Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014213.1 Kokia drynarioides strain JFW-HI SEQ_129246, 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: 212405
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:162 original size:4 final size:4
Alignment explanation
Indices: 155--204 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
145 TTTCTTCATA
155 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
203 GT
1 GT
205 GACATACCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:6316 original size:2 final size:2
Alignment explanation
Indices: 6274--6304 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6264 ACATACATAC
6274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6305 CACATGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9825 original size:20 final size:20
Alignment explanation
Indices: 9780--9825 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
9770 TACAACACGT
*
9780 TAACGTAAGTGACTAAAACG
1 TAACATAAGTGACTAAAACG
9800 -AGACATAAGTGACTAAAACG
1 TA-ACATAAGTGACTAAAACG
9820 TAACAT
1 TAACAT
9826 TTCAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (20 bp):
TAACATAAGTGACTAAAACG
Found at i:10390 original size:178 final size:175
Alignment explanation
Indices: 10167--10487 Score: 475
Period size: 178 Copynumber: 1.8 Consensus size: 175
10157 ACTAACAAAT
* * *
10167 ATTAAATTGCTCCAATTTTTTTTGAAATAGATCAATTTAATCAATTTCG-AAATTAAGTGAAACT
1 ATTAAATTGCTCAAATTTTTTTTGAAAAAGATCAATTTAATCAATTT-GAAAATTAAGAGAAACT
* *
10231 AGAGAAATCCTTTTACCTACATTTTGTTATTCAAAATTTTTATTTTTTACAAAATACCAGTTTTT
65 AGAGAAATCCTCTTACCTACATTTTGTTATTCAAAATTTTTA-TTTTTACAAAATACCA-ATTTT
*
10296 TGACATATATATAAATAAATGAATTTTAAAAAAATTAAATTAATAAAG
128 TAACATATATATAAATAAATGAATTTTAAAAAAATTAAATTAATAAAG
* *
10344 ATTAAATTGCTCAAATTTTCTTTTGAGAAAAG-TCAATTTAATCAATTTGAAAATTGAGAGAAAT
1 ATTAAATTGCTCAAATTTT-TTTTGA-AAAAGATCAATTTAATCAATTTGAAAATTAAGAGAAAC
* ** *
10408 TAGAGAAATCCTCTTACTTACATTTTGTTATTCGGAATTTTTATTTTTACAAAATTCCAATTTTT
64 TAGAGAAATCCTCTTACCTACATTTTGTTATTCAAAATTTTTATTTTTACAAAATACCAATTTTT
10473 AACATATATATAAAT
129 AACATATATATAAAT
10488 TTAAAAAGAA
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
176 19 0.15
177 34 0.26
178 72 0.56
179 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (175 bp):
ATTAAATTGCTCAAATTTTTTTTGAAAAAGATCAATTTAATCAATTTGAAAATTAAGAGAAACTA
GAGAAATCCTCTTACCTACATTTTGTTATTCAAAATTTTTATTTTTACAAAATACCAATTTTTAA
CATATATATAAATAAATGAATTTTAAAAAAATTAAATTAATAAAG
Found at i:12950 original size:2 final size:2
Alignment explanation
Indices: 12938--12981 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
12928 CAGTACCTAA
12938 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12979 AT A
1 AT A
12982 GTTTCAGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14781 original size:26 final size:28
Alignment explanation
Indices: 14729--14786 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
14719 TGAACATGTT
14729 AATAAACGAACATGAATACAAATAAATTTA
1 AATAAACGAACATG-A-ACAAATAAATTTA
14759 AATAAACGAACATG-ACAAA-AAATTTA
1 AATAAACGAACATGAACAAATAAATTTA
14785 AA
1 AA
14787 ATTCTTAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.32
27 5 0.18
30 14 0.50
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (28 bp):
AATAAACGAACATGAACAAATAAATTTA
Found at i:15143 original size:13 final size:13
Alignment explanation
Indices: 15107--15154 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
15097 TCAAATTATA
15107 ATAAAATTAAAAT
1 ATAAAATTAAAAT
*
15120 ATAAAGATTAAATT
1 ATAAA-ATTAAAAT
*
15134 ATAAATTTAAACAT
1 ATAAAATTAAA-AT
15148 GATAAAA
1 -ATAAAA
15155 AGACCAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.36
14 13 0.46
15 5 0.18
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (13 bp):
ATAAAATTAAAAT
Found at i:18912 original size:9 final size:9
Alignment explanation
Indices: 18891--18919 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
18881 AAGGCATAAC
18891 AAAATTTTT
1 AAAATTTTT
18900 -AAATTTTT
1 AAAATTTTT
18908 AAAATTTTT
1 AAAATTTTT
18917 AAA
1 AAA
18920 CCAAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:19607 original size:22 final size:20
Alignment explanation
Indices: 19582--19625 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19572 TTTAAATTCA
* *
19582 TTATTCAATCTAAAGTAATTAT
1 TTATCCAAT-TAAA-TAAATAT
19604 TTATCCAATTAAATAAATAT
1 TTATCCAATTAAATAAATAT
19624 TT
1 TT
19626 GAAGTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (20 bp):
TTATCCAATTAAATAAATAT
Found at i:23886 original size:13 final size:13
Alignment explanation
Indices: 23868--23894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23858 TAATTTTACT
23868 ATAATGACAAAAG
1 ATAATGACAAAAG
23881 ATAATGACAAAAG
1 ATAATGACAAAAG
23894 A
1 A
23895 ACGAAGAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
ATAATGACAAAAG
Found at i:27826 original size:32 final size:35
Alignment explanation
Indices: 27781--27845 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 35
27771 TTTTAAGATA
27781 AATTTGACTTTTAA-ATTTA-AAAAAA-AAAATCT
1 AATTTGACTTTTAACATTTAGAAAAAATAAAATCT
*
27813 AATTTGA-TCTTTAACTTTTAGAAAAAATAAAAT
1 AATTTGACT-TTTAACATTTAGAAAAAATAAAAT
27846 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 1 0.04
32 12 0.43
33 4 0.14
34 6 0.21
35 5 0.18
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (35 bp):
AATTTGACTTTTAACATTTAGAAAAAATAAAATCT
Found at i:33025 original size:14 final size:14
Alignment explanation
Indices: 33006--33033 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32996 CACTTCCATT
33006 TTTCCAACTACTTA
1 TTTCCAACTACTTA
33020 TTTCCAACTACTTA
1 TTTCCAACTACTTA
33034 ATGATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCCAACTACTTA
Found at i:36310 original size:24 final size:26
Alignment explanation
Indices: 36283--36330 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
36273 AGAGAAATGT
36283 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
36307 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
36331 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:36423 original size:23 final size:23
Alignment explanation
Indices: 36393--36488 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 23
36383 ACACTAGCGC
*
36393 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGGTTAGCACTGTCT-GT
*
36416 GCTCTCTGGTTAGCACTGTGTGT
1 GCTCTCTGGTTAGCACTGTCTGT
***
36439 GCTCTCAAATTAGCACT-TCGTGT
1 GCTCTCTGGTTAGCACTGTC-TGT
* * * * *
36462 GCTTTCTGATTAACACTTTGTGT
1 GCTCTCTGGTTAGCACTGTCTGT
36485 GCTC
1 GCTC
36489 AGTACTTTGT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
22 1 0.02
23 53 0.91
24 4 0.07
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGGTTAGCACTGTCTGT
Found at i:37445 original size:17 final size:20
Alignment explanation
Indices: 37423--37465 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
37413 GATGTTTCGT
37423 TTTCTAGTT-TTTT-TTAA-
1 TTTCTAGTTGTTTTGTTAAC
*
37440 TTTCTATTTGTTTTGTTAAC
1 TTTCTAGTTGTTTTGTTAAC
37460 TTTCTA
1 TTTCTA
37466 CTACATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 4 0.18
20 6 0.27
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTCTAGTTGTTTTGTTAAC
Found at i:37570 original size:18 final size:18
Alignment explanation
Indices: 37543--37583 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
37533 TAAAAAAAAC
* *
37543 ATATTGAAATACTATATA
1 ATATTAAAATACTATACA
*
37561 ATATTAAAATATTATACA
1 ATATTAAAATACTATACA
37579 ATATT
1 ATATT
37584 TTTTTAATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
ATATTAAAATACTATACA
Found at i:38476 original size:26 final size:26
Alignment explanation
Indices: 38427--38481 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
38417 AATATTTATA
38427 TTTTTTTTATTAATGTTACTCTT-AC
1 TTTTTTTTATTAATGTTACTCTTAAC
38452 TTTTTTTTAATTAAAT-TTAAC-CTTAAC
1 TTTTTTTT-ATT-AATGTT-ACTCTTAAC
38479 TTT
1 TTT
38482 AAAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
25 8 0.31
26 8 0.31
27 10 0.38
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTTTTTATTAATGTTACTCTTAAC
Found at i:38673 original size:19 final size:20
Alignment explanation
Indices: 38637--38683 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
38627 TTTTTTGTTT
*
38637 TTTTTTTAATTTATAAA-TA
1 TTTTTATAATTTATAAATTA
38656 TTTTTATAATTT-TCAAATTA
1 TTTTTATAATTTAT-AAATTA
38676 TTTATTAT
1 TTT-TTAT
38684 CATGACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 5 0.21
21 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTTATAAATTA
Found at i:40702 original size:106 final size:105
Alignment explanation
Indices: 40508--40746 Score: 392
Period size: 106 Copynumber: 2.3 Consensus size: 105
40498 GGAAACAACT
*
40508 CTCC-CACCATCTCACAAATACTCGAACCTAACCTTCCTTCACCACTCGACTAAACATGCATCAA
1 CTCCTCACCATCTCACAAATACTCGAACCTAACCTTCCTTCACCACTCGACTAAACATGAATCAA
* * *
40572 TAGAACACTCGAGCCCAGACCCTTGCCTTAAAGGTACTAAA
66 TAGAACACTCGAACCCAGAACCTTG-CTTAAAGGTACCAAA
*
40613 CTCCTCACCATCTCACAAATACTCGAGCCTAACCTTCCTTCACCACTCGACTAAACATGAATCAA
1 CTCCTCACCATCTCACAAATACTCGAACCTAACCTTCCTTCACCACTCGACTAAACATGAATCAA
40678 TAGAACACTCGAACCC-GAAACCTTGCTTAAAGGTACCAAA
66 TAGAACACTCGAACCCAG-AACCTTGCTTAAAGGTACCAAA
*
40718 CTCCTCACCATCTCACAAATACTTGAACC
1 CTCCTCACCATCTCACAAATACTCGAACC
40747 CGAAACCTTG
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
105 46 0.37
106 79 0.63
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.21
Consensus pattern (105 bp):
CTCCTCACCATCTCACAAATACTCGAACCTAACCTTCCTTCACCACTCGACTAAACATGAATCAA
TAGAACACTCGAACCCAGAACCTTGCTTAAAGGTACCAAA
Found at i:42835 original size:5 final size:5
Alignment explanation
Indices: 42825--42851 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
42815 CCATCCCCTC
42825 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
42852 ATTCAATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:45960 original size:18 final size:18
Alignment explanation
Indices: 45937--45971 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
45927 CAAACTCTTT
45937 AAGAAATCAACTTCTGTG
1 AAGAAATCAACTTCTGTG
45955 AAGAAATCAACTTCTGT
1 AAGAAATCAACTTCTGT
45972 ATCAGTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGAAATCAACTTCTGTG
Found at i:50998 original size:31 final size:31
Alignment explanation
Indices: 50956--51016 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
50946 TAAAATGCTC
* *
50956 ATTGAATTATTCGAAAGTTTTCATTTAAGTT
1 ATTGAACTATTCAAAAGTTTTCATTTAAGTT
*
50987 ATTGAACTATTCAAAAGTTTTTATTTAAGT
1 ATTGAACTATTCAAAAGTTTTCATTTAAGT
51017 CAATGAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (31 bp):
ATTGAACTATTCAAAAGTTTTCATTTAAGTT
Found at i:57465 original size:17 final size:16
Alignment explanation
Indices: 57445--57479 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
57435 TATTCTTAAA
*
57445 ATAATATAATTTATTTT
1 ATAAAATAATTT-TTTT
57462 ATAAAATAATTTTTTT
1 ATAAAATAATTTTTTT
57478 AT
1 AT
57480 TATTCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATAAAATAATTTTTTT
Found at i:61262 original size:16 final size:17
Alignment explanation
Indices: 61237--61270 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
61227 GTTTAAAAAA
61237 AAATTAATTTTTT-TTT
1 AAATTAATTTTTTATTT
*
61253 AAATTTATTTTTTATTT
1 AAATTAATTTTTTATTT
61270 A
1 A
61271 GTAAACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AAATTAATTTTTTATTT
Found at i:61968 original size:22 final size:22
Alignment explanation
Indices: 61907--61968 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
61897 CAGCAACCTC
61907 TCTTGGAAAACCAACAGCATCT
1 TCTTGGAAAACCAACAGCATCT
*
61929 TCTTGAAAAACCAACAGCATCT
1 TCTTGGAAAACCAACAGCATCT
* *
61951 TCTTGGAAAGCCAGCAGC
1 TCTTGGAAAACCAACAGC
61969 CAAGAACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.21
Consensus pattern (22 bp):
TCTTGGAAAACCAACAGCATCT
Found at i:67307 original size:21 final size:22
Alignment explanation
Indices: 67282--67339 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
67272 AAGTTCACAG
67282 AAGAAG-ATAGAAAATCCAGAA
1 AAGAAGAATAGAAAATCCAGAA
* *
67303 AAGAAGAAAAAAAAATCCAGAA
1 AAGAAGAATAGAAAATCCAGAA
67325 ACAGAAAGAATAGAA
1 A-AG-AAGAATAGAA
67340 CAAGCAACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.20
22 14 0.47
23 2 0.07
24 8 0.27
ACGTcount: A:0.67, C:0.09, G:0.17, T:0.07
Consensus pattern (22 bp):
AAGAAGAATAGAAAATCCAGAA
Found at i:70215 original size:14 final size:16
Alignment explanation
Indices: 70178--70215 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
70168 ATATATTTTT
70178 ATAATAAAATATTGTA
1 ATAATAAAATATTGTA
*
70194 AAAATAAAA-ATT-TA
1 ATAATAAAATATTGTA
70208 ATAATAAA
1 ATAATAAA
70216 TTTAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAATAAAATATTGTA
Found at i:71750 original size:15 final size:15
Alignment explanation
Indices: 71730--71764 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
71720 CTTTTAAATG
71730 ATTAATTAGACAATA
1 ATTAATTAGACAATA
* *
71745 ATTAATTAGATAATT
1 ATTAATTAGACAATA
71760 ATTAA
1 ATTAA
71765 CCTTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (15 bp):
ATTAATTAGACAATA
Found at i:72759 original size:4 final size:4
Alignment explanation
Indices: 72750--72776 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
72740 ATATACCTAT
72750 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
72777 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:73085 original size:154 final size:158
Alignment explanation
Indices: 72780--73077 Score: 363
Period size: 161 Copynumber: 1.9 Consensus size: 158
72770 ATACATATAT
* * ** *
72780 ATATATAAAATATGCTGCATGCTTGGCCCCTAAAGCGGAGAAAAGAAGGTGAACTTAAATGAGAT
1 ATATATAAAATATGCTGAATGCTTGGCCCCTAAAACGGAGAAAAGAAGACGAACGTAAATGAGAT
*
72845 TTGTAGTTATACTAATTGGGGCTTTTATTATAGTTTGATACACTCTAGACTGGGCTGGTTTTGTG
66 ATGTAGTTATACTAATTGGGGCTTTTATTATAGTTTGATACACTCT--A-TGGGCTGGTTTTGTG
72910 TGTGTTAGATATTTGCAACACAAACATATCC
128 TGTGTTAGATATTTGCAACACAAACATATCC
* * ** * *
72941 ATATATATAATATGCTGAATGCTTTGCCTGTAAAATGGAGAAAAGATGACGAACGTAAATGA-A-
1 ATATATAAAATATGCTGAATGCTTGGCCCCTAAAACGGAGAAAAGAAGACGAACGTAAATGAGAT
* * * * *
73004 AT-TAGTTGTACTAATTGGGGTTTTTGTTATAGTTTGGTATACTCT-TGGGCT-GTATTTGTGTG
66 ATGTAGTTATACTAATTGGGGCTTTTATTATAGTTTGATACACTCTATGGGCTGGT-TTTGTGTG
*
73066 TTTTAGATATTT
130 TGTTAGATATTT
73078 TTAACACACA
Statistics
Matches: 118, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
153 2 0.02
154 25 0.21
158 38 0.32
159 1 0.01
160 1 0.01
161 51 0.43
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (158 bp):
ATATATAAAATATGCTGAATGCTTGGCCCCTAAAACGGAGAAAAGAAGACGAACGTAAATGAGAT
ATGTAGTTATACTAATTGGGGCTTTTATTATAGTTTGATACACTCTATGGGCTGGTTTTGTGTGT
GTTAGATATTTGCAACACAAACATATCC
Found at i:78829 original size:23 final size:23
Alignment explanation
Indices: 78803--78871 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
78793 TTCATTTAAC
*
78803 TTAATCGAACATGTTCACGAACA
1 TTAATCAAACATGTTCACGAACA
*
78826 TTAAACAAACATGTT-ACGAACA
1 TTAATCAAACATGTTCACGAACA
*
78848 TATAATTAAACATGTTCACGAACA
1 T-TAATCAAACATGTTCACGAACA
78872 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 8 0.20
23 25 0.62
24 7 0.17
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (23 bp):
TTAATCAAACATGTTCACGAACA
Found at i:83720 original size:16 final size:17
Alignment explanation
Indices: 83699--83738 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
83689 GCCTTTTTTT
83699 TTTATTTTAAAAT-TTA
1 TTTATTTTAAAATATTA
*
83715 TTTATTGTAAAATATTA
1 TTTATTTTAAAATATTA
83732 -TTATTTT
1 TTTATTTT
83739 TAGACTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTATTTTAAAATATTA
Found at i:87420 original size:10 final size:10
Alignment explanation
Indices: 87384--87422 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
87374 AAAAAACAAA
87384 ATAAAAATTT
1 ATAAAAATTT
*
87394 ATAGAAAGTTT
1 ATA-AAAATTT
*
87405 ATAAAAATTC
1 ATAAAAATTT
87415 ATAAAAAT
1 ATAAAAAT
87423 ATCAATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:88048 original size:5 final size:5
Alignment explanation
Indices: 88038--88066 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
88028 CTAGTTAAAA
88038 TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTAT
88067 AAAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:94640 original size:29 final size:30
Alignment explanation
Indices: 94574--94640 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 30
94564 GTTTAACTTT
94574 ATTTGATTCTTTTGAATAATAGATGAACTA
1 ATTTGATTCTTTTGAATAATAGATGAACTA
* * *
94604 AATCGATT-TATTTG-ATAGTAGAATG-ACTA
1 ATTTGATTCT-TTTGAATAATAG-ATGAACTA
94633 ATTTGATT
1 ATTTGATT
94641 GGATCCCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (30 bp):
ATTTGATTCTTTTGAATAATAGATGAACTA
Found at i:100687 original size:13 final size:12
Alignment explanation
Indices: 100653--100683 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
100643 TAACAAAAAA
100653 AAAATTAAATTT
1 AAAATTAAATTT
100665 AACAATTAAATTT
1 AA-AATTAAATTT
100678 AAAATT
1 AAAATT
100684 TAAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:101256 original size:19 final size:18
Alignment explanation
Indices: 101232--101268 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
101222 AATTTCTATC
101232 AAAAATCAAAGAAGAAAAA
1 AAAAATCAAAGAA-AAAAA
*
101251 AAAAATCAGAGAAAAAAA
1 AAAAATCAAAGAAAAAAA
101269 TGGGAGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.78, C:0.05, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAATCAAAGAAAAAAA
Found at i:104939 original size:18 final size:18
Alignment explanation
Indices: 104904--104939 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
104894 GTTTGTAATA
* *
104904 TTATATATTATTTTATTT
1 TTATATATTATGTAATTT
104922 TTATATATTATGTAATTT
1 TTATATATTATGTAATTT
104940 ATAATAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATATATTATGTAATTT
Found at i:104969 original size:22 final size:23
Alignment explanation
Indices: 104935--104979 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
104925 TATATTATGT
104935 AATTTATAATAAT-TAAAAATTA
1 AATTTATAATAATATAAAAATTA
** *
104957 AATTTATTGTAATATAAATATTA
1 AATTTATAATAATATAAAAATTA
104980 TTATAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTTATAATAATATAAAAATTA
Found at i:104986 original size:17 final size:16
Alignment explanation
Indices: 104955--104991 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
104945 AATTAAAAAT
*
104955 TAAATTTATTGTAATA
1 TAAATTTATTATAATA
104971 TAAATATTATTATAATA
1 TAAAT-TTATTATAATA
104988 TAAA
1 TAAA
104992 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TAAATTTATTATAATA
Found at i:105051 original size:40 final size:40
Alignment explanation
Indices: 105007--105083 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
104997 TTAAAAAAAT
* *
105007 TAAAATGATTATAT-TTAAAATTATAATAAATACAAATACA
1 TAAAATGATTAAATATT-AAATTAAAATAAATACAAATACA
* *
105047 TAAAATGATTAAATATTATATTAAAATAAATATAAAT
1 TAAAATGATTAAATATTAAATTAAAATAAATACAAAT
105084 GTATATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 30 0.94
41 2 0.06
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (40 bp):
TAAAATGATTAAATATTAAATTAAAATAAATACAAATACA
Found at i:106570 original size:100 final size:98
Alignment explanation
Indices: 106254--106573 Score: 321
Period size: 100 Copynumber: 3.2 Consensus size: 98
106244 AATCATGTTG
* * *
106254 GATGTGAT-AGATGTGATTTGATGGAGCTTGGCGT-AGACC-CCATTAAATGAGTATTTTATTGT
1 GATGTGATAAGATGTCACTTGAT-GAGCTTGGTGTAAG-CCTCC-TTAAATGAGTATTTTATTGT
* *
106316 GTCAGGTTTGTAGTAAGATCATGGAGAATTCTATTGA
63 GTAAGGTTTGTAGTAAGGTCATGGAGAATT-TATTGA
* * *
106353 GATGTGATAAGATGTCACTTGATGAAGCTTGGTGTATGCCTCGTTAAA-G-G-ATTTTATTGTGC
1 GATGTGATAAGATGTCACTTGATG-AGCTTGGTGTAAGCCTCCTTAAATGAGTATTTTATTGTGT
** * *
106415 AAGGACTGTAGTAAGGTCATGGAGAACTTTGTTGG
65 AAGGTTTGTAGTAAGGTCATGGAGAA-TTTATTGA
* * * *
106450 GATGTAATAAGATGCCACTTGATCGAGCTTGGTGTAAGCCTCCCTAAATGAGTATCTTATTGTGT
1 GATGTGATAAGATGTCACTTGAT-GAGCTTGGTGTAAGCCTCCTTAAATGAGTATTTTATTGTGT
* * * *
106515 AAGGTTTGTAGTAAGGTGACGAAGAATATTATTCA
65 AAGGTTTGTAGTAAGGTCATGGAGAAT-TTATTGA
*
106550 GATGTGAT-AGAATGTGACTTGATG
1 GATGTGATAAG-ATGTCACTTGATG
106574 GTAACGTATA
Statistics
Matches: 180, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
97 78 0.43
98 5 0.03
99 15 0.08
100 80 0.44
101 2 0.01
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (98 bp):
GATGTGATAAGATGTCACTTGATGAGCTTGGTGTAAGCCTCCTTAAATGAGTATTTTATTGTGTA
AGGTTTGTAGTAAGGTCATGGAGAATTTATTGA
Found at i:120581 original size:27 final size:26
Alignment explanation
Indices: 120529--120587 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
120519 ATGATTATAT
120529 ATAAAATTTTAATATCTGAAAAAATAA
1 ATAAAATTTTAATATCTGAAAAAAT-A
*
120556 ATAAAATTATTAATAT-T-AAATTAATA
1 ATAAAATT-TTAATATCTGAAA-AAATA
120582 ATAAAA
1 ATAAAA
120588 AATATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 10 0.34
27 12 0.41
28 7 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
ATAAAATTTTAATATCTGAAAAAATA
Found at i:121586 original size:33 final size:34
Alignment explanation
Indices: 121550--121612 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
121540 ATTTGTGTGT
*
121550 TTTTTTATAAAAT-TTATAAATAT-TTTTTTCGA
1 TTTTTTATAAAATATTATAAAAATATTTTTTCGA
121582 TTTTTTATAAAATATTATAAAAATATTTTTT
1 TTTTTTATAAAATATTATAAAAATATTTTTT
121613 ATATCAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 13 0.46
33 9 0.32
34 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (34 bp):
TTTTTTATAAAATATTATAAAAATATTTTTTCGA
Found at i:121811 original size:28 final size:25
Alignment explanation
Indices: 121775--121831 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
121765 GGTATCTATG
*
121775 TTATTCAAAGAATGAGTATTAAATATTT
1 TTATACAAAGAAT-A-TA-TAAATATTT
* *
121803 TTATACAAATAATATATAAATTTTT
1 TTATACAAAGAATATATAAATATTT
121828 TTAT
1 TTAT
121832 GGGTTTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 12 0.46
26 2 0.08
27 1 0.04
28 11 0.42
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (25 bp):
TTATACAAAGAATATATAAATATTT
Found at i:122948 original size:8 final size:8
Alignment explanation
Indices: 122935--122969 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
122925 TATAAGATAA
*
122935 ATGGTGTC
1 ATGGTGCC
122943 ATGGTGCC
1 ATGGTGCC
122951 ATGGTGCC
1 ATGGTGCC
122959 ATGGTGCC
1 ATGGTGCC
122967 ATG
1 ATG
122970 TTAGCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.14, C:0.20, G:0.37, T:0.29
Consensus pattern (8 bp):
ATGGTGCC
Found at i:124487 original size:15 final size:15
Alignment explanation
Indices: 124467--124495 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
124457 GAGCAGTACG
124467 GTGCAGTGCAATGCA
1 GTGCAGTGCAATGCA
124482 GTGCAGTGCAATGC
1 GTGCAGTGCAATGC
124496 GTTTAGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (15 bp):
GTGCAGTGCAATGCA
Found at i:156063 original size:25 final size:26
Alignment explanation
Indices: 156035--156087 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
156025 ATTATATAGA
156035 AAATTTCAATAAATA-AAAAAT-ATAT
1 AAATTT-AATAAATATAAAAATAATAT
* *
156060 AAATTTATTAAATATTAAAATAATAT
1 AAATTTAATAAATATAAAAATAATAT
156086 AA
1 AA
156088 TATAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 11 0.46
26 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATTTAATAAATATAAAAATAATAT
Found at i:157537 original size:2 final size:2
Alignment explanation
Indices: 157530--157554 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
157520 TTCTTTTGCT
157530 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 T
157555 CAGGCTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:167469 original size:19 final size:18
Alignment explanation
Indices: 167458--167496 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
167448 AAATTATTAC
167458 AAAATTTAAAAAATATAA
1 AAAATTTAAAAAATATAA
167476 AAAATATT--AAAATATAA
1 AAAAT-TTAAAAAATATAA
167493 AAAA
1 AAAA
167497 AGTAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.65
18 5 0.25
19 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTTAAAAAATATAA
Found at i:167476 original size:9 final size:9
Alignment explanation
Indices: 167458--167496 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
167448 AAATTATTAC
*
167458 AAAATTTAA
1 AAAATATAA
167467 AAAATATAA
1 AAAATATAA
*
167476 AAAATAT-T
1 AAAATATAA
167484 AAAATATAA
1 AAAATATAA
167493 AAAA
1 AAAA
167497 AGTAATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATATAA
Found at i:167497 original size:19 final size:18
Alignment explanation
Indices: 167458--167497 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
167448 AAATTATTAC
*
167458 AAAATTTAAAAAATATAA
1 AAAATTTAAAAAATAAAA
*
167476 AAAATATTAAAATATAAAA
1 AAAAT-TTAAAAAATAAAA
167495 AAA
1 AAA
167498 GTAATGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATTTAAAAAATAAAA
Found at i:167507 original size:19 final size:18
Alignment explanation
Indices: 167467--167515 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
167457 CAAAATTTAA
*
167467 AAAATAT-AAAAAATATT
1 AAAATATAAAAAAATAAT
167484 AAAATATAAAAAAAGTAAT
1 AAAATATAAAAAAA-TAAT
*
167503 GAAATTATAAAAA
1 -AAAATATAAAAA
167516 TGGTAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 3 0.11
20 11 0.41
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (18 bp):
AAAATATAAAAAAATAAT
Found at i:171831 original size:29 final size:29
Alignment explanation
Indices: 171759--171825 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
171749 CCCAGTCAGT
171759 TGACTAAAAGATAACATTTCAAACATAAG
1 TGACTAAAAGATAACATTTCAAACATAAG
* *
171788 TGACTAAACGATAACATTTCAAATATAAG
1 TGACTAAAAGATAACATTTCAAACATAAG
171817 TGACTAAAA
1 TGACTAAAA
171826 TGTAACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.25
Consensus pattern (29 bp):
TGACTAAAAGATAACATTTCAAACATAAG
Found at i:171870 original size:31 final size:31
Alignment explanation
Indices: 171817--171878 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
171807 CAAATATAAG
** *
171817 TGACTAAAATGTAACTTAAGACAAACAAAAA
1 TGACTAAAATGTAACCGAAGACAAAAAAAAA
*
171848 TGACTAAAATGTAACCGGAGACAAAAAAAAA
1 TGACTAAAATGTAACCGAAGACAAAAAAAAA
171879 AATGTAACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (31 bp):
TGACTAAAATGTAACCGAAGACAAAAAAAAA
Found at i:173413 original size:20 final size:20
Alignment explanation
Indices: 173376--173414 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
173366 AATTTTACAG
* * *
173376 AATAATATAATATTAAAGTA
1 AATAAAATAAAATAAAAGTA
173396 AATAAAATAAAATAAAAGT
1 AATAAAATAAAATAAAAGT
173415 GATAAACAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
AATAAAATAAAATAAAAGTA
Found at i:176742 original size:86 final size:85
Alignment explanation
Indices: 176633--176803 Score: 324
Period size: 86 Copynumber: 2.0 Consensus size: 85
176623 TAATGAGAAG
*
176633 TTTTAATAATGTTGGGGACCAATAGAAAATATTGAAGCTTACGTGGAATGTCATCATTTGCAAAT
1 TTTTAATAATGTTGGGGACCAATAGAAAATATTGAAGCTTAAGTGGAATGTCATCATTTGCAAAT
176698 GAGTACCTTCATTTTTCATA
66 GAGTACCTTCATTTTTCATA
176718 TTTTCAATAATGTTGGGGACCAATAGAAAATATTGAAGCTTAAGTGGAATGTCATCATTTGCAAA
1 TTTT-AATAATGTTGGGGACCAATAGAAAATATTGAAGCTTAAGTGGAATGTCATCATTTGCAAA
176783 TGAGTACCTTCATTTTTCATA
65 TGAGTACCTTCATTTTTCATA
176804 GAAGTTCACC
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 4 0.05
86 80 0.95
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (85 bp):
TTTTAATAATGTTGGGGACCAATAGAAAATATTGAAGCTTAAGTGGAATGTCATCATTTGCAAAT
GAGTACCTTCATTTTTCATA
Found at i:186035 original size:4 final size:4
Alignment explanation
Indices: 186028--186064 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
186018 AGCATATATA
186028 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
186065 GCATATTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:187988 original size:18 final size:18
Alignment explanation
Indices: 187965--187999 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
187955 CATCTATTGC
187965 TATCTCTATCGATATAAG
1 TATCTCTATCGATATAAG
187983 TATCTCTATCGATATAA
1 TATCTCTATCGATATAA
188000 ATGAGGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (18 bp):
TATCTCTATCGATATAAG
Found at i:192638 original size:18 final size:18
Alignment explanation
Indices: 192617--192659 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
192607 AAATAAAATT
192617 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
192635 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
192653 TTAATTA
1 TTAATTA
192660 CAACTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:195358 original size:176 final size:171
Alignment explanation
Indices: 195061--195380 Score: 478
Period size: 176 Copynumber: 1.8 Consensus size: 171
195051 GATTATAAAC
* * * *
195061 GGAAACCAACATATATAATGATCCAACAAACCTGCACACCCAATGTTAGACGCCTATTTCCGCTT
1 GGAAACCAACATATATAATGATCCAACAAACCTGCACACCAAATGTAAGACGCCTATTGCCGCGT
* * * *
195126 AATATGAGCTAAAACTTTCTGATTTCACAGATATTCATACACAATATCAACCTATTTCGGCTTAA
66 AATATGACCTAAAACTTCCCGATTTCACAGATATTCATACACAATATCAACCTATTTCAGCTTAA
*
195191 GTATGACATAAAACCATGTGGATTCACGGATATCAATCGAT
131 GTATAACATAAAACCATGTGGATTCACGGATATCAATCGAT
195232 GGAAACCAACATATATAATGATCCAACAAACCTGCACACCAAATGCTAAGACAGACACCTATTGC
1 GGAAACCAACATATATAATGATCCAACAAACCTGCACACCAAATG-TAAGAC-G---CCTATTGC
* * * *
195297 CGCGTAATATGTCCTAAAACTTCCCGATTTCGCAGATATTCATAGACAATATCAGCCTATTTCAG
61 CGCGTAATATGACCTAAAACTTCCCGATTTCACAGATATTCATACACAATATCAACCTATTTCAG
195362 CTTAAGTATAACATAAAAC
126 CTTAAGTATAACATAAAAC
195381 ATAGCGGATT
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
171 44 0.34
172 5 0.04
173 1 0.01
176 81 0.62
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (171 bp):
GGAAACCAACATATATAATGATCCAACAAACCTGCACACCAAATGTAAGACGCCTATTGCCGCGT
AATATGACCTAAAACTTCCCGATTTCACAGATATTCATACACAATATCAACCTATTTCAGCTTAA
GTATAACATAAAACCATGTGGATTCACGGATATCAATCGAT
Found at i:200356 original size:1 final size:1
Alignment explanation
Indices: 200350--200384 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
200340 TATAATTCAT
200350 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
200385 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.