Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004248.1 Hibiscus syriacus cultivar Beakdansim tig00009316_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: 135317
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9748 original size:27 final size:27
Alignment explanation
Indices: 9706--9761 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
9696 AGAGTCAATG
*
9706 TTCTCAACATCTTCAATTGTTGAAATC
1 TTCTCAACATCCTCAATTGTTGAAATC
9733 TTCTCAACATCCTCAATTGTTGAAATC
1 TTCTCAACATCCTCAATTGTTGAAATC
9760 TT
1 TT
9762 TGGCATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (27 bp):
TTCTCAACATCCTCAATTGTTGAAATC
Found at i:25628 original size:5 final size:5
Alignment explanation
Indices: 25604--25652 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
25594 GTACGCTCCC
* *
25604 TTTTCA TTTTA -TTCA TTTTA TTTTA --TTA TCTTA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
25652 T
1 T
25653 CTAATTATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
3 3 0.08
4 3 0.08
5 27 0.73
6 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:25628 original size:14 final size:13
Alignment explanation
Indices: 25604--25643 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
25594 GTACGCTCCC
25604 TTTTCATTTTATTCA
1 TTTT-ATTTTATT-A
25619 TTTTATTTTATTA
1 TTTTATTTTATTA
*
25632 TCTTATTTTATT
1 TTTTATTTTATT
25644 TTATTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 8 0.33
15 4 0.17
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:25639 original size:13 final size:14
Alignment explanation
Indices: 25609--25643 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
25599 CTCCCTTTTC
*
25609 ATTTTATTCATTTT
1 ATTTTATTCATCTT
25623 ATTTTATT-ATCTT
1 ATTTTATTCATCTT
25636 ATTTTATT
1 ATTTTATT
25644 TTATTTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTATTCATCTT
Found at i:25659 original size:28 final size:27
Alignment explanation
Indices: 25609--25663 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
25599 CTCCCTTTTC
* *
25609 ATTTTATTCATTTTATTTTATTATCTT
1 ATTTTATTCATTTTATCTAATTATCTT
*
25636 ATTTTATTTTATTTTATCTAATTATCTT
1 ATTTTA-TTCATTTTATCTAATTATCTT
25664 TGTCGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTATTCATTTTATCTAATTATCTT
Found at i:53999 original size:96 final size:96
Alignment explanation
Indices: 53815--54001 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
53805 ACAGGATTTT
* * ** * *
53815 TCAAGCCAGGAGATGAAACTCTTCCTAATTCAGACCCAAATTGTCTTTCTTCAGCACCAAGCGAA
1 TCAAGCCAGGAGACGAAACCCTTCCTAATTCAGACCCAAACAGCCTTTCCTCAGCACCAAGCGAA
* *
53880 GGAAAATCACGTTCGAATTCAGATTTATTAA
66 GGAAAATCACGCTCGAATGCAGATTTATTAA
* * *
53911 TCAAGCCAGGAGACGAAACCCTTCCTACTTCAGACCCTACCAGCCTTTCCTCAGCACCAAGCGAA
1 TCAAGCCAGGAGACGAAACCCTTCCTAATTCAGACCCAAACAGCCTTTCCTCAGCACCAAGCGAA
*
53976 TGAAAATCACGCTCAGAA-GCAGATTT
66 GGAAAATCACGCTC-GAATGCAGATTT
54002 TTCACGGACA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 75 0.96
97 3 0.04
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (96 bp):
TCAAGCCAGGAGACGAAACCCTTCCTAATTCAGACCCAAACAGCCTTTCCTCAGCACCAAGCGAA
GGAAAATCACGCTCGAATGCAGATTTATTAA
Found at i:56315 original size:60 final size:59
Alignment explanation
Indices: 56229--56345 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 59
56219 TTCAAATTCG
** *
56229 TCCTTAAACTTTTAAATGTTCTAATTTCATCCTCAAACTATGACTC-TCATTCTAAATTAA
1 TCCTTAAACTTTTAAACATTCGAATTTCATCCT-AAACTATGAC-CGTCATTCTAAATTAA
* * *
56289 TCCTTAAACTTTTGAACATTCGAATTTCATCCTATACTATGACCGTCTTTCTAAATT
1 TCCTTAAACTTTTAAACATTCGAATTTCATCCTAAACTATGACCGTCATTCTAAATT
56346 GGTCTCCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 1 0.02
59 20 0.40
60 29 0.58
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (59 bp):
TCCTTAAACTTTTAAACATTCGAATTTCATCCTAAACTATGACCGTCATTCTAAATTAA
Found at i:57099 original size:2 final size:2
Alignment explanation
Indices: 57092--57130 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
57082 CTTCCACCAT
57092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57131 TGTGGTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68776 original size:19 final size:19
Alignment explanation
Indices: 68754--68801 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
68744 TTCATCAATA
68754 TGAACTTATTCATATATTC
1 TGAACTTATTCATATATTC
*
68773 TGAACTTATTCATATATTT
1 TGAACTTATTCATATATTC
*
68792 TAAACTTATT
1 TGAACTTATT
68802 ATTTTCTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.50
Consensus pattern (19 bp):
TGAACTTATTCATATATTC
Found at i:69920 original size:12 final size:12
Alignment explanation
Indices: 69905--69948 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
69895 CTTCGTGAGC
69905 ATATTCGTTTAT
1 ATATTCGTTTAT
** *
69917 ATATTCGTCAAC
1 ATATTCGTTTAT
*
69929 ATGTTCGTTTAT
1 ATATTCGTTTAT
69941 ATATTCGT
1 ATATTCGT
69949 CAACAAGTCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (12 bp):
ATATTCGTTTAT
Found at i:69935 original size:24 final size:24
Alignment explanation
Indices: 69908--69953 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
69898 CGTGAGCATA
69908 TTCGTTTATATATTCGTCAACATG
1 TTCGTTTATATATTCGTCAACATG
69932 TTCGTTTATATATTCGTCAACA
1 TTCGTTTATATATTCGTCAACA
69954 AGTCTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (24 bp):
TTCGTTTATATATTCGTCAACATG
Found at i:71954 original size:27 final size:27
Alignment explanation
Indices: 71924--71981 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
71914 ATATAAATAA
*
71924 TAATAATATATGTATATCT-AATTTTTT
1 TAATAA-ACATGTATATCTAAATTTTTT
*
71951 TAAT-AGCATGTATATCTAAATTTTTT
1 TAATAAACATGTATATCTAAATTTTTT
71977 TAATA
1 TAATA
71982 GTAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.37
26 13 0.48
27 4 0.15
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (27 bp):
TAATAAACATGTATATCTAAATTTTTT
Found at i:71962 original size:25 final size:26
Alignment explanation
Indices: 71933--71982 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
71923 ATAATAATAT
71933 ATGTATATCT-AATTTTTTTAATAGC
1 ATGTATATCTAAATTTTTTTAATAGC
71958 ATGTATATCTAAATTTTTTTAATAG
1 ATGTATATCTAAATTTTTTTAATAG
71983 TAAAGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (26 bp):
ATGTATATCTAAATTTTTTTAATAGC
Found at i:72388 original size:12 final size:12
Alignment explanation
Indices: 72371--72397 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
72361 ACACAATTTC
72371 TTCCTTATTAAT
1 TTCCTTATTAAT
72383 TTCCTTATTAAT
1 TTCCTTATTAAT
72395 TTC
1 TTC
72398 ACAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCCTTATTAAT
Found at i:75055 original size:43 final size:43
Alignment explanation
Indices: 74989--75094 Score: 176
Period size: 43 Copynumber: 2.5 Consensus size: 43
74979 ATGGAGAGTT
* * *
74989 GATATGTAGATAAATATTCCTACAGTCTTCCAAAACGTGGCTG
1 GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
75032 GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
1 GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
*
75075 GATAAGTAGATATATATTTC
1 GATAAGTAGATAAATATTTC
75095 ACCCTGCCGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (43 bp):
GATAAGTAGATAAATATTTCTACAGTCTCCCAAAACGTGGCTG
Found at i:77269 original size:29 final size:29
Alignment explanation
Indices: 77236--77293 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
77226 TAATAGCACC
*
77236 GGTTTTTGGATAACTTTGTTCATTCCGGT
1 GGTTTTTGAATAACTTTGTTCATTCCGGT
77265 GGTTTTTGAATAACTTTGTTCATTCCGGT
1 GGTTTTTGAATAACTTTGTTCATTCCGGT
77294 CTGCACACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.48
Consensus pattern (29 bp):
GGTTTTTGAATAACTTTGTTCATTCCGGT
Found at i:77883 original size:21 final size:21
Alignment explanation
Indices: 77859--77898 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
77849 TCACCTACCA
77859 AAGATGAATTTTTCAATAATC
1 AAGATGAATTTTTCAATAATC
*
77880 AAGATGAATTTTTTAATAA
1 AAGATGAATTTTTCAATAA
77899 ATTGGCTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
AAGATGAATTTTTCAATAATC
Found at i:77947 original size:25 final size:25
Alignment explanation
Indices: 77919--77978 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
77909 AACCAAATAT
77919 GTCAATTTTG-CAAACTTTCAACTTC
1 GTCAATTTTGTC-AACTTTCAACTTC
* *
77944 GTCAATTTTGTCAACTTTCAATTTT
1 GTCAATTTTGTCAACTTTCAACTTC
77969 GTCAACTTTT
1 GTCAA-TTTT
77979 AATTTTGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (25 bp):
GTCAATTTTGTCAACTTTCAACTTC
Found at i:77966 original size:16 final size:16
Alignment explanation
Indices: 77945--78012 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
77935 TTCAACTTCG
77945 TCAATTTTGTCAACTT
1 TCAATTTTGTCAACTT
77961 TCAATTTTGTCAACTT
1 TCAATTTTGTCAACTT
*
77977 TTAATTTTGTCAACTT
1 TCAATTTTGTCAACTT
* *
77993 TAAACTTTGTCAACTT
1 TCAATTTTGTCAACTT
78009 TCAA
1 TCAA
78013 GCCAAATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (16 bp):
TCAATTTTGTCAACTT
Found at i:78009 original size:9 final size:9
Alignment explanation
Indices: 77936--78009 Score: 61
Period size: 9 Copynumber: 8.9 Consensus size: 9
77926 TTGCAAACTT
*
77936 TCAACTTCG
1 TCAACTTTG
*
77945 TCAATTTTG
1 TCAACTTTG
77954 TCAAC-TT-
1 TCAACTTTG
*
77961 TCAATTTTG
1 TCAACTTTG
77970 TCAACTTT-
1 TCAACTTTG
*
77978 T-AATTTTG
1 TCAACTTTG
77986 TCAAC-TT-
1 TCAACTTTG
*
77993 TAAACTTTG
1 TCAACTTTG
78002 TCAACTTT
1 TCAACTTT
78010 CAAGCCAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
7 13 0.26
8 10 0.20
9 27 0.54
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.49
Consensus pattern (9 bp):
TCAACTTTG
Found at i:79547 original size:20 final size:20
Alignment explanation
Indices: 79511--79550 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
79501 TGTTTGAATC
*
79511 AAATTAATTAGATATTATTA
1 AAATTAATTAGAAATTATTA
79531 AAATTAATT-GTAAATTATTA
1 AAATTAATTAG-AAATTATTA
79551 TTTTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTAATTAGAAATTATTA
Found at i:79889 original size:18 final size:18
Alignment explanation
Indices: 79850--79885 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
79840 TGATTATATG
79850 ATAATTATAAATTGTTTT
1 ATAATTATAAATTGTTTT
79868 ATAATTATAAATT-TTTT
1 ATAATTATAAATTGTTTT
79885 A
1 A
79886 ATAAGAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATAATTATAAATTGTTTT
Found at i:81413 original size:23 final size:23
Alignment explanation
Indices: 81380--81428 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
81370 ATGTTGAAAA
* *
81380 GTCAAAATTTTCATCTTAGAATG
1 GTCAAAATTTTCAGCTTACAATG
*
81403 GTCAAAGTTTTCAGCTTACAATG
1 GTCAAAATTTTCAGCTTACAATG
81426 GTC
1 GTC
81429 CAATTTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
GTCAAAATTTTCAGCTTACAATG
Found at i:106768 original size:4 final size:4
Alignment explanation
Indices: 106759--106823 Score: 130
Period size: 4 Copynumber: 16.2 Consensus size: 4
106749 AAAGGTACAA
106759 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
106807 ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC A
106824 GTATTTGTGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:112798 original size:37 final size:37
Alignment explanation
Indices: 112694--112801 Score: 128
Period size: 37 Copynumber: 2.9 Consensus size: 37
112684 CACCCGCAAT
* * * *
112694 GAGAAGATTAATCATGGTTATCGGCAATAGATACTCC
1 GAGAAGATTAGTCATGATTATCGACAATGGATACTCC
*
112731 GAGAAGATTAGTCAT-AGTTATCGACGATGGATACTCC
1 GAGAAGATTAGTCATGA-TTATCGACAATGGATACTCC
* * *
112768 GAGAATATTAGTCATGATAATCGCCAATGGATAC
1 GAGAAGATTAGTCATGATTATCGACAATGGATAC
112802 CCTGATTTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
37 59 0.98
38 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (37 bp):
GAGAAGATTAGTCATGATTATCGACAATGGATACTCC
Found at i:114884 original size:17 final size:17
Alignment explanation
Indices: 114862--114895 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
114852 CGTTAACAAA
114862 AATTAAATCATAGCTTG
1 AATTAAATCATAGCTTG
114879 AATTAAATCATAGCTTG
1 AATTAAATCATAGCTTG
114896 TAAGCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AATTAAATCATAGCTTG
Found at i:115791 original size:2 final size:2
Alignment explanation
Indices: 115784--115821 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
115774 TAATAGATAA
115784 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
115822 GAAACTCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:121764 original size:2 final size:2
Alignment explanation
Indices: 121757--121797 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
121747 TCATGTGGTC
121757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
121798 CCTTGTTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:129722 original size:22 final size:23
Alignment explanation
Indices: 129697--129742 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
129687 CATTTAAATG
*
129697 ATAAACGAACAT-AACGAATATA
1 ATAAACGAACATAAACGAACATA
*
129719 ATAAACGAATATAAACGAACATA
1 ATAAACGAACATAAACGAACATA
129742 A
1 A
129743 ACGAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.61, C:0.13, G:0.09, T:0.17
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACATA
Found at i:129734 original size:10 final size:10
Alignment explanation
Indices: 129697--129749 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
129687 CATTTAAATG
129697 ATAAACGAAC
1 ATAAACGAAC
*
129707 AT-AACGAATATA
1 ATAAACG-A-A-C
*
129719 ATAAACGAAT
1 ATAAACGAAC
129729 ATAAACGAAC
1 ATAAACGAAC
129739 ATAAACGAAC
1 ATAAACGAAC
129749 A
1 A
129750 ACACAAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.11
10 23 0.64
11 2 0.06
12 3 0.08
13 4 0.11
ACGTcount: A:0.60, C:0.15, G:0.09, T:0.15
Consensus pattern (10 bp):
ATAAACGAAC
Done.