Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005961.1 Hibiscus syriacus cultivar Beakdansim tig00014006_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: 95812
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3721 original size:2 final size:2
Alignment explanation
Indices: 3711--3830 Score: 53
Period size: 2 Copynumber: 62.5 Consensus size: 2
3701 AAATTGAAAA
*
3711 AT AT A- AT AT AT AT AT AT AT AT AT A- AT A- AA AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3748 AA ACT AT AT TT AT AT -T AT A- ACT AT AT AT -T AT -T AT AA ACT
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* * * *
3787 AT AT AT AA AT -T AT AT TT AT GT AA ACT AT AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT
3830 A
1 A
3831 AACTATATTG
Statistics
Matches: 89, Mismatches: 14, Indels: 30
0.67 0.11 0.23
Matches are distributed among these distances:
1 10 0.11
2 73 0.82
3 6 0.07
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3735 original size:19 final size:19
Alignment explanation
Indices: 3711--3793 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 19
3701 AAATTGAAAA
3711 ATATAATATATATATATAT
1 ATATAATATATATATATAT
3730 ATATAATA-A-A-AT-TAT
1 ATATAATATATATATATAT
*
3745 ATA-AA-ACTATATTTATAT
1 ATATAATA-TATATATATAT
3763 -TATAACTATATAT-TAT-T
1 ATATAA-TATATATATATAT
3780 ATA-AACTATATATA
1 ATATAA-TATATATA
3794 AATTATATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 21
0.71 0.01 0.28
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
15 7 0.13
16 3 0.06
17 15 0.28
18 11 0.21
19 13 0.25
20 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAATATATATATATAT
Found at i:3786 original size:34 final size:32
Alignment explanation
Indices: 3711--3800 Score: 94
Period size: 34 Copynumber: 2.8 Consensus size: 32
3701 AAATTGAAAA
*
3711 ATATAATA-TATATATATATATATAATAAAATT
1 ATATAAAACTATATATATAT-TATAATAAAATT
* *
3743 ATATAAAACTATATTTATATTATAACTATATATT
1 ATATAAAACTATATATATATTATAA-TA-AAATT
*
3777 AT-TATAAACTATATATAAATTATA
1 ATATA-AAACTATATATATATTATA
3801 TTTATGTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 12 0.24
33 14 0.29
34 23 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAAAACTATATATATATTATAATAAAATT
Found at i:3833 original size:48 final size:50
Alignment explanation
Indices: 3719--3852 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 50
3709 AAATATAATA
* *
3719 TATATATATATATATAATAAAAT-TATATAAAACTATATTTATATTATAAC
1 TATATATATATATAT-ATAAACTATATATAAAACTATATTTATAGTATAAC
*
3769 --TATATAT-TAT-TATAAACTATATAT-AAATTATATTTAT-GTA-AAC
1 TATATATATATATATATAAACTATATATAAAACTATATTTATAGTATAAC
*
3812 TATAGTATATATATATATAAACTATATTGTATAAACTATAT
1 TATA-TATATATATATATAAACTATA-TATA-AAACTATAT
3853 AAAATATATG
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
43 3 0.04
44 2 0.03
45 20 0.29
46 11 0.16
47 6 0.09
48 18 0.26
49 2 0.03
51 8 0.11
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (50 bp):
TATATATATATATATATAAACTATATATAAAACTATATTTATAGTATAAC
Found at i:3844 original size:22 final size:21
Alignment explanation
Indices: 3742--3869 Score: 67
Period size: 22 Copynumber: 6.1 Consensus size: 21
3732 ATAATAAAAT
3742 TATATA-AAACTATAT-T-TA
1 TATATATAAACTATATGTATA
3760 TAT-TAT-AACTATA--TAT-
1 TATATATAAACTATATGTATA
*
3776 TAT-TATAAACTATATATAAATTA
1 TATATATAAACTATATGT--A-TA
* *
3799 TATTTATGTAAACTATAGTATATA
1 TA--TATATAAACTATA-TGTATA
3823 TATATATAAACTATATTGTATA
1 TATATATAAACTATA-TGTATA
* * *
3845 AACTATATAAAATATATGTTTA
1 TA-TATATAAACTATATGTATA
3867 TAT
1 TAT
3870 GTTATAATTT
Statistics
Matches: 88, Mismatches: 8, Indels: 25
0.73 0.07 0.21
Matches are distributed among these distances:
16 7 0.08
17 17 0.19
18 3 0.03
19 1 0.01
21 2 0.02
22 25 0.28
23 14 0.16
24 4 0.05
25 2 0.02
26 10 0.11
27 3 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
TATATATAAACTATATGTATA
Found at i:4037 original size:18 final size:18
Alignment explanation
Indices: 3999--4037 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3989 AGTATTTACT
* *
3999 TTATATAGTTTATATATA
1 TTATATAGTTTATACACA
*
4017 TTATATGGTTTATACACA
1 TTATATAGTTTATACACA
4035 TTA
1 TTA
4038 GGTTTATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (18 bp):
TTATATAGTTTATACACA
Found at i:4083 original size:14 final size:14
Alignment explanation
Indices: 4038--4139 Score: 61
Period size: 14 Copynumber: 7.4 Consensus size: 14
4028 ATACACATTA
* *
4038 GGTTTATAGTTTAT
1 GGTTTAGAGTTTAG
* *
4052 GATTTA-AGGTTAG
1 GGTTTAGAGTTTAG
*
4065 TGTTTAGAGTTTAG
1 GGTTTAGAGTTTAG
*
4079 GGTTTA-ACATTTA-
1 GGTTTAGA-GTTTAG
* *
4092 TGTTTAAAGTTTAG
1 GGTTTAGAGTTTAG
4106 GGTTTATGA-TTTAG
1 GGTTTA-GAGTTTAG
*
4120 GATTTAG-GATTTAG
1 GGTTTAGAG-TTTAG
4134 GGTTTA
1 GGTTTA
4140 AGGTTTATAT
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
13 20 0.30
14 46 0.69
15 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (14 bp):
GGTTTAGAGTTTAG
Found at i:4084 original size:27 final size:26
Alignment explanation
Indices: 4035--4144 Score: 87
Period size: 27 Copynumber: 4.1 Consensus size: 26
4025 TTTATACACA
* * *
4035 TTAGGTTTATAGTTTATGATTTAAGG
1 TTAGGTTTAGAGTTTAGGGTTTAAGG
**
4061 TTAGTGTTTAGAGTTTAGGGTTTAACAT
1 TTAG-GTTTAGAGTTTAGGGTTTAA-GG
* * * *
4089 TTATGTTTAAAGTTTAGGGTTTATGAT
1 TTAGGTTTAGAGTTTAGGGTTTAAG-G
4116 TTAGGATTTAG-GATTTAGGGTTTAAGG
1 TTAGG-TTTAGAG-TTTAGGGTTTAAGG
4143 TT
1 TT
4145 TATATAAACT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
26 4 0.06
27 43 0.65
28 19 0.29
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (26 bp):
TTAGGTTTAGAGTTTAGGGTTTAAGG
Found at i:4146 original size:14 final size:14
Alignment explanation
Indices: 4054--4146 Score: 68
Period size: 14 Copynumber: 6.8 Consensus size: 14
4044 TAGTTTATGA
*
4054 TTTAAGG-TTAGTG
1 TTTAAGGTTTAGGG
4067 TTT-AGAGTTTAGGG
1 TTTAAG-GTTTAGGG
** *
4081 TTTAACATTTA-TG
1 TTTAAGGTTTAGGG
*
4094 TTTAAAGTTTAGGG
1 TTTAAGGTTTAGGG
* * *
4108 TTTATGATTTAGGA
1 TTTAAGGTTTAGGG
4122 TTT-AGGATTTAGGG
1 TTTAAGG-TTTAGGG
4136 TTTAAGGTTTA
1 TTTAAGGTTTA
4147 TATAAACTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
12 2 0.03
13 15 0.25
14 39 0.65
15 4 0.07
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:4968 original size:37 final size:36
Alignment explanation
Indices: 4926--5005 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
4916 TGCACTCTCC
* *
4926 ATGCATCAATGCACTC-GGGTTTTAATGAAAACATCGA
1 ATGCATCAATGCACTCAGGCTTTT--TCAAAACATCGA
**
4963 ATGCATTTGATGCACTCAGGCTTTTTCAAAACATCGA
1 ATGCA-TCAATGCACTCAGGCTTTTTCAAAACATCGA
5000 ATGCAT
1 ATGCAT
5006 TTGATGCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
36 1 0.03
37 21 0.57
38 9 0.24
39 6 0.16
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (36 bp):
ATGCATCAATGCACTCAGGCTTTTTCAAAACATCGA
Found at i:8184 original size:64 final size:63
Alignment explanation
Indices: 8031--8171 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
8021 CATCTTCAAT
* * *
8031 GTGCATCGATGCACTCTCA-AATAA--CAAACATCGAATGTAATTAATGCATCGATGTATAAGGA
1 GTGCATCGATGCAC-CCCATAA-AATGCAAACATCGAATGTAATTAATGCACCGATGCATAAGGA
* * * *
8093 GTGCATCGATGCATCCCCTTAAAATGCAAACATCGAATGTCATTTATGCACCGATGCA-CAGGCA
1 GTGCATCGATGCA-CCCCATAAAATGCAAACATCGAATGTAATTAATGCACCGATGCATAAGG-A
8157 GTGCATCGATGCACC
1 GTGCATCGATGCACC
8172 GATAAGGAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
62 17 0.25
63 8 0.12
64 42 0.63
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (63 bp):
GTGCATCGATGCACCCCATAAAATGCAAACATCGAATGTAATTAATGCACCGATGCATAAGGA
Found at i:14691 original size:200 final size:200
Alignment explanation
Indices: 14343--14748 Score: 803
Period size: 200 Copynumber: 2.0 Consensus size: 200
14333 ATATTGGGTA
*
14343 TTATAATACCCAAGGGAAAGAAACAAGAGTTTCCAGATAACTCTTGATTCTTCTTTCTTCTTCAA
1 TTATGATACCCAAGGGAAAGAAACAAGAGTTTCCAGATAACTCTTGATTCTTCTTTCTTCTTCAA
14408 CGTGAAGCACCCAAACCTAAGGTAAGTTTGATTTCTTTTGGTTAATCTTTCAAATTAAAGTATGA
66 CGTGAAGCACCCAAACCTAAGGTAAGTTTGATTTCTTTTGGTTAATCTTTCAAATTAAAGTATGA
14473 GTTTGATTTATGAAGCTTTAGGAAAGATTATGGAGATGAAAAATATTATAGAAACTCAAAGATTG
131 GTTTGATTTATGAAGCTTTAGGAAAGATTATGGAGATGAAAAATATTATAGAAACTCAAAGATTG
14538 GTGAG
196 GTGAG
14543 TTATGATACCCAAGGGAAAGAAACAAGAGTTTCCAGATAACTCTTGATTCTTCTTTCTTCTTCAA
1 TTATGATACCCAAGGGAAAGAAACAAGAGTTTCCAGATAACTCTTGATTCTTCTTTCTTCTTCAA
14608 CGTGAAGCACCCAAACCTAAGGTAAGTTTGATTTCTTTTGGTTAATCTTTCAAATTAAAGTATGA
66 CGTGAAGCACCCAAACCTAAGGTAAGTTTGATTTCTTTTGGTTAATCTTTCAAATTAAAGTATGA
14673 GTTTGATTTATGAAGCTTTAGGAAAGATTATGGAGATGAAAAATATTATAGAAACTCAAAGATTG
131 GTTTGATTTATGAAGCTTTAGGAAAGATTATGGAGATGAAAAATATTATAGAAACTCAAAGATTG
14738 GTGAG
196 GTGAG
14743 TTATGA
1 TTATGA
14749 AGGATTAAAG
Statistics
Matches: 205, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 205 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (200 bp):
TTATGATACCCAAGGGAAAGAAACAAGAGTTTCCAGATAACTCTTGATTCTTCTTTCTTCTTCAA
CGTGAAGCACCCAAACCTAAGGTAAGTTTGATTTCTTTTGGTTAATCTTTCAAATTAAAGTATGA
GTTTGATTTATGAAGCTTTAGGAAAGATTATGGAGATGAAAAATATTATAGAAACTCAAAGATTG
GTGAG
Found at i:15901 original size:23 final size:23
Alignment explanation
Indices: 15857--15901 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
15847 ATTATTATAT
*
15857 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* * *
15880 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTACAATTATACG
15902 AGCTGTGGTG
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:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:23977 original size:2 final size:2
Alignment explanation
Indices: 23970--24008 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
23960 TATGTTTAAT
*
23970 TA TA TA TA TA TA TA TA TA TG TA TA TA CT- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA T
24009 TATTCAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24104 original size:19 final size:19
Alignment explanation
Indices: 24080--24118 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
24070 TTGATTTTAT
24080 TTGGG-AATTTAGAGGGAAA
1 TTGGGAAATTTAGA-GGAAA
24099 TTGGGAAATTTAGAGGAAA
1 TTGGGAAATTTAGAGGAAA
24118 T
1 T
24119 AGAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.28
Consensus pattern (19 bp):
TTGGGAAATTTAGAGGAAA
Found at i:24126 original size:19 final size:20
Alignment explanation
Indices: 24085--24128 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
24075 TTTATTTGGG
* **
24085 AATTTAGAGGGAAATTGGGA
1 AATTTAGAGGGAAATAGAAA
24105 AATTTAGA-GGAAATAGAAA
1 AATTTAGAGGGAAATAGAAA
24124 AATTT
1 AATTT
24129 GGGAAGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (20 bp):
AATTTAGAGGGAAATAGAAA
Found at i:24351 original size:18 final size:18
Alignment explanation
Indices: 24328--24365 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
24318 ATATAAAGTA
*
24328 ATAAATTATATAGTTTAT
1 ATAAATGATATAGTTTAT
*
24346 ATAAATGGTATAGTTTAT
1 ATAAATGATATAGTTTAT
24364 AT
1 AT
24366 TTGTATTATT
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:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
ATAAATGATATAGTTTAT
Found at i:24521 original size:22 final size:21
Alignment explanation
Indices: 24470--24524 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
24460 CGTTTAATAC
24470 TAATATTCATTTATTATCAAAT
1 TAATATT-ATTTATTATCAAAT
24492 TAATTATTATTTATTATCAAAAT
1 TAA-TATTATTTATTATC-AAAT
*
24515 TTATATTATT
1 TAATATTATT
24525 AATGTAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATTATTTATTATCAAAT
Found at i:24619 original size:22 final size:24
Alignment explanation
Indices: 24583--24631 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
24573 TTATTTTTTC
24583 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
24606 TTTATAT-AATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
24629 TTT
1 TTT
24632 TCTTTGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:24907 original size:16 final size:16
Alignment explanation
Indices: 24890--24953 Score: 92
Period size: 16 Copynumber: 4.0 Consensus size: 16
24880 TCATTTACAT
*
24890 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAG
24906 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAG
* *
24922 GCCAGGTTGAAAACAG
1 GTCAGGTTAAAAACAG
*
24938 GTCAGGTTGAAAACAG
1 GTCAGGTTAAAAACAG
24954 ATCGGGTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:26076 original size:17 final size:15
Alignment explanation
Indices: 26046--26079 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
26036 TTTTCTTATT
26046 ATTTTGATTTATAAA
1 ATTTTGATTTATAAA
26061 ATTTTAGATATTATAAA
1 ATTTT-GAT-TTATAAA
26078 AT
1 AT
26080 GATCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 3 0.18
17 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTTTGATTTATAAA
Found at i:26294 original size:30 final size:31
Alignment explanation
Indices: 26260--26340 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 31
26250 AATGTTCGTA
* *
26260 AAATTTTAAAAATATATAATT-TATTTTCTG
1 AAATTTTAAAAATATATAATTAGATTTTATG
* *
26290 AAATTATAAAAAAATATAATTACGATTTTATG
1 AAATTTTAAAAATATATAATTA-GATTTTATG
26322 AATATTTTAAAAATGATAT
1 AA-ATTTTAAAAAT-ATAT
26341 GTAAAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 19 0.46
32 9 0.22
33 9 0.22
34 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (31 bp):
AAATTTTAAAAATATATAATTAGATTTTATG
Found at i:28305 original size:24 final size:25
Alignment explanation
Indices: 28254--28307 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
28244 TTTATAAATA
28254 AAAAAGTTAGATCCTTAATTACACT
1 AAAAAGTTAGATCCTTAATTACACT
*
28279 AAAAAGTTAGA-CATTTAATTACA-T
1 AAAAAGTTAGATC-CTTAATTACACT
28303 AAAAA
1 AAAAA
28308 AATAAGTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAAAGTTAGATCCTTAATTACACT
Found at i:28689 original size:3 final size:3
Alignment explanation
Indices: 28681--28738 Score: 71
Period size: 3 Copynumber: 18.0 Consensus size: 3
28671 ATTTATTTAT
*
28681 TTA TTA TTA TTA CTA TTA TTA TTA TTA TATA TATA TATA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA T-TA T-TA TTA TTA
28730 TTA TTA TTA
1 TTA TTA TTA
28739 AAAAATAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 37 0.71
4 15 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:30054 original size:9 final size:9
Alignment explanation
Indices: 30040--30064 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30030 GTTTACTTTT
30040 TATTATTAC
1 TATTATTAC
30049 TATTATTAC
1 TATTATTAC
30058 TATTATT
1 TATTATT
30065 TAACTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATTAC
Found at i:30271 original size:20 final size:19
Alignment explanation
Indices: 30246--30287 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
30236 TTATTTTATA
30246 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
30266 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
30285 AAT
1 AAT
30288 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:30289 original size:119 final size:119
Alignment explanation
Indices: 30144--30360 Score: 267
Period size: 120 Copynumber: 1.8 Consensus size: 119
30134 TTTAATCCTA
* * * * *
30144 TTTTAATATTTATTTATTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CAT
* *
30207 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTAATATTTCTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
** * ** * *
30262 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCTT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
*
30327 TTTCTAATATTTCTAAATAAATAAATATTTTATT
65 TTTCTAATATTTCTAAATAAATAAATATCTTATT
30361 AATATATATT
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
118 6 0.07
119 19 0.23
120 36 0.44
121 20 0.25
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (119 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TTCTAATATTTCTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
Found at i:30904 original size:18 final size:18
Alignment explanation
Indices: 30860--30904 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
30850 TTTCTTTCAA
30860 TTATTTATTACTTATTAT
1 TTATTTATTACTTATTAT
* *
30878 TT-TTATATTATTTTTTAT
1 TTATT-TATTACTTATTAT
30896 TTATTTATT
1 TTATTTATT
30905 TTATTCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTATTACTTATTAT
Found at i:35520 original size:2 final size:2
Alignment explanation
Indices: 35513--35572 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
35503 TATCCTTTTA
35513 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
35555 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
35573 CTTTTGTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35887 original size:1 final size:1
Alignment explanation
Indices: 35881--35943 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
35871 AAAGAAGAAG
* * ** * ** *
35881 AAAAAAAAACAAAAAAAAAACAAAAAGGAAAAAAACAAAAAGGAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35944 GGAAAATTGA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:35912 original size:15 final size:15
Alignment explanation
Indices: 35894--35930 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
35884 AAAAAACAAA
35894 AAAAAAACAAAAAGG
1 AAAAAAACAAAAAGG
35909 AAAAAAACAAAAAGG
1 AAAAAAACAAAAAGG
35924 AAAAAAA
1 AAAAAAA
35931 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAAAGG
Found at i:35918 original size:26 final size:26
Alignment explanation
Indices: 35882--35941 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
35872 AAGAAGAAGA
35882 AAAAAAAACAAAAA-AAAAACAAAAAG
1 AAAAAAAACAAAAAGAAAAA-AAAAAG
* *
35908 GAAAAAAACAAAAAGGAAAAAAAAAG
1 AAAAAAAACAAAAAGAAAAAAAAAAG
35934 AAAAAAAA
1 AAAAAAAA
35942 AAGGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (26 bp):
AAAAAAAACAAAAAGAAAAAAAAAAG
Found at i:35927 original size:22 final size:22
Alignment explanation
Indices: 35880--35949 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
35870 GAAAGAAGAA
*
35880 GAAAAAAAAACAAAAAAAAAA-
1 GAAAAAAAAAGAAAAAAAAAAG
* * *
35901 CAAAAAGGAAA-AAAACAAAAAG
1 GAAAAA-AAAAGAAAAAAAAAAG
35923 GAAAAAAAAAGAAAAAAAAAAG
1 GAAAAAAAAAGAAAAAAAAAAG
35945 GAAAA
1 GAAAA
35950 TTGAATCAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 17 0.43
22 23 0.57
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAGAAAAAAAAAAG
Found at i:35942 original size:15 final size:15
Alignment explanation
Indices: 35875--35943 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
35865 GCAAAGAAAG
35875 AAGAAGAAAAAAAAACA
1 AAGAA-AAAAAAAAA-A
*
35892 AA-AAAAAAACAAAA
1 AAGAAAAAAAAAAAA
* *
35906 AGGAAAAAAACAAAA
1 AAGAAAAAAAAAAAA
*
35921 AGGAAAAAAAAAGAAA
1 AAGAAAAAAAAA-AAA
35937 AA-AAAAA
1 AAGAAAAA
35944 GGAAAATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
14 2 0.04
15 36 0.78
16 6 0.13
17 2 0.04
ACGTcount: A:0.86, C:0.04, G:0.10, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAAA
Found at i:35944 original size:11 final size:11
Alignment explanation
Indices: 35881--35949 Score: 68
Period size: 11 Copynumber: 6.3 Consensus size: 11
35871 AAAGAAGAAG
*
35881 AAAAAAAAACA
1 AAAAAAAAAGA
*
35892 AAAAAAAAACA
1 AAAAAAAAAGA
**
35903 AAAAGGAAA-A
1 AAAAAAAAAGA
* *
35913 AAACAAAAAGG
1 AAAAAAAAAGA
35924 AAAAAAAAAGA
1 AAAAAAAAAGA
35935 AAAAAAAAAGGA
1 AAAAAAAAA-GA
35947 AAA
1 AAA
35950 TTGAATCAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
10 7 0.15
11 36 0.75
12 5 0.10
ACGTcount: A:0.86, C:0.04, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:35949 original size:10 final size:10
Alignment explanation
Indices: 35867--35942 Score: 66
Period size: 10 Copynumber: 7.3 Consensus size: 10
35857 CTCATCCAGC
*
35867 AAAGAAAGAA
1 AAAGAAAAAA
*
35877 GAAGAAAAAA
1 AAAGAAAAAA
*
35887 AAACAAAAAA
1 AAAGAAAAAA
35897 AAA-ACAAAAA
1 AAAGA-AAAAA
35907 GGAAA-AAAACAA
1 --AAAGAAAA-AA
35919 AAAGGAAAAAA
1 AAA-GAAAAAA
35930 AAAGAAAAAA
1 AAAGAAAAAA
35940 AAA
1 AAA
35943 AGGAAAATTG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
9 1 0.02
10 37 0.66
11 8 0.14
12 10 0.18
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:40825 original size:22 final size:22
Alignment explanation
Indices: 40796--40850 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
40786 ATCTACACTC
40796 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
40818 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
40840 TTCAAAGATGA
1 TTCAAAGATGA
40851 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:41654 original size:76 final size:76
Alignment explanation
Indices: 41528--41709 Score: 260
Period size: 76 Copynumber: 2.4 Consensus size: 76
41518 CTATTTCCCA
* *
41528 CATCTGTAAGTCCTATAGTGTATGATGTTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
* *
41593 AGCCTTAGGGT
66 AACCTTAGAGT
*
41604 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT-TGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCT-GGAGCTTTTTGATGTTTTCA
*
41668 AAACCTTCGAGT
65 AAACCTTAGAGT
* *
41680 CAGCTGTAAGCCCTACAGTGCA-GAATGTTT
1 CATCTGTAAGTCCTACAGTGCATG-ATGTTT
41710 TTTTATTATT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
75 2 0.02
76 93 0.98
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
AACCTTAGAGT
Found at i:41939 original size:113 final size:112
Alignment explanation
Indices: 41727--42263 Score: 722
Period size: 113 Copynumber: 4.8 Consensus size: 112
41717 ATTATTAAAA
*
41727 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTA-AGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* ** *
41792 GAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCA-TTCGATGGATCAG
65 GAAGAATTTGTTCAACCTTTT-GCTCAAATCCATCACTT-GATGGATCAG
* * * * *
41840 CATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAA
1 CATTTCCAGGT-AAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
*
41905 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGAATCAG
65 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* ** * *
41953 CTTTTCCAGAAAAAGTTCATAATAAAAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGA
1 CATTTCCAG-GTAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
42017 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
65 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* ** *
42065 CTTTTCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGA
1 CATTTCCAG-GTAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* ** * *
42130 GAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAG
65 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
* * *
42178 CATTGCCAGGTAGAGTTCATAATAAAAAAAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTA-AGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
42243 GAA-AATTTTGTTCAACCTTTT
65 GAAGAA-TTTGTTCAACCTTTT
42264 TCATGACTCT
Statistics
Matches: 385, Mismatches: 32, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
112 111 0.29
113 266 0.69
114 8 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (112 bp):
CATTTCCAGGTAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAG
Found at i:42126 original size:225 final size:227
Alignment explanation
Indices: 41740--42263 Score: 743
Period size: 225 Copynumber: 2.3 Consensus size: 227
41730 TTCCAGGTAG
* * *
41740 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATAAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
** * *** *
41805 AA-CTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAG
66 AACCTTTTCGCTCAAATCCATCATTCGATGGATCAGCATTACCAGAAAAAGTTCATAATGAAAAG
41869 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAAT
131 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAAT
* *
41934 CCATCACTTGATGAATCAGCTTTTCCAGAAAA
196 CCATCACTTGATGAATCAGCATTGCCAGAAAA
*
41966 AGTTCATAATAAAAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATAAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
42030 AACCTTTT-GCTCAAATCCATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAAAA
66 AACCTTTTCGCTCAAATCCATCA-TTCGATGGATCAGCATTACCAGAAAAAGTTCATAATGAAAA
* * * * **
42093 GAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAA
130 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAA
* * * ** *
42158 TTCATCATTTGATGGATCAGCATTGCCAGGTAG
195 TCCATCACTTGATGAATCAGCATTGCCAGAAAA
*
42191 AGTTCATAATAAAAAAAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAA-AATTTTGTT
1 AGTTCATAATAAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAA-TTTGTT
42255 CAACCTTTT
65 CAACCTTTT
42264 TCATGACTCT
Statistics
Matches: 265, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
225 192 0.72
226 73 0.28
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (227 bp):
AGTTCATAATAAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTCGCTCAAATCCATCATTCGATGGATCAGCATTACCAGAAAAAGTTCATAATGAAAAG
AACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAAT
CCATCACTTGATGAATCAGCATTGCCAGAAAA
Found at i:42278 original size:113 final size:114
Alignment explanation
Indices: 41727--42384 Score: 689
Period size: 113 Copynumber: 5.8 Consensus size: 114
41717 ATTATTAAAA
* *
41727 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* * * *
41792 GAAGAACTTGTTCAA-CTTTTCGCTTGAAT-TCATCATTCGATGGATCAG
66 GAAGAATTTGTTCAACCTTTTCTCATGAATCT-ATCATTTGATGGATCAG
* * * * * *
41840 CATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAA
1 CATTTCCAGGTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* * *
41905 GAAGAATTTGTTCAACCTTTTGCTCA--AATCCATCACTTGATGAATCAG
66 GAAGAATTTGTTCAACCTTTT-CTCATGAATCTATCATTTGATGGATCAG
* ** * *
41953 CTTTTCCAGAAAAAGTTCATAATAAAAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* *
42017 GAAGAATTTGTTCAACCTTTTGCTCA--AATCCATCACTTGATGGATCAG
66 GAAGAATTTGTTCAACCTTTT-CTCATGAATCTATCATTTGATGGATCAG
* ** *
42065 CTTTTCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* *
42130 GAAGAATTTGTTCAACCTTTTGT-TTGAAT-TCATCATTTGATGGATCAG
66 GAAGAATTTGTTCAACCTTTTCTCATGAATCT-ATCATTTGATGGATCAG
* * * *
42178 CATTGCCAGGTAGAGTTCATAATAAAAAAAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
1 CATTTCCAGGTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
* ** * *
42243 GAA-AATTTTGTTCAACCTTTT-TCATGACTCTATCATAAAAGGAGATAGATCAACAT
66 GAAGAA-TTTGTTCAACCTTTTCTCATGAATCTATCAT-----TTGATGGAT---CAG
* *
42299 CAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG-A-AAA-AAGAATAAGTTCATA
1 C-A--TTTCCAG-GTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATA
**
42360 ATGAGAAGAGCTTGTTCAACCTTTT
62 ATGAGAAGAATTTGTTCAACCTTTT
42385 GCATAACTCT
Statistics
Matches: 471, Mismatches: 51, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
112 112 0.24
113 270 0.57
114 6 0.01
115 2 0.00
118 6 0.01
121 38 0.08
122 5 0.01
123 1 0.00
124 30 0.06
125 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (114 bp):
CATTTCCAGGTAAAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTCTCATGAATCTATCATTTGATGGATCAG
Found at i:42408 original size:121 final size:121
Alignment explanation
Indices: 42191--42529 Score: 400
Period size: 121 Copynumber: 2.8 Consensus size: 121
42181 TGCCAGGTAG
* * * * **
42191 AGTTCATAATAAAAAAAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAAATTTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTG-A-AAA-AAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * * * *
42256 AACCTTTTTCATGACTCTATCATAAAAGGAGATAGATCAACATCAACTTTTCCAG-AGAA
63 AACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAG-A
*
42315 AGTTCATAATGAGAAGAACTCATCTGAAAAAAGAATAAGTTCATAATGAGAAGAGCTTGTTCAAC
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
* * * *
42380 CTTTTGCATAACTCTATCACAGAAGGAGATATATCATCATCAGCATTTCCAGAAGG
66 CTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAGA
* * * *
42436 AGTTCACAATGAGAAGAACTCATCTG-AAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTGCAAC
1 AGTTCATAATGAGAAGAACTCATCTGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
*
42500 C-TTTGC-TAGATTAC-ATCACAGAAGGAGATA
66 CTTTTGCATA-ACT-CTATCACAGAAGGAGATA
42530 AATTGTCATC
Statistics
Matches: 190, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
118 2 0.01
119 23 0.12
120 36 0.19
121 100 0.53
122 5 0.03
123 1 0.01
124 23 0.12
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (121 bp):
AGTTCATAATGAGAAGAACTCATCTGAAAAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
CTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAAGA
Found at i:42488 original size:17 final size:17
Alignment explanation
Indices: 42430--42488 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
42420 CAGCATTTCC
*
42430 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
42447 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
42465 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
42483 AGAAGA
1 AGAAGA
42489 GCTTGTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 2 0.06
19 10 0.30
20 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:42750 original size:3 final size:3
Alignment explanation
Indices: 42742--42806 Score: 96
Period size: 3 Copynumber: 21.0 Consensus size: 3
42732 ATTTATTTAT
42742 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA
42788 TATA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
42807 AAAAATAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 47 0.80
4 10 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44311 original size:20 final size:19
Alignment explanation
Indices: 44286--44327 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
44276 TTATTTTATA
44286 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
44306 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
44325 AAT
1 AAT
44328 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:44320 original size:119 final size:119
Alignment explanation
Indices: 44184--44400 Score: 285
Period size: 120 Copynumber: 1.8 Consensus size: 119
44174 TTTAATCCTA
* * * * *
44184 TTTTAATATTTATTTATTTTCCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCAT
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-T
*
44247 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTGATATTTCTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
** * ** *
44302 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCT
*
44367 TTTCTGATATTTCTAAATAAATAAATATTTTATT
65 TTTCTGATATTTCTAAATAAATAAATATCTTATT
44401 AATATATATT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
118 6 0.07
119 19 0.23
120 36 0.43
121 22 0.27
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (119 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTT
TTCTGATATTTCTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
Found at i:53796 original size:22 final size:21
Alignment explanation
Indices: 53771--53831 Score: 50
Period size: 22 Copynumber: 2.8 Consensus size: 21
53761 CTTAAGAAGT
53771 GGTCATTCGAGACAAATAAAGA
1 GGTC-TTCGAGACAAATAAAGA
** * *
53793 GGTCTTTTAGGAAAAATACAGA
1 GGTCTTCGA-GACAAATAAAGA
*
53815 GGTCCTTCGGGACAAAT
1 GGT-CTTCGAGACAAAT
53832 TTCATATGCC
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
21 3 0.10
22 23 0.79
23 3 0.10
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (21 bp):
GGTCTTCGAGACAAATAAAGA
Found at i:53959 original size:3 final size:3
Alignment explanation
Indices: 53951--53983 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53941 AGGTAATTAC
53951 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53984 GTTTACATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:57228 original size:252 final size:252
Alignment explanation
Indices: 56772--57317 Score: 966
Period size: 252 Copynumber: 2.2 Consensus size: 252
56762 TAAAGCTGAT
*
56772 ACATGCACCAGAGTCCATAATACATGCTTCTTTGGACTAATGTTTCTACTCGAACCTATTAGAAG
1 ACATGCACCAGAGTCCATAATACATGCTTCTTTGGACTAATGTTTCTACTCGAACCTATTACAAG
*
56837 AACAAAGTCTCGAAGATTCAAAGCATATATATTCAGTAACTATAATGTGAATGAATCATTAAACG
66 AACAAAGTCTCGAAGATTCAAAGCATATATATTCAGTAACTATAATGTGAATGAATCATCAAACG
56902 ATTCTAATGTTGCTCCCTTTAATGTTTTAGATTCAAGGTCGAATCTTTTAAAAAAAAGGGAGGAT
131 ATTCTAATGTTGCTCCCTTTAATGTTTTAGATTCAAGGTCGAATCTTTTAAAAAAAAGGGAGGAT
*
56967 GATACATGCATCACAAGACTCACATCAAAGGAAGAAGTAATAAATCTTCCAAATGAG
196 GAAACATGCATCACAAGACTCACATCAAAGGAAGAAGTAATAAATCTTCCAAATGAG
* * *
57024 ACATGAACCAGAGTCCATAATACATGCTTTTTTGGACAAATGTTTCTACTCGAACCTATTACAAG
1 ACATGCACCAGAGTCCATAATACATGCTTCTTTGGACTAATGTTTCTACTCGAACCTATTACAAG
* * * *
57089 AACAAAGTCTCGAAGATTCAAAGCATATCTATTCGGTAACTATAATGTGAATGAATTATCAAATG
66 AACAAAGTCTCGAAGATTCAAAGCATATATATTCAGTAACTATAATGTGAATGAATCATCAAACG
** *
57154 ATTCTAATGTTGCTCCCTTTAATGTTTTAGATTCAAGGTCGAATCTTTTTGAAGAAAGGGAGGAT
131 ATTCTAATGTTGCTCCCTTTAATGTTTTAGATTCAAGGTCGAATCTTTTAAAAAAAAGGGAGGAT
*
57219 GAAACATGCATCACAAGACTCACATCAAAGGAAGAAGTAATAAATCTTCCAAATGAT
196 GAAACATGCATCACAAGACTCACATCAAAGGAAGAAGTAATAAATCTTCCAAATGAG
57276 ACATGCACCAGAGTCCATAATACATGCTTCTTTGGACTAATG
1 ACATGCACCAGAGTCCATAATACATGCTTCTTTGGACTAATG
57318 ATACAATTCG
Statistics
Matches: 277, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
252 277 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (252 bp):
ACATGCACCAGAGTCCATAATACATGCTTCTTTGGACTAATGTTTCTACTCGAACCTATTACAAG
AACAAAGTCTCGAAGATTCAAAGCATATATATTCAGTAACTATAATGTGAATGAATCATCAAACG
ATTCTAATGTTGCTCCCTTTAATGTTTTAGATTCAAGGTCGAATCTTTTAAAAAAAAGGGAGGAT
GAAACATGCATCACAAGACTCACATCAAAGGAAGAAGTAATAAATCTTCCAAATGAG
Found at i:58392 original size:2 final size:2
Alignment explanation
Indices: 58380--58410 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
58370 TGTGAACGAG
58380 AT AT GAT 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
58411 TTATGTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60274 original size:3 final size:3
Alignment explanation
Indices: 60223--60255 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
60213 AGGTAATTGC
60223 ATT ATT ATT AATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT
60256 ATGTTATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:60701 original size:21 final size:21
Alignment explanation
Indices: 60652--60702 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
60642 GCCGAAAATT
*
60652 ACTGTAGCAGGGTATCGGTAC
1 ACTGTAGCAGGGTATCGATAC
*
60673 ACTATAGCAGGGTATCGATAC
1 ACTGTAGCAGGGTATCGATAC
*
60694 CCTGTAGCA
1 ACTGTAGCA
60703 TTCTGGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCGATAC
Found at i:60778 original size:22 final size:22
Alignment explanation
Indices: 60726--60779 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
60716 TAACATTTGG
* *
60726 TATTGTTCACGATATTGTTCAT
1 TATTGTTCACGATACTGTACAT
* * * *
60748 TAATATTCATGGTACTGTACAT
1 TATTGTTCACGATACTGTACAT
60770 TATTGTTCAC
1 TATTGTTCAC
60780 AATATTGTTC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (22 bp):
TATTGTTCACGATACTGTACAT
Found at i:62357 original size:31 final size:31
Alignment explanation
Indices: 62285--62358 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
62275 AACCTGTGAT
* *
62285 GATCACATCTTAATTAAATAAAAATGAAAGT
1 GATCACATCTTAATTAAATAAAAACGAAAGC
*
62316 GACCACATCTTAATTAAATAAAAACGAAAGC
1 GATCACATCTTAATTAAATAAAAACGAAAGC
*
62347 GATCATATCTTA
1 GATCACATCTTA
62359 TGTTTTTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (31 bp):
GATCACATCTTAATTAAATAAAAACGAAAGC
Found at i:76674 original size:19 final size:19
Alignment explanation
Indices: 76636--76687 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
76626 TTTTGAATTG
76636 GTCAAAGTCAACGG--TGC
1 GTCAAAGTCAACGGTCTGC
*
76653 GTCAAAGTCAATGGTCTGC
1 GTCAAAGTCAACGGTCTGC
*
76672 GTCAAAATCAACGGTC
1 GTCAAAGTCAACGGTC
76688 CGGAAAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 13 0.43
19 17 0.57
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (19 bp):
GTCAAAGTCAACGGTCTGC
Found at i:77470 original size:9 final size:9
Alignment explanation
Indices: 77451--77529 Score: 53
Period size: 9 Copynumber: 9.1 Consensus size: 9
77441 AATAAAAAAT
77451 ATTATATATA
1 ATTA-ATATA
77461 ATTAATATA
1 ATTAATATA
77470 A--AATAT-
1 ATTAATATA
*
77476 A-TAAAAT-
1 ATTAATATA
77483 ATTATATATA
1 ATTA-ATATA
77493 ATTAATATA
1 ATTAATATA
** *
77502 AAAAATATT
1 ATTAATATA
77511 A-TATATATA
1 ATTA-ATATA
77520 ATTAATATA
1 ATTAATATA
77529 A
1 A
77530 AAAATAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
6 1 0.02
7 10 0.18
8 3 0.05
9 32 0.57
10 10 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTAATATA
Found at i:77470 original size:25 final size:25
Alignment explanation
Indices: 77442--77535 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 25
77432 AAATAGAAAA
77442 ATAAAAAATATTATATATAATTAATAT
1 ATAAAAAATATTATATATAATT-A-AT
77469 AAAATATATAAAATATTATATATAATTAAT
1 ---ATA-A-AAAATATTATATATAATTAAT
77499 ATAAAAAATATTATATATATAATTAAT
1 ATAAAAAATA-T-TATATATAATTAAT
77526 ATAAAAAATA
1 ATAAAAAATA
77536 AAAAAATATT
Statistics
Matches: 60, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.10
26 2 0.03
27 27 0.45
30 5 0.08
31 2 0.03
32 18 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAAAAAATATTATATATAATTAAT
Found at i:77485 original size:32 final size:31
Alignment explanation
Indices: 77433--77552 Score: 149
Period size: 32 Copynumber: 3.9 Consensus size: 31
77423 TCATTAAAAA
*
77433 AATAGAAAAATAAAAAATATTATATATAATT
1 AATATAAAAATAAAAAATATTATATATAATT
*
77464 AATATAAAATATATAAAATATTATATATAATT
1 AATATAAAA-ATAAAAAATATTATATATAATT
* *
77496 AATAT--AAA-AAATATTA-TATATATAATT
1 AATATAAAAATAAAAAATATTATATATAATT
77523 AATATAAAAAATAAAAAAATATTATATATA
1 AATAT-AAAAAT-AAAAAATATTATATATA
77553 TATATATATA
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
27 16 0.21
28 5 0.07
29 1 0.01
30 5 0.07
31 8 0.11
32 32 0.43
33 8 0.11
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
AATATAAAAATAAAAAATATTATATATAATT
Found at i:78997 original size:298 final size:299
Alignment explanation
Indices: 78561--79156 Score: 1004
Period size: 298 Copynumber: 2.0 Consensus size: 299
78551 GTTTATTTAT
**
78561 TTTTAATAAAATTATTTTGATTTTTGCATGAAATTACACAATACGTAAAATCTAGTATAGGAAAA
1 TTTTAATAAAATTATTTAAATTTTTGCATGAAATTACACAATACGTAAAATCTAGTATAGGAAAA
78626 CTTTGAAGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAGTATTTCTTTT
66 CTTTGAAGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAGTATTTCTTTT
78691 ACAAAATGATGATGATGATGATGATAAATATTTTATAATTT-AAAAA-T-TAAAAATTTCATATT
131 ACAAAATGATGATGATGATGATGATAAATATTTTATAATTTAAAAAATTATAAAAATTTCATA-T
*
78753 TTTTTTAAAAAAAATTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATA
195 CTTTTT-AAAAAAATTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATA
78818 AAC-TTTAATTACAATTGAAGGATCAAAAGAATTATTATTA
259 AACTTTTAATTACAATTGAAGGATCAAAAGAATTATTATTA
* * *
78858 TTTTATATAAAATTATTTAAAATTTTT-CATGAAATTACACAATATGTATAATCTATTATAGGAA
1 TTTTA-ATAAAATTATTT-AAATTTTTGCATGAAATTACACAATACGTAAAATCTAGTATAGGAA
* *
78922 AACTTTGAGGGTAAGTATTTTAAAATATGAATAGTTTTATAAAAGTTTTATAACCAGTATTTCTT
64 AACTTTGAAGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAGTATTTCTT
78987 TTACAAAATGATGATGATGATGATGATAAATATTTTATAATTTAAAAAATTATAAAAATTTCATA
129 TTACAAAATGATGATGATGATGATGATAAATATTTTATAATTTAAAAAATTATAAAAATTTCATA
* **
79052 TCTTTTTGAAAATTTTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATA
194 TCTTTTTAAAAAAATTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATA
* *
79117 AACTTTTAATTACAATTGAGGGATCAAATGAATTATTATT
259 AACTTTTAATTACAATTGAAGGATCAAAAGAATTATTATT
79157 CATTAATTAT
Statistics
Matches: 280, Mismatches: 13, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
297 5 0.02
298 152 0.54
299 69 0.25
300 41 0.15
301 13 0.05
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (299 bp):
TTTTAATAAAATTATTTAAATTTTTGCATGAAATTACACAATACGTAAAATCTAGTATAGGAAAA
CTTTGAAGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAGTATTTCTTTT
ACAAAATGATGATGATGATGATGATAAATATTTTATAATTTAAAAAATTATAAAAATTTCATATC
TTTTTAAAAAAATTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAA
CTTTTAATTACAATTGAAGGATCAAAAGAATTATTATTA
Found at i:87106 original size:21 final size:21
Alignment explanation
Indices: 87055--87107 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
87045 ATTATGACTA
87055 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
87076 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
87097 TCGCAATGCGA
1 TCGCAATGCGA
87108 ATAAGCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:87127 original size:41 final size:41
Alignment explanation
Indices: 87082--87190 Score: 105
Period size: 41 Copynumber: 2.7 Consensus size: 41
87072 AATTTCGCGT
*
87082 TGCGATTTTCCCAATTCGCAATGCGA-A-TAAGCAAATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGATACTAA-C-AATCGCAA
* ** * * *
87123 TGCGAATTTGGAAAATAGCAATGCGATACTAACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGATACTAACAATCGCAA
* *
87164 TGCGATTTTCCTAATTCGCATTGCGAT
1 TGCGATTTTCCAAATTCGCAATGCGAT
87191 TTACGTATTC
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
41 47 0.90
42 2 0.04
43 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCAAATTCGCAATGCGATACTAACAATCGCAA
Found at i:87188 original size:21 final size:21
Alignment explanation
Indices: 87158--87230 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
87148 ATACTAACTA
*
87158 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
87179 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
***
87199 TCGTGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
87220 TCGCAATGCGA
1 TCGCAATGCGA
87231 ATACGTAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:87245 original size:20 final size:20
Alignment explanation
Indices: 87220--87331 Score: 129
Period size: 20 Copynumber: 5.5 Consensus size: 20
87210 TTTTCATAAT
87220 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
87240 TCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAA-TACGTAAA
* * *
87260 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAA-TACGTAAA
87281 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
87301 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
87321 TCGCAATGCGA
1 TCGCAATGCGA
87332 TTTACATAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.75
21 17 0.21
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:87292 original size:41 final size:41
Alignment explanation
Indices: 87220--87313 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
87210 TTTTCATAAT
*
87220 TCGCAATGCGAA-TACGTAAATCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAA-TACGTAAA
* * *
87260 TCGCATTGCGAATTATGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
87301 TCGCAATGCGAAT
1 TCGCAATGCGAAT
87314 CTTACTATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATACGTAAA
Found at i:87974 original size:33 final size:34
Alignment explanation
Indices: 87926--87991 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
87916 TTTCATTTCG
**
87926 CGTTGCGATTTTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
87959 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
87992 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:87993 original size:20 final size:19
Alignment explanation
Indices: 87904--88016 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
87894 GAAACCAAAA
*
87904 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
87923 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
87942 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
87956 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
87975 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
87995 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
88015 TC
1 TC
88017 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 32 0.41
20 31 0.39
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:89291 original size:18 final size:18
Alignment explanation
Indices: 89268--89314 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
89258 CTCCACTTCG
89268 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
89286 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
89304 AGAGCCATCAC
1 AGAGCCATCAC
89315 TTGATCGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.30, C:0.47, G:0.13, T:0.11
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:89873 original size:95 final size:87
Alignment explanation
Indices: 89716--89895 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 87
89706 TAGATTGCTT
89716 AGTAAATGTATTCGGTTGCTGCCATACTGCTAAACTGTTATTAACACTGTGAAGTTAGTATTTGT
1 AGTAAATGTATTCGGTTGCTGCCATACTGCTAAACTGTTATTAACACTGTGAAGTTAGTATTTGT
89781 CTTTTTGTTTTGTCTTTTGGTTGA
66 C--TTTGTTTTGTCTTTTGGTTGA
* * *
89805 AGTAAATTTATTCGGTTTCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATGTATTCGGTTGCTGCC-ATACTGCTAAACTGT-TA----TTAACACTGTGAAGTTAGT
89870 ATTTGTCTTTGTTTTGTCTTTTGGTT
60 ATTTGTCTTTGTTTTGTCTTTTGGTT
89896 AAAAGTTTGA
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
89 21 0.26
90 14 0.17
91 2 0.02
93 19 0.23
95 26 0.32
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.48
Consensus pattern (87 bp):
AGTAAATGTATTCGGTTGCTGCCATACTGCTAAACTGTTATTAACACTGTGAAGTTAGTATTTGT
CTTTGTTTTGTCTTTTGGTTGA
Found at i:90199 original size:42 final size:42
Alignment explanation
Indices: 90120--90199 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
90110 GACTCGCCTG
* * *
90120 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
* * * *
90162 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCC
90200 ATTGTCATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
Found at i:91607 original size:14 final size:14
Alignment explanation
Indices: 91588--91623 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
91578 ATTGTTTAAT
91588 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
91602 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
91616 TGATTTGT
1 TGATTTGT
91624 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:91763 original size:33 final size:33
Alignment explanation
Indices: 91726--91815 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
91716 AAAAAGTACT
* * * *
91726 ATCGCAATGCGAAATGAAGATCGCAATGAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
91759 ATCGCAACGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
91792 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
91816 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:91833 original size:19 final size:19
Alignment explanation
Indices: 91811--91885 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 19
91801 CGAAATTAAA
91811 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
91830 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
91845 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
91863 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
91882 TTCG
1 TTCG
91886 TATTGTGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 8 0.18
16 3 0.07
17 3 0.07
19 31 0.69
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:91873 original size:52 final size:52
Alignment explanation
Indices: 91811--91928 Score: 173
Period size: 52 Copynumber: 2.2 Consensus size: 52
91801 CGAAATTAAA
** *
91811 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAAT
* * *
91863 TTCGCGTTGCGATTTTCATTTCGTATTGTGATTCTCTCGTTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAAT
91915 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
91929 AGACATTAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 48 0.81
53 11 0.19
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (52 bp):
TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAAT
Found at i:91895 original size:19 final size:19
Alignment explanation
Indices: 91811--91895 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
91801 CGAAATTAAA
*
91811 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
91830 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
91846 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
91863 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
91882 TTCGTATTGTGATT
1 TTCGCATTGCGATT
91896 CTCTCGTTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
14 6 0.11
16 6 0.11
17 6 0.11
19 35 0.66
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:95241 original size:21 final size:20
Alignment explanation
Indices: 95194--95245 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
95184 TTTTCCTAAT
*
95194 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
95214 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
95235 TCGCAATGCGA
1 TCGCAATGCGA
95246 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:95259 original size:20 final size:20
Alignment explanation
Indices: 95234--95291 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
95224 AATTTGGAAA
* *
95234 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
*
95254 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
95274 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
95292 AAATCGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:95298 original size:20 final size:20
Alignment explanation
Indices: 95230--95300 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
95220 TGCGAATTTG
* * *
95230 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
**
95250 GACTATCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
***
95270 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
95290 GAAAATCGCAA
1 GAAAATCGCAA
95301 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:95584 original size:14 final size:14
Alignment explanation
Indices: 95565--95618 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
95555 GAAAATCGCA
95565 TTGCGATTTTTTCG
1 TTGCGATTTTTTCG
95579 TTGCGATTTTTATTTCG
1 TTGCGA--TTT-TTTCG
*
95596 CATTGCGATTTTCTCG
1 --TTGCGATTTTTTCG
95612 TTGCGAT
1 TTGCGAT
95619 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 13 0.38
16 7 0.21
17 8 0.24
19 6 0.18
ACGTcount: A:0.11, C:0.17, G:0.20, T:0.52
Consensus pattern (14 bp):
TTGCGATTTTTTCG
Found at i:95584 original size:33 final size:33
Alignment explanation
Indices: 95547--95617 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
95537 AAAATTGCAA
*
95547 TGCGAAATGAAAATCGCATTGCGATTTTTTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
95580 TGCGATTTTTATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
95613 TGCGA
1 TGCGA
95618 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:95603 original size:19 final size:18
Alignment explanation
Indices: 95560--95607 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
95550 GAAATGAAAA
95560 TCGCATTGCGA--TTTTT
1 TCGCATTGCGATTTTTTT
95576 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTT-TT
95593 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
95608 CTCGTTGCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.22
16 6 0.22
17 5 0.19
19 10 0.37
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (18 bp):
TCGCATTGCGATTTTTTT
Done.