Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011905.1 Kokia drynarioides strain JFW-HI SEQ_126903, 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: 186543
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:20878 original size:21 final size:21
Alignment explanation
Indices: 20852--20895 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20842 TCATTCATCA
20852 CAAAGACAAACAACATGTGGT
1 CAAAGACAAACAACATGTGGT
20873 CAAAGACAAACAACATGTGGT
1 CAAAGACAAACAACATGTGGT
20894 CA
1 CA
20896 CATTTACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (21 bp):
CAAAGACAAACAACATGTGGT
Found at i:24438 original size:25 final size:26
Alignment explanation
Indices: 24404--24466 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
24394 ACATATTTTC
24404 TCAAAATTTTACC-AAGGTAAAATCG
1 TCAAAATTTTACCGAAGGTAAAATCG
* * *
24429 TCAAACTTTTACCGAGGGTAAAATTG
1 TCAAAATTTTACCGAAGGTAAAATCG
*
24455 TTAAAATTTTAC
1 TCAAAATTTTAC
24467 TAGGAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACCGAAGGTAAAATCG
Found at i:26554 original size:74 final size:74
Alignment explanation
Indices: 26433--26580 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
26423 TTTTACTTAA
26433 TAGAACTTGTGTAGAACTATGGATGATATTAGTAATCTTGTAGTGCAGAGGTGGGATGAAAGTTA
1 TAGAACTTGTGTAGAACTATGGATGATATTAGTAATCTTGTAGTGCAGAGGTGGGATGAAAGTTA
26498 CTGGTGTAG
66 CTGGTGTAG
26507 TAGAACTTGTGTAGAACTATGGATGATATTAGTAATCTTGTAGTGCAGAGGTGGGATGAAAGTTA
1 TAGAACTTGTGTAGAACTATGGATGATATTAGTAATCTTGTAGTGCAGAGGTGGGATGAAAGTTA
26572 CTGGTGTAG
66 CTGGTGTAG
26581 AACTAATAGC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.30, C:0.07, G:0.31, T:0.32
Consensus pattern (74 bp):
TAGAACTTGTGTAGAACTATGGATGATATTAGTAATCTTGTAGTGCAGAGGTGGGATGAAAGTTA
CTGGTGTAG
Found at i:28465 original size:32 final size:34
Alignment explanation
Indices: 28429--28514 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 34
28419 GTTGGATATT
* *
28429 GATATTGAAATTATTATGTTTTAAGCTTGTTGGATATTA
1 GATATTGAAATTATTATGTTTTAACCTTGATGG-----A
28468 GATATTGAAATTATTATGTTTTAACCTTGAT-G-
1 GATATTGAAATTATTATGTTTTAACCTTGATGGA
28500 GATATTGAAATTATT
1 GATATTGAAATTATT
28515 GACAATGACA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 15 0.33
38 1 0.02
39 29 0.64
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (34 bp):
GATATTGAAATTATTATGTTTTAACCTTGATGGA
Found at i:28483 original size:39 final size:39
Alignment explanation
Indices: 28388--28505 Score: 154
Period size: 39 Copynumber: 3.1 Consensus size: 39
28378 TATGTATGTT
*
28388 TTAG-TATT-AAATTATTATTTTTTAAATG-TTGGTTGGATA
1 TTAGATATTGAAATTATTATGTTTT-AA-GCTT-GTTGGATA
28427 TT-GATATTGAAATTATTATGTTTTAAGCTTGTTGGATA
1 TTAGATATTGAAATTATTATGTTTTAAGCTTGTTGGATA
* *
28465 TTAGATATTGAAATTATTATGTTTTAACCTTGATGGATA
1 TTAGATATTGAAATTATTATGTTTTAAGCTTGTTGGATA
28504 TT
1 TT
28506 GAAATTATTG
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
38 12 0.17
39 46 0.64
40 14 0.19
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.51
Consensus pattern (39 bp):
TTAGATATTGAAATTATTATGTTTTAAGCTTGTTGGATA
Found at i:29779 original size:20 final size:22
Alignment explanation
Indices: 29740--29780 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
29730 ATGTAAAAAC
*
29740 AATATAAAATATAAATTTAATA
1 AATATAAAATATAAACTTAATA
29762 AATAT-AAA-ATAAACTTAAT
1 AATATAAAATATAAACTTAAT
29781 TAAACAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATAAAATATAAACTTAATA
Found at i:31059 original size:15 final size:14
Alignment explanation
Indices: 31010--31060 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
31000 TAAAATTTTA
*
31010 ATAAATAAAAATAT
1 ATAAATTAAAATAT
31024 ATAAAATTATTAAATAT
1 AT-AAATTA--AAATAT
31041 -TAAATTAAAATAAT
1 ATAAATTAAAAT-AT
31055 ATAAAT
1 ATAAAT
31061 ATATATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 16 0.52
16 1 0.03
17 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAATTAAAATAT
Found at i:34037 original size:21 final size:20
Alignment explanation
Indices: 34003--34045 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
33993 TTATTGATTT
*
34003 ATATTGAATAGATTGTTATA
1 ATATTGAATAGATTGTGATA
*
34023 ATATTCGAATTGATTGTGATA
1 ATATT-GAATAGATTGTGATA
34044 AT
1 AT
34046 CTTTATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.44
Consensus pattern (20 bp):
ATATTGAATAGATTGTGATA
Found at i:38463 original size:24 final size:22
Alignment explanation
Indices: 38434--38477 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
38424 TTTAAGGCAA
38434 AATTTGATATTTTACAATTTTTTT
1 AATTTGATA-TTTA-AATTTTTTT
*
38458 AATTTGGTATTTAAATTTTT
1 AATTTGATATTTAAATTTTT
38478 ATGATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
AATTTGATATTTAAATTTTTTT
Found at i:38524 original size:55 final size:56
Alignment explanation
Indices: 38450--38587 Score: 181
Period size: 55 Copynumber: 2.5 Consensus size: 56
38440 ATATTTTACA
* *
38450 ATTTTTTTAATTTGGTATTTAAATTTTTATGATTTAATTTAATATTTAAATTT-G-
1 ATTTTTTTAATTTGGTATTTAAATTTTTATGATCTAATTTAATATCTAAATTTAGT
* * **
38504 ATATTTTTTAATTTGGTATTTAAATTTTTTTTATCTAATTTGGTATCTAAATTTAGT
1 AT-TTTTTTAATTTGGTATTTAAATTTTTATGATCTAATTTAATATCTAAATTTAGT
*
38561 ATTTTTTCTAATGTGGTATTTAAATTT
1 ATTTTTT-TAATTTGGTATTTAAATTT
38588 ATTAAATATT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
54 2 0.03
55 45 0.62
56 6 0.08
57 20 0.27
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (56 bp):
ATTTTTTTAATTTGGTATTTAAATTTTTATGATCTAATTTAATATCTAAATTTAGT
Found at i:38588 original size:30 final size:29
Alignment explanation
Indices: 38450--38587 Score: 137
Period size: 27 Copynumber: 4.9 Consensus size: 29
38440 ATATTTTACA
*
38450 ATTTTTT-TAATTTGGTATTTAAATTTTT
1 ATTTTTTCTAATTTGGTATTTAAATTTGT
** **
38478 A-TGATT-TAATTTAATATTTAAATTTG-
1 ATTTTTTCTAATTTGGTATTTAAATTTGT
38504 ATATTTTT-TAATTTGGTATTTAAATTT-T
1 AT-TTTTTCTAATTTGGTATTTAAATTTGT
* *
38532 -TTTTATCTAATTTGGTATCTAAATTTAGT
1 ATTTTTTCTAATTTGGTATTTAAATTT-GT
*
38561 ATTTTTTCTAATGTGGTATTTAAATTT
1 ATTTTTTCTAATTTGGTATTTAAATTT
38588 ATTAAATATT
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
26 5 0.06
27 39 0.44
28 21 0.24
29 1 0.01
30 23 0.26
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (29 bp):
ATTTTTTCTAATTTGGTATTTAAATTTGT
Found at i:38860 original size:31 final size:30
Alignment explanation
Indices: 38784--38868 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
38774 ACCCCAAAAT
* * *
38784 ATTTAAATATCAACTTAACAAAAAATGACAA
1 ATTTACATACCAAATTAA-AAAAAATGACAA
* *
38815 ATTTAGATATCAAATTAAGAAAAAAT-ATCAA
1 ATTTACATACCAAATTAA-AAAAAATGA-CAA
*
38846 GTTTACATACCAAATTAAAAAAA
1 ATTTACATACCAAATTAAAAAAA
38869 GTCAAATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.27
Consensus pattern (30 bp):
ATTTACATACCAAATTAAAAAAAATGACAA
Found at i:46135 original size:22 final size:23
Alignment explanation
Indices: 46107--46157 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
46097 GGATTAGTAT
46107 TTAAAAATAACATACAAT-AATA
1 TTAAAAATAACATACAATAAATA
46129 TTAAAAATAACATACAATAAATA
1 TTAAAAATAACATACAATAAATA
*
46152 ATAAAA
1 TTAAAA
46158 TGTATGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (23 bp):
TTAAAAATAACATACAATAAATA
Found at i:47479 original size:3 final size:3
Alignment explanation
Indices: 47473--47505 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
47463 AAGTCATTAA
47473 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47506 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47510 original size:3 final size:3
Alignment explanation
Indices: 47504--47544 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
47494 AATAATAATA
47504 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47545 TAATAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:47554 original size:20 final size:20
Alignment explanation
Indices: 47512--47554 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
47502 TAATTATTAT
* *
47512 TATTATTATTATTATTATTA
1 TATTATTATTATTAATATAA
47532 TATTATTATTATTTAATA-AA
1 TATTATTATTA-TTAATATAA
47552 TAT
1 TAT
47555 ATTGATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATTATTATTAATATAA
Found at i:47804 original size:2 final size:2
Alignment explanation
Indices: 47797--47825 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47787 AATCATGTTT
47797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47826 CTTACTTGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48872 original size:33 final size:33
Alignment explanation
Indices: 48835--48909 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
48825 TTAATTCGAT
* * *
48835 TTAAAATATATATCTTTATGAAAGGTTATCTCA
1 TTAAAAGATATATCCTTATGAAAGGATATCTCA
* *
48868 TTAAAAGATATATCCTTATGATATGATATCTCA
1 TTAAAAGATATATCCTTATGAAAGGATATCTCA
*
48901 TAAAAAGAT
1 TTAAAAGAT
48910 GCACTTAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (33 bp):
TTAAAAGATATATCCTTATGAAAGGATATCTCA
Found at i:49247 original size:7 final size:7
Alignment explanation
Indices: 49235--49259 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49225 TTAAGAAATA
49235 TATTTAT
1 TATTTAT
49242 TATTTAT
1 TATTTAT
49249 TATTTAT
1 TATTTAT
49256 TATT
1 TATT
49260 ATTTTACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:50955 original size:16 final size:16
Alignment explanation
Indices: 50934--50964 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50924 GTTTTAATTA
50934 AAATATAAAATTAAAT
1 AAATATAAAATTAAAT
*
50950 AAATATAAGATTAAA
1 AAATATAAAATTAAA
50965 ATTTAGTTTT
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:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATATAAAATTAAAT
Found at i:52174 original size:17 final size:18
Alignment explanation
Indices: 52152--52185 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52142 TTGTTTATAA
52152 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
52169 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
52186 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:54289 original size:38 final size:38
Alignment explanation
Indices: 54258--54334 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
54248 ATATTTTTAT
54258 ACATCACTCAATCACCAATAGTCATTCAATATGTACTA
1 ACATCACTCAATCACCAATAGTCATTCAATATGTACTA
54296 ACATCACTCAATCACCAATAGTCATTCAATATGTACTA
1 ACATCACTCAATCACCAATAGTCATTCAATATGTACTA
54334 A
1 A
54335 TAATATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (38 bp):
ACATCACTCAATCACCAATAGTCATTCAATATGTACTA
Found at i:54377 original size:19 final size:19
Alignment explanation
Indices: 54353--54403 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 19
54343 TTATACATAA
54353 TTTTATTTGAATTATCAAT
1 TTTTATTTGAATTATCAAT
*
54372 TTTTA--T--A-CAT-AAT
1 TTTTATTTGAATTATCAAT
54385 TTTTATTTGAATTATCAAT
1 TTTTATTTGAATTATCAAT
54404 ATGTGTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 12
0.63 0.05 0.32
Matches are distributed among these distances:
13 8 0.33
14 2 0.08
15 2 0.08
17 2 0.08
18 2 0.08
19 8 0.33
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTATTTGAATTATCAAT
Found at i:54377 original size:31 final size:32
Alignment explanation
Indices: 54339--54403 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
54329 TACTAATAAT
54339 ATTTTTATACATAA-TTTTATTTGAATTATCA
1 ATTTTTATACATAATTTTTATTTGAATTATCA
54370 ATTTTTATACATAATTTTTATTTGAATTATCA
1 ATTTTTATACATAATTTTTATTTGAATTATCA
54402 AT
1 AT
54404 ATGTGTTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.42
32 19 0.58
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (32 bp):
ATTTTTATACATAATTTTTATTTGAATTATCA
Found at i:93187 original size:20 final size:20
Alignment explanation
Indices: 93162--93229 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 20
93152 ATTCCAAAAA
93162 TAATATTATTTTAATATATT
1 TAATATTATTTTAATATATT
*
93182 TAATATTAAATTTAATACTTATCT
1 TAATATT-ATTTTAATA--TAT-T
* * *
93206 AAATAATATTTTATTA-ATT
1 TAATATTATTTTAATATATT
93225 TAATA
1 TAATA
93230 AGATTTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 5 0.13
20 9 0.24
21 8 0.21
23 10 0.26
24 6 0.16
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATATTATTTTAATATATT
Found at i:93235 original size:19 final size:21
Alignment explanation
Indices: 93207--93249 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
93197 TACTTATCTA
*
93207 AATAATATTT-TATT-AATTT
1 AATAAGATTTATATTAAATTT
93226 AATAAGATTTAATATTAAATTT
1 AATAAGATTT-ATATTAAATTT
93248 AA
1 AA
93250 ATTATAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATAAGATTTATATTAAATTT
Found at i:93280 original size:59 final size:52
Alignment explanation
Indices: 93164--93287 Score: 131
Period size: 53 Copynumber: 2.2 Consensus size: 52
93154 TCCAAAAATA
* * *
93164 ATATTATTTTAATATATTTAATATTAAATTTAATACTTATCTAAATAATATT
1 ATATTAATTTAATAGATTTAATATTAAATTTAATAATTATCTAAATAATATT
* **
93216 TTATTAATTTAATAAGATTTAATATTAAATTTAAATTATAATTCATCTTGATAAGTATT
1 ATATTAATTTAAT-AGATTTAATATTAAATTT--A--ATAATT-ATCTAAATAA-TATT
93275 ATATTAATTTAAT
1 ATATTAATTTAAT
93288 TTTAAAGTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
52 11 0.19
53 17 0.29
55 1 0.02
57 5 0.09
58 8 0.14
59 16 0.28
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (52 bp):
ATATTAATTTAATAGATTTAATATTAAATTTAATAATTATCTAAATAATATT
Found at i:93659 original size:21 final size:22
Alignment explanation
Indices: 93624--93667 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
93614 CAGTAAATTA
* *
93624 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATCATT
93646 TTTTAAAAAT-TTAAAATCATT
1 TTTTAAAAATATTAAAATCATT
93667 T
1 T
93668 GCTGACGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATCATT
Found at i:99366 original size:66 final size:66
Alignment explanation
Indices: 99260--99391 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
99250 TCTAAAAACT
99260 TTTTGCACCCATTCAAGGCACAACGTTAGTTTCCAAAAAACACAAATATTCTTCTCAAAGAATGT
1 TTTTGCACCCATTCAAGGCACAACGTTAGTTTCCAAAAAACACAAATATTCTTCTCAAAGAATGT
99325 C
66 C
* * * *
99326 TTTTGCACCTATTCAGGGCACAACGTTAGTTTCTAGAAAACACAAATATTCTTCTCAAAGAATGT
1 TTTTGCACCCATTCAAGGCACAACGTTAGTTTCCAAAAAACACAAATATTCTTCTCAAAGAATGT
99391 C
66 C
99392 CTTCCCAAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (66 bp):
TTTTGCACCCATTCAAGGCACAACGTTAGTTTCCAAAAAACACAAATATTCTTCTCAAAGAATGT
C
Found at i:103461 original size:22 final size:23
Alignment explanation
Indices: 103435--103485 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
103425 TTAGATTGTT
* *
103435 ATTAATAATAATATTTAA-AAAA
1 ATTAATAAAAACATTTAATAAAA
103457 ATTAATAAAAACATTTAATAAAA
1 ATTAATAAAAACATTTAATAAAA
103480 A-TAATA
1 ATTAATA
103486 TATTTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTAATAAAAACATTTAATAAAA
Found at i:105513 original size:59 final size:59
Alignment explanation
Indices: 105381--105514 Score: 180
Period size: 59 Copynumber: 2.3 Consensus size: 59
105371 GGTATCCAAA
* *
105381 TTTTTTGACTCAATTTAATACTTGAACTTGACACTTTTTTCTAATTTGATACCTAAACT
1 TTTTTTGACTCAATTTAATACTTAAACTTGACACTTTTTCCTAATTTGATACCTAAACT
* * * * *
105440 TTTTTTTACCCAATTTAATATTTAAACTTGACA-TTTTTCCTAATTTGGTACCTAAGCT
1 TTTTTTGACTCAATTTAATACTTAAACTTGACACTTTTTCCTAATTTGATACCTAAACT
*
105498 TTTTTTAGATTCAATTT
1 TTTTTT-GACTCAATTT
105515 GACACCTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 28 0.44
59 36 0.56
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.50
Consensus pattern (59 bp):
TTTTTTGACTCAATTTAATACTTAAACTTGACACTTTTTCCTAATTTGATACCTAAACT
Found at i:111574 original size:26 final size:27
Alignment explanation
Indices: 111512--111576 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
111502 AATAGCACCC
*
111512 TTAGTTTAACATTACTTTTAAAAAGTG
1 TTAGTTTAAAATTACTTTTAAAAAGTG
** *
111539 TTA-TGAAAAATTACTTTTAAAATGT-
1 TTAGTTTAAAATTACTTTTAAAAAGTG
111564 TTAGTTTAAAATT
1 TTAGTTTAAAATT
111577 TAACTGTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.10
26 25 0.81
27 3 0.10
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (27 bp):
TTAGTTTAAAATTACTTTTAAAAAGTG
Found at i:115540 original size:17 final size:18
Alignment explanation
Indices: 115503--115542 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
115493 TTGAAACTTC
*
115503 AAAA-AAGCAAATAAGTG
1 AAAACAAGCAAAGAAGTG
115520 -AAACAAGCAAAGAA-TG
1 AAAACAAGCAAAGAAGTG
115536 AAAACAA
1 AAAACAA
115543 AAAGGCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.68, C:0.10, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAACAAGCAAAGAAGTG
Found at i:117713 original size:29 final size:29
Alignment explanation
Indices: 117680--117748 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
117670 CTTACATGTG
117680 TTCTTACATTTTGTTAAATACAAAT-AGAT
1 TTCTTACATTTTGTTAAATACAAATGA-AT
* *
117709 TTCTTACATTTTGTTTAATGCAAATGAAT
1 TTCTTACATTTTGTTAAATACAAATGAAT
117738 TTCTTACATTT
1 TTCTTACATTT
117749 CCAAATGTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (29 bp):
TTCTTACATTTTGTTAAATACAAATGAAT
Found at i:125937 original size:16 final size:18
Alignment explanation
Indices: 125904--125941 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
125894 AATATATACT
125904 AAAAAAATGATTGATGAA
1 AAAAAAATGATTGATGAA
125922 AAAAAAATGA-TG-TGAA
1 AAAAAAATGATTGATGAA
125938 AAAA
1 AAAA
125942 GTTTTTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (18 bp):
AAAAAAATGATTGATGAA
Found at i:126228 original size:18 final size:18
Alignment explanation
Indices: 126207--126248 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
126197 TTATAATTAC
126207 AAAAATA-ATTAAAAATA
1 AAAAATATATTAAAAATA
126224 AAAAATATATTAAAAATA
1 AAAAATATATTAAAAATA
126242 ATAAAAT
1 A-AAAAT
126249 TGATTTCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.30
18 11 0.48
19 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATATATTAAAAATA
Found at i:128730 original size:21 final size:20
Alignment explanation
Indices: 128695--128733 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
128685 ATATATTTAT
*
128695 AAAATTTTATTTTAAAAATA
1 AAAATTTTATATTAAAAATA
128715 AAAATATTTATATTAAAAA
1 AAAAT-TTTATATTAAAAA
128734 CTAACGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTTATATTAAAAATA
Found at i:133025 original size:43 final size:42
Alignment explanation
Indices: 132954--133118 Score: 133
Period size: 43 Copynumber: 3.9 Consensus size: 42
132944 TTTCACTGAA
*
132954 TCATAAGTCTCTTCCTTTTTAAAC--AATCTTATGCTCTAT-CAAG
1 TCATAAG--TCTTCC-TTTTAAACATAATCTCATGCTC-ATCCAAG
*
132997 TCATAAGTCTTCCTTTTCAAACATAATCTCATGCTCATCCCGAG
1 TCATAAGTCTTCCTTTT-AAACATAATCTCATGCTCAT-CCAAG
* * * *
133041 ACATGAGTCTTCC-TTTAAACATATTCTCATGCTCATTCCGAG
1 TCATAAGTCTTCCTTTTAAACATAATCTCATGCTCA-TCCAAG
** * *
133083 TCACGAGTCTTCCATTTATACA-AATTCTCATGCTCA
1 TCATAAGTCTTCCTTTTAAACATAA-TCTCATGCTCA
133119 ACCCGAGACA
Statistics
Matches: 105, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
40 4 0.04
41 10 0.10
42 37 0.35
43 40 0.38
44 14 0.13
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.37
Consensus pattern (42 bp):
TCATAAGTCTTCCTTTTAAACATAATCTCATGCTCATCCAAG
Found at i:133069 original size:42 final size:43
Alignment explanation
Indices: 133002--133148 Score: 188
Period size: 43 Copynumber: 3.4 Consensus size: 43
132992 TCAAGTCATA
* * *
133002 AGTCTTCCTTTTCAAACATAATCTCATGCTCATCCCGAGACATG
1 AGTCTTCCATTT-AAACATATTCTCATGCTCATCCCGAGACACG
* *
133046 AGTCTTCC-TTTAAACATATTCTCATGCTCATTCCGAGTCACG
1 AGTCTTCCATTTAAACATATTCTCATGCTCATCCCGAGACACG
* * *
133088 AGTCTTCCATTTATACAAATTCTCATGCTCAACCCGAGACACG
1 AGTCTTCCATTTAAACATATTCTCATGCTCATCCCGAGACACG
* *
133131 AGTCTTCCGTTTATACAT
1 AGTCTTCCATTTAAACAT
133149 TAAGTGATTC
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
42 35 0.38
43 48 0.53
44 8 0.09
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (43 bp):
AGTCTTCCATTTAAACATATTCTCATGCTCATCCCGAGACACG
Found at i:136474 original size:30 final size:29
Alignment explanation
Indices: 136440--136770 Score: 337
Period size: 30 Copynumber: 11.2 Consensus size: 29
136430 GGTCAAAACA
* *
136440 TAATTTTAAAAAAGTTTGAGGGTAAAAATG
1 TAATTTTAGAAAAGTTT-AGGGTTAAAATG
* * *
136470 TAATTATGGAAAAGTTAAAGGGTTAAAATG
1 TAATTTTAGAAAAGTT-TAGGGTTAAAATG
* * *
136500 TAATTTTAGAGAATTTTGAGGGTTAAAATT
1 TAATTTTAGAAAAGTTT-AGGGTTAAAATG
*
136530 TAATTTTGGAAAAGTTTAGGGGTTAAAATG
1 TAATTTTAGAAAAGTTTA-GGGTTAAAATG
* * *
136560 TAATTTTGGAAAAGTTTATGGGTCAAAATA
1 TAATTTTAGAAAAGTTTA-GGGTTAAAATG
*
136590 TAA-TGTAGAAAAGTTTGAGGGGTTAAAATG
1 TAATTTTAGAAAAGTTT-A-GGGTTAAAATG
* * *
136620 CAATTTTAGGAAATTTTAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGGGTTAAAATG
136649 TAATTTT-GAAAAGTTTAGGG-TAAAATG
1 TAATTTTAGAAAAGTTTAGGGTTAAAATG
* * *
136676 TAATTTTGGAAAAGTTTGGGGTTTATAATG
1 TAATTTTAGAAAAGTTTAGGG-TTAAAATG
* *
136706 AAATTTTGGAAAAGTTTAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGGGTTAAAATG
* *
136735 TAATTTTA-AAAAATTTAAGGGTCAAAATG
1 TAATTTTAGAAAAGTTT-AGGGTTAAAATG
*
136764 TGATTTT
1 TAATTTT
136771 CAAAGAAAAT
Statistics
Matches: 252, Mismatches: 40, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
27 14 0.06
28 30 0.12
29 59 0.23
30 139 0.55
31 10 0.04
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (29 bp):
TAATTTTAGAAAAGTTTAGGGTTAAAATG
Found at i:136493 original size:90 final size:90
Alignment explanation
Indices: 136406--136681 Score: 212
Period size: 90 Copynumber: 3.1 Consensus size: 90
136396 ACGGGGTTGA
*
136406 AAAATG-AAGTTTCAGAGGA-TATG-GGGTCAAAACATAATTTTAAAAAAGTTT-GAGGGTAAAA
1 AAAATGTAA-TTTCAGAGAATTATGAGGGTCAAAACATAATTTTAAAAAAGTTTAG-GGGTAAAA
136467 ATGTAATTATGGAAAAGTTAAAGGGTT
64 ATGTAATTATGGAAAAGTTAAAGGGTT
* * * ** ** *
136494 AAAATGTAATTTTAGAGAATTTTGAGGGTTAAAATTTAATTTTGGAAAAGTTTAGGGGTTAAAAT
1 AAAATGTAATTTCAGAGAATTATGAGGGTCAAAACATAATTTTAAAAAAGTTTAGGGGTAAAAAT
* * * *
136559 GTAATTTTGGAAAAGTTTATGGGTC
66 GTAATTATGGAAAAGTTAAAGGGTT
* * * * *** ** * *
136584 AAAATATAATGT-AGAAAAGTT-TGAGGGGTTAAAATGCAATTTTAGGAAATTTTA-GGGTTAAA
1 AAAATGTAATTTCAGAGAA-TTATGA-GGGTCAAAACATAATTTTAAAAAAGTTTAGGGGTAAAA
* *
136646 ATGTAATT-TTGAAAAGTT-TAGGG-T
64 ATGTAATTATGGAAAAGTTAAAGGGTT
136670 AAAATGTAATTT
1 AAAATGTAATTT
136682 TGGAAAAGTT
Statistics
Matches: 155, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
86 10 0.06
87 3 0.02
88 23 0.15
89 29 0.19
90 89 0.57
91 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (90 bp):
AAAATGTAATTTCAGAGAATTATGAGGGTCAAAACATAATTTTAAAAAAGTTTAGGGGTAAAAAT
GTAATTATGGAAAAGTTAAAGGGTT
Found at i:153060 original size:26 final size:26
Alignment explanation
Indices: 153009--153076 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
152999 GATCCTCTTA
* * *
153009 TGCAACGATAACTCTGAAATTATTCC
1 TGCAGCGATAATTCTGAAAATATTCC
153035 TGCAGCGATAATTCTGAACAAT-TTCC
1 TGCAGCGATAATTCTGAA-AATATTCC
* * *
153061 TACAGTGACAATTCTG
1 TGCAGCGATAATTCTG
153077 GGCGCATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 33 0.94
27 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (26 bp):
TGCAGCGATAATTCTGAAAATATTCC
Found at i:157930 original size:28 final size:28
Alignment explanation
Indices: 157883--157940 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
157873 GCTCAGATAA
*
157883 AGCGATATTCTGATTTTAGCTTGAATAG
1 AGCGATATTCTGATTTTAGCTCGAATAG
*
157911 AGCGATATTCTG-TTTCTAGCTCGGATAG
1 AGCGATATTCTGATTT-TAGCTCGAATAG
157939 AG
1 AG
157941 ATAATTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (28 bp):
AGCGATATTCTGATTTTAGCTCGAATAG
Found at i:158040 original size:56 final size:55
Alignment explanation
Indices: 157919--158041 Score: 124
Period size: 56 Copynumber: 2.2 Consensus size: 55
157909 AGAGCGATAT
* * *
157919 TCTGTTTCTAGCTCGGATAGAGATAATTCTAATTCTGGGTCGAGTAAAGCGTTAC
1 TCTGTTTCTGGCTCGGATAGACATAATTCTAATTCTAGGTCGAGTAAAGCGTTAC
* ** * * *
157974 TTTGAATCTGGCTCGAGTATAG-CATTATTCTAATTCTAGTTCGAGTAGAGCGTT-C
1 TCTGTTTCTGGCTCG-G-ATAGACATAATTCTAATTCTAGGTCGAGTAAAGCGTTAC
158029 ATCTGTTTCTGGC
1 -TCTGTTTCTGGC
158042 ATAAAAAGAG
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
55 12 0.23
56 37 0.70
57 4 0.08
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (55 bp):
TCTGTTTCTGGCTCGGATAGACATAATTCTAATTCTAGGTCGAGTAAAGCGTTAC
Found at i:160546 original size:46 final size:46
Alignment explanation
Indices: 160448--160604 Score: 147
Period size: 46 Copynumber: 3.4 Consensus size: 46
160438 AGTTTCCAAT
* * * * *
160448 AAATGCGAGAACTGGGAACGTAAAT-CAGTATTCACCAGTTCGCAAC
1 AAATGCAAGAACTGGGAACCTAAATCCA-TATTCACCAATCCGTAAC
** * ** *
160494 GTATGCAAGAACTGGGAACCTAATTTTGA-ATTCACCAATCTGTAAC
1 AAATGCAAGAACTGGGAACCTAA-ATCCATATTCACCAATCCGTAAC
* * *
160540 AAATGCAAGAAATGGGACCCTAAATCCATATTCACCAGTCCGTAAC
1 AAATGCAAGAACTGGGAACCTAAATCCATATTCACCAATCCGTAAC
*
160586 AAATGCAAGAGCTGGGAAC
1 AAATGCAAGAACTGGGAAC
160605 TTGAACAGTA
Statistics
Matches: 86, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
45 2 0.02
46 82 0.95
47 1 0.01
48 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (46 bp):
AAATGCAAGAACTGGGAACCTAAATCCATATTCACCAATCCGTAAC
Found at i:161795 original size:28 final size:28
Alignment explanation
Indices: 161750--161868 Score: 96
Period size: 28 Copynumber: 4.2 Consensus size: 28
161740 TTTGACATAG
* * *
161750 ATAGCCATAGAGGCGTCCTTGAA-AAAAC
1 ATAGCCACAAAGGTGTCCTT-AAGAAAAC
* * *
161778 ATAGCCACAAAGTTGTCCTTAAGTAAAG
1 ATAGCCACAAAGGTGTCCTTAAGAAAAC
* *
161806 ATAGCCACAAAGGTGTCCTTAAGCAAAG
1 ATAGCCACAAAGGTGTCCTTAAGAAAAC
* * * * * *
161834 ATAGTCACAATGGCGTCCTTACGCAAAG
1 ATAGCCACAAAGGTGTCCTTAAGAAAAC
161862 ATAGCCA
1 ATAGCCA
161869 TAGAGGCTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 2 0.03
28 75 0.97
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (28 bp):
ATAGCCACAAAGGTGTCCTTAAGAAAAC
Found at i:161808 original size:56 final size:56
Alignment explanation
Indices: 161748--161875 Score: 141
Period size: 56 Copynumber: 2.3 Consensus size: 56
161738 CTTTTGACAT
** *
161748 AGATAGCCATAGAGGCGTCCTTGAA-AAAACATAGCCACAAAGTTGTCCTTAAGTAA
1 AGATAGCCATAGAGGCGTCCTT-AAGAAAACATAGCCACAAAGGCGTCCTTAAGCAA
* * * * * * * *
161804 AGATAGCCACAAAGGTGTCCTTAAGCAAAGATAGTCACAATGGCGTCCTTACGCAA
1 AGATAGCCATAGAGGCGTCCTTAAGAAAACATAGCCACAAAGGCGTCCTTAAGCAA
161860 AGATAGCCATAGAGGC
1 AGATAGCCATAGAGGC
161876 TTTTCAATCA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
55 2 0.04
56 55 0.96
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (56 bp):
AGATAGCCATAGAGGCGTCCTTAAGAAAACATAGCCACAAAGGCGTCCTTAAGCAA
Found at i:162053 original size:28 final size:28
Alignment explanation
Indices: 161990--162074 Score: 116
Period size: 29 Copynumber: 3.0 Consensus size: 28
161980 ACTTCATTAT
161990 CAGAATCAACCACAAAGGCTTCATTTTAA
1 CAGAATCAACCACAAAGGCTTC-TTTTAA
*
162019 CAGAATCAACCACAAAGTCTTCTTTTAA
1 CAGAATCAACCACAAAGGCTTCTTTTAA
* * *
162047 TAGAATCAGCCAAAAAGGCTTCCTTTTA
1 CAGAATCAACCACAAAGGCTT-CTTTTA
162075 CGAAAAATGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 23 0.46
29 27 0.54
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (28 bp):
CAGAATCAACCACAAAGGCTTCTTTTAA
Found at i:167975 original size:26 final size:26
Alignment explanation
Indices: 167946--167995 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
167936 TCACATCCCA
*
167946 ATTTTACCCCTGATAAAATTTTGATG
1 ATTTTACCACTGATAAAATTTTGATG
*
167972 ATTTTACCATTGATAAAATTTTGA
1 ATTTTACCACTGATAAAATTTTGA
167996 GAAAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (26 bp):
ATTTTACCACTGATAAAATTTTGATG
Found at i:171877 original size:27 final size:25
Alignment explanation
Indices: 171815--171886 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
171805 CAGTTTAGCA
*
171815 AACTAGGGGTTTGCCAATTGGTTGGC
1 AACTA-GGGTTCGCCAATTGGTTGGC
* *
171841 AAGTTGGGGTTCGCCAATTGGTTTGGC
1 AA-CTAGGGTTCGCCAATTGG-TTGGC
*
171868 GAACTAGGGTTCACCAATT
1 -AACTAGGGTTCGCCAATT
171887 ATAAGTCGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
26 16 0.43
27 19 0.51
28 2 0.05
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.31
Consensus pattern (25 bp):
AACTAGGGTTCGCCAATTGGTTGGC
Found at i:173613 original size:18 final size:18
Alignment explanation
Indices: 173590--173661 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
173580 GAAACTATAT
*
173590 TGTTATTATGTGAACCTA
1 TGTTATTATGCGAACCTA
*
173608 TGTTATTATGCAAACCTACAA
1 TGTTATTATGCGAACCT---A
*
173629 TGTTA-TATGCGAACCTC
1 TGTTATTATGCGAACCTA
* *
173646 TGCTATTATGTGAACC
1 TGTTATTATGCGAACC
173662 CTTAATAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.09
18 24 0.55
20 10 0.23
21 6 0.14
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (18 bp):
TGTTATTATGCGAACCTA
Found at i:177359 original size:38 final size:38
Alignment explanation
Indices: 177266--177352 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 38
177256 GTACCTCTGC
* * *
177266 AAAACCATTCCCCTTTTCTTTTAAATGACATCCCTCCAC
1 AAAACCATT-TCCTTTTCTTTTAAATCACATCCCTCCAA
* *
177305 AAAGCCATTTCCTTTTCTTTTAAGTCACATCCCTCCAA
1 AAAACCATTTCCTTTTCTTTTAAATCACATCCCTCCAA
*
177343 AAAACGATTT
1 AAAACCATTT
177353 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 33 0.80
39 8 0.20
ACGTcount: A:0.30, C:0.31, G:0.05, T:0.34
Consensus pattern (38 bp):
AAAACCATTTCCTTTTCTTTTAAATCACATCCCTCCAA
Found at i:183183 original size:50 final size:50
Alignment explanation
Indices: 183022--183168 Score: 224
Period size: 50 Copynumber: 2.9 Consensus size: 50
183012 GACAAAACAA
* ** *
183022 TGAATCTTATACACCTAAAG-CTATAGAGGAGCAGATTGAAGCCACAATGG
1 TGAATCTTATACACCTAAAGTC-GTAGAGGAATAGATTGAAGCCGCAATGG
* *
183072 TGAATCTCATACACCTAAAGTCGTAGAGGAATAGATTGAGGCCGCAATGG
1 TGAATCTTATACACCTAAAGTCGTAGAGGAATAGATTGAAGCCGCAATGG
183122 TGAATCTTATACACCTAAAGTCGTAGAGGAATAGATTGAAGCCGCAA
1 TGAATCTTATACACCTAAAGTCGTAGAGGAATAGATTGAAGCCGCAA
183169 GAACGAATCT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 87 0.99
51 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (50 bp):
TGAATCTTATACACCTAAAGTCGTAGAGGAATAGATTGAAGCCGCAATGG
Found at i:185441 original size:17 final size:17
Alignment explanation
Indices: 185402--185435 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
185392 TTTGATGACA
185402 TTTATTGTGATGATTAT
1 TTTATTGTGATGATTAT
185419 TTTATTGTG-T-ATTAT
1 TTTATTGTGATGATTAT
185434 TT
1 TT
185436 GTTATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (17 bp):
TTTATTGTGATGATTAT
Found at i:186030 original size:36 final size:36
Alignment explanation
Indices: 185990--186061 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
185980 TTATGGTTTC
185990 AAAGACCAAAATTTGTTTCAATGATTTTAAAATATT
1 AAAGACCAAAATTTGTTTCAATGATTTTAAAATATT
186026 AAAGACCAAAATTTGTTTCAATGATTTTAAAATATT
1 AAAGACCAAAATTTGTTTCAATGATTTTAAAATATT
186062 CCAAGGTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (36 bp):
AAAGACCAAAATTTGTTTCAATGATTTTAAAATATT
Found at i:186527 original size:17 final size:17
Alignment explanation
Indices: 186499--186540 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
186489 TTGGAAATTG
186499 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
186515 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
186532 AATTTATTT
1 AATTTATTT
186541 GAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.