Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006929.1 Hibiscus syriacus cultivar Beakdansim tig00017783_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: 63884
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:799 original size:2 final size:2
Alignment explanation
Indices: 794--827 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
784 TGTTTGTGGG
794 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
828 GGCTGGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1864 original size:26 final size:25
Alignment explanation
Indices: 1835--1907 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 25
1825 ATTCGTTTTC
1835 ATTATTATTTTATTATTATTATTATT
1 ATTATTA-TTTATTATTATTATTATT
*
1861 ATTATTAATTATTATTATTTATTATT
1 ATTATTATTTATTATTA-TTATTATT
1887 ATTATTAACTTTATTA-TATTA
1 ATTATT-A-TTTATTATTATTA
1908 CAAACCCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.21
26 24 0.57
27 3 0.07
28 6 0.14
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTATTATTTATTATTATTATTATT
Found at i:1903 original size:3 final size:3
Alignment explanation
Indices: 1835--1893 Score: 93
Period size: 3 Copynumber: 19.3 Consensus size: 3
1825 ATTCGTTTTC
1835 ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A-TT
1881 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
1894 ACTTTATTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2493 original size:34 final size:34
Alignment explanation
Indices: 2454--2562 Score: 218
Period size: 34 Copynumber: 3.2 Consensus size: 34
2444 AGAGAACCAA
2454 CAGCAAACGGGAACAACATCGACAGCAACCAAAG
1 CAGCAAACGGGAACAACATCGACAGCAACCAAAG
2488 CAGCAAACGGGAACAACATCGACAGCAACCAAAG
1 CAGCAAACGGGAACAACATCGACAGCAACCAAAG
2522 CAGCAAACGGGAACAACATCGACAGCAACCAAAG
1 CAGCAAACGGGAACAACATCGACAGCAACCAAAG
2556 CAGCAAA
1 CAGCAAA
2563 TAGAACAGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.48, C:0.29, G:0.20, T:0.03
Consensus pattern (34 bp):
CAGCAAACGGGAACAACATCGACAGCAACCAAAG
Found at i:3394 original size:26 final size:26
Alignment explanation
Indices: 3333--3402 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
3323 ATTAGGGTAT
* * *
3333 CTAATTTTAATATGTTATAATTTAGTTA
1 CTAATTTTAATA-CTT-TCATTTAATTA
3361 CTAATTTTAATACTTTCATTTAATTA
1 CTAATTTTAATACTTTCATTTAATTA
*
3387 C-AAGTTTTATTACTTT
1 CTAA-TTTTAATACTTT
3403 TTATATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 21 0.57
27 2 0.05
28 12 0.32
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (26 bp):
CTAATTTTAATACTTTCATTTAATTA
Found at i:3469 original size:14 final size:14
Alignment explanation
Indices: 3450--3477 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3440 GATATATTTT
3450 AATATGTTTAATTA
1 AATATGTTTAATTA
3464 AATATGTTTAATTA
1 AATATGTTTAATTA
3478 TTTTTATTAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATATGTTTAATTA
Found at i:3518 original size:27 final size:28
Alignment explanation
Indices: 3470--3531 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
3460 ATTAAATATG
* * *
3470 TTTAATTATTTTTATTATATTAAT-ATA
1 TTTATTTAATTTTATTAAATTAATGATA
3497 TATTATTTAATTTTA-TAAATTAATGATA
1 T-TTATTTAATTTTATTAAATTAATGATA
3525 TTTATTT
1 TTTATTT
3532 TAAATATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTATTTAATTTTATTAAATTAATGATA
Found at i:4415 original size:16 final size:15
Alignment explanation
Indices: 4387--4420 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4377 AAAATTTTTA
4387 TATATACTTATTACT
1 TATATACTTATTACT
*
4402 TATATACATTATTATT
1 TATATAC-TTATTACT
4418 TAT
1 TAT
4421 TTATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATACTTATTACT
Found at i:5922 original size:7 final size:7
Alignment explanation
Indices: 5906--5946 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
5896 TTTCCATACA
5906 TGCA-TT
1 TGCATTT
5912 TGCATTT
1 TGCATTT
5919 TGCATCTT
1 TGCAT-TT
5927 TGCATTT
1 TGCATTT
5934 T-CATTT
1 TGCATTT
5940 TGCATTT
1 TGCATTT
5947 ATACTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 15 0.47
8 7 0.22
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:11586 original size:75 final size:75
Alignment explanation
Indices: 11475--11636 Score: 220
Period size: 75 Copynumber: 2.2 Consensus size: 75
11465 TTGGAGCAAA
* * *
11475 CTGAAAGCCCATTTCAATTAGAATCAAGAATATTGAC-TCATTTTGAACGTTTGTATCAGCCAAT
1 CTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACGT-ATTTTGAACGCTTGTATCAGCAAAT
11539 GTTGGGGAATG
65 GTTGGGGAATG
* * *
11550 CTGAAAGCCCATTTCAATCAGAAT-AATGAATGTTGACGTATTTTGAGCGCTTGTATCATCAAAT
1 CTGAAAGCCCATTTCAATCAGAATCAA-GAATATTGACGTATTTTGAACGCTTGTATCAGCAAAT
*
11614 GTTGGGGCATG
65 GTTGGGGAATG
*
11625 CTGAAGGCCCAT
1 CTGAAAGCCCAT
11637 ATTACGTGGA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
74 2 0.03
75 74 0.96
76 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (75 bp):
CTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACGTATTTTGAACGCTTGTATCAGCAAATG
TTGGGGAATG
Found at i:12489 original size:22 final size:22
Alignment explanation
Indices: 12462--12503 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12452 ATCTACATTC
*
12462 TTCAAAGATTATAAATTCTCTA
1 TTCAAAGATGATAAATTCTCTA
12484 TTCAAAGATGATAAATTCTC
1 TTCAAAGATGATAAATTCTC
12504 CTAAAGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAAATTCTCTA
Found at i:13077 original size:113 final size:113
Alignment explanation
Indices: 12881--13317 Score: 483
Period size: 113 Copynumber: 3.8 Consensus size: 113
12871 CCATAATTCA
* * * * *
12881 ATGGATCAATATTTCCGGA-AGAGTTCATGATGAGAAGAACTCATCTGAA-AAAGAAGAAGAAGT
1 ATGGATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
12944 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGAATTCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGAATTCATCACTCG
* * *
12992 ATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCCTCTGAAGAAGGAAGAAGAAA
1 ATGGATCAACATTGCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* * *
13056 TTCATAATGAGAAGAATTTGTTCAACCTTTTTCTTGAATTCATCACTCG
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGAATTCATCACTCG
* * * *
13105 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* **
13170 TCATAATGAGAAGAACTTGTTCAACC-TTTGC-ATG-ACTCTATCACAGAAGAAG
66 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTA-GAATTC-ATCAC-----TCG
* * * *
13222 ATAGATCAACATCAATATTTCCAGAAAGAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGA
1 ATGGATC-A-A-C---ATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
13286 AGAAGTTCATAATGAGAAGAACTTATTCAACC
60 AGAAGTTCATAATGAGAAGAACTTGTTCAACC
13318 GTGTCTTAAT
Statistics
Matches: 277, Mismatches: 32, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
111 17 0.06
112 38 0.14
113 137 0.49
114 1 0.00
117 7 0.03
118 1 0.00
119 1 0.00
120 1 0.00
122 38 0.14
123 36 0.13
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (113 bp):
ATGGATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTTGCTAGAATTCATCACTCG
Found at i:13691 original size:16 final size:17
Alignment explanation
Indices: 13670--13751 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 17
13660 GTCCATTCGT
13670 TTTTATTATT-TTATTA
1 TTTTATTATTATTATTA
*
13686 TTTTATTATTATTAATAA
1 TTTTATTATTATT-ATTA
*
13704 TTAATATTATTATTATTA
1 TT-TTATTATTATTATTA
13722 -TTTATTATTATTATTAA
1 TTTTATTATTATTATT-A
*
13739 CTTTATTA-TATTA
1 TTTTATTATTATTA
13752 CAGGCCCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
16 23 0.40
17 9 0.16
18 15 0.26
19 10 0.18
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATTATTATTATTA
Found at i:13696 original size:19 final size:20
Alignment explanation
Indices: 13672--13751 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 20
13662 CCATTCGTTT
13672 TTATTATTTTATTATT-TTA
1 TTATTATTTTATTATTATTA
* * *
13691 TTATTA-TTAATAATTAATA
1 TTATTATTTTATTATTATTA
13710 TTATTATTATTATTTATTATTA
1 TTATTATT-TTA-TTATTATTA
*
13732 TTATTAACTTTATTA-TATTA
1 TTATT-ATTTTATTATTATTA
13752 CAGGCCCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
18 7 0.14
19 14 0.29
20 6 0.12
21 5 0.10
22 15 0.31
23 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTTTATTATTATTA
Found at i:13744 original size:22 final size:21
Alignment explanation
Indices: 13672--13751 Score: 82
Period size: 19 Copynumber: 4.0 Consensus size: 21
13662 CCATTCGTTT
*
13672 TTATTATT--TTATTATTTTA
1 TTATTATTAATTATTATATTA
*
13691 TTATTATTAATAATTA-A-TA
1 TTATTATTAATTATTATATTA
13710 TTATTATT-ATTATT-TATTA
1 TTATTATTAATTATTATATTA
13729 TTATTATTAACTTTATTATATTA
1 TTATTATTAA--TTATTATATTA
13752 CAGGCCCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.12
19 28 0.56
20 1 0.02
21 5 0.10
22 5 0.10
23 5 0.10
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTATTAATTATTATATTA
Found at i:13747 original size:3 final size:3
Alignment explanation
Indices: 13672--13737 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
13662 CCATTCGTTT
* *
13672 TTA TTA TT- TTA TTA TT- TTA TTA TTA TTAA TAA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
13716 TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA
13738 ACTTTATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 46 0.84
4 5 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:14175 original size:21 final size:21
Alignment explanation
Indices: 14149--14196 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
14139 CTATGGTGAG
*
14149 TCACCGTCATAGCTTGGCGAC
1 TCACCGCCATAGCTTGGCGAC
*
14170 TCACCGCCATAGCTTGGTGAC
1 TCACCGCCATAGCTTGGCGAC
14191 TCACCG
1 TCACCG
14197 AAGACCGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (21 bp):
TCACCGCCATAGCTTGGCGAC
Found at i:14940 original size:15 final size:15
Alignment explanation
Indices: 14920--14952 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
14910 CCGAATTAGC
14920 CATTATGATTTTAAT
1 CATTATGATTTTAAT
*
14935 CATTATTATTTTAAT
1 CATTATGATTTTAAT
14950 CAT
1 CAT
14953 AAACAGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (15 bp):
CATTATGATTTTAAT
Found at i:15149 original size:26 final size:26
Alignment explanation
Indices: 15088--15157 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
15078 ATTAGGGTAT
* * *
15088 CTAATTTTAATATGTTATAATTTAGTTA
1 CTAATTTTAATA-CTT-TCATTTAATTA
15116 CTAATTTTAATACTTTCATTTAATTA
1 CTAATTTTAATACTTTCATTTAATTA
*
15142 C-AAGTTTTATTACTTT
1 CTAA-TTTTAATACTTT
15158 TTATATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 21 0.57
27 2 0.05
28 12 0.32
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (26 bp):
CTAATTTTAATACTTTCATTTAATTA
Found at i:15225 original size:14 final size:14
Alignment explanation
Indices: 15206--15233 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15196 GATATATTTT
15206 AATATGTTTAATTA
1 AATATGTTTAATTA
15220 AATATGTTTAATTA
1 AATATGTTTAATTA
15234 TTGTTATTAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATATGTTTAATTA
Found at i:15301 original size:27 final size:28
Alignment explanation
Indices: 15237--15302 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
15227 TTAATTATTG
*
15237 TTATTATATTAATATATATTATTTAATT
1 TTATAATATTAATATATATTATTTAATT
*
15265 TTATAA-ATTAATGATAT-TTATTTATTT
1 TTATAATATTAAT-ATATATTATTTAATT
15292 TTA-AATATTAA
1 TTATAATATTAA
15303 GAAAAGGGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 23 0.68
28 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTATAATATTAATATATATTATTTAATT
Found at i:18577 original size:31 final size:32
Alignment explanation
Indices: 18537--18606 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
18527 TTTATTTTTA
18537 TTTTACCCCTCATTTTCTATAATTAATTATAC
1 TTTTACCCCTCATTTTCTATAATTAATTATAC
* * *
18569 TTTT-CCCCTTATTTTTTATGATTAATTATA-
1 TTTTACCCCTCATTTTCTATAATTAATTATAC
*
18599 TTCTACCC
1 TTTTACCC
18607 TTTGAGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.24, C:0.21, G:0.01, T:0.53
Consensus pattern (32 bp):
TTTTACCCCTCATTTTCTATAATTAATTATAC
Found at i:19604 original size:2 final size:2
Alignment explanation
Indices: 19597--19629 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19587 AGATGAAATG
19597 AT 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 AT A
19630 AAGAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21068 original size:13 final size:13
Alignment explanation
Indices: 21050--21074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21040 AAAATTCCAA
21050 ACCCTAAAACTCT
1 ACCCTAAAACTCT
21063 ACCCTAAAACTC
1 ACCCTAAAACTC
21075 AAACTCTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (13 bp):
ACCCTAAAACTCT
Found at i:23166 original size:31 final size:31
Alignment explanation
Indices: 23131--23194 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
23121 TAATGGTATG
*
23131 CACCTAAAAGTGTAAC-AGAGAAAAC-TGTAGA
1 CACCTAAAACTGTAACGA-AGAAAACAT-TAGA
23162 CACCTAAAACTGTAACGAAGAAAACATTAGA
1 CACCTAAAACTGTAACGAAGAAAACATTAGA
23193 CA
1 CA
23195 TCTCTTGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (31 bp):
CACCTAAAACTGTAACGAAGAAAACATTAGA
Found at i:23555 original size:2 final size:2
Alignment explanation
Indices: 23548--23598 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
23538 CATTTTAAAC
*
23548 AT AT AT AT AT GT 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
23590 AT AT AT AT A
1 AT AT AT AT A
23599 CTATTTATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28433 original size:18 final size:19
Alignment explanation
Indices: 28412--28452 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
28402 ATCCCCAATC
28412 TATACACAATT-TCCTATT
1 TATACACAATTATCCTATT
*
28430 TATA-ACATTTATCCTATT
1 TATACACAATTATCCTATT
*
28448 CATAC
1 TATAC
28453 GACTTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (19 bp):
TATACACAATTATCCTATT
Found at i:30427 original size:4 final size:4
Alignment explanation
Indices: 30418--31490 Score: 2118
Period size: 4 Copynumber: 269.2 Consensus size: 4
30408 CCCTATCTTC
30418 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30466 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30514 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30562 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30610 TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30656 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30704 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30752 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30800 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30848 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30896 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30944 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
30992 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31040 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31088 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31134 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31182 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31230 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31278 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31326 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31374 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31422 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
31470 TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA T
31491 TTATATATAT
Statistics
Matches: 1065, Mismatches: 0, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
2 4 0.00
4 1061 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:34506 original size:32 final size:32
Alignment explanation
Indices: 34464--34534 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
34454 TGCTATCATG
* *
34464 TAAGGATGAGTTTAAAATATAATTAACTAATA
1 TAAGGTTGAGTCTAAAATATAATTAACTAATA
34496 TAAGGTTGAGTCTAAAATATAATTAACTAATA
1 TAAGGTTGAGTCTAAAATATAATTAACTAATA
34528 TAAGGTT
1 TAAGGTT
34535 ATGCCGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (32 bp):
TAAGGTTGAGTCTAAAATATAATTAACTAATA
Found at i:36237 original size:18 final size:19
Alignment explanation
Indices: 36216--36257 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
36206 TTTAATTATT
*
36216 TTTTATTTGTTTATAA-TA
1 TTTTATTTATTTATAACTA
* *
36234 TTTTTTTTATTTTTAACTA
1 TTTTATTTATTTATAACTA
36253 TTTTA
1 TTTTA
36258 GATTGCTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATTTATTTATAACTA
Found at i:36254 original size:19 final size:19
Alignment explanation
Indices: 36206--36256 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
36196 ATTTTTTAAA
36206 TTTAATTATTTTTTATTTGT
1 TTTAA-TATTTTTTATTTGT
36226 TTATAATATTTTTT-TTAT-T
1 TT-TAATATTTTTTATT-TGT
36245 TTTAACTATTTT
1 TTTAA-TATTTT
36257 AGATTGCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.11
19 11 0.39
20 11 0.39
21 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTAATATTTTTTATTTGT
Found at i:41261 original size:20 final size:20
Alignment explanation
Indices: 41238--41281 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
41228 TTTGTTAAGA
41238 CAAATCAAAAGTTGTGAAGG
1 CAAATCAAAAGTTGTGAAGG
41258 CAAATCAAAAGTTGTGAAGG
1 CAAATCAAAAGTTGTGAAGG
41278 CAAA
1 CAAA
41282 GATTAGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (20 bp):
CAAATCAAAAGTTGTGAAGG
Found at i:43211 original size:20 final size:20
Alignment explanation
Indices: 43186--43378 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
43176 GATTTTCCAG
* ** *
43186 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
43206 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
43226 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
43246 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43266 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43286 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
43306 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
43326 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
43347 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
43367 AATCGCAACGCG
1 AATCGCAACGCG
43379 ATTTTTAAAG
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.01
20 133 0.87
21 19 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:43968 original size:20 final size:20
Alignment explanation
Indices: 43943--44128 Score: 232
Period size: 20 Copynumber: 9.3 Consensus size: 20
43933 AGAAGTAGTA
*
43943 CGCAACGCGTATCCGTAAAC
1 CGCAACGCGTATCCGTAAAT
*
43963 CGCAACGTGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
43983 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
44003 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
44023 CGCAACGCGTATCCATAAAT
1 CGCAACGCGTATCCGTAAAT
*
44043 CGCAACG-ATAATCCGTAAAT
1 CGCAACGCGT-ATCCGTAAAT
* * * *
44063 CACAACGAGAATCTGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
44083 CGCAACG-ATAATCCGTAAAT
1 CGCAACGCGT-ATCCGTAAAT
* * *
44103 CGCAACGAGAATCTGTAAAT
1 CGCAACGCGTATCCGTAAAT
44123 CGCAAC
1 CGCAAC
44129 ACTGAAATTT
Statistics
Matches: 145, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 144 0.99
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.19
Consensus pattern (20 bp):
CGCAACGCGTATCCGTAAAT
Found at i:44859 original size:24 final size:24
Alignment explanation
Indices: 44820--44866 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44810 AAATTTGGTC
44820 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
44844 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
44867 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:47458 original size:72 final size:72
Alignment explanation
Indices: 47349--47558 Score: 264
Period size: 72 Copynumber: 2.9 Consensus size: 72
47339 GCAACGAGAG
* *
47349 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATAAAAATACCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
47414 AAATGAA
66 AAATGAA
* *
47421 AATCGCAATGCGAAATAAAAATAGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATAAAAATACCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
47485 GAAATGAA
65 GAAATGAA
* * *** * * *
47493 AATCGCAACGAGAGAATCGCAATGCGGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCATTG
1 AATCGCAATGCGA-AATAAAAATAC-CAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
47556 CGA
64 CGA
47559 TTCTCTCGTT
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
72 98 0.82
73 20 0.17
74 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATAAAAATACCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:47549 original size:53 final size:52
Alignment explanation
Indices: 47335--47552 Score: 293
Period size: 53 Copynumber: 4.1 Consensus size: 52
47325 CGGAAATTAC
*
47335 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
47382 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
47440 AATAGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
47493 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
47546 AATCGCA
1 AATCGCA
47553 TTGCGATTCT
Statistics
Matches: 152, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
47 8 0.05
49 1 0.01
50 1 0.01
52 14 0.09
53 114 0.75
55 2 0.01
56 1 0.01
58 11 0.07
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:47613 original size:52 final size:52
Alignment explanation
Indices: 47548--47664 Score: 209
Period size: 52 Copynumber: 2.2 Consensus size: 52
47538 GAAATGAAAA
47548 TCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
47600 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
47652 TCCGCATTGCGAT
1 T-CGCATTGCGAT
47665 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 44 0.70
53 19 0.30
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:47672 original size:20 final size:19
Alignment explanation
Indices: 47567--47664 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
47557 GATTCTCTCG
47567 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
47586 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
47605 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
47619 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47638 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
47658 TTGCGAT
1 TTGCGAT
47665 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 31 0.44
20 19 0.27
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:47790 original size:14 final size:14
Alignment explanation
Indices: 47771--47807 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
47761 CATCAATTAC
47771 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
47785 ACAAATCATCTTTT
1 ACAAATCAACTTTT
47799 ACAAATCAA
1 ACAAATCAA
47808 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:49766 original size:19 final size:19
Alignment explanation
Indices: 49724--49896 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
49714 TAGTTTACTT
* *
49724 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
49744 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
49763 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* * **
49782 TCGTAATGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
49801 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49820 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
49834 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49853 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
49867 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49886 TCGCAATGCGA
1 TCGCAACGCGA
49897 TTTGGTTTCG
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 18 0.15
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 78 0.63
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:49837 original size:14 final size:14
Alignment explanation
Indices: 49818--49874 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
49808 GCGAAATGAA
*
49818 AATCGCAACGACAG
1 AATCGCAACGAAAG
49832 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
49849 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
49865 AATCGCAACG
1 AATCGCAACG
49875 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:49845 original size:33 final size:33
Alignment explanation
Indices: 49799--49891 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
49789 GCGAAACCAA
49799 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
49832 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
49865 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
49892 TGCGATTTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:49888 original size:52 final size:52
Alignment explanation
Indices: 49758--49896 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
49748 AACGCGAAAT
* * * *
49758 GAGAATCGCAACGAGAAACCAAAATCGTAATGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
49810 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
49862 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
49897 TTTGGTTTCG
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:49913 original size:18 final size:18
Alignment explanation
Indices: 49886--49949 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
49876 GAAATGAAAA
*
49886 TCGCAATGCGATTTGGTT
1 TCGCATTGCGATTTGGTT
*
49904 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTGGTT
49920 T-G--TTGCGATTTGGTT
1 TCGCATTGCGATTTGGTT
*
49935 TCGCGTTGCGATTTG
1 TCGCATTGCGATTTG
49950 CGTGCGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
13 9 0.24
15 3 0.08
16 3 0.08
18 23 0.61
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTGGTT
Found at i:49967 original size:31 final size:31
Alignment explanation
Indices: 49892--49976 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
49882 AAAATCGCAA
* * *
49892 TGCGATTTGGTTTCGCATTGCGATTTTGTGT
1 TGCGATTTAGTTTCGCGTTGCGATTTTGCGT
*
49923 TGCGATTTGGTTTCGCGTTGCGA-TTTGCG-
1 TGCGATTTAGTTTCGCGTTGCGATTTTGCGT
*
49952 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGA-TTT-AGTTTCGCGTTGCGA
49977 AAGTGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.10
30 8 0.17
31 35 0.73
ACGTcount: A:0.11, C:0.14, G:0.31, T:0.45
Consensus pattern (31 bp):
TGCGATTTAGTTTCGCGTTGCGATTTTGCGT
Found at i:51889 original size:21 final size:20
Alignment explanation
Indices: 51837--51933 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
51827 TTTTGGTTGA
51837 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
51857 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
51877 TAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
51896 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
51911 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
51931 AAT
1 AAT
51934 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:51903 original size:14 final size:14
Alignment explanation
Indices: 51884--51940 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
51874 GAGTAATGAA
51884 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
51898 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
51917 AATCGCAACGAGAG
1 AATCGCAACGAGAG
51931 AATCGCAACG
1 AATCGCAACG
51941 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:51918 original size:33 final size:33
Alignment explanation
Indices: 51835--51957 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
51825 TCTTTTGGTT
*
51835 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
51874 GAGTAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GA--AATGAAAATCGCAACGAGAGAATCGCAACGC
51909 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
51942 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
51958 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 47 0.58
35 10 0.12
38 1 0.01
39 2 0.02
40 1 0.01
41 20 0.25
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:52053 original size:21 final size:21
Alignment explanation
Indices: 51982--52057 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
51972 CGCGTTGCGA
*
51982 TTCTCTTGTTGCGA-TTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
52002 TTTTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
52024 TT-TCACGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
52044 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
52058 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
20 19 0.42
21 20 0.44
22 6 0.13
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:52179 original size:33 final size:33
Alignment explanation
Indices: 52137--52207 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
52127 AATACTAACT
52137 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
52170 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
52203 TGAAA
1 TGAAA
52208 TCTAAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:52183 original size:19 final size:19
Alignment explanation
Indices: 52159--52207 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
52149 CGAGAGAATA
52159 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
52178 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
52192 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
52208 TCTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:52193 original size:14 final size:14
Alignment explanation
Indices: 52141--52197 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
52131 CTAACTTGAA
52141 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
52155 AATAGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
52174 AATCGCAACGAGAG
1 AATCGCAACGAGAG
52188 AATCGCAACG
1 AATCGCAACG
52198 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:52612 original size:20 final size:20
Alignment explanation
Indices: 52587--52779 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
52577 CTTTAAAAAT
52587 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52607 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
52627 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
52648 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
52668 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52688 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
52708 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
52728 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
52748 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
52768 CGCGTTGCGATT
1 CGCGTTGCGATT
52780 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:54090 original size:24 final size:24
Alignment explanation
Indices: 54063--54110 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
54053 TAGCACAAAG
54063 TGAGCTCAAATTTTAGGCTTCAAT
1 TGAGCTCAAATTTTAGGCTTCAAT
*
54087 TGAGCTCCAATTTTAGGCTTCAAT
1 TGAGCTCAAATTTTAGGCTTCAAT
54111 CGAACTTCTA
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:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (24 bp):
TGAGCTCAAATTTTAGGCTTCAAT
Found at i:59366 original size:15 final size:15
Alignment explanation
Indices: 59346--59375 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59336 TTATCGTTTG
59346 AATTGAACTAGTTAA
1 AATTGAACTAGTTAA
*
59361 AATTGAATTAGTTAA
1 AATTGAACTAGTTAA
59376 TTTTTTCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (15 bp):
AATTGAACTAGTTAA
Found at i:60614 original size:20 final size:21
Alignment explanation
Indices: 60581--60621 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
60571 ATTAATAATG
* *
60581 AAAATGAAATAAAATAAAATT
1 AAAATGAAAAAAAAGAAAATT
60602 AAAA-GAAAAAAAAGAAAATT
1 AAAATGAAAAAAAAGAAAATT
60622 CTAATTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAATGAAAAAAAAGAAAATT
Found at i:61803 original size:3 final size:3
Alignment explanation
Indices: 61792--61852 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
61782 AAAAATGAAA
**
61792 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT TTT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT
* *
61840 AAA AAT AAA AAT A
1 AAT AAT AAT AAT A
61853 TAAGACCCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 38 0.79
4 10 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:61827 original size:32 final size:32
Alignment explanation
Indices: 61776--61852 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
61766 TAAACAAAAA
* *
61776 AAAAAAAAAAATGAA-AAATATATAATAATAAT
1 AAAAATAAAAAT-AATAAATAAATAATAATAAT
* * **
61808 AATAATAATAATAATAAATAAATTTTAATAAT
1 AAAAATAAAAATAATAAATAAATAATAATAAT
61840 AAAAATAAAAATA
1 AAAAATAAAAATA
61853 TAAGACCCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
31 2 0.06
32 34 0.94
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (32 bp):
AAAAATAAAAATAATAAATAAATAATAATAAT
Done.