Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003276.1 Hibiscus syriacus cultivar Beakdansim tig00006888_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: 96782
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3027 original size:12 final size:12
Alignment explanation
Indices: 3010--3034 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3000 AATTAGCCGA
3010 GGCCAAGTGATG
1 GGCCAAGTGATG
3022 GGCCAAGTGATG
1 GGCCAAGTGATG
3034 G
1 G
3035 AAGTGATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GGCCAAGTGATG
Found at i:6214 original size:15 final size:15
Alignment explanation
Indices: 6170--6221 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
6160 TTAATGTCAT
6170 ATTAAAATAAAAATA
1 ATTAAAATAAAAATA
* *
6185 A--AATAATTCAGAATA
1 ATTAA-AA-TAAAAATA
6200 ATTAAAATAAAAATA
1 ATTAAAATAAAAATA
6215 ATTAAAA
1 ATTAAAA
6222 ATTCATTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 21 0.72
16 2 0.07
17 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
ATTAAAATAAAAATA
Found at i:8698 original size:2 final size:2
Alignment explanation
Indices: 8691--8730 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8681 CACTGGGCTA
8691 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
8731 CATAGGCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8808 original size:2 final size:2
Alignment explanation
Indices: 8801--8842 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
8791 AAATTTACAT
8801 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8842 T
1 T
8843 TACTTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8810 original size:19 final size:19
Alignment explanation
Indices: 8788--8835 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
8778 TTTTTATTTT
* *
8788 TATAAATTTACATTATATA
1 TATAAATATACATAATATA
* *
8807 TATATATATATATAATATA
1 TATAAATATACATAATATA
*
8826 TATATATATA
1 TATAAATATA
8836 TATATATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATAAATATACATAATATA
Found at i:9119 original size:21 final size:20
Alignment explanation
Indices: 9071--9267 Score: 115
Period size: 21 Copynumber: 9.7 Consensus size: 20
9061 GTTTCCAGAT
*
9071 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAA-TTCGACTA
*
9092 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
*
9113 TCGCAATG-GAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
*
9132 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
* *
9153 TCGCAATGCGAAAAT-GTA-AA
1 TCGCAATGCG-AATTCG-ACTA
*
9173 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
*
9194 TCGCAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
*
9214 TCGCAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
*
9234 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
*
9255 TTGCAATGCGAAT
1 TCGCAATGCGAAT
9268 ATGTAAATCG
Statistics
Matches: 145, Mismatches: 15, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
19 12 0.08
20 61 0.42
21 71 0.49
22 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATTCGACTA
Found at i:9182 original size:41 final size:41
Alignment explanation
Indices: 9091--9224 Score: 218
Period size: 41 Copynumber: 3.3 Consensus size: 41
9081 AACTTCGACT
* *
9091 ATCGCAATGCGA-ACTTGGACTATCGCAATG-GAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
*
9131 ATCGCAATGCGATAGTCGACTATCGCAATGCGAAAATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
9172 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
9213 ATCGCAATGCGA
1 ATCGCAATGCGA
9225 ATATGTAAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
40 26 0.30
41 62 0.70
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:9217 original size:61 final size:61
Alignment explanation
Indices: 9152--9285 Score: 250
Period size: 61 Copynumber: 2.2 Consensus size: 61
9142 ATAGTCGACT
9152 ATCGCAATGCGAAAATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAAAATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
* *
9213 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATTGCAATGCGAATATGTAA
1 ATCGCAATGCGAAAATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
9274 ATCGCAATGCGA
1 ATCGCAATGCGA
9286 TAGTCGAAGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (61 bp):
ATCGCAATGCGAAAATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:9227 original size:102 final size:102
Alignment explanation
Indices: 9085--9292 Score: 348
Period size: 102 Copynumber: 2.0 Consensus size: 102
9075 AACGCGAACT
*
9085 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGGAATATGTAAATCGCAATGCGATAGTCGA
1 TCGACTATCGCAATGCGAACTTGGACAATCGCAATGGAATATGTAAATCGCAATGCGATAGTCGA
9150 CTATCGCAATGCGAAAATGTAAATCGCAATGCGATAG
66 CTATCGCAATGCGAAAATGTAAATCGCAATGCGATAG
*
9187 TCGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 TCGACTATCGCAATGCGAACT-TGGACAATCGCAATG-GAATATGTAAATCGCAATGCGATAGTC
* *
9250 GACTATTGCAATGCGAATATGTAAATCGCAATGCGATAG
64 GACTATCGCAATGCGAAAATGTAAATCGCAATGCGATAG
9289 TCGA
1 TCGA
9293 AGTTCGCATT
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
101 10 0.10
102 90 0.90
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (102 bp):
TCGACTATCGCAATGCGAACTTGGACAATCGCAATGGAATATGTAAATCGCAATGCGATAGTCGA
CTATCGCAATGCGAAAATGTAAATCGCAATGCGATAG
Found at i:9306 original size:41 final size:41
Alignment explanation
Indices: 9214--9306 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
9204 AATATGTAAA
9214 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTAT
1 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAC-AT
9256 T-GCAATGCGAATATGTAAATCGCAATGCGATAGTCGA-AGT
1 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACA-T
*
9296 TCGCATTGCGA
1 TCGCAATGCGA
9307 TTTACATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
39 1 0.02
40 2 0.04
41 44 0.92
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACAT
Found at i:9973 original size:6 final size:6
Alignment explanation
Indices: 9951--9988 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
9941 CCGCCGTCTC
*
9951 GGTCG- GGTCGT GATCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
9989 AATACGTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.03, C:0.16, G:0.50, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:10129 original size:21 final size:21
Alignment explanation
Indices: 10077--10134 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
10067 CGTTGCGATT
*
10077 TTGGACTATCGTAA--CGAAT
1 TTGGACTATCGTAATGCGAAC
*
10096 TTGGAATAAATCGTAATGCGAAC
1 TTGGACT--ATCGTAATGCGAAC
*
10119 TTGGACTATCGCAATG
1 TTGGACTATCGTAATG
10135 GACTATCGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 6 0.19
21 15 0.48
23 10 0.32
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGGACTATCGTAATGCGAAC
Found at i:10138 original size:13 final size:13
Alignment explanation
Indices: 10120--10201 Score: 62
Period size: 13 Copynumber: 6.2 Consensus size: 13
10110 AATGCGAACT
10120 TGGACTATCGCAA
1 TGGACTATCGCAA
10133 TGGACTATCGCAA
1 TGGACTATCGCAA
* *
10146 TGCGAATAT-GTAAA
1 TG-GACTATCG-CAA
* *
10160 TCG-CAAT-GCGAA
1 TGGACTATCGC-AA
10172 CTTGGACTATCGCAA
1 --TGGACTATCGCAA
10187 TGGACTATCGCAA
1 TGGACTATCGCAA
10200 TG
1 TG
10202 CGAATATGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 5 0.09
13 32 0.59
14 10 0.19
15 5 0.09
16 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (13 bp):
TGGACTATCGCAA
Found at i:10164 original size:20 final size:20
Alignment explanation
Indices: 10139--10225 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
10129 GCAATGGACT
10139 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
10159 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTA-A
*
10180 ATCGCAATG-G---A-CT--
1 ATCGCAATGCGAATATGTAA
10193 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
10213 ATCGCAATGCGAA
1 ATCGCAATGCGAA
10226 CTTGGACTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
13 9 0.17
14 1 0.02
17 1 0.02
18 1 0.02
20 30 0.58
21 10 0.19
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:10168 original size:54 final size:54
Alignment explanation
Indices: 10102--10242 Score: 273
Period size: 54 Copynumber: 2.6 Consensus size: 54
10092 GAATTTGGAA
*
10102 TAAATCGTAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
1 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
10156 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
1 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
10210 TAAATCGCAATGCGAACTTGGACTATCGCAATG
1 TAAATCGCAATGCGAACTTGGACTATCGCAATG
10243 CGAACTTCGA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (54 bp):
TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
Found at i:10239 original size:21 final size:21
Alignment explanation
Indices: 10187--10266 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
10177 ACTATCGCAA
10187 TGGACTATCGCAATGCGAA-T
1 TGGACTATCGCAATGCGAACT
* *
10207 ATGTA-AATCGCAATGCGAACT
1 -TGGACTATCGCAATGCGAACT
10228 TGGACTATCGCAATGCGAACT
1 TGGACTATCGCAATGCGAACT
* *
10249 TCGACTATCGCATTGCGA
1 TGGACTATCGCAATGCGA
10267 TTTACATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
TGGACTATCGCAATGCGAACT
Found at i:10321 original size:21 final size:20
Alignment explanation
Indices: 10275--10400 Score: 110
Period size: 21 Copynumber: 6.6 Consensus size: 20
10265 GATTTACATA
* * *
10275 TTCGCATTGTGATAGTCGAC
1 TTCGCATTGCGATAGTCAAG
10295 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGT-CAAG
10317 TTCGCATTGCG--A-T--AG
1 TTCGCATTGCGATAGTCAAG
10332 TTCGCATTGCG--A-T--AG
1 TTCGCATTGCGATAGTCAAG
10347 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAG
10368 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAG
*
10389 TTCGCGTTGCGA
1 TTCGCATTGCGA
10401 ATCTGGAAAC
Statistics
Matches: 93, Mismatches: 4, Indels: 17
0.82 0.04 0.15
Matches are distributed among these distances:
15 28 0.30
17 1 0.01
18 2 0.02
19 1 0.01
20 2 0.02
21 56 0.60
22 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAG
Found at i:10335 original size:15 final size:15
Alignment explanation
Indices: 10315--10362 Score: 96
Period size: 15 Copynumber: 3.2 Consensus size: 15
10305 CGATAGTCCA
10315 AGTTCGCATTGCGAT
1 AGTTCGCATTGCGAT
10330 AGTTCGCATTGCGAT
1 AGTTCGCATTGCGAT
10345 AGTTCGCATTGCGAT
1 AGTTCGCATTGCGAT
10360 AGT
1 AGT
10363 CCAAGTTCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (15 bp):
AGTTCGCATTGCGAT
Found at i:10809 original size:23 final size:24
Alignment explanation
Indices: 10774--10819 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
10764 GTGACACATA
** *
10774 AATTAAATTAAAATTAAT-TAATT
1 AATTAAAAGAAAATAAATGTAATT
10797 AATTAAAAGAAAATAAATGTAAT
1 AATTAAAAGAAAATAAATGTAAT
10820 AATCAAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AATTAAAAGAAAATAAATGTAATT
Found at i:10988 original size:100 final size:100
Alignment explanation
Indices: 10797--11106 Score: 440
Period size: 100 Copynumber: 3.1 Consensus size: 100
10787 TTAATTAATT
* * * * *
10797 AATTAAAAGAAAATAAATGTAATAATCAAATTGAATGGTGACATGGCACCGTCACCATTCAATTT
1 AATTAAAATAAAATAAATGTAATCATCAAATTGAATGGTGACA---CA-TGACACCATTCCATTT
10862 GAAGATTAATTTTATTTTAATTTATTAAAATTAGGACTA
62 GAAGATTAATTTTATTTTAATTTATTAAAATTAGGACTA
* * *
10901 AATTAAAATAAAATAAATATAATCATCAAATTGAATGGTGACACATGGCATCATTCCATTTGAAG
1 AATTAAAATAAAATAAATGTAATCATCAAATTGAATGGTGACACATGACACCATTCCATTTGAAG
*
10966 ATTAATTTTATTTTAATTTATTAAAATTAGGATTA
66 ATTAATTTTATTTTAATTTATTAAAATTAGGACTA
* * *
11001 AATTAAAATAAAATAAATGTAATCATCAAATTGAATGGTGATACTTGACACCATCCCATTTGAAG
1 AATTAAAATAAAATAAATGTAATCATCAAATTGAATGGTGACACATGACACCATTCCATTTGAAG
** * *
11066 ATTAATTTTATTTTAACGTATTAAAATTATGACAA
66 ATTAATTTTATTTTAATTTATTAAAATTAGGACTA
11101 AATTAA
1 AATTAA
11107 TAGAATATAT
Statistics
Matches: 187, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
100 145 0.78
101 2 0.01
104 40 0.21
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (100 bp):
AATTAAAATAAAATAAATGTAATCATCAAATTGAATGGTGACACATGACACCATTCCATTTGAAG
ATTAATTTTATTTTAATTTATTAAAATTAGGACTA
Found at i:16782 original size:21 final size:22
Alignment explanation
Indices: 16753--16808 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
16743 TTGTCCAGGT
*
16753 TTTTTTTATTTAACT-TTATTG
1 TTTTATTATTTAACTATTATTG
* *
16774 TTTTATTATTATTACTATTATTT
1 TTTTATTATT-TAACTATTATTG
16797 TTATTATTATTT
1 TT-TTATTATTT
16809 TAATACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.31
22 4 0.14
23 8 0.28
24 8 0.28
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTATTTAACTATTATTG
Found at i:16808 original size:12 final size:12
Alignment explanation
Indices: 16776--16809 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16766 CTTTATTGTT
*
16776 TTATTATTATTA
1 TTATTATTTTTA
*
16788 CTATTATTTTTA
1 TTATTATTTTTA
16800 TTATTATTTT
1 TTATTATTTT
16810 AATACAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:17555 original size:32 final size:34
Alignment explanation
Indices: 17514--17621 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 34
17504 GGTAAGACAT
* *
17514 TTATTTTTATGTTAGTAT-TTT-T-TAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
17546 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
* *
17580 TT-TTTTT-TATTAAAATAATATTTATATAATTATTA
1 TTATTTTTATATT--AAT-ATATTTATGTAAATATTA
17615 TTTATTT
1 -TTATTT
17622 AGAATTATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
32 20 0.31
33 8 0.12
34 9 0.14
35 22 0.34
36 2 0.03
37 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:17785 original size:17 final size:17
Alignment explanation
Indices: 17763--17816 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
17753 AATGTTAATA
17763 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
17780 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
17797 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
17814 TTT
1 TTT
17817 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:19376 original size:21 final size:21
Alignment explanation
Indices: 19346--19393 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19336 GCAGGGGTAC
* *
19346 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
19367 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
19388 ATGCCA
1 ATGCCA
19394 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:19423 original size:21 final size:21
Alignment explanation
Indices: 19397--19469 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
19387 TATGCCATCT
*
19397 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
*
19418 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
19439 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
19460 CCGCAGGGTT
1 CCGCAGGGTT
19470 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:19430 original size:42 final size:41
Alignment explanation
Indices: 19384--19478 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 41
19374 GCCCACCAGT
* *
19384 TTATATGCCATCTCCG-CAGGGTTACATTCCGAGCCCGCAGGG
1 TTATATACCATC-CCGCCA-GGTTACATGCCGAGCCCGCAGGG
* * *
19426 TTATATTCCTAGCCCGCCAGGTTACATGCCTAGCCCGCAGGG
1 TTATATACC-ATCCCGCCAGGTTACATGCCGAGCCCGCAGGG
*
19468 TTTTATACCAT
1 TTATATACCAT
19479 ATGGAGGTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.02
42 39 0.89
43 4 0.09
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (41 bp):
TTATATACCATCCCGCCAGGTTACATGCCGAGCCCGCAGGG
Found at i:20042 original size:34 final size:34
Alignment explanation
Indices: 19992--20089 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
19982 AAATGTTTTT
*
19992 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
20026 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
20060 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
20090 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:20717 original size:125 final size:123
Alignment explanation
Indices: 20490--20728 Score: 417
Period size: 125 Copynumber: 1.9 Consensus size: 123
20480 TTACCTGATT
20490 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
20555 TGACAAAATAATGGAAGGCGCCCCCGGGAACGCCCTTCATGTGAATAGTGAAATAATAGG
66 TG--AAAATAATGGAAGGCGCCCCCGGGAACGCCCTTCATGTGAATAGTGAAATAATAGG
*
20615 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
20680 TG-AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGAAAATAATGGAA-G-GCGCCCCCGGGAACGC-CCTTCATGTGAATAGT
20729 ACTCCGATTA
Statistics
Matches: 110, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
122 11 0.10
123 1 0.01
124 16 0.15
125 82 0.75
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (123 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGAAAATAATGGAAGGCGCCCCCGGGAACGCCCTTCATGTGAATAGTGAAATAATAGG
Found at i:20812 original size:8 final size:8
Alignment explanation
Indices: 20799--20839 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
20789 TCACAAGCTT
20799 TCAAATTC
1 TCAAATTC
20807 TCAAATTC
1 TCAAATTC
* *
20815 CCAAACTC
1 TCAAATTC
20823 T-AAATTC
1 TCAAATTC
20830 TCAAATTC
1 TCAAATTC
20838 TC
1 TC
20840 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:23766 original size:23 final size:24
Alignment explanation
Indices: 23740--23786 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
23730 TATTCAAATG
*
23740 AATGTTTTTG-TTTCTA-ATAATTT
1 AATGTTATTGATTT-TATATAATTT
23763 AATGTTATTGATTTTATATAATTT
1 AATGTTATTGATTTTATATAATTT
23787 GTCAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (24 bp):
AATGTTATTGATTTTATATAATTT
Found at i:26096 original size:20 final size:20
Alignment explanation
Indices: 26073--26111 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26063 TTTTATTTCA
26073 CTATTAATTT-ATATATTTAG
1 CTATTAATTTCA-ATATTTAG
*
26093 CTATTTATTTCAATATTTA
1 CTATTAATTTCAATATTTA
26112 TTTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
CTATTAATTTCAATATTTAG
Found at i:26122 original size:13 final size:13
Alignment explanation
Indices: 26094--26126 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
26084 TATATTTAGC
*
26094 TATTTA-TTTCAA
1 TATTTATTTTAAA
26106 TATTTATTTTAAA
1 TATTTATTTTAAA
26119 TATTTATT
1 TATTTATT
26127 ATCTAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATTTTAAA
Found at i:32154 original size:23 final size:23
Alignment explanation
Indices: 32124--32168 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
32114 TGTTATGTGT
*
32124 GGCTTGCAAGTTGGCAAGTTGAA
1 GGCTTGCAAGTTGACAAGTTGAA
32147 GGCTTGCAAGTTGACAAGTTGA
1 GGCTTGCAAGTTGACAAGTTGA
32169 CAAGTTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.27
Consensus pattern (23 bp):
GGCTTGCAAGTTGACAAGTTGAA
Found at i:32157 original size:15 final size:15
Alignment explanation
Indices: 32137--32191 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
32127 TTGCAAGTTG
32137 GCAAGTTGAAGGCTT
1 GCAAGTTGAAGGCTT
*
32152 GCAAGTTGACAAG-TT
1 GCAAGTTGA-AGGCTT
*
32167 GACAAGTTGAAGACTT
1 G-CAAGTTGAAGGCTT
32183 GCAAGTTGA
1 GCAAGTTGA
32192 CAAGTTGGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (15 bp):
GCAAGTTGAAGGCTT
Found at i:32173 original size:31 final size:31
Alignment explanation
Indices: 32130--32204 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
32120 GTGTGGCTTG
*
32130 CAAGTTGGCAAGTTGAAGGCTTGCAAGTTGA
1 CAAGTTGGCAAGTTGAAGACTTGCAAGTTGA
*
32161 CAAGTTGACAAGTTGAAGACTTGCAAGTTGA
1 CAAGTTGGCAAGTTGAAGACTTGCAAGTTGA
32192 CAAGTTGGCAAGT
1 CAAGTTGGCAAGT
32205 GGCCAACTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.25
Consensus pattern (31 bp):
CAAGTTGGCAAGTTGAAGACTTGCAAGTTGA
Found at i:32255 original size:60 final size:60
Alignment explanation
Indices: 32183--32360 Score: 313
Period size: 60 Copynumber: 3.0 Consensus size: 60
32173 TTGAAGACTT
32183 GCAAGTTGACAAGTTGGCAAGTGGCCAACTTGTGCACATGGGATAATTCATCTTTGGTTG
1 GCAAGTTGACAAGTTGGCAAGTGGCCAACTTGTGCACATGGGATAATTCATCTTTGGTTG
*
32243 GCAAGTTGACAAGTTGGCAAGTGTCCAACTTGTGCACATGGGATAATTCATCTTTGGTTG
1 GCAAGTTGACAAGTTGGCAAGTGGCCAACTTGTGCACATGGGATAATTCATCTTTGGTTG
* *
32303 GCAAGTTGACAAATTGTGCAAGTGGCCAACTTGTGCACATGGGA-ATTTCATCTTTGGT
1 GCAAGTTGACAAGTTG-GCAAGTGGCCAACTTGTGCACATGGGATAATTCATCTTTGGT
32361 CCATAAAATA
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 87 0.77
61 26 0.23
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (60 bp):
GCAAGTTGACAAGTTGGCAAGTGGCCAACTTGTGCACATGGGATAATTCATCTTTGGTTG
Found at i:36072 original size:29 final size:29
Alignment explanation
Indices: 36038--36096 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
36028 CTTAAATTAA
36038 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
36067 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
36096 T
1 T
36097 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:40748 original size:29 final size:29
Alignment explanation
Indices: 40714--40772 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
40704 CCTAAATTAA
40714 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
40743 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
40772 T
1 T
40773 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:46792 original size:18 final size:19
Alignment explanation
Indices: 46771--46806 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46761 AAAATAAAAA
*
46771 AATATTTA-AATTACAATG
1 AATATTTATAACTACAATG
46789 AATATTTATAACTACAAT
1 AATATTTATAACTACAAT
46807 CGTAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
AATATTTATAACTACAATG
Found at i:52566 original size:15 final size:15
Alignment explanation
Indices: 52548--52578 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52538 AAATTCTAAA
52548 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
52563 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
52578 T
1 T
52579 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:56397 original size:21 final size:21
Alignment explanation
Indices: 56355--56397 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
56345 TTTCTGGGAT
*
56355 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
56376 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
56397 A
1 A
56398 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:56449 original size:19 final size:19
Alignment explanation
Indices: 56425--56461 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56415 GAACGCTAGA
*
56425 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
56444 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
56462 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:57268 original size:103 final size:103
Alignment explanation
Indices: 56940--57260 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
56930 GTAGAGGGTC
*
56940 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
57005 TTGATCCTTGGCATAAGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
57043 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
57108 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
57146 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
57211 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
57249 TATGTGTTCCTT
1 TATGTGGTCCTT
57261 ATGGACATTA
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:57335 original size:23 final size:23
Alignment explanation
Indices: 57276--57339 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
57266 CATTATTATA
57276 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* * *
57299 CGGCACTCCA-GTGCAATTTTACG
1 TGGCACT-TAGGTGCAATTCTACG
57322 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
57340 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
25 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:63420 original size:21 final size:21
Alignment explanation
Indices: 63380--63420 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
63370 TCTGGGCTAA
*
63380 GGGAATCGATACCCATTCAAG
1 GGGAATCGATACCCACTCAAG
*
63401 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
63421 ACAAATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCACTCAAG
Found at i:64150 original size:103 final size:103
Alignment explanation
Indices: 63966--64286 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
63956 GTAGAGGGTC
*
63966 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
64031 TTGGTCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
64069 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGAGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
64134 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
64172 TATGTGGTCCTTCGGGGCATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
64237 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
64275 TATGTGGTCCTT
1 TATGTGGTCCTT
64287 ATGGACATTA
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:64336 original size:23 final size:23
Alignment explanation
Indices: 64303--64365 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
64293 ATTATTATAT
64303 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * * *
64326 GTCACTCCGGTGCAATTTTACGT
1 GGCACTACGGTGCAATTCTACGC
64349 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
64366 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:65296 original size:21 final size:21
Alignment explanation
Indices: 65250--65296 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
65240 GATTTTGACT
* *
65250 ATCGCTTTGCGATTTTCCAAA
1 ATCGCGTTGCGATTTTACAAA
* *
65271 TTCGCGTTGCGATTTTAGAAA
1 ATCGCGTTGCGATTTTACAAA
65292 ATCGC
1 ATCGC
65297 AATGCGAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTACAAA
Found at i:65355 original size:41 final size:41
Alignment explanation
Indices: 65310--65586 Score: 482
Period size: 41 Copynumber: 6.8 Consensus size: 41
65300 GCGAATATGT
* *
65310 AAATCGCAACGCGATTCTAACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* *
65351 AAATCGTAACGCGATTCTGACTATCGCAAAGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
65392 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
65433 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
65474 AAATCGCAACACGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* * *
65515 AAATCGCAATGCGATTCTGACTATCGCAACACGATAATAAA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
65556 AAATCGCAACGCGATTCTGACTATCGCAACG
1 AAATCGCAACGCGATTCTGACTATCGCAACG
65587 TGATTTTCCA
Statistics
Matches: 224, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 224 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:66060 original size:19 final size:19
Alignment explanation
Indices: 66036--66144 Score: 101
Period size: 19 Copynumber: 5.4 Consensus size: 19
66026 TTATTTTGGA
66036 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
66055 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
66077 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * *
66099 ATTTTAACTATCGCAACAA
1 TTTTTCACTATCGCAACAC
* *
66118 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
66137 ATTTTTCA
1 -TTTTTCA
66145 AAATTGTGTT
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
19 42 0.56
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:68381 original size:96 final size:96
Alignment explanation
Indices: 68206--68396 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 96
68196 TACTATTATA
*
68206 TATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
1 TATACAATAAAGCTTGAGATATCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
* *
68271 ATCCATCTAGCCTGATAAAGGTGATTATATC
66 ATCCAGCTAACCTGATAAAGGTGATTATATC
* * *
68302 TATACAATAAAGCTTGAGCTATCCCTCTAAGGCAATTGGTTAAACGTCCCGACTTTATGGATAAG
1 TATACAATAAAGCTTGAGATATCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
* *
68367 ATTCAGCTAACCTGATAAAGGTGTTTATAT
66 ATCCAGCTAACCTGATAAAGGTGATTATAT
68397 ATTGAGCTGT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (96 bp):
TATACAATAAAGCTTGAGATATCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGATAAG
ATCCAGCTAACCTGATAAAGGTGATTATATC
Found at i:70117 original size:116 final size:118
Alignment explanation
Indices: 69787--70246 Score: 471
Period size: 116 Copynumber: 3.8 Consensus size: 118
69777 CAATACAAGC
* * * * * *
69787 TTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGAGGCCAT
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCAT
* * * * *
69852 CCACGGTTTCAACTTCATGGCGAAAGGAATCGTGCTCACCAGCAACATTCAT-CTTTAAA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCCCACAAGCAACA---ATGC----AA
* * * * *
69911 TTGGATTTGAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCAT
* * * *
69976 CCACAGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACCAA-CAAC-ATTC-A
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCCCA-CAAGCAACAATGCAA
* * *
70027 TTGGATTTCAACTTCACTACGAAAGATATCCAATTCAAGGATCAACTTCACAACTAAGGGGTCAT
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCAT
* *
70092 CCACGGTTTCAAGTTCACGACGAAGGGAATCGTGCCCACAAGCAGCAATGCAA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCCCACAAGCAACAATGCAA
* * * * * * *
70145 CCCCTGGATTTCAACTTCACGACGAATGCTATCCAATTTAAGGCTTAACTTCACGACGAAGGGGT
1 ---TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGT
* *
70210 AATCCACGATTTCAACTTCACGACGAA-GGATATCGTG
63 CATCCACGGTTTCAACTTCACGACGAAGGGA-ATCGTG
70247 TTCATTTGCA
Statistics
Matches: 288, Mismatches: 39, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
115 3 0.01
116 95 0.33
117 3 0.01
118 1 0.00
120 5 0.02
121 84 0.29
124 95 0.33
125 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (118 bp):
TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCCCACAAGCAACAATGCAA
Found at i:70196 original size:121 final size:118
Alignment explanation
Indices: 69786--70246 Score: 507
Period size: 124 Copynumber: 3.8 Consensus size: 118
69776 ACAATACAAG
* * *
69786 CTTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAAGAGGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* * * *
69851 TCCACGGTTTCAACTTCATGGCGAAAGGAATCGTGCTCACCAGCAACATTCATCTTTAA
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACAAGCAACA-T--TC---AA
* * * * *
69910 ATTGGATTTGAACTTCACAATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* *
69975 TCCACAGTTTCAACTTCACGAAGAAGGGAATCGTGCTCACCAA-CAACATTC-A
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCA-CAAGCAACATTCAA
* * * * *
70027 -TTGGATTTCAACTTCACTACGAAAGATATCCAATTCAAGGATCAACTTCACAACTAAGGGGTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
* * * *
70091 TCCACGGTTTCAAGTTCACGACGAAGGGAATCGTGCCCACAAGCAGCAATGCAA
66 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACAAGCAAC-ATTCAA
* * * * * * *
70145 CCCCTGGATTTCAACTTCACGACGAATGCTATCCAATTTAAGGCTTAACTTCACGACGAAGGGGT
1 --CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGC
* *
70210 AATCCACGATTTCAACTTCACGACGAA-GGATATCGTG
64 CATCCACGGTTTCAACTTCACGACGAAGGGA-ATCGTG
70247 TTCATTTGCA
Statistics
Matches: 289, Mismatches: 40, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
115 3 0.01
116 94 0.33
117 4 0.01
118 1 0.00
120 3 0.01
121 85 0.29
123 1 0.00
124 96 0.33
125 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (118 bp):
CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCA
TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACAAGCAACATTCAA
Found at i:70424 original size:78 final size:77
Alignment explanation
Indices: 70327--70551 Score: 237
Period size: 80 Copynumber: 2.9 Consensus size: 77
70317 AGCTCCAAGG
* *
70327 CACATCATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACAAAAGAATTTCGAGTTCG
1 CACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTG-CAAC-AAAGAATTTCGAGTTCG
70392 ATTCCACTCAT-G-
64 ATTCCACTCATCGA
* * * * **
70404 CATCATCATTTGCAGCATAACTCAAGGCGAGAGGGGTTATATGC--TAAAGACCTTCGAGTTCGA
1 CA-CATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCAACAAAGAATTTCGAGTTCGA
70467 TTCCACTCATCCCGAAGA
65 TTCCACTCAT--C---GA
*
70485 CACATCATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAAC-AA-AATTATCGAGTTCG
1 CACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTG-CAACAAAGAATT-TCGAGTTCG
70548 ATTC
64 ATTC
70552 GATTCAGCTC
Statistics
Matches: 122, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
74 26 0.21
77 3 0.02
78 36 0.30
80 37 0.30
81 5 0.04
82 15 0.12
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (77 bp):
CACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCAACAAAGAATTTCGAGTTCGAT
TCCACTCATCGA
Found at i:71211 original size:27 final size:28
Alignment explanation
Indices: 71181--71240 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
71171 TCAAAAAATG
*
71181 GTTTCCGAAAA-TATATATATTATATAC
1 GTTTCCGAAAACTATATATAATATATAC
** *
71208 GTTTTTGAAAACTTATATATAATATATAG
1 GTTTCCGAAAAC-TATATATAATATATAC
71237 GTTT
1 GTTT
71241 TAAAACATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.33
29 18 0.67
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (28 bp):
GTTTCCGAAAACTATATATAATATATAC
Found at i:71245 original size:27 final size:29
Alignment explanation
Indices: 71192--71246 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
71182 TTTCCGAAAA
* *
71192 TATATATATTATATACGTTTTTGAAAACT
1 TATATATAATATATACGGTTTTGAAAACT
71221 TATATATAATATATA-GGTTTT-AAAAC
1 TATATATAATATATACGGTTTTGAAAAC
71247 ATTTTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 5 0.21
29 14 0.58
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (29 bp):
TATATATAATATATACGGTTTTGAAAACT
Found at i:71292 original size:33 final size:34
Alignment explanation
Indices: 71223--71289 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 34
71213 TGAAAACTTA
71223 TATATAATATATAGGTTTTAAAACATTTTGAAAAT
1 TATATAATATATAGGTTTTAAAACATTTT-AAAAT
*
71258 TATATAATATATA-GTTTTGAAATCATTTTAAA
1 TATATAATATATAGGTTTT-AAAACATTTTAAA
71290 TTAAAAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 8 0.27
35 22 0.73
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (34 bp):
TATATAATATATAGGTTTTAAAACATTTTAAAAT
Found at i:71416 original size:24 final size:23
Alignment explanation
Indices: 71358--71417 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
71348 TTATATAATA
*
71358 TTTTTAAA-ATCATTTTTGAAAAC
1 TTTTTAAATAT-AGTTTTGAAAAC
* *
71381 TATATAATATATAGTTTTGAAAAC
1 TTTTTAA-ATATAGTTTTGAAAAC
71405 TTTTTTAAATATA
1 -TTTTTAAATATA
71418 ATAATATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (23 bp):
TTTTTAAATATAGTTTTGAAAAC
Found at i:71480 original size:3 final size:3
Alignment explanation
Indices: 71467--71530 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
71457 ATATAATCTA
* * *
71467 TAT TA- TAT TAT TAT TAG TATT TAT TAT TAT TAG TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
*
71512 T-T TAT ATAT TAT AAT TAT T
1 TAT TAT -TAT TAT TAT TAT T
71531 TTGTGGGCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 3 0.06
3 41 0.84
4 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:71493 original size:16 final size:16
Alignment explanation
Indices: 71467--71510 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
71457 ATATAATCTA
71467 TATTATATTATTATTAG
1 TATT-TATTATTATTAG
71484 TATTTATTATTATTAG
1 TATTTATTATTATTAG
71500 TA-TTATTATTA
1 TATTTATTATTA
71511 ATTTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.33
16 14 0.52
17 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TATTTATTATTATTAG
Found at i:72745 original size:21 final size:20
Alignment explanation
Indices: 72712--72760 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
72702 CATTCCACTA
*
72712 TATTCATTATTTTATTATTTT
1 TATT-ATTATTTTATTACTTT
*
72733 TATTATTATTTTTTTTACTTT
1 TATTATTA-TTTTATTACTTT
72754 TATTATT
1 TATTATT
72761 TTATTCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTATTATTTTATTACTTT
Found at i:73804 original size:19 final size:19
Alignment explanation
Indices: 73780--73818 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
73770 GACTATTAAA
73780 AATTATAAAATGATATTTT
1 AATTATAAAATGATATTTT
* *
73799 AATTATAGAATGTTATTTT
1 AATTATAAAATGATATTTT
73818 A
1 A
73819 TTAAGTCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
AATTATAAAATGATATTTT
Found at i:73809 original size:60 final size:60
Alignment explanation
Indices: 73740--73853 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
73730 AATGTCTCCT
** **
73740 ATTATAGAATATTATTTTATTATTTCTTTCGACTATTAAAAATTATAAAATGATATTTTA
1 ATTATAGAATATTATTTTATTAAGTCACTCGACTATTAAAAATTATAAAATGATATTTTA
* *
73800 ATTATAGAATGTTATTTTATTAAGTCACTCGATTATTAAAAATTATAAAATGAT
1 ATTATAGAATATTATTTTATTAAGTCACTCGACTATTAAAAATTATAAAATGAT
73854 CATCTGATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (60 bp):
ATTATAGAATATTATTTTATTAAGTCACTCGACTATTAAAAATTATAAAATGATATTTTA
Found at i:75903 original size:14 final size:15
Alignment explanation
Indices: 75868--75910 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
75858 TTTTAATATC
75868 AAAT-TTTTATTTTT
1 AAATATTTTATTTTT
75882 AAAATATTTTATTTTT
1 -AAATATTTTATTTTT
75898 -AATATTTTATTTT
1 AAATATTTTATTTT
75911 GAGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.48
15 4 0.15
16 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AAATATTTTATTTTT
Found at i:76773 original size:23 final size:23
Alignment explanation
Indices: 76743--76794 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
76733 CTTAAGGATC
76743 ACTTTTACTTGCGTAGTTGACTT
1 ACTTTTACTTGCGTAGTTGACTT
*
76766 ACTTTTACTTGCGTAGTTGATTT
1 ACTTTTACTTGCGTAGTTGACTT
*
76789 AATTTT
1 ACTTTT
76795 TCATTTTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.52
Consensus pattern (23 bp):
ACTTTTACTTGCGTAGTTGACTT
Found at i:77393 original size:20 final size:20
Alignment explanation
Indices: 77344--77483 Score: 77
Period size: 20 Copynumber: 6.9 Consensus size: 20
77334 ACAGTTTCCA
* *
77344 AATTCGCAACACGAAATTTCG
1 AATTCGCAACGCG-ATTTTCG
* *
77365 AATTTGCAACTCGATTTAT-G
1 AATTCGCAACGCGATTT-TCG
*
77385 AATTCGCAACGCGATTTTCA
1 AATTCGCAACGCGATTTTCG
* *** *
77405 AATTCGCAACAC-AAACTCC
1 AATTCGCAACGCGATTTTCG
* * *
77424 AATTTCGCAACTCGAATTTGG
1 AA-TTCGCAACGCGATTTTCG
* * * *
77445 TATTCGCAACACGGAATTTCA
1 AATTCGCAACGC-GATTTTCG
77466 AATTCGCAACGCGATTTT
1 AATTCGCAACGCGATTTT
77484 TAAATTAACA
Statistics
Matches: 91, Mismatches: 23, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
19 6 0.07
20 53 0.58
21 32 0.35
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (20 bp):
AATTCGCAACGCGATTTTCG
Found at i:77412 original size:61 final size:61
Alignment explanation
Indices: 77342--77475 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
77332 ACACAGTTTC
* * * * *
77342 CAAATTCGCAACACGAAATTTCGAATTT-GCAACTCG-ATTTATGAATTCGCAACGC-GATTTT
1 CAAATTCGCAACAC-AAA-CTCCAATTTCGCAACTCGAATTT-GGAATTCGCAACACGGAATTT
*
77403 CAAATTCGCAACACAAACTCCAATTTCGCAACTCGAATTTGGTATTCGCAACACGGAATTT
1 CAAATTCGCAACACAAACTCCAATTTCGCAACTCGAATTTGGAATTCGCAACACGGAATTT
77464 CAAATTCGCAAC
1 CAAATTCGCAAC
77476 GCGATTTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 7 0.11
60 22 0.34
61 35 0.55
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (61 bp):
CAAATTCGCAACACAAACTCCAATTTCGCAACTCGAATTTGGAATTCGCAACACGGAATTT
Found at i:77425 original size:81 final size:81
Alignment explanation
Indices: 77340--77543 Score: 193
Period size: 81 Copynumber: 2.5 Consensus size: 81
77330 CAACACAGTT
* *
77340 TCCAAATTCGCAACACGAAATTTCGAATTTGCAACTC-G-ATTT-ATGAATTCGCAACGCGATTT
1 TCCAAATTCGCAACACG-AATTTCGAATTCGCAACACGGAATTTCA--AATTCGCAACGCGATTT
**
77402 TCAAATTCGCAACACAAAC
63 TCAAATTAACAACACAAAC
* * * * *
77421 TCCAATTTCGCAACTCGAATTTGGTATTCGCAACACGGAATTTCAAATTCGCAACGCGATTTTTA
1 TCCAAATTCGCAACACGAATTTCGAATTCGCAACACGGAATTTCAAATTCGCAACGCGATTTTCA
**
77486 AATTAACAACACAAGTT
66 AATTAACAACACAA-AC
** * * *
77503 TCC-TTTTCGCAACAAGATTTTCTAATTCGCAACAC-GAATTT
1 TCCAAATTCGCAACACGAATTTCGAATTCGCAACACGGAATTT
77544 TGTTTTTGCA
Statistics
Matches: 101, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
80 21 0.21
81 72 0.71
82 7 0.07
83 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (81 bp):
TCCAAATTCGCAACACGAATTTCGAATTCGCAACACGGAATTTCAAATTCGCAACGCGATTTTCA
AATTAACAACACAAAC
Found at i:77431 original size:40 final size:40
Alignment explanation
Indices: 77387--77542 Score: 125
Period size: 40 Copynumber: 3.9 Consensus size: 40
77377 GATTTATGAA
*
77387 TTCGCAACGCGATTTTCAAATTCGCAACACAAACTCCAAT
1 TTCGCAACGCGATTTTCAAATTCGCAACACAAATTCCAAT
* * *** * * *
77427 TTCGCAACTCGAATTTGGTATTCGCAACACGGAATTTCAAA
1 TTCGCAACGCGATTTTCAAATTCGCAACAC-AAATTCCAAT
* ** * *
77468 TTCGCAACGCGATTTTTAAATTAACAACACAAGTTTCC-TT
1 TTCGCAACGCGATTTTCAAATTCGCAACACAA-ATTCCAAT
** * *
77508 TTCGCAACAAGATTTTCTAATTCGCAACACGAATT
1 TTCGCAACGCGATTTTCAAATTCGCAACACAAATT
77543 TTGTTTTTGC
Statistics
Matches: 85, Mismatches: 29, Indels: 5
0.71 0.24 0.04
Matches are distributed among these distances:
39 2 0.02
40 51 0.60
41 32 0.38
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (40 bp):
TTCGCAACGCGATTTTCAAATTCGCAACACAAATTCCAAT
Found at i:77555 original size:40 final size:40
Alignment explanation
Indices: 77506--77596 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
77496 ACAAGTTTCC
* *
77506 TTTTCGCAACAAGATTTTCTAATTCGCAACACGAATTTTG
1 TTTTCGCAACAAGATTTCCGAATTCGCAACACGAATTTTG
* ** * *
77546 TTTTTGCAACTCGATTTCCGAATTCGCAATACGAATTTTA
1 TTTTCGCAACAAGATTTCCGAATTCGCAACACGAATTTTG
*
77586 ATTTCGCAACA
1 TTTTCGCAACA
77597 GCTTTTATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTCCGAATTCGCAACACGAATTTTG
Found at i:78541 original size:24 final size:24
Alignment explanation
Indices: 78514--78581 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
78504 GTGAGTACTA
*
78514 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
* *
78538 GTCAATACTCGGACTTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
* *
78562 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGAAATTTGAT
78582 TACGTTTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
GTCAATACTCGAAATTTGATCTTG
Found at i:80739 original size:21 final size:21
Alignment explanation
Indices: 80627--80759 Score: 99
Period size: 21 Copynumber: 6.3 Consensus size: 21
80617 CGAATGCCAT
* *
80627 GTGGATCCTGAACAGTGGGCG
1 GTGGATCCTGAACAATGGGAG
* *
80648 GTAGATCCTGAACGATGGGAG
1 GTGGATCCTGAACAATGGGAG
* *
80669 G-GG-TCTCTTGAACGATGGGAT
1 GTGGATC-C-TGAACAATGGGAG
** * * **
80690 GTGCCTCTTGAACGATGACAG
1 GTGGATCCTGAACAATGGGAG
* *
80711 ATGAATCCTGAACAATGGGAG
1 GTGGATCCTGAACAATGGGAG
*
80732 GTGGATCCTGAACAATGGTAG
1 GTGGATCCTGAACAATGGGAG
80753 GTGGATC
1 GTGGATC
80760 AGGCTTATTC
Statistics
Matches: 87, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 80 0.92
22 1 0.01
23 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.23
Consensus pattern (21 bp):
GTGGATCCTGAACAATGGGAG
Found at i:80909 original size:4 final size:4
Alignment explanation
Indices: 80893--80926 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
80883 GGGCCGCTAA
*
80893 AAAT AAAT TAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
80927 TGCCGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:81067 original size:21 final size:20
Alignment explanation
Indices: 81043--81225 Score: 100
Period size: 21 Copynumber: 8.7 Consensus size: 20
81033 TCTCACATAG
81043 AGCAGCTACCTCATCACGTAA
1 AGCA-CTACCTCATCACGTAA
* *
81064 AGCAAAC-ACCTCACCACATAA
1 AGC--ACTACCTCATCACGTAA
* **
81085 AGCACCATTGTCATCACGT-A
1 AGCACTA-CCTCATCACGTAA
* * *
81105 AGACAGCTATCTTACCACGTAA
1 AG-CA-CTACCTCATCACGTAA
* **
81127 AGACCCTACCTCATCACGCCA
1 AG-CACTACCTCATCACGTAA
* * **
81148 TGCACCATTGTCATCACGTAA
1 AGCACTA-CCTCATCACGTAA
*
81169 AGCACCGACCTCATCACGTAA
1 AGCA-CTACCTCATCACGTAA
81190 AGCACTGACCTCATCACGTAA
1 AGCACT-ACCTCATCACGTAA
*
81211 AGCACCTAACTCATC
1 AGCA-CTACCTCATC
81226 CCGTGGAGGT
Statistics
Matches: 122, Mismatches: 29, Indels: 22
0.71 0.17 0.13
Matches are distributed among these distances:
19 2 0.02
20 8 0.07
21 99 0.81
22 12 0.10
23 1 0.01
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.19
Consensus pattern (20 bp):
AGCACTACCTCATCACGTAA
Found at i:81216 original size:63 final size:62
Alignment explanation
Indices: 81050--81216 Score: 176
Period size: 63 Copynumber: 2.6 Consensus size: 62
81040 TAGAGCAGCT
* * * *
81050 ACCTCATCACGTAAAGCAAAC-ACCTCACCACATAAAGCACCATTGTCATCACGTAAGACAGCT
1 ACCTCATCACGTAAAGC--ACTACCTCATCACGTAAAGCACCATTGTCATCACGTAAGACACCG
* * * * ** *
81113 ATCTTACCACGTAAAGACCCTACCTCATCACGCCATGCACCATTGTCATCACGTAA-AGCACCG
1 ACCTCATCACGTAAAG-CACTACCTCATCACGTAAAGCACCATTGTCATCACGTAAGA-CACCG
81176 ACCTCATCACGTAAAGCACTGACCTCATCACGTAAAGCACC
1 ACCTCATCACGTAAAGCACT-ACCTCATCACGTAAAGCACC
81217 TAACTCATCC
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
62 5 0.06
63 76 0.93
64 1 0.01
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.19
Consensus pattern (62 bp):
ACCTCATCACGTAAAGCACTACCTCATCACGTAAAGCACCATTGTCATCACGTAAGACACCG
Found at i:81422 original size:41 final size:42
Alignment explanation
Indices: 81325--81429 Score: 176
Period size: 42 Copynumber: 2.5 Consensus size: 42
81315 GTGATGGAAT
*
81325 AGGTGATGGCTCTCGGTATCGAGGTATAGAATCGACTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGGTATAGAATCGACTCGATC
*
81367 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCG-CTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGGTATAGAATCGACTCGATC
*
81408 AGGTGATGGATCTCGGTGTCGA
1 AGGTGATGGCTCTCGGTGTCGA
81430 AGTGAGTGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
41 28 0.47
42 32 0.53
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGGTATAGAATCGACTCGATC
Found at i:83575 original size:20 final size:20
Alignment explanation
Indices: 83550--83599 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
83540 GTTTCGAATT
*
83550 CGAAAATAAAATTCGCTTTG
1 CGAAAATAAAATTCGCGTTG
83570 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATTCGCGTTG
*
83590 CAAAAATAAA
1 CGAAAATAAA
83600 CGTGCTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (20 bp):
CGAAAATAAAATTCGCGTTG
Found at i:83609 original size:19 final size:20
Alignment explanation
Indices: 83552--83612 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
83542 TTCGAATTCG
* *
83552 AAAATAAAATTCGCTTTGCG
1 AAAATAAAAGTCGCTTTGCA
* *
83572 AAAATAAAATTCGCGTTGCA
1 AAAATAAAAGTCGCTTTGCA
*
83592 AAAATAAACGT-GCTTTGCA
1 AAAATAAAAGTCGCTTTGCA
83611 AA
1 AA
83613 TTTGACTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 9 0.25
20 27 0.75
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAATAAAAGTCGCTTTGCA
Found at i:83748 original size:20 final size:20
Alignment explanation
Indices: 83714--83759 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
83704 TCGCGTTGCC
*
83714 AATTTGGAATCTGTGCTGCT
1 AATTTGGAATCTGTGCTGCG
* * *
83734 AATTTGGAGTTTGTGTTGCG
1 AATTTGGAATCTGTGCTGCG
83754 AATTTG
1 AATTTG
83760 TTGGTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.43
Consensus pattern (20 bp):
AATTTGGAATCTGTGCTGCG
Found at i:90850 original size:70 final size:70
Alignment explanation
Indices: 90737--90868 Score: 201
Period size: 70 Copynumber: 1.9 Consensus size: 70
90727 CATCGTCTTT
* * * * * *
90737 TGTCGTAGATGAAGTTTCACCTGACCTCCCCTTCCCTTAGCAACCAAAACCTCTATGAAATCATG
1 TGTCGTAGATGAAGTTTCACCCGACCTCACATCCCCTCAGCAACCAAAACCTCCATGAAATCATG
90802 AATGA
66 AATGA
*
90807 TGTCGTAGATGAAGTTTCACCCGACCTCACATCCCCTCAGCAACCAAAACTTCCATGAAATC
1 TGTCGTAGATGAAGTTTCACCCGACCTCACATCCCCTCAGCAACCAAAACCTCCATGAAATC
90869 GTGACCGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (70 bp):
TGTCGTAGATGAAGTTTCACCCGACCTCACATCCCCTCAGCAACCAAAACCTCCATGAAATCATG
AATGA
Found at i:92346 original size:60 final size:60
Alignment explanation
Indices: 92250--92366 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
92240 TAAACTACAT
* * * *
92250 AAATGATCTTTCGATTATAAGGTATTATTTTATTAAGT-TCATTGATTATTAAAAGTTATA
1 AAATGATCATTCGATTATAAGATATTACTTTATTAAGTCTC-TTGACTATTAAAAGTTATA
* *
92310 AAATGATCATTCGATTAT-AGAATATTGCTTTGTTAAGTCTCTTGACTATTAAAAGTT
1 AAATGATCATTCGATTATAAG-ATATTACTTTATTAAGTCTCTTGACTATTAAAAGTT
92367 GAAGGTTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 45 0.92
61 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (60 bp):
AAATGATCATTCGATTATAAGATATTACTTTATTAAGTCTCTTGACTATTAAAAGTTATA
Found at i:93970 original size:2 final size:2
Alignment explanation
Indices: 93965--94010 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
93955 TTTTTTGTTG
* *
93965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94007 AT AT
1 AT AT
94011 TAGCTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Done.