Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010905.1 Kokia drynarioides strain JFW-HI SEQ_125873, 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: 20349
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2577 original size:27 final size:27
Alignment explanation
Indices: 2538--2598 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
2528 CAATTTTCAA
*
2538 TTAATGATTGTTTCCTTTGATCCTCCCT
1 TTAAT-ATTGTTTCCTTCGATCCTCCCT
**
2566 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTGTTTCCTTCGATCCTCCCT
2593 TTAATA
1 TTAATA
2599 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.52
Consensus pattern (27 bp):
TTAATATTGTTTCCTTCGATCCTCCCT
Found at i:5244 original size:27 final size:27
Alignment explanation
Indices: 5205--5265 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
5195 CAATTTTCAA
*
5205 TTAATGATTGTTTCCTTTGATCCTCCCT
1 TTAAT-ATTGTTTCCTTCGATCCTCCCT
**
5233 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTGTTTCCTTCGATCCTCCCT
5260 TTAATA
1 TTAATA
5266 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.52
Consensus pattern (27 bp):
TTAATATTGTTTCCTTCGATCCTCCCT
Found at i:6127 original size:190 final size:191
Alignment explanation
Indices: 5815--6502 Score: 873
Period size: 190 Copynumber: 3.5 Consensus size: 191
5805 CATGCTCGAT
5815 GTAAGC-AAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAGAA
1 GTAAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAGAA
* * *
5879 GGTCAACTTCCTGATGAGATACCGAGAAGTGAACCAAATCCGCCTTCCTGATGAGATACAAAGAA
66 GGTCAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATCTGCCTTCCTGATGAGATACAAAGAA
* * *
5944 GCGAACGACACAGTCATCTTCCTGATAAGACACTAAGAAGAAGACCCAAACCATGCTCGAT
131 GCGAACGACACAGTCATCTTCCTGATAAGACACTAAGAAGAAGACCCAAACCAGGCTCAAA
*
6005 GTAAGC-AAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAA
1 GTAAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAGAA
* * *
6069 GGTCAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATCTGCCTTTCTGATGAGATACAGAGAA
66 GGTCAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATCTGCCTTCCTGATGAGATACAAAGAA
** * * * *
6134 GCGAACGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCAAA
131 GCGAACGACACAGTCATCTTCCTGATAAGACACTAAGAAGAAGACCCAAACCAGGCTCAAA
* *
6195 GTGAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAGAA
1 GTAAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAGAA
* * * * *
6260 GGTTAGCTTCCTGATGAGGTACTGAGAAGTGAACCAAAT-TCGTCTTCCGGATGAAATACGGAGA
66 GGTCAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATCT-GCCTTCCTGATGAGATAC--A-A
** * * * * *
6324 AGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGATGAGGTGC-CGAA-AAGAAGACCTAA
127 A--GAAGCG-AAC-GACA-C-A-G---TCATCTTCCTGAT-AAG-ACACTAAGAAGAAGACCCAA
*
6387 ACGAGGCTCAAA
180 ACCAGGCTCAAA
* * *
6399 GTGAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAGAA
1 GTAAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAGAA
* *
6464 GGTTAGCTTCCTGATGAGGTACTGAGAAGTGAACCAAAT
66 GGTCAGCTTCCTGATGAGATACTGAGAAGTGAACCAAAT
6503 TCGAAGAAGC
Statistics
Matches: 441, Mismatches: 40, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
190 180 0.41
191 106 0.24
193 1 0.00
194 1 0.00
196 4 0.01
197 3 0.01
198 1 0.00
199 1 0.00
201 1 0.00
204 139 0.32
205 3 0.01
206 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (191 bp):
GTAAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAGAA
GGTCAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATCTGCCTTCCTGATGAGATACAAAGAA
GCGAACGACACAGTCATCTTCCTGATAAGACACTAAGAAGAAGACCCAAACCAGGCTCAAA
Found at i:6656 original size:186 final size:186
Alignment explanation
Indices: 6321--6678 Score: 524
Period size: 186 Copynumber: 1.9 Consensus size: 186
6311 TGAAATACGG
* * *
6321 AGAAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGATGAGGTGCCGAAAAGAAGACCTA
1 AGAAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGAAGAGATGCCGAAAAGAAGACCCA
** * * * * *
6386 AACGAGGCTCAAAGTGAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGT
66 AACGAGGCTCAAAACGAGCAAAGTCTTCGAACCACAGCTTCCCGATGAGACACGAAGAAGCAAGT
*
6451 CGAAGCAATAGAAGGTTAGCTTCCT-GATGAGGTACTGAGAAGTGAACCAAATTCGA
131 CGAAGCAATAGAAGGTTAGC-TCCTCGATGAGATACTGAGAAGTGAACCAAATTCGA
*
6507 AGAAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGAAGAGATGCTGAAAAGAAGACCCA
1 AGAAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGAAGAGATGCCGAAAAGAAGACCCA
* * *
6572 AACGAGGCTTAAAACGAGCAAA-TCTTCGAACCACAGCTTCCCGATGAGACGCGGAGAAGCAAGT
66 AACGAGGCTCAAAACGAGCAAAGTCTTCGAACCACAGCTTCCCGATGAGACACGAAGAAGCAAGT
*
6636 CGAAGCCATA-AAGTGGTTAGCTCCTCGATGAGATACTGAGAAG
131 CGAAGCAATAGAA--GGTTAGCTCCTCGATGAGATACTGAGAAG
6679 AAGGCCAAGT
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
184 2 0.01
185 48 0.31
186 103 0.67
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (186 bp):
AGAAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGAAGAGATGCCGAAAAGAAGACCCA
AACGAGGCTCAAAACGAGCAAAGTCTTCGAACCACAGCTTCCCGATGAGACACGAAGAAGCAAGT
CGAAGCAATAGAAGGTTAGCTCCTCGATGAGATACTGAGAAGTGAACCAAATTCGA
Found at i:7012 original size:17 final size:16
Alignment explanation
Indices: 6962--7018 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
6952 TAAAATTTTG
*
6962 AATTTATTTTAAATTTA
1 AATTTAATTT-AATTTA
*
6979 AATTT-GTCTTGAATTTA
1 AATTTAAT-TT-AATTTA
6996 AATTTAATTTAAGTTTA
1 AATTTAATTTAA-TTTA
7013 AATTTA
1 AATTTA
7019 TTTTCAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.09
17 30 0.88
18 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (16 bp):
AATTTAATTTAATTTA
Found at i:7016 original size:23 final size:23
Alignment explanation
Indices: 6969--7018 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6959 TTGAATTTAT
*
6969 TTTAAATTTAAATTTGTCTTGAA
1 TTTAAATTTAAATTTGTCTTAAA
6992 TTTAAATTT-AATTTAAGT-TTAAA
1 TTTAAATTTAAATTT--GTCTTAAA
7015 TTTA
1 TTTA
7019 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (23 bp):
TTTAAATTTAAATTTGTCTTAAA
Found at i:7775 original size:13 final size:13
Alignment explanation
Indices: 7757--7787 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7747 TTTATAACTG
*
7757 TTAATAATCATTA
1 TTAATAATCAATA
7770 TTAATAATCAATA
1 TTAATAATCAATA
7783 TTAAT
1 TTAAT
7788 TATTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAATAATCAATA
Found at i:8824 original size:29 final size:29
Alignment explanation
Indices: 8787--9157 Score: 184
Period size: 30 Copynumber: 12.9 Consensus size: 29
8777 GTCCCTGAGC
8787 CTTCTAAAAATTACCATTTTACCCCCGAA
1 CTTCTAAAAATTACCATTTTACCCCCGAA
* * * **
8816 CTTCCAAAAA-TCCCATTTTTAACCTTGAA
1 CTTCTAAAAATTACCA-TTTTACCCCCGAA
8845 CTTTCTAAAAATTACCATTTTA---CC---
1 C-TTCTAAAAATTACCATTTTACCCCCGAA
** ** ** **
8869 C--C-AAAAATCCCATTTTTGTCCCTAAA
1 CTTCTAAAAATTACCATTTTACCCCCGAA
8895 CCTTCTAAAAATTACCATTTTACCCCCGAA
1 -CTTCTAAAAATTACCATTTTACCCCCGAA
* ** ***
8925 CTTCCAAAAA-CCCCATTTTTTA-TGTCGAA
1 CTTCTAAAAATTACCA--TTTTACCCCCGAA
*
8954 CCTTCTAAAAATTACCATTTTACCCTCGAA
1 -CTTCTAAAAATTACCATTTTACCCCCGAA
* * *
8984 CTTCCAAAAA-TCCCATTTTTGA-CCTCGAA
1 CTTCTAAAAATTACCA-TTTT-ACCCCCGAA
* * *
9013 CCTTCTTAAAATTACTATTTTACCCCCAAA
1 -CTTCTAAAAATTACCATTTTACCCCCGAA
* *
9043 CTTCTTAAAA-TCCCATTTTTGA-CCCCGAA
1 CTTCTAAAAATTACCA-TTTT-ACCCCCGAA
* *
9072 CCTTCTAAAAAATACCATTTTACCCCCAAA
1 -CTTCTAAAAATTACCATTTTACCCCCGAA
* *
9102 CTTCCAAAAA-TCCCATTTTTGA-CCCCGAA
1 CTTCTAAAAATTACCA-TTTT-ACCCCCGAA
*
9131 CCTTCTAAAAACTACCATTTTACCCCC
1 -CTTCTAAAAATTACCATTTTACCCCC
9158 ATGCATCCGA
Statistics
Matches: 256, Mismatches: 53, Indels: 65
0.68 0.14 0.17
Matches are distributed among these distances:
20 11 0.04
21 1 0.00
23 1 0.00
24 1 0.00
27 1 0.00
28 18 0.07
29 101 0.39
30 104 0.41
31 18 0.07
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (29 bp):
CTTCTAAAAATTACCATTTTACCCCCGAA
Found at i:8881 original size:50 final size:50
Alignment explanation
Indices: 8819--8920 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
8809 CCCCGAACTT
* * *
8819 CCAAAAATCCCATTTTTAACCTTGAACTTTCTAAAAATTACCATTTTACC
1 CCAAAAATCCCATTTTTAACCCTAAACCTTCTAAAAATTACCATTTTACC
**
8869 CCAAAAATCCCATTTTTGTCCCTAAACCTTCTAAAAATTACCATTTTACC
1 CCAAAAATCCCATTTTTAACCCTAAACCTTCTAAAAATTACCATTTTACC
8919 CC
1 CC
8921 CGAACTTCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (50 bp):
CCAAAAATCCCATTTTTAACCCTAAACCTTCTAAAAATTACCATTTTACC
Found at i:8940 original size:59 final size:59
Alignment explanation
Indices: 8869--9158 Score: 395
Period size: 59 Copynumber: 4.9 Consensus size: 59
8859 CCATTTTACC
* * *
8869 CCAAAAATCCCATTTTTGTCCCTAAACCTTCTAAAAATTACCATTTTACCCCCGAACTT
1 CCAAAAATCCCATTTTTGACCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTT
* * ** * *
8928 CCAAAAACCCCATTTTTTA-TGTCGAACCTTCTAAAAATTACCATTTTACCCTCGAACTT
1 CCAAAAATCCCATTTTTGACCCT-GAACCTTCTAAAAATTACCATTTTACCCCCAAACTT
* *
8987 CCAAAAATCCCATTTTTGA-CCTCGAACCTTCTTAAAATTACTATTTTACCCCCAAACTT
1 CCAAAAATCCCATTTTTGACCCT-GAACCTTCTAAAAATTACCATTTTACCCCCAAACTT
** * *
9046 CTTAAAATCCCATTTTTGACCCCGAACCTTCTAAAAAATACCATTTTACCCCCAAACTT
1 CCAAAAATCCCATTTTTGACCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTT
* *
9105 CCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAACTACCATTTTACCCCCA
1 CCAAAAATCCCATTTTTGACCCTGAACCTTCTAAAAATTACCATTTTACCCCCA
9159 TGCATCCGAA
Statistics
Matches: 205, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
58 1 0.00
59 202 0.99
60 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (59 bp):
CCAAAAATCCCATTTTTGACCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTT
Found at i:10108 original size:37 final size:38
Alignment explanation
Indices: 10051--10136 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
10041 ATAAGTGATT
* *
10051 TTAAAATTATTAAAAATATTTTTTGAAATAAAAAATTA
1 TTAAAATTATTAAAAATATTTTTTAAAATAAAAAACTA
* * *
10089 TTAAAATTATT-ATATTATTTTTTAAAATATAAAACTA
1 TTAAAATTATTAAAAATATTTTTTAAAATAAAAAACTA
10126 TTAAAATTATT
1 TTAAAATTATT
10137 TGGTTGTTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 32 0.74
38 11 0.26
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (38 bp):
TTAAAATTATTAAAAATATTTTTTAAAATAAAAAACTA
Found at i:11200 original size:38 final size:38
Alignment explanation
Indices: 11144--11236 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
11134 TATATGCATT
*
11144 TAATCATTTTAATAATTTTATATTTCAAAAAA-ATAATA
1 TAATAATTTTAATAATTTTATATTTCAAAAAATAT-ATA
* * *
11182 TAATAATTTTAATAATTTTTTATTTCAAAAAATATTTT
1 TAATAATTTTAATAATTTTATATTTCAAAAAATATATA
11220 TAATAATTTTAA-AATTT
1 TAATAATTTTAATAATTT
11237 ATTGAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 5 0.10
38 43 0.86
39 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (38 bp):
TAATAATTTTAATAATTTTATATTTCAAAAAATATATA
Found at i:12705 original size:51 final size:49
Alignment explanation
Indices: 12640--12749 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 49
12630 AATTAAAAGT
12640 TGAAATTAAATGAAATGAAAATGAAAATGAATTAAAAGTTGAAATTAGAA
1 TGAAATTAAATGAAATGAAAATGAAAATGAATTAAAAGTTGAAATTA-AA
* * *
12690 TGAAATTCTAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATTAAA
1 TGAAATT-AAATGAAATGAAAATGAAAATGAATTAAAAGTTGAAATTAAA
*
12740 TGAATTTAAA
1 TGAAATTAAA
12750 AAAACATAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.04
50 15 0.28
51 37 0.69
ACGTcount: A:0.55, C:0.01, G:0.14, T:0.30
Consensus pattern (49 bp):
TGAAATTAAATGAAATGAAAATGAAAATGAATTAAAAGTTGAAATTAAA
Found at i:14232 original size:17 final size:16
Alignment explanation
Indices: 14212--14245 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14202 ATATTTAATT
*
14212 TAAAATTTGAATTGAAA
1 TAAAATTT-AAATGAAA
14229 TAAAATTTAAATGAAA
1 TAAAATTTAAATGAAA
14245 T
1 T
14246 TTATACAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
TAAAATTTAAATGAAA
Found at i:15799 original size:40 final size:41
Alignment explanation
Indices: 15722--15825 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 41
15712 ATCTTTCATT
* * *
15722 TAAT-TTTTTATTTAATTTAAATTTAAATTATTTTTTTAAA
1 TAATATTTTTATTTAATTTAAATTAAAATAATTATTTTAAA
*
15762 TAATATTTTTATTT-ATTT-AATTAAAATCAATTATTTTAAT
1 TAATATTTTTATTTAATTTAAATTAAAAT-AATTATTTTAAA
* *
15802 TAATATGTCTAATTTAA-TTAAATT
1 TAATAT-TTTTATTTAATTTAAATT
15826 TTATTTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
39 8 0.15
40 23 0.43
41 17 0.32
42 5 0.09
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (41 bp):
TAATATTTTTATTTAATTTAAATTAAAATAATTATTTTAAA
Found at i:15844 original size:19 final size:19
Alignment explanation
Indices: 15817--15858 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
15807 TGTCTAATTT
*
15817 AATTAAATTTTATT-TTTTA
1 AATTAAA-TTTATTGTCTTA
*
15836 AATTTAATTTATTGTCTTA
1 AATTAAATTTATTGTCTTA
15855 AATT
1 AATT
15859 GATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTAAATTTATTGTCTTA
Found at i:17882 original size:16 final size:17
Alignment explanation
Indices: 17859--17900 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
17849 TTTTTAAAAT
*
17859 ATTTTTTTATTTTCGAA
1 ATTTTTTTATTATCGAA
17876 ATTTTTTTATTATCG-A
1 ATTTTTTTATTATCGAA
17892 ATTTTTTTA
1 ATTTTTTTA
17901 AATTAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (17 bp):
ATTTTTTTATTATCGAA
Found at i:17921 original size:11 final size:11
Alignment explanation
Indices: 17905--17934 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
17895 TTTTTAAATT
17905 AATATTTTCGA
1 AATATTTTCGA
17916 AATATTTTCGA
1 AATATTTTCGA
17927 AATATTTT
1 AATATTTT
17935 TTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (11 bp):
AATATTTTCGA
Found at i:18698 original size:12 final size:12
Alignment explanation
Indices: 18670--18713 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
18660 ATTTAGATTT
*
18670 CGAGCTCGAGGA
1 CGAGCTCGAGTA
*
18682 TGAGCTCGAGTA
1 CGAGCTCGAGTA
*
18694 CGAGCACGAGTA
1 CGAGCTCGAGTA
*
18706 CTAGCTCG
1 CGAGCTCG
18714 CGGACCAACC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.16
Consensus pattern (12 bp):
CGAGCTCGAGTA
Found at i:19458 original size:390 final size:389
Alignment explanation
Indices: 18785--19514 Score: 918
Period size: 390 Copynumber: 1.9 Consensus size: 389
18775 GTTGCAAGAC
* ***** *
18785 CAATATCATCATTCCATAGAGGAGATTTTTGGCGTTTTTGTCGACCCTCAACGTTCATATTACTC
1 CAATATCATCATTCCATAGAGGAGATTTTTGGCATCGACATCGACCATCAACGTTCATATTACTC
*
18850 CAATTCATCCTCAAATTAATTAGAAATTCATCGGGAAGAACGTACACCAAAAATGGAGAATATTT
66 CAATTCATCCTCAAATTAATTAGAAATCCATCGGGAAGAACGTACACCAAAAATGGAGAATATTT
* * * *
18915 TGGCTCGATGCCTTCGATCACTCAACATACTCCCGATGACGATGACGATATGTACGATTTTACCA
131 TGGCTCGATACCTCCAATCACTCAACATACTCCCGATGACGATGACGATACGTACGATTTTACCA
* * *
18980 CTTTTCTACGTACGTCGATCGGGACTCCGAGCGTTGAGACCACTGAGGTCGAACCAATGAACACC
196 CTTTTCTACGTACGTCGATCGGGACTCCAAACGTTGAGACCACTAAGGTCGAACCAATGAACACC
* * * * ***
19045 TATGTAACGCCTCCTCAACGAGGTGCACTATGGCCTCGACCTCTTTGAG-CCGAGAAGAACCCGA
261 TATGTAACACCTCATCAACGAGGTGCACTACGACCTCGACCTCGCCGAGCCCG-GAAGAACCCGA
19109 TCCGTTACACGCCAGCCCGTGCCCCAATATCAAGCATCAGAGTCTTCGTCTTTTTGCCACAAAAT
325 TCCGTTACACGCCAGCCCGTGCCCCAATATCAAGCATCAGAGTCTTCGTCTTTTTGCCACAAAAT
* * *
19174 CAATATCATCGTTCCATGGAGGAGATTTTTGGCATCGACATCGACCATCAATGTTCATATTACTC
1 CAATATCATCATTCCATAGAGGAGATTTTTGGCATCGACATCGACCATCAACGTTCATATTACTC
* * * ** * *
19239 CGATTCATCCTCATATTAA-TCGAAGATCCATCGGGAAGAACGTACACTGACAATGGAGGATATT
66 CAATTCATCCTCAAATTAATTAGAA-ATCCATCGGGAAGAACGTACACCAAAAATGGAGAATA-T
* *
19303 TTTGGTTCG-TCACCTCCAATCACTCAACATACTCCCGATGACGATGACGATACGTATGATTTTA
129 TTTGGCTCGAT-ACCTCCAATCACTCAACATACTCCCGATGACGATGACGATACGTACGATTTTA
* * * *
19367 CCATCTTTT-TACGTATGTTGATCGGGACAT-TAAACGTTGAGACTA-TCAAGG-CTGAACCGAA
193 CCA-CTTTTCTACGTACGTCGATCGGGAC-TCCAAACGTTGAGACCACT-AAGGTC-GAACC-AA
* * * * *
19428 -GAATACCTATGTAACACTTTATCAACGAGGTGCACTACGACCTCGGCCTCGCCGAGCCCGGAGG
253 TGAACACCTATGTAACACCTCATCAACGAGGTGCACTACGACCTCGACCTCGCCGAGCCCGGAAG
* *
19492 AACTCGATTCGTTACACGCCAGC
318 AACCCGATCCGTTACACGCCAGC
19515 ATCGGGGACG
Statistics
Matches: 287, Mismatches: 45, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
388 4 0.01
389 107 0.37
390 165 0.57
391 11 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (389 bp):
CAATATCATCATTCCATAGAGGAGATTTTTGGCATCGACATCGACCATCAACGTTCATATTACTC
CAATTCATCCTCAAATTAATTAGAAATCCATCGGGAAGAACGTACACCAAAAATGGAGAATATTT
TGGCTCGATACCTCCAATCACTCAACATACTCCCGATGACGATGACGATACGTACGATTTTACCA
CTTTTCTACGTACGTCGATCGGGACTCCAAACGTTGAGACCACTAAGGTCGAACCAATGAACACC
TATGTAACACCTCATCAACGAGGTGCACTACGACCTCGACCTCGCCGAGCCCGGAAGAACCCGAT
CCGTTACACGCCAGCCCGTGCCCCAATATCAAGCATCAGAGTCTTCGTCTTTTTGCCACAAAAT
Found at i:20139 original size:13 final size:13
Alignment explanation
Indices: 20123--20159 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
20113 AAATTGAAGG
20123 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
20136 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
20149 AGAAAGAAGAA
1 A-AAA-AAGAA
20160 GAAGGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
14 3 0.14
15 5 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:20168 original size:25 final size:24
Alignment explanation
Indices: 20122--20205 Score: 62
Period size: 28 Copynumber: 3.3 Consensus size: 24
20112 AAAATTGAAG
**
20122 GAAAAAAGAAAGAA-AAAAAAGAAA
1 GAAAAAAG-AAGAAGAAGGAAGAAA
20146 GAAAGAAAGAAGAAGAAGGAAGAAGGA
1 GAAA-AAAGAAGAAGAAGGAAGAA--A
* * *
20173 GAAAAAGGGCAAGAAGGAGAAAGAAA
1 GAAAAA-AG-AAGAAGAAGGAAGAAA
20199 GAAAAAA
1 GAAAAAA
20206 TGTAATGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
24 9 0.19
25 11 0.23
26 9 0.19
27 6 0.12
28 13 0.27
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (24 bp):
GAAAAAAGAAGAAGAAGGAAGAAA
Done.