Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 81 of 126
Found at i:16418338 original size:20 final size:20
Alignment explanation
Indices: 16418313--16418350 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16418303 TCAATTTGAT
16418313 TTTTTTGTCACTATTCTCCA
1 TTTTTTGTCACTATTCTCCA
16418333 TTTTTTGTCACTATTCTC
1 TTTTTTGTCACTATTCTC
16418351 TTTTTATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.24, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTTGTCACTATTCTCCA
Found at i:16419443 original size:5 final size:5
Alignment explanation
Indices: 16419421--16419462 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
16419411 ACTTATTTTC
*
16419421 TTAAT TTATT TTAA- TTAAT TTAAT TTAAT TTAAT TT-AT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
16419463 CTAACTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:16419445 original size:19 final size:19
Alignment explanation
Indices: 16419421--16419462 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
16419411 ACTTATTTTC
*
16419421 TTAATTTATTTTAATTAAT
1 TTAATTTAATTTAATTAAT
*
16419440 TTAATTTAATTTAATTTAT
1 TTAATTTAATTTAATTAAT
16419459 TTAA
1 TTAA
16419463 CTAACTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTTAATTTAATTAAT
Found at i:16425651 original size:37 final size:37
Alignment explanation
Indices: 16425601--16425711 Score: 222
Period size: 37 Copynumber: 3.0 Consensus size: 37
16425591 TTCCTTAACG
16425601 TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
1 TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
16425638 TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
1 TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
16425675 TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
1 TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
16425712 CAACCCCTAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (37 bp):
TAGAATCATTGTTATTTCCATATCCAGCTAAAGACCA
Found at i:16426365 original size:34 final size:34
Alignment explanation
Indices: 16426300--16426366 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
16426290 GATATCTATC
* **
16426300 ATTTTCAAAAAATTATACCATTTTATTAAAATAG
1 ATTTTCAAAAAATTATACCACTTTACAAAAATAG
**
16426334 ATTTTCAAAAAATTATAGTACTTTACAAAAATA
1 ATTTTCAAAAAATTATACCACTTTACAAAAATA
16426367 AAATTTTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (34 bp):
ATTTTCAAAAAATTATACCACTTTACAAAAATAG
Found at i:16426781 original size:16 final size:16
Alignment explanation
Indices: 16426760--16426790 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16426750 AAAAAATAAT
16426760 AAAATTTAAATTTATA
1 AAAATTTAAATTTATA
*
16426776 AAAATTTATATTTAT
1 AAAATTTAAATTTAT
16426791 TATTTTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATTTAAATTTATA
Found at i:16427027 original size:27 final size:27
Alignment explanation
Indices: 16426992--16427043 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
16426982 TACATTTTTT
**
16426992 AGAAATATTATGATTTCTCAAAAATAG
1 AGAAATATTACAATTTCTCAAAAATAG
*
16427019 AGAAATATTACAATTTTTCAAAAAT
1 AGAAATATTACAATTTCTCAAAAAT
16427044 TCATTTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (27 bp):
AGAAATATTACAATTTCTCAAAAATAG
Found at i:16427548 original size:52 final size:51
Alignment explanation
Indices: 16427486--16427603 Score: 116
Period size: 52 Copynumber: 2.3 Consensus size: 51
16427476 ATCAATTTAG
*
16427486 ATTTAAAATAATTAAAGGGATAAATTTATTATTTTTTATTT-TGG-TAAAT-TTTT
1 ATTT-AAATAATTAAA---ATAAA-TTATTATTTTTTATTTATGGATAAATAATTT
* * *
16427539 ATTTAAATAAGTAAAATTAATTCTTATTTTTTATTTATGGATTAAATAATTT
1 ATTTAAATAATTAAAATAAATTATTATTTTTTATTTATGGA-TAAATAATTT
*
16427591 ATTTAAAAAATTA
1 ATTTAAATAATTA
16427604 TTGGTAATCC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
48 15 0.27
49 7 0.13
51 5 0.09
52 24 0.44
53 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.51
Consensus pattern (51 bp):
ATTTAAATAATTAAAATAAATTATTATTTTTTATTTATGGATAAATAATTT
Found at i:16427750 original size:11 final size:11
Alignment explanation
Indices: 16427734--16427760 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16427724 TTTTAAAATT
16427734 TAATTTTCTAA
1 TAATTTTCTAA
16427745 TAATTTTCTAA
1 TAATTTTCTAA
16427756 TAATT
1 TAATT
16427761 AGTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (11 bp):
TAATTTTCTAA
Found at i:16428175 original size:21 final size:21
Alignment explanation
Indices: 16428149--16428189 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16428139 CATCAATTTG
16428149 ATTTTTTTGTCACTATTCTCC
1 ATTTTTTTGTCACTATTCTCC
*
16428170 ATTTTTTTGTCACTGTTCTC
1 ATTTTTTTGTCACTATTCTC
16428190 TTTTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTTTTTGTCACTATTCTCC
Found at i:16431478 original size:11 final size:11
Alignment explanation
Indices: 16431464--16431502 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
16431454 TATTTATTTT
16431464 ATTTTTATTAA
1 ATTTTTATTAA
*
16431475 ATTTATATATAA
1 ATTTTTAT-TAA
16431487 ATTTTTATTAA
1 ATTTTTATTAA
16431498 ATTTT
1 ATTTT
16431503 AAATCGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTATTAA
Found at i:16431514 original size:23 final size:23
Alignment explanation
Indices: 16431463--16431506 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16431453 ATATTTATTT
*
16431463 TATTTTTATTAAATTTATATATA
1 TATTTTTATTAAATTTATAAATA
*
16431486 AATTTTTATTAAATTT-TAAAT
1 TATTTTTATTAAATTTATAAAT
16431507 CGTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTATTAAATTTATAAATA
Found at i:16433142 original size:24 final size:24
Alignment explanation
Indices: 16433096--16433143 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
16433086 GTTTACATTT
* *
16433096 CAATAAGTATATTTGTTAGTTTAA
1 CAATAAGTATATTTGTCAATTTAA
16433120 CAATAAGTATATTTGTCAATTTAA
1 CAATAAGTATATTTGTCAATTTAA
16433144 TAATTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (24 bp):
CAATAAGTATATTTGTCAATTTAA
Found at i:16434314 original size:2 final size:2
Alignment explanation
Indices: 16434307--16434337 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16434297 GGATCTCTAT
16434307 TA TA 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 TA TA T
16434338 GATCTACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16434594 original size:24 final size:24
Alignment explanation
Indices: 16434562--16434609 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16434552 CGATATGTTC
*
16434562 TTATTCACTAATAATATATAAAAT
1 TTATACACTAATAATATATAAAAT
* * *
16434586 TTATACACTGATAATGTATCAAAT
1 TTATACACTAATAATATATAAAAT
16434610 ATAAATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (24 bp):
TTATACACTAATAATATATAAAAT
Found at i:16441511 original size:12 final size:12
Alignment explanation
Indices: 16441476--16441524 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
16441466 GTCGAGTTAT
16441476 TTTTTTATTTTGA
1 TTTTTTATTTT-A
*
16441489 TATTTTATTTTA
1 TTTTTTATTTTA
*
16441501 TTTTTTGTTTTA
1 TTTTTTATTTTA
16441513 TTTATTTATTTT
1 TTT-TTTATTTT
16441525 TTATTCATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 14 0.45
13 17 0.55
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:16441511 original size:25 final size:25
Alignment explanation
Indices: 16441476--16441524 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16441466 GTCGAGTTAT
16441476 TTTTTTATTTTGATAT-TTTATTTTA
1 TTTTTTATTTT-ATATATTTATTTTA
* *
16441501 TTTTTTGTTTTATTTATTTATTTT
1 TTTTTTATTTTATATATTTATTTT
16441525 TTATTCATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTTATTTTATATATTTATTTTA
Found at i:16441863 original size:10 final size:10
Alignment explanation
Indices: 16441850--16441906 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
16441840 AAATAAATTT
16441850 TTTTAAAAAA
1 TTTTAAAAAA
16441860 TTTTAAATGATAA
1 TTTTAAA--A-AA
16441873 TTTT-AAAAA
1 TTTTAAAAAA
*
16441882 TTTTAGAAAAT
1 TTTTA-AAAAA
16441893 TTTTAAAAAA
1 TTTTAAAAAA
16441903 TTTT
1 TTTT
16441907 TAAGGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 6 0.15
10 16 0.40
11 9 0.22
12 3 0.08
13 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:16441985 original size:19 final size:19
Alignment explanation
Indices: 16441924--16441986 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
16441914 AAAATTTTTT
16441924 AAAAATTTAATTCAAATGATA
1 AAAAATTTAATT-AAAT-ATA
* *
16441945 AAATAATTT-AGTAAATTTTA
1 AAA-AATTTAATTAAA-TATA
16441965 AAAAATTTAATTAAATATA
1 AAAAATTTAATTAAATATA
16441984 AAA
1 AAA
16441987 TTAATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 11 0.31
20 13 0.37
21 6 0.17
22 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAAATTTAATTAAATATA
Found at i:16442047 original size:19 final size:19
Alignment explanation
Indices: 16442023--16442068 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
16442013 ATCTTTTCAT
*
16442023 ATATAATTTAAAAATTAAA
1 ATATAAATTAAAAATTAAA
*
16442042 ATATAAATTAAAAATTTAA
1 ATATAAATTAAAAATTAAA
*
16442061 ATAAAAAT
1 ATATAAAT
16442069 ATTTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAATTAAAAATTAAA
Found at i:16442055 original size:20 final size:21
Alignment explanation
Indices: 16442021--16442061 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16442011 ATATCTTTTC
*
16442021 ATATATAATTTAAAAATTAAA
1 ATATATAATTAAAAAATTAAA
*
16442042 ATATA-AATTAAAAATTTAAA
1 ATATATAATTAAAAAATTAAA
16442062 TAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATATAATTAAAAAATTAAA
Found at i:16443709 original size:16 final size:17
Alignment explanation
Indices: 16443669--16443710 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
16443659 TTATTTAGTC
16443669 TAATTTTATTCATAATA
1 TAATTTTATTCATAATA
*
16443686 TCATTTTATTC-T-ATCA
1 TAATTTTATTCATAAT-A
16443702 TAATTTTAT
1 TAATTTTAT
16443711 GTGCTTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 10 0.45
17 10 0.45
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTATTCATAATA
Found at i:16446142 original size:20 final size:20
Alignment explanation
Indices: 16446119--16446174 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
16446109 AAAATTCAGC
16446119 TTTTTATTAAAAATATG-ATA
1 TTTTTATTAAAAATATGTA-A
* *
16446139 TTTTTAATATATAA-ATGTAA
1 TTTTTATTA-AAAATATGTAA
16446159 TTTTTATTAAAAATAT
1 TTTTTATTAAAAATAT
16446175 AAAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTTATTAAAAATATGTAA
Found at i:16447116 original size:15 final size:15
Alignment explanation
Indices: 16447085--16447114 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16447075 TGAAATGATA
16447085 TATTTTAAATATTTT
1 TATTTTAAATATTTT
16447100 TATTTTAAA-ATTTT
1 TATTTTAAATATTTT
16447114 T
1 T
16447115 TAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTAAATATTTT
Found at i:16449449 original size:20 final size:20
Alignment explanation
Indices: 16449424--16449477 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
16449414 TGGATATGTG
16449424 ATAAAATTAAAAGAGA-CAAA
1 ATAAAATTAAAA-AGATCAAA
*
16449444 ATAAAAAATAAAAAGATTCAAA
1 AT-AAAATTAAAAAGA-TCAAA
16449466 A-AAAATTAAAAA
1 ATAAAATTAAAAA
16449478 AAATCTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 15 0.52
21 9 0.31
22 5 0.17
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.17
Consensus pattern (20 bp):
ATAAAATTAAAAAGATCAAA
Found at i:16449465 original size:22 final size:21
Alignment explanation
Indices: 16449426--16449470 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
16449416 GATATGTGAT
*
16449426 AAAATTAAAAGAGACAAAATAA
1 AAAATAAAAAGAGACAAAA-AA
**
16449448 AAAATAAAAAGATTCAAAAAA
1 AAAATAAAAAGAGACAAAAAA
16449469 AA
1 AA
16449471 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (21 bp):
AAAATAAAAAGAGACAAAAAA
Found at i:16453662 original size:6 final size:6
Alignment explanation
Indices: 16453635--16453702 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
16453625 TCTTTTTTGT
* * *
16453635 AATATA AAT-TA TATATT TATATA AATATA AATATA TAATATA ATATTATA
1 AATATA AATATA AATATA AATATA AATATA AATATA -AATATA A-A-TATA
* *
16453685 AATATA AAAATT AATATA
1 AATATA AATATA AATATA
16453703 TTATATAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
5 4 0.08
6 33 0.66
7 8 0.16
8 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AATATA
Found at i:16454258 original size:39 final size:40
Alignment explanation
Indices: 16454215--16454291 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
16454205 TATCCCTTTG
**
16454215 ATTTTCATAAAGATTAAGAA-AAAACTTTTACTTTAATGT
1 ATTTTCATAAAGATTAAGAACAAAAAATTTACTTTAATGT
16454254 ATTTTCATAAAGATTAAGAACAAAAAATTTACTTTAAT
1 ATTTTCATAAAGATTAAGAACAAAAAATTTACTTTAAT
16454292 TATGAGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (40 bp):
ATTTTCATAAAGATTAAGAACAAAAAATTTACTTTAATGT
Found at i:16455025 original size:3 final size:3
Alignment explanation
Indices: 16455017--16455063 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
16455007 ATTTTAAACC
*
16455017 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16455064 ATCTCCAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:16458042 original size:30 final size:31
Alignment explanation
Indices: 16458008--16458076 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
16457998 ATCATTGACC
*
16458008 TTTAATTTACATTCGAATAAATTTTTAA-TT
1 TTTAATTTACATTCAAATAAATTTTTAATTT
* *
16458038 TTTAATTTATATTCAAATAAGTTTTTAATTT
1 TTTAATTTACATTCAAATAAATTTTTAATTT
16458069 TTTAATTT
1 TTTAATTT
16458077 CTACCTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTAATTTACATTCAAATAAATTTTTAATTT
Found at i:16458087 original size:31 final size:30
Alignment explanation
Indices: 16458008--16458096 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
16457998 ATCATTGACC
* * *
16458008 TTTAATTTACATTCGAATAAATTTTTAATT
1 TTTAATTTATACTCAAATAAATTTTTAATT
* *
16458038 TTTAATTTATATTCAAATAAGTTTTTAATTT
1 TTTAATTTATACTCAAATAAATTTTTAA-TT
* *
16458069 TTTAATTTCTAC-CTAAATAAATCTTTAA
1 TTTAATTTATACTC-AAATAAATTTTTAA
16458097 CATAAATCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 26 0.52
31 24 0.48
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTAATTTATACTCAAATAAATTTTTAATT
Found at i:16458352 original size:15 final size:17
Alignment explanation
Indices: 16458320--16458352 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16458310 GTGAGAATAC
16458320 TGGGGGATAGGAAGGAT
1 TGGGGGATAGGAAGGAT
16458337 TGGGGGA-AGG-AGGAT
1 TGGGGGATAGGAAGGAT
16458352 T
1 T
16458353 TTATTTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.55, T:0.18
Consensus pattern (17 bp):
TGGGGGATAGGAAGGAT
Found at i:16462157 original size:28 final size:28
Alignment explanation
Indices: 16462099--16462170 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
16462089 CATTTTTATA
* * ***
16462099 ATAATATATATTATATATTTATCTTTTT
1 ATAATATAAATTATATATTTATATAAAT
16462127 ATAATATAAATTATATATTTATATAAAT
1 ATAATATAAATTATATATTTATATAAAT
*
16462155 ATAATTATAAAATATA
1 ATAA-TATAAATTATA
16462171 AAAATTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (28 bp):
ATAATATAAATTATATATTTATATAAAT
Found at i:16462188 original size:19 final size:19
Alignment explanation
Indices: 16462134--16462190 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
16462124 TTTATAATAT
*
16462134 AAATT-ATATATT-TATAT
1 AAATTAATATATTATATAA
**
16462151 AAATATAATTATAAAATATAA
1 AAAT-TAA-TATATTATATAA
16462172 AAATTAATATATTATATAA
1 AAATTAATATATTATATAA
16462191 TCCAGATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 4 0.13
18 1 0.03
19 11 0.35
20 7 0.23
21 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTAATATATTATATAA
Found at i:16466406 original size:30 final size:31
Alignment explanation
Indices: 16466361--16466419 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
16466351 AAATCATTAC
*
16466361 ATTCGAATAAATTTTTAA-TTTTTAATTTTT
1 ATTCAAATAAATTTTTAATTTTTTAATTTTT
*
16466391 ATTCAAATAAGTTTTTAATTTTTTAATTT
1 ATTCAAATAAATTTTTAATTTTTTAATTT
16466420 ATACCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
ATTCAAATAAATTTTTAATTTTTTAATTTTT
Found at i:16466430 original size:31 final size:30
Alignment explanation
Indices: 16466366--16466439 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
16466356 ATTACATTCG
* *
16466366 AATAAATTTTTAATTTTTAATTTTTATTCA
1 AATAAATTTTTAATTTTTAATTTATATCCA
*
16466396 AATAAGTTTTTAATTTTTTAATTTATA-CCAA
1 AATAAATTTTTAA-TTTTTAATTTATATCC-A
*
16466427 AATAAATCTTTAA
1 AATAAATTTTTAA
16466440 CATAAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.35
31 24 0.65
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (30 bp):
AATAAATTTTTAATTTTTAATTTATATCCA
Found at i:16466489 original size:27 final size:30
Alignment explanation
Indices: 16466459--16466515 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
16466449 ATTTTTTGTT
16466459 TCAAAA-AAT-AG-CTTATTTAAGTATAAA
1 TCAAAATAATAAGACTTATTTAAGTATAAA
*
16466486 TCAAAATAATAAAGATTTATTTAAGTATAA
1 TCAAAATAAT-AAGACTTATTTAAGTATAA
16466516 TAAACATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 3 0.12
30 2 0.08
31 14 0.56
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (30 bp):
TCAAAATAATAAGACTTATTTAAGTATAAA
Found at i:16470524 original size:28 final size:28
Alignment explanation
Indices: 16470466--16470526 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
16470456 AGTTTTTATA
* * * ***
16470466 ATAAGATATATTATATATTTATCTTTTT
1 ATAATATAAATTATATATTTATATAAAT
16470494 ATAATATAAATTATATATTTATATAAAT
1 ATAATATAAATTATATATTTATATAAAT
16470522 ATAAT
1 ATAAT
16470527 TATATAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
ATAATATAAATTATATATTTATATAAAT
Found at i:16471852 original size:3 final size:3
Alignment explanation
Indices: 16471844--16471881 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16471834 ATTTTAAATC
16471844 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16471882 ATCTCGAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16475234 original size:30 final size:30
Alignment explanation
Indices: 16475198--16475266 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
16475188 AGTTATAATG
*
16475198 TCCAAATAAA-TCATTGACTTGTAATTTACA
1 TCCAAATAAATTC-TTAACTTGTAATTTACA
* * *
16475228 TTCAAATAAATTCTTAACTTTTAATTTATA
1 TCCAAATAAATTCTTAACTTGTAATTTACA
16475258 TCCAAATAA
1 TCCAAATAA
16475267 GTATTTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (30 bp):
TCCAAATAAATTCTTAACTTGTAATTTACA
Found at i:16484283 original size:16 final size:16
Alignment explanation
Indices: 16484262--16484295 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16484252 AAATTTTATT
16484262 GATCAATTGCTATATA
1 GATCAATTGCTATATA
*
16484278 GATCAATTGCTGTATA
1 GATCAATTGCTATATA
16484294 GA
1 GA
16484296 AGCAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (16 bp):
GATCAATTGCTATATA
Found at i:16485286 original size:1 final size:1
Alignment explanation
Indices: 16485280--16485309 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16485270 GGGCATACTT
16485280 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16485310 GGCTTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16486486 original size:19 final size:19
Alignment explanation
Indices: 16486458--16486494 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16486448 ATCCGGTTTA
16486458 ATTCTCATAACTATGATTG
1 ATTCTCATAACTATGATTG
*
16486477 ATTCTTATAACTATGATT
1 ATTCTCATAACTATGATT
16486495 AAGGGTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTCTCATAACTATGATTG
Found at i:16493785 original size:15 final size:15
Alignment explanation
Indices: 16493765--16493797 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
16493755 GAATGTAGAA
16493765 CTCTGAATCATAAAC
1 CTCTGAATCATAAAC
16493780 CTCTGAATCATAAAC
1 CTCTGAATCATAAAC
16493795 CTC
1 CTC
16493798 CTGACAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.27
Consensus pattern (15 bp):
CTCTGAATCATAAAC
Found at i:16493900 original size:27 final size:27
Alignment explanation
Indices: 16493861--16493932 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
16493851 CTCCCTTCTC
* * *
16493861 TTTTTTCTCTCTCTGTTTTTTCTGATT
1 TTTTTTCTTTCTCTGCTTTTTCTGACT
16493888 TTTTTTCTTTCTCTGCTTTTTCTGACT
1 TTTTTTCTTTCTCTGCTTTTTCTGACT
*
16493915 TTTCTTCTTTCTCTGCTT
1 TTTTTTCTTTCTCTGCTT
16493933 GATTTTCGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.03, C:0.22, G:0.07, T:0.68
Consensus pattern (27 bp):
TTTTTTCTTTCTCTGCTTTTTCTGACT
Found at i:16496575 original size:13 final size:15
Alignment explanation
Indices: 16496544--16496578 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
16496534 AAAAAACTAA
16496544 AGATAAAATAAACAT
1 AGATAAAATAAACAT
16496559 AGATAAAA-AAA-AT
1 AGATAAAATAAACAT
16496572 AGATAAA
1 AGATAAA
16496579 TAGCATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 3 0.15
15 8 0.40
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (15 bp):
AGATAAAATAAACAT
Found at i:16499092 original size:2 final size:2
Alignment explanation
Indices: 16499085--16499115 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16499075 TTTTGACAGT
16499085 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16499116 AGTGAACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16499637 original size:22 final size:22
Alignment explanation
Indices: 16499590--16499637 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
16499580 TGATGTTATT
* * *
16499590 TTATTAATTTTTTAATTTTAAT
1 TTATAAATTTTTTAATTTAAAA
16499612 TTATAAATTTATTTAA-TTAAAA
1 TTATAAATTT-TTTAATTTAAAA
16499634 TTAT
1 TTAT
16499638 TGACAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATAAATTTTTTAATTTAAAA
Found at i:16500927 original size:27 final size:28
Alignment explanation
Indices: 16500853--16500927 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 28
16500843 TGTCATGAGT
* *
16500853 TATT-TTTAAATTATATTAAAATATTTAA
1 TATTATTTAATTTATA-AAAAATATTTAA
16500881 TATAATATTTATATTT-TAAAAAAT-TTTAA
1 TAT--TATTTA-ATTTATAAAAAATATTTAA
16500910 TATTATTTAATTTATAAA
1 TATTATTTAATTTATAAA
16500928 TATATTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
26 4 0.10
27 10 0.25
28 3 0.08
29 8 0.20
30 6 0.15
31 6 0.15
32 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATTATTTAATTTATAAAAAATATTTAA
Found at i:16500949 original size:32 final size:29
Alignment explanation
Indices: 16500870--16500950 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 29
16500860 AAATTATATT
16500870 AAAATATTTAATATAATATTTATATTTTAA
1 AAAAT-TTTAATATAATATTTATATTTTAA
16500900 AAAATTTTAATAT--TATTTA-ATTTATAA
1 AAAATTTTAATATAATATTTATATTT-TAA
*
16500927 ATATATTAATTAATATAATATTTA
1 A-AAATT--TTAATATAATATTTA
16500951 CTTTTAACGT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
26 4 0.09
27 10 0.23
28 4 0.09
29 8 0.18
30 12 0.27
32 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AAAATTTTAATATAATATTTATATTTTAA
Found at i:16501203 original size:23 final size:24
Alignment explanation
Indices: 16501132--16501206 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 24
16501122 TTTTTGTTTA
*
16501132 TATTTTTTATGAATGTTTCAAAATTAT
1 TATTTTTTAT--ATATTT-AAAATTAT
* *
16501159 ATATTTTTTA-ATATCTATAATTAT
1 -TATTTTTTATATATTTAAAATTAT
16501183 TATTTTTTATAT-TTTAAAATTAT
1 TATTTTTTATATATTTAAAATTAT
16501206 T
1 T
16501207 TATTATTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
23 19 0.46
24 9 0.22
25 4 0.10
28 9 0.22
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (24 bp):
TATTTTTTATATATTTAAAATTAT
Found at i:16504549 original size:14 final size:15
Alignment explanation
Indices: 16504530--16504558 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16504520 TTGGATTTCC
16504530 TTTT-CCTTTTTTTT
1 TTTTCCCTTTTTTTT
16504544 TTTTCCCTTTTTTTT
1 TTTTCCCTTTTTTTT
16504559 CTTCTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCCCTTTTTTTT
Found at i:16505915 original size:23 final size:23
Alignment explanation
Indices: 16505846--16505916 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
16505836 ATTTATTTTA
* *
16505846 TTATTTTATTATTTTTTA-GGAT
1 TTATTTTTTTATTTTTTATGGTT
**
16505868 TTATTTTTGTTATTTCTAAAT--TT
1 TTATTTTT-TTATTT-TTTATGGTT
16505891 TTATTTTTTTATTTTTTATGGTT
1 TTATTTTTTTATTTTTTATGGTT
16505914 TTA
1 TTA
16505917 AAGCAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
21 3 0.08
22 13 0.34
23 20 0.53
24 2 0.05
ACGTcount: A:0.20, C:0.01, G:0.07, T:0.72
Consensus pattern (23 bp):
TTATTTTTTTATTTTTTATGGTT
Found at i:16507743 original size:24 final size:25
Alignment explanation
Indices: 16507711--16507757 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
16507701 AAATAGTATA
* *
16507711 ATAATAAGAATA-AAATAAATAAGG
1 ATAAAAAGAATACAAAGAAATAAGG
16507735 ATAAAAAGAATACAAAGAAATAA
1 ATAAAAAGAATACAAAGAAATAA
16507758 AACCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (25 bp):
ATAAAAAGAATACAAAGAAATAAGG
Found at i:16508075 original size:24 final size:24
Alignment explanation
Indices: 16508030--16508076 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16508020 TTCCCCTTCA
* *
16508030 TTTCTATTTTTTTCCTCTTTTTTT
1 TTTCTATTTCTTTCCTCCTTTTTT
16508054 TTTCTTATTTCTTT-CTCCTTTTT
1 TTTC-TATTTCTTTCCTCCTTTTT
16508077 CATTTTCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTCTATTTCTTTCCTCCTTTTTT
Found at i:16508430 original size:17 final size:17
Alignment explanation
Indices: 16508410--16508445 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16508400 CTCTAGTTAA
16508410 AACTACAGCTAATCAAT
1 AACTACAGCTAATCAAT
*
16508427 AACTAGAGCTAATCAAT
1 AACTACAGCTAATCAAT
16508444 AA
1 AA
16508446 GTAGTGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.22
Consensus pattern (17 bp):
AACTACAGCTAATCAAT
Found at i:16509239 original size:24 final size:24
Alignment explanation
Indices: 16509212--16509259 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16509202 TCTTTAGTGG
*
16509212 ACAAAGTAACACATTTTTATAACT
1 ACAAAGTAACACACTTTTATAACT
* *
16509236 ACAAGGTAACACACTTTTGTAACT
1 ACAAAGTAACACACTTTTATAACT
16509260 TAGACTGCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (24 bp):
ACAAAGTAACACACTTTTATAACT
Found at i:16516846 original size:2 final size:2
Alignment explanation
Indices: 16516839--16516863 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16516829 AAATCACCTA
16516839 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16516864 GACACATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16522087 original size:14 final size:14
Alignment explanation
Indices: 16522068--16522097 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16522058 GGTATCAGAG
16522068 CGAGGTTCCAGGTT
1 CGAGGTTCCAGGTT
*
16522082 CGAGGTTCTAGGTT
1 CGAGGTTCCAGGTT
16522096 CG
1 CG
16522098 TGGGTCCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.37, T:0.30
Consensus pattern (14 bp):
CGAGGTTCCAGGTT
Found at i:16527449 original size:18 final size:17
Alignment explanation
Indices: 16527426--16527460 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
16527416 ATTCTATTAA
16527426 TTTTTATTTTTTAGTTAT
1 TTTTTA-TTTTTAGTTAT
16527444 TTTTTATTTTTAGTTAT
1 TTTTTATTTTTAGTTAT
16527461 ATAGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTAGTTAT
Found at i:16528633 original size:16 final size:15
Alignment explanation
Indices: 16528609--16528638 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16528599 AAAGAAAAAC
16528609 AAAAAAAAAATTTTT
1 AAAAAAAAAATTTTT
16528624 AAAAACAAAAATTTT
1 AAAAA-AAAAATTTT
16528639 AATCTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAAAAAATTTTT
Found at i:16530286 original size:3 final size:3
Alignment explanation
Indices: 16530278--16530319 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
16530268 AAATTTTAAG
16530278 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16530320 TGTAGGTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16530777 original size:31 final size:31
Alignment explanation
Indices: 16530742--16530806 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
16530732 ACTCGAGATA
16530742 TAAATGTCAATTATAAGTAAGAATAATATTT
1 TAAATGTCAATTATAAGTAAGAATAATATTT
16530773 TAAATGTCAATTATAAGTAAGAATAATATTT
1 TAAATGTCAATTATAAGTAAGAATAATATTT
16530804 TAA
1 TAA
16530807 TCATTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.38
Consensus pattern (31 bp):
TAAATGTCAATTATAAGTAAGAATAATATTT
Found at i:16532820 original size:2 final size:2
Alignment explanation
Indices: 16532813--16532838 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16532803 TAAAATTATC
16532813 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
16532839 TGCAAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16532981 original size:2 final size:2
Alignment explanation
Indices: 16532974--16533012 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
16532964 AAGCAACCAC
*
16532974 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16533013 TGAAATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:16533622 original size:2 final size:2
Alignment explanation
Indices: 16533610--16533643 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
16533600 GTCATTCTTT
*
16533610 TA TA TA AA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16533644 TTTTTCTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16535310 original size:65 final size:65
Alignment explanation
Indices: 16535241--16535371 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
16535231 AAAATTAAAT
* * *
16535241 ATAATATATACATTAATATCCTATGTCTATATATACTAGTCACATTCAAATACAAAATTAAGTTA
1 ATAATATATACATTAATAACCTATGTCTATACATACTAATCACATTCAAATACAAAATTAAGTTA
*
16535306 ATAATATATACATTAATAACCTATGTCTATACATACTAATCTCATTCAAATACAAAATTAAGTTA
1 ATAATATATACATTAATAACCTATGTCTATACATACTAATCACATTCAAATACAAAATTAAGTTA
16535371 A
1 A
16535372 CTAAGTATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (65 bp):
ATAATATATACATTAATAACCTATGTCTATACATACTAATCACATTCAAATACAAAATTAAGTTA
Found at i:16535454 original size:15 final size:15
Alignment explanation
Indices: 16535422--16535452 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16535412 TATCATAATT
16535422 AATTTTTATTATAAA
1 AATTTTTATTATAAA
16535437 AATTTTTATT-TAAA
1 AATTTTTATTATAAA
16535451 AA
1 AA
16535453 ATAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTTTATTATAAA
Found at i:16537153 original size:37 final size:36
Alignment explanation
Indices: 16537086--16537156 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
16537076 AATCTTTCTC
**
16537086 TTTTTTTAAACTTTTATTTTATTTTTATTTTTTAGT
1 TTTTTTTAAACTTTTATTTTATTTGGATTTTTTAGT
*
16537122 TTTTTTTAAAGTATTTACTTTT-TTTGGATTTTTTA
1 TTTTTTTAAACT-TTTA-TTTTATTTGGATTTTTTA
16537157 ATAATATGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 11 0.37
37 15 0.50
38 4 0.13
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.72
Consensus pattern (36 bp):
TTTTTTTAAACTTTTATTTTATTTGGATTTTTTAGT
Found at i:16538454 original size:20 final size:20
Alignment explanation
Indices: 16538417--16538455 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16538407 CTTTTCCTCA
* * *
16538417 TTTTTTTCTTTTTTTTTTTG
1 TTTTTTTCCTTCTCTTTTTG
16538437 TTTTTTTCCTTCTCTTTTT
1 TTTTTTTCCTTCTCTTTTT
16538456 TCATTTTCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (20 bp):
TTTTTTTCCTTCTCTTTTTG
Found at i:16540671 original size:3 final size:3
Alignment explanation
Indices: 16540663--16540718 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
16540653 TTTGTTTTAT
16540663 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16540711 TTA TTA TT
1 TTA TTA TT
16540719 GTGCCTTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16542007 original size:16 final size:17
Alignment explanation
Indices: 16541979--16542010 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16541969 TTTAAATAAT
16541979 ATAAAAAACAATAAAAA
1 ATAAAAAACAATAAAAA
16541996 ATAAAAAA-AATAAAA
1 ATAAAAAACAATAAAA
16542011 TGTTTGTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (17 bp):
ATAAAAAACAATAAAAA
Found at i:16547438 original size:15 final size:16
Alignment explanation
Indices: 16547407--16547448 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
16547397 TCATGTTTGT
16547407 TGTTTACTTTT-TTTTA
1 TGTTT-CTTTTATTTTA
16547423 TG-TTCTTTTATTTTA
1 TGTTTCTTTTATTTTA
16547438 TGTTTCTTTTA
1 TGTTTCTTTTA
16547449 CATAAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 9 0.38
16 10 0.42
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (16 bp):
TGTTTCTTTTATTTTA
Found at i:16549159 original size:22 final size:22
Alignment explanation
Indices: 16549130--16549182 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
16549120 TTGTCTAATG
* *
16549130 AAATTTATTGATGTTATTTTAT
1 AAATTTATTAATGTTAATTTAT
* *
16549152 TAATTTATTAATTTTAATTTAT
1 AAATTTATTAATGTTAATTTAT
16549174 AAATTTATT
1 AAATTTATT
16549183 TAATTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
AAATTTATTAATGTTAATTTAT
Found at i:16549160 original size:8 final size:8
Alignment explanation
Indices: 16549147--16549187 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
16549137 TTGATGTTAT
16549147 TTTATTAA
1 TTTATTAA
16549155 TTTATTAA
1 TTTATTAA
16549163 -TT-TTAA
1 TTTATTAA
*
16549169 TTTATAAA
1 TTTATTAA
16549177 TTTATTTAA
1 TTTA-TTAA
16549186 TT
1 TT
16549188 AAAATTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 4 0.14
7 4 0.14
8 15 0.54
9 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATTAA
Found at i:16549195 original size:22 final size:22
Alignment explanation
Indices: 16549148--16549195 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
16549138 TGATGTTATT
* * *
16549148 TTATTAATTTATTAATTTTAAT
1 TTATAAATTTATTAATTTAAAA
16549170 TTATAAATTTATTTAA-TTAAAA
1 TTATAAATTTA-TTAATTTAAAA
16549192 TTAT
1 TTAT
16549196 TGACAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAAATTTATTAATTTAAAA
Found at i:16549856 original size:27 final size:27
Alignment explanation
Indices: 16549804--16549871 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
16549794 TTAAATTATA
16549804 TTAAAATATTTAATATAATATTTAAATT
1 TTAAAATATTTAATAT-ATATTTAAATT
*
16549832 TTAAAATTTTTTAATAT-TATTTAAATT
1 TTAAAA-TATTTAATATATATTTAAATT
* *
16549859 AT-AAATAATTAAT
1 TTAAAATATTTAAT
16549872 TAATATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 6 0.17
26 3 0.09
27 11 0.31
28 6 0.17
29 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAAAATATTTAATATATATTTAAATT
Found at i:16550882 original size:15 final size:14
Alignment explanation
Indices: 16550823--16550873 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
16550813 GTTAACTTTT
*
16550823 AAAATTAAAAAAT-
1 AAAATTAAAATATC
* * *
16550836 ATAATTAAATCTATA
1 AAAATTAAA-ATATC
16550851 AAAATTAAAATATC
1 AAAATTAAAATATC
16550865 AAAATTAAA
1 AAAATTAAA
16550874 TGATTCAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 8 0.27
14 14 0.47
15 8 0.27
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTAAAATATC
Found at i:16554904 original size:11 final size:11
Alignment explanation
Indices: 16554890--16554920 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16554880 CATTTTTCAT
16554890 TCATTGCATTC
1 TCATTGCATTC
16554901 TCATTGCATTC
1 TCATTGCATTC
16554912 TCATT-CATT
1 TCATTGCATT
16554921 ACACTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.19, C:0.26, G:0.06, T:0.48
Consensus pattern (11 bp):
TCATTGCATTC
Found at i:16562200 original size:7 final size:7
Alignment explanation
Indices: 16562139--16562209 Score: 58
Period size: 8 Copynumber: 9.7 Consensus size: 7
16562129 ATGCTTAAAA
16562139 AAAAATG
1 AAAAATG
16562146 AAAAA--
1 AAAAATG
16562151 AAAAA-G
1 AAAAATG
16562157 AAAAGATG
1 AAAA-ATG
16562165 AAAAATGG
1 AAAAAT-G
16562173 AAAAATG
1 AAAAATG
*
16562180 AAAAAATAAA
1 -AAAAAT--G
16562190 AAAAATG
1 AAAAATG
16562197 AAAAAATG
1 -AAAAATG
16562205 AAAAA
1 AAAAA
16562210 AAAGAAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
5 5 0.09
6 4 0.07
7 14 0.26
8 25 0.46
9 6 0.11
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:16562203 original size:17 final size:17
Alignment explanation
Indices: 16562136--16562218 Score: 91
Period size: 17 Copynumber: 4.9 Consensus size: 17
16562126 ACTATGCTTA
*
16562136 AAAAAAAATGAAAAAAA
1 AAAAAAAATGAAAAAAT
16562153 AAAGAAAAGATG-AAAAAT
1 AAA-AAAA-ATGAAAAAAT
**
16562171 -GGAAAAATGAAAAAAT
1 AAAAAAAATGAAAAAAT
16562187 AAAAAAAATGAAAAAAT
1 AAAAAAAATGAAAAAAT
16562204 GAAAAAAAA-GAAAAA
1 -AAAAAAAATGAAAAA
16562219 GTGAAAAAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.05
16 10 0.18
17 23 0.41
18 17 0.30
19 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (17 bp):
AAAAAAAATGAAAAAAT
Found at i:16562227 original size:8 final size:8
Alignment explanation
Indices: 16562149--16562226 Score: 77
Period size: 8 Copynumber: 9.6 Consensus size: 8
16562139 AAAAATGAAA
*
16562149 AAAAAAAG
1 AAAAAATG
*
16562157 AAAAGATG
1 AAAAAATG
16562165 -AAAAATG
1 AAAAAATG
*
16562172 GAAAAATG
1 AAAAAATG
*
16562180 AAAAAATAA
1 AAAAAAT-G
16562189 AAAAAATG
1 AAAAAATG
16562197 AAAAAATG
1 AAAAAATG
*
16562205 AAAAAAAAG
1 -AAAAAATG
*
16562214 AAAAAGTG
1 AAAAAATG
16562222 AAAAA
1 AAAAA
16562227 GGAGGACTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
7 6 0.10
8 38 0.66
9 14 0.24
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:16563282 original size:41 final size:41
Alignment explanation
Indices: 16563237--16563531 Score: 395
Period size: 41 Copynumber: 7.1 Consensus size: 41
16563227 ATGATTGTCA
16563237 AGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAG
* *
16563278 AGGAGCAATTTA-TTTTCCAAAGTTCCGTGGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTTTCGTTGCCTCTGTTTAG
*
16563319 AGGAGCAATTTACTTTTCAAAGTTTCGTGGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAG
* *
16563360 AGGAGCAATTTACTTTCCAAAGTTTCGTTGCTTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAG
*
16563401 AGGAGCAATTTATTTTTCAAAGTTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAG
*
16563442 AGGAGCAATTTAC-TTTCAAAAG--TCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTTTCGT--TGCCTCTGTTTAG
* *
16563483 AGGAGCAATTTATGTTTCTCAAAG--TCGTTGAGCCTTTGTTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTTTCGTT--GCCTCTGTTTAG
16563526 AGGAGC
1 AGGAGC
16563532 TTTGGTAAAA
Statistics
Matches: 230, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
39 4 0.02
40 8 0.03
41 186 0.81
42 4 0.02
43 26 0.11
44 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAG
Found at i:16563868 original size:31 final size:26
Alignment explanation
Indices: 16563832--16563895 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 26
16563822 TTTAGATTAG
*
16563832 ATTTATATGTATTTTATGTATATAGTTATAT
1 ATTTATAT-TATATTAT-TAT-TA-TTAT-T
16563863 ATTTATTATTATATTATTATTATTATT
1 ATTTA-TATTATATTATTATTATTATT
16563890 ATTTAT
1 ATTTAT
16563896 TATTTAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.03
27 6 0.19
28 4 0.13
29 2 0.06
30 3 0.10
31 12 0.39
32 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (26 bp):
ATTTATATTATATTATTATTATTATT
Found at i:16563873 original size:3 final size:3
Alignment explanation
Indices: 16563865--16563899 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
16563855 AGTTATATAT
16563865 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT
16563900 TAGTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16563876 original size:14 final size:14
Alignment explanation
Indices: 16563857--16563899 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
16563847 ATGTATATAG
16563857 TTATATATTTATTA
1 TTATATATTTATTA
16563871 TTATAT-TATTATTA
1 TTATATAT-TTATTA
16563885 TTAT-TATTTATTA
1 TTATATATTTATTA
16563898 TT
1 TT
16563900 TAGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATATATTTATTA
Found at i:16564779 original size:17 final size:16
Alignment explanation
Indices: 16564744--16564814 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
16564734 CCGCTCCAGG
*
16564744 TTTTTTTT-TTTTTGGA
1 TTTTTTTTATTTTT-TA
16564760 TTTTTTTTATTTGTTTA
1 TTTTTTTTATTT-TTTA
*
16564777 TTTGTTTTATTTATTTA
1 TTTTTTTTATTT-TTTA
*
16564794 TTCATTTATTATTTTTTA
1 TT--TTTTTTATTTTTTA
16564812 TTT
1 TTT
16564815 ATTAGATTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
16 9 0.20
17 21 0.46
18 8 0.17
19 8 0.17
ACGTcount: A:0.14, C:0.01, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTTTTTATTTTTTA
Found at i:16564833 original size:4 final size:4
Alignment explanation
Indices: 16564765--16564817 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
16564755 TTGGATTTTT
* * *
16564765 TTTA TTTG TTTA TTTGT TTTA TTTA TTTA TTCA TTTA -TTA TTT- TTTA
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
16564812 TTTA TT
1 TTTA TT
16564818 AGATTAGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
3 6 0.15
4 31 0.77
5 3 0.08
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:16564833 original size:22 final size:23
Alignment explanation
Indices: 16564782--16564833 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
16564772 GTTTATTTGT
* *
16564782 TTTATTTATTTATTCATTTATTA
1 TTTATTTATTTATTCAATTATGA
16564805 TTT-TTTATTTATT-AGATTA-GA
1 TTTATTTATTTATTCA-ATTATGA
16564826 TTTATTTA
1 TTTATTTA
16564834 ATATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 5 0.20
22 17 0.68
23 3 0.12
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTATTTATTTATTCAATTATGA
Found at i:16564893 original size:21 final size:22
Alignment explanation
Indices: 16564869--16564909 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
16564859 TTATTTTTTG
16564869 TTTTATTTT-TGTTATTTTCAC
1 TTTTATTTTGTGTTATTTTCAC
*
16564890 TTTTATTTTGTTTTATTTTC
1 TTTTATTTTGTGTTATTTTC
16564910 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTTATTTTGTGTTATTTTCAC
Found at i:16565005 original size:60 final size:59
Alignment explanation
Indices: 16564924--16565559 Score: 702
Period size: 60 Copynumber: 10.7 Consensus size: 59
16564914 AATAAAAATC
*
16564924 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTCA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCA
* *
16564982 AAAAAAGGAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCA
1 AAAAAA-TA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCA
* *
16565043 AAAAAATATTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATATCCA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAAT-TTCA
*
16565102 AAAAAACT-TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCCAA
1 AAAAAA-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTT-C-A
* *
16565162 AAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTC-
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCA
* ** * *
16565219 AAAAAATA-TTTAGTTGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAGTTTCCAGA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTT-C--A
* * * * *
16565280 AAAAAATAATTTTAGGGGAAAAGTTAAAAGTATCAATTTTCCTTTAAAATCAAAGTTTCCAGA
1 AAAAAAT-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTT-C--A
* * * *
16565343 AAAAAATAATTTT-AGGAGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAGTTTCC
1 AAAAAATATTTTTGA-G-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCA
** * * * * **
16565403 AAAAAAGGTTTTCGAAGAAAAATTGAAAGTATCAATTTTCCTTTAAAATCCAAGTTTTCA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-CAAAATTTCA
* * * *
16565463 AAAAAATA-TTTTCAGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAATAT-AAATTTTC-
1 AAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT-TAAAA-ATCAAAATTTCA
*
16565522 -AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
16565560 TTCTAAACAA
Statistics
Matches: 505, Mismatches: 49, Indels: 48
0.84 0.08 0.08
Matches are distributed among these distances:
56 35 0.07
57 13 0.03
58 78 0.15
59 101 0.20
60 114 0.23
61 58 0.11
62 9 0.02
63 97 0.19
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (59 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCA
Found at i:16565133 original size:59 final size:58
Alignment explanation
Indices: 16564923--16565559 Score: 694
Period size: 59 Copynumber: 10.7 Consensus size: 58
16564913 AAATAAAAAT
* *
16564923 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTC
1 CAAAAAA-ATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* * *
16564981 AAAAAAAGGAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTT-
1 CAAAAAA--ATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* * *
16565041 CAAAAAAATATTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATATC
1 CAAAAAAAT-TTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
*
16565100 CAAAAAAACTTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTC
1 CAAAAAAA-TTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* * *
16565159 CAAAAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTT-
1 C-AAAAAAA-TTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* *
16565218 CAAAAAATATTTAGTT--GAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAGTTTC
1 CAAAAAA-ATTT-TTTGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* * *
16565276 CAGAAAAAAATAATTTTAGGGGAAAAGTTAAAAGTATCAATTTTCCTTTAAAATCAAAGTTTC
1 C--AAAAAAAT--TTTT-TGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* *
16565339 CAGAAAAAAATAATTTTAGGAGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAGTTTC
1 C--AAAAAAAT--TTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
** * * * * * *
16565402 CAAAAAAGGTTTTCGAAGAAAAATTGAAAGTATCAATTTTCCTTTAAAATCCAAGTTTT
1 CAAAAAAATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
* * ** *
16565461 CAAAAAAATATTTTCAGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAAT-ATAAATTTT
1 CAAAAAAAT-TTTT-TGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCA-AAATTTC
* *
16565521 CAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 CAAAAAAATTTTTTGGGAAAAGTTGAAAGTATCAATTTT
16565560 TTCTAAACAA
Statistics
Matches: 509, Mismatches: 46, Indels: 48
0.84 0.08 0.08
Matches are distributed among these distances:
56 31 0.06
57 6 0.01
58 81 0.16
59 127 0.25
60 114 0.22
61 48 0.09
62 2 0.00
63 100 0.20
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (58 bp):
CAAAAAAATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATCAAAATTTC
Found at i:16566278 original size:16 final size:16
Alignment explanation
Indices: 16566257--16566288 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16566247 TTGTATTATT
16566257 TTGAGTTTAAATCAAA
1 TTGAGTTTAAATCAAA
16566273 TTGAGTTTAAATCAAA
1 TTGAGTTTAAATCAAA
16566289 AATTTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (16 bp):
TTGAGTTTAAATCAAA
Found at i:16569318 original size:52 final size:51
Alignment explanation
Indices: 16569203--16569357 Score: 197
Period size: 52 Copynumber: 3.0 Consensus size: 51
16569193 TATAACCATA
* * *
16569203 CAAACTTGCCTATTAAGAATCTCTCTCCTCTTA-AATT-TTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATC-CTTTCCTCTTAGAATTCTTCTCTTGCAAGT
*
16569253 CAAACTTGCCTATTAAGAATCCATTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-TTTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * *
16569305 TAAACTTACCTATTAAGAATCCTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCT-TTCCTCTTAGAATTCTTCTCTTGCAAGT
16569357 C
1 C
16569358 TTCTTGTCCA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
49 1 0.01
50 29 0.32
51 5 0.05
52 56 0.62
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.41
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:16569670 original size:25 final size:25
Alignment explanation
Indices: 16569640--16569717 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
16569630 CAAACCATGT
16569640 TCTTCCCACATCTTGAACCTTCAGC
1 TCTTCCCACATCTTGAACCTTCAGC
* *
16569665 TCTTCCCACGTCTTGAACCTT-TGAC
1 TCTTCCCACATCTTGAACCTTCAG-C
**
16569690 TCTTTTCACAT-TTCGAACCTTCAGC
1 TCTTCCCACATCTT-GAACCTTCAGC
16569715 TCT
1 TCT
16569718 GATATCATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 3 0.07
25 40 0.91
26 1 0.02
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.37
Consensus pattern (25 bp):
TCTTCCCACATCTTGAACCTTCAGC
Found at i:16570355 original size:22 final size:22
Alignment explanation
Indices: 16570330--16570376 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16570320 TTTCCCCTCG
16570330 TTTCCCCTTCTTTTCTATTCTT
1 TTTCCCCTTCTTTTCTATTCTT
* * * *
16570352 TTTCTCCTTTTTTTTTCTTCTT
1 TTTCCCCTTCTTTTCTATTCTT
16570374 TTT
1 TTT
16570377 TTTTTTTCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTCCCCTTCTTTTCTATTCTT
Found at i:16570376 original size:14 final size:14
Alignment explanation
Indices: 16570350--16570390 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
16570340 TTTTCTATTC
16570350 TTTTTC-TCCTTTT
1 TTTTTCTTCCTTTT
16570363 TTTTTCTT-CTTTT
1 TTTTTCTTCCTTTT
*
16570376 TTTTTTTTCCTTTT
1 TTTTTCTTCCTTTT
16570390 T
1 T
16570391 CATATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTCCTTTT
Found at i:16587550 original size:21 final size:21
Alignment explanation
Indices: 16587524--16587563 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16587514 AGTCGTTCTT
16587524 TTATATAAATATAAATATAAA
1 TTATATAAATATAAATATAAA
* *
16587545 TTATATATATATATATATA
1 TTATATAAATATAAATATA
16587564 TTCTAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATATAAATATAAATATAAA
Found at i:16589063 original size:22 final size:22
Alignment explanation
Indices: 16589036--16589079 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16589026 AGTTTTAATT
* *
16589036 TTTTTTCCTTTAAAAGATGTCA
1 TTTTTTCATATAAAAGATGTCA
*
16589058 TTTTTTTATATAAAAGATGTCA
1 TTTTTTCATATAAAAGATGTCA
16589080 CAACTTAAAT
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:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTTTTCATATAAAAGATGTCA
Found at i:16589511 original size:19 final size:18
Alignment explanation
Indices: 16589489--16589527 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16589479 ATTTTATCAT
16589489 AATTAATATTTATTATAAA
1 AATTAATATTTATT-TAAA
* *
16589508 AATTATTTTTTATTTAAA
1 AATTAATATTTATTTAAA
16589526 AA
1 AA
16589528 ATAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAATATTTATTTAAA
Found at i:16590939 original size:20 final size:20
Alignment explanation
Indices: 16590893--16590941 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
16590883 TGTATTATTT
**
16590893 AATTAAAATATTATATTTTA
1 AATTAAAATATTATATTAAA
*
16590913 AAGTAAAATA-TATAATTAAA
1 AATTAAAATATTAT-ATTAAA
16590933 AATTAAAAT
1 AATTAAAAT
16590942 CTAAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AATTAAAATATTATATTAAA
Found at i:16591663 original size:20 final size:20
Alignment explanation
Indices: 16591606--16591665 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
16591596 GGTTACTTTT
16591606 ATATATCAATTTAATTAAAA
1 ATATATCAATTTAATTAAAA
* **
16591626 A-AT-T-ATTTTTTGTTAAAA
1 ATATATCA-ATTTAATTAAAA
16591644 ATATATCAATTTAATTAAAA
1 ATATATCAATTTAATTAAAA
16591664 AT
1 AT
16591666 GATAACATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
17 1 0.03
18 11 0.37
19 4 0.13
20 13 0.43
21 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATATCAATTTAATTAAAA
Found at i:16594937 original size:58 final size:59
Alignment explanation
Indices: 16594842--16595002 Score: 172
Period size: 58 Copynumber: 2.7 Consensus size: 59
16594832 GGTAAAAAAT
* *
16594842 AAAAAATATTTTTAATGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAAACTT-TC-
1 AAAAAATATTTTTAACGAAAAGTTGAAAGCATCAATTTTTC-TTGAAAATAAAA-TTATCA
* *
16594900 AAAAAATATTTTT-ACGAGAAATTTGAAAGCATTAATTTTTCTTGAAAATAAAATTATCA
1 AAAAAATATTTTTAACGA-AAAGTTGAAAGCATCAATTTTTCTTGAAAATAAAATTATCA
* *
16594959 AGAAAAATATTTTTTTAA--AAAAGTTGAAAGTATAAATTTTTCTT
1 A-AAAAATA--TTTTTAACGAAAAGTTGAAAGCATCAATTTTTCTT
16595003 ATATAAAAGC
Statistics
Matches: 88, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
57 5 0.06
58 41 0.47
59 6 0.07
60 29 0.33
61 1 0.01
62 5 0.06
63 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.39
Consensus pattern (59 bp):
AAAAAATATTTTTAACGAAAAGTTGAAAGCATCAATTTTTCTTGAAAATAAAATTATCA
Found at i:16594987 original size:60 final size:58
Alignment explanation
Indices: 16594842--16595002 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 58
16594832 GGTAAAAAAT
*
16594842 AAAAAATA--TTTTTAATGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAAACTTTC
1 AAAAAATATTTTTTTAA--AAAAGTTGAAAGTATAAATTTTTC-TTGAAAATAAAACTTTC
*** * * * *
16594900 AAAAAATATTTTTACGAGAAATTTGAAAGCATTAATTTTTCTTGAAAATAAAA-TTATC
1 AAAAAATATTTTTTTAAAAAAGTTGAAAGTATAAATTTTTCTTGAAAATAAAACTT-TC
16594958 AAGAAAAATATTTTTTTAAAAAAGTTGAAAGTATAAATTTTTCTT
1 -A-AAAAATATTTTTTTAAAAAAGTTGAAAGTATAAATTTTTCTT
16595003 ATATAAAAGC
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
57 2 0.02
58 36 0.43
59 6 0.07
60 39 0.47
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.39
Consensus pattern (58 bp):
AAAAAATATTTTTTTAAAAAAGTTGAAAGTATAAATTTTTCTTGAAAATAAAACTTTC
Found at i:16600012 original size:46 final size:46
Alignment explanation
Indices: 16599951--16600162 Score: 230
Period size: 46 Copynumber: 4.5 Consensus size: 46
16599941 TGATGAAGTC
* *
16599951 TTGAGTTTTCAAATGATAATCTTTAAGAAATCTTCAAATGAAAATCT
1 TTGAGTCTT-AAATGAAAATCTTTAAGAAATCTTCAAATGAAAATCT
* *
16599998 TTGAGTCTTAAATGAAAATCTTTAAAAAATTTTCAAAT-AAGAATCT
1 TTGAGTCTTAAATGAAAATCTTTAAGAAATCTTCAAATGAA-AATCT
* * * * *
16600044 TTGAGTCTTAAATGAGAATATTTGAGAAATTTTCAAATGAGAATCT
1 TTGAGTCTTAAATGAAAATCTTTAAGAAATCTTCAAATGAAAATCT
* * *
16600090 TTAAATCTTAAATGAAAATCTTTAAGAAAGTCTT-AAATGGAAATCT
1 TTGAGTCTTAAATGAAAATCTTTAAGAAA-TCTTCAAATGAAAATCT
*
16600136 TTAAGATGTTTTCAAATGAAAATCTTT
1 TT--GA-GTCTT-AAATGAAAATCTTT
16600163 GAGTTTGAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
45 2 0.01
46 106 0.77
47 12 0.09
48 1 0.01
49 3 0.02
50 14 0.10
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (46 bp):
TTGAGTCTTAAATGAAAATCTTTAAGAAATCTTCAAATGAAAATCT
Found at i:16600114 original size:14 final size:13
Alignment explanation
Indices: 16600092--16600136 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
16600082 GAGAATCTTT
16600092 AAATCTTAAATGA
1 AAATCTTAAATGA
*
16600105 AAATCTTTAA-GA
1 AAATCTTAAATGA
* *
16600117 AAGTCTTAAATGG
1 AAATCTTAAATGA
16600130 AAATCTT
1 AAATCTT
16600137 TAAGATGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (13 bp):
AAATCTTAAATGA
Found at i:16600162 original size:117 final size:114
Alignment explanation
Indices: 16599956--16600279 Score: 383
Period size: 117 Copynumber: 2.8 Consensus size: 114
16599946 AAGTCTTGAG
* *
16599956 TTTTCAAATGATAATCTTTAAGAAATCTTCAAATGAAAATCTTT-G--AGTCTTAAATGAAAATC
1 TTTTCAAATGAGAATCTTT---AAATCTT-AAATGAAAATCTTTAGAAAGTCTTAAATGGAAATC
* *
16600018 TTTAAAAAATTTTCAAATAAGAATCTTTGAGTCTT-AAATGAGAATATTTGAGAAA
62 TTT--AAAGTTTTCAAATAAGAATCTTTGAGT-TTGAAATGAGAATATTTAAGAAA
16600073 TTTTCAAATGAGAATCTTTAAATCTTAAATGAAAATCTTTAAGAAAGTCTTAAATGGAAATCTTT
1 TTTTCAAATGAGAATCTTTAAATCTTAAATGAAAATCTTT-AGAAAGTCTTAAATGGAAATCTTT
*
16600138 AAGATGTTTTCAAATGAA-AATCTTTGAGTTTGAAATGAGAATCTTTAAGAAA
65 AA-A-GTTTTCAAAT-AAGAATCTTTGAGTTTGAAATGAGAATATTTAAGAAA
* * * * *
16600190 TTCTCAAATGAGAATCTTTGAATCTTAAATGAGAATCTTTAGAAAATCCTCAAAT-GAGAAT-TT
1 TTTTCAAATGAGAATCTTTAAATCTTAAATGAAAATCTTTAGAAAGT-CTTAAATGGA-AATCTT
*
16600253 TTAAGTTTTCAAATAAGAATCTTTGAG
64 TAAAGTTTTCAAATAAGAATCTTTGAG
16600280 ATGTAAAACC
Statistics
Matches: 185, Mismatches: 11, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
113 16 0.09
114 27 0.15
115 4 0.02
116 15 0.08
117 121 0.65
118 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.37
Consensus pattern (114 bp):
TTTTCAAATGAGAATCTTTAAATCTTAAATGAAAATCTTTAGAAAGTCTTAAATGGAAATCTTTA
AAGTTTTCAAATAAGAATCTTTGAGTTTGAAATGAGAATATTTAAGAAA
Found at i:16600220 original size:46 final size:47
Alignment explanation
Indices: 16599959--16600276 Score: 173
Period size: 46 Copynumber: 6.8 Consensus size: 47
16599949 TCTTGAGTTT
* * * *
16599959 TCAAATGATAATCTTTAAGAAATCTTCAAATGAAAATCTTT-G--AGTC
1 TCAAATGAAAATCTTT--GAAGTCTTCAAATGAGAATCTTTAGAAATTC
* * * * * *
16600005 TTAAATGAAAATCTTTAAAAAATTTTCAAATAAGAATCTTT-G--AGTC
1 TCAAATGAAAATCTTT--GAAGTCTTCAAATGAGAATCTTTAGAAATTC
* * * * *
16600051 TTAAATGAGAATATTTGAGAAATTTTCAAATGAGAATCTTT--AAA-TC
1 TCAAATGAAAATCTTT--GAAGTCTTCAAATGAGAATCTTTAGAAATTC
* ** *
16600097 TTAAATGAAAATCTTTAAGAAAGTCTT-AAATG-GAAATCTTTAAGATGTTT
1 TCAAATGAAAATCTTT--G-AAGTCTTCAAATGAG-AATCTTT-AGAAATTC
*
16600147 TCAAATGAAAATCTTTG-AGT-TTGAAATGAGAATCTTTAAGAAATTC
1 TCAAATGAAAATCTTTGAAGTCTTCAAATGAGAATCTTT-AGAAATTC
* *
16600193 TCAAATGAGAATCTTTGAA-TCTT-AAATGAGAATCTTTAGAAAATCC
1 TCAAATGAAAATCTTTGAAGTCTTCAAATGAGAATCTTTAG-AAATTC
* * * *
16600239 TCAAATGAGAAT-TTTTAAGTTTTCAAATAAGAATCTTT
1 TCAAATGAAAATCTTTGAAGTCTTCAAATGAGAATCTTT
16600277 GAGATGTAAA
Statistics
Matches: 229, Mismatches: 28, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
45 10 0.04
46 178 0.78
47 23 0.10
48 1 0.00
49 1 0.00
50 16 0.07
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (47 bp):
TCAAATGAAAATCTTTGAAGTCTTCAAATGAGAATCTTTAGAAATTC
Found at i:16600832 original size:41 final size:41
Alignment explanation
Indices: 16600763--16600842 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
16600753 TGACTATCGA
* * *
16600763 GGAGCCTTTTATTTTTCAAAGTCATTGAGTCTCTGTTTAGG
1 GGAGCCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGG
* * **
16600804 GGAGCCCTTTGTTTTTCTAAGTTGTTGAGCCTCTATTTA
1 GGAGCCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTA
16600843 AAGAGGCTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.45
Consensus pattern (41 bp):
GGAGCCCTTTATTTTTCAAAGTCATTGAGCCTCTATTTAGG
Found at i:16602791 original size:57 final size:59
Alignment explanation
Indices: 16602640--16602798 Score: 225
Period size: 59 Copynumber: 2.7 Consensus size: 59
16602630 AGTAAAAAAT
*
16602640 AAAAAATATTTTTGAGTAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTA
* * * *
16602699 AAAAAATATTTTTGAGGAAAAGTTAAAATTTTCAA-TTTTCTTTAAAAATAAAA-TTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAAATTTTTA
* *
16602757 AAAAAA-CTTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT
16602799 GTATAAAAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
57 25 0.28
58 20 0.23
59 43 0.49
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (59 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTTA
Found at i:16606947 original size:10 final size:10
Alignment explanation
Indices: 16606924--16607242 Score: 92
Period size: 10 Copynumber: 32.9 Consensus size: 10
16606914 ATCTTTAAAA
16606924 TAAAAAA-TT
1 TAAAAAATTT
*
16606933 CAAAAAATTT
1 TAAAAAATTT
*
16606943 T--AAAA-GT
1 TAAAAAATTT
*
16606950 T-AAAATTTT
1 TAAAAAATTT
*
16606959 TTAAAAATTT
1 TAAAAAATTT
16606969 CT-AAAAATTT
1 -TAAAAAATTT
** *
16606979 TTCAAACTTT
1 TAAAAAATTT
16606989 CTAAAAAA-TT
1 -TAAAAAATTT
* **
16606999 AAAAAAAAAT
1 TAAAAAATTT
* * *
16607009 TCAAATATTA
1 TAAAAAATTT
* *
16607019 TAACAAATTC
1 TAAAAAATTT
*
16607029 T-AAAAATTC
1 TAAAAAATTT
16607038 TAAAAAATTCT
1 TAAAAAATT-T
*
16607049 AAAAAAATTT
1 TAAAAAATTT
* **
16607059 T-TAAAATCC
1 TAAAAAATTT
*
16607068 TAACAAATTT
1 TAAAAAATTT
* * *
16607078 TCATAAATTC
1 TAAAAAATTT
*
16607088 T-AAAAATTC
1 TAAAAAATTT
*
16607097 TAAAATAATAT
1 TAAAA-AATTT
**
16607108 TAAAACTTTT
1 TAAAAAATTT
* *
16607118 TAGAAAATTC
1 TAAAAAATTT
** *
16607128 CCAAAAATTC
1 TAAAAAATTT
16607138 TAAAAAATTT
1 TAAAAAATTT
16607148 TAAAAAATTT
1 TAAAAAATTT
* *
16607158 TAAAAACTTC
1 TAAAAAATTT
**
16607168 TAAAATTTTT
1 TAAAAAATTT
*
16607178 TTAAAAATTT
1 TAAAAAATTT
* *
16607188 CAAAAAA--C
1 TAAAAAATTT
16607196 T--AAAA-TT
1 TAAAAAATTT
* *
16607203 TCACAAATTT
1 TAAAAAATTT
*
16607213 TCAAAAAATTC
1 T-AAAAAATTT
*
16607224 TAGAAAATTT
1 TAAAAAATTT
16607234 TAAAAAATT
1 TAAAAAATT
16607243 CAAAAAGAAT
Statistics
Matches: 219, Mismatches: 73, Indels: 35
0.67 0.22 0.11
Matches are distributed among these distances:
6 4 0.02
7 3 0.01
8 7 0.03
9 40 0.18
10 137 0.63
11 28 0.13
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.36
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:16607184 original size:30 final size:29
Alignment explanation
Indices: 16606926--16607248 Score: 132
Period size: 30 Copynumber: 11.2 Consensus size: 29
16606916 CTTTAAAATA
*
16606926 AAAAATTC-AAAAAATTTT--AAAAGTT-
1 AAAAATTCTAAAAAATTTTAAAAAATTTC
* * * *
16606951 AAAATTTTTTAAAAATTTCTAAAAATTTTTC
1 AAAAATTCTAAAAAATTT-TAAAAA-ATTTC
** ** *
16606982 AAACTTTCTAAAAAATTAAAAAAAAATTC
1 AAAAATTCTAAAAAATTTTAAAAAATTTC
* * * * *
16607011 AAATATTATAACAAATTCT-AAAAATTCTA
1 AAAAATTCTAAAAAATTTTAAAAAATT-TC
* *
16607040 AAAAATTCTAAAAAAATTTT-TAAAA-TCC
1 AAAAATTCT-AAAAAATTTTAAAAAATTTC
* * * * *
16607068 TAACAAATTTTCATAAATTCT-AAAAATTCTA
1 -AA-AAATTCTAAAAAATTTTAAAAAATT-TC
** * *
16607099 AAATAATAT-TAAAACTTTTTAGAAAATTCCC
1 AAA-AAT-TCTAAAAAATTTTAAAAAATT-TC
*
16607130 AAAAATTCTAAAAAATTTTAAAAAATTTT
1 AAAAATTCTAAAAAATTTTAAAAAATTTC
** *
16607159 AAAAACTTCTAAAATTTTTTTAAAAATTTC
1 AAAAA-TTCTAAAAAATTTTAAAAAATTTC
* * * *
16607189 AAAAA-ACT--AAAATTTCACAAATTTTC
1 AAAAATTCTAAAAAATTTTAAAAAATTTC
*
16607215 AAAAAATTCTAGAAAATTTTAAAAAA-TTC
1 -AAAAATTCTAAAAAATTTTAAAAAATTTC
16607244 AAAAA
1 AAAAA
16607249 GAATTAAGGA
Statistics
Matches: 215, Mismatches: 62, Indels: 39
0.68 0.20 0.12
Matches are distributed among these distances:
25 6 0.03
26 20 0.09
27 6 0.03
28 15 0.07
29 51 0.24
30 92 0.43
31 25 0.12
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35
Consensus pattern (29 bp):
AAAAATTCTAAAAAATTTTAAAAAATTTC
Found at i:16607243 original size:20 final size:19
Alignment explanation
Indices: 16606924--16607248 Score: 159
Period size: 20 Copynumber: 16.8 Consensus size: 19
16606914 ATCTTTAAAA
*
16606924 TAAAAAATTCAAAAAATTT
1 TAAAAAATTCTAAAAATTT
* *
16606943 T--AAAAGT-TAAAATTTTT
1 TAAAAAATTCTAAAA-ATTT
*
16606960 TAAAAATTTCTAAAAATTTT
1 TAAAAAATTCTAAAAA-TTT
* ** *
16606980 TCAAACTTTCTAAAAAATTAA
1 TAAAAAATTCT-AAAAATT-T
* * *
16607001 AAAAAAATTC-AAATATTA
1 TAAAAAATTCTAAAAATTT
* *
16607019 TAACAAATTCTAAAAATTC
1 TAAAAAATTCTAAAAATTT
16607038 TAAAAAATTCTAAAAAAATTT
1 TAAAAAATTCT--AAAAATTT
* *
16607059 T-TAAAATCCTAACAAATTT
1 TAAAAAATTCTAA-AAATTT
* * *
16607078 TCATAAATTCTAAAAATTC
1 TAAAAAATTCTAAAAATTT
*
16607097 TAAAATAATAT-TAAAACTTTT
1 TAAAA-AAT-TCTAAAA-ATTT
* * *
16607118 TAGAAAATTCCCAAAAATTC
1 TAAAAAATT-CTAAAAATTT
*
16607138 TAAAAAATTTTAAAAAATTT
1 TAAAAAATTCT-AAAAATTT
* *
16607158 TAAAAACTTCTAAAATTTTT
1 TAAAAAATTCTAAAA-ATTT
* **
16607178 TTAAAAATT-TCAAAAA-AC
1 TAAAAAATTCT-AAAAATTT
* *
16607196 T-AAAATTTC-ACAAATTT
1 TAAAAAATTCTAAAAATTT
16607213 TCAAAAAATTCTAGAAAATTT
1 T-AAAAAATTCTA-AAAATTT
16607234 TAAAAAATTC-AAAAA
1 TAAAAAATTCTAAAAA
16607249 GAATTAAGGA
Statistics
Matches: 228, Mismatches: 52, Indels: 53
0.68 0.16 0.16
Matches are distributed among these distances:
16 8 0.04
17 16 0.07
18 16 0.07
19 56 0.25
20 95 0.42
21 37 0.16
ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35
Consensus pattern (19 bp):
TAAAAAATTCTAAAAATTT
Found at i:16607248 original size:10 final size:10
Alignment explanation
Indices: 16606987--16607248 Score: 109
Period size: 10 Copynumber: 26.9 Consensus size: 10
16606977 TTTTCAAACT
16606987 TTCTAAAAAA
1 TTCTAAAAAA
**
16606997 TTAAAAAAAAA
1 TT-CTAAAAAA
*
16607008 TTC--AAATA
1 TTCTAAAAAA
* *
16607016 TTATAACAAA
1 TTCTAAAAAA
16607026 TTCT-AAAAA
1 TTCTAAAAAA
16607035 TTCTAAAAAA
1 TTCTAAAAAA
16607045 TTCTAAAAAAA
1 TTCT-AAAAAA
**
16607056 TT-TTTAAAA
1 TTCTAAAAAA
* *
16607065 TCCTAACAAA
1 TTCTAAAAAA
* * *
16607075 TTTTCATAAA
1 TTCTAAAAAA
16607085 TTCT-AAAAA
1 TTCTAAAAAA
16607094 TTCTAAAATAA
1 TTCTAAAA-AA
**
16607105 TAT-TAAAACT
1 T-TCTAAAAAA
* *
16607115 TTTTAGAAAA
1 TTCTAAAAAA
**
16607125 TTCCCAAAAA
1 TTCTAAAAAA
16607135 TTCTAAAAAA
1 TTCTAAAAAA
*
16607145 TTTTAAAAAA
1 TTCTAAAAAA
* *
16607155 TTTTAAAAAC
1 TTCTAAAAAA
**
16607165 TTCTAAAATT
1 TTCTAAAAAA
* *
16607175 TTTTTAAAAA
1 TTCTAAAAAA
16607185 TT-TCAAAAAA
1 TTCT-AAAAAA
16607195 --CT--AAAA
1 TTCTAAAAAA
* *
16607201 TT-TCACAAA
1 TTCTAAAAAA
*
16607210 TTTTCAAAAAA
1 TTCT-AAAAAA
*
16607221 TTCTAGAAAA
1 TTCTAAAAAA
*
16607231 TTTTAAAAAA
1 TTCTAAAAAA
16607241 TTC-AAAAA
1 TTCTAAAAA
16607249 GAATTAAGGA
Statistics
Matches: 184, Mismatches: 50, Indels: 37
0.68 0.18 0.14
Matches are distributed among these distances:
6 4 0.02
7 1 0.01
8 6 0.03
9 34 0.18
10 107 0.58
11 31 0.17
12 1 0.01
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (10 bp):
TTCTAAAAAA
Found at i:16607308 original size:18 final size:17
Alignment explanation
Indices: 16607285--16607326 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
16607275 AAAATTTTCC
16607285 AAAATTAAAAAAATATAA
1 AAAATTAAAAAAATA-AA
* *
16607303 ATAATTAAAAGAATAAA
1 AAAATTAAAAAAATAAA
16607320 AAAATTA
1 AAAATTA
16607327 TGATTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAATTAAAAAAATAAA
Found at i:16607626 original size:8 final size:8
Alignment explanation
Indices: 16607615--16607658 Score: 52
Period size: 8 Copynumber: 5.0 Consensus size: 8
16607605 AAAATTTTGA
16607615 AATTTTTT
1 AATTTTTT
16607623 AATTTTTT
1 AATTTTTT
16607631 AAAATTTTTTT
1 --AA-TTTTTT
16607642 AATTTTTT
1 AATTTTTT
16607650 AGATTTTTT
1 A-ATTTTTT
16607659 CTTTTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 15 0.47
9 9 0.28
10 2 0.06
11 6 0.19
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
AATTTTTT
Found at i:16607629 original size:9 final size:9
Alignment explanation
Indices: 16607617--16607658 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
16607607 AATTTTGAAA
16607617 TTTTTTAAT
1 TTTTTTAAT
*
16607626 TTTTTAAAAT
1 TTTTT-TAAT
16607636 TTTTTTAA-
1 TTTTTTAAT
16607644 TTTTTTAGAT
1 TTTTTTA-AT
16607654 TTTTT
1 TTTTT
16607659 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 8 0.29
10 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:16607921 original size:7 final size:8
Alignment explanation
Indices: 16607907--16607970 Score: 64
Period size: 8 Copynumber: 8.1 Consensus size: 8
16607897 AATTTAAAAA
16607907 TAAATTTT
1 TAAATTTT
16607915 T-AATTTT
1 TAAATTTT
16607922 TAAAAATTTT
1 T--AAATTTT
16607932 TAAATTTT
1 TAAATTTT
16607940 TAAATTTT
1 TAAATTTT
16607948 T---TTTT
1 TAAATTTT
*
16607953 TGAATTTT
1 TAAATTTT
16607961 TAAAATTTT
1 T-AAATTTT
16607970 T
1 T
16607971 TTAATATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
5 5 0.10
7 7 0.15
8 22 0.46
9 7 0.15
10 7 0.15
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (8 bp):
TAAATTTT
Found at i:16607930 original size:17 final size:18
Alignment explanation
Indices: 16607908--16607943 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16607898 ATTTAAAAAT
16607908 AAATTTTT-AATTTTTAA
1 AAATTTTTAAATTTTTAA
16607925 AAATTTTTAAATTTTTAA
1 AAATTTTTAAATTTTTAA
16607943 A
1 A
16607944 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATTTTTAAATTTTTAA
Found at i:16607958 original size:21 final size:21
Alignment explanation
Indices: 16607928--16607972 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
16607918 TTTTTAAAAA
*
16607928 TTTTTAAATTTTTAAATTTTT
1 TTTTTAAATTTTTAAAATTTT
*
16607949 TTTTTGAATTTTTAAAATTTT
1 TTTTTAAATTTTTAAAATTTT
16607970 TTT
1 TTT
16607973 AATATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTAAATTTTTAAAATTTT
Done.