Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002038.1 Hibiscus syriacus cultivar Beakdansim tig00004157_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56332
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3324 original size:14 final size:15
Alignment explanation
Indices: 3292--3326 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3282 ATTATTCAAA
*
3292 TTGAATTATTTTATT
1 TTGAATTATTATATT
3307 TTGAATTATTAT-TT
1 TTGAATTATTATATT
3321 TTGAAT
1 TTGAAT
3327 CACTCATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (15 bp):
TTGAATTATTATATT
Found at i:13161 original size:55 final size:55
Alignment explanation
Indices: 12409--13175 Score: 1282
Period size: 55 Copynumber: 13.9 Consensus size: 55
12399 GCATACCTAA
* * *
12409 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
12464 TGCCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
12519 TGCCCATACGAAAATTCATAAACTTACTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
12574 TGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
12629 TGCCCATACGGAAATTCATTAACTTATTATGATTTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
12684 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
** *
12739 TGCCCATACAAAAATTCATAAACTTATTATTAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
12794 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
12849 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACATACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
** * * *
12904 TGCCCATACAAAAATTCATTAACTTATTATGAATTTCTTAGTTTTGCACATACAA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * *
12959 TTCCCATACTGAAATTCATAAACTTATTATGAATTTCTTTGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * *
13014 TGCCTATACGGATATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACGG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
13069 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACATACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
13124 TGCCCATACGGAAATTCATAAACTTATTATGAGTTTCTTAGTTTTGCACACA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
13176 TATAGTGCCA
Statistics
Matches: 667, Mismatches: 45, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 667 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (55 bp):
TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
Found at i:14442 original size:21 final size:22
Alignment explanation
Indices: 14401--14455 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
14391 ATACTTAAGA
*
14401 AAGTATCGATACCTCATACTAT
1 AAGTATCGATACCTCAAACTAT
14423 AAGTATCGATA-CTCAAACTA-
1 AAGTATCGATACCTCAAACTAT
* *
14443 GAGTATTGATACC
1 AAGTATCGATACC
14456 ATCCCCTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 9 0.31
22 11 0.38
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (22 bp):
AAGTATCGATACCTCAAACTAT
Found at i:25706 original size:184 final size:185
Alignment explanation
Indices: 25391--25743 Score: 480
Period size: 184 Copynumber: 1.9 Consensus size: 185
25381 TAACGTTTAA
* *
25391 TGATCAAATCTTAATAAAACGATAATATAAATGACCAAAACTTATGGTTTTTTAATCGAGTGACT
1 TGATCAAATCTTAATAAAACGATAACATAAATGACCAAAACTTATAGTTTTTTAATCGAGTGACT
* * * *
25456 ATACGTTTATAAAACTGAAGCAAAAATGACCAAATAAGTAATTTACCCTTCCAAGTCAGCTCAAC
66 ATACGTTTATAAAACTAAAACAAAAATGACCAAATAAGTAATTTACCCTTCCAAGCCAGATCAAC
* *
25521 -A-A-AGTGGTTTAATGTTATGACCAAATCTTATTTCTCGACACCTAACGCTCAG
131 AATATAGTGGTATAATGTGATGACCAAATCTTATTTCTCGACACCTAACGCTCAG
* * * * *
25573 TGATCAAATCTTAATAAAACGATAACATAAATTACCAAAATTTTATATTTTTTTGAATTGAGTGG
1 TGATCAAATCTTAATAAAACGATAACATAAATGACCAAAA-CTTATAGTTTTTT-AATCGAGTGA
* * *
25638 CTATACGTTTATAAAACTAAAACAAAAATGATCAAATACA-TAGTTTACCCTTCTAAGCCAGATC
64 CTATACGTTTATAAAACTAAAACAAAAATGACCAAATA-AGTAATTTACCCTTCCAAGCCAGATC
25702 AACAAATAGTTAGTGGTATAATGTGATGACCAAATCTTATTT
128 AAC-AATA--TAGTGGTATAATGTGATGACCAAATCTTATTT
25744 AAATTAAAAC
Statistics
Matches: 146, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
182 38 0.26
183 10 0.07
184 66 0.45
185 1 0.01
186 1 0.01
187 1 0.01
190 29 0.20
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (185 bp):
TGATCAAATCTTAATAAAACGATAACATAAATGACCAAAACTTATAGTTTTTTAATCGAGTGACT
ATACGTTTATAAAACTAAAACAAAAATGACCAAATAAGTAATTTACCCTTCCAAGCCAGATCAAC
AATATAGTGGTATAATGTGATGACCAAATCTTATTTCTCGACACCTAACGCTCAG
Found at i:29454 original size:31 final size:31
Alignment explanation
Indices: 29419--29486 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
29409 TGATTTATAG
*
29419 ATTTTGTAAATTCAATTCAAGTCCAAAAACT
1 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
29450 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
1 ATTTTGTAAATTCAATTCAAGTCCAAAAACC
29481 ATTTTG
1 ATTTTG
29487 CCTTAAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTTGTAAATTCAATTCAAGTCCAAAAACC
Found at i:29844 original size:21 final size:21
Alignment explanation
Indices: 29820--29873 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
29810 TATCGCAAAT
29820 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
29841 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
29862 TCGCGTTGCGAT
1 TCGCGTTGCGAT
29874 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:29887 original size:20 final size:20
Alignment explanation
Indices: 29862--29933 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
29852 TAGTTGAAAA
29862 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
29882 TCGCGTTGTGATTTTTCGTT
1 TCGCGTTGCGATTTTCCATT
*
29902 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCATT
29922 TCGCGTTGCGAT
1 TCGCGTTGCGAT
29934 AGTCTACAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.08, C:0.22, G:0.25, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:29950 original size:22 final size:22
Alignment explanation
Indices: 29925--29996 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
29915 TTCCAGTTCG
29925 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * *
29947 CGTTGCGAT-TTTTGA-A-AT-T
1 CGTTGCGATAGTCT-ACAGTTGT
29966 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
29988 CGTTGCGAT
1 CGTTGCGAT
29997 TTTTGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:29970 original size:19 final size:19
Alignment explanation
Indices: 29946--30014 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
29936 TCTACAGTTG
29946 TCGTTGCGATTTTTGAAAT
1 TCGTTGCGATTTTTGAAAT
* * *
29965 TCGTTGCGATAGTCT-ACAGTT
1 TCGTTGCGAT-TTTTGA-A-AT
29986 GTCGTTGCGATTTTTGAAAT
1 -TCGTTGCGATTTTTGAAAT
30006 TCGTTGCGA
1 TCGTTGCGA
30015 AAATCGCGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 20 0.51
20 4 0.10
21 4 0.10
22 11 0.28
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTTGAAAT
Found at i:29977 original size:41 final size:41
Alignment explanation
Indices: 29925--30089 Score: 186
Period size: 41 Copynumber: 4.2 Consensus size: 41
29915 TTCCAGTTCG
*
29925 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTGAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
*
29966 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTGAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
* * *
30007 CGTTGCGA-A----A-A-TCG-CGTTGCGA-TTTTCCAGTT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
* *
30039 CGCGTTGCGATAGTCTGCAGTTGTCGTTGCGATTTTCCAAATT
1 --CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
30082 CGTTGCGA
1 CGTTGCGA
30090 AAATTCGTTG
Statistics
Matches: 104, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
32 7 0.07
33 8 0.08
34 10 0.10
35 2 0.02
36 1 0.01
40 2 0.02
41 59 0.57
42 8 0.08
43 7 0.07
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
Found at i:30043 original size:20 final size:20
Alignment explanation
Indices: 30018--30077 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
30008 GTTGCGAAAA
30018 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
30038 TCGCGTTGCGATAGTCTGCAGT
1 TCGCGTTGCGAT--TTTCCAGT
30060 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
30078 AATTCGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.12, C:0.23, G:0.27, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:30878 original size:22 final size:22
Alignment explanation
Indices: 30849--30941 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
30839 AATTTGGAAA
30849 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
30871 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
30893 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
30912 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
30933 ATCGCAACG
1 ATCGCAACG
30942 CGAAATGGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 13 0.23
22 27 0.48
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:30900 original size:19 final size:20
Alignment explanation
Indices: 30827--30941 Score: 72
Period size: 22 Copynumber: 5.6 Consensus size: 20
30817 TTTTTTTTTA
* *
30827 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
**
30846 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACG--AACTGTAG
* *
30868 ACTTTCGCAACAACAACTGTAG
1 ACTATCGCAAC--GAACTGTAG
* *
30890 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
** *
30909 AAAATCGCAACGACATTGTAG
1 ACTATCGCAACGA-ACTGTAG
30930 ACTATCGCAACG
1 ACTATCGCAACG
30942 CGAAATGGAA
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
19 24 0.34
20 3 0.04
21 15 0.21
22 29 0.41
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGAACTGTAG
Found at i:30917 original size:41 final size:40
Alignment explanation
Indices: 30872--30960 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
30862 CTGTAGACTT
*
30872 TCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAAA
1 TCGCAACAAC-ACTGTAGACTATCGCAACCGAA-ATGGAAAA
* *
30913 TCGCAACGACATTGTAGACTATCGCAACGCGAAATGGAAAA
1 TCGCAACAACACTGTAGACTATCGCAAC-CGAAATGGAAAA
30954 TCGCAAC
1 TCGCAAC
30961 GCGATTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 16 0.37
41 23 0.53
42 4 0.09
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (40 bp):
TCGCAACAACACTGTAGACTATCGCAACCGAAATGGAAAA
Found at i:30958 original size:20 final size:20
Alignment explanation
Indices: 30933--31018 Score: 102
Period size: 20 Copynumber: 4.2 Consensus size: 20
30923 ATTGTAGACT
30933 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
30953 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
30974 ATCGCAACGC-AACATGGAAA
1 ATCGCAACGCGAA-ATGGAAA
30994 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
31014 ATCGC
1 ATCGC
31019 GATCGCAACG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:30975 original size:41 final size:42
Alignment explanation
Indices: 30885--31005 Score: 155
Period size: 41 Copynumber: 3.0 Consensus size: 42
30875 CAACAACAAC
**
30885 TGTAGACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-AT
1 TGTAGACTATCGCAACGCGAACATGGAAAATCGCAACG-CGAT
30925 TGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAACGCGAT
1 TGTAGACTATCGCAACGCGAACATGGAAAATCGCAACGCGAT
*
30966 TTTCA-ACTATCGCAACGC-AACATGGAAAATCGCAACGCGA
1 TGT-AGACTATCGCAACGCGAACATGGAAAATCGCAACGCGA
31006 AATGGAAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
40 18 0.24
41 51 0.69
42 5 0.07
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (42 bp):
TGTAGACTATCGCAACGCGAACATGGAAAATCGCAACGCGAT
Found at i:31026 original size:41 final size:41
Alignment explanation
Indices: 30933--31027 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
30923 ATTGTAGACT
** * *
30933 ATCGCAACGCGAA-ATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGC-AACATGGAAAATCGCAACGCGAAATGCAACA
*
30974 ATCGCAACGCAACATGGAAAATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCAACATGGAAAATCGCAACGCGAAATGCAACA
*
31014 ATCGCGATCGCAAC
1 ATCGC-AACGCAAC
31028 GCGAAATGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 7 0.15
41 39 0.85
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (41 bp):
ATCGCAACGCAACATGGAAAATCGCAACGCGAAATGCAACA
Found at i:32288 original size:2 final size:2
Alignment explanation
Indices: 32283--32341 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
32273 ATTTCGTGTG
32283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32325 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
32342 GAAACCAACG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33409 original size:3 final size:3
Alignment explanation
Indices: 33401--33444 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
33391 GAAATTAAAT
33401 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
33445 TTTTTGTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34357 original size:44 final size:45
Alignment explanation
Indices: 34308--34403 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 45
34298 TTTCCCGTTT
*
34308 TCTTTGCTTTTTCTTTTGA-TT-TTTTCTCTTTGCTTTTTATTT-GC
1 TCTTTGCTTTTTC-TTT-ACTTATTTTCTCTTTGCTTTTTATTTGGA
* *
34352 TCTTTGTTTTTTCTTTACTTATTTTCTCTTTGCTTTTTCTTTGGA
1 TCTTTGCTTTTTCTTTACTTATTTTCTCTTTGCTTTTTATTTGGA
34397 TCTTTGC
1 TCTTTGC
34404 ACTTGGCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
42 1 0.02
43 5 0.11
44 32 0.71
45 7 0.16
ACGTcount: A:0.05, C:0.17, G:0.09, T:0.69
Consensus pattern (45 bp):
TCTTTGCTTTTTCTTTACTTATTTTCTCTTTGCTTTTTATTTGGA
Found at i:34380 original size:26 final size:26
Alignment explanation
Indices: 34344--34393 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
34334 TCTTTGCTTT
*
34344 TTATTTGCTCTTTGTTTTTTCTTTAC
1 TTATTTGCTCTTTGCTTTTTCTTTAC
*
34370 TTATTTTCTCTTTGCTTTTTCTTT
1 TTATTTGCTCTTTGCTTTTTCTTT
34394 GGATCTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.72
Consensus pattern (26 bp):
TTATTTGCTCTTTGCTTTTTCTTTAC
Found at i:39035 original size:16 final size:16
Alignment explanation
Indices: 39014--39052 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
39004 GTAATCGTTC
39014 TATGGTTCACTATATG
1 TATGGTTCACTATATG
39030 TATGGTTCACTATATG
1 TATGGTTCACTATATG
*
39046 CATGGTT
1 TATGGTT
39053 TTGGCTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (16 bp):
TATGGTTCACTATATG
Found at i:42334 original size:12 final size:12
Alignment explanation
Indices: 42282--42334 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
42272 TGTAAATTAA
*
42282 AATA-TAATAAC
1 AATATTAATAAT
*
42293 AATAGTAATAAT
1 AATATTAATAAT
*
42305 AATATTAATATT
1 AATATTAATAAT
*
42317 ATTATTAATAAT
1 AATATTAATAAT
42329 AATATT
1 AATATT
42335 TTTGTAGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
11 4 0.11
12 31 0.89
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:51019 original size:22 final size:22
Alignment explanation
Indices: 50994--51052 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
50984 TTCATATTTG
*
50994 AAATTTTAATAAAAGATAT-ATT
1 AAATTTTAATAAAA-ATATCATA
* *
51016 AAATATTAAATTAAAATATCATA
1 AAAT-TTTAATAAAAATATCATA
51039 AATATTTTAATAAA
1 AA-ATTTTAATAAA
51053 TAAAAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 8 0.28
23 19 0.66
24 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATTTTAATAAAAATATCATA
Done.