Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005138.1 Hibiscus syriacus cultivar Beakdansim tig00011574_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: 81849
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1148 original size:2 final size:2
Alignment explanation
Indices: 1141--1185 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1131 TACATTCTTT
1141 TA TA TA TA TA -A TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1181 TA TA T
1 TA TA T
1186 TAATTACCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2862 original size:28 final size:27
Alignment explanation
Indices: 2830--2896 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
2820 TCTTTACAAA
* *
2830 CAAAAGCAAAAATATGAAAACTAAGAAT
1 CAAAAACAAAAATA-GAAAACTAAAAAT
* *
2858 CAAAAACAAAAGTAGGAAACTAAAAAT
1 CAAAAACAAAAATAGAAAACTAAAAAT
*
2885 TAAAAACAAAAA
1 CAAAAACAAAAA
2897 CAATTAAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.69, C:0.10, G:0.09, T:0.12
Consensus pattern (27 bp):
CAAAAACAAAAATAGAAAACTAAAAAT
Found at i:2907 original size:114 final size:118
Alignment explanation
Indices: 2757--2972 Score: 307
Period size: 114 Copynumber: 1.9 Consensus size: 118
2747 GCACACAAGC
* * * * *
2757 AGGAAACTAAGAATAAAAAATAAAAGCAATCAAAAGCACCATTAAGAGAAGAATCAAAAGGT-TT
1 AGGAAACTAAAAATAAAAAACAAAAACAATCAAAAGCACCATTAACAGAAGAATCAAAAGATGTT
2821 CTTT-AC--AAACAAAAGC-AAAAATATGAAAACTAAGAATCAAAAACAAAAGT
66 CTTTGACATAAAC-AAAGCAAAAAATATGAAAACTAAGAATCAAAAACAAAAGT
* *
2871 AGGAAACTAAAAATTAAAAACAAAAACAATTAAAAGCACCATTAACAGAAGAATCAAAAGATGTT
1 AGGAAACTAAAAATAAAAAACAAAAACAATCAAAAGCACCATTAACAGAAGAATCAAAAGATGTT
* *
2936 CTTTGACATAAACAACGCAAAAAATATGACAACTAAG
66 CTTTGACATAAACAAAGCAAAAAATATGAAAACTAAG
2973 TATTAATAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
114 55 0.62
115 6 0.07
116 2 0.02
117 4 0.05
118 21 0.24
ACGTcount: A:0.58, C:0.13, G:0.12, T:0.17
Consensus pattern (118 bp):
AGGAAACTAAAAATAAAAAACAAAAACAATCAAAAGCACCATTAACAGAAGAATCAAAAGATGTT
CTTTGACATAAACAAAGCAAAAAATATGAAAACTAAGAATCAAAAACAAAAGT
Found at i:3457 original size:92 final size:90
Alignment explanation
Indices: 3300--3534 Score: 303
Period size: 92 Copynumber: 2.6 Consensus size: 90
3290 TCAATTCCAT
*
3300 ACCATCAGGAGAAGAATCAAAAGGTTTTCTTTGACAGAAACGAAAGCACAAAAGCAGGAAACTAA
1 ACCATTAGGAGAAGAATCAAAAGGTTTTCTTTGACAGAAAC-AAAGCA-AAAAGCAGGAAACTAA
* *
3365 GAATAAAAAATAAAAGCAA-TCAAAAGC
64 GAATAAAAAACAAAAACAACT-AAAAGC
*
3392 ACCATTAGGAGAAGAATCAAAAGGTTTTCTTTAACAGAAACAAAAGCAAAAA-CTATGGAAACTA
1 ACCATTAGGAGAAGAATCAAAAGGTTTTCTTTGACAGAAAC-AAAGCAAAAAGC-A-GGAAACTA
*
3456 AGAATCAAAAACAAAAACAACTAAAAGC
63 AGAATAAAAAACAAAAACAACTAAAAGC
** * * * *
3484 ACCATTAACAAAAGAATCAAAAGATGTTCTTTGACATAAACAAAGCAAAAA
1 ACCATTAGGAGAAGAATCAAAAGGTTTTCTTTGACAGAAACAAAGCAAAAA
3535 AATATGACAA
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 15 0.12
92 110 0.87
93 1 0.01
ACGTcount: A:0.54, C:0.15, G:0.14, T:0.16
Consensus pattern (90 bp):
ACCATTAGGAGAAGAATCAAAAGGTTTTCTTTGACAGAAACAAAGCAAAAAGCAGGAAACTAAGA
ATAAAAAACAAAAACAACTAAAAGC
Found at i:11850 original size:21 final size:21
Alignment explanation
Indices: 11826--11865 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11816 TTTTCAAAGG
11826 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
11847 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
11866 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:11915 original size:19 final size:19
Alignment explanation
Indices: 11891--11929 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
11881 TCGAATGCAT
11891 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
**
11910 TCCATGCATTGATGCACTC
1 TCCATGCACCGATGCACTC
11929 T
1 T
11930 GATTTAATTA
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:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:11953 original size:64 final size:64
Alignment explanation
Indices: 11826--12038 Score: 195
Period size: 64 Copynumber: 3.3 Consensus size: 64
11816 TTTTCAAAGG
* * *
11826 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGC
11889 ATT
62 ATT
*
11892 CCATGCACCGATGCACTCTCCATGCATTGATGCACTC-TGATTTAATTAAAACATCGAATGCATT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-T
11956 T
64 T
* * * ** * *
11957 GATGCATCAATGCACAATCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-
12019 TT
63 TT
*
12021 CATGCATCGATGCACTCT
1 CATGCACCGATGCACTCT
12039 TAGTGCACTA
Statistics
Matches: 123, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
63 1 0.01
64 83 0.67
65 16 0.13
66 7 0.06
67 14 0.11
68 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATT
Found at i:20089 original size:33 final size:34
Alignment explanation
Indices: 20041--20113 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 34
20031 GAAATGACTT
20041 CCAG-AAAATTCCTCTGCTTACTGAACCCGACCA
1 CCAGAAAAATTCCTCTGCTTACTGAACCCGACCA
*
20074 CCAGAAAAATT-CTCTGCTTATTGAACCCGACCA
1 CCAGAAAAATTCCTCTGCTTACTGAACCCGACCA
*
20107 CGAGAAA
1 CCAGAAA
20114 TCCCAATCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 31 0.84
34 6 0.16
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.21
Consensus pattern (34 bp):
CCAGAAAAATTCCTCTGCTTACTGAACCCGACCA
Found at i:21996 original size:16 final size:16
Alignment explanation
Indices: 21951--21996 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
21941 GAGAATATTA
21951 GATA-AATATATACAT
1 GATATAATATATACAT
*
21966 G-TAT-ATCTATAACAT
1 GATATAATATAT-ACAT
21981 GATATAATATATACAT
1 GATATAATATATACAT
21997 ACATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 7 0.28
17 5 0.20
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (16 bp):
GATATAATATATACAT
Found at i:22278 original size:16 final size:16
Alignment explanation
Indices: 22257--22288 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22247 ATTAAATAAC
*
22257 AAAAATAAAATGAAAT
1 AAAAATAAAATAAAAT
22273 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
22289 GTTAGTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:22428 original size:16 final size:17
Alignment explanation
Indices: 22392--22429 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
22382 AGCAATTAGC
*
22392 AGTTAGAAATGTTAACT
1 AGTTAGAAAAGTTAACT
22409 -GTTAGAAAAGTTAA-T
1 AGTTAGAAAAGTTAACT
22424 AGTTAG
1 AGTTAG
22430 TAGTTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (17 bp):
AGTTAGAAAAGTTAACT
Found at i:22475 original size:39 final size:39
Alignment explanation
Indices: 22384--22475 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 39
22374 TAACAATTAG
* * *
22384 CAATTAGCAGTTAGAAATGTTAACTGTTAGAAAAGTTAA
1 CAATTAGTAGTTAGAAATATTAACTGGTAGAAAAGTTAA
* * * *
22423 TAGTTAGTAGTTAGAAATATTAGCTGGTAGAAAAGTTAG
1 CAATTAGTAGTTAGAAATATTAACTGGTAGAAAAGTTAA
* *
22462 CAATTTGTGGTTAG
1 CAATTAGTAGTTAG
22476 CAGAATCTGT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (39 bp):
CAATTAGTAGTTAGAAATATTAACTGGTAGAAAAGTTAA
Found at i:23862 original size:17 final size:18
Alignment explanation
Indices: 23828--23860 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
23818 TTTTGTTTGT
23828 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
23846 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
23861 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:27450 original size:2 final size:2
Alignment explanation
Indices: 27443--27472 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27433 ATTAGGGTAT
27443 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27473 ATAGAAACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31204 original size:22 final size:23
Alignment explanation
Indices: 31179--31229 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
31169 TCTCAGAATT
31179 AAATTATTTTCT-TCTCTT-GAAA
1 AAATTATTTTCTCTC-CTTAGAAA
31201 AAA-TATTTTCTCTCCTTAGAAA
1 AAATTATTTTCTCTCCTTAGAAA
*
31223 ATATTAT
1 AAATTAT
31230 CTTCCACTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.44
22 11 0.44
23 3 0.12
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (23 bp):
AAATTATTTTCTCTCCTTAGAAA
Found at i:31209 original size:21 final size:21
Alignment explanation
Indices: 31183--31233 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
31173 AGAATTAAAT
31183 TATTTTCTTCT-CTTGAAAAAA
1 TATTTTCTTCTCCTT-AAAAAA
*
31204 TATTTTC-TCTCCTTAGAAAA
1 TATTTTCTTCTCCTTAAAAAA
*
31224 TATTATCTTC
1 TATTTTCTTC
31234 CACTAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (21 bp):
TATTTTCTTCTCCTTAAAAAA
Found at i:33457 original size:184 final size:183
Alignment explanation
Indices: 33140--33790 Score: 795
Period size: 184 Copynumber: 3.6 Consensus size: 183
33130 ATTACAGGTA
33140 AAAATATGACAAAACCGGTAAA-ACGATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAG
1 AAAA-ATGACAAAACCGGTAAAGA-GATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAG
*
33204 TATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGCCTATAAAAG-GTCGAATACTTTA
64 TATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAT-AAAGTGTC-AATACTTTA
* * *
33268 AAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT-AAGTCTC
127 AAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGA-TCTC
* *
33325 AAAAATGACAAAACCGGTAAA-AAATACTTA-ATATGTTGAAAGTGTCGATAATTTAATATAAGT
1 AAAAATGACAAAACCGGTAAAGAGATAC-CAGATATGTTGAAAGTGTCGATAATTTAATATAAGT
* * * *
33388 ATCGAAATTTTTTGGAGTTTAAAAGAGAAGGAGTTATAGCGCCTATAAAGTGTCAATACTTTAAA
65 ATCGACA-CTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCAATACTTT-AA
* *
33453 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGATC-C
128 AAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGATCTC
* ** * *
33508 CAAAATGA-AAAATCATGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGT
1 AAAAATGACAAAA-CCGGTAAAGAGATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGT
* * ***
33572 AT-----C-----G-A--TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTTTGA
65 ATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCAATACTTTAAAA
* *
33624 AAATGTATCGATCCATAACAATATAACAACTAAAAATATGATAAAATCGATCTC
130 AAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGATCTC
* ** * *
33678 -AAAATGACAAAACCGATAAAGATCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTA
1 AAAAATGACAAAACCGGTAAAGAGATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
* *
33742 TTGACACTTGTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGT
66 TCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGT
33791 ATCTACACTC
Statistics
Matches: 405, Mismatches: 38, Indels: 49
0.82 0.08 0.10
Matches are distributed among these distances:
169 102 0.25
170 45 0.11
173 1 0.00
174 1 0.00
179 1 0.00
180 1 0.00
182 35 0.09
183 70 0.17
184 144 0.36
185 5 0.01
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (183 bp):
AAAAATGACAAAACCGGTAAAGAGATACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
TCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCAATACTTTAAAAA
AATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGATCTC
Found at i:33713 original size:169 final size:169
Alignment explanation
Indices: 33407--33742 Score: 487
Period size: 169 Copynumber: 2.0 Consensus size: 169
33397 TTTTGGAGTT
* *
33407 TAAAAGAGAAGGAGTTATAGCGCCTATAAAGTGTCAATACTTTAAAAAAAATGTATCGATCCATA
1 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAATACTTTAAAAAAAATGTATCGATCCATA
** * *
33472 ACAATATAACAGGTAAAAATATGACAAAACCGATCCCAAAATGAAAAATCATGTAAAGCGCTACC
66 ACAATATAACAACTAAAAATATGACAAAACCGATCCCAAAATGAAAAACCA-GTAAAGAGCTACC
33537 AGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
130 AGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
* ***
33577 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTT-TTGAAAATGTATCGATCCATA
1 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAATACTTTAAAAAAAATGTATCGATCCATA
* * * *
33641 ACAATATAACAACTAAAAATATGATAAAATCGATCTCAAAATGACAAAACC-GATAAAGATCTAC
66 ACAATATAACAACTAAAAATATGACAAAACCGATCCCAAAATGA-AAAACCAG-TAAAGAGCTAC
* *
33705 CGGATATGTTGAAAGTGTCGATACTTTAATATAAGTAT
129 CAGATATGTTGAAAGTGTCGATAATTTAATATAAGTAT
33743 TGACACTTGT
Statistics
Matches: 148, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
168 1 0.01
169 102 0.69
170 45 0.30
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (169 bp):
TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCAATACTTTAAAAAAAATGTATCGATCCATA
ACAATATAACAACTAAAAATATGACAAAACCGATCCCAAAATGAAAAACCAGTAAAGAGCTACCA
GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
Found at i:34104 original size:20 final size:21
Alignment explanation
Indices: 34079--34121 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
34069 CGATAATTAT
34079 AATGTAATAGGTT-AATTTAC
1 AATGTAATAGGTTAAATTTAC
*
34099 AATGTAATCGGTTGAAATTTAC
1 AATGTAATAGGTT-AAATTTAC
34121 A
1 A
34122 GGTTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
AATGTAATAGGTTAAATTTAC
Found at i:34247 original size:23 final size:23
Alignment explanation
Indices: 34221--34278 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
34211 GGTTAAATGT
*
34221 CTATTTTATTATATAAGCGCTAC
1 CTATTATATTATATAAGCGCTAC
34244 CTATTATATTATATAAGCGCTAC
1 CTATTATATTATATAAGCGCTAC
*
34267 CTAATATATTAT
1 CTATTATATTAT
34279 TGTGCTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (23 bp):
CTATTATATTATATAAGCGCTAC
Found at i:34255 original size:87 final size:87
Alignment explanation
Indices: 34144--34305 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 87
34134 AAATAAGTCA
* * * * *
34144 ATATAAGCGCTATCTATTACATTATATAAGCGTTATCTAATATGTTATTATACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
*
34209 CTGGTTAAATGTCTATTTTATT
66 CTAGTTAAATGTCTATTTTATT
* * *
34231 ATATAAGCGCTACCTATTATATTATATAAGCGCTACCTAATATATTATTGTGCTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
*
34296 TTAGTTAAAT
66 CTAGTTAAAT
34306 AATATAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTATACTTAATAATATTT
CTAGTTAAATGTCTATTTTATT
Found at i:35544 original size:2 final size:2
Alignment explanation
Indices: 35537--35569 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35527 TAATGACATA
35537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35570 AGAAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35655 original size:2 final size:2
Alignment explanation
Indices: 35648--35672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35638 GTATACTTAA
35648 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35673 CTAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37218 original size:106 final size:107
Alignment explanation
Indices: 37044--37275 Score: 331
Period size: 106 Copynumber: 2.2 Consensus size: 107
37034 ATCTTCTGTC
* * * * * **
37044 GTGAAGTTGAATTTGGTTCTGGAACTGGGAAATTGTTTTGTTGATAGTCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
*
37109 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATGCCCTTCAAT
66 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
*
37151 GTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTG-TTTGTTGACAACCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
* * * **
37215 TGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCT
66 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
37257 GTGAAGTTGAAATTGGCTC
1 GTGAAGTTGAAATTGGCTC
37276 TAGCTAAAAC
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 81 0.73
107 30 0.27
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (107 bp):
GTGAAGTTGAAATTGGCTCCGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
Found at i:37766 original size:67 final size:67
Alignment explanation
Indices: 37594--37780 Score: 230
Period size: 67 Copynumber: 2.7 Consensus size: 67
37584 AAAAAGATAG
* * * * *
37594 AATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCAAGGGAG
1 AATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCAAGGGAG
37659 ACAA
64 ACAA
* * * * * *
37663 AATTTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCGAGGGAGA
1 AA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAGGGAGA
*
37728 CGA
65 CAA
*
37731 AATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
37781 ATTTTCAAAG
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
67 44 0.44
68 29 0.29
69 5 0.05
70 23 0.23
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (67 bp):
AATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAGGGAGAC
AA
Found at i:37842 original size:36 final size:35
Alignment explanation
Indices: 37735--37851 Score: 170
Period size: 35 Copynumber: 3.4 Consensus size: 35
37725 AGACGAAATT
* *
37735 TGTTTCAAGGGAAACAATCTCAAAGG----TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTG
*
37766 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTG
37801 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTT-TTTTTG
37837 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
37852 TGTATCAAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
31 23 0.30
35 33 0.43
36 21 0.27
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTG
Found at i:37932 original size:37 final size:36
Alignment explanation
Indices: 37891--38519 Score: 203
Period size: 37 Copynumber: 18.4 Consensus size: 36
37881 CAAGGATTGA
37891 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTT
* * *
37928 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAAC-TGTCTCAAG-GAGACAAAATTT
*
37965 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTT
* *
38001 TGTTT-AATGTA-AAA-TATATTCAA--AG-----ATTT
1 TGTTTCAA-G-AGAAACTGT-CTCAAGGAGACAAAATTT
* *
38030 TGTTTCAAGGGAAACTGTTTTCAA--AG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAAATTT
*
38059 ATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 -TGTTTCAAGAGAAACTGTCTC-AAGGAGACAAAATTT
* *
38096 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTT
** * * *
38132 CATTTCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAAATTT
*
38160 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTT
* *
38198 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTT
* * * *
38232 TATTTCAAGGGAAA-TGCTTTCAA--TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAAATTT
38260 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTT
* * * *
38298 TGTTCCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAAATTT
38326 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTT
* *
38364 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTT
* * * *
38400 TATTTCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGGAGACAAAATTT
*
38428 ATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTT
1 -TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAA-TTT
* * * * *
38467 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCT
1 -TGTTTCAAGAGAAACTGTCTCAAG-GAGACAAAATTT
* *
38505 TGTTTTAAGAAAAAC
1 TGTTTCAAGAGAAAC
38520 AATCTTGAGG
Statistics
Matches: 448, Mismatches: 69, Indels: 150
0.67 0.10 0.22
Matches are distributed among these distances:
28 10 0.02
29 83 0.19
30 35 0.08
31 2 0.00
32 6 0.01
33 5 0.01
34 21 0.05
35 11 0.02
36 102 0.23
37 115 0.26
38 27 0.06
39 31 0.07
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGGAGACAAAATTT
Found at i:38055 original size:30 final size:30
Alignment explanation
Indices: 38019--38077 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
38009 GTAAAATATA
*
38019 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
38049 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
38078 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:38267 original size:100 final size:101
Alignment explanation
Indices: 38032--38311 Score: 465
Period size: 100 Copynumber: 2.8 Consensus size: 101
38022 AAAGATTTTG
* * *
38032 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
38096 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTCA
*
38134 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
38199 GTTTCAAGGGAAACTATCTCAAGAGAGAC-AATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAATTCA
*
38234 TTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
38299 GTTCCAAGGGAAA
66 GTTTCAAGGGAAA
38312 TGTTTTCAAT
Statistics
Matches: 169, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
100 80 0.47
101 45 0.27
102 44 0.26
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAATTCA
Found at i:38329 original size:166 final size:166
Alignment explanation
Indices: 38096--38481 Score: 623
Period size: 166 Copynumber: 2.3 Consensus size: 166
38086 AGACAAAATT
* * *
38096 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TTCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TTGTTCAAGGGAAATGTTTTCAATGTTT
*
38160 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
38225 GAC-AATTTATTTCAAGGGAAATGCTTTCAATGTTTA
130 GACAAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
*
38261 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT-CAAGGGAAATGTTTTCAATGTTT
38326 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
38391 GACAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
130 GAC-AAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
* * *
38429 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTT-TG-TTCAAGGGAAA
38482 CTATCTCAAG
Statistics
Matches: 205, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
164 1 0.00
165 35 0.17
166 90 0.44
168 64 0.31
169 3 0.01
170 10 0.05
171 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (166 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:38332 original size:66 final size:65
Alignment explanation
Indices: 38198--38377 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 65
38188 GACAAAATTT
* * *
38198 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
38260 A
65 A
*
38261 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
38326 A
65 A
38327 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
38378 CTATCTCAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 7 0.06
66 71 0.66
67 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:38439 original size:102 final size:105
Alignment explanation
Indices: 38261--38508 Score: 378
Period size: 102 Copynumber: 2.4 Consensus size: 105
38251 TCAATGTTTA
* * *
38261 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
*
38326 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-
66 ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
38364 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTAT-TT-CAAGGGAAATGTTTTCAATGTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT-TGTTCCAAGGGAAATGTTTTCAATGTT
*
38427 TATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTC
65 TATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
* * * *
38468 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTGTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTGTT
38509 TTAAGAAAAA
Statistics
Matches: 132, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
102 56 0.42
103 40 0.30
104 36 0.27
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (105 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
Found at i:40005 original size:183 final size:183
Alignment explanation
Indices: 39697--40050 Score: 654
Period size: 183 Copynumber: 1.9 Consensus size: 183
39687 ATCAGGTTTA
39697 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
39762 GCCAAGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
39827 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCATAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
39880 ACTAAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
39945 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
40010 TCCTCTATAACCAATTGCCATAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCATAGTGGAATAGCTCAGCTTTA
40051 CGGATTTAAT
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 165 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTAAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCATAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:44100 original size:21 final size:21
Alignment explanation
Indices: 44062--44112 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
44052 ACATAGTATT
44062 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
44082 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
44103 ACATATAGAA
1 AAATA-AGAA
44113 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:44291 original size:2 final size:2
Alignment explanation
Indices: 44284--44336 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
44274 ATATACTTAA
44284 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
44326 AT AT AT AT AT A
1 AT AT AT AT AT A
44337 CTAATATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46467 original size:45 final size:45
Alignment explanation
Indices: 46417--46556 Score: 149
Period size: 45 Copynumber: 3.1 Consensus size: 45
46407 GTATACCTAG
*
46417 GTCACACAACATCAG-CATCTCCCAAGTATCTCAGGTGAGGTCTGA
1 GTCACACAACAT-AGACATCTCCCAAGTATCTCAGGCGAGGTCTGA
* * *
46462 GTCACAGAGCATTGACATCTCCCAAGTATCTCAGGCGAGGTCTGA
1 GTCACACAACATAGACATCTCCCAAGTATCTCAGGCGAGGTCTGA
* * * * * * * *
46507 GTCACATAGCATCGACACCTCCCAAG-ACCTTAGGCTAGGTCTGG
1 GTCACACAACATAGACATCTCCCAAGTATCTCAGGCGAGGTCTGA
46551 GTCACA
1 GTCACA
46557 TAAGATCGAC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 21 0.25
45 62 0.75
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (45 bp):
GTCACACAACATAGACATCTCCCAAGTATCTCAGGCGAGGTCTGA
Found at i:46557 original size:44 final size:45
Alignment explanation
Indices: 46435--46569 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
46425 ACATCAGCAT
* * * * *
46435 CTCCCAAGTATCTCAGGTGAGGTCTGAGTCACAGAGCATTGACAT
1 CTCCCAAGTACCTCAGGCGAGGTCTGAGTCACATAGCATCGACAC
*
46480 CTCCCAAGTATCTCAGGCGAGGTCTGAGTCACATAGCATCGACAC
1 CTCCCAAGTACCTCAGGCGAGGTCTGAGTCACATAGCATCGACAC
* * *
46525 CTCCCAAG-ACCTTAGGCTAGGTCTGGGTCACATAAG-ATCGACAC
1 CTCCCAAGTACCTCAGGCGAGGTCTGAGTCACAT-AGCATCGACAC
46569 C
1 C
46570 ATGCTTGGCT
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 30 0.37
45 51 0.63
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (45 bp):
CTCCCAAGTACCTCAGGCGAGGTCTGAGTCACATAGCATCGACAC
Found at i:47638 original size:41 final size:41
Alignment explanation
Indices: 47587--47665 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
47577 CAAAGAAGGG
*
47587 ATCGATCATTTTCT-CCAAGTGATCGATCCTTTTGAAAAGAT
1 ATCGATCA-TTTCTGCCAAGGGATCGATCCTTTTGAAAAGAT
* * *
47628 ATCGATCATTTCTGTCGAGGGATCGATTCTTTTGAAAA
1 ATCGATCATTTCTGCCAAGGGATCGATCCTTTTGAAAA
47666 TGTATTGATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
ATCGATCATTTCTGCCAAGGGATCGATCCTTTTGAAAAGAT
Found at i:47710 original size:31 final size:31
Alignment explanation
Indices: 47675--47742 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
47665 ATGTATTGAT
47675 CCTTTGCTGGATAGAAACTTTGGGATCGATC
1 CCTTTGCTGGATAGAAACTTTGGGATCGATC
47706 CCTTTGCTGGATAGAAACTTTGGGATCGATC
1 CCTTTGCTGGATAGAAACTTTGGGATCGATC
47737 CCTTTG
1 CCTTTG
47743 GTCGAGGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (31 bp):
CCTTTGCTGGATAGAAACTTTGGGATCGATC
Found at i:47743 original size:15 final size:15
Alignment explanation
Indices: 47692--47743 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
47682 TGGATAGAAA
47692 CTTTGGGATCGATCC
1 CTTTGGGATCGATCC
* **
47707 CTTTGCTGGATAGA-AA
1 CTTTG--GGATCGATCC
47723 CTTTGGGATCGATCC
1 CTTTGGGATCGATCC
47738 CTTTGG
1 CTTTGG
47744 TCGAGGGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 6 0.21
15 11 0.39
16 5 0.18
17 6 0.21
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (15 bp):
CTTTGGGATCGATCC
Found at i:49408 original size:27 final size:26
Alignment explanation
Indices: 49364--49444 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
49354 TTCATAATCA
*
49364 TTTATATT-ACTAACTTAAAAAATATTT
1 TTTATATTAACTTA-TT-AAAAATATTT
*
49391 TTTATATTAACTTATTAAATATATTT
1 TTTATATTAACTTATTAAAAATATTT
*
49417 TAT-TATTAACTTAATTTAAAAATATTT
1 TTTATATTAACTT-A-TTAAAAATATTT
49444 T
1 T
49445 CATTTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.19
26 12 0.26
27 22 0.47
28 4 0.09
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTATATTAACTTATTAAAAATATTT
Found at i:49423 original size:25 final size:25
Alignment explanation
Indices: 49363--49444 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 25
49353 ATTCATAATC
* **
49363 ATTTATATTACTAACTTAAAAAATAT
1 ATTT-TATTATTAACTTATTAAATAT
*
49389 TTTTTA-TATTAACTTATTAAATAT
1 ATTTTATTATTAACTTATTAAATAT
*
49413 ATTTTATTATTAACTTAATTTAAAAAT
1 ATTTTATTATTAACTT-A-TTAAATAT
49440 ATTTT
1 ATTTT
49445 CATTTAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
24 20 0.43
25 11 0.23
26 4 0.09
27 12 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTATTATTAACTTATTAAATAT
Found at i:49471 original size:20 final size:21
Alignment explanation
Indices: 49435--49473 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
49425 ACTTAATTTA
49435 AAAATATTTTCATTTAAAAAT
1 AAAATATTTTCATTTAAAAAT
49456 AAAA-ATTTT-ATGTTAAAA
1 AAAATATTTTCAT-TTAAAA
49474 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 11 0.65
21 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAATATTTTCATTTAAAAAT
Found at i:49688 original size:17 final size:16
Alignment explanation
Indices: 49668--49715 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
49658 TTTAGTAATT
*
49668 TATTTTTAGTATTTTTA
1 TATTTTTA-TATTTTAA
49685 TATTTTGTATATTTTAA
1 TATTTT-TATATTTTAA
*
49702 TATTTTTTTATTTT
1 TATTTTTATATTTT
49716 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 19 0.68
18 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
TATTTTTATATTTTAA
Found at i:49716 original size:17 final size:15
Alignment explanation
Indices: 49666--49707 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
49656 TTTTTAGTAA
49666 TTTAT-TTTTAGTATT
1 TTTATATTTT-GTATT
49681 TTTATATTTTGTATAT
1 TTTATATTTTGTAT-T
49697 TTTAATATTTT
1 TTT-ATATTTT
49708 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.38
16 8 0.33
17 7 0.29
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (15 bp):
TTTATATTTTGTATT
Found at i:50758 original size:27 final size:27
Alignment explanation
Indices: 50719--50780 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
50709 ATTTTAAGTT
*
50719 AAAAATATGAATTCAAAAATAAAAA-ATA
1 AAAAAT-TAAATT-AAAAATAAAAATATA
** *
50747 AAAAATTAAATTATTAATAAAAATATT
1 AAAAATTAAATTAAAAATAAAAATATA
50774 AAAAATT
1 AAAAATT
50781 TGAAGTACGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 9 0.31
27 14 0.48
28 6 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAAATTAAATTAAAAATAAAAATATA
Found at i:50906 original size:23 final size:23
Alignment explanation
Indices: 50853--50914 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
50843 GATTTTATGG
* * *
50853 TAAAGAAAAATTTATAA-AATTT
1 TAAATAAAAATATAAAATAATTT
50875 TAAATAAAAATA-AAAATAATTT
1 TAAATAAAAATATAAAATAATTT
*
50897 TTAATAAAAAATATAAAA
1 TAAAT-AAAAATATAAAA
50915 ATATATAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 7 0.21
24 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
TAAATAAAAATATAAAATAATTT
Found at i:54892 original size:54 final size:54
Alignment explanation
Indices: 54805--55162 Score: 486
Period size: 54 Copynumber: 6.6 Consensus size: 54
54795 TGAACGACCA
* *
54805 ATGAACGACCATATC-AGCACTAAATGTGCAACCCACAAAATTCATAATAAGTTT
1 ATGAACGACCGTATCGA-CACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * * * * *
54859 ATGAATGACCGTATTGGCACTAAATGTGTAACCCACAGAATTCATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * *
54913 ATGAACGATCGTATCGACACTAAGTGTGCAACCCCCAAAATTTATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* *
54967 ATGAACGACCGTATCGACACTAAGTATGCAACACACAAAATTCATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * **
55021 ATGAATGACCGTATCGGCACTAAGTGTGCAACCCATGAAATTCATAATAAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* * * *
55075 ATGAACGACTGTATCGACACTAAGTATGCAACCCACATAATTCATAATGAGTTT
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
* *
55129 ATGAACGACCGTATTGACACTACGTGTGC-ACCCA
1 ATGAACGACCGTATCGACACTAAGTGTGCAACCCA
55163 AAAGAACTTA
Statistics
Matches: 265, Mismatches: 38, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
53 5 0.02
54 260 0.98
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (54 bp):
ATGAACGACCGTATCGACACTAAGTGTGCAACCCACAAAATTCATAATAAGTTT
Found at i:61785 original size:54 final size:54
Alignment explanation
Indices: 61700--61885 Score: 293
Period size: 54 Copynumber: 3.4 Consensus size: 54
61690 CTATGTGTAC
**
61700 TATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGAATG
1 TATCGACACTAAGTGTGCAACCCAC-ATAATTCATAATAAGTTTATGAACGACCG
* *
61754 TATCGACACTAAGTGTACAACTCACATAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCG
*
61808 TATCGACACTAAGTGTGCAACCCACATAATTCATAATGAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCG
* *
61862 TATCGACACTATGTGTGCACCCCA
1 TATCGACACTAAGTGTGCAACCCA
61886 AAGAACTTAT
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
53 1 0.01
54 121 0.99
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCG
Found at i:68915 original size:20 final size:20
Alignment explanation
Indices: 68890--68942 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
68880 ATAATGTTAT
68890 CAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
68910 CAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
68930 CAGGGTATCTATA
1 CAGGGTATCTATA
68943 TCTCAGTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:70412 original size:21 final size:21
Alignment explanation
Indices: 70386--70425 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
70376 CTGTAGTAGT
70386 ACTGTAACAGTGCATCGATGC
1 ACTGTAACAGTGCATCGATGC
*
70407 ACTGTAGCAGTGCATCGAT
1 ACTGTAACAGTGCATCGAT
70426 ACACAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAACAGTGCATCGATGC
Found at i:70476 original size:22 final size:22
Alignment explanation
Indices: 70451--70493 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
70441 AAAATATTTC
* *
70451 ACTGTTCATAGTACTGTTCATG
1 ACTGTTCACAGCACTGTTCATG
70473 ACTGTTCACAGCACTGTTCAT
1 ACTGTTCACAGCACTGTTCAT
70494 ACCGTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (22 bp):
ACTGTTCACAGCACTGTTCATG
Found at i:70478 original size:10 final size:12
Alignment explanation
Indices: 70451--70494 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
70441 AAAATATTTC
70451 ACTGTTCATAGT
1 ACTGTTCATAGT
70463 ACTGTTCAT-G-
1 ACTGTTCATAGT
* *
70473 ACTGTTCACAGC
1 ACTGTTCATAGT
70485 ACTGTTCATA
1 ACTGTTCATA
70495 CCGTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.29
11 2 0.07
12 18 0.64
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (12 bp):
ACTGTTCATAGT
Found at i:73897 original size:31 final size:31
Alignment explanation
Indices: 73810--73918 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
73800 AGAGTCGAGG
*
73810 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ***
73841 TTTTTACCTATG-TCTTTTGAGACATATGGACA
1 -GTTTACCTATGTTCTAAGGA-ACATATGGACA
* **
73873 GTATACCTATGTTCTAAGGAACATATATACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
*
73904 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
73919 TCGGGACCTA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
31 36 0.58
32 26 0.42
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:74099 original size:2 final size:2
Alignment explanation
Indices: 74092--74132 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
74082 TATTGAACAT
74092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74133 GTGATTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77296 original size:13 final size:13
Alignment explanation
Indices: 77278--77303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
77268 TCCAAACACT
77278 GAGGCGAGCATTC
1 GAGGCGAGCATTC
77291 GAGGCGAGCATTC
1 GAGGCGAGCATTC
77304 AAAGCTCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.38, T:0.15
Consensus pattern (13 bp):
GAGGCGAGCATTC
Found at i:79101 original size:22 final size:23
Alignment explanation
Indices: 79073--79131 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
79063 TTGCAGCTGC
*
79073 CAATTTGGACTTTAACAGGCTCT
1 CAATTTGGACTTTAACAAGCTCT
*
79096 -AATTTGGACTTTTAACAAGCTGT
1 CAATTTGGAC-TTTAACAAGCTCT
*
79119 CAATTTAGACTTT
1 CAATTTGGACTTT
79132 TTAACAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 9 0.29
23 14 0.45
24 8 0.26
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (23 bp):
CAATTTGGACTTTAACAAGCTCT
Done.