Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 91 of 128
Found at i:29856108 original size:16 final size:15
Alignment explanation
Indices: 29856087--29856122 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
29856077 TTAAGATCTT
29856087 ATATATCTAGATAAAA
1 ATATATCTAGA-AAAA
*
29856103 ATATATCTATAAAAA
1 ATATATCTAGAAAAA
29856118 ATATA
1 ATATA
29856123 GATAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (15 bp):
ATATATCTAGAAAAA
Found at i:29858629 original size:18 final size:21
Alignment explanation
Indices: 29858606--29858645 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
29858596 ATTTTTTTTA
29858606 ATATAAT-T-TTTAAAA-AAT
1 ATATAATATCTTTAAAATAAT
29858624 ATATAATATCTTTAAAATAAT
1 ATATAATATCTTTAAAATAAT
29858645 A
1 A
29858646 ACAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 7 0.37
21 4 0.21
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATATCTTTAAAATAAT
Found at i:29875938 original size:18 final size:18
Alignment explanation
Indices: 29875917--29875963 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
29875907 TGAAAATTGA
29875917 TTATAATTTTTTTA-GTTT
1 TTATAATTTTTTTATG-TT
*
29875935 TTATAA-TCTTTTATGTT
1 TTATAATTTTTTTATGTT
*
29875952 TTATTATTTTTT
1 TTATAATTTTTT
29875964 ATTTTCTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (18 bp):
TTATAATTTTTTTATGTT
Found at i:29877488 original size:32 final size:32
Alignment explanation
Indices: 29877447--29877512 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
29877437 TACTTTTTTT
*
29877447 TTACTATTTTACTATAATTTCACCTATCTTAA
1 TTACTATTTTACTATAATTTCACCCATCTTAA
*
29877479 TTACTATTTTACTATCATTTCACCCATCTTAA
1 TTACTATTTTACTATAATTTCACCCATCTTAA
29877511 TT
1 TT
29877513 GGATTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (32 bp):
TTACTATTTTACTATAATTTCACCCATCTTAA
Found at i:29880550 original size:21 final size:21
Alignment explanation
Indices: 29880526--29880565 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29880516 ACTTTTTCTA
29880526 AAGTTAAAA-GTCAAAACTATT
1 AAGTTAAAAGGT-AAAACTATT
29880547 AAGTTAAAAGGTAAAACTA
1 AAGTTAAAAGGTAAAACTA
29880566 CGTCGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATT
Found at i:29881682 original size:26 final size:27
Alignment explanation
Indices: 29881639--29881689 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29881629 ATTTATTTTA
**
29881639 ATATTTTTTTATTGTATTTGATATATT
1 ATATTTTTAAATTGTATTTGATATATT
*
29881666 ATATTTTTAAATT-TATTTTATATA
1 ATATTTTTAAATTGTATTTGATATA
29881690 AAAAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (27 bp):
ATATTTTTAAATTGTATTTGATATATT
Found at i:29883949 original size:38 final size:39
Alignment explanation
Indices: 29883907--29883983 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
29883897 TATAACATTT
* * *
29883907 TAAAA-ATTATATTATACTTATTGTA-TTTTTTAATATAA
1 TAAAATATT-TATTACACTTATGGTAGTTTTTTAAAATAA
*
29883945 TAAAATATTTATTACATTTATGGTAGTTTTTTAAAATAA
1 TAAAATATTTATTACACTTATGGTAGTTTTTTAAAATAA
29883984 GTACTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 18 0.55
39 15 0.45
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (39 bp):
TAAAATATTTATTACACTTATGGTAGTTTTTTAAAATAA
Found at i:29884071 original size:14 final size:15
Alignment explanation
Indices: 29884054--29884083 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29884044 TTAGTGTATT
29884054 ATATTTTTAAA-AAA
1 ATATTTTTAAATAAA
29884068 ATATTTTTAAATAAA
1 ATATTTTTAAATAAA
29884083 A
1 A
29884084 ACTAATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTTTAAATAAA
Found at i:29889784 original size:16 final size:16
Alignment explanation
Indices: 29889765--29889803 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
29889755 AAAATCAAAT
*
29889765 AAAATTATATTATATA
1 AAAATTACATTATATA
*
29889781 AAAAATACATTATATA
1 AAAATTACATTATATA
29889797 AAAATTA
1 AAAATTA
29889804 AATGAGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:29890079 original size:23 final size:23
Alignment explanation
Indices: 29890016--29890079 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
29890006 ATATATATTT
* *
29890016 AAATA-TTTTTAATAAAAATAAA
1 AAATATTTTTTAATATAAACAAA
* * *
29890038 AATTAATATTTT-ATTTAAACAAA
1 AAAT-ATTTTTTAATATAAACAAA
29890061 AAATATTTTTTAATATAAA
1 AAATATTTTTTAATATAAA
29890080 AAATTGATTC
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
22 9 0.29
23 18 0.58
24 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATTTTTTAATATAAACAAA
Found at i:29891179 original size:16 final size:17
Alignment explanation
Indices: 29891159--29891517 Score: 143
Period size: 17 Copynumber: 21.0 Consensus size: 17
29891149 ACGAAAGTTT
*
29891159 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
29891176 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
29891194 TTTGT-AAACACGAAAA
1 TTTTTAAAACACGAAAA
*
29891210 -TTTTAGAAACGCGAAAA
1 TTTTTA-AAACACGAAAA
29891227 TTTTTAGAAGA-ACGAAAA
1 TTTTTA-AA-ACACGAAAA
**
29891245 TTTTTAAAACACGACATTT
1 TTTTTAAAACACGA-A-AA
*
29891264 TTTTTTAAACACG---A
1 TTTTTAAAACACGAAAA
*
29891278 --TTTAAAAAAC-AAAA
1 TTTTTAAAACACGAAAA
** * * * *
29891292 -AATGAAATGCAAGAATA
1 TTTTTAAA-ACACGAAAA
* **
29891309 -TTTTGAAACACGAATT
1 TTTTTAAAACACGAAAA
* * *
29891325 TTTTTTAAACGCGAGAA
1 TTTTTAAAACACGAAAA
*
29891342 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAAAA
* * * *
29891360 -CTTTGAAACACCG-GAG
1 TTTTTAAAACA-CGAAAA
*
29891376 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
* *
29891394 TTTGTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
* ***
29891411 TTTGTGAAAACACGTATTT
1 TTT-TTAAAACACG-AAAA
29891430 TTTTTAAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* * *
29891448 TTTTTGAAACGCCG-GAA
1 TTTTTAAAAC-ACGAAAA
*
29891465 TTTTTAAAAACACGAAGA
1 TTTTT-AAAACACGAAAA
*
29891483 TTTTTAAAACATGAAAA
1 TTTTTAAAACACGAAAA
29891500 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
29891518 CACAAAATTT
Statistics
Matches: 251, Mismatches: 64, Indels: 53
0.68 0.17 0.14
Matches are distributed among these distances:
12 8 0.03
14 1 0.00
15 7 0.03
16 24 0.10
17 93 0.37
18 93 0.37
19 25 0.10
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:29891392 original size:52 final size:54
Alignment explanation
Indices: 29891314--29891518 Score: 140
Period size: 52 Copynumber: 3.9 Consensus size: 54
29891304 GAATATTTTG
* ** * *
29891314 AAACACGAAT-TTTTTTTAAACGCGAGAATTTTTGAAAACATGAAAACTT-TG-
1 AAACACGGATGTTTTTAAAAACACGAGAATTTTTGAAAACACGAAAACTTGTGA
* * *
29891365 AAACACCGGA-GTTTTTGAAAACACGAGAATTTGTG-AAACACGAAAATTTGTGA
1 AAACA-CGGATGTTTTTAAAAACACGAGAATTTTTGAAAACACGAAAACTTGTGA
* * * * * * * *
29891418 AAACACGTATTTTTTTTAAAAACACGAAAATTTTTG-AAACGCCG-GAATTTTTAA
1 AAACACGGA-TGTTTTTAAAAACACGAGAATTTTTGAAAAC-ACGAAAACTTGTGA
* * *
29891472 AAACAC-GAAGATTTTT-AAAACATGAAAATTTTTGAAAACACGAAAAC
1 AAACACGGATG-TTTTTAAAAACACGAGAATTTTTGAAAACACGAAAAC
29891519 ACAAAATTTG
Statistics
Matches: 121, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
51 17 0.14
52 47 0.39
53 17 0.14
54 38 0.31
55 2 0.02
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (54 bp):
AAACACGGATGTTTTTAAAAACACGAGAATTTTTGAAAACACGAAAACTTGTGA
Found at i:29891475 original size:89 final size:88
Alignment explanation
Indices: 29891342--29891513 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 88
29891332 AACGCGAGAA
* * * * *
29891342 TTTTTGAAAACATGAAAACTTTGAAACACCGGAGTTTTTGAAAACACG-AGAATTTGTGAAACAC
1 TTTTTAAAAACACGAAAACTTTGAAACACCGGAATTTTTAAAAACACGAAG-ATTTGTAAAACAC
29891406 GAAAATTTGTGAAAACACGTATTT
65 GAAAATTTGTGAAAACACGTATTT
* * * *
29891430 TTTTTAAAAACACGAAAATTTTTGAAACGCCGGAATTTTTAAAAACACGAAGATTTTTAAAACAT
1 TTTTTAAAAACACGAAAA-CTTTGAAACACCGGAATTTTTAAAAACACGAAGATTTGTAAAACAC
*
29891495 GAAAATTTTTGAAAACACG
65 GAAAATTTGTGAAAACACG
29891514 AAAACACAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
88 16 0.22
89 54 0.75
90 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (88 bp):
TTTTTAAAAACACGAAAACTTTGAAACACCGGAATTTTTAAAAACACGAAGATTTGTAAAACACG
AAAATTTGTGAAAACACGTATTT
Found at i:29891515 original size:35 final size:35
Alignment explanation
Indices: 29891158--29891517 Score: 137
Period size: 35 Copynumber: 10.5 Consensus size: 35
29891148 AACGAAAGTT
* * *
29891158 TTTTTTAAAACACGAGAATTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAAA
* *
29891194 --TTTGTAAACACGAAAA-TTTTAGAAACGCGAAAA
1 TTTTTGAAAACACGAAAATTTTTA-AAACACGAAAA
* **
29891227 TTTTTAGAAGA-ACGAAAATTTTTAAAACACGACATT
1 TTTTT-GAAAACACGAAAATTTTTAAAACACGA-AAA
** *
29891263 TTTTTTTAAACACG---A--TTTAAAAAAC-AAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
** * * * * *
29891292 --AATGAAATGCAAGAATA-TTTTGAAACACG-AAT
1 TTTTTGAAA-ACACGAAAATTTTTAAAACACGAAAA
** * * *
29891324 TTTTTTTAAACGCGAGAATTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACGAAAA
* * * *
29891360 -CTTTG-AAACACCG-GAGTTTTTGAAAACACGAGAA
1 TTTTTGAAAACA-CGAAAATTTTT-AAAACACGAAAA
* * ***
29891394 TTTGTG-AAACACGAAAATTTGTGAAAACACGTATTT
1 TTTTTGAAAACACGAAAATTT-TTAAAACACG-AAAA
* * * *
29891430 TTTTTAAAAACACGAAAATTTTTGAAACGCCG-GAA
1 TTTTTGAAAACACGAAAATTTTTAAAAC-ACGAAAA
* * *
29891465 TTTTTAAAAACACGAAGATTTTTAAAACATGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
29891500 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
29891518 CACAAAATTT
Statistics
Matches: 232, Mismatches: 66, Indels: 53
0.66 0.19 0.15
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 1 0.00
30 1 0.00
31 10 0.04
32 11 0.05
33 18 0.08
34 45 0.19
35 94 0.41
36 30 0.13
37 16 0.07
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACGAAAA
Found at i:29891517 original size:18 final size:18
Alignment explanation
Indices: 29891158--29891517 Score: 156
Period size: 18 Copynumber: 21.0 Consensus size: 18
29891148 AACGAAAGTT
* *
29891158 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
29891176 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
29891194 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
29891210 TTTTAG-AAACGCGAAAA
1 TTTTTGAAAACACGAAAA
*
29891227 TTTTTAGAAGA-ACGAAAA
1 TTTTT-GAAAACACGAAAA
**
29891245 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
**
29891263 TTTTTTTAAACACG---A
1 TTTTTGAAAACACGAAAA
*
29891278 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
** * * *
29891292 --AATGAAATGCAAGAATA
1 TTTTTGAAA-ACACGAAAA
*
29891309 -TTTTG-AAACACG-AAT
1 TTTTTGAAAACACGAAAA
** * *
29891324 TTTTTTTAAACGCGAGAA
1 TTTTTGAAAACACGAAAA
*
29891342 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
29891360 -CTTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
29891376 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
29891394 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* ***
29891411 TTTGTGAAAACACGTATTT
1 TTTTTGAAAACACG-AAAA
*
29891430 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
29891448 TTTTTG-AAACGCCG-GAA
1 TTTTTGAAAAC-ACGAAAA
* *
29891465 TTTTTAAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
*
29891483 TTTTT-AAAACATGAAAA
1 TTTTTGAAAACACGAAAA
29891500 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
29891518 CACAAAATTT
Statistics
Matches: 253, Mismatches: 62, Indels: 54
0.69 0.17 0.15
Matches are distributed among these distances:
12 5 0.02
13 3 0.01
14 2 0.01
15 4 0.02
16 31 0.12
17 84 0.33
18 102 0.40
19 22 0.09
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:29891519 original size:43 final size:43
Alignment explanation
Indices: 29891471--29891557 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
29891461 GGAATTTTTA
* * *
29891471 AAAACACGAAGATTTTTAAAACATGAAAA-TTTTTGAAAACACG
1 AAAACAC-AAAATTTGTAAAACACGAAAATTTTTTGAAAACACG
**
29891514 AAAACACAAAATTTGTCGAACACGAAAATTTTTTGAAAACACG
1 AAAACACAAAATTTGTAAAACACGAAAATTTTTTGAAAACACG
29891557 A
1 A
29891558 TAATATCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 16 0.42
43 22 0.58
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (43 bp):
AAAACACAAAATTTGTAAAACACGAAAATTTTTTGAAAACACG
Found at i:29891645 original size:25 final size:27
Alignment explanation
Indices: 29891599--29891648 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
29891589 ATTTTTTTTG
29891599 AAACACGAGATTTTTTTGAAAACACGA
1 AAACACGAGATTTTTTTGAAAACACGA
29891626 AAACACGA-ATTTTTTT-AAAACAC
1 AAACACGAGATTTTTTTGAAAACAC
29891649 AGGAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (27 bp):
AAACACGAGATTTTTTTGAAAACACGA
Found at i:29891689 original size:17 final size:17
Alignment explanation
Indices: 29891667--29891705 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29891657 TATTATTATT
29891667 ATTTTGAA-ACACGAGAA
1 ATTTTGAAGACACGA-AA
*
29891684 ATTTTGAAGACATGAAA
1 ATTTTGAAGACACGAAA
29891701 ATTTT
1 ATTTT
29891706 TTAAAAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (17 bp):
ATTTTGAAGACACGAAA
Found at i:29893084 original size:29 final size:29
Alignment explanation
Indices: 29892956--29893086 Score: 133
Period size: 29 Copynumber: 4.4 Consensus size: 29
29892946 AAATATGGGC
* *
29892956 CAAAATGTAATTTATTA-AGAGTTTAGGGGT
1 CAAAATGTAAATT-TTAGAAAGTTTA-GGGT
* * *
29892986 TAAAGTG-AAATTTTGAGAAAGTCTAAGGGT
1 CAAAATGTAAATTTT-AGAAAGT-TTAGGGT
*
29893016 CGAAATGT-AATTTTAGAAAGTTTTAGGGT
1 CAAAATGTAAATTTTAGAAAG-TTTAGGGT
*
29893045 CAAAATGTAAATTTTAGAAAGTTTGGGGT
1 CAAAATGTAAATTTTAGAAAGTTTAGGGT
29893074 CAAAATGTAAATT
1 CAAAATGTAAATT
29893087 GTGAAAAGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.02
29 44 0.52
30 36 0.43
31 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (29 bp):
CAAAATGTAAATTTTAGAAAGTTTAGGGT
Found at i:29893605 original size:19 final size:18
Alignment explanation
Indices: 29893558--29893605 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
29893548 ATTACCTTTT
29893558 TTCTT-TCTTTCTTCTTC
1 TTCTTCTCTTTCTTCTTC
29893575 TTCTTCTCCTTTCTCTCTT-
1 TTCTTCT-CTTTCT-TCTTC
29893594 TTCTTTCTCTTT
1 TTC-TTCTCTTT
29893606 TCCGGTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 13 0.48
20 8 0.30
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTCTTCTCTTTCTTCTTC
Found at i:29897538 original size:21 final size:21
Alignment explanation
Indices: 29897508--29897548 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29897498 AAGCAGAGAT
*
29897508 GGTGGTGGAAGGGGTGGAAAC
1 GGTGGCGGAAGGGGTGGAAAC
*
29897529 GGTGGCGGAAGTGGTGGAAA
1 GGTGGCGGAAGGGGTGGAAA
29897549 AGGTAGCAAC
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:0.05, G:0.56, T:0.15
Consensus pattern (21 bp):
GGTGGCGGAAGGGGTGGAAAC
Found at i:29901173 original size:42 final size:42
Alignment explanation
Indices: 29901125--29901435 Score: 480
Period size: 42 Copynumber: 7.4 Consensus size: 42
29901115 CACAATTAGA
29901125 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
29901167 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
29901209 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
29901251 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
* *
29901293 CCCACCTCAATTAGGATTTATGTTTCTAGTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
* ** * *
29901335 CTCAGGTCAATTAGGATTTATGTTTTTAGTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
* * * * * *
29901377 CCTACATCAATTAAGATTTATGTTTTTACTTTTTCATTTAAT
1 CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
*
29901419 CCCTA-CTCAAGTAGGAT
1 CCC-ACCTCAATTAGGAT
29901436 ACTTCTGTTC
Statistics
Matches: 252, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
42 251 1.00
43 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.48
Consensus pattern (42 bp):
CCCACCTCAATTAGGATTTATCTTTGTAGTTTTTCATTTAAT
Found at i:29906977 original size:8 final size:9
Alignment explanation
Indices: 29906903--29906979 Score: 55
Period size: 9 Copynumber: 7.8 Consensus size: 9
29906893 TCTTTAAAAA
*
29906903 TAAAATTAT
1 TAAAAATAT
29906912 TAAAAATAT
1 TAAAAATAT
*
29906921 ATAAAAATGT
1 -TAAAAATAT
*
29906931 TAAAAGACAATT
1 TAAAA-A-TA-T
29906943 ATAAAAATAT
1 -TAAAAATAT
*
29906953 TCAAATATTAT
1 T-AAA-AATAT
29906964 TAAAAATAT
1 TAAAAATAT
29906973 TAAAAAT
1 TAAAAAT
29906980 CAATAAATGG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
9 25 0.46
10 16 0.30
11 6 0.11
12 2 0.04
13 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
TAAAAATAT
Found at i:29906986 original size:19 final size:19
Alignment explanation
Indices: 29906901--29906986 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 19
29906891 AATCTTTAAA
*
29906901 AATAAAATTATTAAAAAT-
1 AATAAAAATATTAAAAATC
*
29906919 ATATAAAAATGTTAAAAGA-C
1 A-ATAAAAATATTAAAA-ATC
* *
29906939 AATTATAAAAATATTCAAATATT
1 -A--ATAAAAATATT-AAAAATC
*
29906962 ATTAAAAATATTAAAAATC
1 AATAAAAATATTAAAAATC
29906981 AATAAA
1 AATAAA
29906987 TGGCAAATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
18 1 0.02
19 23 0.44
20 11 0.21
21 1 0.02
22 13 0.25
23 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAAAAATATTAAAAATC
Found at i:29913329 original size:23 final size:23
Alignment explanation
Indices: 29913278--29913321 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29913268 TGAGTCGTTT
*
29913278 AAAATAAAAGTCAACGACCAATC
1 AAAATAAAAGTCAAAGACCAATC
*
29913301 AAAATAAAAGTGAAAGACCAA
1 AAAATAAAAGTCAAAGACCAA
29913322 ATCCAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.11, T:0.11
Consensus pattern (23 bp):
AAAATAAAAGTCAAAGACCAATC
Found at i:29921721 original size:39 final size:37
Alignment explanation
Indices: 29921662--29921751 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 37
29921652 TGCTGCCAAA
* *
29921662 AATTTATAATTTCTT-TCTTTT-T-ATATAATTTTTAAT
1 AATTTTTAATTT-TTATCTTTTATGATA-AATTTATAAT
29921698 AAATTTTCTATATTTTTATCTTTTATGATAAATTTATAAT
1 -AATTTT-TA-ATTTTTATCTTTTATGATAAATTTATAAT
29921738 AATTTTTAATTTTT
1 AATTTTTAATTTTT
29921752 TAAAGAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
37 11 0.24
38 6 0.13
39 16 0.35
40 10 0.22
41 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (37 bp):
AATTTTTAATTTTTATCTTTTATGATAAATTTATAAT
Found at i:29932109 original size:39 final size:37
Alignment explanation
Indices: 29932050--29932139 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 37
29932040 TGCTGCCAAA
* *
29932050 AATTTATAATTTCTT-TCTTTT-T-ATATAATTTTTAAT
1 AATTTTTAATTT-TTATCTTTTATGATA-AATTTATAAT
29932086 AAATTTTCTATATTTTTATCTTTTATGATAAATTTATAAT
1 -AATTTT-TA-ATTTTTATCTTTTATGATAAATTTATAAT
29932126 AATTTTTAATTTTT
1 AATTTTTAATTTTT
29932140 TAAAGAGTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
37 11 0.24
38 6 0.13
39 16 0.35
40 10 0.22
41 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (37 bp):
AATTTTTAATTTTTATCTTTTATGATAAATTTATAAT
Found at i:29941742 original size:149 final size:149
Alignment explanation
Indices: 29941580--29941882 Score: 597
Period size: 149 Copynumber: 2.0 Consensus size: 149
29941570 TGTCATAAAC
29941580 TTGAAACCTTAACTAATTTATTTAGGTCTCAAAATTATTATTTTAGAAAATTTTTAAAATTTTAA
1 TTGAAACCTTAACTAATTTATTTAGGTCTCAAAATTATTATTTTAGAAAATTTTTAAAATTTTAA
*
29941645 CTTTATTTATATATTCTTTAATATTTTTTTAAAATTTTTGTATTTTTTTTAAAAAAATAAAGATT
66 CTTTATTTATATATTCTTTAATATTTTTTTAAAATTTTTGTATTTTTTTTAAAAAAATAAAAATT
29941710 TGGAGCTTTTATAAATGTT
131 TGGAGCTTTTATAAATGTT
29941729 TTGAAACCTTAACTAATTTATTTAGGTCTCAAAATTATTATTTTAGAAAATTTTTAAAATTTTAA
1 TTGAAACCTTAACTAATTTATTTAGGTCTCAAAATTATTATTTTAGAAAATTTTTAAAATTTTAA
29941794 CTTTATTTATATATTCTTTAATATTTTTTTAAAATTTTTGTATTTTTTTTAAAAAAATAAAAATT
66 CTTTATTTATATATTCTTTAATATTTTTTTAAAATTTTTGTATTTTTTTTAAAAAAATAAAAATT
29941859 TGGAGCTTTTATAAATGTT
131 TGGAGCTTTTATAAATGTT
29941878 TTGAA
1 TTGAA
29941883 TTTTAAAAAT
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (149 bp):
TTGAAACCTTAACTAATTTATTTAGGTCTCAAAATTATTATTTTAGAAAATTTTTAAAATTTTAA
CTTTATTTATATATTCTTTAATATTTTTTTAAAATTTTTGTATTTTTTTTAAAAAAATAAAAATT
TGGAGCTTTTATAAATGTT
Found at i:29944116 original size:16 final size:17
Alignment explanation
Indices: 29944095--29944131 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
29944085 TTTTCAAAAG
29944095 TAATTTTTATT-TTTTA
1 TAATTTTTATTATTTTA
29944111 TAATTTTTATTATTTTA
1 TAATTTTTATTATTTTA
29944128 TAAT
1 TAAT
29944132 ATCTCAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TAATTTTTATTATTTTA
Found at i:29944287 original size:31 final size:31
Alignment explanation
Indices: 29944240--29944356 Score: 111
Period size: 31 Copynumber: 3.9 Consensus size: 31
29944230 TTAATATAAT
* * *
29944240 ATTTGGTATCTGAACTTGACAATTTTTCCTA
1 ATTTGGTACCTAAACTTGACATTTTTTCCTA
*
29944271 ATTTGATACCTAAACTT----TTTTTGGTCC-A
1 ATTTGGTACCTAAACTTGACATTTTT--TCCTA
*
29944299 ATTTGGTA-CTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACATTTTTTCCTA
*
29944330 ATTTGGTACCTAGACTTGACATTTTTT
1 ATTTGGTACCTAAACTTGACATTTTTT
29944357 TTTAAAGTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
27 6 0.09
28 14 0.20
29 3 0.04
30 3 0.04
31 37 0.54
32 6 0.09
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACATTTTTTCCTA
Found at i:29952313 original size:3 final size:3
Alignment explanation
Indices: 29952293--29952387 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
29952283 TTAATTTTAA
* * * * * * * * *
29952293 TAT TTT TAT TAT TGT TAT TAT TAT TAA TAC CAT CAT CAT CAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
29952341 TAT TAT TAA TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29952388 AATTGTTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:29956845 original size:17 final size:18
Alignment explanation
Indices: 29956811--29956856 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
29956801 CCGTTATGTC
29956811 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
29956826 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
29956843 CGCGACCGCGACCG
1 CGCGACCGCGACCG
29956857 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:29972499 original size:6 final size:6
Alignment explanation
Indices: 29972484--29972532 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
29972474 AAGCAATGGG
* *
29972484 ATTCCA ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT ATTCCC ATTCCT
1 ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT ATTCCT
29972532 A
1 A
29972533 ACCAAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTCCT
Found at i:29977859 original size:30 final size:30
Alignment explanation
Indices: 29977823--29977898 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
29977813 ATGTTAAGAT
29977823 GTTCAAATCTCAGCATTCATTAGGCTTACA
1 GTTCAAATCTCAGCATTCATTAGGCTTACA
*
29977853 GTTCAAATCTCAGCATTCATTAGGCTTACG
1 GTTCAAATCTCAGCATTCATTAGGCTTACA
* *
29977883 GTTCAAACCCCAGCAT
1 GTTCAAATCTCAGCAT
29977899 CCAACAGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (30 bp):
GTTCAAATCTCAGCATTCATTAGGCTTACA
Found at i:29982627 original size:37 final size:37
Alignment explanation
Indices: 29982543--29982627 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 37
29982533 TTAGATACAT
* * *
29982543 ATATTTTTAT-ATTTATAATTTCTTTTATATTTTAAG
1 ATATTTTTATAATATATAATTTATTTTAAATTTTAAG
* *
29982579 AAATTTATATAATATAT-ATATTATTTTAAATTTTTAA-
1 ATATTTTTATAATATATAAT-TTATTTTAAA-TTTTAAG
29982616 ATATTTTTATAA
1 ATATTTTTATAA
29982628 AAAATTAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
36 10 0.26
37 23 0.59
38 6 0.15
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (37 bp):
ATATTTTTATAATATATAATTTATTTTAAATTTTAAG
Found at i:29983099 original size:30 final size:30
Alignment explanation
Indices: 29983038--29983106 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
29983028 AGTGTGACCA
* *
29983038 AAATAGAAACAATCTAAAATGTAAGTGACT
1 AAATAGAAACAATCTAAAATATAAGTAACT
** **
29983068 AAATAGAAATGATCTAAAATATTGGTAACT
1 AAATAGAAACAATCTAAAATATAAGTAACT
*
29983098 AAATTGAAA
1 AAATAGAAA
29983107 ATTTTTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (30 bp):
AAATAGAAACAATCTAAAATATAAGTAACT
Found at i:29984613 original size:22 final size:22
Alignment explanation
Indices: 29984585--29984628 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29984575 GAGGTAACCC
29984585 CATCTTTGTTTTTCGCATTATT
1 CATCTTTGTTTTTCGCATTATT
29984607 CATCTTTGTTTTTCGCATTATT
1 CATCTTTGTTTTTCGCATTATT
29984629 TTGTGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.09, T:0.59
Consensus pattern (22 bp):
CATCTTTGTTTTTCGCATTATT
Found at i:29989099 original size:9 final size:9
Alignment explanation
Indices: 29989085--29989133 Score: 82
Period size: 9 Copynumber: 5.4 Consensus size: 9
29989075 GTAGTGATTC
29989085 AATTCGGTT
1 AATTCGGTT
29989094 AATTCGGTT
1 AATTCGGTT
29989103 AATTCAGG-T
1 AATTC-GGTT
29989112 AATTCGGTT
1 AATTCGGTT
29989121 AATTCGGTT
1 AATTCGGTT
29989130 AATT
1 AATT
29989134 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 2 0.05
9 34 0.89
10 2 0.05
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29990410 original size:18 final size:18
Alignment explanation
Indices: 29990389--29990432 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
29990379 ATATAAGGGT
29990389 TAGGATACAAAAAAAGGC
1 TAGGATACAAAAAAAGGC
*
29990407 TAGGATACATAAAAAGGC
1 TAGGATACAAAAAAAGGC
29990425 TAGGATAC
1 TAGGATAC
29990433 GCACCTGGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.16
Consensus pattern (18 bp):
TAGGATACAAAAAAAGGC
Found at i:29992269 original size:11 final size:11
Alignment explanation
Indices: 29992248--29992307 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
29992238 CTTTTAAATA
29992248 GAAATTTGAGAG
1 GAAA-TTGAGAG
29992260 GAAATTGAGAG
1 GAAATTGAGAG
* *
29992271 GAATTTAAGA-
1 GAAATTGAGAG
29992281 GAATATT-AGAG
1 GAA-ATTGAGAG
29992292 AGAAATTGAGA-
1 -GAAATTGAGAG
29992303 GAAAT
1 GAAAT
29992308 GATTTAGTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
10 11 0.27
11 20 0.49
12 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.23
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:29992281 original size:22 final size:23
Alignment explanation
Indices: 29992247--29992298 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
29992237 TCTTTTAAAT
*
29992247 AGAAATTTGAGAGGAA-ATT-GAG
1 AGAAATTTAAGA-GAATATTAGAG
*
29992269 AGGAATTTAAGAGAATATTAGAG
1 AGAAATTTAAGAGAATATTAGAG
29992292 AGAAATT
1 AGAAATT
29992299 GAGAGAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (23 bp):
AGAAATTTAAGAGAATATTAGAG
Found at i:29993213 original size:32 final size:32
Alignment explanation
Indices: 29993175--29993240 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
29993165 TACAATGGGG
* *
29993175 TTTTAGGTTCCTTAAAAGTT-GGAGAAAAATTT
1 TTTTAGGTCCCATAAAAGTTAGGA-AAAAATTT
*
29993207 TTTTAGGTCCCATAAAAGTTAGTAAAAAATTT
1 TTTTAGGTCCCATAAAAGTTAGGAAAAAATTT
29993239 TT
1 TT
29993241 GGATCCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (32 bp):
TTTTAGGTCCCATAAAAGTTAGGAAAAAATTT
Found at i:29998251 original size:9 final size:9
Alignment explanation
Indices: 29998237--29998267 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
29998227 GTAGTGATTC
29998237 AATTCGGTT
1 AATTCGGTT
29998246 AATTCGGTT
1 AATTCGGTT
29998255 AATTCGGTT
1 AATTCGGTT
29998264 AATT
1 AATT
29998268 TTTAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:30007917 original size:14 final size:14
Alignment explanation
Indices: 30007886--30007947 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
30007876 GAAAATGTAT
*
30007886 TAATTTAATGTTT-T
1 TAATTTAAT-TTTAA
30007900 TAATTTAATTTTAA
1 TAATTTAATTTTAA
30007914 TAATGTATAA-TTTAA
1 TAAT-T-TAATTTTAA
*
30007929 -AATTTTATTTTAA
1 TAATTTAATTTTAA
30007942 -AATTTA
1 TAATTTA
30007948 TCAAATTATG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.05
13 14 0.34
14 16 0.39
15 6 0.15
16 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TAATTTAATTTTAA
Found at i:30009917 original size:19 final size:18
Alignment explanation
Indices: 30009876--30009916 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
30009866 CGTAGATCTC
30009876 AAAAATTTATTCGAAATA
1 AAAAATTTATTCGAAATA
30009894 AAAAATTTATTCGAAATA
1 AAAAATTTATTCGAAATA
30009912 AAAAA
1 AAAAA
30009917 AAACCGTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAAATTTATTCGAAATA
Found at i:30010186 original size:30 final size:29
Alignment explanation
Indices: 30010119--30010186 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
30010109 GATTTCGCGG
*
30010119 AAAATGGCCCATTCCGGTAAATAATTAAA
1 AAAACGGCCCATTCCGGTAAATAATTAAA
* * *
30010148 AAATCGGCCCATTTCGGTAAAT-TTTGAAAA
1 AAAACGGCCCATTCCGGTAAATAATT--AAA
30010178 AAAACGGCC
1 AAAACGGCC
30010187 TTTATTGGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.06
29 19 0.59
30 11 0.34
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAACGGCCCATTCCGGTAAATAATTAAA
Found at i:30013672 original size:17 final size:17
Alignment explanation
Indices: 30013650--30013684 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30013640 AATTGTGTAT
30013650 ATCTATACC-ATTATTTA
1 ATCTAT-CCTATTATTTA
30013667 ATCTATCCTATTATTTA
1 ATCTATCCTATTATTTA
30013684 A
1 A
30013685 GTGTGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (17 bp):
ATCTATCCTATTATTTA
Found at i:30018163 original size:13 final size:13
Alignment explanation
Indices: 30018145--30018170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30018135 CTCATCCATC
30018145 ACTCAATCATTTT
1 ACTCAATCATTTT
30018158 ACTCAATCATTTT
1 ACTCAATCATTTT
30018171 GAGCATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ACTCAATCATTTT
Found at i:30019587 original size:43 final size:43
Alignment explanation
Indices: 30019432--30019596 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 43
30019422 TTTCGATATG
* *
30019432 TGATTTCGTGTAAGATCACGTCTGGGACGTTGGCATC-G-ATT
1 TGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCGGTATT
* * *
30019473 TGAGATTTACGTGTAAGACCATGTCTGGGACATTGACATCGTGTA--
1 T--GA-TTACGTGTAAGACCACGTCTGGGACGTTGGCATCG-GTATT
** *
30019518 TGATTTTGTGTAAGACC-CTGTTTGGGACAG-TGGCATCGGTATT
1 TGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGGTATT
*
30019561 TGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
30019597 TGTACAAGCT
Statistics
Matches: 97, Mismatches: 15, Indels: 22
0.72 0.11 0.16
Matches are distributed among these distances:
41 4 0.04
42 28 0.29
43 32 0.33
44 30 0.31
45 1 0.01
46 1 0.01
47 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
TGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCGGTATT
Found at i:30027978 original size:46 final size:46
Alignment explanation
Indices: 30027920--30028123 Score: 291
Period size: 46 Copynumber: 4.4 Consensus size: 46
30027910 TGATGATAAA
*
30027920 ATGTTGTCCGAATGTTGTTGAAATGCTGTCCATTTTTGAGCATATT
1 ATGTTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTGAGCATATT
* *
30027966 ATGTTGTTCGAATGTTGTTTAAATGATGTCCATTTTTGAGCATATT
1 ATGTTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTGAGCATATT
* *
30028012 ATGATGTCCGAATGTTGTTTAAATGCTGTCCGTTTTTGAGCATATT
1 ATGTTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTGAGCATATT
* ** * *
30028058 ATGCTGTCCGAATGTTGTTTAAATATTGTCCATTTTTGAGCAAATCA
1 ATGTTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTGAGCATAT-T
* *
30028105 ATGCTGTCCGAATATTGTT
1 ATGTTGTCCGAATGTTGTT
30028124 ACTGCTGTTC
Statistics
Matches: 143, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
46 125 0.87
47 18 0.13
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (46 bp):
ATGTTGTCCGAATGTTGTTTAAATGCTGTCCATTTTTGAGCATATT
Found at i:30028684 original size:11 final size:11
Alignment explanation
Indices: 30028668--30028693 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30028658 TTATTATTCA
30028668 TTTTATTTTAT
1 TTTTATTTTAT
30028679 TTTTATTTTAT
1 TTTTATTTTAT
30028690 TTTT
1 TTTT
30028694 TGGTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:30028688 original size:16 final size:17
Alignment explanation
Indices: 30028657--30028692 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30028647 TATTATTCCC
30028657 TTTATTATTCATTTTAT
1 TTTATTATTCATTTTAT
*
30028674 TTTATT-TTTATTTTAT
1 TTTATTATTCATTTTAT
30028690 TTT
1 TTT
30028693 TTGGTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTATTCATTTTAT
Found at i:30029451 original size:3 final size:3
Alignment explanation
Indices: 30029443--30029656 Score: 428
Period size: 3 Copynumber: 71.3 Consensus size: 3
30029433 TTTAGCAACT
30029443 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
30029491 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
30029539 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
30029587 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
30029635 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
30029657 NNNNNNNNNN
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 211 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30043713 original size:11 final size:11
Alignment explanation
Indices: 30043697--30043722 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30043687 TTATTATTCA
30043697 TTTTATTTTAT
1 TTTTATTTTAT
30043708 TTTTATTTTAT
1 TTTTATTTTAT
30043719 TTTT
1 TTTT
30043723 TGGTTTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:30043717 original size:16 final size:17
Alignment explanation
Indices: 30043686--30043721 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30043676 TATTATTCCC
30043686 TTTATTATTCATTTTAT
1 TTTATTATTCATTTTAT
*
30043703 TTTATT-TTTATTTTAT
1 TTTATTATTCATTTTAT
30043719 TTT
1 TTT
30043722 TTGGTTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTATTCATTTTAT
Found at i:30044476 original size:3 final size:3
Alignment explanation
Indices: 30044468--30044682 Score: 430
Period size: 3 Copynumber: 71.7 Consensus size: 3
30044458 TTTAGCAACT
30044468 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
30044516 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
30044564 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
30044612 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
30044660 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
30044683 TTTTATAGTT
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 212 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30046726 original size:58 final size:56
Alignment explanation
Indices: 30046656--30046823 Score: 295
Period size: 55 Copynumber: 3.0 Consensus size: 56
30046646 TATTATCAGC
*
30046656 GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTCATGATTTTCGTGAATT
1 GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTCAT--TTTCCGTGAATT
30046714 GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTC-TTTTCCGTGAATT
1 GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTCATTTTCCGTGAATT
30046769 GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTCA-TTTCCGTGAATT
1 GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTCATTTTCCGTGAATT
30046824 AAGGGAAAAA
Statistics
Matches: 108, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
55 65 0.60
57 1 0.01
58 42 0.39
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (56 bp):
GAAGAACTTTTGATTCATTCCCCTTTTATCACTCATTTGGTCATTTTCCGTGAATT
Found at i:30046842 original size:55 final size:55
Alignment explanation
Indices: 30046670--30046842 Score: 161
Period size: 55 Copynumber: 3.1 Consensus size: 55
30046660 AACTTTTGAT
* ***** *
30046670 TCATTCCCCTTTTATCACTCATTTGGTCATGATTTTCGTGAATTGAAGAACTTTTGAT
1 TCATTCCCCTTTTATCACTCATTTGGTC---ATTTCCGTGAATTGAAGAACAAAAAAG
* ***** *
30046728 TCATTCCCCTTTTATCACTCATTTGGTCTTTTCCGTGAATTGAAGAACTTTTGAT
1 TCATTCCCCTTTTATCACTCATTTGGTCATTTCCGTGAATTGAAGAACAAAAAAG
30046783 TCATTCCCCTTTTATCACTCATTTGGTCATTTCCGTGAATT-AAGGGAA-AAAAAAG
1 TCATTCCCCTTTTATCACTCATTTGGTCATTTCCGTGAATTGAA--GAACAAAAAAG
30046838 TCATT
1 TCATT
30046843 TTCGAATTTC
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
54 2 0.02
55 71 0.68
56 3 0.03
58 28 0.27
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.42
Consensus pattern (55 bp):
TCATTCCCCTTTTATCACTCATTTGGTCATTTCCGTGAATTGAAGAACAAAAAAG
Found at i:30048126 original size:22 final size:22
Alignment explanation
Indices: 30048087--30048128 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30048077 GGAATAGTAA
*
30048087 ATTATATATATTTGTATTATAT
1 ATTATATATATTTCTATTATAT
30048109 ATTATAT-TATTTTCTATTAT
1 ATTATATATA-TTTCTATTAT
30048129 TTTAATGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTATATATATTTCTATTATAT
Found at i:30053708 original size:18 final size:18
Alignment explanation
Indices: 30053687--30053740 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
30053677 ATTTTGAATT
*
30053687 TTTTATAAA-TATTTTAGA
1 TTTTAAAAATTATTTT-GA
30053705 TTTTAAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
** *
30053723 TTTTTGAAATTTTTTTGA
1 TTTTAAAAATTATTTTGA
30053741 AATTTTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 25 0.81
19 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
TTTTAAAAATTATTTTGA
Found at i:30053746 original size:10 final size:11
Alignment explanation
Indices: 30053723--30053747 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30053713 ATTATTTTGA
30053723 TTTTTGAAATT
1 TTTTTGAAATT
30053734 TTTTTGAAATT
1 TTTTTGAAATT
30053745 TTT
1 TTT
30053748 GTTAAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTGAAATT
Found at i:30054669 original size:16 final size:16
Alignment explanation
Indices: 30054648--30054689 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
30054638 TGTATATATT
30054648 TATATTTTTAATCAAA
1 TATATTTTTAATCAAA
* *
30054664 TATATTTTTTATTAAA
1 TATATTTTTAATCAAA
30054680 TATATATTTT
1 TATAT-TTTT
30054690 TTATACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTTTTAATCAAA
Found at i:30055142 original size:42 final size:42
Alignment explanation
Indices: 30055024--30055203 Score: 238
Period size: 43 Copynumber: 4.2 Consensus size: 42
30055014 CTAACTTTTT
*
30055024 GCGGCGCTTACAGAAAAAACGCCGCTAAAGATTATGTTCTTTA
1 GCGGCGCTTA-AGAAAAAACGCCGCTAAAGATCATGTTCTTTA
30055067 GCGGCGC-TAAGATAATAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAAGA-AA-AAACGCCGCTAAAGATCATGTTCTTTA
* *
30055110 GCGGCGCTTATGAAAAAACGTCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTA
** * *
30055152 GCGGCGCTTTGGAAGAAAACGCCGCTAAA-AGTAATGTTCTATA
1 GCGGCGCTTAAGAA-AAAACGCCGCTAAAGA-TCATGTTCTTTA
30055195 GCGGCGCTT
1 GCGGCGCTT
30055204 GTTCAAAAAC
Statistics
Matches: 124, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
41 3 0.02
42 43 0.35
43 74 0.60
44 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (42 bp):
GCGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTTCTTTA
Found at i:30055212 original size:85 final size:85
Alignment explanation
Indices: 30055024--30055218 Score: 243
Period size: 85 Copynumber: 2.3 Consensus size: 85
30055014 CTAACTTTTT
* *
30055024 GCGGCGCTTACAGAAAAAACGCCGCTAAAGATTATGTTCTTTAGCGGCGCTAAGATAATAAACGC
1 GCGGCGCTTA-TGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGATAATAAACGC
* *
30055089 CGCTAAAGATCATGTTCTTTA
65 CGCTAAAGATAATGTTCTATA
* **
30055110 GCGGCGCTTATGAAAAAACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGA-AGA-AAACG
1 GCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TAAGATA-ATAAACG
30055173 CCGCTAAA-AGTAATGTTCTATA
64 CCGCTAAAGA-TAATGTTCTATA
* **
30055195 GCGGCGCTTGTTCAAAAACGCCGC
1 GCGGCGCTTATGAAAAAACGCCGC
30055219 GAATAATAGT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
84 1 0.01
85 80 0.84
86 14 0.15
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (85 bp):
GCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGATAATAAACGCC
GCTAAAGATAATGTTCTATA
Found at i:30055237 original size:85 final size:85
Alignment explanation
Indices: 30055024--30055245 Score: 211
Period size: 85 Copynumber: 2.6 Consensus size: 85
30055014 CTAACTTTTT
* * * * * **
30055024 GCGGCGCTTACAGAAAAAACGCCGCTAAAGATTATGTTCTTTAGCGGCGC-TAAGATA-ATAAAC
1 GCGGCGCTTA-TGAAAAAACGCCGCGAAAGATCATGTTATTTAGAGGCGCTTTGGA-AGA-AAAC
* *
30055087 GCCGCTAAAGATCATGTTCTTTA
63 GCCGCTAAAGATAATGTTCTATA
* * * *
30055110 GCGGCGCTTATGAAAAAACGTCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAAGAAAACGCC
1 GCGGCGCTTATGAAAAAACGCCGCGAAAGATCATGTTATTTAGAGGCGCTTTGGAAGAAAACGCC
30055175 GCTAAA-AGTAATGTTCTATA
66 GCTAAAGA-TAATGTTCTATA
* **
30055195 GCGGCGCTTGTTCAAAAACGCCGCGAATA-AT-AGTGTTATTTAGAGGCGCTT
1 GCGGCGCTTATGAAAAAACGCCGCGAA-AGATCA-TGTTATTTAGAGGCGCTT
30055246 ATTTCACAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
84 2 0.02
85 100 0.85
86 15 0.13
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (85 bp):
GCGGCGCTTATGAAAAAACGCCGCGAAAGATCATGTTATTTAGAGGCGCTTTGGAAGAAAACGCC
GCTAAAGATAATGTTCTATA
Found at i:30055846 original size:344 final size:344
Alignment explanation
Indices: 30055219--30055907 Score: 1362
Period size: 344 Copynumber: 2.0 Consensus size: 344
30055209 AAAACGCCGC
30055219 GAATAATAGTGTTATTTAGAGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTTAGCGG
1 GAATAATAGTGTTATTTAGAGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTTAGCGG
30055284 CGCTTTTTTAAAAAAGCCACTAATTTTAGGATTTTTTTAAAATAAAATTTTCTGTTTTTTTCAGC
66 CGCTTTTTTAAAAAAGCCACTAATTTTAGGATTTTTTTAAAATAAAATTTTCTGTTTTTTTCAGC
30055349 CCTCCTGCAACAACAAATCAAAAGCAACCAGATCTAAACTAACCAAAAACAATAAATTTATATAA
131 CCTCCTGCAACAACAAATCAAAAGCAACCAGATCTAAACTAACCAAAAACAATAAATTTATATAA
30055414 TATAATGACTAAAATAATATTAATTGATATAAATAAAAGTGAATTCATACTTTTCTTTACAAAAA
196 TATAATGACTAAAATAATATTAATTGATATAAATAAAAGTGAATTCATACTTTTCTTTACAAAAA
30055479 AGTTTAAAGTTAAAATAAT-AAAAATATTTATGCAATATACAGTATGACGGCGGAAGTTGCGACT
261 AGTTTAAAGTTAAAATAATAAAAAATATTTAT-CAATATACAGTATGACGGCGGAAGTTGCGACT
30055543 GCTGAAACATCTTCATCATA
325 GCTGAAACATCTTCATCATA
30055563 GAATAATAGTGTTATTTAGAGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTTAGCGG
1 GAATAATAGTGTTATTTAGAGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTTAGCGG
30055628 CGCTTTTTTAAAAAAGCCACTAATTTTAGGATTTTTTTAAAATAAAATTTTCTGTTTTTTTCAGC
66 CGCTTTTTTAAAAAAGCCACTAATTTTAGGATTTTTTTAAAATAAAATTTTCTGTTTTTTTCAGC
30055693 CCTCCTGCAACAACAAATCAAAAGCAACCAGATCTAAACTAACCAAAAACAATAAATTTATATAA
131 CCTCCTGCAACAACAAATCAAAAGCAACCAGATCTAAACTAACCAAAAACAATAAATTTATATAA
30055758 TATAATGACTAAAATAATATTAATTGATATAAATAAAAGTGAATTCATACTTTTCTTTACAAAAA
196 TATAATGACTAAAATAATATTAATTGATATAAATAAAAGTGAATTCATACTTTTCTTTACAAAAA
30055823 AGTTTAAAGTTAAAATAATAAAAAATATTTATCAATATACAGTATGACGGCGGAAGTTGCGACTG
261 AGTTTAAAGTTAAAATAATAAAAAATATTTATCAATATACAGTATGACGGCGGAAGTTGCGACTG
30055888 CTGAAACATCTTCATCATA
326 CTGAAACATCTTCATCATA
30055907 G
1 G
30055908 TCTGAGGTTG
Statistics
Matches: 344, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
344 332 0.97
345 12 0.03
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (344 bp):
GAATAATAGTGTTATTTAGAGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTTAGCGG
CGCTTTTTTAAAAAAGCCACTAATTTTAGGATTTTTTTAAAATAAAATTTTCTGTTTTTTTCAGC
CCTCCTGCAACAACAAATCAAAAGCAACCAGATCTAAACTAACCAAAAACAATAAATTTATATAA
TATAATGACTAAAATAATATTAATTGATATAAATAAAAGTGAATTCATACTTTTCTTTACAAAAA
AGTTTAAAGTTAAAATAATAAAAAATATTTATCAATATACAGTATGACGGCGGAAGTTGCGACTG
CTGAAACATCTTCATCATA
Found at i:30056048 original size:12 final size:12
Alignment explanation
Indices: 30056016--30056062 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
30056006 TTTTGAACAT
*
30056016 CTGCTTCTATCG
1 CTGCTTCTCTCG
30056028 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
30056040 CTGCTTCTCTTG
1 CTGCTTCTCTCG
*
30056052 TTGCTTCTCTC
1 CTGCTTCTCTC
30056063 ACTGTGGCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.15, T:0.47
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:30056079 original size:21 final size:21
Alignment explanation
Indices: 30056053--30056100 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
30056043 CTTCTCTTGT
* *
30056053 TGCTTCTCTCACTGTGGCCTC
1 TGCTTCTCTCACTGTAGCATC
*
30056074 TGCTTCTCTCGCTGTAGCATC
1 TGCTTCTCTCACTGTAGCATC
30056095 TGCTTC
1 TGCTTC
30056101 CCTCNNNNNN
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.35, G:0.19, T:0.40
Consensus pattern (21 bp):
TGCTTCTCTCACTGTAGCATC
Found at i:30071983 original size:147 final size:147
Alignment explanation
Indices: 30071783--30072120 Score: 371
Period size: 147 Copynumber: 2.3 Consensus size: 147
30071773 GCCTCGTATA
* * * *
30071783 GATAAATGTTAAAACATTTTTGCGGCGTTTT-AGTTCAAGCCCCACTAACTATAA-ATCAAAACG
1 GATAAATGTTAAAACAATTTTGCGGCGTTTTAAG-TAAAGCGCCACTAAATATAAGATC-AAACG
* * * *
30071846 CAGTCGCTTCAGCAACACTTACCTCAAACCCGTGGCGTTT-TAAAAAAATCGCCACTAATAACAT
64 AAGTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAA-CGCCACTAATAACAT
* * *
30071910 TTAAAAAAC-AGCAGCGTTTC
128 TGAAAAAACGA-CAACATTTC
* * *
30071930 TATAAATGTTAGAACAATGTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATCAAACGAA
1 GATAAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATCAAACGAA
* * * * ** *
30071995 GTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCGTTTCCAAAAAAACGCCACTAATACCATTGA
66 GTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAACGCCACTAATAACATTGA
*
30072060 CAAAACGACAACATTTC
131 AAAAACGACAACATTTC
** *
30072077 GATAAA-CATAAATACAATTTTGCGGCGTTTTATGTAAAGCGCCA
1 GATAAATGTTAAA-ACAATTTTGCGGCGTTTTAAGTAAAGCGCCA
30072121 GTAATAGCAA
Statistics
Matches: 158, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
146 3 0.02
147 142 0.90
148 13 0.08
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (147 bp):
GATAAATGTTAAAACAATTTTGCGGCGTTTTAAGTAAAGCGCCACTAAATATAAGATCAAACGAA
GTCGCTTCACCAACACTTAACTCAAACCCGTGGCGTTTCCAAAAAAACGCCACTAATAACATTGA
AAAAACGACAACATTTC
Found at i:30073110 original size:15 final size:16
Alignment explanation
Indices: 30073077--30073114 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
30073067 AAACATTAAA
30073077 CCTTAAACTATAAAACC
1 CCTTAAACTAT-AAACC
*
30073094 CCTTAAACTAT-AGCC
1 CCTTAAACTATAAACC
30073109 CCTTAA
1 CCTTAA
30073115 GCCTCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (16 bp):
CCTTAAACTATAAACC
Found at i:30081524 original size:18 final size:18
Alignment explanation
Indices: 30081501--30081537 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30081491 CCTACCTATC
30081501 TAATTGTATTAGTGTCTA
1 TAATTGTATTAGTGTCTA
30081519 TAATTGTATTAGTGTCTA
1 TAATTGTATTAGTGTCTA
30081537 T
1 T
30081538 GTAATACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (18 bp):
TAATTGTATTAGTGTCTA
Found at i:30082547 original size:54 final size:55
Alignment explanation
Indices: 30082451--30082564 Score: 196
Period size: 54 Copynumber: 2.1 Consensus size: 55
30082441 ATATTATCAG
* *
30082451 TGAAGAACTTTTGATTTATTCCCCTTTTATCACTCATTTGGTCATTTTCGTGAAT
1 TGAAGAACTTTTGATTCATTCCCCCTTTATCACTCATTTGGTCATTTTCGTGAAT
30082506 TGAAGAACTTTTGATTCA-TCCCCCTTTATCACTCATTTGGTCATTTTCGTGAAT
1 TGAAGAACTTTTGATTCATTCCCCCTTTATCACTCATTTGGTCATTTTCGTGAAT
30082560 T-AAGA
1 TGAAGA
30082565 GAAAAAAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
53 4 0.07
54 36 0.63
55 17 0.30
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (55 bp):
TGAAGAACTTTTGATTCATTCCCCCTTTATCACTCATTTGGTCATTTTCGTGAAT
Found at i:30083557 original size:15 final size:15
Alignment explanation
Indices: 30083539--30083569 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30083529 ATTTGTAATA
30083539 TTTTTTTTTGAGAAT
1 TTTTTTTTTGAGAAT
*
30083554 TTTTTTTTTTAGAAT
1 TTTTTTTTTGAGAAT
30083569 T
1 T
30083570 AGGCTGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTTTTTTTGAGAAT
Found at i:30083868 original size:22 final size:22
Alignment explanation
Indices: 30083840--30083881 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
30083830 AGAATAGTAA
30083840 ATTATATATATTTT-TATTATAT
1 ATTATAT-TATTTTCTATTATAT
30083862 ATTATATTATTTTCTATTAT
1 ATTATATTATTTTCTATTAT
30083882 TTTAATGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTATATTATTTTCTATTATAT
Found at i:30084467 original size:18 final size:18
Alignment explanation
Indices: 30084437--30084471 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30084427 AAACAATTTA
30084437 TTTAATAAAATTAAAATG
1 TTTAATAAAATTAAAATG
30084455 TTTAA-AAATATTAAAAT
1 TTTAATAAA-ATTAAAAT
30084472 ATCACTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TTTAATAAAATTAAAATG
Found at i:30088027 original size:152 final size:153
Alignment explanation
Indices: 30087749--30088054 Score: 587
Period size: 152 Copynumber: 2.0 Consensus size: 153
30087739 CGGTGATCGG
30087749 AAAATTCATGTCGGCAACTTGGAAGGACAAAGCCCCGGTCAGTAGGGGTGAGCGATGATAAATAT
1 AAAATTCATG-CGGCAACTTGGAAGGACAAAGCCCCGGTCAGTAGGGGTGAGCGATGATAAATAT
30087814 TAAAAGTAACATATTTTAATCTTATTTTTAATATATATATATATATATTTTTTGTGATTATTCGA
65 TAAAAGTAACATATTTTAATCTTATTTTTAATATATATATATATATATTTTTTGTGATTATTCGA
30087879 TCTTAACCATAAATTTTATACTTT
130 TCTTAACCATAAATTTTATACTTT
30087903 AAAATTCATG-GGCAACTTGGAAGGACAAAGCCCCGGTCAGTAGGGGTGAGCGATGATAAATATT
1 AAAATTCATGCGGCAACTTGGAAGGACAAAGCCCCGGTCAGTAGGGGTGAGCGATGATAAATATT
*
30087967 AAAAGTAACATATTTTAATCTTATTTTTTATATATATATATATATATTTTTTGTGATTATTCGAT
66 AAAAGTAACATATTTTAATCTTATTTTTAATATATATATATATATATTTTTTGTGATTATTCGAT
30088032 CTTAACCATAAATTTTATACTTT
131 CTTAACCATAAATTTTATACTTT
30088055 CAATCATTTA
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
152 141 0.93
154 10 0.07
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (153 bp):
AAAATTCATGCGGCAACTTGGAAGGACAAAGCCCCGGTCAGTAGGGGTGAGCGATGATAAATATT
AAAAGTAACATATTTTAATCTTATTTTTAATATATATATATATATATTTTTTGTGATTATTCGAT
CTTAACCATAAATTTTATACTTT
Found at i:30091702 original size:25 final size:26
Alignment explanation
Indices: 30091668--30091716 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
30091658 AAAATTTTCA
30091668 AATCGAGTCGAA-TGAAGTGAAATTCG
1 AATCGAGTCGAATTG-AGTGAAATTCG
30091694 AATC-AGTCGAATTGAGTGAAATT
1 AATCGAGTCGAATTGAGTGAAATT
30091717 ATTCGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (26 bp):
AATCGAGTCGAATTGAGTGAAATTCG
Found at i:30092011 original size:18 final size:18
Alignment explanation
Indices: 30091947--30092011 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
30091937 TATTTTCAGG
30091947 ATTTTTTTGAATTTTTTATAA
1 ATTTTTTTG-A-TTTTTA-AA
* * *
30091968 ATATTTTAGATTTTAAAA
1 ATTTTTTTGATTTTTAAA
* *
30091986 ATTATTTTGATTTTTGAA
1 ATTTTTTTGATTTTTAAA
30092004 ATTTTTTT
1 ATTTTTTT
30092012 TGTAATTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
18 22 0.63
19 5 0.14
20 1 0.03
21 7 0.20
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATTTTTTTGATTTTTAAA
Found at i:30094028 original size:13 final size:14
Alignment explanation
Indices: 30094003--30094031 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30093993 TGACAAAATC
30094003 AAAATGTATTTAAA
1 AAAATGTATTTAAA
30094017 AAAATGTA-TTAAA
1 AAAATGTATTTAAA
30094030 AA
1 AA
30094032 TGTCAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (14 bp):
AAAATGTATTTAAA
Found at i:30107710 original size:3 final size:3
Alignment explanation
Indices: 30107702--30107738 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
30107692 TTACACTTAC
30107702 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30107739 TACTCTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30115260 original size:31 final size:29
Alignment explanation
Indices: 30115229--30115286 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
30115219 ATTTGAACCA
* **
30115229 AAATTAGAGCTTCACGTGTATAATTGCACC
1 AAATTACAG-TTCACGTACATAATTGCACC
*
30115259 AAATTACAGTTCATGTACATAATTGCAC
1 AAATTACAGTTCACGTACATAATTGCAC
30115287 GTTAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (29 bp):
AAATTACAGTTCACGTACATAATTGCACC
Found at i:30118117 original size:278 final size:278
Alignment explanation
Indices: 30117620--30118175 Score: 1103
Period size: 278 Copynumber: 2.0 Consensus size: 278
30117610 ATTTTAAAAA
30117620 AAAACTATAAAGAGATAAATTCCTAAAAATAAAATCCAAATTCAAATTTACGAAAATTAATAACA
1 AAAACTATAAAGAGATAAATTCCTAAAAATAAAATCCAAATTCAAATTTACGAAAATTAATAACA
30117685 AATTTCCTTCCCCCGACTCTTAAAAGCCGCTTAATGCGAAGCATATGTACCTTCACCTATTAAAG
66 AATTTCCTTCCCCCGACTCTTAAAAGCCGCTTAATGCGAAGCATATGTACCTTCACCTATTAAAG
30117750 CTTCTCCACTACTAAAGAACGACTAAGCTTAATTTCTGAGAATAAAATAAGTCAAAACTTCTAGA
131 CTTCTCCACTACTAAAGAACGACTAAGCTTAATTTCTGAGAATAAAATAAGTCAAAACTTCTAGA
30117815 AAAAAAAGAAAGGGTTTCATCTTTTTTTTTCTTAAATGTGCAATTACTACCATCTTTAAAATTAT
196 AAAAAAAGAAAGGGTTTCATCTTTTTTTTTCTTAAATGTGCAATTACTACCATCTTTAAAATTAT
30117880 TGTAACCGCAGATTGTGT
261 TGTAACCGCAGATTGTGT
30117898 AAAACTATAAAGAGATAAATTCCTAAAAATAAAATCCAAATTCAAATTTACGAAAATTAATAACA
1 AAAACTATAAAGAGATAAATTCCTAAAAATAAAATCCAAATTCAAATTTACGAAAATTAATAACA
30117963 AATTTCCTTCCCCCGACTCTTAAAAGCCGCTTAATGCGAAGCATATGTACCTTCACCTATTAAAG
66 AATTTCCTTCCCCCGACTCTTAAAAGCCGCTTAATGCGAAGCATATGTACCTTCACCTATTAAAG
30118028 CTTCTCCACTACTAAAGAACGACTAAGCTTAATTTCTGAGAATAAAATAAGTCAAAACTTCTAGA
131 CTTCTCCACTACTAAAGAACGACTAAGCTTAATTTCTGAGAATAAAATAAGTCAAAACTTCTAGA
30118093 AAAAAAAGAAAGGGTTTCATCTTTTTTTTTCTTAAATGTGCAATTACTACCATCTTTAAAATTAT
196 AAAAAAAGAAAGGGTTTCATCTTTTTTTTTCTTAAATGTGCAATTACTACCATCTTTAAAATTAT
*
30118158 TGTAACCGCCGATTGTGT
261 TGTAACCGCAGATTGTGT
30118176 CTTAACTCGA
Statistics
Matches: 277, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 277 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (278 bp):
AAAACTATAAAGAGATAAATTCCTAAAAATAAAATCCAAATTCAAATTTACGAAAATTAATAACA
AATTTCCTTCCCCCGACTCTTAAAAGCCGCTTAATGCGAAGCATATGTACCTTCACCTATTAAAG
CTTCTCCACTACTAAAGAACGACTAAGCTTAATTTCTGAGAATAAAATAAGTCAAAACTTCTAGA
AAAAAAAGAAAGGGTTTCATCTTTTTTTTTCTTAAATGTGCAATTACTACCATCTTTAAAATTAT
TGTAACCGCAGATTGTGT
Found at i:30120698 original size:16 final size:16
Alignment explanation
Indices: 30120679--30120709 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30120669 CAACATTATA
30120679 TATGTATACATATATG
1 TATGTATACATATATG
*
30120695 TATGTATATATATAT
1 TATGTATACATATAT
30120710 CGCTGATTGA
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:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (16 bp):
TATGTATACATATATG
Found at i:30126075 original size:25 final size:24
Alignment explanation
Indices: 30126033--30126080 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
30126023 CCCATATATT
30126033 ATACTTTCAATTCTTTCACATTTA
1 ATACTTTCAATTCTTTCACATTTA
30126057 ATACATTTCAATGTC-TTCACATTT
1 ATAC-TTTCAAT-TCTTTCACATTT
30126081 TTCCCATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.29, C:0.21, G:0.02, T:0.48
Consensus pattern (24 bp):
ATACTTTCAATTCTTTCACATTTA
Found at i:30126707 original size:21 final size:22
Alignment explanation
Indices: 30126674--30126718 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
30126664 GTATGTTTGT
30126674 AAAGTTGGGGGTTTCAAGGGGG
1 AAAGTTGGGGGTTTCAAGGGGG
* *
30126696 AAAGTT-GGGGTTTGAGGGGGG
1 AAAGTTGGGGGTTTCAAGGGGG
30126717 AA
1 AA
30126719 GGGATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.24, C:0.02, G:0.51, T:0.22
Consensus pattern (22 bp):
AAAGTTGGGGGTTTCAAGGGGG
Found at i:30126900 original size:133 final size:136
Alignment explanation
Indices: 30126741--30127004 Score: 320
Period size: 144 Copynumber: 1.9 Consensus size: 136
30126731 AATGGGATTT
* *
30126741 TTTTTTCAAAGTAAAATTATTTTTTGTGAC-GTTTTT-A-TATTGCTTATCTTTTGTGGTATTTT
1 TTTTTTCAAAGTAAAATTATTTTTTGTG-CTGTTTTTAACTATTGCTTATCTTTTGCGGCATTTT
* * *
30126803 TCATAAAAATACCATAGAAAATTATTTTATTTGGAATAAAACGATATTGTTTTACTATATAAAAT
65 TCATAAAAATACCACAAAAAATTATTTCATTTGGAATAAAACGATATTGTTTTACTATATAAAAT
30126868 GTCGTTA
130 GTCGTTA
*
30126875 TTTTTT-AAAGTAAAATTATTTTTTGTGCTTTTTTTTAAAAACGTCGCTATTGCTTATCTTTTGC
1 TTTTTTCAAAGTAAAATTATTTTTTGTGC-TGTTTTT---AA-----CTATTGCTTATCTTTTGC
* * * *
30126939 GGCGTTTTTCATAAAAATGCCGCAAAAAATTATTTCATTTGGAATAAAACGATATTGTTTTGCTA
57 GGCATTTTTCATAAAAATACCACAAAAAATTATTTCATTTGGAATAAAACGATATTGTTTTACTA
30127004 T
122 T
30127005 GTTAAAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
132 1 0.01
133 21 0.19
134 11 0.10
138 1 0.01
144 74 0.69
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (136 bp):
TTTTTTCAAAGTAAAATTATTTTTTGTGCTGTTTTTAACTATTGCTTATCTTTTGCGGCATTTTT
CATAAAAATACCACAAAAAATTATTTCATTTGGAATAAAACGATATTGTTTTACTATATAAAATG
TCGTTA
Found at i:30127055 original size:144 final size:144
Alignment explanation
Indices: 30126778--30127061 Score: 306
Period size: 144 Copynumber: 2.0 Consensus size: 144
30126768 GACGTTTTTA
* * * * *
30126778 TATTGCTTATCTTTTGTGGTATTTTTCATAAAAATACCATAGAAAATTATTTTATTTGGAATAAA
1 TATTGCTTATCTTTTGCGGCATTTTTCATAAAAATACCACAAAAAATTATTTCATTTGGAATAAA
* * ** ** *
30126843 ACGATATTGTTTTACTATATAAAATGTCGTTATTTTTTAAAGTAAAATTATTTTTTGTGCT-TTT
66 ACGATATTGTTTTACTATATAAAATATCGTTATTTTGTAAAGTAAAATTATTAGTTAAGCTGATT
*
30126907 TTTTAAAAACGTCGC
131 TTAT-AAAACGTCGC
* * *
30126922 TATTGCTTATCTTTTGCGGCGTTTTTCATAAAAATGCCGCAAAAAATTATTTCATTTGGAATAAA
1 TATTGCTTATCTTTTGCGGCATTTTTCATAAAAATACCACAAAAAATTATTTCATTTGGAATAAA
* * * **
30126987 ACGATATTGTTTTGCTATGTTAAAAATAT-TTTATTTTGT-CTGTTAAAAATTATTAGTTAAG-T
66 ACGATATTGTTTTACTAT-AT-AAAATATCGTTATTTTGTAAAG-T-AAAATTATTAGTTAAGCT
30127049 GATTTTATAAAAC
127 GATTTTATAAAAC
30127062 ATTTATTATT
Statistics
Matches: 114, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
144 75 0.66
145 16 0.14
146 23 0.20
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (144 bp):
TATTGCTTATCTTTTGCGGCATTTTTCATAAAAATACCACAAAAAATTATTTCATTTGGAATAAA
ACGATATTGTTTTACTATATAAAATATCGTTATTTTGTAAAGTAAAATTATTAGTTAAGCTGATT
TTATAAAACGTCGC
Found at i:30127841 original size:15 final size:15
Alignment explanation
Indices: 30127821--30127850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30127811 CCCTAACCTG
*
30127821 ACCCTAAATCTCTAA
1 ACCCTAAATCACTAA
30127836 ACCCTAAATCACTAA
1 ACCCTAAATCACTAA
30127851 CTCTTAACCC
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:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
ACCCTAAATCACTAA
Found at i:30127972 original size:88 final size:89
Alignment explanation
Indices: 30127868--30128030 Score: 265
Period size: 88 Copynumber: 1.8 Consensus size: 89
30127858 CCCCAAACCT
*
30127868 CTAACCACTAACCCCTAAACCTTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAACCAT
1 CTAACCACTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCAT
30127932 AAACCCTAACCCAACCTCGAATCC
66 AAACCCTAACCCAACCTCGAATCC
* * * *
30127956 CTAACCCCTAACCCCTAAACATTGTTTAATATATAAATTAAAACACACTAATTAATTTAAACCCT
1 CTAACCACTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCAT
*
30128021 AAACCTTAAC
66 AAACCCTAAC
30128031 TTGAACTGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
88 40 0.59
89 28 0.41
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (89 bp):
CTAACCACTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCAT
AAACCCTAACCCAACCTCGAATCC
Found at i:30128062 original size:89 final size:88
Alignment explanation
Indices: 30127870--30128054 Score: 248
Period size: 88 Copynumber: 2.1 Consensus size: 88
30127860 CCAAACCTCT
*
30127870 AACCACTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCATAAA
1 AACC-CTAACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCATAAA
*
30127935 CCCTAACCCAACCTCGAATCCCTA
65 CCCTAACCCAACCTCGAATCCATA
* * * *
30127959 ACCCCTAACCCCTAAACATTGTTTAATATATAAATTAAAACACACTAATTAATTTAAACCCTAAA
1 AACCCTAACCCCTAAACATTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAACCATAAA
* **
30128024 CCTTAACTTGAA-CT-GAATCCATA
65 CCCTAAC-CCAACCTCGAATCCATA
30128047 AACCCTAA
1 AACCCTAA
30128055 ATCCCTAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
88 49 0.58
89 33 0.39
90 2 0.02
ACGTcount: A:0.44, C:0.27, G:0.02, T:0.26
Consensus pattern (88 bp):
AACCCTAACCCCTAAACATTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCATAAAC
CCTAACCCAACCTCGAATCCATA
Found at i:30128613 original size:41 final size:41
Alignment explanation
Indices: 30128555--30128681 Score: 128
Period size: 41 Copynumber: 3.1 Consensus size: 41
30128545 AAATGTTTTT
* * * *
30128555 GCGGCGCTTTTTCAAAAACGGCACTAAAGCCCCGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCACTAAAGACCCGAGCATTA
* * * *
30128596 GCGGCGCTTCTTGAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCACTAAAGACCCGAGCATTA
* * * * * *
30128637 GCGGCACTTCTTAAAAAATGCCGCTAAATATCTGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCACTAAAGACCCGAGCATTA
30128678 GCGG
1 GCGG
30128682 TGTTTTTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTCTTAAAAAACGCCACTAAAGACCCGAGCATTA
Found at i:30134174 original size:24 final size:24
Alignment explanation
Indices: 30134147--30134198 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
30134137 CTATATATCA
30134147 GTTTCCTAGTTGTTCTCATCATAT
1 GTTTCCTAGTTGTTCTCATCATAT
30134171 GTTTCCTAGTTGTTCTCATCATAT
1 GTTTCCTAGTTGTTCTCATCATAT
30134195 GTTT
1 GTTT
30134199 ATGTATATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.52
Consensus pattern (24 bp):
GTTTCCTAGTTGTTCTCATCATAT
Found at i:30134379 original size:1 final size:1
Alignment explanation
Indices: 30134375--30134402 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
30134365 TTTTTTTTTT
30134375 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
30134403 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:30145406 original size:31 final size:31
Alignment explanation
Indices: 30145371--30145434 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
30145361 GAGGAATTAT
30145371 GAATATTTTCTGTGAATGGTCACTTAATTGG
1 GAATATTTTCTGTGAATGGTCACTTAATTGG
30145402 GAATATTTTCTGTGAATGGTCACTTAATTGG
1 GAATATTTTCTGTGAATGGTCACTTAATTGG
30145433 GA
1 GA
30145435 TGCCCAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (31 bp):
GAATATTTTCTGTGAATGGTCACTTAATTGG
Found at i:30154077 original size:25 final size:25
Alignment explanation
Indices: 30154043--30154094 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
30154033 GTACGTGTGT
30154043 TCGAATGCGATAAAGCGCATTATCC
1 TCGAATGCGATAAAGCGCATTATCC
30154068 TCGAATGCGATAAAGCGCATTATCC
1 TCGAATGCGATAAAGCGCATTATCC
30154093 TC
1 TC
30154095 TTATTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (25 bp):
TCGAATGCGATAAAGCGCATTATCC
Found at i:30157457 original size:12 final size:12
Alignment explanation
Indices: 30157440--30157464 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30157430 GGTGTTCATT
30157440 CGGTTAACCGAC
1 CGGTTAACCGAC
30157452 CGGTTAACCGAC
1 CGGTTAACCGAC
30157464 C
1 C
30157465 CGAAATAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:30157638 original size:9 final size:9
Alignment explanation
Indices: 30157624--30157735 Score: 134
Period size: 9 Copynumber: 12.4 Consensus size: 9
30157614 TTTGGTTAAA
30157624 AATTAACCG
1 AATTAACCG
*
30157633 AATTAACCA
1 AATTAACCG
30157642 AATTAACCG
1 AATTAACCG
*
30157651 AATTACCCG
1 AATTAACCG
*
30157660 AATTAACCA
1 AATTAACCG
*
30157669 AATTACCCG
1 AATTAACCG
**
30157678 AATTAATTG
1 AATTAACCG
30157687 AATTAACCG
1 AATTAACCG
*
30157696 AATTACCCG
1 AATTAACCG
*
30157705 AATTACCCG
1 AATTAACCG
*
30157714 AATTAACCT
1 AATTAACCG
*
30157723 AATTAACCT
1 AATTAACCG
30157732 AATT
1 AATT
30157736 GAATCATACA
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 88 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:30157824 original size:6 final size:6
Alignment explanation
Indices: 30157774--30157808 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
30157764 ACTTTTATAC
30157774 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
30157809 AATTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:30157832 original size:20 final size:20
Alignment explanation
Indices: 30157774--30157821 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
30157764 ACTTTTATAC
30157774 TTTAGTTTTAGTTTTAG--T
1 TTTAGTTTTAGTTTTAGAAT
30157792 TTTAGTTTTAGTTTTAGAAT
1 TTTAGTTTTAGTTTTAGAAT
*
30157812 TTTATTTTTA
1 TTTAGTTTTA
30157822 TTTGTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 17 0.63
20 10 0.37
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGTTTTAGAAT
Found at i:30159859 original size:8 final size:8
Alignment explanation
Indices: 30159846--30159870 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30159836 GTAAATGTTT
30159846 TCAAAATA
1 TCAAAATA
30159854 TCAAAATA
1 TCAAAATA
30159862 TCAAAATA
1 TCAAAATA
30159870 T
1 T
30159871 GTAAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (8 bp):
TCAAAATA
Found at i:30165125 original size:37 final size:39
Alignment explanation
Indices: 30165051--30165128 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 39
30165041 CTTACTCATG
*
30165051 ATCATTTATTTAGTTCGATGAATGAACAATAACAAACAAAA
1 ATCATTTATTTAGTCCGATGAATGAAC-A-AACAAACAAAA
* *
30165092 ATCATTTATTTCGTCCGGTGAATGAAC-AA-AAACAAAA
1 ATCATTTATTTAGTCCGATGAATGAACAAACAAACAAAA
30165129 GTAGAACCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 8 0.24
38 2 0.06
41 24 0.71
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (39 bp):
ATCATTTATTTAGTCCGATGAATGAACAAACAAACAAAA
Found at i:30176312 original size:12 final size:13
Alignment explanation
Indices: 30176295--30176323 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30176285 GTATATTAAA
30176295 TTTATAGTTTTT-
1 TTTATAGTTTTTG
30176307 TTTATAGTTTTTG
1 TTTATAGTTTTTG
30176320 TTTA
1 TTTA
30176324 AAAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (13 bp):
TTTATAGTTTTTG
Found at i:30178218 original size:83 final size:82
Alignment explanation
Indices: 30178079--30178244 Score: 246
Period size: 83 Copynumber: 2.0 Consensus size: 82
30178069 TTTACCCTAA
*
30178079 ATACAATTGTGTTGAATTCTAATTTTATTTAGTTGGTGGATTGATAATAAATTTTAATAAAGTTT
1 ATACAATTGTGTTGAATTCTAATTTTATTTAGTTGGTGGATTAATAATAAATTTTAATAAAGTTT
30178144 TAATTTTGACTAATGAC
66 TAATTTTGACTAATGAC
* * *
30178161 ATACAATTGTGTTGACTTTTAATTTTTATTTAGTTGGTCGG-TTAATAAT-AATATTTAATAAAT
1 ATACAATTGTGTTGAATTCTAA-TTTTATTTAGTTGGT-GGATTAATAATAAAT-TTTAATAAAG
*
30178224 TTTTATTTTTGACTAATGAC
63 TTTTAATTTTGACTAATGAC
30178244 A
1 A
30178245 CCAAATGGTC
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
82 23 0.30
83 51 0.67
84 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.48
Consensus pattern (82 bp):
ATACAATTGTGTTGAATTCTAATTTTATTTAGTTGGTGGATTAATAATAAATTTTAATAAAGTTT
TAATTTTGACTAATGAC
Found at i:30178689 original size:19 final size:18
Alignment explanation
Indices: 30178646--30178690 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
30178636 TTAATAATTG
*
30178646 TAAAAATATTCAAAAAAA
1 TAAAAAAATTCAAAAAAA
*
30178664 TATAAAAAATTCATAAAAAC
1 TA-AAAAAATTCA-AAAAAA
30178684 TAAAAAA
1 TAAAAAA
30178691 GATAGTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAAAATTCAAAAAAA
Found at i:30199488 original size:45 final size:45
Alignment explanation
Indices: 30199415--30199504 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
30199405 ACTATTAACA
*
30199415 ATCTACTGAAAAGCAAAAGAAATATGAAAAGGTATCTACCACTTT
1 ATCTACTGAAAAGCAAAAGAAATATGAAAAGGTACCTACCACTTT
* * *
30199460 ATCTACTGAAAAGTAAAAGGAATGTGAAAAGGTACCTACCACTTT
1 ATCTACTGAAAAGCAAAAGAAATATGAAAAGGTACCTACCACTTT
30199505 CTTTTAAGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (45 bp):
ATCTACTGAAAAGCAAAAGAAATATGAAAAGGTACCTACCACTTT
Found at i:30205280 original size:26 final size:27
Alignment explanation
Indices: 30205244--30205309 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
30205234 AAAATAAAAT
*
30205244 TTTACCAAAATATTAT-CCTTTTTTTA
1 TTTACCAAAATATTATACATTTTTTTA
*
30205270 TTTACCAAAATATTATATATTTTTTTA
1 TTTACCAAAATATTATACATTTTTTTA
* *
30205297 ATTACGAAAATAT
1 TTTACCAAAATAT
30205310 ATCAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 16 0.46
27 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTACCAAAATATTATACATTTTTTTA
Found at i:30205292 original size:27 final size:26
Alignment explanation
Indices: 30205244--30205313 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
30205234 AAAATAAAAT
*
30205244 TTTACCAAAATATTATCCTTTTTTTA
1 TTTACCAAAATATTATCATTTTTTTA
*
30205270 TTTACCAAAATATTATATATTTTTTTA
1 TTTACCAAAATATTAT-CATTTTTTTA
* *
30205297 ATTACGAAAATA-TATCA
1 TTTACCAAAATATTATCA
30205314 AAAAAACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
25 1 0.03
26 19 0.50
27 18 0.47
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (26 bp):
TTTACCAAAATATTATCATTTTTTTA
Found at i:30205464 original size:4 final size:4
Alignment explanation
Indices: 30205455--30205640 Score: 113
Period size: 4 Copynumber: 45.8 Consensus size: 4
30205445 GAAGGAGAGG
* *
30205455 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAAA GGAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GA-AA GAAA GAAA
* * * *
30205506 GAAA -AAG GAAA GAAAA GGAAG GAGAG GAAA GAAA GAAA -AAG GAAA GGAGAA
1 GAAA GAAA GAAA G-AAA -GAAA GA-AA GAAA GAAA GAAA GAAA GAAA -GA-AA
30205557 -AAA -AAA GAAA G-AA G-AA GAAGA GGAAA GGAGAA GAAA -AAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA -GA-AA GAAA GAAA GAAA
* *
30205600 G-AA -AAA GAAA GAAA GAAA GAAA G-GA GAAGA GAAA AAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAA
30205641 GAAGAAGAAG
Statistics
Matches: 150, Mismatches: 12, Indels: 40
0.74 0.06 0.20
Matches are distributed among these distances:
3 24 0.16
4 86 0.57
5 31 0.21
6 9 0.06
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:30205502 original size:39 final size:39
Alignment explanation
Indices: 30205457--30205654 Score: 146
Period size: 41 Copynumber: 5.1 Consensus size: 39
30205447 AGGAGAGGGA
30205457 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGGAAGGAG
1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGGAAGGAG
*
30205496 -AG---GAAAGAAAGAAA-AAGGAAAGAAAAGGAAGGAG
1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGGAAGGAG
* * * * *
30205530 AGGAAAGAAAGAAAAAGGAAAG-GAGAAAAAAAAGAAAGAAG
1 AAGAAAGAAAG--AAA-GAAAGAAAGAAAGAAAAGGAAGGAG
* *
30205571 AAGAAGAGGAAAGGAGAAGAAA-AAAGAAAGAAAAAGAAAGA-
1 AAGAA-A-GAAA-GA-AAGAAAGAAAGAAAGAAAAGGAAGGAG
* * *
30205612 AAGAAAGAAAG-GAGAAGAGAAAAAAAGAAGAA-GAAGAAG
1 AAGAAAGAAAGAAAGAA-AGAAAGAAAGAA-AAGGAAGGAG
30205651 AAGA
1 AAGA
30205655 GGGGAGGAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 34
0.70 0.10 0.19
Matches are distributed among these distances:
34 19 0.15
35 13 0.10
36 4 0.03
37 1 0.01
38 21 0.17
39 10 0.08
40 4 0.03
41 27 0.22
42 18 0.15
43 6 0.05
44 1 0.01
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (39 bp):
AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGGAAGGAG
Found at i:30205503 original size:19 final size:19
Alignment explanation
Indices: 30205479--30205539 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
30205469 AAGAAAGAAA
30205479 GAAAGAAAAGGAAGGAGAG
1 GAAAGAAAAGGAAGGAGAG
*
30205498 GAAAG-AAA-GAA--AAAG
1 GAAAGAAAAGGAAGGAGAG
30205513 GAAAGAAAAGGAAGGAGAG
1 GAAAGAAAAGGAAGGAGAG
30205532 GAAAGAAA
1 GAAAGAAA
30205540 GAAAAAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 8 0.22
16 3 0.08
17 6 0.17
18 3 0.08
19 16 0.44
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAGGAAGGAGAG
Found at i:30205522 original size:34 final size:34
Alignment explanation
Indices: 30205463--30205551 Score: 160
Period size: 34 Copynumber: 2.6 Consensus size: 34
30205453 GGGAAAGAAA
*
30205463 GAAAGAAAGAAAGAAAGAAAGAAAAGGAAGGAGAG
1 GAAAGAAAGAAA-AAGGAAAGAAAAGGAAGGAGAG
30205498 GAAAGAAAGAAAAAGGAAAGAAAAGGAAGGAGAG
1 GAAAGAAAGAAAAAGGAAAGAAAAGGAAGGAGAG
30205532 GAAAGAAAGAAAAAGGAAAG
1 GAAAGAAAGAAAAAGGAAAG
30205552 GAGAAAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 41 0.77
35 12 0.23
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (34 bp):
GAAAGAAAGAAAAAGGAAAGAAAAGGAAGGAGAG
Found at i:30205540 original size:23 final size:23
Alignment explanation
Indices: 30205513--30205593 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 23
30205503 AAAGAAAAAG
30205513 GAAAGAAAAGGAAGGAGAGGAAA
1 GAAAGAAAAGGAAGGAGAGGAAA
30205536 GAAAGAAAAAGGAAAGGAGA--AAA
1 GAAAG-AAAAGG-AAGGAGAGGAAA
* * *
30205559 AAAAGAAAGAAGAAGAAGAGGAAA
1 GAAAGAAA-AGGAAGGAGAGGAAA
30205583 GGAGAAGAAAA
1 -GA-AAGAAAA
30205594 AAGAAAGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
22 9 0.19
23 14 0.30
24 9 0.19
25 9 0.19
26 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAAGAAAAGGAAGGAGAGGAAA
Found at i:30205543 original size:57 final size:56
Alignment explanation
Indices: 30205473--30205646 Score: 155
Period size: 57 Copynumber: 3.1 Consensus size: 56
30205463 GAAAGAAAGA
*
30205473 AAGAAAGAAAGAAAAGG-AAGGAGAGGAAAGAAAGAAA-AAGGAAAGAAAAGG-AAGGAG
1 AAGAAAGAAAGAAAAGGAAAGGAGA--AAAAAAAGAAAGAA-G-AAGAAAAGGAAAGGAG
* *
30205530 AGGAAAGAAAGAAAAAGGAAAGGAGAAAAAAAAGAAAGAAGAAGAAGAGGAAAGGAG
1 AAGAAAGAAAG-AAAAGGAAAGGAGAAAAAAAAGAAAGAAGAAGAAAAGGAAAGGAG
* * * * *
30205587 AAGAAA-AAAG-AAAGAAAAAGA-AAGAAAGAAAGAAAGGAGAAGAGAAA-AAAAGAAG
1 AAGAAAGAAAGAAAAGGAAAGGAGAA-AAA-AAAGAAAGAAGAAGA-AAAGGAAAGGAG
30205642 AAGAA
1 AAGAA
30205647 GAAGAAGAGG
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
53 2 0.02
54 12 0.12
55 25 0.25
56 14 0.14
57 32 0.32
58 8 0.08
59 7 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (56 bp):
AAGAAAGAAAGAAAAGGAAAGGAGAAAAAAAAGAAAGAAGAAGAAAAGGAAAGGAG
Found at i:30205571 original size:3 final size:3
Alignment explanation
Indices: 30205565--30205654 Score: 53
Period size: 3 Copynumber: 29.3 Consensus size: 3
30205555 AAAAAAAAGA
* * *
30205565 AAG AAG AAG AAG AGG AAAG GAG AAG AA- AA- AAG AAAG AAA AAG AAAG
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG -AAG AAG AAG -AAG
* *
30205611 AAAG AAAG AAAG GAG AAG -AG AA- AAA AAG AAG AAG AAG AAG AAG A
1 -AAG -AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
30205655 GGGGAGGAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
2 8 0.11
3 44 0.61
4 20 0.28
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:30205646 original size:34 final size:34
Alignment explanation
Indices: 30205461--30205646 Score: 112
Period size: 34 Copynumber: 5.1 Consensus size: 34
30205451 GAGGGAAAGA
* * *
30205461 AAGAAAGAAAGAAAGAAAGAA-AGAAAAGGAAGGAG
1 AAGAAAGAAAGAAAG-GAGAAGAGAAAA-AAAGAAG
* ** *
30205496 AGGAAAGAAAGAAAAAGGA-AAGA-AAAGGAAGGAG
1 AAGAAAGAAAG--AAAGGAGAAGAGAAAAAAAGAAG
*
30205530 AGGAAAGAAAGAAAAAGGA-AAGGAGAAAAAAAAGAAAG
1 AAGAAAGAAAG--AAAGGAGAA-GAG-AAAAAAAG-AAG
*
30205568 AAG-AAGAAGAGGAAAGGAGAAGAAAAAAGAAAGAAAAAG
1 AAGAAAGAA-A-GAAAGGAGAAGAGAAAA-AAAG---AAG
30205607 AAAGAAAGAAAGAAAGGAGAAGAGAAAAAAAGAAG
1 -AAGAAAGAAAGAAAGGAGAAGAGAAAAAAAGAAG
30205642 AAGAA
1 AAGAA
30205647 GAAGAAGAGG
Statistics
Matches: 127, Mismatches: 9, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
34 33 0.26
35 20 0.16
36 6 0.05
37 27 0.21
38 11 0.09
39 21 0.17
40 4 0.03
41 5 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (34 bp):
AAGAAAGAAAGAAAGGAGAAGAGAAAAAAAGAAG
Found at i:30205649 original size:22 final size:22
Alignment explanation
Indices: 30205590--30205651 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
30205580 AAAGGAGAAG
*
30205590 AAAAAAGAAAGAAAAAGAA-AGA
1 AAAAAAG-AAGAAGAAGAAGAGA
* *
30205612 AAGAAAG-A-AAGGAGAAGAGA
1 AAAAAAGAAGAAGAAGAAGAGA
30205632 AAAAAAGAAGAAGAAGAAGA
1 AAAAAAGAAGAAGAAGAAGA
30205652 AGAGGGGAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 6 0.19
20 10 0.31
21 1 0.03
22 15 0.47
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAGAAGAAGAAGAGA
Found at i:30205810 original size:26 final size:26
Alignment explanation
Indices: 30205736--30205819 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 26
30205726 TTAAAAATTT
* *
30205736 ATGTTATTTATATTATACGTATTTTAA
1 ATGTTATGTACATTATACGTATTTT-A
* *
30205763 TATTTTATTTAGCA-TATA--TATTTTA
1 -ATGTTATGTA-CATTATACGTATTTTA
30205788 ATGTTATGTACATTATACGTA-TTT-
1 ATGTTATGTACATTATACGTATTTTA
30205812 ATGTTATG
1 ATGTTATG
30205820 GTATGTACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.04
24 20 0.42
25 4 0.08
26 8 0.17
28 13 0.27
29 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (26 bp):
ATGTTATGTACATTATACGTATTTTA
Found at i:30206405 original size:22 final size:23
Alignment explanation
Indices: 30206377--30206427 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
30206367 TTGATTTACC
30206377 AAAAAA-TTATATTTTGATAAAT
1 AAAAAATTTATATTTTGATAAAT
*
30206399 AAAAAATTTATATTTTGATAACT
1 AAAAAATTTATATTTTGATAAAT
30206422 AAAAAA
1 AAAAAA
30206428 AAGTTATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAAAATTTATATTTTGATAAAT
Found at i:30206815 original size:37 final size:35
Alignment explanation
Indices: 30206731--30206797 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
30206721 TAATAAGTTT
* *
30206731 ATAAAATTAGAAATTATGATATTTTTTAAAATATC
1 ATAAAATGAGAAATTATGATATTTTTTAAAAAATC
* *
30206766 ATAAAATTAGAAATTATGATATTTTTTTAAAA
1 ATAAAATGAGAAATTATGATATTTTTTAAAAA
30206798 GAATAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.43
Consensus pattern (35 bp):
ATAAAATGAGAAATTATGATATTTTTTAAAAAATC
Found at i:30209538 original size:27 final size:27
Alignment explanation
Indices: 30209508--30209560 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
30209498 TAAAATTGCA
30209508 CCATTGGTGCCGCCAATGGCATTGGCG
1 CCATTGGTGCCGCCAATGGCATTGGCG
30209535 CCATTGGTGCCGCCAATGGCATTGGC
1 CCATTGGTGCCGCCAATGGCATTGGC
30209561 CTGACCCGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.32, T:0.23
Consensus pattern (27 bp):
CCATTGGTGCCGCCAATGGCATTGGCG
Done.