Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 16 of 182
Found at i:6688817 original size:30 final size:31
Alignment explanation
Indices: 6688740--6688820 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
6688730 AAATGAATAG
* *
6688740 TAAATAGAG-GACTATTTTGTCACTTTTCGA
1 TAAATTGAGTGACTGTTTTGTCACTTTTCGA
* *
6688770 TAACTTTAGTGACTGTTTTGTCACATTTTC-A
1 TAAATTGAGTGACTGTTTTGTCAC-TTTTCGA
*
6688801 -AAATTGAGTGATTGTTTTGT
1 TAAATTGAGTGACTGTTTTGT
6688821 TAAATATAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 23 0.55
31 14 0.33
32 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (31 bp):
TAAATTGAGTGACTGTTTTGTCACTTTTCGA
Found at i:6696852 original size:17 final size:16
Alignment explanation
Indices: 6696832--6696876 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
6696822 GTTTGATTTT
*
6696832 TAAAAGTATTTTTGAGA
1 TAAAAGTATTTTT-AAA
*
6696849 TAAAAGTATTATTAAA
1 TAAAAGTATTTTTAAA
6696865 TAAAA-TATTTTT
1 TAAAAGTATTTTT
6696877 TGATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.24
16 7 0.28
17 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
TAAAAGTATTTTTAAA
Found at i:6696879 original size:52 final size:52
Alignment explanation
Indices: 6696823--6696922 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 52
6696813 TTTATTTAAG
*
6696823 TTTGA-TTTTTAAAAGTATTTTTGAG-AT-AAAAGTATTATTAAATAAAATATTT
1 TTTGATTTTTTAAAAGTATTTTTG-GTATCAAAAATATT-TTAAA-AAAATATTT
6696875 TTTGATTTTTTAAAAGTATTTTTGGTATCAAAAATATTTTAAAAAAAT
1 TTTGATTTTTTAAAAGTATTTTTGGTATCAAAAATATTTTAAAAAAAT
6696923 TTCCAAAAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
52 11 0.25
53 25 0.57
54 8 0.18
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (52 bp):
TTTGATTTTTTAAAAGTATTTTTGGTATCAAAAATATTTTAAAAAAATATTT
Found at i:6701630 original size:24 final size:24
Alignment explanation
Indices: 6701591--6701655 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
6701581 CCGGATTTTT
* *
6701591 TAAAAGATTTACTATTTATTAGCA
1 TAAAATATTTAATATTTATTAGCA
* *
6701615 TAATATATTTAATATTTATTAGTA
1 TAAAATATTTAATATTTATTAGCA
* *
6701639 TAAAATTTTTATTATTT
1 TAAAATATTTAATATTT
6701656 CTTTTCATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (24 bp):
TAAAATATTTAATATTTATTAGCA
Found at i:6703639 original size:88 final size:89
Alignment explanation
Indices: 6703483--6703649 Score: 210
Period size: 89 Copynumber: 1.9 Consensus size: 89
6703473 ACTTGATATA
* * * * * * * *
6703483 TTTTTTTAATTTGGTATTTAAATTTTTTTGATCTAATGTGGTACTCAAATTTAAATTTTTTTTTT
1 TTTTTTTAAGTTGGTACTTAAACTTTTTGGATCCAATGTGATACCCAAATTTAAATTTTTTTCTT
*
6703548 AATTTGGTATCTAAACTTGACACT
66 AATTTGGTACCTAAACTTGACACT
* * * *
6703572 TTTTTTTAAGTTGGTACTTAAACTTTTTGGGTCCAATTTGAT-CCCAAATTTGACTTTTTTTCTT
1 TTTTTTTAAGTTGGTACTTAAACTTTTTGGATCCAATGTGATACCCAAATTTAAATTTTTTTCTT
6703636 AATTTGGTACCTAA
66 AATTTGGTACCTAA
6703650 TATTTTTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
88 31 0.48
89 34 0.52
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (89 bp):
TTTTTTTAAGTTGGTACTTAAACTTTTTGGATCCAATGTGATACCCAAATTTAAATTTTTTTCTT
AATTTGGTACCTAAACTTGACACT
Found at i:6704576 original size:10 final size:10
Alignment explanation
Indices: 6704563--6704599 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
6704553 TTTTTTACAT
6704563 AATTTTTTTA
1 AATTTTTTTA
6704573 AATTTTTTTA
1 AATTTTTTTA
*
6704583 AATTTTTAATA
1 AATTTTT-TTA
6704594 AATTTT
1 AATTTT
6704600 AACTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:6704613 original size:17 final size:18
Alignment explanation
Indices: 6704578--6704613 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6704568 TTTTAAATTT
6704578 TTTTAAATTTTTAATAAA
1 TTTTAAATTTTTAATAAA
*
6704596 TTTTAACTTTTTAA-AAA
1 TTTTAAATTTTTAATAAA
6704613 T
1 T
6704614 CATAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAATTTTTAATAAA
Found at i:6705040 original size:23 final size:20
Alignment explanation
Indices: 6705016--6705059 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6705006 AATACGAAAA
6705016 TAATA-ATATATATTAATGAT
1 TAATATATATATATT-ATGAT
*
6705036 TAATATCTATATATTATGAT
1 TAATATATATATATTATGAT
6705056 TAAT
1 TAAT
6705060 TGACGTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TAATATATATATATTATGAT
Found at i:6710811 original size:20 final size:21
Alignment explanation
Indices: 6710788--6710826 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6710778 TTTGCAATGT
*
6710788 AGTTAGTTATTG-TAGTTAAA
1 AGTTAGTTAATGATAGTTAAA
6710808 AGTTAGTTAATGATAGTTA
1 AGTTAGTTAATGATAGTTA
6710827 GTTAATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44
Consensus pattern (21 bp):
AGTTAGTTAATGATAGTTAAA
Found at i:6721025 original size:100 final size:100
Alignment explanation
Indices: 6720850--6721048 Score: 317
Period size: 100 Copynumber: 2.0 Consensus size: 100
6720840 ATCACCCAGC
* *
6720850 ACTTAATACATGCTCAACTGTAACAACTGAGCATCAATGACGAGCAGTATTAAACTTCCAAAATG
1 ACTTAATACATGCTCAACTGTAACAACTGAGCACCAATCACGAGCAGTATTAAACTTCCAAAATG
* *
6720915 TATTGCTAAATCCCAGTAAGCAAGTTAGCCAAGCA
66 TATTGATAAATCCCAGTAAGCAACTTAGCCAAGCA
* * *
6720950 ACTTAATACATGCTCAATTGTAATAACTGAGCACCAGTCACGAGCAGTATTAAACTTCCAAAATG
1 ACTTAATACATGCTCAACTGTAACAACTGAGCACCAATCACGAGCAGTATTAAACTTCCAAAATG
* *
6721015 TATTGATAAATTCTAGTAAGCAACTTAGCCAAGC
66 TATTGATAAATCCCAGTAAGCAACTTAGCCAAGC
6721049 CAAAACTAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (100 bp):
ACTTAATACATGCTCAACTGTAACAACTGAGCACCAATCACGAGCAGTATTAAACTTCCAAAATG
TATTGATAAATCCCAGTAAGCAACTTAGCCAAGCA
Found at i:6726302 original size:18 final size:18
Alignment explanation
Indices: 6726279--6726313 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6726269 TTACAAAGCA
*
6726279 TTTATTTCAAAAGTATTT
1 TTTATTTCAAAAATATTT
6726297 TTTATTTCAAAAATATT
1 TTTATTTCAAAAATATT
6726314 CGGAGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTATTTCAAAAATATTT
Found at i:6729953 original size:90 final size:91
Alignment explanation
Indices: 6729799--6729992 Score: 241
Period size: 90 Copynumber: 2.1 Consensus size: 91
6729789 TTAATATAAT
*** *
6729799 ATTTGGTACCTAAACTTGACACTTTTTTCCTAGTTTGGTACCTAAACTCTTTTTGGTCCAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTTAAAAGTTTGGTACCTAAACTCTTTTGGGTCCAATTTG
*
6729864 ATACTCAAACTTGA-TACTTTTTCCTG
66 ATACTCAAACTTGACT-CTTTTTCCTA
* * *
6729890 ATTTGGTACCTAAGCTTGACATTTTTTTAAAAG-TTGGTACTTAAACT-TTTTGGGGTCCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTTTAAAAGTTTGGTACCTAAACTCTTTT-GGGTCCAATTT
** *
6729953 GATACTTGAACTTGACTCTTTTTTCTA
65 GATACTCAAACTTGACTCTTTTTCCTA
*
6729980 ATTTGATACCTAA
1 ATTTGGTACCTAA
6729993 TCTTTTTTAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
89 4 0.04
90 56 0.63
91 29 0.33
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTTAAAAGTTTGGTACCTAAACTCTTTTGGGTCCAATTTG
ATACTCAAACTTGACTCTTTTTCCTA
Found at i:6730243 original size:58 final size:58
Alignment explanation
Indices: 6730158--6730298 Score: 201
Period size: 58 Copynumber: 2.4 Consensus size: 58
6730148 AAATTGAATC
* * *
6730158 TAAAAAAAGTTTAGGTATCAAAATAGGAAAAAATACCAAGTTCAAGTACCAATTTGGG
1 TAAAAAAAATTTAGGTACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAATTTGGG
* ** *
6730216 TAAAAAAAATTTAGGTACCGAATTAGGAAAAAATGTCAAGTTCAAGTATCAATTTGGG
1 TAAAAAAAATTTAGGTACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAATTTGGG
* *
6730274 TCAAAAAAATTTAGGTGCCAAATTA
1 TAAAAAAAATTTAGGTACCAAATTA
6730299 AAAAAAAGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (58 bp):
TAAAAAAAATTTAGGTACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAATTTGGG
Found at i:6730305 original size:58 final size:58
Alignment explanation
Indices: 6730158--6730315 Score: 190
Period size: 58 Copynumber: 2.7 Consensus size: 58
6730148 AAATTGAATC
* * * ** **
6730158 TAAAAAAAGTTTAGGTATCAAAATAGGAAAAAATACCAAGTTCAAGTACCAATTTGGG
1 TAAAAAAAATTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCAATTTGGG
* ** *
6730216 TAAAAAAAATTTAGGTACCGAATTAGGAAAAAATGTCAAGTTCAAGTATCAATTTGGG
1 TAAAAAAAATTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCAATTTGGG
* * *
6730274 TCAAAAAAATTTAGGTGCCAAATTAAAAAAAAGTGTCAAGTT
1 TAAAAAAAATTTAGGTACCAAATTAAAAAAAAATGTCAAGTT
6730316 TAGATACCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 87 1.00
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.26
Consensus pattern (58 bp):
TAAAAAAAATTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCAATTTGGG
Found at i:6742819 original size:22 final size:22
Alignment explanation
Indices: 6742771--6742820 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6742761 TACCTAAATT
6742771 TTGAAATTTAAAAAAATAAGAG
1 TTGAAATTTAAAAAAATAAGAG
* **
6742793 ATGAAATTTTTAAAAATATA-AG
1 TTGAAATTTAAAAAAATA-AGAG
6742815 TTGAAA
1 TTGAAA
6742821 GACTAAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (22 bp):
TTGAAATTTAAAAAAATAAGAG
Found at i:6744092 original size:11 final size:11
Alignment explanation
Indices: 6744074--6744115 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
6744064 ATTTCATGCT
6744074 ATTTTTTATGA
1 ATTTTTTATGA
*
6744085 ACTTTTTAT-A
1 ATTTTTTATGA
*
6744095 ATTTTTTTTGA
1 ATTTTTTATGA
6744106 ATTTTTTATG
1 ATTTTTTATG
6744116 TTTTTAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (11 bp):
ATTTTTTATGA
Found at i:6744120 original size:21 final size:21
Alignment explanation
Indices: 6744074--6744114 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6744064 ATTTCATGCT
6744074 ATTTTTTATGAACTTTTTATA
1 ATTTTTTATGAACTTTTTATA
* *
6744095 ATTTTTTTTGAATTTTTTAT
1 ATTTTTTATGAACTTTTTAT
6744115 GTTTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTTTTTATGAACTTTTTATA
Found at i:6744128 original size:17 final size:17
Alignment explanation
Indices: 6744099--6744131 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6744089 TTTATAATTT
6744099 TTTTTGAATTTTTTATG
1 TTTTTGAATTTTTTATG
6744116 TTTTT-AATATTTTTAT
1 TTTTTGAAT-TTTTTAT
6744132 TTATTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTTGAATTTTTTATG
Found at i:6744581 original size:21 final size:22
Alignment explanation
Indices: 6744557--6744603 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
6744547 TTAAGTCTCA
*
6744557 AAATTATTATTT-TAATTTTTT
1 AAATTATTATTTAGAATTTTTT
*
6744578 AAA-TATTCTTTAGAATTTTTT
1 AAATTATTATTTAGAATTTTTT
*
6744599 TAATT
1 AAATT
6744604 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
AAATTATTATTTAGAATTTTTT
Found at i:6744649 original size:28 final size:28
Alignment explanation
Indices: 6744566--6744645 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 28
6744556 AAAATTATTA
* * * *
6744566 TTTTAATTTTTTAAATATTCTTTAGAATTT
1 TTTTAATTTTTAAAAAAAT-TTTA-AATAT
*
6744596 TTTTAATTTTTTAAAAAAATTATAAATAT
1 TTTTAA-TTTTTAAAAAAATTTTAAATAT
*
6744625 TTTTAA-TTTTAAAAGAATTTT
1 TTTTAATTTTTAAAAAAATTTT
6744646 TAAAAATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 13 0.31
29 10 0.24
30 9 0.21
31 10 0.24
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTTAATTTTTAAAAAAATTTTAAATAT
Found at i:6747071 original size:18 final size:19
Alignment explanation
Indices: 6747027--6747071 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
6747017 AATTTATCTA
6747027 AAAT-TTTAAAAATATAAT
1 AAATATTTAAAAATATAAT
6747045 AAATA-TTAAAAATA-AA-
1 AAATATTTAAAAATATAAT
6747061 AAATAGTTTAA
1 AAATA-TTTAA
6747072 TTTTAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.21
17 2 0.08
18 17 0.71
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATATTTAAAAATATAAT
Found at i:6747210 original size:18 final size:17
Alignment explanation
Indices: 6747168--6747219 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
6747158 TCTATTTTTG
*
6747168 AAAATTATAAAA-ATTCA
1 AAAATT-TAAAATTTTCA
6747185 AAAGATTTAAAATTTTCA
1 AAA-ATTTAAAATTTTCA
6747203 TAAAATTTTAAAATTTT
1 -AAAA-TTTAAAATTTT
6747220 GTTTTATGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.27
18 8 0.27
19 14 0.47
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATTTAAAATTTTCA
Found at i:6747415 original size:42 final size:42
Alignment explanation
Indices: 6747368--6747449 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
6747358 TTTTTTTATG
6747368 AAATTATGAAATTTTCAAAAACATTTAATTATAAACAAACTC
1 AAATTATGAAATTTTCAAAAACATTTAATTATAAACAAACTC
* * *
6747410 AAATTATGAAATTTTCAGAAACCTTTAATTCTAAACAAAC
1 AAATTATGAAATTTTCAAAAACATTTAATTATAAACAAAC
6747450 GCATTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (42 bp):
AAATTATGAAATTTTCAAAAACATTTAATTATAAACAAACTC
Found at i:6747464 original size:42 final size:42
Alignment explanation
Indices: 6747368--6747466 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 42
6747358 TTTTTTTATG
* *
6747368 AAATTATGAAATTTTCAAAAACATTTAATTATAAACAAACTC
1 AAATTATAAAATTTTCAAAAACATTTAATTATAAACAAACGC
* * * *
6747410 AAATTATGAAATTTTCAGAAACCTTTAATTCTAAACAAACGC
1 AAATTATAAAATTTTCAAAAACATTTAATTATAAACAAACGC
** *
6747452 ATTTTTTAAAATTTT
1 AAATTATAAAATTTT
6747467 TTTAAATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.37
Consensus pattern (42 bp):
AAATTATAAAATTTTCAAAAACATTTAATTATAAACAAACGC
Found at i:6747534 original size:21 final size:22
Alignment explanation
Indices: 6747484--6747537 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
6747474 TTTGCGAACT
**
6747484 TATTGTTTTTAAAAATATTTTGA
1 TATT-TTTTTAAAAATAAATTGA
*
6747507 TA-ATTTTTAAAAATAAATT-A
1 TATTTTTTTAAAAATAAATTGA
6747527 TATTTTTTTAA
1 TATTTTTTTAA
6747538 TATGTGATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
23 2 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTTTTTTAAAAATAAATTGA
Found at i:6750595 original size:4 final size:4
Alignment explanation
Indices: 6750586--6750627 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
6750576 CCCTGTACCT
6750586 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
6750628 ATATTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:6755835 original size:41 final size:42
Alignment explanation
Indices: 6755783--6755863 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 42
6755773 CCCCCCCCTT
6755783 TTTTTAAGGAAAATAAATCATTAATTTTTG-GAATTGAAATTC
1 TTTTTAAGGAAAATAAATCATTAA-TTTTGAGAATTGAAATTC
6755825 TTTTT-AGGAAAATAAATCATTAATTTTGAGAATTGAAAT
1 TTTTTAAGGAAAATAAATCATTAATTTTGAGAATTGAAAT
6755864 AATAGTGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
40 5 0.13
41 28 0.74
42 5 0.13
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTTTAAGGAAAATAAATCATTAATTTTGAGAATTGAAATTC
Found at i:6763215 original size:14 final size:14
Alignment explanation
Indices: 6763196--6763225 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6763186 ACTTATTACA
6763196 AAAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
6763210 AAAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
6763224 AA
1 AA
6763226 GCCATTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (14 bp):
AAAGAGAGAGAGAG
Found at i:6767572 original size:27 final size:27
Alignment explanation
Indices: 6767522--6767573 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
6767512 TATTTTTGGG
**
6767522 TGGTGCCTACCTAGTAAGCAGCACCAA
1 TGGTGCCTACCTACCAAGCAGCACCAA
* *
6767549 TGGTGCCTACCTACCAGGCGGCACC
1 TGGTGCCTACCTACCAAGCAGCACC
6767574 TGCATGCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (27 bp):
TGGTGCCTACCTACCAAGCAGCACCAA
Found at i:6767894 original size:17 final size:17
Alignment explanation
Indices: 6767874--6767907 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6767864 AAAAAAATTT
*
6767874 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
6767891 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
6767908 TTATGTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:6770233 original size:12 final size:12
Alignment explanation
Indices: 6770216--6770254 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
6770206 ACTTTCAGTC
6770216 GCCTGAGCTTGA
1 GCCTGAGCTTGA
*
6770228 GCCTGAGC-CGCA
1 GCCTGAGCTTG-A
6770240 GCCTGAGCTTGA
1 GCCTGAGCTTGA
6770252 GCC
1 GCC
6770255 GCAGCACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.18
Consensus pattern (12 bp):
GCCTGAGCTTGA
Found at i:6770252 original size:18 final size:18
Alignment explanation
Indices: 6770225--6770259 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6770215 CGCCTGAGCT
6770225 TGAGCCTGAGCCGCAGCC
1 TGAGCCTGAGCCGCAGCC
*
6770243 TGAGCTTGAGCCGCAGC
1 TGAGCCTGAGCCGCAGC
6770260 ACTATTCGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.14
Consensus pattern (18 bp):
TGAGCCTGAGCCGCAGCC
Found at i:6770855 original size:26 final size:26
Alignment explanation
Indices: 6770800--6770875 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
6770790 GCTAAACCTT
**
6770800 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
6770826 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
6770852 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
6770876 CTTCATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:6773677 original size:26 final size:26
Alignment explanation
Indices: 6773648--6773708 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
6773638 TTCTACTAAC
* * *
6773648 CTTTTGTTTCCTTTTCTTCTTCAAAA
1 CTTTTGCTTCATTTCCTTCTTCAAAA
6773674 CTTTTGCTTCATTTCCTTCTTCAAAA
1 CTTTTGCTTCATTTCCTTCTTCAAAA
*
6773700 -ATTTGCTTC
1 CTTTTGCTTC
6773709 TCTTCTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.54
Consensus pattern (26 bp):
CTTTTGCTTCATTTCCTTCTTCAAAA
Found at i:6774793 original size:11 final size:11
Alignment explanation
Indices: 6774762--6774803 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
6774752 GAAGAGAATG
6774762 TATTATTTTAA
1 TATTATTTTAA
6774773 TA-TA---TAA
1 TATTATTTTAA
6774780 TATTATTTTAA
1 TATTATTTTAA
6774791 TATTATTTTAA
1 TATTATTTTAA
6774802 TA
1 TA
6774804 AAAAACCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
7 5 0.19
8 2 0.07
10 2 0.07
11 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:6776590 original size:27 final size:27
Alignment explanation
Indices: 6776561--6776613 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
6776551 TATAAAATTT
6776561 TTTTAATGTAT-TTTTAAT-TTATTTAA
1 TTTTAATGTATGTTTTAATGTT-TTTAA
*
6776587 TTTTAATGTTTGTTTTAATGTTTTTAA
1 TTTTAATGTATGTTTTAATGTTTTTAA
6776614 ATATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 12 0.50
28 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (27 bp):
TTTTAATGTATGTTTTAATGTTTTTAA
Found at i:6776668 original size:28 final size:28
Alignment explanation
Indices: 6776609--6776670 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
6776599 TTTTAATGTT
* * *
6776609 TTTAAATATATTTATATATTATATATAT
1 TTTAAATATATTTATATAATATAAATAG
*
6776637 TTTAAATTTATTGTATATAATA-AAATAG
1 TTTAAATATATT-TATATAATATAAATAG
6776665 TTTAAA
1 TTTAAA
6776671 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TTTAAATATATTTATATAATATAAATAG
Found at i:6781418 original size:90 final size:89
Alignment explanation
Indices: 6781266--6781444 Score: 340
Period size: 90 Copynumber: 2.0 Consensus size: 89
6781256 GCCCGTCTTT
*
6781266 TCATAGCTTTAAGTTCTTATACAAATTTTTATTTATTACAAGTAAATCAATAAATTGAATAAAAA
1 TCATAGCTTTAAGTTCTTACACAAATTTTTATTTATTACAAGTAAATCAATAAATTGAATAAAAA
6781331 CAAAAACACCAACCCAATATAATG
66 CAAAAACACCAACCCAATATAATG
6781355 TCATAGCTTTAAGTTCTTACACAAATTTTTTATTTATTACAAGTAAATCAATAAATTGAATAAAA
1 TCATAGCTTTAAGTTCTTACACAAA-TTTTTATTTATTACAAGTAAATCAATAAATTGAATAAAA
6781420 ACAAAAACACCAACCCAATATAATG
65 ACAAAAACACCAACCCAATATAATG
6781445 CTTTAATAAC
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
89 24 0.27
90 64 0.73
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (89 bp):
TCATAGCTTTAAGTTCTTACACAAATTTTTATTTATTACAAGTAAATCAATAAATTGAATAAAAA
CAAAAACACCAACCCAATATAATG
Found at i:6791093 original size:30 final size:30
Alignment explanation
Indices: 6791059--6791116 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
6791049 ATTATAATAA
*
6791059 AAAAT-ATATAAATTTATTAAATATTAAATG
1 AAAATAATATAAATTTAATAAA-ATTAAATG
*
6791089 AAAATAATATAATTTTAATAAAATTAAA
1 AAAATAATATAAATTTAATAAAATTAAA
6791117 AATTAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATAATATAAATTTAATAAAATTAAATG
Found at i:6794466 original size:62 final size:60
Alignment explanation
Indices: 6794313--6794537 Score: 253
Period size: 61 Copynumber: 3.8 Consensus size: 60
6794303 AGTCATTGTC
* * * *
6794313 AAAAAAATAC-AATTTTTTGATGTTGGCCATCAAATGGCCGACACCCT-ATTTTCT-TGA
1 AAAAAAATTCAAATTTTTTGATGTTGACCATCAAATGGCCGACACCCTCCTTTTCTAAGA
* * *
6794370 AAAAAAATT-ACATTTTTGGGTGTTGACCATCAAATGGCCGACACCCTCCTTTTCTCAAGA
1 AAAAAAATTCAAATTTTTTGATGTTGACCATCAAATGGCCGACACCCTCCTTTTCT-AAGA
* * *
6794430 AAAAAAATTCAAATTTTTTTCATGTTGACCATCAAATGGCCGACA-CCTCCTTTTTTGAATA
1 AAAAAAATTCAAA-TTTTTTGATGTTGACCATCAAATGGCCGACACCCTCCTTTTCT-AAGA
* * * *
6794491 AAAAAATTTCAAATTTTTTTGGTGTTGGCCATCTAATGGCCGACACC
1 AAAAAAATTCAAA-TTTTTTGATGTTGACCATCAAATGGCCGACACC
6794538 AACTTCTTTT
Statistics
Matches: 142, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
57 41 0.29
58 6 0.04
60 11 0.08
61 55 0.39
62 29 0.20
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (60 bp):
AAAAAAATTCAAATTTTTTGATGTTGACCATCAAATGGCCGACACCCTCCTTTTCTAAGA
Found at i:6795981 original size:3 final size:3
Alignment explanation
Indices: 6795973--6796005 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
6795963 AAAGTGTTAT
6795973 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6796006 AATAATAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6798462 original size:10 final size:10
Alignment explanation
Indices: 6798439--6798523 Score: 70
Period size: 10 Copynumber: 8.7 Consensus size: 10
6798429 GATCATACCC
6798439 AAAAAA-TAT
1 AAAAAATTAT
*
6798448 TAAAAATTAT
1 AAAAAATTAT
6798458 AAAAAA-TATT
1 AAAAAATTA-T
*
6798468 TAAAAA-TAT
1 AAAAAATTAT
*
6798477 ATAAAATTAT
1 AAAAAATTAT
6798487 AAAATAA-TAT
1 AAAA-AATTAT
*
6798497 ATAAAATTAT
1 AAAAAATTAT
**
6798507 AAAAAATCGT
1 AAAAAATTAT
6798517 AAAAAAT
1 AAAAAAT
6798524 AAAAAATATA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
9 14 0.23
10 45 0.74
11 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:6798463 original size:19 final size:21
Alignment explanation
Indices: 6798439--6798482 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
6798429 GATCATACCC
6798439 AAAAAATA-TTAAAAAT-TAT
1 AAAAAATATTTAAAAATATAT
6798458 AAAAAATATTTAAAAATATAT
1 AAAAAATATTTAAAAATATAT
6798479 AAAA
1 AAAA
6798483 TTATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.35
20 8 0.35
21 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAAATATTTAAAAATATAT
Found at i:6798489 original size:8 final size:9
Alignment explanation
Indices: 6798441--6798533 Score: 55
Period size: 10 Copynumber: 9.9 Consensus size: 9
6798431 TCATACCCAA
6798441 AAAATAT-T
1 AAAATATAT
*
6798449 AAAAATTATAA
1 -AAAA-TATAT
*
6798460 AAAATATTT
1 AAAATATAT
6798469 AAAAATATAT
1 -AAAATATAT
*
6798479 AAAATTATAA
1 AAAA-TATAT
6798489 AATAATATAT
1 AA-AATATAT
6798499 AAAAT-TAT
1 AAAATATAT
* *
6798507 AAAAAATCGT
1 AAAATAT-AT
* *
6798517 AAAAAATAA
1 AAAATATAT
6798526 AAAATATA
1 AAAATATA
6798534 AACTACACTA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 7 0.11
9 22 0.33
10 35 0.53
11 2 0.03
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAATATAT
Found at i:6798495 original size:20 final size:20
Alignment explanation
Indices: 6798472--6798510 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
6798462 AATATTTAAA
6798472 AATATATAAAATTATAAAAT
1 AATATATAAAATTATAAAAT
6798492 AATATATAAAATTATAAAA
1 AATATATAAAATTATAAAA
6798511 AATCGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATATAAAATTATAAAAT
Found at i:6803437 original size:2 final size:2
Alignment explanation
Indices: 6803430--6803456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6803420 TTTAAAAGAA
6803430 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6803457 ATGTTTAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6818239 original size:16 final size:16
Alignment explanation
Indices: 6818218--6818252 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
6818208 TTAGCTTTAC
6818218 TGATGTGGCATACACG
1 TGATGTGGCATACACG
6818234 TGATGTGGCATACACG
1 TGATGTGGCATACACG
6818250 TGA
1 TGA
6818253 AAATGCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (16 bp):
TGATGTGGCATACACG
Found at i:6819044 original size:30 final size:31
Alignment explanation
Indices: 6818970--6819046 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
6818960 AATTAATAAG
* * *
6818970 TATAAAATTATATTTTGATCTTTTTAAAAAT
1 TATAAAAATATAATTTAATCTTTTTAAAAAT
* *
6819001 AAT-AAAATTTAATTTAAT-TTTTTAAAAAT
1 TATAAAAATATAATTTAATCTTTTTAAAAAT
6819030 TATAAAAATATAATTTA
1 TATAAAAATATAATTTA
6819047 TTTAAATGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 13 0.34
30 23 0.61
31 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
TATAAAAATATAATTTAATCTTTTTAAAAAT
Found at i:6820795 original size:61 final size:60
Alignment explanation
Indices: 6820665--6820852 Score: 207
Period size: 60 Copynumber: 3.1 Consensus size: 60
6820655 TTAATCTAAT
* * * * *
6820665 ATTTGGTACTTGAACTTGATGTTTTTTTCCTAATTTGGTACCTAAACTTTTTTTG-ACTCA
1 ATTTCGTACCTGAACTTGATATTTTTTT-CTAATTTGGCACCTAAACTTTTTTTGAATTCA
*
6820725 ATTTTGTACCTGAACTTGATATTTTTTTCTAATTTGGCACCTAAACATTTTTTTGAATTCA
1 ATTTCGTACCTGAACTTGATATTTTTTTCTAATTTGGCACCTAAAC-TTTTTTTGAATTCA
* ** ** * *
6820786 ATTTCGTACCTAAACTTGGCATTTTTCCCCTAATTTGGCACCTAAGCTTTTTATTTAGATTCA
1 ATTTCGTACCTGAACTTGATATTTTT-TTCTAATTTGGCACCTAAACTTTTT-TTGA-ATTCA
6820849 ATTT
1 ATTT
6820853 GATACCTAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
59 17 0.15
60 33 0.30
61 31 0.28
62 20 0.18
63 9 0.08
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (60 bp):
ATTTCGTACCTGAACTTGATATTTTTTTCTAATTTGGCACCTAAACTTTTTTTGAATTCA
Found at i:6820797 original size:30 final size:28
Alignment explanation
Indices: 6820696--6820802 Score: 99
Period size: 31 Copynumber: 3.6 Consensus size: 28
6820686 TTTTTTTCCT
*
6820696 AATTTGGTACCTAAACTTTTTTTGACTC
1 AATTTGGTACCTAAACTTTTTTTGATTC
* * *
6820724 AATTTTGTACCTGAACTTGATATTTT-TTTC
1 AATTTGGTACCTAAACTT--T-TTTTGATTC
*
6820754 TAATTTGGCACCTAAACATTTTTTTGAATTC
1 -AATTTGGTACCTAAAC-TTTTTTTG-ATTC
*
6820785 AATTTCGTACCTAAACTT
1 AATTTGGTACCTAAACTT
6820803 GGCATTTTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
28 16 0.26
29 6 0.10
30 18 0.29
31 20 0.32
32 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTTGATTC
Found at i:6821128 original size:31 final size:31
Alignment explanation
Indices: 6821062--6821202 Score: 126
Period size: 31 Copynumber: 4.6 Consensus size: 31
6821052 TGGATCCCAA
* * *
6821062 AAAGTTTACGTACCAACTTTAATAAAAAATGT
1 AAAGTTTAAGTACCAA-ATTAAGAAAAAATGT
* *
6821094 CAAGTTTAAGTACCAAATTAAGAAAATATGT
1 AAAGTTTAAGTACCAAATTAAGAAAAAATGT
* * * *
6821125 CAAGTTTGAGTATCAAATT-GGACAAAAA-G-
1 AAAGTTTAAGTACCAAATTAAGA-AAAAATGT
* *
6821154 AAAGTTTAGGTACCAAATTAAGAAAAAATAT
1 AAAGTTTAAGTACCAAATTAAGAAAAAATGT
* *
6821185 AAAGTTCAAATACCAAAT
1 AAAGTTTAAGTACCAAAT
6821203 GTTATATTAA
Statistics
Matches: 87, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
29 20 0.23
30 5 0.06
31 48 0.55
32 14 0.16
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.27
Consensus pattern (31 bp):
AAAGTTTAAGTACCAAATTAAGAAAAAATGT
Found at i:6821180 original size:91 final size:91
Alignment explanation
Indices: 6821012--6821202 Score: 217
Period size: 91 Copynumber: 2.1 Consensus size: 91
6821002 AAAATACTAG
**
6821012 ATACCAAATTAAGAAAAAGAGTCAAGTTCAAATATCAAATTGGATCCCAAAAAGTTTACGTACCA
1 ATACCAAATTAAGAAAAAGAGTCAAGTTCAAATATCAAATTGGATCAAAAAAAGTTTACGTACCA
* * * * *
6821077 ACTTTAATAAAAAATGTCAAGTTTAA
66 ACATTAAGAAAAAATATAAAGTTCAA
* * ** * *
6821103 GTACCAAATTAAGAAAATA-TGTCAAGTTTGAGTATCAAATTGGA-CAAAAAGAAAGTTTAGGTA
1 ATACCAAATTAAGAAAA-AGAGTCAAGTTCAAATATCAAATTGGATC-AAAA-AAAGTTTACGTA
6821166 CCAA-ATTAAGAAAAAATATAAAGTTCAA
63 CCAACATTAAGAAAAAATATAAAGTTCAA
6821194 ATACCAAAT
1 ATACCAAAT
6821203 GTTATATTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
90 1 0.01
91 66 0.80
92 16 0.19
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.26
Consensus pattern (91 bp):
ATACCAAATTAAGAAAAAGAGTCAAGTTCAAATATCAAATTGGATCAAAAAAAGTTTACGTACCA
ACATTAAGAAAAAATATAAAGTTCAA
Found at i:6834258 original size:23 final size:24
Alignment explanation
Indices: 6834232--6834278 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
6834222 AAAAAAATTA
6834232 AAATTCTAAATTTTTT-TAAATAT
1 AAATTCTAAATTTTTTATAAATAT
* *
6834255 AAATTTTGAATTTTTTATAAATAT
1 AAATTCTAAATTTTTTATAAATAT
6834279 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AAATTCTAAATTTTTTATAAATAT
Found at i:6834300 original size:28 final size:29
Alignment explanation
Indices: 6834263--6834317 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
6834253 ATAAATTTTG
*
6834263 AATTTTTTATAAATATTTT-TAATTTTAA
1 AATTTATTATAAATATTTTGTAATTTTAA
* *
6834291 AATTTATTATGAATTTTTTGTAATTTT
1 AATTTATTATAAATATTTTGTAATTTT
6834318 TGTTGAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
AATTTATTATAAATATTTTGTAATTTTAA
Found at i:6841653 original size:29 final size:30
Alignment explanation
Indices: 6841621--6841687 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
6841611 TTTCAACTTT
* * *
6841621 TTTTTTTTATTAAATTAATCATATATGT-A
1 TTTTTTTTATTAAATTAACCAAATAGGTCA
* *
6841650 TTTTTTTTCTTTAATTAACCAAATAGGTCA
1 TTTTTTTTATTAAATTAACCAAATAGGTCA
6841680 TTTTTTTT
1 TTTTTTTT
6841688 TTAGATTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTTTTTTATTAAATTAACCAAATAGGTCA
Found at i:6844554 original size:22 final size:24
Alignment explanation
Indices: 6844527--6844572 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6844517 TTTTAATTGA
6844527 TTCAA-TCGATTC-AAGAACATTT
1 TTCAATTCGATTCAAAGAACATTT
* *
6844549 TTCAATTTGATTCAAATAACATTT
1 TTCAATTCGATTCAAAGAACATTT
6844573 CCTCCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (24 bp):
TTCAATTCGATTCAAAGAACATTT
Found at i:6846105 original size:2 final size:2
Alignment explanation
Indices: 6846098--6846138 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
6846088 CGTTCTTTCG
* * *
6846098 TC TC TC TC TC TG TC TC TC TC TC TG TC TC TC TC TC AC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6846139 AGTTAGTCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.02, C:0.44, G:0.05, T:0.49
Consensus pattern (2 bp):
TC
Found at i:6846138 original size:12 final size:12
Alignment explanation
Indices: 6846097--6846131 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
6846087 TCGTTCTTTC
6846097 GTCTCTCTCTCT
1 GTCTCTCTCTCT
6846109 GTCTCTCTCTCT
1 GTCTCTCTCTCT
6846121 GTCTCTCTCTC
1 GTCTCTCTCTC
6846132 ACTCTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.09, T:0.49
Consensus pattern (12 bp):
GTCTCTCTCTCT
Found at i:6847680 original size:4 final size:4
Alignment explanation
Indices: 6847671--6847699 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6847661 TTTGATGTAA
6847671 GAAT GAAT GAAT GAAT GAAT GAAT GAAT G
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT G
6847700 TGGGATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (4 bp):
GAAT
Found at i:6853615 original size:2 final size:2
Alignment explanation
Indices: 6853608--6853634 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6853598 ATTAATAATT
6853608 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
6853635 TAATAAAAAT
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:6858016 original size:5 final size:5
Alignment explanation
Indices: 6858008--6858045 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
6857998 AAAAAAAAAA
6858008 GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG GTG
1 GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG GTG
6858046 AGCAGGAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.79, T:0.21
Consensus pattern (5 bp):
GTGGG
Found at i:6860444 original size:18 final size:18
Alignment explanation
Indices: 6860414--6860470 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
6860404 TTTATTTTTT
6860414 ATATAAAA-A-TAAAAAA
1 ATATAAAATATTAAAAAA
*
6860430 ATATAATATATTAAAAACA
1 ATATAAAATATTAAAAA-A
*
6860449 CTA-AAAATATTAAAATAA
1 ATATAAAATATTAAAA-AA
6860467 ATAT
1 ATAT
6860471 TTACTTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 7 0.22
17 1 0.03
18 20 0.62
19 4 0.12
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
ATATAAAATATTAAAAAA
Found at i:6860559 original size:3 final size:3
Alignment explanation
Indices: 6860551--6860598 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
6860541 ATACCTTTAA
* *
6860551 AAT AAT AAT AAT AAT AAT AAT ATT CA- AAT AAT AACT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T A-AT AAT AAT
6860597 AA
1 AA
6860599 AATGTTGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 32 0.84
4 4 0.11
5 1 0.03
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6861203 original size:22 final size:22
Alignment explanation
Indices: 6861131--6861204 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
6861121 AATTTAATCC
*
6861131 TTTAAATATTATAAAAATATAAAC
1 TTTAAA-ATTATAAAAAT-TAAAA
**
6861155 TATTAAAATTAT-AAAATTACATT
1 T-TTAAAATTATAAAAATTA-AAA
**
6861178 TTTACCATTATAAAAATTAAAA
1 TTTAAAATTATAAAAATTAAAA
6861200 TTTAA
1 TTTAA
6861205 TTTCCACTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 15 0.38
23 14 0.35
24 6 0.15
25 5 0.12
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATTATAAAAATTAAAA
Found at i:6862629 original size:31 final size:32
Alignment explanation
Indices: 6862589--6862655 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
6862579 AAAATTTCAG
* * **
6862589 AATTTGAAAAGTGCAGGGACTAAAATTGA-CA
1 AATTCGAAAAGTACAGAAACTAAAATTGATCA
*
6862620 AATTCGAAAAGTATAGAAACTAAAATTGATCA
1 AATTCGAAAAGTACAGAAACTAAAATTGATCA
6862652 AATT
1 AATT
6862656 AAAGTATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (32 bp):
AATTCGAAAAGTACAGAAACTAAAATTGATCA
Found at i:6862670 original size:29 final size:29
Alignment explanation
Indices: 6862606--6862672 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 29
6862596 AAAGTGCAGG
6862606 GACTAAAATTGACAAATTCGAAAAGTATAGA
1 GACTAAAATTGACAAATT--AAAAGTATAGA
*
6862637 AACTAAAATTGATCAAATT-AAAGTATAGA
1 GACTAAAATTGA-CAAATTAAAAGTATAGA
6862666 GACTAAA
1 GACTAAA
6862673 TCTACAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 16 0.48
31 11 0.33
32 6 0.18
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (29 bp):
GACTAAAATTGACAAATTAAAAGTATAGA
Found at i:6868624 original size:22 final size:22
Alignment explanation
Indices: 6868575--6868616 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6868565 TTTTGTTTCA
*
6868575 AATGTTTTAAATGTTAGGCTCC
1 AATGTTTTAAATGTTAGGATCC
6868597 AATGTTTTAAATGTTAGGAT
1 AATGTTTTAAATGTTAGGAT
6868617 GGGATGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (22 bp):
AATGTTTTAAATGTTAGGATCC
Found at i:6881599 original size:9 final size:9
Alignment explanation
Indices: 6881587--6881611 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6881577 CTTACATTTC
6881587 TTATTTTAG
1 TTATTTTAG
6881596 TTATTTTAG
1 TTATTTTAG
6881605 TTATTTT
1 TTATTTT
6881612 TCTAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (9 bp):
TTATTTTAG
Found at i:6889603 original size:27 final size:27
Alignment explanation
Indices: 6889565--6889627 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
6889555 GTATAAATGG
6889565 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
6889592 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
6889619 ATGGTGCCT
1 GTGGTGCCT
6889628 TTCTATCAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:6889636 original size:27 final size:27
Alignment explanation
Indices: 6889566--6889646 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
6889556 TATAAATGGG
*
6889566 TGGTGCCTACCTGA-CAGGCGGCACCAG
1 TGGTGCCTACCT-ATCAGGCGGCACCAA
*
6889593 TGGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
** *
6889620 TGGTGCCTTTCTATCAGGTGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
6889647 CTCGTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.21
Consensus pattern (27 bp):
TGGTGCCTACCTATCAGGCGGCACCAA
Found at i:6889790 original size:20 final size:23
Alignment explanation
Indices: 6889753--6889793 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
6889743 TTTTAATAAA
6889753 TATAAGAATTGTAGAAAAAATAT
1 TATAAGAATTGTAGAAAAAATAT
6889776 TATAA-AATT-TA-AAAAAAT
1 TATAAGAATTGTAGAAAAAAT
6889794 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TATAAGAATTGTAGAAAAAATAT
Found at i:6889912 original size:57 final size:55
Alignment explanation
Indices: 6889798--6889928 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 55
6889788 AAAAATTAAA
* *
6889798 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
** *
6889853 TTATTTATCAAAATAATAATAATCTCCAA-ATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CT-CAATATTTTTA-AATAAATAATATAA-AAAATAT
6889910 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
6889929 CACTTTTATA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
55 13 0.20
56 15 0.23
57 27 0.42
58 9 0.14
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
Found at i:6890035 original size:27 final size:27
Alignment explanation
Indices: 6889994--6890054 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
6889984 TTTGACAAGA
6889994 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
**
6890021 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
6890048 GGTGCCT
1 GGTGCCT
6890055 TTGTCAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.21
Consensus pattern (27 bp):
GGTGCCTACCAGGTAGGCGGCACTAGT
Found at i:6890160 original size:26 final size:27
Alignment explanation
Indices: 6890115--6890179 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
6890105 AAGAAAGAAT
* *
6890115 AACAGTAAATTTTTGAAGAAGGAAAGGA
1 AACAG-AAAGTTTTGAAGAAGAAAAGGA
*
6890143 AACA-AAAGTTTTGTAGAAGAAAAGGA
1 AACAGAAAGTTTTGAAGAAGAAAAGGA
*
6890169 AATAGAAAGTT
1 AACAGAAAGTT
6890180 AGCAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 22 0.69
27 6 0.19
28 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (27 bp):
AACAGAAAGTTTTGAAGAAGAAAAGGA
Found at i:6892987 original size:28 final size:28
Alignment explanation
Indices: 6892934--6892991 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
6892924 CATTTTTCTG
*
6892934 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
6892962 TTGGAATTAATTTTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
6892990 TT
1 TT
6892992 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:6893032 original size:26 final size:26
Alignment explanation
Indices: 6892983--6893032 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
6892973 TTTATTTAAA
* **
6892983 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTAATTTAATAAGGTTTATG
*
6893009 TTTGAATTAATTTAATTAGGTTTA
1 TTTGAATTAATTTAATAAGGTTTA
6893033 GCAAATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAAGGTTTATG
Found at i:6893109 original size:6 final size:6
Alignment explanation
Indices: 6893098--6893144 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
6893088 ATATTTGCAT
*
6893098 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATA
6893145 TTTAATGGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:6893586 original size:6 final size:6
Alignment explanation
Indices: 6893577--6893607 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
6893567 CTGCGACTGC
6893577 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
6893608 CCGGCTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:6895478 original size:13 final size:13
Alignment explanation
Indices: 6895462--6895489 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6895452 TAATTTTTCG
6895462 TTTTAAAAAATAT
1 TTTTAAAAAATAT
6895475 TTTTAAAAAATAT
1 TTTTAAAAAATAT
6895488 TT
1 TT
6895490 AATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAAAATAT
Found at i:6895513 original size:17 final size:16
Alignment explanation
Indices: 6895481--6895512 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6895471 ATATTTTTAA
6895481 AAAATATTTAATATAT
1 AAAATATTTAATATAT
6895497 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
6895512 A
1 A
6895513 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:6895573 original size:10 final size:10
Alignment explanation
Indices: 6895558--6895590 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
6895548 CTCTTTTTTT
6895558 CTTTCTTGTG
1 CTTTCTTGTG
6895568 CTTTCTTGTG
1 CTTTCTTGTG
6895578 CTTTCTTGTG
1 CTTTCTTGTG
6895588 CTT
1 CTT
6895591 GCCATGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.21, G:0.18, T:0.61
Consensus pattern (10 bp):
CTTTCTTGTG
Found at i:6909604 original size:39 final size:39
Alignment explanation
Indices: 6909529--6909604 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
6909519 TGGAATAAAT
* *
6909529 TATATTATTTACCCACATGAATTAACATGAGCATAAACC
1 TATATTATTTAACCACATGAATTAACACGAGCATAAACC
** * *
6909568 TATATTATTTAATGACATGAATTAATACGAGTATAAA
1 TATATTATTTAACCACATGAATTAACACGAGCATAAA
6909605 TAACGTCCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (39 bp):
TATATTATTTAACCACATGAATTAACACGAGCATAAACC
Found at i:6922694 original size:15 final size:16
Alignment explanation
Indices: 6922648--6922694 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
6922638 TTTTTGGATA
6922648 AAAAATACTTTTTAAAT
1 AAAAATA-TTTTTAAAT
**
6922665 AAAAATATTACTAAAT
1 AAAAATATTTTTAAAT
*
6922681 -AAGATATTTTTAAA
1 AAAAATATTTTTAAA
6922695 CTTTTCAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 11 0.44
16 7 0.28
17 7 0.28
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAAATATTTTTAAAT
Found at i:6927694 original size:26 final size:26
Alignment explanation
Indices: 6927665--6927717 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
6927655 ATAAATATTA
6927665 TTTTTTTA-T-TAAAATAATACGACT
1 TTTTTTTACTATAAAATAATACGACT
*
6927689 TTTTTTTACTATATAATAATACGACT
1 TTTTTTTACTATAAAATAATACGACT
6927715 TTT
1 TTT
6927718 AAGAGTGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 8 0.31
25 1 0.04
26 17 0.65
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTTTTACTATAAAATAATACGACT
Found at i:6928476 original size:32 final size:31
Alignment explanation
Indices: 6928409--6928498 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
6928399 ATATCTAGTT
* *
6928409 TTTTTTTTTAAGTTGATACTTAAACTCGACA
1 TTTTTTTTTAAGTTGGTACTTAAACTTGACA
* * *
6928440 TTTTTTCTTAATTTGGTACATAAACTTGACA
1 TTTTTTTTTAAGTTGGTACTTAAACTTGACA
6928471 CTTTTTTTTTAAGTTGGTACTTAAACTT
1 -TTTTTTTTTAAGTTGGTACTTAAACTT
6928499 TTTGGGATCC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 26 0.52
32 24 0.48
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (31 bp):
TTTTTTTTTAAGTTGGTACTTAAACTTGACA
Found at i:6928829 original size:13 final size:12
Alignment explanation
Indices: 6928811--6928860 Score: 64
Period size: 13 Copynumber: 4.0 Consensus size: 12
6928801 AAGAAAAAGT
6928811 TATCAAATTCAAA
1 TATCAAATT-AAA
6928824 TATCAAATTAAA
1 TATCAAATTAAA
**
6928836 TAAAAAATTTAAA
1 TATCAAA-TTAAA
6928849 TATCAAATTAAA
1 TATCAAATTAAA
6928861 AAAAATATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 13 0.41
13 19 0.59
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
TATCAAATTAAA
Found at i:6928843 original size:25 final size:24
Alignment explanation
Indices: 6928815--6928865 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
6928805 AAAAGTTATC
6928815 AAATTCAAATATCAAATTAAATAAA
1 AAATTCAAATATCAAATTAAA-AAA
*
6928840 AAATTTAAATATCAAATTAAAAAA
1 AAATTCAAATATCAAATTAAAAAA
6928864 AA
1 AA
6928866 TATCAAGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATTCAAATATCAAATTAAAAAA
Found at i:6930765 original size:2 final size:2
Alignment explanation
Indices: 6930760--6930790 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6930750 CACTTAAATA
6930760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6930791 CACGCACAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6932198 original size:9 final size:9
Alignment explanation
Indices: 6932158--6932198 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
6932148 TTTTAGAAAA
6932158 TTTTT-AAT
1 TTTTTAAAT
*
6932166 TTTTTAATT
1 TTTTTAAAT
6932175 TTTTTAGAA-
1 TTTTTA-AAT
6932184 TTTTTAAAT
1 TTTTTAAAT
6932193 TTTTTA
1 TTTTTA
6932199 TATTAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 20 0.71
10 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:6933272 original size:13 final size:13
Alignment explanation
Indices: 6933254--6933282 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6933244 CATTTCCATT
6933254 AAATGATTAACAA
1 AAATGATTAACAA
6933267 AAATGATTAACAA
1 AAATGATTAACAA
6933280 AAA
1 AAA
6933283 AATTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATGATTAACAA
Found at i:6934106 original size:31 final size:30
Alignment explanation
Indices: 6934071--6934153 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
6934061 TCATCATGGC
*
6934071 AGTGACTGTTTTGTCACATTTCGATCACGTT
1 AGTGACTGTTTTGTCA-ATTTCGATAACGTT
*
6934102 AGTGACTGTTTTGTCAATTTTCGATAATGTT
1 AGTGACTGTTTTGTCAA-TTTCGATAACGTT
* *
6934133 AGTGACTATTTTATCATATTT
1 AGTGACTGTTTTGTCA-ATTT
6934154 TTAAAGTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (30 bp):
AGTGACTGTTTTGTCAATTTCGATAACGTT
Found at i:6934516 original size:9 final size:9
Alignment explanation
Indices: 6934494--6934602 Score: 55
Period size: 10 Copynumber: 11.8 Consensus size: 9
6934484 ACAAATATAT
6934494 TAAAAA-TA
1 TAAAAATTA
*
6934502 TTAAAATTA
1 TAAAAATTA
6934511 TAAAAAACTTA
1 T-AAAAA-TTA
*
6934522 TAAATATTA
1 TAAAAATTA
6934531 TAAAAA-TA
1 TAAAAATTA
*
6934539 CAAAAGAATTA
1 -TAAA-AATTA
*
6934550 TACTAAATTA
1 TA-AAAATTA
6934560 TAAAAA--A
1 TAAAAATTA
*
6934567 TATAAATTAA
1 TAAAAATT-A
*
6934577 TAAAACTTA
1 TAAAAATTA
*
6934586 TTTAAAATTA
1 -TAAAAATTA
*
6934596 AAAAAAT
1 TAAAAAT
6934603 GTATTAGAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 21
0.68 0.14 0.19
Matches are distributed among these distances:
7 6 0.08
8 7 0.09
9 23 0.31
10 32 0.43
11 7 0.09
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:6934524 original size:11 final size:10
Alignment explanation
Indices: 6934504--6934572 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
6934494 TAAAAATATT
6934504 AAAATTATAA
1 AAAATTATAA
6934514 AAAACTTAT-A
1 AAAA-TTATAA
*
6934524 AATATTAT-A
1 AAAATTATAA
*
6934533 AAAA-TACAA
1 AAAATTATAA
*
6934542 AAGAATTATAC
1 AA-AATTATAA
*
6934553 TAAATTATAA
1 AAAATTATAA
6934563 AAAA-TATAA
1 AAAATTATAA
6934572 A
1 A
6934573 TTAATAAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 2 0.04
9 17 0.36
10 20 0.43
11 8 0.17
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:6934607 original size:20 final size:20
Alignment explanation
Indices: 6934570--6934607 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6934560 TAAAAAATAT
*
6934570 AAATTAATAAAACTTATTTA
1 AAATTAATAAAAATTATTTA
6934590 AAATTAA-AAAAATGTATT
1 AAATTAATAAAAAT-TATT
6934608 AGAATTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATTAATAAAAATTATTTA
Found at i:6935062 original size:11 final size:9
Alignment explanation
Indices: 6935046--6935263 Score: 57
Period size: 10 Copynumber: 22.6 Consensus size: 9
6935036 CCAGTTCAAG
6935046 TTTTTATGATA
1 TTTTTAT-A-A
6935057 TTTTTATAA
1 TTTTTATAA
6935066 TTTTTATAA
1 TTTTTATAA
* *
6935075 GTATATATCAA
1 -TTTTTAT-AA
** **
6935086 TTTAACATTT
1 TTT-TTATAA
6935096 TTTTTATAA
1 TTTTTATAA
*
6935105 TTTTTTATGA
1 -TTTTTATAA
*
6935115 TTTTTAAAGAA
1 TTTTT--ATAA
*
6935126 TTTTCAT-A
1 TTTTTATAA
6935134 TGTTTTATAAAA
1 T-TTTTAT--AA
* *
6935146 TTTTAATAC
1 TTTTTATAA
*
6935155 GTTTTATTAA
1 TTTTTA-TAA
*
6935165 TTTTATAAAA
1 TTTT-TATAA
6935175 TTTATTATAA
1 TTT-TTATAA
6935185 -TTTTATAA
1 TTTTTATAA
* *
6935193 TTTTTGTTAG
1 TTTTT-ATAA
**
6935203 TTTAAATAAA
1 TTTTTAT-AA
6935213 TTTTTAT-A
1 TTTTTATAA
6935221 TTATTTATAA
1 TT-TTTATAA
* *
6935231 TATTTAATCA
1 T-TTTTATAA
6935241 TTTTTAT-A
1 TTTTTATAA
*
6935249 TTTTTTTACA
1 TTTTTATA-A
6935259 TTTTT
1 TTTTT
6935264 TTTTTTATTT
Statistics
Matches: 150, Mismatches: 36, Indels: 43
0.66 0.16 0.19
Matches are distributed among these distances:
8 18 0.12
9 45 0.30
10 58 0.39
11 27 0.18
12 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:6935197 original size:29 final size:29
Alignment explanation
Indices: 6935136--6935196 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
6935126 TTTTCATATG
*
6935136 TTTTATAAAATTTTAATACGTTTTATTAA
1 TTTTATAAAATTTTAATACATTTTATTAA
*
6935165 TTTTATAAAATTTATTATA-ATTTTA-TAA
1 TTTTATAAAATTT-TAATACATTTTATTAA
6935193 TTTT
1 TTTT
6935197 TGTTAGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.24
29 18 0.62
30 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTATAAAATTTTAATACATTTTATTAA
Found at i:6935254 original size:10 final size:10
Alignment explanation
Indices: 6935241--6935311 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
6935231 TATTTAATCA
6935241 TTTTTATATT
1 TTTTTATATT
*
6935251 TTTTTACATT
1 TTTTTATATT
6935261 TTTTT-T-TT
1 TTTTTATATT
*
6935269 TATTTGATA-T
1 T-TTTTATATT
*
6935279 TTTATA-ATT
1 TTTTTATATT
6935288 TTTTTATGATT
1 TTTTTAT-ATT
**
6935299 TTTAAATATT
1 TTTTTATATT
6935309 TTT
1 TTT
6935312 ATGGAAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 4 0.09
9 12 0.26
10 23 0.49
11 8 0.17
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (10 bp):
TTTTTATATT
Found at i:6935255 original size:38 final size:36
Alignment explanation
Indices: 6935213--6935309 Score: 90
Period size: 38 Copynumber: 2.6 Consensus size: 36
6935203 TTTAAATAAA
6935213 TTTTTATATTATTTATAATATTTAATCATTTT-TATATT
1 TTTTTATATT-TTTATAATATTTAAT-ATTTTATA-ATT
* * ** *
6935251 TTTTTACATTTTTTTTTTTATTTGATATTTTATAATT
1 TTTTTATA-TTTTTATAATATTTAATATTTTATAATT
6935288 TTTTTATGATTTTTA-AATATTT
1 TTTTTAT-ATTTTTATAATATTT
6935310 TTATGGAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
36 5 0.11
37 19 0.40
38 21 0.45
39 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (36 bp):
TTTTTATATTTTTATAATATTTAATATTTTATAATT
Found at i:6935297 original size:21 final size:19
Alignment explanation
Indices: 6935240--6935314 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
6935230 ATATTTAATC
* *
6935240 ATTTTTATATTTTTTTA-C
1 ATTTTTAAATTTTTTTATG
*
6935258 ATTTTT---TTTTTTATTTG
1 ATTTTTAAATTTTTT-TATG
6935275 ATATTTTATAATTTTTTTATG
1 AT-TTTTA-AATTTTTTTATG
*
6935296 ATTTTTAAATATTTTTATG
1 ATTTTTAAATTTTTTTATG
6935315 GAAAAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
15 6 0.13
16 1 0.02
17 2 0.04
18 10 0.22
19 11 0.24
20 5 0.11
21 5 0.11
22 6 0.13
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTAAATTTTTTTATG
Found at i:6942955 original size:33 final size:33
Alignment explanation
Indices: 6942918--6943013 Score: 86
Period size: 33 Copynumber: 3.1 Consensus size: 33
6942908 ATGAAAATAA
6942918 TGGAATTTATAAATCATTTAAATAAAAGTAAAT
1 TGGAATTTATAAATCATTTAAATAAAAGTAAAT
*
6942951 TGGAA---AT--A--ATGTAACTATGAAAA-T-AA-
1 TGGAATTTATAAATCATTTAA--AT-AAAAGTAAAT
6942977 TGGAATTTATAAATCATTTAAATAAAAGTAAAT
1 TGGAATTTATAAATCATTTAAATAAAAGTAAAT
6943010 TGGA
1 TGGA
6943014 TGTTGTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 26
0.63 0.03 0.34
Matches are distributed among these distances:
26 10 0.21
27 2 0.04
28 4 0.08
29 6 0.12
30 6 0.12
31 4 0.08
32 2 0.04
33 14 0.29
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.33
Consensus pattern (33 bp):
TGGAATTTATAAATCATTTAAATAAAAGTAAAT
Found at i:6942967 original size:59 final size:59
Alignment explanation
Indices: 6942895--6943013 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
6942885 CCCAAAACTC
6942895 AAATAATGTAACTATGAAAATAATGGAATTTATAAATCATTTAAATAAAAGTAAATTGG
1 AAATAATGTAACTATGAAAATAATGGAATTTATAAATCATTTAAATAAAAGTAAATTGG
6942954 AAATAATGTAACTATGAAAATAATGGAATTTATAAATCATTTAAATAAAAGTAAATTGG
1 AAATAATGTAACTATGAAAATAATGGAATTTATAAATCATTTAAATAAAAGTAAATTGG
6943013 A
1 A
6943014 TGTTGTTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (59 bp):
AAATAATGTAACTATGAAAATAATGGAATTTATAAATCATTTAAATAAAAGTAAATTGG
Found at i:6946755 original size:14 final size:14
Alignment explanation
Indices: 6946736--6946781 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
6946726 TTTTACTTTG
6946736 TTATCATTCATTCT
1 TTATCATTCATTCT
*
6946750 TTATCATT--TT-G
1 TTATCATTCATTCT
6946761 TTATCATTCATTCT
1 TTATCATTCATTCT
6946775 TTATCAT
1 TTATCAT
6946782 ATTTACATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 2 0.07
14 15 0.56
ACGTcount: A:0.22, C:0.17, G:0.02, T:0.59
Consensus pattern (14 bp):
TTATCATTCATTCT
Found at i:6946762 original size:25 final size:25
Alignment explanation
Indices: 6946732--6946781 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6946722 TTAGTTTTAC
6946732 TTTGTTATCATTCATTCTTTATCAT
1 TTTGTTATCATTCATTCTTTATCAT
6946757 TTTGTTATCATTCATTCTTTATCAT
1 TTTGTTATCATTCATTCTTTATCAT
6946782 ATTTACATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTGTTATCATTCATTCTTTATCAT
Found at i:6952358 original size:27 final size:28
Alignment explanation
Indices: 6952323--6952379 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
6952313 ACTCGAAGTT
6952323 GGGTTTTG-CTTGGTTTTCATTTTATTG
1 GGGTTTTGCCTTGGTTTTCATTTTATTG
**
6952350 GGGTTTTGCTCTTTTTTTTCATTTTATTG
1 GGGTTTTGC-CTTGGTTTTCATTTTATTG
6952379 G
1 G
6952380 TTCTATAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 8 0.31
29 18 0.69
ACGTcount: A:0.07, C:0.09, G:0.23, T:0.61
Consensus pattern (28 bp):
GGGTTTTGCCTTGGTTTTCATTTTATTG
Found at i:6957715 original size:131 final size:133
Alignment explanation
Indices: 6957466--6957730 Score: 335
Period size: 131 Copynumber: 2.0 Consensus size: 133
6957456 ATCAACTTAT
* ** *
6957466 TATTTCCACATAATACTCACTAAAAATCCAATTAATGGATTATTGACTATCATTTGCGTTTATGA
1 TATTTCCACATAATACTCACTAAAAATCCAATTAATGGAATATCAACTATCATTTACGTTTATGA
*
6957531 CTGAATTTAAAGACATAGAATGATCCAATTGAAAAAAATAAACTACATCTACAATTATACACATA
66 C-GAATGTAAAGACATAGAATGATCCAATTGAAAAAAATAAACTACATCTACAATTATACACATA
6957596 ATAC
130 ATAC
* *
6957600 TATTTCCACAT-ATCATTCGCTAAAAATCCAATTAATGGAATA-CAACTATCATTTACG-TTATG
1 TATTTCCACATAAT-ACTCACTAAAAATCCAATTAATGGAATATCAACTATCATTTACGTTTATG
* * * * *
6957662 AC-AA-GTACAAGGATC-TAGAATGATCCAATTGGAAAAAATGAACTATATTTACAATTGTACAC
65 ACGAATGTA-AA-GA-CATAGAATGATCCAATTGAAAAAAATAAACTACATCTACAATTATACAC
6957724 ATAATAC
127 ATAATAC
6957731 AAAAATAATA
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
129 2 0.02
130 4 0.03
131 51 0.44
132 8 0.07
133 14 0.12
134 36 0.31
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (133 bp):
TATTTCCACATAATACTCACTAAAAATCCAATTAATGGAATATCAACTATCATTTACGTTTATGA
CGAATGTAAAGACATAGAATGATCCAATTGAAAAAAATAAACTACATCTACAATTATACACATAA
TAC
Found at i:6960778 original size:27 final size:28
Alignment explanation
Indices: 6960709--6960781 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
6960699 TTTTTAAGAT
*
6960709 TTTTTATACGTTTTATAAAAATTTAACTA
1 TTTTTATATG-TTTATAAAAATTTAACTA
* *
6960738 -TTTTATTAAT-TTTATAAAATTTTTA-TA
1 TTTTTA-T-ATGTTTATAAAAATTTAACTA
6960765 TTTTTATATGTTTATAA
1 TTTTTATATGTTTATAA
6960782 TACTTATAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.05
27 10 0.27
28 23 0.62
29 1 0.03
30 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTTATATGTTTATAAAAATTTAACTA
Found at i:6961504 original size:28 final size:29
Alignment explanation
Indices: 6961473--6961527 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
6961463 ACTAAATTAA
*
6961473 TCTATTTAATAATGAGA-GACTAATTTTT
1 TCTATTTAATAATAAGAGGACTAATTTTT
* *
6961501 TCTATTTGATAATAAGAGGATTAATTT
1 TCTATTTAATAATAAGAGGACTAATTT
6961528 GATCTAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.45
Consensus pattern (29 bp):
TCTATTTAATAATAAGAGGACTAATTTTT
Found at i:6964879 original size:30 final size:31
Alignment explanation
Indices: 6964836--6964910 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
6964826 ATTACATTTA
*
6964836 ACAAAATAGTCACTCAAC-TT-T-GAAAATGTG
1 ACAAAACAGTCACT-AACGTTATCGAAAA-GTG
*
6964866 ACAAAACAATCACTAACGTTATCGAAAAGTG
1 ACAAAACAGTCACTAACGTTATCGAAAAGTG
6964897 ACAAAACAGTCACT
1 ACAAAACAGTCACT
6964911 GATAAATAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.08
30 14 0.36
31 17 0.44
32 5 0.13
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAACGTTATCGAAAAGTG
Found at i:6966528 original size:51 final size:51
Alignment explanation
Indices: 6966444--6966728 Score: 416
Period size: 51 Copynumber: 5.6 Consensus size: 51
6966434 TTTCCTTTAA
** *
6966444 TACTCACGATGACA-TATAGTCATCGGGCCTTTAATCCGTAAAGTATTCATT
1 TACTCACGATGACACT-TAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
*
6966495 TACTCACGATGACACTTAGTCATCGAACTTTTAAT-C-TATAA-GATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTA-AAGGATTCATT
*
6966544 TACTCACGATGACACTTAGTCATCAAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
* *
6966595 TACTCACGATGACACTTAGTCATCGAACTTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
* * *
6966646 TACTCACGATAACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
* *
6966697 TACTCACAATGACACTTAATCATCGAACCTTT
1 TACTCACGATGACACTTAGTCATCGAACCTTT
6966729 TCATTTATAG
Statistics
Matches: 210, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
49 42 0.20
50 6 0.03
51 161 0.77
52 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATCCGTAAAGGATTCATT
Found at i:6966617 original size:100 final size:102
Alignment explanation
Indices: 6966444--6966729 Score: 452
Period size: 100 Copynumber: 2.8 Consensus size: 102
6966434 TTTCCTTTAA
* *
6966444 TACTCACGATGACA-TATAGTCATCGGGCCTTTAATCCGTAAAGTATTCATTTACTCACGATGAC
1 TACTCACGATGACACT-TAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGAC
6966508 ACTTAGTCATCGAACTTTTAATCTAT-AA-GATTCATT
65 ACTTAGTCATCGAACTTTTAATCTATAAAGGATTCATT
**
6966544 TACTCACGATGACACTTAGTCATCAAACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACA
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACA
*
6966609 CTTAGTCATCGAACTTTTAATCTGTAAAGGATTCATT
66 CTTAGTCATCGAACTTTTAATCTATAAAGGATTCATT
* * *
6966646 TACTCACGATAACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATTTACTCACAATGACA
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACA
*
6966711 CTTAATCATCGAACCTTTT
66 CTTAGTCATCGAA-CTTTT
6966730 CATTTATAGC
Statistics
Matches: 171, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
100 83 0.49
101 3 0.02
102 80 0.47
103 5 0.03
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (102 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACA
CTTAGTCATCGAACTTTTAATCTATAAAGGATTCATT
Found at i:6968224 original size:30 final size:31
Alignment explanation
Indices: 6968153--6968227 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
6968143 CCATGATTTC
6968153 AGTGACTGTTTTGTCACTTTTCGATAATGTT
1 AGTGACTGTTTTGTCACTTTTCGATAATGTT
6968184 AGTGACTGTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGTCAC-TTTTCGATAATGTT
*
6968213 GAGTGATTGTTTTGT
1 -AGTGACTGTTTTGT
6968228 TAAATGTAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 3 0.07
30 15 0.37
31 18 0.44
32 5 0.12
ACGTcount: A:0.20, C:0.11, G:0.21, T:0.48
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTCGATAATGTT
Found at i:6973366 original size:8 final size:8
Alignment explanation
Indices: 6973353--6973402 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
6973343 TTTTAGTTGT
6973353 TTTATATA
1 TTTATATA
6973361 TTTATATA
1 TTTATATA
6973369 TTT-TAT-
1 TTTATATA
6973375 TTTAT-T-
1 TTTATATA
*
6973381 TTTATAAA
1 TTTATATA
*
6973389 TTTATAAA
1 TTTATATA
6973397 TTTATA
1 TTTATA
6973403 AATTATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
6 9 0.24
7 4 0.11
8 25 0.66
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATATA
Found at i:6973403 original size:8 final size:8
Alignment explanation
Indices: 6973381--6973406 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6973371 TTATTTTATT
6973381 TTTATAAA
1 TTTATAAA
6973389 TTTATAAA
1 TTTATAAA
6973397 TTTATAAA
1 TTTATAAA
6973405 TT
1 TT
6973407 ATTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTATAAA
Found at i:6973411 original size:28 final size:28
Alignment explanation
Indices: 6973352--6973419 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
6973342 TTTTTAGTTG
* **
6973352 TTTTATATATTTATATATTTTATTTTAT
1 TTTTATATATTTATAAATTTTAAATTAT
*
6973380 TTTTATAAATTTATAAATTTATAAATTA-
1 TTTTATATATTTATAAATTT-TAAATTAT
6973408 TTTTATATATTT
1 TTTTATATATTT
6973420 TCAAAATACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTATATATTTATAAATTTTAAATTAT
Found at i:6980920 original size:23 final size:22
Alignment explanation
Indices: 6980869--6980920 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
6980859 AAGGGATCAA
* *
6980869 AATT-AAATTGTAATTTTTACG
1 AATTAAAAATGTAATTTTTAAG
*
6980890 ATAATAAAAATGTAATTTTTAAAG
1 A-ATTAAAAATGTAATTTTT-AAG
6980914 AATTAAA
1 AATTAAA
6980921 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 2 0.08
23 18 0.75
24 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTAAAAATGTAATTTTTAAG
Found at i:6984534 original size:1 final size:1
Alignment explanation
Indices: 6984528--6984552 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
6984518 GATGTAAGTC
6984528 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
6984553 ATTATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6986804 original size:22 final size:22
Alignment explanation
Indices: 6986763--6986804 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6986753 ATTAAATTCT
*
6986763 TAAAATTAAAAATTATAAAAAC
1 TAAAATTAAAAATTACAAAAAC
* *
6986785 TAAAATTTAAATTTACAAAA
1 TAAAATTAAAAATTACAAAA
6986805 GGCATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATTAAAAATTACAAAAAC
Found at i:6989232 original size:15 final size:15
Alignment explanation
Indices: 6989212--6989241 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6989202 TAGATTCATG
*
6989212 ATTATCTTTTTTAAT
1 ATTATCGTTTTTAAT
6989227 ATTATCGTTTTTAAT
1 ATTATCGTTTTTAAT
6989242 GTTGGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTATCGTTTTTAAT
Found at i:6991481 original size:31 final size:30
Alignment explanation
Indices: 6991443--6991503 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
6991433 TTGCCGCTTC
* *
6991443 ACATGACAGTATACAATTCAACTCCGACAAT
1 ACATGACAATATACAATTCAACCCCG-CAAT
*
6991474 ACATGACAATATATAATTCAACCCCGCAAT
1 ACATGACAATATACAATTCAACCCCGCAAT
6991504 TCGGTTACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.23
Consensus pattern (30 bp):
ACATGACAATATACAATTCAACCCCGCAAT
Found at i:6992616 original size:25 final size:25
Alignment explanation
Indices: 6992583--6992631 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
6992573 AAGCCCAGAT
6992583 AGAAGTACGCTCTTACGAGCCAAAC
1 AGAAGTACGCTCTTACGAGCCAAAC
*
6992608 AGAATTACGCTCTTACGAGCCAAA
1 AGAAGTACGCTCTTACGAGCCAAA
6992632 ATTCAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (25 bp):
AGAAGTACGCTCTTACGAGCCAAAC
Done.