Multiple sequence alignment - TraesCS2D01G074200

Loading Multiple Alignment...

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 TraesCS2D01G074200 chr2D 100.000 2987 0 0 462 3448 31730500 31727514 0.000000e+00 5517
1 TraesCS2D01G074200 chr2D 86.332 1573 154 23 916 2454 31608542 31606997 0.000000e+00 1657
2 TraesCS2D01G074200 chr2D 90.122 1144 108 5 1334 2474 31561241 31560100 0.000000e+00 1482
3 TraesCS2D01G074200 chr2D 100.000 178 0 0 1 178 31730961 31730784 2.570000e-86 329
4 TraesCS2D01G074200 chr2D 94.393 107 6 0 996 1102 346045621 346045727 7.660000e-37 165
5 TraesCS2D01G074200 chr2A 91.212 2549 190 21 885 3420 33564401 33561874 0.000000e+00 3435
6 TraesCS2D01G074200 chr2A 86.430 1577 154 26 916 2459 33382694 33381145 0.000000e+00 1672
7 TraesCS2D01G074200 chr2A 89.750 1122 114 1 1334 2454 33343997 33342876 0.000000e+00 1434
8 TraesCS2D01G074200 chr2A 84.281 598 46 22 2797 3392 33554711 33554160 1.090000e-149 540
9 TraesCS2D01G074200 chr2A 93.678 174 11 0 707 880 33564618 33564445 9.490000e-66 261
10 TraesCS2D01G074200 chr2B 89.419 2117 160 29 1345 3444 52123408 52125477 0.000000e+00 2610
11 TraesCS2D01G074200 chr2B 87.613 1550 155 20 916 2454 51706992 51705469 0.000000e+00 1764
12 TraesCS2D01G074200 chr2B 91.546 414 24 4 895 1305 52122996 52123401 8.360000e-156 560
13 TraesCS2D01G074200 chr2B 93.909 197 10 1 3248 3444 51703644 51703450 2.600000e-76 296
14 TraesCS2D01G074200 chr2B 88.750 160 17 1 1 159 52121997 52122156 9.760000e-46 195
15 TraesCS2D01G074200 chr2B 91.270 126 9 1 3260 3385 51704668 51704545 1.650000e-38 171
16 TraesCS2D01G074200 chrUn 88.942 1049 112 1 1388 2436 17252922 17253966 0.000000e+00 1291
17 TraesCS2D01G074200 chr7D 81.366 1025 173 13 1410 2431 154376804 154377813 0.000000e+00 819
18 TraesCS2D01G074200 chr7A 81.110 1027 172 17 1410 2431 156267808 156268817 0.000000e+00 802


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 TraesCS2D01G074200 chr2D 31727514 31730961 3447 True 2923.000000 5517 100.000000 1 3448 2 chr2D.!!$R3 3447
1 TraesCS2D01G074200 chr2D 31606997 31608542 1545 True 1657.000000 1657 86.332000 916 2454 1 chr2D.!!$R2 1538
2 TraesCS2D01G074200 chr2D 31560100 31561241 1141 True 1482.000000 1482 90.122000 1334 2474 1 chr2D.!!$R1 1140
3 TraesCS2D01G074200 chr2A 33561874 33564618 2744 True 1848.000000 3435 92.445000 707 3420 2 chr2A.!!$R4 2713
4 TraesCS2D01G074200 chr2A 33381145 33382694 1549 True 1672.000000 1672 86.430000 916 2459 1 chr2A.!!$R2 1543
5 TraesCS2D01G074200 chr2A 33342876 33343997 1121 True 1434.000000 1434 89.750000 1334 2454 1 chr2A.!!$R1 1120
6 TraesCS2D01G074200 chr2A 33554160 33554711 551 True 540.000000 540 84.281000 2797 3392 1 chr2A.!!$R3 595
7 TraesCS2D01G074200 chr2B 52121997 52125477 3480 False 1121.666667 2610 89.905000 1 3444 3 chr2B.!!$F1 3443
8 TraesCS2D01G074200 chr2B 51703450 51706992 3542 True 743.666667 1764 90.930667 916 3444 3 chr2B.!!$R1 2528
9 TraesCS2D01G074200 chrUn 17252922 17253966 1044 False 1291.000000 1291 88.942000 1388 2436 1 chrUn.!!$F1 1048
10 TraesCS2D01G074200 chr7D 154376804 154377813 1009 False 819.000000 819 81.366000 1410 2431 1 chr7D.!!$F1 1021
11 TraesCS2D01G074200 chr7A 156267808 156268817 1009 False 802.000000 802 81.110000 1410 2431 1 chr7A.!!$F1 1021

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
56 57 0.119155 AGGGGTCAGTTGAGGATCCA 59.881 55.0 15.82 0.0 37.27 3.41 F
589 695 0.180406 ACAAGCTCGGTTGGACAGTT 59.820 50.0 12.75 0.0 0.00 3.16 F
909 1091 0.398318 AGAACCCAGCACTTGACTCC 59.602 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 2106 0.098200 CGACGTAGATGAAGCCGTGA 59.902 55.000 0.0 0.0 33.03 4.35 R
2148 2368 2.649034 GAAGAGGTCACCGTCGCA 59.351 61.111 0.0 0.0 0.00 5.10 R
2841 4411 2.009774 CCAAGAAACAGTAGCCCATCG 58.990 52.381 0.0 0.0 0.00 3.84 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
47 48 2.501261 GCGAAGTTTTAGGGGTCAGTT 58.499 47.619 0.00 0.00 0.00 3.16
50 51 3.746492 CGAAGTTTTAGGGGTCAGTTGAG 59.254 47.826 0.00 0.00 0.00 3.02
56 57 0.119155 AGGGGTCAGTTGAGGATCCA 59.881 55.000 15.82 0.00 37.27 3.41
69 71 1.869648 AGGATCCAGGTCATAGGAGGT 59.130 52.381 15.82 0.00 37.34 3.85
80 82 2.433239 TCATAGGAGGTAAAAGGGCGTC 59.567 50.000 0.00 0.00 0.00 5.19
83 85 2.760581 AGGAGGTAAAAGGGCGTCTAT 58.239 47.619 0.00 0.00 0.00 1.98
92 94 1.680338 AGGGCGTCTATTTTCCATGC 58.320 50.000 0.00 0.00 0.00 4.06
100 102 5.701290 GCGTCTATTTTCCATGCTAGGTATT 59.299 40.000 0.00 0.00 0.00 1.89
101 103 6.347725 GCGTCTATTTTCCATGCTAGGTATTG 60.348 42.308 0.00 0.00 0.00 1.90
116 118 6.238211 GCTAGGTATTGTGTTGCTGATAGTTG 60.238 42.308 0.00 0.00 0.00 3.16
121 123 7.114811 GGTATTGTGTTGCTGATAGTTGTTTTG 59.885 37.037 0.00 0.00 0.00 2.44
122 124 4.358851 TGTGTTGCTGATAGTTGTTTTGC 58.641 39.130 0.00 0.00 0.00 3.68
481 583 2.640316 AGTTCCAGACAAAGTCCACC 57.360 50.000 0.00 0.00 32.18 4.61
482 584 1.202651 AGTTCCAGACAAAGTCCACCG 60.203 52.381 0.00 0.00 32.18 4.94
484 586 0.679505 TCCAGACAAAGTCCACCGAG 59.320 55.000 0.00 0.00 32.18 4.63
489 595 1.006102 CAAAGTCCACCGAGTCGCT 60.006 57.895 7.12 0.00 0.00 4.93
496 602 0.443869 CCACCGAGTCGCTGAATTTG 59.556 55.000 7.12 0.00 0.00 2.32
498 604 1.298859 ACCGAGTCGCTGAATTTGCC 61.299 55.000 7.12 0.00 0.00 4.52
501 607 0.796312 GAGTCGCTGAATTTGCCGAA 59.204 50.000 0.00 0.00 0.00 4.30
538 644 4.588278 GACAAAGTTCAGAAACAACTCGG 58.412 43.478 0.00 0.00 37.88 4.63
558 664 0.316689 CGTTGTGTTTGGCGAGTTCC 60.317 55.000 0.00 0.00 0.00 3.62
563 669 1.161563 TGTTTGGCGAGTTCCGTTCC 61.162 55.000 0.00 0.00 41.15 3.62
578 684 2.258013 TTCCCGGCAAACAAGCTCG 61.258 57.895 0.00 0.00 34.17 5.03
580 686 2.978010 CCGGCAAACAAGCTCGGT 60.978 61.111 0.00 0.00 40.82 4.69
589 695 0.180406 ACAAGCTCGGTTGGACAGTT 59.820 50.000 12.75 0.00 0.00 3.16
590 696 0.588252 CAAGCTCGGTTGGACAGTTG 59.412 55.000 1.09 0.00 0.00 3.16
592 698 1.045407 AGCTCGGTTGGACAGTTGTA 58.955 50.000 0.00 0.00 0.00 2.41
602 708 5.414454 GGTTGGACAGTTGTAAGCAATCATA 59.586 40.000 0.00 0.00 36.92 2.15
632 738 7.539712 TGCTAGTTTCTATTATTGTGCACTC 57.460 36.000 19.41 0.00 0.00 3.51
635 741 6.893958 AGTTTCTATTATTGTGCACTCGAG 57.106 37.500 19.41 11.84 0.00 4.04
650 756 7.386573 TGTGCACTCGAGAAACATTTAAATAGA 59.613 33.333 21.68 0.00 0.00 1.98
656 762 9.708222 CTCGAGAAACATTTAAATAGACATTGG 57.292 33.333 6.58 0.00 0.00 3.16
664 770 8.749354 ACATTTAAATAGACATTGGGGAGTTTC 58.251 33.333 0.00 0.00 0.00 2.78
692 799 5.069501 ACGATAACTCAGGAAACTACCAC 57.930 43.478 0.00 0.00 40.21 4.16
798 941 2.295909 GCTATGTCTAGAGGCCACAGAG 59.704 54.545 5.01 8.05 33.39 3.35
845 988 1.134946 AGCACACAAAGTTTGTCAGCC 59.865 47.619 26.34 14.07 43.23 4.85
880 1023 8.815912 AGTTTAAATGATTATTCCCAGCACTTT 58.184 29.630 0.00 0.00 0.00 2.66
881 1024 9.435688 GTTTAAATGATTATTCCCAGCACTTTT 57.564 29.630 0.00 0.00 0.00 2.27
906 1088 1.569479 GCGAGAACCCAGCACTTGAC 61.569 60.000 0.00 0.00 0.00 3.18
909 1091 0.398318 AGAACCCAGCACTTGACTCC 59.602 55.000 0.00 0.00 0.00 3.85
1037 1225 2.040939 CTCATGGCTCCTCAGACATCT 58.959 52.381 0.00 0.00 46.68 2.90
1068 1256 1.742761 CGATGCCATGGACAAGAACT 58.257 50.000 18.40 0.00 0.00 3.01
1135 1324 6.210396 ACGTATCGTGCATATGTACAATTG 57.790 37.500 21.64 3.24 39.18 2.32
1137 1326 6.074516 ACGTATCGTGCATATGTACAATTGAC 60.075 38.462 21.64 11.37 39.18 3.18
1142 1331 5.959527 CGTGCATATGTACAATTGACTTGAC 59.040 40.000 21.64 2.73 38.29 3.18
1237 1433 2.640316 AGGGCGAATAATGGAGGAAC 57.360 50.000 0.00 0.00 0.00 3.62
1241 1437 3.004734 GGGCGAATAATGGAGGAACAATG 59.995 47.826 0.00 0.00 0.00 2.82
1246 1442 5.764686 CGAATAATGGAGGAACAATGATGGA 59.235 40.000 0.00 0.00 0.00 3.41
1314 1513 1.291877 CCAAGGTGAAGCGGTCGAAG 61.292 60.000 0.00 0.00 0.00 3.79
1806 2026 1.453379 CTCTTCCTCTCCGGCCGTA 60.453 63.158 26.12 7.53 0.00 4.02
2079 2299 2.043852 AGATCGACCCAGACGGCT 60.044 61.111 0.00 0.00 33.26 5.52
2324 2544 2.048503 GACTACGTGTGCGCCCTT 60.049 61.111 4.18 0.00 42.83 3.95
2436 2656 0.104120 TGATAGGCCCGTCAACATCG 59.896 55.000 0.00 0.00 0.00 3.84
2461 2681 7.081976 GGCATGGCCTAATAAATTTTACTACG 58.918 38.462 8.35 0.00 46.69 3.51
2464 2684 9.445786 CATGGCCTAATAAATTTTACTACGTTG 57.554 33.333 3.32 0.00 0.00 4.10
2466 2686 8.667463 TGGCCTAATAAATTTTACTACGTTGTC 58.333 33.333 5.77 0.00 0.00 3.18
2468 2688 9.911980 GCCTAATAAATTTTACTACGTTGTCTC 57.088 33.333 5.77 0.00 0.00 3.36
2475 2695 9.511144 AAATTTTACTACGTTGTCTCAAAAAGG 57.489 29.630 5.77 0.00 0.00 3.11
2476 2696 7.846644 TTTTACTACGTTGTCTCAAAAAGGA 57.153 32.000 5.77 0.00 0.00 3.36
2662 4231 9.443283 TTTGTAAATTATGTGCAAATTTGTTGC 57.557 25.926 19.03 6.84 45.11 4.17
2667 4236 3.965292 TGTGCAAATTTGTTGCCATTG 57.035 38.095 19.03 0.00 44.32 2.82
2731 4301 4.876107 GCCACTAATTCATTCTTCCTTCGA 59.124 41.667 0.00 0.00 0.00 3.71
2752 4322 8.980143 TTCGAAAACTTCATTTCTTTTGTTCT 57.020 26.923 0.00 0.00 37.20 3.01
2754 4324 9.072294 TCGAAAACTTCATTTCTTTTGTTCTTC 57.928 29.630 0.00 0.00 37.20 2.87
2824 4394 4.753107 GGGTCAGTTTCTGTTATGTTTCGA 59.247 41.667 0.00 0.00 32.61 3.71
2841 4411 3.814005 TCGAACCAAGCCTAAGTATCC 57.186 47.619 0.00 0.00 0.00 2.59
2857 4427 2.622064 ATCCGATGGGCTACTGTTTC 57.378 50.000 0.00 0.00 0.00 2.78
2873 4443 0.467804 TTTCTTGGTTGCAAAGGGCC 59.532 50.000 0.00 0.00 43.89 5.80
2914 4486 7.865706 AATGTCTAATAAGCCTAGTTTGGTG 57.134 36.000 0.00 0.00 0.00 4.17
2921 4493 6.879367 ATAAGCCTAGTTTGGTGGTAAGTA 57.121 37.500 0.00 0.00 0.00 2.24
2928 4500 7.468220 GCCTAGTTTGGTGGTAAGTATTTATGC 60.468 40.741 0.00 0.00 0.00 3.14
2929 4501 7.773690 CCTAGTTTGGTGGTAAGTATTTATGCT 59.226 37.037 0.00 0.00 0.00 3.79
3004 4581 8.950007 TTTTATTTGAAGGATAAACCACTCCT 57.050 30.769 0.00 0.00 43.86 3.69
3042 4619 8.209917 TCCTTAGAAAGAGTTTGTTTGTCTTC 57.790 34.615 0.00 0.00 30.07 2.87
3118 4696 6.510879 AAGAAACGTGGTCTTCTTTCTTTT 57.489 33.333 7.06 0.00 39.02 2.27
3119 4697 6.510879 AGAAACGTGGTCTTCTTTCTTTTT 57.489 33.333 0.00 0.00 30.39 1.94
3257 5091 6.914757 GTCGAGTAAAAAGGTACTATACGCAT 59.085 38.462 0.00 0.00 38.49 4.73
3315 5149 0.976641 AGCCACGAGTCCAGATTTGA 59.023 50.000 0.00 0.00 0.00 2.69
3361 5196 3.360249 AATCAAGTTGAAGCAGCACAC 57.640 42.857 10.14 0.00 0.00 3.82
3369 5204 1.942657 TGAAGCAGCACACTCAGAAAC 59.057 47.619 0.00 0.00 0.00 2.78
3388 5223 4.329462 AACCTCGAAGATAAGATGAGCC 57.671 45.455 0.00 0.00 33.89 4.70
3424 5259 1.402787 TCTAGCGTCATCCAGCATGA 58.597 50.000 0.00 0.00 39.69 3.07
3444 5279 6.620949 GCATGAGAAGCTTGCATATAGATGTG 60.621 42.308 2.10 0.00 44.57 3.21
3445 5280 5.922053 TGAGAAGCTTGCATATAGATGTGT 58.078 37.500 2.10 0.00 35.30 3.72
3446 5281 7.054491 TGAGAAGCTTGCATATAGATGTGTA 57.946 36.000 2.10 0.00 35.30 2.90
3447 5282 7.674120 TGAGAAGCTTGCATATAGATGTGTAT 58.326 34.615 2.10 0.00 35.30 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.399303 CCTTCTCGGCCAAATTCAGTATTT 59.601 41.667 2.24 0.00 36.90 1.40
29 30 4.072839 CCTCAACTGACCCCTAAAACTTC 58.927 47.826 0.00 0.00 0.00 3.01
47 48 2.158249 CCTCCTATGACCTGGATCCTCA 60.158 54.545 14.23 9.04 0.00 3.86
50 51 2.407340 ACCTCCTATGACCTGGATCC 57.593 55.000 4.20 4.20 0.00 3.36
56 57 2.778270 GCCCTTTTACCTCCTATGACCT 59.222 50.000 0.00 0.00 0.00 3.85
69 71 4.097286 GCATGGAAAATAGACGCCCTTTTA 59.903 41.667 0.00 0.00 0.00 1.52
80 82 7.807977 ACACAATACCTAGCATGGAAAATAG 57.192 36.000 0.00 0.00 0.00 1.73
83 85 5.336372 GCAACACAATACCTAGCATGGAAAA 60.336 40.000 0.00 0.00 0.00 2.29
92 94 6.818644 ACAACTATCAGCAACACAATACCTAG 59.181 38.462 0.00 0.00 0.00 3.02
100 102 4.358851 GCAAAACAACTATCAGCAACACA 58.641 39.130 0.00 0.00 0.00 3.72
101 103 3.421888 CGCAAAACAACTATCAGCAACAC 59.578 43.478 0.00 0.00 0.00 3.32
116 118 2.116366 CTAAGTTGTGTGCCGCAAAAC 58.884 47.619 3.01 3.01 43.88 2.43
121 123 0.240945 ATTGCTAAGTTGTGTGCCGC 59.759 50.000 0.00 0.00 0.00 6.53
122 124 1.535028 TCATTGCTAAGTTGTGTGCCG 59.465 47.619 0.00 0.00 0.00 5.69
481 583 1.059369 CGGCAAATTCAGCGACTCG 59.941 57.895 0.00 0.00 0.00 4.18
482 584 0.796312 TTCGGCAAATTCAGCGACTC 59.204 50.000 0.00 0.00 0.00 3.36
484 586 2.262572 AATTCGGCAAATTCAGCGAC 57.737 45.000 0.00 0.00 31.78 5.19
496 602 1.657822 GAGTTCCCTCTGAATTCGGC 58.342 55.000 9.58 0.00 34.90 5.54
501 607 3.325135 ACTTTGTCGAGTTCCCTCTGAAT 59.675 43.478 0.00 0.00 34.90 2.57
517 623 3.181500 GCCGAGTTGTTTCTGAACTTTGT 60.181 43.478 0.00 0.00 33.71 2.83
519 625 2.031683 CGCCGAGTTGTTTCTGAACTTT 59.968 45.455 0.00 0.00 33.71 2.66
538 644 0.928451 GAACTCGCCAAACACAACGC 60.928 55.000 0.00 0.00 0.00 4.84
563 669 2.551912 AACCGAGCTTGTTTGCCGG 61.552 57.895 0.00 0.00 45.44 6.13
571 677 0.588252 CAACTGTCCAACCGAGCTTG 59.412 55.000 0.00 0.00 0.00 4.01
572 678 0.180406 ACAACTGTCCAACCGAGCTT 59.820 50.000 0.00 0.00 0.00 3.74
573 679 1.045407 TACAACTGTCCAACCGAGCT 58.955 50.000 0.00 0.00 0.00 4.09
574 680 1.798813 CTTACAACTGTCCAACCGAGC 59.201 52.381 0.00 0.00 0.00 5.03
578 684 3.568007 TGATTGCTTACAACTGTCCAACC 59.432 43.478 0.00 0.00 38.99 3.77
580 686 7.517614 TTTATGATTGCTTACAACTGTCCAA 57.482 32.000 0.00 0.00 38.99 3.53
611 717 7.768240 TCTCGAGTGCACAATAATAGAAACTA 58.232 34.615 21.04 0.00 0.00 2.24
632 738 7.915397 CCCCAATGTCTATTTAAATGTTTCTCG 59.085 37.037 11.05 0.00 0.00 4.04
635 741 8.749354 ACTCCCCAATGTCTATTTAAATGTTTC 58.251 33.333 11.05 0.32 0.00 2.78
650 756 3.181470 CGTTTTTGGAAACTCCCCAATGT 60.181 43.478 0.00 0.00 42.63 2.71
656 762 5.239963 TGAGTTATCGTTTTTGGAAACTCCC 59.760 40.000 9.74 0.00 42.35 4.30
664 770 6.313744 AGTTTCCTGAGTTATCGTTTTTGG 57.686 37.500 0.00 0.00 0.00 3.28
672 778 5.069501 ACGTGGTAGTTTCCTGAGTTATC 57.930 43.478 0.00 0.00 0.00 1.75
673 779 5.479124 AACGTGGTAGTTTCCTGAGTTAT 57.521 39.130 0.00 0.00 0.00 1.89
682 789 4.084900 CGTTTCACCTAACGTGGTAGTTTC 60.085 45.833 0.00 0.00 44.28 2.78
798 941 4.077188 GTGTTGAGCGCGTGGAGC 62.077 66.667 8.43 0.00 43.95 4.70
819 962 4.094887 TGACAAACTTTGTGTGCTCTCTTC 59.905 41.667 11.97 0.00 45.52 2.87
882 1025 0.383949 GTGCTGGGTTCTCGCAAAAA 59.616 50.000 0.00 0.00 36.14 1.94
890 1072 0.398318 GGAGTCAAGTGCTGGGTTCT 59.602 55.000 0.00 0.00 0.00 3.01
909 1091 0.673022 GAGCAGCTTCACTCCACCAG 60.673 60.000 0.00 0.00 0.00 4.00
1037 1225 0.821301 TGGCATCGCAAGTGGACAAA 60.821 50.000 0.00 0.00 39.48 2.83
1068 1256 8.429641 GTCACTTTGAGACCTATATTATTCCCA 58.570 37.037 0.00 0.00 0.00 4.37
1135 1324 9.900710 ATCGATACACTAATCTATTGTCAAGTC 57.099 33.333 0.00 0.00 0.00 3.01
1137 1326 8.642885 GCATCGATACACTAATCTATTGTCAAG 58.357 37.037 0.00 0.00 0.00 3.02
1142 1331 7.063780 TGCATGCATCGATACACTAATCTATTG 59.936 37.037 18.46 0.00 0.00 1.90
1237 1433 6.762187 GCTCATACTCATATCCTCCATCATTG 59.238 42.308 0.00 0.00 0.00 2.82
1241 1437 5.395103 GGTGCTCATACTCATATCCTCCATC 60.395 48.000 0.00 0.00 0.00 3.51
1246 1442 2.232452 GCGGTGCTCATACTCATATCCT 59.768 50.000 0.00 0.00 0.00 3.24
1314 1513 5.125739 TGCTTCTCTTACTAACTCCTGCTAC 59.874 44.000 0.00 0.00 0.00 3.58
1806 2026 2.108514 CGACCTGCCGCATGTCAAT 61.109 57.895 23.30 0.00 30.40 2.57
1886 2106 0.098200 CGACGTAGATGAAGCCGTGA 59.902 55.000 0.00 0.00 33.03 4.35
2148 2368 2.649034 GAAGAGGTCACCGTCGCA 59.351 61.111 0.00 0.00 0.00 5.10
2304 2524 4.065281 GGCGCACACGTAGTCCCT 62.065 66.667 10.83 0.00 41.61 4.20
2436 2656 7.255346 ACGTAGTAAAATTTATTAGGCCATGCC 60.255 37.037 5.01 0.00 46.32 4.40
2452 2672 7.846644 TCCTTTTTGAGACAACGTAGTAAAA 57.153 32.000 0.00 0.00 45.00 1.52
2505 2732 5.975988 TCCTCCCAAATATAGCAAAGAGT 57.024 39.130 0.00 0.00 0.00 3.24
2700 4270 7.939588 GGAAGAATGAATTAGTGGCTATTACCT 59.060 37.037 0.00 0.00 0.00 3.08
2824 4394 3.181454 CCATCGGATACTTAGGCTTGGTT 60.181 47.826 0.00 0.00 0.00 3.67
2841 4411 2.009774 CCAAGAAACAGTAGCCCATCG 58.990 52.381 0.00 0.00 0.00 3.84
2857 4427 2.339712 CGGCCCTTTGCAACCAAG 59.660 61.111 0.00 0.00 43.89 3.61
2901 4473 5.774102 AATACTTACCACCAAACTAGGCT 57.226 39.130 0.00 0.00 0.00 4.58
2904 4476 8.732746 AGCATAAATACTTACCACCAAACTAG 57.267 34.615 0.00 0.00 0.00 2.57
2982 4559 7.510675 AGAGGAGTGGTTTATCCTTCAAATA 57.489 36.000 0.00 0.00 46.12 1.40
2987 4564 6.154706 TGAACTAGAGGAGTGGTTTATCCTTC 59.845 42.308 0.00 0.00 46.12 3.46
3004 4581 7.179338 ACTCTTTCTAAGGAAGCATGAACTAGA 59.821 37.037 0.00 0.00 32.61 2.43
3119 4697 9.793252 CTCAAAGAAGAAATGAAAGAAAACTGA 57.207 29.630 0.00 0.00 0.00 3.41
3204 4782 9.218440 ACAAAATAATACAAAAATCCCTTGCAG 57.782 29.630 0.00 0.00 0.00 4.41
3257 5091 6.297582 TCTTGTTTTCCCGAGTAAACCATAA 58.702 36.000 0.00 0.00 33.61 1.90
3315 5149 4.612264 ATGAACAAGCAGCTGGAAATTT 57.388 36.364 17.12 0.00 0.00 1.82
3361 5196 6.800543 TCATCTTATCTTCGAGGTTTCTGAG 58.199 40.000 0.00 0.00 0.00 3.35
3369 5204 4.157656 CCTAGGCTCATCTTATCTTCGAGG 59.842 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.