Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004354.1 Hibiscus syriacus cultivar Beakdansim tig00009540_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: 177989
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:298 original size:22 final size:22
Alignment explanation
Indices: 263--315 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
253 ACATCCTACA
*
263 ACGTAATA-GTGCATTCCCCAC
1 ACGTAAGATGTGCATTCCCCAC
284 ACGTAAGATGTGCATTCCCCAC
1 ACGTAAGATGTGCATTCCCCAC
306 ACGTAAGATG
1 ACGTAAGATG
316 GAATGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (22 bp):
ACGTAAGATGTGCATTCCCCAC
Found at i:4152 original size:30 final size:31
Alignment explanation
Indices: 4118--4184 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
4108 TTAAAAAACA
4118 TAAGATATGCCCACTTTTGTTTT-ATTTAAT
1 TAAGATATGCCCACTTTTGTTTTAATTTAAT
* **
4148 TAAGATTTGTTCACTTTTGTTTTAATTTAAT
1 TAAGATATGCCCACTTTTGTTTTAATTTAAT
4179 TAAGAT
1 TAAGAT
4185 GTGATCACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.52
Consensus pattern (31 bp):
TAAGATATGCCCACTTTTGTTTTAATTTAAT
Found at i:4560 original size:24 final size:26
Alignment explanation
Indices: 4520--4577 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
4510 ATATATTAAG
*
4520 TATTTT-TAATTAACTT-A-TTGAAA
1 TATTTTATTATTAACTTAATTTGAAA
*
4543 TATTTTATTATTAACTTAATTTTAAA
1 TATTTTATTATTAACTTAATTTGAAA
4569 TATTTTATT
1 TATTTTATT
4578 TTCATTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 6 0.20
24 9 0.30
25 1 0.03
26 14 0.47
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTTTATTATTAACTTAATTTGAAA
Found at i:10521 original size:23 final size:24
Alignment explanation
Indices: 10483--10540 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
10473 AAATGAATTT
*
10483 ATAAAATTTTAA--AAAATA-AAA
1 ATAAATTTTTAATTAAAATATAAA
*
10504 ATAAATTTTTAATTAAAATATATA
1 ATAAATTTTTAATTAAAATATAAA
10528 AT-AATTTTTAATT
1 ATAAATTTTTAATT
10541 TTTTATAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 11 0.34
23 17 0.53
24 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAATTTTTAATTAAAATATAAA
Found at i:10844 original size:43 final size:42
Alignment explanation
Indices: 10779--10866 Score: 158
Period size: 43 Copynumber: 2.1 Consensus size: 42
10769 GAATTGAAGT
10779 GCAAAAATTTGATGGTTTTCAATTGTGTTAATACAGAACAAA
1 GCAAAAATTTGATGGTTTTCAATTGTGTTAATACAGAACAAA
*
10821 GCAAAAATTTTGATGGTTTTCAATTGTGTTCATACAGAACAAA
1 GCAAAAA-TTTGATGGTTTTCAATTGTGTTAATACAGAACAAA
10864 GCA
1 GCA
10867 TAAGCCGGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 7 0.16
43 37 0.84
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (42 bp):
GCAAAAATTTGATGGTTTTCAATTGTGTTAATACAGAACAAA
Found at i:12446 original size:14 final size:14
Alignment explanation
Indices: 12427--12453 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12417 TTTATTTTTT
12427 TAATATATATATAA
1 TAATATATATATAA
12441 TAATATATATATA
1 TAATATATATATA
12454 TATATGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATATATATAA
Found at i:12448 original size:12 final size:11
Alignment explanation
Indices: 12427--12458 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
12417 TTTATTTTTT
12427 TAATATATATA
1 TAATATATATA
12438 TAATA-ATATA
1 TAATATATATA
12448 T-ATATATATA
1 TAATATATATA
12458 T
1 T
12459 GGATGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.15
10 12 0.60
11 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATATATATA
Found at i:12716 original size:4 final size:4
Alignment explanation
Indices: 12707--12731 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12697 AGGCAATTGG
12707 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
12732 AAGATAAGAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:13273 original size:37 final size:36
Alignment explanation
Indices: 13198--13273 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
13188 TTTTTATATT
*
13198 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
13234 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
13271 TTT
1 TTT
13274 GTAGCATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:14527 original size:30 final size:30
Alignment explanation
Indices: 14492--14555 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
14482 ACATTTTATC
14492 TTAATTTACTAAATAT-TTTATATTATTACT
1 TTAATTTACTAAATATATTT-TATTATTACT
** * *
14522 TTAATTTTTTAAATATATTTTATTTTTATT
1 TTAATTTACTAAATATATTTTATTATTACT
14552 TTAA
1 TTAA
14556 CTTCAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTAATTTACTAAATATATTTTATTATTACT
Found at i:15044 original size:31 final size:31
Alignment explanation
Indices: 15009--15077 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
14999 AAAACATAAC
* *
15009 ATTTGGTCACTTTCATTTCATTTTGATTAAG
1 ATTTGGTCACTTTCATTTCACTTTAATTAAG
** * *
15040 ATTTGAACATTTTCGTTTCACTTTAATTAAG
1 ATTTGGTCACTTTCATTTCACTTTAATTAAG
*
15071 ATGTGGT
1 ATTTGGT
15078 AACTGAAGGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTTGGTCACTTTCATTTCACTTTAATTAAG
Found at i:18798 original size:14 final size:16
Alignment explanation
Indices: 18769--18800 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
18759 CGTTCGTGAA
18769 CGTTCGATTATATGTT
1 CGTTCGATTATATGTT
18785 CGTTC-ATT-TATGTT
1 CGTTCGATTATATGTT
18799 CG
1 CG
18801 AACAGAGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (16 bp):
CGTTCGATTATATGTT
Found at i:19069 original size:23 final size:24
Alignment explanation
Indices: 19043--19092 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
19033 GTTCGAATAA
* *
19043 GTTTTTTTGTGTTTGTGT-TGTTC
1 GTTTTATTGTGTTCGTGTATGTTC
*
19066 G-TTTATTGTGTTCGTTTATGTTC
1 GTTTTATTGTGTTCGTGTATGTTC
19089 GTTT
1 GTTT
19093 ATTATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 13 0.59
23 7 0.32
24 2 0.09
ACGTcount: A:0.04, C:0.06, G:0.24, T:0.66
Consensus pattern (24 bp):
GTTTTATTGTGTTCGTGTATGTTC
Found at i:23793 original size:171 final size:172
Alignment explanation
Indices: 23427--23830 Score: 555
Period size: 171 Copynumber: 2.3 Consensus size: 172
23417 GCCGTCGGTT
* * *
23427 AACTTGTTTCCAACACCAGGACTCGGACCGGAGTCAGTAAACTTGTTCCCTACACCGGGGCTCGG
1 AACTTATTTCCCACACCAGGACTCGGACCGGAGTCGGTAAACTTGTTCCCTACACCGGGGCTCGG
* * * * *
23492 CCCTCCATTCTTAATGCCTCCTATAATCTGACGACTATCGATTAACTTATTTTCGAAACCAGGAC
66 CCCCCCATTCTTAATGCCTCCAATAACCT-A-GACTATCGATTAACTTATTTTCCAAACCAGAAC
* * *
23557 TTGAAACGAAGTTTTTAATTCCACCTAGAGTGAAGCTATTAGTA
129 TTGAAACGAAGGTTTTAATGCCACCTAGAGTGAAGCTATCAGTA
* *
23601 AACTTATTTCCCACGCCAGGACTCGGACCGGAGTCGGTAAACTTGTTCCCTACACCTGGGCTCGG
1 AACTTATTTCCCACACCAGGACTCGGACCGGAGTCGGTAAACTTGTTCCCTACACCGGGGCTCGG
* * *
23666 CCCCCCATTCTTTATGCCTCCAATGACCT-GACTATC-AGTTAACTTA-TTTCCATCACCAGAAC
66 CCCCCCATTCTTAATGCCTCCAATAACCTAGACTATCGA-TTAACTTATTTTCCA-AACCAGAAC
*
23728 TTG-AACTGGAGGTTTTAATGCCACCTAGAGTGAAGCTATCAGTA
129 TTGAAAC-GAAGGTTTTAATGCCACCTAGAGTGAAGCTATCAGTA
* * *
23772 AATTTATTTCCCACACCAGGACTCGGACCGGACTCGGTAAACTTGTTCCCTACGCCGGG
1 AACTTATTTCCCACACCAGGACTCGGACCGGAGTCGGTAAACTTGTTCCCTACACCGGG
23831 ACTTGGACCT
Statistics
Matches: 205, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
170 9 0.04
171 112 0.55
174 84 0.41
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (172 bp):
AACTTATTTCCCACACCAGGACTCGGACCGGAGTCGGTAAACTTGTTCCCTACACCGGGGCTCGG
CCCCCCATTCTTAATGCCTCCAATAACCTAGACTATCGATTAACTTATTTTCCAAACCAGAACTT
GAAACGAAGGTTTTAATGCCACCTAGAGTGAAGCTATCAGTA
Found at i:27097 original size:60 final size:59
Alignment explanation
Indices: 26984--27097 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
26974 ATGTTCCCTC
* *
26984 ATTATAGAGTATTGTTTTATTAAATCTTATACTATTAAAAGTTATAAAATGATCTATGA
1 ATTATAGAATATTGTTTTATTAAATCTCATACTATTAAAAGTTATAAAATGATCTATGA
*
27043 ATTATAGAATATTGTTTTATTAAGTCCCTCA-ACTATT-AAAGATTATAAAATGATC
1 ATTATAGAATATTGTTTTATTAAAT--CTCATACTATTAAAAG-TTATAAAATGATC
27098 ATCCGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
59 27 0.55
60 19 0.39
61 3 0.06
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (59 bp):
ATTATAGAATATTGTTTTATTAAATCTCATACTATTAAAAGTTATAAAATGATCTATGA
Found at i:27384 original size:19 final size:21
Alignment explanation
Indices: 27360--27406 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
27350 AATAAAATAA
27360 CATTTTAT-A-GTTAGAGGAT
1 CATTTTATAACGTTAGAGGAT
*
27379 CATTTTATAACTTTTAGAGGAT
1 CATTTTATAAC-GTTAGAGGAT
27401 CATTTT
1 CATTTT
27407 TGTAGATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 1 0.04
22 15 0.62
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (21 bp):
CATTTTATAACGTTAGAGGAT
Found at i:27977 original size:29 final size:29
Alignment explanation
Indices: 27943--28001 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
27933 CCTAAATTAA
27943 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
27972 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
28001 T
1 T
28002 AGGTGAAAAT
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:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:32662 original size:29 final size:29
Alignment explanation
Indices: 32628--32686 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
32618 CCTAAATTAA
32628 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
32657 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
32686 T
1 T
32687 AGGTGAAAAT
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:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:42887 original size:12 final size:12
Alignment explanation
Indices: 42870--42898 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42860 AGATGAGCCT
42870 GAGCAGCCCGAG
1 GAGCAGCCCGAG
42882 GAGCAGCCCGAG
1 GAGCAGCCCGAG
42894 GAGCA
1 GAGCA
42899 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:55305 original size:19 final size:19
Alignment explanation
Indices: 55281--55332 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
55271 AAATAGCCTG
55281 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
55300 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
55319 GTGCATCGATGCAT
1 GTGCATCGATGCAT
55333 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTT
Found at i:55305 original size:83 final size:84
Alignment explanation
Indices: 55213--55396 Score: 212
Period size: 83 Copynumber: 2.2 Consensus size: 84
55203 CGTTGGAACA
*
55213 CTTGATGCATCGGTGCACCAAGTGTGCATCGATGCATTAAATGCATTCGATG-TTTGAAAAATAG
1 CTTG-TGCATCGGTGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATA-
55277 CCT-G-GTGCATCGATGCATGG
63 CCTAGAGTGCATCGATGCATGG
* ***** **
55297 CTTGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTT
1 CTTGTGCATCGGTGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATACCT
55362 AGAGTGCATCGATGCATGG
66 AGAGTGCATCGATGCATGG
***
55381 AGAGTGCATCGGTGCA
1 CTTGTGCATCGGTGCA
55397 TGGAATGCAT
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
82 1 0.01
83 47 0.56
84 36 0.43
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (84 bp):
CTTGTGCATCGGTGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATACCT
AGAGTGCATCGATGCATGG
Found at i:55386 original size:19 final size:19
Alignment explanation
Indices: 55362--55412 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
55352 GAAAATATTT
55362 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
55381 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
55400 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
55413 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:55398 original size:84 final size:83
Alignment explanation
Indices: 55235--55399 Score: 226
Period size: 83 Copynumber: 2.0 Consensus size: 83
55225 GTGCACCAAG
* ***
55235 TGTGCATCGATGCATTAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGCTT
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGAGA
55300 GTGCATCGATGCATGGCT
66 GTGCATCGATGCATGGCT
**
55318 TGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATA-TTTAGAGTGCATCGATGCATGG
1 TGTGCATCGATGCATCAAATGCATTCGATG-TTTGAAAAATAGCCT-G-GTGCATCGATGCATGG
*
55381 AGAGTGCATCGGTGCATGG
63 AGAGTGCATCGATGCATGG
55400 AATGCATTCG
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
82 1 0.01
83 36 0.50
84 35 0.49
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (83 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGAGA
GTGCATCGATGCATGGCT
Found at i:55453 original size:20 final size:20
Alignment explanation
Indices: 55428--55483 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
55418 TTAATTCATC
*
55428 GATGCATCGATGCATGGACT
1 GATGCATCGGTGCATGGACT
55448 GATGCATCGGTGCATGGACT
1 GATGCATCGGTGCATGGACT
55468 GATGCATCGGTGCATG
1 GATGCATCGGTGCATG
55484 CATTTGAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (20 bp):
GATGCATCGGTGCATGGACT
Found at i:60723 original size:30 final size:30
Alignment explanation
Indices: 60687--60746 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
60677 CTATGTATGG
*
60687 AACGAATAGCGCATGCAATTCAAGGAAGTA
1 AACGAATAGCGCACGCAATTCAAGGAAGTA
60717 AACGAATAGCGCACGCAATTCAAGGAAGTA
1 AACGAATAGCGCACGCAATTCAAGGAAGTA
60747 TTGAGGCCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.15
Consensus pattern (30 bp):
AACGAATAGCGCACGCAATTCAAGGAAGTA
Found at i:62958 original size:29 final size:30
Alignment explanation
Indices: 62902--62971 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
62892 GATTGTATAT
* * *
62902 AATAATTTAAATACCTAATTTAATAAAA-A
1 AATAATTTAAATACCCAATATAAAAAAACA
62931 AATAATTTAAATACCCAGA-ATAAAAAAACA
1 AATAATTTAAATACCCA-ATATAAAAAAACA
62961 ACATAATTTAA
1 A-ATAATTTAA
62972 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 23 0.66
30 3 0.09
31 9 0.26
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (30 bp):
AATAATTTAAATACCCAATATAAAAAAACA
Found at i:64265 original size:13 final size:14
Alignment explanation
Indices: 64235--64276 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
64225 GATTGATAAA
64235 ATTA-CTCATATTT
1 ATTATCTCATATTT
64248 ATTATCTCATATTTTT
1 ATTATCTCATA--TTT
*
64264 ATTATCTCGTATT
1 ATTATCTCATATT
64277 ACTTTAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
16 13 0.52
ACGTcount: A:0.26, C:0.14, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTATCTCATATTT
Found at i:64266 original size:16 final size:16
Alignment explanation
Indices: 64245--64276 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64235 ATTACTCATA
64245 TTTATTATCTCATATT
1 TTTATTATCTCATATT
*
64261 TTTATTATCTCGTATT
1 TTTATTATCTCATATT
64277 ACTTTAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTATTATCTCATATT
Found at i:70721 original size:16 final size:16
Alignment explanation
Indices: 70700--70738 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
70690 GGCAGCCTAC
*
70700 TACCCCACCTCTCACT
1 TACCCCACCTCCCACT
70716 TACCCCACCTCCCACT
1 TACCCCACCTCCCACT
70732 TACCCCA
1 TACCCCA
70739 TTGCATATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (16 bp):
TACCCCACCTCCCACT
Found at i:75025 original size:60 final size:60
Alignment explanation
Indices: 74908--75065 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
74898 TGAATTTGGG
* ** * * *
74908 GATGAAATTGAAATATTC-AAAGTTTGGGGA-CTAATTTATAAAGAGGGTCATAGTTTAGA
1 GATGAAATTAAAATATTCAAAAGTTTAAGGATC-AATTTAGAAAGAGAGTCACAGTTTAGA
* *
74967 GATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTTAGAATGAGAGTCACGGTTTAGA
1 GATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTTAGAAAGAGAGTCACAGTTTAGA
* * *
75027 GATGAAACTAGAATATTCAAAAGTTTAAGGATTAATTTA
1 GATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTTA
75066 AAGTTAAAGA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 17 0.20
60 68 0.79
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (60 bp):
GATGAAATTAAAATATTCAAAAGTTTAAGGATCAATTTAGAAAGAGAGTCACAGTTTAGA
Found at i:75070 original size:19 final size:19
Alignment explanation
Indices: 75046--75084 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
75036 AGAATATTCA
*
75046 AAAGTTTAAGGAT-TAATTT
1 AAAG-TTAAAGATATAATTT
75065 AAAGTTAAAGATATAATTT
1 AAAGTTAAAGATATAATTT
75084 A
1 A
75085 GGGACATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (19 bp):
AAAGTTAAAGATATAATTT
Found at i:80113 original size:29 final size:26
Alignment explanation
Indices: 80079--80152 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
80069 TTATTATAAA
80079 TATAAAATATTGATATTAATATTATTTAT
1 TATAAAATATT-ATA-TAATATTATTT-T
80108 TATAAAAT-TTCA-ATAATATTATTTT
1 TATAAAATATT-ATATAATATTATTTT
*
80133 TA-AAAGTATTATAGTAATAT
1 TATAAAATATTATA-TAATAT
80153 AAGCTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 5 0.12
25 6 0.15
26 17 0.43
27 1 0.03
28 3 0.08
29 8 0.20
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (26 bp):
TATAAAATATTATATAATATTATTTT
Found at i:80382 original size:26 final size:27
Alignment explanation
Indices: 80353--80405 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
80343 ATAACTGAAT
*
80353 ATATGATTATAA-TATTGAA-AAATATA
1 ATATGATTAAAATTATT-AATAAATATA
80379 ATATGATTAAAATTATTAATAAATATA
1 ATATGATTAAAATTATTAATAAATATA
80406 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATGATTAAAATTATTAATAAATATA
Found at i:85495 original size:9 final size:9
Alignment explanation
Indices: 85481--85546 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
85471 GGCTGCTGGA
85481 AACCGGTTT
1 AACCGGTTT
85490 AACCGGTTTT
1 AACCGG-TTT
85500 CAACCGGTTCT
1 -AACCGGTT-T
* *
85511 GACTGGTTT
1 AACCGGTTT
*
85520 CAACCGGTTCG
1 -AACCGGTT-T
85531 AACCGGTTT
1 AACCGGTTT
*
85540 GACCGGT
1 AACCGGT
85547 CTGAATCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
9 13 0.29
10 25 0.56
11 7 0.16
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:85506 original size:20 final size:21
Alignment explanation
Indices: 85481--85539 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
85471 GGCTGCTGGA
85481 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
* *
85501 AACCGGTTCTGACTGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
85521 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
85540 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:85528 original size:10 final size:10
Alignment explanation
Indices: 85481--85539 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
85471 GGCTGCTGGA
85481 AACCGGTTT-
1 AACCGGTTTC
85490 AACCGGTTTTC
1 AACCGG-TTTC
85501 AACCGG-TTC
1 AACCGGTTTC
* *
85510 TGACTGGTTTC
1 -AACCGGTTTC
85521 AACCGG-TTC
1 AACCGGTTTC
85530 GAACCGGTTT
1 -AACCGGTTT
85540 GACCGGTCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 12 0.30
10 17 0.43
11 11 0.28
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:85535 original size:30 final size:28
Alignment explanation
Indices: 85485--85542 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
85475 GCTGGAAACC
85485 GGTTTAACCGGTTTTCAACCGGTTCTGACT
1 GGTTTAACCGG-TTTCAACCGGTT-TGACT
85515 GGTTTCAACCGG-TTCGAACCGGTTTGAC
1 GGTTT-AACCGGTTTC-AACCGGTTTGAC
85543 CGGTCTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.27
30 13 0.50
31 6 0.23
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (28 bp):
GGTTTAACCGGTTTCAACCGGTTTGACT
Found at i:85546 original size:19 final size:20
Alignment explanation
Indices: 85522--85574 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
85512 ACTGGTTTCA
*
85522 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGATTTG
*
85541 ACCGG-TCTGAATCGATTTG
1 ACCGGTTCTGAACCGATTTG
*
85560 ACCGG-TCTGACCCGA
1 ACCGGTTCTGAACCGA
85575 CCCAACCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 2 0.07
19 27 0.93
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (20 bp):
ACCGGTTCTGAACCGATTTG
Found at i:85589 original size:17 final size:17
Alignment explanation
Indices: 85567--85627 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
85557 TTGACCGGTC
85567 TGACCCGACCCAACCGT
1 TGACCCGACCCAACCGT
85584 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCC-A----ACCGT
*
85606 TGACCCGACCCGACCGT
1 TGACCCGACCCAACCGT
85623 TGACC
1 TGACC
85628 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 21 0.55
18 1 0.03
22 16 0.42
ACGTcount: A:0.20, C:0.48, G:0.21, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCAACCGT
Found at i:85593 original size:22 final size:22
Alignment explanation
Indices: 85568--85620 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
85558 TGACCGGTCT
85568 GACCCGACCCAACCGTTGACCC
1 GACCCGACCCAACCGTTGACCC
*
85590 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCAACCGTTGACCC
85612 GACCCGACC
1 GACCCGACC
85621 GTTGACCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.08
Consensus pattern (22 bp):
GACCCGACCCAACCGTTGACCC
Found at i:92582 original size:10 final size:9
Alignment explanation
Indices: 92547--92646 Score: 74
Period size: 10 Copynumber: 10.4 Consensus size: 9
92537 CTGCTCGAAA
*
92547 ACCGGTTTA
1 ACCGGTTTG
*
92556 ACCGGTTTTCA
1 ACCGG-TTT-G
92567 ACCGGTTCTG
1 ACCGGTT-TG
92577 ACCGGTTTG
1 ACCGGTTTG
*
92586 ACCGGTTTCA
1 ACCGGTTT-G
*
92596 ACCGGTTCG
1 ACCGGTTTG
*
92605 AACCAGTTTG
1 -ACCGGTTTG
*
92615 ACCGGTCTG
1 ACCGGTTTG
*
92624 AATCGGTTTG
1 -ACCGGTTTG
*
92634 ACCAGTTTG
1 ACCGGTTTG
92643 ACCG
1 ACCG
92647 TTGACCGTTG
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:92591 original size:19 final size:18
Alignment explanation
Indices: 92547--92646 Score: 74
Period size: 19 Copynumber: 5.2 Consensus size: 18
92537 CTGCTCGAAA
* *
92547 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGG-TTT-G
92567 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTTTG
* *
92586 ACCGGTTTCAACCGGTTCG
1 ACCGGTTT-GACCGGTTTG
* *
92605 AACCAGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTTTG
* *
92624 AATCGGTTTGACCAGTTTG
1 -ACCGGTTTGACCGGTTTG
92643 ACCG
1 ACCG
92647 TTGACCGTTG
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
18 4 0.06
19 37 0.58
20 17 0.27
21 6 0.09
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:97097 original size:2 final size:2
Alignment explanation
Indices: 97085--97114 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
97075 TTTGTAGTGA
97085 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
97115 AGCTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:97871 original size:16 final size:17
Alignment explanation
Indices: 97838--97871 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
97828 CCTTCTGTTT
*
97838 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
97855 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
97871 T
1 T
97872 AATAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:103445 original size:15 final size:15
Alignment explanation
Indices: 103400--103447 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
103390 AGACCTTACT
* *
103400 CGCCCCGCATCCGCT
1 CGCCCCACATCCGCC
*
103415 CGCCCCATATCCGCC
1 CGCCCCACATCCGCC
*
103430 CGCCCCACATCTGCC
1 CGCCCCACATCCGCC
103445 CGC
1 CGC
103448 ACACTAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.10, C:0.60, G:0.17, T:0.12
Consensus pattern (15 bp):
CGCCCCACATCCGCC
Found at i:103731 original size:22 final size:20
Alignment explanation
Indices: 103704--103743 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
103694 ATTAATAGTG
103704 TAATTAAAATGTTAATAATTGT
1 TAATTAAAAT-TTAA-AATTGT
103726 TAATTAAAATTTAAAATT
1 TAATTAAAATTTAAAATT
103744 AACATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAATTAAAATTTAAAATTGT
Found at i:105287 original size:2 final size:2
Alignment explanation
Indices: 105280--105314 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
105270 ATTCTAACAA
105280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
105315 AAATTTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105492 original size:10 final size:10
Alignment explanation
Indices: 105477--105507 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
105467 CGATTTTAAT
105477 TTTAATCTAA
1 TTTAATCTAA
105487 TTTAATCTAA
1 TTTAATCTAA
*
105497 TTTAATTTAA
1 TTTAATCTAA
105507 T
1 T
105508 AAAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTAATCTAA
Found at i:110437 original size:20 final size:20
Alignment explanation
Indices: 110412--110457 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
110402 TATTCCCTGG
* *
110412 TAATCTTTTATTTCTAGTGA
1 TAATCTTTTATTTCCACTGA
110432 TAATC-TTTATTTCCACTGA
1 TAATCTTTTATTTCCACTGA
110451 TAATCTT
1 TAATCTT
110458 ACATTCCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (20 bp):
TAATCTTTTATTTCCACTGA
Found at i:112549 original size:29 final size:28
Alignment explanation
Indices: 112476--112565 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
112466 AAAAGAATAA
112476 GGCCCTAGA-TGTAAAGATTAAAA-AAGGG
1 GGCCCTA-ATTGTAAA-ATTAAAAGAAGGG
* *
112504 GGCCCTAGTTATAAAAATTAAAAGAAGGG
1 GGCCCTAATTGT-AAAATTAAAAGAAGGG
*
112533 GGCCCTAATTGTGAAAATTAAAAG-AGCG
1 GGCCCTAATTGT-AAAATTAAAAGAAGGG
112561 GGCCC
1 GGCCC
112566 ATGAGCAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 24 0.45
29 29 0.55
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (28 bp):
GGCCCTAATTGTAAAATTAAAAGAAGGG
Found at i:118645 original size:30 final size:31
Alignment explanation
Indices: 118606--118678 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
118596 TTCAACGTCA
* *
118606 AAGTGACCAAAACTTAATAAAACTATAACAT
1 AAGTAACCAAAACTTAATAAAACGATAACAT
* *
118637 -AGTAACCAAAATTTAATAAAACGATAACTT
1 AAGTAACCAAAACTTAATAAAACGATAACAT
*
118667 AAGTGACCAAAA
1 AAGTAACCAAAA
118679 GTGTACAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.55, C:0.15, G:0.08, T:0.22
Consensus pattern (31 bp):
AAGTAACCAAAACTTAATAAAACGATAACAT
Found at i:119546 original size:22 final size:21
Alignment explanation
Indices: 119493--119534 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
119483 AAAAAAAGAT
119493 AAAT-GAAAAAATAGCCAAAA
1 AAATCGAAAAAATAGCCAAAA
119513 AAATCGAAAAAATATGCCAAAA
1 AAATCGAAAAAATA-GCCAAAA
119535 CATATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.67, C:0.12, G:0.10, T:0.12
Consensus pattern (21 bp):
AAATCGAAAAAATAGCCAAAA
Found at i:120532 original size:37 final size:37
Alignment explanation
Indices: 120459--120533 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
120449 GTTGAAAAAT
* *
120459 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
120496 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
120533 A
1 A
120534 GGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:127213 original size:18 final size:17
Alignment explanation
Indices: 127192--127233 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
127182 AATATGATAT
*
127192 AATTATATAATTTTATTA
1 AATTATATAATTTTA-AA
*
127210 AATTTTATAATTTTAAA
1 AATTATATAATTTTAAA
127227 AATTATA
1 AATTATA
127234 ATTTAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATATAATTTTAAA
Found at i:154018 original size:7 final size:8
Alignment explanation
Indices: 154003--154035 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
153993 TATGAATATA
154003 TTAAATTT
1 TTAAATTT
154011 TT-AATTT
1 TTAAATTT
154018 TTAAATTT
1 TTAAATTT
154026 TTAAATTT
1 TTAAATTT
154034 TT
1 TT
154036 TCAGTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTAAATTT
Found at i:154023 original size:15 final size:16
Alignment explanation
Indices: 154003--154035 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
153993 TATGAATATA
154003 TTAAATTTTT-AATTT
1 TTAAATTTTTAAATTT
154018 TTAAATTTTTAAATTT
1 TTAAATTTTTAAATTT
154034 TT
1 TT
154036 TCAGTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAAATTTTTAAATTT
Found at i:158183 original size:26 final size:26
Alignment explanation
Indices: 158154--158204 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
158144 AACACTGCTA
* * * *
158154 TTATTATAAATCATCGTCAGATTTTT
1 TTATTAAAAATAATCATCAAATTTTT
158180 TTATTAAAAATAATCATCAAATTTT
1 TTATTAAAAATAATCATCAAATTTT
158205 ATTCTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (26 bp):
TTATTAAAAATAATCATCAAATTTTT
Found at i:158475 original size:31 final size:31
Alignment explanation
Indices: 158440--158515 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
158430 TCAGAAAACA
158440 TAAGATATGATCACTTTCATTTTTATTTAAT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
* **
158471 TAAGATATGATTACTTTTGTTTTTATTTAAT
1 TAAGATATGATCACTTTCATTTTTATTTAAT
*
158502 TAAGATGTGATCAC
1 TAAGATATGATCAC
158516 CCCGAGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (31 bp):
TAAGATATGATCACTTTCATTTTTATTTAAT
Found at i:159570 original size:31 final size:31
Alignment explanation
Indices: 159481--159572 Score: 148
Period size: 31 Copynumber: 3.0 Consensus size: 31
159471 TGACCACATC
*
159481 TTAATTAAATAAAAACGAAAATAACCATATT
1 TTAATTAAATAAAAACGAAAATAATCATATT
*
159512 TTAATTAAATAAAAACGAAAATGATCATATT
1 TTAATTAAATAAAAACGAAAATAATCATATT
* *
159543 TTAATTAAATAAAAACGAAAGTTATCATAT
1 TTAATTAAATAAAAACGAAAATAATCATAT
159573 CTTATGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAATAATCATATT
Found at i:159865 original size:2 final size:2
Alignment explanation
Indices: 159858--159895 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
159848 TTTATATTCG
159858 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
159896 CGTATGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:163032 original size:20 final size:22
Alignment explanation
Indices: 162998--163040 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
162988 TTGATTAATT
162998 TTAATATAAAATTTTT-ATATG
1 TTAATATAAAATTTTTAATATG
*
163019 TTAA-ATAAATTTTTTAATATG
1 TTAATATAAAATTTTTAATATG
163040 T
1 T
163041 ATTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTAATATAAAATTTTTAATATG
Found at i:163359 original size:12 final size:11
Alignment explanation
Indices: 163327--163365 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
163317 TATTAGTTGA
*
163327 ATAAAATTAAT
1 ATAAAAATAAT
163338 -TAAAAATAAT
1 ATAAAAATAAT
163348 ATAAATAATAAT
1 ATAAA-AATAAT
163360 ATAAAA
1 ATAAAA
163366 TTTGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:171706 original size:5 final size:5
Alignment explanation
Indices: 171696--171794 Score: 171
Period size: 5 Copynumber: 19.8 Consensus size: 5
171686 CTCATATTAA
171696 ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG
1 ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG
* * *
171746 ATCAG ATCAG ATCAG ATCAA ATCAG ATCAG ATCAA ATCAC ATCAG ATCA
1 ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCAG ATCA
171795 AAATCACCAG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 89 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (5 bp):
ATCAG
Done.