Multiple sequence alignment - TraesCS5A01G327800

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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 TraesCS5A01G327800 chr5A 100.000 6571 0 0 1 6571 537132931 537126361 0.000000e+00 12135
1 TraesCS5A01G327800 chr5A 84.722 144 11 6 5933 6076 537122002 537121870 4.130000e-27 134
2 TraesCS5A01G327800 chr5B 94.500 6054 221 43 494 6480 511401695 511395687 0.000000e+00 9232
3 TraesCS5A01G327800 chr5B 80.835 527 51 25 115 633 638648281 638647797 1.040000e-97 368
4 TraesCS5A01G327800 chr5D 94.732 2373 56 16 3245 5598 423539881 423537559 0.000000e+00 3626
5 TraesCS5A01G327800 chr5D 96.857 1877 50 6 1373 3245 423541876 423540005 0.000000e+00 3131
6 TraesCS5A01G327800 chr5D 88.666 1297 91 22 70 1334 423543156 423541884 0.000000e+00 1530
7 TraesCS5A01G327800 chr5D 90.144 974 53 15 5618 6563 423537572 423536614 0.000000e+00 1227
8 TraesCS5A01G327800 chr5D 83.333 156 16 5 5934 6089 423532710 423532565 1.150000e-27 135
9 TraesCS5A01G327800 chr2B 82.737 643 89 13 3414 4047 801190560 801191189 2.680000e-153 553
10 TraesCS5A01G327800 chr2B 79.478 536 87 18 116 645 422237261 422236743 6.260000e-95 359
11 TraesCS5A01G327800 chr2B 82.957 399 53 12 276 663 100985293 100984899 4.880000e-91 346
12 TraesCS5A01G327800 chr3A 84.464 560 66 15 115 662 343228050 343228600 3.490000e-147 532
13 TraesCS5A01G327800 chr2D 80.286 629 90 19 2731 3345 282939278 282938670 1.680000e-120 444
14 TraesCS5A01G327800 chr2D 84.383 397 51 8 276 663 64628452 64628058 4.810000e-101 379
15 TraesCS5A01G327800 chr2D 80.892 314 41 10 2731 3034 87847451 87847755 5.130000e-56 230
16 TraesCS5A01G327800 chr6B 80.000 625 94 21 2731 3345 550811294 550810691 3.640000e-117 433
17 TraesCS5A01G327800 chr1D 80.810 568 84 19 115 669 408539859 408539304 7.880000e-114 422
18 TraesCS5A01G327800 chr3D 80.736 571 70 17 116 674 349640238 349639696 6.130000e-110 409
19 TraesCS5A01G327800 chr7A 80.790 557 73 27 111 657 486709756 486709224 7.930000e-109 405
20 TraesCS5A01G327800 chr1B 80.903 487 67 9 126 610 133219842 133219380 1.740000e-95 361
21 TraesCS5A01G327800 chr1B 79.710 207 36 5 1806 2010 121773697 121773899 1.910000e-30 145
22 TraesCS5A01G327800 chr2A 80.122 493 69 18 197 662 62137758 62137268 2.270000e-89 340
23 TraesCS5A01G327800 chr6D 77.442 563 103 21 113 664 308923962 308924511 1.380000e-81 315
24 TraesCS5A01G327800 chr4B 79.283 251 32 14 2802 3041 588065939 588065698 2.450000e-34 158


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 TraesCS5A01G327800 chr5A 537126361 537132931 6570 True 12135.0 12135 100.0000 1 6571 1 chr5A.!!$R2 6570
1 TraesCS5A01G327800 chr5B 511395687 511401695 6008 True 9232.0 9232 94.5000 494 6480 1 chr5B.!!$R1 5986
2 TraesCS5A01G327800 chr5D 423532565 423543156 10591 True 1929.8 3626 90.7464 70 6563 5 chr5D.!!$R1 6493
3 TraesCS5A01G327800 chr2B 801190560 801191189 629 False 553.0 553 82.7370 3414 4047 1 chr2B.!!$F1 633
4 TraesCS5A01G327800 chr2B 422236743 422237261 518 True 359.0 359 79.4780 116 645 1 chr2B.!!$R2 529
5 TraesCS5A01G327800 chr3A 343228050 343228600 550 False 532.0 532 84.4640 115 662 1 chr3A.!!$F1 547
6 TraesCS5A01G327800 chr2D 282938670 282939278 608 True 444.0 444 80.2860 2731 3345 1 chr2D.!!$R2 614
7 TraesCS5A01G327800 chr6B 550810691 550811294 603 True 433.0 433 80.0000 2731 3345 1 chr6B.!!$R1 614
8 TraesCS5A01G327800 chr1D 408539304 408539859 555 True 422.0 422 80.8100 115 669 1 chr1D.!!$R1 554
9 TraesCS5A01G327800 chr3D 349639696 349640238 542 True 409.0 409 80.7360 116 674 1 chr3D.!!$R1 558
10 TraesCS5A01G327800 chr7A 486709224 486709756 532 True 405.0 405 80.7900 111 657 1 chr7A.!!$R1 546
11 TraesCS5A01G327800 chr6D 308923962 308924511 549 False 315.0 315 77.4420 113 664 1 chr6D.!!$F1 551

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
66 67 0.605589 AAGACTGTCTGAAGCTCCCG 59.394 55.000 11.71 0.0 0.00 5.14 F
94 95 0.678950 TGACAGATCGCCACACAAGA 59.321 50.000 0.00 0.0 0.00 3.02 F
762 837 1.696097 ATTTACCGCCGCTGGATCCT 61.696 55.000 14.23 0.0 0.00 3.24 F
1182 1266 0.968901 TCATGCGTCCGAACCCTAGT 60.969 55.000 0.00 0.0 0.00 2.57 F
2746 2835 0.535335 TGACCCGACATACCTTGCTC 59.465 55.000 0.00 0.0 0.00 4.26 F
3632 3861 2.748388 AGGACGGGAGCTTATACTTGT 58.252 47.619 0.00 0.0 0.00 3.16 F
4276 4512 3.878237 ATCACATGGATGGATGCTCTT 57.122 42.857 0.00 0.0 34.06 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1240 0.103208 GGTTCGGACGCATGATCTCT 59.897 55.000 0.00 0.00 0.00 3.10 R
1161 1243 0.387929 TAGGGTTCGGACGCATGATC 59.612 55.000 14.07 0.00 40.90 2.92 R
2486 2573 1.739466 ACCAGAGCATATGCAACAACG 59.261 47.619 28.62 13.01 45.16 4.10 R
3018 3116 3.627577 AGACCAATGCATTTATCACCGTC 59.372 43.478 9.83 6.86 0.00 4.79 R
4712 4950 0.034767 CTGGGCCATCTTCAGCTTCA 60.035 55.000 6.72 0.00 0.00 3.02 R
5195 5445 3.772572 TGTTTGAGTTATCCGGATCTCCA 59.227 43.478 23.08 11.40 35.14 3.86 R
5993 6248 0.482446 AACCACATGAGGGCTCCAAA 59.518 50.000 14.11 0.00 0.00 3.28 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
26 27 9.394477 GATGTTGATTACTGTTTAACAAAGTCC 57.606 33.333 0.00 0.00 35.23 3.85
27 28 7.708998 TGTTGATTACTGTTTAACAAAGTCCC 58.291 34.615 0.00 0.00 0.00 4.46
28 29 7.558444 TGTTGATTACTGTTTAACAAAGTCCCT 59.442 33.333 0.00 0.00 0.00 4.20
29 30 9.059260 GTTGATTACTGTTTAACAAAGTCCCTA 57.941 33.333 0.00 0.00 0.00 3.53
30 31 8.842358 TGATTACTGTTTAACAAAGTCCCTAG 57.158 34.615 0.00 0.00 0.00 3.02
31 32 8.434392 TGATTACTGTTTAACAAAGTCCCTAGT 58.566 33.333 0.00 0.00 0.00 2.57
32 33 9.281371 GATTACTGTTTAACAAAGTCCCTAGTT 57.719 33.333 0.00 0.00 0.00 2.24
34 35 9.546428 TTACTGTTTAACAAAGTCCCTAGTTAC 57.454 33.333 0.00 0.00 0.00 2.50
35 36 6.994496 ACTGTTTAACAAAGTCCCTAGTTACC 59.006 38.462 0.00 0.00 0.00 2.85
36 37 7.140522 TGTTTAACAAAGTCCCTAGTTACCT 57.859 36.000 0.00 0.00 0.00 3.08
37 38 6.993902 TGTTTAACAAAGTCCCTAGTTACCTG 59.006 38.462 0.00 0.00 0.00 4.00
38 39 6.752285 TTAACAAAGTCCCTAGTTACCTGT 57.248 37.500 0.00 0.00 0.00 4.00
39 40 4.886496 ACAAAGTCCCTAGTTACCTGTC 57.114 45.455 0.00 0.00 0.00 3.51
40 41 4.228824 ACAAAGTCCCTAGTTACCTGTCA 58.771 43.478 0.00 0.00 0.00 3.58
41 42 4.657039 ACAAAGTCCCTAGTTACCTGTCAA 59.343 41.667 0.00 0.00 0.00 3.18
42 43 5.131475 ACAAAGTCCCTAGTTACCTGTCAAA 59.869 40.000 0.00 0.00 0.00 2.69
43 44 5.899631 AAGTCCCTAGTTACCTGTCAAAA 57.100 39.130 0.00 0.00 0.00 2.44
44 45 5.899631 AGTCCCTAGTTACCTGTCAAAAA 57.100 39.130 0.00 0.00 0.00 1.94
65 66 2.849294 AAAGACTGTCTGAAGCTCCC 57.151 50.000 11.71 0.00 0.00 4.30
66 67 0.605589 AAGACTGTCTGAAGCTCCCG 59.394 55.000 11.71 0.00 0.00 5.14
67 68 1.216710 GACTGTCTGAAGCTCCCGG 59.783 63.158 0.00 0.00 0.00 5.73
68 69 2.125350 CTGTCTGAAGCTCCCGGC 60.125 66.667 0.00 0.00 42.19 6.13
94 95 0.678950 TGACAGATCGCCACACAAGA 59.321 50.000 0.00 0.00 0.00 3.02
383 388 3.972950 TGTTCGCCGAATCAAGAAAAA 57.027 38.095 1.55 0.00 0.00 1.94
388 393 5.614923 TCGCCGAATCAAGAAAAATGTTA 57.385 34.783 0.00 0.00 0.00 2.41
390 395 5.049336 TCGCCGAATCAAGAAAAATGTTACA 60.049 36.000 0.00 0.00 0.00 2.41
391 396 5.627367 CGCCGAATCAAGAAAAATGTTACAA 59.373 36.000 0.00 0.00 0.00 2.41
392 397 6.183359 CGCCGAATCAAGAAAAATGTTACAAG 60.183 38.462 0.00 0.00 0.00 3.16
480 495 9.567917 GATTTTAGAAAATGTTCGAAACTTTGC 57.432 29.630 0.00 1.40 37.86 3.68
482 497 7.678194 TTAGAAAATGTTCGAAACTTTGCAG 57.322 32.000 0.00 0.00 38.90 4.41
692 757 9.790344 ATAAAATATCTAGTGCAAGCTCAAGAT 57.210 29.630 0.00 1.92 0.00 2.40
743 818 6.976088 TCAATGCGAAAAATAGAAGGTGAAA 58.024 32.000 0.00 0.00 0.00 2.69
752 827 5.830000 AATAGAAGGTGAAATTTACCGCC 57.170 39.130 1.11 2.04 43.06 6.13
762 837 1.696097 ATTTACCGCCGCTGGATCCT 61.696 55.000 14.23 0.00 0.00 3.24
867 947 3.192922 CGGGACCGGACATTTCGC 61.193 66.667 9.46 1.51 35.56 4.70
988 1070 4.821589 GAGAACCTCCGCCTGCCG 62.822 72.222 0.00 0.00 0.00 5.69
1017 1099 2.771943 GGGGATGGTGAAGATAGTGACA 59.228 50.000 0.00 0.00 0.00 3.58
1156 1238 3.394606 TCCTTCCCACCCATTATTCTAGC 59.605 47.826 0.00 0.00 0.00 3.42
1158 1240 4.597507 CCTTCCCACCCATTATTCTAGCTA 59.402 45.833 0.00 0.00 0.00 3.32
1159 1241 5.280215 CCTTCCCACCCATTATTCTAGCTAG 60.280 48.000 15.01 15.01 0.00 3.42
1160 1242 5.087923 TCCCACCCATTATTCTAGCTAGA 57.912 43.478 19.72 19.72 0.00 2.43
1161 1243 5.087323 TCCCACCCATTATTCTAGCTAGAG 58.913 45.833 22.19 12.10 33.21 2.43
1182 1266 0.968901 TCATGCGTCCGAACCCTAGT 60.969 55.000 0.00 0.00 0.00 2.57
1209 1295 4.954118 TCTGTGGTCACCCCGCCT 62.954 66.667 0.00 0.00 43.57 5.52
1277 1363 3.855255 TTATGCTCCATGAAATCCGGA 57.145 42.857 6.61 6.61 0.00 5.14
1368 1454 7.563724 TTACTAGATGAAGTGGGGTTAAGTT 57.436 36.000 0.00 0.00 0.00 2.66
1395 1481 1.073897 GGTTCAGCTGACCTTGCCT 59.926 57.895 18.03 0.00 0.00 4.75
1620 1707 2.869801 TGACACTTTGCTGGTTAAGTCG 59.130 45.455 0.00 0.00 32.50 4.18
2356 2443 5.717178 AGCTCTTTCCCCTTTCCTTTTTATC 59.283 40.000 0.00 0.00 0.00 1.75
2357 2444 5.717178 GCTCTTTCCCCTTTCCTTTTTATCT 59.283 40.000 0.00 0.00 0.00 1.98
2486 2573 5.465935 TGACAACCTGTTTCACAAGAAAAC 58.534 37.500 0.00 0.00 44.75 2.43
2519 2606 7.040892 GCATATGCTCTGGTGATAATTTTCTCA 60.041 37.037 20.64 0.00 38.21 3.27
2521 2608 7.893124 ATGCTCTGGTGATAATTTTCTCAAT 57.107 32.000 0.00 0.00 0.00 2.57
2681 2769 2.693762 CCCATTCACAGCTGCACGG 61.694 63.158 15.27 7.44 0.00 4.94
2719 2808 4.986659 CGTATTACCTTCACCCCTAATTCG 59.013 45.833 0.00 0.00 0.00 3.34
2746 2835 0.535335 TGACCCGACATACCTTGCTC 59.465 55.000 0.00 0.00 0.00 4.26
2954 3052 8.656849 TCGAGCAGAGTAAAAAGATACAAAATC 58.343 33.333 0.00 0.00 0.00 2.17
3378 3604 2.921069 GCACTACTATGCACGTATCCGG 60.921 54.545 0.00 0.00 45.39 5.14
3435 3661 9.733556 TTTTTGTAGCTACTGATTTCCATCTTA 57.266 29.630 23.84 0.00 0.00 2.10
3485 3713 3.200329 ATGTGGCAGGCTGTGAGCA 62.200 57.895 17.16 10.54 44.75 4.26
3632 3861 2.748388 AGGACGGGAGCTTATACTTGT 58.252 47.619 0.00 0.00 0.00 3.16
4161 4397 8.338259 GTCATTCTATTAACATAAGCCACAGTG 58.662 37.037 0.00 0.00 0.00 3.66
4276 4512 3.878237 ATCACATGGATGGATGCTCTT 57.122 42.857 0.00 0.00 34.06 2.85
4315 4551 7.412672 CGGTTACTAAACTTGCTTCAGGATTAC 60.413 40.741 0.00 0.00 35.81 1.89
4482 4719 9.139734 AGTTTATATACGGTATCCAGTTCAGAA 57.860 33.333 3.47 0.00 0.00 3.02
4580 4818 9.347777 TGATACACCTTCCTAGATATAGGTAGA 57.652 37.037 18.69 2.43 38.93 2.59
4829 5067 6.761714 AGGAAGAATTAGCAACTGGTATAACG 59.238 38.462 0.00 0.00 0.00 3.18
5118 5368 7.862512 ACAGTACCTAGTTCAGTAGATACAC 57.137 40.000 0.00 0.00 0.00 2.90
5148 5398 7.814264 AAGATGGATGAATTATGTTCTCCAC 57.186 36.000 11.96 8.75 35.73 4.02
5238 5488 9.903682 CAAACATATCATCTTCACTTTCAACTT 57.096 29.630 0.00 0.00 0.00 2.66
5460 5710 6.390721 AGGAGTAGTTATAATATGCTGTGCG 58.609 40.000 0.00 0.00 0.00 5.34
5605 5855 0.313672 GTCATTTTCTGCCGTTGCCA 59.686 50.000 0.00 0.00 36.33 4.92
5656 5906 6.609237 TTGATGCAAGTAATATCAGCAGTC 57.391 37.500 0.00 0.00 38.75 3.51
5825 6075 6.438425 AGATGGTCCTTATTCAGTGCAAATTT 59.562 34.615 0.00 0.00 0.00 1.82
5826 6076 6.024552 TGGTCCTTATTCAGTGCAAATTTC 57.975 37.500 0.00 0.00 0.00 2.17
5901 6156 2.433436 CCGGTACCCTCCTTTTCTTTG 58.567 52.381 6.25 0.00 0.00 2.77
5963 6218 6.949578 AGTCAAACAAACAAAATGTGACTG 57.050 33.333 2.79 0.00 34.58 3.51
6022 6277 3.384467 CCCTCATGTGGTTCTGTTTGTTT 59.616 43.478 12.65 0.00 0.00 2.83
6125 6384 8.435982 TGGAAAAATCAACTGAACCCAATTATT 58.564 29.630 0.00 0.00 0.00 1.40
6129 6388 8.831715 AAATCAACTGAACCCAATTATTTGTC 57.168 30.769 0.00 0.00 0.00 3.18
6135 6394 9.927668 AACTGAACCCAATTATTTGTCAATAAG 57.072 29.630 0.00 0.00 38.09 1.73
6138 6397 9.703892 TGAACCCAATTATTTGTCAATAAGTTG 57.296 29.630 0.00 0.00 38.09 3.16
6149 6408 6.785488 TGTCAATAAGTTGTGATGTGACTC 57.215 37.500 0.00 0.00 35.92 3.36
6156 6415 6.867662 AAGTTGTGATGTGACTCCTTAAAG 57.132 37.500 0.00 0.00 0.00 1.85
6164 6423 9.220767 GTGATGTGACTCCTTAAAGATAAGTTT 57.779 33.333 0.00 0.00 37.42 2.66
6185 6444 7.686434 AGTTTAACTTTGGCTAATACTGGAGA 58.314 34.615 0.00 0.00 0.00 3.71
6196 6455 6.098982 GGCTAATACTGGAGATATGCACCTAT 59.901 42.308 0.00 0.00 0.00 2.57
6197 6456 7.365117 GGCTAATACTGGAGATATGCACCTATT 60.365 40.741 0.00 0.00 0.00 1.73
6216 6475 9.817809 CACCTATTTCGTGCCAGTATTATATAT 57.182 33.333 0.00 0.00 0.00 0.86
6236 6498 3.300852 TTAGCCATGTTGTTGTGCATG 57.699 42.857 0.00 0.00 41.37 4.06
6238 6500 1.141645 GCCATGTTGTTGTGCATGTG 58.858 50.000 0.00 0.00 40.42 3.21
6254 6516 7.030768 TGTGCATGTGTATCAATCAAGAAATG 58.969 34.615 0.00 0.00 0.00 2.32
6255 6517 6.020121 GTGCATGTGTATCAATCAAGAAATGC 60.020 38.462 0.00 0.00 37.72 3.56
6257 6519 4.661125 TGTGTATCAATCAAGAAATGCGC 58.339 39.130 0.00 0.00 0.00 6.09
6258 6520 4.037690 GTGTATCAATCAAGAAATGCGCC 58.962 43.478 4.18 0.00 0.00 6.53
6259 6521 3.693578 TGTATCAATCAAGAAATGCGCCA 59.306 39.130 4.18 0.00 0.00 5.69
6283 6562 2.492088 CTGATACAGTCTGGTTCGGACA 59.508 50.000 4.53 0.00 41.77 4.02
6294 6573 1.526887 GGTTCGGACATGTATGCATCG 59.473 52.381 0.19 0.00 31.99 3.84
6308 6593 9.025020 CATGTATGCATCGAAGGATAAGTATAC 57.975 37.037 0.19 0.00 31.07 1.47
6422 6708 8.599774 GTTCATCTATTAGAGAAGAAGCAACAC 58.400 37.037 0.00 0.00 41.37 3.32
6489 6775 3.942829 ACACCATGTGGAGTTATCAGTG 58.057 45.455 5.96 0.00 35.43 3.66
6491 6777 2.305635 ACCATGTGGAGTTATCAGTGCA 59.694 45.455 5.96 0.00 38.94 4.57
6496 6782 2.939103 GTGGAGTTATCAGTGCATGGTC 59.061 50.000 0.00 0.00 0.00 4.02
6502 6788 2.160822 ATCAGTGCATGGTCGATAGC 57.839 50.000 0.00 0.00 0.00 2.97
6544 6830 3.821033 GGTAGGATGCAATATGTTGGACC 59.179 47.826 4.23 5.90 38.55 4.46
6563 6849 5.310594 TGGACCAGGGAATTCCTTCTATATG 59.689 44.000 23.63 10.80 45.47 1.78
6565 6851 6.441088 ACCAGGGAATTCCTTCTATATGTC 57.559 41.667 23.63 3.33 45.47 3.06
6567 6853 6.043706 ACCAGGGAATTCCTTCTATATGTCTG 59.956 42.308 23.63 16.38 45.47 3.51
6568 6854 6.270927 CCAGGGAATTCCTTCTATATGTCTGA 59.729 42.308 23.63 0.00 45.47 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.394477 GGACTTTGTTAAACAGTAATCAACATC 57.606 33.333 0.00 0.00 0.00 3.06
1 2 8.357402 GGGACTTTGTTAAACAGTAATCAACAT 58.643 33.333 0.00 0.00 0.00 2.71
3 4 7.937649 AGGGACTTTGTTAAACAGTAATCAAC 58.062 34.615 0.00 0.00 27.25 3.18
4 5 9.280174 CTAGGGACTTTGTTAAACAGTAATCAA 57.720 33.333 0.00 0.00 41.75 2.57
8 9 9.546428 GTAACTAGGGACTTTGTTAAACAGTAA 57.454 33.333 0.00 0.00 41.75 2.24
9 10 8.150296 GGTAACTAGGGACTTTGTTAAACAGTA 58.850 37.037 0.00 0.00 41.75 2.74
10 11 6.994496 GGTAACTAGGGACTTTGTTAAACAGT 59.006 38.462 0.00 0.00 41.75 3.55
11 12 7.430992 GGTAACTAGGGACTTTGTTAAACAG 57.569 40.000 0.00 0.00 41.75 3.16
44 45 3.481453 GGGAGCTTCAGACAGTCTTTTT 58.519 45.455 0.00 0.00 0.00 1.94
45 46 2.548920 CGGGAGCTTCAGACAGTCTTTT 60.549 50.000 0.00 0.00 0.00 2.27
46 47 1.001406 CGGGAGCTTCAGACAGTCTTT 59.999 52.381 0.00 0.00 0.00 2.52
47 48 0.605589 CGGGAGCTTCAGACAGTCTT 59.394 55.000 0.00 0.00 0.00 3.01
48 49 1.254284 CCGGGAGCTTCAGACAGTCT 61.254 60.000 0.00 0.00 0.00 3.24
49 50 1.216710 CCGGGAGCTTCAGACAGTC 59.783 63.158 0.00 0.00 0.00 3.51
50 51 2.948720 GCCGGGAGCTTCAGACAGT 61.949 63.158 2.18 0.00 38.99 3.55
51 52 2.125350 GCCGGGAGCTTCAGACAG 60.125 66.667 2.18 0.00 38.99 3.51
52 53 3.706373 GGCCGGGAGCTTCAGACA 61.706 66.667 2.18 0.00 43.05 3.41
53 54 3.378399 GAGGCCGGGAGCTTCAGAC 62.378 68.421 2.18 0.00 46.54 3.51
54 55 3.077556 GAGGCCGGGAGCTTCAGA 61.078 66.667 2.18 0.00 46.54 3.27
65 66 3.432051 GATCTGTCACGGGAGGCCG 62.432 68.421 0.00 0.00 39.31 6.13
66 67 2.501610 GATCTGTCACGGGAGGCC 59.498 66.667 0.00 0.00 0.00 5.19
67 68 2.105128 CGATCTGTCACGGGAGGC 59.895 66.667 0.00 0.00 0.00 4.70
68 69 2.105128 GCGATCTGTCACGGGAGG 59.895 66.667 0.00 0.00 0.00 4.30
75 76 0.678950 TCTTGTGTGGCGATCTGTCA 59.321 50.000 0.00 0.00 0.00 3.58
94 95 2.029290 ACGAGCAATAACGACAGAGGTT 60.029 45.455 0.00 0.00 0.00 3.50
201 202 7.404139 ACTATTTTGTAAGTCACGAACAGTC 57.596 36.000 0.00 0.00 29.77 3.51
320 324 5.885449 TTTTTGGAGATTGGTGGAACATT 57.115 34.783 0.00 0.00 44.52 2.71
353 358 4.932799 TGATTCGGCGAACATTTCTAGAAA 59.067 37.500 26.22 19.83 34.46 2.52
480 495 9.858247 CATTTTTCAAATTCATGAACACTTCTG 57.142 29.630 11.07 2.52 38.95 3.02
581 632 5.504853 TGACCATATTTTGCTACATCACCA 58.495 37.500 0.00 0.00 0.00 4.17
692 757 4.759693 CCCTAACGCTCCAATATTTGCATA 59.240 41.667 0.00 0.00 0.00 3.14
743 818 1.227853 GGATCCAGCGGCGGTAAAT 60.228 57.895 12.74 8.28 0.00 1.40
752 827 0.246086 GATGAGGCTAGGATCCAGCG 59.754 60.000 22.08 9.51 40.05 5.18
762 837 1.527433 CGATGGGAGCGATGAGGCTA 61.527 60.000 0.00 0.00 44.93 3.93
849 929 2.263540 CGAAATGTCCGGTCCCGT 59.736 61.111 0.00 0.00 37.81 5.28
954 1036 3.744719 CGAGAGCCCACGACGGAA 61.745 66.667 0.00 0.00 36.56 4.30
1017 1099 1.296056 GCAGCCCGTTCACGTTGTAT 61.296 55.000 0.00 0.00 37.74 2.29
1156 1238 2.605823 GGTTCGGACGCATGATCTCTAG 60.606 54.545 0.00 0.00 0.00 2.43
1158 1240 0.103208 GGTTCGGACGCATGATCTCT 59.897 55.000 0.00 0.00 0.00 3.10
1159 1241 0.876342 GGGTTCGGACGCATGATCTC 60.876 60.000 5.94 0.00 38.50 2.75
1160 1242 1.144057 GGGTTCGGACGCATGATCT 59.856 57.895 5.94 0.00 38.50 2.75
1161 1243 0.387929 TAGGGTTCGGACGCATGATC 59.612 55.000 14.07 0.00 40.90 2.92
1182 1266 2.037251 GGTGACCACAGACAGCTAAGAA 59.963 50.000 0.00 0.00 34.08 2.52
1277 1363 2.645838 ACAGTGCAGACTTGGTGAAT 57.354 45.000 0.00 0.00 0.00 2.57
1368 1454 2.143122 GTCAGCTGAACCGAATCACAA 58.857 47.619 20.19 0.00 0.00 3.33
1395 1481 5.001232 GTCTCCTAAAGCACACCAAACATA 58.999 41.667 0.00 0.00 0.00 2.29
2356 2443 4.925068 AGTTTTAGTGCAAGCAAGTCAAG 58.075 39.130 0.00 0.00 0.00 3.02
2357 2444 4.981806 AGTTTTAGTGCAAGCAAGTCAA 57.018 36.364 0.00 0.00 0.00 3.18
2421 2508 7.809331 TGCACATCTTATGTTCTTCATTTTCAC 59.191 33.333 0.00 0.00 42.70 3.18
2486 2573 1.739466 ACCAGAGCATATGCAACAACG 59.261 47.619 28.62 13.01 45.16 4.10
2519 2606 9.573133 GCTCATAGCAAAATTTACACTTACATT 57.427 29.630 0.00 0.00 41.89 2.71
2592 2679 9.955208 CTCATGCTATTAACTGATTGCATTAAA 57.045 29.630 4.49 0.00 42.87 1.52
2604 2691 7.445402 ACACAGTTGTTTCTCATGCTATTAACT 59.555 33.333 0.00 0.00 28.43 2.24
2681 2769 7.269477 AGGTAATACGATACAAGTCAGGTAC 57.731 40.000 0.00 0.00 0.00 3.34
2719 2808 5.086104 AGGTATGTCGGGTCATTATATGC 57.914 43.478 0.00 0.00 0.00 3.14
2842 2939 5.670792 ATGCATTCATCACAAGTGGAAAT 57.329 34.783 0.00 0.00 0.00 2.17
2954 3052 8.889000 GCAAAGTGTAAACAGTTCTTATTAACG 58.111 33.333 3.75 0.00 38.47 3.18
3018 3116 3.627577 AGACCAATGCATTTATCACCGTC 59.372 43.478 9.83 6.86 0.00 4.79
3378 3604 3.664025 GCGTGCTTTCAAAATCTACACAC 59.336 43.478 0.00 0.00 0.00 3.82
3485 3713 8.749354 GTTGATCCCACTAAATAATTTTCCTGT 58.251 33.333 0.00 0.00 0.00 4.00
3632 3861 8.474025 TCTTCAGCTCCAACTTTTTGATTAAAA 58.526 29.630 0.00 0.00 34.24 1.52
4161 4397 6.346896 AGCTAAGGCATACAGTAGTTTAACC 58.653 40.000 0.00 0.00 41.70 2.85
4221 4457 4.044426 CAGGCAGTTGCTTACAAAGTTTC 58.956 43.478 3.88 0.00 41.70 2.78
4276 4512 1.349688 AGTAACCGCATCCAACCAAGA 59.650 47.619 0.00 0.00 0.00 3.02
4467 4704 5.063880 ACAGTGTTTTCTGAACTGGATACC 58.936 41.667 10.89 0.00 44.49 2.73
4580 4818 5.898174 ACATGATGAAATGCACATTCGAAT 58.102 33.333 4.39 4.39 0.00 3.34
4712 4950 0.034767 CTGGGCCATCTTCAGCTTCA 60.035 55.000 6.72 0.00 0.00 3.02
4829 5067 6.947644 TGGTTAACACCTTTAGAAAACTCC 57.052 37.500 8.10 0.00 44.61 3.85
5148 5398 7.137490 TGTTTTCTTGCAGACTATCATCTTG 57.863 36.000 0.00 0.00 0.00 3.02
5195 5445 3.772572 TGTTTGAGTTATCCGGATCTCCA 59.227 43.478 23.08 11.40 35.14 3.86
5605 5855 5.413833 CAGAAAGTAGTCATTTGACCTGCAT 59.586 40.000 7.07 0.00 45.85 3.96
5639 5889 4.696479 AGGGGACTGCTGATATTACTTG 57.304 45.455 0.00 0.00 41.13 3.16
5656 5906 3.624777 AGCATCAACACATTCTTAGGGG 58.375 45.455 0.00 0.00 0.00 4.79
5826 6076 9.924650 ACAAACTATGTACCTCTGTTAGTAAAG 57.075 33.333 0.00 0.00 41.63 1.85
5901 6156 3.118920 GGAGGAGGCTACTTCTCTTCAAC 60.119 52.174 0.00 0.00 46.80 3.18
5963 6218 1.975660 TTAGCCACCCAACAACAGAC 58.024 50.000 0.00 0.00 0.00 3.51
5993 6248 0.482446 AACCACATGAGGGCTCCAAA 59.518 50.000 14.11 0.00 0.00 3.28
6022 6277 8.023021 TCTCAAGATAAGCTAAGCCAGAATTA 57.977 34.615 0.00 0.00 0.00 1.40
6125 6384 6.204688 GGAGTCACATCACAACTTATTGACAA 59.795 38.462 0.00 0.00 39.30 3.18
6127 6386 5.934625 AGGAGTCACATCACAACTTATTGAC 59.065 40.000 0.00 0.00 39.30 3.18
6129 6388 6.808008 AAGGAGTCACATCACAACTTATTG 57.192 37.500 0.00 0.00 41.98 1.90
6135 6394 8.547967 TTATCTTTAAGGAGTCACATCACAAC 57.452 34.615 0.00 0.00 0.00 3.32
6138 6397 8.779354 AACTTATCTTTAAGGAGTCACATCAC 57.221 34.615 0.00 0.00 39.36 3.06
6164 6423 7.878127 GCATATCTCCAGTATTAGCCAAAGTTA 59.122 37.037 0.00 0.00 0.00 2.24
6165 6424 6.712547 GCATATCTCCAGTATTAGCCAAAGTT 59.287 38.462 0.00 0.00 0.00 2.66
6166 6425 6.183361 TGCATATCTCCAGTATTAGCCAAAGT 60.183 38.462 0.00 0.00 0.00 2.66
6169 6428 5.513094 GGTGCATATCTCCAGTATTAGCCAA 60.513 44.000 0.00 0.00 0.00 4.52
6171 6430 4.223923 AGGTGCATATCTCCAGTATTAGCC 59.776 45.833 0.00 0.00 0.00 3.93
6178 6437 4.345257 ACGAAATAGGTGCATATCTCCAGT 59.655 41.667 0.00 0.00 0.00 4.00
6196 6455 8.315482 TGGCTAATATATAATACTGGCACGAAA 58.685 33.333 0.00 0.00 0.00 3.46
6197 6456 7.842982 TGGCTAATATATAATACTGGCACGAA 58.157 34.615 0.00 0.00 0.00 3.85
6216 6475 2.627221 ACATGCACAACAACATGGCTAA 59.373 40.909 7.78 0.00 46.35 3.09
6220 6482 2.512485 ACACATGCACAACAACATGG 57.488 45.000 7.78 0.34 46.35 3.66
6236 6498 4.037690 GGCGCATTTCTTGATTGATACAC 58.962 43.478 10.83 0.00 0.00 2.90
6238 6500 4.291540 TGGCGCATTTCTTGATTGATAC 57.708 40.909 10.83 0.00 0.00 2.24
6254 6516 2.398498 CAGACTGTATCAGTATGGCGC 58.602 52.381 14.26 0.00 46.10 6.53
6259 6521 4.338682 GTCCGAACCAGACTGTATCAGTAT 59.661 45.833 0.93 0.00 45.44 2.12
6275 6554 2.469826 TCGATGCATACATGTCCGAAC 58.530 47.619 0.00 0.00 36.35 3.95
6283 6562 8.749354 TGTATACTTATCCTTCGATGCATACAT 58.251 33.333 0.00 0.00 39.98 2.29
6335 6620 3.585990 CCAAATAGCGCCTGCCGG 61.586 66.667 2.29 0.00 44.31 6.13
6402 6688 4.864806 TGCGTGTTGCTTCTTCTCTAATAG 59.135 41.667 0.00 0.00 46.63 1.73
6489 6775 5.362556 AAATGTATTGCTATCGACCATGC 57.637 39.130 0.00 0.00 0.00 4.06
6491 6777 5.620206 TGGAAATGTATTGCTATCGACCAT 58.380 37.500 0.00 0.00 0.00 3.55
6496 6782 6.603237 TCTGTTGGAAATGTATTGCTATCG 57.397 37.500 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.