Multiple sequence alignment - TraesCS7D01G425700

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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 TraesCS7D01G425700 chr7D 100.000 4804 0 0 1 4804 545693063 545697866 0.000000e+00 8872.0
1 TraesCS7D01G425700 chr7D 100.000 263 0 0 4987 5249 545698049 545698311 2.200000e-133 486.0
2 TraesCS7D01G425700 chr7D 93.443 61 4 0 3937 3997 101137360 101137300 2.010000e-14 91.6
3 TraesCS7D01G425700 chr7D 92.727 55 4 0 3937 3991 407071698 407071644 4.360000e-11 80.5
4 TraesCS7D01G425700 chr7A 92.286 4524 256 51 1 4481 628660472 628664945 0.000000e+00 6335.0
5 TraesCS7D01G425700 chr7A 85.742 512 47 9 3042 3538 634306589 634306089 7.790000e-143 518.0
6 TraesCS7D01G425700 chr7A 93.436 259 14 3 4992 5249 628665709 628665965 1.070000e-101 381.0
7 TraesCS7D01G425700 chr7A 85.878 262 34 1 2438 2699 634307483 634307225 5.180000e-70 276.0
8 TraesCS7D01G425700 chr7A 90.805 174 12 3 4468 4639 628665129 628665300 4.090000e-56 230.0
9 TraesCS7D01G425700 chr7A 92.617 149 10 1 4644 4791 628665356 628665504 4.120000e-51 213.0
10 TraesCS7D01G425700 chr7A 91.803 61 5 0 3937 3997 103398557 103398497 9.370000e-13 86.1
11 TraesCS7D01G425700 chr7B 94.253 3950 149 39 595 4515 589958309 589962209 0.000000e+00 5965.0
12 TraesCS7D01G425700 chr7B 86.437 435 39 9 127 554 589957813 589958234 4.790000e-125 459.0
13 TraesCS7D01G425700 chr7B 93.822 259 12 3 4994 5249 590006160 590006417 2.290000e-103 387.0
14 TraesCS7D01G425700 chr7B 92.884 267 15 3 4987 5249 589963255 589963521 8.250000e-103 385.0
15 TraesCS7D01G425700 chr7B 90.476 273 19 5 30 298 290387294 290387563 2.330000e-93 353.0
16 TraesCS7D01G425700 chr7B 88.125 160 19 0 4645 4804 589962752 589962911 1.930000e-44 191.0
17 TraesCS7D01G425700 chr7B 93.443 61 4 0 3937 3997 57678771 57678711 2.010000e-14 91.6
18 TraesCS7D01G425700 chr5B 89.897 485 34 11 4149 4628 573006650 573006176 1.250000e-170 610.0
19 TraesCS7D01G425700 chr6D 76.480 608 113 26 3504 4094 24829816 24829222 2.380000e-78 303.0
20 TraesCS7D01G425700 chr6B 77.046 562 97 29 3504 4046 40452344 40452892 1.430000e-75 294.0
21 TraesCS7D01G425700 chr6A 76.391 593 108 27 3470 4046 23363958 23363382 1.850000e-74 291.0


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 TraesCS7D01G425700 chr7D 545693063 545698311 5248 False 4679.00 8872 100.00000 1 5249 2 chr7D.!!$F1 5248
1 TraesCS7D01G425700 chr7A 628660472 628665965 5493 False 1789.75 6335 92.28600 1 5249 4 chr7A.!!$F1 5248
2 TraesCS7D01G425700 chr7A 634306089 634307483 1394 True 397.00 518 85.81000 2438 3538 2 chr7A.!!$R2 1100
3 TraesCS7D01G425700 chr7B 589957813 589963521 5708 False 1750.00 5965 90.42475 127 5249 4 chr7B.!!$F3 5122
4 TraesCS7D01G425700 chr6D 24829222 24829816 594 True 303.00 303 76.48000 3504 4094 1 chr6D.!!$R1 590
5 TraesCS7D01G425700 chr6B 40452344 40452892 548 False 294.00 294 77.04600 3504 4046 1 chr6B.!!$F1 542
6 TraesCS7D01G425700 chr6A 23363382 23363958 576 True 291.00 291 76.39100 3470 4046 1 chr6A.!!$R1 576

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
362 373 0.035056 CCCAGCAATCCTCCGAAACT 60.035 55.0 0.00 0.00 0.00 2.66 F
1053 1151 0.032403 TCGTCATTTCGGTGGTCGTT 59.968 50.0 0.00 0.00 40.32 3.85 F
1055 1153 0.110373 GTCATTTCGGTGGTCGTTGC 60.110 55.0 0.00 0.00 40.32 4.17 F
1431 1529 0.612174 TCAGCTACAACCGCCTCTCT 60.612 55.0 0.00 0.00 0.00 3.10 F
2415 2513 1.195115 GTCTGACTGGCCAGATACCA 58.805 55.0 39.19 25.51 44.09 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2342 0.806868 AGAACATGCCGCTGATGTTG 59.193 50.000 12.45 0.00 42.74 3.33 R
2508 2606 0.739561 GGTCCACGTAGTAGAGCCTG 59.260 60.000 0.00 0.00 40.53 4.85 R
2766 3323 1.088340 CCTGCAGCGTCTTCATCTGG 61.088 60.000 8.66 0.00 0.00 3.86 R
2847 3404 3.876320 GGAGGTCAAGAATCTCAATCTGC 59.124 47.826 0.00 0.00 0.00 4.26 R
4316 4908 0.099082 GTCTCACCGATCGACTCCAC 59.901 60.000 18.66 3.69 0.00 4.02 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
36 38 2.287117 TGGATGCCCCCTGTCCAT 60.287 61.111 0.00 0.00 37.12 3.41
41 43 3.246684 TGGATGCCCCCTGTCCATATATA 60.247 47.826 0.00 0.00 37.12 0.86
65 67 4.996434 CCAGATCCGATGGGGCGC 62.996 72.222 0.00 0.00 33.94 6.53
96 104 1.959226 CCTCCGGTGGTGTTTGTCG 60.959 63.158 14.67 0.00 0.00 4.35
104 112 0.678366 TGGTGTTTGTCGGCAGTTGT 60.678 50.000 0.00 0.00 0.00 3.32
114 122 3.660111 GCAGTTGTCGGGTGGCAC 61.660 66.667 9.70 9.70 0.00 5.01
139 147 2.048222 CCGTGTGTGTGGCTCGAT 60.048 61.111 0.00 0.00 0.00 3.59
175 183 3.244981 TGGGTTAGGGGTGTGTGTTATTC 60.245 47.826 0.00 0.00 0.00 1.75
203 211 0.608856 TCCGTTGCAATCCACATGCT 60.609 50.000 0.59 0.00 44.14 3.79
265 275 0.611062 TACACCCCGAGAGTCACCTG 60.611 60.000 0.00 0.00 0.00 4.00
300 310 2.730672 CTTCGAAACGCCAGCGAGG 61.731 63.158 20.32 4.68 42.83 4.63
322 333 4.201608 GGCAACGAAACGATAACGATAACA 60.202 41.667 0.00 0.00 42.66 2.41
357 368 0.611896 AAAACCCCAGCAATCCTCCG 60.612 55.000 0.00 0.00 0.00 4.63
361 372 1.032114 CCCCAGCAATCCTCCGAAAC 61.032 60.000 0.00 0.00 0.00 2.78
362 373 0.035056 CCCAGCAATCCTCCGAAACT 60.035 55.000 0.00 0.00 0.00 2.66
363 374 1.089920 CCAGCAATCCTCCGAAACTG 58.910 55.000 0.00 0.00 0.00 3.16
364 375 0.449388 CAGCAATCCTCCGAAACTGC 59.551 55.000 0.00 0.00 0.00 4.40
365 376 0.036732 AGCAATCCTCCGAAACTGCA 59.963 50.000 0.00 0.00 32.21 4.41
366 377 0.449388 GCAATCCTCCGAAACTGCAG 59.551 55.000 13.48 13.48 0.00 4.41
367 378 1.945819 GCAATCCTCCGAAACTGCAGA 60.946 52.381 23.35 0.00 0.00 4.26
368 379 2.005451 CAATCCTCCGAAACTGCAGAG 58.995 52.381 23.35 6.02 0.00 3.35
370 381 0.832135 TCCTCCGAAACTGCAGAGGT 60.832 55.000 23.35 4.27 45.16 3.85
371 382 0.390472 CCTCCGAAACTGCAGAGGTC 60.390 60.000 23.35 12.87 40.91 3.85
373 384 1.738099 CCGAAACTGCAGAGGTCCG 60.738 63.158 23.35 14.95 0.00 4.79
374 385 2.383527 CGAAACTGCAGAGGTCCGC 61.384 63.158 23.35 1.24 0.00 5.54
375 386 2.357517 AAACTGCAGAGGTCCGCG 60.358 61.111 23.35 0.00 0.00 6.46
385 396 1.352156 GAGGTCCGCGCACAACTAAG 61.352 60.000 8.75 0.00 0.00 2.18
386 397 2.474712 GTCCGCGCACAACTAAGC 59.525 61.111 8.75 0.00 0.00 3.09
387 398 2.027625 GTCCGCGCACAACTAAGCT 61.028 57.895 8.75 0.00 0.00 3.74
389 400 2.740714 CCGCGCACAACTAAGCTCC 61.741 63.158 8.75 0.00 0.00 4.70
390 401 2.027073 CGCGCACAACTAAGCTCCA 61.027 57.895 8.75 0.00 0.00 3.86
392 403 0.804989 GCGCACAACTAAGCTCCATT 59.195 50.000 0.30 0.00 0.00 3.16
393 404 1.466360 GCGCACAACTAAGCTCCATTG 60.466 52.381 0.30 0.00 0.00 2.82
394 405 2.076100 CGCACAACTAAGCTCCATTGA 58.924 47.619 9.95 0.00 0.00 2.57
395 406 2.159653 CGCACAACTAAGCTCCATTGAC 60.160 50.000 9.95 2.69 0.00 3.18
396 407 2.159653 GCACAACTAAGCTCCATTGACG 60.160 50.000 9.95 3.45 0.00 4.35
398 409 3.935203 CACAACTAAGCTCCATTGACGAT 59.065 43.478 9.95 0.00 0.00 3.73
399 410 4.033358 CACAACTAAGCTCCATTGACGATC 59.967 45.833 9.95 0.00 0.00 3.69
400 411 4.183865 CAACTAAGCTCCATTGACGATCA 58.816 43.478 0.00 0.00 0.00 2.92
401 412 4.471904 ACTAAGCTCCATTGACGATCAA 57.528 40.909 0.00 0.00 41.09 2.57
402 413 4.832248 ACTAAGCTCCATTGACGATCAAA 58.168 39.130 0.00 0.00 40.12 2.69
403 414 5.245531 ACTAAGCTCCATTGACGATCAAAA 58.754 37.500 0.00 0.00 40.12 2.44
404 415 5.882557 ACTAAGCTCCATTGACGATCAAAAT 59.117 36.000 0.00 0.00 40.12 1.82
405 416 4.889832 AGCTCCATTGACGATCAAAATC 57.110 40.909 0.00 0.00 40.12 2.17
406 417 3.629398 AGCTCCATTGACGATCAAAATCC 59.371 43.478 0.00 0.00 40.12 3.01
407 418 3.243201 GCTCCATTGACGATCAAAATCCC 60.243 47.826 0.00 0.00 40.12 3.85
408 419 2.942376 TCCATTGACGATCAAAATCCCG 59.058 45.455 0.00 0.00 40.12 5.14
409 420 2.541588 CCATTGACGATCAAAATCCCGC 60.542 50.000 0.00 0.00 40.12 6.13
410 421 0.724549 TTGACGATCAAAATCCCGCG 59.275 50.000 0.00 0.00 32.71 6.46
427 438 2.764314 CGGTCGACGTACCCGGAAT 61.764 63.158 9.92 0.00 38.09 3.01
446 461 1.213537 CCCGAACACGTCCGTACAT 59.786 57.895 0.00 0.00 0.00 2.29
454 469 2.028748 ACACGTCCGTACATAAAAGCCT 60.029 45.455 0.00 0.00 0.00 4.58
506 526 3.562973 GGTCACATCACATGATCACATCC 59.437 47.826 0.00 0.00 34.15 3.51
532 552 4.450757 CACATCATTCACTAACCAACACGA 59.549 41.667 0.00 0.00 0.00 4.35
552 572 4.691685 ACGACCATTTTTATCGTACAAGCA 59.308 37.500 0.00 0.00 46.63 3.91
553 573 5.353123 ACGACCATTTTTATCGTACAAGCAT 59.647 36.000 0.00 0.00 46.63 3.79
554 574 5.901884 CGACCATTTTTATCGTACAAGCATC 59.098 40.000 0.00 0.00 0.00 3.91
555 575 6.238103 CGACCATTTTTATCGTACAAGCATCT 60.238 38.462 0.00 0.00 0.00 2.90
556 576 6.785191 ACCATTTTTATCGTACAAGCATCTG 58.215 36.000 0.00 0.00 0.00 2.90
580 610 0.532573 GATCAGACGGAGCAACCTGA 59.467 55.000 0.00 0.00 39.60 3.86
591 621 1.004277 GCAACCTGACTGACGACTCG 61.004 60.000 0.00 0.00 0.00 4.18
592 622 0.591659 CAACCTGACTGACGACTCGA 59.408 55.000 5.20 0.00 0.00 4.04
596 655 2.571096 GACTGACGACTCGACGCG 60.571 66.667 3.53 3.53 36.70 6.01
609 668 1.445224 CGACGCGCGCTAAACAAATG 61.445 55.000 32.58 12.54 0.00 2.32
624 683 1.545582 CAAATGGCAACTTGGATCGGT 59.454 47.619 0.00 0.00 37.61 4.69
643 706 2.351111 GGTGTCTTACGTACTCGAGAGG 59.649 54.545 21.68 10.84 40.62 3.69
699 762 3.023116 CCCTTGGAGGCCCCATCA 61.023 66.667 13.07 0.00 46.10 3.07
729 792 0.178992 CAAAAGTCAGACCTGCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
734 797 2.045536 CAGACCTGCCCCAAGAGC 60.046 66.667 0.00 0.00 0.00 4.09
735 798 2.204059 AGACCTGCCCCAAGAGCT 60.204 61.111 0.00 0.00 0.00 4.09
770 847 4.564116 CACTACGCTACGCCCCGG 62.564 72.222 0.00 0.00 0.00 5.73
793 870 2.519441 CCTCCCTCCATGGCCATG 59.481 66.667 34.82 34.82 38.51 3.66
823 900 1.200716 CTCGCGCCGGATAAACCTATA 59.799 52.381 5.05 0.00 36.31 1.31
848 925 5.332280 CGTAGTATATTACCACGACGACGAA 60.332 44.000 15.32 0.00 44.55 3.85
887 964 0.687757 TGGGACGCTAGCTTCTCCAT 60.688 55.000 17.73 0.00 0.00 3.41
1013 1096 3.056536 GGCCTCGCTATGATCATCAGTTA 60.057 47.826 12.53 0.00 0.00 2.24
1016 1099 4.021981 CCTCGCTATGATCATCAGTTACCA 60.022 45.833 12.53 0.00 0.00 3.25
1017 1100 5.126396 TCGCTATGATCATCAGTTACCAG 57.874 43.478 12.53 2.39 0.00 4.00
1024 1107 1.089920 CATCAGTTACCAGCACCAGC 58.910 55.000 0.00 0.00 42.56 4.85
1053 1151 0.032403 TCGTCATTTCGGTGGTCGTT 59.968 50.000 0.00 0.00 40.32 3.85
1055 1153 0.110373 GTCATTTCGGTGGTCGTTGC 60.110 55.000 0.00 0.00 40.32 4.17
1063 1161 2.962786 TGGTCGTTGCGTCGTTGG 60.963 61.111 0.00 0.00 0.00 3.77
1072 1170 3.636043 CGTCGTTGGCGTTGCTGT 61.636 61.111 0.00 0.00 39.49 4.40
1075 1173 2.109739 TCGTTGGCGTTGCTGTTGT 61.110 52.632 0.00 0.00 39.49 3.32
1077 1175 1.199852 CGTTGGCGTTGCTGTTGTTC 61.200 55.000 0.00 0.00 0.00 3.18
1137 1235 3.123620 GCGCTGCTGACCTTCCTG 61.124 66.667 0.00 0.00 0.00 3.86
1431 1529 0.612174 TCAGCTACAACCGCCTCTCT 60.612 55.000 0.00 0.00 0.00 3.10
1702 1800 4.742201 GGAACTGCTCGCGCCTCA 62.742 66.667 0.00 0.00 34.43 3.86
1716 1814 3.073735 CTCAGGGTCCTCAGCGCT 61.074 66.667 2.64 2.64 0.00 5.92
2062 2160 3.358076 GACTTCTCCCGCCTCACCG 62.358 68.421 0.00 0.00 0.00 4.94
2104 2202 3.353836 CCAACAACCTCACCGGCG 61.354 66.667 0.00 0.00 35.61 6.46
2244 2342 3.969981 CGTTGACCGTGAACAATTTTACC 59.030 43.478 1.73 0.00 0.00 2.85
2293 2391 4.704833 GCTGCAAGGACCTCGCCA 62.705 66.667 0.92 0.00 0.00 5.69
2319 2417 3.189910 TGCTCGTGTCGTACAACTTCTAT 59.810 43.478 0.00 0.00 0.00 1.98
2403 2501 1.979693 GGAGGAGTGCGGTCTGACT 60.980 63.158 7.85 0.00 0.00 3.41
2415 2513 1.195115 GTCTGACTGGCCAGATACCA 58.805 55.000 39.19 25.51 44.09 3.25
2735 3292 1.929836 GCTCAACCTCAGCGATAACAG 59.070 52.381 0.00 0.00 0.00 3.16
3567 4147 2.261671 CACGAGAACCTGGTCCCG 59.738 66.667 0.00 6.86 0.00 5.14
4267 4859 0.599204 ACGTGGTCTGTGTAAAGCGG 60.599 55.000 0.00 0.00 0.00 5.52
4269 4861 1.870580 CGTGGTCTGTGTAAAGCGGAA 60.871 52.381 0.00 0.00 0.00 4.30
4283 4875 1.448540 CGGAAATGGAGCGCTCTGT 60.449 57.895 34.46 21.31 0.00 3.41
4287 4879 2.129555 AAATGGAGCGCTCTGTGGGT 62.130 55.000 34.46 14.14 0.00 4.51
4288 4880 2.129555 AATGGAGCGCTCTGTGGGTT 62.130 55.000 34.46 17.59 0.00 4.11
4290 4882 3.426568 GAGCGCTCTGTGGGTTGC 61.427 66.667 29.88 0.00 0.00 4.17
4291 4883 4.254709 AGCGCTCTGTGGGTTGCA 62.255 61.111 2.64 0.00 0.00 4.08
4294 4886 1.503542 CGCTCTGTGGGTTGCAATC 59.496 57.895 0.59 0.00 0.00 2.67
4295 4887 1.885871 GCTCTGTGGGTTGCAATCC 59.114 57.895 22.52 22.52 0.00 3.01
4297 4889 1.171308 CTCTGTGGGTTGCAATCCTG 58.829 55.000 28.51 18.07 0.00 3.86
4309 4901 2.108075 TGCAATCCTGAGAGTTTTGGGA 59.892 45.455 0.00 0.00 0.00 4.37
4316 4908 1.003118 TGAGAGTTTTGGGACGATGGG 59.997 52.381 0.00 0.00 0.00 4.00
4329 4921 1.364171 GATGGGTGGAGTCGATCGG 59.636 63.158 16.41 0.00 0.00 4.18
4335 4927 0.099082 GTGGAGTCGATCGGTGAGAC 59.901 60.000 16.41 5.47 35.30 3.36
4422 5021 4.728772 TCCACCATCCATAATCACATTCC 58.271 43.478 0.00 0.00 0.00 3.01
4423 5022 4.167697 TCCACCATCCATAATCACATTCCA 59.832 41.667 0.00 0.00 0.00 3.53
4481 5277 0.393537 CTGATTGGTGGAGGTGGAGC 60.394 60.000 0.00 0.00 0.00 4.70
4515 5311 2.813172 GTTTGCCACAAAAATGGATGGG 59.187 45.455 0.00 0.00 43.02 4.00
4531 5327 0.968405 TGGGGCATTGCTCTTTGTTC 59.032 50.000 8.71 0.00 0.00 3.18
4533 5329 0.881118 GGGCATTGCTCTTTGTTCGA 59.119 50.000 8.82 0.00 0.00 3.71
4535 5331 1.266718 GGCATTGCTCTTTGTTCGACA 59.733 47.619 8.82 0.00 0.00 4.35
4559 5356 0.396060 GATCCCTGGTCTCTGCATCC 59.604 60.000 0.00 0.00 0.00 3.51
4677 5913 2.837532 ACACAATCACCCAATTTGGC 57.162 45.000 10.10 0.00 35.79 4.52
4730 5966 5.027460 TGGCTACACCTAGAGACCAAAATA 58.973 41.667 0.00 0.00 40.22 1.40
4738 5974 6.314896 CACCTAGAGACCAAAATAAGCTTCAG 59.685 42.308 0.00 0.00 0.00 3.02
4752 5988 9.914131 AAATAAGCTTCAGGAACTTGATAAAAC 57.086 29.630 0.00 0.00 34.60 2.43
4753 5989 6.959639 AAGCTTCAGGAACTTGATAAAACA 57.040 33.333 0.00 0.00 34.60 2.83
4754 5990 7.530426 AAGCTTCAGGAACTTGATAAAACAT 57.470 32.000 0.00 0.00 34.60 2.71
4755 5991 7.150783 AGCTTCAGGAACTTGATAAAACATC 57.849 36.000 0.00 0.00 34.60 3.06
4792 6029 4.191544 TGATGGTATTGTAGCAGTTCTGC 58.808 43.478 15.88 15.88 39.81 4.26
4799 6036 0.453390 GTAGCAGTTCTGCATTGCCC 59.547 55.000 23.69 4.25 38.58 5.36
5016 6414 5.505286 CCATCTCGCAAACATATTTGAGAC 58.495 41.667 0.00 0.00 45.96 3.36
5073 6472 1.070134 ACTCACCACGAAAGCTAAGCA 59.930 47.619 0.00 0.00 0.00 3.91
5095 6496 1.126488 TGGGCATGAAAAGGCAAACA 58.874 45.000 0.00 0.00 0.00 2.83
5108 6509 5.957842 AAGGCAAACATTGAATTCGTCTA 57.042 34.783 0.04 0.00 0.00 2.59
5148 6549 9.238368 CTTATCAAAATTACCCCTTTACACAGA 57.762 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.568780 CCTCTATATATGGACAGGGGGCA 60.569 52.174 0.00 0.00 0.00 5.36
36 38 2.856864 TCGGATCTGGCCCCTCTATATA 59.143 50.000 0.00 0.00 0.00 0.86
41 43 1.840650 CATCGGATCTGGCCCCTCT 60.841 63.158 0.00 0.00 0.00 3.69
83 85 1.381165 AACTGCCGACAAACACCACC 61.381 55.000 0.00 0.00 0.00 4.61
86 94 0.028902 GACAACTGCCGACAAACACC 59.971 55.000 0.00 0.00 0.00 4.16
96 104 4.947147 TGCCACCCGACAACTGCC 62.947 66.667 0.00 0.00 0.00 4.85
114 122 1.665916 CACACACACGGAGGCTCTG 60.666 63.158 21.66 21.66 0.00 3.35
124 132 2.863153 GCATCGAGCCACACACAC 59.137 61.111 0.00 0.00 37.23 3.82
125 133 2.738139 CGCATCGAGCCACACACA 60.738 61.111 0.00 0.00 41.38 3.72
175 183 3.243704 TGGATTGCAACGGAAGGAAAAAG 60.244 43.478 0.00 0.00 0.00 2.27
265 275 3.050275 GCTGCTCGGGGTGTTCAC 61.050 66.667 0.00 0.00 0.00 3.18
300 310 4.715905 GTGTTATCGTTATCGTTTCGTTGC 59.284 41.667 0.00 0.00 38.33 4.17
322 333 2.632136 TTTTGACGTCGGTGGCTCGT 62.632 55.000 11.62 0.00 40.49 4.18
364 375 2.486636 TAGTTGTGCGCGGACCTCTG 62.487 60.000 28.22 0.00 0.00 3.35
365 376 1.812686 TTAGTTGTGCGCGGACCTCT 61.813 55.000 28.22 24.84 0.00 3.69
366 377 1.352156 CTTAGTTGTGCGCGGACCTC 61.352 60.000 28.22 19.53 0.00 3.85
367 378 1.374252 CTTAGTTGTGCGCGGACCT 60.374 57.895 28.22 20.13 0.00 3.85
368 379 3.023591 GCTTAGTTGTGCGCGGACC 62.024 63.158 28.22 13.61 0.00 4.46
370 381 1.736645 GAGCTTAGTTGTGCGCGGA 60.737 57.895 8.83 0.00 0.00 5.54
371 382 2.740714 GGAGCTTAGTTGTGCGCGG 61.741 63.158 8.83 0.00 0.00 6.46
373 384 0.804989 AATGGAGCTTAGTTGTGCGC 59.195 50.000 0.00 0.00 0.00 6.09
374 385 2.076100 TCAATGGAGCTTAGTTGTGCG 58.924 47.619 0.00 0.00 0.00 5.34
375 386 2.159653 CGTCAATGGAGCTTAGTTGTGC 60.160 50.000 0.00 0.00 0.00 4.57
376 387 3.325870 TCGTCAATGGAGCTTAGTTGTG 58.674 45.455 0.00 0.00 0.00 3.33
377 388 3.678056 TCGTCAATGGAGCTTAGTTGT 57.322 42.857 0.00 0.00 0.00 3.32
378 389 4.183865 TGATCGTCAATGGAGCTTAGTTG 58.816 43.478 0.00 0.00 0.00 3.16
379 390 4.471904 TGATCGTCAATGGAGCTTAGTT 57.528 40.909 0.00 0.00 0.00 2.24
385 396 3.243201 GGGATTTTGATCGTCAATGGAGC 60.243 47.826 2.09 0.00 36.11 4.70
386 397 3.002656 CGGGATTTTGATCGTCAATGGAG 59.997 47.826 2.09 0.00 36.11 3.86
387 398 2.942376 CGGGATTTTGATCGTCAATGGA 59.058 45.455 2.09 0.00 36.11 3.41
389 400 2.719798 GCGGGATTTTGATCGTCAATG 58.280 47.619 2.09 0.00 36.11 2.82
390 401 1.330521 CGCGGGATTTTGATCGTCAAT 59.669 47.619 0.00 0.00 36.11 2.57
392 403 1.087202 CCGCGGGATTTTGATCGTCA 61.087 55.000 20.10 0.00 0.00 4.35
393 404 1.087771 ACCGCGGGATTTTGATCGTC 61.088 55.000 31.76 0.00 0.00 4.20
394 405 1.078708 ACCGCGGGATTTTGATCGT 60.079 52.632 31.76 0.00 0.00 3.73
395 406 1.641677 GACCGCGGGATTTTGATCG 59.358 57.895 31.76 0.00 0.00 3.69
396 407 0.808453 TCGACCGCGGGATTTTGATC 60.808 55.000 31.76 14.17 38.28 2.92
398 409 1.738830 GTCGACCGCGGGATTTTGA 60.739 57.895 31.76 14.93 38.28 2.69
399 410 2.782615 GTCGACCGCGGGATTTTG 59.217 61.111 31.76 12.52 38.28 2.44
400 411 2.211619 TACGTCGACCGCGGGATTTT 62.212 55.000 31.76 7.71 41.42 1.82
401 412 2.699768 TACGTCGACCGCGGGATTT 61.700 57.895 31.76 8.20 41.42 2.17
402 413 3.133464 TACGTCGACCGCGGGATT 61.133 61.111 31.76 8.67 41.42 3.01
403 414 3.880846 GTACGTCGACCGCGGGAT 61.881 66.667 31.76 9.62 41.42 3.85
409 420 2.652893 GATTCCGGGTACGTCGACCG 62.653 65.000 10.58 15.90 46.79 4.79
410 421 1.064783 GATTCCGGGTACGTCGACC 59.935 63.158 10.58 0.00 38.78 4.79
427 438 1.243342 ATGTACGGACGTGTTCGGGA 61.243 55.000 7.73 0.00 41.85 5.14
454 469 0.108992 CGGTTTTGATCGAGACGGGA 60.109 55.000 3.86 0.00 0.00 5.14
506 526 4.518590 TGTTGGTTAGTGAATGATGTGGTG 59.481 41.667 0.00 0.00 0.00 4.17
532 552 6.597672 TCAGATGCTTGTACGATAAAAATGGT 59.402 34.615 0.00 0.00 0.00 3.55
555 575 1.767759 TGCTCCGTCTGATCAGATCA 58.232 50.000 27.51 16.65 39.97 2.92
556 576 2.468831 GTTGCTCCGTCTGATCAGATC 58.531 52.381 27.51 18.90 39.97 2.75
580 610 4.738345 GCGCGTCGAGTCGTCAGT 62.738 66.667 13.12 0.00 0.00 3.41
591 621 1.125847 CCATTTGTTTAGCGCGCGTC 61.126 55.000 32.35 22.88 0.00 5.19
592 622 1.154301 CCATTTGTTTAGCGCGCGT 60.154 52.632 32.35 20.00 0.00 6.01
596 655 2.064573 AGTTGCCATTTGTTTAGCGC 57.935 45.000 0.00 0.00 0.00 5.92
609 668 0.321653 AGACACCGATCCAAGTTGCC 60.322 55.000 0.00 0.00 0.00 4.52
624 683 2.234661 TCCCTCTCGAGTACGTAAGACA 59.765 50.000 13.13 0.00 43.62 3.41
699 762 1.600916 GACTTTTGGAGGTGCGGCT 60.601 57.895 0.00 0.00 0.00 5.52
705 768 1.202818 GCAGGTCTGACTTTTGGAGGT 60.203 52.381 7.85 0.00 0.00 3.85
729 792 1.719600 GCGAGTCATGTTGAGCTCTT 58.280 50.000 16.19 0.00 0.00 2.85
734 797 0.368227 GCTTCGCGAGTCATGTTGAG 59.632 55.000 9.59 1.00 0.00 3.02
735 798 0.319469 TGCTTCGCGAGTCATGTTGA 60.319 50.000 9.59 0.00 0.00 3.18
770 847 3.174265 CATGGAGGGAGGGAGGGC 61.174 72.222 0.00 0.00 0.00 5.19
772 849 3.174265 GCCATGGAGGGAGGGAGG 61.174 72.222 18.40 0.00 38.09 4.30
773 850 3.174265 GGCCATGGAGGGAGGGAG 61.174 72.222 18.40 0.00 38.09 4.30
774 851 3.367604 ATGGCCATGGAGGGAGGGA 62.368 63.158 20.04 0.00 38.09 4.20
775 852 2.780040 ATGGCCATGGAGGGAGGG 60.780 66.667 20.04 0.00 38.09 4.30
776 853 2.519441 CATGGCCATGGAGGGAGG 59.481 66.667 34.31 9.41 38.09 4.30
957 1040 5.124776 GTCAACAACATGGGGAATAATCGAA 59.875 40.000 0.00 0.00 0.00 3.71
961 1044 3.699038 CCGTCAACAACATGGGGAATAAT 59.301 43.478 0.00 0.00 0.00 1.28
1025 1108 2.746277 AAATGACGACCCGCTGCC 60.746 61.111 0.00 0.00 0.00 4.85
1055 1153 3.163110 AACAGCAACGCCAACGACG 62.163 57.895 0.00 0.00 43.93 5.12
1063 1161 2.725815 GGCGAACAACAGCAACGC 60.726 61.111 0.00 0.00 46.79 4.84
1066 1164 3.959975 GCCGGCGAACAACAGCAA 61.960 61.111 12.58 0.00 34.54 3.91
1117 1215 3.123620 GAAGGTCAGCAGCGCCTG 61.124 66.667 2.29 5.38 32.16 4.85
1281 1379 4.632458 GAGATCGTCCCGCCGAGC 62.632 72.222 0.00 0.00 43.18 5.03
1500 1598 1.746615 CCCGGACAGATGGTTGCTG 60.747 63.158 0.73 0.00 39.26 4.41
1551 1649 3.417275 ATTGAGCGAGACGAGGCCG 62.417 63.158 0.00 0.00 42.50 6.13
1698 1796 4.154347 GCGCTGAGGACCCTGAGG 62.154 72.222 0.00 0.00 40.04 3.86
1701 1799 4.463879 CCAGCGCTGAGGACCCTG 62.464 72.222 38.06 15.18 0.00 4.45
1716 1814 1.525077 GGTGAGGTTGTTGCGACCA 60.525 57.895 0.45 0.00 40.26 4.02
1719 1817 2.280524 CCGGTGAGGTTGTTGCGA 60.281 61.111 0.00 0.00 34.51 5.10
1835 1933 1.674221 GCTTGACGAGGTTGATGAGCT 60.674 52.381 0.00 0.00 39.22 4.09
1839 1937 0.994995 CGAGCTTGACGAGGTTGATG 59.005 55.000 3.29 0.00 39.22 3.07
2062 2160 1.134965 CAGGTCCAAGACGGTGAGATC 60.135 57.143 0.00 0.00 35.57 2.75
2197 2295 1.018226 AACTGCAGCTCTCGCATGTC 61.018 55.000 15.27 0.00 39.02 3.06
2244 2342 0.806868 AGAACATGCCGCTGATGTTG 59.193 50.000 12.45 0.00 42.74 3.33
2361 2459 2.125512 ATCAGCCGGACGTTGCTC 60.126 61.111 5.05 0.00 35.12 4.26
2403 2501 1.829456 CCACGATGGTATCTGGCCA 59.171 57.895 4.71 4.71 40.68 5.36
2508 2606 0.739561 GGTCCACGTAGTAGAGCCTG 59.260 60.000 0.00 0.00 40.53 4.85
2589 2687 2.203126 GCCATGGCCTTCTCCGAG 60.203 66.667 27.24 0.00 34.56 4.63
2766 3323 1.088340 CCTGCAGCGTCTTCATCTGG 61.088 60.000 8.66 0.00 0.00 3.86
2847 3404 3.876320 GGAGGTCAAGAATCTCAATCTGC 59.124 47.826 0.00 0.00 0.00 4.26
3567 4147 1.823041 GATGCAGAAGCCCTGGAGC 60.823 63.158 0.00 2.27 46.51 4.70
4267 4859 1.372087 CCCACAGAGCGCTCCATTTC 61.372 60.000 32.94 9.05 0.00 2.17
4269 4861 2.129555 AACCCACAGAGCGCTCCATT 62.130 55.000 32.94 15.29 0.00 3.16
4283 4875 1.067295 ACTCTCAGGATTGCAACCCA 58.933 50.000 13.79 0.00 0.00 4.51
4287 4879 2.892852 CCCAAAACTCTCAGGATTGCAA 59.107 45.455 0.00 0.00 0.00 4.08
4288 4880 2.108075 TCCCAAAACTCTCAGGATTGCA 59.892 45.455 0.00 0.00 0.00 4.08
4290 4882 2.744202 CGTCCCAAAACTCTCAGGATTG 59.256 50.000 0.00 0.00 0.00 2.67
4291 4883 2.637872 TCGTCCCAAAACTCTCAGGATT 59.362 45.455 0.00 0.00 0.00 3.01
4294 4886 2.350522 CATCGTCCCAAAACTCTCAGG 58.649 52.381 0.00 0.00 0.00 3.86
4295 4887 2.350522 CCATCGTCCCAAAACTCTCAG 58.649 52.381 0.00 0.00 0.00 3.35
4297 4889 1.003233 ACCCATCGTCCCAAAACTCTC 59.997 52.381 0.00 0.00 0.00 3.20
4309 4901 1.725557 CGATCGACTCCACCCATCGT 61.726 60.000 10.26 0.00 37.16 3.73
4316 4908 0.099082 GTCTCACCGATCGACTCCAC 59.901 60.000 18.66 3.69 0.00 4.02
4329 4921 7.846644 ATTCTGATTCTGATTTCTGTCTCAC 57.153 36.000 0.00 0.00 0.00 3.51
4422 5021 1.659098 GTTGCTTTAGTCGACGGGATG 59.341 52.381 10.46 3.95 0.00 3.51
4423 5022 1.274167 TGTTGCTTTAGTCGACGGGAT 59.726 47.619 10.46 0.00 0.00 3.85
4481 5277 6.751514 TTGTGGCAAACCTATGTAACTATG 57.248 37.500 0.00 0.00 36.63 2.23
4515 5311 1.266718 TGTCGAACAAAGAGCAATGCC 59.733 47.619 0.00 0.00 0.00 4.40
4531 5327 1.827969 AGACCAGGGATCTCTTTGTCG 59.172 52.381 13.74 0.00 0.00 4.35
4559 5356 4.993905 AGATGATTGTGTGTGCATCAATG 58.006 39.130 11.83 0.00 39.57 2.82
4659 5895 1.672441 CGGCCAAATTGGGTGATTGTG 60.672 52.381 14.59 0.00 38.19 3.33
4677 5913 2.400399 TGTAGCTCGAACTTTGTTCGG 58.600 47.619 25.60 18.88 41.78 4.30
4730 5966 6.959639 TGTTTTATCAAGTTCCTGAAGCTT 57.040 33.333 0.00 0.00 0.00 3.74
4738 5974 6.095377 CCAAGCAGATGTTTTATCAAGTTCC 58.905 40.000 0.00 0.00 0.00 3.62
4752 5988 5.359009 ACCATCATTCTTAACCAAGCAGATG 59.641 40.000 0.00 0.00 35.76 2.90
4753 5989 5.513233 ACCATCATTCTTAACCAAGCAGAT 58.487 37.500 0.00 0.00 0.00 2.90
4754 5990 4.922206 ACCATCATTCTTAACCAAGCAGA 58.078 39.130 0.00 0.00 0.00 4.26
4755 5991 6.949352 ATACCATCATTCTTAACCAAGCAG 57.051 37.500 0.00 0.00 0.00 4.24
4988 6386 1.376543 ATGTTTGCGAGATGGCTCTG 58.623 50.000 0.00 0.00 39.06 3.35
5016 6414 4.693283 TCAATATTTCCCGTGTAGCTCAG 58.307 43.478 0.00 0.00 0.00 3.35
5025 6423 3.426615 TGTGGCTTTCAATATTTCCCGT 58.573 40.909 0.00 0.00 0.00 5.28
5073 6472 1.941377 TTGCCTTTTCATGCCCATCT 58.059 45.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.