Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014212.1 Kokia drynarioides strain JFW-HI SEQ_129245, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 204688
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:14688 original size:12 final size:12
Alignment explanation
Indices: 14671--14709 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
14661 TCTCTATTTT
14671 AAAAAAAGAAAAA
1 AAAAAAAG-AAAA
14684 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
14696 AGAAAAAGAAAA
1 AAAAAAAGAAAA
14708 AA
1 AA
14710 TTTGTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:14689 original size:13 final size:13
Alignment explanation
Indices: 14671--14709 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
14661 TCTCTATTTT
14671 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
14684 AAAAAAAG-AAAA
1 AAAAAAAGAAAAA
*
14696 AGAAAAAGAAAAA
1 AAAAAAAGAAAAA
14709 A
1 A
14710 TTTGTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:18147 original size:21 final size:20
Alignment explanation
Indices: 18123--18185 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
18113 ATATTACTGC
18123 TAAATATTAAACCCTAACCTT
1 TAAATATTAAA-CCTAACCTT
*
18144 TAAATATTAATA-CTAAACTT
1 TAAATATTAA-ACCTAACCTT
18164 TAAATATTAAACTCTAAACCTT
1 TAAATATTAAAC-CT-AACCTT
18186 AATACTAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.03
20 17 0.47
21 12 0.33
22 6 0.17
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATATTAAACCTAACCTT
Found at i:18164 original size:20 final size:20
Alignment explanation
Indices: 18123--18187 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
18113 ATATTACTGC
*
18123 TAAATATTAAACCCTAACCTT
1 TAAATATTAAA-CCTAAACTT
18144 TAAATATTAATA-CTAAACTT
1 TAAATATTAA-ACCTAAACTT
*
18164 TAAATATTAAACTCTAAACCT
1 TAAATATTAAAC-CTAAACTT
18185 TAA
1 TAA
18188 TACTAATGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.44
21 20 0.51
22 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATTAAACCTAAACTT
Found at i:38862 original size:30 final size:30
Alignment explanation
Indices: 38822--38881 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
38812 TAGAATTTTT
* *
38822 AATACTTTTAAATAATAGAAATTCTAAAAA
1 AATACTTTTAAAAAATAGAAATTCCAAAAA
*
38852 AATATTTTTAAAAAATAGAAATTCCAAAAA
1 AATACTTTTAAAAAATAGAAATTCCAAAAA
38882 TTATAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (30 bp):
AATACTTTTAAAAAATAGAAATTCCAAAAA
Found at i:56621 original size:40 final size:38
Alignment explanation
Indices: 56560--56639 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 38
56550 CAAAACTAAA
*
56560 AAAGTTTAAAAATATAAAAAAATATTAAT-AATTATTTT
1 AAAGTTTAAAAATATAAAAAAAAATTAATAAATT-TTTT
56598 AAAGTTCTAAAAA-ATGAAAAAAAAAATTAATAAATTTTTT
1 AAAGTT-TAAAAATAT--AAAAAAAAATTAATAAATTTTTT
56638 AA
1 AA
56640 GGGATAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
38 8 0.22
39 6 0.16
40 19 0.51
41 4 0.11
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (38 bp):
AAAGTTTAAAAATATAAAAAAAAATTAATAAATTTTTT
Found at i:56963 original size:29 final size:30
Alignment explanation
Indices: 56929--56987 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
56919 TTACGTGTAT
*
56929 AATTGTAC-CAAATTAAAATTCATGTATAC
1 AATTGTACACAAATTAAAATTAATGTATAC
*
56958 AATTGTACATTAAATTAAAATTAATGTATA
1 AATTGTACA-CAAATTAAAATTAATGTATA
56988 ATTTTAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (30 bp):
AATTGTACACAAATTAAAATTAATGTATAC
Found at i:56990 original size:29 final size:27
Alignment explanation
Indices: 56924--56990 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
56914 GAATTTTACG
*
56924 TGTATAATTGTACCAAATTAAAATTCA
1 TGTATAATTGTACCAAATTAAAATTAA
*
56951 TGTATACAATTGTACATTAAATTAAAATTAA
1 TGTAT--AATTGTAC--CAAATTAAAATTAA
56982 TGTATAATT
1 TGTATAATT
56991 TTAAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.35
31 17 0.50
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (27 bp):
TGTATAATTGTACCAAATTAAAATTAA
Found at i:58621 original size:23 final size:23
Alignment explanation
Indices: 58567--58621 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
58557 TAAAGGAGGT
* *
58567 AAAAGTTAAATTATAATTTTTAA
1 AAAAGTAAAAGTATAATTTTTAA
* *
58590 GATAGTAAAAGTATAATTTTTAA
1 AAAAGTAAAAGTATAATTTTTAA
*
58613 AAAATTAAA
1 AAAAGTAAA
58622 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AAAAGTAAAAGTATAATTTTTAA
Found at i:58661 original size:30 final size:29
Alignment explanation
Indices: 58605--58669 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
58595 TAAAAGTATA
*
58605 ATTTTT-AAAAAATTAAATTAAAATTTTAT
1 ATTTTTAAAAAAATTAAAGTAAAATTTT-T
**
58634 CATTTTTAAAAAAATTAAAGT-GTATTTTT
1 -ATTTTTAAAAAAATTAAAGTAAAATTTTT
58663 ATTTTTA
1 ATTTTTA
58670 CTAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 7 0.23
29 1 0.03
30 11 0.35
31 12 0.39
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTTTAAAAAAATTAAAGTAAAATTTTT
Found at i:78616 original size:24 final size:25
Alignment explanation
Indices: 78564--78616 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
78554 ACTATACTAT
*
78564 TAAATACAAAAATATTATAAACTCA
1 TAAATACAAAAATACTATAAACTCA
*
78589 -AAATA-AATAAATACTATAAA-TTA
1 TAAATACAA-AAATACTATAAACTCA
78612 TAAAT
1 TAAAT
78617 CTAAAAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAATACAAAAATACTATAAACTCA
Found at i:80968 original size:3 final size:3
Alignment explanation
Indices: 80960--80985 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
80950 GTAAAAGTCC
80960 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
80986 AGGTTGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:86399 original size:21 final size:21
Alignment explanation
Indices: 86344--86399 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
86334 CTAGATATCC
86344 GAACCCATAACCCCAAACCATT
1 GAACCCA-AACCCCAAACCATT
86366 GAACCCTAAACCCCAAACACA-T
1 GAACCC-AAACCCCAAAC-CATT
*
86388 GATCCCAAACCC
1 GAACCCAAACCC
86400 TTAAATCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 6 0.19
22 22 0.71
23 3 0.10
ACGTcount: A:0.41, C:0.43, G:0.05, T:0.11
Consensus pattern (21 bp):
GAACCCAAACCCCAAACCATT
Found at i:86799 original size:31 final size:31
Alignment explanation
Indices: 86763--86863 Score: 143
Period size: 31 Copynumber: 3.3 Consensus size: 31
86753 ATCTCAAAAT
* *
86763 TATACACGAACTTTAATTTAATGTGCGATTA
1 TATACATGAACTTTAATTTAATGTGCAATTA
*
86794 TATACATGAACTTTAATTTAATGTGCAATTG
1 TATACATGAACTTTAATTTAATGTGCAATTA
*
86825 TATGCATGAACTTTAATTTAA--TGCAATTA
1 TATACATGAACTTTAATTTAATGTGCAATTA
*
86854 TACACATGAA
1 TATACATGAA
86864 ACTCTAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 15 0.24
31 48 0.76
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
TATACATGAACTTTAATTTAATGTGCAATTA
Found at i:86887 original size:60 final size:60
Alignment explanation
Indices: 86759--86904 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 60
86749 ATAAATCTCA
* * * * *
86759 AAAT-TATACACGAACTTTAATTTAATGTGCGATTATATACATGAACTTTAATTTAATGTGC
1 AAATGTATACATGAACTTTAATTTAA-GTGCAATTATACACATGAACTCTAATTT-AGGTGC
* * *
86820 AATTGTATGCATGAACTTTAATTTAA-TGCAATTATACACATGAAACTCTAATATT-GGTTC
1 AAATGTATACATGAACTTTAATTTAAGTGCAATTATACACATG-AACTCTAAT-TTAGGTGC
*
86880 AAATGTATACGTGAAACTTTAATTT
1 AAATGTATACATG-AACTTTAATTT
86905 TGATTTAATC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
60 27 0.39
61 22 0.31
62 21 0.30
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (60 bp):
AAATGTATACATGAACTTTAATTTAAGTGCAATTATACACATGAACTCTAATTTAGGTGC
Found at i:87066 original size:30 final size:29
Alignment explanation
Indices: 87032--87090 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
87022 GAATTAGATC
* *
87032 AAATAAAAATTACATGTATAGAATTGCACA
1 AAATAAAAACT-CATGTATACAATTGCACA
*
87062 AAATAAAAGCTCATGTATACAATTGCACA
1 AAATAAAAACTCATGTATACAATTGCACA
87091 TTAAACTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (29 bp):
AAATAAAAACTCATGTATACAATTGCACA
Found at i:108290 original size:21 final size:21
Alignment explanation
Indices: 108266--108327 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
108256 GAAAAGAAAG
108266 AAACTTGATAATGGAAGAGCA
1 AAACTTGATAATGGAAGAGCA
* *
108287 AAACGTG--CAT-GAAGAG--
1 AAACTTGATAATGGAAGAGCA
108303 AAACTTGATAATGGAAGAGCA
1 AAACTTGATAATGGAAGAGCA
108324 AAAC
1 AAAC
108328 GTGCATGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 6 0.19
18 8 0.25
19 8 0.25
21 10 0.31
ACGTcount: A:0.48, C:0.11, G:0.24, T:0.16
Consensus pattern (21 bp):
AAACTTGATAATGGAAGAGCA
Found at i:108302 original size:18 final size:18
Alignment explanation
Indices: 108279--108343 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 18
108269 CTTGATAATG
108279 GAAGAGCAAAACGTGCAT
1 GAAGAGCAAAACGTGCAT
* *
108297 GAAGAG--AAACTTGATAAT
1 GAAGAGCAAAACGTG--CAT
108315 GGAAGAGCAAAACGTGCAT
1 -GAAGAGCAAAACGTGCAT
108334 GAAGATGCAA
1 GAAGA-GCAA
108344 CGTAACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
16 6 0.16
18 13 0.35
19 12 0.32
21 6 0.16
ACGTcount: A:0.46, C:0.12, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAGAGCAAAACGTGCAT
Found at i:108314 original size:37 final size:37
Alignment explanation
Indices: 108264--108338 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
108254 AGGAAAAGAA
108264 AGAAACTTGATAATGGAAGAGCAAAACGTGCATGAAG
1 AGAAACTTGATAATGGAAGAGCAAAACGTGCATGAAG
108301 AGAAACTTGATAATGGAAGAGCAAAACGTGCATGAAG
1 AGAAACTTGATAATGGAAGAGCAAAACGTGCATGAAG
108338 A
1 A
108339 TGCAACGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.11, G:0.27, T:0.16
Consensus pattern (37 bp):
AGAAACTTGATAATGGAAGAGCAAAACGTGCATGAAG
Found at i:108321 original size:19 final size:19
Alignment explanation
Indices: 108264--108321 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
108254 AGGAAAAGAA
108264 AGAAACTTGATAATGGAAG
1 AGAAACTTGATAATGGAAG
* *
108283 AGCAAAACGTG--CAT-GAAG
1 AG--AAACTTGATAATGGAAG
108301 AGAAACTTGATAATGGAAG
1 AGAAACTTGATAATGGAAG
108320 AG
1 AG
108322 CAAAACGTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 6 0.20
18 8 0.27
19 10 0.33
21 6 0.20
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.17
Consensus pattern (19 bp):
AGAAACTTGATAATGGAAG
Found at i:112054 original size:59 final size:58
Alignment explanation
Indices: 111972--112161 Score: 202
Period size: 60 Copynumber: 3.2 Consensus size: 58
111962 AAAAAACTTT
* *
111972 GGTGTTGGCCATTGCATGATCGACACCCCTTTTAATCTGATCAAAAAATCAAATTTTTG
1 GGTGTTGGCCA-TGCATGATCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTG
* * * * * *
112031 GGTGTTGGCCATGCAATGGTCGACACCCCCTTTTTCTCAGATGAAAAATTCAAATTTTTT
1 GGTGTTGGCCATGC-ATGATCGACA-CCCCTTTTTATCTGATAAAAAAATCAAATTTTTG
** * * *
112091 GGTGTTGATCATGCCATAACCGACA-CTCTTATTTATCTGATAAAAAAAATCAAATTTTTG
1 GGTGTTGGCCATG-CATGATCGACACCCCTT-TTTATCTGAT-AAAAAAATCAAATTTTTG
112151 GGTGTTGGCCA
1 GGTGTTGGCCA
112162 AAAAAAAAAT
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
58 7 0.07
59 28 0.26
60 70 0.66
61 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (58 bp):
GGTGTTGGCCATGCATGATCGACACCCCTTTTTATCTGATAAAAAAATCAAATTTTTG
Found at i:112341 original size:62 final size:64
Alignment explanation
Indices: 112232--112425 Score: 222
Period size: 61 Copynumber: 3.1 Consensus size: 64
112222 CAAAATTTTG
*
112232 ATTTTTTATTCAGATAAAAAAGGAGGTGTCGGCCATGACATGACCAACACAAAAAAAAATTGAAA
1 ATTTTTTATTCAGATAAAAAA-GAGGTGTCGGTCATGACATGACCAACACAAAAAAAAATTGAAA
* * ** **
112297 ATTTTTTA-TCAGAT-AAATAGAGGTGTCGGTCATGACATGGCCAACAC-CCAAAATTTTG---
1 ATTTTTTATTCAGATAAAAAAGAGGTGTCGGTCATGACATGACCAACACAAAAAAAAATTGAAA
* * * *
112355 ATTTTTTATTCAGATAAAAAAAGGGGTATCGATCATGGCATGACCAACACAAAAAAAAATT-AAA
1 ATTTTTTATTCAGAT-AAAAAAGAGGTGTCGGTCATGACATGACCAACACAAAAAAAAATTGAAA
112419 ATTTTTT
1 ATTTTTT
112426 TATTTGATAA
Statistics
Matches: 105, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
58 8 0.08
59 6 0.06
61 34 0.32
62 32 0.30
63 4 0.04
64 13 0.12
65 8 0.08
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (64 bp):
ATTTTTTATTCAGATAAAAAAGAGGTGTCGGTCATGACATGACCAACACAAAAAAAAATTGAAA
Found at i:112349 original size:123 final size:121
Alignment explanation
Indices: 112162--112818 Score: 444
Period size: 123 Copynumber: 5.5 Consensus size: 121
112152 GTGTTGGCCA
* * *
112162 AAAAAAAAATTG--ATTTTTTTATCAG-TAAATAGGGGTGTCGGTCATGGA-ATGACTAACATTC
1 AAAAAAAAATTGAAAATTTTTTATCAGATAAATAGGGGTGTCGGTCAT-GACATGACCAACA-CC
*
112223 -AAAATTTTGATTTTTTATTCAGATAAAAAAGGAGGTGTCGGCCATGACATGACCAACAC
64 AAAAAATTTGATTTTTTATTCAGATAAAAAAGG-GGTGTCGGCCATG-CATGACCAACAC
* * *
112282 AAAAAAAAATTGAAAATTTTTTATCAGATAAATAGAGGTGTCGGTCATGACATGGCCAACACCCA
1 AAAAAAAAATTGAAAATTTTTTATCAGATAAATAGGGGTGTCGGTCATGACATGACCAACACCAA
* * **
112347 AAATTTTGATTTTTTATTCAGATAAAAAAAGGGGTATCGATCATGGCATGACCAACAC
66 AAAATTTGATTTTTTATTCAGAT-AAAAAAGGGGTGTCGGCCAT-GCATGACCAACAC
** * ** *
112405 AAAAAAAAATT-AAAATTTTTTTATTTGATAAATA------------AT--CATGGCCGGCACCT
1 AAAAAAAAATTGAAAA-TTTTTTATCAGATAAATAGGGGTGTCGGTCATGACATGACCAACACCA
* * **
112455 AAAAATTTGATTTTTTATTCAGATAAAAAAGGGATGTCAGCCATGGCATGGTCAACAC
65 AAAAATTTGATTTTTTATTCAGATAAAAAAGGGGTGTCGGCCAT-GCATGACCAACAC
* * ** *
112513 AAAAAAAAAAATTGAAATTTTTTTATCTA-ATAAATAGGAGTGTCGACCAT-AGCATGACCAGCA
1 --AAAAAAAAATTGAAAATTTTTTATC-AGATAAATAGGGGTGTCGGTCATGA-CATGACCAACA
* ** * * * * *
112576 TCAAAAAAAATGGGATTTTTTATT-TGACAAAAATGGGGTGTCGGCCATTGTATGGCCAACAC
62 -C-CAAAAAATTTGATTTTTTATTCAGATAAAAAAGGGGTGTCGGCCA-TGCATGACCAACAC
*** * *
112638 -AAAAAAAATTGATTTTTTTTTATCAG-TAAATAGGGGTGTCGGTCATGGCATGACCGACACCAA
1 AAAAAAAAATTGAAAATTTTTTATCAGATAAATAGGGGTGTCGGTCATGACATGACCAACACCAA
* * * * * ** *
112701 AAAAATTGAATTTTTCA-TCTGA-CAAAAAGGAGTGTCAACCATTGCATGATCAACAC
66 AAAATTTG-ATTTTTTATTCAGATAAAAAAGGGGTGTCGGCCA-TGCATGACCAACAC
* * * *
112757 -AAAAAAATTTG---ATTATTTTATCAAATTAAA-AGGGGTGTCGGCCATG-CAATGGCCAACAC
1 AAAAAAAAATTGAAAATT-TTTTATCAGA-TAAATAGGGGTGTCGGTCATGAC-ATGACCAACAC
112816 CAA
63 CAA
112819 CTTTTTTTTT
Statistics
Matches: 436, Mismatches: 64, Indels: 76
0.76 0.11 0.13
Matches are distributed among these distances:
108 27 0.06
109 34 0.08
110 26 0.06
111 5 0.01
116 2 0.00
117 9 0.02
118 27 0.06
119 48 0.11
120 23 0.05
121 27 0.06
122 43 0.10
123 99 0.23
124 18 0.04
125 30 0.07
126 18 0.04
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (121 bp):
AAAAAAAAATTGAAAATTTTTTATCAGATAAATAGGGGTGTCGGTCATGACATGACCAACACCAA
AAAATTTGATTTTTTATTCAGATAAAAAAGGGGTGTCGGCCATGCATGACCAACAC
Found at i:112519 original size:60 final size:59
Alignment explanation
Indices: 112455--112815 Score: 184
Period size: 59 Copynumber: 6.0 Consensus size: 59
112445 GCCGGCACCT
* **
112455 AAAAATTTGATTTTTTATTCAGATAAAAAAGGGATGTCAGCCATGGCATGGTCAACACAAAAA
1 AAAAATTTGATTTTTTATTCAGAT-AAAAAGGGATGTCGGCCATGGCATGACCAACAC---AA
* * * * *
112518 AAAAAATTGAAATTTTTT-TATCTA-ATAAATA-GGAGTGTCGACCATAGCATGACCAGCATCAA
1 AAAAATTTG--ATTTTTTAT-TC-AGATAAAAAGGGA-TGTCGGCCATGGCATGACCAACA-C-A
112580 A
59 A
** * * * * * *
112581 AAAAATGGGATTTTTTATT-TGACAAAAATGGGGTGTCGGCCATTGTATGGCCAACACAA
1 AAAAATTTGATTTTTTATTCAGATAAAAA-GGGATGTCGGCCATGGCATGACCAACACAA
* * * * * *
112640 AAAAAATTGATTTTTTTTTATCAG-TAAATAGGGGTGTCGGTCATGGCATGACCGACACCAA
1 AAAAATTTGA-TTTTTTAT-TCAGATAAAAAGGGATGTCGGCCATGGCATGACCAACA-CAA
* * * ** * *
112701 AAAAA-TTGAATTTTTCA-TCTGACAAAAA-GGAGTGTCAACCATTGCATGATCAACACAA
1 AAAAATTTG-ATTTTTTATTCAGATAAAAAGGGA-TGTCGGCCATGGCATGACCAACACAA
* * * *
112759 AAAAATTTGATTATTTTA-TCAAATTAAAAGGGGTGTCGGCCAT-GCAATGGCCAACAC
1 AAAAATTTGATT-TTTTATTCAGATAAAAAGGGATGTCGGCCATGGC-ATGACCAACAC
112816 CAACTTTTTT
Statistics
Matches: 223, Mismatches: 54, Indels: 46
0.69 0.17 0.14
Matches are distributed among these distances:
58 18 0.08
59 61 0.27
60 45 0.20
61 40 0.18
62 4 0.02
63 20 0.09
64 22 0.10
65 12 0.05
66 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (59 bp):
AAAAATTTGATTTTTTATTCAGATAAAAAGGGATGTCGGCCATGGCATGACCAACACAA
Found at i:112546 original size:110 final size:109
Alignment explanation
Indices: 112332--112548 Score: 285
Period size: 109 Copynumber: 2.0 Consensus size: 109
112322 TCGGTCATGA
* * *
112332 CATGGCCAACACCCAAAATTTTGATTTTTTATTCAGATAAAAAAAGGGGTATCGATCATGGCATG
1 CATGGCCAACACCCAAAAATTTGATTTTTTATTCAGATAAAAAAAGGGATATCGACCATGGCATG
* *
112397 ACCAACACAAAAAAAAATTAAAATTTTTTTATTTGATAAATAAT
66 ACCAACACAAAAAAAAATTAAAATTTTTTTATCTAATAAATAAT
** * *
112441 CATGGCCGGCACCTAAAAATTTGATTTTTTATTCAGAT-AAAAAAGGGATGTC-AGCCATGGCAT
1 CATGGCCAACACCCAAAAATTTGATTTTTTATTCAGATAAAAAAAGGGATATCGA-CCATGGCAT
** *
112504 GGTCAACACAAAAAAAAAAATTGAAATTTTTTTATCTAATAAATA
65 GACCAACAC--AAAAAAAAATTAAAATTTTTTTATCTAATAAATA
112549 GGAGTGTCGA
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 27 0.29
109 34 0.37
110 31 0.33
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (109 bp):
CATGGCCAACACCCAAAAATTTGATTTTTTATTCAGATAAAAAAAGGGATATCGACCATGGCATG
ACCAACACAAAAAAAAATTAAAATTTTTTTATCTAATAAATAAT
Found at i:112617 original size:61 final size:59
Alignment explanation
Indices: 112552--112777 Score: 188
Period size: 59 Copynumber: 3.8 Consensus size: 59
112542 ATAAATAGGA
* *
112552 GTGTCGACCATAGCATGACCAGCATCAAAAAAAATGGGATTTTTTATTTGACAAAAATGGG
1 GTGTCGACCATTGCATGACCAACA-CAAAAAAAAT-GGATTTTTTATTTGACAAAAATGGG
* * * * *
112613 GTGTCGGCCATTGTATGGCCAACACAAAAAAAATTGATTTTTT-TTT-ATCAGTAAATAGGG
1 GTGTCGACCATTGCATGACCAACACAAAAAAAATGGATTTTTTATTTGA-CA-AAAAT-GGG
** * * * * * * *
112673 GTGTCGGTCATGGCATGACCGACACCAAAAAAATTGAATTTTTCATCTGACAAAAA-GGA
1 GTGTCGACCATTGCATGACCAACA-CAAAAAAAATGGATTTTTTATTTGACAAAAATGGG
* * * *
112732 GTGTCAACCATTGCATGATCAACACAAAAAAATTTGATTATTTTAT
1 GTGTCGACCATTGCATGACCAACACAAAAAAAATGGATT-TTTTAT
112778 CAAATTAAAA
Statistics
Matches: 130, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
57 1 0.01
58 18 0.14
59 37 0.28
60 32 0.25
61 37 0.28
62 4 0.03
63 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (59 bp):
GTGTCGACCATTGCATGACCAACACAAAAAAAATGGATTTTTTATTTGACAAAAATGGG
Found at i:112637 original size:233 final size:232
Alignment explanation
Indices: 112223--112645 Score: 516
Period size: 233 Copynumber: 1.8 Consensus size: 232
112213 ACTAACATTC
* * *
112223 AAAATTTTGATTTTTTATTCAGATAAAAAAGGAGGTGTCGGCCATGACATGACCAACACAAAAAA
1 AAAAATTTGATTTTTTATTCAGATAAAAAAGGAGATGTCAGCCATGACATGACCAACACAAAAAA
** * ** * *
112288 AAATTGAAAATTTTTTATCAGATAAATAGAGGTGTCGGTCATGACATGGCCAACACCCAAAATTT
66 AAATTGAAAATTTTTTATCAGATAAATAGAGGTGTCGACCATGACATGACCAACACAAAAAAATG
* *
112353 TGATTTTTTATTCAGATAAAAAAAGGGGTATCGATCATGGCATGACCAACACAAAAAAAAATTAA
131 GGATTTTTTATTCAGATAAAAAAAGGGGTATCGACCATGGCATGACCAACACAAAAAAAAATTAA
112418 AATTTTTTTATTTGATAAATAATCATGGCCGGCACCT
196 AATTTTTTTATTTGATAAATAATCATGGCCGGCACCT
* **
112455 AAAAATTTGATTTTTTATTCAGATAAAAAAGG-GATGTCAGCCATGGCATGGTCAACACAAAAAA
1 AAAAATTTGATTTTTTATTCAGATAAAAAAGGAGATGTCAGCCATGACATGACCAACAC--AAAA
* *
112519 AAAAATTGAAATTTTTTTATCTA-ATAAATAG-GAGTGTCGACCAT-AGCATGACCAGCATCAAA
64 AAAAATTGAAAATTTTTTATC-AGATAAATAGAG-GTGTCGACCATGA-CATGACCAACA-C-AA
* * * * * * * *
112581 AAAAATGGGATTTTTTATT-TGA-CAAAAATGGGGTGTCGGCCATTGTATGGCCAACACAAAAAA
124 AAAAATGGGATTTTTTATTCAGATAAAAAAAGGGGTATCGACCATGGCATGACCAACACAAAAAA
112644 AA
189 AA
112646 TTGATTTTTT
Statistics
Matches: 159, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
231 21 0.13
232 33 0.21
233 85 0.53
234 4 0.03
235 16 0.10
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (232 bp):
AAAAATTTGATTTTTTATTCAGATAAAAAAGGAGATGTCAGCCATGACATGACCAACACAAAAAA
AAATTGAAAATTTTTTATCAGATAAATAGAGGTGTCGACCATGACATGACCAACACAAAAAAATG
GGATTTTTTATTCAGATAAAAAAAGGGGTATCGACCATGGCATGACCAACACAAAAAAAAATTAA
AATTTTTTTATTTGATAAATAATCATGGCCGGCACCT
Found at i:112748 original size:59 final size:59
Alignment explanation
Indices: 112516--112778 Score: 215
Period size: 60 Copynumber: 4.4 Consensus size: 59
112506 TCAACACAAA
* * * * *
112516 AAAAAAAATTGAAATTTTTTTATCTAATAAATAGGAGTGTCGACCATAGCATGACCAGCATC
1 AAAAAAAATTG-AA-TTTTTTATCTGACAAAAAGGAGTGTCGACCATTGCATGACCAACA-C
* * * * * * *
112578 AAAAAAAATGGGATTTTTTATTTGACAAAAATGGGGTGTCGGCCATTGTATGGCCAACAC
1 AAAAAAAATTGAATTTTTTATCTGACAAAAA-GGAGTGTCGACCATTGCATGACCAACAC
* * * * * ** * *
112638 AAAAAAAATTGATTTTTTTTTATCAG-TAAATAGGGGTGTCGGTCATGGCATGACCGACAC
1 AAAAAAAATTGA--ATTTTTTATCTGACAAAAAGGAGTGTCGACCATTGCATGACCAACAC
* * * *
112698 CAAAAAAATTGAATTTTTCATCTGACAAAAAGGAGTGTCAACCATTGCATGATCAACAC
1 AAAAAAAATTGAATTTTTTATCTGACAAAAAGGAGTGTCGACCATTGCATGACCAACAC
*
112757 AAAAAAATTTG-ATTATTTTATC
1 AAAAAAAATTGAATT-TTTTATC
112779 AAATTAAAAG
Statistics
Matches: 156, Mismatches: 40, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
58 12 0.08
59 40 0.26
60 59 0.38
61 26 0.17
62 19 0.12
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (59 bp):
AAAAAAAATTGAATTTTTTATCTGACAAAAAGGAGTGTCGACCATTGCATGACCAACAC
Found at i:112814 original size:59 final size:55
Alignment explanation
Indices: 112517--112815 Score: 168
Period size: 60 Copynumber: 5.0 Consensus size: 55
112507 CAACACAAAA
* * * * *
112517 AAAAAAATTGAAATTTTTTTATCTAATAAATAGGAGTGTCGACCATAGCATGACCAGCATC
1 AAAAAAATTG--A-TTTTTTATC-ACTAAA-AGGGGTGTCGGCCATTGCATGACCAACA-C
* * * * *
112578 AAAAAAAATGGGATTTTTTATTTGACAAAAATGGGGTGTCGGCCATTGTATGGCCAACAC
1 -AAAAAAAT-TGATTTTTTA--TCACTAAAA-GGGGTGTCGGCCATTGCATGACCAACAC
* * * *
112638 AAAAAAAATTGATTTTTTTTTATCAGTAAATAGGGGTGTCGGTCATGGCATGACCGACACC
1 -AAAAAAATTGA---TTTTTTATCACTAAA-AGGGGTGTCGGCCATTGCATGACCAACA-C
* * * ** *
112699 AAAAAAATTGAATTTTTCATCTGACAAAAAGGAGTGTCAACCATTGCATGATCAACAC
1 AAAAAAATTG-ATTTTTTATC--ACTAAAAGGGGTGTCGGCCATTGCATGACCAACAC
* *
112757 AAAAAAATTTGATTATTTTATCAAATTAAAAGGGGTGTCGGCCA-TGCAATGGCCAACAC
1 AAAAAAA-TTGATT-TTTTATC--ACTAAAAGGGGTGTCGGCCATTGC-ATGACCAACAC
112816 CAACTTTTTT
Statistics
Matches: 183, Mismatches: 39, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
58 22 0.12
59 56 0.31
60 59 0.32
61 29 0.16
62 16 0.09
63 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (55 bp):
AAAAAAATTGATTTTTTATCACTAAAAGGGGTGTCGGCCATTGCATGACCAACAC
Found at i:119295 original size:23 final size:22
Alignment explanation
Indices: 119245--119297 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
119235 AAAATGTTAT
*
119245 TTTAATATAAATAATAAAATAA
1 TTTAATATAAATAATAAAAGAA
* *
119267 TATTAATATGATTATATAAAAGAA
1 T-TTAATATAAATA-ATAAAAGAA
119291 TTTAATA
1 TTTAATA
119298 AATAAAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 16 0.62
24 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTAATATAAATAATAAAAGAA
Found at i:122932 original size:2 final size:2
Alignment explanation
Indices: 122925--122966 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
122915 TCATACATAC
* * *
122925 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122967 GTATGCATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:122967 original size:6 final size:6
Alignment explanation
Indices: 122926--122970 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
122916 CATACATACA
* * *
122926 TATATA TATATA TATATA TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TAT
122971 GCATGAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:136188 original size:12 final size:12
Alignment explanation
Indices: 136171--136196 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
136161 ACTTTGTATG
136171 TGTGTGAGAGAA
1 TGTGTGAGAGAA
136183 TGTGTGAGAGAA
1 TGTGTGAGAGAA
136195 TG
1 TG
136197 AGGGAGGCTA
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:0.31, C:0.00, G:0.42, T:0.27
Consensus pattern (12 bp):
TGTGTGAGAGAA
Found at i:137614 original size:4 final size:4
Alignment explanation
Indices: 137605--137634 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
137595 CGTTAGGCCT
137605 CAAC CAAC CAAC CAAC CAAC CAAC CAAC CA
1 CAAC CAAC CAAC CAAC CAAC CAAC CAAC CA
137635 TGCAAACTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAC
Found at i:138191 original size:22 final size:22
Alignment explanation
Indices: 138166--138207 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
138156 TTTGTTTTTA
*
138166 TTTTATTGTCATTTTACTATTG
1 TTTTACTGTCATTTTACTATTG
*
138188 TTTTACTGTCATTTTCCTAT
1 TTTTACTGTCATTTTACTAT
138208 CGTATTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTTACTGTCATTTTACTATTG
Found at i:138916 original size:17 final size:18
Alignment explanation
Indices: 138877--138916 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
138867 TGTAATTTGG
138877 TCCTTTTTTTTCATTTTTA
1 TCCTTTTTTTT-ATTTTTA
138896 --CTTTTTTTT-TTTTTA
1 TCCTTTTTTTTATTTTTA
138911 TCCTTT
1 TCCTTT
138917 CACCTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
15 6 0.32
17 13 0.68
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (18 bp):
TCCTTTTTTTTATTTTTA
Found at i:141176 original size:36 final size:36
Alignment explanation
Indices: 141136--141204 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
141126 AAGGATCAGA
* *
141136 TAGTTTGA-TTTAATTAAATAAATTATTAATTATTTT
1 TAGTTTGAGTTT-ATTAAATAAATAATAAATTATTTT
141172 TAGTTTGAGTTTATTAAATAAATAATAAATTAT
1 TAGTTTGAGTTTATTAAATAAATAATAAATTAT
141205 ATTAGTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (36 bp):
TAGTTTGAGTTTATTAAATAAATAATAAATTATTTT
Found at i:147657 original size:16 final size:17
Alignment explanation
Indices: 147638--147669 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
147628 AGAGGATCTC
147638 AACAGTACC-GAGCTCT
1 AACAGTACCTGAGCTCT
147654 AACAGTACCTGAGCTC
1 AACAGTACCTGAGCTC
147670 ACCCAGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (17 bp):
AACAGTACCTGAGCTCT
Found at i:157263 original size:24 final size:25
Alignment explanation
Indices: 157216--157266 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
157206 TAATTTCTTT
*
157216 AAGAATTGAAATAGGTTTCTTACTA
1 AAGAATTGAAACAGGTTTCTTACTA
* *
157241 AAGATTTGAAACAGTTTTC-TACTA
1 AAGAATTGAAACAGGTTTCTTACTA
157265 AA
1 AA
157267 CTAATGCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (25 bp):
AAGAATTGAAACAGGTTTCTTACTA
Found at i:165480 original size:4 final size:4
Alignment explanation
Indices: 165471--165499 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
165461 AAAATTTTAG
165471 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
165500 GGCTTTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:172530 original size:91 final size:91
Alignment explanation
Indices: 172433--172617 Score: 318
Period size: 91 Copynumber: 2.0 Consensus size: 91
172423 TTTTTCATTA
172433 TTTTAAATTTAAATTTAAATATATATCAATTATTTTTTTATTCTATATC-TAATTATTTTAAAAC
1 TTTTAAATTTAAATTTAAATATATATCAATTA-TTTTTTATTCTATATCTTAATTATTTTAAAAC
172497 ATATATACTAAAAAGCTTTTTCCTCGT
65 ATATATACTAAAAAGCTTTTTCCTCGT
* * * *
172524 TTTTAAATTTAAATTTAAATATATGTTAGTTATTTTTTATTTTATATCTTAATTATTTTAAAACA
1 TTTTAAATTTAAATTTAAATATATATCAATTATTTTTTATTCTATATCTTAATTATTTTAAAACA
172589 TATATACTAAAAAGCTTTTTCCTCGT
66 TATATACTAAAAAGCTTTTTCCTCGT
172615 TTT
1 TTT
172618 ATTATCATAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 15 0.17
91 74 0.83
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (91 bp):
TTTTAAATTTAAATTTAAATATATATCAATTATTTTTTATTCTATATCTTAATTATTTTAAAACA
TATATACTAAAAAGCTTTTTCCTCGT
Found at i:173279 original size:77 final size:77
Alignment explanation
Indices: 173186--173339 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
173176 TCGACTGTAA
* *
173186 GAGAAATGCAACTGATTTGCCAAAGCTTCAGCAAAGTACATTAACTCTTTATAACAGGAGATGTT
1 GAGAAATGAAACTGATTTGCCAAAGCTTCAGCAAAGTACATTAACTCTTCATAACAGGAGATGTT
173251 TGTCAGGCACCT
66 TGTCAGGCACCT
*
173263 GAGAAATGAAACTGATTTGCCAAAGCTTCAGCAAAGTACATTAACTCTTCATATCAGGAGATGTT
1 GAGAAATGAAACTGATTTGCCAAAGCTTCAGCAAAGTACATTAACTCTTCATAACAGGAGATGTT
173328 TGTCAGGCACCT
66 TGTCAGGCACCT
173340 TCATAAAGTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (77 bp):
GAGAAATGAAACTGATTTGCCAAAGCTTCAGCAAAGTACATTAACTCTTCATAACAGGAGATGTT
TGTCAGGCACCT
Found at i:179845 original size:7 final size:7
Alignment explanation
Indices: 179833--179860 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
179823 TTATTCTTGT
179833 CATTTCC
1 CATTTCC
179840 CATTTCC
1 CATTTCC
179847 CATTTCC
1 CATTTCC
179854 CATTTCC
1 CATTTCC
179861 TCCACCTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CATTTCC
Found at i:190700 original size:22 final size:22
Alignment explanation
Indices: 190675--190740 Score: 87
Period size: 24 Copynumber: 2.9 Consensus size: 22
190665 ATTAATAACA
*
190675 AAATAGTAACAACATAATAGTG
1 AAATGGTAACAACATAATAGTG
190697 AAATGGTAGAGCAACATAATAGTG
1 AAATGGTA-A-CAACATAATAGTG
* *
190721 AAATGGTAGCAAAATAATAG
1 AAATGGTAACAACATAATAG
190741 GGTTTTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 17 0.44
23 1 0.03
24 21 0.54
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.21
Consensus pattern (22 bp):
AAATGGTAACAACATAATAGTG
Found at i:190715 original size:24 final size:24
Alignment explanation
Indices: 190684--190729 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
190674 AAAATAGTAA
190684 CAACATAATAGTGAAATGGTAGAG
1 CAACATAATAGTGAAATGGTAGAG
190708 CAACATAATAGTGAAATGGTAG
1 CAACATAATAGTGAAATGGTAG
190730 CAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.22
Consensus pattern (24 bp):
CAACATAATAGTGAAATGGTAGAG
Found at i:191590 original size:24 final size:24
Alignment explanation
Indices: 191548--191621 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
191538 AATAGCAAAA
*
191548 CAACAAAAATTACAACAAAAACAG
1 CAACAAAAATAACAACAAAAACAG
* *
191572 CAACAAAAATAACAGCAAAAATAG
1 CAACAAAAATAACAACAAAAACAG
*
191596 CAACAAAAATAAAAACATCAAAACAG
1 CAACAAAAATAACAACA--AAAACAG
191622 TAAACATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 36 0.86
26 6 0.14
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (24 bp):
CAACAAAAATAACAACAAAAACAG
Found at i:191612 original size:12 final size:12
Alignment explanation
Indices: 191546--191612 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
191536 AAAATAGCAA
191546 AACAACAAAAAT
1 AACAACAAAAAT
* *
191558 TACAACAAAAAC
1 AACAACAAAAAT
*
191570 AGCAACAAAAAT
1 AACAACAAAAAT
*
191582 AACAGCAAAAAT
1 AACAACAAAAAT
*
191594 AGCAACAAAAAT
1 AACAACAAAAAT
*
191606 AAAAACA
1 AACAACA
191613 TCAAAACAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:191704 original size:33 final size:32
Alignment explanation
Indices: 191614--191710 Score: 124
Period size: 34 Copynumber: 3.0 Consensus size: 32
191604 ATAAAAACAT
* *
191614 CAAAACAGT-AAACATAACACAAAACAACAAC
1 CAAAACAGTAAAAAAAAACACAAAACAACAAC
*
191645 CAAAACAGTAAAAAATAAAAACCAAAACAACAAC
1 CAAAACAGTAAAAAA-AAACA-CAAAACAACAAC
*
191679 TAAAACAGTAAAAAAAAACATCAAAACAACAA
1 CAAAACAGTAAAAAAAAACA-CAAAACAACAA
191711 TATAATTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.16
32 4 0.07
33 18 0.32
34 26 0.46
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.07
Consensus pattern (32 bp):
CAAAACAGTAAAAAAAAACACAAAACAACAAC
Found at i:193237 original size:18 final size:20
Alignment explanation
Indices: 193197--193240 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
193187 CAAAGCATAA
*
193197 TAAAAATTAAAAAAATATTT
1 TAAAAATTAAAAAAATATGT
*
193217 TAAAAA-TAAAAATA-ATGT
1 TAAAAATTAAAAAAATATGT
193235 TAAAAA
1 TAAAAA
193241 ATGTTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAAATTAAAAAAATATGT
Found at i:204476 original size:42 final size:42
Alignment explanation
Indices: 204430--204557 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 42
204420 GCAATACTCG
* *
204430 CCACCTGCTCAAGGTCGCACACCACCTACACAAGCTCATTCA
1 CCACCTGCTCAAGGTCGCACACCACCTACTCAAGCTCATCCA
** * **
204472 CCACCAACGCAATACTCGC-CA-C-CC-ACTCAAGCTCATCCA
1 CCACCTGCTCAA-GGTCGCACACCACCTACTCAAGCTCATCCA
* *
204511 CCACCTGCTCAAGGTTGCACCCCACCTACTCAAGCTCATCCA
1 CCACCTGCTCAAGGTCGCACACCACCTACTCAAGCTCATCCA
204553 CCACC
1 CCACC
204558 AACACAATAC
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
38 3 0.04
39 23 0.34
40 3 0.04
41 3 0.04
42 31 0.46
43 4 0.06
ACGTcount: A:0.27, C:0.47, G:0.10, T:0.16
Consensus pattern (42 bp):
CCACCTGCTCAAGGTCGCACACCACCTACTCAAGCTCATCCA
Found at i:204514 original size:21 final size:21
Alignment explanation
Indices: 204449--204557 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 21
204439 CAAGGTCGCA
* *
204449 CACCACCTACACAAGCTCATT
1 CACCACCTACTCAAGCTCATC
* *
204470 CACCACCAACGCAA--T-A-C
1 CACCACCTACTCAAGCTCATC
* *
204487 TCGCCACCCACTCAAGCTCATC
1 -CACCACCTACTCAAGCTCATC
* *
204509 CACCACCTGCTCAAGGTTGCA-C
1 CACCACCTACTCAA-GCT-CATC
204531 C-CCACCTACTCAAGCTCATC
1 CACCACCTACTCAAGCTCATC
204551 CACCACC
1 CACCACC
204558 AACACAATAC
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
18 12 0.18
19 3 0.04
20 5 0.07
21 40 0.60
22 5 0.07
23 2 0.03
ACGTcount: A:0.28, C:0.48, G:0.08, T:0.16
Consensus pattern (21 bp):
CACCACCTACTCAAGCTCATC
Found at i:204572 original size:18 final size:18
Alignment explanation
Indices: 204551--204641 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 18
204541 CAAGCTCATC
204551 CACCACCAACACAATACT
1 CACCACCAACACAATACT
*
204569 CACCACCTATAGCTC-AT-C-
1 CACCACC-A-A-CACAATACT
* * * *
204587 CTCCACCAAGACAAAACC
1 CACCACCAACACAATACT
**
204605 CACCACCAAGGCAATACT
1 CACCACCAACACAATACT
*
204623 CACCACCCACACAA-ACT
1 CACCACCAACACAATACT
204640 CA
1 CA
204642 TACCCCACCA
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 7 0.13
18 38 0.69
19 2 0.04
20 3 0.05
21 2 0.04
ACGTcount: A:0.40, C:0.45, G:0.04, T:0.11
Consensus pattern (18 bp):
CACCACCAACACAATACT
Found at i:204576 original size:39 final size:39
Alignment explanation
Indices: 204449--204611 Score: 143
Period size: 39 Copynumber: 4.2 Consensus size: 39
204439 CAAGGTCGCA
* * *
204449 CACCACCTACACAAGCTCATTCACCACCAACGCAATACT
1 CACCACCTACTCAAGCTCATCCACCACCAACACAATACT
* * ** * * *
204488 CGCCACCCACTCAAGCTCATCCACCACCTGCTCAAGGTTGCA
1 CACCACCTACTCAAGCTCATCCACCACCAACACAA---TACT
*
204530 CCCCACCTACTCAAGCTCATCCACCACCAACACAATACT
1 CACCACCTACTCAAGCTCATCCACCACCAACACAATACT
* * * *
204569 CACCACCTA-T--AGCTCATCCTCCACCAAGACAAAACC
1 CACCACCTACTCAAGCTCATCCACCACCAACACAATACT
204605 CACCACC
1 CACCACC
204612 AAGGCAATAC
Statistics
Matches: 100, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
36 29 0.29
38 1 0.01
39 38 0.38
42 32 0.32
ACGTcount: A:0.32, C:0.47, G:0.07, T:0.15
Consensus pattern (39 bp):
CACCACCTACTCAAGCTCATCCACCACCAACACAATACT
Found at i:204593 original size:36 final size:36
Alignment explanation
Indices: 204543--204611 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
204533 CACCTACTCA
* *
204543 AGCTCATCCACCACCAACACAATACTCACCACCTAT
1 AGCTCATCCACCACCAACACAAAACCCACCACCTAT
* *
204579 AGCTCATCCTCCACCAAGACAAAACCCACCACC
1 AGCTCATCCACCACCAACACAAAACCCACCACC
204612 AAGGCAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.36, C:0.46, G:0.04, T:0.13
Consensus pattern (36 bp):
AGCTCATCCACCACCAACACAAAACCCACCACCTAT
Found at i:204594 original size:81 final size:80
Alignment explanation
Indices: 204430--204593 Score: 233
Period size: 81 Copynumber: 2.1 Consensus size: 80
204420 GCAATACTCG
* * *
204430 CCACCTGCTCAAGGTCGCACACCACCTACACAAGCTCATTCACCACCAACGCAATACTCGCCACC
1 CCACCTGCTCAAGGTCGCACACCACCTACACAAGCTCATCCACCACCAACACAATACTCACCACC
204495 CACTCAAGCTCATCCA
66 CACT-AAGCTCATCCA
* * *
204511 CCACCTGCTCAAGGTTGCACCCCACCTACTCAAGCTCATCCACCACCAACACAATACTCACCACC
1 CCACCTGCTCAAGGTCGCACACCACCTACACAAGCTCATCCACCACCAACACAATACTCACCACC
* *
204576 TA-T-AGCTCATCCT
66 CACTAAGCTCATCCA
204589 CCACC
1 CCACC
204594 AAGACAAAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
78 14 0.19
80 1 0.01
81 60 0.80
ACGTcount: A:0.29, C:0.46, G:0.09, T:0.16
Consensus pattern (80 bp):
CCACCTGCTCAAGGTCGCACACCACCTACACAAGCTCATCCACCACCAACACAATACTCACCACC
CACTAAGCTCATCCA
Found at i:204652 original size:24 final size:24
Alignment explanation
Indices: 204623--204675 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
204613 AGGCAATACT
*
204623 CACCACCCACACAAACTCATACC-C
1 CACCACCCACACAAACACAT-CCAC
*
204647 CACCACCCACTCAAACACATCCAC
1 CACCACCCACACAAACACATCCAC
204671 CACCA
1 CACCA
204676 ATGCAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.38, C:0.55, G:0.00, T:0.08
Consensus pattern (24 bp):
CACCACCCACACAAACACATCCAC
Done.