Multiple sequence alignment - TraesCS5D01G545200

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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 TraesCS5D01G545200 chr5D 100.000 3699 0 0 1 3699 554473675 554477373 0.000000e+00 6831.0
1 TraesCS5D01G545200 chr5D 95.122 123 3 2 3424 3546 554476994 554477113 1.360000e-44 191.0
2 TraesCS5D01G545200 chr5D 95.122 123 3 2 3320 3439 554477098 554477220 1.360000e-44 191.0
3 TraesCS5D01G545200 chr5D 78.571 252 31 12 1423 1659 307392326 307392569 1.070000e-30 145.0
4 TraesCS5D01G545200 chr5D 96.970 33 1 0 2698 2730 412464740 412464772 5.160000e-04 56.5
5 TraesCS5D01G545200 chr5B 91.740 1925 70 44 1559 3439 696190110 696188231 0.000000e+00 2591.0
6 TraesCS5D01G545200 chr5B 85.455 1265 92 49 327 1528 696191869 696190634 0.000000e+00 1232.0
7 TraesCS5D01G545200 chr5B 98.551 276 4 0 3424 3699 696188353 696188078 4.290000e-134 488.0
8 TraesCS5D01G545200 chr5B 91.221 262 21 2 64 324 696192570 696192310 4.540000e-94 355.0
9 TraesCS5D01G545200 chr5B 100.000 35 0 0 2701 2735 508618261 508618227 8.570000e-07 65.8
10 TraesCS5D01G545200 chr4A 95.158 950 26 10 2055 2997 614107388 614106452 0.000000e+00 1482.0
11 TraesCS5D01G545200 chr4A 91.570 866 34 22 1125 1988 614108319 614107491 0.000000e+00 1158.0
12 TraesCS5D01G545200 chr4A 87.537 1027 73 18 327 1306 614109222 614108204 0.000000e+00 1136.0
13 TraesCS5D01G545200 chr4A 87.164 335 30 6 1 324 614109956 614109624 5.840000e-98 368.0
14 TraesCS5D01G545200 chr4A 84.452 283 37 5 3424 3699 614106241 614105959 4.710000e-69 272.0
15 TraesCS5D01G545200 chr4A 94.872 39 2 0 378 416 737180163 737180201 1.110000e-05 62.1
16 TraesCS5D01G545200 chr1B 83.408 223 25 5 1249 1464 39999135 39999352 2.910000e-46 196.0
17 TraesCS5D01G545200 chr1B 77.972 286 33 15 1389 1659 27275151 27275421 6.400000e-33 152.0
18 TraesCS5D01G545200 chr6D 78.322 286 32 15 1389 1659 349182898 349182628 1.380000e-34 158.0
19 TraesCS5D01G545200 chr6D 78.175 252 32 12 1423 1659 349020666 349020909 4.980000e-29 139.0
20 TraesCS5D01G545200 chr6D 77.922 231 26 17 1339 1559 349183139 349182924 1.800000e-23 121.0
21 TraesCS5D01G545200 chrUn 77.622 286 34 15 1389 1659 29486378 29486648 2.980000e-31 147.0
22 TraesCS5D01G545200 chrUn 77.778 225 25 17 1339 1553 29486137 29486346 8.390000e-22 115.0
23 TraesCS5D01G545200 chr3D 78.486 251 33 10 1423 1659 604728586 604728829 1.070000e-30 145.0
24 TraesCS5D01G545200 chr3D 78.175 252 32 12 1423 1659 433045226 433045469 4.980000e-29 139.0
25 TraesCS5D01G545200 chr3D 95.349 43 1 1 378 419 419929867 419929825 2.380000e-07 67.6
26 TraesCS5D01G545200 chr1A 78.696 230 25 17 1339 1559 5951254 5951468 8.340000e-27 132.0
27 TraesCS5D01G545200 chr2A 78.571 224 25 16 1339 1553 770215172 770215381 3.880000e-25 126.0
28 TraesCS5D01G545200 chr1D 77.729 229 30 16 1339 1559 393217807 393217592 1.800000e-23 121.0
29 TraesCS5D01G545200 chr7A 77.729 229 27 17 1340 1559 373292383 373292170 6.490000e-23 119.0
30 TraesCS5D01G545200 chr7A 100.000 36 0 0 2701 2736 586277323 586277358 2.380000e-07 67.6
31 TraesCS5D01G545200 chr7A 94.444 36 1 1 381 416 156101948 156101914 2.000000e-03 54.7
32 TraesCS5D01G545200 chr7A 94.286 35 1 1 2695 2728 78508299 78508333 7.000000e-03 52.8
33 TraesCS5D01G545200 chr5A 88.506 87 7 3 2997 3082 553463081 553463165 6.540000e-18 102.0
34 TraesCS5D01G545200 chr3A 88.506 87 7 3 2997 3082 63180621 63180537 6.540000e-18 102.0
35 TraesCS5D01G545200 chr3A 87.952 83 9 1 3001 3083 33422538 33422457 3.040000e-16 97.1
36 TraesCS5D01G545200 chr3A 88.732 71 7 1 3012 3082 15696156 15696087 6.580000e-13 86.1
37 TraesCS5D01G545200 chr3A 89.394 66 5 2 2997 3061 723564783 723564847 8.510000e-12 82.4
38 TraesCS5D01G545200 chr2B 85.542 83 9 3 2997 3078 308427348 308427428 2.370000e-12 84.2
39 TraesCS5D01G545200 chr2D 97.500 40 0 1 2701 2739 60617 60578 2.380000e-07 67.6
40 TraesCS5D01G545200 chr2D 97.143 35 0 1 2701 2735 94447319 94447352 1.430000e-04 58.4
41 TraesCS5D01G545200 chr3B 100.000 35 0 0 2699 2733 780341682 780341648 8.570000e-07 65.8
42 TraesCS5D01G545200 chr6B 97.222 36 1 0 381 416 437842062 437842027 1.110000e-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 TraesCS5D01G545200 chr5D 554473675 554477373 3698 False 2404.333333 6831 96.74800 1 3699 3 chr5D.!!$F3 3698
1 TraesCS5D01G545200 chr5B 696188078 696192570 4492 True 1166.500000 2591 91.74175 64 3699 4 chr5B.!!$R2 3635
2 TraesCS5D01G545200 chr4A 614105959 614109956 3997 True 883.200000 1482 89.17620 1 3699 5 chr4A.!!$R1 3698

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
657 1131 0.100325 TGCGGCAAATATGAAAGCGG 59.900 50.0 0.0 0.0 0.0 5.52 F
911 1396 0.178950 TCCCTCCTCTCCATCCATCG 60.179 60.0 0.0 0.0 0.0 3.84 F
1586 2678 0.313672 TCCTGAATTTTGTGGCGTGC 59.686 50.0 0.0 0.0 0.0 5.34 F
1991 3083 0.530650 CCGCCATGATGAAGTACGCT 60.531 55.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 2688 0.032515 TCCTTGATGCTCGGGTCCTA 60.033 55.000 0.00 0.0 0.00 2.94 R
2141 3269 0.174617 CTCCTCCTCTGCTTCGGTTC 59.825 60.000 0.00 0.0 0.00 3.62 R
2562 3708 1.015109 TCGAGCTCCATCGTCAGTAC 58.985 55.000 8.47 0.0 43.20 2.73 R
2983 4152 1.288932 AGGTGGCAGCCCAAGATAAAT 59.711 47.619 13.95 0.0 44.33 1.40 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
72 73 8.967552 AACTGAAACTAGTACTAAAGATGACG 57.032 34.615 3.76 0.00 0.00 4.35
73 74 7.536855 ACTGAAACTAGTACTAAAGATGACGG 58.463 38.462 3.76 0.95 0.00 4.79
76 77 8.454106 TGAAACTAGTACTAAAGATGACGGTAC 58.546 37.037 3.76 0.00 34.69 3.34
79 80 7.563906 ACTAGTACTAAAGATGACGGTACTCT 58.436 38.462 3.76 0.00 41.09 3.24
84 85 4.602340 AAAGATGACGGTACTCTGTGTT 57.398 40.909 0.00 0.00 32.75 3.32
170 171 3.752665 TCCTCGATCGGCTTATAAGACT 58.247 45.455 16.85 0.00 0.00 3.24
171 172 4.903054 TCCTCGATCGGCTTATAAGACTA 58.097 43.478 16.85 5.78 0.00 2.59
186 187 9.209175 CTTATAAGACTAAGCCCATGTGTATTC 57.791 37.037 6.64 0.00 0.00 1.75
189 190 4.716784 AGACTAAGCCCATGTGTATTCTCA 59.283 41.667 0.00 0.00 0.00 3.27
193 194 2.092212 AGCCCATGTGTATTCTCAAGGG 60.092 50.000 9.57 9.57 44.18 3.95
217 218 1.005687 ACTAGGGCTTAGTCGACCTGT 59.994 52.381 13.01 0.00 38.20 4.00
220 221 2.100989 AGGGCTTAGTCGACCTGTAAG 58.899 52.381 13.01 14.42 30.71 2.34
333 781 6.373186 AAAGTACAAAGTACAAAGTGCCTC 57.627 37.500 9.68 0.00 0.00 4.70
401 860 4.463879 CCGGAGTGGCAGGCAGAG 62.464 72.222 0.00 0.00 0.00 3.35
402 861 4.463879 CGGAGTGGCAGGCAGAGG 62.464 72.222 0.00 0.00 0.00 3.69
403 862 4.106925 GGAGTGGCAGGCAGAGGG 62.107 72.222 0.00 0.00 0.00 4.30
404 863 4.106925 GAGTGGCAGGCAGAGGGG 62.107 72.222 0.00 0.00 0.00 4.79
405 864 4.664267 AGTGGCAGGCAGAGGGGA 62.664 66.667 0.00 0.00 0.00 4.81
406 865 4.106925 GTGGCAGGCAGAGGGGAG 62.107 72.222 0.00 0.00 0.00 4.30
409 868 3.478274 GCAGGCAGAGGGGAGGAG 61.478 72.222 0.00 0.00 0.00 3.69
410 869 2.366167 CAGGCAGAGGGGAGGAGA 59.634 66.667 0.00 0.00 0.00 3.71
411 870 1.306482 CAGGCAGAGGGGAGGAGAA 60.306 63.158 0.00 0.00 0.00 2.87
448 907 1.050988 TGGAGCTATGAGGGGAGCAC 61.051 60.000 0.00 0.00 41.36 4.40
458 917 2.574018 GGGGAGCACAACTTTGCCC 61.574 63.158 0.00 0.00 44.14 5.36
656 1130 2.124011 ATGCGGCAAATATGAAAGCG 57.876 45.000 6.82 0.00 0.00 4.68
657 1131 0.100325 TGCGGCAAATATGAAAGCGG 59.900 50.000 0.00 0.00 0.00 5.52
658 1132 0.380378 GCGGCAAATATGAAAGCGGA 59.620 50.000 0.00 0.00 0.00 5.54
659 1133 1.597937 GCGGCAAATATGAAAGCGGAG 60.598 52.381 0.00 0.00 0.00 4.63
726 1201 7.921786 TCCTGTGGTAAATGAACATTCTTAG 57.078 36.000 0.45 0.00 0.00 2.18
793 1269 7.326968 TGTTGTAAATCAAAGTGATGTGTCA 57.673 32.000 0.00 0.00 37.15 3.58
797 1273 9.814899 TTGTAAATCAAAGTGATGTGTCAAAAT 57.185 25.926 0.00 0.00 37.15 1.82
798 1274 9.814899 TGTAAATCAAAGTGATGTGTCAAAATT 57.185 25.926 0.00 0.00 37.15 1.82
863 1339 1.840198 ACCGGGAAAAGGAGACCGT 60.840 57.895 6.32 0.00 44.57 4.83
911 1396 0.178950 TCCCTCCTCTCCATCCATCG 60.179 60.000 0.00 0.00 0.00 3.84
1008 1515 3.381983 TCGCTCGACATGGCCACT 61.382 61.111 8.16 0.00 0.00 4.00
1018 1525 1.705186 ACATGGCCACTACTCAAGGTT 59.295 47.619 8.16 0.00 0.00 3.50
1026 1533 2.100989 ACTACTCAAGGTTAGGAGCCG 58.899 52.381 0.00 0.00 34.48 5.52
1030 1537 1.412710 CTCAAGGTTAGGAGCCGCATA 59.587 52.381 0.00 0.00 0.00 3.14
1033 1540 2.808543 CAAGGTTAGGAGCCGCATATTC 59.191 50.000 0.00 0.00 0.00 1.75
1092 1626 4.443978 TTGGGGAGATGATGGAGAAATC 57.556 45.455 0.00 0.00 0.00 2.17
1093 1627 3.673343 TGGGGAGATGATGGAGAAATCT 58.327 45.455 0.00 0.00 33.36 2.40
1094 1628 4.050037 TGGGGAGATGATGGAGAAATCTT 58.950 43.478 0.00 0.00 30.83 2.40
1172 1770 4.760047 CAGCCTTCCCCCACGTCG 62.760 72.222 0.00 0.00 0.00 5.12
1412 2010 4.566004 ACTTGCTCAACGTAATCAAGCTA 58.434 39.130 15.21 5.91 38.06 3.32
1413 2011 4.389077 ACTTGCTCAACGTAATCAAGCTAC 59.611 41.667 15.21 0.00 38.06 3.58
1414 2012 3.920446 TGCTCAACGTAATCAAGCTACA 58.080 40.909 0.00 0.00 34.11 2.74
1415 2013 3.678072 TGCTCAACGTAATCAAGCTACAC 59.322 43.478 0.00 0.00 34.11 2.90
1416 2014 3.927142 GCTCAACGTAATCAAGCTACACT 59.073 43.478 0.00 0.00 0.00 3.55
1417 2015 4.201628 GCTCAACGTAATCAAGCTACACTG 60.202 45.833 0.00 0.00 0.00 3.66
1418 2016 5.128992 TCAACGTAATCAAGCTACACTGA 57.871 39.130 0.00 0.00 0.00 3.41
1419 2017 5.534407 TCAACGTAATCAAGCTACACTGAA 58.466 37.500 0.00 0.00 0.00 3.02
1420 2018 6.163476 TCAACGTAATCAAGCTACACTGAAT 58.837 36.000 0.00 0.00 0.00 2.57
1421 2019 6.649141 TCAACGTAATCAAGCTACACTGAATT 59.351 34.615 0.00 0.00 0.00 2.17
1433 2031 5.798934 GCTACACTGAATTCTGAAGCATTTG 59.201 40.000 18.13 7.20 0.00 2.32
1475 2074 5.377358 CAATACTCTGTTTTGCTCTGTTCG 58.623 41.667 0.00 0.00 0.00 3.95
1482 2081 4.799678 TGTTTTGCTCTGTTCGTTTCAAA 58.200 34.783 0.00 0.00 0.00 2.69
1483 2082 5.406649 TGTTTTGCTCTGTTCGTTTCAAAT 58.593 33.333 0.00 0.00 0.00 2.32
1485 2084 6.690957 TGTTTTGCTCTGTTCGTTTCAAATAG 59.309 34.615 0.00 0.00 0.00 1.73
1486 2085 6.371809 TTTGCTCTGTTCGTTTCAAATAGT 57.628 33.333 0.00 0.00 0.00 2.12
1488 2087 7.667043 TTGCTCTGTTCGTTTCAAATAGTAT 57.333 32.000 0.00 0.00 0.00 2.12
1489 2088 7.060600 TGCTCTGTTCGTTTCAAATAGTATG 57.939 36.000 0.00 0.00 0.00 2.39
1490 2089 6.871492 TGCTCTGTTCGTTTCAAATAGTATGA 59.129 34.615 0.00 0.00 0.00 2.15
1491 2090 7.063426 TGCTCTGTTCGTTTCAAATAGTATGAG 59.937 37.037 0.00 0.00 0.00 2.90
1492 2091 7.275779 GCTCTGTTCGTTTCAAATAGTATGAGA 59.724 37.037 0.00 0.00 0.00 3.27
1493 2092 9.307121 CTCTGTTCGTTTCAAATAGTATGAGAT 57.693 33.333 0.00 0.00 0.00 2.75
1494 2093 9.653287 TCTGTTCGTTTCAAATAGTATGAGATT 57.347 29.630 0.00 0.00 0.00 2.40
1533 2605 5.777802 TGTATGCAAATTTGAATCGGTTGT 58.222 33.333 22.31 0.00 0.00 3.32
1561 2633 3.059188 TGCTTCGATTTCACGGAAGAAAC 60.059 43.478 4.34 0.00 40.03 2.78
1586 2678 0.313672 TCCTGAATTTTGTGGCGTGC 59.686 50.000 0.00 0.00 0.00 5.34
1859 2951 2.501610 GCCATGTCCTCCGTCCTC 59.498 66.667 0.00 0.00 0.00 3.71
1988 3080 1.498865 CCGCCGCCATGATGAAGTAC 61.499 60.000 0.00 0.00 0.00 2.73
1989 3081 1.821241 CGCCGCCATGATGAAGTACG 61.821 60.000 0.00 0.00 0.00 3.67
1991 3083 0.530650 CCGCCATGATGAAGTACGCT 60.531 55.000 0.00 0.00 0.00 5.07
1995 3087 2.477825 CCATGATGAAGTACGCTCCTG 58.522 52.381 0.00 0.00 0.00 3.86
1996 3088 2.101415 CCATGATGAAGTACGCTCCTGA 59.899 50.000 0.00 0.00 0.00 3.86
1997 3089 3.430790 CCATGATGAAGTACGCTCCTGAA 60.431 47.826 0.00 0.00 0.00 3.02
1998 3090 3.232213 TGATGAAGTACGCTCCTGAAC 57.768 47.619 0.00 0.00 0.00 3.18
2005 3097 2.826128 AGTACGCTCCTGAACATCTTCA 59.174 45.455 0.00 0.00 35.04 3.02
2006 3098 3.449018 AGTACGCTCCTGAACATCTTCAT 59.551 43.478 0.00 0.00 35.78 2.57
2007 3099 3.340814 ACGCTCCTGAACATCTTCATT 57.659 42.857 0.00 0.00 35.78 2.57
2008 3100 3.679389 ACGCTCCTGAACATCTTCATTT 58.321 40.909 0.00 0.00 35.78 2.32
2010 3102 3.686241 CGCTCCTGAACATCTTCATTTCA 59.314 43.478 0.00 0.00 35.78 2.69
2015 3130 6.487828 TCCTGAACATCTTCATTTCATTCCT 58.512 36.000 0.00 0.00 35.78 3.36
2017 3132 6.183360 CCTGAACATCTTCATTTCATTCCTCC 60.183 42.308 0.00 0.00 35.78 4.30
2018 3133 5.355071 TGAACATCTTCATTTCATTCCTCCG 59.645 40.000 0.00 0.00 31.00 4.63
2019 3134 4.202441 ACATCTTCATTTCATTCCTCCGG 58.798 43.478 0.00 0.00 0.00 5.14
2022 3137 0.539518 TCATTTCATTCCTCCGGCGA 59.460 50.000 9.30 0.00 0.00 5.54
2166 3294 2.183679 GAAGCAGAGGAGGAGGAAGAA 58.816 52.381 0.00 0.00 0.00 2.52
2202 3330 0.708802 AAGGGGAGTACGAGGAGGAA 59.291 55.000 0.00 0.00 0.00 3.36
2546 3692 3.485431 CCTGCTTGCTCGCTGACG 61.485 66.667 6.33 0.00 42.01 4.35
2904 4073 8.624776 GGTAGAATTTATCTGGTTTCTGGATTG 58.375 37.037 0.00 0.00 39.30 2.67
3099 4268 5.520022 TCTTCGTGGTTTATTTCGTAAGC 57.480 39.130 0.00 0.00 37.18 3.09
3136 4306 6.317789 TGCATCTTACCTTTTGTTTCTCTG 57.682 37.500 0.00 0.00 0.00 3.35
3263 4435 3.494398 GGCGAGCCTTATATCTTTGGACA 60.494 47.826 6.90 0.00 0.00 4.02
3312 4484 5.957910 AAGCGAGATGAAAGTCTATTTCG 57.042 39.130 0.00 0.00 34.99 3.46
3420 4592 8.873215 CTTATATAGGACATAAACCGGCTATG 57.127 38.462 18.26 18.26 33.71 2.23
3421 4593 8.598202 TTATATAGGACATAAACCGGCTATGA 57.402 34.615 24.07 7.98 32.20 2.15
3422 4594 3.753294 AGGACATAAACCGGCTATGAG 57.247 47.619 24.07 5.22 32.20 2.90
3423 4595 3.305720 AGGACATAAACCGGCTATGAGA 58.694 45.455 24.07 0.00 32.20 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.254470 TGAATTTTGATGCCATGCTGG 57.746 42.857 0.00 0.00 41.55 4.85
17 18 3.998341 AGTGTTGAATTTTGATGCCATGC 59.002 39.130 0.00 0.00 0.00 4.06
51 52 8.672815 AGTACCGTCATCTTTAGTACTAGTTTC 58.327 37.037 0.00 0.00 41.28 2.78
53 54 8.046107 AGAGTACCGTCATCTTTAGTACTAGTT 58.954 37.037 0.00 0.00 42.68 2.24
55 56 7.495279 ACAGAGTACCGTCATCTTTAGTACTAG 59.505 40.741 2.23 0.00 42.68 2.57
62 63 5.717078 AACACAGAGTACCGTCATCTTTA 57.283 39.130 0.00 0.00 0.00 1.85
72 73 5.497474 ACATCCCATTTAACACAGAGTACC 58.503 41.667 0.00 0.00 0.00 3.34
73 74 7.448748 AAACATCCCATTTAACACAGAGTAC 57.551 36.000 0.00 0.00 0.00 2.73
76 77 7.661040 AGAAAAACATCCCATTTAACACAGAG 58.339 34.615 0.00 0.00 0.00 3.35
79 80 7.925483 CAGAAGAAAAACATCCCATTTAACACA 59.075 33.333 0.00 0.00 0.00 3.72
84 85 7.818930 GCATTCAGAAGAAAAACATCCCATTTA 59.181 33.333 0.00 0.00 37.29 1.40
170 171 4.385199 CCCTTGAGAATACACATGGGCTTA 60.385 45.833 0.00 0.00 41.87 3.09
171 172 3.624777 CCTTGAGAATACACATGGGCTT 58.375 45.455 0.00 0.00 31.80 4.35
186 187 0.618968 AGCCCTAGTCACCCCTTGAG 60.619 60.000 0.00 0.00 33.71 3.02
189 190 1.080666 ACTAAGCCCTAGTCACCCCTT 59.919 52.381 0.00 0.00 35.90 3.95
324 334 0.475906 AGAGCTGGTTGAGGCACTTT 59.524 50.000 0.00 0.00 41.55 2.66
325 335 0.036022 GAGAGCTGGTTGAGGCACTT 59.964 55.000 0.00 0.00 41.55 3.16
401 860 1.135960 CCTCTTGGATTCTCCTCCCC 58.864 60.000 0.00 0.00 37.46 4.81
402 861 1.488393 CACCTCTTGGATTCTCCTCCC 59.512 57.143 0.00 0.00 37.46 4.30
403 862 2.998316 CACCTCTTGGATTCTCCTCC 57.002 55.000 0.00 0.00 37.46 4.30
416 875 2.765807 CTCCATCGGGCCACCTCT 60.766 66.667 4.39 0.00 33.28 3.69
424 883 1.548357 CCCCTCATAGCTCCATCGGG 61.548 65.000 0.00 0.00 0.00 5.14
448 907 2.700773 GGCGGCTAGGGCAAAGTTG 61.701 63.158 0.00 0.00 40.87 3.16
458 917 3.280920 CTTGAGCTAAGGCGGCTAG 57.719 57.895 13.71 11.28 44.37 3.42
501 960 9.643693 ATTTAAAAATTATGGCAGACAAGACAG 57.356 29.630 0.00 0.00 0.00 3.51
593 1063 2.304761 TGCCTAGGAGAAAACGAATGGT 59.695 45.455 14.75 0.00 0.00 3.55
700 1175 7.595819 AAGAATGTTCATTTACCACAGGAAA 57.404 32.000 0.00 0.00 0.00 3.13
704 1179 7.383102 AGCTAAGAATGTTCATTTACCACAG 57.617 36.000 0.00 0.00 0.00 3.66
793 1269 2.295070 ACGCTTGGCCGACTAAAATTTT 59.705 40.909 8.75 8.75 0.00 1.82
797 1273 0.589223 CAACGCTTGGCCGACTAAAA 59.411 50.000 0.00 0.00 0.00 1.52
798 1274 1.847890 GCAACGCTTGGCCGACTAAA 61.848 55.000 0.00 0.00 0.00 1.85
863 1339 0.032615 ACCAACCAAAGCCAACCAGA 60.033 50.000 0.00 0.00 0.00 3.86
911 1396 2.576615 GGAAGATGATAAGGTGGTGGC 58.423 52.381 0.00 0.00 0.00 5.01
1008 1515 0.822164 GCGGCTCCTAACCTTGAGTA 59.178 55.000 0.00 0.00 0.00 2.59
1026 1533 4.084011 AGAAGGAAGCAGGAGAATATGC 57.916 45.455 0.00 0.00 42.87 3.14
1030 1537 2.025510 CCCAAGAAGGAAGCAGGAGAAT 60.026 50.000 0.00 0.00 41.22 2.40
1033 1540 0.695347 ACCCAAGAAGGAAGCAGGAG 59.305 55.000 0.00 0.00 41.22 3.69
1092 1626 2.806608 ACAATCCACAAGCAAGCAAG 57.193 45.000 0.00 0.00 0.00 4.01
1093 1627 3.196463 CAAACAATCCACAAGCAAGCAA 58.804 40.909 0.00 0.00 0.00 3.91
1094 1628 2.483363 CCAAACAATCCACAAGCAAGCA 60.483 45.455 0.00 0.00 0.00 3.91
1178 1776 2.896443 GTCTTCTCCTCTGCCGGG 59.104 66.667 2.18 0.00 0.00 5.73
1184 1782 1.363145 CGACGCTCGTCTTCTCCTCT 61.363 60.000 18.51 0.00 42.54 3.69
1203 1801 2.896443 CTCCTCCTCCGCCTTGAC 59.104 66.667 0.00 0.00 0.00 3.18
1204 1802 3.077556 GCTCCTCCTCCGCCTTGA 61.078 66.667 0.00 0.00 0.00 3.02
1205 1803 4.168291 GGCTCCTCCTCCGCCTTG 62.168 72.222 0.00 0.00 40.62 3.61
1211 1809 2.770475 GGGGAAGGCTCCTCCTCC 60.770 72.222 5.26 0.00 46.94 4.30
1412 2010 4.038282 TGCAAATGCTTCAGAATTCAGTGT 59.962 37.500 8.44 0.00 42.66 3.55
1413 2011 4.552355 TGCAAATGCTTCAGAATTCAGTG 58.448 39.130 8.44 0.00 42.66 3.66
1414 2012 4.280174 ACTGCAAATGCTTCAGAATTCAGT 59.720 37.500 8.44 0.00 42.66 3.41
1415 2013 4.806330 ACTGCAAATGCTTCAGAATTCAG 58.194 39.130 8.44 0.00 42.66 3.02
1416 2014 4.859304 ACTGCAAATGCTTCAGAATTCA 57.141 36.364 8.44 0.00 42.66 2.57
1417 2015 5.924825 AGAAACTGCAAATGCTTCAGAATTC 59.075 36.000 6.97 0.00 42.66 2.17
1418 2016 5.694910 CAGAAACTGCAAATGCTTCAGAATT 59.305 36.000 6.97 0.00 42.66 2.17
1419 2017 5.227908 CAGAAACTGCAAATGCTTCAGAAT 58.772 37.500 6.97 0.00 42.66 2.40
1420 2018 4.613944 CAGAAACTGCAAATGCTTCAGAA 58.386 39.130 6.97 0.00 42.66 3.02
1421 2019 4.233123 CAGAAACTGCAAATGCTTCAGA 57.767 40.909 6.97 0.00 42.66 3.27
1513 2112 7.903995 ATTAACAACCGATTCAAATTTGCAT 57.096 28.000 13.54 8.24 0.00 3.96
1515 2114 8.420807 CAAATTAACAACCGATTCAAATTTGC 57.579 30.769 13.54 0.00 36.57 3.68
1533 2605 5.614923 TCCGTGAAATCGAAGCAAATTAA 57.385 34.783 0.00 0.00 0.00 1.40
1561 2633 3.922240 CGCCACAAAATTCAGGATTCAAG 59.078 43.478 0.00 0.00 0.00 3.02
1586 2678 2.264794 GGGTCCTACAGTGCACGG 59.735 66.667 15.82 15.82 0.00 4.94
1596 2688 0.032515 TCCTTGATGCTCGGGTCCTA 60.033 55.000 0.00 0.00 0.00 2.94
1988 3080 3.686241 TGAAATGAAGATGTTCAGGAGCG 59.314 43.478 11.32 0.00 45.96 5.03
1989 3081 5.831702 ATGAAATGAAGATGTTCAGGAGC 57.168 39.130 11.32 1.81 45.96 4.70
1991 3083 6.487828 AGGAATGAAATGAAGATGTTCAGGA 58.512 36.000 11.32 0.00 45.96 3.86
1995 3087 5.814783 CGGAGGAATGAAATGAAGATGTTC 58.185 41.667 0.00 0.00 0.00 3.18
1996 3088 5.824904 CGGAGGAATGAAATGAAGATGTT 57.175 39.130 0.00 0.00 0.00 2.71
2015 3130 1.514657 CGTTAATGTCGTCGCCGGA 60.515 57.895 5.05 0.00 33.95 5.14
2017 3132 2.992313 CCGTTAATGTCGTCGCCG 59.008 61.111 0.00 0.00 0.00 6.46
2018 3133 2.699212 GCCGTTAATGTCGTCGCC 59.301 61.111 0.00 0.00 0.00 5.54
2019 3134 2.153945 TCGCCGTTAATGTCGTCGC 61.154 57.895 0.00 0.00 30.10 5.19
2022 3137 1.802715 CGGTCGCCGTTAATGTCGT 60.803 57.895 9.69 0.00 42.73 4.34
2024 3139 1.416050 GACCGGTCGCCGTTAATGTC 61.416 60.000 20.85 11.39 46.80 3.06
2025 3140 1.446618 GACCGGTCGCCGTTAATGT 60.447 57.895 20.85 7.06 46.80 2.71
2027 3142 2.202650 CGACCGGTCGCCGTTAAT 60.203 61.111 40.78 0.00 46.80 1.40
2037 3152 3.056107 TGAATTCAGAAAGATCGACCGGT 60.056 43.478 6.92 6.92 0.00 5.28
2038 3153 3.521560 TGAATTCAGAAAGATCGACCGG 58.478 45.455 3.38 0.00 0.00 5.28
2041 3156 6.254589 CAGTACCTGAATTCAGAAAGATCGAC 59.745 42.308 32.49 17.79 46.59 4.20
2044 3159 6.644347 TCCAGTACCTGAATTCAGAAAGATC 58.356 40.000 32.49 17.03 46.59 2.75
2050 3165 3.830178 TCGTTCCAGTACCTGAATTCAGA 59.170 43.478 32.49 14.21 46.59 3.27
2051 3166 3.927142 GTCGTTCCAGTACCTGAATTCAG 59.073 47.826 25.75 25.75 43.40 3.02
2053 3168 3.259902 GGTCGTTCCAGTACCTGAATTC 58.740 50.000 0.00 0.00 32.44 2.17
2139 3267 1.153745 CTCCTCTGCTTCGGTTCCG 60.154 63.158 4.74 4.74 0.00 4.30
2141 3269 0.174617 CTCCTCCTCTGCTTCGGTTC 59.825 60.000 0.00 0.00 0.00 3.62
2143 3271 1.684049 CCTCCTCCTCTGCTTCGGT 60.684 63.158 0.00 0.00 0.00 4.69
2148 3276 1.078656 ACTTCTTCCTCCTCCTCTGCT 59.921 52.381 0.00 0.00 0.00 4.24
2166 3294 3.469863 TTCCTCGCCGGCAACAACT 62.470 57.895 28.98 0.00 0.00 3.16
2202 3330 1.620819 GCCGTCTGGTGGATGATAGAT 59.379 52.381 0.00 0.00 37.67 1.98
2265 3393 3.220999 CTCGTCCTTGTCCACGCCA 62.221 63.158 0.00 0.00 35.93 5.69
2562 3708 1.015109 TCGAGCTCCATCGTCAGTAC 58.985 55.000 8.47 0.00 43.20 2.73
2713 3864 3.730761 GATGGCGATGGCGATGGC 61.731 66.667 7.17 7.17 37.76 4.40
2714 3865 3.417224 CGATGGCGATGGCGATGG 61.417 66.667 1.13 0.00 37.76 3.51
2715 3866 4.081030 GCGATGGCGATGGCGATG 62.081 66.667 1.13 0.00 37.76 3.84
2726 3877 1.512996 GACTGATGGCATGGCGATGG 61.513 60.000 15.27 7.58 0.00 3.51
2728 3879 1.596203 CGACTGATGGCATGGCGAT 60.596 57.895 15.27 9.18 0.00 4.58
2826 3987 4.377839 TGAATTACAGCCGAAGAGAGAG 57.622 45.455 0.00 0.00 0.00 3.20
2983 4152 1.288932 AGGTGGCAGCCCAAGATAAAT 59.711 47.619 13.95 0.00 44.33 1.40
3099 4268 4.346734 AAGATGCAAGCACAGAAATACG 57.653 40.909 0.00 0.00 0.00 3.06
3165 4335 5.116084 ACATATAGTGGTTTCACAGGCAT 57.884 39.130 0.00 0.00 45.91 4.40
3251 4423 4.755266 AGTAACCGCTGTCCAAAGATAT 57.245 40.909 0.00 0.00 0.00 1.63
3395 4567 8.692710 TCATAGCCGGTTTATGTCCTATATAAG 58.307 37.037 20.44 1.25 31.85 1.73
3396 4568 8.598202 TCATAGCCGGTTTATGTCCTATATAA 57.402 34.615 20.44 3.51 31.85 0.98
3397 4569 8.057011 TCTCATAGCCGGTTTATGTCCTATATA 58.943 37.037 20.44 5.43 31.85 0.86
3398 4570 6.895756 TCTCATAGCCGGTTTATGTCCTATAT 59.104 38.462 20.44 0.00 31.85 0.86
3399 4571 6.250711 TCTCATAGCCGGTTTATGTCCTATA 58.749 40.000 20.44 6.45 31.85 1.31
3400 4572 5.084519 TCTCATAGCCGGTTTATGTCCTAT 58.915 41.667 20.44 7.73 31.85 2.57
3401 4573 4.476297 TCTCATAGCCGGTTTATGTCCTA 58.524 43.478 20.44 5.98 31.85 2.94
3402 4574 3.305720 TCTCATAGCCGGTTTATGTCCT 58.694 45.455 20.44 4.12 31.85 3.85
3403 4575 3.746045 TCTCATAGCCGGTTTATGTCC 57.254 47.619 20.44 0.00 31.85 4.02
3404 4576 4.883083 TGATCTCATAGCCGGTTTATGTC 58.117 43.478 20.44 14.35 31.85 3.06
3405 4577 4.955811 TGATCTCATAGCCGGTTTATGT 57.044 40.909 20.44 8.07 31.85 2.29
3406 4578 6.035005 CGTAATGATCTCATAGCCGGTTTATG 59.965 42.308 17.17 17.17 35.10 1.90
3407 4579 6.071560 TCGTAATGATCTCATAGCCGGTTTAT 60.072 38.462 1.90 0.00 35.10 1.40
3408 4580 5.242171 TCGTAATGATCTCATAGCCGGTTTA 59.758 40.000 1.90 0.00 35.10 2.01
3409 4581 4.038763 TCGTAATGATCTCATAGCCGGTTT 59.961 41.667 1.90 0.00 35.10 3.27
3410 4582 3.572682 TCGTAATGATCTCATAGCCGGTT 59.427 43.478 1.90 0.00 35.10 4.44
3411 4583 3.154710 TCGTAATGATCTCATAGCCGGT 58.845 45.455 1.90 0.00 35.10 5.28
3412 4584 3.850122 TCGTAATGATCTCATAGCCGG 57.150 47.619 0.00 0.00 35.10 6.13
3413 4585 8.560374 TCTATAATCGTAATGATCTCATAGCCG 58.440 37.037 0.00 0.00 35.84 5.52
3414 4586 9.672086 GTCTATAATCGTAATGATCTCATAGCC 57.328 37.037 0.00 0.00 35.84 3.93


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

AutoCloner maintained by Alex Coulton.