Multiple sequence alignment - TraesCS5A01G350300

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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 TraesCS5A01G350300 chr5A 100.000 2498 0 0 1 2498 553098456 553095959 0.000000e+00 4614.0
1 TraesCS5A01G350300 chr6A 97.353 1020 21 4 1482 2498 234065300 234064284 0.000000e+00 1729.0
2 TraesCS5A01G350300 chr6A 97.047 1016 26 3 1486 2498 208573935 208574949 0.000000e+00 1707.0
3 TraesCS5A01G350300 chr6A 96.961 1020 25 4 1482 2498 268847696 268846680 0.000000e+00 1707.0
4 TraesCS5A01G350300 chr6A 96.866 1021 27 4 1482 2498 241768487 241767468 0.000000e+00 1703.0
5 TraesCS5A01G350300 chr2A 97.056 1019 27 2 1482 2497 128817104 128816086 0.000000e+00 1712.0
6 TraesCS5A01G350300 chr4A 96.866 1021 29 2 1480 2498 576322400 576323419 0.000000e+00 1705.0
7 TraesCS5A01G350300 chr4A 96.676 1023 29 3 1479 2498 325774654 325775674 0.000000e+00 1696.0
8 TraesCS5A01G350300 chr4A 78.488 172 35 2 1141 1311 725785706 725785536 7.300000e-21 111.0
9 TraesCS5A01G350300 chr3A 96.866 1021 26 4 1482 2498 207300972 207299954 0.000000e+00 1703.0
10 TraesCS5A01G350300 chr1A 96.863 1020 29 2 1482 2498 404753912 404754931 0.000000e+00 1703.0
11 TraesCS5A01G350300 chr5D 90.582 807 52 9 1 786 438151473 438150670 0.000000e+00 1048.0
12 TraesCS5A01G350300 chr7B 82.378 698 114 9 790 1483 713133785 713134477 1.280000e-167 599.0
13 TraesCS5A01G350300 chr5B 85.326 552 45 19 4 522 532702840 532702292 2.830000e-149 538.0
14 TraesCS5A01G350300 chr5B 91.549 71 2 4 655 724 532700958 532700891 7.360000e-16 95.3
15 TraesCS5A01G350300 chr2B 78.107 169 35 2 1141 1308 753634536 753634703 3.400000e-19 106.0
16 TraesCS5A01G350300 chr2B 94.444 36 2 0 324 359 215851811 215851776 3.470000e-04 56.5


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 TraesCS5A01G350300 chr5A 553095959 553098456 2497 True 4614.00 4614 100.0000 1 2498 1 chr5A.!!$R1 2497
1 TraesCS5A01G350300 chr6A 234064284 234065300 1016 True 1729.00 1729 97.3530 1482 2498 1 chr6A.!!$R1 1016
2 TraesCS5A01G350300 chr6A 208573935 208574949 1014 False 1707.00 1707 97.0470 1486 2498 1 chr6A.!!$F1 1012
3 TraesCS5A01G350300 chr6A 268846680 268847696 1016 True 1707.00 1707 96.9610 1482 2498 1 chr6A.!!$R3 1016
4 TraesCS5A01G350300 chr6A 241767468 241768487 1019 True 1703.00 1703 96.8660 1482 2498 1 chr6A.!!$R2 1016
5 TraesCS5A01G350300 chr2A 128816086 128817104 1018 True 1712.00 1712 97.0560 1482 2497 1 chr2A.!!$R1 1015
6 TraesCS5A01G350300 chr4A 576322400 576323419 1019 False 1705.00 1705 96.8660 1480 2498 1 chr4A.!!$F2 1018
7 TraesCS5A01G350300 chr4A 325774654 325775674 1020 False 1696.00 1696 96.6760 1479 2498 1 chr4A.!!$F1 1019
8 TraesCS5A01G350300 chr3A 207299954 207300972 1018 True 1703.00 1703 96.8660 1482 2498 1 chr3A.!!$R1 1016
9 TraesCS5A01G350300 chr1A 404753912 404754931 1019 False 1703.00 1703 96.8630 1482 2498 1 chr1A.!!$F1 1016
10 TraesCS5A01G350300 chr5D 438150670 438151473 803 True 1048.00 1048 90.5820 1 786 1 chr5D.!!$R1 785
11 TraesCS5A01G350300 chr7B 713133785 713134477 692 False 599.00 599 82.3780 790 1483 1 chr7B.!!$F1 693
12 TraesCS5A01G350300 chr5B 532700891 532702840 1949 True 316.65 538 88.4375 4 724 2 chr5B.!!$R1 720


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
866 2151 0.105453 TGCCTCCCTACCTCTCCATC 60.105 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 3214 0.912006 GGTGGGCTTCCCTCTCTCTT 60.912 60.0 3.27 0.0 45.7 2.85 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
89 91 7.408756 TTTCATTGTTTCTAGCATGGCTAAT 57.591 32.000 0.00 0.00 40.82 1.73
242 256 7.772757 TGTCTTGGCAAATTTAATTTTTGACCT 59.227 29.630 12.34 0.00 40.65 3.85
328 342 4.627035 GCATTTGCTTCCCATTTGTAAGAC 59.373 41.667 0.00 0.00 38.21 3.01
330 344 2.432444 TGCTTCCCATTTGTAAGACCG 58.568 47.619 0.00 0.00 0.00 4.79
405 420 1.980036 AGGCCACCATTTCTTTTGCAT 59.020 42.857 5.01 0.00 0.00 3.96
419 446 5.522456 TCTTTTGCATGAACAAGTGTCATC 58.478 37.500 0.00 0.00 0.00 2.92
428 455 4.141733 TGAACAAGTGTCATCTCCAACAGA 60.142 41.667 0.00 0.00 34.78 3.41
469 496 3.192541 ACACCTTTTTGGGCATGAAAC 57.807 42.857 0.00 0.00 41.11 2.78
527 561 1.202770 GGCGGCAAGTATATGAGGGTT 60.203 52.381 3.07 0.00 0.00 4.11
530 564 3.244112 GCGGCAAGTATATGAGGGTTACT 60.244 47.826 0.00 0.00 0.00 2.24
540 574 1.078159 TGAGGGTTACTGCTAGGGTCA 59.922 52.381 0.00 0.00 0.00 4.02
549 583 0.618680 TGCTAGGGTCACAGGAGCAT 60.619 55.000 0.00 0.00 43.32 3.79
628 662 2.361992 TCCGGAACTAGCCTCGCA 60.362 61.111 0.00 0.00 0.00 5.10
716 2000 2.063015 AATGCACGGACCCCTCAACA 62.063 55.000 0.00 0.00 0.00 3.33
732 2016 4.815308 CCTCAACAAAAATGAAATGCACCA 59.185 37.500 0.00 0.00 0.00 4.17
747 2031 4.567318 CCAGCACTGGGCCTATTC 57.433 61.111 8.93 0.00 46.81 1.75
786 2070 6.147821 CCTAATGCTAATTTGATACGGGAGTG 59.852 42.308 0.00 0.00 46.80 3.51
787 2071 4.746535 TGCTAATTTGATACGGGAGTGA 57.253 40.909 0.00 0.00 46.80 3.41
788 2072 4.693283 TGCTAATTTGATACGGGAGTGAG 58.307 43.478 0.00 0.00 46.80 3.51
817 2101 5.652324 TCTAGTTAGGGTTTCTGTTCCTCT 58.348 41.667 0.00 0.00 32.46 3.69
818 2102 4.893829 AGTTAGGGTTTCTGTTCCTCTC 57.106 45.455 0.00 0.00 32.46 3.20
819 2103 4.232091 AGTTAGGGTTTCTGTTCCTCTCA 58.768 43.478 0.00 0.00 32.46 3.27
821 2105 1.981495 AGGGTTTCTGTTCCTCTCAGG 59.019 52.381 0.00 0.00 36.46 3.86
823 2107 1.700186 GGTTTCTGTTCCTCTCAGGGT 59.300 52.381 0.00 0.00 35.59 4.34
840 2124 4.595538 TGACTTGTCGCCGCCGTT 62.596 61.111 0.00 0.00 35.54 4.44
844 2128 4.287781 TTGTCGCCGCCGTTGAGA 62.288 61.111 0.00 0.00 35.54 3.27
862 2147 1.146982 AGATCTGCCTCCCTACCTCTC 59.853 57.143 0.00 0.00 0.00 3.20
866 2151 0.105453 TGCCTCCCTACCTCTCCATC 60.105 60.000 0.00 0.00 0.00 3.51
867 2152 0.105453 GCCTCCCTACCTCTCCATCA 60.105 60.000 0.00 0.00 0.00 3.07
871 2156 3.439260 CCTCCCTACCTCTCCATCAATCT 60.439 52.174 0.00 0.00 0.00 2.40
876 2161 1.063183 CCTCTCCATCAATCTCCCCC 58.937 60.000 0.00 0.00 0.00 5.40
878 2163 0.764369 TCTCCATCAATCTCCCCCGG 60.764 60.000 0.00 0.00 0.00 5.73
879 2164 0.764369 CTCCATCAATCTCCCCCGGA 60.764 60.000 0.73 0.00 0.00 5.14
898 2183 3.771160 CTGCTCGCGGTTAGGGGT 61.771 66.667 6.13 0.00 0.00 4.95
903 2188 2.125673 CGCGGTTAGGGGTGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
912 2197 2.920912 GGGTGTCTGGTGGGACGA 60.921 66.667 0.00 0.00 38.91 4.20
917 2202 1.906824 GTCTGGTGGGACGACCTGA 60.907 63.158 3.44 8.58 40.56 3.86
919 2204 3.302347 CTGGTGGGACGACCTGAGC 62.302 68.421 3.44 1.61 41.11 4.26
921 2206 2.997897 GTGGGACGACCTGAGCCT 60.998 66.667 3.44 0.00 41.11 4.58
922 2207 2.680352 TGGGACGACCTGAGCCTC 60.680 66.667 3.44 0.00 41.11 4.70
925 2210 2.341101 GGACGACCTGAGCCTCGAA 61.341 63.158 4.99 0.00 33.96 3.71
926 2211 1.585006 GACGACCTGAGCCTCGAAA 59.415 57.895 4.99 0.00 33.96 3.46
928 2213 1.179814 ACGACCTGAGCCTCGAAAGT 61.180 55.000 4.99 0.00 33.96 2.66
931 2216 0.526662 ACCTGAGCCTCGAAAGTACG 59.473 55.000 0.00 0.00 0.00 3.67
932 2217 0.179134 CCTGAGCCTCGAAAGTACGG 60.179 60.000 0.00 0.00 0.00 4.02
937 2222 1.880819 GCCTCGAAAGTACGGGTGGA 61.881 60.000 0.00 0.00 31.23 4.02
944 2229 0.408700 AAGTACGGGTGGAGGAGAGT 59.591 55.000 0.00 0.00 0.00 3.24
945 2230 0.323542 AGTACGGGTGGAGGAGAGTG 60.324 60.000 0.00 0.00 0.00 3.51
946 2231 1.000019 TACGGGTGGAGGAGAGTGG 60.000 63.158 0.00 0.00 0.00 4.00
947 2232 1.797018 TACGGGTGGAGGAGAGTGGT 61.797 60.000 0.00 0.00 0.00 4.16
956 2241 2.236644 GGAGGAGAGTGGTTTAGGGTTC 59.763 54.545 0.00 0.00 0.00 3.62
957 2242 1.900486 AGGAGAGTGGTTTAGGGTTCG 59.100 52.381 0.00 0.00 0.00 3.95
958 2243 1.622312 GGAGAGTGGTTTAGGGTTCGT 59.378 52.381 0.00 0.00 0.00 3.85
959 2244 2.353505 GGAGAGTGGTTTAGGGTTCGTC 60.354 54.545 0.00 0.00 0.00 4.20
962 2247 1.071228 AGTGGTTTAGGGTTCGTCCAC 59.929 52.381 0.00 0.00 43.61 4.02
965 2250 2.148768 GGTTTAGGGTTCGTCCACAAG 58.851 52.381 2.42 0.00 38.11 3.16
966 2251 1.534163 GTTTAGGGTTCGTCCACAAGC 59.466 52.381 2.42 0.00 38.11 4.01
974 2259 1.520787 CGTCCACAAGCCCCGATAC 60.521 63.158 0.00 0.00 0.00 2.24
976 2261 1.117150 GTCCACAAGCCCCGATACTA 58.883 55.000 0.00 0.00 0.00 1.82
980 2265 2.550208 CCACAAGCCCCGATACTATTCC 60.550 54.545 0.00 0.00 0.00 3.01
983 2268 3.394606 ACAAGCCCCGATACTATTCCATT 59.605 43.478 0.00 0.00 0.00 3.16
987 2272 2.618045 CCCCGATACTATTCCATTGGGC 60.618 54.545 2.09 0.00 42.57 5.36
1012 2297 2.552315 GGTTTCGAGATGGCTTCAAACA 59.448 45.455 13.25 0.00 32.05 2.83
1014 2299 4.499019 GGTTTCGAGATGGCTTCAAACAAA 60.499 41.667 13.25 2.00 32.05 2.83
1015 2300 3.896648 TCGAGATGGCTTCAAACAAAC 57.103 42.857 3.03 0.00 0.00 2.93
1022 2307 1.679153 GGCTTCAAACAAACCTTCGGA 59.321 47.619 0.00 0.00 0.00 4.55
1023 2308 2.296190 GGCTTCAAACAAACCTTCGGAT 59.704 45.455 0.00 0.00 0.00 4.18
1027 2312 3.745799 TCAAACAAACCTTCGGATGCTA 58.254 40.909 0.00 0.00 0.00 3.49
1030 2315 3.418684 ACAAACCTTCGGATGCTACTT 57.581 42.857 0.00 0.00 0.00 2.24
1032 2317 3.244422 ACAAACCTTCGGATGCTACTTCA 60.244 43.478 0.00 0.00 0.00 3.02
1050 2335 4.496336 GCAGGGGCGCAGGAGATT 62.496 66.667 10.83 0.00 0.00 2.40
1056 2341 1.227380 GGCGCAGGAGATTGACGAT 60.227 57.895 10.83 0.00 0.00 3.73
1059 2344 0.926155 CGCAGGAGATTGACGATGTG 59.074 55.000 0.00 0.00 0.00 3.21
1063 2348 3.193263 CAGGAGATTGACGATGTGGAAG 58.807 50.000 0.00 0.00 0.00 3.46
1085 2370 3.028850 CAATGATGCAGGAATTGGGTCT 58.971 45.455 9.74 0.00 0.00 3.85
1087 2372 3.173953 TGATGCAGGAATTGGGTCTTT 57.826 42.857 0.00 0.00 0.00 2.52
1089 2374 1.631405 TGCAGGAATTGGGTCTTTGG 58.369 50.000 0.00 0.00 0.00 3.28
1113 2398 2.366916 GGAGGACCTAGATGATGTGGTG 59.633 54.545 0.00 0.00 32.30 4.17
1117 2402 3.941483 GGACCTAGATGATGTGGTGTTTG 59.059 47.826 0.00 0.00 32.30 2.93
1125 2410 4.097551 TGATGTGGTGTTTGATGAGGAA 57.902 40.909 0.00 0.00 0.00 3.36
1126 2411 4.665451 TGATGTGGTGTTTGATGAGGAAT 58.335 39.130 0.00 0.00 0.00 3.01
1128 2413 4.371624 TGTGGTGTTTGATGAGGAATCT 57.628 40.909 0.00 0.00 36.15 2.40
1137 2422 1.211457 GATGAGGAATCTGCACCACCT 59.789 52.381 0.00 0.00 32.01 4.00
1139 2424 0.326264 GAGGAATCTGCACCACCTGT 59.674 55.000 0.00 0.00 0.00 4.00
1155 2440 4.175337 GTGGCTGCCCGCTGGATA 62.175 66.667 17.53 0.00 38.62 2.59
1177 2462 0.034186 CCTGGCTAGGGTTCATTGCA 60.034 55.000 8.57 0.00 40.63 4.08
1188 2473 3.554129 GGGTTCATTGCACCAAAACCTAC 60.554 47.826 7.78 1.71 35.65 3.18
1191 2476 2.295909 TCATTGCACCAAAACCTACAGC 59.704 45.455 0.00 0.00 0.00 4.40
1205 2490 3.844211 ACCTACAGCCAATTCTGGTTCTA 59.156 43.478 0.00 0.00 45.53 2.10
1224 2509 1.800805 ACAGGAACATGAGAACAGCG 58.199 50.000 0.00 0.00 0.00 5.18
1228 2513 1.608025 GGAACATGAGAACAGCGTGGA 60.608 52.381 0.00 0.00 0.00 4.02
1236 2521 0.955428 GAACAGCGTGGAATCTGGCA 60.955 55.000 0.00 0.00 34.76 4.92
1258 2543 2.943033 CAAGAGGTGAAGTTCAAACCGT 59.057 45.455 7.25 0.00 39.07 4.83
1272 2557 2.185004 AACCGTTGGAGGACAATCTG 57.815 50.000 0.00 0.00 41.95 2.90
1279 2564 3.961480 TGGAGGACAATCTGTACACAG 57.039 47.619 2.84 2.84 45.08 3.66
1281 2566 3.646162 TGGAGGACAATCTGTACACAGTT 59.354 43.478 9.11 0.00 44.12 3.16
1311 2596 2.124151 CTTGGGGATTGGGAGCGG 60.124 66.667 0.00 0.00 0.00 5.52
1312 2597 2.612430 TTGGGGATTGGGAGCGGA 60.612 61.111 0.00 0.00 0.00 5.54
1315 2600 0.696143 TGGGGATTGGGAGCGGATTA 60.696 55.000 0.00 0.00 0.00 1.75
1320 2605 2.548920 GGATTGGGAGCGGATTACTCAG 60.549 54.545 0.00 0.00 35.79 3.35
1326 2611 1.757699 GAGCGGATTACTCAGGAAGGT 59.242 52.381 0.00 0.00 34.18 3.50
1329 2614 2.108168 CGGATTACTCAGGAAGGTCCA 58.892 52.381 0.00 0.00 39.61 4.02
1331 2616 3.493350 CGGATTACTCAGGAAGGTCCATG 60.493 52.174 0.00 0.00 39.61 3.66
1332 2617 3.181450 GGATTACTCAGGAAGGTCCATGG 60.181 52.174 4.97 4.97 39.61 3.66
1341 2626 2.026262 GGAAGGTCCATGGCACTTTAGA 60.026 50.000 18.11 0.00 36.28 2.10
1348 2633 4.345257 GTCCATGGCACTTTAGAGGAGATA 59.655 45.833 6.96 0.00 0.00 1.98
1353 2638 7.445121 CATGGCACTTTAGAGGAGATATTGTA 58.555 38.462 0.00 0.00 0.00 2.41
1356 2641 9.154632 TGGCACTTTAGAGGAGATATTGTAATA 57.845 33.333 0.00 0.00 0.00 0.98
1375 2660 2.747396 ACTAAAACCGTACGATGGCA 57.253 45.000 18.76 0.00 0.00 4.92
1395 2680 3.792401 CATAGCCAAACCATCGACAGTA 58.208 45.455 0.00 0.00 0.00 2.74
1397 2682 1.346395 AGCCAAACCATCGACAGTACA 59.654 47.619 0.00 0.00 0.00 2.90
1404 2689 2.497675 ACCATCGACAGTACAGCTTGAT 59.502 45.455 0.00 0.00 0.00 2.57
1405 2690 3.055819 ACCATCGACAGTACAGCTTGATT 60.056 43.478 0.00 0.00 0.00 2.57
1410 2695 3.553511 CGACAGTACAGCTTGATTCCATC 59.446 47.826 0.00 0.00 0.00 3.51
1413 2698 4.141846 ACAGTACAGCTTGATTCCATCGAT 60.142 41.667 0.00 0.00 0.00 3.59
1440 2725 2.539003 GCAAGTGCATGACGTACCA 58.461 52.632 0.00 0.00 41.59 3.25
1446 2731 0.973632 TGCATGACGTACCACCTCTT 59.026 50.000 0.00 0.00 0.00 2.85
1449 2734 3.196901 TGCATGACGTACCACCTCTTTAT 59.803 43.478 0.00 0.00 0.00 1.40
1470 2755 2.187946 CATCTGGTGCCGTCCCTC 59.812 66.667 0.00 0.00 0.00 4.30
2029 3322 4.069232 CCTCGCGCCAGAAGGACA 62.069 66.667 2.64 0.00 36.89 4.02
2125 3418 4.715523 CCACGCGACCCCCATGTT 62.716 66.667 15.93 0.00 0.00 2.71
2187 3480 3.080765 TCCCGCACCATGGTCGAT 61.081 61.111 27.55 2.78 0.00 3.59
2295 3588 2.690881 CCCTCCCCACCGATCCAA 60.691 66.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
318 332 5.116882 GCTATTGGAGACGGTCTTACAAAT 58.883 41.667 23.61 15.08 31.06 2.32
328 342 1.227674 GGGCTGCTATTGGAGACGG 60.228 63.158 0.00 0.00 40.96 4.79
330 344 3.778954 AATAGGGCTGCTATTGGAGAC 57.221 47.619 0.00 0.00 39.13 3.36
397 412 5.526115 AGATGACACTTGTTCATGCAAAAG 58.474 37.500 0.00 0.00 0.00 2.27
405 420 4.129380 CTGTTGGAGATGACACTTGTTCA 58.871 43.478 0.00 0.00 0.00 3.18
419 446 4.884164 CCTTTTATAGGGCTTCTGTTGGAG 59.116 45.833 0.00 0.00 40.67 3.86
445 472 4.227864 TCATGCCCAAAAAGGTGTTTTT 57.772 36.364 0.00 0.00 45.01 1.94
501 535 0.249398 ATATACTTGCCGCCGATCCC 59.751 55.000 0.00 0.00 0.00 3.85
505 539 0.317160 CCTCATATACTTGCCGCCGA 59.683 55.000 0.00 0.00 0.00 5.54
513 547 5.780793 CCCTAGCAGTAACCCTCATATACTT 59.219 44.000 0.00 0.00 0.00 2.24
527 561 1.960471 GCTCCTGTGACCCTAGCAGTA 60.960 57.143 0.00 0.00 33.38 2.74
530 564 0.618680 ATGCTCCTGTGACCCTAGCA 60.619 55.000 5.51 5.51 46.30 3.49
540 574 2.441532 GCCATGGCATGCTCCTGT 60.442 61.111 32.08 0.00 41.49 4.00
575 609 0.696143 TAAATCCCTGGATCCGCCCA 60.696 55.000 7.39 0.00 33.08 5.36
579 613 0.602905 GCCGTAAATCCCTGGATCCG 60.603 60.000 7.39 1.76 33.08 4.18
586 620 4.540735 CCGCGGCCGTAAATCCCT 62.541 66.667 28.70 0.00 0.00 4.20
618 652 1.750193 TCCCAAAAATGCGAGGCTAG 58.250 50.000 0.00 0.00 0.00 3.42
619 653 2.091541 CTTCCCAAAAATGCGAGGCTA 58.908 47.619 0.00 0.00 0.00 3.93
628 662 7.775561 AGAATATCTAGCGAACTTCCCAAAAAT 59.224 33.333 0.00 0.00 0.00 1.82
706 1990 4.141528 TGCATTTCATTTTTGTTGAGGGGT 60.142 37.500 0.00 0.00 0.00 4.95
732 2016 2.907458 AAAAGAATAGGCCCAGTGCT 57.093 45.000 0.00 0.00 40.92 4.40
762 2046 6.929049 TCACTCCCGTATCAAATTAGCATTAG 59.071 38.462 0.00 0.00 0.00 1.73
807 2091 1.148027 AGTCACCCTGAGAGGAACAGA 59.852 52.381 0.00 0.00 37.67 3.41
808 2092 1.638529 AGTCACCCTGAGAGGAACAG 58.361 55.000 0.00 0.00 37.67 3.16
810 2094 1.694696 ACAAGTCACCCTGAGAGGAAC 59.305 52.381 0.00 0.00 37.67 3.62
817 2101 2.741092 GGCGACAAGTCACCCTGA 59.259 61.111 0.72 0.00 0.00 3.86
818 2102 2.738521 CGGCGACAAGTCACCCTG 60.739 66.667 0.00 0.00 0.00 4.45
819 2103 4.681978 GCGGCGACAAGTCACCCT 62.682 66.667 12.98 0.00 0.00 4.34
823 2107 4.595538 AACGGCGGCGACAAGTCA 62.596 61.111 38.93 0.00 0.00 3.41
840 2124 0.937441 AGGTAGGGAGGCAGATCTCA 59.063 55.000 0.00 0.00 35.58 3.27
844 2128 0.189822 GGAGAGGTAGGGAGGCAGAT 59.810 60.000 0.00 0.00 0.00 2.90
862 2147 3.986054 TCCGGGGGAGATTGATGG 58.014 61.111 0.00 0.00 0.00 3.51
876 2161 4.492160 TAACCGCGAGCAGCTCCG 62.492 66.667 17.16 19.08 45.59 4.63
878 2163 2.583593 CCTAACCGCGAGCAGCTC 60.584 66.667 12.94 12.94 45.59 4.09
879 2164 4.148825 CCCTAACCGCGAGCAGCT 62.149 66.667 8.23 0.00 45.59 4.24
890 2175 0.838987 TCCCACCAGACACCCCTAAC 60.839 60.000 0.00 0.00 0.00 2.34
898 2183 2.200370 AGGTCGTCCCACCAGACA 59.800 61.111 0.00 0.00 39.16 3.41
903 2188 4.083862 GGCTCAGGTCGTCCCACC 62.084 72.222 0.00 0.00 36.58 4.61
912 2197 0.526662 CGTACTTTCGAGGCTCAGGT 59.473 55.000 15.95 5.10 0.00 4.00
917 2202 1.590147 CACCCGTACTTTCGAGGCT 59.410 57.895 0.00 0.00 0.00 4.58
919 2204 0.172803 CTCCACCCGTACTTTCGAGG 59.827 60.000 0.00 0.00 0.00 4.63
921 2206 0.251297 TCCTCCACCCGTACTTTCGA 60.251 55.000 0.00 0.00 0.00 3.71
922 2207 0.172803 CTCCTCCACCCGTACTTTCG 59.827 60.000 0.00 0.00 0.00 3.46
925 2210 0.408700 ACTCTCCTCCACCCGTACTT 59.591 55.000 0.00 0.00 0.00 2.24
926 2211 0.323542 CACTCTCCTCCACCCGTACT 60.324 60.000 0.00 0.00 0.00 2.73
928 2213 1.000019 CCACTCTCCTCCACCCGTA 60.000 63.158 0.00 0.00 0.00 4.02
931 2216 1.555533 CTAAACCACTCTCCTCCACCC 59.444 57.143 0.00 0.00 0.00 4.61
932 2217 1.555533 CCTAAACCACTCTCCTCCACC 59.444 57.143 0.00 0.00 0.00 4.61
937 2222 1.900486 CGAACCCTAAACCACTCTCCT 59.100 52.381 0.00 0.00 0.00 3.69
944 2229 1.129917 TGTGGACGAACCCTAAACCA 58.870 50.000 0.00 0.00 38.00 3.67
945 2230 2.148768 CTTGTGGACGAACCCTAAACC 58.851 52.381 0.00 0.00 38.00 3.27
946 2231 1.534163 GCTTGTGGACGAACCCTAAAC 59.466 52.381 0.00 0.00 38.00 2.01
947 2232 1.543871 GGCTTGTGGACGAACCCTAAA 60.544 52.381 0.00 0.00 38.00 1.85
956 2241 1.520787 GTATCGGGGCTTGTGGACG 60.521 63.158 0.00 0.00 0.00 4.79
957 2242 1.117150 TAGTATCGGGGCTTGTGGAC 58.883 55.000 0.00 0.00 0.00 4.02
958 2243 2.097110 ATAGTATCGGGGCTTGTGGA 57.903 50.000 0.00 0.00 0.00 4.02
959 2244 2.550208 GGAATAGTATCGGGGCTTGTGG 60.550 54.545 0.00 0.00 0.00 4.17
962 2247 3.703001 ATGGAATAGTATCGGGGCTTG 57.297 47.619 0.00 0.00 0.00 4.01
965 2250 2.618045 CCCAATGGAATAGTATCGGGGC 60.618 54.545 0.00 0.00 0.00 5.80
966 2251 2.618045 GCCCAATGGAATAGTATCGGGG 60.618 54.545 0.00 0.00 36.12 5.73
974 2259 3.884037 AACCCTAGCCCAATGGAATAG 57.116 47.619 0.00 2.22 0.00 1.73
976 2261 2.686715 CGAAACCCTAGCCCAATGGAAT 60.687 50.000 0.00 0.00 0.00 3.01
980 2265 1.209504 TCTCGAAACCCTAGCCCAATG 59.790 52.381 0.00 0.00 0.00 2.82
983 2268 0.830648 CATCTCGAAACCCTAGCCCA 59.169 55.000 0.00 0.00 0.00 5.36
987 2272 2.168521 TGAAGCCATCTCGAAACCCTAG 59.831 50.000 0.00 0.00 0.00 3.02
1027 2312 4.711949 CTGCGCCCCTGCTGAAGT 62.712 66.667 4.18 0.00 36.04 3.01
1039 2324 0.807667 ACATCGTCAATCTCCTGCGC 60.808 55.000 0.00 0.00 0.00 6.09
1041 2326 1.134699 TCCACATCGTCAATCTCCTGC 60.135 52.381 0.00 0.00 0.00 4.85
1050 2335 2.470983 TCATTGCTTCCACATCGTCA 57.529 45.000 0.00 0.00 0.00 4.35
1072 2357 2.450476 CTCCCAAAGACCCAATTCCTG 58.550 52.381 0.00 0.00 0.00 3.86
1085 2370 2.317900 TCATCTAGGTCCTCCTCCCAAA 59.682 50.000 0.00 0.00 43.94 3.28
1087 2372 1.620515 TCATCTAGGTCCTCCTCCCA 58.379 55.000 0.00 0.00 43.94 4.37
1089 2374 2.896685 CACATCATCTAGGTCCTCCTCC 59.103 54.545 0.00 0.00 43.94 4.30
1107 2392 4.074259 CAGATTCCTCATCAAACACCACA 58.926 43.478 0.00 0.00 33.75 4.17
1113 2398 3.084039 TGGTGCAGATTCCTCATCAAAC 58.916 45.455 0.00 0.00 33.75 2.93
1117 2402 1.211457 AGGTGGTGCAGATTCCTCATC 59.789 52.381 0.00 0.00 0.00 2.92
1161 2446 0.323360 TGGTGCAATGAACCCTAGCC 60.323 55.000 8.15 0.00 36.83 3.93
1173 2458 1.036707 GGCTGTAGGTTTTGGTGCAA 58.963 50.000 0.00 0.00 0.00 4.08
1177 2462 3.573967 CAGAATTGGCTGTAGGTTTTGGT 59.426 43.478 0.00 0.00 0.00 3.67
1205 2490 1.070758 ACGCTGTTCTCATGTTCCTGT 59.929 47.619 0.00 0.00 0.00 4.00
1212 2497 2.350804 CAGATTCCACGCTGTTCTCATG 59.649 50.000 0.00 0.00 0.00 3.07
1218 2503 1.073025 TGCCAGATTCCACGCTGTT 59.927 52.632 0.00 0.00 0.00 3.16
1219 2504 1.672356 GTGCCAGATTCCACGCTGT 60.672 57.895 0.00 0.00 0.00 4.40
1224 2509 1.271597 ACCTCTTGTGCCAGATTCCAC 60.272 52.381 0.00 0.00 0.00 4.02
1228 2513 2.107204 ACTTCACCTCTTGTGCCAGATT 59.893 45.455 0.00 0.00 45.03 2.40
1236 2521 2.943033 CGGTTTGAACTTCACCTCTTGT 59.057 45.455 0.00 0.00 0.00 3.16
1254 2539 1.056660 ACAGATTGTCCTCCAACGGT 58.943 50.000 0.00 0.00 35.44 4.83
1258 2543 3.646162 ACTGTGTACAGATTGTCCTCCAA 59.354 43.478 18.18 0.00 46.59 3.53
1272 2557 4.757149 AGGCAAGAGAATTGAACTGTGTAC 59.243 41.667 0.00 0.00 0.00 2.90
1279 2564 2.232208 CCCCAAGGCAAGAGAATTGAAC 59.768 50.000 0.00 0.00 0.00 3.18
1281 2566 1.710244 TCCCCAAGGCAAGAGAATTGA 59.290 47.619 0.00 0.00 0.00 2.57
1311 2596 3.745797 GCCATGGACCTTCCTGAGTAATC 60.746 52.174 18.40 0.00 37.46 1.75
1312 2597 2.173569 GCCATGGACCTTCCTGAGTAAT 59.826 50.000 18.40 0.00 37.46 1.89
1315 2600 0.842030 TGCCATGGACCTTCCTGAGT 60.842 55.000 18.40 0.00 37.46 3.41
1320 2605 2.026262 TCTAAAGTGCCATGGACCTTCC 60.026 50.000 18.40 0.00 36.96 3.46
1326 2611 2.832838 TCTCCTCTAAAGTGCCATGGA 58.167 47.619 18.40 0.00 0.00 3.41
1329 2614 6.506538 ACAATATCTCCTCTAAAGTGCCAT 57.493 37.500 0.00 0.00 0.00 4.40
1331 2616 9.425577 GTATTACAATATCTCCTCTAAAGTGCC 57.574 37.037 0.00 0.00 0.00 5.01
1348 2633 7.042523 GCCATCGTACGGTTTTAGTATTACAAT 60.043 37.037 16.52 0.00 0.00 2.71
1353 2638 4.757594 TGCCATCGTACGGTTTTAGTATT 58.242 39.130 16.52 0.00 0.00 1.89
1356 2641 2.747396 TGCCATCGTACGGTTTTAGT 57.253 45.000 16.52 0.00 0.00 2.24
1359 2644 1.937899 GCTATGCCATCGTACGGTTTT 59.062 47.619 16.52 0.00 0.00 2.43
1375 2660 3.196901 TGTACTGTCGATGGTTTGGCTAT 59.803 43.478 0.00 0.00 0.00 2.97
1380 2665 2.688507 AGCTGTACTGTCGATGGTTTG 58.311 47.619 1.46 0.00 0.00 2.93
1386 2671 3.195610 TGGAATCAAGCTGTACTGTCGAT 59.804 43.478 1.46 0.00 0.00 3.59
1389 2674 3.553511 CGATGGAATCAAGCTGTACTGTC 59.446 47.826 1.46 0.00 45.97 3.51
1395 2680 5.236282 CAGATATCGATGGAATCAAGCTGT 58.764 41.667 8.54 0.00 45.97 4.40
1397 2682 4.323333 CCCAGATATCGATGGAATCAAGCT 60.323 45.833 8.54 0.00 45.97 3.74
1404 2689 2.046292 TGCACCCAGATATCGATGGAA 58.954 47.619 8.54 0.00 39.02 3.53
1405 2690 1.715785 TGCACCCAGATATCGATGGA 58.284 50.000 8.54 1.57 39.02 3.41
1410 2695 0.940126 GCACTTGCACCCAGATATCG 59.060 55.000 0.00 0.00 41.59 2.92
1434 2719 1.208535 TGGGCATAAAGAGGTGGTACG 59.791 52.381 0.00 0.00 0.00 3.67
1437 2722 2.092212 CAGATGGGCATAAAGAGGTGGT 60.092 50.000 0.00 0.00 0.00 4.16
1440 2725 2.092212 CACCAGATGGGCATAAAGAGGT 60.092 50.000 3.48 0.00 42.05 3.85
1446 2731 1.152984 CGGCACCAGATGGGCATAA 60.153 57.895 3.48 0.00 42.05 1.90
1449 2734 4.408821 GACGGCACCAGATGGGCA 62.409 66.667 3.48 0.00 42.05 5.36
1470 2755 1.334960 GGGTGTGACACTTTTGATGCG 60.335 52.381 16.07 0.00 34.40 4.73
1473 2758 3.073062 AGCTAGGGTGTGACACTTTTGAT 59.927 43.478 16.07 1.45 31.80 2.57
1474 2759 2.438021 AGCTAGGGTGTGACACTTTTGA 59.562 45.455 16.07 0.00 31.80 2.69
1923 3214 0.912006 GGTGGGCTTCCCTCTCTCTT 60.912 60.000 3.27 0.00 45.70 2.85
2122 3415 1.079490 AGTGAGGATGAGAGGGGAACA 59.921 52.381 0.00 0.00 0.00 3.18
2125 3418 1.010795 TGAGTGAGGATGAGAGGGGA 58.989 55.000 0.00 0.00 0.00 4.81
2366 3661 3.718210 GACCGGAGCGAGGCGAATT 62.718 63.158 9.46 0.00 0.00 2.17
2442 3737 1.535462 CAAACGCGTGGGAAAGAAGAT 59.465 47.619 14.98 0.00 0.00 2.40



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

AutoCloner maintained by Alex Coulton.