Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003504.1 Hibiscus syriacus cultivar Beakdansim tig00007406_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: 232423
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4836 original size:19 final size:19
Alignment explanation
Indices: 4812--4856 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
4802 AATTGTGTAC
4812 CGATGCATGGATAGTGCAT
1 CGATGCATGGATAGTGCAT
4831 CGATGCATGGATAGTGCAT
1 CGATGCATGGATAGTGCAT
4850 CGATGCA
1 CGATGCA
4857 CATGTTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (19 bp):
CGATGCATGGATAGTGCAT
Found at i:4872 original size:24 final size:20
Alignment explanation
Indices: 4826--4902 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
4816 GCATGGATAG
* * *
4826 TGCATCGATGCA-TGGATAG
1 TGCATCGATGCACTGTAGAA
4845 TGCATCGATGCACATGTTAAGGAA
1 TGCATCGATGCAC-TG-T-A-GAA
4869 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
4889 TGTATCGATGCACT
1 TGCATCGATGCACT
4903 TCAAAGGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 12 0.24
20 16 0.33
21 3 0.06
22 1 0.02
23 3 0.06
24 14 0.29
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:5240 original size:19 final size:21
Alignment explanation
Indices: 5201--5250 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
5191 GAGCATATGT
5201 TTGATATGTTACATGTGTGTTA
1 TTGATATGTTACA-GTGTGTTA
5223 TTGAT-TGTTACA-TGTGTTA
1 TTGATATGTTACAGTGTGTTA
* *
5242 ATGGTATGT
1 TTGATATGT
5251 GTGAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.40
20 3 0.12
21 7 0.28
22 5 0.20
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.50
Consensus pattern (21 bp):
TTGATATGTTACAGTGTGTTA
Found at i:5681 original size:32 final size:33
Alignment explanation
Indices: 5640--5795 Score: 105
Period size: 32 Copynumber: 4.9 Consensus size: 33
5630 AGTCGAGGGT
*
5640 TTACCTATGTTC-TACGGAACATATGGATAGAA
1 TTACCTATGTTCTTACGGAACATATGGACAGAA
* *
5672 TTACCTATG-TCTTTCGGGACATATGGACAGAA
1 TTACCTATGTTCTTACGGAACATATGGACAGAA
* **
5704 TTACATATG-TCTT-TTGAGACATATGGAC--AA
1 TTACCTATGTTCTTACGGA-ACATATGGACAGAA
* * * **
5734 TATACCTATGTTC-TAAGTAGCATATGGACA-TT
1 T-TACCTATGTTCTTACGGAACATATGGACAGAA
* * *
5766 TTACCTAGGTTCTT-CGGGACCTATGGACAG
1 TTACCTATGTTCTTACGGAACATATGGACAG
5796 TTGCCGAGGT
Statistics
Matches: 96, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
30 3 0.03
31 40 0.42
32 53 0.55
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (33 bp):
TTACCTATGTTCTTACGGAACATATGGACAGAA
Found at i:14270 original size:37 final size:37
Alignment explanation
Indices: 14192--14282 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
14182 ATTAGTTTAT
* *
14192 TTTTATTAGGAGT-TTTATTAGGCAACGTTTATTCAA
1 TTTTATTAGGAGTCTTTAATAGGCAACGTTTATGCAA
*
14228 CTTTATTAGGAGTCTTTAATAGGCAAC-TGTTATGCAA
1 TTTTATTAGGAGTCTTTAATAGGCAACGT-TTATGCAA
14265 TTTTATTAGGAGTCTTTA
1 TTTTATTAGGAGTCTTTA
14283 TCAGGTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 13 0.27
37 36 0.73
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (37 bp):
TTTTATTAGGAGTCTTTAATAGGCAACGTTTATGCAA
Found at i:27841 original size:23 final size:23
Alignment explanation
Indices: 27815--27892 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
27805 CACCACAGCT
*
27815 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
27838 CATATAATTGCACCGTAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
* * *
27861 CGTAGAATTACACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
27884 TATAATAAT
1 CAT-ATAAT
27893 GTCTATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:28070 original size:103 final size:103
Alignment explanation
Indices: 27899--28116 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
27889 TAATGTCTAT
* * *
27899 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
27964 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
28002 AAGGACCACATATCATTCCTTAAAAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
28067 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
28105 AAAGACCACATA
1 AAGGACCACATA
28117 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:29056 original size:64 final size:63
Alignment explanation
Indices: 28902--29063 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 63
28892 TTCCCTATCG
* * ** * ** *
28902 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTGCCTGTGCATCGATGCACCAAATACATTCGATGTTTGTTGATTAAAGA
* * * *
28965 GATGCATCGATGCA-TGCCTTATACATCGATGCACCAATTTCATTCGATGTTT-TTGGATTAAAA
1 G-TGCATCGATGCACTGCC-TGTGCATCGATGCACCAAATACATTCGATGTTTGTT-GATT-AAA
29028 GA
62 GA
*
29030 GTGCATCGATGCACTGCCTGTGCATCGATACACC
1 GTGCATCGATGCACTGCCTGTGCATCGATGCACC
29064 TTCAAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
63 6 0.08
64 66 0.84
65 7 0.09
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTGCCTGTGCATCGATGCACCAAATACATTCGATGTTTGTTGATTAAAGA
Found at i:32289 original size:23 final size:23
Alignment explanation
Indices: 32263--32326 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
32253 CAGCTCATAT
* *
32263 AATTGCACCTAAGTTCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
32286 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
32309 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
32327 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:32518 original size:103 final size:103
Alignment explanation
Indices: 32342--32765 Score: 812
Period size: 103 Copynumber: 4.1 Consensus size: 103
32332 TAATGTCCAT
*
32342 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
32407 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
32445 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCAAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
32510 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
32548 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
32613 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
32651 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
32716 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
32754 AAGGACCACATA
1 AAGGACCACATA
32766 GACCCTCTAC
Statistics
Matches: 315, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 315 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:33268 original size:20 final size:20
Alignment explanation
Indices: 33243--33280 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33233 TCTTTTTTTA
*
33243 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
33263 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
33281 TTGAATGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:37717 original size:50 final size:50
Alignment explanation
Indices: 37656--37757 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
37646 AAAATTATTG
37656 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
37706 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
37756 AA
1 AA
37758 ATAGGATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:37959 original size:30 final size:30
Alignment explanation
Indices: 37904--37960 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
37894 AACGGTATGG
*
37904 CGCCCAGACCACTCGACGACTTTCATTGGT
1 CGCCCAGACCACTCGACGACCTTCATTGGT
*
37934 CGCCCAGACCA-TCCGGCGACCTTCATT
1 CGCCCAGACCACT-CGACGACCTTCATT
37961 CGAACTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (30 bp):
CGCCCAGACCACTCGACGACCTTCATTGGT
Found at i:38388 original size:5 final size:5
Alignment explanation
Indices: 38341--38387 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
38331 CTGGGACAAC
* * *
38341 TCCGT TCCGT TCCGT TCCGT TCCGT TCCGT TCTGT TCTGT TCTGT TC
1 TCCGT TCCGT TCCGT TCCGT TCCGT TCCGT TCCGT TCCGT TCCGT TC
38388 TATTCTGTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.00, C:0.34, G:0.19, T:0.47
Consensus pattern (5 bp):
TCCGT
Found at i:38393 original size:5 final size:5
Alignment explanation
Indices: 38344--38395 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
38334 GGACAACTCC
* * * * * *
38344 GTTCC GTTCC GTTCC GTTCC GTTCC GTTCT GTTCT GTTCT GTTCT ATTCT
1 GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT GTTCT
38394 GT
1 GT
38396 CTTTCCATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.02, C:0.29, G:0.19, T:0.50
Consensus pattern (5 bp):
GTTCT
Found at i:41883 original size:36 final size:36
Alignment explanation
Indices: 41836--41907 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
41826 CCGTTGCCGT
*
41836 TGCCATTGTCGACATTGCGATCGGATTTACATAGGC
1 TGCCATTGTCGACATTGCGATCGGATTTACAAAGGC
41872 TGCCATTGTCGACATTGCGATCGGATTTACAAAGGC
1 TGCCATTGTCGACATTGCGATCGGATTTACAAAGGC
41908 AGAATTTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (36 bp):
TGCCATTGTCGACATTGCGATCGGATTTACAAAGGC
Found at i:42763 original size:18 final size:18
Alignment explanation
Indices: 42740--42776 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42730 CAAACAATTG
42740 AAAACATCAACATTGGAA
1 AAAACATCAACATTGGAA
* *
42758 AAAACATTAACTTTGGAA
1 AAAACATCAACATTGGAA
42776 A
1 A
42777 TTTCAGTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (18 bp):
AAAACATCAACATTGGAA
Found at i:46076 original size:2 final size:2
Alignment explanation
Indices: 46069--46093 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46059 TTAAAAGAAT
46069 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46094 TAGCACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47227 original size:18 final size:19
Alignment explanation
Indices: 47192--47228 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
47182 CACGGAATGT
47192 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
47212 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
47229 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:50817 original size:34 final size:31
Alignment explanation
Indices: 50717--50822 Score: 95
Period size: 34 Copynumber: 3.3 Consensus size: 31
50707 GGTAAGAAAT
* * * * *
50717 TTATTTTTATGTTAGTATTTTTTAAATAGTTA
1 TTATTTTTATATTAATA-TATTTATATAATTA
* *
50749 TTATATTTTATATTAATATATTTATGTAAATA
1 TTAT-TTTTATATTAATATATTTATATAATTA
*
50781 TTATTTTTCTATTAAAATAATATTTATATAATTA
1 TTATTTTTATATT--AAT-ATATTTATATAATTA
50815 TTATTTTT
1 TTATTTTT
50823 TTAAAATTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
31 8 0.13
32 17 0.28
33 14 0.23
34 21 0.35
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (31 bp):
TTATTTTTATATTAATATATTTATATAATTA
Found at i:50989 original size:17 final size:17
Alignment explanation
Indices: 50967--51020 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
50957 AATGTTAATA
50967 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
50984 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
51001 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
51018 TTT
1 TTT
51021 TTATAATGCA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:52581 original size:21 final size:21
Alignment explanation
Indices: 52551--52619 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
52541 GCAGGGGTAC
* * *
52551 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCAGTTCAT
52572 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCAGTTCAT
52593 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCAGTTCAT
52614 ATGCCA
1 ATGCCA
52620 TCTCCGCAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (21 bp):
ATGCCAAGCCCACCAGTTCAT
Found at i:52645 original size:42 final size:42
Alignment explanation
Indices: 52623--52758 Score: 229
Period size: 42 Copynumber: 3.2 Consensus size: 42
52613 TATGCCATCT
*
52623 CCGCAGGGTTACATTCCGAGCCCG-CAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGCCCGCCA-GGTTACATTCCGAGC
52665 CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATTCCGAGC
* *
52707 CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATGCCTAGC
1 CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATTCCGAGC
52749 CCGCAGGGTT
1 CCGCAGGGTT
52759 TTATACCATA
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
42 88 0.98
43 2 0.02
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (42 bp):
CCGCAGGGTTACATTCCTAGCCCGCCAGGTTACATTCCGAGC
Found at i:52649 original size:21 final size:21
Alignment explanation
Indices: 52623--52758 Score: 204
Period size: 21 Copynumber: 6.5 Consensus size: 21
52613 TATGCCATCT
52623 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
52644 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
52665 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
52686 CCGCCA-GGTTACATTCCGAGC
1 CCG-CAGGGTTACATTCCGAGC
*
52707 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
52728 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
52749 CCGCAGGGTT
1 CCGCAGGGTT
52759 TTATACCATA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.04
21 99 0.93
22 4 0.04
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:53316 original size:40 final size:40
Alignment explanation
Indices: 53272--53356 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
53262 AAATGTTTTT
* * *
53272 AAAATACAAATTATATTATTCAAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTCAAAATTTAAAATTAAAATA
*
53312 AAAATAAAAATAATATTATTCGAAATTTAAAATTAAAATA
1 AAAATAAAAATAATATTATTCAAAATTTAAAATTAAAATA
*
53352 TAAAT
1 AAAAT
53357 TATAGTATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (40 bp):
AAAATAAAAATAATATTATTCAAAATTTAAAATTAAAATA
Found at i:53381 original size:34 final size:34
Alignment explanation
Indices: 53300--53382 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
53290 TTCAAAATTT
* *
53300 AAATTTAAAATAAAAATAAAAATAATATTATTCG
1 AAATTTAAAATTAAAATAAAAATAATAGTATTCG
* *
53334 AAATTTAAAATTAAAATATAAATTATAGTATTCG
1 AAATTTAAAATTAAAATAAAAATAATAGTATTCG
*
53368 AAATTTAACATTAAA
1 AAATTTAAAATTAAA
53383 TTTCAACTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (34 bp):
AAATTTAAAATTAAAATAAAAATAATAGTATTCG
Found at i:53382 original size:40 final size:39
Alignment explanation
Indices: 53270--53382 Score: 119
Period size: 34 Copynumber: 3.0 Consensus size: 39
53260 ATAAATGTTT
* *
53270 TTAAAATACAAATTATATTATTCAAAATTTAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA-TTAAAA
* *
53310 TAAAAATAAAAATAATATTATTCGAAA--T---TTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAATTAAAA
* *
53344 TTAAAATATAAATTATAGTATTCGAAATTTAACATTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAA-ATTAAA
53383 TTTCAACTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
34 29 0.49
36 1 0.02
38 1 0.02
40 28 0.47
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (39 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAATTAAAA
Found at i:54012 original size:128 final size:128
Alignment explanation
Indices: 53776--54074 Score: 544
Period size: 128 Copynumber: 2.3 Consensus size: 128
53766 ACAATCCATC
53776 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
53841 GGAAGGCGCGCCCCCGGGAACGCTCCTTCAAGTCCCCTAAGAAATAATAGGTACTGATATGAA
66 AGAAGGCGCGCCCCCGGGAACGCACCTTCAAGTCCCCTAAGAAATAATAGGTACTGATATGAA
* *
53904 TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
53969 AGAAGGCGCGCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 AGAAGGCGCGCCCCCGGGAACGCACCTTCAAGTCCCCTAAGAAATAATAGGTACTGATATGAA
*
54032 TAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATA
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATA
54075 TCCATACCTC
Statistics
Matches: 164, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 164 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
AGAAGGCGCGCCCCCGGGAACGCACCTTCAAGTCCCCTAAGAAATAATAGGTACTGATATGAA
Found at i:55401 original size:30 final size:32
Alignment explanation
Indices: 55337--55415 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
55327 AAAAAAATTC
*
55337 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
55371 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
55401 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
55416 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
31 4 0.10
32 8 0.20
33 18 0.45
34 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:57955 original size:58 final size:58
Alignment explanation
Indices: 57852--57965 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
57842 GAATGATGGA
* * *
57852 GATCTGGTTCAGAAATACTCTCTGTTCTTCTACCCTTTGAACTATGCTTTTGTTTGGG
1 GATCTGATTCAGAAATACTCTCTGTTCTTCTACCCTTTGAACTATGATTGTGTTTGGG
* **
57910 GATCTGATTCAGAAATGA-TCTCTGTTTTTCTACCCTTTGCTCTATGATTGTGTTTG
1 GATCTGATTCAGAAAT-ACTCTCTGTTCTTCTACCCTTTGAACTATGATTGTGTTTG
57966 TGCGATTACT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 48 0.98
59 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (58 bp):
GATCTGATTCAGAAATACTCTCTGTTCTTCTACCCTTTGAACTATGATTGTGTTTGGG
Found at i:66802 original size:11 final size:11
Alignment explanation
Indices: 66786--66810 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
66776 TTTGCTATTT
66786 AAAAAAAACAA
1 AAAAAAAACAA
66797 AAAAAAAACAA
1 AAAAAAAACAA
66808 AAA
1 AAA
66811 GACAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:72445 original size:101 final size:103
Alignment explanation
Indices: 72261--72468 Score: 332
Period size: 101 Copynumber: 2.0 Consensus size: 103
72251 TGCTTCGAGT
*
72261 AAAACTGGACTTAATTCAAAAAATAGATTTTTTTAATTCGACTCGAGAAAATTCAACTCGAATTG
1 AAAACTGGACTTAATTCAAAAAATAGATTTTTTTAACTCGACTCGAGAAAATTCAACTCGAATTG
72326 CCTTCAAATTATAATTTCATAAACTCGAATCGAATAAA
66 CCTTCAAATTATAATTTCATAAACTCGAATCGAATAAA
**
72364 AAAACTCGG-CTTAATTCGGAAAATAGA-TTTTTT-ACTCGACTCGAGAAAATTCAACTCGAATT
1 AAAACT-GGACTTAATTCAAAAAATAGATTTTTTTAACTCGACTCGAGAAAATTCAACTCGAATT
* * *
72426 GGCTTCAAATTGTAGTTTCATAAACTCGAATCGAATAAA
65 GCCTTCAAATTATAATTTCATAAACTCGAATCGAATAAA
72465 AAAA
1 AAAA
72469 TTAAGTTCAA
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
101 68 0.69
102 6 0.06
103 22 0.22
104 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (103 bp):
AAAACTGGACTTAATTCAAAAAATAGATTTTTTTAACTCGACTCGAGAAAATTCAACTCGAATTG
CCTTCAAATTATAATTTCATAAACTCGAATCGAATAAA
Found at i:74908 original size:2 final size:2
Alignment explanation
Indices: 74901--74950 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
74891 ATAAATTTAC
74901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74943 AT AT AT AT
1 AT AT AT AT
74951 TTGTATCTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82130 original size:22 final size:22
Alignment explanation
Indices: 82098--82141 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
82088 CATGATTATA
*
82098 ATTAAAACATAAATTTAAAATT
1 ATTAAAACATAAACTTAAAATT
* *
82120 ATTAAATCATATACTTAAAATT
1 ATTAAAACATAAACTTAAAATT
82142 CATATCCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAAAACATAAACTTAAAATT
Found at i:82367 original size:31 final size:31
Alignment explanation
Indices: 82329--82394 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
82319 AATATAAATA
*
82329 TAATAAATCAATAATATAAATGATCAAAACT
1 TAATAAATCAATAACATAAATGATCAAAACT
* * *
82360 TAATAAATTAATAACATAAATGATTAAAATT
1 TAATAAATCAATAACATAAATGATCAAAACT
82391 TAAT
1 TAAT
82395 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (31 bp):
TAATAAATCAATAACATAAATGATCAAAACT
Found at i:84106 original size:60 final size:60
Alignment explanation
Indices: 84042--84167 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
84032 ATGGTTCCCT
* * * * *
84042 GACTATAGAA-TATT-ATTTTATTAAGT-TTCTCGAGTATTAAAAGTTATAAAATGGTCATTC
1 GACTATA-AAGTATTGATTTT-TTAAGTATT-TCGACTATTAAAAGCTACAAAATGCTCATCC
* *
84102 GACTATAAAGTGTTGCTTTTTTAAGTATTTCGACTATTAAAAGCTACAAAATGCTCATCC
1 GACTATAAAGTATTGATTTTTTAAGTATTTCGACTATTAAAAGCTACAAAATGCTCATCC
84162 GACTAT
1 GACTAT
84168 TTATTGTGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.04
60 48 0.86
61 6 0.11
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (60 bp):
GACTATAAAGTATTGATTTTTTAAGTATTTCGACTATTAAAAGCTACAAAATGCTCATCC
Found at i:85064 original size:24 final size:24
Alignment explanation
Indices: 85037--85085 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
85027 TAGAAGATTG
85037 AAAATAAGAT-AAAAAATGTTATAA
1 AAAATAA-ATCAAAAAATGTTATAA
* *
85061 AAAATGAATCAAAACATGTTATAA
1 AAAATAAATCAAAAAATGTTATAA
85085 A
1 A
85086 CGTTTATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (24 bp):
AAAATAAATCAAAAAATGTTATAA
Found at i:90333 original size:21 final size:21
Alignment explanation
Indices: 90307--90350 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
90297 ATTTCTGGGT
* *
90307 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
90328 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
90349 AA
1 AA
90351 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:90902 original size:23 final size:24
Alignment explanation
Indices: 90859--90905 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
90849 ATATGGCATG
*
90859 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
90883 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
90906 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:91121 original size:31 final size:31
Alignment explanation
Indices: 91083--91238 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
91073 AGGGTCGAGG
91083 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
91114 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
91145 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
91176 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
91207 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
91238 G
1 G
91239 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:94384 original size:21 final size:21
Alignment explanation
Indices: 94358--94401 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
94348 ATTTCTGGGT
* *
94358 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
94379 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
94400 AA
1 AA
94402 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:94955 original size:23 final size:24
Alignment explanation
Indices: 94912--94958 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
94902 ATATGGCATG
*
94912 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
94936 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
94959 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:95174 original size:31 final size:31
Alignment explanation
Indices: 95136--95291 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
95126 AGGGTCGAGG
95136 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
95167 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
95198 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
95229 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
95260 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
95291 G
1 G
95292 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:98440 original size:21 final size:21
Alignment explanation
Indices: 98414--98457 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
98404 ATTTCTGGGT
* *
98414 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
98435 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
98456 AA
1 AA
98458 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:99011 original size:23 final size:24
Alignment explanation
Indices: 98968--99014 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
98958 ATATGGCATG
*
98968 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
98992 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
99015 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:99230 original size:31 final size:31
Alignment explanation
Indices: 99192--99347 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
99182 AGGGTCGAGG
99192 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
99223 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
99254 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
99285 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
99316 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
99347 G
1 G
99348 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:115819 original size:21 final size:21
Alignment explanation
Indices: 115795--115848 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
115785 AATTGAAGCG
*
115795 AGAGAATTGGGGGAAATGGAC
1 AGAGAATTAGGGGAAATGGAC
*
115816 AGAGAATTAGGGGAAATGGAT
1 AGAGAATTAGGGGAAATGGAC
*
115837 AAAGAATTAGGG
1 AGAGAATTAGGG
115849 ATTGAGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.02, G:0.39, T:0.17
Consensus pattern (21 bp):
AGAGAATTAGGGGAAATGGAC
Found at i:118970 original size:90 final size:90
Alignment explanation
Indices: 118764--118970 Score: 288
Period size: 90 Copynumber: 2.3 Consensus size: 90
118754 ACCCAACGTC
* * * * * * * *
118764 ACATAATCATCAAAAAAGAAAAAGCCAATTGACTTGCAATAGTCCTGCTGAATTCATGGGACCAT
1 ACATGATCATCAAAAAAGCACAAGCCAACTGACCTGCAATAGTCATGCAGAATTCATGGGAACAT
118829 ACTCTCCAATTTCGTCATCAACATT
66 ACTCTCCAATTTCGTCATCAACATT
* *
118854 ACATGATCATAAAAAAAACACAAGCCAACTGACCTGCAATAGTCATGCAGAATTCATGGGAACAT
1 ACATGATCATCAAAAAAGCACAAGCCAACTGACCTGCAATAGTCATGCAGAATTCATGGGAACAT
* *
118919 ACTCTCCAATTTCTTCATTAACATT
66 ACTCTCCAATTTCGTCATCAACATT
* *
118944 ACATGATTATCAAAAAAGCACTAGCCA
1 ACATGATCATCAAAAAAGCACAAGCCA
118971 CGACAATGTT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 101 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (90 bp):
ACATGATCATCAAAAAAGCACAAGCCAACTGACCTGCAATAGTCATGCAGAATTCATGGGAACAT
ACTCTCCAATTTCGTCATCAACATT
Found at i:122385 original size:2 final size:2
Alignment explanation
Indices: 122378--122431 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
122368 AAGCTCCACA
122378 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
122420 AT AT AT AT AT AT
1 AT AT AT AT AT AT
122432 TCTCCACCTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123596 original size:21 final size:21
Alignment explanation
Indices: 123570--123623 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
123560 GCGTTGCATT
123570 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
123591 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
123612 TCTCGTTGCGAT
1 TCGCGTTGCGAT
123624 TTTCCATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:123642 original size:20 final size:20
Alignment explanation
Indices: 123615--123875 Score: 224
Period size: 20 Copynumber: 12.4 Consensus size: 20
123605 TTGAAAATCT
123615 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* *
123635 CATTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCG
123655 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
*
123675 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCG
* *
123695 CGTTGCGATTTTTCAGTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
123715 CGTTGCGATAGTCTACAGTT-G
1 CGTTGCGAT--TTTCCATTTCG
*
123736 TCGTTGCGATTTTCCAAATT--
1 -CGTTGCGATTTTCC-ATTTCG
* *
123756 CGTTGCGATAGTTTACAGTT-G
1 CGTTGCGAT--TTTCCATTTCG
123777 TCGTTGCGATTTTCCAAATTCGTTGCGTCG
1 -CGTTGCGATTTTCC--A----TT---TCG
*
123807 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCG
123827 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
*
123847 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCG
*
123867 TGTTGCGAT
1 CGTTGCGAT
123876 AGTTGAAAAT
Statistics
Matches: 204, Mismatches: 19, Indels: 36
0.79 0.07 0.14
Matches are distributed among these distances:
19 9 0.04
20 142 0.70
21 8 0.04
22 26 0.13
23 1 0.00
26 1 0.00
27 1 0.00
29 15 0.07
30 1 0.00
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:123663 original size:40 final size:40
Alignment explanation
Indices: 123615--123875 Score: 278
Period size: 40 Copynumber: 6.2 Consensus size: 40
123605 TTGAAAATCT
*
123615 CGTTGCGATTTTCCATTTCGCATTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
123655 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
* * * *
123695 CGTTGCGATTTTTCAGTTCGCGTTGCGATAGTCTACAGTT-G
1 CGTTGCGATTTTCCATTTCGCGTTGCGAT--TTTCCAGTTCG
* *
123736 TCGTTGCGATTTTCCAAATT--CGTTGCGATAGTTTACAGTT-G
1 -CGTTGCGATTTTCC-ATTTCGCGTTGCGAT--TTTCCAGTTCG
123777 TCGTTGCGATTTTCCAAATTCGTTGCGTCGCGTTGCGATTTTCCAGTTCG
1 -CGTTGCGATTTTCC--A----TT---TCGCGTTGCGATTTTCCAGTTCG
123827 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
*
123867 TGTTGCGAT
1 CGTTGCGAT
123876 AGTTGAAAAT
Statistics
Matches: 195, Mismatches: 11, Indels: 30
0.83 0.05 0.13
Matches are distributed among these distances:
40 97 0.50
41 36 0.18
42 22 0.11
43 5 0.03
46 1 0.01
47 1 0.01
49 23 0.12
50 1 0.01
51 9 0.05
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.41
Consensus pattern (40 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
Found at i:123761 original size:41 final size:41
Alignment explanation
Indices: 123715--123803 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
123705 TTTCAGTTCG
123715 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
123756 CGTTGCGATAGTTTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
123797 CGTTGCG
1 CGTTGCG
123804 TCGCGTTGCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:123909 original size:132 final size:131
Alignment explanation
Indices: 123672--123935 Score: 397
Period size: 132 Copynumber: 2.0 Consensus size: 131
123662 ATTTTCCATT
*
123672 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTTCAGTTCGCGTTGCGATAGTCTACAGTTGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATA-TCTACAGTTGT
* * * *
123737 CGTTGCGATTTTCCAAATTCGTTGCGATAGTTTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
65 CGTTGCGATGTTCAAAATGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
123802 CG
130 CG
* * *
123804 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCAGTTCGT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATATCTACAGTT-GT
*
123868 -GTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGT
65 CGTTGCGAT-GTTCAAAAT-GCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGT
123932 TGCG
128 TGCG
123936 ATAGTCTACA
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
130 15 0.12
131 8 0.07
132 97 0.81
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (131 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATATCTACAGTTGTC
GTTGCGATGTTCAAAATGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
G
Found at i:123916 original size:22 final size:21
Alignment explanation
Indices: 123888--123959 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
123878 TTGAAAATCG
123888 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * **
123910 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGTTT
123929 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTT-T
123951 CGTTGCGAT
1 CGTTGCGAT
123960 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:123933 original size:19 final size:19
Alignment explanation
Indices: 123909--123974 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
123899 TCTACAGTTG
123909 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
123928 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
123949 ATCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
123969 TCGTTG
1 TCGTTG
123975 TGATAGGTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:123933 original size:41 final size:41
Alignment explanation
Indices: 123888--123980 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
123878 TTGAAAATCG
*
123888 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
123929 CGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
*
123970 CGTTGTGATAG
1 CGTTGCGATAG
123981 GTAAAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTATCGTTGCGATTTTCCAAATT
Found at i:124070 original size:6 final size:6
Alignment explanation
Indices: 124059--124089 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
124049 GACACGCACT
124059 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
124090 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:124096 original size:5 final size:5
Alignment explanation
Indices: 124086--124119 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
124076 GACCACGACC
124086 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGA
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGA
124120 ACGGCGTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.38, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:124599 original size:6 final size:6
Alignment explanation
Indices: 124590--124645 Score: 112
Period size: 6 Copynumber: 9.3 Consensus size: 6
124580 GCCGCCGTCC
124590 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
124638 GTCGTG GT
1 GTCGTG GT
124646 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:124785 original size:21 final size:20
Alignment explanation
Indices: 124732--124788 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
124722 ACTATCGCAC
124732 TGTAGACTATCGCAACGAAT
1 TGTAGACTATCGCAACGAAT
* **
124752 T-TGGAAAATCGCAACGACAT
1 TGTAGACTATCGCAACGA-AT
124772 TGTAGACTATCGCAACG
1 TGTAGACTATCGCAACG
124789 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
TGTAGACTATCGCAACGAAT
Found at i:124805 original size:20 final size:20
Alignment explanation
Indices: 124780--124852 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
124770 ATTGTAGACT
124780 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
124800 ATCGCATCGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
124821 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
124841 ATCGCAACGCGA
1 ATCGCAACGCGA
124853 TTTCCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:124822 original size:41 final size:41
Alignment explanation
Indices: 124737--124877 Score: 175
Period size: 41 Copynumber: 3.5 Consensus size: 41
124727 CGCACTGTAG
*
124737 ACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-ATTGT--A
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATT-TCCA
* *
124776 GACTATCGCAACGCGAAATGGAAAATCGCATCGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
124818 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
*
124859 ACTATCGCAACACGAAATG
1 ACTATCGCAACGCGAAATG
124878 CAACGCGAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
40 12 0.13
41 74 0.81
42 5 0.05
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCA
Found at i:124881 original size:21 final size:21
Alignment explanation
Indices: 124777--124881 Score: 88
Period size: 21 Copynumber: 5.1 Consensus size: 21
124767 GACATTGTAG
*
124777 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
124798 A-AATCGCATCGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
124818 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
124839 A-AATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATGCA
*
124859 ACTATCGCAACACGAAATGCA
1 ACTATCGCAACGCGAAATGCA
124880 AC
1 AC
124882 GCGAATTTGC
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 31 0.52
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:127055 original size:18 final size:19
Alignment explanation
Indices: 127015--127062 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
127005 CAAAGGGCTG
*
127015 GTATCGATACTCCTTCTTGA
1 GTATCGATACT-CTTCATGA
127035 GTATCGATACT-TTCATGA
1 GTATCGATACTCTTCATGA
*
127053 GTACCGATAC
1 GTATCGATAC
127063 CAAATTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (19 bp):
GTATCGATACTCTTCATGA
Found at i:131472 original size:20 final size:20
Alignment explanation
Indices: 131443--131501 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
131433 TTGCATTTGG
131443 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
* * *
131463 TATCGGTACTGTTCA-AATAA
1 TATCGATACTG-TAAGAACAA
*
131483 TATTGATACTGTAAGAACA
1 TATCGATACTGTAAGAACA
131502 GTCTCGGTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (20 bp):
TATCGATACTGTAAGAACAA
Found at i:131808 original size:34 final size:34
Alignment explanation
Indices: 131765--131829 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
131755 TCAAGGTAGT
131765 ATCAATACCCCAGTAGAGGAGTATCGATACTCTA
1 ATCAATACCCCAGTAGAGGAGTATCGATACTCTA
131799 ATCAATACCCCAGTAGAGGAGTATCGATACT
1 ATCAATACCCCAGTAGAGGAGTATCGATACT
131830 TTAGCTAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (34 bp):
ATCAATACCCCAGTAGAGGAGTATCGATACTCTA
Found at i:131857 original size:21 final size:21
Alignment explanation
Indices: 131817--131875 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
131807 CCCAGTAGAG
*
131817 GAGTATCGATACT-TTAGCTA
1 GAGTATCGATACTCCTAGCTA
131837 GAGTATCGATACTCCTAGCTA
1 GAGTATCGATACTCCTAGCTA
*
131858 AAGTATCGATACTACCTA
1 GAGTATCGATACT-CCTA
131876 TTTCTCTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.37
21 18 0.51
22 4 0.11
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (21 bp):
GAGTATCGATACTCCTAGCTA
Found at i:131928 original size:19 final size:20
Alignment explanation
Indices: 131904--131941 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
131894 ATTCATTTTT
131904 GGTATCGATAC-CAAGGGTG
1 GGTATCGATACTCAAGGGTG
*
131923 GGTATCGGTACTCAAGGGT
1 GGTATCGATACTCAAGGGT
131942 TAGTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.24
Consensus pattern (20 bp):
GGTATCGATACTCAAGGGTG
Found at i:132311 original size:22 final size:22
Alignment explanation
Indices: 132240--132315 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
132230 TATTAATGCT
* *
132240 GAGACACTTTAGTATCAATGCA
1 GAGACACTTTAGTATCAGTGTA
*
132262 AATG-CACTTTAGTATCAGTGTA
1 GA-GACACTTTAGTATCAGTGTA
* *
132284 GTGACACTTTAGTATTAGTGGT-
1 GAGACACTTTAGTATCAGT-GTA
132306 GAGACACTTT
1 GAGACACTTT
132316 TGTTATACGA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.02
22 40 0.91
23 3 0.07
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (22 bp):
GAGACACTTTAGTATCAGTGTA
Found at i:133258 original size:2 final size:2
Alignment explanation
Indices: 133246--133287 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
133236 AAATAATTTT
*
133246 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
133287 T
1 T
133288 TTGATTTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:138974 original size:15 final size:15
Alignment explanation
Indices: 138956--138994 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
138946 TAACTTATTA
138956 ATGCATAATGTACGT
1 ATGCATAATGTACGT
*
138971 ATGCATAATGTATGT
1 ATGCATAATGTACGT
138986 ATGCATAAT
1 ATGCATAAT
138995 TAATAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (15 bp):
ATGCATAATGTACGT
Found at i:139064 original size:15 final size:15
Alignment explanation
Indices: 139044--139112 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
139034 GTATAATGTG
139044 TGTATAATTTATTAA
1 TGTATAATTTATTAA
*
139059 TGTATAATGTATGT-A
1 TGTATAATTTAT-TAA
* *
139074 TGTAT-GTGTGTATTTA
1 TGTATAAT-T-TATTAA
* *
139090 TGTATAATTAATTAG
1 TGTATAATTTATTAA
139105 TGTATAAT
1 TGTATAAT
139113 ATATGTAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.02
15 29 0.69
16 11 0.26
17 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (15 bp):
TGTATAATTTATTAA
Found at i:139231 original size:33 final size:33
Alignment explanation
Indices: 139182--139303 Score: 158
Period size: 33 Copynumber: 3.7 Consensus size: 33
139172 ATTTTTAGTG
*
139182 TATACTATATAATTTATATATACTAATGAACTA
1 TATATTATATAATTTATATATACTAATGAACTA
* *
139215 TATATTATATAGTTTATATAAACTAATGAACTA
1 TATATTATATAATTTATATATACTAATGAACTA
* *
139248 TATAATT-TAT-ATGTACTATATAATAATGAACTA
1 TAT-ATTATATAATTTA-TATATACTAATGAACTA
*
139281 TATAATATATAATTTATATATAC
1 TATATTATATAATTTATATATAC
139304 CATATAGTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 5 0.07
33 63 0.84
34 7 0.09
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (33 bp):
TATATTATATAATTTATATATACTAATGAACTA
Found at i:139448 original size:2 final size:2
Alignment explanation
Indices: 139375--139433 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
139365 AAGCTGTGCA
* *
139375 AT AT AT AT AT AT AT AT AT AT AT GT -T TT AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
139414 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
139434 TGCATGGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:139504 original size:26 final size:27
Alignment explanation
Indices: 139475--139532 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 27
139465 AAATACAAAT
*
139475 TATATAGTTTATATATAT-TATATTAA
1 TATATACTTTATATATATATATATTAA
*
139501 TATATACTTTATATATATATCTATTAA
1 TATATACTTTATATATATATATATTAA
139528 TATAT
1 TATAT
139533 TATAATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (27 bp):
TATATACTTTATATATATATATATTAA
Found at i:139505 original size:15 final size:14
Alignment explanation
Indices: 139485--139532 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
139475 TATATAGTTT
139485 ATATATATTATATTA
1 ATATATATT-TATTA
139500 ATATATACTTTA-T-
1 ATATATA-TTTATTA
*
139513 ATATATATCTATTA
1 ATATATATTTATTA
139527 ATATAT
1 ATATAT
139533 TATAATTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 3 0.10
13 8 0.28
14 7 0.24
15 9 0.31
16 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATTTATTA
Found at i:140478 original size:26 final size:27
Alignment explanation
Indices: 140422--140478 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
140412 ACTCTATATT
* * *
140422 ATTTTATTATTATTTTAATACAACATG
1 ATTTTATTATTATTTTAATAAAAAATA
140449 ATTTT-TTATTA-TTTAATATAAAAATA
1 ATTTTATTATTATTTTAATA-AAAAATA
140475 ATTT
1 ATTT
140479 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 7 0.27
26 14 0.54
27 5 0.19
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTTTATTATTATTTTAATAAAAAATA
Found at i:151621 original size:20 final size:20
Alignment explanation
Indices: 151596--151990 Score: 193
Period size: 20 Copynumber: 19.4 Consensus size: 20
151586 GATTTTCCAG
**
151596 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
* ** *
151616 AATCGCAACGCGATTCTTAC
1 AATCGCAACGCGAATCCGAA
* * * *
151636 TATCGCAACGAGTATTCGTAAA
1 AATCGCAACGCGAATCCG--AA
* *
151658 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
151678 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* *
151699 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
151719 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
151739 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * *
151759 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
151780 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
151800 AATCGCAACAAC-AATACGTAA
1 AATCGCAAC-GCGAATCCG-AA
* *
151821 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
151841 AATCGTAACGAGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
151862 AATCGCAACGCGATTCTGAT
1 AATCGCAACGCGAATCCGAA
* * * **
151882 TATCGCAAC-CAAAATACGTT
1 AATCGCAACGC-GAATCCGAA
* * * *
151902 AATCGTAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGAA
** *
151922 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGAA
** *
151942 AATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
151962 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGAA
151982 AATCGCAAC
1 AATCGCAAC
151991 ACTTAAATTT
Statistics
Matches: 284, Mismatches: 79, Indels: 24
0.73 0.20 0.06
Matches are distributed among these distances:
19 1 0.00
20 206 0.73
21 61 0.21
22 16 0.06
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:151713 original size:41 final size:41
Alignment explanation
Indices: 151596--151990 Score: 382
Period size: 41 Copynumber: 9.7 Consensus size: 41
151586 GATTTTCCAG
* * * *
151596 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTCTTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* * *
151635 CTATCGCAACGAGTATTCGTAAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCGTA
*
151678 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
151719 AATCGCAACGAGAATACGT-AAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * * *
151758 CTATCGCAACGAGTATCCGTAAAATTGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
151800 AATCGCAACAACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
151841 AATCGTAACGAGAATACGTAAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * * * * * * *
151881 TTATCGCAACCAAAATACGT-TAATCGTAACGAGAATCTGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* * *
151922 AATCGCAACGATAATCCGT-AAATCGCAACG-ATAATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGT-ATCCGTA
151962 AATCGCAACGAGAAT-CTGT-AAATCGCAAC
1 AATCGCAACGAGAATAC-GTAAAATCGCAAC
151991 ACTTAAATTT
Statistics
Matches: 294, Mismatches: 47, Indels: 28
0.80 0.13 0.08
Matches are distributed among these distances:
38 1 0.00
39 6 0.02
40 112 0.38
41 135 0.46
42 34 0.12
43 6 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:152673 original size:12 final size:12
Alignment explanation
Indices: 152652--152685 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
152642 ACCACATTTC
*
152652 CAATACCAAACA
1 CAATATCAAACA
152664 CAATATCAAACA
1 CAATATCAAACA
*
152676 CAATCTCAAA
1 CAATATCAAA
152686 ACCTACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:152862 original size:24 final size:24
Alignment explanation
Indices: 152811--152864 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
152801 GTATTCGAAA
*
152811 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
152835 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
152859 TTTGAT
1 TTTGAT
152865 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:155375 original size:14 final size:14
Alignment explanation
Indices: 155356--155443 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
155346 CGGAAATTAC
155356 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
155370 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
155389 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
155403 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
155422 AATCGCAACGAGAG
1 AATCGCAACGAGAG
155436 AATCGCAA
1 AATCGCAA
155444 TGTGAAATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:155393 original size:33 final size:33
Alignment explanation
Indices: 155337--155462 Score: 207
Period size: 33 Copynumber: 3.8 Consensus size: 33
155327 TCATTTTACT
* * *
155337 ATCGCAACGCGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
155371 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
155404 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
155437 ATCGCAATGTGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
155463 TGCGAAATGA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 79 0.90
34 9 0.10
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:155459 original size:52 final size:52
Alignment explanation
Indices: 155403--155514 Score: 206
Period size: 52 Copynumber: 2.2 Consensus size: 52
155393 GCAACGAGAG
**
155403 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAA
155455 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAA
155507 AATCGCAA
1 AATCGCAA
155515 CGAGAGAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAA
Found at i:155481 original size:85 final size:85
Alignment explanation
Indices: 155370--155547 Score: 338
Period size: 85 Copynumber: 2.1 Consensus size: 85
155360 GCAACGAGAG
*
155370 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
*
155435 GAATCGCAATGTGAAATGAA
66 GAATCGCAATGCGAAATGAA
155455 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
155520 GAATCGCAATGCGAAATGAA
66 GAATCGCAATGCGAAATGAA
155540 AATCGCAA
1 AATCGCAA
155548 CGAGAGAATC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.13
Consensus pattern (85 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
GAATCGCAATGCGAAATGAA
Found at i:155492 original size:33 final size:33
Alignment explanation
Indices: 155455--155557 Score: 197
Period size: 33 Copynumber: 3.1 Consensus size: 33
155445 GTGAAATGAA
155455 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
155488 AATCGCAATGCAAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
155521 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
155554 AATC
1 AATC
155558 ACACTCGTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:155493 original size:14 final size:14
Alignment explanation
Indices: 155474--155557 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
155464 GCGAAATGAA
155474 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
155488 AATCGCAATGCAAAATGAA
1 AATCGCAA--C--GA-GAG
155507 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
155521 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
155540 AATCGCAACGAGAG
1 AATCGCAACGAGAG
155554 AATC
1 AATC
155558 ACACTCGTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
14 24 0.44
15 2 0.04
16 3 0.06
17 3 0.06
18 2 0.04
19 20 0.37
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:155556 original size:118 final size:119
Alignment explanation
Indices: 155337--155557 Score: 399
Period size: 118 Copynumber: 1.9 Consensus size: 119
155327 TCATTTTACT
* * *
155337 ATCGCAACGCGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
155402 GAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAA
66 GAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAA
*
155456 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
155520 GAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
66 GAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
155558 ACACTCGTTG
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
118 89 0.91
119 9 0.09
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (119 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGAGA
GAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAA
Found at i:155716 original size:14 final size:14
Alignment explanation
Indices: 155697--155733 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
155687 CATCAATTAA
155697 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
155711 ACAAATCATCTTTT
1 ACAAATCAACTTTT
155725 ACAAATCAA
1 ACAAATCAA
155734 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:155874 original size:82 final size:84
Alignment explanation
Indices: 155700--155876 Score: 331
Period size: 83 Copynumber: 2.1 Consensus size: 84
155690 CAATTAAACA
155700 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
155765 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
*
155784 AATCAACTTTTACAAATCATCTTTTAC-AATGAATTAAACAATCAAAAAATAAGCAATAATTC-T
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
155847 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
155866 AATCAACTTTT
1 AATCAACTTTT
155877 GCAGCCATAC
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 31 0.34
83 34 0.37
84 27 0.29
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (84 bp):
AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTT
ATTTCCTCATCTACTATTG
Found at i:157254 original size:42 final size:41
Alignment explanation
Indices: 157169--157291 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
157159 GTGAATCGGG
* * * *
157169 CTCTTGAATGGTGGGA-GGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
157211 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
157253 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
157292 CAAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:157679 original size:21 final size:21
Alignment explanation
Indices: 157655--157707 Score: 83
Period size: 19 Copynumber: 2.6 Consensus size: 21
157645 GCAGAAGAAA
157655 CGCAACGAGAGAAATGAAAAT
1 CGCAACGAGAGAAATGAAAAT
*
157676 CGCAAC--GCGAAATGAAAAT
1 CGCAACGAGAGAAATGAAAAT
157695 CGCAACGAGAGAA
1 CGCAACGAGAGAA
157708 TCGCAACGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 18 0.64
21 10 0.36
ACGTcount: A:0.49, C:0.19, G:0.25, T:0.08
Consensus pattern (21 bp):
CGCAACGAGAGAAATGAAAAT
Found at i:157687 original size:19 final size:19
Alignment explanation
Indices: 157665--157734 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
157655 CGCAACGAGA
157665 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
157684 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
157701 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
157717 AAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
157735 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 1 0.02
17 2 0.05
18 1 0.02
19 28 0.65
ACGTcount: A:0.49, C:0.20, G:0.21, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:157711 original size:14 final size:14
Alignment explanation
Indices: 157692--157748 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
157682 GCGAAATGAA
157692 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
157706 AATCGCAACGCAAAATGAA
1 AATCGCAACG----A-GAG
157725 AATCGCAACGAGAG
1 AATCGCAACGAGAG
157739 AATCGCAACG
1 AATCGCAACG
157749 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
18 1 0.03
19 12 0.33
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:157715 original size:33 final size:33
Alignment explanation
Indices: 157673--157764 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
157663 GAGAAATGAA
157673 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
157706 AATCGCAACGCAAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
157739 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
157765 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:157782 original size:19 final size:19
Alignment explanation
Indices: 157760--157842 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 19
157750 GAAACCAAAA
*
157760 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
157779 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
157793 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
157812 TCGCGTTGCGATATTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
157832 TCGTGTTGCGA
1 TCGCGTTGCGA
157843 AAGTAAACTA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 3 0.06
19 24 0.46
20 12 0.23
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:158004 original size:63 final size:63
Alignment explanation
Indices: 157894--158019 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
157884 ATTGCATTAC
*
157894 TTCAACCAAAAGACAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAG
1 TTCAACCAAAAGACAAACAAAGACAAATAATAACTTCAGAGTATTAAAGAATACACAGTTTAG
* * *
157957 TTCAACCAAAAGACAAAACAAAGACAAATAAT-ATTTCATAGTGTTAAAGAATACACAGTTTAG
1 TTCAACCAAAAGAC-AAACAAAGACAAATAATAACTTCAGAGTATTAAAGAATACACAGTTTAG
158020 CAGAATTGGC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 42 0.72
64 16 0.28
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (63 bp):
TTCAACCAAAAGACAAACAAAGACAAATAATAACTTCAGAGTATTAAAGAATACACAGTTTAG
Found at i:158088 original size:82 final size:81
Alignment explanation
Indices: 157976--158131 Score: 258
Period size: 82 Copynumber: 1.9 Consensus size: 81
157966 AAGACAAAAC
* * *
157976 AAAGACAAATAATATTTCATAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
1 AAAGACAAATAATACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAAT
158041 AAATTTACTTCAACCA
66 AAATTTACTTCAACCA
* *
158057 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAA
1 AAAGACAAATAAT-ACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
158122 TAAATTTACT
65 TAAATTTACT
158132 AAGTAATCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 12 0.17
82 57 0.83
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (81 bp):
AAAGACAAATAATACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAAT
AAATTTACTTCAACCA
Found at i:159804 original size:14 final size:14
Alignment explanation
Indices: 159785--159841 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
159775 TTGAAATGAA
159785 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
159799 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
159818 AATCGCAACGAGAG
1 AATCGCAACGAGAG
159832 AATCGCAACG
1 AATCGCAACG
159842 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:159817 original size:33 final size:33
Alignment explanation
Indices: 159777--159858 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
159767 TCTTTTTGTT
159777 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
159810 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
159843 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
159859 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:159823 original size:19 final size:19
Alignment explanation
Indices: 159799--159863 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
159789 GCAACGAGAG
159799 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
159818 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
159832 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
159851 AATCGCAATGCGA
1 AATCGCAACGCGA
159864 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:159920 original size:21 final size:19
Alignment explanation
Indices: 159859--159924 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
159849 AAAATCGCAA
**
159859 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTCATTTCTCGT
*
159878 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCTCGT
159897 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCTCGT
159918 TGCGATT
1 TGCGATT
159925 CTTCTGCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 27 0.66
20 2 0.05
21 12 0.29
ACGTcount: A:0.09, C:0.20, G:0.21, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCATTTCTCGT
Found at i:160465 original size:20 final size:20
Alignment explanation
Indices: 160440--160597 Score: 151
Period size: 20 Copynumber: 7.7 Consensus size: 20
160430 CTTTAAAAAT
160440 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
160460 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
160480 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
160501 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
160521 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
160542 CGCATTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
* * * *
160564 CTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGAT-TTACGGATA
160584 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
160598 TATGTTCGCG
Statistics
Matches: 113, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.02
20 54 0.48
21 39 0.35
22 18 0.16
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:160499 original size:41 final size:41
Alignment explanation
Indices: 160442--160596 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
160432 TTAAAAATCG
160442 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
160483 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * **
160524 CGTTGCGATTTACGGATACGCATTGCGATTTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTTACGTATTGT
* * *
160566 CGTTGCGATAGTAAGAAT-CGCGTTGCGATTT
1 CGTTGCGAT-TTACGGATACGCGTTGCGATTT
160597 ATATGTTCGC
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 71 0.68
42 28 0.27
43 5 0.05
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
Found at i:160606 original size:20 final size:20
Alignment explanation
Indices: 160583--160718 Score: 100
Period size: 20 Copynumber: 6.8 Consensus size: 20
160573 ATAGTAAGAA
*
160583 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
160603 TCGCGTTGTGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
** * *
160623 TCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGATT-TTCATAT
**
160644 TCGCAATGCGAATTTGT-ACTA-
1 TCGCGTTGCG-ATTT-TCA-TAT
* *
160665 TCGCATTGCGATTTTTAT-T
1 TCGCGTTGCGATTTTCATAT
*
160684 TCGCATTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
160704 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
160719 GTTGGTCATT
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.21
20 48 0.51
21 22 0.23
22 4 0.04
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:160610 original size:82 final size:81
Alignment explanation
Indices: 160438--160616 Score: 218
Period size: 82 Copynumber: 2.2 Consensus size: 81
160428 CGCTTTAAAA
* * ** * * *
160438 ATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 ATCGCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCGATGTAAGAATACG
160503 CGTTGCGATTTTACGT
66 CGTTGCGATTTTACGT
*
160519 ATTGTCGTTGCGATTTACGGATACGCATTGCGATTTTTACGGATACTCGTTGCGATAGTAAGAAT
1 ATCG-CGTTGCGATTTACGGATACGCATTGCGA-TTTTACGGATACTCGTTGCGAT-GTAAGAAT
*
160584 -CGCGTTGCGATTTATATGT
63 ACGCGTTGCGATTT-TACGT
*
160603 -TCGCGTTGTGATTT
1 ATCGCGTTGCGATTT
160617 TCATATTCGC
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
81 3 0.04
82 37 0.45
83 34 0.41
84 9 0.11
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (81 bp):
ATCGCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACTCGTTGCGATGTAAGAATACG
CGTTGCGATTTTACGT
Found at i:160689 original size:19 final size:20
Alignment explanation
Indices: 160665--160718 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
160655 ATTTGTACTA
*
160665 TCGCATTGCGATTTTTAT-T
1 TCGCATTGCGATTTTCATAT
160684 TCGCATTGCGATTTTCATAT
1 TCGCATTGCGATTTTCATAT
*
160704 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
160719 GTTGGTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (20 bp):
TCGCATTGCGATTTTCATAT
Found at i:161059 original size:27 final size:27
Alignment explanation
Indices: 161029--161090 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
161019 CGTACAATAT
161029 ATATTTTTAAATAAAAATAA-AGATAAA
1 ATATTTTTAAATAAAAATAATA-ATAAA
* *
161056 ATA-TTTTAAATTAAATTAATAATAAA
1 ATATTTTTAAATAAAAATAATAATAAA
*
161082 ATATATTTA
1 ATATTTTTA
161091 GTAAGTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATTTTTAAATAAAAATAATAATAAA
Found at i:161107 original size:25 final size:23
Alignment explanation
Indices: 161066--161127 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
161056 ATATTTTAAA
* *
161066 TTAAATTAATA-ATAAAATATATT
1 TTAAGTTAATATATAAAACAT-TT
161089 TAGTAAGTTAATATA-AAAACATTT
1 T--TAAGTTAATATATAAAACATTT
161113 TTAAGTTAATATATA
1 TTAAGTTAATATATA
161128 TAAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 12 0.36
23 2 0.06
24 3 0.09
25 15 0.45
26 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (23 bp):
TTAAGTTAATATATAAAACATTT
Found at i:161126 original size:24 final size:25
Alignment explanation
Indices: 161065--161132 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
161055 AATATTTTAA
* *
161065 ATTAAATTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAA-ACATTT
*
161090 AGTAAGTT-A-ATATAAAAACATTT
1 ATTAAGTTAATATATAAAAACATTT
161113 -TTAAGTTAATATATATAAAA
1 ATTAAGTTAATATATA-AAAA
161133 AAGAATATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.17
23 7 0.20
24 12 0.34
25 10 0.29
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTAAGTTAATATATAAAAACATTT
Found at i:163923 original size:19 final size:20
Alignment explanation
Indices: 163890--163928 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
163880 TGCACTTTTC
*
163890 ATTTAATATTAATTTGTTTA
1 ATTTAATATTAATTTATTTA
*
163910 ATTT-ATATTCATTTATTTA
1 ATTTAATATTAATTTATTTA
163929 GTTAGCCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTAATATTAATTTATTTA
Found at i:165177 original size:18 final size:18
Alignment explanation
Indices: 165147--165193 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
165137 GATGTAAATG
165147 ATAAA-AAACTGAAATAAA
1 ATAAAGAAACTGAAA-AAA
165165 ATAAAGAAA-TGAAAAAA
1 ATAAAGAAACTGAAAAAA
165182 ATGAAAGGAAAC
1 AT-AAA-GAAAC
165194 AAAAAAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
18 13 0.52
19 7 0.28
ACGTcount: A:0.70, C:0.04, G:0.13, T:0.13
Consensus pattern (18 bp):
ATAAAGAAACTGAAAAAA
Found at i:166269 original size:16 final size:16
Alignment explanation
Indices: 166244--166289 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
166234 TAAAAAAGAT
166244 AAAA-AAATAAAGTTA
1 AAAATAAATAAAGTTA
**
166259 AAAATAAATAAAAATA
1 AAAATAAATAAAGTTA
*
166275 ATAATAAA-AAAGTTA
1 AAAATAAATAAAGTTA
166290 GTATTAAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 9 0.36
16 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAATAAATAAAGTTA
Found at i:167677 original size:21 final size:23
Alignment explanation
Indices: 167633--167685 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
167623 TTCTCAATTT
* *
167633 TTTTTAAAACTATATAATATATA
1 TTTTCAAAACCATATAATATATA
167656 TTTTCAAAACCATAT-A-ATATA
1 TTTTCAAAACCATATAATATATA
167677 TTTTCAAAA
1 TTTTCAAAA
167686 AATATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 14 0.50
22 1 0.04
23 13 0.46
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTTCAAAACCATATAATATATA
Found at i:167694 original size:57 final size:59
Alignment explanation
Indices: 167565--167787 Score: 172
Period size: 57 Copynumber: 3.7 Consensus size: 59
167555 AAATCATAAA
* * * * ** *
167565 TTTCGAAAATATTTTTTAAATTATATAT-TATATATTTTTTAAAACGTTTTCAA-AATATT
1 TTTCAAAAATATTTTTAAAACTATATATATATATA-TTTTCAAAACCATAT-AATAATATT
* * *
167624 TCTC--AATTTTTTTTAAAACTATATA-ATATATATTTTCAAAACCATATAAT-ATA-T
1 TTTCAAAAATATTTTTAAAACTATATATATATATATTTTCAAAACCATATAATAATATT
*
167678 TTTCAAAAAATATTTTTAAAACTATATAATATATTTCAAAAATATTTTCAAAACTATATAATAAA
1 TTTC-AAAAATATTTTTAAAACTATAT-ATATA--T-----ATATTTTCAAAACCATATAAT-AA
167743 TATTT
56 TA-TT
167748 TTTCAAAAATATTTTTAAAACTATATATTATATATATTTT
1 TTTCAAAAATATTTTTAAAACTATATA-TATATATATTTT
167788 TTAAAAATGT
Statistics
Matches: 132, Mismatches: 13, Indels: 35
0.73 0.07 0.19
Matches are distributed among these distances:
54 4 0.03
55 5 0.04
56 11 0.08
57 41 0.31
58 1 0.01
59 6 0.05
61 1 0.01
62 7 0.05
66 20 0.15
67 1 0.01
68 4 0.03
69 26 0.20
70 5 0.04
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (59 bp):
TTTCAAAAATATTTTTAAAACTATATATATATATATTTTCAAAACCATATAATAATATT
Found at i:167754 original size:37 final size:37
Alignment explanation
Indices: 167653--167968 Score: 273
Period size: 37 Copynumber: 8.7 Consensus size: 37
167643 TATATAATAT
*
167653 ATATTTTCAAAACCATAT-A-ATATA--TTTTCAAAAA
1 ATATTTTCAAAACTATATAATATATATGTTTTC-AAAA
*
167687 ATATTTTTAAAACTATAT-A-ATATA---TTTCAAAA
1 ATATTTTCAAAACTATATAATATATATGTTTTCAAAA
* *
167719 ATATTTTCAAAACTATATAATAAATATTTTTTCAAAA
1 ATATTTTCAAAACTATATAATATATATGTTTTCAAAA
* *
167756 ATATTTTTAAAACTATATATTATATATAT-TTTTTAAAA
1 ATATTTTCAAAACTATATA--ATATATATGTTTTCAAAA
* * *
167794 ATGTTTTTAAAACTATATATTATATATGTTTT-AAAA
1 ATATTTTCAAAACTATATAATATATATGTTTTCAAAA
* * *
167830 ATGTTTTCAAAAACTATATATTATATAGGTTTTC-AAA
1 ATATTTTC-AAAACTATATAATATATATGTTTTCAAAA
* * * *
167867 ATGTTTTCAAAACTATATATTATATACGTTTT-TAAA
1 ATATTTTCAAAACTATATAATATATATGTTTTCAAAA
* * * *
167903 ATGTTTTTAAAAAGCTATATATTATATAAGTTTTC-AAA
1 AT-ATTTTCAAAA-CTATATAATATATATGTTTTCAAAA
* *
167941 ATGTTTTCAAAAACTATATTATATATAT
1 ATATTTTC-AAAACTATATAATATATAT
167969 ATATATATAT
Statistics
Matches: 247, Mismatches: 20, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
32 21 0.09
33 5 0.02
34 26 0.11
36 46 0.19
37 88 0.36
38 54 0.22
39 7 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (37 bp):
ATATTTTCAAAACTATATAATATATATGTTTTCAAAA
Found at i:167890 original size:111 final size:111
Alignment explanation
Indices: 167653--167969 Score: 368
Period size: 111 Copynumber: 2.9 Consensus size: 111
167643 TATATAATAT
* ** *
167653 ATATTTTCAAAAC--CATA-TA-ATATATTTTCAAAAAATATTTTTAAAACTATATA--ATATA-
1 ATATTTTCAAAACTATATATTATATATATTTTTTAAAAATGTTTTTAAAACTATATATTATATAG
* * * * **
167711 TTTCAAAAATATTTTC-AAAACTATATAATAAATATTTTTTCAAAA
66 TTTTAAAAATGTTTTCAAAAACTATATATTATATAGGTTTTCAAAA
*
167756 ATATTTTTAAAACTATATATTATATATATTTTTTAAAAATGTTTTTAAAACTATATATTATATAT
1 ATATTTTCAAAACTATATATTATATATATTTTTTAAAAATGTTTTTAAAACTATATATTATATA-
167821 GTTTTAAAAATGTTTTCAAAAACTATATATTATATAGGTTTTC-AAA
65 GTTTTAAAAATGTTTTCAAAAACTATATATTATATAGGTTTTCAAAA
* **
167867 ATGTTTTCAAAACTATATATTATATA-CGTTTTT-AAAATGTTTTTAAAAAGCTATATATTATAT
1 ATATTTTCAAAACTATATATTATATATATTTTTTAAAAATGTTTTT-AAAA-CTATATATTATAT
*
167930 AAGTTTTCAAAATGTTTTCAAAAACTATATTATATATATA
64 -AGTTTTAAAAATGTTTTCAAAAACTATA-TAT-TATATA
167970 TATATATATT
Statistics
Matches: 184, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
103 12 0.07
105 3 0.02
106 2 0.01
107 31 0.17
109 16 0.09
110 9 0.05
111 80 0.43
112 25 0.14
113 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (111 bp):
ATATTTTCAAAACTATATATTATATATATTTTTTAAAAATGTTTTTAAAACTATATATTATATAG
TTTTAAAAATGTTTTCAAAAACTATATATTATATAGGTTTTCAAAA
Found at i:168255 original size:35 final size:36
Alignment explanation
Indices: 168186--168267 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
168176 GTTGTTGATA
168186 ATCTC-TATTTCATTTGAATCTATACACTTAAAATT
1 ATCTCATATTTCATTTGAATCTATACACTTAAAATT
168221 ATCTCATATTTCATTTGAATCTATACACTT-AAATT
1 ATCTCATATTTCATTTGAATCTATACACTTAAAATT
168256 ATCTCATATTTC
1 ATCTCATATTTC
168268 TATCTTTCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 22 0.48
36 24 0.52
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.46
Consensus pattern (36 bp):
ATCTCATATTTCATTTGAATCTATACACTTAAAATT
Found at i:169159 original size:21 final size:22
Alignment explanation
Indices: 169135--169179 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
169125 AAACATTTTC
169135 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
169156 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
169178 TT
1 TT
169180 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Done.