Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001240.1 Hibiscus syriacus cultivar Beakdansim tig00002439_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: 166992
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2030 original size:17 final size:17
Alignment explanation
Indices: 2008--2040 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1998 TATCCTACCA
2008 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
2025 TATACCCTAACCATTT
1 TATACCATAACCATTT
2041 TTTAAGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:6171 original size:27 final size:26
Alignment explanation
Indices: 6114--6174 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
6104 CTTTCTTTCT
*
6114 TTTCTTTTTTCTTTTGGAATGTTGAA
1 TTTCTTTTTTCTTTTGGAATGTTCAA
* *
6140 CTTCTTTCTTTC-TTTGGAGTGCTTCAA
1 TTTCTTT-TTTCTTTTGGAATG-TTCAA
6167 TTTCTTTT
1 TTTCTTTT
6175 CTGATTTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (26 bp):
TTTCTTTTTTCTTTTGGAATGTTCAA
Found at i:23605 original size:45 final size:45
Alignment explanation
Indices: 23555--23650 Score: 165
Period size: 45 Copynumber: 2.1 Consensus size: 45
23545 AGAGTGAAGG
*
23555 ACAAATTTTACCTAACAAATCTTCTTCTACTATTTCTTTTTCCTA
1 ACAAATTTTACCAAACAAATCTTCTTCTACTATTTCTTTTTCCTA
* *
23600 ACAAATTTTACCAAACAAATCTTTTTCTACTATTTCTTTTTTCTA
1 ACAAATTTTACCAAACAAATCTTCTTCTACTATTTCTTTTTCCTA
23645 ACAAAT
1 ACAAAT
23651 ATGTCTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (45 bp):
ACAAATTTTACCAAACAAATCTTCTTCTACTATTTCTTTTTCCTA
Found at i:34767 original size:15 final size:15
Alignment explanation
Indices: 34756--34785 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34746 ATTCAAAAAG
34756 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
34771 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
34785 A
1 A
34786 GTTGAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:40866 original size:13 final size:13
Alignment explanation
Indices: 40848--40905 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
40838 ACTATATGTT
40848 CATCACCATCTTC
1 CATCACCATCTTC
*
40861 CATCACCAT-TTT
1 CATCACCATCTTC
* **
40873 CA-CACC-TATAA
1 CATCACCATCTTC
*
40884 CATCGCCATCTTC
1 CATCACCATCTTC
40897 CATCACCAT
1 CATCACCAT
40906 TGCACGCCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.21
12 7 0.21
13 19 0.56
ACGTcount: A:0.28, C:0.41, G:0.02, T:0.29
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:40928 original size:35 final size:35
Alignment explanation
Indices: 40847--40997 Score: 221
Period size: 35 Copynumber: 4.3 Consensus size: 35
40837 CACTATATGT
* *
40847 TCATCACCATCTTCCATCACCATTTTCACACCTATA
1 TCATCACCATCTTCCATCACCA-TTGCACGCCTATA
* *
40883 ACATCGCCATCTTCCATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
*
40918 TCATCACCATCTTCTATCACCATTGCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
* * *
40953 TCATCCCCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTGCACGCCTATA
40988 TCATCACCAT
1 TCATCACCAT
40998 TCCCTTATCA
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
35 85 0.81
36 20 0.19
ACGTcount: A:0.26, C:0.39, G:0.04, T:0.31
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTGCACGCCTATA
Found at i:47201 original size:35 final size:35
Alignment explanation
Indices: 47155--47232 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
47145 AACCTAAAAT
47155 ATCACCATCTTCCATCACCATTGCACGCCTATATC
1 ATCACCATCTTCCATCACCATTGCACGCCTATATC
* *
47190 ATCACCATCTTCTATCACCATTGCATGCCTATATC
1 ATCACCATCTTCCATCACCATTGCACGCCTATATC
47225 ATCACCAT
1 ATCACCAT
47233 TTCACGCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.27, C:0.37, G:0.05, T:0.31
Consensus pattern (35 bp):
ATCACCATCTTCCATCACCATTGCACGCCTATATC
Found at i:47229 original size:22 final size:22
Alignment explanation
Indices: 47203--47255 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
47193 ACCATCTTCT
*
47203 ATCACCATTGCATGCCTATATC
1 ATCACCATTGCACGCCTATATC
*
47225 ATCACCATTTCACGCCTATATC
1 ATCACCATTGCACGCCTATATC
47247 ATCACCATT
1 ATCACCATT
47256 CCCTTATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.32
Consensus pattern (22 bp):
ATCACCATTGCACGCCTATATC
Found at i:47655 original size:18 final size:17
Alignment explanation
Indices: 47634--47670 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
47624 AAGCAACAAA
*
47634 AAGAGAAAAAGAGAGAAG
1 AAGAAAAAAAGAGA-AAG
47652 AAGAAAAAAAGAGAAAG
1 AAGAAAAAAAGAGAAAG
47669 AA
1 AA
47671 AATACTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAGAGAAAG
Found at i:53193 original size:13 final size:11
Alignment explanation
Indices: 53116--53234 Score: 64
Period size: 11 Copynumber: 10.2 Consensus size: 11
53106 TGTTCATCAC
53116 CATCACCATTTT
1 CATCACCA-TTT
**
53128 CA-CACCTATAA
1 CATCACC-ATTT
53139 CATCACCATCTT
1 CATCACCAT-TT
*
53151 CCATCACCATTG
1 -CATCACCATTT
* *
53163 CA-CGCCTATAT
1 CATCACC-ATTT
53174 CATCACCATCTT
1 CATCACCAT-TT
*
53186 CTATCACCATTG
1 C-ATCACCATTT
*
53198 CAT-ACCTATAT
1 CATCACC-ATTT
53209 CATCACCATCTT
1 CATCACCAT-TT
53221 CTATCACCATTT
1 C-ATCACCATTT
53233 CA
1 CA
53235 CGCCTATATA
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
10 6 0.07
11 27 0.33
12 23 0.28
13 25 0.31
ACGTcount: A:0.29, C:0.37, G:0.03, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:53213 original size:70 final size:71
Alignment explanation
Indices: 53117--53248 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 71
53107 GTTCATCACC
* *
53117 ATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACGCCTATATCATCACCA
1 ATCACCATTTGCACACCTATAACATCACCATCTTCCATCACCATTGCACGCCTATATAATCACCA
53182 TCTTCT
66 TCTTCT
* * * *
53188 ATCACCA-TTGCATACCTATATCATCACCATCTTCTATCACCATTTCACGCCTATATAATCA
1 ATCACCATTTGCACACCTATAACATCACCATCTTCCATCACCATTGCACGCCTATATAATCA
53249 TCATTCCTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
70 48 0.87
71 7 0.13
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.32
Consensus pattern (71 bp):
ATCACCATTTGCACACCTATAACATCACCATCTTCCATCACCATTGCACGCCTATATAATCACCA
TCTTCT
Found at i:53261 original size:35 final size:35
Alignment explanation
Indices: 53117--53248 Score: 183
Period size: 35 Copynumber: 3.7 Consensus size: 35
53107 GTTCATCACC
* * * *
53117 ATCACCATTTTCACACCTATAACATCACCATCTTCC
1 ATCACCA-TTGCACGCCTATATCATCACCATCTTCT
53153 ATCACCATTGCACGCCTATATCATCACCATCTTCT
1 ATCACCATTGCACGCCTATATCATCACCATCTTCT
**
53188 ATCACCATTGCATACCTATATCATCACCATCTTCT
1 ATCACCATTGCACGCCTATATCATCACCATCTTCT
* *
53223 ATCACCATTTCACGCCTATATAATCA
1 ATCACCATTGCACGCCTATATCATCA
53249 TCATTCCTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 79 0.92
36 7 0.08
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.32
Consensus pattern (35 bp):
ATCACCATTGCACGCCTATATCATCACCATCTTCT
Found at i:53581 original size:23 final size:23
Alignment explanation
Indices: 53555--53612 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
53545 GTTAGCTTAG
*
53555 AGGAGGCACATGCACGCCTAACA
1 AGGAGACACATGCACGCCTAACA
53578 AGGAGACACATGCACGCCTAACA
1 AGGAGACACATGCACGCCTAACA
53601 AGTGA-ACACATG
1 AG-GAGACACATG
53613 ACCAGCCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 31 0.94
24 2 0.06
ACGTcount: A:0.38, C:0.28, G:0.24, T:0.10
Consensus pattern (23 bp):
AGGAGACACATGCACGCCTAACA
Found at i:64065 original size:13 final size:13
Alignment explanation
Indices: 64043--64072 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
64033 ACTAGACACA
64043 TTTC-ACATACCT
1 TTTCAACATACCT
64055 TTTCAACATACCT
1 TTTCAACATACCT
64068 TTTCA
1 TTTCA
64073 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:68756 original size:16 final size:17
Alignment explanation
Indices: 68724--68757 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
68714 CACTTTGCAC
*
68724 TTCTTTTTGTATTTTGT
1 TTCTTTTTGTATATTGT
68741 TTCTTTTTGT-TATTGT
1 TTCTTTTTGTATATTGT
68757 T
1 T
68758 ACACGTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (17 bp):
TTCTTTTTGTATATTGT
Found at i:72102 original size:23 final size:23
Alignment explanation
Indices: 72074--72120 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
72064 CTCTTGCTGA
72074 TTTTG-ATTGCTTGCACCTGTAAT
1 TTTTGAATT-CTTGCACCTGTAAT
* *
72097 TTTTGAATTCTTTCACTTGTAAT
1 TTTTGAATTCTTGCACCTGTAAT
72120 T
1 T
72121 CACGTGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (23 bp):
TTTTGAATTCTTGCACCTGTAAT
Found at i:75774 original size:13 final size:13
Alignment explanation
Indices: 75756--75785 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
75746 GATAATTGTG
75756 TTTAAATTATGCA
1 TTTAAATTATGCA
*
75769 TTTAAATTATGTA
1 TTTAAATTATGCA
75782 TTTA
1 TTTA
75786 GGAAAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTAAATTATGCA
Found at i:92908 original size:15 final size:15
Alignment explanation
Indices: 92888--92928 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
92878 AGAAGACGTT
92888 GGAGTTGAAAATGAG
1 GGAGTTGAAAATGAG
*
92903 GGAGTTAAAAATGAG
1 GGAGTTGAAAATGAG
*
92918 AGAGTTGAAAA
1 GGAGTTGAAAA
92929 GGATGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (15 bp):
GGAGTTGAAAATGAG
Found at i:93090 original size:24 final size:25
Alignment explanation
Indices: 93063--93117 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
93053 AAAATCATGG
*
93063 CTTTTGGAA-AACTAAAAGAT-GTGA
1 CTTTTGGAAGAACCAAAAG-TCGTGA
93087 CTTTT-GAAGAACCAAAAGTCGTGA
1 CTTTTGGAAGAACCAAAAGTCGTGA
93111 CTTTTGG
1 CTTTTGG
93118 CGATTCACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.15
24 22 0.81
25 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (25 bp):
CTTTTGGAAGAACCAAAAGTCGTGA
Found at i:95456 original size:22 final size:21
Alignment explanation
Indices: 95420--95460 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
95410 CATCTTTATT
95420 TCATCATCAACACCATCAAAA
1 TCATCATCAACACCATCAAAA
*
95441 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
95461 TTCCGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAAAA
Found at i:97182 original size:17 final size:17
Alignment explanation
Indices: 97090--97195 Score: 83
Period size: 17 Copynumber: 6.1 Consensus size: 17
97080 ATTAACTAAG
*
97090 TAGTTCATTGATTAAAC
1 TAGTTCATTAATTAAAC
* *
97107 TAGTTTATTAATCAAAC
1 TAGTTCATTAATTAAAC
*
97124 TTGTTCATTCAAGATT--AC
1 TAGTTCATT--A-ATTAAAC
* *
97142 AAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
97160 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
97177 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
97194 TA
1 TA
97196 ACTCTTAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
15 1 0.01
16 1 0.01
17 43 0.62
18 21 0.30
19 1 0.01
20 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:97853 original size:21 final size:21
Alignment explanation
Indices: 97829--97879 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
97819 GAAAGTAAGG
97829 CTAAATTCAACCTCAAATTGT
1 CTAAATTCAACCTCAAATTGT
*
97850 CTAAATTCAACCTTAAATTGT
1 CTAAATTCAACCTCAAATTGT
97871 CTAAATTCA
1 CTAAATTCA
97880 TCCACAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (21 bp):
CTAAATTCAACCTCAAATTGT
Found at i:101782 original size:17 final size:17
Alignment explanation
Indices: 101760--101831 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
101750 AATTAAGAGT
*
101760 TAGTTTAATAAATTAAC
1 TAGTTTAATAAATGAAC
* *
101777 TAGTTTGATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
101794 TAGTTTAATTAATGAGC
1 TAGTTTAATAAATGAAC
* *
101811 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
101829 TAG
1 TAG
101832 ATGCATAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 31 0.70
18 13 0.30
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:101840 original size:17 final size:17
Alignment explanation
Indices: 101820--101901 Score: 51
Period size: 17 Copynumber: 4.8 Consensus size: 17
101810 CTAACTTTAT
101820 TAAATGAACTAGATGCA
1 TAAATGAACTAGATGCA
* * *
101837 TAAATGAAGTAGCT-TA
1 TAAATGAACTAGATGCA
* *
101853 CTATAT-AATCTAAATGCA
1 -TAAATGAA-CTAGATGCA
** * *
101871 TAAATGAACTACTTCCC
1 TAAATGAACTAGATGCA
101888 TAAATGAACTAGAT
1 TAAATGAACTAGAT
101902 TATTTAAATG
Statistics
Matches: 46, Mismatches: 15, Indels: 8
0.67 0.22 0.12
Matches are distributed among these distances:
16 3 0.07
17 40 0.87
18 3 0.07
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAATGAACTAGATGCA
Found at i:102814 original size:72 final size:71
Alignment explanation
Indices: 102697--102834 Score: 163
Period size: 72 Copynumber: 1.9 Consensus size: 71
102687 ATACATCCTT
* * * * * *
102697 TGGCTGAATTCATCCCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGAA
1 TGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGAA
102762 TGTATCC
65 TGTATCC
* *
102769 TGGCTGAAATTCTTCGC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATGA
1 TGGCTG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATGA
102832 ATG
64 ATG
102835 GATGAATTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
71 17 0.30
72 30 0.54
73 9 0.16
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (71 bp):
TGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAAT
GTATCC
Found at i:108003 original size:336 final size:336
Alignment explanation
Indices: 107390--108064 Score: 1350
Period size: 336 Copynumber: 2.0 Consensus size: 336
107380 AAGTCCTTTG
107390 TGATGTGGTGCCCATGAGTGCAAGCCACCTTATACTCGGGCGTCCTTGGCAATATGATAAGAAGG
1 TGATGTGGTGCCCATGAGTGCAAGCCACCTTATACTCGGGCGTCCTTGGCAATATGATAAGAAGG
107455 CTACCCATGATGGATTCTCTAACAAGTACTCTTTCCAGCATCAAGGGAGAAAAATCATATTAGCA
66 CTACCCATGATGGATTCTCTAACAAGTACTCTTTCCAGCATCAAGGGAGAAAAATCATATTAGCA
107520 CCAATGCTTCCAAGCCAAGTTCATGAATGTCAAGTGACCCTCAAGTCACACATAGAATAATGGGA
131 CCAATGCTTCCAAGCCAAGTTCATGAATGTCAAGTGACCCTCAAGTCACACATAGAATAATGGGA
107585 GAAATATAAGAAGGCCAAAGAAATTCATACTCCGAAGATGAATATCTATGCCAGCAGAGGAGATA
196 GAAATATAAGAAGGCCAAAGAAATTCATACTCCGAAGATGAATATCTATGCCAGCAGAGGAGATA
107650 TCCGGAAACATTTATCAACTAAGAAGGCTCTACTTATACTTATGTATAAGGAAAGTTTTCTTCTT
261 TCCGGAAACATTTATCAACTAAGAAGGCTCTACTTATACTTATGTATAAGGAAAGTTTTCTTCTT
107715 ACTAACCCTCC
326 ACTAACCCTCC
107726 TGATGTGGTGCCCATGAGTGCAAGCCACCTTATACTCGGGCGTCCTTGGCAATATGATAAGAAGG
1 TGATGTGGTGCCCATGAGTGCAAGCCACCTTATACTCGGGCGTCCTTGGCAATATGATAAGAAGG
107791 CTACCCATGATGGATTCTCTAACAAGTACTCTTTCCAGCATCAAGGGAGAAAAATCATATTAGCA
66 CTACCCATGATGGATTCTCTAACAAGTACTCTTTCCAGCATCAAGGGAGAAAAATCATATTAGCA
107856 CCAATGCTTCCAAGCCAAGTTCATGAATGTCAAGTGACCCTCAAGTCACACATAGAATAATGGGA
131 CCAATGCTTCCAAGCCAAGTTCATGAATGTCAAGTGACCCTCAAGTCACACATAGAATAATGGGA
107921 GAAATATAAGAAGGCCAAAGAAATTCATACTCCGAAGATGAATATCTATGCCAGCAGAGGAGATA
196 GAAATATAAGAAGGCCAAAGAAATTCATACTCCGAAGATGAATATCTATGCCAGCAGAGGAGATA
107986 TCCGGAAACATTTATCAACTAAGAAGGCTCTACTTATACTTATGTATAAGGAAAGTTTTCTTCTT
261 TCCGGAAACATTTATCAACTAAGAAGGCTCTACTTATACTTATGTATAAGGAAAGTTTTCTTCTT
108051 ACTAACCCTCC
326 ACTAACCCTCC
108062 TGA
1 TGA
108065 AGGCTTGCCT
Statistics
Matches: 339, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
336 339 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (336 bp):
TGATGTGGTGCCCATGAGTGCAAGCCACCTTATACTCGGGCGTCCTTGGCAATATGATAAGAAGG
CTACCCATGATGGATTCTCTAACAAGTACTCTTTCCAGCATCAAGGGAGAAAAATCATATTAGCA
CCAATGCTTCCAAGCCAAGTTCATGAATGTCAAGTGACCCTCAAGTCACACATAGAATAATGGGA
GAAATATAAGAAGGCCAAAGAAATTCATACTCCGAAGATGAATATCTATGCCAGCAGAGGAGATA
TCCGGAAACATTTATCAACTAAGAAGGCTCTACTTATACTTATGTATAAGGAAAGTTTTCTTCTT
ACTAACCCTCC
Found at i:109748 original size:11 final size:13
Alignment explanation
Indices: 109716--109745 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
109706 TGGCCAAAGA
109716 TGAAAAGGTATGT
1 TGAAAAGGTATGT
109729 TGAAAAGGTATG-
1 TGAAAAGGTATGT
109741 TGAAA
1 TGAAA
109746 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:120841 original size:23 final size:23
Alignment explanation
Indices: 120811--120864 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
120801 GCATTCAATC
120811 TTGAATCTCCATGGTTAGGTTTA
1 TTGAATCTCCATGGTTAGGTTTA
120834 TTGAATCTCCATGGTTAGGTTTA
1 TTGAATCTCCATGGTTAGGTTTA
120857 TTGAATCT
1 TTGAATCT
120865 TCCCTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (23 bp):
TTGAATCTCCATGGTTAGGTTTA
Found at i:125660 original size:18 final size:18
Alignment explanation
Indices: 125639--125673 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
125629 AATAATGATG
*
125639 AAAATAAACCTCACCAAC
1 AAAAAAAACCTCACCAAC
*
125657 AAAAAAAATCTCACCAA
1 AAAAAAAACCTCACCAA
125674 TACACTCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.29, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAAAACCTCACCAAC
Found at i:134894 original size:12 final size:12
Alignment explanation
Indices: 134864--134898 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
134854 TATCTTTTGT
134864 TTATCTTGTTT-
1 TTATCTTGTTTC
*
134875 TAATCTTGTTTC
1 TTATCTTGTTTC
134887 TTATCTTGTTTC
1 TTATCTTGTTTC
134899 CAGCACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:135125 original size:11 final size:12
Alignment explanation
Indices: 135096--135130 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
135086 TTTTGTGCTG
135096 GAAACAAGATAA
1 GAAACAAGATAA
*
135108 GAAACAAGATTA
1 GAAACAAGATAA
135120 -AAACAAGATAA
1 GAAACAAGATAA
135131 ATAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:141934 original size:13 final size:13
Alignment explanation
Indices: 141916--141984 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
141906 CTACCTATAA
*
141916 CATCACCATCTTC
1 CATCACCATATTC
141929 CATCACCAT-TTC
1 CATCACCATATTC
* **
141941 CA-CGCC-TATAA
1 CATCACCATATTC
*
141952 CATCACCATCTTC
1 CATCACCATATTC
*
141965 CATCACCATAGTC
1 CATCACCATATTC
141978 CATCACC
1 CATCACC
141985 TTCACGCCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 8 0.18
13 29 0.66
ACGTcount: A:0.28, C:0.43, G:0.03, T:0.26
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:142412 original size:7 final size:6
Alignment explanation
Indices: 142381--142433 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
142371 GTGCTGCAAC
* * * *
142381 AAAAGCA AAAAAA AAAAGA AAAAGA AAGAAGA AATACA AAAAGA GAAAGA
1 AAAAG-A AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA
142431 AAA
1 AAA
142434 GACCCATACA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:142726 original size:17 final size:17
Alignment explanation
Indices: 142704--142736 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
142694 ATCCTACCCA
142704 TATACCATAACCATTTC
1 TATACCATAACCATTTC
*
142721 TATACCCTAACCATTT
1 TATACCATAACCATTT
142737 TTTTAAGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.36
Consensus pattern (17 bp):
TATACCATAACCATTTC
Found at i:146858 original size:27 final size:28
Alignment explanation
Indices: 146828--146889 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
146818 CTTTTCTTTG
*
146828 CTTTTCTTCTTTTGGAATG-TTGAACTT
1 CTTTTCTTCTTTTGGAATGCTTCAACTT
* *
146855 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAACTT
146883 CTTTTCT
1 CTTTTCT
146890 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.13, T:0.58
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAACTT
Found at i:162632 original size:17 final size:17
Alignment explanation
Indices: 162610--162649 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
162600 CTGCCATCAC
162610 CTTCACACCTACTACAT
1 CTTCACACCTACTACAT
**
162627 CTTCACTTCTACTACAT
1 CTTCACACCTACTACAT
162644 CTTCAC
1 CTTCAC
162650 TTCTATCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.40, G:0.00, T:0.35
Consensus pattern (17 bp):
CTTCACACCTACTACAT
Found at i:162650 original size:17 final size:17
Alignment explanation
Indices: 162618--162654 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
162608 ACCTTCACAC
162618 CTACTACATCTTCACTT
1 CTACTACATCTTCACTT
162635 CTACTACATCTTCACTT
1 CTACTACATCTTCACTT
162652 CTA
1 CTA
162655 TCACCATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (17 bp):
CTACTACATCTTCACTT
Found at i:164314 original size:45 final size:45
Alignment explanation
Indices: 164264--164359 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
164254 AGAGTGAAGG
164264 ACAAATTTTACCTAACAAATCTTCTTCTACTATTTCTTTTTCCTA
1 ACAAATTTTACCTAACAAATCTTCTTCTACTATTTCTTTTTCCTA
* *
164309 ACAAATTTTACCTAACAAATCTTTTTCTACTATTTCTTTTTTCTA
1 ACAAATTTTACCTAACAAATCTTCTTCTACTATTTCTTTTTCCTA
164354 ACAAAT
1 ACAAAT
164360 ATGTCTTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (45 bp):
ACAAATTTTACCTAACAAATCTTCTTCTACTATTTCTTTTTCCTA
Done.