACTGGATATTCAAGGGAA 58.747 41.667 0.00 0.00 37.80 3.97
2061 4467 7.054124 GTGTGAACTGGATATTCAAGGGAATA 58.946 38.462 0.16 0.16 46.88 1.75
2096 4502 3.611025 ACCCACAAAAATCTCCTTCCA 57.389 42.857 0.00 0.00 0.00 3.53
2141 7784 8.372459 TGATGTGTACTATAAAGTCAAAGGTGT 58.628 33.333 0.00 0.00 37.15 4.16
2181 7824 2.147958 TCCCAAAATGTGTGCTACGAC 58.852 47.619 0.00 0.00 0.00 4.34
2183 7826 1.136085 CCAAAATGTGTGCTACGACCG 60.136 52.381 0.00 0.00 0.00 4.79
2204 7847 5.298276 ACCGTCTTCAACTTGAAAAATGCTA 59.702 36.000 5.72 0.00 35.73 3.49
2216 7859 8.515414 ACTTGAAAAATGCTATACTGAAGAACC 58.485 33.333 0.00 0.00 0.00 3.62
2220 7863 5.700402 AATGCTATACTGAAGAACCCACT 57.300 39.130 0.00 0.00 0.00 4.00
2233 7876 3.395941 AGAACCCACTCTTTGTCCTCATT 59.604 43.478 0.00 0.00 0.00 2.57
2249 7892 3.696548 CCTCATTAACCCCTTTCAGAAGC 59.303 47.826 0.00 0.00 0.00 3.86
2286 7929 5.405571 GCTGAATCGTAACTTGAGACAAAGA 59.594 40.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.555325 CAATGTGTTGACAGGTGCTCAT 59.445 45.455 0.00 0.00 37.53 2.90
1 2 1.948834 CAATGTGTTGACAGGTGCTCA 59.051 47.619 0.00 0.00 37.53 4.26
15 16 1.203052 CACCTTAAGCCAGGCAATGTG 59.797 52.381 15.80 9.66 37.47 3.21
36 37 1.153784 CACGCATCACATTTGGGGC 60.154 57.895 0.00 0.00 0.00 5.80
40 41 1.202177 GCTACCCACGCATCACATTTG 60.202 52.381 0.00 0.00 0.00 2.32
90 91 1.875157 AACGACCTTTCGGTTAGTGGC 60.875 52.381 0.00 0.00 45.19 5.01
115 116 6.238842 CGTAGATCAATTGCTCCATTCCATTT 60.239 38.462 5.68 0.00 0.00 2.32
120 121 4.084849 CGACGTAGATCAATTGCTCCATTC 60.085 45.833 5.68 0.00 0.00 2.67
134 135 2.097825 AGTGTAAAGGGCGACGTAGAT 58.902 47.619 0.00 0.00 0.00 1.98
139 140 1.725164 GAGAAAGTGTAAAGGGCGACG 59.275 52.381 0.00 0.00 0.00 5.12
189 216 2.417516 CCATCACCGACGGGCTAG 59.582 66.667 20.00 5.21 36.48 3.42
190 217 2.363276 ACCATCACCGACGGGCTA 60.363 61.111 20.00 2.95 36.48 3.93
199 226 4.464597 AGAGAAACTCTACTCACCATCACC 59.535 45.833 0.00 0.00 39.28 4.02
204 231 7.280428 CGAAGTATAGAGAAACTCTACTCACCA 59.720 40.741 10.11 0.00 44.47 4.17
257 284 2.328992 TACACTACACACCCCATCCA 57.671 50.000 0.00 0.00 0.00 3.41
261 289 3.039743 TCACTTTACACTACACACCCCA 58.960 45.455 0.00 0.00 0.00 4.96
320 351 4.942483 AGAGCATTTGATCAGACCTGAAAG 59.058 41.667 3.62 0.00 43.58 2.62
333 364 8.242729 TCAGTATCTATCTTCAGAGCATTTGA 57.757 34.615 0.00 0.00 0.00 2.69
380 411 4.911390 AGGTATTCAGGTTTTGACTGGAG 58.089 43.478 0.00 0.00 34.94 3.86
408 465 9.436957 ACATTTCGTAAAGAGTTGAATGTAGAT 57.563 29.630 0.00 0.00 0.00 1.98
428 485 8.003784 CGAAGCCAAAGAAACATAAAACATTTC 58.996 33.333 0.00 0.00 33.40 2.17
445 502 5.713792 TCCATTTTATTGACGAAGCCAAA 57.286 34.783 0.00 0.00 0.00 3.28
465 522 9.529325 AAAAAGTTGAGCATAACTAGTTTTTCC 57.471 29.630 14.49 0.59 39.86 3.13
492 550 6.761099 TTGTTAACTGGTTAAAGAACAGCA 57.239 33.333 7.22 0.00 36.86 4.41
555 613 4.720902 TGGTGGACTGCATGCCCG 62.721 66.667 16.68 8.96 0.00 6.13
556 614 2.283101 TTGGTGGACTGCATGCCC 60.283 61.111 16.68 10.02 0.00 5.36
617 675 3.468266 AACAAAGCCACGCGCACTG 62.468 57.895 5.73 0.83 41.38 3.66
630 688 6.039270 AGCAACTCAATTACTAGCACAACAAA 59.961 34.615 0.00 0.00 0.00 2.83
670 728 2.711542 AGGATTGGCAAGTTTAGTCGG 58.288 47.619 5.96 0.00 0.00 4.79
743 802 4.677673 ATGGAAGACATGATGACGATGA 57.322 40.909 0.00 0.00 38.70 2.92
846 910 5.005203 CGAATTTCGATCAAGAGAGTTCAGG 59.995 44.000 13.45 0.00 43.74 3.86
903 974 1.537202 GCTTTGGATGGTGTGAGTGTC 59.463 52.381 0.00 0.00 0.00 3.67
908 979 1.355381 AGATGGCTTTGGATGGTGTGA 59.645 47.619 0.00 0.00 0.00 3.58
955 1027 5.189659 AGAAATGTAGATCGACTGGTAGC 57.810 43.478 7.51 0.00 0.00 3.58
1043 1115 3.704231 ATCATCAGCACCACCGCCC 62.704 63.158 0.00 0.00 0.00 6.13
1205 1277 0.608640 CTGCTTCAGGTTAGGGTCGT 59.391 55.000 0.00 0.00 0.00 4.34
1212 1284 3.319972 AGTTGACGTACTGCTTCAGGTTA 59.680 43.478 0.00 0.00 35.51 2.85
1309 1388 1.137825 CTGGGCTCTCGTTCTCGTC 59.862 63.158 0.00 0.00 38.33 4.20
1310 1389 2.995872 GCTGGGCTCTCGTTCTCGT 61.996 63.158 0.00 0.00 38.33 4.18
1312 1391 2.185608 GGCTGGGCTCTCGTTCTC 59.814 66.667 0.00 0.00 0.00 2.87
1313 1392 2.604686 TGGCTGGGCTCTCGTTCT 60.605 61.111 0.00 0.00 0.00 3.01
1314 1393 2.125350 CTGGCTGGGCTCTCGTTC 60.125 66.667 0.00 0.00 0.00 3.95
1315 1394 2.925170 ACTGGCTGGGCTCTCGTT 60.925 61.111 0.00 0.00 0.00 3.85
1316 1395 3.699894 CACTGGCTGGGCTCTCGT 61.700 66.667 0.00 0.00 0.00 4.18
1317 1396 4.463879 CCACTGGCTGGGCTCTCG 62.464 72.222 0.00 0.00 36.18 4.04
1395 1481 2.365617 CAGATACATCGGGGTTGCTACT 59.634 50.000 0.00 0.00 0.00 2.57
1401 1487 4.480115 TCAGATACAGATACATCGGGGTT 58.520 43.478 0.00 0.00 0.00 4.11
1472 1604 0.690192 TCTTTCTCCCATCAACGCCA 59.310 50.000 0.00 0.00 0.00 5.69
1522 1658 4.088648 CGTTCGAGAAAAACATATGCCAC 58.911 43.478 1.58 0.00 0.00 5.01
1568 1704 7.352739 CGCGCTTATCCTTTTATATTTGTCTT 58.647 34.615 5.56 0.00 0.00 3.01
1569 1705 6.073222 CCGCGCTTATCCTTTTATATTTGTCT 60.073 38.462 5.56 0.00 0.00 3.41
1570 1706 6.077838 CCGCGCTTATCCTTTTATATTTGTC 58.922 40.000 5.56 0.00 0.00 3.18
1571 1707 5.562113 GCCGCGCTTATCCTTTTATATTTGT 60.562 40.000 5.56 0.00 0.00 2.83
1572 1708 4.851558 GCCGCGCTTATCCTTTTATATTTG 59.148 41.667 5.56 0.00 0.00 2.32
1573 1709 4.082949 GGCCGCGCTTATCCTTTTATATTT 60.083 41.667 5.56 0.00 0.00 1.40
1574 1710 3.439129 GGCCGCGCTTATCCTTTTATATT 59.561 43.478 5.56 0.00 0.00 1.28
1576 1712 2.038033 AGGCCGCGCTTATCCTTTTATA 59.962 45.455 5.56 0.00 0.00 0.98
1591 1727 1.835483 CGTAATGATGCAGAGGCCGC 61.835 60.000 0.00 0.00 40.13 6.53
1659 1795 9.195411 CGTTTGTGGTAGTATCTACTTTTGTTA 57.805 33.333 6.83 0.00 37.73 2.41
1660 1796 7.927629 TCGTTTGTGGTAGTATCTACTTTTGTT 59.072 33.333 6.83 0.00 37.73 2.83
1674 1810 6.879962 TCTAATTTTTCGTCGTTTGTGGTAG 58.120 36.000 0.00 0.00 0.00 3.18
1675 1811 6.841443 TCTAATTTTTCGTCGTTTGTGGTA 57.159 33.333 0.00 0.00 0.00 3.25
1676 1812 5.738118 TCTAATTTTTCGTCGTTTGTGGT 57.262 34.783 0.00 0.00 0.00 4.16
1713 1849 5.470098 AGTGTGGTTCGATTATGGAATATGC 59.530 40.000 0.00 0.00 0.00 3.14
1721 1857 7.169308 GTGATAAGGTAGTGTGGTTCGATTATG 59.831 40.741 0.00 0.00 0.00 1.90
1724 1860 5.416947 GTGATAAGGTAGTGTGGTTCGATT 58.583 41.667 0.00 0.00 0.00 3.34
1727 1863 3.194968 AGGTGATAAGGTAGTGTGGTTCG 59.805 47.826 0.00 0.00 0.00 3.95
1729 1865 3.518303 GGAGGTGATAAGGTAGTGTGGTT 59.482 47.826 0.00 0.00 0.00 3.67
1870 4223 8.515695 TCGATGTATACGGACCTCATAAATAT 57.484 34.615 0.00 0.00 0.00 1.28
1928 4281 3.855689 ACAAGATTCTTTCCATTGGCG 57.144 42.857 0.00 0.00 0.00 5.69
1964 4317 0.882042 GTGCGTAGGCTGATGATGGG 60.882 60.000 9.11 0.00 40.82 4.00
1965 4318 0.105593 AGTGCGTAGGCTGATGATGG 59.894 55.000 9.11 0.00 40.82 3.51
1974 4327 2.286025 CCGGTAAATTTAGTGCGTAGGC 59.714 50.000 0.00 0.00 40.52 3.93
2002 4355 4.395231 GCTCGATTTAGTGCCTAGGTTTTT 59.605 41.667 11.31 0.00 0.00 1.94
2003 4356 3.939592 GCTCGATTTAGTGCCTAGGTTTT 59.060 43.478 11.31 0.00 0.00 2.43
2004 4357 3.532542 GCTCGATTTAGTGCCTAGGTTT 58.467 45.455 11.31 0.00 0.00 3.27
2005 4358 2.158943 GGCTCGATTTAGTGCCTAGGTT 60.159 50.000 11.31 0.00 44.71 3.50
2006 4359 1.413077 GGCTCGATTTAGTGCCTAGGT 59.587 52.381 11.31 0.00 44.71 3.08
2007 4360 2.156343 GGCTCGATTTAGTGCCTAGG 57.844 55.000 3.67 3.67 44.71 3.02
2059 4465 4.979039 TGTGGGTACAATATTGGGGACTAT 59.021 41.667 19.37 0.00 32.88 2.12
2061 4467 3.194620 TGTGGGTACAATATTGGGGACT 58.805 45.455 19.37 0.78 32.88 3.85
2090 4496 5.940192 TTATAATAGCGTGCAATGGAAGG 57.060 39.130 0.00 0.00 0.00 3.46
2091 4497 8.075574 TCATTTTATAATAGCGTGCAATGGAAG 58.924 33.333 0.00 0.00 0.00 3.46
2096 4502 8.352201 ACACATCATTTTATAATAGCGTGCAAT 58.648 29.630 0.00 0.00 0.00 3.56
2169 7812 0.039798 GAAGACGGTCGTAGCACACA 60.040 55.000 1.89 0.00 0.00 3.72
2181 7824 4.610945 AGCATTTTTCAAGTTGAAGACGG 58.389 39.130 17.36 9.43 37.70 4.79
2183 7826 9.334693 CAGTATAGCATTTTTCAAGTTGAAGAC 57.665 33.333 17.36 7.60 37.70 3.01
2204 7847 5.513267 GGACAAAGAGTGGGTTCTTCAGTAT 60.513 44.000 0.00 0.00 36.42 2.12
2216 7859 4.010349 GGGTTAATGAGGACAAAGAGTGG 58.990 47.826 0.00 0.00 0.00 4.00
2220 7863 5.163034 TGAAAGGGGTTAATGAGGACAAAGA 60.163 40.000 0.00 0.00 0.00 2.52
2233 7876 0.672401 CGCGCTTCTGAAAGGGGTTA 60.672 55.000 5.56 0.00 43.68 2.85
2249 7892 2.597505 CGATTCAGCCAAATTACTCGCG 60.598 50.000 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.