Multiple sequence alignment - TraesCS4A01G198700

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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 TraesCS4A01G198700 chr4A 100.000 3096 0 0 1 3096 484733719 484730624 0.000000e+00 5718.0
1 TraesCS4A01G198700 chr4A 93.798 129 8 0 1355 1483 645308493 645308621 8.760000e-46 195.0
2 TraesCS4A01G198700 chr4D 93.308 1853 45 22 643 2435 95278157 95279990 0.000000e+00 2662.0
3 TraesCS4A01G198700 chr4D 88.443 623 22 11 7 617 95277473 95278057 0.000000e+00 706.0
4 TraesCS4A01G198700 chr4D 92.086 417 15 6 2685 3096 95280433 95280836 3.460000e-159 571.0
5 TraesCS4A01G198700 chr4D 97.122 139 4 0 2463 2601 95279982 95280120 5.160000e-58 235.0
6 TraesCS4A01G198700 chr4B 89.822 1906 100 28 777 2620 134812860 134814733 0.000000e+00 2359.0
7 TraesCS4A01G198700 chr4B 85.060 502 40 14 131 617 134811866 134812347 2.160000e-131 479.0
8 TraesCS4A01G198700 chr4B 84.450 418 22 15 2680 3096 134814756 134815131 3.770000e-99 372.0
9 TraesCS4A01G198700 chr4B 94.531 128 7 0 1355 1482 590429248 590429121 6.770000e-47 198.0
10 TraesCS4A01G198700 chr4B 93.478 92 5 1 643 734 134812447 134812537 5.390000e-28 135.0
11 TraesCS4A01G198700 chr4B 100.000 36 0 0 94 129 134811553 134811588 1.990000e-07 67.6
12 TraesCS4A01G198700 chr2D 91.908 346 25 1 1237 1582 85755798 85756140 6.000000e-132 481.0
13 TraesCS4A01G198700 chr6A 82.609 138 18 3 2489 2620 615699445 615699308 1.950000e-22 117.0
14 TraesCS4A01G198700 chr6A 78.322 143 24 5 2480 2617 101857786 101857926 5.500000e-13 86.1
15 TraesCS4A01G198700 chr6D 80.952 147 20 5 2480 2620 470867786 470867642 3.260000e-20 110.0
16 TraesCS4A01G198700 chr5D 80.000 145 22 5 2480 2617 450217011 450217155 1.960000e-17 100.0
17 TraesCS4A01G198700 chr3B 80.000 130 24 2 2487 2615 412701717 412701845 9.140000e-16 95.3
18 TraesCS4A01G198700 chr3D 79.310 116 19 3 2487 2598 308818600 308818486 3.310000e-10 76.8
19 TraesCS4A01G198700 chr3A 75.694 144 28 5 2487 2626 428457153 428457013 7.170000e-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 TraesCS4A01G198700 chr4A 484730624 484733719 3095 True 5718.00 5718 100.00000 1 3096 1 chr4A.!!$R1 3095
1 TraesCS4A01G198700 chr4D 95277473 95280836 3363 False 1043.50 2662 92.73975 7 3096 4 chr4D.!!$F1 3089
2 TraesCS4A01G198700 chr4B 134811553 134815131 3578 False 682.52 2359 90.56200 94 3096 5 chr4B.!!$F1 3002

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
446 736 0.097674 GCTATTGTGCAAGGTGAGCG 59.902 55.0 0.0 0.0 33.85 5.03 F
1109 1809 0.249657 CATTCCCAGCTCGCCTACTC 60.250 60.0 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 2237 0.959372 GGTGCTCTTGCTGCTGATGT 60.959 55.0 0.0 0.0 40.48 3.06 R
2867 3928 0.036164 AGGTGTGTGTGTGTGTGTGT 59.964 50.0 0.0 0.0 0.00 3.72 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
62 63 2.249139 ACACTGACAAGTACTCCCTCC 58.751 52.381 0.00 0.00 33.79 4.30
66 67 2.299297 CTGACAAGTACTCCCTCCGTTT 59.701 50.000 0.00 0.00 0.00 3.60
74 75 6.309389 AGTACTCCCTCCGTTTCATAAATT 57.691 37.500 0.00 0.00 0.00 1.82
75 76 6.718294 AGTACTCCCTCCGTTTCATAAATTT 58.282 36.000 0.00 0.00 0.00 1.82
90 91 7.502177 TCATAAATTTCTTGTCGTCGTACTC 57.498 36.000 0.00 0.00 0.00 2.59
202 481 3.065371 GGATCGCCAACCAAAACTCTATG 59.935 47.826 0.00 0.00 0.00 2.23
203 482 3.410631 TCGCCAACCAAAACTCTATGA 57.589 42.857 0.00 0.00 0.00 2.15
204 483 3.071479 TCGCCAACCAAAACTCTATGAC 58.929 45.455 0.00 0.00 0.00 3.06
205 484 2.161609 CGCCAACCAAAACTCTATGACC 59.838 50.000 0.00 0.00 0.00 4.02
206 485 2.492088 GCCAACCAAAACTCTATGACCC 59.508 50.000 0.00 0.00 0.00 4.46
207 486 3.814316 GCCAACCAAAACTCTATGACCCT 60.814 47.826 0.00 0.00 0.00 4.34
208 487 4.566907 GCCAACCAAAACTCTATGACCCTA 60.567 45.833 0.00 0.00 0.00 3.53
209 488 5.755849 CCAACCAAAACTCTATGACCCTAT 58.244 41.667 0.00 0.00 0.00 2.57
214 493 6.098982 ACCAAAACTCTATGACCCTATCTCTG 59.901 42.308 0.00 0.00 0.00 3.35
401 691 3.114065 CTGGCTTAGTTTATCCGTCGTC 58.886 50.000 0.00 0.00 0.00 4.20
446 736 0.097674 GCTATTGTGCAAGGTGAGCG 59.902 55.000 0.00 0.00 33.85 5.03
470 781 3.040795 GCAATAACATGCATGCTCGAAG 58.959 45.455 26.53 13.03 45.70 3.79
474 785 2.907910 ACATGCATGCTCGAAGTTTC 57.092 45.000 26.53 0.00 0.00 2.78
555 866 3.395941 ACTTCCTCAGGACAATGAAAGGT 59.604 43.478 0.00 0.00 0.00 3.50
556 867 4.597507 ACTTCCTCAGGACAATGAAAGGTA 59.402 41.667 0.00 0.00 0.00 3.08
557 868 4.553330 TCCTCAGGACAATGAAAGGTAC 57.447 45.455 0.00 0.00 0.00 3.34
559 870 4.223032 TCCTCAGGACAATGAAAGGTACTC 59.777 45.833 0.00 0.00 38.49 2.59
600 911 3.264998 ACTGTACGAGTCTACTCCTCC 57.735 52.381 4.58 0.00 39.79 4.30
601 912 2.839425 ACTGTACGAGTCTACTCCTCCT 59.161 50.000 4.58 0.00 39.79 3.69
602 913 3.118665 ACTGTACGAGTCTACTCCTCCTC 60.119 52.174 4.58 0.00 39.79 3.71
640 1033 1.199097 CACACCGGAAGCCATGTAAAC 59.801 52.381 9.46 0.00 0.00 2.01
641 1034 1.073284 ACACCGGAAGCCATGTAAACT 59.927 47.619 9.46 0.00 0.00 2.66
642 1035 2.159382 CACCGGAAGCCATGTAAACTT 58.841 47.619 9.46 0.00 0.00 2.66
643 1036 2.095263 CACCGGAAGCCATGTAAACTTG 60.095 50.000 9.46 0.00 0.00 3.16
644 1037 2.159382 CCGGAAGCCATGTAAACTTGT 58.841 47.619 0.00 0.00 0.00 3.16
645 1038 3.244630 ACCGGAAGCCATGTAAACTTGTA 60.245 43.478 9.46 0.00 0.00 2.41
646 1039 3.754323 CCGGAAGCCATGTAAACTTGTAA 59.246 43.478 0.00 0.00 0.00 2.41
647 1040 4.216687 CCGGAAGCCATGTAAACTTGTAAA 59.783 41.667 0.00 0.00 0.00 2.01
691 1084 1.600356 ATGCCATGTCACGCACACA 60.600 52.632 0.00 0.00 38.04 3.72
806 1486 2.125106 GGCCTCGGCTGTTGGTAG 60.125 66.667 8.00 0.00 41.60 3.18
870 1550 1.000731 GAGCATCACAGCCTAGCTAGG 59.999 57.143 32.12 32.12 40.10 3.02
921 1606 0.942962 GGAGGAATGATGAGCAAGCG 59.057 55.000 0.00 0.00 0.00 4.68
1106 1806 2.443394 CCCATTCCCAGCTCGCCTA 61.443 63.158 0.00 0.00 0.00 3.93
1108 1808 1.690219 CCATTCCCAGCTCGCCTACT 61.690 60.000 0.00 0.00 0.00 2.57
1109 1809 0.249657 CATTCCCAGCTCGCCTACTC 60.250 60.000 0.00 0.00 0.00 2.59
1110 1810 0.687757 ATTCCCAGCTCGCCTACTCA 60.688 55.000 0.00 0.00 0.00 3.41
1111 1811 1.605058 TTCCCAGCTCGCCTACTCAC 61.605 60.000 0.00 0.00 0.00 3.51
1391 2091 2.510238 CTTCCTCCGCGAGCAAGG 60.510 66.667 8.23 9.14 34.79 3.61
1483 2183 3.141488 ACCAGCTACGCCTCCTCG 61.141 66.667 0.00 0.00 0.00 4.63
1641 2365 4.048241 AGCAGAAGAAGAGGTATTACGC 57.952 45.455 0.00 0.00 0.00 4.42
1879 2603 3.842923 GAGCTCTGCGCCCAGCTA 61.843 66.667 25.44 0.00 46.31 3.32
1972 2705 0.753479 TGAGGTCTCGAGATCCTGGC 60.753 60.000 29.51 20.38 0.00 4.85
1980 2713 3.017581 AGATCCTGGCACCACCCC 61.018 66.667 0.00 0.00 37.83 4.95
2093 2826 1.079503 CGAGCACTAGGACAAAAGCC 58.920 55.000 0.00 0.00 0.00 4.35
2154 2887 2.025321 AGTCTGTTCTTGTTGGTGGGTT 60.025 45.455 0.00 0.00 0.00 4.11
2296 3054 0.321564 TGCATGGACAGTGCCACTAC 60.322 55.000 0.00 0.00 41.56 2.73
2348 3106 7.438757 CAGAGTGAGTAACTAAGCTATCTACGA 59.561 40.741 0.00 0.00 40.07 3.43
2349 3107 8.152246 AGAGTGAGTAACTAAGCTATCTACGAT 58.848 37.037 0.00 0.00 40.07 3.73
2350 3108 8.680039 AGTGAGTAACTAAGCTATCTACGATT 57.320 34.615 0.00 0.00 37.36 3.34
2351 3109 8.776470 AGTGAGTAACTAAGCTATCTACGATTC 58.224 37.037 0.00 0.00 37.36 2.52
2353 3111 9.993454 TGAGTAACTAAGCTATCTACGATTCTA 57.007 33.333 0.00 0.00 0.00 2.10
2396 3154 8.504005 AGTGTAGTGTTTTGTGTTATATGAAGC 58.496 33.333 0.00 0.00 0.00 3.86
2409 3167 9.169592 GTGTTATATGAAGCCCTTGTAACTTTA 57.830 33.333 0.00 0.00 31.94 1.85
2430 3188 7.868415 ACTTTACTACTGAATGAGACTGTGTTC 59.132 37.037 0.00 0.00 0.00 3.18
2433 3191 7.151999 ACTACTGAATGAGACTGTGTTCTAG 57.848 40.000 0.00 0.00 0.00 2.43
2434 3192 4.815269 ACTGAATGAGACTGTGTTCTAGC 58.185 43.478 0.00 0.00 0.00 3.42
2435 3193 3.838120 TGAATGAGACTGTGTTCTAGCG 58.162 45.455 0.00 0.00 0.00 4.26
2436 3194 2.285827 ATGAGACTGTGTTCTAGCGC 57.714 50.000 0.00 0.00 0.00 5.92
2437 3195 1.248486 TGAGACTGTGTTCTAGCGCT 58.752 50.000 17.26 17.26 0.00 5.92
2438 3196 2.433436 TGAGACTGTGTTCTAGCGCTA 58.567 47.619 17.75 17.75 0.00 4.26
2439 3197 2.420372 TGAGACTGTGTTCTAGCGCTAG 59.580 50.000 33.92 33.92 34.56 3.42
2440 3198 2.420722 GAGACTGTGTTCTAGCGCTAGT 59.579 50.000 36.45 23.09 34.84 2.57
2441 3199 2.820787 AGACTGTGTTCTAGCGCTAGTT 59.179 45.455 36.45 17.30 34.84 2.24
2442 3200 3.256136 AGACTGTGTTCTAGCGCTAGTTT 59.744 43.478 36.45 16.39 34.84 2.66
2443 3201 3.576648 ACTGTGTTCTAGCGCTAGTTTC 58.423 45.455 36.45 27.28 34.84 2.78
2444 3202 2.924290 CTGTGTTCTAGCGCTAGTTTCC 59.076 50.000 36.45 24.70 34.84 3.13
2445 3203 2.297880 TGTGTTCTAGCGCTAGTTTCCA 59.702 45.455 36.45 26.50 34.84 3.53
2485 3244 8.896320 TGTGTTCTAGCTTACAGTGAAATTTA 57.104 30.769 0.00 0.00 0.00 1.40
2538 3297 0.379669 TAAGATCGAACGCCGTCCTC 59.620 55.000 0.00 0.00 39.75 3.71
2629 3687 8.597662 TTGTAGATTCAGTTAATATTACCGGC 57.402 34.615 0.00 0.00 0.00 6.13
2630 3688 7.156673 TGTAGATTCAGTTAATATTACCGGCC 58.843 38.462 0.00 0.00 0.00 6.13
2631 3689 6.182507 AGATTCAGTTAATATTACCGGCCA 57.817 37.500 0.00 0.00 0.00 5.36
2632 3690 6.231211 AGATTCAGTTAATATTACCGGCCAG 58.769 40.000 0.00 0.00 0.00 4.85
2633 3691 5.362105 TTCAGTTAATATTACCGGCCAGT 57.638 39.130 0.00 0.00 0.00 4.00
2634 3692 5.362105 TCAGTTAATATTACCGGCCAGTT 57.638 39.130 0.00 0.00 0.00 3.16
2635 3693 5.120399 TCAGTTAATATTACCGGCCAGTTG 58.880 41.667 0.00 0.00 0.00 3.16
2636 3694 3.881089 AGTTAATATTACCGGCCAGTTGC 59.119 43.478 0.00 0.00 40.16 4.17
2637 3695 2.428544 AATATTACCGGCCAGTTGCA 57.571 45.000 0.00 0.00 43.89 4.08
2639 3697 1.961793 TATTACCGGCCAGTTGCATC 58.038 50.000 0.00 0.00 43.89 3.91
2641 3699 0.037590 TTACCGGCCAGTTGCATCTT 59.962 50.000 0.00 0.00 43.89 2.40
2642 3700 0.037590 TACCGGCCAGTTGCATCTTT 59.962 50.000 0.00 0.00 43.89 2.52
2643 3701 1.244019 ACCGGCCAGTTGCATCTTTC 61.244 55.000 0.00 0.00 43.89 2.62
2644 3702 1.243342 CCGGCCAGTTGCATCTTTCA 61.243 55.000 2.24 0.00 43.89 2.69
2645 3703 0.169672 CGGCCAGTTGCATCTTTCAG 59.830 55.000 2.24 0.00 43.89 3.02
2646 3704 1.538047 GGCCAGTTGCATCTTTCAGA 58.462 50.000 0.00 0.00 43.89 3.27
2647 3705 1.471684 GGCCAGTTGCATCTTTCAGAG 59.528 52.381 0.00 0.00 43.89 3.35
2648 3706 1.471684 GCCAGTTGCATCTTTCAGAGG 59.528 52.381 0.00 0.00 40.77 3.69
2652 3710 3.819188 GCATCTTTCAGAGGCGGG 58.181 61.111 0.00 0.00 42.34 6.13
2653 3711 1.821332 GCATCTTTCAGAGGCGGGG 60.821 63.158 0.00 0.00 42.34 5.73
2654 3712 1.153086 CATCTTTCAGAGGCGGGGG 60.153 63.158 0.00 0.00 0.00 5.40
2655 3713 3.049080 ATCTTTCAGAGGCGGGGGC 62.049 63.158 0.00 0.00 0.00 5.80
2656 3714 3.721706 CTTTCAGAGGCGGGGGCT 61.722 66.667 0.00 0.00 42.48 5.19
2657 3715 3.984193 CTTTCAGAGGCGGGGGCTG 62.984 68.421 0.00 0.00 38.98 4.85
2668 3726 2.766660 GGGGCTGAGCCTCCTTTT 59.233 61.111 24.52 0.00 44.86 2.27
2669 3727 1.379176 GGGGCTGAGCCTCCTTTTC 60.379 63.158 24.52 4.09 44.86 2.29
2670 3728 2.142292 GGGGCTGAGCCTCCTTTTCA 62.142 60.000 24.52 0.00 44.86 2.69
2671 3729 2.865492 GGCTGAGCCTCCTTTTCAG 58.135 57.895 17.96 0.00 46.69 3.02
2672 3730 0.326264 GGCTGAGCCTCCTTTTCAGA 59.674 55.000 17.96 0.00 46.69 3.27
2673 3731 1.271597 GGCTGAGCCTCCTTTTCAGAA 60.272 52.381 17.96 0.00 46.69 3.02
2674 3732 2.508526 GCTGAGCCTCCTTTTCAGAAA 58.491 47.619 0.00 0.00 40.54 2.52
2675 3733 2.487372 GCTGAGCCTCCTTTTCAGAAAG 59.513 50.000 0.00 0.00 40.54 2.62
2676 3734 3.808618 GCTGAGCCTCCTTTTCAGAAAGA 60.809 47.826 0.00 0.00 44.03 2.52
2677 3735 4.392940 CTGAGCCTCCTTTTCAGAAAGAA 58.607 43.478 0.00 0.00 44.03 2.52
2678 3736 4.792068 TGAGCCTCCTTTTCAGAAAGAAA 58.208 39.130 0.00 0.00 44.03 2.52
2799 3860 0.180171 AACAAAAACAGGGCCCAAGC 59.820 50.000 27.56 0.00 38.76 4.01
2829 3890 0.321653 GGTACTGTGGCAGGGAAGTG 60.322 60.000 0.00 0.00 35.51 3.16
2833 3894 0.620556 CTGTGGCAGGGAAGTGGTAT 59.379 55.000 0.00 0.00 0.00 2.73
2843 3904 5.565045 GCAGGGAAGTGGTATAAGTAGATCG 60.565 48.000 0.00 0.00 0.00 3.69
2864 3925 4.308526 CAGGGTGCATCTGGACAC 57.691 61.111 10.94 0.00 40.34 3.67
2865 3926 1.376086 CAGGGTGCATCTGGACACA 59.624 57.895 6.85 0.00 42.67 3.72
2866 3927 0.957395 CAGGGTGCATCTGGACACAC 60.957 60.000 6.85 0.00 42.67 3.82
2867 3928 1.073025 GGGTGCATCTGGACACACA 59.927 57.895 0.00 0.00 39.75 3.72
2870 3931 0.588252 GTGCATCTGGACACACACAC 59.412 55.000 0.00 0.00 36.77 3.82
2871 3932 0.179936 TGCATCTGGACACACACACA 59.820 50.000 0.00 0.00 0.00 3.72
2872 3933 0.588252 GCATCTGGACACACACACAC 59.412 55.000 0.00 0.00 0.00 3.82
2873 3934 1.952193 CATCTGGACACACACACACA 58.048 50.000 0.00 0.00 0.00 3.72
3037 4100 1.923316 GCTCGCAAGTTGCTTCTGTTG 60.923 52.381 24.61 8.18 42.25 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.703298 TTTTGAATCTCACAGAAAAGCATTG 57.297 32.000 0.00 0.00 0.00 2.82
29 30 9.310716 GTACTTGTCAGTGTTTCTTTACTAACT 57.689 33.333 0.00 0.00 34.06 2.24
39 40 4.308265 GAGGGAGTACTTGTCAGTGTTTC 58.692 47.826 0.00 0.00 34.06 2.78
62 63 6.068931 ACGACGACAAGAAATTTATGAAACG 58.931 36.000 0.00 12.32 0.00 3.60
66 67 6.529125 GGAGTACGACGACAAGAAATTTATGA 59.471 38.462 0.00 0.00 0.00 2.15
74 75 5.571784 AATATGGAGTACGACGACAAGAA 57.428 39.130 0.00 0.00 0.00 2.52
75 76 5.819379 ACTAATATGGAGTACGACGACAAGA 59.181 40.000 0.00 0.00 0.00 3.02
202 481 0.103208 CGTGCCACAGAGATAGGGTC 59.897 60.000 0.00 0.00 0.00 4.46
203 482 0.614979 ACGTGCCACAGAGATAGGGT 60.615 55.000 0.00 0.00 0.00 4.34
204 483 1.067212 GTACGTGCCACAGAGATAGGG 59.933 57.143 0.00 0.00 0.00 3.53
205 484 2.025155 AGTACGTGCCACAGAGATAGG 58.975 52.381 0.00 0.00 0.00 2.57
206 485 3.439293 CAAGTACGTGCCACAGAGATAG 58.561 50.000 0.00 0.00 0.00 2.08
207 486 2.416836 GCAAGTACGTGCCACAGAGATA 60.417 50.000 21.39 0.00 38.66 1.98
208 487 1.673033 GCAAGTACGTGCCACAGAGAT 60.673 52.381 21.39 0.00 38.66 2.75
209 488 0.319555 GCAAGTACGTGCCACAGAGA 60.320 55.000 21.39 0.00 38.66 3.10
382 671 2.114825 CGACGACGGATAAACTAAGCC 58.885 52.381 0.00 0.00 35.72 4.35
491 802 9.827411 CTCGATCGTTGATTGACTAGATTTATA 57.173 33.333 15.94 0.00 30.26 0.98
492 803 8.568794 TCTCGATCGTTGATTGACTAGATTTAT 58.431 33.333 15.94 0.00 30.26 1.40
493 804 7.927048 TCTCGATCGTTGATTGACTAGATTTA 58.073 34.615 15.94 0.00 30.26 1.40
494 805 6.796426 TCTCGATCGTTGATTGACTAGATTT 58.204 36.000 15.94 0.00 30.26 2.17
495 806 6.261158 TCTCTCGATCGTTGATTGACTAGATT 59.739 38.462 15.94 0.00 30.26 2.40
496 807 5.760743 TCTCTCGATCGTTGATTGACTAGAT 59.239 40.000 15.94 0.00 30.26 1.98
497 808 5.116882 TCTCTCGATCGTTGATTGACTAGA 58.883 41.667 15.94 5.39 30.26 2.43
498 809 5.235401 TCTCTCTCGATCGTTGATTGACTAG 59.765 44.000 15.94 0.71 30.26 2.57
499 810 5.116882 TCTCTCTCGATCGTTGATTGACTA 58.883 41.667 15.94 0.00 30.26 2.59
500 811 3.942115 TCTCTCTCGATCGTTGATTGACT 59.058 43.478 15.94 0.00 30.26 3.41
501 812 4.280101 TCTCTCTCGATCGTTGATTGAC 57.720 45.455 15.94 0.00 30.26 3.18
502 813 4.965119 TTCTCTCTCGATCGTTGATTGA 57.035 40.909 15.94 11.76 32.26 2.57
503 814 6.580963 AATTTCTCTCTCGATCGTTGATTG 57.419 37.500 15.94 9.95 0.00 2.67
504 815 8.703604 TTAAATTTCTCTCTCGATCGTTGATT 57.296 30.769 15.94 6.87 0.00 2.57
505 816 8.879342 ATTAAATTTCTCTCTCGATCGTTGAT 57.121 30.769 15.94 0.00 0.00 2.57
506 817 8.703604 AATTAAATTTCTCTCTCGATCGTTGA 57.296 30.769 15.94 13.31 0.00 3.18
509 820 9.804758 AGTAAATTAAATTTCTCTCTCGATCGT 57.195 29.630 15.94 0.00 33.82 3.73
579 890 4.029520 AGGAGGAGTAGACTCGTACAGTA 58.970 47.826 15.18 0.00 42.56 2.74
600 911 7.465111 CGGTGTGAATATCTTGTTGATTCTGAG 60.465 40.741 0.00 0.00 36.65 3.35
601 912 6.313658 CGGTGTGAATATCTTGTTGATTCTGA 59.686 38.462 0.00 0.00 36.65 3.27
602 913 6.457392 CCGGTGTGAATATCTTGTTGATTCTG 60.457 42.308 0.00 0.00 36.65 3.02
640 1033 2.811431 TCCGTGTTGATGGCTTTACAAG 59.189 45.455 0.00 0.00 0.00 3.16
641 1034 2.852449 TCCGTGTTGATGGCTTTACAA 58.148 42.857 0.00 0.00 0.00 2.41
642 1035 2.552599 TCCGTGTTGATGGCTTTACA 57.447 45.000 0.00 0.00 0.00 2.41
643 1036 3.071479 TCTTCCGTGTTGATGGCTTTAC 58.929 45.455 0.00 0.00 0.00 2.01
644 1037 3.071479 GTCTTCCGTGTTGATGGCTTTA 58.929 45.455 0.00 0.00 0.00 1.85
645 1038 1.880027 GTCTTCCGTGTTGATGGCTTT 59.120 47.619 0.00 0.00 0.00 3.51
646 1039 1.523758 GTCTTCCGTGTTGATGGCTT 58.476 50.000 0.00 0.00 0.00 4.35
647 1040 0.670546 CGTCTTCCGTGTTGATGGCT 60.671 55.000 0.00 0.00 0.00 4.75
806 1486 1.268692 GGGAAAAACCGTTTGTCCGTC 60.269 52.381 21.98 9.57 40.11 4.79
843 1523 0.457851 GGCTGTGATGCTCTAGTCGT 59.542 55.000 0.00 0.00 0.00 4.34
844 1524 0.743688 AGGCTGTGATGCTCTAGTCG 59.256 55.000 0.00 0.00 0.00 4.18
845 1525 2.288152 GCTAGGCTGTGATGCTCTAGTC 60.288 54.545 0.00 0.00 36.79 2.59
870 1550 0.613777 ATTGACCTTGACCGTCCTCC 59.386 55.000 0.00 0.00 0.00 4.30
921 1606 3.428664 TGGGCCATGTGGGGGATC 61.429 66.667 0.00 0.00 37.04 3.36
1483 2183 3.764972 AGGAGTAGTAGTTGGAGCAGTTC 59.235 47.826 0.00 0.00 0.00 3.01
1537 2237 0.959372 GGTGCTCTTGCTGCTGATGT 60.959 55.000 0.00 0.00 40.48 3.06
1641 2365 1.667724 CCATAGCTGCTTTGTTCTCCG 59.332 52.381 16.92 0.00 0.00 4.63
1951 2684 1.409521 CCAGGATCTCGAGACCTCAGT 60.410 57.143 24.82 8.38 31.06 3.41
2104 2837 8.603304 AGAAATCAAACACCTGGTACTACTAAT 58.397 33.333 0.00 0.00 0.00 1.73
2105 2838 7.876068 CAGAAATCAAACACCTGGTACTACTAA 59.124 37.037 0.00 0.00 0.00 2.24
2109 2842 5.308497 TCCAGAAATCAAACACCTGGTACTA 59.692 40.000 0.00 0.00 43.54 1.82
2296 3054 9.744468 GTAATTAGCAAACCCTACCAATTATTG 57.256 33.333 0.00 0.00 0.00 1.90
2343 3101 6.632035 GGACTTTGACATACGTAGAATCGTAG 59.368 42.308 0.08 3.08 46.70 3.51
2348 3106 5.125097 ACTCGGACTTTGACATACGTAGAAT 59.875 40.000 0.08 0.00 0.00 2.40
2349 3107 4.456911 ACTCGGACTTTGACATACGTAGAA 59.543 41.667 0.08 0.00 0.00 2.10
2350 3108 4.005650 ACTCGGACTTTGACATACGTAGA 58.994 43.478 0.08 0.00 0.00 2.59
2351 3109 4.096311 CACTCGGACTTTGACATACGTAG 58.904 47.826 0.08 0.00 0.00 3.51
2353 3111 2.295349 ACACTCGGACTTTGACATACGT 59.705 45.455 0.00 0.00 0.00 3.57
2354 3112 2.942710 ACACTCGGACTTTGACATACG 58.057 47.619 0.00 0.00 0.00 3.06
2396 3154 8.311836 TCTCATTCAGTAGTAAAGTTACAAGGG 58.688 37.037 4.14 0.00 36.12 3.95
2409 3167 6.349777 GCTAGAACACAGTCTCATTCAGTAGT 60.350 42.308 0.00 0.00 0.00 2.73
2452 3210 7.011482 CACTGTAAGCTAGAACACAGTCTTTTT 59.989 37.037 16.34 0.00 46.52 1.94
2453 3211 6.480320 CACTGTAAGCTAGAACACAGTCTTTT 59.520 38.462 16.34 0.00 46.52 2.27
2454 3212 5.986135 CACTGTAAGCTAGAACACAGTCTTT 59.014 40.000 16.34 0.00 46.52 2.52
2456 3214 4.827835 TCACTGTAAGCTAGAACACAGTCT 59.172 41.667 16.34 0.29 46.52 3.24
2457 3215 5.122512 TCACTGTAAGCTAGAACACAGTC 57.877 43.478 16.34 0.00 46.52 3.51
2459 3217 7.426929 AATTTCACTGTAAGCTAGAACACAG 57.573 36.000 13.45 13.45 43.21 3.66
2460 3218 7.801716 AAATTTCACTGTAAGCTAGAACACA 57.198 32.000 0.00 0.00 37.60 3.72
2485 3244 9.772973 GGTCAAGAAAATTAACTTACCCAAAAT 57.227 29.630 0.00 0.00 0.00 1.82
2507 3266 5.690409 GCGTTCGATCTTAATCTAATGGTCA 59.310 40.000 0.00 0.00 28.90 4.02
2538 3297 5.069318 AGAAAGCTGGAGGAAGAAGAAAAG 58.931 41.667 0.00 0.00 0.00 2.27
2609 3667 5.995897 ACTGGCCGGTAATATTAACTGAATC 59.004 40.000 18.00 0.00 0.00 2.52
2620 3678 1.488812 AGATGCAACTGGCCGGTAATA 59.511 47.619 20.05 7.44 43.89 0.98
2636 3694 1.153086 CCCCCGCCTCTGAAAGATG 60.153 63.158 0.00 0.00 45.62 2.90
2637 3695 3.049080 GCCCCCGCCTCTGAAAGAT 62.049 63.158 0.00 0.00 45.62 2.40
2639 3697 3.721706 AGCCCCCGCCTCTGAAAG 61.722 66.667 0.00 0.00 34.57 2.62
2653 3711 4.673732 CTTTCTGAAAAGGAGGCTCAGCC 61.674 52.174 17.69 8.01 42.50 4.85
2654 3712 2.191128 TTCTGAAAAGGAGGCTCAGC 57.809 50.000 17.69 0.00 37.17 4.26
2655 3713 4.013267 TCTTTCTGAAAAGGAGGCTCAG 57.987 45.455 17.69 4.79 41.88 3.35
2656 3714 4.437682 TTCTTTCTGAAAAGGAGGCTCA 57.562 40.909 17.69 0.00 41.88 4.26
2657 3715 5.774498 TTTTCTTTCTGAAAAGGAGGCTC 57.226 39.130 5.78 5.78 46.20 4.70
2682 3740 4.079253 AGATGTCCGGCAATGTTAACTTT 58.921 39.130 7.22 3.94 0.00 2.66
2685 3743 3.063997 CAGAGATGTCCGGCAATGTTAAC 59.936 47.826 0.00 0.00 0.00 2.01
2694 3752 1.066858 TCTGTTTCAGAGATGTCCGGC 60.067 52.381 0.00 0.00 35.39 6.13
2699 3757 4.063689 CAGTGCTTCTGTTTCAGAGATGT 58.936 43.478 0.00 0.00 41.75 3.06
2760 3818 6.367374 TGTTGAGATATTCACCCTTGTGTA 57.633 37.500 0.00 0.00 43.26 2.90
2773 3831 3.769300 GGGCCCTGTTTTTGTTGAGATAT 59.231 43.478 17.04 0.00 0.00 1.63
2829 3890 3.056749 CCCTGGTGCGATCTACTTATACC 60.057 52.174 0.00 0.00 0.00 2.73
2833 3894 1.754803 CACCCTGGTGCGATCTACTTA 59.245 52.381 2.89 0.00 39.39 2.24
2862 3923 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2863 3924 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2864 3925 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2865 3926 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2866 3927 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2867 3928 0.036164 AGGTGTGTGTGTGTGTGTGT 59.964 50.000 0.00 0.00 0.00 3.72
2870 3931 1.375853 CCCAGGTGTGTGTGTGTGTG 61.376 60.000 0.00 0.00 0.00 3.82
2871 3932 1.077787 CCCAGGTGTGTGTGTGTGT 60.078 57.895 0.00 0.00 0.00 3.72
2872 3933 1.077787 ACCCAGGTGTGTGTGTGTG 60.078 57.895 0.00 0.00 0.00 3.82
2873 3934 1.077787 CACCCAGGTGTGTGTGTGT 60.078 57.895 8.75 0.00 40.91 3.72


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

AutoCloner maintained by Alex Coulton.