Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012391.1 Kokia drynarioides strain JFW-HI SEQ_127395, 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: 125583
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 209 characters in sequence are not A, C, G, or T
Found at i:497 original size:24 final size:27
Alignment explanation
Indices: 440--494 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
430 TTATATTTTT
*
440 TATTTAATTTAATTTAAATAAAAATTAC
1 TATTTAATTTAACTTAAATAAAAA-TAC
468 TCATTTAATTTAACTTAAATAAAAATA
1 T-ATTTAATTTAACTTAAATAAAAATA
495 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
TATTTAATTTAACTTAAATAAAAATAC
Found at i:2153 original size:16 final size:17
Alignment explanation
Indices: 2128--2160 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2118 TCTTCATAAT
2128 TTTTAAAAAA-TTAAAA
1 TTTTAAAAAATTTAAAA
*
2144 TTTTATAAAATTTAAAA
1 TTTTAAAAAATTTAAAA
2161 GATCTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAATTTAAAA
Found at i:2719 original size:63 final size:63
Alignment explanation
Indices: 2641--2767 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
2631 AGTTTTCATT
*
2641 TAAGTCATTGAATTGTTAAAATAGTTATACTATGGCCTTATCTGTTCGCACCTTCTGCACCTA
1 TAAGTCATTGAATTGTTAAAATAGTTATACTATGGCCTTATCTGTTCACACCTTCTGCACCTA
*
2704 TAAGTCATTGGATTGTTAAAATAGTTATACTATGGCCTTATCTGTTCACACCTTCTGCACCTA
1 TAAGTCATTGAATTGTTAAAATAGTTATACTATGGCCTTATCTGTTCACACCTTCTGCACCTA
2767 T
1 T
2768 CAAAAGCTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (63 bp):
TAAGTCATTGAATTGTTAAAATAGTTATACTATGGCCTTATCTGTTCACACCTTCTGCACCTA
Found at i:3591 original size:31 final size:31
Alignment explanation
Indices: 3556--3619 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3546 CAGCCAAATT
* *
3556 ACTTAAATAGAAACTTTCGAATAGCTCAGTG
1 ACTTAAATAAAAACTTTCAAATAGCTCAGTG
*
3587 ACTTAAATAAAAACTTTCAAATAGTTCAGTG
1 ACTTAAATAAAAACTTTCAAATAGCTCAGTG
3618 AC
1 AC
3620 CATTTTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGCTCAGTG
Found at i:21152 original size:3 final size:3
Alignment explanation
Indices: 21144--21172 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21134 ATAGTGGTAC
21144 CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
21173 GCAGCAGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:32830 original size:2 final size:2
Alignment explanation
Indices: 32823--32851 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
32813 ATTTTGAGAA
32823 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32852 TTTTGGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:44901 original size:94 final size:94
Alignment explanation
Indices: 44792--44981 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 94
44782 TGAAACCCAA
44792 AATAATGCTAATCGAAAACAAACTGAATTTGAAATGACACAAACATGAACTAACCAAAACTTAAA
1 AATAATGCTAATCGAAAACAAACTGAATTTGAAATGACACAAACATGAACTAACCAAAACTTAAA
44857 AAGATCTGAACTTGTGATGACCCGACTCG
66 AAGATCTGAACTTGTGATGACCCGACTCG
* *
44886 AATAGTGCTAATCGAAAACAAACTGAATTTGAAATGACACAAACTTGAACTAACCAAAACTTAAA
1 AATAATGCTAATCGAAAACAAACTGAATTTGAAATGACACAAACATGAACTAACCAAAACTTAAA
44951 AAGATCTGAACTTGTGATGACCCGACTCG
66 AAGATCTGAACTTGTGATGACCCGACTCG
44980 AA
1 AA
44982 AAACCCAATC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (94 bp):
AATAATGCTAATCGAAAACAAACTGAATTTGAAATGACACAAACATGAACTAACCAAAACTTAAA
AAGATCTGAACTTGTGATGACCCGACTCG
Found at i:50585 original size:105 final size:105
Alignment explanation
Indices: 50403--50614 Score: 289
Period size: 105 Copynumber: 2.0 Consensus size: 105
50393 CTCCTTTTCT
* * * * * * *
50403 TGTAACAAGAGTAAACCATCGTAGATGCTCCAGAGTTCAGGATCAAAGACTGAACAAACACTTAA
1 TGTAACAAGAGTAAACCATCGTAGATACTCCAAAATTCAAGACCAAAGACTAAACAAACACCTAA
* * *
50468 ATTATGATTGAACTCAATAATCCAATCTCCAAATCGACTA
66 ACTATGATTGAACCCAATAATCCAATCTCCAAACCGACTA
* ** *
50508 TGTAACAAGAGTAAACTATTTTAGATACTCCAAAATTTAAGACCAAAGACTAAACAAACACCTAA
1 TGTAACAAGAGTAAACCATCGTAGATACTCCAAAATTCAAGACCAAAGACTAAACAAACACCTAA
*
50573 ACTATGATTGAACCCGATAATCCAATCTCCAAACCGACTA
66 ACTATGATTGAACCCAATAATCCAATCTCCAAACCGACTA
50613 TG
1 TG
50615 ATAATCAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 92 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (105 bp):
TGTAACAAGAGTAAACCATCGTAGATACTCCAAAATTCAAGACCAAAGACTAAACAAACACCTAA
ACTATGATTGAACCCAATAATCCAATCTCCAAACCGACTA
Found at i:63307 original size:33 final size:33
Alignment explanation
Indices: 63237--63310 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
63227 TAAATTGGTG
*
63237 CAATTATAC--ACATGAAACTTGAATTCTGATT
1 CAATTATACATACACGAAACTTGAATTCTGATT
** *
63268 C-A-TATACATACACGAAACTTTTATTTTGATT
1 CAATTATACATACACGAAACTTGAATTCTGATT
63299 CAATTATACATA
1 CAATTATACATA
63311 TTTAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 5 0.14
30 1 0.03
31 20 0.57
32 1 0.03
33 8 0.23
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (33 bp):
CAATTATACATACACGAAACTTGAATTCTGATT
Found at i:81460 original size:5 final size:5
Alignment explanation
Indices: 81450--81475 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
81440 ATTAGTTTCT
81450 ACAAA ACAAA ACAAA ACAAA ACAAA A
1 ACAAA ACAAA ACAAA ACAAA ACAAA A
81476 ACTGGGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:88294 original size:6 final size:6
Alignment explanation
Indices: 88285--88345 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
88275 ATTGATTTTG
* * *
88285 AATTTA AATTT- ATTTTAA AATTTA AATTT- AATTTA AATTTG GATTTA
1 AATTTA AATTTA AATTT-A AATTTA AATTTA AATTTA AATTTA AATTTA
*
88332 TATTTA AATTTA AA
1 AATTTA AATTTA AA
88346 ACTTATTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 9 0.20
6 32 0.71
7 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:88308 original size:18 final size:17
Alignment explanation
Indices: 88252--88345 Score: 91
Period size: 17 Copynumber: 5.4 Consensus size: 17
88242 TTAAACCCAT
*
88252 TTTAAGATTCATTTTAAGA
1 TTTAA-ATTTATTTTAA-A
* *
88271 -TTAAATTGATTTTGAA
1 TTTAAATTTATTTTAAA
88287 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
*
88305 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
**
88322 TTTGGATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
88340 TTTAAA
1 TTTAAA
88346 ACTTATTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
16 1 0.02
17 32 0.52
18 29 0.47
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:88310 original size:35 final size:35
Alignment explanation
Indices: 88252--88345 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
88242 TTAAACCCAT
* * * *
88252 TTTAAGATTCATTTTAAGA-TTAAATTGATTTTGAA
1 TTTAA-ATTTATTTTAAAATTTAAATTGAATTTAAA
*
88287 TTTAAATTTATTTTAAAATTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAAATTTAAATTGAATTTAAA
**
88322 TTTGGATTTATATTT-AAATTTAAA
1 TTTAAATTTAT-TTTAAAATTTAAA
88346 ACTTATTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 11 0.22
35 36 0.72
36 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAATTTAAATTGAATTTAAA
Found at i:88453 original size:36 final size:36
Alignment explanation
Indices: 88411--88486 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
88401 CAAAAACCCA
*
88411 AATTGGGGTCCAATTACAAATTAACCCAAACAAATC
1 AATTGGGGTCCAATTACAAATTAACCCAAACAAACC
*
88447 AATTGGGGTCCAATTACAAATTAATCCAAACAAACC
1 AATTGGGGTCCAATTACAAATTAACCCAAACAAACC
88483 AATT
1 AATT
88487 ACACCCCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (36 bp):
AATTGGGGTCCAATTACAAATTAACCCAAACAAACC
Found at i:89076 original size:12 final size:12
Alignment explanation
Indices: 89061--89147 Score: 68
Period size: 12 Copynumber: 7.1 Consensus size: 12
89051 TTAATACCAT
*
89061 CATTAATAATAG
1 CATTAATAATAA
89073 CATTAATAATAA
1 CATTAATAATAA
* **
89085 TATTTCTAATAA
1 CATTAATAATAA
89097 CATTAATAATAAA
1 CATTAATAAT-AA
* *
89110 CAGTAGTAATAA
1 CATTAATAATAA
*
89122 -ATGATATTAATAA
1 CAT--TAATAATAA
*
89135 TATTAATAATAA
1 CATTAATAATAA
89147 C
1 C
89148 TGTTTCAATA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
11 1 0.02
12 37 0.64
13 18 0.31
14 2 0.03
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (12 bp):
CATTAATAATAA
Found at i:89178 original size:16 final size:16
Alignment explanation
Indices: 89154--89205 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
89144 TAACTGTTTC
* *
89154 AATAATAATAATAATT
1 AATATTAATAATAATA
*
89170 AATATTAATATTAATA
1 AATATTAATAATAATA
*
89186 AATTTTAATAAATAA-A
1 AATATTAAT-AATAATA
89202 AATA
1 AATA
89206 AAAAGGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 25 0.86
17 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTAATAATAATA
Found at i:90357 original size:29 final size:29
Alignment explanation
Indices: 90301--90502 Score: 182
Period size: 29 Copynumber: 7.0 Consensus size: 29
90291 AATTATATTG
* *
90301 ACCCTCAAACTTCTCCAAAATTATATTTTTA
1 ACCC-CAAACTT-TCTAAAATTACATTTTTA
* *
90332 ACCTCGAACTTTCTAAAATTACA-TTTT-
1 ACCCCAAACTTTCTAAAATTACATTTTTA
*
90359 ACCCCAAACTTCTCCAAAATTACA-TTTTA
1 ACCCCAAACTT-TCTAAAATTACATTTTTA
*
90388 ACCCCTAAACTTTTTAAAAATTACA-TTTTA
1 ACCCC-AAACTTTCT-AAAATTACATTTTTA
* * *
90418 CCCCCGAACTTT-TCAAAATT-CATTTTTG
1 ACCCCAAACTTTCT-AAAATTACATTTTTA
* *
90446 ACCCCAAACTTCCAAAAATTACATTTTTA
1 ACCCCAAACTTTCTAAAATTACATTTTTA
* * *
90475 CCCCCAAACTTCCTAAAATTCCATTTTT
1 ACCCCAAACTTTCTAAAATTACATTTTT
90503 TGACTTCGAT
Statistics
Matches: 143, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.08
28 45 0.31
29 54 0.38
30 30 0.21
31 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (29 bp):
ACCCCAAACTTTCTAAAATTACATTTTTA
Found at i:90377 original size:57 final size:58
Alignment explanation
Indices: 90287--90592 Score: 236
Period size: 57 Copynumber: 5.3 Consensus size: 58
90277 ATAAACTGTC
* * *
90287 CAAAAATTATA-TTGACCCTCAAACTTCTCCAAAATTATATTTTTAACCTCGAACTTT
1 CAAAAATTACATTTTACCCCCAAACTTCTCCAAAATTATATTTTTAACCTCGAACTTT
* * * *
90344 CTAAAATTACATTTTA-CCCCAAACTTCTCCAAAATTACA-TTTTAACCCCTAAACTTTT
1 CAAAAATTACATTTTACCCCCAAACTTCTCCAAAATTATATTTTTAACCTC-GAAC-TTT
* * * * * * * *
90402 TAAAAATTACATTTTACCCCCGAACTT-TTCAAAATT-CATTTTTGACCCCAAACTTC
1 CAAAAATTACATTTTACCCCCAAACTTCTCCAAAATTATATTTTTAACCTCGAACTTT
* * * *
90458 CAAAAATTACATTTTTACCCCCAAACTTC-CTAAAATTCCAT-TTTTTGACTTCG-ATTTT
1 CAAAAATTACA-TTTTACCCCCAAACTTCTCCAAAATT--ATATTTTTAACCTCGAACTTT
* * *
90516 ACCAAAAATTACCATTTTACCCCCCGAA-TGC-CTAAAATTATATTTTTAACCTCGAACTTT
1 --CAAAAATTA-CATTTTA-CCCCCAAACTTCTCCAAAATTATATTTTTAACCTCGAACTTT
*
90576 CCCAAAATTACTATTTT
1 -CAAAAATTAC-ATTTT
90593 GCCCTTGGGT
Statistics
Matches: 203, Mismatches: 29, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
56 21 0.10
57 60 0.30
58 43 0.21
59 42 0.21
60 28 0.14
61 9 0.04
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
CAAAAATTACATTTTACCCCCAAACTTCTCCAAAATTATATTTTTAACCTCGAACTTT
Found at i:90501 original size:28 final size:28
Alignment explanation
Indices: 90279--90501 Score: 159
Period size: 28 Copynumber: 7.8 Consensus size: 28
90269 GGAGGTCCAT
* * * *
90279 AAACTGTCCAAAAATTATA-TTGACCCTC
1 AAACT-TCCTAAAATTACATTTTACCCCC
* * * *
90307 AAACTTCTCCAAAATTATATTTTTAACCTC
1 AAACTTC-CTAAAATTACA-TTTTACCCCC
* *
90337 GAACTTTCTAAAATTACATTTTA-CCCC
1 AAACTTCCTAAAATTACATTTTACCCCC
* *
90364 AAACTTCTCCAAAATTACATTTTAACCCCT
1 AAACTTC-CTAAAATTACATTTT-ACCCCC
**
90394 AAACTTTTTAAAAATTACATTTTACCCCC
1 AAACTTCCT-AAAATTACATTTTACCCCC
* *
90423 GAACTT-TTCAAAATT-CATTTTTGA-CCCC
1 AAACTTCCT-AAAATTACA-TTTT-ACCCCC
*
90451 AAACTTCCAAAAATTACATTTTTACCCCC
1 AAACTTCCTAAAATTACA-TTTTACCCCC
*
90480 AAACTTCCTAAAATTCCATTTT
1 AAACTTCCTAAAATTACATTTT
90502 TTGACTTCGA
Statistics
Matches: 160, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
27 12 0.08
28 66 0.41
29 48 0.30
30 34 0.21
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (28 bp):
AAACTTCCTAAAATTACATTTTACCCCC
Found at i:90585 original size:30 final size:30
Alignment explanation
Indices: 90315--90592 Score: 152
Period size: 29 Copynumber: 9.5 Consensus size: 30
90305 TCAAACTTCT
* *
90315 CCAAAATTATATTTTTAACCTCGAACTTT-
1 CCAAAATTACATTTTTAACCCCGAACTTTC
* *
90344 CTAAAATTACA-TTTT-ACCCCAAAC-TTC
1 CCAAAATTACATTTTTAACCCCGAACTTTC
* *
90371 TCCAAAATTACA-TTTTAACCCCTAAACTTTT
1 -CCAAAATTACATTTTTAACCCC-GAACTTTC
** *
90402 TAAAAATTACA-TTTTACCCCCGAACTTT-
1 CCAAAATTACATTTTTAACCCCGAACTTTC
* * *
90430 TCAAAATT-CATTTTTGACCCCAAAC-TTC
1 CCAAAATTACATTTTTAACCCCGAACTTTC
* * *
90458 CAAAAATTACATTTTTACCCCCAAAC-TTC
1 CCAAAATTACATTTTTAACCCCGAACTTTC
* * * ** *
90487 CTAAAATTCCATTTTTTGACTTCG-ATTTTAC
1 CCAAAATTACA-TTTTTAACCCCGAACTTT-C
* * *
90518 CAAAAATTACCA-TTTTACCCCCCGAA--TGC
1 CCAAAATTA-CATTTTTA-ACCCCGAACTTTC
* * *
90547 CTAAAATTATATTTTTAACCTCGAACTTTC
1 CCAAAATTACATTTTTAACCCCGAACTTTC
90577 CCAAAATTACTATTTT
1 CCAAAATTAC-ATTTT
90593 GCCCTTGGGT
Statistics
Matches: 191, Mismatches: 40, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
26 2 0.01
27 11 0.06
28 49 0.26
29 62 0.32
30 46 0.24
31 18 0.09
32 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
CCAAAATTACATTTTTAACCCCGAACTTTC
Found at i:94295 original size:32 final size:35
Alignment explanation
Indices: 94256--94348 Score: 111
Period size: 32 Copynumber: 2.6 Consensus size: 35
94246 CCTATATAAA
94256 AAATAGTTTGATACCCTGTGCATTTGG-ATA-TAT
1 AAATAGTTTGATACCCTGTGCATTTGGTATATTAT
*
94289 -AATAGTTTGATACCTTGTGCAAATTTGGTTATATTAT
1 AAATAGTTTGATACCCTGTGC--ATTTGG-TATATTAT
*
94326 AAACTAGTTCGATACCCTGTGCA
1 AAA-TAGTTTGATACCCTGTGCA
94349 CTGCACAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
32 19 0.38
34 6 0.12
36 3 0.06
37 4 0.08
38 2 0.04
39 16 0.32
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (35 bp):
AAATAGTTTGATACCCTGTGCATTTGGTATATTAT
Found at i:100670 original size:3 final size:3
Alignment explanation
Indices: 100662--100686 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
100652 GTATTCATCT
100662 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
100687 AAAAAGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:115646 original size:31 final size:32
Alignment explanation
Indices: 115597--115656 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
115587 AACAACTCAG
*
115597 TGACTTAAATAAAAAACTTTTAAATAATTTAA
1 TGACTTAAATAAAAAACTTTCAAATAATTTAA
*
115629 TGACTTAAAT-AAAAACTTTCGAATAATT
1 TGACTTAAATAAAAAACTTTCAAATAATT
115657 CAGTGATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (32 bp):
TGACTTAAATAAAAAACTTTCAAATAATTTAA
Found at i:118435 original size:48 final size:48
Alignment explanation
Indices: 118373--118484 Score: 197
Period size: 48 Copynumber: 2.3 Consensus size: 48
118363 AGCCGTAACA
* *
118373 GCTGAATCCGTAAAGCAGGGGGTTACTAATACTCCATCAGTCTCGAAG
1 GCTGAATCCATAAAGCAGGAGGTTACTAATACTCCATCAGTCTCGAAG
*
118421 GCTGAATTCATAAAGCAGGAGGTTACTAATACTCCATCAGTCTCGAAG
1 GCTGAATCCATAAAGCAGGAGGTTACTAATACTCCATCAGTCTCGAAG
118469 GCTGAATCCATAAAGC
1 GCTGAATCCATAAAGC
118485 GAGATGTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (48 bp):
GCTGAATCCATAAAGCAGGAGGTTACTAATACTCCATCAGTCTCGAAG
Found at i:125175 original size:27 final size:27
Alignment explanation
Indices: 125137--125191 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
125127 ATACCTGACC
125137 CCAATGGAGGAACA-CGAAGTGGCGGCA
1 CCAATGGAGGAACATC-AAGTGGCGGCA
*
125164 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAACATCAAGTGGCGGCA
125191 C
1 C
125192 TAAGCGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.22, G:0.35, T:0.11
Consensus pattern (27 bp):
CCAATGGAGGAACATCAAGTGGCGGCA
Found at i:125376 original size:4 final size:4
Alignment explanation
Indices: 125367--125452 Score: 77
Period size: 4 Copynumber: 21.2 Consensus size: 4
125357 AAATAAACGG
* * *
125367 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
125417 G-AA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
125453 GTAATGTGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
3 6 0.09
4 51 0.74
5 12 0.17
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:125389 original size:17 final size:17
Alignment explanation
Indices: 125367--125452 Score: 92
Period size: 17 Copynumber: 5.3 Consensus size: 17
125357 AAATAAACGG
125367 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
125384 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* *
125400 GAAGGAGAGGAAA-GAAA
1 GAAAGA-AAGAAAGGAAA
* *
125417 G-AAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
125433 GAAAG-AAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
125448 GAAAG
1 GAAAG
125453 GTAATGTGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
15 16 0.27
16 18 0.31
17 25 0.42
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:125422 original size:20 final size:20
Alignment explanation
Indices: 125366--125445 Score: 108
Period size: 20 Copynumber: 3.9 Consensus size: 20
125356 CAAATAAACG
*
125366 GGAAAGAAAGAAAGGAAAGA-A
1 GGAAAGAAAG-AA-GAAGGAGA
*
125387 AGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAA-GAAGAAGGAGA
125408 GGAAAGAAAGAAGAAGGAGA
1 GGAAAGAAAGAAGAAGGAGA
125428 GGAAAGAAAGAAGAAGGA
1 GGAAAGAAAGAAGAAGGA
125446 AAGAAAGGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
20 34 0.63
21 19 0.35
22 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAGGAGA
Done.