Multiple sequence alignment - TraesCS1A01G225600

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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 TraesCS1A01G225600 chr1A 100.000 3932 0 0 1 3932 396099633 396103564 0.000000e+00 7262.0
1 TraesCS1A01G225600 chr1B 94.828 2494 115 9 539 3024 427216251 427213764 0.000000e+00 3879.0
2 TraesCS1A01G225600 chr1B 94.118 867 34 4 3077 3932 427213767 427212907 0.000000e+00 1303.0
3 TraesCS1A01G225600 chr1B 88.060 536 63 1 1 535 165549509 165550044 5.540000e-178 634.0
4 TraesCS1A01G225600 chr1B 100.000 28 0 0 3059 3086 535979643 535979670 7.000000e-03 52.8
5 TraesCS1A01G225600 chr1D 95.103 2389 97 13 640 3024 315536339 315538711 0.000000e+00 3746.0
6 TraesCS1A01G225600 chr1D 93.426 867 42 3 3077 3932 315538708 315539570 0.000000e+00 1271.0
7 TraesCS1A01G225600 chr1D 88.577 534 59 2 7 539 644999 644467 0.000000e+00 647.0
8 TraesCS1A01G225600 chr1D 93.878 98 4 1 539 636 315529239 315529334 3.170000e-31 147.0
9 TraesCS1A01G225600 chr5D 89.925 536 52 2 7 541 500227244 500226710 0.000000e+00 689.0
10 TraesCS1A01G225600 chr5D 88.561 542 57 5 1 541 464060619 464061156 0.000000e+00 652.0
11 TraesCS1A01G225600 chr2D 89.033 538 58 1 1 537 467999384 467999921 0.000000e+00 665.0
12 TraesCS1A01G225600 chr2D 88.060 536 60 4 7 540 566709545 566709012 1.990000e-177 632.0
13 TraesCS1A01G225600 chr3A 88.662 538 59 2 1 537 509080 509616 0.000000e+00 654.0
14 TraesCS1A01G225600 chr6D 88.082 537 62 2 7 542 230823114 230822579 1.540000e-178 636.0
15 TraesCS1A01G225600 chr5B 87.985 541 61 3 1 537 622615576 622616116 1.540000e-178 636.0
16 TraesCS1A01G225600 chr4B 96.552 58 1 1 3023 3080 670245990 670245934 1.160000e-15 95.3
17 TraesCS1A01G225600 chr5A 94.828 58 1 1 3023 3080 690307536 690307481 5.410000e-14 89.8
18 TraesCS1A01G225600 chr5A 87.692 65 4 4 2998 3059 39114841 39114778 5.450000e-09 73.1
19 TraesCS1A01G225600 chr4A 93.103 58 1 2 3023 3080 548307452 548307506 9.060000e-12 82.4
20 TraesCS1A01G225600 chr6B 87.013 77 2 5 3010 3080 144010320 144010246 3.260000e-11 80.5
21 TraesCS1A01G225600 chr3B 97.826 46 1 0 3019 3064 173115961 173116006 3.260000e-11 80.5
22 TraesCS1A01G225600 chr3D 89.831 59 4 1 3022 3080 566681951 566681895 1.520000e-09 75.0
23 TraesCS1A01G225600 chr7B 88.333 60 5 2 3022 3080 684464028 684463970 1.960000e-08 71.3
24 TraesCS1A01G225600 chr7B 88.333 60 5 2 3022 3080 690053021 690052963 1.960000e-08 71.3


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 TraesCS1A01G225600 chr1A 396099633 396103564 3931 False 7262.0 7262 100.0000 1 3932 1 chr1A.!!$F1 3931
1 TraesCS1A01G225600 chr1B 427212907 427216251 3344 True 2591.0 3879 94.4730 539 3932 2 chr1B.!!$R1 3393
2 TraesCS1A01G225600 chr1B 165549509 165550044 535 False 634.0 634 88.0600 1 535 1 chr1B.!!$F1 534
3 TraesCS1A01G225600 chr1D 315536339 315539570 3231 False 2508.5 3746 94.2645 640 3932 2 chr1D.!!$F2 3292
4 TraesCS1A01G225600 chr1D 644467 644999 532 True 647.0 647 88.5770 7 539 1 chr1D.!!$R1 532
5 TraesCS1A01G225600 chr5D 500226710 500227244 534 True 689.0 689 89.9250 7 541 1 chr5D.!!$R1 534
6 TraesCS1A01G225600 chr5D 464060619 464061156 537 False 652.0 652 88.5610 1 541 1 chr5D.!!$F1 540
7 TraesCS1A01G225600 chr2D 467999384 467999921 537 False 665.0 665 89.0330 1 537 1 chr2D.!!$F1 536
8 TraesCS1A01G225600 chr2D 566709012 566709545 533 True 632.0 632 88.0600 7 540 1 chr2D.!!$R1 533
9 TraesCS1A01G225600 chr3A 509080 509616 536 False 654.0 654 88.6620 1 537 1 chr3A.!!$F1 536
10 TraesCS1A01G225600 chr6D 230822579 230823114 535 True 636.0 636 88.0820 7 542 1 chr6D.!!$R1 535
11 TraesCS1A01G225600 chr5B 622615576 622616116 540 False 636.0 636 87.9850 1 537 1 chr5B.!!$F1 536

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
666 673 0.250234 TGTTGAGGAGGCGAAGATGG 59.750 55.0 0.0 0.0 0.0 3.51 F
1423 1438 0.032615 AAGATGCCTCTCGACCTCCT 60.033 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1610 0.390340 GAGGACAGCAATCACGAGCA 60.390 55.0 0.00 0.0 0.00 4.26 R
3022 3038 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 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
50 51 2.592574 CGGCGGTGATGATGGCAT 60.593 61.111 0.00 0.00 37.47 4.40
69 70 0.608856 TGACCATGGTGGCACATGTC 60.609 55.000 25.52 18.01 45.21 3.06
94 95 0.745845 GCGACATGATTGGTGGAGCT 60.746 55.000 0.00 0.00 0.00 4.09
95 96 1.742761 CGACATGATTGGTGGAGCTT 58.257 50.000 0.00 0.00 0.00 3.74
140 141 0.958382 TTTGGCGGACGGGAGAAATG 60.958 55.000 0.00 0.00 0.00 2.32
289 293 1.226575 CAGCGGCGTCTTCATCGTA 60.227 57.895 9.37 0.00 0.00 3.43
331 335 1.591863 GTATGCGGAGGTTCGAGGC 60.592 63.158 0.00 0.00 0.00 4.70
354 359 1.867363 AGGAGCGAGGTGGTAATCTT 58.133 50.000 0.00 0.00 0.00 2.40
364 369 1.259142 TGGTAATCTTCGGTGGGCGA 61.259 55.000 0.00 0.00 0.00 5.54
365 370 0.529992 GGTAATCTTCGGTGGGCGAG 60.530 60.000 0.00 0.00 0.00 5.03
459 465 1.702182 TCTTTTGGGCATGCTTGTGA 58.298 45.000 18.92 6.14 0.00 3.58
463 469 2.212812 TTGGGCATGCTTGTGATGTA 57.787 45.000 18.92 0.00 0.00 2.29
472 478 1.683011 GCTTGTGATGTATGCCCCAGT 60.683 52.381 0.00 0.00 0.00 4.00
474 480 3.470709 CTTGTGATGTATGCCCCAGTAG 58.529 50.000 0.00 0.00 0.00 2.57
552 558 7.709613 GCCTATTTCGTCAATCTAAGGAGTAAA 59.290 37.037 0.00 0.00 0.00 2.01
556 562 6.829229 TCGTCAATCTAAGGAGTAAAGACA 57.171 37.500 0.00 0.00 0.00 3.41
590 596 4.142902 GCTGAAGTGCGTAAAGAATAGCAA 60.143 41.667 0.00 0.00 41.56 3.91
596 602 8.712285 AAGTGCGTAAAGAATAGCAACTTATA 57.288 30.769 0.00 0.00 41.56 0.98
597 603 8.888579 AGTGCGTAAAGAATAGCAACTTATAT 57.111 30.769 0.00 0.00 41.56 0.86
620 626 6.925610 TGTCATTTGTATCACTAGAATGGC 57.074 37.500 0.00 0.00 34.01 4.40
666 673 0.250234 TGTTGAGGAGGCGAAGATGG 59.750 55.000 0.00 0.00 0.00 3.51
668 675 1.552799 TTGAGGAGGCGAAGATGGCA 61.553 55.000 0.00 0.00 36.77 4.92
678 685 2.005451 CGAAGATGGCAGGTGAAGAAG 58.995 52.381 0.00 0.00 0.00 2.85
749 757 5.471116 TGTCTCATGTGCATAATAAGCATCC 59.529 40.000 0.00 0.00 44.79 3.51
908 921 2.990740 ACCAAAATGGGCCAACTCTA 57.009 45.000 11.89 0.00 43.37 2.43
909 922 2.525368 ACCAAAATGGGCCAACTCTAC 58.475 47.619 11.89 0.00 43.37 2.59
952 965 2.930562 ACCCAGCCCAGTGGAGAC 60.931 66.667 11.95 0.00 40.44 3.36
954 967 2.997315 CCAGCCCAGTGGAGACGA 60.997 66.667 11.95 0.00 40.44 4.20
976 989 3.816523 ACAACAAAACCATACTACCACGG 59.183 43.478 0.00 0.00 0.00 4.94
977 990 3.775261 ACAAAACCATACTACCACGGT 57.225 42.857 0.00 0.00 0.00 4.83
978 991 3.667360 ACAAAACCATACTACCACGGTC 58.333 45.455 0.00 0.00 0.00 4.79
979 992 3.004862 CAAAACCATACTACCACGGTCC 58.995 50.000 0.00 0.00 0.00 4.46
980 993 2.242882 AACCATACTACCACGGTCCT 57.757 50.000 0.00 0.00 0.00 3.85
1168 1183 2.592861 GCCCTCATCGCCACATCC 60.593 66.667 0.00 0.00 0.00 3.51
1259 1274 3.190849 CGCGCCACATCTGACCTG 61.191 66.667 0.00 0.00 0.00 4.00
1314 1329 3.391382 GGCCTGCTACCCAGTCGT 61.391 66.667 0.00 0.00 40.06 4.34
1346 1361 1.002087 ACTTTCAGCGAGATCCCGTTT 59.998 47.619 0.00 0.00 0.00 3.60
1423 1438 0.032615 AAGATGCCTCTCGACCTCCT 60.033 55.000 0.00 0.00 0.00 3.69
1457 1472 3.857309 AAGACGACGACGAGGGGGT 62.857 63.158 15.32 0.00 42.66 4.95
1639 1654 2.725759 CGATTCAATCACGCACACAAGG 60.726 50.000 0.00 0.00 0.00 3.61
2296 2311 1.339438 GGTGCTTTGAGGAGATGCAGA 60.339 52.381 0.00 0.00 34.15 4.26
2300 2315 2.641305 CTTTGAGGAGATGCAGAAGGG 58.359 52.381 0.00 0.00 0.00 3.95
2352 2367 1.035139 GCTTGCTTGTGGGATATGGG 58.965 55.000 0.00 0.00 0.00 4.00
2360 2375 2.948115 TGTGGGATATGGGAATGCAAG 58.052 47.619 0.00 0.00 0.00 4.01
2382 2397 2.389059 CGAATGGATAGAGTGACTGCG 58.611 52.381 0.00 0.00 0.00 5.18
2391 2406 1.344438 AGAGTGACTGCGATGTTGGAA 59.656 47.619 0.00 0.00 0.00 3.53
2439 2454 0.675208 ATGGCCGAACGTACAATGCA 60.675 50.000 0.00 0.00 0.00 3.96
2460 2475 4.671250 GCACTGATTAAGCTGCTCAAGAAC 60.671 45.833 1.00 0.00 33.05 3.01
2535 2550 2.346803 CTTGAACCCACTGTCCATACG 58.653 52.381 0.00 0.00 0.00 3.06
2676 2691 8.609176 GTGTTTATTAATGGTCACATACGACAT 58.391 33.333 0.00 0.00 37.66 3.06
2837 2852 6.004574 AGAAGGTGAAGTTTACAGGGAAATC 58.995 40.000 0.00 0.00 0.00 2.17
2999 3015 5.008415 CCTGCTATTTATGAAAGAGGTGCTG 59.992 44.000 0.00 0.00 30.60 4.41
3020 3036 7.759886 GTGCTGTAGTTTCTCTGATGTTGTATA 59.240 37.037 0.00 0.00 0.00 1.47
3021 3037 7.976175 TGCTGTAGTTTCTCTGATGTTGTATAG 59.024 37.037 0.00 0.00 0.00 1.31
3022 3038 7.976734 GCTGTAGTTTCTCTGATGTTGTATAGT 59.023 37.037 0.00 0.00 0.00 2.12
3027 3043 8.688151 AGTTTCTCTGATGTTGTATAGTACTCC 58.312 37.037 0.00 0.00 0.00 3.85
3028 3044 7.584122 TTCTCTGATGTTGTATAGTACTCCC 57.416 40.000 0.00 0.00 0.00 4.30
3029 3045 6.912426 TCTCTGATGTTGTATAGTACTCCCT 58.088 40.000 0.00 0.00 0.00 4.20
3030 3046 6.999272 TCTCTGATGTTGTATAGTACTCCCTC 59.001 42.308 0.00 0.00 0.00 4.30
3031 3047 6.069331 TCTGATGTTGTATAGTACTCCCTCC 58.931 44.000 0.00 0.00 0.00 4.30
3032 3048 4.825634 TGATGTTGTATAGTACTCCCTCCG 59.174 45.833 0.00 0.00 0.00 4.63
3033 3049 4.240881 TGTTGTATAGTACTCCCTCCGT 57.759 45.455 0.00 0.00 0.00 4.69
3034 3050 4.202441 TGTTGTATAGTACTCCCTCCGTC 58.798 47.826 0.00 0.00 0.00 4.79
3035 3051 3.498774 TGTATAGTACTCCCTCCGTCC 57.501 52.381 0.00 0.00 0.00 4.79
3036 3052 2.224378 TGTATAGTACTCCCTCCGTCCG 60.224 54.545 0.00 0.00 0.00 4.79
3037 3053 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
3038 3054 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
3039 3055 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3040 3056 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3041 3057 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3042 3058 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3043 3059 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3044 3060 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3045 3061 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3046 3062 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3047 3063 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3048 3064 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3049 3065 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
3050 3066 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
3051 3067 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
3052 3068 3.490419 CCGTCCGGAAATACTTGTCCTAG 60.490 52.174 5.23 0.00 37.50 3.02
3053 3069 3.379372 CGTCCGGAAATACTTGTCCTAGA 59.621 47.826 5.23 0.00 0.00 2.43
3054 3070 4.142315 CGTCCGGAAATACTTGTCCTAGAA 60.142 45.833 5.23 0.00 0.00 2.10
3055 3071 5.622914 CGTCCGGAAATACTTGTCCTAGAAA 60.623 44.000 5.23 0.00 0.00 2.52
3056 3072 6.346896 GTCCGGAAATACTTGTCCTAGAAAT 58.653 40.000 5.23 0.00 0.00 2.17
3057 3073 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
3058 3074 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
3059 3075 6.113411 CGGAAATACTTGTCCTAGAAATGGT 58.887 40.000 0.00 0.00 0.00 3.55
3060 3076 7.270047 CGGAAATACTTGTCCTAGAAATGGTA 58.730 38.462 0.00 0.00 0.00 3.25
3061 3077 7.931948 CGGAAATACTTGTCCTAGAAATGGTAT 59.068 37.037 0.00 0.00 0.00 2.73
3062 3078 9.628500 GGAAATACTTGTCCTAGAAATGGTATT 57.372 33.333 0.00 0.00 32.36 1.89
3065 3081 9.628500 AATACTTGTCCTAGAAATGGTATTTCC 57.372 33.333 9.89 0.00 0.00 3.13
3066 3082 6.113411 ACTTGTCCTAGAAATGGTATTTCCG 58.887 40.000 9.89 3.49 39.52 4.30
3067 3083 5.031066 TGTCCTAGAAATGGTATTTCCGG 57.969 43.478 9.89 0.00 39.52 5.14
3068 3084 4.717778 TGTCCTAGAAATGGTATTTCCGGA 59.282 41.667 0.00 0.00 39.52 5.14
3069 3085 5.055144 GTCCTAGAAATGGTATTTCCGGAC 58.945 45.833 22.97 22.97 39.75 4.79
3070 3086 4.056050 CCTAGAAATGGTATTTCCGGACG 58.944 47.826 1.83 0.00 39.52 4.79
3071 3087 2.914059 AGAAATGGTATTTCCGGACGG 58.086 47.619 1.83 3.96 39.52 4.79
3072 3088 2.502538 AGAAATGGTATTTCCGGACGGA 59.497 45.455 1.83 9.76 43.52 4.69
3073 3089 2.614829 AATGGTATTTCCGGACGGAG 57.385 50.000 13.64 0.00 46.06 4.63
3074 3090 0.756903 ATGGTATTTCCGGACGGAGG 59.243 55.000 13.64 0.00 46.06 4.30
3075 3091 1.332144 TGGTATTTCCGGACGGAGGG 61.332 60.000 13.64 0.00 46.06 4.30
3170 3186 4.222124 AGTTTCTGTGAAACTCAGGTGT 57.778 40.909 16.93 0.00 35.76 4.16
3171 3187 5.353394 AGTTTCTGTGAAACTCAGGTGTA 57.647 39.130 16.93 0.00 35.76 2.90
3213 3240 6.017109 CACTCTGCAATTGTTTTGTAGGTACT 60.017 38.462 7.40 0.00 46.37 2.73
3275 3302 2.299993 TTCTATCTTGCAGTGGCTCG 57.700 50.000 0.00 0.00 41.91 5.03
3420 3447 4.216411 TGTAGGCTTAGACATTGGAACC 57.784 45.455 0.00 0.00 0.00 3.62
3441 3468 1.207329 AGCTGGAACTTAAGGGCTACG 59.793 52.381 7.53 0.00 0.00 3.51
3491 3518 7.654022 ATTTACACCCTTTTGAGTTTGAAGA 57.346 32.000 0.00 0.00 0.00 2.87
3500 3527 9.546428 CCCTTTTGAGTTTGAAGATAACAAAAT 57.454 29.630 0.00 0.00 38.63 1.82
3542 3569 0.030101 CGTTTTGGGTGCACGTTCAT 59.970 50.000 11.45 0.00 0.00 2.57
3554 3581 3.439825 TGCACGTTCATTGCATATTCTGT 59.560 39.130 0.00 0.00 45.06 3.41
3601 3628 5.152623 TGTAGCTTGATGGATACCTATGC 57.847 43.478 0.00 0.00 0.00 3.14
3667 3694 5.702865 CTTAAGGTGTCATCATGGTGTTTG 58.297 41.667 5.73 0.00 0.00 2.93
3668 3695 3.507162 AGGTGTCATCATGGTGTTTGA 57.493 42.857 5.73 0.00 0.00 2.69
3669 3696 4.038271 AGGTGTCATCATGGTGTTTGAT 57.962 40.909 5.73 0.00 34.15 2.57
3693 3720 4.271291 GGAAGTTCTTTGTCGATGCTATCC 59.729 45.833 2.25 0.00 0.00 2.59
3785 3812 7.101652 TGAGTCCACTCTAATACAGTGATTC 57.898 40.000 8.19 0.00 43.54 2.52
3798 3825 3.769844 ACAGTGATTCGAGTCCCAGTATT 59.230 43.478 5.38 0.00 0.00 1.89
3849 3876 7.276658 AGTTTTCTGCATTACTATCTCTTGTCG 59.723 37.037 0.00 0.00 0.00 4.35
3869 3896 6.837992 TGTCGTAAATTTCTATCAAAGTGCC 58.162 36.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.608856 GACATGTGCCACCATGGTCA 60.609 55.000 16.53 10.72 45.21 4.02
69 70 2.472059 CCAATCATGTCGCCCACCG 61.472 63.158 0.00 0.00 38.61 4.94
94 95 1.134818 CATCCTCGAATGGTCCGACAA 60.135 52.381 0.00 0.00 32.18 3.18
95 96 0.459899 CATCCTCGAATGGTCCGACA 59.540 55.000 0.00 0.00 32.18 4.35
276 277 2.795470 GGAAGGAATACGATGAAGACGC 59.205 50.000 0.00 0.00 0.00 5.19
364 369 4.778143 GATCACCCGCAACCGCCT 62.778 66.667 0.00 0.00 33.11 5.52
378 383 5.899318 GTCAGATCGACGAAAATGATGATC 58.101 41.667 0.00 0.00 34.19 2.92
459 465 3.115390 AGTTCACTACTGGGGCATACAT 58.885 45.455 0.00 0.00 35.19 2.29
463 469 1.958288 AGAGTTCACTACTGGGGCAT 58.042 50.000 0.00 0.00 37.17 4.40
472 478 5.011329 ACCCGATACAACAAAGAGTTCACTA 59.989 40.000 0.00 0.00 38.74 2.74
474 480 4.062991 ACCCGATACAACAAAGAGTTCAC 58.937 43.478 0.00 0.00 38.74 3.18
537 543 9.003658 ACAAATGTGTCTTTACTCCTTAGATTG 57.996 33.333 0.00 0.00 29.49 2.67
552 558 4.036027 CACTTCAGCTTCACAAATGTGTCT 59.964 41.667 12.87 6.66 45.76 3.41
556 562 2.287188 CGCACTTCAGCTTCACAAATGT 60.287 45.455 0.00 0.00 0.00 2.71
568 574 5.120830 AGTTGCTATTCTTTACGCACTTCAG 59.879 40.000 0.00 0.00 31.24 3.02
596 602 7.285566 AGCCATTCTAGTGATACAAATGACAT 58.714 34.615 0.00 0.00 30.64 3.06
597 603 6.653020 AGCCATTCTAGTGATACAAATGACA 58.347 36.000 0.00 0.00 30.64 3.58
641 648 4.647611 TCTTCGCCTCCTCAACAAATAAA 58.352 39.130 0.00 0.00 0.00 1.40
648 655 1.092345 GCCATCTTCGCCTCCTCAAC 61.092 60.000 0.00 0.00 0.00 3.18
711 719 5.522824 CACATGAGACATCATCATCGACTTT 59.477 40.000 0.00 0.00 44.58 2.66
716 724 3.128349 TGCACATGAGACATCATCATCG 58.872 45.455 0.00 0.00 44.58 3.84
718 726 8.857694 TTATTATGCACATGAGACATCATCAT 57.142 30.769 0.00 0.00 44.58 2.45
719 727 7.094933 GCTTATTATGCACATGAGACATCATCA 60.095 37.037 0.00 0.00 44.58 3.07
825 835 9.276590 TCATTGATTAAATAGCACCAGTCATAG 57.723 33.333 0.00 0.00 0.00 2.23
826 836 9.625747 TTCATTGATTAAATAGCACCAGTCATA 57.374 29.630 0.00 0.00 0.00 2.15
827 837 8.523915 TTCATTGATTAAATAGCACCAGTCAT 57.476 30.769 0.00 0.00 0.00 3.06
834 844 6.138761 CGGCTCTTCATTGATTAAATAGCAC 58.861 40.000 0.00 0.00 30.68 4.40
887 900 2.407562 AGAGTTGGCCCATTTTGGTTT 58.592 42.857 0.00 0.00 35.17 3.27
888 901 2.101640 AGAGTTGGCCCATTTTGGTT 57.898 45.000 0.00 0.00 35.17 3.67
908 921 6.565247 CGTTAAAAACCATTCTGCGTCTTAGT 60.565 38.462 0.00 0.00 0.00 2.24
909 922 5.788531 CGTTAAAAACCATTCTGCGTCTTAG 59.211 40.000 0.00 0.00 0.00 2.18
952 965 4.376615 CGTGGTAGTATGGTTTTGTTGTCG 60.377 45.833 0.00 0.00 0.00 4.35
954 967 3.816523 CCGTGGTAGTATGGTTTTGTTGT 59.183 43.478 0.00 0.00 0.00 3.32
976 989 4.338400 GGAATAATGTTGGGTTAGCAGGAC 59.662 45.833 0.00 0.00 0.00 3.85
977 990 4.017958 TGGAATAATGTTGGGTTAGCAGGA 60.018 41.667 0.00 0.00 0.00 3.86
978 991 4.277476 TGGAATAATGTTGGGTTAGCAGG 58.723 43.478 0.00 0.00 0.00 4.85
979 992 5.221303 CCATGGAATAATGTTGGGTTAGCAG 60.221 44.000 5.56 0.00 0.00 4.24
980 993 4.648762 CCATGGAATAATGTTGGGTTAGCA 59.351 41.667 5.56 0.00 0.00 3.49
1305 1320 4.065281 GGTAGCGCACGACTGGGT 62.065 66.667 11.47 0.00 32.83 4.51
1311 1326 1.131883 GAAAGTAGAGGTAGCGCACGA 59.868 52.381 11.47 0.00 0.00 4.35
1314 1329 1.135083 GCTGAAAGTAGAGGTAGCGCA 60.135 52.381 11.47 0.00 35.30 6.09
1437 1452 2.484203 CCCTCGTCGTCGTCTTCC 59.516 66.667 1.33 0.00 38.33 3.46
1595 1610 0.390340 GAGGACAGCAATCACGAGCA 60.390 55.000 0.00 0.00 0.00 4.26
1639 1654 2.401195 GAAGAAGCGGCGTGATGC 59.599 61.111 9.37 0.00 45.38 3.91
1839 1854 3.754850 CACCAACTGCATTCTTGATCTCA 59.245 43.478 0.00 0.00 0.00 3.27
1943 1958 4.479993 CTGCCTCCTTCCCCAGCG 62.480 72.222 0.00 0.00 0.00 5.18
2352 2367 3.141398 TCTATCCATTCGCCTTGCATTC 58.859 45.455 0.00 0.00 0.00 2.67
2360 2375 2.748605 CAGTCACTCTATCCATTCGCC 58.251 52.381 0.00 0.00 0.00 5.54
2382 2397 3.507233 TCTGTGCCATTTCTTCCAACATC 59.493 43.478 0.00 0.00 0.00 3.06
2391 2406 0.779997 ACCCCTTCTGTGCCATTTCT 59.220 50.000 0.00 0.00 0.00 2.52
2439 2454 4.645535 TGTTCTTGAGCAGCTTAATCAGT 58.354 39.130 0.00 0.00 0.00 3.41
2460 2475 3.418047 TGCATCATCTGGCATATTCCTG 58.582 45.455 0.00 0.00 34.58 3.86
2526 2541 5.331876 TCATCATGTTGTACGTATGGACA 57.668 39.130 0.00 0.00 0.00 4.02
2527 2542 5.983118 TCATCATCATGTTGTACGTATGGAC 59.017 40.000 0.00 0.00 0.00 4.02
2535 2550 7.700322 ATACGACTTCATCATCATGTTGTAC 57.300 36.000 3.76 0.00 32.46 2.90
2593 2608 1.278537 TGCATCTCATCCCACACTGA 58.721 50.000 0.00 0.00 0.00 3.41
2676 2691 1.203441 ATGCTTCCTCAGGTCTGCCA 61.203 55.000 0.00 0.00 37.19 4.92
3020 3036 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
3021 3037 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
3022 3038 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3023 3039 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3024 3040 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3025 3041 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3026 3042 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3027 3043 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3028 3044 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3029 3045 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
3030 3046 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
3031 3047 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
3032 3048 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
3033 3049 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
3034 3050 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
3035 3051 6.113411 ACCATTTCTAGGACAAGTATTTCCG 58.887 40.000 0.00 0.00 36.95 4.30
3036 3052 9.628500 AATACCATTTCTAGGACAAGTATTTCC 57.372 33.333 0.00 0.00 0.00 3.13
3039 3055 9.628500 GGAAATACCATTTCTAGGACAAGTATT 57.372 33.333 10.53 0.00 38.79 1.89
3040 3056 7.931948 CGGAAATACCATTTCTAGGACAAGTAT 59.068 37.037 10.53 0.00 38.90 2.12
3041 3057 7.270047 CGGAAATACCATTTCTAGGACAAGTA 58.730 38.462 10.53 0.00 38.90 2.24
3042 3058 6.113411 CGGAAATACCATTTCTAGGACAAGT 58.887 40.000 10.53 0.00 38.90 3.16
3043 3059 5.527582 CCGGAAATACCATTTCTAGGACAAG 59.472 44.000 0.00 0.00 38.90 3.16
3044 3060 5.190132 TCCGGAAATACCATTTCTAGGACAA 59.810 40.000 0.00 4.97 38.90 3.18
3045 3061 4.717778 TCCGGAAATACCATTTCTAGGACA 59.282 41.667 0.00 5.42 38.90 4.02
3046 3062 5.055144 GTCCGGAAATACCATTTCTAGGAC 58.945 45.833 25.30 25.30 42.42 3.85
3047 3063 4.202182 CGTCCGGAAATACCATTTCTAGGA 60.202 45.833 5.23 17.28 38.90 2.94
3048 3064 4.056050 CGTCCGGAAATACCATTTCTAGG 58.944 47.826 5.23 12.90 38.90 3.02
3049 3065 4.056050 CCGTCCGGAAATACCATTTCTAG 58.944 47.826 5.23 6.27 38.90 2.43
3050 3066 3.705579 TCCGTCCGGAAATACCATTTCTA 59.294 43.478 5.23 0.00 42.05 2.10
3051 3067 2.502538 TCCGTCCGGAAATACCATTTCT 59.497 45.455 5.23 0.00 42.05 2.52
3052 3068 2.870411 CTCCGTCCGGAAATACCATTTC 59.130 50.000 5.23 3.52 44.66 2.17
3053 3069 2.420967 CCTCCGTCCGGAAATACCATTT 60.421 50.000 5.23 0.00 44.66 2.32
3054 3070 1.140252 CCTCCGTCCGGAAATACCATT 59.860 52.381 5.23 0.00 44.66 3.16
3055 3071 0.756903 CCTCCGTCCGGAAATACCAT 59.243 55.000 5.23 0.00 44.66 3.55
3056 3072 1.332144 CCCTCCGTCCGGAAATACCA 61.332 60.000 5.23 0.00 44.66 3.25
3057 3073 1.044790 TCCCTCCGTCCGGAAATACC 61.045 60.000 5.23 0.00 44.66 2.73
3058 3074 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3059 3075 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3060 3076 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3061 3077 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
3062 3078 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
3063 3079 0.846015 TATTACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
3064 3080 0.957362 GTATTACTCCCTCCGTCCGG 59.043 60.000 0.00 0.00 0.00 5.14
3065 3081 1.978454 AGTATTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
3066 3082 6.041296 TCAATAAAGTATTACTCCCTCCGTCC 59.959 42.308 0.00 0.00 0.00 4.79
3067 3083 7.047460 TCAATAAAGTATTACTCCCTCCGTC 57.953 40.000 0.00 0.00 0.00 4.79
3068 3084 7.343833 TCTTCAATAAAGTATTACTCCCTCCGT 59.656 37.037 0.00 0.00 36.31 4.69
3069 3085 7.723324 TCTTCAATAAAGTATTACTCCCTCCG 58.277 38.462 0.00 0.00 36.31 4.63
3170 3186 3.678289 AGTGATGCTTTGATGTGCAGTA 58.322 40.909 0.00 0.00 42.74 2.74
3171 3187 2.486982 GAGTGATGCTTTGATGTGCAGT 59.513 45.455 0.00 0.00 42.74 4.40
3213 3240 1.760613 GGTGCATACTAGGCCACTACA 59.239 52.381 5.01 0.00 0.00 2.74
3275 3302 8.230472 AGATCATTAAATTGGAAGATGTGGTC 57.770 34.615 0.00 0.00 0.00 4.02
3420 3447 2.633488 GTAGCCCTTAAGTTCCAGCTG 58.367 52.381 6.78 6.78 0.00 4.24
3441 3468 0.239347 GTGACATCAAGCAGGTGCAC 59.761 55.000 8.80 8.80 45.16 4.57
3500 3527 6.027131 CGACAAAGTCAACTTGTTTGATGAA 58.973 36.000 10.36 0.00 46.14 2.57
3523 3550 0.030101 ATGAACGTGCACCCAAAACG 59.970 50.000 12.15 0.00 42.82 3.60
3601 3628 1.475280 ACAAGGCTACAAGCATGCATG 59.525 47.619 22.70 22.70 44.75 4.06
3667 3694 3.686726 AGCATCGACAAAGAACTTCCATC 59.313 43.478 0.00 0.00 0.00 3.51
3668 3695 3.679389 AGCATCGACAAAGAACTTCCAT 58.321 40.909 0.00 0.00 0.00 3.41
3669 3696 3.126001 AGCATCGACAAAGAACTTCCA 57.874 42.857 0.00 0.00 0.00 3.53
3693 3720 3.492383 CAGTGGCTCATATTTCGCTACAG 59.508 47.826 0.00 0.00 37.57 2.74
3785 3812 3.066900 CACAGGAGTAATACTGGGACTCG 59.933 52.174 7.43 0.00 40.55 4.18
3812 3839 9.066892 AGTAATGCAGAAAACTAGACAAAATCA 57.933 29.630 0.00 0.00 0.00 2.57
3818 3845 8.972127 AGAGATAGTAATGCAGAAAACTAGACA 58.028 33.333 0.00 0.00 0.00 3.41
3869 3896 3.130633 GGGGTGCTTTACTTTGCAAAAG 58.869 45.455 13.84 8.70 41.10 2.27


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

AutoCloner maintained by Alex Coulton.