Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003044.1 Hibiscus syriacus cultivar Beakdansim tig00006334_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: 61711
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:3148 original size:6 final size:5
Alignment explanation
Indices: 3115--3161 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 5
3105 TAGTTAGTAT
3115 TTAT- TTAT- TTAT- TTATA TTATA -TATA TTAGTA TTATA TTAT- TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA
3161 T
1 T
3162 GTACTCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
4 20 0.51
5 14 0.36
6 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:3153 original size:11 final size:10
Alignment explanation
Indices: 3115--3161 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
3105 TAGTTAGTAT
3115 TTAT-TTAT-
1 TTATATTATA
3123 TTAT-TTATA
1 TTATATTATA
3132 TTATA-TATA
1 TTATATTATA
3141 TTAGTATTATA
1 TTA-TATTATA
3152 TTAT-TTATA
1 TTATATTATA
3161 T
1 T
3162 GTACTCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.23
9 17 0.49
10 3 0.09
11 7 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTATATTATA
Found at i:4383 original size:93 final size:92
Alignment explanation
Indices: 4212--4448 Score: 280
Period size: 83 Copynumber: 2.7 Consensus size: 92
4202 TAATATTATA
* ** *
4212 TATACAATAAAGGTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGGCTTTATGGATAATA
1 TATACAATAAAGCTTGAACTGTCCCTCTAGAGCAATTGGTTAACGCCCCGGCTTTATGGATAAGA
*
4277 TTCAGCTAGCCTGATAAAGGCGATTAC
66 TTCAGCTAACCTGATAAAGGCGATTAC
*
4304 TATACAATAAAGCTTGAACTGTCCCTCTA-AGGCAATTGGTTAAACGCCTCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAACTGTCCCTCTAGA-GCAATTGGTT-AACGCCCCGGCTTTATGGATAA
*
4368 GATTCAGCTAACCTGATGAA-G-G--TA-
64 GATTCAGCTAACCTGATAAAGGCGATTAC
* * *
4392 TTTAC-AT--A--TTGAGCTGTCCCTCTAGAGTAATTGGTTAAACGCCCCGGCTTTATGGAT
1 TATACAATAAAGCTTGAACTGTCCCTCTAGAGCAATTGGTT-AACGCCCCGGCTTTATGGAT
4449 CCAGCTAGCC
Statistics
Matches: 131, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
83 44 0.34
84 1 0.01
85 1 0.01
87 2 0.02
88 4 0.03
89 2 0.02
91 2 0.02
92 37 0.28
93 38 0.29
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (92 bp):
TATACAATAAAGCTTGAACTGTCCCTCTAGAGCAATTGGTTAACGCCCCGGCTTTATGGATAAGA
TTCAGCTAACCTGATAAAGGCGATTAC
Found at i:5867 original size:37 final size:37
Alignment explanation
Indices: 5811--5882 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
5801 TTTAAAGAAG
* *
5811 ATTTTATCTCGATTGAGATAGTTTC-CGTTGAAACAAA
1 ATTTTATCTCCATTAAGATAGTTTCTC-TTGAAACAAA
*
5848 ATTTTATCTCCCTTAAGATAGTTTCTCTTGAAACA
1 ATTTTATCTCCATTAAGATAGTTTCTCTTGAAACA
5883 TAAACATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (37 bp):
ATTTTATCTCCATTAAGATAGTTTCTCTTGAAACAAA
Found at i:6049 original size:37 final size:37
Alignment explanation
Indices: 5982--6073 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
5972 ATTGAAAACA
** * *
5982 TTTCCCTTGAAA-TGAACTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAACTTTGTCTCCCTTGAGACAG
*
6018 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAACTTTGTCTCCCTTGAGACAG
* *
6055 TTTCTCTTGGAACATAAAC
1 TTTCCCTTGAAACA-AAAC
6074 ATTGAAAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 12 0.26
37 31 0.67
38 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAACTTTGTCTCCCTTGAGACAG
Found at i:6170 original size:36 final size:35
Alignment explanation
Indices: 6083--6171 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 35
6073 CATTGAAAAC
** *
6083 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGAT
1 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAG
* *
6118 AGTTTCTCTTGGAACAAATTTTGTCTCTCTTGAGACG
1 A-TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA-G
6155 ATTTCCCTTGAAACAAA
1 ATTTCCCTTGAAACAAA
6172 AACTTTGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
35 1 0.02
36 43 0.96
37 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (35 bp):
ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAG
Found at i:6210 original size:101 final size:101
Alignment explanation
Indices: 5899--6733 Score: 501
Period size: 101 Copynumber: 8.2 Consensus size: 101
5889 TTGAAATGAA
* *** * *
5899 TTTTGTCTCTCTTGAGATAGTTTCCCAGGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1 TTTT-TCTCTCTTGAGATAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTT
* * **** * * ** *
5964 G--A-AATAACATTGAAAACATTTCCCTTGAAATGAAC
64 GAAACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
* * * * *
5999 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTTCTCTCTTGAGATAGTTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * **** * * **
6064 GAACATAAACATTGAAAACATTTCCCTTGAAATGAA-
65 AAACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
**
6100 TTTTGTCTCTCTTGAGATAGTTTCTCTTGGAACAAATTTTGTCTCTCTTGAGAC-GATTTCCCTT
1 TTTT-TCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG-TTTCCCTT
6164 GAAACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
64 GAAACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
* * * *
6202 TTTTTCTCTCTAGAGATATTTTCTCTTAAAACAAATTTTGTCTCTCTTGGGACGGTTTCCCTTGA
1 TTTTTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
6267 AACAAAAACTTTGAATTAT-TTTTCTTTGAAACAAAG
66 AACAAAAACTTTGAATT-TGTTTTCTTTGAAACAAAG
* * * * *
6303 TTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTATCTCTTTTGAGACAGTTTCCCTTGA
1 TTTTTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
* * * * *
6368 AACAAAATCTTTGAATCTGTTTTCCTTAAAATAAA-
66 AACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
* * * * * * * *
6403 TTTCGTCTCCCTTGAAACAGTTTC-CATTGAAACAAA------ATCT-TTGA-ATCTGTTTTCCT
1 TTT-TTCTCTCTTGAGATAGTTTCTC-TTAAAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCT
* ** **
6459 TTAAACAAATTTCGTCTCTCTTGAGA-CAG-TTTCTTTTAG-AACTAAA-
63 TGAAACAAA------AACT-TTGA-ATTTGTTTTC-TTT-GAAAC-AAAG
* * * * **
6505 TTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGATTATCTTG
1 TTTT-TCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
6570 AAACAAAATCTCTGAATCTGTTTTCCTTGAAACAAAC
65 AAACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
** * * **
6607 TTGCGTCTCCCTTGAGATAGTTTCT-TTAGGAACTAAATTTTGTCTCTCTTGAGACAGTTTATCT
1 TT-TTTCTCTCTTGAGATAGTTTCTCTTA-AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
* ** *
6671 TGAAACAAAATCTTTGAAGCTGTTTTCCATT-AAACAAA-
63 TGAAACAAAAACTTTGAATTTGTTTT-CTTTGAAACAAAG
* * *
6709 TTTTGTCTCACTCGAGACAGTTTCT
1 TTTT-TCTCTCTTGAGATAGTTTCT
6734 TTTGAGATAG
Statistics
Matches: 610, Mismatches: 83, Indels: 82
0.79 0.11 0.11
Matches are distributed among these distances:
93 1 0.00
94 20 0.03
95 3 0.00
99 59 0.10
100 16 0.03
101 274 0.45
102 144 0.24
103 68 0.11
104 3 0.00
108 3 0.00
109 18 0.03
110 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (101 bp):
TTTTTCTCTCTTGAGATAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAAAACTTTGAATTTGTTTTCTTTGAAACAAAG
Found at i:6335 original size:36 final size:36
Alignment explanation
Indices: 6286--6373 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
6276 TTTGAATTAT
*
6286 TTTTCT-TTGAAACAAAGTTTGTCTCTCTTGAGACA
1 TTTTCTCTTGAAACAAAGTTTATCTCTCTTGAGACA
* * *
6321 TTTTCTCTTAAAACAAATTTTATCTCTTTTGAGACA
1 TTTTCTCTTGAAACAAAGTTTATCTCTCTTGAGACA
* *
6357 GTTTCCCTTGAAACAAA
1 TTTTCTCTTGAAACAAA
6374 ATCTTTGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 6 0.13
36 39 0.87
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (36 bp):
TTTTCTCTTGAAACAAAGTTTATCTCTCTTGAGACA
Found at i:6398 original size:166 final size:168
Alignment explanation
Indices: 6220--6528 Score: 428
Period size: 166 Copynumber: 1.9 Consensus size: 168
6210 TCTAGAGATA
* * ** * *
6220 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGGGACGGTTTCCCTTGAAACAAAAACTTTGAAT-T
1 TTTTCTCTTAAAACAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAAACTTTGAATCT
* *
6284 ATTTTTCTTTGAAACAAAGTTT-GTCTCTCTTGAGACATTTTCTCTTAAAAC-AAATTTTATCTC
66 ATTTTCCTTT-AAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTCTTAAAACTAAATTTTATCTC
*
6347 TTTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG
129 TCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG
* *
6387 TTTTC-CTTAAAATAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAATCTTTGAATCT
1 TTTTCTCTTAAAACAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAAACTTTGAATCT
* * * *
6451 GTTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTC
66 ATTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTAAAACTAAATTTTATCTCTC
*
6516 TTGAGACATTTTC
131 TTGAGACAGTTTC
6529 TCGTAAAACA
Statistics
Matches: 123, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
165 3 0.02
166 82 0.67
167 38 0.31
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (168 bp):
TTTTCTCTTAAAACAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAAACTTTGAATCT
ATTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTAAAACTAAATTTTATCTCTC
TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG
Found at i:6433 original size:65 final size:65
Alignment explanation
Indices: 6321--6630 Score: 286
Period size: 65 Copynumber: 4.6 Consensus size: 65
6311 TCTTGAGACA
** * *
6321 TTTTCTCTTAAAACAAATTTTATCTCTTTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
1 TTTTC-CTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCATTGAAACAAAATCTTTGAATCT
6386 G
65 G
* * *
6387 TTTTCCTTAAAATAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAATCTTTGAATCTG
1 TTTTCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCATTGAAACAAAATCTTTGAATCTG
* * * * **
6452 TTTTCCTTTAAACAAATTTCGTCTCTCTTGAGACAGTTT-CTTTTAGAACTAAAT-TTTGTCTCT
1 TTTTCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCATTGA-AACAAAATCTTTG--AAT
6515 CTTGAG
63 C-T--G
* * *
6521 ACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGATTAT-C-TTGAAACAAAATCTCTG
1 ---TTTTC-CTTAAAACAAATTTCGTCTCTCTTGAGACAG-TT-TCCATTGAAACAAAATCTTTG
6584 AATCTG
60 AATCTG
* * * *
6590 TTTTCCTTGAAACAAACTTGCGTCTCCCTTGAGATAGTTTC
1 TTTTCCTTAAAACAAA-TTTCGTCTCTCTTGAGACAGTTTC
6631 TTTAGGAACT
Statistics
Matches: 199, Mismatches: 30, Indels: 31
0.77 0.12 0.12
Matches are distributed among these distances:
64 9 0.05
65 106 0.53
66 28 0.14
67 1 0.01
69 2 0.01
71 1 0.01
72 7 0.04
73 35 0.18
74 8 0.04
75 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (65 bp):
TTTTCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCATTGAAACAAAATCTTTGAATCTG
Found at i:6549 original size:36 final size:36
Alignment explanation
Indices: 6461--6560 Score: 146
Period size: 37 Copynumber: 2.8 Consensus size: 36
6451 GTTTTCCTTT
* **
6461 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
* *
6497 GAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
6534 AAACAAATTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAG
6561 ATTATCTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 25 0.45
37 31 0.55
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
Found at i:6573 original size:138 final size:139
Alignment explanation
Indices: 6394--6662 Score: 402
Period size: 138 Copynumber: 1.9 Consensus size: 139
6384 CTGTTTTCCT
* *
6394 TAAAATAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAATCTTTGAATCTGTTTTCCT
1 TAAAACAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAATCTCTGAATCTGTTTTCCT
* * *
6459 TTAAACAAA-TTTCGTCTCTCTTGAGACAGTTTCTTTTA-GAACTAAATTTTGTCTCTCTTGAGA
66 TGAAACAAACTTGCGTCTCCCTTGAGACAGTTTC-TTTAGGAACTAAATTTTGTCTCTCTTGAGA
6522 CATTTTCTCG
130 CATTTTCTCG
* * *
6532 TAAAACAAATTTTGTCTCTCTTGAGACAGATTAT-C-TTGAAACAAAATCTCTGAATCTGTTTTC
1 TAAAACAAATTTCGTCTCCCTTGAAACAG-TT-TCCATTGAAACAAAATCTCTGAATCTGTTTTC
*
6595 CTTGAAACAAACTTGCGTCTCCCTTGAGATAGTTTCTTTAGGAACTAAATTTTGTCTCTCTTGAG
64 CTTGAAACAAACTTGCGTCTCCCTTGAGACAGTTTCTTTAGGAACTAAATTTTGTCTCTCTTGAG
6660 ACA
129 ACA
6663 GTTTATCTTG
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
138 66 0.56
139 51 0.43
140 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (139 bp):
TAAAACAAATTTCGTCTCCCTTGAAACAGTTTCCATTGAAACAAAATCTCTGAATCTGTTTTCCT
TGAAACAAACTTGCGTCTCCCTTGAGACAGTTTCTTTAGGAACTAAATTTTGTCTCTCTTGAGAC
ATTTTCTCG
Found at i:6574 original size:36 final size:34
Alignment explanation
Indices: 6461--6576 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 34
6451 GTTTTCCTTT
*
6461 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTC--TTA
* *
6497 GAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCT--TA
*
6534 AAACAAATTTTGTCTCTCTTGAGACAGATTATCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAG-TT-TCTTA
6570 AAACAAA
1 AAACAAA
6577 ATCTCTGAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
35 1 0.01
36 33 0.48
37 32 0.46
38 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (34 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTA
Found at i:6652 original size:103 final size:102
Alignment explanation
Indices: 6538--6735 Score: 299
Period size: 103 Copynumber: 1.9 Consensus size: 102
6528 CTCGTAAAAC
*
6538 AAATTTTGTCTCTCTTGAGACAGATTATCTTGAAACAAAATCTCTGAATCTGTTTTCC-TTGAAA
1 AAATTTTGTCTCTCTTGAGACAGATTATCTTGAAACAAAATCTCTGAAGCTGTTTTCCATT-AAA
* * *
6602 CAAACTTGCGTCTCCCTTGAGATAGTTTCTTTAGGAACT
65 CAAA-TTGCGTCTCACTCGAGACAGTTTCTTTAGGAACT
* *
6641 AAATTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAAATCTTTGAAGCTGTTTTCCATTAAAC
1 AAATTTTGTCTCTCTTGAGACAGATTATCTTGAAACAAAATCTCTGAAGCTGTTTTCCATTAAAC
**
6706 AAATTTTGTCTCACTCGAGACAGTTTCTTT
66 AAATTGCGTCTCACTCGAGACAGTTTCTTT
6736 TGAGATAGTT
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
102 22 0.26
103 62 0.72
104 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (102 bp):
AAATTTTGTCTCTCTTGAGACAGATTATCTTGAAACAAAATCTCTGAAGCTGTTTTCCATTAAAC
AAATTGCGTCTCACTCGAGACAGTTTCTTTAGGAACT
Found at i:8388 original size:2 final size:2
Alignment explanation
Indices: 8373--8413 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
8363 TACTATATTT
*
8373 TA TA -A TA T- TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8413 T
1 T
8414 TTCTATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:8603 original size:19 final size:19
Alignment explanation
Indices: 8569--8614 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
8559 TTTACCTTTA
* *
8569 CTTTATTTTTTTTTATCTT
1 CTTTATTTTATATTATCTT
*
8588 CTTTATTTTATATTATTTT
1 CTTTATTTTATATTATCTT
*
8607 CCTTATTT
1 CTTTATTT
8615 CGTTCGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (19 bp):
CTTTATTTTATATTATCTT
Found at i:10019 original size:2 final size:2
Alignment explanation
Indices: 10012--10037 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10002 TAAAAATTAT
10012 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
10038 AACTCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15711 original size:13 final size:13
Alignment explanation
Indices: 15693--15717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15683 TTCATTTAGG
15693 TTTTTTTTCTTTC
1 TTTTTTTTCTTTC
15706 TTTTTTTTCTTT
1 TTTTTTTTCTTT
15718 TAATTCAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Found at i:18194 original size:22 final size:22
Alignment explanation
Indices: 18160--18203 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18150 GGCTTGATTT
18160 TTTGTTTTCATTTAATTTTGAG
1 TTTGTTTTCATTTAATTTTGAG
*
18182 TTTGATTTT-ATTTTATTTTGAG
1 TTTG-TTTTCATTTAATTTTGAG
18204 ATATATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.66
Consensus pattern (22 bp):
TTTGTTTTCATTTAATTTTGAG
Found at i:18211 original size:22 final size:23
Alignment explanation
Indices: 18164--18211 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
18154 TGATTTTTTG
*
18164 TTTTCATTTAATTTTGAGTTTGA
1 TTTTCATTTAATTTTGAGTATGA
*
18187 TTTT-ATTTTATTTTGAGATAT-A
1 TTTTCATTTAATTTTGAG-TATGA
18209 TTT
1 TTT
18212 GATAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (23 bp):
TTTTCATTTAATTTTGAGTATGA
Found at i:27008 original size:2 final size:2
Alignment explanation
Indices: 27003--27044 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
26993 ATTATTAATA
27003 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT
27045 CTTATCTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30975 original size:20 final size:20
Alignment explanation
Indices: 30952--31008 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
30942 TTCTAGAATG
*
30952 TAGGCAGGATATCTATACCA
1 TAGGCAGGGTATCTATACCA
30972 TAGGCAGGGTATCTATACCA
1 TAGGCAGGGTATCTATACCA
*
30992 TAGACAGGGTATCTATA
1 TAGGCAGGGTATCTATA
31009 TCTCAGTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (20 bp):
TAGGCAGGGTATCTATACCA
Found at i:31568 original size:22 final size:21
Alignment explanation
Indices: 31543--31595 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
31533 GTTTATAGTA
*
31543 GTCCTTCGGATCTTATCCAGTG
1 GTCCTTCGGA-CATATCCAGTG
31565 GTCCTTCGGGACATATCCAGTG
1 GTCCTTC-GGACATATCCAGTG
*
31587 GTCATTCGG
1 GTCCTTCGG
31596 GACGTAGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.32
Consensus pattern (21 bp):
GTCCTTCGGACATATCCAGTG
Found at i:31596 original size:22 final size:22
Alignment explanation
Indices: 31556--31598 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31546 CTTCGGATCT
*
31556 TATCCAGTGGTCCTTCGGGACA
1 TATCCAGTGGTCATTCGGGACA
31578 TATCCAGTGGTCATTCGGGAC
1 TATCCAGTGGTCATTCGGGAC
31599 GTAGTGGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (22 bp):
TATCCAGTGGTCATTCGGGACA
Found at i:41488 original size:13 final size:13
Alignment explanation
Indices: 41472--41496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41462 TTTCATTAAA
41472 TTTTTATTTTTAC
1 TTTTTATTTTTAC
41485 TTTTTATTTTTA
1 TTTTTATTTTTA
41497 TTCGATCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:50224 original size:19 final size:18
Alignment explanation
Indices: 50197--50234 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
50187 ATTTAAATTG
50197 ATTTTATTT-ATTTTTACC
1 ATTTTATTTCA-TTTTACC
50215 ATTTTAATTTCATTTTACC
1 ATTTT-ATTTCATTTTACC
50234 A
1 A
50235 AAACCCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 12 0.67
20 1 0.06
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATTTCATTTTACC
Found at i:52822 original size:98 final size:99
Alignment explanation
Indices: 52652--52848 Score: 369
Period size: 98 Copynumber: 2.0 Consensus size: 99
52642 GAATAGTTCA
52652 GTGATTTATTCGGAAGTATTTCTTGAAAATTATTAGTAATTATCAAAGGAATTAAAGGGTAAAAT
1 GTGATTTATTCGGAAGTATTTCTTGAAAATTATTAGTAATTATCAAAGGAATTAAAGGGTAAAAT
*
52717 GGTCATTTGACATAAAAGATTTTTATTTCCTTAT
66 GGTCATTTGACAGAAAAGATTTTTATTTCCTTAT
52751 GTGATTTATTCGGAAGTATTTCTTGAAAATTA-TAGTAATTATCAAAGGAATTAAAGGGTAAAAT
1 GTGATTTATTCGGAAGTATTTCTTGAAAATTATTAGTAATTATCAAAGGAATTAAAGGGTAAAAT
*
52815 GGTCATTTGATAGAAAAGATTTTTATTTCCTTAT
66 GGTCATTTGACAGAAAAGATTTTTATTTCCTTAT
52849 AATATAAGGA
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 64 0.67
99 32 0.33
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (99 bp):
GTGATTTATTCGGAAGTATTTCTTGAAAATTATTAGTAATTATCAAAGGAATTAAAGGGTAAAAT
GGTCATTTGACAGAAAAGATTTTTATTTCCTTAT
Found at i:55424 original size:14 final size:14
Alignment explanation
Indices: 55405--55434 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55395 CATTTAAGGA
*
55405 AAAATATATTAATT
1 AAAATAGATTAATT
55419 AAAATAGATTAATT
1 AAAATAGATTAATT
55433 AA
1 AA
55435 TTTCTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AAAATAGATTAATT
Found at i:58153 original size:25 final size:26
Alignment explanation
Indices: 58125--58176 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
58115 CTACAATGAG
*
58125 TGGCATTCA-TGCAATACACCACTAA
1 TGGCATTCATTGAAATACACCACTAA
*
58150 TGGCATTCATTGAAATGCACCACTAA
1 TGGCATTCATTGAAATACACCACTAA
58176 T
1 T
58177 ATAAAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (26 bp):
TGGCATTCATTGAAATACACCACTAA
Found at i:59303 original size:24 final size:24
Alignment explanation
Indices: 59273--59319 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
59263 GTTTACTCCT
59273 TTCTTATGGGTACATTAACCCCCC
1 TTCTTATGGGTACATTAACCCCCC
59297 TTCTTATGGGTACATTAACCCCC
1 TTCTTATGGGTACATTAACCCCC
59320 ACAAAGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (24 bp):
TTCTTATGGGTACATTAACCCCCC
Found at i:60494 original size:3 final size:3
Alignment explanation
Indices: 60486--60558 Score: 107
Period size: 3 Copynumber: 24.7 Consensus size: 3
60476 CGAATACCCT
60486 TTA TTA TTA TTA TTTA TTA TTA TT- TTA TTA TTA TTTA TTA TTA -TA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
60531 TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
60559 TTACATTTTG
Statistics
Matches: 65, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.09
3 53 0.82
4 6 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Done.