Multiple sequence alignment - TraesCS6D01G304300

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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 TraesCS6D01G304300 chr6D 100.000 4841 0 0 1 4841 413273565 413268725 0.000000e+00 8940
1 TraesCS6D01G304300 chr6A 92.903 4072 165 65 507 4488 558789340 558785303 0.000000e+00 5805
2 TraesCS6D01G304300 chr6A 85.201 473 16 13 5 443 558790194 558789742 2.070000e-118 436
3 TraesCS6D01G304300 chr6A 94.382 178 4 2 4670 4841 558783957 558783780 7.990000e-68 268
4 TraesCS6D01G304300 chr6A 91.500 200 10 7 4471 4669 558784191 558783998 7.990000e-68 268
5 TraesCS6D01G304300 chr6B 90.978 3558 160 68 1 3464 623085310 623081820 0.000000e+00 4643
6 TraesCS6D01G304300 chr6B 90.999 1422 37 23 3474 4838 623081769 623080382 0.000000e+00 1832
7 TraesCS6D01G304300 chr7A 78.526 475 80 17 2560 3020 124069304 124068838 4.740000e-75 292
8 TraesCS6D01G304300 chr7D 78.059 474 82 17 2560 3019 119567531 119567066 3.690000e-71 279
9 TraesCS6D01G304300 chr7B 84.932 219 33 0 2560 2778 80661154 80660936 6.310000e-54 222
10 TraesCS6D01G304300 chr7B 82.857 140 24 0 2873 3012 80660833 80660694 5.090000e-25 126
11 TraesCS6D01G304300 chr1B 89.431 123 13 0 1193 1315 377969155 377969033 6.490000e-34 156
12 TraesCS6D01G304300 chr1A 88.462 130 14 1 1193 1321 350400269 350400140 6.490000e-34 156
13 TraesCS6D01G304300 chr1D 88.618 123 14 0 1193 1315 278109820 278109698 3.020000e-32 150


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 TraesCS6D01G304300 chr6D 413268725 413273565 4840 True 8940.00 8940 100.0000 1 4841 1 chr6D.!!$R1 4840
1 TraesCS6D01G304300 chr6A 558783780 558790194 6414 True 1694.25 5805 90.9965 5 4841 4 chr6A.!!$R1 4836
2 TraesCS6D01G304300 chr6B 623080382 623085310 4928 True 3237.50 4643 90.9885 1 4838 2 chr6B.!!$R1 4837

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
956 1428 0.234884 GAAGCAAACGACGTGGGAAG 59.765 55.0 0.00 0.0 0.00 3.46 F
1187 1677 0.106708 ATCTTCTGTGGTGTGCGTGT 59.893 50.0 0.00 0.0 0.00 4.49 F
1610 2118 0.389817 TCAAGAACGTCATCTGCCCG 60.390 55.0 0.00 0.0 0.00 6.13 F
2262 2775 0.458543 CGTTCATGGACTCGGTGAGG 60.459 60.0 1.86 0.0 33.35 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2814 3338 0.317799 ATCGCAATGTGGCAAAGCAA 59.682 45.000 0.00 0.0 0.00 3.91 R
2824 3348 1.003839 ACACACCCGATCGCAATGT 60.004 52.632 10.32 10.3 0.00 2.71 R
3476 4052 0.948623 CTGCATTCCGTCGAACACCA 60.949 55.000 0.00 0.0 0.00 4.17 R
4091 4673 0.162507 GAAGAAGACGACGACGACGA 59.837 55.000 25.15 0.0 42.66 4.20 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 6.785191 TCTTTTCTTTGTTTAGTCAGCACTG 58.215 36.000 0.00 0.00 33.62 3.66
27 28 6.597672 TCTTTTCTTTGTTTAGTCAGCACTGA 59.402 34.615 0.00 0.00 37.24 3.41
81 82 2.462456 TAGTGCAGAAACAGCAGAGG 57.538 50.000 0.00 0.00 43.63 3.69
82 83 0.250640 AGTGCAGAAACAGCAGAGGG 60.251 55.000 0.00 0.00 43.63 4.30
348 375 1.153901 CTGTACCGGCACTGTACCG 60.154 63.158 12.50 12.50 46.18 4.02
394 421 2.542595 GACGAGTAGAGCTGTAGAGAGC 59.457 54.545 0.00 0.00 39.46 4.09
402 429 1.484653 AGCTGTAGAGAGCGAGAGAGA 59.515 52.381 0.00 0.00 44.24 3.10
443 494 0.673985 CCAACGAGGCCATAGATCGA 59.326 55.000 17.25 0.00 39.66 3.59
444 495 1.336332 CCAACGAGGCCATAGATCGAG 60.336 57.143 17.25 9.27 39.66 4.04
446 497 1.154131 CGAGGCCATAGATCGAGCG 60.154 63.158 5.01 0.00 38.72 5.03
447 498 1.445238 GAGGCCATAGATCGAGCGC 60.445 63.158 5.01 0.00 0.00 5.92
448 499 2.807045 GGCCATAGATCGAGCGCG 60.807 66.667 2.41 2.41 39.35 6.86
449 500 2.049985 GCCATAGATCGAGCGCGT 60.050 61.111 10.30 0.00 38.98 6.01
450 501 2.368105 GCCATAGATCGAGCGCGTG 61.368 63.158 10.30 0.00 38.98 5.34
451 502 1.008424 CCATAGATCGAGCGCGTGT 60.008 57.895 10.30 0.00 38.98 4.49
452 503 0.999228 CCATAGATCGAGCGCGTGTC 60.999 60.000 10.30 9.62 38.98 3.67
453 504 0.999228 CATAGATCGAGCGCGTGTCC 60.999 60.000 10.30 0.00 38.98 4.02
454 505 2.131294 ATAGATCGAGCGCGTGTCCC 62.131 60.000 10.30 0.00 38.98 4.46
607 1025 2.282603 CGGGGCGGGGAAAGAAAA 60.283 61.111 0.00 0.00 0.00 2.29
608 1026 2.340328 CGGGGCGGGGAAAGAAAAG 61.340 63.158 0.00 0.00 0.00 2.27
627 1056 3.018423 AGCTCCTCTCTCTTCTCTTCC 57.982 52.381 0.00 0.00 0.00 3.46
628 1057 2.311542 AGCTCCTCTCTCTTCTCTTCCA 59.688 50.000 0.00 0.00 0.00 3.53
629 1058 3.096092 GCTCCTCTCTCTTCTCTTCCAA 58.904 50.000 0.00 0.00 0.00 3.53
746 1200 1.738432 CTGGCTCGCTGCATCTCTA 59.262 57.895 0.00 0.00 45.15 2.43
855 1316 2.428890 AGGCATCTGTCTATATAGCGCC 59.571 50.000 2.29 9.22 34.44 6.53
856 1317 2.455032 GCATCTGTCTATATAGCGCCG 58.545 52.381 2.29 0.00 0.00 6.46
857 1318 2.455032 CATCTGTCTATATAGCGCCGC 58.545 52.381 2.29 0.00 0.00 6.53
861 1326 2.014857 TGTCTATATAGCGCCGCCTAG 58.985 52.381 4.98 2.27 0.00 3.02
863 1328 3.201290 GTCTATATAGCGCCGCCTAGTA 58.799 50.000 4.98 0.00 0.00 1.82
873 1338 1.266446 GCCGCCTAGTACTAGCACTAC 59.734 57.143 22.39 8.08 31.95 2.73
891 1356 0.963856 ACACCTCGATCGTAGCACCA 60.964 55.000 15.94 0.00 0.00 4.17
892 1357 0.248661 CACCTCGATCGTAGCACCAG 60.249 60.000 15.94 2.75 0.00 4.00
893 1358 1.299468 CCTCGATCGTAGCACCAGC 60.299 63.158 15.94 0.00 42.56 4.85
913 1378 1.423056 CAGCGCTGCTTCTTGCTAC 59.577 57.895 26.68 0.00 43.37 3.58
915 1380 0.532573 AGCGCTGCTTCTTGCTACTA 59.467 50.000 10.39 0.00 43.37 1.82
917 1382 1.737363 GCGCTGCTTCTTGCTACTAGT 60.737 52.381 0.00 0.00 43.37 2.57
920 1385 2.189342 CTGCTTCTTGCTACTAGTCGC 58.811 52.381 12.27 12.27 43.37 5.19
925 1397 0.248539 CTTGCTACTAGTCGCCGGAC 60.249 60.000 16.05 0.00 43.76 4.79
952 1424 1.487231 CTCGAAGCAAACGACGTGG 59.513 57.895 0.00 0.00 35.88 4.94
953 1425 1.886861 CTCGAAGCAAACGACGTGGG 61.887 60.000 0.00 0.00 35.88 4.61
954 1426 1.952133 CGAAGCAAACGACGTGGGA 60.952 57.895 0.00 0.00 0.00 4.37
955 1427 1.492319 CGAAGCAAACGACGTGGGAA 61.492 55.000 0.00 0.00 0.00 3.97
956 1428 0.234884 GAAGCAAACGACGTGGGAAG 59.765 55.000 0.00 0.00 0.00 3.46
963 1435 2.182030 GACGTGGGAAGCCGAGAG 59.818 66.667 0.00 0.00 0.00 3.20
1106 1584 4.806571 GCTCGAGGCGTATGTGAA 57.193 55.556 15.58 0.00 0.00 3.18
1107 1585 3.274393 GCTCGAGGCGTATGTGAAT 57.726 52.632 15.58 0.00 0.00 2.57
1109 1587 1.523095 GCTCGAGGCGTATGTGAATTC 59.477 52.381 15.58 0.00 0.00 2.17
1110 1588 2.809446 CTCGAGGCGTATGTGAATTCA 58.191 47.619 3.38 3.38 0.00 2.57
1112 1590 2.165641 TCGAGGCGTATGTGAATTCACT 59.834 45.455 32.57 22.18 46.55 3.41
1114 1592 2.535984 GAGGCGTATGTGAATTCACTCG 59.464 50.000 32.57 30.18 46.55 4.18
1115 1593 2.094182 AGGCGTATGTGAATTCACTCGT 60.094 45.455 32.57 22.31 46.55 4.18
1116 1594 2.281762 GGCGTATGTGAATTCACTCGTC 59.718 50.000 32.57 28.70 46.55 4.20
1117 1595 2.281762 GCGTATGTGAATTCACTCGTCC 59.718 50.000 32.57 19.56 46.55 4.79
1118 1596 2.858344 CGTATGTGAATTCACTCGTCCC 59.142 50.000 32.57 16.60 46.55 4.46
1119 1597 3.428999 CGTATGTGAATTCACTCGTCCCT 60.429 47.826 32.57 14.62 46.55 4.20
1120 1598 3.703001 ATGTGAATTCACTCGTCCCTT 57.297 42.857 32.57 9.96 46.55 3.95
1121 1599 3.040147 TGTGAATTCACTCGTCCCTTC 57.960 47.619 32.57 8.91 46.55 3.46
1122 1600 2.289444 TGTGAATTCACTCGTCCCTTCC 60.289 50.000 32.57 8.43 46.55 3.46
1124 1602 0.618981 AATTCACTCGTCCCTTCCCC 59.381 55.000 0.00 0.00 0.00 4.81
1125 1603 1.272554 ATTCACTCGTCCCTTCCCCC 61.273 60.000 0.00 0.00 0.00 5.40
1145 1623 3.058160 CCGCCCTTGCCTCTGTTG 61.058 66.667 0.00 0.00 0.00 3.33
1146 1624 2.032528 CGCCCTTGCCTCTGTTGA 59.967 61.111 0.00 0.00 0.00 3.18
1147 1625 1.377725 CGCCCTTGCCTCTGTTGAT 60.378 57.895 0.00 0.00 0.00 2.57
1148 1626 0.962356 CGCCCTTGCCTCTGTTGATT 60.962 55.000 0.00 0.00 0.00 2.57
1149 1627 1.260544 GCCCTTGCCTCTGTTGATTT 58.739 50.000 0.00 0.00 0.00 2.17
1150 1628 1.203287 GCCCTTGCCTCTGTTGATTTC 59.797 52.381 0.00 0.00 0.00 2.17
1151 1629 2.800250 CCCTTGCCTCTGTTGATTTCT 58.200 47.619 0.00 0.00 0.00 2.52
1152 1630 3.160269 CCCTTGCCTCTGTTGATTTCTT 58.840 45.455 0.00 0.00 0.00 2.52
1153 1631 3.192212 CCCTTGCCTCTGTTGATTTCTTC 59.808 47.826 0.00 0.00 0.00 2.87
1154 1632 3.822735 CCTTGCCTCTGTTGATTTCTTCA 59.177 43.478 0.00 0.00 0.00 3.02
1155 1633 4.461781 CCTTGCCTCTGTTGATTTCTTCAT 59.538 41.667 0.00 0.00 33.34 2.57
1156 1634 5.047519 CCTTGCCTCTGTTGATTTCTTCATT 60.048 40.000 0.00 0.00 33.34 2.57
1175 1653 5.176592 TCATTGTCTCTTGCTCATCTTCTG 58.823 41.667 0.00 0.00 0.00 3.02
1177 1655 3.922910 TGTCTCTTGCTCATCTTCTGTG 58.077 45.455 0.00 0.00 0.00 3.66
1187 1677 0.106708 ATCTTCTGTGGTGTGCGTGT 59.893 50.000 0.00 0.00 0.00 4.49
1319 1813 1.534175 CGGACTCAGATGAAGGTACGC 60.534 57.143 0.00 0.00 0.00 4.42
1341 1849 1.272313 CCCATCCCATCATCCATGTCC 60.272 57.143 0.00 0.00 0.00 4.02
1346 1854 0.949397 CCATCATCCATGTCCGCAAG 59.051 55.000 0.00 0.00 0.00 4.01
1367 1875 3.333680 AGCCATCTTTTTCACCCTCCTTA 59.666 43.478 0.00 0.00 0.00 2.69
1610 2118 0.389817 TCAAGAACGTCATCTGCCCG 60.390 55.000 0.00 0.00 0.00 6.13
1704 2212 2.743126 CTCAAAGAAGAGGCAAGCAGAG 59.257 50.000 0.00 0.00 31.94 3.35
1735 2243 0.685458 TAACTACCACTCCGCCTCCC 60.685 60.000 0.00 0.00 0.00 4.30
1959 2472 4.087892 CTGGACCTGGACCCGCTG 62.088 72.222 12.66 0.00 0.00 5.18
2262 2775 0.458543 CGTTCATGGACTCGGTGAGG 60.459 60.000 1.86 0.00 33.35 3.86
2263 2776 0.741221 GTTCATGGACTCGGTGAGGC 60.741 60.000 0.00 0.00 36.87 4.70
2382 2906 0.750546 TCCCGACTATCGTGACCAGG 60.751 60.000 0.00 0.00 38.40 4.45
2461 2985 4.077184 TAAGGCCAGACCACCGCG 62.077 66.667 5.01 0.00 43.14 6.46
2527 3051 0.530650 ATTAGGCGCACATGGACGAG 60.531 55.000 10.83 0.00 0.00 4.18
2536 3060 2.420022 GCACATGGACGAGCATTTTACT 59.580 45.455 0.00 0.00 0.00 2.24
2646 3170 4.081185 TGCCGGCAGATCGAGCAA 62.081 61.111 29.03 0.00 34.97 3.91
2810 3334 1.449601 CGGCGGCTTAGTTCACCAT 60.450 57.895 7.61 0.00 0.00 3.55
2814 3338 2.017049 GCGGCTTAGTTCACCATCATT 58.983 47.619 0.00 0.00 0.00 2.57
2816 3340 3.731867 GCGGCTTAGTTCACCATCATTTG 60.732 47.826 0.00 0.00 0.00 2.32
2824 3348 1.969208 TCACCATCATTTGCTTTGCCA 59.031 42.857 0.00 0.00 0.00 4.92
3147 3678 4.624364 CAGCAGCACCGGTGGACA 62.624 66.667 34.58 0.00 0.00 4.02
3153 3684 2.590575 CACCGGTGGACAACGCTT 60.591 61.111 27.57 0.00 40.82 4.68
3304 3835 2.029964 GGGTGTTCGCCTTCGTGA 59.970 61.111 2.41 0.00 36.96 4.35
3354 3885 4.680237 CTCTCGCACGGCAACCCA 62.680 66.667 0.00 0.00 0.00 4.51
3387 3918 4.473520 CGCATCCCCAACGGCTCT 62.474 66.667 0.00 0.00 0.00 4.09
3476 4052 5.687285 CAGACGTAGGTGTTTAACTTAACGT 59.313 40.000 14.33 14.33 41.01 3.99
3896 4475 1.075896 AGTAAGAGCTCCTCCCCCG 60.076 63.158 10.93 0.00 0.00 5.73
3897 4476 2.444140 TAAGAGCTCCTCCCCCGC 60.444 66.667 10.93 0.00 0.00 6.13
3919 4498 1.473258 TTCATTCCCATTCAAGGCGG 58.527 50.000 0.00 0.00 0.00 6.13
4032 4614 1.225704 GCTGGGGTTCATCCTCTGG 59.774 63.158 0.00 0.00 37.63 3.86
4092 4674 4.436998 CCACTCGCCCACGACCTC 62.437 72.222 0.00 0.00 45.12 3.85
4093 4675 4.778415 CACTCGCCCACGACCTCG 62.778 72.222 0.00 0.00 45.12 4.63
4228 4810 3.862124 GCACAAGCACGTCTCGAT 58.138 55.556 0.00 0.00 41.58 3.59
4229 4811 1.704582 GCACAAGCACGTCTCGATC 59.295 57.895 0.00 0.00 41.58 3.69
4230 4812 0.734253 GCACAAGCACGTCTCGATCT 60.734 55.000 0.00 0.00 41.58 2.75
4231 4813 1.263776 CACAAGCACGTCTCGATCTC 58.736 55.000 0.00 0.00 0.00 2.75
4232 4814 0.179187 ACAAGCACGTCTCGATCTCG 60.179 55.000 0.00 0.00 41.45 4.04
4368 4956 3.895232 TCTTCTCCTCCCTTTTGATCG 57.105 47.619 0.00 0.00 0.00 3.69
4378 4966 2.565841 CCTTTTGATCGTCCTCCCATC 58.434 52.381 0.00 0.00 0.00 3.51
4460 5064 8.689061 CCTCCAATCAATTAATGAACATTCAGA 58.311 33.333 3.23 0.00 42.54 3.27
4532 6270 4.927425 CAGTACAACGTGTATAAAGCTGGT 59.073 41.667 0.00 0.00 35.05 4.00
4575 6313 2.546778 CTCATCATTGCCATTTGCCAC 58.453 47.619 0.00 0.00 40.16 5.01
4687 6465 2.551912 GCTTGTGGTGGTGTTCGGG 61.552 63.158 0.00 0.00 0.00 5.14
4707 6485 1.892819 CTTGAAGGAGAGCCCGCAGA 61.893 60.000 0.00 0.00 40.87 4.26
4708 6486 1.892819 TTGAAGGAGAGCCCGCAGAG 61.893 60.000 0.00 0.00 40.87 3.35
4709 6487 3.731653 GAAGGAGAGCCCGCAGAGC 62.732 68.421 0.00 0.00 40.87 4.09
4802 6594 1.079888 GCACCCCTTCAATTTGCCG 60.080 57.895 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.785191 TCAGTGCTGACTAAACAAAGAAAAG 58.215 36.000 0.00 0.00 34.14 2.27
76 77 0.463295 CCACAGCACTATGCCCTCTG 60.463 60.000 0.00 0.00 46.52 3.35
77 78 0.618680 TCCACAGCACTATGCCCTCT 60.619 55.000 0.00 0.00 46.52 3.69
81 82 1.815421 CCGTCCACAGCACTATGCC 60.815 63.158 0.00 0.00 46.52 4.40
82 83 0.807667 CTCCGTCCACAGCACTATGC 60.808 60.000 0.00 0.00 45.46 3.14
139 158 4.838152 CAGCACGGCATAGCGGGT 62.838 66.667 1.74 0.00 35.48 5.28
143 162 4.247612 GCAGCAGCACGGCATAGC 62.248 66.667 0.00 0.50 39.55 2.97
144 163 1.227350 TAGCAGCAGCACGGCATAG 60.227 57.895 3.17 0.00 45.49 2.23
145 164 1.521457 GTAGCAGCAGCACGGCATA 60.521 57.895 3.17 0.00 45.49 3.14
146 165 2.821366 GTAGCAGCAGCACGGCAT 60.821 61.111 3.17 0.00 45.49 4.40
147 166 2.237534 TATGTAGCAGCAGCACGGCA 62.238 55.000 3.17 0.00 45.49 5.69
204 223 4.144727 TCTCCCTCTCCCTCGGCC 62.145 72.222 0.00 0.00 0.00 6.13
348 375 3.106672 CTCTTTCGTACTCGTATGGTGC 58.893 50.000 0.00 0.00 38.33 5.01
394 421 0.533308 CGTCTACCCCCTCTCTCTCG 60.533 65.000 0.00 0.00 0.00 4.04
402 429 2.409870 CGCGTTACGTCTACCCCCT 61.410 63.158 6.63 0.00 36.87 4.79
490 541 7.233553 TCTCTCTCTCTCTCTCTCCAACTATAG 59.766 44.444 0.00 0.00 0.00 1.31
604 1022 4.222810 GGAAGAGAAGAGAGAGGAGCTTTT 59.777 45.833 0.00 0.00 0.00 2.27
605 1023 3.769300 GGAAGAGAAGAGAGAGGAGCTTT 59.231 47.826 0.00 0.00 0.00 3.51
606 1024 3.245586 TGGAAGAGAAGAGAGAGGAGCTT 60.246 47.826 0.00 0.00 0.00 3.74
607 1025 2.311542 TGGAAGAGAAGAGAGAGGAGCT 59.688 50.000 0.00 0.00 0.00 4.09
608 1026 2.733956 TGGAAGAGAAGAGAGAGGAGC 58.266 52.381 0.00 0.00 0.00 4.70
627 1056 1.760029 GGAAGGAGAGGGAGCTAGTTG 59.240 57.143 0.00 0.00 0.00 3.16
628 1057 1.343580 GGGAAGGAGAGGGAGCTAGTT 60.344 57.143 0.00 0.00 0.00 2.24
629 1058 0.263468 GGGAAGGAGAGGGAGCTAGT 59.737 60.000 0.00 0.00 0.00 2.57
838 1299 1.405821 GGCGGCGCTATATAGACAGAT 59.594 52.381 32.30 0.00 0.00 2.90
855 1316 2.290093 GGTGTAGTGCTAGTACTAGGCG 59.710 54.545 27.24 7.55 34.05 5.52
856 1317 3.553904 AGGTGTAGTGCTAGTACTAGGC 58.446 50.000 27.24 20.07 34.05 3.93
857 1318 3.808726 CGAGGTGTAGTGCTAGTACTAGG 59.191 52.174 27.24 12.18 34.05 3.02
861 1326 3.059733 CGATCGAGGTGTAGTGCTAGTAC 60.060 52.174 10.26 2.24 0.00 2.73
863 1328 1.941294 CGATCGAGGTGTAGTGCTAGT 59.059 52.381 10.26 0.00 0.00 2.57
873 1338 0.248661 CTGGTGCTACGATCGAGGTG 60.249 60.000 24.34 9.36 0.00 4.00
902 1367 1.562017 GGCGACTAGTAGCAAGAAGC 58.438 55.000 26.27 7.04 46.19 3.86
903 1368 1.534175 CCGGCGACTAGTAGCAAGAAG 60.534 57.143 26.27 12.91 32.66 2.85
904 1369 0.454600 CCGGCGACTAGTAGCAAGAA 59.545 55.000 26.27 0.00 32.66 2.52
906 1371 0.248539 GTCCGGCGACTAGTAGCAAG 60.249 60.000 26.27 19.23 35.99 4.01
907 1372 1.805254 GTCCGGCGACTAGTAGCAA 59.195 57.895 26.27 10.78 35.99 3.91
952 1424 2.776913 CGGTCTCCTCTCGGCTTCC 61.777 68.421 0.00 0.00 0.00 3.46
953 1425 1.720694 CTCGGTCTCCTCTCGGCTTC 61.721 65.000 0.00 0.00 0.00 3.86
954 1426 1.751162 CTCGGTCTCCTCTCGGCTT 60.751 63.158 0.00 0.00 0.00 4.35
955 1427 2.124487 CTCGGTCTCCTCTCGGCT 60.124 66.667 0.00 0.00 0.00 5.52
956 1428 3.213402 CCTCGGTCTCCTCTCGGC 61.213 72.222 0.00 0.00 0.00 5.54
963 1435 3.151022 CCTGCCTCCTCGGTCTCC 61.151 72.222 0.00 0.00 34.25 3.71
1056 1534 4.710167 GGGGTGTGGCGGTGGTAC 62.710 72.222 0.00 0.00 0.00 3.34
1077 1555 0.459078 CCTCGAGCTGCTGAATCTGA 59.541 55.000 7.01 0.00 0.00 3.27
1104 1582 1.407025 GGGGAAGGGACGAGTGAATTC 60.407 57.143 0.00 0.00 0.00 2.17
1105 1583 0.618981 GGGGAAGGGACGAGTGAATT 59.381 55.000 0.00 0.00 0.00 2.17
1106 1584 1.272554 GGGGGAAGGGACGAGTGAAT 61.273 60.000 0.00 0.00 0.00 2.57
1107 1585 1.916777 GGGGGAAGGGACGAGTGAA 60.917 63.158 0.00 0.00 0.00 3.18
1128 1606 2.826777 ATCAACAGAGGCAAGGGCGG 62.827 60.000 0.00 0.00 42.47 6.13
1129 1607 0.962356 AATCAACAGAGGCAAGGGCG 60.962 55.000 0.00 0.00 42.47 6.13
1130 1608 1.203287 GAAATCAACAGAGGCAAGGGC 59.797 52.381 0.00 0.00 40.13 5.19
1131 1609 2.800250 AGAAATCAACAGAGGCAAGGG 58.200 47.619 0.00 0.00 0.00 3.95
1132 1610 3.822735 TGAAGAAATCAACAGAGGCAAGG 59.177 43.478 0.00 0.00 34.30 3.61
1135 1613 4.828939 ACAATGAAGAAATCAACAGAGGCA 59.171 37.500 0.00 0.00 42.54 4.75
1136 1614 5.182760 AGACAATGAAGAAATCAACAGAGGC 59.817 40.000 0.00 0.00 42.54 4.70
1138 1616 7.670009 AGAGACAATGAAGAAATCAACAGAG 57.330 36.000 0.00 0.00 42.54 3.35
1139 1617 7.521099 GCAAGAGACAATGAAGAAATCAACAGA 60.521 37.037 0.00 0.00 42.54 3.41
1141 1619 6.263842 AGCAAGAGACAATGAAGAAATCAACA 59.736 34.615 0.00 0.00 42.54 3.33
1142 1620 6.675987 AGCAAGAGACAATGAAGAAATCAAC 58.324 36.000 0.00 0.00 42.54 3.18
1143 1621 6.487668 TGAGCAAGAGACAATGAAGAAATCAA 59.512 34.615 0.00 0.00 42.54 2.57
1145 1623 6.492007 TGAGCAAGAGACAATGAAGAAATC 57.508 37.500 0.00 0.00 0.00 2.17
1146 1624 6.885376 AGATGAGCAAGAGACAATGAAGAAAT 59.115 34.615 0.00 0.00 0.00 2.17
1147 1625 6.236409 AGATGAGCAAGAGACAATGAAGAAA 58.764 36.000 0.00 0.00 0.00 2.52
1148 1626 5.802465 AGATGAGCAAGAGACAATGAAGAA 58.198 37.500 0.00 0.00 0.00 2.52
1149 1627 5.417754 AGATGAGCAAGAGACAATGAAGA 57.582 39.130 0.00 0.00 0.00 2.87
1150 1628 5.875910 AGAAGATGAGCAAGAGACAATGAAG 59.124 40.000 0.00 0.00 0.00 3.02
1151 1629 5.642491 CAGAAGATGAGCAAGAGACAATGAA 59.358 40.000 0.00 0.00 0.00 2.57
1152 1630 5.176592 CAGAAGATGAGCAAGAGACAATGA 58.823 41.667 0.00 0.00 0.00 2.57
1153 1631 4.936411 ACAGAAGATGAGCAAGAGACAATG 59.064 41.667 0.00 0.00 0.00 2.82
1154 1632 4.936411 CACAGAAGATGAGCAAGAGACAAT 59.064 41.667 0.00 0.00 0.00 2.71
1155 1633 4.313282 CACAGAAGATGAGCAAGAGACAA 58.687 43.478 0.00 0.00 0.00 3.18
1156 1634 3.306571 CCACAGAAGATGAGCAAGAGACA 60.307 47.826 0.00 0.00 0.00 3.41
1187 1677 2.667874 TTGAACATCCTGCGCGCA 60.668 55.556 34.12 34.12 0.00 6.09
1319 1813 1.146359 ACATGGATGATGGGATGGGTG 59.854 52.381 0.00 0.00 36.23 4.61
1341 1849 1.669795 GGGTGAAAAAGATGGCTTGCG 60.670 52.381 0.00 0.00 33.79 4.85
1346 1854 2.222227 AGGAGGGTGAAAAAGATGGC 57.778 50.000 0.00 0.00 0.00 4.40
1367 1875 4.122776 CAGGAATCATCTCGTTCCGAAAT 58.877 43.478 0.00 0.00 46.68 2.17
1523 2031 1.301716 GCGGAGGAAGCAGTTGTCA 60.302 57.895 0.00 0.00 34.19 3.58
1718 2226 2.363925 GGGAGGCGGAGTGGTAGT 60.364 66.667 0.00 0.00 0.00 2.73
2262 2775 2.663119 GGATGTCAAAATGCAACGAAGC 59.337 45.455 0.00 0.00 0.00 3.86
2263 2776 3.899734 TGGATGTCAAAATGCAACGAAG 58.100 40.909 0.00 0.00 0.00 3.79
2370 2894 4.201679 CGCGCCCTGGTCACGATA 62.202 66.667 0.00 0.00 0.00 2.92
2461 2985 0.893727 ACCCGTGCAAAATGGACTCC 60.894 55.000 0.00 0.00 36.50 3.85
2810 3334 2.144730 GCAATGTGGCAAAGCAAATGA 58.855 42.857 0.00 0.00 0.00 2.57
2814 3338 0.317799 ATCGCAATGTGGCAAAGCAA 59.682 45.000 0.00 0.00 0.00 3.91
2816 3340 1.135699 CGATCGCAATGTGGCAAAGC 61.136 55.000 0.26 0.00 0.00 3.51
2824 3348 1.003839 ACACACCCGATCGCAATGT 60.004 52.632 10.32 10.30 0.00 2.71
2852 3383 1.323534 GACCGAACGATCAATTCCACG 59.676 52.381 0.00 0.00 0.00 4.94
3354 3885 3.314331 CGGGACACCTCCTGCACT 61.314 66.667 0.00 0.00 36.06 4.40
3387 3918 2.933287 ATGGAGTTGCCCGGGTGA 60.933 61.111 24.63 8.28 34.97 4.02
3476 4052 0.948623 CTGCATTCCGTCGAACACCA 60.949 55.000 0.00 0.00 0.00 4.17
3648 4224 2.679716 GGCAGGATGGTGAAGCCT 59.320 61.111 0.00 0.00 42.01 4.58
3651 4227 1.450312 GTCGGGCAGGATGGTGAAG 60.450 63.158 0.00 0.00 35.86 3.02
3896 4475 2.484241 GCCTTGAATGGGAATGAATGGC 60.484 50.000 0.00 0.00 0.00 4.40
3897 4476 2.223876 CGCCTTGAATGGGAATGAATGG 60.224 50.000 0.00 0.00 0.00 3.16
3919 4498 1.044231 AACCAACCAAAACCCCGGTC 61.044 55.000 0.00 0.00 33.17 4.79
4088 4670 1.895280 GAAGACGACGACGACGAGGT 61.895 60.000 25.15 10.76 42.66 3.85
4089 4671 1.225691 GAAGACGACGACGACGAGG 60.226 63.158 25.15 7.50 42.66 4.63
4090 4672 0.163360 AAGAAGACGACGACGACGAG 59.837 55.000 25.15 9.88 42.66 4.18
4091 4673 0.162507 GAAGAAGACGACGACGACGA 59.837 55.000 25.15 0.00 42.66 4.20
4092 4674 0.788645 GGAAGAAGACGACGACGACG 60.789 60.000 17.60 17.60 42.66 5.12
4093 4675 0.236711 TGGAAGAAGACGACGACGAC 59.763 55.000 15.32 8.08 42.66 4.34
4094 4676 0.236711 GTGGAAGAAGACGACGACGA 59.763 55.000 15.32 0.00 42.66 4.20
4215 4797 2.467962 TCGAGATCGAGACGTGCTT 58.532 52.632 0.00 0.00 44.22 3.91
4227 4809 2.704572 CAAAGCCTCCAACTTCGAGAT 58.295 47.619 0.00 0.00 0.00 2.75
4228 4810 1.878102 GCAAAGCCTCCAACTTCGAGA 60.878 52.381 0.00 0.00 0.00 4.04
4229 4811 0.519077 GCAAAGCCTCCAACTTCGAG 59.481 55.000 0.00 0.00 0.00 4.04
4230 4812 0.179032 TGCAAAGCCTCCAACTTCGA 60.179 50.000 0.00 0.00 0.00 3.71
4231 4813 0.883833 ATGCAAAGCCTCCAACTTCG 59.116 50.000 0.00 0.00 0.00 3.79
4232 4814 1.888512 TCATGCAAAGCCTCCAACTTC 59.111 47.619 0.00 0.00 0.00 3.01
4368 4956 4.899239 CTGCGGCGATGGGAGGAC 62.899 72.222 12.98 0.00 0.00 3.85
4378 4966 4.519437 TCATCCTCTGCTGCGGCG 62.519 66.667 13.96 0.51 42.25 6.46
4460 5064 6.551227 GGATACTATCTTGGGCAAAGGAAAAT 59.449 38.462 0.88 0.00 36.46 1.82
4532 6270 1.550327 AAGAGATCGACTCCACAGCA 58.450 50.000 10.24 0.00 45.96 4.41
4575 6313 3.117171 GCAGCGAGCAGGTCACAG 61.117 66.667 0.00 0.00 44.79 3.66
4687 6465 2.821810 GCGGGCTCTCCTTCAAGC 60.822 66.667 0.00 0.00 37.80 4.01
4707 6485 0.531532 CATTACAGCCTGCGCTAGCT 60.532 55.000 17.38 17.38 46.25 3.32
4708 6486 1.937391 CATTACAGCCTGCGCTAGC 59.063 57.895 9.73 11.92 46.25 3.42
4709 6487 1.937391 GCATTACAGCCTGCGCTAG 59.063 57.895 9.73 4.25 46.25 3.42
4710 6488 4.124910 GCATTACAGCCTGCGCTA 57.875 55.556 9.73 0.00 46.25 4.26
4802 6594 4.687483 CGACCCAACGACCCATATTAATAC 59.313 45.833 0.00 0.00 35.09 1.89


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

AutoCloner maintained by Alex Coulton.