Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 17 of 21
Found at i:1907504 original size:2 final size:2
Alignment explanation
Indices: 1907497--1907524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1907487 CTTTCTACGA
1907497 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1907525 GTGTGGGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1909422 original size:25 final size:24
Alignment explanation
Indices: 1909358--1909422 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 24
1909348 TTTAATTAAA
1909358 TTTATAAGTTTAATTAATAATTTATT
1 TTTATAA-TTT-ATTAATAATTTATT
*
1909384 TTTATTAAAGTTATTAA-AACTTTATT
1 TTTA-T-AATTTATTAATAA-TTTATT
1909410 TTATATAATTTAT
1 TT-TATAATTTAT
1909423 AATTAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
25 8 0.24
26 18 0.55
27 5 0.15
28 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTATAATTTATTAATAATTTATT
Found at i:1909461 original size:20 final size:20
Alignment explanation
Indices: 1909429--1909491 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 20
1909419 TTATAATTAA
1909429 ATTTAAA-TAAAAATATATT
1 ATTTAAATTAAAAATATATT
1909448 ATTTAAATTAAAAAT-TATT
1 ATTTAAATTAAAAATATATT
*
1909467 ATTTAAAATT--AAATAAATT
1 ATTT-AAATTAAAAATATATT
1909486 ATTTAA
1 ATTTAA
1909492 TTTTTAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.15
19 22 0.55
20 12 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAATTAAAAATATATT
Found at i:1909500 original size:25 final size:22
Alignment explanation
Indices: 1909425--1909488 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 22
1909415 TAATTTATAA
1909425 TTAAATTTAAATAAAAATATATTA-T
1 TTAAA-TTAAAT--AAAT-TATTATT
1909450 TTAAATT-AA-AAATTATTATT
1 TTAAATTAAATAAATTATTATT
*
1909470 TAAAATTAAATAAATTATT
1 TTAAATTAAATAAATTATT
1909489 TAATTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 2 0.06
22 8 0.23
23 2 0.06
24 2 0.06
25 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAATTAAATAAATTATTATT
Found at i:1909950 original size:22 final size:22
Alignment explanation
Indices: 1909925--1909991 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1909915 ACTGATGCGT
*
1909925 TATTGTTTTTAAATTTTTATTA
1 TATTATTTTTAAATTTTTATTA
* * *
1909947 TATTAATTTTAAA-ATATATATA
1 TATTATTTTTAAATTTTTAT-TA
1909969 TATTATATTTTAAATATTTTATT
1 TATTAT-TTTTAAAT-TTTTATT
1909992 TAAATTACAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 4 0.12
22 18 0.53
23 7 0.21
24 1 0.03
25 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
TATTATTTTTAAATTTTTATTA
Found at i:1910027 original size:12 final size:12
Alignment explanation
Indices: 1909968--1910037 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
1909958 AAATATATAT
1909968 ATATTATATTTTAA
1 ATATTATA-TTT-A
*
1909982 ATATTTTATTTA
1 ATATTATATTTA
*
1909994 A-ATTACATCTTTA
1 ATATT--ATATTTA
*
1910007 CA-ATCATATTTA
1 -ATATTATATTTA
1910019 ATATTATATTTA
1 ATATTATATTTA
1910031 ATATTAT
1 ATATTAT
1910038 TAAATTTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 4 0.09
12 24 0.52
13 8 0.17
14 10 0.22
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:1910216 original size:18 final size:20
Alignment explanation
Indices: 1910193--1910255 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1910183 AATTTGCGTG
1910193 TTTATATTT-ATATTAT-TT
1 TTTATATTTAATATTATATT
1910211 TTTATATTTAAAATATTATATT
1 TTTATATTT--AATATTATATT
1910233 TTTATATATTAATAATTA-ATT
1 TTTATAT-TTAAT-ATTATATT
1910254 TT
1 TT
1910256 ATTTCATGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.23
21 15 0.38
22 13 0.33
23 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATATTTAATATTATATT
Found at i:1910250 original size:22 final size:22
Alignment explanation
Indices: 1910195--1910255 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1910185 TTTGCGTGTT
*
1910195 TATATTTAT-ATTAT-TTTTTA
1 TATATTAATAATTATATTTTTA
*
1910215 TAT-TTAAAATATTATATTTTTA
1 TATATTAATA-ATTATATTTTTA
1910237 TATATTAATAATTA-ATTTT
1 TATATTAATAATTATATTTT
1910256 ATTTCATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 10 0.29
22 13 0.38
23 5 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATTAATAATTATATTTTTA
Found at i:1910257 original size:20 final size:22
Alignment explanation
Indices: 1910202--1910244 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1910192 GTTTATATTT
1910202 ATATTAT-TTTTTATATTTAAA
1 ATATTATATTTTTATATTTAAA
1910223 ATATTATATTTTTATATATTAA
1 ATATTATATTTTTATAT-TTAA
1910245 TAATTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATATTTTTATATTTAAA
Found at i:1911189 original size:19 final size:19
Alignment explanation
Indices: 1911159--1911204 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
1911149 AATTATTATT
1911159 TAATA-AAATTTATT-TT-A
1 TAATATAAATTT-TTATTAA
1911176 TAAT-TAAATTTTTATTAA
1 TAATATAAATTTTTATTAA
1911194 TAATATAAATT
1 TAATATAAATT
1911205 AACTACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 12 0.48
18 5 0.20
19 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATAAATTTTTATTAA
Found at i:1911480 original size:14 final size:11
Alignment explanation
Indices: 1911447--1911485 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1911437 CACATGATAT
1911447 TTATTTTTATA
1 TTATTTTTATA
1911458 TTATTTTTATA
1 TTATTTTTATA
*
1911469 TTATGTTT-T-
1 TTATTTTTATA
1911478 TTATTTTT
1 TTATTTTT
1911486 CGTATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 7 0.27
10 1 0.04
11 18 0.69
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:1912059 original size:10 final size:10
Alignment explanation
Indices: 1912046--1912075 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1912036 TATAATTTAA
1912046 TATTATTATT
1 TATTATTATT
1912056 TATTATTATT
1 TATTATTATT
1912066 TATT-TTATT
1 TATTATTATT
1912075 T
1 T
1912076 TTAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTATTATT
Found at i:1912062 original size:13 final size:13
Alignment explanation
Indices: 1912029--1912070 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1912019 TAAATAAATT
*
1912029 TTTATTA-TATAA
1 TTTATTATTATTA
*
1912041 TTTAATATTATTA
1 TTTATTATTATTA
1912054 TTTATTATTATTTA
1 TTTATTATTA-TTA
1912068 TTT
1 TTT
1912071 TATTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 6 0.24
13 13 0.52
14 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:1912436 original size:14 final size:12
Alignment explanation
Indices: 1912411--1912448 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1912401 AAAAATAATT
1912411 ATATAATTAAAA
1 ATATAATTAAAA
1912423 ATATAATTAAAA
1 ATATAATTAAAA
* *
1912435 AAATGA-TAAAA
1 ATATAATTAAAA
1912446 ATA
1 ATA
1912449 GTATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
ATATAATTAAAA
Found at i:1913097 original size:12 final size:12
Alignment explanation
Indices: 1913063--1913099 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
1913053 TATTTTTATT
1913063 TTTTTAATTTAAA
1 TTTTTAA-TTAAA
1913076 TTTTT-A-TAAA
1 TTTTTAATTAAA
1913086 TTTTTAATTAAA
1 TTTTTAATTAAA
1913098 TT
1 TT
1913100 GATTCCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
12 7 0.32
13 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTAATTAAA
Found at i:1913227 original size:17 final size:19
Alignment explanation
Indices: 1913183--1913228 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
1913173 AAATATTTTA
*
1913183 AAATAATTTTAATATAAAGT
1 AAATAA-TTAAATATAAAGT
1913203 AAAT-ATTAAATAT-AA-T
1 AAATAATTAAATATAAAGT
1913219 AAATAATTAA
1 AAATAATTAA
1913229 TAAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 5 0.21
17 7 0.29
18 7 0.29
19 1 0.04
20 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATAATTAAATATAAAGT
Found at i:1913553 original size:9 final size:9
Alignment explanation
Indices: 1913539--1913564 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1913529 CGTCAGAAAC
1913539 AGTTATATT
1 AGTTATATT
1913548 AGTTATATT
1 AGTTATATT
1913557 AGTTATAT
1 AGTTATAT
1913565 ATCTTAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (9 bp):
AGTTATATT
Found at i:1915283 original size:26 final size:25
Alignment explanation
Indices: 1915185--1915284 Score: 69
Period size: 25 Copynumber: 3.8 Consensus size: 25
1915175 ATCTAAATTC
* *
1915185 ATATTAATTTGAATTTTATTTTATTATT
1 ATATTAA-TT-AAATTTATTTTATTA-A
1915213 ATATT-ATTAAATATTATTTTAATT-A
1 ATATTAATTAAAT-TTATTTT-ATTAA
* **
1915238 ATATTTAAATAAAAATATTTTATTAA
1 ATA-TTAATTAAATTTATTTTATTAA
* *
1915264 ATATTAATTTAATTTAATTTA
1 ATATTAATTAAATTTATTTTA
1915285 ATTTAAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
25 22 0.39
26 21 0.37
27 9 0.16
28 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
ATATTAATTAAATTTATTTTATTAA
Found at i:1916716 original size:18 final size:16
Alignment explanation
Indices: 1916693--1916731 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1916683 TCCCTCCTCT
1916693 CCTCCTACACCGCCACCG
1 CCTCCTACACCG--ACCG
*
1916711 CCTCCTCCACCGACCG
1 CCTCCTACACCGACCG
1916727 CCTCC
1 CCTCC
1916732 AACCTCCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.13, C:0.64, G:0.10, T:0.13
Consensus pattern (16 bp):
CCTCCTACACCGACCG
Found at i:1916722 original size:12 final size:12
Alignment explanation
Indices: 1916705--1916765 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
1916695 TCCTACACCG
1916705 CCACCGCCTCCT
1 CCACCGCCTCCT
*
1916717 CCACCGACCGCCT
1 CCACCG-CCTCCT
*
1916730 CCAACCTCCTCCT
1 CC-ACCGCCTCCT
* * *
1916743 CCTCCACCTCCG
1 CCACCGCCTCCT
*
1916755 CCTCCGCCTCC
1 CCACCGCCTCC
1916766 ACCGTCTCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
12 23 0.57
13 14 0.35
14 3 0.08
ACGTcount: A:0.10, C:0.66, G:0.08, T:0.16
Consensus pattern (12 bp):
CCACCGCCTCCT
Found at i:1916753 original size:15 final size:15
Alignment explanation
Indices: 1916727--1916831 Score: 77
Period size: 15 Copynumber: 6.5 Consensus size: 15
1916717 CCACCGACCG
1916727 CCTCCAACCTCCTCCT
1 CCTCC-ACCTCCTCCT
*
1916743 CCTCCACCTCCGCCTCCG
1 CCTCCACCT---CCTCCT
1916761 CCTCCACCGT-CTCCT
1 CCTCCACC-TCCTCCT
*
1916776 CCTCCACCACCGCTCCT
1 CCTCCACC-TC-CTCCT
* *
1916793 CCACGCACCGCCTCCT
1 CCTC-CACCTCCTCCT
* *
1916809 CCACCACCGCCTCCT
1 CCTCCACCTCCTCCT
1916824 CCTCCACC
1 CCTCCACC
1916832 CCCAAAGAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
15 34 0.45
16 14 0.19
17 9 0.12
18 17 0.23
19 1 0.01
ACGTcount: A:0.10, C:0.65, G:0.07, T:0.18
Consensus pattern (15 bp):
CCTCCACCTCCTCCT
Found at i:1916765 original size:47 final size:46
Alignment explanation
Indices: 1916677--1916769 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 46
1916667 TCCCAACGCC
** *
1916677 ACCGCCTCCCTCCTCTCCTCCTACACCGCCACCGCCTCCTCCACCG
1 ACCGCCTCCAACCTCTCCTCCTACACCGCCACCGCCGCCTCCACCG
* * * *
1916723 ACCGCCTCCAACCTCCTCCTCCTCCACCTCCGCCTCCGCCTCCACCG
1 ACCGCCTCCAACCT-CTCCTCCTACACCGCCACCGCCGCCTCCACCG
1916770 TCTCCTCCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 12 0.31
47 27 0.69
ACGTcount: A:0.11, C:0.63, G:0.09, T:0.17
Consensus pattern (46 bp):
ACCGCCTCCAACCTCTCCTCCTACACCGCCACCGCCGCCTCCACCG
Found at i:1916776 original size:18 final size:18
Alignment explanation
Indices: 1916735--1916794 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
1916725 CGCCTCCAAC
1916735 CTCCTCCTCCTCCACC-T
1 CTCCTCCTCCTCCACCGT
* *
1916752 CCGCCTCCGCCTCCACCGT
1 -CTCCTCCTCCTCCACCGT
*
1916771 CTCCTCCTCCACCACCG-
1 CTCCTCCTCCTCCACCGT
1916788 CTCCTCC
1 CTCCTCC
1916795 ACGCACCGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.19
18 28 0.78
19 1 0.03
ACGTcount: A:0.07, C:0.65, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCTCCTCCTCCACCGT
Found at i:1919060 original size:17 final size:17
Alignment explanation
Indices: 1919025--1919074 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1919015 AATATTTTTA
*
1919025 ATAAAA-ATTATTAATAT
1 ATAAAACATTAATAA-AT
*
1919042 ATTAAAC-TTATATAAAT
1 ATAAAACATTA-ATAAAT
1919059 ATAAAACATTAATAAA
1 ATAAAACATTAATAAA
1919075 AAAAATCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAACATTAATAAAT
Found at i:1919281 original size:16 final size:16
Alignment explanation
Indices: 1919239--1919283 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1919229 GATTAATTTA
1919239 ATTTATAAAA-TTTTT
1 ATTTATAAAATTTTTT
* *
1919254 ATGATATTAAATTTTTT
1 AT-TTATAAAATTTTTT
1919271 ATTTATAAAATTT
1 ATTTATAAAATTT
1919284 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.08
16 15 0.62
17 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTATAAAATTTTTT
Found at i:1919528 original size:15 final size:15
Alignment explanation
Indices: 1919502--1919545 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1919492 AATCCAATTT
*
1919502 TTAATATTAATTTTAA
1 TTAAT-TTAATTTAAA
1919518 TTAATTTAATTTAAA
1 TTAATTTAATTTAAA
* *
1919533 TCAAATTAATTTA
1 TTAATTTAATTTA
1919546 TTATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATTTAATTTAAA
Found at i:1922532 original size:54 final size:54
Alignment explanation
Indices: 1922450--1922557 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1922440 TATATGAGCT
* * *
1922450 GGAGAAAGGCCTACTATGGCCACAACTGGTCTCTGTTAGGAGTCAAGATAAGAA
1 GGAGAAAGGCCCACCATGGCCACAACTGGTCCCTGTTAGGAGTCAAGATAAGAA
1922504 GGAGAAAGGCCCACCATGGCCACAACTGGTCCCTGTTAGGAGTCAAGATAAGAA
1 GGAGAAAGGCCCACCATGGCCACAACTGGTCCCTGTTAGGAGTCAAGATAAGAA
1922558 ATAGAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (54 bp):
GGAGAAAGGCCCACCATGGCCACAACTGGTCCCTGTTAGGAGTCAAGATAAGAA
Found at i:1924409 original size:225 final size:229
Alignment explanation
Indices: 1924066--1924640 Score: 638
Period size: 225 Copynumber: 2.5 Consensus size: 229
1924056 AACGTCTACG
* * * * * * * *
1924066 AGGACTCCACCCTCCGCTTGGTTCTTCGTCTTCGTGGTGACATGCAAATATTCGTCAAACTCTCA
1 AGGAGTCCACCCTCCACCTGGTGCTTCGTCTTCGAGGTGGCATGCAAATATTTGTCAAACCCTCA
* * * * * * * * *
1924131 CCGGAAAGACGATTACCTTGGAGGTCGAAAGCTCTGACGCTATTGATAATGTCAAGTCTAAGATC
66 CTGGAAAGACAATTACCTTGGAGGTTGAGAGTTCTGACACCATTGATAATGTCAAGGCAAAGATC
* * * * * *
1924196 CAAGATAATGAAGGAATCCCCCCTGAGCAAC-AGA-GGCTTATCTTTGCTGG-AAGCAGCTTGAA
131 CAAGACAAGGAAGGAATCCCACCGGACCAACTAGATGGCTAATCTTTGCTGGAAAGCAGCTTGAA
* * * *
1924258 GAGGGCCGCACATTGGC-AATTATTACATCCAGA
196 GAGGGCCGCACACTAGCGAACTATAACATCCAGA
* * *
1924291 AGGAGTCTACCCTCCACCTGGTGCTTCGTCTTCGAGGTGGCGTGCAAATTTTTGTCAAACCCTCA
1 AGGAGTCCACCCTCCACCTGGTGCTTCGTCTTCGAGGTGGCATGCAAATATTTGTCAAACCCTCA
* * * * *
1924356 CTGGCAAGACCATTACCCTT-GAAGTTTAGAGTTCTGACACCATTGACAATGTCAAGGCAAAGAT
66 CTGGAAAGACAATTA-CCTTGGAGGTTGAGAGTTCTGACACCATTGATAATGTCAAGGCAAAGAT
* * * * *
1924420 TCAAGACAAGGAAGGGATCCCACCGGACCAGCTTGAAGATGGCTAATTTTTGTTGGAAAGCAGCT
130 CCAAGACAAGGAAGGAATCCCACCGGACCAAC-T--AGATGGCTAATCTTTGCTGGAAAGCAGCT
* * * *
1924485 TGAAGATGGCTGCACCCTAGCGGACTATAACATCCAGA
192 TGAAGAGGGCCGCACACTAGCGAACTATAACATCCAGA
* *
1924523 AGGAGTCCACCCTCCACCTCGTGCTTCGTCTTCGATGTGGCATGCAAATATTTGTCAAGACCCTC
1 AGGAGTCCACCCTCCACCTGGTGCTTCGTCTTCGAGGTGGCATGCAAATATTTGTCAA-ACCCTC
* *
1924588 ACTGGAAAGATAATTACCTTGGAGGTTGAGAGTTCTGATACCATTGATAATGT
65 ACTGGAAAGACAATTACCTTGGAGGTTGAGAGTTCTGACACCATTGATAATGT
1924641 GAAAGCCAAA
Statistics
Matches: 285, Mismatches: 55, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
225 124 0.44
226 4 0.01
229 3 0.01
230 13 0.05
231 24 0.08
232 70 0.25
233 47 0.16
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (229 bp):
AGGAGTCCACCCTCCACCTGGTGCTTCGTCTTCGAGGTGGCATGCAAATATTTGTCAAACCCTCA
CTGGAAAGACAATTACCTTGGAGGTTGAGAGTTCTGACACCATTGATAATGTCAAGGCAAAGATC
CAAGACAAGGAAGGAATCCCACCGGACCAACTAGATGGCTAATCTTTGCTGGAAAGCAGCTTGAA
GAGGGCCGCACACTAGCGAACTATAACATCCAGA
Found at i:1924946 original size:227 final size:227
Alignment explanation
Indices: 1924603--1925067 Score: 497
Period size: 228 Copynumber: 2.0 Consensus size: 227
1924593 AAAGATAATT
* * * * * *
1924603 ACCTTGGAGGTTGAGAGTTCTGATACCATTGATAATGTGAAAGCCAAAATTCAGGACAAAGAAGC
1 ACCTTGGAGGTTGAAAGTTCAGACACCATCGACAATGTGAAAGCCAAAATCCAGGACAAAGAAGC
* * * ** * * * *
1924668 ATTCCACCATACCAGCAAAGACTGATTTTTGCGGGAAAACACCTTGAAGATGGAAGGAC-TCTTA
66 ATACCACCAGACCAGCAAAGACTCACCTTTGCAGGAAAACAACTCGAAGATGGAAGGACGTC-GA
** * * * * * * * * *
1924732 TTGATTATAACATCTAGAAGGAGT-AACTCTACATTTGGT-TCTCCGCCTTCGTGGTGGTATGCA
130 CCGACTACAACATCCAAAAGGAGTCAACCCTACACTGGGTGT-TCCGCCTTCGTGGCGGGATGCA
*
1924795 GATCTTCGTGGAGACCTTAACCAGAAAAACGATC
194 GATCTTCGTGAAGACCTTAACCAGAAAAACGATC
* *
1924829 ACCTTGGAGGTTGAAAGTTCAGACACCATCGACAATGTGAAAG-CAAAGATCCAGGACAAGGAGG
1 ACCTTGGAGGTTGAAAGTTCAGACACCATCGACAATGTGAAAGCCAAA-ATCCAGGACAAAGA-A
* * * * *
1924893 GTATACCCCCAGACCAGCAAAGACTCACCTTTGCAGGCAAGCAACTCGAAGATGGGAGGACGTCG
64 GCATACCACCAGACCAGCAAAGACTCACCTTTGCAGGAAAACAACTCGAAGATGGAAGGACGTCG
* * * **
1924958 GCCGACTACAATATCCAAAAGGAGTCAACCCTTCACTGGGTGTTGTGCCTTCGTGGCGGGATGCA
129 ACCGACTACAACATCCAAAAGGAGTCAACCCTACACTGGGTGTTCCGCCTTCGTGGCGGGATGCA
*
1925023 GATCTTCGTGAAGACCTTAACCAGAAAGACGATC
194 GATCTTCGTGAAGACCTTAACCAGAAAAACGATC
*
1925057 ACTTTGGAGGT
1 ACCTTGGAGGT
1925068 CGAATATATG
Statistics
Matches: 193, Mismatches: 41, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
225 4 0.02
226 50 0.26
227 65 0.34
228 73 0.38
229 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (227 bp):
ACCTTGGAGGTTGAAAGTTCAGACACCATCGACAATGTGAAAGCCAAAATCCAGGACAAAGAAGC
ATACCACCAGACCAGCAAAGACTCACCTTTGCAGGAAAACAACTCGAAGATGGAAGGACGTCGAC
CGACTACAACATCCAAAAGGAGTCAACCCTACACTGGGTGTTCCGCCTTCGTGGCGGGATGCAGA
TCTTCGTGAAGACCTTAACCAGAAAAACGATC
Found at i:1926410 original size:18 final size:17
Alignment explanation
Indices: 1926383--1926416 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1926373 TAAATTTTAA
1926383 TTTATAATAATAAATTT
1 TTTATAATAATAAATTT
1926400 TTTATTAATAATAAATT
1 TTTA-TAATAATAAATT
1926417 ATAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATAATAATAAATTT
Found at i:1926410 original size:21 final size:20
Alignment explanation
Indices: 1926373--1926416 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1926363 TTAATTAAAT
*
1926373 TAAATTTTAATTTATAATAA
1 TAAATTTTAATTAATAATAA
*
1926393 TAAATTTT--TTATTAATAA
1 TAAATTTTAATTAATAATAA
1926411 TAAATT
1 TAAATT
1926417 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
20 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATTTTAATTAATAATAA
Found at i:1926474 original size:25 final size:23
Alignment explanation
Indices: 1926399--1926474 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 23
1926389 ATAATAAATT
1926399 TTTTATTAATAATAAATTATAAAA
1 TTTTATTAA-AATAAATTATAAAA
1926423 TTTTAAATTAAAATAAAATT-TAAAAA
1 TTTT--ATTAAAAT-AAATTAT-AAAA
1926449 TTTTATTAACAATAAATTATATAAA
1 TTTTATTAA-AATAAATTATA-AAA
1926474 T
1 T
1926475 CTTCTAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
24 15 0.33
25 12 0.27
26 18 0.40
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTTATTAAAATAAATTATAAAA
Found at i:1926662 original size:17 final size:18
Alignment explanation
Indices: 1926631--1926664 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1926621 TTTTTAAATA
*
1926631 AAAACTATATTATTTTTG
1 AAAACTATATCATTTTTG
1926649 AAAA-TATATCATTTTT
1 AAAACTATATCATTTTT
1926665 CCAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
AAAACTATATCATTTTTG
Found at i:1926864 original size:2 final size:2
Alignment explanation
Indices: 1926857--1926885 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1926847 AATTTAATCT
1926857 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1926886 TTCTTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1927378 original size:58 final size:58
Alignment explanation
Indices: 1927315--1927481 Score: 230
Period size: 58 Copynumber: 2.9 Consensus size: 58
1927305 TAATAATTCG
*
1927315 TATATTC-ATATTATATTTTTATTATTTTTTATATATTATTATCATGTTTAAAATTTTA
1 TATATTCGA-ATTATATTTTTATTATTTTTTATATATTATTATTATGTTTAAAATTTTA
* * *
1927373 TATATTCGAATTGTATTTTTATTATTTTTTACATATTATTATTGTGTTTAAAATTTTA
1 TATATTCGAATTATATTTTTATTATTTTTTATATATTATTATTATGTTTAAAATTTTA
* * ** *
1927431 TATATTCGAATCATATTCTTATTA-TTTTCGTATATTATTATTAAGTTTAAA
1 TATATTCGAATTATATTTTTATTATTTTTTATATATTATTATTATGTTTAAA
1927482 GTTTAAAACA
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
57 22 0.23
58 73 0.76
59 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (58 bp):
TATATTCGAATTATATTTTTATTATTTTTTATATATTATTATTATGTTTAAAATTTTA
Found at i:1927744 original size:2 final size:2
Alignment explanation
Indices: 1927737--1927767 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1927727 TTATACCTCA
*
1927737 AT AT AT AT CT 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
1927768 GACTTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1928099 original size:2 final size:2
Alignment explanation
Indices: 1928092--1928133 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1928082 TTCTTGGTTA
1928092 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1928134 AGTCCTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1928315 original size:18 final size:19
Alignment explanation
Indices: 1928272--1928315 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1928262 AATTTCAAAA
*
1928272 TAATATTGTAATATTAATTT
1 TAATATTG-AATATTAATAT
*
1928292 TTATATTG-ATATTAATAT
1 TAATATTGAATATTAATAT
1928310 TAATAT
1 TAATAT
1928316 AAATTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
20 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TAATATTGAATATTAATAT
Found at i:1928373 original size:15 final size:16
Alignment explanation
Indices: 1928354--1928392 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1928344 TAAATTTAAC
1928354 TAATTTAAATTAAAAA
1 TAATTTAAATTAAAAA
* *
1928370 -AATTTTATTTAAAAA
1 TAATTTAAATTAAAAA
1928385 TAATTTAA
1 TAATTTAA
1928393 TACGAGTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTAAATTAAAAA
Found at i:1928688 original size:21 final size:21
Alignment explanation
Indices: 1928639--1928692 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
1928629 ATATTTATCA
1928639 TTAAATTTAAATAAAAATAATT
1 TTAAA-TTAAATAAAAATAATT
* *
1928661 TTTAATTACATAAATAATAA-T
1 TTAAATTAAATAAA-AATAATT
1928682 TTAAATTAAAT
1 TTAAATTAAAT
1928693 TAATTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATTAAATAAAAATAATT
Found at i:1929925 original size:31 final size:33
Alignment explanation
Indices: 1929867--1929929 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
1929857 GAAATATAAA
* *
1929867 ATTATTTTATTATTTTTTGTATCTTTAAATTTTT
1 ATTATTTTATAATTATTTGTA-CTTTAAATTTTT
1929901 ATTATTTTATAATTATTT-TA-TTTAAATTT
1 ATTATTTTATAATTATTTGTACTTTAAATTT
1929930 AATCCAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 9 0.33
33 2 0.07
34 16 0.59
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (33 bp):
ATTATTTTATAATTATTTGTACTTTAAATTTTT
Found at i:1930471 original size:177 final size:177
Alignment explanation
Indices: 1930165--1930508 Score: 422
Period size: 177 Copynumber: 1.9 Consensus size: 177
1930155 TGGAAACGAC
* * * * *
1930165 AATCAGTTTGAAGATCAGAATCCAAATGCTTGTCAGCCAGCTGTCGATGTATCACAGTGTAATAA
1 AATCAGTTTGAAGATCAGAATCCAAATGCTTGGCAGCCAACTGTCGATGCATCACAGTATAACAA
* * *
1930230 TGAAACATCTTTAACGGCTGGAAACAGTAGTATTGCGGTGTCTGAATATCAGAATTCGAATGCTT
66 TGAAACATCTTTAACGGCTGGAAACAATAGTATTGCGGCGTCTGAATATCAGAATTCAAATGCTT
* *
1930295 CTCCTCGGCAATCTGTTGATGGAGCTTCTTTAATGGCTCGAAACAAT
131 CTCCTCGGCAAGCTGTTAATGGAGCTTCTTTAATGGCTCGAAACAAT
** * * *
1930342 AATCAGTTTGAAGATTGGAATCCGAATGCTTGGCAGCCAACTTTTGATGCATCACAGTATAACAA
1 AATCAGTTTGAAGATCAGAATCCAAATGCTTGGCAGCCAACTGTCGATGCATCACAGTATAACAA
* * * ** * *
1930407 T-AAAGCGTCTTTAATGGCTGGGAACAATGAG-ATTGTTGCGTCTGAATATCCGTATTCAAATGC
66 TGAAA-CATCTTTAACGGCTGGAAACAAT-AGTATTGCGGCGTCTGAATATCAGAATTCAAATGC
* * * *
1930470 TTTTTCTTGGCAAGCTGTTAATGGAGCTTCTTTCATGGC
129 TTCTCCTCGGCAAGCTGTTAATGGAGCTTCTTTAATGGC
1930509 AAGGAACAAT
Statistics
Matches: 139, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
176 3 0.02
177 134 0.96
178 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (177 bp):
AATCAGTTTGAAGATCAGAATCCAAATGCTTGGCAGCCAACTGTCGATGCATCACAGTATAACAA
TGAAACATCTTTAACGGCTGGAAACAATAGTATTGCGGCGTCTGAATATCAGAATTCAAATGCTT
CTCCTCGGCAAGCTGTTAATGGAGCTTCTTTAATGGCTCGAAACAAT
Found at i:1930598 original size:81 final size:82
Alignment explanation
Indices: 1930415--1930599 Score: 212
Period size: 84 Copynumber: 2.2 Consensus size: 82
1930405 AATAAAGCGT
* * * * * *
1930415 CTTTAATGGCTGGGAACAATGAGATTGTTGCGTCTGAATATCCGTATTCAAATGCTTTTTCTTGG
1 CTTTAATGGCT-GGAACAATAAGATTGCTGCGTCTGAATATCAGAATTCAAATGCTCTTTC-TAG
**
1930480 CAAGCTGTTAATGGAGCTT
64 CAAGCTGTTAATGGAGCAC
* * * *
1930499 CTTTCATGGCAAGGAACAATAATATTGCTGCGTCTGAATATCAGAATTCGAATGC-CTTTC-AGC
1 CTTTAATGGC-TGGAACAATAAGATTGCTGCGTCTGAATATCAGAATTCAAATGCTCTTTCTAGC
1930562 AAGCTGTTAATGGAGCAC
65 AAGCTGTTAATGGAGCAC
1930580 CTTTAATGGCTGGAAACAAT
1 CTTTAATGGCTGG-AACAAT
1930600 TCGAATGCTT
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
80 2 0.02
81 33 0.39
83 4 0.05
84 46 0.54
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (82 bp):
CTTTAATGGCTGGAACAATAAGATTGCTGCGTCTGAATATCAGAATTCAAATGCTCTTTCTAGCA
AGCTGTTAATGGAGCAC
Found at i:1930628 original size:57 final size:54
Alignment explanation
Indices: 1930543--1930652 Score: 166
Period size: 57 Copynumber: 2.0 Consensus size: 54
1930533 TGAATATCAG
1930543 AATTCGAATGCCTTTCAGCAAGCTGTTAATGGAGCACCTTTAATGGCTGGAAAC
1 AATTCGAATGCCTTTCAGCAAGCTGTTAATGGAGCACCTTTAATGGCTGGAAAC
* * *
1930597 AATTCGAATGCTTCTTCTCGGCAAGCTGTTAATGGGGCATCTTTAATGGCTGGAAA
1 AATTCGAATGC--CTT-TCAGCAAGCTGTTAATGGAGCACCTTTAATGGCTGGAAA
1930653 AAATAATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
54 11 0.22
56 3 0.06
57 36 0.72
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (54 bp):
AATTCGAATGCCTTTCAGCAAGCTGTTAATGGAGCACCTTTAATGGCTGGAAAC
Found at i:1930746 original size:87 final size:87
Alignment explanation
Indices: 1930607--1931059 Score: 517
Period size: 87 Copynumber: 5.3 Consensus size: 87
1930597 AATTCGAATG
** * **
1930607 CTTCTTCTCGGCAAGCTGTTAATGGGGCATCTTTAATGGCTGGAAAAAATAATATTATTGGATCT
1 CTTCTTCTCGGCAAGCTGTTAATGAAGCATCTTCAATGGCTGGAAACTATAATATTATTGGATCT
* * *
1930672 GCATATCAGGATTCGAAAGCTT
66 GAATATCAGCATTCGAATGCTT
* * * *
1930694 CTTCTTCTCGGCAAGCTGTTAGTGCAGCATCTTCAATGGCTGAAAACTATAATATTATTGGGTCT
1 CTTCTTCTCGGCAAGCTGTTAATGAAGCATCTTCAATGGCTGGAAACTATAATATTATTGGATCT
*
1930759 GAATATCAGCATTTGAATGCTT
66 GAATATCAGCATTCGAATGCTT
* * * * *
1930781 CTTCTTCTTGGCAAGCGGTTAATGAAGCATCTTTAATGGATGGAAACTATATTATTATT-GAGTC
1 CTTCTTCTCGGCAAGCTGTTAATGAAGCATCTTCAATGGCTGGAAACTATAATATTATTGGA-TC
*
1930845 TGAATATCAGCATTTGAATGCTT
65 TGAATATCAGCATTCGAATGCTT
* * * * *
1930868 CTTCTTCTTGGCAGGCGGTTAATGAAGCATCTTCAATGGATGGAAACTATATTATTATT-GAGTC
1 CTTCTTCTCGGCAAGCTGTTAATGAAGCATCTTCAATGGCTGGAAACTATAATATTATTGGA-TC
* * *
1930932 TGAATATCGGTATCCGAATGCTT
65 TGAATATCAGCATTCGAATGCTT
* * * *
1930955 CTTCTTTTCGGCAAGCTGTTAATGGAGCATC-TC-----CTGGAAACTATAATATTGTTGGGTCT
1 CTTCTTCTCGGCAAGCTGTTAATGAAGCATCTTCAATGGCTGGAAACTATAATATTATTGGATCT
* *
1931014 GAATATAAGTATTCGAATGCTT
66 GAATATCAGCATTCGAATGCTT
* *
1931036 CTTCTCCTTGGCAAGCTGTTAATG
1 CTTCTTCTCGGCAAGCTGTTAATG
1931060 GGGCGTCTTT
Statistics
Matches: 322, Mismatches: 42, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
81 60 0.19
82 1 0.00
86 3 0.01
87 258 0.80
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (87 bp):
CTTCTTCTCGGCAAGCTGTTAATGAAGCATCTTCAATGGCTGGAAACTATAATATTATTGGATCT
GAATATCAGCATTCGAATGCTT
Found at i:1931753 original size:12 final size:12
Alignment explanation
Indices: 1931712--1931763 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
1931702 AGATTCAAAA
1931712 ATTTATATTAAT
1 ATTTATATTAAT
* *
1931724 ATTTAAAATAAT
1 ATTTATATTAAT
*
1931736 TTTTATATTAAT
1 ATTTATATTAAT
1931748 ATTTATAATTAA-
1 ATTTAT-ATTAAT
1931760 ATTT
1 ATTT
1931764 GAATATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 28 0.85
13 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATTAAT
Found at i:1931839 original size:21 final size:20
Alignment explanation
Indices: 1931780--1931845 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
1931770 AAATAGTTTT
*
1931780 ATTATTTAAATAATAATTTAAA
1 ATTATTAAAAT-ATAATTT-AA
* *
1931802 ATAAAATAAAATA-AATTTAA
1 AT-TATTAAAATATAATTTAA
*
1931822 ATTATTAAAATATTAATTCAA
1 ATTATTAAAATA-TAATTTAA
1931843 ATT
1 ATT
1931846 TAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 8 0.23
20 4 0.11
21 14 0.40
22 3 0.09
23 6 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATTAAAATATAATTTAA
Found at i:1931848 original size:11 final size:11
Alignment explanation
Indices: 1931815--1931897 Score: 61
Period size: 11 Copynumber: 7.9 Consensus size: 11
1931805 AAATAAAATA
1931815 AATTTAAA-TT
1 AATTTAAATTT
*
1931825 -ATTAAAATATT
1 AATTTAAAT-TT
*
1931836 AATTCAAATTT
1 AATTTAAATTT
1931847 AATTTAAA-TT
1 AATTTAAATTT
*
1931857 ATTTATAAATTT
1 AATT-TAAATTT
*
1931869 AATTTAAATAT
1 AATTTAAATTT
1931880 -A-TT-AATTT
1 AATTTAAATTT
*
1931888 AATTCAAATT
1 AATTTAAATT
1931898 ATAAATAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 4 0.07
9 9 0.16
10 7 0.12
11 25 0.44
12 12 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:1931869 original size:22 final size:21
Alignment explanation
Indices: 1931841--1931899 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
1931831 ATATTAATTC
1931841 AAATTTAATTTAAATTATTTAT
1 AAATTTAATTTAAATTA-TTAT
1931863 AAATTTAATTTAAA-TA-TAT
1 AAATTTAATTTAAATTATTAT
* *
1931882 TAATTTAATTCAAATTAT
1 AAATTTAATTTAAATTAT
1931900 AAATAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 15 0.45
20 2 0.06
21 2 0.06
22 14 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTAATTTAAATTATTAT
Found at i:1933235 original size:2 final size:2
Alignment explanation
Indices: 1933228--1933288 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1933218 AAGAAATTAA
1933228 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1933270 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1933289 ACTTTGAAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1940379 original size:22 final size:22
Alignment explanation
Indices: 1940354--1940397 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1940344 TTTTGATTTG
1940354 AATTAAATTA-ATAAAATTTAAT
1 AATTAAA-TAGATAAAATTTAAT
* *
1940376 AATTTAATAGATTAAATTTAAT
1 AATTAAATAGATAAAATTTAAT
1940398 GCCCCTCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAATAGATAAAATTTAAT
Found at i:1946325 original size:19 final size:22
Alignment explanation
Indices: 1946303--1946358 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
1946293 AGAATTTTGT
1946303 TATTTTTATA-T-TAA-TATTA
1 TATTTTTATATTATAATTATTA
*
1946322 TATTTATATATTATAATTATTA
1 TATTTTTATATTATAATTATTA
*
1946344 TA-TTTTAAATTATAA
1 TATTTTTATATTATAA
1946359 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 9 0.29
20 1 0.03
21 14 0.45
22 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTATATTATAATTATTA
Found at i:1946345 original size:22 final size:21
Alignment explanation
Indices: 1946317--1946358 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1946307 TTTATATTAA
*
1946317 TATTATATTTATATATTATAAT
1 TATTATATTT-TAAATTATAAT
1946339 TATTATATTTTAAATTATAA
1 TATTATATTTTAAATTATAA
1946359 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATATTTTAAATTATAAT
Found at i:1947299 original size:26 final size:29
Alignment explanation
Indices: 1947236--1947299 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1947226 ATCTTGGGTT
*
1947236 AAATAGATTAAAAATATATTTTTATTATTA
1 AAATA-ATTAAAAATATATTATTATTATTA
*
1947266 AATTTAATTAAAAAT-TATTATT-TTA-TA
1 AA-ATAATTAAAAATATATTATTATTATTA
1947293 AAATAAT
1 AAATAAT
1947300 AATTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 4 0.13
27 4 0.13
28 3 0.10
29 6 0.20
30 11 0.37
31 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
AAATAATTAAAAATATATTATTATTATTA
Found at i:1947302 original size:29 final size:31
Alignment explanation
Indices: 1947237--1947303 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
1947227 TCTTGGGTTA
* *
1947237 AATAGATTAAAAATATATTTTTATTATTAAAT
1 AATA-ATTAAAAATATATTATTATTATAAAAT
*
1947269 -TTAATTAAAAAT-TATTATT-TTATAAAAT
1 AATAATTAAAAATATATTATTATTATAAAAT
1947297 AATAATT
1 AATAATT
1947304 TTAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 9 0.30
31 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
AATAATTAAAAATATATTATTATTATAAAAT
Found at i:1949395 original size:24 final size:24
Alignment explanation
Indices: 1949349--1949395 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1949339 TTTTTTTAAG
* *
1949349 TTTAAAAATTATATTTTATAATAT
1 TTTAAAAATTATATTTAAAAATAT
* *
1949373 TTTAAAATTTTTATTTAAAAATA
1 TTTAAAAATTATATTTAAAAATA
1949396 AAATATTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAAAATTATATTTAAAAATAT
Found at i:1950273 original size:46 final size:47
Alignment explanation
Indices: 1950223--1950311 Score: 123
Period size: 46 Copynumber: 1.9 Consensus size: 47
1950213 ATTAAAATAT
1950223 TAAAAA-ATTATATATTAATATT-TATATTTTTAT-AA-TTAAATTTAAA
1 TAAAAATATTAT-TATTAA-ATTATA-ATTTTTATCAATTTAAATTTAAA
1950269 TAAAAATATTATTATTAAATTATAATTTTTATCAATTTAAATT
1 TAAAAATATTATTATTAAATTATAATTTTTATCAATTTAAATT
1950312 ATTAAAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
45 11 0.28
46 16 0.41
47 12 0.31
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (47 bp):
TAAAAATATTATTATTAAATTATAATTTTTATCAATTTAAATTTAAA
Found at i:1951910 original size:26 final size:24
Alignment explanation
Indices: 1951881--1951937 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 24
1951871 ATAATTTAGT
1951881 TTTAAGTTATCTAATAAAATAAATAA
1 TTTAA-TTATCTAATAAAATAAAT-A
*
1951907 TTTATATTATCTAATAAATTAAATA
1 TTTA-ATTATCTAATAAAATAAATA
1951932 TTTAAT
1 TTTAAT
1951938 AAGGTGGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 2 0.07
25 5 0.17
26 21 0.72
27 1 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTAATTATCTAATAAAATAAATA
Found at i:1952056 original size:20 final size:20
Alignment explanation
Indices: 1951998--1952096 Score: 64
Period size: 19 Copynumber: 5.5 Consensus size: 20
1951988 TATATATATC
*
1951998 ATATTT-TATAATATTATAAT
1 ATATTTATATAAAATT-TAAT
1952018 -TATTT-TA-AAATATTT--T
1 ATATTTATATAAA-ATTTAAT
1952034 ATATTTATATAAAATTTAAT
1 ATATTTATATAAAATTTAAT
1952054 ATA-TTA-AT--AA-TT-A-
1 ATATTTATATAAAATTTAAT
*
1952067 ATA-TTATATAAATTTTAAT
1 ATATTTATATAAAATTTAAT
1952086 ATATTTATATA
1 ATATTTATATA
1952097 TTAATTATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 6 0.09
14 3 0.05
15 2 0.03
16 4 0.06
17 7 0.11
18 12 0.19
19 19 0.30
20 11 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTATATAAAATTTAAT
Found at i:1952068 original size:7 final size:8
Alignment explanation
Indices: 1952049--1952105 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
1952039 TATATAAAAT
1952049 TTAATATA
1 TTAATATA
1952057 TTAATA-A
1 TTAATATA
1952064 TTAATATTA
1 TTAATA-TA
*
1952073 TATAA-ATT
1 T-TAATATA
1952081 TTAATATA
1 TTAATATA
*
1952089 TTTATATA
1 TTAATATA
1952097 TTAAT-TA
1 TTAATATA
1952104 TT
1 TT
1952106 TTTTATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 14 0.34
8 21 0.51
9 3 0.07
10 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTAATATA
Found at i:1952075 original size:32 final size:33
Alignment explanation
Indices: 1952038--1952101 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1952028 TATTTTATAT
1952038 TTATATAAAATTTAATATATTAATA-ATTAATA
1 TTATATAAAATTTAATATATTAATATATTAATA
* *
1952070 TTATATAAATTTTAATATATTTATATATTAAT
1 TTATATAAAATTTAATATATTAATATATTAAT
1952102 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TTATATAAAATTTAATATATTAATATATTAATA
Found at i:1953228 original size:15 final size:15
Alignment explanation
Indices: 1953194--1953280 Score: 61
Period size: 15 Copynumber: 5.6 Consensus size: 15
1953184 TTTTATTATT
* *
1953194 TTAAATTTAAATTATT
1 TTAATTTTAAATTA-A
*
1953210 TTAATTTTAATTTAA
1 TTAATTTTAAATTAA
* *
1953225 TTAA-ATTAAAATAA
1 TTAATTTTAAATTAA
1953239 TTAAAGTTATTAAATTTAA
1 TT-AA-TT-TTAAA-TTAA
1953258 TT-ATTTTAAATTAA
1 TTAATTTTAAATTAA
*
1953272 TTTATTTTA
1 TTAATTTTA
1953281 GTTTCACGAG
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
14 15 0.26
15 17 0.30
16 14 0.25
17 1 0.02
18 5 0.09
19 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
TTAATTTTAAATTAA
Found at i:1954132 original size:35 final size:37
Alignment explanation
Indices: 1954093--1954192 Score: 100
Period size: 39 Copynumber: 2.7 Consensus size: 37
1954083 GATTATTGTT
1954093 TAAA-TAATAAAAATATTTTT-ATTTAAAT-TTAATTA
1 TAAATTAATAAAAATATTTTTAATTTAAATATT-ATTA
* *
1954128 TAAATATTAATATAAAATATTTTTAATTTTAATATTATTT
1 T-AA-ATTAATA-AAAATATTTTTAATTTAAATATTATTA
* *
1954168 TAAATTAATATAAAT-TTTTAAATTT
1 TAAATTAATAAAAATATTTTTAATTT
1954193 TTACTTAAGC
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
35 1 0.02
36 11 0.20
37 5 0.09
38 12 0.22
39 13 0.24
40 11 0.20
41 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TAAATTAATAAAAATATTTTTAATTTAAATATTATTA
Found at i:1954290 original size:17 final size:18
Alignment explanation
Indices: 1954268--1954301 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1954258 TTTATATGTG
1954268 TAAATAAAAT-TTTATTT
1 TAAATAAAATATTTATTT
1954285 TAAATAAAATATTTATT
1 TAAATAAAATATTTATT
1954302 CATATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATAAAATATTTATTT
Found at i:1954774 original size:32 final size:29
Alignment explanation
Indices: 1954712--1954788 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 29
1954702 TTTTATTTTT
*
1954712 AATTATATTTTAATATTTTTAAAAATATA
1 AATTATTTTTTAATATTTTTAAAAATATA
*
1954741 AATTATTTTATTAATCTTATTTATAAAATATA
1 AATTATTTT-TTAATATT-TTTA-AAAATATA
1954773 AA-TATTTGATTTAATA
1 AATTATTT--TTTAATA
1954789 ATGTATAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 8 0.20
30 7 0.17
31 9 0.22
32 15 0.38
33 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
AATTATTTTTTAATATTTTTAAAAATATA
Found at i:1955129 original size:2 final size:2
Alignment explanation
Indices: 1955122--1955149 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1955112 AGCCCTTTTA
1955122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1955150 TTAACGGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1955389 original size:19 final size:19
Alignment explanation
Indices: 1955353--1955390 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1955343 TATATATTAA
*
1955353 TTTTATATTCATATTATTT
1 TTTTATATTCATAATATTT
*
1955372 TTTTATATTTATAATATTT
1 TTTTATATTCATAATATTT
1955391 AAAAAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATATTCATAATATTT
Found at i:1956855 original size:21 final size:21
Alignment explanation
Indices: 1956816--1956869 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1956806 ATTATATTTT
* * *
1956816 TTATTTATATTAATTTAAATTA
1 TTATTTA-AATAATATAAAATA
1956838 TTATTTAAATAATATAAAATA
1 TTATTTAAATAATATAAAATA
*
1956859 TT-TTTATATAA
1 TTATTTAAATAA
1956870 ATTTAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 8 0.29
21 13 0.46
22 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTTAAATAATATAAAATA
Found at i:1956889 original size:21 final size:21
Alignment explanation
Indices: 1956863--1956909 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
1956853 AAAATATTTT
1956863 TATATAAAT-TTAATTATAAAA
1 TATATAAATATTAA-TATAAAA
1956884 TATATAAATATTAATATAAAA
1 TATATAAATATTAATATAAAA
*
1956905 AATAT
1 TATAT
1956910 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:1956974 original size:20 final size:20
Alignment explanation
Indices: 1956949--1956990 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1956939 AATTTAAACA
1956949 AAAAAATTAAATAAAAATTT
1 AAAAAATTAAATAAAAATTT
* * *
1956969 AAAAAATTTAATTATAATTT
1 AAAAAATTAAATAAAAATTT
1956989 AA
1 AA
1956991 TCTATAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTAAATAAAAATTT
Found at i:1961252 original size:16 final size:16
Alignment explanation
Indices: 1961231--1961300 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
1961221 ATCAAAAAAT
1961231 TATAATATAAAATTTA
1 TATAATATAAAATTTA
* *
1961247 TATAAT-T-TAA-TTC
1 TATAATATAAAATTTA
1961260 TAT-AT-TAAAATTTA
1 TATAATATAAAATTTA
*
1961274 TATAAATATAAAATATTT
1 TAT-AATATAAAAT-TTA
1961292 TA-AATATAA
1 TATAATATAA
1961301 TTATATTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 3 0.07
13 7 0.16
14 7 0.16
15 1 0.02
16 15 0.35
17 6 0.14
18 4 0.09
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAATATAAAATTTA
Found at i:1961294 original size:27 final size:27
Alignment explanation
Indices: 1961238--1961295 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1961228 AATTATAATA
* **
1961238 TAAAATTTATATAATTTAATTCTATAT
1 TAAAATTTATATAATATAATAATATAT
*
1961265 TAAAATTTATATAAATATAA-AATATTT
1 TAAAATTTATAT-AATATAATAATATAT
1961292 TAAA
1 TAAA
1961296 TATAATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATTTATATAATATAATAATATAT
Found at i:1966789 original size:12 final size:11
Alignment explanation
Indices: 1966772--1966802 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1966762 GTAAAAAAAA
1966772 TTAAAAAGTAT
1 TTAAAAAGTAT
1966783 TTAAAAAGTAT
1 TTAAAAAGTAT
1966794 TTAAAAAGT
1 TTAAAAAGT
1966803 GGTTACCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (11 bp):
TTAAAAAGTAT
Found at i:1967150 original size:2 final size:2
Alignment explanation
Indices: 1967143--1967177 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1967133 AATCCAATTA
1967143 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1967178 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1969241 original size:23 final size:21
Alignment explanation
Indices: 1969193--1969241 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
1969183 TATAAAGATA
**
1969193 AAATTTTAAAAATATTTTAAT
1 AAATTTTAAAAATATTCAAAT
1969214 AAATTTTAAATAATAATTCAAAT
1 AAATTTTAAA-AAT-ATTCAAAT
1969237 AAATT
1 AAATT
1969242 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTTTAAAAATATTCAAAT
Found at i:1969269 original size:21 final size:21
Alignment explanation
Indices: 1969228--1969271 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1969218 TTTAAATAAT
*
1969228 AATTCAAATAAATTATATTTA
1 AATTCAAATAAATAATATTTA
*
1969249 AATTTAAATAAA-AATACTTTA
1 AATTCAAATAAATAATA-TTTA
1969270 AA
1 AA
1969272 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTCAAATAAATAATATTTA
Found at i:1969473 original size:23 final size:21
Alignment explanation
Indices: 1969447--1969491 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
1969437 ATATATAAAA
1969447 ATTTTAAAATAATATATATTTAT
1 ATTTTAAAAT--TATATATTTAT
* *
1969470 ATTTTTAAATTATGTATTTAT
1 ATTTTAAAATTATATATTTAT
1969491 A
1 A
1969492 ACGCAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTAAAATTATATATTTAT
Found at i:1969688 original size:2 final size:2
Alignment explanation
Indices: 1969681--1969710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1969671 ACAACACCGC
1969681 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1969711 ATTTTCTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1970216 original size:2 final size:2
Alignment explanation
Indices: 1970209--1970242 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1970199 GAGTTTCATA
1970209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1970243 TCATTCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1970787 original size:190 final size:190
Alignment explanation
Indices: 1970464--1970845 Score: 613
Period size: 190 Copynumber: 2.0 Consensus size: 190
1970454 TGATTTGCCT
* * *
1970464 AGAAATGGAAATTCACAGTAAAATTAAGACTAATTTCTTTATTTAGCGCCGATTAACTGCCAGTT
1 AGAAATGGAAATTCACAGTAAAATTAAGACTAATTGCTTTATTTAGCGCCAATTAACGGCCAGTT
*
1970529 GTTTGAATCAATTGTTTAATGAGGGGCATCATTACTGCAAAATCTTGTAGTTCTAAATAAATGTA
66 GTTTAAATCAATTGTTTAATGAGGGGCATCATTACTGCAAAATCTTGTAGTTCTAAATAAATGTA
* * * *
1970594 CTCTATCGCTTTAGGTATTACGTTATTAATTTAATCATGCATTTAAAATGTCAGTCTTAG
131 CTCTATCGCTTTAGGTATTACATTATTAATTTAATCATACATTTAAAATGCCAATCTTAG
* **
1970654 AGAAATGGAAATTCACAGTAACATTATA-ACTAATTGCTTTATTTAGCGCCAATTAACGGCTGGT
1 AGAAATGGAAATTCACAGTAAAATTA-AGACTAATTGCTTTATTTAGCGCCAATTAACGGCCAGT
*
1970718 TGTTTAAATCAATTGTTTAATGGGGGGCATCATTACTGCAAAATCTTGTAGTTCTAAATAAATGT
65 TGTTTAAATCAATTGTTTAATGAGGGGCATCATTACTGCAAAATCTTGTAGTTCTAAATAAATGT
* * *
1970783 ACTCTATTGCTTTAGGTATTACATTATTAATTTAATCATACTTTTTAAATGCCAATCTTAG
130 ACTCTATCGCTTTAGGTATTACATTATTAATTTAATCATACATTTAAAATGCCAATCTTAG
1970844 AG
1 AG
1970846 CAAAAGTTTG
Statistics
Matches: 176, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
190 175 0.99
191 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (190 bp):
AGAAATGGAAATTCACAGTAAAATTAAGACTAATTGCTTTATTTAGCGCCAATTAACGGCCAGTT
GTTTAAATCAATTGTTTAATGAGGGGCATCATTACTGCAAAATCTTGTAGTTCTAAATAAATGTA
CTCTATCGCTTTAGGTATTACATTATTAATTTAATCATACATTTAAAATGCCAATCTTAG
Found at i:1974259 original size:6 final size:7
Alignment explanation
Indices: 1974243--1974275 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1974233 TTTTCTTTTT
1974243 AAATATAA
1 AAAT-TAA
1974251 AAATTAA
1 AAATTAA
1974258 AAATTAA
1 AAATTAA
1974265 AAATTAA
1 AAATTAA
1974272 AAAT
1 AAAT
1974276 ATTATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATTAA
Found at i:1974265 original size:14 final size:15
Alignment explanation
Indices: 1974243--1974277 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
1974233 TTTTCTTTTT
1974243 AAATATAAAAATTAA
1 AAATATAAAAATTAA
1974258 AAAT-TAAAAATTAA
1 AAATATAAAAATTAA
1974272 AAATAT
1 AAATAT
1974278 TATATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATAAAAATTAA
Found at i:1974944 original size:16 final size:18
Alignment explanation
Indices: 1974923--1974957 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1974913 AATATTTATA
1974923 TTTTAT-TTATA-ATATT
1 TTTTATATTATATATATT
1974939 TTTTATATTATATATATT
1 TTTTATATTATATATATT
1974957 T
1 T
1974958 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATATTATATATATT
Found at i:1974961 original size:31 final size:33
Alignment explanation
Indices: 1974910--1974999 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 33
1974900 TTAGTTATAA
1974910 TTAA-ATATT-TATAT-TTTATTTATAAT-ATT
1 TTAATATATTATATATATTTATTTATAATAATT
* *
1974939 TT-TTATATTATATATATTTATTTTTAATAAATT
1 TTAATATATTATATATATTTATTTATAAT-AATT
*
1974972 TTAATATATTTATATTAAATTTATTTAT
1 TTAATATA-TTATA-TATATTTATTTAT
1975000 GAGTAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 7 0.15
30 5 0.10
31 11 0.23
33 5 0.10
34 4 0.08
35 5 0.10
36 11 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTAATATATTATATATATTTATTTATAATAATT
Found at i:1974964 original size:21 final size:19
Alignment explanation
Indices: 1974913--1974964 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
1974903 GTTATAATTA
1974913 AATATTTATATTTTATTTAT
1 AATATTTAT-TTTTATTTAT
*
1974933 AATATTT-TTTATA-TTAT
1 AATATTTATTTTTATTTAT
1974950 ATATATTTATTTTTA
1 A-ATATTTATTTTTA
1974965 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 10 0.36
19 6 0.21
20 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
AATATTTATTTTTATTTAT
Found at i:1974997 original size:25 final size:26
Alignment explanation
Indices: 1974940--1974997 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
1974930 TATAATATTT
* * *
1974940 TTTATATTATATATATTTATTTTTAA
1 TTTATTTTATATATATTTATATTAAA
**
1974966 TAAATTTTA-ATATATTTATATTAAA
1 TTTATTTTATATATATTTATATTAAA
1974991 TTTATTT
1 TTTATTT
1974998 ATGAGTAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATTTTATATATATTTATATTAAA
Found at i:1975063 original size:12 final size:12
Alignment explanation
Indices: 1975033--1975104 Score: 58
Period size: 12 Copynumber: 5.9 Consensus size: 12
1975023 TATAAAATTT
1975033 TTATT-TAAAT-
1 TTATTATAAATA
1975043 TTAATTATAAATA
1 TT-ATTATAAATA
* *
1975056 TTAGTATAAAAA
1 TTATTATAAATA
*
1975068 TTATTTTTAATATA
1 TTA-TTATAA-ATA
*
1975082 TTATTTTAAATA
1 TTATTATAAATA
*
1975094 TTAATATAAAT
1 TTATTATAAAT
1975105 TCAATTTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 28 0.56
13 12 0.24
14 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (12 bp):
TTATTATAAATA
Found at i:1976243 original size:3 final size:3
Alignment explanation
Indices: 1976235--1976273 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1976225 TCTTCGCTTT
1976235 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1976274 ATTTTTTGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1976607 original size:2 final size:2
Alignment explanation
Indices: 1976600--1976634 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1976590 GAAGTCAGAA
1976600 AT AT 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 AT AT A
1976635 AATAAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1983157 original size:9 final size:9
Alignment explanation
Indices: 1983136--1983173 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1983126 TTGATAAAAA
1983136 TTAATTATAT
1 TTAATTA-AT
*
1983146 TTAATTTAT
1 TTAATTAAT
1983155 TT-ATTAAT
1 TTAATTAAT
1983163 TTAATTAAT
1 TTAATTAAT
1983172 TT
1 TT
1983174 TATAAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTAATTAAT
Found at i:1983166 original size:17 final size:17
Alignment explanation
Indices: 1983139--1983187 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1983129 ATAAAAATTA
1983139 ATTATATTTAATTTATTT
1 ATTA-ATTTAATTTATTT
*
1983157 ATTAATTTAATTAATTT
1 ATTAATTTAATTTATTT
*
1983174 -TATAAGTTAATTTA
1 AT-TAATTTAATTTA
1983188 AATGAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 1 0.04
17 22 0.81
18 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTAATTTAATTTATTT
Found at i:1983175 original size:22 final size:21
Alignment explanation
Indices: 1983135--1983210 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 21
1983125 ATTGATAAAA
*
1983135 ATTAATTATATTTAATTTATTT
1 ATTAATT-TAATTAATTTATTT
*
1983157 ATTAATTTAATTAATTT-TATA
1 ATTAATTTAATTAATTTAT-TT
* *
1983178 AGTTAATTTAAATGAATTTATTC
1 A-TTAATTT-AATTAATTTATTT
1983201 AGTTAATTTA
1 A-TTAATTTA
1983211 TAAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.02
21 11 0.24
22 15 0.33
23 18 0.39
24 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (21 bp):
ATTAATTTAATTAATTTATTT
Found at i:1983204 original size:23 final size:23
Alignment explanation
Indices: 1983148--1983210 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1983138 AATTATATTT
* *
1983148 AATTTATTTA-TTAATTT-AATT
1 AATTTATTAAGTTAATTTAAATG
1983169 AATTT-TATAAGTTAATTTAAATG
1 AATTTAT-TAAGTTAATTTAAATG
*
1983192 AATTTATTCAGTTAATTTA
1 AATTTATTAAGTTAATTTA
1983211 TAAATTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 7 0.20
22 7 0.20
23 19 0.54
24 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
AATTTATTAAGTTAATTTAAATG
Found at i:1983658 original size:2 final size:2
Alignment explanation
Indices: 1983651--1983676 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1983641 AAGAACTAGA
1983651 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1983677 GATGAAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1985751 original size:19 final size:19
Alignment explanation
Indices: 1985727--1985778 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1985717 TTAACTTGGA
1985727 ATATATAATAATTTATATT
1 ATATATAATAATTTATATT
*
1985746 ATATAT-ATATTATTATATT
1 ATATATAATAAT-TTATATT
1985765 ATA-ATAAT-ATTTAT
1 ATATATAATAATTTAT
1985779 GATATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 4 0.14
18 7 0.24
19 18 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATAATAATTTATATT
Found at i:1985828 original size:28 final size:28
Alignment explanation
Indices: 1985788--1985852 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1985778 TGATATTTTT
* * *
1985788 TATTTTTATAAATTTTAATAT-TTTAAA
1 TATTTATATAAATTTTAAAATATTCAAA
1985815 TATATTATATAAATTTTAAAATATTCAAA
1 TAT-TTATATAAATTTTAAAATATTCAAA
1985844 TATTTATAT
1 TATTTATAT
1985853 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 3 0.09
28 22 0.67
29 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TATTTATATAAATTTTAAAATATTCAAA
Found at i:1985874 original size:9 final size:9
Alignment explanation
Indices: 1985730--1985857 Score: 52
Period size: 9 Copynumber: 14.1 Consensus size: 9
1985720 ACTTGGAATA
1985730 TATAATAATT
1 TATAAT-ATT
* *
1985740 TATATTATA
1 TATAATATT
1985749 TAT-ATA-T
1 TATAATATT
*
1985756 TATTATATT
1 TATAATATT
1985765 ATAATAATATT
1 -T-ATAATATT
*
1985776 TATGATATT
1 TATAATATT
* * *
1985785 TTTTATTTT
1 TATAATATT
1985794 TATAA-ATT
1 TATAATATT
1985802 T-TAATATT
1 TATAATATT
1985810 T-TAAATATAT
1 TAT-AATAT-T
*
1985820 TATATAAATTT
1 TATA-ATA-TT
*
1985831 TAAAATATT
1 TATAATATT
*
1985840 CA-AATATT
1 TATAATATT
*
1985848 TATATTATT
1 TATAATATT
1985857 T
1 T
1985858 TTTATATAAT
Statistics
Matches: 89, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.07
8 20 0.22
9 36 0.40
10 12 0.13
11 14 0.16
12 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (9 bp):
TATAATATT
Found at i:1986857 original size:15 final size:15
Alignment explanation
Indices: 1986837--1986903 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1986827 TAAATACTTA
*
1986837 AATTATAATAATTAT
1 AATTATAATAAATAT
* *
1986852 ATTTATTATAAATAT
1 AATTATAATAAATAT
*
1986867 AATTATTATTATAAT-T
1 AATTA-TAATA-AATAT
*
1986883 AATTATAATTAA-A-
1 AATTATAATAAATAT
1986896 AATTATAA
1 AATTATAA
1986904 AATTCAACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 19 0.46
16 9 0.22
17 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTATAATAAATAT
Found at i:1986859 original size:18 final size:19
Alignment explanation
Indices: 1986838--1986893 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
1986828 AAATACTTAA
1986838 ATTATAATAATTATAT-TT
1 ATTATAATAATTATATATT
*
1986856 ATTATAA-ATATAAT-TATT
1 ATTATAATA-ATTATATATT
1986874 ATTATAATTAATTATA-ATT
1 ATTATAA-TAATTATATATT
1986893 A
1 A
1986894 AAAATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 2 0.06
18 20 0.65
19 8 0.26
20 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATAATAATTATATATT
Found at i:1986878 original size:21 final size:22
Alignment explanation
Indices: 1986844--1986893 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1986834 TTAAATTATA
*
1986844 ATAATTATATTTATTA-TAAAT
1 ATAATTATATTTATAATTAAAT
*
1986865 ATAATTAT-TATTATAATTAATT
1 ATAATTATAT-TTATAATTAAAT
1986887 ATAATTA
1 ATAATTA
1986894 AAAATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTATATTTATAATTAAAT
Found at i:1987386 original size:21 final size:22
Alignment explanation
Indices: 1987360--1987438 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 22
1987350 TTGAAAAAAT
1987360 TTAAATTTAAATTAATT-ATTA
1 TTAAATTTAAATTAATTAATTA
*
1987381 TTAAATTT-AAGTAATTTAATTAA
1 TTAAATTTAAATTAA-TTAATT-A
* * *
1987404 TTATATTTAAA-TATTTAAATA
1 TTAAATTTAAATTAATTAATTA
*
1987425 TTTAATTTAAATTA
1 TTAAATTTAAATTA
1987439 TTTATAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 5 0.11
21 20 0.43
22 10 0.21
23 10 0.21
24 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TTAAATTTAAATTAATTAATTA
Found at i:1987399 original size:30 final size:30
Alignment explanation
Indices: 1987363--1987451 Score: 87
Period size: 30 Copynumber: 2.9 Consensus size: 30
1987353 AAAAAATTTA
*
1987363 AATTTAAATTAATTATTATTAAATTTAAGT
1 AATTTAAATTAATTATTATTAAATTTAAAT
1987393 AATTT-AATTAATTA-TATTTAAATATTTAAAT
1 AATTTAAATTAATTATTA-TT-AA-ATTTAAAT
*
1987424 -ATTTAATTTAAATTATT-TATAAATTTAA
1 AATTTAAATT-AATTATTAT-TAAATTTAA
1987452 TTAAATTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
28 2 0.04
29 11 0.22
30 17 0.34
31 13 0.26
32 6 0.12
33 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
AATTTAAATTAATTATTATTAAATTTAAAT
Found at i:1987440 original size:22 final size:22
Alignment explanation
Indices: 1987358--1987463 Score: 87
Period size: 22 Copynumber: 4.9 Consensus size: 22
1987348 GCTTGAAAAA
* *
1987358 ATTTAAATTTAAATTAATT-ATT
1 ATTT-AATTTAAATTATTTAAAT
* * * *
1987380 ATTAAATTTAAGTAATTTAATT
1 ATTTAATTTAAATTATTTAAAT
*
1987402 AATTATATTTAAA-TATTTAAAT
1 ATTTA-ATTTAAATTATTTAAAT
1987424 ATTTAATTTAAATTATTTATAA-
1 ATTTAATTTAAATTATTTA-AAT
1987446 ATTTAA-TTAAATT-TTTAA
1 ATTTAATTTAAATTATTTAA
1987464 TTAATATTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.01
20 4 0.06
21 25 0.36
22 32 0.46
23 8 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
ATTTAATTTAAATTATTTAAAT
Found at i:1987455 original size:21 final size:21
Alignment explanation
Indices: 1987361--1987462 Score: 58
Period size: 21 Copynumber: 5.0 Consensus size: 21
1987351 TGAAAAAATT
1987361 TAAATTTAAATT-AATTA-TTA
1 TAAATTT-AATTAAATTATTTA
* *
1987381 TTAAATTTAAGT-AA-T-TTAA
1 -TAAATTTAATTAAATTATTTA
* *
1987400 TTAATTATATTTAAA-TATTTA
1 TAAATT-TAATTAAATTATTTA
*
1987421 -AATATTTAATTTAAATTATTTA
1 TAA-ATTT-AATTAAATTATTTA
1987443 TAAATTTAATTAAATT-TTTA
1 TAAATTTAATTAAATTATTTA
1987463 ATTAATATTG
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
18 5 0.08
19 6 0.09
20 14 0.22
21 28 0.43
22 10 0.15
23 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (21 bp):
TAAATTTAATTAAATTATTTA
Found at i:1987471 original size:61 final size:58
Alignment explanation
Indices: 1987355--1987479 Score: 141
Period size: 61 Copynumber: 2.1 Consensus size: 58
1987345 TTTGCTTGAA
*
1987355 AAAATTT-AA-ATTTAAATTAATTATTATTAAATTTAAGTAATTTAATTAATTATATTT
1 AAAATTTAAATATTTAAATTAATTATTATTAAATTTAAGTAATTT-ATTAATTATATTG
* *
1987412 AAATATTTAAATATTTAATTTAAATTATT-TATAAATTTAATTAAATTT-TTAATTAATATTG
1 AAA-ATTTAAATATTTAAATT-AATTATTAT-TAAATTTAAGT-AATTTATTAATT-ATATTG
1987473 AAAATTT
1 AAAATTT
1987480 TTAATTTCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
57 3 0.05
58 4 0.07
59 2 0.03
60 19 0.33
61 25 0.43
62 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (58 bp):
AAAATTTAAATATTTAAATTAATTATTATTAAATTTAAGTAATTTATTAATTATATTG
Found at i:1987496 original size:19 final size:18
Alignment explanation
Indices: 1987445--1987498 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1987435 ATTATTTATA
1987445 AATTTAAT-TAAATTTTT
1 AATTTAATGTAAATTTTT
* *
1987462 AATTAATATTGAAAATTTTT
1 AATT--TAATGTAAATTTTT
1987482 AATTTCAATGTAAATTT
1 AATTT-AATGTAAATTT
1987499 AAATAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 4 0.14
18 1 0.03
19 12 0.41
20 12 0.41
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
AATTTAATGTAAATTTTT
Found at i:1987568 original size:22 final size:23
Alignment explanation
Indices: 1987520--1987585 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1987510 TATTTTAAAT
* *
1987520 TAAATTTAAATTTCAAA--AAA-
1 TAAATTTTAATTTAAAATCAAAC
1987540 TAAATTTTAA-TTAAAATCAAAC
1 TAAATTTTAATTTAAAATCAAAC
*
1987562 TAAATTTTAATTTAAATTCAAAC
1 TAAATTTTAATTTAAAATCAAAC
1987585 T
1 T
1987586 TTACTTCATG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.13
20 9 0.23
21 3 0.08
22 10 0.26
23 12 0.31
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTTTAATTTAAAATCAAAC
Found at i:1987885 original size:24 final size:25
Alignment explanation
Indices: 1987863--1987907 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
1987853 AAATTTTATT
1987863 TATAAAAA-AATA-ATTA-AAATTA
1 TATAAAAATAATAGATTATAAATTA
1987885 TATAAAAATAATAGATTATAAAT
1 TATAAAAATAATAGATTATAAAT
1987908 AAAAAAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 4 0.20
25 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
TATAAAAATAATAGATTATAAATTA
Found at i:1988051 original size:2 final size:2
Alignment explanation
Indices: 1988039--1988072 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1988029 GATAATTAGA
*
1988039 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1988073 GAATGATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1988864 original size:17 final size:17
Alignment explanation
Indices: 1988817--1988878 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
1988807 TATAATATTT
1988817 AATTTATATTTAAAT-A
1 AATTTATATTTAAATAA
* *
1988833 AATATTAAATATAAATAA
1 AAT-TTATATTTAAATAA
*
1988851 AATTTTTATTTAAAATAA
1 AATTTATATTT-AAATAA
1988869 AATTT-TATTT
1 AATTTATATTT
1988879 GTTAGAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
16 3 0.08
17 20 0.53
18 15 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTATATTTAAATAA
Found at i:1989028 original size:20 final size:20
Alignment explanation
Indices: 1989003--1989040 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1988993 ATGGATGCCA
1989003 AGTTGCCAAGTCGAAAGTCC
1 AGTTGCCAAGTCGAAAGTCC
1989023 AGTTGCCAAGTCGAAAGT
1 AGTTGCCAAGTCGAAAGT
1989041 AAGTTGCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (20 bp):
AGTTGCCAAGTCGAAAGTCC
Found at i:1989244 original size:19 final size:21
Alignment explanation
Indices: 1989180--1989245 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 21
1989170 TATAAATCAA
1989180 TTTAATTTAAATATAATATTAAT
1 TTTAATTT--ATATAATATTAAT
* *
1989203 ATT-ATTTATATAA-ATTTAT
1 TTTAATTTATATAATATTAAT
1989222 TTTAATTTA-A-AATATTAAT
1 TTTAATTTATATAATATTAAT
1989241 TTTAA
1 TTTAA
1989246 AATTTAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.05
19 18 0.49
20 11 0.30
22 4 0.11
23 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATTTATATAATATTAAT
Found at i:1989251 original size:41 final size:41
Alignment explanation
Indices: 1989180--1989259 Score: 94
Period size: 41 Copynumber: 1.9 Consensus size: 41
1989170 TATAAATCAA
1989180 TTTAATTTAAATATAATATTAATATTATTT-ATATAAATTTAT
1 TTTAATTTAAATATAATATTAATA-TATTTAAT-TAAATTTAT
*
1989222 TTTAATTTAAAATATTAATTTTAA-A-ATTTAATTAAATT
1 TTTAATTT-AAATA-TAATATTAATATATTTAATTAAATT
1989260 GGTTAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
41 10 0.29
42 10 0.29
43 6 0.18
44 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
TTTAATTTAAATATAATATTAATATATTTAATTAAATTTAT
Found at i:1989313 original size:23 final size:23
Alignment explanation
Indices: 1989283--1989329 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1989273 AAATAATTAG
1989283 TTTAAATTT-ATTTATATTATATT
1 TTTAAATTTAATTTATATTA-ATT
*
1989306 TTTAAATTTAATTTTTATTAATT
1 TTTAAATTTAATTTATATTAATT
1989329 T
1 T
1989330 AATATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTAAATTTAATTTATATTAATT
Found at i:1989454 original size:25 final size:25
Alignment explanation
Indices: 1989407--1989469 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1989397 TATTTATTTT
1989407 TTATAT-A-ATAAAATTATATAATA
1 TTATATAATATAAAATTATATAATA
1989430 -TATATAAATATAAAATTA-ATAAATA
1 TTATAT-AATATAAAATTATAT-AATA
1989455 TTATATAAT-TAAAAT
1 TTATATAATATAAAAT
1989470 GTAAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 5 0.14
24 9 0.26
25 16 0.46
26 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TTATATAATATAAAATTATATAATA
Found at i:1989530 original size:14 final size:15
Alignment explanation
Indices: 1989508--1989536 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1989498 TATTGAAGTA
1989508 AAAATTTAATTTTTT
1 AAAATTTAATTTTTT
1989523 AAAA-TTAATTTTTT
1 AAAATTTAATTTTTT
1989537 GTTTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAAATTTAATTTTTT
Found at i:1992975 original size:24 final size:22
Alignment explanation
Indices: 1992943--1992986 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
1992933 AATTTATTAT
*
1992943 ATTACATATTCAATAAATATAAAA
1 ATTAAATATT-AAT-AATATAAAA
1992967 ATTAAATATTAATAATATAA
1 ATTAAATATTAATAATATAA
1992987 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTAAATATTAATAATATAAAA
Found at i:1993043 original size:22 final size:23
Alignment explanation
Indices: 1992995--1993050 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
1992985 AATTTTATTT
1992995 TTAAATTT-TTT-AATTATAATA
1 TTAAATTTATTTAAATTATAATA
**
1993016 AAAAATTTATTTAAATTAT-ATA
1 TTAAATTTATTTAAATTATAATA
*
1993038 TTAAATATATTTA
1 TTAAATTTATTTA
1993051 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.21
22 16 0.57
23 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAATTTATTTAAATTATAATA
Found at i:1993057 original size:17 final size:19
Alignment explanation
Indices: 1993031--1993069 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1993021 TTTATTTAAA
*
1993031 TTATATATT-AAATAT-AT
1 TTATAAATTAAAATATAAT
1993048 TTATAAATTAAAATATAAT
1 TTATAAATTAAAATATAAT
1993067 TTA
1 TTA
1993070 AAAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATAAATTAAAATATAAT
Found at i:1993153 original size:30 final size:32
Alignment explanation
Indices: 1993119--1993198 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 32
1993109 TATATTAATA
1993119 TTATATATATTTTTTAA-AATTTAAATAAAT-
1 TTATATATATTTTTTAATAATTTAAATAAATC
**
1993149 TTATAT-T-TTTAAATAATAATTTAAATAAATC
1 TTATATATATTT-TTTAATAATTTAAATAAATC
1993180 TTAATTAGTATATTTTTTA
1 TT-A-TA-TATATTTTTTA
1993199 TTCAAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
28 3 0.08
29 4 0.11
30 19 0.50
31 2 0.05
32 1 0.03
33 2 0.05
34 1 0.03
35 3 0.08
36 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TTATATATATTTTTTAATAATTTAAATAAATC
Done.