Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2678
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: 95644
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Found at i:4301 original size:34 final size:34
Alignment explanation
Indices: 4263--4398 Score: 254
Period size: 34 Copynumber: 4.0 Consensus size: 34
4253 CTTTGTTAAG
4263 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
4297 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
4331 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
* *
4365 TGTGTTTGGTGAGAATGTTAAGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
4399 GAATGTTAGG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 100 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:4391 original size:22 final size:22
Alignment explanation
Indices: 4365--4420 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
4355 TGTTAGGTGA
*
4365 TGTGTTTGGTGAGAATGTTAAG
1 TGTGTTAGGTGAGAATGTTAAG
*
4387 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAAG
*
4409 TGTGCTAGGTGA
1 TGTGTTAGGTGA
4421 TGTATTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.02, G:0.39, T:0.38
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAAG
Found at i:4402 original size:56 final size:56
Alignment explanation
Indices: 4338--4449 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
4328 TGATGTATTT
* *
4338 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAAGTGTGTTA
1 GGTGAGAATGTTAGGTGTGCTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTA
*
4394 GGTGAGAATGTTAGGTGTGCTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGCTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTA
4450 ACATGTATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.21, C:0.01, G:0.39, T:0.38
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGCTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTA
Found at i:4432 original size:68 final size:66
Alignment explanation
Indices: 4266--4449 Score: 199
Period size: 68 Copynumber: 2.9 Consensus size: 66
4256 TGTTAAGTGT
* *
4266 ATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 ATTTGGT-AG-ATGCTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTAGGTGA
*
4331 TGT
64 TGA
* *
4334 ATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAAGTGTGTTAGGTGA
1 ATTTGGT-AG-ATGCTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTAGGTGA
4399 -GA
64 TGA
* *
4401 A-----T-G-T--TAGGTGTGCTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 ATTTGGTAGATGCTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTA
4450 ACATGTATAT
Statistics
Matches: 110, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
56 42 0.38
58 1 0.01
60 1 0.01
62 1 0.01
67 2 0.02
68 63 0.57
ACGTcount: A:0.21, C:0.01, G:0.38, T:0.40
Consensus pattern (66 bp):
ATTTGGTAGATGCTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAAGTGTGTTAGGTGATG
A
Found at i:9143 original size:52 final size:52
Alignment explanation
Indices: 9066--9167 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
9056 GAATTTAAAT
* * *
9066 AATAAAAAAAATTATCTTTAACTTTTTATTAGTCTGTG-TTATTGAAATTGA
1 AATAAAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATTGA
** * *
9117 AATAGAAAAAAATTAGCTTTGGCTTTTTGTTAATCTGAGTTTTTTGAAATT
1 AATA-AAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATT
9168 TTGGTTAGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 4 0.10
52 28 0.67
53 10 0.24
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (52 bp):
AATAAAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATTGA
Found at i:9179 original size:26 final size:26
Alignment explanation
Indices: 9140--9202 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
9130 TAGCTTTGGC
* * *
9140 TTTTTGTTAATCTGAGTTTTTTGAAA
1 TTTTGGTTAGTCTGAGTTTTTTAAAA
9166 TTTTGGTTAGTCTGAGTTTTTTAAAA
1 TTTTGGTTAGTCTGAGTTTTTTAAAA
*
9192 TTTTGTTTAGT
1 TTTTGGTTAGT
9203 TCGTGATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.03, G:0.17, T:0.59
Consensus pattern (26 bp):
TTTTGGTTAGTCTGAGTTTTTTAAAA
Found at i:9960 original size:17 final size:16
Alignment explanation
Indices: 9926--9971 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
9916 TAGAGGAAAA
*
9926 TTATGAAA-CTACTTT
1 TTATGAAATCTACTCT
9941 TTATGAAATTCTACTCT
1 TTATGAAA-TCTACTCT
9958 TTATGAAACTCTAC
1 TTATGAAA-TCTAC
9972 AGTGTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.30
17 19 0.70
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (16 bp):
TTATGAAATCTACTCT
Found at i:10173 original size:21 final size:21
Alignment explanation
Indices: 10132--10177 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10122 TCAGAAGTGT
*
10132 TATTTCTTTTAACCTTGATAA
1 TATTTCTTTTAACCTTAATAA
10153 TATTTCATTTTAACC-TAATAA
1 TATTTC-TTTTAACCTTAATAA
10174 -ATTT
1 TATTT
10178 AGGTGGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTCTTTTAACCTTAATAA
Found at i:10677 original size:46 final size:46
Alignment explanation
Indices: 10621--10712 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
10611 CTTCCAATGT
* *
10621 ATTTGAGCTTGGCATCAATCAAATGAATCTCG-AGTAAATTTGTTA
1 ATTTGAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
**
10666 ATTTCGAGCTTGACATCAATAAAATGAATCTCGTAGTAGTTTTGTTA
1 ATTT-GAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
10713 TTTAGGTGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 4 0.10
46 26 0.63
47 11 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (46 bp):
ATTTGAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
Found at i:23686 original size:23 final size:21
Alignment explanation
Indices: 23650--23698 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
23640 AATATTTTAA
23650 TTAAAAATTAATAATGAAAATAT
1 TTAAAAATTAATAA--AAAATAT
*
23673 TTAAAAA-TATATAAATAATAT
1 TTAAAAATTA-ATAAAAAATAT
23694 TTAAA
1 TTAAA
23699 TAAATCAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAAAATTAATAAAAAATAT
Found at i:23698 original size:11 final size:11
Alignment explanation
Indices: 23668--23701 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
23658 TAATAATGAA
23668 AATATTTAAA-
1 AATATTTAAAT
*
23678 AATATATAAAT
1 AATATTTAAAT
23689 AATATTTAAAT
1 AATATTTAAAT
23700 AA
1 AA
23702 ATCAACTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATTTAAAT
Found at i:29819 original size:32 final size:30
Alignment explanation
Indices: 29770--29829 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
29760 TGTCACTACA
29770 GTCAAGTTTGGTAGAAAAAAAATATTTCACCG
1 GTCAAGTTTGGTAG--AAAAAATATTTCACCG
* *
29802 GTCAGGTTTGGTTGAAAAAATATTTCAC
1 GTCAAGTTTGGTAGAAAAAATATTTCAC
29830 TCATGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
32 12 0.46
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (30 bp):
GTCAAGTTTGGTAGAAAAAATATTTCACCG
Found at i:35381 original size:16 final size:16
Alignment explanation
Indices: 35332--35387 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
35322 GATTTAAATA
*
35332 TAAATATGAAATATTT
1 TAAATATAAAATATTT
* * *
35348 AAAAAAGT-AAAT-TAT
1 TAAATA-TAAAATATTT
35363 TAAATATAAAATATTT
1 TAAATATAAAATATTT
35379 TAAATATAA
1 TAAATATAA
35388 TAAATAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 19 0.61
17 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:43785 original size:52 final size:52
Alignment explanation
Indices: 43708--43809 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
43698 GAATTTAAAT
* *
43708 AATAAAAAAAATTAGCTTTAACTTTTTATTAGTCTGTG-TTATTGAAATTGA
1 AATAAAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATTGA
** * *
43759 AATAGAAAAAAATTAGCTTTGGCTTTTTGTTAATCTGAGTTTTTTGAAATT
1 AATA-AAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATT
43810 TTGGTTAGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 4 0.09
52 29 0.67
53 10 0.23
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (52 bp):
AATAAAAAAAATTAGCTTTAACTTTTTATTAATCTGAGTTTATTGAAATTGA
Found at i:43821 original size:26 final size:26
Alignment explanation
Indices: 43782--43844 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
43772 TAGCTTTGGC
* * *
43782 TTTTTGTTAATCTGAGTTTTTTGAAA
1 TTTTGGTTAGTCTGAGTTTTTTAAAA
43808 TTTTGGTTAGTCTGAGTTTTTTAAAA
1 TTTTGGTTAGTCTGAGTTTTTTAAAA
*
43834 TTTTGTTTAGT
1 TTTTGGTTAGT
43845 TCGTGATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.21, C:0.03, G:0.17, T:0.59
Consensus pattern (26 bp):
TTTTGGTTAGTCTGAGTTTTTTAAAA
Found at i:44603 original size:17 final size:16
Alignment explanation
Indices: 44569--44614 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
44559 TAGAGGAAAA
*
44569 TTATGAAA-CTACTTT
1 TTATGAAATCTACTCT
44584 TTATGAAATTCTACTCT
1 TTATGAAA-TCTACTCT
44601 TTATGAAACTCTAC
1 TTATGAAA-TCTAC
44615 AGTGTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.30
17 19 0.70
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (16 bp):
TTATGAAATCTACTCT
Found at i:44816 original size:21 final size:21
Alignment explanation
Indices: 44775--44820 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
44765 TCAGAAGTGT
*
44775 TATTTCTTTTAACCTTGATAA
1 TATTTCTTTTAACCTTAATAA
44796 TATTTCATTTTAACC-TAATAA
1 TATTTC-TTTTAACCTTAATAA
44817 -ATTT
1 TATTT
44821 AGGTGGGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTTCTTTTAACCTTAATAA
Found at i:45320 original size:46 final size:46
Alignment explanation
Indices: 45264--45355 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
45254 CTTCCAATGT
* *
45264 ATTTGAGCTTGGCATCAATCAAATGAATCTCG-AGTAAATTTGTTA
1 ATTTGAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
**
45309 ATTTCGAGCTTGACATCAATAAAATGAATCTCGTAGTAGTTTTGTTA
1 ATTT-GAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
45356 TTTAGGTGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 4 0.10
46 26 0.63
47 11 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (46 bp):
ATTTGAGCTTGACATCAATAAAATGAATCTCGTAGTAAATTTGTTA
Found at i:58350 original size:23 final size:21
Alignment explanation
Indices: 58314--58362 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
58304 AATATTTTAA
58314 TTAAAAATTAATAATGAAAATAT
1 TTAAAAATTAATAA--AAAATAT
*
58337 TTAAAAA-TATATAAATAATAT
1 TTAAAAATTA-ATAAAAAATAT
58358 TTAAA
1 TTAAA
58363 TAAATCAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAAAATTAATAAAAAATAT
Found at i:58362 original size:11 final size:11
Alignment explanation
Indices: 58332--58365 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
58322 TAATAATGAA
58332 AATATTTAAA-
1 AATATTTAAAT
*
58342 AATATATAAAT
1 AATATTTAAAT
58353 AATATTTAAAT
1 AATATTTAAAT
58364 AA
1 AA
58366 ATCAACTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATTTAAAT
Found at i:64487 original size:32 final size:30
Alignment explanation
Indices: 64438--64497 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
64428 TGTCACTACA
64438 GTCAAGTTTGGTAGAAAAAAAATATTTCACCG
1 GTCAAGTTTGGTAG--AAAAAATATTTCACCG
* *
64470 GTCAGGTTTGGTTGAAAAAATATTTCAC
1 GTCAAGTTTGGTAGAAAAAATATTTCAC
64498 TCATGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
32 12 0.46
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (30 bp):
GTCAAGTTTGGTAGAAAAAATATTTCACCG
Found at i:70048 original size:16 final size:16
Alignment explanation
Indices: 69999--70054 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
69989 GATTTAAATA
*
69999 TAAATATGAAATATTT
1 TAAATATAAAATATTT
* * *
70015 AAAAAAGT-AAAT-TAT
1 TAAATA-TAAAATATTT
70030 TAAATATAAAATATTT
1 TAAATATAAAATATTT
70046 TAAATATAA
1 TAAATATAA
70055 TAAATAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 19 0.61
17 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:77004 original size:10 final size:10
Alignment explanation
Indices: 76987--77024 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
76977 TTGTTCATTA
*
76987 AATT-AAATT
1 AATTAAAATC
76996 AATTAAAATC
1 AATTAAAATC
77006 AATTAAAATC
1 AATTAAAATC
77016 AATTAAAAT
1 AATTAAAAT
77025 GAAAAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 4 0.15
10 23 0.85
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTAAAATC
Found at i:77858 original size:11 final size:11
Alignment explanation
Indices: 77842--77876 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
77832 TATGTAATAT
77842 TTTTATTTTTA
1 TTTTATTTTTA
77853 TTTTATTTTTA
1 TTTTATTTTTA
*
77864 TTCTA-TTTTA
1 TTTTATTTTTA
77874 TTT
1 TTT
77877 CAAGGAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:78651 original size:11 final size:12
Alignment explanation
Indices: 78630--78667 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
78620 TAAATTAATT
78630 TTTTAAAATATA
1 TTTTAAAATATA
78642 TTTT-AAATATA
1 TTTTAAAATATA
*
78653 TATTTGAAATATA
1 T-TTTAAAATATA
78666 TT
1 TT
78668 ATTTAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.33
12 8 0.33
13 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTTAAAATATA
Found at i:78874 original size:2 final size:2
Alignment explanation
Indices: 78867--78896 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
78857 ATCACTGATA
78867 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
78897 TTGGATTCAA
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:82614 original size:22 final size:23
Alignment explanation
Indices: 82571--82618 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
82561 TATTTTTATA
82571 TTTTTATAATTAAATTTAAATAAT
1 TTTTTATAATTAAA-TTAAATAAT
82595 TTTTTATTAATTAAA-T-AATAAT
1 TTTTTA-TAATTAAATTAAATAAT
82617 TT
1 TT
82619 GAGTCGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
23 1 0.04
24 6 0.26
25 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTATAATTAAATTAAATAAT
Found at i:82996 original size:16 final size:16
Alignment explanation
Indices: 82947--83002 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
82937 GATTTAAATA
*
82947 TAAATATGAAATATTT
1 TAAATATAAAATATTT
* * *
82963 AAAAAAGT-AAAT-TAT
1 TAAATA-TAAAATATTT
82978 TAAATATAAAATATTT
1 TAAATATAAAATATTT
82994 TAAATATAA
1 TAAATATAA
83003 TAAATAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 19 0.61
17 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:90425 original size:34 final size:34
Alignment explanation
Indices: 90387--90522 Score: 254
Period size: 34 Copynumber: 4.0 Consensus size: 34
90377 CTTTGTTAAG
90387 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
90421 TGTATTTGGTGAGAATGTTATGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
90455 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
90489 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
90523 GAATGTTAGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 99 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:90454 original size:22 final size:22
Alignment explanation
Indices: 90428--90544 Score: 87
Period size: 22 Copynumber: 5.2 Consensus size: 22
90418 TGATGTATTT
90428 GGTGAGAATGTTATGTGTGTTA
1 GGTGAGAATGTTATGTGTGTTA
* * *
90450 GGTGATGTAT-TTGGTGAGAATGTTA
1 GGTGA-GAATGTT-ATGTG--TGTTA
* * * *
90475 GGTGTGTTAGGTGATGTGT-TT-
1 GGTGAG-AATGTTATGTGTGTTA
*
90496 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTATGTGTGTTA
*
90518 GGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTATGTGTGTTA
90540 GGTGA
1 GGTGA
90545 TGTATTTGGT
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
20 8 0.11
21 7 0.09
22 36 0.49
23 7 0.09
24 1 0.01
25 14 0.19
26 1 0.01
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.39
Consensus pattern (22 bp):
GGTGAGAATGTTATGTGTGTTA
Found at i:90488 original size:56 final size:54
Alignment explanation
Indices: 90462--90573 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 54
90452 TGATGTATTT
90462 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGT-AG-ATGTTAGGTGTGTTA
*
90518 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGT-AG-ATGTTAGGTGTGTTA
90574 ACATGTATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.39
Consensus pattern (54 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTAGATGTTAGGTGTGTTA
Found at i:91973 original size:35 final size:30
Alignment explanation
Indices: 91919--92007 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 30
91909 CTCTAACAGT
*
91919 CACCTAA-ACACATTAACATTCTCACAAAACACA
1 CACCTAACACAC-CTAACATTCTCAC--AA-ACA
*
91952 GCACCTAACACCACCTAACATTCTCACAAATA
1 -CACCTAACA-CACCTAACATTCTCACAAACA
91984 CACCTAACACACC-AACATTCTCAC
1 CACCTAACACACCTAACATTCTCAC
92008 CACATAACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
29 11 0.22
30 4 0.08
31 9 0.18
32 2 0.04
33 2 0.04
34 7 0.14
35 13 0.25
36 3 0.06
ACGTcount: A:0.43, C:0.38, G:0.01, T:0.18
Consensus pattern (30 bp):
CACCTAACACACCTAACATTCTCACAAACA
Done.