Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002116.1 Hibiscus syriacus cultivar Beakdansim tig00004339_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: 161355
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:295 original size:54 final size:54
Alignment explanation
Indices: 232--473 Score: 271
Period size: 54 Copynumber: 4.5 Consensus size: 54
222 TAGAATTAAC
*
232 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAGT
* ** *
286 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG---CCAAAGT
* ** * *
343 GACTGAGCACCTCTGTGCTTCAGCCG-GAGCTGACACCTCTGTGTAG-CTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAG-T
*
396 GATTGAGCACCTCTGTCCTTCAATCGAG-GACTGACACCTCTGTGCAGCCAACTA-T
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAGCCAA--AGT
*
451 GACTGAGCA-C-CTGTGCTTCAATC
1 GATTGAGCACCTCTGTGCTTCAATC
474 TAAATTCTGG
Statistics
Matches: 158, Mismatches: 21, Indels: 19
0.80 0.11 0.10
Matches are distributed among these distances:
52 2 0.01
53 36 0.23
54 63 0.40
55 11 0.07
56 18 0.11
57 28 0.18
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAGT
Found at i:323 original size:27 final size:26
Alignment explanation
Indices: 239--440 Score: 110
Period size: 27 Copynumber: 7.4 Consensus size: 26
229 AACGATTGAG
239 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGA-CTGA
* * * *
266 CACCTCTGTG-TAGCCAA-AGTGATTGA
1 CACCTCTGTGCT--TCAATCGAGACTGA
292 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAG-ACTGA
* ***
320 CACCTCTGTGCAGTTAAAAAAATGACTGA
1 CACCTCTGTGC--TTCAATCGA-GACTGA
**
349 GCACCTCTGTGCTTCAGCCG-GAGCTGA
1 -CACCTCTGTGCTTCAATCGAGA-CTGA
* *
376 CACCTCTGTG-TAGCTAA--GATGATTGA
1 CACCTCTGTGCT-TC-AATCGA-GACTGA
*
402 GCACCTCTGTCCTTCAATCGAGGACTGA
1 -CACCTCTGTGCTTCAATCGA-GACTGA
430 CACCTCTGTGC
1 CACCTCTGTGC
441 AGCCAACTAT
Statistics
Matches: 131, Mismatches: 25, Indels: 38
0.68 0.13 0.20
Matches are distributed among these distances:
25 2 0.02
26 25 0.19
27 63 0.48
28 19 0.15
29 10 0.08
30 12 0.09
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (26 bp):
CACCTCTGTGCTTCAATCGAGACTGA
Found at i:387 original size:110 final size:111
Alignment explanation
Indices: 235--442 Score: 348
Period size: 110 Copynumber: 1.9 Consensus size: 111
225 AATTAACGAT
*
235 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAG-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAG-CAAAGATGATTGAGCACCTC
*
299 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAATGAC
65 TGTCCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAATGAC
* *
346 TGAGCACCTCTGTGCTTCAGCCG-GAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCAAAGATGATTGAGCACCTCT
*
410 GTCCTTCAATCGAGGACTGACACCTCTGTGCAG
66 GTCCTTCAATCGAGAACTGACACCTCTGTGCAG
443 CCAACTATGA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
109 4 0.04
110 66 0.73
111 21 0.23
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (111 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCAAAGATGATTGAGCACCTCT
GTCCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAATGAC
Found at i:1317 original size:82 final size:84
Alignment explanation
Indices: 1188--1352 Score: 264
Period size: 82 Copynumber: 2.0 Consensus size: 84
1178 TAAAACATTA
* *
1188 AATGCTTGAAAAGATGACAAGCTTATTCTAACCCTGCCACTAGCCCTATACAT-GGTTGGCCTTG
1 AATGCTTGAAAAGAGGACAAGCTTATTCTAACCCTACCACTAGCCCTATACATAGGTTGGCCTTG
*
1252 GTGTACCTACCC-GTTGTG
66 GCGTACCTACCCAGTTGTG
*
1270 AATGCTTGAAAAGAGGACAAGCTTATTCT-ACCCTACCACTAGACCCTATACATAGTTTGGCCTT
1 AATGCTTGAAAAGAGGACAAGCTTATTCTAACCCTACCACTAG-CCCTATACATAGGTTGGCCTT
1334 GGCGTACCTACCCAGTTGT
65 GGCGTACCTACCCAGTTGT
1353 TGCCCCATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
81 12 0.16
82 38 0.50
83 21 0.28
84 5 0.07
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (84 bp):
AATGCTTGAAAAGAGGACAAGCTTATTCTAACCCTACCACTAGCCCTATACATAGGTTGGCCTTG
GCGTACCTACCCAGTTGTG
Found at i:5652 original size:12 final size:12
Alignment explanation
Indices: 5626--5659 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5616 GAGTCGATTG
5626 AAGCTCGAGACTC
1 AAGCTCGA-ACTC
5639 AAGCTCGAACTC
1 AAGCTCGAACTC
*
5651 AAACTCGAA
1 AAGCTCGAA
5660 TTTGAACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (12 bp):
AAGCTCGAACTC
Found at i:10774 original size:26 final size:28
Alignment explanation
Indices: 10737--10800 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
10727 TATGTATTTG
10737 TTTCTA-ATATTT-CAATGTAAT-TGCAT
1 TTTCTACATATTTCCAATGT-ATGTGCAT
*
10763 TTTCTACA-ATTTCCCAATGTATGTGTAT
1 TTTCTACATATTT-CCAATGTATGTGCAT
10791 TTTCTACATA
1 TTTCTACATA
10801 AATTTCTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 18 0.56
29 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTCTACATATTTCCAATGTATGTGCAT
Found at i:10887 original size:25 final size:25
Alignment explanation
Indices: 10858--10938 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
10848 ATCGAACCTT
*
10858 ACCCTAAACCACTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTACAAA
** * *
10883 ACCCTTGACCA-TTCTCACCTTAAAAA
1 ACCCTAAACCACTT-TAACC-TACAAA
*
10909 ACCCTAAACCGCTTTAACCTACAAA
1 ACCCTAAACCACTTTAACCTACAAA
10934 ACCCT
1 ACCCT
10939 TCATCACTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
24 2 0.05
25 23 0.53
26 16 0.37
27 2 0.05
ACGTcount: A:0.37, C:0.38, G:0.02, T:0.22
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTACAAA
Found at i:10924 original size:51 final size:51
Alignment explanation
Indices: 10858--10980 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
10848 ATCGAACCTT
* *
10858 ACCCTAAACCACTTTAACCTACACAACCCTTGACCA-TTCTCACCTTAAAAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTT-TCACCTTAAAAA
* * **
10909 ACCCTAAACCGCTTTAACCTACAAAACCCTTCATCACTTTCACCTTAACGA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTTTCACCTTAAAAA
* *
10960 ACCTTATACCACTTTAACCTA
1 ACCCTAAACCACTTTAACCTA
10981 AAATCACTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 60 0.97
52 2 0.03
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (51 bp):
ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTTTCACCTTAAAAA
Found at i:10948 original size:25 final size:25
Alignment explanation
Indices: 10858--10980 Score: 81
Period size: 25 Copynumber: 4.8 Consensus size: 25
10848 ATCGAACCTT
* *
10858 ACCCTAAACCACTTTAACCTACACA
1 ACCCTTAACCACTTTAACCTACAAA
* * *
10883 ACCCTTGACCA-TTCTCACCTTAAAAA
1 ACCCTTAACCACTT-TAACC-TACAAA
* *
10909 ACCCTAAACCGCTTTAACCTACAAA
1 ACCCTTAACCACTTTAACCTACAAA
* * * *
10934 ACCCTTCATCACTTTCACCTTA-ACGA
1 ACCCTTAACCACTTTAACC-TACA-AA
10960 A-CCTTATACCACTTTAACCTA
1 ACCCTTA-ACCACTTTAACCTA
10981 AAATCACTCA
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
24 2 0.03
25 39 0.53
26 30 0.41
27 2 0.03
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (25 bp):
ACCCTTAACCACTTTAACCTACAAA
Found at i:11935 original size:18 final size:18
Alignment explanation
Indices: 11912--11948 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11902 CCTGGAGCAG
11912 ACGTGATTTTATATCTGC
1 ACGTGATTTTATATCTGC
11930 ACGTGATTTTATATCTGC
1 ACGTGATTTTATATCTGC
11948 A
1 A
11949 AACGTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (18 bp):
ACGTGATTTTATATCTGC
Found at i:11992 original size:12 final size:12
Alignment explanation
Indices: 11975--12025 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
11965 TTCAAAGAGG
11975 TTTTATATTTAA
1 TTTTATATTTAA
11987 TTTTATA-TTATA
1 TTTTATATTTA-A
*
11999 TTTGAT-TTTAA
1 TTTTATATTTAA
12010 TTTTA-ATATTAA
1 TTTTATAT-TTAA
12022 TTTT
1 TTTT
12026 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:12041 original size:24 final size:27
Alignment explanation
Indices: 12008--12076 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 27
11998 ATTTGATTTT
*
12008 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
12033 AATTA-AATATTAA-TTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
12058 TATTATAGATATTAATTTT
1 AATTATA-ATATTAATTTT
12077 AATTTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 7 0.19
24 9 0.24
25 10 0.27
26 1 0.03
27 7 0.19
28 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:12074 original size:27 final size:23
Alignment explanation
Indices: 12014--12076 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 23
12004 TTTTAATTTT
12014 AATATTAATTTTTTAAATAAATTA
1 AATATTAA-TTTTTAAATAAATTA
*
12038 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAA-A-TAAATTA
12063 TAGATATTAATTTT
1 -A-ATATTAATTTT
12077 AATTTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.21
24 9 0.26
25 6 0.18
26 1 0.03
27 11 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATTAATTTTTAAATAAATTA
Found at i:12086 original size:12 final size:12
Alignment explanation
Indices: 11983--12143 Score: 78
Period size: 12 Copynumber: 12.8 Consensus size: 12
11973 GGTTTTATAT
11983 TTAATTTT-ATA
1 TTAATTTTAATA
* *
11994 TT-ATATTTGATT
1 TTAAT-TTTAATA
12006 TTAATTTTAATA
1 TTAATTTTAATA
12018 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
* *
12031 -TAAATTAAATA
1 TTAATTTTAATA
12042 TTAATTTTTAATA
1 TTAA-TTTTAATA
*
12055 TTATATTATAGATA
1 TTA-ATTTTA-ATA
*
12069 TTAATTTTAATT
1 TTAATTTTAATA
**
12081 TTAATTTTTTTAA
1 TTAATTTTAAT-A
* * *
12094 ATAAATTAAATA
1 TTAATTTTAATA
12106 TTAATTTTTTAATA
1 TTAA--TTTTAATA
*
12120 TTATATTATAGATA
1 TTA-ATTTTA-ATA
12134 TTTAATTTTA
1 -TTAATTTTA
12144 TATCATATAA
Statistics
Matches: 111, Mismatches: 23, Indels: 29
0.68 0.14 0.18
Matches are distributed among these distances:
10 6 0.05
11 6 0.05
12 34 0.31
13 31 0.28
14 30 0.27
15 4 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:12127 original size:65 final size:63
Alignment explanation
Indices: 11983--12143 Score: 249
Period size: 64 Copynumber: 2.6 Consensus size: 63
11973 GGTTTTATAT
*
11983 TTAA-TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
*
12042 TTAATTTTTAATATTATATTATAGATATTAATTTTAATTTTAATTTTTTTAAATAAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTTTAAATAAATTAAATA
12106 TTAATTTTTTAATATTATATTATAGATATTTAATTTTA
1 TTAA-TTTTTAATATTATATTATAGATA-TTAATTTTA
12144 TATCATATAA
Statistics
Matches: 93, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
59 4 0.04
60 4 0.04
61 10 0.11
62 1 0.01
63 18 0.19
64 24 0.26
65 23 0.25
66 9 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (63 bp):
TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
Found at i:12155 original size:60 final size:62
Alignment explanation
Indices: 11983--12143 Score: 179
Period size: 65 Copynumber: 2.6 Consensus size: 62
11973 GGTTTTATAT
* * *
11983 TTAA-TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATT-TTTTAAATAAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTT-A-ATTAATTCATATAAATAAATTAAATA
** *
12042 TTAATTTTTAATATTATATTATAGATATTAATTTTAATTTTAATTTTTTTAAATAAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAA--TTAATTCATATAAATAAATTAAATA
12106 TTAATTTTTTAATATTATATTATAGATATTTAATTTTA
1 TTAA-TTTTTAATATTATATTATAGATA-TTAATTTTA
12144 TATCATATAA
Statistics
Matches: 92, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
59 4 0.04
60 4 0.04
61 11 0.12
62 2 0.02
63 17 0.18
64 22 0.24
65 23 0.25
66 9 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (62 bp):
TTAATTTTTAATATTATATTATAGATATTAATTTTAATTAATTCATATAAATAAATTAAATA
Found at i:12702 original size:31 final size:31
Alignment explanation
Indices: 12667--12726 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12657 TAGTTGTATG
* * *
12667 AATTATTTAAATTTTAGTATTGTAAAACTAA
1 AATTATTTAAATCTTAATATTGCAAAACTAA
12698 AATTATTTAAATCTTAATATTGCAAAACT
1 AATTATTTAAATCTTAATATTGCAAAACT
12727 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATCTTAATATTGCAAAACTAA
Found at i:19342 original size:33 final size:33
Alignment explanation
Indices: 19299--19370 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
19289 TTTAACACTA
19299 GATGATCATAATGAAACCAAAATGTAACATTAGT
1 GATGATCATAATGAAACCAAAATGTAACATT-GT
19333 GATGA-CATAATGAAACCAAAATGTAACATTGT
1 GATGATCATAATGAAACCAAAATGTAACATTGT
19365 GATGAT
1 GATGAT
19371 TATGGGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
32 7 0.19
33 25 0.68
34 5 0.14
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (33 bp):
GATGATCATAATGAAACCAAAATGTAACATTGT
Found at i:19553 original size:3 final size:3
Alignment explanation
Indices: 19545--19573 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19535 TTTATTTGTT
19545 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19574 CAAATATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:22849 original size:4 final size:4
Alignment explanation
Indices: 22840--22864 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22830 AGGGCCCTCA
22840 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
22865 CATTTCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:25922 original size:20 final size:22
Alignment explanation
Indices: 25897--25947 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
25887 ATTATAAACT
*
25897 TTTTTTAATTT-GATCATTA-A
1 TTTTTTAATTTGGATAATTAGA
25917 TTTTTT-ATTTGGATAATTAGA
1 TTTTTTAATTTGGATAATTAGA
*
25938 TTATTTAATT
1 TTTTTTAATT
25948 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 13 0.50
21 6 0.23
22 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (22 bp):
TTTTTTAATTTGGATAATTAGA
Found at i:27135 original size:16 final size:16
Alignment explanation
Indices: 27114--27152 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
27104 AGAAATTTAG
*
27114 CTTGTTCGTGTTTATT
1 CTTGTTCGTGTTCATT
27130 CTTGTTCGTGTTCATT
1 CTTGTTCGTGTTCATT
*
27146 ATTGTTC
1 CTTGTTC
27153 ATTCGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.15, G:0.18, T:0.59
Consensus pattern (16 bp):
CTTGTTCGTGTTCATT
Found at i:27195 original size:24 final size:24
Alignment explanation
Indices: 27167--27229 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
27157 GTTAAAATGA
* * *
27167 TAAACTAACACAAACGAATGAACT
1 TAAACGAACACAAACGAATAAACG
*
27191 TAAACGAACACAAGCGAATAAACG
1 TAAACGAACACAAACGAATAAACG
* *
27215 TAAATGAGCACAAAC
1 TAAACGAACACAAAC
27230 AAACGAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
TAAACGAACACAAACGAATAAACG
Found at i:29402 original size:12 final size:12
Alignment explanation
Indices: 29385--29409 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29375 CCACCGTCAC
29385 CCTCATTATCTT
1 CCTCATTATCTT
29397 CCTCATTATCTT
1 CCTCATTATCTT
29409 C
1 C
29410 TCTTAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCATTATCTT
Found at i:30861 original size:10 final size:10
Alignment explanation
Indices: 30846--30870 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30836 TGGATATACA
30846 ATTTTTTTAT
1 ATTTTTTTAT
30856 ATTTTTTTAT
1 ATTTTTTTAT
30866 ATTTT
1 ATTTT
30871 CCCTTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:31737 original size:21 final size:21
Alignment explanation
Indices: 31713--31760 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31703 TAACTAATTG
31713 AAGAAAACTCAAATTTCAGTA
1 AAGAAAACTCAAATTTCAGTA
* ** *
31734 AAGAAAATTCGGATTTCAGTG
1 AAGAAAACTCAAATTTCAGTA
31755 AAGAAA
1 AAGAAA
31761 TTTCGGATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (21 bp):
AAGAAAACTCAAATTTCAGTA
Found at i:31765 original size:21 final size:21
Alignment explanation
Indices: 31725--31773 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
31715 GAAAACTCAA
31725 ATTTCAGTAAAGAAAATTCGG
1 ATTTCAGTAAAGAAAATTCGG
* *
31746 ATTTCAGTGAAGAAATTTCGG
1 ATTTCAGTAAAGAAAATTCGG
31767 ATTTCAG
1 ATTTCAG
31774 AATAAGCACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (21 bp):
ATTTCAGTAAAGAAAATTCGG
Found at i:35904 original size:17 final size:18
Alignment explanation
Indices: 35871--35908 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
35861 CCCAAGGAAC
35871 AAAAGAAATCATATAATA
1 AAAAGAAATCATATAATA
35889 AAAAGAAA-CA-AGTAATA
1 AAAAGAAATCATA-TAATA
35906 AAA
1 AAA
35909 CCTAGGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 10 0.53
18 8 0.42
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (18 bp):
AAAAGAAATCATATAATA
Found at i:37420 original size:19 final size:18
Alignment explanation
Indices: 37393--37430 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
37383 CATGACGACA
37393 TTCATTTCTC-AAAATCTT
1 TTCATTTCTCTAAAA-CTT
37411 TTCATATTCTCTAAAACTT
1 TTCAT-TTCTCTAAAACTT
37430 T
1 T
37431 GGATTCTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
TTCATTTCTCTAAAACTT
Found at i:41311 original size:54 final size:55
Alignment explanation
Indices: 41193--41438 Score: 282
Period size: 54 Copynumber: 4.5 Consensus size: 55
41183 CCAGAATTTA
* ** * *
41193 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCTCC-C
*
41248 GATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCTCCC
** * * * * *
41302 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGCTCCC
* * *
41360 GATT-AAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCTCCC
*
41414 GATTGAAGCACAGATGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
41439 GTTAATTCTA
Statistics
Matches: 163, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
54 71 0.44
55 47 0.29
57 20 0.12
58 25 0.15
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGCTCCC
Found at i:41395 original size:112 final size:109
Alignment explanation
Indices: 41196--41435 Score: 338
Period size: 112 Copynumber: 2.2 Consensus size: 109
41186 GAATTTAGAT
**
41196 TGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAG
1 TGAAGCACAGAGGTGCTCAGTCATAGTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAG
*
41261 AGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCCGGC
66 AGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCCGAC
** *
41305 TGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGATT-AAGCA
1 TGAAGCACAGAGGTGCTCAGTCA---TAGTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCA
* * * *
41369 CAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTCGAT
63 CAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCCCGAC
*
41417 TGAAGCACAGATGTGCTCA
1 TGAAGCACAGAGGTGCTCA
41436 ATCGTTAATT
Statistics
Matches: 116, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
109 23 0.20
111 21 0.18
112 72 0.62
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (109 bp):
TGAAGCACAGAGGTGCTCAGTCATAGTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAG
AGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCCGAC
Found at i:41689 original size:81 final size:81
Alignment explanation
Indices: 41554--41711 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 81
41544 GCGAGTTACA
*
41554 AAGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
41619 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
*
41635 AAGAATGGTTCGCACACGAAATGGCGGA-TCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCT
1 AAGAATGGTTCGCACACGAAATGGCGGAGT-AACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCT
41699 ACCGAGCCAGTTG
65 ACCGAGCCAGTTG
41712 TGCAAGAGAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 1 0.01
81 71 0.99
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCGCACACGAAATGGCGGAGTAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:47275 original size:55 final size:55
Alignment explanation
Indices: 47057--47478 Score: 405
Period size: 55 Copynumber: 7.8 Consensus size: 55
47047 CCACTGGGTT
* * * **
47057 TGCTCCCT-TTTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTC
1 TGCTCCCTATTT-CTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAACGTGTC
* * * * *
47112 TGTTCTCTATTCCTTCAGAGAGTATAGGACT---A-AATCTTCAACAAATGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * *
47163 CGCTCCCCATTCCTTCAGAGAGTATAGGACT----CAATCTTCAATCAAACGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAAACGTGTC
* * * * *
47215 CGCTCCCTATTTTTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * * **
47270 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAATAATTTTCAACATTCGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * ** *
47325 TGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* * * * *
47380 TGCTCCCTATTGCTTAAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTC
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
* *
47435 TGCTCTCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA
47479 TTTGCTTCAC
Statistics
Matches: 309, Mismatches: 50, Indels: 16
0.82 0.13 0.04
Matches are distributed among these distances:
50 1 0.00
51 50 0.16
52 37 0.12
55 210 0.68
56 11 0.04
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (55 bp):
TGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTC
Found at i:66077 original size:64 final size:63
Alignment explanation
Indices: 65997--66267 Score: 195
Period size: 64 Copynumber: 4.3 Consensus size: 63
65987 AATGTATTTG
* *
65997 ATCTTTTTAATTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAAT
1 ATCTATTTAAGTTTGAATATTAAAAG-TAATTATATACTTTTGTATATTTCAAATTAAAATAAT
* * * * ** *
66061 ATCTATTTAAGTTTGAATAATAAAAGGAGTT-TA-CCTTTTG-ACCGTTGCAAATT-AAAT-AT
1 ATCTATTTAAGTTTGAATATTAAAAGTAATTATATACTTTTGTA-TATTTCAAATTAAAATAAT
* * * *
66120 A-CTATTTAA-TTTGAATATTAGTAAG-AA-TAT-TACTCTTTGAATATGTCAATTTAAAA-AGA
1 ATCTATTTAAGTTTGAATATTA-AAAGTAATTATATACT-TTTGTATATTTCAAATTAAAATA-A
66179 T
63 T
* * * * *
66180 ATTTGTTACGTTTTTAACTTTGAATATTAAAAATAATTCTATACTTTTGTATATTTCAAACTAAA
1 A-----T-C-TATTTAAGTTTGAATATTAAAAGTAATTATATACTTTTGTATATTTCAAATTAAA
66245 ATAAT
59 ATAAT
66250 ATCTATTTAAGTTTGAAT
1 ATCTATTTAAGTTTGAAT
66268 GGTAAAAGGC
Statistics
Matches: 157, Mismatches: 28, Indels: 45
0.68 0.12 0.20
Matches are distributed among these distances:
56 1 0.01
57 14 0.09
58 21 0.13
59 7 0.04
60 8 0.05
61 14 0.09
62 2 0.01
63 16 0.10
64 24 0.15
65 1 0.01
67 1 0.01
68 8 0.05
69 13 0.08
70 22 0.14
71 5 0.03
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (63 bp):
ATCTATTTAAGTTTGAATATTAAAAGTAATTATATACTTTTGTATATTTCAAATTAAAATAAT
Found at i:66247 original size:189 final size:188
Alignment explanation
Indices: 65936--66281 Score: 536
Period size: 189 Copynumber: 1.8 Consensus size: 188
65926 AACGATATTT
* * *
65936 TTTAATTTGAATATTAGTAGGATAATTACTTTTTTAATAAGTCAATTTAAAAATGTATTTGATCT
1 TTTAATTTGAATATTAGTAGAATAATTACTCTTTGAATAAGTCAATTTAAAAATGTATTTGATCT
* *
66001 TTTTAATTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATCTA
66 TTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAACTAAAATAATATCTA
66066 TTTAAGTTTGAATAATAAAAGGAGTTTACCTTTTGACCGTTGCAAATTAAATATACTA
131 TTTAAGTTTGAATAATAAAAGGAGTTTACCTTTTGACCGTTGCAAATTAAATATACTA
* *
66124 TTTAATTTGAATATTAGTAAGAAT-ATTACTCTTTGAATATGTCAATTTAAAAA-GATATTTGTT
1 TTTAATTTGAATATTAGT-AGAATAATTACTCTTTGAATAAGTCAATTTAAAAATG-TATTTGAT
*
66187 ACGTTTTTAACTTTGAATATTAAAA-ATAATTCTATACTTTTGTATATTTCAAACTAAAATAATA
64 -C-TTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAACTAAAATAATA
** *
66251 TCTATTTAAGTTTGAATGGTAAAAGGCGTTT
127 TCTATTTAAGTTTGAATAATAAAAGGAGTTT
66282 TATATTTGAA
Statistics
Matches: 143, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
187 1 0.01
188 51 0.36
189 70 0.49
190 21 0.15
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.45
Consensus pattern (188 bp):
TTTAATTTGAATATTAGTAGAATAATTACTCTTTGAATAAGTCAATTTAAAAATGTATTTGATCT
TTTTAACTTTGAATATTAAAAGATAATTATATACTTTTGTATATTTCAAACTAAAATAATATCTA
TTTAAGTTTGAATAATAAAAGGAGTTTACCTTTTGACCGTTGCAAATTAAATATACTA
Found at i:67610 original size:34 final size:32
Alignment explanation
Indices: 67555--67619 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
67545 AACCATAAAT
*
67555 TTATAGATAAAATTGAGTATGAATAATTTAATAC
1 TTATAGATAAAATAGAGTATG-A-AATTTAATAC
*
67589 TTATATATAAAA-AGAGCTATGAAATTTAATA
1 TTATAGATAAAATAGAG-TATGAAATTTAATA
67620 TTTGGGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 9 0.32
33 4 0.14
34 15 0.54
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (32 bp):
TTATAGATAAAATAGAGTATGAAATTTAATAC
Found at i:75124 original size:31 final size:31
Alignment explanation
Indices: 75049--75124 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
75039 TTAAAATACA
*
75049 TAAGATATGATCACTTATATTTTTATTTAAT
1 TAAGATATGGTCACTTATATTTTTATTTAAT
*
75080 TAAGATATTGTCACTT-TCATTTTTATTTAAT
1 TAAGATATGGTCACTTAT-ATTTTTATTTAAT
*
75111 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
75125 CCCTAGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (31 bp):
TAAGATATGGTCACTTATATTTTTATTTAAT
Found at i:75906 original size:25 final size:24
Alignment explanation
Indices: 75873--75929 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 24
75863 ATATATTAAC
75873 TTAAAATATTTTTA-TATTAACTTT
1 TTAAAATA-TTTTACTATTAACTTT
75897 TTAAATATATTTTACTATTAACTTAAT
1 TTAAA-ATATTTTACTATTAACTT--T
75924 TTAAAA
1 TTAAAA
75930 ATAATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 10 0.34
25 12 0.41
26 1 0.03
27 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAAATATTTTACTATTAACTTT
Found at i:75937 original size:27 final size:24
Alignment explanation
Indices: 75883--75938 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
75873 TTAAAATATT
* *
75883 TTTATATTAACTTTTTAAATATAT
1 TTTATATTAACTTTTTAAAAATAA
75907 TTTACTATTAACTTAATTTAAAAATAA
1 TTTA-TATTAACTT--TTTAAAAATAA
75934 TTTAT
1 TTTAT
75939 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 9 0.33
26 1 0.04
27 13 0.48
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATATTAACTTTTTAAAAATAA
Found at i:77838 original size:21 final size:22
Alignment explanation
Indices: 77814--77862 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
77804 GATCACTATT
77814 ATAATTTACCCTTT-A-TTTTAA
1 ATAATTTA-CCTTTAATTTTTAA
*
77835 ATAAGTTACCTTTAATTTTTAA
1 ATAATTTACCTTTAATTTTTAA
*
77857 CTAATT
1 ATAATT
77863 CATAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 8 0.35
22 10 0.43
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATTTACCTTTAATTTTTAA
Found at i:78228 original size:22 final size:21
Alignment explanation
Indices: 78200--78246 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
78190 CGTGAAATTA
* *
78200 TAAATTAGTTGAAATTTAAAGG
1 TAAATTA-TTGAAAATAAAAGG
*
78222 TAAATTATTTAAAATAAAAGG
1 TAAATTATTGAAAATAAAAGG
78243 TAAA
1 TAAA
78247 CTATACTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (21 bp):
TAAATTATTGAAAATAAAAGG
Found at i:81656 original size:12 final size:12
Alignment explanation
Indices: 81641--81683 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
81631 GTTATTTAAA
81641 CGGGTATTGGGC
1 CGGGTATTGGGC
81653 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
81665 CGAGAATCGGGC
1 CGGGTATTGGGC
81677 CGGGTAT
1 CGGGTAT
81684 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.14, C:0.19, G:0.47, T:0.21
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:81688 original size:2 final size:2
Alignment explanation
Indices: 81681--81772 Score: 61
Period size: 2 Copynumber: 49.0 Consensus size: 2
81671 TCGGGCCGGG
* * * *
81681 TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA AA TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
81721 TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81759 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
81773 ATTATTTTTA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81819 original size:13 final size:12
Alignment explanation
Indices: 81788--81824 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
81778 TTTTAATATT
*
81788 TATCGGGTCGGG
1 TATCGGGGCGGG
81800 TATCGGGGCGGG
1 TATCGGGGCGGG
81812 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
81825 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:84262 original size:20 final size:20
Alignment explanation
Indices: 84237--84280 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
84227 TTTTATTTAA
* * *
84237 AATTTAAAGTTTAAAGTTAT
1 AATTTAAAATATAAAATTAT
84257 AATTTAAAATATAAAATTAT
1 AATTTAAAATATAAAATTAT
84277 AATT
1 AATT
84281 GCATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
AATTTAAAATATAAAATTAT
Found at i:84414 original size:19 final size:21
Alignment explanation
Indices: 84390--84429 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
84380 TTTTTTCGAT
84390 GTTTTAA-CTT-TAATAATTG
1 GTTTTAATCTTGTAATAATTG
*
84409 GTTTTAATTTTGTAATAATTG
1 GTTTTAATCTTGTAATAATTG
84430 TAATTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (21 bp):
GTTTTAATCTTGTAATAATTG
Found at i:88614 original size:18 final size:18
Alignment explanation
Indices: 88568--88618 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
88558 AATTATATGG
88568 TGATTTTCAGTTATCAGA
1 TGATTTTCAGTTATCAGA
*
88586 T-ATTTAT-AGTTATTAGA
1 TGATTT-TCAGTTATCAGA
88603 TGATTTTCAGTTATCA
1 TGATTTTCAGTTATCA
88619 TACGTAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (18 bp):
TGATTTTCAGTTATCAGA
Found at i:97954 original size:25 final size:24
Alignment explanation
Indices: 97920--97972 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
97910 AAACAATTAG
* *
97920 TTTTTTTTTTT-AATTTGAATGAT
1 TTTTTTTTTTTAAACTTAAATGAT
*
97943 TTTTTTTATTTTAAACTTAAATTAT
1 TTTTTTT-TTTTAAACTTAAATGAT
97968 TTTTT
1 TTTTT
97973 AATGAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 4 0.16
25 14 0.56
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTTTTTTTAAACTTAAATGAT
Found at i:108598 original size:19 final size:20
Alignment explanation
Indices: 108560--108607 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
108550 CAGCTGATGT
*
108560 TAATTGATATATGGTTGTAA
1 TAATTGATATATGATTGTAA
*
108580 TAATTGA-ATCTGATTGTAA
1 TAATTGATATATGATTGTAA
*
108599 TAGTTGATA
1 TAATTGATA
108608 CGATAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (20 bp):
TAATTGATATATGATTGTAA
Found at i:112407 original size:21 final size:19
Alignment explanation
Indices: 112360--112407 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
112350 TTAAATTCTT
*
112360 ATTAAATTATAGATTAATG
1 ATTAAATTATAGATCAATG
*
112379 ATTTAAATTAGTCGATCAATAG
1 A-TTAAATTA-TAGATCAAT-G
112401 ATTAAAT
1 ATTAAAT
112408 ATCAATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
21 13 0.54
22 2 0.08
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (19 bp):
ATTAAATTATAGATCAATG
Found at i:120131 original size:17 final size:16
Alignment explanation
Indices: 120104--120155 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 16
120094 TATCGCTATT
120104 TTAATTATTATTTTTATA
1 TTAA-TATTATTTTT-TA
*
120122 TTTATATTATTATTTTA
1 TTAATATTATT-TTTTA
120139 TTAATATTATATTTTTA
1 TTAATATTAT-TTTTTA
120156 CATATTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATATTATTTTTTA
Found at i:120134 original size:14 final size:15
Alignment explanation
Indices: 120108--120152 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
120098 GCTATTTTAA
*
120108 TTATTATTTTTATAT
1 TTATTATTATTATAT
120123 TTA-TATTATTAT-T
1 TTATTATTATTATAT
*
120136 TTATTAATATTATAT
1 TTATTATTATTATAT
120151 TT
1 TT
120153 TTACATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 16 0.62
15 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:127548 original size:4 final size:4
Alignment explanation
Indices: 127539--127591 Score: 76
Period size: 4 Copynumber: 14.0 Consensus size: 4
127529 GATCGAGAAA
*
127539 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
127585 A-AT ACAT
1 ACAT ACAT
127592 CAAACATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 39 0.89
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:128209 original size:156 final size:153
Alignment explanation
Indices: 127917--128200 Score: 380
Period size: 156 Copynumber: 1.8 Consensus size: 153
127907 AATTCAGTCT
* * * * *
127917 CTTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATCTC
1 CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACATAAAACAAAATTAATCTC
* *
127982 ATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCACAAATTTTG
66 ACTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCAC--A-TTTG
128047 AGAATTTTAAAACAAATTGTGTTTCG
128 AGAATTTTAAAACAAATTGTGTTTCG
128073 CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-TAAAAACAAAATTAATCT
1 CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACAT-AAAACAAAATTAATCT
* * * *
128137 CACCTT-AGATTCTTGTTTCTTTCAAAACAAATTTCGTCTCGCTTGAGAC-CTTTTCC-C-TTTG
65 CA-CTTGAGA-TCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCACATTTG
128198 AGA
128 AGA
128201 TCCAAATTTC
Statistics
Matches: 114, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
151 7 0.06
155 2 0.02
156 68 0.60
157 37 0.32
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (153 bp):
CTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACATAAAACAAAATTAATCTC
ACTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCACATTTGAGA
ATTTTAAAACAAATTGTGTTTCG
Found at i:128284 original size:36 final size:36
Alignment explanation
Indices: 128261--128358 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 36
128251 TCGTTTCCTC
128261 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
1 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
* ** * *
128297 AAAAACAAATTTTGTCTCATTTGAGACTATAT--CT
1 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
* *
128331 TAAAGCAAA-TCTTGTCTCGCTTGAGACA
1 AAAAACAAACT-TTGTCTCGCTTGAGACA
128359 TCATTTTCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
33 1 0.02
34 23 0.45
36 27 0.53
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (36 bp):
AAAAACAAACTTTGTCTCGCTTGAGACAATTTCACT
Found at i:128647 original size:27 final size:27
Alignment explanation
Indices: 128610--128737 Score: 184
Period size: 27 Copynumber: 4.6 Consensus size: 27
128600 CTTTTGAGGA
128610 AAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAATCTTTGAGTTTGTTCCTCTTG
128637 AAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAATCTTTGAGTTTGTTCCTCTTG
*
128664 AAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAATCTTTGAGTTTGTTCCTCTTG
* *
128691 AATAAAAATCTTGGAGTTTGTTCCTTTTG
1 -A-AAAAATCTTTGAGTTTGTTCCTCTTG
*
128720 AATAAAATTTTTTGAGTT
1 AA-AAAA-TCTTTGAGTT
128738 GTTTCGTTTG
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
27 54 0.58
28 6 0.06
29 33 0.35
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTTGTTCCTCTTG
Found at i:128669 original size:29 final size:29
Alignment explanation
Indices: 128609--128765 Score: 182
Period size: 27 Copynumber: 5.6 Consensus size: 29
128599 TCTTTTGAGG
128609 AAAAAAATCTTTGAGTTTGTTCCTCTTG-
1 AAAAAAATCTTTGAGTTTGTTCCTCTTGA
128637 -AAAAAATCTTTGAGTTTGTTCCTCTTG-
1 AAAAAAATCTTTGAGTTTGTTCCTCTTGA
*
128664 -AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAAATCTTTGAGTTTGTTCCTCTTGA
* * *
128692 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 AAAAAAATCTTTGAGTTTGTTCCTCTTGA
* * * *
128721 ATAAAATTTTTTGAG-TTGTTTCGT-TTGA
1 AAAAAAATCTTTGAGTTTG-TTCCTCTTGA
128749 AACAAAAATCTTTGAGT
1 AA-AAAAATCTTTGAGT
128766 CTATTTATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
27 53 0.46
28 8 0.07
29 53 0.46
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
AAAAAAATCTTTGAGTTTGTTCCTCTTGA
Found at i:128692 original size:54 final size:56
Alignment explanation
Indices: 128610--128765 Score: 201
Period size: 54 Copynumber: 2.8 Consensus size: 56
128600 CTTTTGAGGA
*
128610 AAAAAATCTTTGAGTTTGTTCCTCTTG-A-AAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAATCTTTGAGTTTGTTCCTTTTGAACAAAAATCTTTGAGTTTGTTCCTCTTG
* * *
128664 AAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAAATCTTTGAGTTTGTTCCTTTTGAACAAAAATCTTTGAGTTTGTTCCTCTTG
* * *
128720 AATAAAATTTTTTGAG-TTGTTTCGTTTGAAACAAAAATCTTTGAGT
1 AA-AAAA-TCTTTGAGTTTGTTCCTTTTG-AACAAAAATCTTTGAGT
128766 CTATTTATTT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
54 26 0.29
55 1 0.01
56 26 0.29
57 14 0.16
58 22 0.25
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (56 bp):
AAAAAATCTTTGAGTTTGTTCCTTTTGAACAAAAATCTTTGAGTTTGTTCCTCTTG
Found at i:129226 original size:121 final size:118
Alignment explanation
Indices: 129056--129280 Score: 258
Period size: 121 Copynumber: 1.9 Consensus size: 118
129046 CTTAACAAAA
* * * *
129056 TCATCCTTGATTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATGAAAAA
1 TCATCCTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAA
*
129121 CTAACTTTTGAGATTGTTTCATTTTGAAAC-AAATTTGGTCTCACTTAAGATGTGAT
66 --AAC-TTTGAGATTGTTTC-CTTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
* * * **
129177 TCATCTTTGAGTCTGTTTCTTTTAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAA
1 TCATCCTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATGAAA
* * *
129240 AAATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
64 AAAACTTTGAGATTGTTTCCTTTGAAACAAAATTTGGTCTC
129281 TCAAGACAAC
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
117 8 0.09
118 24 0.27
119 2 0.02
120 7 0.08
121 43 0.49
122 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.44
Consensus pattern (118 bp):
TCATCCTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAA
AACTTTGAGATTGTTTCCTTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
Found at i:129305 original size:63 final size:63
Alignment explanation
Indices: 129179--129304 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
129169 GATGTGATTC
* *
129179 ATCTTTGAGTCTGTTTCTTTTAAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTAAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
* * * *
129242 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC-TCAAGACAACTTCTTTTGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTAAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
129304 A
1 A
129305 AAACATCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 22 0.39
63 35 0.61
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTAAAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAA
Found at i:129769 original size:38 final size:35
Alignment explanation
Indices: 129727--129815 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
129717 CATTTGAATC
129727 TGTTTTTCTTGAAACAAAACAAACAAAGTCTTTGAGTA
1 TGTTTTTCTTGAAACAAAA-AAA-AAA-TCTTTGAGTA
* * *
129765 TGTTTTTCTTAAAACAAAAAAAACATCTTTGAGTT
1 TGTTTTTCTTGAAACAAAAAAAAAATCTTTGAGTA
* *
129800 TGTTTCTCTCGAAACA
1 TGTTTTTCTTGAAACA
129816 CTAATCTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 22 0.49
36 2 0.04
37 3 0.07
38 18 0.40
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (35 bp):
TGTTTTTCTTGAAACAAAAAAAAAATCTTTGAGTA
Found at i:129804 original size:35 final size:38
Alignment explanation
Indices: 129727--129804 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
129717 CATTTGAATC
*
129727 TGTTTTTCTTGAAACAAAACAAACAAAGTCTTTGAGTA
1 TGTTTTTCTTAAAACAAAACAAACAAAGTCTTTGAGTA
* *
129765 TGTTTTTCTTAAAACAAAA-AAA-ACA-TCTTTGAGTT
1 TGTTTTTCTTAAAACAAAACAAACAAAGTCTTTGAGTA
129800 TGTTT
1 TGTTT
129805 CTCTCGAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 14 0.38
36 2 0.05
37 3 0.08
38 18 0.49
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (38 bp):
TGTTTTTCTTAAAACAAAACAAACAAAGTCTTTGAGTA
Found at i:129873 original size:36 final size:35
Alignment explanation
Indices: 129820--129933 Score: 109
Period size: 36 Copynumber: 3.4 Consensus size: 35
129810 GAAACACTAA
*
129820 TCTTTGAGATCA-ATTCCCTTTAAACGAATTTTGTC
1 TCTTTGAGA-CAGTTTCCCTTTAAACGAATTTTGTC
*
129855 TCATTTGAGACAGTTTCCCTTTAAACG----TCG--
1 TC-TTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
* *
129885 TCTTTGAGTC-GTTTCCCTTAAAACGAATTTTGTC
1 TCTTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
129919 TCTTTTGAGACAGTT
1 TC-TTTGAGACAGTT
129934 GCTTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
28 14 0.22
29 7 0.11
30 2 0.03
32 4 0.06
34 2 0.03
35 11 0.17
36 23 0.37
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (35 bp):
TCTTTGAGACAGTTTCCCTTTAAACGAATTTTGTC
Found at i:130155 original size:43 final size:44
Alignment explanation
Indices: 130064--130299 Score: 181
Period size: 43 Copynumber: 5.5 Consensus size: 44
130054 TGGCCAGCCG
* * *
130064 TCCTCATCATGTAGGAACCGTGTCATCACC--AG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCAT-ACCATAGATAACCAGACC
130104 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* * * ** *
130146 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGACC
* * * ** * *
130193 TCTTCATCACGTATGAGCCGTGTCATTCC--CCA-AATCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
130234 TCCTCATCACGTATGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
130276 GTCCTCATCACGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAGCCGTGT
130300 TATCACCCTT
Statistics
Matches: 154, Mismatches: 28, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
38 3 0.02
40 27 0.18
41 29 0.19
42 4 0.03
43 54 0.35
45 5 0.03
46 31 0.20
47 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
Found at i:130283 original size:130 final size:132
Alignment explanation
Indices: 130067--130392 Score: 446
Period size: 130 Copynumber: 2.5 Consensus size: 132
130057 CCAGCCGTCC
* * * *
130067 TCATCATGTAGGAACCGTGTCATCACCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTACGAGCCGTGTCATCACCAAACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
*
130132 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA-CCTT-T-AGATGGCCAGAACT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCTAAGATGGCAAGAACT
130194 CT
131 CT
* * * *
130196 TCATCACGTATGAGCCGTGTCATTCCCCAAATCAGATCTCCTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTACGAGCCGTGTCA-TCACCAAACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
130261 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAAGA
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTT-CT-AAGATGGCAAGA
130326 ACTCT
128 ACTCT
* * *
130331 TCATCACGTACGAGCCGTGTCA-C-CCTAGATAACCAGCTGTCCTCATCACGTAGGAACCGTGT
1 TCATCACGTACGAGCCGTGTCATCACC---A-AACCAGATCTCCTCATCACGTAGGAGCCGTGT
130393 TATCACCCTT
Statistics
Matches: 173, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
129 19 0.11
130 82 0.47
131 4 0.02
132 2 0.01
133 2 0.01
135 37 0.21
136 27 0.16
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (132 bp):
TCATCACGTACGAGCCGTGTCATCACCAAACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCTAAGATGGCAAGAACT
CT
Found at i:130397 original size:93 final size:94
Alignment explanation
Indices: 130237--130444 Score: 364
Period size: 93 Copynumber: 2.2 Consensus size: 94
130227 TCAGATCTCC
130237 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
130302 TCACCCTTCCTAAAGATGGCAAGAACTCT
66 TCACCCTTCCTAAAGATGGCAAGAACTCT
* * *
130331 TCATCACGTACGAGCCGTGTC-ACCCTAGATAACCAGCTGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
*
130395 TCACCCTTCCTAAAGATGGCCAGAACTCT
66 TCACCCTTCCTAAAGATGGCAAGAACTCT
*
130424 TCATCACGTATGAGCAGTGTC
1 TCATCACGTATGAGCCGTGTC
130445 GTCCCCACCA
Statistics
Matches: 108, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 88 0.81
94 20 0.19
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (94 bp):
TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCCTTCCTAAAGATGGCAAGAACTCT
Found at i:130642 original size:17 final size:16
Alignment explanation
Indices: 130615--130666 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 16
130605 TATCGCTATT
130615 TTAATTATTATTTTTATA
1 TTAA-TATTATTTTT-TA
*
130633 TTTATATTATTATTTTA
1 TTAATATTATT-TTTTA
130650 TTAATATTATATTTTTA
1 TTAATATTAT-TTTTTA
130667 CATATTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATATTATTTTTTA
Found at i:130645 original size:14 final size:15
Alignment explanation
Indices: 130619--130663 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
130609 GCTATTTTAA
*
130619 TTATTATTTTTATAT
1 TTATTATTATTATAT
130634 TTA-TATTATTAT-T
1 TTATTATTATTATAT
*
130647 TTATTAATATTATAT
1 TTATTATTATTATAT
130662 TT
1 TT
130664 TTACATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 16 0.62
15 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:138080 original size:15 final size:15
Alignment explanation
Indices: 138060--138094 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
138050 AGCAAGGCTC
*
138060 TTCGAGTGATGCTTG
1 TTCGAGTGAAGCTTG
*
138075 TTCGAGTGAAGTTTG
1 TTCGAGTGAAGCTTG
138090 TTCGA
1 TTCGA
138095 ATGGTGAGCA
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:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (15 bp):
TTCGAGTGAAGCTTG
Found at i:139816 original size:8 final size:8
Alignment explanation
Indices: 139803--139833 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
139793 TGAGTTCATT
139803 CTTTCTAG
1 CTTTCTAG
139811 CTTTCTAG
1 CTTTCTAG
*
139819 CTTGCTAG
1 CTTTCTAG
139827 CTTTCTA
1 CTTTCTA
139834 ACCTTGTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (8 bp):
CTTTCTAG
Found at i:143136 original size:23 final size:23
Alignment explanation
Indices: 143102--143162 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
143092 CATAATTGTC
143102 CCGAAG-GACCACATAGGCCTGCA
1 CCGAAGTG-CCACATAGGCCTGCA
* **
143125 TCGAAGTGCCACATAGGTTTGCA
1 CCGAAGTGCCACATAGGCCTGCA
*
143148 CCGAAGTGTCACATA
1 CCGAAGTGCCACATA
143163 TTTGTCCCCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
CCGAAGTGCCACATAGGCCTGCA
Found at i:143202 original size:21 final size:22
Alignment explanation
Indices: 143157--143206 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
143147 ACCGAAGTGT
*
143157 CACATATTTGTCCCCGAAAGAC
1 CACATAATTGTCCCCGAAAGAC
143179 CACATAATTGT-CCC-AAATGAC
1 CACATAATTGTCCCCGAAA-GAC
143200 CACATAA
1 CACATAA
143207 AACCCTCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 10 0.38
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.22
Consensus pattern (22 bp):
CACATAATTGTCCCCGAAAGAC
Found at i:146859 original size:29 final size:29
Alignment explanation
Indices: 146817--146875 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
146807 TATTTGTGAA
146817 CTAACCCTAACGTTAATATATCAACAAAT
1 CTAACCCTAACGTTAATATATCAACAAAT
146846 CTAACCCTAACGTTAATATATCAACAAAT
1 CTAACCCTAACGTTAATATATCAACAAAT
146875 C
1 C
146876 CTTAGATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.27
Consensus pattern (29 bp):
CTAACCCTAACGTTAATATATCAACAAAT
Found at i:149095 original size:31 final size:30
Alignment explanation
Indices: 149029--149141 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
149019 ATATATATAT
* **
149029 ATATATATTATT-TTATTCTTAACTTATTAA
1 ATATATTTTATTCTTATT-TTAACTTAAAAA
* * *
149059 GTATATCTTATTTTTATTTTAACTTACAAAA
1 ATATATTTTATTCTTATTTTAACTTA-AAAA
* * *
149090 ATATATTTTAGTCCTATTTTAACTTAAAAT
1 ATATATTTTATTCTTATTTTAACTTAAAAA
*
149120 ATATATTTTATTCTTATCTTAA
1 ATATATTTTATTCTTATTTTAA
149142 TTTTTAAACA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
30 40 0.59
31 28 0.41
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (30 bp):
ATATATTTTATTCTTATTTTAACTTAAAAA
Found at i:149199 original size:29 final size:26
Alignment explanation
Indices: 149146--149215 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 26
149136 TCTTAATTTT
*
149146 TAAACATATATTTAAATTAAAATAAAG
1 TAAA-ATATATTTAAATTAAAATAAAA
*
149173 TAAAATATATTTCATAAGTTAAGATAAAA
1 TAAAATATATTT-A-AA-TTAAAATAAAA
*
149202 TAAAATATTTTTAA
1 TAAAATATATTTAA
149216 TTTTAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.22
27 6 0.16
28 3 0.08
29 20 0.54
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (26 bp):
TAAAATATATTTAAATTAAAATAAAA
Found at i:149329 original size:59 final size:59
Alignment explanation
Indices: 149266--149380 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 59
149256 TTAAGGTAAT
* * *
149266 AATAAAATATATTT-TTAAGTTGAA-ATAAGATGAAAATATTTTTTTTAA-ATTAAAATTAA
1 AATAAAATATATTTAATAAGTT-AAGATAAAAT-AAAATA-TATTTTTAATATTAAAATTAA
*
149325 AATAAAATATATTTAATAAGTTAAGGTAAAATAAAATATATTTTTAATATTAAAAT
1 AATAAAATATATTTAATAAGTTAAGATAAAATAAAATATATTTTTAATATTAAAAT
149381 GTGAATTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
58 8 0.16
59 30 0.61
60 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (59 bp):
AATAAAATATATTTAATAAGTTAAGATAAAATAAAATATATTTTTAATATTAAAATTAA
Found at i:149377 original size:29 final size:29
Alignment explanation
Indices: 149237--149377 Score: 103
Period size: 29 Copynumber: 4.8 Consensus size: 29
149227 GAATTTAATT
* *
149237 TAAAATACATTTTTAAAAATTAAGGTAATAA
1 TAAAATATATTTTT-AATATTAAGGTAA-AA
* * *
149268 TAAAATATATTTTTAAGT-TGAA-ATAAGA
1 TAAAATATATTTTTAA-TATTAAGGTAAAA
* **
149296 TGAAAATATTTTTTTTAA-ATTAAAATTAAAA
1 T-AAAATA-TATTTTTAATATT-AAGGTAAAA
149327 TAAAATATA--TTTAATAAGTTAAGGTAAAA
1 TAAAATATATTTTTAAT-A-TTAAGGTAAAA
149356 TAAAATATATTTTTAATATTAA
1 TAAAATATATTTTTAATATTAA
149378 AATGTGAATT
Statistics
Matches: 87, Mismatches: 12, Indels: 24
0.71 0.10 0.20
Matches are distributed among these distances:
27 5 0.06
28 2 0.02
29 32 0.37
30 24 0.28
31 24 0.28
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
TAAAATATATTTTTAATATTAAGGTAAAA
Found at i:149611 original size:22 final size:19
Alignment explanation
Indices: 149584--149630 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
149574 AAATATATTG
149584 AATTAAAATAAATAATCTCTCT
1 AATTAAAAT--ATAATCT-TCT
149606 AATT-AAATATAATCTTCT
1 AATTAAAATATAATCTTCT
149624 AATTAAA
1 AATTAAA
149631 TGATGATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.29
19 9 0.38
21 4 0.17
22 4 0.17
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAATATAATCTTCT
Found at i:149626 original size:18 final size:19
Alignment explanation
Indices: 149595--149631 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
149585 ATTAAAATAA
149595 ATAATCTCTCTAATTAAAT
1 ATAATCTCTCTAATTAAAT
149614 ATAATCT-TCTAATTAAAT
1 ATAATCTCTCTAATTAAAT
149632 GATGATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATCTCTCTAATTAAAT
Found at i:149843 original size:44 final size:45
Alignment explanation
Indices: 149763--149856 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 45
149753 TGAATAAATT
149763 AAATAGTTATGTGATCTTATTAATAAAATTAAAAGATCGATAGTA
1 AAATAGTTATGTGATCTTATTAATAAAATTAAAAGATCGATAGTA
* *
149808 AAATAGTTATGTGAT-TTTTTGATAAAATTAAAAGATCGATAGTA
1 AAATAGTTATGTGATCTTATTAATAAAATTAAAAGATCGATAGTA
149852 AAATA
1 AAATA
149857 AAAAAACTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 32 0.68
45 15 0.32
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (45 bp):
AAATAGTTATGTGATCTTATTAATAAAATTAAAAGATCGATAGTA
Found at i:150428 original size:12 final size:13
Alignment explanation
Indices: 150411--150439 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
150401 CTTAGTTGCG
150411 AAAATTAAAA-TT
1 AAAATTAAAATTT
150423 AAAATTAAAATTT
1 AAAATTAAAATTT
150436 AAAA
1 AAAA
150440 CATTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:150437 original size:93 final size:94
Alignment explanation
Indices: 150278--150462 Score: 318
Period size: 93 Copynumber: 2.0 Consensus size: 94
150268 CTTGAACTGC
* *
150278 CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTGAAATTGAAATTT
1 CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
150343 AAAACATTCAATTCAAAATA-TTACCTGT
66 AAAACATTCAATTCAAAATACTTACCTGT
* *
150371 CCTTTCGGTACCATTTAATTTGCTGATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
1 CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
*
150436 AAAACATTCGATTCAAAATACTTACCT
66 AAAACATTCAATTCAAAATACTTACCT
150463 TTGATTGGTT
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
93 80 0.93
94 6 0.07
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (94 bp):
CCTTTCGATACCATTTAATTTGCTAATTGTCTTAGTTGCGAAAATTAAAATTAAAATTAAAATTT
AAAACATTCAATTCAAAATACTTACCTGT
Found at i:151822 original size:3 final size:3
Alignment explanation
Indices: 151808--151851 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
151798 ACAAAAACAC
151808 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT -AT AATT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A
151852 TTTTTTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:153113 original size:24 final size:22
Alignment explanation
Indices: 153086--153140 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
153076 ACAACATTTA
153086 ATAAATTACGAATTTTAT-ATAATT
1 ATAAATTA--AATTTTATAATAA-T
153110 ATAAATTTAAATTTTATAATAAT
1 ATAAA-TTAAATTTTATAATAAT
*
153133 ATTAATTA
1 ATAAATTA
153141 TATAACATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 3 0.11
23 13 0.46
24 9 0.32
25 3 0.11
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAATTAAATTTTATAATAAT
Found at i:153828 original size:19 final size:20
Alignment explanation
Indices: 153800--153839 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
153790 TATTATTAAC
*
153800 TAATT-AAAAATATTAAATT
1 TAATTAAAAAATAATAAATT
*
153819 TAATTTAAAAATAATAAATT
1 TAATTAAAAAATAATAAATT
153839 T
1 T
153840 GTTTTTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTAAAAAATAATAAATT
Found at i:157822 original size:30 final size:30
Alignment explanation
Indices: 157788--157844 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
157778 CATGAAGTAC
* *
157788 TAGAATTTAAATCTAATTTAAATTTTTAAT
1 TAGAATTCAAATCAAATTTAAATTTTTAAT
*
157818 TAGAATTCAAATCAAATTTAATTTTTT
1 TAGAATTCAAATCAAATTTAAATTTTT
157845 TAACTGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (30 bp):
TAGAATTCAAATCAAATTTAAATTTTTAAT
Found at i:161211 original size:42 final size:42
Alignment explanation
Indices: 161097--161341 Score: 303
Period size: 43 Copynumber: 5.8 Consensus size: 42
161087 GAACCAAAAT
*
161097 GCCGCAAAAGGTTGAGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * ** *
161140 GCCGCAAAAGGTTGATATCTATATAGGCGTTTTTGGAACTAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
161183 GTCGCAAAAGGTGATATCTATAGCGGCG-TTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
161224 GCCGCAATAGGTCACATATATAGCGGCGTTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCG-TTTTTGGAACAAAC
* **
161267 GCCGCAATAGGTCAGATAGATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* *
161309 ACCGCAAAAGGTCAGATCTATAGAGGCGTTTTT
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTT
161342 TATACAACGC
Statistics
Matches: 180, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
41 35 0.19
42 57 0.32
43 88 0.49
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (42 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Done.