Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015150.1 Corchorus capsularis cultivar CVL-1 contig15171, 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: 151752
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1640 original size:50 final size:50
Alignment explanation
Indices: 1560--1992 Score: 455
Period size: 50 Copynumber: 9.5 Consensus size: 50
1550 GAACACGCGA
* *
1560 AGACACGAAGGTACACAAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
* * *
1610 AGACACGAAGCTACACGAAAAGACAAAGGCCTCCGCAATGAGGCGAGGCC
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
* * *
1660 AGACATGAAGCTACACGAGAAGACAGAGGCCTCCACAGTGAGGTGA----
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1706 AG-C-C--AG--ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGA----
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1746 AG-C-C--AG--ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGA----
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1786 AG-C-C--AG--ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
* *
1830 AGACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGTGAGGCGAGGCC
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
*
1880 AGACACGAAGCTACACGAGAAGACAAAGGCCT---C--T---GC-A-G--
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
* *
1918 TGACACGAAGCTACACGAGAAGACAGAGGCCTCTGCAGTGAGGCGAGGCC
1 AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1968 AGACACGAAGCTACACGAGAAGACA
1 AGACACGAAGCTACACGAGAAGACA
1993 CGACCCATTT
Statistics
Matches: 342, Mismatches: 19, Indels: 44
0.84 0.05 0.11
Matches are distributed among these distances:
38 30 0.09
40 113 0.33
41 2 0.01
42 4 0.01
43 1 0.00
44 2 0.01
45 3 0.01
46 5 0.01
47 2 0.01
48 3 0.01
50 177 0.52
ACGTcount: A:0.35, C:0.26, G:0.32, T:0.07
Consensus pattern (50 bp):
AGACACGAAGCTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
Found at i:1717 original size:40 final size:40
Alignment explanation
Indices: 1672--1975 Score: 315
Period size: 40 Copynumber: 7.2 Consensus size: 40
1662 ACATGAAGCT
* *
1672 ACACGAGAAGACAGAGGCCTCCACAGTGAGGTGAAGCCAG
1 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
1712 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
1 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
1752 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
1 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
1792 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACACGAAG
1 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGA----AG-C-C--AG
* *
1840 CTACACGAGAAGACAAAGGCCTCTGCAGTGAGGCGAGGCCAGACACGAAG
1 --ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGA----AG-C-C--AG
* * ** *
1890 CTACACGAGAAGACAAAGGCCTCTGCAGTGACACGAAG-C-T
1 --ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
* *
1930 ACACGAGAAGACAGAGGCCTCTGCAGTGAGGCGAGGCCAG
1 ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
1970 ACACGA
1 ACACGA
1976 AGCTACACGA
Statistics
Matches: 240, Mismatches: 12, Indels: 24
0.87 0.04 0.09
Matches are distributed among these distances:
38 32 0.13
39 1 0.00
40 118 0.49
43 1 0.00
44 2 0.01
45 1 0.00
46 3 0.01
48 2 0.01
50 80 0.33
ACGTcount: A:0.34, C:0.27, G:0.33, T:0.07
Consensus pattern (40 bp):
ACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAAGCCAG
Found at i:1924 original size:38 final size:38
Alignment explanation
Indices: 1881--1958 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
1871 GGCGAGGCCA
1881 GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGT
1 GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGT
*
1919 GACACGAAGCTACACGAGAAGACAGAGGCCTCTGCAGT
1 GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGT
1957 GA
1 GA
1959 GGCGAGGCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.26, G:0.28, T:0.10
Consensus pattern (38 bp):
GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGT
Found at i:1949 original size:88 final size:88
Alignment explanation
Indices: 1831--1992 Score: 315
Period size: 88 Copynumber: 1.8 Consensus size: 88
1821 GGCGAGGCCA
1831 GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGTGAGGCGAGGCCAGACACGAAGCTACAC
1 GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGTGAGGCGAGGCCAGACACGAAGCTACAC
1896 GAGAAGACAAAGGCCTCTGCAGT
66 GAGAAGACAAAGGCCTCTGCAGT
*
1919 GACACGAAGCTACACGAGAAGACAGAGGCCTCTGCAGTGAGGCGAGGCCAGACACGAAGCTACAC
1 GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGTGAGGCGAGGCCAGACACGAAGCTACAC
1984 GAGAAGACA
66 GAGAAGACA
1993 CGACCCATTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.36, C:0.26, G:0.30, T:0.08
Consensus pattern (88 bp):
GACACGAAGCTACACGAGAAGACAAAGGCCTCTGCAGTGAGGCGAGGCCAGACACGAAGCTACAC
GAGAAGACAAAGGCCTCTGCAGT
Found at i:12243 original size:10 final size:10
Alignment explanation
Indices: 12228--12261 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
12218 AGAATTTGGC
12228 AAAAAACAAA
1 AAAAAACAAA
12238 AAAAAACAAA
1 AAAAAACAAA
12248 AAAACAACAAA
1 AAAA-AACAAA
12259 AAA
1 AAA
12262 CAAGTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:12249 original size:11 final size:11
Alignment explanation
Indices: 12228--12261 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12218 AGAATTTGGC
12228 AAAAAAC-AAA
1 AAAAAACAAAA
12238 AAAAAACAAAA
1 AAAAAACAAAA
*
12249 AAACAACAAAA
1 AAAAAACAAAA
12260 AA
1 AA
12262 CAAGTTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:12251 original size:18 final size:18
Alignment explanation
Indices: 12228--12264 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12218 AGAATTTGGC
12228 AAAAAACAAAAAAAAACA
1 AAAAAACAAAAAAAAACA
*
12246 AAAAAACAACAAAAAACA
1 AAAAAACAAAAAAAAACA
12264 A
1 A
12265 GTTCAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAACA
Found at i:12262 original size:10 final size:10
Alignment explanation
Indices: 12227--12264 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
12217 AAGAATTTGG
12227 CAAAAAACAA
1 CAAAAAACAA
*
12237 AAAAAAAC-A
1 CAAAAAACAA
12246 -AAAAAACAA
1 CAAAAAACAA
12255 CAAAAAACAA
1 CAAAAAACAA
12265 GTTCAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 7 0.28
9 2 0.08
10 16 0.64
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAAACAA
Found at i:18923 original size:18 final size:18
Alignment explanation
Indices: 18894--18928 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18884 TAGATCATAA
18894 ATTCCTAACCAGAGAATCC
1 ATTCCTAACCAGA-AATCC
18913 ATTCC-AACCAGAAATC
1 ATTCCTAACCAGAAATC
18929 AATTTAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (18 bp):
ATTCCTAACCAGAAATCC
Found at i:26020 original size:87 final size:87
Alignment explanation
Indices: 25874--26047 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
25864 CCATCTCCAA
25874 GCATCGGAGGAAGAGGCCAAAACCAATCTTGGGCACATATCTCTATTAGAAAAGACTCAAGAATC
1 GCATCGGAGGAAGAGGCCAAAACCAATCTTGGGCACATATCTCTATTAGAAAAGACTCAAGAATC
25939 TTGTTAAACGAGAACCTAAATT
66 TTGTTAAACGAGAACCTAAATT
25961 GCATCGGAGGAAGAGGCCAAAACCAATCTTGGGCACATATCTCTATTAGAAAAGACTCAAGAATC
1 GCATCGGAGGAAGAGGCCAAAACCAATCTTGGGCACATATCTCTATTAGAAAAGACTCAAGAATC
26026 TTGTTAAACGAGAACCTAAATT
66 TTGTTAAACGAGAACCTAAATT
26048 TATTATGTTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (87 bp):
GCATCGGAGGAAGAGGCCAAAACCAATCTTGGGCACATATCTCTATTAGAAAAGACTCAAGAATC
TTGTTAAACGAGAACCTAAATT
Found at i:38753 original size:119 final size:120
Alignment explanation
Indices: 38542--38801 Score: 416
Period size: 119 Copynumber: 2.2 Consensus size: 120
38532 ATTCGGTGCT
*
38542 AGCATTCTTCACTCGCGCGG-TCGGCACTCTAAATTGAGCACTCTTCTTTCGCGCGTTGGTAATT
1 AGCATTCTTCACTCGCGCGGTTCGGCACTCTAAATTGAGCACTCTTCTTTCGCGCATTGGTAATT
* *
38606 GCACGTGCTTAGGGGAGTTGCACATGTTCAGAAGAGCATTCGGTGCTCTTCATTA
66 GCACGTGCTTAGGGGAGTTGAACATGTTCAGAAGAGCATCCGGTGCTCTTCATTA
** *
38661 AGCATTCTTCACTCGCGCGGTTC-GCACTCTTCATTGAGCACTCTTCTTTCGCGCATTGGTGATT
1 AGCATTCTTCACTCGCGCGGTTCGGCACTCTAAATTGAGCACTCTTCTTTCGCGCATTGGTAATT
* * **
38725 GCACGTGCTTGGGGGAGTTGAACGTGTTCAGGGGAGCATCCGGTGCTCTTCATTA
66 GCACGTGCTTAGGGGAGTTGAACATGTTCAGAAGAGCATCCGGTGCTCTTCATTA
38780 AGCATTCTTCACTCGCGCGGTT
1 AGCATTCTTCACTCGCGCGGTT
38802 GGTCATCATG
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
119 128 0.98
120 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (120 bp):
AGCATTCTTCACTCGCGCGGTTCGGCACTCTAAATTGAGCACTCTTCTTTCGCGCATTGGTAATT
GCACGTGCTTAGGGGAGTTGAACATGTTCAGAAGAGCATCCGGTGCTCTTCATTA
Found at i:39286 original size:24 final size:24
Alignment explanation
Indices: 39254--39299 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
39244 TTTTACAATT
*
39254 GCTCGCCCTTTTGACTTGTTGGTC
1 GCTCACCCTTTTGACTTGTTGGTC
39278 GCTCACCCTTTTGACTTGTTGG
1 GCTCACCCTTTTGACTTGTTGG
39300 AGATGGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.07, C:0.28, G:0.24, T:0.41
Consensus pattern (24 bp):
GCTCACCCTTTTGACTTGTTGGTC
Found at i:47075 original size:29 final size:29
Alignment explanation
Indices: 47038--47097 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
47028 AAATAAAAAC
* *
47038 TACCCATTTTAGATAAAAACTACCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
47067 TACCAATTTTAGAAAAAAACTACCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
47096 TA
1 TA
47098 AGATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (29 bp):
TACCAATTTTAGAAAAAAACTACCCATTA
Found at i:61959 original size:17 final size:18
Alignment explanation
Indices: 61929--61963 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61919 CAAGACACCA
61929 GAAGAAAAAGGCAGACAG
1 GAAGAAAAAGGCAGACAG
61947 GAAGAAAAA-GCAGACAG
1 GAAGAAAAAGGCAGACAG
61964 AAGCAGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.11, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAGGCAGACAG
Found at i:68121 original size:17 final size:18
Alignment explanation
Indices: 68089--68123 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
68079 TTAGACACCA
*
68089 GAAGAGAAAGGCAGACAG
1 GAAGAGAAAAGCAGACAG
68107 GAAGA-AAAAGCAGACAG
1 GAAGAGAAAAGCAGACAG
68124 AAGCAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.54, C:0.11, G:0.34, T:0.00
Consensus pattern (18 bp):
GAAGAGAAAAGCAGACAG
Found at i:75794 original size:1 final size:1
Alignment explanation
Indices: 75790--75814 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
75780 TCCAAATTCT
75790 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
75815 CAAAGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:78538 original size:16 final size:16
Alignment explanation
Indices: 78517--78550 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
78507 ATTTATCTCC
78517 TTTCCTTATTTTGCTT
1 TTTCCTTATTTTGCTT
78533 TTTCCTTATTTTGCTT
1 TTTCCTTATTTTGCTT
78549 TT
1 TT
78551 GCTGCTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTCCTTATTTTGCTT
Found at i:78780 original size:44 final size:44
Alignment explanation
Indices: 78693--78793 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
78683 ATTTACACAA
* * * *
78693 TATTTACATTATTATTTATTTACGCGTTGCTTATGTATGCTCTC
1 TATTTACATTATTATTTAATTACCCATTGCTTATGTATACTCTC
78737 TATTTACATTATTATTTTAATTACCCATTGCTTAT-TATACTCTC
1 TATTTACATTATTA-TTTAATTACCCATTGCTTATGTATACTCTC
*
78781 TAATTACATTATT
1 TATTTACATTATT
78794 TGGCAGCCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 34 0.67
45 17 0.33
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (44 bp):
TATTTACATTATTATTTAATTACCCATTGCTTATGTATACTCTC
Found at i:79076 original size:11 final size:11
Alignment explanation
Indices: 79060--79085 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
79050 GCTATTGTCA
79060 AAAAAAAAAAG
1 AAAAAAAAAAG
79071 AAAAAAAAAAG
1 AAAAAAAAAAG
79082 AAAA
1 AAAA
79086 CTAGACAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:90545 original size:15 final size:15
Alignment explanation
Indices: 90522--90554 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
90512 CCATCTCATG
90522 TCATAAACATCAGTA
1 TCATAAACATCAGTA
*
90537 TCATCAACATCAGTA
1 TCATAAACATCAGTA
90552 TCA
1 TCA
90555 GCAAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (15 bp):
TCATAAACATCAGTA
Found at i:92235 original size:27 final size:25
Alignment explanation
Indices: 92181--92241 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 25
92171 GACTAGGATG
*
92181 AAAAAAATAAGAGAATTTTCACCAA
1 AAAAAAATAAGAGAATTTTCACAAA
*
92206 AAAAAAATAAGAGAATTGTTTCAAAGAA
1 AAAAAAATAAGAGAA-T-TTTCACA-AA
92234 AAAAAAAT
1 AAAAAAAT
92242 CTAGGTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 15 0.48
26 1 0.03
27 5 0.16
28 10 0.32
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.20
Consensus pattern (25 bp):
AAAAAAATAAGAGAATTTTCACAAA
Found at i:112126 original size:12 final size:12
Alignment explanation
Indices: 112109--112138 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
112099 AAAAAATAGG
112109 TAGAGAGAGAGA
1 TAGAGAGAGAGA
112121 TAGAGAGAGAGA
1 TAGAGAGAGAGA
112133 TAGAGA
1 TAGAGA
112139 AGGTCAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (12 bp):
TAGAGAGAGAGA
Found at i:114999 original size:83 final size:83
Alignment explanation
Indices: 114897--115063 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
114887 AACCACTTTG
*
114897 AATCTCGACTAATTTGGAATTTAATTATGCCGGACATCATATAAGTAATCTTGATTAATTTTGGA
1 AATCTCGACTAATTTGGAATTTAATTATGCCGGACATCAAATAAGTAATCTTGATTAATTTTGGA
*
114962 ATTTGGTCGTGTCGAATA
66 ATTTAGTCGTGTCGAATA
*
114980 AATCTCGACTAATTTGGAATTTAATTGTGCCGGACATCAAATAAGTAATCTTGATTAATTTTGGA
1 AATCTCGACTAATTTGGAATTTAATTATGCCGGACATCAAATAAGTAATCTTGATTAATTTTGGA
115045 ATTTAGTCGTGTCGAATA
66 ATTTAGTCGTGTCGAATA
115063 A
1 A
115064 TTTAGAATTT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (83 bp):
AATCTCGACTAATTTGGAATTTAATTATGCCGGACATCAAATAAGTAATCTTGATTAATTTTGGA
ATTTAGTCGTGTCGAATA
Found at i:116311 original size:162 final size:163
Alignment explanation
Indices: 116113--116416 Score: 502
Period size: 162 Copynumber: 1.9 Consensus size: 163
116103 CAATTGGAAC
* *
116113 ATTGACTTGTTGTGGTGCAAATGCAACATGGACATAGTCTTGGCCAGTGTCCTCACGTTTCACAG
1 ATTGACTTGTTGTGGTGCAAATGCAACATGGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
116178 GCTTAGCTGCACTTGGAAC-ATTGACTTGCTGTGGTGCAAATGCAACATTGACATAGCCTTGGCC
66 GCTTAGCTGCACTTGGAACTATTGACTTGCTGTGGTGCAAATGCAACATTGACATAGCCTTGGCC
116242 AGTGACCTCATGCTTAGCTGCACTTGGAACATT
131 AGTGACCTCATGCTTAGCTGCACTTGGAACATT
* * * *
116275 ATTGGCTTGTTGTGGTGCAAATGCAATATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACTG
1 ATTGACTTGTTGTGGTGCAAATGCAACATGGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
* * *
116340 GCTTAGCTGCACTTGGAACATTATTGGCTTGTTGTGGTGCAAATGCAACATTGACATAGTCTTGG
66 GCTTAGCTGCACTTGGAAC--TATTGACTTGCTGTGGTGCAAATGCAACATTGACATAGCCTTGG
116405 CCAGTGACCTCA
129 CCAGTGACCTCA
116417 CGTTTCACAG
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
162 78 0.60
165 52 0.40
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (163 bp):
ATTGACTTGTTGTGGTGCAAATGCAACATGGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
GCTTAGCTGCACTTGGAACTATTGACTTGCTGTGGTGCAAATGCAACATTGACATAGCCTTGGCC
AGTGACCTCATGCTTAGCTGCACTTGGAACATT
Found at i:116404 original size:87 final size:87
Alignment explanation
Indices: 116113--116437 Score: 485
Period size: 87 Copynumber: 3.9 Consensus size: 87
116103 CAATTGGAAC
* * *
116113 ATTGACTTGTTGTGGTGCAAATGCAACATGGACATAGTCTTGGCCAGTGTCCTCACGTTTCACAG
1 ATTGACTTGTTGTGGTGCAAATGCAACATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
116178 GCTTAGCTGCACTTGGAAC---
66 GCTTAGCTGCACTTGGAACATT
*
116197 ATTGACTTGCTGTGGTGCAAATGCAACATTGACATAGCCTTGGCCAGTGACCTCA----T-----
1 ATTGACTTGTTGTGGTGCAAATGCAACATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
116253 GCTTAGCTGCACTTGGAACATT
66 GCTTAGCTGCACTTGGAACATT
* * *
116275 ATTGGCTTGTTGTGGTGCAAATGCAATATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACTG
1 ATTGACTTGTTGTGGTGCAAATGCAACATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
116340 GCTTAGCTGCACTTGGAACATT
66 GCTTAGCTGCACTTGGAACATT
* *
116362 ATTGGCTTGTTGTGGTGCAAATGCAACATTGACATAGTCTTGGCCAGTGACCTCACGTTTCACAG
1 ATTGACTTGTTGTGGTGCAAATGCAACATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
116427 GCTTAGCTGCA
66 GCTTAGCTGCA
116438 TTGACAGCTT
Statistics
Matches: 219, Mismatches: 10, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
75 19 0.09
78 52 0.24
80 1 0.00
82 1 0.00
84 51 0.23
87 95 0.43
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (87 bp):
ATTGACTTGTTGTGGTGCAAATGCAACATTGACATAGCCTTGGCCAGTGACCTCACGTTTCACAG
GCTTAGCTGCACTTGGAACATT
Found at i:116712 original size:23 final size:23
Alignment explanation
Indices: 116686--116730 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
116676 TACTTGTGTC
*
116686 CCCAGTGGTTAAAGCTTGGGACA
1 CCCAGTGGTTAAAACTTGGGACA
116709 CCCAGTGGTTAAAACTTGGGAC
1 CCCAGTGGTTAAAACTTGGGAC
116731 TTCTTCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (23 bp):
CCCAGTGGTTAAAACTTGGGACA
Found at i:117414 original size:36 final size:36
Alignment explanation
Indices: 117374--117481 Score: 162
Period size: 39 Copynumber: 2.9 Consensus size: 36
117364 GTACTAATTT
117374 TTTTTTTTTTGAGTAATATAGTAGTACTAAATCACA
1 TTTTTTTTTTGAGTAATATAGTAGTACTAAATCACA
* * *
117410 TTTTTTTTTTGAGTAGTAATATAGTTGTACTAAATCTCT
1 TTTTTTTTTT--G-AGTAATATAGTAGTACTAAATCACA
117449 TTTTTTTTTTGAGTAATATAGTAGTACTAAATC
1 TTTTTTTTTTGAGTAATATAGTAGTACTAAATC
117482 TCGATTCTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
36 31 0.48
37 1 0.02
38 1 0.02
39 32 0.49
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (36 bp):
TTTTTTTTTTGAGTAATATAGTAGTACTAAATCACA
Found at i:117482 original size:36 final size:36
Alignment explanation
Indices: 117357--117483 Score: 179
Period size: 36 Copynumber: 3.5 Consensus size: 36
117347 AATGAATATT
117357 TATAGTAGTACT-AAT-T-TTTTTTTTTTTGAGTAA
1 TATAGTAGTACTAAATCTCTTTTTTTTTTTGAGTAA
* *
117390 TATAGTAGTACTAAATCACATTTTTTTTTTGAGTAGTAA
1 TATAGTAGTACTAAATCTC-TTTTTTTTTT-TG-AGTAA
*
117429 TATAGTTGTACTAAATCTCTTTTTTTTTTTGAGTAA
1 TATAGTAGTACTAAATCTCTTTTTTTTTTTGAGTAA
117465 TATAGTAGTACTAAATCTC
1 TATAGTAGTACTAAATCTC
117484 GATTCTAGTA
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
33 12 0.15
34 3 0.04
36 23 0.28
37 11 0.13
38 11 0.13
39 22 0.27
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (36 bp):
TATAGTAGTACTAAATCTCTTTTTTTTTTTGAGTAA
Found at i:117792 original size:10 final size:11
Alignment explanation
Indices: 117763--117791 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
117753 AAATGATTTC
117763 AAAAAAAAGAA
1 AAAAAAAAGAA
117774 AAAAAAAAGAA
1 AAAAAAAAGAA
117785 AAAAAAA
1 AAAAAAA
117792 GTTATTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:139932 original size:6 final size:6
Alignment explanation
Indices: 139921--139946 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
139911 ATTGATTTTG
139921 CATATT CATATT CATATT CATATT CA
1 CATATT CATATT CATATT CATATT CA
139947 AGTAAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (6 bp):
CATATT
Found at i:141225 original size:6 final size:6
Alignment explanation
Indices: 141214--141247 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
141204 ATGAGGCCGT
141214 GCCACA GCCACA GCCACA GCCACA GCCACA GCCA
1 GCCACA GCCACA GCCACA GCCACA GCCACA GCCA
141248 GAGGCAGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GCCACA
Found at i:141331 original size:18 final size:18
Alignment explanation
Indices: 141320--141518 Score: 281
Period size: 18 Copynumber: 11.1 Consensus size: 18
141310 ACTGGAAGAG
*
141320 GAAGATCAACTGGAGGAA
1 GAAGATCAATTGGAGGAA
* *
141338 GGAGATCAATTGGAGGAG
1 GAAGATCAATTGGAGGAA
*
141356 GAAGATCAACTGGAGGAA
1 GAAGATCAATTGGAGGAA
141374 GAAGATCAATTGGAGGAA
1 GAAGATCAATTGGAGGAA
* *
141392 GAAGATGAAGTGGAGGAA
1 GAAGATCAATTGGAGGAA
*
141410 GAAGATCAATTGGAGGAG
1 GAAGATCAATTGGAGGAA
*
141428 GAAGATCAATTGCAGGAA
1 GAAGATCAATTGGAGGAA
141446 GAAGATCAATTGGAGGAA
1 GAAGATCAATTGGAGGAA
141464 GAAGATCAATTGGAGGAA
1 GAAGATCAATTGGAGGAA
* *
141482 GGAGATCAACTGGAGGAA
1 GAAGATCAATTGGAGGAA
* * *
141500 GAAGAACAAGTGGGGGAA
1 GAAGATCAATTGGAGGAA
141518 G
1 G
141519 CAGAACAAGT
Statistics
Matches: 160, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 160 1.00
ACGTcount: A:0.42, C:0.07, G:0.37, T:0.14
Consensus pattern (18 bp):
GAAGATCAATTGGAGGAA
Found at i:149543 original size:15 final size:15
Alignment explanation
Indices: 149505--149553 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
149495 TCTTGGAAAA
*
149505 ATCAAAGTATTCAATC
1 ATCAAAGTA-ACAATC
149521 -TCAAAGTAACAATC
1 ATCAAAGTAACAATC
* *
149535 ATCACAGTAAAAATC
1 ATCAAAGTAACAATC
149550 ATCA
1 ATCA
149554 TCACTAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.24
Consensus pattern (15 bp):
ATCAAAGTAACAATC
Done.