Multiple sequence alignment - TraesCS7D01G182700

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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 TraesCS7D01G182700 chr7D 100.000 3101 0 0 1 3101 136206245 136203145 0.000000e+00 5727
1 TraesCS7D01G182700 chr7D 82.222 225 33 6 1514 1737 582458606 582458824 1.470000e-43 187
2 TraesCS7D01G182700 chr7A 91.441 2617 109 45 10 2589 135691170 135688632 0.000000e+00 3485
3 TraesCS7D01G182700 chr7A 88.997 309 22 3 2602 2910 135688350 135688054 3.780000e-99 372
4 TraesCS7D01G182700 chr7A 97.727 176 4 0 2926 3101 135688069 135687894 1.400000e-78 303
5 TraesCS7D01G182700 chr7B 91.343 2495 92 44 1 2446 99090912 99088493 0.000000e+00 3297
6 TraesCS7D01G182700 chr7B 93.254 252 13 2 2657 2908 99088295 99088048 4.890000e-98 368
7 TraesCS7D01G182700 chr7B 84.699 183 11 7 2926 3092 99088061 99087880 1.910000e-37 167
8 TraesCS7D01G182700 chr7B 87.826 115 8 3 2483 2593 99088426 99088314 2.510000e-26 130
9 TraesCS7D01G182700 chr6D 91.606 274 21 2 1562 1834 388951402 388951130 8.120000e-101 377
10 TraesCS7D01G182700 chr6B 90.511 274 24 2 1562 1834 581867818 581867546 8.180000e-96 361
11 TraesCS7D01G182700 chr6A 90.146 274 25 2 1562 1834 535403369 535403097 3.800000e-94 355
12 TraesCS7D01G182700 chr5A 83.803 284 28 12 1548 1828 393917964 393918232 1.430000e-63 254
13 TraesCS7D01G182700 chr5D 82.927 287 31 12 1548 1831 304163191 304162920 3.090000e-60 243
14 TraesCS7D01G182700 chr5B 82.927 287 31 10 1548 1831 348571415 348571144 3.090000e-60 243
15 TraesCS7D01G182700 chr2B 81.726 197 33 2 1545 1738 555384969 555385165 8.900000e-36 161


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 TraesCS7D01G182700 chr7D 136203145 136206245 3100 True 5727.000000 5727 100.000000 1 3101 1 chr7D.!!$R1 3100
1 TraesCS7D01G182700 chr7A 135687894 135691170 3276 True 1386.666667 3485 92.721667 10 3101 3 chr7A.!!$R1 3091
2 TraesCS7D01G182700 chr7B 99087880 99090912 3032 True 990.500000 3297 89.280500 1 3092 4 chr7B.!!$R1 3091

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
725 736 0.790866 GCTCGCATGCAAAGTTCGTC 60.791 55.0 19.57 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2698 3068 1.079543 CTCTCACAAGCCTCACGGG 60.08 63.158 0.0 0.0 38.36 5.28 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
66 67 3.559384 CCCCAGTGGTAGTCCTCTTTTTC 60.559 52.174 8.74 0.00 35.65 2.29
67 68 3.072476 CCCAGTGGTAGTCCTCTTTTTCA 59.928 47.826 8.74 0.00 35.65 2.69
68 69 4.263506 CCCAGTGGTAGTCCTCTTTTTCAT 60.264 45.833 8.74 0.00 35.65 2.57
69 70 4.938226 CCAGTGGTAGTCCTCTTTTTCATC 59.062 45.833 0.00 0.00 35.65 2.92
72 73 6.486657 CAGTGGTAGTCCTCTTTTTCATCAAA 59.513 38.462 0.00 0.00 35.65 2.69
74 75 7.725844 AGTGGTAGTCCTCTTTTTCATCAAATT 59.274 33.333 0.00 0.00 34.35 1.82
75 76 8.023706 GTGGTAGTCCTCTTTTTCATCAAATTC 58.976 37.037 0.00 0.00 34.23 2.17
170 171 1.266175 GATGGGCATGAATGAGCGAAG 59.734 52.381 0.00 0.00 0.00 3.79
257 262 4.263572 CGTCAGCCACACCCCCAA 62.264 66.667 0.00 0.00 0.00 4.12
259 264 2.776526 TCAGCCACACCCCCAACT 60.777 61.111 0.00 0.00 0.00 3.16
262 267 2.034221 GCCACACCCCCAACTCTC 59.966 66.667 0.00 0.00 0.00 3.20
330 335 1.561076 CATTCACACCCTCCTCCATCA 59.439 52.381 0.00 0.00 0.00 3.07
430 435 1.965930 CCACACCACACCATCACCG 60.966 63.158 0.00 0.00 0.00 4.94
431 436 2.281484 ACACCACACCATCACCGC 60.281 61.111 0.00 0.00 0.00 5.68
432 437 3.055719 CACCACACCATCACCGCC 61.056 66.667 0.00 0.00 0.00 6.13
433 438 3.565214 ACCACACCATCACCGCCA 61.565 61.111 0.00 0.00 0.00 5.69
434 439 2.045045 CCACACCATCACCGCCAT 60.045 61.111 0.00 0.00 0.00 4.40
435 440 2.114670 CCACACCATCACCGCCATC 61.115 63.158 0.00 0.00 0.00 3.51
436 441 1.377072 CACACCATCACCGCCATCA 60.377 57.895 0.00 0.00 0.00 3.07
437 442 1.377202 ACACCATCACCGCCATCAC 60.377 57.895 0.00 0.00 0.00 3.06
438 443 2.114670 CACCATCACCGCCATCACC 61.115 63.158 0.00 0.00 0.00 4.02
439 444 2.271821 CCATCACCGCCATCACCA 59.728 61.111 0.00 0.00 0.00 4.17
440 445 1.378382 CCATCACCGCCATCACCAA 60.378 57.895 0.00 0.00 0.00 3.67
441 446 1.378882 CCATCACCGCCATCACCAAG 61.379 60.000 0.00 0.00 0.00 3.61
442 447 1.750399 ATCACCGCCATCACCAAGC 60.750 57.895 0.00 0.00 0.00 4.01
443 448 2.482796 ATCACCGCCATCACCAAGCA 62.483 55.000 0.00 0.00 0.00 3.91
444 449 2.672996 ACCGCCATCACCAAGCAC 60.673 61.111 0.00 0.00 0.00 4.40
447 452 4.465512 GCCATCACCAAGCACGCG 62.466 66.667 3.53 3.53 0.00 6.01
449 454 3.725459 CATCACCAAGCACGCGCA 61.725 61.111 5.73 0.00 42.27 6.09
467 472 4.263572 CACACCCACGGCCCTCAA 62.264 66.667 0.00 0.00 0.00 3.02
468 473 4.265056 ACACCCACGGCCCTCAAC 62.265 66.667 0.00 0.00 0.00 3.18
548 556 1.473080 CCCAAACCCAAACACAGCAAG 60.473 52.381 0.00 0.00 0.00 4.01
658 666 4.202409 GCTATTAGATCAGGCAAGAAGGGT 60.202 45.833 0.00 0.00 0.00 4.34
667 675 1.480498 GGCAAGAAGGGTTTCCTGGAA 60.480 52.381 4.68 4.68 44.07 3.53
723 734 1.207339 TGCTCGCATGCAAAGTTCG 59.793 52.632 19.57 0.00 40.29 3.95
725 736 0.790866 GCTCGCATGCAAAGTTCGTC 60.791 55.000 19.57 0.00 0.00 4.20
880 894 1.597854 CCTTCAGGTTGCTCGCACA 60.598 57.895 0.00 0.00 0.00 4.57
881 895 1.571460 CTTCAGGTTGCTCGCACAC 59.429 57.895 0.00 0.00 0.00 3.82
882 896 1.845809 CTTCAGGTTGCTCGCACACC 61.846 60.000 12.35 12.35 0.00 4.16
883 897 3.716006 CAGGTTGCTCGCACACCG 61.716 66.667 13.59 8.14 34.58 4.94
972 1005 3.923461 TCGGTTTCTGCACAAAAAGTTTG 59.077 39.130 0.00 0.00 0.00 2.93
987 1020 9.161629 ACAAAAAGTTTGGATTTTTCGATCTTT 57.838 25.926 5.76 0.00 37.67 2.52
1152 1185 1.450312 CACCTCCACCTCGCCATTC 60.450 63.158 0.00 0.00 0.00 2.67
1234 1273 0.466372 GCCCCAAGAATCCTGCTACC 60.466 60.000 0.00 0.00 0.00 3.18
1242 1281 1.348775 AATCCTGCTACCTCCCTGCC 61.349 60.000 0.00 0.00 0.00 4.85
1266 1305 3.576982 CCTCCTCTTACAGTTACACCACA 59.423 47.826 0.00 0.00 0.00 4.17
1288 1327 1.600636 CAAGCTCCGTTTGCTCCCA 60.601 57.895 0.00 0.00 40.22 4.37
1462 1501 1.449956 CAGCTCTTCCTCCAGCAGC 60.450 63.158 0.00 0.00 38.18 5.25
1463 1502 1.917282 AGCTCTTCCTCCAGCAGCA 60.917 57.895 0.00 0.00 38.18 4.41
1464 1503 1.449956 GCTCTTCCTCCAGCAGCAG 60.450 63.158 0.00 0.00 35.56 4.24
1465 1504 1.449956 CTCTTCCTCCAGCAGCAGC 60.450 63.158 0.00 0.00 42.56 5.25
1466 1505 2.181445 CTCTTCCTCCAGCAGCAGCA 62.181 60.000 3.17 0.00 45.49 4.41
1467 1506 1.745864 CTTCCTCCAGCAGCAGCAG 60.746 63.158 3.17 0.00 45.49 4.24
1468 1507 3.914579 TTCCTCCAGCAGCAGCAGC 62.915 63.158 3.17 0.46 45.49 5.25
1469 1508 4.717313 CCTCCAGCAGCAGCAGCA 62.717 66.667 12.92 0.00 45.49 4.41
1470 1509 3.128188 CTCCAGCAGCAGCAGCAG 61.128 66.667 12.92 3.65 45.49 4.24
1817 1865 0.102120 CTCGACTCCATCTGCCAGAC 59.898 60.000 0.00 0.00 0.00 3.51
1851 1899 2.126580 CCGTCGTCCAAGTCGTCC 60.127 66.667 0.00 0.00 0.00 4.79
2129 2192 1.401539 GCAAACGGAAGCTCCATGAAC 60.402 52.381 0.00 0.00 35.91 3.18
2136 2199 3.621268 CGGAAGCTCCATGAACGAATTAA 59.379 43.478 0.00 0.00 35.91 1.40
2137 2200 4.273480 CGGAAGCTCCATGAACGAATTAAT 59.727 41.667 0.00 0.00 35.91 1.40
2138 2201 5.559035 CGGAAGCTCCATGAACGAATTAATC 60.559 44.000 0.00 0.00 35.91 1.75
2170 2233 1.447317 AATTAATCCTGCAGCGGCCG 61.447 55.000 24.05 24.05 40.13 6.13
2244 2307 2.202388 TTCGCCATCGTCGTCGTC 60.202 61.111 1.33 0.00 38.33 4.20
2245 2308 3.987777 TTCGCCATCGTCGTCGTCG 62.988 63.158 5.50 5.50 38.33 5.12
2246 2309 4.806481 CGCCATCGTCGTCGTCGT 62.806 66.667 11.41 0.00 38.33 4.34
2259 2322 1.127582 GTCGTCGTAGTAGCAGTCGTT 59.872 52.381 0.00 0.00 0.00 3.85
2283 2346 9.459640 GTTAAGAAGGGTTTAAGCTTAAGTTTG 57.540 33.333 17.91 0.00 33.29 2.93
2384 2450 2.426024 GGCCAGTCGAGAGTGTAATGTA 59.574 50.000 0.00 0.00 0.00 2.29
2385 2451 3.068307 GGCCAGTCGAGAGTGTAATGTAT 59.932 47.826 0.00 0.00 0.00 2.29
2386 2452 4.045104 GCCAGTCGAGAGTGTAATGTATG 58.955 47.826 7.11 0.00 0.00 2.39
2387 2453 4.045104 CCAGTCGAGAGTGTAATGTATGC 58.955 47.826 7.11 0.00 0.00 3.14
2454 2526 8.532186 ACTAGTCTCATTGTGATCTATCTTGT 57.468 34.615 0.00 0.00 0.00 3.16
2470 2542 8.565896 TCTATCTTGTGCATATTTCAGTTGTT 57.434 30.769 0.00 0.00 0.00 2.83
2471 2543 9.013229 TCTATCTTGTGCATATTTCAGTTGTTT 57.987 29.630 0.00 0.00 0.00 2.83
2473 2545 7.697352 TCTTGTGCATATTTCAGTTGTTTTG 57.303 32.000 0.00 0.00 0.00 2.44
2474 2546 7.487484 TCTTGTGCATATTTCAGTTGTTTTGA 58.513 30.769 0.00 0.00 0.00 2.69
2475 2547 8.143193 TCTTGTGCATATTTCAGTTGTTTTGAT 58.857 29.630 0.00 0.00 0.00 2.57
2477 2549 8.074474 TGTGCATATTTCAGTTGTTTTGATTG 57.926 30.769 0.00 0.00 0.00 2.67
2478 2550 7.924947 TGTGCATATTTCAGTTGTTTTGATTGA 59.075 29.630 0.00 0.00 0.00 2.57
2485 2584 5.518812 TCAGTTGTTTTGATTGATGTTCCG 58.481 37.500 0.00 0.00 0.00 4.30
2491 2590 5.751028 TGTTTTGATTGATGTTCCGAAAACC 59.249 36.000 0.00 0.00 33.09 3.27
2500 2599 4.785511 TGTTCCGAAAACCTCTCTCTAG 57.214 45.455 0.00 0.00 0.00 2.43
2501 2600 3.056749 TGTTCCGAAAACCTCTCTCTAGC 60.057 47.826 0.00 0.00 0.00 3.42
2502 2601 3.088789 TCCGAAAACCTCTCTCTAGCT 57.911 47.619 0.00 0.00 0.00 3.32
2503 2602 4.232188 TCCGAAAACCTCTCTCTAGCTA 57.768 45.455 0.00 0.00 0.00 3.32
2504 2603 4.794334 TCCGAAAACCTCTCTCTAGCTAT 58.206 43.478 0.00 0.00 0.00 2.97
2506 2605 5.998981 TCCGAAAACCTCTCTCTAGCTATAG 59.001 44.000 0.00 0.00 0.00 1.31
2593 2695 5.471257 AGAACGGAGAGAACAGTAACATTC 58.529 41.667 0.00 0.00 0.00 2.67
2594 2696 4.866508 ACGGAGAGAACAGTAACATTCA 57.133 40.909 0.00 0.00 0.00 2.57
2595 2697 4.810790 ACGGAGAGAACAGTAACATTCAG 58.189 43.478 0.00 0.00 0.00 3.02
2596 2698 4.177026 CGGAGAGAACAGTAACATTCAGG 58.823 47.826 0.00 0.00 0.00 3.86
2598 2700 5.415221 GGAGAGAACAGTAACATTCAGGAG 58.585 45.833 0.00 0.00 0.00 3.69
2602 2704 7.684529 AGAGAACAGTAACATTCAGGAGAATT 58.315 34.615 0.00 0.00 42.46 2.17
2603 2705 8.160106 AGAGAACAGTAACATTCAGGAGAATTT 58.840 33.333 0.00 0.00 42.46 1.82
2604 2706 8.697507 AGAACAGTAACATTCAGGAGAATTTT 57.302 30.769 0.00 0.00 42.46 1.82
2606 2708 7.823745 ACAGTAACATTCAGGAGAATTTTGT 57.176 32.000 0.00 0.00 42.46 2.83
2608 2710 7.502226 ACAGTAACATTCAGGAGAATTTTGTGA 59.498 33.333 0.00 0.00 42.46 3.58
2610 2712 8.571336 AGTAACATTCAGGAGAATTTTGTGAAG 58.429 33.333 0.00 0.00 42.46 3.02
2611 2713 7.587037 AACATTCAGGAGAATTTTGTGAAGA 57.413 32.000 0.00 0.00 42.46 2.87
2652 3022 7.663043 ACTTTTGTGAAGGGTTTTGGTTATA 57.337 32.000 0.00 0.00 0.00 0.98
2653 3023 8.080363 ACTTTTGTGAAGGGTTTTGGTTATAA 57.920 30.769 0.00 0.00 0.00 0.98
2654 3024 8.541234 ACTTTTGTGAAGGGTTTTGGTTATAAA 58.459 29.630 0.00 0.00 0.00 1.40
2655 3025 8.719560 TTTTGTGAAGGGTTTTGGTTATAAAC 57.280 30.769 0.00 0.00 35.31 2.01
2656 3026 7.663043 TTGTGAAGGGTTTTGGTTATAAACT 57.337 32.000 1.50 0.00 36.12 2.66
2671 3041 9.965824 TGGTTATAAACTTATACCGTAAGCTAC 57.034 33.333 1.50 0.00 0.00 3.58
2697 3067 2.093447 GGGAGACTCAAGTACCATGTGG 60.093 54.545 4.53 0.00 42.17 4.17
2698 3068 2.622436 GAGACTCAAGTACCATGTGGC 58.378 52.381 0.00 0.00 39.32 5.01
2719 3089 1.423395 CGTGAGGCTTGTGAGAGTTC 58.577 55.000 0.00 0.00 0.00 3.01
2814 3184 1.202533 ACCGAGCTATTCCATTGACCG 60.203 52.381 0.00 0.00 0.00 4.79
2866 3236 3.869272 CGCAGCCTTAGCCGCAAG 61.869 66.667 0.00 0.00 42.89 4.01
2960 3332 6.584563 GCATTGGAAACGCAAAAGAAATAGTA 59.415 34.615 0.00 0.00 0.00 1.82
3003 3375 2.050077 GCACGCTGGGTCAAAAGC 60.050 61.111 0.00 0.00 36.03 3.51
3038 3410 1.270550 GCAATCCAACCTTCCACACAG 59.729 52.381 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.351874 TGAAAAAGAGGACTACCACTGG 57.648 45.455 0.00 0.00 37.20 4.00
66 67 9.236691 TCGTCTTCTTTCTTTTTGAATTTGATG 57.763 29.630 0.00 0.00 34.24 3.07
67 68 9.971922 ATCGTCTTCTTTCTTTTTGAATTTGAT 57.028 25.926 0.00 0.00 34.24 2.57
68 69 9.801873 AATCGTCTTCTTTCTTTTTGAATTTGA 57.198 25.926 0.00 0.00 34.24 2.69
72 73 9.617975 GATGAATCGTCTTCTTTCTTTTTGAAT 57.382 29.630 0.00 0.00 34.24 2.57
74 75 8.153479 TGATGAATCGTCTTCTTTCTTTTTGA 57.847 30.769 3.95 0.00 0.00 2.69
75 76 8.961294 ATGATGAATCGTCTTCTTTCTTTTTG 57.039 30.769 3.95 0.00 0.00 2.44
89 90 6.017605 GCTTTGAGGTTGATATGATGAATCGT 60.018 38.462 0.00 0.00 0.00 3.73
90 91 6.017687 TGCTTTGAGGTTGATATGATGAATCG 60.018 38.462 0.00 0.00 0.00 3.34
138 139 2.323580 GCCCATCGCATGAGCTAGC 61.324 63.158 6.62 6.62 39.10 3.42
139 140 1.070275 TGCCCATCGCATGAGCTAG 59.930 57.895 0.00 0.00 44.64 3.42
140 141 3.229271 TGCCCATCGCATGAGCTA 58.771 55.556 0.00 0.00 44.64 3.32
170 171 4.704833 TTGACCTGGCGAGCTGGC 62.705 66.667 12.95 12.95 45.12 4.85
175 176 2.046892 CCTGGTTGACCTGGCGAG 60.047 66.667 12.40 0.00 46.05 5.03
257 262 3.805307 CTCGCGCCGTGAGAGAGT 61.805 66.667 22.46 0.00 46.37 3.24
276 281 2.479650 GAGTGGACGACGACGAGG 59.520 66.667 15.32 0.00 42.66 4.63
430 435 4.465512 CGCGTGCTTGGTGATGGC 62.466 66.667 0.00 0.00 0.00 4.40
431 436 4.465512 GCGCGTGCTTGGTGATGG 62.466 66.667 15.02 0.00 38.39 3.51
432 437 3.725459 TGCGCGTGCTTGGTGATG 61.725 61.111 23.16 0.00 43.34 3.07
433 438 3.726517 GTGCGCGTGCTTGGTGAT 61.727 61.111 23.16 0.00 43.34 3.06
435 440 4.962122 GTGTGCGCGTGCTTGGTG 62.962 66.667 23.16 0.00 43.34 4.17
437 442 4.962122 GTGTGTGCGCGTGCTTGG 62.962 66.667 23.16 0.00 43.34 3.61
438 443 4.962122 GGTGTGTGCGCGTGCTTG 62.962 66.667 23.16 0.00 43.34 4.01
469 474 3.334891 TCGTGGGTTGGATGGGGG 61.335 66.667 0.00 0.00 0.00 5.40
472 477 2.045340 GGGTCGTGGGTTGGATGG 60.045 66.667 0.00 0.00 0.00 3.51
474 479 2.602676 CCTGGGTCGTGGGTTGGAT 61.603 63.158 0.00 0.00 0.00 3.41
475 480 3.246112 CCTGGGTCGTGGGTTGGA 61.246 66.667 0.00 0.00 0.00 3.53
478 483 4.265056 GTGCCTGGGTCGTGGGTT 62.265 66.667 0.00 0.00 0.00 4.11
582 590 1.209747 GGGAGGAAATCTTACCTGCGT 59.790 52.381 0.00 0.00 43.82 5.24
633 641 4.996122 CCTTCTTGCCTGATCTAATAGCAG 59.004 45.833 0.00 0.00 41.47 4.24
681 689 6.479095 AAGCGAAAGAAGAAGAAGAAGATG 57.521 37.500 0.00 0.00 0.00 2.90
682 690 6.567511 GCAAAGCGAAAGAAGAAGAAGAAGAT 60.568 38.462 0.00 0.00 0.00 2.40
683 691 5.277538 GCAAAGCGAAAGAAGAAGAAGAAGA 60.278 40.000 0.00 0.00 0.00 2.87
694 705 0.874390 ATGCGAGCAAAGCGAAAGAA 59.126 45.000 0.57 0.00 37.44 2.52
695 706 0.166597 CATGCGAGCAAAGCGAAAGA 59.833 50.000 0.57 0.00 37.44 2.52
699 710 3.049074 TGCATGCGAGCAAAGCGA 61.049 55.556 14.09 7.32 42.46 4.93
723 734 3.675698 CGTCCTAGCAAGAACAAGAAGAC 59.324 47.826 0.00 0.00 0.00 3.01
725 736 3.914312 TCGTCCTAGCAAGAACAAGAAG 58.086 45.455 0.00 0.00 0.00 2.85
880 894 1.375326 GAAGAAGAACAGGGGCGGT 59.625 57.895 0.00 0.00 0.00 5.68
881 895 1.741770 CGAAGAAGAACAGGGGCGG 60.742 63.158 0.00 0.00 0.00 6.13
882 896 2.391389 GCGAAGAAGAACAGGGGCG 61.391 63.158 0.00 0.00 0.00 6.13
883 897 0.606673 AAGCGAAGAAGAACAGGGGC 60.607 55.000 0.00 0.00 0.00 5.80
929 956 6.589139 ACCGAACTAAAAGGTAGAAATCGAAG 59.411 38.462 0.00 0.00 36.34 3.79
942 975 4.545823 TGTGCAGAAACCGAACTAAAAG 57.454 40.909 0.00 0.00 0.00 2.27
972 1005 7.273598 GCCAACTAGAAAAAGATCGAAAAATCC 59.726 37.037 0.00 0.00 0.00 3.01
987 1020 1.173043 CCGCCATTGCCAACTAGAAA 58.827 50.000 0.00 0.00 0.00 2.52
1152 1185 0.824109 TGGAGGTGGCGTAGAATGAG 59.176 55.000 0.00 0.00 0.00 2.90
1234 1273 0.263172 TAAGAGGAGGAGGCAGGGAG 59.737 60.000 0.00 0.00 0.00 4.30
1242 1281 4.082136 GTGGTGTAACTGTAAGAGGAGGAG 60.082 50.000 0.00 0.00 37.43 3.69
1266 1305 1.230324 GAGCAAACGGAGCTTGAAGT 58.770 50.000 0.00 0.00 43.58 3.01
1294 1333 3.118454 CGACGATGTGGTGGTGGC 61.118 66.667 0.00 0.00 0.00 5.01
1297 1336 1.469335 AAGGACGACGATGTGGTGGT 61.469 55.000 0.00 0.00 0.00 4.16
1305 1344 1.429825 CTGCGAGAAGGACGACGAT 59.570 57.895 0.00 0.00 0.00 3.73
1833 1881 2.804090 GACGACTTGGACGACGGC 60.804 66.667 0.00 0.00 34.70 5.68
2170 2233 5.392767 TGTCTAATATTCCATCGAGCCTC 57.607 43.478 0.00 0.00 0.00 4.70
2244 2307 4.341099 CCTTCTTAACGACTGCTACTACG 58.659 47.826 0.00 0.00 0.00 3.51
2245 2308 4.157472 ACCCTTCTTAACGACTGCTACTAC 59.843 45.833 0.00 0.00 0.00 2.73
2246 2309 4.338879 ACCCTTCTTAACGACTGCTACTA 58.661 43.478 0.00 0.00 0.00 1.82
2259 2322 7.504574 AGCAAACTTAAGCTTAAACCCTTCTTA 59.495 33.333 19.10 0.00 38.01 2.10
2454 2526 8.927721 CATCAATCAAAACAACTGAAATATGCA 58.072 29.630 0.00 0.00 0.00 3.96
2470 2542 5.534654 AGAGGTTTTCGGAACATCAATCAAA 59.465 36.000 15.75 0.00 33.81 2.69
2471 2543 5.070001 AGAGGTTTTCGGAACATCAATCAA 58.930 37.500 15.75 0.00 33.81 2.57
2473 2545 4.938226 AGAGAGGTTTTCGGAACATCAATC 59.062 41.667 15.75 8.33 33.81 2.67
2474 2546 4.911390 AGAGAGGTTTTCGGAACATCAAT 58.089 39.130 15.75 4.95 33.81 2.57
2475 2547 4.040461 AGAGAGAGGTTTTCGGAACATCAA 59.960 41.667 15.75 0.00 33.81 2.57
2477 2549 4.195225 AGAGAGAGGTTTTCGGAACATC 57.805 45.455 8.51 8.51 0.00 3.06
2478 2550 4.382147 GCTAGAGAGAGGTTTTCGGAACAT 60.382 45.833 0.00 0.00 0.00 2.71
2485 2584 7.811117 TCACTATAGCTAGAGAGAGGTTTTC 57.189 40.000 21.87 0.00 0.00 2.29
2491 2590 7.337689 AGCATTGATCACTATAGCTAGAGAGAG 59.662 40.741 21.87 10.83 29.69 3.20
2506 2605 9.630098 TCTTCAGAAATTTTAAGCATTGATCAC 57.370 29.630 0.00 0.00 0.00 3.06
2574 2676 4.082190 TCCTGAATGTTACTGTTCTCTCCG 60.082 45.833 0.00 0.00 0.00 4.63
2616 2986 7.446931 ACCCTTCACAAAAGTTTTGAACAAAAT 59.553 29.630 30.20 11.13 41.64 1.82
2621 2991 6.795098 AAACCCTTCACAAAAGTTTTGAAC 57.205 33.333 30.20 0.00 0.00 3.18
2671 3041 1.477295 GGTACTTGAGTCTCCCTTCCG 59.523 57.143 0.00 0.00 0.00 4.30
2698 3068 1.079543 CTCTCACAAGCCTCACGGG 60.080 63.158 0.00 0.00 38.36 5.28
2747 3117 3.982372 TTGCGTGAGGTCGATCGGC 62.982 63.158 16.41 14.41 0.00 5.54
2814 3184 9.017509 TGCATGATCCATAGAATTCTTAAATCC 57.982 33.333 14.36 0.88 0.00 3.01
2866 3236 6.728089 AGCTACTACCTGTAATAAAGTCCC 57.272 41.667 0.00 0.00 0.00 4.46
2935 3305 4.730600 ATTTCTTTTGCGTTTCCAATGC 57.269 36.364 0.00 0.00 43.70 3.56
2936 3306 8.687824 ATACTATTTCTTTTGCGTTTCCAATG 57.312 30.769 0.00 0.00 0.00 2.82
2938 3308 9.615295 GTTATACTATTTCTTTTGCGTTTCCAA 57.385 29.630 0.00 0.00 0.00 3.53
2939 3309 7.958567 CGTTATACTATTTCTTTTGCGTTTCCA 59.041 33.333 0.00 0.00 0.00 3.53
2940 3310 8.170553 TCGTTATACTATTTCTTTTGCGTTTCC 58.829 33.333 0.00 0.00 0.00 3.13
2945 3315 9.749490 TTCTTTCGTTATACTATTTCTTTTGCG 57.251 29.630 0.00 0.00 0.00 4.85
2960 3332 6.570654 TCCCCCTAATTCTTCTTTCGTTAT 57.429 37.500 0.00 0.00 0.00 1.89
3003 3375 2.358267 GGATTGCAAGAGAAGGATGCTG 59.642 50.000 4.94 0.00 40.66 4.41
3038 3410 7.955502 ACACCAATTTGAAAAACGTACTTTTC 58.044 30.769 15.42 15.42 42.93 2.29


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

AutoCloner maintained by Alex Coulton.