Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001490.1 Hibiscus syriacus cultivar Beakdansim tig00002895_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: 94939
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:9663 original size:20 final size:20
Alignment explanation
Indices: 9634--9673 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
9624 ATTTGATTGA
9634 ATTTTAAATT-AGATGAAAT
1 ATTTTAAATTCAGATGAAAT
9653 ATTTCTAAATTCAGATGAAAT
1 ATTT-TAAATTCAGATGAAAT
9674 TGGATGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
ATTTTAAATTCAGATGAAAT
Found at i:13905 original size:23 final size:25
Alignment explanation
Indices: 13868--13913 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
13858 TCCCCCTTAG
13868 TTATAGATTCCATTATATATCTACA
1 TTATAGATTCCATTATATATCTACA
*
13893 TTATA-ATT-CATTATTTATCTA
1 TTATAGATTCCATTATATATCTA
13914 TTTATTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 3 0.15
25 5 0.25
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATAGATTCCATTATATATCTACA
Found at i:17516 original size:21 final size:21
Alignment explanation
Indices: 17492--17531 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17482 TTTATTTTAT
*
17492 AACTTTATTTCAATTATCGTA
1 AACTTTACTTCAATTATCGTA
*
17513 AACTTTGCTTCAATTATCG
1 AACTTTACTTCAATTATCG
17532 AACTTGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (21 bp):
AACTTTACTTCAATTATCGTA
Found at i:17580 original size:33 final size:32
Alignment explanation
Indices: 17526--17624 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
17516 TTTGCTTCAA
17526 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
17558 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
17591 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
17624 T
1 T
17625 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:17653 original size:13 final size:13
Alignment explanation
Indices: 17610--17664 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
17600 TTGGAAGTAT
17610 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
17623 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
17637 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
17650 TTAAGTATTTGAA
1 TTAAGTATTTCAA
17663 TT
1 TT
17665 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:17886 original size:21 final size:21
Alignment explanation
Indices: 17860--17916 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
17850 TGGAGCGTGG
*
17860 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
* *
17881 GGGAATCGATTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
17902 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
17917 AAGTGTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:18257 original size:15 final size:17
Alignment explanation
Indices: 18231--18262 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18221 TCTATGGGAA
18231 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
18247 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
18263 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:23161 original size:75 final size:75
Alignment explanation
Indices: 22998--23291 Score: 414
Period size: 75 Copynumber: 4.0 Consensus size: 75
22988 CATCATCAAG
* ** * * *
22998 TTCTGCCAAAGGACTTGGTTTGGGACAACCAACCAAGGGTAAGCCTGAAATTCCC--G-AGAAGC
1 TTCTGTCAAAGGTGTTGGTTCGGGACAACCAACCACGGGGAAGCCTGAAATTCCCGAGAAGAAGC
23060 CGGTTAGCCC
66 CGGTTAGCCC
* *
23070 TTCTGTCAAATGTGTTGGTTCGGGACAACCAGCCACGGGGAAGCCTGAAATTCCCGAGAAGAAGC
1 TTCTGTCAAAGGTGTTGGTTCGGGACAACCAACCACGGGGAAGCCTGAAATTCCCGAGAAGAAGC
23135 CGGTTAGCCC
66 CGGTTAGCCC
**
23145 TTCTGTCAAAGGTGTTGGTTCGGGACAACCAACCACGGAAAAGCCTGAAATTCCCGAGAAGAAGC
1 TTCTGTCAAAGGTGTTGGTTCGGGACAACCAACCACGGGGAAGCCTGAAATTCCCGAGAAGAAGC
*
23210 CAGTTAGCCC
66 CGGTTAGCCC
* * * ** *
23220 TTCTGTTAGAGGTGTTGGTTCGGGACAATCGGCCACGGGGAAGCCTGAAATTCCCGAGAAGAATC
1 TTCTGTCAAAGGTGTTGGTTCGGGACAACCAACCACGGGGAAGCCTGAAATTCCCGAGAAGAAGC
23285 CGGTTAG
66 CGGTTAG
23292 GCCCCGCGAA
Statistics
Matches: 197, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
72 47 0.24
74 1 0.01
75 149 0.76
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (75 bp):
TTCTGTCAAAGGTGTTGGTTCGGGACAACCAACCACGGGGAAGCCTGAAATTCCCGAGAAGAAGC
CGGTTAGCCC
Found at i:26210 original size:21 final size:21
Alignment explanation
Indices: 26174--26231 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
26164 ATAACGTTAT
*
26174 TTAAAAT-GTTATTTTTTTA-
1 TTAAAATAATTATTTTTTTAC
*
26193 TTAAAATTATTAATTTTTTTAC
1 TTAAAATAATT-ATTTTTTTAC
26215 TTAAAATAATTATTTTT
1 TTAAAATAATTATTTTT
26232 ATAAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.21
20 2 0.06
21 15 0.44
22 10 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTAAAATAATTATTTTTTTAC
Found at i:26242 original size:19 final size:20
Alignment explanation
Indices: 26187--26248 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
26177 AAATGTTATT
*
26187 TTTTTATTAAAATTATTAATT-
1 TTTTTACTAAAA-TA-TAATTA
*
26208 TTTTTACTTAAA-ATAATTA
1 TTTTTACTAAAATATAATTA
26227 TTTTTA-TAAAATATAA-TA
1 TTTTTACTAAAATATAATTA
26245 TTTT
1 TTTT
26249 AAGTAACGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 15 0.42
19 11 0.31
21 10 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTACTAAAATATAATTA
Found at i:26246 original size:18 final size:19
Alignment explanation
Indices: 26187--26248 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
26177 AAATGTTATT
*
26187 TTTTTATTAAAATTATTAATT
1 TTTTTATTAAAA-TA-TAATA
*
26208 TTTTTACTTAAAATA-ATTA
1 TTTTTA-TTAAAATATAATA
26227 TTTTTA-TAAAATATAATA
1 TTTTTATTAAAATATAATA
26245 TTTT
1 TTTT
26249 AAGTAACGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 7 0.19
18 7 0.19
19 8 0.22
21 8 0.22
22 6 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTATTAAAATATAATA
Found at i:27846 original size:62 final size:62
Alignment explanation
Indices: 27758--27879 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
27748 ATATGTCACG
* * *
27758 TCATTAGGATAAAGAAAGTTAACAACTTAATTGTTAAATTATACCAAAATCGACAATATAACA
1 TCATTAGAATAAAGAAAGTTAACAACTTAATAGTTAAATTATAAC-AAATCGACAATATAACA
* *
27821 TCATTAGAATAAGGAAA-TTAACAACTTAATAGTTAAATTATAACAAATCGATAATATAA
1 TCATTAGAATAAAGAAAGTTAACAACTTAATAGTTAAATTATAACAAATCGACAATATAA
27880 ATGACCGGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 14 0.26
62 25 0.46
63 15 0.28
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (62 bp):
TCATTAGAATAAAGAAAGTTAACAACTTAATAGTTAAATTATAACAAATCGACAATATAACA
Found at i:32592 original size:16 final size:16
Alignment explanation
Indices: 32554--32592 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32544 TTTCCCCCAA
32554 TCCAAAAACCGGATTT
1 TCCAAAAACCGGATTT
** *
32570 TAAAAAAATCGGATTT
1 TCCAAAAACCGGATTT
32586 TCCAAAA
1 TCCAAAA
32593 TCCAGTTTCG
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (16 bp):
TCCAAAAACCGGATTT
Found at i:33923 original size:22 final size:22
Alignment explanation
Indices: 33866--33924 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
33856 ACGTGATTCT
33866 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
33888 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
33909 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
33925 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:33938 original size:20 final size:20
Alignment explanation
Indices: 33913--33984 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
33903 TTTTCCGACT
33913 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
33933 ATCGCAATTCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
33953 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
33973 ATCGCAATGCGA
1 ATCGCAATGCGA
33985 TTCTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:33996 original size:20 final size:20
Alignment explanation
Indices: 33973--34020 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
33963 GAATATGTAA
*
33973 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
33993 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
34013 GTCGCAAC
1 ATCGCAAC
34021 ACTGAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:33997 original size:40 final size:40
Alignment explanation
Indices: 33909--34004 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
33899 GCGATTTTCC
*
33909 GACTATCGCAATGCGAATATGTAAATCGCAATTCGAATAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
* * *
33949 GTA-AATCGCAATGCGAATATGTAAATCGCAATGCGATTCT
1 G-ACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
*
33989 GACTATCGCAACGCGA
1 GACTATCGCAATGCGA
34005 TTCTGACTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.02
40 46 0.96
41 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
Found at i:34892 original size:24 final size:24
Alignment explanation
Indices: 34839--34893 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
34829 GGTATTCGAA
34839 ATTTT-ATCTTGGTCAATACCCGG
1 ATTTTGATCTTGGTCAATACCCGG
** *
34862 ACATTGATCTTGGTCAATACTCGG
1 ATTTTGATCTTGGTCAATACCCGG
34886 ATTTTGAT
1 ATTTTGAT
34894 GATGTTTTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTTTGATCTTGGTCAATACCCGG
Found at i:35101 original size:12 final size:13
Alignment explanation
Indices: 35086--35118 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
35076 AAAAGAAAAA
35086 GAAGAAA-TCCCC
1 GAAGAAAGTCCCC
35098 GAAGAAAAGTCCCC
1 GAAG-AAAGTCCCC
35112 GAAGAAA
1 GAAGAAA
35119 ATGCCACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 6 0.32
14 9 0.47
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.06
Consensus pattern (13 bp):
GAAGAAAGTCCCC
Found at i:35112 original size:14 final size:14
Alignment explanation
Indices: 35093--35119 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35083 AAAGAAGAAA
35093 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
35107 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
35120 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:37180 original size:18 final size:18
Alignment explanation
Indices: 37157--37191 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37147 AGAAAAAGGC
*
37157 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
37175 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
37192 CAACCGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:37503 original size:140 final size:140
Alignment explanation
Indices: 37251--37516 Score: 469
Period size: 140 Copynumber: 1.9 Consensus size: 140
37241 AAACGTTGTA
* *
37251 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATTTTGAACATTGTTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
37316 TGATCTGTTCAGTTGTTATTACTTATTACACATTCATTTGAATATCGCAAAACGAATTTGACTAT
66 TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAAAACGAATTTGACTAT
37381 TATGTGTATT
131 TATGTGTATT
37391 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
**
37456 TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAAAACGAATTTGA
37517 TTATCGCAAC
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 119 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAAAACGAATTTGACTAT
TATGTGTATT
Found at i:37516 original size:20 final size:20
Alignment explanation
Indices: 37491--37688 Score: 137
Period size: 20 Copynumber: 10.8 Consensus size: 20
37481 TTACACATTC
37491 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
37511 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
37530 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
37545 ATTTGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
*
37564 A----AA-ATCACAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
37579 ATTTGACTATCGCAACG-GCT
1 ATTTGAATATCGCAACGCG-A
*
37599 ATTTGACTATCGCAA--CG-
1 ATTTGAATATCGCAACGCGA
* *
37616 A---GAAAATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
*
37633 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
37653 ATTTGAGTATCGTAACGCGA
1 ATTTGAATATCGCAACGCGA
*
37673 ATTTGATTATCGCAAC
1 ATTTGAATATCGCAAC
37689 AGGTATTTGA
Statistics
Matches: 139, Mismatches: 19, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
14 27 0.19
15 6 0.04
16 2 0.01
17 2 0.01
19 8 0.06
20 94 0.68
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:37542 original size:34 final size:34
Alignment explanation
Indices: 37499--37595 Score: 167
Period size: 34 Copynumber: 2.9 Consensus size: 34
37489 TCATTTGAAT
* *
37499 ATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
37533 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
*
37567 ATCACAACGCGAATTTGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
37596 GCTATTTGAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:37591 original size:54 final size:55
Alignment explanation
Indices: 37533--37670 Score: 201
Period size: 54 Copynumber: 2.5 Consensus size: 55
37523 CAACTCAAAA
*
37533 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAAATCACAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCAGAAAATCACAACACGAATTTGACT
* *
37587 ATCGCAACG-GCTATTTGACTATCGCAACG-AGAAAATCGCAACACGAATTTGACT
1 ATCGCAACGCG-AATTTGACTATCGCAACGCAGAAAATCACAACACGAATTTGACT
* *
37641 ATCGCAACGCGAATTTGAGTATCGTAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACGC
37671 GAATTTGATT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
53 2 0.03
54 71 0.96
55 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (55 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAGAAAATCACAACACGAATTTGACT
Found at i:37698 original size:40 final size:40
Alignment explanation
Indices: 37491--37688 Score: 119
Period size: 34 Copynumber: 5.4 Consensus size: 40
37481 TTACACATTC
* * *
37491 ATTTGAATATCGCAACGCGAATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACACGA
* * *
37530 A----A-AATCGCAACGCGAATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACACGA
* * * * *
37564 A----A-AATCACAACGCGAATTTGACTATCGCAAC-GGCT
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACACG-A
*
37599 ATTTGACTATCGCAACGAGAA----A--ATCGCAACACGA
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACACGA
* *
37633 ATTTGACTATCGCAACGCGAATTTGAGTATCGTAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACACGA
*
37673 ATTTGATTATCGCAAC
1 ATTTGACTATCGCAAC
37689 AGGTATTTGA
Statistics
Matches: 130, Mismatches: 15, Indels: 27
0.76 0.09 0.16
Matches are distributed among these distances:
34 87 0.67
35 3 0.02
36 1 0.01
38 1 0.01
39 2 0.02
40 36 0.28
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
ATTTGACTATCGCAACGCGAATTTGAGTATCGCAACACGA
Found at i:37964 original size:14 final size:14
Alignment explanation
Indices: 37904--37965 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
37894 CACAAATAAG
*
37904 AATTATTTACACATC
1 AATT-TTTACAAATC
**
37919 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
37934 AACTTTTACAAATC
1 AATTTTTACAAATC
*
37948 AATTTTTATAAATC
1 AATTTTTACAAATC
37962 AATT
1 AATT
37966 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:39466 original size:42 final size:42
Alignment explanation
Indices: 39386--39478 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
39376 CCTCTTTAAC
* * * *
39386 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGGCTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAGGAGGCTCTTGAGG
* **
39428 GATGATAGGGGCCTCTTGAACGATAGG-GGAGGCTTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATAGGAGGAGGC-TCTTGAGG
39470 GATGACAGG
1 GATGACAGG
39479 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 5 0.12
42 37 0.88
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAGGAGGCTCTTGAGG
Found at i:39987 original size:18 final size:19
Alignment explanation
Indices: 39964--40008 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
39954 GAAACTTAAA
39964 ATCGCAACACG-AATGAAT
1 ATCGCAACACGAAATGAAT
* *
39982 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGAAT
40002 ATCGCAA
1 ATCGCAA
40009 TGCGAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAACACGAAATGAAT
Found at i:40004 original size:20 final size:20
Alignment explanation
Indices: 39975--40030 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
39965 TCGCAACACG
*
39975 AATGAATATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
39995 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
**
40015 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
40031 AGAGAATCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:40101 original size:20 final size:20
Alignment explanation
Indices: 40073--40116 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
40063 GCGATTCTTT
*
40073 CGTTGCGATAGTCAAATTCG
1 CGTTACGATAGTCAAATTCG
**
40093 CGTTACGATAGTCATTTTCG
1 CGTTACGATAGTCAAATTCG
40113 CGTT
1 CGTT
40117 GCGAAAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTACGATAGTCAAATTCG
Found at i:42036 original size:20 final size:20
Alignment explanation
Indices: 42013--42108 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
42003 TCTGAAACTT
*
42013 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
42033 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
42053 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** ** *
42073 ACTATCGCAACGTG-AAATA
1 AAAATCGCAACACGAAAATG
*
42092 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
42109 CTAAAATCAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
19 13 0.21
20 49 0.79
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:42100 original size:19 final size:20
Alignment explanation
Indices: 42006--42114 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
41996 AATAGTTTCT
* **
42006 GAAACTTAAAATCGCAACAT
1 GAAACTAAAAATCGCAACGC
* * *
42026 GAAAATGAAAATCGCAACAC
1 GAAACTAAAAATCGCAACGC
* * **
42046 GAAAATGACTATCGCAACGC
1 GAAACTAAAAATCGCAACGC
** * ** *
42066 GAATTTGACTATCGCAACGT
1 GAAACTAAAAATCGCAACGC
42086 GAAA-TAAAAATCGCAACGC
1 GAAACTAAAAATCGCAACGC
42105 GAAACTAAAA
1 GAAACTAAAA
42115 TCACATTGCG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 15 0.20
20 59 0.80
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.17
Consensus pattern (20 bp):
GAAACTAAAAATCGCAACGC
Found at i:42532 original size:22 final size:22
Alignment explanation
Indices: 42506--42548 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42496 GAGATAGACG
42506 GATTTCGCCAGAGATGGGGACT
1 GATTTCGCCAGAGATGGGGACT
* *
42528 GATTTCGTCGGAGATGGGGAC
1 GATTTCGCCAGAGATGGGGAC
42549 GGATGTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (22 bp):
GATTTCGCCAGAGATGGGGACT
Found at i:42754 original size:20 final size:20
Alignment explanation
Indices: 42731--42835 Score: 122
Period size: 20 Copynumber: 5.2 Consensus size: 20
42721 AAATCGCATA
**
42731 GCGATAGTCA-ATATCGTATT
1 GCGATAGTCAGA-ATCGCGTT
*
42751 GCGACAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
42771 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
*
42791 ACGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
* * *
42811 GCGATAGTCATACTCGCATT
1 GCGATAGTCAGAATCGCGTT
42831 GCGAT
1 GCGAT
42836 TTACATATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 72 0.99
21 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:52954 original size:32 final size:33
Alignment explanation
Indices: 52901--52963 Score: 119
Period size: 32 Copynumber: 1.9 Consensus size: 33
52891 TTTGATAGAT
52901 TTTGATGATTATTTTTGCAATAGTTCGATAAAA
1 TTTGATGATTATTTTTGCAATAGTTCGATAAAA
52934 TTTGATGATTA-TTTTGCAATAGTTCGATAA
1 TTTGATGATTATTTTTGCAATAGTTCGATAA
52964 TTTCACTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (33 bp):
TTTGATGATTATTTTTGCAATAGTTCGATAAAA
Found at i:53959 original size:16 final size:15
Alignment explanation
Indices: 53934--53965 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
53924 TTTGAGAATA
53934 TTTTTAAGTTCAAGT
1 TTTTTAAGTTCAAGT
53949 TTTTTAGAGTTCAAGT
1 TTTTTA-AGTTCAAGT
53965 T
1 T
53966 GTATTCCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTTTAAGTTCAAGT
Found at i:56202 original size:16 final size:17
Alignment explanation
Indices: 56181--56214 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
56171 GAGTTAGATT
56181 ATTTAATT-TTTTTTAA
1 ATTTAATTATTTTTTAA
56197 ATTTAATTATTTTTTAA
1 ATTTAATTATTTTTTAA
56214 A
1 A
56215 AATATAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTAATTATTTTTTAA
Found at i:58896 original size:29 final size:29
Alignment explanation
Indices: 58854--58909 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
58844 TGTTTGTCGT
**
58854 AGGTCGCTGGGAGGGCATGACGACCTACA
1 AGGTCGCCCGGAGGGCATGACGACCTACA
* *
58883 AGGTCGCCCGGAGGGTATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGACGACCTA
58910 TGTGTTGGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.25, G:0.39, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGACGACCTACA
Found at i:59085 original size:14 final size:14
Alignment explanation
Indices: 59041--59086 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
59031 GCGAGAGCAT
*
59041 CCGAGGCCATCTGA
1 CCGAGGCCATCCGA
* *
59055 CCAAGGGCATCCGA
1 CCGAGGCCATCCGA
59069 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
59083 CCGA
1 CCGA
59087 ATTATGTGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.39, G:0.28, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:59130 original size:23 final size:23
Alignment explanation
Indices: 59100--59144 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
59090 ATGTGAGGGC
59100 ATGCGAGGACAGCCGAGCGAGCT
1 ATGCGAGGACAGCCGAGCGAGCT
* *
59123 ATGCGAGGGCATCCGAGCGAGC
1 ATGCGAGGACAGCCGAGCGAGC
59145 GAGCAAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.40, T:0.09
Consensus pattern (23 bp):
ATGCGAGGACAGCCGAGCGAGCT
Found at i:59197 original size:29 final size:29
Alignment explanation
Indices: 59155--59267 Score: 163
Period size: 29 Copynumber: 3.9 Consensus size: 29
59145 GAGCAAGGGT
* * *
59155 AGGTTGCCCGGAGTGCTTGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
*
59184 AGGTCGCCAGGAGTGCATGGCGACTTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
*
59213 AGGTCGCCAGGAGTGCATGGCGACTTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
* *
59242 AGGTCGCCAGAATTGCATGGCGACCT
1 AGGTCGCCAGGAGTGCATGGCGACCT
59268 TGTACCTATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.19
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:63971 original size:15 final size:16
Alignment explanation
Indices: 63951--63983 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
63941 CCAAATTTAT
63951 AATTATACAAATT-AA
1 AATTATACAAATTGAA
*
63966 AATTATATAAATTGAA
1 AATTATACAAATTGAA
63982 AA
1 AA
63984 AATAACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AATTATACAAATTGAA
Found at i:72597 original size:24 final size:23
Alignment explanation
Indices: 72531--72599 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 23
72521 GGACCACGGA
*
72531 AAGAAGGAAAAGAAGATGAAAGAC
1 AAGAAGGAAAAGAA-AAGAAAGAC
*
72555 AACAAGGAGAAGAAAGAAAAGAAAGAC
1 AAGAA-G-G-A-AAAGAAAAGAAAGAC
72582 AAGAAGGAAAAGGAAAAG
1 AAGAAGGAAAA-GAAAAG
72600 GAAAAGAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
23 3 0.08
24 11 0.30
25 2 0.05
26 2 0.05
27 13 0.35
28 6 0.16
ACGTcount: A:0.65, C:0.04, G:0.29, T:0.01
Consensus pattern (23 bp):
AAGAAGGAAAAGAAAAGAAAGAC
Found at i:81719 original size:23 final size:26
Alignment explanation
Indices: 81693--81739 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
81683 GGCTTATTTG
81693 ATTT-TAAGAAAAAA-A-TAAAAATA
1 ATTTATAAGAAAAAATATTAAAAATA
*
81716 ATTTATAATAAAAAATATTAAAAA
1 ATTTATAAGAAAAAATATTAAAAA
81740 ATTAAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 9 0.45
25 1 0.05
26 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
ATTTATAAGAAAAAATATTAAAAATA
Found at i:81980 original size:27 final size:27
Alignment explanation
Indices: 81922--81981 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
81912 AATTTCATTG
** *
81922 AAATTTTATAAAAAAATTCATTTAATT
1 AAATTTTATAAAAAAATTCATGAAATA
*
81949 CAATTTTATAAAAAAATT-AGTGAAATA
1 AAATTTTATAAAAAAATTCA-TGAAATA
81976 AAATTT
1 AAATTT
81982 AAAAATCACT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (27 bp):
AAATTTTATAAAAAAATTCATGAAATA
Found at i:89016 original size:24 final size:25
Alignment explanation
Indices: 88971--89018 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
88961 TTTAAAGATC
*
88971 ATTTTTAATAATGTAATAATAATTT
1 ATTTTTAATAATATAATAATAATTT
88996 ATTTTATAA-AATATAAT-ATAATT
1 ATTTT-TAATAATATAATAATAATT
89019 AAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 12 0.57
26 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTTTTAATAATATAATAATAATTT
Found at i:92571 original size:14 final size:14
Alignment explanation
Indices: 92552--92580 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
92542 GCAAAGTGTC
92552 CTGGAGCCTTGAGG
1 CTGGAGCCTTGAGG
92566 CTGGAGCCTTGAGG
1 CTGGAGCCTTGAGG
92580 C
1 C
92581 GCGAGGCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.24, G:0.41, T:0.21
Consensus pattern (14 bp):
CTGGAGCCTTGAGG
Done.