Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004334.1 Hibiscus syriacus cultivar Beakdansim tig00009501_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: 56399
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1092 original size:31 final size:31
Alignment explanation
Indices: 1039--1107 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1029 ACACATAATA
* * *
1039 AACTCATCATAACATGAACTTTCATGGAAAG
1 AACTTATCAAAACATGAACTTTCATGCAAAG
* * *
1070 AACTTATCAAAACATGATCTTTCTTGCCAAG
1 AACTTATCAAAACATGAACTTTCATGCAAAG
1101 AACTTAT
1 AACTTAT
1108 ATAGTAACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (31 bp):
AACTTATCAAAACATGAACTTTCATGCAAAG
Found at i:1212 original size:33 final size:33
Alignment explanation
Indices: 1162--1253 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
1152 TCATCATATG
**
1162 ACTTTCATGA-TATAACTTATATCATAAGTTGA
1 ACTTTCATGACTATAACTTATATCATAACATGA
*
1194 ATTTTCATGACTATAACTTATATCATAACATGA
1 ACTTTCATGACTATAACTTATATCATAACATGA
* * **
1227 ACTTTCATGGCAAGCACTTATATCATA
1 ACTTTCATGACTATAACTTATATCATA
1254 TACCTAGCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 9 0.18
33 42 0.82
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (33 bp):
ACTTTCATGACTATAACTTATATCATAACATGA
Found at i:2100 original size:16 final size:16
Alignment explanation
Indices: 2079--2116 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2069 CAAGCATAGA
2079 ATCAAACATAAAATT-T
1 ATCAAACA-AAAATTGT
*
2095 ATCAAACAAACATTGT
1 ATCAAACAAAAATTGT
2111 ATCAAA
1 ATCAAA
2117 TTAACTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (16 bp):
ATCAAACAAAAATTGT
Found at i:3860 original size:20 final size:21
Alignment explanation
Indices: 3835--3885 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3825 GTTTTAAAAA
*
3835 GGTATCAATATCTT-CCCTTC
1 GGTATCGATATCTTCCCCTTC
*
3855 GGTATCGATA-CTTCCCCTTT
1 GGTATCGATATCTTCCCCTTC
3875 GGTATCGATAT
1 GGTATCGATAT
3886 TGATTAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
GGTATCGATATCTTCCCCTTC
Found at i:9840 original size:28 final size:28
Alignment explanation
Indices: 9800--9866 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
9790 AAATCCTTCG
*
9800 TATCATAACCAAACTCTGCTCGTTTTAT
1 TATCATAACCAAACTCTGCTCATTTTAT
* *
9828 TATCATAACCAAACTTTGGTCATTTTAT
1 TATCATAACCAAACTCTGCTCATTTTAT
*
9856 CATCATAACCA
1 TATCATAACCA
9867 TTCTAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (28 bp):
TATCATAACCAAACTCTGCTCATTTTAT
Found at i:10039 original size:46 final size:46
Alignment explanation
Indices: 9947--10240 Score: 408
Period size: 46 Copynumber: 6.3 Consensus size: 46
9937 TCCATGATAT
* * * *
9947 ATTTAAATTATGGCATCCTTTCATGCATTTTAATTATGTATCCTTTCATTC
1 ATTTTAATTATGGCATCCTTTCATGC--CTT-A--ATGCATCCTTTCATGC
* *
9998 ATTTTAATTATGGCATCCTTTTATTCCTTAATGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
10044 ATTTTAATTATGGAATCATTTCATGCCTTAATGCAACCTTTCAAGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
10090 ATTTTAATTATGGCATCCTTTCATGCCTTAATGTATCATTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
10136 ATTTTAATTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
10182 ATTTTAATTATGGCATCATTTCATGCCTTAATGCATCTTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
10228 ATTTTAATTATGG
1 ATTTTAATTATGG
10241 ATTCGATTTA
Statistics
Matches: 219, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
46 193 0.88
48 1 0.00
49 2 0.01
51 23 0.11
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:10133 original size:20 final size:20
Alignment explanation
Indices: 10102--10227 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
10092 TTTAATTATG
*
10102 GCATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
* *
10122 GTATCATTTCATGCATTTTAATTAT
1 GCATCATTTCATGC--CTT-A--AT
* *
10147 GGTATCCTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
* *
10168 GCATCCTTTCATGCATTTTAATTAT
1 GCATCATTTCATGC--CTT-A--AT
10193 GGCATCATTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
*
10214 GCATCTTTTCATGC
1 GCATCATTTCATGC
10228 ATTTTAATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
20 38 0.45
21 4 0.05
22 4 0.05
23 4 0.05
24 4 0.05
25 4 0.05
26 26 0.31
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATCATTTCATGCCTTAAT
Found at i:10205 original size:138 final size:141
Alignment explanation
Indices: 9947--10240 Score: 450
Period size: 138 Copynumber: 2.1 Consensus size: 141
9937 TCCATGATAT
* * * *
9947 ATTTAAATTATGGCATCCTTTCATGCATTTTAATTATGTATCCTTTCATTCATTTTAATTATGGC
1 ATTTTAATTATGGCATCCTTTCATGCA-CTTAA-TATGTATCATTTCATGCATTTTAATTATGGC
* *
10012 ATCCTTTTATTCCTTAATGCATCCTTTCATGCATTTTAATTATGGAATCATTTCATGCCTTAATG
64 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGAATCATTTCATGCCTTAATG
10077 CAACCTTTCAAGC
129 CAACCTTTCAAGC
*
10090 ATTTTAATTATGGCATCCTTTCATGC-CTT-A-ATGTATCATTTCATGCATTTTAATTATGGTAT
1 ATTTTAATTATGGCATCCTTTCATGCACTTAATATGTATCATTTCATGCATTTTAATTATGGCAT
*
10152 CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAATGCA
66 CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGAATCATTTCATGCCTTAATGCA
* * *
10217 TCTTTTCATGC
131 ACCTTTCAAGC
10228 ATTTTAATTATGG
1 ATTTTAATTATGG
10241 ATTCGATTTA
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
138 112 0.80
140 1 0.01
141 2 0.01
143 25 0.18
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (141 bp):
ATTTTAATTATGGCATCCTTTCATGCACTTAATATGTATCATTTCATGCATTTTAATTATGGCAT
CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGAATCATTTCATGCCTTAATGCA
ACCTTTCAAGC
Found at i:10748 original size:20 final size:20
Alignment explanation
Indices: 10723--10813 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
10713 ATATTACCTA
*
10723 GTATCGATACTCTTACCATG
1 GTATCGATACTCCTACCATG
10743 GTATCGATAC-CCTTACCATG
1 GTATCGATACTCC-TACCATG
*
10763 GTATCGATACTACCCTACTATG
1 GTATCGATACT--CCTACCATG
* **
10785 GTACCGATAC-CCTATTATG
1 GTATCGATACTCCTACCATG
10804 GTATCGATAC
1 GTATCGATAC
10814 CTTCCCTTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
19 18 0.29
20 27 0.44
22 15 0.24
23 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (20 bp):
GTATCGATACTCCTACCATG
Found at i:10792 original size:22 final size:23
Alignment explanation
Indices: 10734--10794 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
10724 TATCGATACT
*
10734 CTTACCATGGTATCG--A-TACC
1 CTTACCATGGTACCGATACTACC
*
10754 CTTACCATGGTATCGATACTACC
1 CTTACCATGGTACCGATACTACC
*
10777 C-TACTATGGTACCGATAC
1 CTTACCATGGTACCGATAC
10795 CCTATTATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.42
22 16 0.44
23 5 0.14
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (23 bp):
CTTACCATGGTACCGATACTACC
Found at i:10793 original size:42 final size:39
Alignment explanation
Indices: 10723--10813 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 39
10713 ATATTACCTA
* *
10723 GTATCGATACTCTTACCATGGTATCGATACCCTTACCATG
1 GTATCGATACTCCTACCATGGTACCGATACCC-TACCATG
* **
10763 GTATCGATACTACCCTACTATGGTACCGATACCCTATTATG
1 GTATCGATACT--CCTACCATGGTACCGATACCCTACCATG
10804 GTATCGATAC
1 GTATCGATAC
10814 CTTCCCTTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
40 11 0.25
41 15 0.34
42 18 0.41
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (39 bp):
GTATCGATACTCCTACCATGGTACCGATACCCTACCATG
Found at i:15541 original size:21 final size:21
Alignment explanation
Indices: 15511--15574 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
15501 AATGGCCCAA
15511 TTTC-ACATTCTAACATCAAT
1 TTTCAACATTCTAACATCAAT
15531 TTTCAACATTCTAACATCAAT
1 TTTCAACATTCTAACATCAAT
*
15552 TTTCAACATTCTAACATTAAT
1 TTTCAACATTCTAACATCAAT
15573 TT
1 TT
15575 CTAGCATAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 4 0.10
21 38 0.90
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTCAACATTCTAACATCAAT
Found at i:18060 original size:55 final size:54
Alignment explanation
Indices: 17964--18069 Score: 133
Period size: 55 Copynumber: 1.9 Consensus size: 54
17954 CATTTTCGAC
*
17964 ACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATGACCATTTCGGT
1 ACTAAATGTGCAACCCATGGTATTCATAATGAGTTTATGAATGACCATTTCGGT
* * * **
18018 ACTATATGTGCAACCCAT-TTAAATTCATAATGAGTTTGTGAATTTCCATTTC
1 ACTAAATGTGCAACCCATGGT--ATTCATAATGAGTTTATGAATGACCATTTC
18070 AGCACTTCGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.02
54 17 0.39
55 26 0.59
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (54 bp):
ACTAAATGTGCAACCCATGGTATTCATAATGAGTTTATGAATGACCATTTCGGT
Found at i:22389 original size:67 final size:67
Alignment explanation
Indices: 22308--22446 Score: 160
Period size: 67 Copynumber: 2.1 Consensus size: 67
22298 AAACGATCAA
* *
22308 TTTTTCCTTCTTC-TTATTT-TT-TTCG-AACAAGGATCTGTTTTTTTTTGCTGTTCGAAACAAT
1 TTTTTCCTTCTTCTTTATTTGTTGTTCGAAACAAGGA----TTTTTTTCTACTGTTCGAAACAAT
22369 GAACAT
62 GAACAT
* * * *
22375 TTTTTCTTTTTTCTTTTTTTGTTGTTCGAAACAATGATTTTTTTCTACTGTTCGAAACAATGAAC
1 TTTTTCCTTCTTCTTTATTTGTTGTTCGAAACAAGGATTTTTTTCTACTGTTCGAAACAATGAAC
22440 AT
66 AT
22442 TTTTT
1 TTTTT
22447 GACCTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
67 44 0.71
68 5 0.08
69 2 0.03
70 4 0.06
71 7 0.11
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (67 bp):
TTTTTCCTTCTTCTTTATTTGTTGTTCGAAACAAGGATTTTTTTCTACTGTTCGAAACAATGAAC
AT
Found at i:26902 original size:25 final size:24
Alignment explanation
Indices: 26874--26984 Score: 62
Period size: 25 Copynumber: 4.4 Consensus size: 24
26864 TAAAACTATT
26874 TAAAATAAAATACCTAAAACAAAAA
1 TAAAATAAAATA-CTAAAACAAAAA
* * *
26899 TAAAATATAAA-AATAATATCCTAAAAC
1 TAAAATA-AAATACTAA-A-AC-AAAAA
* * ** **
26926 TTAATTAAAATACTAAAACTTATT
1 TAAAATAAAATACTAAAACAAAAA
* *
26950 TAAACTAAAATACCTAAAACAAAGA
1 TAAAATAAAATA-CTAAAACAAAAA
26975 TAAAATAAAA
1 TAAAATAAAA
26985 ATAATATCCT
Statistics
Matches: 62, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
24 14 0.23
25 27 0.44
26 8 0.13
27 13 0.21
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.24
Consensus pattern (24 bp):
TAAAATAAAATACTAAAACAAAAA
Found at i:26922 original size:32 final size:34
Alignment explanation
Indices: 26875--26943 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
26865 AAAACTATTT
26875 AAAATAAAATACCTAAAACAAAAATAAAATA-TA
1 AAAATAAAATACCTAAAACAAAAATAAAATACTA
* ** *
26908 AAAATAATAT-CCTAAAACTTAATTAAAATACTA
1 AAAATAAAATACCTAAAACAAAAATAAAATACTA
26941 AAA
1 AAA
26944 CTTATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (34 bp):
AAAATAAAATACCTAAAACAAAAATAAAATACTA
Found at i:27012 original size:74 final size:76
Alignment explanation
Indices: 26864--27034 Score: 287
Period size: 74 Copynumber: 2.3 Consensus size: 76
26854 TAAAAACACT
*
26864 TAAAAC-TATTTAAAATAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAACTT
1 TAAAACTTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAACTT
26928 AATTAAAATAC
66 AATTAAAATAC
*
26939 TAAAACTTATTTAAACTAAAATACCTAAAACAAAGAT-AAA-ATAAAAATAATATCCTAAAACTT
1 TAAAACTTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAACTT
27002 AATTAAAATAC
66 AATTAAAATAC
27013 TAAAA-TCTATTTAAACTAAAAT
1 TAAAACT-TATTTAAACTAAAAT
27035 GCAAAGATAA
Statistics
Matches: 92, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
73 1 0.01
74 54 0.59
75 9 0.10
76 28 0.30
ACGTcount: A:0.60, C:0.11, G:0.01, T:0.28
Consensus pattern (76 bp):
TAAAACTTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAATATCCTAAAACTT
AATTAAAATAC
Found at i:31621 original size:54 final size:54
Alignment explanation
Indices: 31558--31660 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
31548 ACATTAAATA
** * *
31558 TGCAACCCATGGTTTTCATAATGCGTTTATGAATGACCTTTTCGGCACTATGTG
1 TGCAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACTATGTG
* **
31612 TGCAACCCATGGAATTCATAATGAGTTTGTGAATTTCCATTTCGGCACT
1 TGCAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACT
31661 TCGGTGCAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCAACCCATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACTATGTG
Found at i:36105 original size:45 final size:45
Alignment explanation
Indices: 36036--36229 Score: 309
Period size: 45 Copynumber: 4.3 Consensus size: 45
36026 CATTTATTTT
* *
36036 CCATTTATCCCATAAGCTCGTAAGCTTATTTTACTAATATACTTA
1 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
* * * *
36081 CAATTTAATCCATAAGCTCATAAGCTTATTTTACCAATGTACTTA
1 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
36126 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
1 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
* *
36171 CCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAACATACTTA
1 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
36216 CCATTT-TTCCATAA
1 CCATTTATTCCATAA
36230 CCATATATCG
Statistics
Matches: 137, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 8 0.06
45 129 0.94
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (45 bp):
CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
Found at i:36452 original size:61 final size:61
Alignment explanation
Indices: 36331--36452 Score: 156
Period size: 61 Copynumber: 2.0 Consensus size: 61
36321 ATAGTTCTAA
* * *
36331 ACCTGCACTAAGCTTACGCCATTGTGCTAATCCCGACAATACACATAAGGGCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCCGACAATACACATAAGGGCGTACCCACC
* * * * *
36392 ACCTACACTAAGCTTACGCTATAGTGCTAATCCGGAC-ATGATACATAAGGTCGTATCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCCGACAAT-ACACATAAGGGCGTACCCACC
36453 TTTCCCGCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 2 0.04
61 50 0.96
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCCGACAATACACATAAGGGCGTACCCACC
Found at i:40797 original size:25 final size:25
Alignment explanation
Indices: 40763--40820 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
40753 TTGACTGTCA
40763 TGATTTTTATAAAATCATGAGATAT
1 TGATTTTTATAAAATCATGAGATAT
40788 TGATTTTTATAAAATCATGAGATAT
1 TGATTTTTATAAAATCATGAGATAT
40813 TGATTTTT
1 TGATTTTT
40821 TAGGTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (25 bp):
TGATTTTTATAAAATCATGAGATAT
Found at i:43337 original size:19 final size:19
Alignment explanation
Indices: 43289--43338 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
43279 TTTGTTCTAC
43289 AAAAAAAAAAAAGAAGAAG
1 AAAAAAAAAAAAGAAGAAG
*
43308 AAAACATAAAAAAG-AGAAG
1 AAAA-AAAAAAAAGAAGAAG
43327 AAACAAAAAAAA
1 AAA-AAAAAAAA
43339 CTAGTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAGAAGAAG
Found at i:44149 original size:37 final size:37
Alignment explanation
Indices: 44108--44222 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 37
44098 TTTAGTTTAA
44108 ATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTT
1 ATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTT
*** **** * * * **
44145 ATTTGAA-TA-TTTTTAGGATTTATCTTTAG--CTAA
1 ATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTT
44178 ATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTT
1 ATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTT
44215 ATTTGAAT
1 ATTTGAAT
44223 ATTTTTAGGA
Statistics
Matches: 50, Mismatches: 24, Indels: 8
0.61 0.29 0.10
Matches are distributed among these distances:
33 8 0.16
34 2 0.04
35 22 0.44
36 2 0.04
37 16 0.32
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.51
Consensus pattern (37 bp):
ATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTT
Found at i:44218 original size:70 final size:70
Alignment explanation
Indices: 44105--44246 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
44095 GACTTTAGTT
44105 TAAATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTTATTTGAATATTTTTAGGATTTATCT
1 TAAATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTTATTTGAATATTTTTAGGATTTATCT
44170 TTAGC
66 TTAGC
44175 TAAATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTTATTTGAATATTTTTAGGATTTATCT
1 TAAATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTTATTTGAATATTTTTAGGATTTATCT
44240 TTAGC
66 TTAGC
44245 TA
1 TA
44247 TTTTTTCTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.51
Consensus pattern (70 bp):
TAAATTTGAATTAGAAATTATCCCTTGTTTTTAGAATTTTATTTGAATATTTTTAGGATTTATCT
TTAGC
Found at i:44371 original size:8 final size:9
Alignment explanation
Indices: 44354--44383 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44344 TTTTATAAAG
44354 TTTTCATTT
1 TTTTCATTT
44363 TTTTC-TTT
1 TTTTCATTT
44371 TTTTCATTT
1 TTTTCATTT
44380 TTTT
1 TTTT
44384 ACTTTTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTCATTT
Found at i:44374 original size:17 final size:18
Alignment explanation
Indices: 44354--44389 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
44344 TTTTATAAAG
44354 TTTTCATTTTTTT-CTTT
1 TTTTCATTTTTTTACTTT
44371 TTTTCATTTTTTTACTTT
1 TTTTCATTTTTTTACTTT
44389 T
1 T
44390 AAGTTCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCATTTTTTTACTTT
Found at i:46665 original size:14 final size:15
Alignment explanation
Indices: 46646--46678 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46636 CTAACACCCA
46646 CTCAACACT-AATGC
1 CTCAACACTAAATGC
*
46660 CTCAACCCTAAATGC
1 CTCAACACTAAATGC
46675 CTCA
1 CTCA
46679 CTATTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.33, C:0.39, G:0.06, T:0.21
Consensus pattern (15 bp):
CTCAACACTAAATGC
Found at i:47811 original size:16 final size:16
Alignment explanation
Indices: 47779--47808 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47769 AACTTATTCT
47779 TTTTTTTCGTTCATTA
1 TTTTTTTCGTTCATTA
47795 TTTTTTTC-TTCATT
1 TTTTTTTCGTTCATT
47809 TATGTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTTTCGTTCATTA
Found at i:53142 original size:35 final size:35
Alignment explanation
Indices: 53096--53167 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
53086 AATGTATTGT
*
53096 TACCATTGATTTACATAATGTAGAAATGGTATCGA
1 TACCATTGATTTACATAATGCAGAAATGGTATCGA
*
53131 TACCATTGATTTACATAATGCAGAAATGGTATTGA
1 TACCATTGATTTACATAATGCAGAAATGGTATCGA
53166 TA
1 TA
53168 ACGTAATAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (35 bp):
TACCATTGATTTACATAATGCAGAAATGGTATCGA
Found at i:53866 original size:55 final size:56
Alignment explanation
Indices: 53646--54031 Score: 510
Period size: 56 Copynumber: 6.9 Consensus size: 56
53636 TACCAAATGA
* *
53646 CACTGTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTAGTATGGG
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * **
53702 CACTTTGTATGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAAG
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * **
53758 CATTTTGTGTGCAAAAACTAAGAAATTCATAACGAGTTTATGAA-TTTCAGTATGGG
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGG
* * *
53814 TACTTTGTGTGC-AAAGCTAATAAATTCATAATAAGTTTATGAATTTTCGTATGGA
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * * * * * *
53869 CACTTTGTGTGCAAAAACTATGAAATTCATATTGAGTTTATGAATTTCCTTATTGG
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * *
53925 AACTTTGTGTGC-AAAGCTAAGAAATTCATAATAAGTTTATGAATTTACATATGGG
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* *
53980 CACTTTGTGTGTAAAA-CTAAGAAATTCATAATAAGTATATGAATTTTCGTAT
1 CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
54032 TGGTAGTGGG
Statistics
Matches: 282, Mismatches: 44, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
55 126 0.45
56 156 0.55
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (56 bp):
CACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
Found at i:53885 original size:111 final size:111
Alignment explanation
Indices: 53644--54025 Score: 525
Period size: 111 Copynumber: 3.4 Consensus size: 111
53634 ATTACCAAAT
* * * *
53644 GACACTGTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTAGTATGGGCACTTTG
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGGAACTTTG
* *
53709 TATGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-
66 TGTGC-AAAGCTAAGAAATTCATAATAAGTTTATGAATTTACGTATG
* * ** *
53755 AAGCATTTTGTGTGCAAAAACTAAGAAATTCATAACGAGTTTATGAATTTCAGTATGGGTACTTT
1 GA-CACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGGAACTTT
* *
53820 GTGTGCAAAGCTAATAAATTCATAATAAGTTTATGAATTTTCGTATG
65 GTGTGCAAAGCTAAGAAATTCATAATAAGTTTATGAATTTACGTATG
* * * ** *
53867 GACACTTTGTGTGCAAAAACTATGAAATTCATATTGAGTTTATGAATTTCCTTATTGGAACTTTG
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGGAACTTTG
*
53932 TGTGCAAAGCTAAGAAATTCATAATAAGTTTATGAATTTACATATG
66 TGTGCAAAGCTAAGAAATTCATAATAAGTTTATGAATTTACGTATG
* * *
53978 GGCACTTTGTGTG-TAAAACTAAGAAATTCATAATAAGTATATGAATTT
1 GACACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTT
54026 TCGTATTGGT
Statistics
Matches: 240, Mismatches: 29, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
110 30 0.12
111 149 0.62
112 61 0.25
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (111 bp):
GACACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGGGAACTTTG
TGTGCAAAGCTAAGAAATTCATAATAAGTTTATGAATTTACGTATG
Done.