Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004076.1 Hibiscus syriacus cultivar Beakdansim tig00008922_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: 85911
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3076 original size:65 final size:64
Alignment explanation
Indices: 3007--3167 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 64
2997 AATTAAATTG
* * *
3007 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCAGCGATGCACTAAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCAGCGATGCACTAAGGATATT-TG-
3071 A
64 A
* ** *
3072 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCAGCGATGCACTAAGGATATTTGA
* *
3135 AACATCGAATACACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
3168 TTAGTGTACC
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 30 0.35
64 4 0.05
65 51 0.60
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCAGCGATGCACTAAGGATATTTGA
Found at i:8960 original size:24 final size:23
Alignment explanation
Indices: 8933--9013 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 23
8923 ACACTTAACA
8933 GTGCACCGATGCATCCCTTTGAAT
1 GTGCACCGATGCATCCC-TTGAAT
** * **
8957 GTGCTTCGATACATCAGTTG-A-
1 GTGCACCGATGCATCCCTTGAAT
8978 -TGCACCGATGCATGCCCTTGAAT
1 GTGCACCGATGCAT-CCCTTGAAT
*
9001 GTGCATCGATGCA
1 GTGCACCGATGCA
9014 CAAGAGCCAT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
20 10 0.24
21 4 0.10
22 2 0.05
23 3 0.07
24 23 0.55
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
GTGCACCGATGCATCCCTTGAAT
Found at i:11708 original size:38 final size:37
Alignment explanation
Indices: 11665--11745 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
11655 ACCATGCACC
*
11665 GATGCACTAAGGAT-TTTATGAAAACATCGAATGCATTT
1 GATGCACTAAGGATATTT-TG-AAACATCGAATGCACTT
** * *
11703 GATGCACTCTGGCTATTTTGAAACATCGAATGTACTT
1 GATGCACTAAGGATATTTTGAAACATCGAATGCACTT
11740 GATGCA
1 GATGCA
11746 TCGATGCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 21 0.57
38 13 0.35
39 3 0.08
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (37 bp):
GATGCACTAAGGATATTTTGAAACATCGAATGCACTT
Found at i:20618 original size:17 final size:17
Alignment explanation
Indices: 20593--20629 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20583 AAAAAATAAC
*
20593 TTAATTAATATTTTATT
1 TTAAATAATATTTTATT
20610 TTAAATAATATTTTATT
1 TTAAATAATATTTTATT
20627 TTA
1 TTA
20630 TTTTACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAAATAATATTTTATT
Found at i:20881 original size:20 final size:20
Alignment explanation
Indices: 20856--20902 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20846 GTTTCCAAAT
20856 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
20876 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
20896 TCGCAAC
1 TCGCAAC
20903 ACAGAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:20919 original size:20 final size:20
Alignment explanation
Indices: 20896--21003 Score: 146
Period size: 20 Copynumber: 5.3 Consensus size: 20
20886 AATCTGTAAA
20896 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
20916 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
20936 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
20956 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
20976 TCGCAACACTGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
20997 TCGCAAC
1 TCGCAAC
21004 TGAATTTCAA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
19 1 0.01
20 63 0.80
21 15 0.19
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:20940 original size:60 final size:60
Alignment explanation
Indices: 20896--21062 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 60
20886 AATCTGTAAA
20896 TCGCAACACAGA-AGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GATAGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAGTCAAAT
* * ** **
20956 TCGCAACGCGATAGTCAAATTCGCAACAC-TGAATTTCAAATTCGCAAC-TGAATTTCAAAT
1 TCGCAACACGATAGTCAAATTCGCAACACAT-AA-GTCAAATTCGCAACACAAAAGTCAAAT
* ** * * * *
21016 TCGCAACTCGATTTTTAAATTCGCAACACA-AATTTAATTTCGCAACA
1 TCGCAACACGATAGTCAAATTCGCAACACATAAGTCAAATTCGCAACA
21063 AGTTTTAGTT
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
58 12 0.13
59 5 0.06
60 60 0.67
61 13 0.14
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (60 bp):
TCGCAACACGATAGTCAAATTCGCAACACATAAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:21007 original size:19 final size:19
Alignment explanation
Indices: 20970--21042 Score: 101
Period size: 19 Copynumber: 3.7 Consensus size: 19
20960 AACGCGATAG
20970 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
20991 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
21010 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
21030 TTAAATTCGCAAC
1 TCAAATTCGCAAC
21043 ACAAATTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 22 0.45
20 17 0.35
21 10 0.20
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:21014 original size:40 final size:40
Alignment explanation
Indices: 20851--21042 Score: 148
Period size: 40 Copynumber: 4.8 Consensus size: 40
20841 ACCCAGTTTC
* *
20851 CAAATTCGCAACGCGAATATGT-AAA-TCGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-TCAAATTCGCAACGC-AAT-AGT
* *
20893 -AAA-TCGCAACACAGAA-GTCAAATTCGCAACAC-ATAAGT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACGCAAT-AGT
* ** *
20931 CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACGAATTTCAAATTCGCAACGCAATAGT
*
20971 CAAATTCGCAACACTGAATTTCAAATTCGCAACTG-AAT-TT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAAC-GCAATAGT
* * *
21011 CAAATTCGCAACTCGATTTTTAAATTCGCAAC
1 CAAATTCGCAACACGAATTTCAAATTCGCAAC
21043 ACAAATTTAA
Statistics
Matches: 126, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
38 5 0.04
39 24 0.19
40 71 0.56
41 25 0.20
42 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.23
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACGCAATAGT
Found at i:21037 original size:20 final size:20
Alignment explanation
Indices: 20930--21061 Score: 117
Period size: 20 Copynumber: 6.7 Consensus size: 20
20920 AACACATAAG
* * **
20930 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACTCGAATT
* *
20950 TCAAATTCGCAACGCG-ATAG
1 TCAAATTCGCAACTCGAAT-T
*
20970 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACTC-GAATT
20991 TCAAATTCGCAACT-GAATT
1 TCAAATTCGCAACTCGAATT
*
21010 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACTCGAATT
* * *
21030 TTAAATTCGCAACACAAATT
1 TCAAATTCGCAACTCGAATT
*
21050 T-AATTTCGCAAC
1 TCAAATTCGCAAC
21062 AAGTTTTAGT
Statistics
Matches: 96, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
19 30 0.31
20 50 0.52
21 14 0.15
22 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (20 bp):
TCAAATTCGCAACTCGAATT
Found at i:21058 original size:39 final size:40
Alignment explanation
Indices: 20896--21062 Score: 121
Period size: 40 Copynumber: 4.2 Consensus size: 40
20886 AATCTGTAAA
* * *
20896 TCGCAACACAGAA-GTCAAATTCGCAACACATAA-GTCAAAT
1 TCGCAACACTGAATTTCAAATTCGCAAC-CA-AATTTCAAAT
* ** * *
20936 TCGCAACAC-AAAAGTCAAATTCGCAACGC-GATAGTCAAAT
1 TCGCAACACTGAATTTCAAATTCGCAAC-CAAAT-TTCAAAT
**
20976 TCGCAACACTGAATTTCAAATTCGCAACTGAATTTCAAAT
1 TCGCAACACTGAATTTCAAATTCGCAACCAAATTTCAAAT
* * * *
21016 TCGCAACTC-GATTTTTAAATTCGCAACACAAATTT-AATT
1 TCGCAACACTGAATTTCAAATTCGCAAC-CAAATTTCAAAT
21055 TCGCAACA
1 TCGCAACA
21063 AGTTTTAGTT
Statistics
Matches: 105, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
38 1 0.01
39 28 0.27
40 59 0.56
41 17 0.16
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (40 bp):
TCGCAACACTGAATTTCAAATTCGCAACCAAATTTCAAAT
Found at i:21069 original size:18 final size:19
Alignment explanation
Indices: 20975--21083 Score: 76
Period size: 19 Copynumber: 5.6 Consensus size: 19
20965 GATAGTCAAA
* *
20975 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC--AATTTTAAT
** * *
20996 TTCGCAACTGAATTTCAAA
1 TTCGCAACACAATTTTAAT
* * *
21015 TTCGCAACTCGATTTTTAAA
1 TTCGCAACAC-AATTTTAAT
*
21035 TTCGCAACACAAATTTAAT
1 TTCGCAACACAATTTTAAT
* *
21054 TTCGCAACA-AGTTTTAGT
1 TTCGCAACACAATTTTAAT
21072 TTCGCAACACAA
1 TTCGCAACACAA
21084 ATGTTTTGGG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.21
19 34 0.47
20 16 0.22
21 8 0.11
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (19 bp):
TTCGCAACACAATTTTAAT
Found at i:22018 original size:24 final size:24
Alignment explanation
Indices: 21991--22044 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
21981 GTATTCGAAA
21991 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
22015 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
22039 TTTGAT
1 TTTGAT
22045 GACGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:22696 original size:20 final size:20
Alignment explanation
Indices: 22671--22744 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
22661 TAAACGCGCT
22671 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGCG
22691 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGCG
*
22711 TTGCGAATTTGACTATTGCG
1 TTGCGAATTTGACTATCGCG
*
22731 TTACGAATTTGACT
1 TTGCGAATTTGACT
22745 TCTGTATTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:22755 original size:60 final size:61
Alignment explanation
Indices: 22674--22849 Score: 161
Period size: 60 Copynumber: 2.9 Consensus size: 61
22664 ACGCGCTTTG
** * *
22674 CGAATTTGACTATC-GCGTTGCGAATTTGACTA-TCGCGTTGCGAATTTGAC-TATT-GCGTTA
1 CGAATTTGACT-TCTGTATTGCGAATTTGACTATTCGCGTTCCG-ATTT-ACAGATTCGCGTTA
* *
22734 CGAATTTGACTTCTGTATTGCG-ATTT-ACAAATTCGCGTTCCGATTTACAGATTCGCGTTG
1 CGAATTTGACTTCTGTATTGCGAATTTGAC-TATTCGCGTTCCGATTTACAGATTCGCGTTA
* * * *
22794 CGAATTTGACTTTTGTATTGCGAATTTGAC--TTCTGTGTTGCAATTTACAGATTCGC
1 CGAATTTGACTTCTGTATTGCGAATTTGACTATTC-GCGTTCCGATTTACAGATTCGC
22850 ATTGTGAATT
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
58 4 0.04
59 17 0.17
60 71 0.72
61 4 0.04
62 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (61 bp):
CGAATTTGACTTCTGTATTGCGAATTTGACTATTCGCGTTCCGATTTACAGATTCGCGTTA
Found at i:22772 original size:40 final size:41
Alignment explanation
Indices: 22671--22803 Score: 109
Period size: 40 Copynumber: 3.3 Consensus size: 41
22661 TAAACGCGCT
* * *
22671 TTGCGAATTTGACTA-TCGCGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACAATTCGCGTTACGAATTTGACTATCGCA
* *
22711 TTGCGAATTTGACTATT-GCGTTACGAATTTGACT-TCTGTA
1 TTGCGAATTTGACAATTCGCGTTACGAATTTGACTATC-GCA
* * *
22751 TTGCG-ATTT-ACAAATTCGCGTTCCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-AATTCGCGTTACGAATTTGAC-TA-TCGCA
22791 TTGCGAATTTGAC
1 TTGCGAATTTGAC
22804 TTTTGTATTG
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
38 4 0.05
39 13 0.17
40 50 0.66
41 7 0.09
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (41 bp):
TTGCGAATTTGACAATTCGCGTTACGAATTTGACTATCGCA
Found at i:22779 original size:20 final size:20
Alignment explanation
Indices: 22754--22792 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
22744 TTCTGTATTG
22754 CGATTTACAAATTCGCGTTC
1 CGATTTACAAATTCGCGTTC
*
22774 CGATTTACAGATTCGCGTT
1 CGATTTACAAATTCGCGTT
22793 GCGAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTC
Found at i:22816 original size:20 final size:20
Alignment explanation
Indices: 22791--22839 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
22781 CAGATTCGCG
*
22791 TTGCGAATTTGACTTTTGTA
1 TTGCGAATTTGACTTCTGTA
*
22811 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTA
22831 TTGC-AATTT
1 TTGCGAATTT
22840 ACAGATTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.49
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTA
Found at i:22870 original size:21 final size:21
Alignment explanation
Indices: 22846--22902 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
22836 ATTTACAGAT
* *
22846 TCGCATTGTGAATTTGGAAAA
1 TCGCAATGTGAATTTAGAAAA
* *
22867 TCGCAACGCGAATTTAGAAAA
1 TCGCAATGTGAATTTAGAAAA
22888 TCGCAATGT-AATTTA
1 TCGCAATGTGAATTTA
22903 CATATTCGCG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (21 bp):
TCGCAATGTGAATTTAGAAAA
Found at i:24932 original size:2 final size:2
Alignment explanation
Indices: 24920--24952 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
24910 AAATAAATAA
24920 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24953 TAATTTGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44646 original size:22 final size:20
Alignment explanation
Indices: 44630--44667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44620 GTAAATTTAA
*
44630 ACCGGTTACATTATAAATTT
1 ACCGATTACATTATAAATTT
*
44650 ACCTATTACATTATAAAT
1 ACCGATTACATTATAAAT
44668 ATTGGTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (20 bp):
ACCGATTACATTATAAATTT
Found at i:44981 original size:198 final size:198
Alignment explanation
Indices: 44635--45113 Score: 529
Period size: 198 Copynumber: 2.4 Consensus size: 198
44625 TTTAAACCGG
* * * * *
44635 TTACATTATAAATTTACCTATTACATTATAAATATTGGTTTTGATGTTTTCGGGATCGATACAAT
1 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGATTTCGGGATCGATAC-TT
* * ** * * *
44700 TTT-AAATGTATTGACACTTTTTGCGTGTAACTCGTTTGTGCTTTATTTTGGAAAAAAGTATTGA
65 TTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTATCGA
* * * *
44764 AACATATTTAAAGAGTGTCGATACATAATGTAAACATATT-TGCTAATTAA-CCGATATATTT-T
130 AACAAATTAAAAAAGTGTCGATACATAATGTAAACATATTCT-CTAATGAACCCGATATATTTCT
44826 AATCGA
194 -ATCGA
* * * *
44832 TTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATG-TTTCGAGGATCGATACTT
1 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGATTTCG-GGATCGATACTT
* *
44896 TTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATTCATTTTGGAAAAATGTATC
65 TTTA-AAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTCATTTTGGAAAAAAGTATC
* * * ** * *
44960 GACACAAATTAAAAAAGTGTCGATACTTTATGTTGACATATTCTCTCATGAACCCGGTATATTTC
128 GAAACAAATTAAAAAAGTGTCGATACATAATGTAAACATATTCTCTAATGAACCCGATATATTTC
*
45025 TATCGG
193 TATCGA
* * ** * *
45031 TTACATTGGAAATTTACCTATTACATTATAATTATTGGTCTCTTTGATTTTGGGATCGATACTTG
1 TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGATTTCGGGATCGATACTTT
45096 TTATAAATGTATCGACAC
66 TTA-AAATGTATCGACAC
45114 AAAATCTAAC
Statistics
Matches: 234, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
196 9 0.04
197 50 0.21
198 88 0.38
199 82 0.35
200 5 0.02
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (198 bp):
TTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGATTTCGGGATCGATACTTT
TTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAAAAAGTATCGAA
ACAAATTAAAAAAGTGTCGATACATAATGTAAACATATTCTCTAATGAACCCGATATATTTCTAT
CGA
Found at i:48276 original size:18 final size:19
Alignment explanation
Indices: 48236--48279 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
48226 TTTGGTTTAC
* *
48236 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTAACAG-G
48256 GGAATAAAAGATTAACA-G
1 GGAATAAAAGATTAACAGG
48274 GGAATA
1 GGAATA
48280 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTAACAGG
Found at i:49637 original size:200 final size:199
Alignment explanation
Indices: 49248--50322 Score: 1420
Period size: 200 Copynumber: 5.4 Consensus size: 199
49238 TGTTTTTGGG
** * *
49248 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTTGACACAAATGT
1 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAAAGTATCGACACAAATGT
49313 ATAAAGTATCGATACATTATGTATACC-TT-TTTTTTAATAACCGATATATTTAGACCGGTTACA
66 ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCG-TATATTTAGACCGGTTACA
49376 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
130 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
49441 AATGT
195 AATGT
** *
49446 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
1 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAAAGTATCGACACAAATGT
49511 ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCAGTATATTTAGACCGGTTACA
66 ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACC-GTATATTTAGACCGGTTACA
49576 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
130 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
49641 AATGT
195 AATGT
* ** *
49646 ATCGACACTTTTTTGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
1 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAAAGTATCGACACAAATGT
* *
49711 ATAAAGTATCGATACATCATGTATACGTTTCTTTTTTAATAACCGATATATTTAGACCGGTTACA
66 ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCG-TATATTTAGACCGGTTACA
49776 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
130 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
49841 AATGT
195 AATGT
* * * *
49846 ATTGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATTTTGGACA-ACATGTATCGACACAAA
1 ATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATACATTATGGACATA-AAGTATCGACACAAA
* * * ** * * * *
49909 T-TAATAAAGTGTCAATACA-TATTGTAGACCTATT-TTCTCATAA-AACTGGTAAATTTAAACT
63 TGT-ATAAAGTATCGATACATTA-TGTATACCT-TTCTT-TTTTAATAAC-CGTATATTTAGACC
* * * * * *
49970 GGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGGGATCGACACT
123 GGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACT
*
50035 TGATATAAATGT
188 TGTTATAAATGT
*
50047 ATCGACACTTATTT-GTGAACTTGTTTTGGTTGGAAAATACATTATGGACACAAAGTATCGACAC
1 ATCGACACTT-TTTCGTGAACTTG---T--TTGGAAAATACATTATGGACATAAAGTATCGACAC
* * * * * *
50111 AAATGTATAAAGTGTCGATACTTTATGTATA--TCTCTTTTCTCATAAATCGGTATATTTAGACC
60 AAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAAT-AA-CCGTATATTTAGACC
* * * *
50174 GGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACT
123 GGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACT
*
50239 TTTTATAAATGT
188 TGTTATAAATGT
* * *
50251 ATCGACACTTTGTTCGTGCACTTGGTTTGG-AAATACATTATGGACA-ACATGTATCGACACGAA
1 ATCGACACTTT-TTCGTGAACTT-GTTTGGAAAATACATTATGGACATA-AAGTATCGACACAAA
*
50314 TGAATAAAG
63 TGTATAAAG
50323 CAAATTCATT
Statistics
Matches: 789, Mismatches: 58, Indels: 58
0.87 0.06 0.06
Matches are distributed among these distances:
198 91 0.12
199 5 0.01
200 353 0.45
201 159 0.20
202 18 0.02
203 5 0.01
204 96 0.12
205 57 0.07
206 5 0.01
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (199 bp):
ATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGGACATAAAGTATCGACACAAATGT
ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCGTATATTTAGACCGGTTACAT
TGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
ATGT
Found at i:50280 original size:405 final size:398
Alignment explanation
Indices: 49248--50322 Score: 1525
Period size: 401 Copynumber: 2.7 Consensus size: 398
49238 TGTTTTTGGG
*
49248 ATCGACACTT-TTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTTGACACAAATG
1 ATCGACACTTATTT-GTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATG
* *
49312 TATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGATATATTTAGACCGGTTACAT
65 TATAAAGTATCGATACATTATGTATATCTCTTTTTTAATAACCGATATATTTAGACCGGTTACAT
49377 TGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
130 TGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
* ** * *
49442 ATGTATCGACACTTTTTCGTGAACTT-GTTTGGAAAATTTATTATGGACATA-AAGTGTCGACAC
195 ATGTATCGACACTTTTTCGTGCACTTGGTTTGG-AAATACATTATGGACA-ACATGTATCGACAC
* * ** * *
49505 AAATGT-ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCAGTATATTTAGACC
258 AAAT-TAATAAAGTATCAATACATTATGTAGACCTTTCTTTCATAATAACCAGTAAATTTAAACC
* * * * *
49569 GGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACT
322 GGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACT
*
49634 TGTTATAAATGT
387 TGATATAAATGT
*
49646 ATCGACACTTTTTTGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
1 ATCGACACTTATTTGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
* *
49711 ATAAAGTATCGATACATCATGTATACGTTTCTTTTTTAATAACCGATATATTTAGACCGGTTACA
66 ATAAAGTATCGATACATTATGTATA--TCTCTTTTTTAATAACCGATATATTTAGACCGGTTACA
49776 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
129 TTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATA
* *
49841 AATGTATTGACACTTTTTTCGTGCACTTGGTTTGGAAATACATTTTGGACAACATGTATCGACAC
194 AATGTATCGACAC-TTTTTCGTGCACTTGGTTTGGAAATACATTATGGACAACATGTATCGACAC
* **
49906 AAATTAATAAAGTGTCAATACA-TATTGTAGACCTATT-TTCTCATAA-AACTGGTAAATTTAAA
258 AAATTAATAAAGTATCAATACATTA-TGTAGACCT-TTCTT-TCATAATAACCAGTAAATTTAAA
* *
49968 CTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTTTTTGGGATCGACA
320 CCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACA
50033 CTTGATATAAATGT
385 CTTGATATAAATGT
** * *
50047 ATCGACACTTATTTGTGAACTTGTTTTGGTTGGAAAATACATTATGGACACAAAGTATCGACACA
1 ATCGACACTTATTTGTGAACTTG---T--TTGGAAAATTTATTATGGACATAAAGTGTCGACACA
* * * * * *
50112 AATGTATAAAGTGTCGATACTTTATGTATATCTCTTTTCTCATAAATCGGTATATTTAGACCGGT
61 AATGTATAAAGTATCGATACATTATGTATATCTCTTTTTTAAT-AACCGATATATTTAGACCGGT
* * * * *
50177 TACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTTT
125 TACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGT
50242 TATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGGAAATACATTATGGACAACATGTATCG
190 TATAAATGTATCGACACTTT-TTCGTGCACTTGGTTTGGAAATACATTATGGACAACATGTATCG
* *
50307 ACACGAATGAATAAAG
254 ACACAAATTAATAAAG
50323 CAAATTCATT
Statistics
Matches: 609, Mismatches: 51, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
398 84 0.14
399 3 0.00
400 116 0.19
401 169 0.28
402 12 0.02
404 14 0.02
405 152 0.25
406 59 0.10
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (398 bp):
ATCGACACTTATTTGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
ATAAAGTATCGATACATTATGTATATCTCTTTTTTAATAACCGATATATTTAGACCGGTTACATT
GTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTATAAA
TGTATCGACACTTTTTCGTGCACTTGGTTTGGAAATACATTATGGACAACATGTATCGACACAAA
TTAATAAAGTATCAATACATTATGTAGACCTTTCTTTCATAATAACCAGTAAATTTAAACCGGTT
ACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTGGGATCGACACTTGAT
ATAAATGT
Found at i:54339 original size:21 final size:22
Alignment explanation
Indices: 54308--54350 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
54298 TATGAGAAAT
54308 TGTTTATAAAATAT-AAAAATGA
1 TGTTTATAAAAT-TGAAAAATGA
54330 TGTTT-TAAAATTGAAAAATGA
1 TGTTTATAAAATTGAAAAATGA
54351 AAATAAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
TGTTTATAAAATTGAAAAATGA
Found at i:58791 original size:23 final size:23
Alignment explanation
Indices: 58773--58831 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
58763 CTCGTATAAA
58773 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
58796 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
58818 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
58832 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:59973 original size:21 final size:21
Alignment explanation
Indices: 59949--59993 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59939 TCTTGTTCGT
* *
59949 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
59970 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
59991 TTG
1 TTG
59994 CCCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:61441 original size:21 final size:21
Alignment explanation
Indices: 61417--61456 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
61407 ACCGTCAACC
*
61417 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
* *
61438 AAATCTAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
61457 AATCCCATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:65682 original size:15 final size:15
Alignment explanation
Indices: 65662--65714 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
65652 TGATTTCCTC
65662 AGAAGAGCTGGGTTG
1 AGAAGAGCTGGGTTG
*
65677 AGAAGAGGTGGGTTG
1 AGAAGAGCTGGGTTG
*
65692 AGAAGAGATGGGTTG
1 AGAAGAGCTGGGTTG
65707 AGAAGAGC
1 AGAAGAGC
65715 CCCGATTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.47, T:0.17
Consensus pattern (15 bp):
AGAAGAGCTGGGTTG
Found at i:66352 original size:198 final size:198
Alignment explanation
Indices: 66189--67152 Score: 1654
Period size: 198 Copynumber: 4.9 Consensus size: 198
66179 TGACCATTTA
*
66189 CATTCTGGACA-AAACGTATCGACACAAATTCAA-AGAGTGTTGATACTTTATGTACACCTGTTT
1 CATTCTGGACACAAA-GTATCGACACAAATTCAACA-AGTGTCGATACTTTATGTACACCTGTTT
*
66252 TCTCATAAACCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTACATTATAATTATGGG
64 TCTCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGG
* * *
66317 TCTCGAT-ATTTTGGGATTGATACTTTTTATAAATGTATCGACACA-TT--ATGGTGACCTTGGT
129 TCTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAGTTCCAT-G-CA-CTTGGT
66378 AAGGAAAT
191 AAGGAAAT
* *
66386 CATTCTGGACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACATGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
* * * *
66451 TCATAAACCGGTATATTTAGACCGATTAGATTGATAATTTACTTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
*
66516 TCGATGTTTTTGGGATCGATA-TTTTTATAAATGTATCAACACAGTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAGTTCCATGCACTTGGTAAGGA
66580 AAT
196 AAT
*
66583 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCAATACTTTATGTACACCTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
66648 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* *
66713 TCGATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAGTTCCATGCACTTGGTAAGGA
66778 AAT
196 AAT
* *
66781 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTATACTTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
66846 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
* *
66911 TCGATGTTTTTGGGATTGATACTTTTTATAAATGTATCGACACAGTTCCATGCACTTGGTAAGAA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAGTTCCATGCACTTGGTAAGGA
66976 AAT
196 AAT
66979 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
1 CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
67044 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
66 TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
*
67109 TCAATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACA
131 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACA
67153 TATGTTTACC
Statistics
Matches: 729, Mismatches: 31, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
197 302 0.41
198 424 0.58
199 1 0.00
200 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (198 bp):
CATTCTGGACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTGTTTTC
TCATAAACCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGGGTC
TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACAGTTCCATGCACTTGGTAAGGA
AAT
Found at i:67495 original size:18 final size:18
Alignment explanation
Indices: 67468--67535 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 18
67458 TTCTCATCTC
* * *
67468 ATACATAATTACATTCGT
1 ATACAAAATTAAAATCGT
67486 ATACAAAATTATAAATCGT
1 ATACAAAATTA-AAATCGT
*
67505 ATACAAAATTAAAAATCTT
1 ATACAAAATT-AAAATCGT
67524 ATACAAAATTAA
1 ATACAAAATTAA
67536 CCCTACATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
18 12 0.27
19 31 0.70
20 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (18 bp):
ATACAAAATTAAAATCGT
Found at i:67506 original size:19 final size:19
Alignment explanation
Indices: 67482--67535 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
67472 ATAATTACAT
*
67482 TCGTATACAAAATTATAAA
1 TCGTATACAAAATTAAAAA
67501 TCGTATACAAAATTAAAAA
1 TCGTATACAAAATTAAAAA
*
67520 TCTTATACAAAATTAA
1 TCGTATACAAAATTAA
67536 CCCTACATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.31
Consensus pattern (19 bp):
TCGTATACAAAATTAAAAA
Found at i:68707 original size:17 final size:17
Alignment explanation
Indices: 68685--68720 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
68675 GAATCATTAG
68685 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
68702 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
68719 GA
1 GA
68721 AATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (17 bp):
GATTAATATCTTTTCAT
Found at i:69045 original size:18 final size:18
Alignment explanation
Indices: 69022--69060 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
69012 TTCTCCTCAT
*
69022 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTATTC
*
69040 TTCCTCTATCTTTTATTC
1 TTCCTCCATCTTTTATTC
69058 TTC
1 TTC
69061 AAATTTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTCCATCTTTTATTC
Found at i:69738 original size:22 final size:24
Alignment explanation
Indices: 69710--69765 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
69700 AACCTGAATT
69710 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
69732 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
69756 TATAAAAAAA
1 TATAATAAAA
69766 ACCAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 14 0.52
25 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:72260 original size:183 final size:181
Alignment explanation
Indices: 71646--72245 Score: 733
Period size: 182 Copynumber: 3.3 Consensus size: 181
71636 GTAGCGCTTT
* * * *
71646 ACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTCATAAAGTATCAA
1 ACCGGTTTTATCATATTTTTACCTATTATATTGCTATGGATCGATACATTTTTATAAAGTATCGA
* * *
71711 CACTTTTTAGGCGTTATAACTTCTTCTCTTTTAAATTACGAAAA-TGTCGATACTTATATTAATT
66 CACTTTATAGGCGTTATAACTTCTTCTCTTTTAAATTTCAAAAAGTGTCGATACTTATATTAA-T
* * *
71775 TATCGACACTTTCAATATATCTGATAGCTTTTTACCGGTTTTATCATTTCTA
130 TATCGACACTTTCAATATATCCGATAGCTCTTTACCGGTTTTATCATTTCGA
* * * * * * * *
71827 GACCTGTTTTGTCATATTCTTACATGTTATATTGCTATAGATCGATACATTTGTATAACGTATCG
1 -ACCGGTTTTATCATATTTTTACCTATTATATTGCTATGGATCGATACATTTTTATAAAGTATCG
*
71892 ACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAA-TTCAAAAAGTGTCGATACTTATATTAAG
65 ACACTTTATAGGCGTTATAACTTCTTCTCTTTTAAATTTCAAAAAGTGTCGATACTTATATTAA-
* * *
71956 GTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGTG
129 TTATCGACACTTTCAATATATCCGATAGCTCTTTACCGGTTTTATCATTTCG-A
* * * * * * *
72010 ACTGGTTTTATCATATTTATACTTGTTATATTGTTATGGATCGATACGTTTTTATTAAGTATCGA
1 ACCGGTTTTATCATATTTTTACCTATTATATTGCTATGGATCGATACATTTTTATAAAGTATCGA
*
72075 CACTTTATAGGCGTTATTACTTCTTCTCTTTTAAATTTC-AAAAGTGTCGATACTTAT-TTAAAT
66 CACTTTATAGGCGTTATAACTTCTTCTCTTTTAAATTTCAAAAAGTGTCGATACTTATATT-AAT
* * * ** ** *
72138 CTAATCGATACTTTCGATATATCCAATAGCGGTTTACCAATTTTATCATAAT-GA
130 -T-ATCGACACTTTCAATATATCCGATAGCTCTTTACCGGTTTTATCAT-TTCGA
*
72192 ACCCGGTTTTATCATATTTTTACCTATTATATTGCTATGGAGCGATACATTTTT
1 A-CCGGTTTTATCATATTTTTACCTATTATATTGCTATGGATCGATACATTTTT
72246 CATTTGTATC
Statistics
Matches: 357, Mismatches: 53, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
181 8 0.02
182 261 0.73
183 87 0.24
184 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (181 bp):
ACCGGTTTTATCATATTTTTACCTATTATATTGCTATGGATCGATACATTTTTATAAAGTATCGA
CACTTTATAGGCGTTATAACTTCTTCTCTTTTAAATTTCAAAAAGTGTCGATACTTATATTAATT
ATCGACACTTTCAATATATCCGATAGCTCTTTACCGGTTTTATCATTTCGA
Found at i:76417 original size:22 final size:22
Alignment explanation
Indices: 76368--76413 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
76358 TTTGACGTGT
* **
76368 TTATAATTTTTGTAGAAAGTAA
1 TTATATTTTTTGTAGAAAAAAA
76390 TTATATTTTTTGTA-AAAAAAA
1 TTATATTTTTTGTAGAAAAAAA
76411 TTA
1 TTA
76414 ATATCTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
TTATATTTTTTGTAGAAAAAAA
Found at i:79810 original size:64 final size:63
Alignment explanation
Indices: 79695--79817 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 63
79685 TTGTTTGAAG
* * **
79695 GTGTATCGATGCACAGGTAGGCATCGATGCACTCTTTTAAAATATAAACATCGAATGCAATTA
1 GTGTATCGATGCAAAGGCAGGCATCGATGCACTCCATTAAAATATAAACATCGAATGCAATTA
* *
79758 GTGTATCGATGCATAAGGCATGCATCGATGCATTCCATTAATAATA-AAACATCGAATGCA
1 GTGTATCGATGCA-AAGGCAGGCATCGATGCACTCCATTAA-AATATAAACATCGAATGCA
79818 TTTTATGCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 13 0.25
64 35 0.67
65 4 0.08
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (63 bp):
GTGTATCGATGCAAAGGCAGGCATCGATGCACTCCATTAAAATATAAACATCGAATGCAATTA
Found at i:79832 original size:64 final size:64
Alignment explanation
Indices: 79701--79854 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 64
79691 GAAGGTGTAT
* * * ** * *
79701 CGATGCACAGGTAG-GCATCGATGCACTCTTTTAAAATATAAACATCGAATGCAATTAGTGTAT
1 CGATGCACAAGCAGTGCATCGATGCATTCCATTAAAATATAAACATCGAATGCAATTAGTGCAC
* *
79764 CGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAATA-AAACATCGAATGCATTTTA-TGC
1 CGATGCACAA-GCAGTGCATCGATGCATTCCATTAA-AATATAAACATCGAATGCA-ATTAGTGC
79826 AC
63 AC
*
79828 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
79855 GCCTCATTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
63 10 0.13
64 58 0.77
65 7 0.09
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
CGATGCACAAGCAGTGCATCGATGCATTCCATTAAAATATAAACATCGAATGCAATTAGTGCAC
Found at i:80262 original size:29 final size:29
Alignment explanation
Indices: 80219--80299 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
80209 GATATGTGAT
*
80219 GAGAACATGCCATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
80249 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
80278 GAGAAATGGCATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
80300 ACATATGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:80401 original size:15 final size:15
Alignment explanation
Indices: 80383--80416 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
80373 GAGGGCATAA
*
80383 TAGTCCTTCGGGACG
1 TAGTCATTCGGGACG
*
80398 TAGTCATTCGGGATG
1 TAGTCATTCGGGACG
80413 TAGT
1 TAGT
80417 GGTCCTACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCATTCGGGACG
Done.