Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008810.1 Kokia drynarioides strain JFW-HI SEQ_123493, 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: 166952
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 281 characters in sequence are not A, C, G, or T
Found at i:3241 original size:23 final size:24
Alignment explanation
Indices: 3203--3251 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
3193 CAAAAGAAAA
*
3203 TAATTGTAATGCATTTAATATAAT
1 TAATTGTAATGAATTTAATATAAT
* *
3227 TAATT-TAATGAATTTATTATTAT
1 TAATTGTAATGAATTTAATATAAT
3250 TA
1 TA
3252 TTAGTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (24 bp):
TAATTGTAATGAATTTAATATAAT
Found at i:13207 original size:35 final size:35
Alignment explanation
Indices: 13161--13230 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
13151 CGCTATTCAC
13161 CTGTTTTTTGTTATGACTATTTTATACTACTAAAA
1 CTGTTTTTTGTTATGACTATTTTATACTACTAAAA
* *
13196 CTGTTTTTTGTTATGACTATTTTATGCTTCTAAAA
1 CTGTTTTTTGTTATGACTATTTTATACTACTAAAA
13231 TTTCATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (35 bp):
CTGTTTTTTGTTATGACTATTTTATACTACTAAAA
Found at i:29382 original size:3 final size:3
Alignment explanation
Indices: 29376--29402 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29366 GCTATTGCTG
29376 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
29403 TTCAAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:30042 original size:8 final size:8
Alignment explanation
Indices: 30026--30069 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
30016 AAGTACAAAT
30026 TATATACA
1 TATATACA
*
30034 TATAGACA
1 TATATACA
*
30042 TACATACA
1 TATATACA
*
30050 TATATATA
1 TATATACA
*
30058 CATATACA
1 TATATACA
30066 TATA
1 TATA
30070 GGCCTTATCA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (8 bp):
TATATACA
Found at i:34668 original size:45 final size:39
Alignment explanation
Indices: 34586--34661 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
34576 AAAAGTGAAG
34586 TTAGAATTATAATTGAAACTTGAAAGATCAATCTAAATC
1 TTAGAATTATAATTGAAACTTGAAAGATCAATCTAAATC
34625 TTAGAATTATAATTGAAACTTGAAAGATCAATCTAAA
1 TTAGAATTATAATTGAAACTTGAAAGATCAATCTAAA
34662 ACTAAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (39 bp):
TTAGAATTATAATTGAAACTTGAAAGATCAATCTAAATC
Found at i:39953 original size:24 final size:24
Alignment explanation
Indices: 39919--40029 Score: 159
Period size: 24 Copynumber: 4.6 Consensus size: 24
39909 AGAAATAATC
* * *
39919 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
39943 TTTCAAATAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
39967 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
39991 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
40015 TTTGAGTTAAACTCT
1 TTTCAATTAAACTCT
40030 TATTAGTCTA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 78 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:41047 original size:22 final size:22
Alignment explanation
Indices: 41019--41068 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
41009 ATAAACCTGA
41019 AATTGATTGAATTACATGTTGT
1 AATTGATTGAATTACATGTTGT
* *
41041 AATTGATTGAATTGCTTGTTGT
1 AATTGATTGAATTACATGTTGT
*
41063 ACTTGA
1 AATTGA
41069 CTATATATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (22 bp):
AATTGATTGAATTACATGTTGT
Found at i:47096 original size:31 final size:32
Alignment explanation
Indices: 47032--47096 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
47022 ACTTATTTAG
* ** *
47032 TTAAGTGACTGAAACAAAAACTTACCCACAAT
1 TTAAGTGACTAAAACAAAAACTTAAACAAAAT
47064 TTAA-TGACTAAAACAAAAACTTAAACAAAAT
1 TTAAGTGACTAAAACAAAAACTTAAACAAAAT
47095 TT
1 TT
47097 TTTGAATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.25
Consensus pattern (32 bp):
TTAAGTGACTAAAACAAAAACTTAAACAAAAT
Found at i:57659 original size:19 final size:20
Alignment explanation
Indices: 57635--57678 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
57625 TTAAAAACAT
* *
57635 TAAATTATTATA-TATATAA
1 TAAATTATTAAATTAAATAA
57654 TAAATTATTAAATTAAATAA
1 TAAATTATTAAATTAAATAA
57674 TAAAT
1 TAAAT
57679 ATCAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATTATTAAATTAAATAA
Found at i:63930 original size:153 final size:153
Alignment explanation
Indices: 63652--63962 Score: 559
Period size: 153 Copynumber: 2.0 Consensus size: 153
63642 AGAACCAATG
*
63652 CAGAGATATAATAAGGGAGTTAGCAAATATCCATCATTGCCGGTTCAGAATTCTTCTGGAGAAGG
1 CAGAGAGATAATAAGGGAGTTAGCAAATATCCATCATTGCCGGTTCAGAATTCTTCTGGAGAAGG
*
63717 GATTGATTTATCATTTAACAATGTAGGTTCTGAGTTCCCAGATGACGACGACTTTGAGACAACTG
66 GATTGATTTATCATTTAACAATGTAGGTTCTGAGTTCCCAGATGACGACGACTTCGAGACAACTG
63782 ATGAATCCAATCCTTATGGGGTT
131 ATGAATCCAATCCTTATGGGGTT
* *
63805 CAGAGAGATAATAAGGGAGTTAGCAAATATCCATCATTTCCGGTTCAGAATTCTTGTGGAGAAGG
1 CAGAGAGATAATAAGGGAGTTAGCAAATATCCATCATTGCCGGTTCAGAATTCTTCTGGAGAAGG
* *
63870 GATTGATTTATCATTTAACAATGTAGGTTCTGAGTTCCCAGATGATGACGACTTCGAGACAATTG
66 GATTGATTTATCATTTAACAATGTAGGTTCTGAGTTCCCAGATGACGACGACTTCGAGACAACTG
*
63935 ATGCATCCAATCCTTATGGGGTT
131 ATGAATCCAATCCTTATGGGGTT
63958 CAGAG
1 CAGAG
63963 TTTTGATAAT
Statistics
Matches: 151, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (153 bp):
CAGAGAGATAATAAGGGAGTTAGCAAATATCCATCATTGCCGGTTCAGAATTCTTCTGGAGAAGG
GATTGATTTATCATTTAACAATGTAGGTTCTGAGTTCCCAGATGACGACGACTTCGAGACAACTG
ATGAATCCAATCCTTATGGGGTT
Found at i:67374 original size:9 final size:9
Alignment explanation
Indices: 67360--67391 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
67350 CATGAATTTT
*
67360 ATAATTCAA
1 ATAATTCGA
67369 ATAATTCGA
1 ATAATTCGA
67378 ATAATTCGA
1 ATAATTCGA
67387 ATAAT
1 ATAAT
67392 ATATTAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (9 bp):
ATAATTCGA
Found at i:77190 original size:29 final size:30
Alignment explanation
Indices: 77128--77207 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
77118 ATACCAAAAC
* * *
77128 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAACTG
77159 TATACATGAACTTTGATTT-TGTGCAACTG
1 TATACATGAACTTTGATTTATGTGCAACTG
*
77188 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
77208 GATTCAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 17 0.39
30 10 0.23
31 17 0.39
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAACTG
Found at i:84815 original size:22 final size:22
Alignment explanation
Indices: 84790--84890 Score: 193
Period size: 22 Copynumber: 4.6 Consensus size: 22
84780 TATTTAATAT
*
84790 TTTTATTATTATTTTGTGACCG
1 TTTTATTATTATTTTGTGATCG
84812 TTTTATTATTATTTTGTGATCG
1 TTTTATTATTATTTTGTGATCG
84834 TTTTATTATTATTTTGTGATCG
1 TTTTATTATTATTTTGTGATCG
84856 TTTTATTATTATTTTGTGATCG
1 TTTTATTATTATTTTGTGATCG
84878 TTTTATTATTATT
1 TTTTATTATTATT
84891 ATCGACATTT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 78 1.00
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.64
Consensus pattern (22 bp):
TTTTATTATTATTTTGTGATCG
Found at i:89077 original size:197 final size:197
Alignment explanation
Indices: 88742--89135 Score: 743
Period size: 197 Copynumber: 2.0 Consensus size: 197
88732 CCATAGCAGA
*
88742 CATACTCCTTTTTATTAAATCAGATGGATAGTGCTTCATATGTTCTACCTATTTGCTGCATGAAT
1 CATACTCCATTTTATTAAATCAGATGGATAGTGCTTCATATGTTCTACCTATTTGCTGCATGAAT
*
88807 GAAATACTCTATTTTATTATATAAAGGGATTGAGAGAAACATGCAACAAACTATGTTATACAGCT
66 GAAATACTCTATTTTATTATATAAAGGGATTGAGAGAAACATGCAACAAACTATGTTATAAAGCT
88872 CAGCTCAAATAGCTCATCAAACTAACCACAAAAAAAAAAAAAAAAAGCAATCTGATATATATGAT
131 CAGCTCAAATAGCTCATCAAACTAACCACAAAAAAAAAAAAAAAAAGCAATCTGATATATATGAT
88937 GC
196 GC
* *
88939 CATACTCCATTTTATTATATCAGATGGATAGTGCTTCATATGTTTTACCTATTTGCTGCATGAAT
1 CATACTCCATTTTATTAAATCAGATGGATAGTGCTTCATATGTTCTACCTATTTGCTGCATGAAT
*
89004 GAAATACTCTATTTTATTATATAAAGGGATTGAGATAAACATGCAACAAACTATGTTATAAAGCT
66 GAAATACTCTATTTTATTATATAAAGGGATTGAGAGAAACATGCAACAAACTATGTTATAAAGCT
89069 CAGCTCAAATAGCTCATCAAACTAACCACAAAAAAAAAAAAAAAAAGCAATCTGATATATATGAT
131 CAGCTCAAATAGCTCATCAAACTAACCACAAAAAAAAAAAAAAAAAGCAATCTGATATATATGAT
89134 GC
196 GC
89136 GTTAAATATC
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
197 192 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (197 bp):
CATACTCCATTTTATTAAATCAGATGGATAGTGCTTCATATGTTCTACCTATTTGCTGCATGAAT
GAAATACTCTATTTTATTATATAAAGGGATTGAGAGAAACATGCAACAAACTATGTTATAAAGCT
CAGCTCAAATAGCTCATCAAACTAACCACAAAAAAAAAAAAAAAAAGCAATCTGATATATATGAT
GC
Found at i:99170 original size:15 final size:16
Alignment explanation
Indices: 99140--99172 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
99130 TATAAATAAT
99140 TAAAAAAGTTTAAAAA
1 TAAAAAAGTTTAAAAA
*
99156 TAAAAAATTTTAAAAA
1 TAAAAAAGTTTAAAAA
99172 T
1 T
99173 TTCAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAAAAAAGTTTAAAAA
Found at i:99194 original size:24 final size:24
Alignment explanation
Indices: 99131--99195 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
99121 TATATAATAT
* *
99131 ATAAATAATTAAAAAAGTTTAAAA
1 ATAAAAAATTAAAAAAATTTAAAA
** *
99155 ATAAAAAATTTTAAAAATTTCAAAG
1 ATAAAAAATTAAAAAAATTT-AAAA
99180 A-AAAAAATTAAAAAAA
1 ATAAAAAATTAAAAAAA
99196 CTCTAAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (24 bp):
ATAAAAAATTAAAAAAATTTAAAA
Found at i:104647 original size:22 final size:21
Alignment explanation
Indices: 104621--104661 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
104611 TACACCGTTT
104621 CAATTGTTAAATTTTTTTATTC
1 CAATT-TTAAATTTTTTTATTC
**
104643 CAATTTTTTATTTTTTTAT
1 CAATTTTAAATTTTTTTAT
104662 CAGTTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
CAATTTTAAATTTTTTTATTC
Found at i:107681 original size:8 final size:8
Alignment explanation
Indices: 107610--107683 Score: 50
Period size: 8 Copynumber: 9.8 Consensus size: 8
107600 ACATTTATAT
107610 TATTTTAA
1 TATTTTAA
107618 -A-TTTAA
1 TATTTTAA
107624 TA-TTTAA
1 TATTTTAA
*
107631 TATTTTTA
1 TATTTTAA
*
107639 TATTTTTA
1 TATTTTAA
107647 T-TTATTAA
1 TATT-TTAA
*
107655 -ATTTTTA
1 TATTTTAA
** *
107662 TAAGTAAA
1 TATTTTAA
107670 TATTTTAA
1 TATTTTAA
107678 TATTTT
1 TATTTT
107684 TTCAACATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
6 5 0.10
7 14 0.27
8 32 0.63
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (8 bp):
TATTTTAA
Found at i:109831 original size:16 final size:16
Alignment explanation
Indices: 109810--109840 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
109800 AGAAACACAG
109810 CTTTGAAAGATCCCCC
1 CTTTGAAAGATCCCCC
109826 CTTTGAAAGATCCCC
1 CTTTGAAAGATCCCC
109841 TACAGATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (16 bp):
CTTTGAAAGATCCCCC
Found at i:120668 original size:56 final size:56
Alignment explanation
Indices: 120603--120712 Score: 220
Period size: 56 Copynumber: 2.0 Consensus size: 56
120593 TGAATCTGAC
120603 GGAGTCGACACTTCATTCTTTATAGTAAGGCTTTGAGATATTTTATGGCTCTTAAT
1 GGAGTCGACACTTCATTCTTTATAGTAAGGCTTTGAGATATTTTATGGCTCTTAAT
120659 GGAGTCGACACTTCATTCTTTATAGTAAGGCTTTGAGATATTTTATGGCTCTTA
1 GGAGTCGACACTTCATTCTTTATAGTAAGGCTTTGAGATATTTTATGGCTCTTA
120713 CTTATGGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (56 bp):
GGAGTCGACACTTCATTCTTTATAGTAAGGCTTTGAGATATTTTATGGCTCTTAAT
Found at i:123013 original size:34 final size:34
Alignment explanation
Indices: 122966--123069 Score: 172
Period size: 34 Copynumber: 3.1 Consensus size: 34
122956 CAAAGGACTT
122966 TATAATTGGCTTACATATTATATCTCATCAGGAA
1 TATAATTGGCTTACATATTATATCTCATCAGGAA
* *
123000 TATAATTGCCTTACATCTTATATCTCATCAGGAA
1 TATAATTGGCTTACATATTATATCTCATCAGGAA
* *
123034 TACAATCGGCTTACATATTATATCTCATCAGGAA
1 TATAATTGGCTTACATATTATATCTCATCAGGAA
123068 TA
1 TA
123070 CAGTTGCACG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (34 bp):
TATAATTGGCTTACATATTATATCTCATCAGGAA
Found at i:128450 original size:83 final size:83
Alignment explanation
Indices: 128311--128559 Score: 426
Period size: 83 Copynumber: 3.0 Consensus size: 83
128301 ATTTGCCACC
* * *
128311 ATATTAACTGCACATCTAGTAAATGCAAACCAAACCAAATTAAAATGCTTAGCTGCTTCCTCTAT
1 ATATTAACTGCACGTCTAGTAAATACAAACCGAACCAAATTAAAATGCTTAGCTGCTTCCTCTAT
128376 TTGCCGAACCAACGTTGT
66 TTGCCGAACCAACGTTGT
128394 ATATTAACTGCACGTCTAGTAAATACAAACCGAACCAAATTAAAATGCTTAGCTGCTTCCTCTAT
1 ATATTAACTGCACGTCTAGTAAATACAAACCGAACCAAATTAAAATGCTTAGCTGCTTCCTCTAT
128459 TTGCCGAACCAACGTTGT
66 TTGCCGAACCAACGTTGT
* * ** *
128477 ATATTAACTGCACGTTTAATAAATACAAACCGAACCAAATTAAAATGCTTAATTACTTCCTCTAT
1 ATATTAACTGCACGTCTAGTAAATACAAACCGAACCAAATTAAAATGCTTAGCTGCTTCCTCTAT
128542 TTGCCGAACCAACGTTGT
66 TTGCCGAACCAACGTTGT
128560 CATCGTTGCA
Statistics
Matches: 158, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 158 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (83 bp):
ATATTAACTGCACGTCTAGTAAATACAAACCGAACCAAATTAAAATGCTTAGCTGCTTCCTCTAT
TTGCCGAACCAACGTTGT
Found at i:130143 original size:38 final size:38
Alignment explanation
Indices: 130092--130247 Score: 285
Period size: 38 Copynumber: 4.1 Consensus size: 38
130082 GACCCAACAA
130092 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
1 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
130130 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
1 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
* * *
130168 ACAAACAAGTATTACCAGATTCAATCATGAACATGATT
1 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
130206 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
1 ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
130244 ACAA
1 ACAA
130248 AGTAATACAG
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 112 1.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (38 bp):
ACAAGCAAGTATCACCAGATTCAATCATGAACACGATT
Found at i:134308 original size:19 final size:19
Alignment explanation
Indices: 134281--134319 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
134271 TTATACATCA
*
134281 TGTAATTTTTATTTTTTTT
1 TGTAATTTTGATTTTTTTT
* *
134300 TGTAGTTTTGCTTTTTTTT
1 TGTAATTTTGATTTTTTTT
134319 T
1 T
134320 TTTGTGACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (19 bp):
TGTAATTTTGATTTTTTTT
Found at i:137356 original size:18 final size:17
Alignment explanation
Indices: 137329--137362 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
137319 CTTTGAAGTT
137329 TATAAAATTATAAATTAG
1 TATAAAATTA-AAATTAG
*
137347 TATAATATTAAAATTA
1 TATAAAATTAAAATTA
137363 TATTTTCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TATAAAATTAAAATTAG
Found at i:139038 original size:95 final size:92
Alignment explanation
Indices: 138843--139038 Score: 241
Period size: 95 Copynumber: 2.1 Consensus size: 92
138833 GACTAACTAA
* * *
138843 TTATATTATAAAAATTAATAAAAAATTATTTCAAATTAAAGTATAATACTAAATCTAAAATTGAG
1 TTATATTATAAAAATAAATAAAAAATTATGTCAAATTAAAGTATAATACTAAATCTAAAATTGAA
*
138908 TATAATAAAAGAAATAAAAACACAAAT
66 TATAATAAAAGAAACAAAAACACAAAT
* * * *
138935 TAACATTATAAAAATAAATGAAAAAATTATGTCAAATTAAATTATAGGA-ACTAAATCTTAAATC
1 TTATATTATAAAAATAAAT-AAAAAATTATGTCAAATTAAAGTATA--ATACTAAATCTAAAAT-
* * * *
138999 TGAATATAATAAAAGAACCCAAACCATAAAT
62 TGAATATAATAAAAGAAACAAAAACACAAAT
139030 TTATATTAT
1 TTATATTAT
139039 TTTTCTTACA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
92 16 0.19
93 24 0.28
94 13 0.15
95 33 0.38
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (92 bp):
TTATATTATAAAAATAAATAAAAAATTATGTCAAATTAAAGTATAATACTAAATCTAAAATTGAA
TATAATAAAAGAAACAAAAACACAAAT
Found at i:154920 original size:15 final size:16
Alignment explanation
Indices: 154900--154929 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
154890 AAATAAAGGG
154900 CTTTTTCTTT-TTTTC
1 CTTTTTCTTTATTTTC
154915 CTTTTTCTTTATTTT
1 CTTTTTCTTTATTTT
154930 TTTAAACCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
CTTTTTCTTTATTTTC
Found at i:162573 original size:15 final size:15
Alignment explanation
Indices: 162549--162581 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
162539 AATAATGTTG
162549 TGGACATAGGACTCT
1 TGGACATAGGACTCT
*
162564 TGGACGTAGGACTCT
1 TGGACATAGGACTCT
162579 TGG
1 TGG
162582 GAGAAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.27
Consensus pattern (15 bp):
TGGACATAGGACTCT
Found at i:166583 original size:13 final size:12
Alignment explanation
Indices: 166552--166586 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
166542 AGGTTTTTTT
166552 CAAAAAAATACG
1 CAAAAAAATACG
166564 -AAAAAAATACG
1 CAAAAAAATACG
166575 ACAAAAAAATAC
1 -CAAAAAAATAC
166587 CTAACACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.71, C:0.14, G:0.06, T:0.09
Consensus pattern (12 bp):
CAAAAAAATACG
Found at i:166814 original size:9 final size:9
Alignment explanation
Indices: 166800--166861 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
166790 AACGGGAAAA
166800 AAAGAAAGG
1 AAAGAAAGG
166809 AAAGAAA-G
1 AAAGAAAGG
*
166817 AAAGGAAGG
1 AAAGAAAGG
*
166826 AAGAATGAGAGG
1 -A-AA-GAAAGG
166838 AAAGAAA-G
1 AAAGAAAGG
166846 -AAG-AAGG
1 AAAGAAAGG
166853 AAAGAAAGG
1 AAAGAAAGG
166862 TAATGTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.05
7 4 0.10
8 11 0.26
9 15 0.36
10 3 0.07
11 3 0.07
12 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:166815 original size:4 final size:4
Alignment explanation
Indices: 166795--166860 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
166785 AAATAAACGG
* * * * *
166795 GAAA AAAA GAAA GGAAA GAAA GAAA GGAA GGAA GAAT GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
166845 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
166861 GTAATGTATT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.80
5 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:166816 original size:13 final size:13
Alignment explanation
Indices: 166794--166860 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
166784 CAAATAAACG
*
166794 GGAAAAAAAGAAA
1 GGAAAGAAAGAAA
166807 GGAAAGAAAGAAA
1 GGAAAGAAAGAAA
* *
166820 GGAAGGAAGAATGAGA
1 GG-A--AAGAAAGAAA
166836 GGAAAGAAAGAAGAA
1 GGAAAGAAAG-A-AA
166851 GGAAAGAAAG
1 GGAAAGAAAG
166861 GTAATGTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 20 0.45
14 2 0.05
15 12 0.27
16 10 0.23
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.01
Consensus pattern (13 bp):
GGAAAGAAAGAAA
Done.