Multiple sequence alignment - TraesCS2A01G311000

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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 TraesCS2A01G311000 chr2A 100.000 3587 0 0 1 3587 534622808 534626394 0.000000e+00 6625
1 TraesCS2A01G311000 chr2D 90.340 2909 106 40 657 3449 396660097 396662946 0.000000e+00 3653
2 TraesCS2A01G311000 chr2D 89.074 659 39 18 3 650 396651684 396652320 0.000000e+00 787
3 TraesCS2A01G311000 chr2B 87.712 1530 93 42 692 2168 470057412 470058899 0.000000e+00 1696
4 TraesCS2A01G311000 chr2B 95.015 682 26 4 2914 3587 470059683 470060364 0.000000e+00 1064
5 TraesCS2A01G311000 chr2B 87.811 763 48 15 2188 2932 470058893 470059628 0.000000e+00 852
6 TraesCS2A01G311000 chr2B 83.713 307 20 13 3 293 470031353 470031645 2.750000e-66 263
7 TraesCS2A01G311000 chr2B 89.796 196 12 5 436 630 470031701 470031889 9.950000e-61 244
8 TraesCS2A01G311000 chr6B 100.000 40 0 0 2346 2385 353181440 353181479 1.380000e-09 75


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 TraesCS2A01G311000 chr2A 534622808 534626394 3586 False 6625.0 6625 100.000000 1 3587 1 chr2A.!!$F1 3586
1 TraesCS2A01G311000 chr2D 396660097 396662946 2849 False 3653.0 3653 90.340000 657 3449 1 chr2D.!!$F2 2792
2 TraesCS2A01G311000 chr2D 396651684 396652320 636 False 787.0 787 89.074000 3 650 1 chr2D.!!$F1 647
3 TraesCS2A01G311000 chr2B 470057412 470060364 2952 False 1204.0 1696 90.179333 692 3587 3 chr2B.!!$F2 2895
4 TraesCS2A01G311000 chr2B 470031353 470031889 536 False 253.5 263 86.754500 3 630 2 chr2B.!!$F1 627

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
873 922 0.174617 GCCCTAGTGCACTCAGAGTC 59.825 60.0 25.56 5.81 0.0 3.36 F
942 995 0.179070 GGCCAAATCTCTCCGTCTCC 60.179 60.0 0.00 0.00 0.0 3.71 F
1397 1490 0.181114 AGTGCAGCTGTGTTCTTGGA 59.819 50.0 16.64 0.00 0.0 3.53 F
1398 1491 0.590195 GTGCAGCTGTGTTCTTGGAG 59.410 55.0 16.64 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1805 0.161446 GCTTTGCGCAATTGTTTCCG 59.839 50.0 25.64 6.29 38.92 4.30 R
2086 2203 0.465460 TTGGAACTGTGACCTGTGCC 60.465 55.0 6.00 0.00 38.44 5.01 R
2496 2619 2.172082 CAGATTGGATGCCTTCCTCTCA 59.828 50.0 4.59 0.00 45.68 3.27 R
2973 3182 2.426024 GGACGTCTCATAGCCTTGTGTA 59.574 50.0 16.46 0.00 0.00 2.90 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
25 33 5.220835 CGATGCTGAAGTGCAATGGTATAAA 60.221 40.000 0.00 0.00 46.61 1.40
35 43 6.818142 AGTGCAATGGTATAAAAGAATTTGCC 59.182 34.615 0.00 0.00 39.02 4.52
36 44 6.593382 GTGCAATGGTATAAAAGAATTTGCCA 59.407 34.615 0.00 0.00 39.02 4.92
63 73 3.671928 CGAAAGAGGCTGATTTGCAAAAG 59.328 43.478 17.19 11.18 34.04 2.27
72 82 5.289434 GGCTGATTTGCAAAAGTAATGCTAC 59.711 40.000 17.19 0.92 44.14 3.58
73 83 6.095377 GCTGATTTGCAAAAGTAATGCTACT 58.905 36.000 17.19 0.00 44.14 2.57
95 112 4.910746 ATGTGATAACGCGCTTGATATC 57.089 40.909 5.73 7.69 0.00 1.63
96 113 3.057019 TGTGATAACGCGCTTGATATCC 58.943 45.455 5.73 2.82 0.00 2.59
97 114 2.090658 GTGATAACGCGCTTGATATCCG 59.909 50.000 5.73 0.00 0.00 4.18
112 129 4.693566 TGATATCCGTTTGTGTTTCAGGTC 59.306 41.667 0.00 0.00 0.00 3.85
194 211 5.304614 TCCTACTTGTTTCAGCAGTACTCTT 59.695 40.000 0.00 0.00 0.00 2.85
230 247 3.054728 TGTCCCTCAAATCTCGGCAAATA 60.055 43.478 0.00 0.00 0.00 1.40
259 276 4.074970 CACCTGTCAGATAGGCTGTTTTT 58.925 43.478 13.10 0.00 45.14 1.94
296 313 1.063469 GCAAGCGTGTATATTTGCCGT 59.937 47.619 0.59 0.00 39.88 5.68
348 373 8.237267 CAGTGGGTTTTAGAATTCTCAACATAC 58.763 37.037 22.72 19.99 0.00 2.39
350 375 8.237267 GTGGGTTTTAGAATTCTCAACATACAG 58.763 37.037 22.72 0.00 0.00 2.74
351 376 7.942341 TGGGTTTTAGAATTCTCAACATACAGT 59.058 33.333 22.72 0.00 0.00 3.55
352 377 9.444600 GGGTTTTAGAATTCTCAACATACAGTA 57.555 33.333 22.72 0.00 0.00 2.74
363 388 9.996554 TTCTCAACATACAGTATATGGTAATGG 57.003 33.333 0.00 0.00 0.00 3.16
377 402 5.825593 TGGTAATGGTATGGGAAGATCTC 57.174 43.478 0.00 0.00 0.00 2.75
480 513 1.536072 CGCATAGTGAGCTAAAGCGGA 60.536 52.381 13.26 0.00 44.51 5.54
510 545 0.928451 GTTGCGCAACCGAACAAGAC 60.928 55.000 37.19 13.66 35.36 3.01
511 546 1.092921 TTGCGCAACCGAACAAGACT 61.093 50.000 21.02 0.00 36.29 3.24
512 547 1.204312 GCGCAACCGAACAAGACTC 59.796 57.895 0.30 0.00 36.29 3.36
529 564 1.997928 CTCGCGGCACATGAGAGAGA 61.998 60.000 6.13 0.00 34.47 3.10
530 565 1.067084 CGCGGCACATGAGAGAGAT 59.933 57.895 0.00 0.00 0.00 2.75
532 567 0.879400 GCGGCACATGAGAGAGATGG 60.879 60.000 0.00 0.00 0.00 3.51
533 568 0.879400 CGGCACATGAGAGAGATGGC 60.879 60.000 0.00 0.00 0.00 4.40
534 569 0.179702 GGCACATGAGAGAGATGGCA 59.820 55.000 0.00 0.00 35.99 4.92
535 570 1.297664 GCACATGAGAGAGATGGCAC 58.702 55.000 0.00 0.00 0.00 5.01
536 571 1.134461 GCACATGAGAGAGATGGCACT 60.134 52.381 0.00 0.00 0.00 4.40
665 700 9.201989 TCAATATTGATTGTACTAGGTCTGAGT 57.798 33.333 14.23 0.00 42.71 3.41
718 760 5.198207 TGGATGCTTTGTCATCATGAATCT 58.802 37.500 0.00 0.00 43.44 2.40
741 783 2.887151 AGAAATGGGGGAGTCAACTG 57.113 50.000 0.00 0.00 0.00 3.16
828 876 5.163416 GGGGATCGATGATGGAAAAACAAAT 60.163 40.000 0.54 0.00 0.00 2.32
838 886 5.957910 TGGAAAAACAAATAACAAGTGCG 57.042 34.783 0.00 0.00 0.00 5.34
856 904 2.115291 GCCGGGAGATCAGTTTGCC 61.115 63.158 2.18 0.00 0.00 4.52
873 922 0.174617 GCCCTAGTGCACTCAGAGTC 59.825 60.000 25.56 5.81 0.00 3.36
887 936 6.874134 GCACTCAGAGTCATAACCTTTTTCTA 59.126 38.462 0.00 0.00 0.00 2.10
942 995 0.179070 GGCCAAATCTCTCCGTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
966 1019 1.118965 TCCTGCTCCGTTCTTGGTCA 61.119 55.000 0.00 0.00 0.00 4.02
976 1029 3.437049 CCGTTCTTGGTCATCTTCCTTTC 59.563 47.826 0.00 0.00 0.00 2.62
989 1042 2.066999 CCTTTCGGGAGGAGGAGGG 61.067 68.421 0.00 0.00 39.25 4.30
992 1045 2.531483 TTTCGGGAGGAGGAGGGAGG 62.531 65.000 0.00 0.00 0.00 4.30
993 1046 3.430497 CGGGAGGAGGAGGGAGGA 61.430 72.222 0.00 0.00 0.00 3.71
994 1047 3.010226 CGGGAGGAGGAGGGAGGAA 62.010 68.421 0.00 0.00 0.00 3.36
995 1048 1.074850 GGGAGGAGGAGGGAGGAAG 60.075 68.421 0.00 0.00 0.00 3.46
996 1049 1.764454 GGAGGAGGAGGGAGGAAGC 60.764 68.421 0.00 0.00 0.00 3.86
997 1050 1.002274 GAGGAGGAGGGAGGAAGCA 59.998 63.158 0.00 0.00 0.00 3.91
998 1051 0.399806 GAGGAGGAGGGAGGAAGCAT 60.400 60.000 0.00 0.00 0.00 3.79
1030 1083 1.070289 AGTTGTGAGTTCCTCCCGTTC 59.930 52.381 0.00 0.00 0.00 3.95
1064 1136 3.191669 TGTACATCTCCCGTTAATTGCG 58.808 45.455 0.00 0.00 0.00 4.85
1090 1162 2.224137 TGTTCTGCTCTGGTGAACTGAG 60.224 50.000 0.00 0.00 45.11 3.35
1213 1290 8.531982 TCCGTGAGTTTCTTACTACTACTACTA 58.468 37.037 0.00 0.00 37.17 1.82
1217 1294 9.883142 TGAGTTTCTTACTACTACTACTACTCC 57.117 37.037 0.00 0.00 37.17 3.85
1226 1303 5.012328 ACTACTACTACTCCTTGCAATGC 57.988 43.478 0.00 0.00 0.00 3.56
1267 1349 0.729690 GCGCCATCTTCCTTCTCAAC 59.270 55.000 0.00 0.00 0.00 3.18
1279 1361 7.223584 TCTTCCTTCTCAACATCACACATAAA 58.776 34.615 0.00 0.00 0.00 1.40
1280 1362 7.719193 TCTTCCTTCTCAACATCACACATAAAA 59.281 33.333 0.00 0.00 0.00 1.52
1281 1363 7.815840 TCCTTCTCAACATCACACATAAAAA 57.184 32.000 0.00 0.00 0.00 1.94
1379 1472 1.153667 GAGTGGCTTCTCCTCGCAG 60.154 63.158 0.00 0.00 35.26 5.18
1396 1489 0.309922 CAGTGCAGCTGTGTTCTTGG 59.690 55.000 16.64 0.00 40.27 3.61
1397 1490 0.181114 AGTGCAGCTGTGTTCTTGGA 59.819 50.000 16.64 0.00 0.00 3.53
1398 1491 0.590195 GTGCAGCTGTGTTCTTGGAG 59.410 55.000 16.64 0.00 0.00 3.86
1399 1492 1.168407 TGCAGCTGTGTTCTTGGAGC 61.168 55.000 16.64 0.00 0.00 4.70
1414 1507 1.202498 TGGAGCATGATTCTCTCGCTG 60.202 52.381 0.00 0.00 31.86 5.18
1418 1511 2.432146 AGCATGATTCTCTCGCTGGTTA 59.568 45.455 0.00 0.00 0.00 2.85
1461 1569 6.038050 GGTTCTTCTCTGATCCATTGATTGAC 59.962 42.308 0.00 0.00 0.00 3.18
1559 1667 5.241506 CCCTATTCTTCTTCACAAGTTTGCA 59.758 40.000 0.00 0.00 0.00 4.08
1579 1687 4.216257 TGCATCTCCTTCAAAGTTTGCTAC 59.784 41.667 10.90 0.00 0.00 3.58
1580 1688 4.457257 GCATCTCCTTCAAAGTTTGCTACT 59.543 41.667 10.90 0.00 39.32 2.57
1582 1690 6.149474 GCATCTCCTTCAAAGTTTGCTACTTA 59.851 38.462 10.90 0.00 46.34 2.24
1612 1720 3.758554 AGGGATATGTTGTCACTTGCAAC 59.241 43.478 0.00 0.00 44.50 4.17
1614 1722 3.505680 GGATATGTTGTCACTTGCAACCA 59.494 43.478 0.00 0.00 43.86 3.67
1629 1737 4.573900 TGCAACCATCAACTTTTTGTGTT 58.426 34.783 0.00 0.00 34.02 3.32
1697 1805 1.026718 AACTGCATTCTACTGCCGGC 61.027 55.000 22.73 22.73 41.58 6.13
1733 1841 2.472695 AGCAGAAACCGTAATGCTCA 57.527 45.000 0.00 0.00 45.57 4.26
1755 1863 8.252417 GCTCACAATCTCATCTCATATCAGTAT 58.748 37.037 0.00 0.00 0.00 2.12
1866 1975 2.159085 CGTAAGTCTCATCTCCCCAACC 60.159 54.545 0.00 0.00 0.00 3.77
2020 2137 1.219522 ACAAGTACGCCAACGACAGC 61.220 55.000 0.00 0.00 43.93 4.40
2083 2200 1.298413 CAGGGTCGTCGATACTGCG 60.298 63.158 13.75 0.00 0.00 5.18
2086 2203 1.585521 GGTCGTCGATACTGCGGTG 60.586 63.158 8.92 0.00 0.00 4.94
2132 2249 4.818546 CCCTTTTGCATTCGAGATACTGAT 59.181 41.667 0.00 0.00 0.00 2.90
2133 2250 5.297776 CCCTTTTGCATTCGAGATACTGATT 59.702 40.000 0.00 0.00 0.00 2.57
2134 2251 6.425504 CCTTTTGCATTCGAGATACTGATTC 58.574 40.000 0.00 0.00 0.00 2.52
2135 2252 6.037500 CCTTTTGCATTCGAGATACTGATTCA 59.962 38.462 0.00 0.00 0.00 2.57
2166 2283 4.727507 AGGCTCTGTCTGTATACTTGTG 57.272 45.455 4.17 0.00 0.00 3.33
2214 2331 6.030228 GTGGAAAATGAATCAATTCCTCGTC 58.970 40.000 22.97 12.47 41.51 4.20
2228 2345 3.401577 TCGTCTGTCGATGCTGAAC 57.598 52.632 0.00 0.00 44.01 3.18
2248 2365 7.583762 GCTGAACTTGTTTTGTTGCATATTTTC 59.416 33.333 0.00 0.00 0.00 2.29
2285 2408 1.214589 GCAAATCAGTGCAGGCCTG 59.785 57.895 29.34 29.34 44.29 4.85
2343 2466 4.940046 AGTGCTAAAGAGTCCATCAATGTG 59.060 41.667 0.00 0.00 0.00 3.21
2407 2530 4.201763 GGTAGAAGAGCAAATGAGCTTTCG 60.202 45.833 0.00 0.00 46.75 3.46
2457 2580 6.465948 TGTTTTTGGAATGCTTATGCTGATT 58.534 32.000 1.96 0.00 40.48 2.57
2496 2619 2.849536 AGCAAAGCTGGAGGCCTT 59.150 55.556 6.77 0.00 43.05 4.35
2616 2751 2.513666 TAAAGCATCCCAGCGGCG 60.514 61.111 0.51 0.51 40.15 6.46
2648 2783 7.086856 CCTTCCAGGAATCAGGATGAAAATGA 61.087 42.308 1.09 0.00 44.32 2.57
2726 2861 4.899502 AGCTGCAAACTGTATCAGTAAGT 58.100 39.130 1.02 0.00 44.62 2.24
2729 2864 5.179368 GCTGCAAACTGTATCAGTAAGTGAA 59.821 40.000 2.80 0.00 44.62 3.18
2789 2924 7.500227 ACATATGTCGAAATCATGTCAGGAAAT 59.500 33.333 1.41 0.00 0.00 2.17
2795 2930 7.064609 GTCGAAATCATGTCAGGAAATTCTGTA 59.935 37.037 11.96 0.21 36.25 2.74
2868 3003 4.276678 GCCATATTGCAATCTGCTAACTGA 59.723 41.667 16.86 0.00 45.31 3.41
2938 3146 5.465532 ACAGATACAGATACAGATGCAGG 57.534 43.478 0.00 0.00 0.00 4.85
3106 3328 0.840288 TAGCTGGAGGGGAAACTGCA 60.840 55.000 0.00 0.00 37.28 4.41
3280 3532 2.712709 TGTTGAACTCAAACCCGAACA 58.287 42.857 0.00 0.00 37.63 3.18
3516 3768 4.816385 GCTGCACTAATTAGAATACCAGCA 59.184 41.667 24.66 18.05 41.85 4.41
3553 3805 1.915141 CTGAACCACTTGCATCCCTT 58.085 50.000 0.00 0.00 0.00 3.95
3562 3814 4.022589 CCACTTGCATCCCTTAAGCATATG 60.023 45.833 0.00 0.00 38.19 1.78
3572 3824 5.592688 TCCCTTAAGCATATGCAAAACTACC 59.407 40.000 28.62 0.00 45.16 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.524816 CCATTGCACTTCAGCATCGC 60.525 55.000 0.00 0.00 45.19 4.58
1 2 0.806868 ACCATTGCACTTCAGCATCG 59.193 50.000 0.00 0.00 45.19 3.84
25 33 3.507233 TCTTTCGATGCTGGCAAATTCTT 59.493 39.130 0.00 0.00 0.00 2.52
36 44 2.681848 CAAATCAGCCTCTTTCGATGCT 59.318 45.455 0.00 0.00 41.06 3.79
63 73 5.442909 GCGCGTTATCACATAGTAGCATTAC 60.443 44.000 8.43 0.00 0.00 1.89
72 82 5.004821 GGATATCAAGCGCGTTATCACATAG 59.995 44.000 8.43 0.00 0.00 2.23
73 83 4.862574 GGATATCAAGCGCGTTATCACATA 59.137 41.667 8.43 0.00 0.00 2.29
95 112 0.666374 GGGACCTGAAACACAAACGG 59.334 55.000 0.00 0.00 0.00 4.44
96 113 0.306533 CGGGACCTGAAACACAAACG 59.693 55.000 0.00 0.00 0.00 3.60
97 114 1.385528 ACGGGACCTGAAACACAAAC 58.614 50.000 7.51 0.00 0.00 2.93
112 129 3.181455 TGTTTGGATCCATCAGATACGGG 60.181 47.826 17.06 0.00 38.89 5.28
145 162 2.158959 CGTCTTGTGATCGCCCGAC 61.159 63.158 3.31 9.06 0.00 4.79
194 211 2.046314 GACAAGCTAGCCGCCCAA 60.046 61.111 12.13 0.00 40.39 4.12
230 247 2.433604 CCTATCTGACAGGTGTCTGCAT 59.566 50.000 11.31 8.64 44.59 3.96
233 250 2.106566 AGCCTATCTGACAGGTGTCTG 58.893 52.381 11.31 10.61 44.99 3.51
259 276 3.864921 GCTTGCTCTCTTTCTACCGGAAA 60.865 47.826 9.46 0.00 41.11 3.13
318 335 8.451748 GTTGAGAATTCTAAAACCCACTGATAC 58.548 37.037 8.25 0.00 0.00 2.24
348 373 8.146053 TCTTCCCATACCATTACCATATACTG 57.854 38.462 0.00 0.00 0.00 2.74
350 375 8.993424 AGATCTTCCCATACCATTACCATATAC 58.007 37.037 0.00 0.00 0.00 1.47
351 376 9.213777 GAGATCTTCCCATACCATTACCATATA 57.786 37.037 0.00 0.00 0.00 0.86
352 377 7.147655 CGAGATCTTCCCATACCATTACCATAT 60.148 40.741 0.00 0.00 0.00 1.78
355 380 4.283467 CGAGATCTTCCCATACCATTACCA 59.717 45.833 0.00 0.00 0.00 3.25
356 381 4.322801 CCGAGATCTTCCCATACCATTACC 60.323 50.000 0.00 0.00 0.00 2.85
357 382 4.283722 ACCGAGATCTTCCCATACCATTAC 59.716 45.833 0.00 0.00 0.00 1.89
358 383 4.283467 CACCGAGATCTTCCCATACCATTA 59.717 45.833 0.00 0.00 0.00 1.90
359 384 3.071602 CACCGAGATCTTCCCATACCATT 59.928 47.826 0.00 0.00 0.00 3.16
360 385 2.634940 CACCGAGATCTTCCCATACCAT 59.365 50.000 0.00 0.00 0.00 3.55
361 386 2.039418 CACCGAGATCTTCCCATACCA 58.961 52.381 0.00 0.00 0.00 3.25
362 387 1.270358 GCACCGAGATCTTCCCATACC 60.270 57.143 0.00 0.00 0.00 2.73
363 388 1.603172 CGCACCGAGATCTTCCCATAC 60.603 57.143 0.00 0.00 0.00 2.39
463 496 1.757118 TGCTCCGCTTTAGCTCACTAT 59.243 47.619 0.00 0.00 40.73 2.12
464 497 1.135139 CTGCTCCGCTTTAGCTCACTA 59.865 52.381 0.00 0.00 40.73 2.74
470 503 1.308783 AAAGGCTGCTCCGCTTTAGC 61.309 55.000 0.00 0.00 40.77 3.09
471 504 0.449388 CAAAGGCTGCTCCGCTTTAG 59.551 55.000 0.00 0.00 40.77 1.85
472 505 0.960364 CCAAAGGCTGCTCCGCTTTA 60.960 55.000 0.00 0.00 40.77 1.85
473 506 2.270986 CCAAAGGCTGCTCCGCTTT 61.271 57.895 0.00 0.00 40.77 3.51
476 509 2.985847 AACCAAAGGCTGCTCCGC 60.986 61.111 0.00 0.00 40.77 5.54
477 510 2.956987 CAACCAAAGGCTGCTCCG 59.043 61.111 0.00 0.00 40.77 4.63
478 511 2.653115 GCAACCAAAGGCTGCTCC 59.347 61.111 4.27 0.00 41.12 4.70
480 513 3.982241 GCGCAACCAAAGGCTGCT 61.982 61.111 0.30 0.00 42.03 4.24
510 545 1.588403 CTCTCTCATGTGCCGCGAG 60.588 63.158 8.23 0.00 0.00 5.03
511 546 1.387295 ATCTCTCTCATGTGCCGCGA 61.387 55.000 8.23 0.00 0.00 5.87
512 547 1.067084 ATCTCTCTCATGTGCCGCG 59.933 57.895 0.00 0.00 0.00 6.46
536 571 2.515757 TTGAACCGCTGCAGTGCA 60.516 55.556 22.03 18.58 36.92 4.57
651 686 5.972107 TTGTTGGTACTCAGACCTAGTAC 57.028 43.478 5.09 5.09 45.62 2.73
652 687 5.479375 CCTTTGTTGGTACTCAGACCTAGTA 59.521 44.000 0.00 0.00 40.46 1.82
653 688 4.283722 CCTTTGTTGGTACTCAGACCTAGT 59.716 45.833 0.00 0.00 40.46 2.57
654 689 4.822026 CCTTTGTTGGTACTCAGACCTAG 58.178 47.826 0.00 0.00 40.46 3.02
655 690 3.007614 GCCTTTGTTGGTACTCAGACCTA 59.992 47.826 0.00 0.00 40.46 3.08
665 700 1.227586 TCGCGTGCCTTTGTTGGTA 60.228 52.632 5.77 0.00 0.00 3.25
718 760 5.076873 CAGTTGACTCCCCCATTTCTTTAA 58.923 41.667 0.00 0.00 0.00 1.52
727 769 1.630369 CTGATTCAGTTGACTCCCCCA 59.370 52.381 5.46 0.00 0.00 4.96
741 783 1.386533 CCTGCACATGACCCTGATTC 58.613 55.000 0.00 0.00 0.00 2.52
801 849 0.392706 TTCCATCATCGATCCCCACG 59.607 55.000 0.00 0.00 0.00 4.94
802 850 2.638480 TTTCCATCATCGATCCCCAC 57.362 50.000 0.00 0.00 0.00 4.61
803 851 3.287222 GTTTTTCCATCATCGATCCCCA 58.713 45.455 0.00 0.00 0.00 4.96
804 852 3.287222 TGTTTTTCCATCATCGATCCCC 58.713 45.455 0.00 0.00 0.00 4.81
828 876 1.895020 ATCTCCCGGCGCACTTGTTA 61.895 55.000 10.83 0.00 0.00 2.41
838 886 2.115291 GGCAAACTGATCTCCCGGC 61.115 63.158 0.00 0.00 0.00 6.13
856 904 4.440802 GGTTATGACTCTGAGTGCACTAGG 60.441 50.000 21.73 15.35 0.00 3.02
873 922 7.362142 GCTTCTCAAGGGTAGAAAAAGGTTATG 60.362 40.741 0.00 0.00 32.77 1.90
887 936 1.905894 GAGAAGAGGCTTCTCAAGGGT 59.094 52.381 24.68 0.00 43.25 4.34
942 995 0.038159 AAGAACGGAGCAGGAAGTCG 60.038 55.000 0.00 0.00 0.00 4.18
976 1029 2.937959 CTTCCTCCCTCCTCCTCCCG 62.938 70.000 0.00 0.00 0.00 5.14
989 1042 0.743097 GTTGCCCATGATGCTTCCTC 59.257 55.000 0.00 0.00 0.00 3.71
992 1045 0.379669 CTCGTTGCCCATGATGCTTC 59.620 55.000 0.00 0.00 0.00 3.86
993 1046 0.322816 ACTCGTTGCCCATGATGCTT 60.323 50.000 0.00 0.00 0.00 3.91
994 1047 0.322816 AACTCGTTGCCCATGATGCT 60.323 50.000 0.00 0.00 0.00 3.79
995 1048 0.179156 CAACTCGTTGCCCATGATGC 60.179 55.000 0.00 0.00 33.45 3.91
996 1049 1.135603 CACAACTCGTTGCCCATGATG 60.136 52.381 9.55 0.00 44.03 3.07
997 1050 1.167851 CACAACTCGTTGCCCATGAT 58.832 50.000 9.55 0.00 44.03 2.45
998 1051 0.107643 TCACAACTCGTTGCCCATGA 59.892 50.000 9.55 3.69 44.03 3.07
1030 1083 4.804139 GGAGATGTACATACACGGAAACAG 59.196 45.833 8.71 0.00 39.30 3.16
1064 1136 1.072159 ACCAGAGCAGAACAGCCAC 59.928 57.895 0.00 0.00 34.23 5.01
1090 1162 0.449388 CAGGACAAGAGCGGCATTTC 59.551 55.000 1.45 0.00 0.00 2.17
1213 1290 1.973281 CACCCGCATTGCAAGGAGT 60.973 57.895 16.56 5.66 0.00 3.85
1216 1293 2.053865 ATCCACCCGCATTGCAAGG 61.054 57.895 6.76 6.76 0.00 3.61
1217 1294 1.140161 CATCCACCCGCATTGCAAG 59.860 57.895 9.69 1.28 0.00 4.01
1218 1295 2.349672 CCATCCACCCGCATTGCAA 61.350 57.895 9.69 0.00 0.00 4.08
1219 1296 2.755064 CCATCCACCCGCATTGCA 60.755 61.111 9.69 0.00 0.00 4.08
1226 1303 1.836999 TTGGTCAGTCCATCCACCCG 61.837 60.000 0.00 0.00 46.60 5.28
1267 1349 6.072008 TCAGGACCATGTTTTTATGTGTGATG 60.072 38.462 0.00 0.00 0.00 3.07
1279 1361 6.983906 AGAAGAAAAATCAGGACCATGTTT 57.016 33.333 0.00 0.00 0.00 2.83
1280 1362 6.550854 TGAAGAAGAAAAATCAGGACCATGTT 59.449 34.615 0.00 0.00 0.00 2.71
1281 1363 6.070656 TGAAGAAGAAAAATCAGGACCATGT 58.929 36.000 0.00 0.00 0.00 3.21
1379 1472 0.590195 CTCCAAGAACACAGCTGCAC 59.410 55.000 15.27 2.69 0.00 4.57
1396 1489 1.202510 ACCAGCGAGAGAATCATGCTC 60.203 52.381 0.00 0.00 44.37 4.26
1397 1490 0.829333 ACCAGCGAGAGAATCATGCT 59.171 50.000 0.00 0.00 46.59 3.79
1398 1491 1.661341 AACCAGCGAGAGAATCATGC 58.339 50.000 0.00 0.00 37.82 4.06
1399 1492 5.757320 AGAAATAACCAGCGAGAGAATCATG 59.243 40.000 0.00 0.00 37.82 3.07
1414 1507 7.881775 ACCAAACATAGGATGAGAAATAACC 57.118 36.000 0.00 0.00 0.00 2.85
1418 1511 8.112183 AGAAGAACCAAACATAGGATGAGAAAT 58.888 33.333 0.00 0.00 0.00 2.17
1559 1667 8.103305 TGATAAGTAGCAAACTTTGAAGGAGAT 58.897 33.333 9.43 0.00 46.61 2.75
1579 1687 7.169308 GTGACAACATATCCCTTACGTGATAAG 59.831 40.741 0.00 0.00 40.19 1.73
1580 1688 6.982141 GTGACAACATATCCCTTACGTGATAA 59.018 38.462 0.00 0.00 0.00 1.75
1581 1689 6.322969 AGTGACAACATATCCCTTACGTGATA 59.677 38.462 0.00 0.00 0.00 2.15
1582 1690 5.128827 AGTGACAACATATCCCTTACGTGAT 59.871 40.000 0.00 0.00 0.00 3.06
1606 1714 4.573900 ACACAAAAAGTTGATGGTTGCAA 58.426 34.783 0.00 0.00 38.20 4.08
1612 1720 6.734104 TTCCAAAACACAAAAAGTTGATGG 57.266 33.333 0.00 0.00 38.20 3.51
1614 1722 8.558973 TCATTTCCAAAACACAAAAAGTTGAT 57.441 26.923 0.00 0.00 38.20 2.57
1629 1737 4.487804 TGGGGAATCAGTTCATTTCCAAA 58.512 39.130 3.59 0.00 40.59 3.28
1697 1805 0.161446 GCTTTGCGCAATTGTTTCCG 59.839 50.000 25.64 6.29 38.92 4.30
1710 1818 1.985684 GCATTACGGTTTCTGCTTTGC 59.014 47.619 0.00 0.00 0.00 3.68
1733 1841 9.758021 AGAGATACTGATATGAGATGAGATTGT 57.242 33.333 0.00 0.00 0.00 2.71
1755 1863 3.820467 CCCACTGTTGTAAATGCAAGAGA 59.180 43.478 13.76 0.00 40.77 3.10
1866 1975 5.502214 TGCAGTTTTTGTTGTTGTTTACG 57.498 34.783 0.00 0.00 0.00 3.18
2020 2137 1.130613 GACAAGTAGCTTGCGCACG 59.869 57.895 11.12 10.43 44.43 5.34
2083 2200 1.152963 AACTGTGACCTGTGCCACC 60.153 57.895 0.00 0.00 32.61 4.61
2086 2203 0.465460 TTGGAACTGTGACCTGTGCC 60.465 55.000 6.00 0.00 38.44 5.01
2132 2249 6.155221 ACAGACAGAGCCTAGTTTATGATGAA 59.845 38.462 0.00 0.00 0.00 2.57
2133 2250 5.658634 ACAGACAGAGCCTAGTTTATGATGA 59.341 40.000 0.00 0.00 0.00 2.92
2134 2251 5.911752 ACAGACAGAGCCTAGTTTATGATG 58.088 41.667 0.00 0.00 0.00 3.07
2135 2252 7.847711 ATACAGACAGAGCCTAGTTTATGAT 57.152 36.000 0.00 0.00 0.00 2.45
2166 2283 2.433664 ACGACGAATTCCCGTGCC 60.434 61.111 16.57 0.00 43.49 5.01
2214 2331 3.885484 AAACAAGTTCAGCATCGACAG 57.115 42.857 0.00 0.00 0.00 3.51
2228 2345 9.584839 GCTTAAGAAAATATGCAACAAAACAAG 57.415 29.630 6.67 0.00 0.00 3.16
2248 2365 4.389890 TGCATTGCCCATTTAGCTTAAG 57.610 40.909 6.12 0.00 0.00 1.85
2285 2408 3.072184 AGGAATACCCATCTCATCAGCAC 59.928 47.826 0.00 0.00 37.41 4.40
2457 2580 5.029807 TGTGGATCAGACACACAAGTTTA 57.970 39.130 6.55 0.00 43.35 2.01
2496 2619 2.172082 CAGATTGGATGCCTTCCTCTCA 59.828 50.000 4.59 0.00 45.68 3.27
2648 2783 2.821969 GAGGTTCACATTTGGCAGATGT 59.178 45.455 17.11 17.11 38.21 3.06
2726 2861 3.440228 TCGATACGAACATGCGAATTCA 58.560 40.909 6.22 0.00 31.06 2.57
2729 2864 3.902150 AGATCGATACGAACATGCGAAT 58.098 40.909 0.00 0.00 39.99 3.34
2789 2924 9.314321 GATTAGAGAACCATCGAAATTACAGAA 57.686 33.333 0.00 0.00 0.00 3.02
2795 2930 6.037610 GTGCTGATTAGAGAACCATCGAAATT 59.962 38.462 0.00 0.00 0.00 1.82
2868 3003 8.902806 TGTAAATTCACTGTCTTTCAGATTGTT 58.097 29.630 1.79 0.00 46.27 2.83
2967 3176 6.040247 CGTCTCATAGCCTTGTGTATGTAAA 58.960 40.000 0.00 0.00 0.00 2.01
2969 3178 4.643334 ACGTCTCATAGCCTTGTGTATGTA 59.357 41.667 0.00 0.00 0.00 2.29
2970 3179 3.447586 ACGTCTCATAGCCTTGTGTATGT 59.552 43.478 0.00 0.00 0.00 2.29
2973 3182 2.426024 GGACGTCTCATAGCCTTGTGTA 59.574 50.000 16.46 0.00 0.00 2.90
3012 3234 4.770531 TCTCCTAGTTCCGATTTGAGTTCA 59.229 41.667 0.00 0.00 0.00 3.18
3106 3328 3.534554 TCGCAGATTGCATGATGTTACT 58.465 40.909 0.00 0.00 45.36 2.24
3149 3371 9.586150 GTACATGCTTTTTCATATGTAGATTCG 57.414 33.333 1.90 0.00 36.87 3.34
3280 3532 2.883026 ACCTATCAAGCTATCTCGCCT 58.117 47.619 0.00 0.00 0.00 5.52
3451 3703 9.984190 GGGACCTAACATAACAACATTTTTAAA 57.016 29.630 0.00 0.00 0.00 1.52
3503 3755 6.611613 CATCCCTCTATGCTGGTATTCTAA 57.388 41.667 0.00 0.00 0.00 2.10
3533 3785 0.610232 AGGGATGCAAGTGGTTCAGC 60.610 55.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.