Multiple sequence alignment - TraesCS3B01G034800

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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 TraesCS3B01G034800 chr3B 100.000 3422 0 0 1 3422 16759159 16755738 0.000000e+00 6320.0
1 TraesCS3B01G034800 chr3B 94.293 1542 64 7 965 2506 16692581 16694098 0.000000e+00 2338.0
2 TraesCS3B01G034800 chr3B 95.382 1126 35 3 816 1930 16958397 16959516 0.000000e+00 1775.0
3 TraesCS3B01G034800 chr3B 87.907 1414 156 8 1007 2407 25219962 25221373 0.000000e+00 1650.0
4 TraesCS3B01G034800 chr3B 87.270 1414 165 8 1007 2407 16079711 16078300 0.000000e+00 1600.0
5 TraesCS3B01G034800 chr3B 92.865 939 47 9 2498 3422 16695413 16696345 0.000000e+00 1345.0
6 TraesCS3B01G034800 chr3B 92.570 821 56 5 2 819 16957554 16958372 0.000000e+00 1173.0
7 TraesCS3B01G034800 chr3B 85.533 553 57 15 2189 2735 16733754 16734289 1.070000e-154 556.0
8 TraesCS3B01G034800 chr3B 85.741 540 52 17 2204 2735 16850969 16850447 6.460000e-152 547.0
9 TraesCS3B01G034800 chr3B 91.444 374 29 3 303 674 16676471 16676843 8.470000e-141 510.0
10 TraesCS3B01G034800 chr3B 80.569 633 74 19 3 612 16980629 16981235 3.130000e-120 442.0
11 TraesCS3B01G034800 chr3B 86.364 264 20 9 2478 2740 16977122 16977370 1.210000e-69 274.0
12 TraesCS3B01G034800 chr3D 91.399 1465 120 5 965 2425 11795099 11796561 0.000000e+00 2002.0
13 TraesCS3B01G034800 chr3D 87.974 1397 154 7 1024 2407 11417736 11416341 0.000000e+00 1637.0
14 TraesCS3B01G034800 chr3D 83.477 1392 216 9 1029 2407 707947 709337 0.000000e+00 1284.0
15 TraesCS3B01G034800 chr3D 86.567 402 45 6 2754 3149 522779257 522779655 5.240000e-118 435.0
16 TraesCS3B01G034800 chr3A 87.535 1412 163 6 1007 2406 25896118 25897528 0.000000e+00 1620.0
17 TraesCS3B01G034800 chr3A 84.505 1394 210 5 1018 2405 8910250 8908857 0.000000e+00 1373.0
18 TraesCS3B01G034800 chr3A 88.442 796 92 0 1286 2081 25232500 25231705 0.000000e+00 961.0
19 TraesCS3B01G034800 chr3A 85.801 824 117 0 1584 2407 25770241 25771064 0.000000e+00 874.0
20 TraesCS3B01G034800 chr3A 79.412 204 31 9 3198 3400 582346688 582346881 2.140000e-27 134.0
21 TraesCS3B01G034800 chr3A 79.227 207 31 10 3201 3406 679701993 679701798 2.140000e-27 134.0
22 TraesCS3B01G034800 chr3A 93.651 63 1 2 758 818 25233345 25233284 1.310000e-14 91.6
23 TraesCS3B01G034800 chr6B 81.093 677 82 25 2754 3422 75643853 75644491 1.830000e-137 499.0
24 TraesCS3B01G034800 chr4D 88.119 404 38 8 2754 3150 497517656 497518056 4.000000e-129 472.0
25 TraesCS3B01G034800 chr1B 80.325 676 89 29 2754 3422 682168590 682167952 4.000000e-129 472.0
26 TraesCS3B01G034800 chr2D 87.065 402 42 8 2755 3149 614342098 614342496 2.420000e-121 446.0
27 TraesCS3B01G034800 chr2D 85.536 401 50 5 2754 3148 636537270 636537668 2.460000e-111 412.0
28 TraesCS3B01G034800 chr2A 86.284 401 46 7 2754 3148 718930333 718930730 8.780000e-116 427.0
29 TraesCS3B01G034800 chr6A 85.644 404 48 7 2754 3150 584892600 584892200 1.900000e-112 416.0
30 TraesCS3B01G034800 chr6A 78.261 207 33 11 3201 3406 531047898 531047703 4.640000e-24 122.0
31 TraesCS3B01G034800 chr7B 82.143 224 30 9 3201 3422 63573681 63573896 2.100000e-42 183.0


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 TraesCS3B01G034800 chr3B 16755738 16759159 3421 True 6320.0 6320 100.0000 1 3422 1 chr3B.!!$R2 3421
1 TraesCS3B01G034800 chr3B 16692581 16696345 3764 False 1841.5 2338 93.5790 965 3422 2 chr3B.!!$F4 2457
2 TraesCS3B01G034800 chr3B 25219962 25221373 1411 False 1650.0 1650 87.9070 1007 2407 1 chr3B.!!$F3 1400
3 TraesCS3B01G034800 chr3B 16078300 16079711 1411 True 1600.0 1600 87.2700 1007 2407 1 chr3B.!!$R1 1400
4 TraesCS3B01G034800 chr3B 16957554 16959516 1962 False 1474.0 1775 93.9760 2 1930 2 chr3B.!!$F5 1928
5 TraesCS3B01G034800 chr3B 16733754 16734289 535 False 556.0 556 85.5330 2189 2735 1 chr3B.!!$F2 546
6 TraesCS3B01G034800 chr3B 16850447 16850969 522 True 547.0 547 85.7410 2204 2735 1 chr3B.!!$R3 531
7 TraesCS3B01G034800 chr3B 16977122 16981235 4113 False 358.0 442 83.4665 3 2740 2 chr3B.!!$F6 2737
8 TraesCS3B01G034800 chr3D 11795099 11796561 1462 False 2002.0 2002 91.3990 965 2425 1 chr3D.!!$F2 1460
9 TraesCS3B01G034800 chr3D 11416341 11417736 1395 True 1637.0 1637 87.9740 1024 2407 1 chr3D.!!$R1 1383
10 TraesCS3B01G034800 chr3D 707947 709337 1390 False 1284.0 1284 83.4770 1029 2407 1 chr3D.!!$F1 1378
11 TraesCS3B01G034800 chr3A 25896118 25897528 1410 False 1620.0 1620 87.5350 1007 2406 1 chr3A.!!$F2 1399
12 TraesCS3B01G034800 chr3A 8908857 8910250 1393 True 1373.0 1373 84.5050 1018 2405 1 chr3A.!!$R1 1387
13 TraesCS3B01G034800 chr3A 25770241 25771064 823 False 874.0 874 85.8010 1584 2407 1 chr3A.!!$F1 823
14 TraesCS3B01G034800 chr3A 25231705 25233345 1640 True 526.3 961 91.0465 758 2081 2 chr3A.!!$R3 1323
15 TraesCS3B01G034800 chr6B 75643853 75644491 638 False 499.0 499 81.0930 2754 3422 1 chr6B.!!$F1 668
16 TraesCS3B01G034800 chr1B 682167952 682168590 638 True 472.0 472 80.3250 2754 3422 1 chr1B.!!$R1 668

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
200 201 0.110238 CGCGGATCAACTGTGTTTGG 60.110 55.0 0.00 0.0 0.00 3.28 F
681 684 0.179084 TCGCTCCCCGCAAAATAGAG 60.179 55.0 0.00 0.0 39.08 2.43 F
1452 1842 0.323360 GGAACCTGCATGGGCTAACA 60.323 55.0 7.06 0.0 41.91 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2407 1.352083 TCCTTGGTCCTCTCCACAAG 58.648 55.0 0.0 0.00 39.88 3.16 R
2275 2677 0.178967 TTGTCTTGGCCAGCCATCAA 60.179 50.0 13.1 14.62 46.64 2.57 R
2627 4363 0.257328 TTGCCCAGACCAGTGTTGAA 59.743 50.0 0.0 0.00 0.00 2.69 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
38 39 3.079578 ACAGTGAACATTGCATGAGAGG 58.920 45.455 0.00 0.00 0.00 3.69
64 65 2.731217 CTCTTTCACCTTTGTTTGCCG 58.269 47.619 0.00 0.00 0.00 5.69
80 81 4.481368 TTGCCGACTTGGTTGTATAGAT 57.519 40.909 0.00 0.00 41.21 1.98
82 83 2.544267 GCCGACTTGGTTGTATAGATGC 59.456 50.000 0.00 0.00 41.21 3.91
85 86 3.731216 CGACTTGGTTGTATAGATGCTCG 59.269 47.826 0.00 0.00 0.00 5.03
104 105 2.019249 CGCCATCCTTGTCATGTCAAT 58.981 47.619 5.84 0.00 0.00 2.57
110 111 4.707030 TCCTTGTCATGTCAATTGATGC 57.293 40.909 12.12 0.00 0.00 3.91
139 140 4.486125 TCTAGCCAACATGCTACAATCA 57.514 40.909 0.00 0.00 42.75 2.57
159 160 2.140065 TGCTTTATGCTCTCCGATCG 57.860 50.000 8.51 8.51 43.37 3.69
200 201 0.110238 CGCGGATCAACTGTGTTTGG 60.110 55.000 0.00 0.00 0.00 3.28
210 211 2.936202 ACTGTGTTTGGATGTGAAGCT 58.064 42.857 0.00 0.00 0.00 3.74
232 233 5.181690 TCTACCGGCATATTTGATTTTGC 57.818 39.130 0.00 0.00 0.00 3.68
239 240 5.895216 GCATATTTGATTTTGCCTAGTGC 57.105 39.130 0.00 0.00 41.77 4.40
241 242 3.508744 ATTTGATTTTGCCTAGTGCCG 57.491 42.857 1.42 0.00 40.16 5.69
282 283 8.896320 ATATTAACCGTATGCTAAACATGTCA 57.104 30.769 0.00 0.00 40.06 3.58
300 301 8.585471 ACATGTCAAGAATTCACCATTTAGAT 57.415 30.769 8.44 0.00 0.00 1.98
326 327 9.625747 TTAATATAGCTTGATGGTTTGACATGA 57.374 29.630 0.00 0.00 0.00 3.07
336 337 7.443477 TGATGGTTTGACATGATTTGATTGTT 58.557 30.769 0.00 0.00 0.00 2.83
356 358 6.959639 TGTTGAGATTATTGAATTAGCCCC 57.040 37.500 0.00 0.00 0.00 5.80
399 401 1.059173 GATGATGACGCATCTCGAGC 58.941 55.000 7.81 0.00 41.06 5.03
404 406 0.248784 TGACGCATCTCGAGCTGATG 60.249 55.000 19.99 13.74 42.86 3.07
409 411 1.940294 GCATCTCGAGCTGATGGATGG 60.940 57.143 19.99 0.00 40.98 3.51
457 459 7.148641 CCGATCTGATTTTTCTTAGCTAGCTA 58.851 38.462 20.67 20.67 0.00 3.32
468 470 7.757097 TTCTTAGCTAGCTAAACGAATGAAG 57.243 36.000 31.43 20.85 37.97 3.02
481 483 9.555727 CTAAACGAATGAAGATATAAAGGGGAA 57.444 33.333 0.00 0.00 0.00 3.97
493 495 5.796502 ATAAAGGGGAAAACATGAGGAGA 57.203 39.130 0.00 0.00 0.00 3.71
519 521 1.187087 GTGATGGAGAGAGGTCGGTT 58.813 55.000 0.00 0.00 0.00 4.44
529 531 6.211986 TGGAGAGAGGTCGGTTAAAAGATAAA 59.788 38.462 0.00 0.00 0.00 1.40
534 536 7.447594 AGAGGTCGGTTAAAAGATAAAGTTGA 58.552 34.615 0.00 0.00 0.00 3.18
557 559 0.902531 GGGAAAGACCGATGGACTCA 59.097 55.000 0.00 0.00 40.11 3.41
626 629 4.651045 AGTTTGTGATTGAAGCTTTTCCCT 59.349 37.500 0.00 0.00 0.00 4.20
645 648 0.179156 TAGTCTTAAACTCCGCCGCG 60.179 55.000 5.59 5.59 39.55 6.46
670 673 1.602377 CGAATGGTAAAATCGCTCCCC 59.398 52.381 0.00 0.00 0.00 4.81
677 680 0.894835 AAAATCGCTCCCCGCAAAAT 59.105 45.000 0.00 0.00 39.08 1.82
681 684 0.179084 TCGCTCCCCGCAAAATAGAG 60.179 55.000 0.00 0.00 39.08 2.43
728 731 6.465948 TGCCAAAATTTCATGTTTAGCTCAT 58.534 32.000 0.00 0.00 0.00 2.90
735 738 3.609853 TCATGTTTAGCTCATCCCACAC 58.390 45.455 0.00 0.00 0.00 3.82
744 747 1.676635 CATCCCACACAGCCACAGG 60.677 63.158 0.00 0.00 0.00 4.00
827 859 4.035792 GTCTGCGCGTGATCCTATCTATAT 59.964 45.833 8.43 0.00 0.00 0.86
852 884 4.081807 TCAGATCTGGCGATATGAATCTGG 60.082 45.833 22.42 0.00 42.95 3.86
863 895 1.687563 TGAATCTGGATGCATGCTGG 58.312 50.000 21.77 13.60 0.00 4.85
864 896 1.213430 TGAATCTGGATGCATGCTGGA 59.787 47.619 21.77 17.73 0.00 3.86
890 1079 7.890515 TGACAAACATGCTGTTGGATAAATTA 58.109 30.769 9.53 0.00 40.14 1.40
896 1085 9.590451 AACATGCTGTTGGATAAATTAATTCTG 57.410 29.630 0.10 0.00 39.45 3.02
911 1100 7.757242 ATTAATTCTGTCTTCCTTCCCTACT 57.243 36.000 0.00 0.00 0.00 2.57
937 1131 0.525761 CCCCCAAAGCAATACACACG 59.474 55.000 0.00 0.00 0.00 4.49
1328 1718 2.435059 GCTTCTGTCGGGGCTCAC 60.435 66.667 0.00 0.00 0.00 3.51
1452 1842 0.323360 GGAACCTGCATGGGCTAACA 60.323 55.000 7.06 0.00 41.91 2.41
1995 2397 2.286197 GACCCCCTGGCCTACCTT 60.286 66.667 3.32 0.00 36.63 3.50
2025 2427 1.912043 CTTGTGGAGAGGACCAAGGAT 59.088 52.381 0.00 0.00 41.87 3.24
2243 2645 1.153745 GAGTGCAGCCGACGAAGAT 60.154 57.895 0.00 0.00 0.00 2.40
2275 2677 4.473520 CGGCGGCAGTGAGGGAAT 62.474 66.667 10.53 0.00 0.00 3.01
2307 2709 2.597510 GACAAAGGCGCCCAGGTT 60.598 61.111 26.15 8.05 0.00 3.50
2311 2713 0.394352 CAAAGGCGCCCAGGTTAGAT 60.394 55.000 26.15 0.00 0.00 1.98
2358 2760 2.040813 AGCCATGGAAGCTCTTCTTGAA 59.959 45.455 18.40 0.00 34.91 2.69
2408 2814 2.899838 GGTGCGCAAGTGGACACA 60.900 61.111 14.00 0.00 41.68 3.72
2454 2862 4.080863 CCTACCTACACATCTTGCTCCTTT 60.081 45.833 0.00 0.00 0.00 3.11
2627 4363 2.033141 AAGCGCCACATGAGCAGT 59.967 55.556 2.29 0.00 0.00 4.40
2664 4400 2.744494 GCAAGTTAGGGCTCTCCATGAG 60.744 54.545 0.00 0.00 45.33 2.90
2672 4408 2.237392 GGGCTCTCCATGAGTAACTTGT 59.763 50.000 0.00 0.00 44.41 3.16
2702 4438 9.500864 GAGTATAGTTTTAGGACTAACTTGACG 57.499 37.037 0.00 0.00 35.86 4.35
2703 4439 9.018582 AGTATAGTTTTAGGACTAACTTGACGT 57.981 33.333 0.00 0.00 35.86 4.34
2719 4455 3.075884 TGACGTACACCCCAAAATTAGC 58.924 45.455 0.00 0.00 0.00 3.09
2747 4483 8.654230 TTAGATCTATGAGAGTGAATTGCAAC 57.346 34.615 0.00 0.00 0.00 4.17
2753 4489 6.833342 ATGAGAGTGAATTGCAACAAAAAC 57.167 33.333 0.00 0.00 0.00 2.43
2756 4497 6.648310 TGAGAGTGAATTGCAACAAAAACAAA 59.352 30.769 0.00 0.00 0.00 2.83
2778 4555 3.214328 AGACACACCACATTTCAAGTCC 58.786 45.455 0.00 0.00 0.00 3.85
2878 4656 8.736742 CACTAATGATTAATTTGACACGATTGC 58.263 33.333 0.00 0.00 0.00 3.56
3093 6433 3.406361 CGTGAGCACTGTCACCGC 61.406 66.667 0.00 0.00 43.45 5.68
3174 6514 0.670854 GGACTCGAACAAGGAGTGCC 60.671 60.000 0.00 0.00 44.25 5.01
3201 6541 2.594131 TGAAAGTCTTCTCTCCGGTCA 58.406 47.619 0.00 0.00 32.33 4.02
3280 8254 1.005037 ATGCGCTGTTGTTCCTCGA 60.005 52.632 9.73 0.00 0.00 4.04
3339 8313 0.453793 CACGCCGAAGATCTCAGAGT 59.546 55.000 0.00 0.00 0.00 3.24
3364 8338 4.735132 CGGCTCGCCAAACTCCGA 62.735 66.667 8.87 0.00 42.43 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.316167 TCACTGTTGTTGCCAGAGAATATT 58.684 37.500 0.00 0.00 34.04 1.28
5 6 2.288666 GTTCACTGTTGTTGCCAGAGA 58.711 47.619 0.00 0.00 34.04 3.10
24 25 1.399714 CATGCCCTCTCATGCAATGT 58.600 50.000 0.00 0.00 46.80 2.71
38 39 1.615392 ACAAAGGTGAAAGAGCATGCC 59.385 47.619 15.66 6.03 0.00 4.40
64 65 3.491267 GCGAGCATCTATACAACCAAGTC 59.509 47.826 0.00 0.00 0.00 3.01
80 81 0.745486 CATGACAAGGATGGCGAGCA 60.745 55.000 0.00 0.00 37.40 4.26
82 83 1.293924 GACATGACAAGGATGGCGAG 58.706 55.000 0.00 0.00 37.40 5.03
85 86 3.444742 TCAATTGACATGACAAGGATGGC 59.555 43.478 15.47 0.00 33.22 4.40
104 105 2.102925 TGGCTAGATCATCACGCATCAA 59.897 45.455 0.00 0.00 0.00 2.57
110 111 2.222678 GCATGTTGGCTAGATCATCACG 59.777 50.000 0.00 0.00 0.00 4.35
179 180 1.262950 CAAACACAGTTGATCCGCGAA 59.737 47.619 8.23 0.00 0.00 4.70
182 183 1.234821 TCCAAACACAGTTGATCCGC 58.765 50.000 0.00 0.00 0.00 5.54
200 201 0.175760 TGCCGGTAGAGCTTCACATC 59.824 55.000 1.90 0.00 0.00 3.06
210 211 5.181690 GCAAAATCAAATATGCCGGTAGA 57.818 39.130 1.90 0.00 32.73 2.59
239 240 1.185315 ATCATTTTTGAGTGCCCCGG 58.815 50.000 0.00 0.00 0.00 5.73
241 242 6.280643 GGTTAATATCATTTTTGAGTGCCCC 58.719 40.000 0.00 0.00 0.00 5.80
300 301 9.625747 TCATGTCAAACCATCAAGCTATATTAA 57.374 29.630 0.00 0.00 0.00 1.40
336 337 7.353525 TCAAAGGGGCTAATTCAATAATCTCA 58.646 34.615 0.00 0.00 0.00 3.27
390 392 1.343789 ACCATCCATCAGCTCGAGATG 59.656 52.381 24.40 24.40 41.91 2.90
391 393 1.343789 CACCATCCATCAGCTCGAGAT 59.656 52.381 18.75 7.13 0.00 2.75
399 401 0.323633 TGGCAACCACCATCCATCAG 60.324 55.000 0.00 0.00 33.75 2.90
409 411 2.649129 GGCTTCCCATGGCAACCAC 61.649 63.158 6.09 0.00 35.80 4.16
431 433 5.333721 GCTAGCTAAGAAAAATCAGATCGGC 60.334 44.000 7.70 0.00 0.00 5.54
435 437 8.821894 CGTTTAGCTAGCTAAGAAAAATCAGAT 58.178 33.333 30.45 2.54 39.36 2.90
440 442 9.162764 TCATTCGTTTAGCTAGCTAAGAAAAAT 57.837 29.630 30.45 24.25 39.36 1.82
457 459 8.817092 TTTCCCCTTTATATCTTCATTCGTTT 57.183 30.769 0.00 0.00 0.00 3.60
468 470 7.518188 TCTCCTCATGTTTTCCCCTTTATATC 58.482 38.462 0.00 0.00 0.00 1.63
474 476 4.469469 TTTCTCCTCATGTTTTCCCCTT 57.531 40.909 0.00 0.00 0.00 3.95
481 483 6.152323 CCATCACTCATTTTCTCCTCATGTTT 59.848 38.462 0.00 0.00 0.00 2.83
493 495 4.382470 CGACCTCTCTCCATCACTCATTTT 60.382 45.833 0.00 0.00 0.00 1.82
529 531 3.570912 TCGGTCTTTCCCTTTTCAACT 57.429 42.857 0.00 0.00 0.00 3.16
534 536 2.375509 AGTCCATCGGTCTTTCCCTTTT 59.624 45.455 0.00 0.00 0.00 2.27
557 559 1.065709 ACAACACTGTTGTCCTCCGTT 60.066 47.619 19.88 0.00 33.55 4.44
596 598 3.751621 CTTCAATCACAAACTCATCCGC 58.248 45.455 0.00 0.00 0.00 5.54
626 629 0.179156 CGCGGCGGAGTTTAAGACTA 60.179 55.000 15.84 0.00 39.19 2.59
645 648 1.593793 GCGATTTTACCATTCGACGGC 60.594 52.381 0.00 0.00 34.92 5.68
651 654 1.602377 CGGGGAGCGATTTTACCATTC 59.398 52.381 0.00 0.00 0.00 2.67
688 691 0.606604 GGCAACTTCCGAGTCTACCA 59.393 55.000 0.00 0.00 34.21 3.25
689 692 0.606604 TGGCAACTTCCGAGTCTACC 59.393 55.000 0.00 0.00 34.21 3.18
691 694 3.478857 TTTTGGCAACTTCCGAGTCTA 57.521 42.857 0.00 0.00 34.21 2.59
692 695 2.341846 TTTTGGCAACTTCCGAGTCT 57.658 45.000 0.00 0.00 34.21 3.24
693 696 3.643159 AATTTTGGCAACTTCCGAGTC 57.357 42.857 0.00 0.00 34.21 3.36
728 731 2.772191 ACCTGTGGCTGTGTGGGA 60.772 61.111 0.00 0.00 0.00 4.37
735 738 3.057969 TCATTTACTCACCTGTGGCTG 57.942 47.619 0.00 0.00 0.00 4.85
744 747 6.477688 CCCAATCATTTGCATCATTTACTCAC 59.522 38.462 0.00 0.00 0.00 3.51
827 859 6.183360 CCAGATTCATATCGCCAGATCTGATA 60.183 42.308 24.62 13.86 38.97 2.15
852 884 2.164827 TGTTTGTCATCCAGCATGCATC 59.835 45.455 21.98 2.43 31.70 3.91
890 1079 7.757242 ATAAGTAGGGAAGGAAGACAGAATT 57.243 36.000 0.00 0.00 0.00 2.17
896 1085 6.409005 GGGGTTTATAAGTAGGGAAGGAAGAC 60.409 46.154 0.00 0.00 0.00 3.01
911 1100 6.017192 TGTGTATTGCTTTGGGGGTTTATAA 58.983 36.000 0.00 0.00 0.00 0.98
937 1131 2.985139 GTTGTGCTTGACCTCGTACTAC 59.015 50.000 0.00 0.00 0.00 2.73
1312 1702 2.125912 CGTGAGCCCCGACAGAAG 60.126 66.667 0.00 0.00 0.00 2.85
1452 1842 2.532854 CGGGAGGTGGAGGATGAAT 58.467 57.895 0.00 0.00 0.00 2.57
1995 2397 4.649705 TCCACAAGCCCCTCCGGA 62.650 66.667 2.93 2.93 0.00 5.14
2005 2407 1.352083 TCCTTGGTCCTCTCCACAAG 58.648 55.000 0.00 0.00 39.88 3.16
2067 2469 2.343758 GTGGCCTCGTGAGCAAGA 59.656 61.111 3.32 0.00 0.00 3.02
2143 2545 2.592574 CCACGCGATCATGGGCAT 60.593 61.111 15.93 0.00 31.83 4.40
2231 2633 0.457851 CTCCTTCATCTTCGTCGGCT 59.542 55.000 0.00 0.00 0.00 5.52
2233 2635 1.066303 CTCCTCCTTCATCTTCGTCGG 59.934 57.143 0.00 0.00 0.00 4.79
2243 2645 1.221840 GCCGCAATCTCCTCCTTCA 59.778 57.895 0.00 0.00 0.00 3.02
2275 2677 0.178967 TTGTCTTGGCCAGCCATCAA 60.179 50.000 13.10 14.62 46.64 2.57
2291 2693 1.303317 CTAACCTGGGCGCCTTTGT 60.303 57.895 28.56 17.53 0.00 2.83
2307 2709 0.319555 GCGCCGCCACATTAGATCTA 60.320 55.000 0.00 0.00 0.00 1.98
2311 2713 2.511373 CAGCGCCGCCACATTAGA 60.511 61.111 4.98 0.00 0.00 2.10
2337 2739 1.632409 TCAAGAAGAGCTTCCATGGCT 59.368 47.619 6.96 0.00 43.26 4.75
2408 2814 5.169295 GTTTCTTCACCTAGCAATACTCGT 58.831 41.667 0.00 0.00 0.00 4.18
2439 2847 3.567164 ACAGACAAAAGGAGCAAGATGTG 59.433 43.478 0.00 0.00 0.00 3.21
2454 2862 2.168326 ATCACGATGCACACAGACAA 57.832 45.000 0.00 0.00 0.00 3.18
2568 4304 4.989279 AGTGTATGCAAAATAGCCCTTG 57.011 40.909 0.00 0.00 0.00 3.61
2627 4363 0.257328 TTGCCCAGACCAGTGTTGAA 59.743 50.000 0.00 0.00 0.00 2.69
2664 4400 9.508567 CCTAAAACTATACTCCGTACAAGTTAC 57.491 37.037 3.46 0.00 31.63 2.50
2672 4408 9.686683 AAGTTAGTCCTAAAACTATACTCCGTA 57.313 33.333 0.00 0.00 34.91 4.02
2702 4438 8.919777 ATCTAATAGCTAATTTTGGGGTGTAC 57.080 34.615 0.00 0.00 0.00 2.90
2703 4439 8.945193 AGATCTAATAGCTAATTTTGGGGTGTA 58.055 33.333 0.00 0.00 0.00 2.90
2704 4440 7.816411 AGATCTAATAGCTAATTTTGGGGTGT 58.184 34.615 0.00 0.00 0.00 4.16
2705 4441 9.965902 ATAGATCTAATAGCTAATTTTGGGGTG 57.034 33.333 6.52 0.00 27.90 4.61
2747 4483 6.479095 AATGTGGTGTGTCTTTTGTTTTTG 57.521 33.333 0.00 0.00 0.00 2.44
2753 4489 5.410067 ACTTGAAATGTGGTGTGTCTTTTG 58.590 37.500 0.00 0.00 0.00 2.44
2756 4497 3.632145 GGACTTGAAATGTGGTGTGTCTT 59.368 43.478 0.00 0.00 0.00 3.01
2778 4555 2.227626 TGTGGTGGCAAATTCGTATGTG 59.772 45.455 0.00 0.00 0.00 3.21
2862 4640 8.531622 AATTGAATTGCAATCGTGTCAAATTA 57.468 26.923 21.82 6.06 46.25 1.40
2878 4656 5.636543 GCCCTTTCTGTCAGAAATTGAATTG 59.363 40.000 24.69 13.11 42.66 2.32
3047 6288 2.046892 CTCCGTGCAAGGGGTCAG 60.047 66.667 19.08 4.77 43.54 3.51
3093 6433 2.992114 CGCCTATCTCCCCTCCGG 60.992 72.222 0.00 0.00 0.00 5.14
3165 6505 2.363306 TTCATGTTGTGGCACTCCTT 57.637 45.000 19.83 4.58 0.00 3.36
3174 6514 4.151335 CGGAGAGAAGACTTTCATGTTGTG 59.849 45.833 0.00 0.00 35.70 3.33
3201 6541 2.685380 AGCCTTCCCTAGTGCGCT 60.685 61.111 9.73 4.58 0.00 5.92
3263 6603 1.954146 GTCGAGGAACAACAGCGCA 60.954 57.895 11.47 0.00 0.00 6.09
3268 6608 2.029964 GCCCGTCGAGGAACAACA 59.970 61.111 6.70 0.00 45.00 3.33
3364 8338 1.006639 GTCTGTCCTCCTCCTCCTCTT 59.993 57.143 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.