Multiple sequence alignment - TraesCS3A01G377300

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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 TraesCS3A01G377300 chr3A 100.000 3336 0 0 1 3336 627251453 627254788 0.000000e+00 6161.0
1 TraesCS3A01G377300 chr3D 93.206 2826 119 32 1 2784 484286346 484289140 0.000000e+00 4087.0
2 TraesCS3A01G377300 chr3B 91.004 2790 159 40 598 3336 647077780 647080528 0.000000e+00 3677.0
3 TraesCS3A01G377300 chr3B 86.166 506 27 17 1 470 647077184 647077682 1.070000e-139 507.0
4 TraesCS3A01G377300 chr5D 86.401 603 82 0 1574 2176 388861 388259 0.000000e+00 660.0
5 TraesCS3A01G377300 chr5D 83.871 589 95 0 1592 2180 538789145 538788557 2.250000e-156 562.0
6 TraesCS3A01G377300 chr5D 90.932 397 36 0 1167 1563 389377 388981 4.900000e-148 534.0
7 TraesCS3A01G377300 chr5D 81.250 400 71 4 1166 1563 210375786 210375389 1.490000e-83 320.0
8 TraesCS3A01G377300 chr4A 85.741 540 77 0 1641 2180 629859598 629860137 3.730000e-159 571.0
9 TraesCS3A01G377300 chr4A 80.065 617 119 4 1565 2179 576702780 576702166 3.920000e-124 455.0
10 TraesCS3A01G377300 chr4A 84.500 400 62 0 1164 1563 576703438 576703039 2.410000e-106 396.0
11 TraesCS3A01G377300 chr5B 83.871 589 95 0 1592 2180 680359997 680359409 2.250000e-156 562.0
12 TraesCS3A01G377300 chr5B 81.220 410 72 5 1166 1572 223984941 223984534 3.210000e-85 326.0
13 TraesCS3A01G377300 chr5A 90.250 400 39 0 1164 1563 228156 228555 1.060000e-144 523.0
14 TraesCS3A01G377300 chr4B 80.484 620 117 4 1562 2179 39121253 39121870 3.900000e-129 472.0
15 TraesCS3A01G377300 chr4B 84.131 397 63 0 1164 1560 39120606 39121002 5.220000e-103 385.0
16 TraesCS3A01G377300 chr4D 80.161 620 119 4 1562 2179 26669097 26669714 8.430000e-126 460.0
17 TraesCS3A01G377300 chr4D 83.879 397 64 0 1164 1560 26668444 26668840 2.430000e-101 379.0
18 TraesCS3A01G377300 chr1B 87.013 77 8 2 2267 2342 492787717 492787642 5.930000e-13 86.1
19 TraesCS3A01G377300 chr1D 88.235 68 8 0 2267 2334 370013325 370013258 7.670000e-12 82.4


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 TraesCS3A01G377300 chr3A 627251453 627254788 3335 False 6161.0 6161 100.0000 1 3336 1 chr3A.!!$F1 3335
1 TraesCS3A01G377300 chr3D 484286346 484289140 2794 False 4087.0 4087 93.2060 1 2784 1 chr3D.!!$F1 2783
2 TraesCS3A01G377300 chr3B 647077184 647080528 3344 False 2092.0 3677 88.5850 1 3336 2 chr3B.!!$F1 3335
3 TraesCS3A01G377300 chr5D 388259 389377 1118 True 597.0 660 88.6665 1167 2176 2 chr5D.!!$R3 1009
4 TraesCS3A01G377300 chr5D 538788557 538789145 588 True 562.0 562 83.8710 1592 2180 1 chr5D.!!$R2 588
5 TraesCS3A01G377300 chr4A 629859598 629860137 539 False 571.0 571 85.7410 1641 2180 1 chr4A.!!$F1 539
6 TraesCS3A01G377300 chr4A 576702166 576703438 1272 True 425.5 455 82.2825 1164 2179 2 chr4A.!!$R1 1015
7 TraesCS3A01G377300 chr5B 680359409 680359997 588 True 562.0 562 83.8710 1592 2180 1 chr5B.!!$R2 588
8 TraesCS3A01G377300 chr4B 39120606 39121870 1264 False 428.5 472 82.3075 1164 2179 2 chr4B.!!$F1 1015
9 TraesCS3A01G377300 chr4D 26668444 26669714 1270 False 419.5 460 82.0200 1164 2179 2 chr4D.!!$F1 1015

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
356 388 0.327576 TGATTTCCTCCCCCTCCTCC 60.328 60.0 0.0 0.0 0.00 4.30 F
1157 1263 0.176219 TGAACAACCGTCCTTCGTGT 59.824 50.0 0.0 0.0 37.94 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2676 0.175073 GGCCGGTTTCATCGTACTCT 59.825 55.0 1.9 0.0 0.0 3.24 R
2940 3362 0.036388 ATCAGCCACCGACACGATTT 60.036 50.0 0.0 0.0 0.0 2.17 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
67 68 1.079819 AGGAGCACGATGTTGTCCG 60.080 57.895 0.00 0.00 32.14 4.79
84 85 3.110178 GGGTCGTCGTTCCGCTTG 61.110 66.667 0.00 0.00 0.00 4.01
90 91 1.134694 GTCGTTCCGCTTGAATGCC 59.865 57.895 1.34 0.00 39.42 4.40
91 92 1.003839 TCGTTCCGCTTGAATGCCT 60.004 52.632 1.34 0.00 39.42 4.75
93 94 1.153958 GTTCCGCTTGAATGCCTGC 60.154 57.895 0.00 0.00 34.90 4.85
299 319 4.838486 CTCGCGTCACTCCGAGCC 62.838 72.222 5.77 0.00 43.49 4.70
336 368 4.090588 CCCGCCCGAGCAAAGGTA 62.091 66.667 0.00 0.00 39.83 3.08
338 370 2.180204 CCGCCCGAGCAAAGGTATG 61.180 63.158 0.00 0.00 39.83 2.39
339 371 1.153449 CGCCCGAGCAAAGGTATGA 60.153 57.895 0.00 0.00 39.83 2.15
340 372 0.532862 CGCCCGAGCAAAGGTATGAT 60.533 55.000 0.00 0.00 39.83 2.45
341 373 1.680338 GCCCGAGCAAAGGTATGATT 58.320 50.000 0.00 0.00 39.53 2.57
344 376 2.618709 CCCGAGCAAAGGTATGATTTCC 59.381 50.000 0.00 0.00 0.00 3.13
348 380 3.885901 GAGCAAAGGTATGATTTCCTCCC 59.114 47.826 0.00 0.00 33.09 4.30
355 387 1.826447 ATGATTTCCTCCCCCTCCTC 58.174 55.000 0.00 0.00 0.00 3.71
356 388 0.327576 TGATTTCCTCCCCCTCCTCC 60.328 60.000 0.00 0.00 0.00 4.30
362 394 1.690985 CTCCCCCTCCTCCCTGAAC 60.691 68.421 0.00 0.00 0.00 3.18
444 485 3.313249 CGTAGTTTTTCCGGTGGTTTTCT 59.687 43.478 0.00 0.00 0.00 2.52
461 502 3.944250 CTCGCTGGCATGGGGGTTT 62.944 63.158 0.00 0.00 0.00 3.27
470 514 0.470833 CATGGGGGTTTGGTGGTTGA 60.471 55.000 0.00 0.00 0.00 3.18
491 535 1.153978 GTTGGTACGACGCGATCCA 60.154 57.895 15.93 10.64 33.72 3.41
542 617 4.646572 GGATTGGTAGGATCTTTAGCTGG 58.353 47.826 0.00 0.00 0.00 4.85
557 632 2.432456 TGGTAGCTTGCGCGACAG 60.432 61.111 12.10 5.25 42.66 3.51
594 669 3.021695 TCGATGATACACGAGTTCCCTT 58.978 45.455 0.00 0.00 34.49 3.95
595 670 3.066342 TCGATGATACACGAGTTCCCTTC 59.934 47.826 0.00 0.00 34.49 3.46
596 671 3.718815 GATGATACACGAGTTCCCTTCC 58.281 50.000 0.00 0.00 0.00 3.46
597 672 1.829222 TGATACACGAGTTCCCTTCCC 59.171 52.381 0.00 0.00 0.00 3.97
598 673 2.108970 GATACACGAGTTCCCTTCCCT 58.891 52.381 0.00 0.00 0.00 4.20
630 705 0.392998 CCACGGGCTGCAGTATCTTT 60.393 55.000 16.64 0.00 0.00 2.52
647 722 1.597663 CTTTTCTGTTGACCGCTTCGT 59.402 47.619 0.00 0.00 0.00 3.85
655 730 3.562779 GACCGCTTCGTGTTCGGGA 62.563 63.158 4.89 0.00 46.78 5.14
676 751 4.381612 GGATGACCAGTGAATCGTGAACTA 60.382 45.833 0.00 0.00 35.97 2.24
680 755 5.056894 ACCAGTGAATCGTGAACTAGTAC 57.943 43.478 0.00 0.00 0.00 2.73
681 756 4.765856 ACCAGTGAATCGTGAACTAGTACT 59.234 41.667 0.00 0.00 0.00 2.73
690 765 8.522542 AATCGTGAACTAGTACTATCTTTCCT 57.477 34.615 2.33 0.00 0.00 3.36
726 801 6.532657 GTGATTTGCGAAAGATTGGATCAATT 59.467 34.615 0.00 0.00 33.90 2.32
830 913 0.933097 CGAGAAATCCTGCGTGATGG 59.067 55.000 0.00 0.00 0.00 3.51
839 922 4.776647 GCGTGATGGCCGGCAAAC 62.777 66.667 30.85 17.86 0.00 2.93
869 952 2.222213 TGTTATCACGCGTTTGTCTTGG 59.778 45.455 10.22 0.00 0.00 3.61
895 980 9.440773 GATCCATCTGTATATATGTGAGCAAAA 57.559 33.333 0.00 0.00 0.00 2.44
896 981 9.797642 ATCCATCTGTATATATGTGAGCAAAAA 57.202 29.630 0.00 0.00 0.00 1.94
939 1032 9.028284 CAATACCATGCCCTGATCTTTTATTAT 57.972 33.333 0.00 0.00 0.00 1.28
943 1036 6.430925 CCATGCCCTGATCTTTTATTATCGAA 59.569 38.462 0.00 0.00 0.00 3.71
944 1037 7.040478 CCATGCCCTGATCTTTTATTATCGAAA 60.040 37.037 0.00 0.00 0.00 3.46
1023 1121 0.179089 CTGAAGAGGATGTCCAGCCG 60.179 60.000 1.30 0.00 42.82 5.52
1064 1162 2.076863 CGGAATGGTCAAGGTCAGTTC 58.923 52.381 0.00 0.00 0.00 3.01
1069 1167 0.325272 GGTCAAGGTCAGTTCCCCTC 59.675 60.000 0.00 0.00 0.00 4.30
1127 1228 3.926616 AGTGCAGAGTACATTTTAGCGT 58.073 40.909 0.00 0.00 0.00 5.07
1128 1229 4.315803 AGTGCAGAGTACATTTTAGCGTT 58.684 39.130 0.00 0.00 0.00 4.84
1129 1230 4.389077 AGTGCAGAGTACATTTTAGCGTTC 59.611 41.667 0.00 0.00 0.00 3.95
1144 1245 0.505231 CGTTCGCGCTAACTGAACAA 59.495 50.000 20.74 0.00 41.52 2.83
1147 1248 1.129809 CGCGCTAACTGAACAACCG 59.870 57.895 5.56 0.00 0.00 4.44
1157 1263 0.176219 TGAACAACCGTCCTTCGTGT 59.824 50.000 0.00 0.00 37.94 4.49
1496 1602 4.111198 CAGATCATGTTCGAGACCTTCAG 58.889 47.826 0.00 0.00 0.00 3.02
1980 2361 3.316868 TCATGAAGTGCGACGTGGATATA 59.683 43.478 0.11 0.00 0.00 0.86
2013 2394 2.482374 GGCAATGTCGTGCTCAGC 59.518 61.111 0.00 0.00 44.31 4.26
2187 2568 2.507407 TCCAGCAGGTACCCATTTTC 57.493 50.000 8.74 0.00 35.89 2.29
2188 2569 1.005450 TCCAGCAGGTACCCATTTTCC 59.995 52.381 8.74 0.00 35.89 3.13
2197 2578 2.846665 ACCCATTTTCCCCCTACATG 57.153 50.000 0.00 0.00 0.00 3.21
2205 2591 5.987019 TTTTCCCCCTACATGCTACTAAT 57.013 39.130 0.00 0.00 0.00 1.73
2206 2592 4.974645 TTCCCCCTACATGCTACTAATG 57.025 45.455 0.00 0.00 0.00 1.90
2207 2593 2.637872 TCCCCCTACATGCTACTAATGC 59.362 50.000 0.00 0.00 0.00 3.56
2208 2594 2.639839 CCCCCTACATGCTACTAATGCT 59.360 50.000 0.00 0.00 0.00 3.79
2255 2644 0.861837 CGAGATTAATGGCGTGCCTC 59.138 55.000 12.84 0.53 36.94 4.70
2344 2733 1.550327 AGTGCTTCTGATCAGTCCGA 58.450 50.000 21.92 0.03 0.00 4.55
2408 2797 0.448990 TCGCAGATGCTTGAATGTGC 59.551 50.000 2.95 1.03 41.98 4.57
2420 2809 2.538222 TGAATGTGCCATGGTTTCCAT 58.462 42.857 14.67 7.60 46.37 3.41
2434 2823 3.487202 CCATGGCGTCGTGGTTCG 61.487 66.667 20.44 0.00 43.41 3.95
2678 3067 0.035739 GTAGCGGGGGTTTCTTGTCA 59.964 55.000 0.00 0.00 0.00 3.58
2699 3088 1.374758 CCACCTGGTCAGTTCTCGC 60.375 63.158 0.00 0.00 0.00 5.03
2747 3140 9.410556 GTACTTCAGCATTTGTACATTTTGAAT 57.589 29.630 0.00 0.00 36.32 2.57
2748 3141 8.891671 ACTTCAGCATTTGTACATTTTGAATT 57.108 26.923 0.00 0.00 0.00 2.17
2749 3142 9.979578 ACTTCAGCATTTGTACATTTTGAATTA 57.020 25.926 0.00 0.00 0.00 1.40
2818 3240 3.078837 GTTGATCCGGTTGGTGTGTTAT 58.921 45.455 0.00 0.00 36.30 1.89
2821 3243 2.172851 TCCGGTTGGTGTGTTATGAC 57.827 50.000 0.00 0.00 36.30 3.06
2846 3268 2.325082 AAGCGTCACAATCCCGTGC 61.325 57.895 0.00 0.00 36.80 5.34
2849 3271 1.809619 CGTCACAATCCCGTGCGAT 60.810 57.895 0.00 0.00 38.09 4.58
2863 3285 1.028130 TGCGATGGAAGTTTGCAACA 58.972 45.000 0.00 0.00 30.57 3.33
2867 3289 2.034558 CGATGGAAGTTTGCAACAGGTT 59.965 45.455 0.00 0.00 30.51 3.50
2868 3290 3.642705 GATGGAAGTTTGCAACAGGTTC 58.357 45.455 0.00 0.00 30.51 3.62
2889 3311 7.068348 AGGTTCATGTATACTCTCGAAAGCTAA 59.932 37.037 4.17 0.00 0.00 3.09
2900 3322 6.704493 ACTCTCGAAAGCTAAACAACAATGTA 59.296 34.615 0.00 0.00 39.40 2.29
2930 3352 3.871594 GCGTATGGCCTTGGATACATATC 59.128 47.826 3.32 0.00 41.26 1.63
2952 3375 1.069513 TCAACCTCAAATCGTGTCGGT 59.930 47.619 0.00 0.00 34.84 4.69
2961 3384 1.323271 ATCGTGTCGGTGGCTGATCT 61.323 55.000 0.00 0.00 0.00 2.75
2965 3388 1.153549 GTCGGTGGCTGATCTGTCC 60.154 63.158 1.40 4.26 0.00 4.02
2970 3393 1.202698 GGTGGCTGATCTGTCCATACC 60.203 57.143 15.18 7.47 31.83 2.73
2989 3412 1.739466 CCACATCCTTGGTGATTGTCG 59.261 52.381 0.00 0.00 38.54 4.35
3003 3428 2.651232 GTCGATTCGAGTCGGGCG 60.651 66.667 26.94 13.61 41.74 6.13
3020 3445 2.031333 GGGCGATCAGAGATGAAATTGC 60.031 50.000 0.00 0.00 0.00 3.56
3021 3446 2.877168 GGCGATCAGAGATGAAATTGCT 59.123 45.455 0.00 0.00 0.00 3.91
3022 3447 3.059051 GGCGATCAGAGATGAAATTGCTC 60.059 47.826 0.00 0.00 0.00 4.26
3023 3448 3.558829 GCGATCAGAGATGAAATTGCTCA 59.441 43.478 0.00 0.00 0.00 4.26
3024 3449 4.034858 GCGATCAGAGATGAAATTGCTCAA 59.965 41.667 0.00 0.00 0.00 3.02
3025 3450 5.448225 GCGATCAGAGATGAAATTGCTCAAA 60.448 40.000 0.00 0.00 0.00 2.69
3026 3451 6.549061 CGATCAGAGATGAAATTGCTCAAAA 58.451 36.000 0.00 0.00 0.00 2.44
3027 3452 6.468319 CGATCAGAGATGAAATTGCTCAAAAC 59.532 38.462 0.00 0.00 0.00 2.43
3028 3453 6.017400 TCAGAGATGAAATTGCTCAAAACC 57.983 37.500 0.00 0.00 0.00 3.27
3029 3454 5.047802 TCAGAGATGAAATTGCTCAAAACCC 60.048 40.000 0.00 0.00 0.00 4.11
3030 3455 4.834496 AGAGATGAAATTGCTCAAAACCCA 59.166 37.500 0.00 0.00 0.00 4.51
3031 3456 4.886579 AGATGAAATTGCTCAAAACCCAC 58.113 39.130 0.00 0.00 0.00 4.61
3032 3457 3.467374 TGAAATTGCTCAAAACCCACC 57.533 42.857 0.00 0.00 0.00 4.61
3033 3458 2.768527 TGAAATTGCTCAAAACCCACCA 59.231 40.909 0.00 0.00 0.00 4.17
3038 3463 2.392662 TGCTCAAAACCCACCATTCAA 58.607 42.857 0.00 0.00 0.00 2.69
3072 3498 5.928839 TGAGACTCAAGAAAATCTTCTTCCG 59.071 40.000 1.64 0.00 46.88 4.30
3078 3504 3.326747 AGAAAATCTTCTTCCGTGTCCG 58.673 45.455 0.00 0.00 38.89 4.79
3092 3518 2.096174 CGTGTCCGTTTTCAACTGGAAA 59.904 45.455 2.98 0.00 43.59 3.13
3120 3546 2.287608 GCTCAAAGAAAACCTTCACCCG 60.288 50.000 0.00 0.00 33.02 5.28
3131 3557 2.143925 CCTTCACCCGAGTCTGTTTTC 58.856 52.381 0.00 0.00 0.00 2.29
3149 3575 9.753674 TCTGTTTTCCTAATAATCACCTCAAAT 57.246 29.630 0.00 0.00 0.00 2.32
3157 3583 9.220767 CCTAATAATCACCTCAAATAAGCCTAC 57.779 37.037 0.00 0.00 0.00 3.18
3158 3584 9.778741 CTAATAATCACCTCAAATAAGCCTACA 57.221 33.333 0.00 0.00 0.00 2.74
3180 3606 3.332034 ACACGCCTTTTAGTGGTATCAC 58.668 45.455 0.00 0.00 42.25 3.06
3247 3674 7.210873 CCTTTTATAGGCTCTTGGTAGTGTAG 58.789 42.308 0.00 0.00 37.17 2.74
3267 3694 6.535508 GTGTAGAAATGACCACCAATACTCTC 59.464 42.308 0.00 0.00 0.00 3.20
3291 3718 5.561679 GTGGGAGAGAAAAGTAAGGTCAAT 58.438 41.667 0.00 0.00 0.00 2.57
3323 3750 6.396829 AAAGGAGAAAGGAAAACATGTCTG 57.603 37.500 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 222 2.944129 TGGGGAGCAGTTTTATATGCC 58.056 47.619 0.00 0.00 43.60 4.40
329 361 3.205282 AGGGGGAGGAAATCATACCTTTG 59.795 47.826 0.00 0.00 36.57 2.77
330 362 3.463704 GAGGGGGAGGAAATCATACCTTT 59.536 47.826 0.00 0.00 36.57 3.11
332 364 2.700540 GGAGGGGGAGGAAATCATACCT 60.701 54.545 0.00 0.00 39.41 3.08
334 366 2.640332 GAGGAGGGGGAGGAAATCATAC 59.360 54.545 0.00 0.00 0.00 2.39
336 368 1.700576 GGAGGAGGGGGAGGAAATCAT 60.701 57.143 0.00 0.00 0.00 2.45
338 370 1.063070 GGGAGGAGGGGGAGGAAATC 61.063 65.000 0.00 0.00 0.00 2.17
339 371 1.006227 GGGAGGAGGGGGAGGAAAT 59.994 63.158 0.00 0.00 0.00 2.17
340 372 2.191846 AGGGAGGAGGGGGAGGAAA 61.192 63.158 0.00 0.00 0.00 3.13
341 373 2.543637 AGGGAGGAGGGGGAGGAA 60.544 66.667 0.00 0.00 0.00 3.36
344 376 1.690985 GTTCAGGGAGGAGGGGGAG 60.691 68.421 0.00 0.00 0.00 4.30
348 380 0.983378 AATCGGTTCAGGGAGGAGGG 60.983 60.000 0.00 0.00 0.00 4.30
362 394 1.648504 GGAACTACGGACCAAATCGG 58.351 55.000 0.00 0.00 42.50 4.18
444 485 3.978193 AAACCCCCATGCCAGCGA 61.978 61.111 0.00 0.00 0.00 4.93
461 502 2.898612 TCGTACCAACTATCAACCACCA 59.101 45.455 0.00 0.00 0.00 4.17
470 514 1.002033 GGATCGCGTCGTACCAACTAT 60.002 52.381 5.77 0.00 0.00 2.12
557 632 2.946762 GACTTGACCAGCAACGGC 59.053 61.111 0.00 0.00 41.61 5.68
571 646 2.358267 GGGAACTCGTGTATCATCGACT 59.642 50.000 0.00 0.00 32.65 4.18
594 669 3.311110 GTCAGCGGTCACCAGGGA 61.311 66.667 0.00 0.00 0.00 4.20
595 670 4.394712 GGTCAGCGGTCACCAGGG 62.395 72.222 1.54 0.00 32.33 4.45
596 671 3.625897 TGGTCAGCGGTCACCAGG 61.626 66.667 6.15 0.00 37.78 4.45
597 672 2.357517 GTGGTCAGCGGTCACCAG 60.358 66.667 11.80 0.00 43.56 4.00
598 673 4.293648 CGTGGTCAGCGGTCACCA 62.294 66.667 6.15 6.15 40.56 4.17
630 705 0.179094 ACACGAAGCGGTCAACAGAA 60.179 50.000 0.00 0.00 0.00 3.02
647 722 1.052617 TTCACTGGTCATCCCGAACA 58.947 50.000 0.00 0.00 39.74 3.18
655 730 3.685139 AGTTCACGATTCACTGGTCAT 57.315 42.857 0.00 0.00 0.00 3.06
690 765 7.353497 TCTTTCGCAAATCACGTGTTTAATTA 58.647 30.769 16.51 0.00 0.00 1.40
749 824 5.796350 AATCAGCTACAATCACGGTAAAC 57.204 39.130 0.00 0.00 0.00 2.01
839 922 2.855963 ACGCGTGATAACAAACGGATAG 59.144 45.455 12.93 0.00 40.12 2.08
869 952 9.440773 TTTTGCTCACATATATACAGATGGATC 57.559 33.333 0.00 0.00 0.00 3.36
916 1001 6.878923 CGATAATAAAAGATCAGGGCATGGTA 59.121 38.462 0.00 0.00 0.00 3.25
939 1032 6.918892 TTCAGTCTGTTTCTTCAATTTCGA 57.081 33.333 0.00 0.00 0.00 3.71
1064 1162 1.133976 GGATTGACACCATGAGAGGGG 60.134 57.143 0.00 0.00 38.34 4.79
1069 1167 4.463539 TGAATTTGGGATTGACACCATGAG 59.536 41.667 0.00 0.00 36.48 2.90
1127 1228 0.863144 GGTTGTTCAGTTAGCGCGAA 59.137 50.000 12.10 0.00 0.00 4.70
1128 1229 1.279527 CGGTTGTTCAGTTAGCGCGA 61.280 55.000 12.10 0.00 0.00 5.87
1129 1230 1.129809 CGGTTGTTCAGTTAGCGCG 59.870 57.895 0.00 0.00 0.00 6.86
1134 1235 2.746269 CGAAGGACGGTTGTTCAGTTA 58.254 47.619 0.00 0.00 38.46 2.24
1147 1248 1.261619 CTGCAGTTTGACACGAAGGAC 59.738 52.381 5.25 0.00 0.00 3.85
1157 1263 3.429372 AACCCCGCCTGCAGTTTGA 62.429 57.895 13.81 0.00 0.00 2.69
1695 2076 0.395862 TGAAGGAGTAGCCCCTCTCG 60.396 60.000 0.78 0.00 37.37 4.04
1980 2361 1.568504 TGCCGTACAGATCCTTCCTT 58.431 50.000 0.00 0.00 0.00 3.36
2187 2568 2.639839 AGCATTAGTAGCATGTAGGGGG 59.360 50.000 0.00 0.00 0.00 5.40
2188 2569 4.067896 CAAGCATTAGTAGCATGTAGGGG 58.932 47.826 0.00 0.00 0.00 4.79
2197 2578 5.006165 CAGTAACAGAGCAAGCATTAGTAGC 59.994 44.000 0.00 0.00 0.00 3.58
2205 2591 1.800805 GAGCAGTAACAGAGCAAGCA 58.199 50.000 0.00 0.00 0.00 3.91
2206 2592 0.718343 CGAGCAGTAACAGAGCAAGC 59.282 55.000 0.00 0.00 0.00 4.01
2207 2593 2.071688 ACGAGCAGTAACAGAGCAAG 57.928 50.000 0.00 0.00 0.00 4.01
2208 2594 2.526304 AACGAGCAGTAACAGAGCAA 57.474 45.000 0.00 0.00 0.00 3.91
2255 2644 1.135603 CCACATCTGCGACACAAATGG 60.136 52.381 0.00 0.00 0.00 3.16
2287 2676 0.175073 GGCCGGTTTCATCGTACTCT 59.825 55.000 1.90 0.00 0.00 3.24
2344 2733 0.473886 AGGTACAGGTTGGTCAGCCT 60.474 55.000 0.31 0.31 43.18 4.58
2434 2823 3.068024 TCCATGACCAAAACACTTTCAGC 59.932 43.478 0.00 0.00 0.00 4.26
2682 3071 0.036952 ATGCGAGAACTGACCAGGTG 60.037 55.000 0.00 0.00 0.00 4.00
2691 3080 3.601443 AAGCTTCTACATGCGAGAACT 57.399 42.857 6.57 6.81 0.00 3.01
2699 3088 8.730680 AGTACCAACAAAATAAGCTTCTACATG 58.269 33.333 0.00 0.00 0.00 3.21
2821 3243 1.929836 GGATTGTGACGCTTGCTAGAG 59.070 52.381 0.00 0.00 0.00 2.43
2863 3285 5.361285 AGCTTTCGAGAGTATACATGAACCT 59.639 40.000 5.50 0.87 0.00 3.50
2867 3289 7.768240 TGTTTAGCTTTCGAGAGTATACATGA 58.232 34.615 5.50 0.00 0.00 3.07
2868 3290 7.987268 TGTTTAGCTTTCGAGAGTATACATG 57.013 36.000 5.50 0.00 0.00 3.21
2900 3322 1.202114 CAAGGCCATACGCACACAAAT 59.798 47.619 5.01 0.00 40.31 2.32
2909 3331 4.112634 CGATATGTATCCAAGGCCATACG 58.887 47.826 5.01 0.00 0.00 3.06
2930 3352 1.124297 CGACACGATTTGAGGTTGACG 59.876 52.381 0.00 0.00 0.00 4.35
2936 3358 1.635663 GCCACCGACACGATTTGAGG 61.636 60.000 0.00 0.00 34.23 3.86
2938 3360 0.948623 CAGCCACCGACACGATTTGA 60.949 55.000 0.00 0.00 0.00 2.69
2940 3362 0.036388 ATCAGCCACCGACACGATTT 60.036 50.000 0.00 0.00 0.00 2.17
2952 3375 1.486310 GTGGTATGGACAGATCAGCCA 59.514 52.381 0.00 0.00 35.91 4.75
2970 3393 2.698803 TCGACAATCACCAAGGATGTG 58.301 47.619 0.00 0.00 35.01 3.21
2985 3408 2.488355 GCCCGACTCGAATCGACA 59.512 61.111 19.07 0.00 45.13 4.35
2986 3409 2.389866 ATCGCCCGACTCGAATCGAC 62.390 60.000 19.07 8.48 45.13 4.20
2988 3411 1.726322 GATCGCCCGACTCGAATCG 60.726 63.158 9.70 9.70 39.54 3.34
2989 3412 0.661780 CTGATCGCCCGACTCGAATC 60.662 60.000 0.00 0.00 39.54 2.52
3003 3428 6.750963 GGTTTTGAGCAATTTCATCTCTGATC 59.249 38.462 0.00 0.00 0.00 2.92
3029 3454 7.998329 GAGTCTCAAACTTCCATTTGAATGGTG 60.998 40.741 19.33 15.76 46.33 4.17
3030 3455 6.015940 GAGTCTCAAACTTCCATTTGAATGGT 60.016 38.462 19.33 1.35 46.33 3.55
3031 3456 6.016024 TGAGTCTCAAACTTCCATTTGAATGG 60.016 38.462 15.14 15.14 46.98 3.16
3032 3457 6.973843 TGAGTCTCAAACTTCCATTTGAATG 58.026 36.000 0.00 0.00 45.52 2.67
3033 3458 7.503566 TCTTGAGTCTCAAACTTCCATTTGAAT 59.496 33.333 15.97 0.00 45.52 2.57
3038 3463 7.645058 TTTTCTTGAGTCTCAAACTTCCATT 57.355 32.000 15.97 0.00 38.74 3.16
3092 3518 5.305128 TGAAGGTTTTCTTTGAGCATTGGAT 59.695 36.000 0.00 0.00 35.50 3.41
3120 3546 8.041323 TGAGGTGATTATTAGGAAAACAGACTC 58.959 37.037 0.00 0.00 0.00 3.36
3131 3557 9.220767 GTAGGCTTATTTGAGGTGATTATTAGG 57.779 37.037 0.00 0.00 0.00 2.69
3157 3583 3.749088 TGATACCACTAAAAGGCGTGTTG 59.251 43.478 0.00 0.00 0.00 3.33
3158 3584 3.749609 GTGATACCACTAAAAGGCGTGTT 59.250 43.478 0.00 0.00 40.10 3.32
3159 3585 3.332034 GTGATACCACTAAAAGGCGTGT 58.668 45.455 0.00 0.00 40.10 4.49
3180 3606 3.583806 AGTCATCTCTCGTTGAGCAAAG 58.416 45.455 3.89 0.00 42.38 2.77
3204 3631 3.272574 AGGCACACCATAGATCACTTG 57.727 47.619 0.00 0.00 39.06 3.16
3241 3668 6.213600 AGAGTATTGGTGGTCATTTCTACACT 59.786 38.462 0.00 0.00 34.42 3.55
3242 3669 6.407202 AGAGTATTGGTGGTCATTTCTACAC 58.593 40.000 0.00 0.00 0.00 2.90
3247 3674 4.504858 ACGAGAGTATTGGTGGTCATTTC 58.495 43.478 0.00 0.00 46.88 2.17
3267 3694 3.006537 TGACCTTACTTTTCTCTCCCACG 59.993 47.826 0.00 0.00 0.00 4.94
3291 3718 5.656549 TTCCTTTCTCCTTTTTGAGGGTA 57.343 39.130 0.00 0.00 46.31 3.69
3311 3738 6.560253 ACCAAGTACATCAGACATGTTTTC 57.440 37.500 0.00 0.00 33.76 2.29


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

AutoCloner maintained by Alex Coulton.