Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009621.1 Kokia drynarioides strain JFW-HI SEQ_124337, 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: 147245
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6485 original size:23 final size:20
Alignment explanation
Indices: 6437--6474 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6427 TTTACAAATT
6437 AAATCTCTAATATTATAATC
1 AAATCTCTAATATTATAATC
6457 AAATCTCTAATATTATAA
1 AAATCTCTAATATTATAA
6475 GGATCATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATCTCTAATATTATAATC
Found at i:11132 original size:22 final size:24
Alignment explanation
Indices: 11098--11149 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
11088 TAAAAAATGT
*
11098 ATAA-ATTTATT-AAATATTAAAA
1 ATAATATTTATTAAAAAATTAAAA
*
11120 A-AATATTTTTTAAAAAATTAAAA
1 ATAATATTTATTAAAAAATTAAAA
11143 ATAATAT
1 ATAATAT
11150 GGGTGGGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 7 0.28
23 11 0.44
24 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATATTTATTAAAAAATTAAAA
Found at i:11404 original size:23 final size:23
Alignment explanation
Indices: 11341--11406 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
11331 AATGTTCACG
* * *
11341 AACATGTTCATT-TAATTTAATCG
1 AACATGTTCATTATCA-TTAAACA
** *
11364 AACATGTTCACGAACATTAAACA
1 AACATGTTCATTATCATTAAACA
11387 AACATGTTCATTATCATTAA
1 AACATGTTCATTATCATTAA
11407 TATATAATTG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
AACATGTTCATTATCATTAAACA
Found at i:22742 original size:10 final size:8
Alignment explanation
Indices: 22713--22738 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
22703 AAAGAGAACT
22713 TGAGAGAA
1 TGAGAGAA
22721 TGAGAGAA
1 TGAGAGAA
22729 TGAGAGAA
1 TGAGAGAA
22737 TG
1 TG
22739 TGAGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (8 bp):
TGAGAGAA
Found at i:24065 original size:12 final size:12
Alignment explanation
Indices: 24040--24073 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24030 ATTGAGCAAA
* *
24040 CTTTTGTTTGCT
1 CTTTTTTTTTCT
24052 CTTTTTTTTTCT
1 CTTTTTTTTTCT
24064 CTTTTTTTTT
1 CTTTTTTTTT
24074 TCAGCATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (12 bp):
CTTTTTTTTTCT
Found at i:26184 original size:50 final size:50
Alignment explanation
Indices: 26121--26244 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 50
26111 TAGTGAACAA
*
26121 ATATTTATATAAAATACAAGATCTAAACAAAAC-AATATAAATAAATATTT
1 ATATTTATATAAAACACAAGATCTAAACAAAACAAAT-TAAATAAATATTT
* * *
26171 ATGTTTATGTAAAACACCAGATCTAAACAAAACAAATTAAATAAATATTT
1 ATATTTATATAAAACACAAGATCTAAACAAAACAAATTAAATAAATATTT
*
26221 ATATTTATTTAAAACATC-AGATCT
1 ATATTTATATAAAACA-CAAGATCT
26245 GAAAACAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 62 0.94
51 4 0.06
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (50 bp):
ATATTTATATAAAACACAAGATCTAAACAAAACAAATTAAATAAATATTT
Found at i:28182 original size:36 final size:36
Alignment explanation
Indices: 28141--28253 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 36
28131 GTAGATTAAT
28141 GTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGA
1 GTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGA
* * ** *
28177 GTAAAATTG-TAAATTTGGA---AATTTTGTAGATTA-A
1 GTAAAAATGAGAAATAGGGAGTTAA-ATT-TAG-TTAGA
28211 TGTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGA
1 -GTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGA
28248 GTAAAA
1 GTAAAA
28254 TTGTTTGTGC
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
32 2 0.03
33 2 0.03
34 4 0.07
35 18 0.31
36 24 0.41
37 4 0.07
38 2 0.03
39 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (36 bp):
GTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGA
Found at i:28197 original size:71 final size:71
Alignment explanation
Indices: 28116--28257 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
28106 AGTGAAGACC
28116 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGAGTAA
1 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGAGTAA
28181 AATTGT
66 AATTGT
28187 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGAGTAA
1 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGAGTAA
28252 AATTGT
66 AATTGT
28258 TTGTGCATTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (71 bp):
AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAGAAATAGGGAGTTAAATTTAGTTAGAGTAA
AATTGT
Found at i:28216 original size:35 final size:36
Alignment explanation
Indices: 28116--28226 Score: 106
Period size: 36 Copynumber: 3.1 Consensus size: 36
28106 AGTGAAGACC
28116 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAG
1 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAG
** * * *
28152 AAATAGGGAGTTAA-ATT-TAG-TTAGA-GTAAAATTG-T
1 AAATTTGGA---AATTTTGTAGATTA-ATGTAAAAATGAG
28187 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAG
1 AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAG
28223 AAAT
1 AAAT
28227 AGGGAGTTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
32 2 0.04
33 2 0.04
34 4 0.07
35 18 0.32
36 22 0.39
37 4 0.07
38 2 0.04
39 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (36 bp):
AAATTTGGAAATTTTGTAGATTAATGTAAAAATGAG
Found at i:35939 original size:29 final size:30
Alignment explanation
Indices: 35907--35971 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
35897 ATTTTATTTT
35907 AAAATGGTGTTTTGACCCTCTAAA-TTTCCA
1 AAAATGGTGTTTTGACCCT-TAAATTTTCCA
**
35937 AAAATTTTGTTTTGACCCTTAAATTTTCCA
1 AAAATGGTGTTTTGACCCTTAAATTTTCCA
35967 AAAAT
1 AAAAT
35972 TATATTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (30 bp):
AAAATGGTGTTTTGACCCTTAAATTTTCCA
Found at i:35948 original size:30 final size:30
Alignment explanation
Indices: 35914--36043 Score: 124
Period size: 30 Copynumber: 4.3 Consensus size: 30
35904 TTTAAAATGG
35914 TGTTTTGACCCTCTAAA-TTTCCAAAAATTT
1 TGTTTTGACCCTC-AAACTTTCCAAAAATTT
* * *
35944 TGTTTTGACCCTTAAATTTTCCAAAAATTA
1 TGTTTTGACCCTCAAACTTTCCAAAAATTT
* **
35974 TATTTTGATCCC-CAAACTTT-CAAAAAAAT
1 TGTTTTGA-CCCTCAAACTTTCCAAAAATTT
* *
36003 TGAATTTGGCCCTCAAACTTTCC-AAAATTT
1 TG-TTTTGACCCTCAAACTTTCCAAAAATTT
36033 TGTTTTTGACC
1 TG-TTTTGACC
36044 TCATTTTTCC
Statistics
Matches: 79, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
29 13 0.16
30 62 0.78
31 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.41
Consensus pattern (30 bp):
TGTTTTGACCCTCAAACTTTCCAAAAATTT
Found at i:40159 original size:12 final size:13
Alignment explanation
Indices: 40137--40175 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
40127 TCTTGTCCTC
40137 AAGCAAACAAGAA
1 AAGCAAACAAGAA
40150 AAGC-AACAAGAA
1 AAGCAAACAAGAA
**
40162 AATAAAACAAGAA
1 AAGCAAACAAGAA
40175 A
1 A
40176 GAAAAGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.72, C:0.13, G:0.13, T:0.03
Consensus pattern (13 bp):
AAGCAAACAAGAA
Found at i:43722 original size:24 final size:23
Alignment explanation
Indices: 43695--43741 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
43685 AAGAGTTAAT
43695 TTGTCA-ACGCAAATATAAAATAAA
1 TTGTCAGA-GCAAAT-TAAAATAAA
*
43719 TTGTCAGAGCAAATTAAGATAAA
1 TTGTCAGAGCAAATTAAAATAAA
43742 AATAAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.26
Consensus pattern (23 bp):
TTGTCAGAGCAAATTAAAATAAA
Found at i:46094 original size:21 final size:21
Alignment explanation
Indices: 46051--46098 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
46041 TTGAAGTTTT
**
46051 TTGTATTGGTAGTTACATGAC
1 TTGTATTGGTAGAAACATGAC
46072 TTGTATTGGTAGAAATCAT-AC
1 TTGTATTGGTAGAAA-CATGAC
46093 TTGTAT
1 TTGTAT
46099 CGTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGTATTGGTAGAAACATGAC
Found at i:55872 original size:22 final size:23
Alignment explanation
Indices: 55834--55878 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
55824 AGTGAAAACA
55834 ACAAAAAAAAATTGAGT-AGAAAT
1 ACAAAAAAAAA-TGAGTAAGAAAT
55857 ACAAAAAGAAAA-GAGTAAGAAA
1 ACAAAAA-AAAATGAGTAAGAAA
55879 ATGTGTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.69, C:0.04, G:0.16, T:0.11
Consensus pattern (23 bp):
ACAAAAAAAAATGAGTAAGAAAT
Found at i:60741 original size:39 final size:39
Alignment explanation
Indices: 60687--60762 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
60677 AAAACCATAC
60687 TTTCGCTAACAATGTCAAGTATTCTCTGTGACAAGTACG
1 TTTCGCTAACAATGTCAAGTATTCTCTGTGACAAGTACG
60726 TTTCGCTAACAATGTCAAGTATTCTCTGTGACAAGTA
1 TTTCGCTAACAATGTCAAGTATTCTCTGTGACAAGTA
60763 TGAACTCCAC
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:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (39 bp):
TTTCGCTAACAATGTCAAGTATTCTCTGTGACAAGTACG
Found at i:61943 original size:9 final size:9
Alignment explanation
Indices: 61929--61960 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
61919 TATCAATTTA
61929 AAAATAAAT
1 AAAATAAAT
61938 AAAATAAAT
1 AAAATAAAT
61947 AAAATAAAAT
1 AAAAT-AAAT
61957 AAAA
1 AAAA
61961 ACTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:61944 original size:5 final size:5
Alignment explanation
Indices: 61929--61960 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
61919 TATCAATTTA
61929 AAAAT -AAAT AAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
61961 ACTTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.32
5 17 0.68
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:62579 original size:324 final size:325
Alignment explanation
Indices: 61984--62636 Score: 1033
Period size: 324 Copynumber: 2.0 Consensus size: 325
61974 TATTTAAAAT
* * * *
61984 ATTTACAGAAAAAGATAATTAATTTTAGTATTTACAAAAGAAACAACCAAATTTTACAAAAAATT
1 ATTTACAGAAAAAGACAACTAATTTCAATATTTACAAAAGAAACAACCAAATTTTACAAAAAATT
* * *
62049 CGATTACGTCATTGAACTCAAAATAATTTAAAAAATTGGGTTGCAATTAAAATTTGGATAAAAAA
66 CAATTAAGTCATTGAACTCAAAATAATTTAAAAAATTAGGTTGCAATTAAAATTTGGATAAAAAA
* *
62114 TTAAACCTTTCTATTTGAAAATTTCAAAATTCAAAATTTATTTTCTTACTTTGGAAATAATTTCT
131 TTAAACCTTTCTATTTGAAAAATTCAAAATACAAAATTTATTTTCTTACTTTGGAAATAATTTCT
* *
62179 TAGAAGATAGTGTTAAAATTAATTTTCAAGAAAGATTGGAGGGGTCACAAGCGATCCCACTTAAG
196 TAGAAGATAGTGTTAAAATTAATTTCCAAGAAAGATTGAAGGGGTCACAAGCGATCCCACTTAAG
* *
62244 TTCCAATCTCCTGGACAAAATTCATTTCAACATATTAATCC-AGAAAATATAACCTAAATTAGCC
261 TTCCAATCTCCTAGACAAAATTCATTTCAACATACTAATCCAAGAAAATATAACCTAAATTAGCC
* *
62308 ATTTATAGAAAAAGACAACTAATTTCAATATTTACAAAAGGAACAACCAAATTTTACAAAAAATT
1 ATTTACAGAAAAAGACAACTAATTTCAATATTTACAAAAGAAACAACCAAATTTTACAAAAAATT
*
62373 CAATTAAGTCATTGAACTCAAAATATTTTAAAAAATTAGGTTGCAATT-AAATCTTGGATAAAAA
66 CAATTAAGTCATTGAACTCAAAATAATTTAAAAAATTAGGTTGCAATTAAAAT-TTGGATAAAAA
* * *
62437 ATTGACCCTTTTTATTTGAAAAATTCAAAATACAAAATTTATTTTCTTACTTTGGAAATAATTTC
130 ATTAAACCTTTCTATTTGAAAAATTCAAAATACAAAATTTATTTTCTTACTTTGGAAATAATTTC
* * * * * *
62502 TTGGAAGATTA-TGTTAAAATTAATTTCCAAGAAATATTGAAGGGGTCATAAGTGGTCTCACTTA
195 TTAGAAGA-TAGTGTTAAAATTAATTTCCAAGAAAGATTGAAGGGGTCACAAGCGATCCCACTTA
*
62566 AGTTCCAATCTCCTAGACAAAATTCATTTCAACATACTAATCCAAGAAAATATAACCTAAGTTAG
259 AGTTCCAATCTCCTAGACAAAATTCATTTCAACATACTAATCCAAGAAAATATAACCTAAATTAG
62631 CC
324 CC
62633 ATTT
1 ATTT
62637 TATTCAAATA
Statistics
Matches: 300, Mismatches: 26, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
323 4 0.01
324 268 0.89
325 28 0.09
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (325 bp):
ATTTACAGAAAAAGACAACTAATTTCAATATTTACAAAAGAAACAACCAAATTTTACAAAAAATT
CAATTAAGTCATTGAACTCAAAATAATTTAAAAAATTAGGTTGCAATTAAAATTTGGATAAAAAA
TTAAACCTTTCTATTTGAAAAATTCAAAATACAAAATTTATTTTCTTACTTTGGAAATAATTTCT
TAGAAGATAGTGTTAAAATTAATTTCCAAGAAAGATTGAAGGGGTCACAAGCGATCCCACTTAAG
TTCCAATCTCCTAGACAAAATTCATTTCAACATACTAATCCAAGAAAATATAACCTAAATTAGCC
Found at i:71182 original size:23 final size:24
Alignment explanation
Indices: 71156--71202 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
71146 ACAATTCATT
71156 TTTATCTTA-ATTTGC-TCTGACAA
1 TTTATCTTATATTTGCAT-TGACAA
*
71179 TTTATTTTATATTTGCATTGACAA
1 TTTATCTTATATTTGCATTGACAA
71203 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTATCTTATATTTGCATTGACAA
Found at i:75078 original size:18 final size:18
Alignment explanation
Indices: 75055--75091 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
75045 ACAATTCATA
75055 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
75073 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
75091 T
1 T
75092 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:81573 original size:12 final size:12
Alignment explanation
Indices: 81556--81582 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
81546 AAAATAAAGT
81556 AAATAAAATAGG
1 AAATAAAATAGG
81568 AAATAAAATAGG
1 AAATAAAATAGG
81580 AAA
1 AAA
81583 ATGAGATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATAAAATAGG
Found at i:97316 original size:11 final size:11
Alignment explanation
Indices: 97296--97327 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
97286 ATAGAAAACA
97296 TTTT-TTTTTC
1 TTTTCTTTTTC
97306 TTTTCTTTTTC
1 TTTTCTTTTTC
97317 -TTTCTTTTTC
1 TTTTCTTTTTC
97327 T
1 T
97328 CATTTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:97751 original size:18 final size:19
Alignment explanation
Indices: 97714--97753 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
97704 TTAACAAAAG
*
97714 AAATGCAATGACAAAATAAA
1 AAATGAAATGAC-AAATAAA
97734 AAATGAAATGAC-AATAAA
1 AAATGAAATGACAAATAAA
97752 AA
1 AA
97754 TGCATGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (19 bp):
AAATGAAATGACAAATAAA
Found at i:102202 original size:21 final size:21
Alignment explanation
Indices: 102176--102217 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
102166 GATCCAATTC
*
102176 CTAATTTCCTGAATTTAGACA
1 CTAATTTCCTAAATTTAGACA
102197 CTAATTTCCTAAATTTAGACA
1 CTAATTTCCTAAATTTAGACA
102218 AAGGTATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (21 bp):
CTAATTTCCTAAATTTAGACA
Found at i:103922 original size:6 final size:6
Alignment explanation
Indices: 103913--103960 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
103903 AACATAACAA
* * * *
103913 TAAAAT TAAAAT TAAAAT TAATAT TAACAAT AAAAAT GAAAAA TAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAA-AAT TAAAAT TAAAAT TAAAA
103961 ATTTCAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 31 0.89
7 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (6 bp):
TAAAAT
Found at i:104533 original size:21 final size:21
Alignment explanation
Indices: 104507--104553 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
104497 CTCACTGGCT
104507 TGCTTTAGATCCAAATTTAAC
1 TGCTTTAGATCCAAATTTAAC
*
104528 TGCTTTAGATCTAAATTTAAC
1 TGCTTTAGATCCAAATTTAAC
104549 TGCTT
1 TGCTT
104554 CAAAGCCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (21 bp):
TGCTTTAGATCCAAATTTAAC
Found at i:138273 original size:15 final size:15
Alignment explanation
Indices: 138253--138304 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
138243 TGATTAAAAT
138253 TAAATGCAAATAATC
1 TAAATGCAAATAATC
* *
138268 TAAATGCAATTGATCC
1 TAAATGCAAATAAT-C
*
138284 TTAATGCAAATTAATC
1 TAAATGCAAA-TAATC
138300 TAAAT
1 TAAAT
138305 ATGCAAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (15 bp):
TAAATGCAAATAATC
Found at i:140113 original size:16 final size:17
Alignment explanation
Indices: 140084--140116 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
140074 ACATCACACT
140084 CATATTTATACATTAAA
1 CATATTTATACATTAAA
*
140101 CATA-TTATTCATTAAA
1 CATATTTATACATTAAA
140117 TTAAGAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
CATATTTATACATTAAA
Found at i:142329 original size:79 final size:80
Alignment explanation
Indices: 142047--142427 Score: 376
Period size: 79 Copynumber: 4.8 Consensus size: 80
142037 TAACCAATTT
* ** * * ** *
142047 CGTCAATTCATGGCACCCAGTGCCTAGCAAATAAACCGCGATAAGTGAGCCTAGCTCTTTTTGGT
1 CGTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCAC-AAAAGTGAGCCTAGCTCTAGTTGGA
* *
142112 TTAACCAACGATAGTTT
65 TTAACCAACAATAG-TC
* ** ** * *
142129 TGTCAATTCCTAACACCCAGTGCCTAGCGGATAAACTGCAAAAGTGAGCCTAGCTCTAGTTAGTT
1 CGTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCACAAAAGTGAGCCTAGCTCTAGTTGGAT
* *
142194 TCACCAACGATAGTTC
66 TAACCAACAATAG-TC
* * * * *
142210 CGTCAATTCCTGACATCCAATGCCTAGTGGATAAACCACAAAAGTGAGCCCAGCTCTAGTTGGAT
1 CGTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCACAAAAGTGAGCCTAGCTCTAGTTGGAT
142275 TAACCAACAATA-TC
66 TAACCAACAATAGTC
* * *
142289 CGTCAAATCCTGGCACCCAGTGCCTAGCAGATAAATCACAAAAGTGAG-CTGAGCTCTAGTTGGA
1 CGTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCACAAAAGTGAGCCT-AGCTCTAGTTGGA
* *
142353 TTAACCAATAATA-TA
65 TTAACCAACAATAGTC
* * * *
142368 CGTCAAATCCTGGCACTCAAG-GCCTAGCGGATAAACTGA-AAAAGTGTGCCTAGCTCTAGT
1 CGTCAATTCCTGGCAC-CCAGTGCCTAGCGGATAAAC-CACAAAAGTGAGCCTAGCTCTAGT
142428 CAGTTAAATT
Statistics
Matches: 255, Mismatches: 40, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
78 1 0.00
79 115 0.45
80 6 0.02
81 101 0.40
82 32 0.13
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (80 bp):
CGTCAATTCCTGGCACCCAGTGCCTAGCGGATAAACCACAAAAGTGAGCCTAGCTCTAGTTGGAT
TAACCAACAATAGTC
Done.