Multiple sequence alignment - TraesCS2D01G410800

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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 TraesCS2D01G410800 chr2D 100.000 2929 0 0 1 2929 525700307 525697379 0.000000e+00 5409.0
1 TraesCS2D01G410800 chr2D 91.667 48 4 0 2568 2615 483871560 483871513 1.880000e-07 67.6
2 TraesCS2D01G410800 chr2D 74.825 143 29 5 171 306 605727005 605727147 1.130000e-04 58.4
3 TraesCS2D01G410800 chr2A 92.614 2559 123 41 47 2577 670880155 670882675 0.000000e+00 3618.0
4 TraesCS2D01G410800 chr2A 91.275 298 9 6 2641 2929 670882678 670882967 9.840000e-105 390.0
5 TraesCS2D01G410800 chr2A 87.500 56 4 2 2579 2634 34674958 34674906 8.760000e-06 62.1
6 TraesCS2D01G410800 chr2B 94.493 1362 45 19 1221 2575 621775400 621776738 0.000000e+00 2073.0
7 TraesCS2D01G410800 chr2B 89.058 1252 57 31 44 1259 621774181 621775388 0.000000e+00 1480.0
8 TraesCS2D01G410800 chr2B 95.973 298 10 1 2632 2929 621776736 621777031 1.580000e-132 483.0
9 TraesCS2D01G410800 chr2B 89.831 59 4 2 180 237 689326743 689326686 1.130000e-09 75.0
10 TraesCS2D01G410800 chr6D 88.636 88 10 0 1342 1429 325600191 325600278 1.110000e-19 108.0
11 TraesCS2D01G410800 chr6D 96.429 56 1 1 1 55 294494229 294494284 1.120000e-14 91.6
12 TraesCS2D01G410800 chr6B 87.500 88 11 0 1342 1429 497434166 497434079 5.160000e-18 102.0
13 TraesCS2D01G410800 chr6A 87.778 90 7 4 1342 1429 464249992 464250079 5.160000e-18 102.0
14 TraesCS2D01G410800 chr6A 90.625 64 4 2 1 64 60091074 60091135 1.870000e-12 84.2
15 TraesCS2D01G410800 chr6A 89.655 58 4 1 2579 2636 615776074 615776019 4.050000e-09 73.1
16 TraesCS2D01G410800 chr6A 95.455 44 2 0 2579 2622 8346549 8346506 1.460000e-08 71.3
17 TraesCS2D01G410800 chr1B 100.000 52 0 0 1 52 518903209 518903260 2.400000e-16 97.1
18 TraesCS2D01G410800 chr1B 94.737 57 3 0 1 57 220821174 220821230 4.020000e-14 89.8
19 TraesCS2D01G410800 chr1B 82.278 79 10 3 171 245 259256525 259256603 6.780000e-07 65.8
20 TraesCS2D01G410800 chr1B 94.737 38 1 1 171 207 327476965 327476928 1.130000e-04 58.4
21 TraesCS2D01G410800 chr5B 98.113 53 1 0 1 53 546304425 546304477 3.110000e-15 93.5
22 TraesCS2D01G410800 chr5B 89.552 67 7 0 1 67 614829117 614829183 5.200000e-13 86.1
23 TraesCS2D01G410800 chr5D 98.113 53 0 1 1 52 564666402 564666454 1.120000e-14 91.6
24 TraesCS2D01G410800 chr1D 94.915 59 1 2 1 58 162069710 162069653 1.120000e-14 91.6
25 TraesCS2D01G410800 chr3D 93.333 60 2 1 1 60 425122794 425122737 1.450000e-13 87.9
26 TraesCS2D01G410800 chr4D 90.196 51 5 0 2572 2622 138259178 138259128 1.880000e-07 67.6
27 TraesCS2D01G410800 chr4A 93.333 45 3 0 2579 2623 165711899 165711855 1.880000e-07 67.6
28 TraesCS2D01G410800 chr1A 91.667 48 3 1 2576 2622 13315352 13315399 6.780000e-07 65.8
29 TraesCS2D01G410800 chr3B 97.297 37 1 0 2579 2615 679626428 679626464 2.440000e-06 63.9
30 TraesCS2D01G410800 chr7B 86.207 58 7 1 2576 2633 662010939 662010995 8.760000e-06 62.1


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 TraesCS2D01G410800 chr2D 525697379 525700307 2928 True 5409.000000 5409 100.000000 1 2929 1 chr2D.!!$R2 2928
1 TraesCS2D01G410800 chr2A 670880155 670882967 2812 False 2004.000000 3618 91.944500 47 2929 2 chr2A.!!$F1 2882
2 TraesCS2D01G410800 chr2B 621774181 621777031 2850 False 1345.333333 2073 93.174667 44 2929 3 chr2B.!!$F1 2885

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
708 742 0.605319 TTCACGGCGGCTTGAATCTT 60.605 50.0 24.14 0.0 0.0 2.40 F
1724 1840 0.248289 TTGTAGCCAAGGTCGGTAGC 59.752 55.0 0.00 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2006 0.535102 ACCGGCACAAGAGAACAAGG 60.535 55.0 0.0 0.0 0.0 3.61 R
2806 2947 3.195661 GCACTATTAGTTCCCGGTCTTG 58.804 50.0 0.0 0.0 0.0 3.02 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
25 26 7.461182 TTCAATACACCAAAATCACTAAGGG 57.539 36.000 0.00 0.00 0.00 3.95
26 27 5.949354 TCAATACACCAAAATCACTAAGGGG 59.051 40.000 0.00 0.00 0.00 4.79
27 28 2.525368 ACACCAAAATCACTAAGGGGC 58.475 47.619 0.00 0.00 0.00 5.80
28 29 2.158385 ACACCAAAATCACTAAGGGGCA 60.158 45.455 0.00 0.00 0.00 5.36
29 30 2.231235 CACCAAAATCACTAAGGGGCAC 59.769 50.000 0.00 0.00 0.00 5.01
30 31 2.110011 ACCAAAATCACTAAGGGGCACT 59.890 45.455 0.00 0.00 0.00 4.40
31 32 3.332485 ACCAAAATCACTAAGGGGCACTA 59.668 43.478 0.00 0.00 0.00 2.74
32 33 3.947834 CCAAAATCACTAAGGGGCACTAG 59.052 47.826 0.00 0.00 0.00 2.57
33 34 4.324254 CCAAAATCACTAAGGGGCACTAGA 60.324 45.833 0.00 0.00 0.00 2.43
34 35 5.440610 CAAAATCACTAAGGGGCACTAGAT 58.559 41.667 0.00 0.00 0.00 1.98
35 36 4.696479 AATCACTAAGGGGCACTAGATG 57.304 45.455 0.00 0.00 0.00 2.90
93 94 3.892918 ATATACGCACGTACACTCTCC 57.107 47.619 4.84 0.00 33.01 3.71
111 112 3.445805 TCTCCTGTATGAACGCACACATA 59.554 43.478 0.00 0.00 29.83 2.29
118 119 1.202592 TGAACGCACACATACACACCT 60.203 47.619 0.00 0.00 0.00 4.00
138 139 1.015609 TATCCCTGTGAGGACCTCCA 58.984 55.000 19.11 14.43 39.24 3.86
141 142 0.838122 CCCTGTGAGGACCTCCAAGT 60.838 60.000 19.11 0.00 37.67 3.16
183 209 6.198650 TCTTATGATTTAGTCGACGGAACA 57.801 37.500 10.46 8.71 0.00 3.18
188 214 5.100259 TGATTTAGTCGACGGAACATCTTC 58.900 41.667 10.46 4.15 0.00 2.87
209 235 1.352017 TCCCACTGAATGCACATCACT 59.648 47.619 0.00 0.00 0.00 3.41
245 271 4.717233 AAATCCAATAAATGCGAGCACA 57.283 36.364 0.00 0.00 0.00 4.57
317 343 1.613437 CATCCAACCGAACCTTGCTTT 59.387 47.619 0.00 0.00 0.00 3.51
471 497 4.032900 GTGCACGGTTCATCTATACAACAG 59.967 45.833 0.00 0.00 0.00 3.16
473 499 4.433615 CACGGTTCATCTATACAACAGCT 58.566 43.478 0.00 0.00 0.00 4.24
526 552 2.719426 ACGCAGTGTCCACTAGTAAC 57.281 50.000 0.00 0.00 42.51 2.50
569 596 2.900122 ATCAATCGTTCGGCAGTTTG 57.100 45.000 0.00 0.00 0.00 2.93
624 651 0.964358 AAAGACGTCGACCCGGAGAT 60.964 55.000 10.58 0.00 0.00 2.75
644 671 5.303971 AGATATTCATGTGTAGCTTCAGCC 58.696 41.667 0.00 0.00 43.38 4.85
663 697 1.026718 CCACCCAGCATCCGTTTCTC 61.027 60.000 0.00 0.00 0.00 2.87
692 726 4.787551 TGGACTTGGCTAGAAGTTTTTCA 58.212 39.130 2.20 0.00 36.27 2.69
698 732 1.136057 GCTAGAAGTTTTTCACGGCGG 60.136 52.381 13.24 0.00 35.70 6.13
708 742 0.605319 TTCACGGCGGCTTGAATCTT 60.605 50.000 24.14 0.00 0.00 2.40
713 747 1.382522 GGCGGCTTGAATCTTGATCA 58.617 50.000 0.00 0.00 0.00 2.92
717 751 3.208594 CGGCTTGAATCTTGATCATGGA 58.791 45.455 8.60 5.23 0.00 3.41
786 824 6.337356 GGTAGATCTATCTAGCCAATTCAGC 58.663 44.000 15.26 0.00 46.71 4.26
787 825 6.071108 GGTAGATCTATCTAGCCAATTCAGCA 60.071 42.308 15.26 0.00 46.71 4.41
788 826 6.430962 AGATCTATCTAGCCAATTCAGCAA 57.569 37.500 0.00 0.00 34.85 3.91
789 827 7.018487 AGATCTATCTAGCCAATTCAGCAAT 57.982 36.000 0.00 0.00 34.85 3.56
790 828 7.460071 AGATCTATCTAGCCAATTCAGCAATT 58.540 34.615 0.00 0.00 34.85 2.32
791 829 7.607223 AGATCTATCTAGCCAATTCAGCAATTC 59.393 37.037 0.00 0.00 34.85 2.17
792 830 6.594744 TCTATCTAGCCAATTCAGCAATTCA 58.405 36.000 0.15 0.00 28.97 2.57
802 840 1.068402 TCAGCAATTCACCGTGCAATG 60.068 47.619 0.00 0.00 43.42 2.82
978 1016 1.062428 CCCTACATGTCCACCCCTCTA 60.062 57.143 0.00 0.00 0.00 2.43
1282 1396 3.762823 AGTGACCAACCACTAGCTAGTAC 59.237 47.826 25.63 16.87 44.82 2.73
1291 1405 6.636562 ACCACTAGCTAGTACATGTATGTC 57.363 41.667 25.63 0.00 41.97 3.06
1309 1423 6.980978 TGTATGTCTTCTAGCTAATCTTGCAC 59.019 38.462 0.00 0.00 0.00 4.57
1315 1429 7.858879 GTCTTCTAGCTAATCTTGCACTAGTAC 59.141 40.741 0.00 0.00 33.59 2.73
1316 1430 7.556635 TCTTCTAGCTAATCTTGCACTAGTACA 59.443 37.037 0.00 0.00 33.59 2.90
1317 1431 7.825331 TCTAGCTAATCTTGCACTAGTACAT 57.175 36.000 0.00 0.00 33.59 2.29
1318 1432 7.877003 TCTAGCTAATCTTGCACTAGTACATC 58.123 38.462 0.00 0.00 33.59 3.06
1319 1433 5.524284 AGCTAATCTTGCACTAGTACATCG 58.476 41.667 0.00 0.00 0.00 3.84
1342 1458 3.664107 TCTTTCTCATATATGCGGTGCC 58.336 45.455 7.92 0.00 0.00 5.01
1433 1549 2.673341 TGCCTCAGCGACGTCTCT 60.673 61.111 14.70 8.35 44.31 3.10
1463 1579 1.448922 GGAGGAGCGCGTCTACATCT 61.449 60.000 8.43 0.00 0.00 2.90
1486 1602 4.704833 GCAGCAGGCCTCCGTCAA 62.705 66.667 0.00 0.00 36.11 3.18
1497 1613 0.530744 CTCCGTCAACCAGGATTCGA 59.469 55.000 0.00 0.00 35.75 3.71
1631 1747 6.491403 AGGACGTCCTTTGTTAGAAACTAGTA 59.509 38.462 31.69 0.00 46.09 1.82
1632 1748 6.805760 GGACGTCCTTTGTTAGAAACTAGTAG 59.194 42.308 27.64 0.00 0.00 2.57
1633 1749 7.282332 ACGTCCTTTGTTAGAAACTAGTAGT 57.718 36.000 0.00 0.00 0.00 2.73
1634 1750 7.720442 ACGTCCTTTGTTAGAAACTAGTAGTT 58.280 34.615 9.85 9.85 40.80 2.24
1635 1751 7.650903 ACGTCCTTTGTTAGAAACTAGTAGTTG 59.349 37.037 16.22 0.85 38.66 3.16
1724 1840 0.248289 TTGTAGCCAAGGTCGGTAGC 59.752 55.000 0.00 0.00 0.00 3.58
1725 1841 0.613853 TGTAGCCAAGGTCGGTAGCT 60.614 55.000 0.00 0.00 37.58 3.32
1726 1842 1.341285 TGTAGCCAAGGTCGGTAGCTA 60.341 52.381 0.00 0.00 35.03 3.32
1738 1854 9.570488 CAAGGTCGGTAGCTATATATTAGTTTC 57.430 37.037 0.00 0.00 31.75 2.78
1760 1876 8.376203 GTTTCATCGATGTGCATATATGAGTAC 58.624 37.037 24.09 11.53 0.00 2.73
1890 2006 5.035443 CACAGTTTATCTAGCACGTACTCC 58.965 45.833 0.00 0.00 0.00 3.85
1992 2108 4.095610 GCATGTTACGTGATTACTTTGCC 58.904 43.478 8.96 0.00 0.00 4.52
2009 2125 1.000955 TGCCGTCCTCTTCTCAACTTC 59.999 52.381 0.00 0.00 0.00 3.01
2046 2162 0.383983 GCATCGTGCATGAATCGAGC 60.384 55.000 13.65 8.57 44.26 5.03
2074 2190 0.452618 CAACGAAGTCGCCGTACGTA 60.453 55.000 15.21 0.00 45.00 3.57
2437 2566 0.872388 GGTTAATTATCCCGCGCCTG 59.128 55.000 0.00 0.00 0.00 4.85
2492 2621 6.761714 CGTTAATTAGCCTCCAAATCTACACT 59.238 38.462 0.00 0.00 0.00 3.55
2577 2709 6.436532 TCACTCTTCTCCTCCTTTTATACGTT 59.563 38.462 0.00 0.00 0.00 3.99
2579 2711 6.664384 ACTCTTCTCCTCCTTTTATACGTTCT 59.336 38.462 0.00 0.00 0.00 3.01
2580 2712 7.098074 TCTTCTCCTCCTTTTATACGTTCTC 57.902 40.000 0.00 0.00 0.00 2.87
2581 2713 5.848833 TCTCCTCCTTTTATACGTTCTCC 57.151 43.478 0.00 0.00 0.00 3.71
2582 2714 4.648307 TCTCCTCCTTTTATACGTTCTCCC 59.352 45.833 0.00 0.00 0.00 4.30
2583 2715 4.617593 TCCTCCTTTTATACGTTCTCCCT 58.382 43.478 0.00 0.00 0.00 4.20
2584 2716 5.769835 TCCTCCTTTTATACGTTCTCCCTA 58.230 41.667 0.00 0.00 0.00 3.53
2585 2717 6.379579 TCCTCCTTTTATACGTTCTCCCTAT 58.620 40.000 0.00 0.00 0.00 2.57
2586 2718 6.267014 TCCTCCTTTTATACGTTCTCCCTATG 59.733 42.308 0.00 0.00 0.00 2.23
2587 2719 6.041751 CCTCCTTTTATACGTTCTCCCTATGT 59.958 42.308 0.00 0.00 0.00 2.29
2588 2720 7.232127 CCTCCTTTTATACGTTCTCCCTATGTA 59.768 40.741 0.00 0.00 0.00 2.29
2589 2721 8.537728 TCCTTTTATACGTTCTCCCTATGTAA 57.462 34.615 0.00 0.00 0.00 2.41
2590 2722 8.980596 TCCTTTTATACGTTCTCCCTATGTAAA 58.019 33.333 0.00 0.00 0.00 2.01
2591 2723 9.257651 CCTTTTATACGTTCTCCCTATGTAAAG 57.742 37.037 0.00 0.00 0.00 1.85
2605 2737 9.841295 TCCCTATGTAAAGAAATATAAAAGCGT 57.159 29.630 0.00 0.00 0.00 5.07
2616 2748 9.391006 AGAAATATAAAAGCGTTTAGATCACCA 57.609 29.630 11.74 0.00 31.44 4.17
2620 2752 9.998106 ATATAAAAGCGTTTAGATCACCATAGT 57.002 29.630 10.55 0.00 32.76 2.12
2622 2754 7.535489 AAAAGCGTTTAGATCACCATAGTAC 57.465 36.000 0.00 0.00 0.00 2.73
2623 2755 5.847111 AGCGTTTAGATCACCATAGTACA 57.153 39.130 0.00 0.00 0.00 2.90
2624 2756 5.833082 AGCGTTTAGATCACCATAGTACAG 58.167 41.667 0.00 0.00 0.00 2.74
2625 2757 5.593095 AGCGTTTAGATCACCATAGTACAGA 59.407 40.000 0.00 0.00 0.00 3.41
2626 2758 5.915758 GCGTTTAGATCACCATAGTACAGAG 59.084 44.000 0.00 0.00 0.00 3.35
2627 2759 6.439599 CGTTTAGATCACCATAGTACAGAGG 58.560 44.000 0.00 0.00 0.00 3.69
2628 2760 6.515200 CGTTTAGATCACCATAGTACAGAGGG 60.515 46.154 0.00 0.00 0.00 4.30
2629 2761 4.816048 AGATCACCATAGTACAGAGGGA 57.184 45.455 5.59 0.00 0.00 4.20
2630 2762 4.735369 AGATCACCATAGTACAGAGGGAG 58.265 47.826 5.59 0.00 0.00 4.30
2631 2763 4.169068 AGATCACCATAGTACAGAGGGAGT 59.831 45.833 5.59 0.00 0.00 3.85
2632 2764 5.372959 AGATCACCATAGTACAGAGGGAGTA 59.627 44.000 5.59 0.00 0.00 2.59
2633 2765 4.789807 TCACCATAGTACAGAGGGAGTAC 58.210 47.826 5.59 0.00 41.59 2.73
2806 2947 0.321298 TTAAGCCGGCCTCAACTGTC 60.321 55.000 26.15 0.00 0.00 3.51
2818 2959 1.202604 TCAACTGTCAAGACCGGGAAC 60.203 52.381 6.32 0.00 0.00 3.62
2850 2991 1.463831 ACTACGTAGACGAGCACACAG 59.536 52.381 28.74 0.17 43.02 3.66
2852 2993 1.801913 CGTAGACGAGCACACAGGC 60.802 63.158 0.00 0.00 43.02 4.85
2913 3054 1.507562 CTACCGTGCATGTGTGAACA 58.492 50.000 4.96 0.00 33.05 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.362920 CCCCTTAGTGATTTTGGTGTATTGAAG 60.363 40.741 0.00 0.00 0.00 3.02
1 2 6.435904 CCCCTTAGTGATTTTGGTGTATTGAA 59.564 38.462 0.00 0.00 0.00 2.69
2 3 5.949354 CCCCTTAGTGATTTTGGTGTATTGA 59.051 40.000 0.00 0.00 0.00 2.57
3 4 5.394115 GCCCCTTAGTGATTTTGGTGTATTG 60.394 44.000 0.00 0.00 0.00 1.90
4 5 4.709886 GCCCCTTAGTGATTTTGGTGTATT 59.290 41.667 0.00 0.00 0.00 1.89
5 6 4.264172 TGCCCCTTAGTGATTTTGGTGTAT 60.264 41.667 0.00 0.00 0.00 2.29
6 7 3.074687 TGCCCCTTAGTGATTTTGGTGTA 59.925 43.478 0.00 0.00 0.00 2.90
7 8 2.158385 TGCCCCTTAGTGATTTTGGTGT 60.158 45.455 0.00 0.00 0.00 4.16
8 9 2.231235 GTGCCCCTTAGTGATTTTGGTG 59.769 50.000 0.00 0.00 0.00 4.17
9 10 2.110011 AGTGCCCCTTAGTGATTTTGGT 59.890 45.455 0.00 0.00 0.00 3.67
10 11 2.807676 AGTGCCCCTTAGTGATTTTGG 58.192 47.619 0.00 0.00 0.00 3.28
11 12 4.843728 TCTAGTGCCCCTTAGTGATTTTG 58.156 43.478 0.00 0.00 0.00 2.44
12 13 5.440610 CATCTAGTGCCCCTTAGTGATTTT 58.559 41.667 0.00 0.00 0.00 1.82
13 14 5.041191 CATCTAGTGCCCCTTAGTGATTT 57.959 43.478 0.00 0.00 0.00 2.17
14 15 4.696479 CATCTAGTGCCCCTTAGTGATT 57.304 45.455 0.00 0.00 0.00 2.57
58 59 7.095102 ACGTGCGTATATATGAGTGTATGTGTA 60.095 37.037 6.12 0.00 0.00 2.90
111 112 1.909302 CCTCACAGGGATAAGGTGTGT 59.091 52.381 1.93 0.00 41.91 3.72
118 119 1.364678 TGGAGGTCCTCACAGGGATAA 59.635 52.381 20.72 0.00 37.73 1.75
138 139 0.546122 TTGTGTCAGCCCAGTCACTT 59.454 50.000 0.00 0.00 0.00 3.16
141 142 0.473755 ATGTTGTGTCAGCCCAGTCA 59.526 50.000 0.00 0.00 0.00 3.41
183 209 2.306805 TGTGCATTCAGTGGGAGAAGAT 59.693 45.455 0.00 0.00 0.00 2.40
188 214 1.741706 GTGATGTGCATTCAGTGGGAG 59.258 52.381 2.81 0.00 0.00 4.30
245 271 2.158143 AGGGTTCAACTCCTAGACACCT 60.158 50.000 0.00 0.00 0.00 4.00
471 497 1.007849 GCTGCTAGCTAGTCCGAGC 60.008 63.158 21.62 18.10 43.19 5.03
526 552 4.158384 GGCATGTGAAATGAAACGTACAG 58.842 43.478 0.00 0.00 0.00 2.74
624 651 3.199727 TGGGCTGAAGCTACACATGAATA 59.800 43.478 0.00 0.00 41.70 1.75
644 671 1.002134 AGAAACGGATGCTGGGTGG 60.002 57.895 0.00 0.00 0.00 4.61
663 697 3.685139 TCTAGCCAAGTCCAGTTGAAG 57.315 47.619 0.00 0.00 0.00 3.02
692 726 0.392998 ATCAAGATTCAAGCCGCCGT 60.393 50.000 0.00 0.00 0.00 5.68
698 732 4.608951 GCTTCCATGATCAAGATTCAAGC 58.391 43.478 0.00 4.62 0.00 4.01
708 742 1.451927 GCCACCGCTTCCATGATCA 60.452 57.895 0.00 0.00 0.00 2.92
713 747 3.064324 GCTTGCCACCGCTTCCAT 61.064 61.111 0.00 0.00 35.36 3.41
717 751 3.289834 CAGTGCTTGCCACCGCTT 61.290 61.111 0.00 0.00 45.83 4.68
785 823 1.199789 TCTCATTGCACGGTGAATTGC 59.800 47.619 13.29 0.00 39.33 3.56
786 824 3.557577 TTCTCATTGCACGGTGAATTG 57.442 42.857 13.29 8.50 0.00 2.32
787 825 4.789012 AATTCTCATTGCACGGTGAATT 57.211 36.364 13.29 15.64 34.31 2.17
788 826 4.789012 AAATTCTCATTGCACGGTGAAT 57.211 36.364 13.29 6.19 0.00 2.57
789 827 4.582701 AAAATTCTCATTGCACGGTGAA 57.417 36.364 13.29 0.00 0.00 3.18
790 828 4.582701 AAAAATTCTCATTGCACGGTGA 57.417 36.364 13.29 0.00 0.00 4.02
899 937 2.381961 AGAGAGAGAAAGGTGGAGAGGT 59.618 50.000 0.00 0.00 0.00 3.85
940 978 1.920835 GGTGAGGGCTGAAGAGGGT 60.921 63.158 0.00 0.00 0.00 4.34
1209 1275 2.543067 ATCAAGAAGTGGCGGAGGGC 62.543 60.000 0.00 0.00 42.51 5.19
1210 1276 0.830648 TATCAAGAAGTGGCGGAGGG 59.169 55.000 0.00 0.00 0.00 4.30
1262 1328 3.770046 TGTACTAGCTAGTGGTTGGTCA 58.230 45.455 32.21 17.05 37.10 4.02
1265 1331 4.737855 ACATGTACTAGCTAGTGGTTGG 57.262 45.455 32.21 20.21 37.10 3.77
1269 1383 6.885952 AGACATACATGTACTAGCTAGTGG 57.114 41.667 32.21 21.11 41.95 4.00
1282 1396 7.654923 TGCAAGATTAGCTAGAAGACATACATG 59.345 37.037 0.00 0.00 0.00 3.21
1291 1405 7.708051 TGTACTAGTGCAAGATTAGCTAGAAG 58.292 38.462 11.58 0.00 34.77 2.85
1315 1429 6.020041 CACCGCATATATGAGAAAGATCGATG 60.020 42.308 17.10 1.30 0.00 3.84
1316 1430 6.038985 CACCGCATATATGAGAAAGATCGAT 58.961 40.000 17.10 0.00 0.00 3.59
1317 1431 5.402398 CACCGCATATATGAGAAAGATCGA 58.598 41.667 17.10 0.00 0.00 3.59
1318 1432 4.032217 GCACCGCATATATGAGAAAGATCG 59.968 45.833 17.10 7.41 0.00 3.69
1319 1433 4.331168 GGCACCGCATATATGAGAAAGATC 59.669 45.833 17.10 0.00 0.00 2.75
1433 1549 2.285668 CTCCTCCTGGCCTTCCCA 60.286 66.667 3.32 0.00 42.79 4.37
1463 1579 4.039092 GAGGCCTGCTGCTTCCCA 62.039 66.667 12.00 0.00 40.05 4.37
1486 1602 4.107029 TCGTGGTCGAATCCTGGT 57.893 55.556 0.00 0.00 43.34 4.00
1497 1613 3.066814 GGAGTAGCCCGTCGTGGT 61.067 66.667 0.00 0.00 35.15 4.16
1631 1747 1.026718 GCAAGATGGCGCCTACAACT 61.027 55.000 29.70 15.77 0.00 3.16
1632 1748 1.305219 TGCAAGATGGCGCCTACAAC 61.305 55.000 29.70 13.22 36.28 3.32
1633 1749 1.002746 TGCAAGATGGCGCCTACAA 60.003 52.632 29.70 7.47 36.28 2.41
1634 1750 1.450134 CTGCAAGATGGCGCCTACA 60.450 57.895 29.70 14.78 34.07 2.74
1635 1751 2.182842 CCTGCAAGATGGCGCCTAC 61.183 63.158 29.70 20.74 34.07 3.18
1738 1854 7.031975 ACAGTACTCATATATGCACATCGATG 58.968 38.462 23.68 23.68 0.00 3.84
1760 1876 9.624697 AACACATAAGCAAACAAACATATACAG 57.375 29.630 0.00 0.00 0.00 2.74
1890 2006 0.535102 ACCGGCACAAGAGAACAAGG 60.535 55.000 0.00 0.00 0.00 3.61
1992 2108 2.708386 ACGAAGTTGAGAAGAGGACG 57.292 50.000 0.00 0.00 37.78 4.79
2009 2125 3.579147 TGCACGAGTGTTTTAAGAACG 57.421 42.857 5.07 0.00 0.00 3.95
2046 2162 1.058695 GCGACTTCGTTGTCATTACCG 59.941 52.381 0.00 0.00 42.22 4.02
2074 2190 6.718593 TCCTTAATTCCCCATATGTATGCT 57.281 37.500 1.24 0.00 32.40 3.79
2248 2377 2.926420 GCTAGCTAGCTCCGGCCTC 61.926 68.421 33.71 6.02 45.62 4.70
2249 2378 2.915137 GCTAGCTAGCTCCGGCCT 60.915 66.667 33.71 0.00 45.62 5.19
2579 2711 9.841295 ACGCTTTTATATTTCTTTACATAGGGA 57.159 29.630 0.00 0.00 0.00 4.20
2590 2722 9.391006 TGGTGATCTAAACGCTTTTATATTTCT 57.609 29.630 0.00 0.00 0.00 2.52
2594 2726 9.998106 ACTATGGTGATCTAAACGCTTTTATAT 57.002 29.630 0.00 0.00 0.00 0.86
2596 2728 9.257651 GTACTATGGTGATCTAAACGCTTTTAT 57.742 33.333 0.00 0.00 0.00 1.40
2597 2729 8.252417 TGTACTATGGTGATCTAAACGCTTTTA 58.748 33.333 0.00 0.00 0.00 1.52
2598 2730 7.101054 TGTACTATGGTGATCTAAACGCTTTT 58.899 34.615 0.00 0.00 0.00 2.27
2599 2731 6.636705 TGTACTATGGTGATCTAAACGCTTT 58.363 36.000 0.00 0.00 0.00 3.51
2600 2732 6.096423 TCTGTACTATGGTGATCTAAACGCTT 59.904 38.462 0.00 0.00 0.00 4.68
2601 2733 5.593095 TCTGTACTATGGTGATCTAAACGCT 59.407 40.000 0.00 0.00 0.00 5.07
2602 2734 5.828747 TCTGTACTATGGTGATCTAAACGC 58.171 41.667 0.00 0.00 0.00 4.84
2603 2735 6.439599 CCTCTGTACTATGGTGATCTAAACG 58.560 44.000 0.00 0.00 0.00 3.60
2604 2736 6.550108 TCCCTCTGTACTATGGTGATCTAAAC 59.450 42.308 0.00 0.00 0.00 2.01
2605 2737 6.679542 TCCCTCTGTACTATGGTGATCTAAA 58.320 40.000 0.00 0.00 0.00 1.85
2606 2738 6.126156 ACTCCCTCTGTACTATGGTGATCTAA 60.126 42.308 0.00 0.00 0.00 2.10
2607 2739 5.372959 ACTCCCTCTGTACTATGGTGATCTA 59.627 44.000 0.00 0.00 0.00 1.98
2608 2740 4.169068 ACTCCCTCTGTACTATGGTGATCT 59.831 45.833 0.00 0.00 0.00 2.75
2609 2741 4.475345 ACTCCCTCTGTACTATGGTGATC 58.525 47.826 0.00 0.00 0.00 2.92
2610 2742 4.544564 ACTCCCTCTGTACTATGGTGAT 57.455 45.455 0.00 0.00 0.00 3.06
2611 2743 4.477581 AGTACTCCCTCTGTACTATGGTGA 59.522 45.833 4.94 0.00 45.86 4.02
2612 2744 4.794334 AGTACTCCCTCTGTACTATGGTG 58.206 47.826 4.94 0.00 45.86 4.17
2613 2745 6.587560 TTAGTACTCCCTCTGTACTATGGT 57.412 41.667 0.00 0.00 46.39 3.55
2614 2746 7.463431 AGATTAGTACTCCCTCTGTACTATGG 58.537 42.308 0.00 0.00 46.39 2.74
2615 2747 8.927675 AAGATTAGTACTCCCTCTGTACTATG 57.072 38.462 0.00 0.00 46.39 2.23
2619 2751 9.577222 AGATTAAGATTAGTACTCCCTCTGTAC 57.423 37.037 0.00 0.00 40.19 2.90
2621 2753 8.919145 CAAGATTAAGATTAGTACTCCCTCTGT 58.081 37.037 0.00 0.00 0.00 3.41
2622 2754 8.919145 ACAAGATTAAGATTAGTACTCCCTCTG 58.081 37.037 0.00 0.00 0.00 3.35
2623 2755 9.495382 AACAAGATTAAGATTAGTACTCCCTCT 57.505 33.333 0.00 0.00 0.00 3.69
2624 2756 9.752961 GAACAAGATTAAGATTAGTACTCCCTC 57.247 37.037 0.00 0.00 0.00 4.30
2625 2757 8.414778 CGAACAAGATTAAGATTAGTACTCCCT 58.585 37.037 0.00 0.00 0.00 4.20
2626 2758 8.411683 TCGAACAAGATTAAGATTAGTACTCCC 58.588 37.037 0.00 0.00 0.00 4.30
2627 2759 9.968870 ATCGAACAAGATTAAGATTAGTACTCC 57.031 33.333 0.00 0.00 0.00 3.85
2632 2764 9.167311 AGCAAATCGAACAAGATTAAGATTAGT 57.833 29.630 0.00 0.00 39.69 2.24
2633 2765 9.643652 GAGCAAATCGAACAAGATTAAGATTAG 57.356 33.333 0.00 0.00 39.69 1.73
2806 2947 3.195661 GCACTATTAGTTCCCGGTCTTG 58.804 50.000 0.00 0.00 0.00 3.02
2818 2959 4.209870 GTCTACGTAGTGCGCACTATTAG 58.790 47.826 42.93 38.64 44.73 1.73


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

AutoCloner maintained by Alex Coulton.