Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002955.1 Hibiscus syriacus cultivar Beakdansim tig00006106_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: 155346
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3057 original size:21 final size:22
Alignment explanation
Indices: 3011--3070 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
3001 ACTCCCATGA
*
3011 GGAACCGATTCCCCCTTTAAAGG
1 GGAACCGATTCCCCC-TCAAAGG
*
3034 GGAACCGATTCCCCC-CACAGG
1 GGAACCGATTCCCCCTCAAAGG
* *
3055 GGAATCGATACCCCCT
1 GGAACCGATTCCCCCT
3071 GGGGTTCTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.53
23 15 0.47
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.17
Consensus pattern (22 bp):
GGAACCGATTCCCCCTCAAAGG
Found at i:12043 original size:33 final size:34
Alignment explanation
Indices: 12001--12067 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 34
11991 TCATTTAGGG
12001 GGGAATCGATA-CCCCTAGGGGGAATCTGTTCAC
1 GGGAATCGATACCCCCTAGGGGGAATCTGTTCAC
*
12034 GGGAATCGATACCCCCCCTGGGGGGAATCTGTTC
1 GGGAATCGATA--CCCCCTAGGGGGAATCTGTTC
12068 CCCCTGCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 11 0.37
36 19 0.63
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (34 bp):
GGGAATCGATACCCCCTAGGGGGAATCTGTTCAC
Found at i:15893 original size:31 final size:31
Alignment explanation
Indices: 15858--15997 Score: 210
Period size: 31 Copynumber: 4.5 Consensus size: 31
15848 ATAGATTCCA
* * * *
15858 AAGAACCTAGGTAATCAGTCCATATGTCCTG
1 AAGAACATAGGTAAACAATCCATATGTCCCG
15889 AAGAACATAGGTAAACAATCCATATGTCCCG
1 AAGAACATAGGTAAACAATCCATATGTCCCG
15920 AAGAACATAGGTAAACAA-CTCATATGTCCCG
1 AAGAACATAGGTAAACAATC-CATATGTCCCG
*
15951 AAGAACATAGGTAAGCAATCCATATGTCCCG
1 AAGAACATAGGTAAACAATCCATATGTCCCG
*
15982 AATAACATAGGTAAAC
1 AAGAACATAGGTAAAC
15998 CCTCGACTCT
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 1 0.01
31 98 0.98
32 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (31 bp):
AAGAACATAGGTAAACAATCCATATGTCCCG
Found at i:20016 original size:99 final size:98
Alignment explanation
Indices: 19877--20090 Score: 331
Period size: 99 Copynumber: 2.2 Consensus size: 98
19867 TAAAGGTTTT
* * * * *
19877 ATTTTTT-AATGTTTTTATTATGAGTTCAATTTTTTTAATAATTATTATTAAGTGTTACTCTTAT
1 ATTTTTTCAATATTTTTATTATGAGTTCAAATTTTCTAATAATTATTATTAAGGGCTACTCTTAT
19941 AATTTATTTTTTCTAATATTTAATAAATGCCTA
66 AATTTATTTTTTCTAATATTTAATAAATGCCTA
* *
19974 ATTTTTTCAATATTTATTATTATGGGTTCAAATTTTCTAATAATTATTATTAGGGGCTACTCTTA
1 ATTTTTTCAATATTT-TTATTATGAGTTCAAATTTTCTAATAATTATTATTAAGGGCTACTCTTA
*
20039 TAATTTATTTTTTCTAATATTTAATAAATGTCTA
65 TAATTTATTTTTTCTAATATTTAATAAATGCCTA
20073 ATTTTTTCCAATATTTTT
1 ATTTTTT-CAATATTTTT
20091 TTTTCTAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
97 7 0.07
98 6 0.06
99 85 0.80
100 8 0.08
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (98 bp):
ATTTTTTCAATATTTTTATTATGAGTTCAAATTTTCTAATAATTATTATTAAGGGCTACTCTTAT
AATTTATTTTTTCTAATATTTAATAAATGCCTA
Found at i:22295 original size:36 final size:36
Alignment explanation
Indices: 22248--22318 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
22238 GCTAAGTTTG
22248 GGGTTTTTTGCATTGACATCATATTTCTATCATATA
1 GGGTTTTTTGCATTGACATCATATTTCTATCATATA
22284 GGGTTTTTTGCATTGACATCATATTTCTATCATAT
1 GGGTTTTTTGCATTGACATCATATTTCTATCATAT
22319 TTCTATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (36 bp):
GGGTTTTTTGCATTGACATCATATTTCTATCATATA
Found at i:23126 original size:22 final size:22
Alignment explanation
Indices: 23101--23155 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
23091 ACTATATGGT
*
23101 ATGAACAGTACTGTGAATAGTA
1 ATGAACAATACTGTGAATAGTA
23123 ATGAACAATACTGTGAATAGTA
1 ATGAACAATACTGTGAATAGTA
23145 ATGAACAATAC
1 ATGAACAATAC
23156 CAAATGCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (22 bp):
ATGAACAATACTGTGAATAGTA
Found at i:23975 original size:23 final size:23
Alignment explanation
Indices: 23933--23976 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
23923 AATACACATA
*
23933 TGTCCCGAAGGACCATGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
23956 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
23977 CCCTCTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:26529 original size:16 final size:16
Alignment explanation
Indices: 26510--26552 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
26500 TTTCGGGTTG
26510 GGTTACTTTCGGTTCA
1 GGTTACTTTCGGTTCA
* *
26526 GGTTAATTTCTGTTCA
1 GGTTACTTTCGGTTCA
*
26542 AGTTACTTTCG
1 GGTTACTTTCG
26553 AGTCGGGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (16 bp):
GGTTACTTTCGGTTCA
Found at i:26562 original size:32 final size:32
Alignment explanation
Indices: 26511--26572 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
26501 TTCGGGTTGG
* *
26511 GTTACTTTCGGTTCAGGTTAATTTCTGTTCAA
1 GTTACTTTCGGTTCAGGTTAAATTCAGTTCAA
*
26543 GTTACTTTCGAG-TCGGGTTAAATTCAGTTC
1 GTTACTTTCG-GTTCAGGTTAAATTCAGTTC
26573 GGGTCGCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (32 bp):
GTTACTTTCGGTTCAGGTTAAATTCAGTTCAA
Found at i:26662 original size:16 final size:16
Alignment explanation
Indices: 26612--26662 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
26602 ATTCAGTTTC
26612 TTTCGGTTTGGATTAA
1 TTTCGGTTTGGATTAA
* **
26628 TTT-GGTTCTAG-TTGT
1 TTTCGGTT-TGGATTAA
26643 TTTCGGTTTGGATTAA
1 TTTCGGTTTGGATTAA
26659 TTTC
1 TTTC
26663 ATTTTGGGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.14, C:0.08, G:0.24, T:0.55
Consensus pattern (16 bp):
TTTCGGTTTGGATTAA
Found at i:26704 original size:32 final size:32
Alignment explanation
Indices: 26668--26730 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
26658 ATTTCATTTT
* * *
26668 GGGTTGCTTTTGGTTCGAGTTAATTTTGGTTC
1 GGGTTGCTTTCGATTCGAGTTAATTTCGGTTC
*
26700 GGGTTGCTTTCGATTCGGGTTAATTTCGGTT
1 GGGTTGCTTTCGATTCGAGTTAATTTCGGTT
26731 TGAATTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.11, G:0.32, T:0.48
Consensus pattern (32 bp):
GGGTTGCTTTCGATTCGAGTTAATTTCGGTTC
Found at i:38118 original size:19 final size:20
Alignment explanation
Indices: 38086--38131 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
38076 ATTATATATA
*
38086 TTTTTTGTTATTTTTCTGAT
1 TTTTTTATTATTTTTCTGAT
* *
38106 TTTTTTATT-TTTTTGTTAT
1 TTTTTTATTATTTTTCTGAT
38125 TTTTTTA
1 TTTTTTA
38132 CTTTCTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTTATTATTTTTCTGAT
Found at i:38140 original size:13 final size:13
Alignment explanation
Indices: 38124--38154 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
38114 TTTTTTGTTA
38124 TTTTTTTACTTTC
1 TTTTTTTACTTTC
38137 TTTTTTTACTTTC
1 TTTTTTTACTTTC
38150 TTTTT
1 TTTTT
38155 CTTTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTACTTTC
Found at i:38271 original size:15 final size:17
Alignment explanation
Indices: 38253--38284 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
38243 CATAATATAA
38253 TAAATT-CAA-ATAGAT
1 TAAATTGCAAGATAGAT
38268 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
38285 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:41874 original size:9 final size:9
Alignment explanation
Indices: 41860--42179 Score: 239
Period size: 9 Copynumber: 36.2 Consensus size: 9
41850 AATTAAATAA
*
41860 ATAATATGT
1 ATAATATAT
41869 ATAATATAT
1 ATAATATAT
*
41878 AT-ATGCTAT
1 ATAAT-ATAT
41887 ATAATATA-
1 ATAATATAT
*
41895 ATACTATAT
1 ATAATATAT
*
41904 AATAATACA-
1 -ATAATATAT
41913 ATAATATAT
1 ATAATATAT
41922 AT-ATATAT
1 ATAATATAT
41930 AT--TATAT
1 ATAATATAT
*
41937 ATAATATAA
1 ATAATATAT
41946 AT-ATA-AT
1 ATAATATAT
41953 ATAATATAT
1 ATAATATAT
*
41962 ATATTATAT
1 ATAATATAT
41971 AT-A-ATAT
1 ATAATATAT
41978 A-AATATAT
1 ATAATATAT
*
41986 ATATTATAT
1 ATAATATAT
*
41995 ATATTATAT
1 ATAATATAT
42004 ATAATATAT
1 ATAATATAT
42013 A-ATATATAAT
1 ATA-ATAT-AT
42023 ATAATATAT
1 ATAATATAT
*
42032 ATACTATAT
1 ATAATATAT
* *
42041 AGTATTGTATT
1 A-TAATATA-T
*
42052 ATAACATAT
1 ATAATATAT
42061 AT-ATATAT
1 ATAATATAT
42069 ATATATATAT
1 ATA-ATATAT
*
42079 ATACTATAT
1 ATAATATAT
42088 A-ATATAATAT
1 ATA-AT-ATAT
*
42098 ATAACATAT
1 ATAATATAT
42107 ATAA-A-AT
1 ATAATATAT
42114 ATAATACTAT
1 ATAATA-TAT
42124 ATAATATATT
1 ATAATATA-T
42134 ATAATA-AT
1 ATAATATAT
42142 AT-ATATACT
1 ATAATATA-T
42151 ATACACTATAT
1 ATA-A-TATAT
*
42162 AT-A-CTAT
1 ATAATATAT
42169 ATAATATAT
1 ATAATATAT
42178 AT
1 AT
42180 GTAAAAGGTC
Statistics
Matches: 253, Mismatches: 25, Indels: 66
0.74 0.07 0.19
Matches are distributed among these distances:
7 30 0.12
8 51 0.20
9 106 0.42
10 54 0.21
11 8 0.03
12 4 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (9 bp):
ATAATATAT
Found at i:41878 original size:7 final size:7
Alignment explanation
Indices: 41868--42178 Score: 194
Period size: 7 Copynumber: 44.6 Consensus size: 7
41858 AAATAATATG
41868 TATAATA
1 TATAATA
41875 TAT-ATA
1 TATAATA
*
41881 TGCTATATAA
1 T-ATA-AT-A
41891 TATAATA
1 TATAATA
41898 CTAT-ATA
1 -TATAATA
41905 -ATAATA
1 TATAATA
*
41911 CAATAATA
1 -TATAATA
41919 TATATATA
1 TATA-ATA
*
41927 TATATTA
1 TATAATA
41934 TAT-ATAA
1 TATAAT-A
41941 TATAA-A
1 TATAATA
41947 TATAATA
1 TATAATA
41954 TAATATATA
1 T-ATA-ATA
*
41963 TATTATA
1 TATAATA
41970 TATAATA
1 TATAATA
41977 TA-AATA
1 TATAATA
41983 TAT-ATA
1 TATAATA
41989 T-TATATA
1 TATA-ATA
*
41996 TATTATA
1 TATAATA
42003 TATAATA
1 TATAATA
42010 TATAATA
1 TATAATA
42017 TATAATA
1 TATAATA
42024 TA-ATATA
1 TATA-ATA
*
42031 TATACTA
1 TATAATA
*
42038 TATAGTA
1 TATAATA
*
42045 T-T-GTA
1 TATAATA
*
42050 TTATAACA
1 -TATAATA
42058 TAT-ATA
1 TATAATA
42064 TAT-ATA
1 TATAATA
42070 TATATATA
1 TATA-ATA
*
42078 TATACTA
1 TATAATA
42085 TAT-A-A
1 TATAATA
42090 TATAATA
1 TATAATA
*
42097 TATAACA
1 TATAATA
42104 TAT-ATA
1 TATAATA
42110 -A-AATA
1 TATAATA
*
42115 TAATACTA
1 T-ATAATA
42123 TATAATA
1 TATAATA
*
42130 TATTATA
1 TATAATA
42137 -ATAATA
1 TATAATA
42143 TAT-ATA
1 TATAATA
42149 CTATACACTA
1 -TATA-A-TA
42159 TATATACTA
1 TATA-A-TA
42168 TATAATA
1 TATAATA
42175 TATA
1 TATA
42179 TGTAAAAGGT
Statistics
Matches: 245, Mismatches: 23, Indels: 72
0.72 0.07 0.21
Matches are distributed among these distances:
5 14 0.06
6 49 0.20
7 118 0.48
8 39 0.16
9 21 0.09
10 4 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (7 bp):
TATAATA
Found at i:41879 original size:2 final size:2
Alignment explanation
Indices: 41863--42179 Score: 239
Period size: 2 Copynumber: 170.0 Consensus size: 2
41853 TAAATAAATA
* *
41863 AT AT GT AT A- AT AT AT AT AT GCT AT AT A- AT AT A- AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A-T AT AT
*
41904 A- AT A- AT AC A- AT A- AT AT AT AT AT AT AT AT -T 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 AT
*
41940 AT AT AA AT AT A- AT AT A- AT AT AT AT AT -T AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
41978 AA AT AT AT AT AT -T AT AT AT AT -T AT AT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
42016 AT AT A- AT AT A- AT AT AT AT ACT AT AT AGT AT -T GT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
*
42055 AC AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
42096 AT AT A- AC AT AT AT A- AA AT AT A- AT ACT AT AT A- AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
42134 AT A- AT A- AT AT AT AT ACT AT AC ACT AT AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT
42174 AT AT AT
1 AT AT AT
42180 GTAAAAGGTC
Statistics
Matches: 259, Mismatches: 15, Indels: 82
0.73 0.04 0.23
Matches are distributed among these distances:
1 32 0.12
2 211 0.81
3 16 0.06
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:41893 original size:5 final size:5
Alignment explanation
Indices: 41844--42176 Score: 156
Period size: 5 Copynumber: 66.6 Consensus size: 5
41834 TTAGACCTGA
* *
41844 ATAAT -TAAT -TAA- ATAA- ATAAT AT-GT ATAAT ATATAT ATGCTAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT AT--AAT
*
41887 ATAAT ATAAT ACT-AT ATAAT AATACA- ATAAT AT-AT ATATAT ATATT
1 ATAAT ATAAT A-TAAT ATAAT -ATA-AT ATAAT ATAAT ATA-AT ATAAT
*
41933 AT-AT ATAAT ATAAAT ATAAT ATAAT AT-AT ATATT AT-AT ATAAT ATAA-
1 ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
41980 ATATAT ATATT AT-AT ATATT AT-AT ATAAT AT-AT A-ATAT ATAAT ATAAT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT
* * * * *
42028 AT-AT ATACT AT-AT AGTATT GTATT ATAAC AT-AT ATATAT ATATAT
1 ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT
*
42073 ATATAT ATACTAT ATAAT ATAAT AT-AT A-ACAT AT-AT AAAAT ATAAT
1 ATA-AT ATA--AT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT
* *
42119 ACT-AT ATAAT ATATT ATAAT AATATAT ATACT ATACACT AT-AT ATACTAT
1 A-TAAT ATAAT ATAAT ATAAT -ATA-AT ATAAT ATA-A-T ATAAT ATA--AT
42169 ATAAT ATA
1 ATAAT ATA
42177 TATGTAAAAG
Statistics
Matches: 259, Mismatches: 26, Indels: 86
0.70 0.07 0.23
Matches are distributed among these distances:
4 64 0.25
5 127 0.49
6 47 0.18
7 21 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:45761 original size:21 final size:22
Alignment explanation
Indices: 45723--45763 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
45713 GTGATATATG
*
45723 AATATGAAATTATATGAAAAGT
1 AATATGAAATTACATGAAAAGT
*
45745 AATATG-AATTACGTGAAAA
1 AATATGAAATTACATGAAAA
45764 AAAGCTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (22 bp):
AATATGAAATTACATGAAAAGT
Found at i:45917 original size:18 final size:18
Alignment explanation
Indices: 45894--45951 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 18
45884 AGGGTTCTAC
45894 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
45912 GTGGTCCTTCGGGAAATTTCATA
1 GTGGTCCTTCGGG--A---CATA
45935 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
45952 TTCATAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 16 0.46
20 1 0.03
21 1 0.03
23 17 0.49
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:45938 original size:23 final size:23
Alignment explanation
Indices: 45908--45971 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
45898 TCCTTCGGGA
45908 CATAGTGGTCCTTCGGGAAATTT
1 CATAGTGGTCCTTCGGGAAATTT
*
45931 CATAGTGGTCCTTCGGGACATTT
1 CATAGTGGTCCTTCGGGAAATTT
* * *
45954 CATAATAGTCATTCGGGA
1 CATAGTGGTCCTTCGGGA
45972 CAAATTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (23 bp):
CATAGTGGTCCTTCGGGAAATTT
Found at i:46118 original size:18 final size:20
Alignment explanation
Indices: 46097--46134 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
46087 ATAACTTTGA
46097 ATACA-ATG-TATGTAATAT
1 ATACATATGATATGTAATAT
*
46115 ATACATATGATGTGTAATAT
1 ATACATATGATATGTAATAT
46135 GAATTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
ATACATATGATATGTAATAT
Found at i:50414 original size:18 final size:20
Alignment explanation
Indices: 50393--50430 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
50383 ATAACTTTGA
50393 ATACA-ATG-TATGTAATAT
1 ATACATATGATATGTAATAT
*
50411 ATACATATGATGTGTAATAT
1 ATACATATGATATGTAATAT
50431 GAATTGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
ATACATATGATATGTAATAT
Found at i:57253 original size:18 final size:18
Alignment explanation
Indices: 57230--57264 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57220 AGGGTTCTAC
*
57230 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAAGACATA
57248 GTGGTCCTTCAAGACAT
1 GTGGTCCTTCAAGACAT
57265 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCAAGACATA
Found at i:63837 original size:2 final size:2
Alignment explanation
Indices: 63832--63873 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
63822 AAAAATGGAA
63832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63874 GCGAAAGGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67029 original size:24 final size:24
Alignment explanation
Indices: 66974--67029 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
66964 ACAGAGGCCA
*
66974 GTGCTTTTGTAGAAGACGAAGCTT
1 GTGCTTTTATAGAAGACGAAGCTT
* * *
66998 GCAG-TTTTATAGCAGATGAAGCTT
1 G-TGCTTTTATAGAAGACGAAGCTT
67022 GTGCTTTT
1 GTGCTTTT
67030 GCAGTAGATG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 1 0.04
24 23 0.92
25 1 0.04
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (24 bp):
GTGCTTTTATAGAAGACGAAGCTT
Found at i:68976 original size:3 final size:3
Alignment explanation
Indices: 68968--68999 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
68958 GGATACTATC
68968 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
69000 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:77699 original size:8 final size:8
Alignment explanation
Indices: 77680--77756 Score: 74
Period size: 9 Copynumber: 9.8 Consensus size: 8
77670 TTAAAGATAA
77680 AAAAAATG
1 AAAAAATG
77688 -AAAAATG
1 AAAAAATG
77695 AAAAAAATGG
1 -AAAAAAT-G
77705 AAAAAATG
1 AAAAAATG
77713 AAAAAATG
1 AAAAAATG
*
77721 -AAATA-G
1 AAAAAATG
77727 -AAAAATAG
1 AAAAAAT-G
77735 AAAAAATGG
1 AAAAAAT-G
77744 AAAAAAT-
1 AAAAAATG
77751 AAAAAA
1 AAAAAA
77757 AAAGAAGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.08
7 17 0.28
8 10 0.17
9 27 0.45
10 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:77700 original size:9 final size:9
Alignment explanation
Indices: 77679--77768 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
77669 GTTAAAGATA
77679 AAAAAAATG
1 AAAAAAATG
77688 --AAAAATG
1 AAAAAAATG
77695 AAAAAAATG
1 AAAAAAATG
*
77704 GAAAAAATG
1 AAAAAAATG
77713 -AAAAAATG
1 AAAAAAATG
77721 AAATAGAAAAAT-
1 --A-A-AAAAATG
77733 AGAAAAAATG
1 A-AAAAAATG
* *
77743 GAAAAAATA
1 AAAAAAATG
*
77752 AAAAAAAAG
1 AAAAAAATG
77761 AAGAAAAA
1 AA-AAAAA
77769 AAACAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
7 7 0.11
8 8 0.12
9 36 0.55
10 7 0.11
12 1 0.02
13 6 0.09
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:77731 original size:39 final size:38
Alignment explanation
Indices: 77683--77757 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 38
77673 AAGATAAAAA
*
77683 AAATGAAAAAT-GAAAAAAATGGAAAAAATGAAAAAATG
1 AAATGAAAAATAG-AAAAAATGGAAAAAATAAAAAAATG
77721 AAATAGAAAAATAGAAAAAATGGAAAAAATAAAAAAA
1 AAAT-GAAAAATAGAAAAAATGGAAAAAATAAAAAAA
77758 AAGAAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 4 0.12
39 29 0.85
40 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (38 bp):
AAATGAAAAATAGAAAAAATGGAAAAAATAAAAAAATG
Found at i:77767 original size:18 final size:17
Alignment explanation
Indices: 77676--77785 Score: 66
Period size: 18 Copynumber: 6.4 Consensus size: 17
77666 TTGGTTAAAG
*
77676 ATAAAAAAAATG-AAAA
1 ATAAAAAAAAAGAAAAA
**
77692 ATGAAAAAAATGGAAAAA
1 AT-AAAAAAAAAGAAAAA
*
77710 ATGAAAAAATGAAATAGAAAA
1 AT-AAAAAA--AAAGA-AAAA
**
77731 ATAGAAAAAATGGAAAAA
1 ATA-AAAAAAAAGAAAAA
*
77749 ATAAAAAAAAAG-AAGA
1 ATAAAAAAAAAGAAAAA
*
77765 A-AAAAAACAA-AAAAA
1 ATAAAAAAAAAGAAAAA
77780 ATAAAA
1 ATAAAA
77786 GGGGGTTCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
15 12 0.16
16 10 0.14
17 15 0.21
18 20 0.27
19 2 0.03
20 3 0.04
21 11 0.15
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.10
Consensus pattern (17 bp):
ATAAAAAAAAAGAAAAA
Found at i:77771 original size:31 final size:29
Alignment explanation
Indices: 77705--77785 Score: 72
Period size: 31 Copynumber: 2.7 Consensus size: 29
77695 AAAAAAATGG
* * * *
77705 AAAAAATGAAAAAATGAAATAGAAAAATAG
1 AAAAAATGAAAAAAT-AAAAAAAAAAAGAA
77735 AAAAAATGGAAAAAATAAAAAAAAAGAAGAA
1 AAAAAAT-GAAAAAATAAAAAAAAA-AAGAA
**
77766 AAAAAACAAAAAAAATAAAA
1 AAAAAA-TGAAAAAATAAAA
77786 GGGGGTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 14 0.33
31 28 0.67
ACGTcount: A:0.80, C:0.01, G:0.10, T:0.09
Consensus pattern (29 bp):
AAAAAATGAAAAAATAAAAAAAAAAAGAA
Found at i:77778 original size:39 final size:38
Alignment explanation
Indices: 77678--77779 Score: 100
Period size: 39 Copynumber: 2.7 Consensus size: 38
77668 GGTTAAAGAT
* ** *
77678 AAAAA-AAATGAAAAATGAAAAAAATGGAAAAAATGAA
1 AAAAAGAAATAAAAAAACAAAAAAATGGAAAAAATAAA
* * *
77715 AAAATGAAATAGAAAAATAGAAAAAATGGAAAAAATAAAA
1 AAAAAGAAATAAAAAAACA-AAAAAATGGAAAAAAT-AAA
77755 AAAAAGAAGA-AAAAAAACAAAAAAA
1 AAAAAGAA-ATAAAAAAACAAAAAAA
77780 ATAAAAGGGG
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
37 4 0.08
38 9 0.17
39 22 0.42
40 16 0.31
41 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (38 bp):
AAAAAGAAATAAAAAAACAAAAAAATGGAAAAAATAAA
Found at i:79172 original size:55 final size:55
Alignment explanation
Indices: 79073--79350 Score: 447
Period size: 55 Copynumber: 5.1 Consensus size: 55
79063 TGAAGCAAAA
79073 GAAGATTGTTCGAGTCTTATA--CTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
79126 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
79181 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGAGGCAGACGCGATCTTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
79234 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
79289 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
79344 GGAGATT
1 GAAGATT
79351 ATTGTTCGAG
Statistics
Matches: 204, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
53 65 0.32
54 6 0.03
55 133 0.65
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:79262 original size:108 final size:110
Alignment explanation
Indices: 79073--79353 Score: 471
Period size: 108 Copynumber: 2.6 Consensus size: 110
79063 TGAAGCAAAA
79073 GAAGATTGTTCGAGTCTTATA--CTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
79136 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* * * *
79181 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGAGGCAGACGCGATCTTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
79244 CGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
*
79289 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
79354 GTTCGAGTTC
Statistics
Matches: 158, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
106 7 0.04
107 3 0.02
108 98 0.62
109 3 0.02
110 47 0.30
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:79406 original size:52 final size:52
Alignment explanation
Indices: 79346--79742 Score: 686
Period size: 52 Copynumber: 7.6 Consensus size: 52
79336 CGATCGTTGG
* *
79346 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
79398 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
79450 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
79502 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
79554 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * *
79606 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
*
79658 AGATTATTGTTTGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
79710 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
79743 TAGAGAGCGA
Statistics
Matches: 325, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 325 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
Found at i:80008 original size:3 final size:3
Alignment explanation
Indices: 80000--80031 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
79990 GGATACTATC
80000 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
80032 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:81297 original size:146 final size:146
Alignment explanation
Indices: 81027--81301 Score: 345
Period size: 146 Copynumber: 1.9 Consensus size: 146
81017 TCTCGCCGGA
* *
81027 GATCGGGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
* ** * ** *
81092 TTGAAAATTCAAGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAACATATCCGGACGGTTT
66 TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
81157 TTAGCCTCTTGCTGGT
131 TTAGCCTCTTGCTGGT
* * * * * *
81173 GATCGGAATCTTCGATCAATATTCCGAACGGTGAAAAGTTGTGTG-ATGCCAACACGAACAACCT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGGCCAACACGAACAACAT
* * * * * *
81237 ATTGAAAAATCAGGACGATTGGACGGTGGATGACGGCAGATCAAAGAAAATACATTCGGACGGTT
65 ATTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTT
81302 ATCTTTGTAT
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
146 106 0.99
147 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (146 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCAACACGAACAACATA
TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
TTAGCCTCTTGCTGGT
Found at i:84678 original size:23 final size:20
Alignment explanation
Indices: 84639--84707 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 20
84629 AAAATTAACC
* *
84639 TAAAGAATAAATCAAATTAATGT
1 TAAATAATAAAT-AAATTAA--A
84662 TAAATAATAAAATAAA-TAAA
1 TAAATAAT-AAATAAATTAAA
84682 TAAATAATAAATAAA-TAAA
1 TAAATAATAAATAAATTAAA
84701 TAAATAA
1 TAAATAA
84708 AAGAATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 18 0.42
20 8 0.19
22 3 0.07
23 10 0.23
24 4 0.09
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAATAATAAATAAATTAAA
Found at i:84679 original size:12 final size:12
Alignment explanation
Indices: 84676--84721 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
84666 TAATAAAATA
*
84676 AATAAAT-AAAT
1 AATAAATAAAAG
84687 AATAAATAAATA-
1 AATAAATAAA-AG
84699 AATAAATAAAAG
1 AATAAATAAAAG
84711 AATAAA-AAAAG
1 AATAAATAAAAG
84722 GAAAATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 13 0.41
12 18 0.56
13 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (12 bp):
AATAAATAAAAG
Found at i:84680 original size:4 final size:4
Alignment explanation
Indices: 84662--84708 Score: 71
Period size: 4 Copynumber: 12.0 Consensus size: 4
84652 AAATTAATGT
84662 TAAA T-AA TAAAA TAAA TAAA TAAA T-AA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
84709 AGAATAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.15
4 31 0.77
5 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:86255 original size:5 final size:5
Alignment explanation
Indices: 85998--86239 Score: 369
Period size: 5 Copynumber: 49.6 Consensus size: 5
85988 TTGGATCTGA
*
85998 ATAAT -TAAT -TAA- ATAA- ATAA- ATAAT ATAAT A-AAT AATATGT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATA-AT ATAAT
86044 ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAA-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
86091 ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
86140 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
86190 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AATATAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATA-AT ATAAT ATA
86240 CATTATATAT
Statistics
Matches: 224, Mismatches: 2, Indels: 22
0.90 0.01 0.09
Matches are distributed among these distances:
3 2 0.01
4 31 0.14
5 178 0.79
6 10 0.04
7 3 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:86476 original size:16 final size:16
Alignment explanation
Indices: 86457--86513 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
86447 TTATAATCAT
86457 AATAATTTAATTAAAA
1 AATAATTTAATTAAAA
*
86473 AATAGTTTAATTAAAA
1 AATAATTTAATTAAAA
86489 AATAATTTAATTAAAA
1 AATAATTTAATTAAAA
86505 AATAATTTA
1 AATAATTTA
86514 CGGATCCCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATAATTTAATTAAAA
Found at i:87917 original size:2 final size:2
Alignment explanation
Indices: 87910--87959 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
87900 TATTTGGCAG
87910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87952 AT AT AT AT
1 AT AT AT AT
87960 CGCTTAATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93262 original size:2 final size:2
Alignment explanation
Indices: 93255--93298 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
93245 TACTTGAAAT
93255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
93297 TA
1 TA
93299 ACTGAATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101719 original size:113 final size:111
Alignment explanation
Indices: 101507--101728 Score: 302
Period size: 113 Copynumber: 2.0 Consensus size: 111
101497 AGAGATCCAC
* * *
101507 CCAAAACCAACCCACTTAAGTTGAAAAACTGTCTTTAACAAAGTAAATTGACCGGTTACCAATAC
1 CCAAAACCAACCCACTTAAGTTGAAAAACTGTCTTTAACAAAGTAAATGGACCAGTGACCAATAC
* *
101572 CAAATGGAAAATTTACATGGGAAGTGTCAAAGATCCACCCAATAGG
66 CAAATGGAAAATTTACATGGGAAATATCAAAGATCCACCCAATAGG
* * *
101618 CCAATACCAACCCGCTTACGTTGAAAAACTGTGCCTTTAACAAAGTAAATGGACCAGTGACCAAT
1 CCAAAACCAACCCACTTAAGTTGAAAAACTGT--CTTTAACAAAGTAAATGGACCAGTGACCAAT
* * * *
101683 ACC-ACTCGGAGAATTTTCATGGGAAATATCAGAGATCCACCCAATA
64 ACCAAAT-GGAAAATTTACATGGGAAATATCAAAGATCCACCCAATA
101729 CGAACCCGCA
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
111 29 0.30
112 2 0.02
113 65 0.68
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (111 bp):
CCAAAACCAACCCACTTAAGTTGAAAAACTGTCTTTAACAAAGTAAATGGACCAGTGACCAATAC
CAAATGGAAAATTTACATGGGAAATATCAAAGATCCACCCAATAGG
Found at i:103287 original size:11 final size:11
Alignment explanation
Indices: 103271--103334 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
103261 TGGGGCAATG
103271 TCGAGCTTGAA
1 TCGAGCTTGAA
*
103282 TCGAGCTCAGAA
1 TCGAGCT-TGAA
103294 TCGAGCTTGAA
1 TCGAGCTTGAA
*
103305 TCGAGCTAAGAA
1 TCGAGCT-TGAA
* *
103317 TCAAGCTTCAA
1 TCGAGCTTGAA
103328 TCGAGCT
1 TCGAGCT
103335 CGAGTCTCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 25 0.57
12 19 0.43
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:103296 original size:12 final size:12
Alignment explanation
Indices: 103279--103335 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
103269 TGTCGAGCTT
103279 GAATCGAGCTCA
1 GAATCGAGCTCA
*
103291 GAATCGAGCT-T
1 GAATCGAGCTCA
*
103302 GAATCGAGCTAA
1 GAATCGAGCTCA
*
103314 GAATCAAGCTTC-
1 GAATCGAGC-TCA
103326 -AATCGAGCTC
1 GAATCGAGCTC
103336 GAGTCTCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 2 0.05
11 17 0.45
12 18 0.47
13 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (12 bp):
GAATCGAGCTCA
Found at i:103301 original size:23 final size:23
Alignment explanation
Indices: 103271--103335 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
103261 TGGGGCAATG
103271 TCGAGCTTGAATCGAGCTCAGAA
1 TCGAGCTTGAATCGAGCTCAGAA
*
103294 TCGAGCTTGAATCGAGCTAAGAA
1 TCGAGCTTGAATCGAGCTCAGAA
* *
103317 TCAAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
103336 GAGTCTCGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCAGAA
Found at i:103644 original size:53 final size:55
Alignment explanation
Indices: 103562--103684 Score: 205
Period size: 53 Copynumber: 2.3 Consensus size: 55
103552 CTTATGTTCG
103562 TATTCGTTTATGTTCTTTTATTTATTAAATAAACGAACATGAACAAAAAA-AA-T
1 TATTCGTTTATGTTCTTTTATTTATTAAATAAACGAACATGAACAAAAAATAATT
* * *
103615 TGTTCGTATATGTTCTTTTATTTATTAAATGAACGAACATGAACAAAAAATAATT
1 TATTCGTTTATGTTCTTTTATTTATTAAATAAACGAACATGAACAAAAAATAATT
103670 TATTCGTTTATGTTC
1 TATTCGTTTATGTTC
103685 GTGTTCGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 47 0.75
54 2 0.03
55 14 0.22
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (55 bp):
TATTCGTTTATGTTCTTTTATTTATTAAATAAACGAACATGAACAAAAAATAATT
Found at i:103693 original size:16 final size:16
Alignment explanation
Indices: 103672--103702 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
103662 AAATAATTTA
103672 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
103688 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
103703 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:108730 original size:25 final size:27
Alignment explanation
Indices: 108678--108744 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 27
108668 TAGAGGGAAA
* * *
108678 AAATGAATAAATGAAAAAATGAAGAAT
1 AAATAAATAAATAAAAAAAGGAAGAAT
108705 -AA-AAATAAATAAAAAAAGGATA-AAT
1 AAATAAATAAATAAAAAAAGGA-AGAAT
108730 AAATAAATAAATAAA
1 AAATAAATAAATAAA
108745 TGAAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 18 0.53
26 5 0.15
27 11 0.32
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (27 bp):
AAATAAATAAATAAAAAAAGGAAGAAT
Found at i:108764 original size:2 final size:2
Alignment explanation
Indices: 108757--108819 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
108747 AAATATTAAA
108757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
108799 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
108820 AATGAGTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:108885 original size:18 final size:18
Alignment explanation
Indices: 108836--108889 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
108826 TAAATAGAAA
*
108836 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
108857 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
108876 AATA-TAATATAAAA
1 AATAGTAATATAAAA
108890 AAAACCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:108891 original size:19 final size:19
Alignment explanation
Indices: 108836--108890 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
108826 TAAATAGAAA
* *
108836 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAAAAAT-AT
*
108857 AATAGTAATATGAAAATAT
1 AATAGTAATATAAAAATAT
108876 AATA-TAATATAAAAA
1 AATAGTAATATAAAAA
108891 AAACCAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 6 0.20
21 8 0.27
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAGTAATATAAAAATAT
Found at i:109122 original size:19 final size:19
Alignment explanation
Indices: 109091--109128 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
109081 AAAAGTATAT
*
109091 ATATATATATAAATAATAA
1 ATATATATATAAAAAATAA
109110 ATATAGTAT-TAAAAAATAA
1 ATATA-TATATAAAAAATAA
109129 CCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATATATATAAAAAATAA
Found at i:109746 original size:37 final size:37
Alignment explanation
Indices: 109661--109754 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
109651 GGATCTTATC
* * * * *
109661 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGCAAAACTCTATCATATT
*
109698 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGCAAAACTCTATCATATT
*
109735 TTTAGGAGTTTGAATTCTAG
1 TTTAGGAGTTTGAATCCTAG
109755 TAGGACGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGCAAAACTCTATCATATT
Found at i:110806 original size:106 final size:106
Alignment explanation
Indices: 110488--112173 Score: 2564
Period size: 106 Copynumber: 16.0 Consensus size: 106
110478 GCATTGTTCT
* ** * *
110488 GAGTCCAATATCC-TCTG-TCGTGAAGTTGAAATTGGCTCTGGAATCAGGAAATTATTTGTTGAC
1 GAGTCCAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* * *
110551 AACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
110594 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
110653 TCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
110695 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
110759 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
110800 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
110865 CCAGCGGTCTCTTCGTAGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
110906 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
110971 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
111012 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
111077 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
111118 GAGTCCAATATCCTTCGATGTGACGTTGAAATTGGATCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
111183 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
111224 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
111289 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * **
111330 GAGTCCAATATACTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
111395 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
111436 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
111501 CCAGCGGTCCCTTCGTCTTGAAGTTGAATTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
111542 GAGTCCAATATTCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
111607 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
111648 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
111713 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
111754 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
111819 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
111860 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
111925 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
111966 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
112031 CCAGCAATCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
112072 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
112137 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
112174 CCTTGAGTGG
Statistics
Matches: 1445, Mismatches: 124, Indels: 22
0.91 0.08 0.01
Matches are distributed among these distances:
99 1 0.00
100 78 0.05
101 5 0.00
102 4 0.00
104 3 0.00
105 5 0.00
106 1346 0.93
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:113012 original size:22 final size:22
Alignment explanation
Indices: 112986--113062 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
112976 TTATGTTTGG
*
112986 TCAAAGGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
113008 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
113030 T-AATAGGTTTGGCATTTGATGC
1 TCAA-AGGTTTGGCATTTGATGC
*
113052 TCAACGGTTTG
1 TCAAAGGTTTG
113063 ATGGGGTAGC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.04
22 47 0.92
23 2 0.04
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:113756 original size:172 final size:171
Alignment explanation
Indices: 113459--113805 Score: 597
Period size: 172 Copynumber: 2.0 Consensus size: 171
113449 TAAATAGGCC
*
113459 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTTCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATC----TCTG
113524 CTCAAAATGTCTCTCTCTCGATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCGGGAATG
62 CTCAAAATGTCTCTCTCTCGATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCGGGAATG
113589 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
127 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
*
113634 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTCAATC-CTGCTCA
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATCTCTGCTCA
* *
113698 AAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGAT
66 AAATG--TCTCTCTCTCGATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCGGGAATGAT
113763 TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
113806 GTCTTTAGGG
Statistics
Matches: 166, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
170 12 0.07
172 99 0.60
175 55 0.33
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (171 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAATCTCTGCTCA
AAATGTCTCTCTCTCGATGCTCTATGATCTTCGAGTGAAATGATTCAGTGATTCGGGAATGATTG
TGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:113857 original size:23 final size:24
Alignment explanation
Indices: 113831--113880 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
113821 TTGCATGTGT
113831 TTTTTGTCCCT-TTTTCTTTTTTC
1 TTTTTGTCCCTGTTTTCTTTTTTC
* *
113854 TTTTTGTTCTTGTTTTCTTTTTTC
1 TTTTTGTCCCTGTTTTCTTTTTTC
113878 TTT
1 TTT
113881 GTTTTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (24 bp):
TTTTTGTCCCTGTTTTCTTTTTTC
Found at i:113879 original size:31 final size:31
Alignment explanation
Indices: 113841--113926 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 31
113831 TTTTTGTCCC
113841 TTTTTCTTTTTTCTTTTTGTTCTTGTT-TTCT
1 TTTTTCTTTTTTCTTTTTGTTCTTGTTGTT-T
*
113872 TTTTTCTTTGTT-TTTTTGTT-TT-TTGTTT
1 TTTTTCTTTTTTCTTTTTGTTCTTGTTGTTT
*
113900 TTTTGCTTCTTTTCTTTTTTGTTCTTG
1 TTTTTCTT-TTTTC-TTTTTGTTCTTG
113927 ATTGGATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 10 0.22
29 7 0.15
30 8 0.17
31 19 0.41
32 2 0.04
ACGTcount: A:0.00, C:0.10, G:0.09, T:0.80
Consensus pattern (31 bp):
TTTTTCTTTTTTCTTTTTGTTCTTGTTGTTT
Found at i:113890 original size:24 final size:24
Alignment explanation
Indices: 113842--113893 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
113832 TTTTGTCCCT
113842 TTTTCTTTTTTCTTTTTGTTCTTG
1 TTTTCTTTTTTCTTTTTGTTCTTG
*
113866 TTTTCTTTTTTCTTTGTT-TTTTTG
1 TTTTCTTTTTTCTTT-TTGTTCTTG
113890 TTTT
1 TTTT
113894 TTGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.83
Consensus pattern (24 bp):
TTTTCTTTTTTCTTTTTGTTCTTG
Found at i:113900 original size:24 final size:24
Alignment explanation
Indices: 113849--113922 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
113839 CCTTTTTCTT
*
113849 TTTTCTTT-TTGTTCTTGTTTTCTT-
1 TTTTCTTTGTT-TTTTTGTTTT-TTG
113873 TTTTCTTTGTTTTTTTGTTTTTTG
1 TTTTCTTTGTTTTTTTGTTTTTTG
* *
113897 TTTT-TTTGCTTCTTTTCTTTTTTG
1 TTTTCTTTG-TTTTTTTGTTTTTTG
113921 TT
1 TT
113923 CTTGATTGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.14
24 36 0.82
25 2 0.05
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (24 bp):
TTTTCTTTGTTTTTTTGTTTTTTG
Found at i:113924 original size:15 final size:14
Alignment explanation
Indices: 113848--113925 Score: 77
Period size: 15 Copynumber: 5.1 Consensus size: 14
113838 CCCTTTTTCT
113848 TTTTTCTTTTTGTTC
1 TTTTT-TTTTTGTTC
113863 TTGTTTTCTTTT-TTC
1 TT-TTTT-TTTTGTTC
*
113878 TTTGTTTTTTTGTTT
1 TTT-TTTTTTTGTTC
113893 TTTGTTTTTTTGCTTC
1 TTT-TTTTTTTG-TTC
113909 TTTTCTTTTTTGTTC
1 TTTT-TTTTTTGTTC
113924 TT
1 TT
113926 GATTGGATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 5 0.09
15 31 0.56
16 19 0.35
ACGTcount: A:0.00, C:0.10, G:0.09, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTGTTC
Found at i:118104 original size:25 final size:27
Alignment explanation
Indices: 118047--118118 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 27
118037 TGTGTTAGAG
* * * *
118047 AGAAAAAATGAATAAATGAAAAAATGA
1 AGAATAAATAAATAAATAAAAAAAGGA
118074 AGAAT-AA-AAATAAATAAAAAAAGGA
1 AGAATAAATAAATAAATAAAAAAAGGA
118099 TA-AATAAATAAATAAATAAA
1 -AGAATAAATAAATAAATAAA
118119 TGAAATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
25 18 0.47
26 5 0.13
27 15 0.39
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (27 bp):
AGAATAAATAAATAAATAAAAAAAGGA
Found at i:119069 original size:36 final size:36
Alignment explanation
Indices: 119003--119097 Score: 136
Period size: 36 Copynumber: 2.6 Consensus size: 36
118993 GGATCTTATC
* * *
119003 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATC-TAGTAAAACTCTATCATATT
*
119040 TTTAGGAGTTTGAATCTAGTAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCTAGTAAAACTCTATCATATT
119076 TTTAGGAGTTTGAATTCTAGTA
1 TTTAGGAGTTTGAA-TCTAGTA
119098 GGACGAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 31 0.58
37 22 0.42
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (36 bp):
TTTAGGAGTTTGAATCTAGTAAAACTCTATCATATT
Found at i:121219 original size:23 final size:21
Alignment explanation
Indices: 121166--121226 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
121156 ATCAATACCC
121166 CCTTG-ATATGTATCGATACA
1 CCTTGAATATGTATCGATACA
*
121186 -CTATGAATATGTACCGATACA
1 CCT-TGAATATGTATCGATACA
121207 TTCCTTGAATATGTATCGAT
1 --CCTTGAATATGTATCGAT
121227 GCACTCCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 14 0.41
23 14 0.41
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (21 bp):
CCTTGAATATGTATCGATACA
Found at i:121234 original size:23 final size:23
Alignment explanation
Indices: 121166--121234 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
121156 ATCAATACCC
121166 CCTTG-ATATGTATCGATACACT
1 CCTTGAATATGTATCGATACACT
* * *
121188 --ATGAATATGTACCGATACATT
1 CCTTGAATATGTATCGATACACT
*
121209 CCTTGAATATGTATCGATGCACT
1 CCTTGAATATGTATCGATACACT
121232 CCT
1 CCT
121235 AGGTGTACCA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.05
21 15 0.41
23 20 0.54
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (23 bp):
CCTTGAATATGTATCGATACACT
Found at i:121667 original size:17 final size:19
Alignment explanation
Indices: 121641--121680 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
121631 AAAAAATTGA
121641 TTTTATTTTAAAT-TGTTT
1 TTTTATTTTAAATATGTTT
*
121659 TTTTA-TTTAATTATGTTT
1 TTTTATTTTAAATATGTTT
121677 TTTT
1 TTTT
121681 CATGAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTTATTTTAAATATGTTT
Found at i:125687 original size:42 final size:42
Alignment explanation
Indices: 125640--125731 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
125630 ATTTCAATAA
* * * *
125640 TGACAAAAATAATTGTCGTCGC-AAATTACCAATTAAGACTAG
1 TGACAAAAACAATTGTCATC-CTAAATTACCAACTAAAACTAG
*
125682 TGACAAAAACAATTGTCATCCTCAATTACCAACTAAAACTAG
1 TGACAAAAACAATTGTCATCCTAAATTACCAACTAAAACTAG
*
125724 TAACAAAA
1 TGACAAAA
125732 TGTTTTCATC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.24
Consensus pattern (42 bp):
TGACAAAAACAATTGTCATCCTAAATTACCAACTAAAACTAG
Found at i:126453 original size:7 final size:7
Alignment explanation
Indices: 126441--126465 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
126431 AGAAGCCTGA
126441 AATCTGG
1 AATCTGG
126448 AATCTGG
1 AATCTGG
126455 AATCTGG
1 AATCTGG
126462 AATC
1 AATC
126466 CCAGAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (7 bp):
AATCTGG
Found at i:127877 original size:20 final size:20
Alignment explanation
Indices: 127852--127898 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
127842 CACCCGCAGC
127852 ATCCATCCACCCATTAATAT
1 ATCCATCCACCCATTAATAT
*
127872 ATCCATCCACTCATTAATAT
1 ATCCATCCACCCATTAATAT
127892 ATCCATC
1 ATCCATC
127899 TATCCATATA
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:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (20 bp):
ATCCATCCACCCATTAATAT
Found at i:127903 original size:24 final size:22
Alignment explanation
Indices: 127855--127904 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
127845 CCGCAGCATC
127855 CATCCACCCATTAATATATC--
1 CATCCACCCATTAATATATCAT
*
127875 CATCCACTCATTAATATATCCAT
1 CATCCACCCATTAATATAT-CAT
127898 CTATCCA
1 C-ATCCA
127905 TATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 18 0.72
21 1 0.04
23 1 0.04
24 5 0.20
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (22 bp):
CATCCACCCATTAATATATCAT
Found at i:128275 original size:17 final size:17
Alignment explanation
Indices: 128226--128275 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
128216 TTGTTCATGT
128226 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
128243 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
128257 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
128274 TT
1 TT
128276 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:128908 original size:7 final size:7
Alignment explanation
Indices: 128890--128926 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
128880 AAACAGGATT
128890 AAATTAAA
1 AAATT-AA
128898 AAATTAA
1 AAATTAA
128905 AAATTAA
1 AAATTAA
128912 AAA-TAA
1 AAATTAA
128918 AAA-TAA
1 AAATTAA
128924 AAA
1 AAA
128927 CTATTGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.41
7 12 0.41
8 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAATTAA
Found at i:132192 original size:18 final size:18
Alignment explanation
Indices: 132171--132221 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
132161 GTTAAAGTTA
**
132171 ATTTATTTAATTTTTCTT
1 ATTTATTTAATTTTAATT
*
132189 ATTTATTTTATTTTAATT
1 ATTTATTTAATTTTAATT
132207 A-TTACTTTAATTTTA
1 ATTTA-TTTAATTTTA
132222 CTGACATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTTAATTTTAATT
Found at i:136218 original size:3 final size:3
Alignment explanation
Indices: 136212--136272 Score: 54
Period size: 3 Copynumber: 19.3 Consensus size: 3
136202 CACCCCCAGG
*
136212 TCT TCT TCT TCT TCCT TCT T-T AT-T TCT TCCT CCT TCAT TCT TCCT
1 TCT TCT TCT TCT T-CT TCT TCT -TCT TCT T-CT TCT TC-T TCT T-CT
136257 TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT T
136273 GTTGCACAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 2 0.04
3 37 0.74
4 11 0.22
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:137176 original size:3 final size:3
Alignment explanation
Indices: 137168--137214 Score: 58
Period size: 3 Copynumber: 14.3 Consensus size: 3
137158 GCCACTGTGC
137168 AAG AAG AAG AAG AAG AAG AAAG AAAG AAAG AAGG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG -AAG -AAG -AAG AA-G AAG AAG AAG AAG A
137215 CCTGGGGGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 28 0.67
4 14 0.33
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:138267 original size:111 final size:113
Alignment explanation
Indices: 138065--138268 Score: 288
Period size: 111 Copynumber: 1.8 Consensus size: 113
138055 TTGGGATAAC
** *
138065 AATAGTGGCGTTTGTTTGAAAAAAAATCGTCGCAATAGGTCCATCTATAGTGGTGTTTATTGAAA
1 AATAGTGGCGTTTGTTTG-AAAAAAATCGTCGCAATAAATCCATCTATAGTGGTATTTATTGAAA
* * *
138130 AAACGTCACTATATATTTTCTTTTTTGGATTTTTGGGGGCCTGCGTAAT
65 AAACGTCACTATATATATACTATTTTGGATTTTTGGGGGCCTGCGTAAT
*
138179 AATAGTGGCGTTT-TTCTG-AAAAAA-CGTCGCAATAAATCTATCTATAGTGGTATTTATTGAAA
1 AATAGTGGCGTTTGTT-TGAAAAAAATCGTCGCAATAAATCCATCTATAGTGGTATTTATTGAAA
* *
138241 AAATGTCATTATATATATACTATTTTGG
65 AAACGTCACTATATATATACTATTTTGG
138269 GGCCCTGCGC
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 57 0.71
112 6 0.08
113 2 0.03
114 15 0.19
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (113 bp):
AATAGTGGCGTTTGTTTGAAAAAAATCGTCGCAATAAATCCATCTATAGTGGTATTTATTGAAAA
AACGTCACTATATATATACTATTTTGGATTTTTGGGGGCCTGCGTAAT
Found at i:138699 original size:24 final size:23
Alignment explanation
Indices: 138672--138726 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
138662 AAATTAAACA
*
138672 AGCTTATAAGCGAACTTATAAATG
1 AGCTTATAA-CGAACGTATAAATG
* * *
138696 AGCTTGTTCATGAACGTATAAATG
1 AGCTT-ATAACGAACGTATAAATG
138720 AGCTTAT
1 AGCTTAT
138727 GAACTAGCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 22 0.88
25 2 0.08
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (23 bp):
AGCTTATAACGAACGTATAAATG
Found at i:140316 original size:36 final size:36
Alignment explanation
Indices: 140269--140500 Score: 317
Period size: 36 Copynumber: 6.5 Consensus size: 36
140259 ACGAAAGAAT
* * *
140269 GCATCG-CACTTCTGATTCAAGTCAAAAGGAAGGAA
1 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
140304 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
1 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
* *
140340 GCATCGACACTTCCGATTCAAGTCAAACGGAGGGAA
1 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
*
140376 GCATCGACACTTCCGATTCAAGTCGAACGGAGGGAA
1 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
* *
140412 GCATCGGCAC-TCCGATTCAAGTCGAACGGAATGAA
1 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
* * * *
140447 GCATCAACACTTCCGATTCAAGTTGAACAGAAGGAT
1 GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
* *
140483 GTATC-ACACTTTCGATTC
1 GCATCGACACTTCCGATTC
140501 GAGTGTTCAT
Statistics
Matches: 178, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
35 49 0.28
36 129 0.72
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (36 bp):
GCATCGACACTTCCGATTCAAGTCGAACGGAAGGAA
Found at i:140457 original size:107 final size:107
Alignment explanation
Indices: 140269--140469 Score: 323
Period size: 107 Copynumber: 1.9 Consensus size: 107
140259 ACGAAAGAAT
*
140269 GCATCGCACTTCTGATTCAAGTCAAAAGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACGG
1 GCATCGCACTTCCGATTCAAGTCAAAAGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACGG
*
140334 AAGGAAGCATCGACACTTCCGATTCAAGTCAAACGGAGGGAA
66 AAGGAAGCATCAACACTTCCGATTCAAGTCAAACGGAGGGAA
* * * *
140376 GCATCGACACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC-TCCGATTCAAGTCGAACG
1 GCATCG-CACTTCCGATTCAAGTCAAAAGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
*
140440 GAATGAAGCATCAACACTTCCGATTCAAGT
65 GAAGGAAGCATCAACACTTCCGATTCAAGT
140470 TGAACAGAAG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 52 0.60
108 34 0.40
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (107 bp):
GCATCGCACTTCCGATTCAAGTCAAAAGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACGG
AAGGAAGCATCAACACTTCCGATTCAAGTCAAACGGAGGGAA
Found at i:140499 original size:71 final size:72
Alignment explanation
Indices: 140269--140500 Score: 326
Period size: 71 Copynumber: 3.3 Consensus size: 72
140259 ACGAAAGAAT
* *
140269 GCATCG-CACTTCTGATTCAAGTCAAAAGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
1 GCATCGACACTTCCGATTCAAGTCAAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
140333 GAAGGAA
66 GAAGGAA
*
140340 GCATCGACACTTCCGATTCAAGTCAAACGGAGGGAAGCATCGACACTTCCGATTCAAGTCGAACG
1 GCATCGACACTTCCGATTCAAGTCAAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
*
140405 GAGGGAA
66 GAAGGAA
* * * * * *
140412 GCATCGGCAC-TCCGATTCAAGTCGAACGGAATGAAGCATCAACACTTCCGATTCAAGTTGAACA
1 GCATCGACACTTCCGATTCAAGTCAAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
*
140476 GAAGGAT
66 GAAGGAA
* *
140483 GTATC-ACACTTTCGATTC
1 GCATCGACACTTCCGATTC
140501 GAGTGTTCAT
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
70 3 0.02
71 70 0.49
72 70 0.49
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (72 bp):
GCATCGACACTTCCGATTCAAGTCAAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACG
GAAGGAA
Found at i:142035 original size:17 final size:18
Alignment explanation
Indices: 142013--142054 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
142003 CTATAGATTA
142013 TTTATTTAATTATTAT-T
1 TTTATTTAATTATTATAT
*
142030 TTTATTTAATTCTTATAT
1 TTTATTTAATTATTATAT
142048 TTTATTT
1 TTTATTT
142055 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:142105 original size:13 final size:13
Alignment explanation
Indices: 142087--142131 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
142077 TCTTTTTATC
142087 TTTATTATTATTA
1 TTTATTATTATTA
142100 TTTATTA-TATTTA
1 TTTATTATTA-TTA
142113 TTTAATTATTATT-
1 TTT-ATTATTATTA
142126 TTTATT
1 TTTATT
142132 TAATTCTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.17
13 16 0.55
14 6 0.21
15 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:142123 original size:17 final size:17
Alignment explanation
Indices: 142101--142150 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
142091 TTATTATTAT
142101 TTATTATATTTATTTAA
1 TTATTATATTTATTTAA
*
142118 TTATTATTTTTATTTAA
1 TTATTATATTTATTTAA
*
142135 TTCTTATATTTTATTT
1 TTATTATA-TTTATTT
142151 TAAAAATAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 22 0.76
18 7 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTATATTTATTTAA
Found at i:142145 original size:96 final size:96
Alignment explanation
Indices: 142011--142209 Score: 389
Period size: 96 Copynumber: 2.1 Consensus size: 96
142001 CTCTATAGAT
142011 TATTTATTTAATTATTATTTTTATTTAATTCTTATATTTTATTTTAAAAACAACTTTTAAAAACC
1 TATTTATTTAATTATTATTTTTATTTAATTCTTATATTTTATTTTAAAAACAACTTTTAAAAACC
142076 CTCTTTTTATCTTTATTATTATTATTTATTA
66 CTCTTTTTATCTTTATTATTATTATTTATTA
*
142107 TATTTATTTAATTATTATTTTTATTTAATTCTTATATTTTATTTTAAAAATAACTTTTAAAAACC
1 TATTTATTTAATTATTATTTTTATTTAATTCTTATATTTTATTTTAAAAACAACTTTTAAAAACC
142172 CTCTTTTTATCTTTATTATTATTATTTATTA
66 CTCTTTTTATCTTTATTATTATTATTTATTA
142203 TATTTAT
1 TATTTAT
142210 ATTTTTTTAT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 102 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (96 bp):
TATTTATTTAATTATTATTTTTATTTAATTCTTATATTTTATTTTAAAAACAACTTTTAAAAACC
CTCTTTTTATCTTTATTATTATTATTTATTA
Found at i:142220 original size:26 final size:24
Alignment explanation
Indices: 142190--142240 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 24
142180 ATCTTTATTA
142190 TTATTATT-TATTATATTTATATTTTT
1 TTATTATTATATT-T-TTT-TATTTTT
142216 TTATTATTATATTTTTTTATTTTT
1 TTATTATTATATTTTTTTATTTTT
142240 T
1 T
142241 CCCACTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 8 0.33
25 3 0.12
26 9 0.38
27 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (24 bp):
TTATTATTATATTTTTTTATTTTT
Found at i:142231 original size:16 final size:16
Alignment explanation
Indices: 142183--142236 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
142173 TCTTTTTATC
142183 TTTATTATTAT-TATTT
1 TTTATTATTATAT-TTT
*
142199 ATTA-TATTTATATTTT
1 TTTATTA-TTATATTTT
142215 TTTATTATTATATTTT
1 TTTATTATTATATTTT
142231 TTTATT
1 TTTATT
142237 TTTTCCCACT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 28 0.85
17 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTATTATATTTT
Found at i:142307 original size:17 final size:17
Alignment explanation
Indices: 142196--142310 Score: 58
Period size: 17 Copynumber: 6.7 Consensus size: 17
142186 ATTATTATTA
*
142196 TTTATTA-TATTTATAT
1 TTTATTATTTTTTATAT
* *
142212 TTTTTTA-TTATTATAT
1 TTTATTATTTTTTATAT
* **
142228 TTTTTTATTTTTTCCCACT
1 TTTATTATTTTTT-ATA-T
* *
142247 TTT-TTATTTTATTTTGT
1 TTTATTATTTT-TTATAT
* *
142264 TTTATT-TTTACTTTCTCT
1 TTTATTATTT--TTTATAT
*
142282 TTTAATATTTTTTATAT
1 TTTATTATTTTTTATAT
142299 TTTATTATTTTT
1 TTTATTATTTTT
142311 CTTTTCTGAA
Statistics
Matches: 76, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
16 20 0.26
17 27 0.36
18 19 0.25
19 10 0.13
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTATTATTTTTTATAT
Found at i:145188 original size:22 final size:22
Alignment explanation
Indices: 145157--145209 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
145147 GTGTTTTTCT
*
145157 GCTTTCGAATAGAAAAATAATA
1 GCTTTTGAATAGAAAAATAATA
*
145179 GCTTTTGAATAGGAAAATAATA
1 GCTTTTGAATAGAAAAATAATA
*
145201 GATTTTGAA
1 GCTTTTGAA
145210 AACGTGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (22 bp):
GCTTTTGAATAGAAAAATAATA
Found at i:146599 original size:41 final size:41
Alignment explanation
Indices: 146554--146705 Score: 184
Period size: 41 Copynumber: 3.8 Consensus size: 41
146544 ATACTCTTAA
*
146554 TTTAGTGGTGTTTGTGACAAAACGCCGCAATAACCATGTAC
1 TTTAGTGGCGTTTGTGACAAAACGCCGCAATAACCATGTAC
* * * * *
146595 TTTAGTGGCATTTGTGAGAAAACGCCACAATAGCCCTGTAC
1 TTTAGTGGCGTTTGTGACAAAACGCCGCAATAACCATGTAC
* * * *
146636 TTTAGTGGCGTCTGTGACCAAATGCCGCAATATCCATGTAC
1 TTTAGTGGCGTTTGTGACAAAACGCCGCAATAACCATGTAC
*
146677 TTTAGCGGCGTTT-T-AC-AAACGCCGCAATA
1 TTTAGTGGCGTTTGTGACAAAACGCCGCAATA
146706 GTTTTGTCCT
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
38 12 0.13
39 2 0.02
40 1 0.01
41 79 0.84
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (41 bp):
TTTAGTGGCGTTTGTGACAAAACGCCGCAATAACCATGTAC
Found at i:146798 original size:41 final size:41
Alignment explanation
Indices: 146693--146804 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 41
146683 GGCGTTTTAC
*
146693 AAACGCCGCAATAGTTTTGTCCTTTAGTGGCTTTTTTCAAT
1 AAACGCCGCAATAGTTTTGTCCCTTAGTGGCTTTTTTCAAT
* * *
146734 AAACACCGTAGTAGTTTTGTCCCTTAGTGGCATTTTTGT-AAT
1 AAACGCCGCAATAGTTTTGTCCCTTAGTGGC-TTTTT-TCAAT
* *
146776 AAATGCCGCAAAAGTTTT-TCCCTTAGTGG
1 AAACGCCGCAATAGTTTTGTCCCTTAGTGG
146805 TGTTTTTAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
41 38 0.63
42 21 0.35
43 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (41 bp):
AAACGCCGCAATAGTTTTGTCCCTTAGTGGCTTTTTTCAAT
Found at i:152615 original size:23 final size:21
Alignment explanation
Indices: 152582--152659 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
152572 GAAGCGAGGA
* *
152582 AAGCAGAGAGAGCAGCAGCGG
1 AAGCACAGAGAGAAGCAGCGG
152603 AAGCACAGAGAGAAGCAGCGG
1 AAGCACAGAGAGAAGCAGCGG
152624 AAGCACAGAGAGAAGCAGCGG
1 AAGCACAGAGAGAAGCAGCGG
*
152645 CAGCACAGAGAGAAG
1 AAGCACAGAGAGAAG
152660 TAACATATCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.42, C:0.19, G:0.38, T:0.00
Consensus pattern (21 bp):
AAGCACAGAGAGAAGCAGCGG
Found at i:153141 original size:44 final size:44
Alignment explanation
Indices: 153059--153217 Score: 132
Period size: 44 Copynumber: 3.8 Consensus size: 44
153049 AATTTAAATA
* * *
153059 TTTTGCGGCGTTTGTA-ACAAAAAATGCCACTATATACCAGACC
1 TTTTGCGGCGTTTGTATACAAAAAACGCCGCTATATACCACACC
* * * * *
153102 TTTTGCGGTGTTTGTATCCGAAAAACGCCGCTATATACCATACA
1 TTTTGCGGCGTTTGTATACAAAAAACGCCGCTATATACCACACC
* * * * *
153146 TTTTGCGGAGTTTTTATAC---GAACACCGCTATATATCACACC
1 TTTTGCGGCGTTTGTATACAAAAAACGCCGCTATATACCACACC
* * *
153187 TTCTGCGGCG--TGTATCCAAAAAATGCCGCTA
1 TTTTGCGGCGTTTGTATACAAAAAACGCCGCTA
153218 AATTCATAAA
Statistics
Matches: 90, Mismatches: 22, Indels: 9
0.74 0.18 0.07
Matches are distributed among these distances:
39 5 0.06
41 25 0.28
42 8 0.09
43 15 0.17
44 37 0.41
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TTTTGCGGCGTTTGTATACAAAAAACGCCGCTATATACCACACC
Done.