Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009537.1 Kokia drynarioides strain JFW-HI SEQ_124249, 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: 165714
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:11190 original size:18 final size:18
Alignment explanation
Indices: 11163--11204 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11153 CTTCCCAGCA
*
11163 ATCCAGTATGCAGACATC
1 ATCCATTATGCAGACATC
*
11181 ATCCATTATGCAGCCATC
1 ATCCATTATGCAGACATC
*
11199 AGCCAT
1 ATCCAT
11205 GCAATCAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (18 bp):
ATCCATTATGCAGACATC
Found at i:11539 original size:3 final size:3
Alignment explanation
Indices: 11526--11556 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11516 CTAGTAGTCT
*
11526 GCA GCA ACA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G
11557 TTAATGGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:24164 original size:17 final size:18
Alignment explanation
Indices: 24131--24167 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
24121 AAATTTTCTT
24131 TTTTAAATTCAATTTAAA
1 TTTTAAATTCAATTTAAA
*
24149 TTTTCAATTC-ATTTAAA
1 TTTTAAATTCAATTTAAA
24166 TT
1 TT
24168 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAAATTCAATTTAAA
Found at i:28322 original size:188 final size:188
Alignment explanation
Indices: 27999--28374 Score: 716
Period size: 188 Copynumber: 2.0 Consensus size: 188
27989 ATTATAAAAA
*
27999 AACATATTTCTCGTGTTTAAAATTTTGTTTATTTTAAAAATATATATTAAAAAATTAAATTAAAT
1 AACATATTTCTCGTGTTTAAAATTTTGTTTATTGTAAAAATATATATTAAAAAATTAAATTAAAT
*
28064 TAAAGTGCGACAGAATATAAATGAAATTCATAATAAAAGAACGAATAATAGAATAAAATATGTCA
66 TAAAGTGCGACAAAATATAAATGAAATTCATAATAAAAGAACGAATAATAGAATAAAATATGTCA
28129 ATTGTGGAGCAATTATGAATTTAACAACATTTACTCGTTGTATGTTAATATCCTAATT
131 ATTGTGGAGCAATTATGAATTTAACAACATTTACTCGTTGTATGTTAATATCCTAATT
*
28187 AACATATTTCTCGTGTTTAAAATTTTGTTTATTGTAAAAATATATATTAAAAATTTAAATTAAAT
1 AACATATTTCTCGTGTTTAAAATTTTGTTTATTGTAAAAATATATATTAAAAAATTAAATTAAAT
*
28252 TAAAGTGCGACAAAATATAAATGAAATTCATAATAAAAGAACGAATAATAGAATAAAATATGTTA
66 TAAAGTGCGACAAAATATAAATGAAATTCATAATAAAAGAACGAATAATAGAATAAAATATGTCA
28317 ATTGTGGAGCAATTATGAATTTAACAACATTTACTCGTTGTATGTTAATATCCTAATT
131 ATTGTGGAGCAATTATGAATTTAACAACATTTACTCGTTGTATGTTAATATCCTAATT
28375 TTCATGTTGT
Statistics
Matches: 184, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
188 184 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (188 bp):
AACATATTTCTCGTGTTTAAAATTTTGTTTATTGTAAAAATATATATTAAAAAATTAAATTAAAT
TAAAGTGCGACAAAATATAAATGAAATTCATAATAAAAGAACGAATAATAGAATAAAATATGTCA
ATTGTGGAGCAATTATGAATTTAACAACATTTACTCGTTGTATGTTAATATCCTAATT
Found at i:28519 original size:17 final size:20
Alignment explanation
Indices: 28479--28524 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28469 GATGAGAATT
*
28479 AGGAGAGAAGAGAAGAAAGC
1 AGGAGAGAAAAGAAGAAAGC
28499 AGGAGAGAAAAG-AG-AAG-
1 AGGAGAGAAAAGAAGAAAGC
28516 AGGAGAGAA
1 AGGAGAGAA
28525 GGGAAGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 3 0.12
19 2 0.08
20 11 0.44
ACGTcount: A:0.57, C:0.02, G:0.41, T:0.00
Consensus pattern (20 bp):
AGGAGAGAAAAGAAGAAAGC
Found at i:38686 original size:20 final size:20
Alignment explanation
Indices: 38640--38686 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
38630 AAAAATACTC
*
38640 ACTTAATAATCATTTAATAA
1 ACTTAAAAATCATTTAATAA
**
38660 AAATAAAAAT-ATTATAATAA
1 ACTTAAAAATCATT-TAATAA
38680 ACTTAAA
1 ACTTAAA
38687 TTAAATATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
ACTTAAAAATCATTTAATAA
Found at i:38721 original size:12 final size:12
Alignment explanation
Indices: 38704--38729 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38694 TTTTTAAATA
38704 AAATTTATAATT
1 AAATTTATAATT
38716 AAATTTATAATT
1 AAATTTATAATT
38728 AA
1 AA
38730 CAAGACTAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATTTATAATT
Found at i:56967 original size:25 final size:23
Alignment explanation
Indices: 56938--56984 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
56928 AGTTGGATCC
56938 AAATTAAATTCTAAAAAAATAATTA
1 AAATTAAA-TCT-AAAAAATAATTA
*
56963 AAATTAAATCTAAACAATAATT
1 AAATTAAATCTAAAAAATAATT
56985 TCCTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 3 0.14
25 8 0.38
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATTAAATCTAAAAAATAATTA
Found at i:57023 original size:21 final size:21
Alignment explanation
Indices: 56999--57042 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
56989 AATTGGATTC
56999 AAATTAAACTCTAAATTATAA
1 AAATTAAACTCTAAATTATAA
57020 AAATTAAACTCTAAATTATAA
1 AAATTAAACTCTAAATTATAA
57041 AA
1 AA
57043 CCTAAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATTAAACTCTAAATTATAA
Found at i:57048 original size:21 final size:21
Alignment explanation
Indices: 57003--57048 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
56993 GGATTCAAAT
*
57003 TAAACTCTAAATTATAAAAAT
1 TAAACTCTAAATTATAAAAAC
*
57024 TAAACTCTAAATTATAAAACC
1 TAAACTCTAAATTATAAAAAC
57045 TAAA
1 TAAA
57049 AGATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACTCTAAATTATAAAAAC
Found at i:58077 original size:15 final size:15
Alignment explanation
Indices: 58059--58097 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
58049 CTTTTTTTTC
58059 TTTTTTTTTTCTCAA
1 TTTTTTTTTTCTCAA
58074 -TTTTTTTTT-TCAA
1 TTTTTTTTTTCTCAA
*
58087 TTTTTCTTTTC
1 TTTTTTTTTTC
58098 AACTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTTCTCAA
Found at i:58120 original size:13 final size:13
Alignment explanation
Indices: 58050--58119 Score: 76
Period size: 13 Copynumber: 5.6 Consensus size: 13
58040 CTTTTGTCTC
*
58050 TTTTTTTTC-TTT
1 TTTTTTTTCAATT
58062 TTTTTTTCTCAATT
1 TTTTTTT-TCAATT
58076 TTTTTTTTCAATT
1 TTTTTTTTCAATT
* *
58089 TTTCTTTTCAA-C
1 TTTTTTTTCAATT
58101 TTTTTTTTC--TT
1 TTTTTTTTCAATT
58112 TTTTTTTT
1 TTTTTTTT
58120 TAAACAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
11 8 0.16
12 15 0.30
13 18 0.36
14 9 0.18
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:63097 original size:25 final size:23
Alignment explanation
Indices: 63068--63113 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
63058 GTTGGATCTA
63068 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
63093 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
63114 CCCTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:66285 original size:22 final size:22
Alignment explanation
Indices: 66260--66316 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
66250 GGGATTTGGA
* *
66260 GGGAGTGGGTAGAGACAT-GAGT
1 GGGAGAGGG-AGAGAAATGGAGT
66282 GGGAGAGGGAGAGAAATGGAGT
1 GGGAGAGGGAGAGAAATGGAGT
* *
66304 GGGAAAAGGAGAG
1 GGGAGAGGGAGAG
66317 GTGAGGGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.35, C:0.02, G:0.53, T:0.11
Consensus pattern (22 bp):
GGGAGAGGGAGAGAAATGGAGT
Found at i:67177 original size:33 final size:34
Alignment explanation
Indices: 67133--67196 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
67123 AAGTACTCTT
*
67133 TTTTTTCCCCCTATAGT-AGGCTAAATAGTTATAA
1 TTTTTTCCCCCTATAGTAAGG-TAAACAGTTATAA
67167 TTTTTT-CCCCTATAGTAAGGTAAACAGTTA
1 TTTTTTCCCCCTATAGTAAGGTAAACAGTTA
67197 CCTTAATGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
TTTTTTCCCCCTATAGTAAGGTAAACAGTTATAA
Found at i:68395 original size:18 final size:20
Alignment explanation
Indices: 68358--68395 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
68348 CGAAAATAAA
*
68358 CAAAAAAACCTGAATGTTGT
1 CAAAAAAACCTGAATCTTGT
68378 CAAAAAAA-CT-AATCTTGT
1 CAAAAAAACCTGAATCTTGT
68396 TTCCCAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (20 bp):
CAAAAAAACCTGAATCTTGT
Found at i:73942 original size:20 final size:21
Alignment explanation
Indices: 73903--73942 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
73893 AAAATATTTT
*
73903 ATATTAATATTTTAATAATAA
1 ATATAAATATTTTAATAATAA
73924 ATATAAATATTTT-ATAATA
1 ATATAAATATTTTAATAATA
73943 TAGATACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAAATATTTTAATAATAA
Found at i:75758 original size:18 final size:16
Alignment explanation
Indices: 75735--75769 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
75725 AATAAGATTA
75735 AATTTATCATTTAGTCTT
1 AATTTATC-TTTAG-CTT
75753 AATTTATCTTTAGCTT
1 AATTTATCTTTAGCTT
75769 A
1 A
75770 TAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (16 bp):
AATTTATCTTTAGCTT
Found at i:77668 original size:15 final size:15
Alignment explanation
Indices: 77648--77681 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
77638 AATTAAAAAT
77648 TAATAA-AAATTTAAA
1 TAATAATAAA-TTAAA
77663 TAATAATAAATTAAA
1 TAATAATAAATTAAA
77678 TAAT
1 TAAT
77682 TTTGATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAATAAATTAAA
Found at i:93709 original size:28 final size:30
Alignment explanation
Indices: 93677--93732 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
93667 AAATAGATAA
93677 AATTTAATG-A-AAAAATTAATTTATTTTT
1 AATTTAATGCATAAAAATTAATTTATTTTT
93705 AATTTAATGCATAAAAATTAATTTATTT
1 AATTTAATGCATAAAAATTAATTTATTT
93733 ATTTTTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 9 0.35
29 1 0.04
30 16 0.62
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (30 bp):
AATTTAATGCATAAAAATTAATTTATTTTT
Found at i:100595 original size:20 final size:21
Alignment explanation
Indices: 100546--100596 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
100536 AATGGTTTTT
100546 AATTAA-TTTTTATTTGGTTC
1 AATTAATTTTTTATTTGGTTC
*
100566 TATTAATTTTTTA-TTGGTTC
1 AATTAATTTTTTATTTGGTTC
100586 AATT--TTTTTTA
1 AATTAATTTTTTA
100597 AATTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.25
20 15 0.54
21 6 0.21
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.65
Consensus pattern (21 bp):
AATTAATTTTTTATTTGGTTC
Found at i:107989 original size:2 final size:2
Alignment explanation
Indices: 107982--108013 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
107972 ATAGAAGAGC
107982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
108014 CAGTATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108722 original size:1 final size:1
Alignment explanation
Indices: 108682--108706 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
108672 TTCTTTAGGA
108682 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
108707 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:109974 original size:183 final size:183
Alignment explanation
Indices: 109654--110023 Score: 506
Period size: 183 Copynumber: 2.0 Consensus size: 183
109644 CAAATGGCAC
109654 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAACCTCAACTAC
1 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAACCTCAACTAC
* * * * *
109719 ATCCTGAGACCTAACAAACTGAGTAACAGGCCCCTTTCGCAACGCTTGCTGCTCTTCGAACTCAC
66 ATCCTGAAACCTAACAAACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
* *
109784 AGAGGGCATATTGAATTCCTTGGCCATGTTCCAAGCTAGCACTAATCTTTGAT
131 AGAGGGCATATTGAATTCCTTGGCCATATTCCAAGCTAGCACTAATCTTTAAT
* *** * * **
109837 AAATTGTCCCATGAACTGGTTCTGTCTTCTAAGGGGATCTTTGGTTGCTTTGAAGTCTCAACTAC
1 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAACCTCAACTAC
* ** * * *
109902 ATCTTGAAACCTGGCAGACTGAGTAACAGACCCCTTTTGCAACCCTTGCAGCTCTTCAAACTCGC
66 ATCCTGAAACCTAACAAACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
* ** * *
109967 TGAGGGCATATTGAATTCCTTGGCCATATTCTGAGCTATCACTAGTCTTTAAT
131 AGAGGGCATATTGAATTCCTTGGCCATATTCCAAGCTAGCACTAATCTTTAAT
110020 AAAT
1 AAAT
110024 GACTGATTCT
Statistics
Matches: 161, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (183 bp):
AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAACCTCAACTAC
ATCCTGAAACCTAACAAACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
AGAGGGCATATTGAATTCCTTGGCCATATTCCAAGCTAGCACTAATCTTTAAT
Found at i:116296 original size:16 final size:16
Alignment explanation
Indices: 116252--116296 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
116242 TTTGGTAGGA
116252 TTAAAATATTAATTATT
1 TTAAAAT-TTAATTATT
116269 TATAAACA-TTAATTATT
1 T-TAAA-ATTTAATTATT
116286 TTAAAATTTAA
1 TTAAAATTTAA
116297 ACACTTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.04
16 8 0.32
17 11 0.44
18 4 0.16
19 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAAATTTAATTATT
Found at i:152026 original size:8 final size:8
Alignment explanation
Indices: 152015--152055 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
152005 ATTAATCCTT
152015 TAAAATTA
1 TAAAATTA
152023 TAAAA-TA
1 TAAAATTA
152030 T-AAATTA
1 TAAAATTA
*
152037 TTAAAATAA
1 -TAAAATTA
152046 TAAAATTA
1 TAAAATTA
152054 TA
1 TA
152056 TTTTTACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 3 0.11
7 5 0.18
8 15 0.54
9 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAAATTA
Found at i:159675 original size:30 final size:33
Alignment explanation
Indices: 159619--159678 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
159609 TGTTTGTATG
*
159619 AAATTGAAGAAAGAGGGAAGAAGGAGAAAGACC
1 AAATTGAAGAAAGAAGGAAGAAGGAGAAAGACC
159652 AAATTGAAGAAA-AAGG-A-AAGGAGAAAG
1 AAATTGAAGAAAGAAGGAAGAAGGAGAAAG
159679 CTAAGGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 1 0.04
32 3 0.12
33 12 0.46
ACGTcount: A:0.58, C:0.03, G:0.32, T:0.07
Consensus pattern (33 bp):
AAATTGAAGAAAGAAGGAAGAAGGAGAAAGACC
Found at i:160792 original size:6 final size:6
Alignment explanation
Indices: 160781--160829 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
160771 TGATCAAAAT
* * *
160781 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
160829 T
1 T
160830 AATATGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:162403 original size:28 final size:28
Alignment explanation
Indices: 162320--162409 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
162310 AACGTACTTA
* * * *
162320 AAAATGCAATTTTTGGATGCCCTAGGGT
1 AAAATGCAATTTTTAGATGCTCGAGGGC
* * * * *
162348 AAAATGCTAAATTTGAGAAGTTTG-GGGC
1 AAAATGC-AATTTTTAGATGCTCGAGGGC
162376 AAAATGCAATTTTTAGATGCTCGAGGGC
1 AAAATGCAATTTTTAGATGCTCGAGGGC
162404 AAAATG
1 AAAATG
162410 GTAATTTGGA
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
27 11 0.24
28 27 0.59
29 8 0.17
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (28 bp):
AAAATGCAATTTTTAGATGCTCGAGGGC
Found at i:162617 original size:171 final size:171
Alignment explanation
Indices: 162383--162708 Score: 374
Period size: 171 Copynumber: 1.9 Consensus size: 171
162373 GGCAAAATGC
** *
162383 AATTTTTAGATGCTCGAGGGCAAAATGGTAATTTGGAATTATCAGGGGTAAAACGGTAATTTTTT
1 AATTTTTAGATGCTCGAGGGCAAAATGGTAATTTAAAAGTATCAGGGGTAAAACGGTAATTTTTT
* * * ** ** *
162448 TACATATGAGGGCAAAATGGCAATTTCTGGACGTTCGAGGTTAAAATAATAATTTTTAGATA-CT
66 GACATACGAGGGAAAAATGGCAATTTCTGGACACTCGAGGGAAAAATAATAATTTTTAGACATC-
**
162512 CGAGGGCAAAATGATAATTTTTGGACATACATGGTAAACGGT
130 CGAGGGCAAAACAATAATTTTTGGACATACATGGTAAACGGT
* *
162554 AATTTTTGGATGCTC-AGGGGCAAAATGGTAATTTTTAAAAGT-TC-GGGGTCAAAA-TGTAATT
1 AATTTTTAGATGCTCGA-GGGCAAAATGGTAA--TTTAAAAGTATCAGGGGT-AAAACGGTAATT
* * * ** *
162615 TTTTGACATCCGAGGGAAAAATGGTAATTTTTGGACACTCGAGGGAAAAATGGTAATTTTTGGAC
62 TTTTGACATACGAGGGAAAAATGGCAATTTCTGGACACTCGAGGGAAAAATAATAATTTTTAGAC
*
162680 ATCCGAGGGTAAAACAATAATTTTTGGAC
127 ATCCGAGGGCAAAACAATAATTTTTGGAC
162709 GCTCGGGGGC
Statistics
Matches: 128, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
170 1 0.01
171 114 0.89
172 7 0.05
173 6 0.05
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (171 bp):
AATTTTTAGATGCTCGAGGGCAAAATGGTAATTTAAAAGTATCAGGGGTAAAACGGTAATTTTTT
GACATACGAGGGAAAAATGGCAATTTCTGGACACTCGAGGGAAAAATAATAATTTTTAGACATCC
GAGGGCAAAACAATAATTTTTGGACATACATGGTAAACGGT
Found at i:162641 original size:29 final size:29
Alignment explanation
Indices: 162604--162819 Score: 151
Period size: 29 Copynumber: 7.5 Consensus size: 29
162594 GTTCGGGGTC
*
162604 AAAAT-GTAATTTTTTGACATCCGAGGGA
1 AAAATGGTAATTTTTGGACATCCGAGGGA
162632 AAAATGGTAATTTTTGGACA-CTCGAGGGA
1 AAAATGGTAATTTTTGGACATC-CGAGGGA
*
162661 AAAATGGTAATTTTTGGACATCCGAGGGT
1 AAAATGGTAATTTTTGGACATCCGAGGGA
*** * * *
162690 AAAACAATAATTTTTGGAC-GCTCGGGGGC
1 AAAATGGTAATTTTTGGACATC-CGAGGGA
* * * **
162719 AAAATGTTAATTTTTGAAAATTTTG-GGGTAA
1 AAAATGGTAATTTTTGGACA-TCCGAGGG--A
* *
162750 AAAAT-ATAATTTTTGGACATCC--TGGA
1 AAAATGGTAATTTTTGGACATCCGAGGGA
** *
162776 TAAAATGGTAATTTTTGGATGTTCG-GGGA
1 -AAAATGGTAATTTTTGGACATCCGAGGGA
162805 TAAAATGGTAATTTT
1 -AAAATGGTAATTTT
162820 GGAAAGTTTG
Statistics
Matches: 149, Mismatches: 28, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 22 0.15
29 103 0.69
30 13 0.09
31 5 0.03
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGACATCCGAGGGA
Found at i:162701 original size:58 final size:58
Alignment explanation
Indices: 162604--162794 Score: 185
Period size: 58 Copynumber: 3.3 Consensus size: 58
162594 GTTCGGGGTC
* **
162604 AAAAT-GTAATTTTTTGACATCCGAGGG-AAAAATGGTAATTTTTGGACACTCGAGGGA
1 AAAATGGTAATTTTTGGACATCCGAGGGTAAAAA-AATAATTTTTGGACACTCGAGGGA
* * * *
162661 AAAATGGTAATTTTTGGACATCCGAGGGTAAAACAATAATTTTTGGACGCTCGGGGGC
1 AAAATGGTAATTTTTGGACATCCGAGGGTAAAAAAATAATTTTTGGACACTCGAGGGA
* * * ** **
162719 AAAATGTTAATTTTTGAAAATTTTG-GGGTAAAAAATATAATTTTTGGACA-TC-CTGGA
1 AAAATGGTAATTTTTGGACA-TCCGAGGGTAAAAAA-ATAATTTTTGGACACTCGAGGGA
162776 TAAAATGGTAATTTTTGGA
1 -AAAATGGTAATTTTTGGA
162795 TGTTCGGGGA
Statistics
Matches: 110, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
57 7 0.06
58 84 0.76
59 19 0.17
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGACATCCGAGGGTAAAAAAATAATTTTTGGACACTCGAGGGA
Found at i:162780 original size:87 final size:87
Alignment explanation
Indices: 162668--162866 Score: 231
Period size: 87 Copynumber: 2.3 Consensus size: 87
162658 GGAAAAATGG
* * *
162668 TAATTTTTGGACATCCGAGGGTAAAACAATAATTTTTGGACGCTCGGGGGCAAAATGTTAATTTT
1 TAATTTTTGGACATCCGAGGATAAAACAATAATTTTTGGACGCTCGGGGACAAAATGGTAA-TTT
*
162733 TGAAAATTTTGGGGTAAAAAATA
65 TGAAAAGTTTGGGGTAAAAAATA
* *** * * *
162756 TAATTTTTGGACATCC-TGGATAAAATGGTAATTTTTGGATGTTCGGGGATAAAATGGTAATTTT
1 TAATTTTTGGACATCCGAGGATAAAACAATAATTTTTGGACGCTCGGGGACAAAATGGTAATTTT
* *
162820 GGAAAGTTTGGGGTCAAAAATA
66 GAAAAGTTTGGGGTAAAAAATA
* * *
162842 T-ATTTTTTGACATTCGAGGGTAAAA
1 TAATTTTTGGACATCCGAGGATAAAA
162867 TGGTAATATT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
85 12 0.13
86 31 0.33
87 34 0.37
88 16 0.17
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.35
Consensus pattern (87 bp):
TAATTTTTGGACATCCGAGGATAAAACAATAATTTTTGGACGCTCGGGGACAAAATGGTAATTTT
GAAAAGTTTGGGGTAAAAAATA
Found at i:162849 original size:58 final size:57
Alignment explanation
Indices: 162784--163171 Score: 248
Period size: 58 Copynumber: 6.7 Consensus size: 57
162774 GATAAAATGG
*
162784 TAATTTTTGGATGTTCGGGGATAAAATGGTAATTTTGGAAAGTTTGGGGTCAAAAATA
1 TAATTTTTGGAAGTTCGGGG-TAAAATGGTAATTTTGGAAAGTTTGGGGTCAAAAATA
* * *
162842 T-ATTTTTTGACA-TTCGAGGGTAAAATGGTAATATTTGGAAAGTTTGGGGTCAGAAATG
1 TAATTTTTGGA-AGTTCG-GGGTAAAATGGTAAT-TTTGGAAAGTTTGGGGTCAAAAATA
* *
162900 TAATTTTTGGACAGTT-GGGGTAAAATGGTAATTTTGG-ATGTTCGAGGGT--AAAATAA
1 TAATTTTTGGA-AGTTCGGGGTAAAATGGTAATTTTGGAAAGTTTG-GGGTCAAAAAT-A
* ** * *
162956 TAATTTTTGAAAAGTTCATGGTCAAAAT-GTGAGTTTTGG-AAGTTTAGGGGT-AAAAATG
1 TAATTTTTG-GAAGTTCGGGGT-AAAATGGT-AATTTTGGAAAGTTT-GGGGTCAAAAATA
* * * * * *
163014 TAATTATTGAGAAGTTTGAGGTCAAAAT-GTGATTTTTGG-AA-TTTGAGGAT-AAAAATG
1 TAATTTTTG-GAAGTTCGGGGT-AAAATGGT-AATTTTGGAAAGTTTG-GGGTCAAAAATA
* * * * * *
163071 TAACTTTTGGGAAGTTCGAGGTTAAAAT-ATAATTTTTGGAAAGTTAGGGGGCCAAAATA
1 TAA-TTTTTGGAAGTTCG-GGGTAAAATGGTAA-TTTTGGAAAGTTTGGGGTCAAAAATA
* * *
163130 TAATTTTTGTGAAGTTTGAAGGTCAAAAT-GTGATTTTGGAAA
1 TAATTTTTG-GAAGTTCG-GGGT-AAAATGGTAATTTTGGAAA
163172 AGTGTAAGGG
Statistics
Matches: 267, Mismatches: 41, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
55 4 0.01
56 20 0.07
57 74 0.28
58 113 0.42
59 47 0.18
60 9 0.03
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
TAATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTGGAAAGTTTGGGGTCAAAAATA
Found at i:162850 original size:30 final size:29
Alignment explanation
Indices: 162719--163171 Score: 208
Period size: 29 Copynumber: 15.7 Consensus size: 29
162709 GCTCGGGGGC
* *
162719 AAAATGTTAATTTTTGAAAATTTTGGGGTAA
1 AAAATG-TAATTTTTGGAAAGTTTGGGGT-A
* * * *
162750 AAAATATAATTTTTGGACA-TCCT-GGAT-
1 AAAATGTAATTTTTGGAAAGT-TTGGGGTA
* *
162777 AAAATGGTAATTTTTGG-ATGTTCGGGG-A
1 AAAAT-GTAATTTTTGGAAAGTTTGGGGTA
162805 TAAAATGGTAA-TTTTGGAAAGTTTGGGGTCA
1 -AAAAT-GTAATTTTTGGAAAGTTTGGGGT-A
* * * *
162836 AAAATAT-ATTTTTTGACA-TTCGAGGGT-
1 AAAATGTAATTTTTGGAAAGTTTG-GGGTA
*
162863 AAAATGGTAATATTTGGAAAGTTTGGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTTGGGGT-A
* *
162894 GAAATGTAATTTTTGGACAG-TTGGGGT-
1 AAAATGTAATTTTTGGAAAGTTTGGGGTA
* *
162921 AAAATGGTAA-TTTTGG-ATGTTCGAGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTTG-GGGTA
* * *** *
162949 AAAATAATAATTTTTGAAAAGTTCATGGTC
1 AAAAT-GTAATTTTTGGAAAGTTTGGGGTA
* *
162979 AAAATGTGAGTTTTGG-AAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAAGTTT-GGGGTA
* * *
163008 AAAATGTAATTATT-GAGAAGTTTGAGGTC
1 AAAATGTAATTTTTGGA-AAGTTTGGGGTA
* *
163037 AAAATGTGATTTTTGG-AA-TTTGAGGATA
1 AAAATGTAATTTTTGGAAAGTTTG-GGGTA
* * * * *
163065 AAAATGTAACTTTTGGGAAGTTCGAGGTT
1 AAAATGTAATTTTTGGAAAGTTTGGGGTA
* * **
163094 AAAATATAATTTTTGGAAAGTTAGGGGGCC
1 AAAATGTAATTTTTGGAAAGTT-TGGGGTA
* * *
163124 AAAATATAATTTTTGTG-AAGTTTGAAGGTC
1 AAAATGTAATTTTTG-GAAAGTTTG-GGGTA
*
163154 AAAATGTGA-TTTTGGAAA
1 AAAATGTAATTTTTGGAAA
163172 AGTGTAAGGG
Statistics
Matches: 318, Mismatches: 71, Indels: 68
0.70 0.16 0.15
Matches are distributed among these distances:
26 1 0.00
27 26 0.08
28 65 0.20
29 129 0.41
30 86 0.27
31 11 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTTGGGGTA
Found at i:162868 original size:86 final size:88
Alignment explanation
Indices: 162668--162964 Score: 259
Period size: 86 Copynumber: 3.4 Consensus size: 88
162658 GGAAAAATGG
* *** * *
162668 TAATTTTTGGACATCCGAGGGTAAAACAATAATTTTTGGACGCTCGGGGGCAAAATGTTAATTTT
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGACGCTCGGGGACAAAATGGTAATTTT
*
162733 TGAAAATTTTGGGGTAAAAAATA
66 TGAAAAGTTTGGGGTAAAAAATA
** * * * *
162756 TAATTTTTGGACA-TCCTGGATAAAATGGTAATTTTTGGATGTTCGGGGATAAAATGGTAA-TTT
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGACGCTCGGGGACAAAATGGTAATTTT
* *
162819 TGGAAAGTTTGGGGTCAAAAATA
66 TGAAAAGTTTGGGGTAAAAAATA
* * * * * *
162842 T-ATTTTTTGACATTCGAGGGTAAAATGGTAATATTTGGAAAGTTTGGGGTCAGAAAT-GTAATT
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGG-ACGCTCGGGGACA-AAATGGTAATT
* * *
162905 TTTGGACAG-TTGGGGT--AAAATGG
64 TTTGAAAAGTTTGGGGTAAAAAAT-A
** **
162928 TAA-TTTTGGATGTTCGAGGGTAAAATAATAATTTTTG
1 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTG
162965 AAAAGTTCAT
Statistics
Matches: 171, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
85 15 0.09
86 74 0.43
87 56 0.33
88 26 0.15
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (88 bp):
TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGACGCTCGGGGACAAAATGGTAATTTT
TGAAAAGTTTGGGGTAAAAAATA
Found at i:162970 original size:144 final size:144
Alignment explanation
Indices: 162575--163138 Score: 469
Period size: 144 Copynumber: 3.9 Consensus size: 144
162565 GCTCAGGGGC
* * * *
162575 AAAATGGTAATTTTTAAAAGTTCGGGGTCAAAATGTAATTTTTTGACATCCGAGGGA-AAAATGG
1 AAAATGGTAATTTTGAAAAGTTTGGGGTCAAAATGTAATTTTTGGACATCTGA-GGATAAAATGG
*** * * * * *
162639 TAATTTTTGGACACTCGAGGGAAAAATGGTAATTTTTGGACA-TCCGAGGGTAAAACAATA-ATT
65 TAATTTTTGGATGTTCGAGGGTAAAATGATAATTTTTGGAAAGTTCG-GGGTCAAA-AATATATT
** * *
162702 TTTGGACGCTCGGGGGC
128 TTTGGACATTCGAGGGT
* * * *
162719 AAAATGTTAATTTTTGAAAATTTTGGGGTAAAAAATATAATTTTTGGACATCCT--GGATAAAAT
1 AAAATGGTAA-TTTTGAAAAGTTTGGGGT-CAAAATGTAATTTTTGGACAT-CTGAGGATAAAAT
* *
162782 GGTAATTTTTGGATGTTCG-GGGATAAAATGGTAA-TTTTGGAAAGTTTGGGGTCAAAAATATAT
63 GGTAATTTTTGGATGTTCGAGGG-TAAAATGATAATTTTTGGAAAGTTCGGGGTCAAAAATATAT
*
162845 TTTTTGACATTCGAGGGT
127 TTTTGGACATTCGAGGGT
* *
162863 AAAATGGTAATATTTGGAAAGTTTGGGGTCAGAAATGTAATTTTTGGACAGT-TG-GGGTAAAAT
1 AAAATGGTAAT-TTTGAAAAGTTTGGGGTCA-AAATGTAATTTTTGGACA-TCTGAGGATAAAAT
* * ** * *
162926 GGTAA-TTTTGGATGTTCGAGGGTAAAATAATAATTTTTGAAAAGTTCATGGTC-AAAATGTGAG
63 GGTAATTTTTGGATGTTCGAGGGTAAAATGATAATTTTTGGAAAGTTCGGGGTCAAAAATAT-AT
*
162989 TTTTGGA-AGTT-TAGGGGT
127 TTTTGGACA-TTCGA-GGGT
* * * *
163007 AAAAAT-GTAATTATTGAGAAGTTTGAGGTCAAAATGTGATTTTTGGA-ATTTGAGGATAAAAAT
1 -AAAATGGTAATT-TTGAAAAGTTTGGGGTCAAAATGTAATTTTTGGACATCTGAGGAT-AAAAT
* * * * * *
163070 -GTAACTTTTGGGAAGTTCGAGGTTAAAAT-ATAATTTTTGGAAAGTTAGGGGGCCAAAATATAA
63 GGTAA-TTTTTGGATGTTCGAGGGTAAAATGATAATTTTTGGAAAGTTCGGGGTCAAAAATAT-A
163133 TTTTTG
126 TTTTTG
163139 TGAAGTTTGA
Statistics
Matches: 343, Mismatches: 53, Indels: 47
0.77 0.12 0.11
Matches are distributed among these distances:
141 1 0.00
142 3 0.01
143 60 0.17
144 174 0.51
145 86 0.25
146 18 0.05
147 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (144 bp):
AAAATGGTAATTTTGAAAAGTTTGGGGTCAAAATGTAATTTTTGGACATCTGAGGATAAAATGGT
AATTTTTGGATGTTCGAGGGTAAAATGATAATTTTTGGAAAGTTCGGGGTCAAAAATATATTTTT
GGACATTCGAGGGT
Found at i:162971 original size:86 final size:86
Alignment explanation
Indices: 162806--163018 Score: 211
Period size: 86 Copynumber: 2.5 Consensus size: 86
162796 GTTCGGGGAT
* * * ** *
162806 AAAATGGTAA-TTTTGGAAAGTTT-GGGGTCAAAAATATATTTTTTGACATTCGAGGGTAAAATG
1 AAAAT-GTAAGTTTTGG-AAGTTTAGGGGT-AAAAATGTAATTTTGGATGTTCGAGGGTAAAATA
* * **
162869 GTAATATTTGGAAAGTTTGGGGTC
63 ATAATATTTGAAAAGTTCAGGGTC
*
162893 AGAAATGTAATTTTTGGACAG-TT-GGGGT-AAAATGGTAATTTTGGATGTTCGAGGGTAAAATA
1 A-AAATGTAAGTTTTGGA-AGTTTAGGGGTAAAAAT-GTAATTTTGGATGTTCGAGGGTAAAATA
* *
162955 ATAATTTTTGAAAAGTTCATGGTC
63 ATAATATTTGAAAAGTTCAGGGTC
*
162979 AAAATGTGAGTTTTGGAAGTTTAGGGGTAAAAATGTAATT
1 AAAATGTAAGTTTTGGAAGTTTAGGGGTAAAAATGTAATT
163019 ATTGAGAAGT
Statistics
Matches: 105, Mismatches: 14, Indels: 15
0.78 0.10 0.11
Matches are distributed among these distances:
84 2 0.02
85 21 0.20
86 52 0.50
87 18 0.17
88 12 0.11
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (86 bp):
AAAATGTAAGTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTGGATGTTCGAGGGTAAAATAATA
ATATTTGAAAAGTTCAGGGTC
Found at i:164108 original size:22 final size:22
Alignment explanation
Indices: 164083--164124 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
164073 TAACTTCCCT
164083 TTTATTATTA-TTAATAATATCA
1 TTTATTATTATTTAA-AATATCA
164105 TTTATTATTATTTAAAATAT
1 TTTATTATTATTTAAAATAT
164125 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATTATTATTTAAAATATCA
Found at i:164188 original size:25 final size:26
Alignment explanation
Indices: 164132--164198 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
164122 TATTTTTTGA
* *
164132 AAATAAATAAATATATTAAATGATTAT
1 AAATACAT-AATATAATAAATGATTAT
164159 AAATA-ATAATATAATAAAT-ATATAT
1 AAATACATAATATAATAAATGAT-TAT
*
164184 TAATACATATATATA
1 AAATACATA-ATATA
164199 CCAAACATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.06
25 18 0.51
26 5 0.14
27 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (26 bp):
AAATACATAATATAATAAATGATTAT
Found at i:164193 original size:14 final size:14
Alignment explanation
Indices: 164133--164197 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
164123 ATTTTTTGAA
*
164133 AATAAATAAATA-T
1 AATAAATATATATT
* *
164146 ATTAAATGAT-TATA
1 AATAAAT-ATATATT
164160 AAT-AATA-ATA-T
1 AATAAATATATATT
164171 AATAAATATATATT
1 AATAAATATATATT
*
164185 AATACATATATAT
1 AATAAATATATAT
164198 ACCAAACATC
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
11 3 0.08
12 7 0.17
13 14 0.35
14 16 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
AATAAATATATATT
Found at i:164864 original size:18 final size:17
Alignment explanation
Indices: 164827--164886 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
164817 GGACATTATT
*
164827 AATTTAAATTTAGGATA
1 AATTTAAATTTAAGATA
164844 AATTTAAATTTAAGAATA
1 AATTTAAATTTAAG-ATA
*
164862 AATTTAAACTTAAGATA
1 AATTTAAATTTAAGATA
*
164879 AATCTAAA
1 AATTTAAA
164887 ATCAAATAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
17 23 0.59
18 16 0.41
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAGATA
Done.