Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001093.1 Hibiscus syriacus cultivar Beakdansim tig00002162_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: 167491
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:4757 original size:13 final size:13
Alignment explanation
Indices: 4736--4770 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4726 CCCACTTACT
4736 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
4749 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
4762 TTTCACTTT
1 TTTCACTTT
4771 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:6779 original size:20 final size:20
Alignment explanation
Indices: 6754--6796 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6744 TCTATGAGCA
*
6754 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
6774 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
6794 CAT
1 CAT
6797 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:10599 original size:10 final size:10
Alignment explanation
Indices: 10584--10608 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10574 TGCACAACAT
10584 TTTAGTTGCA
1 TTTAGTTGCA
10594 TTTAGTTGCA
1 TTTAGTTGCA
10604 TTTAG
1 TTTAG
10609 GTTATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:12616 original size:19 final size:20
Alignment explanation
Indices: 12594--12632 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12584 ATATGTAATT
12594 AATATACATAT-AT-GTTTTA
1 AATAT-CATATGATAGTTTTA
12613 AATATCATATGATAGTTTTA
1 AATATCATATGATAGTTTTA
12633 CTTGAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (20 bp):
AATATCATATGATAGTTTTA
Found at i:18583 original size:40 final size:40
Alignment explanation
Indices: 18539--18689 Score: 230
Period size: 40 Copynumber: 3.8 Consensus size: 40
18529 AGGACACTAA
*
18539 GTGTATATGGTGGGCATGACCTCATGTGTAATGCACTTCG
1 GTGTATATGGTGGGCATGACCTTATGTGTAATGCACTTCG
* *
18579 GTGTATATGGTGGACATGACCTTATGTGTAATGTACTTCG
1 GTGTATATGGTGGGCATGACCTTATGTGTAATGCACTTCG
* * *
18619 GTGTATATGGTGTGCATGACCGTATGTGTAATGCACTTAG
1 GTGTATATGGTGGGCATGACCTTATGTGTAATGCACTTCG
* *
18659 GTGTATATGGTGAGCACGACCTTATGTGTAA
1 GTGTATATGGTGGGCATGACCTTATGTGTAA
18690 CAACCCGAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (40 bp):
GTGTATATGGTGGGCATGACCTTATGTGTAATGCACTTCG
Found at i:19460 original size:9 final size:9
Alignment explanation
Indices: 19434--19496 Score: 81
Period size: 9 Copynumber: 6.7 Consensus size: 9
19424 TCAGTTTTCA
19434 ACCGGTTCTG
1 ACCGGTT-TG
19444 ACCGGTTTG
1 ACCGGTTTG
*
19453 ACCAGTTTTG
1 ACC-GGTTTG
19463 ACCGGTTTG
1 ACCGGTTTG
*
19472 ACCGGTCTG
1 ACCGGTTTG
19481 AACCGGTTTG
1 -ACCGGTTTG
19491 ACCGGT
1 ACCGGT
19497 CAGACCCGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
9 24 0.51
10 23 0.49
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:19466 original size:19 final size:18
Alignment explanation
Indices: 19434--19502 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
19424 TCAGTTTTCA
19434 ACCGGTTCTGACCGGTTTG
1 ACCGG-TCTGACCGGTTTG
* *
19453 ACCAGTTTTGACCGGTTTG
1 ACC-GGTCTGACCGGTTTG
19472 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTG-ACCGGTTTG
*
19491 ACCGGTCAGACC
1 ACCGGTCTGACC
19503 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 7 0.16
19 35 0.81
20 1 0.02
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:19509 original size:5 final size:5
Alignment explanation
Indices: 19499--19550 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
19489 TGACCGGTCA
* * *
19499 GACCC GACCC GACCC GACCC GA-CT GACCC GACCC -AACT GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC
19547 GACC
1 GACC
19551 GTTGACGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 5 0.13
5 34 0.87
ACGTcount: A:0.23, C:0.54, G:0.19, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:19526 original size:14 final size:14
Alignment explanation
Indices: 19499--19549 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
19489 TGACCGGTCA
*
19499 GACCCGACCCGACCC
1 GACCCGA-CTGACCC
19514 GACCCGACTGACCC
1 GACCCGACTGACCC
*
19528 GACCCAACTGACCC
1 GACCCGACTGACCC
19542 GACCCGAC
1 GACCCGAC
19550 CGTTGACGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 26 0.79
15 7 0.21
ACGTcount: A:0.24, C:0.53, G:0.20, T:0.04
Consensus pattern (14 bp):
GACCCGACTGACCC
Found at i:19526 original size:19 final size:20
Alignment explanation
Indices: 19499--19550 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
19489 TGACCGGTCA
*
19499 GACCCGACCCGACCCGACCC
1 GACCCGACCCGACCCAACCC
* *
19519 GA-CTGACCCGACCCAA-CT
1 GACCCGACCCGACCCAACCC
19537 GACCCGACCCGACC
1 GACCCGACCCGACC
19551 GTTGACGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.11
19 22 0.81
20 2 0.07
ACGTcount: A:0.23, C:0.54, G:0.19, T:0.04
Consensus pattern (20 bp):
GACCCGACCCGACCCAACCC
Found at i:26702 original size:20 final size:21
Alignment explanation
Indices: 26670--26753 Score: 99
Period size: 20 Copynumber: 4.3 Consensus size: 21
26660 AGGGCTGGAA
*
26670 ACCGGTT-TG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTTCG
*
26689 ATCGGTTCTG-ACCGGTTTCG
1 ACCGGTTCTGAACCGGTTTCG
*
26709 ACCGGTTC-GAACTGGTTTCG
1 ACCGGTTCTGAACCGGTTTCG
26729 ACCGG-TCTGAACCGGTTT-G
1 ACCGGTTCTGAACCGGTTTCG
26748 ACCGGT
1 ACCGGT
26754 CAGACCCGAC
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
19 15 0.27
20 41 0.73
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
ACCGGTTCTGAACCGGTTTCG
Found at i:26704 original size:10 final size:9
Alignment explanation
Indices: 26670--26753 Score: 69
Period size: 10 Copynumber: 8.7 Consensus size: 9
26660 AGGGCTGGAA
26670 ACCGGTTTG
1 ACCGGTTTG
*
26679 ACCGGTTTCA
1 ACCGGTTT-G
*
26689 ATCGGTTCTG
1 ACCGGTT-TG
26699 ACCGGTTTCG
1 ACCGGTTT-G
*
26709 ACCGGTTCG
1 ACCGGTTTG
*
26718 AACTGGTTTCG
1 -ACCGGTTT-G
*
26729 ACCGGTCTG
1 ACCGGTTTG
26738 AACCGGTTTG
1 -ACCGGTTTG
26748 ACCGGT
1 ACCGGT
26754 CAGACCCGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 17 0.29
10 40 0.68
11 2 0.03
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:28922 original size:14 final size:15
Alignment explanation
Indices: 28897--28926 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28887 ATGTGACATC
28897 TATAATCTATATGGG
1 TATAATCTATATGGG
28912 TATAA-CTATATGGG
1 TATAATCTATATGGG
28926 T
1 T
28927 TTTTGGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
TATAATCTATATGGG
Found at i:30637 original size:20 final size:21
Alignment explanation
Indices: 30612--30651 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
30602 GTCCCTTACT
*
30612 TTCTTTCTTT-TGTCTTTAAG
1 TTCTTTATTTATGTCTTTAAG
30632 TTCTTTATTTCATGTCTTTA
1 TTCTTTATTT-ATGTCTTTA
30652 TTTATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.12, C:0.15, G:0.07, T:0.65
Consensus pattern (21 bp):
TTCTTTATTTATGTCTTTAAG
Found at i:32791 original size:75 final size:73
Alignment explanation
Indices: 32701--32857 Score: 192
Period size: 75 Copynumber: 2.1 Consensus size: 73
32691 TTTAACTATT
* * *
32701 AATTATAAT-TAATAAAT-ATAATTAAAAATCATTTATTTCATTAAAAAAAATTAAAAATAAATA
1 AATTAT-ATGTAATAAATAAAAACTAAAAATCATTTATTCCATT-AAAAAAATT-AAAATAAAT-
32764 AAAAATATTATA
62 AAAAATATTATA
* * * *
32776 AATTATATGTAATAAATAAAAACTAAGAATTATTTCTTCCATTAAAAAAATTAAAATATATAAAA
1 AATTATATGTAATAAATAAAAACTAAAAATCATTTATTCCATTAAAAAAATTAAAATAAATAAAA
*
32841 ATATTGTA
66 ATATTATA
32849 AATTATATG
1 AATTATATG
32858 CAAATAAGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
73 20 0.28
74 10 0.14
75 23 0.32
76 19 0.26
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (73 bp):
AATTATATGTAATAAATAAAAACTAAAAATCATTTATTCCATTAAAAAAATTAAAATAAATAAAA
ATATTATA
Found at i:33723 original size:32 final size:32
Alignment explanation
Indices: 33672--33744 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
33662 ACTTTAACTT
* *
33672 ACTAATAAAGGGGGGTTACATTTCCAGGGATC
1 ACTAGTAAACGGGGGTTACATTTCCAGGGATC
33704 ACTAGTAAACGGGGGTTACATTTCCAGGGATC
1 ACTAGTAAACGGGGGTTACATTTCCAGGGATC
33736 ACTAGTAAA
1 ACTAGTAAA
33745 GGGAAGTCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (32 bp):
ACTAGTAAACGGGGGTTACATTTCCAGGGATC
Found at i:41170 original size:71 final size:72
Alignment explanation
Indices: 41054--41199 Score: 249
Period size: 71 Copynumber: 2.0 Consensus size: 72
41044 AAAACGCCGA
* *
41054 TAATTTACCACTCTATTGCGACATTTTTTGTATAAACGCCACTAAATGTTAAATATATTGCGGCG
1 TAATTTACCAATCTATTGCGACATTTTTGGTATAAACGCCACTAAATGTTAAATATATTGCGGCG
41119 TTTT-GC
66 TTTTAGC
* *
41125 TAATTTACCAATCTATTGCGGCATTTTTGGTATAAACGCCGCTAAATGTTAAATATATTGCGGCG
1 TAATTTACCAATCTATTGCGACATTTTTGGTATAAACGCCACTAAATGTTAAATATATTGCGGCG
41190 TTTTAGC
66 TTTTAGC
41197 TAA
1 TAA
41200 AACGCCGCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 65 0.93
72 5 0.07
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (72 bp):
TAATTTACCAATCTATTGCGACATTTTTGGTATAAACGCCACTAAATGTTAAATATATTGCGGCG
TTTTAGC
Found at i:41185 original size:42 final size:42
Alignment explanation
Indices: 41138--41251 Score: 160
Period size: 41 Copynumber: 2.7 Consensus size: 42
41128 TTTACCAATC
* *
41138 TATTGCGGCATTTTTGGTATAAACGCCGCTAAATGT-TAAATA
1 TATTGCGGCGTTTTTGCTATAAACGCCGCTAAATGTCT-AATA
* *
41180 TATTGCGGCGTTTTAGCTA-AAACGCCGCTAAATGTCTACTA
1 TATTGCGGCGTTTTTGCTATAAACGCCGCTAAATGTCTAATA
*
41221 TATTGCGGCGTTTTTACTATAAACGCCGCTA
1 TATTGCGGCGTTTTTGCTATAAACGCCGCTA
41252 TTGTTTAACC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
41 36 0.56
42 28 0.44
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (42 bp):
TATTGCGGCGTTTTTGCTATAAACGCCGCTAAATGTCTAATA
Found at i:41211 original size:41 final size:42
Alignment explanation
Indices: 41138--41251 Score: 153
Period size: 42 Copynumber: 2.7 Consensus size: 42
41128 TTTACCAATC
* * *
41138 TATTGCGGCATTTTTGGTATAAACGCCGCTAAATGT-TAAATA
1 TATTGCGGCGTTTTAGCTATAAACGCCGCTAAATGTCT-AATA
*
41180 TATTGCGGCGTTTTAGCTA-AAACGCCGCTAAATGTCTACTA
1 TATTGCGGCGTTTTAGCTATAAACGCCGCTAAATGTCTAATA
41221 TATTGCGGCGTTTTTA-CTATAAACGCCGCTA
1 TATTGCGGCG-TTTTAGCTATAAACGCCGCTA
41252 TTGTTTAACC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
41 32 0.49
42 33 0.51
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (42 bp):
TATTGCGGCGTTTTAGCTATAAACGCCGCTAAATGTCTAATA
Found at i:41560 original size:20 final size:20
Alignment explanation
Indices: 41521--41560 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41511 GCTATGAATC
*
41521 CAATCCCAACATGCCCAATG
1 CAATCCCAACATGCACAATG
* *
41541 CAATCCCACCATGCATAATG
1 CAATCCCAACATGCACAATG
41561 AAAGCCCATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.38, G:0.10, T:0.17
Consensus pattern (20 bp):
CAATCCCAACATGCACAATG
Found at i:43412 original size:3 final size:3
Alignment explanation
Indices: 43404--43507 Score: 82
Period size: 3 Copynumber: 32.7 Consensus size: 3
43394 TAAGTTTTTC
* * *
43404 ATT ATT ATT ATT ATT AATT ATT ATT ATT AATT ACT ATT ACTA ATT ATA
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT -ATT ATT ATT A-TT ATT ATT
* * * *
43452 ATT ATT ATT GTT AATT ACT ATT ACTA ATT ATT TTT ATT ATT AATT ATT
1 ATT ATT ATT ATT -ATT ATT ATT A-TT ATT ATT ATT ATT ATT -ATT ATT
*
43500 ACT ATT AT
1 ATT ATT AT
43508 AAACAAAATA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
3 64 0.81
4 15 0.19
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:43425 original size:13 final size:13
Alignment explanation
Indices: 43407--43506 Score: 84
Period size: 13 Copynumber: 8.0 Consensus size: 13
43397 GTTTTTCATT
43407 ATTATTATTATTA
1 ATTATTATTATTA
43420 ATTATTATTATTA
1 ATTATTATTATTA
* *
43433 ATTACTATTACTA
1 ATTATTATTATTA
*
43446 ATTATAATTATT-
1 ATTATTATTATTA
*
43458 ATTGTTA--ATT-
1 ATTATTATTATTA
* *
43468 ACTATTACTAATT-
1 ATTATTA-TTATTA
*
43481 ATTTTTATTATTA
1 ATTATTATTATTA
*
43494 ATTATTACTATTA
1 ATTATTATTATTA
43507 TAAACAAAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
10 8 0.12
12 9 0.13
13 52 0.75
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:43454 original size:32 final size:32
Alignment explanation
Indices: 43413--43506 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
43403 CATTATTATT
43413 ATTATTAATTATTATTATTAATTACTATTACTA
1 ATTA-TAATTATTATTATTAATTACTATTACTA
*
43446 ATTATAATTATTATTGTTAATTACTATTACTA
1 ATTATAATTATTATTATTAATTACTATTACTA
**
43478 ATTATTTTTATTATTAATT-ATTACTATTA
1 ATTATAATTATTATT-ATTAATTACTATTA
43507 TAAACAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 50 0.89
33 6 0.11
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (32 bp):
ATTATAATTATTATTATTAATTACTATTACTA
Found at i:43751 original size:2 final size:2
Alignment explanation
Indices: 43746--43786 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43736 ATTATAGCTC
43746 AT AT AT AT 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 AT AT AT AT A
43787 AAATAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44113 original size:26 final size:26
Alignment explanation
Indices: 44083--44136 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
44073 ATGATAACAA
* *
44083 TATTTTTATGATATTTT-ATTTTATTT
1 TATTTTCATGA-ATTTTCATTTAATTT
*
44109 TATTTTCATTAATTTTCATTTAATTT
1 TATTTTCATGAATTTTCATTTAATTT
44135 TA
1 TA
44137 GTATTGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (26 bp):
TATTTTCATGAATTTTCATTTAATTT
Found at i:44133 original size:11 final size:11
Alignment explanation
Indices: 44095--44135 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
44085 TTTTTATGAT
*
44095 ATTTTATTTT-
1 ATTTAATTTTC
*
44105 ATTTTATTTTC
1 ATTTAATTTTC
44116 A-TTAATTTTC
1 ATTTAATTTTC
44126 ATTTAATTTT
1 ATTTAATTTT
44136 AGTATTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTAATTTTC
Found at i:59422 original size:23 final size:22
Alignment explanation
Indices: 59389--59436 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
59379 ATTACACCTG
*
59389 AAAAAATAAGA-AAAAAAATAA
1 AAAAAATAAGAGAAAAAAAGAA
*
59410 AAAAAATTAAAGAGAGAAAAAGAA
1 AAAAAA-T-AAGAGAAAAAAAGAA
59434 AAA
1 AAA
59437 TGAATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 4 0.18
24 11 0.50
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAATAAGAGAAAAAAAGAA
Found at i:60927 original size:3 final size:3
Alignment explanation
Indices: 60919--61003 Score: 98
Period size: 3 Copynumber: 27.0 Consensus size: 3
60909 ATAAGTTTTG
* *
60919 TAT TAT TAT TAT TAT TAAT TAT TAT TAT TATT TAC AAT TAT TATT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT
* *
60967 TACT AAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61004 AAACAAAATA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
3 59 0.84
4 11 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:60941 original size:16 final size:16
Alignment explanation
Indices: 60920--61002 Score: 105
Period size: 16 Copynumber: 5.0 Consensus size: 16
60910 TAAGTTTTGT
60920 ATTATTATTATTATTA
1 ATTATTATTATTATTA
60936 ATTATTATTATTATTTACA
1 ATTATTATTATTA-TT--A
*
60955 ATTATTATTTATTACTA
1 ATTATTA-TTATTATTA
*
60972 ATTATAATTATTATT-
1 ATTATTATTATTATTA
60987 ATTATTATTATTATTA
1 ATTATTATTATTATTA
61003 TAAACAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
15 14 0.24
16 20 0.34
17 9 0.16
19 9 0.16
20 6 0.10
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTATTATTATTA
Found at i:62996 original size:5 final size:5
Alignment explanation
Indices: 62986--63031 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
62976 ATAGAAATAT
* **
62986 TTTTA TTTTA TTTTG TTTTA TTTTTA TGATA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
63032 AAAATGTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:63007 original size:21 final size:21
Alignment explanation
Indices: 62983--63030 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
62973 ATGATAGAAA
** *
62983 TATTTTTATTTTATTTTGTTT
1 TATTTTTATGATATTTTATTT
63004 TATTTTTATGATATTTTATTT
1 TATTTTTATGATATTTTATTT
63025 TATTTT
1 TATTTT
63031 AAAAATGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (21 bp):
TATTTTTATGATATTTTATTT
Found at i:63491 original size:22 final size:24
Alignment explanation
Indices: 63459--63502 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
63449 TAAACAAAGT
63459 TTTGTCTTTAAAA-TAATTTTTTA
1 TTTGTCTTTAAAAGTAATTTTTTA
*
63482 TTTGT-TTTAAAAGTCATTTTT
1 TTTGTCTTTAAAAGTAATTTTT
63503 AGGTATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTGTCTTTAAAAGTAATTTTTTA
Found at i:67250 original size:214 final size:212
Alignment explanation
Indices: 66881--67306 Score: 807
Period size: 214 Copynumber: 2.0 Consensus size: 212
66871 CTTGCATCAC
66881 TGTAACAACCCAAATATTTACAAAATAATATTTAATTGAAATTGGAGGTTAATTGTGAAAATTGG
1 TGTAACAACCCAAATATTTACAAAATAATATTTAATTGAAATTGGAGGTTAATTGTGAAAATTGG
* *
66946 TGAAAATTGGGGACTAAATTGAAAGATTTTAAATTTTGGAGCTTGTTTTAGAGTTAGAGGAAATT
66 TGAAAATTGGGGACTAAATTGAAAGATTTTAAAATTTGGAGCTTGTTTTAGAGTTAAAGGAAATT
67011 TAGGGACTAAGCCCTGAATTTACCCAATAAAATTAGGTAAGTTTAGTTTTTGATGATATATATAC
131 TAGGGACTAAGCCCTGAATTTACCCAATAAAATTAGGTAAGTTTAGTTTTTGATG--ATATATAC
67076 GTGGGGTGGTTTTCTGTTT
194 GTGGGGTGGTTTTCTGTTT
*
67095 TGTAACAACCCAAATATTTACAAAATAATATTTAATTGAACTTGGAGGTTAATTGTGAAAATTGG
1 TGTAACAACCCAAATATTTACAAAATAATATTTAATTGAAATTGGAGGTTAATTGTGAAAATTGG
67160 TGAAAATTGGGGACTAAATTGAAAGATTTTAAAATTTGGAGCTTGTTTTAGAGTTAAAGGAAATT
66 TGAAAATTGGGGACTAAATTGAAAGATTTTAAAATTTGGAGCTTGTTTTAGAGTTAAAGGAAATT
67225 TAGGGACTAAGCCCTGAATTTACCCAATAAAATTAGGTAAGTTTAGTTTTTGATGATATATACGT
131 TAGGGACTAAGCCCTGAATTTACCCAATAAAATTAGGTAAGTTTAGTTTTTGATGATATATACGT
67290 GGGGTGGTTTTCTGTTT
196 GGGGTGGTTTTCTGTTT
67307 CAAAACAGAA
Statistics
Matches: 209, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
212 27 0.13
214 182 0.87
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (212 bp):
TGTAACAACCCAAATATTTACAAAATAATATTTAATTGAAATTGGAGGTTAATTGTGAAAATTGG
TGAAAATTGGGGACTAAATTGAAAGATTTTAAAATTTGGAGCTTGTTTTAGAGTTAAAGGAAATT
TAGGGACTAAGCCCTGAATTTACCCAATAAAATTAGGTAAGTTTAGTTTTTGATGATATATACGT
GGGGTGGTTTTCTGTTT
Found at i:74645 original size:20 final size:19
Alignment explanation
Indices: 74620--74671 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
74610 AGGGCTAGAA
*
74620 AACCGGTCTGACCGGTTTTC
1 AACCGGTCTGACCGG-TCTC
* *
74640 AACCGGTTTGACCGGTCTG
1 AACCGGTCTGACCGGTCTC
74659 AACCGGTCTGACC
1 AACCGGTCTGACC
74672 CGACCCGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (19 bp):
AACCGGTCTGACCGGTCTC
Found at i:74688 original size:17 final size:17
Alignment explanation
Indices: 74666--74699 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
74656 CTGAACCGGT
74666 CTGACCCGACCCGACCG
1 CTGACCCGACCCGACCG
74683 CTGACCCGACCCGACCG
1 CTGACCCGACCCGACCG
74700 TTAACCGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.53, G:0.24, T:0.06
Consensus pattern (17 bp):
CTGACCCGACCCGACCG
Found at i:84520 original size:18 final size:19
Alignment explanation
Indices: 84497--84535 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
84487 TTTAAGTAGT
*
84497 AATAAAAACGATTAAA-TA
1 AATAAAAACAATTAAAGTA
*
84515 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
84534 AA
1 AA
84536 AATAAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:85656 original size:25 final size:22
Alignment explanation
Indices: 85628--85678 Score: 57
Period size: 25 Copynumber: 2.2 Consensus size: 22
85618 TCTTTAATGT
85628 ATATTTAATTTGAATTAATTAAATA
1 ATATTTAATTT--ATTAATTAAA-A
* *
85653 ATATTTTATTTATTAATTCAAA
1 ATATTTAATTTATTAATTAAAA
85675 ATAT
1 ATAT
85679 ATCAATTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
25 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTAATTTATTAATTAAAA
Found at i:92498 original size:37 final size:37
Alignment explanation
Indices: 92422--92498 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
92412 TTTTTATATT
*
92422 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
92459 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
92496 TTT
1 TTT
92499 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:102938 original size:18 final size:19
Alignment explanation
Indices: 102903--102940 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
102893 CACTGAATGT
102903 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
102923 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
102941 GATTACTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:103732 original size:18 final size:18
Alignment explanation
Indices: 103709--103746 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
103699 GTCACGATCT
*
103709 GACCCGTTGACCCGACCC
1 GACCCGTTGACCAGACCC
103727 GACCCGTTGACCAGACCC
1 GACCCGTTGACCAGACCC
103745 GA
1 GA
103747 TCGTTGACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.24, T:0.11
Consensus pattern (18 bp):
GACCCGTTGACCAGACCC
Found at i:103852 original size:29 final size:29
Alignment explanation
Indices: 103792--103859 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
103782 ATTCGGTTTT
* * * *
103792 GGTGCTAATCTGGTAATTAATTCGAAATG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
* *
103821 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
103850 GGTGCTATTT
1 GGTGCTATTT
103860 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCAAAAAG
Found at i:108291 original size:10 final size:9
Alignment explanation
Indices: 108276--108346 Score: 61
Period size: 10 Copynumber: 7.3 Consensus size: 9
108266 CCGGTTTTCA
108276 ACCGGTTCTG
1 ACCGGTT-TG
*
108286 ACCGGTTTCA
1 ACCGGTTT-G
*
108296 ACCGGTTCG
1 ACCGGTTTG
108305 AACCGGTTTG
1 -ACCGGTTTG
*
108315 ACCGGTTTCA
1 ACCGGTTT-G
*
108325 ACCGGTTCG
1 ACCGGTTTG
108334 AACCGGTTTG
1 -ACCGGTTTG
108344 ACC
1 ACC
108347 AGTCTGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 12 0.24
10 37 0.76
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:108294 original size:20 final size:19
Alignment explanation
Indices: 108258--108346 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 19
108248 TGCTGGAAAT
*
108258 CGGTTTAACCGGTTTTCAAC
1 CGGTTTGACCGG-TTTCAAC
108278 CGGTTCTGACCGGTTTCAAC
1 CGGTT-TGACCGGTTTCAAC
* *
108298 CGGTTCGAACCGGTTT-GAC
1 CGGTTTG-ACCGGTTTCAAC
*
108317 CGGTTTCAACCGG-TTCGAAC
1 CGGTTT-GACCGGTTTC-AAC
108337 CGGTTTGACC
1 CGGTTTGACC
108347 AGTCTGACCC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.04
19 16 0.28
20 33 0.58
21 6 0.11
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (19 bp):
CGGTTTGACCGGTTTCAAC
Found at i:108323 original size:29 final size:29
Alignment explanation
Indices: 108258--108346 Score: 137
Period size: 29 Copynumber: 3.0 Consensus size: 29
108248 TGCTGGAAAT
108258 CGGTTT-AACCGGTTTTC-AACCGGTTCTGAC
1 CGGTTTCAACCGG--TTCGAACCGGTT-TGAC
108288 CGGTTTCAACCGGTTCGAACCGGTTTGAC
1 CGGTTTCAACCGGTTCGAACCGGTTTGAC
108317 CGGTTTCAACCGGTTCGAACCGGTTTGAC
1 CGGTTTCAACCGGTTCGAACCGGTTTGAC
108346 C
1 C
108347 AGTCTGACCC
Statistics
Matches: 57, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
29 37 0.65
30 14 0.25
31 6 0.11
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
CGGTTTCAACCGGTTCGAACCGGTTTGAC
Found at i:108379 original size:17 final size:17
Alignment explanation
Indices: 108357--108394 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
108347 AGTCTGACCC
108357 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
108374 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
108391 GACC
1 GACC
108395 GTTGACTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:108394 original size:7 final size:7
Alignment explanation
Indices: 108384--108414 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
108374 GACCCGACCC
108384 GACCGTT
1 GACCGTT
108391 GACCGTT
1 GACCGTT
*
108398 GACTGTT
1 GACCGTT
108405 GACCGTT
1 GACCGTT
108412 GAC
1 GAC
108415 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:115588 original size:9 final size:9
Alignment explanation
Indices: 115575--115681 Score: 106
Period size: 9 Copynumber: 11.3 Consensus size: 9
115565 GCTGCTGGAA
*
115575 ACCGGTTTA
1 ACCGGTTTG
115584 ACCGGTTCTG
1 ACCGGTT-TG
115594 ACCGGTTCTG
1 ACCGGTT-TG
115604 ACCGGTTTG
1 ACCGGTTTG
*
115613 ACCGGTTTCA
1 ACCGGTTT-G
*
115623 ACCGGTTCG
1 ACCGGTTTG
115632 AACCGGTTTG
1 -ACCGGTTTG
**
115642 ACCGGTCTAA
1 ACCGGT-TTG
*
115652 ACCGGCTTG
1 ACCGGTTTG
115661 ACCGGTTTG
1 ACCGGTTTG
*
115670 ACCGGTCTG
1 ACCGGTTTG
115679 ACC
1 ACC
115682 CGACCCGACC
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
9 43 0.52
10 39 0.48
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:115599 original size:19 final size:19
Alignment explanation
Indices: 115575--115681 Score: 105
Period size: 19 Copynumber: 5.6 Consensus size: 19
115565 GCTGCTGGAA
*
115575 ACCGGTTTAACCGGTTCTG
1 ACCGGTTTGACCGGTTCTG
115594 ACCGGTTCTGACCGGTT-TG
1 ACCGGTT-TGACCGGTTCTG
*
115613 ACCGGTTTCAACCGGTTC-G
1 ACCGGTTT-GACCGGTTCTG
*
115632 AACCGGTTTGACCGG-TCTAA
1 -ACCGGTTTGACCGGTTCT-G
*
115652 ACCGGCTTGACCGGTT-TG
1 ACCGGTTTGACCGGTTCTG
*
115670 ACCGGTCTGACC
1 ACCGGTTTGACC
115682 CGACCCGACC
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
18 13 0.18
19 43 0.59
20 17 0.23
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCTG
Found at i:115617 original size:29 final size:29
Alignment explanation
Indices: 115575--115677 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
115565 GCTGCTGGAA
* *
115575 ACCGGTTTAACCGGTTCT-GACCGGTTCTG
1 ACCGGTTTGACCGG-TCTAAACCGGTTCTG
* *
115604 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTCTAAACCGGTTCTG
*
115632 AACCGGTTTGACCGGTCTAAACCGGCT-TG
1 -ACCGGTTTGACCGGTCTAAACCGGTTCTG
115661 ACCGGTTTGACCGGTCT
1 ACCGGTTTGACCGGTCT
115678 GACCCGACCC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
28 20 0.31
29 45 0.69
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (29 bp):
ACCGGTTTGACCGGTCTAAACCGGTTCTG
Found at i:115691 original size:28 final size:28
Alignment explanation
Indices: 115603--115692 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
115593 GACCGGTTCT
* * ***
115603 GACCGGTTTGACCGGTTTCAACCGGTTC
1 GACCGGTTTGACCGGTCTAAACCGACCC
* **
115631 GAACCGGTTTGACCGGTCTAAACCGGCTT
1 G-ACCGGTTTGACCGGTCTAAACCGACCC
* *
115660 GACCGGTTTGACCGGTCTGACCCGACCC
1 GACCGGTTTGACCGGTCTAAACCGACCC
115688 GACCG
1 GACCG
115693 TTGACCCGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 28 0.54
29 24 0.46
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (28 bp):
GACCGGTTTGACCGGTCTAAACCGACCC
Found at i:115699 original size:17 final size:17
Alignment explanation
Indices: 115677--115727 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
115667 TTGACCGGTC
115677 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
115694 T-----GACCCGACCGT
1 TGACCCGACCCGACCGT
*
115706 TGACCCGACCTGACCGT
1 TGACCCGACCCGACCGT
115723 TGACC
1 TGACC
115728 GTTGACTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
12 12 0.43
17 16 0.57
ACGTcount: A:0.18, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:115727 original size:12 final size:12
Alignment explanation
Indices: 115683--115715 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
115673 GGTCTGACCC
115683 GACCCGACCGTT
1 GACCCGACCGTT
115695 GACCCGACCGTT
1 GACCCGACCGTT
115707 GACCCGACC
1 GACCCGACC
115716 TGACCGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:120893 original size:13 final size:13
Alignment explanation
Indices: 120875--120911 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
120865 GACCGGTCAC
120875 GACCCGACCCGTT
1 GACCCGACCCGTT
120888 GACCCGACCCGTT
1 GACCCGACCCGTT
*
120901 GACCAGACCCG
1 GACCCGACCCG
120912 ATCGTTGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:121024 original size:29 final size:29
Alignment explanation
Indices: 120929--121002 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
120919 ACTGTTGACC
120929 GGTGCTATTCTGGTAAATAATTCAATTTT
1 GGTGCTATTCTGGTAAATAATTCAATTTT
*
120958 GGTGTTATTCTGGTAAATAATTCAATTTT
1 GGTGCTATTCTGGTAAATAATTCAATTTT
120987 GGTGCTATTCTGGTAA
1 GGTGCTATTCTGGTAA
121003 TTAAATCGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAATTTT
Found at i:121047 original size:29 final size:29
Alignment explanation
Indices: 120987--121054 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
120977 ATTCAATTTT
* * *
120987 GGTGCTATTCTGGTAATTAAATCGAAATG
1 GGTGCTATTTTGGTAATTAAATCAAAAAG
** *
121016 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAAATCAAAAAG
121045 GGTGCTATTT
1 GGTGCTATTT
121055 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAAATCAAAAAG
Found at i:134241 original size:44 final size:44
Alignment explanation
Indices: 134192--134285 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
134182 TGGTACATGG
* * *
134192 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATAGCAAGTATATTGGTAAAATAAGCTTACAAGC
*
134236 TTATGGATAAATAGTAAGTATATTGGTAAAATAAGCTTACAAGC
1 TTATGGATAAATAGCAAGTATATTGGTAAAATAAGCTTACAAGC
134280 TTATGG
1 TTATGG
134286 TATTAAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATAGCAAGTATATTGGTAAAATAAGCTTACAAGC
Found at i:134286 original size:24 final size:24
Alignment explanation
Indices: 134215--134287 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
134205 GCAAGTGTAT
*
134215 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACAAGCTTA
**
134239 TGG-ATAAAT-AG--T--AAGTATA
1 TGGTA-AAATAAGCTTACAAGCTTA
134258 TTGGTAAAATAAGCTTACAAGCTTA
1 -TGGTAAAATAAGCTTACAAGCTTA
134283 TGGTA
1 TGGTA
134288 TTAAATGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 16
0.63 0.09 0.28
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 4 0.11
23 4 0.11
24 12 0.33
25 5 0.14
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACAAGCTTA
Found at i:141728 original size:44 final size:44
Alignment explanation
Indices: 141679--141782 Score: 147
Period size: 44 Copynumber: 2.3 Consensus size: 44
141669 TGGTATATGA
* *
141679 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGCAAGTATATTGGTAAAATAAGCTTACAAGC
*
141723 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
1 TTATGGATAAATGGCAAGTATATTGGTAAAATAAGCTTACAAGC
141767 TTATGGTATTAAATGG
1 TTATGG-A-TAAATGG
141783 TAAAATATTG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
44 45 0.83
45 2 0.04
46 7 0.13
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (44 bp):
TTATGGATAAATGGCAAGTATATTGGTAAAATAAGCTTACAAGC
Found at i:144976 original size:44 final size:44
Alignment explanation
Indices: 144926--145156 Score: 408
Period size: 44 Copynumber: 5.2 Consensus size: 44
144916 CCATCCTTGC
* *
144926 ACACAAAGTACTCTTACCATAGTACACAAAGTACTACTCTAAGT
1 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
144970 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
1 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
* * *
145014 ACAAAAAGTAATCTTGCCATAGTACACAAAGTACTACTCCAAGA
1 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
145058 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
1 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
*
145102 ACACAAAGTACTCTTACCATAGTACACAAAGTACTACTCCAAGT
1 ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
145146 ACACAAAGTAC
1 ACACAAAGTAC
145157 GAAAATGCAA
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 178 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (44 bp):
ACACAAAGTACTCTTGCCATAGTACACAAAGTACTACTCCAAGT
Found at i:151384 original size:21 final size:21
Alignment explanation
Indices: 151360--151547 Score: 218
Period size: 21 Copynumber: 8.7 Consensus size: 21
151350 AAAGTGCCAT
151360 AGTACACAAAGTACTACTCCA
1 AGTACACAAAGTACTACTCCA
*
151381 AGTACACAAAGTACTCCTACCA
1 AGTACACAAAGTACTACT-CCA
*
151403 TAGTACACAAAGTACTACTCAA
1 -AGTACACAAAGTACTACTCCA
151425 AGTACACAAAGTACTACTCCA
1 AGTACACAAAGTACTACTCCA
151446 AGTACACAAAGTACT-CTTGCCA
1 AGTACACAAAGTACTAC-T-CCA
*
151468 TAGTACACAAACTACTACTCCA
1 -AGTACACAAAGTACTACTCCA
* *
151490 AGTACAGAATGTACT-CTTACCA
1 AGTACACAAAGTACTAC-T-CCA
* *
151512 TAGTACATAAAGTACTACTTCA
1 -AGTACACAAAGTACTACTCCA
*
151534 AGTACAAAAAGTAC
1 AGTACACAAAGTAC
151548 ACAAAGTACT
Statistics
Matches: 145, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.01
21 79 0.54
22 16 0.11
23 46 0.32
24 2 0.01
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (21 bp):
AGTACACAAAGTACTACTCCA
Found at i:151406 original size:44 final size:42
Alignment explanation
Indices: 151360--151579 Score: 201
Period size: 44 Copynumber: 4.9 Consensus size: 42
151350 AAAGTGCCAT
151360 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTACCA
1 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCT-CCA
* *
151403 TAGTACACAAAGTACTACTCAAAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTCCA
* *
151446 AGTACACAAAGTACT-CTTGCCATAGTACACAAACTACTACTCCA
1 AGTACACAAAGTACTAC-T-CCA-AGTACACAAAGTACTCCTCCA
* * * *
151490 AGTACAGAATGTACT-CTTACCATAGTACATAAAGTACTACTTCAAGTACAAAA
1 AGTACACAAAGTACTAC-T-CCA-AGTACACAAAGTACT-C--C---T-C--CA
151543 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTC
1 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTC
151580 TTATGAAAAT
Statistics
Matches: 149, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 16 0.11
43 5 0.03
44 90 0.60
47 1 0.01
50 2 0.01
51 15 0.10
52 3 0.02
53 15 0.10
54 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (42 bp):
AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTCCA
Found at i:151436 original size:65 final size:65
Alignment explanation
Indices: 151360--151578 Score: 260
Period size: 65 Copynumber: 3.2 Consensus size: 65
151350 AAAGTGCCAT
*
151360 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACTACTCAA
1 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACTACTCCA
* * *
151425 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCTTGCCATAGTACACAAACTACTACTCCA
1 AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACTACTCCA
* * * * *
151490 AGTACAGAATGTACT-CTTACCATAGTACATAAAGTACTACTTCAAGTACAAAAAGTACACAAAG
1 AGTACACAAAGTACTAC-T-CCA-AGTACACAAAGTACT-C--C---TAC-CATAGTACACAAAG
151554 TACTACTCCA
56 TACTACTCCA
151564 AGTACACAAAGTACT
1 AGTACACAAAGTACT
151579 CTTATGAAAA
Statistics
Matches: 130, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
64 1 0.01
65 75 0.58
66 3 0.02
67 14 0.11
68 1 0.01
73 2 0.02
74 34 0.26
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (65 bp):
AGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACTACTCCA
Found at i:151548 original size:30 final size:30
Alignment explanation
Indices: 151513--151577 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
151503 CTCTTACCAT
* *
151513 AGTACATAAAGTACTACTTCAAGTACAAAA
1 AGTACACAAAGTACTACTCCAAGTACAAAA
*
151543 AGTACACAAAGTACTACTCCAAGTACACAA
1 AGTACACAAAGTACTACTCCAAGTACAAAA
151573 AGTAC
1 AGTAC
151578 TCTTATGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.20
Consensus pattern (30 bp):
AGTACACAAAGTACTACTCCAAGTACAAAA
Found at i:151568 original size:109 final size:108
Alignment explanation
Indices: 151354--151556 Score: 304
Period size: 109 Copynumber: 1.9 Consensus size: 108
151344 GCACATAAAG
*
151354 TGCCATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACT
1 TGCCATAGTACACAAACTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACT
* *
151419 ACTCAAAGTACACAAAGTACTACTCCAAGTACACAAAGTACTCT
66 ACTCAAAGTACAAAAAGTACTAC-CAAAGTACACAAAGTACTCT
* * * *
151463 TGCCATAGTACACAAACTACTACTCCAAGTACAGAATGTACTCTTACCATAGTACATAAAGTACT
1 TGCCATAGTACACAAACTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACT
151528 ACTTC-AAGTACAAAAAGTAC-A-CAAAGTAC
66 AC-TCAAAGTACAAAAAGTACTACCAAAGTAC
151557 TACTCCAAGT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
106 7 0.08
108 1 0.01
109 76 0.88
110 2 0.02
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (108 bp):
TGCCATAGTACACAAACTACTACTCCAAGTACACAAAGTACTCCTACCATAGTACACAAAGTACT
ACTCAAAGTACAAAAAGTACTACCAAAGTACACAAAGTACTCT
Found at i:154169 original size:12 final size:11
Alignment explanation
Indices: 154140--154177 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
154130 TATTTAATAT
154140 TTTAAAAAATC
1 TTTAAAAAATC
154151 TTTAAAAAATC
1 TTTAAAAAATC
*
154162 TTTAAAAAATA
1 TTTAAAAAATC
154173 TTTAA
1 TTTAA
154178 TAGTACAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (11 bp):
TTTAAAAAATC
Found at i:165739 original size:12 final size:12
Alignment explanation
Indices: 165712--165754 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
165702 GAAAGAACAC
*
165712 AAAAACTTAAAG
1 AAAAACTTAATG
165724 -AAAACTTAATG
1 AAAAACTTAATG
*
165735 AAAAACTTGATG
1 AAAAACTTAATG
*
165747 TAAAACTT
1 AAAAACTT
165755 CATGCCCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (12 bp):
AAAAACTTAATG
Found at i:167059 original size:26 final size:27
Alignment explanation
Indices: 167023--167073 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
167013 GAATGATTTC
*
167023 TTTAATTCAAATAATA-TTTT-TTGAGT
1 TTTAAATCAAA-AATAGTTTTCTTGAGT
167049 TTTAAATCAAAAATAGTTTTCTTGA
1 TTTAAATCAAAAATAGTTTTCTTGA
167074 TGGACAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (27 bp):
TTTAAATCAAAAATAGTTTTCTTGAGT
Done.