Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002671.1 Kokia drynarioides strain JFW-HI SEQ_114925, 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: 134759
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:135 original size:7 final size:7
Alignment explanation
Indices: 118--158 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
108 CTTCCCCTTA
118 TTCTCTCC
1 TTCT-TCC
126 TTCTTCC
1 TTCTTCC
133 TTCTTCC
1 TTCTTCC
140 TTCTTCC
1 TTCTTCC
*
147 TTCTTCT
1 TTCTTCC
154 TTCTT
1 TTCTT
159 TCTTTCTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (7 bp):
TTCTTCC
Found at i:149 original size:21 final size:22
Alignment explanation
Indices: 100--158 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
90 TTTTTTTTCC
* *
100 CTCTCCTTCTTCC-CCTT-ATT
1 CTCTCCTTCTTCCTTCTTCCTT
120 CTCTCCTTCTTCCTTCTTCCTT
1 CTCTCCTTCTTCCTTCTTCCTT
*
142 CT-TCCTTCTTCTTTCTT
1 CTCTCCTTCTTCCTTCTT
159 TCTTTCTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.38
21 17 0.50
22 4 0.12
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (22 bp):
CTCTCCTTCTTCCTTCTTCCTT
Found at i:157 original size:4 final size:4
Alignment explanation
Indices: 150--192 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
140 TTCTTCCTTC
*
150 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
193 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:189 original size:11 final size:11
Alignment explanation
Indices: 147--203 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
137 TCCTTCTTCC
*
147 TTCTTCTTTCT
1 TTCTTTTTTCT
158 TTCTTTCTTTCTT
1 TTCTTT-TTTC-T
171 TCTCTTTTTTCT
1 T-TCTTTTTTCT
*
183 TTCTTTTTTCC
1 TTCTTTTTTCT
*
194 TTCATTTTTC
1 TTCTTTTTTC
204 GTTGGTCCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 23 0.57
12 6 0.15
13 6 0.15
14 5 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:201 original size:12 final size:11
Alignment explanation
Indices: 136--203 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
126 TTCTTCCTTC
**
136 TTCCTTCTTCC
1 TTCCTTCTTTT
147 TT-CTTCTTTCT
1 TTCCTTCTTT-T
*
158 TTCTTTCTTTCT
1 TTCCTTCTTT-T
170 TT-C-TCTTTT
1 TTCCTTCTTTT
*
179 TTCTTTCTTTT
1 TTCCTTCTTTT
*
190 TTCCTTCATTT
1 TTCCTTCTTTT
201 TTC
1 TTC
204 GTTGGTCCCC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
9 3 0.07
10 11 0.24
11 22 0.48
12 10 0.22
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (11 bp):
TTCCTTCTTTT
Found at i:2577 original size:90 final size:91
Alignment explanation
Indices: 2419--2602 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 91
2409 GGGAAGTCTG
* *
2419 ATTACCAGAATGTTATGATCTTTCAGGTATTTTATGGTCCCATTTTATCTTGCTTCTTTTTTCTC
1 ATTACCAGAATATTATGATCTTTCAGGTATTTCATGGTCCCATTTTATCTTGCTTCTTTTTTCTC
* *
2484 CCTGTTTAGTTTCTTTTAAAATTTTA
66 CCTGTTTAGTTACTTTAAAAATTTTA
* *
2510 ATTACCAGAATATTATGGTCTTTCAGGTATTTCATGGT-CCATTTTATCTTTCTTCTTTTTTCTC
1 ATTACCAGAATATTATGATCTTTCAGGTATTTCATGGTCCCATTTTATCTTGCTTCTTTTTTCTC
2574 CCTGTTTAGTTACTTTAAAAATTTTA
66 CCTGTTTAGTTACTTTAAAAATTTTA
2600 ATT
1 ATT
2603 TTTGAAGCAC
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 52 0.60
91 35 0.40
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.52
Consensus pattern (91 bp):
ATTACCAGAATATTATGATCTTTCAGGTATTTCATGGTCCCATTTTATCTTGCTTCTTTTTTCTC
CCTGTTTAGTTACTTTAAAAATTTTA
Found at i:14171 original size:96 final size:96
Alignment explanation
Indices: 14053--14228 Score: 235
Period size: 96 Copynumber: 1.8 Consensus size: 96
14043 ATTATTATTA
* * * * * * *
14053 AAACGTTTATTGTTTATTTAATTATTTAATGCTTTAACACGCGGAAACGTTCAATTATTGTCAAT
1 AAACATTTATTGTTTATTTAATTATCTAATGCTGTAACACACGGAAACGTACAATTATTATAAAT
* *
14118 ATTCAAATAATTTCAAATTTAAAACAAAGTT
66 ATTAAAATAAGTTCAAATTTAAAACAAAGTT
* * * *
14149 AAACATTTATTTTTTATTTAATTATCTAGTGCTGTAACACATGTAAACGTACAATTATTATAAAT
1 AAACATTTATTGTTTATTTAATTATCTAATGCTGTAACACACGGAAACGTACAATTATTATAAAT
14214 ATTAAAATAAGTTCA
66 ATTAAAATAAGTTCA
14229 TGACATAAAA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 67 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (96 bp):
AAACATTTATTGTTTATTTAATTATCTAATGCTGTAACACACGGAAACGTACAATTATTATAAAT
ATTAAAATAAGTTCAAATTTAAAACAAAGTT
Found at i:15172 original size:7 final size:7
Alignment explanation
Indices: 15155--15183 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
15145 GCTCATCACA
15155 TCCAA-T
1 TCCAACT
15161 TCCAACT
1 TCCAACT
15168 TCCAACT
1 TCCAACT
15175 TCCAACT
1 TCCAACT
15182 TC
1 TC
15184 TATAACCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (7 bp):
TCCAACT
Found at i:31576 original size:34 final size:34
Alignment explanation
Indices: 31528--31592 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
31518 TATTGGTAAG
*
31528 AATGATTTGGAAGGGATCACATGCTTAAAGCAAA
1 AATGATTTGAAAGGGATCACATGCTTAAAGCAAA
31562 AATGATTTGAAAGGGATCACATGCTTAAAGC
1 AATGATTTGAAAGGGATCACATGCTTAAAGC
31593 GTGGTTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (34 bp):
AATGATTTGAAAGGGATCACATGCTTAAAGCAAA
Found at i:32506 original size:35 final size:37
Alignment explanation
Indices: 32458--32526 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 37
32448 ATTTAAATTT
* *
32458 TTTAAAAT-TTTAAATTAATAAAA-ATAAATTTATAC
1 TTTAAAATCTTAAAAATAATAAAATATAAATTTATAC
* *
32493 TTTAAACTCTTAAAAATAATAAAATATTAATTTA
1 TTTAAAATCTTAAAAATAATAAAATATAAATTTA
32527 ATTTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 7 0.25
36 13 0.46
37 8 0.29
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (37 bp):
TTTAAAATCTTAAAAATAATAAAATATAAATTTATAC
Found at i:48051 original size:196 final size:194
Alignment explanation
Indices: 47698--48083 Score: 576
Period size: 196 Copynumber: 2.0 Consensus size: 194
47688 TCTTTTTCCT
*
47698 CATCTCTTTTATAGTTCAATTTTTTTCATAAAATAGCTTTGAATGACACAAATTTGCAAATCAAA
1 CATCTCTTCTATAGTTCAATTTTTTTCATAAAATAGCTTTGAATGACACAAATTTGCAAATCAAA
* * *
47763 ATTCACAATTTTCTTCTTTGATCTCCAACATTGACCGTTAGATCAACTTGAAATTAAGGTATATT
66 ATTCACAACTTTCTTCTTCGATCTCCAACATTGACCGTTAGATCAACTTGAAACTAAGGTATATT
*
47828 CTTCTACACATTGATGGAGATTGATTCATCATACTGATCGTCAATTGGAACTCACTAGTTCCCC
131 CTTCTACACATTGATGGAGATTGATTCACCATACTGATCGTCAATTGGAACTCACTAGTTCCCC
* * ** * *
47892 CATCTCTTCTATAGTTCAAATTTTTTTTTATGAAATAGCTTTGAATGACATGAATTT-CTGATTC
1 CATCTCTTCTATAGTTC-AA-TTTTTTTCATAAAATAGCTTTGAATGACACAAATTTGC-AAATC
* * * *
47956 AAAATTCATAACTTTCTTCTTCGATCTTCGATATTGACCGTTAGATCAACTTGAAACTAAGGTAT
63 AAAATTCACAACTTTCTTCTTCGATCTCCAACATTGACCGTTAGATCAACTTGAAACTAAGGTAT
* * *
48021 ATTCTTCTACATATTGATGGAGATTGATTCACCATATTGATTGTCAATTGGAACTCACTAGTT
128 ATTCTTCTACACATTGATGGAGATTGATTCACCATACTGATCGTCAATTGGAACTCACTAGTT
48084 GGACTTTTTT
Statistics
Matches: 171, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
194 16 0.09
195 3 0.02
196 152 0.89
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (194 bp):
CATCTCTTCTATAGTTCAATTTTTTTCATAAAATAGCTTTGAATGACACAAATTTGCAAATCAAA
ATTCACAACTTTCTTCTTCGATCTCCAACATTGACCGTTAGATCAACTTGAAACTAAGGTATATT
CTTCTACACATTGATGGAGATTGATTCACCATACTGATCGTCAATTGGAACTCACTAGTTCCCC
Found at i:51314 original size:31 final size:31
Alignment explanation
Indices: 51271--51352 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
51261 GCTCAAACAA
*
51271 CAAAATGGTACCTAAACTATACTAGTTTT-CT
1 CAAATTGGTACCTAAACTATACTA-TTTTGCT
** *
51302 CAAATTGGTACCTAAAC-ATTTTATTTTGGT
1 CAAATTGGTACCTAAACTATACTATTTTGCT
*
51332 CAGAATTGGTACCAAAACTAT
1 CA-AATTGGTACCTAAACTAT
51353 TAAACCGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 7 0.16
31 30 0.70
32 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (31 bp):
CAAATTGGTACCTAAACTATACTATTTTGCT
Found at i:53364 original size:31 final size:31
Alignment explanation
Indices: 53329--53389 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
53319 AAAAAATCTT
53329 ATCTCCTTAGGAAATTTGGACTAAAAGGCTC
1 ATCTCCTTAGGAAATTTGGACTAAAAGGCTC
53360 ATCTCCTTAGGAAATTTGGACTAAAAGGCT
1 ATCTCCTTAGGAAATTTGGACTAAAAGGCT
53390 GTAGAATAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
ATCTCCTTAGGAAATTTGGACTAAAAGGCTC
Found at i:54870 original size:28 final size:28
Alignment explanation
Indices: 54808--54870 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
54798 GTTACGTATT
* *
54808 TAATTAAAAAAGTGGATCATTTTTTAAA
1 TAATTAAAAAAGTAGATCATTTTATAAA
*
54836 TAA-TAAAAAATTAGATCATTTTGATAAA
1 TAATTAAAAAAGTAGATCATTTT-ATAAA
54864 -AATTAAA
1 TAATTAAA
54871 TTTTATAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (28 bp):
TAATTAAAAAAGTAGATCATTTTATAAA
Found at i:55014 original size:15 final size:16
Alignment explanation
Indices: 54994--55026 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54984 ATCGAGAAAC
*
54994 AAAAT-AAACTAAAAA
1 AAAATAAAACCAAAAA
55009 AAAATAAAACCAAAAA
1 AAAATAAAACCAAAAA
55025 AA
1 AA
55027 TAAAAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAATAAAACCAAAAA
Found at i:55314 original size:16 final size:17
Alignment explanation
Indices: 55271--55317 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
55261 ATTAGTAATT
55271 AAATTTAAT-TATAAAA
1 AAATTTAATATATAAAA
* *
55287 AAATGTAAAATATTAAAA
1 AAATTTAATATA-TAAAA
55305 AAATTTAATATAT
1 AAATTTAATATAT
55318 TTTAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 7 0.28
17 3 0.12
18 15 0.60
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATTTAATATATAAAA
Found at i:58227 original size:18 final size:18
Alignment explanation
Indices: 58204--58239 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58194 TGAAAGTTCT
*
58204 AGAAGATATAATTATTTG
1 AGAAGAGATAATTATTTG
*
58222 AGAAGAGCTAATTATTTG
1 AGAAGAGATAATTATTTG
58240 GTAAAACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (18 bp):
AGAAGAGATAATTATTTG
Found at i:58957 original size:21 final size:19
Alignment explanation
Indices: 58933--58971 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
58923 GAAAATACAC
*
58933 AATATTCTTTTGAAAGTTTTG
1 AATACTCTTTT-AAA-TTTTG
58954 AATACTCTTTTAAATTTT
1 AATACTCTTTTAAATTTT
58972 ATCTTGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (19 bp):
AATACTCTTTTAAATTTTG
Found at i:69229 original size:58 final size:59
Alignment explanation
Indices: 69167--69317 Score: 182
Period size: 58 Copynumber: 2.6 Consensus size: 59
69157 TTTTATTAAG
* * *
69167 ATTATTATTAAATATTATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
* * * *
69225 ATTATTATTAAATACAATTTAAT-AAAACAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
* *
69283 ATTATTATTAAAATATGAA-TTAGTAAAAATCATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
69318 TATATAACAT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 20 0.26
58 39 0.51
59 9 0.12
60 9 0.12
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:74938 original size:23 final size:23
Alignment explanation
Indices: 74909--74955 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
74899 TGACCATTGC
74909 TATTATTAATATACTAGTATGTT
1 TATTATTAATATACTAGTATGTT
74932 TATTATTAATATACTAGTATGTT
1 TATTATTAATATACTAGTATGTT
74955 T
1 T
74956 CTAATCTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
TATTATTAATATACTAGTATGTT
Found at i:79064 original size:2 final size:2
Alignment explanation
Indices: 79059--79087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
79049 AATGAACTTT
79059 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
79088 TAACCTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:82912 original size:3 final size:3
Alignment explanation
Indices: 82904--82933 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
82894 GTTCATCCAT
82904 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
82934 CTATATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:84116 original size:12 final size:12
Alignment explanation
Indices: 84099--84123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84089 AGTTTATTAT
84099 AAATATATAATA
1 AAATATATAATA
84111 AAATATATAATA
1 AAATATATAATA
84123 A
1 A
84124 TTCAACTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATATAATA
Found at i:96791 original size:2 final size:2
Alignment explanation
Indices: 96784--96810 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
96774 TTATTTGATA
96784 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
96811 AATGAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113768 original size:21 final size:21
Alignment explanation
Indices: 113739--113780 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
113729 TTTAACTTTC
* *
113739 ATTATATTTTTTTAGAATTTT
1 ATTAAATTTTTCTAGAATTTT
*
113760 ATTAAATTTTTCTATAATTTT
1 ATTAAATTTTTCTAGAATTTT
113781 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTAAATTTTTCTAGAATTTT
Found at i:113809 original size:18 final size:18
Alignment explanation
Indices: 113788--113825 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
113778 TTTTAAAAAA
113788 TATAAA-ATTTGAAAGTTT
1 TATAAATATTTGAAA-TTT
*
113806 TATAAATATTTTAAATTT
1 TATAAATATTTGAAATTT
113824 TA
1 TA
113826 AAAGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATAAATATTTGAAATTT
Found at i:115661 original size:16 final size:16
Alignment explanation
Indices: 115640--115673 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
115630 CGTATATGTT
115640 GTACTTATGTATTGGA
1 GTACTTATGTATTGGA
115656 GTACTTATGTATTGGA
1 GTACTTATGTATTGGA
115672 GT
1 GT
115674 GTTTGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (16 bp):
GTACTTATGTATTGGA
Found at i:115865 original size:48 final size:48
Alignment explanation
Indices: 115808--115899 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
115798 GGTTAACAGA
*
115808 CAATATAGAGGAAATTAAGAAAACCCATGGCAGTACATAAATTATTTT
1 CAATATAGAGGAAATTAAGAAAACCCATGACAGTACATAAATTATTTT
*
115856 CAATATAGAGGAAATTAAGAAAACCCATGACAGTACATATATTA
1 CAATATAGAGGAAATTAAGAAAACCCATGACAGTACATAAATTA
115900 ATATTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (48 bp):
CAATATAGAGGAAATTAAGAAAACCCATGACAGTACATAAATTATTTT
Found at i:115974 original size:64 final size:64
Alignment explanation
Indices: 115873--116001 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
115863 GAGGAAATTA
* *
115873 AGAAAACCCATGACAGTACATATATTAATATTGAAAATACAAAGCAGCAGAATTACTTTGCAGC
1 AGAAAACCCATGACAGTACATAAATTAATATTGAAAATACAAAGCAACAGAATTACTTTGCAGC
*
115937 AGAAAACCCATGGCAGTACATAAATTAATATTGAAAATACAAAGCAACAGAATTACTTTGCAGC
1 AGAAAACCCATGACAGTACATAAATTAATATTGAAAATACAAAGCAACAGAATTACTTTGCAGC
116001 A
1 A
116002 AGAAGTCACC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (64 bp):
AGAAAACCCATGACAGTACATAAATTAATATTGAAAATACAAAGCAACAGAATTACTTTGCAGC
Found at i:126352 original size:17 final size:18
Alignment explanation
Indices: 126322--126356 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
126312 ACATTTCGTT
126322 ATAACAATCAATTTTTTA
1 ATAACAATCAATTTTTTA
*
126340 ATAA-AATCTATTTTTTA
1 ATAACAATCAATTTTTTA
126357 TACTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAACAATCAATTTTTTA
Done.