Multiple sequence alignment - TraesCS5B01G193100

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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 TraesCS5B01G193100 chr5B 100.000 3835 0 0 1 3835 348451149 348447315 0.000000e+00 7083.0
1 TraesCS5B01G193100 chr5D 92.219 2519 70 47 751 3190 303761262 303758791 0.000000e+00 3450.0
2 TraesCS5B01G193100 chr5D 84.028 432 19 19 3414 3835 303758164 303757773 1.680000e-98 370.0
3 TraesCS5B01G193100 chr5A 90.681 2511 89 55 770 3190 394183478 394181023 0.000000e+00 3206.0
4 TraesCS5B01G193100 chr5A 91.026 390 27 5 3446 3835 394180374 394179993 1.580000e-143 520.0
5 TraesCS5B01G193100 chr7A 100.000 751 0 0 1 751 514823619 514824369 0.000000e+00 1387.0
6 TraesCS5B01G193100 chr7A 82.162 555 55 24 206 752 348206751 348207269 1.640000e-118 436.0
7 TraesCS5B01G193100 chr4A 100.000 751 0 0 1 751 666112557 666111807 0.000000e+00 1387.0
8 TraesCS5B01G193100 chr2A 100.000 751 0 0 1 751 61505661 61506411 0.000000e+00 1387.0
9 TraesCS5B01G193100 chr7B 80.311 772 95 29 21 751 706414550 706413795 7.290000e-147 531.0
10 TraesCS5B01G193100 chr7B 97.917 48 1 0 1731 1778 97974193 97974146 2.460000e-12 84.2
11 TraesCS5B01G193100 chr6D 87.940 199 24 0 2590 2788 388538515 388538317 6.410000e-58 235.0
12 TraesCS5B01G193100 chr6D 82.803 157 27 0 1273 1429 388540037 388539881 1.440000e-29 141.0
13 TraesCS5B01G193100 chr6D 81.699 153 26 2 2509 2660 323715240 323715391 4.020000e-25 126.0
14 TraesCS5B01G193100 chr6D 86.022 93 11 2 1531 1621 388539768 388539676 8.770000e-17 99.0
15 TraesCS5B01G193100 chr6D 95.652 46 2 0 1733 1778 388539566 388539521 1.480000e-09 75.0
16 TraesCS5B01G193100 chr6A 87.437 199 25 0 2590 2788 535152681 535152483 2.980000e-56 230.0
17 TraesCS5B01G193100 chr6A 79.605 152 31 0 2509 2660 461146925 461147076 4.050000e-20 110.0
18 TraesCS5B01G193100 chr6A 86.022 93 11 2 1531 1621 535153984 535153892 8.770000e-17 99.0
19 TraesCS5B01G193100 chr6A 93.478 46 3 0 1733 1778 535153734 535153689 6.870000e-08 69.4
20 TraesCS5B01G193100 chr6B 86.432 199 27 0 2590 2788 581080112 581079914 6.450000e-53 219.0
21 TraesCS5B01G193100 chr6B 85.350 157 23 0 1273 1429 581081927 581081771 3.070000e-36 163.0
22 TraesCS5B01G193100 chr6B 83.761 117 17 2 2545 2660 500210534 500210419 4.050000e-20 110.0
23 TraesCS5B01G193100 chr6B 90.000 80 8 0 1531 1610 581081662 581081583 1.880000e-18 104.0
24 TraesCS5B01G193100 chr6B 95.652 46 2 0 1733 1778 581081147 581081102 1.480000e-09 75.0
25 TraesCS5B01G193100 chr2D 85.981 107 13 2 1308 1413 112180690 112180585 3.130000e-21 113.0
26 TraesCS5B01G193100 chr7D 97.917 48 1 0 1731 1778 136014861 136014814 2.460000e-12 84.2


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 TraesCS5B01G193100 chr5B 348447315 348451149 3834 True 7083 7083 100.0000 1 3835 1 chr5B.!!$R1 3834
1 TraesCS5B01G193100 chr5D 303757773 303761262 3489 True 1910 3450 88.1235 751 3835 2 chr5D.!!$R1 3084
2 TraesCS5B01G193100 chr5A 394179993 394183478 3485 True 1863 3206 90.8535 770 3835 2 chr5A.!!$R1 3065
3 TraesCS5B01G193100 chr7A 514823619 514824369 750 False 1387 1387 100.0000 1 751 1 chr7A.!!$F2 750
4 TraesCS5B01G193100 chr7A 348206751 348207269 518 False 436 436 82.1620 206 752 1 chr7A.!!$F1 546
5 TraesCS5B01G193100 chr4A 666111807 666112557 750 True 1387 1387 100.0000 1 751 1 chr4A.!!$R1 750
6 TraesCS5B01G193100 chr2A 61505661 61506411 750 False 1387 1387 100.0000 1 751 1 chr2A.!!$F1 750
7 TraesCS5B01G193100 chr7B 706413795 706414550 755 True 531 531 80.3110 21 751 1 chr7B.!!$R2 730

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
989 1048 1.065782 GCTTCTCCTTCTCCTTGGACC 60.066 57.143 0.0 0.0 0.0 4.46 F
1444 1503 0.607489 CCTGTTCACCCTGCTTCCTG 60.607 60.000 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1956 0.609662 CCCACAAAAATGGAGCTGGG 59.390 55.0 0.00 0.00 43.02 4.45 R
3376 3607 0.451383 TTCGCATTACACCTGCATGC 59.549 50.0 11.82 11.82 39.64 4.06 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
799 847 2.202756 GCCGGATTCGCGTCTTCT 60.203 61.111 5.05 0.00 34.56 2.85
872 921 4.763793 ACACCAATCATTTCCTCTTCACTG 59.236 41.667 0.00 0.00 0.00 3.66
875 924 5.222007 ACCAATCATTTCCTCTTCACTGTCT 60.222 40.000 0.00 0.00 0.00 3.41
960 1016 2.583593 CGCGCTTCTAGGACCTGC 60.584 66.667 5.56 0.00 0.00 4.85
975 1034 1.153469 CTGCCCCTCGAAGCTTCTC 60.153 63.158 23.50 0.00 0.00 2.87
989 1048 1.065782 GCTTCTCCTTCTCCTTGGACC 60.066 57.143 0.00 0.00 0.00 4.46
1044 1103 4.101448 GAGGTGGGCATGACGGCT 62.101 66.667 0.00 0.00 40.90 5.52
1444 1503 0.607489 CCTGTTCACCCTGCTTCCTG 60.607 60.000 0.00 0.00 0.00 3.86
1477 1536 2.687200 TACCCGCCATGCACCTCT 60.687 61.111 0.00 0.00 0.00 3.69
1478 1537 3.030168 TACCCGCCATGCACCTCTG 62.030 63.158 0.00 0.00 0.00 3.35
1480 1539 4.790962 CCGCCATGCACCTCTGCT 62.791 66.667 0.00 0.00 44.57 4.24
1481 1540 3.200593 CGCCATGCACCTCTGCTC 61.201 66.667 0.00 0.00 44.57 4.26
1482 1541 2.045634 GCCATGCACCTCTGCTCA 60.046 61.111 0.00 0.00 44.57 4.26
1483 1542 2.113433 GCCATGCACCTCTGCTCAG 61.113 63.158 0.00 0.00 44.57 3.35
1624 1684 1.153628 GTACTACACCCGCCAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
1625 1685 3.014085 TACTACACCCGCCAGCAGC 62.014 63.158 0.00 0.00 38.52 5.25
1626 1686 4.393155 CTACACCCGCCAGCAGCA 62.393 66.667 0.00 0.00 44.04 4.41
1627 1687 4.697756 TACACCCGCCAGCAGCAC 62.698 66.667 0.00 0.00 44.04 4.40
1716 1797 3.624326 TCAATTTCGCAGGTGTTTGAG 57.376 42.857 0.00 0.00 0.00 3.02
1776 1857 1.307309 CATGGACATCAAGGGCCCA 59.693 57.895 27.56 2.74 0.00 5.36
1805 1886 5.576563 TCCTCAAAGTCCAAGGTGAATTA 57.423 39.130 0.00 0.00 0.00 1.40
1829 1915 2.242926 CTCCTCTCGCCCATCATCTAA 58.757 52.381 0.00 0.00 0.00 2.10
1861 1948 2.152297 CTAGCATGGCCGCTCGATCT 62.152 60.000 8.56 0.00 42.62 2.75
1869 1956 1.335496 GGCCGCTCGATCTATCTATCC 59.665 57.143 0.00 0.00 0.00 2.59
1910 1997 4.636206 GGCACGAATATTCCCATATCTTCC 59.364 45.833 9.87 0.00 0.00 3.46
2049 2141 4.433615 TCATTCGCACCAGAAATCTAGTC 58.566 43.478 0.00 0.00 33.43 2.59
2050 2142 4.160439 TCATTCGCACCAGAAATCTAGTCT 59.840 41.667 0.00 0.00 33.43 3.24
2051 2143 5.359860 TCATTCGCACCAGAAATCTAGTCTA 59.640 40.000 0.00 0.00 33.43 2.59
2052 2144 4.902443 TCGCACCAGAAATCTAGTCTAG 57.098 45.455 0.00 0.00 0.00 2.43
2053 2145 4.270834 TCGCACCAGAAATCTAGTCTAGT 58.729 43.478 6.77 0.00 0.00 2.57
2284 2376 8.642432 GCTTTCCTTCCCATTTATAGCTTTATT 58.358 33.333 0.00 0.00 0.00 1.40
2302 2394 0.122435 TTTATCCCTCCCCACCACCT 59.878 55.000 0.00 0.00 0.00 4.00
2333 2425 1.337823 ACTTAACCACCGCTAGTGCTG 60.338 52.381 0.00 0.00 45.83 4.41
2334 2426 0.672401 TTAACCACCGCTAGTGCTGC 60.672 55.000 0.00 0.00 45.83 5.25
2335 2427 1.541310 TAACCACCGCTAGTGCTGCT 61.541 55.000 0.00 0.00 45.83 4.24
2336 2428 1.541310 AACCACCGCTAGTGCTGCTA 61.541 55.000 0.00 0.00 45.83 3.49
2337 2429 1.519455 CCACCGCTAGTGCTGCTAC 60.519 63.158 0.00 0.00 45.83 3.58
2338 2430 1.513158 CACCGCTAGTGCTGCTACT 59.487 57.895 0.00 5.63 40.28 2.57
2339 2431 0.738975 CACCGCTAGTGCTGCTACTA 59.261 55.000 0.00 6.50 40.28 1.82
2425 2523 5.984695 ACTTAACTAGTGACTGATCAGCA 57.015 39.130 22.83 17.59 34.75 4.41
2429 2527 5.611128 AACTAGTGACTGATCAGCATCAT 57.389 39.130 22.83 12.93 38.42 2.45
2430 2528 4.946445 ACTAGTGACTGATCAGCATCATG 58.054 43.478 22.83 14.58 38.42 3.07
2431 2529 4.648307 ACTAGTGACTGATCAGCATCATGA 59.352 41.667 22.83 10.32 38.42 3.07
2432 2530 4.691326 AGTGACTGATCAGCATCATGAT 57.309 40.909 22.83 1.18 42.62 2.45
2433 2531 4.381411 AGTGACTGATCAGCATCATGATG 58.619 43.478 28.04 28.04 40.02 3.07
2797 2907 0.108233 GAGTGGAAGCAGCTCTCCAG 60.108 60.000 20.47 0.00 32.30 3.86
2855 2993 1.554160 TCCAACGGCCGGACTAATTAA 59.446 47.619 31.76 2.12 0.00 1.40
2862 3000 4.099881 ACGGCCGGACTAATTAATTCACTA 59.900 41.667 31.76 0.00 0.00 2.74
2864 3002 4.446719 GGCCGGACTAATTAATTCACTACG 59.553 45.833 5.05 4.86 0.00 3.51
2865 3003 5.045872 GCCGGACTAATTAATTCACTACGT 58.954 41.667 5.05 0.00 0.00 3.57
2866 3004 5.051240 GCCGGACTAATTAATTCACTACGTG 60.051 44.000 5.05 0.00 34.45 4.49
2867 3005 6.038356 CCGGACTAATTAATTCACTACGTGT 58.962 40.000 3.39 0.00 34.79 4.49
2868 3006 7.195646 CCGGACTAATTAATTCACTACGTGTA 58.804 38.462 3.39 0.00 34.79 2.90
2870 3008 7.096722 CGGACTAATTAATTCACTACGTGTAGC 60.097 40.741 3.39 0.00 36.66 3.58
2871 3009 7.919621 GGACTAATTAATTCACTACGTGTAGCT 59.080 37.037 3.39 0.00 36.66 3.32
2872 3010 9.298774 GACTAATTAATTCACTACGTGTAGCTT 57.701 33.333 3.39 0.00 36.66 3.74
3112 3256 5.654209 AGGAACCATGGAATAAAGAAAGAGC 59.346 40.000 21.47 0.00 0.00 4.09
3130 3274 5.365021 AGAGCAACCTGAGTAAATAGCAT 57.635 39.130 0.00 0.00 0.00 3.79
3138 3282 7.944729 ACCTGAGTAAATAGCATCAACAAAT 57.055 32.000 0.00 0.00 0.00 2.32
3158 3302 1.086634 GCCTTCTCTGTCCGTGCATC 61.087 60.000 0.00 0.00 0.00 3.91
3190 3377 9.260002 ACCATCATCAAAATTTGTTTCAACTAC 57.740 29.630 5.56 0.00 0.00 2.73
3205 3396 9.903682 TGTTTCAACTACTACTACACTACAATC 57.096 33.333 0.00 0.00 0.00 2.67
3208 3399 9.964354 TTCAACTACTACTACACTACAATCCTA 57.036 33.333 0.00 0.00 0.00 2.94
3209 3400 9.610705 TCAACTACTACTACACTACAATCCTAG 57.389 37.037 0.00 0.00 0.00 3.02
3210 3401 9.393512 CAACTACTACTACACTACAATCCTAGT 57.606 37.037 0.00 0.00 0.00 2.57
3215 3406 9.393512 ACTACTACACTACAATCCTAGTACAAG 57.606 37.037 0.00 0.00 0.00 3.16
3216 3407 7.642082 ACTACACTACAATCCTAGTACAAGG 57.358 40.000 0.00 0.00 38.06 3.61
3217 3408 5.934402 ACACTACAATCCTAGTACAAGGG 57.066 43.478 0.00 0.00 37.24 3.95
3218 3409 5.586877 ACACTACAATCCTAGTACAAGGGA 58.413 41.667 0.00 0.00 37.24 4.20
3219 3410 5.421374 ACACTACAATCCTAGTACAAGGGAC 59.579 44.000 0.00 0.00 37.24 4.46
3234 3456 5.801380 ACAAGGGACATGTTATTCGTAAGT 58.199 37.500 0.00 0.00 36.65 2.24
3240 3462 6.035758 GGGACATGTTATTCGTAAGTTGTCTC 59.964 42.308 0.00 0.00 34.23 3.36
3245 3467 9.825972 CATGTTATTCGTAAGTTGTCTCAAAAT 57.174 29.630 0.00 0.00 39.48 1.82
3271 3496 5.800438 GTCAATTCAAATTTCCTAGCCGTTC 59.200 40.000 0.00 0.00 0.00 3.95
3278 3503 2.579207 TTCCTAGCCGTTCGATTCAG 57.421 50.000 0.00 0.00 0.00 3.02
3285 3510 2.158900 AGCCGTTCGATTCAGATCCAAT 60.159 45.455 0.00 0.00 0.00 3.16
3288 3513 2.032549 CGTTCGATTCAGATCCAATGGC 60.033 50.000 0.00 0.00 0.00 4.40
3291 3516 1.266175 CGATTCAGATCCAATGGCTGC 59.734 52.381 0.00 0.00 0.00 5.25
3296 3521 1.884579 CAGATCCAATGGCTGCCATAC 59.115 52.381 32.71 20.26 44.40 2.39
3304 3529 2.238942 TGGCTGCCATACGTCTTATG 57.761 50.000 19.30 0.00 37.86 1.90
3315 3540 6.511767 GCCATACGTCTTATGTCATCCTTTTG 60.512 42.308 0.00 0.00 36.54 2.44
3319 3544 4.273318 GTCTTATGTCATCCTTTTGCCCT 58.727 43.478 0.00 0.00 0.00 5.19
3322 3547 5.191722 TCTTATGTCATCCTTTTGCCCTAGT 59.808 40.000 0.00 0.00 0.00 2.57
3333 3558 3.314541 TTGCCCTAGTTTCTTCTCGAC 57.685 47.619 0.00 0.00 0.00 4.20
3335 3562 1.201880 GCCCTAGTTTCTTCTCGACGT 59.798 52.381 0.00 0.00 0.00 4.34
3337 3564 2.748532 CCCTAGTTTCTTCTCGACGTCT 59.251 50.000 14.70 0.00 0.00 4.18
3340 3567 4.154556 CCTAGTTTCTTCTCGACGTCTTCT 59.845 45.833 14.70 1.65 0.00 2.85
3387 3618 4.722700 GGTCGGGCATGCAGGTGT 62.723 66.667 21.36 0.00 0.00 4.16
3388 3619 2.267642 GTCGGGCATGCAGGTGTA 59.732 61.111 21.36 0.00 0.00 2.90
3389 3620 1.376683 GTCGGGCATGCAGGTGTAA 60.377 57.895 21.36 0.00 0.00 2.41
3390 3621 0.748005 GTCGGGCATGCAGGTGTAAT 60.748 55.000 21.36 0.00 0.00 1.89
3391 3622 0.747644 TCGGGCATGCAGGTGTAATG 60.748 55.000 21.36 0.00 0.00 1.90
3393 3624 1.064621 GGCATGCAGGTGTAATGCG 59.935 57.895 21.36 0.00 46.87 4.73
3394 3625 1.375853 GGCATGCAGGTGTAATGCGA 61.376 55.000 21.36 0.00 46.87 5.10
3396 3627 1.135431 GCATGCAGGTGTAATGCGAAA 60.135 47.619 14.21 0.00 46.87 3.46
3397 3628 2.518949 CATGCAGGTGTAATGCGAAAC 58.481 47.619 0.00 0.00 46.87 2.78
3398 3629 0.515127 TGCAGGTGTAATGCGAAACG 59.485 50.000 0.00 0.00 46.87 3.60
3418 3999 2.280389 CGCCTACCTCGCATGCAT 60.280 61.111 19.57 0.00 0.00 3.96
3420 4001 1.650912 GCCTACCTCGCATGCATTG 59.349 57.895 19.57 7.15 0.00 2.82
3465 4059 0.659427 ATGCATGTGATGTGCGCTAC 59.341 50.000 9.73 5.95 45.37 3.58
3474 4068 1.873270 ATGTGCGCTACTGGTGTCGA 61.873 55.000 9.73 0.00 0.00 4.20
3494 4088 1.656652 TAGAGTACACGTACGCCTCC 58.343 55.000 16.72 1.05 40.80 4.30
3523 4117 1.539827 CCTACCAAAAACCGAAGCCAG 59.460 52.381 0.00 0.00 0.00 4.85
3537 4131 1.413118 AGCCAGTGGTTTTCCCTTTG 58.587 50.000 11.74 0.00 39.73 2.77
3548 4142 5.163216 TGGTTTTCCCTTTGCTTGATTGATT 60.163 36.000 0.00 0.00 39.73 2.57
3594 4190 2.100631 GCTCGGGTTCACGTGATGG 61.101 63.158 20.80 9.04 34.94 3.51
3595 4191 2.047655 TCGGGTTCACGTGATGGC 60.048 61.111 20.80 12.43 34.94 4.40
3596 4192 2.358125 CGGGTTCACGTGATGGCA 60.358 61.111 20.80 0.31 0.00 4.92
3597 4193 2.677003 CGGGTTCACGTGATGGCAC 61.677 63.158 20.80 14.22 41.67 5.01
3605 4201 3.029810 GTGATGGCACGCACAACA 58.970 55.556 15.12 0.00 36.48 3.33
3664 4272 2.353839 CGTCGTCGTTTGTCCCGT 60.354 61.111 0.00 0.00 0.00 5.28
3667 4275 1.300080 TCGTCGTTTGTCCCGTTCC 60.300 57.895 0.00 0.00 0.00 3.62
3672 4280 0.604243 CGTTTGTCCCGTTCCCATGA 60.604 55.000 0.00 0.00 0.00 3.07
3675 4283 1.285280 TTGTCCCGTTCCCATGATCT 58.715 50.000 0.00 0.00 0.00 2.75
3680 4288 0.833287 CCGTTCCCATGATCTGTCCT 59.167 55.000 0.00 0.00 0.00 3.85
3696 4304 4.778415 CTGGTCTCCGACGTGGCG 62.778 72.222 0.00 0.00 37.80 5.69
3738 4346 4.508124 GCTAGTTAAGCGTAGTACTCCGTA 59.492 45.833 9.72 0.00 42.53 4.02
3754 4362 2.094906 TCCGTACCTCTGAACAATCGTG 60.095 50.000 0.00 0.00 0.00 4.35
3761 4372 2.233922 CTCTGAACAATCGTGGTACCCT 59.766 50.000 10.07 0.00 0.00 4.34
3822 4433 2.414138 GCGACCGTAGCTACAAATGTTT 59.586 45.455 23.21 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
799 847 1.870941 TAGGTGGAGGGAAGCGAGGA 61.871 60.000 0.00 0.00 0.00 3.71
847 896 5.474876 AGTGAAGAGGAAATGATTGGTGTTC 59.525 40.000 0.00 0.00 0.00 3.18
872 921 3.694043 AGGCAGAAAAGGAGAAGAGAC 57.306 47.619 0.00 0.00 0.00 3.36
875 924 2.711009 TGGAAGGCAGAAAAGGAGAAGA 59.289 45.455 0.00 0.00 0.00 2.87
960 1016 0.176910 GAAGGAGAAGCTTCGAGGGG 59.823 60.000 20.43 0.00 0.00 4.79
975 1034 1.296715 CACGGGTCCAAGGAGAAGG 59.703 63.158 0.00 0.00 0.00 3.46
989 1048 3.876198 GCGCCATACCAAGCACGG 61.876 66.667 0.00 0.00 0.00 4.94
1158 1217 3.415087 AGGCCACTGAGCATCCCC 61.415 66.667 5.01 0.00 0.00 4.81
1444 1503 4.509230 GGCGGGTACTATAAAAACTACTGC 59.491 45.833 0.00 0.00 0.00 4.40
1451 1510 3.628487 GTGCATGGCGGGTACTATAAAAA 59.372 43.478 0.00 0.00 0.00 1.94
1478 1537 0.739112 GCAGGTAGTGAGCACTGAGC 60.739 60.000 13.12 7.76 42.52 4.26
1479 1538 0.457509 CGCAGGTAGTGAGCACTGAG 60.458 60.000 13.12 2.10 42.52 3.35
1480 1539 0.893727 TCGCAGGTAGTGAGCACTGA 60.894 55.000 13.12 0.00 42.52 3.41
1481 1540 0.038251 TTCGCAGGTAGTGAGCACTG 60.038 55.000 13.12 0.00 42.52 3.66
1482 1541 0.038159 GTTCGCAGGTAGTGAGCACT 60.038 55.000 8.35 8.35 45.02 4.40
1483 1542 0.319555 TGTTCGCAGGTAGTGAGCAC 60.320 55.000 0.00 0.00 42.04 4.40
1624 1684 3.429410 GGGAGTTCATTAATTGCTGGTGC 60.429 47.826 0.00 0.00 40.20 5.01
1625 1685 3.763360 TGGGAGTTCATTAATTGCTGGTG 59.237 43.478 0.00 0.00 0.00 4.17
1626 1686 4.046286 TGGGAGTTCATTAATTGCTGGT 57.954 40.909 0.00 0.00 0.00 4.00
1627 1687 5.353938 CAATGGGAGTTCATTAATTGCTGG 58.646 41.667 0.00 0.00 35.78 4.85
1628 1688 4.807304 GCAATGGGAGTTCATTAATTGCTG 59.193 41.667 10.14 0.00 43.98 4.41
1629 1689 4.141869 GGCAATGGGAGTTCATTAATTGCT 60.142 41.667 15.37 0.00 45.69 3.91
1630 1690 4.122046 GGCAATGGGAGTTCATTAATTGC 58.878 43.478 9.15 9.15 45.68 3.56
1631 1691 5.341872 TGGCAATGGGAGTTCATTAATTG 57.658 39.130 0.00 0.00 35.78 2.32
1632 1692 5.221303 CGATGGCAATGGGAGTTCATTAATT 60.221 40.000 0.00 0.00 35.78 1.40
1716 1797 2.357034 TCCGCCAGCTTCACGAAC 60.357 61.111 1.54 0.00 0.00 3.95
1776 1857 2.978156 TGGACTTTGAGGATTTGGCT 57.022 45.000 0.00 0.00 0.00 4.75
1805 1886 1.340399 TGATGGGCGAGAGGAGCATT 61.340 55.000 0.00 0.00 36.08 3.56
1851 1938 1.950909 GGGGATAGATAGATCGAGCGG 59.049 57.143 0.00 0.00 0.00 5.52
1861 1948 5.134339 ACAAAAATGGAGCTGGGGATAGATA 59.866 40.000 0.00 0.00 0.00 1.98
1869 1956 0.609662 CCCACAAAAATGGAGCTGGG 59.390 55.000 0.00 0.00 43.02 4.45
2284 2376 0.623324 CAGGTGGTGGGGAGGGATAA 60.623 60.000 0.00 0.00 0.00 1.75
2285 2377 1.004230 CAGGTGGTGGGGAGGGATA 59.996 63.158 0.00 0.00 0.00 2.59
2286 2378 1.833055 TACAGGTGGTGGGGAGGGAT 61.833 60.000 0.00 0.00 0.00 3.85
2287 2379 1.833055 ATACAGGTGGTGGGGAGGGA 61.833 60.000 0.00 0.00 0.00 4.20
2302 2394 4.393680 GCGGTGGTTAAGTGAATGAATACA 59.606 41.667 0.00 0.00 0.00 2.29
2340 2432 9.865321 GGACAAAAGGGAGGTTTAATTTTATAC 57.135 33.333 0.00 0.00 0.00 1.47
2350 2445 3.061369 ACTAGGGACAAAAGGGAGGTTT 58.939 45.455 0.00 0.00 0.00 3.27
2425 2523 1.477014 CCCAGCTCTGCACATCATGAT 60.477 52.381 1.18 1.18 0.00 2.45
2429 2527 2.672908 CCCCAGCTCTGCACATCA 59.327 61.111 0.00 0.00 0.00 3.07
2430 2528 2.827642 GCCCCAGCTCTGCACATC 60.828 66.667 0.00 0.00 35.50 3.06
2431 2529 4.790962 CGCCCCAGCTCTGCACAT 62.791 66.667 0.00 0.00 36.60 3.21
2837 2947 3.623960 TGAATTAATTAGTCCGGCCGTTG 59.376 43.478 26.12 10.11 0.00 4.10
2871 3009 9.793259 CAGGGGATTCATTAACTAGCTAATTAA 57.207 33.333 9.62 9.62 0.00 1.40
2872 3010 7.883311 GCAGGGGATTCATTAACTAGCTAATTA 59.117 37.037 0.00 0.00 0.00 1.40
2873 3011 6.717084 GCAGGGGATTCATTAACTAGCTAATT 59.283 38.462 0.00 0.00 0.00 1.40
2874 3012 6.044871 AGCAGGGGATTCATTAACTAGCTAAT 59.955 38.462 0.00 0.00 0.00 1.73
3112 3256 6.741992 TGTTGATGCTATTTACTCAGGTTG 57.258 37.500 0.00 0.00 0.00 3.77
3130 3274 3.149196 GGACAGAGAAGGCATTTGTTGA 58.851 45.455 0.00 0.00 0.00 3.18
3138 3282 1.830587 ATGCACGGACAGAGAAGGCA 61.831 55.000 0.00 0.00 0.00 4.75
3158 3302 2.945447 ATTTTGATGATGGTGTGCGG 57.055 45.000 0.00 0.00 0.00 5.69
3190 3377 8.838365 CCTTGTACTAGGATTGTAGTGTAGTAG 58.162 40.741 17.42 0.00 37.50 2.57
3204 3395 6.183360 CGAATAACATGTCCCTTGTACTAGGA 60.183 42.308 23.03 9.65 37.50 2.94
3205 3396 5.983720 CGAATAACATGTCCCTTGTACTAGG 59.016 44.000 15.64 15.64 34.92 3.02
3208 3399 5.416271 ACGAATAACATGTCCCTTGTACT 57.584 39.130 0.00 0.00 0.00 2.73
3209 3400 6.815142 ACTTACGAATAACATGTCCCTTGTAC 59.185 38.462 0.00 0.00 0.00 2.90
3210 3401 6.938507 ACTTACGAATAACATGTCCCTTGTA 58.061 36.000 0.00 0.00 0.00 2.41
3212 3403 6.148811 ACAACTTACGAATAACATGTCCCTTG 59.851 38.462 0.00 0.00 0.00 3.61
3213 3404 6.235664 ACAACTTACGAATAACATGTCCCTT 58.764 36.000 0.00 0.00 0.00 3.95
3215 3406 5.873164 AGACAACTTACGAATAACATGTCCC 59.127 40.000 0.00 0.00 34.35 4.46
3216 3407 6.588756 TGAGACAACTTACGAATAACATGTCC 59.411 38.462 0.00 0.00 34.35 4.02
3217 3408 7.576750 TGAGACAACTTACGAATAACATGTC 57.423 36.000 0.00 0.00 34.19 3.06
3218 3409 7.956420 TTGAGACAACTTACGAATAACATGT 57.044 32.000 0.00 0.00 0.00 3.21
3219 3410 9.825972 ATTTTGAGACAACTTACGAATAACATG 57.174 29.630 0.00 0.00 0.00 3.21
3245 3467 6.177610 ACGGCTAGGAAATTTGAATTGACTA 58.822 36.000 0.00 0.00 0.00 2.59
3246 3468 5.010282 ACGGCTAGGAAATTTGAATTGACT 58.990 37.500 0.00 0.00 0.00 3.41
3249 3471 4.793216 CGAACGGCTAGGAAATTTGAATTG 59.207 41.667 0.00 0.00 0.00 2.32
3255 3480 4.258543 TGAATCGAACGGCTAGGAAATTT 58.741 39.130 0.00 0.00 0.00 1.82
3257 3482 3.132289 TCTGAATCGAACGGCTAGGAAAT 59.868 43.478 0.00 0.00 0.00 2.17
3261 3486 2.608261 GGATCTGAATCGAACGGCTAGG 60.608 54.545 0.00 0.00 32.24 3.02
3264 3489 0.824109 TGGATCTGAATCGAACGGCT 59.176 50.000 0.00 0.00 32.24 5.52
3271 3496 1.266175 GCAGCCATTGGATCTGAATCG 59.734 52.381 6.95 0.00 32.24 3.34
3278 3503 0.877071 CGTATGGCAGCCATTGGATC 59.123 55.000 32.20 15.51 42.23 3.36
3285 3510 1.484653 ACATAAGACGTATGGCAGCCA 59.515 47.619 18.99 18.99 43.53 4.75
3291 3516 6.511767 GCAAAAGGATGACATAAGACGTATGG 60.512 42.308 12.21 0.00 43.53 2.74
3296 3521 3.065371 GGGCAAAAGGATGACATAAGACG 59.935 47.826 0.00 0.00 0.00 4.18
3304 3529 4.336280 AGAAACTAGGGCAAAAGGATGAC 58.664 43.478 0.00 0.00 0.00 3.06
3315 3540 1.201880 ACGTCGAGAAGAAACTAGGGC 59.798 52.381 0.00 0.00 0.00 5.19
3319 3544 5.686159 AAGAAGACGTCGAGAAGAAACTA 57.314 39.130 10.46 0.00 0.00 2.24
3349 3576 2.034879 CGTCGGTGGCAAGAGCAAT 61.035 57.895 0.00 0.00 44.61 3.56
3371 3602 0.748005 ATTACACCTGCATGCCCGAC 60.748 55.000 16.68 0.00 0.00 4.79
3372 3603 0.747644 CATTACACCTGCATGCCCGA 60.748 55.000 16.68 0.00 0.00 5.14
3373 3604 1.729276 CATTACACCTGCATGCCCG 59.271 57.895 16.68 7.44 0.00 6.13
3374 3605 1.438814 GCATTACACCTGCATGCCC 59.561 57.895 16.68 0.00 37.88 5.36
3375 3606 1.064621 CGCATTACACCTGCATGCC 59.935 57.895 16.68 0.00 40.26 4.40
3376 3607 0.451383 TTCGCATTACACCTGCATGC 59.549 50.000 11.82 11.82 39.64 4.06
3378 3609 1.130373 CGTTTCGCATTACACCTGCAT 59.870 47.619 0.00 0.00 39.64 3.96
3380 3611 3.290098 CGTTTCGCATTACACCTGC 57.710 52.632 0.00 0.00 36.26 4.85
3393 3624 3.551915 GAGGTAGGCGCGCGTTTC 61.552 66.667 32.36 22.88 0.00 2.78
3402 3633 1.650912 CAATGCATGCGAGGTAGGC 59.349 57.895 14.09 0.00 0.00 3.93
3403 3634 1.650912 GCAATGCATGCGAGGTAGG 59.349 57.895 14.09 0.00 46.87 3.18
3412 3643 3.642705 CTGATCATCCTTGCAATGCATG 58.357 45.455 9.39 11.74 38.76 4.06
3418 3999 1.100510 GCAGCTGATCATCCTTGCAA 58.899 50.000 20.43 0.00 0.00 4.08
3420 4001 1.001268 CATGCAGCTGATCATCCTTGC 60.001 52.381 20.43 4.98 0.00 4.01
3465 4059 2.676839 ACGTGTACTCTATCGACACCAG 59.323 50.000 0.00 0.00 40.29 4.00
3474 4068 2.216898 GGAGGCGTACGTGTACTCTAT 58.783 52.381 17.90 0.00 34.04 1.98
3478 4072 3.044059 GCGGAGGCGTACGTGTACT 62.044 63.158 17.90 10.12 34.04 2.73
3494 4088 2.136196 TTTTTGGTAGGCAAGCCGCG 62.136 55.000 5.28 0.00 43.84 6.46
3523 4117 3.751479 ATCAAGCAAAGGGAAAACCAC 57.249 42.857 0.00 0.00 43.89 4.16
3537 4131 3.442977 AGCAACTCCTCAATCAATCAAGC 59.557 43.478 0.00 0.00 0.00 4.01
3579 4175 2.358125 TGCCATCACGTGAACCCG 60.358 61.111 24.13 11.18 0.00 5.28
3595 4191 4.235025 TGCGTGCTGTTGTGCGTG 62.235 61.111 0.00 0.00 35.36 5.34
3596 4192 4.236416 GTGCGTGCTGTTGTGCGT 62.236 61.111 0.00 0.00 35.36 5.24
3597 4193 4.235025 TGTGCGTGCTGTTGTGCG 62.235 61.111 0.00 0.00 35.36 5.34
3598 4194 2.352686 CTGTGCGTGCTGTTGTGC 60.353 61.111 0.00 0.00 0.00 4.57
3599 4195 2.352686 GCTGTGCGTGCTGTTGTG 60.353 61.111 0.00 0.00 0.00 3.33
3600 4196 3.585990 GGCTGTGCGTGCTGTTGT 61.586 61.111 0.00 0.00 0.00 3.32
3601 4197 4.332637 GGGCTGTGCGTGCTGTTG 62.333 66.667 0.00 0.00 0.00 3.33
3602 4198 4.873810 TGGGCTGTGCGTGCTGTT 62.874 61.111 0.00 0.00 0.00 3.16
3730 4338 3.376234 CGATTGTTCAGAGGTACGGAGTA 59.624 47.826 0.00 0.00 45.11 2.59
3732 4340 2.163815 ACGATTGTTCAGAGGTACGGAG 59.836 50.000 0.00 0.00 0.00 4.63
3733 4341 2.094906 CACGATTGTTCAGAGGTACGGA 60.095 50.000 0.00 0.00 0.00 4.69
3734 4342 2.259618 CACGATTGTTCAGAGGTACGG 58.740 52.381 0.00 0.00 0.00 4.02
3735 4343 2.259618 CCACGATTGTTCAGAGGTACG 58.740 52.381 0.00 0.00 0.00 3.67
3738 4346 2.028385 GGTACCACGATTGTTCAGAGGT 60.028 50.000 7.15 0.00 0.00 3.85
3775 4386 2.281484 TTGGCGCCCACAGAGAAC 60.281 61.111 26.77 0.00 30.78 3.01


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

AutoCloner maintained by Alex Coulton.