Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007576.1 Hibiscus syriacus cultivar Beakdansim tig00021598_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: 38408
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:919 original size:59 final size:59
Alignment explanation
Indices: 768--1093 Score: 453
Period size: 59 Copynumber: 5.6 Consensus size: 59
758 GATTACCAGA
** * ** *
768 AGGGCACTTTATGTGCTAAAATGTCAAGGAATTCATACTAA--GTATGAATTTTCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
825 AGGGCACTTC--GTGCTAACATGAGAAGGAATTCATACTAAGGGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * *
882 AGGGCACTTTGTGTGCTAACATGAAAAGGAGTTCATACTAAGTATATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
** * ** *
941 AGGGTTCTCCGTGTGCTAACATGAGAAACAATTCAAACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
1000 AGGGCACTTCGTGTGCTAACATGAGAATGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
1059 AGGGCACTTCGTATGCTAACATGAGAAGGAATTCA
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCA
1094 GATAACTCCG
Statistics
Matches: 237, Mismatches: 28, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
55 26 0.11
57 33 0.14
59 178 0.75
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:10503 original size:3 final size:3
Alignment explanation
Indices: 10497--10545 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
10487 TTATTTTAAA
* *
10497 ATT ATT ATT ATT ATT ATT ATT A-T ATT AAT ATAT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
10542 ATT A
1 ATT A
10546 CAAAGCCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:10532 original size:18 final size:17
Alignment explanation
Indices: 10497--10545 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
10487 TTATTTTAAA
*
10497 ATTATTATTATTATTATT
1 ATTA-TATTAATATTATT
10515 ATTATATTAATA-TA-T
1 ATTATATTAATATTATT
10530 ATTATTATTAATATTA
1 ATTA-TATTAATATTA
10546 CAAAGCCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 9 0.32
18 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATATTAATATTATT
Found at i:15780 original size:15 final size:15
Alignment explanation
Indices: 15760--15791 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15750 ATCAATACCT
15760 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
15775 TTTTGCATACATTCA
1 TTTTGCATACATGCA
15790 TT
1 TT
15792 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:23095 original size:1 final size:1
Alignment explanation
Indices: 23084--23145 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
23074 ATGCTTGAAG
* * * * * * *
23084 AAAAAAGAAAAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23146 GGGGGGTCAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:23099 original size:10 final size:10
Alignment explanation
Indices: 23084--23145 Score: 92
Period size: 10 Copynumber: 6.2 Consensus size: 10
23074 ATGCTTGAAG
23084 AAAAAAGAAA
1 AAAAAAGAAA
23094 AAAAAAG--A
1 AAAAAAGAAA
23102 AAAAAAGAAA
1 AAAAAAGAAA
23112 AAAAAAGAAA
1 AAAAAAGAAA
23122 AAAAAAGAAAA
1 AAAAAAG-AAA
23133 AGAAAAAGAAA
1 A-AAAAAGAAA
23144 AA
1 AA
23146 GGGGGGTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.17
10 26 0.54
11 8 0.17
12 6 0.12
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:23107 original size:18 final size:18
Alignment explanation
Indices: 23084--23139 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
23074 ATGCTTGAAG
23084 AAAAAAGAAAAAAAAAGA
1 AAAAAAGAAAAAAAAAGA
23102 AAAAAAGAAAAAAAAAG-
1 AAAAAAGAAAAAAAAAGA
*
23119 AAAAAA-AAAGAAAAAGA
1 AAAAAAGAAAAAAAAAGA
23136 AAAA
1 AAAA
23140 GAAAAAGGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 9 0.25
17 10 0.28
18 17 0.47
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAGA
Found at i:23120 original size:28 final size:28
Alignment explanation
Indices: 23084--23146 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
23074 ATGCTTGAAG
23084 AAAAAAGAAAAAAAAAGAAAAA-AAGAAA
1 AAAAAAGAAAAAAAAAGAAAAAGAA-AAA
23112 AAAAAAGAAAAAAAAAGAAAAAGAAAAA
1 AAAAAAGAAAAAAAAAGAAAAAGAAAAA
*
23140 GAAAAAG
1 AAAAAAG
23147 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAAAAAAAAGAAAAAGAAAAA
Found at i:23144 original size:18 final size:17
Alignment explanation
Indices: 23081--23146 Score: 82
Period size: 17 Copynumber: 3.8 Consensus size: 17
23071 ATTATGCTTG
23081 AAGAAAAAAGAAAA-AAA
1 AAGAAAAAA-AAAAGAAA
*
23098 AAGAAAAAAAGAAAAAAA
1 AAGAAAAAAA-AAAGAAA
23116 AAG-AAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
23132 AAGAAAAAGAAAAAG
1 AAGAAAAA-AAAAAG
23147 GGGGGTCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
16 10 0.23
17 22 0.50
18 12 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:24314 original size:187 final size:185
Alignment explanation
Indices: 23999--24475 Score: 766
Period size: 187 Copynumber: 2.6 Consensus size: 185
23989 ACAAGTGCCG
*
23999 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTT--GTTATCTGATCTGGTTTGGTATAAACCCCG-
24064 AAAAACCAATCATT-A-TTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
63 AAAAACCAATCATTGATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
24127 TATCTGATCTGGTTTGGTATGAACCCCGAAAAAACCAATCATTGAATTTGGAAGATGAA
128 TAACTGATCTGGTTTGGTATGAACCCCG-AAAAACCAATCATTGAATTTGGAAGATGAA
*
24186 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTT-TAACTCTGATCTGGTTTGGTATAAACCCCGAA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGTTA-TCTGATCTGGTTTGGTATAAACCCCGAA
24250 AAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
65 AAACCAATCATTG-ATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
24315 AACTGATCTGGTTTGGTATGAACCCCGAAAAACCAATCATTGAATTTGGAAGATGAA
129 AACTGATCTGGTTTGGTATGAACCCCGAAAAACCAATCATTGAATTTGGAAGATGAA
* *
24372 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAAACCAC--
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTT--GTTATCTGATCTGGTTTGGTATAAACCCCGA
* *
24435 AAAACCAATCATTGGATATTGAAAGATGAATTTGCTCATAG
64 AAAACCAATCATT-GAT-TTGGAAGATGAATGTGCTCATAG
24476 TAGAAATAAG
Statistics
Matches: 273, Mismatches: 8, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
184 16 0.06
185 25 0.09
186 78 0.29
187 129 0.47
188 23 0.08
189 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (185 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGTTATCTGATCTGGTTTGGTATAAACCCCGAAA
AACCAATCATTGATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAA
CTGATCTGGTTTGGTATGAACCCCGAAAAACCAATCATTGAATTTGGAAGATGAA
Found at i:24379 original size:94 final size:94
Alignment explanation
Indices: 23999--24475 Score: 783
Period size: 92 Copynumber: 5.1 Consensus size: 94
23989 ACAAGTGCCG
23999 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG-
24064 AAAAACCAATCATT--A-TTGGAAGATGAA
65 AAAAACCAATCATTGAATTTGGAAGATGAA
24091 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCG-
24156 AAAAACCAATCATTGAATTTGGAAGATGAA
65 AAAAACCAATCATTGAATTTGGAAGATGAA
* *
24186 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTT---TAACTCTGATCTGGTTTGGTATAAACCCCG
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA-TCTGATCTGGTTTGGTATGAACCCCG
24248 AAAAACCAATCATTGAATTTGGAAGATGAA
65 AAAAACCAATCATTGAATTTGGAAGATGAA
*
24278 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAACTGATCTGGTTTGGTATGAACCCCGA
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
24343 AAAACCAATCATTGAATTTGGAAGATGAA
66 AAAACCAATCATTGAATTTGGAAGATGAA
*
24372 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAA-ACC-A
1 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
* *
24434 CAAAACCAATCATTGGATATTGAAAGATGAA
66 -AAAACCAATCATTGAAT-TTGGAAGATGAA
*
24465 TTTGCTCATAG
1 TGTGCTCATAG
24476 TAGAAATAAG
Statistics
Matches: 366, Mismatches: 10, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
91 1 0.00
92 161 0.44
93 49 0.13
94 109 0.30
95 46 0.13
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (94 bp):
TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCGA
AAAACCAATCATTGAATTTGGAAGATGAA
Found at i:25027 original size:95 final size:95
Alignment explanation
Indices: 24864--25061 Score: 387
Period size: 95 Copynumber: 2.1 Consensus size: 95
24854 TATTCTCCTC
24864 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
*
24929 AAAGATCACTTCATAATCAGATGAGTTGTT
66 AAAGATCACTTCATAATCAGATGAGTAGTT
24959 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
1 ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
25024 AAAGATCACTTCATAATCAGATGAGTAGTT
66 AAAGATCACTTCATAATCAGATGAGTAGTT
25054 ATCAGAAT
1 ATCAGAAT
25062 TAACATGTTG
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 102 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (95 bp):
ATCAGAATCAGAATTCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTG
AAAGATCACTTCATAATCAGATGAGTAGTT
Found at i:25589 original size:113 final size:114
Alignment explanation
Indices: 25394--26160 Score: 949
Period size: 113 Copynumber: 6.7 Consensus size: 114
25384 AGTGTCAGTT
25394 AAAGTTCATAATAAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* *
25458 TCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGC-TTTGCCAGAG
66 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTTCCAGAG
25506 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* *
25571 TCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGC-TTTGCCAGAG
66 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTTCCAGAG
*
25619 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* * *
25684 TCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTTCCAG-G
66 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTTCCAGAG
* * *
25732 TAGAGTTCATAATGAGAAGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAAT
1 -AAAGTTCATAATAAGAAGAACTCA-T-C-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
* **
25797 TTGTTCAACCTTATGCTCAAATCCATCACTTGATGGATCAGC-TTTTCCAGTT
62 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTTCCAGAG
* * * *
25849 AGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGAGAAGAACTTG
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTG
* * * * *
25913 TTTAACCTTTTGTTTAAATTCATCACTTGATGGATCAACA-TTTCCAGAG
65 TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTTCCAGAG
* * * * **
25962 AAAGTTCATAATAAGAAGAACTTATTTGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* * ** * *
26026 TCAACCTTTTGCAT-AATTCTATCACAGAAGCAGATAGATTAGCATAAACCTTTCCAGAG
66 TCAACCTTTTGC-TCAAATCCATCAC-----TTGATGGATCAGCAT-----TTTCCAGAG
* * * * * * *
26085 AAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGAAGAACTTAT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
26150 TCAACCTTTTG
66 TCAACCTTTTG
26161 AATGACTCTA
Statistics
Matches: 584, Mismatches: 48, Indels: 34
0.88 0.07 0.05
Matches are distributed among these distances:
112 81 0.14
113 280 0.48
114 31 0.05
115 2 0.00
116 32 0.05
117 82 0.14
123 37 0.06
124 39 0.07
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (114 bp):
AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTTTCCAGAG
Found at i:25830 original size:230 final size:229
Alignment explanation
Indices: 25394--26160 Score: 962
Period size: 230 Copynumber: 3.3 Consensus size: 229
25384 AGTGTCAGTT
*
25394 AAAGTTCATAATAAGAAGAACTCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
* *
25458 TCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATAAGAA
66 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAA
*
25523 GAACTCA-T-C-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
131 GAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
25585 AAATCCATCACTTGATGGATTAGCTTTGCCAGAG
196 AAATCCATCACTTGATGGATTAGCTTTTCCAGAG
* *
25619 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
* * * *
25684 TCAACCTTTTGCTCAAATCCATAATTTGATGGATCAGCTTTTTCCAG-GTAGAGTTCATAATGAG
66 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGC-TTTTCCAGAG-AAAGTTCATAATAAG
*
25748 AAGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGC
129 AAGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* **
25813 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTT
194 TCAAATCCATCACTTGATGGATTAGCTTTTCCAGAG
* * *
25849 AGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGAGAAGAACTTG
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGAGAAGAACTTG
* * * * * *
25913 TTTAACCTTTTGTTTAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGA
65 TTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGA
* * * **
25978 AGAA--C-TTATTTGAA-GAGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCA
130 AGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-
* * ** *
26039 T-AATTCTATCACAGAAGCAGATAGATTAGCATAAACCTTTCCAGAG
194 TCAAATCCATCAC-----TTGATGGATTAGC-T-----TTTCCAGAG
* * * * * *
26085 AAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGAAGAACTTAT
1 AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
26150 TCAACCTTTTG
66 TCAACCTTTTG
26161 AATGACTCTA
Statistics
Matches: 471, Mismatches: 50, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
225 82 0.17
226 76 0.16
227 30 0.06
228 1 0.00
229 29 0.06
230 180 0.38
231 1 0.00
236 70 0.15
237 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (229 bp):
AAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAA
GAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
AAATCCATCACTTGATGGATTAGCTTTTCCAGAG
Found at i:26105 original size:123 final size:124
Alignment explanation
Indices: 25953--26179 Score: 348
Period size: 124 Copynumber: 1.8 Consensus size: 124
25943 TGGATCAACA
* * * * * *
25953 TTTCCAGAGAAAGTTCATAATAAGAAGAACTTATTTG-AAGAGGAAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGA
* * * *
26017 AGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATAAACC
66 AGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAGATAGATTAGCATAAACC
26076 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGA
1 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGA
*
26141 AGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
66 AGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAG
26180 GAAATAGGTC
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
123 35 0.38
124 57 0.62
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGA
AGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAGATAGATTAGCATAAACC
Found at i:26244 original size:124 final size:122
Alignment explanation
Indices: 25955--26244 Score: 278
Period size: 124 Copynumber: 2.4 Consensus size: 122
25945 GATCAACATT
* *** * * * *
25955 TCCAGAGAAAGTTCATAATAAGAAGAACTTAT-TTGAAGAGGAAGAAGAAGTTCACAATGAGAAG
1 TCCAGAGAAAGTTCATAATAAGAAGAACTAATCCCAAAAAGAAAGAAGAAGTTCAAAATAAGAAG
* * * * * * *
26019 AGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATAAACC
66 AACTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATAAACC
* **
26076 TTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAAAAGAAAGAAGAAGTTCAAAATAAGA
1 --TCCAGAGAAAGTTCATAATAAGAAGAACTAATCCCAAAAAGAAAGAAGAAGTTCAAAATAAGA
* * * * *
26141 AGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
64 AGAACTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATAAACC
* * * *
26200 -CCAGTGGAAAAGTTCGTAATGAGAAGAGCTAATCCCAAAGAAGAA
1 TCCAG-AG-AAAGTTCATAATAAGAAGAACTAATCCCAAA-AAGAA
26245 TTATTTCAAC
Statistics
Matches: 137, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
121 4 0.03
122 1 0.01
123 56 0.41
124 76 0.55
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (122 bp):
TCCAGAGAAAGTTCATAATAAGAAGAACTAATCCCAAAAAGAAAGAAGAAGTTCAAAATAAGAAG
AACTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATAAACC
Found at i:26390 original size:3 final size:3
Alignment explanation
Indices: 26384--26432 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
26374 ATTTTAAAAT
*
26384 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA
26430 TTA
1 TTA
26433 CAAAGCCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:35446 original size:59 final size:59
Alignment explanation
Indices: 35380--35851 Score: 730
Period size: 59 Copynumber: 8.0 Consensus size: 59
35370 GATTACCAGA
* **
35380 AGGGCACTTCGTGTGCTAAAATGTCAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
35439 AGGGCACTTCGTGTGCTAACATGAGAACGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
35498 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
35557 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAACTGTATGAATTTCTATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
35616 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACGAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
35675 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATAAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * * **
35734 AGGGCACTTAGTGTACCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * *
35793 TGGACACCTT-GTGTGCCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCA-CTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
35852 GGAAAATAAT
Statistics
Matches: 386, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
59 383 0.99
60 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Done.