Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 95 of 131
Found at i:17075958 original size:16 final size:16
Alignment explanation
Indices: 17075937--17075987 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
17075927 CGAATAACTA
17075937 AACTAAAGAAAGAAAG
1 AACTAAAGAAAGAAAG
**
17075953 AACTAAAG-AACTAAG
1 AACTAAAGAAAGAAAG
17075968 AACTAAAAGAAAGAAGAG
1 AACT-AAAGAAAGAA-AG
17075986 AA
1 AA
17075988 GTGATGAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 12 0.43
17 3 0.11
18 4 0.14
ACGTcount: A:0.67, C:0.08, G:0.18, T:0.08
Consensus pattern (16 bp):
AACTAAAGAAAGAAAG
Found at i:17075960 original size:8 final size:8
Alignment explanation
Indices: 17075937--17075974 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
17075927 CGAATAACTA
17075937 AACTAAAG
1 AACTAAAG
**
17075945 AAAGAAAG
1 AACTAAAG
17075953 AACTAAAG
1 AACTAAAG
17075961 AACT-AAG
1 AACTAAAG
17075968 AACTAAA
1 AACTAAA
17075975 AGAAAGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.66, C:0.11, G:0.13, T:0.11
Consensus pattern (8 bp):
AACTAAAG
Found at i:17085062 original size:22 final size:22
Alignment explanation
Indices: 17085023--17085065 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17085013 CTCTATTTTT
17085023 TTTTAGTTTTTAGTTTTAGTTC
1 TTTTAGTTTTTAGTTTTAGTTC
*
17085045 TTTTATTTCTTTAG-TTTAGTT
1 TTTTAGTT-TTTAGTTTTAGTT
17085066 ATTAGCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.70
Consensus pattern (22 bp):
TTTTAGTTTTTAGTTTTAGTTC
Found at i:17092219 original size:50 final size:50
Alignment explanation
Indices: 17092152--17092251 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
17092142 CCACCTATTA
17092152 CTTCAAGTGTATTCTTGTAGTTCTCTGCATATTAGCTCACATCCACCAAC
1 CTTCAAGTGTATTCTTGTAGTTCTCTGCATATTAGCTCACATCCACCAAC
17092202 CTTCAAGTGTATTCTTGTAGTTCTCTGCATATTAGCTCACATCCACCAAC
1 CTTCAAGTGTATTCTTGTAGTTCTCTGCATATTAGCTCACATCCACCAAC
17092252 AGTTCCTTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTCAAGTGTATTCTTGTAGTTCTCTGCATATTAGCTCACATCCACCAAC
Found at i:17110221 original size:2 final size:2
Alignment explanation
Indices: 17110214--17110246 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17110204 AGAAATACCA
17110214 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 A
17110247 AGCATGGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17114789 original size:3 final size:3
Alignment explanation
Indices: 17114781--17114831 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
17114771 TCGTTTCCTT
17114781 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
17114829 TTC
1 TTC
17114832 CACCTTCAGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:17115287 original size:7 final size:7
Alignment explanation
Indices: 17115271--17115340 Score: 63
Period size: 7 Copynumber: 10.3 Consensus size: 7
17115261 TGTAAAAGCA
*
17115271 TTTTTCT
1 TTTTTAT
17115278 TTTTTAT
1 TTTTTAT
*
17115285 TTTCTA-
1 TTTTTAT
17115291 TTTTTAT
1 TTTTTAT
17115298 TTTTTA-
1 TTTTTAT
**** *
17115304 AAAGTAC
1 TTTTTAT
17115311 TTTTTAT
1 TTTTTAT
17115318 TTTTTAT
1 TTTTTAT
17115325 TTTTTAT
1 TTTTTAT
17115332 TTTTTAT
1 TTTTTAT
17115339 TT
1 TT
17115341 CATTTAAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
6 7 0.14
7 42 0.86
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTAT
Found at i:17115322 original size:40 final size:41
Alignment explanation
Indices: 17115263--17115349 Score: 115
Period size: 40 Copynumber: 2.1 Consensus size: 41
17115253 GTTTGGTTTG
*
17115263 TAAAAGCATTTTTCTTTTTTATTTTCTA-TTTTTATTT-TT
1 TAAAAGCATTTTTATTTTTTATTTTCTATTTTTTATTTATT
* *
17115302 TAAAAGTACTTTTTATTTTTTATTTTTTATTTTTTATTTCATT
1 TAAAAGCA-TTTTTATTTTTTATTTTCTATTTTTTATTT-ATT
17115345 TAAAA
1 TAAAA
17115350 ATGTGTTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
39 7 0.17
40 18 0.44
41 9 0.22
43 7 0.17
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (41 bp):
TAAAAGCATTTTTATTTTTTATTTTCTATTTTTTATTTATT
Found at i:17120008 original size:16 final size:16
Alignment explanation
Indices: 17119987--17120017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17119977 AAACGATCAA
17119987 ATCATTTCAAGTTTGG
1 ATCATTTCAAGTTTGG
*
17120003 ATCATTTCAATTTTG
1 ATCATTTCAAGTTTG
17120018 AATTAAGTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
ATCATTTCAAGTTTGG
Found at i:17120203 original size:14 final size:15
Alignment explanation
Indices: 17120167--17120208 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
17120157 AATATAATTC
17120167 AATTATATAAAAATGA
1 AATTAT-TAAAAATGA
*
17120183 AACTATTAAAAAT-A
1 AATTATTAAAAATGA
17120197 AATTATTTAAAA
1 AATTA-TTAAAA
17120209 GTAATTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATTATTAAAAATGA
Found at i:17120557 original size:26 final size:26
Alignment explanation
Indices: 17120527--17120627 Score: 121
Period size: 26 Copynumber: 3.9 Consensus size: 26
17120517 GGCCCGAACA
*
17120527 GCCCAATTAGACCCATTGGTGTCCGG
1 GCCCAATTAGGCCCATTGGTGTCCGG
** * *
17120553 GCCCAATTAGGCTTATTGGTGTTCAG
1 GCCCAATTAGGCCCATTGGTGTCCGG
* *
17120579 GCCCAATTAGGCCCATTGGTGTTCGA
1 GCCCAATTAGGCCCATTGGTGTCCGG
* *
17120605 GCCTAATTAGGCCCATTGATGTC
1 GCCCAATTAGGCCCATTGGTGTC
17120628 ACTATTATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (26 bp):
GCCCAATTAGGCCCATTGGTGTCCGG
Found at i:17120657 original size:6 final size:6
Alignment explanation
Indices: 17120646--17120670 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17120636 TTGATTATTA
17120646 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
17120671 CTTTCTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:17121716 original size:11 final size:11
Alignment explanation
Indices: 17121675--17121708 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17121665 CAACAAAAAA
17121675 ATAATAAAATAT
1 ATAA-AAAATAT
*
17121687 ATAAAATATAT
1 ATAAAAAATAT
17121698 ATAAAAAATAT
1 ATAAAAAATAT
17121709 TAGAAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:17125624 original size:12 final size:11
Alignment explanation
Indices: 17125611--17125734 Score: 53
Period size: 12 Copynumber: 10.6 Consensus size: 11
17125601 AACAAAAGAG
17125611 AAAGAGAAAAA
1 AAAGAGAAAAA
*
17125622 GAAACAAGAAAAA
1 -AAA-GAGAAAAA
* *
17125635 AATGTGCAAAAA
1 AAAGAG-AAAAA
17125647 AAAGAGAAAAAA
1 AAAGAG-AAAAA
*
17125659 ATAAAAGTTAAAAA
1 A-AAGAG--AAAAA
17125673 AAA-AGAAAAA
1 AAAGAGAAAAA
17125683 AAAGCA-AAAAA
1 AAAG-AGAAAAA
17125694 AAA-A-AAACAA
1 AAAGAGAAA-AA
17125704 ACAAGA-AAAGAA
1 A-AAGAGAAA-AA
17125716 AAA-ATGAAAGAA
1 AAAGA-GAAA-AA
17125728 AAAGAGA
1 AAAGAGA
17125735 CAAAGGAGGA
Statistics
Matches: 90, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
9 4 0.04
10 12 0.13
11 13 0.14
12 41 0.46
13 14 0.16
14 6 0.07
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAGAGAAAAA
Found at i:17125691 original size:18 final size:19
Alignment explanation
Indices: 17125670--17125719 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
17125660 TAAAAGTTAA
*
17125670 AAAAAAAGAAAAAA-AAGC
1 AAAAAAAGAAAAAACAAAC
17125688 AAAAAAA-AAAAAACAAAC
1 AAAAAAAGAAAAAACAAAC
*
17125706 AAGAAAAGAAAAAA
1 AAAAAAAGAAAAAA
17125720 TGAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 16 0.57
19 6 0.21
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAACAAAC
Found at i:17125695 original size:14 final size:15
Alignment explanation
Indices: 17125668--17125718 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
17125658 AATAAAAGTT
17125668 AAAAA-AAAAGAAAA
1 AAAAACAAAAGAAAA
*
17125682 AAAAGCAAAA-AAAA
1 AAAAACAAAAGAAAA
17125696 AAAAACAAACAAGAAAA
1 AAAAAC-AA-AAGAAAA
17125713 GAAAAA
1 -AAAAA
17125719 ATGAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 13 0.43
15 6 0.20
16 2 0.07
17 4 0.13
18 5 0.17
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAGAAAA
Found at i:17125698 original size:27 final size:27
Alignment explanation
Indices: 17125642--17125700 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
17125632 AAAAATGTGC
* ***
17125642 AAAAAAAAGAGAAAAAAATAAAAGTTA
1 AAAAAAAAGAGAAAAAAACAAAAAAAA
17125669 AAAAAAAAGA-AAAAAAAGCAAAAAAAA
1 AAAAAAAAGAGAAAAAAA-CAAAAAAAA
17125696 AAAAA
1 AAAAA
17125701 CAAACAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.05
Consensus pattern (27 bp):
AAAAAAAAGAGAAAAAAACAAAAAAAA
Found at i:17126820 original size:85 final size:84
Alignment explanation
Indices: 17126669--17126848 Score: 195
Period size: 85 Copynumber: 2.1 Consensus size: 84
17126659 TTATGAAATC
* ** *
17126669 TTTGTGAATCTATAACCTTTGAGAAACTTGGGGTCTTGTGAATTTTTTTTCTTACAAACCTGAAA
1 TTTGTGAATCTAGAACCTTTGAGAAACTTGGGGTCTTACGAATTTTTTTTCTTACAAACCTAAAA
*
17126734 AT-TCTTGTGAATTTTACATT
66 ATCT-TTGTGAATCTTACA-T
** ** *
17126754 TTTGTGAATCTAGGTCCTTTGCA-AAACTT-GGGTCTTACGAATCTTTTTTTCTTATGAACTTAA
1 TTTGTGAATCTAGAACCTTTG-AGAAACTTGGGGTCTTACGAAT-TTTTTTTCTTACAAACCTAA
*
17126817 AAATCTTTGTGAATCTTGCAT
64 AAATCTTTGTGAATCTTACAT
*
17126838 CTTGTGAATCT
1 TTTGTGAATCT
17126849 TTTATTTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
84 22 0.28
85 56 0.70
86 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (84 bp):
TTTGTGAATCTAGAACCTTTGAGAAACTTGGGGTCTTACGAATTTTTTTTCTTACAAACCTAAAA
ATCTTTGTGAATCTTACAT
Found at i:17127640 original size:26 final size:25
Alignment explanation
Indices: 17127604--17127677 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
17127594 ACACCTATTT
17127604 GTGTCCAGACCCAATTAGGCCAATTG
1 GTGTCC-GACCCAATTAGGCCAATTG
* * * * *
17127630 GTGTCTTGACCTAATTTGGCCCATTT
1 GTGTC-CGACCCAATTAGGCCAATTG
17127656 GTGTCCGAGCCCAATTAGGCCA
1 GTGTCCGA-CCCAATTAGGCCA
17127678 TTGATGTTCG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
25 2 0.05
26 35 0.95
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (25 bp):
GTGTCCGACCCAATTAGGCCAATTG
Found at i:17127729 original size:26 final size:26
Alignment explanation
Indices: 17127664--17127736 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
17127654 TTGTGTCCGA
* *
17127664 GCCCAATTAGG-CCATTGATGTTCGG
1 GCCCAATTAGGCCCATTAATGTTCAG
** *
17127689 GCCCAATTAAACCCATTAATGTTTAG
1 GCCCAATTAGGCCCATTAATGTTCAG
* *
17127715 GCCCAACTAGGCCCATTTATGT
1 GCCCAATTAGGCCCATTAATGT
17127737 CACTATTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (26 bp):
GCCCAATTAGGCCCATTAATGTTCAG
Found at i:17127807 original size:3 final size:3
Alignment explanation
Indices: 17127799--17127841 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
17127789 TCTATGTTTA
17127799 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17127842 TTCTTCTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17128648 original size:20 final size:21
Alignment explanation
Indices: 17128625--17128670 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
17128615 TCTATTTTCA
*
17128625 TTTTATT-TTTTGGTTTGATT
1 TTTTATTGTTTTGATTTGATT
*
17128645 TTTT-TTGTTTTGATTTTATT
1 TTTTATTGTTTTGATTTGATT
17128665 TATTTA
1 T-TTTA
17128671 ACTTCACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.10
20 16 0.76
21 3 0.14
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (21 bp):
TTTTATTGTTTTGATTTGATT
Found at i:17128650 original size:15 final size:15
Alignment explanation
Indices: 17128630--17128661 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17128620 TTTCATTTTA
17128630 TTTTTTGGTTTGATT
1 TTTTTTGGTTTGATT
*
17128645 TTTTTTGTTTTGATT
1 TTTTTTGGTTTGATT
17128660 TT
1 TT
17128662 ATTTATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.00, G:0.16, T:0.78
Consensus pattern (15 bp):
TTTTTTGGTTTGATT
Found at i:17128807 original size:9 final size:9
Alignment explanation
Indices: 17128793--17128835 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
17128783 TATTTACAAC
17128793 AAAAAAAAT
1 AAAAAAAAT
17128802 -AAAAAAAT
1 AAAAAAAAT
*
17128810 AAAAAATAT
1 AAAAAAAAT
* *
17128819 ATATAAAAT
1 AAAAAAAAT
17128828 AAAAAAAA
1 AAAAAAAA
17128836 ACCTTTTAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:17134867 original size:27 final size:26
Alignment explanation
Indices: 17134836--17134894 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 26
17134826 GAGATTGTAT
17134836 TGAAAGCAAAAACAAAAGTGTAAAGG
1 TGAAAGCAAAAACAAAAGTGTAAAGG
17134862 T---AG--AAAACAAAAGTGTAAAGG
1 TGAAAGCAAAAACAAAAGTGTAAAGG
*
17134883 TAGAAAACAAAA
1 T-GAAAGCAAAA
17134895 GCTAGACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 11
0.68 0.03 0.29
Matches are distributed among these distances:
21 19 0.73
23 2 0.08
25 1 0.04
26 1 0.04
27 3 0.12
ACGTcount: A:0.61, C:0.07, G:0.20, T:0.12
Consensus pattern (26 bp):
TGAAAGCAAAAACAAAAGTGTAAAGG
Found at i:17134868 original size:21 final size:21
Alignment explanation
Indices: 17134844--17134895 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
17134834 ATTGAAAGCA
17134844 AAAACAAAAGTGTAAAGGTAG
1 AAAACAAAAGTGTAAAGGTAG
17134865 AAAACAAAAGTGTAAAGGTAG
1 AAAACAAAAGTGTAAAGGTAG
17134886 AAAACAAAAG
1 AAAACAAAAG
17134896 CTAGACAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.06, G:0.21, T:0.12
Consensus pattern (21 bp):
AAAACAAAAGTGTAAAGGTAG
Found at i:17139482 original size:20 final size:20
Alignment explanation
Indices: 17139445--17139482 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17139435 TTCAAATTAT
*
17139445 ATTTTGCAACTTTATTTTCG
1 ATTTTGCAACTATATTTTCG
17139465 ATTTTG-AACTATAGTTTT
1 ATTTTGCAACTATA-TTTT
17139483 GGTTTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTTTGCAACTATATTTTCG
Found at i:17142216 original size:84 final size:82
Alignment explanation
Indices: 17142076--17142241 Score: 262
Period size: 84 Copynumber: 2.0 Consensus size: 82
17142066 AAGCCAACCT
*
17142076 TATTAATGCCATACAAAACCCCATTCTATCCTATGATATATGTGAAAGATCCTATTCCTCATAAA
1 TATTAATGCCATAAAAAACCCCATTCTATCCTATGATATATGTGAAAGATCCTATTCCTCATAAA
17142141 GATGCCAGTATAGGATA
66 GATGCCAGTATAGGATA
* * *
17142158 TATTAATGCCATAAAAAACCCCATTTTCTATCCTATGATGTATGTGAAGGA-CTTTATTCCTCAT
1 TATTAATGCCATAAAAAACCCCA--TTCTATCCTATGATATATGTGAAAGATC-CTATTCCTCAT
17142222 AAAGATGCCAGTATAGGATA
63 AAAGATGCCAGTATAGGATA
17142242 CAACCAGTCT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
82 22 0.29
83 1 0.01
84 54 0.70
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (82 bp):
TATTAATGCCATAAAAAACCCCATTCTATCCTATGATATATGTGAAAGATCCTATTCCTCATAAA
GATGCCAGTATAGGATA
Found at i:17150735 original size:21 final size:21
Alignment explanation
Indices: 17150681--17150736 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
17150671 GCAATAAATT
* *
17150681 GATCT-CTCATTGAAATGATC
1 GATCTCCTCCTTGAAAGGATC
* *
17150701 -ATCACCTTCTTGAAAGGATC
1 GATCTCCTCCTTGAAAGGATC
17150721 GATCTCCTCCTTGAAA
1 GATCTCCTCCTTGAAA
17150737 AGATTAATCC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 13 0.46
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (21 bp):
GATCTCCTCCTTGAAAGGATC
Found at i:17154772 original size:19 final size:19
Alignment explanation
Indices: 17154723--17154779 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
17154713 AAAAGGTTAT
* * *
17154723 GGTTTGGTTTAAGATTTAG
1 GGTTTGATTTAGGGTTTAG
17154742 GGTTTGATTTAGGGTTTAG
1 GGTTTGATTTAGGGTTTAG
*
17154761 GGTTTGTTTTAGGGTTTAG
1 GGTTTGATTTAGGGTTTAG
17154780 TTTAAGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (19 bp):
GGTTTGATTTAGGGTTTAG
Found at i:17154772 original size:31 final size:31
Alignment explanation
Indices: 17154737--17154796 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
17154727 TGGTTTAAGA
* *
17154737 TTTAGGGTTT-GATTTAGGGTTTAGGGTTTGT
1 TTTAGGGTTTAG-TTTAAGGTTTAAGGTTTGT
17154768 TTTAGGGTTTAGTTTAAGGTTTAAGGTTT
1 TTTAGGGTTTAGTTTAAGGTTTAAGGTTT
17154797 CAAGTAGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.52
Consensus pattern (31 bp):
TTTAGGGTTTAGTTTAAGGTTTAAGGTTTGT
Found at i:17156380 original size:20 final size:20
Alignment explanation
Indices: 17156357--17156401 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17156347 CCTTTTAGTT
*
17156357 TTGATCCAAGTCTGACCAAG
1 TTGACCCAAGTCTGACCAAG
* *
17156377 TTGACCCGAGTTTGACCAAG
1 TTGACCCAAGTCTGACCAAG
17156397 TTGAC
1 TTGAC
17156402 TTAGATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (20 bp):
TTGACCCAAGTCTGACCAAG
Found at i:17156430 original size:20 final size:20
Alignment explanation
Indices: 17156369--17156431 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
17156359 GATCCAAGTC
**
17156369 TGACCAAGTTGACCCGAGTT
1 TGACCAAGTTGACTTGAGTT
17156389 TGACCAAGTTGACTT-AGATT
1 TGACCAAGTTGACTTGAG-TT
* *
17156409 TGACCAATTTGATTTGAGTT
1 TGACCAAGTTGACTTGAGTT
17156429 TGA
1 TGA
17156432 TTGAGGGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (20 bp):
TGACCAAGTTGACTTGAGTT
Found at i:17156928 original size:24 final size:24
Alignment explanation
Indices: 17156892--17156940 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
17156882 GTCTACTAAC
* *
17156892 ATATAACATTTATTTATTTATTTA
1 ATATAAAAATTATTTATTTATTTA
17156916 ATATAAAAATTATTTATTTATTTA
1 ATATAAAAATTATTTATTTATTTA
17156940 A
1 A
17156941 AATGTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATAAAAATTATTTATTTATTTA
Found at i:17156949 original size:24 final size:24
Alignment explanation
Indices: 17156901--17156952 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17156891 CATATAACAT
*
17156901 TTATTTATTTATTTAATATAAAAA
1 TTATTTATTTATTTAAAATAAAAA
**
17156925 TTATTTATTTATTTAAAATGTAAA
1 TTATTTATTTATTTAAAATAAAAA
17156949 TTAT
1 TTAT
17156953 GAAAATATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTATTTATTTATTTAAAATAAAAA
Found at i:17157047 original size:25 final size:24
Alignment explanation
Indices: 17156992--17157044 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
17156982 AATTATAAAT
* * *
17156992 TTAAATTTAAAAATTTTGTTTTTG
1 TTAAACTTAAAAATGTGGTTTTTG
17157016 TTAAACTTAAAAATGTGGTTTTTG
1 TTAAACTTAAAAATGTGGTTTTTG
17157040 TTAAA
1 TTAAA
17157045 ACTATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (24 bp):
TTAAACTTAAAAATGTGGTTTTTG
Found at i:17157179 original size:89 final size:90
Alignment explanation
Indices: 17157064--17157235 Score: 260
Period size: 89 Copynumber: 1.9 Consensus size: 90
17157054 TGAAAAAAAA
* *
17157064 TTTAGACTTAAAAATGTTGTATTTGTTGAAACTATAAAATTTTGAAAAA-TAA-ATTTTTTTCAT
1 TTTAAACTTAAAAATGGTGTATTTGTTGAAACTATAAAATTTT-AAAAATTAATATTTTTTTCAT
17157127 AATATAGTTTCAACAAAAAACATGTT
65 AATATAGTTTCAACAAAAAACATGTT
* *
17157153 TTTAAACTTAAAAATGGTGCT-TTTGTTGAAACTATAGAATTTTAAAAATTAATTTTTTTTTCAT
1 TTTAAACTTAAAAATGGTG-TATTTGTTGAAACTATAAAATTTTAAAAATTAATATTTTTTTCAT
*
17157217 GATATAGTTTCAACAAAAA
65 AATATAGTTTCAACAAAAA
17157236 TCACATATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
88 5 0.07
89 41 0.55
90 29 0.39
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42
Consensus pattern (90 bp):
TTTAAACTTAAAAATGGTGTATTTGTTGAAACTATAAAATTTTAAAAATTAATATTTTTTTCATA
ATATAGTTTCAACAAAAAACATGTT
Found at i:17160018 original size:8 final size:9
Alignment explanation
Indices: 17159986--17160026 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
17159976 AATTTATAAA
17159986 ATAAATATT
1 ATAAATATT
17159995 ATAAATATT
1 ATAAATATT
17160004 ATAAATATT
1 ATAAATATT
17160013 -TAAATATT
1 ATAAATATT
17160021 -TAAATA
1 ATAAATA
17160027 CATAATTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 14 0.44
9 18 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAAATATT
Found at i:17164145 original size:29 final size:31
Alignment explanation
Indices: 17164080--17164139 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
17164070 CAAAACTCAT
*
17164080 GAAATTATTGAAATAAATGAAGTTTTTTTAA
1 GAAATTATTGAAATAAATGAAATTTTTTTAA
*
17164111 GAAATTATT-AAA-AAATTAAATTTTTTTAA
1 GAAATTATTGAAATAAATGAAATTTTTTTAA
17164140 AGAATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.56
30 3 0.11
31 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.43
Consensus pattern (31 bp):
GAAATTATTGAAATAAATGAAATTTTTTTAA
Found at i:17168751 original size:6 final size:6
Alignment explanation
Indices: 17168740--17168766 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17168730 ACATAATCTA
17168740 AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAA
17168767 AAATAGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:17169298 original size:12 final size:13
Alignment explanation
Indices: 17169282--17169315 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
17169272 AGAAATGAAT
17169282 AAAAAAATTAAAG
1 AAAAAAATTAAAG
17169295 AAAAAAATTAAA-
1 AAAAAAATTAAAG
17169307 AATAAAAAT
1 AA-AAAAAT
17169316 GGTTGGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAAAAATTAAAG
Found at i:17170592 original size:21 final size:21
Alignment explanation
Indices: 17170567--17170609 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17170557 TAATTGTTAG
*
17170567 ATAATAA-CAAGTAGTAAATAA
1 ATAATAATAAAGTAG-AAATAA
17170588 ATAATAATAAAGTAGAAATAA
1 ATAATAATAAAGTAGAAATAA
17170609 A
1 A
17170610 AAATGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (21 bp):
ATAATAATAAAGTAGAAATAA
Found at i:17170750 original size:14 final size:13
Alignment explanation
Indices: 17170711--17170755 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
17170701 GGAAAATTAT
*
17170711 TAAATAATAAAAA
1 TAAATAATAATAA
17170724 TTAAAATAATAATAA
1 -T-AAATAATAATAA
17170739 TAAATGAATAATAA
1 TAAAT-AATAATAA
17170753 TAA
1 TAA
17170756 TAAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 11 0.39
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
TAAATAATAATAA
Found at i:17170750 original size:17 final size:17
Alignment explanation
Indices: 17170728--17170760 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17170718 TAAAAATTAA
17170728 AATAATAATAATAAATG
1 AATAATAATAATAAATG
17170745 AATAATAATAATAAAT
1 AATAATAATAATAAAT
17170761 TTTTTTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAAATG
Found at i:17170864 original size:72 final size:71
Alignment explanation
Indices: 17170716--17170873 Score: 166
Period size: 72 Copynumber: 2.2 Consensus size: 71
17170706 ATTATTAAAT
* * * * *
17170716 AATAAA-AATTAAAATAATAATAATAAATGAATAATAATAATAAATTTTTTTATGAAAAGGGGAA
1 AATAAATAATAAAAATAAAAATAATAAATAAATAATAATAATAAATTTTTTAATGAAAA-GAGAA
17170780 AACAATC
65 AACAATC
17170787 AATAAATAATAAAAATAAAAATAATAAAGGTAAATAAATAATAATAAA-TTTTTAAT-AAAA-AG
1 AATAAATAATAAAAATAAAAATAATAAA--TAAAT-AATAATAATAAATTTTTTAATGAAAAGAG
*
17170849 AAAA-AATAT
63 AAAACAAT-C
17170858 ATATAAAT-ATAAAAAT
1 A-ATAAATAATAAAAAT
17170874 TCATTTTTCT
Statistics
Matches: 75, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
70 3 0.04
71 20 0.27
72 25 0.33
73 4 0.05
74 11 0.15
75 12 0.16
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (71 bp):
AATAAATAATAAAAATAAAAATAATAAATAAATAATAATAATAAATTTTTTAATGAAAAGAGAAA
ACAATC
Found at i:17171014 original size:19 final size:18
Alignment explanation
Indices: 17170979--17171083 Score: 104
Period size: 19 Copynumber: 5.6 Consensus size: 18
17170969 CCCTAAACAA
*
17170979 AACCCTAAATCTTAGGTG
1 AACCCTAAACCTTAGGTG
*
17170997 AACCACTAAACCTGAGGTG
1 AACC-CTAAACCTTAGGTG
*
17171016 AAACCCAAAACCTTTA-GTG
1 -AACCCTAAACC-TTAGGTG
17171035 AACCCTAAACCTTAGGTG
1 AACCCTAAACCTTAGGTG
* * *
17171053 AAGCCTAAAACCTTTAGCTA
1 AACCCT-AAACC-TTAGGTG
17171073 AACCCTAAACC
1 AACCCTAAACC
17171084 CTAAGCGAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
17 3 0.04
18 22 0.31
19 31 0.43
20 16 0.22
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (18 bp):
AACCCTAAACCTTAGGTG
Found at i:17171052 original size:37 final size:37
Alignment explanation
Indices: 17170994--17171098 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 37
17170984 TAAATCTTAG
*
17170994 GTGAACCACTAAACCTGAGGTGAAACCCAAAACCTTTA
1 GTGAACC-CTAAACCTTAGGTGAAACCCAAAACCTTTA
* *
17171032 GTGAACCCTAAACCTTAGGTGAAGCCTAAAACCTTTA
1 GTGAACCCTAAACCTTAGGTGAAACCCAAAACCTTTA
* * * *
17171069 GCTAAACCCTAAACCCTAAGCGAAACCCAA
1 G-TGAACCCTAAACCTTAGGTGAAACCCAA
17171099 GACCCTAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 28 0.49
38 29 0.51
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (37 bp):
GTGAACCCTAAACCTTAGGTGAAACCCAAAACCTTTA
Found at i:17171094 original size:19 final size:19
Alignment explanation
Indices: 17171072--17171133 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
17171062 ACCTTTAGCT
17171072 AAACCCTAAACCCTAAGCG
1 AAACCCTAAACCCTAAGCG
**
17171091 AAACCC-AAGACCCTAAATG
1 AAACCCTAA-ACCCTAAGCG
* * *
17171110 AAATCCTAAACCATAAGCA
1 AAACCCTAAACCCTAAGCG
17171129 AAACC
1 AAACC
17171134 TTGAGATCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 2 0.06
19 29 0.88
20 2 0.06
ACGTcount: A:0.48, C:0.32, G:0.08, T:0.11
Consensus pattern (19 bp):
AAACCCTAAACCCTAAGCG
Found at i:17171348 original size:12 final size:13
Alignment explanation
Indices: 17171324--17171363 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
17171314 TTAAATGTAA
17171324 AAATAATAAAATT
1 AAATAATAAAATT
17171337 AAATAA-AAAATT
1 AAATAATAAAATT
*
17171349 AAA-ATTAAAATT
1 AAATAATAAAATT
17171361 AAA
1 AAA
17171364 ATTTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 1 0.04
12 18 0.72
13 6 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAAAATT
Found at i:17174311 original size:33 final size:33
Alignment explanation
Indices: 17174269--17174346 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
17174259 CTAAGATGTC
17174269 ATGAAAACTTTCGTTTTACATTCAATACTAGTT
1 ATGAAAACTTTCGTTTTACATTCAATACTAGTT
17174302 ATGAAAACTTTCGTTTTACATTCAATACTAGTT
1 ATGAAAACTTTCGTTTTACATTCAATACTAGTT
17174335 ATGAAAACTTTC
1 ATGAAAACTTTC
17174347 TTCCTTTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (33 bp):
ATGAAAACTTTCGTTTTACATTCAATACTAGTT
Found at i:17179443 original size:9 final size:9
Alignment explanation
Indices: 17179420--17179491 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
17179410 AACAAAGAAC
*
17179420 AAAAAAAGG
1 AAAAAAAGA
*
17179429 ATAAAAAGA
1 AAAAAAAGA
*
17179438 AAAAAAATA
1 AAAAAAAGA
* *
17179447 AAAACAACA
1 AAAAAAAGA
*
17179456 AAACAAAAAA
1 AAA-AAAAGA
*
17179466 AATATAAAATA
1 AA-A-AAAAGA
17179477 AAAAAAAGA
1 AAAAAAAGA
17179486 AAAAAA
1 AAAAAA
17179492 TTCGGACTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
9 35 0.70
10 7 0.14
11 8 0.16
ACGTcount: A:0.83, C:0.04, G:0.06, T:0.07
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:17179465 original size:25 final size:25
Alignment explanation
Indices: 17179437--17179491 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
17179427 GGATAAAAAG
*
17179437 AAAAAAAATAAAA-ACAACAAAACAA
1 AAAAAAAATAAAATA-AAAAAAACAA
* *
17179462 AAAAAATATAAAATAAAAAAAAGAA
1 AAAAAAAATAAAATAAAAAAAACAA
17179487 AAAAA
1 AAAAA
17179492 TTCGGACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.85, C:0.05, G:0.02, T:0.07
Consensus pattern (25 bp):
AAAAAAAATAAAATAAAAAAAACAA
Found at i:17179492 original size:24 final size:25
Alignment explanation
Indices: 17179431--17179492 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
17179421 AAAAAAGGAT
17179431 AAAAAGAAAAAAA-ATAAAAACAAC
1 AAAAAGAAAAAAATATAAAAACAAC
17179455 AAAACA-AAAAAAATATAAAATA-AA-
1 AAAA-AGAAAAAAATATAAAA-ACAAC
17179479 AAAAAGAAAAAAAT
1 AAAAAGAAAAAAAT
17179493 TCGGACTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
23 1 0.03
24 23 0.68
25 9 0.26
26 1 0.03
ACGTcount: A:0.84, C:0.05, G:0.03, T:0.08
Consensus pattern (25 bp):
AAAAAGAAAAAAATATAAAAACAAC
Found at i:17180732 original size:36 final size:35
Alignment explanation
Indices: 17180682--17180819 Score: 91
Period size: 34 Copynumber: 3.9 Consensus size: 35
17180672 CTTGTTTCTA
**
17180682 GACTTATGACTTAGTCCTGGTCATCTTTTATTTGTC
1 GACTTATGACTTAGTCCTAATCATCTTTTATTT-TC
** * *
17180718 GACTTATGGTTTAGTCCTAATTATC-ATTATTTTC
1 GACTTATGACTTAGTCCTAATCATCTTTTATTTTC
* * * * *
17180752 AACTTATGATTTAATCTTGATCAT-TTTTATTTCTC
1 GACTTATGACTTAGTCCTAATCATCTTTTATTT-TC
* * * * *
17180787 GACTTGTGGCCTAGTCCTAGTCATTTCTTTATT
1 GACTTATGACTTAGTCCTAATCATCT-TTTATT
17180820 CTTTGGCCTG
Statistics
Matches: 76, Mismatches: 22, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
34 26 0.34
35 23 0.30
36 21 0.28
37 6 0.08
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (35 bp):
GACTTATGACTTAGTCCTAATCATCTTTTATTTTC
Found at i:17181143 original size:13 final size:13
Alignment explanation
Indices: 17181121--17181156 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
17181111 TTTCAGTTTC
*
17181121 AACAAAAAAAAAA
1 AACAAAAAAAACA
17181134 AACCAAAAAAAACA
1 AA-CAAAAAAAACA
17181148 AACAAAAAA
1 AACAAAAAA
17181157 TTTTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AACAAAAAAAACA
Found at i:17182672 original size:21 final size:20
Alignment explanation
Indices: 17182648--17182687 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
17182638 GAAGGCGAAG
* *
17182648 AAAAAACGAAGTAAGAAAAGC
1 AAAAAAAGAACTAA-AAAAGC
17182669 AAAAAAAGAACTAAAAAAG
1 AAAAAAAGAACTAAAAAAG
17182688 AAGTTGAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.07, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAGAACTAAAAAAGC
Found at i:17182827 original size:20 final size:20
Alignment explanation
Indices: 17182804--17182842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17182794 CTGTAGTAAA
*
17182804 AAAAAGACCAAATAAAAAAG
1 AAAAAGAACAAATAAAAAAG
*
17182824 AAAAAGAAGAAATAAAAAA
1 AAAAAGAACAAATAAAAAA
17182843 AAATGGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (20 bp):
AAAAAGAACAAATAAAAAAG
Found at i:17183983 original size:26 final size:26
Alignment explanation
Indices: 17183954--17184014 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
17183944 AATAAATTCT
* *
17183954 TAAAATTAAGACCCTAAATGGAACCC
1 TAAAATTAAGACCCTAAACGAAACCC
*
17183980 TAAAATTAAGACCTTAAACGAAACCC
1 TAAAATTAAGACCCTAAACGAAACCC
*
17184006 TGAAATTAA
1 TAAAATTAA
17184015 ATCCCTAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.21
Consensus pattern (26 bp):
TAAAATTAAGACCCTAAACGAAACCC
Found at i:17184063 original size:15 final size:15
Alignment explanation
Indices: 17184043--17184072 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17184033 AAGTCTTAAT
17184043 TAAACTTTACAACCC
1 TAAACTTTACAACCC
*
17184058 TAAACTTTGCAACCC
1 TAAACTTTACAACCC
17184073 AAAAATCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.33, G:0.03, T:0.27
Consensus pattern (15 bp):
TAAACTTTACAACCC
Found at i:17187707 original size:20 final size:20
Alignment explanation
Indices: 17187661--17187720 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
17187651 AATCTTTCTT
* *
17187661 AAAAGGGAAAATGGAAAAGAAG
1 AAAAGTGAAAAT-GAAAA-ATG
* *
17187683 AAAAGTGAGATTGAAAAATG
1 AAAAGTGAAAATGAAAAATG
17187703 AAAAGTGAAAATGAAAAA
1 AAAAGTGAAAATGAAAAA
17187721 AAAAGATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 18 0.56
21 5 0.16
22 9 0.28
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (20 bp):
AAAAGTGAAAATGAAAAATG
Found at i:17188097 original size:18 final size:16
Alignment explanation
Indices: 17188074--17188109 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
17188064 GTGAAAAATG
17188074 ATGAAAAAAAGATGAAAA
1 ATGAAAAAAA-AT-AAAA
17188092 ATGAAAAAAAATAAAA
1 ATGAAAAAAAATAAAA
17188108 AT
1 AT
17188110 AAAGGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
ATGAAAAAAAATAAAA
Found at i:17188108 original size:28 final size:28
Alignment explanation
Indices: 17188041--17188113 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
17188031 AAATAAAGCC
* *
17188041 AAAAAAA-AAAAAAAAGATACAGAGTGA
1 AAAAAAATAAAAAAAAGATACAAAATGA
** *
17188068 AAAATGATGAAAAAAAGATGA-AAAATGA
1 AAAAAAATAAAAAAAAGAT-ACAAAATGA
17188096 AAAAAAATAAAAATAAAG
1 AAAAAAATAAAAA-AAAG
17188114 GAAAATGAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
27 5 0.14
28 25 0.71
29 5 0.14
ACGTcount: A:0.74, C:0.01, G:0.14, T:0.11
Consensus pattern (28 bp):
AAAAAAATAAAAAAAAGATACAAAATGA
Found at i:17189177 original size:23 final size:23
Alignment explanation
Indices: 17189134--17189178 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17189124 CTAATAACTG
* *
17189134 CATATCTTTATTTAGATTAGTAT
1 CATATCTTTATTGAGAATAGTAT
17189157 CATAT-TTTATTGATGAATAGTA
1 CATATCTTTATTGA-GAATAGTA
17189179 ATTGTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (23 bp):
CATATCTTTATTGAGAATAGTAT
Found at i:17193224 original size:15 final size:16
Alignment explanation
Indices: 17193204--17193236 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17193194 TGAGAATCCA
17193204 AACAATA-AAAAAATT
1 AACAATACAAAAAATT
*
17193219 AACAATACATAAAATT
1 AACAATACAAAAAATT
17193235 AA
1 AA
17193237 ACTCACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
AACAATACAAAAAATT
Found at i:17197095 original size:67 final size:65
Alignment explanation
Indices: 17196922--17197107 Score: 204
Period size: 61 Copynumber: 2.9 Consensus size: 65
17196912 TCCAATTCAA
* * * * * *
17196922 TCCAAGTC-ATTTCATTCTTAGTTTTGGTTTAGTCTAAGTCTTTTTGTTTTTCACCTTCAATTTA
1 TCCAAGTCAATTTCATTCTTAG-CTTAGTTTAGTCCAAGTCTTTTTATTTTTCAACTTTAATTTA
17196986 G
65 G
* * *
17196987 TCAAAGTCAATTTCATTCTTAGGCTTA----A-TCCAAATCTTTTTATTTTTCAACTTTAGTTTA
1 TCCAAGTCAATTTCATTCTTA-GCTTAGTTTAGTCCAAGTCTTTTTATTTTTCAACTTTAATTTA
17197047 G
65 G
*
17197048 TCCAAGTCAATTTCATTCTTAGACTTCAGTTTAGTCCAAGTCCTTTTATTTTTCAACTTT
1 TCCAAGTCAATTTCATTCTTAG-CTT-AGTTTAGTCCAAGTCTTTTTATTTTTCAACTTT
17197108 GACTCAATTT
Statistics
Matches: 100, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
60 1 0.01
61 50 0.50
62 2 0.02
65 7 0.07
66 15 0.15
67 25 0.25
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (65 bp):
TCCAAGTCAATTTCATTCTTAGCTTAGTTTAGTCCAAGTCTTTTTATTTTTCAACTTTAATTTAG
Found at i:17197122 original size:67 final size:66
Alignment explanation
Indices: 17197051--17197308 Score: 297
Period size: 67 Copynumber: 3.9 Consensus size: 66
17197041 AGTTTAGTCC
* * * * *
17197051 AAGTCAATTTCATTCTTAGACTTCAGTTTAGTCCAAGTCCTTTTATTTTTCA-ACTTTGACTCAA
1 AAGTCAATTTCATTTTTAGACTTCA-TTCAATCCAAGTCATTTTATTTTT-AGACTTTGGCTCAA
17197115 TTT
64 TTT
* * * *
17197118 AAGTCATTTTCATTTTTAGACTTCCATTCAATCTAAGTCATTTCATTTTTAGGCTTTGGCTCAAT
1 AAGTCAATTTCATTTTTAGACTT-CATTCAATCCAAGTCATTTTATTTTTAGACTTTGGCTCAAT
**
17197183 CC
65 TT
* * *
17197185 AAGT-AATTTC-TTTTTCCGACTTCTATTCAATCAAAGTCATTTTATTTTTAGACTTTGGCTTAA
1 AAGTCAATTTCATTTTT-AGACTTC-ATTCAATCCAAGTCATTTTATTTTTAGACTTTGGCTCAA
17197248 TTT
64 TTT
* *
17197251 AAGTCATTTTCATTTTTAGACTTCAATTCAATCCAAGCCATTTTATTTTTAGACTTTG
1 AAGTCAATTTCATTTTTAGACTTC-ATTCAATCCAAGTCATTTTATTTTTAGACTTTG
17197309 CTCTGCTCAA
Statistics
Matches: 161, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
65 6 0.04
66 51 0.32
67 97 0.60
68 7 0.04
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (66 bp):
AAGTCAATTTCATTTTTAGACTTCATTCAATCCAAGTCATTTTATTTTTAGACTTTGGCTCAATT
T
Found at i:17197167 original size:33 final size:33
Alignment explanation
Indices: 17197111--17197306 Score: 164
Period size: 33 Copynumber: 5.9 Consensus size: 33
17197101 CAACTTTGAC
*
17197111 TCAATTTAAGTCATTTTCATTTTTAGACTTCCAT
1 TCAATCTAAGTCA-TTTCATTTTTAGACTTCCAT
* ****
17197145 TCAATCTAAGTCATTTCATTTTTAGGCTTTGGC
1 TCAATCTAAGTCATTTCATTTTTAGACTTCCAT
* * * *
17197178 TCAATCCAAGTAATTTC-TTTTTCCGACTTCTAT
1 TCAATCTAAGTCATTTCATTTTT-AGACTTCCAT
* * *
17197211 TCAATCAAAGTCATTTTATTTTTAGACTTTGGC-T
1 TCAATCTAAGTCATTTCATTTTTAGAC-TT-CCAT
* *
17197245 T-AATTTAAGTCATTTTCATTTTTAGACTTCAAT
1 TCAATCTAAGTCA-TTTCATTTTTAGACTTCCAT
* * *
17197278 TCAATCCAAGCCATTTTATTTTTAGACTT
1 TCAATCTAAGTCATTTCATTTTTAGACTT
17197307 TGCTCTGCTC
Statistics
Matches: 126, Mismatches: 29, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
32 5 0.04
33 79 0.63
34 42 0.33
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (33 bp):
TCAATCTAAGTCATTTCATTTTTAGACTTCCAT
Found at i:17197453 original size:28 final size:28
Alignment explanation
Indices: 17197399--17197458 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17197389 TCATTTTCAT
* *
17197399 TTTTTAGACTATGGTTTAATCCTAGTCA
1 TTTTTAGACTATGGCTTAATCCAAGTCA
* **
17197427 TTTTTAGACTTTGGCTTCGTCCAAGTCA
1 TTTTTAGACTATGGCTTAATCCAAGTCA
17197455 TTTT
1 TTTT
17197459 ATTCTCAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (28 bp):
TTTTTAGACTATGGCTTAATCCAAGTCA
Found at i:17200006 original size:23 final size:20
Alignment explanation
Indices: 17199951--17200008 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
17199941 AGAAGAAATT
*
17199951 TAAATGCAAGAACCAAAAAC
1 TAAATGCAAGAACAAAAAAC
* *
17199971 TAAGTGCATGAACAATAAGAAC
1 TAAATGCAAGAACAA-AA-AAC
17199993 TAAAATGCAAGAACAA
1 T-AAATGCAAGAACAA
17200009 GTAAAATGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 4 0.13
23 12 0.40
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (20 bp):
TAAATGCAAGAACAAAAAAC
Found at i:17200333 original size:31 final size:30
Alignment explanation
Indices: 17200270--17200334 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
17200260 TAGATTAAAC
*
17200270 TGAATTTAAATGCAACAAATTGAAGATGCT
1 TGAATTTAAATGCAACAAATTGAAAATGCT
*
17200300 TGAATTTAAATGCAAGCGAA-TGTAAAATGCT
1 TGAATTTAAATGCAA-CAAATTG-AAAATGCT
17200331 TGAA
1 TGAA
17200335 CCAAAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.29
Consensus pattern (30 bp):
TGAATTTAAATGCAACAAATTGAAAATGCT
Found at i:17201123 original size:16 final size:16
Alignment explanation
Indices: 17201102--17201146 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
17201092 AGAAAATGAA
17201102 CAAGAAATGTAAATTG
1 CAAGAAATGTAAATTG
17201118 CAAGAAATGTAAATTG
1 CAAGAAATGTAAATTG
17201134 CAAGAAATGTAAA
1 CAAGAAATGTAAA
17201147 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (16 bp):
CAAGAAATGTAAATTG
Found at i:17214375 original size:124 final size:124
Alignment explanation
Indices: 17214155--17214402 Score: 451
Period size: 124 Copynumber: 2.0 Consensus size: 124
17214145 TAGATTAGTG
17214155 CTATAAAAGGAAAATAAAAAGAAATCTAATATCACCTCGCTAAAAACAAACCTTCTAGTTGGTTC
1 CTATAAAAGGAAAATAAAAAGAAATCTAATATCACCTCGCTAAAAACAAACCTTCTAGTTGGTTC
*
17214220 CCTTTTAGTTTTAGTTAGGTTTTCTTATATTTGAATTTAAAAGAAAGTGAAAAAAATAA
66 CCTTTTAGTTTTAGTTAGGTTTTCTTATATTTGAATTTAAAAGAAAGGGAAAAAAATAA
* *
17214279 CTATAAAAGGAAAATAAAAAGAAATCTAATATCACCTCGTTAGAAACAAACCTTCTAGTTGGTTC
1 CTATAAAAGGAAAATAAAAAGAAATCTAATATCACCTCGCTAAAAACAAACCTTCTAGTTGGTTC
* *
17214344 CCTTTTAGTTTTAGTTAGGTTTTCTTATATTTGAATTTAAAGGAAAGGGAAAATAATAA
66 CCTTTTAGTTTTAGTTAGGTTTTCTTATATTTGAATTTAAAAGAAAGGGAAAAAAATAA
17214403 ATGGTTCCAA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (124 bp):
CTATAAAAGGAAAATAAAAAGAAATCTAATATCACCTCGCTAAAAACAAACCTTCTAGTTGGTTC
CCTTTTAGTTTTAGTTAGGTTTTCTTATATTTGAATTTAAAAGAAAGGGAAAAAAATAA
Found at i:17215915 original size:4 final size:4
Alignment explanation
Indices: 17215906--17215934 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
17215896 CGTGTATCTG
17215906 TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
17215935 AAGCCTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:17220208 original size:2 final size:2
Alignment explanation
Indices: 17220201--17220228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17220191 TAATGTACCT
17220201 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
17220229 CCCCCTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17221886 original size:24 final size:24
Alignment explanation
Indices: 17221854--17221904 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
17221844 ACTGGCAATG
17221854 TAAGTATTGGCCTTGTTTAGACAT
1 TAAGTATTGGCCTTGTTTAGACAT
17221878 TAAGTATTGGCCTTGTTTAGACAT
1 TAAGTATTGGCCTTGTTTAGACAT
17221902 TAA
1 TAA
17221905 TTGCTATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (24 bp):
TAAGTATTGGCCTTGTTTAGACAT
Found at i:17223267 original size:2 final size:2
Alignment explanation
Indices: 17223260--17223302 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
17223250 TTTGTTTGGT
17223260 TA TA 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 TA TA
17223302 T
1 T
17223303 CCTTCCCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17232520 original size:10 final size:9
Alignment explanation
Indices: 17232500--17232529 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
17232490 GGATGAGGTG
17232500 AAAAAATAA
1 AAAAAATAA
17232509 AAAAAATAA
1 AAAAAATAA
*
17232518 AAAAAATGA
1 AAAAAATAA
17232527 AAA
1 AAA
17232530 GTGACAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:17233542 original size:45 final size:45
Alignment explanation
Indices: 17233441--17233548 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 45
17233431 CATGATTGGA
* * * *
17233441 TGAAAC-CTTAAAACTTTTGAATGGGAACCTTTGAAATATTGGATG
1 TGAAACAC-TAAAATTTTTGAATGAGAACCTTTGAAATATTGAAAG
* *
17233486 TGAAACACTAAAATTTTTGAATGAGAATCTTTGAAATCTTGAAAG
1 TGAAACACTAAAATTTTTGAATGAGAACCTTTGAAATATTGAAAG
* *
17233531 T-AAATCCCTAAAGTTTTT
1 TGAAA-CACTAAAATTTTT
17233549 CAAATAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 3 0.06
45 49 0.92
46 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (45 bp):
TGAAACACTAAAATTTTTGAATGAGAACCTTTGAAATATTGAAAG
Found at i:17233651 original size:23 final size:23
Alignment explanation
Indices: 17233622--17233665 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17233612 AGCCTTGAAA
17233622 TTTTGAAT-CAGAATCTTTAAAAT
1 TTTTGAATGCA-AATCTTTAAAAT
*
17233645 TTTTGAATGTAAATCTTTAAA
1 TTTTGAATGCAAATCTTTAAA
17233666 TGTTGGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (23 bp):
TTTTGAATGCAAATCTTTAAAAT
Found at i:17233827 original size:18 final size:18
Alignment explanation
Indices: 17233804--17233854 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
17233794 ACTCCTTTCG
*
17233804 AATCTTCAAATATTTGCA
1 AATCTTCAAATACTTGCA
*
17233822 AATCTTCAAATACTTGCG
1 AATCTTCAAATACTTGCA
*
17233840 AATCTTCTAATACTT
1 AATCTTCAAATACTT
17233855 ATGAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (18 bp):
AATCTTCAAATACTTGCA
Found at i:17233860 original size:18 final size:18
Alignment explanation
Indices: 17233822--17233877 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
17233812 AATATTTGCA
* **
17233822 AATCTTCAAATACTTGCG
1 AATCTTCTAATACTTATG
17233840 AATCTTCTAATACTTATG
1 AATCTTCTAATACTTATG
*
17233858 AATATT-TAATACTTATG
1 AATCTTCTAATACTTATG
17233875 AAT
1 AAT
17233878 TTGAAATCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 14 0.41
18 20 0.59
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (18 bp):
AATCTTCTAATACTTATG
Found at i:17234005 original size:67 final size:67
Alignment explanation
Indices: 17233931--17234083 Score: 157
Period size: 67 Copynumber: 2.3 Consensus size: 67
17233921 TCATGAATAT
* * *
17233931 AAATTCTTGCAAATCTAAAAATTCTTACTAA-CATAAAATTTTTAAGAATCAAATTCTTGTGAAA
1 AAATTCTTGCAAATCTAAAAATTCTTACGAATC-TAAAA-ATTTAAGAATCAAATTCTTGCGAAA
*
17233995 CT-G
64 CTAA
* * * * * *** *
17233998 ATATTCTTGCGAATTTAAAATTTTTTACGAATCTAAAAATTTGCTAATCAAATTCTTGCGAATCT
1 AAATTCTTGCAAATCTAAAAATTCTTACGAATCTAAAAATTTAAGAATCAAATTCTTGCGAAACT
17234063 AA
66 AA
17234065 AAATTCTTGCAAATCTAAA
1 AAATTCTTGCAAATCTAAA
17234084 TTCTTGCAAG
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
66 21 0.31
67 46 0.68
68 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (67 bp):
AAATTCTTGCAAATCTAAAAATTCTTACGAATCTAAAAATTTAAGAATCAAATTCTTGCGAAACT
AA
Found at i:17234060 original size:31 final size:34
Alignment explanation
Indices: 17234025--17234090 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 34
17234015 AAATTTTTTA
*
17234025 CGAATCTAAAAA-T-TTGCTAATC-AAATTCTTG
1 CGAATCTAAAAATTCTTGCAAATCTAAATTCTTG
17234056 CGAATCTAAAAATTCTTGCAAATCTAAATTCTTG
1 CGAATCTAAAAATTCTTGCAAATCTAAATTCTTG
17234090 C
1 C
17234091 AAGTCTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 12 0.39
32 1 0.03
33 8 0.26
34 10 0.32
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (34 bp):
CGAATCTAAAAATTCTTGCAAATCTAAATTCTTG
Found at i:17234070 original size:18 final size:18
Alignment explanation
Indices: 17234000--17234083 Score: 79
Period size: 18 Copynumber: 4.9 Consensus size: 18
17233990 TGAAACTGAT
*
17234000 ATTCTTGCGAATTTAAAA
1 ATTCTTGCGAATCTAAAA
* * *
17234018 TTTTTTACGAATCTAAAA
1 ATTCTTGCGAATCTAAAA
*
17234036 A-T-TTGCTAATC---AA
1 ATTCTTGCGAATCTAAAA
17234049 ATTCTTGCGAATCTAAAA
1 ATTCTTGCGAATCTAAAA
*
17234067 ATTCTTGCAAATCTAAA
1 ATTCTTGCGAATCTAAA
17234084 TTCTTGCAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
13 3 0.06
14 1 0.02
15 8 0.15
16 7 0.13
17 1 0.02
18 32 0.62
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.38
Consensus pattern (18 bp):
ATTCTTGCGAATCTAAAA
Found at i:17234086 original size:16 final size:16
Alignment explanation
Indices: 17234038--17234092 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 16
17234028 ATCTAAAAAT
*
17234038 TTGCTAATC-AAATTC
1 TTGCAAATCTAAATTC
*
17234053 TTGCGAATCTAAAAATTC
1 TTGCAAATCT--AAATTC
17234071 TTGCAAATCTAAATTC
1 TTGCAAATCTAAATTC
17234087 TTGCAA
1 TTGCAA
17234093 GTCTTTGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 8 0.23
16 12 0.34
18 15 0.43
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (16 bp):
TTGCAAATCTAAATTC
Found at i:17235240 original size:23 final size:23
Alignment explanation
Indices: 17235193--17235252 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
17235183 GGGGAAACAT
* *
17235193 TGATGATAGAAGTAGTAACCATTG
1 TGATGATTGAA-TGGTAACCATTG
*
17235217 TGATGATTGAATGGTAGCCATTG
1 TGATGATTGAATGGTAACCATTG
17235240 TGAT-ATGTGAATG
1 TGATGAT-TGAATG
17235253 CCCTGAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.06
23 20 0.62
24 10 0.31
ACGTcount: A:0.32, C:0.07, G:0.28, T:0.33
Consensus pattern (23 bp):
TGATGATTGAATGGTAACCATTG
Found at i:17237467 original size:20 final size:18
Alignment explanation
Indices: 17237425--17237482 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
17237415 CTTATTTTTA
*
17237425 TATTTATTGCATGGT-ATT
1 TATTT-TTGCATGATAATT
17237443 TATTTTTGCATGACTAATAT
1 TATTTTTGCATGA-TAAT-T
17237463 TA-TTTTGCATGATAATT
1 TATTTTTGCATGATAATT
17237480 TAT
1 TAT
17237483 CTACCTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 10 0.29
18 10 0.29
19 12 0.34
20 3 0.09
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (18 bp):
TATTTTTGCATGATAATT
Found at i:17237535 original size:25 final size:26
Alignment explanation
Indices: 17237488--17237606 Score: 109
Period size: 21 Copynumber: 5.0 Consensus size: 26
17237478 TTTATCTACC
17237488 TAATATATTTATTTGTATGATTA-A-
1 TAATATATTTATTTGTATGATTATAT
*
17237512 T-AT-T-TTTATTTGTGTGATT-TAT
1 TAATATATTTATTTGTATGATTATAT
*
17237534 TAATATATTTGTTTGTATGATTATAT
1 TAATATATTTATTTGTATGATTATAT
*
17237560 T--TA-ATTTGA-TTGCATGA-T-TAT
1 TAATATATTT-ATTTGTATGATTATAT
*
17237581 TAATATATTTATTTGCATGATTATAT
1 TAATATATTTATTTGTATGATTATAT
17237607 GTTTATTTGT
Statistics
Matches: 77, Mismatches: 5, Indels: 24
0.73 0.05 0.23
Matches are distributed among these distances:
21 19 0.25
22 3 0.04
23 18 0.23
24 16 0.21
25 14 0.18
26 7 0.09
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (26 bp):
TAATATATTTATTTGTATGATTATAT
Found at i:17237563 original size:27 final size:25
Alignment explanation
Indices: 17237488--17237602 Score: 104
Period size: 25 Copynumber: 4.9 Consensus size: 25
17237478 TTTATCTACC
17237488 TAATATATTTATTTGTATG----AT
1 TAATATATTTATTTGTATGATTTAT
* *
17237509 TAATATTTTTATTTGTGTGATTTAT
1 TAATATATTTATTTGTATGATTTAT
*
17237534 TAATATATTTGTTTGTATGATTATAT
1 TAATATATTTATTTGTATGATT-TAT
*
17237560 T--TA-ATTTGA-TTGCATGA-TTAT
1 TAATATATTT-ATTTGTATGATTTAT
*
17237581 TAATATATTTATTTGCATGATT
1 TAATATATTTATTTGTATGATT
17237603 ATATGTTTAT
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
21 21 0.28
22 1 0.01
23 14 0.18
24 14 0.18
25 22 0.29
26 4 0.05
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (25 bp):
TAATATATTTATTTGTATGATTTAT
Found at i:17237576 original size:23 final size:24
Alignment explanation
Indices: 17237540--17237615 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
17237530 TTATTAATAT
* *
17237540 ATTTGTTTGTATGATTATAT-TTA
1 ATTTGATTGCATGATTATATATTA
*
17237563 ATTTGATTGCATGATTAT-TAATA
1 ATTTGATTGCATGATTATATATTA
* *
17237586 TATTT-ATTTGCATGATTATATGTTT
1 -ATTTGA-TTGCATGATTATATATTA
17237611 ATTTG
1 ATTTG
17237616 TATGTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 19 0.45
24 20 0.48
25 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.57
Consensus pattern (24 bp):
ATTTGATTGCATGATTATATATTA
Found at i:17237589 original size:47 final size:44
Alignment explanation
Indices: 17237488--17237625 Score: 163
Period size: 47 Copynumber: 3.0 Consensus size: 44
17237478 TTTATCTACC
17237488 TAATATATTTATTTGTATGATTAATATTTTTATTTGTGTGATTTAT
1 TAATATATTTATTTGTATGATT-ATA-TTTTATTTGTGTGATTTAT
* *
17237534 TAATATATTTGTTTGTATGATTATATTTAATTTGAT-TGCATGATTAT
1 TAATATATTTATTTGTATGATTATATTTTATTTG-TGTG-AT--TTAT
* *
17237581 TAATATATTTATTTGCATGATTATATGTTTATTTGTATG-TTTAT
1 TAATATATTTATTTGTATGATTATAT-TTTATTTGTGTGATTTAT
17237625 T
1 T
17237626 TGCTTGTTTA
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
44 15 0.19
45 6 0.07
46 22 0.27
47 29 0.36
48 9 0.11
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (44 bp):
TAATATATTTATTTGTATGATTATATTTTATTTGTGTGATTTAT
Found at i:17237604 original size:12 final size:12
Alignment explanation
Indices: 17237605--17237648 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
17237595 GCATGATTAT
*
17237605 ATGTTTATTTGT
1 ATGTTTATTTGC
17237617 ATGTTTATTTGC
1 ATGTTTATTTGC
*
17237629 TTGTTTATTTGC
1 ATGTTTATTTGC
*
17237641 ATGATTAT
1 ATGTTTAT
17237649 ATATTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (12 bp):
ATGTTTATTTGC
Found at i:17237611 original size:20 final size:20
Alignment explanation
Indices: 17237583--17237662 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
17237573 ATGATTATTA
17237583 ATATATTTATTTGCATGATT
1 ATATATTTATTTGCATGATT
* * *
17237603 ATATGTTTATTTGTATGTTT
1 ATATATTTATTTGCATGATT
* *
17237623 ATTTGCTTGTTTATTTGCATGATT
1 A--T--ATATTTATTTGCATGATT
*
17237647 ATATATTTAATTGCAT
1 ATATATTTATTTGCAT
17237663 ATTTGTTTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
20 29 0.62
22 2 0.04
24 16 0.34
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.57
Consensus pattern (20 bp):
ATATATTTATTTGCATGATT
Found at i:17237613 original size:24 final size:24
Alignment explanation
Indices: 17237493--17237820 Score: 87
Period size: 23 Copynumber: 13.1 Consensus size: 24
17237483 CTACCTAATA
*
17237493 TATTTATTTGTATGATTA-ATA-T
1 TATTTATTTGCATGATTATATATT
** *
17237515 T-TTTATTTGTGTGATT-TATTAATA
1 TATTTATTTGCATGATTATA-T-ATT
* *
17237539 TATTTGTTTGTATGATTATAT-TT
1 TATTTATTTGCATGATTATATATT
* *
17237562 AATTTGA-TTGCATGATTAT-TAATA
1 TATTT-ATTTGCATGATTATAT-ATT
17237586 TATTTATTTGCATGA-T-TATA--
1 TATTTATTTGCATGATTATATATT
* * * * **
17237606 TGTTTATTTGTATGTTTATTTGCT
1 TATTTATTTGCATGATTATATATT
*
17237630 TGTTTATTTGCATGATTATATATT
1 TATTTATTTGCATGATTATATATT
*
17237654 TAATTGCATATTTGTTTGCATGACT-TATATGT
1 T-ATT---TA----TTTGCATGATTATATAT-T
*
17237686 TA-TTATTTGTATGATTATATATTTAATT
1 TATTTATTTGCATGA-T-TATA--T-ATT
17237714 GCATATTTATTTGCATGATT-TATATAT
1 ---TATTTATTTGCATGATTATATAT-T
*
17237741 TA-TTATTTGTATGATTATATATTTAAT
1 TATTTATTTGCATGATTATATA--T--T
17237768 TACATGTTTATTTGCATGATT-TATATAT
1 T--A--TTTATTTGCATGATTATATAT-T
*
17237796 TA-TTATTTGCATGATAATATATT
1 TATTTATTTGCATGATTATATATT
17237819 TA
1 TA
17237821 ATTGCAAGTT
Statistics
Matches: 233, Mismatches: 28, Indels: 89
0.67 0.08 0.25
Matches are distributed among these distances:
20 12 0.05
21 16 0.07
22 7 0.03
23 57 0.24
24 45 0.19
25 17 0.07
26 8 0.03
27 7 0.03
28 7 0.03
29 6 0.03
30 2 0.01
31 13 0.06
32 36 0.15
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (24 bp):
TATTTATTTGCATGATTATATATT
Found at i:17237672 original size:44 final size:44
Alignment explanation
Indices: 17237588--17237736 Score: 127
Period size: 55 Copynumber: 3.1 Consensus size: 44
17237578 TATTAATATA
* * * *
17237588 TTTATTTGCATGATTATATGTTTATTTGTATGTTTATTTGCTTG
1 TTTATTTGCATGATTATATATTTAATTGCATATTTATTTGCTTG
*
17237632 TTTATTTGCATGATTATATATTTAATTGCATATTTGTTTGCATGACTTATATG
1 TTTATTTGCATGATTATATATTTAATTGCATATTT-ATT---TG-C---T-TG
* *
17237685 TTATTATTTGTATGATTATATATTTAATTGCATATTTATTTGCATG
1 -T-TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCTTG
17237731 ATTTAT
1 -TTTAT
17237737 ATATTATTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
44 31 0.36
45 6 0.07
46 3 0.04
48 2 0.02
49 1 0.01
50 1 0.01
51 2 0.02
52 1 0.01
53 2 0.02
54 3 0.04
55 33 0.39
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (44 bp):
TTTATTTGCATGATTATATATTTAATTGCATATTTATTTGCTTG
Found at i:17237700 original size:55 final size:55
Alignment explanation
Indices: 17237633--17237826 Score: 316
Period size: 55 Copynumber: 3.5 Consensus size: 55
17237623 ATTTGCTTGT
* * *
17237633 TTATTTGCATGATTATATATTTAATTGCATATTTGTTTGCATGACTTATATGTTA
1 TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTA
*
17237688 TTATTTGTATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTA
1 TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTA
* * *
17237743 TTATTTGTATGATTATATATTTAATTACATGTTTATTTGCATGATTTATATATTA
1 TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTA
*
17237798 TTATTTGCATGATAATATATTTAATTGCA
1 TTATTTGCATGATTATATATTTAATTGCA
17237827 AGTTTGTATG
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 130 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.54
Consensus pattern (55 bp):
TTATTTGCATGATTATATATTTAATTGCATATTTATTTGCATGATTTATATATTA
Found at i:17237726 original size:32 final size:31
Alignment explanation
Indices: 17237688--17237796 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 31
17237678 TTATATGTTA
*
17237688 TTATTTGTATGATTATATATTTAATTGCATAT
1 TTATTTGCATGATTATATATTTAATT-CATAT
17237720 TTATTTGCATGATT-TATA--T-A-T--TA-
1 TTATTTGCATGATTATATATTTAATTCATAT
* *
17237743 TTATTTGTATGATTATATATTTAATTACATGT
1 TTATTTGCATGATTATATATTTAATT-CATAT
17237775 TTATTTGCATGATTTATATATT
1 TTATTTGCATGA-TTATATATT
17237797 ATTATTTGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
23 13 0.21
24 6 0.10
26 1 0.02
27 2 0.03
28 2 0.03
29 1 0.02
31 5 0.08
32 24 0.38
33 9 0.14
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (31 bp):
TTATTTGCATGATTATATATTTAATTCATAT
Found at i:17237857 original size:24 final size:24
Alignment explanation
Indices: 17237830--17237875 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
17237820 AATTGCAAGT
*
17237830 TTGTATGATTATTAATATATTTGC
1 TTGTACGATTATTAATATATTTGC
17237854 TTGTACGATTATTAATATATTT
1 TTGTACGATTATTAATATATTT
17237876 ATTTACATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (24 bp):
TTGTACGATTATTAATATATTTGC
Found at i:17243968 original size:21 final size:20
Alignment explanation
Indices: 17243942--17243995 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 20
17243932 AGAGATGTAC
17243942 AAAAAAAGAAAAAAAGTAAA
1 AAAAAAAGAAAAAAAGTAAA
17243962 AAAAAAAGAAAAAAAGTAAA
1 AAAAAAAGAAAAAAAGTAAA
17243982 ATAAAAAAGAAAAA
1 A-AAAAAAGAAAAA
17243996 GAGAAAGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAGTAAA
Found at i:17244016 original size:28 final size:27
Alignment explanation
Indices: 17243953--17244022 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 27
17243943 AAAAAAGAAA
* *
17243953 AAAAGTAAAAA-AAAAAGAAAAAAAGT
1 AAAATTAAAAAGAAAAAGAAAAAAAGG
* *
17243979 AAAATAAAAAAGAAAAAGAGAAAGAAGG
1 AAAATTAAAAAGAAAAAGA-AAAAAAGG
* *
17244007 AAACTTAAAATGAAAA
1 AAAATTAAAAAGAAAA
17244023 CTCAAAAGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 9 0.26
27 7 0.20
28 19 0.54
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.09
Consensus pattern (27 bp):
AAAATTAAAAAGAAAAAGAAAAAAAGG
Found at i:17245529 original size:34 final size:35
Alignment explanation
Indices: 17245465--17245541 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 35
17245455 TTTCCAAAAG
17245465 TTTCAAAGCCTCAGTTGTGGAGAAGTATTTTA-TT
1 TTTCAAAGCCTCAGTTGTGGAGAAGTATTTTAGTT
*
17245499 TTTCAAAGCCTTAGTTGTGG-G-AGATCATTTTAGTT
1 TTTCAAAGCCTCAGTTGTGGAGAAG-T-ATTTTAGTT
*
17245534 TTTAAAAG
1 TTTCAAAG
17245542 TTTCAAAGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 2 0.05
33 2 0.05
34 25 0.66
35 9 0.24
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (35 bp):
TTTCAAAGCCTCAGTTGTGGAGAAGTATTTTAGTT
Found at i:17245865 original size:12 final size:13
Alignment explanation
Indices: 17245846--17245881 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
17245836 TTATTTGTAT
17245846 TTTAATTTTTTAG
1 TTTAATTTTTTAG
*
17245859 TTT-ATTTTTTGG
1 TTTAATTTTTTAG
17245871 TTTAATTTTTT
1 TTTAATTTTTT
17245882 TTAGTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (13 bp):
TTTAATTTTTTAG
Found at i:17246528 original size:20 final size:18
Alignment explanation
Indices: 17246503--17246540 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
17246493 TTTTGCATGA
17246503 ATTTGCATGACTAATGTTAT
1 ATTTGCATGA-TAAT-TTAT
17246523 ATTTGCATGATAATTTAT
1 ATTTGCATGATAATTTAT
17246541 TTGCCTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (18 bp):
ATTTGCATGATAATTTAT
Found at i:17246557 original size:17 final size:16
Alignment explanation
Indices: 17246522--17246560 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17246512 ACTAATGTTA
*
17246522 TATTTGCATGATAATT
1 TATTTGCATAATAATT
*
17246538 TATTTGCCTAATATATT
1 TATTTGCATAATA-ATT
17246555 TATTTG
1 TATTTG
17246561 AATGATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (16 bp):
TATTTGCATAATAATT
Found at i:17246570 original size:21 final size:21
Alignment explanation
Indices: 17246546--17246601 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
17246536 TTTATTTGCC
17246546 TAATATATTTATTTGAATGAT
1 TAATATATTTATTTGAATGAT
*
17246567 TAATATATTTATTTGTATGAT
1 TAATATATTTATTTGAATGAT
*
17246588 T-ATAT-TTAATTTGA
1 TAATATATTTATTTGA
17246602 TTGCATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 7 0.22
20 4 0.12
21 21 0.66
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
TAATATATTTATTTGAATGAT
Found at i:17246658 original size:24 final size:24
Alignment explanation
Indices: 17246546--17246782 Score: 126
Period size: 24 Copynumber: 10.0 Consensus size: 24
17246536 TTTATTTGCC
*
17246546 TAATATATTTATTTG-A--ATGAT
1 TAATATATTTATTTGCATGATTAT
*
17246567 TAATATATTTATTTGTATGATTA-
1 TAATATATTTATTTGCATGATTAT
*
17246590 T-ATTTAATTTGA-TTGCATGATTAT
1 TAATAT-ATTT-ATTTGCATGATTAT
* * * *
17246614 TGATATATCTAATTGCTTGATTAT
1 TAATATATTTATTTGCATGATTAT
*
17246638 TAATATATTTATTTTCATGA-T-T
1 TAATATATTTATTTGCATGATTAT
17246660 TATATATTATTT-TTTGCATGATAATAT
1 TA-ATA-TATTTATTTGCATGAT--TAT
* *
17246687 GT-TTA-ATTGCATGTTTGCATGATTAT
1 -TAATATATT---TATTTGCATGATTAT
17246713 TAATATATTT-TGCTTGCATGATTAT
1 TAATATATTTAT--TTGCATGATTAT
* * *
17246738 TAATATGTTTATTTACAT-AATA-
1 TAATATATTTATTTGCATGATTAT
*
17246760 TGATATTATTTA-TTGCATGATTA
1 TAATA-TATTTATTTGCATGATTA
17246783 ATATTTGATT
Statistics
Matches: 169, Mismatches: 21, Indels: 50
0.70 0.09 0.21
Matches are distributed among these distances:
21 15 0.09
22 16 0.09
23 40 0.24
24 48 0.28
25 25 0.15
26 9 0.05
27 5 0.03
28 11 0.07
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.53
Consensus pattern (24 bp):
TAATATATTTATTTGCATGATTAT
Found at i:17246766 original size:99 final size:100
Alignment explanation
Indices: 17246546--17246786 Score: 256
Period size: 99 Copynumber: 2.5 Consensus size: 100
17246536 TTTATTTGCC
*
17246546 TAATATATTTATTTGA-ATGAT-TA-ATA-TATTTATTTGTATGATT-ATA--TTTAATT---TG
1 TAATATATTTATTT-ACATGATATATATATTATTTA-TTGCATGATTAATATGTTTAATTGCATG
* * *
17246601 ATTGCATGATTATTGATATATCTAATTGCTTGATTAT
64 TTTGCATGATTATTAATATATCTAATTGCATGATTAT
* * *
17246638 TAATATATTTATTTTCATGATTTATATATTATTTTTTGCATGA-TAATATGTTTAATTGCATGTT
1 TAATATATTTATTTACATGATATATATATTATTTATTGCATGATTAATATGTTTAATTGCATGTT
* **
17246702 TGCATGATTATTAATATATTTTGCTTGCATGATTAT
66 TGCATGATTATTAATATA-TCTAATTGCATGATTAT
*
17246738 TAATATGTTTATTTACAT-A-ATATGATATTATTTATTGCATGATTAATAT
1 TAATATATTTATTTACATGATATAT-ATATTATTTATTGCATGATTAATAT
17246787 TTGATTTGCA
Statistics
Matches: 123, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
92 19 0.15
93 3 0.02
94 13 0.11
95 5 0.04
96 7 0.06
98 3 0.02
99 38 0.31
100 35 0.28
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (100 bp):
TAATATATTTATTTACATGATATATATATTATTTATTGCATGATTAATATGTTTAATTGCATGTT
TGCATGATTATTAATATATCTAATTGCATGATTAT
Found at i:17248515 original size:143 final size:142
Alignment explanation
Indices: 17248352--17248610 Score: 324
Period size: 143 Copynumber: 1.8 Consensus size: 142
17248342 TAAAAGAATC
* * * *
17248352 AAAATACCCTTAGGGGTATTTGCT-TAATTTGACCTTCCTGAGGGCGGTTTTTCATGAAATGCTT
1 AAAATACACTTAGGGATATTT-CTCTAATTTGACCTTCCTGAGGGCGATTTTT-ATGAAACGCTT
* * * * *
17248416 TAGATTATGTTTTTATATTATTTCATGA-TTTTTAGTGTATTAAAAACCTTGATCACACCATAGA
64 TAGATCAAGATTTGATATTATTTCATGATTTTTTA-TGCATTAAAAACCTTGATCACACCATAGA
17248480 AGGTGTGAAATTACT
128 AGGTGTGAAATTACT
* * * * * *
17248495 AAAATACACTTAGGGATATTTTTCTAATTTGACTTTCTTGAGGTCGATTTTTTTGAAACGTTTTA
1 AAAATACACTTAGGGATATTTCTCTAATTTGACCTTCCTGAGGGCGATTTTTATGAAACGCTTTA
* *
17248560 GATCAAGATTTGATATTATTTGATGATTTTTTATGCATTAAAAACTTTGAT
66 GATCAAGATTTGATATTATTTCATGATTTTTTATGCATTAAAAACCTTGAT
17248611 TAAGTGTGAA
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
142 48 0.49
143 49 0.51
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.43
Consensus pattern (142 bp):
AAAATACACTTAGGGATATTTCTCTAATTTGACCTTCCTGAGGGCGATTTTTATGAAACGCTTTA
GATCAAGATTTGATATTATTTCATGATTTTTTATGCATTAAAAACCTTGATCACACCATAGAAGG
TGTGAAATTACT
Found at i:17248695 original size:21 final size:21
Alignment explanation
Indices: 17248669--17248711 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17248659 AACTTTTCGA
17248669 TGTTAGTTTTCCATGAAAACT
1 TGTTAGTTTTCCATGAAAACT
17248690 TGTTAGTTTTCCATGAAAACT
1 TGTTAGTTTTCCATGAAAACT
17248711 T
1 T
17248712 TCAAATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (21 bp):
TGTTAGTTTTCCATGAAAACT
Found at i:17250085 original size:60 final size:60
Alignment explanation
Indices: 17250017--17250130 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
17250007 TCATGCATTC
* *
17250017 AAGTTTGCATTTTCATTAATGGTATTTTGGTAATTTTTGTCACAT-CACTCTCATTCACCA
1 AAGTTTGCATTTTCATCAATGGTATTTTAGTAA-TTTTGTCACATGCACTCTCATTCACCA
* *
17250077 AAGTTTGCATTTTTATCAATGGTATTTTAGTAATTTTGTCACATGCATTCTCAT
1 AAGTTTGCATTTTCATCAATGGTATTTTAGTAATTTTGTCACATGCACTCTCAT
17250131 GAAACCCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 11 0.22
60 38 0.78
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (60 bp):
AAGTTTGCATTTTCATCAATGGTATTTTAGTAATTTTGTCACATGCACTCTCATTCACCA
Found at i:17250167 original size:19 final size:19
Alignment explanation
Indices: 17250140--17250239 Score: 101
Period size: 19 Copynumber: 5.3 Consensus size: 19
17250130 TGAAACCCCA
* *
17250140 AAACTACCATCCAAATCCT
1 AAACCACCATCCAAACCCT
* * *
17250159 AAACCACCATGCAAGCCCC
1 AAACCACCATCCAAACCCT
*
17250178 AAACCACCATCTAAACCCT
1 AAACCACCATCCAAACCCT
* *
17250197 AAACCACCATCCAAGCTCT
1 AAACCACCATCCAAACCCT
* * *
17250216 AAACCACTATCAAAACCAT
1 AAACCACCATCCAAACCCT
17250235 AAACC
1 AAACC
17250240 TAAACCCTAA
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.14
Consensus pattern (19 bp):
AAACCACCATCCAAACCCT
Found at i:17250198 original size:38 final size:38
Alignment explanation
Indices: 17250135--17250239 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 38
17250125 TCTCATGAAA
* * * *
17250135 CCCCAAAACTACCATCCAAATCCTAAACCACCATGCAAG
1 CCCC-AAACCACCATCAAAACCCTAAACCACCATCCAAG
*
17250174 CCCCAAACCACCATCTAAACCCTAAACCACCATCCAAG
1 CCCCAAACCACCATCAAAACCCTAAACCACCATCCAAG
* * * *
17250212 CTCTAAACCACTATCAAAACCATAAACC
1 CCCCAAACCACCATCAAAACCCTAAACC
17250240 TAAACCCTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
38 53 0.93
39 4 0.07
ACGTcount: A:0.42, C:0.42, G:0.03, T:0.13
Consensus pattern (38 bp):
CCCCAAACCACCATCAAAACCCTAAACCACCATCCAAG
Found at i:17250353 original size:19 final size:19
Alignment explanation
Indices: 17250291--17250359 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 19
17250281 AAACCCTAAA
*
17250291 CTAAACTCTAAACCACCAT
1 CTAAACCCTAAACCACCAT
* * * *
17250310 CCAAGCTCC-AACCCACTAT
1 CTAAAC-CCTAAACCACCAT
*
17250329 C-CAACCCTAAACCACCAT
1 CTAAACCCTAAACCACCAT
*
17250347 CTAAACCTTAAAC
1 CTAAACCCTAAAC
17250360 ACTAAACCAA
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
17 2 0.06
18 11 0.31
19 22 0.61
20 1 0.03
ACGTcount: A:0.39, C:0.42, G:0.01, T:0.17
Consensus pattern (19 bp):
CTAAACCCTAAACCACCAT
Found at i:17250376 original size:26 final size:26
Alignment explanation
Indices: 17250347--17250443 Score: 88
Period size: 26 Copynumber: 3.5 Consensus size: 26
17250337 AAACCACCAT
17250347 CTAAACCTTAAACACTAAACCAAACC
1 CTAAACCTTAAACACTAAACCAAACC
*
17250373 CT-AACCTTAAACTCTTAAACCAAAACC
1 CTAAACCTTAAACAC-TAAACC-AAACC
* *
17250400 CTAACCTAACCTTAAACCCTAAACCAACCC
1 CT-A---AACCTTAAACACTAAACCAAACC
*
17250430 CCAAACCTTCAAAC
1 CTAAACCTT-AAAC
17250444 TAACTAGATC
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
25 11 0.19
26 14 0.24
27 11 0.19
29 1 0.02
30 5 0.08
31 6 0.10
32 11 0.19
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (26 bp):
CTAAACCTTAAACACTAAACCAAACC
Found at i:17250384 original size:32 final size:31
Alignment explanation
Indices: 17250348--17250437 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
17250338 AACCACCATC
*
17250348 TAAACCTTAAACACTAAA-CCAAACCCTAACCT
1 TAAACCTTAAAC-CAAAACCCAAA-CCTAACCT
*
17250380 TAAACTCTTAAACCAAAACCCTAACCTAACCT
1 TAAAC-CTTAAACCAAAACCCAAACCTAACCT
* **
17250412 TAAACCCTAAACCAACCCCCAAACCT
1 TAAACCTTAAACCAAAACCCAAACCT
17250438 TCAAACTAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
31 17 0.34
32 22 0.44
33 11 0.22
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (31 bp):
TAAACCTTAAACCAAAACCCAAACCTAACCT
Found at i:17250689 original size:19 final size:19
Alignment explanation
Indices: 17250662--17250780 Score: 130
Period size: 19 Copynumber: 6.3 Consensus size: 19
17250652 TGAAACCCCA
* *
17250662 AAACTACCATCCAAATCCT
1 AAACCACCATCCAAACCCT
* * *
17250681 AAACCACCATGCAAGCCCC
1 AAACCACCATCCAAACCCT
*
17250700 AAACCACCATCTAAACCCT
1 AAACCACCATCCAAACCCT
*
17250719 AAACCACCATCTAAACCCT
1 AAACCACCATCCAAACCCT
* *
17250738 AAACCACCATCCAAGCTCT
1 AAACCACCATCCAAACCCT
* * *
17250757 AAACCACTATCAAAACCAT
1 AAACCACCATCCAAACCCT
17250776 AAACC
1 AAACC
17250781 TAAACCCTAA
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.14
Consensus pattern (19 bp):
AAACCACCATCCAAACCCT
Found at i:17250743 original size:57 final size:57
Alignment explanation
Indices: 17250662--17250780 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 57
17250652 TGAAACCCCA
* * * * *
17250662 AAACTACCATCCAAATCCTAAACCACCATGCAAGCCCCAAACCACCATCTAAACCCT
1 AAACCACCATCCAAACCCTAAACCACCATCCAAGCCCCAAACCACCATCAAAACCAT
* * * *
17250719 AAACCACCATCTAAACCCTAAACCACCATCCAAGCTCTAAACCACTATCAAAACCAT
1 AAACCACCATCCAAACCCTAAACCACCATCCAAGCCCCAAACCACCATCAAAACCAT
17250776 AAACC
1 AAACC
17250781 TAAACCCTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.14
Consensus pattern (57 bp):
AAACCACCATCCAAACCCTAAACCACCATCCAAGCCCCAAACCACCATCAAAACCAT
Found at i:17250894 original size:19 final size:19
Alignment explanation
Indices: 17250832--17250900 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 19
17250822 AAACCCTAAA
*
17250832 CTAAACTCTAAACCACCAT
1 CTAAACCCTAAACCACCAT
* * * *
17250851 CCAAGCTCC-AACCCACTAT
1 CTAAAC-CCTAAACCACCAT
*
17250870 C-CAACCCTAAACCACCAT
1 CTAAACCCTAAACCACCAT
*
17250888 CTAAACCTTAAAC
1 CTAAACCCTAAAC
17250901 ACTAAACCAA
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
17 2 0.06
18 11 0.31
19 22 0.61
20 1 0.03
ACGTcount: A:0.39, C:0.42, G:0.01, T:0.17
Consensus pattern (19 bp):
CTAAACCCTAAACCACCAT
Found at i:17250917 original size:26 final size:26
Alignment explanation
Indices: 17250888--17250984 Score: 88
Period size: 26 Copynumber: 3.5 Consensus size: 26
17250878 AAACCACCAT
17250888 CTAAACCTTAAACACTAAACCAAACC
1 CTAAACCTTAAACACTAAACCAAACC
*
17250914 CT-AACCTTAAACTCTTAAACCAAAACC
1 CTAAACCTTAAACAC-TAAACC-AAACC
* *
17250941 CTAACCTAACCTTAAACCCTAAACCAACCC
1 CT-A---AACCTTAAACACTAAACCAAACC
*
17250971 CCAAACCTTCAAAC
1 CTAAACCTT-AAAC
17250985 TAACTAGATC
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
25 11 0.19
26 14 0.24
27 11 0.19
29 1 0.02
30 5 0.08
31 6 0.10
32 11 0.19
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (26 bp):
CTAAACCTTAAACACTAAACCAAACC
Found at i:17250925 original size:32 final size:31
Alignment explanation
Indices: 17250889--17250978 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
17250879 AACCACCATC
*
17250889 TAAACCTTAAACACTAAA-CCAAACCCTAACCT
1 TAAACCTTAAAC-CAAAACCCAAA-CCTAACCT
*
17250921 TAAACTCTTAAACCAAAACCCTAACCTAACCT
1 TAAAC-CTTAAACCAAAACCCAAACCTAACCT
* **
17250953 TAAACCCTAAACCAACCCCCAAACCT
1 TAAACCTTAAACCAAAACCCAAACCT
17250979 TCAAACTAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
31 17 0.34
32 22 0.44
33 11 0.22
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (31 bp):
TAAACCTTAAACCAAAACCCAAACCTAACCT
Done.