Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004539.1 Hibiscus syriacus cultivar Beakdansim tig00010032_pilon, 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: 86348
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3570 original size:38 final size:38
Alignment explanation
Indices: 3516--3707 Score: 276
Period size: 38 Copynumber: 5.1 Consensus size: 38
3506 GTTCTTTGTA
* ** *
3516 TGGATGATATTCTGTCATGCACATACCATGCTCGGAGT
1 TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
*
3554 TGGATGATATTGTGTCACGTGCATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
* *
3592 TCGATGATATTGTGTCACGTGCATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
* ** *
3630 TGGATGATATTATGTCATGTGTGTATCATGCTCGGATT
1 TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
*
3668 TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
3706 TG
1 TG
3708 TTCTAGAACC
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 137 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (38 bp):
TGGATGATATTGTGTCATGTGCATACCATGCTCGGATT
Found at i:4826 original size:44 final size:45
Alignment explanation
Indices: 4762--4849 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
4752 TGTCAACATC
*
4762 TATTAGAAGATTTGACTGTTAAGTAA-T-TAATATATATATATATA
1 TATTAGAAGATTTGAATGTTAAGTAATTGTAATATATATA-ATATA
*
4806 TATTAGAAGATTTGAATGTTAGGTAATTGTAATATATATAATAT
1 TATTAGAAGATTTGAATGTTAAGTAATTGTAATATATATAATAT
4850 TGGTGATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
44 24 0.60
45 5 0.12
46 11 0.28
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (45 bp):
TATTAGAAGATTTGAATGTTAAGTAATTGTAATATATATAATATA
Found at i:10675 original size:27 final size:27
Alignment explanation
Indices: 10637--10698 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
10627 TGACATTAGA
10637 TTCAGTTCGGGTTCAGGTCGGGTTAAT
1 TTCAGTTCGGGTTCAGGTCGGGTTAAT
10664 TTCAGTTCGGGTTCAGGTCGGGTTAAT
1 TTCAGTTCGGGTTCAGGTCGGGTTAAT
10691 TTCAGTTC
1 TTCAGTTC
10699 AGATCGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.15, C:0.16, G:0.31, T:0.39
Consensus pattern (27 bp):
TTCAGTTCGGGTTCAGGTCGGGTTAAT
Found at i:10694 original size:16 final size:16
Alignment explanation
Indices: 10648--10695 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
10638 TCAGTTCGGG
10648 TTCAGGTCGGGTTAAT
1 TTCAGGTCGGGTTAAT
*
10664 TTCAGTTCGGG-----
1 TTCAGGTCGGGTTAAT
10675 TTCAGGTCGGGTTAAT
1 TTCAGGTCGGGTTAAT
10691 TTCAG
1 TTCAG
10696 TTCAGATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
11 10 0.40
16 15 0.60
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.38
Consensus pattern (16 bp):
TTCAGGTCGGGTTAAT
Found at i:10797 original size:11 final size:11
Alignment explanation
Indices: 10783--10809 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
10773 GACTTCAGTT
10783 AGATCTCATTC
1 AGATCTCATTC
10794 AGATCTCATTC
1 AGATCTCATTC
10805 AGATC
1 AGATC
10810 GGGTGACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (11 bp):
AGATCTCATTC
Found at i:11386 original size:2 final size:2
Alignment explanation
Indices: 11381--11610 Score: 98
Period size: 2 Copynumber: 117.5 Consensus size: 2
11371 AACAATGATA
* *
11381 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AA AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
11421 AG A- AT AT A- AT AT AGT TT AT AT AT A- AT AGT AT AT AA AT AT AA
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
11462 ACT AT AT GAT TT AT AT AT AGT TT AT A- AT A- AT AA ACT AT AT A-
1 A-T AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
* * *
11503 AT TT AT AT AT AGT AT AT AT A- AT TT AT A- AT -T AT AC AT AGT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
11544 AT AT AT -T A- AT AT CAG CT AT AT AT AT AA AT -T AT AT AT ACT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
11585 AT AGT -T GAT AT -T A- AT AT AT AT AT AT A
1 AT A-T AT -AT AT AT AT AT AT AT AT AT AT A
11611 CTATGTATAA
Statistics
Matches: 171, Mismatches: 28, Indels: 58
0.67 0.11 0.23
Matches are distributed among these distances:
1 17 0.10
2 137 0.80
3 17 0.10
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11477 original size:69 final size:66
Alignment explanation
Indices: 11378--11523 Score: 154
Period size: 67 Copynumber: 2.2 Consensus size: 66
11368 TGAAACAATG
* * * * *
11378 ATAATATATATATATGTATA-TATATATATATATA-AATTATATAAGAATATA-ATATAGTTTAT
1 ATAATATATATAAATATAAACTATATATATATATATAATT-TATAAGAATAAACATATAATTTAT
11440 AT
65 AT
* * *
11442 ATAATAGTATATAAATATAAACTATATGATTTATATATAGTTTATAATAATAAACTATATAATTT
1 ATAATA-TATATAAATATAAACTATAT-ATATATATATAATTTATAAGAATAAAC-ATATAATTT
11507 ATAT
63 ATAT
*
11511 ATAGTATATATAA
1 ATAATATATATAA
11524 TTTATAATTA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
64 6 0.09
65 11 0.16
66 5 0.07
67 18 0.27
68 10 0.15
69 17 0.25
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (66 bp):
ATAATATATATAAATATAAACTATATATATATATATAATTTATAAGAATAAACATATAATTTATA
T
Found at i:11488 original size:33 final size:34
Alignment explanation
Indices: 11439--11520 Score: 123
Period size: 33 Copynumber: 2.4 Consensus size: 34
11429 ATATAGTTTA
*
11439 TATATAATAGTATATAAAT-ATAAACTATATGATT
1 TATAT-ATAGTATATAAATAATAAACTATATAATT
*
11473 TATATATAGTTTAT-AATAATAAACTATATAATT
1 TATATATAGTATATAAATAATAAACTATATAATT
11506 TATATATAGTATATA
1 TATATATAGTATATA
11521 TAATTTATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 3 0.07
33 35 0.81
34 5 0.12
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (34 bp):
TATATATAGTATATAAATAATAAACTATATAATT
Found at i:11632 original size:28 final size:27
Alignment explanation
Indices: 11565--11643 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
11555 TCAGCTATAT
*
11565 ATATAAATTATATATACTA-TATAGTTG
1 ATATAAATTATATATA-TACTATAGTTA
*
11592 ATATTAATATATATATATACTAT-GTATA
1 ATATAAAT-TATATATATACTATAGT-TA
11620 ATTATAAATTATATACTAT-CTATA
1 A-TATAAATTATATA-TATACTATA
11644 AATTATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
27 11 0.26
28 23 0.53
29 9 0.21
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (27 bp):
ATATAAATTATATATATACTATAGTTA
Found at i:11633 original size:30 final size:27
Alignment explanation
Indices: 11565--11643 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 27
11555 TCAGCTATAT
*
11565 ATATAAATTATATATACTATATAGTTG
1 ATATAAATTATATATACTATATAGTTA
*
11592 ATATTAA-TATATATA-TATACTATGTATA
1 ATATAAATTATATATACTATA-TA-GT-TA
11620 ATTATAAATTATATACTATCTATA
1 A-TATAAATTATATA-TA-CTATA
11644 AATTATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
25 4 0.10
26 10 0.24
27 8 0.20
28 2 0.05
29 5 0.12
30 6 0.15
31 2 0.05
33 4 0.10
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (27 bp):
ATATAAATTATATATACTATATAGTTA
Found at i:11733 original size:22 final size:24
Alignment explanation
Indices: 11699--11765 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 24
11689 ATAAATTATA
* * *
11699 TATAAACTATATAAACTGTATAGT
1 TATAAATTATATAAACTATATAAT
* *
11723 T-TATATT-TATACACTATATAAT
1 TATAAATTATATAAACTATATAAT
11745 TATAAATTATATAAACTATAT
1 TATAAATTATATAAACTATAT
11766 TTTATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 13 0.38
23 9 0.26
24 12 0.35
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (24 bp):
TATAAATTATATAAACTATATAAT
Found at i:11775 original size:18 final size:18
Alignment explanation
Indices: 11752--11801 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
11742 AATTATAAAT
* *
11752 TATATAAACTATATTTTA
1 TATATAAACTATAGTCTA
11770 TATATAAACTATAGTCTA
1 TATATAAACTATAGTCTA
11788 TATATAAACTATAG
1 TATATAAACTATAG
11802 AGTTTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (18 bp):
TATATAAACTATAGTCTA
Found at i:11906 original size:33 final size:34
Alignment explanation
Indices: 11845--11961 Score: 112
Period size: 35 Copynumber: 3.4 Consensus size: 34
11835 ATGGCTTATA
* *
11845 TATATAGTTTATATTAATATATATACTATGTATAAAT
1 TATATAG-TT-TATTAATATACA-ACTATGTATAAAC
* *
11882 TATATAGTTTATTAATATA-AACTATATATAAGC
1 TATATAGTTTATTAATATACAACTATGTATAAAC
* *
11915 CATATAGTTTATACTTATATACAACTATGTA-AAAC
1 TATATAGTTTAT--TAATATACAACTATGTATAAAC
*
11950 TCTATAGTTTAT
1 TATATAGTTTAT
11962 ATATATAGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
33 21 0.31
34 1 0.01
35 29 0.43
36 10 0.15
37 7 0.10
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (34 bp):
TATATAGTTTATTAATATACAACTATGTATAAAC
Found at i:11956 original size:35 final size:34
Alignment explanation
Indices: 11847--11968 Score: 117
Period size: 33 Copynumber: 3.5 Consensus size: 34
11837 GGCTTATATA
* *
11847 TATAGTTTATATTAATATATATACTATGTATAAATTA
1 TATAGTTTATATT-ATATA-A-ACTATGTATAAACTC
* * *
11884 TATAGTTTAT-TAATATAAACTATATATAAGC-C
1 TATAGTTTATATTATATAAACTATGTATAAACTC
11916 ATATAGTTTATACTTATATACAACTATGTA-AAACTC
1 -TATAGTTTATA-TTATATA-AACTATGTATAAACTC
11952 TATAGTTTATA-TATATA
1 TATAGTTTATATTATATA
11969 GTATATATGG
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
33 26 0.36
34 1 0.01
35 25 0.35
36 10 0.14
37 10 0.14
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (34 bp):
TATAGTTTATATTATATAAACTATGTATAAACTC
Found at i:13357 original size:24 final size:24
Alignment explanation
Indices: 13328--13375 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
13318 TACAAACAAA
*
13328 TTTATTTATTGACTTATTTATAAG
1 TTTATTTATCGACTTATTTATAAG
13352 TTTATTTATCGACTTATTTATAAG
1 TTTATTTATCGACTTATTTATAAG
13376 CTCGTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTATTTATCGACTTATTTATAAG
Found at i:13383 original size:24 final size:24
Alignment explanation
Indices: 13331--13384 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
13321 AAACAAATTT
* * *
13331 ATTTATTGACTTATTTATAAGTTT
1 ATTTATCGACTTATTTATAAGCTC
13355 ATTTATCGACTTATTTATAAGCTC
1 ATTTATCGACTTATTTATAAGCTC
*
13379 GTTTAT
1 ATTTAT
13385 TCGATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (24 bp):
ATTTATCGACTTATTTATAAGCTC
Found at i:13596 original size:23 final size:23
Alignment explanation
Indices: 13566--13609 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
13556 GTTGGTTGAA
* *
13566 GAATATATTCGCAGACGTTAAAC
1 GAATATATTCACAAACGTTAAAC
13589 GAATATATTCACAAACGTTAA
1 GAATATATTCACAAACGTTAA
13610 GCGTACACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (23 bp):
GAATATATTCACAAACGTTAAAC
Found at i:17095 original size:21 final size:20
Alignment explanation
Indices: 17039--17095 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
17029 CCAAATTTTT
*
17039 TCAGTAGGTATCGATACTCTC
1 TCAG-AGGTATCGATACTCAC
* *
17060 TCAGAGGTATTGATAGTCAC
1 TCAGAGGTATCGATACTCAC
*
17080 TCATATGGTATCGATA
1 TCAGA-GGTATCGATA
17096 AGTTAGGGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (20 bp):
TCAGAGGTATCGATACTCAC
Found at i:18068 original size:30 final size:30
Alignment explanation
Indices: 18029--18095 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
18019 TAAAGTTTGG
* *
18029 AAAAATTTAGGGACTAAA-ATGTTAATTTTC
1 AAAAGTTTAGGGACCAAATATG-TAATTTTC
* *
18059 AAAAGTTTAGGGACCAAATATGTACTTTTT
1 AAAAGTTTAGGGACCAAATATGTAATTTTC
18089 AAAAGTT
1 AAAAGTT
18096 AGGTGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (30 bp):
AAAAGTTTAGGGACCAAATATGTAATTTTC
Found at i:23076 original size:19 final size:19
Alignment explanation
Indices: 23052--23139 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 19
23042 TATGTATTGG
23052 GCTATGAA-CTTGAAAATAA
1 GCTATGAATC-TGAAAATAA
*
23071 GCTATGAATCTGAAATTAA
1 GCTATGAATCTGAAAATAA
*
23090 GTTATGAATCT-AAAATAA
1 GCTATGAATCTGAAAATAA
* * * *
23108 GTTATGAGTCCGAAAACAA
1 GCTATGAATCTGAAAATAA
*
23127 GTTATGAATCTGA
1 GCTATGAATCTGA
23140 GAATGAGTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
18 15 0.25
19 43 0.73
20 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:23106 original size:37 final size:37
Alignment explanation
Indices: 23064--23137 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
23054 TATGAACTTG
* **
23064 AAAATAAGCTATGAATCTGAAATTAAGTTATGAATCT
1 AAAATAAGCTATGAATCCGAAAACAAGTTATGAATCT
* *
23101 AAAATAAGTTATGAGTCCGAAAACAAGTTATGAATCT
1 AAAATAAGCTATGAATCCGAAAACAAGTTATGAATCT
23138 GAGAATGAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (37 bp):
AAAATAAGCTATGAATCCGAAAACAAGTTATGAATCT
Found at i:23148 original size:19 final size:19
Alignment explanation
Indices: 23062--23153 Score: 105
Period size: 19 Copynumber: 4.9 Consensus size: 19
23052 GCTATGAACT
*
23062 TGAAAATAAGCTATGAATC
1 TGAAAATAAGTTATGAATC
*
23081 TGAAATTAAGTTATGAATC
1 TGAAAATAAGTTATGAATC
*
23100 T-AAAATAAGTTATGAGTC
1 TGAAAATAAGTTATGAATC
* *
23118 CGAAAACAAGTTATGAATC
1 TGAAAATAAGTTATGAATC
* * *
23137 TGAGAATGAGTTCTGAA
1 TGAAAATAAGTTATGAA
23154 ATGTGAAAGT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
18 15 0.25
19 45 0.75
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.29
Consensus pattern (19 bp):
TGAAAATAAGTTATGAATC
Found at i:23280 original size:18 final size:18
Alignment explanation
Indices: 23257--23321 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
23247 TGAAAAAGAA
23257 TATGATATGACTATTATG
1 TATGATATGACTATTATG
** *
23275 TATGATATTGTTTATCATGG
1 TATGATA-TGACTATTAT-G
*
23295 TTTTGATATGACTATTATG
1 -TATGATATGACTATTATG
23314 TATGATAT
1 TATGATAT
23322 TGTTTATCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 14 0.39
19 8 0.22
20 8 0.22
21 6 0.17
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (18 bp):
TATGATATGACTATTATG
Found at i:23307 original size:39 final size:39
Alignment explanation
Indices: 23259--23341 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
23249 AAAAAGAATA
23259 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
23298 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
23337 TGATA
1 TGATA
23342 AAGTCATGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.51
Consensus pattern (39 bp):
TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
Found at i:23762 original size:2 final size:2
Alignment explanation
Indices: 23755--23786 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23745 GTTTTAGATA
23755 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
23787 TGACAGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24835 original size:19 final size:20
Alignment explanation
Indices: 24810--24906 Score: 107
Period size: 19 Copynumber: 5.0 Consensus size: 20
24800 ACCGGTTTTC
*
24810 AACCGGTTCTGACCGG-TTTG
1 AACCGGTT-TGACCGGATCTG
* *
24830 -ACCGGTTTTAACCGGTTC-G
1 AACCGG-TTTGACCGGATCTG
24849 AACCGGTTTGACC-GATCTG
1 AACCGGTTTGACCGGATCTG
24868 AACCGGTTTGACC-GATCTG
1 AACCGGTTTGACCGGATCTG
24887 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGATCTG
24906 A
1 A
24907 CCCGACCCGA
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
18 3 0.04
19 56 0.82
20 9 0.13
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (20 bp):
AACCGGTTTGACCGGATCTG
Found at i:24847 original size:29 final size:29
Alignment explanation
Indices: 24800--24908 Score: 109
Period size: 29 Copynumber: 3.8 Consensus size: 29
24790 GCTGCTGGAA
24800 ACCGGTTTTCAACCGGTTCTGACCGGTTTG
1 ACCGGTTTT-AACCGGTTCTGACCGGTTTG
24830 ACCGGTTTTAACCGGTTC-GAACCGGTTTG
1 ACCGGTTTTAACCGGTTCTG-ACCGGTTTG
* * * * *
24859 ACCGATCTGAACCGGTT-TGACCGATCTG
1 ACCGGTTTTAACCGGTTCTGACCGGTTTG
*
24887 AACCGG-TTTGACCGG-TCTGACC
1 -ACCGGTTTTAACCGGTTCTGACC
24909 CGACCCGACC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
27 1 0.02
28 19 0.29
29 37 0.56
30 9 0.14
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (29 bp):
ACCGGTTTTAACCGGTTCTGACCGGTTTG
Found at i:24915 original size:5 final size:5
Alignment explanation
Indices: 24905--24962 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
24895 TGACCGGTCT
* * *
24905 GACCC GACCC GACCC GACCGTT GACCT GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
24954 GACCC GACC
1 GACCC GACC
24963 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.50, G:0.22, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:24930 original size:22 final size:22
Alignment explanation
Indices: 24904--24962 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
24894 TTGACCGGTC
24904 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
*
24926 TGACCTGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
24948 TGACCCGACCCGACC
1 TGACCCGACCCGACC
24963 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:24935 original size:17 final size:17
Alignment explanation
Indices: 24931--24969 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
24921 ACCGTTGACC
24931 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
24948 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
24965 TGACC
1 TGACC
24970 GTTGACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:26793 original size:12 final size:12
Alignment explanation
Indices: 26778--26812 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
26768 TCGATTTAAC
26778 AATAATTTATTA
1 AATAATTTATTA
26790 AATAATTTATTA
1 AATAATTTATTA
*
26802 ATTAATTTATT
1 AATAATTTATT
26813 GTTGTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATAATTTATTA
Found at i:29006 original size:35 final size:34
Alignment explanation
Indices: 28932--29008 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 34
28922 ATATAGTTTT
* *
28932 TAATTTTTTATATTTAATGTATTAAATATCTTAA
1 TAATTTTTTATATTTAATATATTAAATATATTAA
*
28966 TAATTTTTTATATTTTAA-AT-TTAAATTTATATAA
1 TAATTTTTTATA-TTTAATATATTAAATATAT-TAA
29000 TGAATTTTT
1 T-AATTTTT
29009 ATAATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 8 0.22
34 17 0.46
35 12 0.32
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (34 bp):
TAATTTTTTATATTTAATATATTAAATATATTAA
Found at i:29346 original size:18 final size:19
Alignment explanation
Indices: 29320--29375 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
29310 ATTTTTTATT
*
29320 AAACCATTTA-AAATCGTA
1 AAACAATTTATAAATCGTA
*
29338 AAACAATTTATAAAT-GAA
1 AAACAATTTATAAATCGTA
29356 AACACAATTTCATAAATCGT
1 AA-ACAATTT-ATAAATCGT
29376 TCATAAATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 13 0.42
19 11 0.35
20 6 0.19
21 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
AAACAATTTATAAATCGTA
Found at i:34210 original size:31 final size:32
Alignment explanation
Indices: 34167--34254 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
34157 TGCAACTGTT
* *
34167 CATAGGTCCCGAAGAACCTAGGTAA-AATGTC
1 CATATGTCCCGAAGAACATAGGTAATAATGTC
* * *
34198 CATATGTCCCGAAGGATATAGGTAATCATGTC
1 CATATGTCCCGAAGAACATAGGTAATAATGTC
**
34230 CATATGTCTTGAA-AGACATAGGTAA
1 CATATGTCCCGAAGA-ACATAGGTAA
34255 CCCTCGACTC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 21 0.46
32 25 0.54
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (32 bp):
CATATGTCCCGAAGAACATAGGTAATAATGTC
Found at i:39410 original size:31 final size:30
Alignment explanation
Indices: 39350--39444 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 30
39340 GAACCTCGGC
*
39350 AACTGTCCATA-GTTCTCGAAGAACCTAGGTA
1 AACTGTCCATATG-TCTCGAAG-ACATAGGTA
*
39381 AACTGTCCATATGTCCCGAATGACATAGGTA
1 AACTGTCCATATGTCTCGAA-GACATAGGTA
*
39412 ATCATGTCCATATGTCTCGAAAGACATAGGTA
1 AAC-TGTCCATATGTCTCG-AAGACATAGGTA
39444 A
1 A
39445 CCCTCGACTC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
31 27 0.48
32 27 0.48
33 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (30 bp):
AACTGTCCATATGTCTCGAAGACATAGGTA
Found at i:39422 original size:32 final size:31
Alignment explanation
Indices: 39350--39444 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 31
39340 GAACCTCGGC
* *
39350 AACTGTCCATA-GTTCTCG-AAGAACCTAGGTA
1 AACTGTCCATATG-TCCCGAAAG-ACATAGGTA
*
39381 AACTGTCCATATGTCCCGAATGACATAGGTA
1 AACTGTCCATATGTCCCGAAAGACATAGGTA
* *
39412 ATCATGTCCATATGTCTCGAAAGACATAGGTA
1 AAC-TGTCCATATGTCCCGAAAGACATAGGTA
39444 A
1 A
39445 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
31 25 0.45
32 30 0.55
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAAGACATAGGTA
Found at i:39531 original size:22 final size:22
Alignment explanation
Indices: 39503--39562 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
39493 AACATGGGCA
* *
39503 TTCTCTTATAATCACGTGTTTC
1 TTCTCTTATAATCACATGTTCC
39525 TTCTCTTATAATCACATGTTCC
1 TTCTCTTATAATCACATGTTCC
*
39547 TTCTCTTCT-ATCACAT
1 TTCTCTTATAATCACAT
39563 ACCCCATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 7 0.20
22 28 0.80
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.48
Consensus pattern (22 bp):
TTCTCTTATAATCACATGTTCC
Found at i:39770 original size:2 final size:2
Alignment explanation
Indices: 39763--39833 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
39753 ACTTATGTAA
39763 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
39805 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
39834 TATATATATA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:39838 original size:2 final size:2
Alignment explanation
Indices: 39833--39951 Score: 114
Period size: 2 Copynumber: 56.0 Consensus size: 2
39823 ACACACACAC
39833 AT AT AT 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
* * * * *
39875 AT AT AT AT CGT TT AT ACT AGT -T CCT AT ACT CT AT CAC ACT AGT AT
1 AT AT AT AT -AT AT AT A-T A-T AT -AT AT A-T AT AT -AT A-T A-T AT
39920 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
39952 TCATACAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
1 1 0.01
2 89 0.89
3 10 0.10
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40501 original size:66 final size:67
Alignment explanation
Indices: 40428--40553 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 67
40418 ACACTTCCTA
* ** * *
40428 GGGTATCGGTGCCATCATTGTATTCTGTTAGTT-TTTC-ATTTAAGAGGGTATCGGTACCTTACT
1 GGGTATCGGTACCATCATTACATTATGTGA-TTCTTTCTATTTAAGAGGGTATCGGTACCTTACT
40491 GGT
65 GGT
* * *
40494 GGGTATCGGTACCCTCATTACATTATGTGATTCTTTCTGTTTGAGAGGGTATCGGTACCT
1 GGGTATCGGTACCATCATTACATTATGTGATTCTTTCTATTTAAGAGGGTATCGGTACCT
40554 GTTGAATGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
65 2 0.04
66 28 0.56
67 20 0.40
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (67 bp):
GGGTATCGGTACCATCATTACATTATGTGATTCTTTCTATTTAAGAGGGTATCGGTACCTTACTG
GT
Found at i:41954 original size:10 final size:9
Alignment explanation
Indices: 41936--41965 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
41926 TTTTAAGATT
41936 AAATATTAA
1 AAATATTAA
41945 AAATTATTAA
1 AAA-TATTAA
41955 AAATATTAA
1 AAATATTAA
41964 AA
1 AA
41966 TTCTATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATATTAA
Found at i:50472 original size:25 final size:25
Alignment explanation
Indices: 50421--50472 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
50411 TTGTACTTTT
* * *
50421 AATTGATAATATGTTTTTTCTCTTA
1 AATTGATAATATGTTTTTACCCCTA
50446 AATTGATAATATGTTTTTACCCCTA
1 AATTGATAATATGTTTTTACCCCTA
50471 AA
1 AA
50473 ATTTTATAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (25 bp):
AATTGATAATATGTTTTTACCCCTA
Found at i:52382 original size:24 final size:26
Alignment explanation
Indices: 52344--52392 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
52334 AAAATTATTT
**
52344 TTTATTCTAGCATAA-ATT-TTTTAA
1 TTTATTCTAAAATAATATTATTTTAA
52368 TTTATTCTAAAATAATATTATTTTA
1 TTTATTCTAAAATAATATTATTTTA
52393 TGCCGCATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 3 0.14
26 5 0.24
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTATTCTAAAATAATATTATTTTAA
Found at i:57069 original size:31 final size:31
Alignment explanation
Indices: 57014--57090 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
57004 TCAAAAAACA
*
57014 TAATATATAGTCACATTCGCTTTTATCAAAT
1 TAATATATGGTCACATTCGCTTTTATCAAAT
* * * **
57045 TAATATATGGTCACTTTTGTTTTTATTTAAT
1 TAATATATGGTCACATTCGCTTTTATCAAAT
* *
57076 TAAGATGTGGTCACA
1 TAATATATGGTCACA
57091 ACATGTTAAC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (31 bp):
TAATATATGGTCACATTCGCTTTTATCAAAT
Found at i:63109 original size:18 final size:18
Alignment explanation
Indices: 63083--63117 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63073 TAATATAATT
*
63083 TTTAGTTTTTGATATTTA
1 TTTAGTTTTTAATATTTA
*
63101 TTTATTTTTTAATATTT
1 TTTAGTTTTTAATATTT
63118 TATATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTAGTTTTTAATATTTA
Found at i:68086 original size:55 final size:57
Alignment explanation
Indices: 68000--68106 Score: 155
Period size: 55 Copynumber: 1.9 Consensus size: 57
67990 TCAGCCACTG
* * *
68000 ATCTGTGAAAAAAAAAAGTTCCTAGAGATCAGATG-TGTCTCTCGGTTTTTGGTTTGT
1 ATCTGTG-AAAAAAAAAGTCCCCAGAGATCAGATGCCGTCTCTCGGTTTTTGGTTTGT
*
68057 ATCTGTG-AAAAAAAGGTCCCCAGAGATCAGATGCCGTCTCTCGGTTTTTG
1 ATCTGTGAAAAAAAAAGTCCCCAGAGATCAGATGCCGTCTCTCGGTTTTTG
68107 TTTCTGAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
55 23 0.51
56 15 0.33
57 7 0.16
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (57 bp):
ATCTGTGAAAAAAAAAGTCCCCAGAGATCAGATGCCGTCTCTCGGTTTTTGGTTTGT
Found at i:71889 original size:2 final size:2
Alignment explanation
Indices: 71882--71906 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71872 CTCGTAATAA
71882 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 A
71907 ATAAATTTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72337 original size:20 final size:20
Alignment explanation
Indices: 72312--72620 Score: 451
Period size: 20 Copynumber: 15.4 Consensus size: 20
72302 ACCAAAAGGG
72312 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
72332 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72352 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
72372 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
72392 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72412 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72432 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
72452 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
72472 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72492 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
72512 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
72532 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
72552 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
72572 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
72592 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
72612 GTTGCGATT
1 GTTGCGATT
72621 ATGGAAAATC
Statistics
Matches: 261, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
19 2 0.01
20 256 0.98
21 3 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:76067 original size:9 final size:9
Alignment explanation
Indices: 76049--76117 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
76039 TTCAATTATT
*
76049 AATAACATA
1 AATAAAATA
76058 AATAAAAT-
1 AATAAAATA
76066 AATAATAATAA
1 AATAA-AAT-A
76077 TAATAATAATA
1 -AATAA-AATA
76088 AATAAAAT-
1 AATAAAATA
76096 -ATAAATATA
1 AATAAA-ATA
*
76105 AATAAAATT
1 AATAAAATA
76114 AATA
1 AATA
76118 GCAGTAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
7 5 0.10
8 7 0.14
9 19 0.37
10 10 0.20
11 1 0.02
12 9 0.18
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (9 bp):
AATAAAATA
Found at i:76071 original size:3 final size:3
Alignment explanation
Indices: 76058--76088 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
76048 TAATAACATA
76058 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
76089 ATAAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:76096 original size:12 final size:13
Alignment explanation
Indices: 76062--76102 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
76052 AACATAAATA
76062 AAATAATAATAAT
1 AAATAATAATAAT
76075 -AATAATAATAAT
1 AAATAATAATAAT
76087 AAATAA-AAT-AT
1 AAATAATAATAAT
76098 AAATA
1 AAATA
76103 TAAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.26
12 15 0.56
13 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:76109 original size:30 final size:30
Alignment explanation
Indices: 76055--76117 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
76045 TATTAATAAC
76055 ATAAATAAAATAATAATAATAATAATAA-TA
1 ATAAATAAAATAATAATAATAATAA-AATTA
76085 ATAAATAAAAT-ATAA-ATATAAATAAAATTA
1 ATAAATAAAATAATAATA-AT-AATAAAATTA
76115 ATA
1 ATA
76118 GCAGTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
28 1 0.03
29 8 0.27
30 21 0.70
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (30 bp):
ATAAATAAAATAATAATAATAATAAAATTA
Found at i:76322 original size:3 final size:3
Alignment explanation
Indices: 76314--76361 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
76304 TTTCTTAACA
76314 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
76360 TA
1 TA
76362 GTAGTAGTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:76366 original size:3 final size:3
Alignment explanation
Indices: 76360--76387 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
76350 TTATTATTAT
76360 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG T
76388 TTTATAGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TAG
Found at i:76532 original size:24 final size:24
Alignment explanation
Indices: 76483--76617 Score: 207
Period size: 24 Copynumber: 5.6 Consensus size: 24
76473 CAACATCAAT
*
76483 GTGCCACGTAGAATATGCACACAAA
1 GTGCCTCGTAGAAT-TGCACACAAA
*
76508 GTGCCTCGTAGAATTGCACATAAA
1 GTGCCTCGTAGAATTGCACACAAA
* *
76532 GTGTCTCATAGAATTGCACACAAA
1 GTGCCTCGTAGAATTGCACACAAA
76556 GTGCCTCGTAGAATTGCACACAAA
1 GTGCCTCGTAGAATTGCACACAAA
* *
76580 GTGCCTCATAGAATTGCACACAAG
1 GTGCCTCGTAGAATTGCACACAAA
76604 GTGCCTCGTAGAAT
1 GTGCCTCGTAGAAT
76618 ATGTCAAAAT
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
24 87 0.87
25 13 0.13
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (24 bp):
GTGCCTCGTAGAATTGCACACAAA
Found at i:80117 original size:18 final size:18
Alignment explanation
Indices: 80094--80148 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 18
80084 CTATGTTTAT
80094 ATAAAAATAAATTTTAAA
1 ATAAAAATAAATTTTAAA
80112 ATAAAATTAATATAATATTTAAA
1 AT-AAA--AATA-AAT-TTTAAA
*
80135 ATAATAATAAATTT
1 ATAAAAATAAATTT
80149 AATATGTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 4 0.13
19 6 0.19
20 4 0.13
21 4 0.13
22 5 0.16
23 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATAAATTTTAAA
Found at i:80131 original size:24 final size:24
Alignment explanation
Indices: 80100--80172 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
80090 TTATATAAAA
80100 ATAA-ATTTTAAAATAAAATTAAT
1 ATAATATTTTAAAATAAAATTAAT
*
80123 ATAATA-TTTAAAATAATAATAAAT
1 ATAATATTTTAAAATAA-AATTAAT
* *
80147 TTAATATGTATTAAAATAAATTTAAT
1 ATAATAT-T-TTAAAATAAAATTAAT
80173 TTTTAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 14 0.34
24 12 0.29
26 6 0.15
27 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
ATAATATTTTAAAATAAAATTAAT
Found at i:80148 original size:17 final size:18
Alignment explanation
Indices: 80113--80150 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
80103 AATTTTAAAA
80113 TAAAATTAATATAATATT
1 TAAAATTAATATAATATT
80131 TAAAA-TAATAATAA-ATT
1 TAAAATTAAT-ATAATATT
80148 TAA
1 TAA
80151 TATGTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTAATATAATATT
Found at i:86106 original size:21 final size:22
Alignment explanation
Indices: 86060--86119 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
86050 CCCCCCTGAA
*
86060 GGAACCGATTCCCCCTTTAAAGG
1 GGAACCGATTCCCCC-TCAAAGG
*
86083 GGAACCGATTCCCCC-CACAGG
1 GGAACCGATTCCCCCTCAAAGG
* *
86104 GGAATCGATACCCCCT
1 GGAACCGATTCCCCCT
86120 GGGTTCTGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.53
23 15 0.47
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.17
Consensus pattern (22 bp):
GGAACCGATTCCCCCTCAAAGG
Done.