Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 18 of 18
Found at i:3370292 original size:19 final size:21
Alignment explanation
Indices: 3370264--3370313 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
3370254 AAATTATTAT
3370264 TATT-TTTTATTTTT-T-AAA
1 TATTATTTTATTTTTATAAAA
3370282 TATTATTTTATTTTTATAAAA
1 TATTATTTTATTTTTATAAAA
3370303 TAATTATTTTA
1 T-ATTATTTTA
3370314 ATATAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.14
19 10 0.36
20 1 0.04
21 4 0.14
22 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATTTTATTTTTATAAAA
Found at i:3370310 original size:25 final size:25
Alignment explanation
Indices: 3370235--3370310 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
3370225 TATTTTATAA
*
3370235 TATTTTATTTTAATAAATTAAATTAT
1 TATTTTATTTTTATAAATT-AATTAT
* *** *
3370261 TATTAT-TTTTTATTTTTTAAATAT
1 TATTTTATTTTTATAAATTAATTAT
*
3370285 TATTTTATTTTTATAAAATAATTAT
1 TATTTTATTTTTATAAATTAATTAT
3370310 T
1 T
3370311 TTAATATAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
24 10 0.27
25 22 0.59
26 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTTATTTTTATAAATTAATTAT
Found at i:3370325 original size:16 final size:16
Alignment explanation
Indices: 3370208--3370327 Score: 61
Period size: 16 Copynumber: 7.4 Consensus size: 16
3370198 AAATAAAAAA
*
3370208 TTATTTTAA-AAAATT
1 TTATTTTAATATAATT
3370223 TATATTTT-ATA-ATATT
1 T-TATTTTAATATA-ATT
3370239 TTATTTTAATA-AATT
1 TTATTTTAATATAATT
** * *
3370254 AAATTATTATTAT-TTT
1 TTATT-TTAATATAATT
*
3370270 TTATTTTTTAAATATTATT
1 TTA--TTTT-AATATAATT
* * *
3370289 TTATTTTTATAAAATAA
1 TTATTTTAATATAAT-T
3370306 TTATTTTAATATAATT
1 TTATTTTAATATAATT
3370322 TTATTT
1 TTATTT
3370328 AATTTAAATA
Statistics
Matches: 79, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
15 15 0.19
16 34 0.43
17 19 0.24
18 6 0.08
19 5 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTTAATATAATT
Found at i:3370804 original size:14 final size:15
Alignment explanation
Indices: 3370777--3370806 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3370767 GAGTCAGATG
3370777 AAAAATTTTAAAAAA
1 AAAAATTTTAAAAAA
3370792 AAAAATTTTAAAAAA
1 AAAAATTTTAAAAAA
3370807 GGAAGAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATTTTAAAAAA
Found at i:3371012 original size:39 final size:38
Alignment explanation
Indices: 3370967--3371071 Score: 101
Period size: 39 Copynumber: 2.8 Consensus size: 38
3370957 TATCATTTTT
*
3370967 ATTTTAATATTATTATATATTAATATATTTTAATATATC
1 ATTTTAATATTATTATATATTAATATATTTTAA-ATATA
* * *
3371006 ATTTTAA-ATTTATCAAATTTTAATAT-TTTTAAATATA
1 ATTTTAATA-TTATTATATATTAATATATTTTAAATATA
* *
3371043 AATTAAATAATT-TTATATATTAA-ATATTT
1 ATTTTAAT-ATTATTATATATTAATATATTT
3371072 ATCAATTTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
36 2 0.04
37 20 0.38
38 9 0.17
39 22 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (38 bp):
ATTTTAATATTATTATATATTAATATATTTTAAATATA
Found at i:3371056 original size:21 final size:22
Alignment explanation
Indices: 3371027--3371067 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3371017 ATCAAATTTT
*
3371027 AATATTTTTAAATA-TAAATTA
1 AATAATTTTAAATATTAAATTA
*
3371048 AATAATTTTATATATTAAAT
1 AATAATTTTAAATATTAAAT
3371068 ATTTATCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAAATATTAAATTA
Found at i:3371505 original size:13 final size:13
Alignment explanation
Indices: 3371487--3371511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3371477 TTAATTAAAA
3371487 ATTAATACATACC
1 ATTAATACATACC
3371500 ATTAATACATAC
1 ATTAATACATAC
3371512 AACCATGCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATACATACC
Found at i:3376992 original size:28 final size:28
Alignment explanation
Indices: 3376957--3377014 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3376947 TCTCAAAAGT
3376957 AAAACTTCATAGAACCTCGACATTCACA
1 AAAACTTCATAGAACCTCGACATTCACA
3376985 AAAACTTCATAGAACCTCGACATTCACA
1 AAAACTTCATAGAACCTCGACATTCACA
3377013 AA
1 AA
3377015 CTGAAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (28 bp):
AAAACTTCATAGAACCTCGACATTCACA
Found at i:3381793 original size:17 final size:17
Alignment explanation
Indices: 3381767--3381807 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
3381757 TTAAAAATAA
*
3381767 ATATTAAATATATAAAT
1 ATATTTAATATATAAAT
3381784 ATATTT-A-ATATAAAT
1 ATATTTAATATATAAAT
3381799 ATATTTAAT
1 ATATTTAAT
3381808 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 14 0.67
16 2 0.10
17 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTAATATATAAAT
Found at i:3381794 original size:15 final size:15
Alignment explanation
Indices: 3381776--3381807 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3381766 AATATTAAAT
3381776 ATATAAATATATTTA
1 ATATAAATATATTTA
3381791 ATATAAATATATTTA
1 ATATAAATATATTTA
3381806 AT
1 AT
3381808 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAAATATATTTA
Found at i:3381830 original size:17 final size:19
Alignment explanation
Indices: 3381810--3381853 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3381800 TATTTAATTT
*
3381810 TTTAAAA-ATTTTA-TATA
1 TTTAAAATATTATATTATA
3381827 TTTAAAATATTATATTATA
1 TTTAAAATATTATATTATA
*
3381846 TATAAAAT
1 TTTAAAAT
3381854 TAAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 5 0.22
19 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAAATATTATATTATA
Found at i:3381833 original size:16 final size:16
Alignment explanation
Indices: 3381814--3381871 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 16
3381804 TAATTTTTTA
3381814 AAAATTTTATATATTT
1 AAAATTTTATATATTT
*
3381830 AAAATATTATATTATATAT
1 AAAAT-TT-TA-TATATTT
**
3381849 AAAATTAAATATATATT
1 AAAATTTTATATAT-TT
3381866 AAAATT
1 AAAATT
3381872 AATATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 10 0.29
17 10 0.29
18 3 0.09
19 11 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATTTTATATATTT
Found at i:3382840 original size:10 final size:10
Alignment explanation
Indices: 3382825--3382874 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
3382815 CACTCATTTA
3382825 TTTATATATT
1 TTTATATATT
*
3382835 TTTATATTATA
1 TTTATA-TATT
3382846 TTT-TATATT
1 TTTATATATT
*
3382855 TTTATAAATT
1 TTTATATATT
*
3382865 TTAATATATT
1 TTTATATATT
3382875 AATAATTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 6 0.18
10 21 0.64
11 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTATATATT
Found at i:3382872 original size:20 final size:21
Alignment explanation
Indices: 3382823--3382874 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3382813 TGCACTCATT
*
3382823 TATTTATATATTTTTATATTA
1 TATTTATATATTTTTATATAA
3382844 TATTT-TATATTTTTATA-AA
1 TATTTATATATTTTTATATAA
3382863 T-TTTAATATATT
1 TATTT-ATATATT
3382875 AATAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 2 0.07
20 18 0.64
21 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTATATATTTTTATATAA
Found at i:3382893 original size:32 final size:32
Alignment explanation
Indices: 3382823--3382906 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
3382813 TGCACTCATT
*
3382823 TATTTATAT--ATTTT--TATATTATATTTTA
1 TATTTATATAAATTTTAATATATTATAATTTA
*
3382851 TATTTTTATAAATTTTAATATATTAATAATTTA
1 TATTTATATAAATTTTAATATATT-ATAATTTA
*
3382884 TA-TTATATAAATTTTAAAATATT
1 TATTTATATAAATTTTAATATATT
3382907 TTTTATATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.17
30 5 0.11
32 25 0.53
33 9 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTTATATAAATTTTAATATATTATAATTTA
Found at i:3385789 original size:15 final size:15
Alignment explanation
Indices: 3385769--3385797 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3385759 CCCTAGAGTT
3385769 TGCTCAGGAGGAGCC
1 TGCTCAGGAGGAGCC
3385784 TGCTCAGGAGGAGC
1 TGCTCAGGAGGAGC
3385798 TTGCCCCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.24, G:0.41, T:0.14
Consensus pattern (15 bp):
TGCTCAGGAGGAGCC
Found at i:3389579 original size:2 final size:2
Alignment explanation
Indices: 3389524--3389566 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3389514 TGCGATATCC
3389524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3389566 T
1 T
3389567 GTCTCATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3390748 original size:63 final size:64
Alignment explanation
Indices: 3390633--3390756 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 64
3390623 AATCAATTTA
*
3390633 GATTTGATTTCAAATCTTAGTAAAAACAAATTCAGACTTTCACTTGACTTAATTCATAAACTTG
1 GATTTGATTTCAAATCTTAGTAAAAACAAATTCAGACTTTCACTTAACTTAATTCATAAACTTG
* *
3390697 GATTTGATTTTAAATCTTAGTAAAAA-AAATTCAGACTTTCACTTAACTTAATTCGTAAAC
1 GATTTGATTTCAAATCTTAGTAAAAACAAATTCAGACTTTCACTTAACTTAATTCATAAAC
3390757 ATTTTTAACT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 32 0.56
64 25 0.44
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (64 bp):
GATTTGATTTCAAATCTTAGTAAAAACAAATTCAGACTTTCACTTAACTTAATTCATAAACTTG
Found at i:3393677 original size:7 final size:8
Alignment explanation
Indices: 3393658--3393707 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
3393648 GATATTCAAA
3393658 TTATATAT
1 TTATATAT
3393666 TTATAT-T
1 TTATATAT
3393673 TTATA-AT
1 TTATATAT
* *
3393680 ATATAAATT
1 TTATATA-T
3393689 TTAATATAT
1 TT-ATATAT
3393698 TTATATAT
1 TTATATAT
3393706 TT
1 TT
3393708 TTAAATGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
7 11 0.31
8 15 0.43
9 5 0.14
10 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTATATAT
Found at i:3393707 original size:18 final size:18
Alignment explanation
Indices: 3393660--3393708 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3393650 TATTCAAATT
3393660 ATATATTTATAT-TTTATA
1 ATATATTTATATATTT-TA
3393678 ATATA--TA-A-ATTTTA
1 ATATATTTATATATTTTA
3393692 ATATATTTATATATTTT
1 ATATATTTATATATTTT
3393709 TAAATGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
14 7 0.27
15 4 0.15
16 4 0.15
17 1 0.04
18 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTTATATATTTTA
Found at i:3393726 original size:23 final size:24
Alignment explanation
Indices: 3393692--3393737 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3393682 ATAAATTTTA
* *
3393692 ATATATTTATA-TATTTTTAAATG
1 ATATATTAATATTATATTTAAATG
3393715 ATATATTAATATTATATTTAAAT
1 ATATATTAATATTATATTTAAAT
3393738 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATATTAATATTATATTTAAATG
Found at i:3403844 original size:2 final size:2
Alignment explanation
Indices: 3403837--3403863 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3403827 ATCGTAGTTT
3403837 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3403864 TTTACTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3404436 original size:28 final size:26
Alignment explanation
Indices: 3404395--3404448 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
3404385 CTTTAACTAC
3404395 AAATGAAAATAATTATACATATATAATAT
1 AAATGAAAATAATTA-A-AT-TATAATAT
3404424 AAAT-AAAATAATTAAATTATAATAT
1 AAATGAAAATAATTAAATTATAATAT
3404449 GATGTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 8 0.32
26 2 0.08
27 1 0.04
28 10 0.40
29 4 0.16
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATGAAAATAATTAAATTATAATAT
Found at i:3404527 original size:7 final size:8
Alignment explanation
Indices: 3404510--3404610 Score: 53
Period size: 8 Copynumber: 11.9 Consensus size: 8
3404500 TGTTAAAATT
3404510 TATATAAA
1 TATATAAA
3404518 TATA-AAA
1 TATATAAA
*
3404525 TATTTTAAA
1 TA-TATAAA
3404534 TATGATTATAA
1 TAT-A-TA-AA
*
3404545 CATAATAAAA
1 TAT-AT-AAA
3404555 TATATAAA
1 TATATAAA
3404563 T-TATTAAA
1 TATA-TAAA
* *
3404571 TTTAATATA
1 TAT-ATAAA
*
3404580 TATATATA
1 TATATAAA
*
3404588 TATATATA
1 TATATAAA
*
3404596 TATATATA
1 TATATAAA
3404604 TATATAA
1 TATATAA
3404611 TCTGCTTTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
7 7 0.09
8 42 0.55
9 13 0.17
10 8 0.11
11 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (8 bp):
TATATAAA
Found at i:3404582 original size:2 final size:2
Alignment explanation
Indices: 3404575--3404609 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3404565 ATTAAATTTA
3404575 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
3404610 ATCTGCTTTC
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:3406312 original size:16 final size:16
Alignment explanation
Indices: 3406291--3406321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3406281 TTTTTCAAAA
3406291 TTTATTTATAGTATTT
1 TTTATTTATAGTATTT
*
3406307 TTTATTTTTAGTATT
1 TTTATTTATAGTATT
3406322 AACGAAATGA
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:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTATTTATAGTATTT
Found at i:3406464 original size:3 final size:3
Alignment explanation
Indices: 3406458--3406491 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3406448 GATGATGATG
3406458 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3406492 GTTGTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3410082 original size:2 final size:2
Alignment explanation
Indices: 3410075--3410112 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3410065 AAATAAGGGT
3410075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3410113 ATTATGGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3410806 original size:3 final size:3
Alignment explanation
Indices: 3410800--3410830 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3410790 TTCATCATAC
3410800 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3410831 ATCCCTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3412687 original size:13 final size:15
Alignment explanation
Indices: 3412659--3412693 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
3412649 TAAGAATATC
3412659 TTTTTATAATTAATA
1 TTTTTATAATTAATA
3412674 TTTTT-TAA-TAATA
1 TTTTTATAATTAATA
3412687 TTTTTAT
1 TTTTTAT
3412694 TTAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTATAATTAATA
Found at i:3412842 original size:21 final size:20
Alignment explanation
Indices: 3412793--3412853 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
3412783 CCGTTAACAA
*
3412793 AATTATTTAATTAAAATATG
1 AATTATTTTATTAAAATATG
*
3412813 ATTTCATTTTATTAAATTATAT-
1 AATT-ATTTTATTAAA--ATATG
3412835 AATTA-TTT-TTAAAATATG
1 AATTATTTTATTAAAATATG
3412853 A
1 A
3412854 TATTTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 5 0.15
20 6 0.18
21 11 0.32
22 3 0.09
23 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (20 bp):
AATTATTTTATTAAAATATG
Found at i:3412870 original size:42 final size:40
Alignment explanation
Indices: 3412791--3412887 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 40
3412781 ATCCGTTAAC
* *
3412791 AAAATTATTTAATTAAAATATGATTTCATTTTATT-AAATTAT
1 AAAATTATTT--TTAAAATATGATTTCAATATATTAAAATT-T
* *
3412833 ATAATTATTTTTAAAATATGATATTTAATATATTTAAAATTT
1 AAAATTATTTTTAAAATATGAT-TTCAATATA-TTAAAATTT
3412875 AAAATTTATTTTT
1 AAAA-TTATTTTT
3412888 TATATTCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
40 12 0.26
41 6 0.13
42 15 0.33
43 13 0.28
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (40 bp):
AAAATTATTTTTAAAATATGATTTCAATATATTAAAATTT
Found at i:3423019 original size:12 final size:13
Alignment explanation
Indices: 3422994--3423026 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3422984 TTTAAAATTA
3422994 ATATATTATTTAT
1 ATATATTATTTAT
3423007 ATATATT-TTTAT
1 ATATATTATTTAT
*
3423019 AAATATTA
1 ATATATTA
3423027 CTTGAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATATTATTTAT
Found at i:3429045 original size:3 final size:3
Alignment explanation
Indices: 3429037--3429089 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3429027 TATTTCAAAG
3429037 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3429085 ATT AT
1 ATT AT
3429090 ACTTATGAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3429726 original size:2 final size:2
Alignment explanation
Indices: 3429719--3429748 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3429709 TCAAAGCTTA
*
3429719 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3429749 TTCTTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3434864 original size:2 final size:2
Alignment explanation
Indices: 3434857--3434894 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3434847 CAAAGTTCGC
3434857 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3434895 GAACAATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3435168 original size:26 final size:26
Alignment explanation
Indices: 3435080--3435169 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
3435070 TATTGTTAGT
* *
3435080 ATATATAAATTTATATATTATTAATAA
1 ATATATATATTTATAT-TTATTTATAA
*
3435107 AT-TATATGATCTTAT-TTTA-TTAAAA
1 ATATATAT-AT-TTATATTTATTTATAA
* *
3435132 ATA-AAATTATTTATATTTATTTATAT
1 ATATATA-TATTTATATTTATTTATAA
3435158 ATATATATATTT
1 ATATATATATTT
3435170 TTTTAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
24 4 0.08
25 14 0.29
26 20 0.41
27 7 0.14
28 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
ATATATATATTTATATTTATTTATAA
Found at i:3435902 original size:27 final size:27
Alignment explanation
Indices: 3435864--3435916 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3435854 TTTTCTATGC
3435864 ATATTCATTAGCTCATAAAATATTGAA
1 ATATTCATTAGCTCATAAAATATTGAA
3435891 ATATTCATTAGCTCATAAAATATTGA
1 ATATTCATTAGCTCATAAAATATTGA
3435917 GAGTGAAGGG
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:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (27 bp):
ATATTCATTAGCTCATAAAATATTGAA
Found at i:3436926 original size:3 final size:3
Alignment explanation
Indices: 3436920--3436956 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3436910 AAAAAAGGAC
3436920 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
3436957 TGCCCCTTCT
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:3438390 original size:11 final size:10
Alignment explanation
Indices: 3438374--3438457 Score: 50
Period size: 10 Copynumber: 8.3 Consensus size: 10
3438364 TTAAATTTTA
3438374 ATATAAATAT
1 ATATAAATAT
*
3438384 GATATAAGTAT
1 -ATATAAATAT
3438395 ATAT-AATAT
1 ATATAAATAT
* *
3438404 -TTTAAATTT
1 ATATAAATAT
*
3438413 ATATAAAATAA
1 ATAT-AAATAT
3438424 ATTATTAAA-AT
1 A-TA-TAAATAT
*
3438435 AT-TAAAATTT
1 ATAT-AAATAT
3438445 ATATAAATAT
1 ATATAAATAT
3438455 ATA
1 ATA
3438458 ATATTTTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 17
0.67 0.12 0.21
Matches are distributed among these distances:
8 3 0.05
9 11 0.20
10 18 0.33
11 17 0.31
12 5 0.09
13 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
ATATAAATAT
Found at i:3438452 original size:18 final size:17
Alignment explanation
Indices: 3438394--3438454 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
3438384 GATATAAGTA
*
3438394 TATATAATATTTTAAATT
1 TATATAA-ATATTAAATT
3438412 TATATAAA-A-TAAA-T
1 TATATAAATATTAAATT
3438426 TAT-TAAAATATTAAAATT
1 TATAT-AAATATT-AAATT
3438444 TATATAAATAT
1 TATATAAATAT
3438455 ATAATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
13 1 0.03
14 7 0.19
15 5 0.14
16 1 0.03
17 4 0.11
18 17 0.47
19 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATAAATATTAAATT
Found at i:3438469 original size:16 final size:16
Alignment explanation
Indices: 3438448--3438494 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
3438438 AAAATTTATA
3438448 TAAATATATAATATTT
1 TAAATATATAATATTT
* *
3438464 TAAATATAATTATAATT
1 TAAATAT-ATAATATTT
*
3438481 TAAAAATATAATAT
1 TAAATATATAATAT
3438495 AAATTATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATATAATATTT
Found at i:3453112 original size:5 final size:5
Alignment explanation
Indices: 3453099--3453149 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
3453089 ACAGTGCCAT
* ** * *
3453099 ACCAC ACCAG ACCAG ACCAG A-CTT ACCAC ACCAC ACCAG ACCAG ACCAG
1 ACCAG ACCAG ACCAG ACCAG ACCAG ACCAG ACCAG ACCAG ACCAG ACCAG
3453148 AC
1 AC
3453150 TCTTGCTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
4 2 0.05
5 37 0.95
ACGTcount: A:0.39, C:0.45, G:0.12, T:0.04
Consensus pattern (5 bp):
ACCAG
Found at i:3453130 original size:24 final size:24
Alignment explanation
Indices: 3453098--3453144 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3453088 AACAGTGCCA
*
3453098 TACCACACCAGACCAGACCAGACT
1 TACCACACCACACCAGACCAGACT
3453122 TACCACACCACACCAGACCAGAC
1 TACCACACCACACCAGACCAGAC
3453145 CAGACTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.45, G:0.11, T:0.06
Consensus pattern (24 bp):
TACCACACCACACCAGACCAGACT
Found at i:3457231 original size:2 final size:2
Alignment explanation
Indices: 3457224--3457255 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3457214 CATTTTTCTC
3457224 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
3457256 CTTTAGAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3457501 original size:2 final size:2
Alignment explanation
Indices: 3457494--3457520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3457484 ACAGAATTTG
3457494 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3457521 ATAGTGTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3464848 original size:2 final size:2
Alignment explanation
Indices: 3464841--3464876 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3464831 TAGAAAGAAC
3464841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3464877 TTTTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3466845 original size:21 final size:21
Alignment explanation
Indices: 3466821--3466905 Score: 63
Period size: 21 Copynumber: 4.0 Consensus size: 21
3466811 ATTTATATAT
3466821 ATATATATTTA-AATTATTAAA
1 ATATA-ATTTATAATTATTAAA
* *
3466842 ATATGAA-CTCTAATTATTAAA
1 ATAT-AATTTATAATTATTAAA
3466863 A-AT-ATATTACGTAATTATT-AA
1 ATATAAT-TTA--TAATTATTAAA
3466884 ATATAATTTAATAATTATTAAA
1 ATATAATTT-ATAATTATTAAA
3466906 CATAATCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 19
0.68 0.05 0.26
Matches are distributed among these distances:
18 1 0.02
20 4 0.08
21 27 0.54
22 15 0.30
23 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATAATTTATAATTATTAAA
Found at i:3466910 original size:21 final size:23
Alignment explanation
Indices: 3466852--3466911 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
3466842 ATATGAACTC
*
3466852 TAATTATTAAAAAT-ATATTACG
1 TAATTATTAAAAATAATATTACA
*
3466874 TAATTATTAAATATAAT-TTA-A
1 TAATTATTAAAAATAATATTACA
*
3466895 TAATTATTAAACATAAT
1 TAATTATTAAAAATAAT
3466912 CTTTTATCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.47
22 16 0.47
23 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATTATTAAAAATAATATTACA
Found at i:3468280 original size:16 final size:17
Alignment explanation
Indices: 3468249--3468281 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3468239 TGAGTATTTC
3468249 TTTAATAAATAAATATT
1 TTTAATAAATAAATATT
*
3468266 TTTAATTAA-AAATATT
1 TTTAATAAATAAATATT
3468282 AACTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAATAAATAAATATT
Found at i:3470597 original size:17 final size:18
Alignment explanation
Indices: 3470560--3470598 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3470550 TTTTTAAAAA
*
3470560 AATTATTTATTTTTACAT
1 AATTATTTATTTTAACAT
*
3470578 AATT-TTTATTTTAACGT
1 AATTATTTATTTTAACAT
3470595 AATT
1 AATT
3470599 CATGCGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTATTTATTTTAACAT
Found at i:3478497 original size:2 final size:2
Alignment explanation
Indices: 3478490--3478516 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3478480 TGAAACAAAT
3478490 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3478517 TAATAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3479668 original size:3 final size:3
Alignment explanation
Indices: 3479662--3479704 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3479652 TGTTTCCTCC
*
3479662 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3479705 TAAAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3484696 original size:26 final size:25
Alignment explanation
Indices: 3484649--3484706 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3484639 TGCAGTATTT
* *
3484649 TTAAAAATATTAATATTAATTTTTAA
1 TTAAAAATATAAAAATTAA-TTTTAA
*
3484675 TTAAAAATAATAAAAATT-ATTTTAT
1 TTAAAAAT-ATAAAAATTAATTTTAA
3484700 TTAAAAA
1 TTAAAAA
3484707 AAATTAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.43
26 9 0.32
27 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAAAAATATAAAAATTAATTTTAA
Found at i:3484921 original size:11 final size:13
Alignment explanation
Indices: 3484883--3484973 Score: 54
Period size: 13 Copynumber: 7.2 Consensus size: 13
3484873 TTATTCTGTT
3484883 AATTAT-ATATTAA
1 AATTATAATATT-A
3484896 AATTATAATATTA
1 AATTATAATATTA
3484909 AATTA-AATA-TA
1 AATTATAATATTA
*
3484920 AATTTTTAATATT-
1 AA-TTATAATATTA
* *
3484933 TATT-TAATATAA
1 AATTATAATATTA
3484945 TAATTAT-ATATTTA
1 -AATTATAATA-TTA
3484959 ATATT-TAA-ATTA
1 A-ATTATAATATTA
3484971 AAT
1 AAT
3484974 AATCTAATAC
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
11 12 0.19
12 12 0.19
13 26 0.41
14 13 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTATAATATTA
Found at i:3484976 original size:31 final size:27
Alignment explanation
Indices: 3484866--3484976 Score: 77
Period size: 25 Copynumber: 4.0 Consensus size: 27
3484856 ATATGAGATT
* * * *
3484866 TAAATTTTTATTCTGTT-AATTATATAT
1 TAAATTTTTAATAT-TTAAATTAAATAA
* *
3484893 TAAAATTATAATA-TTAAATTAAAT-A
1 TAAATTTTTAATATTTAAATTAAATAA
*
3484918 TAAATTTTTAATATTT-ATTTAATATAA
1 TAAATTTTTAATATTTAAATTAA-ATAA
3484945 TAATTATATATTTAATATTTAAATTAAATAA
1 TAA--AT-T-TTTAATATTTAAATTAAATAA
3484976 T
1 T
3484977 CTAATACAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
25 18 0.28
26 11 0.17
27 13 0.20
29 2 0.03
30 1 0.02
31 15 0.23
32 5 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TAAATTTTTAATATTTAAATTAAATAA
Found at i:3486185 original size:3 final size:3
Alignment explanation
Indices: 3486177--3486210 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3486167 GAGCACCGAA
*
3486177 CTG CTG CTG CTG CTG CTG CTG CTG CTA CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
3486211 GTCTGCTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.35, G:0.29, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:3494473 original size:13 final size:13
Alignment explanation
Indices: 3494451--3494494 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3494441 GAAAATTTAA
*
3494451 ATTTTATAATTAT
1 ATTTTTTAATTAT
*
3494464 ATTTTTTAATTTT
1 ATTTTTTAATTAT
*
3494477 AATTTTTTATTTAT
1 -ATTTTTTAATTAT
3494491 ATTT
1 ATTT
3494495 AAAAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTTTTAATTAT
Found at i:3494501 original size:27 final size:27
Alignment explanation
Indices: 3494442--3494512 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
3494432 TATTATTATG
* *
3494442 AAAATTTAAATTTTATAATTATATTTT
1 AAAATTTTAATTTTATAATTATATTTA
** * *
3494469 TTAATTTTAATTTTTTATTTATATTTA
1 AAAATTTTAATTTTATAATTATATTTA
*
3494496 AAAATTTTTA-TTTATAA
1 AAAATTTTAATTTTATAA
3494513 AAATTTTAAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
AAAATTTTAATTTTATAATTATATTTA
Found at i:3494513 original size:16 final size:16
Alignment explanation
Indices: 3494494--3494524 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3494484 TATTTATATT
*
3494494 TAAAAATTTTTATTTA
1 TAAAAATTTTAATTTA
3494510 TAAAAATTTTAATTT
1 TAAAAATTTTAATTT
3494525 CCATAAATAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAAAATTTTAATTTA
Found at i:3494804 original size:18 final size:17
Alignment explanation
Indices: 3494773--3494816 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3494763 GGAAAAAGAG
*
3494773 TTTAATTTTTATTTAAT
1 TTTAATTTTAATTTAAT
3494790 TTTATATTTTAATTTAATT
1 TTTA-ATTTTAATTTAA-T
3494809 TTTAATTT
1 TTTAATTT
3494817 GATAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATTTTAATTTAAT
Found at i:3494915 original size:7 final size:7
Alignment explanation
Indices: 3494905--3494930 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3494895 AAATATTAAT
3494905 TTAATAA
1 TTAATAA
3494912 TTAATAA
1 TTAATAA
3494919 TTAATAA
1 TTAATAA
3494926 TTAAT
1 TTAAT
3494931 TAAAATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTAATAA
Found at i:3494997 original size:18 final size:21
Alignment explanation
Indices: 3494976--3495020 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3494966 ATTATCATGA
3494976 AAAAATAT-AAA-AA-TTTTT
1 AAAAATATAAAATAATTTTTT
3494994 AAAAATATAAAATAATTTTTT
1 AAAAATATAAAATAATTTTTT
3495015 AAAAAT
1 AAAAAT
3495021 TTTTTATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.33
19 3 0.12
20 2 0.08
21 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATATAAAATAATTTTTT
Found at i:3496771 original size:2 final size:2
Alignment explanation
Indices: 3496766--3496808 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3496756 AGACTTGAAC
3496766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3496808 A
1 A
3496809 CACACGCGCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3498367 original size:38 final size:38
Alignment explanation
Indices: 3498324--3498409 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
3498314 CAAAATTTGT
* * **
3498324 ATTATTTTTTTATATAATAAATTTGAAT-TC-AAATTA
1 ATTATTTTTTCAGATAATAAATTCAAATATCTAAATTA
*
3498360 ATTTTATTTATTCAGATAATAAATTCAAATATCTAAATTA
1 A--TTATTTTTTCAGATAATAAATTCAAATATCTAAATTA
3498400 ATTATTTTTT
1 ATTATTTTTT
3498410 ATTTGTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
36 1 0.03
38 30 0.75
39 2 0.05
40 7 0.17
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (38 bp):
ATTATTTTTTCAGATAATAAATTCAAATATCTAAATTA
Found at i:3504018 original size:2 final size:2
Alignment explanation
Indices: 3504011--3504054 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3504001 CTGCGAGTTC
*
3504011 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3504053 AT
1 AT
3504055 TCTCCTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3507890 original size:2 final size:2
Alignment explanation
Indices: 3507883--3507913 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3507873 TCACACTTGT
*
3507883 TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3507914 TGATTATTTA
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:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3512168 original size:2 final size:2
Alignment explanation
Indices: 3512161--3512221 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
3512151 ATAAAGTGAT
3512161 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
3512203 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
3512222 TTTTAAGCTT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3517445 original size:2 final size:2
Alignment explanation
Indices: 3517432--3517477 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3517422 TTTATTCTAT
*
3517432 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3517474 TA TA
1 TA TA
3517478 GAGAGAGAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3517482 original size:2 final size:2
Alignment explanation
Indices: 3517477--3517530 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3517467 ATATATATAT
3517477 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
3517519 AG AG AG AG AG AG
1 AG AG AG AG AG AG
3517531 TTCATTGTCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3517860 original size:2 final size:2
Alignment explanation
Indices: 3517853--3517879 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3517843 AATGTGTTAG
3517853 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3517880 GATGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3521558 original size:30 final size:29
Alignment explanation
Indices: 3521489--3521561 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
3521479 TATATTTTTA
* *
3521489 TTAACTTTTAATTTATATCTAAGTAGACTC
1 TTAAATTTTAA-TTATATCTAAATAGACTC
* *
3521519 TTAATTTTTAATTATATCTAAATA-AGTC
1 TTAAATTTTAATTATATCTAAATAGACTC
3521547 TTCAAAATTTTAATT
1 TT--AAATTTTAATT
3521562 TGAATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.14
29 12 0.32
30 20 0.54
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (29 bp):
TTAAATTTTAATTATATCTAAATAGACTC
Found at i:3521650 original size:19 final size:20
Alignment explanation
Indices: 3521626--3521667 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3521616 TTGAATATAA
3521626 TAAAAAT-ATATAAATTTAT
1 TAAAAATAATATAAATTTAT
* *
3521645 TAAAAATAATTTAAATTTTT
1 TAAAAATAATATAAATTTAT
3521665 TAA
1 TAA
3521668 TATTTTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAATAATATAAATTTAT
Found at i:3546488 original size:3 final size:3
Alignment explanation
Indices: 3546482--3546510 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3546472 ATTAATTAAT
3546482 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3546511 CTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3568936 original size:12 final size:12
Alignment explanation
Indices: 3568919--3568944 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3568909 GTGAAAAGGA
3568919 AGAGAGAGAGAC
1 AGAGAGAGAGAC
3568931 AGAGAGAGAGAC
1 AGAGAGAGAGAC
3568943 AG
1 AG
3568945 CGTCGGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGAC
Found at i:3577024 original size:2 final size:2
Alignment explanation
Indices: 3577017--3577047 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3577007 AATTTCCCTC
3577017 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3577048 CAACCCTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3579706 original size:20 final size:21
Alignment explanation
Indices: 3579681--3579731 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
3579671 ATATTTATAT
3579681 ATAATAATTATTTA-TCAAAA
1 ATAATAATTATTTATTCAAAA
* *
3579701 ATAATAATTGTTTATTGAAAA
1 ATAATAATTATTTATTCAAAA
3579722 ATAATTAATT
1 ATAA-TAATT
3579732 GGAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 13 0.48
21 9 0.33
22 5 0.19
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
ATAATAATTATTTATTCAAAA
Found at i:3584063 original size:3 final size:3
Alignment explanation
Indices: 3584055--3584101 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3584045 TTAACTAATG
3584055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3584102 AGATTAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3585798 original size:22 final size:22
Alignment explanation
Indices: 3585773--3585816 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3585763 ATGATCGAAA
3585773 AATGTCAGATCATTACTGTTGG
1 AATGTCAGATCATTACTGTTGG
3585795 AATGTCAGATCATTACTGTTGG
1 AATGTCAGATCATTACTGTTGG
3585817 GGTCAAAGAA
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:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (22 bp):
AATGTCAGATCATTACTGTTGG
Found at i:3588134 original size:27 final size:28
Alignment explanation
Indices: 3588100--3588165 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
3588090 GTCACCCATT
*
3588100 TGTTTGTCAAAAATTGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
*
3588127 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
3588155 -GATTTGTCAAA
1 TG-TTTGTCAAA
3588166 TATAGAGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 22 0.63
28 13 0.37
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTATCTTTG
Found at i:3588272 original size:20 final size:20
Alignment explanation
Indices: 3588247--3588292 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3588237 AAATAGAGGC
3588247 TCCCTCATCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
3588267 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
3588287 TCCCTC
1 TCCCTC
3588293 TTCAATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:3592726 original size:28 final size:27
Alignment explanation
Indices: 3592668--3592736 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
3592658 CACCCATTTG
* **
3592668 TTTGTCAAAAATGGTTGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTGAA
3592695 TTTGTCAAAAATGGTGGTT-TCCTTTGAA
1 TTTGTCAAAAATGGTGGTTAT--TTTGAA
*
3592723 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
3592737 AGGCTTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTGAA
Found at i:3597854 original size:11 final size:11
Alignment explanation
Indices: 3597838--3597882 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
3597828 TAGATATAAT
*
3597838 ATTAAAAAATA
1 ATTAAAATATA
3597849 ATTAAAATATA
1 ATTAAAATATA
3597860 ATATAAAATATA
1 AT-TAAAATATA
*
3597872 A-TATAATATA
1 ATTAAAATATA
3597882 A
1 A
3597883 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 9 0.29
11 12 0.39
12 10 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAAATATA
Found at i:3597858 original size:41 final size:39
Alignment explanation
Indices: 3597807--3597921 Score: 119
Period size: 41 Copynumber: 2.9 Consensus size: 39
3597797 AATTTGGTTA
*
3597807 AATTTAAATATATTAAAAATTTAGATATAATATTAAAAAAT
1 AATTAAAATATATTAAAAATTTA-ATATAATA-TAAAAAAT
* *
3597848 AATTAAAATATAATATAAAATATAATATAATATAAAAAAT
1 AATTAAAATATATTA-AAAATTTAATATAATATAAAAAAT
* * *
3597888 AA-AATAAATATATCAAAAA-TT-ATATAACATAAAA
1 AATTA-AAATATATTAAAAATTTAATATAATATAAAA
3597922 TATTAATAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
37 12 0.19
38 1 0.02
39 5 0.08
40 18 0.28
41 21 0.33
42 7 0.11
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (39 bp):
AATTAAAATATATTAAAAATTTAATATAATATAAAAAAT
Found at i:3597868 original size:12 final size:12
Alignment explanation
Indices: 3597831--3597899 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
3597821 AAAAATTTAG
3597831 ATATAATATTAAA
1 ATATAATA-TAAA
*
3597844 AAATAAT-TAAA
1 ATATAATATAAA
3597855 ATATAATATAAA
1 ATATAATATAAA
*
3597867 ATATAATATAAT
1 ATATAATATAAA
* *
3597879 ATAAAAAATAAA
1 ATATAATATAAA
3597891 ATA-AATATA
1 ATATAATATA
3597900 TCAAAAATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
11 15 0.31
12 27 0.56
13 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:3597876 original size:17 final size:17
Alignment explanation
Indices: 3597854--3597921 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
3597844 AAATAATTAA
*
3597854 AATATAATATAAAATAT
1 AATATAATATAAAAAAT
3597871 AATATAATATAAAAAAT
1 AATATAATATAAAAAAT
*
3597888 AAAATAAATATATCAAAAAT
1 AATAT-AATATA--AAAAAT
* *
3597908 TATATAACATAAAA
1 AATATAATATAAAA
3597922 TATTAATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 23 0.53
18 6 0.14
19 5 0.12
20 9 0.21
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATAATATAAAAAAT
Found at i:3597924 original size:12 final size:12
Alignment explanation
Indices: 3597851--3597924 Score: 60
Period size: 12 Copynumber: 6.1 Consensus size: 12
3597841 AAAAAATAAT
*
3597851 TAAAATATAATA
1 TAAAATAAAATA
*
3597863 TAAAATATAATA
1 TAAAATAAAATA
* *
3597875 TAATATAAAAAA
1 TAAAATAAAATA
3597887 TAAAATAAATATA
1 TAAAATAAA-ATA
**
3597900 TCAAAA-ATTATA
1 T-AAAATAAAATA
*
3597912 TAACATAAAATA
1 TAAAATAAAATA
3597924 T
1 T
3597925 TAATAATATC
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
11 3 0.06
12 38 0.78
13 4 0.08
14 4 0.08
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATAAAATA
Found at i:3599475 original size:25 final size:24
Alignment explanation
Indices: 3599447--3599507 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
3599437 TATGTTCTCG
3599447 AATTATTTTTTATAATATTA-TATA
1 AATT-TTTTTTATAATATTATTATA
* *
3599471 TAATTTTTTTAAATTATATTATTATA
1 -AATTTTTTT-TATAATATTATTATA
3599497 AATTTTTTTTA
1 AATTTTTTTTA
3599508 AAAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.19
25 21 0.68
26 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AATTTTTTTTATAATATTATTATA
Found at i:3599496 original size:28 final size:26
Alignment explanation
Indices: 3599456--3599523 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
3599446 GAATTATTTT
3599456 TTATAATATTATATATAATTTTTTTAAA
1 TTATAATATTATA-A-AATTTTTTTAAA
* *
3599484 TTATATTATTATAAATTTTTTTTAAA
1 TTATAATATTATAAAATTTTTTTAAA
3599510 --A-AATATTA-AAAATT
1 TTATAATATTATAAAATT
3599524 GTCAGAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.14
23 6 0.17
24 1 0.03
26 11 0.31
27 1 0.03
28 12 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATAATATTATAAAATTTTTTTAAA
Found at i:3599515 original size:26 final size:25
Alignment explanation
Indices: 3599460--3599517 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
3599450 TATTTTTTAT
*
3599460 AATATTATATATAATTTTTTTAAAT
1 AATATTATATATAATTTTTTTAAAA
*
3599485 TATATTAT-TATAAATTTTTTTTAAAA
1 AATATTATATAT-AA-TTTTTTTAAAA
3599511 AATATTA
1 AATATTA
3599518 AAAATTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 9 0.32
26 16 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTATATATAATTTTTTTAAAA
Found at i:3606702 original size:14 final size:13
Alignment explanation
Indices: 3606675--3606725 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
3606665 GAATTATAGA
3606675 TTAAAATTAATTT
1 TTAAAATTAATTT
*
3606688 TTAAATATTATTTT
1 TTAAA-ATTAATTT
3606702 TTAATAA-TAA-TT
1 TTAA-AATTAATTT
3606714 TTATAAATTAAT
1 TTA-AAATTAAT
3606726 AAATTTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 7 0.23
13 11 0.35
14 12 0.39
15 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAAATTAATTT
Done.