Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007718.1 Hibiscus syriacus cultivar Beakdansim tig00109949_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: 1062497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1012364 original size:12 final size:13
Alignment explanation
Indices: 1012300--1012365 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 13
1012290 CCATATTGAT
*
1012300 TTATTATTAT-TA
1 TTATTATAATATA
1012312 TTATTATAAT-TA
1 TTATTATAATATA
*
1012324 TTATTATTATCATTA
1 TTATTATAAT-A-TA
*
1012339 TTATTATTAT-TA
1 TTATTATAATATA
1012351 TTATTA-AATATA
1 TTATTATAATATA
1012363 TTA
1 TTA
1012366 AATATATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
11 2 0.04
12 33 0.70
15 12 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATAATATA
Found at i:1013791 original size:13 final size:13
Alignment explanation
Indices: 1013775--1013814 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
1013765 ATATAATAAA
1013775 TAAATATTTATTT
1 TAAATATTTATTT
*
1013788 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1013802 T-AATATTTATTT
1 TAAATATTTATTT
1013814 T
1 T
1013815 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1025135 original size:7 final size:7
Alignment explanation
Indices: 1025123--1025167 Score: 63
Period size: 7 Copynumber: 6.0 Consensus size: 7
1025113 TGCTTGAAGA
1025123 AAAAAAG
1 AAAAAAG
1025130 AAAAAAG
1 AAAAAAG
1025137 AAAAAAG
1 AAAAAAG
1025144 AAAAAAGAG
1 -AAAAA-AG
1025153 AAAAAAG
1 AAAAAAG
1025160 AAGAAAAG
1 AA-AAAAG
1025168 GGGGGGTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 18 0.51
8 15 0.43
9 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1025154 original size:23 final size:23
Alignment explanation
Indices: 1025119--1025167 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
1025109 ATTATGCTTG
1025119 AAGAAAAAAAGAAAAAAGAA-AA
1 AAGAAAAAAAGAAAAAAGAAGAA
1025141 AAGAAAAAAGAGAAAAAAGAAGAA
1 AAGAAAAAA-AGAAAAAAGAAGAA
1025165 AAG
1 AAG
1025168 GGGGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 9 0.36
23 11 0.44
24 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAGAAAAAAAGAAAAAAGAAGAA
Found at i:1026445 original size:83 final size:84
Alignment explanation
Indices: 1026303--1026619 Score: 530
Period size: 83 Copynumber: 3.8 Consensus size: 84
1026293 ACATTAACTG
* * *
1026303 GAAAGATGAATGTGCTC-ATATCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGT
1 GAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
* *
1026367 AAAACCAATCATTGAATTT
66 AAAACCAGTTATTGAATTT
* *
1026386 GAAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGT
1 GAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
*
1026450 AAAACGAGTTATTGAATTT
66 AAAACCAGTTATTGAATTT
1026469 GAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
1 GAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
1026534 AAAACCAGTTATTGAATTT
66 AAAACCAGTTATTGAATTT
*
1026553 GGAAAGATGAATGTGCCCAATAGCATCTTCCGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 -GAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1026618 TA
65 TA
1026620 TGAACCCCAA
Statistics
Matches: 222, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
83 93 0.42
84 64 0.29
85 65 0.29
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (84 bp):
GAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
AAAACCAGTTATTGAATTT
Found at i:1027849 original size:226 final size:226
Alignment explanation
Indices: 1027455--1027989 Score: 808
Period size: 226 Copynumber: 2.4 Consensus size: 226
1027445 GCAAAGATTT
*
1027455 AAATCTATCACTTGATGGATTATCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1027520 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAACTTGATG
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAACTTGATG
* *
1027585 GATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCA
131 GATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1027650 TAATGAGAAGAATTTGTTCAACCTTTTGCTC
196 TAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
1027681 AAATCTATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATATTGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1027746 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATG
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAACTTGATG
1027811 GATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
131 GATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
* * *
1027876 TAATGAGAAGAATTTGTTCGA-CTTTAG-TT
196 TAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
1027905 TAATC-A--AC---AT-CA--A-CTTTTCCAGAG-AAAGTTCATAATGAGAAGAATTTATCTGAA
1 AAATCTATCACTTGATGGATTAGCTTTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAA
*
1027959 GAAGGAAGAAGAGAGTTCATAATGAGAAGAA
65 GAAGGATGAAGA-AGTTCATAATGAGAAGAA
1027990 CTCATCTGAA
Statistics
Matches: 287, Mismatches: 20, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
214 45 0.16
215 19 0.07
217 1 0.00
218 2 0.01
221 2 0.01
223 1 0.00
224 5 0.02
225 5 0.02
226 207 0.72
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (226 bp):
AAATCTATCACTTGATGGATTAGCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATAACTTGATG
GATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:1027916 original size:113 final size:113
Alignment explanation
Indices: 1027455--1027894 Score: 790
Period size: 113 Copynumber: 3.9 Consensus size: 113
1027445 GCAAAGATTT
* * * *
1027455 AAATCTATCACTTGATGGATTATCTTTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1027520 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
1027568 AAATCCATAACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1027633 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
1027681 AAATCTATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATATTGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
1027746 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1027794 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
1027859 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTC
1027895 GACTTTAGTT
Statistics
Matches: 314, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 314 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:1028013 original size:36 final size:37
Alignment explanation
Indices: 1027927--1028027 Score: 132
Period size: 41 Copynumber: 2.6 Consensus size: 37
1027917 ACTTTTCCAG
* *
1027927 AGAAAGTTCATAATGAGAAGAATTTATCTGAAGAAGGA
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
1027965 AGAAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-A
1 AG-A-A-AGTTCATAATGAGAAGAACTCATCTGAAGAAGA
*
1028004 AGAAAGTTCAAAATGAGAAGAACT
1 AGAAAGTTCATAATGAGAAGAACT
1028028 TGGTTAACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
36 19 0.33
37 1 0.02
38 3 0.05
39 4 0.07
40 1 0.02
41 29 0.51
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.20
Consensus pattern (37 bp):
AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:1028398 original size:3 final size:3
Alignment explanation
Indices: 1028386--1028444 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
1028376 TATTGATTTT
*
1028386 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1028433 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1028445 AATATATTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1029778 original size:13 final size:13
Alignment explanation
Indices: 1029762--1029801 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
1029752 ATATAATAAA
1029762 TAAATATTTATTT
1 TAAATATTTATTT
*
1029775 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1029789 T-AATATTTATTT
1 TAAATATTTATTT
1029801 T
1 T
1029802 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1031146 original size:26 final size:27
Alignment explanation
Indices: 1031109--1031160 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
1031099 TTTAAAAAAG
1031109 AAAAATAATAATAAAAACAAACAAATT
1 AAAAATAATAATAAAAACAAACAAATT
* * *
1031136 AAAAAT-ATAATGAAAATAAATAAAT
1 AAAAATAATAATAAAAACAAACAAAT
1031161 AATATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (27 bp):
AAAAATAATAATAAAAACAAACAAATT
Found at i:1031156 original size:22 final size:22
Alignment explanation
Indices: 1031131--1031207 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
1031121 AAAAACAAAC
1031131 AAATTAAAAATAT-AATGAAAAT
1 AAATTAAAAATATAAAT-AAAAT
1031153 AAA-TAAATAATATAAATAAAAT
1 AAATTAAA-AATATAAATAAAAT
* * *
1031175 -AATAAAAAATTTATATATAAA-
1 AAATTAAAAATATAAATA-AAAT
1031196 AAATATAAAAAT
1 AAAT-TAAAAAT
1031208 GTATGTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 14 0.31
22 22 0.49
23 9 0.20
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (22 bp):
AAATTAAAAATATAAATAAAAT
Found at i:1031202 original size:13 final size:14
Alignment explanation
Indices: 1031151--1031202 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
1031141 TATAATGAAA
1031151 ATAAATAAATA-AT
1 ATAAATAAATATAT
1031164 ATAAATAAA-ATA-
1 ATAAATAAATATAT
1031176 ATAAA-AAATTTATAT
1 ATAAATAAA--TATAT
1031191 ATAAA-AAATATA
1 ATAAATAAATATA
1031203 AAAATGTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.09
12 6 0.18
13 14 0.41
14 3 0.09
15 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAATAAATATAT
Found at i:1031216 original size:25 final size:23
Alignment explanation
Indices: 1031163--1031227 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
1031153 AAATAAATAA
*
1031163 TATAAATAAAATAATAAAAAATT
1 TATATATAAAATAATAAAAAATT
*
1031186 TATATATAAAA-AATATAAAAATG
1 TATATATAAAATAATA-AAAAATT
* *
1031209 TATGTATAATATAATAAAA
1 TATATATAAAATAATAAAA
1031228 TACTAGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.11
23 28 0.78
24 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
TATATATAAAATAATAAAAAATT
Found at i:1031253 original size:10 final size:10
Alignment explanation
Indices: 1031238--1031264 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1031228 TACTAGTAAT
1031238 AATAATAAAA
1 AATAATAAAA
1031248 AATAATAAAA
1 AATAATAAAA
1031258 AATAATA
1 AATAATA
1031265 TACATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AATAATAAAA
Found at i:1031253 original size:13 final size:14
Alignment explanation
Indices: 1031234--1031316 Score: 50
Period size: 13 Copynumber: 6.1 Consensus size: 14
1031224 AAAATACTAG
1031234 TAATAATAATAAAA
1 TAATAATAATAAAA
1031248 -AATAATAA-AAAA
1 TAATAATAATAAAA
*
1031260 TAAT-ATACATATAA
1 TAATAATA-ATAAAA
* *
1031274 TATTAACTAAAAAAA
1 TAATAA-TAATAAAA
* *
1031289 TAGTAATCATAGAAA
1 TAATAATAATA-AAA
*
1031304 -CATAA-AATAAAA
1 TAATAATAATAAAA
1031316 T
1 T
1031317 GAAATAAGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
12 10 0.19
13 15 0.29
14 12 0.23
15 13 0.25
16 2 0.04
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:1031421 original size:69 final size:69
Alignment explanation
Indices: 1031283--1031416 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 69
1031273 ATATTAACTA
1031283 AAAAAATAGTAATCATAGAAACATAAAATAAAATGAAATAAGAATATATATATAACGTTAGGAAA
1 AAAAAATAGTAATCATAGAAACATAAAATAAAA-GAAATAAGAATATATATATAAC--TAGGAAA
1031348 ATATAGT
63 ATATAGT
* *
1031355 AAAAAATAGTAA--ATAAGTAAACAT-AGATAAAA-AAATAATAATATATATATAA-TAGGAAAA
1 AAAAAATAGTAATCAT-AG-AAACATAAAATAAAAGAAATAAGAATATATATATAACTAGGAAAA
1031415 TA
64 TA
1031417 ATATAATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
66 10 0.17
69 19 0.33
70 2 0.03
71 9 0.16
72 18 0.31
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.25
Consensus pattern (69 bp):
AAAAAATAGTAATCATAGAAACATAAAATAAAAGAAATAAGAATATATATATAACTAGGAAAATA
TAGT
Found at i:1032000 original size:37 final size:37
Alignment explanation
Indices: 1031959--1032043 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
1031949 GGATCCTATC
* *
1031959 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
* * ** *
1031996 TTTAGGATTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
1032033 TTTAGGAGTTT
1 TTTAGGAGTTT
1032044 GAATCCTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
Found at i:1032989 original size:106 final size:106
Alignment explanation
Indices: 1032805--1034066 Score: 1942
Period size: 106 Copynumber: 11.9 Consensus size: 106
1032795 GCATTGTTCC
* * * * * *
1032805 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTAGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
1032870 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGCTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1032911 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
* *
1032975 ACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1033017 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
*
1033081 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1033123 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1033188 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1033229 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGAGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
1033293 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1033335 GAG-CACAATATCTTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTC-CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
1033399 ACCAGCGATCCCTTCGTCATGAAGTTGAACTTACGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1033441 AAGTCTAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1033506 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
1033547 GAGTCCAATAT-CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
**
1033611 CCAGCGGTCCCTTCGTAATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1033652 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1033717 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1033758 GAGTCCAATATACTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1033823 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1033864 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1033929 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1033970 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1034035 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTG
1034067 TGTTATCTCA
Statistics
Matches: 1068, Mismatches: 80, Indels: 16
0.92 0.07 0.01
Matches are distributed among these distances:
105 103 0.10
106 962 0.90
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1035686 original size:6 final size:6
Alignment explanation
Indices: 1035675--1035733 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
1035665 TTTTTTGTCC
* * *
1035675 CTTTTT CTTTTT GATTTTT CTTTTTT CTTTTT GTTTTT CTTCTTT -TTCTT
1 CTTTTT CTTTTT -CTTTTT C-TTTTT CTTTTT CTTTTT CTT-TTT CTTTTT
1035725 CTTTTT CTT
1 CTTTTT CTT
1035734 CTTTTTTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 2 0.05
6 27 0.63
7 14 0.33
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:1035699 original size:19 final size:18
Alignment explanation
Indices: 1035675--1035746 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
1035665 TTTTTTGTCC
1035675 CTTTTTCTTTTTGATTTTT
1 CTTTTTCTTTTTG-TTTTT
1035694 CTTTTTTCTTTTTGTTTTT
1 C-TTTTTCTTTTTGTTTTT
* *
1035713 CTTCTTT-TTCTTCTTTTT
1 CTT-TTTCTTTTTGTTTTT
*
1035731 C-TTCT-TTTTTGTTTTT
1 CTTTTTCTTTTTGTTTTT
1035747 GCCCTTATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 11 0.24
17 1 0.02
18 12 0.26
19 10 0.22
20 12 0.26
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.81
Consensus pattern (18 bp):
CTTTTTCTTTTTGTTTTT
Found at i:1035722 original size:9 final size:9
Alignment explanation
Indices: 1035689--1035739 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
1035679 TTCTTTTTGA
*
1035689 TTTTTCTTT
1 TTTTTCTTC
* *
1035698 TTTCTTTTTG
1 TTT-TTCTTC
1035708 TTTTTCTTC
1 TTTTTCTTC
1035717 TTTTTCTTC
1 TTTTTCTTC
1035726 TTTTTCTTC
1 TTTTTCTTC
1035735 TTTTT
1 TTTTT
1035740 TGTTTTTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
9 30 0.81
10 7 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:1040220 original size:17 final size:17
Alignment explanation
Indices: 1040191--1040248 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
1040181 AATATAATGA
*
1040191 AAATAAATAAATAGTAT
1 AAATAAATAAATAATAT
1040208 AAATAAA-ATAATAATAT
1 AAATAAATA-AATAATAT
* * *
1040225 ATATATATATATAATAT
1 AAATAAATAAATAATAT
1040242 AAA-AAAT
1 AAATAAAT
1040249 GTATGTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 4 0.12
17 28 0.85
18 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATAAATAAATAATAT
Found at i:1040340 original size:28 final size:28
Alignment explanation
Indices: 1040273--1040356 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 28
1040263 ATAAAATACT
*
1040273 AAATAGTAAT-A-ATAATAATAAATGAAA
1 AAATAGTAATCATATAATATTAAAT-AAA
1040300 ATAA-A-T-ATACATATAATATTAAATAAA
1 A-AATAGTAAT-CATATAATATTAAATAAA
* *
1040327 AAATAGTAATCATAGAAATATAAAATAAA
1 AAATAGTAATCATA-TAATATTAAATAAA
1040356 A
1 A
1040357 TGAAGTAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 8 0.17
28 18 0.39
29 15 0.33
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (28 bp):
AAATAGTAATCATATAATATTAAATAAA
Found at i:1040374 original size:2 final size:2
Alignment explanation
Indices: 1040367--1040395 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1040357 TGAAGTAAGA
1040367 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 A
1040396 ACGTTAGGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1040541 original size:2 final size:2
Alignment explanation
Indices: 1040534--1040561 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1040524 AAAATATAAT
1040534 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1040562 ATAATAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1041105 original size:37 final size:37
Alignment explanation
Indices: 1041012--1041113 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
1041002 ATGCTTGTGG
* * * ** *
1041012 ATCCTATCTTTAGAAGTTTAAATAATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
1041049 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
1041086 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
1041114 TAGTACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:1046784 original size:16 final size:14
Alignment explanation
Indices: 1046751--1046780 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1046741 TAAATCAACC
1046751 TTGTATACATCCTT
1 TTGTATACATCCTT
1046765 TTGTATACATCCTT
1 TTGTATACATCCTT
1046779 TT
1 TT
1046781 TTGTCCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (14 bp):
TTGTATACATCCTT
Found at i:1046808 original size:3 final size:3
Alignment explanation
Indices: 1046800--1046869 Score: 70
Period size: 3 Copynumber: 22.7 Consensus size: 3
1046790 TTTTAATTGT
* * *
1046800 TTA TTA TTA GTTA TTA TAA TTA TTA TT- TTAA TTA TTA TCA CTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
*
1046846 TTA GTA TTA TTA TTTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TT
1046870 TTTCTTTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 45 0.82
4 8 0.15
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1049436 original size:16 final size:16
Alignment explanation
Indices: 1049417--1049469 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1049407 ACCAATCATT
1049417 AAAAACACAAATATCC
1 AAAAACACAAATATCC
*
1049433 AAAAACAATCAAATATTC
1 AAAAAC-A-CAAATATCC
*
1049451 AAACAAC-CAAACATCC
1 AAA-AACACAAATATCC
1049467 AAA
1 AAA
1049470 TCATTCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 16 0.52
17 1 0.03
18 11 0.35
19 3 0.10
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAACACAAATATCC
Found at i:1051520 original size:22 final size:21
Alignment explanation
Indices: 1051495--1051551 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
1051485 ATTCTATGCT
1051495 AGTAGTATCGATACCTA-GAAAG
1 AGTAGTATCGATACCTATG--AG
*
1051517 AGTAGTATCGATA-CTATGTG
1 AGTAGTATCGATACCTATGAG
1051537 AGTAGTATCGATACC
1 AGTAGTATCGATACC
1051552 AAGTGCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 14 0.44
21 4 0.12
22 14 0.44
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (21 bp):
AGTAGTATCGATACCTATGAG
Found at i:1056512 original size:18 final size:18
Alignment explanation
Indices: 1056491--1056525 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1056481 CGAATAATTG
* *
1056491 AATCGAATATAATATTTA
1 AATCGAACATAAAATTTA
1056509 AATCGAACATAAAATTT
1 AATCGAACATAAAATTT
1056526 TAAAATTAAT
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:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (18 bp):
AATCGAACATAAAATTTA
Found at i:1058371 original size:35 final size:35
Alignment explanation
Indices: 1058324--1058441 Score: 114
Period size: 35 Copynumber: 3.3 Consensus size: 35
1058314 GTCTCTGCAA
* *
1058324 GTTCAGTTCGATCAAACTGGTAATTCCTTATATAG
1 GTTCAGTCCGATCAAATTGGTAATTCCTTATATAG
*
1058359 GTTCAGTCCGATCGAATTGGTAATTACC-TATATTAG
1 GTTCAGTCCGATCAAATTGGTAATT-CCTTATA-TAG
* * * * *
1058395 GTTTAG-CTTGGTTAAATTGGTAATTCTTTATATAG
1 GTTCAGTC-CGATCAAATTGGTAATTCCTTATATAG
*
1058430 GTTCAGACCGAT
1 GTTCAGTCCGAT
1058442 GGAGGTGTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
35 38 0.58
36 28 0.42
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.39
Consensus pattern (35 bp):
GTTCAGTCCGATCAAATTGGTAATTCCTTATATAG
Done.