Multiple sequence alignment - TraesCS1B01G193800

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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 TraesCS1B01G193800 chr1B 100.000 4014 0 0 1 4014 348860799 348864812 0.000000e+00 7413
1 TraesCS1B01G193800 chr1D 94.430 2675 87 25 672 3315 263071619 263074262 0.000000e+00 4058
2 TraesCS1B01G193800 chr1D 88.467 711 73 5 3310 4014 439753530 439754237 0.000000e+00 850
3 TraesCS1B01G193800 chr1D 86.452 465 29 14 136 572 263071078 263071536 2.810000e-131 479
4 TraesCS1B01G193800 chr1A 91.316 2925 134 49 460 3315 337149648 337152521 0.000000e+00 3884
5 TraesCS1B01G193800 chr1A 91.503 459 27 5 1 453 337149015 337149467 4.410000e-174 621
6 TraesCS1B01G193800 chr7D 90.395 708 64 4 3309 4014 596927514 596928219 0.000000e+00 928
7 TraesCS1B01G193800 chr7D 90.254 708 65 4 3309 4014 596944349 596945054 0.000000e+00 922
8 TraesCS1B01G193800 chr7D 87.712 708 82 3 3310 4014 549094030 549094735 0.000000e+00 821
9 TraesCS1B01G193800 chr6A 88.017 726 65 10 3310 4014 435338385 435339109 0.000000e+00 839
10 TraesCS1B01G193800 chr7A 87.870 709 80 4 3309 4014 731246557 731245852 0.000000e+00 828
11 TraesCS1B01G193800 chr4D 87.465 710 78 6 3310 4014 484940931 484941634 0.000000e+00 808
12 TraesCS1B01G193800 chr4D 83.884 242 24 10 1514 1743 482158438 482158676 2.430000e-52 217
13 TraesCS1B01G193800 chr4D 89.431 123 13 0 1834 1956 482158823 482158945 5.370000e-34 156
14 TraesCS1B01G193800 chr4D 90.110 91 9 0 2095 2185 482159062 482159152 7.050000e-23 119
15 TraesCS1B01G193800 chr2D 87.377 713 79 7 3310 4014 639517585 639516876 0.000000e+00 808
16 TraesCS1B01G193800 chr6D 87.518 705 79 5 3310 4011 456792687 456793385 0.000000e+00 806
17 TraesCS1B01G193800 chr7B 75.397 630 119 26 3310 3907 637841767 637841142 5.110000e-69 272
18 TraesCS1B01G193800 chr4B 83.058 242 26 9 1514 1743 611853334 611853572 5.260000e-49 206
19 TraesCS1B01G193800 chr4B 89.431 123 13 0 1834 1956 611853724 611853846 5.370000e-34 156
20 TraesCS1B01G193800 chr4B 89.011 91 10 0 2095 2185 611853947 611854037 3.280000e-21 113
21 TraesCS1B01G193800 chr5A 82.857 245 24 10 1514 1743 660443055 660442814 1.890000e-48 204
22 TraesCS1B01G193800 chr5A 89.431 123 13 0 1834 1956 660442663 660442541 5.370000e-34 156
23 TraesCS1B01G193800 chr5A 90.217 92 9 0 2095 2186 660442427 660442336 1.960000e-23 121


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 TraesCS1B01G193800 chr1B 348860799 348864812 4013 False 7413.0 7413 100.0000 1 4014 1 chr1B.!!$F1 4013
1 TraesCS1B01G193800 chr1D 263071078 263074262 3184 False 2268.5 4058 90.4410 136 3315 2 chr1D.!!$F2 3179
2 TraesCS1B01G193800 chr1D 439753530 439754237 707 False 850.0 850 88.4670 3310 4014 1 chr1D.!!$F1 704
3 TraesCS1B01G193800 chr1A 337149015 337152521 3506 False 2252.5 3884 91.4095 1 3315 2 chr1A.!!$F1 3314
4 TraesCS1B01G193800 chr7D 596927514 596928219 705 False 928.0 928 90.3950 3309 4014 1 chr7D.!!$F2 705
5 TraesCS1B01G193800 chr7D 596944349 596945054 705 False 922.0 922 90.2540 3309 4014 1 chr7D.!!$F3 705
6 TraesCS1B01G193800 chr7D 549094030 549094735 705 False 821.0 821 87.7120 3310 4014 1 chr7D.!!$F1 704
7 TraesCS1B01G193800 chr6A 435338385 435339109 724 False 839.0 839 88.0170 3310 4014 1 chr6A.!!$F1 704
8 TraesCS1B01G193800 chr7A 731245852 731246557 705 True 828.0 828 87.8700 3309 4014 1 chr7A.!!$R1 705
9 TraesCS1B01G193800 chr4D 484940931 484941634 703 False 808.0 808 87.4650 3310 4014 1 chr4D.!!$F1 704
10 TraesCS1B01G193800 chr2D 639516876 639517585 709 True 808.0 808 87.3770 3310 4014 1 chr2D.!!$R1 704
11 TraesCS1B01G193800 chr6D 456792687 456793385 698 False 806.0 806 87.5180 3310 4011 1 chr6D.!!$F1 701
12 TraesCS1B01G193800 chr7B 637841142 637841767 625 True 272.0 272 75.3970 3310 3907 1 chr7B.!!$R1 597

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
931 1180 0.034186 GCATCATTCCACCACCTCCA 60.034 55.0 0.0 0.0 0.00 3.86 F
963 1217 0.041576 CACACGACACGAGACGAGAA 60.042 55.0 11.7 0.0 36.75 2.87 F
2280 2565 0.302589 GTTTGTGTTGTCGGTCGGTC 59.697 55.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2357 1.229428 CGCTGCAACAAAGAGGAAGA 58.771 50.000 0.0 0.0 0.00 2.87 R
2289 2574 2.430582 CAAATGCAACCACGCCGG 60.431 61.111 0.0 0.0 42.50 6.13 R
3531 3896 0.467659 AGACGGTAGCTCGGCCTATT 60.468 55.000 0.0 0.0 39.34 1.73 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
29 30 6.258230 TCATGAACTCACAATGATGGAAAC 57.742 37.500 0.00 0.00 0.00 2.78
33 34 3.831323 ACTCACAATGATGGAAACCACA 58.169 40.909 0.00 0.00 35.80 4.17
38 39 4.022155 CACAATGATGGAAACCACATGTGA 60.022 41.667 27.46 6.25 35.80 3.58
53 54 8.579850 ACCACATGTGACACTTATCATTTAAT 57.420 30.769 27.46 0.00 0.00 1.40
93 94 8.906636 TTAGTGTTCTTTGTACTATCACGATC 57.093 34.615 0.00 0.00 0.00 3.69
288 305 4.042398 GGTTTTTCCAAAGTCGCTTTCTC 58.958 43.478 2.45 0.00 30.60 2.87
296 313 3.371063 TCGCTTTCTCGGAGGCGT 61.371 61.111 20.89 0.00 46.37 5.68
320 337 1.737793 GCGAATTCTTCCACACCGATT 59.262 47.619 3.52 0.00 0.00 3.34
346 363 2.817423 CTGCTTGATTCGCGGCCTC 61.817 63.158 6.13 0.98 0.00 4.70
351 368 0.036388 TTGATTCGCGGCCTCTTTCT 60.036 50.000 6.13 0.00 0.00 2.52
419 436 0.690762 TGTACTGTTCCCTCCCAAGC 59.309 55.000 0.00 0.00 0.00 4.01
421 438 0.178873 TACTGTTCCCTCCCAAGCCT 60.179 55.000 0.00 0.00 0.00 4.58
453 470 1.228124 CACGGGGAGCTTCAAACCA 60.228 57.895 0.00 0.00 0.00 3.67
472 663 2.353011 CCAGGTTGATGGTTGTTGATGC 60.353 50.000 0.00 0.00 35.47 3.91
476 667 3.680937 GGTTGATGGTTGTTGATGCAATG 59.319 43.478 0.00 0.00 0.00 2.82
479 670 5.211174 TGATGGTTGTTGATGCAATGAAA 57.789 34.783 0.00 0.00 0.00 2.69
500 691 2.934107 CAACGCGTGCAAGTAAGTAA 57.066 45.000 14.98 0.00 0.00 2.24
501 692 3.241783 CAACGCGTGCAAGTAAGTAAA 57.758 42.857 14.98 0.00 0.00 2.01
502 693 3.805823 CAACGCGTGCAAGTAAGTAAAT 58.194 40.909 14.98 0.00 0.00 1.40
507 701 3.610585 GCGTGCAAGTAAGTAAATTGGCA 60.611 43.478 0.59 0.00 0.00 4.92
538 742 3.431725 GTACCGCTGCCCAACTGC 61.432 66.667 0.00 0.00 39.69 4.40
547 751 0.609957 TGCCCAACTGCATTCCTCAG 60.610 55.000 0.00 0.00 36.04 3.35
565 774 3.130633 TCAGAACAACCACGATCAACAG 58.869 45.455 0.00 0.00 0.00 3.16
592 832 4.351192 CACAGTGGCAAAAACTTCAGTAC 58.649 43.478 0.00 0.00 0.00 2.73
594 834 3.632145 CAGTGGCAAAAACTTCAGTACCT 59.368 43.478 0.00 0.00 0.00 3.08
598 838 3.883489 GGCAAAAACTTCAGTACCTGACT 59.117 43.478 0.00 0.00 40.46 3.41
601 841 5.758784 GCAAAAACTTCAGTACCTGACTACT 59.241 40.000 0.00 0.00 40.46 2.57
603 843 5.373981 AAACTTCAGTACCTGACTACTCG 57.626 43.478 0.00 0.00 40.46 4.18
605 845 2.783609 TCAGTACCTGACTACTCGCT 57.216 50.000 0.00 0.00 35.39 4.93
629 869 2.536365 ACATGCGTATGTGAACCGTAG 58.464 47.619 18.78 0.00 45.54 3.51
630 870 2.094390 ACATGCGTATGTGAACCGTAGT 60.094 45.455 18.78 0.00 45.54 2.73
631 871 3.129113 ACATGCGTATGTGAACCGTAGTA 59.871 43.478 18.78 0.00 45.54 1.82
632 872 3.135414 TGCGTATGTGAACCGTAGTAC 57.865 47.619 0.00 0.00 0.00 2.73
633 873 2.749076 TGCGTATGTGAACCGTAGTACT 59.251 45.455 0.00 0.00 0.00 2.73
634 874 3.938334 TGCGTATGTGAACCGTAGTACTA 59.062 43.478 0.00 0.00 0.00 1.82
635 875 4.201812 TGCGTATGTGAACCGTAGTACTAC 60.202 45.833 21.06 21.06 0.00 2.73
636 876 4.201812 GCGTATGTGAACCGTAGTACTACA 60.202 45.833 28.03 13.31 35.87 2.74
637 877 5.496387 CGTATGTGAACCGTAGTACTACAG 58.504 45.833 28.03 21.17 35.87 2.74
638 878 5.063944 CGTATGTGAACCGTAGTACTACAGT 59.936 44.000 28.03 21.79 35.87 3.55
639 879 5.557891 ATGTGAACCGTAGTACTACAGTC 57.442 43.478 28.03 21.23 35.87 3.51
640 880 4.645535 TGTGAACCGTAGTACTACAGTCT 58.354 43.478 28.03 15.54 35.87 3.24
641 881 5.793817 TGTGAACCGTAGTACTACAGTCTA 58.206 41.667 28.03 14.88 35.87 2.59
644 884 5.871524 TGAACCGTAGTACTACAGTCTACAG 59.128 44.000 28.03 12.14 35.87 2.74
649 889 6.421501 CCGTAGTACTACAGTCTACAGATGAG 59.578 46.154 28.03 9.94 35.87 2.90
682 922 5.075493 ACACTCTTTGAGCATTCTTCCAAT 58.925 37.500 0.00 0.00 32.04 3.16
689 929 2.428530 GAGCATTCTTCCAATCCAACCC 59.571 50.000 0.00 0.00 0.00 4.11
852 1098 2.739913 GGCCACGCAGCGATTATAATAA 59.260 45.455 24.65 0.00 0.00 1.40
931 1180 0.034186 GCATCATTCCACCACCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
939 1188 1.146930 CACCACCTCCATCCCATCG 59.853 63.158 0.00 0.00 0.00 3.84
943 1192 0.394216 CACCTCCATCCCATCGCAAA 60.394 55.000 0.00 0.00 0.00 3.68
952 1201 1.502990 CCCATCGCAAACACACGACA 61.503 55.000 0.00 0.00 41.76 4.35
953 1202 0.384230 CCATCGCAAACACACGACAC 60.384 55.000 0.00 0.00 41.76 3.67
954 1203 0.717896 CATCGCAAACACACGACACG 60.718 55.000 0.00 0.00 41.76 4.49
955 1204 0.872451 ATCGCAAACACACGACACGA 60.872 50.000 0.00 0.00 41.76 4.35
956 1205 1.084290 CGCAAACACACGACACGAG 60.084 57.895 0.00 0.00 0.00 4.18
963 1217 0.041576 CACACGACACGAGACGAGAA 60.042 55.000 11.70 0.00 36.75 2.87
997 1251 4.355720 CTGCCAAGCCAGCCAGGA 62.356 66.667 0.00 0.00 41.22 3.86
999 1253 2.363406 GCCAAGCCAGCCAGGAAT 60.363 61.111 0.00 0.00 41.22 3.01
1760 2029 2.808761 TAGGCCCCCGTCACAGCTAA 62.809 60.000 0.00 0.00 0.00 3.09
1761 2030 2.590092 GCCCCCGTCACAGCTAAT 59.410 61.111 0.00 0.00 0.00 1.73
1831 2103 3.729965 CTCCGATTGCGCCTGCTCT 62.730 63.158 4.18 0.00 43.34 4.09
2075 2352 5.904362 ATGGCGCTAAAATCTTCTTCTTT 57.096 34.783 7.64 0.00 0.00 2.52
2076 2353 8.500753 TTATGGCGCTAAAATCTTCTTCTTTA 57.499 30.769 7.64 0.00 0.00 1.85
2077 2354 7.573968 ATGGCGCTAAAATCTTCTTCTTTAT 57.426 32.000 7.64 0.00 0.00 1.40
2078 2355 7.016361 TGGCGCTAAAATCTTCTTCTTTATC 57.984 36.000 7.64 0.00 0.00 1.75
2079 2356 6.823689 TGGCGCTAAAATCTTCTTCTTTATCT 59.176 34.615 7.64 0.00 0.00 1.98
2080 2357 7.336931 TGGCGCTAAAATCTTCTTCTTTATCTT 59.663 33.333 7.64 0.00 0.00 2.40
2168 2451 4.437587 GGCCATGGAGCAGCAGGT 62.438 66.667 18.40 0.00 0.00 4.00
2269 2554 4.561735 AACCATCGATTTCGTTTGTGTT 57.438 36.364 0.00 4.22 40.80 3.32
2278 2563 1.146957 TCGTTTGTGTTGTCGGTCGG 61.147 55.000 0.00 0.00 0.00 4.79
2279 2564 1.422950 CGTTTGTGTTGTCGGTCGGT 61.423 55.000 0.00 0.00 0.00 4.69
2280 2565 0.302589 GTTTGTGTTGTCGGTCGGTC 59.697 55.000 0.00 0.00 0.00 4.79
2281 2566 1.146957 TTTGTGTTGTCGGTCGGTCG 61.147 55.000 0.00 0.00 0.00 4.79
2282 2567 2.026590 GTGTTGTCGGTCGGTCGT 59.973 61.111 0.00 0.00 0.00 4.34
2283 2568 1.282570 GTGTTGTCGGTCGGTCGTA 59.717 57.895 0.00 0.00 0.00 3.43
2285 2570 1.165907 TGTTGTCGGTCGGTCGTAGT 61.166 55.000 0.00 0.00 0.00 2.73
2289 2574 2.503375 CGGTCGGTCGTAGTGCAC 60.503 66.667 9.40 9.40 0.00 4.57
2661 2953 4.532521 AGTCCTAAGATAACACAAGTGGCT 59.467 41.667 5.08 0.00 34.19 4.75
2690 2982 6.023435 CACCTTACATGTTTCATCATTCACG 58.977 40.000 2.30 0.00 0.00 4.35
2701 2993 7.600752 TGTTTCATCATTCACGTCACATTACTA 59.399 33.333 0.00 0.00 0.00 1.82
2702 2994 8.604035 GTTTCATCATTCACGTCACATTACTAT 58.396 33.333 0.00 0.00 0.00 2.12
2705 2997 7.978975 TCATCATTCACGTCACATTACTATTGA 59.021 33.333 0.00 0.00 0.00 2.57
2824 3130 0.946221 CTTTGAACGAGGCGCTCACT 60.946 55.000 7.64 0.00 31.69 3.41
2968 3274 2.532256 GCAGCAGCAGCAGATACCG 61.532 63.158 4.63 0.00 45.49 4.02
3056 3362 7.699878 ACCCAATCAAGTTCTAGTCCTTTTAT 58.300 34.615 0.00 0.00 0.00 1.40
3120 3426 3.875134 TGCACGTTGATCTCGTCTATAGA 59.125 43.478 12.08 0.00 39.55 1.98
3194 3500 3.790089 ATGTTCTTTTCGTCCCTTCCT 57.210 42.857 0.00 0.00 0.00 3.36
3195 3501 2.846193 TGTTCTTTTCGTCCCTTCCTG 58.154 47.619 0.00 0.00 0.00 3.86
3367 3693 1.878088 AGAATGATGCATGCGGTCATC 59.122 47.619 28.03 22.17 39.49 2.92
3447 3788 8.208855 CTCTCAAAGAGCGAAAAACATAAAAG 57.791 34.615 0.00 0.00 35.30 2.27
3475 3833 1.135228 GCCACAACCGGCGAAATAAAT 60.135 47.619 9.30 0.00 43.52 1.40
3476 3834 2.097791 GCCACAACCGGCGAAATAAATA 59.902 45.455 9.30 0.00 43.52 1.40
3528 3893 2.167662 GATCACCATCCAAACCGGTTT 58.832 47.619 26.87 26.87 35.57 3.27
3531 3896 3.563223 TCACCATCCAAACCGGTTTAAA 58.437 40.909 31.17 21.74 35.57 1.52
3536 3901 5.186215 ACCATCCAAACCGGTTTAAAATAGG 59.814 40.000 31.17 25.13 35.57 2.57
3552 3917 1.381928 TAGGCCGAGCTACCGTCTTG 61.382 60.000 0.00 0.00 0.00 3.02
3582 3947 3.786553 AGACCCAGTAACCATACACTCA 58.213 45.455 0.00 0.00 34.29 3.41
3621 3986 2.029623 AGTAGCGACCACATACGGATT 58.970 47.619 0.00 0.00 0.00 3.01
3639 4004 1.737838 TTAATGCAGTGGCTCGGAAG 58.262 50.000 0.00 0.00 41.91 3.46
3642 4007 0.463295 ATGCAGTGGCTCGGAAGATG 60.463 55.000 0.00 0.00 41.91 2.90
3661 4026 6.939132 AGATGACCTGCAAGAAATGAATAG 57.061 37.500 0.00 0.00 34.07 1.73
3741 4106 2.163815 ACATACTCCTACGCGGATATGC 59.836 50.000 12.47 0.00 42.12 3.14
3746 4111 0.039437 CCTACGCGGATATGCTTCGT 60.039 55.000 12.47 13.74 37.19 3.85
3754 4119 3.554324 GCGGATATGCTTCGTTGTTTCTA 59.446 43.478 0.00 0.00 0.00 2.10
3781 4146 1.043116 TCCATCTAGCCACGTCCCAG 61.043 60.000 0.00 0.00 0.00 4.45
3880 4245 4.301628 GCAATCAAGAAAGAGGTGTTTGG 58.698 43.478 0.00 0.00 0.00 3.28
3895 4260 5.882557 AGGTGTTTGGTAGATTCATCATGAC 59.117 40.000 0.00 0.00 0.00 3.06
3913 4278 3.930336 TGACCACAGAAGCTACATCTTG 58.070 45.455 0.00 0.00 0.00 3.02
3914 4279 3.578282 TGACCACAGAAGCTACATCTTGA 59.422 43.478 0.00 0.00 0.00 3.02
3927 4292 4.213564 ACATCTTGAAGATCCTGTCCAC 57.786 45.455 4.39 0.00 31.32 4.02
3939 4304 1.944024 CCTGTCCACTTACGTTTTGCA 59.056 47.619 0.00 0.00 0.00 4.08
3972 4338 6.483307 CCTTAGTGAGAATGACTTGTTTGTGA 59.517 38.462 0.00 0.00 32.18 3.58
3989 4359 4.998671 TGTGAACAAACCACATGAACAT 57.001 36.364 0.00 0.00 39.36 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.859427 AAATTAAATGATAAGTGTCACATGTGG 57.141 29.630 25.16 7.43 0.00 4.17
131 132 5.133941 CCAGATGTACTGCTTACTCTCCTA 58.866 45.833 0.00 0.00 44.52 2.94
132 133 3.957497 CCAGATGTACTGCTTACTCTCCT 59.043 47.826 0.00 0.00 44.52 3.69
133 134 3.491792 GCCAGATGTACTGCTTACTCTCC 60.492 52.174 0.00 0.00 44.52 3.71
134 135 3.491792 GGCCAGATGTACTGCTTACTCTC 60.492 52.174 0.00 0.00 44.52 3.20
141 144 1.050988 ATCCGGCCAGATGTACTGCT 61.051 55.000 2.24 0.00 44.52 4.24
346 363 0.531200 ACGGGTCGGAAGCTAGAAAG 59.469 55.000 0.00 0.00 0.00 2.62
351 368 2.992689 TGCACGGGTCGGAAGCTA 60.993 61.111 0.00 0.00 0.00 3.32
392 409 3.315418 GAGGGAACAGTACAGTTCGTTC 58.685 50.000 20.73 16.87 46.81 3.95
393 410 2.036862 GGAGGGAACAGTACAGTTCGTT 59.963 50.000 20.73 13.25 46.81 3.85
394 411 1.617357 GGAGGGAACAGTACAGTTCGT 59.383 52.381 20.73 12.87 46.81 3.85
395 412 1.067071 GGGAGGGAACAGTACAGTTCG 60.067 57.143 20.73 0.00 46.81 3.95
421 438 2.735478 CGTGTTACGCTTGCCGGA 60.735 61.111 5.05 0.00 42.52 5.14
453 470 2.596346 TGCATCAACAACCATCAACCT 58.404 42.857 0.00 0.00 0.00 3.50
497 688 4.437390 CGGATGAGTCACTTGCCAATTTAC 60.437 45.833 0.00 0.00 0.00 2.01
499 690 2.489329 CGGATGAGTCACTTGCCAATTT 59.511 45.455 0.00 0.00 0.00 1.82
500 691 2.086869 CGGATGAGTCACTTGCCAATT 58.913 47.619 0.00 0.00 0.00 2.32
501 692 1.679944 CCGGATGAGTCACTTGCCAAT 60.680 52.381 0.00 0.00 0.00 3.16
502 693 0.321564 CCGGATGAGTCACTTGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
507 701 0.815734 CGGTACCGGATGAGTCACTT 59.184 55.000 27.00 0.00 35.56 3.16
538 742 2.766313 TCGTGGTTGTTCTGAGGAATG 58.234 47.619 0.00 0.00 33.71 2.67
547 751 1.601903 TGCTGTTGATCGTGGTTGTTC 59.398 47.619 0.00 0.00 0.00 3.18
565 774 0.809636 GTTTTTGCCACTGTGGGTGC 60.810 55.000 27.02 13.95 44.08 5.01
592 832 1.454201 TGTCAGAGCGAGTAGTCAGG 58.546 55.000 0.00 0.00 0.00 3.86
594 834 1.133216 GCATGTCAGAGCGAGTAGTCA 59.867 52.381 0.00 0.00 0.00 3.41
603 843 1.926561 TCACATACGCATGTCAGAGC 58.073 50.000 0.00 0.00 43.73 4.09
605 845 2.616960 GGTTCACATACGCATGTCAGA 58.383 47.619 0.00 0.00 43.73 3.27
629 869 8.199449 ACTCTACTCATCTGTAGACTGTAGTAC 58.801 40.741 12.89 0.00 42.54 2.73
630 870 8.308851 ACTCTACTCATCTGTAGACTGTAGTA 57.691 38.462 12.89 0.00 42.54 1.82
631 871 7.190335 ACTCTACTCATCTGTAGACTGTAGT 57.810 40.000 12.89 0.00 42.54 2.73
632 872 8.418662 AGTACTCTACTCATCTGTAGACTGTAG 58.581 40.741 0.00 9.54 42.54 2.74
633 873 8.308851 AGTACTCTACTCATCTGTAGACTGTA 57.691 38.462 0.00 0.00 42.54 2.74
634 874 7.190335 AGTACTCTACTCATCTGTAGACTGT 57.810 40.000 0.00 0.00 42.54 3.55
635 875 8.198778 TGTAGTACTCTACTCATCTGTAGACTG 58.801 40.741 0.00 0.00 44.74 3.51
636 876 8.199449 GTGTAGTACTCTACTCATCTGTAGACT 58.801 40.741 0.00 0.00 44.74 3.24
637 877 8.199449 AGTGTAGTACTCTACTCATCTGTAGAC 58.801 40.741 0.00 0.00 44.74 2.59
638 878 8.308851 AGTGTAGTACTCTACTCATCTGTAGA 57.691 38.462 0.00 4.62 44.74 2.59
658 898 5.227569 TGGAAGAATGCTCAAAGAGTGTA 57.772 39.130 0.00 0.00 31.39 2.90
659 899 4.090761 TGGAAGAATGCTCAAAGAGTGT 57.909 40.909 0.00 0.00 31.39 3.55
660 900 5.392811 GGATTGGAAGAATGCTCAAAGAGTG 60.393 44.000 0.00 0.00 31.39 3.51
661 901 4.704057 GGATTGGAAGAATGCTCAAAGAGT 59.296 41.667 0.00 0.00 31.39 3.24
662 902 4.703575 TGGATTGGAAGAATGCTCAAAGAG 59.296 41.667 0.00 0.00 0.00 2.85
663 903 4.665451 TGGATTGGAAGAATGCTCAAAGA 58.335 39.130 0.00 0.00 0.00 2.52
667 907 3.091545 GGTTGGATTGGAAGAATGCTCA 58.908 45.455 0.00 0.00 0.00 4.26
765 1011 1.822114 TTCCGTCGTGGGATTCTGCA 61.822 55.000 0.00 0.00 38.76 4.41
931 1180 0.321210 TCGTGTGTTTGCGATGGGAT 60.321 50.000 0.00 0.00 31.76 3.85
939 1188 0.043310 GTCTCGTGTCGTGTGTTTGC 60.043 55.000 0.00 0.00 0.00 3.68
943 1192 1.156034 TCTCGTCTCGTGTCGTGTGT 61.156 55.000 4.24 0.00 0.00 3.72
992 1246 0.819259 CGTGGTGCCCATATTCCTGG 60.819 60.000 0.00 0.00 35.28 4.45
994 1248 0.916086 TTCGTGGTGCCCATATTCCT 59.084 50.000 0.00 0.00 35.28 3.36
997 1251 0.250793 TCGTTCGTGGTGCCCATATT 59.749 50.000 0.00 0.00 35.28 1.28
999 1253 1.216977 CTCGTTCGTGGTGCCCATA 59.783 57.895 0.00 0.00 35.28 2.74
1946 2218 3.300934 ATGAGTCAGCTGCGCGGAA 62.301 57.895 23.20 0.53 34.22 4.30
1952 2224 1.480137 ACCTGTAGATGAGTCAGCTGC 59.520 52.381 21.00 19.56 33.40 5.25
1964 2236 2.225420 TGGTGGTGGATGTACCTGTAGA 60.225 50.000 0.00 0.00 41.43 2.59
2075 2352 4.697352 GCTGCAACAAAGAGGAAGAAGATA 59.303 41.667 0.00 0.00 0.00 1.98
2076 2353 3.505293 GCTGCAACAAAGAGGAAGAAGAT 59.495 43.478 0.00 0.00 0.00 2.40
2077 2354 2.880890 GCTGCAACAAAGAGGAAGAAGA 59.119 45.455 0.00 0.00 0.00 2.87
2078 2355 2.350197 CGCTGCAACAAAGAGGAAGAAG 60.350 50.000 0.00 0.00 0.00 2.85
2079 2356 1.603802 CGCTGCAACAAAGAGGAAGAA 59.396 47.619 0.00 0.00 0.00 2.52
2080 2357 1.229428 CGCTGCAACAAAGAGGAAGA 58.771 50.000 0.00 0.00 0.00 2.87
2269 2554 2.969806 GCACTACGACCGACCGACA 61.970 63.158 3.56 0.00 0.00 4.35
2278 2563 4.712425 ACGCCGGTGCACTACGAC 62.712 66.667 25.52 11.60 37.32 4.34
2279 2564 4.710695 CACGCCGGTGCACTACGA 62.711 66.667 25.52 0.00 37.35 3.43
2289 2574 2.430582 CAAATGCAACCACGCCGG 60.431 61.111 0.00 0.00 42.50 6.13
2494 2783 2.780595 CAAGAAATGGATCCGGCGT 58.219 52.632 7.39 0.00 0.00 5.68
2555 2847 6.094881 CGGAGCCTTCTTGGATTTATTAACAA 59.905 38.462 0.00 0.00 38.35 2.83
2661 2953 7.943079 ATGATGAAACATGTAAGGTGATTGA 57.057 32.000 0.00 0.00 0.00 2.57
2690 2982 5.764686 TCCATGGCATCAATAGTAATGTGAC 59.235 40.000 6.96 0.00 0.00 3.67
2701 2993 5.715279 CAGATTAAGGATCCATGGCATCAAT 59.285 40.000 15.82 13.20 35.21 2.57
2702 2994 5.074804 CAGATTAAGGATCCATGGCATCAA 58.925 41.667 15.82 10.23 35.21 2.57
2705 2997 4.736611 ACAGATTAAGGATCCATGGCAT 57.263 40.909 15.82 1.16 35.21 4.40
2752 3044 8.037758 CAGGATACCAAAATATAGCACTCCTAG 58.962 40.741 0.00 0.00 37.17 3.02
2968 3274 3.450028 CTGCTCCAGCTGGTAGAAC 57.550 57.895 31.58 17.35 42.66 3.01
3120 3426 1.603455 CCCGGACAGGCACAAACAT 60.603 57.895 0.73 0.00 39.21 2.71
3141 3447 1.816074 TACACTGCCGGAACATTTCC 58.184 50.000 5.05 0.00 46.62 3.13
3142 3448 5.751243 ATAATACACTGCCGGAACATTTC 57.249 39.130 5.05 0.00 0.00 2.17
3146 3452 5.968528 AAAAATAATACACTGCCGGAACA 57.031 34.783 5.05 0.00 0.00 3.18
3194 3500 1.031235 CCAGCCACAATGTGTGTTCA 58.969 50.000 12.79 0.00 46.45 3.18
3195 3501 1.317613 TCCAGCCACAATGTGTGTTC 58.682 50.000 12.79 0.00 46.45 3.18
3317 3626 3.451540 AGACCGGGAGATAACCTCTTTTC 59.548 47.826 6.32 0.00 41.66 2.29
3321 3630 1.854280 AGAGACCGGGAGATAACCTCT 59.146 52.381 6.32 0.00 41.66 3.69
3389 3719 3.804786 TTGAGACTTGGACACGTTGTA 57.195 42.857 0.00 0.00 0.00 2.41
3394 3724 1.264288 GCCTTTTGAGACTTGGACACG 59.736 52.381 0.00 0.00 0.00 4.49
3434 3775 6.531594 GTGGCTATCCTGCTTTTATGTTTTTC 59.468 38.462 0.00 0.00 0.00 2.29
3447 3788 1.819632 CCGGTTGTGGCTATCCTGC 60.820 63.158 0.00 0.00 0.00 4.85
3510 3875 2.953284 TAAACCGGTTTGGATGGTGA 57.047 45.000 36.94 15.96 42.00 4.02
3528 3893 2.034124 ACGGTAGCTCGGCCTATTTTA 58.966 47.619 0.00 0.00 0.00 1.52
3531 3896 0.467659 AGACGGTAGCTCGGCCTATT 60.468 55.000 0.00 0.00 39.34 1.73
3536 3901 2.886124 GCAAGACGGTAGCTCGGC 60.886 66.667 0.00 0.00 38.69 5.54
3552 3917 2.547826 GTTACTGGGTCTATCCGTTGC 58.452 52.381 0.00 0.00 37.00 4.17
3582 3947 2.680352 ACTCCGACGGATGCCAGT 60.680 61.111 18.71 8.57 0.00 4.00
3621 3986 0.901827 TCTTCCGAGCCACTGCATTA 59.098 50.000 0.00 0.00 41.13 1.90
3639 4004 5.591877 ACCTATTCATTTCTTGCAGGTCATC 59.408 40.000 0.00 0.00 30.41 2.92
3642 4007 4.702131 ACACCTATTCATTTCTTGCAGGTC 59.298 41.667 0.00 0.00 32.57 3.85
3680 4045 3.745799 TGGAACTGCAGGAACGATTTAA 58.254 40.909 19.93 0.00 0.00 1.52
3681 4046 3.410631 TGGAACTGCAGGAACGATTTA 57.589 42.857 19.93 0.00 0.00 1.40
3741 4106 6.954944 TGGAATTGAGTTAGAAACAACGAAG 58.045 36.000 0.00 0.00 33.50 3.79
3746 4111 7.336931 GGCTAGATGGAATTGAGTTAGAAACAA 59.663 37.037 0.00 0.00 0.00 2.83
3754 4119 3.055094 ACGTGGCTAGATGGAATTGAGTT 60.055 43.478 0.00 0.00 0.00 3.01
3781 4146 4.334203 TCCAAATACCATGCACACGTTATC 59.666 41.667 0.00 0.00 0.00 1.75
3880 4245 5.236047 GCTTCTGTGGTCATGATGAATCTAC 59.764 44.000 0.00 0.00 0.00 2.59
3895 4260 4.825422 TCTTCAAGATGTAGCTTCTGTGG 58.175 43.478 0.00 0.00 0.00 4.17
3939 4304 8.571336 CAAGTCATTCTCACTAAGGACAATTTT 58.429 33.333 4.49 0.00 41.42 1.82


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

AutoCloner maintained by Alex Coulton.