Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007226.1 Hibiscus syriacus cultivar Beakdansim tig00019121_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: 69782
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:270 original size:31 final size:31
Alignment explanation
Indices: 226--312 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
216 TTTGTGGGTA
*
226 AAATTGGTATTTTATCCAAAGTTTAAGAG-TC
1 AAATTAGTATTTTATCCAAA-TTTAAGAGATC
* * * *
257 AAATTAGTGTTTTATCGAAATTTTAGAGATG
1 AAATTAGTATTTTATCCAAATTTAAGAGATC
* *
288 AAATTAATATTTTATCTAAAATTTA
1 AAATTAGTATTTTATC-CAAATTTA
313 TGAATTAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 7 0.16
31 32 0.71
32 6 0.13
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.43
Consensus pattern (31 bp):
AAATTAGTATTTTATCCAAATTTAAGAGATC
Found at i:323 original size:31 final size:30
Alignment explanation
Indices: 233--325 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
223 GTAAAATTGG
* * *
233 TATTTTATCCAAAGTTTAAGAGTCAAATTAG
1 TATTTTATCCAAAATTT-AGAATCAAATTAA
* * * *
264 TGTTTTATCGAAATTTTAGAGATGAAATTAA
1 TATTTTATCCAAAATTTAGA-ATCAAATTAA
* *
295 TATTTTATCTAAAATTTATGAATTAAATTAA
1 TATTTTATCCAAAATTTA-GAATCAAATTAA
326 AGATCAACTC
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 3 0.06
31 45 0.90
32 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
TATTTTATCCAAAATTTAGAATCAAATTAA
Found at i:1982 original size:2 final size:2
Alignment explanation
Indices: 1975--2006 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1965 TAGTACGACA
1975 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2007 GAAGAACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5839 original size:57 final size:57
Alignment explanation
Indices: 5766--5878 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
5756 TTATGGAATG
* ** * *
5766 AAACGTTAAGCACCAAACTGGAATGAAAAAATGTTAGACACTAAACTAGAACGAAAA
1 AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGACACCAAACTAGAACGAAAA
* * *
5823 AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGGCACCAAATTGGAACGAAA
1 AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGACACCAAACTAGAACGAAA
5879 GACATACGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (57 bp):
AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGACACCAAACTAGAACGAAAA
Found at i:5850 original size:28 final size:28
Alignment explanation
Indices: 5766--5867 Score: 109
Period size: 28 Copynumber: 3.6 Consensus size: 28
5756 TTATGGAATG
* **
5766 AAACGTTAAGCACCAAACTGGAATGAAA
1 AAACGTTAAGCACCAAACTGAAACAAAA
* *
5794 AAATGTT-AGACACTAAACT-AGAACGAAAA
1 AAACGTTAAG-CACCAAACTGA-AAC-AAAA
5823 AAACGTTAAGCACCAAACTGAAACAAAA
1 AAACGTTAAGCACCAAACTGAAACAAAA
*
5851 AAACGTTAGGCACCAAA
1 AAACGTTAAGCACCAAA
5868 TTGGAACGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.03
28 36 0.59
29 20 0.33
30 3 0.05
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.14
Consensus pattern (28 bp):
AAACGTTAAGCACCAAACTGAAACAAAA
Found at i:7231 original size:40 final size:40
Alignment explanation
Indices: 7173--7252 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
7163 GTAAGTCTGG
*
7173 ATCAAAATACTATGAAGAGTGAAAGCATAAAATCCAATCC
1 ATCAAAATACTATCAAGAGTGAAAGCATAAAATCCAATCC
* *
7213 ATCAAAATACTATCAAGAGTGAAAGCGTAAAATTCAATCC
1 ATCAAAATACTATCAAGAGTGAAAGCATAAAATCCAATCC
7253 TACAAACATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.21
Consensus pattern (40 bp):
ATCAAAATACTATCAAGAGTGAAAGCATAAAATCCAATCC
Found at i:12128 original size:30 final size:30
Alignment explanation
Indices: 12083--12192 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 30
12073 TTGGGCAGTA
*
12083 CTCGACTCGTGCTCGTTAAAAAAATTTGTTG
1 CTCGACTCG-ACTCGTTAAAAAAATTTGTTG
* ***
12114 CTCGATTCGACTCGTTGCTCGTTAAAA-TTG-TG
1 CTCGACTCGACTCG-T--T-AAAAAAATTTGTTG
*
12146 CTCGACTCGTGCTCGTTAAAAAAATTTGTTG
1 CTCGACTCG-ACTCGTTAAAAAAATTTGTTG
*
12177 CTCAACTCGACTCGTT
1 CTCGACTCGACTCGTT
12193 GCTCGTTAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
29 4 0.07
30 14 0.23
31 19 0.32
32 11 0.18
33 8 0.13
34 4 0.07
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (30 bp):
CTCGACTCGACTCGTTAAAAAAATTTGTTG
Found at i:12137 original size:37 final size:34
Alignment explanation
Indices: 12084--12201 Score: 126
Period size: 37 Copynumber: 3.5 Consensus size: 34
12074 TGGGCAGTAC
12084 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCGA
1 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTC-A
12119 TTCGACTCGTTGCTCGTT---AAAA-TTG-TG--C-
1 -TCGACTCG-TGCTCGTTAAAAAAATTTGTTGCTCA
12147 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAA
1 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTC-A
12182 CTCGACTCGTTGCTCGTTAA
1 -TCGACTCG-TGCTCGTTAA
12202 GCTCACTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 23
0.75 0.00 0.25
Matches are distributed among these distances:
26 8 0.11
27 8 0.11
29 4 0.06
30 4 0.06
31 2 0.03
32 2 0.03
33 4 0.06
34 4 0.06
36 16 0.23
37 18 0.26
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (34 bp):
TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCA
Found at i:12187 original size:63 final size:63
Alignment explanation
Indices: 12083--12201 Score: 220
Period size: 63 Copynumber: 1.9 Consensus size: 63
12073 TTGGGCAGTA
* *
12083 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCGATTCGACTCGTTGCTCGTTAAAATTGTG
1 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAAAATTGTG
12146 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAA
1 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAA
12202 GCTCACTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (63 bp):
CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAAAATTGTG
Found at i:12382 original size:21 final size:21
Alignment explanation
Indices: 12294--12382 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
12284 TTGGGTATTA
12294 AAATTA-TATTATTAATTAAT
1 AAATTATTATTATTAATTAAT
12314 AATATT-TTATTATTAATTAA-
1 AA-ATTATTATTATTAATTAAT
* *
12334 AAATAATAGATTAGTTAACTT-AT
1 AAATTAT-TATTA-TTAA-TTAAT
* *
12357 -TATTATTATTATTTATTAAT
1 AAATTATTATTATTAATTAAT
12377 AAATTA
1 AAATTA
12383 ATAAATTAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
19 4 0.08
20 10 0.19
21 28 0.53
22 9 0.17
23 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATTATTATTATTAATTAAT
Found at i:12463 original size:23 final size:23
Alignment explanation
Indices: 12420--12464 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12410 ATTTTTTGAA
**
12420 TAAAATAATTTTGAAGTAATTAC
1 TAAAATAATTTTGAAAAAATTAC
12443 TAAAATATATTTT-AAAAAATTA
1 TAAAATA-ATTTTGAAAAAATTA
12465 ATAAGATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAAATAATTTTGAAAAAATTAC
Found at i:13158 original size:223 final size:223
Alignment explanation
Indices: 12770--13218 Score: 871
Period size: 223 Copynumber: 2.0 Consensus size: 223
12760 GTACAAGGCA
*
12770 CAAAAGAAGTGCAATGTAACCATGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
1 CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
*
12835 CATTTGTGAAATGGCAAGGCTGCAAAGCAGTAATCATTATTGAAAAATAAATTACCTTCTTCATT
66 CATTTGTGAAATGGCAAGGCTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
12900 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
131 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
12965 TGAATCCATGTCGAACAAGGGTCTCTTT
196 TGAATCCATGTCGAACAAGGGTCTCTTT
12993 CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
1 CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
*
13058 CATTTGTGAAATGGCAAGGTTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
66 CATTTGTGAAATGGCAAGGCTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
13123 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
131 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
13188 TGAATCCATGTCGAACAAGGGTCTCTTT
196 TGAATCCATGTCGAACAAGGGTCTCTTT
13216 CAA
1 CAA
13219 GACCTGAAAA
Statistics
Matches: 223, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
223 223 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (223 bp):
CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
CATTTGTGAAATGGCAAGGCTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
TGAATCCATGTCGAACAAGGGTCTCTTT
Found at i:18917 original size:21 final size:21
Alignment explanation
Indices: 18875--18917 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18865 TTTTCGGGTT
* * *
18875 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
18896 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
18917 A
1 A
18918 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:19001 original size:12 final size:12
Alignment explanation
Indices: 18984--19009 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18974 ATTCCCCCAT
18984 AAGAAAAGAAAG
1 AAGAAAAGAAAG
18996 AAGAAAAGAAAG
1 AAGAAAAGAAAG
19008 AA
1 AA
19010 AGACTAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAG
Found at i:19591 original size:149 final size:149
Alignment explanation
Indices: 19385--19688 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
19375 GGGTAGAAGG
19385 TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* * *
19450 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATAATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
19515 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
19534 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
19599 ACTTGATCCATAGTATATGTATATAATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATAATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
19664 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
19683 TCTACG
1 TCTACG
19689 GGGCACTTCG
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATAATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:19711 original size:23 final size:23
Alignment explanation
Indices: 19667--19711 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19657 ATCATTATAT
*
19667 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
19690 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
19712 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:25806 original size:21 final size:21
Alignment explanation
Indices: 25764--25806 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
25754 TTTTCGGGTT
* * *
25764 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
25785 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
25806 A
1 A
25807 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:26539 original size:149 final size:149
Alignment explanation
Indices: 26347--26650 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
26337 GGGTAGAGGG
*
26347 TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAATACACAT
1 TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
26412 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
26477 TATGGCACTACGATGCAAT
131 TATGGCACTACGATGCAAT
*
26496 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
26561 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTTGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
26626 TATGGCACTACGGTGCAAT
131 TATGGCACTACGATGCAAT
26645 TCTACG
1 TCTACG
26651 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGAACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGATGCAAT
Found at i:26673 original size:23 final size:23
Alignment explanation
Indices: 26629--26673 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
26619 ATCATTATAT
*
26629 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
26652 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
26674 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:38620 original size:22 final size:22
Alignment explanation
Indices: 38603--38669 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
38593 CTCGTATAAA
38603 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38625 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38647 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38669 T
1 T
38670 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:38930 original size:30 final size:31
Alignment explanation
Indices: 38889--38948 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
38879 TAGCCATAGT
*
38889 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
38919 ATTTACATACCTTTATCCCATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
38949 AACGTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:39005 original size:29 final size:29
Alignment explanation
Indices: 38963--39034 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
38953 TTTTCTGCAT
**
38963 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
* *
38992 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
39021 ATTCATGTCATGTA
1 ATTCATGTCATGTA
39035 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:39485 original size:68 final size:69
Alignment explanation
Indices: 39338--39490 Score: 209
Period size: 69 Copynumber: 2.2 Consensus size: 69
39328 TTTTCTCATG
* * * *
39338 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
*
39403 TGAG
66 TGAA
* * * * *
39407 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
39471 TGAA
66 TGAA
39475 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
39491 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 27 0.36
69 47 0.64
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
TGAA
Found at i:39500 original size:21 final size:21
Alignment explanation
Indices: 39470--39512 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39460 ATCATATTCG
* *
39470 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
39491 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
39512 T
1 T
39513 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:45568 original size:22 final size:22
Alignment explanation
Indices: 45543--45593 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
45533 CACCACAGCT
*
45543 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
45565 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
45587 CGTAGAA
1 CGTAGAA
45594 TTTTGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:45594 original size:22 final size:22
Alignment explanation
Indices: 45551--45595 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
45541 CTCGTATAAA
45551 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
45573 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
45595 T
1 T
45596 TTGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:45856 original size:30 final size:31
Alignment explanation
Indices: 45815--45874 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
45805 TAGCCATAGT
*
45815 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
45845 ATTTACATACCTTTATCCCATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
45875 AACGTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:45931 original size:29 final size:29
Alignment explanation
Indices: 45889--45960 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
45879 TTTTCTGCAT
**
45889 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
* *
45918 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
45947 ATTCATGTCATGTA
1 ATTCATGTCATGTA
45961 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:46411 original size:68 final size:69
Alignment explanation
Indices: 46264--46416 Score: 209
Period size: 69 Copynumber: 2.2 Consensus size: 69
46254 TTTTCTCATG
* * * *
46264 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
*
46329 TGAG
66 TGAA
* * * * *
46333 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
46397 TGAA
66 TGAA
46401 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
46417 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 27 0.36
69 47 0.64
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
TGAA
Found at i:46426 original size:21 final size:21
Alignment explanation
Indices: 46396--46438 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
46386 ATCATATTCG
* *
46396 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
46417 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
46438 T
1 T
46439 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:48511 original size:21 final size:21
Alignment explanation
Indices: 48469--48511 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
48459 TTTCTGGGCT
* *
48469 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
48490 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
48511 A
1 A
48512 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:49288 original size:103 final size:103
Alignment explanation
Indices: 49063--49277 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
49053 GTAGAGGGTC
*
49063 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
49128 TTGATCCTTGGTATATGTATATGATTCTTAAAGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
49166 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
49231 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
49269 TATGTGGTC
1 TATGTGGTC
49278 CTTATGGACA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
Found at i:49330 original size:23 final size:23
Alignment explanation
Indices: 49297--49359 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
49287 ATTATTATAT
*
49297 GGCACTACGGTGCGATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
49320 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
49343 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
49360 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:55446 original size:21 final size:21
Alignment explanation
Indices: 55404--55446 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
55394 TTTCTGGGCT
* *
55404 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
55425 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
55446 A
1 A
55447 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:56182 original size:103 final size:103
Alignment explanation
Indices: 55993--56210 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
55983 GTAGAGGGTC
55993 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
56058 TTGATCCTTGGTATATATATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
*
56096 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
56161 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
56199 TATGTGGTCCTT
1 TATGTGGTCCTT
56211 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
Found at i:56260 original size:23 final size:23
Alignment explanation
Indices: 56227--56289 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
56217 ATTATTATAT
56227 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
56250 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
56273 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
56290 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:57733 original size:22 final size:22
Alignment explanation
Indices: 57702--57773 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
57692 CTGAGTGGCA
57702 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
* *
57725 TGTGAATTTTTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
57747 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
57768 TATGAA
1 TATGAA
57774 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.44
22 21 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:57761 original size:21 final size:21
Alignment explanation
Indices: 57710--57772 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
57700 CATATGAAAT
* *
57710 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
*
57732 TTTTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
57753 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
57773 AACCCTCGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:59250 original size:64 final size:64
Alignment explanation
Indices: 59150--59310 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
59140 TAATGAAGGT
* * *
59150 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
59213 GG
63 GC
* *
59215 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
59279 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
59311 CCTTAACAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 57 0.67
65 25 0.29
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:60294 original size:31 final size:31
Alignment explanation
Indices: 60256--60334 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
60246 AGGGTTGAGG
*
60256 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
60287 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
60318 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
60335 AGAATCTATG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:60345 original size:31 final size:31
Alignment explanation
Indices: 60258--60349 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 31
60248 GGTTGAGGGT
* * * * *
60258 TTACCTATGTTTTTCGGGACATATGGACTGT
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
* * *
60289 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTAGGTTCTTCAGAACATATGGACTGA
60320 TTACCTAGGTTCTTCAGAATC-TATGGACTG
1 TTACCTAGGTTCTTCAGAA-CATATGGACTG
60350 GTCTTTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTAGGTTCTTCAGAACATATGGACTGA
Found at i:61539 original size:18 final size:19
Alignment explanation
Indices: 61516--61552 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
61506 ATTTTACACT
61516 TAGGGA-ACCGATTCCCCA
1 TAGGGAGACCGATTCCCCA
61534 TAGGGAGTACCGATTCCCC
1 TAGGGAG-ACCGATTCCCC
61553 CCACGCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (19 bp):
TAGGGAGACCGATTCCCCA
Done.