Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000896.1 Hibiscus syriacus cultivar Beakdansim tig00001759_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: 46360
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:4107 original size:20 final size:22
Alignment explanation
Indices: 4073--4112 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
4063 GATATATTAT
*
4073 TTAATAATATTAATT-TTAAGA
1 TTAATAATATAAATTCTTAAGA
4094 TTAA-AATATAAATTCTTAA
1 TTAATAATATAAATTCTTAA
4113 AAATATAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (22 bp):
TTAATAATATAAATTCTTAAGA
Found at i:6365 original size:31 final size:31
Alignment explanation
Indices: 6309--6384 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
6299 GTCTTTCGGG
* *
6309 ACATATGGACAATATACCTATGTTCTAAAGA
1 ACATATGGACAATTTACCTAGGTTCTAAAGA
* ** *
6340 ACATATGGACAATTTACTTAGGTTCTTCAGG
1 ACATATGGACAATTTACCTAGGTTCTAAAGA
*
6371 ACCTATGGACAATT
1 ACATATGGACAATT
6385 GCTGAGGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (31 bp):
ACATATGGACAATTTACCTAGGTTCTAAAGA
Found at i:7056 original size:21 final size:21
Alignment explanation
Indices: 7030--7069 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
7020 CTGTAGCATA
*
7030 ACTGTAGTAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
7051 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
7070 ACACAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:10257 original size:3 final size:3
Alignment explanation
Indices: 10237--10285 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
10227 TCTGGGTTTG
* * *
10237 TAA TAAA TAA TATT TAA TAA TAA TAA TAT TAA TAA AAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10284 TA
1 TA
10286 TAACAGTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:10539 original size:59 final size:59
Alignment explanation
Indices: 10398--10539 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
10388 TTCTTCCTAG
* * *
10398 TACATAAATGGTCCCTCGATTATAGGACACTATTTTATTGAGTCCCTTGACTATTAAAAGT
1 TACA-AAATGGTCCCT-GACTATAGGACACTATTTTATTGAGTACCTCGACTATTAAAAGT
* * * * *
10459 TACAAAACGGTTGTCC-AACTATATGACATTATTTT-TTGAGTACCTCGACTATTAAAAGT
1 TACAAAATGG-T-CCCTGACTATAGGACACTATTTTATTGAGTACCTCGACTATTAAAAGT
10518 TACAAAATGGTCACCTGACTAT
1 TACAAAATGGTC-CCTGACTAT
10540 TCATATCTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
58 3 0.05
59 36 0.55
60 20 0.30
61 5 0.08
62 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (59 bp):
TACAAAATGGTCCCTGACTATAGGACACTATTTTATTGAGTACCTCGACTATTAAAAGT
Found at i:13744 original size:44 final size:44
Alignment explanation
Indices: 13677--13769 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
13667 CTAATTAAAT
*
13677 AATTGAAATTTGAGGGGGGAAACAAGTTCCAATAGATGGAAAAG
1 AATTGAAATTTGAGGGGGAAAACAAGTTCCAATAGATGGAAAAG
13721 AATTGAAATTTGAGGGGGAAAACAAGTTCCAATAGATGGAAAAG
1 AATTGAAATTTGAGGGGGAAAACAAGTTCCAATAGATGGAAAAG
13765 AATTG
1 AATTG
13770 CAAGAGGAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (44 bp):
AATTGAAATTTGAGGGGGAAAACAAGTTCCAATAGATGGAAAAG
Found at i:13763 original size:21 final size:21
Alignment explanation
Indices: 13696--13763 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
13686 TTGAGGGGGG
13696 AAACAAGTTCCAATAGATGGA
1 AAACAAGTTCCAATAGATGGA
* ** **
13717 AAAGAA-TTGAAATTTGAGGGGGA
1 AAACAAGTTCCAA--T-AGATGGA
13740 AAACAAGTTCCAATAGATGGA
1 AAACAAGTTCCAATAGATGGA
13761 AAA
1 AAA
13764 GAATTGCAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
22 2 0.06
23 10 0.30
24 4 0.12
ACGTcount: A:0.49, C:0.09, G:0.24, T:0.19
Consensus pattern (21 bp):
AAACAAGTTCCAATAGATGGA
Found at i:14597 original size:19 final size:19
Alignment explanation
Indices: 14576--14611 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14566 TTTTAATAAA
14576 AAAATACATAA-AATTTTT
1 AAAATACATAATAATTTTT
*
14594 AAAATATATAATAATTTT
1 AAAATACATAATAATTTT
14612 AAACTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATACATAATAATTTTT
Found at i:21149 original size:24 final size:25
Alignment explanation
Indices: 21097--21153 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
21087 TGATACTCTA
21097 ATTGGAGTATCAATACCCATTTTTT
1 ATTGGAGTATCAATACCCATTTTTT
* *
21122 ATTGGAGTGTCAATACCTA-TTTTT
1 ATTGGAGTATCAATACCCATTTTTT
21146 ATTGGAGT
1 ATTGGAGT
21154 TGTGCTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (25 bp):
ATTGGAGTATCAATACCCATTTTTT
Found at i:21818 original size:49 final size:49
Alignment explanation
Indices: 21746--21846 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
21736 CTTGGTAACA
21746 GAACATGTTTTTCTATCTGACCACAATGAACTATGCTAAGTTCTTAAAG
1 GAACATGTTTTTCTATCTGACCACAATGAACTATGCTAAGTTCTTAAAG
21795 GAACATGTTTTTCTATCTGACCACAATGAACTATGCTAAGTTCTTAAAG
1 GAACATGTTTTTCTATCTGACCACAATGAACTATGCTAAGTTCTTAAAG
21844 GAA
1 GAA
21847 GATCATCCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (49 bp):
GAACATGTTTTTCTATCTGACCACAATGAACTATGCTAAGTTCTTAAAG
Found at i:27718 original size:84 final size:84
Alignment explanation
Indices: 27602--27845 Score: 310
Period size: 84 Copynumber: 2.9 Consensus size: 84
27592 TTGTTGGAAG
* * * * *
27602 ATAACCCTTCTAGTCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCCGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC
*
27667 GGAGATCTTATG-TTATCAA
66 GAAGATCTT-TGATTATCAA
* * *
27686 ATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTTGTCAAACTC
1 ATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC
* * *
27751 GAAGGTCTTTGATTGTCAG
66 GAAGATCTTTGATTATCAA
* * * * * *
27770 ATAACGCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGAAGTCAAACCC
1 ATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC
27835 GAAGATCTTTG
66 GAAGATCTTTG
27846 TGTTTCAAGA
Statistics
Matches: 137, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
83 2 0.01
84 135 0.99
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (84 bp):
ATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTC
GAAGATCTTTGATTATCAA
Found at i:27999 original size:36 final size:35
Alignment explanation
Indices: 27997--28184 Score: 241
Period size: 36 Copynumber: 5.1 Consensus size: 35
27987 GAAACATATT
27997 CAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAA-ATTT-GTTTCAAGGGAAACTGT-TCAAGAGAGA
28035 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGT-TCAAGAGAGA
*
28071 CAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGT-TCAAGAGAGA
* * *
28107 CTAAACTTTGTTTCAAGGGAAATTGCCTCAAGAGAGA
1 C-AAAATTTGTTTCAAGGGAAACTG-TTCAAGAGAGA
* * *
28144 GAGAATTTGTTTCAAGGGAAACAGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGGGAAACTGT-TCAAGAGAGA
28180 CAAAA
1 CAAAA
28185 CTTTATTTTG
Statistics
Matches: 134, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
36 96 0.72
37 34 0.25
38 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (35 bp):
CAAAATTTGTTTCAAGGGAAACTGTTCAAGAGAGA
Found at i:28055 original size:65 final size:68
Alignment explanation
Indices: 27951--28184 Score: 224
Period size: 73 Copynumber: 3.4 Consensus size: 68
27941 AGTTAAAAAA
* ** * *
27951 GAAACTGTTTCAAGAGAGACGGAATTTGTTTCAAGGGAAACATAT-TC-A-A-ATATTTTGTTTC
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-TATCTCAAGACAAAATTTGTTTC
*
28012 AAGG
65 AAAG
*
28016 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTC---A-AGACAAAATTTGT
28081 TTCAAAG
62 TTCAAAG
* * ** *
28088 GAAACTGTCTCAAGAGAGACTAAACTTTGTTTCAAGGGAAATTGCCTCAAGAGAGAGAGAATTTG
1 GAAACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGGGAAACTATCTC-A-AGACA-A-AATTTG
*
28153 TTTCAAGG
61 TTTCAAAG
*
28161 GAAACAGTCTCAAGAGAGACAAAA
1 GAAACTGTCTCAAGAGAGACAAAA
28185 CTTTATTTTG
Statistics
Matches: 143, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
64 2 0.01
65 40 0.28
70 1 0.01
71 7 0.05
72 37 0.26
73 56 0.39
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (68 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGACAAAATTTGTTTCA
AAG
Found at i:28211 original size:73 final size:73
Alignment explanation
Indices: 28004--28188 Score: 300
Period size: 73 Copynumber: 2.5 Consensus size: 73
27994 ATTCAAATAT
*
28004 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAG
28068 AGACAAAA
66 AGACAAAA
* * *
28076 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACTAAACTTTGTTTCAAGGGAAATTGCCTCAAGAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAG
* *
28141 AGAGAGAA
66 AGACAAAA
*
28149 TTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAACTTT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTT
28189 ATTTTGAGTA
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 34 0.33
73 69 0.67
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (73 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAG
AGACAAAA
Found at i:28500 original size:124 final size:124
Alignment explanation
Indices: 28275--28519 Score: 400
Period size: 124 Copynumber: 2.0 Consensus size: 124
28265 CTTATTCCTG
* * * *
28275 AAGATAAATTTTGCTGGTGTGTACGATTCCCTTCGTCATGAAGTTGAAACCGTGGATGACCCCTT
1 AAGATAAATGTTGCTGGTGAGCACGATTCCCTTCGTCATGAAGTTAAAACCGTGGATGACCCCTT
28340 CGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
66 CGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
* * * *
28399 AAGATGAATGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTAAAACCGTGGATGGCCCTTT
1 AAGATAAATGTTGCTGGTGAGCACGATTCCCTTCGTCATGAAGTTAAAACCGTGGATGACCCCTT
* *
28464 CGTTGTGAAGTTGAGCCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAAT
66 CGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
28520 GTAAGTTGCG
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 111 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (124 bp):
AAGATAAATGTTGCTGGTGAGCACGATTCCCTTCGTCATGAAGTTAAAACCGTGGATGACCCCTT
CGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
Found at i:28871 original size:106 final size:106
Alignment explanation
Indices: 28556--28906 Score: 504
Period size: 106 Copynumber: 3.3 Consensus size: 106
28546 ATCCTCCTCC
* *
28556 GTGAAGTTGAAATTGGCTCTGAAACTGAGAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGT
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGT
* *
28621 GAAGTTGAGCTTGTGATGTCTCGAGTCCAATATCCTTTGTT
66 GAAGTTGAGCTTGTGATGTCTCGAGTCCAATATCCTTCGAT
* * * * *
28662 GTAAAGTTGAAATTGGCTATAAAACTGGGAAGTTTATTTATTGACAGTCAGCCGCCCCTTCGCTG
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAG-TTGTTTGTTGACAGTCAGCCGCCCCTTCGCTG
* * * *
28727 TGAAGTTGATCCTGTGCTGTCTGGAGTCCAATATCCTTCGAT
65 TGAAGTTGAGCTTGTGATGTCTCGAGTCCAATATCCTTCGAT
** * *
28769 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAACCAGTCGCCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGT
* * * *
28834 GAAGTTGAGCTTGTGTTATCTTGAGTCCAATATCCTTCGCT
66 GAAGTTGAGCTTGTGATGTCTCGAGTCCAATATCCTTCGAT
28875 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAG
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAG
28907 CTCCTTCGTC
Statistics
Matches: 216, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
106 121 0.56
107 95 0.44
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
GTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGT
GAAGTTGAGCTTGTGATGTCTCGAGTCCAATATCCTTCGAT
Found at i:32971 original size:22 final size:23
Alignment explanation
Indices: 32930--32972 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
32920 AATGTGTTAG
*
32930 ATAAAAAAATGAAAATAAATAAA
1 ATAAAAAAATGAAAAAAAATAAA
*
32953 ATAAAAAAGT-AAAAAAAATA
1 ATAAAAAAATGAAAAAAAATA
32973 TAGAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (23 bp):
ATAAAAAAATGAAAAAAAATAAA
Found at i:34723 original size:31 final size:31
Alignment explanation
Indices: 34687--34745 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
34677 AACTTAAAAG
*
34687 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
34718 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
34746 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:34796 original size:22 final size:22
Alignment explanation
Indices: 34770--34812 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
34760 TAATAAATTA
34770 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
34792 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
34813 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:34821 original size:22 final size:22
Alignment explanation
Indices: 34772--34820 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
34762 ATAAATTATT
**
34772 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
34794 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
34817 TAAA
1 TAAA
34821 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:34824 original size:54 final size:54
Alignment explanation
Indices: 34760--35230 Score: 466
Period size: 54 Copynumber: 8.6 Consensus size: 54
34750 ACAACTACAA
34760 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
34814 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATT
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA-C
** * ** *
34873 TAA-AAA-TAAAT-CAATCCATACAAAT--ATATTATTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATA-T-TTTAAAATAAATCAATCCATAC
* *
34926 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
34980 TAATAAATTATTTAAAATAAATCAAT-C-TA---TACAACTACAAT-AATAAATA-
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTA-AAATA-AATCAATCCATAC
**
35029 -AATTCA-TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAATCCATAC
* * *
35092 TAATAAATTATTTAAAATATATCAATCTATATTTTAAAATAAATCAATCAATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
35146 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
35200 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
35231 CAACTACAAT
Statistics
Matches: 345, Mismatches: 36, Indels: 72
0.76 0.08 0.16
Matches are distributed among these distances:
47 2 0.01
48 20 0.06
49 2 0.01
50 10 0.03
51 3 0.01
52 2 0.01
53 6 0.02
54 201 0.58
55 9 0.03
56 17 0.05
57 8 0.02
58 25 0.07
59 3 0.01
61 3 0.01
62 10 0.03
63 2 0.01
64 20 0.06
65 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:34830 original size:32 final size:32
Alignment explanation
Indices: 34792--35011 Score: 179
Period size: 32 Copynumber: 7.7 Consensus size: 32
34782 CAATCCATAT
34792 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
34824 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
34854 --T--AATAAATCAATCC--A-T-AT---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
34875 ---AAAATAAATCAATCCATACAAATATATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
34904 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
34936 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
34958 TTTAAAACAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
34990 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
35012 AACTACAATA
Statistics
Matches: 153, Mismatches: 9, Indels: 52
0.71 0.04 0.24
Matches are distributed among these distances:
21 1 0.01
22 29 0.19
23 3 0.02
24 3 0.02
26 18 0.12
28 4 0.03
29 3 0.02
30 2 0.01
31 4 0.03
32 86 0.56
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:34880 original size:22 final size:22
Alignment explanation
Indices: 34822--34892 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 22
34812 ACTAATAAAT
34822 TATTT-AAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATCCA
**
34843 TACAACTACAATAATAAATCAATCCA
1 T--ATTTA-AA-AATAAATCAATCCA
34869 TATTTAAAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATCCA
34891 TA
1 TA
34893 CAAATATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 1 0.02
22 16 0.39
23 4 0.10
24 3 0.07
25 2 0.05
26 15 0.37
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (22 bp):
TATTTAAAAATAAATCAATCCA
Found at i:34945 original size:166 final size:166
Alignment explanation
Indices: 34760--35176 Score: 717
Period size: 166 Copynumber: 2.5 Consensus size: 166
34750 ACAACTACAA
34760 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
34825 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTAAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATAAATCCATATTTAAAAATAAATCAATCC
*
34890 ATACAAATATATTATTTAAAATAAATCAATACATAC
131 ATACAAATAAATTATTTAAAATAAATCAATACATAC
* *
34926 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAATCAATACATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* * * *
34991 TTAAAATAAATCAATCTATACAACTACAATAATAAATAAATTCATATTTTAAAATAAATCAATCT
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATAAATCCATATTTAAAAATAAATCAATCC
* *
35056 ATACTAATAAATTATTTAAAATAAATCAATCCATAC
131 ATACAAATAAATTATTTAAAATAAATCAATACATAC
* * *
35092 TAATAAATTATTTAAAATATATCAATCTATATTTTAAAATAAATCAATCAATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
35157 TTAAAATAAATCAATCCATA
66 TTAAAATAAATCAATCCATA
35177 TTTTAAAATA
Statistics
Matches: 235, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
166 235 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (166 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATAAATCCATATTTAAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATACATAC
Found at i:34962 original size:22 final size:22
Alignment explanation
Indices: 34936--34978 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34926 TAATAAATTA
* *
34936 TTTAAAATAAATCAATCCATAT
1 TTTAAAACAAATCAATACATAT
34958 TTTAAAACAAATCAATACATA
1 TTTAAAACAAATCAATACATA
34979 CTAATAAATT
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:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAACAAATCAATACATAT
Found at i:35064 original size:18 final size:18
Alignment explanation
Indices: 35043--35099 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
35033 CATATTTTAA
35043 AATAAATCAATCTATACT
1 AATAAATCAATCTATACT
* *
35061 AATAAAT-TAT-T-TA-A
1 AATAAATCAATCTATACT
*
35075 AATAAATCAATCCATACT
1 AATAAATCAATCTATACT
35093 AATAAAT
1 AATAAAT
35100 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 1 0.03
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATCTATACT
Found at i:35077 original size:32 final size:32
Alignment explanation
Indices: 35038--35231 Score: 221
Period size: 32 Copynumber: 6.7 Consensus size: 32
35028 AAATTCATAT
*
35038 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35070 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
35102 TTTAAAAT--AT--ATCAAT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
35124 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35156 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35178 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
35210 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
35232 AACTACAATA
Statistics
Matches: 139, Mismatches: 3, Indels: 40
0.76 0.02 0.22
Matches are distributed among these distances:
22 24 0.17
23 3 0.02
24 4 0.03
26 11 0.08
27 4 0.03
28 10 0.07
30 4 0.03
31 2 0.01
32 77 0.55
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:35148 original size:220 final size:220
Alignment explanation
Indices: 34904--35301 Score: 717
Period size: 220 Copynumber: 1.8 Consensus size: 220
34894 AAATATATTA
34904 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAA
* *
34969 TCAATACATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATAAATTC
66 TCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATAAATCC
*
35034 ATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAA
131 ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAA
35099 TTATTTAAAATATATCAATCTATAT
196 TTATTTAAAATATATCAATCTATAT
*
35124 TTTAAAATAAATCAAT-CAATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATAC-ATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAA
* *
35188 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATC
65 ATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATAAATC
*
35253 CATATTTTAAAATAAATCAATCCCTACTAATAAATTATTTAAAATAAAT
130 CATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
35302 TATTTTAAAA
Statistics
Matches: 170, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
219 1 0.01
220 169 0.99
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (220 bp):
TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAA
TCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATAAATCC
ATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAA
TTATTTAAAATATATCAATCTATAT
Found at i:35182 original size:22 final size:22
Alignment explanation
Indices: 35156--35198 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
35146 TAATAAATTA
35156 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
35178 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
35199 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:35207 original size:22 final size:22
Alignment explanation
Indices: 35158--35206 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35148 ATAAATTATT
**
35158 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
35180 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
35203 TAAA
1 TAAA
35207 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:35214 original size:86 final size:86
Alignment explanation
Indices: 35038--35301 Score: 298
Period size: 86 Copynumber: 3.1 Consensus size: 86
35028 AAATTCATAT
* ** * *
35038 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAA
* * **
35103 TTAAAAT--ATA-TCAATCTA-TA
65 AT-CAATCCATACT-AATAAATTA
35123 TTTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
1 -TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
35188 ATCAATCCATACTAATAAATTA
65 ATCAATCCATACTAATAAATTA
* *
35210 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCAATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
*
35268 ATCAATCCCTACTAATAAATTA
65 ATCAATCCATACTAATAAATTA
35290 TTTAAAATAAAT
1 TTTAAAATAAAT
35302 TATTTTAAAA
Statistics
Matches: 161, Mismatches: 12, Indels: 16
0.85 0.06 0.08
Matches are distributed among these distances:
80 60 0.37
82 1 0.01
84 4 0.02
85 10 0.06
86 83 0.52
87 3 0.02
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (86 bp):
TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTA
Found at i:35247 original size:166 final size:163
Alignment explanation
Indices: 34760--35256 Score: 618
Period size: 166 Copynumber: 3.0 Consensus size: 163
34750 ACAACTACAA
*
34760 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTAT
* *
34825 TTAAAATAAATCAATCCATA-CAACTACAATAATAAAT-CAATCCATATTTAAAAATAAATCAAT
66 TTAAAATAAATCAATCCATATAAACTACAATAATAAATACAATACATATTT-AAAATAAATCAAT
* *
34888 CCATACAAATATATTATTTAAAATAAATCAATACATAC
130 CCATAC-AATA-AATA-TT-AAATAAATCAATCCATAC
*
34926 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAACAAATCAAT-ACATACTAATAAATTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCA-ATACTAATAAATTA
*
34990 TTTAAAATAAATCAAT-C-TATACAACTACAATAATAAATA-AATTCATATTTTAAAATAAATCA
65 TTTAAAATAAATCAATCCATATA-AACTACAATAATAAATACAATACATA-TTTAAAATAAATCA
*
35052 ATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC
128 ATCCATAC-AATAAA-TA-TT-AAATAAATCAATCCATAC
* *
35092 TAATAAATTATTTAAAATATATCAATCTATATTTTAAAATAAATCAATCAATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTAT
* ** *
35157 TTAAAATAAATCAATCCATATTTTAAAATA-AATCAATCCATACTAATAAATTATTTAAAATAAA
66 TTAAAATAAATCAATCCATA---TAAACTACAAT-AATAAATAC-AATACA-TATTTAAAATAAA
*
35221 TCAATCCATACAACTACA-A-T-AATAAATCAATCCATA
125 TCAATCCATACAA-TAAATATTAAATAAATCAATCCATA
35257 TTTTAAAATA
Statistics
Matches: 296, Mismatches: 18, Indels: 34
0.85 0.05 0.10
Matches are distributed among these distances:
164 2 0.01
165 2 0.01
166 236 0.80
167 5 0.02
168 3 0.01
169 3 0.01
170 11 0.04
171 4 0.01
172 28 0.09
173 2 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (163 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACTAATAAATTAT
TTAAAATAAATCAATCCATATAAACTACAATAATAAATACAATACATATTTAAAATAAATCAATC
CATACAATAAATATTAAATAAATCAATCCATAC
Found at i:35266 original size:22 final size:22
Alignment explanation
Indices: 35241--35338 Score: 79
Period size: 22 Copynumber: 4.3 Consensus size: 22
35231 CAACTACAAT
35241 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
* **
35263 AATAAATCAATCCCTACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
35286 ATTATTTAAAATAAATTATTTTAA
1 AATAAAT-CAATCCA-TATTTTAA
*
35310 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
35332 AATAAAT
1 AATAAAT
35339 TATTTTGAAA
Statistics
Matches: 54, Mismatches: 19, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
22 29 0.54
23 12 0.22
24 11 0.20
25 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:35300 original size:14 final size:15
Alignment explanation
Indices: 35281--35316 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
35271 AATCCCTACT
35281 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
35295 AATAAATTATTTTAA
1 AATAAATTATTTTAA
35310 AATAAAT
1 AATAAAT
35317 CAATCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:35319 original size:47 final size:45
Alignment explanation
Indices: 35201--35325 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 45
35191 AATCCATACT
35201 AATAAATTA-TTTAAAATAAATCAATCCATACAACTACAATAATA
1 AATAAATTATTTTAAAATAAATCAATCCATACAACTACAATAATA
* * *
35245 AATCAATCCATATTTTAAAATAAATCAATCCCTACTAA-TA-AATTATTTAA
1 AATAAAT---TATTTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-A
35295 AATAAATTATTTTAAAATAAATCAATCCATA
1 AATAAATTATTTTAAAATAAATCAATCCATA
35326 TTTTATAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
44 6 0.09
47 27 0.40
48 25 0.37
49 3 0.04
50 7 0.10
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (45 bp):
AATAAATTATTTTAAAATAAATCAATCCATACAACTACAATAATA
Done.