Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006171.1 Hibiscus syriacus cultivar Beakdansim tig00014660_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: 115224
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:189 original size:27 final size:26
Alignment explanation
Indices: 132--195 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
122 ACATACTATT
**
132 CATCGATGCACTCAGTGCATTTGATG
1 CATCGATGCACTCAGTGCATTTGAAA
*
158 CATCGATGCACTCTG-GCTATTTTGAAA
1 CATCGATGCACTCAGTGC-A-TTTGAAA
185 CATCGAATGCA
1 CATCG-ATGCA
196 TTTTATGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.06
26 15 0.47
27 10 0.31
28 5 0.16
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (26 bp):
CATCGATGCACTCAGTGCATTTGAAA
Found at i:5702 original size:21 final size:21
Alignment explanation
Indices: 5676--5725 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
5666 ACTGATGCAC
*
5676 CGATGCACCATTGGTATGAAT
1 CGATGCACCATGGGTATGAAT
*
5697 CGATGCACCATGGGTATGCAT
1 CGATGCACCATGGGTATGAAT
5718 CGATGCAC
1 CGATGCAC
5726 TGACGCTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
CGATGCACCATGGGTATGAAT
Found at i:6719 original size:387 final size:386
Alignment explanation
Indices: 5957--6724 Score: 1078
Period size: 387 Copynumber: 2.0 Consensus size: 386
5947 CAAGAACACA
* *
5957 ATTGTGCTCAATTGTATTTATCTTTGAGTGTTCTTATCTTGTTTTAGAATTGTGCAAACAATCTA
1 ATTGTACTCAATTGTATTTATCTTTGAGTGTTCTTATCTTGTTCTAGAATTGTGCAAACAATCTA
*
6022 CCTTATGAGTTTTCCTTGCAAGTTTATGAATTTGTATATTTCTCTTTGAAAAAGAGTGTGCTCAA
66 CCTTATGAGTTTTCCTTGCAAGTTTATAAATTTGTATATTTCTCTTTGAAAAAGAGTGTGCTCAA
* *
6087 TAATTGGGGTATAATTCTTGAGGGTGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAA
131 GAATTGGGGTATAATTATTGAGGGTGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAA
6152 TTAGTGAATTTGTTGGAAAATCCTTAGTGGATAGCTAAGGTAGTGGATAGACTTTGATTGAGAAA
196 TTAGTGAATTTGTTGGAAAATCCTTAGTGGATAGCTAAGGTAGTGGATAGACTTTGATTGAGAAA
*
6217 GTCGAACCACTATAAATCGCTGTGCAAATCTTTTCAATTTTCTGCAAAAGCTTCCACCAAAATTT
261 GTCGAACCACTATAAATCGCTGTGCAAATCATTTCAATTTTCTGCAAAAGCTTCCACCAAAATTT
*
6282 TAATTGCCAATTCACCCCCCTCTTGGTCGATTCCATCGATCGATTAACTCAACAAACACTT
326 TAATTGCCAATTCACCCCCCTCTTGGTCCATTCCATCGATCGATTAACTCAACAAACACTT
*
6343 ATTGTACTCAATTGTA-TTAT-TCTTGAGTGTTCTT-TCTTTGTTCTAGAATTGTGCAAA-TATC
1 ATTGTACTCAATTGTATTTATCT-TTGAGTGTTCTTATC-TTGTTCTAGAATTGTGCAAACAATC
* * ** *
6404 TTGCCTTATGAGGATTTT-CTTGTAAGTTTGCA-AAATTTGTAT-TGTTCTCTTTGGGAGAGAGT
64 -TACCTTATGA-G-TTTTCCTTGCAAGTTT--ATAAATTTGTATAT-TTCTCTTTGAAAAAGAGT
* * *
6466 GTTCTCAAGAATTTGTGGTATAATTATTGAGGGAT-TTGTAAGGTTA-CTCTTTGTCCTCAAAAG
123 GTGCTCAAGAA-TTGGGGTATAATTATTGAGGG-TGTTGTAAGGTTATCTCTTTGGCCTCAAAAG
*
6529 AAAG-ACAAATTAGTGAATTTG-TGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGT
186 AAAGAACAAATTAGTGAATTTGTTGGAAAATCCTTA--GTGGATAGCTAAGGTAGTGGA--TAGA
* * * *
6592 CTTTGGTTGAGAAAGTCGAACCACTTTAAATCGTTGTGCAAAT-ATTTCAATTTTTTGCAAAAGC
247 CTTTGATTGAGAAAGTCGAACCACTATAAATCGCTGTGCAAATCATTTCAATTTTCTGCAAAAGC
* * * *
6656 TTCCACCGAAATTTTAATTGCCAATTCACCCTCCTCTT-G-CCATATTCGTCGATCGATTAACTC
312 TTCCACCAAAATTTTAATTGCCAATTCACCCCCCTCTTGGTCCAT-TCCATCGATCGATTAACTC
6719 AACAAA
376 AACAAA
6725 ATTATATATA
Statistics
Matches: 342, Mismatches: 25, Indels: 29
0.86 0.06 0.07
Matches are distributed among these distances:
384 6 0.02
385 57 0.17
386 47 0.14
387 102 0.30
388 86 0.25
389 44 0.13
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (386 bp):
ATTGTACTCAATTGTATTTATCTTTGAGTGTTCTTATCTTGTTCTAGAATTGTGCAAACAATCTA
CCTTATGAGTTTTCCTTGCAAGTTTATAAATTTGTATATTTCTCTTTGAAAAAGAGTGTGCTCAA
GAATTGGGGTATAATTATTGAGGGTGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAAAGAACAAA
TTAGTGAATTTGTTGGAAAATCCTTAGTGGATAGCTAAGGTAGTGGATAGACTTTGATTGAGAAA
GTCGAACCACTATAAATCGCTGTGCAAATCATTTCAATTTTCTGCAAAAGCTTCCACCAAAATTT
TAATTGCCAATTCACCCCCCTCTTGGTCCATTCCATCGATCGATTAACTCAACAAACACTT
Found at i:6747 original size:18 final size:18
Alignment explanation
Indices: 6724--6854 Score: 72
Period size: 18 Copynumber: 6.9 Consensus size: 18
6714 AACTCAACAA
6724 AATTA-TATATAACTATAT
1 AATTATTATA-AACTATAT
6742 AATTATTATAAACTATAT
1 AATTATTATAAACTATAT
* ** *
6760 -ATAAATTAT-ATTTATGT
1 AAT-TATTATAAACTATAT
6777 GAACTATATATATAAACTATGTAT
1 -AA-T-TAT-TATAAACTA--TAT
**
6801 ATAAAATTATAAACTATAT
1 A-ATTATTATAAACTATAT
*
6820 -TTATATTATAAACTATAT
1 AAT-TATTATAAACTATAT
*
6838 AATTATTATAAGCTATA
1 AATTATTATAAACTATA
6855 ATATAAATTA
Statistics
Matches: 86, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
17 7 0.08
18 45 0.52
19 9 0.10
20 4 0.05
21 12 0.14
22 5 0.06
23 1 0.01
24 3 0.03
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
AATTATTATAAACTATAT
Found at i:6796 original size:13 final size:13
Alignment explanation
Indices: 6748--6918 Score: 59
Period size: 13 Copynumber: 12.8 Consensus size: 13
6738 ATATAATTAT
6748 TATAAACTATATA
1 TATAAACTATATA
*
6761 TA-AATTA-TATTTA
1 TATAA--ACTATATA
* *
6774 TGTGAACTATATA
1 TATAAACTATATA
*
6787 TATAAACTATGTA
1 TATAAACTATATA
*
6800 TATAAAAT-TATA
1 TATAAACTATATA
* * *
6812 AACTATA-TTTATA
1 TA-TAAACTATATA
6825 TTATAAACTATATAA
1 -TATAAACTATAT-A
6840 TTATTATAAGCTATA-A
1 -TA-TA-AA-CTATATA
* *
6856 TATAAATTATGTTTA
1 TATAAACTA--TATA
* *
6871 TGTGAA-T-TATA
1 TATAAACTATATA
* *
6882 TACAAACTATGTA
1 TATAAACTATATA
*
6895 TATAAACTATATG
1 TATAAACTATATA
6908 TATAAACTATA
1 TATAAACTATA
6919 AAAGTATAGT
Statistics
Matches: 115, Mismatches: 26, Indels: 34
0.66 0.15 0.19
Matches are distributed among these distances:
11 6 0.05
12 11 0.10
13 66 0.57
14 11 0.10
15 11 0.10
16 3 0.03
17 2 0.02
18 5 0.04
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (13 bp):
TATAAACTATATA
Found at i:6824 original size:21 final size:18
Alignment explanation
Indices: 6781--6865 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
6771 TTATGTGAAC
6781 TATATA-TATAAACTATGTA
1 TATATATTATAAACTA--TA
*
6800 TATAAAATTATAAACTATA
1 TAT-ATATTATAAACTATA
*
6819 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
*
6837 TA-ATTATTATAAGCTATAA
1 TATA-TATTATAAACTAT-A
*
6856 TATAAATTAT
1 TATATATTAT
6866 GTTTATGTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
17 1 0.02
18 27 0.49
19 15 0.27
20 3 0.05
21 9 0.16
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:6918 original size:22 final size:22
Alignment explanation
Indices: 6893--6935 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6883 ACAAACTATG
6893 TATATAAACTATA-TGTATAAAC
1 TATA-AAACTATAGTGTATAAAC
* *
6915 TATAAAAGTATAGTTTATAAA
1 TATAAAACTATAGTGTATAAA
6936 ATATTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (22 bp):
TATAAAACTATAGTGTATAAAC
Found at i:7178 original size:7 final size:7
Alignment explanation
Indices: 7158--7222 Score: 60
Period size: 7 Copynumber: 9.4 Consensus size: 7
7148 TATACATACA
7158 TTAGGGT
1 TTAGGGT
7165 TTA-GGT
1 TTAGGGT
7171 TTAGGGT
1 TTAGGGT
7178 TTAGGGT
1 TTAGGGT
***
7185 TTATTAT
1 TTAGGGT
**
7192 TTAAAGT
1 TTAGGGT
*
7199 TTAGGAT
1 TTAGGGT
7206 TTAGGGT
1 TTAGGGT
*
7213 TTAAGGT
1 TTAGGGT
7220 TTA
1 TTA
7223 TATAACTATA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
6 6 0.13
7 40 0.87
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:7611 original size:14 final size:13
Alignment explanation
Indices: 7588--7622 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
7578 CTCACTTTGA
7588 ATAATATATATAT
1 ATAATATATATAT
7601 ATAAGTATATATAT
1 ATAA-TATATATAT
7615 ATAATATA
1 ATAATATA
7623 ATTAAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:8057 original size:2 final size:2
Alignment explanation
Indices: 8046--8076 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8036 CTTATGTTTA
8046 AT AT -T 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
8077 TCAAAGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:8606 original size:23 final size:24
Alignment explanation
Indices: 8580--8627 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
8570 CTAATATTCA
*
8580 TTTATTATC-AAATTAATTATTAT
1 TTTATTACCAAAATTAATTATTAT
* *
8603 TTTATTGCCAAAATTATTTATTAT
1 TTTATTACCAAAATTAATTATTAT
8627 T
1 T
8628 AATATAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTATTACCAAAATTAATTATTAT
Found at i:8706 original size:14 final size:14
Alignment explanation
Indices: 8689--8735 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
8679 ATTATTTCTT
8689 TATATAAATTAAAC
1 TATATAAATTAAAC
8703 TATAT-AATT----
1 TATATAAATTAAAC
8712 TATATAAATTAAAC
1 TATATAAATTAAAC
*
8726 TATATTAATT
1 TATATAAATT
8736 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:8713 original size:23 final size:24
Alignment explanation
Indices: 8687--8736 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
8677 TTATTATTTC
8687 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
8710 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
8734 TTT
1 TTT
8737 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:8845 original size:29 final size:28
Alignment explanation
Indices: 8776--8856 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
8766 AATTTACATT
8776 TAAATAATTTTATTAAATAATTTATATAA
1 TAAAT-ATTTTATTAAATAATTTATATAA
** *
8805 TAGGTCTATTTATTAATATAA-TTATCATAA
1 TAAATAT-TTTATTAA-ATAATTTAT-ATAA
*
8835 TAAATATTTTATTATA-AATTTA
1 TAAATATTTTATTAAATAATTTA
8857 AAAAATAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.05
28 5 0.12
29 22 0.54
30 12 0.29
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TAAATATTTTATTAAATAATTTATATAA
Found at i:9019 original size:15 final size:15
Alignment explanation
Indices: 8983--9031 Score: 73
Period size: 16 Copynumber: 3.2 Consensus size: 15
8973 TCATTTACAG
8983 GTCAGGTTAAAAACAT
1 GTCAGGTT-AAAACAT
8999 GTCAGGTTGAAAACA-
1 GTCAGGTT-AAAACAT
9014 GTCAGGTTAAAACAT
1 GTCAGGTTAAAACAT
9029 GTC
1 GTC
9032 GGGTAATACC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 6 0.19
15 11 0.35
16 14 0.45
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.24
Consensus pattern (15 bp):
GTCAGGTTAAAACAT
Found at i:9707 original size:15 final size:15
Alignment explanation
Indices: 9644--9729 Score: 66
Period size: 15 Copynumber: 5.5 Consensus size: 15
9634 TCCAAAAGCT
*
9644 GAGAAGAAGCCTGCC
1 GAGAAGAAGCCAGCC
*
9659 GAGAAGAAGCCAGCA
1 GAGAAGAAGCCAGCC
*** *
9674 GA-AGAGAAAAAAGCT
1 GAGA-AGAAGCCAGCC
9689 GAGAAGAAGCCAGCC
1 GAGAAGAAGCCAGCC
*
9704 GAGAAAAAGCCTAGAGCC
1 GAGAAGAAGCC---AGCC
9722 GAGAAGAA
1 GAGAAGAA
9730 ACTACCCAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
14 1 0.02
15 41 0.76
16 1 0.02
18 11 0.20
ACGTcount: A:0.47, C:0.19, G:0.31, T:0.03
Consensus pattern (15 bp):
GAGAAGAAGCCAGCC
Found at i:13054 original size:32 final size:32
Alignment explanation
Indices: 13017--13079 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
13007 GAAAACATAG
13017 TTTTTAACATATGCATAAATAAAAGTTAAATA
1 TTTTTAACATATGCATAAATAAAAGTTAAATA
*
13049 TTTTTAATATATGCATAAATAAAAGTTAAAT
1 TTTTTAACATATGCATAAATAAAAGTTAAAT
13080 CATATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (32 bp):
TTTTTAACATATGCATAAATAAAAGTTAAATA
Found at i:15072 original size:17 final size:18
Alignment explanation
Indices: 15046--15087 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
15036 GGATTATCAA
* *
15046 TGGTCCTTCGGGATA-AG
1 TGGTCATTCGGGACATAG
15063 TGGTCATTCGGGACATAG
1 TGGTCATTCGGGACATAG
15081 TGGTCAT
1 TGGTCAT
15088 CCAAGACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (18 bp):
TGGTCATTCGGGACATAG
Found at i:16487 original size:20 final size:20
Alignment explanation
Indices: 16464--16621 Score: 183
Period size: 20 Copynumber: 7.9 Consensus size: 20
16454 ATTTTCTAAT
16464 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
16484 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* *
16504 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
16524 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
16544 TTGGC-ATGCGATTACGTAAA
1 -TCGCAATGCGAATACGTAAA
* *
16564 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
16584 TCGGTATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
16604 TTGCAATGCAAATACGTA
1 TCGCAATGCGAATACGTA
16622 TTCGCATTGC
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 3 0.03
20 112 0.95
21 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:16508 original size:40 final size:40
Alignment explanation
Indices: 16464--16642 Score: 209
Period size: 40 Copynumber: 4.5 Consensus size: 40
16454 ATTTTCTAAT
* * *
16464 TCGCAATGCGAATACGTAAATCGCAATGCGAATACATAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATACGTAAA
*
16504 TCGCAACGCGATTACGTAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATACGTAAA
* *
16544 TTGGC-ATGCGATTACGTAAATCGCAACGCGATTACGTAAA
1 -TCGCAATGCGATTACGTAAATCGCAACGCGAATACGTAAA
** * * * *
16584 TCGGTATGCGATTACGTAAATTGCAATGCAAATACGT-AT
1 TCGCAATGCGATTACGTAAATCGCAACGCGAATACGTAAA
*
16623 TCGCATTGCGATTTACGTAA
1 TCGCAATGCGA-TTACGTAA
16643 TCGTGTTACA
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
39 11 0.09
40 105 0.88
41 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (40 bp):
TCGCAATGCGATTACGTAAATCGCAACGCGAATACGTAAA
Found at i:16639 original size:20 final size:20
Alignment explanation
Indices: 16616--16686 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
16606 GCAATGCAAA
* *
16616 TACGTATTCGCATTGCGATT
1 TACGTAATCGCGTTGCGATT
* * *
16636 TACGTAATCGTGTTACAATT
1 TACGTAATCGCGTTGCGATT
16656 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCGTTGCGATT
16676 TA-GTAAATCGC
1 TACGT-AATCGC
16687 AACGAGATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 2 0.05
20 40 0.95
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (20 bp):
TACGTAATCGCGTTGCGATT
Found at i:16642 original size:60 final size:60
Alignment explanation
Indices: 16464--16621 Score: 228
Period size: 60 Copynumber: 2.6 Consensus size: 60
16454 ATTTTCTAAT
* *
16464 TCGCAATGCGAATACGTAAATCGCAATGCGAATACATAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATTGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
* *
16524 TCGCAACGCGAATACGTAAATTGGC-ATGCGATTACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATT-GCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
** * *
16584 TCGGTATGCGATTACGTAAATTGCAATGCAAATACGTA
1 TCGCAATGCGAATACGTAAATTGCAATGCGAATACGTA
16622 TTCGCATTGC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 2 0.02
60 82 0.95
61 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATTGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
Found at i:17579 original size:24 final size:24
Alignment explanation
Indices: 17552--17605 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
17542 GTATTCGAAA
17552 TTTGATATTGGTCAATACTCAGAC
1 TTTGATATTGGTCAATACTCAGAC
* * *
17576 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCAGAC
17600 TTTGAT
1 TTTGAT
17606 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCAGAC
Found at i:20100 original size:14 final size:14
Alignment explanation
Indices: 20081--20144 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
20071 TCATTTGACT
*
20081 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
20095 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
20114 ATCGCAACGTGAAA
1 ATCGCAACGAGAAA
*
20128 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
20142 ATC
1 ATC
20145 ACAAAGCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 26 0.63
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:20198 original size:19 final size:19
Alignment explanation
Indices: 20174--20214 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20164 GCAACGGGAA
20174 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
20193 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
20212 TTT
1 TTT
20215 GTCGTTACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:20235 original size:33 final size:33
Alignment explanation
Indices: 20184--20277 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
20174 TTTAGTTTCG
* * *
20184 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
20217 CGTTACGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
20250 CGTTGCGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
20278 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:20403 original size:14 final size:14
Alignment explanation
Indices: 20384--20420 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
20374 CATCAATTAA
20384 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
20398 ACAAATCATCTTTT
1 ACAAATCAACTTTT
20412 ACAAATCAA
1 ACAAATCAA
20421 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:21824 original size:21 final size:21
Alignment explanation
Indices: 21758--21824 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
21748 GTGAATCGGG
*
21758 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
21778 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
21800 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
21821 CTCT
1 CTCT
21825 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:21843 original size:42 final size:41
Alignment explanation
Indices: 21758--21880 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
21748 GTGAATCGGG
* * * *
21758 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
21800 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
21842 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
21881 TGAGTCTGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:24149 original size:20 final size:20
Alignment explanation
Indices: 24084--24174 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
24074 CGATTATCTC
*
24084 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
24103 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
24123 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
24144 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
24164 GTTGCGATTTT
1 GTTGCGATTTT
24175 AAGTTTAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
19 13 0.21
20 32 0.52
21 17 0.27
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:24761 original size:20 final size:20
Alignment explanation
Indices: 24736--24880 Score: 131
Period size: 20 Copynumber: 7.3 Consensus size: 20
24726 AAAAATCGCA
*
24736 TTGCGATTTACGGATATGCG
1 TTGCGATTTACGTATATGCG
*
24756 TTGCGATTT-TGTAT-TGTCG
1 TTGCGATTTACGTATATG-CG
* * *
24775 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATATGCG
* *
24795 TTGCGATTTACGTAT-TCTCA
1 TTGCGATTTACGTATAT-GCG
*
24815 TTGCGATTTACAG-ATACGCG
1 TTGCGATTTAC-GTATATGCG
24835 TTGCGATTTACGTA-ATCGCG
1 TTGCGATTTACGTATAT-GCG
24855 TTGCGATTTACGTA-ATCGCG
1 TTGCGATTTACGTATAT-GCG
24875 TTGCGA
1 TTGCGA
24881 ATTAGGAAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.02
19 16 0.15
20 84 0.81
21 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATATGCG
Found at i:24821 original size:40 final size:40
Alignment explanation
Indices: 24734--24880 Score: 181
Period size: 40 Copynumber: 3.7 Consensus size: 40
24724 TTAAAAATCG
* * *
24734 CATTGCGATTTACGGATATGCGTTGCGATTT-TGTATTGT
1 CATTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* *
24773 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CATTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
24813 CATTGCGATTTACAGATACGCGTTGCGATTTACGTAATCG
1 CATTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* *
24853 CGTTGCGATTTACGTA-ATCGCGTTGCGA
1 CATTGCGATTTACGGATA-CGCGTTGCGA
24881 ATTAGGAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 29 0.31
40 64 0.69
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
CATTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:24894 original size:21 final size:20
Alignment explanation
Indices: 24831--24894 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
24821 TTTACAGATA
* *
24831 CGCGTTGCGATTTACGTAAT
1 CGCGTTGCGAATTACGAAAT
* *
24851 CGCGTTGCGATTTACGTAAT
1 CGCGTTGCGAATTACGAAAT
*
24871 CGCGTTGCGAATTAGGAAAAT
1 CGCGTTGCGAATTACG-AAAT
24892 CGC
1 CGC
24895 AACGCGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 34 0.85
21 6 0.15
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (20 bp):
CGCGTTGCGAATTACGAAAT
Found at i:24901 original size:21 final size:21
Alignment explanation
Indices: 24877--24922 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
24867 TAATCGCGTT
24877 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
24898 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
24919 GCGA
1 GCGA
24923 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:26480 original size:35 final size:34
Alignment explanation
Indices: 26434--26545 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
26424 AAAACAATCC
* *
26434 TCAATTTCATTCTAAATCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
26469 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
** ** *
26504 TCAATTAAATTCTAAACCCCAAATTTTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
26539 TCAATTT
1 TCAATTT
26546 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 3 0.04
35 61 0.91
36 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:27924 original size:35 final size:35
Alignment explanation
Indices: 27876--27987 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
27866 TCTAACCCTT
* * * *
27876 AAATTAAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
27911 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
27946 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
27981 AAATTGA
1 AAATTGA
27988 GGACTATTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:31446 original size:21 final size:21
Alignment explanation
Indices: 31399--31489 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
31389 AGTCTAAATT
*
31399 CGTTGAGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
* *
31420 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCA
** *
31441 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCA
* * *
31460 CGTTGCGACAATCTAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
31481 CGTTGCGAT
1 CGTTGCGAT
31490 TTTGGAAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 14 0.25
21 41 0.75
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCA
Found at i:31915 original size:19 final size:20
Alignment explanation
Indices: 31890--31980 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
31880 CTTATTTTGG
31890 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
31910 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
31930 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
31954 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
31973 ATTTTTCA
1 ATTTTTCA
31981 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:31952 original size:44 final size:41
Alignment explanation
Indices: 31901--31982 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
31891 TTTTTCACTA
* *
31901 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
31945 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
31983 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:32340 original size:17 final size:16
Alignment explanation
Indices: 32294--32346 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
32284 CGAGAATAAG
*
32294 ATTACCGGAATGTTAC
1 ATTACTGGAATGTTAC
32310 ATTACTGGAATGTTAC
1 ATTACTGGAATGTTAC
32326 ATTACTGGAAATGTTAC
1 ATTACTGG-AATGTTAC
32343 ATTA
1 ATTA
32347 TTGTGTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (16 bp):
ATTACTGGAATGTTAC
Found at i:32731 original size:14 final size:14
Alignment explanation
Indices: 32712--32743 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32702 ATATTTTTGA
32712 AATAAAGTTATGAT
1 AATAAAGTTATGAT
*
32726 AATAAATTTATGAT
1 AATAAAGTTATGAT
32740 AATA
1 AATA
32744 TACTATAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AATAAAGTTATGAT
Found at i:39464 original size:4 final size:4
Alignment explanation
Indices: 39403--39429 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39393 ATGTTAGAAG
39403 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
39430 ATACTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41221 original size:14 final size:14
Alignment explanation
Indices: 41202--41279 Score: 88
Period size: 14 Copynumber: 5.4 Consensus size: 14
41192 GCAATAATGT
41202 ATATTATAAAAATA
1 ATATTATAAAAATA
*
41216 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
41232 A-ATTATAAAAATA
1 ATATTATAAAAATA
*
41245 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
41261 A-ATTATAAAAATA
1 ATATTATAAAAATA
41274 ATATTA
1 ATATTA
41280 ATCAAAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 14 0.26
14 16 0.30
15 10 0.19
16 14 0.26
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATTATAAAAATA
Found at i:41246 original size:29 final size:29
Alignment explanation
Indices: 41204--41287 Score: 168
Period size: 29 Copynumber: 2.9 Consensus size: 29
41194 AATAATGTAT
41204 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
41233 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
41262 ATTATAAAAATAATATTAATCAAAAG
1 ATTATAAAAATAATATTAATCAAAAG
41288 GGACGAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
ATTATAAAAATAATATTAATCAAAAGTAA
Found at i:41868 original size:43 final size:43
Alignment explanation
Indices: 41807--41962 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
41797 ACCAGCGGTC
*
41807 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
41850 CCTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
*
41900 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
41944 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
41963 ATTGGCTCTG
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 39 0.48
44 1 0.01
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 1 0.01
51 21 0.26
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:42042 original size:98 final size:98
Alignment explanation
Indices: 41784--42454 Score: 1233
Period size: 98 Copynumber: 6.9 Consensus size: 98
41774 AATTGGGAAG
41784 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
41849 TCCTTCATTGTGAAGTTGAAATTGG----GAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
41878 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
41943 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
*
41976 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
42041 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
* *
42074 TTGTTTATTAACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
42139 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
42172 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
42237 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
* *
42270 TTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
42335 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
* *
42368 TTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
42433 TCCTTCGTTGTGAAGTTGAAAT
66 TCCTTCGTTGTGAAGTTGAAAT
42455 CAACTCTGGG
Statistics
Matches: 561, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
94 89 0.16
98 472 0.84
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (98 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
Found at i:42158 original size:43 final size:43
Alignment explanation
Indices: 42097--42256 Score: 113
Period size: 43 Copynumber: 3.4 Consensus size: 43
42087 ACCAGCGGTC
*
42097 CCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
42140 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCA-ATAT
42194 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CC-TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
42238 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
42257 ATTGGCCCTG
Statistics
Matches: 85, Mismatches: 20, Indels: 24
0.66 0.16 0.19
Matches are distributed among these distances:
43 35 0.41
44 4 0.05
45 3 0.04
46 5 0.06
47 1 0.01
48 3 0.04
50 3 0.04
51 1 0.01
52 5 0.06
53 3 0.04
54 4 0.05
55 18 0.21
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:42243 original size:294 final size:290
Alignment explanation
Indices: 41674--42454 Score: 1319
Period size: 294 Copynumber: 2.7 Consensus size: 290
41664 TTGGAATTGG
* * * *
41674 GAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGGGCCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
41739 AATCTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCTG--A-----AA-TTGTTTATTGACAACCAGCG
*
41804 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAA
123 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
41869 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
188 ATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
41934 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
253 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCT
*
41972 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCT
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
42037 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTAACAACCAGCGGTCCCTTC
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTC
*
42102 GTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCC
131 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG---
42167 TGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
193 -GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
42232 CAATATCCTTCGTTGTGAAGTTGAAATTGGCCCT
257 CAATATCCTTCGTTGTGAAGTTGAAATTGGCCCT
* *
42266 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
42331 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGTGGTCCCTTC
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTC
*
42396 GTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
131 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
42455 CAACTCTGGG
Statistics
Matches: 461, Mismatches: 18, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
290 87 0.19
291 2 0.00
294 279 0.61
296 1 0.00
298 92 0.20
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (290 bp):
GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTC
GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAA
ATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
ATCCTTCGTTGTGAAGTTGAAATTGGCCCT
Found at i:42354 original size:43 final size:43
Alignment explanation
Indices: 42293--42452 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
42283 ACCAGCGGTC
*
42293 CCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
* * * * ** * *
42336 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGTGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C----ATTG--TCTGGA-GTCCAAT-AT
42390 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
*
42434 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
42453 ATCAACTCTG
Statistics
Matches: 87, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
43 37 0.43
44 2 0.02
45 4 0.05
46 5 0.06
48 4 0.05
50 4 0.05
52 5 0.06
53 4 0.05
54 2 0.02
55 20 0.23
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
Found at i:47022 original size:20 final size:20
Alignment explanation
Indices: 46946--47030 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
46936 AACAGAACCC
*
46946 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
**
46967 GTGGGGGGAATC-AGTTCCCCTT
1 CAGGGGGGAATCGA-TT-CCC-T
* *
46989 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
47010 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
47030 C
1 C
47031 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
20 18 0.36
21 17 0.34
22 4 0.08
23 11 0.22
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:63302 original size:4 final size:4
Alignment explanation
Indices: 63293--63357 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
63283 ATGTTAGAAG
* * * *
63293 AAAT AAAT AAAT AAAT AAAT AAA- ATACT AAAT AAGT CAAAT GAAAG GAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT -AAAT AAAT
*
63343 AAAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAA
63358 AAAAATAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
3 1 0.02
4 39 0.83
5 7 0.15
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:65044 original size:22 final size:22
Alignment explanation
Indices: 65018--65068 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
65008 GGGCATTCTG
65018 TTGGGCCCCGTATAATATGATC
1 TTGGGCCCCGTATAATATGATC
65040 TTGGGCCCCGTATAATATGATC
1 TTGGGCCCCGTATAATATGATC
65062 TTGGGCC
1 TTGGGCC
65069 TGACACAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (22 bp):
TTGGGCCCCGTATAATATGATC
Found at i:65143 original size:14 final size:14
Alignment explanation
Indices: 65124--65201 Score: 88
Period size: 14 Copynumber: 5.4 Consensus size: 14
65114 GCAATAATGT
65124 ATATTATAAAAATA
1 ATATTATAAAAATA
*
65138 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
65154 A-ATTATAAAAATA
1 ATATTATAAAAATA
*
65167 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
65183 A-ATTATAAAAATA
1 ATATTATAAAAATA
65196 ATATTA
1 ATATTA
65202 ATCAAAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 14 0.26
14 16 0.30
15 10 0.19
16 14 0.26
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATTATAAAAATA
Found at i:65168 original size:29 final size:29
Alignment explanation
Indices: 65126--65209 Score: 168
Period size: 29 Copynumber: 2.9 Consensus size: 29
65116 AATAATGTAT
65126 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
65155 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
65184 ATTATAAAAATAATATTAATCAAAAG
1 ATTATAAAAATAATATTAATCAAAAG
65210 GGACGAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
ATTATAAAAATAATATTAATCAAAAGTAA
Found at i:71946 original size:13 final size:13
Alignment explanation
Indices: 71919--71953 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
71909 CATGCTATTG
*
71919 TCTTTG-TTTTCT
1 TCTTTGATTCTCT
71931 TCTTTGATTCTCT
1 TCTTTGATTCTCT
71944 TCTTTGATTC
1 TCTTTGATTC
71954 ATATGGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.06, C:0.20, G:0.09, T:0.66
Consensus pattern (13 bp):
TCTTTGATTCTCT
Found at i:75790 original size:21 final size:22
Alignment explanation
Indices: 75764--75806 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
75754 AACTTGATTT
75764 TAAAATAATTTATAT-TTTTAA
1 TAAAATAATTTATATATTTTAA
*
75785 TAAAATTATTTATATATTTTAA
1 TAAAATAATTTATATATTTTAA
75807 CTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAATAATTTATATATTTTAA
Found at i:75988 original size:32 final size:32
Alignment explanation
Indices: 75921--75988 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
75911 TATCCAACTT
*
75921 AAAAATATATTTTATCTCATATTAACTTTTAA
1 AAAAATATATTTTATATCATATTAACTTTTAA
75953 AAAAATATAATTTTATTATCAT-TTAACTTTTAA
1 AAAAATAT-ATTTTA-TATCATATTAACTTTTAA
75986 AAA
1 AAA
75989 TGTATTGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 8 0.24
33 20 0.61
34 5 0.15
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAAATATATTTTATATCATATTAACTTTTAA
Found at i:76084 original size:29 final size:28
Alignment explanation
Indices: 76036--76103 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
76026 TATTTATATA
* * *
76036 TTAACATAAAAAATATTTTAATCTTATT
1 TTAACTTAAAAAATACTTTAATCTTATC
* * *
76064 TTAGCTTAAAAATATACTTTATTCTTGTC
1 TTAACTTAAAAA-ATACTTTAATCTTATC
76093 TTAACTTAAAA
1 TTAACTTAAAA
76104 TGTACATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (28 bp):
TTAACTTAAAAAATACTTTAATCTTATC
Found at i:76143 original size:30 final size:29
Alignment explanation
Indices: 75858--76204 Score: 140
Period size: 30 Copynumber: 11.7 Consensus size: 29
75848 TATCAAATTA
** *
75858 AATTAAATTATATATTTTATTCTTATTTT
1 AATTAAAAAATATATTTTATTCTTATCTT
** ** * *
75887 TGTTTTAAAATATTTTTTAATTCTTATC-C
1 AATTAAAAAATATATTTT-ATTCTTATCTT
* *
75916 AACTT-AAAAATATATTTTA-TCTCATATT
1 AA-TTAAAAAATATATTTTATTCTTATCTT
* *
75944 AACTTTTAAAAAAATATAATTTTATTATCAT-TT
1 AA---TT-AAAAAATAT-ATTTTATTCTTATCTT
* * *
75977 AACTTTTAAAAATGTATTGTATTCTTA-CTTT
1 AA--TTAAAAAATATATTTTATTCTTATC-TT
** * *
76008 AAATTATTAAATATGTTTTATT-TATATATT
1 -AATTAAAAAATATATTTTATTCT-TATCTT
* * *
76038 AA-CATAAAAA-ATATTTTAATCTTATTTT
1 AATTA-AAAAATATATTTTATTCTTATCTT
* * *
76066 AGCTT-AAAAATATACTTTATTCTTGTCTT
1 A-ATTAAAAAATATATTTTATTCTTATCTT
** * *
76095 AACTTAAAATGTACATTTTATTCTTATATT
1 AA-TTAAAAAATATATTTTATTCTTATCTT
*
76125 GATATAAAAAATATATTTTATT-TTAATCTT
1 AAT-TAAAAAATATATTTTATTCTT-ATCTT
*
76155 AACTTTAAAAATATATATTTTATTTTTATCTT
1 AA--TTAAAAA-ATATATTTTATTCTTATCTT
*
76187 AATTTAAAAATAT-TTTTA
1 AATTAAAAAATATATTTTA
76205 ACATATATTT
Statistics
Matches: 234, Mismatches: 57, Indels: 55
0.68 0.16 0.16
Matches are distributed among these distances:
27 5 0.02
28 28 0.12
29 53 0.23
30 83 0.35
31 15 0.06
32 33 0.14
33 12 0.05
34 5 0.02
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (29 bp):
AATTAAAAAATATATTTTATTCTTATCTT
Found at i:76155 original size:60 final size:61
Alignment explanation
Indices: 75866--76204 Score: 167
Period size: 60 Copynumber: 5.7 Consensus size: 61
75856 TAAATTAAAT
* * ** ** * *
75866 TATATATTTTATTCTTATTTTTGTTTTAAAATATTTTTTAATTCTTATC-CAAC-TTAAAAA
1 TATACATTTTATTCTTATATTAATTAAAAAATATATTTT-ATTCTTATCTTAACTTTAAAAA
* * *
75926 TAT--ATTTTA-TCTCATATTAACTTTTAAAAAAATATAATTTTATTATCAT-TTAACTTTTAAA
1 TATACATTTTATTCTTATATTAA---TT-AAAAAATAT-ATTTTATTCTTATCTTAAC-TTTAAA
75987 AA
60 AA
* * ** * * *
75989 TGT--ATTGTATTCTTACT-TTAAATTATTAAATATGTTTTATT-TATATATTAAC-ATAAAAA
1 TATACATTTTATTCTTA-TATT-AATTAAAAAATATATTTTATTCT-TATCTTAACTTTAAAAA
* * * * *
76048 -AT--ATTTTAATCTTATTTTAGCTT-AAAAATATACTTTATTCTTGTCTTAAC-TT-AAAA
1 TATACATTTTATTCTTATATTA-ATTAAAAAATATATTTTATTCTTATCTTAACTTTAAAAA
* *
76104 TGTACATTTTATTCTTATATTGATATAAAAAATATATTTTATT-TTAATCTTAACTTTAAAAA
1 TATACATTTTATTCTTATATTAAT-TAAAAAATATATTTTATTCTT-ATCTTAACTTTAAAAA
* * * *
76166 TATATATTTTATTTTTATCTTAATTTAAAAATAT-TTTTA
1 TATACATTTTATTCTTATATTAATTAAAAAATATATTTTA
76205 ACATATATTT
Statistics
Matches: 213, Mismatches: 42, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
56 4 0.02
57 30 0.14
58 23 0.11
59 24 0.11
60 41 0.19
61 39 0.18
62 29 0.14
63 14 0.07
64 6 0.03
65 3 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (61 bp):
TATACATTTTATTCTTATATTAATTAAAAAATATATTTTATTCTTATCTTAACTTTAAAAA
Found at i:76176 original size:32 final size:31
Alignment explanation
Indices: 76129--76199 Score: 117
Period size: 32 Copynumber: 2.3 Consensus size: 31
76119 TATATTGATA
76129 TAAAAA-ATATATTTTATTTTAATCTTAACTT
1 TAAAAATATATATTTTATTTTAATCTTAA-TT
*
76160 TAAAAATATATATTTTATTTTTATCTTAATT
1 TAAAAATATATATTTTATTTTAATCTTAATT
76191 TAAAAATAT
1 TAAAAATAT
76200 TTTTAACATA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 17 0.45
32 21 0.55
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (31 bp):
TAAAAATATATATTTTATTTTAATCTTAATT
Found at i:76391 original size:28 final size:28
Alignment explanation
Indices: 76280--76391 Score: 77
Period size: 28 Copynumber: 4.0 Consensus size: 28
76270 TATATTTGGA
* *
76280 ATATA-TTTAAA-TTATGATAA-AATAAA
1 ATATATTTTAAAGTTAAGATAAGAAT-AT
* * *
76306 ATATATTTTTAAAATTTAAGATAAGAACGAA
1 ATATA-TTTT-AAAGTTAAGATAAGAA-TAT
** * *
76337 ATATATTTTTCAGTTAAAATAAAAATAT
1 ATATATTTTAAAGTTAAGATAAGAATAT
*
76365 ATATATTTTAAAGTTGAGATAAGAATA
1 ATATATTTTAAAGTTAAGATAAGAATA
76392 AAATAAATAT
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
26 5 0.08
28 26 0.39
29 14 0.21
30 12 0.18
31 9 0.14
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (28 bp):
ATATATTTTAAAGTTAAGATAAGAATAT
Found at i:76396 original size:57 final size:55
Alignment explanation
Indices: 76297--76454 Score: 141
Period size: 57 Copynumber: 2.9 Consensus size: 55
76287 TAAATTATGA
* *
76297 TAAAATAAAATATATTTTTAAAATTTAAGATAAGAACGAAAT-ATATTTTTCAGT
1 TAAAATAAAATATATTTTTAAAAGTTAAGATAAGAACAAAATAATATTTTTCAGT
* * *
76351 TAAAATAAAAATATATATATTTTAAAGTTGAGATAAGAATAAAATAAATATTTTT---T
1 TAAAAT-AAAATATAT-T-TTTAAAAGTTAAGATAAGAACAAAAT-AATATTTTTCAGT
* * *
76407 TAAAAATAAAATAT-TTTCTTAAAA-TTAAGTTTAGAATAAAAT-ATATTT
1 T-AAAATAAAATATATTT-TTAAAAGTTAAGATAAGAACAAAATAATATTT
76455 AATAATTTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
51 6 0.07
53 16 0.18
54 12 0.14
55 10 0.11
56 10 0.11
57 26 0.30
59 8 0.09
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (55 bp):
TAAAATAAAATATATTTTTAAAAGTTAAGATAAGAACAAAATAATATTTTTCAGT
Found at i:76414 original size:18 final size:19
Alignment explanation
Indices: 76391--76430 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
76381 AGATAAGAAT
*
76391 AAAAT-AAATATTTTTTTA
1 AAAATAAAATATTTTCTTA
76409 AAAATAAAATATTTTCTTA
1 AAAATAAAATATTTTCTTA
76428 AAA
1 AAA
76431 TTAAGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAAAATATTTTCTTA
Found at i:88605 original size:234 final size:232
Alignment explanation
Indices: 88180--88648 Score: 879
Period size: 234 Copynumber: 2.0 Consensus size: 232
88170 AACAAGGTGA
88180 ATACAAAATTCACTAGCAAATGCAATCACAAGGGACCTGGGCCTAAGTTGCAAATTACGTAGGGA
1 ATACAAAATTCACTAGCAAATGCAATCACAAGGGACCTGGGCCTAAGTTGCAAATTACGTAGGGA
88245 CATTGCAAATGAATAATGTACAAAAATAAAACGAATTCGAGCATTACAATAGAAGCATATACGAA
66 CATTGCAAATGAATAATGTACAAAAATAAAACGAATTCGAGCATTACAATAGAAGCATATACGAA
88310 TGTAAATTCCGTAGGGTCGTTAGTCGACAGAATGTCAACATCTGAGTATTATACAGTCCTAGATG
131 TGTAAATTCCGTAGGGTCGTTAGTCGACAGAATGTCAACATCTGAGTATTATACAGTCCTAGATG
*
88375 GAAATC-T-TAACCTGAGAGTGTAAGAAGCAAAATAT
196 GAAATCTTATAACCTGAGAGTGTAAGAAGCAAAAAAT
88410 ATACAAAAATTCACTAGCAAAAATGCAATCACAAGGGACCTGGGCCTAAGTTGCAAATTACGTAG
1 ATAC-AAAATTCACTAGC--AAATGCAATCACAAGGGACCTGGGCCTAAGTTGCAAATTACGTAG
88475 GGACATTGCAAATGAATAATGTACAAAAATAAAAACGAATTCGAGCATTACAATAGAAGCATATA
63 GGACATTGCAAATGAATAATGTACAAAAAT-AAAACGAATTCGAGCATTACAATAGAAGCATATA
88540 CGAATGTAAATTCCGTAGGGTCGTTAGTCGACAGAATGTCAACATCTGAGTATTATACAGTCCTA
127 CGAATGTAAATTCCGTAGGGTCGTTAGTCGACAGAATGTCAACATCTGAGTATTATACAGTCCTA
88605 GATGGAAATCTTATAACCTGAGAGTGTAAGAAGCAAAAAAT
192 GATGGAAATCTTATAACCTGAGAGTGTAAGAAGCAAAAAAT
88646 ATA
1 ATA
88649 GTAGCAGGAT
Statistics
Matches: 232, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
230 4 0.02
231 13 0.06
233 75 0.32
234 109 0.47
235 1 0.00
236 30 0.13
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (232 bp):
ATACAAAATTCACTAGCAAATGCAATCACAAGGGACCTGGGCCTAAGTTGCAAATTACGTAGGGA
CATTGCAAATGAATAATGTACAAAAATAAAACGAATTCGAGCATTACAATAGAAGCATATACGAA
TGTAAATTCCGTAGGGTCGTTAGTCGACAGAATGTCAACATCTGAGTATTATACAGTCCTAGATG
GAAATCTTATAACCTGAGAGTGTAAGAAGCAAAAAAT
Found at i:90934 original size:15 final size:17
Alignment explanation
Indices: 90901--90936 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
90891 GCTGAAAATG
*
90901 ATGTGTGTGTATGGTAT
1 ATGTGTGTATATGGTAT
*
90918 ATGTGTGTATATGATAT
1 ATGTGTGTATATGGTAT
90935 AT
1 AT
90937 ATATTCAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (17 bp):
ATGTGTGTATATGGTAT
Found at i:104359 original size:18 final size:18
Alignment explanation
Indices: 104322--104364 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
104312 TAAAGCTCCA
* *
104322 AAGCAAGCTAACGGGGAG
1 AAGCAAGCTAACAGGAAG
104340 AAGCAAGCTAACAGGAAG
1 AAGCAAGCTAACAGGAAG
104358 AATGCAA
1 AA-GCAA
104365 CAACTCTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.47, C:0.16, G:0.30, T:0.07
Consensus pattern (18 bp):
AAGCAAGCTAACAGGAAG
Found at i:105372 original size:23 final size:24
Alignment explanation
Indices: 105354--105443 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 24
105344 TTTAAATACT
105354 AAAATATTA-TTTAAATAAAAAATA
1 AAAATA-TACTTTAAATAAAAAATA
105378 AAAATATACTTTAAATACTAAAATATA
1 AAAATATACTTTAAATA--AAAA-ATA
*
105405 ATTAAA-ATA-TTCAAAT-AAAAATA
1 A--AAATATACTTTAAATAAAAAATA
* *
105428 ATACTATACTTTAAAT
1 AAAATATACTTTAAAT
105444 TAGGCCTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
21 1 0.02
22 3 0.06
23 12 0.22
24 18 0.33
26 4 0.07
27 10 0.19
28 3 0.06
29 3 0.06
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAATATACTTTAAATAAAAAATA
Found at i:105391 original size:43 final size:44
Alignment explanation
Indices: 105338--105432 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 44
105328 TATAACTAAT
* *
105338 AATA-ACTTTAAATACTAAAATATTATTTAAATA-AAAAATAAA
1 AATATACTTTAAATACTAAAATATAATTAAAATATAAAAATAAA
**
105380 AATATACTTTAAATACTAAAATATAATTAAAATATTCAAATAAA
1 AATATACTTTAAATACTAAAATATAATTAAAATATAAAAATAAA
105424 AATAATACT
1 AAT-ATACT
105433 ATACTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 4 0.09
43 27 0.59
44 10 0.22
45 5 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (44 bp):
AATATACTTTAAATACTAAAATATAATTAAAATATAAAAATAAA
Found at i:105402 original size:19 final size:19
Alignment explanation
Indices: 105332--105404 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 19
105322 TGTTTATATA
105332 ACTAATAATA-ACTTTAAAT
1 ACTAA-AATATACTTTAAAT
105351 ACTAAAATATTA-TTTAAAT
1 ACTAAAATA-TACTTTAAAT
*
105370 AAAAAATAAAAATATACTTTAAAT
1 ----ACT-AAAATATACTTTAAAT
105394 ACTAAAATATA
1 ACTAAAATATA
105405 ATTAAAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
18 4 0.09
19 20 0.45
20 3 0.07
23 4 0.09
24 13 0.30
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (19 bp):
ACTAAAATATACTTTAAAT
Found at i:105643 original size:14 final size:14
Alignment explanation
Indices: 105624--105671 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
105614 TATATTTTCG
105624 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
105638 TTTA---T-GTTCA
1 TTTATGTTCGTTCA
*
105648 TTTATGTCCGTTCA
1 TTTATGTTCGTTCA
105662 TTTATGTTCG
1 TTTATGTTCG
105672 AACAGATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.32
11 1 0.04
14 18 0.64
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:105659 original size:24 final size:24
Alignment explanation
Indices: 105606--105670 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
105596 CGTTCGTGAA
* * *
105606 CGTTCGATTATATTTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTC
105632 CGTTCATTTATGTTCATTTATGTC
1 CGTTCATTTATGTTCATTTATGTC
105656 CGTTCATTTATGTTC
1 CGTTCATTTATGTTC
105671 GAACAGATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 28 0.78
25 3 0.08
26 5 0.14
ACGTcount: A:0.15, C:0.15, G:0.14, T:0.55
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTC
Found at i:106521 original size:13 final size:13
Alignment explanation
Indices: 106503--106529 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
106493 AAAATACCCA
106503 TTTAAGTTCACGC
1 TTTAAGTTCACGC
106516 TTTAAGTTCACGC
1 TTTAAGTTCACGC
106529 T
1 T
106530 CTGCTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTAAGTTCACGC
Done.