Multiple sequence alignment - TraesCS4B01G005600

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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 TraesCS4B01G005600 chr4B 100.000 3422 0 0 1 3422 3832262 3828841 0.000000e+00 6320.0
1 TraesCS4B01G005600 chr4B 82.929 1441 217 20 1000 2425 3820815 3822241 0.000000e+00 1271.0
2 TraesCS4B01G005600 chr4D 91.981 2469 138 15 978 3421 3250777 3248344 0.000000e+00 3408.0
3 TraesCS4B01G005600 chr4D 84.427 1387 196 16 1049 2425 3241649 3243025 0.000000e+00 1347.0
4 TraesCS4B01G005600 chr4D 92.141 369 16 6 591 947 3251130 3250763 3.050000e-140 508.0
5 TraesCS4B01G005600 chr4D 89.130 414 32 11 2 403 3251706 3251294 1.420000e-138 503.0
6 TraesCS4B01G005600 chr4D 94.690 113 5 1 472 583 3251281 3251169 1.260000e-39 174.0
7 TraesCS4B01G005600 chr4A 92.779 1454 92 5 972 2416 602272623 602274072 0.000000e+00 2091.0
8 TraesCS4B01G005600 chr4A 83.309 1390 206 17 1049 2425 602307884 602306508 0.000000e+00 1258.0
9 TraesCS4B01G005600 chr4A 84.550 589 56 15 1 585 602271680 602272237 4.990000e-153 551.0
10 TraesCS4B01G005600 chr4A 90.164 366 20 7 594 944 602272276 602272640 2.410000e-126 462.0
11 TraesCS4B01G005600 chr4A 98.039 51 1 0 2510 2560 602274125 602274175 4.700000e-14 89.8
12 TraesCS4B01G005600 chr2B 78.116 722 143 12 1053 1765 6341824 6341109 8.710000e-121 444.0
13 TraesCS4B01G005600 chr2D 77.641 729 144 14 1053 1770 5079495 5080215 3.160000e-115 425.0
14 TraesCS4B01G005600 chr1B 94.595 37 2 0 2068 2104 589920008 589919972 1.330000e-04 58.4


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 TraesCS4B01G005600 chr4B 3828841 3832262 3421 True 6320.00 6320 100.0000 1 3422 1 chr4B.!!$R1 3421
1 TraesCS4B01G005600 chr4B 3820815 3822241 1426 False 1271.00 1271 82.9290 1000 2425 1 chr4B.!!$F1 1425
2 TraesCS4B01G005600 chr4D 3241649 3243025 1376 False 1347.00 1347 84.4270 1049 2425 1 chr4D.!!$F1 1376
3 TraesCS4B01G005600 chr4D 3248344 3251706 3362 True 1148.25 3408 91.9855 2 3421 4 chr4D.!!$R1 3419
4 TraesCS4B01G005600 chr4A 602306508 602307884 1376 True 1258.00 1258 83.3090 1049 2425 1 chr4A.!!$R1 1376
5 TraesCS4B01G005600 chr4A 602271680 602274175 2495 False 798.45 2091 91.3830 1 2560 4 chr4A.!!$F1 2559
6 TraesCS4B01G005600 chr2B 6341109 6341824 715 True 444.00 444 78.1160 1053 1765 1 chr2B.!!$R1 712
7 TraesCS4B01G005600 chr2D 5079495 5080215 720 False 425.00 425 77.6410 1053 1770 1 chr2D.!!$F1 717

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
402 415 0.114364 GTTTGTGGGGACTGGGGAAT 59.886 55.0 0.0 0.0 0.00 3.01 F
2167 2241 0.314302 CGACCAGTTCCTCAACGAGT 59.686 55.0 0.0 0.0 37.61 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2285 0.322322 TGGCCTTGTCGTTACCGAAT 59.678 50.0 3.32 0.00 46.26 3.34 R
3316 3403 0.883153 TCATGCCATTGTCTGTGCAC 59.117 50.0 10.75 10.75 35.01 4.57 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
24 25 7.368480 GGCTAAAAAGAAACATTACGGTAGA 57.632 36.000 0.00 0.00 0.00 2.59
25 26 7.461918 GGCTAAAAAGAAACATTACGGTAGAG 58.538 38.462 0.00 0.00 0.00 2.43
26 27 7.332678 GGCTAAAAAGAAACATTACGGTAGAGA 59.667 37.037 0.00 0.00 0.00 3.10
118 122 3.049674 ACAACGTCATGGCTGCCG 61.050 61.111 14.98 3.82 0.00 5.69
121 125 3.958147 AACGTCATGGCTGCCGAGG 62.958 63.158 14.98 13.60 0.00 4.63
169 173 2.298593 GAGACGCTCCATAAACGGC 58.701 57.895 0.00 0.00 34.19 5.68
175 179 1.807981 CTCCATAAACGGCGCGTCA 60.808 57.895 12.89 0.00 39.99 4.35
261 265 3.953775 CCTCCACCACGCCCACTT 61.954 66.667 0.00 0.00 0.00 3.16
264 268 2.203280 CCACCACGCCCACTTCAA 60.203 61.111 0.00 0.00 0.00 2.69
273 277 1.002134 CCCACTTCAACGCCCTCAT 60.002 57.895 0.00 0.00 0.00 2.90
324 328 0.390603 GCGTACACATACACCAGCCA 60.391 55.000 0.00 0.00 0.00 4.75
353 360 4.764308 GCTCCCATGGAAAAGATTCTATCC 59.236 45.833 15.22 10.21 34.84 2.59
361 368 3.821421 AAAGATTCTATCCCGCTCGTT 57.179 42.857 0.00 0.00 0.00 3.85
373 386 1.512734 GCTCGTTGCCATGCTTTCG 60.513 57.895 0.00 0.00 35.15 3.46
377 390 3.746889 TTGCCATGCTTTCGCCGG 61.747 61.111 0.00 0.00 34.43 6.13
382 395 4.101790 ATGCTTTCGCCGGCGTTG 62.102 61.111 44.16 33.35 40.74 4.10
394 407 2.725641 GCGTTGGTTTGTGGGGAC 59.274 61.111 0.00 0.00 0.00 4.46
395 408 1.826487 GCGTTGGTTTGTGGGGACT 60.826 57.895 0.00 0.00 0.00 3.85
396 409 2.029743 CGTTGGTTTGTGGGGACTG 58.970 57.895 0.00 0.00 0.00 3.51
398 411 1.112916 GTTGGTTTGTGGGGACTGGG 61.113 60.000 0.00 0.00 0.00 4.45
399 412 2.117423 GGTTTGTGGGGACTGGGG 59.883 66.667 0.00 0.00 0.00 4.96
400 413 2.466186 GGTTTGTGGGGACTGGGGA 61.466 63.158 0.00 0.00 0.00 4.81
401 414 1.539665 GTTTGTGGGGACTGGGGAA 59.460 57.895 0.00 0.00 0.00 3.97
402 415 0.114364 GTTTGTGGGGACTGGGGAAT 59.886 55.000 0.00 0.00 0.00 3.01
403 416 1.356398 GTTTGTGGGGACTGGGGAATA 59.644 52.381 0.00 0.00 0.00 1.75
404 417 1.295020 TTGTGGGGACTGGGGAATAG 58.705 55.000 0.00 0.00 0.00 1.73
405 418 1.279025 TGTGGGGACTGGGGAATAGC 61.279 60.000 0.00 0.00 0.00 2.97
431 444 2.322658 CAAGGGGAATGGGAATGATGG 58.677 52.381 0.00 0.00 0.00 3.51
446 459 5.337813 GGAATGATGGTTTTCCTTTGCTGAT 60.338 40.000 0.00 0.00 38.68 2.90
447 460 4.789012 TGATGGTTTTCCTTTGCTGATC 57.211 40.909 0.00 0.00 41.38 2.92
448 461 3.191162 TGATGGTTTTCCTTTGCTGATCG 59.809 43.478 0.00 0.00 41.38 3.69
449 462 2.857483 TGGTTTTCCTTTGCTGATCGA 58.143 42.857 0.00 0.00 41.38 3.59
467 480 3.130633 TCGAGTTGATCAAGTGGTTGTG 58.869 45.455 20.46 3.75 34.98 3.33
503 516 4.368315 CTCACCGTTGCACTGCTATATAA 58.632 43.478 1.98 0.00 0.00 0.98
541 554 2.390225 ATTGCTACTCCCTCCGATCT 57.610 50.000 0.00 0.00 0.00 2.75
614 659 7.990055 TGATCAGAGGGAGTATAATCTACTCA 58.010 38.462 19.71 7.55 44.18 3.41
663 708 5.063944 CGGACATCAAGGAAAATGTCTGTAG 59.936 44.000 13.60 2.90 46.85 2.74
672 717 5.421056 AGGAAAATGTCTGTAGGATCACGTA 59.579 40.000 0.00 0.00 0.00 3.57
739 787 0.388520 GTCTTTTGGCCCGTTGCATC 60.389 55.000 0.00 0.00 43.89 3.91
837 896 6.158175 TGTGTTTTGTTTTGTTGAATTCCG 57.842 33.333 2.27 0.00 0.00 4.30
881 940 3.535561 AGATTCCTTAAGCACATGGACG 58.464 45.455 0.00 0.00 0.00 4.79
882 941 2.107950 TTCCTTAAGCACATGGACGG 57.892 50.000 0.00 0.00 0.00 4.79
885 944 1.382522 CTTAAGCACATGGACGGCAT 58.617 50.000 0.00 0.00 0.00 4.40
886 945 1.745087 CTTAAGCACATGGACGGCATT 59.255 47.619 0.00 0.00 0.00 3.56
932 991 8.150945 TCCTATTAGATAGAGGCACATTTTCAC 58.849 37.037 0.00 0.00 34.77 3.18
933 992 7.933577 CCTATTAGATAGAGGCACATTTTCACA 59.066 37.037 0.00 0.00 34.77 3.58
934 993 6.985188 TTAGATAGAGGCACATTTTCACAC 57.015 37.500 0.00 0.00 0.00 3.82
935 994 4.265073 AGATAGAGGCACATTTTCACACC 58.735 43.478 0.00 0.00 0.00 4.16
936 995 2.363306 AGAGGCACATTTTCACACCA 57.637 45.000 0.00 0.00 0.00 4.17
937 996 2.880443 AGAGGCACATTTTCACACCAT 58.120 42.857 0.00 0.00 0.00 3.55
938 997 3.233507 AGAGGCACATTTTCACACCATT 58.766 40.909 0.00 0.00 0.00 3.16
939 998 3.006110 AGAGGCACATTTTCACACCATTG 59.994 43.478 0.00 0.00 0.00 2.82
940 999 2.037511 AGGCACATTTTCACACCATTGG 59.962 45.455 0.00 0.00 0.00 3.16
941 1000 2.224257 GGCACATTTTCACACCATTGGT 60.224 45.455 1.37 1.37 35.62 3.67
942 1001 3.006323 GGCACATTTTCACACCATTGGTA 59.994 43.478 8.31 0.00 32.11 3.25
943 1002 3.987220 GCACATTTTCACACCATTGGTAC 59.013 43.478 8.31 0.00 32.11 3.34
944 1003 4.500545 GCACATTTTCACACCATTGGTACA 60.501 41.667 8.31 0.00 32.11 2.90
945 1004 5.221880 CACATTTTCACACCATTGGTACAG 58.778 41.667 8.31 0.00 42.39 2.74
946 1005 4.236935 CATTTTCACACCATTGGTACAGC 58.763 43.478 8.31 0.00 42.39 4.40
947 1006 2.949177 TTCACACCATTGGTACAGCT 57.051 45.000 8.31 0.00 42.39 4.24
948 1007 2.949177 TCACACCATTGGTACAGCTT 57.051 45.000 8.31 0.00 42.39 3.74
949 1008 3.222173 TCACACCATTGGTACAGCTTT 57.778 42.857 8.31 0.00 42.39 3.51
950 1009 3.561143 TCACACCATTGGTACAGCTTTT 58.439 40.909 8.31 0.00 42.39 2.27
951 1010 3.957497 TCACACCATTGGTACAGCTTTTT 59.043 39.130 8.31 0.00 42.39 1.94
952 1011 4.050553 CACACCATTGGTACAGCTTTTTG 58.949 43.478 8.31 0.00 42.39 2.44
953 1012 3.704061 ACACCATTGGTACAGCTTTTTGT 59.296 39.130 8.31 0.00 42.39 2.83
954 1013 4.890581 ACACCATTGGTACAGCTTTTTGTA 59.109 37.500 8.31 0.00 42.39 2.41
955 1014 5.009610 ACACCATTGGTACAGCTTTTTGTAG 59.990 40.000 8.31 0.00 42.39 2.74
956 1015 4.022329 ACCATTGGTACAGCTTTTTGTAGC 60.022 41.667 6.54 8.07 46.79 3.58
957 1016 6.214220 ACCATTGGTACAGCTTTTTGTAGCT 61.214 40.000 6.54 0.00 46.75 3.32
958 1017 7.959066 ACCATTGGTACAGCTTTTTGTAGCTC 61.959 42.308 6.54 0.00 46.75 4.09
966 1025 4.522297 GCTTTTTGTAGCTCGATCGATT 57.478 40.909 19.78 12.55 38.15 3.34
967 1026 4.509891 GCTTTTTGTAGCTCGATCGATTC 58.490 43.478 19.78 13.40 38.15 2.52
968 1027 4.268884 GCTTTTTGTAGCTCGATCGATTCT 59.731 41.667 19.78 19.57 38.15 2.40
969 1028 5.220491 GCTTTTTGTAGCTCGATCGATTCTT 60.220 40.000 19.78 7.12 38.15 2.52
970 1029 5.950965 TTTTGTAGCTCGATCGATTCTTC 57.049 39.130 19.78 15.75 0.00 2.87
971 1030 4.902443 TTGTAGCTCGATCGATTCTTCT 57.098 40.909 19.78 12.56 0.00 2.85
972 1031 4.902443 TGTAGCTCGATCGATTCTTCTT 57.098 40.909 19.78 2.23 0.00 2.52
973 1032 4.849883 TGTAGCTCGATCGATTCTTCTTC 58.150 43.478 19.78 9.10 0.00 2.87
974 1033 4.576873 TGTAGCTCGATCGATTCTTCTTCT 59.423 41.667 19.78 8.08 0.00 2.85
975 1034 4.223320 AGCTCGATCGATTCTTCTTCTC 57.777 45.455 19.78 0.00 0.00 2.87
976 1035 2.970609 GCTCGATCGATTCTTCTTCTCG 59.029 50.000 19.78 3.18 0.00 4.04
998 1057 2.886604 GTTGGTACCGCGCGCATA 60.887 61.111 32.61 19.83 0.00 3.14
999 1058 2.886604 TTGGTACCGCGCGCATAC 60.887 61.111 32.61 28.90 0.00 2.39
1000 1059 3.644399 TTGGTACCGCGCGCATACA 62.644 57.895 31.61 22.02 0.00 2.29
1001 1060 2.660552 GGTACCGCGCGCATACAT 60.661 61.111 31.61 16.73 0.00 2.29
1247 1309 4.161295 CGAGCTCCCATTCCCGCA 62.161 66.667 8.47 0.00 0.00 5.69
1520 1582 2.251642 GGCTTCTTCACAACGGCGT 61.252 57.895 6.77 6.77 0.00 5.68
1848 1922 2.094854 GGTCGTCTATGTCTGTTTCGGT 60.095 50.000 0.00 0.00 0.00 4.69
1946 2020 1.187087 GTGGTGAAGGAGTCCGAGAT 58.813 55.000 2.76 0.00 0.00 2.75
1956 2030 2.100631 GTCCGAGATGGTGTTGCCG 61.101 63.158 0.00 0.00 41.21 5.69
2022 2096 0.695462 AGGGGCTCATAGTGCATGGA 60.695 55.000 0.00 0.00 35.16 3.41
2035 2109 1.753848 CATGGATGGGCGCCTCAAA 60.754 57.895 28.56 10.38 0.00 2.69
2043 2117 2.800736 GCGCCTCAAATCGCCATT 59.199 55.556 0.00 0.00 45.01 3.16
2046 2120 1.581934 CGCCTCAAATCGCCATTCTA 58.418 50.000 0.00 0.00 0.00 2.10
2076 2150 2.665777 CGTAGGTGGCTTCATGACG 58.334 57.895 0.00 0.00 0.00 4.35
2115 2189 4.498520 CTGGAGTCCGTCGCGCAT 62.499 66.667 8.75 0.00 0.00 4.73
2130 2204 4.538233 CATGGCGTGCCTGTCATA 57.462 55.556 12.84 0.00 31.05 2.15
2167 2241 0.314302 CGACCAGTTCCTCAACGAGT 59.686 55.000 0.00 0.00 37.61 4.18
2175 2249 1.302033 CCTCAACGAGTGGCTTGCT 60.302 57.895 0.00 0.00 0.00 3.91
2193 2267 0.320421 CTGTGGACGTACTTGGGGTG 60.320 60.000 0.00 0.00 0.00 4.61
2276 2359 4.899239 GTCGGAGCTGATGGGCGG 62.899 72.222 0.00 0.00 37.29 6.13
2320 2403 2.972713 AGGAGAAAGTGCAAGGAGTACA 59.027 45.455 0.00 0.00 35.00 2.90
2321 2404 3.391296 AGGAGAAAGTGCAAGGAGTACAA 59.609 43.478 0.00 0.00 35.00 2.41
2358 2441 0.465705 CCATAGCGAAAGGAGGCTCA 59.534 55.000 17.69 0.00 40.58 4.26
2416 2499 1.073722 TGGAGTGGCAGCAAGGAAG 59.926 57.895 0.00 0.00 0.00 3.46
2439 2522 4.704965 AGTAGATTCGGAATTGTTAGGCC 58.295 43.478 4.47 0.00 0.00 5.19
2440 2523 3.933861 AGATTCGGAATTGTTAGGCCT 57.066 42.857 11.78 11.78 0.00 5.19
2441 2524 3.809905 AGATTCGGAATTGTTAGGCCTC 58.190 45.455 9.68 0.00 0.00 4.70
2442 2525 3.199946 AGATTCGGAATTGTTAGGCCTCA 59.800 43.478 9.68 0.00 0.00 3.86
2444 2527 3.644966 TCGGAATTGTTAGGCCTCAAT 57.355 42.857 9.68 11.69 36.07 2.57
2474 2558 4.573900 CTCTGCTAGGTGAAGTGTGAATT 58.426 43.478 0.00 0.00 0.00 2.17
2494 2578 4.893424 TTGTGCTAAACTGTCAAAGGAC 57.107 40.909 0.00 0.00 44.57 3.85
2670 2755 9.087871 TCTGGATTGATAAATTTTCAAGAACCA 57.912 29.630 20.65 20.65 36.60 3.67
2671 2756 9.362539 CTGGATTGATAAATTTTCAAGAACCAG 57.637 33.333 25.22 25.22 41.08 4.00
2672 2757 9.087871 TGGATTGATAAATTTTCAAGAACCAGA 57.912 29.630 19.57 10.09 36.60 3.86
2735 2820 1.615392 GGCGGTAAGGTATGTCGGTAT 59.385 52.381 0.00 0.00 0.00 2.73
2739 2824 4.022849 GCGGTAAGGTATGTCGGTATAAGT 60.023 45.833 0.00 0.00 0.00 2.24
2744 2829 7.981225 GGTAAGGTATGTCGGTATAAGTTTCAA 59.019 37.037 0.00 0.00 0.00 2.69
2777 2862 7.142306 TGGATGTATACGCAAGAGACTATAC 57.858 40.000 0.00 0.00 43.62 1.47
2845 2930 8.671384 TTTATGGTATAACTGCTATGGTTCAC 57.329 34.615 0.00 0.00 0.00 3.18
2878 2963 0.323725 AGAGGAAAACCCATGCGCAT 60.324 50.000 19.28 19.28 37.41 4.73
2932 3019 8.693120 TTTTGTCTAGTCTCTTAGAGAACTCA 57.307 34.615 14.06 6.63 40.59 3.41
2952 3039 2.380084 TTAACACCAGATGACTCCGC 57.620 50.000 0.00 0.00 0.00 5.54
2964 3051 1.071542 TGACTCCGCTTTCATGGTCAA 59.928 47.619 0.00 0.00 31.99 3.18
2969 3056 1.508088 GCTTTCATGGTCAAGGGCG 59.492 57.895 0.00 0.00 0.00 6.13
2977 3064 1.462616 TGGTCAAGGGCGATTGAATG 58.537 50.000 5.47 0.00 40.72 2.67
2994 3081 4.037858 GAATGTCAATGAGGGCACATTC 57.962 45.455 8.36 8.36 44.66 2.67
3108 3195 7.745620 AAGACTTACTTGTTTGTATCCTTGG 57.254 36.000 0.00 0.00 37.45 3.61
3111 3198 5.699458 ACTTACTTGTTTGTATCCTTGGACG 59.301 40.000 0.00 0.00 0.00 4.79
3113 3200 4.906618 ACTTGTTTGTATCCTTGGACGAT 58.093 39.130 0.00 0.00 0.00 3.73
3149 3236 5.474578 TGATGTATGCTAGAAGGATCACC 57.525 43.478 0.00 0.00 0.00 4.02
3182 3269 2.158957 AGTATCATGCGTAACAGGGTGG 60.159 50.000 0.00 0.00 0.00 4.61
3184 3271 0.036765 TCATGCGTAACAGGGTGGTC 60.037 55.000 0.00 0.00 0.00 4.02
3190 3277 2.287368 GCGTAACAGGGTGGTCAAAAAG 60.287 50.000 0.00 0.00 0.00 2.27
3196 3283 2.499693 CAGGGTGGTCAAAAAGGTTGTT 59.500 45.455 0.00 0.00 0.00 2.83
3201 3288 5.053811 GGTGGTCAAAAAGGTTGTTATTGG 58.946 41.667 0.00 0.00 0.00 3.16
3211 3298 9.816787 AAAAAGGTTGTTATTGGGTTATCTAGA 57.183 29.630 0.00 0.00 0.00 2.43
3214 3301 8.024145 AGGTTGTTATTGGGTTATCTAGAGAG 57.976 38.462 0.00 0.00 0.00 3.20
3291 3378 5.897050 AGAGATACTTTTAGGCTTCACTCG 58.103 41.667 0.00 0.00 0.00 4.18
3301 3388 2.567615 AGGCTTCACTCGGTATGAAAGT 59.432 45.455 0.00 0.00 35.70 2.66
3305 3392 5.234543 GGCTTCACTCGGTATGAAAGTATTC 59.765 44.000 0.00 0.00 35.70 1.75
3328 3415 3.193267 ACAAACAAGTGTGCACAGACAAT 59.807 39.130 22.40 4.00 0.00 2.71
3377 3464 4.000988 TGAATACAGGAACGAGAAAAGGC 58.999 43.478 0.00 0.00 0.00 4.35
3383 3470 2.232941 AGGAACGAGAAAAGGCGTCATA 59.767 45.455 0.00 0.00 40.23 2.15
3421 3508 8.783660 ATAAGTAGACATAGTGATTGAAGGGA 57.216 34.615 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 184 3.066814 GGGCGTACCACTCCGTCT 61.067 66.667 0.00 0.00 39.85 4.18
324 328 0.112995 TTTTCCATGGGAGCAGCAGT 59.887 50.000 13.02 0.00 31.21 4.40
373 386 4.639171 CCACAAACCAACGCCGGC 62.639 66.667 19.07 19.07 0.00 6.13
377 390 1.826487 AGTCCCCACAAACCAACGC 60.826 57.895 0.00 0.00 0.00 4.84
382 395 2.014033 TTCCCCAGTCCCCACAAACC 62.014 60.000 0.00 0.00 0.00 3.27
394 407 2.854253 TGGGCTAGCTATTCCCCAG 58.146 57.895 21.88 1.44 42.41 4.45
395 408 1.140312 CTTGGGCTAGCTATTCCCCA 58.860 55.000 21.88 20.06 45.45 4.96
396 409 0.402121 CCTTGGGCTAGCTATTCCCC 59.598 60.000 21.88 18.21 39.30 4.81
398 411 0.402121 CCCCTTGGGCTAGCTATTCC 59.598 60.000 15.72 7.77 35.35 3.01
399 412 1.435256 TCCCCTTGGGCTAGCTATTC 58.565 55.000 15.72 0.00 43.94 1.75
400 413 1.907240 TTCCCCTTGGGCTAGCTATT 58.093 50.000 15.72 0.00 43.94 1.73
401 414 1.707427 CATTCCCCTTGGGCTAGCTAT 59.293 52.381 15.72 0.00 43.94 2.97
402 415 1.140312 CATTCCCCTTGGGCTAGCTA 58.860 55.000 15.72 0.96 43.94 3.32
403 416 1.649271 CCATTCCCCTTGGGCTAGCT 61.649 60.000 15.72 0.00 43.94 3.32
404 417 1.152673 CCATTCCCCTTGGGCTAGC 60.153 63.158 6.04 6.04 43.94 3.42
417 430 5.682234 AAGGAAAACCATCATTCCCATTC 57.318 39.130 1.10 0.00 45.08 2.67
418 431 5.804120 GCAAAGGAAAACCATCATTCCCATT 60.804 40.000 1.10 0.00 45.08 3.16
431 444 4.024048 TCAACTCGATCAGCAAAGGAAAAC 60.024 41.667 0.00 0.00 0.00 2.43
446 459 3.130633 CACAACCACTTGATCAACTCGA 58.869 45.455 3.38 0.00 0.00 4.04
447 460 2.349817 GCACAACCACTTGATCAACTCG 60.350 50.000 3.38 0.00 0.00 4.18
448 461 2.349817 CGCACAACCACTTGATCAACTC 60.350 50.000 3.38 0.00 0.00 3.01
449 462 1.603802 CGCACAACCACTTGATCAACT 59.396 47.619 3.38 0.00 0.00 3.16
463 476 2.591429 CAGCCACCACTCGCACAA 60.591 61.111 0.00 0.00 0.00 3.33
467 480 4.687215 TGAGCAGCCACCACTCGC 62.687 66.667 0.00 0.00 32.98 5.03
503 516 9.367444 GTAGCAATAGAACAAACACAGTACTAT 57.633 33.333 0.00 0.00 0.00 2.12
585 599 9.120538 GTAGATTATACTCCCTCTGATCAGATC 57.879 40.741 25.30 15.20 36.76 2.75
587 601 8.225863 AGTAGATTATACTCCCTCTGATCAGA 57.774 38.462 23.75 23.75 35.85 3.27
588 602 8.106462 TGAGTAGATTATACTCCCTCTGATCAG 58.894 40.741 17.07 17.07 42.32 2.90
589 603 7.990055 TGAGTAGATTATACTCCCTCTGATCA 58.010 38.462 14.25 0.00 42.32 2.92
591 605 7.019153 ACCTGAGTAGATTATACTCCCTCTGAT 59.981 40.741 14.25 0.00 42.32 2.90
592 606 6.333168 ACCTGAGTAGATTATACTCCCTCTGA 59.667 42.308 14.25 0.00 42.32 3.27
593 607 6.432783 CACCTGAGTAGATTATACTCCCTCTG 59.567 46.154 14.25 3.23 42.32 3.35
594 608 6.548321 CACCTGAGTAGATTATACTCCCTCT 58.452 44.000 14.25 0.00 42.32 3.69
595 609 5.184287 GCACCTGAGTAGATTATACTCCCTC 59.816 48.000 14.25 2.24 42.32 4.30
596 610 5.081032 GCACCTGAGTAGATTATACTCCCT 58.919 45.833 14.25 0.00 42.32 4.20
597 611 5.081032 AGCACCTGAGTAGATTATACTCCC 58.919 45.833 14.25 0.00 42.32 4.30
598 612 5.770663 TGAGCACCTGAGTAGATTATACTCC 59.229 44.000 14.25 1.06 42.32 3.85
599 613 6.566942 CGTGAGCACCTGAGTAGATTATACTC 60.567 46.154 10.82 10.82 43.06 2.59
614 659 1.414919 TGGTTTCTAACGTGAGCACCT 59.585 47.619 17.68 0.00 0.00 4.00
672 717 0.039888 GCGGGTTGCACGTGTAATTT 60.040 50.000 21.92 0.00 45.45 1.82
739 787 1.805539 ATGCATGTCGTGTCGTCCG 60.806 57.895 0.00 0.00 0.00 4.79
743 796 1.423721 CTCCCATGCATGTCGTGTCG 61.424 60.000 24.58 7.82 0.00 4.35
837 896 1.534163 GAAAAGGGAACACGTACAGCC 59.466 52.381 0.00 0.00 0.00 4.85
881 940 1.384222 CCCCAACGCCTCTAAATGCC 61.384 60.000 0.00 0.00 0.00 4.40
882 941 0.393808 TCCCCAACGCCTCTAAATGC 60.394 55.000 0.00 0.00 0.00 3.56
885 944 1.551883 GTAGTCCCCAACGCCTCTAAA 59.448 52.381 0.00 0.00 0.00 1.85
886 945 1.188863 GTAGTCCCCAACGCCTCTAA 58.811 55.000 0.00 0.00 0.00 2.10
932 991 4.320608 ACAAAAAGCTGTACCAATGGTG 57.679 40.909 16.41 0.00 36.19 4.17
933 992 4.022329 GCTACAAAAAGCTGTACCAATGGT 60.022 41.667 10.81 10.81 39.50 3.55
934 993 4.485163 GCTACAAAAAGCTGTACCAATGG 58.515 43.478 0.00 0.00 39.50 3.16
945 1004 4.268884 AGAATCGATCGAGCTACAAAAAGC 59.731 41.667 23.84 0.00 43.11 3.51
946 1005 5.957910 AGAATCGATCGAGCTACAAAAAG 57.042 39.130 23.84 0.00 0.00 2.27
947 1006 6.100004 AGAAGAATCGATCGAGCTACAAAAA 58.900 36.000 23.84 0.00 0.00 1.94
948 1007 5.651530 AGAAGAATCGATCGAGCTACAAAA 58.348 37.500 23.84 0.00 0.00 2.44
949 1008 5.250235 AGAAGAATCGATCGAGCTACAAA 57.750 39.130 23.84 0.00 0.00 2.83
950 1009 4.902443 AGAAGAATCGATCGAGCTACAA 57.098 40.909 23.84 0.00 0.00 2.41
951 1010 4.576873 AGAAGAAGAATCGATCGAGCTACA 59.423 41.667 23.84 0.00 0.00 2.74
952 1011 5.103290 AGAAGAAGAATCGATCGAGCTAC 57.897 43.478 23.84 13.48 0.00 3.58
953 1012 4.084276 CGAGAAGAAGAATCGATCGAGCTA 60.084 45.833 23.84 0.00 38.72 3.32
954 1013 3.303725 CGAGAAGAAGAATCGATCGAGCT 60.304 47.826 23.84 19.04 38.72 4.09
955 1014 2.970609 CGAGAAGAAGAATCGATCGAGC 59.029 50.000 23.84 17.11 38.72 5.03
956 1015 2.970609 GCGAGAAGAAGAATCGATCGAG 59.029 50.000 23.84 6.11 38.72 4.04
957 1016 2.354821 TGCGAGAAGAAGAATCGATCGA 59.645 45.455 21.86 21.86 38.72 3.59
958 1017 2.465839 GTGCGAGAAGAAGAATCGATCG 59.534 50.000 9.36 9.36 38.72 3.69
959 1018 2.792116 GGTGCGAGAAGAAGAATCGATC 59.208 50.000 0.00 0.00 38.72 3.69
960 1019 2.796383 CGGTGCGAGAAGAAGAATCGAT 60.796 50.000 0.00 0.00 38.72 3.59
961 1020 1.467543 CGGTGCGAGAAGAAGAATCGA 60.468 52.381 0.00 0.00 38.72 3.59
962 1021 0.917259 CGGTGCGAGAAGAAGAATCG 59.083 55.000 0.00 0.00 39.40 3.34
963 1022 1.997669 ACGGTGCGAGAAGAAGAATC 58.002 50.000 0.00 0.00 0.00 2.52
964 1023 2.069273 CAACGGTGCGAGAAGAAGAAT 58.931 47.619 0.00 0.00 0.00 2.40
965 1024 1.497991 CAACGGTGCGAGAAGAAGAA 58.502 50.000 0.00 0.00 0.00 2.52
966 1025 0.319555 CCAACGGTGCGAGAAGAAGA 60.320 55.000 0.00 0.00 0.00 2.87
967 1026 0.600255 ACCAACGGTGCGAGAAGAAG 60.600 55.000 0.00 0.00 32.98 2.85
968 1027 0.675083 TACCAACGGTGCGAGAAGAA 59.325 50.000 0.00 0.00 36.19 2.52
969 1028 0.038892 GTACCAACGGTGCGAGAAGA 60.039 55.000 0.00 0.00 36.19 2.87
970 1029 1.012486 GGTACCAACGGTGCGAGAAG 61.012 60.000 7.15 0.00 39.20 2.85
971 1030 1.005867 GGTACCAACGGTGCGAGAA 60.006 57.895 7.15 0.00 39.20 2.87
972 1031 2.652530 GGTACCAACGGTGCGAGA 59.347 61.111 7.15 0.00 39.20 4.04
973 1032 2.807895 CGGTACCAACGGTGCGAG 60.808 66.667 13.54 0.00 39.20 5.03
993 1052 2.453080 GCCATTGTTGACATGTATGCG 58.547 47.619 0.00 0.00 0.00 4.73
994 1053 2.453080 CGCCATTGTTGACATGTATGC 58.547 47.619 0.00 0.00 0.00 3.14
997 1056 0.808125 GGCGCCATTGTTGACATGTA 59.192 50.000 24.80 0.00 0.00 2.29
998 1057 1.586028 GGCGCCATTGTTGACATGT 59.414 52.632 24.80 0.00 0.00 3.21
999 1058 1.153784 GGGCGCCATTGTTGACATG 60.154 57.895 30.85 0.00 0.00 3.21
1000 1059 2.699768 CGGGCGCCATTGTTGACAT 61.700 57.895 30.85 0.00 0.00 3.06
1001 1060 3.361158 CGGGCGCCATTGTTGACA 61.361 61.111 30.85 0.00 0.00 3.58
1277 1339 2.094182 AGGACATTGTCGCTATTGTCGT 60.094 45.455 10.56 0.00 39.45 4.34
1432 1494 1.306141 TGAAGGTGAGCCGAGGGAT 60.306 57.895 0.00 0.00 40.50 3.85
1599 1673 1.296715 CTCCACGAACTTCCCCCAG 59.703 63.158 0.00 0.00 0.00 4.45
1878 1952 1.065928 GCCGTGTCCGACCTCATAG 59.934 63.158 0.00 0.00 35.63 2.23
1881 1955 4.988716 AGGCCGTGTCCGACCTCA 62.989 66.667 0.00 0.00 44.32 3.86
1899 1973 1.984570 CGGCTTCCCAGAGTCCTCA 60.985 63.158 0.00 0.00 0.00 3.86
1956 2030 2.359230 AGCCACTCTTGCGCTTCC 60.359 61.111 9.73 0.00 0.00 3.46
2022 2096 3.211963 GCGATTTGAGGCGCCCAT 61.212 61.111 26.15 10.58 46.93 4.00
2035 2109 0.667487 CGGTGCGATAGAATGGCGAT 60.667 55.000 0.00 0.00 36.74 4.58
2076 2150 3.050275 GAGTTCCACCCGCAGTGC 61.050 66.667 4.58 4.58 45.83 4.40
2115 2189 1.739929 CGTTATGACAGGCACGCCA 60.740 57.895 11.35 0.00 38.92 5.69
2167 2241 1.301401 GTACGTCCACAGCAAGCCA 60.301 57.895 0.00 0.00 0.00 4.75
2175 2249 1.749665 CACCCCAAGTACGTCCACA 59.250 57.895 0.00 0.00 0.00 4.17
2211 2285 0.322322 TGGCCTTGTCGTTACCGAAT 59.678 50.000 3.32 0.00 46.26 3.34
2320 2403 2.880770 CTCCGTGAGCTCTCTCCTT 58.119 57.895 16.19 0.00 38.58 3.36
2321 2404 4.655921 CTCCGTGAGCTCTCTCCT 57.344 61.111 16.19 0.00 38.58 3.69
2358 2441 0.447801 GCGTCAGGTTTTCATGCGAT 59.552 50.000 0.00 0.00 34.88 4.58
2398 2481 1.073722 CTTCCTTGCTGCCACTCCA 59.926 57.895 0.00 0.00 0.00 3.86
2416 2499 4.750598 GGCCTAACAATTCCGAATCTACTC 59.249 45.833 0.00 0.00 0.00 2.59
2442 2525 3.054139 TCACCTAGCAGAGCAATGGAATT 60.054 43.478 0.00 0.00 36.63 2.17
2444 2527 1.908619 TCACCTAGCAGAGCAATGGAA 59.091 47.619 0.00 0.00 0.00 3.53
2446 2529 2.286872 CTTCACCTAGCAGAGCAATGG 58.713 52.381 0.00 0.00 0.00 3.16
2448 2531 2.304180 ACACTTCACCTAGCAGAGCAAT 59.696 45.455 0.00 0.00 0.00 3.56
2474 2558 3.879998 TGTCCTTTGACAGTTTAGCACA 58.120 40.909 0.00 0.00 46.40 4.57
2494 2578 6.824305 ACTAGAGATTTGGACCATTTGTTG 57.176 37.500 0.00 0.00 0.00 3.33
2712 2797 0.317603 CGACATACCTTACCGCCTCG 60.318 60.000 0.00 0.00 0.00 4.63
2739 2824 8.941977 GCGTATACATCCAATGGTATATTGAAA 58.058 33.333 3.32 0.00 35.56 2.69
2744 2829 7.847096 TCTTGCGTATACATCCAATGGTATAT 58.153 34.615 3.32 0.00 35.56 0.86
2750 2835 5.292765 AGTCTCTTGCGTATACATCCAATG 58.707 41.667 3.32 0.86 0.00 2.82
2751 2836 5.537300 AGTCTCTTGCGTATACATCCAAT 57.463 39.130 3.32 0.00 0.00 3.16
2826 2911 6.479001 ACATTCGTGAACCATAGCAGTTATAC 59.521 38.462 0.00 0.00 0.00 1.47
2845 2930 5.163814 GGTTTTCCTCTGAATCTCACATTCG 60.164 44.000 0.00 0.00 36.94 3.34
2863 2948 2.740668 CACATGCGCATGGGTTTTC 58.259 52.632 43.46 0.00 42.91 2.29
2932 3019 2.501723 AGCGGAGTCATCTGGTGTTAAT 59.498 45.455 0.00 0.00 41.02 1.40
2952 3039 1.755179 ATCGCCCTTGACCATGAAAG 58.245 50.000 0.00 0.00 0.00 2.62
2964 3051 2.947652 CTCATTGACATTCAATCGCCCT 59.052 45.455 0.00 0.00 43.03 5.19
2969 3056 3.444742 TGTGCCCTCATTGACATTCAATC 59.555 43.478 0.00 0.00 43.03 2.67
2977 3064 2.821969 ACAAGAATGTGCCCTCATTGAC 59.178 45.455 0.80 0.00 38.69 3.18
3032 3119 8.072567 ACCAATAACAACGTCTCGTAGTATATC 58.927 37.037 0.00 0.00 39.99 1.63
3088 3175 5.929992 TCGTCCAAGGATACAAACAAGTAAG 59.070 40.000 0.00 0.00 41.41 2.34
3099 3186 3.381908 ACACTCTCATCGTCCAAGGATAC 59.618 47.826 0.00 0.00 0.00 2.24
3108 3195 4.362932 TCATCTCAACACTCTCATCGTC 57.637 45.455 0.00 0.00 0.00 4.20
3111 3198 6.145858 GCATACATCATCTCAACACTCTCATC 59.854 42.308 0.00 0.00 0.00 2.92
3113 3200 5.128335 AGCATACATCATCTCAACACTCTCA 59.872 40.000 0.00 0.00 0.00 3.27
3169 3256 1.310904 TTTTGACCACCCTGTTACGC 58.689 50.000 0.00 0.00 0.00 4.42
3182 3269 8.364894 AGATAACCCAATAACAACCTTTTTGAC 58.635 33.333 0.00 0.00 0.00 3.18
3184 3271 9.855021 CTAGATAACCCAATAACAACCTTTTTG 57.145 33.333 0.00 0.00 0.00 2.44
3190 3277 7.793036 ACTCTCTAGATAACCCAATAACAACC 58.207 38.462 0.00 0.00 0.00 3.77
3244 3331 9.030452 TCTCTATTATCTAGAGGAGCAATTTCC 57.970 37.037 8.89 0.00 40.95 3.13
3291 3378 8.349983 ACACTTGTTTGTGAATACTTTCATACC 58.650 33.333 1.47 0.00 43.49 2.73
3316 3403 0.883153 TCATGCCATTGTCTGTGCAC 59.117 50.000 10.75 10.75 35.01 4.57
3377 3464 3.984508 ATCCTCGTTACTGGTATGACG 57.015 47.619 0.00 0.00 36.89 4.35
3383 3470 5.503927 TGTCTACTTATCCTCGTTACTGGT 58.496 41.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.