Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004138.1 Hibiscus syriacus cultivar Beakdansim tig00009052_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: 79093
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2493 original size:164 final size:164
Alignment explanation
Indices: 2011--2470 Score: 708
Period size: 164 Copynumber: 2.8 Consensus size: 164
2001 GAGGTGAAGG
* * * *
2011 GATCCAAACTCGATTTGATCAATTAAACCTTATTGATAAGATGAGATTGAAAGCTATTTGCCATG
1 GATCCAAGCTTGATTTGATCAATTAAGCCTTATTGATGAGATGAGATTGAAAGCTATTTGCCATG
2076 GCAGATATATCAAAAACGGATGATGAAAGATCATAACAAGAAAGTACATCTAAGAGAGTTCCAAG
66 GCAGATATATCAAAAACGGATGATGAAAGATCATAACAAGAAAGTACATCTAAGAGAGTTCCAAG
* *
2141 ATGTTGATCTAGTGCTAAAAAAGGAGACTGGATA
131 ATGTTGATCTAGTGCTAAAAAAGGAGATTGAATA
2175 GATCCAAGCTTGATTTGATCAATTAAGCCTTA-TGATGAGATGAGATTGAAAGCTATTTGCCATA
1 GATCCAAGCTTGATTTGATCAATTAAGCCTTATTGATGAGATGAGATTGAAAGCTATTTGCCAT-
* *
2239 GGCAGATATATCAAAAACGGATGATGAAATATCATAACAAGAAAGTACATCCAAGAGAGTTCCAA
65 GGCAGATATATCAAAAACGGATGATGAAAGATCATAACAAGAAAGTACATCTAAGAGAGTTCCAA
2304 GATGTTGATCTAGTGCTAAAAAAGGAGATTGAATA
130 GATGTTGATCTAGTGCTAAAAAAGGAGATTGAATA
** * *
2339 GATCCAAGCTTGATTTGATCAATTAAGGTTTATTGATGAGAATG-TATTGAAAGTTATTTGCCAT
1 GATCCAAGCTTGATTTGATCAATTAAGCCTTATTGATGAG-ATGAGATTGAAAGCTATTTGCCAT
* * * ** * *
2403 GGGTAGATGTATCAGAAGTGGATGATGAAAGATCACAACAAGAAAGTACATCTGAGAGAGTTCCA
65 -GGCAGATATATCAAAAACGGATGATGAAAGATCATAACAAGAAAGTACATCTAAGAGAGTTCCA
2468 AGA
129 AGA
2471 GAGCGATCTA
Statistics
Matches: 271, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
163 30 0.11
164 155 0.57
165 83 0.31
166 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (164 bp):
GATCCAAGCTTGATTTGATCAATTAAGCCTTATTGATGAGATGAGATTGAAAGCTATTTGCCATG
GCAGATATATCAAAAACGGATGATGAAAGATCATAACAAGAAAGTACATCTAAGAGAGTTCCAAG
ATGTTGATCTAGTGCTAAAAAAGGAGATTGAATA
Found at i:2674 original size:9 final size:8
Alignment explanation
Indices: 2670--2722 Score: 70
Period size: 8 Copynumber: 6.4 Consensus size: 8
2660 GAAAAAATAG
*
2670 AAAAAGGA
1 AAAAAGAA
2678 AAAAAGAA
1 AAAAAGAA
2686 AAAGAAGAA
1 AAA-AAGAA
*
2695 AAAAAAAA
1 AAAAAGAA
2703 AAAAAGGAA
1 AAAAA-GAA
2712 AAAAAGAA
1 AAAAAGAA
2720 AAA
1 AAA
2723 TTGAACCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
8 25 0.62
9 15 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2681 original size:16 final size:15
Alignment explanation
Indices: 2660--2722 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
2650 TATTATGCTT
*
2660 GAAAAAATAGAAAAAG
1 GAAAAAA-AAAAAAAG
2676 GAAAAAAGAAAAAGAAG
1 GAAAAAA-AAAAA-AAG
*
2693 AAAAAAAAAAAAAAAG
1 -GAAAAAAAAAAAAAG
2709 GAAAAAAAGAAAAA
1 GAAAAAAA-AAAAA
2723 TTGAACCAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.17
16 19 0.47
17 8 0.20
18 6 0.15
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAAAAAAG
Found at i:3235 original size:32 final size:32
Alignment explanation
Indices: 3199--3261 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3189 GTCAGACACA
* *
3199 AGAAGTATCTCTACGATATGAGCATAACAATG
1 AGAAGTATCTCTACAAGATGAGCATAACAATG
3231 AGAAGTATCTCTACAAGATGAGCATAACAAT
1 AGAAGTATCTCTACAAGATGAGCATAACAAT
3262 CATTTCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAATG
Found at i:5116 original size:114 final size:114
Alignment explanation
Indices: 4881--5107 Score: 409
Period size: 114 Copynumber: 2.0 Consensus size: 114
4871 GTTCCACGTT
*
4881 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTG
* *
4946 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTA
66 GTTCGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTA
4995 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTG
* *
5060 GTTCGGTATGAACCCTATAACCAATCATTGGATTTAAAAGATGAATTT
66 GTTCGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTT
5108 GATGATAGTC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATCTG
GTTCGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTA
Found at i:8393 original size:113 final size:113
Alignment explanation
Indices: 8181--8855 Score: 874
Period size: 113 Copynumber: 5.9 Consensus size: 113
8171 TAGCAAAGAT
* *
8181 TCAAATCCATCAC--AATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
8244 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
8292 TCAAATCCATCACTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
8357 AGAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
8405 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
8470 AGAAGGAACAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * * * *
8518 TTGAATTCATCATTTGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * *
8582 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *
8631 TCAAATTCATCACTCGATGGATTAACTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
8696 AGAA-GAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * * *
8743 TTAACTCTATCATAGAAGGATATAGATCAGCATCAACATTTCCAGATAAAGTTCATAATGAGAAG
1 TCAAATC---CAT--CA--CT-T-GAT--GGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAG
*
8808 AACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
55 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
8856 GACTTTAGCT
Statistics
Matches: 495, Mismatches: 53, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
111 13 0.03
112 43 0.09
113 353 0.71
115 3 0.01
117 1 0.00
119 1 0.00
121 3 0.01
122 1 0.00
123 77 0.16
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:8855 original size:20 final size:20
Alignment explanation
Indices: 8793--8855 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
8783 TCCAGATAAA
8793 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
8813 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
8832 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
8852 GTTC
1 GTTC
8856 GACTTTAGCT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 14 0.47
21 3 0.10
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:8942 original size:139 final size:134
Alignment explanation
Indices: 8774--9133 Score: 427
Period size: 139 Copynumber: 2.6 Consensus size: 134
8764 ATAGATCAGC
** *
8774 ATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGACGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * *
8839 ATGAGAAGAACTTGTTCGACTTTAG-CTTGATTCATCACCTATGGAGTTGAATGAAAGAAGAACC
66 ATGAGAAGAACTTGTTCAACCTT-GCCTTAATTCATCACATATGAAGTTGAAT----CAA-AACC
8903 TCACTTGAGG
125 TCACTTGAGG
* * *
8913 ATCAACATTTTCAGACGAAGTTCATAATGAGAAGAACTCGTCTGAAAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGACGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * **
8978 ATGATAATAACTTATTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAACACCTCTTTT
66 ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAACCTCACTT
9043 GAGG
131 GAGG
* * * * *
9047 ATCATCATTTCCAGAAGGAA-TTCATAATGAGAAGAACTCACCTGAAGAAGAAAAAGAAGTTCAT
1 ATCAACATTTCCAG-ACGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
*
9111 AATAAGAAGAACTTGTTCAACCT
65 AATGAGAAGAACTTGTTCAACCT
9134 CTTGTTAGAT
Statistics
Matches: 189, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
134 81 0.43
135 6 0.03
138 1 0.01
139 101 0.53
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (134 bp):
ATCAACATTTCCAGACGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAACCTCACTT
GAGG
Found at i:9781 original size:3 final size:3
Alignment explanation
Indices: 9773--9818 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
9763 TTTGAATCTG
9773 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9819 TTTCAAACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:14933 original size:29 final size:29
Alignment explanation
Indices: 14896--14987 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
14886 TATAAATTAG
14896 TCCTTAAACTTTTAAACATTCTAATTTCA
1 TCCTTAAACTTTTAAACATTCTAATTTCA
* * * * * *
14925 TCCTAAAACTATGACACTCATTCTAAATTGA
1 TCCTTAAACTTTTA-A-ACATTCTAATTTCA
* *
14956 TCCTTAAACTTTTGAACATTCTAGTTTCA
1 TCCTTAAACTTTTAAACATTCTAATTTCA
14985 TCC
1 TCC
14988 CATACTATGA
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 24 0.51
30 2 0.04
31 21 0.45
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (29 bp):
TCCTTAAACTTTTAAACATTCTAATTTCA
Found at i:14963 original size:60 final size:59
Alignment explanation
Indices: 14870--15027 Score: 167
Period size: 60 Copynumber: 2.7 Consensus size: 59
14860 ACATGTTCTC
* * * *
14870 AAACTATGACCCTTAATATAAATT-AGTCCTTAAACTTTTAAACATTCTAATTTCATCCTA
1 AAACTATGACACTCATTCTAAATTGA-TCCTTAAACTTTTAAACATTCTAATTTCATCC-A
* * *
14930 AAACTATGACACTCATTCTAAATTGATCCTTAAACTTTTGAACATTCTAGTTTCATCCC
1 AAACTATGACACTCATTCTAAATTGATCCTTAAACTTTTAAACATTCTAATTTCATCCA
* * * * *
14989 ATACTATGATTA-TCATTCAAAATTGGTCCCTAAACTTTT
1 AAACTATGA-CACTCATTCTAAATTGATCCTTAAACTTTT
15028 GCATCTTCCA
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 32 0.38
60 51 0.61
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (59 bp):
AAACTATGACACTCATTCTAAATTGATCCTTAAACTTTTAAACATTCTAATTTCATCCA
Found at i:15024 original size:59 final size:60
Alignment explanation
Indices: 14889--15028 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 60
14879 CCCTTAATAT
* * *
14889 AAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCTAAAACTATGACACTCATTCT
1 AAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCTAAAACTATGACACTCATTCA
* * * * *
14949 AAATTGATCCTTAAACTTTTGAACATTCTAGTTTCATCC-CATACTATGATTA-TCATTCA
1 AAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCTAAAACTATGA-CACTCATTCA
*
15008 AAATTGGTCCCTAAACTTTTG
1 AAATTGGTCCTTAAACTTTTG
15029 CATCTTCCAA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 33 0.48
60 36 0.52
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (60 bp):
AAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCTAAAACTATGACACTCATTCA
Found at i:15314 original size:58 final size:56
Alignment explanation
Indices: 15172--15341 Score: 162
Period size: 58 Copynumber: 2.9 Consensus size: 56
15162 GTATATACGT
* * *
15172 ATAATTTAGGATCAAATTGAAATGTAAAAAGTTTGAGGCCTAATTTAAAATGAAGATC
1 ATAATTTAGGATGAAATTGAAATGT-TAAAGTTTGAGGACTAA-TTAAAATGAAGATC
* * * * * *
15230 ATAGTTTGGGGATGAAAATGGAATGTTAGAAGTTTGAGGACTAATTAGAATGTTAG-TC
1 ATAATTT-AGGATGAAATTGAAATGTTA-AAGTTTGAGGACTAATTAAAATG-AAGATC
* *
15288 ATAATTTAGAGATGAAATTGAAATGTTTAAAGTTTAAGGATTAATTTAAAATGA
1 ATAATTTAG-GATGAAATTGAAATG-TTAAAGTTTGAGGACTAA-TTAAAATGA
15342 GGGTCATATA
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
57 1 0.01
58 48 0.54
59 40 0.45
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (56 bp):
ATAATTTAGGATGAAATTGAAATGTTAAAGTTTGAGGACTAATTAAAATGAAGATC
Found at i:15743 original size:31 final size:31
Alignment explanation
Indices: 15703--15769 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
15693 TACAATATAA
15703 TCCCCCAACATTTAGTTC-GTTTGCAACATGG
1 TCCCCCAACATTTAG-TCGGTTTGCAACATGG
* *
15734 TCCCTCAACATTTAGTCGGTTTGCAATATGG
1 TCCCCCAACATTTAGTCGGTTTGCAACATGG
15765 TCCCC
1 TCCCC
15770 GACGTAACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCGGTTTGCAACATGG
Found at i:17051 original size:31 final size:31
Alignment explanation
Indices: 17009--17086 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
16999 CAGTTACGTC
*
17009 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACAATATTGCAAACGGACTAAATGTTG
*
17040 AGGGACAATATTGCAAACGGACTAAATTTTG
1 AGGGACAATATTGCAAACGGACTAAATGTTG
**
17071 AGGGATTATATTGCAA
1 AGGGACAATATTGCAA
17087 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (31 bp):
AGGGACAATATTGCAAACGGACTAAATGTTG
Found at i:17790 original size:18 final size:19
Alignment explanation
Indices: 17754--17795 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
17744 ATTTTAATAA
*
17754 ATTATGATTGTAAACATTT
1 ATTATAATTGTAAACATTT
*
17773 ATTATAATT-TAAATATTT
1 ATTATAATTGTAAACATTT
*
17791 TTTAT
1 ATTAT
17796 TTTTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTATAATTGTAAACATTT
Found at i:17912 original size:217 final size:218
Alignment explanation
Indices: 17535--17957 Score: 787
Period size: 217 Copynumber: 1.9 Consensus size: 218
17525 TTAATTTACT
*
17535 ATTATGATTGTAAACATTTATTATAATTTTAATATTTTTATTTTTATTAAAATTAACTACTTCTG
1 ATTATGATTGTAAACATTTATTATAATTTAAATATTTTTATTTTTATTAAAATTAACTACTTC-G
17600 TATAAAAAAAATGGATAAACTATACATGTGACCATTCAACTATGATAAAAAAATAACGGTTAACG
65 TATAAAAAAAATGGATAAACTATACATGTGACCATTCAACTATGATAAAAAAATAACGGTTAACG
17665 GAACAGGTGACATGATAGTTAAAATATTTTTAGTATAATTACACAATTGGCCCATGTTACTTATA
130 GAACAGGTGACATGATAGTTAAAATATTTTTAGTATAATTACACAATTGGCCCATGTTACTTATA
17730 TATTCTTTCAACTCATTTTAATAA
195 TATTCTTTCAACTCATTTTAATAA
17754 ATTATGATTGTAAACATTTATTATAATTTAAATATTTTTTATTTTTATTAAAATTAACTACTTC-
1 ATTATGATTGTAAACATTTATTATAATTTAAATA-TTTTTATTTTTATTAAAATTAACTACTTCG
*
17818 TAT-AAAAAGATGGATAAACTATACATGTGACCATTCAACTATGATAAAAAAATAACGGTTAACG
65 TATAAAAAAAATGGATAAACTATACATGTGACCATTCAACTATGATAAAAAAATAACGGTTAACG
*
17882 GAACAGGTGATATGATAGTTAAAATATTTTTAGTATAATTACACAATTGGCCCATGTTACTTATA
130 GAACAGGTGACATGATAGTTAAAATATTTTTAGTATAATTACACAATTGGCCCATGTTACTTATA
17947 TATTCTTTCAA
195 TATTCTTTCAA
17958 TTTGGTTCTC
Statistics
Matches: 200, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
217 135 0.68
218 3 0.01
219 33 0.17
220 29 0.14
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (218 bp):
ATTATGATTGTAAACATTTATTATAATTTAAATATTTTTATTTTTATTAAAATTAACTACTTCGT
ATAAAAAAAATGGATAAACTATACATGTGACCATTCAACTATGATAAAAAAATAACGGTTAACGG
AACAGGTGACATGATAGTTAAAATATTTTTAGTATAATTACACAATTGGCCCATGTTACTTATAT
ATTCTTTCAACTCATTTTAATAA
Found at i:18318 original size:24 final size:26
Alignment explanation
Indices: 18285--18340 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
18275 ATAAAAATAC
*
18285 TTTTTGTTAA-TGAAAAATATTTATA
1 TTTTTGTTAAGTGAAAAATATTCATA
18310 TTTTT-TTAATGTGAAAAATATTCATA
1 TTTTTGTTAA-GTGAAAAATATTCATA
18336 TTTTT
1 TTTTT
18341 AATATGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 4 0.14
25 5 0.18
26 19 0.68
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (26 bp):
TTTTTGTTAAGTGAAAAATATTCATA
Found at i:18359 original size:31 final size:33
Alignment explanation
Indices: 18323--18383 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
18313 TTTTAATGTG
* *
18323 AAAAATATTCATAT-TTTTA-ATATGATTAAAT
1 AAAAATATTAATATGTTTTATATATAATTAAAT
18354 AAAAATATTAATATGTTTTATATATAATTA
1 AAAAATATTAATATGTTTTATATATAATTA
18384 TTAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 13 0.50
32 5 0.19
33 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (33 bp):
AAAAATATTAATATGTTTTATATATAATTAAAT
Found at i:21710 original size:21 final size:21
Alignment explanation
Indices: 21659--21718 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
21649 TATTATAATG
** *
21659 TTGATGTGACAGTTTACGATA
1 TTGATGTGACAGTCCACAATA
* **
21680 CTGACATGACAGTCCACAATA
1 TTGATGTGACAGTCCACAATA
21701 TTGATGTGACAGTCCACA
1 TTGATGTGACAGTCCACA
21719 CTAGTTGACA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TTGATGTGACAGTCCACAATA
Found at i:23335 original size:2 final size:2
Alignment explanation
Indices: 23323--23353 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
23313 TCTAAAATTA
23323 AT AT A- 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
23354 TTACGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25497 original size:2 final size:2
Alignment explanation
Indices: 25490--25541 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
25480 CAAAATCGTA
25490 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
25532 AT AT AT AT AT
1 AT AT AT AT AT
25542 TGAAATACTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37478 original size:81 final size:80
Alignment explanation
Indices: 37380--38674 Score: 1827
Period size: 81 Copynumber: 16.0 Consensus size: 80
37370 TATTCCAAAA
* *
37380 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGATGTCAATTATGCTAGTTATATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAG-TGTCAATTATGCCAGTTAGATGAAAG
*
37445 GTTAAATACCATTGAG
65 GTTAAATACCTTTGAG
* * *
37461 TAAAAGATTAATAGCCTAGCTGTGCATTTAACAGAAAGGTGCCAATTATTCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
*
37526 GTTAAATATCTTTGAG
65 GTTAAATACCTTTGAG
** * *
37542 TAAAAGATTAATAGCCTATATGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAT
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
* * *
37607 GTTAAATGCCTTTAAC
65 GTTAAATACCTTTGAG
* *
37623 TAAAATATTAAT-GACCTAGCTGTGCATTTGACAGAAATGTCTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATAG-CCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAA
*
37687 GGTTAAATACCTTTTAG
64 GGTTAAATACCTTTGAG
*
37704 TAAAAGATTAATAGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
37769 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* *
37785 TAAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
* * *
37850 GATAAATACATTTGAA
65 GTTAAATACCTTTGAG
* *
37866 TAAAAGATTAATAACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATAAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
37931 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* * * *
37947 TAAAAGATTAATAACCTAGCTGTGTATTTGATAGAAATGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
38012 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* * * * *
38028 TAAAATATTAATGGCCTAGCTGTGCATTTGATATAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
*
38093 GTTAAATACCTATGAG
65 GTTAAATACCTTTGAG
* * * *
38109 TAAAAGAGTAATAGCATAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGAAAT
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
38174 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* *
38190 TAAAAGAGTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
38255 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* * * *
38271 TAAAAGATTAATAACCTAGTTATGCATTTGACATAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
*
38336 GTTAAATATCTTTGAG
65 GTTAAATACCTTTGAG
* * * *
38352 TAAAAGATTAATGGCTTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
* * *
38417 GCTATATGCCTTTGAG
65 GTTAAATACCTTTGAG
* *
38433 TAAAAGATTAATAGCATGGCTGTGCATTTGACAGAAAGTTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAG-TGTCAATTATGCCAGTTAGATGAAAG
38498 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* * *
38514 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
*
38579 GTTAAATACCTTTAAG
65 GTTAAATACCTTTGAG
* * * **
38595 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTTTCAATCATGTAAGTTAGATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAG
* * *
38660 GCTATATGCCTTTGA
65 GTTAAATACCTTTGA
38675 CATAAATGAA
Statistics
Matches: 1095, Mismatches: 114, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
80 2 0.00
81 1090 1.00
82 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (80 bp):
TAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGTGTCAATTATGCCAGTTAGATGAAAGG
TTAAATACCTTTGAG
Found at i:43606 original size:23 final size:24
Alignment explanation
Indices: 43565--43613 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
43555 GGGGTTTTCA
43565 TTATTCAAGGACATTGTAAAAGTT
1 TTATTCAAGGACATTGTAAAAGTT
*
43589 TTATGTCAAGG-C-TTGTAAGAGTT
1 TTAT-TCAAGGACATTGTAAAAGTT
43612 TT
1 TT
43614 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 5 0.22
25 6 0.26
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (24 bp):
TTATTCAAGGACATTGTAAAAGTT
Found at i:45698 original size:6 final size:6
Alignment explanation
Indices: 45687--45719 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
45677 ACGGCTCGGC
45687 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCG
45720 AGGACTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:45896 original size:22 final size:22
Alignment explanation
Indices: 45871--45925 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
45861 TCAGGAGTTA
* *
45871 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
45893 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
45915 CGGGAGTTATA
1 CAGGAGTTATA
45926 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:51479 original size:5 final size:5
Alignment explanation
Indices: 51460--51503 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
51450 GTCCGTCCGT
* * * *
51460 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
51504 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:51512 original size:6 final size:6
Alignment explanation
Indices: 51501--51567 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
51491 ACGGCTCGGC
* *
51501 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
51549 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
51568 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:51867 original size:22 final size:22
Alignment explanation
Indices: 51842--51896 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
51832 TCAGGAGTTA
* *
51842 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
51864 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
51886 CGGGAGTTATA
1 CAGGAGTTATA
51897 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:56225 original size:20 final size:21
Alignment explanation
Indices: 56200--56239 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56190 AGTTTATTTA
56200 AATATT-AC-AAAGGTAGTATC
1 AATATTCACTAAAGG-AGTATC
56220 AATATTCACTAAAGGAGTAT
1 AATATTCACTAAAGGAGTAT
56240 TGGTGCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (21 bp):
AATATTCACTAAAGGAGTATC
Found at i:57253 original size:2 final size:2
Alignment explanation
Indices: 57246--57277 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57236 ATGGAAGAGG
57246 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
57278 TGATTTCACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65485 original size:9 final size:9
Alignment explanation
Indices: 65471--65531 Score: 79
Period size: 9 Copynumber: 6.7 Consensus size: 9
65461 TTTTTTTTAA
65471 AAAAAAAAC
1 AAAAAAAAC
65480 AAAAAAAAC
1 AAAAAAAAC
65489 AAAAAAAGAC
1 AAAAAAA-AC
*
65499 -AAAAAGAC
1 AAAAAAAAC
*
65507 AAAAAACAAA
1 AAAAAA-AAC
65517 AAAAAAAAC
1 AAAAAAAAC
65526 AAAAAA
1 AAAAAA
65532 GCCAAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 2 0.04
9 34 0.76
10 9 0.20
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:65549 original size:1 final size:1
Alignment explanation
Indices: 65469--65531 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
65459 TATTTTTTTT
* * * * * * * *
65469 AAAAAAAAAACAAAAAAAACAAAAAAAGACAAAAAGACAAAAAACAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
65532 GCCAAAATTT
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:71012 original size:27 final size:27
Alignment explanation
Indices: 70982--71069 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 27
70972 AGTGTTATTG
70982 GTATAAACAATCTATCGTAGTTAAGTT
1 GTATAAACAATCTATCGTAGTTAAGTT
* * * *
71009 GTATGTCAAGACTATCAAAT-GTA-TCAAGTG
1 GTA--T-AA-ACAATC-TATCGTAGTTAAGTT
71039 GTATAAACAATCTATCGTAGTTAAGTT
1 GTATAAACAATCTATCGTAGTTAAGTT
71066 GTAT
1 GTAT
71070 GTCAAGACCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 2 0.04
26 8 0.17
27 14 0.30
28 1 0.02
29 1 0.02
30 10 0.22
31 8 0.17
32 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (27 bp):
GTATAAACAATCTATCGTAGTTAAGTT
Found at i:71068 original size:57 final size:57
Alignment explanation
Indices: 70980--71094 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
70970 GAAGTGTTAT
*
70980 TGGTATAAACAATCTATCGTAGTTAAGTTGTATGTCAAGACTATCAAATGTATCAAG
1 TGGTATAAACAATCTATCGTAGTTAAGTTGTATGTCAAGACCATCAAATGTATCAAG
71037 TGGTATAAACAATCTATCGTAGTTAAGTTGTATGTCAAGACCATCAAATGTATCAAG
1 TGGTATAAACAATCTATCGTAGTTAAGTTGTATGTCAAGACCATCAAATGTATCAAG
71094 T
1 T
71095 TTTTCAGGTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (57 bp):
TGGTATAAACAATCTATCGTAGTTAAGTTGTATGTCAAGACCATCAAATGTATCAAG
Found at i:73231 original size:15 final size:15
Alignment explanation
Indices: 73211--73276 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
73201 TTCTAGAAAA
*
73211 TGAATTACTGTAATT
1 TGAATTACTGAAATT
73226 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
73241 TGAATTACTGCAAA-A
1 TGAATTACTG-AAATT
*
73256 TGAATTACTGGAATT
1 TGAATTACTGAAATT
73271 TGAATT
1 TGAATT
73277 CTAGAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
14 2 0.04
15 40 0.89
16 3 0.07
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:73247 original size:30 final size:30
Alignment explanation
Indices: 73211--73292 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
73201 TTCTAGAAAA
* **
73211 TGAATTACTGTAATTTGAATTACTGAAATT
1 TGAATTACTGCAAAATGAATTACTGAAATT
*
73241 TGAATTACTGCAAAATGAATTACTGGAATT
1 TGAATTACTGCAAAATGAATTACTGAAATT
73271 TGAATT-CTAG-AAAATGAATTAC
1 TGAATTACT-GCAAAATGAATTAC
73293 ATTTTTGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
29 14 0.30
30 33 0.70
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (30 bp):
TGAATTACTGCAAAATGAATTACTGAAATT
Found at i:73271 original size:45 final size:44
Alignment explanation
Indices: 73207--73292 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 44
73197 GGTTTTCTAG
* *
73207 AAAATGAATTACTGTAATTTGAATTACT-GAAATTTGAATTACTGC
1 AAAATGAATTACTGGAATTTGAATT-CTAGAAA-ATGAATTACTGC
73252 AAAATGAATTACTGGAATTTGAATTCTAGAAAATGAATTAC
1 AAAATGAATTACTGGAATTTGAATTCTAGAAAATGAATTAC
73293 ATTTTTGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 10 0.26
45 28 0.74
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (44 bp):
AAAATGAATTACTGGAATTTGAATTCTAGAAAATGAATTACTGC
Found at i:73290 original size:14 final size:15
Alignment explanation
Indices: 73203--73292 Score: 71
Period size: 15 Copynumber: 6.1 Consensus size: 15
73193 AATTGGTTTT
73203 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
**
73218 CT-GTAATTTGAATTA
1 CTAG-AAAATGAATTA
*
73233 CT-GAAATTTGAATTA
1 CTAGAAA-ATGAATTA
73248 CT-GCAAAATGAATTA
1 CTAG-AAAATGAATTA
* **
73263 CTGGAATTTGAATT-
1 CTAGAAAATGAATTA
73277 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
73292 C
1 C
73293 ATTTTTGGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
14 14 0.23
15 43 0.70
16 4 0.07
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (15 bp):
CTAGAAAATGAATTA
Found at i:73761 original size:74 final size:79
Alignment explanation
Indices: 73677--73842 Score: 190
Period size: 74 Copynumber: 2.2 Consensus size: 79
73667 TAAATACCTT
73677 TATT-AAAATATTAGATTAT-TATATTA-ATAATATTATTCATTATTA-AATATATAAAAA-ATA
1 TATTAAAAATATTA-A-TATCTATATTATATAATATTATTCATTATTATAATAT-TAAAAATATA
*
73737 TTA-TATATT-TTTAAA
63 ATATTATATTATTTAAA
**
73752 -A-TAAAAATA-TAATATCTATATTATTATAATATTATTTTTTATTATAATATTAAAAATATAAT
1 TATTAAAAATATTAATATCTATATTA-TATAATATTATTCATTATTATAATATTAAAAATATAAT
73814 ATTATATTATTTAAA
65 ATTATATTATTTAAA
73829 TATTAATAAATATT
1 TATTAA-AAATATT
73843 TTAAATATTT
Statistics
Matches: 76, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
71 3 0.04
72 8 0.11
73 3 0.04
74 30 0.39
75 10 0.13
76 6 0.08
77 6 0.08
78 1 0.01
79 3 0.04
80 5 0.07
81 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (79 bp):
TATTAAAAATATTAATATCTATATTATATAATATTATTCATTATTATAATATTAAAAATATAATA
TTATATTATTTAAA
Found at i:73831 original size:30 final size:33
Alignment explanation
Indices: 73776--73841 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
73766 TCTATATTAT
* *
73776 TATAATATTATTTTTTATTATAATATTAA-AAA
1 TATAATATTATATTATATTATAATATTAATAAA
73808 TATAATATTATATTAT-TTA-AATATTAATAAA
1 TATAATATTATATTATATTATAATATTAATAAA
73839 TAT
1 TAT
73842 TTTAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 9 0.29
32 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TATAATATTATATTATATTATAATATTAATAAA
Found at i:73850 original size:49 final size:49
Alignment explanation
Indices: 73732--73851 Score: 135
Period size: 48 Copynumber: 2.5 Consensus size: 49
73722 AATATATAAA
73732 AAATATT-ATATAT-TTTTAAA-A-TAAAAATATAATATCTATATTATT
1 AAATATTAATATATATTTTAAATATTAAAAATATAATATCTATATTATT
* * * *
73777 ATAATATTATTTTTTATTAT-AATATTAAAAATATAATAT-TATATTATTT
1 A-AATATTAATATATATTTTAAATATTAAAAATATAATATCTATATTA-TT
*
73826 AAATATTAATAAATATTTTAAATATT
1 AAATATTAATATATATTTTAAATATT
73852 TTAATAATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
45 1 0.02
46 6 0.10
47 5 0.08
48 24 0.41
49 23 0.39
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (49 bp):
AAATATTAATATATATTTTAAATATTAAAAATATAATATCTATATTATT
Found at i:74381 original size:64 final size:65
Alignment explanation
Indices: 74304--74427 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
74294 CGGTGCACTA
**
74304 GTGCACCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGTCTGAGTGCATCGATGCATTGCT
1 GTGCACCGATGCATAAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATTGCT
74367 G
65 G
* *
74368 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
1 GTGCACCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
74428 GAAATGCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
64 27 0.50
65 24 0.44
66 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCACCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATTGCTG
Found at i:74441 original size:64 final size:64
Alignment explanation
Indices: 74305--74442 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
74295 GGTGCACTAG
* ** ***
74305 TGCACCGATGCATAAAATGCATTCGATGTTTCAAAATAGTCTGAGTGCATCGATGCATTGCTGG
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATTGCAAA
*
74369 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCA-TG-AA
1 TGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATACCCTGAGTGCATCGATGCATTGCAA
74431 A
64 A
74432 TGCATTCGATG
1 TGCA-TCGATG
74443 TTCAATTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 4 0.06
64 34 0.53
65 23 0.36
66 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGCATTGCAAA
Found at i:77159 original size:21 final size:21
Alignment explanation
Indices: 77131--77210 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
77121 GCATGGCCTT
77131 GTGCATCGATGCACATTCAAG
1 GTGCATCGATGCACATTCAAG
* * * *
77152 GCGCATCGGTGCACCTTCACG
1 GTGCATCGATGCACATTCAAG
* *
77173 TTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AA-G
77196 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
77211 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
21 30 0.68
22 1 0.02
23 1 0.02
24 12 0.27
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCACATTCAAG
Found at i:78254 original size:18 final size:18
Alignment explanation
Indices: 78231--78268 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
78221 CAAAAAATGG
*
78231 AAAAAAATAATATAAAAT
1 AAAAAAATAAAATAAAAT
*
78249 AAAAAAATAAAATGAAAT
1 AAAAAAATAAAATAAAAT
78267 AA
1 AA
78269 CCAAGAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAAATAAAATAAAAT
Done.