Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006729.1 Hibiscus syriacus cultivar Beakdansim tig00016858_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: 59540
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:8707 original size:9 final size:9
Alignment explanation
Indices: 8693--8727 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
8683 GAAATCGGTT
8693 AATTAACCG
1 AATTAACCG
*
8702 AATTAATCG
1 AATTAACCG
8711 AATTAACCG
1 AATTAACCG
8720 AATTAACC
1 AATTAACC
8728 CTTAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:10626 original size:20 final size:19
Alignment explanation
Indices: 10601--10653 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
10591 ATTGTATTGT
10601 AATAGTACTGATACTGTATG
1 AATAGTACTGATACT-TATG
* *
10621 AATAGTACTAATA-TTGTG
1 AATAGTACTGATACTTATG
*
10639 AACAGTACTGATACT
1 AATAGTACTGATACT
10654 CAAAAACTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.50
19 2 0.07
20 12 0.43
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (19 bp):
AATAGTACTGATACTTATG
Found at i:12824 original size:25 final size:24
Alignment explanation
Indices: 12796--12852 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
12786 GTCATACTAA
* *
12796 TAAATTAAAATAAATTATATATTTT
1 TAAATTAAAATAAA-AAAATATTTT
*
12821 TAAATGAAAATAAAAAAATATTTT
1 TAAATTAAAATAAAAAAATATTTT
12845 TAAATTAA
1 TAAATTAA
12853 GTTAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATTAAAATAAAAAAATATTTT
Found at i:12867 original size:27 final size:27
Alignment explanation
Indices: 12814--12903 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 27
12804 AATAAATTAT
* *
12814 ATATTTTTAAATGAA---AATAAAAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
12838 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
* *
12865 ATATATTT-AA-TAAGTTGAT-ATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
*
12889 A-ATGTTTTAAGTTAA
1 ATAT-TTTTAAATTAA
12904 TAGATATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.04
24 23 0.43
25 9 0.17
26 5 0.09
27 15 0.28
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATTAAGTTAATAATAAA
Found at i:12890 original size:25 final size:26
Alignment explanation
Indices: 12834--12921 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 26
12824 ATGAAAATAA
* *
12834 AAAAATATTTTTAAATTAAGTTAATA-
1 AAAAATATATTT-AATTAAGTTGATAT
12860 ATAAAATATATTTAA-TAAGTTGATAT
1 A-AAAATATATTTAATTAAGTTGATAT
* *
12886 AAAAATGT-TTTAAGTTAA-TAGATAT
1 AAAAATATATTTAA-TTAAGTTGATAT
*
12911 AAAATTATATT
1 AAAAATATATT
12922 ATATATAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 5 0.10
25 27 0.53
26 9 0.18
27 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (26 bp):
AAAAATATATTTAATTAAGTTGATAT
Found at i:13051 original size:23 final size:22
Alignment explanation
Indices: 13025--13105 Score: 57
Period size: 23 Copynumber: 3.8 Consensus size: 22
13015 AAATATTAAA
13025 AAATAATTTAGAATGTTAATGTG
1 AAATAATTTAGAA-GTTAATGTG
* *
13048 AAATATTTTA-AA--AAAT-T-
1 AAATAATTTAGAAGTTAATGTG
*
13065 -AAGAATTTAGAACGTTAATGTG
1 AAATAATTTAGAA-GTTAATGTG
*
13087 AAATAATTTAAGAAATTAA
1 AAATAATTT-AGAAGTTAA
13106 GAATTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
16 7 0.16
17 2 0.05
18 1 0.02
19 3 0.07
20 3 0.07
21 1 0.02
22 2 0.05
23 20 0.47
24 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (22 bp):
AAATAATTTAGAAGTTAATGTG
Found at i:13076 original size:39 final size:39
Alignment explanation
Indices: 13029--13171 Score: 166
Period size: 39 Copynumber: 3.7 Consensus size: 39
13019 ATTAAAAAAT
*
13029 AATTTAGAATGTTAATGTGAAATATTTTAAAAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAAAAATTAAG
* *
13068 AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAAAAATTAAG
* * **
13107 AATTTAGAATGTT-ATGTTGTCAA-AATTTAAGAAATTGGG
1 AATTTAGAATGTTAATG-TG-AAATAATTTAAAAAATTAAG
*
13146 ATTTTAGAATGTTAGA-GTGAAATAAT
1 AATTTAGAATGTTA-ATGTGAAATAAT
13172 ATGAGGATTA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
38 5 0.06
39 81 0.90
40 3 0.03
41 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.17, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAAAAATTAAG
Found at i:13208 original size:19 final size:21
Alignment explanation
Indices: 13184--13222 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13174 GAGGATTATG
13184 AATAAAAT-T-TAATATAAAA
1 AATAAAATGTATAATATAAAA
13203 AATAAAATGTATAATATAAA
1 AATAAAATGTATAATATAAA
13223 TCGGGTACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
AATAAAATGTATAATATAAAA
Found at i:15392 original size:32 final size:32
Alignment explanation
Indices: 15356--15420 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
15346 AAAGTTCAAC
15356 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
1 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
15388 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
1 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
15420 G
1 G
15421 TCAGAGGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.48, T:0.09
Consensus pattern (32 bp):
GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
Found at i:16971 original size:9 final size:9
Alignment explanation
Indices: 16957--17049 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
16947 GGCTGCTGGA
16957 AACCGGTTT
1 AACCGGTTT
16966 AACCGGTTTT
1 AACCGG-TTT
16976 CAACCGGTTCT
1 -AACCGGTT-T
*
16987 GACCGGTTT
1 AACCGGTTT
*
16996 GACC-GTTT
1 AACCGGTTT
*
17004 CAACCGGTTCG
1 -AACCGGTT-T
17015 AACCGGTTT
1 AACCGGTTT
* *
17024 GACCGGTCT
1 AACCGGTTT
*
17033 GACTCGGTTT
1 AAC-CGGTTT
*
17043 GACCGGT
1 AACCGGT
17050 CTGACCCGAC
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.06
9 28 0.40
10 31 0.44
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:16982 original size:20 final size:21
Alignment explanation
Indices: 16957--16995 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16947 GGCTGCTGGA
16957 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
16977 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
16996 GACCGTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:17008 original size:28 final size:29
Alignment explanation
Indices: 16957--17028 Score: 103
Period size: 28 Copynumber: 2.5 Consensus size: 29
16947 GGCTGCTGGA
*
16957 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACC-GTTTTCAACCGGTTC-G
16988 -ACCGGTTTGACCG-TTTCAACCGGTTCG
1 AACCGGTTTGACCGTTTTCAACCGGTTCG
17015 AACCGGTTTGACCG
1 AACCGGTTTGACCG
17029 GTCTGACTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 1 0.03
28 26 0.67
29 1 0.03
30 11 0.28
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.29
Consensus pattern (29 bp):
AACCGGTTTGACCGTTTTCAACCGGTTCG
Found at i:17028 original size:19 final size:19
Alignment explanation
Indices: 16957--17049 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 19
16947 GGCTGCTGGA
*
16957 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTGACCGG--TTCG
*
16977 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
*
16997 -ACC-GTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
17015 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
17034 -ACTCGGTTTGACCGGT
1 AAC-CGGTTTGACCGGT
17050 CTGACCCGAC
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
17 1 0.02
18 15 0.25
19 26 0.43
20 12 0.20
21 6 0.10
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:17050 original size:19 final size:19
Alignment explanation
Indices: 17018--17054 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17008 CGGTTCGAAC
17018 CGGTTTGACCGGTCTGACT
1 CGGTTTGACCGGTCTGACT
17037 CGGTTTGACCGGTCTGAC
1 CGGTTTGACCGGTCTGAC
17055 CCGACCCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.27, G:0.32, T:0.30
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGACT
Found at i:17054 original size:9 final size:9
Alignment explanation
Indices: 17016--17055 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
17006 ACCGGTTCGA
*
17016 ACCGGTTTG
1 ACCGGTCTG
17025 ACCGGTCTG
1 ACCGGTCTG
*
17034 ACTCGGTTTG
1 AC-CGGTCTG
17044 ACCGGTCTG
1 ACCGGTCTG
17053 ACC
1 ACC
17056 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:17062 original size:5 final size:5
Alignment explanation
Indices: 17052--17109 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
17042 TGACCGGTCT
* *
17052 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
17101 GACCC GACC
1 GACCC GACC
17110 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:17078 original size:22 final size:22
Alignment explanation
Indices: 17052--17116 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
17042 TGACCGGTCT
17052 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
17074 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
17096 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
17117 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:17118 original size:7 final size:7
Alignment explanation
Indices: 17106--17143 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
17096 GACCCGACCC
17106 GACCGTT
1 GACCGTT
17113 GACCGTT
1 GACCGTT
17120 GACCGTT
1 GACCGTT
17127 GACCGTT
1 GACCGTT
17134 GACCGTT
1 GACCGTT
17141 GAC
1 GAC
17144 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:24304 original size:9 final size:9
Alignment explanation
Indices: 24290--24383 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
24280 GGCTGCTGGA
24290 AACCGGTTT
1 AACCGGTTT
24299 AACCGGTTTT
1 AACCGG-TTT
24309 CAACCGGTTCT
1 -AACCGGTT-T
*
24320 GACCGGTTT
1 AACCGGTTT
*
24329 GACCGGTTT
1 AACCGGTTT
* *
24338 CAATCGGTTCG
1 -AACCGGTT-T
24349 AACCGGTTT
1 AACCGGTTT
* *
24358 GACCGGTCT
1 AACCGGTTT
*
24367 GACTCGGTTT
1 AAC-CGGTTT
*
24377 GACCGGT
1 AACCGGT
24384 CTGACCCGAC
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
9 30 0.43
10 33 0.47
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:24315 original size:20 final size:21
Alignment explanation
Indices: 24290--24328 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24280 GGCTGCTGGA
24290 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
24310 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
24329 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:24335 original size:19 final size:19
Alignment explanation
Indices: 24292--24389 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
24282 CTGCTGGAAA
* * *
24292 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
24312 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
* *
24331 CCGGTTTCAATCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
24351 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
24369 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
24388 CC
1 CC
24390 CGACCCGACC
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
18 6 0.09
19 37 0.56
20 15 0.23
21 8 0.12
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.31
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:24353 original size:29 final size:30
Alignment explanation
Indices: 24290--24364 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
24280 GGCTGCTGGA
*
24290 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
24321 -ACCGGTTTGACCGGTTTCAATCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
24349 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
24365 CTGACTCGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.66
30 13 0.32
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:24373 original size:29 final size:28
Alignment explanation
Indices: 24291--24389 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
24281 GCTGCTGGAA
* * *
24291 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAATCGGTTC-G
*
24321 ACCGGTTTGACCGGTTTCAATCGGTTCG
1 ACCGGTTTGACCGGTCTCAATCGGTTCG
* * *
24349 AACCGGTTTGACCGGTCTGACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAATCGGTTCG
*
24378 ACCGGTCTGACC
1 ACCGGTTTGACC
24390 CGACCCGACC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
28 12 0.20
29 36 0.59
30 13 0.21
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAATCGGTTCG
Found at i:24388 original size:9 final size:9
Alignment explanation
Indices: 24350--24389 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
24340 ATCGGTTCGA
*
24350 ACCGGTTTG
1 ACCGGTCTG
24359 ACCGGTCTG
1 ACCGGTCTG
*
24368 ACTCGGTTTG
1 AC-CGGTCTG
24378 ACCGGTCTG
1 ACCGGTCTG
24387 ACC
1 ACC
24390 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:24396 original size:5 final size:5
Alignment explanation
Indices: 24386--24443 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
24376 TGACCGGTCT
* *
24386 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
24435 GACCC GACC
1 GACCC GACC
24444 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:24412 original size:22 final size:22
Alignment explanation
Indices: 24386--24450 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
24376 TGACCGGTCT
24386 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
24408 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
24430 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
24451 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:24452 original size:7 final size:7
Alignment explanation
Indices: 24440--24477 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
24430 GACCCGACCC
24440 GACCGTT
1 GACCGTT
24447 GACCGTT
1 GACCGTT
24454 GACCGTT
1 GACCGTT
24461 GACCGTT
1 GACCGTT
24468 GACCGTT
1 GACCGTT
24475 GAC
1 GAC
24478 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:29005 original size:13 final size:15
Alignment explanation
Indices: 28977--29008 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
28967 AATCACAGAA
28977 GAAATAAGATAGGGG
1 GAAATAAGATAGGGG
28992 GAAATAA-A-AGGGG
1 GAAATAAGATAGGGG
29005 GAAA
1 GAAA
29009 AGGGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (15 bp):
GAAATAAGATAGGGG
Found at i:34008 original size:21 final size:21
Alignment explanation
Indices: 33965--34008 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33955 AAAACGTCTG
* *
33965 ATAATAATAAATTTGATATAA
1 ATAATAATAAATTTAATAAAA
**
33986 ATAATAATATTTTTAATAAAA
1 ATAATAATAAATTTAATAAAA
34007 AT
1 AT
34009 TTACCTATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATAATAATAAATTTAATAAAA
Found at i:42641 original size:16 final size:16
Alignment explanation
Indices: 42620--42657 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
42610 TTTCCTAATT
42620 ATGTGCTTAATTTACA
1 ATGTGCTTAATTTACA
42636 ATGTGCTTAATTTACA
1 ATGTGCTTAATTTACA
42652 ACTGTG
1 A-TGTG
42658 ATTGTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (16 bp):
ATGTGCTTAATTTACA
Found at i:42818 original size:35 final size:34
Alignment explanation
Indices: 42778--42858 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 34
42768 CTTGACTCGT
42778 TGCTCGTTAAACTAATTAAAA-TCTTGCTCGACTCA
1 TGCTCGTTAAACTAA--AAAACTCTTGCTCGACTCA
* *
42813 TGCTCGTTAAA--AAAAAACTTGTTGCTCTACTCA
1 TGCTCGTTAAACTAAAAAAC-TCTTGCTCGACTCA
42846 TGCTCGTTAAACT
1 TGCTCGTTAAACT
42859 CGTTGCTCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 4 0.10
33 25 0.62
35 11 0.28
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (34 bp):
TGCTCGTTAAACTAAAAAACTCTTGCTCGACTCA
Found at i:42878 original size:16 final size:16
Alignment explanation
Indices: 42859--42907 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
42849 TCGTTAAACT
42859 CGTTGCTCGTTTAGCC
1 CGTTGCTCGTTTAGCC
* *
42875 CGTT-C-C--TCAGCT
1 CGTTGCTCGTTTAGCC
42887 CGTTGCTCGTTTAGCC
1 CGTTGCTCGTTTAGCC
42903 CGTTG
1 CGTTG
42908 AAATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 8 0.32
13 1 0.04
14 2 0.08
15 1 0.04
16 13 0.52
ACGTcount: A:0.06, C:0.33, G:0.24, T:0.37
Consensus pattern (16 bp):
CGTTGCTCGTTTAGCC
Found at i:45873 original size:2 final size:2
Alignment explanation
Indices: 45866--45896 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
45856 GGTAAAATGA
*
45866 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45897 CATAAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46171 original size:18 final size:18
Alignment explanation
Indices: 46149--46198 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
46139 AAAAAATAGT
*
46149 AATAATAGAAATAATAAG
1 AATAATAAAAATAATAAG
* * * *
46167 GATAATATAAAGAATAAT
1 AATAATAAAAATAATAAG
46185 AATAATAAAAATAA
1 AATAATAAAAATAA
46199 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AATAATAAAAATAATAAG
Found at i:46264 original size:12 final size:13
Alignment explanation
Indices: 46252--46299 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 13
46242 TATACGTATA
46252 ATAATAATAATA-
1 ATAATAATAATAT
*
46264 ACAATAATAATAT
1 ATAATAATAATAT
46277 ATATATATATATATAT
1 ATA-ATA-ATA-ATAT
46293 ATAATAA
1 ATAATAA
46300 AACGTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 11 0.37
13 2 0.07
14 4 0.13
15 6 0.20
16 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:47521 original size:22 final size:23
Alignment explanation
Indices: 47480--47527 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
47470 AGAAAAAATG
47480 TAAATATAATATAATTTATAATA
1 TAAATATAATATAATTTATAATA
47503 TAAATAT-ATAT-ATTATATAATA
1 TAAATATAATATAATT-TATAATA
47525 TAA
1 TAA
47528 GGACGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 14 0.58
23 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATAATATAATTTATAATA
Found at i:47763 original size:20 final size:20
Alignment explanation
Indices: 47740--47781 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
47730 GAATCCTTCG
47740 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
*
47760 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
47780 TC
1 TC
47782 AGAGTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:48036 original size:105 final size:105
Alignment explanation
Indices: 47839--48472 Score: 1133
Period size: 105 Copynumber: 6.0 Consensus size: 105
47829 CGTTGTGAAG
* * * *
47839 CTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTG
1 CTGAATTTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* *
47904 TCTGGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTTGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
47945 CTGAATTTAAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
48010 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
48050 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
48115 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
48155 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
48220 CCGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
48260 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
48325 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* * *
48365 CTGAAATTGATAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
48430 CTGGAGTCCAATATCCTTCGTTGGGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
48470 CTG
1 CTG
48473 GGTAAAACCT
Statistics
Matches: 512, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
105 501 0.98
106 11 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Done.