Multiple sequence alignment - TraesCS1B01G428600

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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 TraesCS1B01G428600 chr1B 100.000 2560 0 0 920 3479 653835170 653837729 0.000000e+00 4728.0
1 TraesCS1B01G428600 chr1B 100.000 580 0 0 1 580 653834251 653834830 0.000000e+00 1072.0
2 TraesCS1B01G428600 chr1B 80.353 1415 183 45 920 2317 653527598 653526262 0.000000e+00 985.0
3 TraesCS1B01G428600 chr1B 81.026 1170 195 19 1070 2233 653487588 653486440 0.000000e+00 905.0
4 TraesCS1B01G428600 chr1B 78.565 1199 207 27 1064 2231 653314033 653312854 0.000000e+00 745.0
5 TraesCS1B01G428600 chr1B 78.512 954 170 24 1287 2233 653727135 653726210 8.310000e-166 593.0
6 TraesCS1B01G428600 chr1B 77.401 1031 198 24 1083 2110 653794939 653793941 6.470000e-162 580.0
7 TraesCS1B01G428600 chr1B 84.191 272 43 0 1962 2233 653689974 653689703 7.400000e-67 265.0
8 TraesCS1B01G428600 chr1B 97.222 36 0 1 545 580 653834709 653834743 3.750000e-05 60.2
9 TraesCS1B01G428600 chr1B 97.222 36 0 1 459 493 653834795 653834830 3.750000e-05 60.2
10 TraesCS1B01G428600 chr1D 95.327 2568 82 18 928 3477 470545540 470542993 0.000000e+00 4043.0
11 TraesCS1B01G428600 chr1D 84.703 791 107 11 1078 1859 470532212 470531427 0.000000e+00 778.0
12 TraesCS1B01G428600 chr1D 85.366 328 29 14 99 409 470545862 470545537 4.330000e-84 322.0
13 TraesCS1B01G428600 chr1D 77.578 223 47 2 1675 1894 458872833 458873055 7.840000e-27 132.0
14 TraesCS1B01G428600 chr1D 77.143 210 27 10 1770 1976 470523705 470523514 6.140000e-18 102.0
15 TraesCS1B01G428600 chr1D 90.909 44 3 1 322 365 470537315 470537273 1.350000e-04 58.4
16 TraesCS1B01G428600 chr1D 92.857 42 0 3 462 502 470545569 470545530 1.350000e-04 58.4
17 TraesCS1B01G428600 chr1D 100.000 28 0 0 425 452 470545591 470545564 6.000000e-03 52.8
18 TraesCS1B01G428600 chr1A 94.531 2578 108 19 920 3477 564141060 564138496 0.000000e+00 3949.0
19 TraesCS1B01G428600 chr1A 83.161 677 78 24 920 1587 564118932 564118283 1.390000e-163 586.0
20 TraesCS1B01G428600 chr1A 75.580 905 175 30 1083 1981 564261562 564262426 4.180000e-109 405.0
21 TraesCS1B01G428600 chr1A 89.952 209 12 6 128 330 564141313 564141108 9.580000e-66 261.0
22 TraesCS1B01G428600 chr1A 97.143 35 1 0 546 580 564118971 564118937 3.750000e-05 60.2
23 TraesCS1B01G428600 chr1A 97.143 35 1 0 517 551 564118971 564118937 3.750000e-05 60.2
24 TraesCS1B01G428600 chr1A 97.143 35 1 0 488 522 564118971 564118937 3.750000e-05 60.2
25 TraesCS1B01G428600 chr6A 86.777 121 16 0 1675 1795 17946780 17946660 6.060000e-28 135.0
26 TraesCS1B01G428600 chr3A 90.541 74 6 1 32 104 624632739 624632666 2.860000e-16 97.1
27 TraesCS1B01G428600 chr7B 80.342 117 23 0 1674 1790 713513388 713513272 4.780000e-14 89.8
28 TraesCS1B01G428600 chr6B 78.049 123 27 0 1676 1798 708482390 708482512 1.040000e-10 78.7


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 TraesCS1B01G428600 chr1B 653834251 653837729 3478 False 1480.10 4728 98.6110 1 3479 4 chr1B.!!$F1 3478
1 TraesCS1B01G428600 chr1B 653526262 653527598 1336 True 985.00 985 80.3530 920 2317 1 chr1B.!!$R3 1397
2 TraesCS1B01G428600 chr1B 653486440 653487588 1148 True 905.00 905 81.0260 1070 2233 1 chr1B.!!$R2 1163
3 TraesCS1B01G428600 chr1B 653312854 653314033 1179 True 745.00 745 78.5650 1064 2231 1 chr1B.!!$R1 1167
4 TraesCS1B01G428600 chr1B 653726210 653727135 925 True 593.00 593 78.5120 1287 2233 1 chr1B.!!$R5 946
5 TraesCS1B01G428600 chr1B 653793941 653794939 998 True 580.00 580 77.4010 1083 2110 1 chr1B.!!$R6 1027
6 TraesCS1B01G428600 chr1D 470542993 470545862 2869 True 1119.05 4043 93.3875 99 3477 4 chr1D.!!$R4 3378
7 TraesCS1B01G428600 chr1D 470531427 470532212 785 True 778.00 778 84.7030 1078 1859 1 chr1D.!!$R2 781
8 TraesCS1B01G428600 chr1A 564138496 564141313 2817 True 2105.00 3949 92.2415 128 3477 2 chr1A.!!$R2 3349
9 TraesCS1B01G428600 chr1A 564261562 564262426 864 False 405.00 405 75.5800 1083 1981 1 chr1A.!!$F1 898

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
21 22 0.179032 TGAAAGCAAACCGAGCCTCA 60.179 50.0 0.0 0.0 0.00 3.86 F
109 110 0.382515 AGACGCTCTTATCAGTCGGC 59.617 55.0 0.0 0.0 38.53 5.54 F
1059 1098 0.606401 CTGCCCCACATCGTCAAAGT 60.606 55.0 0.0 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 1098 0.107508 GATCTTGTGGGCTAGCAGCA 60.108 55.0 18.24 8.98 44.75 4.41 R
1060 1099 1.156645 CGATCTTGTGGGCTAGCAGC 61.157 60.0 18.24 6.26 41.46 5.25 R
2640 2789 0.389817 CGACAATGGAGAAGCCGTCA 60.390 55.0 0.00 0.00 40.66 4.35 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
19 20 2.633860 CTGAAAGCAAACCGAGCCT 58.366 52.632 0.00 0.00 0.00 4.58
20 21 0.519077 CTGAAAGCAAACCGAGCCTC 59.481 55.000 0.00 0.00 0.00 4.70
21 22 0.179032 TGAAAGCAAACCGAGCCTCA 60.179 50.000 0.00 0.00 0.00 3.86
22 23 0.519077 GAAAGCAAACCGAGCCTCAG 59.481 55.000 0.00 0.00 0.00 3.35
23 24 0.890996 AAAGCAAACCGAGCCTCAGG 60.891 55.000 0.00 0.00 0.00 3.86
24 25 2.032681 GCAAACCGAGCCTCAGGT 59.967 61.111 0.00 2.93 43.68 4.00
25 26 2.328099 GCAAACCGAGCCTCAGGTG 61.328 63.158 8.63 0.54 41.21 4.00
26 27 2.032681 AAACCGAGCCTCAGGTGC 59.967 61.111 8.63 0.00 41.21 5.01
27 28 3.553095 AAACCGAGCCTCAGGTGCC 62.553 63.158 8.63 0.00 41.21 5.01
30 31 3.842923 CGAGCCTCAGGTGCCGAT 61.843 66.667 0.00 0.00 0.00 4.18
31 32 2.107953 GAGCCTCAGGTGCCGATC 59.892 66.667 0.00 0.00 0.00 3.69
32 33 2.364842 AGCCTCAGGTGCCGATCT 60.365 61.111 0.00 0.00 0.00 2.75
33 34 1.075970 AGCCTCAGGTGCCGATCTA 60.076 57.895 0.00 0.00 0.00 1.98
34 35 1.112315 AGCCTCAGGTGCCGATCTAG 61.112 60.000 0.00 0.00 0.00 2.43
35 36 1.365633 CCTCAGGTGCCGATCTAGC 59.634 63.158 0.00 0.00 0.00 3.42
36 37 1.007964 CTCAGGTGCCGATCTAGCG 60.008 63.158 0.00 0.00 0.00 4.26
37 38 2.659897 CAGGTGCCGATCTAGCGC 60.660 66.667 0.00 0.00 40.04 5.92
38 39 2.835431 AGGTGCCGATCTAGCGCT 60.835 61.111 17.26 17.26 40.59 5.92
39 40 2.659897 GGTGCCGATCTAGCGCTG 60.660 66.667 22.90 10.49 40.59 5.18
40 41 2.659897 GTGCCGATCTAGCGCTGG 60.660 66.667 22.90 19.16 37.75 4.85
41 42 4.592192 TGCCGATCTAGCGCTGGC 62.592 66.667 24.58 24.58 45.91 4.85
62 63 4.821935 CCCTCAGGCCGTTCTTTT 57.178 55.556 0.00 0.00 0.00 2.27
63 64 3.036431 CCCTCAGGCCGTTCTTTTT 57.964 52.632 0.00 0.00 0.00 1.94
64 65 0.881796 CCCTCAGGCCGTTCTTTTTC 59.118 55.000 0.00 0.00 0.00 2.29
65 66 0.517316 CCTCAGGCCGTTCTTTTTCG 59.483 55.000 0.00 0.00 0.00 3.46
70 71 2.127003 CCGTTCTTTTTCGGCGCC 60.127 61.111 19.07 19.07 40.28 6.53
71 72 2.613506 CCGTTCTTTTTCGGCGCCT 61.614 57.895 26.68 0.00 40.28 5.52
72 73 1.440353 CGTTCTTTTTCGGCGCCTG 60.440 57.895 26.68 18.23 0.00 4.85
73 74 1.081442 GTTCTTTTTCGGCGCCTGG 60.081 57.895 26.68 10.37 0.00 4.45
74 75 2.265182 TTCTTTTTCGGCGCCTGGG 61.265 57.895 26.68 9.50 0.00 4.45
75 76 2.671619 CTTTTTCGGCGCCTGGGA 60.672 61.111 26.68 12.15 0.00 4.37
76 77 2.671619 TTTTTCGGCGCCTGGGAG 60.672 61.111 26.68 8.63 0.00 4.30
77 78 4.715523 TTTTCGGCGCCTGGGAGG 62.716 66.667 26.68 7.77 38.80 4.30
109 110 0.382515 AGACGCTCTTATCAGTCGGC 59.617 55.000 0.00 0.00 38.53 5.54
139 141 6.143758 TGTGAGCGTTCTTCAAAAATAAATGC 59.856 34.615 0.00 0.00 33.17 3.56
190 196 0.901580 CAATTGGGCCAGCAGGACTT 60.902 55.000 6.23 0.00 45.05 3.01
213 219 3.781307 AGCCCACCGCGCAGAATA 61.781 61.111 8.75 0.00 44.76 1.75
315 336 0.914417 AAATCCCTCGCCTCCTTCCA 60.914 55.000 0.00 0.00 0.00 3.53
318 339 3.382832 CCTCGCCTCCTTCCACGT 61.383 66.667 0.00 0.00 0.00 4.49
348 369 2.488355 TCGCCGTCGATCACTTCC 59.512 61.111 0.00 0.00 40.21 3.46
380 401 3.123620 CGCAGAGCACTTCCCAGC 61.124 66.667 0.00 0.00 0.00 4.85
410 431 3.900855 CAGATCACTGCCCTGCAC 58.099 61.111 0.00 0.00 37.33 4.57
411 432 1.002990 CAGATCACTGCCCTGCACA 60.003 57.895 0.00 0.00 37.33 4.57
412 433 1.025113 CAGATCACTGCCCTGCACAG 61.025 60.000 1.47 1.47 41.08 3.66
413 434 2.360852 ATCACTGCCCTGCACAGC 60.361 61.111 2.87 0.00 38.79 4.40
414 435 2.816601 GATCACTGCCCTGCACAGCT 62.817 60.000 2.87 0.00 38.79 4.24
415 436 2.816601 ATCACTGCCCTGCACAGCTC 62.817 60.000 2.87 0.00 38.79 4.09
416 437 3.247648 ACTGCCCTGCACAGCTCT 61.248 61.111 2.87 0.00 38.79 4.09
417 438 2.436292 CTGCCCTGCACAGCTCTC 60.436 66.667 4.93 0.00 33.79 3.20
418 439 3.972971 CTGCCCTGCACAGCTCTCC 62.973 68.421 4.93 0.00 33.79 3.71
419 440 4.792804 GCCCTGCACAGCTCTCCC 62.793 72.222 0.00 0.00 0.00 4.30
420 441 4.106925 CCCTGCACAGCTCTCCCC 62.107 72.222 0.00 0.00 0.00 4.81
421 442 3.007920 CCTGCACAGCTCTCCCCT 61.008 66.667 0.00 0.00 0.00 4.79
422 443 2.268280 CTGCACAGCTCTCCCCTG 59.732 66.667 0.00 0.00 36.41 4.45
423 444 3.972971 CTGCACAGCTCTCCCCTGC 62.973 68.421 0.00 0.00 33.65 4.85
444 465 4.521062 GCCTCGCCGCAGATCACT 62.521 66.667 0.00 0.00 0.00 3.41
445 466 2.584418 CCTCGCCGCAGATCACTG 60.584 66.667 0.00 0.00 45.91 3.66
453 474 3.900855 CAGATCACTGCCCTGCAC 58.099 61.111 0.00 0.00 37.33 4.57
454 475 1.002990 CAGATCACTGCCCTGCACA 60.003 57.895 0.00 0.00 37.33 4.57
455 476 1.025113 CAGATCACTGCCCTGCACAG 61.025 60.000 1.47 1.47 41.08 3.66
456 477 2.360852 ATCACTGCCCTGCACAGC 60.361 61.111 2.87 0.00 38.79 4.40
457 478 2.816601 GATCACTGCCCTGCACAGCT 62.817 60.000 2.87 0.00 38.79 4.24
458 479 2.816601 ATCACTGCCCTGCACAGCTC 62.817 60.000 2.87 0.00 38.79 4.09
459 480 3.247648 ACTGCCCTGCACAGCTCT 61.248 61.111 2.87 0.00 38.79 4.09
460 481 2.436292 CTGCCCTGCACAGCTCTC 60.436 66.667 4.93 0.00 33.79 3.20
493 514 2.995574 CCGTCGACCACTCCCCTT 60.996 66.667 10.58 0.00 0.00 3.95
494 515 2.261671 CGTCGACCACTCCCCTTG 59.738 66.667 10.58 0.00 0.00 3.61
495 516 2.047179 GTCGACCACTCCCCTTGC 60.047 66.667 3.51 0.00 0.00 4.01
496 517 3.691342 TCGACCACTCCCCTTGCG 61.691 66.667 0.00 0.00 0.00 4.85
517 538 4.477975 CCTCGCCGTCGACCACTC 62.478 72.222 10.58 0.00 40.21 3.51
518 539 4.477975 CTCGCCGTCGACCACTCC 62.478 72.222 10.58 0.00 40.21 3.85
522 543 2.995574 CCGTCGACCACTCCCCTT 60.996 66.667 10.58 0.00 0.00 3.95
523 544 2.261671 CGTCGACCACTCCCCTTG 59.738 66.667 10.58 0.00 0.00 3.61
524 545 2.047179 GTCGACCACTCCCCTTGC 60.047 66.667 3.51 0.00 0.00 4.01
525 546 3.691342 TCGACCACTCCCCTTGCG 61.691 66.667 0.00 0.00 0.00 4.85
546 567 4.477975 CCTCGCCGTCGACCACTC 62.478 72.222 10.58 0.00 40.21 3.51
547 568 4.477975 CTCGCCGTCGACCACTCC 62.478 72.222 10.58 0.00 40.21 3.85
551 572 2.995574 CCGTCGACCACTCCCCTT 60.996 66.667 10.58 0.00 0.00 3.95
552 573 2.261671 CGTCGACCACTCCCCTTG 59.738 66.667 10.58 0.00 0.00 3.61
553 574 2.047179 GTCGACCACTCCCCTTGC 60.047 66.667 3.51 0.00 0.00 4.01
554 575 3.691342 TCGACCACTCCCCTTGCG 61.691 66.667 0.00 0.00 0.00 4.85
575 596 4.477975 CCTCGCCGTCGACCACTC 62.478 72.222 10.58 0.00 40.21 3.51
576 597 4.477975 CTCGCCGTCGACCACTCC 62.478 72.222 10.58 0.00 40.21 3.85
948 970 3.330720 CCTGCCGAAACCCTCCCT 61.331 66.667 0.00 0.00 0.00 4.20
980 1002 4.803908 CCCAAGCCGCCTCTTCCC 62.804 72.222 0.00 0.00 0.00 3.97
981 1003 4.803908 CCAAGCCGCCTCTTCCCC 62.804 72.222 0.00 0.00 0.00 4.81
982 1004 4.803908 CAAGCCGCCTCTTCCCCC 62.804 72.222 0.00 0.00 0.00 5.40
989 1011 3.420482 CCTCTTCCCCCGCCCATT 61.420 66.667 0.00 0.00 0.00 3.16
990 1012 2.193248 CTCTTCCCCCGCCCATTC 59.807 66.667 0.00 0.00 0.00 2.67
991 1013 2.612430 TCTTCCCCCGCCCATTCA 60.612 61.111 0.00 0.00 0.00 2.57
992 1014 2.210144 CTCTTCCCCCGCCCATTCAA 62.210 60.000 0.00 0.00 0.00 2.69
993 1015 2.036572 TTCCCCCGCCCATTCAAC 59.963 61.111 0.00 0.00 0.00 3.18
994 1016 3.929334 TTCCCCCGCCCATTCAACG 62.929 63.158 0.00 0.00 0.00 4.10
1059 1098 0.606401 CTGCCCCACATCGTCAAAGT 60.606 55.000 0.00 0.00 0.00 2.66
1060 1099 0.888736 TGCCCCACATCGTCAAAGTG 60.889 55.000 0.00 0.00 0.00 3.16
1061 1100 1.875963 CCCCACATCGTCAAAGTGC 59.124 57.895 0.00 0.00 32.09 4.40
1121 1160 0.809636 CGTATCCGTCATTGCTGGCA 60.810 55.000 0.00 0.00 0.00 4.92
1279 1330 0.676466 GGACAATCATGGGTCGCACA 60.676 55.000 0.00 0.00 34.87 4.57
1546 1610 4.023291 GAGAGGACCTTGAGAAGTCAGAT 58.977 47.826 0.00 0.00 32.98 2.90
1673 1741 1.751351 TGAGCCATCTCTTAGTGACGG 59.249 52.381 0.00 0.00 40.03 4.79
1713 1781 1.043116 TTCGAGGTCGGCCATGAGAT 61.043 55.000 9.71 0.00 40.29 2.75
1945 2085 3.488090 GAGGTTACGTGGCTGCGC 61.488 66.667 0.00 0.00 34.88 6.09
2203 2343 1.347707 TCCGTTCTGAACCAGCTCATT 59.652 47.619 14.48 0.00 0.00 2.57
2416 2563 4.142227 GCTTCAGCAATCTCCATGTTGATT 60.142 41.667 5.04 5.04 37.76 2.57
2640 2789 1.135068 TTGGGTCGTTGGTGGGGTAT 61.135 55.000 0.00 0.00 0.00 2.73
2760 2909 1.279496 CATGGTGGAGACCTTGGAGA 58.721 55.000 0.00 0.00 43.58 3.71
2832 2982 1.359475 GGAGGTCGATGTAGACGGC 59.641 63.158 0.00 0.00 41.81 5.68
2889 3039 0.944311 CAGTGCGTCAGGTACCACAC 60.944 60.000 15.94 13.32 33.91 3.82
3169 3320 3.100671 GGTTGTCACATCCTCCTAGTCT 58.899 50.000 0.00 0.00 0.00 3.24
3305 3456 5.012046 TCACAAGATGACAACTGTGAGGTAT 59.988 40.000 11.51 0.00 33.21 2.73
3477 3633 0.904649 ATGACAATGGACTCGAGCCA 59.095 50.000 24.41 24.41 40.24 4.75
3478 3634 0.037326 TGACAATGGACTCGAGCCAC 60.037 55.000 24.61 15.28 38.44 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.081175 GGCTCGGTTTGCTTTCAGC 60.081 57.895 0.00 0.00 42.82 4.26
1 2 0.519077 GAGGCTCGGTTTGCTTTCAG 59.481 55.000 0.00 0.00 0.00 3.02
2 3 0.179032 TGAGGCTCGGTTTGCTTTCA 60.179 50.000 10.42 0.00 0.00 2.69
3 4 0.519077 CTGAGGCTCGGTTTGCTTTC 59.481 55.000 15.39 0.00 0.00 2.62
4 5 0.890996 CCTGAGGCTCGGTTTGCTTT 60.891 55.000 21.38 0.00 0.00 3.51
5 6 1.302832 CCTGAGGCTCGGTTTGCTT 60.303 57.895 21.38 0.00 0.00 3.91
6 7 2.348998 CCTGAGGCTCGGTTTGCT 59.651 61.111 21.38 0.00 0.00 3.91
7 8 2.032681 ACCTGAGGCTCGGTTTGC 59.967 61.111 21.38 0.00 0.00 3.68
8 9 2.328099 GCACCTGAGGCTCGGTTTG 61.328 63.158 22.58 18.70 0.00 2.93
9 10 2.032681 GCACCTGAGGCTCGGTTT 59.967 61.111 22.58 8.29 0.00 3.27
10 11 4.021925 GGCACCTGAGGCTCGGTT 62.022 66.667 22.58 7.90 0.00 4.44
13 14 3.781770 GATCGGCACCTGAGGCTCG 62.782 68.421 10.42 0.00 0.00 5.03
14 15 1.109920 TAGATCGGCACCTGAGGCTC 61.110 60.000 7.79 7.79 0.00 4.70
15 16 1.075970 TAGATCGGCACCTGAGGCT 60.076 57.895 0.00 0.00 0.00 4.58
16 17 1.365633 CTAGATCGGCACCTGAGGC 59.634 63.158 0.00 0.00 0.00 4.70
17 18 1.365633 GCTAGATCGGCACCTGAGG 59.634 63.158 0.00 0.00 0.00 3.86
18 19 1.007964 CGCTAGATCGGCACCTGAG 60.008 63.158 12.68 0.00 0.00 3.35
19 20 3.120105 CGCTAGATCGGCACCTGA 58.880 61.111 12.68 0.00 0.00 3.86
20 21 2.659897 GCGCTAGATCGGCACCTG 60.660 66.667 0.00 0.13 0.00 4.00
21 22 2.835431 AGCGCTAGATCGGCACCT 60.835 61.111 8.99 6.38 0.00 4.00
22 23 2.659897 CAGCGCTAGATCGGCACC 60.660 66.667 10.99 4.59 0.00 5.01
23 24 2.659897 CCAGCGCTAGATCGGCAC 60.660 66.667 10.99 4.55 0.00 5.01
24 25 4.592192 GCCAGCGCTAGATCGGCA 62.592 66.667 25.91 0.00 42.50 5.69
25 26 4.292178 AGCCAGCGCTAGATCGGC 62.292 66.667 24.10 24.10 46.08 5.54
45 46 0.881796 GAAAAAGAACGGCCTGAGGG 59.118 55.000 0.00 0.00 0.00 4.30
46 47 0.517316 CGAAAAAGAACGGCCTGAGG 59.483 55.000 0.00 0.00 0.00 3.86
47 48 0.517316 CCGAAAAAGAACGGCCTGAG 59.483 55.000 0.00 0.00 42.55 3.35
48 49 2.624169 CCGAAAAAGAACGGCCTGA 58.376 52.632 0.00 0.00 42.55 3.86
54 55 1.440353 CAGGCGCCGAAAAAGAACG 60.440 57.895 23.20 0.00 0.00 3.95
55 56 1.081442 CCAGGCGCCGAAAAAGAAC 60.081 57.895 23.20 0.00 0.00 3.01
56 57 2.265182 CCCAGGCGCCGAAAAAGAA 61.265 57.895 23.20 0.00 0.00 2.52
57 58 2.671619 CCCAGGCGCCGAAAAAGA 60.672 61.111 23.20 0.00 0.00 2.52
58 59 2.671619 TCCCAGGCGCCGAAAAAG 60.672 61.111 23.20 8.22 0.00 2.27
59 60 2.671619 CTCCCAGGCGCCGAAAAA 60.672 61.111 23.20 6.08 0.00 1.94
60 61 4.715523 CCTCCCAGGCGCCGAAAA 62.716 66.667 23.20 7.67 0.00 2.29
79 80 4.421479 AGCGTCTCCAGCCGTTCG 62.421 66.667 0.00 0.00 34.64 3.95
80 81 2.493907 AAGAGCGTCTCCAGCCGTTC 62.494 60.000 3.66 0.00 34.98 3.95
81 82 1.248785 TAAGAGCGTCTCCAGCCGTT 61.249 55.000 3.66 0.00 34.64 4.44
82 83 1.038130 ATAAGAGCGTCTCCAGCCGT 61.038 55.000 3.66 0.00 34.64 5.68
83 84 0.318275 GATAAGAGCGTCTCCAGCCG 60.318 60.000 3.66 0.00 34.64 5.52
84 85 0.747255 TGATAAGAGCGTCTCCAGCC 59.253 55.000 3.66 0.00 34.64 4.85
85 86 1.407258 ACTGATAAGAGCGTCTCCAGC 59.593 52.381 3.66 0.00 0.00 4.85
86 87 2.286713 CGACTGATAAGAGCGTCTCCAG 60.287 54.545 3.66 6.36 0.00 3.86
87 88 1.671328 CGACTGATAAGAGCGTCTCCA 59.329 52.381 3.66 0.00 0.00 3.86
88 89 1.002251 CCGACTGATAAGAGCGTCTCC 60.002 57.143 3.66 0.00 0.00 3.71
89 90 1.598430 GCCGACTGATAAGAGCGTCTC 60.598 57.143 0.00 0.00 0.00 3.36
90 91 0.382515 GCCGACTGATAAGAGCGTCT 59.617 55.000 0.00 0.00 0.00 4.18
91 92 0.382515 AGCCGACTGATAAGAGCGTC 59.617 55.000 0.00 0.00 0.00 5.19
92 93 2.494677 AGCCGACTGATAAGAGCGT 58.505 52.632 0.00 0.00 0.00 5.07
109 110 2.140065 TGAAGAACGCTCACACTCAG 57.860 50.000 0.00 0.00 0.00 3.35
149 151 2.913777 AGGGCTTTTACGCGAAATTC 57.086 45.000 15.93 4.14 0.00 2.17
150 152 3.502979 TGTTAGGGCTTTTACGCGAAATT 59.497 39.130 15.93 0.00 0.00 1.82
190 196 3.972276 GCGCGGTGGGCTGAAAAA 61.972 61.111 8.83 0.00 40.44 1.94
237 249 2.621526 GAGCAGGAGAGAGCTAGGTTAC 59.378 54.545 0.00 0.00 42.04 2.50
287 308 1.376683 CGAGGGATTTGGCGTTGGA 60.377 57.895 0.00 0.00 0.00 3.53
332 353 2.582498 GGGAAGTGATCGACGGCG 60.582 66.667 2.87 2.87 39.35 6.46
333 354 1.519455 CTGGGAAGTGATCGACGGC 60.519 63.158 0.00 0.00 0.00 5.68
334 355 1.519455 GCTGGGAAGTGATCGACGG 60.519 63.158 0.00 0.00 0.00 4.79
335 356 1.874019 CGCTGGGAAGTGATCGACG 60.874 63.158 0.00 0.00 0.00 5.12
336 357 2.167861 GCGCTGGGAAGTGATCGAC 61.168 63.158 0.00 0.00 0.00 4.20
337 358 2.184322 GCGCTGGGAAGTGATCGA 59.816 61.111 0.00 0.00 0.00 3.59
338 359 2.892425 GGCGCTGGGAAGTGATCG 60.892 66.667 7.64 0.00 0.00 3.69
339 360 2.892425 CGGCGCTGGGAAGTGATC 60.892 66.667 8.83 0.00 0.00 2.92
366 387 4.400961 GGCGCTGGGAAGTGCTCT 62.401 66.667 7.64 0.00 44.03 4.09
403 424 4.106925 GGGGAGAGCTGTGCAGGG 62.107 72.222 4.41 0.00 0.00 4.45
404 425 3.007920 AGGGGAGAGCTGTGCAGG 61.008 66.667 4.41 0.00 0.00 4.85
405 426 2.268280 CAGGGGAGAGCTGTGCAG 59.732 66.667 4.41 0.00 0.00 4.41
406 427 4.025858 GCAGGGGAGAGCTGTGCA 62.026 66.667 4.41 0.00 34.18 4.57
427 448 4.521062 AGTGATCTGCGGCGAGGC 62.521 66.667 12.98 0.00 0.00 4.70
428 449 2.584418 CAGTGATCTGCGGCGAGG 60.584 66.667 12.98 1.36 34.79 4.63
436 457 1.002990 TGTGCAGGGCAGTGATCTG 60.003 57.895 0.00 1.29 40.08 2.90
437 458 1.298993 CTGTGCAGGGCAGTGATCT 59.701 57.895 0.00 0.00 40.08 2.75
438 459 2.404995 GCTGTGCAGGGCAGTGATC 61.405 63.158 0.00 0.00 40.08 2.92
439 460 2.360852 GCTGTGCAGGGCAGTGAT 60.361 61.111 0.00 0.00 40.08 3.06
440 461 3.541950 GAGCTGTGCAGGGCAGTGA 62.542 63.158 12.44 0.00 40.08 3.41
441 462 3.054503 GAGCTGTGCAGGGCAGTG 61.055 66.667 12.44 0.00 40.08 3.66
442 463 3.247648 AGAGCTGTGCAGGGCAGT 61.248 61.111 12.44 0.00 40.08 4.40
443 464 2.436292 GAGAGCTGTGCAGGGCAG 60.436 66.667 12.44 6.08 40.08 4.85
444 465 4.025858 GGAGAGCTGTGCAGGGCA 62.026 66.667 12.44 0.00 35.60 5.36
445 466 4.792804 GGGAGAGCTGTGCAGGGC 62.793 72.222 4.41 2.94 0.00 5.19
446 467 4.106925 GGGGAGAGCTGTGCAGGG 62.107 72.222 4.41 0.00 0.00 4.45
447 468 3.007920 AGGGGAGAGCTGTGCAGG 61.008 66.667 4.41 0.00 0.00 4.85
448 469 2.268280 CAGGGGAGAGCTGTGCAG 59.732 66.667 4.41 0.00 0.00 4.41
449 470 4.025858 GCAGGGGAGAGCTGTGCA 62.026 66.667 4.41 0.00 34.18 4.57
505 526 2.995574 AAGGGGAGTGGTCGACGG 60.996 66.667 9.92 0.00 0.00 4.79
506 527 2.261671 CAAGGGGAGTGGTCGACG 59.738 66.667 9.92 0.00 0.00 5.12
507 528 2.047179 GCAAGGGGAGTGGTCGAC 60.047 66.667 7.13 7.13 0.00 4.20
508 529 3.691342 CGCAAGGGGAGTGGTCGA 61.691 66.667 0.00 0.00 0.00 4.20
534 555 2.995574 AAGGGGAGTGGTCGACGG 60.996 66.667 9.92 0.00 0.00 4.79
535 556 2.261671 CAAGGGGAGTGGTCGACG 59.738 66.667 9.92 0.00 0.00 5.12
536 557 2.047179 GCAAGGGGAGTGGTCGAC 60.047 66.667 7.13 7.13 0.00 4.20
537 558 3.691342 CGCAAGGGGAGTGGTCGA 61.691 66.667 0.00 0.00 0.00 4.20
977 999 4.418328 CGTTGAATGGGCGGGGGA 62.418 66.667 0.00 0.00 0.00 4.81
981 1003 4.114997 GTGGCGTTGAATGGGCGG 62.115 66.667 0.00 0.00 0.00 6.13
982 1004 4.114997 GGTGGCGTTGAATGGGCG 62.115 66.667 0.00 0.00 0.00 6.13
983 1005 3.758931 GGGTGGCGTTGAATGGGC 61.759 66.667 0.00 0.00 0.00 5.36
984 1006 2.035626 AGGGTGGCGTTGAATGGG 59.964 61.111 0.00 0.00 0.00 4.00
985 1007 2.046285 GGAGGGTGGCGTTGAATGG 61.046 63.158 0.00 0.00 0.00 3.16
986 1008 2.046285 GGGAGGGTGGCGTTGAATG 61.046 63.158 0.00 0.00 0.00 2.67
987 1009 2.355115 GGGAGGGTGGCGTTGAAT 59.645 61.111 0.00 0.00 0.00 2.57
988 1010 3.961414 GGGGAGGGTGGCGTTGAA 61.961 66.667 0.00 0.00 0.00 2.69
989 1011 4.974438 AGGGGAGGGTGGCGTTGA 62.974 66.667 0.00 0.00 0.00 3.18
990 1012 4.722700 CAGGGGAGGGTGGCGTTG 62.723 72.222 0.00 0.00 0.00 4.10
1044 1083 0.518636 CAGCACTTTGACGATGTGGG 59.481 55.000 10.00 0.00 34.79 4.61
1059 1098 0.107508 GATCTTGTGGGCTAGCAGCA 60.108 55.000 18.24 8.98 44.75 4.41
1060 1099 1.156645 CGATCTTGTGGGCTAGCAGC 61.157 60.000 18.24 6.26 41.46 5.25
1061 1100 1.156645 GCGATCTTGTGGGCTAGCAG 61.157 60.000 18.24 4.75 0.00 4.24
1143 1185 2.717044 ATGTCCGATTCCGCCGACA 61.717 57.895 0.00 0.00 39.79 4.35
2140 2280 1.003355 CCAGTCACTGGTCGCCATT 60.003 57.895 16.65 0.00 45.82 3.16
2203 2343 0.390124 CTTTGGAAGCAAGCTTGGCA 59.610 50.000 27.10 2.08 36.26 4.92
2416 2563 4.022935 GCCATTTTCAGGATCGCATTATCA 60.023 41.667 0.00 0.00 0.00 2.15
2420 2567 1.410153 GGCCATTTTCAGGATCGCATT 59.590 47.619 0.00 0.00 0.00 3.56
2640 2789 0.389817 CGACAATGGAGAAGCCGTCA 60.390 55.000 0.00 0.00 40.66 4.35
2760 2909 1.751924 GTTCTAGACGGTGCTCCTCAT 59.248 52.381 2.85 0.00 0.00 2.90
2808 2957 1.816835 TCTACATCGACCTCCACACAC 59.183 52.381 0.00 0.00 0.00 3.82
3087 3238 0.032515 TCGAGGGGAGTGAATAGGCA 60.033 55.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.