Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013935.1 Kokia drynarioides strain JFW-HI SEQ_128965, 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: 177514
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 173 characters in sequence are not A, C, G, or T
Found at i:13452 original size:17 final size:16
Alignment explanation
Indices: 13430--13484 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
13420 TAATAAATTA
13430 TTAATAAAATTATTATT
1 TTAATAAAATT-TTATT
*
13447 TTAAT-AAATTGTT-TA
1 TTAATAAAATT-TTATT
* *
13462 ATATTAAAATTTTATT
1 TTAATAAAATTTTATT
13478 TTAATAA
1 TTAATAA
13485 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
15 6 0.21
16 18 0.62
17 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTAATAAAATTTTATT
Found at i:13494 original size:32 final size:31
Alignment explanation
Indices: 13432--13512 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
13422 ATAAATTATT
*** *
13432 AATAAAATTATTATTTTAATAAATTGTTTAAT
1 AATAAAATT-TTATTTTAATAAAAAATTTAAC
*
13464 ATTAAAATTTTATTTTAATAATAAAATTTAAC
1 AATAAAATTTTATTTTAATAA-AAAATTTAAC
13496 AATAATAATTTTATTTT
1 AATAA-AATTTTATTTT
13513 TATTAAATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 12 0.29
32 18 0.44
33 11 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
AATAAAATTTTATTTTAATAAAAAATTTAAC
Found at i:18716 original size:40 final size:40
Alignment explanation
Indices: 18601--18719 Score: 141
Period size: 41 Copynumber: 3.0 Consensus size: 40
18591 CATGAAATTA
* *
18601 TGTTTAAAGAAAGACTTATGT-CTCAATTAGATCATAAGAT
1 TGTTTAAAGGAAGACTTAT-TACTCAATTAGAGCATAAGAT
* ** *
18641 TGTTTTAAAGGAAGACTTATGACTCCGTTAAAGCATAAGAT
1 TG-TTTAAAGGAAGACTTATTACTCAATTAGAGCATAAGAT
* *
18682 TGTTTAAAGGAAGATTTATTACTCAATTGGAGCATAAG
1 TGTTTAAAGGAAGACTTATTACTCAATTAGAGCATAAG
18720 GTTAATTTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
40 32 0.49
41 33 0.51
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (40 bp):
TGTTTAAAGGAAGACTTATTACTCAATTAGAGCATAAGAT
Found at i:19687 original size:31 final size:31
Alignment explanation
Indices: 19646--19718 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
19636 GTTTTGGGTG
*
19646 TTACATTATGTTAGTTGGATCAGAGACAACT
1 TTACACTATGTTAGTTGGATCAGAGACAACT
19677 TTACACTATGTTAGTTGGATCAGAGACAACT
1 TTACACTATGTTAGTTGGATCAGAGACAACT
*
19708 TCA-ACTATGTT
1 TTACACTATGTT
19719 CAATTCCTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 8 0.20
31 32 0.80
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.36
Consensus pattern (31 bp):
TTACACTATGTTAGTTGGATCAGAGACAACT
Found at i:21773 original size:16 final size:14
Alignment explanation
Indices: 21737--21801 Score: 62
Period size: 15 Copynumber: 4.6 Consensus size: 14
21727 TTTAAAATAT
21737 TTTAGTTTA-TTTA
1 TTTAGTTTATTTTA
21750 TTTA-TTTATTTTA
1 TTTAGTTTATTTTA
21763 GTATTAGTTTATTTTA
1 -T-TTAGTTTATTTTA
* * *
21779 TTAAATTTAATTTTT
1 TTTAGTTT-ATTTTA
21794 TTTAGTTT
1 TTTAGTTT
21802 TTCTTTCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.10
13 8 0.19
14 6 0.14
15 15 0.36
16 9 0.21
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTAGTTTATTTTA
Found at i:26836 original size:3 final size:3
Alignment explanation
Indices: 26828--26854 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
26818 AAATGTAAGT
26828 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
26855 ATCATATCTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:36016 original size:14 final size:14
Alignment explanation
Indices: 35989--36021 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35979 CAGATCAGAC
35989 CTTCCCAAACATGG
1 CTTCCCAAACATGG
36003 CTTCACCAAA-ATGG
1 CTTC-CCAAACATGG
36017 CTTCC
1 CTTCC
36022 ATTCTCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 12 0.67
15 5 0.28
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.24
Consensus pattern (14 bp):
CTTCCCAAACATGG
Found at i:38740 original size:2 final size:2
Alignment explanation
Indices: 38733--38758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38723 GGAGTAAAAT
38733 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
38759 ATAAGGGGAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43044 original size:25 final size:26
Alignment explanation
Indices: 42990--43048 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
42980 TTAATTTTTA
*
42990 AAAATAAATAAAATTAAAAAAGTTTG
1 AAAATAAATAAAATTAAAAAAGTTTC
*
43016 AAAATACA-AAAATTAAAAAA-TTGTC
1 AAAATAAATAAAATTAAAAAAGTT-TC
43041 AAAA-AAAT
1 AAAATAAAT
43049 CAGAAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 7 0.25
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (26 bp):
AAAATAAATAAAATTAAAAAAGTTTC
Found at i:57912 original size:35 final size:35
Alignment explanation
Indices: 57866--57933 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
57856 AAAGATAGTA
57866 ACTGATTTGGACATGGTCGAAATCCAATTCTAGCT
1 ACTGATTTGGACATGGTCGAAATCCAATTCTAGCT
*
57901 ACTGATTTGGACATGGTTGAAATCCAATTCTAG
1 ACTGATTTGGACATGGTCGAAATCCAATTCTAG
57934 TTCTGTTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (35 bp):
ACTGATTTGGACATGGTCGAAATCCAATTCTAGCT
Found at i:78401 original size:2 final size:2
Alignment explanation
Indices: 78389--78419 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
78379 GACAAAACAA
*
78389 GT GT CT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
78420 CGCCTAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
GT
Found at i:79451 original size:10 final size:10
Alignment explanation
Indices: 79433--79483 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
79423 ATTTTATTAA
79433 TTTTATAATT
1 TTTTATAATT
79443 TTTTATAATT
1 TTTTATAATT
**
79453 TAGTATAATT
1 TTTTATAATT
79463 TTTT-T-ATT
1 TTTTATAATT
79471 TTTTATAAATT
1 TTTTAT-AATT
79482 TT
1 TT
79484 AATTTTTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 20 0.59
11 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:79461 original size:20 final size:19
Alignment explanation
Indices: 79411--79483 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 19
79401 AGTTTTATAA
79411 AATTTTA-AATATATTTTATT
1 AATTTTATAAT-T-TTTTATT
79431 AATTTTATAATTTTTTA-T
1 AATTTTATAATTTTTTATT
79449 AATTTAGTATAATTTTTTTATT
1 AATTT--TATAA-TTTTTTATT
79471 --TTTTATAAATTTT
1 AATTTTAT-AATTTT
79484 AATTTTTAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
18 13 0.28
19 7 0.15
20 16 0.34
21 10 0.21
22 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (19 bp):
AATTTTATAATTTTTTATT
Found at i:81033 original size:29 final size:29
Alignment explanation
Indices: 80976--81033 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
80966 AATTTTAATC
*
80976 AAATAAAAATTTCATATATAAATTACACA
1 AAATAAAAATTTCATATATAAACTACACA
* *
81005 AAATCAAAATTTGCATATA-AAACTGCACA
1 AAATAAAAATTT-CATATATAAACTACACA
81034 TTAAAACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (29 bp):
AAATAAAAATTTCATATATAAACTACACA
Found at i:81426 original size:25 final size:26
Alignment explanation
Indices: 81398--81453 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
81388 ATTTTATTTT
81398 TTAAAAT-TATTTTT-AAAATTTGTAA
1 TTAAAATATATTTTTCAAAATTT-TAA
* *
81423 TT-AAATATATTTTTCAATATTTTAT
1 TTAAAATATATTTTTCAAAATTTTAA
81448 TTAAAA
1 TTAAAA
81454 AAACACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 13 0.50
26 9 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAAAATATATTTTTCAAAATTTTAA
Found at i:82025 original size:18 final size:20
Alignment explanation
Indices: 82002--82038 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
81992 TCTTTTCTCT
82002 GTTGTGTTG-GTT-AGTTTG
1 GTTGTGTTGTGTTGAGTTTG
82020 GTTGTGTTGTGTTGAGTTT
1 GTTGTGTTGTGTTGAGTTT
82039 TTTCAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.05, C:0.00, G:0.38, T:0.57
Consensus pattern (20 bp):
GTTGTGTTGTGTTGAGTTTG
Found at i:82890 original size:18 final size:18
Alignment explanation
Indices: 82867--82905 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
82857 GTAGGTGGAG
82867 GAGGATTAATCTGATATT
1 GAGGATTAATCTGATATT
*
82885 GAGGATTAATTTGATATT
1 GAGGATTAATCTGATATT
82903 GAG
1 GAG
82906 AATCAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (18 bp):
GAGGATTAATCTGATATT
Found at i:88023 original size:20 final size:20
Alignment explanation
Indices: 88000--88055 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
87990 ATAAATAATC
88000 GAATTTGAAAGGTAATAAGG
1 GAATTTGAAAGGTAATAAGG
*
88020 GAATTTGAAAGGTCATAAGG
1 GAATTTGAAAGGTAATAAGG
*
88040 GAACTTGAAAGGTAAT
1 GAATTTGAAAGGTAAT
88056 TTGGAGCATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.25
Consensus pattern (20 bp):
GAATTTGAAAGGTAATAAGG
Found at i:89883 original size:15 final size:15
Alignment explanation
Indices: 89865--89907 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
89855 TGAAAAACAC
89865 AAAATCAAAAATTAA
1 AAAATCAAAAATTAA
* *
89880 AAAATTAAAAAATAA
1 AAAATCAAAAATTAA
*
89895 ATAAATGAAAAAT
1 A-AAATCAAAAAT
89908 ATTGCTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATCAAAAATTAA
Found at i:104081 original size:59 final size:59
Alignment explanation
Indices: 103989--104106 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
103979 TTGATCAGAT
103989 CAATTAGAAGTTCACACTATCCGCCAGAAGTTATGGTAGACTCTTGATTTATTGAGTCG
1 CAATTAGAAGTTCACACTATCCGCCAGAAGTTATGGTAGACTCTTGATTTATTGAGTCG
104048 CAATTAGAAGTTCACACTATCCGCCAGAAGTTATGGTAGACTCTTGATTTATTGAGTCG
1 CAATTAGAAGTTCACACTATCCGCCAGAAGTTATGGTAGACTCTTGATTTATTGAGTCG
104107 ATCTAAGTGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (59 bp):
CAATTAGAAGTTCACACTATCCGCCAGAAGTTATGGTAGACTCTTGATTTATTGAGTCG
Found at i:108276 original size:186 final size:187
Alignment explanation
Indices: 107947--108290 Score: 467
Period size: 186 Copynumber: 1.8 Consensus size: 187
107937 TTATAAAATA
* * * * * * * *
107947 TGTCTCAGATTACATTTTAGTTATTTATGTTTGAAATGATATGTTTTAGTTATTTACGTTATCGT
1 TGTCTCAAATTACATTTTAGTTACTTATGTTTAAAATGATACGTATTAGTTACTCACATTATCGT
* ** * * *
108012 TATGTTACGAAATGATCACTCTGTCGTTAAGATCTGTTACCTCCCAAATGACAGTCTGACGTGAT
66 TATGTTACAAAATGATCACTCTACCGTTAAAATCTGTTACCTCCCAAACGACAGTCTGACGTGAC
108077 AGTTAAAATGAGTTTTAAAAGCCAACGTGAATGTTTAACAAAATTGTCACTTTTGTT
131 AGTTAAAATGAGTTTTAAAAGCCAACGTGAATGTTTAACAAAATTGTCACTTTTGTT
*
108134 TGTCTCAAATTACA-TTTAGTTACTTATGTTTAAAATGTTACGTATTAGTTACTCACATTATCGT
1 TGTCTCAAATTACATTTTAGTTACTTATGTTTAAAATGATACGTATTAGTTACTCACATTATCGT
* * * ** *
108198 TTTGTTACAAAATTATCACTCTACCGTTAAAATCTGTTATCTCCCAAACGACAGT-TCGGTGTGG
66 TATGTTACAAAATGATCACTCTACCGTTAAAATCTGTTACCTCCCAAACGACAGTCT-GACGTGA
*
108262 CAGTTAAAATGAGTTTTAAATGCCAACGT
130 CAGTTAAAATGAGTTTTAAAAGCCAACGT
108291 AAACGTTCAA
Statistics
Matches: 134, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
185 1 0.01
186 120 0.90
187 13 0.10
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (187 bp):
TGTCTCAAATTACATTTTAGTTACTTATGTTTAAAATGATACGTATTAGTTACTCACATTATCGT
TATGTTACAAAATGATCACTCTACCGTTAAAATCTGTTACCTCCCAAACGACAGTCTGACGTGAC
AGTTAAAATGAGTTTTAAAAGCCAACGTGAATGTTTAACAAAATTGTCACTTTTGTT
Found at i:108817 original size:3 final size:3
Alignment explanation
Indices: 108809--108842 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
108799 TTGGTGCGTT
108809 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
108843 CTACATTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:115350 original size:14 final size:14
Alignment explanation
Indices: 115331--115361 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
115321 GACTTAAGTT
115331 ATTTTTAGTAACCA
1 ATTTTTAGTAACCA
115345 ATTTTTAGTAACCA
1 ATTTTTAGTAACCA
115359 ATT
1 ATT
115362 GTGTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (14 bp):
ATTTTTAGTAACCA
Found at i:116796 original size:26 final size:26
Alignment explanation
Indices: 116739--116795 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
116729 ATGTATTTTC
* *
116739 TCAAAATTTTATCAGGGGTAAAATTA
1 TCAAAATGTTATCAGAGGTAAAATTA
*
116765 TCAAAATGTTATC-GAGGTGAAATTA
1 TCAAAATGTTATCAGAGGTAAAATTA
116790 TCAAAA
1 TCAAAA
116796 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (26 bp):
TCAAAATGTTATCAGAGGTAAAATTA
Found at i:120691 original size:19 final size:20
Alignment explanation
Indices: 120676--120717 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
120666 TATTTTAACT
120676 TTTTTA-AATTTATTTAATA
1 TTTTTATAATTTATTTAATA
120695 TTTTTATAA-TT-TTTAATA
1 TTTTTATAATTTATTTAATA
120713 TTTTT
1 TTTTT
120718 TTTACAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.55
19 8 0.36
20 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTATAATTTATTTAATA
Found at i:123633 original size:20 final size:19
Alignment explanation
Indices: 123608--123649 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
123598 GCATGTTTGT
123608 TTATTTTAAAAAAAATTTAA
1 TTATTTT-AAAAAAATTTAA
* *
123628 TTATTTTTAAATAATTTAA
1 TTATTTTAAAAAAATTTAA
123647 TTA
1 TTA
123650 AAGTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTTTAAAAAAATTTAA
Found at i:125050 original size:171 final size:176
Alignment explanation
Indices: 124732--125082 Score: 439
Period size: 172 Copynumber: 2.0 Consensus size: 176
124722 AGAGTAAAAT
* *
124732 TTTGAGGGGAAGTAAATAGGGGAATAAAATTTTGGAGGAAAAATATTCAAAAAAAAAAAAATTGG
1 TTTGAGGGAAAGTAAATAGGGGAATAAAATTTTAGAGGAAAAATATT---AAAAAAAAAAATT-G
* * * * *
124797 AGAGGGAGGAATGTGTTTGGGGTTGATGGGGGTGGGATGGGAGGGAATTAAAAGTTTTAGGGGGA
62 AGAGGGA-GAATGGGTTTGGGGTAGATGGGGGTGGGATGGAAGGGAAGTAAAAATTTTAGGGGGA
*
124862 AAGTGGGAGGTAGTAAAAGTTTT-GGGGAAAAAT-AAAAAGTTTTGAGGGTG
126 AAGTGGGAGGTAGTAAAAGTTTTAGGCGAAAAATAAAAAAG-TTTGAGGGTG
* * * * *
124912 TTTGA-GGAAAGTAAATGGGGGAGTAAAATTTTAGAGGGAAAATATT-AAAAACAAAATT-TGAG
1 TTTGAGGGAAAGTAAATAGGGGAATAAAATTTTAGAGGAAAAATATTAAAAAAAAAAATTGAGAG
*
124974 GGA-AATGGGTTTGGGGTAGATGGAGGGTGGGATGGAAGGGGAGTAAAAATTTT-GGGGGAAAGT
66 GGAGAATGGGTTTGGGGTAGATGG-GGGTGGGATGGAAGGGAAGTAAAAATTTTAGGGGGAAAGT
*
125037 GGGAAGG-AGTAAAAGTTTTAGGCGAAAAGTAAAAAAGTTTGAGGGT
130 GGG-AGGTAGTAAAAGTTTTAGGCGAAAAATAAAAAAGTTTGAGGGT
125083 TTGGGGTTAA
Statistics
Matches: 152, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
171 43 0.28
172 45 0.30
173 12 0.08
175 11 0.07
179 36 0.24
180 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.37, T:0.24
Consensus pattern (176 bp):
TTTGAGGGAAAGTAAATAGGGGAATAAAATTTTAGAGGAAAAATATTAAAAAAAAAAATTGAGAG
GGAGAATGGGTTTGGGGTAGATGGGGGTGGGATGGAAGGGAAGTAAAAATTTTAGGGGGAAAGTG
GGAGGTAGTAAAAGTTTTAGGCGAAAAATAAAAAAGTTTGAGGGTG
Found at i:125145 original size:19 final size:19
Alignment explanation
Indices: 125115--125170 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
125105 TATAGTTTGA
125115 TATTCG-GTTTATTCGAAT
1 TATTCGAGTTTATTCGAAT
125133 TATTCGAGTTTATTCGAAT
1 TATTCGAGTTTATTCGAAT
*
125152 TATTCAAG-TTATTCGAAT
1 TATTCGAGTTTATTCGAAT
125170 T
1 T
125171 TGAAAACTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 17 0.47
19 19 0.53
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (19 bp):
TATTCGAGTTTATTCGAAT
Found at i:125154 original size:9 final size:9
Alignment explanation
Indices: 125123--125170 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
125113 GATATTCGGT
125123 TTATTCGAA
1 TTATTCGAA
*
125132 TTATTCGAGT
1 TTATTCGA-A
125142 TTATTCGAA
1 TTATTCGAA
125151 TTATTC-AA
1 TTATTCGAA
125159 GTTATTCGAA
1 -TTATTCGAA
125169 TT
1 TT
125171 TGAAAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 2 0.06
9 22 0.65
10 10 0.29
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:125661 original size:19 final size:19
Alignment explanation
Indices: 125634--125693 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 19
125624 TATGCCAGAT
* *
125634 ATGCGCTTTGTGCGCCATG
1 ATGCACTTTGTGTGCCATG
125653 ATGCACTTTGTGTGCCATG
1 ATGCACTTTGTGTGCCATG
*
125672 ATGCACTTTGTGTGCCAAG
1 ATGCACTTTGTGTGCCATG
125691 ATG
1 ATG
125694 TGCTTCATGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (19 bp):
ATGCACTTTGTGTGCCATG
Found at i:126048 original size:66 final size:66
Alignment explanation
Indices: 125942--126073 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
125932 CCTTGGGGGC
125942 CCAAACGGATATGAATGAGTTGGTAGACTCCAAAATTTAGTGAATAATGTGATATTAAGAAGTGA
1 CCAAACGGATATGAATGAGTTGGTAGACTCCAAAATTTAGTGAATAATGTGATATTAAGAAGTGA
126007 A
66 A
126008 CCAAACGGATATGAATGAGTTGGTAGACTCCAAAATTTAGTGAATAATGTGATATTAAGAAGTGA
1 CCAAACGGATATGAATGAGTTGGTAGACTCCAAAATTTAGTGAATAATGTGATATTAAGAAGTGA
126073 A
66 A
126074 TTATATGTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (66 bp):
CCAAACGGATATGAATGAGTTGGTAGACTCCAAAATTTAGTGAATAATGTGATATTAAGAAGTGA
A
Found at i:127108 original size:30 final size:31
Alignment explanation
Indices: 127041--127125 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
127031 TATTTAATTT
* * *
127041 TTTTTTGTTCAATTTGATACTTAAACTTGATA
1 TTTTTTCTT-AATTTGATACCTAAACTTGACA
*
127073 TTTTTTCTTAATTTGGTACCTAAAC-TGACA
1 TTTTTTCTTAATTTGATACCTAAACTTGACA
* *
127103 TTTTTTTTTAATTTGATAGCTAA
1 TTTTTTCTTAATTTGATACCTAA
127126 TTTTTTTAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
30 24 0.52
31 14 0.30
32 8 0.17
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (31 bp):
TTTTTTCTTAATTTGATACCTAAACTTGACA
Found at i:128957 original size:21 final size:21
Alignment explanation
Indices: 128931--128970 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
128921 TAGAGGATGC
128931 TGAATTCGTTAAAAAGAAATA
1 TGAATTCGTTAAAAAGAAATA
*
128952 TGAATTCGTTATAAAGAAA
1 TGAATTCGTTAAAAAGAAA
128971 ACTACTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (21 bp):
TGAATTCGTTAAAAAGAAATA
Found at i:136615 original size:147 final size:147
Alignment explanation
Indices: 136348--136644 Score: 558
Period size: 147 Copynumber: 2.0 Consensus size: 147
136338 ATAAATGTAT
*
136348 TAATGATGTTAATGAAATATTAATTGTGATTATCACATGAATAAAAAATACTATACCATTCTATT
1 TAATGATGTTAATGAAATATTAATTGTGATTATCACATGAATAAAAAATACTATACCATTCGATT
* *
136413 ACAATTAAACATAATTTATATCATTAAGAAAACCTAAAAGTATGAATTCATAATTAATCAATATT
66 ACAATTAAACATAAATTATATCACTAAGAAAACCTAAAAGTATGAATTCATAATTAATCAATATT
136478 GAAAATTAAAACCCTAA
131 GAAAATTAAAACCCTAA
*
136495 TAATGATGTTAATGAAATATTAATTGTGATTATCACATGAATAAAAAATACTATACCCTTCGATT
1 TAATGATGTTAATGAAATATTAATTGTGATTATCACATGAATAAAAAATACTATACCATTCGATT
136560 ACAATTAAACATAAATTATATCACTAAGAAAACCTAAAAGTATGAATTCATAATTAATCAATATT
66 ACAATTAAACATAAATTATATCACTAAGAAAACCTAAAAGTATGAATTCATAATTAATCAATATT
136625 GAAAATTAAAACCCTAA
131 GAAAATTAAAACCCTAA
136642 TAA
1 TAA
136645 ATATAAATCC
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (147 bp):
TAATGATGTTAATGAAATATTAATTGTGATTATCACATGAATAAAAAATACTATACCATTCGATT
ACAATTAAACATAAATTATATCACTAAGAAAACCTAAAAGTATGAATTCATAATTAATCAATATT
GAAAATTAAAACCCTAA
Found at i:146983 original size:17 final size:16
Alignment explanation
Indices: 146958--146988 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
146948 TTTCTTTTTT
*
146958 TTTTTTTTTTAAAATA
1 TTTTTATTTTAAAATA
146974 TTTTTATTTTAAAAT
1 TTTTTATTTTAAAAT
146989 CTAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTATTTTAAAATA
Found at i:148298 original size:22 final size:22
Alignment explanation
Indices: 148273--148314 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
148263 AATTAAATAA
*
148273 TTTCTTTTACGAGATTTAAGAT
1 TTTCTTTAACGAGATTTAAGAT
*
148295 TTTCTTTAACGAGTTTTAAG
1 TTTCTTTAACGAGATTTAAG
148315 GTTTGAAAAT
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:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTCTTTAACGAGATTTAAGAT
Found at i:152528 original size:32 final size:32
Alignment explanation
Indices: 152455--152530 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
152445 AATGTAGGGT
* * * *
152455 ATTTTGGGTTTTAGATTTCAAAATTTTTGGGA
1 ATTTTGGGATTTAGATTTCAAAAATTTCGAGA
* * *
152487 ATTTGGGGATTTAGGTTTTAAAAATTTCGAGA
1 ATTTTGGGATTTAGATTTCAAAAATTTCGAGA
*
152519 TTTTTGGGATTT
1 ATTTTGGGATTT
152531 TTAAGGTTGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.03, G:0.24, T:0.49
Consensus pattern (32 bp):
ATTTTGGGATTTAGATTTCAAAAATTTCGAGA
Found at i:152575 original size:63 final size:62
Alignment explanation
Indices: 152496--152647 Score: 198
Period size: 62 Copynumber: 2.4 Consensus size: 62
152486 AATTTGGGGA
* * * * *
152496 TTTAGGTTTTAAAAATTTCGAGATTTTTGGGATTTTTAAGGTTGTTGGGTTTGGGGAATTCGG
1 TTTAGG-TTTAAAAATTTGGGGATTTTCGAGATTTTTAAGGTTGTTGGGCTTGGGGAATTCGG
* * *
152559 TTTAGGTTTAAGAAATTTGGGGA-TTTCGAGATTTTTGAGGTTGTTGGGCTTGGGGATTTTGG
1 TTTAGGTTTAA-AAATTTGGGGATTTTCGAGATTTTTAAGGTTGTTGGGCTTGGGGAATTCGG
*
152621 TTTAAGTTTAAAAATTTGGGGATTTTC
1 TTTAGGTTTAAAAATTTGGGGATTTTC
152648 AGGACTTAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
61 11 0.14
62 52 0.67
63 15 0.19
ACGTcount: A:0.21, C:0.03, G:0.30, T:0.45
Consensus pattern (62 bp):
TTTAGGTTTAAAAATTTGGGGATTTTCGAGATTTTTAAGGTTGTTGGGCTTGGGGAATTCGG
Found at i:154015 original size:23 final size:23
Alignment explanation
Indices: 153985--154037 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
153975 AATGACCTAA
153985 ACAAAACGATAAGGGCCAAAATG
1 ACAAAACGATAAGGGCCAAAATG
154008 ACAAAACGATAAGGGCCAAAATG
1 ACAAAACGATAAGGGCCAAAATG
154031 ACAAAAC
1 ACAAAAC
154038 CACCAAACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.55, C:0.19, G:0.19, T:0.08
Consensus pattern (23 bp):
ACAAAACGATAAGGGCCAAAATG
Found at i:156438 original size:19 final size:17
Alignment explanation
Indices: 156416--156466 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
156406 AAAATAGAGG
*
156416 AAAAACGAGAAAAAGGGA
1 AAAAAAGAGAAAAA-GGA
*
156434 AAAAAAGAAGATAAAGGA
1 AAAAAAG-AGAAAAAGGA
156452 AAAACAAGAGAAAAA
1 AAAA-AAGAGAAAAA
156467 AACCTTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.02
Consensus pattern (17 bp):
AAAAAAGAGAAAAAGGA
Found at i:167844 original size:22 final size:21
Alignment explanation
Indices: 167799--167846 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
167789 GTTAGACTTT
*
167799 CATTATTAAGCTTAATTAACC
1 CATTTTTAAGCTTAATTAACC
* *
167820 CATTTTTAATCTTGATTAAACC
1 CATTTTTAAGCTTAATT-AACC
167842 CATTT
1 CATTT
167847 ATACTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (21 bp):
CATTTTTAAGCTTAATTAACC
Found at i:170345 original size:9 final size:9
Alignment explanation
Indices: 170333--170438 Score: 54
Period size: 10 Copynumber: 10.9 Consensus size: 9
170323 ATACAAATCA
170333 ATAAAAATT
1 ATAAAAATT
170342 AT-AAAATT
1 ATAAAAATT
**
170350 AATTAAATTTT
1 -A-TAAAAATT
170361 AATAAAAA-T
1 -ATAAAAATT
170370 ATTAAAAATT
1 A-TAAAAATT
*
170380 AGAAAAAATT
1 A-TAAAAATT
170390 ATAAAAATCAT
1 ATAAAAAT--T
*
170401 AAAAAGAATT
1 ATAAA-AATT
170411 ATAAAAAATT
1 AT-AAAAATT
* *
170421 GTAAAATTTT
1 ATAAAA-ATT
170431 ATAAAAAT
1 ATAAAAAT
170439 CGTAAAAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
8 7 0.09
9 21 0.28
10 29 0.39
11 14 0.19
12 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:170356 original size:19 final size:18
Alignment explanation
Indices: 170334--170405 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
170324 TACAAATCAA
*
170334 TAAAAATTATAAAATTAAT
1 TAAAAATTATAAAAAT-AT
**
170353 TAAATTTTAATAAAAATAT
1 TAAAAATT-ATAAAAATAT
*
170372 TAAAAATTAGAAAAA-ATT
1 TAAAAATTATAAAAATA-T
*
170390 ATAAAAATCATAAAAA
1 -TAAAAATTATAAAAA
170406 GAATTATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.02
18 7 0.17
19 27 0.64
20 7 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (18 bp):
TAAAAATTATAAAAATAT
Found at i:170405 original size:10 final size:10
Alignment explanation
Indices: 170354--170455 Score: 64
Period size: 10 Copynumber: 10.0 Consensus size: 10
170344 AAAATTAATT
*
170354 AAATTTTAATA
1 AAATTATAA-A
* *
170365 AAAATATTAA
1 AAATTATAAA
*
170375 AAATTAGAAA
1 AAATTATAAA
170385 AAATTAT-AA
1 AAATTATAAA
*
170394 AAATCATAAAA
1 AAATTAT-AAA
170405 AGAATTATAAA
1 A-AATTATAAA
*
170416 AAATTGTAAA
1 AAATTATAAA
**
170426 ATTTTAT-AA
1 AAATTATAAA
**
170435 AAATCGTAAA
1 AAATTATAAA
170445 AAATTTATAAA
1 AAA-TTATAAA
170456 CTATATAGAA
Statistics
Matches: 67, Mismatches: 19, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
9 13 0.19
10 31 0.46
11 18 0.27
12 5 0.07
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (10 bp):
AAATTATAAA
Found at i:170438 original size:19 final size:20
Alignment explanation
Indices: 170382--170455 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
170372 TAAAAATTAG
*
170382 AAAAAA-TTATAAAAATCAT
1 AAAAAATTTATAAAAATCGT
* *
170401 AAAAAGAATTATAAAAAATTGT
1 AAAAA-ATTTAT-AAAAATCGT
*
170423 -AAAATTTTATAAAAATCGT
1 AAAAAATTTATAAAAATCGT
170442 AAAAAATTTATAAA
1 AAAAAATTTATAAA
170456 CTATATAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 13 0.29
20 17 0.38
21 8 0.18
22 7 0.16
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAAAATTTATAAAAATCGT
Found at i:170462 original size:29 final size:29
Alignment explanation
Indices: 170412--170467 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
170402 AAAAGAATTA
* *
170412 TAAAAAATTGTAAAATTTTATAAAAATCG
1 TAAAAAATTGTAAAACTATATAAAAATCG
*
170441 TAAAAAATT-TATAAACTATATAGAAAT
1 TAAAAAATTGTA-AAACTATATAAAAAT
170468 ATAGGATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAAAAATTGTAAAACTATATAAAAATCG
Found at i:170523 original size:19 final size:20
Alignment explanation
Indices: 170491--170547 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
170481 TTATAAAGTC
*
170491 GTAAGAAAATTATAAAAAAT
1 GTAAAAAAATTATAAAAAAT
* **
170511 GTAAAGAAA-TATAAAATTT
1 GTAAAAAAATTATAAAAAAT
170530 GTAAAAAAATTATAAAAA
1 GTAAAAAAATTATAAAAA
170548 TTTTCATACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAAAT
Found at i:170754 original size:19 final size:19
Alignment explanation
Indices: 170732--170889 Score: 92
Period size: 20 Copynumber: 8.2 Consensus size: 19
170722 TTTTGATGCA
*
170732 TTTTATAAATTTTTATGAT
1 TTTTATAAATTTTTATAAT
* * *
170751 TTTTATAAAATTTTACAACG
1 TTTTATAAATTTTTATAA-T
* *
170771 TTTTATAATTTATTTATGAT
1 TTTTATAAATT-TTTATAAT
*
170791 TTTTATAATTATTTTTCTAAT
1 TTTTATAA--ATTTTTATAAT
* * *
170812 TTTAATAAATTTTAAATATT
1 TTTTATAAATTTT-TATAAT
* *
170832 TTTTATTAAAATTTAATAA-
1 TTTTA-TAAATTTTTATAAT
* *
170851 TTTAAT-AACTTTTATTAA-
1 TTTTATAAATTTTTA-TAAT
170869 TTTT-T-AATTTTTATAAT
1 TTTTATAAATTTTTATAAT
170886 TTTT
1 TTTT
170890 TTTTTATCAT
Statistics
Matches: 107, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
16 3 0.03
17 18 0.17
18 7 0.07
19 24 0.22
20 28 0.26
21 25 0.23
22 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTTTTATAAT
Found at i:170794 original size:20 final size:19
Alignment explanation
Indices: 170732--170824 Score: 78
Period size: 19 Copynumber: 4.7 Consensus size: 19
170722 TTTTGATGCA
170732 TTTTATAAATTTTTATGAT
1 TTTTATAAATTTTTATGAT
* ** *
170751 TTTTATAAAATTTTACAACG
1 TTTTATAAATTTTTATGA-T
*
170771 TTTTATAATTTATTTATGAT
1 TTTTATAAATT-TTTATGAT
* *
170791 TTTTATAATTATTTTTCTAAT
1 TTTTATAA--ATTTTTATGAT
*
170812 TTTAATAAATTTT
1 TTTTATAAATTTT
170825 AAATATTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 20 0.35
20 17 0.30
21 18 0.32
22 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTATAAATTTTTATGAT
Found at i:170815 original size:40 final size:37
Alignment explanation
Indices: 170731--170824 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 37
170721 TTTTTGATGC
170731 ATTTTATAAATTTTTATGATTTTTATAAAATTTTACA
1 ATTTTATAAATTTTTATGATTTTTATAAAATTTTACA
* * *
170768 ACGTTTTATAATTTATTTATGATTTTTATAATTATTTTTCTA
1 A--TTTTATAAATT-TTTATGATTTTTATAA-AATTTTAC-A
170810 ATTTTAATAAATTTT
1 ATTTT-ATAAATTTT
170825 AAATATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
37 1 0.02
39 10 0.21
40 22 0.47
41 12 0.26
42 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (37 bp):
ATTTTATAAATTTTTATGATTTTTATAAAATTTTACA
Found at i:170825 original size:10 final size:10
Alignment explanation
Indices: 170809--170876 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
170799 TTATTTTTCT
170809 AATTTTAATA
1 AATTTTAATA
170819 AATTTTAAATA
1 AATTTT-AATA
** *
170830 TTTTTTATTA
1 AATTTTAATA
*
170840 AAATTTAAT-
1 AATTTTAATA
170849 AA-TTTAATA
1 AATTTTAATA
* *
170858 ACTTTTATTA
1 AATTTTAATA
*
170868 ATTTTTAAT
1 AATTTTAAT
170877 TTTTATAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
8 6 0.14
9 3 0.07
10 27 0.61
11 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (10 bp):
AATTTTAATA
Found at i:170857 original size:28 final size:31
Alignment explanation
Indices: 170812--170868 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 31
170802 TTTTTCTAAT
**
170812 TTTAATAAATTTTAAATATTTTTTATTAAAA
1 TTTAATAAATTTTAAATAACTTTTATTAAAA
170843 TTTAAT-AA-TTT-AATAACTTTTATTAA
1 TTTAATAAATTTTAAATAACTTTTATTAA
170869 TTTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 3 0.12
30 2 0.08
31 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTAATAAATTTTAAATAACTTTTATTAAAA
Found at i:170885 original size:9 final size:9
Alignment explanation
Indices: 170732--170889 Score: 61
Period size: 9 Copynumber: 16.4 Consensus size: 9
170722 TTTTGATGCA
170732 TTTTATAAAT
1 TTTTAT-AAT
*
170742 TTTTATGAT
1 TTTTATAAT
*
170751 TTTTATAAAA
1 TTTTAT-AAT
* *
170761 TTTTACAACG
1 TTTTATAA-T
170771 TTTTATAATT
1 TTTTATAA-T
*
170781 TATTTATGAT
1 T-TTTATAAT
170791 TTTTATAATTAT
1 TTTTAT-A--AT
*
170803 TTTTCTAAT
1 TTTTATAAT
*
170812 TTTAATAAAT
1 TTTTAT-AAT
* *
170822 TTTAAATATT
1 TTT-TATAAT
*
170832 TTTTATTAAAA
1 TTTTA-T-AAT
*
170843 TTTAATAA-
1 TTTTATAAT
* *
170851 TTTAATAAC
1 TTTTATAAT
170860 TTTTATTAA-
1 TTTTA-TAAT
170869 TTTT-TAAT
1 TTTTATAAT
170877 TTTTATAAT
1 TTTTATAAT
170886 TTTT
1 TTTT
170890 TTTTTATCAT
Statistics
Matches: 115, Mismatches: 19, Indels: 29
0.71 0.12 0.18
Matches are distributed among these distances:
7 3 0.03
8 12 0.10
9 40 0.35
10 38 0.33
11 15 0.13
12 7 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:170891 original size:28 final size:28
Alignment explanation
Indices: 170789--170891 Score: 70
Period size: 28 Copynumber: 3.6 Consensus size: 28
170779 TTTATTTATG
*
170789 ATTTTTATAATTATTTTT-CTAATTTTAATA
1 ATTTTTATAATT-TTTTTATTAATTTT--TA
* **
170819 AATTTTA-AATATTTTTTATTAAAATTTA
1 ATTTTTATAAT-TTTTTTATTAATTTTTA
* *
170847 ATAATTTAATAA--CTTTTATTAATTTTTA
1 AT--TTTTATAATTTTTTTATTAATTTTTA
170875 ATTTTTATAATTTTTTT
1 ATTTTTATAATTTTTTT
170892 TTTATCATAT
Statistics
Matches: 55, Mismatches: 11, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
26 7 0.13
28 22 0.40
29 8 0.15
30 16 0.29
31 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTTATAATTTTTTTATTAATTTTTA
Found at i:176885 original size:17 final size:17
Alignment explanation
Indices: 176799--176875 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
176789 CCCAATTAGC
* *
176799 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
176816 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
* *
176833 TTAAATTTGGTT-GAAAT
1 TTAAATTT-ATTATAAAT
176850 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
176867 TTAAATTTA
1 TTAAATTTA
176876 AAATTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.04
17 46 0.92
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Done.