Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005368.1 Hibiscus syriacus cultivar Beakdansim tig00012202_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: 98306
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:1252 original size:23 final size:23
Alignment explanation
Indices: 1226--1274 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1216 ATAAAGAACC
* *
1226 AAAATAAA-TTTAAATATACCATT
1 AAAATAAAGTCTAAACAT-CCATT
1249 AAAATAAAGTCTAAACATCCATT
1 AAAATAAAGTCTAAACATCCATT
1272 AAA
1 AAA
1275 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGTCTAAACATCCATT
Found at i:4887 original size:5 final size:5
Alignment explanation
Indices: 4877--4905 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4867 AATTAATTGC
4877 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
4906 GTTTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:11459 original size:23 final size:23
Alignment explanation
Indices: 11433--11481 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
11423 ATAAAGAACC
*
11433 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
11456 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
11479 AAA
1 AAA
11482 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:12813 original size:17 final size:16
Alignment explanation
Indices: 12781--12815 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12771 TAACTATTCA
12781 TGTGAATAGTAAATTT
1 TGTGAATAGTAAATTT
*
12797 TGTGAATAGTAAAATT
1 TGTGAATAGTAAATTT
12813 TGT
1 TGT
12816 TCAACGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
TGTGAATAGTAAATTT
Found at i:17237 original size:26 final size:28
Alignment explanation
Indices: 17176--17237 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
17166 GAGTATTGCT
* *
17176 GAGCTCGACTCGACTCGAAAACTTTGAAAT
1 GAGCTCGACTCGACTCGAAAACTTCG--AC
17206 GAAGCTCGACTCGACTCGAAAAC-TCG-C
1 G-AGCTCGACTCGACTCGAAAACTTCGAC
17233 GAGCT
1 GAGCT
17238 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 3 0.10
31 21 0.72
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTTCGAC
Found at i:19807 original size:103 final size:103
Alignment explanation
Indices: 19675--19881 Score: 324
Period size: 103 Copynumber: 2.0 Consensus size: 103
19665 CATCACCAAA
* * *
19675 ATCATTGTTCGTCGACTCCAGAGCATCATCCCGCTCCTTGTTTCTCTGAACCAAACAAGCTTCAT
1 ATCATTGTTCGTCGACTCCAAAACATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAGCTTCAT
*
19740 TTTGGGCCACTCTATCACTAAAAATATTGTTATCAACC
66 TCTGGGCCACTCTATCACTAAAAATATTGTTATCAACC
* * *
19778 ATCATTGTTCGTCGACTCTAAAACTTCATCCCGCTTCTTGTTTCTCCGAACCAAACAAGCTTCAT
1 ATCATTGTTCGTCGACTCCAAAACATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAGCTTCAT
* * *
19843 TCTGGGCCGCTTTATCACTGAAAATATTGTTATCAACC
66 TCTGGGCCACTCTATCACTAAAAATATTGTTATCAACC
19881 A
1 A
19882 GGAAATCATC
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.33
Consensus pattern (103 bp):
ATCATTGTTCGTCGACTCCAAAACATCATCCCGCTCCTTGTTTCTCCGAACCAAACAAGCTTCAT
TCTGGGCCACTCTATCACTAAAAATATTGTTATCAACC
Found at i:27280 original size:222 final size:222
Alignment explanation
Indices: 26883--27330 Score: 799
Period size: 222 Copynumber: 2.0 Consensus size: 222
26873 AGAATTCAGA
26883 AATCAGTGTTTCTAACATGTTTATAGACTCTTTATGACCCCTATGTTCATACATAAGACTTTAAT
1 AATCAGTGTTTCTAACATGTTTATAGACTCTTTATGACCCCTATGTTCATACATAAGACTTTAAT
26948 AACAATTGGGCACTCAGTAGAATGTTTGGGGGTAGAAAATTAGTATTTTTCAAGCTCAAAATAGG
66 AACAATTGGGCACTCAGTAGAATGTTTGGGGGTAGAAAATTAGTATTTTTCAAGCTCAAAATAGG
* * *
27013 GCATTTTTGTTGGTACTGTAGGAACAGTACAGTAGATATCCATTTTCGTTCAGGGTTCAAATCCA
131 GCATTTTTGTCGGTACTGTAAGAACAGTACAGTAGATACCCATTTTCGTTCAGGGTTCAAATCCA
*
27078 ATTCTAAGTTCCAGTCTAGGTTTGAAG
196 ATTCTAAGTTCCAGTCTAAGTTTGAAG
27105 AATCAGTGTTTCTAACATGTTTATAGACTCTTTATGACCCCTATGTTCATACATAAGACTTTAAT
1 AATCAGTGTTTCTAACATGTTTATAGACTCTTTATGACCCCTATGTTCATACATAAGACTTTAAT
*
27170 AACAATTGGGACACTCAGTAGAATGTTTGGGGGTAGAAAGTTAGTATTTTTCAAGCTCAAAATAG
66 AACAATTGGG-CACTCAGTAGAATGTTTGGGGGTAGAAAATTAGTATTTTTCAAGCTCAAAATAG
* * * *
27235 GGCATTTTT-TCGGTGCTGTAAGAACAGTATAGTATATACCCATTTTCGTTCAGGGTTCAAATCT
130 GGCATTTTTGTCGGTACTGTAAGAACAGTACAGTAGATACCCATTTTCGTTCAGGGTTCAAATCC
27299 AATTCTAAGTTCCAGTCTAAGTTTGAAG
195 AATTCTAAGTTCCAGTCTAAGTTTGAAG
27327 AATC
1 AATC
27331 CATTCAAACC
Statistics
Matches: 216, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
222 154 0.71
223 62 0.29
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (222 bp):
AATCAGTGTTTCTAACATGTTTATAGACTCTTTATGACCCCTATGTTCATACATAAGACTTTAAT
AACAATTGGGCACTCAGTAGAATGTTTGGGGGTAGAAAATTAGTATTTTTCAAGCTCAAAATAGG
GCATTTTTGTCGGTACTGTAAGAACAGTACAGTAGATACCCATTTTCGTTCAGGGTTCAAATCCA
ATTCTAAGTTCCAGTCTAAGTTTGAAG
Found at i:28014 original size:2 final size:2
Alignment explanation
Indices: 28009--28037 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27999 TTTATATGTG
28009 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 T
28038 TACGTATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38999 original size:42 final size:42
Alignment explanation
Indices: 38952--39052 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
38942 AATTATTAAG
* *
38952 GGTAGTATCAATACTAGTTGAAGAGGTTATCGATACTATGTA
1 GGTAGTATCAATACCAGTTGAAGAGGCTATCGATACTATGTA
* * *
38994 GGTAGTATCAATACCAGTTGAAGAGGCTATCTATACTGTGTG
1 GGTAGTATCAATACCAGTTGAAGAGGCTATCGATACTATGTA
*
39036 GGTAGTATCGATACCAG
1 GGTAGTATCAATACCAG
39053 GGGGATGGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (42 bp):
GGTAGTATCAATACCAGTTGAAGAGGCTATCGATACTATGTA
Found at i:39723 original size:21 final size:21
Alignment explanation
Indices: 39694--39751 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
39684 GTCAAAGGTT
*
39694 TTATGTGGTCATTCGGGACAA
1 TTATATGGTCATTCGGGACAA
*
39715 TTATATGGTCATTCAGGACAA
1 TTATATGGTCATTCGGGACAA
*
39736 ATATATGG-CACTTCGG
1 TTATATGGTCA-TTCGG
39752 TGCAAACCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
TTATATGGTCATTCGGGACAA
Found at i:39757 original size:21 final size:22
Alignment explanation
Indices: 39733--39781 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
39723 TCATTCAGGA
39733 CAAA-TATATGGCACTTCGGTG
1 CAAACTATATGGCACTTCGGTG
*
39754 CAAACCTATGTGGCACTTCGGTG
1 CAAA-CTATATGGCACTTCGGTG
39777 CAAAC
1 CAAAC
39782 CTATTTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 1 0.04
23 20 0.80
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
CAAACTATATGGCACTTCGGTG
Found at i:39795 original size:23 final size:23
Alignment explanation
Indices: 39741--39785 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
39731 GACAAATATA
39741 TGGCACTTCGGTGCAAACCTATG
1 TGGCACTTCGGTGCAAACCTATG
39764 TGGCACTTCGGTGCAAACCTAT
1 TGGCACTTCGGTGCAAACCTAT
39786 TTGGTCCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAAACCTATG
Found at i:45891 original size:22 final size:21
Alignment explanation
Indices: 45866--45940 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
45856 ATTAAGGGTA
45866 GTATCGATACTAGTTAAAGAGG
1 GTATCGATACTAGTT-AAGAGG
* *
45888 GTATCGATA-TTGTGT-AG-GTA
1 GTATCGATACTAGT-TAAGAG-G
*
45908 GTATCGATACCAGTTGAAGAGG
1 GTATCGATACTAGTT-AAGAGG
45930 GTATCGATACT
1 GTATCGATACT
45941 GTATGGGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
19 1 0.02
20 12 0.29
21 5 0.12
22 22 0.54
23 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGATACTAGTTAAGAGG
Found at i:45910 original size:42 final size:42
Alignment explanation
Indices: 45862--45962 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
45852 AATTATTAAG
* * *
45862 GGTAGTATCGATACTAGTTAAAGAGGGTATCGATATTGTGTA
1 GGTAGTATCGATACCAGTTAAAGAGGGTATCGATACTGTATA
* *
45904 GGTAGTATCGATACCAGTTGAAGAGGGTATCGATACTGTATG
1 GGTAGTATCGATACCAGTTAAAGAGGGTATCGATACTGTATA
45946 GGTAGTATCGATACCAG
1 GGTAGTATCGATACCAG
45963 GGGGATGGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (42 bp):
GGTAGTATCGATACCAGTTAAAGAGGGTATCGATACTGTATA
Found at i:46668 original size:21 final size:22
Alignment explanation
Indices: 46644--46692 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
46634 TCCTTCAGGA
46644 CAAA-TATCTGGCACTTCGGTG
1 CAAACTATCTGGCACTTCGGTG
*
46665 CAAAGCTATGTGGCACTTCGGTG
1 CAAA-CTATCTGGCACTTCGGTG
*
46688 AAAAC
1 CAAAC
46693 CTATTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 1 0.04
23 19 0.79
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
CAAACTATCTGGCACTTCGGTG
Found at i:46681 original size:23 final size:23
Alignment explanation
Indices: 46652--46696 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
46642 GACAAATATC
* *
46652 TGGCACTTCGGTGCAAAGCTATG
1 TGGCACTTCGGTGAAAACCTATG
46675 TGGCACTTCGGTGAAAACCTAT
1 TGGCACTTCGGTGAAAACCTAT
46697 TTGGTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGAAAACCTATG
Found at i:47937 original size:46 final size:46
Alignment explanation
Indices: 47824--48303 Score: 606
Period size: 46 Copynumber: 10.5 Consensus size: 46
47814 ATGAATGAAT
* * *
47824 AAAATACATAACGGTGCATTAACTA-CATAAAAGGATGCCATAAAT-
1 AAAATGCATAACGGTGCATTATC-AGCATGAAAGGATGCCATAAATG
* * *
47869 AAAATCCATAACGATGCATTATCAGCATAAAAGGATGCCATAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
* * *
47915 AAAATGCATAAGGGTGCTTTATCAGGATGAAAGGATGCCATAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
*
47961 AAAATGCATAACGGTGCATTATC-GAAATGAAAGGATGCCATAAATG
1 AAAATGCATAACGGTGCATTATCAG-CATGAAAGGATGCCATAAATG
* * * ** *
48007 AAAATGCATAATGATACATTATTGGCATAAAAGGATGCCATAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
* * * *
48053 AAAATGCATAACAGTGGATTATCGGTATGAAAGGATGCCATAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
* * * *
48099 AAAATGAATAACGGTGCATTATCAACATGAAATGATGCGATAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
* * *
48145 AAAATGGATAACGGTGCATTATCGGCATGAAAGGATGCCAGAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
** *
48191 AAAATATATAACGGTGCATTATCAGCATGAAAGGATGCAATAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
* * *
48237 AAAATGCATAACGGTGCATTATCGGCATGAAATGATGCCACAAATG
1 AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
* *
48283 AAAATACATAACGGTGTATTA
1 AAAATGCATAACGGTGCATTA
48304 ACGACATAAA
Statistics
Matches: 378, Mismatches: 53, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.00
45 41 0.11
46 335 0.89
47 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (46 bp):
AAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCCATAAATG
Found at i:56679 original size:46 final size:46
Alignment explanation
Indices: 56605--57092 Score: 589
Period size: 46 Copynumber: 10.6 Consensus size: 46
56595 AAATGAATGA
* * * * ** *
56605 ATAAATGAAAATGAATGACTGTGTATTATCAACATGAAAGGATTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
56651 ATAAATGAAAATGCATAGCGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
** *
56697 ATAAATGAAAATGCATAACTTTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
56743 ATAAATAAAAATGCATAATGGTTCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
** * **
56789 ATAAATGAAAATGCATAACACTGCATTATTGGCATGAAAATATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
56835 ATAAATGAAAATGCATAACGATGCATTATCGGTATGAAAGAATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
56881 ATAAATGAAAATGCATAACGGTGTATTATTGGCATGAAAGAATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
56927 ATAAATGAAAATACATAGCGGTGCATTATCGACATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** *
56973 ATTAATGAAAATGCATAATAGTGCATTATCAGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
57019 ATAAATGAAAATACATAATGGTGCATTATCGGCATGGAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * *
57065 ACAAATAAAAATACATAATGGTGTATTA
1 ATAAATGAAAATGCATAACGGTGCATTA
57093 ATGATATAAA
Statistics
Matches: 380, Mismatches: 62, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 380 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:58226 original size:18 final size:19
Alignment explanation
Indices: 58190--58228 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
58180 TTGTTAAATT
*
58190 AAAATATTTATTTTATCAC
1 AAAAAATTTATTTTATCAC
*
58209 AAAAAATTT-TTTTGTCAC
1 AAAAAATTTATTTTATCAC
58227 AA
1 AA
58229 TTAACTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (19 bp):
AAAAAATTTATTTTATCAC
Found at i:58504 original size:32 final size:32
Alignment explanation
Indices: 58372--58504 Score: 101
Period size: 32 Copynumber: 4.2 Consensus size: 32
58362 TATTGTGACT
* * * *
58372 AAATAAATTTTTTACAATTTATTATTGTGA-A
1 AAATAAATTTATTATAATTTGTTATTATGAGA
* * *
58403 AGAATATTATTTATCATAATTTTTTA-T-TGAGA
1 A-AATA-AATTTATTATAATTTGTTATTATGAGA
* * * * **
58435 AATTAATGTTTGTTATAAATTGTTATTATGACT
1 AAATAA-ATTTATTATAATTTGTTATTATGAGA
58468 AAATAAATTTATTATAATTTGTTATTATGAGA
1 AAATAAATTTATTATAATTTGTTATTATGAGA
58500 AAATA
1 AAATA
58505 TTGTAACTAA
Statistics
Matches: 76, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
31 20 0.26
32 34 0.45
33 22 0.29
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (32 bp):
AAATAAATTTATTATAATTTGTTATTATGAGA
Found at i:58937 original size:20 final size:20
Alignment explanation
Indices: 58900--58938 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58890 AATATCATAT
* * *
58900 AAAATATATTTTATTATTAA
1 AAAATAAATTATAATATTAA
58920 AAAATAAATTATAATATTA
1 AAAATAAATTATAATATTA
58939 CCTTCAAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATAAATTATAATATTAA
Found at i:59214 original size:40 final size:40
Alignment explanation
Indices: 59159--59236 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
59149 TAATACATGA
59159 AATAAATATATAACTAAGTCATAAGAAAAAGACAACCGGT
1 AATAAATATATAACTAAGTCATAAGAAAAAGACAACCGGT
59199 AATAAATATATAACTAAGTCATAAGAAAAAGACAACCG
1 AATAAATATATAACTAAGTCATAAGAAAAAGACAACCG
59237 ACAGACTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.56, C:0.13, G:0.12, T:0.19
Consensus pattern (40 bp):
AATAAATATATAACTAAGTCATAAGAAAAAGACAACCGGT
Found at i:59864 original size:15 final size:15
Alignment explanation
Indices: 59844--59872 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59834 ATTTGTATTA
59844 AATTTTGATTGTTTG
1 AATTTTGATTGTTTG
59859 AATTTTGATTGTTT
1 AATTTTGATTGTTT
59873 TTGTCGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (15 bp):
AATTTTGATTGTTTG
Found at i:66640 original size:25 final size:23
Alignment explanation
Indices: 66594--66640 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
66584 AGGCCAGATT
* *
66594 AATTTGTTTAATTCAACTATTAC
1 AATTTGTTTAATCCAACAATTAC
66617 AATTGTGTTTAAATCCAACAATTA
1 AATT-TGTTT-AATCCAACAATTA
66641 AATCATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (23 bp):
AATTTGTTTAATCCAACAATTAC
Found at i:68216 original size:6 final size:6
Alignment explanation
Indices: 68207--68239 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
68197 GGACGTGCTC
68207 GTGGAT GTGGAT GTGGAT GTGGAT GTGGAT GTG
1 GTGGAT GTGGAT GTGGAT GTGGAT GTGGAT GTG
68240 AGAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
GTGGAT
Found at i:69100 original size:22 final size:21
Alignment explanation
Indices: 69075--69119 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
69065 ATAAATTTGA
* *
69075 AAATTCCTAGAAATTATATTTT
1 AAATT-CTAGAAAATAGATTTT
*
69097 AAATTCTTGAAAATAGATTTT
1 AAATTCTAGAAAATAGATTTT
69118 AA
1 AA
69120 TATATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (21 bp):
AAATTCTAGAAAATAGATTTT
Found at i:70043 original size:19 final size:19
Alignment explanation
Indices: 70015--70114 Score: 55
Period size: 19 Copynumber: 5.1 Consensus size: 19
70005 TGTTGTGAAA
*
70015 AGTAAAATTTTTTATTTTT
1 AGTAATATTTTTTATTTTT
*
70034 AGTAATATTTTATCAATTTTT
1 AGTAATATTTT-T-TATTTTT
*
70055 -TTCAAT-TTATTTTATTTTT
1 AGT-AATATT-TTTTATTTTT
*
70074 --TATTATTTTAGTAATATTTTT
1 AGTAATATTTT--T--TATTTTT
*
70095 AGTAATATTTATTATTTTT
1 AGTAATATTTTTTATTTTT
70114 A
1 A
70115 AATTATATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
17 4 0.06
18 3 0.05
19 25 0.40
20 5 0.08
21 19 0.30
23 7 0.11
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
AGTAATATTTTTTATTTTT
Found at i:70094 original size:12 final size:12
Alignment explanation
Indices: 70079--70104 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
70069 TTTTTTATTA
70079 TTTTAGTAATAT
1 TTTTAGTAATAT
70091 TTTTAGTAATAT
1 TTTTAGTAATAT
70103 TT
1 TT
70105 ATTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTTAGTAATAT
Found at i:70209 original size:14 final size:13
Alignment explanation
Indices: 70185--70225 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
70175 TTTTATTTTT
70185 ATTTTGATTTTAAA
1 ATTTT-ATTTTAAA
* *
70199 ATTTTCTTTTTAA
1 ATTTTATTTTAAA
70212 ATTTTATTTTAAA
1 ATTTTATTTTAAA
70225 A
1 A
70226 GTAGTTTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
ATTTTATTTTAAA
Found at i:71363 original size:3 final size:3
Alignment explanation
Indices: 71357--71407 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
71347 GCTTTTTTTG
* * * * *
71357 TTA TTA TT- TTT TTA CTA TTA TTA TTA TTA ATA ATA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
71404 TTA T
1 TTA T
71408 CATTTTCAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:71412 original size:15 final size:15
Alignment explanation
Indices: 71351--71413 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
71341 TCCGAAGCTT
*
71351 TTTTTGTTATTATT-
1 TTTTTATTATTATTA
*
71365 TTTTTACTATTATTA
1 TTTTTATTATTATTA
* * *
71380 TTATTAATAATATTA
1 TTTTTATTATTATTA
*
71395 TTTTTATTATTATCA
1 TTTTTATTATTATTA
71410 TTTT
1 TTTT
71414 CAGGTTACAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTTTATTATTATTA
Found at i:77394 original size:32 final size:32
Alignment explanation
Indices: 77358--77424 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
77348 ATTTTGATAC
*
77358 TACATTTATCTGAGACTCCAAAGTCATACCTT
1 TACATTTATCTGAGACGCCAAAGTCATACCTT
* * * *
77390 TACATTTTTTTGAGACGCCAAATTCATACTTT
1 TACATTTATCTGAGACGCCAAAGTCATACCTT
77422 TAC
1 TAC
77425 CTTCTCGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (32 bp):
TACATTTATCTGAGACGCCAAAGTCATACCTT
Found at i:78208 original size:13 final size:12
Alignment explanation
Indices: 78174--78339 Score: 84
Period size: 13 Copynumber: 13.9 Consensus size: 12
78164 AAATATATAT
78174 AAAAAGATAG-AG
1 AAAAAGA-AGAAG
78186 AAATAA-AAGATAG
1 AAA-AAGAAGA-AG
78199 AAAAAGAAGAAG
1 AAAAAGAAGAAG
78211 AAAAAGAA-AAG
1 AAAAAGAAGAAG
* *
78222 AGAAAA-TA-TAG
1 A-AAAAGAAGAAG
78233 AAAAAGAAGAAG
1 AAAAAGAAGAAG
*
78245 GAAAA-AAGATA-
1 AAAAAGAAGA-AG
*
78256 AAAAA-AAGGAG
1 AAAAAGAAGAAG
* *
78267 -AAAA-TA-TAG
1 AAAAAGAAGAAG
78276 AAAAAGAAGAAG
1 AAAAAGAAGAAG
78288 AAAAAAGATAGAAG
1 -AAAAAGA-AGAAG
*
78302 AAAAAAGAAAAAG
1 -AAAAAGAAGAAG
*
78315 AAAAAAGAAAAAAG
1 -AAAAAG-AAGAAG
*
78329 AAAAAGGAGAA
1 AAAAAGAAGAA
78340 AGGAGAAAGA
Statistics
Matches: 125, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
9 2 0.02
10 14 0.11
11 23 0.18
12 32 0.26
13 35 0.28
14 19 0.15
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.05
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:78227 original size:7 final size:7
Alignment explanation
Indices: 78197--78347 Score: 52
Period size: 7 Copynumber: 21.7 Consensus size: 7
78187 AATAAAAGAT
78197 AGAAAA-
1 AGAAAAG
*
78203 AGAAGA-
1 AGAAAAG
78209 AGAAAA-
1 AGAAAAG
78215 AGAAAAG
1 AGAAAAG
*
78222 AGAAAATAT
1 AG-AAA-AG
78231 AGAAAA-
1 AGAAAAG
78237 AGAAGAAG
1 AGAA-AAG
*
78245 -GAAAAA
1 AGAAAAG
78251 AGATAAA-
1 AGA-AAAG
78258 A-AAAAGG
1 AGAAAA-G
*
78265 AGAAAATAT
1 AG-AAA-AG
78274 AGAAAA-
1 AGAAAAG
78280 AGAAGAAG
1 AGAA-AAG
*
78288 AAAAAAG
1 AGAAAAG
* *
78295 ATAGAAG
1 AGAAAAG
*
78302 AAAAAAG
1 AGAAAAG
78309 A-AAAAG
1 AGAAAAG
*
78315 AAAAAAG
1 AGAAAAG
*
78322 AAAAAAG
1 AGAAAAG
78329 A-AAAAGG
1 AGAAAA-G
*
78336 AGAAAGG
1 AGAAAAG
78343 AGAAA
1 AGAAA
78348 GAAAATAAAT
Statistics
Matches: 117, Mismatches: 11, Indels: 33
0.73 0.07 0.20
Matches are distributed among these distances:
5 3 0.03
6 37 0.32
7 50 0.43
8 18 0.15
9 8 0.07
10 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (7 bp):
AGAAAAG
Found at i:78238 original size:34 final size:35
Alignment explanation
Indices: 78190--78332 Score: 141
Period size: 34 Copynumber: 3.9 Consensus size: 35
78180 ATAGAGAAAT
*
78190 AAAAGATAGAAAAAGAAGAAG-AAAAAGAAAAGAG
1 AAAATATAGAAAAAGAAGAAGAAAAAAGAAAAGAG
78224 AAAATATAGAAAAAGAAGAAGGAAAAAAGATAAAAAAAAGGAG
1 AAAATATAGAAAAAGAAGAA-GAAAAAAG------AAAA-GAG
*
78267 AAAATATAGAAAAAGAAGAAGAAAAAAG-ATAGAAG
1 AAAATATAGAAAAAGAAGAAGAAAAAAGAAAAG-AG
*
78302 AAAA-A-AGAAAAAGAAAAAAGAAAAAAGAAAA
1 AAAATATAGAAAAAG-AAGAAGAAAAAAGAAAA
78333 AGGAGAAAGG
Statistics
Matches: 93, Mismatches: 4, Indels: 23
0.77 0.03 0.19
Matches are distributed among these distances:
33 8 0.09
34 33 0.35
35 11 0.12
36 6 0.06
42 12 0.13
43 23 0.25
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (35 bp):
AAAATATAGAAAAAGAAGAAGAAAAAAGAAAAGAG
Found at i:78252 original size:14 final size:13
Alignment explanation
Indices: 78174--78333 Score: 88
Period size: 14 Copynumber: 12.3 Consensus size: 13
78164 AAATATATAT
78174 AAAAAGATAG-AGA
1 AAAAAGA-AGAAGA
*
78187 AATAA-AAGATAG-
1 AAAAAGAAGA-AGA
78199 AAAAAGAAGAAG-
1 AAAAAGAAGAAGA
78211 AAAAAGAA-AAGA
1 AAAAAGAAGAAGA
* * *
78223 GAAAA-TA-TAG-
1 AAAAAGAAGAAGA
78233 AAAAAGAAGAAGGA
1 AAAAAGAAGAA-GA
78247 AAAAAGATA-AA-A
1 AAAAAGA-AGAAGA
* *
78259 AAAAGGAGAAAATATA
1 AAAA--AGAAGA-AGA
78275 GAAAAAGAAGAAGA
1 -AAAAAGAAGAAGA
78289 AAAAAGATAGAAGA
1 AAAAAGA-AGAAGA
*
78303 AAAAAGAAAAAGA
1 AAAAAGAAGAAGA
*
78316 AAAAAGAAAAAAGA
1 AAAAAG-AAGAAGA
78330 AAAA
1 AAAA
78334 GGAGAAAGGA
Statistics
Matches: 119, Mismatches: 11, Indels: 33
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.03
11 9 0.08
12 25 0.21
13 30 0.25
14 39 0.33
15 7 0.06
16 1 0.01
17 4 0.03
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (13 bp):
AAAAAGAAGAAGA
Found at i:78280 original size:43 final size:41
Alignment explanation
Indices: 78190--78333 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 41
78180 ATAGAGAAAT
*
78190 AAAAGATAGAAAAAGAAGAAGA-AAAAGAAAAGAGAAAATATAGA
1 AAAAGA-AGAAGAA-AA-AAGATAAAA-AAAAGAGAAAATATAGA
78234 AAAAGAAGAAGGAAAAAAGATAAAAAAAAGGAGAAAATATAGA
1 AAAAGAAGAA-GAAAAAAGATAAAAAAAA-GAGAAAATATAGA
*
78277 AAAAGAAGAAGAAAAAAGATAGAAGAAAAA-AGAAAA-AGA-A
1 AAAAGAAGAAGAAAAAAGATA-AA-AAAAAGAGAAAATATAGA
*
78317 AAAAGAAAAAAGAAAAA
1 AAAAG-AAGAAGAAAAA
78334 GGAGAAAGGA
Statistics
Matches: 91, Mismatches: 3, Indels: 15
0.83 0.03 0.14
Matches are distributed among these distances:
40 6 0.07
41 12 0.13
42 25 0.27
43 35 0.38
44 13 0.14
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (41 bp):
AAAAGAAGAAGAAAAAAGATAAAAAAAAGAGAAAATATAGA
Found at i:78315 original size:27 final size:27
Alignment explanation
Indices: 78197--78352 Score: 113
Period size: 27 Copynumber: 5.7 Consensus size: 27
78187 AATAAAAGAT
* *
78197 AGAAAAAG-AAGAAG-AAAAAGAAAAG
1 AGAAAAAGAAAAAAGAAAAAAGAAAAA
* * *
78222 AGAAAATATAGAAAAAGAAGAAGGAAAAA
1 AGAAAA-AGA-AAAAAGAAAAAAGAAAAA
*
78251 AGATAAAA-AAAAGGAGAAAATATAG-AAAA
1 AGA-AAAAGAAAA-AAGAAAA-A-AGAAAAA
* * *
78280 AGAAGAAGAAAAAAGATAGAAGAAAAA
1 AGAAAAAGAAAAAAGAAAAAAGAAAAA
78307 AGAAAAAGAAAAAAGAAAAAAGAAAAA
1 AGAAAAAGAAAAAAGAAAAAAGAAAAA
* * * *
78334 GGAGAAAGGAGAAAGAAAA
1 AGAAAAAGAAAAAAGAAAA
78353 TAAATCAAGT
Statistics
Matches: 102, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
25 6 0.06
26 3 0.03
27 47 0.46
28 18 0.18
29 24 0.24
30 4 0.04
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (27 bp):
AGAAAAAGAAAAAAGAAAAAAGAAAAA
Found at i:78341 original size:20 final size:20
Alignment explanation
Indices: 78199--78352 Score: 89
Period size: 20 Copynumber: 7.5 Consensus size: 20
78189 TAAAAGATAG
*
78199 AAAAAGAAGAA-GAAAAAGA
1 AAAAAGAAAAAGGAAAAAGA
* *
78218 AAAGAGAAAATATAGAAAAAGA
1 AAAAAGAAAA-A-GGAAAAAGA
* * *
78240 AGAAGGAAAAAAGATAAAA-A
1 AAAAAGAAAAAGGA-AAAAGA
* *
78260 AAAGGAGAAAATATAGAAAAAG-
1 AAA-AAGAAAA-A-GGAAAAAGA
* * *
78282 AAGAAGAAAAAAGATAGAAGA
1 AAAAAGAAAAAGGA-AAAAGA
*
78303 AAAAAGAAAAAGAAAAAAGA
1 AAAAAGAAAAAGGAAAAAGA
* *
78323 AAAAAGAAAAAGGAGAAAGG
1 AAAAAGAAAAAGGAAAAAGA
*
78343 AGAAAGAAAA
1 AAAAAGAAAA
78353 TAAATCAAGT
Statistics
Matches: 106, Mismatches: 19, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
19 11 0.10
20 43 0.41
21 27 0.25
22 22 0.21
23 3 0.03
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (20 bp):
AAAAAGAAAAAGGAAAAAGA
Found at i:78719 original size:21 final size:19
Alignment explanation
Indices: 78681--78726 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
78671 AATTAATCGT
78681 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
78701 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
78722 A-TAAT
1 ACTAAT
78727 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:81128 original size:11 final size:11
Alignment explanation
Indices: 81112--81136 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
81102 GCTGTTATAT
81112 AAAAAAATGAA
1 AAAAAAATGAA
81123 AAAAAAATGAA
1 AAAAAAATGAA
81134 AAA
1 AAA
81137 CTACAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:88675 original size:18 final size:20
Alignment explanation
Indices: 88632--88681 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
88622 TCCTTATGGG
88632 GAGTATCGATACTCTACCCTT
1 GAGTATCGATACTC-ACCCTT
88653 G-GTATCGATACTC-CCC-T
1 GAGTATCGATACTCACCCTT
*
88670 GAGTATTGATAC
1 GAGTATCGATAC
88682 CAAAATGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
20 12 0.44
21 1 0.04
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (20 bp):
GAGTATCGATACTCACCCTT
Found at i:88742 original size:20 final size:20
Alignment explanation
Indices: 88717--88767 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
88707 AGCTTTCTCG
88717 GTATCGATACC-ACCCTACGA
1 GTATCGATACCTACCCTAC-A
*
88737 GTATCGATACCTTCCCTACA
1 GTATCGATACCTACCCTACA
*
88757 TTATCGATACC
1 GTATCGATACC
88768 CATTTCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (20 bp):
GTATCGATACCTACCCTACA
Done.