Multiple sequence alignment - TraesCS3A01G297000

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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 TraesCS3A01G297000 chr3A 100.000 2594 0 0 1000 3593 531668657 531666064 0.000000e+00 4791.0
1 TraesCS3A01G297000 chr3A 100.000 692 0 0 1 692 531669656 531668965 0.000000e+00 1279.0
2 TraesCS3A01G297000 chr3A 82.069 580 70 21 1297 1850 531667754 531667183 7.030000e-127 464.0
3 TraesCS3A01G297000 chr3A 82.069 580 70 21 1903 2474 531668360 531667807 7.030000e-127 464.0
4 TraesCS3A01G297000 chr3D 92.281 2267 103 28 1337 3589 419560287 419562495 0.000000e+00 3151.0
5 TraesCS3A01G297000 chr3D 84.114 491 46 14 1391 1850 419560926 419561415 2.550000e-121 446.0
6 TraesCS3A01G297000 chr3D 83.992 481 47 14 1994 2474 419560350 419560800 5.510000e-118 435.0
7 TraesCS3A01G297000 chr3D 90.064 312 30 1 1 311 419520327 419520638 1.550000e-108 403.0
8 TraesCS3A01G297000 chr3D 91.129 248 16 4 437 682 419559752 419559995 7.440000e-87 331.0
9 TraesCS3A01G297000 chr3B 90.204 1715 95 18 1890 3589 546183224 546181568 0.000000e+00 2169.0
10 TraesCS3A01G297000 chr3B 86.974 1520 96 41 1699 3184 545813669 545812218 0.000000e+00 1616.0
11 TraesCS3A01G297000 chr3B 94.607 853 38 5 1013 1858 546184074 546183223 0.000000e+00 1314.0
12 TraesCS3A01G297000 chr3B 92.229 682 44 3 1000 1672 545814343 545813662 0.000000e+00 957.0
13 TraesCS3A01G297000 chr3B 91.176 680 50 7 9 682 545815018 545814343 0.000000e+00 915.0
14 TraesCS3A01G297000 chr3B 87.153 576 52 10 1292 1850 545813469 545812899 5.060000e-178 634.0
15 TraesCS3A01G297000 chr3B 83.406 687 76 21 9 682 546184739 546184078 1.430000e-168 603.0
16 TraesCS3A01G297000 chr3B 88.889 387 28 5 1479 1850 546183035 546182649 2.530000e-126 462.0
17 TraesCS3A01G297000 chr3B 84.100 478 46 17 1997 2474 546183678 546183231 5.510000e-118 435.0
18 TraesCS3A01G297000 chr3B 78.392 398 64 18 1903 2292 545814037 545813654 4.640000e-59 239.0
19 TraesCS3A01G297000 chr3B 90.667 150 12 2 2326 2474 545813665 545813517 7.870000e-47 198.0
20 TraesCS3A01G297000 chr7A 91.667 48 3 1 9 56 54678034 54678080 8.330000e-07 65.8


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 TraesCS3A01G297000 chr3A 531666064 531669656 3592 True 1749.500000 4791 91.034500 1 3593 4 chr3A.!!$R1 3592
1 TraesCS3A01G297000 chr3D 419559752 419562495 2743 False 1090.750000 3151 87.879000 437 3589 4 chr3D.!!$F2 3152
2 TraesCS3A01G297000 chr3B 546181568 546184739 3171 True 996.600000 2169 88.241200 9 3589 5 chr3B.!!$R2 3580
3 TraesCS3A01G297000 chr3B 545812218 545815018 2800 True 759.833333 1616 87.765167 9 3184 6 chr3B.!!$R1 3175


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
538 554 0.394899 GCCCACTAAATCCAGCAGCT 60.395 55.0 0.0 0.0 0.0 4.24 F
1220 1254 0.032615 GAGGAGGAGGAGAGAGCCAA 60.033 60.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2474 2520 0.384669 GCTCTTGCCCTTGATCATGC 59.615 55.0 0.0 0.49 0.00 4.06 R
3093 3158 0.392863 TCAGGATGTGCCATTCACCG 60.393 55.0 0.0 0.00 45.03 4.94 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
35 36 3.694566 ACGGTTCAATTAGGGAGCATTTC 59.305 43.478 0.00 0.00 0.00 2.17
46 47 1.986413 AGCATTTCAGCTCGGGAGT 59.014 52.632 0.00 0.00 42.18 3.85
57 58 1.069091 GCTCGGGAGTAGATACTTCGC 60.069 57.143 0.00 4.98 36.50 4.70
58 59 2.219458 CTCGGGAGTAGATACTTCGCA 58.781 52.381 10.05 2.72 36.50 5.10
121 122 5.123227 CCTTGTTACTTCTTCTCCACACAA 58.877 41.667 0.00 0.00 0.00 3.33
124 125 5.116180 TGTTACTTCTTCTCCACACAAGTG 58.884 41.667 0.00 0.00 45.47 3.16
178 181 0.878523 TGGTCGAGGTGCTTTTGTCG 60.879 55.000 0.00 0.00 0.00 4.35
192 195 5.049267 TGCTTTTGTCGGGTACATCTAAAAC 60.049 40.000 0.00 0.00 38.10 2.43
217 220 6.319141 AGTGCATTTTTAACCTCTTCTGTC 57.681 37.500 0.00 0.00 0.00 3.51
232 235 2.847441 TCTGTCGTATATGGAGCGTCT 58.153 47.619 0.00 0.00 0.00 4.18
263 268 4.314740 TTCATTGCTGGCGTTAGTTTTT 57.685 36.364 0.00 0.00 0.00 1.94
302 307 1.668419 CTCATCCATCCCCAACGTTC 58.332 55.000 0.00 0.00 0.00 3.95
358 366 1.511850 TGATTGTGCGACTGTTGAGG 58.488 50.000 0.00 0.00 0.00 3.86
377 385 1.276989 GGTTCCTCACAATACGACCCA 59.723 52.381 0.00 0.00 0.00 4.51
538 554 0.394899 GCCCACTAAATCCAGCAGCT 60.395 55.000 0.00 0.00 0.00 4.24
582 598 2.539983 GCCCAGAAGTAGGCCCATA 58.460 57.895 0.00 0.00 43.76 2.74
611 627 3.287867 AGAAATGGATTCATCGCACCT 57.712 42.857 0.00 0.00 40.72 4.00
616 632 0.652592 GGATTCATCGCACCTGTTCG 59.347 55.000 0.00 0.00 0.00 3.95
627 643 2.989055 ACCTGTTCGGTCCACAAGCG 62.989 60.000 0.00 0.00 44.93 4.68
682 698 1.471676 CCTAACCCACATCGAGAGCAC 60.472 57.143 0.00 0.00 0.00 4.40
683 699 1.478510 CTAACCCACATCGAGAGCACT 59.521 52.381 0.00 0.00 0.00 4.40
684 700 0.687354 AACCCACATCGAGAGCACTT 59.313 50.000 0.00 0.00 0.00 3.16
685 701 0.687354 ACCCACATCGAGAGCACTTT 59.313 50.000 0.00 0.00 0.00 2.66
686 702 1.338200 ACCCACATCGAGAGCACTTTC 60.338 52.381 0.00 0.00 0.00 2.62
687 703 1.066573 CCCACATCGAGAGCACTTTCT 60.067 52.381 0.00 0.00 0.00 2.52
688 704 2.266554 CCACATCGAGAGCACTTTCTC 58.733 52.381 0.00 0.00 40.16 2.87
689 705 2.353109 CCACATCGAGAGCACTTTCTCA 60.353 50.000 0.00 0.00 43.02 3.27
690 706 3.320626 CACATCGAGAGCACTTTCTCAA 58.679 45.455 0.00 0.00 43.02 3.02
691 707 3.742882 CACATCGAGAGCACTTTCTCAAA 59.257 43.478 0.00 0.00 43.02 2.69
1098 1120 3.782443 GCGATGGGGAAGACGGGT 61.782 66.667 0.00 0.00 0.00 5.28
1099 1121 2.428925 GCGATGGGGAAGACGGGTA 61.429 63.158 0.00 0.00 0.00 3.69
1100 1122 1.740285 CGATGGGGAAGACGGGTAG 59.260 63.158 0.00 0.00 0.00 3.18
1116 1138 1.341778 GGTAGGACGGAGGAGGAGAAA 60.342 57.143 0.00 0.00 0.00 2.52
1119 1141 1.331399 GGACGGAGGAGGAGAAAGGG 61.331 65.000 0.00 0.00 0.00 3.95
1149 1171 1.850755 GGACAAGGGGAAGGGGTCA 60.851 63.158 0.00 0.00 0.00 4.02
1220 1254 0.032615 GAGGAGGAGGAGAGAGCCAA 60.033 60.000 0.00 0.00 0.00 4.52
1635 1669 1.504900 CCTCGACACGGTGATCGAA 59.495 57.895 24.73 14.97 46.01 3.71
1880 1914 0.608035 GTCAATTGCAAGACCCCCGA 60.608 55.000 4.94 0.00 0.00 5.14
1916 1950 1.980765 AGAGGAGGAAGACATGTGCAA 59.019 47.619 1.15 0.00 0.00 4.08
1979 2013 3.721706 AGCGGAGGGGGCAAGAAG 61.722 66.667 0.00 0.00 0.00 2.85
1981 2015 4.115199 CGGAGGGGGCAAGAAGGG 62.115 72.222 0.00 0.00 0.00 3.95
1990 2036 1.377333 GCAAGAAGGGGGAGAACCG 60.377 63.158 0.00 0.00 41.60 4.44
1991 2037 2.067197 CAAGAAGGGGGAGAACCGT 58.933 57.895 0.00 0.00 41.60 4.83
2523 2569 1.137404 GCGCAAGATGTTCGGCATT 59.863 52.632 0.30 0.00 38.06 3.56
2549 2595 0.323542 GACTTCACCGAGGAGGAGGA 60.324 60.000 0.00 0.00 45.00 3.71
2550 2596 0.323908 ACTTCACCGAGGAGGAGGAG 60.324 60.000 0.00 0.00 45.00 3.69
2551 2597 1.000486 TTCACCGAGGAGGAGGAGG 60.000 63.158 0.00 0.00 45.00 4.30
2602 2651 3.002038 TCGAAGAGTAGGAGTCCCTTC 57.998 52.381 5.25 10.37 40.78 3.46
2685 2735 6.349300 TGTTCTGCCTCCTTTATCACTAATC 58.651 40.000 0.00 0.00 0.00 1.75
2703 2753 6.318144 CACTAATCTCCTAGTGGTCGTTTCTA 59.682 42.308 3.34 0.00 43.39 2.10
2706 2756 4.660168 TCTCCTAGTGGTCGTTTCTAAGT 58.340 43.478 0.00 0.00 34.23 2.24
2707 2757 4.699257 TCTCCTAGTGGTCGTTTCTAAGTC 59.301 45.833 0.00 0.00 34.23 3.01
2718 2768 6.419771 GTCGTTTCTAAGTCTTTGTCAAAGG 58.580 40.000 22.23 8.45 39.01 3.11
2722 2772 7.849515 CGTTTCTAAGTCTTTGTCAAAGGTTAC 59.150 37.037 22.23 14.40 39.01 2.50
2750 2800 5.927115 AGTAAGGTCAACTTGATTCGTCTTC 59.073 40.000 0.00 0.00 40.37 2.87
2755 2805 1.345176 CTTGATTCGTCTTCCGCGC 59.655 57.895 0.00 0.00 36.19 6.86
2756 2806 1.351430 CTTGATTCGTCTTCCGCGCA 61.351 55.000 8.75 0.00 36.19 6.09
2774 2825 4.208253 CGCGCACTTAACCTTTTTCATTTT 59.792 37.500 8.75 0.00 0.00 1.82
2775 2826 5.431309 GCGCACTTAACCTTTTTCATTTTG 58.569 37.500 0.30 0.00 0.00 2.44
2782 2833 9.719355 ACTTAACCTTTTTCATTTTGTTCTGTT 57.281 25.926 0.00 0.00 0.00 3.16
2818 2869 6.308041 GGGATCGAATTTGTGTTTAAAGCTTC 59.692 38.462 0.00 0.00 0.00 3.86
2902 2955 4.186159 CCCCATGAATTGCTGTTGAATTC 58.814 43.478 0.00 0.00 39.36 2.17
2931 2984 2.417719 ACTCTTGATCGAAGGTGTTGC 58.582 47.619 0.00 0.00 31.85 4.17
2962 3020 5.609423 ACTATTCTTGATCTGCTTAGCTGG 58.391 41.667 11.04 1.67 0.00 4.85
3087 3152 6.036735 GCAGTGAATATTTGAAATGCTTGCAT 59.963 34.615 1.81 1.81 0.00 3.96
3088 3153 7.398746 CAGTGAATATTTGAAATGCTTGCATG 58.601 34.615 8.98 0.00 0.00 4.06
3089 3154 7.064134 CAGTGAATATTTGAAATGCTTGCATGT 59.936 33.333 8.98 3.13 0.00 3.21
3090 3155 7.064134 AGTGAATATTTGAAATGCTTGCATGTG 59.936 33.333 8.98 0.00 0.00 3.21
3091 3156 6.314152 TGAATATTTGAAATGCTTGCATGTGG 59.686 34.615 8.98 0.00 0.00 4.17
3092 3157 1.798283 TTGAAATGCTTGCATGTGGC 58.202 45.000 8.98 0.00 45.13 5.01
3093 3158 0.037139 TGAAATGCTTGCATGTGGCC 60.037 50.000 8.98 0.00 43.89 5.36
3094 3159 1.079681 AAATGCTTGCATGTGGCCG 60.080 52.632 8.98 0.00 43.89 6.13
3211 3281 7.291182 AGTGAATAGCATATATATCCTGACCCC 59.709 40.741 0.00 0.00 0.00 4.95
3212 3282 7.071196 GTGAATAGCATATATATCCTGACCCCA 59.929 40.741 0.00 0.00 0.00 4.96
3213 3283 7.290948 TGAATAGCATATATATCCTGACCCCAG 59.709 40.741 0.00 0.00 40.09 4.45
3224 3294 1.984026 GACCCCAGGCAATTGGTGG 60.984 63.158 7.72 0.00 36.45 4.61
3225 3295 2.120274 CCCCAGGCAATTGGTGGT 59.880 61.111 7.72 0.00 36.45 4.16
3226 3296 1.386155 CCCCAGGCAATTGGTGGTA 59.614 57.895 7.72 0.00 36.45 3.25
3227 3297 0.032217 CCCCAGGCAATTGGTGGTAT 60.032 55.000 7.72 0.00 36.45 2.73
3228 3298 1.216678 CCCCAGGCAATTGGTGGTATA 59.783 52.381 7.72 0.00 36.45 1.47
3229 3299 2.358721 CCCCAGGCAATTGGTGGTATAA 60.359 50.000 7.72 0.00 36.45 0.98
3230 3300 3.370104 CCCAGGCAATTGGTGGTATAAA 58.630 45.455 7.72 0.00 36.45 1.40
3231 3301 3.384467 CCCAGGCAATTGGTGGTATAAAG 59.616 47.826 7.72 0.00 36.45 1.85
3232 3302 3.384467 CCAGGCAATTGGTGGTATAAAGG 59.616 47.826 7.72 0.00 33.38 3.11
3233 3303 3.384467 CAGGCAATTGGTGGTATAAAGGG 59.616 47.826 7.72 0.00 0.00 3.95
3281 3351 4.572795 TGTGTTTTGCTTGACTACATTCGA 59.427 37.500 0.00 0.00 0.00 3.71
3282 3352 5.238432 TGTGTTTTGCTTGACTACATTCGAT 59.762 36.000 0.00 0.00 0.00 3.59
3284 3354 7.041712 TGTGTTTTGCTTGACTACATTCGATTA 60.042 33.333 0.00 0.00 0.00 1.75
3336 3406 2.460757 AATTTTGGCATGTGGCTCAC 57.539 45.000 8.09 0.00 44.01 3.51
3401 3471 6.957631 ACCTTATCAGTCAATTGTCACCATA 58.042 36.000 5.13 0.00 0.00 2.74
3440 3510 7.919690 TCTTGTCTTGTTCTTATGTTTGAGTG 58.080 34.615 0.00 0.00 0.00 3.51
3445 3515 8.012241 GTCTTGTTCTTATGTTTGAGTGTGATC 58.988 37.037 0.00 0.00 0.00 2.92
3446 3516 7.933577 TCTTGTTCTTATGTTTGAGTGTGATCT 59.066 33.333 0.00 0.00 0.00 2.75
3447 3517 8.450578 TTGTTCTTATGTTTGAGTGTGATCTT 57.549 30.769 0.00 0.00 0.00 2.40
3448 3518 9.554395 TTGTTCTTATGTTTGAGTGTGATCTTA 57.446 29.630 0.00 0.00 0.00 2.10
3449 3519 9.725019 TGTTCTTATGTTTGAGTGTGATCTTAT 57.275 29.630 0.00 0.00 0.00 1.73
3462 3536 7.497595 AGTGTGATCTTATTATTCGCTTGGTA 58.502 34.615 0.00 0.00 0.00 3.25
3506 3581 5.340803 TCTTCTGTATTTCGATGAAGGACG 58.659 41.667 0.00 0.00 35.98 4.79
3508 3583 4.421058 TCTGTATTTCGATGAAGGACGTG 58.579 43.478 0.00 0.00 0.00 4.49
3512 3587 1.014044 TTCGATGAAGGACGTGCTGC 61.014 55.000 11.44 9.83 0.00 5.25
3515 3592 0.723981 GATGAAGGACGTGCTGCTTC 59.276 55.000 16.83 15.30 45.40 3.86
3520 3597 1.230324 AGGACGTGCTGCTTCTTTTC 58.770 50.000 9.49 0.00 0.00 2.29
3525 3602 4.261031 GGACGTGCTGCTTCTTTTCTTTTA 60.261 41.667 0.00 0.00 0.00 1.52
3534 3611 7.639113 TGCTTCTTTTCTTTTACCTTTGAGA 57.361 32.000 0.00 0.00 0.00 3.27
3540 3617 7.920682 TCTTTTCTTTTACCTTTGAGATTGCAC 59.079 33.333 0.00 0.00 0.00 4.57
3545 3622 3.228188 ACCTTTGAGATTGCACCTTCA 57.772 42.857 0.00 0.00 0.00 3.02
3579 3656 4.194640 AGCTGAGTGTATCATTTGCGATT 58.805 39.130 0.00 0.00 37.28 3.34
3580 3657 5.359756 AGCTGAGTGTATCATTTGCGATTA 58.640 37.500 0.00 0.00 37.28 1.75
3589 3666 8.818057 GTGTATCATTTGCGATTAGTAAACTCT 58.182 33.333 0.00 0.00 37.26 3.24
3590 3667 9.031360 TGTATCATTTGCGATTAGTAAACTCTC 57.969 33.333 0.00 0.00 37.26 3.20
3591 3668 9.031360 GTATCATTTGCGATTAGTAAACTCTCA 57.969 33.333 0.00 0.00 37.26 3.27
3592 3669 7.290857 TCATTTGCGATTAGTAAACTCTCAC 57.709 36.000 0.00 0.00 37.26 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.250624 CCTAATTGAACCGTAAAATTGAAACAA 57.749 29.630 0.00 0.00 0.00 2.83
1 2 7.868415 CCCTAATTGAACCGTAAAATTGAAACA 59.132 33.333 0.00 0.00 0.00 2.83
2 3 8.083462 TCCCTAATTGAACCGTAAAATTGAAAC 58.917 33.333 0.00 0.00 0.00 2.78
3 4 8.179509 TCCCTAATTGAACCGTAAAATTGAAA 57.820 30.769 0.00 0.00 0.00 2.69
4 5 7.576098 GCTCCCTAATTGAACCGTAAAATTGAA 60.576 37.037 0.00 0.00 0.00 2.69
5 6 6.127842 GCTCCCTAATTGAACCGTAAAATTGA 60.128 38.462 0.00 0.00 0.00 2.57
6 7 6.033966 GCTCCCTAATTGAACCGTAAAATTG 58.966 40.000 0.00 0.00 0.00 2.32
7 8 5.712917 TGCTCCCTAATTGAACCGTAAAATT 59.287 36.000 0.00 0.00 0.00 1.82
15 16 4.440663 GCTGAAATGCTCCCTAATTGAACC 60.441 45.833 0.00 0.00 0.00 3.62
35 36 2.224549 CGAAGTATCTACTCCCGAGCTG 59.775 54.545 0.00 0.00 35.64 4.24
57 58 3.582998 TGGATTTGAGGGCTTAGGATG 57.417 47.619 0.00 0.00 0.00 3.51
58 59 4.821532 AATGGATTTGAGGGCTTAGGAT 57.178 40.909 0.00 0.00 0.00 3.24
88 89 4.595986 AGAAGTAACAAGGGTTGTGTTGT 58.404 39.130 0.18 0.00 44.59 3.32
146 147 2.432146 CCTCGACCAGATGGATTTCTGA 59.568 50.000 5.72 0.00 44.88 3.27
164 167 1.154197 GTACCCGACAAAAGCACCTC 58.846 55.000 0.00 0.00 0.00 3.85
178 181 3.592059 TGCACTCGTTTTAGATGTACCC 58.408 45.455 0.00 0.00 0.00 3.69
192 195 5.049405 ACAGAAGAGGTTAAAAATGCACTCG 60.049 40.000 0.00 0.00 0.00 4.18
217 220 4.713806 CAAGACTAGACGCTCCATATACG 58.286 47.826 0.00 0.00 0.00 3.06
263 268 1.475034 GGTTCTCTCTTGTGCACCACA 60.475 52.381 15.69 0.00 43.02 4.17
358 366 2.232941 TCTGGGTCGTATTGTGAGGAAC 59.767 50.000 0.00 0.00 0.00 3.62
383 391 5.728637 ATGGAATTGAAAGGTTTCAGACC 57.271 39.130 5.35 10.10 46.68 3.85
403 411 3.976942 CACACGCAAAAGGAAGAAGAATG 59.023 43.478 0.00 0.00 0.00 2.67
446 460 8.363390 TCATGAAGGAGATATAGCAACACTAAG 58.637 37.037 0.00 0.00 33.57 2.18
448 462 7.839680 TCATGAAGGAGATATAGCAACACTA 57.160 36.000 0.00 0.00 34.64 2.74
449 463 6.737720 TCATGAAGGAGATATAGCAACACT 57.262 37.500 0.00 0.00 0.00 3.55
493 509 7.092716 CCATTTGTAATATTATGCTTGAGCCC 58.907 38.462 0.00 0.00 41.18 5.19
538 554 4.016444 ACTGAAACAAGCTGGAGTTTTGA 58.984 39.130 11.88 4.06 38.01 2.69
582 598 2.019984 GAATCCATTTCTTCTGCCGCT 58.980 47.619 0.00 0.00 0.00 5.52
611 627 2.970324 GCGCTTGTGGACCGAACA 60.970 61.111 0.00 0.00 0.00 3.18
627 643 4.819761 TGGCCGAGAGTGCGATGC 62.820 66.667 0.00 0.00 0.00 3.91
630 646 1.447838 GAAATGGCCGAGAGTGCGA 60.448 57.895 0.00 0.00 0.00 5.10
1018 1034 4.880426 TCCCGCCCCCATCTCCTC 62.880 72.222 0.00 0.00 0.00 3.71
1098 1120 1.063867 CCTTTCTCCTCCTCCGTCCTA 60.064 57.143 0.00 0.00 0.00 2.94
1099 1121 0.324830 CCTTTCTCCTCCTCCGTCCT 60.325 60.000 0.00 0.00 0.00 3.85
1100 1122 1.331399 CCCTTTCTCCTCCTCCGTCC 61.331 65.000 0.00 0.00 0.00 4.79
1129 1151 2.933834 CCCCTTCCCCTTGTCCGT 60.934 66.667 0.00 0.00 0.00 4.69
1149 1171 0.898789 TCTCTTCCTTCTCCGCCGTT 60.899 55.000 0.00 0.00 0.00 4.44
1220 1254 1.779061 TTCTCCCTTTTGCTCCGCCT 61.779 55.000 0.00 0.00 0.00 5.52
1622 1656 1.203758 TGCAGTATTCGATCACCGTGT 59.796 47.619 0.00 0.00 39.75 4.49
1880 1914 1.693062 CCTCTATCTGGTGCATCTGCT 59.307 52.381 0.00 0.00 42.66 4.24
1916 1950 4.828072 GGAGTAAGTCCAGAGAACCATT 57.172 45.455 0.00 0.00 46.10 3.16
1979 2013 2.059345 TTGACCAACGGTTCTCCCCC 62.059 60.000 0.00 0.00 35.25 5.40
1981 2015 2.625375 GTTGACCAACGGTTCTCCC 58.375 57.895 0.00 0.00 35.25 4.30
1990 2036 3.047877 CTCCGGCCGTTGACCAAC 61.048 66.667 26.12 2.94 37.92 3.77
1991 2037 4.323477 CCTCCGGCCGTTGACCAA 62.323 66.667 26.12 0.00 0.00 3.67
2474 2520 0.384669 GCTCTTGCCCTTGATCATGC 59.615 55.000 0.00 0.49 0.00 4.06
2523 2569 3.220999 CTCGGTGAAGTCGGTGGCA 62.221 63.158 0.00 0.00 0.00 4.92
2549 2595 2.494073 CTCTCTTTACGCAGTTCCTCCT 59.506 50.000 0.00 0.00 37.78 3.69
2550 2596 2.231721 ACTCTCTTTACGCAGTTCCTCC 59.768 50.000 0.00 0.00 37.78 4.30
2551 2597 3.503891 GACTCTCTTTACGCAGTTCCTC 58.496 50.000 0.00 0.00 37.78 3.71
2602 2651 0.519175 CGCAGAAATGGCTTCGAACG 60.519 55.000 0.00 0.00 39.22 3.95
2685 2735 4.701171 AGACTTAGAAACGACCACTAGGAG 59.299 45.833 0.00 0.00 38.69 3.69
2703 2753 5.751586 TCCTGTAACCTTTGACAAAGACTT 58.248 37.500 26.14 18.45 41.02 3.01
2706 2756 5.367945 ACTCCTGTAACCTTTGACAAAGA 57.632 39.130 26.14 6.61 41.02 2.52
2707 2757 6.204882 CCTTACTCCTGTAACCTTTGACAAAG 59.795 42.308 19.20 19.20 35.14 2.77
2718 2768 5.850614 TCAAGTTGACCTTACTCCTGTAAC 58.149 41.667 0.08 0.00 35.14 2.50
2722 2772 4.627467 CGAATCAAGTTGACCTTACTCCTG 59.373 45.833 7.96 0.00 0.00 3.86
2750 2800 1.002251 TGAAAAAGGTTAAGTGCGCGG 60.002 47.619 8.83 0.00 0.00 6.46
2755 2805 9.150348 ACAGAACAAAATGAAAAAGGTTAAGTG 57.850 29.630 0.00 0.00 0.00 3.16
2756 2806 9.719355 AACAGAACAAAATGAAAAAGGTTAAGT 57.281 25.926 0.00 0.00 0.00 2.24
2774 2825 5.047566 TCCCAATCTTCTTCAACAGAACA 57.952 39.130 0.00 0.00 36.51 3.18
2775 2826 5.163814 CGATCCCAATCTTCTTCAACAGAAC 60.164 44.000 0.00 0.00 36.51 3.01
2782 2833 5.945784 ACAAATTCGATCCCAATCTTCTTCA 59.054 36.000 0.00 0.00 0.00 3.02
2818 2869 1.400629 CCACTTGAAGCATGCAGTTCG 60.401 52.381 21.98 7.59 0.00 3.95
2902 2955 4.358851 CTTCGATCAAGAGTAGCTGAAGG 58.641 47.826 0.00 0.00 33.29 3.46
2931 2984 7.151999 AGCAGATCAAGAATAGTACTATCCG 57.848 40.000 15.72 5.39 0.00 4.18
3092 3157 1.077501 AGGATGTGCCATTCACCGG 60.078 57.895 0.00 0.00 45.03 5.28
3093 3158 0.392863 TCAGGATGTGCCATTCACCG 60.393 55.000 0.00 0.00 45.03 4.94
3094 3159 1.679680 CATCAGGATGTGCCATTCACC 59.320 52.381 1.07 0.00 45.03 4.02
3211 3281 3.384467 CCCTTTATACCACCAATTGCCTG 59.616 47.826 0.00 0.00 0.00 4.85
3212 3282 3.270960 TCCCTTTATACCACCAATTGCCT 59.729 43.478 0.00 0.00 0.00 4.75
3213 3283 3.636764 CTCCCTTTATACCACCAATTGCC 59.363 47.826 0.00 0.00 0.00 4.52
3231 3301 7.090082 AATCCAATGTGGGATAAGAAACTCCC 61.090 42.308 0.49 0.49 46.96 4.30
3232 3302 4.855340 TCCAATGTGGGATAAGAAACTCC 58.145 43.478 0.00 0.00 38.32 3.85
3233 3303 6.378280 ACAATCCAATGTGGGATAAGAAACTC 59.622 38.462 0.00 0.00 46.96 3.01
3315 3385 3.514645 GTGAGCCACATGCCAAAATTAG 58.485 45.455 0.00 0.00 42.71 1.73
3370 3440 8.999431 TGACAATTGACTGATAAGGTTAGTTTC 58.001 33.333 13.59 0.00 0.00 2.78
3401 3471 7.125792 ACAAGACAAGATCCTTATCCGTTAT 57.874 36.000 0.00 0.00 31.98 1.89
3440 3510 8.988934 TGAATACCAAGCGAATAATAAGATCAC 58.011 33.333 0.00 0.00 0.00 3.06
3446 3516 9.990360 TCATACTGAATACCAAGCGAATAATAA 57.010 29.630 0.00 0.00 0.00 1.40
3448 3518 9.155975 GATCATACTGAATACCAAGCGAATAAT 57.844 33.333 0.00 0.00 0.00 1.28
3449 3519 8.367911 AGATCATACTGAATACCAAGCGAATAA 58.632 33.333 0.00 0.00 0.00 1.40
3451 3521 6.763355 AGATCATACTGAATACCAAGCGAAT 58.237 36.000 0.00 0.00 0.00 3.34
3452 3522 6.161855 AGATCATACTGAATACCAAGCGAA 57.838 37.500 0.00 0.00 0.00 4.70
3454 3524 9.809096 ATATAAGATCATACTGAATACCAAGCG 57.191 33.333 0.00 0.00 0.00 4.68
3506 3581 5.188327 AGGTAAAAGAAAAGAAGCAGCAC 57.812 39.130 0.00 0.00 0.00 4.40
3508 3583 6.273071 TCAAAGGTAAAAGAAAAGAAGCAGC 58.727 36.000 0.00 0.00 0.00 5.25
3512 3587 8.972349 GCAATCTCAAAGGTAAAAGAAAAGAAG 58.028 33.333 0.00 0.00 0.00 2.85
3515 3592 7.169813 GGTGCAATCTCAAAGGTAAAAGAAAAG 59.830 37.037 0.00 0.00 0.00 2.27
3520 3597 5.712152 AGGTGCAATCTCAAAGGTAAAAG 57.288 39.130 0.00 0.00 0.00 2.27
3525 3602 3.228188 TGAAGGTGCAATCTCAAAGGT 57.772 42.857 0.00 0.00 0.00 3.50
3534 3611 6.038714 GCTTAATACTAGCTTGAAGGTGCAAT 59.961 38.462 7.22 0.00 35.74 3.56
3540 3617 6.478344 CACTCAGCTTAATACTAGCTTGAAGG 59.522 42.308 1.04 0.00 46.42 3.46
3545 3622 8.239038 TGATACACTCAGCTTAATACTAGCTT 57.761 34.615 0.00 0.00 46.42 3.74
3562 3639 8.718102 AGTTTACTAATCGCAAATGATACACT 57.282 30.769 0.00 0.00 0.00 3.55



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

AutoCloner maintained by Alex Coulton.