Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 36 of 145
Found at i:12895713 original size:45 final size:45
Alignment explanation
Indices: 12895644--12895746 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 45
12895634 ATGTTAACCA
* ** *
12895644 AGTTCATTGCCACAACGTACTAGCAGGTTTTATCTACACTGATGGAT
1 AGTTCA-T-CCACAACGTACTAGCAGCTTTTATCTACACAAACGGAT
*
12895691 AGTTCATCCACAACGTATTAGCAGCTTTTATCTACACAAACGGAT
1 AGTTCATCCACAACGTACTAGCAGCTTTTATCTACACAAACGGAT
*
12895736 GGTTCATCCAC
1 AGTTCATCCAC
12895747 CAATATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 43 0.86
46 1 0.02
47 6 0.12
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
AGTTCATCCACAACGTACTAGCAGCTTTTATCTACACAAACGGAT
Found at i:12895801 original size:21 final size:21
Alignment explanation
Indices: 12895762--12895801 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12895752 TATTTTTATC
**
12895762 ATTAGAAGTTCATTTACAATG
1 ATTAGAAGTTCATCCACAATG
*
12895783 ATTAGTAGTTCATCCACAA
1 ATTAGAAGTTCATCCACAA
12895802 AGTAGTGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
ATTAGAAGTTCATCCACAATG
Found at i:12897775 original size:16 final size:15
Alignment explanation
Indices: 12897756--12897791 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
12897746 TCAAAAACCT
12897756 TTTTCCTTTTTCTTCA
1 TTTTCCTTTTT-TTCA
*
12897772 TTTTCCTTTTTTTCT
1 TTTTCCTTTTTTTCA
12897787 TTTTC
1 TTTTC
12897792 TACTCAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCCTTTTTTTCA
Found at i:12898124 original size:48 final size:49
Alignment explanation
Indices: 12898053--12898151 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 49
12898043 AAATAAATAC
12898053 ATTCTTTCTTAGTCCATTTTCTCTTTTTC-TTCTCTCTCTTTAACTCAA
1 ATTCTTTCTTAGTCCATTTTCTCTTTTTCTTTCTCTCTCTTTAACTCAA
12898101 ATTCTTTCTTAGTCCATTTTCTCTTTTTCTTTTCTCTCTCTTTAACTCAA
1 ATTCTTTCTTAGTCCATTTTCTCTTTTTC-TTTCTCTCTCTTTAACTCAA
12898151 A
1 A
12898152 AGACTCTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 29 0.59
50 20 0.41
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (49 bp):
ATTCTTTCTTAGTCCATTTTCTCTTTTTCTTTCTCTCTCTTTAACTCAA
Found at i:12900266 original size:24 final size:24
Alignment explanation
Indices: 12900239--12900290 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
12900229 TTCTAGAAGT
*
12900239 TTTAGTATTTATTAGTATA-TTATA
1 TTTAGCATTTATTAGTATAGTT-TA
12900263 TTTAGCATTTATTAGTATAGTTTA
1 TTTAGCATTTATTAGTATAGTTTA
12900287 TTTA
1 TTTA
12900291 ACTCACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (24 bp):
TTTAGCATTTATTAGTATAGTTTA
Found at i:12902018 original size:20 final size:20
Alignment explanation
Indices: 12901954--12902018 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
12901944 TATTTTTACA
12901954 ATTTTTAATAGATTTATTAAGT
1 ATTTTTAATA-ATTTATTAA-T
* *
12901976 -TGTTT-ATAGTTT-TTAAT
1 ATTTTTAATAATTTATTAAT
* *
12901993 AATTTTAATATTTTATTAAT
1 ATTTTTAATAATTTATTAAT
12902013 ATTTTT
1 ATTTTT
12902019 CTAGTAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 9 0.26
20 13 0.38
21 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
ATTTTTAATAATTTATTAAT
Found at i:12902138 original size:15 final size:15
Alignment explanation
Indices: 12902094--12902141 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
12902084 TAATTTTTAA
*
12902094 TTTATTTTTAATATTT
1 TTTATTTTTAATA-AT
*
12902110 TTTGAATTTATAATAAT
1 TTT--ATTTTTAATAAT
12902127 TTTATTTTTAATAAT
1 TTTATTTTTAATAAT
12902142 GAATTTTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 11 0.41
16 3 0.11
17 4 0.15
18 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTATTTTTAATAAT
Found at i:12902140 original size:18 final size:18
Alignment explanation
Indices: 12902073--12902149 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
12902063 GTCTTCTATA
**
12902073 AATTTTATTTTTAATTTTT
1 AATTTTATTTTTAA-TAAT
12902092 AA-TTTATTTTTAAT-AT
1 AATTTTATTTTTAATAAT
* *
12902108 -TTTTTGA-ATTT-ATAAT
1 AATTTT-ATTTTTAATAAT
12902124 AATTTTATTTTTAATAAT
1 AATTTTATTTTTAATAAT
12902142 GAATTTTA
1 -AATTTTA
12902150 GTTTGGGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
15 2 0.04
16 10 0.22
17 9 0.20
18 16 0.35
19 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
AATTTTATTTTTAATAAT
Found at i:12907914 original size:22 final size:22
Alignment explanation
Indices: 12907890--12907932 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12907880 GCCTATATAT
*
12907890 AAAACTATAAAGCATTATTATTA
1 AAAAATATAAAGC-TTATTATTA
*
12907913 AAAAATTTAAAGCTTATTAT
1 AAAAATATAAAGCTTATTAT
12907933 ATATATATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAAATATAAAGCTTATTATTA
Found at i:12910968 original size:22 final size:23
Alignment explanation
Indices: 12910920--12910969 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
12910910 CAAAGAAAAT
* * *
12910920 ATAATCATCTAAAAGCTTGTTAT
1 ATAATCATCTAAAAGATTCTTAG
*
12910943 ATAATCATC-AAAAGATTCTTCG
1 ATAATCATCTAAAAGATTCTTAG
12910965 ATAAT
1 ATAAT
12910970 AATTTACTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (23 bp):
ATAATCATCTAAAAGATTCTTAG
Found at i:12921684 original size:13 final size:13
Alignment explanation
Indices: 12921668--12921720 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
12921658 TTTAAACCAA
12921668 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
12921681 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
12921694 ACTTTTCTATAGC
1 ACTTTTCAAAAGC
12921707 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
12921720 A
1 A
12921721 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:12924004 original size:16 final size:16
Alignment explanation
Indices: 12923985--12924026 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
12923975 GCTTTTTGAG
12923985 TTCAGGTTTTTTCAGA
1 TTCAGGTTTTTTCAGA
*
12924001 TTCA-GTTCTTTTCAGG
1 TTCAGGTT-TTTTCAGA
*
12924017 TTCAGATTTT
1 TTCAGGTTTT
12924027 ATCGGGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 17 0.77
17 2 0.09
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (16 bp):
TTCAGGTTTTTTCAGA
Found at i:12925359 original size:3 final size:3
Alignment explanation
Indices: 12925351--12925380 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12925341 TAGTCTTTTG
*
12925351 TTC TTC TTC TTC TTC ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12925381 CATGTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:12928432 original size:28 final size:30
Alignment explanation
Indices: 12928377--12928434 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
12928367 TCATAACTTT
12928377 CTAAAATTGAGTAACCAATATATAAACATA
1 CTAAAATTGAGTAACCAATATATAAACATA
*
12928407 CTAATAATTTAGTAA-C-ATAT-TAAACATA
1 CTAA-AATTGAGTAACCAATATATAAACATA
12928435 TGTATTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.31
29 4 0.15
30 5 0.19
31 9 0.35
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (30 bp):
CTAAAATTGAGTAACCAATATATAAACATA
Found at i:12930047 original size:23 final size:23
Alignment explanation
Indices: 12930021--12930072 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
12930011 TAGTTGAAAG
* *
12930021 CTGTAATATCCCGAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
12930044 CTGTAATACCCCAAAAATTACTA
1 CTGTAATACCCCAAAAATTACTA
*
12930067 CAGTAA
1 CTGTAA
12930073 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (23 bp):
CTGTAATACCCCAAAAATTACTA
Found at i:12935852 original size:23 final size:23
Alignment explanation
Indices: 12935826--12935869 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12935816 ATAAATTATT
12935826 TTTATTACTTTAAAT-ATAAAACA
1 TTTATTAC-TTAAATCATAAAACA
*
12935849 TTTATTTCTTAAATCATAAAA
1 TTTATTACTTAAATCATAAAA
12935870 TAGAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTATTACTTAAATCATAAAACA
Found at i:12936782 original size:199 final size:200
Alignment explanation
Indices: 12936442--12936840 Score: 791
Period size: 199 Copynumber: 2.0 Consensus size: 200
12936432 GGTAGGGAGC
12936442 TTCTGGAATGATAACATTGGTGAAATAATTTATATGAGTTTGAATTTTTTTTAAATGGATGAGTA
1 TTCTGGAATGATAACATTGGTGAAATAATTTATATGAGTTTGAATTTTTTTTAAATGGATGAGTA
12936507 TAAATTTTATTGTTTAATATATTAATAAGTTTGACATTAAACAATTAAGTTTTTCATTATTTTAA
66 TAAATTTTATTGTTTAATATATTAATAAGTTTGACATTAAACAATTAAGTTTTTCATTATTTTAA
12936572 ATAATATAGCTTTTTTTCATTTAAACTATACAACGTATTAGAAAAAGTAATATTAATT-ATTAAT
131 ATAATATAGCTTTTTTTCATTTAAACTATACAACGTATTAGAAAAAGTAATATTAATTAATTAAT
12936636 AATAA
196 AATAA
12936641 TTCTGGAATGATAACATTGGTGAAATAATTTATATGAGTTTGAATTTTTTTTAAATGGATGAGTA
1 TTCTGGAATGATAACATTGGTGAAATAATTTATATGAGTTTGAATTTTTTTTAAATGGATGAGTA
12936706 TAAATTTTATTGTTTAATATATTAATAAGTTTGACATTAAACAATTAAGTTTTTCATTATTTTAA
66 TAAATTTTATTGTTTAATATATTAATAAGTTTGACATTAAACAATTAAGTTTTTCATTATTTTAA
12936771 ATAATATAGCTTTTTTTCATTTAAACTATACAACGTATTAGAAAAAGTAATATTAATTAATTAAT
131 ATAATATAGCTTTTTTTCATTTAAACTATACAACGTATTAGAAAAAGTAATATTAATTAATTAAT
12936836 AATAA
196 AATAA
12936841 ATAAAATCAT
Statistics
Matches: 199, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
199 188 0.94
200 11 0.06
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.45
Consensus pattern (200 bp):
TTCTGGAATGATAACATTGGTGAAATAATTTATATGAGTTTGAATTTTTTTTAAATGGATGAGTA
TAAATTTTATTGTTTAATATATTAATAAGTTTGACATTAAACAATTAAGTTTTTCATTATTTTAA
ATAATATAGCTTTTTTTCATTTAAACTATACAACGTATTAGAAAAAGTAATATTAATTAATTAAT
AATAA
Found at i:12944708 original size:16 final size:16
Alignment explanation
Indices: 12944687--12944718 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12944677 ATTTTGTTGC
*
12944687 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
12944703 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
12944719 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:12945004 original size:51 final size:50
Alignment explanation
Indices: 12944946--12945068 Score: 137
Period size: 48 Copynumber: 2.5 Consensus size: 50
12944936 TCGGTTCACA
* *
12944946 TAGTAGCCTACACATAGTACTACACGTGTGA-CCATCA-CTATCCAATCCACG
1 TAGTAGCCT-CACATAGTACTACACATGTGATCCA--AGCTATCCAATACACG
* **
12944997 TAGTAG-C-CACATAGTACTACACATGTGATCGAAGCTATCCGGTACACG
1 TAGTAGCCTCACATAGTACTACACATGTGATCCAAGCTATCCAATACACG
12945045 TAGTAGCCTGCACATAGTACTACA
1 TAGTAGCCT-CACATAGTACTACA
12945069 TACGTGACTA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
47 1 0.02
48 37 0.60
49 3 0.05
50 1 0.02
51 20 0.32
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTCACATAGTACTACACATGTGATCCAAGCTATCCAATACACG
Found at i:12946664 original size:31 final size:31
Alignment explanation
Indices: 12946607--12946666 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
12946597 AGAGGTGGGA
*
12946607 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
* * *
12946638 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAA
12946667 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:12949107 original size:23 final size:23
Alignment explanation
Indices: 12949077--12949152 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
12949067 CCAATAGGAA
12949077 AAGTGATAGTAACACTATGGTGC
1 AAGTGATAGTAACACTATGGTGC
*** *
12949100 AAGTGATAG-AAGTGTTATAGTGC
1 AAGTGATAGTAA-CACTATGGTGC
**
12949123 AAAGTGATAGTGGCACTATGGTGC
1 -AAGTGATAGTAACACTATGGTGC
12949147 AAGTGA
1 AAGTGA
12949153 CAGAGGCACT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 2 0.05
23 22 0.55
24 16 0.40
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.26
Consensus pattern (23 bp):
AAGTGATAGTAACACTATGGTGC
Found at i:12949160 original size:23 final size:23
Alignment explanation
Indices: 12949119--12949244 Score: 110
Period size: 23 Copynumber: 5.4 Consensus size: 23
12949109 AAGTGTTATA
* *
12949119 GTGCAAAGTGATAGTGGCACTATG
1 GTGC-AAGTGATAGAGGCACTACG
*
12949143 GTGCAAGTGACAGAGGCACTACG
1 GTGCAAGTGATAGAGGCACTACG
* * * * *
12949166 ATGCAAGTGATTGTGACGCTACG
1 GTGCAAGTGATAGAGGCACTACG
* * *
12949189 ATGCAAGTGACAGAGGCACTACA
1 GTGCAAGTGATAGAGGCACTACG
* *
12949212 GTGCAAG-CAGTAGTGGCACTACG
1 GTGCAAGTGA-TAGAGGCACTACG
12949235 GTGCAAGTGA
1 GTGCAAGTGA
12949245 ATGGCACTTC
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
22 1 0.01
23 73 0.92
24 5 0.06
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.19
Consensus pattern (23 bp):
GTGCAAGTGATAGAGGCACTACG
Found at i:12949234 original size:46 final size:46
Alignment explanation
Indices: 12949128--12949244 Score: 148
Period size: 46 Copynumber: 2.5 Consensus size: 46
12949118 AGTGCAAAGT
* *
12949128 GATAGTGGCACTATGGTGCAAGTGACAGAGGCACTACGATGCAAGT
1 GATAGTGGCACTACGGTGCAAGTGACAGAGGCACTACGATGCAAGA
* * * *
12949174 GATTGTGACGCTACGATGCAAGTGACAGAGGCACTAC-AGTGCAAGCA
1 GATAGTGGCACTACGGTGCAAGTGACAGAGGCACTACGA-TGCAAG-A
12949221 G-TAGTGGCACTACGGTGCAAGTGA
1 GATAGTGGCACTACGGTGCAAGTGA
12949245 ATGGCACTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 1 0.02
46 57 0.97
47 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.32, T:0.19
Consensus pattern (46 bp):
GATAGTGGCACTACGGTGCAAGTGACAGAGGCACTACGATGCAAGA
Found at i:12951702 original size:16 final size:17
Alignment explanation
Indices: 12951681--12951712 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12951671 AAATATGCAA
12951681 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
12951697 TCACATAACTTCATAT
1 TCACATAACTTCATAT
12951713 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:12952024 original size:43 final size:42
Alignment explanation
Indices: 12951873--12952036 Score: 169
Period size: 43 Copynumber: 3.9 Consensus size: 42
12951863 GACTCGTACA
* * *
12951873 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-ATCG
12951916 ATGCC-ACTGTCCCAGACAG-GGTCTTACAC--AAATCA-AATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAA-CACAAT-CG
* *
12951957 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
*
12952000 ATGCCAACGTCCCAGACGCT-GTCTTACACGAAAACAC
1 ATGCCAACGTCCCAGACG-TGGTCTTACACGTAAACAC
12952037 GTATCGAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
40 2 0.02
41 29 0.28
42 6 0.06
43 62 0.61
44 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:12959135 original size:21 final size:20
Alignment explanation
Indices: 12959106--12959144 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12959096 TATGAAATTG
*
12959106 GTTTGTTTTTGTTTAACATT
1 GTTTGTTTTTATTTAACATT
*
12959126 GTTTTTTTTTATTTAACAT
1 GTTTGTTTTTATTTAACAT
12959145 GGATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (20 bp):
GTTTGTTTTTATTTAACATT
Found at i:12959151 original size:20 final size:20
Alignment explanation
Indices: 12959111--12959151 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12959101 AATTGGTTTG
* * *
12959111 TTTTTGTTTAACATTGTTTT
1 TTTTTATTTAACATGGATTT
12959131 TTTTTATTTAACATGGATTT
1 TTTTTATTTAACATGGATTT
12959151 T
1 T
12959152 ATATATTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTTATTTAACATGGATTT
Found at i:12960643 original size:9 final size:9
Alignment explanation
Indices: 12960629--12960704 Score: 116
Period size: 9 Copynumber: 8.4 Consensus size: 9
12960619 TTTGGTTAAA
12960629 AATTAACCG
1 AATTAACCG
12960638 AATTAACCG
1 AATTAACCG
12960647 AATTAACCG
1 AATTAACCG
*
12960656 AATTACCCG
1 AATTAACCG
12960665 AATTAACCG
1 AATTAACCG
*
12960674 AATTACCCG
1 AATTAACCG
*
12960683 AATTAACCA
1 AATTAACCG
*
12960692 AATTAACCA
1 AATTAACCG
12960701 AATT
1 AATT
12960705 GAATCACTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:12961310 original size:11 final size:11
Alignment explanation
Indices: 12961286--12961317 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12961276 TTTTTTTTGT
12961286 AAAAATA-T-A
1 AAAAATATTGA
12961295 AAAAATATTGA
1 AAAAATATTGA
12961306 AAAAATATTGA
1 AAAAATATTGA
12961317 A
1 A
12961318 GTGTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.33
10 1 0.05
11 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (11 bp):
AAAAATATTGA
Found at i:12968153 original size:25 final size:25
Alignment explanation
Indices: 12968132--12968309 Score: 94
Period size: 25 Copynumber: 7.1 Consensus size: 25
12968122 TATGAGCGTT
*
12968132 CTGATATTTGGCTCTCACGAGCTTC
1 CTGATACTTGGCTCTCACGAGCTTC
12968157 CTGATACTTGGCTCTCACGAGCTTC
1 CTGATACTTGGCTCTCACGAGCTTC
** * * * *
12968182 CCAACACTTGGATCTTATGAGCTT-
1 CTGATACTTGGCTCTCACGAGCTTC
* * **
12968206 ATCGATTA-ATGGCTCTCTTGAGCTTC
1 CT-GA-TACTTGGCTCTCACGAGCTTC
* * * *
12968232 CCGTTA-TATGGCTATCACGAGATTC
1 CTGATACT-TGGCTCTCACGAGCTTC
* * *
12968257 CTGATA-TATGCCTCTCATGAGTTTC
1 CTGATACT-TGGCTCTCACGAGCTTC
* * * *
12968282 CCGATATTTGGCTCACATGAGCTTC
1 CTGATACTTGGCTCTCACGAGCTTC
12968307 CTG
1 CTG
12968310 TTTATGGCTC
Statistics
Matches: 114, Mismatches: 34, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
24 2 0.02
25 110 0.96
26 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (25 bp):
CTGATACTTGGCTCTCACGAGCTTC
Found at i:12968308 original size:50 final size:50
Alignment explanation
Indices: 12968117--12968382 Score: 150
Period size: 50 Copynumber: 5.3 Consensus size: 50
12968107 ACACACCACA
* * *
12968117 GCTCTTATGAGCGTT-CTGATATTTGGCTCTCACGAGCTTCCTGATACT-TG
1 GCTCTCATGAGC-TTCCCGATATTTGGCTCACACGAGCTTCCTGATA-TATG
* * * * * ** * *
12968167 GCTCTCACGAGCTTCCCAACACTTGGATCTTATGAGCTT-ATCGAT-TAATG
1 GCTCTCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCT-GATAT-ATG
* * * *
12968217 GCTCTCTTGAGCTTCCCGTTATATGGCT-ATCACGAGATTCCTGATATATG
1 GCTCTCATGAGCTTCCCGATATTTGGCTCA-CACGAGCTTCCTGATATATG
* * * *
12968267 CCTCTCATGAGTTTCCCGATATTTGGCTCACATGAGCTTCCTG-TTTATG
1 GCTCTCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCTGATATATG
* * * ** * * * **
12968316 GCTCGT-ATAAGCTTCCAGATAATTGGCTCGTAAGAGTTTCCTGTTATACA
1 GCTC-TCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCTGATATATG
*
12968366 GCTCACATGAGCTTCCC
1 GCTCTCATGAGCTTCCC
12968383 ATTACATGGG
Statistics
Matches: 159, Mismatches: 46, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
48 1 0.01
49 40 0.25
50 115 0.72
51 3 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (50 bp):
GCTCTCATGAGCTTCCCGATATTTGGCTCACACGAGCTTCCTGATATATG
Found at i:12973328 original size:14 final size:14
Alignment explanation
Indices: 12973309--12973336 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12973299 ACCGCTCAAA
12973309 ACCATTGCTACATT
1 ACCATTGCTACATT
12973323 ACCATTGCTACATT
1 ACCATTGCTACATT
12973337 TTACAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
ACCATTGCTACATT
Found at i:12974270 original size:30 final size:31
Alignment explanation
Indices: 12974234--12974298 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
12974224 GTCAATCAAT
*
12974234 TATTCAAAACTTTTCATTTAAGTTACT-AAC
1 TATTCAAAACTTTTCATTTAAGTCACTGAAC
*
12974264 TATTCAAAACTTTTTATTTAAGTCACTGAAC
1 TATTCAAAACTTTTCATTTAAGTCACTGAAC
12974295 TATT
1 TATT
12974299 AAGTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (31 bp):
TATTCAAAACTTTTCATTTAAGTCACTGAAC
Found at i:12975359 original size:12 final size:12
Alignment explanation
Indices: 12975339--12975382 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12975329 AATTATGCTA
*
12975339 TTAACTATTATT
1 TTAAATATTATT
12975351 TTAAATATTATT
1 TTAAATATTATT
**
12975363 TTAAATGAGAATT
1 TTAAAT-ATTATT
12975376 TTAAATA
1 TTAAATA
12975383 ATAGAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (12 bp):
TTAAATATTATT
Found at i:12977158 original size:55 final size:58
Alignment explanation
Indices: 12977111--12977226 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 58
12977101 TTTCATTTAT
12977111 TTTCTCAT-AAATTTGT-A-TAAAAATTATAAATATAT-TTTTTTACAATTTCTTTGAA
1 TTTCT-ATGAAATTTGTAATTAAAAATTATAAATATATATTTTTTACAATTTCTTTGAA
* * *
12977166 TTTCTTTGAATTTTTTAATTAAAAATTATAAATATATATTTTTTACAATTTCTTTGAA
1 TTTCTATGAAATTTGTAATTAAAAATTATAAATATATATTTTTTACAATTTCTTTGAA
12977224 TTT
1 TTT
12977227 TTTAATTGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
54 1 0.02
55 11 0.20
56 1 0.02
57 18 0.33
58 23 0.43
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.54
Consensus pattern (58 bp):
TTTCTATGAAATTTGTAATTAAAAATTATAAATATATATTTTTTACAATTTCTTTGAA
Found at i:12977169 original size:10 final size:10
Alignment explanation
Indices: 12977154--12977178 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12977144 ATTTTTTTAC
12977154 AATTTCTTTG
1 AATTTCTTTG
12977164 AATTTCTTTG
1 AATTTCTTTG
12977174 AATTT
1 AATTT
12977179 TTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (10 bp):
AATTTCTTTG
Found at i:12977255 original size:58 final size:57
Alignment explanation
Indices: 12977128--12977239 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
12977118 TAAATTTGTA
** *
12977128 TAAAAATTATAAATATATTTTTTTACAATTTCTTTGAATTTCTTTGAATTTTTTAAT
1 TAAAAATTATAAATATATTTTTTTACAATTTCTTTGAATTTCTTTGAATTAGTTAAG
12977185 TAAAAATTATAAATATATATTTTTTACAATTTCTTTGAATTT-TTT-AATTGAGTTA
1 TAAAAATTATAAATATAT-TTTTTTACAATTTCTTTGAATTTCTTTGAATT-AGTTA
12977240 GGTAGACATT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
56 4 0.08
57 24 0.47
58 23 0.45
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (57 bp):
TAAAAATTATAAATATATTTTTTTACAATTTCTTTGAATTTCTTTGAATTAGTTAAG
Found at i:12986494 original size:24 final size:24
Alignment explanation
Indices: 12986466--12986517 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12986456 TTAGTAAGTC
* *
12986466 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
12986490 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
12986514 AAAT
1 AAAT
12986518 CCTCTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:12993088 original size:22 final size:22
Alignment explanation
Indices: 12993060--12993108 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12993050 TGACAGGTCA
* *
12993060 TGTCTCGAGACATATAGGCTTT
1 TGTCTCGAGACAAACAGGCTTT
*
12993082 TGTCTCGAGACAAACATGCTTT
1 TGTCTCGAGACAAACAGGCTTT
12993104 TGTCT
1 TGTCT
12993109 AAAGACATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (22 bp):
TGTCTCGAGACAAACAGGCTTT
Found at i:12998700 original size:51 final size:52
Alignment explanation
Indices: 12998620--12998838 Score: 223
Period size: 51 Copynumber: 4.3 Consensus size: 52
12998610 TTAACACGTA
* * *
12998620 TGTAGTACTAAGTGCAGTCTACTACGTGTATC-GATAGATAATGGTCACATG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
* * * * ** *
12998671 TGTACTACTATGTGCAGGCTACTATGTGTACCGAAT-GACCTTGGTCACGTG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
* * * * * * *
12998722 TGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG-C-TTGATCACGTG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
*
12998772 TGTAGTACTATGTGTAGGCTACTACGTGTATCGGAT-GACAATGGTCACATG
1 TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
* *
12998823 GGTGGTACTATGTGCA
1 TGTAGTACTATGTGCA
12998839 AACCACCGAA
Statistics
Matches: 135, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 43 0.32
51 88 0.65
52 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (52 bp):
TGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGACAATGGTCACATG
Found at i:12998780 original size:50 final size:50
Alignment explanation
Indices: 12998710--12998806 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
12998700 ACCGAATGAC
*
12998710 CTTGGTCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG
1 CTTGATCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG
* * *
12998760 CTTGATCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGA
1 CTTGATCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGA
12998807 TGACAATGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
CTTGATCACGTGTGTAGTACTATGTGAAAGCTACTACGTGAATCGGAAAG
Found at i:13002572 original size:43 final size:42
Alignment explanation
Indices: 13002549--13002680 Score: 237
Period size: 43 Copynumber: 3.1 Consensus size: 42
13002539 TTTACGACTC
13002549 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
1 TCTTTTTCTGGGTTTATGGGTTTTTAG-TGTTTCTTTGATGGT
13002592 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
1 TCTTTTTCTGGGTTTATGGGTTTTTAG-TGTTTCTTTGATGGT
13002635 TCTTTTTCTGGGTTTATGGGTTTTTAGTTGTTTCTTTGATGGT
1 TCTTTTTCTGGGTTTATGGGTTTTTAG-TGTTTCTTTGATGGT
13002678 TCT
1 TCT
13002681 AGTTGCATGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.07, C:0.08, G:0.25, T:0.61
Consensus pattern (42 bp):
TCTTTTTCTGGGTTTATGGGTTTTTAGTGTTTCTTTGATGGT
Found at i:13019909 original size:20 final size:20
Alignment explanation
Indices: 13019884--13019921 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13019874 TTTGGTTATC
13019884 ACATGTTCAAATATCTAAGT
1 ACATGTTCAAATATCTAAGT
**
13019904 ACATGTTTGAATATCTAA
1 ACATGTTCAAATATCTAA
13019922 TCCCATTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
ACATGTTCAAATATCTAAGT
Found at i:13022715 original size:51 final size:51
Alignment explanation
Indices: 13022638--13022849 Score: 285
Period size: 51 Copynumber: 4.3 Consensus size: 51
13022628 ACTTCTGATC
* * * *
13022638 AGTGACAAGTGATGAGTGGTAACTTTAGCTACACTTATCTAATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
*
13022689 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
13022740 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * *
13022791 AGTG---A-TG---AGTGGTAGCTTTAGTTACATTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
*
13022835 AATGACAAGTGATAA
1 AGTGACAAGTGATAA
13022850 ATGTGATCCG
Statistics
Matches: 143, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
44 36 0.25
47 3 0.02
48 3 0.02
51 101 0.71
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:13022739 original size:44 final size:44
Alignment explanation
Indices: 13022689--13022848 Score: 194
Period size: 44 Copynumber: 3.5 Consensus size: 44
13022679 ATCAGTGACA
13022689 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAGTGAC
1 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTG---A-T--C
*
13022739 AAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC
1 -AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATC
* * *
13022784 AGTGACAAGTGATGAGTGGTAGCTTTAGTTACATTTATCTGATC
1 AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATC
* * *
13022828 AGGGACAAATGACAAGTGATA
1 AGTGACAAGTGATAAGTGATA
13022849 AATGTGATCC
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
44 56 0.57
45 1 0.01
47 1 0.01
48 1 0.01
51 40 0.40
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATC
Found at i:13027837 original size:14 final size:14
Alignment explanation
Indices: 13027820--13027910 Score: 75
Period size: 14 Copynumber: 6.7 Consensus size: 14
13027810 CAATGTTCTA
* *
13027820 TTCCATATATCTGT
1 TTCCATATAACTAT
13027834 TTCCATATAACTGA-
1 TTCCATATAACT-AT
*
13027848 TT-CATATAACCAT
1 TTCCATATAACTAT
*
13027861 TT-CATATATCTAT
1 TTCCATATAACTAT
*
13027874 TTCCATATAACCAT
1 TTCCATATAACTAT
*
13027888 TT-CATATATCTACT
1 TTCCATATAACTA-T
13027902 TT-CATATAA
1 TTCCATATAA
13027911 TCGATTCATA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
12 1 0.02
13 29 0.46
14 33 0.52
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (14 bp):
TTCCATATAACTAT
Found at i:13027863 original size:27 final size:27
Alignment explanation
Indices: 13027837--13027910 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
13027827 TATCTGTTTC
13027837 CATATAACTGA-TT-CATATAACCATTT
1 CATATAACT-ATTTCCATATAACCATTT
*
13027863 CATATATCTATTTCCATATAACCATTT
1 CATATAACTATTTCCATATAACCATTT
*
13027890 CATATATCTACTTT-CATATAA
1 CATATAACTA-TTTCCATATAA
13027911 TCGATTCATA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 10 0.23
27 30 0.68
28 3 0.07
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.42
Consensus pattern (27 bp):
CATATAACTATTTCCATATAACCATTT
Found at i:13027892 original size:40 final size:41
Alignment explanation
Indices: 13027823--13027909 Score: 115
Period size: 40 Copynumber: 2.1 Consensus size: 41
13027813 TGTTCTATTC
* *
13027823 CATATATCTGTTTCCATATAACTGATTCATATAACCA-TTT
1 CATATATCTATTTCCATATAACTCATTCATATAACCACTTT
* *
13027863 CATATATCTATTTCCATATAAC-CATTTCATATATCTACTTT
1 CATATATCTATTTCCATATAACTCA-TTCATATAACCACTTT
13027904 CATATA
1 CATATA
13027910 ATCGATTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
39 1 0.02
40 31 0.76
41 9 0.22
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (41 bp):
CATATATCTATTTCCATATAACTCATTCATATAACCACTTT
Found at i:13027893 original size:13 final size:13
Alignment explanation
Indices: 13027848--13027910 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 13
13027838 ATATAACTGA
13027848 TTCATATAACCAT
1 TTCATATAACCAT
* *
13027861 TTCATATATCTAT
1 TTCATATAACCAT
13027874 TTCCATATAACCAT
1 TT-CATATAACCAT
* *
13027888 TTCATATATCTACT
1 TTCATATAACCA-T
13027902 TTCATATAA
1 TTCATATAA
13027911 TCGATTCATA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
13 21 0.51
14 20 0.49
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:13027920 original size:27 final size:26
Alignment explanation
Indices: 13027848--13027910 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 26
13027838 ATATAACTGA
13027848 TTCATATAACCATTTCATATATCTAT
1 TTCATATAACCATTTCATATATCTAT
13027874 TTCCATATAACCATTTCATATATCTACT
1 TT-CATATAACCATTTCATATATCTA-T
13027902 TTCATATAA
1 TTCATATAA
13027911 TCGATTCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.06
27 30 0.86
28 3 0.09
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (26 bp):
TTCATATAACCATTTCATATATCTAT
Found at i:13034982 original size:36 final size:37
Alignment explanation
Indices: 13034935--13035008 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
13034925 TTTAAGTGTG
13034935 AAACAATTTAATATGTGAATAAAAAAA-TGTGATAAA
1 AAACAATTTAATATGTGAATAAAAAAATTGTGATAAA
13034971 AAACAATTTAATATGTGAATAAAAAAATTGTGATAAA
1 AAACAATTTAATATGTGAATAAAAAAATTGTGATAAA
13035008 A
1 A
13035009 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 27 0.73
37 10 0.27
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (37 bp):
AAACAATTTAATATGTGAATAAAAAAATTGTGATAAA
Found at i:13035149 original size:14 final size:15
Alignment explanation
Indices: 13035132--13035160 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13035122 AAATATGTTG
13035132 GTGAAATA-ATAGAA
1 GTGAAATACATAGAA
13035146 GTGAAATACATAGAA
1 GTGAAATACATAGAA
13035161 ATTTGATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (15 bp):
GTGAAATACATAGAA
Found at i:13041898 original size:17 final size:16
Alignment explanation
Indices: 13041873--13041922 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
13041863 CGAAAAATTT
13041873 TTAAAACACGAGGATC
1 TTAAAACACGAGGATC
**
13041889 TTAGAAACACGAAAATTC
1 TTA-AAACACGAGGA-TC
13041907 TTAAAAGCACGAGGAT
1 TTAAAA-CACGAGGAT
13041923 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.11
17 13 0.48
18 11 0.41
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (16 bp):
TTAAAACACGAGGATC
Found at i:13041947 original size:17 final size:17
Alignment explanation
Indices: 13041851--13042009 Score: 102
Period size: 18 Copynumber: 8.8 Consensus size: 17
13041841 AATAATTATT
13041851 TTTTTGAGAACACGAAAAA
1 TTTTTGA-AACACG-AAAA
* **
13041870 TTTTTAAAACACGAGGA
1 TTTTTGAAACACGAAAA
* *
13041887 TCTTAGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * **
13041904 TTCTTAAAAGCACGAGGATTT
1 TTTTTGAAA-CACGA--A-AA
13041925 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
13041942 TTTTTGAAAATACGGAAA
1 TTTTTG-AAACACGAAAA
* * *
13041960 TTTTTAAAACACAGGAAT
1 TTTTTGAAACAC-GAAAA
*
13041978 TTTTTGGAAACATGAAAA
1 TTTTT-GAAACACGAAAA
13041996 TTTTTGAAACACGA
1 TTTTTGAAACACGA
13042010 TTAGTTTTTT
Statistics
Matches: 105, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
17 38 0.36
18 43 0.41
19 11 0.10
20 6 0.06
21 7 0.07
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:13041982 original size:36 final size:35
Alignment explanation
Indices: 13041851--13042009 Score: 115
Period size: 36 Copynumber: 4.4 Consensus size: 35
13041841 AATAATTATT
**
13041851 TTTTTGAGAACACGAAAAATTTTT-AAAACACGAGGA
1 TTTTTGA-AACACG-AAAATTTTTGAAAACACGAAAA
* * * **
13041887 TCTTAGAAACACGAAAATTCTT-AAAAGCACGAGGATTT
1 TTTTTGAAACACGAAAATTTTTGAAAA-CACGA--A-AA
* *
13041925 TTTTTGAAACACGAAAATTTTTGAAAATACGGAAA
1 TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
* * * * *
13041960 TTTTTAAAACACAGGAATTTTTTGGAAACATGAAAA
1 TTTTTGAAACAC-GAAAATTTTTGAAAACACGAAAA
13041996 TTTTTGAAACACGA
1 TTTTTGAAACACGA
13042010 TTAGTTTTTT
Statistics
Matches: 95, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
34 12 0.13
35 23 0.24
36 34 0.36
38 22 0.23
39 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (35 bp):
TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:13042018 original size:54 final size:56
Alignment explanation
Indices: 13041893--13042008 Score: 157
Period size: 54 Copynumber: 2.1 Consensus size: 56
13041883 AGGATCTTAG
* * * *
13041893 AAACACGAAAATTCTTAAAAGCACGAGGATTTTTTTTGAAACACGAAAATTTTTGA
1 AAACACGGAAATTTTTAAAAGCACGAGGAATTTTTTGGAAACACGAAAATTTTTGA
* *
13041949 AAATACGGAAATTTTTAAAA-CAC-AGGAATTTTTTGGAAACATGAAAATTTTTG-
1 AAACACGGAAATTTTTAAAAGCACGAGGAATTTTTTGGAAACACGAAAATTTTTGA
13042002 AAACACG
1 AAACACG
13042009 ATTAGTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 6 0.11
54 27 0.51
55 3 0.06
56 17 0.32
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (56 bp):
AAACACGGAAATTTTTAAAAGCACGAGGAATTTTTTGGAAACACGAAAATTTTTGA
Found at i:13042504 original size:20 final size:19
Alignment explanation
Indices: 13042479--13042530 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
13042469 AATTTTGAGC
13042479 CTTTTCCTTTTTTTCTCTTT
1 CTTTT-CTTTTTTTCTCTTT
*
13042499 CTTTTCTCTTTTTTCTTTTT
1 CTTTTCT-TTTTTTCTCTTT
13042519 CTTTTCTTTTTT
1 CTTTTCTTTTTT
13042531 CTTTTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTTCTTTTTTTCTCTTT
Found at i:13042505 original size:11 final size:11
Alignment explanation
Indices: 13042479--13042535 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
13042469 AATTTTGAGC
13042479 CTTTTC-CTTT
1 CTTTTCTCTTT
13042489 -TTTTCTCTTT
1 CTTTTCTCTTT
13042499 CTTTTCTC-TT
1 CTTTTCTCTTT
*
13042509 -TTTTCTTTTT
1 CTTTTCTCTTT
*
13042519 CTTTTCTTTTTT
1 CTTTTC-TCTTT
13042531 CTTTT
1 CTTTT
13042536 TTTCTTCAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 11 0.27
10 8 0.20
11 12 0.29
12 10 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
CTTTTCTCTTT
Found at i:13042541 original size:20 final size:20
Alignment explanation
Indices: 13042487--13042536 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 20
13042477 GCCTTTTCCT
*
13042487 TTTTTTCTCTTTCTTTTCTC
1 TTTTTTCTTTTTCTTTTCTC
13042507 TTTTTTCTTTTTC-TTT-TC
1 TTTTTTCTTTTTCTTTTCTC
13042525 TTTTTTCTTTTT
1 TTTTTTCTTTTT
13042537 TTCTTCAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.48
19 3 0.10
20 12 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTCTTTTCTC
Found at i:13042541 original size:26 final size:26
Alignment explanation
Indices: 13042488--13042537 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
13042478 CCTTTTCCTT
13042488 TTTTTCTCTTTCTTTTCTCTTTTTTC
1 TTTTTCTCTTTCTTTTCTCTTTTTTC
*
13042514 TTTTTCT-TTTCTTTTTTCTTTTTT
1 TTTTTCTCTTTCTTTTCTCTTTTTT
13042538 TCTTCAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTTCTCTTTCTTTTCTCTTTTTTC
Found at i:13042760 original size:18 final size:18
Alignment explanation
Indices: 13042734--13042768 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13042724 CCTAATCTGC
*
13042734 TGGGCCTGCTGGGTGTTG
1 TGGGCCTGCTGGCTGTTG
*
13042752 TGGGTCTGCTGGCTGTT
1 TGGGCCTGCTGGCTGTT
13042769 CCGGGTCGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.37
Consensus pattern (18 bp):
TGGGCCTGCTGGCTGTTG
Found at i:13043021 original size:15 final size:16
Alignment explanation
Indices: 13042997--13043040 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
13042987 TCTCCTCCCC
*
13042997 TTTTCCTTTTCTT-CT
1 TTTTCTTTTTCTTCCT
13043012 TTTTCTTTTTCTTCCT
1 TTTTCTTTTTCTTCCT
* *
13043028 TTGTCTTTCTCTT
1 TTTTCTTTTTCTT
13043041 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTCTTTTTCTTCCT
Found at i:13043504 original size:58 final size:59
Alignment explanation
Indices: 13043428--13043562 Score: 188
Period size: 58 Copynumber: 2.3 Consensus size: 59
13043418 GTAAAATTAT
*
13043428 AATTTT-GAGAAAGTTTAGGGGTT-AATATGTAATTTTGAGAAAGTTTAGAGGTCAAAATGT
1 AATTTTAGA-AAAGTTTAGGGGTTGAA-ATGTAATTTTGAGAAAGTTTAG-GGTCAAAATGA
* *
13043488 AA-TTTA-AAAAGTTTAGGGGTTGAAGTGTAATTTTGAGAAATTTTAGGGTCAAAATGA
1 AATTTTAGAAAAGTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTAGGGTCAAAATGA
13043545 AATTTTAGAAAAGTTTAG
1 AATTTTAGAAAAGTTTAG
13043563 AGGTCAAAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
57 12 0.18
58 38 0.56
59 16 0.24
60 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (59 bp):
AATTTTAGAAAAGTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTAGGGTCAAAATGA
Found at i:13043573 original size:30 final size:30
Alignment explanation
Indices: 13043427--13043573 Score: 167
Period size: 30 Copynumber: 5.0 Consensus size: 30
13043417 GGTAAAATTA
* * *
13043427 TAATTTTGAGAAAGTTTAGGGGTTAATATG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
13043457 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
* * ** *
13043487 TAA-TTT-AAAAAGTTTAGGGGTTGAAGTG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
*
13043515 TAATTTTGAGAAATTTTAG-GGTCAAAATG
1 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
*
13043544 AAATTTT-AGAAAAGTTTAGAGGTCAAAATG
1 TAATTTTGAG-AAAGTTTAGAGGTCAAAATG
13043574 CAAAAAATTA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
28 22 0.22
29 27 0.28
30 49 0.50
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
TAATTTTGAGAAAGTTTAGAGGTCAAAATG
Found at i:13044805 original size:30 final size:28
Alignment explanation
Indices: 13044770--13044836 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
13044760 ATTTAAAATT
* *
13044770 TTATAAAAACGTATGAAAATTCTATAAAAA
1 TTATAAAAAAGTAT-AAAATTATAT-AAAA
* *
13044800 TTATAAAAAAGTATTAAATTATATAAAC
1 TTATAAAAAAGTATAAAATTATATAAAA
13044828 TTATAAAAA
1 TTATAAAAA
13044837 TAAAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 12 0.36
29 8 0.24
30 13 0.39
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (28 bp):
TTATAAAAAAGTATAAAATTATATAAAA
Found at i:13059870 original size:26 final size:27
Alignment explanation
Indices: 13059841--13059897 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
13059831 TTTATGCTTT
*
13059841 TTTTATAAAATCTTA-TAATTTGTAAA
1 TTTTATAAAATCTTATTAATTTGCAAA
* * *
13059867 TTTTATTAAATTTTATTATTTTGCAAA
1 TTTTATAAAATCTTATTAATTTGCAAA
13059894 TTTT
1 TTTT
13059898 CTATATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTATAAAATCTTATTAATTTGCAAA
Found at i:13066677 original size:22 final size:21
Alignment explanation
Indices: 13066599--13066677 Score: 54
Period size: 22 Copynumber: 3.7 Consensus size: 21
13066589 AAAAAATAAT
*
13066599 AAAATTTTAATTTAATACTT-TA
1 AAAATTATAATTT-ATA-TTATA
** * *
13066621 AAAATTATAA-AGATATAATC
1 AAAATTATAATTTATATTATA
*
13066641 AAAATTATATTTTTATTATTATA
1 AAAATTATA-ATTTA-TATTATA
13066664 AAAATTATAATTTA
1 AAAATTATAATTTA
13066678 ATTTCATCCC
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.02
20 13 0.31
22 14 0.33
23 14 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
AAAATTATAATTTATATTATA
Found at i:13067941 original size:16 final size:16
Alignment explanation
Indices: 13067915--13067967 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
13067905 TTAAATATTT
13067915 TTTTCATATTTTTTATA
1 TTTT-ATATTTTTTATA
*
13067932 TTTTATATTTTTCATA
1 TTTTATATTTTTTATA
* * *
13067948 ATATATAATTTTTTTTA
1 TTTTAT-ATTTTTTATA
13067965 TTT
1 TTT
13067968 AAAGATTTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTATATTTTTTATA
Found at i:13068130 original size:231 final size:232
Alignment explanation
Indices: 13067727--13068193 Score: 918
Period size: 231 Copynumber: 2.0 Consensus size: 232
13067717 GAAAGTTTAC
13067727 TTTTTTATTTAAAGATTTCAAATTTAATTTAGGCTTTACATATCAGCCAAATACCTACAAAACAA
1 TTTTTTATTTAAAGATTTCAAATTTAATTTAGGCTTTACATATCAGCCAAATACCTACAAAACAA
13067792 AACAAAAAATGTTTTCATATTTTTTTCATATAATTTTAATTTTTTTTATGAAATCTTATAATATT
66 AACAAAAAATGTTTTCATATTTTTTTCATATAATTTTAATTTTTTTTATGAAATCTTATAATATT
13067857 TTGTAAATTTTATTAATGTTTAAATACTTTTAATAACTTTATATATTTTTAAATATTTTTTTCAT
131 TTGTAAATTTTATTAATGTTTAAATACTTTTAATAACTTTATATATTTTTAAATATTTTTTTCAT
13067922 ATTTTTTATATTTTATATTTTTCATAA-TATATAATT
196 ATTTTTTATATTTTATATTTTTCATAATTATATAATT
13067958 TTTTTTATTTAAAGATTTCAAATTTAATTTAGGCTTTACATATCAGCCAAATACCTACAAAACAA
1 TTTTTTATTTAAAGATTTCAAATTTAATTTAGGCTTTACATATCAGCCAAATACCTACAAAACAA
13068023 AACAAAAAATGTTTTCATATTTTTTTCATATAATTTTAATTTTTTTTATGAAATCTTATAATATT
66 AACAAAAAATGTTTTCATATTTTTTTCATATAATTTTAATTTTTTTTATGAAATCTTATAATATT
13068088 TTGTAAATTTTATTAATGTTTAAATACTTTTAATAACTTTATATATTTTTAAATATTTTTTTCAT
131 TTGTAAATTTTATTAATGTTTAAATACTTTTAATAACTTTATATATTTTTAAATATTTTTTTCAT
13068153 ATTTTTTATATTTTATATTTTTCATAATTTATATAATT
196 ATTTTTTATATTTTATATTTTTCATAA-TTATATAATT
13068191 TTT
1 TTT
13068194 AATTTCATAT
Statistics
Matches: 234, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
231 222 0.95
233 12 0.05
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (232 bp):
TTTTTTATTTAAAGATTTCAAATTTAATTTAGGCTTTACATATCAGCCAAATACCTACAAAACAA
AACAAAAAATGTTTTCATATTTTTTTCATATAATTTTAATTTTTTTTATGAAATCTTATAATATT
TTGTAAATTTTATTAATGTTTAAATACTTTTAATAACTTTATATATTTTTAAATATTTTTTTCAT
ATTTTTTATATTTTATATTTTTCATAATTATATAATT
Found at i:13068172 original size:16 final size:16
Alignment explanation
Indices: 13068146--13068224 Score: 72
Period size: 16 Copynumber: 4.8 Consensus size: 16
13068136 TTAAATATTT
13068146 TTTTCATATTTTTTATA
1 TTTT-ATATTTTTTATA
*
13068163 TTTTATATTTTTCATAA
1 TTTTATATTTTTTAT-A
*
13068180 TTTATATAATTTTTA-A
1 TTT-TATATTTTTTATA
*
13068196 TTTCATA-TTTTTATTA
1 TTTTATATTTTTTA-TA
*
13068212 TTTTGTATTTTTT
1 TTTTATATTTTTT
13068225 CTAGGATGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 20 0.39
17 13 0.25
18 9 0.18
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (16 bp):
TTTTATATTTTTTATA
Found at i:13069972 original size:21 final size:21
Alignment explanation
Indices: 13069946--13069986 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13069936 AATAATGAAA
*
13069946 ATAAAAAAATTAAATTAATAC
1 ATAAAAAAATTAAACTAATAC
**
13069967 ATAAAACTATTAAACTAATA
1 ATAAAAAAATTAAACTAATA
13069987 TACAAATTTG
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:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAAAAATTAAACTAATAC
Found at i:13076531 original size:21 final size:21
Alignment explanation
Indices: 13076473--13076524 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
13076463 GGGAGTAATG
13076473 TCGCGACATTAGCCTTTAGGA
1 TCGCGACATTAGCCTTTAGGA
13076494 TCGCGACATTAGCCTTTAGGA
1 TCGCGACATTAGCCTTTAGGA
13076515 TCGCGACATT
1 TCGCGACATT
13076525 GAGCTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (21 bp):
TCGCGACATTAGCCTTTAGGA
Found at i:13082907 original size:124 final size:124
Alignment explanation
Indices: 13082687--13082950 Score: 528
Period size: 124 Copynumber: 2.1 Consensus size: 124
13082677 AGGTGCTCAT
13082687 GGGCCGGGCCGGGCCGAGCCCGGGCTTTATGAATTTTTCCCGGGCCGGACTTGGGCAAAATTCTA
1 GGGCCGGGCCGGGCCGAGCCCGGGCTTTATGAATTTTTCCCGGGCCGGACTTGGGCAAAATTCTA
13082752 GGCCCATATTTCGGGCCTATATTTTTACCCAAACCCTCCCATATTTCGGGCGGGCCGTC
66 GGCCCATATTTCGGGCCTATATTTTTACCCAAACCCTCCCATATTTCGGGCGGGCCGTC
13082811 GGGCCGGGCCGGGCCGAGCCCGGGCTTTATGAATTTTTCCCGGGCCGGACTTGGGCAAAATTCTA
1 GGGCCGGGCCGGGCCGAGCCCGGGCTTTATGAATTTTTCCCGGGCCGGACTTGGGCAAAATTCTA
13082876 GGCCCATATTTCGGGCCTATATTTTTACCCAAACCCTCCCATATTTCGGGCGGGCCGTC
66 GGCCCATATTTCGGGCCTATATTTTTACCCAAACCCTCCCATATTTCGGGCGGGCCGTC
13082935 GGGCCGGGCCGGGCCG
1 GGGCCGGGCCGGGCCG
13082951 CCCAGCCCAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 140 1.00
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.23
Consensus pattern (124 bp):
GGGCCGGGCCGGGCCGAGCCCGGGCTTTATGAATTTTTCCCGGGCCGGACTTGGGCAAAATTCTA
GGCCCATATTTCGGGCCTATATTTTTACCCAAACCCTCCCATATTTCGGGCGGGCCGTC
Found at i:13084948 original size:13 final size:13
Alignment explanation
Indices: 13084930--13084955 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13084920 AGGATGAATC
13084930 AAATGAAAATAAA
1 AAATGAAAATAAA
13084943 AAATGAAAATAAA
1 AAATGAAAATAAA
13084956 TGAATAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATGAAAATAAA
Found at i:13085072 original size:4 final size:4
Alignment explanation
Indices: 13085059--13085101 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
13085049 TGATTTTTTG
13085059 AATT -ATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
13085102 GAAGTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
AATT
Found at i:13090288 original size:23 final size:24
Alignment explanation
Indices: 13090246--13090295 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
13090236 AACATTGATG
* *
13090246 TGAGTTAATCTTTTGCTTGTTTAAT
1 TGAGTTAA-CTTTTGATTGTTAAAT
13090271 TGAGTTAA-TTTTGATTGTTAAAT
1 TGAGTTAACTTTTGATTGTTAAAT
13090294 TG
1 TG
13090296 TCTTCCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.54
Consensus pattern (24 bp):
TGAGTTAACTTTTGATTGTTAAAT
Found at i:13096655 original size:27 final size:29
Alignment explanation
Indices: 13096616--13096670 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
13096606 TTTACGAGGT
*
13096616 TTTTTTTTTAGAA-TTT-TGATTTTTTAA
1 TTTTTTTTAAGAACTTTATGATTTTTTAA
13096643 TTTTTTTTAAGAACTTTTATGATTTTTT
1 TTTTTTTTAAGAAC-TTTATGATTTTTT
13096671 TTACAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
29 3 0.12
30 9 0.38
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (29 bp):
TTTTTTTTAAGAACTTTATGATTTTTTAA
Found at i:13096660 original size:21 final size:21
Alignment explanation
Indices: 13096635--13096681 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
13096625 AGAATTTTGA
* *
13096635 TTTTTTAATTTTTTTTAAGAAC
1 TTTTATAATTTTTTTT-ACAAC
*
13096657 TTTTATGATTTTTTTTACAAC
1 TTTTATAATTTTTTTTACAAC
13096678 TTTT
1 TTTT
13096682 GTATAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATAATTTTTTTTACAAC
Found at i:13096970 original size:21 final size:22
Alignment explanation
Indices: 13096933--13096984 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
13096923 TAACTTTAAA
**
13096933 AAAATTAAAATTGAAAATGATAT
1 AAAATT-AAATTGAAAAAAATAT
13096956 AAAATTAAA-TGAAAAAAATAT
1 AAAATTAAATTGAAAAAAATAT
13096977 ATAAATTA
1 A-AAATTA
13096985 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
AAAATTAAATTGAAAAAAATAT
Found at i:13096971 original size:22 final size:21
Alignment explanation
Indices: 13096933--13096984 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
13096923 TAACTTTAAA
*
13096933 AAAATTAAAATTGAAAATGATAT
1 AAAATT-AAATTGAAAA-AATAT
13096956 AAAATTAAA-TGAAAAAAATAT
1 AAAATTAAATTG-AAAAAATAT
13096977 ATAAATTA
1 A-AAATTA
13096985 TAAAAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.27
22 13 0.50
23 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
AAAATTAAATTGAAAAAATAT
Found at i:13098056 original size:2 final size:2
Alignment explanation
Indices: 13098049--13098091 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
13098039 AAACTCTCCA
13098049 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13098091 T
1 T
13098092 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:13106620 original size:29 final size:31
Alignment explanation
Indices: 13106579--13106645 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
13106569 TTATTCAAAT
*
13106579 AATAT-TAAAAAAATA-ATTAATTACGAAAA
1 AATATATAAAAAAACATATTAATTACGAAAA
*
13106608 AATATATAAAAAAACATATTAATTATGAAAA
1 AATATATAAAAAAACATATTAATTACGAAAA
*
13106639 TATATAT
1 AATATAT
13106646 TTATTATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 5 0.15
30 9 0.27
31 19 0.58
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (31 bp):
AATATATAAAAAAACATATTAATTACGAAAA
Found at i:13107421 original size:27 final size:29
Alignment explanation
Indices: 13107376--13107433 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
13107366 AAAATGTTTA
*
13107376 TTTTCGTAATTAATCTATTTTTTTA-TAT
1 TTTTCGTAATTAATCTATTTTTGTATTAT
*
13107404 TTTTTGTAATTAAT-TATTTTTGTATTAT
1 TTTTCGTAATTAATCTATTTTTGTATTAT
13107432 TT
1 TT
13107434 AGATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTTCGTAATTAATCTATTTTTGTATTAT
Found at i:13113669 original size:13 final size:13
Alignment explanation
Indices: 13113653--13113679 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13113643 AAACTTAAAA
13113653 TTCTCTATAAATG
1 TTCTCTATAAATG
13113666 TTCTCTATAAATG
1 TTCTCTATAAATG
13113679 T
1 T
13113680 ATTATGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TTCTCTATAAATG
Found at i:13117720 original size:17 final size:15
Alignment explanation
Indices: 13117694--13117740 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
13117684 ACCCGCCAAA
*
13117694 TTATTATTTAATAAT
1 TTATTTTTTAATAAT
13117709 TAATATTTTTTAAT-AT
1 T--TATTTTTTAATAAT
13117725 TTATTCTTTTAATAAT
1 TTATT-TTTTAATAAT
13117741 AATTTGGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 5 0.19
17 10 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTTTTAATAAT
Found at i:13119058 original size:23 final size:23
Alignment explanation
Indices: 13118991--13119066 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
13118981 AGTTAAAATA
* *
13118991 TATATATTATAATGTTATAAT-AT
1 TATATA-TATAATATTATAATAAG
* *
13119014 TATATCT-TAATTATTA-ATTAAG
1 TATATATATAA-TATTATAATAAG
13119036 TATATATATAATATTATAATAAG
1 TATATATATAATATTATAATAAG
*
13119059 TAGATATA
1 TATATATA
13119067 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
21 5 0.12
22 17 0.40
23 20 0.48
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (23 bp):
TATATATATAATATTATAATAAG
Found at i:13119105 original size:16 final size:15
Alignment explanation
Indices: 13119089--13119118 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
13119079 AACAAAAAGA
13119089 AATAGAAAGAAACAG
1 AATAGAAAGAAACAG
13119104 AATAGAAACGAAACA
1 AATAGAAA-GAAACA
13119119 AGGAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.10, G:0.17, T:0.07
Consensus pattern (15 bp):
AATAGAAAGAAACAG
Found at i:13119109 original size:15 final size:16
Alignment explanation
Indices: 13119076--13119118 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
13119066 AATAAATAAA
*
13119076 AGAAAC-AAAAAGAAAT
1 AGAAACGAAACAG-AAT
13119092 AGAAA-GAAACAGAAT
1 AGAAACGAAACAGAAT
13119107 AGAAACGAAACA
1 AGAAACGAAACA
13119119 AGGAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.70, C:0.09, G:0.16, T:0.05
Consensus pattern (16 bp):
AGAAACGAAACAGAAT
Found at i:13119136 original size:26 final size:25
Alignment explanation
Indices: 13119093--13119159 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 25
13119083 AAAAGAAATA
*
13119093 GAAAGAAACAGAATAGAAACGAAACAAGG
1 GAAAGAAA-A-AA-AGAAAAGAAA-AAGG
13119122 AGAAA-AAAAAAAGAAAAGAAAAAGG
1 -GAAAGAAAAAAAGAAAAGAAAAAGG
*
13119147 GAAAGAAAGAAAG
1 GAAAGAAAAAAAG
13119160 GAGAAATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.12
25 11 0.32
26 9 0.26
27 2 0.06
28 1 0.03
29 3 0.09
30 4 0.12
ACGTcount: A:0.70, C:0.04, G:0.24, T:0.01
Consensus pattern (25 bp):
GAAAGAAAAAAAGAAAAGAAAAAGG
Found at i:13125524 original size:43 final size:43
Alignment explanation
Indices: 13125428--13125527 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
13125418 ATGCCGGTAT
* ** *
13125428 AGAACATGACCTTTAGCGGTGCTTTTTCCACAAACACCGCTAT
1 AGAACATGACTTTTAGCGACGCTTTTTCCACAAACACCGCTAA
* *
13125471 AGAACTTGACTTTTAGCGACGCTTTTAT-CATAAACACCGCTAA
1 AGAACATGACTTTTAGCGACGCTTTT-TCCACAAACACCGCTAA
*
13125514 ATAACATGACTTTT
1 AGAACATGACTTTT
13125528 GACTTTTAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (43 bp):
AGAACATGACTTTTAGCGACGCTTTTTCCACAAACACCGCTAA
Found at i:13127882 original size:18 final size:19
Alignment explanation
Indices: 13127847--13127884 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13127837 ACCAATTTTC
13127847 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
13127866 AAAAATTCCAAAT-TTTAT
1 AAAAATTCAAAATATTTAT
13127884 A
1 A
13127885 TTATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:13128288 original size:25 final size:24
Alignment explanation
Indices: 13128241--13128290 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
13128231 CTCACCCATA
*
13128241 ATTTAAATTAAATAATAATTTTTT
1 ATTTAAATTAAATAATAAATTTTT
* * *
13128265 ATTTAAATTTAATTATAAAATTTT
1 ATTTAAATTAAATAATAAATTTTT
13128289 AT
1 AT
13128291 GTCATTAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTAAATTAAATAATAAATTTTT
Found at i:13128430 original size:14 final size:14
Alignment explanation
Indices: 13128401--13128429 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13128391 AATTTCCTTA
13128401 TTCTCTTTCTTTTT
1 TTCTCTTTCTTTTT
13128415 TTCT-TTTCTTTTT
1 TTCTCTTTCTTTTT
13128428 TT
1 TT
13128430 TAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTCTTTCTTTTT
Found at i:13162100 original size:23 final size:21
Alignment explanation
Indices: 13162065--13162107 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
13162055 GTTTCTTGTT
13162065 TAAAACTCAAACTTGGTTCGAGA
1 TAAAACTCAAAC-T-GTTCGAGA
* *
13162088 TAAAAGTCGAACTGTTCGAG
1 TAAAACTCAAACTGTTCGAG
13162108 CTTACTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (21 bp):
TAAAACTCAAACTGTTCGAGA
Found at i:13177303 original size:15 final size:16
Alignment explanation
Indices: 13177283--13177312 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13177273 ATGGGTATTA
13177283 AATAAATTTT-TTAAT
1 AATAAATTTTATTAAT
13177298 AATAAATTTTATTAA
1 AATAAATTTTATTAA
13177313 ATATCCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAAATTTTATTAAT
Found at i:13181029 original size:24 final size:25
Alignment explanation
Indices: 13181002--13181093 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
13180992 TTCCAGATAT
*
13181002 TGGCTCACATGAGTTTCCTGTTA-A
1 TGGCTCACATGAGCTTCCTGTTACA
* *
13181026 TGGCTCTTC-GGAGCTT-CTCGTTACA
1 TGGCTC-ACATGAGCTTCCT-GTTACA
* *
13181051 TGACTCACATGAGCTTCCTGTTATA
1 TGGCTCACATGAGCTTCCTGTTACA
* *
13181076 TGGCTCAAAAGAGCTTCC
1 TGGCTCACATGAGCTTCC
13181094 AGTTTATGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.04
24 16 0.30
25 33 0.62
26 2 0.04
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCTGTTACA
Found at i:13181114 original size:25 final size:25
Alignment explanation
Indices: 13180991--13181106 Score: 69
Period size: 25 Copynumber: 4.7 Consensus size: 25
13180981 GTCGCTTAAC
* *
13180991 CTTCCAGATAT-TGGCTCACATGAG
1 CTTCCAGTTATATGGCTCAAATGAG
* * ****
13181015 TTTCCTGTTA-ATGGCTCTTCGGAG
1 CTTCCAGTTATATGGCTCAAATGAG
* * *
13181039 CTTCTC-GTTACATGACTCACATGAG
1 CTTC-CAGTTATATGGCTCAAATGAG
* *
13181064 CTTCCTGTTATATGGCTCAAAAGAG
1 CTTCCAGTTATATGGCTCAAATGAG
13181089 CTTCCAGTT-TATGTGCTC
1 CTTCCAGTTATATG-GCTC
13181107 GTATGAGCAT
Statistics
Matches: 69, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
24 28 0.41
25 41 0.59
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (25 bp):
CTTCCAGTTATATGGCTCAAATGAG
Found at i:13182224 original size:12 final size:12
Alignment explanation
Indices: 13182207--13182249 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
13182197 TCAGAGAGTT
13182207 ACACGGGTAAGG
1 ACACGGGTAAGG
*
13182219 ACACGGGCT-GGG
1 ACACGGG-TAAGG
13182231 ACACGGGTAAGG
1 ACACGGGTAAGG
13182243 ACACGGG
1 ACACGGG
13182250 CTGGGACACG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.44, T:0.07
Consensus pattern (12 bp):
ACACGGGTAAGG
Found at i:13182239 original size:24 final size:24
Alignment explanation
Indices: 13182207--13182260 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
13182197 TCAGAGAGTT
13182207 ACACGGGTAAGGACACGGGCTGGG
1 ACACGGGTAAGGACACGGGCTGGG
13182231 ACACGGGTAAGGACACGGGCTGGG
1 ACACGGGTAAGGACACGGGCTGGG
13182255 ACACGG
1 ACACGG
13182261 CTGTGTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.44, T:0.07
Consensus pattern (24 bp):
ACACGGGTAAGGACACGGGCTGGG
Found at i:13182256 original size:12 final size:12
Alignment explanation
Indices: 13182217--13182260 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
13182207 ACACGGGTAA
13182217 GGACACGGGCTG
1 GGACACGGGCTG
*
13182229 GGACACGGG-TAA
1 GGACACGGGCT-G
13182241 GGACACGGGCTG
1 GGACACGGGCTG
13182253 GGACACGG
1 GGACACGG
13182261 CTGTGTGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.48, T:0.07
Consensus pattern (12 bp):
GGACACGGGCTG
Found at i:13199303 original size:21 final size:21
Alignment explanation
Indices: 13199279--13199342 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
13199269 ACAGAAACCT
13199279 ATAAGGGTTGAACGGAAGCTC
1 ATAAGGGTTGAACGGAAGCTC
* * * *
13199300 ATAAGAGCTGAACGGAAACCC
1 ATAAGGGTTGAACGGAAGCTC
* *
13199321 ATAAGGGTTAAACTGAAGCTC
1 ATAAGGGTTGAACGGAAGCTC
13199342 A
1 A
13199343 ATAGAGTTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
ATAAGGGTTGAACGGAAGCTC
Found at i:13199303 original size:42 final size:42
Alignment explanation
Indices: 13199251--13199374 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 42
13199241 AGGCTGCACA
* * * *
13199251 GAAGCACATAAGTGCTAAACAGAAACCTATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACG
* * *
13199293 GAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACG
* * *
13199335 GAAGCTCA-ATAGAGTTAAACGGAAACCAAT-AGGGTTAAAC
1 GAAGCTCATA-AGAGCTAAACAGAAACCCATAAGGGTTAAAC
13199375 TAAAACTCAT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
41 11 0.15
42 60 0.85
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACG
Found at i:13199353 original size:21 final size:21
Alignment explanation
Indices: 13199327--13199393 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
13199317 ACCCATAAGG
*
13199327 GTTAAACTGAAGCTCAATAGA
1 GTTAAACTGAAACTCAATAGA
* *
13199348 GTTAAACGGAAAC-CAATAGG
1 GTTAAACTGAAACTCAATAGA
*
13199368 GTTAAACTAAAACTC-ATATGA
1 GTTAAACTGAAACTCAATA-GA
13199389 GTTAA
1 GTTAA
13199394 CACGAAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (21 bp):
GTTAAACTGAAACTCAATAGA
Found at i:13199380 original size:20 final size:21
Alignment explanation
Indices: 13199324--13199383 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
13199314 GAAACCCATA
*
13199324 AGGGTTAAACTGAAGCTCAAT
1 AGGGTTAAACTGAAACTCAAT
* *
13199345 AGAGTTAAACGGAAAC-CAAT
1 AGGGTTAAACTGAAACTCAAT
*
13199365 AGGGTTAAACTAAAACTCA
1 AGGGTTAAACTGAAACTCA
13199384 TATGAGTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
AGGGTTAAACTGAAACTCAAT
Found at i:13199391 original size:41 final size:42
Alignment explanation
Indices: 13199266--13199393 Score: 118
Period size: 42 Copynumber: 3.1 Consensus size: 42
13199256 ACATAAGTGC
* * * ** * *
13199266 TAAACAGAAACCTATAAGGGTTGAACGGAAGCTC-ATAAGAGC
1 TAAACGGAAACCAATAAGGGTTAAACTAAAACTCAAT-AGAGT
* * * *
13199308 TGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAATAGAGT
1 TAAACGGAAACCAATAAGGGTTAAACTAAAACTCAATAGAGT
13199350 TAAACGGAAACCAAT-AGGGTTAAACTAAAACTC-ATATGAGT
1 TAAACGGAAACCAATAAGGGTTAAACTAAAACTCAATA-GAGT
13199391 TAA
1 TAA
13199394 CACGAAAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.04
41 23 0.31
42 46 0.62
43 2 0.03
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.20
Consensus pattern (42 bp):
TAAACGGAAACCAATAAGGGTTAAACTAAAACTCAATAGAGT
Found at i:13206904 original size:42 final size:42
Alignment explanation
Indices: 13206852--13206986 Score: 112
Period size: 42 Copynumber: 3.2 Consensus size: 42
13206842 AGGCTGCATA
* * * * *
13206852 GAAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAACG
1 GAAGCTCATAAGAGCTAAACAGAAACCCAAAAAGGTTAAACG
* ** *
13206894 GAAGCTCATAAGAGCTGAATGGAAACCCAAAAAGGTTAAACT
1 GAAGCTCATAAGAGCTAAACAGAAACCCAAAAAGGTTAAACG
* * * * *
13206936 GAAGCTCA-AGAGAGCTGAAC-GAAAACCAATAGGGTTAAACT
1 GAAGCTCATA-AGAGCTAAACAGAAACCCAAAAAGGTTAAACG
*
13206977 GAAACTCATA
1 GAAGCTCATA
13206987 TGAGTCAACA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 26 0.34
42 51 0.66
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAGAAACCCAAAAAGGTTAAACG
Found at i:13206912 original size:21 final size:21
Alignment explanation
Indices: 13206852--13206917 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
13206842 AGGCTGCATA
* * *
13206852 GAAGCACATAAGTGCTAAACA
1 GAAGCACATAAGAGCTGAACG
* * * *
13206873 GAAACCCATAAGGGTTGAACG
1 GAAGCACATAAGAGCTGAACG
* *
13206894 GAAGCTCATAAGAGCTGAATG
1 GAAGCACATAAGAGCTGAACG
13206915 GAA
1 GAA
13206918 ACCCAAAAAG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (21 bp):
GAAGCACATAAGAGCTGAACG
Found at i:13226781 original size:21 final size:22
Alignment explanation
Indices: 13226755--13226805 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
13226745 GGCCAGTACC
*
13226755 AATAACAA-AAACAATAGC-AAA
1 AATAACAACAAA-AACAGCAAAA
13226776 AATAACAACAAAAACAGCAGAAA
1 AATAACAACAAAAACAGCA-AAA
13226799 AATAACA
1 AATAACA
13226806 GCACCAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 13 0.50
22 3 0.12
23 10 0.38
ACGTcount: A:0.71, C:0.16, G:0.06, T:0.08
Consensus pattern (22 bp):
AATAACAACAAAAACAGCAAAA
Found at i:13226799 original size:23 final size:24
Alignment explanation
Indices: 13226758--13226805 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
13226748 CAGTACCAAT
*
13226758 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
13226782 AACAAAAACAGCAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
13226805 A
1 A
13226806 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:13227356 original size:27 final size:26
Alignment explanation
Indices: 13227307--13227357 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
13227297 TTTGACTCTA
* *
13227307 ATTTTTTTTTAAATTTCTCTCAATTT
1 ATTTATTTTTAAATTTATCTCAATTT
*
13227333 ATTTATTTTTAACTTTATCGTCAAT
1 ATTTATTTTTAAATTTATC-TCAAT
13227358 ATGCTTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTATTTTTAAATTTATCTCAATTT
Found at i:13246397 original size:92 final size:91
Alignment explanation
Indices: 13246236--13246408 Score: 222
Period size: 92 Copynumber: 1.9 Consensus size: 91
13246226 CAAGTACTAA
* * * * * **
13246236 AATAAAACACATATTGATAGTTTAAGTACCACATTGACATTTTCAAAGTACAAGTATTATATTGG
1 AATAAAACACATATTGATAGCTCAAGTACAACATTGACATTTTCAAAGTACAAGTATCACATTAA
*
13246301 ACATTTTATGAAAGTACATGTACCAT
66 ACATTATATGAAAGTACATGTACCAT
* * *
13246327 AATAAAATACATATTGATAGCTC-AGATACAATATTAGACATTTTCAAAGTACAAGTATCGCATT
1 AATAAAACACATATTGATAGCTCAAG-TACAACATT-GACATTTTCAAAGTACAAGTATCACATT
13246391 AAACATTATATGAAAGTA
64 AAACATTATATGAAAGTA
13246409 TAAATACCAA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
90 2 0.03
91 27 0.39
92 40 0.58
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (91 bp):
AATAAAACACATATTGATAGCTCAAGTACAACATTGACATTTTCAAAGTACAAGTATCACATTAA
ACATTATATGAAAGTACATGTACCAT
Found at i:13248614 original size:4 final size:4
Alignment explanation
Indices: 13248607--13248645 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
13248597 ATGAAAAATG
*
13248607 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
13248646 TTACTTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:13252217 original size:26 final size:26
Alignment explanation
Indices: 13252181--13252231 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
13252171 AAGAGTTAAG
13252181 TTAGTGTTTTTCATATATTATATTAC
1 TTAGTGTTTTTCATATATTATATTAC
*
13252207 TTAGTGTTTTTTATATATTATATTA
1 TTAGTGTTTTTCATATATTATATTA
13252232 TTCATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.61
Consensus pattern (26 bp):
TTAGTGTTTTTCATATATTATATTAC
Found at i:13253136 original size:17 final size:17
Alignment explanation
Indices: 13253114--13253174 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
13253104 AATCTTAGAG
13253114 TTCTAATTGTATACAGT
1 TTCTAATTGTATACAGT
* *
13253131 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGT
13253150 TTCTAATTGTATACAGCT
1 TTCTAATTGTATACAG-T
13253168 TT-TAATT
1 TTCTAATT
13253175 ATAGCCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 4 0.11
17 14 0.40
18 4 0.11
19 9 0.26
20 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TTCTAATTGTATACAGT
Found at i:13253147 original size:36 final size:36
Alignment explanation
Indices: 13253106--13253176 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
13253096 GATTATTTAA
13253106 TCTTAGAGTTCTAATTGTATACAG-TTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTT-TAATTATG
13253142 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
13253177 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 31 0.91
37 3 0.09
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTTTAATTATG
Found at i:13253155 original size:19 final size:18
Alignment explanation
Indices: 13253106--13253157 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
13253096 GATTATTTAA
13253106 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
13253123 T-ATACAGTTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
13253142 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
13253158 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:13258042 original size:17 final size:17
Alignment explanation
Indices: 13258020--13258080 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
13258010 AATCTTAGAG
13258020 TTCTAATTGTATACAGT
1 TTCTAATTGTATACAGT
* *
13258037 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGT
13258056 TTCTAATTGTATACAGCT
1 TTCTAATTGTATACAG-T
13258074 TT-TAATT
1 TTCTAATT
13258081 ATAGCCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 4 0.11
17 14 0.40
18 4 0.11
19 9 0.26
20 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TTCTAATTGTATACAGT
Found at i:13258053 original size:36 final size:36
Alignment explanation
Indices: 13258012--13258082 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
13258002 GATTATTTAA
13258012 TCTTAGAGTTCTAATTGTATACAG-TTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTT-TAATTATG
13258048 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
13258083 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 31 0.91
37 3 0.09
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTTTAATTATG
Found at i:13258061 original size:19 final size:18
Alignment explanation
Indices: 13258012--13258063 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
13258002 GATTATTTAA
13258012 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
13258029 T-ATACAGTTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
13258048 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
13258064 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:13259658 original size:3 final size:3
Alignment explanation
Indices: 13259652--13259718 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
13259642 ACCCTCTTCT
* **
13259652 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TTG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13259700 TCAA -AA -AA TAA TAA TAA TA
1 T-AA TAA TAA TAA TAA TAA TA
13259719 CATTTGGCAG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Done.