Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003270.1 Hibiscus syriacus cultivar Beakdansim tig00006875_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: 88363
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:13595 original size:30 final size:31
Alignment explanation
Indices: 13560--13620 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
13550 CAAAATGGTT
13560 TTTGGACTTGAATTGAAT-T-TACAAAATTTA
1 TTTGGACTT-AATTGAATGTATACAAAATTTA
*
13590 TTTGGACTTAATTGAATGTATTCAAAATTTA
1 TTTGGACTTAATTGAATGTATACAAAATTTA
13621 CAAAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 8 0.29
30 10 0.36
31 10 0.36
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (31 bp):
TTTGGACTTAATTGAATGTATACAAAATTTA
Found at i:13714 original size:18 final size:19
Alignment explanation
Indices: 13673--13739 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
13663 AATGTTTTTA
*
13673 TGAATAGTAATTTACTATT
1 TGAACAGTAATTTACTATT
13692 TGAACAGTAATTTACTA-T
1 TGAACAGTAATTTACTATT
* * *
13710 TGAACAGTAAATCACTGTT
1 TGAACAGTAATTTACTATT
13729 TGACACAGTAA
1 TGA-ACAGTAA
13740 CCCGAGGCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 15 0.36
19 20 0.48
20 7 0.17
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAATTTACTATT
Found at i:13871 original size:21 final size:21
Alignment explanation
Indices: 13845--13886 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13835 ATTTGAATAT
*
13845 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
13866 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
13887 CCCATTCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:13948 original size:21 final size:21
Alignment explanation
Indices: 13915--13954 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
13905 TTTTTGCAGA
*
13915 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
13937 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
13955 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:14201 original size:34 final size:32
Alignment explanation
Indices: 14162--14231 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
14152 TTTTGTAAAG
* *
14162 GGGAAAGGTTATAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
14196 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
14228 GGGA
1 GGGA
14232 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:16429 original size:30 final size:31
Alignment explanation
Indices: 16394--16455 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
16384 CAAAATGGTT
16394 TTTGGACTTGAATTGAAT-T-TACAAAATTTA
1 TTTGGACTT-AATTGAATGTATACAAAATTTA
*
16424 TTTGGACTTAATTGAATGTATTCAAAATTTA
1 TTTGGACTTAATTGAATGTATACAAAATTTA
16455 T
1 T
16456 AAAAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 8 0.28
30 10 0.34
31 11 0.38
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (31 bp):
TTTGGACTTAATTGAATGTATACAAAATTTA
Found at i:16603 original size:21 final size:21
Alignment explanation
Indices: 16577--16618 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16567 ATTTGAATAT
* * *
16577 TATGAAGGGGTATCGGTTCCC
1 TATGAAGAGGTACCGATTCCC
16598 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
16619 CCCATTCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:16680 original size:21 final size:21
Alignment explanation
Indices: 16647--16686 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
16637 TTTTTATAGA
*
16647 AAAATCATTCCCAAACGGCTCT
1 AAAATCA-TCCCCAACGGCTCT
16669 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
16687 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCT
Found at i:16945 original size:34 final size:32
Alignment explanation
Indices: 16900--16969 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
16890 TTTTGTAAAG
* * *
16900 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
16934 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
16966 GGGA
1 GGGA
16970 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:25280 original size:3 final size:3
Alignment explanation
Indices: 25274--25383 Score: 184
Period size: 3 Copynumber: 36.7 Consensus size: 3
25264 TTTTTATCCA
* *
25274 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
25322 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25370 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
25384 AATATATTAA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:26793 original size:12 final size:12
Alignment explanation
Indices: 26778--26840 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
26768 TTTTATTATA
26778 TTATTAAATATT
1 TTATTAAATATT
26790 TTATTAAATATT
1 TTATTAAATATT
*
26802 TT-TATAAATATA
1 TTAT-TAAATATT
* *
26814 TAATAAATAGTATT
1 TTATTAA-A-TATT
*
26828 TTTTTAAATATT
1 TTATTAAATATT
26840 T
1 T
26841 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 1 0.03
12 29 0.73
13 3 0.08
14 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:26850 original size:13 final size:12
Alignment explanation
Indices: 26781--26852 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
26771 TATTATATTA
*
26781 TTAAATATTTTA
1 TTAAATATTTTT
26793 TTAAATATTTTT
1 TTAAATATTTTT
* * **
26805 ATAAATATATAA
1 TTAAATATTTTT
*
26817 TAAATAGTATTTTT
1 TTAA-A-TATTTTT
26831 TTAAATATTTATT
1 TTAAATATTT-TT
*
26844 TTTAATATT
1 TTAAATATT
26853 GAAGAAAAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
12 26 0.58
13 12 0.27
14 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (12 bp):
TTAAATATTTTT
Found at i:37557 original size:83 final size:83
Alignment explanation
Indices: 37413--38104 Score: 1174
Period size: 83 Copynumber: 8.4 Consensus size: 83
37403 ATATCCCAGT
37413 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
37478 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
* * *
37496 TCAATCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
37561 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
37579 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
37644 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
37662 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
37727 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
37745 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
37810 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
* * *
37828 TCAATCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * **
37893 TGACCTGGTTTAACAGAA
66 TGATCTGATTGGACAGAA
*
37911 CCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
37976 TGACCTGGTT-TAGCAGAA
66 TGATCTGATTGGA-CAGAA
* * *
37994 -CAATCATCGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
38058 TGATTTGGTTGGACAGAA
66 TGATCTGATTGGACAGAA
*
38076 -CAATCATTGAATTTGGAAGATGAATTTGC
1 TCAAGCATTGAATTTGGAAGATGAATTTGC
38105 TCATAGTAAA
Statistics
Matches: 581, Mismatches: 26, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
82 102 0.18
83 479 0.82
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (83 bp):
TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTGGACAGAA
Found at i:38907 original size:113 final size:113
Alignment explanation
Indices: 38744--39488 Score: 1268
Period size: 113 Copynumber: 6.6 Consensus size: 113
38734 ATGGAGCAGC
*
38744 TTTT-CCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
*
38807 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
*
38855 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
*
38920 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
38968 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
39033 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
39081 TTTTGCCA-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
39145 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
39193 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * *
39258 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCATTTGATGGATCAA
66 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
** * *
39306 CATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 TTTTGCCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
39370 AGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAA
65 AGAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
** *
39419 CATTGCCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCATAATG
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATG
39482 AGAAGAA
65 AGAAGAA
39489 CTCATCAAGA
Statistics
Matches: 614, Mismatches: 14, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
111 6 0.01
112 173 0.28
113 434 0.71
114 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (113 bp):
TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
Found at i:39139 original size:225 final size:224
Alignment explanation
Indices: 38744--39488 Score: 1260
Period size: 225 Copynumber: 3.3 Consensus size: 224
38734 ATGGAGCAGC
38744 TTTT-CCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
1 TTTTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
*
38808 AAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTC
66 AAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTATTTTTGCCA-AGAAGGTTC
*
38873 ATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCT
130 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCT
*
38938 TTTACCTGAATTCATCACTTGATGGATTAT
195 TTTACTTGAATTCATCACTTGATGGATTAT
*
38968 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
39033 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTATTTTTGCCAAGAAGGTTC
65 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTATTTTTGCCAAGAAGGTTC
39098 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCT
130 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCT
39163 TTTACTTGAATTCATCACTTGATGGATTAT
195 TTTACTTGAATTCATCACTTGATGGATTAT
*
39193 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * *** * *
39258 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAAAGTT
65 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTATTTTTGCCAAG-AAGGTT
*
39323 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
129 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
* * * *
39388 TTTTGCTTGAATTCATCATTTGATGGATCAA
194 TTTTACTTGAATTCATCACTTGATGGATTAT
**
39419 CATTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCATAATGA
1 TTTTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATGA
39483 GAAGAA
65 GAAGAA
39489 CTCATCAAGA
Statistics
Matches: 498, Mismatches: 19, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
224 7 0.01
225 279 0.56
226 212 0.43
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (224 bp):
TTTTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTATTTTTGCCAAGAAGGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
TTACTTGAATTCATCACTTGATGGATTAT
Found at i:39347 original size:338 final size:338
Alignment explanation
Indices: 38725--39488 Score: 1284
Period size: 338 Copynumber: 2.3 Consensus size: 338
38715 GATTCAAATC
* * *
38725 CATCATTTGATGGAGCAGCTTTT-CCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCA-ATTTTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
38789 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTA
65 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTA
38854 TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATG
130 TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATG
* *** *
38919 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGT
195 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAACATTGCCAGAGAAAGT
38984 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
260 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
39049 CTTTTACTTGAATT
325 CTTTTACTTGAATT
* * *
39063 CATCACTTGATGGATTATTTTTGCCA-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAATTTTGCCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGA
*
39127 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTA
65 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTA
*
39192 TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
130 TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATG
* *
39257 AGAAGAATTTGTTCAACCTTTTACTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAG
195 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAACATTGCCAGAG-AAAG
*
39321 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
259 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
*
39386 CCTTTTGCTTGAATT
324 CCTTTTACTTGAATT
* **
39401 CATCATTTGATGGATCAACATTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
1 CATCACTTGATGGATCAATTTTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
39466 GAA-AAAGTTCATAATGAGAAGAA
66 GAAGAAA-TTCATAATGAGAAGAA
39489 CTCATCAAGA
Statistics
Matches: 399, Mismatches: 22, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
337 12 0.03
338 383 0.96
339 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (338 bp):
CATCACTTGATGGATCAATTTTGCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA
GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAACATTGCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC
TTTTACTTGAATT
Found at i:39748 original size:3 final size:3
Alignment explanation
Indices: 39742--39842 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
39732 TTTTTATCCA
* *
39742 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
39790 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39838 TAT TA
1 TAT TA
39843 AATATTTAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:41260 original size:13 final size:12
Alignment explanation
Indices: 41232--41257 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41222 TTTTATTATA
41232 TTATTAAATATT
1 TTATTAAATATT
41244 TTATTAAATATT
1 TTATTAAATATT
41256 TT
1 TT
41258 TATAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:41285 original size:34 final size:33
Alignment explanation
Indices: 41219--41290 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
41209 GTAGTATTTG
* *
41219 TATTTTTATTATATTATTAAATATTTTATTAAA
1 TATTTTTATAATATTATAAAATATTTTATTAAA
*
41252 TATTTTTATAATA-TATAAATAGTATTTTTTTAAA
1 TATTTTTATAATATTATAAA-A-TATTTTATTAAA
41286 TATTT
1 TATTT
41291 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 5 0.15
33 13 0.38
34 16 0.47
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTTTTATAATATTATAAAATATTTTATTAAA
Found at i:48523 original size:30 final size:30
Alignment explanation
Indices: 48487--48566 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
48477 TAGTTGGGCG
* *
48487 GGCGGATGTGGGGTGGGTGGATGCAGTGCA
1 GGCGGATGAGGGGCGGGTGGATGCAGTGCA
*
48517 GGCGGATGAGGGGCGGGTGGATGCGGTGCGGA
1 GGCGGATGAGGGGCGGGTGGATGCAGTGC--A
* *
48549 TGCGGATGCGGGGCGGGT
1 GGCGGATGAGGGGCGGGT
48567 AAGGTCTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 26 0.60
32 17 0.40
ACGTcount: A:0.11, C:0.12, G:0.60, T:0.16
Consensus pattern (30 bp):
GGCGGATGAGGGGCGGGTGGATGCAGTGCA
Found at i:48538 original size:15 final size:15
Alignment explanation
Indices: 48482--48565 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
48472 ATATTTAGTT
*
48482 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGAG
* *
48497 GGGTGGGTGGATGCA-
1 GGGCGGGCGGATG-AG
* *
48512 GTGCAGGCGGATGAG
1 GGGCGGGCGGATGAG
* *
48527 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGAG
* *
48542 GTGCGGATGCGGATGCG
1 GGGCGG--GCGGATGAG
48559 GGGCGGG
1 GGGCGGG
48566 TAAGGTCTCA
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
14 1 0.02
15 37 0.73
17 13 0.25
ACGTcount: A:0.11, C:0.13, G:0.62, T:0.14
Consensus pattern (15 bp):
GGGCGGGCGGATGAG
Found at i:48930 original size:14 final size:15
Alignment explanation
Indices: 48902--48936 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
48892 CGTTACACAT
*
48902 TATTTTTTATTATAA
1 TATTTTTTATAATAA
48917 TATTTTTT-TAATAA
1 TATTTTTTATAATAA
48931 TATTTT
1 TATTTT
48937 GCGATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTTTATAATAA
Found at i:51403 original size:24 final size:24
Alignment explanation
Indices: 51370--51423 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
51360 GGAGATGGGA
51370 GAGAAAACGAGGAAGAATTAGGGC
1 GAGAAAACGAGGAAGAATTAGGGC
*
51394 GAGAACACGAGGAAGAATTAGGGC
1 GAGAAAACGAGGAAGAATTAGGGC
51418 GAGAAA
1 GAGAAA
51424 TGTGTATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.09, G:0.37, T:0.07
Consensus pattern (24 bp):
GAGAAAACGAGGAAGAATTAGGGC
Found at i:53825 original size:24 final size:24
Alignment explanation
Indices: 53792--53845 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
53782 GGAGATGGGA
53792 GAGAAAACGAGGAAGAATTAGGGC
1 GAGAAAACGAGGAAGAATTAGGGC
*
53816 GAGAACACGAGGAAGAATTAGGGC
1 GAGAAAACGAGGAAGAATTAGGGC
53840 GAGAAA
1 GAGAAA
53846 TGTGTATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.09, G:0.37, T:0.07
Consensus pattern (24 bp):
GAGAAAACGAGGAAGAATTAGGGC
Found at i:58971 original size:24 final size:24
Alignment explanation
Indices: 58914--58961 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
58904 TGGGAGGAGA
58914 AGGGCGAGAAAACGAGGAAGAATT
1 AGGGCGAGAAAACGAGGAAGAATT
* *
58938 AGGGCGAGAACACGATGAAGAATT
1 AGGGCGAGAAAACGAGGAAGAATT
58962 GGGGGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.35, T:0.10
Consensus pattern (24 bp):
AGGGCGAGAAAACGAGGAAGAATT
Found at i:60024 original size:16 final size:16
Alignment explanation
Indices: 60000--60043 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
59990 CTATAACGCT
*
60000 CGATGAGTACCACTAA
1 CGATAAGTACCACTAA
60016 CGATAAGTACCACTAA
1 CGATAAGTACCACTAA
60032 CGATAAGTACCA
1 CGATAAGTACCA
60044 TTAATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (16 bp):
CGATAAGTACCACTAA
Found at i:60204 original size:21 final size:23
Alignment explanation
Indices: 60157--60204 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
60147 ACGTATGATT
60157 ATAAATTAATTAAAAATTAAAGG
1 ATAAATTAATTAAAAATTAAAGG
*
60180 -TAAATT-ATTTAAAA-TAAAGG
1 ATAAATTAATTAAAAATTAAAGG
60200 ATAAA
1 ATAAA
60205 CTATACTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 11 0.48
22 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.31
Consensus pattern (23 bp):
ATAAATTAATTAAAAATTAAAGG
Found at i:63891 original size:24 final size:24
Alignment explanation
Indices: 63847--63896 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
63837 ATAAAGAACC
*
63847 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
63871 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
63895 AA
1 AA
63897 TCAATCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:74254 original size:24 final size:24
Alignment explanation
Indices: 74210--74259 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
74200 ATAAAGAACC
*
74210 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
74234 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
74258 AA
1 AA
74260 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:75782 original size:16 final size:16
Alignment explanation
Indices: 75761--75792 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
75751 TATAAATTAA
75761 ATTAGTGGTGTTCATC
1 ATTAGTGGTGTTCATC
75777 ATTAGTGGTGTTCATC
1 ATTAGTGGTGTTCATC
75793 CGTGCTCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
ATTAGTGGTGTTCATC
Found at i:75914 original size:22 final size:23
Alignment explanation
Indices: 75871--75919 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
75861 CGTATAATTA
*
75871 TAAATTAGTCAAAAATTTAAAGG
1 TAAATTAGTCAAAAATTAAAAGG
* *
75894 TAAATTATTTAAAAA-TAAAAGG
1 TAAATTAGTCAAAAATTAAAAGG
75916 TAAA
1 TAAA
75920 CTATACCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (23 bp):
TAAATTAGTCAAAAATTAAAAGG
Found at i:79692 original size:21 final size:21
Alignment explanation
Indices: 79652--79692 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
79642 CGGCACTGGT
* *
79652 ATAATTTACCTTTTATTTTAA
1 ATAATTTACCTTTAAATTTAA
*
79673 ATAATTTGCCTTTAAATTTA
1 ATAATTTACCTTTAAATTTA
79693 TGCTAATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTTACCTTTAAATTTAA
Found at i:81250 original size:20 final size:20
Alignment explanation
Indices: 81222--81285 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
81212 ATCTGATTCG
*
81222 CCTGGAATTTTAGTTCGTCC
1 CCTGAAATTTTAGTTCGTCC
*
81242 CCTGAAATTTTAGTTCATCC
1 CCTGAAATTTTAGTTCGTCC
* * * *
81262 TACTTAAGTTTAAGTTCGTCC
1 -CCTGAAATTTTAGTTCGTCC
81283 CCT
1 CCT
81286 AACATAAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (20 bp):
CCTGAAATTTTAGTTCGTCC
Found at i:83682 original size:13 final size:13
Alignment explanation
Indices: 83664--83744 Score: 72
Period size: 13 Copynumber: 5.6 Consensus size: 13
83654 CAAGAAGATA
83664 GAATGAAATTATT
1 GAATGAAATTATT
*
83677 GAATGAAACTCATTT
1 GAATGAAA-TTA-TT
83692 GAGAATGAAATTATT
1 --GAATGAAATTATT
*
83707 GAATGAAACTCATTT
1 GAATGAAA-TTA-TT
83722 GAGAATGAAATTATT
1 --GAATGAAATTATT
83737 GAATGAAA
1 GAATGAAA
83745 CTCATTTGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 24 0.43
14 4 0.07
15 8 0.14
16 4 0.07
17 16 0.29
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (13 bp):
GAATGAAATTATT
Found at i:83699 original size:17 final size:17
Alignment explanation
Indices: 83677--83753 Score: 80
Period size: 13 Copynumber: 5.0 Consensus size: 17
83667 TGAAATTATT
83677 GAATGAAACTCATTTGA
1 GAATGAAACTCATTTGA
*
83694 GAATGAAA-TTA-TT--
1 GAATGAAACTCATTTGA
83707 GAATGAAACTCATTTGA
1 GAATGAAACTCATTTGA
*
83724 GAATGAAA-TTA-TT--
1 GAATGAAACTCATTTGA
83737 GAATGAAACTCATTTGA
1 GAATGAAACTCATTTGA
83754 TGAACAGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
13 16 0.33
14 4 0.08
15 8 0.17
16 4 0.08
17 16 0.33
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (17 bp):
GAATGAAACTCATTTGA
Found at i:83699 original size:30 final size:30
Alignment explanation
Indices: 83663--83753 Score: 182
Period size: 30 Copynumber: 3.0 Consensus size: 30
83653 TCAAGAAGAT
83663 AGAATGAAATTATTGAATGAAACTCATTTG
1 AGAATGAAATTATTGAATGAAACTCATTTG
83693 AGAATGAAATTATTGAATGAAACTCATTTG
1 AGAATGAAATTATTGAATGAAACTCATTTG
83723 AGAATGAAATTATTGAATGAAACTCATTTG
1 AGAATGAAATTATTGAATGAAACTCATTTG
83753 A
1 A
83754 TGAACAGGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (30 bp):
AGAATGAAATTATTGAATGAAACTCATTTG
Done.