Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013412.1 Kokia drynarioides strain JFW-HI SEQ_128437, 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: 114756
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 672 characters in sequence are not A, C, G, or T
Found at i:21110 original size:7 final size:7
Alignment explanation
Indices: 21098--21126 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21088 AATGCCCCCT
21098 CTCTCAA
1 CTCTCAA
21105 CTCTCAA
1 CTCTCAA
21112 CTCTCAA
1 CTCTCAA
21119 CTCTCAA
1 CTCTCAA
21126 C
1 C
21127 AGTCACAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28
Consensus pattern (7 bp):
CTCTCAA
Found at i:28371 original size:58 final size:58
Alignment explanation
Indices: 28231--28379 Score: 146
Period size: 59 Copynumber: 2.6 Consensus size: 58
28221 AGTTTTGAAT
** *
28231 TTTTTTTATCTG-AAAAAGGAGGTGTCGGCCATTGCATGACCAACACCTAAAAATTTGA
1 TTTTTTTATCTGAAAAAAGG-GGTGTCGGCCATTGCATGACCAACACAAAAAAATGTGA
* *
28289 TTTTTTTATC-AAATAAATAGGGGTGTCGGCCATTGTAT-AGCCAACACAAAAAAATAGT-A
1 TTTTTTTATCTGAA-AAA-AGGGGTGTCGGCCATTGCATGA-CCAACACAAAAAAAT-GTGA
* *
28348 -TTTTTTATCTGACAAAAAAGGGTGTCGCCCAT
1 TTTTTTTATCTGA-AAAAAGGGGTGTCGGCCAT
28380 GCAAATTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
58 34 0.45
59 37 0.49
60 5 0.07
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (58 bp):
TTTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGACCAACACAAAAAAATGTGA
Found at i:30095 original size:23 final size:24
Alignment explanation
Indices: 30059--30110 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
30049 ATATAATACA
*
30059 TAAAAAAATATTTTTA-AAAAGTTT
1 TAAAAAAATATTTTTATAAAA-TTC
*
30083 TAAAACAAT-TTTTTATAAAATTC
1 TAAAAAAATATTTTTATAAAATTC
30106 TAAAA
1 TAAAA
30111 TATATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAAAAAATATTTTTATAAAATTC
Found at i:30172 original size:20 final size:20
Alignment explanation
Indices: 30129--30172 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30119 TATAAATTTA
* * *
30129 AAAAATTAGAAATAATATAT
1 AAAAATTAGAAAGAAAATAG
30149 AAAAATTAGAAAGAAAATAG
1 AAAAATTAGAAAGAAAATAG
30169 AAAA
1 AAAA
30173 GGTATTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (20 bp):
AAAAATTAGAAAGAAAATAG
Found at i:30237 original size:8 final size:8
Alignment explanation
Indices: 30224--30283 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
30214 TTTAAATTCC
30224 ATTTTAGA
1 ATTTTAGA
*
30232 ATTTTAAA
1 ATTTTAGA
* *
30240 ATTATA-T
1 ATTTTAGA
30247 ATTTTAGA
1 ATTTTAGA
*
30255 ATTTTAAA
1 ATTTTAGA
* *
30263 ATTATA-T
1 ATTTTAGA
30270 ATTTTAGA
1 ATTTTAGA
30278 ATTTTA
1 ATTTTA
30284 TAAAAAATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
7 10 0.25
8 30 0.75
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (8 bp):
ATTTTAGA
Found at i:30298 original size:23 final size:23
Alignment explanation
Indices: 30224--30283 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
30214 TTTAAATTCC
30224 ATTTTAGAATTTTAAAATTATAT
1 ATTTTAGAATTTTAAAATTATAT
30247 ATTTTAGAATTTTAAAATTATAT
1 ATTTTAGAATTTTAAAATTATAT
30270 ATTTTAGAATTTTA
1 ATTTTAGAATTTTA
30284 TAAAAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
ATTTTAGAATTTTAAAATTATAT
Found at i:31922 original size:16 final size:16
Alignment explanation
Indices: 31903--31938 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31893 TGTAAAAGAG
31903 AATTAAAATAAAATCA
1 AATTAAAATAAAATCA
* *
31919 AATTAAAATTAAATTA
1 AATTAAAATAAAATCA
31935 AATT
1 AATT
31939 TTACTGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAAATAAAATCA
Found at i:32958 original size:188 final size:189
Alignment explanation
Indices: 32636--32988 Score: 471
Period size: 188 Copynumber: 1.9 Consensus size: 189
32626 GATTAACTTA
* * * *
32636 GATCCAAAGTATATTCTTCTACTTGTCAATAGGTATTGATCTACCGTACCGACCATCAGATTGTC
1 GATCCAAAGTATATTCTTCTACTCGTCAATAGATACTGATCTACCGTACCAACCATCAGATTGTC
* ** *
32701 GTTTGGAGGTCGCTGATGAAATTTGAAAAAAAAAAGTAACATCCGAATAATTCCGTGATCCAATT
66 GTTTGGAGCTCGCTGATGAAATTTGAAAAAAAAAAGTAACATCCGAATAATTCAATGATCAAATT
*
32766 GTAAC-GTTTTTTCATTAAATGA-TCAAAACGAAAATTTACTAATAGTTTAATGATTAAT
131 GTAACTGTTTTTTAATTAAATGACT-AAAACGAAAATTTACTAATAGTTTAATGATTAAT
* * * * * * *
32824 GATCTAAAGTATATTTTTCTACTCGTTAATATATACTGATCTACTGTATCAACCATCGGATTGTC
1 GATCCAAAGTATATTCTTCTACTCGTCAATAGATACTGATCTACCGTACCAACCATCAGATTGTC
* * *
32889 GTTTGGAGCTCGTTGGA-GAAATTT-AAAAAAAAAACGTAACATCTGAATTATTCAATGATCAAA
66 GTTTGGAGCTCGCT-GATGAAATTTGAAAAAAAAAA-GTAACATCCGAATAATTCAATGATCAAA
*
32952 TTGTAACTTTTTTTTAATTAAATGACTAAAACGAAAA
129 TTGTAACTGTTTTTTAATTAAATGACTAAAACGAAAA
32989 CTTATCCATA
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
187 10 0.07
188 103 0.73
189 27 0.19
190 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (189 bp):
GATCCAAAGTATATTCTTCTACTCGTCAATAGATACTGATCTACCGTACCAACCATCAGATTGTC
GTTTGGAGCTCGCTGATGAAATTTGAAAAAAAAAAGTAACATCCGAATAATTCAATGATCAAATT
GTAACTGTTTTTTAATTAAATGACTAAAACGAAAATTTACTAATAGTTTAATGATTAAT
Found at i:37365 original size:30 final size:31
Alignment explanation
Indices: 37330--37412 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 31
37320 CTTGAAAAAA
*
37330 ATTAAATACCAACTTAAAAAAAAT-ATAAAT
1 ATTAAATACCAAATTAAAAAAAATGATAAAT
** *
37360 ATTAAATGTCAAATT-AAAAAAATGTTAAAT
1 ATTAAATACCAAATTAAAAAAAATGATAAAT
*
37390 -TTAAGTACCAAATTAAATAAAAA
1 ATTAAATACCAAATTAAA-AAAAA
37413 AAATTAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 19 0.44
30 19 0.44
31 5 0.12
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (31 bp):
ATTAAATACCAAATTAAAAAAAATGATAAAT
Found at i:38086 original size:16 final size:16
Alignment explanation
Indices: 38044--38098 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
38034 ATATAATAAC
*
38044 TTATAAATTCAAATTA
1 TTATATATTCAAATTA
* *
38060 -AATATCTTTCAAATTA
1 TTATAT-ATTCAAATTA
*
38076 TTATATATTCAAATGA
1 TTATATATTCAAATTA
38092 TTA-ATAT
1 TTATATAT
38099 AAATCATTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 7 0.23
16 20 0.65
17 4 0.13
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (16 bp):
TTATATATTCAAATTA
Found at i:38529 original size:30 final size:30
Alignment explanation
Indices: 38473--38530 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
38463 TCCAACTCAA
*
38473 ATTTAAATTAAATAAATTAAAAATATTTTT
1 ATTTAAATTAAATAAATAAAAAATATTTTT
* *
38503 ATTTAAATTTAAT-TATAAAAATATATTT
1 ATTTAAATTAAATAAATAAAAA-ATATTT
38531 AGATCAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTTAAATTAAATAAATAAAAAATATTTTT
Found at i:46261 original size:2 final size:2
Alignment explanation
Indices: 46254--46283 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46244 ATTTTTAAAC
46254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46284 TCAGATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56718 original size:5 final size:6
Alignment explanation
Indices: 56688--56715 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
56678 TGTATTGATA
56688 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
56716 GAATGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:57365 original size:21 final size:22
Alignment explanation
Indices: 57328--57380 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
57318 GTAACATGTT
*
57328 TTGAAGAT-TTAAGATTTTATC
1 TTGAATATATTAAGATTTTATC
* * *
57349 TTGAATTTATTAA-ATTTTTTT
1 TTGAATATATTAAGATTTTATC
57370 TTGAATATATT
1 TTGAATATATT
57381 GGTGTAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (22 bp):
TTGAATATATTAAGATTTTATC
Found at i:59342 original size:8 final size:8
Alignment explanation
Indices: 59331--59356 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
59321 CATTTTAATC
59331 TTTTAAAA
1 TTTTAAAA
59339 TTTTAAAA
1 TTTTAAAA
59347 TTTTAAAA
1 TTTTAAAA
59355 TT
1 TT
59357 AATAAAGATA
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:60414 original size:31 final size:31
Alignment explanation
Indices: 60376--60442 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
60366 TTCCTACCCC
60376 TAAATTTTATATATTAAAAAATAATTAAGAA
1 TAAATTTTATATATTAAAAAATAATTAAGAA
60407 TAAATTTTATATATTAAAAAATAATTAAGAA
1 TAAATTTTATATATTAAAAAATAATTAAGAA
60438 TAAAT
1 TAAAT
60443 AAATGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTTATATATTAAAAAATAATTAAGAA
Found at i:63033 original size:21 final size:21
Alignment explanation
Indices: 62999--63039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62989 CAATTGAACC
62999 AATATTATTATTAT-TTTTTA
1 AATATTATTATTATATTTTTA
*
63019 AATATTTATTTTTATATTTTT
1 AATA-TTATTATTATATTTTT
63040 TGATGATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
AATATTATTATTATATTTTTA
Found at i:63540 original size:20 final size:20
Alignment explanation
Indices: 63507--63545 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
63497 GAGGTTAATA
*
63507 TTCCATATGATCATATATTC
1 TTCCATACGATCATATATTC
* *
63527 TTCCATACGTTCATGTATT
1 TTCCATACGATCATATATT
63546 TTGGAGGCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (20 bp):
TTCCATACGATCATATATTC
Found at i:69026 original size:223 final size:224
Alignment explanation
Indices: 68632--69089 Score: 812
Period size: 223 Copynumber: 2.0 Consensus size: 224
68622 ATCCACCACA
* * *
68632 TCAGTTTCATTTCATCAAATCTTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCTTTCG
1 TCAGTGTCATTTCATCAAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCATTCG
**
68697 ATCACCAATTTATGCAATAATGATATGTATAATTAATCTAAAGAAACTAAAAGAAGTAATTGCAT
66 ATCACCAAAATATGCAATAATGATATGTATAATTAATCTAAAGAAACTAAAAGAAGTAATTGCAT
68762 TATCATCTAAAAACCTATGAGAAACAAGCCCTTAATCATAAAAC-AAGAACGAAGACATGCCTAG
131 TATCATCTAAAAACCTATGAGAAACAAGCCCTTAATCATAAAACAAAGAACGAAGACATGCCTAG
68826 ATAAGAAGTAAGAGCCCACCGATTCCAAC
196 ATAAGAAGTAAGAGCCCACCGATTCCAAC
*
68855 TCAGTGTCATTTCATCCAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCATTCG
1 TCAGTGTCATTTCATCAAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCATTCG
68920 ATCACCAAAATATGCAATAATGATATGTATAATTAATCTAAAGAAA-TGAAAAGAAGTAATTGCA
66 ATCACCAAAATATGCAATAATGATATGTATAATTAATCTAAAGAAACT-AAAAGAAGTAATTGCA
* *
68984 TTATCATCTACAAACCTATGAGAAACAAGCCCTTAATCATAAAACATAAGAATGAAGACATGCCT
130 TTATCATCTAAAAACCTATGAGAAACAAGCCCTTAATCATAAAACA-AAGAACGAAGACATGCCT
69049 AGATAAGAAGTAAGAGCCCACCGATTCCAAC
194 AGATAAGAAGTAAGAGCCCACCGATTCCAAC
69080 TCAGTGTCAT
1 TCAGTGTCAT
69090 CCTCTTCCCT
Statistics
Matches: 224, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
222 1 0.00
223 165 0.74
225 58 0.26
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (224 bp):
TCAGTGTCATTTCATCAAATATTGCTAAATCACCTTTTGATCACGAAAGTAAATAACATCATTCG
ATCACCAAAATATGCAATAATGATATGTATAATTAATCTAAAGAAACTAAAAGAAGTAATTGCAT
TATCATCTAAAAACCTATGAGAAACAAGCCCTTAATCATAAAACAAAGAACGAAGACATGCCTAG
ATAAGAAGTAAGAGCCCACCGATTCCAAC
Found at i:70898 original size:20 final size:20
Alignment explanation
Indices: 70875--70912 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
70865 AGGAATTCAT
* *
70875 TCATTCATAATTGAATAGCA
1 TCATTCAGAAGTGAATAGCA
70895 TCATTCAGAAGTGAATAG
1 TCATTCAGAAGTGAATAG
70913 TATTCAACTC
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:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
TCATTCAGAAGTGAATAGCA
Found at i:80111 original size:8 final size:8
Alignment explanation
Indices: 80080--80135 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
80070 TTAACAATGC
*
80080 ATACATAC
1 ATACATAT
*
80088 ATACATAC
1 ATACATAT
80096 ATAC--AT
1 ATACATAT
80102 ATACATAT
1 ATACATAT
*
80110 ATATATAT
1 ATACATAT
*
80118 ATATATAT
1 ATACATAT
*
80126 ATATATAT
1 ATACATAT
80134 AT
1 AT
80136 CAACAGTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 5 0.11
8 39 0.89
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATACATAT
Found at i:80113 original size:2 final size:2
Alignment explanation
Indices: 80100--80135 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
80090 ACATACATAC
*
80100 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80136 CAACAGTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:88630 original size:30 final size:29
Alignment explanation
Indices: 88574--88631 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
88564 GTACCTTTAG
** * *
88574 AATTTAATTTTTTTGTTTTTATTTTCAAT
1 AATTTAATTTTTTACTTTTGAATTTCAAT
88603 AATTTAATTTTTTACTTTTAGAATTTCAA
1 AATTTAATTTTTTACTTTT-GAATTTCAA
88632 AACTTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (29 bp):
AATTTAATTTTTTACTTTTGAATTTCAAT
Found at i:90219 original size:101 final size:101
Alignment explanation
Indices: 90043--90237 Score: 277
Period size: 101 Copynumber: 1.9 Consensus size: 101
90033 AGCAAAAAGA
* * * *
90043 AAAATTTTAGAACATTTTGAAGATTTTTATATAACTTCTGGAAATATTTAAATTTAAAAATTTTA
1 AAAATTTTAAAACATTTTGAAGATTTTTATATAACTTCTGGAAAGATTTAAATTTAAAAAGTTCA
*
90108 AATTCTTTTTGCATTTGTAGTTTTTTTTTTTTTTCC
66 AATTCTTTTTGCATTTGTAGTTTTATTTTTTTTTCC
* * *
90144 AAAATTTTAAAACATTTTGAATATTTTTATATAA-TTTTGGAAAAAGATTTAAATTTAAAGAGTT
1 AAAATTTTAAAACATTTTGAAGATTTTTATATAACTTCTGG--AAAGATTTAAATTTAAAAAGTT
*
90208 CAAATTC-TTTTGCATTTTTAGTTTTATTTT
64 CAAATTCTTTTTGCATTTGTAGTTTTATTTT
90238 CAAGGTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
100 5 0.06
101 53 0.64
102 25 0.30
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (101 bp):
AAAATTTTAAAACATTTTGAAGATTTTTATATAACTTCTGGAAAGATTTAAATTTAAAAAGTTCA
AATTCTTTTTGCATTTGTAGTTTTATTTTTTTTTCC
Found at i:103142 original size:30 final size:31
Alignment explanation
Indices: 103069--103142 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 31
103059 AAAATTTTAA
* *
103069 ATTAATAATTAT-AGAATTTTATTTTAATTC
1 ATTAATAATTATAAAAATTTGATTTTAATTC
*
103099 ATTAA-AATAATAAAAATTTGA-TTTAA-TC
1 ATTAATAATTATAAAAATTTGATTTTAATTC
*
103127 TTTTAATAATTATAAA
1 -ATTAATAATTATAAA
103143 GATATAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 2 0.06
29 14 0.39
30 20 0.56
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTAATAATTATAAAAATTTGATTTTAATTC
Found at i:104835 original size:2 final size:2
Alignment explanation
Indices: 104787--104819 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
104777 TATCAAAAAN
*
104787 TA TA TA TA TA TA TA CA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
104820 ATAAACTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:110271 original size:17 final size:18
Alignment explanation
Indices: 110251--110295 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
110241 TGAAGATTGA
110251 TTAATATTTTAAAT-AAT
1 TTAATATTTTAAATAAAT
**
110268 TTAAT-TTTTTTATAAAT
1 TTAATATTTTAAATAAAT
110285 TT-ATATTTTAA
1 TTAATATTTTAA
110296 GTGTACAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTTTAAATAAAT
Found at i:113669 original size:31 final size:31
Alignment explanation
Indices: 113631--113699 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
113621 AAAATATTGG
113631 TATTTTTATGCTATCAT-GTTTTAATTATTTT
1 TATTTTTATGCTATC-TCGTTTTAATTATTTT
*
113662 TATTTTTATGTTATCTCGTTTTAATTATTTT
1 TATTTTTATGCTATCTCGTTTTAATTATTTT
113693 TATTTTT
1 TATTTTT
113700 CTATCTTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.68
Consensus pattern (31 bp):
TATTTTTATGCTATCTCGTTTTAATTATTTT
Done.