Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold731
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: 52511
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7572 original size:3 final size:3
Alignment explanation
Indices: 7564--7590 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7554 TGTTTTGCTG
7564 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
7591 GAAAAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:8384 original size:15 final size:17
Alignment explanation
Indices: 8362--8399 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
8352 ATAATTAATT
*
8362 ATAATAAATA-TATAAA
1 ATAATAAAAATTATAAA
8378 A-AATAAAAATTATAAA
1 ATAATAAAAATTATAAA
8394 ATAATA
1 ATAATA
8400 TTTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAATAAAAATTATAAA
Found at i:8748 original size:16 final size:16
Alignment explanation
Indices: 8729--8770 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
8719 ATTTTATGAA
8729 TAAAAAAATTTATTAT
1 TAAAAAAATTTATTAT
* *
8745 TAAAAAAAATTATTTT
1 TAAAAAAATTTATTAT
8761 TAAAATAAAT
1 TAAAA-AAAT
8771 CAATTCGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAAAATTTATTAT
Found at i:9417 original size:35 final size:35
Alignment explanation
Indices: 9352--9466 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
9342 TTATTTTCCT
*
9352 AATTTCTTTATTTA-TTTTTTTATTGTATTCACTC
1 AATTTTTTTATTTATTTTTTTTATTGTATTCACTC
*
9386 AATTTTTTTATTTATTTTTTTTATTGAATTCACTC
1 AATTTTTTTATTTATTTTTTTTATTGTATTCACTC
*
9421 AATTTTTTTATTTATTGTTTGTTTATTGTATTTACTC
1 AATTTTTTTATTTATT-TTT-TTTATTGTATTCACTC
9458 AATTTTTTT
1 AATTTTTTT
9467 TATTACATGT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 13 0.18
35 35 0.47
36 3 0.04
37 23 0.31
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (35 bp):
AATTTTTTTATTTATTTTTTTTATTGTATTCACTC
Found at i:9855 original size:5 final size:6
Alignment explanation
Indices: 9838--9862 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9828 TTAAAATTAG
9838 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
9863 AGTTAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:14655 original size:146 final size:147
Alignment explanation
Indices: 14452--14718 Score: 383
Period size: 146 Copynumber: 1.8 Consensus size: 147
14442 TGGAAGGCGC
* * * * * *
14452 ACTAAATGGTTATTCTAAGACTTTGCAGAATAAAATTAGAATCGATTATTCTGAAAAAAAATCAT
1 ACTAAATAGTTATTCTAAGACTTAGCAAAACAAAATTAGAATCAATTATTCTAAAAAAAAATCAT
14517 TCAACGAATCAAACAATCATATCATTATAATACAACGATTCAAATCATAATGAAATAACTTTTAT
66 TCAACGAATCAAACAATCATATCATTATAATACAACGATTCAAATCATAATGAAATAACTTTTAT
14582 TTTTCAATGAAAAACAT
131 TTTTCAATGAAAAACAT
* * * * *
14599 ACTAAATAGTT-TTCTAAGACTTAGCAAAACAAGATTAGAATTAATTATTTTAAAAAATAATTAT
1 ACTAAATAGTTATTCTAAGACTTAGCAAAACAAAATTAGAATCAATTATTCTAAAAAAAAATCAT
* * * * *
14663 TTAACGAATCAAATAATCATATCATTATAATATAATGATTCAACTCATAATGAAAT
66 TCAACGAATCAAACAATCATATCATTATAATACAACGATTCAAATCATAATGAAAT
14719 TATTATAATG
Statistics
Matches: 104, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
146 94 0.90
147 10 0.10
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (147 bp):
ACTAAATAGTTATTCTAAGACTTAGCAAAACAAAATTAGAATCAATTATTCTAAAAAAAAATCAT
TCAACGAATCAAACAATCATATCATTATAATACAACGATTCAAATCATAATGAAATAACTTTTAT
TTTTCAATGAAAAACAT
Found at i:14758 original size:22 final size:19
Alignment explanation
Indices: 14713--14759 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
14703 CAACTCATAA
14713 TGAAATTATTATAATGAAC
1 TGAAATTATTATAATGAAC
*
14732 T-AAATATATTATAAATGCAAT
1 TGAAAT-TATTAT-AATG-AAC
14753 TGAAATT
1 TGAAATT
14760 TCTCTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 4 0.17
21 4 0.17
22 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (19 bp):
TGAAATTATTATAATGAAC
Found at i:19160 original size:14 final size:14
Alignment explanation
Indices: 19141--19170 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19131 GCTCATGAAT
19141 AATAACAAGAAAAC
1 AATAACAAGAAAAC
19155 AATAACAAGAAAAC
1 AATAACAAGAAAAC
19169 AA
1 AA
19171 ATCAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.13, G:0.07, T:0.07
Consensus pattern (14 bp):
AATAACAAGAAAAC
Found at i:19852 original size:2 final size:2
Alignment explanation
Indices: 19845--19877 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19835 CTTTTGGCAT
19845 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 T
19878 GCAATCTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21680 original size:16 final size:16
Alignment explanation
Indices: 21659--21720 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
21649 CCGAGTTTAA
21659 ATTATTTCAGATTCAG
1 ATTATTTCAGATTCAG
* *
21675 ATTATTTCAAGTTTAAG
1 ATTATTTC-AGATTCAG
* * *
21692 -TTATTTCGGTTTCGG
1 ATTATTTCAGATTCAG
*
21707 ATTATTTCAAATTC
1 ATTATTTCAGATTC
21721 GAGTCAATCA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 5 0.14
16 25 0.69
17 6 0.17
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.48
Consensus pattern (16 bp):
ATTATTTCAGATTCAG
Found at i:21688 original size:32 final size:32
Alignment explanation
Indices: 21652--21716 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
21642 AGTCATTCCG
21652 AGTTTAAATTATTTCAGATTCAGATTATTTCA
1 AGTTTAAATTATTTCAGATTCAGATTATTTCA
* * * *
21684 AGTTTAAGTTATTTCGGTTTCGGATTATTTCA
1 AGTTTAAATTATTTCAGATTCAGATTATTTCA
21716 A
1 A
21717 ATTCGAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (32 bp):
AGTTTAAATTATTTCAGATTCAGATTATTTCA
Found at i:26268 original size:52 final size:52
Alignment explanation
Indices: 26199--26318 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
26189 AAAATTTATT
*
26199 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
26251 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGTC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
26303 TGCATGTATCGATACA
1 TGCATGTATCGATACA
26319 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:26331 original size:52 final size:51
Alignment explanation
Indices: 26190--26338 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
26180 CGAAATATGA
* *
26190 AAATTTATTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
26242 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
26294 AAATTTGTCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGTCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
26339 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATTTGTCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:26345 original size:13 final size:13
Alignment explanation
Indices: 26327--26351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26317 CAAAGATCAG
26327 TGTATCGATACAA
1 TGTATCGATACAA
26340 TGTATCGATACA
1 TGTATCGATACA
26352 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:26433 original size:33 final size:33
Alignment explanation
Indices: 26391--26460 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
26381 GGCAGTAGCT
26391 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
26424 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
26457 TACA
1 TACA
26461 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:26434 original size:13 final size:13
Alignment explanation
Indices: 26416--26440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26406 CAAAAAAATA
26416 TGTATCGATACAT
1 TGTATCGATACAT
26429 TGTATCGATACA
1 TGTATCGATACA
26441 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:28016 original size:36 final size:36
Alignment explanation
Indices: 27973--28066 Score: 179
Period size: 36 Copynumber: 2.6 Consensus size: 36
27963 GAAGGTTGCA
*
27973 GAGCTGCTGCCGGTGTTCGTGGGTTGGAAGCTGATG
1 GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
28009 GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
1 GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
28045 GAGCTGCTGCCAGTGTTCGTGG
1 GAGCTGCTGCCAGTGTTCGTGG
28067 CTAGAAGTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.12, C:0.18, G:0.43, T:0.28
Consensus pattern (36 bp):
GAGCTGCTGCCAGTGTTCGTGGGTTGGAAGCTGATG
Found at i:28281 original size:20 final size:19
Alignment explanation
Indices: 28244--28282 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28234 GAGCAGACGC
*
28244 TGGAAGCTGCTGCTATGGA
1 TGGAAGCTGCTGCAATGGA
*
28263 TGGAAGGCTGCTGGAATGGA
1 TGGAA-GCTGCTGCAATGGA
28283 AGTTGGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (19 bp):
TGGAAGCTGCTGCAATGGA
Found at i:28639 original size:5 final size:5
Alignment explanation
Indices: 28626--28696 Score: 88
Period size: 5 Copynumber: 14.2 Consensus size: 5
28616 GCATGAAAGC
* * * * *
28626 AATGT AATGA AATGC AATGC AATGA AATGA AATGA AATGC AATGC AATGA
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA
*
28676 AATGC AATGA AATGA AATGA A
1 AATGA AATGA AATGA AATGA A
28697 GTGCAATGCA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 59 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (5 bp):
AATGA
Found at i:28644 original size:15 final size:15
Alignment explanation
Indices: 28618--28714 Score: 106
Period size: 15 Copynumber: 6.5 Consensus size: 15
28608 CATTTCATGC
*
28618 ATGAAA-GCAATGTA
1 ATGAAATGCAATGAA
*
28632 ATGAAATGCAATGCA
1 ATGAAATGCAATGAA
*
28647 ATGAAATGAAATGAA
1 ATGAAATGCAATGAA
*
28662 ATGCAATGCAATGAA
1 ATGAAATGCAATGAA
* *
28677 ATGCAATGAAATGAA
1 ATGAAATGCAATGAA
* *
28692 ATGAAGTGCAATGCA
1 ATGAAATGCAATGAA
*
28707 ATAAAATG
1 ATGAAATG
28715 TTTTTGAAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
14 6 0.09
15 64 0.91
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (15 bp):
ATGAAATGCAATGAA
Found at i:28649 original size:20 final size:20
Alignment explanation
Indices: 28624--28714 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
28614 ATGCATGAAA
*
28624 GCAATGTAATGAAATGCAAT
1 GCAATGAAATGAAATGCAAT
*
28644 GCAATGAAATGAAATGAAAT
1 GCAATGAAATGAAATGCAAT
*
28664 GCAATGCAATGAAATGCAAT
1 GCAATGAAATGAAATGCAAT
* *
28684 GAAATGAAATGAAGTGCAAT
1 GCAATGAAATGAAATGCAAT
*
28704 GCAATAAAATG
1 GCAATGAAATG
28715 TTTTTGAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (20 bp):
GCAATGAAATGAAATGCAAT
Found at i:28706 original size:5 final size:5
Alignment explanation
Indices: 28624--28708 Score: 82
Period size: 5 Copynumber: 17.0 Consensus size: 5
28614 ATGCATGAAA
* * * * *
28624 GCAAT GTAAT GAAAT GCAAT GCAAT GAAAT GAAAT GAAAT GCAAT GCAAT
1 GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT
* * *
28674 GAAAT GCAAT GAAAT GAAAT G-AAGT GCAAT GCAAT
1 GCAAT GCAAT GCAAT GCAAT GCAA-T GCAAT GCAAT
28709 AAAATGTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
4 2 0.03
5 66 0.94
6 2 0.03
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.21
Consensus pattern (5 bp):
GCAAT
Found at i:28714 original size:10 final size:10
Alignment explanation
Indices: 28626--28704 Score: 95
Period size: 10 Copynumber: 7.9 Consensus size: 10
28616 GCATGAAAGC
*
28626 AATGTAATGA
1 AATGCAATGA
*
28636 AATGCAATGC
1 AATGCAATGA
*
28646 AATGAAATGA
1 AATGCAATGA
* *
28656 AATGAAATGC
1 AATGCAATGA
28666 AATGCAATGA
1 AATGCAATGA
28676 AATGCAATGA
1 AATGCAATGA
*
28686 AATGAAATGA
1 AATGCAATGA
*
28696 AGTGCAATG
1 AATGCAATG
28705 CAATAAAATG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 59 1.00
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.22
Consensus pattern (10 bp):
AATGCAATGA
Found at i:28774 original size:43 final size:43
Alignment explanation
Indices: 28726--28863 Score: 214
Period size: 43 Copynumber: 3.3 Consensus size: 43
28716 TTTTGAAATG
*
28726 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAG
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
*
28769 TATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
*
28812 CATGAAATG-AAA--ATGCATGCA--ATATGTTACGTGAAAAA
1 CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
28850 CATGAAATGAAAAT
1 CATGAAATGAAAAT
28864 GCATGCAATG
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
38 25 0.28
39 3 0.03
40 9 0.10
42 3 0.03
43 49 0.55
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (43 bp):
CATGAAATGAAAATTATGCATGCATGAAATGTTACGTGAAAAA
Found at i:28839 original size:38 final size:38
Alignment explanation
Indices: 28788--28872 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
28778 AAAATTATGC
28788 ATGCATG-AA-ATGTTACGTGAAAAACATGAAATGAAA
1 ATGCATGCAATATGTTACGTGAAAAACATGAAATGAAA
28824 ATGCATGCAATATGTTACGTGAAAAACATGAAATGAAA
1 ATGCATGCAATATGTTACGTGAAAAACATGAAATGAAA
28862 ATGCATGCAAT
1 ATGCATGCAAT
28873 GAAAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 7 0.15
37 2 0.04
38 38 0.81
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.24
Consensus pattern (38 bp):
ATGCATGCAATATGTTACGTGAAAAACATGAAATGAAA
Found at i:29395 original size:42 final size:42
Alignment explanation
Indices: 29299--30022 Score: 785
Period size: 42 Copynumber: 16.9 Consensus size: 42
29289 AAGAAAATAC
* * * *
29299 TCTCCCGGGTCAAAGCCAACGGGCAGACTTAGGGAAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAAAG
* * * *
29342 TCTTCAAGGTCAAAACCGACAGGCAGACTAAGGGATGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
*
29384 TCTCCAGGGTCAAGGCCGACAGGCAGACTAAGGGAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
* ** **
29426 TCTCCAGGGTCAAAGCCGACAGACAGACTTTAAATG-AG-GCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGAC--TAAGGGAAGAAAAG
** * *
29468 TCTCCAGAATCAAAGCTGACAGGCAGACTGAAGGGAAGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAAGAAAAG
29511 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
* *
29553 TCTCCAGGGCCAAAGCCGACAGGCAGACTTAGGGAAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAAAG
* *
29596 TCTCCAGGGTCAAAGCCGACAGGTAGACTGAGGGAA-AGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGA-AAAG
* * * * *
29638 TCTCTAGGGACGAAGCCGATAGGCAGACTTAGGGAAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-AAGAAAAG
* * * **
29681 TCTCCAGGGTCAAAGCCGACAGGTAGATTGAGGGTTGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
* * * *
29723 TCTTCAGGGACAAAGCCGACAAGCAGACTAAGGGAAGGAAAAA
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAA-GAAAAG
*
29766 TCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
** **
29808 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAAATG-AG-GCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGAC--TAAGGGAAGAAAAG
* *
29850 TCTCCAGAGTCAAAGCTGACAGGCAGACTGAAGGGATAGGAAAGTCTCCAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGA-A-G--A------AAAG
* *
29903 TCTCCAGGGTCAAAGCCAACAGGTAGACTAAGGGAAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
* *
29945 TCTCCAGGGTCAAAGCCGACAGGCAGATTGAA-GGAAGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAAGAAAAG
29987 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
30023 AACAAAAAAG
Statistics
Matches: 569, Mismatches: 85, Indels: 55
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.00
41 9 0.02
42 341 0.60
43 171 0.30
44 10 0.02
48 1 0.00
50 1 0.00
51 1 0.00
52 6 0.01
53 27 0.05
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (42 bp):
TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAG
Found at i:29395 original size:85 final size:85
Alignment explanation
Indices: 29299--30023 Score: 770
Period size: 85 Copynumber: 8.4 Consensus size: 85
29289 AAGAAAATAC
* * * * * * *
29299 TCTCCCGGGTCAAAGCCAACGGGCAGACTTAGGGAAAGAAAAGTCTTCAAGGTCAAAACCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
29364 GCAGACTAAGGGATGAAAAG
66 GCAGACTAAGGGATGAAAAG
*
29384 TCTCCAGGGTCAAGGCCGACAGGCAGACTAAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
* **
29448 ACAGACTTTAA---ATGAGGCAG
66 GCAGAC--TAAGGGATGA-AAAG
** * *
29468 TCTCCAGAATCAAAGCTGACAGGCAGACTGAAGGG-AAGGAAAGTCTCCAGGGTCAAAGCCGACA
1 TCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACA
*
29532 GGCAGACTAAGGGAAGAAAAG
65 GGCAGACTAAGGGATGAAAAG
* *
29553 TCTCCAGGGCCAAAGCCGACAGGCAGACTTAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
* * *
29618 GTAGACTGAGGGA-AAGAAAG
66 GCAGACTAAGGGATGA-AAAG
* * * * *
29638 TCTCTAGGGACGAAGCCGATAGGCAGACTTAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
* * * *
29703 GTAGATTGAGGGTTGAAAAG
66 GCAGACTAAGGGATGAAAAG
* * * * * *
29723 TCTTCAGGGACAAAGCCGACAAGCAGACTAAGGGAAGGAAAAATCTCTAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
*
29788 GCAGACTAAGGGAAGAAAAG
66 GCAGACTAAGGGATGAAAAG
* * ** * *
29808 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA---AATGAGGCAGTCTCCAGAGTCAAAGCTGAC
1 TCTCCAGGGTCAAAGCCGACAGGCAGAC-TAAGGGAAAGA-AAAGTCTCCAGGGTCAAAGCCGAC
29870 AGGCAGACTGAAGGGATAGGAAAGTCTCCAAAG
64 AGGCAGACT-AAGGGAT--G--A------AAAG
* *
29903 TCTCCAGGGTCAAAGCCAACAGGTAGACTAAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
* * *
29967 GCAGATTGAA-GGAAGGAAAG
66 GCAGACT-AAGGGATGAAAAG
29987 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAA
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAA
30024 ACAAAAAAGA
Statistics
Matches: 538, Mismatches: 75, Indels: 54
0.81 0.11 0.08
Matches are distributed among these distances:
83 11 0.02
84 127 0.24
85 319 0.59
86 9 0.02
87 1 0.00
89 1 0.00
92 1 0.00
94 5 0.01
95 61 0.11
96 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (85 bp):
TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAG
GCAGACTAAGGGATGAAAAG
Found at i:29502 original size:127 final size:126
Alignment explanation
Indices: 29339--30021 Score: 759
Period size: 127 Copynumber: 5.3 Consensus size: 126
29329 AGGGAAAGAA
* * * *
29339 AAGTCTTCAAGGTCAAAACCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGTCAAGGCCGAC
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGTCAAAGCCGAC
*
29404 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGACAGACTTTAAATGAGG
66 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAAATGAGG
* ** * * *
29465 CAGTCTCCAGAATCAAAGCTGACAGGCAGACTGAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGA
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGATGAAAAGTCTCCAGGGTCAAAGCCGA
* * *
29530 CAGGCAGACTAAGGGAAGAAAAGTCTCCAGGGCCAAAGCCGACAGGCAGAC-TTAGGGAAAGA-A
65 CAGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTA---AATGAGG
* * * * * *
29593 AAGTCTCCAGGGTCAAAGCCGACAGGTAGACTGAGGGA-AAGAAAGTCTCTAGGGACGAAGCCGA
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGATGA-AAAGTCTCCAGGGTCAAAGCCGA
* * * * ** *
29657 TAGGCAGACTTAGGGAAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGTAGA-TTGAGGGTTGA-A
65 CAGGCAGACTAAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--AATGAGG
* * * * * *
29720 AAGTCTTCAGGGACAAAGCCGACAAGCAGACTAAGGGAAGGAAAAATCTCTAGGGTCAAAGCCGA
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG-ATGAAAAGTCTCCAGGGTCAAAGCCGA
29785 CAGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAAATGAGG
65 CAGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAAATGAGG
* * *
29847 CAGTCTCCAGAGTCAAAGCTGACAGGCAGACTGAAGGGATAGGAAAGTCTCCAAAGTCTCCAGGG
1 AAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAT--G--A------AAAGTCTCCAGGG
* * *
29912 TCAAAGCCAACAGGTAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA--TTG
55 TCAAAGCCGACAGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTA
*
29975 AAGGAAGG
120 AATG-AGG
29983 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGA
1 -AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGA
30022 AAACAAAAAA
Statistics
Matches: 468, Mismatches: 65, Indels: 38
0.82 0.11 0.07
Matches are distributed among these distances:
126 31 0.07
127 214 0.46
128 104 0.22
129 6 0.01
131 1 0.00
135 5 0.01
136 9 0.02
137 98 0.21
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (126 bp):
AAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGATGAAAAGTCTCCAGGGTCAAAGCCGAC
AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAAATGAGG
Found at i:29931 original size:53 final size:51
Alignment explanation
Indices: 29848--29950 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 51
29838 TAAATGAGGC
** *
29848 AGTCTCCAGAGTCAAAGCTGACAGGCAGACTGAAGGGATAGGAAAGTCTCCAA
1 AGTCTCCAGAGTCAAAGCCAACAGGCAGACT-AAGGGA-AGAAAAGTCTCCAA
* *
29901 AGTCTCCAGGGTCAAAGCCAACAGGTAGACTAAGGGAAGAAAAGTCTCCA
1 AGTCTCCAGAGTCAAAGCCAACAGGCAGACTAAGGGAAGAAAAGTCTCCA
29951 GGGTCAAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 12 0.27
52 6 0.13
53 27 0.60
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (51 bp):
AGTCTCCAGAGTCAAAGCCAACAGGCAGACTAAGGGAAGAAAAGTCTCCAA
Found at i:29967 original size:95 final size:92
Alignment explanation
Indices: 29804--29992 Score: 245
Period size: 95 Copynumber: 2.0 Consensus size: 92
29794 TAAGGGAAGA
* * ** *
29804 AAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAAATGAGGCAGTCTCCAGAGTCAAAGCTGA
1 AAAGTCTCCAGGGTCAAAGCCAACAGGCAGAC-TTAAAGGAGAAAGTCTCCAGAGTCAAAGCCGA
29869 CAGGCAGACTGAAGGGATAGGAAAGTCTCC
65 CAGGCAGACTGAA-GGA-AGGAAAGTCTCC
* * *
29899 AAAGTCTCCAGGGTCAAAGCCAACAGGTAGAC-TAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCG
1 AAAGTCTCCAGGGTCAAAGCCAACAGGCAGACTTAAAGG-AG-AAAGTCTCCAGAGTCAAAGCCG
*
29963 ACAGGCAGATTGAAGGAAGGAAAGTCTCC
64 ACAGGCAGACTGAAGGAAGGAAAGTCTCC
29992 A
1 A
29993 GGGTCAAAGC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
93 17 0.20
94 5 0.06
95 61 0.73
ACGTcount: A:0.36, C:0.21, G:0.29, T:0.14
Consensus pattern (92 bp):
AAAGTCTCCAGGGTCAAAGCCAACAGGCAGACTTAAAGGAGAAAGTCTCCAGAGTCAAAGCCGAC
AGGCAGACTGAAGGAAGGAAAGTCTCC
Found at i:43268 original size:5 final size:5
Alignment explanation
Indices: 43255--43348 Score: 107
Period size: 5 Copynumber: 18.8 Consensus size: 5
43245 GCATGAAATC
* * * * *
43255 AATGT AATGA AATGC AATGC AATGA AATGA AATGA AATGA AATGC AATGC
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA
* * * *
43305 AATGA AATGC AATGA AATGA AATGA AGTGC AATGC AATGA AATG
1 AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATGA AATG
43349 TTTTTGAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 78 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (5 bp):
AATGA
Found at i:43278 original size:15 final size:15
Alignment explanation
Indices: 43243--43348 Score: 128
Period size: 15 Copynumber: 7.2 Consensus size: 15
43233 CGGCCATTTC
43243 ATGC-ATGAAAT-CA
1 ATGCAATGAAATGCA
*
43256 ATGTAATGAAATGCA
1 ATGCAATGAAATGCA
*
43271 ATGCAATGAAATGAA
1 ATGCAATGAAATGCA
*
43286 ATGAAATGAAATGCA
1 ATGCAATGAAATGCA
43301 ATGCAATGAAATGCA
1 ATGCAATGAAATGCA
*
43316 ATGAAATGAAATG-A
1 ATGCAATGAAATGCA
* *
43330 AGTGCAATGCAATGAA
1 A-TGCAATGAAATGCA
43346 ATG
1 ATG
43349 TTTTTGAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
13 3 0.04
14 9 0.11
15 66 0.82
16 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.22
Consensus pattern (15 bp):
ATGCAATGAAATGCA
Found at i:43385 original size:22 final size:22
Alignment explanation
Indices: 43357--43433 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
43347 TGTTTTTGAA
43357 ATGCATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
*
43379 ATGCATGAAATG----TTACGTGAA
1 ATGCATGAAATGAAAATTA--TG-C
*
43400 AAGCATGAAATGAAAATTATGC
1 ATGCATGAAATGAAAATTATGC
43422 ATGCATGAAATG
1 ATGCATGAAATG
43434 TTACATGTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 2 0.05
21 11 0.25
22 23 0.52
23 2 0.05
25 3 0.07
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (22 bp):
ATGCATGAAATGAAAATTATGC
Found at i:43406 original size:43 final size:43
Alignment explanation
Indices: 43336--43437 Score: 161
Period size: 43 Copynumber: 2.4 Consensus size: 43
43326 ATGAAGTGCA
** *
43336 ATGCAATGAAATGTT-TTTGAAATGCATGAAATGAAAATTATGC
1 ATGC-ATGAAATGTTACGTGAAAAGCATGAAATGAAAATTATGC
43379 ATGCATGAAATGTTACGTGAAAAGCATGAAATGAAAATTATGC
1 ATGCATGAAATGTTACGTGAAAAGCATGAAATGAAAATTATGC
43422 ATGCATGAAATGTTAC
1 ATGCATGAAATGTTAC
43438 ATGTGCATGA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 10 0.18
43 45 0.82
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (43 bp):
ATGCATGAAATGTTACGTGAAAAGCATGAAATGAAAATTATGC
Found at i:43444 original size:22 final size:22
Alignment explanation
Indices: 43376--43446 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
43366 ATGAAAATTA
43376 TGCATGCATGAAATGTTAC--G
1 TGCATGCATGAAATGTTACATG
* * * * *
43396 TGAAAAGCATGAAATG-AAAATTA
1 TG-CATGCATGAAATGTTACA-TG
43419 TGCATGCATGAAATGTTACATG
1 TGCATGCATGAAATGTTACATG
43441 TGCATG
1 TGCATG
43447 AAATGTTACG
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 3 0.08
21 11 0.31
22 18 0.50
23 4 0.11
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATGCATGAAATGTTACATG
Found at i:43445 original size:61 final size:61
Alignment explanation
Indices: 43380--43498 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
43370 AAATTATGCA
*
43380 TGCATGAAATGTTACGTGAAAAGCATGAAATGAAAATTATGCATGCATGAAATGTTACATG
1 TGCATGAAATGTTACGTGAAAAACATGAAATGAAAATTATGCATGCATGAAATGTTACATG
43441 TGCATGAAATGTTACGTGAAAAACATGAAATGAAAATTATGCATGCATGAAATGTTAC
1 TGCATGAAATGTTACGTGAAAAACATGAAATGAAAATTATGCATGCATGAAATGTTAC
43499 GTGAAAAACA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (61 bp):
TGCATGAAATGTTACGTGAAAAACATGAAATGAAAATTATGCATGCATGAAATGTTACATG
Found at i:43662 original size:17 final size:17
Alignment explanation
Indices: 43620--43679 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
43610 TTTTATTTCA
*
43620 TTATTTTTTT-ATAAAAT
1 TTATTTTTTTGAT-TAAT
*
43637 TT-TTATTTTGATTAAT
1 TTATTTTTTTGATTAAT
*
43653 TTATTTTTTTGTTTAA-
1 TTATTTTTTTGATTAAT
43669 -TATTTTTTTGA
1 TTATTTTTTTGA
43680 AATCTCGGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 10 0.28
16 11 0.31
17 15 0.42
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TTATTTTTTTGATTAAT
Found at i:44318 original size:19 final size:19
Alignment explanation
Indices: 44274--44329 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
44264 CTACCAATTT
**
44274 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
44294 CATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
44313 CATGTATCGATACAATG
1 CATGTATCGATACAATG
44330 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:44332 original size:13 final size:13
Alignment explanation
Indices: 44314--44339 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44304 TATAATGAAC
44314 ATGTATCGATACA
1 ATGTATCGATACA
44327 ATGTATCGATACA
1 ATGTATCGATACA
44340 TCTGGGTGAG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:45257 original size:13 final size:13
Alignment explanation
Indices: 45239--45268 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45229 ATAAACCCAG
*
45239 AATGTATCGATAC
1 AATGTATCAATAC
45252 AATGTATCAATAC
1 AATGTATCAATAC
45265 AATG
1 AATG
45269 AATAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:49551 original size:20 final size:20
Alignment explanation
Indices: 49522--49559 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49512 GTAAAAAGAT
*
49522 AGAATGTATCGATACATTGA
1 AGAATCTATCGATACATTGA
49542 AGAATCTATCGATACATT
1 AGAATCTATCGATACATT
49560 CATACATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATCTATCGATACATTGA
Found at i:49571 original size:20 final size:20
Alignment explanation
Indices: 49522--49574 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
49512 GTAAAAAGAT
*
49522 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTCA
*
49542 AGAATCTATCGATACATTCA
1 AGAATGTATCGATACATTCA
*
49562 TA-CATGTATCGAT
1 -AGAATGTATCGAT
49575 GTATCGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTCA
Done.