Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 88 of 325
Found at i:29574844 original size:20 final size:20
Alignment explanation
Indices: 29574821--29574858 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29574811 GTGGGGGTCA
29574821 ACACACCCATGTGGAAGGGC
1 ACACACCCATGTGGAAGGGC
* *
29574841 ACACGCCCGTGTGGAAGG
1 ACACACCCATGTGGAAGG
29574859 AAGCATATGC
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:0.26, C:0.29, G:0.34, T:0.11
Consensus pattern (20 bp):
ACACACCCATGTGGAAGGGC
Found at i:29580267 original size:24 final size:24
Alignment explanation
Indices: 29580233--29580286 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
29580223 ACTGACCTGG
*
29580233 AATATTATTTATCATTCACCAA-A
1 AATATTATTTATCATCCACCAACA
*
29580256 AAGTATTGTTTATCATCCACCAACA
1 AA-TATTATTTATCATCCACCAACA
29580281 AATATT
1 AATATT
29580287 TAATATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (24 bp):
AATATTATTTATCATCCACCAACA
Found at i:29591773 original size:24 final size:24
Alignment explanation
Indices: 29591729--29591775 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29591719 TATAGTATTA
*
29591729 GAAATATATACATGGGATAATATG
1 GAAATATATACATGAGATAATATG
*
29591753 GAAATATGTACAT-AGAGTAATAT
1 GAAATATATACATGAGA-TAATAT
29591776 ATACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (24 bp):
GAAATATATACATGAGATAATATG
Found at i:29591805 original size:21 final size:21
Alignment explanation
Indices: 29591781--29591862 Score: 58
Period size: 21 Copynumber: 3.7 Consensus size: 21
29591771 AATATATACA
29591781 AAAATATAACTAATAATATTT
1 AAAATATAACTAATAATATTT
*** *
29591802 AAAATAATAA-TAGGGATATTA
1 AAAAT-ATAACTAATAATATTT
* *
29591823 AAAATACTTAGTATATAATATTT
1 AAAATA-TAACTA-ATAATATTT
29591846 AAAATATATACATAATA
1 AAAATATA-AC-TAATA
29591863 CAAAAACATA
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
20 1 0.02
21 19 0.43
22 7 0.16
23 15 0.34
24 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATATAACTAATAATATTT
Found at i:29591868 original size:42 final size:39
Alignment explanation
Indices: 29591770--29591868 Score: 92
Period size: 44 Copynumber: 2.4 Consensus size: 39
29591760 GTACATAGAG
*
29591770 TAATATATACAAAAATATAACTAATAATATTTAAAATAA
1 TAATAGATACAAAAATATAACTAATAATATTTAAAATAA
* * *
29591809 TAATAGGGATATTAAAAATACTTAGTATATAATATTTAAAATATA
1 TAATA--GATA-CAAAAATA-TAACTA-ATAATATTTAAAATA-A
29591854 TACATA-ATACAAAAA
1 TA-ATAGATACAAAAA
29591869 CATATATAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
39 5 0.10
41 3 0.06
42 12 0.25
43 7 0.15
44 15 0.31
45 3 0.06
46 3 0.06
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (39 bp):
TAATAGATACAAAAATATAACTAATAATATTTAAAATAA
Found at i:29593286 original size:46 final size:46
Alignment explanation
Indices: 29593210--29593653 Score: 602
Period size: 46 Copynumber: 9.6 Consensus size: 46
29593200 TGATGTCATA
* * * *
29593210 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCACGTTGCCATG
* * *
29593256 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGTTGCCATG
*
29593303 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* ** *
29593349 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGTTGCCATG
29593396 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* * * *
29593442 GTATCTTTCAACCACGGTCTTATTCATTTCATATCACGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* * * *
29593488 GTATCTTTCAACCACGGTCTTACACATTTCATATCAAGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* * * *
29593534 GTATCTTTCAACCATGGTCCTACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
* * *
29593580 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
*
29593626 GTATCTTTCAACCATGGTCTTACACATT
1 GTATCTTTCAACCATGGTCTTACTCATT
29593654 CCATATCAGA
Statistics
Matches: 365, Mismatches: 30, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
46 283 0.78
47 82 0.22
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGTTGCCATG
Found at i:29597831 original size:73 final size:75
Alignment explanation
Indices: 29597695--29597850 Score: 228
Period size: 73 Copynumber: 2.1 Consensus size: 75
29597685 AAAAACAGAG
* * *
29597695 TTTG-AAAGACAGAATTTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAGACAGAAATTGAAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAAT
29597759 ACGAGTTGATT
65 ACGAGTTGATT
* *
29597770 TTTGAAAAG-CAGAAATTGAAATTACCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTCGCAATA
1 TTTGAAAAGACAGAAATTGAAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATA
*
29597833 TGAGTTGATT
66 CGAGTTGATT
29597843 TTTGAAAA
1 TTTGAAAA
29597851 ATATAGATTG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
73 47 0.64
75 23 0.31
76 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (75 bp):
TTTGAAAAGACAGAAATTGAAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATA
CGAGTTGATT
Found at i:29597930 original size:89 final size:86
Alignment explanation
Indices: 29597774--29598099 Score: 401
Period size: 83 Copynumber: 3.8 Consensus size: 86
29597764 TTGATTTTTG
* * *
29597774 AAAAGCAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
29597839 GATTTTTGAAAAATATAGATT
66 GATTTTTGAAAAACATAGATT
** * *
29597860 GGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTTTCGCAATATAA
1 ---AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
29597925 GTTGA--TTT-AAAAACAGACATT
63 GTTGATTTTTGAAAAACATAGATT
* * *
29597946 AAGAACAGAGATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
29598011 GGTTTTTG-AAAACAT-GAATT
66 GATTTTTGAAAAACATAG-ATT
* ** *
29598031 AAAAACAGAAATTGGAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
29598096 TTGA
64 TTGA
29598100 CTTCTTTTTT
Statistics
Matches: 205, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
83 61 0.30
85 36 0.18
86 10 0.05
87 38 0.19
89 60 0.29
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (86 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAACATAGATT
Found at i:29597986 original size:172 final size:169
Alignment explanation
Indices: 29597779--29598099 Score: 452
Period size: 172 Copynumber: 1.9 Consensus size: 169
29597769 TTTTGAAAAG
*
29597779 CAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * *
29597844 TTGAAAA-ATATAGATTGGAAAAAACAGAAATTGAAAATACCTCAGC-GTG-TCTTGAGGCTCAA
66 TTGAAAACAT-GA-ATT---AAAAACAGAAATTGAAAATACCTCAGCAGTGAGC-CGAGGCTCAA
29597906 CTCACCTT-TCGCAATATAAGTTGATTTAAAAACAGACATTAAGAA
125 CTCA-CTTCTCGCAATATAAGTTGATTTAAAAACAGACATTAAGAA
* * * *
29597951 CAGAGATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTT
1 CAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
29598016 TTGAAAACATGAATTAAAAACAGAAATTGGAAATACCTCAGCATGTGAGCCGAGGCTCAACTCAC
66 TTGAAAACATGAATTAAAAACAGAAATTGAAAATACCTCAGCA-GTGAGCCGAGGCTCAACTCAC
*
29598081 TTCTCGCAATATGAGTTGA
130 TTCTCGCAATATAAGTTGA
29598100 CTTCTTTTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
168 26 0.19
169 3 0.02
170 31 0.23
171 4 0.03
172 68 0.51
173 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (169 bp):
CAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTGAAAACATGAATTAAAAACAGAAATTGAAAATACCTCAGCAGTGAGCCGAGGCTCAACTCACT
TCTCGCAATATAAGTTGATTTAAAAACAGACATTAAGAA
Found at i:29599129 original size:42 final size:42
Alignment explanation
Indices: 29599050--29599129 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
29599040 GTGTTAATCA
29599050 AGATGCCCTTTTCGGGTTTTCACCTTGATCATCTTTTTTTTT
1 AGATGCCCTTTTCGGGTTTTCACCTTGATCATCTTTTTTTTT
* **
29599092 AGATG-CCTTTTCGGGTTTTCATCTTGATTTTCTTTTTT
1 AGATGCCCTTTTCGGGTTTTCACCTTGATCATCTTTTTT
29599130 CAAGCATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 30 0.86
42 5 0.14
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (42 bp):
AGATGCCCTTTTCGGGTTTTCACCTTGATCATCTTTTTTTTT
Found at i:29611565 original size:24 final size:24
Alignment explanation
Indices: 29611521--29611567 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29611511 TATAGTATTA
*
29611521 GAAATATATACATGGGATAATATG
1 GAAATATATACATGAGATAATATG
*
29611545 GAAATATGTACAT-AGAGTAATAT
1 GAAATATATACATGAGA-TAATAT
29611568 ATACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (24 bp):
GAAATATATACATGAGATAATATG
Found at i:29612511 original size:10 final size:8
Alignment explanation
Indices: 29612484--29612508 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29612474 AAAAAGAGAA
29612484 AAGGGGAG
1 AAGGGGAG
29612492 AAGGGGAG
1 AAGGGGAG
29612500 AAGGGGAG
1 AAGGGGAG
29612508 A
1 A
29612509 GAATCCGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (8 bp):
AAGGGGAG
Found at i:29614003 original size:16 final size:14
Alignment explanation
Indices: 29613982--29614031 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 14
29613972 ACCAAGCGGA
29613982 AAAAGAAAAGAGAAGC
1 AAAAGAAAA-AG-AGC
29613998 AAAAGAAAAAGAGC
1 AAAAGAAAAAGAGC
*
29614012 AAAA-AAGAAGA--
1 AAAAGAAAAAGAGC
29614023 AAAAGAAAA
1 AAAAGAAAA
29614032 CAAATGTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 4 0.13
12 3 0.10
13 6 0.19
14 7 0.23
15 2 0.06
16 9 0.29
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAGC
Found at i:29620708 original size:3 final size:3
Alignment explanation
Indices: 29620700--29620731 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29620690 TCCAATTGCA
29620700 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29620732 AACATTCTAT
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:29634415 original size:3 final size:3
Alignment explanation
Indices: 29634409--29634435 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29634399 TAACTTTTAC
29634409 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
29634436 TGGTCCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29636039 original size:3 final size:3
Alignment explanation
Indices: 29636025--29636071 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
29636015 TGTCATGCAG
29636025 CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
29636072 TTTCATTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:29638571 original size:20 final size:22
Alignment explanation
Indices: 29638538--29638581 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
29638528 GAATGATTTT
29638538 TTAACAAGTACTTT-ATTATAA
1 TTAACAAGTACTTTGATTATAA
*
29638559 TTAA-AAGTCCTTTGATTATAA
1 TTAACAAGTACTTTGATTATAA
29638580 TT
1 TT
29638582 TTTTAGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (22 bp):
TTAACAAGTACTTTGATTATAA
Found at i:29642417 original size:6 final size:6
Alignment explanation
Indices: 29642406--29642430 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29642396 ACACCCACAT
29642406 CCCTCC CCCTCC CCCTCC CCCTCC C
1 CCCTCC CCCTCC CCCTCC CCCTCC C
29642431 TAAATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCTCC
Found at i:29644098 original size:17 final size:17
Alignment explanation
Indices: 29644065--29644147 Score: 71
Period size: 18 Copynumber: 4.8 Consensus size: 17
29644055 TTCTAACCTC
* *
29644065 TATAAAAATTTGT-AAA
1 TATAAAAATATATAAAA
29644081 TATTAAAAA-ATATAAAA
1 TA-TAAAAATATATAAAA
*
29644098 TATAAAAATATATATATA
1 TATAAAAATATATA-AAA
* *
29644116 TATATATATATATAAAA
1 TATAAAAATATATAAAA
*
29644133 TTTAGAAAATATATA
1 TATA-AAAATATATA
29644148 TAATCTAGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
16 10 0.19
17 21 0.40
18 22 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TATAAAAATATATAAAA
Found at i:29644144 original size:18 final size:18
Alignment explanation
Indices: 29644123--29644159 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29644113 ATATATATAT
*
29644123 ATATATAAAATTTAGAAA
1 ATATATAAAATCTAGAAA
*
29644141 ATATATATAATCTAGAAA
1 ATATATAAAATCTAGAAA
29644159 A
1 A
29644160 ATAACAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATATAAAATCTAGAAA
Found at i:29644149 original size:2 final size:2
Alignment explanation
Indices: 29644105--29644129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29644095 AAATATAAAA
29644105 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29644130 AAATTTAGAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29644954 original size:15 final size:15
Alignment explanation
Indices: 29644934--29644964 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29644924 CCTTTTTAGA
29644934 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
29644949 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
29644964 A
1 A
29644965 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:29645143 original size:22 final size:21
Alignment explanation
Indices: 29645108--29645172 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
29645098 AATTTAAATA
*
29645108 TTTTTCTATATTTTATGTATT
1 TTTTTCTATATTTTATATATT
*
29645129 TTTTTCTAATTTTTTATATATT
1 TTTTTCT-ATATTTTATATATT
*
29645151 TATTTTC-ATCTTTTATAT-TT
1 T-TTTTCTATATTTTATATATT
29645171 TT
1 TT
29645173 AATGTGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 17 0.44
22 13 0.33
23 5 0.13
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTCTATATTTTATATATT
Found at i:29655378 original size:30 final size:30
Alignment explanation
Indices: 29655291--29655386 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
29655281 GTACAAGTGA
*
29655291 TGGTGGAGCAAGTGTGGCTAGTGGAGTAGG
1 TGGTGGAGCAAGTGTGGCTAGTGGAGTTGG
* *
29655321 TAGTAGAGCAAGTGTGGCTAGTGGAGTTGG
1 TGGTGGAGCAAGTGTGGCTAGTGGAGTTGG
29655351 TGGTGGAGCAAGTGTGGCTAGTGGAGTTGG
1 TGGTGGAGCAAGTGTGGCTAGTGGAGTTGG
29655381 TGGTGG
1 TGGTGG
29655387 CAAAGGCTAG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.19, C:0.06, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGAGCAAGTGTGGCTAGTGGAGTTGG
Found at i:29656506 original size:148 final size:151
Alignment explanation
Indices: 29656210--29657170 Score: 577
Period size: 154 Copynumber: 6.2 Consensus size: 151
29656200 CTCAGCGTCT
* * * *
29656210 TGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAATACCT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TATTTTGAAAG-CAGAAATTAAAAATACCT
* *** * * * *
29656275 CAACTTGTC-TTGAGGCTCAACTCACTTCTTGCAGTATGAGTTGA--ATTTTTTGAAAGACAGAA
64 CAACGTGTCACCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAA
*
29656337 ATTGAAAATACATCAACGTGTCT
129 ATTGAAAATACATCAACGTGTCC
* * * * *
29656360 TGAGGCTCAACTCACTTCTTGTAGTATGAGTTGA-ATTTTGAAA-CAGAAA-TAAAAATTATCTC
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAGCAGAAATTAAAAA-TACCTC
* *
29656422 AGCGTGTC-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAGACAGAAA
65 AACGTGTCACCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAA
* * *
29656486 TTGAAATTACCTCAGCGTGTCC
130 TTGAAAATACATCAACGTGTCC
* *
29656508 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAGGCAGAAATTAAAAATACCT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TATTTTGAAA-GCAGAAATTAAAAATACCT
* * *
29656573 CAACGTGTCAGTCAAGGCTTAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAACCGTAGAAA
64 CAACGTGTCA-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT------T-----
* * * * *
29656638 TTAAAGAACAGAAATGGAAAATACCTCAGCGTATGACC
117 TGAAAG-ACAGAAATTGAAAATACATCAACG--TGTCC
* ** ** * * * *
29656676 CGAGGCTCAACTCACCTCTTACAATATGAGTTTTTTTTTTAAAAAAACAAACAGAAATTGAAAAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTT-----GA-AAGCAGAAATTAAAAAT
* ** * * *
29656741 ACCTCAGCGTG-C-CTTGAGACTCAACTCACCTCTCACAATATGAGTTG--GTTTTTTTGACAA-
60 ACCTCAACGTGTCAC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGA-AAG
* * *
29656801 ACAGAAATTGAAAATACCTCAGCGTGCCC
123 ACAGAAATTGAAAATACATCAACGTGTCC
*
29656830 TGAGGCTCAACTCACCTCTCGCAATATGAGTTG--ATTTTGACAAACAAAGACAGAAATTGAAAA
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTG------AAAG-CAGAAATTAAAAA
* * *
29656893 TACCTCAGCACGTG--AGCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGA--TTTTTTTGAC
59 TACCTCA--ACGTGTCA-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAA
* * * * * *
29656954 A-ATAGAAATTGCAATTACCTCAGCATGTCC
121 AGACAGAAATTGAAAATACATCAACGTGTCC
* * * * * * ** * *
29656984 CGAGGCTCAACTCACCTTTTGCAATATGAGTTTGTTTTTTTTTTATAAAAATAGAATTTGAAAAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAG-TTG----ATATTT-TGAAAGCAGAAATTAAAAAT
* * ** * * *
29657049 ATCTCAGCGTGTC-CTGAGGCTCAACTCACTTATCGCAACATGAGTTGA----TTTTTGACAA-A
60 ACCTCAACGTGTCACCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGA-AAGA
* * * *
29657108 CAGCAATTGAAAATACCTCAGCGTGCCC
124 CAGAAATTGAAAATACATCAACGTGTCC
* * *
29657136 CGAGGCTCAACTCACCTCCCGTAATATGAGTTGAT
1 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
29657171 TTAAAAAATA
Statistics
Matches: 654, Mismatches: 102, Indels: 113
0.75 0.12 0.13
Matches are distributed among these distances:
145 5 0.01
146 46 0.07
147 1 0.00
148 73 0.11
150 35 0.05
151 10 0.02
152 74 0.11
153 61 0.09
154 124 0.19
155 62 0.09
156 27 0.04
157 2 0.00
158 2 0.00
160 1 0.00
161 3 0.00
162 2 0.00
165 6 0.01
166 22 0.03
167 6 0.01
168 38 0.06
170 27 0.04
171 1 0.00
172 24 0.04
173 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (151 bp):
TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAGCAGAAATTAAAAATACCTCA
ACGTGTCACCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAAT
TGAAAATACATCAACGTGTCC
Found at i:29656514 original size:77 final size:75
Alignment explanation
Indices: 29656187--29657402 Score: 719
Period size: 75 Copynumber: 15.8 Consensus size: 75
29656177 TGAAGAACAA
* * * * *
29656187 AAATGGAAAACACCTCAGC--GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
29656250 TGAAAGACAG
66 TGAAAGACAG
* * * * * * *
29656260 AAATTGAAAATACCTCAACTTGTCTTGAGGCTCAACTCACTTCTTGCAGTATGAGTTGAATTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
29656325 TGAAAGACAG
66 TGAAAGACAG
* * * * * * * *
29656335 AAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCACTTCTTGTAGTATGAGTTGA--ATTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
29656398 TG-AA-ACAG
66 TGAAAGACAG
* * **
29656406 AAA-TAAAAATTATCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT
*
29656470 TTTTTAAAGACAG
63 TTTTGAAAGACAG
*
29656483 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
29656548 TTAAAGGCAG
66 TGAAAGACAG
* * * * * *
29656558 AAATTAAAAATACCTCAACGTGTCAGTCAAGGCTTAACTCACCTCTCGCAATATGAGCTGATTTT
1 AAATTGAAAATACCTCAGCGTGTC-CT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* *
29656623 TTTGAACCG-TAG
64 TTTGAA-AGACAG
*** ** * * * * * * *
29656635 AAATT-AAAGA-ACAGAAATG-GAAAATACCTCA-GCGT-ATGACCCGAGGCTCAACTCACCTCT
1 AAATTGAAA-ATAC-CTCA-GCG--TGT-CCTGAGGC-TCA--ACTC-A-CCTC-TCGCA-AT-A
* * * *
29656695 TACAATATGAGTTTTTTTTTTAAAAAAACAAACAG
52 T-GAGT-TGA-TTTT---TTT----GAA-AGACAG
* * *
29656730 AAATTGAAAATACCTCAGCGTG-CCTTGAGACTCAACTCACCTCTCACAATATGAGTTGGTTTTT
1 AAATTGAAAATACCTCAGCGTGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
29656794 TTGACAA-ACAG
65 TTGA-AAGACAG
*
29656805 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT--
****
29656870 CAAACAAAGACAG
64 -TTTGAAAGACAG
* *
29656883 AAATTGAAAATACCTCAGCACGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGAGTTGATTT
1 AAATTGAAAATACCTCAG--CGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* *
29656947 TTTTGACA-ATAG
63 TTTTGAAAGACAG
* * * * * * *
29656959 AAATTGCAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTTTTGCAATATGAGTTTGTTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG-TTG--ATTT
* * *
29657024 TTTTATAAAAATAG
63 TTTT-GAAAGACAG
* * * * *
29657038 AATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAGTTGA--TTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
29657101 TGACAA-ACAG
66 TGA-AAGACAG
* * * * *
29657111 CAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGTAATATGAGTTGATTTAAA
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT---
** * *
29657176 AAATAGACATAAAAACAG
63 -TTTTG----AAAGACAG
* * * * ** *
29657194 AAATTGAAAGTGA-CTCAACACGTGAGCC-AAGGCTCAACTCACCTCTCGTGATATGCA-TTAAT
1 AAATTGAAAAT-ACCTC-A-GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATG-AGTTGAT
*
29657256 TTTTTTGAAAG-TAG
61 TTTTTTGAAAGACAG
* * ** * * **
29657270 AATTTGAAAATACCTCGGCGTG-CC-CCGGCTCAACTCACCTCCCGCAACATGAGTT--TACTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
29657331 TGACAA-ACAG
66 TGA-AAGACAG
* * * *
29657341 CAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCT-TCCGCAATATGAGTTGATTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT-CGCAATATGAGTTGATTT
29657403 AAAAAACAGA
Statistics
Matches: 893, Mismatches: 165, Indels: 168
0.73 0.13 0.14
Matches are distributed among these distances:
70 12 0.01
71 70 0.08
72 29 0.03
73 101 0.11
74 42 0.05
75 211 0.24
76 45 0.05
77 120 0.13
78 35 0.04
79 56 0.06
80 45 0.05
81 7 0.01
82 5 0.01
83 22 0.02
84 5 0.01
85 37 0.04
86 7 0.01
87 5 0.01
88 3 0.00
89 3 0.00
90 4 0.00
91 5 0.01
92 3 0.00
93 2 0.00
94 4 0.00
95 10 0.01
96 5 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (75 bp):
AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
TGAAAGACAG
Found at i:29656785 original size:79 final size:73
Alignment explanation
Indices: 29656644--29657397 Score: 516
Period size: 79 Copynumber: 9.8 Consensus size: 73
29656634 GAAATTAAAG
* **
29656644 AACAGAAATGGAAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTTACAATATGAGTTT
1 AACAGAAATTGAAAATACCTCAGCG--TG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTT
29656709 TTTTTTTAAAAAAACA
63 TTTTTTT-----AACA
* * * *
29656725 AACAGAAATTGAAAATACCTCAGCGTGCCTTGAGACTCAACTCACCTCTCACAATATGAGTTGGT
1 AACAGAAATTGAAAATACCTCAGCGTGCC-CGAGGCTCAACTCACCTCTCGCAATATGAGTT-TT
*
29656790 TTTTTTGACA
64 TTTTTTAACA
29656800 AACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTT--T
****
29656865 TTTGACAAACAA
63 TTTTTTTAAC-A
* *
29656877 AGACAGAAATTGAAAATACCTCAGCACGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGTT
1 A-ACAGAAATTGAAAATACCTCAG--CGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
29656942 GATTTTTTTGAC-
62 -TTTTTTTTAACA
* * * * * *
29656954 AATAGAAATTGCAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTTTTGCAATATGAGTTTGT
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGA----GT
*
29657019 TTTTTTTTTATAAA
61 TTTTTTTTTA-ACA
* * * * * * * **
29657033 AATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAG-TTGA
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTT
*
29657097 TTTTTGACA
65 TTTTTAACA
* * *
29657106 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGTAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTT--T
****
29657171 TTAAAAAATAGACATAAA
63 TT--TTTTTA-AC----A
* * * * **
29657189 AACAGAAATTGAAAGTGA-CTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGTGATATGCA-T
1 AACAGAAATTGAAAAT-ACCTC-A-GCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATG-AGT
* *
29657252 TAATTTTTTTGA-A
61 T-TTTTTTTTAACA
** * * * * * **
29657265 AGTAGAATTTGAAAATACCTCGGCGTGCCC-CGGCTCAACTCACCTCCCGCAACATGAG-TTTAC
1 AACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTTT
*
29657328 TTTTGACA
66 TTTTAACA
* *
29657336 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCT-TCCGCAATATGAGTT
1 AACAGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCT-CGCAATATGAGTT
29657398 GATTTAAAAA
Statistics
Matches: 532, Mismatches: 105, Indels: 79
0.74 0.15 0.11
Matches are distributed among these distances:
70 7 0.01
71 25 0.05
72 24 0.05
73 76 0.14
74 45 0.08
75 63 0.12
76 41 0.08
77 10 0.02
78 29 0.05
79 87 0.16
80 41 0.08
81 27 0.05
82 1 0.00
83 18 0.03
84 5 0.01
85 32 0.06
86 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (73 bp):
AACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTTT
TTTTAACA
Found at i:29656856 original size:154 final size:152
Alignment explanation
Indices: 29656644--29657398 Score: 619
Period size: 154 Copynumber: 4.9 Consensus size: 152
29656634 GAAATTAAAG
* **
29656644 AACAGAAATGGAAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTTACAATATGAGTTT
1 AACAGAAATTGAAAATACCTCAGCG--TGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTT
*
29656709 TTTTTTTAAAAAAACAAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGACTCAACTCACCTCT
64 TTTTTTTAAAAAAA-AAACAGAAATTGAAAATACCTCAGCGTGCC-TGAGGCTCAACTCACCTCT
*
29656774 CACAATATGAGTTGGTTTTTTTGACA
127 CGCAATATGAGTTGGTTTTTTTGACA
*
29656800 AACAGAAATTGAAAATACCTCAGCGTG-CCCTGAGGCTCAACTCACCTCTCGCAATATGAG-TTG
1 AACAGAAATTGAAAATACCTCAGCGTGACCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTTT
* * * *
29656863 ATTTTGACAAACAAAGACAGAAATTGAAAATACCTCAGCACGTGAGCC-GAGGCTCAACTCACCT
65 TTTTTTA-AAAAAAAAACAGAAATTGAAAATACCTCAG--CGT--GCCTGAGGCTCAACTCACCT
* *
29656927 CTTGCAATATGAGTTGATTTTTTTGAC-
125 CTCGCAATATGAGTTGGTTTTTTTGACA
* * * * * * *
29656954 AATAGAAATTGCAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTTTTGCAATATGAGTTTGT
1 AACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTT-T
*** * * * * * *
29657019 TTTTTTTTTATAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCG
65 TTTTTTAAAAAAAAAACAGAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCTCG
* *
29657084 CAACATGAGTT-G-ATTTTTGACA
129 CAATATGAGTTGGTTTTTTTGACA
* * * * *
29657106 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGTAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-TT
**** * * *
29657171 TTAAAAAATAGACATAAAAACAGAAATTGAAAGTGA-CTCAACACGTGAGCC-AAGGCTCAACTC
65 TTTTTTAA-A-A-A-AAAAACAGAAATTGAAAAT-ACCTC-A-GCGT--GCCTGAGGCTCAACTC
** **
29657234 ACCTCTCGTGATATGCA-TTAATTTTTTTGA-A
121 ACCTCTCGCAATATG-AGTTGGTTTTTTTGACA
** * * * * * *
29657265 AGTAGAATTTGAAAATACCTCGGCGTG-CCC-CGGCTCAACTCACCTCCCGCAACATGAG-TTTA
1 AACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTT
* * * * * *
29657327 CTTTT----GACAAACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCT-TCCG
66 TTTTTAAAAAAAAAACAGAAATTGAAAATACCTCAGCGTG-CCTGAGGCTCAACTCACCTCT-CG
29657387 CAATATGAGTTG
129 CAATATGAGTTG
29657399 ATTTAAAAAA
Statistics
Matches: 478, Mismatches: 91, Indels: 71
0.75 0.14 0.11
Matches are distributed among these distances:
143 1 0.00
144 4 0.01
145 26 0.05
146 2 0.00
147 19 0.04
151 9 0.02
152 57 0.12
153 63 0.13
154 85 0.18
155 71 0.15
156 48 0.10
157 30 0.06
158 29 0.06
159 26 0.05
160 8 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (152 bp):
AACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTTT
TTTTTAAAAAAAAAACAGAAATTGAAAATACCTCAGCGTGCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGGTTTTTTTGACA
Found at i:29657165 original size:73 final size:73
Alignment explanation
Indices: 29656644--29657402 Score: 571
Period size: 73 Copynumber: 9.9 Consensus size: 73
29656634 GAAATTAAAG
* * **
29656644 AACAGAAATGGAAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTTACAATATGAGTTT
1 AACAGAAATTGAAAATACCTCAGCG--TGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG-TT
** *
29656709 TTTTTTTAAAAAAACA
63 GATTTTT-----GACA
** * *
29656725 AACAGAAATTGAAAATACCTCAGCGTGCCTTGAGACTCAACTCACCTCTCACAATATGAGTTGGT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-G-
*
29656790 TTTTTTGACA
64 ATTTTTGACA
*
29656800 AACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
29656864 TTTTGACAAACAA
66 TTTTG----AC-A
** *
29656877 AGACAGAAATTGAAAATACCTCAGCACGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGTT
1 A-ACAGAAATTGAAAATACCTCAG--CGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
29656942 GATTTTTTTGAC-
63 GA--TTTTTGACA
* * * * * * *
29656954 AATAGAAATTGCAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTTTTGCAATATGAGTTTGT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAG-TTG-
* * *
29657019 TTTTTTTTTATAAA
64 ---ATTTTT-GACA
* * * * * * * *
29657033 AATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
29657098 TTTTGACA
66 TTTTGACA
* * *
29657106 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGTAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
29657171 TTAAAAAATAGACATAAA
66 TT------TTGAC----A
* * ** * **
29657189 AACAGAAATTGAAAGTGA-CTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGTGATATGCA-T
1 AACAGAAATTGAAAAT-ACCTC-A-GCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATG-AGT
*
29657252 TAATTTTTTTGA-A
62 TGA--TTTTTGACA
** * * * * * *
29657265 AGTAGAATTTGAAAATACCTCGGCGTGCCCC--GGCTCAACTCACCTCCCGCAACATGAGTTTAC
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
29657328 TTTTGACA
66 TTTTGACA
* *
29657336 AACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCT-TCCGCAATATGAGTTGA
1 AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCT-CGCAATATGAGTTGA
29657400 TTT
65 TTT
29657403 AAAAAACAGA
Statistics
Matches: 551, Mismatches: 85, Indels: 92
0.76 0.12 0.13
Matches are distributed among these distances:
70 6 0.01
71 28 0.05
72 29 0.05
73 86 0.16
74 45 0.08
75 66 0.12
76 37 0.07
77 8 0.01
78 28 0.05
79 86 0.16
80 43 0.08
81 27 0.05
83 23 0.04
84 2 0.00
85 33 0.06
86 1 0.00
87 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (73 bp):
AACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGACA
Found at i:29657229 original size:545 final size:542
Alignment explanation
Indices: 29656039--29657503 Score: 1445
Period size: 545 Copynumber: 2.7 Consensus size: 542
29656029 GTGACCCTGA
** * *
29656039 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTT-AAAACTAGACATTAAAAACAGAAATTGA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTAAAAAATAGACATTAAAAACAGAAATTGA
* * **
29656103 AAATAGCTCAACACGTGAGCCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAA
64 AAATACCTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG-T--TTTTTTT-TTA
* * * *
29656168 CACAGAAATTGAAGAACAAAAATGGAAAACACCTCAGCGT--CTTGAGGTTCAACTCACCTCTCG
125 -A-A-AAA---AA-AACAGAAATTGAAAATACCTCAGCGTGCCTTGA-GCTCAACTCACCTCTCG
* * * * *
29656231 CAATATGAGCTGATTTTTTTGA-AAGACAGAAATTGAAAATACCTCAACTTGTCTTGAGGCTCAA
182 CAATATGAGTTG-TTTTTTTGACAA-ACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAA
* * * *** *
29656295 CTCACTTCTTGCAGTATGAGTTGAATTTT---TTGAAAGACAGAAATTGAAAATACATCA-ACGT
245 CTCACCTCTCGCAATATGAGTTG-ATTTTACAAACAAAGACAGAAATTGAAAATACCTCACACGT
* * * *
29656356 G-TCTTGAGGCTCAACTCACTTCTTGTAGTATGAGTTGA--ATTTTGAAACAGAAATAAAAATTA
309 GAGC-CGAGGCTCAACTCACTTCTTGTAATATGAGTTGATTTTTTTGAAACAGAAATAAAAATTA
* * *
29656418 TCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAGACAG
373 CCTCAGCATGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAG
* * * *
29656483 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
438 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAACATGAGTTGATTTTTG
** **
29656548 TTAAAGGCAGAAATTAAAAATACCTCAACGTGTCAGTCAAG
503 ACAAA-GCAGAAATTAAAAATACCTCAACGTGTCACCCAAG
* * * *** * *
29656589 GCTTAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAACCGTAGAAATTAAAGAACAGAAATG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTAAAAAATAGACATTAAA-AACAGAAATT
* *** * * **
29656654 GAAAATACCTCAGCGTATGACCCGAGGCTCAACTCACCTCTTACAATATGAGTTTTTTTTTTAAA
62 GAAAATACCTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTTTTTTTTTAAA
*
29656719 AAAACAAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGACTCAACTCACCTCTCACAATATGA
127 AAAA-AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAG-CTCAACTCACCTCTCGCAATATGA
29656784 GTTGGTTTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCT
190 GTT-GTTTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCT
29656849 CGCAATATGAGTTGATTTTGACAAACAAAGACAGAAATTGAAAATACCTCAGCACGTGAGCCGAG
254 CGCAATATGAGTTGATTTT-ACAAACAAAGACAGAAATTGAAAATACCTCA-CACGTGAGCCGAG
* * * ***
29656914 GCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTGACAATAGAAATTGCAATTACCTCAGCA
317 GCTCAACTCACTTCTTGTAATATGAGTTGATTTTTTTGA-AACAGAAATAAAAATTACCTCAGCA
* * * * * *
29656979 TGTCCCGAGGCTCAACTCACCTTTTGCAATATGAGTTTGTTTTTTTTTTATAAAAATAGAATTTG
381 TGTCCCAAGGCTCAACTCACCTCTCGCAATATGAG-TTGATTTTTTTTT-TAAAAACAGAAATTG
* *
29657044 AAAATATCTCAGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAGTTGATTTTTGACAAA-
444 AAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAACATGAGTTGATTTTTGACAAAG
* * * *
29657108 CAGCAATTGAAAATACCTCAGCGTG-C-CCCGAG
509 CAGAAATTAAAAATACCTCAACGTGTCACCCAAG
* *
29657140 GCTCAACTCACCTCCCGTAATATGAGTTGA-TTTAAAAAATAGACA-TAAAAACAGAAATTGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAATAGACATTAAAAACAGAAATTGAAA
* ** *
29657203 GTGA-CTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGTGATATGCA-TTAATTTTTTT----
66 AT-ACCTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATG-AGTT-TTTTTTTTAAAA
* ** * * ** * *
29657262 -GAAAGTAGAATTTGAAAATACCTCGGCGTGCCCCG-GCTCAACTCACCTCCCGCAACATGAGTT
128 AAAAAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGCTCAACTCACCTCTCGCAATATGAGTT
** * * *
29657325 -TACTTTTGACAAACAGCAATTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCT-TCCGC
193 GTTTTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCT-CGC
* * * *
29657388 AATATGAGTTGATTTAAAAAACAGACATAAAAACAGAAATTGAAAGTGA-CTCAACACGTGAGCC
257 AATATGAGTTGATTT----TACA-A-ACAAAGACAGAAATTGAAAAT-ACCTC-ACACGTGAGCC
* *
29657452 AAGGCTCAACTCACTTCTCGTAATATGAGTTGATTTTTTTGAAAACAGAAAT
314 GAGGCTCAACTCACTTCTTGTAATATGAGTTGATTTTTTTG-AAACAGAAAT
29657504 GAAATATCCA
Statistics
Matches: 761, Mismatches: 119, Indels: 79
0.79 0.12 0.08
Matches are distributed among these distances:
535 1 0.00
536 71 0.09
538 24 0.03
539 4 0.01
540 28 0.04
541 77 0.10
542 3 0.00
543 24 0.03
544 7 0.01
545 141 0.19
546 19 0.02
547 11 0.01
548 25 0.03
549 1 0.00
550 67 0.09
551 33 0.04
552 21 0.03
553 124 0.16
554 12 0.02
555 68 0.09
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (542 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAATAGACATTAAAAACAGAAATTGAAA
ATACCTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTTTTTTTTTAAAAAAA
AAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGCTCAACTCACCTCTCGCAATATGAGTTGTT
TTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTACAAACAAAGACAGAAATTGAAAATACCTCACACGTGAGCCGAGGCTCAACTC
ACTTCTTGTAATATGAGTTGATTTTTTTGAAACAGAAATAAAAATTACCTCAGCATGTCCCAAGG
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCAG
CGTGTCCTGAGGCTCAACTCACCTATCGCAACATGAGTTGATTTTTGACAAAGCAGAAATTAAAA
ATACCTCAACGTGTCACCCAAG
Found at i:29657336 original size:230 final size:232
Alignment explanation
Indices: 29656760--29657495 Score: 768
Period size: 230 Copynumber: 3.2 Consensus size: 232
29656750 TGCCTTGAGA
** ** ** *
29656760 CTCAACTCACCTCTCACAATATGAGTTGGTTTTTTTGACAAACAGAAATTGAAAATACCTCAGCG
1 CTCAACTCACCTCTCGTAATATGAGTTAATTTTTTTGA-AAGTAGAATTTGAAAATACCTCAGCG
* * *
29656825 TGCCCTGAGGCTCAACTCACCT-CTCGCAATATGAGTTGA-TTTTGACAAACAAAGACAGAAATT
65 TGTCCTCAGGCTCAACTCACCTAC-CGCAACATGAGTTGACTTTTGACAAAC--AG-C---AATT
** ** **
29656888 GAAAATACCTCAGCACGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTT----TT
123 GAAAATACCTCAG--CGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAAA
** * * * * ** *
29656949 TTGAC-----AATAGAAATTGCAA-TTACCTCAGCA--TGTCCCGAGG
186 CAGACATAAAAACAGAAATTGAAAGTGA-CTCAACACGTGAGCCAAGG
* * * ** * * *
29656989 CTCAACTCACCTTTTGCAATATGAGTTTGTTTTTTTTTTATAAAAATAGAATTTGAAAATATCTC
1 CTCAACTCACCTCTCGTAATATGA----GTTAATTTTTT-TGAAAGTAGAATTTGAAAATACCTC
* * * *
29657054 AGCGTGTCCTGAGGCTCAACTCACTTATCGCAACATGAGTTGATTTTTGACAAACAGCAATTGAA
61 AGCGTGTCCTCAGGCTCAACTCACCTACCGCAACATGAGTTGACTTTTGACAAACAGCAATTGAA
* *
29657119 AATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGTAATATGAGTTGATTTAAAAAATAGAC
126 AATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAAACAGAC
29657184 ATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGG
191 ATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGG
* *
29657226 CTCAACTCACCTCTCGTGATATGCA-TTAATTTTTTTGAAAGTAGAATTTGAAAATACCTCGGCG
1 CTCAACTCACCTCTCGTAATATG-AGTTAATTTTTTTGAAAGTAGAATTTGAAAATACCTCAGCG
* * *
29657290 TG-CC-CCGGCTCAACTCACCTCCCGCAACATGAGTTTACTTTTGACAAACAGCAATTGAAAATA
65 TGTCCTCAGGCTCAACTCACCTACCGCAACATGAGTTGACTTTTGACAAACAGCAATTGAAAATA
* *
29657353 CCTCAGCGTGCCCCGAGGCTTAACTCACCTTCCGCAATATGAGTTGATTTAAAAAACAGACATAA
130 CCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAAACAGACATAA
29657418 AAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGG
195 AAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGG
* *
29657456 CTCAACTCACTTCTCGTAATATGAGTTGATTTTTTTGAAA
1 CTCAACTCACCTCTCGTAATATGAGTTAATTTTTTTGAAA
29657496 ACAGAAATGA
Statistics
Matches: 434, Mismatches: 52, Indels: 41
0.82 0.10 0.08
Matches are distributed among these distances:
226 39 0.09
228 17 0.04
229 22 0.05
230 190 0.44
231 3 0.01
232 29 0.07
233 74 0.17
234 13 0.03
235 18 0.04
236 2 0.00
237 26 0.06
238 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (232 bp):
CTCAACTCACCTCTCGTAATATGAGTTAATTTTTTTGAAAGTAGAATTTGAAAATACCTCAGCGT
GTCCTCAGGCTCAACTCACCTACCGCAACATGAGTTGACTTTTGACAAACAGCAATTGAAAATAC
CTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGATTTAAAAAACAGACATAAA
AACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGG
Found at i:29657410 original size:71 final size:70
Alignment explanation
Indices: 29657273--29657411 Score: 181
Period size: 71 Copynumber: 2.0 Consensus size: 70
29657263 AAAGTAGAAT
* * * *
29657273 TTGAAAATACCTCGGCGTGCCCCGGCTCAACTCACCTCCCGCAACATGAGTTTACTTTTGACAAA
1 TTGAAAATACCTCAGCGTGCCCCGGCTCAACTCACCTCCCGCAACATGAGTTGAC-TTTAAAAAA
29657338 CAGCAA
65 CAGCAA
* * *
29657344 TTGAAAATACCTCAGCGTGCCCCGAGGCTTAACTCACCTTCCGCAATATGAGTTGA-TTTAAAAA
1 TTGAAAATACCTCAGCGTGCCCC--GGCTCAACTCACCTCCCGCAACATGAGTTGACTTTAAAAA
29657408 ACAG
64 ACAG
29657412 ACATAAAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 32 0.54
73 27 0.46
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (70 bp):
TTGAAAATACCTCAGCGTGCCCCGGCTCAACTCACCTCCCGCAACATGAGTTGACTTTAAAAAAC
AGCAA
Found at i:29662349 original size:14 final size:14
Alignment explanation
Indices: 29662332--29662363 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
29662322 ATGTTCTCGC
29662332 GATCCTTCTTTCCT
1 GATCCTTCTTTCCT
29662346 GATCCTTCTTTCCT
1 GATCCTTCTTTCCT
29662360 GATC
1 GATC
29662364 TTTATTCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.34, G:0.09, T:0.47
Consensus pattern (14 bp):
GATCCTTCTTTCCT
Found at i:29669622 original size:73 final size:73
Alignment explanation
Indices: 29669499--29670184 Score: 568
Period size: 80 Copynumber: 8.9 Consensus size: 73
29669489 TCTGTTTTTT
* * *
29669499 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTCAATTACTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTG
29669564 TTTGTCAA
66 TTTGTCAA
* * * *
29669572 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCGGAGGTATTTTCAAATTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTG
*
29669637 CTT-TCAAAA
66 TTTGTC--AA
* * ** * * *
29669646 AAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTTACTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC--GCTGAGGTATTTTCAATTTC
* **
29669711 TATTTTTATGTCTGTTTTTT
64 ---TGTT-TGTC------AA
* * * *
29669731 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCTTCGGGGCATGCTGAGGTATTTTCAATTGCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTG
29669796 TTTGTCAA
66 TTTGTCAA
* * * * * *
29669804 AAATCAACTCATGTTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC-AATT-TC
* * *
29669869 TTTTTATAAAAAAA
64 TGTTTGT----CAA
* * * * * *
29669883 AAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTAATTGCAATTTCT
1 AAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCT
*
29669948 -ATTGTCAAAA
65 GTTTGTC--AA
* **
29669958 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTATTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC--GCTGAGGTATTTTCAA----
29670023 TGTCTCTGTTTGTC-A
60 T-T-TCTGTTTGTCAA
* * *
29670038 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGGTACGCTGAGGTATTTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTG
*
29670103 TTTGTTTTTAAA
66 TTTG----TCAA
* * * *
29670115 AAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCCATTT
1 AAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGC--ACGCTGAGGTATTTTCAATTT
29670180 CTGTT
63 CTGTT
29670185 CTTTAATTTC
Statistics
Matches: 489, Mismatches: 85, Indels: 71
0.76 0.13 0.11
Matches are distributed among these distances:
72 10 0.02
73 110 0.22
74 80 0.16
75 11 0.02
76 30 0.06
77 8 0.02
78 49 0.10
79 16 0.03
80 112 0.23
81 3 0.01
82 3 0.01
83 21 0.04
85 36 0.07
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (73 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTCTG
TTTGTCAA
Found at i:29669812 original size:232 final size:233
Alignment explanation
Indices: 29669410--29670613 Score: 1025
Period size: 232 Copynumber: 5.2 Consensus size: 233
29669400 TTCTGTTTTC
* *
29669410 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGA-GTCATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGT-ATTTTCA
* **** *
29669474 ATTTCTGTTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGGGG
65 ATTTCTATTTTTATGTCTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGG
* *
29669539 CACGCTGAGGTATTTTCAATTACTGTTTGTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAG
130 CACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * * *
29669604 CCTCGGGGCACGCGGAGGTATTTTCAAATTCTA-CTTTC
195 CCTCAGGACACGCTGAGGTATTTTCAAATTCTATCTTTA
* * * * *
29669642 AAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTTACTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAA
**** *
29669707 TTTCTATTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAG-CTTCGGGG
66 TTTCTATTTTTATGTCTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGGG
* * *
29669771 CATGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGAGAAGTGAGTTGAG
130 CACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
29669836 CCTCAGGACACGCTGAGATATTTTCAAATTCTATTTTTATAAA
195 CCTCAGGACACGCTGAGGTATTTTCAAATTCTA-TCTT-T--A
* * * * * *
29669879 AAAAAAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGG--GACATGCTGAGGTAATTGCA
1 AAAAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCA
* * **
29669942 ATTTCTA----T-TGTC----AAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCT
65 ATTTCTATTTTTATGTCTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGG
29669998 CACGTGCTGAGGTATTTTCAATTTCTGTCTCTGTTTGTC-AAAATCAACTCATATTGCGAGAGGT
130 CAC--GCTGAGGTATTTTCAA--T-TG---CTGTTTGTCAAAAATCAACTCATATTGCGAGAGGT
* ** * * * *
29670062 GAGTTGAGCTTCAGGGTACGCTGAGGTATTTTCAATTTCTGTTTGTTTTT
187 GAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATTC--TAT-CTTTA
* * * * * *
29670112 AAAAAAA-CAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCC
1 AAAAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCA
* * * *
29670176 ATTTCTGTTCTTTAATTTCTATGGTTCAAAAAAATCAGCTCATATTGCGAGAGGTCAGTTGAGCC
65 ATTTCTATT-TTT-ATGTC--T-GTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * * * * *
29670241 TTGACTGACACGTTGAGGCATTTTCAATTTCTGCCTT-TCAAAAAAATCAACTCATATTGCGAGA
124 TTG--GGGCACGCTGAGGTATTTTCAATTGCTG-TTTGTC--AAAAATCAACTCATATTGCGAGA
* * *
29670305 GGTGAGTTGAGCCTCAGGACACGCTGACGTAATTTCAATTTCTATCTTTTAA
184 GGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATTCTATC-TTT-A
* *
29670357 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG--GACACGCTGA-G-A---T--A
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAA
* ** * * * * * * * *** *
29670413 -----ATTTTTATTTCTGTTTCAGAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGAC
66 TTTCTATTTTTATGTCTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGGC
* * * *
29670473 ACG-TCGAGGTATTTTCAATTTCTGTCTT-TCAAAAAATTCAACTCATACTGCAAGAAGTGAGTT
131 ACGCT-GAGGTATTTTCAATTGCTGT-TTGTC-AAAAA-TCAACTCATATTGCGAGAGGTGAGTT
* * * *
29670536 GAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTCTTTCA
192 GAGCCTCAGGACACGCTGAGGTATTTTCAAATTCTATCTTT-A
* *
29670579 AAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
29670614 ACCTCAAGAC
Statistics
Matches: 822, Mismatches: 101, Indels: 108
0.80 0.10 0.10
Matches are distributed among these distances:
222 44 0.05
223 84 0.10
225 28 0.03
226 3 0.00
227 35 0.04
228 2 0.00
229 21 0.03
230 3 0.00
231 10 0.01
232 248 0.30
233 8 0.01
234 79 0.10
235 12 0.01
236 26 0.03
237 8 0.01
238 31 0.04
239 1 0.00
241 4 0.00
242 1 0.00
243 13 0.02
244 7 0.01
245 38 0.05
246 61 0.07
247 1 0.00
249 51 0.06
251 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (233 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAA
TTTCTATTTTTATGTCTGTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGGC
ACGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
CTCAGGACACGCTGAGGTATTTTCAAATTCTATCTTTA
Found at i:29669948 original size:80 final size:76
Alignment explanation
Indices: 29669499--29670618 Score: 853
Period size: 73 Copynumber: 14.5 Consensus size: 76
29669489 TCTGTTTTTT
* * * * *
29669499 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGGGGCACGCTGAGGTATTTTCAATTACTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
*
29669564 T-TTGTC--AA
66 TCTTTTCAAAA
* * * *
29669572 AAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCGGAGGTATTTTCAAATTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
29669637 -C-TTTCAAAA
66 TCTTTTCAAAA
* * ** * * *
29669646 AAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTTACTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC--GCTGAGGTATTTTCAATTTC
* ****
29669711 TATTTTTATGTCTGTTTTTT
64 TA-TCTT-T-TC----AAAA
* * * * * *
29669731 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCTTCGGGGCATGCTGAGGTATTTTCAATTGCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
*
29669796 T-TTGTC--AA
66 TCTTTTCAAAA
* * * * *
29669804 AAATCAACTCATGTTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
* *
29669869 TTTTTATAAAAAAA
66 TCTTT-T--CAAAA
* * * * *
29669883 AAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTAATTGCAATTTCT
1 AAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCT
*
29669948 A--TTGTCAAAA
65 ATCTTTTCAAAA
* **
29669958 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTATTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC--GCTGAGGTATTTTCAATTTC
* ****
29670023 TGTCTCTGTTTGTCA
64 TATCT-T-TTCAAAA
* *
29670038 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGG-TACGCTGAGGTATTTTCAATTTCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTTCAATTTC-
* * *
29670102 GTTTGTTTTTAAAA
64 -TATCTTTTCAAAA
* *
29670116 AAA-CAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCCATTT
1 AAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATTTT-CA---
*
29670180 CTGTTCTTTAATTTCTATGGTTCAAAA
59 AT-TTC--T-A--TCT-T--TTCAAAA
* * * * * *
29670207 AAATCAGCTCATATTGCGAGAGGTCAGTTGAGCCTTGACTGACACGTTGAGGCATTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG--GGACACGCTGAGGTATTTTCAATTTC
* *
29670272 T-GCCTTTCAAAA
64 TATCTTTTCAAAA
* * *
29670284 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGACGTAATTTCAATTTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
*
29670349 TCTTTTAAAAAA
66 TCTTTT-CAAAA
* * *
29670361 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGATAATTTT-TATTTC-
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGT-ATTTTCAATTTCT
* *
29670424 -T-GTTTC--AG
65 ATCTTTTCAAAA
* * * * * * **
29670432 AATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGACACG-TCGAGGTATTTTCAATTTCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT-GAGGTATTTTCAATTTCT
*
29670496 GTC-TTTCAAAA
65 ATCTTTTCAAAA
* * * * ** * *
29670507 AATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
29670572 TC-TTTCAAAAA
66 TCTTTTC-AAAA
* * *
29670583 AAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
29670619 AAGACGCTGA
Statistics
Matches: 843, Mismatches: 144, Indels: 117
0.76 0.13 0.11
Matches are distributed among these distances:
70 6 0.01
71 45 0.05
72 3 0.00
73 118 0.14
74 80 0.09
75 100 0.12
76 74 0.09
77 101 0.12
78 63 0.07
79 12 0.01
80 110 0.13
81 8 0.01
82 1 0.00
83 17 0.02
84 2 0.00
85 41 0.05
86 3 0.00
87 1 0.00
88 2 0.00
89 1 0.00
90 2 0.00
91 51 0.06
92 1 0.00
93 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (76 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTCTA
TCTTTTCAAAA
Found at i:29670144 original size:312 final size:309
Alignment explanation
Indices: 29669570--29670618 Score: 897
Period size: 312 Copynumber: 3.4 Consensus size: 309
29669560 ACTGTTTGTC
* * * * *
29669570 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCGGAGGTATTTTCAAATTC
1 AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
* * * *
29669635 TACTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTTA
66 TA-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTA
* * ** *
29669700 CTTTCAATTTCTATTTTTATGTCTGTTTTTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCT
130 ATTTCAATTTC------TATCTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCT
* * * * * *
29669765 TCGGGGCATGCTGAGGTATTTTCAATTGCTGTTTGTCAAAAATCAACTCATGTTGCGAGAAGTGA
189 TCAGGGCACGCTGAGGTATTTTCAATTGCTGTTTGTAAAAAAACAACTCATATTGCAAGAAGTGA
29669830 GTTGAGCCTCAGG-ACACGCTGAGATATTTTCAAATTCTATT-TTT-A-TA-AAAA
254 GTTGAGCCTCAGGCACACGCTGAGATATTTTCAAATTCTATTCTTTAATTAGAAAA
* * * *
29669881 AAAAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTAATTGCAATTT
1 AAAAAAC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
*
29669946 CTATTGTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGT
65 CTATT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGT
* * *
29670011 ATTTTCAATTTCTGTCTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
129 AATTTCAATTTCTATCTCTGTTT-TAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
* * *
29670076 GGTACGCTGAGGTATTTTCAATTTCTGTTTGTTTTTAAAAAAACAAACTCATATTGCAAGAGGTG
193 GGCACGCTGAGGTATTTTCAATTGCTGTTTG----TAAAAAAAC-AACTCATATTGCAAGAAGTG
* * * * * * **
29670141 AGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCCATTTCTGTTCTTTAATTTCTATGGTTCAA
253 AGTTGAGCCTCAGG-CACACGCTGAGATATTTTCAAATTCTATTCTTTAA--T-TA--G-AAAA
* * * * * * *
29670205 AAAAATCAGCTCATATTGCGAGAGGTCAGTTGAGCCTTGACTGACACGTTGAGGCATTTTCAATT
1 AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCG--GGACACGCTGAGGTATTTTCAATT
* *
29670270 TCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACAC--GCTGA
64 TCT--ATTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACGTGCTGA
* **
29670332 CGTAATTTCAATTTCTATCT-T-TTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
126 GGTAATTTCAATTTCTATCTCTGTT--TTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-C
* * * * * ** * * *
29670395 TT--GGGACACGCTGAGATAATTTT-TATTTCTG-TT-TCAGAATTCAACTCATACTACAAAAAG
188 TTCAGGG-CACGCTGAGGT-ATTTTCAATTGCTGTTTGTAAAAAAACAACTCATATTGCAAGAAG
* * * * *
29670455 TGAGTTGAGCCTCAAG-ACACG-TCGAGGTATTTTCAATTTCT-GTC--T--TT---CAA
251 TGAGTTGAGCCTCAGGCACACGCT-GAGATATTTTCAAATTCTATTCTTTAATTAGAAAA
** * * * ** *
29670505 AAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
* * * *
29670570 TGTCTTTCAAAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTC
66 --TATTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
29670619 AAGACGCTGA
Statistics
Matches: 618, Mismatches: 86, Indels: 80
0.79 0.11 0.10
Matches are distributed among these distances:
298 29 0.05
299 37 0.06
300 35 0.06
306 10 0.02
307 66 0.11
311 16 0.03
312 147 0.24
313 3 0.00
314 44 0.07
315 3 0.00
316 29 0.05
317 5 0.01
320 2 0.00
322 7 0.01
323 78 0.13
324 38 0.06
325 21 0.03
326 44 0.07
327 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (309 bp):
AAAAAACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
TATTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTAA
TTTCAATTTCTATCTCTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGGC
ACGCTGAGGTATTTTCAATTGCTGTTTGTAAAAAAACAACTCATATTGCAAGAAGTGAGTTGAGC
CTCAGGCACACGCTGAGATATTTTCAAATTCTATTCTTTAATTAGAAAA
Found at i:29670173 original size:158 final size:156
Alignment explanation
Indices: 29669499--29670618 Score: 719
Period size: 154 Copynumber: 7.2 Consensus size: 156
29669489 TCTGTTTTTT
* * *
29669499 AAATCAACTCATATTGCGGGAGGTGAGTTGAGCCTTGGG--GCACGCTGAGGTATTTTCAA--T-
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTC
* * *
29669559 TA---CTGTTTGTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCGGAG
66 TATCTCTGTTTGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-GGGCACGCTGAG
* **
29669621 GTATTTTCAAATTC---TACTTTCAAAA
129 GTATTTTCAATTTCTGTTTGTTTCAAAA
* * * ** * * *
29669646 AAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACGTGTTGAGTTACTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTC
* ** * *
29669711 TATTTTTATGTCTGTTT-TTTAAATCAACTCATATTGCGGGAGGTGAGTTGAGCTTCGGGGCATG
66 ------TATCTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-GGGCACG
*
29669775 CTGAGGTATTTTCAATTGCTGTTTG--TC--AA
124 CTGAGGTATTTTCAATTTCTGTTTGTTTCAAAA
* * * * *
29669804 AAATCAACTCATGTTGCGAGAAGTGAGTTGAGCCTCAGG--ACACGCTGAGATATTTTCAAATTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTC
* * * ***** * * * *
29669867 TATTTTTATAAAAAAAAAAACAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGACATGCTGA
66 TATCTCTGT-TTGTCAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGCTTCGGG-CACGCTGA
* * *
29669932 GGTAATTGCAATTTCT-ATTG--TCAAAA
128 GGTATTTTCAATTTCTGTTTGTTTCAAAA
* * **
29669958 AAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACGTGCTGAGGTATTTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTC
* *
29670023 TGTCTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGGTACGCTGAGG
66 TATCTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-GGGCACGCTGAGG
*
29670088 TATTTTCAATTTCTGTTTGTTTTTAAAA
130 TATTTTCAATTTCTGTTTG-TTTCAAAA
* * *
29670116 AAA-CAAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGTATTTTCCATTT
1 AAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTT
* * * * *
29670180 CTGTTCTTTAATTTCTATGGTTCAAAAAAATCAGCTCATATTGCGAGAGGTCAGTTGAGCCTTGA
65 CT-ATC--T-CTGT-T-T-G-TC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTT--
* * * * **
29670245 CTGACACGTTGAGGCATTTTCAATTTCTG--CCTTTCAAAA
116 CGGGCACGCTGAGGTATTTTCAATTTCTGTTTGTTTCAAAA
* * *
29670284 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGACGTAATTTCAATTTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTC
****
29670347 TATCT-T-TTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGGACACGCTGA
66 TATCTCTGTT-TGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCGGG-CACGCTGA
* * *
29670409 GATAATTTT-TATTTC----TGTTTC--AG
128 GGT-ATTTTCAATTTCTGTTTGTTTCAAAA
* * * * * * **
29670432 AATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAG--ACACG-TCGAGGTATTTTCAATTT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT-GAGGTATTTTCAATTT
* *** * * * * * * *
29670494 C--TGTC--TTTCAAAAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGTTGA
65 CTATCTCTGTTTGTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCTTC-GGGCACGCTGA
*
29670555 GGTATTTTCAATTTCTG--TCTTTCAAAAA
128 GGTATTTTCAATTTCTGTTTGTTTC-AAAA
* * *
29670583 AAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
29670619 AAGACGCTGA
Statistics
Matches: 767, Mismatches: 147, Indels: 114
0.75 0.14 0.11
Matches are distributed among these distances:
145 13 0.02
146 44 0.06
147 38 0.05
148 58 0.08
149 14 0.02
150 10 0.01
151 30 0.04
152 25 0.03
153 54 0.07
154 120 0.16
155 11 0.01
156 43 0.06
157 1 0.00
158 101 0.13
159 60 0.08
160 4 0.01
161 8 0.01
162 3 0.00
163 2 0.00
164 1 0.00
165 3 0.00
166 23 0.03
168 42 0.05
169 32 0.04
170 3 0.00
171 23 0.03
172 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Consensus pattern (156 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTC
TATCTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCGGGCACGCTGAGGT
ATTTTCAATTTCTGTTTGTTTCAAAA
Found at i:29670284 original size:77 final size:75
Alignment explanation
Indices: 29670200--29670623 Score: 444
Period size: 77 Copynumber: 5.6 Consensus size: 75
29670190 ATTTCTATGG
* * * * *
29670200 TTCAAAAAAATCAGCTCATATTGCGAGAGGTCAGTTGAGCCTTGACTGACACGTTGAGGCATTTT
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCA-AGACACGTTGAGGTATTTT
29670265 CAATTTCTGCCT
64 CAATTTCTGCCT
* * * *
29670277 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGACGTAATTTCA
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
* *
29670342 ATTTCTATCTT
66 ATTTCT-GCCT
* *** * *
29670353 TTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGACACGCTGAGATAATTTT
1 TT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGT-ATTTT
*
29670418 -TATTTCTG--T
64 CAATTTCTGCCT
* * * * * * * *
29670427 TTC--AGAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGACACGTCGAGGTATTTTCA
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
*
29670490 ATTTCTGTCT
66 ATTTCTGCCT
* * * *
29670500 TTCAAAAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
1 TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
*
29670565 ATTTCTGTCT
66 ATTTCTGCCT
* * *
29670575 TTCAAAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGAC
1 TTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
29670624 GCTGAGGTTG
Statistics
Matches: 294, Mismatches: 44, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
70 5 0.02
71 47 0.16
73 4 0.01
74 3 0.01
75 91 0.31
76 44 0.15
77 96 0.33
78 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (75 bp):
TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
ATTTCTGCCT
Found at i:29670462 original size:71 final size:73
Alignment explanation
Indices: 29670260--29670582 Score: 253
Period size: 75 Copynumber: 4.3 Consensus size: 73
29670250 ACGTTGAGGC
* * * * * * *
29670260 ATTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 ATTTTCAATTTCTG-CTTTC-AAAAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGAC
29670325 ACG-CTGACG-T
64 ACGTC-GA-GAT
* * * * * * * * * ***
29670335 AATTTCAATTTCTATCTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG
1 ATTTTCAATTTCT-GC-TTT--CAAAAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAG
29670400 ACACG-CTGAGAT
62 ACACGTC-GAGAT
* *
29670412 AATTTT-TATTTCTG-TTTC-AGAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGACA
1 -ATTTTCAATTTCTGCTTTCAAAAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGACA
*
29670474 CGTCGAGGT
65 CGTCGAGAT
* *
29670483 ATTTTCAATTTCTGTCTTTCAAAAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGAC
1 ATTTTCAATTTCTG-CTTTC-AAAAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGAC
* *
29670548 ACGTTGAGGT
64 ACGTCGAGAT
29670558 ATTTTCAATTTCTGTCTTTCAAAAA
1 ATTTTCAATTTCTG-CTTTCAAAAA
29670583 AAATTAGCTC
Statistics
Matches: 211, Mismatches: 25, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
70 5 0.02
71 47 0.22
72 1 0.00
73 4 0.02
74 8 0.04
75 82 0.39
76 4 0.02
77 56 0.27
78 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (73 bp):
ATTTTCAATTTCTGCTTTCAAAAATTCAACTCATACTACAAAAAGTGAGTTGAGCCTCAAGACAC
GTCGAGAT
Found at i:29675410 original size:31 final size:31
Alignment explanation
Indices: 29675369--29675436 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
29675359 TACAAAATAA
* *
29675369 TCACTGAACTATTTGAAAA-TTTTCATTTAAG
1 TCACTAAACTA-TTCAAAAGTTTTCATTTAAG
*
29675400 TCACTAAACTATTCAAAAGTTTTTATTTAAG
1 TCACTAAACTATTCAAAAGTTTTCATTTAAG
29675431 TCACTA
1 TCACTA
29675437 GAATGTTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGTTTTCATTTAAG
Found at i:29678094 original size:20 final size:20
Alignment explanation
Indices: 29678069--29678107 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29678059 TTAACAAGTA
29678069 TCCTT-AAAATATTTGATATC
1 TCCTTAAAAAT-TTTGATATC
29678089 TCCTTAAAAATTTTGATAT
1 TCCTTAAAAATTTTGATAT
29678108 ATACCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (20 bp):
TCCTTAAAAATTTTGATATC
Found at i:29679317 original size:20 final size:21
Alignment explanation
Indices: 29679271--29679323 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
29679261 TACTAATTAC
29679271 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
29679292 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
29679312 ATATATTCTAAT
1 AAATATT-TAAT
29679324 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:29679467 original size:11 final size:11
Alignment explanation
Indices: 29679451--29679491 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
29679441 TAATATTAAC
29679451 TAATTTAAATA
1 TAATTTAAATA
29679462 TAATTTAAATA
1 TAATTTAAATA
29679473 TAATTTAAATA
1 TAATTTAAATA
29679484 TATATTTA
1 TA-ATTTA
29679492 TTACTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 24 0.83
12 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TAATTTAAATA
Found at i:29679514 original size:39 final size:35
Alignment explanation
Indices: 29679462--29679568 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 35
29679452 AATTTAAATA
29679462 TAATTTAAATATAATTTAAATATATATTTATTACT
1 TAATTTAAATATAATTTAAATATATATTTATTACT
* * * * *
29679497 TGATTT-ACTAAAATAT-AATATA-ATAATATTAAC-
1 TAATTTAAATATAATTTAAATATATAT-TTATT-ACT
29679530 TAATTTAAATATAATTTAAATATATATTTATTACT
1 TAATTTAAATATAATTTAAATATATATTTATTACT
29679565 TAAT
1 TAAT
29679569 AATAACATGT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
32 2 0.04
33 15 0.27
34 18 0.32
35 19 0.34
36 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (35 bp):
TAATTTAAATATAATTTAAATATATATTTATTACT
Found at i:29679546 original size:11 final size:11
Alignment explanation
Indices: 29679530--29679559 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
29679520 TAATATTAAC
29679530 TAATTTAAATA
1 TAATTTAAATA
29679541 TAATTTAAATA
1 TAATTTAAATA
29679552 TATATTTA
1 TA-ATTTA
29679560 TTACTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTAAATA
Found at i:29680162 original size:44 final size:43
Alignment explanation
Indices: 29680113--29680200 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
29680103 TTTAGGCATC
* * *
29680113 TAGCAGCCCTTATATTCGCCCCAACTTACATCAATATTTTAATA
1 TAGCAGCCCCTATA-TCCCCCCAACATACATCAATATTTTAATA
** *
29680157 TAGCAGCCCCTATATCCCCCCTGCATCCATCAATATTTTAATA
1 TAGCAGCCCCTATATCCCCCCAACATACATCAATATTTTAATA
29680200 T
1 T
29680201 GTTAGTGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
43 25 0.66
44 13 0.34
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.33
Consensus pattern (43 bp):
TAGCAGCCCCTATATCCCCCCAACATACATCAATATTTTAATA
Found at i:29681375 original size:17 final size:16
Alignment explanation
Indices: 29681341--29681375 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29681331 ATCAAATCAT
*
29681341 TGTAATACGAATAGAA
1 TGTAATACGAAAAGAA
29681357 TGTAATACGATAAAGAA
1 TGTAATACGA-AAAGAA
29681374 TG
1 TG
29681376 AACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (16 bp):
TGTAATACGAAAAGAA
Found at i:29681994 original size:11 final size:11
Alignment explanation
Indices: 29681968--29682001 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29681958 TAAGCGAAGA
*
29681968 AAGAATAGAA-
1 AAGATTAGAAT
29681978 AAGATTAGAAT
1 AAGATTAGAAT
29681989 AAGATTAGAAT
1 AAGATTAGAAT
29682000 AA
1 AA
29682002 AATGCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (11 bp):
AAGATTAGAAT
Found at i:29683071 original size:16 final size:16
Alignment explanation
Indices: 29683050--29683083 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29683040 GAGGAAATTC
29683050 TAACGGCAATTAAAGG
1 TAACGGCAATTAAAGG
29683066 TAACGGCAATTAAAGG
1 TAACGGCAATTAAAGG
29683082 TA
1 TA
29683084 TTGCACCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
TAACGGCAATTAAAGG
Found at i:29684217 original size:16 final size:16
Alignment explanation
Indices: 29684196--29684227 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29684186 TGGTGGAGAG
29684196 ATTCAAAAACAAGGAA
1 ATTCAAAAACAAGGAA
29684212 ATTCAAAAACAAGGAA
1 ATTCAAAAACAAGGAA
29684228 GGAAATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (16 bp):
ATTCAAAAACAAGGAA
Found at i:29687749 original size:68 final size:68
Alignment explanation
Indices: 29687659--29687923 Score: 381
Period size: 68 Copynumber: 3.9 Consensus size: 68
29687649 ATGCGGTCAT
* * * *
29687659 GCACTTAATCCAACCGATTTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTTAACAAG
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
*
29687724 ATA
66 ACA
*
29687727 GCACTTAATTCAACCAAATTTGTCTTCAAAA-TTTCACGTTGGACAGCATGTATAACCTCAACAA
1 GCACTTAATTCAACCAAATTTGTCTT-AAAATTTTCACATTGGACAGCATGTATAACCTCAACAA
29687791 GACA
65 GACA
* **
29687795 GCACTTAATTCAACCAAATTTGTCTTAACATTTTCGTATTCGG-CAGCATGTATAACCTCAACAA
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATT-GGACAGCATGTATAACCTCAACAA
29687859 GACA
65 GACA
* * * *
29687863 ACACTTAATTCAACCAAATTTGTCTTAAAATTTTCATATTGGACAGTATGTAAAACCTCAA
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAA
29687924 TCGGACATAC
Statistics
Matches: 178, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
67 5 0.03
68 167 0.94
69 6 0.03
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (68 bp):
GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
ACA
Found at i:29687819 original size:136 final size:136
Alignment explanation
Indices: 29687620--29687923 Score: 389
Period size: 136 Copynumber: 2.2 Consensus size: 136
29687610 CATAAATTTT
* * * * * * *
29687620 TTTTTACATTGGACAGCATGTAAAACCACATGC-GGTCATGCACTTAATCCAACCGATTTTGTCT
1 TTTTCACATTGGACAGCATGTAAAACCTCA-ACAAGACA-GCACTTAATCCAACCAAATTTGTCT
* * *
29687684 TAAAATTTTCACATT-GGACAGCATGTATAACCTTAACAAGATAGCACTTAATTCAACCAAATTT
64 TAAAATTTTCACATTCGG-CAGCATGTATAACCTCAACAAGACAACACTTAATTCAACCAAATTT
29687748 GTCTTCAAAA
128 GTCTT-AAAA
* * *
29687758 -TTTCACGTTGGACAGCATGTATAACCTCAACAAGACAGCACTTAATTCAACCAAATTTGTCTTA
1 TTTTCACATTGGACAGCATGTAAAACCTCAACAAGACAGCACTTAATCCAACCAAATTTGTCTTA
* **
29687822 ACATTTTCGTATTCGGCAGCATGTATAACCTCAACAAGACAACACTTAATTCAACCAAATTTGTC
66 AAATTTTCACATTCGGCAGCATGTATAACCTCAACAAGACAACACTTAATTCAACCAAATTTGTC
29687887 TTAAAA
131 TTAAAA
* *
29687893 TTTTCATATTGGACAGTATGTAAAACCTCAA
1 TTTTCACATTGGACAGCATGTAAAACCTCAA
29687924 TCGGACATAC
Statistics
Matches: 143, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
135 4 0.03
136 109 0.76
137 30 0.21
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (136 bp):
TTTTCACATTGGACAGCATGTAAAACCTCAACAAGACAGCACTTAATCCAACCAAATTTGTCTTA
AAATTTTCACATTCGGCAGCATGTATAACCTCAACAAGACAACACTTAATTCAACCAAATTTGTC
TTAAAA
Found at i:29689015 original size:20 final size:20
Alignment explanation
Indices: 29688990--29689029 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29688980 AATATTTTCT
*
29688990 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
29689010 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
29689030 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:29689032 original size:34 final size:35
Alignment explanation
Indices: 29688978--29689044 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
29688968 CAAACAGCAG
* *
29688978 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
29689013 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
29689045 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:29689036 original size:14 final size:14
Alignment explanation
Indices: 29689013--29689052 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29689003 ACAGAAAAGT
*
29689013 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
29689027 AAATCATTTTACGG
1 AAAACATTTTACAG
29689041 AAAACATTTTAC
1 AAAACATTTTAC
29689053 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:29694981 original size:2 final size:2
Alignment explanation
Indices: 29694974--29695004 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29694964 CAAACATACT
29694974 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
29695005 TATGTATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29696263 original size:28 final size:27
Alignment explanation
Indices: 29696232--29696292 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 27
29696222 CTCATGACAA
*
29696232 TTTTAAAGATTTTTTAATTGTTTATCTT
1 TTTTAAAGAATTTTTAATTGTTTAT-TT
29696260 TTTTAAAGAATTTTTAATTGTTTATTT
1 TTTTAAAGAATTTTTAATTGTTTATTT
29696287 TTTTAA
1 TTTTAA
29696293 TAAACTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.64
Consensus pattern (27 bp):
TTTTAAAGAATTTTTAATTGTTTATTT
Found at i:29696739 original size:28 final size:29
Alignment explanation
Indices: 29696702--29696771 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
29696692 TGTGACAATT
* *
29696702 AAAATAAAAACATTA-AAT-TTAAATTTTA
1 AAAATAAAAA-ATTATAATAATAAATATTA
29696730 AAAATAAAAAATTATAATAATAAATATTA
1 AAAATAAAAAATTATAATAATAAATATTA
*
29696759 AAATATTAAAAAT
1 AAA-ATAAAAAAT
29696772 AGTTTTTGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.11
28 13 0.36
29 11 0.31
30 8 0.22
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAATAAAAAATTATAATAATAAATATTA
Found at i:29697776 original size:17 final size:16
Alignment explanation
Indices: 29697733--29697777 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
29697723 AAAAAATCAC
*
29697733 ATTTTTTACATTTAAT
1 ATTTTTTAAATTTAAT
29697749 ATTTTTT-AATTTAAT
1 ATTTTTTAAATTTAAT
29697764 ATATTTTTAAATTT
1 AT-TTTTTAAATTT
29697778 TAAAATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 12 0.46
17 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTTAAATTTAAT
Found at i:29708853 original size:44 final size:45
Alignment explanation
Indices: 29708805--29708890 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
29708795 GAATTATTCA
*
29708805 TGTCTCCAATGCCATA-TATAATATGGACTTACATGGCTCAATCC
1 TGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAATCC
* * *
29708849 TGTCTCTAAAGTCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA-TTATAATATGGACTTACATGGCTCA
29708891 TTTCTGTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 13 0.36
46 23 0.64
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (45 bp):
TGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAATCC
Found at i:29716261 original size:46 final size:44
Alignment explanation
Indices: 29716159--29716266 Score: 153
Period size: 44 Copynumber: 2.4 Consensus size: 44
29716149 TGTCTTTGAC
** * * *
29716159 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
29716203 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
29716249 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
29716267 TTTCTGTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 33 0.58
46 24 0.42
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:29717618 original size:13 final size:13
Alignment explanation
Indices: 29717600--29717627 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29717590 AAGAACATGG
29717600 CCGTGTGGACAGC
1 CCGTGTGGACAGC
29717613 CCGTGTGGACAGC
1 CCGTGTGGACAGC
29717626 CC
1 CC
29717628 ATGTAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (13 bp):
CCGTGTGGACAGC
Found at i:29720151 original size:26 final size:26
Alignment explanation
Indices: 29720117--29720166 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
29720107 AAGTTAATAA
*
29720117 AAAAATAAT-ATTATAATTTAATATTT
1 AAAAATAATAATT-TAATATAATATTT
29720143 AAAAATAATAATTTAATATAATAT
1 AAAAATAATAATTTAATATAATAT
29720167 CAACAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAAATAATAATTTAATATAATATTT
Found at i:29723714 original size:20 final size:21
Alignment explanation
Indices: 29723689--29723727 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29723679 ACTATTTTCT
*
29723689 GTTAAAAA-GGAAAAAAAATA
1 GTTAAAAATAGAAAAAAAATA
29723709 GTTAAAAATAGAAAAAAAA
1 GTTAAAAATAGAAAAAAAA
29723728 ACAAAAAAGC
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:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (21 bp):
GTTAAAAATAGAAAAAAAATA
Found at i:29724116 original size:153 final size:151
Alignment explanation
Indices: 29723846--29724168 Score: 567
Period size: 153 Copynumber: 2.1 Consensus size: 151
29723836 TATAAAATCT
*
29723846 AGATCCGAAAATTTTAAAAATACAAATAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATA
1 AGATCCGAAAATTTTAAAAATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATA
* *
29723911 AAAAACACTAAAATAATACATTTGAAATATTATGTACTAAAATAATATAAAAAGAATAAAATAGG
66 AAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-AAAA-AATAAAATACG
29723976 AAAATAATATATTTTAAAAAATA
129 AAAATAATATATTTTAAAAAATA
*
29723999 AGATTCGAAAATTTTAAAAATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATA
1 AGATCCGAAAATTTTAAAAATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATA
29724064 AAAAA-ACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAA
66 AAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAA
*
29724128 AATAGTATATTTTAAAAAATA
131 AATAATATATTTTAAAAAATA
*
29724149 AAATCCGAAAATTTTAAAAA
1 AGATCCGAAAATTTTAAAAA
29724169 CTTTAAAAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
150 50 0.31
151 4 0.02
152 41 0.25
153 68 0.42
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (151 bp):
AGATCCGAAAATTTTAAAAATACAAACAAAGGGACAAAATTAGGGTTATTTACTAAATTAATATA
AAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAA
AATAATATATTTTAAAAAATA
Found at i:29724129 original size:25 final size:27
Alignment explanation
Indices: 29724101--29724160 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 27
29724091 ATTATGTACT
29724101 AAAATA-ATA-TAAAAAATAAAATACG
1 AAAATAGATATTAAAAAATAAAATACG
*
29724126 AAAATAGTATATTTTAAAAAATAAAATCCG
1 AAAATAG-ATA--TTAAAAAATAAAATACG
29724156 AAAAT
1 AAAAT
29724161 TTTAAAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.21
27 3 0.10
30 20 0.69
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAATAGATATTAAAAAATAAAATACG
Found at i:29731573 original size:25 final size:25
Alignment explanation
Indices: 29731525--29731573 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29731515 CATAACTAAA
* * *
29731525 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
29731550 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
29731574 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:29732199 original size:22 final size:23
Alignment explanation
Indices: 29732173--29732218 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29732163 CAACCAAACC
29732173 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
29732195 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
29732218 A
1 A
29732219 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:29732224 original size:23 final size:23
Alignment explanation
Indices: 29732180--29732224 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29732170 ACCAATTCAA
*
29732180 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
29732203 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
29732225 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:29738946 original size:15 final size:15
Alignment explanation
Indices: 29738910--29738938 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29738900 GAGAAACCTC
29738910 TGACTGATATATTTT
1 TGACTGATATATTTT
29738925 TGACTGATATATTT
1 TGACTGATATATTT
29738939 CTTTCTGAAC
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:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (15 bp):
TGACTGATATATTTT
Found at i:29739774 original size:22 final size:23
Alignment explanation
Indices: 29739748--29739793 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29739738 CAACCAAACC
29739748 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
29739770 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
29739793 A
1 A
29739794 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:29739799 original size:23 final size:23
Alignment explanation
Indices: 29739755--29739799 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29739745 ACCAATTCAA
*
29739755 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
29739778 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
29739800 CACATACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:29743966 original size:92 final size:92
Alignment explanation
Indices: 29743809--29743993 Score: 336
Period size: 92 Copynumber: 2.0 Consensus size: 92
29743799 AGTGGAAGAC
29743809 TAAGTTTAAAAATGCATAGCATAATTTATTATTCGAATGTATAAGAATCTAGCATGAAAGTATTA
1 TAAGTTTAAAAATGCATAGCATAATTTATTATTCGAATGTATAAGAATCTAGCATGAAAGTATTA
29743874 GATTGT-CGTGACCTGCCCCTACATATT
66 GATT-TCCGTGACCTGCCCCTACATATT
*
29743901 TAAGTTTAGAAATGCATAGCATAATTTATTATTCGAATGTATAAGAATCTAGCATGAAAGTATTA
1 TAAGTTTAAAAATGCATAGCATAATTTATTATTCGAATGTATAAGAATCTAGCATGAAAGTATTA
*
29743966 GATTTCCGTGACTTGCCCCTACATATT
66 GATTTCCGTGACCTGCCCCTACATATT
29743993 T
1 T
29743994 TAATGTTATT
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 1 0.01
92 89 0.99
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (92 bp):
TAAGTTTAAAAATGCATAGCATAATTTATTATTCGAATGTATAAGAATCTAGCATGAAAGTATTA
GATTTCCGTGACCTGCCCCTACATATT
Found at i:29747644 original size:11 final size:12
Alignment explanation
Indices: 29747628--29747659 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
29747618 TACAGTGAAG
29747628 AAAAGGAAAA-A
1 AAAAGGAAAAGA
29747639 AAAAGGAAAAGA
1 AAAAGGAAAAGA
29747651 AAAA-GAAAA
1 AAAAGGAAAA
29747660 TTTAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAGA
Found at i:29747649 original size:17 final size:17
Alignment explanation
Indices: 29747627--29747659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29747617 CTACAGTGAA
29747627 GAAAAGGAAAAA-AAAAG
1 GAAAA-GAAAAAGAAAAG
29747644 GAAAAGAAAAAGAAAA
1 GAAAAGAAAAAGAAAA
29747660 TTTAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAAAGAAAAG
Found at i:29763015 original size:21 final size:21
Alignment explanation
Indices: 29762970--29763015 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
29762960 TGTTATATAT
*
29762970 ATTA-TTTATTTTAAGATTGC
1 ATTATTTTATTTTAAGATTAC
29762990 ATTATTTTATTTTTAA-ATTAC
1 ATTATTTTA-TTTTAAGATTAC
*
29763011 TTTAT
1 ATTAT
29763016 GTATTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 12 0.55
22 6 0.27
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTATTTTATTTTAAGATTAC
Found at i:29764322 original size:20 final size:20
Alignment explanation
Indices: 29764278--29764329 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
29764268 TTTTTACTTC
*
29764278 TAAATTCAACAATTCGACTCA
1 TAAATTCAAC-ATTCCACTCA
* *
29764299 TAAATTCAACATTCCTCTCT
1 TAAATTCAACATTCCACTCA
29764319 TAAATT-AACAT
1 TAAATTCAACAT
29764330 AAATTCCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 5 0.18
20 13 0.46
21 10 0.36
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAATTCAACATTCCACTCA
Found at i:29769076 original size:41 final size:39
Alignment explanation
Indices: 29768981--29769105 Score: 97
Period size: 41 Copynumber: 3.1 Consensus size: 39
29768971 GATGTAAAAT
** * * * *
29768981 TTTTTGCGGCACTTTTACAAAAACACCACTGTATCTCAA
1 TTTTTGCGGCGTTTTTATAAAAACGCCACTATAGCTCAA
* **
29769020 TTTTTTGTGATGTTTTTATTAAAAACGCCACTATAGCTCAA
1 -TTTTTGCGGCGTTTTTA-TAAAAACGCCACTATAGCTCAA
* * * *
29769061 CTTTTTGCGGCGTTTTCACTAAAAACGTCATTATTGCTCAA
1 -TTTTTGCGGCGTTTTTA-TAAAAACGCCACTATAGCTCAA
29769102 TTTT
1 TTTT
29769106 ATTTTTTTTT
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 16 0.24
41 50 0.76
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (39 bp):
TTTTTGCGGCGTTTTTATAAAAACGCCACTATAGCTCAA
Found at i:29769301 original size:7 final size:7
Alignment explanation
Indices: 29769291--29769351 Score: 122
Period size: 7 Copynumber: 8.7 Consensus size: 7
29769281 TTTATTTTTT
29769291 ATTTTCA
1 ATTTTCA
29769298 ATTTTCA
1 ATTTTCA
29769305 ATTTTCA
1 ATTTTCA
29769312 ATTTTCA
1 ATTTTCA
29769319 ATTTTCA
1 ATTTTCA
29769326 ATTTTCA
1 ATTTTCA
29769333 ATTTTCA
1 ATTTTCA
29769340 ATTTTCA
1 ATTTTCA
29769347 ATTTT
1 ATTTT
29769352 TTTAAAGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTCA
Found at i:29770003 original size:6 final size:6
Alignment explanation
Indices: 29769994--29770024 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
29769984 TTTCAAAACC
*
29769994 AAAGGG AAAGGG AAAGGG AAAGGG GAAGGG A
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG A
29770025 TCATATGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:29770241 original size:20 final size:20
Alignment explanation
Indices: 29770218--29770255 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
29770208 TTATATTTCA
29770218 TTTTTATTTA-TTATCAATG
1 TTTTTATTTATTTATCAATG
29770237 TTTTTATTTATTTATCAAT
1 TTTTTATTTATTTATCAAT
29770256 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTTATTTATTTATCAATG
Found at i:29770918 original size:15 final size:15
Alignment explanation
Indices: 29770898--29770928 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29770888 ATAGATTAGT
29770898 GTTTAGGGTTTAAGG
1 GTTTAGGGTTTAAGG
*
29770913 GTTTAGGGTTTTAGG
1 GTTTAGGGTTTAAGG
29770928 G
1 G
29770929 GTTATATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GTTTAGGGTTTAAGG
Found at i:29771052 original size:41 final size:41
Alignment explanation
Indices: 29770990--29771096 Score: 144
Period size: 41 Copynumber: 2.6 Consensus size: 41
29770980 GTTATATGAC
*
29770990 TTTTAGCGGCG-TTTTACCAAAAACGCCACTATTGTTCTATT
1 TTTTAGCGGCGCTTTTA-CAAAAACGCCACTATTGCTCTATT
* * *
29771031 TTTTAGCGGCGCTTTGACAAAAACGCCGCTATTGCTCTGTT
1 TTTTAGCGGCGCTTTTACAAAAACGCCACTATTGCTCTATT
* *
29771072 TTTTAGCGGCTCTTTTCCAAAAACG
1 TTTTAGCGGCGCTTTTACAAAAACG
29771097 TCGCTAATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 54 0.93
42 4 0.07
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGCTTTTACAAAAACGCCACTATTGCTCTATT
Found at i:29771115 original size:41 final size:41
Alignment explanation
Indices: 29770990--29771142 Score: 116
Period size: 41 Copynumber: 3.8 Consensus size: 41
29770980 GTTATATGAC
* * * * *
29770990 TTTTAGCGGCG-TTTTACCAAAAACGCCACTATTGTTCTATT
1 TTTTAGCGGCGCTTTGA-CAAAAACGCCGCTAATGCTATATT
* * *
29771031 TTTTAGCGGCGCTTTGACAAAAACGCCGCTATTGCTCTGTT
1 TTTTAGCGGCGCTTTGACAAAAACGCCGCTAATGCTATATT
* ** * *
29771072 TTTTAGCGGCTCTTTTCCAAAAACGTCGCTAATG-TATAAT
1 TTTTAGCGGCGCTTTGACAAAAACGCCGCTAATGCTATATT
* **
29771112 TTTT-GTGGCG-TTTTTCATAAAACGCCGCTAA
1 TTTTAGCGGCGCTTTGACA-AAAACGCCGCTAA
29771143 AAACGCCGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
38 6 0.06
39 16 0.17
40 7 0.07
41 61 0.65
42 4 0.04
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGCTTTGACAAAAACGCCGCTAATGCTATATT
Found at i:29771145 original size:12 final size:12
Alignment explanation
Indices: 29771130--29771155 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29771120 CGTTTTTCAT
29771130 AAAACGCCGCTA
1 AAAACGCCGCTA
29771142 AAAACGCCGCTA
1 AAAACGCCGCTA
29771154 AA
1 AA
29771156 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:29772653 original size:15 final size:16
Alignment explanation
Indices: 29772633--29772666 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
29772623 TTTTATATCT
29772633 TATTATATA-ATAATA
1 TATTATATACATAATA
29772648 TATTATATATCATAATA
1 TATTATATA-CATAATA
29772665 TA
1 TA
29772667 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTATATACATAATA
Found at i:29772745 original size:24 final size:23
Alignment explanation
Indices: 29772692--29772735 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
29772682 CTTCAAAATT
29772692 TAAAAAAAACTTCACCAATAAGG
1 TAAAAAAAACTTCACCAATAAGG
29772715 TAAAAAAAAC-TCTACCAATAA
1 TAAAAAAAACTTC-ACCAATAA
29772736 AGTTGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (23 bp):
TAAAAAAAACTTCACCAATAAGG
Found at i:29774485 original size:51 final size:50
Alignment explanation
Indices: 29774364--29774499 Score: 125
Period size: 51 Copynumber: 2.7 Consensus size: 50
29774354 TCAAACTATT
29774364 TTATTTATTATTT-AATTAATTAGAGATAAAATAATAATTTAATATTATCAC
1 TTATTTA--ATTTAAATTAATTAGAGATAAAATAATAATTTAATATTATCAC
* * ** * * * *
29774415 TTAATTATTTTATTTTTAATTAGTGTTAATAT-ATAATTTTAATACTTATCTC
1 TTATTTAATTTA-AATTAATTAGAGATAAAATAATAA-TTTAATA-TTATCAC
*
29774467 TTATTTAATTTAAATTAATTAGA-AAAAAATAAT
1 TTATTTAATTTAAATTAATTAGAGATAAAATAAT
29774500 TACGACACAT
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
49 3 0.05
50 8 0.12
51 37 0.58
52 16 0.25
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (50 bp):
TTATTTAATTTAAATTAATTAGAGATAAAATAATAATTTAATATTATCAC
Found at i:29774720 original size:23 final size:24
Alignment explanation
Indices: 29774678--29774726 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
29774668 GCCCAAAACC
29774678 AAAAATAAATAAACAAAAT-ATAA
1 AAAAATAAATAAACAAAATAATAA
*
29774701 AAAAATAAATAATA-ATAATAATAA
1 AAAAATAAATAA-ACAAAATAATAA
29774725 AA
1 AA
29774727 CCTAAGTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (24 bp):
AAAAATAAATAAACAAAATAATAA
Found at i:29776016 original size:34 final size:34
Alignment explanation
Indices: 29775978--29776142 Score: 253
Period size: 34 Copynumber: 4.9 Consensus size: 34
29775968 AAATATGCAG
*
29775978 TAGGGCTTTAGCCCATCATAGTATCAGTACGCAT
1 TAGGGCTTTAGCCCATCACAGTATCAGTACGCAT
*
29776012 TAGGGCCTTAGCCCATCACAGTATCAGTACGCAT
1 TAGGGCTTTAGCCCATCACAGTATCAGTACGCAT
*
29776046 TAGGG-TCTTAGCCCATCACAGTATTAGTACGCAT
1 TAGGGCT-TTAGCCCATCACAGTATCAGTACGCAT
*
29776080 TAGGG-TCTTAGCCCACCACAGTATCAGTACGCAT
1 TAGGGCT-TTAGCCCATCACAGTATCAGTACGCAT
*
29776114 TAGGGCCTTAGCCCATCACAGTATCAGTA
1 TAGGGCTTTAGCCCATCACAGTATCAGTA
29776143 GCAGTCATGC
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
34 121 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (34 bp):
TAGGGCTTTAGCCCATCACAGTATCAGTACGCAT
Found at i:29778355 original size:60 final size:60
Alignment explanation
Indices: 29778269--29778391 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 60
29778259 TGTCCTGGGT
* * *
29778269 TTTGGGATATTTTCCCATTTATCCCCTGTTATTTTTCACGTATTATATTTTAGTCCTTTA
1 TTTGGGATATTCTCCCATTTAGCCCCTGTTATTTTTCACATATTATATTTTAGTCCTTTA
* *
29778329 TTTGGGAATATTCT-CCATTTAGCCCCTTTTATTTTTCACATGTTATATTTTAGTCCTTTA
1 TTTGGG-ATATTCTCCCATTTAGCCCCTGTTATTTTTCACATATTATATTTTAGTCCTTTA
29778389 TTT
1 TTT
29778392 ACTTATTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 51 0.89
61 6 0.11
ACGTcount: A:0.19, C:0.18, G:0.10, T:0.54
Consensus pattern (60 bp):
TTTGGGATATTCTCCCATTTAGCCCCTGTTATTTTTCACATATTATATTTTAGTCCTTTA
Found at i:29778571 original size:3 final size:3
Alignment explanation
Indices: 29778563--29778605 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
29778553 ATTTTCACCC
* *
29778563 TTA TTA TTA TTG TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29778606 GATAGTAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29781935 original size:21 final size:21
Alignment explanation
Indices: 29781896--29781935 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29781886 AATCCTAAAT
* * *
29781896 AAGATTGAAGAGTTGAAGGGA
1 AAGATAGAAGAGCTCAAGGGA
29781917 AAGATAGAAGAGCTCAAGG
1 AAGATAGAAGAGCTCAAGG
29781936 CCGCACTGCA
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:0.45, C:0.05, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGATAGAAGAGCTCAAGGGA
Found at i:29784053 original size:43 final size:42
Alignment explanation
Indices: 29783956--29784053 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
29783946 GACCATGCAT
* * *
29783956 GGGACATCGGCATCGTATCTGATTTCATGTAAGACCCTGTCT
1 GGGACGTCGGTATCGTATCTGATTTCATGTAAGACCCTGTCC
*
29783998 GGGACAG-AGGTATCGATAT-TGAATTTCATGTAAGACCAC-GTCC
1 GGGAC-GTCGGTATCG-TATCTG-ATTTCATGTAAGACC-CTGTCC
29784041 GGGACGTCGGTAT
1 GGGACGTCGGTAT
29784054 TGTACTTGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
42 14 0.30
43 31 0.67
44 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
GGGACGTCGGTATCGTATCTGATTTCATGTAAGACCCTGTCC
Found at i:29787772 original size:10 final size:10
Alignment explanation
Indices: 29787744--29787773 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29787734 TAATTTTAGC
*
29787744 ATTTATCTCT
1 ATTTATCTTT
29787754 ATTTATCTTT
1 ATTTATCTTT
29787764 ATTTATCTTT
1 ATTTATCTTT
29787774 TAGAATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:29796593 original size:44 final size:44
Alignment explanation
Indices: 29796541--29797040 Score: 542
Period size: 44 Copynumber: 11.4 Consensus size: 44
29796531 AGTCCCATAC
*
29796541 CCCTGAAGTTGCAGT-GAGTCAGATTAAAGCTGCAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAG-CAGATTAAAGCTACAAATCTTATCT
* * * * *
29796585 CTCTGAAGTTGTAGTGGAGCAGATTAAAACCACAAATCTAATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * * *
29796629 CCCTGAAGTTGTAGTGGAGCAGATTGAAGTTACAAATTTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * *
29796673 CCCTGAAGTTTCAGTGGAGCAGATTAAAG---CGAACCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
*** *
29796714 CCCTGAAGTTTTTTGTGGAGCAGATTAAAGCTACTAATCTTATCT
1 CCCTGAAG-TTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
** * *
29796759 CATTGAAGTTGCAGTGGAGCAGATTAAAGCTACTAATCTTATTT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * * * *
29796803 CCTTGAAGTTGTAGTGGAGCAGGTTAAAGCCACAAATCTAATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * * *
29796847 CCCTGAAGTTGCAGCGGAGCAGATTGAAGTTGCAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * * * * *
29796891 CCTTGAAGTTGCAGTAGAGCAAATTGAAGCTACGAATATTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* *
29796935 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * * *
29796979 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCGATAAATCCTATAC-
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTAT-CT
**
29797023 CTTTGAAGTTGCAGTGGA
1 CCCTGAAGTTGCAGTGGA
29797041 TTAGAATGAA
Statistics
Matches: 385, Mismatches: 65, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
41 17 0.04
42 19 0.05
44 329 0.85
45 20 0.05
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
Found at i:29797219 original size:13 final size:14
Alignment explanation
Indices: 29797201--29797240 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
29797191 ACCCAAAACT
29797201 AAAAATAAATAA-A
1 AAAAATAAATAACA
*
29797214 AAAAATATAAAAACA
1 AAAAATA-AATAACA
29797229 AAAAATAAATAA
1 AAAAATAAATAA
29797241 TAATAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 8 0.35
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAATAACA
Found at i:29797231 original size:15 final size:14
Alignment explanation
Indices: 29797195--29797237 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29797185 TGTCTGACCC
*
29797195 AAAACTAAAAATAA
1 AAAACAAAAAATAA
*
29797209 ATAA-AAAAAATATA
1 AAAACAAAAAATA-A
29797223 AAAACAAAAAATAA
1 AAAACAAAAAATAA
29797237 A
1 A
29797238 TAATAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 7 0.29
14 9 0.38
15 8 0.33
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAACAAAAAATAA
Found at i:29798190 original size:13 final size:14
Alignment explanation
Indices: 29798169--29798197 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29798159 TGAAAAATGA
29798169 ATTAGAAAATATTT
1 ATTAGAAAATATTT
29798183 ATTA-AAAATATTT
1 ATTAGAAAATATTT
29798196 AT
1 AT
29798198 GAAGTTAATC
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:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTAGAAAATATTT
Found at i:29798760 original size:31 final size:32
Alignment explanation
Indices: 29798711--29798774 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
29798701 ATATTAAATA
*
29798711 AGATATTTATTAATTAAATA-ATTATATTATG
1 AGATATTTATTAATTAAATATATTAAATTATG
*
29798742 AGATTTTTATGTAA-TAAATATATTAAATTATG
1 AGATATTTAT-TAATTAAATATATTAAATTATG
29798774 A
1 A
29798775 CAAATGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
AGATATTTATTAATTAAATATATTAAATTATG
Found at i:29799720 original size:15 final size:15
Alignment explanation
Indices: 29799697--29799740 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
29799687 TATCAAATTT
29799697 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
29799712 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
29799727 ATATTGATTGAAAT
1 ATATTGATTGAAAT
29799741 TTAATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:29800137 original size:23 final size:23
Alignment explanation
Indices: 29800109--29800166 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
29800099 TAATATTCCG
29800109 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
29800132 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
29800155 GGTGTGCTTGGG
1 GGTGTGTTTGGG
29800167 AGGAATCCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.07, C:0.05, G:0.43, T:0.45
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:29800292 original size:18 final size:19
Alignment explanation
Indices: 29800271--29800311 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29800261 AATGAAATGA
29800271 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
29800289 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
29800308 GAAA
1 GAAA
29800312 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:29806011 original size:17 final size:18
Alignment explanation
Indices: 29805985--29806023 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29805975 GCAAGTGTGG
29805985 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
29806001 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
29806019 AAAAT
1 AAAAT
29806024 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:29806200 original size:15 final size:15
Alignment explanation
Indices: 29806180--29806210 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29806170 AAAACAATAT
29806180 AACTCTAGACCTTTC
1 AACTCTAGACCTTTC
*
29806195 AACTCTTGACCTTTC
1 AACTCTAGACCTTTC
29806210 A
1 A
29806211 CTTACATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
AACTCTAGACCTTTC
Found at i:29809579 original size:15 final size:15
Alignment explanation
Indices: 29809569--29809598 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29809559 TCCCTTCTTG
29809569 ACCACGACCTTTTCC
1 ACCACGACCTTTTCC
*
29809584 ACCACGACCATTTCC
1 ACCACGACCTTTTCC
29809599 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCTTTTCC
Found at i:29810364 original size:17 final size:18
Alignment explanation
Indices: 29810338--29810376 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29810328 CAAATTGTGG
29810338 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
29810354 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
29810372 AAAAT
1 AAAAT
29810377 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:29810554 original size:15 final size:15
Alignment explanation
Indices: 29810534--29810564 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29810524 AAAACAATAT
29810534 AACTCTAGACCTTTC
1 AACTCTAGACCTTTC
*
29810549 AACTCTTGACCTTTC
1 AACTCTAGACCTTTC
29810564 A
1 A
29810565 CTTACATGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
AACTCTAGACCTTTC
Found at i:29811206 original size:30 final size:30
Alignment explanation
Indices: 29811170--29811228 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
29811160 CAAAAGAAAA
29811170 TTGTTTAGGAAATTATAAGGTAGAAATTTT
1 TTGTTTAGGAAATTATAAGGTAGAAATTTT
29811200 TTGTTTAGGAAATTATAAGGTAGAAATTT
1 TTGTTTAGGAAATTATAAGGTAGAAATTT
29811229 ATTTAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.42
Consensus pattern (30 bp):
TTGTTTAGGAAATTATAAGGTAGAAATTTT
Found at i:29813813 original size:22 final size:22
Alignment explanation
Indices: 29813785--29813826 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29813775 CAGCTGGATA
*
29813785 GATTTTTATAAT-TTTTATTTTT
1 GATTTTT-TAATAATTTATTTTT
29813807 GATTTTTTAATAATTTATTT
1 GATTTTTTAATAATTTATTT
29813827 GCTTTAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
GATTTTTTAATAATTTATTTTT
Found at i:29814066 original size:28 final size:25
Alignment explanation
Indices: 29814027--29814102 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 25
29814017 GATAATAATG
29814027 AATCTTTGGATTTTTTTATATTTTTAA
1 AATCTTTGGA-TTTTTTAT-TTTTTAA
* *
29814054 AATCATTTTGATTTTTTATTTTTT-G
1 AATC-TTTGGATTTTTTATTTTTTAA
29814079 AAT-TTTAAGGATTTTTTATTTTTT
1 AATCTTT--GGATTTTTTATTTTTT
29814103 TCATAATGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
23 3 0.07
25 18 0.42
26 5 0.12
27 12 0.28
28 5 0.12
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.66
Consensus pattern (25 bp):
AATCTTTGGATTTTTTATTTTTTAA
Found at i:29817920 original size:10 final size:9
Alignment explanation
Indices: 29817905--29817960 Score: 58
Period size: 10 Copynumber: 5.7 Consensus size: 9
29817895 AAATTTTAGG
29817905 ATTTATTTT
1 ATTTATTTT
29817914 CATTTATCTTT
1 -ATTTAT-TTT
29817925 ATTTATTTTT
1 ATTTA-TTTT
*
29817935 AATTATCTTT
1 ATTTAT-TTT
29817945 ATTTATTTGT
1 ATTTATTT-T
29817955 ATTTAT
1 ATTTAT
29817961 CTTTTAGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 3 0.08
10 33 0.82
11 4 0.10
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (9 bp):
ATTTATTTT
Found at i:29817928 original size:20 final size:19
Alignment explanation
Indices: 29817905--29817964 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 19
29817895 AAATTTTAGG
29817905 ATTTATTTTCATTTATCTTT
1 ATTTATTTT-ATTTATCTTT
*
29817925 ATTTATTTTTAATTATCTTT
1 ATTTA-TTTTATTTATCTTT
29817945 ATTTATTTGTATTTATCTTT
1 ATTTATTT-TATTTATCTTT
29817965 TAGAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.08
20 29 0.81
21 4 0.11
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTATTTTATTTATCTTT
Found at i:29817949 original size:30 final size:31
Alignment explanation
Indices: 29817907--29817966 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
29817897 ATTTTAGGAT
29817907 TTATTTTCATTTATCTT-TATTTAT-TTTTAA
1 TTATTTTCATTTAT-TTGTATTTATCTTTTAA
29817937 TTATCTTT-ATTTATTTGTATTTATCTTTTA
1 TTAT-TTTCATTTATTTGTATTTATCTTTTA
29817967 GAATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 2 0.07
30 17 0.63
31 8 0.30
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (31 bp):
TTATTTTCATTTATTTGTATTTATCTTTTAA
Found at i:29826032 original size:130 final size:129
Alignment explanation
Indices: 29825766--29826094 Score: 461
Period size: 130 Copynumber: 2.5 Consensus size: 129
29825756 CTATTCATTC
29825766 AAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATCGTG
1 AAAAATTC-TTAAAACGAAGGCAATGTTCGATGTTTGGCAATTC-GGGAATCGTGCCCTATCGTG
* * *
29825831 CT-GATTGCAATATCTCGTTTGTCCAAAATAATCGAATATTCCTTTGGAATTTCACTCATGTCTT
64 CTGGGTTGCAATATCTCGTTTGTCCAAAATAATCAAATATTCCTTTAGAATTTCACTCATGTCTT
29825895 T
129 T
* *
29825896 AAAAATTCTTCAAAACGAAGGAAATGTTCGATGTTTAGCAATTCGGAGAATCGTGCCCTATCGTG
1 AAAAATTCTT-AAAACGAAGGCAATGTTCGATGTTTGGCAATTCGG-GAATCGTGCCCTATCGTG
*
29825961 CTGGGTTGCAATTTCTCGTTTG-CTCAAAATAATCAAATATTCCTTTAGAATTTCACTCATGT-T
64 CTGGGTTGCAATATCTCGTTTGTC-CAAAATAATCAAATATTCCTTTAGAATTTCACTCATGTCT
29826024 TT
128 TT
** * * * *
29826026 CTAAATTC-TAAAAC-AAGGCAATGTTCAATATTTGGAAATTCAGGGAATCGTGCCCTACCGTGC
1 AAAAATTCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTC-GGGAATCGTGCCCTATCGTGC
29826089 TGGGTT
65 TGGGTT
29826095 TCGATTTTTC
Statistics
Matches: 180, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
127 46 0.26
128 7 0.04
129 5 0.03
130 69 0.38
131 53 0.29
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (129 bp):
AAAAATTCTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGAATCGTGCCCTATCGTGCT
GGGTTGCAATATCTCGTTTGTCCAAAATAATCAAATATTCCTTTAGAATTTCACTCATGTCTTT
Found at i:29828699 original size:53 final size:54
Alignment explanation
Indices: 29828625--29828769 Score: 156
Period size: 53 Copynumber: 2.7 Consensus size: 54
29828615 CTTACACGGT
* *
29828625 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTTTACAGAATCACATTA
1 TCACAT-TCATACCGAAGCCATAGCCCAG-CTATGGTCTTATACAGAATCACATTA
* * *
29828680 TCACATT-ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTCATACCGAAGCCATAGCCCAGCTATGGTCTTATACAGAATCACATTA
* * *
29828733 TTACATT--GACC-AATGTCATAGCCCAGCTATGGTCTTA
1 TCACATTCATACCGAA-GCCATAGCCCAGCTATGGTCTTA
29828770 AACGGGCGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
51 1 0.01
52 26 0.33
53 45 0.57
54 1 0.01
55 6 0.08
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (54 bp):
TCACATTCATACCGAAGCCATAGCCCAGCTATGGTCTTATACAGAATCACATTA
Found at i:29828769 original size:52 final size:53
Alignment explanation
Indices: 29828642--29828774 Score: 162
Period size: 53 Copynumber: 2.5 Consensus size: 53
29828632 TCATACCGAA
* * * * *
29828642 GCCATATCCCAGAC-ATGGTCTTTTACAGAATCACATTATCACATTATACCGAT
1 GCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTAGACCAAT
* *
29828695 GCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATTACATT-GACCAAT
1 GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTAGACCAAT
* *
29828747 GTCATAGCCCAGCTATGGTCTTAAACGG
1 GCCATAGCCCAGCTATGGTCTTATACGG
29828775 GCGCACTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
52 32 0.46
53 38 0.54
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (53 bp):
GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTAGACCAAT
Found at i:29835742 original size:53 final size:53
Alignment explanation
Indices: 29835661--29835811 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
29835651 CTTACACGGT
* * *
29835661 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTTTACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
* *
29835716 TCACATTATACCGATGCCATAGCCCAGCTAGGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
29835769 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
29835812 GCGCACTTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 1 0.01
53 78 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:29847298 original size:264 final size:264
Alignment explanation
Indices: 29846863--29847552 Score: 960
Period size: 264 Copynumber: 2.6 Consensus size: 264
29846853 CGAAGAAACA
* * * * ** * * *
29846863 AGCCTTAACCCCCTAAGTAGCAGGGTAACAGGTTGAATATTACAGGTCTTGTC-TCTTCGAAGTT
1 AGCCTTGA-CCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCGCCCT-GAAGTT
* * * * * *
29846927 GCAGTGGAACAGATCAAAGACGGTGAGCCTTGACCCTCTAAGCAGTA-GGTAACAGGTTGAAGAT
64 GCAGTGGAACAGATCAAAGACGGTAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAAAT
*
29846991 TATAGATCTTGTCTCCCTAAACAGTAGTGGATCAAATCGAAGAAGCAAGCCTTAACCCCCTAAGT
129 TATAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGAAGCAAGCCTTAACCCCCTAAGT
* *
29847056 AGTAAAGTAACAGGCTGAAGATTGCAGA-CTTGTCTCCTCGAAGTTGCAGTGGAACAGATCAAAG
194 AGTAAAGTAACAAGCTGAAGATTGCAGATCTTGTCTCCTCAAAGTTGCAGTGGAACAGATCAAAG
29847120 ACGGTG
259 ACGGTG
29847126 AGCCTTGACCCTCTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCGCCCTGAAGTTG
1 AGCCTTGACCC-CTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCGCCCTGAAGTTG
* * * *
29847191 CAGTGGAACAGATCAAAAATGGTAAGCCTTAACCCCCTAAGTAGCAGGGTAACAGGCTGAATATT
65 CAGTGGAACAGATCAAAGACGGTAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAAATT
*
29847256 GTAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGAAGCAAGCCTTAACCCCCTAAGTA
130 ATAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGAAGCAAGCCTTAACCCCCTAAGTA
* *
29847321 GTAGAGTAACAAGCTGAAGATTGCAGATCTTGTTTCCTCAAAGTTGCAGTGGAACAGATCAAAGA
195 GTAAAGTAACAAGCTGAAGATTGCAGATCTTGTCTCCTCAAAGTTGCAGTGGAACAGATCAAAGA
29847386 CGGTG
260 CGGTG
**
29847391 AGCCTTGACCCCTTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCGCCCT-AAGCAG
1 AGCCTTGACCCC-TAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCGCCCTGAAGTTG
* * * * *
29847455 TAGCGGAGCAGATCGAAGACAGTGAA-CCTTAACCCCCTAAGTAGTAGGGTAAC-GGCCTGAAAA
65 CAGTGGAACAGATCAAAGACGGT-AAGCCTTAACCCCCTAAGTAGTAGGGTAACAGG-CTGAAAA
* * * *
29847518 TTACAGATCCTATCTCCCTAAGCAGTAGTGGAGCA
128 TTATAGATCTTGTCTCCCTAAACAGTAGTGGAGCA
29847553 GACTGAAGAT
Statistics
Matches: 380, Mismatches: 40, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
262 3 0.01
263 90 0.24
264 189 0.50
265 98 0.26
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (264 bp):
AGCCTTGACCCCTAAGTAGTAGGGTAACAGGCTGAAGATTGTAGATCTTGTCGCCCTGAAGTTGC
AGTGGAACAGATCAAAGACGGTAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTGAAAATTA
TAGATCTTGTCTCCCTAAACAGTAGTGGAGCAAATCGAAGAAGCAAGCCTTAACCCCCTAAGTAG
TAAAGTAACAAGCTGAAGATTGCAGATCTTGTCTCCTCAAAGTTGCAGTGGAACAGATCAAAGAC
GGTG
Done.