Multiple sequence alignment - TraesCS4B01G139200

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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 TraesCS4B01G139200 chr4B 100.000 3500 0 0 1 3500 183602445 183605944 0.000000 6464.0
1 TraesCS4B01G139200 chr4D 94.713 3499 112 27 1 3460 120864564 120868028 0.000000 5369.0
2 TraesCS4B01G139200 chr4A 94.646 2596 94 18 767 3337 452342938 452345513 0.000000 3982.0
3 TraesCS4B01G139200 chr4A 92.265 724 17 10 1 708 452342211 452342911 0.000000 990.0
4 TraesCS4B01G139200 chr2A 97.059 34 1 0 204 237 1522317 1522284 0.000136 58.4
5 TraesCS4B01G139200 chr7B 100.000 30 0 0 924 953 605109393 605109422 0.000488 56.5
6 TraesCS4B01G139200 chrUn 100.000 29 0 0 923 951 399089388 399089360 0.002000 54.7
7 TraesCS4B01G139200 chrUn 100.000 29 0 0 923 951 399115687 399115659 0.002000 54.7
8 TraesCS4B01G139200 chrUn 100.000 29 0 0 923 951 399117234 399117206 0.002000 54.7
9 TraesCS4B01G139200 chr7A 100.000 29 0 0 924 952 501088406 501088434 0.002000 54.7
10 TraesCS4B01G139200 chr5B 100.000 29 0 0 923 951 597234935 597234963 0.002000 54.7
11 TraesCS4B01G139200 chr6A 100.000 28 0 0 204 231 24418529 24418556 0.006000 52.8
12 TraesCS4B01G139200 chr5D 100.000 28 0 0 204 231 443876557 443876584 0.006000 52.8


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 TraesCS4B01G139200 chr4B 183602445 183605944 3499 False 6464 6464 100.0000 1 3500 1 chr4B.!!$F1 3499
1 TraesCS4B01G139200 chr4D 120864564 120868028 3464 False 5369 5369 94.7130 1 3460 1 chr4D.!!$F1 3459
2 TraesCS4B01G139200 chr4A 452342211 452345513 3302 False 2486 3982 93.4555 1 3337 2 chr4A.!!$F1 3336

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
44 45 0.176449 CGAGTCCAGACCATGCATCA 59.824 55.0 0.0 0.0 0.0 3.07 F
732 756 0.244994 AGCAGCACCACTCTAGAACG 59.755 55.0 0.0 0.0 0.0 3.95 F
747 771 0.307760 GAACGCAACACCAACAGGAG 59.692 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1547 0.608640 AGAAGGGTGTCCACATCGAC 59.391 55.000 0.0 0.0 34.83 4.20 R
2367 2401 0.396435 AAGGGATCGCGCCATTATCA 59.604 50.000 0.0 0.0 28.71 2.15 R
2624 2662 2.172505 ACCATCACCACTTCACTTGACA 59.827 45.455 0.0 0.0 0.00 3.58 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
21 22 2.348411 ACTAATTGAAGGCCCCATCG 57.652 50.000 0.00 0.00 0.00 3.84
44 45 0.176449 CGAGTCCAGACCATGCATCA 59.824 55.000 0.00 0.00 0.00 3.07
137 138 5.941647 GGTAGGTAGTACAATCCAAAGCAAA 59.058 40.000 2.06 0.00 32.62 3.68
138 139 6.093633 GGTAGGTAGTACAATCCAAAGCAAAG 59.906 42.308 2.06 0.00 32.62 2.77
139 140 4.459337 AGGTAGTACAATCCAAAGCAAAGC 59.541 41.667 2.06 0.00 0.00 3.51
140 141 4.217550 GGTAGTACAATCCAAAGCAAAGCA 59.782 41.667 2.06 0.00 0.00 3.91
141 142 4.243007 AGTACAATCCAAAGCAAAGCAC 57.757 40.909 0.00 0.00 0.00 4.40
142 143 3.636300 AGTACAATCCAAAGCAAAGCACA 59.364 39.130 0.00 0.00 0.00 4.57
413 426 3.194542 GGCATGCATGTTTTGTTACCCTA 59.805 43.478 26.79 0.00 0.00 3.53
441 454 3.392882 GGATTTGTTTGTCTGGCCAAAG 58.607 45.455 7.01 0.00 35.13 2.77
589 606 2.464157 AGCAAAAGAGAAGAGGGACG 57.536 50.000 0.00 0.00 0.00 4.79
732 756 0.244994 AGCAGCACCACTCTAGAACG 59.755 55.000 0.00 0.00 0.00 3.95
747 771 0.307760 GAACGCAACACCAACAGGAG 59.692 55.000 0.00 0.00 0.00 3.69
748 772 1.101049 AACGCAACACCAACAGGAGG 61.101 55.000 0.00 0.00 0.00 4.30
836 860 3.407424 TGTCTTTCTCCCACATCACAG 57.593 47.619 0.00 0.00 0.00 3.66
838 862 1.081892 CTTTCTCCCACATCACAGCG 58.918 55.000 0.00 0.00 0.00 5.18
914 948 4.631813 AGTAGGAATTCAGTTCGTCAATGC 59.368 41.667 7.93 0.00 37.73 3.56
940 974 3.698820 CCTTGCCCTTGCCCTTGC 61.699 66.667 0.00 0.00 36.33 4.01
941 975 3.698820 CTTGCCCTTGCCCTTGCC 61.699 66.667 0.00 0.00 36.33 4.52
945 979 2.999063 CCCTTGCCCTTGCCCTTG 60.999 66.667 0.00 0.00 36.33 3.61
946 980 3.698820 CCTTGCCCTTGCCCTTGC 61.699 66.667 0.00 0.00 36.33 4.01
947 981 3.698820 CTTGCCCTTGCCCTTGCC 61.699 66.667 0.00 0.00 36.33 4.52
951 985 2.999063 CCCTTGCCCTTGCCCTTG 60.999 66.667 0.00 0.00 36.33 3.61
1233 1267 1.374947 CGCCCTCTTCCACCAAGAA 59.625 57.895 0.00 0.00 40.83 2.52
1251 1285 2.039951 CCAACCTACCTCCCGGGA 59.960 66.667 25.06 25.06 38.76 5.14
1311 1345 3.359033 CATGAAAGACCACATCCACCAT 58.641 45.455 0.00 0.00 0.00 3.55
1330 1364 1.944177 TGAGTCCTCCTCCAAGAAGG 58.056 55.000 0.00 0.00 39.65 3.46
1385 1419 3.439540 GGAATGGCGCCGCAAGAA 61.440 61.111 23.90 2.33 43.02 2.52
1536 1570 1.208293 GATGTGGACACCCTTCTCTCC 59.792 57.143 0.00 0.00 0.00 3.71
1632 1666 2.124983 CCGATGCTGTCCCTGGTG 60.125 66.667 0.00 0.00 0.00 4.17
1701 1735 2.680352 GAGGACACTGAGCCCGGA 60.680 66.667 0.73 0.00 0.00 5.14
1887 1921 2.275380 GGCCATTGGTGCCGAGTTT 61.275 57.895 4.26 0.00 39.48 2.66
2061 2095 4.430441 AGTCTAAGAAGTGGATCAAGGGT 58.570 43.478 0.00 0.00 0.00 4.34
2115 2149 1.074405 AGCACCAAGGAATCTGAAGCA 59.926 47.619 0.00 0.00 0.00 3.91
2120 2154 2.165167 CAAGGAATCTGAAGCAGCCAA 58.835 47.619 0.00 0.00 0.00 4.52
2181 2215 1.681780 CGCACAAGGGGATACAATGGT 60.682 52.381 0.00 0.00 39.74 3.55
2235 2269 0.882484 GGAGCTCCTTCGGCAATAGC 60.882 60.000 26.25 0.00 41.10 2.97
2238 2272 1.441729 CTCCTTCGGCAATAGCGGA 59.558 57.895 0.00 0.00 46.68 5.54
2367 2401 2.109387 TACACGCCTTGCACGGTT 59.891 55.556 11.38 0.00 34.00 4.44
2395 2429 1.608025 GCGCGATCCCTTATCCAATCA 60.608 52.381 12.10 0.00 0.00 2.57
2406 2440 0.549950 ATCCAATCAGAGGTGCCCAG 59.450 55.000 0.00 0.00 0.00 4.45
2484 2518 3.002791 CAATTCTTTGCCTCGTAGCTCA 58.997 45.455 0.00 0.00 0.00 4.26
2487 2521 1.618837 TCTTTGCCTCGTAGCTCACTT 59.381 47.619 0.00 0.00 0.00 3.16
2490 2524 0.898326 TGCCTCGTAGCTCACTTGGA 60.898 55.000 0.00 0.00 0.00 3.53
2534 2568 8.325787 TGATTAAGGCAGGTTTATGTTCTTCTA 58.674 33.333 0.00 0.00 0.00 2.10
2537 2571 6.067217 AGGCAGGTTTATGTTCTTCTACAT 57.933 37.500 0.00 0.00 41.43 2.29
2539 2573 6.069963 AGGCAGGTTTATGTTCTTCTACATCT 60.070 38.462 0.00 0.00 39.39 2.90
2624 2662 3.586618 AGGCTCAGATCAGAAGAAAGGTT 59.413 43.478 0.00 0.00 0.00 3.50
2777 2815 7.928908 TTGTCAATTGAATTCAAGTTAGCAC 57.071 32.000 24.17 15.28 39.47 4.40
2804 2842 7.173735 TCTGGCAATAGCAATAACATGATGTAG 59.826 37.037 0.00 0.00 44.61 2.74
2836 2874 3.469008 TCGAATGCCGATAATCTGGTT 57.531 42.857 0.00 0.00 43.23 3.67
2837 2875 4.594123 TCGAATGCCGATAATCTGGTTA 57.406 40.909 0.00 0.00 43.23 2.85
2844 2882 4.189231 GCCGATAATCTGGTTAGTGTTGT 58.811 43.478 0.00 0.00 0.00 3.32
2846 2884 5.462398 GCCGATAATCTGGTTAGTGTTGTAG 59.538 44.000 0.00 0.00 0.00 2.74
2868 2906 6.336842 AGGATGTTTTGGATCTTGTTTGAG 57.663 37.500 0.00 0.00 0.00 3.02
2877 2915 5.624159 TGGATCTTGTTTGAGATTGACAGT 58.376 37.500 0.00 0.00 36.54 3.55
2912 2950 3.343617 GGTCCTTGTTACAGCATAGCAA 58.656 45.455 0.00 0.00 0.00 3.91
2934 2972 2.205022 TGCCATGTTTTCCTCCTCTG 57.795 50.000 0.00 0.00 0.00 3.35
2941 2979 2.155279 GTTTTCCTCCTCTGTTGCTCC 58.845 52.381 0.00 0.00 0.00 4.70
2963 3003 0.818040 GTGGTGTGCCGTTTCTTCCT 60.818 55.000 0.00 0.00 37.67 3.36
2999 3039 4.502105 TCTATGGGTATCTTTTGCTGCA 57.498 40.909 0.00 0.00 0.00 4.41
3018 3060 3.056179 TGCACACTTGATCTAATCCGTCA 60.056 43.478 0.00 0.00 0.00 4.35
3019 3061 3.307242 GCACACTTGATCTAATCCGTCAC 59.693 47.826 0.00 0.00 0.00 3.67
3020 3062 4.494484 CACACTTGATCTAATCCGTCACA 58.506 43.478 0.00 0.00 0.00 3.58
3021 3063 5.111989 CACACTTGATCTAATCCGTCACAT 58.888 41.667 0.00 0.00 0.00 3.21
3027 3069 5.977635 TGATCTAATCCGTCACATTTCACT 58.022 37.500 0.00 0.00 0.00 3.41
3065 3108 5.659463 AGCTGTGCTTATGTTTTTGAAACA 58.341 33.333 8.49 8.49 33.89 2.83
3133 3176 5.378230 TCTGCTGGGTAAATCAGATCATT 57.622 39.130 0.00 0.00 34.36 2.57
3172 3215 1.473258 CCCCATCGCATTTCCTTTCA 58.527 50.000 0.00 0.00 0.00 2.69
3174 3217 2.223876 CCCCATCGCATTTCCTTTCATG 60.224 50.000 0.00 0.00 0.00 3.07
3176 3219 3.119029 CCCATCGCATTTCCTTTCATGTT 60.119 43.478 0.00 0.00 0.00 2.71
3178 3221 4.563976 CCATCGCATTTCCTTTCATGTTTC 59.436 41.667 0.00 0.00 0.00 2.78
3179 3222 4.844998 TCGCATTTCCTTTCATGTTTCA 57.155 36.364 0.00 0.00 0.00 2.69
3316 3366 6.128117 GCACCAAACCGAATCTAAGTTGAATA 60.128 38.462 0.00 0.00 0.00 1.75
3347 3397 2.489329 CCTTATTCCACAAGCACTGGTG 59.511 50.000 0.00 0.00 34.82 4.17
3364 3414 7.858052 CACTGGTGCTAAGTTAAATGAAAAG 57.142 36.000 0.00 0.00 0.00 2.27
3400 3450 4.079253 GTCTATTTGCAGTTGGAGGGAAA 58.921 43.478 0.00 0.00 0.00 3.13
3407 3457 3.585289 TGCAGTTGGAGGGAAAGTGTATA 59.415 43.478 0.00 0.00 31.77 1.47
3413 3463 6.884836 AGTTGGAGGGAAAGTGTATATGTTTC 59.115 38.462 0.00 0.00 0.00 2.78
3420 3470 8.458843 AGGGAAAGTGTATATGTTTCAAATTCG 58.541 33.333 0.00 0.00 32.77 3.34
3460 3510 6.899393 ACAAGATCAATTAACCAGAAGCAA 57.101 33.333 0.00 0.00 0.00 3.91
3461 3511 7.288810 ACAAGATCAATTAACCAGAAGCAAA 57.711 32.000 0.00 0.00 0.00 3.68
3462 3512 7.725251 ACAAGATCAATTAACCAGAAGCAAAA 58.275 30.769 0.00 0.00 0.00 2.44
3463 3513 7.653311 ACAAGATCAATTAACCAGAAGCAAAAC 59.347 33.333 0.00 0.00 0.00 2.43
3464 3514 7.288810 AGATCAATTAACCAGAAGCAAAACA 57.711 32.000 0.00 0.00 0.00 2.83
3465 3515 7.147976 AGATCAATTAACCAGAAGCAAAACAC 58.852 34.615 0.00 0.00 0.00 3.32
3466 3516 6.214191 TCAATTAACCAGAAGCAAAACACA 57.786 33.333 0.00 0.00 0.00 3.72
3467 3517 6.039616 TCAATTAACCAGAAGCAAAACACAC 58.960 36.000 0.00 0.00 0.00 3.82
3468 3518 5.590530 ATTAACCAGAAGCAAAACACACA 57.409 34.783 0.00 0.00 0.00 3.72
3469 3519 5.590530 TTAACCAGAAGCAAAACACACAT 57.409 34.783 0.00 0.00 0.00 3.21
3470 3520 4.470334 AACCAGAAGCAAAACACACATT 57.530 36.364 0.00 0.00 0.00 2.71
3471 3521 4.470334 ACCAGAAGCAAAACACACATTT 57.530 36.364 0.00 0.00 0.00 2.32
3472 3522 4.183101 ACCAGAAGCAAAACACACATTTG 58.817 39.130 0.00 0.00 40.04 2.32
3473 3523 4.183101 CCAGAAGCAAAACACACATTTGT 58.817 39.130 0.00 0.00 39.42 2.83
3474 3524 5.105554 ACCAGAAGCAAAACACACATTTGTA 60.106 36.000 0.00 0.00 39.42 2.41
3475 3525 5.984926 CCAGAAGCAAAACACACATTTGTAT 59.015 36.000 0.00 0.00 39.42 2.29
3476 3526 6.074195 CCAGAAGCAAAACACACATTTGTATG 60.074 38.462 0.00 0.00 39.42 2.39
3477 3527 5.463061 AGAAGCAAAACACACATTTGTATGC 59.537 36.000 6.05 6.05 40.32 3.14
3478 3528 4.691175 AGCAAAACACACATTTGTATGCA 58.309 34.783 13.28 0.00 41.50 3.96
3479 3529 5.114780 AGCAAAACACACATTTGTATGCAA 58.885 33.333 13.28 0.00 41.50 4.08
3480 3530 5.006552 AGCAAAACACACATTTGTATGCAAC 59.993 36.000 13.28 0.00 41.50 4.17
3481 3531 5.736338 CAAAACACACATTTGTATGCAACC 58.264 37.500 0.00 0.00 35.03 3.77
3482 3532 4.662468 AACACACATTTGTATGCAACCA 57.338 36.364 0.00 0.00 35.03 3.67
3483 3533 4.241590 ACACACATTTGTATGCAACCAG 57.758 40.909 0.00 0.00 35.03 4.00
3484 3534 3.888323 ACACACATTTGTATGCAACCAGA 59.112 39.130 0.00 0.00 35.03 3.86
3485 3535 4.340666 ACACACATTTGTATGCAACCAGAA 59.659 37.500 0.00 0.00 35.03 3.02
3486 3536 4.919168 CACACATTTGTATGCAACCAGAAG 59.081 41.667 0.00 0.00 35.03 2.85
3487 3537 3.922240 CACATTTGTATGCAACCAGAAGC 59.078 43.478 0.00 0.00 35.03 3.86
3488 3538 3.573538 ACATTTGTATGCAACCAGAAGCA 59.426 39.130 0.00 0.00 45.92 3.91
3489 3539 3.921119 TTTGTATGCAACCAGAAGCAG 57.079 42.857 0.00 0.00 44.94 4.24
3490 3540 1.167851 TGTATGCAACCAGAAGCAGC 58.832 50.000 0.00 0.00 44.94 5.25
3491 3541 0.453390 GTATGCAACCAGAAGCAGCC 59.547 55.000 0.00 0.00 44.94 4.85
3492 3542 0.329261 TATGCAACCAGAAGCAGCCT 59.671 50.000 0.00 0.00 44.94 4.58
3493 3543 0.541296 ATGCAACCAGAAGCAGCCTT 60.541 50.000 0.00 0.00 44.94 4.35
3494 3544 0.756442 TGCAACCAGAAGCAGCCTTT 60.756 50.000 0.00 0.00 35.51 3.11
3495 3545 1.247567 GCAACCAGAAGCAGCCTTTA 58.752 50.000 0.00 0.00 0.00 1.85
3496 3546 1.613437 GCAACCAGAAGCAGCCTTTAA 59.387 47.619 0.00 0.00 0.00 1.52
3497 3547 2.608016 GCAACCAGAAGCAGCCTTTAAC 60.608 50.000 0.00 0.00 0.00 2.01
3498 3548 2.887152 CAACCAGAAGCAGCCTTTAACT 59.113 45.455 0.00 0.00 0.00 2.24
3499 3549 4.072131 CAACCAGAAGCAGCCTTTAACTA 58.928 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.179124 GCATGGTCTGGACTCGACTC 60.179 60.000 0.00 0.00 0.00 3.36
137 138 0.101759 CTTGTGCTTGTGCTTGTGCT 59.898 50.000 0.00 0.00 40.48 4.40
138 139 1.485032 GCTTGTGCTTGTGCTTGTGC 61.485 55.000 0.00 0.00 40.48 4.57
139 140 0.179132 TGCTTGTGCTTGTGCTTGTG 60.179 50.000 0.00 0.00 40.48 3.33
140 141 0.101759 CTGCTTGTGCTTGTGCTTGT 59.898 50.000 0.00 0.00 40.48 3.16
141 142 1.213094 GCTGCTTGTGCTTGTGCTTG 61.213 55.000 0.00 0.00 40.48 4.01
142 143 1.066918 GCTGCTTGTGCTTGTGCTT 59.933 52.632 0.00 0.00 40.48 3.91
184 185 5.331905 GCACGCTAACTTTCTCTTATGATCG 60.332 44.000 0.00 0.00 0.00 3.69
185 186 5.331905 CGCACGCTAACTTTCTCTTATGATC 60.332 44.000 0.00 0.00 0.00 2.92
186 187 4.504461 CGCACGCTAACTTTCTCTTATGAT 59.496 41.667 0.00 0.00 0.00 2.45
187 188 3.857665 CGCACGCTAACTTTCTCTTATGA 59.142 43.478 0.00 0.00 0.00 2.15
222 223 1.184431 AATTTCCACCGATGCATGCA 58.816 45.000 25.04 25.04 0.00 3.96
223 224 3.004629 TGATAATTTCCACCGATGCATGC 59.995 43.478 11.82 11.82 0.00 4.06
224 225 4.834357 TGATAATTTCCACCGATGCATG 57.166 40.909 2.46 0.00 0.00 4.06
225 226 5.535783 TGAATGATAATTTCCACCGATGCAT 59.464 36.000 0.00 0.00 0.00 3.96
413 426 2.965147 CAGACAAACAAATCCCAAGGGT 59.035 45.455 4.80 0.00 36.47 4.34
441 454 3.502920 CCACATCTGTGTCTAGTTCGAC 58.497 50.000 9.33 0.00 44.21 4.20
465 478 9.809096 TTTGCTTTAACATTTCACTTCATACAA 57.191 25.926 0.00 0.00 0.00 2.41
589 606 1.344438 CACTTTTCCTTTCTTGCCCCC 59.656 52.381 0.00 0.00 0.00 5.40
732 756 1.903404 CCCCTCCTGTTGGTGTTGC 60.903 63.158 0.00 0.00 34.23 4.17
836 860 2.032808 AGAAGAAAGAAACTTGCGACGC 60.033 45.455 14.19 14.19 0.00 5.19
838 862 5.006746 TGAAGAGAAGAAAGAAACTTGCGAC 59.993 40.000 0.00 0.00 0.00 5.19
914 948 3.580604 AAGGGCAAGGAGGCAGCAG 62.581 63.158 0.00 0.00 46.44 4.24
940 974 6.821616 ATCTATATCTATCAAGGGCAAGGG 57.178 41.667 0.00 0.00 0.00 3.95
941 975 8.637986 GTCTATCTATATCTATCAAGGGCAAGG 58.362 40.741 0.00 0.00 0.00 3.61
942 976 8.349245 CGTCTATCTATATCTATCAAGGGCAAG 58.651 40.741 0.00 0.00 0.00 4.01
943 977 8.053355 TCGTCTATCTATATCTATCAAGGGCAA 58.947 37.037 0.00 0.00 0.00 4.52
944 978 7.574607 TCGTCTATCTATATCTATCAAGGGCA 58.425 38.462 0.00 0.00 0.00 5.36
945 979 7.717875 ACTCGTCTATCTATATCTATCAAGGGC 59.282 40.741 0.00 0.00 0.00 5.19
946 980 9.051679 CACTCGTCTATCTATATCTATCAAGGG 57.948 40.741 0.00 0.00 0.00 3.95
947 981 9.825109 TCACTCGTCTATCTATATCTATCAAGG 57.175 37.037 0.00 0.00 0.00 3.61
995 1029 4.320456 CCGGCTGATCCATCCCCG 62.320 72.222 0.00 8.17 39.14 5.73
1513 1547 0.608640 AGAAGGGTGTCCACATCGAC 59.391 55.000 0.00 0.00 34.83 4.20
1887 1921 2.165641 CTGAGCGTGGTGGTACTGATAA 59.834 50.000 0.00 0.00 0.00 1.75
2061 2095 1.741028 TGAGACCCCAGATGTTCCAA 58.259 50.000 0.00 0.00 0.00 3.53
2120 2154 3.379372 CGAGAATGATCTGTTGGCCAAAT 59.621 43.478 22.47 10.74 35.54 2.32
2164 2198 3.189606 TCTGACCATTGTATCCCCTTGT 58.810 45.455 0.00 0.00 0.00 3.16
2181 2215 0.397564 TGTTGCACCTGAGCATCTGA 59.602 50.000 0.00 0.00 45.19 3.27
2367 2401 0.396435 AAGGGATCGCGCCATTATCA 59.604 50.000 0.00 0.00 28.71 2.15
2406 2440 3.740044 TTCTGATTTCGCCGATTGAAC 57.260 42.857 0.00 0.00 0.00 3.18
2484 2518 5.423610 ACTGCTAGATCAGTACATTCCAAGT 59.576 40.000 1.55 0.00 44.77 3.16
2487 2521 4.956075 TCACTGCTAGATCAGTACATTCCA 59.044 41.667 3.07 0.00 44.81 3.53
2490 2524 8.147058 CCTTAATCACTGCTAGATCAGTACATT 58.853 37.037 3.07 7.16 44.81 2.71
2512 2546 7.011499 TGTAGAAGAACATAAACCTGCCTTA 57.989 36.000 0.00 0.00 0.00 2.69
2534 2568 3.019564 GCCAAGGCACATAAGAAGATGT 58.980 45.455 6.14 0.00 40.78 3.06
2537 2571 3.263170 TGTAGCCAAGGCACATAAGAAGA 59.737 43.478 14.40 0.00 44.88 2.87
2539 2573 3.712016 TGTAGCCAAGGCACATAAGAA 57.288 42.857 14.40 0.00 44.88 2.52
2586 2624 7.865706 TCTGAGCCTATAAAAAGTTGATTCC 57.134 36.000 0.00 0.00 0.00 3.01
2624 2662 2.172505 ACCATCACCACTTCACTTGACA 59.827 45.455 0.00 0.00 0.00 3.58
2777 2815 6.016527 ACATCATGTTATTGCTATTGCCAGAG 60.017 38.462 0.00 0.00 38.71 3.35
2804 2842 1.168714 GCATTCGATTCCATAGCCCC 58.831 55.000 0.00 0.00 0.00 5.80
2826 2864 8.090788 ACATCCTACAACACTAACCAGATTAT 57.909 34.615 0.00 0.00 0.00 1.28
2830 2868 5.818678 AACATCCTACAACACTAACCAGA 57.181 39.130 0.00 0.00 0.00 3.86
2836 2874 7.016153 AGATCCAAAACATCCTACAACACTA 57.984 36.000 0.00 0.00 0.00 2.74
2837 2875 5.880901 AGATCCAAAACATCCTACAACACT 58.119 37.500 0.00 0.00 0.00 3.55
2844 2882 7.230747 TCTCAAACAAGATCCAAAACATCCTA 58.769 34.615 0.00 0.00 0.00 2.94
2846 2884 6.331369 TCTCAAACAAGATCCAAAACATCC 57.669 37.500 0.00 0.00 0.00 3.51
2868 2906 6.095377 CCCTGCAATTTTCTTACTGTCAATC 58.905 40.000 0.00 0.00 0.00 2.67
2877 2915 4.479158 ACAAGGACCCTGCAATTTTCTTA 58.521 39.130 0.00 0.00 0.00 2.10
2927 2965 1.610102 CCACAAGGAGCAACAGAGGAG 60.610 57.143 0.00 0.00 36.89 3.69
2934 2972 1.360192 GCACACCACAAGGAGCAAC 59.640 57.895 0.00 0.00 38.69 4.17
2941 2979 0.738389 AAGAAACGGCACACCACAAG 59.262 50.000 0.00 0.00 34.57 3.16
2963 3003 8.757307 ATACCCATAGATTTAGGATTTCTGGA 57.243 34.615 0.00 0.00 0.00 3.86
2999 3039 4.801330 TGTGACGGATTAGATCAAGTGT 57.199 40.909 0.00 0.00 0.00 3.55
3018 3060 9.468532 GCTTAAGAAATGAAGAAAGTGAAATGT 57.531 29.630 6.67 0.00 0.00 2.71
3019 3061 9.688592 AGCTTAAGAAATGAAGAAAGTGAAATG 57.311 29.630 6.67 0.00 0.00 2.32
3020 3062 9.688592 CAGCTTAAGAAATGAAGAAAGTGAAAT 57.311 29.630 6.67 0.00 0.00 2.17
3021 3063 8.686334 ACAGCTTAAGAAATGAAGAAAGTGAAA 58.314 29.630 6.67 0.00 0.00 2.69
3027 3069 6.639632 AGCACAGCTTAAGAAATGAAGAAA 57.360 33.333 6.67 0.00 33.89 2.52
3064 3107 6.128172 CCTGAAAATAAGCAACCTCTGTAGTG 60.128 42.308 0.00 0.00 0.00 2.74
3065 3108 5.940470 CCTGAAAATAAGCAACCTCTGTAGT 59.060 40.000 0.00 0.00 0.00 2.73
3153 3196 1.473258 TGAAAGGAAATGCGATGGGG 58.527 50.000 0.00 0.00 0.00 4.96
3156 3199 5.162794 TGAAACATGAAAGGAAATGCGATG 58.837 37.500 0.00 0.00 0.00 3.84
3176 3219 8.939929 GCTGCTATTGTATATATTGCTTCTGAA 58.060 33.333 0.00 0.00 0.00 3.02
3178 3221 8.489990 AGCTGCTATTGTATATATTGCTTCTG 57.510 34.615 0.00 0.00 0.00 3.02
3179 3222 8.944029 CAAGCTGCTATTGTATATATTGCTTCT 58.056 33.333 0.90 0.00 35.28 2.85
3193 3242 2.686405 TCAAGGCATCAAGCTGCTATTG 59.314 45.455 0.90 0.00 44.79 1.90
3275 3325 1.680338 GTGCCTGGGGTTATGATGAC 58.320 55.000 0.00 0.00 0.00 3.06
3277 3327 0.258484 TGGTGCCTGGGGTTATGATG 59.742 55.000 0.00 0.00 0.00 3.07
3360 3410 7.707467 AATAGACACCCCAGATATACCTTTT 57.293 36.000 0.00 0.00 0.00 2.27
3364 3414 5.221843 TGCAAATAGACACCCCAGATATACC 60.222 44.000 0.00 0.00 0.00 2.73
3400 3450 9.142515 TCGTTACGAATTTGAAACATATACACT 57.857 29.630 4.50 0.00 31.06 3.55
3407 3457 5.997385 AGCTTCGTTACGAATTTGAAACAT 58.003 33.333 20.56 0.00 44.85 2.71
3446 3496 5.590530 TGTGTGTTTTGCTTCTGGTTAAT 57.409 34.783 0.00 0.00 0.00 1.40
3460 3510 5.016051 TGGTTGCATACAAATGTGTGTTT 57.984 34.783 11.21 0.00 39.05 2.83
3461 3511 4.340666 TCTGGTTGCATACAAATGTGTGTT 59.659 37.500 11.21 0.00 39.05 3.32
3462 3512 3.888323 TCTGGTTGCATACAAATGTGTGT 59.112 39.130 11.21 0.00 39.05 3.72
3463 3513 4.502171 TCTGGTTGCATACAAATGTGTG 57.498 40.909 0.00 5.99 38.82 3.82
3464 3514 4.559300 GCTTCTGGTTGCATACAAATGTGT 60.559 41.667 0.00 0.00 42.09 3.72
3465 3515 3.922240 GCTTCTGGTTGCATACAAATGTG 59.078 43.478 0.00 0.00 37.58 3.21
3466 3516 3.573538 TGCTTCTGGTTGCATACAAATGT 59.426 39.130 0.00 0.00 37.58 2.71
3467 3517 4.171005 CTGCTTCTGGTTGCATACAAATG 58.829 43.478 0.00 0.00 37.58 2.32
3468 3518 3.367703 GCTGCTTCTGGTTGCATACAAAT 60.368 43.478 0.00 0.00 37.58 2.32
3469 3519 2.030007 GCTGCTTCTGGTTGCATACAAA 60.030 45.455 0.00 0.00 37.58 2.83
3470 3520 1.541147 GCTGCTTCTGGTTGCATACAA 59.459 47.619 0.00 0.00 38.59 2.41
3471 3521 1.167851 GCTGCTTCTGGTTGCATACA 58.832 50.000 0.00 0.00 38.59 2.29
3472 3522 0.453390 GGCTGCTTCTGGTTGCATAC 59.547 55.000 0.00 0.00 38.59 2.39
3473 3523 0.329261 AGGCTGCTTCTGGTTGCATA 59.671 50.000 0.00 0.00 38.59 3.14
3474 3524 0.541296 AAGGCTGCTTCTGGTTGCAT 60.541 50.000 0.00 0.00 38.59 3.96
3475 3525 0.756442 AAAGGCTGCTTCTGGTTGCA 60.756 50.000 0.00 0.00 37.63 4.08
3476 3526 1.247567 TAAAGGCTGCTTCTGGTTGC 58.752 50.000 0.00 0.00 0.00 4.17
3477 3527 2.887152 AGTTAAAGGCTGCTTCTGGTTG 59.113 45.455 0.00 0.00 0.00 3.77
3478 3528 3.229697 AGTTAAAGGCTGCTTCTGGTT 57.770 42.857 0.00 0.00 0.00 3.67
3479 3529 2.959465 AGTTAAAGGCTGCTTCTGGT 57.041 45.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.