Multiple sequence alignment - TraesCS2D01G319900

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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 TraesCS2D01G319900 chr2D 100.000 3558 0 0 1 3558 411343542 411347099 0.000000e+00 6571
1 TraesCS2D01G319900 chr2D 94.223 1506 45 6 958 2421 411954125 411955630 0.000000e+00 2261
2 TraesCS2D01G319900 chr2D 93.432 1492 56 9 958 2407 411726967 411728458 0.000000e+00 2174
3 TraesCS2D01G319900 chr2D 93.254 1008 65 2 2553 3558 293069135 293070141 0.000000e+00 1482
4 TraesCS2D01G319900 chr2D 93.750 896 28 6 1649 2520 411688627 411689518 0.000000e+00 1319
5 TraesCS2D01G319900 chr2D 81.957 1308 182 22 1018 2293 561323450 561322165 0.000000e+00 1059
6 TraesCS2D01G319900 chr2D 84.701 1072 139 18 958 2011 561288528 561287464 0.000000e+00 1048
7 TraesCS2D01G319900 chr2D 90.717 711 51 6 958 1653 411678470 411679180 0.000000e+00 933
8 TraesCS2D01G319900 chr2B 94.031 1491 59 5 958 2421 485433094 485434581 0.000000e+00 2233
9 TraesCS2D01G319900 chr2B 93.680 1155 46 4 958 2085 485299880 485301034 0.000000e+00 1703
10 TraesCS2D01G319900 chr2B 82.473 1375 184 29 958 2293 670340980 670342336 0.000000e+00 1151
11 TraesCS2D01G319900 chr2B 82.263 919 128 18 1400 2293 670445784 670446692 0.000000e+00 761
12 TraesCS2D01G319900 chr2B 94.218 294 14 1 2128 2421 485301035 485301325 2.520000e-121 446
13 TraesCS2D01G319900 chr2A 94.262 1464 54 4 958 2394 579440414 579441874 0.000000e+00 2211
14 TraesCS2D01G319900 chr2A 92.455 994 68 5 2556 3547 41991584 41990596 0.000000e+00 1413
15 TraesCS2D01G319900 chr2A 83.162 1360 183 23 958 2285 701018828 701017483 0.000000e+00 1201
16 TraesCS2D01G319900 chr2A 83.162 1360 183 23 958 2285 701034200 701032855 0.000000e+00 1201
17 TraesCS2D01G319900 chr3D 94.549 1009 45 7 2555 3558 64695859 64696862 0.000000e+00 1550
18 TraesCS2D01G319900 chr3D 90.973 997 41 17 1 957 441384219 441383232 0.000000e+00 1297
19 TraesCS2D01G319900 chr3D 95.556 540 18 5 1 538 552488614 552489149 0.000000e+00 859
20 TraesCS2D01G319900 chr3D 88.964 444 37 9 522 957 272605147 272605586 4.040000e-149 538
21 TraesCS2D01G319900 chr6D 94.083 1014 52 5 2551 3558 381526466 381527477 0.000000e+00 1533
22 TraesCS2D01G319900 chr6D 88.688 442 40 6 522 957 375533448 375533885 6.760000e-147 531
23 TraesCS2D01G319900 chr5A 93.837 1006 58 3 2556 3558 398188428 398187424 0.000000e+00 1511
24 TraesCS2D01G319900 chr1D 93.657 1009 52 8 2557 3558 62697923 62696920 0.000000e+00 1498
25 TraesCS2D01G319900 chr1D 90.950 442 33 5 522 957 147929507 147929947 3.960000e-164 588
26 TraesCS2D01G319900 chr3A 93.300 1000 57 4 2568 3558 610560523 610561521 0.000000e+00 1467
27 TraesCS2D01G319900 chr3A 91.532 992 70 6 2570 3558 35094429 35095409 0.000000e+00 1354
28 TraesCS2D01G319900 chr3A 89.751 1005 89 9 2557 3558 615052234 615053227 0.000000e+00 1273
29 TraesCS2D01G319900 chr7A 92.644 1006 65 7 2556 3558 605144945 605143946 0.000000e+00 1439
30 TraesCS2D01G319900 chr7A 92.402 408 26 3 354 759 113927414 113927818 8.570000e-161 577
31 TraesCS2D01G319900 chr7D 91.935 992 36 12 1 957 567842370 567843352 0.000000e+00 1349
32 TraesCS2D01G319900 chr7D 95.941 542 16 4 1 538 23119570 23120109 0.000000e+00 874
33 TraesCS2D01G319900 chr7D 95.756 542 15 7 1 538 604034746 604035283 0.000000e+00 867
34 TraesCS2D01G319900 chr7D 95.756 542 12 9 1 537 531794742 531794207 0.000000e+00 863
35 TraesCS2D01G319900 chr7D 90.172 641 39 10 343 959 351112421 351113061 0.000000e+00 813
36 TraesCS2D01G319900 chr7D 91.111 450 25 4 522 957 142321545 142321097 2.360000e-166 595
37 TraesCS2D01G319900 chr7D 89.933 447 33 7 522 957 29508145 29507700 1.850000e-157 566
38 TraesCS2D01G319900 chrUn 83.235 1360 182 23 958 2285 210396864 210395519 0.000000e+00 1206
39 TraesCS2D01G319900 chr5D 90.186 805 53 15 1 799 523952781 523953565 0.000000e+00 1026
40 TraesCS2D01G319900 chr5D 95.772 544 14 8 1 538 121939019 121939559 0.000000e+00 869
41 TraesCS2D01G319900 chr5D 88.964 444 38 6 522 957 38015872 38015432 4.040000e-149 538
42 TraesCS2D01G319900 chr4D 95.749 541 13 9 1 538 127264589 127265122 0.000000e+00 863
43 TraesCS2D01G319900 chr4A 87.237 760 65 20 1 738 664404731 664403982 0.000000e+00 837
44 TraesCS2D01G319900 chr1B 82.031 1024 141 20 1290 2293 646053340 646054340 0.000000e+00 832
45 TraesCS2D01G319900 chr6B 89.116 441 40 5 522 957 375843453 375843016 3.120000e-150 542


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 TraesCS2D01G319900 chr2D 411343542 411347099 3557 False 6571.0 6571 100.000 1 3558 1 chr2D.!!$F2 3557
1 TraesCS2D01G319900 chr2D 411954125 411955630 1505 False 2261.0 2261 94.223 958 2421 1 chr2D.!!$F6 1463
2 TraesCS2D01G319900 chr2D 411726967 411728458 1491 False 2174.0 2174 93.432 958 2407 1 chr2D.!!$F5 1449
3 TraesCS2D01G319900 chr2D 293069135 293070141 1006 False 1482.0 1482 93.254 2553 3558 1 chr2D.!!$F1 1005
4 TraesCS2D01G319900 chr2D 411688627 411689518 891 False 1319.0 1319 93.750 1649 2520 1 chr2D.!!$F4 871
5 TraesCS2D01G319900 chr2D 561322165 561323450 1285 True 1059.0 1059 81.957 1018 2293 1 chr2D.!!$R2 1275
6 TraesCS2D01G319900 chr2D 561287464 561288528 1064 True 1048.0 1048 84.701 958 2011 1 chr2D.!!$R1 1053
7 TraesCS2D01G319900 chr2D 411678470 411679180 710 False 933.0 933 90.717 958 1653 1 chr2D.!!$F3 695
8 TraesCS2D01G319900 chr2B 485433094 485434581 1487 False 2233.0 2233 94.031 958 2421 1 chr2B.!!$F1 1463
9 TraesCS2D01G319900 chr2B 670340980 670342336 1356 False 1151.0 1151 82.473 958 2293 1 chr2B.!!$F2 1335
10 TraesCS2D01G319900 chr2B 485299880 485301325 1445 False 1074.5 1703 93.949 958 2421 2 chr2B.!!$F4 1463
11 TraesCS2D01G319900 chr2B 670445784 670446692 908 False 761.0 761 82.263 1400 2293 1 chr2B.!!$F3 893
12 TraesCS2D01G319900 chr2A 579440414 579441874 1460 False 2211.0 2211 94.262 958 2394 1 chr2A.!!$F1 1436
13 TraesCS2D01G319900 chr2A 41990596 41991584 988 True 1413.0 1413 92.455 2556 3547 1 chr2A.!!$R1 991
14 TraesCS2D01G319900 chr2A 701017483 701018828 1345 True 1201.0 1201 83.162 958 2285 1 chr2A.!!$R2 1327
15 TraesCS2D01G319900 chr2A 701032855 701034200 1345 True 1201.0 1201 83.162 958 2285 1 chr2A.!!$R3 1327
16 TraesCS2D01G319900 chr3D 64695859 64696862 1003 False 1550.0 1550 94.549 2555 3558 1 chr3D.!!$F1 1003
17 TraesCS2D01G319900 chr3D 441383232 441384219 987 True 1297.0 1297 90.973 1 957 1 chr3D.!!$R1 956
18 TraesCS2D01G319900 chr3D 552488614 552489149 535 False 859.0 859 95.556 1 538 1 chr3D.!!$F3 537
19 TraesCS2D01G319900 chr6D 381526466 381527477 1011 False 1533.0 1533 94.083 2551 3558 1 chr6D.!!$F2 1007
20 TraesCS2D01G319900 chr5A 398187424 398188428 1004 True 1511.0 1511 93.837 2556 3558 1 chr5A.!!$R1 1002
21 TraesCS2D01G319900 chr1D 62696920 62697923 1003 True 1498.0 1498 93.657 2557 3558 1 chr1D.!!$R1 1001
22 TraesCS2D01G319900 chr3A 610560523 610561521 998 False 1467.0 1467 93.300 2568 3558 1 chr3A.!!$F2 990
23 TraesCS2D01G319900 chr3A 35094429 35095409 980 False 1354.0 1354 91.532 2570 3558 1 chr3A.!!$F1 988
24 TraesCS2D01G319900 chr3A 615052234 615053227 993 False 1273.0 1273 89.751 2557 3558 1 chr3A.!!$F3 1001
25 TraesCS2D01G319900 chr7A 605143946 605144945 999 True 1439.0 1439 92.644 2556 3558 1 chr7A.!!$R1 1002
26 TraesCS2D01G319900 chr7D 567842370 567843352 982 False 1349.0 1349 91.935 1 957 1 chr7D.!!$F3 956
27 TraesCS2D01G319900 chr7D 23119570 23120109 539 False 874.0 874 95.941 1 538 1 chr7D.!!$F1 537
28 TraesCS2D01G319900 chr7D 604034746 604035283 537 False 867.0 867 95.756 1 538 1 chr7D.!!$F4 537
29 TraesCS2D01G319900 chr7D 531794207 531794742 535 True 863.0 863 95.756 1 537 1 chr7D.!!$R3 536
30 TraesCS2D01G319900 chr7D 351112421 351113061 640 False 813.0 813 90.172 343 959 1 chr7D.!!$F2 616
31 TraesCS2D01G319900 chrUn 210395519 210396864 1345 True 1206.0 1206 83.235 958 2285 1 chrUn.!!$R1 1327
32 TraesCS2D01G319900 chr5D 523952781 523953565 784 False 1026.0 1026 90.186 1 799 1 chr5D.!!$F2 798
33 TraesCS2D01G319900 chr5D 121939019 121939559 540 False 869.0 869 95.772 1 538 1 chr5D.!!$F1 537
34 TraesCS2D01G319900 chr4D 127264589 127265122 533 False 863.0 863 95.749 1 538 1 chr4D.!!$F1 537
35 TraesCS2D01G319900 chr4A 664403982 664404731 749 True 837.0 837 87.237 1 738 1 chr4A.!!$R1 737
36 TraesCS2D01G319900 chr1B 646053340 646054340 1000 False 832.0 832 82.031 1290 2293 1 chr1B.!!$F1 1003

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
633 701 0.037697 TGGTGCGCCACTACTAGTTG 60.038 55.0 16.89 0.59 40.46 3.16 F
827 923 0.108186 GTGGCTCATCGTGGATGTGA 60.108 55.0 10.79 0.00 40.55 3.58 F
2438 2623 0.555769 AGGTTCAGGAAAAGGCACCA 59.444 50.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2633 0.386226 CGGCGCTCTAGCTTAGCTAC 60.386 60.000 10.21 0.01 40.44 3.58 R
2503 2688 1.548269 GACTACTTGAGCACTGCCTCT 59.452 52.381 0.00 0.00 33.02 3.69 R
3310 3516 1.676529 ACGATGGTCTACACGATCTGG 59.323 52.381 0.00 0.00 35.99 3.86 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
325 337 9.288124 GGTTTTTGAGGATTTTGAAAATGTTTG 57.712 29.630 8.03 0.00 0.00 2.93
593 647 2.877786 GTGGAATTTTTGGGCCAAGTTG 59.122 45.455 19.90 0.00 31.18 3.16
600 654 2.685106 TTGGGCCAAGTTGGTAATGA 57.315 45.000 22.85 3.68 40.46 2.57
633 701 0.037697 TGGTGCGCCACTACTAGTTG 60.038 55.000 16.89 0.59 40.46 3.16
762 844 7.046033 AGTTTAACTAGTAATGGCGCACTATT 58.954 34.615 10.83 9.34 0.00 1.73
827 923 0.108186 GTGGCTCATCGTGGATGTGA 60.108 55.000 10.79 0.00 40.55 3.58
870 966 1.603456 AATGACGCACCAACACATGA 58.397 45.000 0.00 0.00 0.00 3.07
888 984 7.102993 ACACATGATGCGCCATTAGTATATAA 58.897 34.615 4.18 0.00 0.00 0.98
891 987 9.830975 ACATGATGCGCCATTAGTATATAATAA 57.169 29.630 4.18 5.20 0.00 1.40
925 1021 2.491298 TGTGTGATGCGCCATTAATGTT 59.509 40.909 14.25 0.00 0.00 2.71
974 1070 4.521062 GCGAGCTCCACGGCATCT 62.521 66.667 8.47 0.00 34.17 2.90
977 1073 1.219124 GAGCTCCACGGCATCTTCA 59.781 57.895 0.87 0.00 34.17 3.02
980 1076 0.674895 GCTCCACGGCATCTTCAACT 60.675 55.000 0.00 0.00 0.00 3.16
1111 1207 3.064987 CTCCGACATCGACGCCCTT 62.065 63.158 2.09 0.00 43.02 3.95
1114 1210 1.736645 CGACATCGACGCCCTTGTT 60.737 57.895 0.00 0.00 43.02 2.83
1132 1228 4.910585 GTCGGGCCCGCCTATGTG 62.911 72.222 39.89 11.44 39.59 3.21
1166 1262 0.946221 CTTCTTCGACGTGCTTGGCT 60.946 55.000 0.00 0.00 0.00 4.75
1216 1312 4.335647 CTGCAGCTGGTTCCCGGT 62.336 66.667 17.12 0.00 31.34 5.28
1463 1575 1.834822 GCGAGGGGCATCTACTCCT 60.835 63.158 0.00 0.00 42.87 3.69
1910 2049 3.164977 TGGACGTGAAGGTGGCCA 61.165 61.111 0.00 0.00 0.00 5.36
2072 2223 1.371267 CGCGTGTCCTTCTTCGTGA 60.371 57.895 0.00 0.00 36.17 4.35
2201 2358 4.119363 GGCCTGGCATGGAGCTGA 62.119 66.667 22.05 0.00 44.79 4.26
2306 2463 1.762222 CGACGATGATTCCGGCAACC 61.762 60.000 0.00 0.00 34.04 3.77
2421 2594 2.736579 TACTGGCAGCAGCACACAGG 62.737 60.000 15.89 0.00 44.61 4.00
2429 2614 0.819259 GCAGCACACAGGTTCAGGAA 60.819 55.000 0.00 0.00 0.00 3.36
2436 2621 1.338020 CACAGGTTCAGGAAAAGGCAC 59.662 52.381 0.00 0.00 0.00 5.01
2438 2623 0.555769 AGGTTCAGGAAAAGGCACCA 59.444 50.000 0.00 0.00 0.00 4.17
2443 2628 3.173953 TCAGGAAAAGGCACCATGATT 57.826 42.857 0.00 0.00 0.00 2.57
2448 2633 3.747529 GGAAAAGGCACCATGATTTGTTG 59.252 43.478 0.00 0.00 0.00 3.33
2480 2665 2.745884 CGCCGCCCACTTGATCAA 60.746 61.111 8.12 8.12 0.00 2.57
2488 2673 2.232208 GCCCACTTGATCAAGGGAAAAG 59.768 50.000 34.45 21.31 44.41 2.27
2503 2688 4.413520 AGGGAAAAGAGCTATAATCAGGCA 59.586 41.667 0.00 0.00 0.00 4.75
2507 2692 4.888326 AAGAGCTATAATCAGGCAGAGG 57.112 45.455 0.00 0.00 0.00 3.69
2520 2705 0.036952 GCAGAGGCAGTGCTCAAGTA 60.037 55.000 16.11 0.00 40.72 2.24
2521 2706 2.006056 GCAGAGGCAGTGCTCAAGTAG 61.006 57.143 16.11 0.37 40.72 2.57
2522 2707 1.274728 CAGAGGCAGTGCTCAAGTAGT 59.725 52.381 16.11 0.00 0.00 2.73
2523 2708 1.548269 AGAGGCAGTGCTCAAGTAGTC 59.452 52.381 16.11 0.00 0.00 2.59
2524 2709 1.273606 GAGGCAGTGCTCAAGTAGTCA 59.726 52.381 16.11 0.00 0.00 3.41
2525 2710 1.694150 AGGCAGTGCTCAAGTAGTCAA 59.306 47.619 16.11 0.00 0.00 3.18
2526 2711 2.072298 GGCAGTGCTCAAGTAGTCAAG 58.928 52.381 16.11 0.00 0.00 3.02
2527 2712 2.548920 GGCAGTGCTCAAGTAGTCAAGT 60.549 50.000 16.11 0.00 0.00 3.16
2528 2713 2.478134 GCAGTGCTCAAGTAGTCAAGTG 59.522 50.000 8.18 0.00 0.00 3.16
2529 2714 3.722147 CAGTGCTCAAGTAGTCAAGTGT 58.278 45.455 0.00 0.00 0.00 3.55
2530 2715 4.796290 GCAGTGCTCAAGTAGTCAAGTGTA 60.796 45.833 8.18 0.00 0.00 2.90
2531 2716 4.681942 CAGTGCTCAAGTAGTCAAGTGTAC 59.318 45.833 0.00 0.00 0.00 2.90
2532 2717 4.585162 AGTGCTCAAGTAGTCAAGTGTACT 59.415 41.667 0.00 0.00 0.00 2.73
2533 2718 4.681942 GTGCTCAAGTAGTCAAGTGTACTG 59.318 45.833 0.00 0.00 29.71 2.74
2534 2719 3.675698 GCTCAAGTAGTCAAGTGTACTGC 59.324 47.826 0.00 0.00 29.71 4.40
2535 2720 4.796290 GCTCAAGTAGTCAAGTGTACTGCA 60.796 45.833 0.00 0.00 32.62 4.41
2536 2721 4.871513 TCAAGTAGTCAAGTGTACTGCAG 58.128 43.478 13.48 13.48 32.62 4.41
2537 2722 4.583073 TCAAGTAGTCAAGTGTACTGCAGA 59.417 41.667 23.35 0.48 32.62 4.26
2538 2723 5.068591 TCAAGTAGTCAAGTGTACTGCAGAA 59.931 40.000 23.35 2.14 32.62 3.02
2539 2724 5.531122 AGTAGTCAAGTGTACTGCAGAAA 57.469 39.130 23.35 4.90 32.62 2.52
2540 2725 6.102897 AGTAGTCAAGTGTACTGCAGAAAT 57.897 37.500 23.35 0.00 32.62 2.17
2541 2726 7.228314 AGTAGTCAAGTGTACTGCAGAAATA 57.772 36.000 23.35 3.26 32.62 1.40
2542 2727 7.667557 AGTAGTCAAGTGTACTGCAGAAATAA 58.332 34.615 23.35 0.00 32.62 1.40
2543 2728 6.787085 AGTCAAGTGTACTGCAGAAATAAC 57.213 37.500 23.35 10.81 0.00 1.89
2544 2729 6.525629 AGTCAAGTGTACTGCAGAAATAACT 58.474 36.000 23.35 12.90 0.00 2.24
2545 2730 6.425114 AGTCAAGTGTACTGCAGAAATAACTG 59.575 38.462 23.35 9.14 40.43 3.16
2546 2731 6.202954 GTCAAGTGTACTGCAGAAATAACTGT 59.797 38.462 23.35 0.00 39.73 3.55
2547 2732 6.765989 TCAAGTGTACTGCAGAAATAACTGTT 59.234 34.615 23.35 0.00 39.73 3.16
2548 2733 7.929245 TCAAGTGTACTGCAGAAATAACTGTTA 59.071 33.333 23.35 2.26 39.73 2.41
2549 2734 8.721478 CAAGTGTACTGCAGAAATAACTGTTAT 58.279 33.333 23.35 7.22 39.73 1.89
2550 2735 8.848474 AGTGTACTGCAGAAATAACTGTTATT 57.152 30.769 23.35 17.71 39.73 1.40
2551 2736 8.721478 AGTGTACTGCAGAAATAACTGTTATTG 58.279 33.333 23.35 14.15 39.73 1.90
3019 3212 3.885901 TCATCTCACTTCTATCGTCCTGG 59.114 47.826 0.00 0.00 0.00 4.45
3101 3294 0.830023 GGATTCCTCCCTCTCCCTCG 60.830 65.000 0.00 0.00 35.28 4.63
3108 3301 0.694783 TCCCTCTCCCTCGCTCTCTA 60.695 60.000 0.00 0.00 0.00 2.43
3219 3421 2.062971 TCGCTAGGTATCGAGGGTTT 57.937 50.000 0.23 0.00 32.13 3.27
3293 3495 1.135721 CCTCTGTCACATCGAGCATCA 59.864 52.381 0.00 0.00 33.17 3.07
3299 3501 2.000429 CACATCGAGCATCACTGTGA 58.000 50.000 13.60 13.60 45.01 3.58
3310 3516 4.722700 ACTGTGACCATGGCCGCC 62.723 66.667 13.04 1.04 0.00 6.13
3442 3648 0.320421 CATTGTTGAGGACGGACGGT 60.320 55.000 0.00 0.00 0.00 4.83
3462 3668 2.640302 GCTGCCACGAGGTGAGAGA 61.640 63.158 0.00 0.00 35.23 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.308825 AGTCCTAGACATCAACAAGGTTTG 58.691 41.667 0.00 0.00 34.60 2.93
195 202 1.390565 CTAGGTGCGCCACTAGTAGT 58.609 55.000 20.59 0.00 37.19 2.73
293 304 8.572855 TTTCAAAATCCTCAAAAACCAAACAT 57.427 26.923 0.00 0.00 0.00 2.71
298 310 8.572855 AACATTTTCAAAATCCTCAAAAACCA 57.427 26.923 0.00 0.00 0.00 3.67
491 507 6.101734 AGTTTCCCATGTGATATGTGGTCTAT 59.898 38.462 0.00 0.00 0.00 1.98
571 625 2.122768 ACTTGGCCCAAAAATTCCACA 58.877 42.857 0.00 0.00 0.00 4.17
593 647 0.107410 TCCCATGGTGCGTCATTACC 60.107 55.000 11.73 0.00 37.48 2.85
633 701 2.018542 TGGTGCGCCATTACTAGTTC 57.981 50.000 16.89 0.00 40.46 3.01
813 909 1.153597 GCGCATCACATCCACGATGA 61.154 55.000 0.30 0.00 42.09 2.92
816 912 2.511373 GGCGCATCACATCCACGA 60.511 61.111 10.83 0.00 0.00 4.35
827 923 3.315191 GTGTCCAAATACTAATGGCGCAT 59.685 43.478 10.83 0.00 36.62 4.73
910 1006 8.284945 AGATAATATGAACATTAATGGCGCAT 57.715 30.769 19.37 18.50 0.00 4.73
948 1044 2.060383 TGGAGCTCGCCACTGCTAT 61.060 57.895 7.83 0.00 39.91 2.97
961 1057 0.674895 AGTTGAAGATGCCGTGGAGC 60.675 55.000 0.00 0.00 0.00 4.70
967 1063 1.651240 CCCAGCAGTTGAAGATGCCG 61.651 60.000 0.00 0.00 43.60 5.69
974 1070 1.165907 CGCTTCACCCAGCAGTTGAA 61.166 55.000 0.00 0.00 40.09 2.69
977 1073 2.281761 CCGCTTCACCCAGCAGTT 60.282 61.111 0.00 0.00 40.09 3.16
980 1076 4.704833 GAGCCGCTTCACCCAGCA 62.705 66.667 0.00 0.00 40.09 4.41
1132 1228 4.309950 AAGTCGTGGTGGCGGTCC 62.310 66.667 0.00 0.00 0.00 4.46
1910 2049 2.200092 GAGATCCTCCTCCCCGCT 59.800 66.667 0.00 0.00 0.00 5.52
2072 2223 1.072159 GTGCTGGCTTGGACAGTCT 59.928 57.895 0.00 0.00 41.48 3.24
2201 2358 3.141522 TTCGGGTGTGCGAGACGTT 62.142 57.895 0.00 0.00 0.00 3.99
2255 2412 3.157881 TCTTGAGACGATCAGTGGAGTT 58.842 45.455 0.00 0.00 39.68 3.01
2256 2413 2.752354 CTCTTGAGACGATCAGTGGAGT 59.248 50.000 0.00 0.00 39.68 3.85
2421 2594 2.238521 TCATGGTGCCTTTTCCTGAAC 58.761 47.619 0.00 0.00 0.00 3.18
2436 2621 5.824904 AGCTTAGCTACAACAAATCATGG 57.175 39.130 4.30 0.00 36.99 3.66
2438 2623 6.481644 GCTCTAGCTTAGCTACAACAAATCAT 59.518 38.462 10.21 0.00 40.44 2.45
2443 2628 3.770666 CGCTCTAGCTTAGCTACAACAA 58.229 45.455 10.21 0.00 40.44 2.83
2448 2633 0.386226 CGGCGCTCTAGCTTAGCTAC 60.386 60.000 10.21 0.01 40.44 3.58
2472 2657 8.688747 ATTATAGCTCTTTTCCCTTGATCAAG 57.311 34.615 25.75 25.75 38.14 3.02
2480 2665 4.413520 TGCCTGATTATAGCTCTTTTCCCT 59.586 41.667 0.00 0.00 0.00 4.20
2488 2673 2.301296 TGCCTCTGCCTGATTATAGCTC 59.699 50.000 0.00 0.00 36.33 4.09
2503 2688 1.548269 GACTACTTGAGCACTGCCTCT 59.452 52.381 0.00 0.00 33.02 3.69
2507 2692 2.478134 CACTTGACTACTTGAGCACTGC 59.522 50.000 0.00 0.00 0.00 4.40
2520 2705 6.425114 CAGTTATTTCTGCAGTACACTTGACT 59.575 38.462 14.67 6.29 0.00 3.41
2521 2706 6.202954 ACAGTTATTTCTGCAGTACACTTGAC 59.797 38.462 14.67 4.15 38.84 3.18
2522 2707 6.288294 ACAGTTATTTCTGCAGTACACTTGA 58.712 36.000 14.67 0.00 38.84 3.02
2523 2708 6.545504 ACAGTTATTTCTGCAGTACACTTG 57.454 37.500 14.67 8.19 38.84 3.16
2524 2709 8.848474 ATAACAGTTATTTCTGCAGTACACTT 57.152 30.769 14.67 0.00 38.84 3.16
2525 2710 8.721478 CAATAACAGTTATTTCTGCAGTACACT 58.279 33.333 14.67 7.23 38.84 3.55
2526 2711 8.717821 TCAATAACAGTTATTTCTGCAGTACAC 58.282 33.333 14.67 5.01 38.84 2.90
2527 2712 8.840833 TCAATAACAGTTATTTCTGCAGTACA 57.159 30.769 14.67 0.00 38.84 2.90
2990 3183 1.846007 AGAAGTGAGATGAGGCGTCT 58.154 50.000 8.06 0.00 31.77 4.18
3019 3212 1.064458 GACTCTTCGAGCGGTAGGC 59.936 63.158 0.00 0.00 44.05 3.93
3101 3294 1.333702 CGTGCACGAGAGATAGAGAGC 60.334 57.143 34.93 0.00 43.02 4.09
3108 3301 1.153939 GTGAGCGTGCACGAGAGAT 60.154 57.895 41.19 20.59 43.02 2.75
3219 3421 1.107114 GGATCAGACCGAGCTCTTGA 58.893 55.000 12.85 10.38 0.00 3.02
3251 3453 4.787999 GGCGACCACGACTCTTAG 57.212 61.111 0.00 0.00 45.04 2.18
3293 3495 4.722700 GGCGGCCATGGTCACAGT 62.723 66.667 18.31 0.00 0.00 3.55
3299 3501 4.195334 GATCTGGGCGGCCATGGT 62.195 66.667 32.84 21.22 0.00 3.55
3310 3516 1.676529 ACGATGGTCTACACGATCTGG 59.323 52.381 0.00 0.00 35.99 3.86
3401 3607 1.734477 CGACTCCTGTGTCCTTGCG 60.734 63.158 0.00 0.00 33.70 4.85
3442 3648 4.056125 CTCACCTCGTGGCAGCGA 62.056 66.667 2.76 10.76 39.22 4.93
3462 3668 2.053244 CCTCCTTACAGGATGAGGCAT 58.947 52.381 0.00 0.00 44.81 4.40


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

AutoCloner maintained by Alex Coulton.