Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004437.1 Hibiscus syriacus cultivar Beakdansim tig00009733_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: 93990
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:647 original size:26 final size:26
Alignment explanation
Indices: 591--644 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
581 TGTGTTTTTC
* * *
591 AATTTCTTTTTTTATTTGATTTACTA
1 AATTTATTTTTTTATTTGAGTCACTA
*
617 AATTTATTTTTATTATTTTAGTCACTA
1 AATTTATTTTT-TTATTTGAGTCACTA
644 A
1 A
645 TTTCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (26 bp):
AATTTATTTTTTTATTTGAGTCACTA
Found at i:5657 original size:20 final size:22
Alignment explanation
Indices: 5618--5658 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
5608 TTTTTTTTGA
*
5618 GTTTTTCAAATTATAATTTTAT
1 GTTTTTCAAATTAAAATTTTAT
5640 GTTTTT-AAA-TAAAATTTTA
1 GTTTTTCAAATTAAAATTTTA
5659 AAATTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
GTTTTTCAAATTAAAATTTTAT
Found at i:6009 original size:17 final size:18
Alignment explanation
Indices: 5987--6024 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5977 AAATCCAACC
5987 TTTTG-TTTTCTAATATT
1 TTTTGTTTTTCTAATATT
*
6004 TTTTGTTTTTTTAATATT
1 TTTTGTTTTTCTAATATT
6022 TTT
1 TTT
6025 GAGCAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTGTTTTTCTAATATT
Found at i:8698 original size:20 final size:20
Alignment explanation
Indices: 8624--8702 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
8614 TTATGAAACA
* * *
8624 TAGTATTGATATTTTTCTTG
1 TAGTATCGATACTATTCTTG
* * *
8644 TAGTATCAATATTGTTCTTG
1 TAGTATCGATACTATTCTTG
8664 TAGTA-CGAATACTATTCTTG
1 TAGTATCG-ATACTATTCTTG
*
8684 TAGTATCGATGCTATTCTT
1 TAGTATCGATACTATTCTT
8703 ACAATATTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.94
21 2 0.04
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.49
Consensus pattern (20 bp):
TAGTATCGATACTATTCTTG
Found at i:8738 original size:45 final size:45
Alignment explanation
Indices: 8687--8774 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
8677 ATTCTTGTAG
*
8687 TATCGATGCTATTCTTACAATATTTGTATTATTATTGTAGTATAA
1 TATCGATACTATTCTTACAATATTTGTATTATTATTGTAGTATAA
* * * * * *
8732 TATCGATATTGTTCTTGCAGTATTTGTATTGTTCTTGTAGTAT
1 TATCGATACTATTCTTACAATATTTGTATTATTATTGTAGTAT
8775 CTGTAATGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (45 bp):
TATCGATACTATTCTTACAATATTTGTATTATTATTGTAGTATAA
Found at i:8763 original size:20 final size:20
Alignment explanation
Indices: 8738--8793 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
8728 ATAATATCGA
* *
8738 TATTGTTCTTGCAGTATTTG
1 TATTGTTCTTGTAGTATCTG
8758 TATTGTTCTTGTAGTATCTG
1 TATTGTTCTTGTAGTATCTG
*
8778 TAATGTTCTTGTAGTA
1 TATTGTTCTTGTAGTA
8794 ATGTCAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.54
Consensus pattern (20 bp):
TATTGTTCTTGTAGTATCTG
Found at i:10092 original size:85 final size:85
Alignment explanation
Indices: 10003--10178 Score: 228
Period size: 85 Copynumber: 2.1 Consensus size: 85
9993 CGCGCAATTA
* * * * *
10003 TGTGTCATAAATCTATGACGCGCATTTATGACGCTCATTACGCGTCATTGAAGCCCCCGTCA-TA
1 TGTGTCATAAATCTATGACACACATGTATGACGCTCATTACGCGTCATTGAAGCACACGTCATTA
*
10067 AATGAAGATGACACACATTCG
66 AA-AAAGATGACACACATTCG
* * * * *
10088 TGTGTCATAAATTTATGGCACACATGTATGACGCTCATTGCGTGTCATTGAAGTACACGTCATTA
1 TGTGTCATAAATCTATGACACACATGTATGACGCTCATTACGCGTCATTGAAGCACACGTCATTA
*
10153 AAAAAGATGACACACATTCT
66 AAAAAGATGACACACATTCG
10173 TGTGTC
1 TGTGTC
10179 GTGATTGTAT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 74 0.95
86 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (85 bp):
TGTGTCATAAATCTATGACACACATGTATGACGCTCATTACGCGTCATTGAAGCACACGTCATTA
AAAAAGATGACACACATTCG
Found at i:11756 original size:2 final size:2
Alignment explanation
Indices: 11749--11786 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11739 GGTGCAAATG
11749 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
11787 GTCCGCCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15203 original size:29 final size:29
Alignment explanation
Indices: 15171--15248 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
15161 CAGTAACGGC
**
15171 CTTTAGTGTAATTTGTGAAAAAAATAT-TT
1 CTTTAGTGTAATTTGT-AAAAAAATATAGA
* **
15200 CTTTAAT-TAATTTGTAATGAAATATAGA
1 CTTTAGTGTAATTTGTAAAAAAATATAGA
*
15228 ATTTAGTGTAATTTGTAAAAA
1 CTTTAGTGTAATTTGTAAAAA
15249 TTCGGGCCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
27 8 0.21
28 13 0.34
29 17 0.45
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (29 bp):
CTTTAGTGTAATTTGTAAAAAAATATAGA
Found at i:17193 original size:43 final size:43
Alignment explanation
Indices: 17145--17233 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
17135 TTCATCCTTT
* * * *
17145 ATCCTTAGTTTGTTTGGGTGCATACTGGAATCCATAACTTACA
1 ATCCTTAGCTTATTTGGGTGCACACTGAAATCCATAACTTACA
*
17188 ATCCTTAGCTTATTTGGGTGCACAGTGAAATCCATAACTTACA
1 ATCCTTAGCTTATTTGGGTGCACACTGAAATCCATAACTTACA
17231 ATC
1 ATC
17234 ACATGGAGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (43 bp):
ATCCTTAGCTTATTTGGGTGCACACTGAAATCCATAACTTACA
Found at i:17493 original size:19 final size:19
Alignment explanation
Indices: 17469--17510 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
17459 GTCCATCTCA
17469 AGCTGATACGATCCAAAAT
1 AGCTGATACGATCCAAAAT
*
17488 AGCTGATACGATCCAAACT
1 AGCTGATACGATCCAAAAT
17507 AGCT
1 AGCT
17511 CCAACTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (19 bp):
AGCTGATACGATCCAAAAT
Found at i:19370 original size:23 final size:24
Alignment explanation
Indices: 19342--19386 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
19332 AAAGAAATCG
19342 AAGCACTC-AAAAGAAGAAAAGTC
1 AAGCACTCAAAAAGAAGAAAAGTC
19365 AAGCACTCAAAAAGAAGAAAAG
1 AAGCACTCAAAAAGAAGAAAAG
19387 AAAAGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.60, C:0.16, G:0.18, T:0.07
Consensus pattern (24 bp):
AAGCACTCAAAAAGAAGAAAAGTC
Found at i:19392 original size:24 final size:23
Alignment explanation
Indices: 19342--19393 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
19332 AAAGAAATCG
**
19342 AAGCACTCAAAAGAAGAAAAGTC
1 AAGCACTCAAAAGAAGAAAAGAA
19365 AAGCACTCAAAAAGAAGAAAAGAA
1 AAGCACTC-AAAAGAAGAAAAGAA
19389 AAGCA
1 AAGCA
19394 AAGACATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.62, C:0.15, G:0.17, T:0.06
Consensus pattern (23 bp):
AAGCACTCAAAAGAAGAAAAGAA
Found at i:20614 original size:24 final size:21
Alignment explanation
Indices: 20580--20622 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
20570 TCCACAAGAC
*
20580 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
20602 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
20623 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:28144 original size:15 final size:15
Alignment explanation
Indices: 28124--28155 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28114 ATCAAGCAAA
28124 ATAGGATGGCATAAG
1 ATAGGATGGCATAAG
28139 ATAGGATGGCATAAG
1 ATAGGATGGCATAAG
28154 AT
1 AT
28156 TGACCATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.31, T:0.22
Consensus pattern (15 bp):
ATAGGATGGCATAAG
Found at i:30008 original size:24 final size:24
Alignment explanation
Indices: 29972--30018 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
29962 CTTAGGTGGC
29972 GAGTGATTCAGTGGGTCAGAGTAG
1 GAGTGATTCAGTGGGTCAGAGTAG
*
29996 GAGTGATTTAGTGGGTCAGAGTA
1 GAGTGATTCAGTGGGTCAGAGTA
30019 TGAGGGACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.40, T:0.28
Consensus pattern (24 bp):
GAGTGATTCAGTGGGTCAGAGTAG
Found at i:35233 original size:13 final size:13
Alignment explanation
Indices: 35215--35249 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
35205 ATTGTTTTTT
35215 ATATATTTATATA
1 ATATATTTATATA
* *
35228 ATATATTTATTTT
1 ATATATTTATATA
35241 ATATATTTA
1 ATATATTTA
35250 CATTTGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATATTTATATA
Found at i:48211 original size:56 final size:55
Alignment explanation
Indices: 48119--48448 Score: 417
Period size: 56 Copynumber: 5.9 Consensus size: 55
48109 AAGGAATAGA
* * *
48119 GAGCGAACCCGTTGCAGATGACTATTCGAGTTCTATACTCCCTGAAAGAAAGAGG
1 GAGCGAACCCGTTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
* *
48174 GAGCGAACCCATTGGTAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
1 GAGCGAACCCGTT-GCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
* * *
48230 GAGTGAACCCGTTGCAGAAGATTATTTGAGTTTTGTACTCCCTGAAAGAAAGAGG
1 GAGCGAACCCGTTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
* * *
48285 GAGCGAACCCGTTGGTAGAAGATTATTCGAGTTCTATACTCCCTAAAAGAAAGAGG
1 GAGCGAACCCGTT-GCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
* ** * * *
48341 GAGTGAACATGTTTGCAAAATATTATTTGAGTTCTATATTCCCTGAAAGAAAGAGG
1 GAGCGAACCCG-TTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
** * * * *
48397 GAGCGAACATGTTTGTAGAAAATTATTTGAGTTTTATATTCCCTGAAAGAAA
1 GAGCGAACCCG-TTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAA
48449 TATTTGTTCA
Statistics
Matches: 242, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
55 63 0.26
56 177 0.73
57 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (55 bp):
GAGCGAACCCGTTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGG
Found at i:48261 original size:111 final size:111
Alignment explanation
Indices: 48123--48448 Score: 472
Period size: 111 Copynumber: 2.9 Consensus size: 111
48113 AATAGAGAGC
* * * *
48123 GAACCCGTTGCAGATGACTATTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCATTG
1 GAACCCGTTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTG
48188 GTAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGT
66 GTAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGT
* *
48234 GAACCCGTTGCAGAAGATTATTTGAGTTTTGTACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTG
1 GAACCCGTTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTG
* *
48299 GTAGAAGATTATTCGAGTTCTATACTCCCTAAAAGAAAGAGGGAGT
66 GTAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGT
** * * * **
48345 GAACATGTTTGCAAAATATTATTTGAGTTCTATATTCCCTGAAAGAAAGAGGGAGCGAACATGTT
1 GAACCCG-TTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTT
* * * *
48410 TGTAGAAAATTATTTGAGTTTTATATTCCCTGAAAGAAA
65 GGTAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAA
48449 TATTTGTTCA
Statistics
Matches: 191, Mismatches: 23, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
111 108 0.57
112 83 0.43
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (111 bp):
GAACCCGTTGCAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTG
GTAGAAGATTATTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGT
Found at i:48323 original size:167 final size:167
Alignment explanation
Indices: 48092--48448 Score: 466
Period size: 167 Copynumber: 2.1 Consensus size: 167
48082 ATTGAGAATC
* * * * * *
48092 GAGTCTTATACTCTCT-AAAGGAATAGAGAGCGAACCCGTTGCAGATGACTATTCGAGTTCTATA
1 GAGTTTTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTGCAGAAGACTATTCGAGTTCTATA
* * * *
48156 CTCCCTGAAAGAAAGAGGGAGCGAACCCATTGGTAGAAGATTATTTGAGTTCTATACTCCCTGAA
66 CTCCCTAAAAGAAAGAGGGAGCGAACACATTGGCAAAAGATTATTTGAGTTCTATACTCCCTGAA
* * *
48221 AGAAAGAGGGAGTGAACCCG-TTGCAGAAGATTATTT
131 AGAAAGAGGGAGCGAACACGTTTGCAGAAAATTATTT
* * *
48257 GAGTTTTGTACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTGGTAGAAGATTATTCGAGTTCTAT
1 GAGTTTTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTT-GCAGAAGACTATTCGAGTTCTAT
* ** * * *
48322 ACTCCCTAAAAGAAAGAGGGAGTGAACATGTTTGCAAAATATTATTTGAGTTCTATATTCCCTGA
65 ACTCCCTAAAAGAAAGAGGGAGCGAACACATTGGCAAAAGATTATTTGAGTTCTATACTCCCTGA
* *
48387 AAGAAAGAGGGAGCGAACATGTTTGTAGAAAATTATTT
130 AAGAAAGAGGGAGCGAACACGTTTGCAGAAAATTATTT
*
48425 GAGTTTTATATTCCCTGAAAGAAA
1 GAGTTTTATACTCCCTGAAAGAAA
48449 TATTTGTTCA
Statistics
Matches: 163, Mismatches: 26, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
165 13 0.08
166 21 0.13
167 93 0.57
168 36 0.22
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (167 bp):
GAGTTTTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTGCAGAAGACTATTCGAGTTCTATA
CTCCCTAAAAGAAAGAGGGAGCGAACACATTGGCAAAAGATTATTTGAGTTCTATACTCCCTGAA
AGAAAGAGGGAGCGAACACGTTTGCAGAAAATTATTT
Found at i:51707 original size:52 final size:52
Alignment explanation
Indices: 51629--51733 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
51619 AACACGATTC
51629 TAACTTGACCATACTGCATGTAGGTCATTGTATGTGCATTTATGGTATGTTT
1 TAACTTGACCATACTGCATGTAGGTCATTGTATGTGCATTTATGGTATGTTT
51681 TAACTTGACCATACTGCATGTAGGTCATTGTATGTGCATTTATGGTATGTTT
1 TAACTTGACCATACTGCATGTAGGTCATTGTATGTGCATTTATGGTATGTTT
51733 T
1 T
51734 GTTCATGGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (52 bp):
TAACTTGACCATACTGCATGTAGGTCATTGTATGTGCATTTATGGTATGTTT
Found at i:52128 original size:18 final size:20
Alignment explanation
Indices: 52105--52150 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
52095 TTTTTGGTAC
52105 CGATACTCAT-GG-GAGTAT
1 CGATACTCATGGGAGAGTAT
52123 CGATAC-CATGGGTAGAGTAT
1 CGATACTCATGGG-AGAGTAT
52143 CGATACTC
1 CGATACTC
52151 CCCACAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
20 12 0.50
21 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (20 bp):
CGATACTCATGGGAGAGTAT
Found at i:55881 original size:29 final size:30
Alignment explanation
Indices: 55834--55892 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
55824 CCTAAATGAG
* *
55834 TAACGGAATGAAATGTTAGACACAAAACTA
1 TAACGAAATGAAACGTTAGACACAAAACTA
*
55864 TAACGAAAT-AAACGTTAGACACTAAACTA
1 TAACGAAATGAAACGTTAGACACAAAACTA
55893 GAACCAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (30 bp):
TAACGAAATGAAACGTTAGACACAAAACTA
Found at i:56108 original size:36 final size:37
Alignment explanation
Indices: 56061--56150 Score: 137
Period size: 36 Copynumber: 2.4 Consensus size: 37
56051 GGAGGATTCG
56061 AAACGATGTCATTTTGGTCTATATTTGAG-TTTTTCA
1 AAACGATGTCATTTTGGTCTATATTTGAGTTTTTTCA
*
56097 AAACGATGTCATTTTGGTGTATATTTGAGTTTTTTTCA
1 AAACGATGTCATTTTGGTCTATATTTGAG-TTTTTTCA
* *
56135 AAATGATGTCGTTTTG
1 AAACGATGTCATTTTG
56151 ATGCTTGTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
36 28 0.57
38 21 0.43
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.48
Consensus pattern (37 bp):
AAACGATGTCATTTTGGTCTATATTTGAGTTTTTTCA
Found at i:57941 original size:17 final size:17
Alignment explanation
Indices: 57919--57955 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
57909 TCGGGGTTGT
57919 TCTATCTTGGTTATTGC
1 TCTATCTTGGTTATTGC
57936 TCTATCTTGGTTATTGC
1 TCTATCTTGGTTATTGC
57953 TCT
1 TCT
57956 TTACATGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.19, G:0.16, T:0.54
Consensus pattern (17 bp):
TCTATCTTGGTTATTGC
Found at i:58717 original size:41 final size:41
Alignment explanation
Indices: 58666--58748 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
58656 GCAATAGATT
*
58666 TCAACATTTATCTTTCCGGGTTCCTAATGAAATACCAATAC
1 TCAACATTTATCTTTCCGGGTTCATAATGAAATACCAATAC
*
58707 TCAACATTTATCTTTCCGGGTTCATAATGAAATCCCAATAC
1 TCAACATTTATCTTTCCGGGTTCATAATGAAATACCAATAC
58748 T
1 T
58749 TACACTCACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (41 bp):
TCAACATTTATCTTTCCGGGTTCATAATGAAATACCAATAC
Found at i:60039 original size:6 final size:6
Alignment explanation
Indices: 60015--60108 Score: 68
Period size: 6 Copynumber: 15.8 Consensus size: 6
60005 AATTTTTGCC
* * * * *
60015 TATT-T TATTTT TATTAT TATAAT TATTAT AATTGT TATAAT TATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
* * * *
60062 AATTAT TACTAT TATTAT TA-TAT T-TATAT TAATAAA TATTAT TATTA
1 TATTAT TATTAT TATTAT TATTAT TAT-TAT T-ATTAT TATTAT TATTA
60109 CATATTACAT
Statistics
Matches: 67, Mismatches: 17, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
5 8 0.12
6 56 0.84
7 2 0.03
8 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (6 bp):
TATTAT
Found at i:60088 original size:9 final size:9
Alignment explanation
Indices: 60027--60079 Score: 81
Period size: 9 Copynumber: 5.9 Consensus size: 9
60017 TTTTATTTTT
60027 ATTATTATA
1 ATTATTATA
60036 ATTATTATA
1 ATTATTATA
*
60045 ATTGTTATA
1 ATTATTATA
60054 ATTATTATA
1 ATTATTATA
60063 ATTATTACT-
1 ATTATTA-TA
60072 ATTATTAT
1 ATTATTAT
60080 TATATTTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
8 1 0.02
9 39 0.95
10 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
ATTATTATA
Found at i:60088 original size:27 final size:26
Alignment explanation
Indices: 60019--60108 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 26
60009 TTTGCCTATT
*
60019 TTATTTTTATTATTATAATTATTATAA
1 TTATTATTATTATTATAATTATTAT-A
* *
60046 TTGTTATAATTATTATAATTATTACTA
1 TTATTATTATTATTATAATTATTA-TA
*
60073 TTATTATTA-TATT-TATATTAATA-A
1 TTATTATTATTATTATA-ATTATTATA
*
60097 ATATTATTATTA
1 TTATTATTATTA
60109 CATATTACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
24 9 0.17
25 4 0.08
26 10 0.19
27 29 0.55
28 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
TTATTATTATTATTATAATTATTATA
Found at i:60911 original size:29 final size:27
Alignment explanation
Indices: 60860--60940 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 27
60850 ATAGTTATTG
60860 TTTAAATT-TTATATGATTATTATCAATATA
1 TTTAAATTATTAT-T-ATTATTAT-AA-ATA
60890 TTTAAATTATTATTATTATTATAAATA
1 TTTAAATTATTATTATTATTATAAATA
*
60917 TTT-ATTTATT-TTATT-TTATTAAAT
1 TTTAAATTATTATTATTATTA-TAAAT
60941 CCTTTATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
24 3 0.06
25 10 0.21
26 6 0.12
27 6 0.12
28 2 0.04
29 8 0.17
30 9 0.19
31 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTAAATTATTATTATTATTATAAATA
Found at i:64943 original size:15 final size:15
Alignment explanation
Indices: 64925--64956 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
64915 GATCAATACC
64925 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
64940 TTTTGCATACATTCA
1 TTTTGCATACATGCA
64955 TT
1 TT
64957 GCATTATTTT
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:68761 original size:8 final size:9
Alignment explanation
Indices: 68736--68764 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
68726 ATGGCAATCG
68736 TTCTTTACA
1 TTCTTTACA
68745 TTCTTTACA
1 TTCTTTACA
68754 TT-TTTACA
1 TTCTTTACA
68762 TTC
1 TTC
68765 ATTATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCTTTACA
Found at i:72315 original size:16 final size:16
Alignment explanation
Indices: 72279--72344 Score: 71
Period size: 16 Copynumber: 4.0 Consensus size: 16
72269 TATTATGCTT
*
72279 GAAGAAAAAAAAAGAAA
1 GAAGAAAAGAAAA-AAA
*
72296 GAAGAAAAGAAAAAAT
1 GAAGAAAAGAAAAAAA
72312 GAAGAAAA-AAGAAAAA
1 GAAGAAAAGAA-AAAAA
*
72328 CAAGAAAGAGAAAAAAA
1 GAAGAAA-AGAAAAAAA
72345 TGTTGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.05
16 20 0.48
17 18 0.43
18 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
GAAGAAAAGAAAAAAA
Found at i:72316 original size:23 final size:22
Alignment explanation
Indices: 72280--72343 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
72270 ATTATGCTTG
*
72280 AAGAAAAAAAAAGAAAGAAGAA
1 AAGAAAAAAAAAGAAAAAAGAA
*
72302 AAGAAAAAATGAAGAAAAAAGAA
1 AAGAAAAAA-AAAGAAAAAAGAA
* *
72325 AA-ACAAGAAAGAGAAAAAA
1 AAGA-AAAAAAAAGAAAAAA
72344 ATGTTGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAAAAGAAAAAAGAA
Found at i:72316 original size:33 final size:33
Alignment explanation
Indices: 72278--72362 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
72268 ATATTATGCT
*
72278 TGAAGAAAAAAAAAGAAAGAAGAAA-AGAAAAAA
1 TGAAGAAAAAAAAA-AAACAAGAAAGAGAAAAAA
*
72311 TGAAGAAAAAAGAAAAACAAGAAAGAGAAAAAAA
1 TGAAGAAAAAAAAAAAACAAGAAAGAG-AAAAAA
**
72345 TGTTGAAAAAATAAAAAA
1 TGAAGAAAAAA-AAAAAA
72363 ATAGAAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 9 0.20
33 15 0.34
34 15 0.34
35 5 0.11
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.07
Consensus pattern (33 bp):
TGAAGAAAAAAAAAAAACAAGAAAGAGAAAAAA
Found at i:72344 original size:34 final size:32
Alignment explanation
Indices: 72278--72371 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 32
72268 ATATTATGCT
*
72278 TGAAGAAAAAAAAAGAAAGAAGAAAAGAAAAAA
1 TGAAGAAAAAAAAA-AAACAAGAAAAGAAAAAA
*
72311 TGAAGAAAAAAGAAAAACAAGAAAGAGAAAAAAA
1 TGAAGAAAAAAAAAAAACAAGAAA-AG-AAAAAA
**
72345 TGTTGAAAAAATAAAAAA-ATAGAAAAG
1 TGAAGAAAAAA-AAAAAACA-AGAAAAG
72372 GAGGGTCAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 9 0.17
33 15 0.29
34 18 0.35
35 10 0.19
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.07
Consensus pattern (32 bp):
TGAAGAAAAAAAAAAAACAAGAAAAGAAAAAA
Found at i:72740 original size:18 final size:18
Alignment explanation
Indices: 72717--72751 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
72707 CAAGTTTATC
72717 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
72735 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
72752 GTTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:74296 original size:124 final size:123
Alignment explanation
Indices: 74040--74402 Score: 599
Period size: 124 Copynumber: 3.0 Consensus size: 123
74030 CATTCGATAG
74040 ATCAACTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAGAAG-A-AAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* *
74102 ATGAGAAGAGCTTGTTCAACCTTTTTGCATGACTCTATCACAGAAGAAGATAAATCAAC
66 ATGAGAAGAGCTTGTTCAACC-TTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
74161 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCAT
*
74226 AATCAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
* * *
74285 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTTACA
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
** *
74350 ATGAGAAGAATTTGTTCAACCTTTTGTATGA-TCTATCACAGAAGGAGATAGAT
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGAT
74403 TAGCATCGAG
Statistics
Matches: 228, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
121 16 0.07
122 55 0.24
123 40 0.18
124 85 0.37
125 32 0.14
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:74423 original size:58 final size:58
Alignment explanation
Indices: 74352--74467 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
74342 AGTTTACAAT
* *
74352 GAGAAGAATTTGTTCAACCTTTTGTATGATCTATCACAGAAGGAGATAGATTAGCATC
1 GAGAAGAACTTGTTCAACCTTTTGTATAATCTATCACAGAAGGAGATAGATTAGCATC
* *
74410 GAGAAGAGCTTGTTCAACCTTTTGTATAATCTATCATAGAAGGAGATAGATTAGCATC
1 GAGAAGAACTTGTTCAACCTTTTGTATAATCTATCACAGAAGGAGATAGATTAGCATC
74468 AACATTTTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (58 bp):
GAGAAGAACTTGTTCAACCTTTTGTATAATCTATCACAGAAGGAGATAGATTAGCATC
Found at i:74755 original size:3 final size:3
Alignment explanation
Indices: 74736--74830 Score: 77
Period size: 3 Copynumber: 32.0 Consensus size: 3
74726 AAATTTTTGC
* * * * *
74736 TTA TT- TTA TTT TTA TTA TTA TAA TTA TTA TAA TTG TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
74783 TAA TTA TTA CTA TTA TTA TTA -TA TTT TTA TTAA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
74828 TTA
1 TTA
74831 CATATTACAG
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 4 0.06
3 63 0.91
4 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:80675 original size:39 final size:36
Alignment explanation
Indices: 80603--80675 Score: 85
Period size: 39 Copynumber: 1.9 Consensus size: 36
80593 TTATACATTT
* *
80603 AATATTAAATTAATATTTTAATATCATTTTAATAAA
1 AATATTAAATTAAAATTTTAATATCATTATAATAAA
80639 AATATTAATTATTAAAATATTTAATATACA-TATAATA
1 AATATTAA--ATTAAAAT-TTTAATAT-CATTATAATA
80676 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 8 0.26
38 7 0.23
39 14 0.45
40 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (36 bp):
AATATTAAATTAAAATTTTAATATCATTATAATAAA
Found at i:80709 original size:19 final size:18
Alignment explanation
Indices: 80668--80711 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
80658 TTTAATATAC
*
80668 ATATAATATAATTTTAAT
1 ATATATTATAATTTTAAT
*
80686 A-ATATTATATTTTTAAT
1 ATATATTATAATTTTAAT
80703 ATTATATTA
1 A-TATATTA
80712 ATATATACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATTATAATTTTAAT
Found at i:80875 original size:19 final size:19
Alignment explanation
Indices: 80837--80876 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
80827 TAATAATGAG
*
80837 TAATATTAATTTATATATT
1 TAATATTAATTAATATATT
80856 TAATATTAATATAATA-ATT
1 TAATATTAAT-TAATATATT
80875 TA
1 TA
80877 GTTTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATTAATTAATATATT
Found at i:81196 original size:30 final size:30
Alignment explanation
Indices: 81162--81228 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
81152 TTCTCAGAAA
*
81162 ATGTAATTCACTTAACATAAATCAGTTTTC
1 ATGTAATTCACTTAACATAAAACAGTTTTC
* * * *
81192 ATGTAATTTATTTTACGTAAAACAGTTTTC
1 ATGTAATTCACTTAACATAAAACAGTTTTC
*
81222 AGGTAAT
1 ATGTAAT
81229 CCATTTTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (30 bp):
ATGTAATTCACTTAACATAAAACAGTTTTC
Found at i:81235 original size:30 final size:30
Alignment explanation
Indices: 81179--81242 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
81169 TCACTTAACA
* * **
81179 TAAATCAGTTTTCATGTAATTTATTTTACG
1 TAAAACAGTTTTCAGGTAATCCATTTTACG
*
81209 TAAAACAGTTTTCAGGTAATCCATTTTATG
1 TAAAACAGTTTTCAGGTAATCCATTTTACG
81239 TAAA
1 TAAA
81243 TTATTTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (30 bp):
TAAAACAGTTTTCAGGTAATCCATTTTACG
Found at i:82074 original size:2 final size:2
Alignment explanation
Indices: 82067--82104 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
82057 TTCTTTTTAA
82067 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
82105 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85807 original size:71 final size:69
Alignment explanation
Indices: 85653--85808 Score: 172
Period size: 73 Copynumber: 2.2 Consensus size: 69
85643 GTATCTGTAT
* * * *
85653 TTTTAAAAGTTATATTTAAGTATTCAAAATATTTATATTAAACAATAAAATTTGAAAATTTTATA
1 TTTTAAAATTTATACTTAAGTATTCAAAATATTTATATTAAACAATAAAATTTGAAAAGTTCATA
85718 AATA
66 AATA
* * *
85722 TTTTAAAAGATTTATACTTAAGTATTTAAAATTATTTATATTTGAA-AATAAAAATTTGAGAAGT
1 TTTT-AAA-ATTTATACTTAAGTATTCAAAA-TATTTATA-TTAAACAAT-AAAATTTGAAAAGT
85786 TCATAACA-A
61 TCATAA-ATA
*
85795 TTTTAAATTTTATA
1 TTTTAAAATTTATA
85809 TTGTTTAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
69 4 0.05
70 3 0.04
71 25 0.34
72 14 0.19
73 26 0.36
74 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (69 bp):
TTTTAAAATTTATACTTAAGTATTCAAAATATTTATATTAAACAATAAAATTTGAAAAGTTCATA
AATA
Found at i:86008 original size:2 final size:2
Alignment explanation
Indices: 86001--86027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
85991 AGATGTTTAT
86001 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
86028 TTAACTCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86086 original size:22 final size:22
Alignment explanation
Indices: 86058--86106 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
86048 TTATGTTCAA
86058 ACAATTATATCTATTTTTTAAT
1 ACAATTATATCTATTTTTTAAT
* *
86080 ACAA-T-TATGTGTTTTTTAAT
1 ACAATTATATCTATTTTTTAAT
86100 ACAATTA
1 ACAATTA
86107 CGTGATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (22 bp):
ACAATTATATCTATTTTTTAAT
Found at i:87042 original size:15 final size:15
Alignment explanation
Indices: 87022--87050 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
87012 GACTAGAAGA
87022 TTCATGTACTTAATG
1 TTCATGTACTTAATG
87037 TTCATGTACTTAAT
1 TTCATGTACTTAAT
87051 AATATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (15 bp):
TTCATGTACTTAATG
Found at i:90129 original size:105 final size:104
Alignment explanation
Indices: 89936--90147 Score: 381
Period size: 105 Copynumber: 2.0 Consensus size: 104
89926 TAAACATCAA
89936 TATTAAATTAATGGAATTTAGGCAAAATCATTCAATGCAGCTCCTATGGATAAGGACATACAGCA
1 TATTAAATTAATGGAATTTAGGCAAAATCATTCAATGCAGCTCCTATGGATAAGGACATACAGCA
90001 TCAAAAAAAAAATGCAATGAAAAAATCTCAAGTTTTCCAT
66 TC-AAAAAAAAATGCAATGAAAAAATCTCAAGTTTTCCAT
* *
90041 TATTAAATTAATGGAATTTAGGCAAAATCCTTCAATGCAGCTCCTATGGATAAGGGCATACAGCA
1 TATTAAATTAATGGAATTTAGGCAAAATCATTCAATGCAGCTCCTATGGATAAGGACATACAGCA
90106 TC-AAAAAAAATGCAATGAAAAAAATCTCAAGTTTTCCAT
66 TCAAAAAAAAATGCAATG-AAAAAATCTCAAGTTTTCCAT
90145 TAT
1 TAT
90148 CCAATCAAAT
Statistics
Matches: 104, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
103 15 0.14
104 24 0.23
105 65 0.62
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (104 bp):
TATTAAATTAATGGAATTTAGGCAAAATCATTCAATGCAGCTCCTATGGATAAGGACATACAGCA
TCAAAAAAAAATGCAATGAAAAAATCTCAAGTTTTCCAT
Found at i:92083 original size:21 final size:21
Alignment explanation
Indices: 92058--92101 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
92048 TTTTTAGTTA
92058 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
92079 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
92100 AT
1 AT
92102 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:92111 original size:28 final size:29
Alignment explanation
Indices: 92078--92140 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 29
92068 TAGTATAAAT
92078 TATTAGTTTGTTAGTTTAAGTTA-TATTA
1 TATTAGTTTGTTAGTTTAAGTTATTATTA
92106 TATTAGTTTGTTAGTTTAAGTTATTTATTA
1 TATTAGTTTGTTAGTTTAAGTTA-TTATTA
92136 TATTA
1 TATTA
92141 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 23 0.70
30 10 0.30
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.59
Consensus pattern (29 bp):
TATTAGTTTGTTAGTTTAAGTTATTATTA
Done.