Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006586.1 Hibiscus syriacus cultivar Beakdansim tig00016148_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: 89695
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:777 original size:20 final size:21
Alignment explanation
Indices: 741--779 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
731 AATTAATGAA
741 TAAATAGATTATTATTATTAT
1 TAAATAGATTATTATTATTAT
*
762 TAAATA-ATTTTTATTATT
1 TAAATAGATTATTATTATT
780 TGTCAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TAAATAGATTATTATTATTAT
Found at i:12075 original size:21 final size:21
Alignment explanation
Indices: 12049--12126 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
12039 GGGTTTCATA
12049 GGTCCTTCGGGACAATACAAT
1 GGTCCTTCGGGACAATACAAT
* *
12070 GGTCCTTCGGGACAATATAGT
1 GGTCCTTCGGGACAATACAAT
*
12091 GATCCTTCGGGACAATACAAT
1 GGTCCTTCGGGACAATACAAT
12112 GGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
12127 ATTTCATATG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAAT
Found at i:12891 original size:11 final size:11
Alignment explanation
Indices: 12857--12891 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12847 ATTTTACGGA
12857 AGTACTGTAGC
1 AGTACTGTAGC
* *
12868 AATCCTGTAGC
1 AGTACTGTAGC
12879 AGTACTGTAGC
1 AGTACTGTAGC
12890 AG
1 AG
12892 GGTATCGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:12925 original size:22 final size:21
Alignment explanation
Indices: 12883--12926 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
12873 TGTAGCAGTA
*
12883 CTGTAGCAGGGTATCGATTCC
1 CTGTAGCAGGGAATCGATTCC
*
12904 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCA-GGGAATCGATTCC
12926 C
1 C
12927 CTTTTTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGATTCC
Found at i:14220 original size:15 final size:16
Alignment explanation
Indices: 14182--14222 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
14172 TCAGAGCCTC
*
14182 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
14198 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
14214 T-AATCATTC
1 TGAATCATTC
14223 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:15885 original size:16 final size:17
Alignment explanation
Indices: 15847--15890 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
15837 ATTTTATATT
15847 TATTTTTTATTAAAGATA
1 TATTTTTT-TTAAAGATA
15865 TATTTTTTTTAAA-AT-
1 TATTTTTTTTAAAGATA
*
15880 TAATTTTTTTA
1 TATTTTTTTTA
15891 TATATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 5 0.20
18 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTTTTTTTAAAGATA
Found at i:18695 original size:21 final size:22
Alignment explanation
Indices: 18671--18716 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
18661 ATATTACACG
18671 TGATGAGAGATTGTTGATT-GT
1 TGATGAGAGATTGTTGATTGGT
*
18692 TGATGTGAGATTGTTGATTGGT
1 TGATGAGAGATTGTTGATTGGT
18714 TGA
1 TGA
18717 GAAATCGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (22 bp):
TGATGAGAGATTGTTGATTGGT
Found at i:18797 original size:21 final size:21
Alignment explanation
Indices: 18773--18813 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18763 ACATTATACG
18773 TGATGAGAGATTGTTGATTGT
1 TGATGAGAGATTGTTGATTGT
*
18794 TGATGTGAGATTGTTGATTG
1 TGATGAGAGATTGTTGATTG
18814 GCTGAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TGATGAGAGATTGTTGATTGT
Found at i:18808 original size:102 final size:103
Alignment explanation
Indices: 18621--18841 Score: 372
Period size: 102 Copynumber: 2.1 Consensus size: 103
18611 GAATAAGATT
18621 ACATGAATGTATTATTTGGCATATTAACATGAATGTTACAATATTACACGTGATGAGAGATTGTT
1 ACATGAATGTATTATTTGGCATATTAACATGAATGTTAC-A-ATTACACGTGATGAGAGATTGTT
*
18686 GATTGTTGATGTGAGATTGTTGATTGGTTGAGAAATCGAC
64 GATTGTTGATGTGAGATTGTTGATTGGCTGAGAAATCGAC
* *
18726 ACATGAATGTATTATTTGGCATATTAACATGAATTTTAC-ATTATACGTGATGAGAGATTGTTGA
1 ACATGAATGTATTATTTGGCATATTAACATGAATGTTACAATTACACGTGATGAGAGATTGTTGA
18790 TTGTTGATGTGAGATTGTTGATTGGCTGAGAAATCGAC
66 TTGTTGATGTGAGATTGTTGATTGGCTGAGAAATCGAC
*
18828 ACATGTTATGTATT
1 ACATG-AATGTATT
18842 TACTTAGTGA
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
102 66 0.59
103 7 0.06
105 38 0.34
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (103 bp):
ACATGAATGTATTATTTGGCATATTAACATGAATGTTACAATTACACGTGATGAGAGATTGTTGA
TTGTTGATGTGAGATTGTTGATTGGCTGAGAAATCGAC
Found at i:19355 original size:138 final size:136
Alignment explanation
Indices: 19100--19381 Score: 386
Period size: 138 Copynumber: 2.1 Consensus size: 136
19090 ACCGAAGTGC
* *
19100 CGAAATAGAAATTCACAAACTCATTATGAATTCCATGGATGCACACATAATGCCGAAAGTACACA
1 CGAAAT-GAAATTCACAAAATCATTATGAATACCATGGATGCACACATAATGCCGAAAGTACACA
* * * *
19165 TAGTACTGATATGAAAATACACCATTATGCATTACACAAAATTGATCAATAACTTTTATACATAA
65 TAATACTGATATAAAAATACACCATTATGCATTACACAAAATCGATCAATAACTTTTATACACAA
19230 TTGTATAT
130 TT-TATAT
** *
19238 CGAAATGATAATTCACAAAATCATTATGAATACCAT-GATTGCACATTTAGTGCCGAAAGTACAC
1 CGAAATGA-AATTCACAAAATCATTATGAATACCATGGA-TGCACACATAATGCCGAAAGTACAC
* * * * *
19302 ATAATATTGATATAAAAATGCACCCTTATGCATTACACAAAATCGATCGATAACTTTTATATACA
64 ATAATACTGATATAAAAATACACCATTATGCATTACACAAAATCGATCAATAACTTTTATACACA
*
19367 ATTTATGT
129 ATTTATAT
19375 CGAAATG
1 CGAAATG
19382 CACCTATGAC
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
137 15 0.12
138 112 0.88
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (136 bp):
CGAAATGAAATTCACAAAATCATTATGAATACCATGGATGCACACATAATGCCGAAAGTACACAT
AATACTGATATAAAAATACACCATTATGCATTACACAAAATCGATCAATAACTTTTATACACAAT
TTATAT
Found at i:28052 original size:30 final size:30
Alignment explanation
Indices: 27997--28081 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
27987 TTTGGCTAGT
* * *
27997 GACTAAAATATAAGTTT-TGAAAGTTTGGTG
1 GACTAAAATATAAATTTGTAAAAGTTTAG-G
28027 GA-TAAAATATAAATTTGTAAAAGTTTAGG
1 GACTAAAATATAAATTTGTAAAAGTTTAGG
*
28056 GACCTAAAATATAATTTTG-AAAAGTT
1 GA-CTAAAATATAAATTTGTAAAAGTT
28082 ATATATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.33
30 18 0.38
31 14 0.29
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.35
Consensus pattern (30 bp):
GACTAAAATATAAATTTGTAAAAGTTTAGG
Found at i:30986 original size:189 final size:188
Alignment explanation
Indices: 30746--31123 Score: 591
Period size: 189 Copynumber: 2.0 Consensus size: 188
30736 ATTAAATTTT
* * * * *
30746 AAATTTTAAATATATTATATATAACATTTGGGCTCAACCCAAACTATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATAAAACATATGAGCTCAACCCAAACCATTTAAAACTCAATTAATAA
* *
30811 TTTAAGATCCAATAATTTTTTAAACCTAAATCAATATTAATTAATTAAAAAAGTTTATAT-AAAT
66 TTTAAGATCCAATAA-CTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-ATTATATGAAA-
*
30875 TTTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TATTTTTTT-AATTAAAA
128 -TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTATTTTTTTGAATTAAAA
*
30935 AAATATTAAATATATTATATAAAACATATGAGCTCACCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATAAAACATATGAGCTCAACCCAAACCATTTAAAACTCAATTAATAA
*
31000 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
* *
31065 TTATTTTATAGTTATATATTATTTAAATTAATTATAAACTTTTTTTTTTGAATTAAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTATTTTTTTGAATTAAAA
31123 A
1 A
31124 CATTTAATTT
Statistics
Matches: 174, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
186 40 0.23
187 13 0.07
188 47 0.27
189 74 0.43
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (188 bp):
AAATATTAAATATATTATATAAAACATATGAGCTCAACCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTATTTTTTTGAATTAAAA
Found at i:37007 original size:3 final size:3
Alignment explanation
Indices: 36981--37039 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
36971 GGCCCACAAA
* *
36981 AAT AAT TAT AAT ATAT AA- AAT AAT AAT AAT AAT AAT AAT AAC AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37026 AAT -AT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
37040 TATTATTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:37395 original size:46 final size:46
Alignment explanation
Indices: 37344--37470 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 46
37334 AAATTAACTC
* *
37344 GAAAATCTAAAAGTTGATCTGAATCAAAACCAA-CTCGAATTGACCT
1 GAAAATCTAAAAGTTGATCCGAACCAAAACCAACCT-GAATTGACCT
* * *
37390 GAAAATCTAAAGGTTGATCCAAACCGAAACCAACCTGAATTGACCT
1 GAAAATCTAAAAGTTGATCCGAACCAAAACCAACCTGAATTGACCT
*
37436 GAAAATCT-AAAGCTTGACCCGAACCAAAACCAACC
1 GAAAATCTAAAAG-TTGATCCGAACCAAAACCAACC
37471 AATCCGATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 3 0.04
46 65 0.93
47 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.19
Consensus pattern (46 bp):
GAAAATCTAAAAGTTGATCCGAACCAAAACCAACCTGAATTGACCT
Found at i:37487 original size:31 final size:31
Alignment explanation
Indices: 37449--37565 Score: 92
Period size: 31 Copynumber: 3.7 Consensus size: 31
37439 AATCTAAAGC
37449 TTGACCCGAACCAAAACCAACCAATCCGATA
1 TTGACCCGAACCAAAACCAACCAATCCGATA
* * * *
37480 TTGACCCG-ACTCAAGACCAATCGATCCGAAA
1 TTGACCCGAAC-CAAAACCAACCAATCCGATA
* * * * *
37511 TTAACCCGACCCACACACCAACCCATCCGATT
1 TTGACCCGAACCA-AAACCAACCAATCCGATA
* * *
37543 TTGTCCCGATTCGAAAACCAACC
1 TTGACCCGA-ACCAAAACCAACC
37566 GACTCAATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
30 2 0.03
31 33 0.50
32 29 0.44
33 2 0.03
ACGTcount: A:0.35, C:0.38, G:0.11, T:0.16
Consensus pattern (31 bp):
TTGACCCGAACCAAAACCAACCAATCCGATA
Found at i:38468 original size:3 final size:3
Alignment explanation
Indices: 38460--38497 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
38450 AATTTAAATT
38460 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38498 TAACTTACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39736 original size:19 final size:19
Alignment explanation
Indices: 39690--39736 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
39680 CATTAATTTG
*
39690 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
39710 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
39730 TATATTT
1 TATATTT
39737 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:42439 original size:29 final size:28
Alignment explanation
Indices: 42407--42472 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 28
42397 TATGCACTTA
* *
42407 AAAGTGCCTCGTGGATATATTTACACTCG
1 AAAGTGCCTCGTCG-TAGATTTACACTCG
*
42436 AAAGTG-CT--TCGTAGATTTGCACTCG
1 AAAGTGCCTCGTCGTAGATTTACACTCG
42461 AAAGTGCCTCGT
1 AAAGTGCCTCGT
42473 AGTATTGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 18 0.58
26 4 0.13
28 3 0.10
29 6 0.19
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (28 bp):
AAAGTGCCTCGTCGTAGATTTACACTCG
Found at i:42459 original size:25 final size:25
Alignment explanation
Indices: 42425--42482 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
42415 TCGTGGATAT
* *
42425 ATTTACACTCGAAAGTGCTTCGTAG
1 ATTTGCACTCGAAAGTGCCTCGTAG
42450 ATTTGCACTCGAAAGTGCCTCGTAG
1 ATTTGCACTCGAAAGTGCCTCGTAG
42475 -TATTGCAC
1 AT-TTGCAC
42483 CATAGGTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (25 bp):
ATTTGCACTCGAAAGTGCCTCGTAG
Found at i:50389 original size:15 final size:15
Alignment explanation
Indices: 50371--50400 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
50361 AAAACCATGT
50371 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
50386 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
50401 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:50407 original size:15 final size:15
Alignment explanation
Indices: 50374--50408 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
50364 ACCATGTTAG
* *
50374 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
50389 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
50404 ATAAA
1 ATAAA
50409 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:50508 original size:44 final size:44
Alignment explanation
Indices: 50440--50549 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 44
50430 AAGAGAAAAC
* * * *
50440 AAATTAAATAAAGAT-AAGATAAAGAAAACA-AAG-ATAAAATAG
1 AAATAAAATAAATATAAAAATAAAGAAAA-AGAAGAAAAAAATAG
*
50482 TAAGTAAAATAAATATAAAAATAAAGAAAAAGAAGAAAAAAATAG
1 -AAATAAAATAAATATAAAAATAAAGAAAAAGAAGAAAAAAATAG
*
50527 AAATAAAA-AAATAAATAAAATAA
1 AAATAAAATAAATATA-AAAATAA
50550 TTAAAAAAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
43 19 0.34
44 29 0.52
45 8 0.14
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (44 bp):
AAATAAAATAAATATAAAAATAAAGAAAAAGAAGAAAAAAATAG
Found at i:50548 original size:9 final size:9
Alignment explanation
Indices: 50402--50623 Score: 73
Period size: 9 Copynumber: 23.3 Consensus size: 9
50392 AAAAGGTAAG
50402 AAATAAATA
1 AAATAAATA
* *
50411 AATTAATTA
1 AAATAAATA
*
50420 AATTAAAATA
1 AAAT-AAATA
*
50430 AAGAGAAA-A
1 AA-ATAAATA
50439 CAAATTAAATA
1 -AAA-TAAATA
50450 AAGATAAGATA
1 AA-ATAA-ATA
*
50461 AAGA-AAACA
1 AA-ATAAATA
50470 AAGATAAA-A
1 AA-ATAAATA
* * *
50479 TAGTAAGTA
1 AAATAAATA
50488 AAATAAATATAA
1 AAAT-AA-AT-A
*
50500 AAATAAAGA
1 AAATAAATA
*
50509 AAA-AGAAGA
1 AAATA-AATA
50518 AAA-AAATA
1 AAATAAATA
50526 GAAATAAA-A
1 -AAATAAATA
50535 AAATAAATA
1 AAATAAATA
*
50544 AAATAATTA
1 AAATAAATA
*
50553 AAA-AAGTA
1 AAATAAATA
50561 AAATAATATA
1 AAATAA-ATA
*
50571 TATATAAATA
1 -AAATAAATA
*
50581 AAAAAAATA
1 AAATAAATA
50590 AAA-AAAGTA
1 AAATAAA-TA
50599 AATATATATATA
1 AA-ATA-A-ATA
*
50611 TAAATTAATA
1 -AAATAAATA
50621 AAA
1 AAA
50624 CTGATAATAA
Statistics
Matches: 166, Mismatches: 22, Indels: 50
0.70 0.09 0.21
Matches are distributed among these distances:
8 24 0.14
9 71 0.43
10 39 0.23
11 19 0.11
12 10 0.06
13 3 0.02
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:50549 original size:5 final size:5
Alignment explanation
Indices: 50418--50592 Score: 53
Period size: 5 Copynumber: 34.0 Consensus size: 5
50408 ATAAATTAAT
* * * * * *
50418 TAAAT TAAAA TAAAGA GAAAA -CAAA TTAAA TAAAGA TAAGA T-AAA GAAAA
1 TAAAA TAAAA TAAA-A TAAAA TAAAA TAAAA TAAA-A TAAAA TAAAA TAAAA
* * *
50468 CAAAGA TAAAA TAGTAAG TAAAA TAAATA TAAAAA TAAAGA -AAAA GAAGAA
1 TAAA-A TAAAA TA--AAA TAAAA TAAA-A T-AAAA TAAA-A TAAAA TAA-AA
*
50519 AAAAA TAGAAA T-AAA -AAAA T-AAA TAAAA TAATTAA -AAAA GTAAAA
1 TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TAA--AA TAAAA -TAAAA
* *
50564 TAATA T-ATA TATAAA TAAAA -AAAA TAAAA
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA
50593 AAAGTAAATA
Statistics
Matches: 131, Mismatches: 16, Indels: 46
0.68 0.08 0.24
Matches are distributed among these distances:
4 26 0.20
5 61 0.47
6 35 0.27
7 9 0.07
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:50608 original size:38 final size:37
Alignment explanation
Indices: 50483--50669 Score: 129
Period size: 38 Copynumber: 5.0 Consensus size: 37
50473 ATAAAATAGT
* * * *
50483 AAGTAAAATAAATATAAAAATAAAGAAAAAGAAGAAAAA
1 AAGTAAAAT-AATATATATATAAATAAAAA-AATAAAAA
* * *
50522 AA-TAGAAATAA-A-A-AAATAAATAAAATAATTAAAA
1 AAGTA-AAATAATATATATATAAATAAAAAAATAAAAA
50556 AAGTAAAATAATATATATATAAATAAAAAAAATAAAAA
1 AAGTAAAATAATATATATATAAAT-AAAAAAATAAAAA
* * *
50594 AAGT-AAAT-ATATATATATAAATTAATAAAACTGATAAT
1 AAGTAAAATAATATATATATAAA-TAA-AAAAAT-AAAAA
*
50632 AA--AAAATAATATTTATATATAATCTAAAAAAATAAAAA
1 AAGTAAAATAATA--TATATATAA-ATAAAAAAATAAAAA
50670 TATATACTAA
Statistics
Matches: 120, Mismatches: 14, Indels: 29
0.74 0.09 0.18
Matches are distributed among these distances:
34 14 0.12
35 14 0.12
36 17 0.14
37 22 0.18
38 30 0.25
39 11 0.09
40 12 0.10
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (37 bp):
AAGTAAAATAATATATATATAAATAAAAAAATAAAAA
Found at i:50643 original size:40 final size:36
Alignment explanation
Indices: 50535--50669 Score: 112
Period size: 41 Copynumber: 3.5 Consensus size: 36
50525 AGAAATAAAA
*
50535 AAATAAATAAAATAATTAAAAAAGTAAAATAATATATATAT
1 AAATAAAAAAAATAA--AAAAAA-T-AAAT-ATATATATAT
*
50576 AAATAAAAAAAATAAAAAAAGTAAATATATATATAT
1 AAATAAAAAAAATAAAAAAAATAAATATATATATAT
* *
50612 AAATTAATAAAACTGATAATAAAAAAT-AATATTTATATAT
1 AAA-TAA-AAAA--AATAA-AAAAAATAAATATATATATAT
*
50652 -AATCTAAAAAAATAAAAA
1 AAAT-AAAAAAAATAAAAA
50670 TATATACTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
35 3 0.04
36 17 0.21
37 7 0.09
38 10 0.12
39 8 0.10
40 16 0.20
41 20 0.25
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (36 bp):
AAATAAAAAAAATAAAAAAAATAAATATATATATAT
Found at i:50696 original size:20 final size:20
Alignment explanation
Indices: 50660--50715 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
50650 ATAATCTAAA
* *
50660 AAAAT-AAAAATATATAC-T
1 AAAATAAAAAAAAAATACAT
*
50678 AAAGTAAAAAAGAAAATACAT
1 AAAATAAAAAA-AAAATACAT
*
50699 AAAATATAAAAAAAATA
1 AAAATAAAAAAAAAATA
50716 TTACATGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.13
19 5 0.17
20 11 0.37
21 10 0.33
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAAAAAAAAAATACAT
Found at i:50720 original size:23 final size:22
Alignment explanation
Indices: 50656--50735 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
50646 ATATATAATC
*
50656 TAAAA-AAATAAAAATATATAC-
1 TAAAATAAAAAAAAATAT-TACA
*
50677 TAAAGTAAAAAAGAAA-A-TACA
1 TAAAATAAAAAA-AAATATTACA
50698 TAAAATATAAAAAAAATATTACA
1 TAAAATA-AAAAAAAATATTACA
*
50721 TGAAAA-AAAAGAAAA
1 T-AAAATAAAAAAAAA
50736 GAAAAATAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
20 3 0.06
21 13 0.27
22 19 0.40
23 9 0.19
24 4 0.08
ACGTcount: A:0.72, C:0.04, G:0.05, T:0.19
Consensus pattern (22 bp):
TAAAATAAAAAAAAATATTACA
Found at i:51077 original size:37 final size:36
Alignment explanation
Indices: 51031--51130 Score: 159
Period size: 34 Copynumber: 2.8 Consensus size: 36
51021 AGTATAACTC
* *
51031 TATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTT
1 TATCCTATTTTTAGGAGTTTGAATCCTAG-AAAATTA
51068 TATCCTATTTTTAGGAGTTTGAATCCT--AAAATTA
1 TATCCTATTTTTAGGAGTTTGAATCCTAGAAAATTA
51102 TATCCTATTTTTAGGAGTTTGAATCCTAG
1 TATCCTATTTTTAGGAGTTTGAATCCTAG
51131 TAGGACGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
34 33 0.56
37 26 0.44
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (36 bp):
TATCCTATTTTTAGGAGTTTGAATCCTAGAAAATTA
Found at i:51898 original size:106 final size:108
Alignment explanation
Indices: 51597--52220 Score: 580
Period size: 109 Copynumber: 5.9 Consensus size: 108
51587 GTTCCGAGTC
* * ** * **
51597 CAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAA-CCAGGAAATTGTTGGTTGACAGTCA
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTGTTGACAACCA
* * * *
51660 GCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-
64 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * *
51703 TAATATCCTTCG-CTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-CTTGTTGACAATCAG
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAG
51761 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * *
51803 CAATATCCTTCG-CTGTGAAGTTGAAATTGGCTATGAAATTTAAAAAATGTTTGTTGACAACCAG
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAG
* *
51867 CTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCA
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * ** * *
51912 CGATATCCTCCGTCGTGGAGTTGAAA-TCGCGGATGAAACTGA-AAAGTTGTTCGTTGACAACCA
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGC-TCTGAAATTGAGAAA-TTGTTTGTTGACAACCA
* * * *
51975 GCCGTCCCTTCATTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCA
64 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * * * *
52021 CGATATCCTCCGTCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCGTTGACAACCAGC
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGC
* *
52086 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGGGTAGCA
66 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * * * *
52130 CGATATCCTCCGTCGTGGAGTTAAAATCGGTTCCGAAATTGGGAAATTG-TTGTTGGCAACCAGC
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGC
52194 CGTCCCTTCGTTGTGAAGTTGAACTTG
66 CGTCCCTTCGTTGTGAAGTTGAACTTG
52221 ACTCTAGCTA
Statistics
Matches: 452, Mismatches: 52, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
100 82 0.18
101 3 0.01
102 5 0.01
104 3 0.01
105 3 0.01
106 83 0.18
108 47 0.10
109 222 0.49
110 4 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (108 bp):
CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGC
CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
Found at i:52102 original size:218 final size:209
Alignment explanation
Indices: 51591--52220 Score: 659
Period size: 218 Copynumber: 3.0 Consensus size: 209
51581 AATATTGTTC
** *
51591 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCAGGAAATTGTTGGTTGACA
1 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAATTAGGAAATTGTTCGTTGACA
** * * * * *
51656 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-CTA--ATATCCTTCG-CT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-ACGATATCCTCCGTC-
* ** * *
51717 GTGAAGTTGAAATTGAC-TCTG-AATGAAA-TCTTGTTGACAATCAGCCGTCCCTTCGTTGTGAA
129 GTGGAGTTGAAA-TG-CGGATGAAATGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAA
51779 GTTGAACTTGTGTTGTCT
192 GTTGAACTTGTGTTGTCT
* * * * * * *
51797 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTTA-AAAAATGTTTGTTGAC
1 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAA-TTAGGAAATTGTTCGTTGAC
* *
51861 AACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCGTC
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACGATATCCTCCGTC
*
51926 GTGGAGTTGAAATCGCGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCATTGT
129 GTGGAGTTGAAAT-GCGGATGAAA-TG-AAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGT
* *
51991 GAAGTTGGACTTGTGTTTTCT
189 GAAGTTGAACTTGTGTTGTCT
* * * * * *
52012 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCGTT
1 CGAGT--C-CAATATCCTCCGCT-GTGAAGTTGAAATTGGTTCTGGAATTAGGAAATTGTTCGTT
* *
52076 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGGGTAGCACGATATCCTCC
62 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACGATATCCTCC
* * *
52141 GTCGTGGAGTTAAAAT-CGGTTCCGAAATTGGGAAATTGTTGTTGGCAACCAGCCGTCCCTTCGT
126 GTCGTGGAGTTGAAATGCGGAT--GAAA-T--GAAATTGTTGTTGACAACCAGCCGTCCCTTCGT
52205 TGTGAAGTTGAACTTG
186 TGTGAAGTTGAACTTG
52221 ACTCTAGCTA
Statistics
Matches: 351, Mismatches: 50, Indels: 35
0.81 0.11 0.08
Matches are distributed among these distances:
206 92 0.26
207 2 0.01
208 3 0.01
209 23 0.07
210 3 0.01
211 2 0.01
212 3 0.01
214 3 0.01
215 48 0.14
216 4 0.01
217 41 0.12
218 123 0.35
219 3 0.01
220 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (209 bp):
CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAATTAGGAAATTGTTCGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATATCCTCCGTCGT
GGAGTTGAAATGCGGATGAAATGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
AACTTGTGTTGTCT
Found at i:52652 original size:37 final size:36
Alignment explanation
Indices: 52609--52680 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
52599 TAAGAAAAAC
52609 TGTCTCA-AGAGAGATAAAACTTAGTTCCAAAAGAAAT
1 TGTCTCACAGAGAGATAAAA-TTAGTTCC-AAAGAAAT
* * *
52646 TGTCTCACGGGGAGATGAAATTAGTTCCAAAGAAA
1 TGTCTCACAGAGAGATAAAATTAGTTCCAAAGAAA
52681 ACATATTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 7 0.23
37 15 0.48
38 9 0.29
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTCTCACAGAGAGATAAAATTAGTTCCAAAGAAAT
Found at i:52866 original size:67 final size:67
Alignment explanation
Indices: 52786--52944 Score: 232
Period size: 67 Copynumber: 2.4 Consensus size: 67
52776 GAAACGAAAT
* *
52786 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
52849 AAAA
64 AAAA
* *
52853 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
52918 AA
66 AA
**
52920 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
52945 GAGAGACGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 78 0.94
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:52943 original size:36 final size:36
Alignment explanation
Indices: 52819--53295 Score: 264
Period size: 36 Copynumber: 13.9 Consensus size: 36
52809 AAAGATTTTG
* * *
52819 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** **
52855 TGTTTCGAGGGAAACAATCTCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
52885 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
52922 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
52958 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
52986 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAA-TT
*
53024 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
53060 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
53088 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
53126 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
53162 CATTTCAA-GGAAAATGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
53190 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
53228 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
53264 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
53296 TGGTGAGCAC
Statistics
Matches: 324, Mismatches: 74, Indels: 86
0.67 0.15 0.18
Matches are distributed among these distances:
28 8 0.02
29 31 0.10
30 18 0.06
31 19 0.06
32 4 0.01
33 4 0.01
34 4 0.01
35 15 0.05
36 122 0.38
37 90 0.28
38 9 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:53038 original size:37 final size:37
Alignment explanation
Indices: 52987--53295 Score: 232
Period size: 37 Copynumber: 8.9 Consensus size: 37
52977 TCAATGTTTA
*
52987 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
53024 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
53060 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
53088 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
53126 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
53162 CATTTCAA-GGAAAATGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
53190 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
53228 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
53264 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
53296 TGGTGAGCAC
Statistics
Matches: 208, Mismatches: 38, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 20 0.10
30 12 0.06
32 1 0.00
33 1 0.00
34 1 0.00
35 11 0.05
36 59 0.28
37 86 0.41
38 11 0.05
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:53059 original size:102 final size:102
Alignment explanation
Indices: 52886--53277 Score: 669
Period size: 102 Copynumber: 3.9 Consensus size: 102
52876 AAAGGTTTTG
* *
52886 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
52950 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
52987 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
53052 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
53089 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
53154 ACAAAACTCATTTCAAGGAAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
53191 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* **
53256 ACAAAGTTTGTTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
53278 CTGTCTCAAG
Statistics
Matches: 275, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
101 33 0.12
102 242 0.88
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:54833 original size:7 final size:7
Alignment explanation
Indices: 54812--54890 Score: 63
Period size: 7 Copynumber: 10.7 Consensus size: 7
54802 TTCTTTTTGA
*
54812 TTCTTAT
1 TTCTTTT
54819 TT-TTTT
1 TTCTTTT
54825 TTCTTTT
1 TTCTTTT
54832 TTCCTTTT
1 TT-CTTTT
54840 GTTCGTGTTT
1 -TTC-T-TTT
*
54850 CTCTTTT
1 TTCTTTT
54857 TTCTTTGT
1 TTCTTT-T
54865 TT-TTTT
1 TTCTTTT
*
54871 TGCTTCTT
1 TTCTT-TT
54879 TTCTTTT
1 TTCTTTT
54886 TTCTT
1 TTCTT
54891 CTTGATTGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
6 7 0.12
7 28 0.47
8 16 0.27
9 5 0.08
10 3 0.05
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.77
Consensus pattern (7 bp):
TTCTTTT
Found at i:54872 original size:32 final size:31
Alignment explanation
Indices: 54821--54893 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
54811 ATTCTTATTT
54821 TTTTTTCTTTTTTCCTTTTG-TTCGTGTTTCTC
1 TTTTTTCTTTTTTCCTTTTGCTTC-T-TTTCTC
* *
54853 TTTTTTCTTTGTTT-TTTTTGCTTCTTTTCTT
1 TTTTTTCTTT-TTTCCTTTTGCTTCTTTTCTC
54884 TTTTCTTCTT
1 TTTT-TTCTT
54894 GATTGGATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 9 0.25
32 21 0.58
33 6 0.17
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (31 bp):
TTTTTTCTTTTTTCCTTTTGCTTCTTTTCTC
Found at i:54877 original size:17 final size:15
Alignment explanation
Indices: 54801--54893 Score: 66
Period size: 15 Copynumber: 6.1 Consensus size: 15
54791 TTTGTTCCTC
**
54801 TTTCTTTTTGATTCT
1 TTTCTTTTTTCTTCT
*
54816 TATTTTTTTTTCTT-T
1 T-TTCTTTTTTCTTCT
* *
54831 TTTCCTTTTGTTCGTGT
1 TTT-CTTTT-TTCTTCT
54848 TTCTCTTTTTTCTT-T
1 TT-TCTTTTTTCTTCT
*
54863 GTTT-TTTTTGCTTCT
1 -TTTCTTTTTTCTTCT
54878 TTTCTTTTTTCTTCT
1 TTTCTTTTTTCTTCT
54893 T
1 T
54894 GATTGGATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.21
15 21 0.34
16 19 0.31
17 8 0.13
18 1 0.02
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:56006 original size:15 final size:15
Alignment explanation
Indices: 55986--56023 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
55976 AATGTAGATG
55986 AAAATGCAAAAGGCA
1 AAAATGCAAAAGGCA
*
56001 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
56016 AGAATGCA
1 AAAATGCA
56024 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.18, T:0.11
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:58475 original size:15 final size:15
Alignment explanation
Indices: 58457--58486 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58447 AAAACCATGT
58457 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
58472 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
58487 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:58493 original size:15 final size:15
Alignment explanation
Indices: 58460--58494 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
58450 ACCATGTTAG
* *
58460 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
58475 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
58490 ATAAA
1 ATAAA
58495 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:58638 original size:18 final size:18
Alignment explanation
Indices: 58631--58687 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
58621 AACAAATAAA
58631 TAAAATAATAAAAAAAAG
1 TAAAATAATAAAAAAAAG
* *
58649 TAAAATATATATATATAAA-
1 TAAAATA-ATA-AAAAAAAG
58668 TAAAA-AAT-AAAAAAAG
1 TAAAATAATAAAAAAAAG
58684 TAAA
1 TAAA
58688 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.16
16 4 0.12
17 2 0.06
18 8 0.25
19 8 0.25
20 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
TAAAATAATAAAAAAAAG
Found at i:58676 original size:48 final size:49
Alignment explanation
Indices: 58572--58682 Score: 122
Period size: 50 Copynumber: 2.3 Consensus size: 49
58562 AATAGTAAGT
58572 AAAATAAATATAAAAATAAAGAAAAAGAAGAAAAAAAATATAGAAATAAA
1 AAAATAAATA-AAAAATAAAGAAAAAGAAGAAAAAAAATATAGAAATAAA
* * * *
58622 ACAAATAAATAAAATAATAAA-AAAAAGTAA-AATATATATATATAAAT-AA
1 A-AAATAAATAAAA-AATAAAGAAAAAG-AAGAAAAAAAATATAGAAATAAA
58671 AAAATAAA-AAAA
1 AAAATAAATAAAA
58683 GTAAATATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
47 4 0.07
48 7 0.13
49 3 0.06
50 23 0.43
51 17 0.31
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.18
Consensus pattern (49 bp):
AAAATAAATAAAAAATAAAGAAAAAGAAGAAAAAAAATATAGAAATAAA
Found at i:58682 original size:36 final size:37
Alignment explanation
Indices: 58626--58704 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
58616 AATAAAACAA
58626 ATAAATAAAATAATAAAAAAAAGTAAA-ATATATATAT
1 ATAAATAAAATAAT-AAAAAAAGTAAATATATATATAT
58663 ATAAATAAAA-AATAAAAAAAGTAAATATATATATAT
1 ATAAATAAAATAATAAAAAAAGTAAATATATATATAT
58699 ATAAAT
1 ATAAAT
58705 TAATAAAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 12 0.29
36 19 0.46
37 10 0.24
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (37 bp):
ATAAATAAAATAATAAAAAAAGTAAATATATATATAT
Found at i:58689 original size:78 final size:79
Alignment explanation
Indices: 58568--58761 Score: 184
Period size: 78 Copynumber: 2.5 Consensus size: 79
58558 ATAAAATAGT
*
58568 AAGTAAAATA-A-ATATAAAAATAAAGAAAAAGAAGAAAAAAAATATAGAAATAAAACAAATAAA
1 AAGTAAAATATATATATATAAATAAA-AAAAAGAA-AAAAAAAATATAGAAAT-AAACAAATAAA
58631 TAAAA-TAATAA-AAAA
63 TAAAACTAATAATAAAA
** * * * * *
58646 AAGTAAAATATATATATATAAATAAAAAATAA-AAAAAGTAAATATATATATATATAAATTAATA
1 AAGTAAAATATATATATATAAATAAAAAA-AAGAAAAAAAAAATATAGAAATAAACAAATAAATA
*
58710 AAACTGATAATAAAA
65 AAACTAATAATAAAA
* * * *
58725 AA-TAATATATTTATATATAATCTAAAAAAAATAAAAA
1 AAGTAAAATATATATATATAA-ATAAAAAAAAGAAAAA
58762 TATATACTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
77 13 0.13
78 46 0.47
79 24 0.25
80 14 0.14
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (79 bp):
AAGTAAAATATATATATATAAATAAAAAAAAGAAAAAAAAAATATAGAAATAAACAAATAAATAA
AACTAATAATAAAA
Found at i:58810 original size:22 final size:21
Alignment explanation
Indices: 58757--58816 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
58747 TAAAAAAAAT
58757 AAAAATATATAC-T-AAAGTAA
1 AAAAATAT-TACATAAAAGTAA
*
58777 AAAAGA-AATACATAAAATGTAA
1 AAAA-ATATTACATAAAA-GTAA
58799 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
58817 AAAAGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 5 0.16
22 14 0.44
23 4 0.12
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.22
Consensus pattern (21 bp):
AAAAATATTACATAAAAGTAA
Found at i:59162 original size:37 final size:36
Alignment explanation
Indices: 59119--59220 Score: 145
Period size: 34 Copynumber: 2.9 Consensus size: 36
59109 ATAGTATAAC
* *
59119 TCTATCCTAATTTTAGGAGTTTTAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
59156 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
59190 TCTATCCTATTTTTAGGAGTTCGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
59221 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 32 0.55
37 26 0.45
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:59620 original size:29 final size:30
Alignment explanation
Indices: 59580--59652 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
59570 CTTTTTCATT
59580 TAAGTACCTAAAGTAT-TGTTTGGTCAAAA
1 TAAGTACCTAAAGTATCTGTTTGGTCAAAA
* * *
59609 TAAGTACTTAAAATTATCTTTTTGGTCAAAA
1 TAAGTACCT-AAAGTATCTGTTTGGTCAAAA
*
59640 TAGGTACCTAAAG
1 TAAGTACCTAAAG
59653 CATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 8 0.22
30 9 0.25
31 19 0.53
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (30 bp):
TAAGTACCTAAAGTATCTGTTTGGTCAAAA
Found at i:59834 original size:29 final size:29
Alignment explanation
Indices: 59739--59837 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 29
59729 GAAAAAGCTT
* * * *
59739 AAATAGTTTAGGTACCTATTTTGAC-ATA
1 AAATACTTTAGATATCTATTTTGACAAAA
*
59767 AAATACTTTAGGTATCTATTTTGACTAAAA
1 AAATACTTTAGATATCTATTTTGAC-AAAA
* * * *
59797 AGATAACTTTATATATTTTTTTTGACAAAA
1 AAAT-ACTTTAGATATCTATTTTGACAAAA
59827 AAATACTTTAG
1 AAATACTTTAG
59838 GTACTTAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
28 23 0.40
29 6 0.10
30 12 0.21
31 17 0.29
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (29 bp):
AAATACTTTAGATATCTATTTTGACAAAA
Found at i:61135 original size:6 final size:6
Alignment explanation
Indices: 61124--61157 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
61114 TCGTCTCGTC
61124 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
61158 ACTTAGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.47, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:62004 original size:35 final size:37
Alignment explanation
Indices: 61933--62005 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
61923 GTTAGAAAAT
* *
61933 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
*
61970 ATTTATATATTTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
62005 A
1 A
62006 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:63430 original size:26 final size:26
Alignment explanation
Indices: 63396--63451 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
63386 TTATCATTCC
63396 TATA-TCTACTACCAAAGTTGAAGAT
1 TATAGTCTACTACCAAAGTTGAAGAT
63421 TATAGTCTACTACCAAAGTTGAAGAT
1 TATAGTCTACTACCAAAGTTGAAGAT
63447 TATAG
1 TATAG
63452 ACTAACAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (26 bp):
TATAGTCTACTACCAAAGTTGAAGAT
Found at i:63828 original size:19 final size:18
Alignment explanation
Indices: 63804--63840 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
63794 AAGACCATGT
*
63804 GCTTAATAATAATAATAAG
1 GCTTAAT-ATAAAAATAAG
63823 GCTTAATATAAAAATAAG
1 GCTTAATATAAAAATAAG
63841 TGCTCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (18 bp):
GCTTAATATAAAAATAAG
Found at i:64454 original size:28 final size:27
Alignment explanation
Indices: 64401--64454 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
64391 AGCTATTTTG
*
64401 GGTTTTTTTATAATTTAAGAAAAATTA
1 GGTTTTTTTATAATATAAGAAAAATTA
64428 GGTTTTTTTATAAATATAA-AAATAATT
1 GGTTTTTTTAT-AATATAAGAAA-AATT
64455 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (27 bp):
GGTTTTTTTATAATATAAGAAAAATTA
Found at i:79647 original size:2 final size:2
Alignment explanation
Indices: 79640--79695 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
79630 ATCATTAAAT
79640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
79681 TA TA TT TA TT TA TA T
1 TA TA TA TA TA TA TA T
79696 TCTATGTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:86431 original size:27 final size:27
Alignment explanation
Indices: 86364--86499 Score: 105
Period size: 27 Copynumber: 4.7 Consensus size: 27
86354 ATTTTATATT
*
86364 TCTTAACTTTAAAAATATTTTATT-TTA
1 TCTTAA-TTTAAATATATTTTATTCTTA
*
86391 T-TTCAACTTATTAAATATATTTTATTCATA
1 TCTT-AA--T-TTAAATATATTTTATTCTTA
* **
86421 TGTTAATTTAAATATATACTATTCTTA
1 TCTTAATTTAAATATATTTTATTCTTA
* *
86448 TTTTAATTTTAAATATAAATTTTATGCTTA
1 TCTTAA-TTTAAATAT--ATTTTATTCTTA
86478 TCTTAATTTAAAAATATATTTT
1 TCTTAATTT--AAATATATTTT
86500 GTTAGCTCCA
Statistics
Matches: 88, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
26 2 0.02
27 25 0.28
28 11 0.12
29 23 0.26
30 19 0.22
31 8 0.09
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (27 bp):
TCTTAATTTAAATATATTTTATTCTTA
Found at i:86449 original size:57 final size:55
Alignment explanation
Indices: 86364--86495 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 55
86354 ATTTTATATT
** *
86364 TCTTAACTTTAAAAATATTTTATTTTATTTCAACTTATTAAATAT-ATTTTATTCATA
1 TCTTAA-TTTAAAAATATACTATTTTATTTCAA-TT-TTAAATATAATTTTATGCATA
* * * *
86421 TGTTAATTTAAATATATACTATTCTTATTTTAATTTTAAATATAAATTTTATGCTTA
1 TCTTAATTTAAAAATATACTATT-TTATTTCAATTTTAAATAT-AATTTTATGCATA
86478 TCTTAATTTAAAAATATA
1 TCTTAATTTAAAAATATA
86496 TTTTGTTAGC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
55 8 0.13
56 16 0.25
57 39 0.62
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (55 bp):
TCTTAATTTAAAAATATACTATTTTATTTCAATTTTAAATATAATTTTATGCATA
Found at i:86718 original size:17 final size:19
Alignment explanation
Indices: 86696--86735 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
86686 AACTTTTAAG
86696 GACAATAT-ACCTTAC-AT
1 GACAATATAACCTTACAAT
*
86713 GACAATGTAACCTTACAAT
1 GACAATATAACCTTACAAT
86732 GACA
1 GACA
86736 CATAAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 7 0.35
19 6 0.30
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (19 bp):
GACAATATAACCTTACAAT
Found at i:87152 original size:21 final size:21
Alignment explanation
Indices: 87085--87181 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
87075 GATTGCAAGA
**
87085 AAGGGATCGATCCTTTAAG-G
1 AAGGGATCGATCCTTTTTGTG
* *
87105 AAAGGGATCGGT-CTTTTTCATCG
1 -AAGGGATCGATCCTTTTT-GT-G
87128 -AGGGATCGATCCTTTTTGTG
1 AAGGGATCGATCCTTTTTGTG
* * *
87148 AAGGGATCAATCCATTTTGTA
1 AAGGGATCGATCCTTTTTGTG
87169 AAGGGATCGATCC
1 AAGGGATCGATCC
87182 CAAACTCACT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
20 5 0.08
21 49 0.80
22 6 0.10
23 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTTGTG
Done.