Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 28 of 193
Found at i:9021289 original size:14 final size:13
Alignment explanation
Indices: 9021263--9021287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9021253 GTCATGTCTT
9021263 TTTTTAATATTTA
1 TTTTTAATATTTA
9021276 TTTTTAATATTT
1 TTTTTAATATTT
9021288 TACAATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:9022193 original size:13 final size:14
Alignment explanation
Indices: 9022161--9022194 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9022151 TATTATATGG
*
9022161 TCAATTTTTTGAGT
1 TCAATTTTTCGAGT
9022175 TCAATTTTTCGAGT
1 TCAATTTTTCGAGT
9022189 T-AATTT
1 TCAATTT
9022195 AAATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (14 bp):
TCAATTTTTCGAGT
Found at i:9023272 original size:17 final size:18
Alignment explanation
Indices: 9023250--9023283 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
9023240 TATTTTTTTG
9023250 TATTTAAAA-AATAAAAT
1 TATTTAAAATAATAAAAT
9023267 TATTTAAAATAATAAAA
1 TATTTAAAATAATAAAA
9023284 CACATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATTTAAAATAATAAAAT
Found at i:9025908 original size:61 final size:61
Alignment explanation
Indices: 9025799--9025945 Score: 141
Period size: 61 Copynumber: 2.4 Consensus size: 61
9025789 ATTCTATTAG
* * * * * * ** * * *
9025799 TTTAATCCTAAATATAATAAATTTAATAAATTTAGCCCTCAATGTTTATAAAATTTGTCAT
1 TTTAGTCCTAACTCTAAAAAATTAAATAAACTTAGCCCTCAACATTTATAAAATCTATCAA
* * * * *
9025860 TTTAGTTCTTATTCTAAAAAATTAAATAAACTTGGCCCTCAACATTTATGAAATCTATCAA
1 TTTAGTCCTAACTCTAAAAAATTAAATAAACTTAGCCCTCAACATTTATAAAATCTATCAA
*
9025921 TTTAGTCCTAACTCTAAAAATTTAA
1 TTTAGTCCTAACTCTAAAAAATTAA
9025946 TTATATTTTA
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (61 bp):
TTTAGTCCTAACTCTAAAAAATTAAATAAACTTAGCCCTCAACATTTATAAAATCTATCAA
Found at i:9029343 original size:16 final size:15
Alignment explanation
Indices: 9029310--9029357 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
9029300 ATATTGATAT
*
9029310 ATTTTATTTTTCAATA
1 ATTTTATTATT-AATA
9029326 ATCTTTATTATTAATA
1 AT-TTTATTATTAATA
*
9029342 ATTTTTTGTATTAATA
1 ATTTTAT-TATTAATA
9029358 TTTGATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 16 0.57
17 8 0.29
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTTTATTATTAATA
Found at i:9029692 original size:60 final size:61
Alignment explanation
Indices: 9029626--9029743 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 61
9029616 AAATTTCAAC
* * *
9029626 ACCAAATCGAATCTAAAAAAAGCTTAGGTACCAAATT-AGAAAAAAATGTCAAGTTCAAAT
1 ACCAAATCGAATCCAAAAAAAGCTTAGGTACCAAATTAAGAAAAAAATATCAAATTCAAAT
* * * *
9029686 ACCAAATTGGATCCAAAAAAAGTTTAGGTACTAAATTAAGAAAAAAATATCAAATTCA
1 ACCAAATCGAATCCAAAAAAAGCTTAGGTACCAAATTAAGAAAAAAATATCAAATTCA
9029744 GATATTAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 32 0.64
61 18 0.36
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.23
Consensus pattern (61 bp):
ACCAAATCGAATCCAAAAAAAGCTTAGGTACCAAATTAAGAAAAAAATATCAAATTCAAAT
Found at i:9029764 original size:60 final size:60
Alignment explanation
Indices: 9029626--9029770 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
9029616 AAATTTCAAC
** * * * *
9029626 ACCAAATCGAATCTAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAAT
1 ACCAAATTAAATCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAATTCAAAT
** * * *
9029686 ACCAAATTGGATCCAAAAAAAGTTTAGGTACTAAATTAAGAAAAAAATATCAAATTCAGAT
1 ACCAAATTAAATCAAAAAAAAGTTTAGGTACCAAATT-AGAAAAAAATATCAAATTCAAAT
**
9029747 ATTAAATTAAAT-AAAAAAAA-TTTA
1 ACCAAATTAAATCAAAAAAAAGTTTA
9029771 AATATCAATA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 4 0.06
60 39 0.55
61 28 0.39
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.25
Consensus pattern (60 bp):
ACCAAATTAAATCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAATTCAAAT
Found at i:9029765 original size:61 final size:60
Alignment explanation
Indices: 9029640--9029766 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 60
9029630 AATCGAATCT
* * ** **
9029640 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAAATACCAAATTGGATCC
1 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATATCAAATTCAAATACCAAATTAAATAA
* * * **
9029700 AAAAAAAGTTTAGGTACTAAATTAAGAAAAAAATATCAAATTCAGATATTAAATTAAATAA
1 AAAAAAAGCTTAGGTACCAAATT-AGAAAAAAATATCAAATTCAAATACCAAATTAAATAA
9029761 AAAAAA
1 AAAAAA
9029767 TTTAAATATC
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
60 21 0.38
61 34 0.62
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (60 bp):
AAAAAAAGCTTAGGTACCAAATTAGAAAAAAATATCAAATTCAAATACCAAATTAAATAA
Found at i:9031556 original size:57 final size:54
Alignment explanation
Indices: 9031492--9031607 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 54
9031482 GAAGAAGAGG
*
9031492 AAGAAGAAGAAAGGTTATTAGATATCTTAAACAAATTAATACCTAAATTAGAATAAA
1 AAGAAGAAGAAAGGTTATTAGAGATCTTAAACAAATTAATACCTAAA-TA-AA-AAA
* *
9031549 AAGAAGAAGAAATGTTGTTAGAGATCTTAAACAAATTAATACCTAAATAAAAAA
1 AAGAAGAAGAAAGGTTATTAGAGATCTTAAACAAATTAATACCTAAATAAAAAA
9031603 AAGAA
1 AAGAA
9031608 ACATTTAGTA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 8 0.14
55 2 0.04
56 2 0.04
57 44 0.79
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (54 bp):
AAGAAGAAGAAAGGTTATTAGAGATCTTAAACAAATTAATACCTAAATAAAAAA
Found at i:9034201 original size:17 final size:18
Alignment explanation
Indices: 9034165--9034202 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9034155 TTTTATTTTC
*
9034165 AAAACTCTATTAAGAACT
1 AAAACTATATTAAGAACT
*
9034183 AAAACTATATTGA-AACT
1 AAAACTATATTAAGAACT
9034200 AAA
1 AAA
9034203 TTTTCAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAACTATATTAAGAACT
Found at i:9034301 original size:19 final size:19
Alignment explanation
Indices: 9034259--9034301 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
9034249 AGAACTAAAA
* *
9034259 CTAAATTGAAACTAAATTT
1 CTAAACTGAAACTAAACTT
* *
9034278 TTAAACTGAAATTAAACTT
1 CTAAACTGAAACTAAACTT
9034297 CTAAA
1 CTAAA
9034302 ATCTACTCTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (19 bp):
CTAAACTGAAACTAAACTT
Found at i:9037867 original size:20 final size:18
Alignment explanation
Indices: 9037817--9037868 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
9037807 TATTAAGATA
9037817 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
9037834 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
9037854 AATATTAAATTAATA
1 AATATTAAATTAATA
9037869 AAAACAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:9038593 original size:17 final size:17
Alignment explanation
Indices: 9038571--9038603 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9038561 ACTTTGGCTC
9038571 TTAAGATTTTTTTGCGT
1 TTAAGATTTTTTTGCGT
9038588 TTAAGATTTTTTTGCG
1 TTAAGATTTTTTTGCG
9038604 CTCACTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (17 bp):
TTAAGATTTTTTTGCGT
Found at i:9038809 original size:20 final size:20
Alignment explanation
Indices: 9038781--9038897 Score: 82
Period size: 20 Copynumber: 5.9 Consensus size: 20
9038771 CCACGTCAGC
*
9038781 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
9038801 AAATTATTTTTAAAA-TA-TA
1 AAATTA-TTTTAAAATTATTA
*
9038820 AAACTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
*
9038840 AAATTAATTTAAAATTATT-
1 AAATTATTTTAAAATTATTA
*** * *
9038859 TTTTTAAATATAAAATTATTA
1 AAATT-ATTTTAAAATTATTA
*
9038880 CAATTATTTTAAAATTAT
1 AAATTATTTTAAAATTAT
9038898 AATCATCATC
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
16 6 0.08
17 2 0.03
19 9 0.12
20 40 0.53
21 10 0.13
22 9 0.12
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:9038827 original size:19 final size:21
Alignment explanation
Indices: 9038787--9038827 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
9038777 CAGCAAATGA
*
9038787 TTTTAAAATTATTAAAATTAT
1 TTTTAAAATTATTAAAACTAT
9038808 TTTTAAAA-TA-TAAAACTAT
1 TTTTAAAATTATTAAAACTAT
9038827 T
1 T
9038828 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAATTATTAAAACTAT
Found at i:9038830 original size:28 final size:27
Alignment explanation
Indices: 9038790--9038899 Score: 122
Period size: 28 Copynumber: 4.1 Consensus size: 27
9038780 CAAATGATTT
9038790 TAAAATTATTAAAATTATTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTAAAATA
*
9038818 TAAAACTATTAAAATTATTTTAAAAT-
1 TAAAATTATTAAAATTATTTTAAAATA
*
9038844 T--AA-T-TTAAAATTATTTTTTTAAATA
1 TAAAATTATTAAAATTA--TTTTAAAATA
*
9038869 TAAAATTATTACAATTATTTTAAAATTA
1 TAAAATTATTAAAATTATTTTAAAA-TA
9038897 TAA
1 TAA
9038900 TCATCATCCC
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
22 9 0.13
23 1 0.01
24 10 0.14
25 1 0.01
26 1 0.01
27 18 0.26
28 22 0.31
29 8 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATTATTAAAATTATTTTAAAATA
Found at i:9038852 original size:22 final size:22
Alignment explanation
Indices: 9038781--9038860 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
9038771 CCACGTCAGC
*
9038781 AAATGATTTTAAAATT-A-TTA
1 AAATTATTTTAAAATTAATTTA
9038801 AAATTATTTTTAAAATATAAAACTATTA
1 AAATTA-TTTTAAAAT-T--AA-T-TTA
9038829 AAATTATTTTAAAATTAATTTA
1 AAATTATTTTAAAATTAATTTA
9038851 AAATTATTTT
1 AAATTATTTT
9038861 TTTAAATATA
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.10
21 9 0.18
22 14 0.27
23 1 0.02
24 2 0.04
25 1 0.02
26 1 0.02
27 9 0.18
28 9 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
AAATTATTTTAAAATTAATTTA
Found at i:9038872 original size:51 final size:49
Alignment explanation
Indices: 9038781--9038896 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 49
9038771 CCACGTCAGC
*
9038781 AAATGATTTTAAAATT-ATTAAAATTATTTTTAAAATATAAAACTATTA
1 AAATTATTTTAAAATTAATTAAAATTATTTTTAAAATATAAAACTATTA
* *
9038829 AAATTATTTTAAAATTAATTTAAAATTATTTTTTTAAATATAAAATTATTA
1 AAATTATTTTAAAATTAA-TTAAAATTA-TTTTTAAAATATAAAACTATTA
*
9038880 CAATTATTTTAAAATTA
1 AAATTATTTTAAAATTA
9038897 TAATCATCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
48 15 0.25
49 1 0.02
50 9 0.15
51 36 0.59
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (49 bp):
AAATTATTTTAAAATTAATTAAAATTATTTTTAAAATATAAAACTATTA
Found at i:9038897 original size:11 final size:11
Alignment explanation
Indices: 9038781--9038860 Score: 68
Period size: 11 Copynumber: 7.9 Consensus size: 11
9038771 CCACGTCAGC
*
9038781 AAATGATTTTA
1 AAATTATTTTA
9038792 AAATTA--TTA
1 AAATTATTTTA
9038801 AAATTATTTTTA
1 AAATTA-TTTTA
9038813 AAA-TA---TA
1 AAATTATTTTA
*
9038820 AAACTA--TTA
1 AAATTATTTTA
9038829 AAATTATTTTA
1 AAATTATTTTA
*
9038840 AAATTAATTTA
1 AAATTATTTTA
9038851 AAATTATTTT
1 AAATTATTTT
9038861 TTTAAATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
7 5 0.09
8 2 0.03
9 16 0.28
11 29 0.50
12 6 0.10
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:9039777 original size:17 final size:17
Alignment explanation
Indices: 9039757--9039808 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
9039747 GAAGATGACA
9039757 AAATGGGGAAGAAAATG
1 AAATGGGGAAGAAAATG
*
9039774 AAATTGGGAAG-AAAT-
1 AAATGGGGAAGAAAATG
*
9039789 -AATGGGGAAGAAGATG
1 AAATGGGGAAGAAAATG
9039805 AAAT
1 AAAT
9039809 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.31
15 3 0.10
16 4 0.14
17 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (17 bp):
AAATGGGGAAGAAAATG
Found at i:9039798 original size:14 final size:15
Alignment explanation
Indices: 9039757--9039800 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
9039747 GAAGATGACA
9039757 AAATGGGGAAGAAAAT
1 AAATGGGGAAG-AAAT
*
9039773 GAAATTGGGAAGAAAT
1 -AAATGGGGAAGAAAT
9039789 -AATGGGGAAGAA
1 AAATGGGGAAGAA
9039801 GATGAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.44
16 4 0.16
17 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (15 bp):
AAATGGGGAAGAAAT
Found at i:9039862 original size:18 final size:17
Alignment explanation
Indices: 9039857--9039920 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 17
9039847 TATTTAAAAA
*
9039857 ATATTTTAAAATATTTT
1 ATATTTAAAAATATTTT
9039874 ATATTTAAAAA-A---T
1 ATATTTAAAAATATTTT
9039887 AT-TTT-AAAATATTTT
1 ATATTTAAAAATATTTT
9039902 ATATTTAAAAAATATTTT
1 ATATTT-AAAAATATTTT
9039920 A
1 A
9039921 AAATATTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 3 0.08
15 3 0.08
16 4 0.10
17 10 0.26
18 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTAAAAATATTTT
Found at i:9039869 original size:10 final size:10
Alignment explanation
Indices: 9039854--9039930 Score: 76
Period size: 10 Copynumber: 8.1 Consensus size: 10
9039844 TTATATTTAA
9039854 AAAATATTTT
1 AAAATATTTT
9039864 AAAATATTTT
1 AAAATATTTT
*
9039874 ---ATATTTAA
1 AAAATATTT-T
9039882 AAAATATTTT
1 AAAATATTTT
9039892 AAAATATTTT
1 AAAATATTTT
*
9039902 ---ATATTTAA
1 AAAATATTT-T
9039910 AAAATATTTT
1 AAAATATTTT
9039920 AAAATATTTT
1 AAAATATTTT
9039930 A
1 A
9039931 TATTTTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
7 12 0.22
10 31 0.56
11 12 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AAAATATTTT
Found at i:9039885 original size:29 final size:28
Alignment explanation
Indices: 9039832--9039960 Score: 199
Period size: 28 Copynumber: 4.6 Consensus size: 28
9039822 TTATTTAATA
*
9039832 ATTTTAATA-ATTTTATATTTAAAAAAT
1 ATTTTAAAATATTTTATATTTAAAAAAT
9039859 ATTTTAAAATATTTTATATTTAAAAAAT
1 ATTTTAAAATATTTTATATTTAAAAAAT
9039887 ATTTTAAAATATTTTATATTTAAAAAAT
1 ATTTTAAAATATTTTATATTTAAAAAAT
9039915 ATTTTAAAATATTTTATATTTTAAAAAAAT
1 ATTTTAAAATATTTTATA-TTT-AAAAAAT
*
9039945 AATTTTAATA-ATTTTA
1 -ATTTTAAAATATTTTA
9039961 AAATCATTTG
Statistics
Matches: 96, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
27 8 0.08
28 64 0.67
29 3 0.03
30 13 0.14
31 8 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTTAAAATATTTTATATTTAAAAAAT
Found at i:9039908 original size:56 final size:58
Alignment explanation
Indices: 9039828--9039960 Score: 227
Period size: 56 Copynumber: 2.3 Consensus size: 58
9039818 AAAATTATTT
9039828 AATAATTTTAATAATTTTATATTTAAAAAATATTTTAAAATATTTTATA-TTT-AAAA
1 AATAATTTTAATAATTTTATATTTAAAAAATATTTTAAAATATTTTATATTTTAAAAA
*
9039884 AAT-ATTTTAAAATATTTTATATTTAAAAAATATTTTAAAATATTTTATATTTTAAAAA
1 AATAATTTTAATA-ATTTTATATTTAAAAAATATTTTAAAATATTTTATATTTTAAAAA
9039942 AATAATTTTAATAATTTTA
1 AATAATTTTAATAATTTTA
9039961 AAATCATTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
55 8 0.11
56 39 0.55
57 3 0.04
58 13 0.18
59 8 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (58 bp):
AATAATTTTAATAATTTTATATTTAAAAAATATTTTAAAATATTTTATATTTTAAAAA
Found at i:9039951 original size:21 final size:22
Alignment explanation
Indices: 9039920--9039963 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
9039910 AAAATATTTT
9039920 AAAATATTTT-AT-ATTTTAAA
1 AAAATATTTTAATAATTTTAAA
9039940 AAAATAATTTTAATAATTTTAAA
1 AAAAT-ATTTTAATAATTTTAAA
9039963 A
1 A
9039964 TCATTTGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 5 0.24
22 2 0.10
23 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATATTTTAATAATTTTAAA
Found at i:9039969 original size:20 final size:17
Alignment explanation
Indices: 9039857--9039940 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 17
9039847 TATTTAAAAA
9039857 ATATTTTAAAATATTTT
1 ATATTTTAAAATATTTT
9039874 ATA-TTTAAAA-A----
1 ATATTTTAAAATATTTT
9039885 ATATTTTAAAATATTTT
1 ATATTTTAAAATATTTT
9039902 ATA-TTTAAAA-A----
1 ATATTTTAAAATATTTT
9039913 ATATTTTAAAATATTTT
1 ATATTTTAAAATATTTT
9039930 ATATTTTAAAA
1 ATATTTTAAAA
9039941 AAATAATTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
11 6 0.11
12 14 0.25
13 2 0.04
15 2 0.04
16 14 0.25
17 17 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTTTAAAATATTTT
Found at i:9041526 original size:35 final size:35
Alignment explanation
Indices: 9041465--9041531 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
9041455 TAAAAAAATA
9041465 TTTATTTACTCAAATAATATACAAAAATTATTTAT
1 TTTATTTACTCAAATAATATACAAAAATTATTTAT
*
9041500 TTTATTTGACT-AAAGTAATAT-TAAAAATTATT
1 TTTATTT-ACTCAAA-TAATATACAAAAATTATT
9041532 ACTTTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
35 20 0.69
36 9 0.31
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
TTTATTTACTCAAATAATATACAAAAATTATTTAT
Found at i:9041945 original size:21 final size:21
Alignment explanation
Indices: 9041921--9041962 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9041911 ATTTATTTTA
9041921 GTATGATATATT-TTTAAATTT
1 GTATGATAT-TTATTTAAATTT
**
9041942 GTATTTTATTTATTTAAATTT
1 GTATGATATTTATTTAAATTT
9041963 TATTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
GTATGATATTTATTTAAATTT
Found at i:9042403 original size:24 final size:24
Alignment explanation
Indices: 9042336--9042406 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
9042326 TGTGGAACTT
*
9042336 GTAGAAAATAAAGATCCAAATCCA
1 GTAGAAAATAAAGATCCAACTCCA
*
9042360 GTAGAAAATGAAA-ATCCAACTCTA
1 GTAGAAAAT-AAAGATCCAACTCCA
9042384 GTAGAAAATAAAGATCCAACTCC
1 GTAGAAAATAAAGATCCAACTCC
9042407 GTGTATGGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
23 3 0.07
24 36 0.86
25 3 0.07
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (24 bp):
GTAGAAAATAAAGATCCAACTCCA
Found at i:9044911 original size:28 final size:28
Alignment explanation
Indices: 9044870--9044935 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
9044860 ATTGAGGCTA
*
9044870 ATGATTTTTAATTTAGGGCTAAAGGTTT
1 ATGATTTATAATTTAGGGCTAAAGGTTT
* * * *
9044898 ATGATTTATGATTTAGGGTTTAGGGTTT
1 ATGATTTATAATTTAGGGCTAAAGGTTT
*
9044926 AAGATTTATA
1 ATGATTTATA
9044936 GGTATGAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (28 bp):
ATGATTTATAATTTAGGGCTAAAGGTTT
Found at i:9044917 original size:21 final size:21
Alignment explanation
Indices: 9044893--9044933 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9044883 TAGGGCTAAA
* *
9044893 GGTTTATGATTTATGATTTAG
1 GGTTTAGGATTTAAGATTTAG
*
9044914 GGTTTAGGGTTTAAGATTTA
1 GGTTTAGGATTTAAGATTTA
9044934 TAGGTATGAA
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:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (21 bp):
GGTTTAGGATTTAAGATTTAG
Found at i:9045322 original size:6 final size:6
Alignment explanation
Indices: 9045287--9045324 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
9045277 CATCCAATGC
* *
9045287 CTCTTC CTCTTC CTCTTG CTCTTG CTCTTG CTCTTG CT
1 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CT
9045325 TTGGCTCTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.11, T:0.50
Consensus pattern (6 bp):
CTCTTG
Found at i:9047177 original size:16 final size:16
Alignment explanation
Indices: 9047156--9047204 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
9047146 GGATGGAGAT
*
9047156 ATTATTTTGGTAATTA
1 ATTATTTTGATAATTA
*
9047172 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
9047187 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
9047202 ATT
1 ATT
9047205 TAGAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:9047332 original size:22 final size:23
Alignment explanation
Indices: 9047299--9047351 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
9047289 TTTAAATAAA
9047299 AATTATTTTAAAT-T-TTATATT
1 AATTATTTTAAATCTATTATATT
*
9047320 AATTCTTTCTAAATCTATTATA-T
1 AATTATTT-TAAATCTATTATATT
*
9047343 AACTATTTT
1 AATTATTTT
9047352 TACCCGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 7 0.27
22 6 0.23
23 8 0.31
24 5 0.19
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTATTTTAAATCTATTATATT
Found at i:9047890 original size:20 final size:21
Alignment explanation
Indices: 9047854--9047906 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
9047844 AAATACATTA
*
9047854 CCTTTCTCTCTTTCTCCTTC-T
1 CCTTTCTTTC-TTCTCCTTCTT
9047875 CCTTTCTTTCTTCTCCTTCTT
1 CCTTTCTTTCTTCTCCTTCTT
9047896 CC-TTCTTTCTT
1 CCTTTCTTTCTT
9047907 TTCTTTAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (21 bp):
CCTTTCTTTCTTCTCCTTCTT
Found at i:9052249 original size:4 final size:4
Alignment explanation
Indices: 9052237--9052268 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
9052227 AACTCAGAGA
9052237 GAGG G-GG GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
9052269 GAGAGAGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:9073296 original size:90 final size:87
Alignment explanation
Indices: 9073130--9073313 Score: 264
Period size: 90 Copynumber: 2.1 Consensus size: 87
9073120 ATATTTATGT
*
9073130 GTTTAAAATTCATTTCACTCGCAATTTTTTTTTTCATTTTAGTACCATACATATTTCATGTGCTA
1 GTTTAAAATTCATTTCACTCACAATTTTTTTTTTCATTTTAGTACC--ACATATTTCATGTGCTA
9073195 TTATTAATTAGTTTCAAACCATAC
64 TTATTAATTAGTTTCAAACCATAC
9073219 GTTTAAAATTCATTTCACTCACAATTTAATTTTTTTTTTCATTTTAGTA-C-CATATTTCATGTG
1 GTTTAAAATTCATTTCACTCAC-----AATTTTTTTTTTCATTTTAGTACCACATATTTCATGTG
* *
9073282 TTATTATTACTTAGTTTCAAACCATAC
61 CTATTATTAATTAGTTTCAAACCATAC
9073309 GTTTA
1 GTTTA
9073314 TTTATTTATT
Statistics
Matches: 87, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
89 21 0.24
90 43 0.49
93 1 0.01
94 22 0.25
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (87 bp):
GTTTAAAATTCATTTCACTCACAATTTTTTTTTTCATTTTAGTACCACATATTTCATGTGCTATT
ATTAATTAGTTTCAAACCATAC
Found at i:9077916 original size:2 final size:2
Alignment explanation
Indices: 9077909--9077957 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
9077899 GGCATCTGAC
*
9077909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9077951 AT TT AT A
1 AT AT AT A
9077958 CACACGAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9083608 original size:29 final size:28
Alignment explanation
Indices: 9083575--9083631 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
9083565 ATTTTTTTCG
*
9083575 AAATAAATATCTTAAATTAATTTCTAATT
1 AAATAAATATCTCAAATTAATTT-TAATT
* * *
9083604 AAATAATTTTCTCAACTTAATTTTAATT
1 AAATAAATATCTCAAATTAATTTTAATT
9083632 CTGGTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATAAATATCTCAAATTAATTTTAATT
Found at i:9084909 original size:22 final size:21
Alignment explanation
Indices: 9084881--9084923 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9084871 CAAAAAATGA
9084881 CAAAAAAGTATCGATACATTTT
1 CAAAAAA-TATCGATACATTTT
* *
9084903 CAAAAAATATTGATACCTTTT
1 CAAAAAATATCGATACATTTT
9084924 ATCAGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (21 bp):
CAAAAAATATCGATACATTTT
Found at i:9085386 original size:36 final size:38
Alignment explanation
Indices: 9085346--9085417 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
9085336 TTGTATCTCT
*
9085346 TTAAGAGG-GTTG-AATCTTAA-ACTTTGGGTAGAAACC
1 TTAAG-GGAGTTGCAATCTTAAGACTTTAGGTAGAAACC
*
9085382 TTAAGGGAGTTGCAATCTTAAGATTTTAGGTAGAAA
1 TTAAGGGAGTTGCAATCTTAAGACTTTAGGTAGAAA
9085418 TCTGAAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.06
36 9 0.29
37 8 0.26
38 12 0.39
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (38 bp):
TTAAGGGAGTTGCAATCTTAAGACTTTAGGTAGAAACC
Found at i:9086225 original size:30 final size:31
Alignment explanation
Indices: 9086182--9086241 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
9086172 TTTAGTACTT
9086182 GAACTTCACATTTTTT-TTAATTTGATACCC
1 GAACTTCACATTTTTTCTTAATTTGATACCC
* * *
9086212 GAACTTGATATTTTTTCTTAATTTGGTACC
1 GAACTTCACATTTTTTCTTAATTTGATACC
9086242 TAAGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (31 bp):
GAACTTCACATTTTTTCTTAATTTGATACCC
Found at i:9086531 original size:31 final size:31
Alignment explanation
Indices: 9086496--9086556 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
9086486 CCAACTTATA
9086496 AAAAAAT-ATCAAGTTT-AGGTACCAAATTAGG
1 AAAAAATGA-CAAGTTTGA-GTACCAAATTAGG
*
9086527 AAAAAGTGACAAGTTTGAGTACCAAATTAG
1 AAAAAATGACAAGTTTGAGTACCAAATTAG
9086557 ATAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.25
Consensus pattern (31 bp):
AAAAAATGACAAGTTTGAGTACCAAATTAGG
Found at i:9086589 original size:90 final size:90
Alignment explanation
Indices: 9086420--9086596 Score: 223
Period size: 90 Copynumber: 2.0 Consensus size: 90
9086410 TGAAAAAAGA
* * ** *
9086420 TTAGGTACCAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACTCCAAAAAATTTAAGC
1 TTAGGTACCAAATTAAGAAAAAGAGACAAGTTCAGGTACCAAATTAGACTAAAAAAAATTGAAGC
* *
9086485 ACCAACTTATAAAAAAATATCAAGT
66 ACCAAATTAAAAAAAAATATCAAGT
* * *
9086510 TTAGGTACCAAATTAGGAAAAAGTGACAAGTT-TGAGTACCAAATTAGA-TAAAAAAAATTGAAG
1 TTAGGTACCAAATTAAGAAAAAGAGACAAGTTCAG-GTACCAAATTAGACTAAAAAAAATTGAAG
* *
9086573 TACCAAATTAAAAAAAAATGTCAA
65 CACCAAATTAAAAAAAAATATCAA
9086597 ATTCAGATAT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
89 33 0.45
90 41 0.55
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (90 bp):
TTAGGTACCAAATTAAGAAAAAGAGACAAGTTCAGGTACCAAATTAGACTAAAAAAAATTGAAGC
ACCAAATTAAAAAAAAATATCAAGT
Found at i:9089970 original size:3 final size:3
Alignment explanation
Indices: 9089962--9089992 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
9089952 GATTCAGCTC
9089962 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9089993 AGAATCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9112062 original size:16 final size:16
Alignment explanation
Indices: 9112039--9112076 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9112029 AATTTTTTGA
*
9112039 AAAATATTTAATATAT
1 AAAATATTAAATATAT
*
9112055 ACAATATTAAATATAT
1 AAAATATTAAATATAT
9112071 AAAATA
1 AAAATA
9112077 AATTAGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTAAATATAT
Found at i:9117122 original size:31 final size:31
Alignment explanation
Indices: 9117084--9117146 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
9117074 TTATATACTT
9117084 AGTTTACTAATTAATAATATTAGTTAAACTA
1 AGTTTACTAATTAATAATATTAGTTAAACTA
9117115 AGTTTACTAATTAATAATATTAGTTAAACTA
1 AGTTTACTAATTAATAATATTAGTTAAACTA
9117146 A
1 A
9117147 TTAAACACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (31 bp):
AGTTTACTAATTAATAATATTAGTTAAACTA
Found at i:9117641 original size:3 final size:3
Alignment explanation
Indices: 9117633--9117713 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
9117623 GTTAATGAAT
9117633 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9117681 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9117714 AACATAAGAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9123551 original size:2 final size:2
Alignment explanation
Indices: 9123544--9123579 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9123534 CAAATAAATC
9123544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9123580 TATTCTAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9132182 original size:21 final size:22
Alignment explanation
Indices: 9132156--9132208 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
9132146 ATATAATTCA
9132156 ATTTGAATTTAA-TTTCAAAGT
1 ATTTGAATTTAATTTTCAAAGT
* *
9132177 ATTTGAATATAATTTTTAAAGT
1 ATTTGAATTTAATTTTCAAAGT
*
9132199 AATTGAATTT
1 ATTTGAATTT
9132209 TCATTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTGAATTTAATTTTCAAAGT
Found at i:9133088 original size:4 final size:4
Alignment explanation
Indices: 9133079--9133105 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9133069 CGCACATCTC
9133079 CCTT CCTT CCTT CCTT CCTT CCTT CCT
1 CCTT CCTT CCTT CCTT CCTT CCTT CCT
9133106 CATTTCTTGA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (4 bp):
CCTT
Found at i:9138936 original size:23 final size:22
Alignment explanation
Indices: 9138909--9138976 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
9138899 ATTCTAACTA
9138909 AAAATAATATATTAAATAATTG
1 AAAATAATATATTAAATAATTG
*
9138931 CAAAATCATATGA-TAAAT-A--G
1 -AAAATAATAT-ATTAAATAATTG
9138951 -AAATAATATATTAAATAATTG
1 AAAATAATATATTAAATAATTG
9138972 AAAAT
1 AAAAT
9138977 TGGGTCGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
17 1 0.03
18 13 0.35
19 1 0.03
20 1 0.03
21 1 0.03
22 5 0.14
23 14 0.38
24 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (22 bp):
AAAATAATATATTAAATAATTG
Found at i:9144661 original size:93 final size:91
Alignment explanation
Indices: 9144515--9144722 Score: 201
Period size: 93 Copynumber: 2.3 Consensus size: 91
9144505 CTCAAACTTA
* *** **
9144515 AAAAAAAAATCAATTAAGCCCCT-CTTTTTTTTTTGCACTCAATTGAGCACTTAAGTTTTCAAAA
1 AAAAAAAAAGCAATTAAGCCCCTAC--TTTTTTCCCCACTCAATTGAGCACTTAAACTTTCAAAA
* * *
9144579 TGCATAAAAAAAAAGGCCTCAAACTTCTTC
64 TACAT-AAAAAAAA-CCCTCAAAATTCTTC
**
9144609 AAAAAAAAAGCAATTAAGCCCCTACTTTTTTCCCCACTCAATT-AGGTTCTTAAACTTTCAAAAT
1 AAAAAAAAAGCAATTAAGCCCCTACTTTTTTCCCCACTCAATTGA-GCACTTAAACTTTCAAAAT
* * *
9144673 ACATCAAAAAGACCCTCAAAATTTTTC
65 ACATAAAAAAAACCCTCAAAATTCTTC
*
9144700 ---AAAAAAGCAATTAAGCCCTTACT
1 AAAAAAAAAGCAATTAAGCCCCTACT
9144723 CTTATTAAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
88 22 0.23
91 12 0.12
92 7 0.07
93 33 0.34
94 22 0.23
95 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (91 bp):
AAAAAAAAAGCAATTAAGCCCCTACTTTTTTCCCCACTCAATTGAGCACTTAAACTTTCAAAATA
CATAAAAAAAACCCTCAAAATTCTTC
Found at i:9144828 original size:21 final size:20
Alignment explanation
Indices: 9144804--9144868 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 20
9144794 TAAAAATTTC
9144804 AAAATTTTTTATAAAAATCGT
1 AAAA-TTTTTATAAAAATCGT
9144825 AAAAAATTTTTA-AAAAATCGT
1 --AAAATTTTTATAAAAATCGT
* *
9144846 -AAATTTTTATAGAAATCAT
1 AAAATTTTTATAAAAATCGT
9144865 AAAA
1 AAAA
9144869 AAATTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.24
19 7 0.18
20 3 0.08
21 9 0.24
22 6 0.16
23 4 0.11
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAATTTTTATAAAAATCGT
Found at i:9145149 original size:19 final size:19
Alignment explanation
Indices: 9145127--9145203 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
9145117 TTCTTTCAAC
9145127 TTTATAAAATTTTATAATT
1 TTTATAAAATTTTATAATT
9145146 TTTAT---ATTTCTAT-ATAT
1 TTTATAAAATTT-TATAAT-T
**
9145163 TTTATAATTTTTTA-AGATT
1 TTTATAAAATTTTATA-ATT
* *
9145182 ATTATAAAATTTTACAATT
1 TTTATAAAATTTTATAATT
9145201 TTT
1 TTT
9145204 TTATATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 16
0.68 0.08 0.24
Matches are distributed among these distances:
16 6 0.13
17 9 0.20
19 24 0.53
20 6 0.13
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTATAAAATTTTATAATT
Found at i:9145211 original size:57 final size:57
Alignment explanation
Indices: 9145088--9145203 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 57
9145078 TTTTAACGAA
* * *
9145088 TTTTATATTTCTTTATATTTTGTATAATTTTCTTTCAACTTTATAAAATTTTATAAT
1 TTTTATATTTCTATATATTTTGTATAATTTTCTTTAAACTTTATAAAATTTTACAAT
*
9145145 TTTTATATTTCTATATA-TTT-TATAA-TTT-TTTAAGATTATTATAAAATTTTACAAT
1 TTTTATATTTCTATATATTTTGTATAATTTTCTTTAA-ACT-TTATAAAATTTTACAAT
9145200 TTTT
1 TTTT
9145204 TTATATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
53 4 0.08
54 5 0.09
55 25 0.47
56 3 0.06
57 16 0.30
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (57 bp):
TTTTATATTTCTATATATTTTGTATAATTTTCTTTAAACTTTATAAAATTTTACAAT
Found at i:9145250 original size:18 final size:16
Alignment explanation
Indices: 9145221--9145254 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
9145211 TTTTTGTGCG
9145221 ATTTTTATATTTTTTA
1 ATTTTTATATTTTTTA
9145237 ATTTTTAATAATTTTTTA
1 ATTTTT-AT-ATTTTTTA
9145255 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTATATTTTTTA
Found at i:9145440 original size:90 final size:88
Alignment explanation
Indices: 9145312--9145537 Score: 276
Period size: 90 Copynumber: 2.5 Consensus size: 88
9145302 TATTTTTAAT
* *
9145312 AAAAGTAGGGGTTTAATTACTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATACATTTTAAAAGTT
1 AAAAGTAGGGGCTTAATTACTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTT
* * *
9145377 CAAGTACTCAATTGAGTGCAAAA
66 CAAATACCCAAATGAGTGCAAAA
** * * *
9145400 AAAAGTAGGGGCTTAATTGTTTATTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAG
1 AAAAGTAGGGGCTTAATT-ACT-TTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAG
9145465 TTCAAATACCCAAATGAGTGCAAAAAA
64 TTCAAATACCCAAATGAGTGC--AAAA
* * * *
9145492 AAAAG-AGGGACTTAAGTGCTTTTTTGAGAAAGTTTGAGGG-CTTTTT
1 AAAAGTAGGGGCTTAATTACTTTTTTGAAAAAGTTTGAGGGCCTTTTT
9145538 ACACTCTTAA
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
88 23 0.19
89 19 0.16
90 57 0.48
91 10 0.08
92 9 0.08
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (88 bp):
AAAAGTAGGGGCTTAATTACTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACATTTTAAAAGTT
CAAATACCCAAATGAGTGCAAAA
Found at i:9150031 original size:21 final size:22
Alignment explanation
Indices: 9149998--9150045 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
9149988 GAATTTTAGA
9149998 TTTTTAGAAAATTTTATGAATT
1 TTTTTAGAAAATTTTATGAATT
* **
9150020 TTTTTA-AGAATTTTATGGTTT
1 TTTTTAGAAAATTTTATGAATT
9150041 TTTTT
1 TTTTT
9150046 TTCAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.62
Consensus pattern (22 bp):
TTTTTAGAAAATTTTATGAATT
Found at i:9150063 original size:24 final size:23
Alignment explanation
Indices: 9150018--9150068 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
9150008 ATTTTATGAA
*
9150018 TTTTTTTAAGAATTTTATGGTTT
1 TTTTTTTAAGAATTTTAGGGTTT
*
9150041 TTTTTTTCAA-AATTTTAGGGGTT
1 TTTTTTT-AAGAATTTTAGGGTTT
9150064 TTTTT
1 TTTTT
9150069 CGTTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.65
Consensus pattern (23 bp):
TTTTTTTAAGAATTTTAGGGTTT
Found at i:9151427 original size:28 final size:28
Alignment explanation
Indices: 9151387--9151442 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
9151377 TAGGATTGCA
*
9151387 TGCAACTCCACTCAATTACGTAAGATTT
1 TGCAACTCCACTCAATTACGCAAGATTT
9151415 TGCAACTCCACTCAATTACGCAAGATTT
1 TGCAACTCCACTCAATTACGCAAGATTT
9151443 ACTTTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (28 bp):
TGCAACTCCACTCAATTACGCAAGATTT
Found at i:9154489 original size:3 final size:3
Alignment explanation
Indices: 9154481--9154529 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
9154471 ACATACAAAT
* *
9154481 TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
9154529 T
1 T
9154530 ATATATATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:9154750 original size:2 final size:2
Alignment explanation
Indices: 9154719--9154761 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
9154709 GGGTATATGT
* * * *
9154719 GA GA GT GA GA GT GA GA GT GA GA GT GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
9154761 G
1 G
9154762 GAAGGGTAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (2 bp):
GA
Found at i:9154761 original size:6 final size:6
Alignment explanation
Indices: 9154717--9154759 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
9154707 GGGGGTATAT
* *
9154717 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GAGAGA GAGAGA G
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA G
9154760 AGGAAGGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.12
Consensus pattern (6 bp):
GTGAGA
Found at i:9161139 original size:2 final size:2
Alignment explanation
Indices: 9161132--9161163 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9161122 CCAAATTTGA
9161132 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9161164 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9173426 original size:32 final size:31
Alignment explanation
Indices: 9173368--9173442 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
9173358 TTTTTGACAT
* *
9173368 AATT-TTTAAATAATGATAAAATTTATAAAAA
1 AATTATTTAAA-AATAATAAAAATTATAAAAA
*
9173399 AATTATTTAAAAATAATAAGAAATTATATAAA
1 AATTATTTAAAAATAATAA-AAATTATAAAAA
*
9173431 AATTATTGAAAA
1 AATTATTTAAAA
9173443 TATTAGAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (31 bp):
AATTATTTAAAAATAATAAAAATTATAAAAA
Found at i:9173435 original size:11 final size:11
Alignment explanation
Indices: 9173383--9173436 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
9173373 TTAAATAATG
*
9173383 ATAAAATTTAT
1 ATAAAAATTAT
*
9173394 AAAAAAATTAT
1 ATAAAAATTAT
*
9173405 TTAAAAA-TA-
1 ATAAAAATTAT
9173414 ATAAGAAATTAT
1 ATAA-AAATTAT
9173426 ATAAAAATTAT
1 ATAAAAATTAT
9173437 TGAAAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 3 0.09
10 5 0.14
11 23 0.66
12 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
ATAAAAATTAT
Found at i:9173443 original size:21 final size:20
Alignment explanation
Indices: 9173392--9173433 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
9173382 GATAAAATTT
*
9173392 ATAA-AAAAATTATTTAAAA
1 ATAATAAAAATTATATAAAA
9173411 ATAATAAGAAATTATATAAAA
1 ATAATAA-AAATTATATAAAA
9173432 AT
1 AT
9173434 TATTGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 2 0.10
21 14 0.70
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
ATAATAAAAATTATATAAAA
Found at i:9176207 original size:6 final size:6
Alignment explanation
Indices: 9176196--9176222 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9176186 CTGTTTGATC
9176196 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
9176223 GAGCGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:9176768 original size:58 final size:58
Alignment explanation
Indices: 9176671--9176782 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
9176661 CGCTTCAAAC
* * * * *
9176671 GTGGTCTCGAATAATCATGGATCAAATACAGAATCAAAAATCATCTCTTACTCTATAT
1 GTGGGCTCGAACAATCACGGATCAAACACAGAATAAAAAATCATCTCTTACTCTATAT
*
9176729 GTGGGCTCGAACAATCACGGATCAAACACAGAATAAAAAATTATCTCTTACTCT
1 GTGGGCTCGAACAATCACGGATCAAACACAGAATAAAAAATCATCTCTTACTCT
9176783 CTTACTTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (58 bp):
GTGGGCTCGAACAATCACGGATCAAACACAGAATAAAAAATCATCTCTTACTCTATAT
Found at i:9180603 original size:25 final size:23
Alignment explanation
Indices: 9180575--9180620 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
9180565 GTTAGATCCA
9180575 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
9180600 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
9180621 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:9185315 original size:24 final size:24
Alignment explanation
Indices: 9185286--9185339 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
9185276 GAGTTTTAAT
9185286 ATATTGGTGTATCGGGGTTAATAA
1 ATATTGGTGTATCGGGGTTAATAA
9185310 ATATTGGTGTATCGGGGTTAATAA
1 ATATTGGTGTATCGGGGTTAATAA
9185334 ATATTG
1 ATATTG
9185340 AAAAGATCTC
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:0.30, C:0.04, G:0.28, T:0.39
Consensus pattern (24 bp):
ATATTGGTGTATCGGGGTTAATAA
Found at i:9186343 original size:37 final size:37
Alignment explanation
Indices: 9186293--9186382 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 37
9186283 ACATCTAAAA
*
9186293 ATTCAGGCTTTGTGCCTAGTAGGCTTCGTGTCGGTGT
1 ATTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGT
9186330 ATTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGT
1 ATTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGT
9186367 ATTCAGGCTTTGTGCC
1 ATTCAGGCTTTGTGCC
9186383 AGTGATCAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.11, C:0.21, G:0.31, T:0.37
Consensus pattern (37 bp):
ATTCAGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGT
Found at i:9186381 original size:21 final size:21
Alignment explanation
Indices: 9186313--9186382 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
9186303 TGTGCCTAGT
*
9186313 AGGCTTCGTGTCGGTGTATTC
1 AGGCTTCGTGCCGGTGTATTC
* *
9186334 AGGCTTTGTGCC----TAGT-
1 AGGCTTCGTGCCGGTGTATTC
9186350 AGGCTTCGTGCCGGTGTATTC
1 AGGCTTCGTGCCGGTGTATTC
*
9186371 AGGCTTTGTGCC
1 AGGCTTCGTGCC
9186383 AGTGATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
16 11 0.29
17 3 0.08
20 3 0.08
21 21 0.55
ACGTcount: A:0.10, C:0.21, G:0.33, T:0.36
Consensus pattern (21 bp):
AGGCTTCGTGCCGGTGTATTC
Found at i:9187628 original size:22 final size:22
Alignment explanation
Indices: 9187585--9187639 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
9187575 AATTAAATTA
**
9187585 AAAATAAAATAATTAAACTCCC
1 AAAATAAAATAACAAAACTCCC
* *
9187607 AAAATAAAATACCAAAATTCCC
1 AAAATAAAATAACAAAACTCCC
9187629 AAAATTAAAAT
1 AAAA-TAAAAT
9187640 TAACTTACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAATAAAATAACAAAACTCCC
Found at i:9193512 original size:30 final size:32
Alignment explanation
Indices: 9193476--9193550 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 32
9193466 AATAATTTAT
9193476 ATTTTTATAAAATTTGA-ATTATTAAA-T-CAA
1 ATTTTTATAAAATTTGATA-TATTAAAGTGCAA
* **
9193506 ATTTTTATCATTTTTGATATATTAAAGTGCAA
1 ATTTTTATAAAATTTGATATATTAAAGTGCAA
9193538 ATTTTATATAAAA
1 ATTTT-TATAAAA
9193551 GACTTAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
30 21 0.60
31 2 0.06
32 8 0.23
33 4 0.11
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (32 bp):
ATTTTTATAAAATTTGATATATTAAAGTGCAA
Found at i:9194062 original size:98 final size:98
Alignment explanation
Indices: 9193947--9194149 Score: 325
Period size: 98 Copynumber: 2.1 Consensus size: 98
9193937 CAATTGACAC
* * * * *
9193947 GGATGTTATTATTATTAATGTTAGAATATGTGGGTTCGAGTATATTTAAACGTGTTATTTTTTTA
1 GGATATTATTATTATTAATGTTAGAATACGTGGGTTCAAGTATATTTAAACATGTTATCTTTTTA
*
9194012 TTTATGGGTTAATGAGAGGTTGTACATAGTTTT
66 TTTATGGGTTAATGAGAGGTTATACATAGTTTT
* *
9194045 GGATATTATTATTATTAATGTTAGAATACGTGGGTTCAAGTATGTTTAAGCATGTTATCTTTTTA
1 GGATATTATTATTATTAATGTTAGAATACGTGGGTTCAAGTATATTTAAACATGTTATCTTTTTA
*
9194110 TTTATGGGTTAATGAGGGGTTATACATAGTTTT
66 TTTATGGGTTAATGAGAGGTTATACATAGTTTT
9194143 GGATATT
1 GGATATT
9194150 TTTTAATAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (98 bp):
GGATATTATTATTATTAATGTTAGAATACGTGGGTTCAAGTATATTTAAACATGTTATCTTTTTA
TTTATGGGTTAATGAGAGGTTATACATAGTTTT
Found at i:9196204 original size:2 final size:2
Alignment explanation
Indices: 9196197--9196221 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9196187 CACACCTACC
9196197 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
9196222 ATTTAGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9199138 original size:27 final size:27
Alignment explanation
Indices: 9199095--9199168 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 27
9199085 AAAATTTGTA
* * *
9199095 TAAAAATATA-AAAAAATTACCATTTT
1 TAAAAATATATTAGAAATTAACATTTT
*
9199121 TACAAAA-ATATTAGAAATTTTAATATTTT
1 TA-AAAATATATTAGAAA--TTAACATTTT
9199150 TAAAAATATATTAGAAATT
1 TAAAAATATATTAGAAATT
9199169 TTAATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
26 5 0.13
27 10 0.26
28 4 0.10
29 20 0.51
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (27 bp):
TAAAAATATATTAGAAATTAACATTTT
Found at i:9199175 original size:27 final size:29
Alignment explanation
Indices: 9199116--9199179 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
9199106 AAAAATTACC
9199116 ATTTTTACAAAAATATTAGAAATTTTAAT
1 ATTTTTACAAAAATATTAGAAATTTTAAT
9199145 ATTTTTA-AAAATATATTAGAAATTTTAAT
1 ATTTTTACAAAA-ATATTAGAAATTTTAAT
*
9199174 TTTTTT
1 ATTTTT
9199180 TAAATTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (29 bp):
ATTTTTACAAAAATATTAGAAATTTTAAT
Found at i:9208200 original size:22 final size:22
Alignment explanation
Indices: 9208167--9208209 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9208157 TGCCACTGTT
9208167 TTGCTATCATTTCGTTATTATA
1 TTGCTATCATTTCGTTATTATA
*
9208189 TTGCTA-CTATTTTGTTATTAT
1 TTGCTATC-ATTTCGTTATTAT
9208210 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (22 bp):
TTGCTATCATTTCGTTATTATA
Found at i:9208728 original size:15 final size:15
Alignment explanation
Indices: 9208708--9208736 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9208698 ACAGCCACCA
9208708 TAATTATAACTTAAT
1 TAATTATAACTTAAT
9208723 TAATTATAACTTAA
1 TAATTATAACTTAA
9208737 AAAATTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTATAACTTAAT
Found at i:9208742 original size:15 final size:15
Alignment explanation
Indices: 9208709--9208747 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9208699 CAGCCACCAT
**
9208709 AATTATAACTTAATT
1 AATTATAACTTAAAA
9208724 AATTATAACTTAAAA
1 AATTATAACTTAAAA
9208739 AATTCATAA
1 AATT-ATAA
9208748 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATAACTTAAAA
Found at i:9210892 original size:19 final size:18
Alignment explanation
Indices: 9210867--9210910 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
9210857 CTTTAGTTAG
*
9210867 TAATTAATTAATCTTAAT
1 TAATTAATTAAACTTAAT
*
9210885 TAAATTAATTAAACTTGAT
1 T-AATTAATTAAACTTAAT
9210904 TAATTAA
1 TAATTAA
9210911 AACTAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATTAATTAAACTTAAT
Found at i:9214961 original size:4 final size:4
Alignment explanation
Indices: 9214954--9214978 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9214944 CAGCTATATA
9214954 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
9214979 GAGATTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:9216946 original size:27 final size:26
Alignment explanation
Indices: 9216903--9216955 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
9216893 AACGTGTTTA
* *
9216903 TTTTTTAAGTTTATTAAATAATATAT
1 TTTTTTAAATTTATTAAAAAATATAT
*
9216929 TTTTTTATAATTTTTTAAAAAATATAT
1 TTTTTTA-AATTTATTAAAAAATATAT
9216956 ATTTACTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTTTAAATTTATTAAAAAATATAT
Found at i:9217318 original size:3 final size:3
Alignment explanation
Indices: 9217268--9217299 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
9217258 TCAAATATCA
9217268 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9217300 CTAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9226872 original size:47 final size:41
Alignment explanation
Indices: 9226774--9226891 Score: 184
Period size: 41 Copynumber: 2.9 Consensus size: 41
9226764 TTCCTTTTAC
*
9226774 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
9226815 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
1 CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
* * *
9226856 CATAATCCCATGCTCAT-TCTGAGTCATGAGTCTTCC
1 CATAATCTCATTCTCATCTC-GAGACATGAGTCTTCC
9226892 ATTTCTTACA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 2 0.03
41 70 0.97
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.38
Consensus pattern (41 bp):
CATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
Found at i:9227780 original size:22 final size:21
Alignment explanation
Indices: 9227733--9227780 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
9227723 GACTTCCATA
*
9227733 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* *
9227754 TTTAACCTTAATTAATCCTATT
1 ATTAA-CTTAATTAATCATATT
9227776 ATTAA
1 ATTAA
9227781 TCAATATCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:9229228 original size:23 final size:22
Alignment explanation
Indices: 9229181--9229228 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
9229171 GGAAAATAAA
**
9229181 AGAAAAAAGAGAGAAAGTGTTG
1 AGAAAAAAGAGAGAAAGAATTG
9229203 AGAAGAAAAGAGA-AAAGAATTCG
1 AGAA-AAAAGAGAGAAAGAATT-G
9229226 AGA
1 AGA
9229229 GTTTGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.58, C:0.02, G:0.29, T:0.10
Consensus pattern (22 bp):
AGAAAAAAGAGAGAAAGAATTG
Found at i:9231311 original size:80 final size:80
Alignment explanation
Indices: 9231120--9232656 Score: 2348
Period size: 80 Copynumber: 19.2 Consensus size: 80
9231110 CTTTATAACT
* * * * *
9231120 TTAGGAGTAAAAGATTAGATTGT-TTCAATCTACCCCATGGTTGGGGTAAGAGATCTGATGGTCT
1 TTAGG-GTAAAAGATTAGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCT
*
9231184 TCAATC-TGCCCTCTAG
64 TCAATCTTGCCCTCTGG
* * *
9231200 TTAAGGTAAAAGATTAGATTTCTTCAATCTACCTCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
**
9231265 AATCTTGCCCTCTAT
66 AATCTTGCCCTCTGG
* * * *
9231280 TTAGGGTAAAAGATTAGATTTCTTCAATCTACCTCATGATCGGGGTAAAAGATCAGATGGTCTTT
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
9231345 AATCTTGCCCTTTGG
66 AATCTTGCCCTCTGG
*
9231360 TTAGGGTAAAAGATTAGATTTCTTCAATTTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
* *
9231425 AATTTTGCCCTCTGA
66 AATCTTGCCCTCTGG
*
9231440 TTAGGGTAAAAGATTAGATTTCTTCAATTTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
9231505 AATCTTGCCCTCTAG
66 AATCTTGCCCTCTGG
* *
9231520 TTAGGGTAAAAAATTAGATTTCTTTAATCTG-CCCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
* *
9231584 AATCTTACCCTCTAG
66 AATCTTGCCCTCTGG
* **
9231599 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATTAGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
9231664 AATCTTGCCCTTTGG
66 AATCTTGCCCTCTGG
*
9231679 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
* *
9231744 AATCTTACCCTTTGG
66 AATCTTGCCCTCTGG
*
9231759 TTAGGGTAAAATATTTA-ATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT
1 TTAGGGTAAAAGA-TTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT
9231823 CAATCTTGCCCTCTGG
65 CAATCTTGCCCTCTGG
* * *
9231839 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAATATCAGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
9231904 AATCTTGCCCACTGG
66 AATCTTGCCCTCTGG
* * * *
9231919 TTAGGGTAAAAGATTAGATTTCTTTAATCTGCTCCATGATCGGGGTAAAAGATCGGATAGTCTTT
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
9231984 AATCTTGCCCTCTGG
66 AATCTTGCCCTCTGG
* * * * *
9231999 TTAGGGCAAAAGATTAGATTTCTTCAATTTACCCTATGATCGGGGTAAAAGATCGGATGGTCTTT
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
9232064 AATCTTGTCCTCTGG
66 AATCTTGCCCTCTGG
* * *
9232079 TTTA-GGTAAAATATTGGATTTCTTCAATATGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT
1 -TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT
* *
9232143 CAATCTTGCCCACTAG
65 CAATCTTGCCCTCTGG
* * *
9232159 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCTCATGATCGGGGTAAAAGATCGTATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
9232224 AATCTTGCCCTCTGG
66 AATCTTGCCCTCTGG
*
9232239 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
* *
9232304 AATCTTGCCCTTTGA
66 AATCTTGCCCTCTGG
* * *
9232319 TTAGAGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
* *
9232384 AATCTTGCCCACTAG
66 AATCTTGCCCTCTGG
*
9232399 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
*
9232464 AATCTTGCCCTCTAG
66 AATCTTGCCCTCTGG
* * * *
9232479 TTAGGGTAAAAGATT-GTAGTTCTTCAATCTGCCTCATGATCAGGGTAAAAGATCGTATGGTCTT
1 TTAGGGTAAAAGATTAG-ATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT
9232543 CAATCTTGCCCTCTGG
65 CAATCTTGCCCTCTGG
* *
9232559 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
9232624 AATCTTGCCCTCTGG
66 AATCTTGCCCTCTGG
9232639 TTAGGGTAAAAGATTAGA
1 TTAGGGTAAAAGATTAGA
9232657 GGTTGTAATT
Statistics
Matches: 1344, Mismatches: 104, Indels: 18
0.92 0.07 0.01
Matches are distributed among these distances:
78 1 0.00
79 138 0.10
80 1199 0.89
81 6 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (80 bp):
TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTC
AATCTTGCCCTCTGG
Found at i:9232900 original size:50 final size:50
Alignment explanation
Indices: 9232731--9232887 Score: 190
Period size: 50 Copynumber: 3.1 Consensus size: 50
9232721 TCCTTTACAA
* * * * * * * * *
9232731 CTTTAAGTGAATGATATTTGCCATTACAGCTTCATTCTGCCCCTCTACAG
1 CTTTAGGTGTATGAGATTTGCCATTGCAGTTTCAATATGCACCTCCACAG
* * *
9232781 CTTTAGGTGCATGAGATTTGCCATTGC-GATTTCAATTTGCACCTCCATAG
1 CTTTAGGTGTATGAGATTTGCCATTGCAG-TTTCAATATGCACCTCCACAG
9232831 CTTTAGGTGTATGAGATTTGCCATTGCAGTTTCAATATGCACCTCCACAG
1 CTTTAGGTGTATGAGATTTGCCATTGCAGTTTCAATATGCACCTCCACAG
9232881 CTTTAGG
1 CTTTAGG
9232888 GGTAAAAAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 90 0.98
51 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (50 bp):
CTTTAGGTGTATGAGATTTGCCATTGCAGTTTCAATATGCACCTCCACAG
Found at i:9234812 original size:19 final size:20
Alignment explanation
Indices: 9234790--9234830 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
9234780 TCTCGACCCC
9234790 TTTTTTTACCT-TTTTTTTA
1 TTTTTTTACCTCTTTTTTTA
9234809 TTTTTTTACCTCCTTTTTTTA
1 TTTTTTTACCT-CTTTTTTTA
9234830 T
1 T
9234831 AACAAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTACCTCTTTTTTTA
Found at i:9238531 original size:11 final size:11
Alignment explanation
Indices: 9238515--9238547 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
9238505 GACAGAGGGG
9238515 TGGAAGGGAAA
1 TGGAAGGGAAA
9238526 TGGAAGGGAAA
1 TGGAAGGGAAA
9238537 TGGAAGGGAAA
1 TGGAAGGGAAA
9238548 AGCTAGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09
Consensus pattern (11 bp):
TGGAAGGGAAA
Found at i:9238884 original size:4 final size:4
Alignment explanation
Indices: 9238877--9238908 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
9238867 ATTTATTTAT
9238877 AATA AAT- AAT- AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
9238909 AATAATAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:9238900 original size:18 final size:18
Alignment explanation
Indices: 9238877--9238927 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
9238867 ATTTATTTAT
9238877 AATAAAT-AATAATAAATA
1 AATAAATAAATAA-AAATA
9238895 AATAAATAAATAAAAAT-
1 AATAAATAAATAAAAATA
*
9238912 AATAAGAAAAATAAAA
1 AATAA-ATAAATAAAA
9238928 TTGGGTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 5 0.17
18 20 0.67
19 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAAATAAATAAAAATA
Found at i:9238902 original size:22 final size:22
Alignment explanation
Indices: 9238878--9238926 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
9238868 TTTATTTATA
* *
9238878 ATAAATAATAATAAATAA-ATAA
1 ATAAATAAAAAT-AATAAGAAAA
9238900 ATAAATAAAAATAATAAGAAAA
1 ATAAATAAAAATAATAAGAAAA
9238922 ATAAA
1 ATAAA
9238927 ATTGGGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAAATAAAAATAATAAGAAAA
Found at i:9241614 original size:18 final size:18
Alignment explanation
Indices: 9241593--9241630 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9241583 ATTACAAAAT
*
9241593 AATT-AAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
9241611 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
9241629 AA
1 AA
9241631 ATTTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:9241621 original size:28 final size:29
Alignment explanation
Indices: 9241580--9241634 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
9241570 TCTCTCAACA
9241580 AAAATTACAAAATAATTA-AAATAATTTTT
1 AAAATTACAAAATAATTATAAA-AATTTTT
*
9241609 AAAATT-CAAAATATTTATAAAAATTT
1 AAAATTACAAAATAATTATAAAAATTT
9241635 CAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATTACAAAATAATTATAAAAATTTTT
Found at i:9241668 original size:12 final size:12
Alignment explanation
Indices: 9241651--9241694 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
9241641 TTATATTTTT
9241651 AAAAAAATTATA
1 AAAAAAATTATA
*
9241663 AAAAAAATTTCTA
1 AAAAAAA-TTATA
9241676 CCAAAAAAATTATA
1 --AAAAAAATTATA
9241690 AAAAA
1 AAAAA
9241695 TTCTAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 12 0.44
13 4 0.15
14 4 0.15
15 7 0.26
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAAATTATA
Found at i:9241705 original size:2 final size:2
Alignment explanation
Indices: 9241700--9241732 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9241690 AAAAATTCTA
*
9241700 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9241733 TAAAGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9249773 original size:2 final size:2
Alignment explanation
Indices: 9249766--9249790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9249756 ACAAAGACAC
9249766 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
9249791 ACACAGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9249826 original size:6 final size:6
Alignment explanation
Indices: 9249817--9249845 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9249807 CAAAGAATCT
9249817 AAAAGG AAAAGG AAAAGG AAAAGG AAAAG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAG
9249846 TGGGGTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:9251570 original size:15 final size:16
Alignment explanation
Indices: 9251547--9251584 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9251537 ATAACTAAAT
*
9251547 TTATTATTATAT-TAA
1 TTATAATTATATATAA
9251562 TTATAATTATATATAA
1 TTATAATTATATATAA
9251578 TTGATAA
1 TT-ATAA
9251585 AAGATGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTATAATTATATATAA
Found at i:9252123 original size:23 final size:22
Alignment explanation
Indices: 9252081--9252123 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
9252071 AAATTAGTTA
*
9252081 TTTTATTGAAAATTTTATTTAT
1 TTTTATTGAAAATTTAATTTAT
*
9252103 TTTTATTGTTAAATTTAATTT
1 TTTTATTG-AAAATTTAATTT
9252124 GTGTACATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTATTGAAAATTTAATTTAT
Found at i:9252593 original size:25 final size:26
Alignment explanation
Indices: 9252536--9252594 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
9252526 ATAAATACAT
9252536 TAATTTATTTTTATATTGAATATATA
1 TAATTTATTTTTATATTGAATATATA
9252562 TAA-TTATTTGTGTATA-T-AATATATA
1 TAATTTATTT-T-TATATTGAATATATA
9252587 -AATTTATT
1 TAATTTATT
9252595 ATATCAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 2 0.07
25 19 0.63
26 5 0.17
27 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (26 bp):
TAATTTATTTTTATATTGAATATATA
Found at i:9252721 original size:14 final size:15
Alignment explanation
Indices: 9252702--9252730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9252692 GTGTTGTCTT
9252702 TTTTTA-ATTTAAAA
1 TTTTTACATTTAAAA
9252716 TTTTTACATTTAAAA
1 TTTTTACATTTAAAA
9252731 ATAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTACATTTAAAA
Found at i:9257202 original size:29 final size:29
Alignment explanation
Indices: 9257148--9257204 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
9257138 CAAAAATATG
*
9257148 TTTTTATAATTTTTATACTTTTATAAATAA
1 TTTTAATAATTTTTATA-TTTTATAAATAA
*
9257178 TTTTAATAATTTTTGT-TTTTAATAAAT
1 TTTTAATAATTTTTATATTTT-ATAAAT
9257205 TTTATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 6 0.25
30 14 0.58
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAATAATTTTTATATTTTATAAATAA
Found at i:9257229 original size:26 final size:26
Alignment explanation
Indices: 9257148--9257242 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 26
9257138 CAAAAATATG
* *
9257148 TTTTTATAATTTTTATACTTTTATAAATAA
1 TTTTAATAATTTTTGT--TTTTAT-AA-AA
9257178 TTTTAATAATTTTTGTTTTTA-ATAAA
1 TTTTAATAATTTTTGTTTTTATA-AAA
9257204 TTTT-ATATATTTTTGAATTTTT-TAAAA
1 TTTTAATA-ATTTTTG--TTTTTATAAAA
*
9257231 TTTTAAAAATTT
1 TTTTAATAATTT
9257243 AATTAATTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
25 3 0.05
26 14 0.25
27 12 0.21
28 13 0.23
30 14 0.25
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTAATAATTTTTGTTTTTATAAAA
Found at i:9257242 original size:27 final size:26
Alignment explanation
Indices: 9257176--9257242 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
9257166 TTTTATAAAT
*
9257176 AATTTTAATAATTTTTGTTTTTAATA
1 AATTTTAAAAATTTTTGTTTTTAATA
* * *
9257202 AATTTTATATATTTTTGAATTTTTTA-A
1 AATTTTAAAAATTTTTG--TTTTTAATA
9257229 AATTTTAAAAATTT
1 AATTTTAAAAATTT
9257243 AATTAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 14 0.42
27 13 0.39
28 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (26 bp):
AATTTTAAAAATTTTTGTTTTTAATA
Found at i:9259521 original size:31 final size:30
Alignment explanation
Indices: 9259468--9259549 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 30
9259458 AATTTCAAAT
* *
9259468 TTTAAAAAATATAAGAATTAAAATTGATCAA
1 TTTAAAAAATATAA-AACTAAAATGGATCAA
9259499 TTTAAAAAATATATAAACTAAAATGGATCAA
1 TTTAAAAAATATA-AAACTAAAATGGATCAA
*
9259530 ATT--AAAATATAGAAACTAAA
1 TTTAAAAAATATA-AAACTAAA
9259550 TTCTCAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 16 0.35
31 29 0.63
32 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (30 bp):
TTTAAAAAATATAAAACTAAAATGGATCAA
Found at i:9261540 original size:21 final size:20
Alignment explanation
Indices: 9261502--9261540 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9261492 GTGCAAAAGA
*
9261502 CTTACAAGAAGGGAGATTGG
1 CTTACAAGAAGCGAGATTGG
9261522 CTTACAAGAAAGCGAGATT
1 CTTACAAG-AAGCGAGATT
9261541 CATTGATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.21
Consensus pattern (20 bp):
CTTACAAGAAGCGAGATTGG
Found at i:9271582 original size:20 final size:20
Alignment explanation
Indices: 9271483--9271582 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 20
9271473 ATTATATTGT
**
9271483 TGTTTTGGTACTTTTTTTAC
1 TGTTTTGGTTGTTTTTTTAC
* *
9271503 TGTTTTGGTTATTTTTGTTGC
1 TGTTTTGGTTGTTTTT-TTAC
*
9271524 TGTTTT--TATGTTGCTTTTTAT
1 TGTTTTGGT-TGTT--TTTTTAC
*
9271545 TGGTTTGG-TGCTTTTTTTAC
1 TGTTTTGGTTG-TTTTTTTAC
9271565 TGTTTTGGTTGTTGTTTT
1 TGTTTTGGTTGTT-TTTT
9271583 CGTGTTGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
19 1 0.02
20 32 0.52
21 24 0.39
22 5 0.08
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.67
Consensus pattern (20 bp):
TGTTTTGGTTGTTTTTTTAC
Found at i:9271604 original size:62 final size:62
Alignment explanation
Indices: 9271486--9271604 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
9271476 ATATTGTTGT
* *
9271486 TTTGGTACTTTTTTTACTGTTTTGGTTATTTTTGTTGCTGTTTTTATGTTGCTTTTTATTGG
1 TTTGGTACTTTTTTTACTGTTTTGGTTATTTTTGTCGCTGTTTTTATGCTGCTTTTTATTGG
* * * *
9271548 TTTGGTGCTTTTTTTACTGTTTTGGTTGTTGTTT-TCG-TGTTGTTTTTGCTGTTTTTT
1 TTTGGTACTTTTTTTACTGTTTTGGTTATT-TTTGTCGCTGTT-TTTATGCTGCTTTTT
9271605 TGCTATTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
61 4 0.08
62 42 0.86
63 3 0.06
ACGTcount: A:0.05, C:0.07, G:0.21, T:0.67
Consensus pattern (62 bp):
TTTGGTACTTTTTTTACTGTTTTGGTTATTTTTGTCGCTGTTTTTATGCTGCTTTTTATTGG
Found at i:9284628 original size:8 final size:8
Alignment explanation
Indices: 9284615--9284640 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9284605 AGAACGTGAC
9284615 CTTTACTG
1 CTTTACTG
9284623 CTTTACTG
1 CTTTACTG
9284631 CTTTACTG
1 CTTTACTG
9284639 CT
1 CT
9284641 CACGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.50
Consensus pattern (8 bp):
CTTTACTG
Found at i:9299439 original size:12 final size:12
Alignment explanation
Indices: 9299422--9299459 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
9299412 TATGTTTTAA
9299422 ATATATATGTAT
1 ATATATATGTAT
9299434 ATATATATGTAT
1 ATATATATGTAT
*
9299446 GA-ATATATATAT
1 -ATATATATGTAT
9299458 AT
1 AT
9299460 TACTATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:9304678 original size:21 final size:21
Alignment explanation
Indices: 9304653--9304713 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
9304643 AGCTATAAAT
*
9304653 ATTATTAAATTTTA-ATAAAAA
1 ATTATTAAAATTTAGA-AAAAA
9304674 ATTATTAAAATTTAGAAAAAA
1 ATTATTAAAATTTAGAAAAAA
* *
9304695 A-TATAAAAATATA-AAAAAA
1 ATTATTAAAATTTAGAAAAAA
9304714 TTGTAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 6 0.17
20 10 0.28
21 19 0.53
22 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTATTAAAATTTAGAAAAAA
Found at i:9304728 original size:21 final size:20
Alignment explanation
Indices: 9304669--9304730 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
9304659 AAATTTTAAT
*
9304669 AAAAAATTATTAAAATTTAGA
1 AAAAAATTA-TAAAATTTATA
*
9304690 AAAAAA-TATAAAA-ATATA
1 AAAAAATTATAAAATTTATA
*
9304708 AAAAAATTGTAAAATTTTATA
1 AAAAAATTATAAAA-TTTATA
9304729 AA
1 AA
9304731 GTTTTAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.26
19 11 0.32
20 2 0.06
21 12 0.35
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAAATTATAAAATTTATA
Found at i:9312850 original size:5 final size:5
Alignment explanation
Indices: 9312840--9312869 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
9312830 CATGCAGCAG
9312840 CTGGT CTGGT CTGGT CTGGT CTGGT -TGGT C
1 CTGGT CTGGT CTGGT CTGGT CTGGT CTGGT C
9312870 CCCTGCCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
CTGGT
Done.