Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003972.1 Kokia drynarioides strain JFW-HI SEQ_117067, 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: 151796
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:804 original size:41 final size:41
Alignment explanation
Indices: 735--859 Score: 160
Period size: 41 Copynumber: 3.0 Consensus size: 41
725 TTTTTATAAA
* *
735 CGCCGCTAATGCTCTGACTTTTAACGGCGCTTTCTTTCAAG
1 CGCCGCTAATGCTATGACTTTTAACGGCGCTTTCCTTCAAG
* * * * *
776 CGCCGTTAATGTTATGACCTTTAGCGGCGTTTTCCTTCAAG
1 CGCCGCTAATGCTATGACTTTTAACGGCGCTTTCCTTCAAG
* * *
817 CGTCGCTAATGCTATGACTTTTAACGACGCTTTCCCTCAAG
1 CGCCGCTAATGCTATGACTTTTAACGGCGCTTTCCTTCAAG
858 CG
1 CG
860 TCATTTCTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (41 bp):
CGCCGCTAATGCTATGACTTTTAACGGCGCTTTCCTTCAAG
Found at i:9345 original size:16 final size:17
Alignment explanation
Indices: 9311--9345 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9301 ACTGCATCAT
*
9311 AAAATTTAAAAAGTAAAA
1 AAAATCTAAAAAG-AAAA
9329 AAAATCTAAAAAGAAAA
1 AAAATCTAAAAAGAAAA
9346 TAATCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATCTAAAAAGAAAA
Found at i:15032 original size:15 final size:16
Alignment explanation
Indices: 14996--15035 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
14986 ATAGTAGAAA
14996 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
15013 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
15028 TATAATTT
1 TATAATTT
15036 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:19923 original size:79 final size:79
Alignment explanation
Indices: 19837--19995 Score: 219
Period size: 79 Copynumber: 2.0 Consensus size: 79
19827 AATGCAAAAC
* * * *
19837 TAATATTTCATTCAATAAATAAAAAATGAATATCGCATGAAAATCCTAATCTATCACCAGAAAAG
1 TAATATTTCACTCAATAAATAAAAAATGAATATCGAATGAAAATCCTAATCTATCACAAGAAAAA
* *
19902 TCATAATTCAAATT
66 TCACAATCCAAATT
* * * * *
19916 TAATATTTCACTCAATCAATAAAAATTGGATATTGAATGAAAATCGTAATCTATCACAAGAAAAA
1 TAATATTTCACTCAATAAATAAAAAATGAATATCGAATGAAAATCCTAATCTATCACAAGAAAAA
19981 TCACAATCCAAATT
66 TCACAATCCAAATT
19995 T
1 T
19996 CTTAAATATT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (79 bp):
TAATATTTCACTCAATAAATAAAAAATGAATATCGAATGAAAATCCTAATCTATCACAAGAAAAA
TCACAATCCAAATT
Found at i:20202 original size:19 final size:18
Alignment explanation
Indices: 20174--20240 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 18
20164 AAGAGAGATG
*
20174 AATTTATTTTATATAAATT
1 AATTTATTTTATA-AAATA
*
20193 AATTTGTTTTATAAAATA
1 AATTTATTTTATAAAATA
* *
20211 AATTT-TATCATAAAAT-
1 AATTTATTTTATAAAATA
20227 AATTT-TTTTATAAA
1 AATTTATTTTATAAA
20241 GTTTTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
16 12 0.29
17 9 0.21
18 9 0.21
19 12 0.29
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
AATTTATTTTATAAAATA
Found at i:21715 original size:27 final size:27
Alignment explanation
Indices: 21685--21739 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21675 GTAAACCAGC
21685 AGAGTTCTATTGGTAATGAAACTTTGA
1 AGAGTTCTATTGGTAATGAAACTTTGA
21712 AGAGTTCTATTGGTAATGAAACTTTGA
1 AGAGTTCTATTGGTAATGAAACTTTGA
21739 A
1 A
21740 TGATTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (27 bp):
AGAGTTCTATTGGTAATGAAACTTTGA
Found at i:26675 original size:22 final size:22
Alignment explanation
Indices: 26644--26685 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
26634 AATGTTCATT
26644 TTTGACACTTGAATTTTTTTAA
1 TTTGACACTTGAATTTTTTTAA
* *
26666 TTTGATACTTGAGTTTTTTT
1 TTTGACACTTGAATTTTTTT
26686 TTTCAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTGACACTTGAATTTTTTTAA
Found at i:34067 original size:8 final size:8
Alignment explanation
Indices: 34056--34081 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34046 CATTTTAATC
34056 TTTTAAAA
1 TTTTAAAA
34064 TTTTAAAA
1 TTTTAAAA
34072 TTTTAAAA
1 TTTTAAAA
34080 TT
1 TT
34082 AATAAAAATA
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:0.00, T:0.54
Consensus pattern (8 bp):
TTTTAAAA
Found at i:41614 original size:3 final size:3
Alignment explanation
Indices: 41606--41632 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41596 TTTACTCGTC
41606 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
41633 CTCGGTGTTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:48310 original size:16 final size:16
Alignment explanation
Indices: 48282--48324 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
48272 TAGTGGATAA
**
48282 AAAAATAATTTTTTTT
1 AAAAATAATTTTTGAT
48298 AAAAAGTAATTTTTGAT
1 AAAAA-TAATTTTTGAT
48315 AAAAATAATT
1 AAAAATAATT
48325 ATATTTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (16 bp):
AAAAATAATTTTTGAT
Found at i:48831 original size:3 final size:3
Alignment explanation
Indices: 48820--48855 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
48810 AAAAAAGCAG
* *
48820 AGA ATA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
48856 GAAAAATTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:49483 original size:29 final size:29
Alignment explanation
Indices: 49425--49482 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
49415 AAATATAAGC
*
49425 ATATTAGGTCATTTACGCAAACAATAAAA
1 ATATTAGGTCATTTACGCAAAAAATAAAA
**
49454 ATATTAGGTCATTTA-TTAAAAAATAAAA
1 ATATTAGGTCATTTACGCAAAAAATAAAA
49482 A
1 A
49483 AGTAAGGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (29 bp):
ATATTAGGTCATTTACGCAAAAAATAAAA
Found at i:52943 original size:26 final size:26
Alignment explanation
Indices: 52895--52946 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
52885 TAAATTATGG
* * *
52895 ATTATTATATTAAATATAGTCTTTTT
1 ATTATTATATGAAATACACTCTTTTT
*
52921 ATTATTATATGAAATACCCTCTTTTT
1 ATTATTATATGAAATACACTCTTTTT
52947 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTATTATATGAAATACACTCTTTTT
Found at i:53558 original size:22 final size:21
Alignment explanation
Indices: 53504--53559 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
53494 AAAGTTTTAT
53504 TTATAA-TTATAATAAATTAAA
1 TTATAATTTAT-ATAAATTAAA
* *
53525 -AATATATATATATAATATTAAA
1 TTATA-ATTTATATAA-ATTAAA
53547 TTATAATTTATAT
1 TTATAATTTATAT
53560 GTAATTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
20 3 0.11
21 5 0.19
22 16 0.59
23 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATAATTTATATAAATTAAA
Found at i:53558 original size:24 final size:24
Alignment explanation
Indices: 53504--53573 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 24
53494 AAAGTTTTAT
53504 TTATAA-TTATA-ATAA-ATTAAA
1 TTATAATTTATATATAATATTAAA
* *
53525 -AAT-ATATATATATAATATTAAA
1 TTATAATTTATATATAATATTAAA
* *
53547 TTATAATTTATATGTAATTTTGAAA
1 TTATAATTTATATATAATATT-AAA
53572 TT
1 TT
53574 CTTCCCTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 1 0.03
20 6 0.16
21 4 0.11
22 6 0.16
23 2 0.05
24 13 0.35
25 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
TTATAATTTATATATAATATTAAA
Found at i:59497 original size:31 final size:31
Alignment explanation
Indices: 59455--59517 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
59445 GATCATCAAC
*
59455 TACCTCTGACTGAAGCAGCAGCTTCTTCTCA
1 TACCTCCGACTGAAGCAGCAGCTTCTTCTCA
59486 TACCTCCGACTGAAGCAGCAGCTTCTTCTCA
1 TACCTCCGACTGAAGCAGCAGCTTCTTCTCA
59517 T
1 T
59518 TATCTGCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (31 bp):
TACCTCCGACTGAAGCAGCAGCTTCTTCTCA
Found at i:60603 original size:2 final size:2
Alignment explanation
Indices: 60596--60621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60586 CAAACCTATC
60596 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
60622 AAGAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:69116 original size:6 final size:6
Alignment explanation
Indices: 69105--69131 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69095 TTTGCCTGCC
69105 CCTTAG CCTTAG CCTTAG CCTTAG CCT
1 CCTTAG CCTTAG CCTTAG CCTTAG CCT
69132 AACCTAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (6 bp):
CCTTAG
Found at i:72554 original size:81 final size:81
Alignment explanation
Indices: 72384--72545 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
72374 GATGAAAAGT
*
72384 AAACATGGTCACGAGACGTTTGTATTTGTGATAAATGACTTGATTACTATTTGATACTAATTAAC
1 AAACATGGTCACGAGACGTTTGTATTTGTAATAAATGACTTGATTACTATTTGATACTAATTAAC
72449 TTTTCATTAAGGAAGA
66 TTTTCATTAAGGAAGA
*
72465 AAACATGGTCACGGGACGTTTGTATTTGTAATAAATGACTTGATTACTATTTGATACTAATTAAC
1 AAACATGGTCACGAGACGTTTGTATTTGTAATAAATGACTTGATTACTATTTGATACTAATTAAC
72530 TTTTCATTAAGGAAGA
66 TTTTCATTAAGGAAGA
72546 TATAATGGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (81 bp):
AAACATGGTCACGAGACGTTTGTATTTGTAATAAATGACTTGATTACTATTTGATACTAATTAAC
TTTTCATTAAGGAAGA
Found at i:79831 original size:11 final size:12
Alignment explanation
Indices: 79815--79845 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
79805 TTTAATCAGG
79815 TTTAAATTGA-T
1 TTTAAATTGATT
79826 TTTAAATTGATT
1 TTTAAATTGATT
79838 TTTAAATT
1 TTTAAATT
79846 TAAATTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TTTAAATTGATT
Found at i:79849 original size:6 final size:6
Alignment explanation
Indices: 79838--79934 Score: 69
Period size: 6 Copynumber: 16.5 Consensus size: 6
79828 TAAATTGATT
**
79838 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATTC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
** ** *
79886 TTTATTC TTTAAA TTTAAA TTT-GC TTTAAA TTTGAA TTT-AA -TTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
79932 TTT
1 TTT
79935 GAGACAATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
4 4 0.06
5 9 0.13
6 47 0.67
7 10 0.14
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:79849 original size:18 final size:19
Alignment explanation
Indices: 79826--79925 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
79816 TTAAATTGAT
*
79826 TTTAAATTGATT-TTTAAA
1 TTTAAATTTATTCTTTAAA
79844 TTTAAATTTA-TC-TTAAA
1 TTTAAATTTATTCTTTAAA
79861 TTTAAATTTATTCTTTAAA
1 TTTAAATTTATTCTTTAAA
79880 TTTAAATTTATTCTTTAAA
1 TTTAAATTTATTCTTTAAA
*
79899 TTTAAA-TT-TGCTTTAAA
1 TTTAAATTTATTCTTTAAA
*
79916 TTTGAATTTA
1 TTTAAATTTA
79926 ATTAAATTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
17 29 0.39
18 15 0.20
19 30 0.41
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTAAATTTATTCTTTAAA
Found at i:79870 original size:29 final size:29
Alignment explanation
Indices: 79815--79870 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
79805 TTTAATCAGG
* **
79815 TTTAAATTGATTTTAAATTGATTTTTAAA
1 TTTAAATTGATCTTAAATTGAAATTTAAA
* *
79844 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTGATCTTAAATTGAAATTTA
79871 TTCTTTAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (29 bp):
TTTAAATTGATCTTAAATTGAAATTTAAA
Found at i:79881 original size:36 final size:36
Alignment explanation
Indices: 79826--79934 Score: 136
Period size: 36 Copynumber: 3.1 Consensus size: 36
79816 TTAAATTGAT
*
79826 TTTAAATTGATT-TTTAAATTTAAATTTATCTTAAA
1 TTTAAATTTATTCTTTAAATTTAAATTTATCTTAAA
79861 TTTAAATTTATTCTTTAAATTTAAATTTATTCTTTAAA
1 TTTAAATTTATTCTTTAAATTTAAATTTA-TC-TTAAA
* * *
79899 TTTAAA-TT-TGCTTTAAATTTGAATTTA-ATTAAA
1 TTTAAATTTATTCTTTAAATTTAAATTTATCTTAAA
79932 TTT
1 TTT
79935 GAGACAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
33 8 0.12
35 11 0.16
36 33 0.49
37 4 0.06
38 11 0.16
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.56
Consensus pattern (36 bp):
TTTAAATTTATTCTTTAAATTTAAATTTATCTTAAA
Found at i:79996 original size:26 final size:26
Alignment explanation
Indices: 79944--79995 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
79934 TGAGACAATT
79944 TAGAACTTAATTAAAAAAGTCTAAAA
1 TAGAACTTAATTAAAAAAGTCTAAAA
* * *
79970 TAGAATTTCAATTACAAATGTCTAAA
1 TAGAACTT-AATTAAAAAAGTCTAAA
79996 TTACAAGCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (26 bp):
TAGAACTTAATTAAAAAAGTCTAAAA
Found at i:81959 original size:18 final size:18
Alignment explanation
Indices: 81932--81975 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
81922 CAGATGTGAA
81932 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
81950 GGAAAGGAAGTGAGAGAT
1 GGAAAAGAAGAAAGAGAT
81968 GAGAAAAG
1 G-GAAAAG
81976 CACGACTGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.07
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:86497 original size:49 final size:49
Alignment explanation
Indices: 86425--87000 Score: 296
Period size: 49 Copynumber: 11.7 Consensus size: 49
86415 TCAGCACTAT
* * * *
86425 GAAACACGAAGGGAAAGATTTAAGCCACAATGGCGAATCCAGTACCACAA
1 GAAACA-GAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCAGTACCACAA
* * **
86475 TGAAACA-AAGGGAAAGGTTTAAGTCGCAACAGCGAA-CCTTGTACC-TTA
1 -GAAACAGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCC-AGTACCACAA
* * * *
86523 GAGACATGAAGGG-AAGGATTTAAGCCACAACGGCGGATCCAGTACCACAAA
1 GAAACA-GAAGGGAAAGG-TTTAAGTCGCAACGGCGAATCCAGTACCAC-AA
* * * * * * * *
86574 GACACA-AAGGGAAAGGTTTAAATCACTATGGAGAACCCAGTACCTC-A
1 GAAACAGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCAGTACCACAA
* * * *
86621 GAAGGCATGAAGGG-AAGGATCTAAGCCGCAACGGCGGATCCAGTATCGCA-AA
1 GAA-ACA-GAAGGGAAAGG-TTTAAGTCGCAACGGCGAATCCAGTA-C-CACAA
* * * * *
86673 GACATA-AAGGGAAAGGTTTAAGTCGCAATGGCGAACCCAGTACCTC-A
1 GAAACAGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCAGTACCACAA
* * * *
86720 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGG-GGATCCAGTACCACGAA
1 GAA-ACA-GAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCAGTACCAC-AA
* * * * **
86771 GACACAG--GGGAATGGTTTAAGTCGCAATGGTGAA-CCTAGTACGTCAA
1 GAAACAGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCC-AGTACCACAA
* * *
86818 -AAGACATGAAGGGAAAGATCTAAG-CAGCAACGGCGGATCCAGTACCAC--
1 GAA-ACA-GAAGGGAAAGGTTTAAGTC-GCAACGGCGAATCCAGTACCACAA
* * * **
86866 GAAGACACATGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTAGTACC-TTA
1 GAA-ACAGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCC-AGTACCACAA
* * * * * *
86915 GAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGC--
1 GAAACA-GAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCAGTACCACAA
* *
86963 GAAGACACAAGGAGAAAGGTTTAAGTCGCAATGGCGAA
1 GAA-ACAGAAGG-GAAAGGTTTAAGTCGCAACGGCGAA
87001 CCTTATACCT
Statistics
Matches: 389, Mismatches: 96, Indels: 82
0.69 0.17 0.14
Matches are distributed among these distances:
46 1 0.00
47 39 0.10
48 58 0.15
49 185 0.48
50 83 0.21
51 19 0.05
52 4 0.01
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (49 bp):
GAAACAGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCAGTACCACAA
Found at i:86822 original size:97 final size:99
Alignment explanation
Indices: 86432--87012 Score: 746
Period size: 98 Copynumber: 5.9 Consensus size: 99
86422 TATGAAACAC
* * * * *
86432 GAAGGGAAAGATTTAAGCCACAATGGCGAATCCAGTACCAC-AATGAAACAAAGGGAAAGGTTTA
1 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAA-GACACAAAGGGAAAGGTTTA
** * * *
86496 AGTCGCAACAGCGAACCTTGTACCT-TAGAGACAT
65 AGTCGCAATGGCGAACCTAGTACCTCAAAAGACAT
* * * *
86530 GAAGGGAAGGATTTAAGCCACAACGGCGGATCCAGTACCACAAAGACACAAAGGGAAAGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAA
* * * * * * *
86595 ATCACTATGGAGAACCCAGTACCTCAGAAGGCAT
66 GTCGCAATGGCGAACCTAGTACCTCAAAAGACAT
* * * * *
86629 GAAGGGAAGGATCTAAGCCGCAACGGCGGATCCAGTATCGCAAAGACATAAAGGGAAAGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAA
* *
86694 GTCGCAATGGCGAACCCAGTACCTCAGAAGACAT
66 GTCGCAATGGCGAACCTAGTACCTCAAAAGACAT
* *
86728 GAAGGGAAAGATCTAAGCCGCAACGG-GGATCCAGTACCACGAAGACAC-AGGGGAATGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAA
* *
86791 GTCGCAATGGTGAACCTAGTACGTCAAAAGACAT
66 GTCGCAATGGCGAACCTAGTACCTCAAAAGACAT
* *
86825 GAAGGGAAAGATCTAAGCAGCAACGGCGGATCCAGTACCACGAAGACAC-ATGGGAAAGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAA
* *
86889 GTCGCAATGGCGAACCTAGTACCT-TAGAGACAT
66 GTCGCAATGGCGAACCTAGTACCTCAAAAGACAT
*
86922 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCGAAGACAC-AAGGAGAAAGGTTTA
1 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACAAAGG-GAAAGGTTTA
86986 AGTCGCAATGGCGAACCTTA-TACCTCA
65 AGTCGCAATGGCGAACC-TAGTACCTCA
87013 GAAGCAGAAA
Statistics
Matches: 429, Mismatches: 48, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
97 125 0.29
98 181 0.42
99 123 0.29
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (99 bp):
GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGACACAAAGGGAAAGGTTTAA
GTCGCAATGGCGAACCTAGTACCTCAAAAGACAT
Found at i:88233 original size:3 final size:3
Alignment explanation
Indices: 88220--88306 Score: 72
Period size: 3 Copynumber: 29.7 Consensus size: 3
88210 AACCGTAAAA
* **
88220 AAT ATT AAT AAT AAT AAT AAT AACT -AT TTT AA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* * * * *
88264 AAT GAT ATT AGT AAT ATT AAT AAT AAT ATT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
88307 AAAGGAAATT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 5 0.08
3 60 0.91
4 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:95442 original size:16 final size:15
Alignment explanation
Indices: 95416--95445 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
95406 AAAGAACATT
95416 TTAATTTTTTAATTA
1 TTAATTTTTTAATTA
95431 TTAATATTTTTAATT
1 TTAAT-TTTTTAATT
95446 TCTGAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAATTTTTTAATTA
Found at i:110048 original size:40 final size:40
Alignment explanation
Indices: 109993--110114 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
109983 CATTGCCAAG
* *
109993 AATGCCAAAACTCTCCTATTTTGGTCCCTTTTCATGACTA
1 AATGCCAAAACTCTCCTATTTTGGTCCCTTTCCATGCCTA
110033 AATGCCAAAACTCTCCTATTTTGGTCCCTTTCCATGCCTA
1 AATGCCAAAACTCTCCTATTTTGGTCCCTTTCCATGCCTA
110073 AATGCCAAAACTCTCCTATTTTGGTCCCTTTCCATGCCTA
1 AATGCCAAAACTCTCCTATTTTGGTCCCTTTCCATGCCTA
110113 AA
1 AA
110115 CCAAATCTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (40 bp):
AATGCCAAAACTCTCCTATTTTGGTCCCTTTCCATGCCTA
Found at i:116435 original size:25 final size:26
Alignment explanation
Indices: 116406--116456 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
116396 TTAAAATATG
116406 AAAAATAAAAAG-TCTTTAAAAATAA
1 AAAAATAAAAAGATCTTTAAAAATAA
* * *
116431 AAAAATAGAAAGATTTTTTAAAATAA
1 AAAAATAAAAAGATCTTTAAAAATAA
116457 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (26 bp):
AAAAATAAAAAGATCTTTAAAAATAA
Found at i:116453 original size:26 final size:25
Alignment explanation
Indices: 116395--116456 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
116385 AAATTTAAAA
*
116395 TTTAAAATATGAAAAATAAAAAGTCT
1 TTTAAAATA-AAAAAATAAAAAGTCT
* * *
116421 TTAAAAATAAAAAAATAGAAAGATTT
1 TTTAAAATAAAAAAATAAAAAG-TCT
116447 TTTAAAATAA
1 TTTAAAATAA
116457 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (25 bp):
TTTAAAATAAAAAAATAAAAAGTCT
Found at i:117426 original size:21 final size:21
Alignment explanation
Indices: 117400--117443 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
117390 AAATAATAAA
*
117400 ATATTAAAAACATATAGTTTT
1 ATATTAAAAACATATACTTTT
* *
117421 ATATTAATATCATATACTTTT
1 ATATTAAAAACATATACTTTT
117442 AT
1 AT
117444 TAGAACTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATTAAAAACATATACTTTT
Found at i:129335 original size:30 final size:32
Alignment explanation
Indices: 129270--129338 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 32
129260 ACCATTAACT
129270 CTTTTTTTTTTTGGTTACATGAACCAATTAATTAA
1 CTTTTTTTTTTTGGTTACATGAACC-A--AATTAA
129305 CTTTTTTTTTTT-GTTACATGAACC-AATTAA
1 CTTTTTTTTTTTGGTTACATGAACCAAATTAA
129335 CTTT
1 CTTT
129339 GATACATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
30 10 0.29
34 12 0.35
35 12 0.35
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (32 bp):
CTTTTTTTTTTTGGTTACATGAACCAAATTAA
Found at i:129394 original size:36 final size:36
Alignment explanation
Indices: 129330--129427 Score: 153
Period size: 36 Copynumber: 2.8 Consensus size: 36
129320 ACATGAACCA
* * *
129330 ATTAACTTTGATACA-TGCACCTATATATCTACAAG
1 ATTAATTTTGATTCATTGCACCTACATATCTACAAG
129365 ATTAATTTTGATTCATTGCACCTACATATCTACAAG
1 ATTAATTTTGATTCATTGCACCTACATATCTACAAG
*
129401 ATTAATTTTGATTCATTGCAGCTACAT
1 ATTAATTTTGATTCATTGCACCTACAT
129428 GCATACTGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 13 0.22
36 45 0.78
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (36 bp):
ATTAATTTTGATTCATTGCACCTACATATCTACAAG
Found at i:137344 original size:11 final size:11
Alignment explanation
Indices: 137296--137346 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
137286 CTACCATTTG
137296 TTATTTTGTTA
1 TTATTTTGTTA
** *
137307 CCATTTTGCTA
1 TTATTTTGTTA
*
137318 TTATATTGTTA
1 TTATTTTGTTA
*
137329 TTATTTTGTTG
1 TTATTTTGTTA
137340 TTATTTT
1 TTATTTT
137347 TTGAATATTA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.67
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:149612 original size:20 final size:20
Alignment explanation
Indices: 149587--149624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
149577 ATATATATTA
**
149587 TTACTGTTTGTGATTTGATT
1 TTACTGTTCATGATTTGATT
149607 TTACTGTTCATGATTTGA
1 TTACTGTTCATGATTTGA
149625 CCCTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.55
Consensus pattern (20 bp):
TTACTGTTCATGATTTGATT
Done.