Multiple sequence alignment - TraesCS3D01G010900

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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 TraesCS3D01G010900 chr3D 100.000 2817 0 0 1 2817 4011144 4013960 0.000000e+00 5203
1 TraesCS3D01G010900 chr3D 96.220 1111 42 0 1249 2359 4046234 4047344 0.000000e+00 1820
2 TraesCS3D01G010900 chr3D 88.174 668 59 10 1249 1914 4059221 4059870 0.000000e+00 778
3 TraesCS3D01G010900 chr3D 92.949 468 29 3 2354 2817 4057576 4058043 0.000000e+00 678
4 TraesCS3D01G010900 chr3D 83.245 567 95 0 1252 1818 4011140 4010574 3.220000e-144 521
5 TraesCS3D01G010900 chr3D 92.982 228 16 0 1 228 4045002 4045229 1.620000e-87 333
6 TraesCS3D01G010900 chr3A 87.406 2128 186 42 78 2154 9573433 9571337 0.000000e+00 2370
7 TraesCS3D01G010900 chr3A 82.038 785 110 17 2041 2817 9563354 9562593 8.510000e-180 640
8 TraesCS3D01G010900 chr3A 91.067 403 31 3 1646 2044 9569011 9568610 8.880000e-150 540
9 TraesCS3D01G010900 chr3A 83.275 568 93 2 1252 1818 9573499 9574065 3.220000e-144 521
10 TraesCS3D01G010900 chr3A 89.266 177 18 1 53 228 9556172 9555996 1.310000e-53 220
11 TraesCS3D01G010900 chr7D 84.737 570 87 0 1260 1829 577201251 577201820 3.150000e-159 571
12 TraesCS3D01G010900 chr7B 84.127 567 90 0 1252 1818 639926308 639926874 1.480000e-152 549
13 TraesCS3D01G010900 chr7B 84.127 567 90 0 1252 1818 639945954 639946520 1.480000e-152 549
14 TraesCS3D01G010900 chr7A 84.211 551 87 0 1260 1810 669293456 669294006 1.150000e-148 536


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 TraesCS3D01G010900 chr3D 4011144 4013960 2816 False 5203.0 5203 100.0000 1 2817 1 chr3D.!!$F1 2816
1 TraesCS3D01G010900 chr3D 4045002 4047344 2342 False 1076.5 1820 94.6010 1 2359 2 chr3D.!!$F2 2358
2 TraesCS3D01G010900 chr3D 4057576 4059870 2294 False 728.0 778 90.5615 1249 2817 2 chr3D.!!$F3 1568
3 TraesCS3D01G010900 chr3D 4010574 4011140 566 True 521.0 521 83.2450 1252 1818 1 chr3D.!!$R1 566
4 TraesCS3D01G010900 chr3A 9568610 9573433 4823 True 1455.0 2370 89.2365 78 2154 2 chr3A.!!$R3 2076
5 TraesCS3D01G010900 chr3A 9562593 9563354 761 True 640.0 640 82.0380 2041 2817 1 chr3A.!!$R2 776
6 TraesCS3D01G010900 chr3A 9573499 9574065 566 False 521.0 521 83.2750 1252 1818 1 chr3A.!!$F1 566
7 TraesCS3D01G010900 chr7D 577201251 577201820 569 False 571.0 571 84.7370 1260 1829 1 chr7D.!!$F1 569
8 TraesCS3D01G010900 chr7B 639926308 639926874 566 False 549.0 549 84.1270 1252 1818 1 chr7B.!!$F1 566
9 TraesCS3D01G010900 chr7B 639945954 639946520 566 False 549.0 549 84.1270 1252 1818 1 chr7B.!!$F2 566
10 TraesCS3D01G010900 chr7A 669293456 669294006 550 False 536.0 536 84.2110 1260 1810 1 chr7A.!!$F1 550

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
975 1067 0.100503 AACGAAGCACCAAACACAGC 59.899 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 3435 0.405198 ATGCCACAACCTCACATCCA 59.595 50.0 0.0 0.0 0.0 3.41 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
39 40 7.038659 TGAATACACAAACAAGGAAAAAGTGG 58.961 34.615 0.00 0.00 0.00 4.00
98 99 6.446781 ACTCAAATATGCAGTGATGAAAGG 57.553 37.500 0.00 0.00 0.00 3.11
141 142 0.458543 AGCTATTGTCCGCGACACAG 60.459 55.000 8.23 10.70 42.60 3.66
147 148 1.733399 GTCCGCGACACAGAAGTCC 60.733 63.158 8.23 0.00 35.07 3.85
189 190 2.009042 GCTAAAGCGTGCCATGAGACT 61.009 52.381 0.00 0.00 0.00 3.24
224 225 1.627834 AGTGAAGAGAAGGAAGCAGGG 59.372 52.381 0.00 0.00 0.00 4.45
234 235 0.112412 GGAAGCAGGGGGAAGACAAA 59.888 55.000 0.00 0.00 0.00 2.83
246 247 3.306294 GGGAAGACAAAGAGGCCATTTTG 60.306 47.826 22.97 22.97 39.55 2.44
251 252 5.385198 AGACAAAGAGGCCATTTTGTTCTA 58.615 37.500 27.81 0.00 44.88 2.10
265 266 6.737254 TTTTGTTCTATCGGAGAAATGGAC 57.263 37.500 2.73 0.00 45.90 4.02
274 275 3.446161 TCGGAGAAATGGACGTTGTCTAT 59.554 43.478 0.00 0.00 35.32 1.98
276 277 3.871594 GGAGAAATGGACGTTGTCTATGG 59.128 47.826 0.00 0.00 34.13 2.74
326 346 2.216898 GTAGCTGATTCTGTGGCCATC 58.783 52.381 9.72 1.58 0.00 3.51
369 402 1.598130 AGCTGACCGAGTTGCCAAC 60.598 57.895 0.00 0.00 0.00 3.77
393 431 2.533266 ATCCAAGGCGTACATAGCAG 57.467 50.000 0.00 0.00 36.08 4.24
444 490 4.155280 GCAACCCACGTGTCTAATTAACAT 59.845 41.667 15.65 0.00 0.00 2.71
550 617 2.821991 GCATGAGGCGACTAGGTTAT 57.178 50.000 0.00 0.00 44.43 1.89
551 618 3.113260 GCATGAGGCGACTAGGTTATT 57.887 47.619 0.00 0.00 44.43 1.40
553 620 4.238514 GCATGAGGCGACTAGGTTATTAG 58.761 47.826 0.00 0.00 44.43 1.73
554 621 4.810790 CATGAGGCGACTAGGTTATTAGG 58.189 47.826 0.00 0.00 44.43 2.69
556 623 2.892215 GAGGCGACTAGGTTATTAGGCT 59.108 50.000 0.00 0.00 44.43 4.58
557 624 4.077822 GAGGCGACTAGGTTATTAGGCTA 58.922 47.826 0.00 0.00 44.43 3.93
558 625 4.080687 AGGCGACTAGGTTATTAGGCTAG 58.919 47.826 0.00 0.00 40.61 3.42
560 627 4.705991 GGCGACTAGGTTATTAGGCTAGAT 59.294 45.833 0.00 0.00 0.00 1.98
561 628 5.163632 GGCGACTAGGTTATTAGGCTAGATC 60.164 48.000 0.00 0.00 0.00 2.75
562 629 5.415077 GCGACTAGGTTATTAGGCTAGATCA 59.585 44.000 0.00 0.00 0.00 2.92
563 630 6.072064 GCGACTAGGTTATTAGGCTAGATCAA 60.072 42.308 0.00 0.00 0.00 2.57
564 631 7.306953 CGACTAGGTTATTAGGCTAGATCAAC 58.693 42.308 0.00 0.00 0.00 3.18
566 633 9.517868 GACTAGGTTATTAGGCTAGATCAACTA 57.482 37.037 0.00 0.00 0.00 2.24
599 666 6.350103 TCAAGGTTACGCCATATATTCAACA 58.650 36.000 0.00 0.00 40.61 3.33
600 667 6.259167 TCAAGGTTACGCCATATATTCAACAC 59.741 38.462 0.00 0.00 40.61 3.32
601 668 5.061179 AGGTTACGCCATATATTCAACACC 58.939 41.667 0.00 0.00 40.61 4.16
662 737 3.006752 TCATGCATGACAGTGACACAGTA 59.993 43.478 25.42 0.00 0.00 2.74
668 743 5.639506 GCATGACAGTGACACAGTATAAAGT 59.360 40.000 8.59 0.00 0.00 2.66
669 744 6.401474 GCATGACAGTGACACAGTATAAAGTG 60.401 42.308 8.59 4.69 41.40 3.16
711 799 1.262417 TATCACGCCAGACCAAGACA 58.738 50.000 0.00 0.00 0.00 3.41
730 818 6.152932 AGACAACGTCAGGTTAGTTTTCTA 57.847 37.500 0.00 0.00 36.49 2.10
768 858 5.865552 CCATACGTAAAGAGACTTCCGAAAA 59.134 40.000 0.00 0.00 0.00 2.29
774 864 7.148623 ACGTAAAGAGACTTCCGAAAATTGATC 60.149 37.037 0.00 0.00 0.00 2.92
775 865 6.502136 AAAGAGACTTCCGAAAATTGATCC 57.498 37.500 0.00 0.00 0.00 3.36
816 906 1.153745 CGCACTCTACACCTGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
830 920 9.574516 CTACACCTGCTCCCTTAATTAAATTAT 57.425 33.333 0.00 0.00 0.00 1.28
859 949 3.056821 CCATTTCTATCTGGCCATGCATG 60.057 47.826 20.19 20.19 0.00 4.06
860 950 1.612676 TTCTATCTGGCCATGCATGC 58.387 50.000 21.69 11.82 0.00 4.06
861 951 0.475044 TCTATCTGGCCATGCATGCA 59.525 50.000 25.04 25.04 0.00 3.96
871 961 3.507786 GCCATGCATGCATACACATATG 58.492 45.455 31.73 18.47 41.16 1.78
912 1002 8.406297 GTTTCACAAAATCACCTACTCTTTCTT 58.594 33.333 0.00 0.00 0.00 2.52
965 1056 1.544686 CCAACAACACAACGAAGCAC 58.455 50.000 0.00 0.00 0.00 4.40
975 1067 0.100503 AACGAAGCACCAAACACAGC 59.899 50.000 0.00 0.00 0.00 4.40
977 1069 1.225855 CGAAGCACCAAACACAGCTA 58.774 50.000 0.00 0.00 36.07 3.32
991 1083 4.925068 ACACAGCTACTTTCAGCAAAAAG 58.075 39.130 8.75 8.75 44.35 2.27
1018 1110 3.137176 TCAAATGGCCTCCTCTTCCTATG 59.863 47.826 3.32 0.00 0.00 2.23
1032 1124 3.019799 TCCTATGTCCTTCTCTTCGCT 57.980 47.619 0.00 0.00 0.00 4.93
1123 1215 2.086869 ACAACAGCTCACATGGTATGC 58.913 47.619 0.00 0.00 0.00 3.14
1199 1304 7.504922 TTTAGCATCGCATTTAATCACAAAC 57.495 32.000 0.00 0.00 0.00 2.93
1207 1312 8.839947 TCGCATTTAATCACAAACTATTGATG 57.160 30.769 0.00 0.00 38.94 3.07
1220 1325 1.742761 ATTGATGGACTCAACTGGCG 58.257 50.000 0.00 0.00 46.37 5.69
1223 1328 1.067142 TGATGGACTCAACTGGCGTAC 60.067 52.381 0.00 0.00 0.00 3.67
1233 1338 6.100004 ACTCAACTGGCGTACATATATATGC 58.900 40.000 20.46 8.18 37.19 3.14
1245 1350 9.062674 CGTACATATATATGCACTCTGTTACAC 57.937 37.037 20.46 0.00 37.19 2.90
1249 1354 9.481340 CATATATATGCACTCTGTTACACAGTT 57.519 33.333 9.75 0.00 46.03 3.16
1272 1670 4.933400 TCCAGTTCTAGTTAACGGATTTGC 59.067 41.667 0.00 0.00 34.46 3.68
1273 1671 4.693566 CCAGTTCTAGTTAACGGATTTGCA 59.306 41.667 0.00 0.00 34.46 4.08
1309 1707 0.106149 ACGTGAAGGCCGAAGACTTT 59.894 50.000 0.00 0.00 0.00 2.66
1833 2241 6.149973 CAGAACTAATGAAGTCTTGCATGGAA 59.850 38.462 0.00 0.00 37.50 3.53
1863 2271 5.470845 AAAAATAGAATCGTCTTGGCTCG 57.529 39.130 0.00 0.00 35.12 5.03
1867 2275 3.085443 AGAATCGTCTTGGCTCGTATG 57.915 47.619 0.00 0.00 0.00 2.39
1917 2325 8.507524 ACTAGCTTGTAAAACATTTATCCTCC 57.492 34.615 0.00 0.00 0.00 4.30
1924 2332 5.859205 AAAACATTTATCCTCCATGGCTC 57.141 39.130 6.96 0.00 35.26 4.70
2035 2443 4.345257 ACCCATAATCAACGATAGCTCAGT 59.655 41.667 0.00 0.00 42.67 3.41
2057 2465 0.103026 TGGTGAGTAGCTAGCATGCG 59.897 55.000 18.83 0.00 38.13 4.73
2082 2490 8.814235 CGGAGCTTAAACTATAGAAAAATCGAA 58.186 33.333 6.78 0.00 0.00 3.71
2207 3067 7.861629 AGTAGTCTAGAGGGAGATGATATGAG 58.138 42.308 0.00 0.00 0.00 2.90
2370 3230 1.407618 GGAACAACCACCACAACCTTC 59.592 52.381 0.00 0.00 38.79 3.46
2401 3261 1.611491 TGACGGTTCATTTTCAAGGCC 59.389 47.619 0.00 0.00 0.00 5.19
2413 3273 5.730296 TTTTCAAGGCCCGAAATCAATAA 57.270 34.783 16.44 1.00 32.66 1.40
2424 3284 5.067153 CCCGAAATCAATAAGGTGCATTACA 59.933 40.000 0.00 0.00 0.00 2.41
2440 3300 4.202151 GCATTACATTCCAGGATTGTTCCC 60.202 45.833 19.81 5.65 43.76 3.97
2446 3306 0.405585 CCAGGATTGTTCCCACCAGT 59.594 55.000 0.00 0.00 43.76 4.00
2451 3311 2.296190 GGATTGTTCCCACCAGTCAAAC 59.704 50.000 0.00 0.00 35.84 2.93
2453 3313 2.818751 TGTTCCCACCAGTCAAACTT 57.181 45.000 0.00 0.00 0.00 2.66
2455 3315 4.237976 TGTTCCCACCAGTCAAACTTAA 57.762 40.909 0.00 0.00 0.00 1.85
2457 3317 3.217681 TCCCACCAGTCAAACTTAACC 57.782 47.619 0.00 0.00 0.00 2.85
2467 3327 6.996282 CCAGTCAAACTTAACCTCCTTTTCTA 59.004 38.462 0.00 0.00 0.00 2.10
2471 3331 7.713942 GTCAAACTTAACCTCCTTTTCTAGTGA 59.286 37.037 0.00 0.00 0.00 3.41
2478 3338 6.056090 ACCTCCTTTTCTAGTGATTCTTCC 57.944 41.667 0.00 0.00 0.00 3.46
2482 3342 4.878397 CCTTTTCTAGTGATTCTTCCGCAT 59.122 41.667 0.00 0.00 0.00 4.73
2494 3354 6.978659 TGATTCTTCCGCATACTACTTGTAAG 59.021 38.462 0.00 0.00 34.45 2.34
2497 3357 6.097356 TCTTCCGCATACTACTTGTAAGTTG 58.903 40.000 2.20 3.77 40.37 3.16
2498 3358 5.395682 TCCGCATACTACTTGTAAGTTGT 57.604 39.130 14.37 14.37 44.80 3.32
2501 3361 6.808212 TCCGCATACTACTTGTAAGTTGTAAC 59.192 38.462 18.10 13.69 45.42 2.50
2514 3374 8.145316 TGTAAGTTGTAACACAATTACCTCAC 57.855 34.615 14.58 0.93 40.59 3.51
2515 3375 7.769507 TGTAAGTTGTAACACAATTACCTCACA 59.230 33.333 14.58 2.75 40.59 3.58
2522 3382 6.478512 AACACAATTACCTCACATGGTTTT 57.521 33.333 0.00 0.00 41.22 2.43
2533 3393 3.010027 TCACATGGTTTTCCTATGGCTCA 59.990 43.478 0.00 0.00 41.38 4.26
2539 3399 5.027460 TGGTTTTCCTATGGCTCACTAGTA 58.973 41.667 0.00 0.00 41.38 1.82
2552 3412 5.988561 GGCTCACTAGTAAATCATTCTCAGG 59.011 44.000 0.00 0.00 0.00 3.86
2554 3414 6.699642 GCTCACTAGTAAATCATTCTCAGGAC 59.300 42.308 0.00 0.00 0.00 3.85
2566 3426 9.685276 AATCATTCTCAGGACATTTTATGTGTA 57.315 29.630 0.00 0.00 45.03 2.90
2568 3428 8.321353 TCATTCTCAGGACATTTTATGTGTAGT 58.679 33.333 0.00 0.00 45.03 2.73
2575 3435 7.491372 CAGGACATTTTATGTGTAGTATGTCGT 59.509 37.037 0.00 0.00 45.03 4.34
2576 3436 7.491372 AGGACATTTTATGTGTAGTATGTCGTG 59.509 37.037 0.00 0.00 45.03 4.35
2612 3472 4.114794 GGCATGGATGTGTTAATGCTTTC 58.885 43.478 6.46 0.00 43.87 2.62
2619 3479 3.626977 TGTGTTAATGCTTTCGTTGCTG 58.373 40.909 0.00 0.00 0.00 4.41
2621 3481 1.985684 GTTAATGCTTTCGTTGCTGCC 59.014 47.619 0.00 0.00 0.00 4.85
2625 3490 2.892334 GCTTTCGTTGCTGCCGTGA 61.892 57.895 0.00 0.00 0.00 4.35
2634 3499 1.658409 GCTGCCGTGAAAGTGTTGC 60.658 57.895 0.00 0.00 0.00 4.17
2636 3501 2.051345 GCCGTGAAAGTGTTGCCG 60.051 61.111 0.00 0.00 0.00 5.69
2655 3520 2.416547 CCGTGGCAGTAATTTCTCACTG 59.583 50.000 2.29 2.29 44.07 3.66
2684 3551 2.158667 CGGCCATGGTAGGGAAATTACT 60.159 50.000 14.67 0.00 0.00 2.24
2753 4218 9.988815 TGGCAACATTGTTGTTAAACTAAATAT 57.011 25.926 25.88 0.00 44.24 1.28
2765 4230 9.548631 TGTTAAACTAAATATGGGGAAAATCCA 57.451 29.630 0.00 0.00 38.64 3.41
2769 4234 9.951866 AAACTAAATATGGGGAAAATCCATAGT 57.048 29.630 8.51 3.64 46.60 2.12
2770 4235 9.588096 AACTAAATATGGGGAAAATCCATAGTC 57.412 33.333 8.51 0.00 46.60 2.59
2773 4238 1.133915 TGGGGAAAATCCATAGTCGCC 60.134 52.381 0.00 0.00 38.64 5.54
2777 4242 2.872858 GGAAAATCCATAGTCGCCACTC 59.127 50.000 0.00 0.00 36.28 3.51
2791 4256 2.791503 CGCCACTCGAGTACTACACATG 60.792 54.545 19.57 2.10 41.67 3.21
2805 4270 5.057149 ACTACACATGTGAAGACCTTTGAC 58.943 41.667 31.94 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.659652 TTTGTAACCACTTTTTCCTTGTTTG 57.340 32.000 0.00 0.00 0.00 2.93
61 62 7.774625 TGCATATTTGAGTTCTTGGATATGTCA 59.225 33.333 0.00 0.00 32.68 3.58
189 190 6.643388 TCTCTTCACTGCTATTCTTGCATTA 58.357 36.000 0.00 0.00 39.86 1.90
224 225 2.222227 AATGGCCTCTTTGTCTTCCC 57.778 50.000 3.32 0.00 0.00 3.97
234 235 3.199946 TCCGATAGAACAAAATGGCCTCT 59.800 43.478 3.32 0.00 39.76 3.69
246 247 4.043037 ACGTCCATTTCTCCGATAGAAC 57.957 45.455 0.27 0.00 44.02 3.01
251 252 2.233922 AGACAACGTCCATTTCTCCGAT 59.766 45.455 0.00 0.00 32.18 4.18
265 266 3.304794 GCTAGCTAGACCCATAGACAACG 60.305 52.174 25.15 0.00 0.00 4.10
274 275 2.028112 CACACAAAGCTAGCTAGACCCA 60.028 50.000 25.15 0.00 0.00 4.51
276 277 3.320673 ACACACAAAGCTAGCTAGACC 57.679 47.619 25.15 7.60 0.00 3.85
326 346 7.674120 TGCAGCCAAGCTATATATATCCATAG 58.326 38.462 0.00 0.00 36.40 2.23
365 398 3.754323 TGTACGCCTTGGATTTTAGTTGG 59.246 43.478 0.00 0.00 0.00 3.77
369 402 4.814234 TGCTATGTACGCCTTGGATTTTAG 59.186 41.667 0.00 0.00 0.00 1.85
393 431 4.399004 AGAGACCATGTCAATCTAGTGC 57.601 45.455 0.00 0.00 34.60 4.40
556 623 5.767665 CCTTGAGAGCTAGCTAGTTGATCTA 59.232 44.000 19.38 11.57 0.00 1.98
557 624 4.584325 CCTTGAGAGCTAGCTAGTTGATCT 59.416 45.833 19.38 17.94 0.00 2.75
558 625 4.340950 ACCTTGAGAGCTAGCTAGTTGATC 59.659 45.833 19.38 15.39 0.00 2.92
560 627 3.702792 ACCTTGAGAGCTAGCTAGTTGA 58.297 45.455 19.38 2.18 0.00 3.18
561 628 4.464069 AACCTTGAGAGCTAGCTAGTTG 57.536 45.455 19.38 7.05 0.00 3.16
562 629 4.096682 CGTAACCTTGAGAGCTAGCTAGTT 59.903 45.833 19.38 16.41 0.00 2.24
563 630 3.628487 CGTAACCTTGAGAGCTAGCTAGT 59.372 47.826 19.38 8.16 0.00 2.57
564 631 3.549221 GCGTAACCTTGAGAGCTAGCTAG 60.549 52.174 19.38 16.84 0.00 3.42
566 633 1.135333 GCGTAACCTTGAGAGCTAGCT 59.865 52.381 19.45 19.45 0.00 3.32
567 634 1.562017 GCGTAACCTTGAGAGCTAGC 58.438 55.000 6.62 6.62 0.00 3.42
699 776 1.502231 CTGACGTTGTCTTGGTCTGG 58.498 55.000 0.00 0.00 33.15 3.86
711 799 5.608449 AGCTTAGAAAACTAACCTGACGTT 58.392 37.500 0.00 0.00 38.57 3.99
730 818 7.554118 TCTTTACGTATGGTGTACTACTAGCTT 59.446 37.037 0.00 0.00 0.00 3.74
768 858 3.323774 ACATGGCCTGAATGGATCAAT 57.676 42.857 3.32 0.00 37.67 2.57
774 864 2.389962 CCAAAACATGGCCTGAATGG 57.610 50.000 3.32 7.59 43.80 3.16
798 888 1.153745 GGAGCAGGTGTAGAGTGCG 60.154 63.158 0.00 0.00 42.26 5.34
830 920 6.012337 TGGCCAGATAGAAATGGTCATTAA 57.988 37.500 0.00 0.00 45.99 1.40
860 950 6.801377 AGTCAACAAAAACGCATATGTGTATG 59.199 34.615 21.64 20.54 40.56 2.39
861 951 6.801377 CAGTCAACAAAAACGCATATGTGTAT 59.199 34.615 21.64 11.44 37.87 2.29
871 961 3.670991 TGTGAAACAGTCAACAAAAACGC 59.329 39.130 0.00 0.00 45.67 4.84
965 1056 2.618241 TGCTGAAAGTAGCTGTGTTTGG 59.382 45.455 0.00 0.00 44.01 3.28
975 1067 8.687824 TTTGAGTTTCTTTTTGCTGAAAGTAG 57.312 30.769 10.69 0.00 36.38 2.57
977 1069 7.064966 CCATTTGAGTTTCTTTTTGCTGAAAGT 59.935 33.333 10.69 0.00 38.20 2.66
991 1083 3.078891 AGAGGAGGCCATTTGAGTTTC 57.921 47.619 5.01 0.00 0.00 2.78
1018 1110 3.249917 CAAGAAGAGCGAAGAGAAGGAC 58.750 50.000 0.00 0.00 0.00 3.85
1032 1124 0.036732 ATGAGGCCAACGCAAGAAGA 59.963 50.000 5.01 0.00 43.62 2.87
1123 1215 2.222027 GTTCACCCAGTGTTGAGAAGG 58.778 52.381 0.00 0.00 34.79 3.46
1171 1276 9.964303 TTGTGATTAAATGCGATGCTAAATATT 57.036 25.926 0.00 0.00 0.00 1.28
1183 1288 7.914871 TCCATCAATAGTTTGTGATTAAATGCG 59.085 33.333 0.00 0.00 32.06 4.73
1188 1293 9.513906 TTGAGTCCATCAATAGTTTGTGATTAA 57.486 29.630 0.00 0.00 43.09 1.40
1207 1312 2.953466 TATGTACGCCAGTTGAGTCC 57.047 50.000 0.00 0.00 0.00 3.85
1220 1325 9.908152 TGTGTAACAGAGTGCATATATATGTAC 57.092 33.333 27.25 27.25 45.67 2.90
1245 1350 5.130292 TCCGTTAACTAGAACTGGAACTG 57.870 43.478 3.71 0.00 32.68 3.16
1247 1352 6.620089 GCAAATCCGTTAACTAGAACTGGAAC 60.620 42.308 3.71 0.00 36.39 3.62
1249 1354 4.933400 GCAAATCCGTTAACTAGAACTGGA 59.067 41.667 3.71 3.85 36.85 3.86
1272 1670 3.188460 CACGTCCTTTGGGTCTTTACATG 59.812 47.826 0.00 0.00 0.00 3.21
1273 1671 3.071892 TCACGTCCTTTGGGTCTTTACAT 59.928 43.478 0.00 0.00 0.00 2.29
1309 1707 1.791103 CGAGTTTGGCCGCCAAGAAA 61.791 55.000 23.64 7.92 44.84 2.52
1833 2241 9.389570 CCAAGACGATTCTATTTTTAACGTTTT 57.610 29.630 5.91 0.00 32.88 2.43
1917 2325 5.739752 TTCAATCGAGTATTTGAGCCATG 57.260 39.130 0.00 0.00 0.00 3.66
1924 2332 9.277565 CCAACAGTTTATTCAATCGAGTATTTG 57.722 33.333 0.00 0.00 0.00 2.32
2006 2414 9.431887 GAGCTATCGTTGATTATGGGTAATAAA 57.568 33.333 0.00 0.00 34.41 1.40
2011 2419 5.538813 ACTGAGCTATCGTTGATTATGGGTA 59.461 40.000 0.00 0.00 0.00 3.69
2035 2443 2.677902 GCATGCTAGCTACTCACCACAA 60.678 50.000 17.23 0.00 0.00 3.33
2082 2490 7.220740 TCAAGAGAGATCGACATGTACTATCT 58.779 38.462 13.93 13.93 31.87 1.98
2370 3230 6.727824 AAATGAACCGTCAGAGATTTACTG 57.272 37.500 0.00 0.00 37.14 2.74
2401 3261 6.130298 TGTAATGCACCTTATTGATTTCGG 57.870 37.500 0.00 0.00 0.00 4.30
2413 3273 3.956199 CAATCCTGGAATGTAATGCACCT 59.044 43.478 0.00 0.00 0.00 4.00
2424 3284 1.715931 TGGTGGGAACAATCCTGGAAT 59.284 47.619 0.00 0.00 45.77 3.01
2440 3300 4.086706 AGGAGGTTAAGTTTGACTGGTG 57.913 45.455 0.00 0.00 0.00 4.17
2446 3306 7.798071 TCACTAGAAAAGGAGGTTAAGTTTGA 58.202 34.615 0.00 0.00 0.00 2.69
2451 3311 9.157104 GAAGAATCACTAGAAAAGGAGGTTAAG 57.843 37.037 0.00 0.00 0.00 1.85
2453 3313 7.578955 CGGAAGAATCACTAGAAAAGGAGGTTA 60.579 40.741 0.00 0.00 0.00 2.85
2455 3315 5.337652 CGGAAGAATCACTAGAAAAGGAGGT 60.338 44.000 0.00 0.00 0.00 3.85
2457 3317 4.568760 GCGGAAGAATCACTAGAAAAGGAG 59.431 45.833 0.00 0.00 0.00 3.69
2467 3327 5.105310 ACAAGTAGTATGCGGAAGAATCACT 60.105 40.000 0.00 0.00 0.00 3.41
2471 3331 6.875076 ACTTACAAGTAGTATGCGGAAGAAT 58.125 36.000 0.00 0.00 37.52 2.40
2478 3338 7.115236 TGTGTTACAACTTACAAGTAGTATGCG 59.885 37.037 0.00 0.00 38.57 4.73
2494 3354 6.016610 ACCATGTGAGGTAATTGTGTTACAAC 60.017 38.462 0.00 0.00 39.62 3.32
2497 3357 6.569179 AACCATGTGAGGTAATTGTGTTAC 57.431 37.500 0.00 0.00 42.25 2.50
2498 3358 7.255660 GGAAAACCATGTGAGGTAATTGTGTTA 60.256 37.037 0.00 0.00 42.25 2.41
2501 3361 5.243730 AGGAAAACCATGTGAGGTAATTGTG 59.756 40.000 0.00 0.00 42.25 3.33
2509 3369 2.689983 GCCATAGGAAAACCATGTGAGG 59.310 50.000 0.00 0.00 0.00 3.86
2514 3374 3.624777 AGTGAGCCATAGGAAAACCATG 58.375 45.455 0.00 0.00 0.00 3.66
2515 3375 4.475016 ACTAGTGAGCCATAGGAAAACCAT 59.525 41.667 0.00 0.00 0.00 3.55
2522 3382 7.510685 AGAATGATTTACTAGTGAGCCATAGGA 59.489 37.037 5.39 0.00 0.00 2.94
2533 3393 9.965902 AAAATGTCCTGAGAATGATTTACTAGT 57.034 29.630 0.00 0.00 0.00 2.57
2539 3399 9.028284 ACACATAAAATGTCCTGAGAATGATTT 57.972 29.630 0.00 0.00 42.70 2.17
2552 3412 7.490079 TCCACGACATACTACACATAAAATGTC 59.510 37.037 0.00 0.00 42.70 3.06
2554 3414 7.764695 TCCACGACATACTACACATAAAATG 57.235 36.000 0.00 0.00 0.00 2.32
2566 3426 2.457598 ACCTCACATCCACGACATACT 58.542 47.619 0.00 0.00 0.00 2.12
2568 3428 2.565391 ACAACCTCACATCCACGACATA 59.435 45.455 0.00 0.00 0.00 2.29
2575 3435 0.405198 ATGCCACAACCTCACATCCA 59.595 50.000 0.00 0.00 0.00 3.41
2576 3436 0.813184 CATGCCACAACCTCACATCC 59.187 55.000 0.00 0.00 0.00 3.51
2612 3472 1.369209 CACTTTCACGGCAGCAACG 60.369 57.895 0.00 0.00 37.36 4.10
2619 3479 2.051345 CGGCAACACTTTCACGGC 60.051 61.111 0.00 0.00 0.00 5.68
2621 3481 1.010125 CCACGGCAACACTTTCACG 60.010 57.895 0.00 0.00 0.00 4.35
2634 3499 2.416547 CAGTGAGAAATTACTGCCACGG 59.583 50.000 0.00 0.00 38.01 4.94
2636 3501 3.674997 TCCAGTGAGAAATTACTGCCAC 58.325 45.455 0.00 0.00 42.21 5.01
2643 3508 4.023536 GCCGTGTTTTCCAGTGAGAAATTA 60.024 41.667 7.37 0.00 35.74 1.40
2655 3520 0.808755 CTACCATGGCCGTGTTTTCC 59.191 55.000 23.39 0.00 0.00 3.13
2712 3579 9.243105 ACAATGTTGCCACTTCTATAAAATAGT 57.757 29.630 0.00 0.00 0.00 2.12
2715 3582 8.367156 ACAACAATGTTGCCACTTCTATAAAAT 58.633 29.630 24.32 0.00 35.91 1.82
2716 3583 7.721402 ACAACAATGTTGCCACTTCTATAAAA 58.279 30.769 24.32 0.00 35.91 1.52
2746 4211 7.148239 GCGACTATGGATTTTCCCCATATTTAG 60.148 40.741 0.00 0.00 43.47 1.85
2750 4215 4.567747 GGCGACTATGGATTTTCCCCATAT 60.568 45.833 0.00 0.00 43.47 1.78
2751 4216 3.244770 GGCGACTATGGATTTTCCCCATA 60.245 47.826 0.00 0.00 43.63 2.74
2752 4217 2.489073 GGCGACTATGGATTTTCCCCAT 60.489 50.000 0.00 0.00 45.64 4.00
2753 4218 1.133915 GGCGACTATGGATTTTCCCCA 60.134 52.381 0.00 0.00 35.03 4.96
2761 4226 0.955178 CTCGAGTGGCGACTATGGAT 59.045 55.000 3.62 0.00 45.59 3.41
2765 4230 2.328819 AGTACTCGAGTGGCGACTAT 57.671 50.000 28.12 0.29 45.59 2.12
2770 4235 0.800631 TGTGTAGTACTCGAGTGGCG 59.199 55.000 28.12 0.00 42.69 5.69
2773 4238 4.680171 TCACATGTGTAGTACTCGAGTG 57.320 45.455 28.12 10.19 0.00 3.51
2777 4242 4.156190 AGGTCTTCACATGTGTAGTACTCG 59.844 45.833 25.91 6.59 31.14 4.18
2783 4248 4.452455 GGTCAAAGGTCTTCACATGTGTAG 59.548 45.833 24.63 23.53 0.00 2.74
2791 4256 4.561105 CTCTACTGGTCAAAGGTCTTCAC 58.439 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.