Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004925.1 Hibiscus syriacus cultivar Beakdansim tig00011088_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: 69560
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:6848 original size:45 final size:45
Alignment explanation
Indices: 6793--6897 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 45
6783 GCACCAATCC
*
6793 ATGCATCGATGCAC-CAATGAATAAATTG-AACATCGAATGCAGTTT
1 ATGCATCGATGCACTC-AGGAATAAA-TGAAACATCGAATGCAGTTT
** * *
6838 ATGCATCGATGCACTCAGGTTTTAATGAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGAATAAATG-AAACATCGAATGCAGTTT
6884 ATGCATCGATGCAC
1 ATGCATCGATGCAC
6898 ACACAATGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 2 0.04
45 19 0.37
46 31 0.60
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGAATAAATGAAACATCGAATGCAGTTT
Found at i:6937 original size:64 final size:65
Alignment explanation
Indices: 6838--6963 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 65
6828 AATGCAGTTT
* * *
6838 ATGCATCGATGCACTCAGGTTTTAATGAAAACATCGAATGCATTTTATGCATCGATGCACACACA
1 ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATGCATCAATGCACACACA
* *
6903 ATGCATCGATGCACTTAGG-CTTACTCAAAACATCGAATGCATTTTATGCATCAATGCACAC
1 ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATGCATCAATGCACAC
6964 TTAGTGCACC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 38 0.68
65 18 0.32
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTTATGCATCAATGCACACACA
Found at i:9165 original size:20 final size:20
Alignment explanation
Indices: 9137--9179 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9127 AATCAGATTG
* *
9137 CCCATGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
9157 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
9177 CCC
1 CCC
9180 TGTTTAACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:9567 original size:34 final size:34
Alignment explanation
Indices: 9528--9618 Score: 164
Period size: 34 Copynumber: 2.7 Consensus size: 34
9518 TTTTGTAAAG
*
9528 GGGAAAGGTTCTAGCCTAGCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAATCTA
9562 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAATCTA
*
9596 GGGAAAGGTTCTAGTTTAGCCCG
1 GGGAAAGGTTCTAGCTTAGCCCG
9619 AAAAAACTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGTAAAATCTA
Found at i:16278 original size:64 final size:65
Alignment explanation
Indices: 16126--16287 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 65
16116 GAATAAATTG
* * * * * * *
16126 AACATCGAATGTAGTTTATGCATTGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
* *
16191 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
16255 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
16288 TTAGTGCACC
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
64 39 0.44
65 49 0.56
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:16301 original size:64 final size:64
Alignment explanation
Indices: 16126--16305 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
16116 GAATAAATTG
* * * * * *
16126 AACATCGAATGTAGTTTATGCATTGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATCAA
* * *
16191 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGTCTTAATCAA
* *
16255 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
16306 AAGTGTTCCA
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 52 0.51
65 48 0.48
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:18155 original size:19 final size:20
Alignment explanation
Indices: 18126--18163 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
18116 AGAAATTTGT
18126 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
18146 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
18164 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:18206 original size:63 final size:62
Alignment explanation
Indices: 18131--18289 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 62
18121 TTTGTTGAAG
* * * *
18131 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
18194 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
18257 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
18290 GCCTCCATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 80 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:19628 original size:18 final size:18
Alignment explanation
Indices: 19605--19640 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19595 AGGAATGATA
19605 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
19623 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
19641 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:19642 original size:62 final size:62
Alignment explanation
Indices: 19576--19763 Score: 146
Period size: 62 Copynumber: 3.1 Consensus size: 62
19566 TGATCCCTAG
19576 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
* * * * * *
19638 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC--
1 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
**
19693 CTAG-
58 CGGGA
*
19697 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
19759 CATAT
1 CATAT
19764 ATGTATTCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 38
0.62 0.12 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 18 0.20
60 12 0.13
61 11 0.12
62 23 0.26
63 7 0.08
64 6 0.07
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (62 bp):
CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGA
Found at i:19701 original size:59 final size:59
Alignment explanation
Indices: 19520--19828 Score: 146
Period size: 59 Copynumber: 5.1 Consensus size: 59
19510 CCTTCGGGAC
19520 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
1 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
* * * * * **
19579 ATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTCGG
1 A--TATAT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC--CTA
19636 GACAT
56 G-CAT
*
19641 ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
1 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
* * * * * * *
19700 ATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTTGG
1 A--TATAT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC-CT-A
19757 GACAT
56 G-CAT
* *
19762 ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTTGATCCCTAGCAT
1 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
*
19821 ATGTATAT
1 ATATATAT
19829 GATTCTTAAG
Statistics
Matches: 178, Mismatches: 34, Indels: 76
0.62 0.12 0.26
Matches are distributed among these distances:
57 12 0.07
58 14 0.08
59 42 0.24
60 24 0.13
61 24 0.13
62 36 0.20
63 14 0.08
64 12 0.07
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (59 bp):
ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
Found at i:19716 original size:121 final size:121
Alignment explanation
Indices: 19504--19867 Score: 687
Period size: 121 Copynumber: 3.0 Consensus size: 121
19494 CGAGGGTCTA
19504 TGTGGTCCTTCGGGACATATA--TATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
19567 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
19623 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
19688 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
19744 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
19809 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCATTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
19865 TGT
1 TGT
19868 TATATGGCAC
Statistics
Matches: 240, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
119 21 0.09
121 219 0.91
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:19749 original size:18 final size:18
Alignment explanation
Indices: 19726--19761 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19716 AGGAATGATA
19726 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
19744 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
19762 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:19940 original size:23 final size:23
Alignment explanation
Indices: 19872--19932 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
19862 CATTGTTATA
19872 TGGCACTAT-GGTGCAATTCTATG
1 TGGCACT-TCGGTGCAATTCTATG
* *
19895 CGGCACTACGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTATG
19918 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
19933 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTATG
Found at i:23777 original size:19 final size:20
Alignment explanation
Indices: 23748--23785 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
23738 AGAAATTTGT
*
23748 TGAAGGTGCATCTATGCATA
1 TGAAGGTGCATCGATGCATA
23768 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
23786 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:23828 original size:63 final size:62
Alignment explanation
Indices: 23753--23911 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 62
23743 TTTGTTGAAG
* * * *
23753 GTGCATCT-ATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCAT-TGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
23816 GTGCATTGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATTGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
*
23879 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATTGATGCAT-AGGAGTGCATCGATGCAT
23912 GCCTCCATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.01
63 77 0.93
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (62 bp):
GTGCATTGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:25230 original size:18 final size:18
Alignment explanation
Indices: 25207--25242 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
25197 AGGAATGATA
25207 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
25225 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
25243 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:25262 original size:121 final size:121
Alignment explanation
Indices: 25104--25469 Score: 705
Period size: 121 Copynumber: 3.0 Consensus size: 121
25094 CGAGGGTCTA
25104 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
25169 GATCCCTAGAATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
25225 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
25290 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
25346 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
25411 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
25467 TGT
1 TGT
25470 TATATGGCAC
Statistics
Matches: 242, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 242 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:25351 original size:18 final size:18
Alignment explanation
Indices: 25328--25363 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25318 AGGAATGATA
25328 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
25346 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
25364 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:25365 original size:62 final size:62
Alignment explanation
Indices: 25179--25365 Score: 144
Period size: 62 Copynumber: 3.1 Consensus size: 62
25169 GATCCCTAGA
*
25179 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGAC
* * * * * * *
25241 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC-CT
1 ATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTT
*
25297 -AG-C
58 GGGAC
25300 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGAC
25362 ATAT
1 ATAT
25366 ATGTATTCTT
Statistics
Matches: 89, Mismatches: 17, Indels: 38
0.62 0.12 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 18 0.20
60 12 0.13
61 11 0.12
62 22 0.25
63 7 0.08
64 6 0.07
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGAC
Found at i:25542 original size:23 final size:23
Alignment explanation
Indices: 25474--25534 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
25464 CATTGTTATA
*
25474 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
25497 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
25520 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
25535 TTTATATGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:25770 original size:4 final size:4
Alignment explanation
Indices: 25761--25785 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25751 ATGAGTTATG
25761 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
25786 TTACTGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:27268 original size:3 final size:3
Alignment explanation
Indices: 27253--27329 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
27243 AATTTTAATT
* * * *
27253 TTA TTA TTG TTA TTA TTA TTA TTA TTA ATG TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
27301 TTA TTGT TTA TTAA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TT-A TTA TTA TTA TTA TTA
27330 ATTACATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 59 0.92
4 5 0.08
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42037 original size:141 final size:141
Alignment explanation
Indices: 41772--42039 Score: 369
Period size: 141 Copynumber: 1.9 Consensus size: 141
41762 ATCAACTGAT
*
41772 CAGATCTCCTCGACACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGA
1 CAGACCTCCTCGACACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGA
* ** *
41837 ACCGAGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTACGAACCATGTCATCTAC
66 ACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTACGAACCATGTCATCTAC
41902 CCTTAGACGAC
131 CCTTAGACGAC
* * * *
41913 CAGACCTCCTC-ATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATTACGTAG
1 CAGACCTCCTCGA-CACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAG
* * * * * *
41976 GAACCTAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATC
64 GAACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTACGAACCATGTCATC
42040 CTTTGACCAG
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
140 1 0.01
141 98 0.89
142 11 0.10
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (141 bp):
CAGACCTCCTCGACACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGA
ACCGAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTACGAACCATGTCATCTAC
CCTTAGACGAC
Found at i:42299 original size:3 final size:3
Alignment explanation
Indices: 42284--42360 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
42274 AATTTTAATT
* * * *
42284 TTA TTA TTG TTA TTA TTA TTA TTA TTA ATG TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
42332 TTA TTGT TTA TTAA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TT-A TTA TTA TTA TTA TTA
42361 ATTACATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 59 0.92
4 5 0.08
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:43967 original size:2 final size:2
Alignment explanation
Indices: 43955--43986 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
43945 GTTATTGTCA
*
43955 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43987 GGTATTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:57924 original size:29 final size:29
Alignment explanation
Indices: 57883--57959 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
57873 ATTTTTTTAA
* *
57883 AATTACGAAAATAGCACCCTTTTCCAAAT
1 AATTACCAGAATAGCACCCTTTTCCAAAT
* * *
57912 AATTACCAGAATAACAACCTTTTCTAAAT
1 AATTACCAGAATAGCACCCTTTTCCAAAT
57941 AATTACCAGAATAGCACCC
1 AATTACCAGAATAGCACCC
57960 GGTTAACGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.26
Consensus pattern (29 bp):
AATTACCAGAATAGCACCCTTTTCCAAAT
Found at i:65135 original size:28 final size:28
Alignment explanation
Indices: 65020--65170 Score: 107
Period size: 29 Copynumber: 5.5 Consensus size: 28
65010 ATCATTTTCA
* * *
65020 AAAACAATTACCAAAATATCACAATTTTT
1 AAAATAATTACCAAAATAACAC-CTTTTT
* * **
65049 AAAATAATTACTAAAATATCATTTTTTT
1 AAAATAATTACCAAAATAACACCTTTTT
* * * *
65077 TAAA-AATTA-CTAAAT--TA-TTTTTT
1 AAAATAATTACCAAAATAACACCTTTTT
*
65100 AAAA-AATTACGAAAATAACACCTTTTT
1 AAAATAATTACCAAAATAACACCTTTTT
* *
65127 AAAATAATTACCAGAATAGCACCTTTTT
1 AAAATAATTACCAAAATAACACCTTTTT
*
65155 CCAAATAATTACCAAA
1 -AAAATAATTACCAAA
65171 TAGCATCTGA
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
23 14 0.14
24 5 0.05
26 5 0.05
27 14 0.14
28 28 0.29
29 32 0.33
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATAATTACCAAAATAACACCTTTTT
Found at i:65172 original size:28 final size:27
Alignment explanation
Indices: 65095--65175 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 27
65085 ACTAAATTAT
* *
65095 TTTTTAAAA-AATTACGAAAATAACACC
1 TTTTTAAAATAATTAC-CAAATAGCACC
65122 TTTTTAAAATAATTACCAGAATAGCACC
1 TTTTTAAAATAATTACCA-AATAGCACC
*
65150 TTTTTCCAAATAATTACCAAATAGCA
1 TTTTT-AAAATAATTACCAAATAGCA
65176 TCTGAACAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
27 10 0.21
28 26 0.54
29 12 0.25
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (27 bp):
TTTTTAAAATAATTACCAAATAGCACC
Done.