Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 83 of 211
Found at i:25625146 original size:6 final size:6
Alignment explanation
Indices: 25625114--25625167 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
25625104 AAAGAAATTG
* * ** *
25625114 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
25625161 AAAGAA A
1 AAAGAA A
25625168 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:25625227 original size:18 final size:18
Alignment explanation
Indices: 25625206--25625240 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25625196 AGAAAAGAAA
25625206 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25625224 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25625241 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25629487 original size:17 final size:17
Alignment explanation
Indices: 25629462--25629515 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
25629452 TATCTTTTTA
*
25629462 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
25629479 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
25629496 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
25629513 TTC
1 TTC
25629516 GCTCTTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:25631191 original size:24 final size:24
Alignment explanation
Indices: 25631163--25631222 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
25631153 TGAGTGAAAA
25631163 TTCTCTTTGAGTTCTTCAAGGATT
1 TTCTCTTTGAGTTCTTCAAGGATT
25631187 TTCTCTTTGAGTTCTTCAAGGATT
1 TTCTCTTTGAGTTCTTCAAGGATT
25631211 TTCTC-TTGAGTT
1 TTCTCTTTGAGTT
25631223 TTCTTTAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 7 0.19
24 29 0.81
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.52
Consensus pattern (24 bp):
TTCTCTTTGAGTTCTTCAAGGATT
Found at i:25639199 original size:18 final size:18
Alignment explanation
Indices: 25639164--25639210 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
25639154 AGACCGTATG
**
25639164 TAATTTTTTTTTTCTTTT
1 TAATTTTTTTTTGATTTT
25639182 TAATTTTTTTTTGATTTT
1 TAATTTTTTTTTGATTTT
* *
25639200 GACTTTTTTTT
1 TAATTTTTTTT
25639211 ATGTACCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (18 bp):
TAATTTTTTTTTGATTTT
Found at i:25639562 original size:22 final size:22
Alignment explanation
Indices: 25639511--25639576 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
25639501 GGTATTTGGG
* *
25639511 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
25639532 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
25639554 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
25639577 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:25646185 original size:11 final size:10
Alignment explanation
Indices: 25646131--25646187 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
25646121 CAACTCCGAC
25646131 CAGCTCAATT
1 CAGCTCAATT
* *
25646141 GAGCTC-TTT
1 CAGCTCAATT
25646150 CAGCTCAA-T
1 CAGCTCAATT
25646159 CGAGCTCAATT
1 C-AGCTCAATT
*
25646170 TAGCTACAATT
1 CAGCT-CAATT
25646181 CAGCTCA
1 CAGCTCA
25646188 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
9 9 0.24
10 18 0.49
11 10 0.27
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25649798 original size:13 final size:13
Alignment explanation
Indices: 25649753--25649785 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
25649743 CCTATAGATC
25649753 ATTAATTGAGTTA
1 ATTAATTGAGTTA
25649766 ATTAATT-AGTTA
1 ATTAATTGAGTTA
25649778 AGTTAATT
1 A-TTAATT
25649786 AATTGAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
ATTAATTGAGTTA
Found at i:25659156 original size:13 final size:12
Alignment explanation
Indices: 25659138--25659171 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
25659128 CATATAGATC
25659138 ATTAATTGAGTTA
1 ATTAATT-AGTTA
25659151 ATTAATTAGTTA
1 ATTAATTAGTTA
25659163 AGTTAATTA
1 A-TTAATTA
25659172 ATTGAGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (12 bp):
ATTAATTAGTTA
Found at i:25661732 original size:30 final size:30
Alignment explanation
Indices: 25661698--25661794 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25661688 AGCTCACTCC
25661698 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
25661728 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
25661758 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
25661788 TAGCTCA
1 TAGCTCA
25661795 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:25663521 original size:13 final size:12
Alignment explanation
Indices: 25663497--25663534 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
25663487 AAAAGAGAAG
25663497 AAATTCAAAAAA
1 AAATTCAAAAAA
25663509 AAATTCAAAAAA
1 AAATTCAAAAAA
*
25663521 AAAATCGAAAAAA
1 AAATTC-AAAAAA
25663534 A
1 A
25663535 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:25664509 original size:35 final size:36
Alignment explanation
Indices: 25664461--25664528 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
25664451 ATTCTTGTAA
25664461 AGAGAAAACAAAGAAAA-GAAAGAAAAAGAAAAAGC
1 AGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
*
25664496 AGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
25664529 GAGAGGCAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (36 bp):
AGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:25664529 original size:35 final size:34
Alignment explanation
Indices: 25664461--25664533 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
25664451 ATTCTTGTAA
25664461 AGAGAAAACAAAGAAAAGAAAGAAAAAGAAAAAG
1 AGAGAAAACAAAGAAAAGAAAGAAAAAGAAAAAG
*
25664495 CAGAGAAGAA-AAAGAAAATGAAATAAAAAG-AAAAG
1 -AGAGAA-AACAAAGAAAA-GAAAGAAAAAGAAAAAG
25664530 AGAG
1 AGAG
25664534 GCAAGAGGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
34 4 0.11
35 19 0.54
36 12 0.34
ACGTcount: A:0.73, C:0.03, G:0.22, T:0.03
Consensus pattern (34 bp):
AGAGAAAACAAAGAAAAGAAAGAAAAAGAAAAAG
Found at i:25664595 original size:12 final size:12
Alignment explanation
Indices: 25664578--25664607 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
25664568 TTGAGAGAAC
25664578 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25664590 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25664602 TTGAAA
1 TTGAAA
25664608 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:25664625 original size:12 final size:12
Alignment explanation
Indices: 25664610--25664642 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25664600 CTTTGAAAGC
25664610 AAAAAGAAAATG
1 AAAAAGAAAATG
*
25664622 AAAAAGGAAATG
1 AAAAAGAAAATG
25664634 AAAAAGAAA
1 AAAAAGAAA
25664643 TTTGAGAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:25665741 original size:22 final size:23
Alignment explanation
Indices: 25665710--25665752 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
25665700 ACCTCTTTGA
25665710 ACCATTACCAATTCATACCAAAT
1 ACCATTACCAATTCATACCAAAT
* *
25665733 ACCA-TACCATTTCGTACCAA
1 ACCATTACCAATTCATACCAA
25665753 TTCATACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCATACCAAAT
Found at i:25665764 original size:20 final size:20
Alignment explanation
Indices: 25665735--25665775 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25665725 TACCAAATAC
*
25665735 CATACCATTTCGTACCAATT
1 CATACCATTTCGAACCAATT
*
25665755 CATACTATTTCGAACCAATT
1 CATACCATTTCGAACCAATT
25665775 C
1 C
25665776 CCAAATACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (20 bp):
CATACCATTTCGAACCAATT
Found at i:25668182 original size:11 final size:11
Alignment explanation
Indices: 25668154--25668186 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
25668144 GAATTGGTAC
25668154 GAAATGGTATG
1 GAAATGGTATG
25668165 G-AATGGTATG
1 GAAATGGTATG
25668175 GAAATGGTATG
1 GAAATGGTATG
25668186 G
1 G
25668187 TATTTGGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:25672563 original size:24 final size:23
Alignment explanation
Indices: 25672509--25672610 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 23
25672499 GGAATAAACA
*
25672509 GAAATGGTATTTGG-TTTAGGTAC
1 GAAATGGTATTTGGAATT-GGTAC
**
25672532 GATTTGGTATTTAGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
25672556 GAAATGGTATATGGAAGTTGGTAC
1 GAAATGGTATTTGGAA-TTGGTAC
*
25672580 GAAATGGTA--TGGTATTTGGTAC
1 GAAATGGTATTTGG-AATTGGTAC
*
25672602 GAATTGGTA
1 GAAATGGTA
25672611 ATGGTTCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
22 18 0.27
23 15 0.22
24 32 0.48
25 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.36
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:25672598 original size:22 final size:22
Alignment explanation
Indices: 25672549--25672615 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 22
25672539 TATTTAGGAA
*
25672549 TTGGTACGAAATGGTATATGGAAG
1 TTGGTACGAAATGG--TATGGTAG
*
25672573 TTGGTACGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATGGTAG
*
25672595 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGT-ATGGT
25672616 TCAAAAAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.51
23 5 0.13
24 14 0.36
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.34
Consensus pattern (22 bp):
TTGGTACGAAATGGTATGGTAG
Found at i:25678934 original size:13 final size:13
Alignment explanation
Indices: 25678918--25678950 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
25678908 AGGAAATTTG
25678918 AAAAAAAAATTCA
1 AAAAAAAAATTCA
25678931 AAAAAAAAATTCA
1 AAAAAAAAATTCA
25678944 AAAAAAA
1 AAAAAAA
25678951 TCGAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:25686134 original size:31 final size:32
Alignment explanation
Indices: 25686089--25686155 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
25686079 ACATGCATGC
*
25686089 ACCTTGCTAAAATGAATCTCCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCACACATTCGGCCA
*
25686121 ACCTTG-TTAAATGATCCCACACATTCGGCCA
1 ACCTTGCTAAAATGATCCCACACATTCGGCCA
25686152 ACCT
1 ACCT
25686156 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCACACATTCGGCCA
Found at i:25688419 original size:20 final size:20
Alignment explanation
Indices: 25688373--25688419 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25688363 AGCTCGTTTC
*
25688373 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25688393 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25688413 CAGCTCA
1 CAGCTCA
25688420 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25702994 original size:20 final size:19
Alignment explanation
Indices: 25702951--25703011 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
25702941 AACTCCGACC
* *
25702951 AGCTCAATTGAGCTCTTTT
1 AGCTCAATCGAGCTCATTT
25702970 CAGCTCAATCGAGCTCAATTT
1 -AGCTCAATCGAGCTC-ATTT
25702991 AGCTACAATTC-AGCTCATTT
1 AGCT-CAA-TCGAGCTCATTT
25703011 A
1 A
25703012 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 23 0.64
21 11 0.31
22 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (19 bp):
AGCTCAATCGAGCTCATTT
Found at i:25703005 original size:11 final size:10
Alignment explanation
Indices: 25702950--25703007 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
25702940 CAACTCCGAC
25702950 CAGCTCAATT
1 CAGCTCAATT
* **
25702960 GAGCTCTTTT
1 CAGCTCAATT
25702970 CAGCTCAA-T
1 CAGCTCAATT
25702979 CGAGCTCAATT
1 C-AGCTCAATT
*
25702990 TAGCTACAATT
1 CAGCT-CAATT
25703001 CAGCTCA
1 CAGCTCA
25703008 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.68
11 10 0.27
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25709687 original size:20 final size:20
Alignment explanation
Indices: 25709664--25709717 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25709654 AGTTTTTCCC
*
25709664 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25709684 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25709704 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25709718 TAATTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:25709697 original size:10 final size:10
Alignment explanation
Indices: 25709684--25709757 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
25709674 AGCTCACATG
25709684 AGCTTAATTT
1 AGCTTAATTT
**
25709694 AGC-TCGTTT
1 AGCTTAATTT
*
25709703 GAGCTCAATTT
1 -AGCTTAATTT
25709714 AGCTTAATTT
1 AGCTTAATTT
**
25709724 AGC-TCGTTT
1 AGCTTAATTT
*
25709733 GAGCTCAATTT
1 -AGCTTAATTT
*
25709744 AGCTTACTTT
1 AGCTTAATTT
25709754 AGCT
1 AGCT
25709758 CGTTTGAGCT
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
9 8 0.17
10 33 0.70
11 6 0.13
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (10 bp):
AGCTTAATTT
Found at i:25709699 original size:30 final size:30
Alignment explanation
Indices: 25709684--25709767 Score: 159
Period size: 30 Copynumber: 2.8 Consensus size: 30
25709674 AGCTCACATG
25709684 AGCTTAATTTAGCTCGTTTGAGCTCAATTT
1 AGCTTAATTTAGCTCGTTTGAGCTCAATTT
25709714 AGCTTAATTTAGCTCGTTTGAGCTCAATTT
1 AGCTTAATTTAGCTCGTTTGAGCTCAATTT
*
25709744 AGCTTACTTTAGCTCGTTTGAGCT
1 AGCTTAATTTAGCTCGTTTGAGCT
25709768 TGGCTTAAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (30 bp):
AGCTTAATTTAGCTCGTTTGAGCTCAATTT
Found at i:25709767 original size:20 final size:20
Alignment explanation
Indices: 25709670--25709768 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
25709660 TCCCAGCTCG
**
25709670 ATTTAGCTCACATGAGCTTA
1 ATTTAGCTCATTTGAGCTTA
* *
25709690 ATTTAGCTCGTTTGAGCTCA
1 ATTTAGCTCATTTGAGCTTA
* *
25709710 ATTTAGCTTAATTT-AGC-TC
1 ATTTAGC-TCATTTGAGCTTA
*
25709729 GTTTGAGCTCAATTT-AGCTTA
1 ATTT-AGCTC-ATTTGAGCTTA
* *
25709750 CTTTAGCTCGTTTGAGCTT
1 ATTTAGCTCATTTGAGCTT
25709769 GGCTTAAGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 7 0.11
20 46 0.75
21 8 0.13
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTTAGCTCATTTGAGCTTA
Found at i:25712442 original size:11 final size:11
Alignment explanation
Indices: 25712426--25712455 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
25712416 AAAGAAATTG
25712426 AAAGAAAACAA
1 AAAGAAAACAA
*
25712437 AAAGAAAACGA
1 AAAGAAAACAA
25712448 AAAGAAAA
1 AAAGAAAA
25712456 AGAAATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAACAA
Found at i:25712449 original size:6 final size:6
Alignment explanation
Indices: 25712426--25712531 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
25712416 AAAGAAATTG
* * ** *
25712426 AAAG-A AAACAA AAAGAA AACG-A AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
25712472 AAAGAA ATCGAA AAAGTG AGAGAA AAA-AA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
25712522 AAAGAA AAAG
1 AAAGAA AAAG
25712532 CGAAAAAAGA
Statistics
Matches: 71, Mismatches: 24, Indels: 11
0.67 0.23 0.10
Matches are distributed among these distances:
5 11 0.15
6 49 0.69
7 7 0.10
8 4 0.06
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:25712487 original size:18 final size:17
Alignment explanation
Indices: 25712429--25712485 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
25712419 GAAATTGAAA
* *
25712429 GAAAACAAAAAGAAAAC
1 GAAAAGAAAAAGAAATC
*
25712446 GAAAAGAAAAAGAAATT
1 GAAAAGAAAAAGAAATC
25712463 GCAAAAGAAAAAGAAATC
1 G-AAAAGAAAAAGAAATC
25712481 GAAAA
1 GAAAA
25712486 AGTGAGAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 19 0.54
18 16 0.46
ACGTcount: A:0.72, C:0.07, G:0.16, T:0.05
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATC
Found at i:25712516 original size:15 final size:15
Alignment explanation
Indices: 25712481--25712543 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 15
25712471 AAAAGAAATC
25712481 GAAAAAGTGAGAGAAAA
1 GAAAAAGTGA-A-AAAA
25712498 -AAAAA-TGAAGAAAA
1 GAAAAAGTGAA-AAAA
*
25712512 G-AAAATTG-AAAAA
1 GAAAAAGTGAAAAAA
*
25712525 GAAAAAGCGAAAAAA
1 GAAAAAGTGAAAAAA
25712540 GAAA
1 GAAA
25712544 TTGAAAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 5 0.12
14 16 0.40
15 14 0.35
16 5 0.12
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (15 bp):
GAAAAAGTGAAAAAA
Found at i:25714405 original size:20 final size:20
Alignment explanation
Indices: 25714382--25714435 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25714372 AGTTTTTCCC
*
25714382 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
25714402 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
25714422 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
25714436 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:25714417 original size:30 final size:30
Alignment explanation
Indices: 25714382--25714455 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
25714372 AGTTTTTCCC
25714382 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
25714412 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
25714442 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
25714456 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:25714445 original size:20 final size:20
Alignment explanation
Indices: 25714382--25714446 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
25714372 AGTTTTTCCC
* * * *
25714382 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
25714402 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
25714421 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
25714442 AGCTC
1 AGCTC
25714447 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:25715949 original size:6 final size:6
Alignment explanation
Indices: 25715931--25716038 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
25715921 AAATAAATTG
* * * ** *
25715931 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
25715978 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
25716029 AAAGAA AAAG
1 AAAGAA AAAG
25716039 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:25715992 original size:18 final size:18
Alignment explanation
Indices: 25715935--25715993 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
25715925 AAATTGAAAG
* *
25715935 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
25715953 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
25715971 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
25715989 AAAAG
1 AAAAG
25715994 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:25716020 original size:14 final size:13
Alignment explanation
Indices: 25715999--25716036 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
25715989 AAAAGTGAGA
25715999 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
25716011 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
25716026 GAAAAAGAAAA
1 GAAAAAGAAAA
25716037 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:25717737 original size:20 final size:20
Alignment explanation
Indices: 25717714--25717756 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
25717704 CTCGTTTCAA
*
25717714 CTCTGACCAGCTCAATTGAG
1 CTCTGACCAGCTCAATCGAG
***
25717734 CTCTTTTCAGCTCAATCGAG
1 CTCTGACCAGCTCAATCGAG
25717754 CTC
1 CTC
25717757 AATTTAGCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (20 bp):
CTCTGACCAGCTCAATCGAG
Found at i:25717765 original size:20 final size:19
Alignment explanation
Indices: 25717722--25717782 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
25717712 AACTCTGACC
* *
25717722 AGCTCAATTGAGCTCTTTT
1 AGCTCAATCGAGCTCATTT
25717741 CAGCTCAATCGAGCTCAATTT
1 -AGCTCAATCGAGCTC-ATTT
25717762 AGCTACAATTC-AGCTCATTT
1 AGCT-CAA-TCGAGCTCATTT
25717782 A
1 A
25717783 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 23 0.64
21 11 0.31
22 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (19 bp):
AGCTCAATCGAGCTCATTT
Found at i:25717776 original size:11 final size:10
Alignment explanation
Indices: 25717721--25717778 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
25717711 CAACTCTGAC
25717721 CAGCTCAATT
1 CAGCTCAATT
* **
25717731 GAGCTCTTTT
1 CAGCTCAATT
25717741 CAGCTCAA-T
1 CAGCTCAATT
25717750 CGAGCTCAATT
1 C-AGCTCAATT
*
25717761 TAGCTACAATT
1 CAGCT-CAATT
25717772 CAGCTCA
1 CAGCTCA
25717779 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.68
11 10 0.27
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:25724863 original size:14 final size:14
Alignment explanation
Indices: 25724846--25724893 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
25724836 AAAAAAATAT
25724846 AAAAAAATTCGAAA
1 AAAAAAATTCGAAA
*
25724860 AAAAAAATTTTTG-AA
1 AAAAAAA--TTCGAAA
25724875 AAAAAAATTC-AAA
1 AAAAAAATTCGAAA
25724888 AAAAAA
1 AAAAAA
25724894 TTTGTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 10 0.34
14 7 0.24
15 9 0.31
16 3 0.10
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (14 bp):
AAAAAAATTCGAAA
Found at i:25724979 original size:27 final size:27
Alignment explanation
Indices: 25724934--25724989 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
25724924 TTTAGTATTG
* *
25724934 AAGAAAAAAAATTCGAAATT-AAAAAA
1 AAGAAAAAAAAATCAAAATTGAAAAAA
25724960 AAGAAGAAAAAAATCAAAATTGAAAAAA
1 AAGAA-AAAAAAATCAAAATTGAAAAAA
25724988 AA
1 AA
25724990 AGAGTGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.19
27 13 0.50
28 8 0.31
ACGTcount: A:0.75, C:0.04, G:0.09, T:0.12
Consensus pattern (27 bp):
AAGAAAAAAAAATCAAAATTGAAAAAA
Found at i:25725827 original size:21 final size:20
Alignment explanation
Indices: 25725798--25725843 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
25725788 AATCTTGAAT
*
25725798 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
25725819 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
25725839 GAAAA
1 GAAAA
25725844 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:25725859 original size:6 final size:6
Alignment explanation
Indices: 25725850--25725885 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
25725840 AAAAAAGAAT
* *
25725850 TTGAGA TTGAGA TTGAGA TTGATA TTGATA TTGAGA
1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA
25725886 AAAAAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (6 bp):
TTGAGA
Found at i:25737514 original size:18 final size:19
Alignment explanation
Indices: 25737470--25737514 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
25737460 TTGAAAAATC
*
25737470 AAAAGAAAATGAGAGAGAG
1 AAAAGAAAATGAGAAAGAG
25737489 AAAA-AAAATGA-AAAGA-
1 AAAAGAAAATGAGAAAGAG
25737505 ATAAAGAAAA
1 A-AAAGAAAA
25737515 GAGTGTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 7 0.30
18 11 0.48
19 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAGAAAATGAGAAAGAG
Found at i:25737604 original size:29 final size:30
Alignment explanation
Indices: 25737554--25737611 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
25737544 TGAGTGATAA
25737554 AAAAAGAGAGAGTGATTCAAAA-GAAAAAG
1 AAAAAGAGAGAGTGATTCAAAATGAAAAAG
*
25737583 AAAAAGAGATGAGTGA-TGAAAATGAAAAA
1 AAAAAGAGA-GAGTGATTCAAAATGAAAAA
25737612 AAGAGTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.62, C:0.02, G:0.24, T:0.12
Consensus pattern (30 bp):
AAAAAGAGAGAGTGATTCAAAATGAAAAAG
Found at i:25737689 original size:36 final size:39
Alignment explanation
Indices: 25737630--25737706 Score: 124
Period size: 37 Copynumber: 2.0 Consensus size: 39
25737620 GTATGTAAAG
25737630 AAAGAGAAGTCAGGAAATCGATGCTGCT-AAGCAACCATT
1 AAAGAGAAG-CAGGAAATCGATGCTGCTAAAGCAACCATT
25737669 AAAGAGAAG-AGG-AATCGATGCTGCTAAAGCAACCATT
1 AAAGAGAAGCAGGAAATCGATGCTGCTAAAGCAACCATT
25737706 A
1 A
25737707 TTGGTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 13 0.35
37 15 0.41
39 9 0.24
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (39 bp):
AAAGAGAAGCAGGAAATCGATGCTGCTAAAGCAACCATT
Found at i:25748425 original size:14 final size:12
Alignment explanation
Indices: 25748389--25748420 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25748379 ATTTTTTTGA
25748389 TTTTTTTC-AAT
1 TTTTTTTCAAAT
25748400 TTTTTTTCAAAT
1 TTTTTTTCAAAT
25748412 TTTTTTTCA
1 TTTTTTTCA
25748421 CAAATCTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:25757727 original size:30 final size:30
Alignment explanation
Indices: 25757691--25757760 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
25757681 GCATAAAAGC
25757691 TGTTCACACCATGGCTGTTCGGTTCAGCCA
1 TGTTCACACCATGGCTGTTCGGTTCAGCCA
25757721 TGTTCACACCATGGCTGTTCGGTTCAGCCA
1 TGTTCACACCATGGCTGTTCGGTTCAGCCA
25757751 TGTTCACACC
1 TGTTCACACC
25757761 TTATGGCCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.30
Consensus pattern (30 bp):
TGTTCACACCATGGCTGTTCGGTTCAGCCA
Found at i:25761203 original size:42 final size:42
Alignment explanation
Indices: 25761144--25761226 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
25761134 AAATTCAAAA
25761144 GGATAAGAACAAGAGTTCAAATGTTTAAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTAAATTTCAAACGTTTT
*
25761186 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTAAATTTCAAACGTTT
25761227 CACACATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATGTTTAAATTTCAAACGTTTT
Found at i:25768653 original size:12 final size:12
Alignment explanation
Indices: 25768636--25768667 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25768626 TCGTATACAA
25768636 TTTTTTTT-GAT
1 TTTTTTTTCGAT
25768647 TTTTTTTTCGAT
1 TTTTTTTTCGAT
25768659 TTTTTTTTC
1 TTTTTTTTC
25768668 AAAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTCGAT
Found at i:25775958 original size:18 final size:18
Alignment explanation
Indices: 25775937--25775971 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25775927 TTTTTCTTTT
25775937 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
25775955 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
25775972 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:25775968 original size:6 final size:6
Alignment explanation
Indices: 25775959--25776063 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
25775949 TCAATCTCAA
* * * ** **
25775959 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
25776011 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
25776057 TTTCTT T
1 TTTCTT T
25776064 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:25776076 original size:6 final size:6
Alignment explanation
Indices: 25776010--25776063 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
25776000 ACTATTTTGA
* ** * *
25776010 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
25776057 TTTCTT T
1 TTTCTT T
25776064 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:25777096 original size:10 final size:10
Alignment explanation
Indices: 25777083--25777115 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
25777073 GACTTTTCAC
25777083 TTTTTTTTCT
1 TTTTTTTTCT
25777093 TTTTTTTTCT
1 TTTTTTTTCT
25777103 TTTTTTTTCT
1 TTTTTTTTCT
25777113 TTT
1 TTT
25777116 AACTCGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:25777155 original size:11 final size:11
Alignment explanation
Indices: 25777139--25777167 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
25777129 TTGTCACTTC
25777139 TTTTTTTTTAT
1 TTTTTTTTTAT
25777150 TTTTTTTTTAT
1 TTTTTTTTTAT
25777161 TTTTTTT
1 TTTTTTT
25777168 GTTACTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:25781563 original size:21 final size:21
Alignment explanation
Indices: 25781538--25781581 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25781528 GTATCAAATA
25781538 CCATACCATTTCATACCAATT
1 CCATACCATTTCATACCAATT
**
25781559 CCATACCATTTTGTACCAATT
1 CCATACCATTTCATACCAATT
25781580 CC
1 CC
25781582 CAAATACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.34, G:0.02, T:0.34
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:25785346 original size:15 final size:14
Alignment explanation
Indices: 25785310--25785364 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
25785300 TCTATTGATC
25785310 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
25785324 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
25785338 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
25785353 GAAAGAAAAGAA
1 GAGA-AAAAGAA
25785365 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:25790491 original size:42 final size:42
Alignment explanation
Indices: 25790432--25790512 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
25790422 ATTCAAAGGA
*
25790432 ATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTGG
1 ATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTTTGG
25790474 ATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 ATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTT
25790513 CACACATATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (42 bp):
ATAAGAAAAAGAGTTCAAATGTTTGAATTTCAAACGTTTTGG
Found at i:25809770 original size:17 final size:18
Alignment explanation
Indices: 25809733--25809770 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25809723 GATTGAGAGT
* *
25809733 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
25809751 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
25809768 GAA
1 GAA
25809771 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:25809783 original size:13 final size:12
Alignment explanation
Indices: 25809752--25809806 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
25809742 TGTGAAACAG
*
25809752 AAAAGAAATTGA
1 AAAAGAAGTTGA
25809764 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
25809776 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
25809788 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
25809800 AAAAGAA
1 AAAAGAA
25809807 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:25818874 original size:20 final size:19
Alignment explanation
Indices: 25818851--25818915 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
25818841 AAGCTCAAAC
25818851 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25818871 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25818891 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
25818911 GAGCT
1 GAGCT
25818916 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:25821968 original size:30 final size:29
Alignment explanation
Indices: 25821911--25821968 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
25821901 TAAACTTGAT
*
25821911 TTTTTTTGCTCACCTTTTTTTTTCTTTTCA
1 TTTTTTTGCTCA-CTTTTTTTTACTTTTCA
25821941 TTTTTTTGCTCGA-TTTTTTTTCACTTTT
1 TTTTTTTGCTC-ACTTTTTTTT-ACTTTT
25821969 TTTTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 16 0.64
31 1 0.04
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTTTTTGCTCACTTTTTTTTACTTTTCA
Found at i:25822022 original size:10 final size:11
Alignment explanation
Indices: 25821930--25822022 Score: 55
Period size: 11 Copynumber: 7.7 Consensus size: 11
25821920 TCACCTTTTT
25821930 TTTTCTTTTC-A
1 TTTT-TTTTCAA
*
25821941 TTTTTTTGCTCGA
1 TTTTTTT--TCAA
*
25821954 TTTTTTTTCAC
1 TTTTTTTTCAA
*
25821965 TTTTTTTTGAA
1 TTTTTTTTCAA
25821976 TTTTTTTTTCAATCAAA
1 --TTTTTTT---TC-AA
25821993 TTTTTTTTTCAA
1 -TTTTTTTTCAA
25822005 TTTTTTTT-AA
1 TTTTTTTTCAA
25822015 TTTTTTTT
1 TTTTTTTT
25822023 GTTACTCCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
10 13 0.19
11 23 0.34
12 4 0.06
13 17 0.25
16 9 0.13
17 2 0.03
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:25832374 original size:19 final size:18
Alignment explanation
Indices: 25832338--25832377 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25832328 TTTCCACTCG
*
25832338 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
25832356 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
25832375 TTT
1 TTT
25832378 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:25832509 original size:18 final size:17
Alignment explanation
Indices: 25832450--25832510 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
25832440 GCACTCCTTC
*
25832450 TTTTCTTTCTCCAATCTTT
1 TTTTCTTT-TTCAAT-TTT
*
25832469 TTCTCTTTTTCAATTTT
1 TTTTCTTTTTCAATTTT
*
25832486 TGTTTCTTTTTCAGTTTCT
1 T-TTTCTTTTTCAATTT-T
25832505 TTTTCT
1 TTTTCT
25832511 CTCGTCACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 23 0.64
19 9 0.25
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTCTTTTTCAATTTT
Found at i:25838062 original size:11 final size:11
Alignment explanation
Indices: 25838046--25838089 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
25838036 ACGGTATTGT
25838046 AAAAAAAATTC
1 AAAAAAAATTC
25838057 AAAAAAAAATTC
1 -AAAAAAAATTC
*
25838069 GAAAAAAATTC
1 AAAAAAAATTC
25838080 AAAAAAAATT
1 AAAAAAAATT
25838090 GTATTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:25838063 original size:12 final size:12
Alignment explanation
Indices: 25838046--25838087 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
25838036 ACGGTATTGT
25838046 AAAAAAAATTCA
1 AAAAAAAATTCA
25838058 AAAAAAAATTC-
1 AAAAAAAATTCA
*
25838069 GAAAAAAATTCA
1 AAAAAAAATTCA
25838081 AAAAAAA
1 AAAAAAA
25838088 TTGTATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:25839119 original size:15 final size:14
Alignment explanation
Indices: 25839078--25839129 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
25839068 TGCGAGCGAG
25839078 AAAATGAAAAAG-A
1 AAAATGAAAAAGAA
* *
25839091 CAAA-GAAAATGAA
1 AAAATGAAAAAGAA
25839104 AGAAATGAAAAAGAA
1 A-AAATGAAAAAGAA
25839119 AAAGATGAAAA
1 AAA-ATGAAAA
25839130 TGAGATTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 6 0.19
13 4 0.13
14 5 0.16
15 16 0.52
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATGAAAAAGAA
Found at i:25839179 original size:12 final size:12
Alignment explanation
Indices: 25839162--25839237 Score: 59
Period size: 12 Copynumber: 6.3 Consensus size: 12
25839152 AGTGAAAAGC
25839162 AAAAAGAGATTG
1 AAAAAGAGATTG
*
25839174 AAAAAGAAATTG
1 AAAAAGAGATTG
25839186 AAAAAGA-A--G
1 AAAAAGAGATTG
*
25839195 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
25839210 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
25839222 AAAGAGAGCTTG
1 AAAAAGAGATTG
25839234 AAAA
1 AAAA
25839238 GAAATCGAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 33 0.65
13 2 0.04
15 7 0.14
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:25840375 original size:10 final size:10
Alignment explanation
Indices: 25840349--25840398 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
25840339 TTAGCTCGTT
25840349 TTCAGCTC-A
1 TTCAGCTCAA
*
25840358 CTCGAGCTCAA
1 TTC-AGCTCAA
*
25840369 GTCAGCTC-A
1 TTCAGCTCAA
*
25840378 TTGAGCTCAA
1 TTCAGCTCAA
25840388 TTCAGCTCAA
1 TTCAGCTCAA
25840398 T
1 T
25840399 CTTAACCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
9 9 0.27
10 21 0.64
11 3 0.09
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:25840385 original size:19 final size:20
Alignment explanation
Indices: 25840350--25840396 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
25840340 TAGCTCGTTT
25840350 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* *
25840370 TCAGCTCA-TTGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
25840389 TCAGCTCA
1 TCAGCTCA
25840397 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:25843733 original size:20 final size:20
Alignment explanation
Indices: 25843687--25843733 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25843677 AGCTCGTTTA
*
25843687 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25843707 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25843727 CAGCTCA
1 CAGCTCA
25843734 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25846420 original size:48 final size:47
Alignment explanation
Indices: 25846341--25846446 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
25846331 GAGTGTCATG
*
25846341 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
25846389 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
25846437 GAAAAAGAAA
1 GAAAAAGAAA
25846447 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:25848161 original size:20 final size:20
Alignment explanation
Indices: 25848115--25848161 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25848105 AGCTCGTTTC
*
25848115 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25848135 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25848155 CAGCTCA
1 CAGCTCA
25848162 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:25849770 original size:21 final size:21
Alignment explanation
Indices: 25849732--25849771 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25849722 CCACGTCTTT
*
25849732 TTCATTTGTTTCTTTTTCTAA
1 TTCATTTGTCTCTTTTTCTAA
25849753 TTCATTT-TCTCTTCTTTCT
1 TTCATTTGTCTCTT-TTTCT
25849772 TTAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (21 bp):
TTCATTTGTCTCTTTTTCTAA
Found at i:25857496 original size:30 final size:30
Alignment explanation
Indices: 25857440--25857496 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
25857430 TGGGCTCAAA
* **
25857440 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
25857470 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
25857497 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:25858791 original size:20 final size:20
Alignment explanation
Indices: 25858775--25858823 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
25858765 TTTAGCTCGT
25858775 TTCAGCTCACTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
* * *
25858795 GTCAGCTCATTCGAGCTCCA
1 TTCAGCTCACTCGAGCTCAA
25858815 TTCAGCTCA
1 TTCAGCTCA
25858824 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (20 bp):
TTCAGCTCACTCGAGCTCAA
Found at i:25860335 original size:40 final size:39
Alignment explanation
Indices: 25860244--25860466 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
25860234 TCCTCGTTCA
* * * **
25860244 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTTTCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25860283 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25860322 GAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
25860362 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
25860402 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
25860443 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25860467 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.25
40 105 0.68
41 12 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:25860407 original size:80 final size:80
Alignment explanation
Indices: 25860242--25860466 Score: 249
Period size: 80 Copynumber: 2.8 Consensus size: 80
25860232 ACTCCTCGTT
* * * ** *
25860242 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTTTCACAATGCCTTCGGGACTTAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACCTAGCACAAAGCCTTCGGGACTTAACCCGGA
25860306 ATTTAATAACTCGCA
66 ATTTAATAACTCGCA
* * * *
25860321 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACCTAGCACAAA-GCCTTCGGGACTTAACCCGG
* *
25860386 AATTT-GTATCTCGCA
65 AATTTAATAACTCGCA
* * * * *
25860401 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-ACCTAGCACAAAGCCTTCGGGACTTAACCCG
25860465 GA
64 GA
25860467 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
79 39 0.32
80 69 0.57
81 14 0.11
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACCTAGCACAAAGCCTTCGGGACTTAACCCGGA
ATTTAATAACTCGCA
Found at i:25860475 original size:41 final size:41
Alignment explanation
Indices: 25860398--25860475 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
25860388 TTTGTATCTC
* * *
25860398 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
25860439 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
25860476 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:25867647 original size:40 final size:39
Alignment explanation
Indices: 25867556--25867777 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
25867546 TCCTCGTTCA
* * * **
25867556 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTTTCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25867595 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25867634 GAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
25867674 AAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
25867713 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
25867754 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25867778 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.01
39 65 0.42
40 80 0.52
41 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:25867657 original size:79 final size:78
Alignment explanation
Indices: 25867554--25867777 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 78
25867544 GCTCCTCGTT
* * * *
25867554 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTTTCACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCACAAAGCCTTCGGGACTTAACCCGGA
25867619 TTTAATAACTCGCA
66 TTT-ATAACTCGCA
* * * *
25867633 CGAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCACAAAGGCCTTCGGG-CTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCACAAA-GCCTTCGGGACTTAACCCGG
* *
25867697 AATTTGTATCTCGCA
65 -ATTTATAACTCGCA
* * * * *
25867712 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTT-GCACAAAGCCTTCGGGACTTAACCCG
25867776 GA
64 GA
25867778 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
78 3 0.02
79 89 0.74
80 29 0.24
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCACAAAGCCTTCGGGACTTAACCCGGA
TTTATAACTCGCA
Found at i:25867786 original size:41 final size:41
Alignment explanation
Indices: 25867709--25867786 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
25867699 TTTGTATCTC
* * *
25867709 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
25867750 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
25867787 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:25880378 original size:23 final size:23
Alignment explanation
Indices: 25880344--25880405 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
25880334 CGATTTTAGG
* **
25880344 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATACGA
**
25880367 TTTGGTTTGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATACGA
25880390 TTTGGTACGAAATGGT
1 TTTGGTACGAAATGGT
25880406 TATGGTTCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.05, G:0.27, T:0.39
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATACGA
Found at i:25892814 original size:30 final size:30
Alignment explanation
Indices: 25892780--25892876 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25892770 AGCTCACTCC
25892780 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
25892810 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
25892840 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
25892870 TAGCTCA
1 TAGCTCA
25892877 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:25894597 original size:24 final size:25
Alignment explanation
Indices: 25894570--25894623 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 25
25894560 GAGAAGAAAT
*
25894570 TCGAAAAAAAAATT-TAAAAAAAAA
1 TCGAAAAAAAAATTAAAAAAAAAAA
25894594 TCGAAAAAAAAATTAAAAAAAAAAA
1 TCGAAAAAAAAATTAAAAAAAAAAA
25894619 TCGAA
1 TCGAA
25894624 GTATATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (25 bp):
TCGAAAAAAAAATTAAAAAAAAAAA
Found at i:25894617 original size:12 final size:12
Alignment explanation
Indices: 25894573--25894617 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
25894563 AAGAAATTCG
*
25894573 AAAAAAAAATTT
1 AAAAAAAAATTA
**
25894585 AAAAAAAAATCG
1 AAAAAAAAATTA
25894597 AAAAAAAAATTA
1 AAAAAAAAATTA
25894609 AAAAAAAAA
1 AAAAAAAAA
25894618 ATCGAAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:25895574 original size:37 final size:37
Alignment explanation
Indices: 25895523--25895593 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
25895513 CATTCTTGTA
25895523 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
25895560 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
25895594 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:25895593 original size:6 final size:6
Alignment explanation
Indices: 25895533--25895582 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
25895523 AAGAGAAAAC
*
25895533 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
25895582 A
1 A
25895583 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:25895675 original size:11 final size:12
Alignment explanation
Indices: 25895643--25895673 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
25895633 TTGAGAGAAC
25895643 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25895655 TTGAAAAAGCCT
1 TTGAAAAAGCCT
25895667 TTGAAAA
1 TTGAAAA
25895674 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:25897849 original size:30 final size:30
Alignment explanation
Indices: 25897815--25897911 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
25897805 AGCTCACTCC
25897815 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
25897845 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
25897875 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
25897905 TAGCTCA
1 TAGCTCA
25897912 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:25921338 original size:4 final size:4
Alignment explanation
Indices: 25921329--25921355 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25921319 AAGTTTTATT
25921329 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
25921356 TACTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:25923163 original size:20 final size:19
Alignment explanation
Indices: 25923075--25923164 Score: 56
Period size: 20 Copynumber: 4.3 Consensus size: 19
25923065 AACTCGAAAC
*
25923075 TTTTTTTTTAGTTCTCAAAAT
1 TTTTTTTTTAATT-TC-AAAT
**
25923096 TTTTTTTAAAATTTC-AAT
1 TTTTTTTTTAATTTCAAAT
25923114 TTAATTTTTTTAATTTCGTATGAAT
1 TT--TTTTTTTAATTTC--A--AAT
*
25923139 ATTTTTTTTAAATTTCAAAT
1 -TTTTTTTTTAATTTCAAAT
25923159 TTTTTT
1 TTTTTT
25923165 GGAACTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
18 5 0.09
19 6 0.11
20 16 0.29
21 10 0.18
22 1 0.02
24 12 0.22
25 3 0.05
26 2 0.04
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTTTTTTAATTTCAAAT
Found at i:25923476 original size:23 final size:23
Alignment explanation
Indices: 25923443--25923504 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
25923433 CGATTTTGGG
* **
25923443 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATACGA
*
25923466 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATACGA
25923489 TTTGGTACGAAATGGT
1 TTTGGTACGAAATGGT
25923505 TATGGTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATACGA
Found at i:25927779 original size:101 final size:101
Alignment explanation
Indices: 25927668--25927872 Score: 410
Period size: 101 Copynumber: 2.0 Consensus size: 101
25927658 CCCTCTTCAT
25927668 TTATTAATTAGGTTTTTTTTTAAGTTTTCCTAATGAGATTAGGAAATAGATAGAAGGCCTATTAA
1 TTATTAATTAGGTTTTTTTTTAAGTTTTCCTAATGAGATTAGGAAATAGATAGAAGGCCTATTAA
25927733 TAGGCATGGCTGGCCACCTTATTGAACACATTACAA
66 TAGGCATGGCTGGCCACCTTATTGAACACATTACAA
25927769 TTATTAATTAGGTTTTTTTTTAAGTTTTCCTAATGAGATTAGGAAATAGATAGAAGGCCTATTAA
1 TTATTAATTAGGTTTTTTTTTAAGTTTTCCTAATGAGATTAGGAAATAGATAGAAGGCCTATTAA
25927834 TAGGCATGGCTGGCCACCTTATTGAACACATTACAA
66 TAGGCATGGCTGGCCACCTTATTGAACACATTACAA
25927870 TTA
1 TTA
25927873 CATTAAATTT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (101 bp):
TTATTAATTAGGTTTTTTTTTAAGTTTTCCTAATGAGATTAGGAAATAGATAGAAGGCCTATTAA
TAGGCATGGCTGGCCACCTTATTGAACACATTACAA
Found at i:25941455 original size:20 final size:20
Alignment explanation
Indices: 25941430--25941470 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
25941420 ATGTTACAGG
25941430 GATCGACTACACTGACCTTT
1 GATCGACTACACTGACCTTT
25941450 GATCGACTACACTGACCTTT
1 GATCGACTACACTGACCTTT
25941470 G
1 G
25941471 CGCAACTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (20 bp):
GATCGACTACACTGACCTTT
Found at i:25942576 original size:40 final size:40
Alignment explanation
Indices: 25942532--25942756 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
25942522 GCTCCTCGTT
*
25942532 CAAATGCCTTCGGGA-TATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACT-TAACCCGGATT-TAGTAACTCGCA
*
25942572 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
25942612 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
25942652 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
25942691 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
25942732 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
25942757 CATCATTCAA
Statistics
Matches: 163, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.20
40 113 0.69
41 16 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:25942716 original size:119 final size:120
Alignment explanation
Indices: 25942534--25942756 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
25942524 TCCTCGTTCA
* *
25942534 AATGCCTTCGGGATATAGCCCGATTATAGTAACTCGCACAAATGCCTTTGGGACTTAACCCGGAT
1 AATGCCTTCGGGATATAGCCCGAATATAGTAACTCGCACAAATGCCTTTCGGACTTAACCCGGAT
* *
25942599 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
25942654 AATGCCTTCGGGCT-TAGCCCGGAAT-TAGTATCTCGCACAAATGCC-TTCGGATCTTAGTCCGG
1 AATGCCTTCGGGATATAGCCC-GAATATAGTAACTCGCACAAATGCCTTTCGGA-CTTAACCCGG
* * *
25942716 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
25942757 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 5 0.06
119 60 0.67
120 24 0.27
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGATATAGCCCGAATATAGTAACTCGCACAAATGCCTTTCGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:25945184 original size:15 final size:15
Alignment explanation
Indices: 25945143--25945196 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
25945133 TCCTTTGAGC
25945143 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
25945157 GAGAG-AAACAAAAA
1 GAGAGAAAAGAAAAA
* *
25945171 GTGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
25945186 GAAAGAAAAGA
1 GAGAGAAAAGA
25945197 CTGACGAAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 15 0.48
15 16 0.52
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.04
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:25954954 original size:21 final size:21
Alignment explanation
Indices: 25954928--25954990 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25954918 TTGGTATTTG
25954928 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
25954949 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
25954970 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
25954991 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:25959724 original size:4 final size:4
Alignment explanation
Indices: 25959707--25959740 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
25959697 GTTGTAAAGT
25959707 TTTA TTT- TTT- TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
25959741 CTTAGTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:25964709 original size:79 final size:82
Alignment explanation
Indices: 25964598--25964782 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
25964588 GCTACTCGTT
* * *
25964598 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
25964661 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
25964678 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
25964741 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
25964758 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25964783 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:25964782 original size:40 final size:40
Alignment explanation
Indices: 25964579--25964782 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
25964569 CGGAATTTAA
** *
25964579 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
25964619 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
25964659 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
25964698 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
25964738 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
25964778 CCGGA
1 CCGGA
25964783 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:25972590 original size:40 final size:39
Alignment explanation
Indices: 25972553--25972644 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
25972543 GCTACTCGTT
*
25972553 CAAATGCCTTCGGGACATAGCCTGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCTGGAAT-TAGTAACTCGCA
* *
25972593 CAAATGCCTTCGGGCTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCTGGAATTAGTAACTCGCA
25972632 CAAATGCCTTCGG
1 CAAATGCCTTCGG
25972645 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCTGGAATTAGTAACTCGCA
Found at i:25972624 original size:39 final size:40
Alignment explanation
Indices: 25972536--25972693 Score: 139
Period size: 40 Copynumber: 4.0 Consensus size: 40
25972526 GAATTTAACC
**
25972536 GGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCT
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACATAGCCT
* *
25972576 GGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCT
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACATAGCCT
* *
25972615 GGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC-
1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CATAG-CCT
* * * *
25972655 GGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCC
1 GGATATAGTAAC-TCGCACAAATGCCTTCGGGACATAGCC
25972694 CGGACATCAT
Statistics
Matches: 100, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.03
39 34 0.34
40 49 0.49
41 14 0.14
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACATAGCCT
Found at i:25978157 original size:15 final size:16
Alignment explanation
Indices: 25978118--25978158 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
25978108 AACAACACTC
25978118 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
25978134 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
25978148 CTTTCTTTTTC
1 CTTTCTTTTTC
25978159 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:25978352 original size:17 final size:15
Alignment explanation
Indices: 25978315--25978353 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
25978305 TATCTCCCAC
25978315 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
25978331 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
25978348 TCATTT
1 TCATTT
25978354 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:25979288 original size:30 final size:32
Alignment explanation
Indices: 25979247--25979325 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 32
25979237 TTTCAATCAC
* *
25979247 TCTTTTTTTTTTCAATTTCG-ATTTTTTTTCT
1 TCTTCTTTTTTTCAATTCCGAATTTTTTTTCT
*
25979278 T-TTCTTTTTTTTAATTCCGAATTTTTTTTCT
1 TCTTCTTTTTTTCAATTCCGAATTTTTTTTCT
*
25979309 TCTTTTTTTTCTTCAAT
1 TCTTCTTTTT-TTCAAT
25979326 ACTAAATACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.38
31 13 0.32
32 7 0.17
33 5 0.12
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.72
Consensus pattern (32 bp):
TCTTCTTTTTTTCAATTCCGAATTTTTTTTCT
Found at i:25979289 original size:31 final size:32
Alignment explanation
Indices: 25979247--25979325 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 32
25979237 TTTCAATCAC
*
25979247 TCTTTTTTTTTTCAATTTCG-ATTTTTTTTCT
1 TCTTTTTTTTTTCAATTCCGAATTTTTTTTCT
25979278 T-TTCTTTTTTTT-AATTCCGAATTTTTTTTCT
1 TCTT-TTTTTTTTCAATTCCGAATTTTTTTTCT
25979309 TCTTTTTTTTCTTCAAT
1 TCTTTTTTTT-TTCAAT
25979326 ACTAAATACA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 8 0.19
31 27 0.64
32 4 0.10
33 3 0.07
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.72
Consensus pattern (32 bp):
TCTTTTTTTTTTCAATTCCGAATTTTTTTTCT
Found at i:25979380 original size:12 final size:12
Alignment explanation
Indices: 25979363--25979406 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
25979353 GAATACAAAC
25979363 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25979375 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25979387 TTTTTTTTTGAA
1 TTTTTTTTTGAA
25979399 TTTTTTTT
1 TTTTTTTT
25979407 CCTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:25979414 original size:24 final size:24
Alignment explanation
Indices: 25979363--25979416 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
25979353 GAATACAAAC
**
25979363 TTTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTTGAATTTTTTTTCCAA
25979387 TTTTTTTTTGAATTTTTTTTCC--
1 TTTTTTTTTGAATTTTTTTTCCAA
25979409 TTTTTTTT
1 TTTTTTTT
25979417 ACAATACCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.29
24 20 0.71
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTTTTTTTGAATTTTTTTTCCAA
Found at i:25990240 original size:25 final size:25
Alignment explanation
Indices: 25990211--25990258 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
25990201 TTGTTGAGTG
*
25990211 CAGAATTTTCT-TTGAGGTTTTCTCC
1 CAGAATTCTCTCTTGA-GTTTTCTCC
25990236 CAGAATTCTCTCTTGAGTTTTCT
1 CAGAATTCTCTCTTGAGTTTTCT
25990259 TTAGAAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.48
Consensus pattern (25 bp):
CAGAATTCTCTCTTGAGTTTTCTCC
Found at i:25997069 original size:10 final size:10
Alignment explanation
Indices: 25997056--25997093 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
25997046 TTGTAGCTAA
25997056 ATTGAGCTCG
1 ATTGAGCTCG
25997066 ATTGAGCT-G
1 ATTGAGCTCG
25997075 ACTTGAGCTCG
1 A-TTGAGCTCG
*
25997086 AGTGAGCT
1 ATTGAGCT
25997094 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:25997073 original size:20 final size:20
Alignment explanation
Indices: 25997033--25997093 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
25997023 ACCAATAAAA
25997033 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
25997053 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
25997073 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
25997093 T
1 T
25997094 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:25997094 original size:20 final size:20
Alignment explanation
Indices: 25997057--25997094 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25997047 TGTAGCTAAA
*
25997057 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
25997077 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
25997095 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:26001137 original size:11 final size:10
Alignment explanation
Indices: 26001115--26001165 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
26001105 ACCAATAAAA
26001115 TAAA-TGAGC
1 TAAATTGAGC
26001124 TAAATTGTAGC
1 TAAATTG-AGC
26001135 TAAATTGAGC
1 TAAATTGAGC
**
26001145 TCGATTGAGC
1 TAAATTGAGC
* *
26001155 TGACTTGAGC
1 TAAATTGAGC
26001165 T
1 T
26001166 CGAGTGAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 4 0.11
10 21 0.60
11 10 0.29
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:26001151 original size:10 final size:10
Alignment explanation
Indices: 26001138--26001175 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
26001128 TTGTAGCTAA
26001138 ATTGAGCTCG
1 ATTGAGCTCG
26001148 ATTGAGCT-G
1 ATTGAGCTCG
26001157 ACTTGAGCTCG
1 A-TTGAGCTCG
*
26001168 AGTGAGCT
1 ATTGAGCT
26001176 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Done.