Multiple sequence alignment - TraesCS2B01G328200

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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 TraesCS2B01G328200 chr2B 100.000 3508 0 0 1 3508 470073282 470069775 0.000000e+00 6479.0
1 TraesCS2B01G328200 chr2B 89.485 466 32 10 2965 3417 725812417 725812878 1.090000e-159 573.0
2 TraesCS2B01G328200 chr2A 93.836 1314 41 19 1597 2881 534636238 534634936 0.000000e+00 1941.0
3 TraesCS2B01G328200 chr2A 91.245 731 41 12 463 1186 534637464 534636750 0.000000e+00 974.0
4 TraesCS2B01G328200 chr2A 94.836 426 15 3 1160 1578 534636647 534636222 0.000000e+00 658.0
5 TraesCS2B01G328200 chr2A 89.474 418 32 6 1 417 534638053 534637647 5.190000e-143 518.0
6 TraesCS2B01G328200 chr2D 95.505 1179 29 12 1597 2757 396713152 396711980 0.000000e+00 1862.0
7 TraesCS2B01G328200 chr2D 94.140 1041 50 8 463 1495 396714443 396713406 0.000000e+00 1574.0
8 TraesCS2B01G328200 chr2D 91.388 418 32 3 1 417 396715040 396714626 1.410000e-158 569.0
9 TraesCS2B01G328200 chr2D 84.586 532 61 17 2965 3486 59717474 59716954 3.120000e-140 508.0
10 TraesCS2B01G328200 chr2D 88.172 93 9 2 3392 3483 489573440 489573531 3.700000e-20 110.0
11 TraesCS2B01G328200 chr2D 87.273 55 4 3 48 101 396714642 396714590 3.780000e-05 60.2
12 TraesCS2B01G328200 chr3B 88.142 506 40 9 2896 3389 41562519 41562022 5.050000e-163 584.0
13 TraesCS2B01G328200 chr3B 95.714 70 3 0 2895 2964 530548735 530548666 2.860000e-21 113.0
14 TraesCS2B01G328200 chr3B 95.714 70 3 0 2895 2964 749027894 749027825 2.860000e-21 113.0
15 TraesCS2B01G328200 chr7B 88.985 463 32 12 2965 3417 705325364 705325817 3.960000e-154 555.0
16 TraesCS2B01G328200 chr5B 87.276 503 43 19 2892 3383 571193602 571194094 3.960000e-154 555.0
17 TraesCS2B01G328200 chr5D 84.794 559 63 14 2965 3508 442103711 442103160 3.080000e-150 542.0
18 TraesCS2B01G328200 chr1B 85.795 528 54 16 2965 3483 673186924 673186409 1.110000e-149 540.0
19 TraesCS2B01G328200 chr7D 85.366 533 50 17 2968 3483 386753308 386752787 8.620000e-146 527.0
20 TraesCS2B01G328200 chr3D 84.544 537 57 17 2895 3417 610435531 610435007 3.120000e-140 508.0
21 TraesCS2B01G328200 chr7A 90.722 97 6 3 3389 3483 607585990 607585895 3.680000e-25 126.0
22 TraesCS2B01G328200 chrUn 88.043 92 11 0 3392 3483 282654178 282654087 3.700000e-20 110.0
23 TraesCS2B01G328200 chrUn 93.243 74 4 1 2895 2968 34110115 34110187 1.330000e-19 108.0
24 TraesCS2B01G328200 chr4B 94.366 71 4 0 2894 2964 23818123 23818053 3.700000e-20 110.0


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 TraesCS2B01G328200 chr2B 470069775 470073282 3507 True 6479.00 6479 100.00000 1 3508 1 chr2B.!!$R1 3507
1 TraesCS2B01G328200 chr2A 534634936 534638053 3117 True 1022.75 1941 92.34775 1 2881 4 chr2A.!!$R1 2880
2 TraesCS2B01G328200 chr2D 396711980 396715040 3060 True 1016.30 1862 92.07650 1 2757 4 chr2D.!!$R2 2756
3 TraesCS2B01G328200 chr2D 59716954 59717474 520 True 508.00 508 84.58600 2965 3486 1 chr2D.!!$R1 521
4 TraesCS2B01G328200 chr5D 442103160 442103711 551 True 542.00 542 84.79400 2965 3508 1 chr5D.!!$R1 543
5 TraesCS2B01G328200 chr1B 673186409 673186924 515 True 540.00 540 85.79500 2965 3483 1 chr1B.!!$R1 518
6 TraesCS2B01G328200 chr7D 386752787 386753308 521 True 527.00 527 85.36600 2968 3483 1 chr7D.!!$R1 515
7 TraesCS2B01G328200 chr3D 610435007 610435531 524 True 508.00 508 84.54400 2895 3417 1 chr3D.!!$R1 522

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
781 949 0.323629 CAAAAGGGGGAGCGTCAGTA 59.676 55.000 0.0 0.0 0.0 2.74 F
782 950 1.065418 CAAAAGGGGGAGCGTCAGTAT 60.065 52.381 0.0 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 2171 0.036732 TTCTTGCTCTGACGGCCAAT 59.963 50.000 2.24 0.0 0.00 3.16 R
2671 3226 1.263217 ACGCAACGGCAGTAAAAGAAG 59.737 47.619 0.00 0.0 41.24 2.85 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
44 45 4.568956 TGTGCCAGGATATGAATGTATCG 58.431 43.478 0.00 0.00 32.93 2.92
67 68 4.387256 GCGACATCTACAAAGCTCATATCC 59.613 45.833 0.00 0.00 0.00 2.59
137 139 5.447818 CGACACTTGACAAAGAAGAGCTTTT 60.448 40.000 0.00 0.00 44.24 2.27
149 151 3.864789 AGAGCTTTTGACCCTTCAGAA 57.135 42.857 0.00 0.00 31.71 3.02
165 167 8.650490 ACCCTTCAGAATTTAACATCACAAAAT 58.350 29.630 0.00 0.00 0.00 1.82
196 198 2.022428 ACATCCCCTACCTACCACATCA 60.022 50.000 0.00 0.00 0.00 3.07
203 205 5.479306 CCCTACCTACCACATCATTTATCG 58.521 45.833 0.00 0.00 0.00 2.92
205 207 4.415881 ACCTACCACATCATTTATCGCA 57.584 40.909 0.00 0.00 0.00 5.10
206 208 4.973168 ACCTACCACATCATTTATCGCAT 58.027 39.130 0.00 0.00 0.00 4.73
217 219 8.412456 ACATCATTTATCGCATCCATTTTGTTA 58.588 29.630 0.00 0.00 0.00 2.41
269 271 7.503521 TGCGTATTGGCATAGATTTAAATGA 57.496 32.000 5.17 0.00 38.17 2.57
305 307 8.324163 AGTTGTGTATAGAACATTGGAACTTC 57.676 34.615 2.40 0.00 41.10 3.01
358 360 5.233476 GTCACAACGTCTACAAAGTTCATCA 59.767 40.000 0.00 0.00 0.00 3.07
421 423 7.749539 AAAACGTTTACAAAGTTCATCAAGG 57.250 32.000 15.03 0.00 0.00 3.61
422 424 6.445357 AACGTTTACAAAGTTCATCAAGGT 57.555 33.333 0.00 0.00 0.00 3.50
423 425 6.056428 ACGTTTACAAAGTTCATCAAGGTC 57.944 37.500 0.00 0.00 0.00 3.85
424 426 5.587043 ACGTTTACAAAGTTCATCAAGGTCA 59.413 36.000 0.00 0.00 0.00 4.02
425 427 6.094325 ACGTTTACAAAGTTCATCAAGGTCAA 59.906 34.615 0.00 0.00 0.00 3.18
426 428 6.970043 CGTTTACAAAGTTCATCAAGGTCAAA 59.030 34.615 0.00 0.00 0.00 2.69
427 429 7.486551 CGTTTACAAAGTTCATCAAGGTCAAAA 59.513 33.333 0.00 0.00 0.00 2.44
428 430 8.807581 GTTTACAAAGTTCATCAAGGTCAAAAG 58.192 33.333 0.00 0.00 0.00 2.27
429 431 6.773976 ACAAAGTTCATCAAGGTCAAAAGA 57.226 33.333 0.00 0.00 0.00 2.52
430 432 7.169158 ACAAAGTTCATCAAGGTCAAAAGAA 57.831 32.000 0.00 0.00 0.00 2.52
431 433 7.035612 ACAAAGTTCATCAAGGTCAAAAGAAC 58.964 34.615 0.00 0.00 35.40 3.01
446 448 5.006358 TCAAAAGAACGTCTACAAAGCTCAC 59.994 40.000 0.00 0.00 0.00 3.51
465 467 5.645497 GCTCACATCCCAATGTTAGGATATC 59.355 44.000 0.00 0.00 43.74 1.63
472 474 3.748048 CCAATGTTAGGATATCTGTGCGG 59.252 47.826 2.05 0.00 0.00 5.69
474 476 3.728076 TGTTAGGATATCTGTGCGGAC 57.272 47.619 0.00 0.00 0.00 4.79
475 477 3.028130 TGTTAGGATATCTGTGCGGACA 58.972 45.455 10.11 10.11 0.00 4.02
476 478 3.449377 TGTTAGGATATCTGTGCGGACAA 59.551 43.478 11.97 2.74 0.00 3.18
498 665 2.746375 GGGGAGCGTCATGACCCAT 61.746 63.158 20.03 6.05 43.67 4.00
499 666 1.224592 GGGAGCGTCATGACCCATT 59.775 57.895 20.03 3.16 41.72 3.16
501 668 1.097547 GGAGCGTCATGACCCATTGG 61.098 60.000 20.03 6.06 37.80 3.16
551 718 2.416547 GGGTTCATCATCACAAGTGTCG 59.583 50.000 0.00 0.00 0.00 4.35
575 742 1.144057 CGCATCCCTCACCTACCAC 59.856 63.158 0.00 0.00 0.00 4.16
698 866 1.742761 ACTCCTTCAATGCACCATCG 58.257 50.000 0.00 0.00 0.00 3.84
700 868 0.394216 TCCTTCAATGCACCATCGGG 60.394 55.000 0.00 0.00 41.29 5.14
780 948 1.073199 CAAAAGGGGGAGCGTCAGT 59.927 57.895 0.00 0.00 0.00 3.41
781 949 0.323629 CAAAAGGGGGAGCGTCAGTA 59.676 55.000 0.00 0.00 0.00 2.74
782 950 1.065418 CAAAAGGGGGAGCGTCAGTAT 60.065 52.381 0.00 0.00 0.00 2.12
953 1121 4.318121 GCAAGACACTCAAAAGTACTCACG 60.318 45.833 0.00 0.00 33.25 4.35
1112 1280 4.668576 TTCGCATCTGATTTGTCTCAAC 57.331 40.909 0.00 0.00 0.00 3.18
1115 1283 4.083855 TCGCATCTGATTTGTCTCAACAAC 60.084 41.667 0.00 0.00 44.90 3.32
1116 1284 4.319694 CGCATCTGATTTGTCTCAACAACA 60.320 41.667 0.00 0.00 44.90 3.33
1120 1288 7.010367 GCATCTGATTTGTCTCAACAACAAAAA 59.990 33.333 5.62 0.00 46.38 1.94
1158 1332 2.040813 AGCAGTGAACATCATGGAACCT 59.959 45.455 0.00 0.00 0.00 3.50
1166 1469 2.768527 ACATCATGGAACCTGATCTCGT 59.231 45.455 0.00 0.00 31.00 4.18
1213 1516 2.125552 CTGGCGCCGATGACAAGA 60.126 61.111 23.90 0.00 0.00 3.02
1254 1557 4.241999 GCAGCCGCACGCCATTAG 62.242 66.667 0.00 0.00 38.78 1.73
1262 1565 1.202325 CGCACGCCATTAGGTACTACA 60.202 52.381 0.00 0.00 42.67 2.74
1306 1609 2.415010 CTCATCTCGGAGGCCACG 59.585 66.667 5.01 9.92 0.00 4.94
1526 2051 2.604132 GCTGCTGCTGTCAGTTTCTTTC 60.604 50.000 8.53 0.00 42.29 2.62
1552 2082 2.253452 GCGGTTGAACTGCTGCTG 59.747 61.111 21.14 4.89 46.62 4.41
1635 2171 4.593956 TCAGCTCTGATCTTCTGTCTGTA 58.406 43.478 0.00 0.00 34.14 2.74
1694 2230 0.955905 GCCGATAGAGAGGACTCCAC 59.044 60.000 0.00 0.00 43.53 4.02
1871 2407 3.355626 TGAGATCGAGGTTCTAATGCG 57.644 47.619 0.00 0.00 0.00 4.73
1874 2418 0.464036 ATCGAGGTTCTAATGCGGCA 59.536 50.000 4.58 4.58 0.00 5.69
2190 2744 3.083349 TGGTGGAGCCCGAGATGG 61.083 66.667 0.00 0.00 36.04 3.51
2199 2753 2.765807 CCGAGATGGCCTGGGAGT 60.766 66.667 3.32 0.00 42.75 3.85
2200 2754 1.457643 CCGAGATGGCCTGGGAGTA 60.458 63.158 3.32 0.00 42.75 2.59
2206 2760 3.834799 GGCCTGGGAGTACGACGG 61.835 72.222 0.00 0.00 0.00 4.79
2336 2890 1.505353 CGAAGAGTACGCCGACCTT 59.495 57.895 0.00 0.00 0.00 3.50
2504 3058 0.182537 CCAAGGGGAATGGCGTGATA 59.817 55.000 0.00 0.00 35.59 2.15
2575 3129 6.015940 CCTCAGTGTGGCTTCTTCTTTTATTT 60.016 38.462 0.00 0.00 0.00 1.40
2576 3130 6.970484 TCAGTGTGGCTTCTTCTTTTATTTC 58.030 36.000 0.00 0.00 0.00 2.17
2578 3132 7.936847 TCAGTGTGGCTTCTTCTTTTATTTCTA 59.063 33.333 0.00 0.00 0.00 2.10
2581 3135 8.017946 GTGTGGCTTCTTCTTTTATTTCTACTG 58.982 37.037 0.00 0.00 0.00 2.74
2651 3206 1.133513 AGGCAACACCAGTTTGGATGA 60.134 47.619 1.40 0.00 41.78 2.92
2671 3226 5.389642 TGATTTTCGATGATTACACTCGC 57.610 39.130 0.00 0.00 32.00 5.03
2697 3252 0.863144 TACTGCCGTTGCGTCTTTTC 59.137 50.000 0.00 0.00 41.78 2.29
2706 3261 2.169832 TGCGTCTTTTCTGCTTAGCT 57.830 45.000 5.60 0.00 0.00 3.32
2738 3293 7.715265 TTTGTAAACTGACTTCTCTGCTTAG 57.285 36.000 0.00 0.00 0.00 2.18
2763 3318 4.022068 TGATTTGCACAAGAGGGAAACATC 60.022 41.667 0.00 0.00 42.75 3.06
2773 3328 3.701664 GAGGGAAACATCTGTGGGATTT 58.298 45.455 0.00 0.00 38.35 2.17
2776 3331 4.284234 AGGGAAACATCTGTGGGATTTTTG 59.716 41.667 0.00 0.00 35.31 2.44
2791 3346 7.657354 GTGGGATTTTTGTAGCAGATTTTTCTT 59.343 33.333 0.00 0.00 0.00 2.52
2819 3376 2.407616 GGGGAATTAAGCGCGCAC 59.592 61.111 35.10 15.79 0.00 5.34
2824 3385 2.574322 GGAATTAAGCGCGCACATATG 58.426 47.619 35.10 0.00 0.00 1.78
2905 3467 7.599245 ACTCCTGTCTTTTAACGAAATCACTAG 59.401 37.037 0.00 0.00 0.00 2.57
2919 3481 9.447157 ACGAAATCACTAGTTAAGTAGTACTCT 57.553 33.333 20.12 7.96 35.76 3.24
2924 3486 7.524912 TCACTAGTTAAGTAGTACTCTTTGCG 58.475 38.462 20.12 7.30 35.76 4.85
2925 3487 6.746364 CACTAGTTAAGTAGTACTCTTTGCGG 59.254 42.308 20.12 3.41 35.76 5.69
2929 3491 6.377712 AGTTAAGTAGTACTCTTTGCGGAGAT 59.622 38.462 2.58 0.00 37.13 2.75
2935 3497 2.175202 ACTCTTTGCGGAGATCACTCT 58.825 47.619 7.91 0.00 42.28 3.24
2936 3498 3.357203 ACTCTTTGCGGAGATCACTCTA 58.643 45.455 7.91 0.00 42.28 2.43
2939 3501 3.764434 TCTTTGCGGAGATCACTCTAACT 59.236 43.478 0.00 0.00 42.28 2.24
2943 3505 3.119101 TGCGGAGATCACTCTAACTTTCC 60.119 47.826 0.00 0.00 42.28 3.13
2949 3511 4.846940 AGATCACTCTAACTTTCCCAGGTT 59.153 41.667 0.00 0.00 0.00 3.50
2955 3517 0.106918 AACTTTCCCAGGTTGCGACA 60.107 50.000 6.39 0.00 0.00 4.35
2956 3518 0.106918 ACTTTCCCAGGTTGCGACAA 60.107 50.000 6.39 0.00 0.00 3.18
2958 3520 0.106918 TTTCCCAGGTTGCGACAAGT 60.107 50.000 6.39 0.00 0.00 3.16
2960 3522 2.260869 CCCAGGTTGCGACAAGTGG 61.261 63.158 6.39 9.17 0.00 4.00
2961 3523 2.639286 CAGGTTGCGACAAGTGGC 59.361 61.111 6.39 0.00 34.76 5.01
2978 3540 2.284150 GTGGCGCAGTTTTTCCTTTTTC 59.716 45.455 10.83 0.00 0.00 2.29
3046 3608 3.303526 CCAAATCTCGAACCGTTTTCGTT 60.304 43.478 14.04 1.95 42.09 3.85
3081 3643 4.167268 GCGTCGAGATCTTCAAAACTAGT 58.833 43.478 0.00 0.00 0.00 2.57
3082 3644 5.330295 GCGTCGAGATCTTCAAAACTAGTA 58.670 41.667 0.00 0.00 0.00 1.82
3083 3645 5.452944 GCGTCGAGATCTTCAAAACTAGTAG 59.547 44.000 0.00 0.00 0.00 2.57
3094 3656 8.041323 TCTTCAAAACTAGTAGATCCCATGTTC 58.959 37.037 3.59 0.00 0.00 3.18
3099 3661 6.597832 ACTAGTAGATCCCATGTTCATAGC 57.402 41.667 3.59 0.00 0.00 2.97
3219 3789 1.197721 GAAATCACAACCGTGCCTCTG 59.802 52.381 0.00 0.00 43.28 3.35
3220 3790 0.396435 AATCACAACCGTGCCTCTGA 59.604 50.000 0.00 0.00 43.28 3.27
3222 3792 1.227527 CACAACCGTGCCTCTGACA 60.228 57.895 0.00 0.00 36.06 3.58
3292 3869 1.497722 CTTTCCGAAAGAGGCACGC 59.502 57.895 14.72 0.00 41.02 5.34
3400 3987 3.535280 TTTCCCTTTGAAAGCACAACC 57.465 42.857 0.00 0.00 38.04 3.77
3401 3988 1.028905 TCCCTTTGAAAGCACAACCG 58.971 50.000 0.00 0.00 0.00 4.44
3402 3989 0.744281 CCCTTTGAAAGCACAACCGT 59.256 50.000 0.00 0.00 0.00 4.83
3403 3990 1.535860 CCCTTTGAAAGCACAACCGTG 60.536 52.381 0.00 0.00 46.56 4.94
3411 3998 2.551270 CACAACCGTGCTTCTCGC 59.449 61.111 0.00 0.00 36.06 5.03
3420 4007 2.663279 GTGCTTCTCGCGAAAGAAAA 57.337 45.000 25.12 10.56 43.27 2.29
3421 4008 2.981875 GTGCTTCTCGCGAAAGAAAAA 58.018 42.857 25.12 10.28 43.27 1.94
3463 4050 1.469335 TTCGTTTCCGAGGAGGCACT 61.469 55.000 0.00 0.00 45.24 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.565307 TCCTGGCACATTGAAGAAGTTT 58.435 40.909 0.00 0.00 38.20 2.66
44 45 4.387256 GGATATGAGCTTTGTAGATGTCGC 59.613 45.833 0.00 0.00 0.00 5.19
67 68 6.868339 TGTCTACGCATATATCTGAACATTGG 59.132 38.462 0.00 0.00 0.00 3.16
105 106 0.666274 TGTCAAGTGTCGACGATGCC 60.666 55.000 11.62 0.10 36.11 4.40
106 107 1.136690 TTGTCAAGTGTCGACGATGC 58.863 50.000 11.62 6.76 36.11 3.91
109 110 2.855660 TCTTTGTCAAGTGTCGACGA 57.144 45.000 11.62 0.00 36.11 4.20
116 118 5.741040 GTCAAAAGCTCTTCTTTGTCAAGTG 59.259 40.000 8.14 0.00 43.84 3.16
137 139 6.303054 TGTGATGTTAAATTCTGAAGGGTCA 58.697 36.000 0.00 0.00 0.00 4.02
149 151 8.353684 TGGTGTACGAATTTTGTGATGTTAAAT 58.646 29.630 0.00 0.00 0.00 1.40
165 167 1.826720 GTAGGGGATGTGGTGTACGAA 59.173 52.381 0.00 0.00 0.00 3.85
171 173 1.129058 GGTAGGTAGGGGATGTGGTG 58.871 60.000 0.00 0.00 0.00 4.17
196 198 8.686334 AGAAGTAACAAAATGGATGCGATAAAT 58.314 29.630 0.00 0.00 0.00 1.40
236 238 2.013400 TGCCAATACGCAATTCGATGT 58.987 42.857 4.65 0.00 41.67 3.06
242 244 9.195411 CATTTAAATCTATGCCAATACGCAATT 57.805 29.630 0.00 0.00 43.24 2.32
325 327 3.194005 AGACGTTGTGACACATTCCTT 57.806 42.857 9.55 0.00 0.00 3.36
402 404 8.696410 TTTTGACCTTGATGAACTTTGTAAAC 57.304 30.769 0.00 0.00 0.00 2.01
403 405 8.744652 TCTTTTGACCTTGATGAACTTTGTAAA 58.255 29.630 0.00 0.00 0.00 2.01
404 406 8.287439 TCTTTTGACCTTGATGAACTTTGTAA 57.713 30.769 0.00 0.00 0.00 2.41
405 407 7.873719 TCTTTTGACCTTGATGAACTTTGTA 57.126 32.000 0.00 0.00 0.00 2.41
406 408 6.773976 TCTTTTGACCTTGATGAACTTTGT 57.226 33.333 0.00 0.00 0.00 2.83
407 409 6.197096 CGTTCTTTTGACCTTGATGAACTTTG 59.803 38.462 0.00 0.00 32.71 2.77
408 410 6.127730 ACGTTCTTTTGACCTTGATGAACTTT 60.128 34.615 0.00 0.00 32.71 2.66
409 411 5.357032 ACGTTCTTTTGACCTTGATGAACTT 59.643 36.000 0.00 0.00 32.71 2.66
410 412 4.881850 ACGTTCTTTTGACCTTGATGAACT 59.118 37.500 0.00 0.00 32.71 3.01
411 413 5.007724 AGACGTTCTTTTGACCTTGATGAAC 59.992 40.000 0.00 0.00 0.00 3.18
412 414 5.123227 AGACGTTCTTTTGACCTTGATGAA 58.877 37.500 0.00 0.00 0.00 2.57
413 415 4.703897 AGACGTTCTTTTGACCTTGATGA 58.296 39.130 0.00 0.00 0.00 2.92
414 416 5.465390 TGTAGACGTTCTTTTGACCTTGATG 59.535 40.000 0.00 0.00 0.00 3.07
415 417 5.607477 TGTAGACGTTCTTTTGACCTTGAT 58.393 37.500 0.00 0.00 0.00 2.57
416 418 5.013568 TGTAGACGTTCTTTTGACCTTGA 57.986 39.130 0.00 0.00 0.00 3.02
417 419 5.728351 TTGTAGACGTTCTTTTGACCTTG 57.272 39.130 0.00 0.00 0.00 3.61
418 420 5.220796 GCTTTGTAGACGTTCTTTTGACCTT 60.221 40.000 0.00 0.00 0.00 3.50
419 421 4.272748 GCTTTGTAGACGTTCTTTTGACCT 59.727 41.667 0.00 0.00 0.00 3.85
420 422 4.272748 AGCTTTGTAGACGTTCTTTTGACC 59.727 41.667 0.00 0.00 0.00 4.02
421 423 5.006358 TGAGCTTTGTAGACGTTCTTTTGAC 59.994 40.000 0.00 0.00 0.00 3.18
422 424 5.006358 GTGAGCTTTGTAGACGTTCTTTTGA 59.994 40.000 0.00 0.00 0.00 2.69
423 425 5.198274 GTGAGCTTTGTAGACGTTCTTTTG 58.802 41.667 0.00 0.00 0.00 2.44
424 426 4.873827 TGTGAGCTTTGTAGACGTTCTTTT 59.126 37.500 0.00 0.00 0.00 2.27
425 427 4.439057 TGTGAGCTTTGTAGACGTTCTTT 58.561 39.130 0.00 0.00 0.00 2.52
426 428 4.054780 TGTGAGCTTTGTAGACGTTCTT 57.945 40.909 0.00 0.00 0.00 2.52
427 429 3.728076 TGTGAGCTTTGTAGACGTTCT 57.272 42.857 0.00 0.00 0.00 3.01
428 430 3.368236 GGATGTGAGCTTTGTAGACGTTC 59.632 47.826 0.00 0.00 0.00 3.95
429 431 3.326747 GGATGTGAGCTTTGTAGACGTT 58.673 45.455 0.00 0.00 0.00 3.99
430 432 2.353803 GGGATGTGAGCTTTGTAGACGT 60.354 50.000 0.00 0.00 0.00 4.34
431 433 2.271800 GGGATGTGAGCTTTGTAGACG 58.728 52.381 0.00 0.00 0.00 4.18
446 448 5.413833 GCACAGATATCCTAACATTGGGATG 59.586 44.000 17.30 6.75 46.49 3.51
490 657 2.713967 GCAAGCGCCAATGGGTCAT 61.714 57.895 2.29 0.00 36.17 3.06
498 665 3.143675 CTCTTCTAGCAAGCGCCAA 57.856 52.632 2.29 0.00 39.83 4.52
499 666 4.919653 CTCTTCTAGCAAGCGCCA 57.080 55.556 2.29 0.00 39.83 5.69
525 692 3.828451 ACTTGTGATGATGAACCCCAAAG 59.172 43.478 0.00 0.00 0.00 2.77
551 718 0.824759 AGGTGAGGGATGCGTTACTC 59.175 55.000 2.11 4.39 0.00 2.59
575 742 5.560966 ACAAATTAGGGCAGTAAACGATG 57.439 39.130 0.00 0.00 0.00 3.84
673 841 3.270877 GGTGCATTGAAGGAGTACGAAT 58.729 45.455 0.00 0.00 0.00 3.34
676 844 2.093306 TGGTGCATTGAAGGAGTACG 57.907 50.000 0.00 0.00 0.00 3.67
700 868 3.499737 CCTGTGGCGCGTTCATCC 61.500 66.667 8.43 0.00 0.00 3.51
780 948 0.739462 CTCGCAAGTGCCCGTCAATA 60.739 55.000 0.00 0.00 37.91 1.90
781 949 2.031919 TCGCAAGTGCCCGTCAAT 59.968 55.556 0.00 0.00 37.91 2.57
782 950 2.652382 TTCTCGCAAGTGCCCGTCAA 62.652 55.000 0.00 0.00 37.91 3.18
953 1121 9.198837 CTTCCTTCTACTACTTCTCTTTGAAAC 57.801 37.037 0.00 0.00 33.79 2.78
1120 1288 4.093998 CACTGCTACTTTCAGATGCGATTT 59.906 41.667 0.00 0.00 35.61 2.17
1158 1332 7.158697 TGAAGGAAGTGAAATTAACGAGATCA 58.841 34.615 0.00 0.00 0.00 2.92
1166 1469 7.010160 ACCCTGAATGAAGGAAGTGAAATTAA 58.990 34.615 0.00 0.00 40.02 1.40
1213 1516 3.553096 GGAAGTTGCCGTATGATCTCGAT 60.553 47.826 0.00 0.00 0.00 3.59
1252 1555 2.020694 GCCCTCTGCGTGTAGTACCTA 61.021 57.143 0.00 0.00 0.00 3.08
1253 1556 1.321074 GCCCTCTGCGTGTAGTACCT 61.321 60.000 0.00 0.00 0.00 3.08
1254 1557 1.141234 GCCCTCTGCGTGTAGTACC 59.859 63.158 0.00 0.00 0.00 3.34
1459 1762 3.804325 CAGAAATCTTACGCATGTCGGAT 59.196 43.478 12.85 4.83 43.86 4.18
1580 2110 9.856803 GCTAAACTTTTCATCGCAAAATAAAAA 57.143 25.926 0.00 0.00 0.00 1.94
1581 2111 9.035607 TGCTAAACTTTTCATCGCAAAATAAAA 57.964 25.926 0.00 0.00 0.00 1.52
1582 2112 8.581057 TGCTAAACTTTTCATCGCAAAATAAA 57.419 26.923 0.00 0.00 0.00 1.40
1583 2113 8.646356 CATGCTAAACTTTTCATCGCAAAATAA 58.354 29.630 0.00 0.00 0.00 1.40
1584 2114 7.812191 ACATGCTAAACTTTTCATCGCAAAATA 59.188 29.630 0.00 0.00 0.00 1.40
1585 2115 6.646240 ACATGCTAAACTTTTCATCGCAAAAT 59.354 30.769 0.00 0.00 0.00 1.82
1586 2116 5.982516 ACATGCTAAACTTTTCATCGCAAAA 59.017 32.000 0.00 0.00 0.00 2.44
1587 2117 5.527951 ACATGCTAAACTTTTCATCGCAAA 58.472 33.333 0.00 0.00 0.00 3.68
1588 2118 5.119931 ACATGCTAAACTTTTCATCGCAA 57.880 34.783 0.00 0.00 0.00 4.85
1589 2119 4.764679 ACATGCTAAACTTTTCATCGCA 57.235 36.364 0.00 0.00 0.00 5.10
1590 2120 5.393962 AGAACATGCTAAACTTTTCATCGC 58.606 37.500 0.00 0.00 0.00 4.58
1591 2121 6.602179 TGAGAACATGCTAAACTTTTCATCG 58.398 36.000 0.00 0.00 0.00 3.84
1592 2122 6.525976 GCTGAGAACATGCTAAACTTTTCATC 59.474 38.462 0.00 0.00 0.00 2.92
1593 2123 6.208204 AGCTGAGAACATGCTAAACTTTTCAT 59.792 34.615 0.00 0.00 35.05 2.57
1594 2124 5.532406 AGCTGAGAACATGCTAAACTTTTCA 59.468 36.000 0.00 0.00 35.05 2.69
1595 2125 6.006759 AGCTGAGAACATGCTAAACTTTTC 57.993 37.500 0.00 0.00 35.05 2.29
1596 2126 5.767168 AGAGCTGAGAACATGCTAAACTTTT 59.233 36.000 0.00 0.00 37.16 2.27
1597 2127 5.180868 CAGAGCTGAGAACATGCTAAACTTT 59.819 40.000 0.00 0.00 37.16 2.66
1598 2128 4.694509 CAGAGCTGAGAACATGCTAAACTT 59.305 41.667 0.00 0.00 37.16 2.66
1635 2171 0.036732 TTCTTGCTCTGACGGCCAAT 59.963 50.000 2.24 0.00 0.00 3.16
1694 2230 4.142049 GGAGAAGTCCATGGAGTAGTTCTG 60.142 50.000 22.61 0.00 43.31 3.02
1874 2418 2.677524 AACCCTGCATGCACGCAT 60.678 55.556 18.46 0.00 42.06 4.73
2190 2744 4.509737 GCCGTCGTACTCCCAGGC 62.510 72.222 0.00 0.00 37.61 4.85
2192 2746 4.189188 CCGCCGTCGTACTCCCAG 62.189 72.222 0.00 0.00 0.00 4.45
2402 2956 1.812708 GCCCGGTTGTACTTGTTCAGT 60.813 52.381 0.00 0.00 39.87 3.41
2575 3129 5.262588 TGATACGACGGTACTACAGTAGA 57.737 43.478 14.94 0.00 0.00 2.59
2576 3130 5.521735 AGTTGATACGACGGTACTACAGTAG 59.478 44.000 6.00 6.00 0.00 2.57
2578 3132 4.256920 AGTTGATACGACGGTACTACAGT 58.743 43.478 0.00 0.00 0.00 3.55
2581 3135 6.530913 TGATAGTTGATACGACGGTACTAC 57.469 41.667 0.00 0.00 0.00 2.73
2651 3206 5.812642 AGAAGCGAGTGTAATCATCGAAAAT 59.187 36.000 0.00 0.00 38.72 1.82
2671 3226 1.263217 ACGCAACGGCAGTAAAAGAAG 59.737 47.619 0.00 0.00 41.24 2.85
2720 3275 3.576118 TCAGCTAAGCAGAGAAGTCAGTT 59.424 43.478 0.00 0.00 0.00 3.16
2738 3293 1.538047 TCCCTCTTGTGCAAATCAGC 58.462 50.000 0.00 0.00 0.00 4.26
2763 3318 5.649782 AATCTGCTACAAAAATCCCACAG 57.350 39.130 0.00 0.00 0.00 3.66
2766 3321 7.301868 AGAAAAATCTGCTACAAAAATCCCA 57.698 32.000 0.00 0.00 0.00 4.37
2802 3359 1.724582 ATGTGCGCGCTTAATTCCCC 61.725 55.000 33.29 8.74 0.00 4.81
2803 3360 0.941542 TATGTGCGCGCTTAATTCCC 59.058 50.000 33.29 9.78 0.00 3.97
2805 3362 1.971962 GCATATGTGCGCGCTTAATTC 59.028 47.619 33.29 14.99 42.28 2.17
2877 3439 7.929785 AGTGATTTCGTTAAAAGACAGGAGTTA 59.070 33.333 0.00 0.00 0.00 2.24
2881 3443 7.439381 ACTAGTGATTTCGTTAAAAGACAGGA 58.561 34.615 0.00 0.00 0.00 3.86
2882 3444 7.653767 ACTAGTGATTTCGTTAAAAGACAGG 57.346 36.000 0.00 0.00 0.00 4.00
2893 3455 9.447157 AGAGTACTACTTAACTAGTGATTTCGT 57.553 33.333 0.00 0.00 37.73 3.85
2905 3467 5.947443 TCTCCGCAAAGAGTACTACTTAAC 58.053 41.667 0.00 0.00 35.28 2.01
2911 3473 4.270834 AGTGATCTCCGCAAAGAGTACTA 58.729 43.478 0.00 0.00 35.28 1.82
2919 3481 4.537135 AAGTTAGAGTGATCTCCGCAAA 57.463 40.909 0.00 0.00 41.26 3.68
2924 3486 4.141824 CCTGGGAAAGTTAGAGTGATCTCC 60.142 50.000 0.00 0.00 41.26 3.71
2925 3487 4.468153 ACCTGGGAAAGTTAGAGTGATCTC 59.532 45.833 0.00 0.00 40.70 2.75
2929 3491 3.496160 GCAACCTGGGAAAGTTAGAGTGA 60.496 47.826 0.00 0.00 0.00 3.41
2935 3497 1.141254 TGTCGCAACCTGGGAAAGTTA 59.859 47.619 0.00 0.00 41.08 2.24
2936 3498 0.106918 TGTCGCAACCTGGGAAAGTT 60.107 50.000 0.00 0.00 41.08 2.66
2939 3501 0.106918 ACTTGTCGCAACCTGGGAAA 60.107 50.000 0.00 0.00 41.08 3.13
2943 3505 2.908073 GCCACTTGTCGCAACCTGG 61.908 63.158 0.00 0.00 0.00 4.45
2955 3517 1.111277 AAGGAAAAACTGCGCCACTT 58.889 45.000 4.18 0.00 0.00 3.16
2956 3518 1.111277 AAAGGAAAAACTGCGCCACT 58.889 45.000 4.18 0.00 0.00 4.00
2958 3520 2.545731 GAAAAAGGAAAAACTGCGCCA 58.454 42.857 4.18 0.00 0.00 5.69
2960 3522 1.521006 CGGAAAAAGGAAAAACTGCGC 59.479 47.619 0.00 0.00 0.00 6.09
2961 3523 2.804647 ACGGAAAAAGGAAAAACTGCG 58.195 42.857 0.00 0.00 0.00 5.18
2962 3524 5.177725 TCTACGGAAAAAGGAAAAACTGC 57.822 39.130 0.00 0.00 0.00 4.40
2963 3525 6.016610 TGGATCTACGGAAAAAGGAAAAACTG 60.017 38.462 0.00 0.00 0.00 3.16
2978 3540 9.801873 AAATGTTTTGAATAAATGGATCTACGG 57.198 29.630 0.00 0.00 0.00 4.02
3015 3577 2.452813 CGAGATTTGGACGCACGGG 61.453 63.158 0.00 0.00 0.00 5.28
3046 3608 1.445410 CGACGCGAGGAATCCAACA 60.445 57.895 15.93 0.00 0.00 3.33
3081 3643 6.767902 GTCAAAAGCTATGAACATGGGATCTA 59.232 38.462 3.86 0.00 0.00 1.98
3082 3644 5.591877 GTCAAAAGCTATGAACATGGGATCT 59.408 40.000 3.86 0.00 0.00 2.75
3083 3645 5.504665 CGTCAAAAGCTATGAACATGGGATC 60.505 44.000 3.86 0.00 0.00 3.36
3165 3734 0.517316 CGTGCCTCTTTCGGAAAAGG 59.483 55.000 19.02 19.02 41.88 3.11
3167 3736 1.512156 GGCGTGCCTCTTTCGGAAAA 61.512 55.000 2.98 0.00 0.00 2.29
3219 3789 0.317854 GGCACGGTTTTGCTTCTGTC 60.318 55.000 0.00 0.00 42.56 3.51
3220 3790 0.751643 AGGCACGGTTTTGCTTCTGT 60.752 50.000 0.00 0.00 42.56 3.41
3222 3792 2.331265 GAGGCACGGTTTTGCTTCT 58.669 52.632 1.28 0.00 43.46 2.85
3384 3971 1.838913 CACGGTTGTGCTTTCAAAGG 58.161 50.000 0.00 0.00 39.67 3.11
3395 3982 2.964438 TTCGCGAGAAGCACGGTTGT 62.964 55.000 9.59 0.00 46.92 3.32
3396 3983 2.307309 TTCGCGAGAAGCACGGTTG 61.307 57.895 9.59 0.00 46.92 3.77
3397 3984 2.028484 TTCGCGAGAAGCACGGTT 59.972 55.556 9.59 0.00 46.92 4.44
3455 4042 3.941657 GAGTCACGGCAGTGCCTCC 62.942 68.421 30.81 15.51 44.88 4.30
3463 4050 3.202216 TTTCGCGAGAGTCACGGCA 62.202 57.895 9.59 0.00 43.69 5.69


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

AutoCloner maintained by Alex Coulton.