Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 6 of 103
Found at i:2283089 original size:29 final size:27
Alignment explanation
Indices: 2283052--2283131 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 27
2283042 GTAAGTAGCT
2283052 TTTTAATTTTTTATAATAAAAAAGTTCAAA
1 TTTT-ATTTTTTA-AATAAAAAA-TTCAAA
*
2283082 TTTTATTTTTTAAAATTAACAAAATTCAAT
1 TTTTATTTTTT-AAA-TAA-AAAATTCAAA
2283112 TTTTATTTTTTAAATAAAAA
1 TTTTATTTTTTAAATAAAAA
2283132 TTATATATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.07
28 3 0.07
29 12 0.26
30 24 0.52
31 4 0.09
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (27 bp):
TTTTATTTTTTAAATAAAAAATTCAAA
Found at i:2293826 original size:69 final size:69
Alignment explanation
Indices: 2293715--2293855 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 69
2293705 TTTAATAAAA
* * * ** * *
2293715 TTATACGTCATGTATAAAAATATGTTACACGTTATGTACAAAAACATGTAACATATCGTGGTTAG
1 TTATACGTCATATACAAAAATATATTACACACTATATACAAAAACATGTAACATATCATGGTTAG
2293780 GTTG
66 GTTG
* * *
2293784 TTATACGTCATATACAAAAATATATTACACACTCTATACAAAAACATGTGACATGTCATGGTTAG
1 TTATACGTCATATACAAAAATATATTACACACTATATACAAAAACATGTAACATATCATGGTTAG
2293849 GTTG
66 GTTG
2293853 TTA
1 TTA
2293856 CACTCTATGA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (69 bp):
TTATACGTCATATACAAAAATATATTACACACTATATACAAAAACATGTAACATATCATGGTTAG
GTTG
Found at i:2293909 original size:24 final size:24
Alignment explanation
Indices: 2293872--2293922 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2293862 ATGATTAAGT
**
2293872 TGTTATACGTCATGTACAAAAACA
1 TGTTATACACCATGTACAAAAACA
2293896 TGTTATACACCATGTACAAAAACA
1 TGTTATACACCATGTACAAAAACA
2293920 TGT
1 TGT
2293923 GACACGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (24 bp):
TGTTATACACCATGTACAAAAACA
Found at i:2293935 original size:90 final size:90
Alignment explanation
Indices: 2293780--2293954 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 90
2293770 TCGTGGTTAG
* *
2293780 GTTGTTATACGTCATATACAAAAATATATTACACACTCTATACAAAAACATGTGACATGTCATGG
1 GTTGTTATACGTCATATACAAAAACATATTACACACTCTATACAAAAACATGTGACACGTCATGG
*
2293845 TTAGGTTGTTACACTCTATGATTAA
66 TTAGGTTGTTACACACTATGATTAA
* * * * *
2293870 GTTGTTATACGTCATGTACAAAAACATGTTATACAC-CATGTACAAAAACATGTGACACGTTATG
1 GTTGTTATACGTCATATACAAAAACATATTACACACTC-TATACAAAAACATGTGACACGTCATG
2293934 GTTAGGTTGTTACACACTATG
65 GTTAGGTTGTTACACACTATG
2293955 TACAAAAACA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 1 0.01
90 75 0.99
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (90 bp):
GTTGTTATACGTCATATACAAAAACATATTACACACTCTATACAAAAACATGTGACACGTCATGG
TTAGGTTGTTACACACTATGATTAA
Found at i:2293960 original size:45 final size:45
Alignment explanation
Indices: 2293896--2294038 Score: 196
Period size: 45 Copynumber: 3.2 Consensus size: 45
2293886 TACAAAAACA
* *
2293896 TGTTATACACCATGTACAAAAACATGTGACACGTTATGGTTAGGT
1 TGTTACACACTATGTACAAAAACATGTGACACGTTATGGTTAGGT
2293941 TGTTACACACTATGTACAAAAACATGTGACACGTTATGGTTAGGT
1 TGTTACACACTATGTACAAAAACATGTGACACGTTATGGTTAGGT
* ** * * * * *
2293986 TATTACATGCTATGTATAAAAATATGTGATATGCTATGGTTAGGT
1 TGTTACACACTATGTACAAAAACATGTGACACGTTATGGTTAGGT
2294031 TGTTACAC
1 TGTTACAC
2294039 GTTATATTGA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (45 bp):
TGTTACACACTATGTACAAAAACATGTGACACGTTATGGTTAGGT
Found at i:2294090 original size:29 final size:29
Alignment explanation
Indices: 2294030--2294124 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
2294020 TATGGTTAGG
* *
2294030 TTGTTACACGTTATATTGAAAAAAAAATTA
1 TTGTTACACGTCATATT-AAAAAAATATTA
*
2294060 TTGTTACACGTCATGTTAAAAAAATATTA
1 TTGTTACACGTCATATTAAAAAAATATTA
* * * *
2294089 TTATTACATGCCATATT-CAAAAATATT-
1 TTGTTACACGTCATATTAAAAAAATATTA
2294116 TTGTTACAC
1 TTGTTACAC
2294125 TTTAATACTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.13
28 9 0.16
29 24 0.44
30 15 0.27
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (29 bp):
TTGTTACACGTCATATTAAAAAAATATTA
Found at i:2298577 original size:14 final size:14
Alignment explanation
Indices: 2298537--2298577 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2298527 GTGTTACAAC
*
2298537 TTTTTGTTATTCTA
1 TTTTTGTTATTCAA
* *
2298551 TTTTTTTTCTTCAA
1 TTTTTGTTATTCAA
2298565 TTTTTGTTATTCA
1 TTTTTGTTATTCA
2298578 TTGTTACAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.71
Consensus pattern (14 bp):
TTTTTGTTATTCAA
Found at i:2301985 original size:2 final size:2
Alignment explanation
Indices: 2301978--2302015 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2301968 CTTCCCACAG
2301978 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2302016 TCCCCTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2306528 original size:21 final size:22
Alignment explanation
Indices: 2306493--2306538 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2306483 TAAATTATCT
* *
2306493 TAATTTTTATATATTTTTAATA
1 TAATTATTATATATTATTAATA
*
2306515 TAATTATT-TATATTATTATTA
1 TAATTATTATATATTATTAATA
2306536 TAA
1 TAA
2306539 AAATATGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATTATTATATATTATTAATA
Found at i:2307257 original size:45 final size:45
Alignment explanation
Indices: 2307208--2307293 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
2307198 TTTACGCCAT
*
2307208 GATTAAGTTGTTACACACTATATGCA-A-AAACATGTGACACGTCAG
1 GATTAAGTTGTTACACAC--CATGCACAGAAACATGTGACACGTCAG
* *
2307253 GATTATGTTGTTACATACCATGCACAGAAACATGTGACACG
1 GATTAAGTTGTTACACACCATGCACAGAAACATGTGACACG
2307294 CCATATACAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 5 0.14
44 1 0.03
45 30 0.83
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (45 bp):
GATTAAGTTGTTACACACCATGCACAGAAACATGTGACACGTCAG
Found at i:2307297 original size:24 final size:24
Alignment explanation
Indices: 2307270--2307601 Score: 222
Period size: 24 Copynumber: 14.2 Consensus size: 24
2307260 TTGTTACATA
*
2307270 CCATGCACAGAAACATGTGACACG
1 CCATGTACAGAAACATGTGACACG
*
2307294 CCATATACAGAAACATGTGACACG
1 CCATGTACAGAAACATGTGACACG
* * *
2307318 CCATGGTTA-AG----TTGTTACACA
1 CCAT-G-TACAGAAACATGTGACACG
* * *
2307339 CTATATACAGAAACATGTGACACA
1 CCATGTACAGAAACATGTGACACG
* *
2307363 TCATGTACAGAAACATATGACACG
1 CCATGTACAGAAACATGTGACACG
*
2307387 CCATGTACAGAAACATGTAACACG
1 CCATGTACAGAAACATGTGACACG
* * * *
2307411 TCATGCATAAAAACATGTGACACG
1 CCATGTACAGAAACATGTGACACG
* * ** * *
2307435 TCATGGT-TAG---GTTGTTACACA
1 CCAT-GTACAGAAACATGTGACACG
2307456 CCATGTACAGAAACATGTGACACG
1 CCATGTACAGAAACATGTGACACG
* * ** * *
2307480 TCATGGT-TAG---GTTGTTACACA
1 CCAT-GTACAGAAACATGTGACACG
* *
2307501 CCATATACAGAAATATGTGACACG
1 CCATGTACAGAAACATGTGACACG
*
2307525 TCATGTACAGAAACATGTGACACG
1 CCATGTACAGAAACATGTGACACG
*
2307549 CCATGTACAGAAACATGTAACACG
1 CCATGTACAGAAACATGTGACACG
* * *
2307573 TCATGCACAAAAACATGTGACACG
1 CCATGTACAGAAACATGTGACACG
*
2307597 TCATG
1 CCATG
2307602 GTTAGGTTGC
Statistics
Matches: 234, Mismatches: 57, Indels: 34
0.72 0.18 0.10
Matches are distributed among these distances:
19 2 0.01
20 5 0.02
21 34 0.15
24 186 0.79
25 5 0.02
26 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (24 bp):
CCATGTACAGAAACATGTGACACG
Found at i:2307316 original size:69 final size:69
Alignment explanation
Indices: 2307220--2307391 Score: 211
Period size: 69 Copynumber: 2.5 Consensus size: 69
2307210 TTAAGTTGTT
* * * * * * *
2307220 ACACACTATATGCAAAAACATGTGACACGTCA-GGATTATGTTGTTACATACCATGCACAGAAAC
1 ACACACCATATACAGAAACATGTGACACGCCATGG-TTAAGTTGTTACACACCATACACAGAAAC
2307284 ATGTG
65 ATGTG
* * *
2307289 ACACGCCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACTATATACAGAAACA
1 ACACACCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACCATACACAGAAACA
2307354 TGTG
66 TGTG
* * *
2307358 ACACATCATGTACAGAAACATATGACACGCCATG
1 ACACACCATATACAGAAACATGTGACACGCCATG
2307392 TACAGAAACA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
69 86 0.98
70 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (69 bp):
ACACACCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACCATACACAGAAACA
TGTG
Found at i:2307415 original size:48 final size:48
Alignment explanation
Indices: 2307269--2307595 Score: 232
Period size: 45 Copynumber: 7.0 Consensus size: 48
2307259 GTTGTTACAT
* * *
2307269 ACCATGCACAGAAACATGTGACACGCCATATACAGAAACATGTGACAC
1 ACCATGTACAGAAACATGTGACACGTCATGTACAGAAACATGTGACAC
* * * * *
2307317 GCCATGGTTA-AG----TTGTTACAC-ACTATATACAGAAACATGTGACAC
1 ACCAT-G-TACAGAAACATGTGACACGTC-ATGTACAGAAACATGTGACAC
* * * *
2307362 ATCATGTACAGAAACATATGACACGCCATGTACAGAAACATGTAACAC
1 ACCATGTACAGAAACATGTGACACGTCATGTACAGAAACATGTGACAC
** * * * * ** *
2307410 GTCATGCATAAAAACATGTGACACGTCATGGT-TAG---GTTGTTACAC
1 ACCATGTACAGAAACATGTGACACGTCAT-GTACAGAAACATGTGACAC
* ** *
2307455 ACCATGTACAGAAACATGTGACACGTCATGGT-TAG---GTTGTTACAC
1 ACCATGTACAGAAACATGTGACACGTCAT-GTACAGAAACATGTGACAC
* *
2307500 ACCATATACAGAAATATGTGACACGTCATGTACAGAAACATGTGACAC
1 ACCATGTACAGAAACATGTGACACGTCATGTACAGAAACATGTGACAC
* * * *
2307548 GCCATGTACAGAAACATGTAACACGTCATGCACAAAAACATGTGACAC
1 ACCATGTACAGAAACATGTGACACGTCATGTACAGAAACATGTGACAC
2307596 GTCATGGTTA
Statistics
Matches: 225, Mismatches: 40, Indels: 28
0.77 0.14 0.10
Matches are distributed among these distances:
43 2 0.01
44 6 0.03
45 107 0.48
48 103 0.46
49 6 0.03
50 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (48 bp):
ACCATGTACAGAAACATGTGACACGTCATGTACAGAAACATGTGACAC
Found at i:2307440 original size:117 final size:117
Alignment explanation
Indices: 2307270--2307484 Score: 326
Period size: 117 Copynumber: 1.8 Consensus size: 117
2307260 TTGTTACATA
*
2307270 CCATGCACAGAAACATGTGACACGCCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTA
1 CCATGCACAGAAACATGTAACACGCCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTA
*
2307335 CACACTATATACAGAAACATGTGACACATCATGTACAGAAACATATGACACG
66 CACACCATATACAGAAACATGTGACACATCATGTACAGAAACATATGACACG
* * * *
2307387 CCATGTACAGAAACATGTAACACGTCATGCATA-A-AAACATGTGACACGTCATGGTTAGGTTGT
1 CCATGCACAGAAACATGTAACACGCCAT--ATACAGAAACATGTGACACGCCATGGTTAAGTTGT
* *
2307450 TACACACCATGTACAGAAACATGTGACACGTCATG
64 TACACACCATATACAGAAACATGTGACACATCATG
2307485 GTTAGGTTGT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
117 84 0.95
118 1 0.01
119 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (117 bp):
CCATGCACAGAAACATGTAACACGCCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTA
CACACCATATACAGAAACATGTGACACATCATGTACAGAAACATATGACACG
Found at i:2307509 original size:162 final size:162
Alignment explanation
Indices: 2307289--2307623 Score: 580
Period size: 162 Copynumber: 2.1 Consensus size: 162
2307279 GAAACATGTG
* *
2307289 ACACGCCATATACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACTATATACAGAAACA
1 ACACGCCATGTACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACCATATACAGAAACA
*
2307354 TGTGACACATCATGTACAGAAACATATGACACGCCATGTACAGAAACATGTAACACGTCATGCAT
66 TGTGACACATCATGTACAGAAACATATGACACGCCATGTACAGAAACATGTAACACGTCATGCAC
*
2307419 AAAAACATGTGACACGTCATGGTTAGGTTGTT
131 AAAAACATGTGACACGTCATGGTTAGGTTGCT
* * * *
2307451 ACACACCATGTACAGAAACATGTGACACGTCATGGTTAGGTTGTTACACACCATATACAGAAATA
1 ACACGCCATGTACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACCATATACAGAAACA
* *
2307516 TGTGACACGTCATGTACAGAAACATGTGACACGCCATGTACAGAAACATGTAACACGTCATGCAC
66 TGTGACACATCATGTACAGAAACATATGACACGCCATGTACAGAAACATGTAACACGTCATGCAC
2307581 AAAAACATGTGACACGTCATGGTTAGGTTGCT
131 AAAAACATGTGACACGTCATGGTTAGGTTGCT
2307613 ACACGCCATGT
1 ACACGCCATGT
2307624 TAAAAAAAAT
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (162 bp):
ACACGCCATGTACAGAAACATGTGACACGCCATGGTTAAGTTGTTACACACCATATACAGAAACA
TGTGACACATCATGTACAGAAACATATGACACGCCATGTACAGAAACATGTAACACGTCATGCAC
AAAAACATGTGACACGTCATGGTTAGGTTGCT
Found at i:2307692 original size:26 final size:25
Alignment explanation
Indices: 2307663--2307877 Score: 114
Period size: 26 Copynumber: 8.0 Consensus size: 25
2307653 TATAAAAACA
2307663 TGTTACACGTCATGGTTAAAAAAAAT
1 TGTTACACGTCAT-GTTAAAAAAAAT
*
2307689 TGTTACACGCCATGTTGAAAAAAAAATACT
1 TGTTACACGTCATGTT---AAAAAAA-A-T
* *
2307719 GCTGTTACACGTCAT-ATACAAAAACA-
1 --TGTTACACGTCATGTTA-AAAAAAAT
* * *
2307745 TGTTATACGCCATGGTTAAAAAAGAT
1 TGTTACACGTCAT-GTTAAAAAAAAT
* *
2307771 TGTTACACATCATATTGAAAAAAAAATACTGT
1 TGTTACACGTCATGTT---AAAAAAA-A---T
*
2307803 TGTTACACGTCAT-ATAAAAAAACA-
1 TGTTACACGTCATGTTAAAAAAA-AT
*
2307827 TGTTACACGTCATTGTTAAAAAAGAT
1 TGTTACACGTCA-TGTTAAAAAAAAT
* *
2307853 TGTTACACGCCATATTGAAAAAAAA
1 TGTTACACGTCATGTT-AAAAAAAA
2307878 ATACTATTGT
Statistics
Matches: 146, Mismatches: 21, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
24 23 0.16
25 16 0.11
26 49 0.34
28 23 0.16
29 7 0.05
30 1 0.01
31 2 0.01
32 25 0.17
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (25 bp):
TGTTACACGTCATGTTAAAAAAAAT
Found at i:2307747 original size:82 final size:82
Alignment explanation
Indices: 2307581--2307893 Score: 417
Period size: 82 Copynumber: 3.9 Consensus size: 82
2307571 CGTCATGCAC
* * * * *
2307581 AAAAACATGTGACACGTCATGGTT-----AGGTTGCTACACGCCATGTT--AAAAAAAATATTGT
1 AAAAACATGTTACACGTCATGGTTAAAAAAGATTGTTACACGCCATATTGAAAAAAAAATACTGT
*
2307639 TGTTACACG-CTATATAT
66 TGTTACACGTC-ATATAA
* * *
2307656 AAAAACATGTTACACGTCATGGTTAAAAAAAATTGTTACACGCCATGTTGAAAAAAAAATACTGC
1 AAAAACATGTTACACGTCATGGTTAAAAAAGATTGTTACACGCCATATTGAAAAAAAAATACTGT
*
2307721 TGTTACACGTCATATAC
66 TGTTACACGTCATATAA
* * **
2307738 AAAAACATGTTATACGCCATGGTTAAAAAAGATTGTTACACATCATATTGAAAAAAAAATACTGT
1 AAAAACATGTTACACGTCATGGTTAAAAAAGATTGTTACACGCCATATTGAAAAAAAAATACTGT
2307803 TGTTACACGTCATATAA
66 TGTTACACGTCATATAA
* *
2307820 AAAAACATGTTACACGTCATTGTTAAAAAAGATTGTTACACGCCATATTGAAAAAAAAATACTAT
1 AAAAACATGTTACACGTCATGGTTAAAAAAGATTGTTACACGCCATATTGAAAAAAAAATACTGT
2307885 TGTTACACG
66 TGTTACACG
2307894 CCTTGTTGAA
Statistics
Matches: 209, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
75 23 0.11
80 17 0.08
82 168 0.80
83 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (82 bp):
AAAAACATGTTACACGTCATGGTTAAAAAAGATTGTTACACGCCATATTGAAAAAAAAATACTGT
TGTTACACGTCATATAA
Found at i:2307748 original size:24 final size:25
Alignment explanation
Indices: 2307720--2307876 Score: 75
Period size: 24 Copynumber: 5.9 Consensus size: 25
2307710 AAAAATACTG
*
2307720 CTGTTACACGTCATATACAAAAACA
1 CTGTTACACGTCATATAAAAAAACA
* * * * *
2307745 -TGTTATACGCCATGGTTAAAAAAGA
1 CTGTTACACGTCAT-ATAAAAAAACA
* * *
2307770 TTGTTACACATCATATTGAAAAAAAAATA
1 CTGTTACACGTCATA-T---AAAAAAACA
2307799 CTGTTGTTACACGTCATATAAAAAAACA
1 C---TGTTACACGTCATATAAAAAAACA
* * *
2307827 -TGTTACACGTCATTGTTAAAAAAGA
1 CTGTTACACGTCA-TATAAAAAAACA
* *
2307852 TTGTTACACGCCATATTGAAAAAAA
1 CTGTTACACGTCATA-T-AAAAAAA
2307877 AATACTATTG
Statistics
Matches: 98, Mismatches: 21, Indels: 24
0.69 0.15 0.17
Matches are distributed among these distances:
24 23 0.23
25 17 0.17
26 23 0.23
27 6 0.06
28 8 0.08
29 7 0.07
31 1 0.01
32 13 0.13
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (25 bp):
CTGTTACACGTCATATAAAAAAACA
Found at i:2307816 original size:32 final size:30
Alignment explanation
Indices: 2307770--2307935 Score: 104
Period size: 29 Copynumber: 5.8 Consensus size: 30
2307760 TTAAAAAAGA
*
2307770 TTGTTACACATCATATTGAAAAAAAAATACT
1 TTGTTACACGTCATATTG-AAAAAAAATACT
2307801 GTTGTTACACGTCATA-T---AAAAAA-AC-
1 -TTGTTACACGTCATATTGAAAAAAAATACT
* ** *
2307826 ATGTTACACGTC--ATTGTTAAAAAAGA--
1 TTGTTACACGTCATATTGAAAAAAAATACT
*
2307852 TTGTTACACGCCATATTGAAAAAAAAATACT
1 TTGTTACACGTCATATTG-AAAAAAAATACT
* * * *
2307883 ATTGTTACACGCCTTGTTG--AAAAAATATT
1 -TTGTTACACGTCATATTGAAAAAAAATACT
*
2307912 ATTGTTACACGTCATATTCAAAAA
1 -TTGTTACACGTCATATTGAAAAA
2307936 CATTTTGTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 27
0.72 0.09 0.18
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 11 0.10
26 18 0.17
27 7 0.07
28 4 0.04
29 31 0.29
31 4 0.04
32 30 0.28
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (30 bp):
TTGTTACACGTCATATTGAAAAAAAATACT
Found at i:2307934 original size:29 final size:27
Alignment explanation
Indices: 2307663--2307945 Score: 104
Period size: 32 Copynumber: 10.2 Consensus size: 27
2307653 TATAAAAACA
*
2307663 TGTTACACGTCATGGTTAAAAAA-A-AT
1 TGTTACACGTCAT-ATTAAAAAATATAT
* * *
2307689 TGTTACACGCCATGTTGAAAAAAAAATACT
1 TGTTACACGTCATATT--AAAAAATATA-T
* *
2307719 GCTGTTACACGTCATA-TACAAAA-ACA-
1 --TGTTACACGTCATATTAAAAAATATAT
* * * *
2307745 TGTTATACGCCATGGTT-AAAAA-AGAT
1 TGTTACACGTCAT-ATTAAAAAATATAT
* *
2307771 TGTTACACATCATATTGAAAAAAAAATACTGT
1 TGTTACACGTCATATT----AAAAAATA-TAT
*
2307803 TGTTACACGTCATA-TAAAAAA-ACA-
1 TGTTACACGTCATATTAAAAAATATAT
* *
2307827 TGTTACACGTCAT-TGTTAAAAA-AGAT
1 TGTTACACGTCATAT-TAAAAAATATAT
*
2307853 TGTTACACGCCATATTGAAAAAAAAATACTAT
1 TGTTACACGTCATATT----AAAAAATA-TAT
* * *
2307885 TGTTACACGCCTTGTTGAAAAAATATTAT
1 TGTTACACGTCATATT-AAAAAATA-TAT
* * *
2307914 TGTTACACGTCATATTCAAAAACATTT
1 TGTTACACGTCATATTAAAAAATATAT
2307941 TGTTA
1 TGTTA
2307946 TACTTTAATG
Statistics
Matches: 196, Mismatches: 34, Indels: 53
0.69 0.12 0.19
Matches are distributed among these distances:
24 24 0.12
25 19 0.10
26 37 0.19
27 20 0.10
28 9 0.05
29 30 0.15
30 11 0.06
31 4 0.02
32 42 0.21
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (27 bp):
TGTTACACGTCATATTAAAAAATATAT
Found at i:2327778 original size:33 final size:32
Alignment explanation
Indices: 2327741--2327819 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
2327731 GACATTAACG
* *
2327741 TGACATGCTAATATATTATAATTGATAATCATA
1 TGACATACTAAT-TATCATAATTGATAATCATA
* * *
2327774 TGACATATTTACTTATCATAATTGATAATGATA
1 TGACATA-CTAATTATCATAATTGATAATCATA
2327807 TGACATACTAATT
1 TGACATACTAATT
2327820 TAACATTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 4 0.11
33 31 0.82
34 3 0.08
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (32 bp):
TGACATACTAATTATCATAATTGATAATCATA
Found at i:2329333 original size:14 final size:14
Alignment explanation
Indices: 2329310--2329340 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2329300 TGATGTTGGC
2329310 TTTGTATTTTTCTT
1 TTTGTATTTTTCTT
*
2329324 TTTGTCTTTTTCTT
1 TTTGTATTTTTCTT
2329338 TTT
1 TTT
2329341 ATGATTTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.10, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTGTATTTTTCTT
Found at i:2329574 original size:20 final size:20
Alignment explanation
Indices: 2329549--2329586 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2329539 AAATTACTTT
2329549 AATGAAATAT-AAAAAGTTCA
1 AATG-AATATGAAAAAGTTCA
2329569 AATGAATATGAAAAAGTT
1 AATGAATATGAAAAAGTT
2329587 TATGAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGAATATGAAAAAGTTCA
Found at i:2329606 original size:23 final size:22
Alignment explanation
Indices: 2329568--2329610 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
2329558 TAAAAAGTTC
2329568 AAATGAATATGAAAAAGTTTATG
1 AAATGAATATGAAAAA-TTTATG
2329591 AAATGGAATATG-AAAATTTA
1 AAAT-GAATATGAAAAATTTA
2329611 GTTTACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (22 bp):
AAATGAATATGAAAAATTTATG
Found at i:2329987 original size:22 final size:22
Alignment explanation
Indices: 2329950--2329991 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2329940 TAAAAAGTTC
2329950 AAATGAATATGAAAAATTTATA
1 AAATGAATATGAAAAATTTATA
2329972 AAATGGAATATG-AAAATTTA
1 AAAT-GAATATGAAAAATTTA
2329992 GTTTGCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (22 bp):
AAATGAATATGAAAAATTTATA
Found at i:2330230 original size:381 final size:382
Alignment explanation
Indices: 2329524--2330286 Score: 1341
Period size: 381 Copynumber: 2.0 Consensus size: 382
2329514 GAAATCGAAA
**
2329524 AATATTAAAATATTAAAATTACTTTAATGAAATATAAAAAGTTCAAATGAATATGAAAAAGTTTA
1 AATATTAAAATATTAAAATTACTTTAACAAAATATAAAAAGTTCAAATGAATATGAAAAAGTTTA
* * * *
2329589 TGAAATGGAATATGAAAATTTAGTTTACATTAGTCAATTTTAATCCTAATCTTAAAAAATAAAAT
66 TAAAATGGAATATGAAAATTTAGTTTACATTAATAAATTTTAATACTAATCTTAAAAAATAAAAT
*
2329654 ATTTAATACTTGTATTTATTATGTAAAAAATTAATTTTATATATTATATAAATATTAACACTTTT
131 ATTTAATACTTGTATTTATTATGCAAAAAATTAATTTTATATATTATATAAATATTAACACTTTT
2329719 TAAATCATTAGAATAATAACAATAATAAAACTCTGACTCAATATATAAATCACATCAAAATGTCT
196 TAAATCATTAGAATAATAACAATAATAAAACTCTGACTCAATATATAAATCACATCAAAATGTCT
* *
2329784 AATTGGGGGCATATCTATCATCTATTCGTTTACTTGATAGCAACATTTTTCTACCAATTTCGTTC
261 AATTGGGGGCATATCTATCATCTATTCGTTTACTTGATAGCAACATATTTCTACCAATCTCGTTC
*
2329849 ATTTGACTTTCATGTACTTTCTCATTAATTTAAAATTCATTATAATCAAAGTATTTT
326 ATTTGACTTTCATGTACGTTCTCATTAATTTAAAATTCATTATAATCAAAGTATTTT
2329906 AATATTAAAATATTAAAATTACTTTAACAAAATATAAAAAGTTCAAATGAATATGAAAAA-TTTA
1 AATATTAAAATATTAAAATTACTTTAACAAAATATAAAAAGTTCAAATGAATATGAAAAAGTTTA
*
2329970 TAAAATGGAATATGAAAATTTAGTTTGCATTAATAAATTTTAATACTAATCTTAAAAAATAAAAT
66 TAAAATGGAATATGAAAATTTAGTTTACATTAATAAATTTTAATACTAATCTTAAAAAATAAAAT
*
2330035 ATTTAATACTTGTATTTATTATGCAAAAATTTAATTTTATATATTATATAAATATTAACACTTTT
131 ATTTAATACTTGTATTTATTATGCAAAAAATTAATTTTATATATTATATAAATATTAACACTTTT
* *
2330100 TAAATTATTAGAATAATAACAATAATAAAACTCTGACTCAGA-ATATAAATCACATCAAAATTTC
196 TAAATCATTAGAATAATAACAATAATAAAACTCTGACTCA-ATATATAAATCACATCAAAATGTC
* *
2330164 TAATTTGGGGCATATCTATCATCTATTCGTTTACTTGATAGCAATATATTTCTACCAATCTCGTT
260 TAATTGGGGGCATATCTATCATCTATTCGTTTACTTGATAGCAACATATTTCTACCAATCTCGTT
* *
2330229 CATTTGACTTTCATGTACGTTCTCCTTAATTTAAAATTCATTATAATCAGAGTATTTT
325 CATTTGACTTTCATGTACGTTCTCATTAATTTAAAATTCATTATAATCAAAGTATTTT
2330287 GTTTAAGATA
Statistics
Matches: 362, Mismatches: 18, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
381 303 0.84
382 59 0.16
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (382 bp):
AATATTAAAATATTAAAATTACTTTAACAAAATATAAAAAGTTCAAATGAATATGAAAAAGTTTA
TAAAATGGAATATGAAAATTTAGTTTACATTAATAAATTTTAATACTAATCTTAAAAAATAAAAT
ATTTAATACTTGTATTTATTATGCAAAAAATTAATTTTATATATTATATAAATATTAACACTTTT
TAAATCATTAGAATAATAACAATAATAAAACTCTGACTCAATATATAAATCACATCAAAATGTCT
AATTGGGGGCATATCTATCATCTATTCGTTTACTTGATAGCAACATATTTCTACCAATCTCGTTC
ATTTGACTTTCATGTACGTTCTCATTAATTTAAAATTCATTATAATCAAAGTATTTT
Found at i:2333383 original size:2 final size:2
Alignment explanation
Indices: 2333378--2333436 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
2333368 TATATATATA
** *
2333378 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CC TG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
**
2333420 TG CA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG T
2333437 ATAATTGGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.02, C:0.07, G:0.46, T:0.46
Consensus pattern (2 bp):
TG
Found at i:2352619 original size:15 final size:15
Alignment explanation
Indices: 2352599--2352636 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
2352589 TTGGACAAAA
2352599 TTACACGTTATGATG
1 TTACACGTTATGATG
2352614 TTACACGTTATGATG
1 TTACACGTTATGATG
2352629 TTACACGT
1 TTACACGT
2352637 CATATACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (15 bp):
TTACACGTTATGATG
Found at i:2352677 original size:21 final size:21
Alignment explanation
Indices: 2352651--2352706 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
2352641 TACAAAAATA
*
2352651 TGTTACACTCCATGATTAAGT
1 TGTTACACACCATGATTAAGT
* *
2352672 TGTTACACGCCATGATTAGGT
1 TGTTACACACCATGATTAAGT
*
2352693 TGTTATACACCATG
1 TGTTACACACCATG
2352707 TACAGAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (21 bp):
TGTTACACACCATGATTAAGT
Found at i:2352743 original size:24 final size:24
Alignment explanation
Indices: 2352702--2352754 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2352692 TTGTTATACA
*
2352702 CCATGTACAGAAACATGTGACACG
1 CCATGTACAAAAACATGTGACACG
* * *
2352726 CCATGTATAAAAATATGTGATACG
1 CCATGTACAAAAACATGTGACACG
*
2352750 TCATG
1 CCATG
2352755 ATTAAGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
CCATGTACAAAAACATGTGACACG
Found at i:2353334 original size:23 final size:23
Alignment explanation
Indices: 2353307--2353357 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2353297 CTTAGTATCT
*
2353307 TGAAAGCGTAAAAAAGAGAAATC
1 TGAAAACGTAAAAAAGAGAAATC
* * * *
2353330 TGAAAATGTGAGAGAGAGAAATC
1 TGAAAACGTAAAAAAGAGAAATC
2353353 TGAAA
1 TGAAA
2353358 CATAACAGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.06, G:0.25, T:0.16
Consensus pattern (23 bp):
TGAAAACGTAAAAAAGAGAAATC
Found at i:2364140 original size:1 final size:1
Alignment explanation
Indices: 2364136--2364172 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
2364126 CTGCACTGCG
* *
2364136 CCCCCCACCCCCCCCCCCCCCCCCCCCCCTCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2364173 AANCCCAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.95, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:2368299 original size:72 final size:72
Alignment explanation
Indices: 2368210--2368358 Score: 298
Period size: 72 Copynumber: 2.1 Consensus size: 72
2368200 CGAAAAGGCA
2368210 TTCTCGCTGCAAAGAATGAAATTTTGTTGCAGCGAAATCCAAGGCAAAATTTTGAACCAACCACC
1 TTCTCGCTGCAAAGAATGAAATTTTGTTGCAGCGAAATCCAAGGCAAAATTTTGAACCAACCACC
2368275 CGAGAGT
66 CGAGAGT
2368282 TTCTCGCTGCAAAGAATGAAATTTTGTTGCAGCGAAATCCAAGGCAAAATTTTGAACCAACCACC
1 TTCTCGCTGCAAAGAATGAAATTTTGTTGCAGCGAAATCCAAGGCAAAATTTTGAACCAACCACC
2368347 CGAGAGT
66 CGAGAGT
2368354 TTCTC
1 TTCTC
2368359 ATTGCAGCGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (72 bp):
TTCTCGCTGCAAAGAATGAAATTTTGTTGCAGCGAAATCCAAGGCAAAATTTTGAACCAACCACC
CGAGAGT
Found at i:2368749 original size:36 final size:36
Alignment explanation
Indices: 2368660--2368795 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 36
2368650 CTCCCCCGGC
* * *
2368660 TCATGTGCACTCCCACATTGCACATTACAAT-ATCA
1 TCATGTGCACTCCCACACTGCACCTCACAATCATCA
* *
2368695 TCATCGGGTGCACTCCCACACTGCACCTCACCATCACCA
1 TCAT---GTGCACTCCCACACTGCACCTCACAATCATCA
* * *
2368734 TCATGTGCACTCCCACACCGCACACGGCATATATCATCA
1 TCATGTGCACTCCCACACTGCAC-C-TCACA-ATCATCA
*
2368773 TCATGTGCTCTCCCACACTGCAC
1 TCATGTGCACTCCCACACTGCAC
2368796 AAGGCATATA
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
35 4 0.05
36 18 0.22
37 1 0.01
38 25 0.30
39 34 0.41
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.23
Consensus pattern (36 bp):
TCATGTGCACTCCCACACTGCACCTCACAATCATCA
Found at i:2368775 original size:39 final size:39
Alignment explanation
Indices: 2368727--2368875 Score: 192
Period size: 39 Copynumber: 3.8 Consensus size: 39
2368717 GCACCTCACC
*
2368727 ATCACCATCATGTGCACTCCCACACCGCACACGGCATAT
1 ATCATCATCATGTGCACTCCCACACCGCACACGGCATAT
* * *
2368766 ATCATCATCATGTGCTCTCCCACACTGCACAAGGCATAT
1 ATCATCATCATGTGCACTCCCACACCGCACACGGCATAT
*
2368805 ATCATCATCATGTGCTA-TCCCACACCGCACATGGCATAT
1 ATCATCATCATGTGC-ACTCCCACACCGCACACGGCATAT
* ** * *
2368844 ATTATCGGCGTGTGCTCTCCCACACCGCACAC
1 ATCATCATCATGTGCACTCCCACACCGCACAC
2368876 TACTAGCACT
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.26, C:0.37, G:0.14, T:0.23
Consensus pattern (39 bp):
ATCATCATCATGTGCACTCCCACACCGCACACGGCATAT
Found at i:2368792 original size:75 final size:76
Alignment explanation
Indices: 2368660--2368912 Score: 253
Period size: 78 Copynumber: 3.3 Consensus size: 76
2368650 CTCCCCCGGC
** *** * *
2368660 TCATGTGCACTCCCACATTGCACATTACA-ATATCATCATCGGGTGCACTCCCACACTGCAC-CT
1 TCATGTGCACTCCCACACCGCACACGGCATATATCATCATCGTGTGCTCTCCCACACTGCACACT
*
2368723 CACCATCACCA
66 CACTATCACCA
* *
2368734 TCATGTGCACTCCCACACCGCACACGGCATATATCATCATCATGTGCTCTCCCACACTGCACAAG
1 TCATGTGCACTCCCACACCGCACACGGCATATATCATCATCGTGTGCTCTCCCACACTGCAC-AC
* * *
2368799 GCATATATCATCA
65 TCA-CTATCACCA
* * ** *
2368812 TCATGTGCTA-TCCCACACCGCACATGGCATATATTATCGGCGTGTGCTCTCCCACACCGCACAC
1 TCATGTGC-ACTCCCACACCGCACACGGCATATATCATCATCGTGTGCTCTCCCACACTGCACAC
* **
2368876 T-ACTAGCACTG
65 TCACTATCACCA
*
2368887 TCATGTGCACTCCCACACTGCACACG
1 TCATGTGCACTCCCACACCGCACACG
2368913 CACGGTTATA
Statistics
Matches: 145, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
74 25 0.17
75 55 0.38
76 1 0.01
77 3 0.02
78 60 0.41
79 1 0.01
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.23
Consensus pattern (76 bp):
TCATGTGCACTCCCACACCGCACACGGCATATATCATCATCGTGTGCTCTCCCACACTGCACACT
CACTATCACCA
Found at i:2369107 original size:55 final size:53
Alignment explanation
Indices: 2369047--2369154 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 53
2369037 GTTCCCATGC
2369047 ATATTTAAAGAAAAGTTCAATAAAATATTTCAAGTGATTCAACCAAATAACATA
1 ATATTTAAAGAAAAGTTCAATAAAATATTTCAAGTGATTCAACCAAAT-ACATA
2369101 NATATTTAAAGAAAAGTTCAATAAAATATTTCAAGTGATTCAACCAAATACATA
1 -ATATTTAAAGAAAAGTTCAATAAAATATTTCAAGTGATTCAACCAAATACATA
2369155 TGCATTTATC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 5 0.09
55 48 0.91
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.30
Consensus pattern (53 bp):
ATATTTAAAGAAAAGTTCAATAAAATATTTCAAGTGATTCAACCAAATACATA
Found at i:2370513 original size:26 final size:27
Alignment explanation
Indices: 2370484--2370553 Score: 63
Period size: 29 Copynumber: 2.5 Consensus size: 27
2370474 TAATGAAAAT
*
2370484 TAAATTAATAAATTAAAAT-TAATTCA
1 TAAATTAATAAATTAAAATATAATTAA
*
2370510 TAAA-AAATTAAATTTAAAATCATAATTAA
1 TAAATTAA-TAAA-TTAAAAT-ATAATTAA
*
2370539 AACAATTAATAAATT
1 TA-AATTAATAAATT
2370554 TTAATAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
25 2 0.06
26 8 0.24
27 7 0.21
29 9 0.26
30 6 0.18
31 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATTAATAAATTAAAATATAATTAA
Found at i:2378103 original size:120 final size:118
Alignment explanation
Indices: 2377879--2378117 Score: 286
Period size: 120 Copynumber: 2.0 Consensus size: 118
2377869 GGAATGGTCC
* * *
2377879 AAACTTTCTTCAGCACCCATCATGATGTCCTCAAGTTCCTCGAGTGTCCATCCAAACTTCACAAG
1 AAACTTTCTTCAGCACCCATCATCATGTCCTCAAGTTCCTCAACTGTCCATCCAAACTTCACAAG
* *
2377944 ATGCAAGTTTTATAACAGTTGATCCTTTTGAACAATCTTCTTTCTCCGATTGA
66 ATGCAAGTTTTACAACAATTGATCCTTTTGAACAATCTTCTTTCTCCGATTGA
* * * *
2377997 AAACTTTCTTCAGC-CCCTATCATCATGTCTTCAAGTTCTTCAACTGTCAATATTCC-ATCTTCA
1 AAACTTTCTTCAGCACCC-ATCATCATGTCCTCAAGTTCCTCAACTGTC--CA-TCCAAACTTCA
* ** * *
2378060 CAAGATTCAAGTTCTT-CAACAATTGATCCTTTTTCACAGTCTTCTTTCTCCGTTTGA
62 CAAGATGCAAGTT-TTACAACAATTGATCCTTTTGAACAATCTTCTTTCTCCGATTGA
2378117 A
1 A
2378118 TTACACCAGT
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
117 3 0.03
118 39 0.38
120 55 0.54
121 5 0.05
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (118 bp):
AAACTTTCTTCAGCACCCATCATCATGTCCTCAAGTTCCTCAACTGTCCATCCAAACTTCACAAG
ATGCAAGTTTTACAACAATTGATCCTTTTGAACAATCTTCTTTCTCCGATTGA
Found at i:2380577 original size:686 final size:684
Alignment explanation
Indices: 2379225--2380601 Score: 2242
Period size: 686 Copynumber: 2.0 Consensus size: 684
2379215 TTATTTCTTG
* *
2379225 GAACATAGAATAGTGACTAAAGTTAATTATTCCTATTACAATTTACATAACATAGGATTATTTTG
1 GAACTTAGAATAGTGACTAAAGTTAATTATTCCTACTACAATTTACATAACATAGGATTATTTTG
*
2379290 TTGCAAACTTTACATAAAATTTTATTATTTTATTACAAATTCATAATATATTATTTTATTTTAAA
66 TTGCAAACTTTACATAAAAATTTATTATTTTATTACAAATTCATAATATATTATTTTATTTTAAA
*
2379355 AATACAATTTACTTGATTATGACATTTAAAAGAATTTCCATATTCAATCTCTCCACTTTTTTTTT
131 AATACAATTTAATTGATTATGACATTTAAAAGAATTTCCATATTCAATCTCTCCACTTTTTTTTT
2379420 TTAAAGTAGAATCAATATTCATTAAAAAAAACACACAAAAAGTAAATTAGTGTCTTCATGCTTGT
196 TTAAAGTAGAATCAATATTCATTAAAAAAAACACACAAAAAGTAAATTAGTGTCTTCATGCTTGT
* * * *
2379485 AAAATCAAAGCTTGTAACAAAACAAAAATATTTGTAGAGTATATCACGGATCCTACATTAGAGAA
261 AAAATCAAAGCTTGCAACAAAACAAAAATATTTGTAGAATATATCACGGATCCTACATTAAAAAA
* * * * *
2379550 AGATATGATGGATTTTAGATATATAAACGTGGATCTTCTATGTGAACTTGTGATTTATAGACTTA
326 AGATAGGATAGATCTTAGATATATAAACGTGAATATTCTATGTGAACTTGTGATTTATAGACTTA
* *
2379615 CTTAAACTTTATTTTCAAAATTTAAAACTGTACAAGGTTAGACTTGAATTTCGACCCATGACAAA
391 CTTAAACTCTATTTTCAAAATTTAAAACTGTACAAGGTTAGACTTGAATTTCAACCCATGACAAA
* * * * * *
2379680 TGGTATTAGAACGTATTTGAATTTTTATTGATGTGGAGTCATCGAAGACTCAGATTACTGTAAGA
456 TGGTATTAGAACATATATCAATTTTTATTAATGTGGAGTCAACGAAGACTCAGACTACTGTAAGA
* *
2379745 GTTATTCTCCTCTATAGGTAAAAAACTAATACAACGAAAGCGTTACACAATTGGGTAGGATAGAA
521 GTTACTCTCCTCTATAGGTAAAAAACTAATACAACGAAAGCGTTACACAATTGAGTAGGATAGAA
* * * *
2379810 TGTCACGGATCCCATATCATTAAGAGATAAAGTGGGTCTTAGATTTATTAAAATGGATCTTTCAC
586 TGTCACGGATCCCACATCATTAAGAGATAAAGTGGGTATTAGATATATTAAAATGGATCTTCCAC
2379875 CACATATTAAGCATGTCTTTTAAGTTAAAAATGT
651 CACATATTAAGCATGTCTTTTAAGTTAAAAATGT
2379909 GAACTTAGAATAGTGACTAAAGTTAATTATTCCTACTACAATTTACATAACATAGGATTATTTTG
1 GAACTTAGAATAGTGACTAAAGTTAATTATTCCTACTACAATTTACATAACATAGGATTATTTTG
2379974 TTGCAAACTTTACATAAAAATTTATTATTTTATTACAAATTCATAATATATTATTTTATTTTAAA
66 TTGCAAACTTTACATAAAAATTTATTATTTTATTACAAATTCATAATATATTATTTTATTTTAAA
2380039 AATACAATTTAATTGATTATGACATTTAAAAGAATTTCCATATTCAATCTCTCCACTTTTTTTTT
131 AATACAATTTAATTGATTATGACATTTAAAAGAATTTCCATATTCAATCTCTCCAC-TTTTTTTT
**
2380104 TTTAAAGTAGAATCGGTATTCATTAAAAAAAAACACACAAAAAGTAAATTAGTGTCTTCATGCTT
195 TTTAAAGTAGAATCAATATTCATT-AAAAAAAACACACAAAAAGTAAATTAGTGTCTTCATGCTT
*
2380169 GTAACATCAAAGCTTGCAACAAAACAAAAATATTTGTAGAATATATCACGGATCCTACATTAAAA
259 GTAAAATCAAAGCTTGCAACAAAACAAAAATATTTGTAGAATATATCACGGATCCTACATTAAAA
* * * * *
2380234 AAAGATAGGATAGATCTTGGATATATAAACGTGAATATTTTATGTGAGCTTGTGATTTATGGGCT
324 AAAGATAGGATAGATCTTAGATATATAAACGTGAATATTCTATGTGAACTTGTGATTTATAGACT
*
2380299 TACTTAAACTCTATTTTCAAAATTTAAAACTGTACAAGGTTAGACTTGAA-TTCTAACTCATGAC
389 TACTTAAACTCTATTTTCAAAATTTAAAACTGTACAAGGTTAGACTTGAATTTC-AACCCATGAC
*
2380363 AAATGGTATTAGAGCATATATCAATTTTTATTAATGTGGAGTCAACGAAGACTC-GAACTACTGT
453 AAATGGTATTAGAACATATATCAATTTTTATTAATGTGGAGTCAACGAAGACTCAG-ACTACTGT
* * * *
2380427 AAGAGTTCCTCTCTTCTATAGGTAAAAAACTAATACAACGAGAGCGTTACACAATTGAGTGGGAT
517 AAGAGTTACTCTCCTCTATAGGTAAAAAACTAATACAACGAAAGCGTTACACAATTGAGTAGGAT
2380492 AGAATGTCACGGATCCCACATCATTAAGAGATAAAGTGGGTATT-GA-ATATATAAACAT-GAGT
582 AGAATGTCACGGATCCCACATCATTAAGAGATAAAGTGGGTATTAGATATAT-TAAA-ATGGA-T
* ** *
2380554 CTTCCACCATATATTTGGCATGTCTTTTGAGTTAAAAATGT
644 CTTCCACCACATATTAAGCATGTCTTTTAAGTTAAAAATGT
*
2380595 GAGCTTA
1 GAACTTA
2380602 TGATTTATGG
Statistics
Matches: 640, Mismatches: 46, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
684 185 0.29
685 42 0.07
686 413 0.65
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (684 bp):
GAACTTAGAATAGTGACTAAAGTTAATTATTCCTACTACAATTTACATAACATAGGATTATTTTG
TTGCAAACTTTACATAAAAATTTATTATTTTATTACAAATTCATAATATATTATTTTATTTTAAA
AATACAATTTAATTGATTATGACATTTAAAAGAATTTCCATATTCAATCTCTCCACTTTTTTTTT
TTAAAGTAGAATCAATATTCATTAAAAAAAACACACAAAAAGTAAATTAGTGTCTTCATGCTTGT
AAAATCAAAGCTTGCAACAAAACAAAAATATTTGTAGAATATATCACGGATCCTACATTAAAAAA
AGATAGGATAGATCTTAGATATATAAACGTGAATATTCTATGTGAACTTGTGATTTATAGACTTA
CTTAAACTCTATTTTCAAAATTTAAAACTGTACAAGGTTAGACTTGAATTTCAACCCATGACAAA
TGGTATTAGAACATATATCAATTTTTATTAATGTGGAGTCAACGAAGACTCAGACTACTGTAAGA
GTTACTCTCCTCTATAGGTAAAAAACTAATACAACGAAAGCGTTACACAATTGAGTAGGATAGAA
TGTCACGGATCCCACATCATTAAGAGATAAAGTGGGTATTAGATATATTAAAATGGATCTTCCAC
CACATATTAAGCATGTCTTTTAAGTTAAAAATGT
Found at i:2380797 original size:80 final size:79
Alignment explanation
Indices: 2380658--2380894 Score: 291
Period size: 80 Copynumber: 3.0 Consensus size: 79
2380648 ACGATATTGG
* * *
2380658 ACTTAAGTTTTAGCTTATGACAATAAACATGCCTCT-GAATCCCCCGATTACAATGAGATTGGAC
1 ACTTAAGTTTTAGCTCATGACAATAAACATGCCTCTAG-AT-CCCCGATCACAACGAGATTGGAC
*
2380722 TTAAGTTCTAACTCC-T
64 TTAAGTTCCAAC-CCGT
* * * * *
2380738 ACTTAAGTTCTAGCCCATGACAATAAACAAGCCTCTAGATCCTCCGATCACAACAAGATTGAACT
1 ACTTAAGTTTTAGCTCATGACAATAAACATGCCTCTAGATCC-CCGATCACAACGAGATTGGACT
2380803 TAAGTTCCAACCCGT
65 TAAGTTCCAACCCGT
* * *
2380818 ACTTAAGTTTTAGCTCGTGACAATAAACATGCCTCTAGATCCCCTAATCACAACGAGATTGGAAT
1 ACTTAAGTTTTAGCTCATGACAATAAACATGCCTCTAGATCCCC-GATCACAACGAGATTGGACT
2380883 TATA-TTCCAACC
65 TA-AGTTCCAACC
2380895 TGTGACAATA
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
79 6 0.04
80 127 0.94
81 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (79 bp):
ACTTAAGTTTTAGCTCATGACAATAAACATGCCTCTAGATCCCCGATCACAACGAGATTGGACTT
AAGTTCCAACCCGT
Found at i:2399514 original size:16 final size:16
Alignment explanation
Indices: 2399490--2399584 Score: 59
Period size: 16 Copynumber: 5.5 Consensus size: 16
2399480 TAGTATTAAA
2399490 AAAACTATTAATTAATT
1 AAAA-TATTAATTAATT
*
2399507 AAAATATTATTTAATT
1 AAAATATTAATTAATT
*
2399523 GATAAATTAATAAATTAA-T
1 -A-AAA-T-ATTAATTAATT
2399542 AATTTATATATTAATTAA-T
1 AA---A-ATATTAATTAATT
* *
2399561 AAAAAATTAATTTATT
1 AAAATATTAATTAATT
2399577 AAAATATT
1 AAAATATT
2399585 TTTCATTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
15 9 0.15
16 20 0.32
17 6 0.10
18 4 0.06
19 13 0.21
20 9 0.15
21 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (16 bp):
AAAATATTAATTAATT
Found at i:2399530 original size:8 final size:8
Alignment explanation
Indices: 2399496--2399571 Score: 50
Period size: 8 Copynumber: 9.8 Consensus size: 8
2399486 TAAAAAAACT
*
2399496 ATTAATTA
1 ATTAATAA
2399504 ATTAA-AA
1 ATTAATAA
* *
2399511 TATTATTTA
1 -ATTAATAA
*
2399520 ATTGATAA
1 ATTAATAA
2399528 ATTAATAA
1 ATTAATAA
2399536 ATTAAT-A
1 ATTAATAA
* *
2399543 ATTTATAT
1 ATTAATAA
*
2399551 ATTAATTA
1 ATTAATAA
*
2399559 A-TAAAAA
1 ATTAATAA
2399566 ATTAAT
1 ATTAAT
2399572 TTATTAAAAT
Statistics
Matches: 49, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
7 12 0.24
8 36 0.73
9 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (8 bp):
ATTAATAA
Found at i:2399568 original size:23 final size:23
Alignment explanation
Indices: 2399519--2399578 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
2399509 AATATTATTT
* * * *
2399519 AATTGATAAATTAATAAATTAAT
1 AATTAATATATTAATAAATAAAA
* *
2399542 AATTTATATATTAATTAATAAAA
1 AATTAATATATTAATAAATAAAA
*
2399565 AATTAATTTATTAA
1 AATTAATATATTAA
2399579 AATATTTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTAATATATTAATAAATAAAA
Found at i:2399571 original size:27 final size:28
Alignment explanation
Indices: 2399495--2399575 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
2399485 TTAAAAAAAC
*
2399495 TATTAATTAATTAAAATATT-ATTTA-AT
1 TATTAATTAA-TAAAAAATTAATTTATAT
* *
2399522 TGATAAATTAATAAATTAA-TAATTTATA-
1 T-ATTAATTAATAAA-AAATTAATTTATAT
2399550 TATTAATTAATAAAAAATTAATTTAT
1 TATTAATTAATAAAAAATTAATTTAT
2399576 TAAAATATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 2 0.05
27 26 0.59
28 15 0.34
29 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TATTAATTAATAAAAAATTAATTTATAT
Found at i:2399782 original size:17 final size:17
Alignment explanation
Indices: 2399762--2399806 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
2399752 GTTCATAATT
2399762 TTAATAAAAAATATTTA
1 TTAATAAAAAATATTTA
2399779 TTAAATATAAAAAATATTTA
1 TT--A-ATAAAAAATATTTA
*
2399799 TTTATAAA
1 TTAATAAA
2399807 CTCAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 7 0.29
19 1 0.04
20 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATAAAAAATATTTA
Found at i:2403553 original size:33 final size:35
Alignment explanation
Indices: 2403516--2403611 Score: 135
Period size: 36 Copynumber: 2.8 Consensus size: 35
2403506 TTTCAAGCAT
2403516 TTGATTAAAATTGTTTAATTAAGTTGT-G-CCTAA
1 TTGATTAAAATTGTTTAATTAAGTTGTGGACCTAA
*
2403549 TTGATTAAATTTGTTTAATTAAGTCAT-TGGACCTAA
1 TTGATTAAAATTGTTTAATTAAGT--TGTGGACCTAA
*
2403585 TTGATTAAAATTGTTTAATTAAATTGT
1 TTGATTAAAATTGTTTAATTAAGTTGT
2403612 TGGGCTTAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
33 23 0.42
34 2 0.04
35 3 0.05
36 27 0.49
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (35 bp):
TTGATTAAAATTGTTTAATTAAGTTGTGGACCTAA
Found at i:2403622 original size:36 final size:35
Alignment explanation
Indices: 2403516--2403622 Score: 128
Period size: 36 Copynumber: 3.1 Consensus size: 35
2403506 TTTCAAGCAT
*
2403516 TTGATTAAAATTGTTTAATT-AA-GTTGTGCCTAA
1 TTGATTAAAATTGTTTAATTAAATGTTGGGCCTAA
* * * *
2403549 TTGATTAAATTTGTTTAATTAAGTCATTGGACCTAA
1 TTGATTAAAATTGTTTAATTAAAT-GTTGGGCCTAA
*
2403585 TTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAA
1 TTGATTAAAATTGTTTAATTAAA-TGTTGGGCCTAA
2403621 TT
1 TT
2403623 AAATTATTGG
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 19 0.32
34 1 0.02
36 39 0.65
37 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.47
Consensus pattern (35 bp):
TTGATTAAAATTGTTTAATTAAATGTTGGGCCTAA
Found at i:2403639 original size:18 final size:18
Alignment explanation
Indices: 2403600--2403640 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2403590 TAAAATTGTT
* * *
2403600 TAATTAAATTGTTGGGCT
1 TAATTAAATTATTGGACC
2403618 TAATTAAATTATTGGACC
1 TAATTAAATTATTGGACC
2403636 TAATT
1 TAATT
2403641 GATTAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (18 bp):
TAATTAAATTATTGGACC
Found at i:2414812 original size:24 final size:22
Alignment explanation
Indices: 2414769--2414812 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2414759 ATACTTATTT
2414769 AAATTTTTTTAAAATAATTTAA
1 AAATTTTTTTAAAATAATTTAA
*
2414791 AAATTTTATTTGAAAATTATTT
1 AAATTTT-TTT-AAAATAATTT
2414813 TTTTTTTTAA
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:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATTTTTTTAAAATAATTTAA
Found at i:2421289 original size:13 final size:13
Alignment explanation
Indices: 2421271--2421295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2421261 TGCAGATTAA
2421271 ATTTTTATTTTTT
1 ATTTTTATTTTTT
2421284 ATTTTTATTTTT
1 ATTTTTATTTTT
2421296 AAAATTGACT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:2422354 original size:75 final size:76
Alignment explanation
Indices: 2422196--2422340 Score: 211
Period size: 76 Copynumber: 1.9 Consensus size: 76
2422186 AAACCTATAC
* * * * * *
2422196 TTATAAATATGTATTTATTAAATGATGATTATTGAAATATTTTTTTTAATATAATTATTAGTAAG
1 TTATAAATATGTATTCATCAAATGAGGATCAGTGAAATATTTTTTTTAATATAATTATTAATAAG
2422261 ATTTAAACCTA
66 ATTTAAACCTA
* *
2422272 TTATAAATGTGTATTCATCAAATGAGGATCAGTGAAATA-TTTTTTTATTATAATTATTAATAAG
1 TTATAAATATGTATTCATCAAATGAGGATCAGTGAAATATTTTTTTTAATATAATTATTAATAAG
2422336 ATTTA
66 ATTTA
2422341 TTCCATTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
75 28 0.46
76 33 0.54
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (76 bp):
TTATAAATATGTATTCATCAAATGAGGATCAGTGAAATATTTTTTTTAATATAATTATTAATAAG
ATTTAAACCTA
Found at i:2422473 original size:20 final size:20
Alignment explanation
Indices: 2422422--2422478 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
2422412 ATTGTATAAT
* *
2422422 TTAAGTATTAATATTTTTAA
1 TTAAATATTAATATTTTAAA
* *
2422442 TTAATTTTTTAATATTTTAAA
1 TTAA-ATATTAATATTTTAAA
*
2422463 TTAAATATTAACATTT
1 TTAAATATTAATATTT
2422479 ATCAAACTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAAATATTAATATTTTAAA
Found at i:2423105 original size:18 final size:20
Alignment explanation
Indices: 2423074--2423111 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2423064 ATTAAAAAGA
*
2423074 AAAAAATAATTGTTT-TTTT
1 AAAAAATAAGTGTTTCTTTT
2423093 AAAAAA-AAGTGTTTCTTTT
1 AAAAAATAAGTGTTTCTTTT
2423112 TTCTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAAAATAAGTGTTTCTTTT
Found at i:2424710 original size:19 final size:19
Alignment explanation
Indices: 2424686--2424752 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
2424676 AAAATATTAA
2424686 TAATATATAATTTAAATAT
1 TAATATATAATTTAAATAT
* *
2424705 TAATATTTTATTTATAAT-T
1 TAATATATAATTTA-AATAT
*
2424724 TAATTATTTATATTTTAAAATAT
1 TAA-TA--TATAATTT-AAATAT
2424747 TAATAT
1 TAATAT
2424753 TTTATTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
19 16 0.43
20 6 0.16
22 10 0.27
23 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATAATTTAAATAT
Found at i:2424712 original size:42 final size:43
Alignment explanation
Indices: 2424668--2424761 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 43
2424658 ATTTTATTTA
2424668 TTTATTTAAAAATATTAATAATATATAATTT-AAATATTAATAT
1 TTTATTTAAAAAT-TTAATAATATATAATTTAAAATATTAATAT
* * * *
2424711 TTTATTT-ATAATTTAATTATTTATATTTTAAAATATTAATAT
1 TTTATTTAAAAATTTAATAATATATAATTTAAAATATTAATAT
2424753 TTTATTTAA
1 TTTATTTAA
2424762 TTTAAATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 14 0.31
42 23 0.51
43 8 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (43 bp):
TTTATTTAAAAATTTAATAATATATAATTTAAAATATTAATAT
Found at i:2424714 original size:15 final size:15
Alignment explanation
Indices: 2424696--2424756 Score: 58
Period size: 16 Copynumber: 4.3 Consensus size: 15
2424686 TAATATATAA
2424696 TTTAAATATTAATAT
1 TTTAAATATTAATAT
*
2424711 TTT--AT-TT-ATAA
1 TTTAAATATTAATAT
* *
2424722 TTTAATTATTTATAT
1 TTTAAATATTAATAT
2424737 TTTAAAATATTAATAT
1 TTT-AAATATTAATAT
2424753 TTTA
1 TTTA
2424757 TTTAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
11 6 0.17
12 2 0.06
13 3 0.08
14 2 0.06
15 10 0.28
16 13 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAATATTAATAT
Found at i:2424731 original size:26 final size:26
Alignment explanation
Indices: 2424691--2424740 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2424681 ATTAATAATA
2424691 TATAATTTAAATATTAATATTTTATT
1 TATAATTTAAATATTAATATTTTATT
* *
2424717 TATAATTTAATTATTTATATTTTA
1 TATAATTTAAATATTAATATTTTA
2424741 AAATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATAATTTAAATATTAATATTTTATT
Found at i:2424738 original size:64 final size:64
Alignment explanation
Indices: 2424632--2424772 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 64
2424622 TATTAGATTT
* * * *
2424632 TTTAAATATTATTATGATTTATTTGTATTTTATTTATTTATTTAAAAATATTAATA-ATATATAA
1 TTTAAATATTAATAT-ATTTATTTATAATTTAATTATTTATTTAAAAATATTAATATATATATAA
* * *
2424696 TTTAAATATTAATAT-TTTATTTATAATTTAATTATTTATATTTTAAAATATTAATATTTTATTT
1 TTTAAATATTAATATATTTATTTATAATTTAATTA-TT-TATTTAAAAATATTAATA-TATATAT
2424760 AA
63 AA
2424762 TTTAAATATTA
1 TTTAAATATTA
2424773 TTATGATCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
62 16 0.24
63 2 0.03
64 31 0.47
66 17 0.26
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (64 bp):
TTTAAATATTAATATATTTATTTATAATTTAATTATTTATTTAAAAATATTAATATATATATAA
Found at i:2425354 original size:12 final size:12
Alignment explanation
Indices: 2425339--2425363 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2425329 TTTATTTATT
2425339 TCTTTAATTTTA
1 TCTTTAATTTTA
2425351 TCTTTAATTTTA
1 TCTTTAATTTTA
2425363 T
1 T
2425364 TTCTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTTTAATTTTA
Found at i:2425374 original size:11 final size:11
Alignment explanation
Indices: 2425345--2425386 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2425335 TATTTCTTTA
*
2425345 ATTTTATCTTTA
1 ATTTTAT-TTTT
2425357 ATTTTATTTCTT
1 ATTTTATTT-TT
2425369 -TTTTATTTTT
1 ATTTTATTTTT
2425379 ATTTTATT
1 ATTTTATT
2425387 AGTTTTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.07
11 17 0.63
12 8 0.30
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:2425392 original size:22 final size:23
Alignment explanation
Indices: 2425346--2425393 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2425336 ATTTCTTTAA
*
2425346 TTTTATCTTTAATTTTATTTCTT
1 TTTTATCTTTAATTTTATTACTT
* *
2425369 TTTTAT-TTTTATTTTATTAGTT
1 TTTTATCTTTAATTTTATTACTT
2425391 TTT
1 TTT
2425394 CAAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTATCTTTAATTTTATTACTT
Found at i:2425519 original size:203 final size:204
Alignment explanation
Indices: 2425151--2425560 Score: 515
Period size: 203 Copynumber: 2.0 Consensus size: 204
2425141 AGTTCAATAC
2425151 TTAATTCTATTTCTTTTCTATTTTTATTTTATTAATTTTTCAAAATAAATAAAAATTCCTGATAC
1 TTAATTCTATTTCTTTTCTATTTTTATTTTATTAATTTTTCAAAATAAATAAAAATTCCTGATAC
* ** * * * *
2425216 TAAATTTTTTTTAAAATCTCCCAAGCCCATGGTAAAATTTTGGAAAATTCTCTCACTTAGAAATT
66 TAAATATTTCCTAAAATCTCCCAAGCCCATGATAAAATTTTGGAAAAATCTCTCACCTAAAAATT
* * ** * * * * *
2425281 CTCAAGAAGTCACTTTTGGTTTTCTTGAAATTTCATCATT-AGAGTTTATTTATTTATTTCTTTA
131 CCCAAAAAACCACTTTTGGTTTTCTTGAAATTTCATCATTGAGAATGTATTTATTTAATTATATA
2425345 ATTTTATCT
196 ATTTTATCT
* * * * * *
2425354 TTAATTTTATTTCTTTTTTATTTTTATTTTATTAGTTTTTCAAAATAAATAAAATTTCTTGATAT
1 TTAATTCTATTTCTTTTCTATTTTTATTTTATTAATTTTTCAAAATAAATAAAAATTCCTGATAC
**
2425419 TGAAA-ATTTCCTAAAATCTCCCAAACGCTTATGATAAAATTTT-GAAAAAT-TCTCACCTAAAA
66 T-AAATATTTCCTAAAATCTCCC-AA-GCCCATGATAAAATTTTGGAAAAATCTCTCACCTAAAA
*
2425481 ATTCCCAAAAAACCACTTTTGGATTTT-TTGAGATTTCATCATTGGAGAATGTATTTATTTAATT
128 ATTCCCAAAAAACCACTTTTGG-TTTTCTTGAAATTTCATCATT-GAGAATGTATTTATTTAATT
2425545 ATATAATTTTATCT
191 ATATAATTTTATCT
2425559 TT
1 TT
2425561 TTTAAAAAAT
Statistics
Matches: 176, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
203 117 0.66
204 15 0.09
205 44 0.25
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (204 bp):
TTAATTCTATTTCTTTTCTATTTTTATTTTATTAATTTTTCAAAATAAATAAAAATTCCTGATAC
TAAATATTTCCTAAAATCTCCCAAGCCCATGATAAAATTTTGGAAAAATCTCTCACCTAAAAATT
CCCAAAAAACCACTTTTGGTTTTCTTGAAATTTCATCATTGAGAATGTATTTATTTAATTATATA
ATTTTATCT
Found at i:2426340 original size:23 final size:22
Alignment explanation
Indices: 2426297--2426340 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2426287 AAATACAAAT
* *
2426297 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAATATAATA
*
2426319 ATATTTTGTATTAGGATATAAT
1 ATATTTT-TATTAGAATATAAT
2426341 TAAACCTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
ATATTTTTATTAGAATATAATA
Found at i:2426426 original size:33 final size:32
Alignment explanation
Indices: 2426384--2426455 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
2426374 TTAAAAGACA
2426384 AAAT-ATATTCTTCATTAAATTTA-AATATTAC
1 AAATAATATTCTTCATTAAATTTATAATATT-C
* * *
2426415 TAAATAATATTCTTTATTACATTTATTATATTC
1 -AAATAATATTCTTCATTAAATTTATAATATTC
2426448 AAATAATA
1 AAATAATA
2426456 ATATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 12 0.34
33 18 0.51
34 5 0.14
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (32 bp):
AAATAATATTCTTCATTAAATTTATAATATTC
Found at i:2426484 original size:44 final size:43
Alignment explanation
Indices: 2426415--2426507 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 43
2426405 TAAATATTAC
*
2426415 TAAATAATATTCTTTATTACATTTATTATA-TTCAAATAATAATAT
1 TAAATAATATTCTTTATAACATTTATTATAGTT-AAATAAT-AT-T
*
2426460 TAAATAATATT-TTTATAATATTTATTATAGTTAAATAATATT
1 TAAATAATATTCTTTATAACATTTATTATAGTTAAATAATATT
2426502 TAAATA
1 TAAATA
2426508 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
42 7 0.16
43 2 0.04
44 23 0.51
45 13 0.29
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (43 bp):
TAAATAATATTCTTTATAACATTTATTATAGTTAAATAATATT
Found at i:2426506 original size:11 final size:11
Alignment explanation
Indices: 2426442--2426507 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
2426432 TACATTTATT
*
2426442 ATATTCAAATA
1 ATATTTAAATA
2426453 ATAATATTAAATA
1 AT-AT-TTAAATA
**
2426466 ATATTTTTATA
1 ATATTTAAATA
*
2426477 ATATTT--ATT
1 ATATTTAAATA
*
2426486 ATAGTTAAATA
1 ATATTTAAATA
2426497 ATATTTAAATA
1 ATATTTAAATA
2426508 TTTTTATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
9 7 0.16
11 25 0.57
12 4 0.09
13 8 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
ATATTTAAATA
Found at i:2435062 original size:22 final size:21
Alignment explanation
Indices: 2435022--2435069 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
2435012 AAATAATGAT
*
2435022 AAAAATTAAAGAAAAAGAA-A
1 AAAAATGAAAGAAAAAGAAGA
2435042 AAAAATGAGAAGATAAAAGAAGA
1 AAAAATGA-AAGA-AAAAGAAGA
2435065 AAAAA
1 AAAAA
2435070 GAACTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 4 0.17
22 7 0.29
23 6 0.25
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (21 bp):
AAAAATGAAAGAAAAAGAAGA
Found at i:2440678 original size:22 final size:21
Alignment explanation
Indices: 2440650--2440729 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 21
2440640 ATTTTTATAA
2440650 TTTTATTTTAAGTAAAATAAAT
1 TTTTATTTTAA-TAAAATAAAT
* *
2440672 TTTTATTATAATTAATAATTAAT
1 TTTTATTTTAA-TAA-AATAAAT
* *
2440695 TATTATTATTAATCAAAATATTAT
1 TTTTATT-TTAAT-AAAATA-AAT
2440719 TTATTATTTTA
1 TT-TTATTTTA
2440730 TATTCATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
22 13 0.29
23 16 0.36
24 11 0.24
25 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTTATTTTAATAAAATAAAT
Found at i:2440915 original size:16 final size:16
Alignment explanation
Indices: 2440894--2440927 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2440884 TATAAAATAA
2440894 TAAATTATATT-TTAAT
1 TAAATTA-ATTATTAAT
2440910 TAAATTAATTATTAAT
1 TAAATTAATTATTAAT
2440926 TA
1 TA
2440928 TAAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTAATTATTAAT
Found at i:2441001 original size:25 final size:25
Alignment explanation
Indices: 2440931--2441001 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 25
2440921 TTAATTATAA
* *
2440931 AAAATTTTATTTAAAATAAAAATAT
1 AAAATTTAATTAAAAATAAAAATAT
*
2440956 AATAATTTATTTAACTCAAAATAAAAATAT
1 AA-AATTTAATT-A---AAAATAAAAATAT
2440986 AAAATTTAATTAAAAA
1 AAAATTTAATTAAAAA
2441002 CAATAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
25 6 0.16
26 7 0.19
28 1 0.03
29 8 0.22
30 15 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAATTTAATTAAAAATAAAAATAT
Found at i:2441010 original size:29 final size:28
Alignment explanation
Indices: 2440943--2441018 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
2440933 AATTTTATTT
* *
2440943 AAAATAAAAATATAATAATTTATTTAACTC
1 AAAATAAAAATATAA-AATTTAATTAAC-A
2440973 AAAATAAAAATATAAAATTTAATTAA-A
1 AAAATAAAAATATAAAATTTAATTAACA
2441000 AACAATAAAAATATTAAAA
1 AA-AATAAAAATA-TAAAA
2441019 AATAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 2 0.05
28 10 0.24
29 15 0.36
30 15 0.36
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
AAAATAAAAATATAAAATTTAATTAACA
Found at i:2450927 original size:27 final size:25
Alignment explanation
Indices: 2450863--2450927 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
2450853 TGAAAAATTA
*
2450863 AATATTAAT-ATTT-TTTAAATATT
1 AATATTGATAATTTATTTAAATATT
2450886 AATATTGATAATTTATTTAAAATATT
1 AATATTGATAATTTATTT-AAATATT
*
2450912 AATAATTGATCATTTA
1 AAT-ATTGATAATTTA
2450928 AATATTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 8 0.22
24 4 0.11
25 3 0.08
26 10 0.28
27 11 0.31
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (25 bp):
AATATTGATAATTTATTTAAATATT
Found at i:2460301 original size:20 final size:20
Alignment explanation
Indices: 2460263--2460302 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2460253 GGCAAGTACG
* * *
2460263 TGCTTTTCATTTGTTTTTTC
1 TGCTTTTCATCTATATTTTC
2460283 TGCTTTTCATCTATATTTTC
1 TGCTTTTCATCTATATTTTC
2460303 ATTATAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.17, G:0.07, T:0.65
Consensus pattern (20 bp):
TGCTTTTCATCTATATTTTC
Found at i:2466894 original size:26 final size:26
Alignment explanation
Indices: 2466858--2466910 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2466848 TACAGGCATG
*
2466858 GTATCTTATAATGTAATGTGAATATA
1 GTATCTTATAATATAATGTGAATATA
* *
2466884 GTATCTTATAATATAATTTGATTATA
1 GTATCTTATAATATAATGTGAATATA
2466910 G
1 G
2466911 GTAATGTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (26 bp):
GTATCTTATAATATAATGTGAATATA
Found at i:2468455 original size:31 final size:29
Alignment explanation
Indices: 2468420--2468477 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2468410 TTTTGTTTGG
* *
2468420 AAAAACATAAAATTATTTTAAATTATTTTT
1 AAAAAAATAAAATAATTTTAAATT-TTTTT
* *
2468450 AAAAAAATTAAATAATTTTTAATTTTTT
1 AAAAAAATAAAATAATTTTAAATTTTTT
2468478 ATTATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAAAAATAAAATAATTTTAAATTTTTTT
Found at i:2468771 original size:28 final size:29
Alignment explanation
Indices: 2468728--2468784 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
2468718 TTAAGTTTAA
*
2468728 AATAAAAATATTAAAATTTGA-TTAAATAT
1 AATAAAAATATAAAAATTT-ATTTAAATAT
2468757 AATAAAAA-ATAAAAATTTATTTAAATAT
1 AATAAAAATATAAAAATTTATTTAAATAT
2468785 TTTTGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 17 0.65
29 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTATTTAAATAT
Found at i:2470744 original size:25 final size:25
Alignment explanation
Indices: 2470716--2470767 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2470706 AAATTTTTTA
2470716 TTCAAAGATT-TTTAAATAGTTTCAT
1 TTCAAAGATTATTT-AATAGTTTCAT
* * *
2470741 TTCAAGGATTATTTTATATTTTCAT
1 TTCAAAGATTATTTAATAGTTTCAT
2470766 TT
1 TT
2470768 GATATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (25 bp):
TTCAAAGATTATTTAATAGTTTCAT
Found at i:2482230 original size:54 final size:54
Alignment explanation
Indices: 2482153--2482255 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
2482143 CCTCGCATCG
2482153 TGGTCAAAGCTGCTATGGCGTGGAGCTGAAGTCCTTGTGTCAAAGCCTGGGTTA
1 TGGTCAAAGCTGCTATGGCGTGGAGCTGAAGTCCTTGTGTCAAAGCCTGGGTTA
* *
2482207 TGGTC-AAGCCTGCTGTGGTGTGGAGCTGAAGTCCTTGTGTCAAAGCCTG
1 TGGTCAAAG-CTGCTATGGCGTGGAGCTGAAGTCCTTGTGTCAAAGCCTG
2482256 ATTTATTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 3 0.07
54 43 0.93
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.28
Consensus pattern (54 bp):
TGGTCAAAGCTGCTATGGCGTGGAGCTGAAGTCCTTGTGTCAAAGCCTGGGTTA
Found at i:2494897 original size:15 final size:16
Alignment explanation
Indices: 2494866--2494921 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
2494856 ATGAAATTCG
2494866 AATTTGAATTGATTTC
1 AATTTGAATTGATTTC
*
2494882 AATTTG-ATTTATTTC
1 AATTTGAATTGATTTC
* *
2494897 AAATTCGAAATGA-TTC
1 -AATTTGAATTGATTTC
2494913 AATTGTGAA
1 AATT-TGAA
2494922 ATAATCCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 12 0.38
16 17 0.53
17 3 0.09
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (16 bp):
AATTTGAATTGATTTC
Found at i:2496352 original size:30 final size:32
Alignment explanation
Indices: 2496296--2496362 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 32
2496286 GTTTTTTTTT
2496296 AATTAATAAAAAATATATAATAATAATTTTAA
1 AATTAATAAAAAATATATAATAATAATTTTAA
*
2496328 AATTAATAAAAAATA-A-AATTATAATTTTAA
1 AATTAATAAAAAATATATAATAATAATTTTAA
*
2496358 TATTA
1 AATTA
2496363 TCATGTCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 17 0.52
31 1 0.03
32 15 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AATTAATAAAAAATATATAATAATAATTTTAA
Found at i:2499608 original size:3 final size:3
Alignment explanation
Indices: 2499600--2499631 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2499590 TCTATGAAAC
2499600 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2499632 TCTTCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2514987 original size:3 final size:3
Alignment explanation
Indices: 2514979--2515016 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2514969 TTACTGCCTC
2514979 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
2515017 CAATCGCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:2525216 original size:12 final size:12
Alignment explanation
Indices: 2525199--2525234 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2525189 AAATCAAGCT
*
2525199 GAGGAAGATGAG
1 GAGGAAGAGGAG
2525211 GAGGAAGAGGAG
1 GAGGAAGAGGAG
*
2525223 GAGGAGGAGGAG
1 GAGGAAGAGGAG
2525235 AATAGGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.58, T:0.03
Consensus pattern (12 bp):
GAGGAAGAGGAG
Found at i:2534357 original size:166 final size:166
Alignment explanation
Indices: 2534076--2534379 Score: 374
Period size: 166 Copynumber: 1.8 Consensus size: 166
2534066 ATTTTTATTT
* ** ** *
2534076 TAAGTTAAATAACACTTTATGCCTAAAAGTTAAGTGATTGTTATTAATCAAAATATTACTTGTTA
1 TAAGTTAAATAACACTTTATGCCTAAAAGTTAACTGATTGCCATTAATCAAAATAACACCTGTTA
* * * * * *
2534141 TTTTATACTCGCATGACACTAACGTGGTATTGATGTGAAAAATGAAAAATATTACATAATCGTGT
66 TATTATACTCACATGACACTAACGTGGTATTGATGTGAAAAATAAAAAATATCACATAATCATAT
2534206 TATCATATCATGTCAACGTCACGTAACATAAAATAA
131 TATCATATCATGTCAACGTCACGTAACATAAAATAA
* * *
2534242 TAAGTTAAATAACACTTTATGCCTAAAAGTTAACTGATTGCCATTAGTTACAATAACACCTGTTA
1 TAAGTTAAATAACACTTTATGCCTAAAAGTTAACTGATTGCCATTAATCAAAATAACACCTGTTA
* * **** * * * * *
2534307 TATTATATTTACATGGTTTTGATGTGGTGTTGATGTGAAAGATAAAAAATATCATATAATCATAT
66 TATTATACTCACATGACACTAACGTGGTATTGATGTGAAAAATAAAAAATATCACATAATCATAT
2534372 TATCATAT
131 TATCATAT
2534380 TACATTCGCA
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
166 112 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.37
Consensus pattern (166 bp):
TAAGTTAAATAACACTTTATGCCTAAAAGTTAACTGATTGCCATTAATCAAAATAACACCTGTTA
TATTATACTCACATGACACTAACGTGGTATTGATGTGAAAAATAAAAAATATCACATAATCATAT
TATCATATCATGTCAACGTCACGTAACATAAAATAA
Found at i:2548094 original size:16 final size:15
Alignment explanation
Indices: 2548056--2548109 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
2548046 TCAAGTTTTT
*
2548056 AATAAATAAATTTAAA
1 AATAAA-AATTTTAAA
2548072 AATTAAAAACTTTTAAA
1 AA-TAAAAA-TTTTAAA
*
2548089 AATAAATATTTTATAA
1 AATAAAAATTTTA-AA
2548105 AATAA
1 AATAA
2548110 TATTTTGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.15
16 16 0.48
17 12 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAAAATTTTAAA
Found at i:2548111 original size:15 final size:15
Alignment explanation
Indices: 2548056--2548115 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
2548046 TCAAGTTTTT
*
2548056 AATAAATAAATTTAAA
1 AATAAAT-ATTTTAAA
*
2548072 AATTAAAAACTTTTAAA
1 AA-TAAATA-TTTTAAA
2548089 AATAAATATTTTATAA
1 AATAAATATTTTA-AA
2548105 AAT-AATATTTT
1 AATAAATATTTT
2548116 GTGATTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.34
16 13 0.34
17 12 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAATATTTTAAA
Found at i:2561290 original size:6 final size:6
Alignment explanation
Indices: 2561279--2561304 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2561269 GAAAAATTCT
2561279 CTGGTG CTGGTG CTGGTG CTGGTG CT
1 CTGGTG CTGGTG CTGGTG CTGGTG CT
2561305 TGCCTTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.46, T:0.35
Consensus pattern (6 bp):
CTGGTG
Found at i:2568367 original size:21 final size:22
Alignment explanation
Indices: 2568330--2568371 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2568320 ACTATGTATT
*
2568330 ATAAAAATATATTTGATTTAAA
1 ATAAAAATATATATGATTTAAA
2568352 ATAAAAATATA-ATGATTTAA
1 ATAAAAATATATATGATTTAA
2568372 TTGAACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
ATAAAAATATATATGATTTAAA
Found at i:2573222 original size:24 final size:24
Alignment explanation
Indices: 2573195--2573242 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2573185 ACACGTCATG
*
2573195 TACAAAAA-TCTGTGACACATTATA
1 TACAAAAACT-TGTGACAAATTATA
2573219 TACAAAAACTTGTGACAAATTATA
1 TACAAAAACTTGTGACAAATTATA
2573243 GTTAGCGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (24 bp):
TACAAAAACTTGTGACAAATTATA
Found at i:2573262 original size:69 final size:69
Alignment explanation
Indices: 2573147--2573418 Score: 314
Period size: 69 Copynumber: 3.9 Consensus size: 69
2573137 GTAACACATA
* * * * * * *
2573147 ATGTATAAAAATTTGTAACAAGTTATGGTTAGCATGTTACACGTCATGTACAAAAATCTGTGACA
1 ATGTACAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAATCTGTGACA
*
2573212 CATT
66 CGTT
* * * * **
2573216 ATATACAAAAA-CTTGTGACAAATTATAGTTAGCGTGTGACATGTCATGTACAAAAA-CATGTGA
1 ATGTACAAAAATC-TGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAATC-TGTGA
*
2573279 TACGTT
64 CACGTT
* * * * *
2573285 ATGTATAAAAATCTGTGACAAGTCATGGTTAGCGTGTTACACATCGTGTACAAAAATTTATGACA
1 ATGTACAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAATCTGTGACA
*
2573350 CGTC
66 CGTT
*
2573354 ATGTACAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAACCTGTGACA
1 ATGTACAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAATCTGTGACA
2573419 AGCTATAGTT
Statistics
Matches: 169, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
68 1 0.01
69 167 0.99
70 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (69 bp):
ATGTACAAAAATCTGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAATCTGTGACA
CGTT
Found at i:2573358 original size:24 final size:24
Alignment explanation
Indices: 2573331--2573380 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2573321 TTACACATCG
* *
2573331 TGTACAAAAATTTATGACACGTCA
1 TGTACAAAAATCTATGACAAGTCA
*
2573355 TGTACAAAAATCTGTGACAAGTCA
1 TGTACAAAAATCTATGACAAGTCA
2573379 TG
1 TG
2573381 GTTAGCGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (24 bp):
TGTACAAAAATCTATGACAAGTCA
Found at i:2573395 original size:45 final size:45
Alignment explanation
Indices: 2573345--2573551 Score: 317
Period size: 45 Copynumber: 4.6 Consensus size: 45
2573335 CAAAAATTTA
*
2573345 TGACACGTCATGTACAAAAATCTGTGACAAGTCATGGTTAGCGTG
1 TGACACGTCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTG
* *
2573390 TGACACATCATGTACAAAAACCTGTGACAAG-CTATAGTTAGCGTG
1 TGACACGTCATGTACAAAAACCTGTGACAAGTC-ATGGTTAGCGTG
* * * *
2573435 TTACATGTCATGTACAAAAACTTGTGACAAGCCATGGTTAGCGTG
1 TGACACGTCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTG
*
2573480 TGACACGTCATGTACAAAAACCTGTGATAAGTCATGGTTAGCGTG
1 TGACACGTCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTG
*
2573525 TTACACGTCATGTACAAAAACCTGTGA
1 TGACACGTCATGTACAAAAACCTGTGA
2573552 AACTTCAAAT
Statistics
Matches: 146, Mismatches: 14, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
44 1 0.01
45 144 0.99
46 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
TGACACGTCATGTACAAAAACCTGTGACAAGTCATGGTTAGCGTG
Found at i:2573401 original size:138 final size:138
Alignment explanation
Indices: 2573147--2573416 Score: 371
Period size: 138 Copynumber: 2.0 Consensus size: 138
2573137 GTAACACATA
* * * *
2573147 ATGTATAAAAATTTGTAACAAGTTATGGTTAGCATGTTACACGTCATGTACAAAAATCTGTGACA
1 ATGTATAAAAATCTGTAACAAGTCATGGTTAGCATGTTACACATCATGTACAAAAATCTATGACA
* * **
2573212 CATTATATACAAAAACTTGTGACAAATTATAGTTAGCGTGTGACATGTCATGTACAAAAACATGT
66 CATCATATACAAAAACTTGTGACAAATCATAGTTAGCGTGTGACACATCATGTACAAAAACATGT
2573277 GATACGTT
131 GATACGTT
* * * *
2573285 ATGTATAAAAATCTGTGACAAGTCATGGTTAGCGTGTTACACATCGTGTACAAAAATTTATGACA
1 ATGTATAAAAATCTGTAACAAGTCATGGTTAGCATGTTACACATCATGTACAAAAATCTATGACA
* * * * *
2573350 CGTCATGTACAAAAA-TCTGTGACAAGTCATGGTTAGCGTGTGACACATCATGTACAAAAACCTG
66 CATCATATACAAAAACT-TGTGACAAATCATAGTTAGCGTGTGACACATCATGTACAAAAACATG
2573414 TGA
130 TGA
2573417 CAAGCTATAG
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
137 1 0.01
138 113 0.99
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (138 bp):
ATGTATAAAAATCTGTAACAAGTCATGGTTAGCATGTTACACATCATGTACAAAAATCTATGACA
CATCATATACAAAAACTTGTGACAAATCATAGTTAGCGTGTGACACATCATGTACAAAAACATGT
GATACGTT
Found at i:2575935 original size:26 final size:27
Alignment explanation
Indices: 2575882--2575935 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
2575872 TCAACGGAGC
*
2575882 AACCTAAAATCAAAATCCCAATTTAAT
1 AACCTAAAATCAAAATACCAATTTAAT
*
2575909 AACC-AAAATGAAAATACC-ATTTGAAT
1 AACCTAAAATCAAAATACCAATTT-AAT
2575935 A
1 A
2575936 TGTAAATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 16 0.67
27 4 0.17
ACGTcount: A:0.54, C:0.19, G:0.04, T:0.24
Consensus pattern (27 bp):
AACCTAAAATCAAAATACCAATTTAAT
Found at i:2576591 original size:26 final size:27
Alignment explanation
Indices: 2576536--2576613 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 27
2576526 AATATGCGAA
* *
2576536 ATGATGATAGGTGACAATAA-ATGATAAT
1 ATGATCATA-GTGAC-ATAATAGGATAAT
*
2576564 ATGAT-ATAGTGACATAATAGGATCAT
1 ATGATCATAGTGACATAATAGGATAAT
*
2576590 ATGATCAT-GTGACATAATATGATA
1 ATGATCATAGTGACATAATAGGATA
2576614 TGGTGATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.09
26 30 0.68
27 5 0.11
28 5 0.11
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (27 bp):
ATGATCATAGTGACATAATAGGATAAT
Found at i:2585482 original size:12 final size:12
Alignment explanation
Indices: 2585465--2585489 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2585455 AGGTTTGGAC
2585465 TCTGCATCTGTT
1 TCTGCATCTGTT
2585477 TCTGCATCTGTT
1 TCTGCATCTGTT
2585489 T
1 T
2585490 GGTTGTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.16, T:0.52
Consensus pattern (12 bp):
TCTGCATCTGTT
Found at i:2592192 original size:55 final size:55
Alignment explanation
Indices: 2592118--2592226 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
2592108 AAACCAAAAT
* * *
2592118 GTACATCATCCTATTCTTTCAAGAGGCTTGTAACCTCTACAAGAACACAAATCAA
1 GTACATCATCCAATACTTTCAAGAGGCTTGTAACCTCTACAAGAACAAAAATCAA
* * * **
2592173 GTACATCATGCAATACTTTCAAGATGCTTGTAATCTCTATTAGAACAAAAATCA
1 GTACATCATCCAATACTTTCAAGAGGCTTGTAACCTCTACAAGAACAAAAATCA
2592227 TATAAAAGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (55 bp):
GTACATCATCCAATACTTTCAAGAGGCTTGTAACCTCTACAAGAACAAAAATCAA
Found at i:2594811 original size:32 final size:32
Alignment explanation
Indices: 2594762--2594838 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 32
2594752 AAATTGTGCC
*
2594762 TTTGCAATAAAACAATC-ATATATTATGCAAAT
1 TTTGTAAT-AAACAATCAATATATTATGCAAAT
2594794 TTTGTAATAAACTAATCATATATATTATGCAAAT
1 TTTGTAATAAAC-AATCA-ATATATTATGCAAAT
2594828 TTTGTAATAAA
1 TTTGTAATAAA
2594839 ATAGTAGCGG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
34 26 0.63
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (32 bp):
TTTGTAATAAACAATCAATATATTATGCAAAT
Found at i:2598561 original size:19 final size:19
Alignment explanation
Indices: 2598537--2598577 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2598527 ATTGCTATTC
2598537 TACTTTTTAACTTCCTAAA
1 TACTTTTTAACTTCCTAAA
2598556 TACTTTTTAACTTCCTAAA
1 TACTTTTTAACTTCCTAAA
2598575 TAC
1 TAC
2598578 ACCTTGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (19 bp):
TACTTTTTAACTTCCTAAA
Found at i:2598589 original size:21 final size:19
Alignment explanation
Indices: 2598544--2598589 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2598534 TTCTACTTTT
* *
2598544 TAACTTCCTAAATACTTTT
1 TAACTTCCTAAATACCTTG
2598563 TAACTTCCTAAATACACCTTG
1 TAACTTCCTAAAT--ACCTTG
2598584 TAACTT
1 TAACTT
2598590 GGCCTTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
21 10 0.43
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (19 bp):
TAACTTCCTAAATACCTTG
Found at i:2599718 original size:125 final size:125
Alignment explanation
Indices: 2599489--2599736 Score: 372
Period size: 125 Copynumber: 2.0 Consensus size: 125
2599479 GGTCGACCTT
* *
2599489 AGAAGTGGCAATATGACTCAATTAAGGGGGAGAAATTATGGACTATGCACTATACTTTTTTTTCC
1 AGAAGTGGCAATATGACTCAATTAAGGGGGAGAAATTATGGACTATGCACTATACTCTTTTGTCC
* * * *
2599554 TTTTGATCGATTTTTGTCCCACTAGGTTTTTATAGCTTAAGGTTTTTAATGAGGCAATCC
66 TTTTGACCAATTTTTGTCCCACTAGATTTTTATAGCTTAAGGTTTTTAATGAGACAATCC
* * * *
2599614 AGAAGTGGCAATATGGCTCAATTGAGGGGGAGCAATTATGGACTATGCACTGTACTCTTTTGTCC
1 AGAAGTGGCAATATGACTCAATTAAGGGGGAGAAATTATGGACTATGCACTATACTCTTTTGTCC
* *
2599679 TTTTGACCAATTTTTGTCCCATTAGATTTTTCT-GACTTAAGGTTTTTAATGAGACAAT
66 TTTTGACCAATTTTTGTCCCACTAGATTTTTATAG-CTTAAGGTTTTTAATGAGACAAT
2599737 ACAATGGACA
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
124 1 0.01
125 109 0.99
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (125 bp):
AGAAGTGGCAATATGACTCAATTAAGGGGGAGAAATTATGGACTATGCACTATACTCTTTTGTCC
TTTTGACCAATTTTTGTCCCACTAGATTTTTATAGCTTAAGGTTTTTAATGAGACAATCC
Found at i:2601646 original size:111 final size:110
Alignment explanation
Indices: 2601448--2601666 Score: 384
Period size: 111 Copynumber: 2.0 Consensus size: 110
2601438 ACTTTTAGTT
2601448 TGAACTAAATAAGTTTTTATATTTTTTATTTTGAGTTAAATAAAATCTTATTATTAATGATTAAC
1 TGAACTAAATAAGTTTTTATATTTTTTATTTTGAGTTAAATAAAATCTTATTATTAATGATTAAC
* *
2601513 TTAATCATAATACTATTTGTCATTTTATATTACGTGAAGATGATG
66 TTAATCATAATACTATTCGTCATTTTATATTAAGTGAAGATGATG
* * *
2601558 TGAACTAAATAAGTTTTTATTTTTTTTTATTTTGAGTTAAATAAACTTTTATTATTAATGATTAA
1 TGAACTAAATAAGTTTTTA-TATTTTTTATTTTGAGTTAAATAAAATCTTATTATTAATGATTAA
2601623 CTTAATCATAATACTATTCGTCATTTTATATTAAGTGAAGATGA
65 CTTAATCATAATACTATTCGTCATTTTATATTAAGTGAAGATGA
2601667 CGTGGCATGT
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 19 0.18
111 84 0.82
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (110 bp):
TGAACTAAATAAGTTTTTATATTTTTTATTTTGAGTTAAATAAAATCTTATTATTAATGATTAAC
TTAATCATAATACTATTCGTCATTTTATATTAAGTGAAGATGATG
Found at i:2601749 original size:33 final size:33
Alignment explanation
Indices: 2601666--2601749 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
2601656 AGTGAAGATG
*
2601666 ACGTGGCATGTTAACATGTTATAATTGATAATA
1 ACGTGGCATGTTAACATATTATAATTGATAATA
** * * *
2601699 ATATCGTATGTTGACATATTATAATTGATAATA
1 ACGTGGCATGTTAACATATTATAATTGATAATA
*
2601732 ACGTGGCATGATAACATA
1 ACGTGGCATGTTAACATA
2601750 ATCATGTGAC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (33 bp):
ACGTGGCATGTTAACATATTATAATTGATAATA
Found at i:2615203 original size:17 final size:17
Alignment explanation
Indices: 2615169--2615204 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2615159 TACTTTTCTT
2615169 ATTTTAAATGAAGATAA
1 ATTTTAAATGAAGATAA
2615186 ATTTATAAATGAAG-TAA
1 ATTT-TAAATGAAGATAA
2615203 AT
1 AT
2615205 GTTTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (17 bp):
ATTTTAAATGAAGATAA
Found at i:2616205 original size:25 final size:25
Alignment explanation
Indices: 2616177--2616229 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
2616167 TCAAAAAATA
2616177 AAATAAAATAAAAATAATAAT-ATTT
1 AAATAAAAT-AAAATAATAATAATTT
* *
2616202 AAATTAAATAAAATATTAATAATTT
1 AAATAAAATAAAATAATAATAATTT
2616227 AAA
1 AAA
2616230 AATTATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AAATAAAATAAAATAATAATAATTT
Found at i:2616269 original size:27 final size:26
Alignment explanation
Indices: 2616239--2616307 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
2616229 AAATTATTGA
2616239 TTAAATTATAAATAAATTATTAATAT
1 TTAAATTATAAATAAATTATTAATAT
*
2616265 TTTAATTA-AATTATAAATTATTAATAT
1 TTAAATTATAA--ATAAATTATTAATAT
**
2616292 TTAAAAAATAAATAAA
1 TTAAATTATAAATAAA
2616308 ATAAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 2 0.06
26 12 0.33
27 20 0.56
28 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAAATTATAAATAAATTATTAATAT
Found at i:2616276 original size:20 final size:19
Alignment explanation
Indices: 2616238--2616290 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
2616228 AAAATTATTG
2616238 ATTAAATTATAAATAAATT
1 ATTAAATTATAAATAAATT
* *
2616257 ATTAATATTTTAATTAAATT
1 ATTAA-ATTATAAATAAATT
*
2616277 A-TAAATTATTAATA
1 ATTAAATTATAAATA
2616291 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 7 0.25
19 8 0.29
20 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAATTATAAATAAATT
Found at i:2616366 original size:17 final size:18
Alignment explanation
Indices: 2616346--2616388 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2616336 ATTTCAAAAT
*
2616346 TATTATTATCAATTA-AA
1 TATTATTATAAATTATAA
*
2616363 TATTATAATAAATTATAA
1 TATTATTATAAATTATAA
2616381 TAATTATT
1 T-ATTATT
2616389 CATCTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 13 0.62
18 3 0.14
19 5 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATTATAAATTATAA
Found at i:2616459 original size:16 final size:16
Alignment explanation
Indices: 2616410--2616461 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2616400 CCGTATCAAA
2616410 TTATATAATAATTATT
1 TTATATAATAATTATT
* * *
2616426 TTATTTTAT-TTTATTT
1 TTATATAATAATTA-TT
2616442 TTATATAATAATTATT
1 TTATATAATAATTATT
2616458 TTAT
1 TTAT
2616462 TATATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 3 0.11
16 22 0.79
17 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATAATAATTATT
Found at i:2617426 original size:18 final size:18
Alignment explanation
Indices: 2617403--2617442 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2617393 ATAATGCCAG
* * *
2617403 GGCTGCTAGGAAAGGTAT
1 GGCTGCCAGAAAAGCTAT
2617421 GGCTGCCAGAAAAGCTAT
1 GGCTGCCAGAAAAGCTAT
2617439 GGCT
1 GGCT
2617443 TCTAAGAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.35, T:0.20
Consensus pattern (18 bp):
GGCTGCCAGAAAAGCTAT
Found at i:2626485 original size:43 final size:43
Alignment explanation
Indices: 2626424--2626509 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
2626414 CTGACTGATT
*
2626424 ACAGAGCTGTTGCGTTATATTTCTTCATCATCTTAAGTTTCCA
1 ACAGAGCTGTTGCGTTATATTTCTTCATCATCTCAAGTTTCCA
* *
2626467 ACAGAGCTGTTTCTTTATATTTCTTCATCATCTCAAGTTTCCA
1 ACAGAGCTGTTGCGTTATATTTCTTCATCATCTCAAGTTTCCA
2626510 GCAAACTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (43 bp):
ACAGAGCTGTTGCGTTATATTTCTTCATCATCTCAAGTTTCCA
Found at i:2627327 original size:15 final size:15
Alignment explanation
Indices: 2627307--2627347 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2627297 TGCCACCTAC
2627307 CTCTCTCTCTCTTCA
1 CTCTCTCTCTCTTCA
2627322 CTCTCT-TCTC-TCA
1 CTCTCTCTCTCTTCA
*
2627335 TTCTCTCTGCTCT
1 CTCTCTCT-CTCT
2627348 CTTTGATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 9 0.41
ACGTcount: A:0.05, C:0.44, G:0.02, T:0.49
Consensus pattern (15 bp):
CTCTCTCTCTCTTCA
Found at i:2633895 original size:21 final size:22
Alignment explanation
Indices: 2633860--2633913 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2633850 AGCTAACCAG
*
2633860 GAGACAAAC-GAAGAAG-AAACA
1 GAGA-AAACAGAAGAAGAAAAAA
*
2633881 GAGGAAACAGAAGAAGAAAAAA
1 GAGAAAACAGAAGAAGAAAAAA
2633903 GAGAAAACAGA
1 GAGAAAACAGA
2633914 GGATTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 10 0.36
22 14 0.50
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (22 bp):
GAGAAAACAGAAGAAGAAAAAA
Found at i:2636774 original size:2 final size:2
Alignment explanation
Indices: 2636767--2636791 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2636757 GTTGCCTCAG
2636767 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 T
2636792 ATAAAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2638217 original size:488 final size:488
Alignment explanation
Indices: 2637293--2638247 Score: 1344
Period size: 488 Copynumber: 2.0 Consensus size: 488
2637283 GCTATTCTTA
* * *
2637293 ATATTCTTTTAATGTCTTTTTACACTTTTCCTTTTTCATCAAAGTCTTAAATTTTAGATCTTTTT
1 ATATTCTTTTAATGTATTCTTACACCTTTCCTTTTTCATCAAAGTCTTAAATTTTAGATCTTTTT
* * *
2637358 CTTCTTAAAAGTTAGTATACCATTCAAGAAGAAAAATTGGTCAAAATACTTGGAAGTTCTTCGTA
66 CTTCCTAAAAGTTAGTATACCATTCAAGAAGAAAAATTGGTCAAAATACTTGAAAGATCTTCGTA
* * ** * * * *
2637423 CTTATGTGTTTTGTTTAATTTAATCTCTTTACTCCAATTTAAAGCAATTTAGTTCCTCGATTTTA
131 CCTATGTATTTTGTACAATTTAATCTCTTTACTCCAATTTAAAGCAATGTAATCCCTCAATTTTA
* * * * * * *
2637488 AGAATTGCTCCAATGTAACCCTTCCTCTTTTAATGATATCTAATTTAGCTGTTAAATAGGATGAT
196 AAAATTACTCCAATGTAACCCCTCCCCTCTTAATGATATCCAATTTAGCTATTAAATAGGATGAT
* * * *
2637553 GTCAATGTTAACGTGATATTGATGTGACATATTTTTGCTGACAAGGCAATGTGGGATAGCAACAT
261 GTCAACGCTAACGTGATATTGATGTGACACATTTTTGCTGACAAGGCAATATGGGATAGCAACAT
* *
2637618 GTTGATGTAGCACTACCATGTCACCCTCACATGCTAATGAGGCAATGCCACATCATCCTTTTAAG
326 GTTGATGTAGCACTACCACGTCACCCTCACATGCTAACGAGGCAATGCCACATCATCCTTTTAAG
* ** *
2637683 TTCGGATTGTTGATGTGGATTGCCATGTAAGCATTAAGGCTCAAGTTGCTGATGTGGCA-TGGCC
391 TTCGGATTGTTGATGTGGACTGCCACATAAGCATTAAGGCTCAAGTTGCTAATGTGGCACT-GCC
2637747 ACATCAACATTAATAATCCAATTGCTGACATGGC
455 ACATCAACATTAATAATCCAATTGCTGACATGGC
* *
2637781 ATATTCTTTTCATGTATTCTTACACCTTTCCTTTTTCATCAAAGTCTTAAATTTTAGTTCTTTTT
1 ATATTCTTTTAATGTATTCTTACACCTTTCCTTTTTCATCAAAGTCTTAAATTTTAGATCTTTTT
**
2637846 CTTCCTAAAAGTTAGTATAGTATTCAAGAAGAAAAATTGGTCAAAATACTTGAAAGATC-TCTGT
66 CTTCCTAAAAGTTAGTATACCATTCAAGAAGAAAAATTGGTCAAAATACTTGAAAGATCTTC-GT
* * *
2637910 ACCTATGTATTTTGTACAATTTAGTCTCTTTACTCCAATTTGAATCAATGTAATCCCTCAATTTT
130 ACCTATGTATTTTGTACAATTTAATCTCTTTACTCCAATTTAAAGCAATGTAATCCCTCAATTTT
* *
2637975 AAAAATTACTCCAATTTAACCCCTCCCCTCTTAATGGTATCCAATTTAGCTATTAAATAGGATGA
195 AAAAATTACTCCAATGTAACCCCTCCCCTCTTAATGATATCCAATTTAGCTATTAAATAGGATGA
* * *** * *
2638040 TGTCAACGCTAACGTGATGTTGATGTGACACATTTTTGCTTATGTGGCAATATGGGGTAGCGACA
260 TGTCAACGCTAACGTGATATTGATGTGACACATTTTTGCTGACAAGGCAATATGGGATAGCAACA
* * * *
2638105 TGTTGATGT-GACACTACCACGTCACCCTCACATGCTAACGTGGTAGTGTCACATCATCCTTTTA
325 TGTTGATGTAG-CACTACCACGTCACCCTCACATGCTAACGAGGCAATGCCACATCATCCTTTTA
* * *
2638169 TGTTC-GAGTTGTTGATGTGGACTGCCACATCAGCATT-AGAGTTCAAGTTGCTAATGTGGCACT
389 AGTTCGGA-TTGTTGATGTGGACTGCCACATAAGCATTAAG-GCTCAAGTTGCTAATGTGGCACT
2638232 GCCACATCAACATTAA
452 GCCACATCAACATTAA
2638248 GACTCGAGTT
Statistics
Matches: 408, Mismatches: 54, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
487 7 0.02
488 400 0.98
489 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (488 bp):
ATATTCTTTTAATGTATTCTTACACCTTTCCTTTTTCATCAAAGTCTTAAATTTTAGATCTTTTT
CTTCCTAAAAGTTAGTATACCATTCAAGAAGAAAAATTGGTCAAAATACTTGAAAGATCTTCGTA
CCTATGTATTTTGTACAATTTAATCTCTTTACTCCAATTTAAAGCAATGTAATCCCTCAATTTTA
AAAATTACTCCAATGTAACCCCTCCCCTCTTAATGATATCCAATTTAGCTATTAAATAGGATGAT
GTCAACGCTAACGTGATATTGATGTGACACATTTTTGCTGACAAGGCAATATGGGATAGCAACAT
GTTGATGTAGCACTACCACGTCACCCTCACATGCTAACGAGGCAATGCCACATCATCCTTTTAAG
TTCGGATTGTTGATGTGGACTGCCACATAAGCATTAAGGCTCAAGTTGCTAATGTGGCACTGCCA
CATCAACATTAATAATCCAATTGCTGACATGGC
Found at i:2638233 original size:40 final size:40
Alignment explanation
Indices: 2638183--2638284 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 40
2638173 CGAGTTGTTG
*
2638183 ATGTGG-ACTGCCACATCAGCATT-AGAGTTCAAGTTGCTA
1 ATGTGGCACTGCCACATCAGCATTAAGA-CTCAAGTTGCTA
* *
2638222 ATGTGGCACTGCCACATCAACATTAAGACTCGAGTTGCTA
1 ATGTGGCACTGCCACATCAGCATTAAGACTCAAGTTGCTA
* * *
2638262 ACGTGGCAGTGCCACGTCAGCAT
1 ATGTGGCACTGCCACATCAGCAT
2638285 GTCAAAGCCA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 6 0.11
40 45 0.83
41 3 0.06
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
ATGTGGCACTGCCACATCAGCATTAAGACTCAAGTTGCTA
Found at i:2641230 original size:32 final size:30
Alignment explanation
Indices: 2641162--2641232 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
2641152 AAAATTTTCA
* *
2641162 AAATTTATTTTATTTTTTTATTATATTTAAT
1 AAATTT-TTTTATTTTTTTATTAAATTAAAT
* *
2641193 CAATTTTTTTATATTTTTATTTTAAATTAAAT
1 AAATTTTTTTAT-TTTTT-TATTAAATTAAAT
2641225 AAATTTTT
1 AAATTTTT
2641233 ATAAATATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 6 0.18
31 10 0.30
32 17 0.52
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (30 bp):
AAATTTTTTTATTTTTTTATTAAATTAAAT
Found at i:2642777 original size:29 final size:28
Alignment explanation
Indices: 2642741--2642816 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
2642731 AATTATTAAT
**
2642741 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAAGGT--AATAAAAA
*
2642771 TATAAAAATTTGACTTAAGGTAATAAAAA
1 TATAAAAATTT-ATTTAAGGTAATAAAAA
*
2642800 TATAAAAAATTATTTAA
1 TATAAAAATTTATTTAA
2642817 ATATTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.12
29 18 0.45
30 11 0.28
31 6 0.15
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (28 bp):
TATAAAAATTTATTTAAGGTAATAAAAA
Found at i:2660005 original size:16 final size:15
Alignment explanation
Indices: 2659984--2660025 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 15
2659974 ATTTATATTG
2659984 AATTAATGAAGTTGTA
1 AATTAATGAAGTTG-A
2660000 AATTAA-GAA--TGA
1 AATTAATGAAGTTGA
2660012 AATTAATGAAGTTG
1 AATTAATGAAGTTG
2660026 GGTATTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
15 5 0.22
16 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (15 bp):
AATTAATGAAGTTGA
Done.