Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009048.1 Hibiscus syriacus cultivar Beakdansim tig00112459_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: 152695
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3754 original size:16 final size:16
Alignment explanation
Indices: 3730--3763 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3720 TATCGCCGAC
*
3730 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3746 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3762 CG
1 CG
3764 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:7515 original size:27 final size:29
Alignment explanation
Indices: 7477--7534 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
7467 GTTATTTATT
*
7477 TAATAATTATTATTATTATA-ATTA-TAA
1 TAATAATTATTATTAATATATATTATTAA
7504 TAATAATTATTATTAATATATATTATTAA
1 TAATAATTATTATTAATATATATTATTAA
7533 TA
1 TA
7535 TTACAAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 19 0.68
28 4 0.14
29 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATAATTATTATTAATATATATTATTAA
Found at i:12920 original size:15 final size:15
Alignment explanation
Indices: 12900--12931 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12890 ATCAATACCT
12900 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
12915 TTTTGCATACATTCA
1 TTTTGCATACATGCA
12930 TT
1 TT
12932 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:20266 original size:7 final size:7
Alignment explanation
Indices: 20246--20284 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
20236 ATTATGCTTG
20246 AAGAGAAA
1 AAGA-AAA
*
20254 AAGAAAG
1 AAGAAAA
20261 AAGAAAA
1 AAGAAAA
20268 AAGAAAA
1 AAGAAAA
20275 AAGAAAA
1 AAGAAAA
20282 AAG
1 AAG
20285 GGAGTTCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:21738 original size:83 final size:83
Alignment explanation
Indices: 21599--21900 Score: 525
Period size: 83 Copynumber: 3.6 Consensus size: 83
21589 AACAAATGCC
21599 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
21664 ATTGAATTTGGAAGAATA
66 ATTGAATTTGGAAGAATA
* *
21682 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
**
21747 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAATA
*
21765 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
*
21830 ATTGAATTTGAAAG-ATAA
66 ATTGAATTTGGAAGAAT-A
*
21848 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
21901 ATATGAAACC
Statistics
Matches: 207, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
83 207 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.39
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAATA
Found at i:22057 original size:115 final size:115
Alignment explanation
Indices: 21855--22170 Score: 553
Period size: 115 Copynumber: 2.8 Consensus size: 115
21845 TAAATGTGCT
*
21855 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCACAGAACCA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCA
**
21920 ATCATTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
66 ATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
21970 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCA
22035 ATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
66 ATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
* * *
22085 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA-GGAACTACAGAACCA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCA
* *
22149 ATCATTGGAATTAAAAGATGAA
66 ATCATTGGATTTGAAAGATGAA
22171 CTGCATGATC
Statistics
Matches: 193, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
114 33 0.17
115 160 0.83
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (115 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCA
ATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
Found at i:23148 original size:22 final size:22
Alignment explanation
Indices: 23106--23151 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
23096 AGTTCATAAT
*
23106 AAGAAGAACTCATCTGAAGAAG
1 AAGAAGAACTCATATGAAGAAG
*
23128 AAGAAGAAGTCATAATG-AGAAG
1 AAGAAGAACTCAT-ATGAAGAAG
23150 AA
1 AA
23152 TTGTTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.54, C:0.09, G:0.24, T:0.13
Consensus pattern (22 bp):
AAGAAGAACTCATATGAAGAAG
Found at i:23513 original size:113 final size:111
Alignment explanation
Indices: 22833--23931 Score: 1530
Period size: 113 Copynumber: 9.8 Consensus size: 111
22823 GCAAAGATTT
*
22833 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAG
* * *
22898 AATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
65 AA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *** *
22946 GAATTCATCA-TGTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTACT
1 AAATCCATCACT-TGATGGATCAGCTTTTCCAGAG-A-AGTTCATAATAAGAAGAACTCA-T-C-
* * *
23009 TGAAGGAGGAAGAA-AAATTCAT-ATGAGAAGAATTTGTTCAACCTTATGCTC
60 TGAA-GAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
23060 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
*
23125 AAGAAGAAGAAG-TCATAATGAGAAGAA-TTGTTCAACCTTTTGCGCC
65 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TC
*
23171 AAATCCATCAC-TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAG
* * *
23235 AAGGAA-AAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
65 AA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *** *
23282 GAATTCTTCA-TGTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTACT
1 AAATCCATCACT-TGATGGATCAGCTTTTCCAGAG-A-AGTTCATAATAAGAAGAACTCA-T-C-
* * *
23345 TGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
60 TGAA-GAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
23398 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
*
23463 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTC
65 AA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
23511 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
23576 AAG--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
23621 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
23686 AG--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
23730 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
**
23795 ATGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 A-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
23842 AAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---G
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAG
*
23904 AAGAAGAAGAATTTCATAATGAGAAGAA
65 AAGAAGAAGAAGTTCATAATGAGAAGAA
23932 CTCATCTGAA
Statistics
Matches: 892, Mismatches: 62, Indels: 68
0.87 0.06 0.07
Matches are distributed among these distances:
109 169 0.19
110 161 0.18
111 55 0.06
112 132 0.15
113 186 0.21
114 73 0.08
115 18 0.02
116 93 0.10
117 4 0.00
118 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (111 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
AGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:23563 original size:17 final size:17
Alignment explanation
Indices: 23541--23601 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
23531 CAGCTTTTCC
23541 AGAAGAAGTTCATAATA
1 AGAAGAAGTTCATAATA
* *
23558 AGAAGAA-CTCATCTGAAGA
1 AGAAGAAGTTCA--T-AATA
*
23577 AGGAAGAAGTTCATAATG
1 A-GAAGAAGTTCATAATA
23595 AGAAGAA
1 AGAAGAA
23602 TTTGTTCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 3 0.09
17 13 0.38
18 4 0.12
19 5 0.15
20 6 0.18
21 3 0.09
ACGTcount: A:0.51, C:0.08, G:0.23, T:0.18
Consensus pattern (17 bp):
AGAAGAAGTTCATAATA
Found at i:23930 original size:17 final size:17
Alignment explanation
Indices: 23908--23968 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
23898 CATCTGAAGA
23908 AGAAGAATTTCATAATG
1 AGAAGAATTTCATAATG
* *
23925 AGAAGAA-CTCAT-CTG
1 AGAAGAATTTCATAATG
*
23940 AAAGAAGAAATTCATAATG
1 --AGAAGAATTTCATAATG
23959 AGAAGAATTT
1 AGAAGAATTT
23969 GTTCAACCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
15 2 0.06
16 4 0.11
17 23 0.66
18 4 0.11
19 2 0.06
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (17 bp):
AGAAGAATTTCATAATG
Found at i:23954 original size:34 final size:36
Alignment explanation
Indices: 23874--23965 Score: 152
Period size: 34 Copynumber: 2.6 Consensus size: 36
23864 GCTTTTCCAG
23874 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 AGAAA-TTCATAATGAGAAGAACTCATCTGAAGAAGA
*
23911 AGAATTTCATAATGAGAAGAACTCATCTG-A-AAGA
1 AGAAATTCATAATGAGAAGAACTCATCTGAAGAAGA
23945 AGAAATTCATAATGAGAAGAA
1 AGAAATTCATAATGAGAAGAA
23966 TTTGTTCAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 24 0.45
35 1 0.02
36 24 0.45
37 4 0.08
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.21
Consensus pattern (36 bp):
AGAAATTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:24033 original size:142 final size:148
Alignment explanation
Indices: 23760--24072 Score: 451
Period size: 142 Copynumber: 2.1 Consensus size: 148
23750 CAGCTTTTCC
*
23760 AGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAGCT
1 AGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACT
* * * *
23825 TGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGA
66 TGTTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGA
23890 GAAGAACTCATCTGAAGA
131 GAAGAACTCATCTGAAGA
* * *
23908 AGAAGAATTTCATAATGAGAAGAACTCATCTG-A-AA-GAAG-A-AA-TTCATAATGAGAAGAAT
1 AG-AGAAGTTCATAATAAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAAC
* * * *
23967 TTGTTCAACC-TTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAAAGTTCATATTG
65 TTGTTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATG
24031 AGAAGAACTCATCTGAAGA
130 AGAAGAACTCATCTGAAGA
24050 AGAGAAAGTTCATAATAAGAAGA
1 AGAG-AAGTTCATAATAAGAAGA
24073 GCTTATTCAA
Statistics
Matches: 149, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
141 2 0.01
142 83 0.56
143 25 0.17
144 2 0.01
145 1 0.01
146 4 0.03
147 2 0.01
148 3 0.02
149 27 0.18
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (148 bp):
AGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACT
TGTTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGA
Found at i:24353 original size:27 final size:27
Alignment explanation
Indices: 24311--24374 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
24301 TTAATGTTAT
*
24311 TTATATAATAATTATTATTATTATA-A
1 TTATATAATAATTATTATTAATATATA
24337 TTATAATAATAATTATTATTAATATATA
1 TTAT-ATAATAATTATTATTAATATATA
*
24365 TTATTTAATA
1 TTATATAATA
24375 TTACAAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 25 0.74
28 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATATAATAATTATTATTAATATATA
Found at i:24809 original size:13 final size:13
Alignment explanation
Indices: 24791--24821 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
24781 GAGAGAGACC
*
24791 AACAAAAACAGAG
1 AACAAAAACAAAG
24804 AACAAAAACAAAG
1 AACAAAAACAAAG
24817 AACAA
1 AACAA
24822 TAACCCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (13 bp):
AACAAAAACAAAG
Found at i:25736 original size:24 final size:23
Alignment explanation
Indices: 25702--25746 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
25692 TATATATAAA
* *
25702 TAATAATTTATTATTATTATTTTT
1 TAATAAATTATT-TTAATATTTTT
25726 TAATAAATTATTTTAATATTT
1 TAATAAATTATTTTAATATTT
25747 ATTTTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATAAATTATTTTAATATTTTT
Found at i:28968 original size:188 final size:189
Alignment explanation
Indices: 28642--29019 Score: 692
Period size: 188 Copynumber: 2.0 Consensus size: 189
28632 CATTCCGTCC
*
28642 TTTATTTATTTATTTATTTTATATTTATGTACTTTCTTTTTTTTGAAAAAATCCGAGTTAGTGTT
1 TTTATTTATTTATTTATATTATATTTATGTACTTTCTTTTTTTTGAAAAAATCCGAGTTAGTGTT
28707 ACCTTGTCTTTGAGTACTAATTTTTAGCCTTCGAAGGATTTCTTGTAAGCTTCATCATTATTAGA
66 ACCTTGTCTTTGAGTACTAATTTTTAGCCTTCGAAGGATTTCTTGTAAGCTTCATCATTATTAGA
28772 AGCAAAATTGTCATTGCATGTAG-GTTCATCGTGTCCATGGTTGGATTCTTATCAGCAA
131 AGCAAAATTGTCATTGCATGTAGTGTTCATCGTGTCCATGGTTGGATTCTTATCAGCAA
28830 TTTATTTA-TTATTTATATT-TATTTATGTACTTTCTTTTTTTTTGAAAAAATCCGAGTTAGTGT
1 TTTATTTATTTATTTATATTATATTTATGTACTTTC-TTTTTTTTGAAAAAATCCGAGTTAGTGT
28893 TACCTTGTC-TTGAGTACTAATTTTTAGCCTTCGAAGGATGTTTCTTGTAAGCTTCATCATTATT
65 TACCTTGTCTTTGAGTACTAATTTTTAGCCTTCGAAGGA--TTTCTTGTAAGCTTCATCATTATT
28957 AGAAGCAAAATTGTCATTGCATGTAGTGTTCATCGTGTCCATGGTTGGATTCTTATCAGCAA
128 AGAAGCAAAATTGTCATTGCATGTAGTGTTCATCGTGTCCATGGTTGGATTCTTATCAGCAA
29019 T
1 T
29020 GGGTACAATG
Statistics
Matches: 185, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
186 44 0.24
187 47 0.25
188 58 0.31
189 36 0.19
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (189 bp):
TTTATTTATTTATTTATATTATATTTATGTACTTTCTTTTTTTTGAAAAAATCCGAGTTAGTGTT
ACCTTGTCTTTGAGTACTAATTTTTAGCCTTCGAAGGATTTCTTGTAAGCTTCATCATTATTAGA
AGCAAAATTGTCATTGCATGTAGTGTTCATCGTGTCCATGGTTGGATTCTTATCAGCAA
Found at i:31160 original size:13 final size:14
Alignment explanation
Indices: 31139--31167 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31129 ATAAGAAGAT
31139 AATGCAAATAAATA
1 AATGCAAATAAATA
31153 AATG-AAATAAATA
1 AATGCAAATAAATA
31166 AA
1 AA
31168 AGGGAGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
AATGCAAATAAATA
Found at i:31225 original size:26 final size:25
Alignment explanation
Indices: 31189--31250 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
31179 AGATAGAAAT
31189 AAAAGAAAAATAAAAAAG-AAAGTA
1 AAAAGAAAAATAAAAAAGAAAAGTA
*
31213 AAAATGAATAAATAAAATAGAAAAGTA
1 AAAA-GAA-AAATAAAAAAGAAAAGTA
31240 AAATAGAAAAA
1 AAA-AGAAAAA
31251 AATAATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.12
25 3 0.09
26 13 0.39
27 12 0.36
28 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (25 bp):
AAAAGAAAAATAAAAAAGAAAAGTA
Found at i:31258 original size:35 final size:37
Alignment explanation
Indices: 31186--31286 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 37
31176 GAAAGATAGA
* *
31186 AATAAAAGAAA-AATAAAAAAGAAAGTAAAAATGAATAAAT
1 AATAATAGAAATAATAAAATAG-AA--AAAAATGAAT-AAT
*
31226 AA-AATAGAAA-AGTAAAATAGAAAAAAAT-AATAAT
1 AATAATAGAAATAATAAAATAGAAAAAAATGAATAAT
*
31260 AATAATAGAAATAATAAAATAGTAAAA
1 AATAATAGAAATAATAAAATAGAAAAA
31287 GAGTATAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
34 5 0.09
35 11 0.20
36 19 0.35
38 2 0.04
39 15 0.28
40 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (37 bp):
AATAATAGAAATAATAAAATAGAAAAAAATGAATAAT
Found at i:31276 original size:12 final size:11
Alignment explanation
Indices: 31181--31273 Score: 64
Period size: 13 Copynumber: 7.9 Consensus size: 11
31171 GAGATGAAAG
31181 ATAGAAATAAA
1 ATAGAAATAAA
* *
31192 AGAAAAATAAA
1 ATAGAAATAAA
*
31203 AAAGAAAGTAAAA
1 ATAGAAA-T-AAA
*
31216 ATGAATAAATAAA
1 AT--AGAAATAAA
31229 ATAGAAAAGTAAA
1 ATAG-AAA-TAAA
31242 ATAGAAA-AAA
1 ATAGAAATAAA
31252 ATA-ATAATAATA
1 ATAGA-AATAA-A
31264 ATAGAAATAA
1 ATAGAAATAA
31274 TAAAATAGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
9 1 0.02
10 8 0.12
11 17 0.26
12 16 0.25
13 18 0.28
14 1 0.02
15 4 0.06
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (11 bp):
ATAGAAATAAA
Found at i:31392 original size:12 final size:12
Alignment explanation
Indices: 31332--31414 Score: 55
Period size: 12 Copynumber: 6.7 Consensus size: 12
31322 TACATATGAA
31332 ATAAAAAT-AAT
1 ATAAAAATAAAT
31343 ATTAAAAAT-AAT
1 A-TAAAAATAAAT
* *
31355 ACTAATAATAGTTAT
1 A-TAAAAATA--AAT
31370 AGTAAAAATAAAT
1 A-TAAAAATAAAT
*
31383 ATAAATATAAAT
1 ATAAAAATAAAT
*
31395 AT-AAAACAAAT
1 ATAAAAATAAAT
31406 AGTAAAAAT
1 A-TAAAAAT
31415 GACCATGACG
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.16
12 30 0.54
13 7 0.12
15 10 0.18
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (12 bp):
ATAAAAATAAAT
Found at i:31393 original size:18 final size:18
Alignment explanation
Indices: 31368--31414 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
31358 AATAATAGTT
*
31368 ATAGTAAAAATAAATATAA
1 ATAGTAAAAATAAA-ACAA
*
31387 ATA-TAAATATAAAACAA
1 ATAGTAAAAATAAAACAA
31404 ATAGTAAAAAT
1 ATAGTAAAAAT
31415 GACCATGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.25
18 15 0.62
19 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
ATAGTAAAAATAAAACAA
Found at i:32695 original size:33 final size:34
Alignment explanation
Indices: 32605--32698 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 34
32595 CAAGAATAAC
32605 GTTTCAAGAGAAACAATTTCAAAAGGTTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTC-AAAGG--TTTTTTTGT
* **
32642 GTTTCAAGAGAGACTGTTTCAAAGG-TTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
32675 GTTTC-AGAGAAAACAATTTCAAAG
1 GTTTCAAGAG-AAACAATTTCAAAG
32699 ATTGGTGCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 4 0.08
33 24 0.48
36 5 0.10
37 17 0.34
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (34 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
Found at i:32764 original size:34 final size:34
Alignment explanation
Indices: 32725--32803 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
32715 GAAACTTCGT
*
32725 TTCAAGGGAAACTATATCAAGAAAGACAAATTTG
1 TTCAAGGGAAACTATATCAAGAAAGACAAAATTG
* * * *
32759 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTG
1 TTCAAGGGAAACTATATCAAGAAAGACAAAATTG
* *
32793 TTTAAAGGAAA
1 TTCAAGGGAAA
32804 ACATATTAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (34 bp):
TTCAAGGGAAACTATATCAAGAAAGACAAAATTG
Found at i:32899 original size:37 final size:37
Alignment explanation
Indices: 32824--32989 Score: 219
Period size: 37 Copynumber: 4.5 Consensus size: 37
32814 AGATTTTGTT
*** *
32824 TCAAGAGAGACAAAATTT-GTTTTACGGGAAAATATC
1 TCAAGAGAGACAAAATTTAGTTTTAAAAGAAAATGTC
*
32860 TCAAGAGAGACAAAATTTAGTTTTAAAAGAAACTGTC
1 TCAAGAGAGACAAAATTTAGTTTTAAAAGAAAATGTC
** *
32897 TCAAGAGAGACAAAATTT-GTTTTACGAGAAAATTTC
1 TCAAGAGAGACAAAATTTAGTTTTAAAAGAAAATGTC
* *
32933 TCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTC
1 TCAAGAGAGACAAAATTTAGTTTTAAAAGAAAATGTC
32970 TCAAGAGAGACAAAACTTTA
1 TCAAGAGAGACAAAA-TTTA
32990 TTTCAAGGAA
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
36 50 0.44
37 59 0.52
38 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (37 bp):
TCAAGAGAGACAAAATTTAGTTTTAAAAGAAAATGTC
Found at i:32943 original size:73 final size:73
Alignment explanation
Indices: 32824--32984 Score: 295
Period size: 73 Copynumber: 2.2 Consensus size: 73
32814 AGATTTTGTT
* *
32824 TCAAGAGAGACAAAATTTGTTTTACGGGAAAATATCTCAAGAGAGACAAAATTTAGTTTTAAAAG
1 TCAAGAGAGACAAAATTTGTTTTACGAGAAAATATCTCAAGAGAGACAAAATTTAGTTCTAAAAG
32889 AAACTGTC
66 AAACTGTC
*
32897 TCAAGAGAGACAAAATTTGTTTTACGAGAAAATTTCTCAAGAGAGACAAAATTTAGTTCTAAAAG
1 TCAAGAGAGACAAAATTTGTTTTACGAGAAAATATCTCAAGAGAGACAAAATTTAGTTCTAAAAG
32962 AAACTGTC
66 AAACTGTC
32970 TCAAGAGAGACAAAA
1 TCAAGAGAGACAAAA
32985 CTTTATTTCA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 85 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (73 bp):
TCAAGAGAGACAAAATTTGTTTTACGAGAAAATATCTCAAGAGAGACAAAATTTAGTTCTAAAAG
AAACTGTC
Found at i:33039 original size:21 final size:21
Alignment explanation
Indices: 33015--33085 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
33005 ATTCAAAGTT
33015 TTTGTTTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAGACAAAA
* *
33036 TTTGTTTTAAGAGA-A-ACAA
1 TTTGTTTCAAGAGAGACAAAA
*
33055 ----TCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAGACAAAA
*
33072 TTTGTTTTAAGAGA
1 TTTGTTTCAAGAGA
33086 AACTGTCTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
15 8 0.22
16 1 0.03
17 3 0.08
19 3 0.08
20 1 0.03
21 21 0.57
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.31
Consensus pattern (21 bp):
TTTGTTTCAAGAGAGACAAAA
Found at i:33068 original size:36 final size:36
Alignment explanation
Indices: 33021--33116 Score: 156
Period size: 36 Copynumber: 2.6 Consensus size: 36
33011 AGTTTTTGTT
33021 TCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATC
1 TCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATC
**
33057 TCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATC
*
33093 TCAAGAGAGACAAAACCTTGTTTT
1 TCAAGAGAGACAAAA-TTTGTTTT
33117 GAGTAAATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 49 0.88
37 7 0.12
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTTGTTTTAAGAGAAACAATC
Found at i:33116 original size:197 final size:192
Alignment explanation
Indices: 32741--33116 Score: 569
Period size: 197 Copynumber: 1.9 Consensus size: 192
32731 GGAAACTATA
* *
32741 TCAAGAAAGACAAATTTGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGTTTAAAGGAAAAC
1 TCAAGAAAGACAAATTTGTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTATTTAAAGGAAAAC
* * *
32806 ATATTAAGAGATTTTGTTTCAAGAGAGACAAAATTTGTTTTACGGGAAAATATCTCAAGAGAGAC
66 AAATTAAGAGATTTTGTTTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATATCTCAAGAGAGAC
*
32871 AAAATTTAGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGAGAAAATTTC
131 AAAATTTAGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAACTTGTTTTACGAGAAAATTTC
* *
32933 TCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGG
1 TCAAGAAAGAC-AAATTT-GTTC-AAAAGAAACTGTCTCAAGAGAGACAAAA--TTATTTAAAGG
*
32998 AAAACAAATTCAA-AGTTTTTGTTTCAAGAGAGACAAAATTTGTTTTAAGAGAAACA-ATCTCAA
61 AAAACAAATT-AAGAGATTTTGTTTCAAGAGAGACAAAATTTGTTTTAAGAGAAA-ATATCTCAA
*
33061 GAGAGACAAAATTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACCTTGTTTT
124 GAGAGACAAAATTTAGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAA-CTTGTTTT
33117 GAGTAAATTA
Statistics
Matches: 166, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
192 10 0.06
193 6 0.04
194 4 0.02
195 27 0.16
196 32 0.19
197 84 0.51
198 3 0.02
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (192 bp):
TCAAGAAAGACAAATTTGTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTATTTAAAGGAAAAC
AAATTAAGAGATTTTGTTTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATATCTCAAGAGAGAC
AAAATTTAGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAACTTGTTTTACGAGAAAATTTC
Found at i:33494 original size:14 final size:14
Alignment explanation
Indices: 33475--33507 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33465 TTGCAAAATT
33475 ATGCTATGGATGCG
1 ATGCTATGGATGCG
33489 ATGCTATGGATGCG
1 ATGCTATGGATGCG
33503 ATGCT
1 ATGCT
33508 CTTATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.30
Consensus pattern (14 bp):
ATGCTATGGATGCG
Found at i:34468 original size:83 final size:87
Alignment explanation
Indices: 34359--34585 Score: 257
Period size: 95 Copynumber: 2.6 Consensus size: 87
34349 GACTAGCTGA
* * *
34359 ATCCATAAAGCCGGGGAATTTTACCAATTGCTCTAGAGGGACAGCTCAA-TAT-GTA-AAT-ACC
1 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
* *
34420 TTTATCAGGTTAGCTGAATCTT
66 TTTATCAGGCTAGCTGAATATT
* *
34442 ATCCATAAAGCTGGGGCGTTTAACCAATTGC-CTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGT
34506 ATAATCACCTTTATCAGGCTAGCTGAATATT
57 ATAATCACCTTTATCAGGCTAGCTGAATATT
* *
34537 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTATAGGGACAACTCAA
1 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAA
34586 GCTTTATTGT
Statistics
Matches: 120, Mismatches: 10, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
82 1 0.01
83 40 0.33
84 1 0.01
89 2 0.02
92 3 0.03
93 3 0.03
94 4 0.03
95 65 0.54
96 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
TTTATCAGGCTAGCTGAATATT
Found at i:34580 original size:95 final size:95
Alignment explanation
Indices: 34417--34598 Score: 303
Period size: 95 Copynumber: 1.9 Consensus size: 95
34407 ATATGTAAAT
* * *
34417 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
34482 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
* *
34512 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGTGTTTAACCAATTG-CTCTATAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGG
34576 GACAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
34599 TAAATAATAT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 2 0.02
95 79 0.98
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:37863 original size:13 final size:13
Alignment explanation
Indices: 37845--37882 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
37835 CCACTTAAAA
*
37845 CGGGTTTGGAGCT
1 CGGGTTTAGAGCT
37858 CGGGTTTAGAGCT
1 CGGGTTTAGAGCT
37871 CGGGTTTAGAGC
1 CGGGTTTAGAGC
37883 CTTAAGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.42, T:0.29
Consensus pattern (13 bp):
CGGGTTTAGAGCT
Found at i:38447 original size:26 final size:26
Alignment explanation
Indices: 38411--38473 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
38401 CGAAAGATAT
38411 GTAAAAAAATGATAATAAATAATAAA
1 GTAAAAAAATGATAATAAATAATAAA
38437 GTAAAAAAATGATAATAAATAATAAA
1 GTAAAAAAATGATAATAAATAATAAA
38463 G-AAAAAAATGA
1 GTAAAAAAATGA
38474 ATGAAGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 10 0.27
26 27 0.73
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.21
Consensus pattern (26 bp):
GTAAAAAAATGATAATAAATAATAAA
Found at i:38497 original size:12 final size:11
Alignment explanation
Indices: 38480--38545 Score: 51
Period size: 13 Copynumber: 5.4 Consensus size: 11
38470 ATGAATGAAG
38480 TAAAGAAAACAA
1 TAAAGAAAA-AA
*
38492 TAAAGAATAAA
1 TAAAGAAAAAA
*
38503 TCAAATAAAAAAA
1 T-AAA-GAAAAAA
38516 TTAAAGATAAAAA
1 -TAAAGA-AAAAA
38529 TAAATGAAATAAA
1 TAAA-GAAA-AAA
38542 TAAA
1 TAAA
38546 ACGAATAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
11 3 0.07
12 18 0.41
13 22 0.50
14 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (11 bp):
TAAAGAAAAAA
Found at i:38520 original size:25 final size:25
Alignment explanation
Indices: 38480--38553 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 25
38470 ATGAATGAAG
*
38480 TAAA-GAAAACAA-TAAAGAATAAA
1 TAAATGAAAAAAATTAAAGAATAAA
*
38503 TCAAAT-AAAAAAATTAAAGATAAAAA
1 T-AAATGAAAAAAATTAAAGA-ATAAA
* *
38529 TAAATGAAATAAATAAAACGAATAA
1 TAAATGAAAAAAATTAAA-GAATAA
38554 CATGGAGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.03
24 9 0.22
25 10 0.25
26 18 0.45
27 2 0.05
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.18
Consensus pattern (25 bp):
TAAATGAAAAAAATTAAAGAATAAA
Found at i:38697 original size:12 final size:12
Alignment explanation
Indices: 38676--38739 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
38666 TGAAATATAG
38676 AAAT-AAAAGAA
1 AAATAAAAAGAA
38687 AAATAAAAAG-A
1 AAATAAAAAGAA
*
38698 AAGTAAAAATGAA
1 AAATAAAAA-GAA
38711 TAAATAAAATAGAA
1 -AAATAAAA-AGAA
*
38725 AAGTAAAATAGAA
1 AAATAAAA-AGAA
38738 AA
1 AA
38740 GAAAATAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
11 13 0.29
12 6 0.13
13 15 0.33
14 10 0.22
15 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (12 bp):
AAATAAAAAGAA
Found at i:38733 original size:43 final size:43
Alignment explanation
Indices: 38672--38764 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
38662 GAGATGAAAT
*
38672 ATAGAAAT--AAAAGAAAAATA-AAAAGAAAGTAAAAATGAATAA
1 ATAGAAATAGAAAAGAAAAATAGAAAAGAAAATAAAAAT-AAT-A
* *
38714 ATA-AAATAGAAAAGTAAAATAGAAAAGAAAATAATAATAATA
1 ATAGAAATAGAAAAGAAAAATAGAAAAGAAAATAAAAATAATA
38756 ATAGAAATA
1 ATAGAAATA
38765 ATAAAATAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 4 0.09
42 7 0.16
43 19 0.43
44 14 0.32
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (43 bp):
ATAGAAATAGAAAAGAAAAATAGAAAAGAAAATAAAAATAATA
Found at i:38742 original size:18 final size:17
Alignment explanation
Indices: 38712--38772 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 17
38702 AAAAATGAAT
38712 AAATAAAATAGAAAAGTA
1 AAATAAAATAGAAAA-TA
38730 AAATAGAAA-AGAAAATA
1 AAATA-AAATAGAAAATA
38747 ATAATAATAATAGAAATAATA
1 A-AATAA-AATAG-AA-AATA
38768 AAATA
1 AAATA
38773 GTAAAAGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.11
18 17 0.46
19 5 0.14
20 6 0.16
21 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (17 bp):
AAATAAAATAGAAAATA
Found at i:38746 original size:12 final size:13
Alignment explanation
Indices: 38683--38779 Score: 71
Period size: 13 Copynumber: 7.5 Consensus size: 13
38673 TAGAAATAAA
*
38683 AGAAAAATAAAA-
1 AGAAAAGTAAAAT
38695 AG-AAAGTAAAA-
1 AGAAAAGTAAAAT
*
38706 ATGAATAAATAAAAT
1 A-GAA-AAGTAAAAT
38721 AGAAAAGTAAAAT
1 AGAAAAGTAAAAT
38734 AGAAAAG-AAAAT
1 AGAAAAGTAAAAT
*
38746 A-ATAA-TAATAAT
1 AGAAAAGTAA-AAT
*
38758 AGAAATAATAAAAT
1 AGAAA-AGTAAAAT
38772 AGTAAAAG
1 AG-AAAAG
38780 AGTATAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
11 14 0.20
12 13 0.19
13 18 0.26
14 17 0.25
15 7 0.10
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (13 bp):
AGAAAAGTAAAAT
Found at i:50425 original size:15 final size:15
Alignment explanation
Indices: 50405--50438 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
50395 GAACCCAATG
*
50405 ACCCGATGCCATTGC
1 ACCCGAGGCCATTGC
*
50420 ACCCGAGGCCTTTGC
1 ACCCGAGGCCATTGC
50435 ACCC
1 ACCC
50439 AAGTCCCATA
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:0.44, G:0.21, T:0.18
Consensus pattern (15 bp):
ACCCGAGGCCATTGC
Found at i:59907 original size:2 final size:2
Alignment explanation
Indices: 59900--59932 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59890 GGAGGCATCT
59900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59933 GAGAACAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72021 original size:37 final size:36
Alignment explanation
Indices: 71960--72081 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
71950 TTATCTCATT
* *
71960 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTG-AAA
*
71996 ATTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
72032 ACCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
72067 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
72082 TTGGTTGTCA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
35 34 0.44
36 14 0.18
37 29 0.38
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:72037 original size:21 final size:20
Alignment explanation
Indices: 72010--72073 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
72000 TTTTTCAAAG
72010 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
72030 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
72045 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
72065 AAATCATTT
1 AAA-CATTT
72074 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:76486 original size:23 final size:23
Alignment explanation
Indices: 76460--76504 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
76450 CACCACAGCT
*
76460 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
76483 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
76505 ATATAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:76647 original size:25 final size:25
Alignment explanation
Indices: 76619--76712 Score: 170
Period size: 25 Copynumber: 3.8 Consensus size: 25
76609 TATATATATA
76619 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
76644 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
76669 TCCCGAAGGACCGCGTATAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
*
76694 TCCCGAAGGACTGCGTAGA
1 TCCCGAAGGACCGCGTAGA
76713 CCCTCTACCC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:83327 original size:23 final size:23
Alignment explanation
Indices: 83301--83345 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
83291 CACCACAGCT
*
83301 CGTATAAATACACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* * *
83324 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
83346 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:89034 original size:16 final size:17
Alignment explanation
Indices: 89015--89051 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
89005 AAGAATGTGA
89015 TTAAATTAC-TTTAATT
1 TTAAATTACATTTAATT
*
89031 TT-AATTACATTTACTT
1 TTAAATTACATTTAATT
89047 TTAAA
1 TTAAA
89052 AATTTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 6 0.33
16 10 0.56
17 2 0.11
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAAATTACATTTAATT
Found at i:90108 original size:48 final size:46
Alignment explanation
Indices: 90063--90224 Score: 141
Period size: 48 Copynumber: 3.5 Consensus size: 46
90053 ATAAAAAACC
* * *
90063 CAAAAAAACAGAAGAAAAAAATCCTCAATATTAAAATCAGAAAAAA
1 CAAAAAAACAGAAGAAAAAAATCCTCAACATTCAAATTAGAAAAAA
* * *
90109 -ATGCAAAAATCAGAATAAAAAAATACTCAACATTCAAATTAGAAAAAA
1 CA---AAAAAACAGAAGAAAAAAATCCTCAACATTCAAATTAGAAAAAA
* * * *
90157 TAAAAAAA-A-AATAAAAAAATCTTCAACATTCAAATTATAAAAAAAA
1 CAAAAAAACAGAAGAAAAAAATCCTCAACATTCAAA-T-TAGAAAAAA
* *
90203 CAAAAAATCAAAAGAAGAAAAA
1 CAAAAAAACAGAAGAA-AAAAA
90225 ATTGTAATGC
Statistics
Matches: 94, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
44 23 0.24
45 3 0.03
46 19 0.20
47 1 0.01
48 42 0.45
49 6 0.06
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.16
Consensus pattern (46 bp):
CAAAAAAACAGAAGAAAAAAATCCTCAACATTCAAATTAGAAAAAA
Found at i:90167 original size:11 final size:11
Alignment explanation
Indices: 90151--90175 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
90141 TTCAAATTAG
90151 AAAAAATAAAA
1 AAAAAATAAAA
90162 AAAAAATAAAA
1 AAAAAATAAAA
90173 AAA
1 AAA
90176 TCTTCAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:90185 original size:44 final size:43
Alignment explanation
Indices: 90077--90209 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 43
90067 AAAACAGAAG
* * * * *
90077 AAAAAAATCCTCAATATTAAAATCAGAAAAAAATGCAAAAATCAGAAT
1 AAAAAAAT-CTCAACATTCAAATTAG-AAAAAAT--AAAAA-AAAAAT
90125 AAAAAAATACTCAACATTCAAATTAGAAAAAATAAAAAAAAAAT
1 AAAAAAAT-CTCAACATTCAAATTAGAAAAAATAAAAAAAAAAT
* *
90169 AAAAAAATCTTCAACATTCAAATTATAAAAAA-AACAAAAAA
1 AAAAAAATC-TCAACATTCAAATTAGAAAAAATAAAAAAAAA
90210 TCAAAAGAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
43 9 0.12
44 33 0.43
45 5 0.07
47 7 0.09
48 22 0.29
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (43 bp):
AAAAAAATCTCAACATTCAAATTAGAAAAAATAAAAAAAAAAT
Found at i:91044 original size:12 final size:12
Alignment explanation
Indices: 91029--91060 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
91019 CCTTTATCCC
*
91029 CACCTTCTGACT
1 CACCTCCTGACT
91041 CACCTCCTGACT
1 CACCTCCTGACT
91053 CACCTCCT
1 CACCTCCT
91061 ATGTCACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.50, G:0.06, T:0.28
Consensus pattern (12 bp):
CACCTCCTGACT
Found at i:91787 original size:17 final size:17
Alignment explanation
Indices: 91765--91804 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
91755 GCCAAACATC
91765 AAATAATTACATATTTT
1 AAATAATTACATATTTT
91782 AAATAATTACATATTTT
1 AAATAATTACATATTTT
91799 ACAATA
1 A-AATA
91805 GTATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAATTACATATTTT
Found at i:92791 original size:16 final size:18
Alignment explanation
Indices: 92770--92804 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
92760 TAAAAATTCT
92770 ACACTAT-ATTT-TATAA
1 ACACTATAATTTCTATAA
92786 ACACTATAATTTCTATAA
1 ACACTATAATTTCTATAA
92804 A
1 A
92805 ATAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (18 bp):
ACACTATAATTTCTATAA
Found at i:104377 original size:20 final size:20
Alignment explanation
Indices: 104352--104444 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
104342 TTTTCCCAAT
104352 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* * *
104372 TCGCAACGCGAATTAGGAAA
1 TCGCAATGCGAATAAGTAAA
104392 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
104413 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
104434 TCGCAATGCGA
1 TCGCAATGCGA
104445 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:104394 original size:41 final size:41
Alignment explanation
Indices: 104349--104444 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
104339 CGATTTTCCC
104349 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGA
*
104390 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGA
*
104431 AAATCGCAATGCGA
1 AATTCGCAATGCGA
104445 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGA
Found at i:104398 original size:21 final size:20
Alignment explanation
Indices: 104352--104444 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
104342 TTTTCCCAAT
*
104352 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* *
104372 TCGCAACGCGAATTAGGAAA
1 TCGCAATGCGAATAAGGAAA
*
104392 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
104413 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
104434 TCGCAATGCGA
1 TCGCAATGCGA
104445 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:104457 original size:41 final size:40
Alignment explanation
Indices: 104371--104505 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 40
104361 GAATAAGTAA
* * *
104371 ATCGCAACGCGAATTAGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATT-GGAAAATCGCAATGCG-ATACTG-ACT
104412 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATT-GGAAAATCGCAATGCGATACTGACT
* * ** * * *
104453 ATCGCAATGCGATAATAAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGAAAATCGCAATGCGATACTGACT
*
104494 TTCGCAACGCGA
1 ATCGCAACGCGA
104506 TACTGACTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 72 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGAATTGGAAAATCGCAATGCGATACTGACT
Found at i:104458 original size:20 final size:20
Alignment explanation
Indices: 104433--104526 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
104423 AATTGGGAAA
*
104433 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
104453 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
104474 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
104494 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
104514 TTCGCAACGCGAT
1 ATCGCAACGCGAT
104527 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:105095 original size:19 final size:19
Alignment explanation
Indices: 105052--105105 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
105042 CGAGAATGAG
* *
105052 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
105072 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
105091 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
105106 CCAAAATCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:105111 original size:19 final size:19
Alignment explanation
Indices: 105073--105113 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
105063 GGAAATGACT
*
105073 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAACAAAA
*
105092 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACAAAA
105111 ATC
1 ATC
105114 ACATTGCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.15, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAACAAAA
Found at i:105137 original size:19 final size:19
Alignment explanation
Indices: 105117--105315 Score: 193
Period size: 19 Copynumber: 10.8 Consensus size: 19
105107 CAAAATCACA
*
105117 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
105136 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
105155 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
105174 TTGCGATTTTAATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
105194 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
105213 TTGCGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
* **
105227 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
105246 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCG
**
105260 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
105280 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
105300 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
105316 AACCAAAAGA
Statistics
Matches: 150, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 19 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 74 0.49
20 48 0.32
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:105240 original size:33 final size:33
Alignment explanation
Indices: 105203--105290 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
105193 GTTGCGATTT
* **
105203 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
105236 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
105269 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
105291 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:105292 original size:20 final size:20
Alignment explanation
Indices: 105269--105315 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
105259 ATTGCGATAG
105269 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
105289 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
105309 TCATTTC
1 TCATTTC
105316 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:107366 original size:42 final size:42
Alignment explanation
Indices: 107306--107428 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
107296 GCCCGACTCG
* * *
107306 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
107348 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
107390 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
107429 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:107386 original size:21 final size:21
Alignment explanation
Indices: 107362--107428 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
107352 TCATTCCTCG
107362 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
107383 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
107404 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
107425 AGAG
1 AGAG
107429 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:108807 original size:13 final size:14
Alignment explanation
Indices: 108782--108816 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
108772 ATTGTTTAAT
108782 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
108796 TGATTTGT-AAAGT
1 TGATTTGTAAAAGG
108809 TGATTTGT
1 TGATTTGT
108817 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:108825 original size:13 final size:14
Alignment explanation
Indices: 108769--108817 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
108759 TTGCTTATTT
*
108769 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
108781 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
108795 GTGATTTG-TAAAG
1 TTGATTTGTTAAAG
108808 TTGATTTGTT
1 TTGATTTGTT
108818 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:109017 original size:19 final size:19
Alignment explanation
Indices: 108995--109112 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
108985 CGAAATTAAA
108995 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
109014 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
109029 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
109047 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
109062 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
109080 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
109099 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
109113 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:109041 original size:33 final size:33
Alignment explanation
Indices: 108999--109092 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
108989 ATTAAATTCG
108999 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
109032 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
109065 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
109093 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:112899 original size:14 final size:14
Alignment explanation
Indices: 112880--112916 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
112870 CATCAATTAA
112880 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
112894 ACAAATCATCTTTT
1 ACAAATCAACATTT
112908 ACAAATCAA
1 ACAAATCAA
112917 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:113287 original size:20 final size:20
Alignment explanation
Indices: 113262--113312 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
113252 ATTCATTTGA
113262 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
113282 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
*
113302 TTATCGCAACG
1 CTATCGCAACG
113313 AGAATATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (20 bp):
CTATCGCAACGTGAAAATGG
Found at i:113362 original size:14 final size:15
Alignment explanation
Indices: 113342--113414 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
113332 TGATAATCGC
113342 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
113357 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
113374 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
113392 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
113408 -TTGCGAT
1 ATTGCGAT
113415 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:113379 original size:19 final size:19
Alignment explanation
Indices: 113338--113404 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
113328 GAAATGATAA
113338 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
113354 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
113371 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
113389 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
113405 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:113538 original size:14 final size:14
Alignment explanation
Indices: 113519--113555 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
113509 CATCAATTAA
113519 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
113533 ACAAATCATCTTTT
1 ACAAATCAACATTT
113547 ACAAATCAA
1 ACAAATCAA
113556 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:115451 original size:20 final size:19
Alignment explanation
Indices: 115416--115481 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 19
115406 GAAACTTAAA
115416 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
115435 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
115455 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
115473 ATCGCAACG
1 ATCGCAACG
115482 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.39
20 17 0.41
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:115490 original size:14 final size:14
Alignment explanation
Indices: 115471--115527 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
115461 ATGCGAAATG
115471 AAATCGCAACGACA
1 AAATCGCAACGACA
*
115485 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
115501 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
115517 AAATCGCAACG
1 AAATCGCAACG
115528 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:115499 original size:32 final size:32
Alignment explanation
Indices: 115455--115532 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
115445 GGAAATGGCT
*
115455 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
115487 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
115519 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
115533 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:115566 original size:19 final size:18
Alignment explanation
Indices: 115544--115603 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
115534 ACAAATCGCA
115544 TTGCGATTTTCATTTTGCG
1 TTGCGA-TTTCATTTTGCG
*
115563 TTGCGA-TT--TTGT-CG
1 TTGCGATTTCATTTTGCG
*
115577 TTGCGATTTCATTTCGCG
1 TTGCGATTTCATTTTGCG
115595 TTGCGATTT
1 TTGCGATTT
115604 TGTCGTTGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
17 4 0.12
18 11 0.32
19 6 0.18
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.50
Consensus pattern (18 bp):
TTGCGATTTCATTTTGCG
Found at i:115578 original size:14 final size:14
Alignment explanation
Indices: 115555--115618 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
115545 TGCGATTTTC
115555 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
115568 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
115582 ATTTCATTTCGCGTTGCG
1 ATTT--TGT--CGTTGCG
*
115600 ATTTTGTCGTTGCA
1 ATTTTGTCGTTGCG
115614 ATTTT
1 ATTTT
115619 CATTTCGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.14
14 22 0.51
16 4 0.09
18 11 0.26
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:115625 original size:33 final size:33
Alignment explanation
Indices: 115544--115634 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
115534 ACAAATCGCA
*
115544 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
115577 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
115609 TTGCAATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
115635 AGCCATTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:115670 original size:20 final size:20
Alignment explanation
Indices: 115621--115673 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
115611 GCAATTTTCA
*
115621 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
115641 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
115661 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
115674 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:115778 original size:6 final size:6
Alignment explanation
Indices: 115730--115764 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
115720 TTACTTCAAC
*
115730 CAAAAGA CAAAAA CAAAAA CAAAAC CAAAAA CAAA
1 CAAAA-A CAAAAA CAAAAA CAAAAA CAAAAA CAAA
115765 TACTAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.77, C:0.20, G:0.03, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:116177 original size:18 final size:18
Alignment explanation
Indices: 116151--116195 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
116141 GTCGATCAGA
*
116151 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
116169 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
116187 TGATGGCTC
1 TGATGGCTC
116196 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:117534 original size:20 final size:20
Alignment explanation
Indices: 117509--117546 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
117499 AATAGTTTCT
117509 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
117529 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
117547 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:117835 original size:22 final size:22
Alignment explanation
Indices: 117810--117853 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
117800 GATTTAGATA
117810 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
117832 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
117854 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:118106 original size:41 final size:42
Alignment explanation
Indices: 118061--118237 Score: 123
Period size: 41 Copynumber: 4.3 Consensus size: 42
118051 CGAAAGCCAG
* * * *
118061 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
118102 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
118144 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
** ** * *
118185 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
118226 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
118238 TTTACTTATT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
40 3 0.03
41 111 0.95
42 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:118112 original size:21 final size:21
Alignment explanation
Indices: 118079--118158 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
118069 TGCGAAAGTA
* * *
118079 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
118100 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
118120 AGTATCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
118142 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
118159 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 26 0.57
22 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:118127 original size:20 final size:20
Alignment explanation
Indices: 118021--118135 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
118011 CGCTTTGAAA
*
118021 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
118042 ATCGCGTTGCGAAAGCCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
118062 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
118082 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
118103 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
118123 ATCGCATTGCGAT
1 ATCGCATTGCGAT
118136 TTTCTCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 1 0.01
20 49 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:118174 original size:82 final size:81
Alignment explanation
Indices: 118104--118257 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 81
118094 TTTTTTATTA
* *
118104 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTATTC
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTC
118167 GCATTGCGAATTTCCCAAT
64 GCATTGCG-ATTTCCCAAT
* * *
118186 TCGCGTTGCGATTTACTTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1 TCGCATTGCGATTCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
118251 ATTGCGA
66 ATTGCGA
118258 ATTGGGAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
80 2 0.03
81 3 0.05
82 60 0.92
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (81 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
ATTGCGATTTCCCAAT
Found at i:118187 original size:21 final size:21
Alignment explanation
Indices: 118124--118260 Score: 129
Period size: 21 Copynumber: 6.7 Consensus size: 21
118114 ATAGTCAGTA
*
118124 TCGCATTGCG-ATTTTCTCAAT
1 TCGCATTGCGAATTTAC-CAAT
* **
118145 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
*
118165 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
118186 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
*
118206 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
118227 TCGCGTTGCG-ATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
118247 TCGCATTGCGAATT
1 TCGCATTGCGAATT
118261 GGGAAAATCG
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
20 43 0.47
21 49 0.53
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGAATTTACCAAT
Found at i:118238 original size:41 final size:41
Alignment explanation
Indices: 118124--118260 Score: 256
Period size: 41 Copynumber: 3.3 Consensus size: 41
118114 ATAGTCAGTA
* *
118124 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
118165 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
118206 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
118247 TCGCATTGCGAATT
1 TCGCATTGCGAATT
118261 GGGAAAATCG
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:121280 original size:21 final size:21
Alignment explanation
Indices: 121256--121297 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
121246 TCTCTTCTCT
121256 AACTACCCTCCTTTCAACTCC
1 AACTACCCTCCTTTCAACTCC
*
121277 AACTACCTTCCTTTCAACTCC
1 AACTACCCTCCTTTCAACTCC
121298 GATCTACTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.31
Consensus pattern (21 bp):
AACTACCCTCCTTTCAACTCC
Found at i:121813 original size:18 final size:18
Alignment explanation
Indices: 121790--121833 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
121780 ACCGGTCATA
* *
121790 ACCCGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTG
121808 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
121826 ACCCGACC
1 ACCCGACC
121834 GAGTATACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:124296 original size:24 final size:23
Alignment explanation
Indices: 124269--124372 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
124259 AATTATTTTA
*
124269 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTCTGT
**
124293 TCTGATACATGACCTGAATTCTGT
1 TCTGAT-TTTGACCTGAATTCTGT
** *
124317 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTT-TGACCTGAATTCTGT
* * **
124341 TCTAATATATGTTCTGAATTCTGT
1 TCTGAT-TTTGACCTGAATTCTGT
*
124365 TTTGATTT
1 TCTGATTT
124373 CTGATATCTC
Statistics
Matches: 61, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
23 1 0.02
24 58 0.95
25 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.49
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTCTGT
Found at i:124321 original size:12 final size:12
Alignment explanation
Indices: 124283--124375 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
124273 ATTTTCGACT
124283 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
124295 TG-ATACATGACC
1 TGAATTC-TGTTC
124307 TGAATTCTGTTC
1 TGAATTCTGTTC
* * *
124319 TGATTTCTGATA
1 TGAATTCTGTTC
*
124331 TGGATTCTGTTC
1 TGAATTCTGTTC
*
124343 T-AATATATGTTC
1 TGAAT-TCTGTTC
*
124355 TGAATTCTGTTT
1 TGAATTCTGTTC
*
124367 TGATTTCTG
1 TGAATTCTG
124376 ATATCTCCGT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 5 0.08
12 48 0.81
13 6 0.10
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:124338 original size:48 final size:48
Alignment explanation
Indices: 124286--124379 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
124276 TTCGACTTGA
*
124286 ATTCTGTTCTGATACATGACCTGAATTCTGTTCTGATTTCTGATATGG
1 ATTCTGTTCTAATACATGACCTGAATTCTGTTCTGATTTCTGATATGG
* ** *
124334 ATTCTGTTCTAATATATGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTAATACATGACCTGAATTCTGTTCTGATTTCTGATAT
124380 CTCCGTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTAATACATGACCTGAATTCTGTTCTGATTTCTGATATGG
Found at i:124550 original size:2 final size:2
Alignment explanation
Indices: 124543--124587 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
124533 GGGATTGGGG
124543 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
124585 TA T
1 TA T
124588 GTTTTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:126487 original size:12 final size:12
Alignment explanation
Indices: 126470--126503 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
126460 TCACGAACAA
126470 ACTCGTTTATTG
1 ACTCGTTTATTG
126482 ACTCGTTTATTG
1 ACTCGTTTATTG
126494 A-TCCGTTTAT
1 ACT-CGTTTAT
126504 AAGCTCGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 20 0.95
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (12 bp):
ACTCGTTTATTG
Found at i:126679 original size:18 final size:19
Alignment explanation
Indices: 126644--126680 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
126634 CACGGAATGT
126644 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
126664 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
126681 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:127709 original size:20 final size:20
Alignment explanation
Indices: 127684--127721 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
127674 TAATCCTATT
127684 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
127704 CACTGGTAATCTTACATT
1 CACTGGTAATCTTACATT
127722 TCATGAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:139654 original size:24 final size:23
Alignment explanation
Indices: 139611--139670 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
139601 TTAAAATGAG
139611 AGAAT-AATTTAT-AAATTTAAAAA
1 AGAATGAA-TTATCAAATTT-AAAA
139634 AGAATGAACTTATCAAA-TTAAAA
1 AGAATGAA-TTATCAAATTTAAAA
139657 A-AATGAATTATCAA
1 AGAATGAATTATCAA
139671 CTGAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.21
22 6 0.18
23 10 0.29
24 8 0.24
25 3 0.09
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (23 bp):
AGAATGAATTATCAAATTTAAAA
Found at i:139657 original size:25 final size:23
Alignment explanation
Indices: 139611--139664 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
139601 TTAAAATGAG
* *
139611 AGAATAATTTATAAATTTAAAAA
1 AGAATAACTTATAAATTAAAAAA
139634 AGAATGAACTTATCAAATTAAAAAA
1 AGAAT-AACTTAT-AAATTAAAAAA
139659 ATGAAT
1 A-GAAT
139665 TATCAACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 6 0.23
25 11 0.42
26 4 0.15
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (23 bp):
AGAATAACTTATAAATTAAAAAA
Found at i:139677 original size:21 final size:23
Alignment explanation
Indices: 139630--139677 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
139620 TATAAATTTA
*
139630 AAAAAGAATGAACTTATCAAATT
1 AAAAAGAATGAACTTATCAAATG
*
139653 AAAAA-AATGAA-TTATCAACTG
1 AAAAAGAATGAACTTATCAAATG
139674 AAAA
1 AAAA
139678 TATAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 6 0.26
23 5 0.22
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (23 bp):
AAAAAGAATGAACTTATCAAATG
Found at i:140507 original size:11 final size:11
Alignment explanation
Indices: 140491--140515 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
140481 TTTTGTCATA
140491 AATTTAAAAAT
1 AATTTAAAAAT
140502 AATTTAAAAAT
1 AATTTAAAAAT
140513 AAT
1 AAT
140516 ACATCTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTTAAAAAT
Found at i:143630 original size:2 final size:2
Alignment explanation
Indices: 143623--143670 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
143613 AATAATGCCC
143623 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
143665 AT AT AT
1 AT AT AT
143671 TATTTTTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143725 original size:19 final size:20
Alignment explanation
Indices: 143694--143735 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
143684 AATCCCTATT
143694 TTTATTGAATAAAAATAATA
1 TTTATTGAATAAAAATAATA
* *
143714 TTTATT-AATAAATATATTA
1 TTTATTGAATAAAAATAATA
143733 TTT
1 TTT
143736 CGGGTCGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTATTGAATAAAAATAATA
Found at i:151653 original size:56 final size:56
Alignment explanation
Indices: 151578--151686 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
151568 CAATCCACTC
*
151578 TGAATTGCTTAACTTTCACATTCACTTCTGATCTAAAGTGACAACTTCAAGCACCA
1 TGAATTGCTTAACTTTCACATTCACTTCTCATCTAAAGTGACAACTTCAAGCACCA
* * *
151634 TGAATTGTTTAACTTTCACATTCACTTCTCTTCTAAAGTGACGACTTCAAGCA
1 TGAATTGCTTAACTTTCACATTCACTTCTCATCTAAAGTGACAACTTCAAGCA
151687 TACTCCAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (56 bp):
TGAATTGCTTAACTTTCACATTCACTTCTCATCTAAAGTGACAACTTCAAGCACCA
Done.