Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002016.1 Hibiscus syriacus cultivar Beakdansim tig00004116_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: 133746
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5926 original size:26 final size:26
Alignment explanation
Indices: 5876--5926 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5866 AACGCCACTT
* *
5876 GAGTAGATCTTTAAGTTTTGCCTGGG
1 GAGTAGATCTTTAAGCTGTGCCTGGG
*
5902 GAGTAGATCTTTAAGCTGTGGCTGG
1 GAGTAGATCTTTAAGCTGTGCCTGG
5927 TGACGATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (26 bp):
GAGTAGATCTTTAAGCTGTGCCTGGG
Found at i:20539 original size:12 final size:12
Alignment explanation
Indices: 20519--20568 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
20509 AAAATCATTT
*
20519 AAATCTATTTTA
1 AAATTTATTTTA
20531 AAATTTATTTTA
1 AAATTTATTTTA
* **
20543 AAATATAAATT-
1 AAATTTATTTTA
20554 -AATTTATTTTA
1 AAATTTATTTTA
20565 AAAT
1 AAAT
20569 ATAGATTGAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTATTTTA
Found at i:20557 original size:22 final size:22
Alignment explanation
Indices: 20533--20897 Score: 486
Period size: 22 Copynumber: 16.6 Consensus size: 22
20523 CTATTTTAAA
* *
20533 ATTTATTTTAAAATATAAATTA
1 ATTTATTTTAAAATATAGATTG
20555 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
20577 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
*
20599 ATTTATTTTAAAATATAGATTA
1 ATTTATTTTAAAATATAGATTG
***
20621 ATTTATTTTAAAATATA-AAAA
1 ATTTATTTTAAAATATAGATTG
*
20642 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATAGATTG
***
20665 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATAGATTG
20686 ATTTTATTTTAAAATATAGATTG
1 A-TTTATTTTAAAATATAGATTG
20709 ATTTATTTTAAAATATTA-ATTG
1 ATTTATTTTAAAATA-TAGATTG
20731 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
20753 ATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
* * ***
20775 AATTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATAGATTG
*
20797 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
*
20819 ATTTATTTTAAAATATAAATTG
1 ATTTATTTTAAAATATAGATTG
*
20841 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
*
20863 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
*
20885 ATTTATTTAAAAA
1 ATTTATTTTAAAA
20898 AAATTATTAT
Statistics
Matches: 307, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
21 9 0.03
22 290 0.94
23 8 0.03
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATAGATTG
Found at i:20978 original size:31 final size:31
Alignment explanation
Indices: 20920--20979 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
20910 TAGTTGTATG
*
20920 AATTATTTAAATTTCAATATTATAAAACTAA
1 AATTATTTAAATTTCAATATTACAAAACTAA
*
20951 AATTATTTAAATTT-AAGTATTGCAAAACT
1 AATTATTTAAATTTCAA-TATTACAAAACT
20980 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAATATTACAAAACTAA
Found at i:25006 original size:31 final size:31
Alignment explanation
Indices: 24968--25092 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
24958 CCCGAAGGAC
* *
24968 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
24999 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
25030 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
25061 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
25092 C
1 C
25093 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:25296 original size:23 final size:24
Alignment explanation
Indices: 25270--25316 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
25260 ATATACTTGT
*
25270 TTTCACATATATA-TTTCATATCA
1 TTTCACATATAAACTTTCATATCA
25293 TTTCACATATAAACTTTCATATCA
1 TTTCACATATAAACTTTCATATCA
25317 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATAAACTTTCATATCA
Found at i:25949 original size:21 final size:21
Alignment explanation
Indices: 25919--25959 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25909 ATTCTGTCGT
* *
25919 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
25940 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
25960 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:28757 original size:31 final size:31
Alignment explanation
Indices: 28719--28843 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
28709 CCCGAAGGAC
* *
28719 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
28750 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
28781 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
28812 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
28843 C
1 C
28844 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:29047 original size:23 final size:24
Alignment explanation
Indices: 29021--29067 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
29011 ATATACTTGT
*
29021 TTTCACATATATA-TTTCATATCA
1 TTTCACATATAAACTTTCATATCA
29044 TTTCACATATAAACTTTCATATCA
1 TTTCACATATAAACTTTCATATCA
29068 CATGTCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATAAACTTTCATATCA
Found at i:30813 original size:111 final size:111
Alignment explanation
Indices: 30591--31149 Score: 845
Period size: 111 Copynumber: 5.0 Consensus size: 111
30581 GGTAAAATTA
* ** * * * * **
30591 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGATATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
* * *
30656 TCCGCTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTG
65 TCCACTTCCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * * *
30703 AATCAGGGTAGACTTGTTCCACTGTCGCTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
*
30768 CCACTTCCTCTGAGAGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* *
30814 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTAAAAGAGAGGGATATGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
*
30879 CCACTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
30925 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
*
30988 CCACTTCCTCTGAGGGAATATCAGATCTGTGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
31034 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* * * *
31099 CCACTTCTTCTAAGGGAATATCAGATATGGGAAAGTTGATCCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
31145 AATCA
1 AATCA
31150 GGGTCGAACC
Statistics
Matches: 412, Mismatches: 32, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
109 103 0.25
110 4 0.01
111 255 0.62
112 50 0.12
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (111 bp):
AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:31054 original size:220 final size:222
Alignment explanation
Indices: 30591--31149 Score: 863
Period size: 220 Copynumber: 2.5 Consensus size: 222
30581 GGTAAAATTA
* ** * * * * **
30591 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGATATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
* * * *
30656 TCCGCTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAGGGTAGACTTGT
65 TCCACTTCCT-CTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCAAGGTAGACTTGT
* *
30720 TCCACTGTCGCTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAGAGA
129 TCCACTATCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAGAGA
30785 ATATCAGATCTGGGAAAGTTGATTCATTG
194 ATATCAGATCTGGGAAAGTTGATTCATTG
* *
30814 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTAAAAGAGAGGGATATGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
*
30879 CCACTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTC
66 CCACTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCAAGGTAGACTTGTTC
* * *
30944 CGCTATCACTCAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTTCCACTTCCTCTGAGGGAAT
131 CACTATCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAGAGAAT
*
31007 ATCAGATCTGTGAAAGTTGATTCATTG
196 ATCAGATCTGGGAAAGTTGATTCATTG
31034 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
31099 CCACTTCTTCTAAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCA
66 CCACTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCA
31150 GGGTCGAACC
Statistics
Matches: 308, Mismatches: 27, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
220 168 0.55
221 2 0.01
222 89 0.29
223 49 0.16
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (222 bp):
AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATCCATTGAATCAAGGTAGACTTGTTC
CACTATCACTCAGGGAATATAAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAGAGAAT
ATCAGATCTGGGAAAGTTGATTCATTG
Found at i:32346 original size:23 final size:22
Alignment explanation
Indices: 32317--32364 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
32307 CCTTCTTTTA
32317 TTTTTCTTT-TTCTTTTTCCTCAT
1 TTTTTCTTTCTT-TTTTT-CTCAT
*
32340 TTTTTCTTTCTTTTTTTTTCAT
1 TTTTTCTTTCTTTTTTTCTCAT
32362 TTT
1 TTT
32365 CTTCCATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 14 0.61
24 2 0.09
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTCTTTTTTTCTCAT
Found at i:32355 original size:22 final size:23
Alignment explanation
Indices: 32317--32364 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
32307 CCTTCTTTTA
*
32317 TTTTTCTTTTTCTTTTTCCTCAT
1 TTTTTCTTTCTCTTTTTCCTCAT
**
32340 TTTTTCTTTCT-TTTTTTTTCAT
1 TTTTTCTTTCTCTTTTTCCTCAT
32362 TTT
1 TTT
32365 CTTCCATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTCTTTCTCTTTTTCCTCAT
Found at i:39559 original size:11 final size:11
Alignment explanation
Indices: 39545--39574 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39535 TGCAATGTAG
39545 ATGCAATATGA
1 ATGCAATATGA
*
39556 ATGCAAGATGA
1 ATGCAATATGA
39567 ATGCAATA
1 ATGCAATA
39575 CAAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:45747 original size:2 final size:2
Alignment explanation
Indices: 45740--45767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45730 TTGAGTCATT
45740 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
45768 ATACCAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:49447 original size:35 final size:35
Alignment explanation
Indices: 49373--49440 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
49363 TTTATGATCA
* *
49373 AAATTCCAAAACACTTCAATTGCATTCTAAACCTC
1 AAATTCCAAAACACTTCAATTACATTATAAACCTC
* * *
49408 AAATTCCAAAATACTTTAATTATATTATAAACC
1 AAATTCCAAAACACTTCAATTACATTATAAACC
49441 CTAAATTAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTATAAACCTC
Found at i:51005 original size:28 final size:28
Alignment explanation
Indices: 50965--51018 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
50955 GTTTGAATAG
* * * *
50965 TTTTTTGATATTTTATATATTTTATAAT
1 TTTTTTCAAATTTAATATATATTATAAT
50993 TTTTTTCAAATTTAATATATATTATA
1 TTTTTTCAAATTTAATATATATTATA
51019 TGTTGTGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTTCAAATTTAATATATATTATAAT
Found at i:52393 original size:57 final size:58
Alignment explanation
Indices: 52311--52447 Score: 213
Period size: 57 Copynumber: 2.4 Consensus size: 58
52301 TAAATCTTTG
* *
52311 TTGAGTCCCCCAACTATTAAAAATTATGAAATGATCCCTTAATTAAGACATTATTTTA
1 TTGAGTCCCCCGACTATTAAAAATTATGAAATGATCCCTTAACTAAGACATTATTTTA
* * * *
52369 TTGAGT-CCCCGACTATTAACAATTATGAAATGATCCCTTAACTAAGATATTGTTTTG
1 TTGAGTCCCCCGACTATTAAAAATTATGAAATGATCCCTTAACTAAGACATTATTTTA
52426 TTGAGTCCCCCGACTATTAAAA
1 TTGAGTCCCCCGACTATTAAAA
52448 GTTACAAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
57 51 0.72
58 20 0.28
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (58 bp):
TTGAGTCCCCCGACTATTAAAAATTATGAAATGATCCCTTAACTAAGACATTATTTTA
Found at i:53227 original size:21 final size:21
Alignment explanation
Indices: 53201--53243 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53191 TTATTCTATA
53201 TATTATTTTTAATTATATATT
1 TATTATTTTTAATTATATATT
53222 TATTATTTTTAATTATATATT
1 TATTATTTTTAATTATATATT
53243 T
1 T
53244 GTTACATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATTTTTAATTATATATT
Found at i:55092 original size:3 final size:3
Alignment explanation
Indices: 55086--55216 Score: 183
Period size: 3 Copynumber: 42.7 Consensus size: 3
55076 TCATTTAAAT
* *
55086 TTA TTA TTA TTGA -AA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
55131 TTA TTA TAA TTA TAA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
55177 TTA TTA TTA TATA TTA TTA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TT
55217 TAATAAATAA
Statistics
Matches: 115, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
2 1 0.01
3 104 0.90
4 10 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:55947 original size:13 final size:13
Alignment explanation
Indices: 55929--55957 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55919 ACCACCGTTA
55929 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
55942 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
55955 CGG
1 CGG
55958 GGAATACGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:61921 original size:11 final size:11
Alignment explanation
Indices: 61905--61944 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
61895 CTCATCCAGC
61905 AAAGAAAGAAA
1 AAAGAAAGAAA
61916 AAAGAAA-AAA
1 AAAGAAAGAAA
61926 AAAG-AAGAAA
1 AAAGAAAGAAA
*
61936 AAAAAAAGA
1 AAAGAAAGA
61945 GAGGAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 13 0.50
11 11 0.42
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:61928 original size:10 final size:10
Alignment explanation
Indices: 61905--61939 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
61895 CTCATCCAGC
61905 AAAGAAAGAAA
1 AAAGAAA-AAA
61916 AAAGAAAAAA
1 AAAGAAAAAA
61926 AAAGAAGAAAA
1 AAAGAA-AAAA
61937 AAA
1 AAA
61940 AAAGAGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:61931 original size:17 final size:17
Alignment explanation
Indices: 61909--61942 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
61899 TCCAGCAAAG
61909 AAAGAA-AAAAGAAAAAA
1 AAAGAAGAAAA-AAAAAA
61926 AAAGAAGAAAAAAAAAA
1 AAAGAAGAAAAAAAAAA
61943 GAGAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAAAAAAAA
Found at i:61935 original size:13 final size:12
Alignment explanation
Indices: 61913--61942 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
61903 GCAAAGAAAG
61913 AAAAAAGAAAAA
1 AAAAAAGAAAAA
61925 AAAAGAAGAAAAA
1 AAAA-AAGAAAAA
61938 AAAAA
1 AAAAA
61943 GAGAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:61941 original size:16 final size:16
Alignment explanation
Indices: 61909--61952 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
61899 TCCAGCAAAG
*
61909 AAAGAAAAAAGAAAAAA
1 AAAGAAGAAA-AAAAAA
61926 AAAGAAGAAAAAAAAA
1 AAAGAAGAAAAAAAAA
* *
61942 AGAGAGGAAAA
1 AAAGAAGAAAA
61953 TTGAATCAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAAAAAAAA
Found at i:66073 original size:54 final size:54
Alignment explanation
Indices: 65974--66085 Score: 134
Period size: 54 Copynumber: 2.1 Consensus size: 54
65964 CAATGATTGA
* * *** *
65974 GAACATCTGAGCATAAGCCACAAAAAAGGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCTGAGCAGAAACCACAAAAAAGGATGAATGCACTATCAAATATTTTAC
* ** *
66028 GAACATCTGAGTAGAAACCACAGGAAAGGATGAATGCACTATCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAAAAAAGGATGAATGCACTATCAAATATTTTAC
66082 GAAC
1 GAAC
66086 CTGCTATTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAAAAAAGGATGAATGCACTATCAAATATTTTAC
Found at i:66514 original size:22 final size:22
Alignment explanation
Indices: 66446--66525 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
66436 TACATCTGCA
* *
66446 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
66468 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
66490 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
66512 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
66526 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:67165 original size:76 final size:76
Alignment explanation
Indices: 67039--67521 Score: 884
Period size: 76 Copynumber: 6.4 Consensus size: 76
67029 TTCTCACATT
67039 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67104 TTCGGGTCATC
66 TTCGGGTCATC
67115 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67180 TTCGGGTCATC
66 TTCGGGTCATC
*
67191 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67256 TTCGGGTCATC
66 TTCGGGTCATC
*
67267 TGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67331 TTC-GGTCATC
66 TTCGGGTCATC
67341 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67406 TTCGGGTCATC
66 TTCGGGTCATC
* * *
67417 TGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCAGGAGC-TTTTAATGTTTTCAAAACC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67480 TTCGGGTCATC
66 TTCGGGTCATC
*
67491 TGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAA
67522 CATTTCCATC
Statistics
Matches: 396, Mismatches: 8, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
74 90 0.23
75 92 0.23
76 214 0.54
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (76 bp):
TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
TTCGGGTCATC
Found at i:67403 original size:150 final size:151
Alignment explanation
Indices: 67039--67521 Score: 882
Period size: 150 Copynumber: 3.2 Consensus size: 151
67029 TTCTCACATT
67039 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
*
67104 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
66 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGAGAGCTTTTTGATG
67169 TTTTCAAATCCTTCGGGTCATC
130 TTTTCAAATCCTTCGGGTCATC
*
67191 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
67256 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGAGAGCTTTTTGATGT
66 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGAGAGCTTTTTGATGT
67321 TTTCAAATCCTTC-GGTCATC
131 TTTCAAATCCTTCGGGTCATC
67341 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
*
67406 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTC-AGGAGC-TTTTAATG
66 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGA-GAGCTTTTTGATG
*
67469 TTTTCAAAACCTTCGGGTCATC
130 TTTTCAAATCCTTCGGGTCATC
*
67491 TGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAA
67522 CATTTCCATC
Statistics
Matches: 323, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
149 21 0.07
150 161 0.50
151 38 0.12
152 103 0.32
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (151 bp):
TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGAGAGCTTTTTGATGT
TTTCAAATCCTTCGGGTCATC
Found at i:67435 original size:226 final size:225
Alignment explanation
Indices: 67039--67521 Score: 878
Period size: 226 Copynumber: 2.1 Consensus size: 225
67029 TTCTCACATT
*
67039 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAATCC
67104 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
65 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
**
67169 TTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGA
130 TTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCAGGA
* *
67234 GCTTTTTGATGTTTTCAAATCCTTCGGGTCATC
194 GC-TTTTAATGTTTTCAAAACCTTCGGGTCATC
67267 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAATCCT
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAATCCT
67332 TC-GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
66 TCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
67396 TTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCAGGAGC
131 TTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCAGGAGC
67461 TTTTAATGTTTTCAAAACCTTCGGGTCATC
196 TTTTAATGTTTTCAAAACCTTCGGGTCATC
*
67491 TGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAA
67522 CATTTCCATC
Statistics
Matches: 249, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
224 58 0.23
225 14 0.06
226 111 0.45
227 38 0.15
228 28 0.11
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (225 bp):
TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAATCCT
TCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
TTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTTCAGGAGC
TTTTAATGTTTTCAAAACCTTCGGGTCATC
Found at i:67653 original size:3 final size:3
Alignment explanation
Indices: 67647--67761 Score: 148
Period size: 3 Copynumber: 38.7 Consensus size: 3
67637 TCATTTAAAT
* *
67647 TTA TTA TTA TTGA -AA TTA TTA TTA -TA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
67691 -TA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
67735 TTA TTA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TT
67762 TAATAAATAA
Statistics
Matches: 99, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
2 7 0.07
3 85 0.86
4 7 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:68494 original size:13 final size:13
Alignment explanation
Indices: 68476--68504 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
68466 ACCACCGTTA
68476 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
68489 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
68502 CGG
1 CGG
68505 AATACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:71615 original size:25 final size:24
Alignment explanation
Indices: 71587--71637 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
71577 CAATTAAATA
71587 TTTTATTCTATA-AATAAATAATAAG
1 TTTTATTCTATAGAAT-AATAA-AAG
*
71612 TTTTATTCTTTAGAATAATAAAAG
1 TTTTATTCTATAGAATAATAAAAG
71636 TT
1 TT
71638 ATTTGTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 16 0.67
26 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTTATTCTATAGAATAATAAAAG
Found at i:81280 original size:30 final size:31
Alignment explanation
Indices: 81225--81300 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
81215 TTATATATAT
*
81225 ATATATATATAATATTAATAAATTTAATTTAA
1 ATATAAATAT-ATATTAATAAATTTAATTTAA
* *
81257 ATA-AAATATATATTTATATATTTAATTTAA
1 ATATAAATATATATTAATAAATTTAATTTAA
*
81287 ATATATATATATAT
1 ATATAAATATATAT
81301 ACCCGGCCCG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 22 0.56
31 14 0.36
32 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATAAATATATATTAATAAATTTAATTTAA
Found at i:81334 original size:12 final size:12
Alignment explanation
Indices: 81319--81353 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
81309 CGATTCTTGG
81319 CCCAATACCCGA
1 CCCAATACCCGA
*
81331 CCCAATACCCGG
1 CCCAATACCCGA
81343 CCCAATACCCG
1 CCCAATACCCG
81354 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:92062 original size:2 final size:2
Alignment explanation
Indices: 92012--92042 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
92002 ATAATTTGGC
92012 TA TA -A 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 TA TA TA
92043 AGTTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:92186 original size:23 final size:23
Alignment explanation
Indices: 92142--92186 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
92132 TTAAAACAAT
*
92142 AACGTAACATGTGACATCATTTA
1 AACGTAACATGTGAAATCATTTA
* * *
92165 AACGTCACTTGTGAAATTATTT
1 AACGTAACATGTGAAATCATTT
92187 TTATATTATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (23 bp):
AACGTAACATGTGAAATCATTTA
Found at i:104194 original size:20 final size:20
Alignment explanation
Indices: 104133--104361 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
104123 GATTTTCCAG
* ** *
104133 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
104153 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
104173 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
104193 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104213 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104233 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104253 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104273 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
104293 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
104313 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
104333 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
104353 AATCACAAC
1 AATCGCAAC
104362 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:105092 original size:24 final size:24
Alignment explanation
Indices: 105053--105099 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
105043 AAATTTGGTC
105053 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
105077 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
105100 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:107574 original size:21 final size:22
Alignment explanation
Indices: 107532--107575 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
107522 ATAATAACAA
*
107532 AATTAGTAATTGTTAAATAATT
1 AATTAGTAATTGTTAAAAAATT
107554 AATTA-TAATT-TTAGAAAAATT
1 AATTAGTAATTGTTA-AAAAATT
107575 A
1 A
107576 TATAGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 12 0.60
22 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
AATTAGTAATTGTTAAAAAATT
Found at i:108478 original size:21 final size:21
Alignment explanation
Indices: 108424--108480 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
108414 TCTTTTGGTT
108424 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
* ***
108445 -TAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
108465 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
108481 TGCGATTTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:108516 original size:14 final size:14
Alignment explanation
Indices: 108497--108551 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
108487 TTTGGTTTCG
108497 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
108511 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
108530 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
108544 CGTTGCGA
1 CGTTGCGA
108552 CAGTCATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:108529 original size:33 final size:33
Alignment explanation
Indices: 108481--108551 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
108471 AAAATCGCAA
**
108481 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
108514 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
108547 TGCGA
1 TGCGA
108552 CAGTCATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:108559 original size:33 final size:33
Alignment explanation
Indices: 108492--108573 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
108482 GCGATTTTGG
***
108492 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
108525 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
108558 TTATCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
108574 TTCATTTCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:108578 original size:20 final size:19
Alignment explanation
Indices: 108508--108583 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 19
108498 GTTGCGATTC
108508 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
*
108527 TCGCGTTGCGA--TTC---
1 TCTCGTTGCGATTTTCATT
***
108541 TCTCGTTGCGACAGTCATT
1 TCTCGTTGCGATTTTCATT
108560 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTTTCATT
108580 TCTC
1 TCTC
108584 TCGTTGCGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 10 0.22
16 2 0.04
17 3 0.07
19 14 0.31
20 16 0.36
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:108587 original size:21 final size:20
Alignment explanation
Indices: 108537--108593 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
108527 TCGCGTTGCG
108537 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
* ***
108557 ATTATCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
108577 ATTTCTCTCGTTGCGAC
1 A-TTCTCTCGTTGCGAC
108594 TCTTCTGCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:108693 original size:14 final size:14
Alignment explanation
Indices: 108676--108732 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
108666 CTAACTTGAA
108676 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
108690 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
108709 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
108723 AATCGTAACG
1 AATCGCAACG
108733 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:108714 original size:33 final size:33
Alignment explanation
Indices: 108672--108742 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
108662 AATACTAACT
108672 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
*
108705 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
108738 TGAAA
1 TGAAA
108743 TCTAAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
Found at i:109285 original size:20 final size:20
Alignment explanation
Indices: 109119--109273 Score: 240
Period size: 20 Copynumber: 7.7 Consensus size: 20
109109 CTTTAAAAAT
109119 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
109139 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
109159 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
109180 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
109200 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
109220 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
109240 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
109260 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
109274 TGTGTTCGCG
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
20 105 0.86
21 17 0.14
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:109291 original size:40 final size:40
Alignment explanation
Indices: 109118--109311 Score: 239
Period size: 40 Copynumber: 4.8 Consensus size: 40
109108 GCTTTAAAAA
*
109118 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGAT
*
109159 T-GTCGTTGCGATTTACGGATACGCGTTGCGATATACGGAT
1 TCG-CGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* *
109199 ACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* * *
109239 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACG-GAT
* * ** *
109279 TCGCGTTACGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
109312 CTGGAAAATC
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
40 104 0.77
41 31 0.23
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
Found at i:109306 original size:60 final size:60
Alignment explanation
Indices: 109119--109311 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
109109 CTTTAAAAAT
*
109119 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTGTTCG-CGTTGCGATTTACGGATA
* * *
109180 CGCGTTGCGATATACGGATACGCATTGCGATTTACG-GATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTG-TTCGCGTTGCGATTTACGGATA
* * * * ** *
109240 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTACGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTGTTCGCGTTGCGATTTACGGATA
109300 CGCGTTGCGATT
1 CGCGTTGCGATT
109312 CTGGAAAATC
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
60 84 0.74
61 30 0.26
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTGTTCGCGTTGCGATTTACGGATA
Found at i:110632 original size:30 final size:30
Alignment explanation
Indices: 110598--110677 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
110588 CAAAATGATT
*
110598 TTTGGACTTGAATTGAATTTACAAAACGTA
1 TTTGGACTTGAATTGAATTTACAAAACATA
* *
110628 TTTGGACTTGAATTAAATTTACAAAATATA
1 TTTGGACTTGAATTGAATTTACAAAACATA
110658 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
110678 TTCAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 10 0.22
30 36 0.78
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACATA
Found at i:110768 original size:19 final size:18
Alignment explanation
Indices: 110741--110806 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
110731 AAATGTTTTA
*
110741 TGAATAGTAATTTACTATT
1 TGAACAGTAA-TTACTATT
110760 TGAACAGTAAATTACTATT
1 TGAACAGT-AATTACTATT
* *
110779 TGAACAGTGAATCACTGTT
1 TGAACAGT-AATTACTATT
110798 TGAACAGTA
1 TGAACAGTA
110807 CCACTGAGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 1 0.02
19 39 0.93
20 2 0.05
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (18 bp):
TGAACAGTAATTACTATT
Found at i:110941 original size:21 final size:21
Alignment explanation
Indices: 110915--110956 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
110905 ATTTGAATAT
110915 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
110936 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
110957 CTCATTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:111018 original size:21 final size:21
Alignment explanation
Indices: 110985--111024 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
110975 TTTTTGCAGA
*
110985 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
111007 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
111025 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:115793 original size:42 final size:42
Alignment explanation
Indices: 115746--115834 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
115736 GCAATTTTCG
115746 ATGGACGAGATAAGCTTCCAACAGCCATTCCCGCAATTGCCC
1 ATGGACGAGATAAGCTTCCAACAGCCATTCCCGCAATTGCCC
115788 ATGGACGAGATAAGCTTCCAACAGCCATTCCCGCAATTGCCC
1 ATGGACGAGATAAGCTTCCAACAGCCATTCCCGCAATTGCCC
115830 ATGGA
1 ATGGA
115835 AGAGGCCACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.19
Consensus pattern (42 bp):
ATGGACGAGATAAGCTTCCAACAGCCATTCCCGCAATTGCCC
Found at i:124685 original size:59 final size:59
Alignment explanation
Indices: 124593--124711 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
124583 AGTGATGATT
124593 GGTGGGATAAAGTAGCTTACATCATTGATTTTACAAAACTCATCTATGACATGCTTAGA
1 GGTGGGATAAAGTAGCTTACATCATTGATTTTACAAAACTCATCTATGACATGCTTAGA
*
124652 GGTGGGATTAAGTAGCTTACATCATTGATTTTACAAAACTCATCTATGACATGCTTAGA
1 GGTGGGATAAAGTAGCTTACATCATTGATTTTACAAAACTCATCTATGACATGCTTAGA
124711 G
1 G
124712 TATATGACAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (59 bp):
GGTGGGATAAAGTAGCTTACATCATTGATTTTACAAAACTCATCTATGACATGCTTAGA
Found at i:125557 original size:11 final size:12
Alignment explanation
Indices: 125541--125569 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
125531 GACACTTTAA
125541 TATTAT-GATTT
1 TATTATGGATTT
125552 TATTATGGATTT
1 TATTATGGATTT
125564 TATTAT
1 TATTAT
125570 TATAGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (12 bp):
TATTATGGATTT
Found at i:125681 original size:75 final size:75
Alignment explanation
Indices: 125522--125673 Score: 182
Period size: 75 Copynumber: 2.0 Consensus size: 75
125512 AGTTATAGTA
* * * *
125522 TTAAGATTTGACACTTTAATATTATGATTTTATTATGGATTTTATTATTATAGAGTTAATATTAT
1 TTAAAATTTGACACTTTAATATTATGATTTTATTATGGATTTTACTATTATAAACTTAATATTAT
125587 GGTTTGAATC
66 GGTTTGAATC
* * * *
125597 TTAAAATTTGACATTTTAATATTGTTG-TTTGT-TTATGGATTTTACTGTTCTAAACTTAATATT
1 TTAAAATTTGACACTTTAATATT-ATGATTT-TATTATGGATTTTACTATTATAAACTTAATATT
* *
125660 ATTGTTTGAGTC
64 ATGGTTTGAATC
125672 TT
1 TT
125674 GACATTTGTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
75 62 0.95
76 3 0.05
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (75 bp):
TTAAAATTTGACACTTTAATATTATGATTTTATTATGGATTTTACTATTATAAACTTAATATTAT
GGTTTGAATC
Done.