Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002135.1 Kokia drynarioides strain JFW-HI SEQ_114073, 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: 83431
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:510 original size:19 final size:20
Alignment explanation
Indices: 488--526 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
478 ATCAAAAAGT
*
488 CGAGAAAAA-AAGAAAAATA
1 CGAGAAAAATAAAAAAAATA
507 CGAGAAAAATAAAAAAAATA
1 CGAGAAAAATAAAAAAAATA
527 AAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (20 bp):
CGAGAAAAATAAAAAAAATA
Found at i:6504 original size:129 final size:129
Alignment explanation
Indices: 6313--6566 Score: 499
Period size: 129 Copynumber: 2.0 Consensus size: 129
6303 AACAATAGGG
6313 AGTAGTCCTAGTAGTCTAGAGATAGTAAGCTTCGATTGTACTCTTTAATTCTTCTTTAACGATGA
1 AGTAGTCCTAGTAGTCTAGAGATAGTAAGCTTCGATTGTACTCTTTAATTCTTCTTTAACGATGA
6378 TAGATTTTGATAACATTAAATGAATACGAGAGTATCTTTTAATACTAGATCATTTTGATTTTGA
66 TAGATTTTGATAACATTAAATGAATACGAGAGTATCTTTTAATACTAGATCATTTTGATTTTGA
*
6442 AGTAGTCCTAGTAGTCTAGAGATAGTAAGTTTCGATTGTACTCTTTAATTCTTCTTTAACGATGA
1 AGTAGTCCTAGTAGTCTAGAGATAGTAAGCTTCGATTGTACTCTTTAATTCTTCTTTAACGATGA
6507 TAGATTTTGATAACATTAAATGAATACGAGAGTATCTTTTAATACTAGATCATTTTGATT
66 TAGATTTTGATAACATTAAATGAATACGAGAGTATCTTTTAATACTAGATCATTTTGATT
6567 CTTATTTTAT
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (129 bp):
AGTAGTCCTAGTAGTCTAGAGATAGTAAGCTTCGATTGTACTCTTTAATTCTTCTTTAACGATGA
TAGATTTTGATAACATTAAATGAATACGAGAGTATCTTTTAATACTAGATCATTTTGATTTTGA
Found at i:10533 original size:17 final size:17
Alignment explanation
Indices: 10513--10545 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10503 TTTAAGGACT
10513 TTTTAGTTTTA-TTTAAG
1 TTTTA-TTTTAGTTTAAG
10530 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
10546 TAAGTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:10822 original size:50 final size:48
Alignment explanation
Indices: 10768--10884 Score: 119
Period size: 50 Copynumber: 2.4 Consensus size: 48
10758 AAGTTTGTAA
*
10768 CATAAATAATGACATGCAGTAAGTAACTTACATGTTAGTTAAATATGCAT
1 CATAAATAATGACATGCAGTAAGTAACTCACATGTTAGTT-AA-ATGCAT
** * * *
10818 CATAAATCCT-ATCATGCATTATGTAACTCCCATGTTAGTTAAATGCAT
1 CATAAATAATGA-CATGCAGTAAGTAACTCACATGTTAGTTAAATGCAT
* *
10866 CATTAAATAAAGTCATGCA
1 CA-TAAATAATGACATGCA
10885 TTTAGTAATC
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
48 8 0.15
49 14 0.26
50 32 0.59
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (48 bp):
CATAAATAATGACATGCAGTAAGTAACTCACATGTTAGTTAAATGCAT
Found at i:21145 original size:42 final size:42
Alignment explanation
Indices: 21099--21321 Score: 306
Period size: 42 Copynumber: 5.3 Consensus size: 42
21089 AAAAAAGAAT
* * * *
21099 ACTCATGTCTCGGGTTGAGCATGAGAATT-TG-TATAAAAGAAG
1 ACTCATGTCTCGAGATGAGAATGAG-ATTATGAT-TAAAGGAAG
21141 ACTCATGTCTCGAGATGAGAATGAGATTATGATTAAAGGAAG
1 ACTCATGTCTCGAGATGAGAATGAGATTATGATTAAAGGAAG
* *
21183 ATTCATGTCTCGAGATGAGAATAAGATTATGATTAAAGGAAG
1 ACTCATGTCTCGAGATGAGAATGAGATTATGATTAAAGGAAG
*
21225 ACTCATGTCTTGAGATGAGAATGAGATTATGATTAAAGGAAG
1 ACTCATGTCTCGAGATGAGAATGAGATTATGATTAAAGGAAG
* * *
21267 ACTCGTGTCTCGAGATGAGAATGAGAATATGACTAAAGGAAG
1 ACTCATGTCTCGAGATGAGAATGAGATTATGATTAAAGGAAG
* *
21309 ACTTATGACTCGA
1 ACTCATGTCTCGA
21322 TAGAGCATAA
Statistics
Matches: 163, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 3 0.02
42 159 0.98
43 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (42 bp):
ACTCATGTCTCGAGATGAGAATGAGATTATGATTAAAGGAAG
Found at i:22477 original size:21 final size:20
Alignment explanation
Indices: 22451--22492 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22441 GTACATTCGC
*
22451 TCTTTTTCTTTTTCTCTTTTT
1 TCTTTTTC-ATTTCTCTTTTT
*
22472 TCTTTTTCATTTCTGTTTTT
1 TCTTTTTCATTTCTCTTTTT
22492 T
1 T
22493 TAGCATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (20 bp):
TCTTTTTCATTTCTCTTTTT
Found at i:23366 original size:14 final size:16
Alignment explanation
Indices: 23343--23376 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
23333 AAATTTATTC
*
23343 AAAAATTAAAT-ACTA
1 AAAAATAAAATAACTA
23358 AAAAATAAAATAACTA
1 AAAAATAAAATAACTA
23374 AAA
1 AAA
23377 TTAAAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATAACTA
Found at i:24987 original size:18 final size:18
Alignment explanation
Indices: 24966--25027 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
24956 CATCTTCAAT
* *
24966 TTCCACAGGATCTCCTTC
1 TTCCTCAGGATCTTCTTC
24984 TTCCTCAGGATCTTCTTC
1 TTCCTCAGGATCTTCTTC
*
25002 TTCCTCAAGATCTTCTTC
1 TTCCTCAGGATCTTCTTC
*
25020 TTCTTCAG
1 TTCCTCAG
25028 CTTGCTGTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.15, C:0.34, G:0.10, T:0.42
Consensus pattern (18 bp):
TTCCTCAGGATCTTCTTC
Found at i:43379 original size:409 final size:409
Alignment explanation
Indices: 42840--43660 Score: 1570
Period size: 409 Copynumber: 2.0 Consensus size: 409
42830 AGATATGTTC
42840 AAGAGATTATTTTAATTTCATGAGTATGTATGTGTATTAACACATTTACTTATTAAAATTTGTTT
1 AAGAGATTATTTTAATTTCATGAGTATGTATGTGTATTAACACATTTACTTATTAAAATTTGTTT
* *
42905 GATTGATTGAATTGACATAGAGATATAGTCAAGATATGAATGGATTTTGGTAAGTGATGTTGTTC
66 GATCGATTGAATTGACATAGAGATATAGTCAAGAGATGAATGGATTTTGGTAAGTGATGTTGTTC
*
42970 ATAAGTTAACAAAATATTGAGTTTCCGTGAATTTATTTCTTAACAAGCATGAACATATGATTATG
131 ATAAGTTAACAAAATATTGAGTTTCCGTGAATTTATTTCGTAACAAGCATGAACATATGATTATG
43035 ATAATATTAAGTTACTAATGCAACTAATCTAACACATATATGTCATATTGATTAAAGTCTTGAAA
196 ATAATATTAAGTTACTAATGCAACTAATCTAACACATATATGTCATATTGATTAAAGTCTTGAAA
*
43100 TCGAGCATTGGAATTAAATTTTATTTTTATTTTTACTTAGATTAATTTTAGTTTAGATTGATCCT
261 TCGAGCATTGGAATTAAATTTTATTTTTATTTTTACTTAGATTAAATTTAGTTTAGATTGATCCT
*
43165 ATTCAAATTATTATATTTCCTTAACCAAATTGTTTATTAATTATTTCATAAATATTTTTCTGACA
326 ATTCAAATTATTATATTTCCCTAACCAAATTGTTTATTAATTATTTCATAAATATTTTTCTGACA
43230 CAGTCCCTATGGGTAAGAT
391 CAGTCCCTATGGGTAAGAT
*
43249 AAGAGATTATTTTAATTTCATGAGTTTGTATGTGTATTAACACATTTACTTATTAAAATTTGTTT
1 AAGAGATTATTTTAATTTCATGAGTATGTATGTGTATTAACACATTTACTTATTAAAATTTGTTT
43314 GATCGATTGAATTGACATAGAGATATAGTCAAGAGATGAATGGATTTTGGTAAGTGATGTTGTTC
66 GATCGATTGAATTGACATAGAGATATAGTCAAGAGATGAATGGATTTTGGTAAGTGATGTTGTTC
43379 ATAAGTTAACAAAATATTGAGTTTCCGTGAATTTATTTCGTAACAAGCATGAACATATGATTATG
131 ATAAGTTAACAAAATATTGAGTTTCCGTGAATTTATTTCGTAACAAGCATGAACATATGATTATG
43444 ATAATATTAAGTTACTAATGCAACTAATCTAACACATATATGTCATATTGATTAAAGTCTTGAAA
196 ATAATATTAAGTTACTAATGCAACTAATCTAACACATATATGTCATATTGATTAAAGTCTTGAAA
* *
43509 TTGAGCATTGGAATTGAATTTTATTTTTATTTTTACTTAGATTAAATTTAGTTTAGATTGATCCT
261 TCGAGCATTGGAATTAAATTTTATTTTTATTTTTACTTAGATTAAATTTAGTTTAGATTGATCCT
43574 ATTCAAATTATTATATTTCCCTAACCAAATTGTTTATTAATTATTTCATAAATATTTTTCTGACA
326 ATTCAAATTATTATATTTCCCTAACCAAATTGTTTATTAATTATTTCATAAATATTTTTCTGACA
43639 CAGTCCCTATGGGTAAGAT
391 CAGTCCCTATGGGTAAGAT
43658 AAG
1 AAG
43661 TCGACATTTA
Statistics
Matches: 404, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
409 404 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.42
Consensus pattern (409 bp):
AAGAGATTATTTTAATTTCATGAGTATGTATGTGTATTAACACATTTACTTATTAAAATTTGTTT
GATCGATTGAATTGACATAGAGATATAGTCAAGAGATGAATGGATTTTGGTAAGTGATGTTGTTC
ATAAGTTAACAAAATATTGAGTTTCCGTGAATTTATTTCGTAACAAGCATGAACATATGATTATG
ATAATATTAAGTTACTAATGCAACTAATCTAACACATATATGTCATATTGATTAAAGTCTTGAAA
TCGAGCATTGGAATTAAATTTTATTTTTATTTTTACTTAGATTAAATTTAGTTTAGATTGATCCT
ATTCAAATTATTATATTTCCCTAACCAAATTGTTTATTAATTATTTCATAAATATTTTTCTGACA
CAGTCCCTATGGGTAAGAT
Found at i:51841 original size:16 final size:17
Alignment explanation
Indices: 51820--51853 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
51810 ACATATGCTC
51820 TTTTTCTTTTTC-TTTT
1 TTTTTCTTTTTCATTTT
51836 TTTTTCTTTTTCATTTT
1 TTTTTCTTTTTCATTTT
51853 T
1 T
51854 GTATGTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTCTTTTTCATTTT
Found at i:54075 original size:18 final size:18
Alignment explanation
Indices: 54052--54086 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54042 ATTTAATTAG
* *
54052 TAAATATATTAACAATTT
1 TAAATAAATTAAAAATTT
54070 TAAATAAATTAAAAATT
1 TAAATAAATTAAAAATT
54087 AGAAGATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATAAATTAAAAATTT
Found at i:67806 original size:21 final size:21
Alignment explanation
Indices: 67761--67807 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
67751 AGTGCAGACT
**
67761 TCTACCGATACAAGTGATAGT
1 TCTACCGATACAAGTGATACA
67782 TCTACCGATACAAGTG-TAACA
1 TCTACCGATACAAGTGAT-ACA
67803 TCTAC
1 TCTAC
67808 TGAAACTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTGATACA
Found at i:68525 original size:40 final size:40
Alignment explanation
Indices: 68480--68569 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
68470 AGTTCATAAT
*
68480 TCTTCCTTTTAATCAATCTTATGCTCTACCGAGTCACAAG
1 TCTTCCTTTTAATCAATCTTATACTCTACCGAGTCACAAG
* * * *
68520 TCTTCCTTTTAATCACTTTTATACTCTATCGAGTCATAAG
1 TCTTCCTTTTAATCAATCTTATACTCTACCGAGTCACAAG
68560 TCTTCCTTTT
1 TCTTCCTTTT
68570 TAAAAGCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.44
Consensus pattern (40 bp):
TCTTCCTTTTAATCAATCTTATACTCTACCGAGTCACAAG
Found at i:68645 original size:41 final size:43
Alignment explanation
Indices: 68595--68750 Score: 199
Period size: 43 Copynumber: 3.6 Consensus size: 43
68585 CGCTCATTTT
* * *
68595 GAGATATGAGTCTTCCTTTAATAT-AA-TCTCATTCTCATCCC
1 GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAACCC
*
68636 GAGACATGAGTCTTCTTTTAATATAAATTCTCATGCTCAACCC
1 GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAACCC
* * *
68679 TAGACATGAGTCTTCCTTTTATATAAATTCTTATGCTCAACCC
1 GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAACCC
* *
68722 GTGACGTGAGTCTTCCATTTAAATATAAA
1 GAGACATGAGTCTTCC-TTT-AATATAAA
68751 ACGTAACAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
41 22 0.22
42 2 0.02
43 65 0.66
44 3 0.03
45 7 0.07
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (43 bp):
GAGACATGAGTCTTCCTTTAATATAAATTCTCATGCTCAACCC
Found at i:73053 original size:21 final size:20
Alignment explanation
Indices: 73025--73063 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
73015 AAAGCAGATA
73025 AATCGATTTTAAATTAATAT
1 AATCGATTTTAAATTAATAT
*
73045 AATCTGATTTTATATTAAT
1 AATC-GATTTTAAATTAAT
73064 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
AATCGATTTTAAATTAATAT
Found at i:74522 original size:20 final size:20
Alignment explanation
Indices: 74473--74524 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
74463 TTTTGTTTAG
74473 GATACATATATATTAAAAAA
1 GATACATATATATTAAAAAA
74493 GTATGA-ATATA-ATTAAATAAA
1 G-AT-ACATATATATTAAA-AAA
74514 GATACATATAT
1 GATACATATAT
74525 TTACTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
19 1 0.04
20 14 0.52
21 11 0.41
22 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (20 bp):
GATACATATATATTAAAAAA
Found at i:75324 original size:9 final size:9
Alignment explanation
Indices: 75307--75368 Score: 70
Period size: 9 Copynumber: 6.2 Consensus size: 9
75297 AAACACTTTT
75307 AATAGAATTA
1 AATA-AATTA
75317 AATAAATTA
1 AATAAATTA
75326 AACTATGGAAATTA
1 AA-TA----AATTA
75340 AATAAATTA
1 AATAAATTA
75349 AATAAATTA
1 AATAAATTA
75358 AATAAATTA
1 AATAAATTA
75367 AA
1 AA
75369 CACTTTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
9 32 0.68
10 6 0.13
13 2 0.04
14 7 0.15
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (9 bp):
AATAAATTA
Found at i:76939 original size:79 final size:79
Alignment explanation
Indices: 76808--76963 Score: 249
Period size: 79 Copynumber: 2.0 Consensus size: 79
76798 TACAAGCACT
* *
76808 AATTTCATTTTAACTCTTATAAGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTAATGTAAT
1 AATTTCATTTTAAATCTTATAAGGAAGCCAATAAGTCATGTCTCTTCATTAGGATCTAATGTAAT
76873 TGAAAAGGCATGGC
66 TGAAAAGGCATGGC
* * * * *
76887 AATTTCGTTTTAAATCTTGTAGGGAAGCCAATAAGTCATGTTTCTTCATTAGGATCTAATGTAGT
1 AATTTCATTTTAAATCTTATAAGGAAGCCAATAAGTCATGTCTCTTCATTAGGATCTAATGTAAT
76952 TGAAAAGGCATG
66 TGAAAAGGCATG
76964 ACATTTCTCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (79 bp):
AATTTCATTTTAAATCTTATAAGGAAGCCAATAAGTCATGTCTCTTCATTAGGATCTAATGTAAT
TGAAAAGGCATGGC
Found at i:79158 original size:80 final size:79
Alignment explanation
Indices: 79026--79177 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 79
79016 TACAAACACT
* * * *
79026 AATTTCATTTTAACTCTGGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGA-TCTGATGTAG
1 AATTTCATTTTAACTCTGATAGAGAAGCCAACGAGTCATGTCTCTTAATTAGGAGT-TGATGTAG
79090 TTGAAAAGAAATGAG
65 TTGAAAAGAAATGAG
* *
79105 AATTTCATTTTTAACTCTTATAGAGAAGCCAACGAGTCATGTTTCTTAATTAGGAGTTGATGTAG
1 AATTTCA-TTTTAACTCTGATAGAGAAGCCAACGAGTCATGTCTCTTAATTAGGAGTTGATGTAG
79170 TTGAAAAG
65 TTGAAAAG
79178 GCATGACATT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 7 0.11
80 57 0.88
81 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (79 bp):
AATTTCATTTTAACTCTGATAGAGAAGCCAACGAGTCATGTCTCTTAATTAGGAGTTGATGTAGT
TGAAAAGAAATGAG
Found at i:81263 original size:18 final size:19
Alignment explanation
Indices: 81231--81266 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
81221 TAAAAAAGTC
81231 GAGAAAAAGAGAAAAATAT
1 GAGAAAAAGAGAAAAATAT
*
81250 GAGAAAAATA-AAAAATA
1 GAGAAAAAGAGAAAAATA
81267 AAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (19 bp):
GAGAAAAAGAGAAAAATAT
Found at i:82882 original size:5 final size:6
Alignment explanation
Indices: 82866--82900 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
82856 TTCTCAAGAG
* *
82866 GAAAAA GAAAAA GAAAAA CAATAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
82901 TGGAAAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:82893 original size:24 final size:24
Alignment explanation
Indices: 82860--82915 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
82850 GGAGAGTTCT
*
82860 CAAGAGGAAAAAGAAAAAGAAAAA
1 CAAGAAGAAAAAGAAAAAGAAAAA
* * *
82884 CAATAAGAAAAAGAAAATGGAAAA
1 CAAGAAGAAAAAGAAAAAGAAAAA
82908 CAAGAAGA
1 CAAGAAGA
82916 TAACCATACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.71, C:0.05, G:0.20, T:0.04
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAAAGAAAAA
Done.