Multiple sequence alignment - TraesCS3D01G312100

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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 TraesCS3D01G312100 chr3D 100.000 3260 0 0 1 3260 426842847 426846106 0.000000e+00 6021
1 TraesCS3D01G312100 chr3D 84.706 340 41 7 144 478 814010 813677 2.420000e-86 329
2 TraesCS3D01G312100 chr3A 89.820 2947 128 68 357 3260 561121845 561119028 0.000000e+00 3622
3 TraesCS3D01G312100 chr3A 84.474 380 51 5 130 504 627696512 627696136 5.140000e-98 368
4 TraesCS3D01G312100 chr3A 91.506 259 19 2 1 256 561122184 561121926 1.440000e-93 353
5 TraesCS3D01G312100 chr3A 84.308 325 43 6 505 822 424721928 424722251 8.780000e-81 311
6 TraesCS3D01G312100 chr3B 92.029 690 38 8 928 1612 556486255 556486932 0.000000e+00 953
7 TraesCS3D01G312100 chr3B 91.392 697 30 7 2569 3257 556487727 556488401 0.000000e+00 928
8 TraesCS3D01G312100 chr3B 91.207 671 42 9 1763 2420 556487016 556487682 0.000000e+00 896
9 TraesCS3D01G312100 chr3B 83.056 360 43 9 134 480 43196372 43196726 8.780000e-81 311
10 TraesCS3D01G312100 chr3B 93.333 75 3 2 839 912 556434188 556434261 3.440000e-20 110
11 TraesCS3D01G312100 chr2D 90.136 294 24 5 505 796 6845911 6846201 8.540000e-101 377
12 TraesCS3D01G312100 chr6D 85.057 348 42 6 135 478 446120233 446119892 2.410000e-91 346
13 TraesCS3D01G312100 chr6D 86.713 143 18 1 362 504 327617833 327617692 1.210000e-34 158
14 TraesCS3D01G312100 chr4D 85.000 340 43 4 143 478 386532522 386532187 4.030000e-89 339
15 TraesCS3D01G312100 chr4D 84.084 333 42 9 505 828 386532119 386531789 8.780000e-81 311
16 TraesCS3D01G312100 chr4A 88.014 292 24 5 503 787 601021861 601021574 5.210000e-88 335
17 TraesCS3D01G312100 chr4A 83.473 357 49 6 128 480 170812967 170812617 1.130000e-84 324
18 TraesCS3D01G312100 chr6A 84.104 346 46 7 505 842 187969934 187969590 3.140000e-85 326
19 TraesCS3D01G312100 chr6A 84.615 325 42 6 505 822 415101095 415101418 1.890000e-82 316
20 TraesCS3D01G312100 chr6B 79.317 498 72 19 19 504 491608263 491607785 1.460000e-83 320
21 TraesCS3D01G312100 chr6B 82.682 358 45 8 136 480 420831780 420832133 5.290000e-78 302
22 TraesCS3D01G312100 chr5B 83.333 360 47 9 128 480 263784661 263784308 1.460000e-83 320
23 TraesCS3D01G312100 chr5B 83.483 333 44 7 505 828 263784256 263783926 1.900000e-77 300
24 TraesCS3D01G312100 chrUn 82.883 333 45 6 503 828 24454752 24454425 4.120000e-74 289
25 TraesCS3D01G312100 chrUn 86.275 102 14 0 22 123 24455242 24455141 9.560000e-21 111
26 TraesCS3D01G312100 chr7A 79.758 331 40 12 505 828 83365817 83366127 7.080000e-52 215
27 TraesCS3D01G312100 chr1D 77.249 189 38 5 23 207 310813037 310813224 4.450000e-19 106


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 TraesCS3D01G312100 chr3D 426842847 426846106 3259 False 6021.000000 6021 100.000000 1 3260 1 chr3D.!!$F1 3259
1 TraesCS3D01G312100 chr3A 561119028 561122184 3156 True 1987.500000 3622 90.663000 1 3260 2 chr3A.!!$R2 3259
2 TraesCS3D01G312100 chr3B 556486255 556488401 2146 False 925.666667 953 91.542667 928 3257 3 chr3B.!!$F3 2329
3 TraesCS3D01G312100 chr4D 386531789 386532522 733 True 325.000000 339 84.542000 143 828 2 chr4D.!!$R1 685
4 TraesCS3D01G312100 chr5B 263783926 263784661 735 True 310.000000 320 83.408000 128 828 2 chr5B.!!$R1 700

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
265 271 0.037590 TCATTGTGTACAGTGGGGCC 59.962 55.0 0.0 0.0 34.77 5.80 F
1429 1572 0.106318 AGCATCAGGGGAGCCAATTC 60.106 55.0 0.0 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1741 0.035056 CTGGTCTGGCCTAGGTTTGG 60.035 60.0 11.31 0.00 38.35 3.28 R
2918 3108 0.107508 CATGCTGAGTGGTACCCCAG 60.108 60.0 10.07 14.52 42.94 4.45 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
107 108 7.177568 TGACTAGATAGGATAGTTTGATGCTCC 59.822 40.741 0.00 0.00 33.64 4.70
154 157 7.803659 CCTAGCTTTCGTTCCTTTTTAAAGAAG 59.196 37.037 0.00 0.56 38.28 2.85
182 186 8.312896 ACTACTAGCTAGCTTTTGTTCTTTTC 57.687 34.615 24.88 0.00 0.00 2.29
255 261 9.665719 AAACATATGTCTACATGTCATTGTGTA 57.334 29.630 9.23 0.00 37.15 2.90
256 262 8.648557 ACATATGTCTACATGTCATTGTGTAC 57.351 34.615 0.00 0.00 37.15 2.90
257 263 8.257306 ACATATGTCTACATGTCATTGTGTACA 58.743 33.333 0.00 0.00 37.15 2.90
258 264 8.758715 CATATGTCTACATGTCATTGTGTACAG 58.241 37.037 0.00 0.00 37.15 2.74
259 265 6.096673 TGTCTACATGTCATTGTGTACAGT 57.903 37.500 0.00 0.00 0.00 3.55
260 266 5.925969 TGTCTACATGTCATTGTGTACAGTG 59.074 40.000 0.00 1.53 35.25 3.66
261 267 5.348724 GTCTACATGTCATTGTGTACAGTGG 59.651 44.000 0.00 0.00 34.77 4.00
262 268 3.411446 ACATGTCATTGTGTACAGTGGG 58.589 45.455 0.00 0.00 34.77 4.61
263 269 2.559698 TGTCATTGTGTACAGTGGGG 57.440 50.000 0.00 0.00 34.77 4.96
264 270 1.165270 GTCATTGTGTACAGTGGGGC 58.835 55.000 0.00 0.00 34.77 5.80
265 271 0.037590 TCATTGTGTACAGTGGGGCC 59.962 55.000 0.00 0.00 34.77 5.80
266 272 1.002624 ATTGTGTACAGTGGGGCCG 60.003 57.895 0.00 0.00 0.00 6.13
267 273 3.835790 TTGTGTACAGTGGGGCCGC 62.836 63.158 14.01 14.01 0.00 6.53
281 287 4.557605 CCGCCGCCATTGCATGTC 62.558 66.667 0.00 0.00 37.32 3.06
282 288 3.813143 CGCCGCCATTGCATGTCA 61.813 61.111 0.00 0.00 37.32 3.58
283 289 2.572812 GCCGCCATTGCATGTCAA 59.427 55.556 5.27 5.27 39.32 3.18
284 290 1.806758 GCCGCCATTGCATGTCAAC 60.807 57.895 4.96 0.00 37.53 3.18
285 291 1.514657 CCGCCATTGCATGTCAACG 60.515 57.895 4.96 5.09 37.53 4.10
286 292 2.153945 CGCCATTGCATGTCAACGC 61.154 57.895 4.96 8.45 37.53 4.84
287 293 1.213537 GCCATTGCATGTCAACGCT 59.786 52.632 4.96 0.00 37.53 5.07
288 294 0.799534 GCCATTGCATGTCAACGCTC 60.800 55.000 4.96 0.00 37.53 5.03
289 295 0.522626 CCATTGCATGTCAACGCTCA 59.477 50.000 4.96 0.00 37.53 4.26
290 296 1.133598 CCATTGCATGTCAACGCTCAT 59.866 47.619 4.96 0.00 37.53 2.90
291 297 2.447250 CATTGCATGTCAACGCTCATC 58.553 47.619 4.96 0.00 37.53 2.92
292 298 1.521580 TTGCATGTCAACGCTCATCA 58.478 45.000 0.00 0.00 0.00 3.07
334 381 2.684881 GGCTACAAATGACATGGACTGG 59.315 50.000 0.00 0.00 0.00 4.00
349 396 2.553028 GGACTGGAAAGGAGCAATGTCA 60.553 50.000 0.00 0.00 0.00 3.58
355 421 4.012374 GGAAAGGAGCAATGTCAGATTCA 58.988 43.478 0.00 0.00 0.00 2.57
379 445 0.978146 GCAAGGGAGCTAGGGTCTGA 60.978 60.000 0.00 0.00 0.00 3.27
396 462 2.892334 GAAGTTTGCACGAGCCGCA 61.892 57.895 1.39 0.00 41.13 5.69
489 574 1.787012 CATGTTTTGCTTGCTCCCAC 58.213 50.000 0.00 0.00 0.00 4.61
490 575 0.681175 ATGTTTTGCTTGCTCCCACC 59.319 50.000 0.00 0.00 0.00 4.61
491 576 1.007387 GTTTTGCTTGCTCCCACCG 60.007 57.895 0.00 0.00 0.00 4.94
494 579 0.179015 TTTGCTTGCTCCCACCGTTA 60.179 50.000 0.00 0.00 0.00 3.18
495 580 0.887387 TTGCTTGCTCCCACCGTTAC 60.887 55.000 0.00 0.00 0.00 2.50
497 582 1.019805 GCTTGCTCCCACCGTTACTC 61.020 60.000 0.00 0.00 0.00 2.59
498 583 0.391263 CTTGCTCCCACCGTTACTCC 60.391 60.000 0.00 0.00 0.00 3.85
499 584 1.122632 TTGCTCCCACCGTTACTCCA 61.123 55.000 0.00 0.00 0.00 3.86
500 585 1.218316 GCTCCCACCGTTACTCCAG 59.782 63.158 0.00 0.00 0.00 3.86
501 586 1.255667 GCTCCCACCGTTACTCCAGA 61.256 60.000 0.00 0.00 0.00 3.86
503 629 1.831736 CTCCCACCGTTACTCCAGATT 59.168 52.381 0.00 0.00 0.00 2.40
626 752 2.093447 ACTCGGGACCAAATCTCATGTC 60.093 50.000 0.00 0.00 0.00 3.06
659 786 4.286813 TCCTGAGAAATCCTACCCTCAT 57.713 45.455 0.00 0.00 35.42 2.90
670 797 9.354673 GAAATCCTACCCTCATTTGATTCATTA 57.645 33.333 0.00 0.00 0.00 1.90
674 801 7.944554 TCCTACCCTCATTTGATTCATTATTCC 59.055 37.037 0.00 0.00 0.00 3.01
859 996 8.414778 ACAGGTATAAATCTAAGTTCTTCTCCG 58.585 37.037 0.00 0.00 0.00 4.63
888 1025 9.221775 GAAATTATAAATCAAGTAGCACAACCG 57.778 33.333 0.00 0.00 0.00 4.44
892 1029 5.545658 AAATCAAGTAGCACAACCGTATG 57.454 39.130 0.00 0.00 0.00 2.39
914 1051 0.736053 AGAAAAACAACGCCGCAGAA 59.264 45.000 0.00 0.00 0.00 3.02
915 1052 1.133407 AGAAAAACAACGCCGCAGAAA 59.867 42.857 0.00 0.00 0.00 2.52
929 1066 1.664302 GCAGAAAGTCTCAAAAGGCGC 60.664 52.381 0.00 0.00 30.24 6.53
1401 1544 1.542472 TGAAGCGTGATGTCGGAGTTA 59.458 47.619 0.00 0.00 0.00 2.24
1429 1572 0.106318 AGCATCAGGGGAGCCAATTC 60.106 55.000 0.00 0.00 0.00 2.17
1433 1576 2.999185 TCAGGGGAGCCAATTCTTTT 57.001 45.000 0.00 0.00 0.00 2.27
1434 1577 4.280819 CATCAGGGGAGCCAATTCTTTTA 58.719 43.478 0.00 0.00 0.00 1.52
1435 1578 3.697166 TCAGGGGAGCCAATTCTTTTAC 58.303 45.455 0.00 0.00 0.00 2.01
1436 1579 3.333680 TCAGGGGAGCCAATTCTTTTACT 59.666 43.478 0.00 0.00 0.00 2.24
1437 1580 4.538490 TCAGGGGAGCCAATTCTTTTACTA 59.462 41.667 0.00 0.00 0.00 1.82
1438 1581 4.884164 CAGGGGAGCCAATTCTTTTACTAG 59.116 45.833 0.00 0.00 0.00 2.57
1439 1582 4.788617 AGGGGAGCCAATTCTTTTACTAGA 59.211 41.667 0.00 0.00 0.00 2.43
1441 1584 6.619852 AGGGGAGCCAATTCTTTTACTAGATA 59.380 38.462 0.00 0.00 0.00 1.98
1442 1585 6.711194 GGGGAGCCAATTCTTTTACTAGATAC 59.289 42.308 0.00 0.00 0.00 2.24
1451 1594 5.607477 TCTTTTACTAGATACGGCCAATGG 58.393 41.667 2.24 0.00 0.00 3.16
1482 1625 2.898729 ACATCTAGCAAGATCCGGTG 57.101 50.000 0.00 0.00 40.65 4.94
1554 1697 5.404366 CAGATGGATTTGTTGAAGTGCAAAG 59.596 40.000 0.00 0.00 38.44 2.77
1558 1701 3.591196 TTTGTTGAAGTGCAAAGCAGT 57.409 38.095 0.00 0.00 44.78 4.40
1582 1725 0.377905 TGATGGTGAATGCGCGAATG 59.622 50.000 12.10 0.00 0.00 2.67
1583 1726 0.317269 GATGGTGAATGCGCGAATGG 60.317 55.000 12.10 0.00 0.00 3.16
1587 1730 2.278142 GAATGCGCGAATGGCACC 60.278 61.111 12.10 0.00 44.23 5.01
1603 1746 2.619013 CACCGATGCTTCTTCCAAAC 57.381 50.000 0.00 0.00 0.00 2.93
1604 1747 1.200020 CACCGATGCTTCTTCCAAACC 59.800 52.381 0.00 0.00 0.00 3.27
1605 1748 1.073923 ACCGATGCTTCTTCCAAACCT 59.926 47.619 0.00 0.00 0.00 3.50
1610 1753 1.271926 TGCTTCTTCCAAACCTAGGCC 60.272 52.381 9.30 0.00 0.00 5.19
1701 1844 1.895131 ACATGTGAAACCCAATCTGGC 59.105 47.619 0.00 0.00 35.79 4.85
1772 1915 9.920946 ACCCAAGCATTCTAGATTTTCTTAATA 57.079 29.630 0.00 0.00 0.00 0.98
1828 1971 9.241317 CAAAGTTGGATTGACTATTTGATATGC 57.759 33.333 0.00 0.00 0.00 3.14
1840 1983 8.859236 ACTATTTGATATGCTGTGCTTCATAT 57.141 30.769 0.00 0.00 38.27 1.78
1841 1984 9.948964 ACTATTTGATATGCTGTGCTTCATATA 57.051 29.630 0.00 0.00 36.38 0.86
1868 2011 8.523464 GCAGTAACAATAACTGATTAAAATGCG 58.477 33.333 7.39 0.00 45.89 4.73
1959 2102 5.362430 ACCCAATAGACTCTGTTGATCTCTC 59.638 44.000 15.24 0.00 35.14 3.20
2148 2303 2.353704 CGTAGTTCAATCAGACCCAGCA 60.354 50.000 0.00 0.00 0.00 4.41
2169 2324 4.024556 GCAGATGCGAGTAACAATATTGCT 60.025 41.667 15.48 5.96 0.00 3.91
2211 2366 2.818130 GCTCCAGAATAGCTCCAGAG 57.182 55.000 0.00 0.00 37.01 3.35
2339 2494 6.295180 GGGTCTTTAGCTGTCTAACTGTAACT 60.295 42.308 0.00 0.00 34.71 2.24
2343 2500 7.447545 TCTTTAGCTGTCTAACTGTAACTGAGA 59.552 37.037 0.00 0.00 34.71 3.27
2344 2501 5.637006 AGCTGTCTAACTGTAACTGAGAG 57.363 43.478 0.00 0.00 0.00 3.20
2345 2502 4.461081 AGCTGTCTAACTGTAACTGAGAGG 59.539 45.833 0.00 0.00 0.00 3.69
2346 2503 4.381079 GCTGTCTAACTGTAACTGAGAGGG 60.381 50.000 0.00 0.00 0.00 4.30
2381 2538 1.745115 GATGTTGCGCTGTAGGCCA 60.745 57.895 9.73 0.00 37.74 5.36
2445 2602 3.489180 AGCAGTGTCGTACTATGTGAC 57.511 47.619 0.00 0.00 37.60 3.67
2524 2681 8.789825 TTTGTACTAGAAACAAAGTGGTGTAA 57.210 30.769 18.08 1.24 40.83 2.41
2551 2716 6.538945 AAAAGAAAGCAACTCCTGGTTAAA 57.461 33.333 0.00 0.00 45.00 1.52
2553 2718 4.793201 AGAAAGCAACTCCTGGTTAAACT 58.207 39.130 0.00 0.00 45.00 2.66
2554 2719 5.201243 AGAAAGCAACTCCTGGTTAAACTT 58.799 37.500 0.00 0.00 45.00 2.66
2555 2720 5.656859 AGAAAGCAACTCCTGGTTAAACTTT 59.343 36.000 0.00 0.30 45.00 2.66
2556 2721 5.515797 AAGCAACTCCTGGTTAAACTTTC 57.484 39.130 0.00 0.00 43.93 2.62
2558 2723 4.580580 AGCAACTCCTGGTTAAACTTTCTG 59.419 41.667 0.00 0.00 36.23 3.02
2559 2724 4.338400 GCAACTCCTGGTTAAACTTTCTGT 59.662 41.667 0.00 0.00 36.23 3.41
2560 2725 5.529800 GCAACTCCTGGTTAAACTTTCTGTA 59.470 40.000 0.00 0.00 36.23 2.74
2561 2726 6.038936 GCAACTCCTGGTTAAACTTTCTGTAA 59.961 38.462 0.00 0.00 36.23 2.41
2563 2728 7.745620 ACTCCTGGTTAAACTTTCTGTAATG 57.254 36.000 0.00 0.00 0.00 1.90
2564 2729 7.287810 ACTCCTGGTTAAACTTTCTGTAATGT 58.712 34.615 0.00 0.00 0.00 2.71
2566 2731 7.936584 TCCTGGTTAAACTTTCTGTAATGTTG 58.063 34.615 0.00 0.00 34.29 3.33
2759 2949 1.547372 GCCAGCATTTCACTGAATGGT 59.453 47.619 9.79 5.86 45.63 3.55
2918 3108 0.525311 GCAGCTTCTTGCCTTCCTTC 59.475 55.000 0.00 0.00 44.23 3.46
3003 3193 3.476552 GAGAATCCCAAGTGTCACAACA 58.523 45.455 5.62 0.00 0.00 3.33
3004 3194 3.480470 AGAATCCCAAGTGTCACAACAG 58.520 45.455 5.62 0.00 35.64 3.16
3005 3195 2.276732 ATCCCAAGTGTCACAACAGG 57.723 50.000 5.62 0.56 35.64 4.00
3006 3196 0.916086 TCCCAAGTGTCACAACAGGT 59.084 50.000 5.62 0.00 35.64 4.00
3007 3197 1.134220 TCCCAAGTGTCACAACAGGTC 60.134 52.381 5.62 0.00 35.64 3.85
3008 3198 1.408127 CCCAAGTGTCACAACAGGTCA 60.408 52.381 5.62 0.00 35.64 4.02
3009 3199 1.670811 CCAAGTGTCACAACAGGTCAC 59.329 52.381 5.62 0.00 35.64 3.67
3010 3200 1.670811 CAAGTGTCACAACAGGTCACC 59.329 52.381 5.62 0.00 35.64 4.02
3011 3201 0.180406 AGTGTCACAACAGGTCACCC 59.820 55.000 5.62 0.00 35.64 4.61
3012 3202 0.180406 GTGTCACAACAGGTCACCCT 59.820 55.000 0.00 0.00 44.02 4.34
3013 3203 0.468226 TGTCACAACAGGTCACCCTC 59.532 55.000 0.00 0.00 39.89 4.30
3014 3204 0.250338 GTCACAACAGGTCACCCTCC 60.250 60.000 0.00 0.00 39.89 4.30
3015 3205 0.692756 TCACAACAGGTCACCCTCCA 60.693 55.000 0.00 0.00 39.89 3.86
3016 3206 0.182537 CACAACAGGTCACCCTCCAA 59.817 55.000 0.00 0.00 39.89 3.53
3087 3277 6.358178 TGTCACAACAGGTTAAATACAAGGA 58.642 36.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 3.281727 TGTGGGAGCATCAAACTATCC 57.718 47.619 0.00 0.00 36.25 2.59
99 100 8.805175 CCAATAATATATTTTGTGGGAGCATCA 58.195 33.333 2.68 0.00 36.25 3.07
107 108 8.028938 GCTAGGCACCAATAATATATTTTGTGG 58.971 37.037 2.68 10.84 0.00 4.17
154 157 7.892778 AGAACAAAAGCTAGCTAGTAGTTTC 57.107 36.000 19.70 15.00 31.35 2.78
182 186 7.674471 AAGCTAGCTAGTAGTTTTTCTTTGG 57.326 36.000 19.70 0.00 28.19 3.28
248 254 1.002624 CGGCCCCACTGTACACAAT 60.003 57.895 0.00 0.00 0.00 2.71
264 270 4.557605 GACATGCAATGGCGGCGG 62.558 66.667 9.78 0.00 46.24 6.13
272 278 2.086094 TGATGAGCGTTGACATGCAAT 58.914 42.857 0.00 0.00 39.03 3.56
273 279 1.521580 TGATGAGCGTTGACATGCAA 58.478 45.000 0.00 0.00 37.39 4.08
274 280 1.521580 TTGATGAGCGTTGACATGCA 58.478 45.000 0.00 0.00 37.39 3.96
275 281 2.159476 ACATTGATGAGCGTTGACATGC 60.159 45.455 0.00 0.00 34.79 4.06
276 282 3.125658 TCACATTGATGAGCGTTGACATG 59.874 43.478 0.00 0.00 0.00 3.21
277 283 3.337358 TCACATTGATGAGCGTTGACAT 58.663 40.909 0.00 0.00 0.00 3.06
278 284 2.765122 TCACATTGATGAGCGTTGACA 58.235 42.857 0.00 0.00 0.00 3.58
279 285 3.740590 CTTCACATTGATGAGCGTTGAC 58.259 45.455 0.00 0.00 0.00 3.18
280 286 2.160219 GCTTCACATTGATGAGCGTTGA 59.840 45.455 0.00 0.00 0.00 3.18
281 287 2.095617 TGCTTCACATTGATGAGCGTTG 60.096 45.455 0.00 0.00 0.00 4.10
282 288 2.153645 TGCTTCACATTGATGAGCGTT 58.846 42.857 0.00 0.00 0.00 4.84
283 289 1.736126 CTGCTTCACATTGATGAGCGT 59.264 47.619 0.00 0.00 0.00 5.07
284 290 1.736126 ACTGCTTCACATTGATGAGCG 59.264 47.619 0.00 0.00 0.00 5.03
285 291 3.189910 TCAACTGCTTCACATTGATGAGC 59.810 43.478 0.00 0.00 0.00 4.26
286 292 5.332707 CATCAACTGCTTCACATTGATGAG 58.667 41.667 16.98 0.00 45.31 2.90
287 293 4.157105 CCATCAACTGCTTCACATTGATGA 59.843 41.667 21.50 0.00 45.31 2.92
288 294 4.082408 ACCATCAACTGCTTCACATTGATG 60.082 41.667 15.58 15.58 44.02 3.07
289 295 4.084287 ACCATCAACTGCTTCACATTGAT 58.916 39.130 0.00 0.00 37.17 2.57
290 296 3.489355 ACCATCAACTGCTTCACATTGA 58.511 40.909 0.00 0.00 33.38 2.57
291 297 3.668757 CGACCATCAACTGCTTCACATTG 60.669 47.826 0.00 0.00 0.00 2.82
292 298 2.485426 CGACCATCAACTGCTTCACATT 59.515 45.455 0.00 0.00 0.00 2.71
334 381 4.096081 CCTGAATCTGACATTGCTCCTTTC 59.904 45.833 0.00 0.00 0.00 2.62
349 396 1.230281 TCCCTTGCCCCCTGAATCT 60.230 57.895 0.00 0.00 0.00 2.40
355 421 2.367512 CTAGCTCCCTTGCCCCCT 60.368 66.667 0.00 0.00 0.00 4.79
379 445 2.899838 TGCGGCTCGTGCAAACTT 60.900 55.556 12.07 0.00 39.87 2.66
396 462 0.249120 TCCAATCGCCGTCTGATGTT 59.751 50.000 0.00 0.00 0.00 2.71
480 565 1.122632 TGGAGTAACGGTGGGAGCAA 61.123 55.000 0.00 0.00 0.00 3.91
481 566 1.534476 TGGAGTAACGGTGGGAGCA 60.534 57.895 0.00 0.00 0.00 4.26
482 567 1.218316 CTGGAGTAACGGTGGGAGC 59.782 63.158 0.00 0.00 0.00 4.70
483 568 1.486211 ATCTGGAGTAACGGTGGGAG 58.514 55.000 0.00 0.00 0.00 4.30
485 570 2.781681 AAATCTGGAGTAACGGTGGG 57.218 50.000 0.00 0.00 0.00 4.61
486 571 6.753107 ATTTAAAATCTGGAGTAACGGTGG 57.247 37.500 0.00 0.00 0.00 4.61
487 572 9.769093 CTAAATTTAAAATCTGGAGTAACGGTG 57.231 33.333 0.00 0.00 0.00 4.94
488 573 8.456471 GCTAAATTTAAAATCTGGAGTAACGGT 58.544 33.333 0.00 0.00 0.00 4.83
489 574 8.674607 AGCTAAATTTAAAATCTGGAGTAACGG 58.325 33.333 0.00 0.00 0.00 4.44
490 575 9.704098 GAGCTAAATTTAAAATCTGGAGTAACG 57.296 33.333 0.00 0.00 0.00 3.18
494 579 9.466497 TCATGAGCTAAATTTAAAATCTGGAGT 57.534 29.630 0.00 0.00 0.00 3.85
495 580 9.727627 GTCATGAGCTAAATTTAAAATCTGGAG 57.272 33.333 0.00 0.00 0.00 3.86
597 723 3.396260 TTTGGTCCCGAGTCAACTTAG 57.604 47.619 0.00 0.00 0.00 2.18
626 752 6.602406 AGGATTTCTCAGGATGTCAATTTGAG 59.398 38.462 0.00 5.08 37.40 3.02
659 786 9.421806 GAACAACATGTGGAATAATGAATCAAA 57.578 29.630 7.39 0.00 0.00 2.69
670 797 6.260493 CCAAAACAATGAACAACATGTGGAAT 59.740 34.615 7.39 0.00 39.39 3.01
674 801 6.659361 TTCCAAAACAATGAACAACATGTG 57.341 33.333 0.00 0.00 39.39 3.21
724 854 5.277974 CCATGCCCTCTATTTTAACATCACG 60.278 44.000 0.00 0.00 0.00 4.35
888 1025 3.223157 CGGCGTTGTTTTTCTGACATAC 58.777 45.455 0.00 0.00 0.00 2.39
892 1029 0.248296 TGCGGCGTTGTTTTTCTGAC 60.248 50.000 9.37 0.00 0.00 3.51
914 1051 0.890996 CTGGGCGCCTTTTGAGACTT 60.891 55.000 28.56 0.00 0.00 3.01
915 1052 1.302832 CTGGGCGCCTTTTGAGACT 60.303 57.895 28.56 0.00 0.00 3.24
929 1066 0.104671 CAGTTGGTTTTGTGGCTGGG 59.895 55.000 0.00 0.00 0.00 4.45
1401 1544 0.549950 CCCCTGATGCTGAATCCAGT 59.450 55.000 0.00 0.00 42.35 4.00
1429 1572 5.365619 ACCATTGGCCGTATCTAGTAAAAG 58.634 41.667 1.54 0.00 0.00 2.27
1433 1576 5.142639 AGTTACCATTGGCCGTATCTAGTA 58.857 41.667 1.54 0.00 0.00 1.82
1434 1577 3.965347 AGTTACCATTGGCCGTATCTAGT 59.035 43.478 1.54 0.00 0.00 2.57
1435 1578 4.602340 AGTTACCATTGGCCGTATCTAG 57.398 45.455 1.54 0.00 0.00 2.43
1436 1579 4.699637 CAAGTTACCATTGGCCGTATCTA 58.300 43.478 1.54 0.00 0.00 1.98
1437 1580 3.541632 CAAGTTACCATTGGCCGTATCT 58.458 45.455 1.54 0.00 0.00 1.98
1438 1581 2.032924 GCAAGTTACCATTGGCCGTATC 59.967 50.000 1.54 0.00 0.00 2.24
1439 1582 2.021457 GCAAGTTACCATTGGCCGTAT 58.979 47.619 1.54 0.00 0.00 3.06
1441 1584 0.251165 AGCAAGTTACCATTGGCCGT 60.251 50.000 1.54 0.00 0.00 5.68
1442 1585 0.171007 CAGCAAGTTACCATTGGCCG 59.829 55.000 1.54 0.00 0.00 6.13
1505 1648 9.523168 TGTTTTGGCACTATAAGTAATAAACCT 57.477 29.630 0.00 0.00 0.00 3.50
1510 1653 9.337396 CCATCTGTTTTGGCACTATAAGTAATA 57.663 33.333 0.00 0.00 0.00 0.98
1511 1654 8.052748 TCCATCTGTTTTGGCACTATAAGTAAT 58.947 33.333 0.00 0.00 34.06 1.89
1518 1661 5.481473 ACAAATCCATCTGTTTTGGCACTAT 59.519 36.000 0.00 0.00 35.23 2.12
1533 1676 4.060205 GCTTTGCACTTCAACAAATCCAT 58.940 39.130 0.00 0.00 35.38 3.41
1554 1697 3.792956 CGCATTCACCATCAAATAACTGC 59.207 43.478 0.00 0.00 0.00 4.40
1558 1701 2.680339 TCGCGCATTCACCATCAAATAA 59.320 40.909 8.75 0.00 0.00 1.40
1587 1730 2.939103 CCTAGGTTTGGAAGAAGCATCG 59.061 50.000 0.00 0.00 0.00 3.84
1598 1741 0.035056 CTGGTCTGGCCTAGGTTTGG 60.035 60.000 11.31 0.00 38.35 3.28
1601 1744 2.301738 GCCTGGTCTGGCCTAGGTT 61.302 63.158 11.31 0.00 46.82 3.50
1602 1745 2.689034 GCCTGGTCTGGCCTAGGT 60.689 66.667 11.31 0.00 46.82 3.08
1701 1844 5.745294 CCAAGTGAATGACAAAAGTGAACAG 59.255 40.000 0.00 0.00 0.00 3.16
1772 1915 7.379098 CTAGATGAGCATGCACATTGATTAT 57.621 36.000 27.78 8.33 0.00 1.28
1841 1984 9.573133 GCATTTTAATCAGTTATTGTTACTGCT 57.427 29.630 0.00 0.00 42.12 4.24
1868 2011 6.803807 GTCTGTATTCAATTTTGCAAGTCCTC 59.196 38.462 0.00 0.00 0.00 3.71
1959 2102 7.927048 TCATATGAATTGAGCAACAATCTCAG 58.073 34.615 1.98 5.58 46.90 3.35
2148 2303 6.422100 CACTAGCAATATTGTTACTCGCATCT 59.578 38.462 16.61 4.13 0.00 2.90
2169 2324 1.410083 GGGATGGCCAAAGCATCACTA 60.410 52.381 10.96 0.00 42.56 2.74
2211 2366 4.520846 CGCGCTTTGTGGATCGCC 62.521 66.667 5.56 0.00 44.12 5.54
2339 2494 3.264706 CGAGATAGGAGATACCCCTCTCA 59.735 52.174 0.00 0.00 42.90 3.27
2343 2500 2.987437 TCACGAGATAGGAGATACCCCT 59.013 50.000 0.00 0.00 40.05 4.79
2344 2501 3.436577 TCACGAGATAGGAGATACCCC 57.563 52.381 0.00 0.00 40.05 4.95
2345 2502 4.337145 ACATCACGAGATAGGAGATACCC 58.663 47.826 0.00 0.00 33.53 3.69
2346 2503 5.704888 CAACATCACGAGATAGGAGATACC 58.295 45.833 0.00 0.00 33.34 2.73
2381 2538 6.882610 TGATGAAGACAAGCAATTAGTTGT 57.117 33.333 4.64 4.64 39.62 3.32
2501 2658 6.480981 GCTTACACCACTTTGTTTCTAGTACA 59.519 38.462 0.00 0.00 0.00 2.90
2519 2676 5.232202 GGAGTTGCTTTCTTTTTGCTTACAC 59.768 40.000 0.00 0.00 0.00 2.90
2524 2681 3.181472 CCAGGAGTTGCTTTCTTTTTGCT 60.181 43.478 0.00 0.00 0.00 3.91
2555 2720 9.699703 GCCCTTTAAATTTTACAACATTACAGA 57.300 29.630 0.00 0.00 0.00 3.41
2556 2721 9.482627 TGCCCTTTAAATTTTACAACATTACAG 57.517 29.630 0.00 0.00 0.00 2.74
2558 2723 9.262358 TGTGCCCTTTAAATTTTACAACATTAC 57.738 29.630 0.00 0.00 0.00 1.89
2560 2725 8.916628 ATGTGCCCTTTAAATTTTACAACATT 57.083 26.923 0.00 0.00 0.00 2.71
2561 2726 8.153550 TGATGTGCCCTTTAAATTTTACAACAT 58.846 29.630 0.00 0.00 0.00 2.71
2563 2728 7.954788 TGATGTGCCCTTTAAATTTTACAAC 57.045 32.000 0.00 0.00 0.00 3.32
2564 2729 8.592809 AGATGATGTGCCCTTTAAATTTTACAA 58.407 29.630 0.00 0.00 0.00 2.41
2566 2731 8.034804 ACAGATGATGTGCCCTTTAAATTTTAC 58.965 33.333 0.00 0.00 41.91 2.01
2759 2949 4.574674 ACTATCACCAAGATGAGGCAAA 57.425 40.909 0.00 0.00 37.57 3.68
2900 3090 1.811359 CAGAAGGAAGGCAAGAAGCTG 59.189 52.381 0.00 0.00 44.79 4.24
2918 3108 0.107508 CATGCTGAGTGGTACCCCAG 60.108 60.000 10.07 14.52 42.94 4.45
3005 3195 2.554032 CACACAGATTTTGGAGGGTGAC 59.446 50.000 0.00 0.00 0.00 3.67
3006 3196 2.862541 CACACAGATTTTGGAGGGTGA 58.137 47.619 0.00 0.00 0.00 4.02
3007 3197 1.270550 GCACACAGATTTTGGAGGGTG 59.729 52.381 0.00 0.00 0.00 4.61
3008 3198 1.145738 AGCACACAGATTTTGGAGGGT 59.854 47.619 0.00 0.00 0.00 4.34
3009 3199 1.542915 CAGCACACAGATTTTGGAGGG 59.457 52.381 0.00 0.00 0.00 4.30
3010 3200 1.542915 CCAGCACACAGATTTTGGAGG 59.457 52.381 0.00 0.00 0.00 4.30
3011 3201 2.233271 ACCAGCACACAGATTTTGGAG 58.767 47.619 0.00 0.00 0.00 3.86
3012 3202 2.363306 ACCAGCACACAGATTTTGGA 57.637 45.000 0.00 0.00 0.00 3.53
3013 3203 3.820467 TCTTACCAGCACACAGATTTTGG 59.180 43.478 0.00 0.00 0.00 3.28
3014 3204 5.633830 ATCTTACCAGCACACAGATTTTG 57.366 39.130 0.00 0.00 0.00 2.44
3015 3205 7.573096 CGTTTATCTTACCAGCACACAGATTTT 60.573 37.037 0.00 0.00 0.00 1.82
3016 3206 6.128282 CGTTTATCTTACCAGCACACAGATTT 60.128 38.462 0.00 0.00 0.00 2.17
3057 3247 2.071778 AACCTGTTGTGACATTGGCT 57.928 45.000 0.00 0.00 34.72 4.75
3087 3277 6.879993 TCAACAAATGATGCATTTTGGCTATT 59.120 30.769 21.88 9.14 40.60 1.73


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

AutoCloner maintained by Alex Coulton.