Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012636.1 Kokia drynarioides strain JFW-HI SEQ_127645, 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: 55550
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:3139 original size:17 final size:17
Alignment explanation
Indices: 3119--3183 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
3109 TCAATTTAAG
3119 TTTAAATTTATTGT-AAA
1 TTTAAATTTATT-TAAAA
** ** *
3136 TTTAAGCTTATTTGGAG
1 TTTAAATTTATTTAAAA
3153 TTTAAATTTATTTTAAAA
1 TTTAAATTTA-TTTAAAA
*
3171 TTTAAAATTATTT
1 TTTAAATTTATTT
3184 TGAAATAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
16 1 0.03
17 22 0.61
18 13 0.36
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTAAAA
Found at i:3176 original size:18 final size:18
Alignment explanation
Indices: 3153--3189 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3143 TTATTTGGAG
*
3153 TTTAAATTTATTTTAAAA
1 TTTAAAATTATTTTAAAA
*
3171 TTTAAAATTATTTTGAAA
1 TTTAAAATTATTTTAAAA
3189 T
1 T
3190 AAAATTTTAA
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:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAAATTATTTTAAAA
Found at i:3182 original size:35 final size:34
Alignment explanation
Indices: 3117--3183 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
3107 ATTCAATTTA
**
3117 AGTTTAAATTTATTGTAAATTTAAGCTTATTTGG
1 AGTTTAAATTTATTGTAAATTTAAAATTATTTGG
*
3151 AGTTTAAATTTATTTTAAAATTTAAAATTATTT
1 AGTTTAAATTTATTGT-AAATTTAAAATTATTT
3184 TGAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 15 0.52
35 14 0.48
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.52
Consensus pattern (34 bp):
AGTTTAAATTTATTGTAAATTTAAAATTATTTGG
Found at i:5032 original size:29 final size:29
Alignment explanation
Indices: 4982--5106 Score: 150
Period size: 30 Copynumber: 4.2 Consensus size: 29
4972 AAAGGTCCCT
4982 AAACTATCCAAAAATTCCATTTTT-ACCCAC
1 AAACT-TCCAAAAATTCCATTTTTGACCC-C
5012 AAACTT-CAAAAATTCCCATTTTTGACCCTC
1 AAACTTCCAAAAATT-CCATTTTTGACCC-C
*
5042 AAACTTCCAAAAA-TCTTATTTTTGACCCCC
1 AAACTTCCAAAAATTC-CATTTTTGA-CCCC
5072 AAACTTCCAAAAATTCCATTTTT-ACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
5100 TAAACTT
1 -AAACTT
5107 TCNNNNNNNN
Statistics
Matches: 85, Mismatches: 3, Indels: 15
0.83 0.03 0.15
Matches are distributed among these distances:
28 12 0.14
29 17 0.20
30 45 0.53
31 11 0.13
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCC
Found at i:5091 original size:60 final size:58
Alignment explanation
Indices: 4978--5106 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 58
4968 CCCTAAAGGT
4978 CCCT-AAACTATCCAAAAATTCCATTTTTACCCACAAACTTCAAAAATTCCCATTTTTGA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTACCCACAAACTTCAAAAATTCCCATTTTT-A
* *
5037 CCCTCAAACTTCCAAAAA-TCTTATTTTTGACCCCCAAACTTCCAAAAATT-CCATTTTTA
1 CCCTCAAACTTCCAAAAATTC-CATTTTT-ACCCACAAACTT-CAAAAATTCCCATTTTTA
5096 CCC-CTAAACTT
1 CCCTC-AAACTT
5107 TCNNNNNNNN
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
58 3 0.05
59 28 0.44
60 24 0.38
61 8 0.13
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.33
Consensus pattern (58 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTACCCACAAACTTCAAAAATTCCCATTTTTA
Found at i:5205 original size:30 final size:30
Alignment explanation
Indices: 5163--5266 Score: 147
Period size: 30 Copynumber: 3.5 Consensus size: 30
5153 NNNNNNNNNN
*
5163 AAAATCCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCA
* **
5193 AAAATTCTATTTTT-ACCCCCGAACTTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCA
* *
5222 AAAATCCCATTTTTAACCCCGAAACTTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCA
5252 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
5267 CCTCGAGTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 25 0.39
30 39 0.61
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCAAAACTTCCA
Found at i:5255 original size:59 final size:57
Alignment explanation
Indices: 5163--5291 Score: 195
Period size: 59 Copynumber: 2.2 Consensus size: 57
5153 NNNNNNNNNN
*
5163 AAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCTATTTTTACCCCCGAACTTCC
1 AAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCC
* * **
5221 AAAAATCCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCTCGAGTTTCC
1 -AAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCC
5279 AAAATCCCATTTT
1 AAAATCCCATTTT
5292 CGACCTCGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 13 0.20
58 9 0.14
59 43 0.66
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (57 bp):
AAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCC
Found at i:5297 original size:28 final size:28
Alignment explanation
Indices: 5217--5300 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 28
5207 ACCCCCGAAC
* * **
5217 TTCCAAAAATCCCATTTTTAACCCCGAAAC
1 TTCCAAAAATCCCA-TTTTGACCTCG-AGT
* *
5247 TTCCAAAAATTCCATTTTTACCTCGAGT
1 TTCCAAAAATCCCATTTTGACCTCGAGT
5275 TTCC-AAAATCCCATTTTCGACCTCGA
1 TTCCAAAAATCCCATTTT-GACCTCGA
5301 AACTCTCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 12 0.26
28 12 0.26
29 9 0.20
30 13 0.28
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.32
Consensus pattern (28 bp):
TTCCAAAAATCCCATTTTGACCTCGAGT
Found at i:16214 original size:18 final size:18
Alignment explanation
Indices: 16191--16227 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16181 TTATTTGGAG
16191 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
16209 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
16227 T
1 T
16228 AAAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:16236 original size:18 final size:18
Alignment explanation
Indices: 16194--16234 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
16184 TTTGGAGTTT
*
16194 AAATTTATTTTAAAATTT
1 AAATTTATTTTAAAATTA
16212 AAATTTATTTTAAAA-TA
1 AAATTTATTTTAAAATTA
16229 AAATTT
1 AAATTT
16235 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATTTATTTTAAAATTA
Found at i:18119 original size:29 final size:29
Alignment explanation
Indices: 18076--18384 Score: 242
Period size: 29 Copynumber: 10.4 Consensus size: 29
18066 AGAGGTCCCT
18076 AAACTATCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* * * *
18106 AAACTTCAAAAAATCCCATTTTGACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * *
18135 GAACTTCCAAAAAATCCCCTTTTTAACCTCG
1 AAACTTCC-AAAAATTCCATTTTT-ACCCCC
* *
18166 AAACTTCCAAAAATTACATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
18195 AAACTTCTAAAAATCCCATTTTTGAACCCCA
1 AAACTTCCAAAAATTCCATTTTT--ACCCCC
** *
18226 AAACTTCCAAAAATTATATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *** * *
18255 GAACTTTTGAAAA-TCACATTTTTGACCTCG
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
* *
18285 AAACTTCCAAAAATTCTATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * *
18314 GAACTTCAAAAAATCCCATTTTTGACTCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
18344 AAACTTCCAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
18373 GAATTTCCAAAA
1 AAACTTCCAAAA
18385 TCCTATTTTC
Statistics
Matches: 210, Mismatches: 61, Indels: 17
0.73 0.21 0.06
Matches are distributed among these distances:
28 1 0.00
29 104 0.50
30 70 0.33
31 35 0.17
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:18217 original size:59 final size:59
Alignment explanation
Indices: 18085--18481 Score: 351
Period size: 59 Copynumber: 6.7 Consensus size: 59
18075 TAAACTATCC
* * * * ** * *
18085 AAAAATTCCATTTTT-ACCCCCAAACTTCAAAAAATCCCATTTTGACCCTCGAACTTCCA
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTT-CT
* *
18144 AAAAATCCCCTTTTTAACCTCGAAACTTCCAAAAATTACATTTTTACCCTCAAACTTCT
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCT
* * * *
18203 AAAAATCCCATTTTTGAACCCCAAAACTTCCAAAAATTATATTTTTACCCTCGAACTTTT
1 AAAAATCCCATTTTT-AACCTCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCT
* * * *
18263 GAAAATCACATTTTTGACCTCGAAACTTCCAAAAATT-CTATTTTTACCCTCGAACTTCA
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTAC-ATTTTTACCCTCGAACTTCT
* * * *
18322 AAAAATCCCATTTTTGA-CTCCGAAACTTCCAAAAATTTCATTTTTACCCCCGAATTTC-
1 AAAAATCCCATTTTTAACCT-CGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCT
* * ** ** * *
18380 CAAAATCCTATTTTCGACCTCGAAAC-TCTC-AAAATTACCCTTTTACCC-CTAAATGT-T
1 AAAAATCCCATTTTTAACCTCGAAACTTC-CAAAAATTACATTTTTACCCTCGAACT-TCT
* * * * * *
18437 TAAAATTCTATTTTTAATCTCGAATCTTCCCAAAATTACCATTTT
1 AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTA-CATTTT
18482 GCCTCCATGC
Statistics
Matches: 282, Mismatches: 44, Indels: 24
0.81 0.13 0.07
Matches are distributed among these distances:
56 4 0.01
57 39 0.14
58 32 0.11
59 120 0.43
60 87 0.31
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCT
Found at i:25027 original size:112 final size:114
Alignment explanation
Indices: 24822--25027 Score: 290
Period size: 112 Copynumber: 1.8 Consensus size: 114
24812 AAGCAAACAA
** * * *
24822 ATCTTCGAATTCCAGCTTCCTGATGAGATACTGAGAAGTAGGTTGAAGAAATAAAATGGTTAGTT
1 ATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGAAATAAAATGGTTAGCT
*
24887 TCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCG
66 TCCTGATGAGATACAGAGAAGTAGACCAACTCAGGGCTCGATGTGAGCG
* * *
24936 ATCTTCGAACCCCAGCTTCTTGATGAG-CACTGAGAAGTAGGTCGAAGCAATCAAA-GGTTAGCT
1 ATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGAAATAAAATGGTTAGCT
* * *
24999 TCCTTATGAGATACTGAGAAGTGGACCAA
66 TCCTGATGAGATACAGAGAAGTAGACCAA
25028 ATTCGTCTTC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
112 32 0.40
113 24 0.30
114 24 0.30
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (114 bp):
ATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGAAATAAAATGGTTAGCT
TCCTGATGAGATACAGAGAAGTAGACCAACTCAGGGCTCGATGTGAGCG
Found at i:25205 original size:205 final size:205
Alignment explanation
Indices: 24922--25467 Score: 765
Period size: 205 Copynumber: 2.7 Consensus size: 205
24912 CCAACTCAGG
* * *
24922 GCTCGATGTGAGC-GATCTTCGAACCCCAGCTTCTTGATGAG-CACTGAGAAGTAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCA
* * *
24985 ATCAAAGGTTAGCTTCCTTATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATAC
* * *
25050 AGAGAGGT-GAATTGAAACAAACGACGTGGTCATCTCCCTGATAAGATACTGAGAAGAAGACCAA
131 AGAGA-ATCGAATTAAAACAAACGACGCGGTCATCTCCCTGATAAGATACTGAGAAGAAGACCAA
* *
25114 ATCGAACCCCC
195 ATCAAACCCAC
* *
25125 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCA
* * * *
25190 ATAAAAGGTTAGCTTCCTGACGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTTATGAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATAC
* * * *
25255 AGAGAATCGGATTAAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAATCGAATTAAAACAAACGACGCGGTCATCTCCCTGATAAGATACTGAGAAGAAGACCAAA
*
25320 TCAAACTCAC
196 TCAAACCCAC
* * * *
25330 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCA
* * * * *
25395 ATAAAAATGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTAATGAAAC
66 AT-AAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGAT
25460 ACAGAGAA
129 ACAGAGAA
25468 ATGGATCAAA
Statistics
Matches: 302, Mismatches: 36, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
203 12 0.04
204 27 0.09
205 203 0.67
206 4 0.01
207 56 0.19
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (205 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATAC
AGAGAATCGAATTAAAACAAACGACGCGGTCATCTCCCTGATAAGATACTGAGAAGAAGACCAAA
TCAAACCCAC
Found at i:25872 original size:17 final size:17
Alignment explanation
Indices: 25844--25923 Score: 117
Period size: 17 Copynumber: 4.7 Consensus size: 17
25834 GGCCCAACAG
*
25844 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTGA
* *
25861 AAATTAAGTTTATTTGA
1 AATTTAAATTTATTTGA
25878 AATTTAAATTTATTTGA
1 AATTTAAATTTATTTGA
25895 AATTTAAATTTATTAT-A
1 AATTTAAATTTATT-TGA
25912 AATTTAAATTTA
1 AATTTAAATTTA
25924 AATTTATTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
17 56 0.98
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTTGA
Found at i:25897 original size:11 final size:10
Alignment explanation
Indices: 25879--25936 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
25869 TTTATTTGAA
25879 ATTTAAATTT
1 ATTTAAATTT
*
25889 ATTTGAA---
1 ATTTAAATTT
25896 ATTTAAATTT
1 ATTTAAATTT
25906 ATTATAAATTT
1 ATT-TAAATTT
25917 AAATTTAAATTT
1 --ATTTAAATTT
25929 ATTTAAAT
1 ATTTAAAT
25937 AATGTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 17 0.43
11 7 0.17
12 7 0.17
13 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:25899 original size:7 final size:6
Alignment explanation
Indices: 25844--25929 Score: 69
Period size: 6 Copynumber: 15.0 Consensus size: 6
25834 GGCCCAACAG
* * *
25844 AATTTA AATTT- ATTTTA AAATTA AGTTT- -ATTTGA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA AATTTA
25889 -ATTTGA AATTTA AATTT- -ATTATA AATTTA AATTTA AATTTA
1 AATTT-A AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA
25930 TTTAAATAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
4 10 0.16
5 5 0.08
6 38 0.59
7 11 0.17
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:25903 original size:23 final size:22
Alignment explanation
Indices: 25889--25936 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
25879 ATTTAAATTT
25889 ATTTGAAATTTAAATTTATTATAA
1 ATTT-AAATTTAAATTTATT-TAA
25913 ATTTAAATTTAAATTTATTTAA
1 ATTTAAATTTAAATTTATTTAA
25935 AT
1 AT
25937 AATGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTAAATTTAAATTTATTTAA
Found at i:27890 original size:30 final size:29
Alignment explanation
Indices: 27854--28025 Score: 186
Period size: 30 Copynumber: 5.8 Consensus size: 29
27844 TTTACCTCTG
*
27854 AACTTCCAAAAATTCCATTTTCAACCCCGA
1 AACTTCCAAAAATTCCATTTT-GACCCCGA
*
27884 AACTTCCAAAAAATTCCATTTTCACCCTC-A
1 AACTTCC-AAAAATTCCATTTTGACCC-CGA
*
27914 AATTTCCAAAAATTCCACTTTTGACCCCGA
1 AACTTCCAAAAATTCCA-TTTTGACCCCGA
*
27944 AACTTCCAAAAATTCCATTTTTACCCTCG-
1 AACTTCCAAAAATTCCATTTTGACCC-CGA
* * * *
27973 AACCTCTAAAATTTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCA-TTTTGACCCCGA
*
28003 AACTTTCAAAAATTACCATTTTG
1 AACTTCCAAAAATT-CCATTTTG
28026 TCCTTAGATG
Statistics
Matches: 120, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
29 34 0.28
30 68 0.57
31 18 0.15
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTGACCCCGA
Found at i:27989 original size:59 final size:58
Alignment explanation
Indices: 27829--28175 Score: 237
Period size: 59 Copynumber: 5.9 Consensus size: 58
27819 CCCTAATTTG
** *
27829 TCCAAAAATTTTATTTTTA-CCTCTGAACTTCCAAAAATTCCATTTTCAACCCCGAAACT
1 TCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTT-GACCCCGAAACT
* * *
27888 TCCAAAAAATTCCATTTTCACCCTCAAATTTCCAAAAATTCCACTTTTGACCCCGAAACT
1 TCC-AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCCCGAAACT
* * * *
27948 TCCAAAAATTCCATTTTTACCCTCGAACCTCTAAAATTTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCCCGAAACT
* * * * * *
28007 TTCAAAAATTACCATTTTGT-CCTTAG-A-TGTCCAAAAAATCCATTTTTGATCTCGAAAC-
1 TCCAAAAATT-CCATTTT-TACCCTCGAACT-TCCAAAAATTCCA-TTTTGACCCCGAAACT
* * * * * * *
28065 TCTC-GAAATTACC-CTTTTACCCTCGAACGTCTAAAAATTCCCTTTTTAACCCC-AAATTT
1 TC-CAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAATT-CCATTTTGACCCCGAAA-CT
* * ** *
28124 TCCCAAAATTACCA-TTTTGCCCTCGAAAATCC-AAAATTACCATTTTGCCCCC
1 TCCAAAAATT-CCATTTTTACCCTCGAACTTCCAAAAATT-CCATTTTGACCCC
28176 CGGGTATTCA
Statistics
Matches: 227, Mismatches: 46, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
56 1 0.00
57 10 0.04
58 42 0.19
59 111 0.49
60 54 0.24
61 9 0.04
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCCCGAAACT
Found at i:28111 original size:29 final size:28
Alignment explanation
Indices: 27832--28112 Score: 108
Period size: 29 Copynumber: 9.6 Consensus size: 28
27822 TAATTTGTCC
** *
27832 AAAAATTTTATTTTTA-CCTCTGAACTTCC
1 AAAAATTCCATTTTTACCCTC-GAAC-TCT
* *
27861 AAAAATTCCATTTTCAACCC-CGAAACTTCCA
1 AAAAATTCCATTTT-TACCCTCG-AAC-T-CT
* * * *
27892 AAAAATTCCATTTTCACCCTCAAATTTCC
1 AAAAATTCCATTTTTACCCTCGAA-CTCT
* *
27921 AAAAATTCCACTTTTGACCC-CGAAACTTCC
1 AAAAATTCCA-TTTTTACCCTCG-AAC-TCT
27951 AAAAATTCCATTTTTACCCTCGAACCTCT
1 AAAAATTCCATTTTTACCCTCGAA-CTCT
* * *
27980 AAAATTTCCATTTTTGACCC-CAAAACTTT
1 AAAAATTCCATTTTT-ACCCTC-GAACTCT
* * ** *
28009 CAAAAATTACCATTTTGT-CCTTAGATGTCC
1 -AAAAATT-CCATTTT-TACCCTCGAACTCT
* *
28039 AAAAAATCCATTTTTGA-TCTCGAAACTCT
1 AAAAATTCCATTTTT-ACCCTCG-AACTCT
** *
28068 CGAAATTACC-CTTTTACCCTCGAACGTCT
1 AAAAATT-CCATTTTTACCCTCGAAC-TCT
*
28097 AAAAATTCCCTTTTTA
1 AAAAATTCCATTTTTA
28113 ACCCCAAATT
Statistics
Matches: 189, Mismatches: 39, Indels: 48
0.68 0.14 0.17
Matches are distributed among these distances:
27 1 0.01
28 15 0.08
29 89 0.47
30 58 0.31
31 25 0.13
32 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTCGAACTCT
Found at i:35062 original size:96 final size:96
Alignment explanation
Indices: 34885--35069 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
34875 GAAATGGATG
* * *
34885 TTCGATTAGCTCGATTTGAAGAAAGGTTGCACCTAGTAGGTTAATGCACAAATTTTCAAAATCGA
1 TTCGATTAGCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAACGCACAAATTTTCAAAATCGA
*
34950 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
** * * *
34981 TTCGATTATTTCGATTTGAAGAACA-ATTGCACCTAGTAAGTTAACGCGCAAATTTTTGAAACTC
1 TTCGATTAGCTCGATTTGAAGAA-AGATTGCACCTAGTAAGTTAACGCACAAA-TTTTCAAAATC
*
35045 GAA-ATAAA-AGAATATTGCCTCGATT
64 GAAGATAAAGA-AACATTGCCTCGATT
35070 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 62 0.82
97 13 0.17
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
TTCGATTAGCTCGATTTGAAGAAAGATTGCACCTAGTAAGTTAACGCACAAATTTTCAAAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:35438 original size:30 final size:28
Alignment explanation
Indices: 35390--35474 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
35380 GGACATTCAG
* *
35390 GGGT-AAAATGGTAATTTTTGCAAGTTTC
1 GGGTAAAAATGG-AATTTTTGAAAGTTTA
35418 GAGGTCAAAAATGGAATTTTTGAAAGTTTA
1 G-GGT-AAAAATGGAATTTTTGAAAGTTTA
* **
35448 GGGTAAAAATGTAATTTTCAAAAGTTT
1 GGGTAAAAATGGAATTTTTGAAAGTTT
35475 TGAGGCTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 21 0.43
29 6 0.12
30 15 0.31
31 7 0.14
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (28 bp):
GGGTAAAAATGGAATTTTTGAAAGTTTA
Found at i:35522 original size:30 final size:29
Alignment explanation
Indices: 35440--35524 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
35430 GGAATTTTTG
*
35440 AAAGTTTA-GGGTAAAAATGTAATTTTCA
1 AAAGTTTAGGGGTAAAAATATAATTTTCA
* * * *
35468 AAAGTTTTGAGGCTAAAAAGATAATTTTGA
1 AAAGTTTAG-GGGTAAAAATATAATTTTCA
*
35498 AGAAGTTTAGGGGTCAAAATATAATTT
1 A-AAGTTTAGGGGTAAAAATATAATTT
35525 ATGGATAGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
28 7 0.16
30 31 0.69
31 7 0.16
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGGTAAAAATATAATTTTCA
Found at i:36585 original size:12 final size:12
Alignment explanation
Indices: 36568--36603 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
36558 AAAAATATTA
*
36568 ATTATTAATAAT
1 ATTATTATTAAT
*
36580 ATTATTATTACT
1 ATTATTATTAAT
36592 ATTATTATTAAT
1 ATTATTATTAAT
36604 GTCATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:36588 original size:15 final size:15
Alignment explanation
Indices: 36548--36601 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
36538 TTTTATTTTT
*
36548 TATT-TTATTAAAAAA
1 TATTATTATT-AATAA
36563 TATTAATTATTAATAA
1 TATT-ATTATTAATAA
* *
36579 TATTATTATTACTAT
1 TATTATTATTAATAA
36594 TATTATTA
1 TATTATTA
36602 ATGTCATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 21 0.62
16 8 0.24
17 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATTATTAATAA
Found at i:37284 original size:17 final size:17
Alignment explanation
Indices: 37264--37341 Score: 84
Period size: 17 Copynumber: 4.6 Consensus size: 17
37254 TATAATTTTT
37264 AATTCAAAATAAATTCA
1 AATTCAAAATAAATTCA
* *
37281 AATTTAAAATAAATTTA
1 AATTCAAAATAAATTCA
* * * *
37298 AACTCAACATGAATTTA
1 AATTCAAAATAAATTCA
*
37315 AATTTAAAATAAATTCA
1 AATTCAAAATAAATTCA
*
37332 AATTAAAAAT
1 AATTCAAAAT
37342 TAAAAGTTGG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (17 bp):
AATTCAAAATAAATTCA
Found at i:37381 original size:16 final size:16
Alignment explanation
Indices: 37360--37397 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
37350 GGATTAGGTG
37360 TTGGGCCCGGTCAAAA
1 TTGGGCCCGGTCAAAA
**
37376 TTGGGCTTGGTCAAAA
1 TTGGGCCCGGTCAAAA
37392 TTGGGC
1 TTGGGC
37398 TTCAACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (16 bp):
TTGGGCCCGGTCAAAA
Found at i:37398 original size:16 final size:16
Alignment explanation
Indices: 37368--37399 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37358 TGTTGGGCCC
37368 GGTCAAAATTGGGCTT
1 GGTCAAAATTGGGCTT
37384 GGTCAAAATTGGGCTT
1 GGTCAAAATTGGGCTT
37400 CAACAACAAG
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:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (16 bp):
GGTCAAAATTGGGCTT
Found at i:37831 original size:30 final size:30
Alignment explanation
Indices: 37782--38040 Score: 265
Period size: 30 Copynumber: 8.6 Consensus size: 30
37772 GGTCGAAAAC
* *
37782 GAAGTTTCAAAGGGATTAAAACGTAATTTTGGA
1 GAAGTTT--AAGGG-TTAAAATGTAATTTTAGA
* * *
37815 AAATTTTAAGGGTTAAAATGTAATTTT-GG
1 GAAGTTTAAGGGTTAAAATGTAATTTTAGA
* *
37844 GAAAGTTTAA-GGTTAAAATGTGATTTTATA
1 G-AAGTTTAAGGGTTAAAATGTAATTTTAGA
* * *
37874 GAAGTTT-GGGGTTAAAATGTGATTTTGGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTAGA
* *
37903 GAAGTTT-AGAGTTAAAATGTGATTTTAGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTAGA
* * *
37932 AAAGTTTAGGGGTCAAAATGTAATTTTAGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTAGA
* *
37962 GAAGTTTATGGGTTAAAATGTAATTTTTGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTAGA
* *
37992 GAAGTGTAAGGGTCAAAATGTAATTTTAGA
1 GAAGTTTAAGGGTTAAAATGTAATTTTAGA
**
38022 GAAGTTCGAGGGTTAAAAT
1 GAAGTTTAAGGGTTAAAAT
38041 AAGATTTTGG
Statistics
Matches: 190, Mismatches: 32, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
29 73 0.38
30 107 0.56
31 5 0.03
33 5 0.03
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
GAAGTTTAAGGGTTAAAATGTAATTTTAGA
Found at i:37892 original size:58 final size:58
Alignment explanation
Indices: 37824--38027 Score: 234
Period size: 58 Copynumber: 3.5 Consensus size: 58
37814 AAAATTTTAA
*
37824 GGGTTAAAATGTAATTTTGG-GAAAGTTTAAGGTTAAAATGTGATTTTATAGAAGTTTG
1 GGGTCAAAATGTAATTTTGGAG-AAGTTTAAGGTTAAAATGTGATTTTATAGAAGTTTG
* * * *
37882 GGGTTAAAATGTGATTTTGGAGAAGTTT-AGAGTTAAAATGTGATTTTAGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAGAAGTTTAAG-GTTAAAATGTGATTTTATAGAAGTTT-G
* * * **
37941 GGGTCAAAATGTAATTTTAGAGAAGTTTATGGGTTAAAATGTAATTTT-TGAGAAGTGTAA
1 GGGTCAAAATGTAATTTTGGAGAAGTTTA-AGGTTAAAATGTGATTTTAT-AGAAGT-TTG
*
38001 GGGTCAAAATGTAATTTTAGAGAAGTT
1 GGGTCAAAATGTAATTTTGGAGAAGTT
38028 CGAGGGTTAA
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
57 2 0.02
58 49 0.39
59 27 0.21
60 47 0.37
61 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (58 bp):
GGGTCAAAATGTAATTTTGGAGAAGTTTAAGGTTAAAATGTGATTTTATAGAAGTTTG
Found at i:38059 original size:90 final size:89
Alignment explanation
Indices: 37797--38033 Score: 226
Period size: 88 Copynumber: 2.7 Consensus size: 89
37787 TTCAAAGGGA
* * * * * * * * * *
37797 TTAAAACGTAATTTTGGAAAATTTTAAGGGTTAAAATGTAATTTTGGGAAAGTTTA-AGGTTAAA
1 TTAAAATGTAATTTTGGAGAA-GTTAAGAGTCAAAATGTAATTTTAGAAAAGTTGAGGGGTCAAA
** * *
37861 ATGTGATTTTATAGAAGTTT-GGGG
65 ATGAAATTTTAGAGAAGTTTATGGG
* * * * *
37885 TTAAAATGTGATTTTGGAGAAGTTTAGAGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTCAAAA
1 TTAAAATGTAATTTTGGAGAAGTTAAGAGTCAAAATGTAATTTTAGAAAAGTTGAGGGGTCAAAA
*
37950 TGTAATTTTAGAGAAGTTTATGGG
66 TGAAATTTTAGAGAAGTTTATGGG
* * *
37974 TTAAAATGTAATTTTTGAGAAGTGTAAGGGTCAAAATGTAATTTTAGAGAAGTTCGAGGG
1 TTAAAATGTAATTTTGGAGAAGT-TAAGAGTCAAAATGTAATTTTAGAAAAGTT-GAGGG
38034 TTAAAATAAG
Statistics
Matches: 123, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
87 28 0.23
88 42 0.34
89 24 0.20
90 25 0.20
91 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (89 bp):
TTAAAATGTAATTTTGGAGAAGTTAAGAGTCAAAATGTAATTTTAGAAAAGTTGAGGGGTCAAAA
TGAAATTTTAGAGAAGTTTATGGG
Found at i:38798 original size:2 final size:2
Alignment explanation
Indices: 38749--38779 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38739 AAAAATAAAG
38749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38780 GTATTTACGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40692 original size:3 final size:3
Alignment explanation
Indices: 40684--40763 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
40674 TTCCATCGTC
40684 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
40732 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
40764 AATCCCTAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:54779 original size:6 final size:6
Alignment explanation
Indices: 54765--54826 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
54755 CCAGGCCCCT
* * *
54765 TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA -TT-AA TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
54811 TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
54827 TTTTCAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 2 0.04
5 5 0.11
6 36 0.78
7 3 0.07
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:54809 original size:23 final size:23
Alignment explanation
Indices: 54765--54824 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
54755 CCAGGCCCCT
* * *
54765 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTAATCTTAAA
*
54788 TTTGAATTTAAATTAATCTTAAA
1 TTTAAATTTAAATTAATCTTAAA
54811 TTTAAATTTAAATT
1 TTTAAATTTAAATT
54825 TATTTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (23 bp):
TTTAAATTTAAATTAATCTTAAA
Done.