Multiple sequence alignment - TraesCS4A01G353100

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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 TraesCS4A01G353100 chr4A 100.000 3278 0 0 1 3278 628326437 628329714 0.000000e+00 6054.0
1 TraesCS4A01G353100 chr4A 89.260 1229 112 11 1036 2245 628483855 628485082 0.000000e+00 1520.0
2 TraesCS4A01G353100 chr5D 93.386 1527 73 9 860 2385 540284784 540286283 0.000000e+00 2235.0
3 TraesCS4A01G353100 chr5D 87.482 1374 133 20 890 2246 540340071 540341422 0.000000e+00 1548.0
4 TraesCS4A01G353100 chr5D 92.278 777 46 7 2422 3187 540286975 540287748 0.000000e+00 1090.0
5 TraesCS4A01G353100 chr5D 95.172 145 6 1 725 869 540283490 540283633 9.150000e-56 228.0
6 TraesCS4A01G353100 chr5D 85.950 121 16 1 3 123 540282622 540282741 9.550000e-26 128.0
7 TraesCS4A01G353100 chr5D 96.970 66 2 0 3213 3278 540287952 540288017 9.610000e-21 111.0
8 TraesCS4A01G353100 chr5B 91.533 1559 113 7 860 2406 682696220 682697771 0.000000e+00 2130.0
9 TraesCS4A01G353100 chr5B 87.127 1375 136 28 890 2246 682817695 682819046 0.000000e+00 1520.0
10 TraesCS4A01G353100 chr5B 91.200 625 38 2 2521 3145 682698799 682699406 0.000000e+00 833.0
11 TraesCS4A01G353100 chr5B 94.444 126 6 1 725 850 682695706 682695830 3.340000e-45 193.0
12 TraesCS4A01G353100 chr5B 100.000 66 0 0 3213 3278 682699591 682699656 4.440000e-24 122.0
13 TraesCS4A01G353100 chr7A 82.921 445 48 15 2841 3278 68889346 68888923 3.090000e-100 375.0
14 TraesCS4A01G353100 chr7A 94.286 35 2 0 388 422 22917084 22917050 2.000000e-03 54.7
15 TraesCS4A01G353100 chr4B 82.511 446 48 11 2841 3278 673189129 673189552 6.680000e-97 364.0
16 TraesCS4A01G353100 chr7B 82.247 445 50 15 2841 3278 6372448 6372026 1.120000e-94 357.0
17 TraesCS4A01G353100 chr7D 82.022 445 51 15 2841 3278 64734100 64733678 5.200000e-93 351.0
18 TraesCS4A01G353100 chr2D 85.099 302 39 1 2823 3118 614875588 614875287 1.480000e-78 303.0
19 TraesCS4A01G353100 chr2D 96.721 61 2 0 3218 3278 614873039 614872979 5.790000e-18 102.0
20 TraesCS4A01G353100 chr5A 81.081 148 22 6 309 455 626159897 626160039 2.670000e-21 113.0
21 TraesCS4A01G353100 chr4D 80.469 128 22 3 373 499 4524242 4524367 9.680000e-16 95.3
22 TraesCS4A01G353100 chr6B 80.315 127 15 9 368 490 135949086 135949206 1.620000e-13 87.9


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 TraesCS4A01G353100 chr4A 628326437 628329714 3277 False 6054.0 6054 100.00000 1 3278 1 chr4A.!!$F1 3277
1 TraesCS4A01G353100 chr4A 628483855 628485082 1227 False 1520.0 1520 89.26000 1036 2245 1 chr4A.!!$F2 1209
2 TraesCS4A01G353100 chr5D 540340071 540341422 1351 False 1548.0 1548 87.48200 890 2246 1 chr5D.!!$F1 1356
3 TraesCS4A01G353100 chr5D 540282622 540288017 5395 False 758.4 2235 92.75120 3 3278 5 chr5D.!!$F2 3275
4 TraesCS4A01G353100 chr5B 682817695 682819046 1351 False 1520.0 1520 87.12700 890 2246 1 chr5B.!!$F1 1356
5 TraesCS4A01G353100 chr5B 682695706 682699656 3950 False 819.5 2130 94.29425 725 3278 4 chr5B.!!$F2 2553
6 TraesCS4A01G353100 chr2D 614872979 614875588 2609 True 202.5 303 90.91000 2823 3278 2 chr2D.!!$R1 455

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
208 209 0.034477 ACATGGTTCCCCGTTCATCC 60.034 55.0 0.00 0.0 0.00 3.51 F
1332 3074 0.328258 AACTGGTCAAAGGATCCGGG 59.672 55.0 5.98 0.0 32.42 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 3487 0.235665 CAAGAAGCGCAACATGTCGT 59.764 50.0 11.47 0.0 0.00 4.34 R
3025 5720 0.035534 CCGTTGTGACCCATCATCCA 60.036 55.0 0.00 0.0 37.14 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
36 37 5.123820 GCACAAATAGGTTCACTCATAAGCA 59.876 40.000 0.00 0.00 0.00 3.91
37 38 6.546395 CACAAATAGGTTCACTCATAAGCAC 58.454 40.000 0.00 0.00 0.00 4.40
38 39 6.149308 CACAAATAGGTTCACTCATAAGCACA 59.851 38.462 0.00 0.00 0.00 4.57
49 50 8.146479 TCACTCATAAGCACATATGAAATGTC 57.854 34.615 10.38 0.00 40.71 3.06
66 67 6.643360 TGAAATGTCTGTGAAATTGATTGCAG 59.357 34.615 0.00 0.00 0.00 4.41
68 69 5.518848 TGTCTGTGAAATTGATTGCAGTT 57.481 34.783 0.00 0.00 0.00 3.16
76 77 6.476380 GTGAAATTGATTGCAGTTTGACTTGA 59.524 34.615 0.00 0.00 35.84 3.02
81 82 9.715121 AATTGATTGCAGTTTGACTTGAATAAT 57.285 25.926 0.00 0.00 0.00 1.28
187 188 7.831690 ACCAAAATAATTGAAAACACCAAGGTT 59.168 29.630 0.00 0.00 0.00 3.50
199 200 2.560981 CACCAAGGTTAACATGGTTCCC 59.439 50.000 24.80 0.14 44.92 3.97
203 204 1.426215 AGGTTAACATGGTTCCCCGTT 59.574 47.619 8.10 0.00 0.00 4.44
206 207 3.086282 GTTAACATGGTTCCCCGTTCAT 58.914 45.455 0.00 0.00 0.00 2.57
208 209 0.034477 ACATGGTTCCCCGTTCATCC 60.034 55.000 0.00 0.00 0.00 3.51
210 211 0.034477 ATGGTTCCCCGTTCATCCAC 60.034 55.000 0.00 0.00 0.00 4.02
212 213 2.046700 TTCCCCGTTCATCCACGC 60.047 61.111 0.00 0.00 38.93 5.34
218 219 0.852777 CCGTTCATCCACGCGAATAG 59.147 55.000 15.93 0.00 38.93 1.73
220 221 2.542205 CCGTTCATCCACGCGAATAGTA 60.542 50.000 15.93 0.00 38.93 1.82
222 223 3.441163 GTTCATCCACGCGAATAGTACA 58.559 45.455 15.93 0.00 0.00 2.90
234 362 8.540492 CACGCGAATAGTACATTTAGAGAAAAT 58.460 33.333 15.93 0.00 38.36 1.82
295 424 4.579454 TGGTATACCATTCTACTCACGC 57.421 45.455 21.05 0.00 42.01 5.34
299 428 0.885879 ACCATTCTACTCACGCGTGA 59.114 50.000 36.96 36.96 38.06 4.35
303 466 3.427098 CCATTCTACTCACGCGTGAAGTA 60.427 47.826 38.11 33.79 39.39 2.24
307 470 1.137513 ACTCACGCGTGAAGTAAAGC 58.862 50.000 38.11 0.00 39.39 3.51
310 473 1.934525 TCACGCGTGAAGTAAAGCAAA 59.065 42.857 37.68 12.17 36.53 3.68
323 486 8.780249 TGAAGTAAAGCAAATACAACTAAGACC 58.220 33.333 0.00 0.00 0.00 3.85
341 504 8.434392 ACTAAGACCTTACTATTCACCAAACAA 58.566 33.333 0.00 0.00 0.00 2.83
391 554 9.535878 TTTGTCAATTTTTACCAAGATTACCAC 57.464 29.630 0.00 0.00 0.00 4.16
392 555 7.364200 TGTCAATTTTTACCAAGATTACCACG 58.636 34.615 0.00 0.00 0.00 4.94
393 556 6.804783 GTCAATTTTTACCAAGATTACCACGG 59.195 38.462 0.00 0.00 0.00 4.94
394 557 6.715718 TCAATTTTTACCAAGATTACCACGGA 59.284 34.615 0.00 0.00 0.00 4.69
395 558 7.394923 TCAATTTTTACCAAGATTACCACGGAT 59.605 33.333 0.00 0.00 0.00 4.18
396 559 6.503589 TTTTTACCAAGATTACCACGGATG 57.496 37.500 0.00 0.00 0.00 3.51
397 560 4.829872 TTACCAAGATTACCACGGATGT 57.170 40.909 0.00 0.00 0.00 3.06
398 561 3.261981 ACCAAGATTACCACGGATGTC 57.738 47.619 0.00 0.00 0.00 3.06
399 562 2.569853 ACCAAGATTACCACGGATGTCA 59.430 45.455 0.00 0.00 0.00 3.58
400 563 3.199946 ACCAAGATTACCACGGATGTCAT 59.800 43.478 0.00 0.00 0.00 3.06
401 564 4.199310 CCAAGATTACCACGGATGTCATT 58.801 43.478 0.00 0.00 0.00 2.57
409 572 2.094258 CCACGGATGTCATTTCTTCGTG 59.906 50.000 0.00 0.00 0.00 4.35
416 579 6.080406 GGATGTCATTTCTTCGTGAAACTTC 58.920 40.000 8.09 5.58 46.08 3.01
426 589 1.931551 TGAAACTTCACACGCGAGC 59.068 52.632 15.93 0.00 31.01 5.03
434 597 1.807165 CACACGCGAGCATAGCAGT 60.807 57.895 15.93 0.00 36.06 4.40
436 599 2.278206 ACGCGAGCATAGCAGTCG 60.278 61.111 15.93 0.00 36.06 4.18
442 605 2.605823 GCGAGCATAGCAGTCGACTATT 60.606 50.000 19.57 11.82 36.44 1.73
457 620 9.638300 CAGTCGACTATTTATGTTAGAAAATGC 57.362 33.333 19.57 0.00 0.00 3.56
515 678 5.880054 ATTTTATTGTTCTAGCTGTGCGT 57.120 34.783 0.00 0.00 0.00 5.24
529 692 2.548057 CTGTGCGTGTAGAACCATGTTT 59.452 45.455 0.00 0.00 0.00 2.83
531 694 2.546368 GTGCGTGTAGAACCATGTTTCA 59.454 45.455 5.73 0.00 0.00 2.69
539 702 7.433719 CGTGTAGAACCATGTTTCAAAAATTCA 59.566 33.333 5.73 0.00 0.00 2.57
543 706 8.369218 AGAACCATGTTTCAAAAATTCATGTC 57.631 30.769 5.73 0.00 35.54 3.06
557 720 8.831715 AAAATTCATGTCCCAAACTAATTGAC 57.168 30.769 0.00 0.00 41.85 3.18
559 722 7.722949 ATTCATGTCCCAAACTAATTGACAT 57.277 32.000 0.00 0.00 41.85 3.06
723 887 6.942005 TGAAATGTATGTGACTTCTGTTGGAT 59.058 34.615 0.00 0.00 0.00 3.41
726 890 8.498054 AATGTATGTGACTTCTGTTGGATAAG 57.502 34.615 0.00 0.00 0.00 1.73
727 891 5.874810 TGTATGTGACTTCTGTTGGATAAGC 59.125 40.000 0.00 0.00 0.00 3.09
728 892 4.350368 TGTGACTTCTGTTGGATAAGCA 57.650 40.909 0.00 0.00 0.00 3.91
729 893 4.713553 TGTGACTTCTGTTGGATAAGCAA 58.286 39.130 0.00 0.00 0.00 3.91
810 1005 3.005554 AGCGACATGACAAAGATTGAGG 58.994 45.455 0.00 0.00 0.00 3.86
869 1444 1.482593 CTAATTGGCCGTGGAGACTCT 59.517 52.381 0.00 0.00 0.00 3.24
1209 2951 3.685214 CTCCCGGTCGCTCTTCGTG 62.685 68.421 0.00 0.00 39.67 4.35
1224 2966 4.157120 GTGGCCGCGGTCACCTAT 62.157 66.667 45.02 0.00 44.18 2.57
1326 3068 2.783135 GATCTGCAACTGGTCAAAGGA 58.217 47.619 0.00 0.00 0.00 3.36
1332 3074 0.328258 AACTGGTCAAAGGATCCGGG 59.672 55.000 5.98 0.00 32.42 5.73
1492 3234 1.607756 TCGCAGAGCTTCACCTCCT 60.608 57.895 0.00 0.00 32.17 3.69
1533 3275 1.351012 CTACGTCTTCGCCGTCGAT 59.649 57.895 0.00 0.00 45.04 3.59
1701 3455 2.430244 CTCGTCAACCCCGTCGTG 60.430 66.667 0.00 0.00 0.00 4.35
1945 3699 4.753877 TCGAGCTCAACGACGCCG 62.754 66.667 15.40 0.00 42.50 6.46
2224 3978 3.589654 CTCCCCAGCGCGTCTTTCA 62.590 63.158 8.43 0.00 0.00 2.69
2262 4016 3.322466 CTCCCCAGTCCGGCTGTT 61.322 66.667 19.93 0.00 43.55 3.16
2263 4017 3.612247 CTCCCCAGTCCGGCTGTTG 62.612 68.421 19.93 12.65 43.55 3.33
2264 4018 3.953775 CCCCAGTCCGGCTGTTGT 61.954 66.667 19.93 0.00 43.55 3.32
2268 4022 4.681978 AGTCCGGCTGTTGTCGCC 62.682 66.667 0.00 0.00 44.11 5.54
2280 4034 4.729856 GTCGCCGGGCACTAACGT 62.730 66.667 20.71 0.00 0.00 3.99
2321 4075 3.303049 AGCCTCCATGGATGATTTTTCC 58.697 45.455 20.12 1.36 38.35 3.13
2326 4080 5.659971 CCTCCATGGATGATTTTTCCTTCTT 59.340 40.000 16.63 0.00 38.35 2.52
2327 4081 6.183360 CCTCCATGGATGATTTTTCCTTCTTC 60.183 42.308 16.63 0.00 38.35 2.87
2329 4083 6.379133 TCCATGGATGATTTTTCCTTCTTCTG 59.621 38.462 11.44 0.00 34.17 3.02
2331 4085 7.340232 CCATGGATGATTTTTCCTTCTTCTGTA 59.660 37.037 5.56 0.00 34.17 2.74
2332 4086 8.742777 CATGGATGATTTTTCCTTCTTCTGTAA 58.257 33.333 0.00 0.00 34.17 2.41
2333 4087 8.704849 TGGATGATTTTTCCTTCTTCTGTAAA 57.295 30.769 0.00 0.00 34.17 2.01
2334 4088 9.142014 TGGATGATTTTTCCTTCTTCTGTAAAA 57.858 29.630 0.00 0.00 34.17 1.52
2335 4089 9.411801 GGATGATTTTTCCTTCTTCTGTAAAAC 57.588 33.333 0.00 0.00 0.00 2.43
2336 4090 9.411801 GATGATTTTTCCTTCTTCTGTAAAACC 57.588 33.333 0.00 0.00 0.00 3.27
2338 4092 8.923270 TGATTTTTCCTTCTTCTGTAAAACCAT 58.077 29.630 0.00 0.00 0.00 3.55
2341 4095 8.754991 TTTTCCTTCTTCTGTAAAACCATACA 57.245 30.769 0.00 0.00 34.72 2.29
2342 4096 7.739498 TTCCTTCTTCTGTAAAACCATACAC 57.261 36.000 0.00 0.00 32.56 2.90
2343 4097 7.074653 TCCTTCTTCTGTAAAACCATACACT 57.925 36.000 0.00 0.00 32.56 3.55
2344 4098 8.197592 TCCTTCTTCTGTAAAACCATACACTA 57.802 34.615 0.00 0.00 32.56 2.74
2345 4099 8.092687 TCCTTCTTCTGTAAAACCATACACTAC 58.907 37.037 0.00 0.00 32.56 2.73
2367 4121 2.704572 ACTACTAGCAAAGCTTGGCAG 58.295 47.619 27.35 22.06 40.44 4.85
2388 4142 1.095228 CGTTGCAGAACTGTGTGGGT 61.095 55.000 3.77 0.00 0.00 4.51
2390 4144 1.065551 GTTGCAGAACTGTGTGGGTTC 59.934 52.381 3.77 0.00 42.15 3.62
2397 4151 2.918712 ACTGTGTGGGTTCAGAGAAG 57.081 50.000 0.00 0.00 35.84 2.85
2417 4178 8.996271 AGAGAAGTAAAATAACACCCTTTTACG 58.004 33.333 10.53 0.00 45.70 3.18
2418 4179 8.102800 AGAAGTAAAATAACACCCTTTTACGG 57.897 34.615 10.53 0.00 45.70 4.02
2419 4180 7.720957 AGAAGTAAAATAACACCCTTTTACGGT 59.279 33.333 10.53 5.22 45.70 4.83
2446 5043 1.656095 GAAGAAATGAGCGTCCGAGTG 59.344 52.381 0.00 0.00 0.00 3.51
2474 5071 3.766545 TCCCCAAGGAAGTGAAATTCAG 58.233 45.455 0.00 0.00 40.08 3.02
2487 5085 3.254166 TGAAATTCAGAACTTCTGGCTGC 59.746 43.478 17.12 0.00 44.39 5.25
2513 5111 3.398406 TCGTCTTTGACTGCAATGCTAA 58.602 40.909 6.82 0.00 33.25 3.09
2515 5113 3.425359 CGTCTTTGACTGCAATGCTAAGG 60.425 47.826 6.82 0.00 33.25 2.69
2518 5116 4.584325 TCTTTGACTGCAATGCTAAGGTTT 59.416 37.500 6.82 0.00 33.25 3.27
2519 5117 5.767665 TCTTTGACTGCAATGCTAAGGTTTA 59.232 36.000 6.82 0.00 33.25 2.01
2539 5219 6.915843 GGTTTATATAAGCATTGAAACCCGTG 59.084 38.462 10.95 0.00 39.82 4.94
2582 5262 7.746475 CAGACACGAAAAAGATTATGTCCTTTC 59.254 37.037 0.00 0.00 37.72 2.62
2676 5360 5.617529 CGCATAAACAAGATGCTGAGTTTCA 60.618 40.000 6.10 0.00 46.16 2.69
2693 5377 7.223584 TGAGTTTCACTGAAAGATGAATGGTA 58.776 34.615 4.36 0.00 35.19 3.25
2694 5378 7.719193 TGAGTTTCACTGAAAGATGAATGGTAA 59.281 33.333 4.36 0.00 35.19 2.85
2705 5389 4.895889 AGATGAATGGTAAGTCCTGATCGA 59.104 41.667 0.00 0.00 37.07 3.59
2730 5414 1.376037 GAACACCGAGCTTCTGGGG 60.376 63.158 1.62 1.62 33.54 4.96
2733 5417 2.203788 ACCGAGCTTCTGGGGACA 60.204 61.111 5.69 0.00 33.54 4.02
2739 5428 1.136329 AGCTTCTGGGGACACATGGT 61.136 55.000 0.00 0.00 35.60 3.55
2751 5440 1.026182 CACATGGTATGGCAGCACGT 61.026 55.000 0.00 0.00 37.50 4.49
2752 5441 1.026182 ACATGGTATGGCAGCACGTG 61.026 55.000 12.28 12.28 37.50 4.49
2763 5452 3.044305 GCACGTGTGTCCTCTGCC 61.044 66.667 18.38 0.00 0.00 4.85
2764 5453 2.357517 CACGTGTGTCCTCTGCCC 60.358 66.667 7.58 0.00 0.00 5.36
2765 5454 2.842462 ACGTGTGTCCTCTGCCCA 60.842 61.111 0.00 0.00 0.00 5.36
2774 5463 1.134371 GTCCTCTGCCCATGTTACCTC 60.134 57.143 0.00 0.00 0.00 3.85
2950 5645 2.222027 GCATCAGCATACCCCTTGTAC 58.778 52.381 0.00 0.00 41.58 2.90
2979 5674 5.931441 AAGTCATACACTTCAAGAAGCAC 57.069 39.130 9.62 0.00 42.07 4.40
2980 5675 5.220710 AGTCATACACTTCAAGAAGCACT 57.779 39.130 9.62 0.92 41.99 4.40
3025 5720 3.623060 CGATCCAAACCTTGAATCGTGAT 59.377 43.478 0.46 0.00 35.66 3.06
3043 5738 1.942657 GATGGATGATGGGTCACAACG 59.057 52.381 0.00 0.00 37.14 4.10
3061 5756 3.443045 GCCCAGGTTGTCCATGCG 61.443 66.667 0.00 0.00 35.89 4.73
3146 7838 2.384899 CAGCAGATGCACATGAATCG 57.615 50.000 7.68 0.00 45.16 3.34
3175 7867 5.652994 TGTTTCTACACAAAAGGCAAAGT 57.347 34.783 0.00 0.00 0.00 2.66
3177 7869 7.341445 TGTTTCTACACAAAAGGCAAAGTAT 57.659 32.000 0.00 0.00 0.00 2.12
3178 7870 7.199766 TGTTTCTACACAAAAGGCAAAGTATG 58.800 34.615 0.00 0.00 0.00 2.39
3179 7871 6.952773 TTCTACACAAAAGGCAAAGTATGT 57.047 33.333 0.00 0.00 0.00 2.29
3180 7872 6.312399 TCTACACAAAAGGCAAAGTATGTG 57.688 37.500 0.00 0.00 42.78 3.21
3189 7881 2.352503 CAAAGTATGTGCAAGGTGCC 57.647 50.000 0.00 0.00 44.23 5.01
3208 7905 2.223377 GCCAAGGTAAACTGAAGACACG 59.777 50.000 0.00 0.00 0.00 4.49
3211 7908 4.389077 CCAAGGTAAACTGAAGACACGATC 59.611 45.833 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.019656 TGAACCTATTTGTGCATGTAAGTTAAT 57.980 29.630 0.00 0.00 0.00 1.40
1 2 8.293867 GTGAACCTATTTGTGCATGTAAGTTAA 58.706 33.333 0.00 0.00 0.00 2.01
5 6 6.149308 TGAGTGAACCTATTTGTGCATGTAAG 59.851 38.462 0.00 0.00 0.00 2.34
38 39 9.309516 GCAATCAATTTCACAGACATTTCATAT 57.690 29.630 0.00 0.00 0.00 1.78
49 50 5.981315 AGTCAAACTGCAATCAATTTCACAG 59.019 36.000 0.00 0.00 0.00 3.66
168 169 7.928706 CCATGTTAACCTTGGTGTTTTCAATTA 59.071 33.333 13.86 0.00 34.43 1.40
172 173 4.712337 ACCATGTTAACCTTGGTGTTTTCA 59.288 37.500 22.71 0.00 46.77 2.69
199 200 0.852777 CTATTCGCGTGGATGAACGG 59.147 55.000 5.77 0.00 43.75 4.44
203 204 4.316205 AATGTACTATTCGCGTGGATGA 57.684 40.909 5.77 0.00 0.00 2.92
206 207 5.297527 TCTCTAAATGTACTATTCGCGTGGA 59.702 40.000 5.77 0.00 0.00 4.02
208 209 7.445900 TTTCTCTAAATGTACTATTCGCGTG 57.554 36.000 5.77 0.00 0.00 5.34
210 211 8.904565 CATTTTCTCTAAATGTACTATTCGCG 57.095 34.615 0.00 0.00 45.25 5.87
295 424 8.492748 TCTTAGTTGTATTTGCTTTACTTCACG 58.507 33.333 0.00 0.00 0.00 4.35
299 428 8.919777 AGGTCTTAGTTGTATTTGCTTTACTT 57.080 30.769 0.00 0.00 0.00 2.24
303 466 8.919777 AGTAAGGTCTTAGTTGTATTTGCTTT 57.080 30.769 0.00 0.00 0.00 3.51
310 473 9.263446 TGGTGAATAGTAAGGTCTTAGTTGTAT 57.737 33.333 3.73 0.00 31.68 2.29
323 486 9.965824 AAAGAACATTGTTTGGTGAATAGTAAG 57.034 29.630 3.08 0.00 0.00 2.34
372 535 6.661805 ACATCCGTGGTAATCTTGGTAAAAAT 59.338 34.615 0.00 0.00 0.00 1.82
377 540 3.770388 TGACATCCGTGGTAATCTTGGTA 59.230 43.478 0.00 0.00 0.00 3.25
378 541 2.569853 TGACATCCGTGGTAATCTTGGT 59.430 45.455 0.00 0.00 0.00 3.67
382 545 5.359194 AGAAATGACATCCGTGGTAATCT 57.641 39.130 0.00 0.00 0.00 2.40
383 546 5.276868 CGAAGAAATGACATCCGTGGTAATC 60.277 44.000 0.00 0.00 0.00 1.75
384 547 4.570772 CGAAGAAATGACATCCGTGGTAAT 59.429 41.667 0.00 0.00 0.00 1.89
386 549 3.056393 ACGAAGAAATGACATCCGTGGTA 60.056 43.478 0.00 0.00 0.00 3.25
387 550 2.289444 ACGAAGAAATGACATCCGTGGT 60.289 45.455 0.00 0.00 0.00 4.16
389 552 2.993220 TCACGAAGAAATGACATCCGTG 59.007 45.455 15.05 15.05 44.71 4.94
390 553 3.313012 TCACGAAGAAATGACATCCGT 57.687 42.857 0.00 0.00 0.00 4.69
391 554 4.661993 TTTCACGAAGAAATGACATCCG 57.338 40.909 0.00 0.00 41.17 4.18
409 572 0.512952 ATGCTCGCGTGTGAAGTTTC 59.487 50.000 5.77 0.00 0.00 2.78
416 579 1.746727 GACTGCTATGCTCGCGTGTG 61.747 60.000 5.77 0.00 0.00 3.82
420 583 2.024729 TCGACTGCTATGCTCGCG 59.975 61.111 0.00 0.00 0.00 5.87
423 586 6.153067 ACATAAATAGTCGACTGCTATGCTC 58.847 40.000 28.12 0.00 30.38 4.26
426 589 9.678941 TTCTAACATAAATAGTCGACTGCTATG 57.321 33.333 28.12 26.72 30.38 2.23
491 654 6.032775 CACGCACAGCTAGAACAATAAAATTG 59.967 38.462 0.00 0.00 0.00 2.32
499 662 2.295070 TCTACACGCACAGCTAGAACAA 59.705 45.455 0.00 0.00 0.00 2.83
507 670 0.443869 CATGGTTCTACACGCACAGC 59.556 55.000 0.00 0.00 0.00 4.40
515 678 9.258826 CATGAATTTTTGAAACATGGTTCTACA 57.741 29.630 23.46 10.66 35.96 2.74
529 692 9.270640 CAATTAGTTTGGGACATGAATTTTTGA 57.729 29.630 0.00 0.00 39.30 2.69
531 694 9.271828 GTCAATTAGTTTGGGACATGAATTTTT 57.728 29.630 0.00 0.00 39.30 1.94
539 702 9.253832 TCATAAATGTCAATTAGTTTGGGACAT 57.746 29.630 0.00 0.00 39.30 3.06
755 950 9.918630 ATGACCAAAAATTCAAAGACTATTCAG 57.081 29.630 0.00 0.00 0.00 3.02
810 1005 0.625849 TTTCCTTGATGGGCCTCTCC 59.374 55.000 4.53 0.00 36.20 3.71
969 2704 2.184579 CGGCGAGGAAGAAGACCC 59.815 66.667 0.00 0.00 0.00 4.46
1314 3056 1.562672 CCCCGGATCCTTTGACCAGT 61.563 60.000 10.75 0.00 0.00 4.00
1326 3068 3.941188 CATAGCACGGCCCCGGAT 61.941 66.667 0.73 1.74 44.69 4.18
1332 3074 2.585247 GACGACCATAGCACGGCC 60.585 66.667 0.00 0.00 0.00 6.13
1492 3234 1.296392 CGGAGGTGAGGTTCATGCA 59.704 57.895 0.00 0.00 0.00 3.96
1701 3455 2.047274 TTGCTGCTGTAGGCGACC 60.047 61.111 0.00 0.00 45.43 4.79
1733 3487 0.235665 CAAGAAGCGCAACATGTCGT 59.764 50.000 11.47 0.00 0.00 4.34
2215 3969 1.129437 GCAGACCTTGATGAAAGACGC 59.871 52.381 0.00 0.00 38.24 5.19
2224 3978 1.604378 CGGGGAAGCAGACCTTGAT 59.396 57.895 0.00 0.00 32.78 2.57
2259 4013 3.166490 TTAGTGCCCGGCGACAACA 62.166 57.895 9.30 0.00 0.00 3.33
2262 4016 4.728102 CGTTAGTGCCCGGCGACA 62.728 66.667 9.30 2.83 0.00 4.35
2263 4017 4.729856 ACGTTAGTGCCCGGCGAC 62.730 66.667 9.30 0.00 0.00 5.19
2264 4018 4.728102 CACGTTAGTGCCCGGCGA 62.728 66.667 9.30 0.00 41.94 5.54
2300 4054 3.052338 AGGAAAAATCATCCATGGAGGCT 60.052 43.478 21.65 9.48 39.55 4.58
2318 4072 7.514721 AGTGTATGGTTTTACAGAAGAAGGAA 58.485 34.615 0.00 0.00 32.92 3.36
2320 4074 8.095169 AGTAGTGTATGGTTTTACAGAAGAAGG 58.905 37.037 0.00 0.00 32.92 3.46
2326 4080 9.745018 AGTAGTAGTAGTGTATGGTTTTACAGA 57.255 33.333 0.00 0.00 32.92 3.41
2329 4083 9.943163 GCTAGTAGTAGTAGTGTATGGTTTTAC 57.057 37.037 12.61 0.00 0.00 2.01
2331 4085 8.585471 TGCTAGTAGTAGTAGTGTATGGTTTT 57.415 34.615 12.61 0.00 0.00 2.43
2332 4086 8.585471 TTGCTAGTAGTAGTAGTGTATGGTTT 57.415 34.615 12.61 0.00 0.00 3.27
2333 4087 8.585471 TTTGCTAGTAGTAGTAGTGTATGGTT 57.415 34.615 12.61 0.00 0.00 3.67
2334 4088 7.201803 GCTTTGCTAGTAGTAGTAGTGTATGGT 60.202 40.741 12.61 0.00 0.00 3.55
2335 4089 7.013464 AGCTTTGCTAGTAGTAGTAGTGTATGG 59.987 40.741 12.61 2.33 36.99 2.74
2336 4090 7.932335 AGCTTTGCTAGTAGTAGTAGTGTATG 58.068 38.462 12.61 3.14 36.99 2.39
2338 4092 7.148120 CCAAGCTTTGCTAGTAGTAGTAGTGTA 60.148 40.741 12.61 0.00 38.25 2.90
2340 4094 6.037098 CCAAGCTTTGCTAGTAGTAGTAGTG 58.963 44.000 12.61 2.78 38.25 2.74
2341 4095 5.394333 GCCAAGCTTTGCTAGTAGTAGTAGT 60.394 44.000 14.95 0.00 38.25 2.73
2342 4096 5.044558 GCCAAGCTTTGCTAGTAGTAGTAG 58.955 45.833 14.95 7.56 38.25 2.57
2343 4097 4.464951 TGCCAAGCTTTGCTAGTAGTAGTA 59.535 41.667 21.73 0.00 38.25 1.82
2344 4098 3.260884 TGCCAAGCTTTGCTAGTAGTAGT 59.739 43.478 21.73 0.00 38.25 2.73
2345 4099 3.861840 TGCCAAGCTTTGCTAGTAGTAG 58.138 45.455 21.73 0.00 38.25 2.57
2367 4121 1.009675 CACACAGTTCTGCAACGGC 60.010 57.895 0.00 0.00 37.61 5.68
2381 4135 7.227910 TGTTATTTTACTTCTCTGAACCCACAC 59.772 37.037 0.00 0.00 0.00 3.82
2388 4142 8.990163 AAAGGGTGTTATTTTACTTCTCTGAA 57.010 30.769 0.00 0.00 0.00 3.02
2416 4177 3.741344 CGCTCATTTCTTCCCTATTACCG 59.259 47.826 0.00 0.00 0.00 4.02
2417 4178 4.704965 ACGCTCATTTCTTCCCTATTACC 58.295 43.478 0.00 0.00 0.00 2.85
2418 4179 4.750598 GGACGCTCATTTCTTCCCTATTAC 59.249 45.833 0.00 0.00 0.00 1.89
2419 4180 4.500887 CGGACGCTCATTTCTTCCCTATTA 60.501 45.833 0.00 0.00 0.00 0.98
2474 5071 2.159170 ACGAGATAGCAGCCAGAAGTTC 60.159 50.000 0.00 0.00 0.00 3.01
2487 5085 4.260132 GCATTGCAGTCAAAGACGAGATAG 60.260 45.833 3.15 0.00 37.67 2.08
2513 5111 6.831868 ACGGGTTTCAATGCTTATATAAACCT 59.168 34.615 12.89 0.00 43.37 3.50
2515 5113 7.699566 TCACGGGTTTCAATGCTTATATAAAC 58.300 34.615 0.00 0.00 0.00 2.01
2518 5116 5.995282 CCTCACGGGTTTCAATGCTTATATA 59.005 40.000 0.00 0.00 0.00 0.86
2519 5117 4.821805 CCTCACGGGTTTCAATGCTTATAT 59.178 41.667 0.00 0.00 0.00 0.86
2539 5219 3.882888 TGTCTGTTGAAATGGTTCACCTC 59.117 43.478 0.00 0.00 43.52 3.85
2582 5262 9.743057 TCAACAATTGTTTTGTTCTGTAATAGG 57.257 29.630 21.10 4.66 40.30 2.57
2676 5360 6.013379 TCAGGACTTACCATTCATCTTTCAGT 60.013 38.462 0.00 0.00 42.04 3.41
2705 5389 1.201429 AAGCTCGGTGTTCCCTGGAT 61.201 55.000 0.00 0.00 0.00 3.41
2730 5414 0.734889 GTGCTGCCATACCATGTGTC 59.265 55.000 0.00 0.00 0.00 3.67
2733 5417 1.026182 CACGTGCTGCCATACCATGT 61.026 55.000 0.82 0.00 0.00 3.21
2739 5428 1.375396 GGACACACGTGCTGCCATA 60.375 57.895 17.22 0.00 0.00 2.74
2751 5440 1.003118 GTAACATGGGCAGAGGACACA 59.997 52.381 0.00 0.00 0.00 3.72
2752 5441 1.679032 GGTAACATGGGCAGAGGACAC 60.679 57.143 0.00 0.00 0.00 3.67
2774 5463 1.819288 TGTTAGCTTGTCCCTCTCTCG 59.181 52.381 0.00 0.00 0.00 4.04
2950 5645 4.188247 TGAAGTGTATGACTTTCCTCCG 57.812 45.455 0.00 0.00 45.48 4.63
2979 5674 1.327303 ATTCGGAGGAGCTCTAGCAG 58.673 55.000 14.64 4.41 45.16 4.24
2980 5675 2.658807 TATTCGGAGGAGCTCTAGCA 57.341 50.000 14.64 0.00 45.16 3.49
3025 5720 0.035534 CCGTTGTGACCCATCATCCA 60.036 55.000 0.00 0.00 37.14 3.41
3043 5738 3.070576 GCATGGACAACCTGGGCC 61.071 66.667 0.00 0.00 37.04 5.80
3145 7837 8.394877 TGCCTTTTGTGTAGAAACATAATATCG 58.605 33.333 0.00 0.00 36.70 2.92
3180 7872 1.000274 CAGTTTACCTTGGCACCTTGC 60.000 52.381 0.00 0.00 44.08 4.01
3181 7873 2.582052 TCAGTTTACCTTGGCACCTTG 58.418 47.619 0.00 0.00 0.00 3.61
3182 7874 3.117663 TCTTCAGTTTACCTTGGCACCTT 60.118 43.478 0.00 0.00 0.00 3.50
3183 7875 2.441750 TCTTCAGTTTACCTTGGCACCT 59.558 45.455 0.00 0.00 0.00 4.00
3184 7876 2.552743 GTCTTCAGTTTACCTTGGCACC 59.447 50.000 0.00 0.00 0.00 5.01
3185 7877 3.003378 GTGTCTTCAGTTTACCTTGGCAC 59.997 47.826 0.00 0.00 0.00 5.01
3186 7878 3.211045 GTGTCTTCAGTTTACCTTGGCA 58.789 45.455 0.00 0.00 0.00 4.92
3187 7879 2.223377 CGTGTCTTCAGTTTACCTTGGC 59.777 50.000 0.00 0.00 0.00 4.52
3188 7880 3.724374 TCGTGTCTTCAGTTTACCTTGG 58.276 45.455 0.00 0.00 0.00 3.61
3189 7881 4.988540 TGATCGTGTCTTCAGTTTACCTTG 59.011 41.667 0.00 0.00 0.00 3.61
3208 7905 5.154222 CGGTAAAGTTCCTTTTGCTTGATC 58.846 41.667 0.00 0.00 35.21 2.92
3211 7908 4.301637 ACGGTAAAGTTCCTTTTGCTTG 57.698 40.909 0.00 0.00 35.21 4.01


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

AutoCloner maintained by Alex Coulton.