Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001102.1 Hibiscus syriacus cultivar Beakdansim tig00002183_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: 83826
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:781 original size:53 final size:54
Alignment explanation
Indices: 550--1069 Score: 700
Period size: 54 Copynumber: 9.8 Consensus size: 54
540 GCATGTTGCT
* * *
550 TAATGAGTTTATGAATTAT-CATATTGGCACTA--TGTGCAACTAAATAAATTCA
1 TAATGAGTTTATGAATT-TCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
*
602 TAATGAG--TATG-ATTTCCGTTTTGGCACTATGTGTGCAACTTAAGAAATTC-
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
* *
652 -AACGAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACTTAAGAAATTCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
*
705 TAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACTTAAG-AATTCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
*
758 TAAGGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTT-AGAAATTCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
*
811 TAAGGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
* * *
865 TAACGAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACTTAAGAAATTCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
* * * * * * *
919 CAATGAGTTTATGAATTTCCATATCGGCACTATGTGTACAACCTAAAAAAATGCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA-CTTAAGAAATTCA
* *
974 TAATGAGTTTATGAATTTCCTTATTGGCACTATGTGTGCAACTTAAGGAATTCA
1 TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
* * * * * *
1028 TAATAAAGTTTATGAATTTTCATATTAGCACTAGGTTTGCAA
1 TAAT-GAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
1070 ACCGTTTAAT
Statistics
Matches: 417, Mismatches: 39, Indels: 21
0.87 0.08 0.04
Matches are distributed among these distances:
48 1 0.00
49 19 0.05
50 4 0.01
51 21 0.05
52 46 0.11
53 98 0.24
54 150 0.36
55 78 0.19
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (54 bp):
TAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCA
Found at i:847 original size:160 final size:160
Alignment explanation
Indices: 550--1069 Score: 712
Period size: 160 Copynumber: 3.3 Consensus size: 160
540 GCATGTTGCT
* * *
550 TAATGAGTTTATGAATTATCATATTGGCACTA--TGTGCAACTAAATAAATTCATAATGAG--TA
1 TAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAA-GAATTCATAATGAGTTTA
*
611 TG-ATTTCCGTTTTGGCACTATGTGTGCAACTTAAGAAATTC--AACGAGTTTATGAATTTCCAT
65 TGAATTTCCGTATTGGCACTATGTGTGCAACTT-AGAAATTCATAACGAGTTTATGAATTTCCAT
673 ATTGGCACTATGTGTGCAACTTAAGAAATTCA
129 ATTGGCACTATGTGTGCAACTTAAGAAATTCA
* *
705 TAATGAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACTTAAGAATTCATAAGGAGTTTAT
1 TAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAATTCATAATGAGTTTAT
* *
770 GAATTTCCGTATTGGCACTATGTGTGCAACTTAGAAATTCATAAGGAGTTTATGAATTTCCGTAT
66 GAATTTCCGTATTGGCACTATGTGTGCAACTTAGAAATTCATAACGAGTTTATGAATTTCCATAT
835 TGGCACTATGTGTGCAACTTAAGAAATTCA
131 TGGCACTATGTGTGCAACTTAAGAAATTCA
* * * *
865 TAACGAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACTTAAGAAATTCACAATGAGTTTA
1 TAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAG-AATTCATAATGAGTTTA
* * * * * * * *
930 TGAATTTCCATATCGGCACTATGTGTACAACCTAAAAAAATGCATAATGAGTTTATGAATTTCCT
65 TGAATTTCCGTATTGGCACTATGTGTGCAA-CT-TAGAAATTCATAACGAGTTTATGAATTTCCA
*
995 TATTGGCACTATGTGTGCAACTTAAGGAATTCA
128 TATTGGCACTATGTGTGCAACTTAAGAAATTCA
* * * *
1028 TAATAAAGTTTATGAATTTTCATATTAGCACTAGGTTTGCAA
1 TAAT-GAGTTTATGAATTTTCATATTGGCACTATGTGTGCAA
1070 ACCGTTTAAT
Statistics
Matches: 326, Mismatches: 28, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
155 30 0.09
156 12 0.04
157 11 0.03
158 12 0.04
159 29 0.09
160 96 0.29
161 42 0.13
162 2 0.01
163 61 0.19
164 31 0.10
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (160 bp):
TAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGCAACTTAAGAATTCATAATGAGTTTAT
GAATTTCCGTATTGGCACTATGTGTGCAACTTAGAAATTCATAACGAGTTTATGAATTTCCATAT
TGGCACTATGTGTGCAACTTAAGAAATTCA
Found at i:9825 original size:13 final size:14
Alignment explanation
Indices: 9806--9847 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
9796 GGCACGAGTC
*
9806 GAGTCAACTCGCTT
1 GAGTCAACTCGATT
*
9820 -AGTCAAATCGATT
1 GAGTCAACTCGATT
9833 GAGTCAACTCG-TT
1 GAGTCAACTCGATT
9846 GA
1 GA
9848 CTTTGTCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
GAGTCAACTCGATT
Found at i:9918 original size:22 final size:22
Alignment explanation
Indices: 9864--9906 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9854 CTGACCGTTG
9864 ACTTTGACCAGA-GTTGACTTTA
1 ACTTTGACCA-ATGTTGACTTTA
9886 ACTTTGACCAATGTTGACTTT
1 ACTTTGACCAATGTTGACTTT
9907 CACATTTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (22 bp):
ACTTTGACCAATGTTGACTTTA
Found at i:12460 original size:47 final size:45
Alignment explanation
Indices: 12386--12511 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
12376 TATAAAATCT
*
12386 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
12431 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
12478 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
12512 GCATGGTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:16609 original size:6 final size:6
Alignment explanation
Indices: 16593--16703 Score: 62
Period size: 6 Copynumber: 17.3 Consensus size: 6
16583 TCTCTCATTT
* * * *
16593 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTCATT TTTTTC TTCTTC GTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC -TTTT--TC TTTTTC TTTTTC TTTTTC
* * * *
16644 ATTTTC TTTTTC TATTTTT TTTCTTC TGTTTTT TTTTTC TTTTGTT TTTTTC
1 TTTTTC TTTTTC T-TTTTC TTT-TTC T-TTTTC TTTTTC TTTT-TC TTTTTC
*
16696 TTCTTC TT
1 TTTTTC TT
16704 ATAATATATA
Statistics
Matches: 80, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
5 5 0.06
6 45 0.56
7 23 0.29
8 6 0.08
9 1 0.01
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:16614 original size:17 final size:17
Alignment explanation
Indices: 16590--16685 Score: 65
Period size: 17 Copynumber: 5.5 Consensus size: 17
16580 TCATCTCTCA
16590 TTTT-TTTCTCTTTTTC
1 TTTTCTTTCTCTTTTTC
*
16606 TTTTCTTTCTCGTTTTC
1 TTTTCTTTCTCTTTTTC
16623 ATTTT-TTTCTTCTTCGTTTTC
1 -TTTTCTTTC-TC-T--TTTTC
*
16644 ATTTTCTTTTTCTATTTT-
1 -TTTTCTTTCTCT-TTTTC
* *
16662 TTTTC-TTCTGTTTTTT
1 TTTTCTTTCTCTTTTTC
16678 TTTTCTTT
1 TTTTCTTT
16686 TGTTTTTTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
15 4 0.06
16 13 0.20
17 22 0.34
18 6 0.09
19 4 0.06
20 1 0.02
21 12 0.18
22 3 0.05
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTCTTTCTCTTTTTC
Found at i:16635 original size:20 final size:22
Alignment explanation
Indices: 16606--16656 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
16596 TCTCTTTTTC
16606 TTTTCTTTC-TCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
16627 TTTTC-TTCTTCGTTTTCATTT
1 TTTTCTTTCTTCGTTTTCATTT
*
16648 TCTT-TTTCT
1 TTTTCTTTCT
16657 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTCTTTCTTCGTTTTCATTT
Found at i:16643 original size:33 final size:30
Alignment explanation
Indices: 16591--16701 Score: 100
Period size: 33 Copynumber: 3.5 Consensus size: 30
16581 CATCTCTCAT
*
16591 TTTTTTCTCTTTTTC-TTTTCTTTCTCGTTTTC
1 TTTTTT-TCTTCTTCGTTTTCTTT-TC-TTTTC
16623 ATTTTTTTCTTCTTCGTTTTCATTTTCTTTTTC
1 -TTTTTTTCTTCTTCGTTTTC-TTTTC-TTTTC
* *
16656 TATTTTTT-TTCTTCTGTTTTTTTTTTCTTTTG
1 T-TTTTTTCTTCTTC-G-TTTTCTTTTCTTTTC
16688 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
16702 TTATAATATA
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
31 6 0.09
32 25 0.37
33 30 0.44
34 7 0.10
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.77
Consensus pattern (30 bp):
TTTTTTTCTTCTTCGTTTTCTTTTCTTTTC
Found at i:16694 original size:32 final size:31
Alignment explanation
Indices: 16624--16702 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
16614 CTCGTTTTCA
16624 TTTTTTTCTTCTTC-GTTTTCATTTTCTTTT
1 TTTTTTTCTTCTTCTGTTTTCATTTTCTTTT
* **
16654 TCTATTTTTTTTCTTCTGTTTTTTTTTTCTTTT
1 T-T-TTTTTCTTCTTCTGTTTTCATTTTCTTTT
16687 GTTTTTTTCTTCTTCT
1 -TTTTTTTCTTCTTCT
16703 TATAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 1 0.02
32 23 0.56
33 15 0.37
34 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (31 bp):
TTTTTTTCTTCTTCTGTTTTCATTTTCTTTT
Found at i:16699 original size:16 final size:16
Alignment explanation
Indices: 16624--16700 Score: 61
Period size: 16 Copynumber: 4.8 Consensus size: 16
16614 CTCGTTTTCA
*
16624 TTTTTTTCTTC-TTCG
1 TTTTTTTCTTCTTTTG
*
16639 TTTTCATT-TTCTTTT-
1 TTTT-TTTCTTCTTTTG
* *
16654 TCTATTTTTTTTCTTCTG
1 T-T-TTTTTCTTCTTTTG
*
16672 TTTTTTTTTTCTTTTG
1 TTTTTTTCTTCTTTTG
16688 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
16701 CTTATAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 8 0.16
16 32 0.64
17 9 0.18
18 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTCTTTTG
Found at i:17803 original size:6 final size:6
Alignment explanation
Indices: 17792--17821 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
17782 ACCCTTGTAT
17792 CATGAC CATGAC CATGAC CATGAC CTATGA
1 CATGAC CATGAC CATGAC CATGAC C-ATGA
17822 GTCTTCCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (6 bp):
CATGAC
Found at i:19591 original size:47 final size:45
Alignment explanation
Indices: 19517--19642 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
19507 TATAAAATCT
*
19517 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
19562 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
19609 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
19643 GCATGGTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:33914 original size:16 final size:16
Alignment explanation
Indices: 33893--33923 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33883 TTGTTTAACT
33893 GTTGACTTTGACCAAC
1 GTTGACTTTGACCAAC
33909 GTTGACTTTGACCAA
1 GTTGACTTTGACCAA
33924 AAAGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (16 bp):
GTTGACTTTGACCAAC
Found at i:36712 original size:89 final size:90
Alignment explanation
Indices: 36579--36766 Score: 272
Period size: 89 Copynumber: 2.1 Consensus size: 90
36569 ATAACTGGCA
* * *
36579 CCTTTTATGCCAATAATGCACCGTTATGCATTTTCATTAGTGGCACCTTTTATGCCGATAATGTA
1 CCTTTTATGACAATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATGCA
* **
36644 TCGTTATGCATTTTCATTTACGGC-
66 CCGTTATAAATTTTCATTTACGGCG
* *
36668 CCTTTTATGATAATAATGCACTGTTATGCATTTTCATTTA-TGGCACATTTTATGCCGATAATGC
1 CCTTTTATGACAATAATGCACCGTTATGCATTTTCA-TTAGTGGCACATTTTATGCCGATAATGC
*
36732 ACCGTTATAAATTTTCATTTATGGCG
65 ACCGTTATAAATTTTCATTTACGGCG
36758 CCTTTTATG
1 CCTTTTATG
36767 CCGATTCATA
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
89 76 0.86
90 12 0.14
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (90 bp):
CCTTTTATGACAATAATGCACCGTTATGCATTTTCATTAGTGGCACATTTTATGCCGATAATGCA
CCGTTATAAATTTTCATTTACGGCG
Found at i:36769 original size:45 final size:45
Alignment explanation
Indices: 36574--36771 Score: 265
Period size: 45 Copynumber: 4.4 Consensus size: 45
36564 ATACCATAAC
*
36574 TGGCACCTTTTATGCCAATAATGCACCGTTATGCATTTTCA-TTA
1 TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTA
* *
36618 GTGGCACCTTTTATGCCGATAATGTATCGTTATGCATTTTCATTTA
1 -TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTA
* *** *
36664 CGGC-CCTTTTATGATAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTA
* **
36708 TGGCACATTTTATGCCGATAATGCACCGTTATAAATTTTCATTTA
1 TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTA
*
36753 TGGCGCCTTTTATGCCGAT
1 TGGCACCTTTTATGCCGAT
36772 TCATAGATTT
Statistics
Matches: 131, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
44 37 0.28
45 91 0.69
46 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (45 bp):
TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTA
Found at i:41827 original size:3 final size:3
Alignment explanation
Indices: 41819--41850 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41809 CTTCTAGGAC
41819 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
41851 GTCATAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:44172 original size:18 final size:18
Alignment explanation
Indices: 44122--44172 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
44112 GTTTCCAATC
* * *
44122 TCTCTTTTTTTCCTCTAT
1 TCTCTGTTTTTCTTTTAT
44140 TCTCTGTTTTT-TTTTAT
1 TCTCTGTTTTTCTTTTAT
44157 TCTCTGTTTTTCTTTT
1 TCTCTGTTTTTCTTTT
44173 TGTTCTCCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.73
Consensus pattern (18 bp):
TCTCTGTTTTTCTTTTAT
Found at i:44641 original size:3 final size:3
Alignment explanation
Indices: 44628--44689 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
44618 GTAATATGTA
** *
44628 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
44672 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
44690 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44690 original size:24 final size:23
Alignment explanation
Indices: 44628--44691 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
44618 GTAATATGTA
* *
44628 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
44651 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
44675 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
44692 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:44982 original size:40 final size:40
Alignment explanation
Indices: 44928--45158 Score: 162
Period size: 40 Copynumber: 5.5 Consensus size: 40
44918 TTATCTAGGG
44928 TGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-A
*
44968 TGACACGGCTCATACGTGATGAAGAGTTCTGGTCTGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
* * * * * *
45008 TGACACGGTTCCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG---TCT---GGGGA
* * * * * ** *
45054 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG---TCTGGGGA
*
45097 TGACACGGCTCATACGTGATGAAGAGATCTGGTCCGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
* * *
45137 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCATACGTGATGA
45159 GGACGGCTGG
Statistics
Matches: 155, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
40 82 0.53
41 5 0.03
42 1 0.01
43 29 0.19
46 38 0.25
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
Found at i:45238 original size:28 final size:28
Alignment explanation
Indices: 45207--45268 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
45197 AAACCAAATT
45207 AAAGATTTATTTCAA-AAGAAACAAACCC
1 AAAGATTTATTTCAAGAA-AAACAAACCC
* * *
45235 AAAGATTTGTTTCAAGAAAAATAAACTC
1 AAAGATTTATTTCAAGAAAAACAAACCC
45263 AAAGAT
1 AAAGAT
45269 GATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (28 bp):
AAAGATTTATTTCAAGAAAAACAAACCC
Found at i:46211 original size:64 final size:63
Alignment explanation
Indices: 46118--46352 Score: 181
Period size: 65 Copynumber: 3.6 Consensus size: 63
46108 TTTCAAAATG
* * * * *
46118 AACATATTCAAAGATTTACTTCAAGAGAAACCGTCTCAAGAGATACAAAATTCAT-TTT-AAGAG
1 AACAGATTCAAAGATTT-TTTCAAAAGAAACCATCTCAAGAGAGACAAAATT-ATGTTTCAA-AG
46181 A
63 A
** * *
46182 AACAGATTCAAAGATTTTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGA
1 AACAGATTCAAAGATTTTTT-CAAAAGAAACCATCTCAAGAGAGACAAAATTATGTTT-CAAAGA
* * ** * *
46247 AACAGACTCAAAGATTTTTGTTTCAAATGAAATTATCT-TA-AGAGACAAAATTTTGTTTCCAAA
1 AACAGATTCAAAGA--TTT-TTTCAAAAGAAACCATCTCAAGAGAGACAAAATTATGTTT-CAAA
46310 GA
62 GA
* *
46312 AACAGACTCAAAGATTTTTGTTTCAAAAGAAACAATCTCAA
1 AACAGATTCAAAGA--TTT-TTTCAAAAGAAACCATCTCAA
46353 AGATTTTTTA
Statistics
Matches: 147, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
63 3 0.02
64 44 0.30
65 76 0.52
66 4 0.03
67 17 0.12
68 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (63 bp):
AACAGATTCAAAGATTTTTTCAAAAGAAACCATCTCAAGAGAGACAAAATTATGTTTCAAAGA
Found at i:46331 original size:65 final size:67
Alignment explanation
Indices: 46179--46343 Score: 275
Period size: 65 Copynumber: 2.5 Consensus size: 67
46169 TCATTTTAAG
* *
46179 AGAAACAGATTCAAAGA-TTTT-TTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
46242 AA
66 AA
*
46244 AGAAACAGACTCAAAGATTTTTGTTTCAAATGAAATTATCTT-A-AGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
46307 AA
66 AA
46309 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAA
46344 CAATCTCAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
65 72 0.77
66 5 0.05
67 17 0.18
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:46587 original size:29 final size:29
Alignment explanation
Indices: 46307--46579 Score: 429
Period size: 29 Copynumber: 9.3 Consensus size: 29
46297 TTTTGTTTCC
* * *
46307 AAAGAAACAGACTCAAAGATTTTTGTTTCA
1 AAAGGAACAAACTCAAAGATTTTT-ATTCA
* *
46337 AAAGAAACAATCTCAAAGATTTTTTATTCA
1 AAAGGAACAAACTCAAAGA-TTTTTATTCA
46367 AAAGGAACAAACTCAAAGATTTTTATTCA
1 AAAGGAACAAACTCAAAGATTTTTATTCA
*
46396 AAATGAACAAACTCAAAGATTTTTATTCA
1 AAAGGAACAAACTCAAAGATTTTTATTCA
46425 AAAGGAACAAACTCAAAGATTTTTATTCA
1 AAAGGAACAAACTCAAAGATTTTTATTCA
*
46454 AAATGAACAAACTCAAAGATTTTTATTCA
1 AAAGGAACAAACTCAAAGATTTTTATTCA
46483 AAAGGAACAAACTCAAAGATTTTTTTATTCA
1 AAAGGAACAAACTCAAAGA--TTTTTATTCA
*
46514 AAATGAACAAACTCAAAGATTTTTATTCA
1 AAAGGAACAAACTCAAAGATTTTTATTCA
*
46543 AAATGAACAAACTCAAAGATTTTTATTCA
1 AAAGGAACAAACTCAAAGATTTTTATTCA
46572 AAAGGAAC
1 AAAGGAAC
46580 TGTCTCAAGA
Statistics
Matches: 229, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
29 158 0.69
30 38 0.17
31 33 0.14
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (29 bp):
AAAGGAACAAACTCAAAGATTTTTATTCA
Found at i:46587 original size:147 final size:147
Alignment explanation
Indices: 46312--46579 Score: 475
Period size: 147 Copynumber: 1.8 Consensus size: 147
46302 TTTCCAAAGA
* * *
46312 AACAGACTCAAAGATTTTTGTTTCAAAAGAAACAATCTCAAAGATTTTTTATTCAAAAGGAACAA
1 AACAAACTCAAAGATTTTTGATTCAAAAGAAACAAACTCAAAGATTTTTTATTCAAAAGGAACAA
46377 ACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAA
66 ACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAA
46442 GATTTTTATTCAAAATG
131 GATTTTTATTCAAAATG
* *
46459 AACAAACTCAAAGATTTTT-ATTCAAAAGGAACAAACTCAAAGATTTTTTTATTCAAAATGAACA
1 AACAAACTCAAAGATTTTTGATTCAAAAGAAACAAACTCAAAGA-TTTTTTATTCAAAAGGAACA
46523 AACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAAC
65 AACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAAC
46580 TGTCTCAAGA
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
146 21 0.18
147 94 0.82
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (147 bp):
AACAAACTCAAAGATTTTTGATTCAAAAGAAACAAACTCAAAGATTTTTTATTCAAAAGGAACAA
ACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAA
GATTTTTATTCAAAATG
Found at i:46904 original size:36 final size:36
Alignment explanation
Indices: 46820--46923 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
46810 GAGAAAATGA
* * *
46820 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
46854 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
46890 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
46924 ACGACAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:47489 original size:4 final size:4
Alignment explanation
Indices: 47480--47547 Score: 118
Period size: 4 Copynumber: 17.0 Consensus size: 4
47470 TTTATGTATC
* *
47480 ATGT ATGT ATGT GTAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
47528 ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT
47548 GTATACTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49403 original size:26 final size:26
Alignment explanation
Indices: 49371--49452 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
49361 TTTCAAGGTG
49371 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
* *
49397 GAGAGAATGCTTCAAGGT-T----GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
49418 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
49443 GATAGAATGT
1 GAAAGAATGT
49453 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 14 0.33
21 3 0.07
25 3 0.07
26 23 0.53
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:49430 original size:46 final size:45
Alignment explanation
Indices: 49362--49451 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 45
49352 AATACAGTGT
* *
49362 TTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGAGAATGC
1 TTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAATGC
*
49407 TTCAAGGTTGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAATG
1 TTCAAGG-TGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAATG
49452 TCAAAAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 7 0.17
46 34 0.83
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (45 bp):
TTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAATGC
Found at i:50830 original size:5 final size:5
Alignment explanation
Indices: 50820--50845 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
50810 CATTATGATG
50820 ATGCA ATGCA ATGCA ATGCA ATGCA A
1 ATGCA ATGCA ATGCA ATGCA ATGCA A
50846 ATGACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGCA
Found at i:50913 original size:31 final size:32
Alignment explanation
Indices: 50857--50918 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
50847 TGACAAAATG
50857 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
50889 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
50919 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:54103 original size:19 final size:19
Alignment explanation
Indices: 54074--54121 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
54064 GTTTCCAATC
54074 TCTCT-TTTTTTCCTCTAT
1 TCTCTGTTTTTTCCTCTAT
** *
54092 TCTCTGTTTTTTTTTTTAT
1 TCTCTGTTTTTTCCTCTAT
54111 TCTCTGTTTTT
1 TCTCTGTTTTT
54122 CTTTTTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.73
Consensus pattern (19 bp):
TCTCTGTTTTTTCCTCTAT
Found at i:54126 original size:19 final size:19
Alignment explanation
Indices: 54089--54133 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
54079 TTTTTTCCTC
*
54089 TATTCTCTGTTTTTTTTTT
1 TATTCTCTGTTTTTCTTTT
54108 TATTCTCTGTTTTTCTTTT
1 TATTCTCTGTTTTTCTTTT
*
54127 TGTTCTC
1 TATTCTC
54134 CCCTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.04, C:0.16, G:0.07, T:0.73
Consensus pattern (19 bp):
TATTCTCTGTTTTTCTTTT
Found at i:54594 original size:3 final size:3
Alignment explanation
Indices: 54581--54642 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
54571 GTAATATGTA
** *
54581 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
54625 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
54643 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54643 original size:24 final size:23
Alignment explanation
Indices: 54581--54644 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
54571 GTAATATGTA
* *
54581 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
54604 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
54628 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
54645 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:55542 original size:45 final size:45
Alignment explanation
Indices: 55486--55775 Score: 438
Period size: 45 Copynumber: 6.4 Consensus size: 45
55476 AATACCATGA
* *
55486 ATGGCACCTTTTATGCCAATAATGCACCGTTATGTATTTTCA-TT
1 ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
* *
55530 AGTGGTACCTTTTATGCCGATAATGCACCGTTATACATTTTCATTT
1 A-TGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
* * *
55576 ATGGCACGTTTTATGCCGATTATGCACCGTTATGCATTTTTATTT
1 ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
* * *
55621 ATGGCACCTTTTATGTCGATAATGCGCCATTATGCATTTTCATTT
1 ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
55666 ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
1 ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
*
55711 ATGGCACCTTTTATGCTGATAATGCACCGTTATGCATTTTCATTT
1 ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
* * *
55756 ATGGTACTTTTTATGACGAT
1 ATGGCACCTTTTATGCCGAT
55776 TCATAGATTT
Statistics
Matches: 221, Mismatches: 23, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
44 1 0.00
45 217 0.98
46 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (45 bp):
ATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
Found at i:55679 original size:26 final size:26
Alignment explanation
Indices: 55650--55726 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
55640 TAATGCGCCA
55650 TTATGCATTTTCATTTATGGCACCTT
1 TTATGCATTTTCATTTATGGCACCTT
* *
55676 TTATGC-----CGA-TAAT-GCACC-G
1 TTATGCATTTTC-ATTTATGGCACCTT
55695 TTATGCATTTTCATTTATGGCACCTT
1 TTATGCATTTTCATTTATGGCACCTT
55721 TTATGC
1 TTATGC
55727 TGATAATGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
19 6 0.16
20 5 0.13
21 4 0.11
22 1 0.03
23 1 0.03
24 4 0.11
25 5 0.13
26 12 0.32
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (26 bp):
TTATGCATTTTCATTTATGGCACCTT
Found at i:62310 original size:17 final size:17
Alignment explanation
Indices: 62290--62325 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
62280 CTCAGCTTTG
62290 TTCATATAGTCTTATTC
1 TTCATATAGTCTTATTC
*
62307 TTCATATAGTTTTATTC
1 TTCATATAGTCTTATTC
62324 TT
1 TT
62326 TAGCAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (17 bp):
TTCATATAGTCTTATTC
Found at i:64033 original size:85 final size:85
Alignment explanation
Indices: 63934--64091 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
63924 ACGACCCCTG
* * * *
63934 AATGTGTGTCATCTT-TTTTAATGACT-GGAGCTTCAATGACGCTCAATG-TAAGTCATACATGC
1 AATGTGTGTCATCTTAATCT-ATGA-TGGGAGCTTCAATGACGCTCAATGCGAA-TCATAAATGC
63996 GTGTCATAAATTTATGAAACACA
63 GTGTCATAAATTTATGAAACACA
*
64019 AATGTGTGTCATCTTAATCTATGATGGGGGCTTCAATGACGCTCAATGCGAATCATAAATGCGTG
1 AATGTGTGTCATCTTAATCTATGATGGGAGCTTCAATGACGCTCAATGCGAATCATAAATGCGTG
64084 TCATAAAT
66 TCATAAAT
64092 GCGCGTCATA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
84 1 0.02
85 60 0.92
86 4 0.06
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (85 bp):
AATGTGTGTCATCTTAATCTATGATGGGAGCTTCAATGACGCTCAATGCGAATCATAAATGCGTG
TCATAAATTTATGAAACACA
Found at i:64099 original size:13 final size:13
Alignment explanation
Indices: 64071--64101 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
64061 TCAATGCGAA
*
64071 TCATAAATGCGTG
1 TCATAAATGCGCG
64084 TCATAAATGCGCG
1 TCATAAATGCGCG
64097 TCATA
1 TCATA
64102 GATTTATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:65471 original size:19 final size:21
Alignment explanation
Indices: 65447--65490 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
65437 CATAAATTAA
65447 TGAATTAATCTT-CCTTGGT-
1 TGAATTAATCTTCCCTTGGTG
*
65466 TGAATTCATCTTCCCTTGGTG
1 TGAATTAATCTTCCCTTGGTG
65487 TGAA
1 TGAA
65491 CATGACGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 7 0.32
21 4 0.18
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (21 bp):
TGAATTAATCTTCCCTTGGTG
Found at i:77855 original size:22 final size:22
Alignment explanation
Indices: 77827--77868 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
77817 CTTAACTAGA
77827 GTTGACTTTGACTTTGACCAGT
1 GTTGACTTTGACTTTGACCAGT
77849 GTTGACTTTGACTTTGACCA
1 GTTGACTTTGACTTTGACCA
77869 AAATGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (22 bp):
GTTGACTTTGACTTTGACCAGT
Found at i:79364 original size:30 final size:30
Alignment explanation
Indices: 79328--79389 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
79318 TTATAGGGAT
79328 ATCATACTGAAATTTAATCAATTTGTAGAA
1 ATCATACTGAAATTTAATCAATTTGTAGAA
79358 ATCATACTGAAATTTAATCAATTTGTAGAA
1 ATCATACTGAAATTTAATCAATTTGTAGAA
79388 AT
1 AT
79390 TTTGTGGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (30 bp):
ATCATACTGAAATTTAATCAATTTGTAGAA
Found at i:82195 original size:17 final size:17
Alignment explanation
Indices: 82175--82208 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
82165 TTGACTTTGA
82175 CCAAAAAGTCAAATTTT
1 CCAAAAAGTCAAATTTT
*
82192 CCAAAAAGTCATATTTT
1 CCAAAAAGTCAAATTTT
82209 ATGTTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (17 bp):
CCAAAAAGTCAAATTTT
Found at i:82794 original size:19 final size:19
Alignment explanation
Indices: 82770--82813 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
82760 GAAATTGAAA
*
82770 ATAACCCTATTAATCGATC
1 ATAACCCTATTAATCAATC
* *
82789 ATAACCTTGTTAATCAATC
1 ATAACCCTATTAATCAATC
82808 ATAACC
1 ATAACC
82814 TTTGAGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAACCCTATTAATCAATC
Found at i:82814 original size:19 final size:19
Alignment explanation
Indices: 82779--82815 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
82769 AATAACCCTA
*
82779 TTAATCGATCATAACCTTG
1 TTAATCAATCATAACCTTG
82798 TTAATCAATCATAACCTT
1 TTAATCAATCATAACCTT
82816 TGAGATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAATCAATCATAACCTTG
Done.