Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 52 of 276
Found at i:16177678 original size:3 final size:3
Alignment explanation
Indices: 16177670--16178485 Score: 1632
Period size: 3 Copynumber: 272.0 Consensus size: 3
16177660 ATAAACAAAT
16177670 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16177718 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16177766 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16177814 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16177862 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16177910 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16177958 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178006 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178054 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178102 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178150 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178198 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178246 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178294 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178342 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178390 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178438 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16178486 CCTTAAAATG
Statistics
Matches: 813, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 813 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16179630 original size:26 final size:26
Alignment explanation
Indices: 16179601--16179708 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
16179591 TGGTACAAAT
16179601 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
16179627 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16179653 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16179679 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16179705 TGAT
1 TGAT
16179709 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16180900 original size:8 final size:8
Alignment explanation
Indices: 16180887--16180917 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
16180877 AGATCGGCAC
16180887 AAGCCGAA
1 AAGCCGAA
16180895 AAGCCGAA
1 AAGCCGAA
*
16180903 ATGCCGAA
1 AAGCCGAA
16180911 AAGCCGA
1 AAGCCGA
16180918 TATTTTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.26, G:0.26, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:16181338 original size:27 final size:26
Alignment explanation
Indices: 16181306--16181445 Score: 165
Period size: 27 Copynumber: 5.2 Consensus size: 26
16181296 AGGAAGCGTC
*
16181306 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
16181333 CTGGTGACTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
16181360 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
16181387 CTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
16181414 CTGGTGGCTCTGCCACAATATCAT-AT
1 CTGGTGGCTCTGCCACATTATC-TGAT
16181440 CTGGTG
1 CTGGTG
16181446 ACTTCGTCAC
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
26 14 0.14
27 81 0.84
28 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:16181388 original size:54 final size:53
Alignment explanation
Indices: 16181306--16181448 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 53
16181296 AGGAAGCGTC
16181306 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
16181360 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* *
16181414 CTGGTGGCTCTGCCACAATATCAT-ATCTGGTGACT
1 CTGGTGGCTATGCCACATTATC-TGATCTGGTGACT
16181449 TCGTCACAAC
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 15 0.18
54 67 0.82
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:16183875 original size:13 final size:13
Alignment explanation
Indices: 16183859--16183936 Score: 80
Period size: 13 Copynumber: 6.5 Consensus size: 13
16183849 ATTTTTAAAT
16183859 TATTTAGTGATAA
1 TATTTAGTGATAA
16183872 TATTTA---A-AA
1 TATTTAGTGATAA
16183881 TTATTTAGTGATAA
1 -TATTTAGTGATAA
16183895 TATTTAGTGATAA
1 TATTTAGTGATAA
*
16183908 TATTTA-AGAT--
1 TATTTAGTGATAA
*
16183918 TATTTTGTGATAA
1 TATTTAGTGATAA
16183931 TATTTA
1 TATTTA
16183937 AGAAAAATCT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
9 2 0.04
10 12 0.23
11 3 0.06
12 3 0.06
13 31 0.58
14 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:16183882 original size:36 final size:35
Alignment explanation
Indices: 16183859--16183936 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 35
16183849 ATTTTTAAAT
16183859 TATTTAGTGATAATATTTAAAATTATTTAGTGATAA
1 TATTTAGTGATAATATTTAAAATTATTTA-TGATAA
* *
16183895 TATTTAGTGATAATATTTAAGATTATTTTGTGATAA
1 TATTTAGTGATAATATTTAAAATTA-TTTATGATAA
16183931 TATTTA
1 TATTTA
16183937 AGAAAAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 36 0.92
37 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (35 bp):
TATTTAGTGATAATATTTAAAATTATTTATGATAA
Found at i:16183883 original size:23 final size:23
Alignment explanation
Indices: 16183855--16183900 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16183845 TTCGATTTTT
16183855 AAATTATTTAGTGATAATATTTA
1 AAATTATTTAGTGATAATATTTA
16183878 AAATTATTTAGTGATAATATTTA
1 AAATTATTTAGTGATAATATTTA
16183901 GTGATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
AAATTATTTAGTGATAATATTTA
Found at i:16183921 original size:23 final size:23
Alignment explanation
Indices: 16183895--16183939 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
16183885 TTAGTGATAA
16183895 TATTTAGTGATAATATTTAAGAT
1 TATTTAGTGATAATATTTAAGAT
*
16183918 TATTTTGTGATAATATTTAAGA
1 TATTTAGTGATAATATTTAAGA
16183940 AAAATCTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (23 bp):
TATTTAGTGATAATATTTAAGAT
Found at i:16185042 original size:10 final size:10
Alignment explanation
Indices: 16185029--16185056 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16185019 AACTGCTCTA
16185029 TACTGCTAAT
1 TACTGCTAAT
16185039 TACTGCTAAT
1 TACTGCTAAT
16185049 TACTGCTA
1 TACTGCTA
16185057 TTTTGTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (10 bp):
TACTGCTAAT
Found at i:16185080 original size:20 final size:20
Alignment explanation
Indices: 16185055--16185103 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
16185045 TAATTACTGC
16185055 TATTTTGTTGTAGGAATTTA
1 TATTTTGTTGTAGGAATTTA
*
16185075 TATTTTATTGTAGGAATTTA
1 TATTTTGTTGTAGGAATTTA
16185095 TATTTTGTT
1 TATTTTGTT
16185104 TGTTTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (20 bp):
TATTTTGTTGTAGGAATTTA
Found at i:16187840 original size:19 final size:19
Alignment explanation
Indices: 16187816--16187855 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
16187806 ATCCGTAGAA
16187816 ATCCCTAGTTTATATTAAT
1 ATCCCTAGTTTATATTAAT
*
16187835 ATCCCTAGTTTATGTTAAT
1 ATCCCTAGTTTATATTAAT
16187854 AT
1 AT
16187856 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (19 bp):
ATCCCTAGTTTATATTAAT
Found at i:16190683 original size:17 final size:17
Alignment explanation
Indices: 16190663--16190705 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
16190653 AGTAAAAATA
16190663 AAAATAAAAACAAAAG-G
1 AAAATAAAAAC-AAAGTG
*
16190680 AAAAGAAAAACAAAGTG
1 AAAATAAAAACAAAGTG
16190697 AAAATAAAA
1 AAAATAAAA
16190706 GGACTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAATAAAAACAAAGTG
Found at i:16192495 original size:13 final size:13
Alignment explanation
Indices: 16192465--16192493 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16192455 GGGAGAAAGG
16192465 GAAAGGAAAGAAA
1 GAAAGGAAAGAAA
16192478 GAAAGG-AAGAAA
1 GAAAGGAAAGAAA
16192490 GAAA
1 GAAA
16192494 AGTAAGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAAGGAAAGAAA
Found at i:16199294 original size:19 final size:19
Alignment explanation
Indices: 16199270--16199309 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
16199260 ATCCGTAGAA
16199270 ATCCCTAGTTTATATTAAT
1 ATCCCTAGTTTATATTAAT
*
16199289 ATCCCTAGTTTATGTTAAT
1 ATCCCTAGTTTATATTAAT
16199308 AT
1 AT
16199310 ATCTCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (19 bp):
ATCCCTAGTTTATATTAAT
Found at i:16202065 original size:23 final size:23
Alignment explanation
Indices: 16202039--16202101 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
16202029 GACTTTTAAA
*
16202039 AGTGACAATATTTAGAATTATTT
1 AGTGATAATATTTAGAATTATTT
16202062 AGTGATAATATTTA-AGATTATTT
1 AGTGATAATATTTAGA-ATTATTT
* *
16202085 TGTAATAATATTTAGAA
1 AGTGATAATATTTAGAA
16202102 AAAATCTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.03
23 33 0.94
24 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (23 bp):
AGTGATAATATTTAGAATTATTT
Found at i:16206002 original size:15 final size:15
Alignment explanation
Indices: 16205982--16206012 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16205972 GATGTGTTAT
16205982 CAAGTTAAATAATTA
1 CAAGTTAAATAATTA
16205997 CAAGTTAAATAATTA
1 CAAGTTAAATAATTA
16206012 C
1 C
16206013 TAATCTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (15 bp):
CAAGTTAAATAATTA
Found at i:16206095 original size:22 final size:23
Alignment explanation
Indices: 16206030--16206095 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 23
16206020 ATCGAGTTAG
* *
16206030 AAATTATTAATACAAATTCAAATAT
1 AAATTATTAAT-TAAACT-AAATAT
* * *
16206055 AAGTTATTTA-TAAACTAAATTT
1 AAATTATTAATTAAACTAAATAT
16206077 AAATTATTAATTAAA-TAAA
1 AAATTATTAATTAAACTAAA
16206096 CTAATCTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 17 0.52
23 8 0.24
25 8 0.24
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATTATTAATTAAACTAAATAT
Found at i:16212477 original size:24 final size:27
Alignment explanation
Indices: 16212412--16212484 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 27
16212402 CCTGTGTAAA
*
16212412 AAGTTTAAAATAAATGATATGTAAGAT
1 AAGTTTAAAATAAATAATATGTAAGAT
*
16212439 AA-TTTAAGATAAATAATA-G-AA-AT
1 AAGTTTAAAATAAATAATATGTAAGAT
* *
16212462 AAGTTTAAAATGAATATTATGTA
1 AAGTTTAAAATAAATAATATGTA
16212485 GTAATAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 4 0.11
24 15 0.39
25 2 0.05
26 15 0.39
27 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.34
Consensus pattern (27 bp):
AAGTTTAAAATAAATAATATGTAAGAT
Found at i:16212607 original size:22 final size:20
Alignment explanation
Indices: 16212575--16212614 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
16212565 AAGTAATAAT
16212575 ATACAAAAAAAAAATTTAAA
1 ATACAAAAAAAAAATTTAAA
*
16212595 ATACATAATAAAACAATTTA
1 ATACA-AA-AAAAAAATTTA
16212615 GAATGGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
ATACAAAAAAAAAATTTAAA
Found at i:16226810 original size:11 final size:12
Alignment explanation
Indices: 16226780--16226805 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16226770 ACTTATCCCC
16226780 TCAAATTTTTCA
1 TCAAATTTTTCA
16226792 TCAAATTTTTCA
1 TCAAATTTTTCA
16226804 TC
1 TC
16226806 CATTTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (12 bp):
TCAAATTTTTCA
Found at i:16227415 original size:19 final size:19
Alignment explanation
Indices: 16227387--16227427 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
16227377 TGAATTATAA
16227387 AAAATAAAATTAAATAACC
1 AAAATAAAATTAAATAACC
* * *
16227406 AAAATTAAATTAGATAATC
1 AAAATAAAATTAAATAACC
16227425 AAA
1 AAA
16227428 TATGCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAAATTAAATAACC
Found at i:16237991 original size:41 final size:41
Alignment explanation
Indices: 16237946--16238027 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
16237936 CGTCAAATGC
*
16237946 ATTCCCGGTTTGACTGATCTATATGCCAAACAATAAGATCA
1 ATTCCCGCTTTGACTGATCTATATGCCAAACAATAAGATCA
*
16237987 ATTCCTGCTTTGACTGATCTATATGCCAAACAATAAGATCA
1 ATTCCCGCTTTGACTGATCTATATGCCAAACAATAAGATCA
16238028 GGCATTAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (41 bp):
ATTCCCGCTTTGACTGATCTATATGCCAAACAATAAGATCA
Found at i:16242661 original size:14 final size:13
Alignment explanation
Indices: 16242638--16242680 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
16242628 GTTGAGATTC
*
16242638 CCTAATCCCCAAA
1 CCTAAACCCCAAA
16242651 CTCTAAACCCCAAA
1 C-CTAAACCCCAAA
*
16242665 CCATAAACCTCAAA
1 CC-TAAACCCCAAA
16242679 CC
1 CC
16242681 CCAAACCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 2 0.08
14 24 0.92
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.14
Consensus pattern (13 bp):
CCTAAACCCCAAA
Found at i:16242665 original size:7 final size:7
Alignment explanation
Indices: 16242644--16242721 Score: 66
Period size: 7 Copynumber: 11.1 Consensus size: 7
16242634 ATTCCCTAAT
16242644 CCCCAAA
1 CCCCAAA
* *
16242651 CTCTAAA
1 CCCCAAA
16242658 CCCCAAA
1 CCCCAAA
**
16242665 CCATAAA
1 CCCCAAA
*
16242672 CCTCAAA
1 CCCCAAA
16242679 CCCCAAA
1 CCCCAAA
*
16242686 CCTCAAA
1 CCCCAAA
*
16242693 TCCCAAA
1 CCCCAAA
* *
16242700 TCACAAA
1 CCCCAAA
16242707 CCCCAAA
1 CCCCAAA
*
16242714 CTCCAAA
1 CCCCAAA
16242721 C
1 C
16242722 GCACCACAAT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.10
Consensus pattern (7 bp):
CCCCAAA
Found at i:16249640 original size:17 final size:16
Alignment explanation
Indices: 16249584--16249639 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
16249574 GTTTATTTTC
16249584 TTGTTTTCAATTTAGT
1 TTGTTTTCAATTTAGT
* *
16249600 TTGTTTTCAGTTTTTGT
1 TTGTTTTCA-ATTTAGT
16249617 TTGTTTTCAATTTAGT
1 TTGTTTTCAATTTAGT
16249633 TTGTTTT
1 TTGTTTT
16249640 TATTATTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 21 0.60
17 14 0.40
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.68
Consensus pattern (16 bp):
TTGTTTTCAATTTAGT
Found at i:16252148 original size:72 final size:72
Alignment explanation
Indices: 16252031--16252223 Score: 260
Period size: 72 Copynumber: 2.7 Consensus size: 72
16252021 TTCGACACTG
* *** * * *
16252031 CTCACACAAGCTTTAGAGAATCGGTAACACATGTTGGATCTCAAGCTATTGGTAAAAAATGATTT
1 CTCACACAAGCTTCAGAGAATCCACAACACGTGTTGGATCTCAAGCCATTGATAAAAAATGATTT
*
16252096 AATGTTA
66 AATGCTA
*
16252103 CTCACACAAGCTTCAGAGAATCCACAACACGTGTTGGATCTCAAGCCATTGATAAAGAATGATTT
1 CTCACACAAGCTTCAGAGAATCCACAACACGTGTTGGATCTCAAGCCATTGATAAAAAATGATTT
* *
16252168 GATGCTG
66 AATGCTA
* * *
16252175 CTCACACAAGCTTCAAATAATCCACAACATGTGTTGGATCTCAAGCCAT
1 CTCACACAAGCTTCAGAGAATCCACAACACGTGTTGGATCTCAAGCCAT
16252224 AGATCATTAA
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 107 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (72 bp):
CTCACACAAGCTTCAGAGAATCCACAACACGTGTTGGATCTCAAGCCATTGATAAAAAATGATTT
AATGCTA
Found at i:16254257 original size:27 final size:27
Alignment explanation
Indices: 16254217--16254327 Score: 82
Period size: 27 Copynumber: 4.0 Consensus size: 27
16254207 AAAAAATTAA
* *
16254217 AAAATTATATATTTTTATAATTTTTTT
1 AAAATTTTAAATTTTTATAATTTTTTT
* *
16254244 AAAATTTTAAATTTTGA-AATTTTTAT
1 AAAATTTTAAATTTTTATAATTTTTTT
* * * *
16254270 AAATATTTTGAATTTTAAAAATTATTTT
1 AAA-ATTTTAAATTTTTATAATTTTTTT
*
16254298 AAATTTTTGAAAATTATTT-TGAATTTTTTT
1 AAAATTTT--AAATT-TTTAT-AATTTTTTT
16254328 TGTAATTTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
26 11 0.17
27 30 0.46
28 10 0.15
29 4 0.06
30 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
AAAATTTTAAATTTTTATAATTTTTTT
Found at i:16254285 original size:19 final size:19
Alignment explanation
Indices: 16254254--16254325 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
16254244 AAAATTTTAA
16254254 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTA-AAATT
*
16254274 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
*
16254293 ATTTTAAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
16254313 ATTTTGAATTTTT
1 ATTTTGAATTTTT
16254326 TTTGTAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.07
19 19 0.41
20 24 0.52
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:16270033 original size:23 final size:24
Alignment explanation
Indices: 16269982--16270038 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
16269972 AATGATCATG
* *
16269982 AATAAGTA-AATAAAAATTGAAGA
1 AATATGTAGAATAAAAATAGAAGA
*
16270005 AATATG-AGAATAAAAATAGAATA
1 AATATGTAGAATAAAAATAGAAGA
*
16270028 ATTATGTAGAA
1 AATATGTAGAA
16270039 AACCACCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.04
23 23 0.82
24 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (24 bp):
AATATGTAGAATAAAAATAGAAGA
Found at i:16273508 original size:17 final size:17
Alignment explanation
Indices: 16273486--16273519 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16273476 GACGGGTTAT
16273486 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
16273503 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
16273520 GGCCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (17 bp):
TGGGTTGTTTGGTTTAG
Found at i:16274283 original size:72 final size:72
Alignment explanation
Indices: 16274185--16274336 Score: 186
Period size: 72 Copynumber: 2.1 Consensus size: 72
16274175 TGAAACTTAA
** ** *
16274185 TTTGAAAAGCAGATCTTGAAAATACCTCAAT-G-AGT-CTTGAGGCTCAACTCATTTCTCGCAAT
1 TTTGAAAAGCAGAAATTGAAAATACCTC-ATCGTA-TCCTT-AGGCTCAACTCACCTCTAGCAAT
16274247 ATGAGTTGAAT
63 ATGAGTTG-AT
*
16274258 TTTGAAAA-CAGAAATTGAAATTACCTCATCGTATCCTTAGGCTCAACTCACCTCTAGCAATATG
1 TTTGAAAAGCAGAAATTGAAAATACCTCATCGTATCCTTAGGCTCAACTCACCTCTAGCAATATG
16274322 AGTTGAT
66 AGTTGAT
16274329 TTTGAAAA
1 TTTGAAAA
16274337 AGTAGGAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
71 12 0.17
72 46 0.66
73 12 0.17
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (72 bp):
TTTGAAAAGCAGAAATTGAAAATACCTCATCGTATCCTTAGGCTCAACTCACCTCTAGCAATATG
AGTTGAT
Found at i:16274416 original size:127 final size:127
Alignment explanation
Indices: 16274238--16274758 Score: 879
Period size: 127 Copynumber: 4.1 Consensus size: 127
16274228 TCAACTCATT
*
16274238 TCTCGCAATATGAGTTGAATT-TTGA-AAACAGAAATTGAAATTACCTCATCGTATCCTTAGGCT
1 TCTCGCAATATGAGTTG-ATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCT
*
16274301 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACC
65 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACC
* * *
16274364 TCTCGCAATATGAGTTGATTCTTGATAGATAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
1 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
*
16274429 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACC
66 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACC
16274491 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
1 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
16274556 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACC
66 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACC
* * *
16274618 TCTCGCAATATGAGTTGATTCTTAACAAACATAAATTGAAATTACCTCATCGTATCCTAAGGCTC
1 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
* * * *
16274683 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAA-CAAAAATGAAAAGGCTT-AACTCACC
66 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGG-TTCAACCCACC
16274744 TCTCGCAATATGAGT
1 TCTCGCAATATGAGT
16274759 CAATTTAAAA
Statistics
Matches: 378, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
125 3 0.01
126 54 0.14
127 321 0.85
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (127 bp):
TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTC
AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACC
Found at i:16274712 original size:254 final size:252
Alignment explanation
Indices: 16274238--16274833 Score: 881
Period size: 254 Copynumber: 2.4 Consensus size: 252
16274228 TCAACTCATT
*
16274238 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCATCGTATCCTTAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTCA
*
16274303 ACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGGTTCAACCCACCTCTC
66 ACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACCTCTC
* * * * *
16274368 GCAATATGAGTTGATTCTTGATAGATAGAAATTGAAATTACCTCATCGTATCCTGAGGCTCAACT
131 GCAATATGAGTTGATTCTTAACAAACAGAAATTGAAATTACCTCATCGTATCCTAAGGCTCAACT
* ** *
16274433 CACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAGGAATTAAAAGG-TTCAACCCACC
196 CACCTCTAGCAATATGAGTTGATTTTGAAAAA-CAAAAATGAAAAGGCTT-AACCCACC
16274491 TCTCGCAATATGAGTTG-ATTCTTGACAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCT
1 TCTCGCAATATGAGTTGAATT-TTGA-AAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCT
16274555 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACCTC
64 CAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACCTC
*
16274620 TCGCAATATGAGTTGATTCTTAACAAACATAAATTGAAATTACCTCATCGTATCCTAAGGCTCAA
129 TCGCAATATGAGTTGATTCTTAACAAACAGAAATTGAAATTACCTCATCGTATCCTAAGGCTCAA
*
16274685 CTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATGAAAAGGCTTAACTCACC
194 CTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATGAAAAGGCTTAACCCACC
* * * * ** *
16274744 TCTCGCAATATGAG-TCAA-TTT-AAAAC-----TAGAAA-TACCTCAGCATGCCCCGAGGCTCA
1 TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTCA
* *
16274800 ACTCACTTCTCGCAATATGAGTTGATTTTGAAAA
66 ACTCACCTCTAGCAATATGAGTTGATTTTGAAAA
16274834 CAAAAATTAA
Statistics
Matches: 317, Mismatches: 22, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
243 51 0.16
244 5 0.02
249 4 0.01
250 1 0.00
251 2 0.01
252 5 0.02
253 53 0.17
254 196 0.62
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (252 bp):
TCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCATCGTATCCTGAGGCTCA
ACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAGTAAGAATTAAAAGGTTCAACCCACCTCTC
GCAATATGAGTTGATTCTTAACAAACAGAAATTGAAATTACCTCATCGTATCCTAAGGCTCAACT
CACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATGAAAAGGCTTAACCCACC
Found at i:16274889 original size:71 final size:71
Alignment explanation
Indices: 16274792--16274970 Score: 349
Period size: 71 Copynumber: 2.5 Consensus size: 71
16274782 AGCATGCCCC
*
16274792 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAAAG
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAAAG
16274857 TGTCTT
66 TGTCTT
16274863 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAAAG
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAAAG
16274928 TGTCTT
66 TGTCTT
16274934 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
16274971 CCTTTAAAAG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 107 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (71 bp):
GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAAAG
TGTCTT
Found at i:16289445 original size:17 final size:17
Alignment explanation
Indices: 16289423--16289456 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16289413 GACGGGTTAT
16289423 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
16289440 TGGGTTGTTTGGTTTAG
1 TGGGTTGTTTGGTTTAG
16289457 GGCCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.41, T:0.53
Consensus pattern (17 bp):
TGGGTTGTTTGGTTTAG
Found at i:16293152 original size:73 final size:73
Alignment explanation
Indices: 16293033--16293177 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
16293023 TAGGAAATTG
16293033 GATGAAGATCTTCAATCTTCATGTAGATCCAACCTCCGAGGTGATTTCGATGGTTGTCCTTGAGT
1 GATGAAGATCTTCAATCTTCATGTAGATCCAACCTCCGAGGTGATTTCGATGGTTGTCCTTGAGT
16293098 ATTTTCTA
66 ATTTTCTA
*
16293106 GATGAAGATCTTCAATCTTGATGTAGATCCAACCTCCGAGGTGATTTCGATGGTTGTCCTTGAGT
1 GATGAAGATCTTCAATCTTCATGTAGATCCAACCTCCGAGGTGATTTCGATGGTTGTCCTTGAGT
16293171 ATTTTCT
66 ATTTTCT
16293178 GCCTTCAACT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (73 bp):
GATGAAGATCTTCAATCTTCATGTAGATCCAACCTCCGAGGTGATTTCGATGGTTGTCCTTGAGT
ATTTTCTA
Found at i:16300730 original size:3 final size:3
Alignment explanation
Indices: 16300722--16300757 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
16300712 CCTTAGTTTG
16300722 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16300758 AAAGCTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:16302757 original size:18 final size:18
Alignment explanation
Indices: 16302734--16302770 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16302724 TATGTTGAGA
16302734 TAGAAACCGAATTACCCT
1 TAGAAACCGAATTACCCT
16302752 TAGAAACCGAATTACCCT
1 TAGAAACCGAATTACCCT
16302770 T
1 T
16302771 GAATGGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (18 bp):
TAGAAACCGAATTACCCT
Found at i:16308998 original size:22 final size:20
Alignment explanation
Indices: 16308973--16309014 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
16308963 ATTATACATA
16308973 AATTATGATTTAATATATAATT
1 AATTATGATTT--TATATAATT
*
16308995 AATTTTGATTTTATATAATT
1 AATTATGATTTTATATAATT
16309015 TTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTATGATTTTATATAATT
Found at i:16309013 original size:16 final size:15
Alignment explanation
Indices: 16308994--16309048 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
16308984 AATATATAAT
16308994 TAATTTTGATTTTATA
1 TAATTTT-ATTTTATA
*
16309010 TAATTTTA-TATATA
1 TAATTTTATTTTATA
* *
16309024 TAATTTTTATTTAATT
1 TAA-TTTTATTTTATA
16309040 TAATTTTAT
1 TAATTTTAT
16309049 AAATTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 8 0.24
15 12 0.36
16 13 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TAATTTTATTTTATA
Found at i:16309020 original size:30 final size:30
Alignment explanation
Indices: 16308986--16309054 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
16308976 TATGATTTAA
*
16308986 TATATAATTAATTTTGATTTTATATAATTT
1 TATATAATTAATTTTGATTTAATATAATTT
* *
16309016 TATAT-ATATAATTTTTATTTAATTTAATTT
1 TATATAAT-TAATTTTGATTTAATATAATTT
16309046 TATA-AATTA
1 TATATAATTA
16309055 TTAACACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TATATAATTAATTTTGATTTAATATAATTT
Found at i:16309025 original size:14 final size:14
Alignment explanation
Indices: 16309006--16309049 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
16308996 ATTTTGATTT
16309006 TATATAATTTTATA
1 TATATAATTTTATA
*
16309020 TATATAATTTTTATT
1 TATATAA-TTTTATA
*
16309035 TAATTTAATTTTATA
1 T-ATATAATTTTATA
16309050 AATTATTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 13 0.52
16 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATAATTTTATA
Found at i:16316727 original size:14 final size:14
Alignment explanation
Indices: 16316710--16316738 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16316700 TCTCCTTGAG
16316710 AGTCGATTTTAACC
1 AGTCGATTTTAACC
16316724 AGTCGATTTTAACC
1 AGTCGATTTTAACC
16316738 A
1 A
16316739 CAAAATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (14 bp):
AGTCGATTTTAACC
Found at i:16319979 original size:39 final size:39
Alignment explanation
Indices: 16319936--16320010 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
16319926 GTTAGTTTTG
* * *
16319936 AGTTTAGGGGCTAAAATGAAAATATTTTGAAATTAAATA
1 AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAAATA
16319975 AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAA
1 AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAA
16320011 CATGAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (39 bp):
AGTTTAGGGACTAAAATAAAAATATTTTAAAATTAAATA
Found at i:16328136 original size:40 final size:40
Alignment explanation
Indices: 16328091--16328233 Score: 146
Period size: 40 Copynumber: 3.5 Consensus size: 40
16328081 TTTGGATATA
*
16328091 TATATATGGCACTTAGTATGCGGTTCGAGATAGTTTCGGC
1 TATATATGGCACTTAGTGTGCGGTTCGAGATAGTTTCGGC
* * * *
16328131 TATATATGGCATTTAGTGTGTGATTCG-GAATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGGTTCGAG-ATAGTTTCGGC
* **
16328171 TATATATAGCACTTAGTGTGCGAGACCGAGATAGCTTT-GGC
1 TATATATGGCACTTAGTGTGCG-GTTCGAGATAG-TTTCGGC
* * *
16328212 TATGTAAGGCACTTAATGTGCG
1 TATATATGGCACTTAGTGTGCG
16328234 AGATTATAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 52 0.63
41 27 0.33
42 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGGTTCGAGATAGTTTCGGC
Found at i:16328213 original size:81 final size:81
Alignment explanation
Indices: 16328091--16328272 Score: 190
Period size: 82 Copynumber: 2.2 Consensus size: 81
16328081 TTTGGATATA
* * ** * * * *
16328091 TATATATGGCACTTAGTATGCGGTTCGAGATAGTTTCGGCTATATATGGCA-TTTA-GTGTGTGA
1 TATATATAGCACTTAGTGTGCGGACCGAGATAGTTTCGGCTATATAAGGCACTTAATGTGCGAGA
* *
16328154 TTCGGAATAGCTTCGGC
66 TT-AGAATAGCTTCGAC
*
16328171 TATATATAGCACTTAGTGTGCGAGACCGAGATAGCTTT-GGCTATGTAAGGCACTTAATGTGCGA
1 TATATATAGCACTTAGTGTGCG-GACCGAGATAG-TTTCGGCTATATAAGGCACTTAATGTGCGA
*
16328235 GATTATAATAGCTTCGAC
64 GATTAGAATAGCTTCGAC
*
16328253 TATGTATAGACACTTAGTGT
1 TATATATAG-CACTTAGTGT
16328273 ATGAGATATT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
80 20 0.24
81 21 0.25
82 25 0.30
83 18 0.21
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (81 bp):
TATATATAGCACTTAGTGTGCGGACCGAGATAGTTTCGGCTATATAAGGCACTTAATGTGCGAGA
TTAGAATAGCTTCGAC
Found at i:16342135 original size:66 final size:65
Alignment explanation
Indices: 16342009--16342145 Score: 179
Period size: 66 Copynumber: 2.1 Consensus size: 65
16341999 AACGATCTCA
* *
16342009 CACACGGGCGTGTGACTGGCCGTGTGGTACAAGTCAGTATACCCCCCTAATTGGCACACGGCCTA
1 CACACGGGCGTGTGACTGGCCGTGTGGCACAAGTCAGTATACCCCACTAATTGG-ACACGGCCTA
16342074 G
65 G
* * *
16342075 CACACGGGCGTGTGACTTGGCCGTGTTGCATAAGTCAGTATACCCTAC-AGGATTGG-CACGGCC
1 CACACGGGCGTGTGAC-TGGCCGTGTGGCACAAGTCAGTATACCCCACTA--ATTGGACACGGCC
16342138 TAG
63 TAG
16342141 CACAC
1 CACAC
16342146 AGCCTGGCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
66 32 0.51
67 26 0.41
68 5 0.08
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.20
Consensus pattern (65 bp):
CACACGGGCGTGTGACTGGCCGTGTGGCACAAGTCAGTATACCCCACTAATTGGACACGGCCTAG
Found at i:16348097 original size:23 final size:24
Alignment explanation
Indices: 16348044--16348122 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 24
16348034 AAAAAATATA
*
16348044 TTTAAAATAAAC-AATACAAAACAG
1 TTTAAAAT-AACTAATATAAAACAG
*
16348068 TTTAAAATAACTAATATAAAA-GG
1 TTTAAAATAACTAATATAAAACAG
* *
16348091 TTTAAAATAAATAATATATAAAATAG
1 TTTAAAATAACT-A-ATATAAAACAG
16348117 TTTAAA
1 TTTAAA
16348123 CTACATAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 15 0.32
24 17 0.36
25 8 0.17
26 7 0.15
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
TTTAAAATAACTAATATAAAACAG
Found at i:16348130 original size:26 final size:25
Alignment explanation
Indices: 16347985--16348290 Score: 144
Period size: 23 Copynumber: 12.4 Consensus size: 25
16347975 AAATAAAAGG
* * *
16347985 TATATAAAAA-CTTAAAGTAAGTAA
1 TATATAAAAAGTTTAAAATAAATAA
* *
16348009 TATATAAAATAGTTAAAAATAACACAA
1 TATATAAAA-AGTTTAAAATAA-ATAA
* *
16348036 -A-A-AATATA-TTTAAAATAAACAA
1 TATATAA-AAAGTTTAAAATAAATAA
* * *
16348058 TACA-AAACAGTTTAAAATAACT-A
1 TATATAAAAAGTTTAAAATAAATAA
*
16348081 -ATATAAAAGGTTTAAAATAAATAA
1 TATATAAAAAGTTTAAAATAAATAA
* *
16348105 TATATAAAATAGTTTAAACTACAT-A
1 TATATAAAA-AGTTTAAAATAAATAA
**
16348130 -AGGT--AAAGTTTAAAATAAATAA
1 TATATAAAAAGTTTAAAATAAATAA
* *
16348152 TGTATATAAAAA-CTCAAAATAAATAA
1 --TATATAAAAAGTTTAAAATAAATAA
* *
16348178 TATGATAAAACAATTTAAAACAAATACCA
1 TAT-ATAAAA-AGTTTAAAATAAATA--A
**
16348207 TATATAAAAAAACTTAAAATAAATAA
1 TATAT-AAAAAGTTTAAAATAAATAA
*
16348233 TA-ATAAAACAGTTCAAAATAAAT-A
1 TATATAAAA-AGTTTAAAATAAATAA
* *
16348257 T-TAT-GAAAGATTTATAATAAATAA
1 TATATAAAAAG-TTTAAAATAAATAA
*
16348281 AATA-AAAAAG
1 TATATAAAAAG
16348291 AAAACAAAAA
Statistics
Matches: 215, Mismatches: 38, Indels: 57
0.69 0.12 0.18
Matches are distributed among these distances:
21 12 0.06
22 11 0.05
23 40 0.19
24 40 0.19
25 39 0.18
26 35 0.16
27 15 0.07
28 15 0.07
29 8 0.04
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.28
Consensus pattern (25 bp):
TATATAAAAAGTTTAAAATAAATAA
Found at i:16348203 original size:53 final size:52
Alignment explanation
Indices: 16348138--16348256 Score: 150
Period size: 53 Copynumber: 2.2 Consensus size: 52
16348128 TAAGGTAAAG
* *
16348138 TTTAAAATAAATA-ATGTATATAAAAACTCAAAATAAATAATATGATAAAACAA
1 TTTAAAATAAATACATATATAAAAAAACTCAAAATAAATAATA--ATAAAACAA
* * *
16348191 TTTAAAACAAATACCATATATAAAAAAACTTAAAATAAATAATAATAAAACAG
1 TTTAAAATAAATA-CATATATAAAAAAACTCAAAATAAATAATAATAAAACAA
*
16348244 TTCAAAATAAATA
1 TTTAAAATAAATA
16348257 TTATGAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 31 0.54
55 26 0.46
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.27
Consensus pattern (52 bp):
TTTAAAATAAATACATATATAAAAAAACTCAAAATAAATAATAATAAAACAA
Found at i:16348223 original size:28 final size:26
Alignment explanation
Indices: 16348139--16348240 Score: 116
Period size: 28 Copynumber: 3.8 Consensus size: 26
16348129 AAGGTAAAGT
* *
16348139 TTAAAATAAATAATGTATATAAAAAC
1 TTAAAATAAATAATATATAAAAAAAC
* * *
16348165 TCAAAATAAATAATATGATAAAACAAT
1 TTAAAATAAATAATAT-ATAAAAAAAC
*
16348192 TTAAAACAAATACCATATATAAAAAAAC
1 TTAAAATAAATA--ATATATAAAAAAAC
16348220 TTAAAATAAATAATA-ATAAAA
1 TTAAAATAAATAATATATAAAA
16348241 CAGTTCAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
25 6 0.10
26 17 0.27
27 17 0.27
28 19 0.30
29 4 0.06
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAAAAAC
Found at i:16348325 original size:22 final size:21
Alignment explanation
Indices: 16348296--16348337 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16348286 AAAAGAAAAC
16348296 AAAAAAGAAT-ACAATATAATG
1 AAAAAAG-ATGACAATATAATG
16348317 AAAATAAGATGACAATATAAT
1 AAAA-AAGATGACAATATAAT
16348338 AATGCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAAAAGATGACAATATAATG
Found at i:16349255 original size:71 final size:71
Alignment explanation
Indices: 16349139--16349276 Score: 267
Period size: 71 Copynumber: 1.9 Consensus size: 71
16349129 GGTGGTGTCA
16349139 GAGAAACGCGCGATGGCAGGTGACAGGCGAGCCGAGCGGTGGTGGCAGAGGCGCTGGGCAAAGGG
1 GAGAAACGCGCGATGGCAGGTGACAGGCGAGCCGAGCGGTGGTGGCAGAGGCGCTGGGCAAAGGG
16349204 GGGACG
66 GGGACG
*
16349210 GAGAAACGCGCGATGGCAGGTGACAGGCGAGCCGAGCGGTGGTGGCAGAGGCGCTGGTCAAAGGG
1 GAGAAACGCGCGATGGCAGGTGACAGGCGAGCCGAGCGGTGGTGGCAGAGGCGCTGGGCAAAGGG
16349275 GG
66 GG
16349277 AACGACTAGG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.22, C:0.20, G:0.50, T:0.08
Consensus pattern (71 bp):
GAGAAACGCGCGATGGCAGGTGACAGGCGAGCCGAGCGGTGGTGGCAGAGGCGCTGGGCAAAGGG
GGGACG
Found at i:16349396 original size:20 final size:20
Alignment explanation
Indices: 16349373--16349411 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16349363 TGGATCATTA
16349373 GTTTTGGGTTTGTAATTTTG
1 GTTTTGGGTTTGTAATTTTG
16349393 GTTTTGGGTTTGTAATTTT
1 GTTTTGGGTTTGTAATTTT
16349412 AAACTGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.28, T:0.62
Consensus pattern (20 bp):
GTTTTGGGTTTGTAATTTTG
Found at i:16349789 original size:51 final size:51
Alignment explanation
Indices: 16349709--16350037 Score: 234
Period size: 51 Copynumber: 6.8 Consensus size: 51
16349699 GAGATAAGAC
* * * *
16349709 TTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGGGATAAGGTTTGTGGT
1 TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGAT
* * * * *
16349760 TTGTAGCTTCAATCTGCCCCACTGCAACTTTAGGGAGATAA-G-AT-TCA-
1 TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGAT
* * * * *
16349807 --CTATCTTCAGCCTGCTCCACTGTAAATTCAGGGAGATAA-------GAT
1 TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGAT
* * * * *
16349849 TTGTAACTTCAACCTGCTCTACTGCAACTTTAGGAAGATAAGGTTTGTGGT
1 TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGAT
* * *
16349900 TTGTAGCTTCAATCTGC-CCTACTGTAACTTCAGGGAGATAAGATTTGCT-AT
1 TTGTAGCTTCAACCTGCTCC-ACTGCAACTTCAGGGAGATAAGGTTTG-TGAT
* *
16349951 CTT-TAG-TT-----TACTCCACTGCAACTTCAGGGAGATAAGATTTGTGAT
1 -TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGAT
* **
16349996 TTGTAGCTTCAATCTGCTCCACTGCAACTTCAATGAGATAAG
1 TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG
16350038 ATTCGCTATC
Statistics
Matches: 216, Mismatches: 40, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
41 1 0.00
44 34 0.16
45 64 0.30
46 4 0.02
48 1 0.00
49 1 0.00
50 4 0.02
51 104 0.48
52 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (51 bp):
TTGTAGCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGAT
Found at i:16349796 original size:140 final size:140
Alignment explanation
Indices: 16349638--16349992 Score: 516
Period size: 140 Copynumber: 2.5 Consensus size: 140
16349628 TCAGTCCATT
*
16349638 CCACTGCAACTTCGGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTCTA-GGAG
1 CCACTGCAACTTCAGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTC-AGGGAG
* * **
16349702 ATAAGACTTGTAACTTCAACCTGCTCCACTGTAACTTCAGGGGGATAAGGTTTGTGGTTTGTAGC
65 ATAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTGGTTTGTAGC
16349767 TTCAATCTGCC
130 TTCAATCTGCC
* * * *
16349778 CCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGCCTGCTCCACTGTAAATTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTCAGGGAGA
* *
16349843 TAAGATTTGTAACTTCAACCTGCTCTACTGCAACTTTAGGAAGATAAGGTTTGTGGTTTGTAGCT
66 TAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTGGTTTGTAGCT
16349908 TCAATCTGCC
131 TCAATCTGCC
* * ** * * *
16349918 CTACTGTAACTTCAGGGAGATAAGATTTGCTATCTTT-AGTTTACTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGGAGATAAGATTCACTAT-TTTCAGTCTGCTCCACTGCAAATTCAGGGAG
16349982 ATAAGATTTGT
65 ATAAGATTTGT
16349993 GATTTGTAGC
Statistics
Matches: 191, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
139 1 0.01
140 188 0.98
141 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (140 bp):
CCACTGCAACTTCAGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTCAGGGAGA
TAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTGGTTTGTAGCT
TCAATCTGCC
Found at i:16349840 original size:45 final size:45
Alignment explanation
Indices: 16349637--16350169 Score: 233
Period size: 45 Copynumber: 11.6 Consensus size: 45
16349627 TTCAGTCCAT
* * **
16349637 TCCACTGCAACTTCGGGGAGATAAGATTCACTATTTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
* * *
16349682 TCCACTGCAAATTCTA-GGAGATAAGACTT--GTAACTTCAACCTGC
1 TCCACTGCAACTTC-AGGGAGATAAGA-TTCACTATCTTCAACCTGC
* * * *** * *
16349726 TCCACTGTAACTTCAGGGGGATAAGGTTTGTGGTTTGTAGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAA-G---AT--TCACTATCTTCAACCTGC
* * *
16349777 CCCACTGCAACTTTAGGGAGATAAGATTCACTATCTTCAGCCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
* * ** *
16349822 TCCACTGTAAATTCAGGGAGATAAGATT-TGTAACTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
* * * * *** * *
16349866 TCTACTGCAACTTTAGGAAGATAAGGTTTGTGGTTTGTAGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAA-G---AT--TCACTATCTTCAACCTGC
* ** * *** *
16349917 -CCTACTGTAACTTCAGGGAGATAAGATTTGCTATCTTTAGTTTAC
1 TCC-ACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
* * * *
16349962 TCCACTGCAACTTCAGGGAGATAAGATTTGTGATTTGTAGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA--T-TCA---CTATCTTCAACCTGC
** * **
16350013 TCCACTGCAACTTCAATGAGATAAGATTCGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
* * * * * **
16350058 TCCATTGCAACTTTAGGGAGACAAGACTT--GTAACTTCAACCCAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCACTATCTTCAACCTGC
* * * *
16350102 TCCACTGCAACTTCAGGGAGATAAGGTTTACTA---T-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
* *
16350143 TCTACTGCAACTTCAGAGAGATAAGAT
1 TCCACTGCAACTTCAGGGAGATAAGAT
16350170 CTGTTATTTA
Statistics
Matches: 368, Mismatches: 91, Indels: 62
0.71 0.17 0.12
Matches are distributed among these distances:
41 27 0.07
42 1 0.00
43 3 0.01
44 91 0.25
45 129 0.35
46 6 0.02
47 4 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 98 0.27
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCACTATCTTCAACCTGC
Found at i:16350002 original size:96 final size:96
Alignment explanation
Indices: 16349637--16350261 Score: 417
Period size: 96 Copynumber: 6.7 Consensus size: 96
16349627 TTCAGTCCAT
* * ** * *
16349637 TCCACTGCAACTTCGGGGAGATAAGATTCACTATTTTCAGTCTGCTCCACTGCAAATTCTA-GGA
1 TCCACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTT-TAGGGA
* *
16349701 GATAAGACTTGT-A-----A-CTTCAACCTGC
65 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * * * *
16349726 TCCACTGTAACTTCAGGGGGATAAGGTTTGTGGTTTGTAGCTTCAATCTGCCCCACTGCAACTTT
1 TCCACTGTAACTTCAGGGAGATAA-GATT-T-G---CTATCTTCAGTCTGCTCCACTGCAACTTT
* * * **
16349791 AGGGAGATAAGA--T-TCA---CTATCTTCAGCCTGC
60 AGGGAGATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * ** * *
16349822 TCCACTGTAAATTCAGGGAGATAAGATTTG-TAACTTCAACCTGCTCTACTGCAACTTTAGGAAG
1 TCCACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
* *
16349886 ATAAGGTTTGTGGTTTGTAGCTTCAATCTGC
66 ATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * *
16349917 -CCTACTGTAACTTCAGGGAGATAAGATTTGCTATCTTTAGTTTACTCCACTGCAACTTCAGGGA
1 TCC-ACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGA
16349981 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
65 GATAAGATTTGTGATTTGTAGCTTCAATCTGC
* ** * *
16350013 TCCACTGCAACTTCAATGAGATAAGATTCGCTATCTTCAGTCTGCTCCATTGCAACTTTAGGGAG
1 TCCACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
* * * **
16350078 ACAAGACTTGT-A-----A-CTTCAACCCAC
66 ATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * * * * *
16350102 TCCACTGCAACTTCAGGGAGATAAGGTTTACTA---TGA-TCTGCTCTACTGCAACTTCAGAGAG
1 TCCACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
* * * *
16350163 ATAAGATCTGTTATTTATAGCTTCAATCTGT
66 ATAAGATTTGTGATTTGTAGCTTCAATCTGC
* * * * * * * * *
16350194 TCCATTGTAATTTCAGGGAGA-AGAGATTTG-TAGCTTCAATCTACTCCGCTGAAACTTCAAGGA
1 TCCACTGTAACTTCAGGGAGATA-AGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGA
16350257 GATAA
65 GATAA
16350262 AAATTGTGGC
Statistics
Matches: 421, Mismatches: 83, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
85 29 0.07
86 3 0.01
89 91 0.22
90 4 0.01
91 5 0.01
92 32 0.08
93 3 0.01
94 7 0.02
95 97 0.23
96 148 0.35
97 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (96 bp):
TCCACTGTAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAG
ATAAGATTTGTGATTTGTAGCTTCAATCTGC
Found at i:16350258 original size:44 final size:44
Alignment explanation
Indices: 16350205--16350347 Score: 135
Period size: 44 Copynumber: 3.2 Consensus size: 44
16350195 CCATTGTAAT
* *
16350205 TTCAGGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAAC
1 TTCAAGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAAC
* * * * ** ** ** *
16350249 TTCAAGGAGATA-AAAATTGTGGCTTCGAGCCGCTCCAATGCCAT
1 TTCAAGGAGA-AGAGATTTGTAGCTTCGATCTACTCCGCTGAAAC
* *
16350293 TTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAAC
1 TTCAAGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAAC
16350337 TTCAAGGAGAA
1 TTCAAGGAGAA
16350348 ACAAATTGTT
Statistics
Matches: 71, Mismatches: 26, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
43 1 0.01
44 69 0.97
45 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
TTCAAGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAAC
Found at i:16350390 original size:88 final size:88
Alignment explanation
Indices: 16350205--16350374 Score: 236
Period size: 88 Copynumber: 1.9 Consensus size: 88
16350195 CCATTGTAAT
16350205 TTCAGGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAACTTCAAGGAGATAAAAATTGTG
1 TTCAGGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAACTTCAAGGAGATAAAAATTGTG
* * * *
16350270 GCTTCGAGCCGCTCCAATGCCAT
66 ACTTCGAACCGCTCCAATACCAC
* *
16350293 TTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGA-AACAAATTGT
1 TTCAGGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAACTTCAAGGAGATAA-AAATTG-
*
16350357 TGATTTC-AACCTGCTCCA
64 TGACTTCGAACC-GCTCCA
16350375 CTACTGCTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
87 2 0.03
88 61 0.82
89 11 0.15
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (88 bp):
TTCAGGGAGAAGAGATTTGTAGCTTCAATCTACTCCGCTGAAACTTCAAGGAGATAAAAATTGTG
ACTTCGAACCGCTCCAATACCAC
Found at i:16356700 original size:24 final size:24
Alignment explanation
Indices: 16356637--16356722 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 24
16356627 ACATAAAAGG
16356637 TTTAAAATAAATACCAT-AAAAGCAA
1 TTTAAAATAAATA--ATAAAAAGCAA
*
16356662 TTTAAAGTAAATAATACAAAA-CAA
1 TTTAAAATAAATAATA-AAAAGCAA
* *
16356686 TTTAAAATCATTAATAAAAAG---
1 TTTAAAATAAATAATAAAAAGCAA
*
16356707 TCTAAAATAAATAATA
1 TTTAAAATAAATAATA
16356723 TGTAAAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 13 0.25
23 6 0.12
24 16 0.31
25 16 0.31
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (24 bp):
TTTAAAATAAATAATAAAAAGCAA
Found at i:16356924 original size:24 final size:25
Alignment explanation
Indices: 16356883--16357004 Score: 70
Period size: 28 Copynumber: 4.7 Consensus size: 25
16356873 TGAATTTATA
* *
16356883 ATAATAAATAGTTCAAAAAT-AATAT
1 ATAA-AAATAATTTAAAAATAAATAT
*
16356908 ATAAAAATAATTT-AAAATAAATAA
1 ATAAAAATAATTTAAAAATAAATAT
* * * *
16356932 ATAAAAAACAATGTGAAGTAATTAATAT
1 AT-AAAAATAAT-TTAA-AAATAAATAT
* *
16356960 ATATAAAATAA-TTCAAAATGACATAT
1 ATA-AAAATAATTTAAAAAT-AAATAT
16356986 ATTAAAAAATAATTTAAAA
1 A-T-AAAAATAATTTAAAA
16357005 CAAATATCAT
Statistics
Matches: 72, Mismatches: 15, Indels: 17
0.69 0.14 0.16
Matches are distributed among these distances:
23 5 0.07
24 13 0.18
25 15 0.21
26 8 0.11
27 10 0.14
28 21 0.29
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (25 bp):
ATAAAAATAATTTAAAAATAAATAT
Found at i:16356934 original size:28 final size:27
Alignment explanation
Indices: 16356899--16357046 Score: 112
Period size: 27 Copynumber: 5.6 Consensus size: 27
16356889 AATAGTTCAA
16356899 AAATAATATATAAAAATAATTTAAAAT
1 AAATAATATATAAAAATAATTTAAAAT
* * * *
16356926 AAATAA-ATA-AAAAACAATGTGAAGT
1 AAATAATATATAAAAATAATTTAAAAT
* *
16356951 AATTAATATATATAAAATAATTCAAAAT
1 AAATAATATATA-AAAATAATTTAAAAT
* *
16356979 GACAT-ATAT-TAAAAAATAATTTAAAAC
1 -AAATAATATAT-AAAAATAATTTAAAAT
* *
16357006 AAAT-ATCATATGAAAAA-AACTTCAAAT
1 AAATAAT-ATAT-AAAAATAATTTAAAAT
16357033 AAATAATA-ATAAAA
1 AAATAATATATAAAA
16357047 CTGTTCAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 18
0.72 0.15 0.14
Matches are distributed among these distances:
25 21 0.22
26 13 0.14
27 35 0.37
28 23 0.24
29 2 0.02
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (27 bp):
AAATAATATATAAAAATAATTTAAAAT
Found at i:16357131 original size:22 final size:21
Alignment explanation
Indices: 16357102--16357143 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
16357092 AAAAGAAAAC
16357102 AAAAAAGAAT-ACAATATAATG
1 AAAAAAG-ATGACAATATAATG
16357123 AAAATAAGATGACAATATAAT
1 AAAA-AAGATGACAATATAAT
16357144 AATGCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAAAAGATGACAATATAATG
Found at i:16365940 original size:19 final size:19
Alignment explanation
Indices: 16365916--16366009 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 19
16365906 AAAATTATTA
16365916 TTTTATAAAATTTTAAATT
1 TTTTATAAAATTTTAAATT
** *
16365935 TTTTATATATTTTTTAGATT
1 TTTTATA-AAATTTTAAATT
*
16365955 TTTT-TAAAATTTATAATTT
1 TTTTATAAAATTT-TAAATT
16365974 TTTTAAATACAAATTTTAGAA-T
1 TTTT--ATA-AAATTTTA-AATT
16365996 TTTTATAAATATTT
1 TTTTATAAA-ATTT
16366010 AGAATTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.07
19 19 0.32
20 20 0.34
22 9 0.15
23 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTAAATT
Found at i:16366027 original size:19 final size:19
Alignment explanation
Indices: 16365984--16366028 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
16365974 TTTTAAATAC
*
16365984 AAAT-TTTAGAATTTTTAT
1 AAATATTTAGAATTTTTAA
16366002 AAATATTTAGAA-TTTTAA
1 AAATATTTAGAATTTTTAA
16366020 AAATTATTT
1 AAA-TATTT
16366029 TCAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
AAATATTTAGAATTTTTAA
Found at i:16367372 original size:23 final size:25
Alignment explanation
Indices: 16367346--16367392 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
16367336 TATCATTCAT
*
16367346 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
16367369 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
16367393 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:16367713 original size:46 final size:46
Alignment explanation
Indices: 16367653--16367910 Score: 280
Period size: 46 Copynumber: 6.0 Consensus size: 46
16367643 TTTGACGTGA
* * * *
16367653 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCAGGT
* * *
16367699 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGT
16367745 TGCCATGGTATCTTTCAACCATGGTCTTA--CA---CA---CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGT
* *
16367783 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGT
*
16367829 TGACATGGTATCTTTCAACCATGGTCTTA--CA---CA---CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGT
* *
16367867 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAG
16367911 AGAGCACACT
Statistics
Matches: 185, Mismatches: 10, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
38 66 0.36
40 4 0.02
41 4 0.02
43 4 0.02
44 3 0.02
45 4 0.02
46 100 0.54
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGT
Found at i:16367794 original size:38 final size:38
Alignment explanation
Indices: 16367743--16367899 Score: 233
Period size: 38 Copynumber: 3.9 Consensus size: 38
16367733 TTCATGTCAC
16367743 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
16367781 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAG
*
16367827 GTTGACATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
16367865 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
16367900 TTTCATATCA
Statistics
Matches: 109, Mismatches: 2, Indels: 16
0.86 0.02 0.13
Matches are distributed among these distances:
38 67 0.61
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 32 0.29
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:16367838 original size:84 final size:84
Alignment explanation
Indices: 16367697--16367910 Score: 374
Period size: 84 Copynumber: 2.5 Consensus size: 84
16367687 TTTCTGTCAT
** * * * *
16367697 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGACATGGTATCTTTCA
16367762 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
16367781 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGACATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGACATGGTATCTTTCA
16367846 ACCATGGTCTTACACACAG
66 ACCATGGTCTTACACACAG
16367865 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
16367911 AGAGCACACT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 124 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (84 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGACATGGTATCTTTCA
ACCATGGTCTTACACACAG
Found at i:16368198 original size:62 final size:62
Alignment explanation
Indices: 16368094--16368247 Score: 238
Period size: 62 Copynumber: 2.5 Consensus size: 62
16368084 ACCCTAATTC
* * * *
16368094 GGATC-CCCGTCCGGGCTAAATCCATTTTACACGTATTTTTCGGGAGGGCTATATCAGAATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGAATA
* *
16368155 GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATTAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGAATA
*
16368217 GGATCACCCATCCGGGCTAGATCCTTTTTAC
1 GGATCACCCGTCCGGGCTAGATCCTTTTTAC
16368248 CGTCAACTCC
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 5 0.06
62 80 0.94
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (62 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTACACATATTCTTCGGGAGGGCTATATCAGAATA
Found at i:16378884 original size:19 final size:18
Alignment explanation
Indices: 16378826--16378884 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
16378816 CTAAAAATAT
*
16378826 ATTTTAAACAATCAATAAA
1 ATTTTAAAAAAT-AATAAA
* * *
16378845 ATTATAAAAAAGAATTCAA
1 ATTTTAAAAAATAA-TAAA
16378864 ATTTTATAAAAATAATAAA
1 ATTTTA-AAAAATAATAAA
16378883 AT
1 AT
16378885 AATTAAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 2 0.06
19 22 0.71
20 7 0.23
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (18 bp):
ATTTTAAAAAATAATAAA
Found at i:16393432 original size:21 final size:20
Alignment explanation
Indices: 16393371--16393432 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
16393361 GAAAAAAATT
*
16393371 AAATTCAA-ATTAAAATACTA
1 AAATTCAAGA-TAAAATACTG
*
16393391 AAATTCAAGATAAAATCCTG
1 AAATTCAAGATAAAATACTG
16393411 AAATTCAAGATAAAAATACTG
1 AAATTCAAGAT-AAAATACTG
16393432 A
1 A
16393433 TGTGGCATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 27 0.73
21 10 0.27
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.26
Consensus pattern (20 bp):
AAATTCAAGATAAAATACTG
Found at i:16395208 original size:6 final size:6
Alignment explanation
Indices: 16395197--16395222 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16395187 CTTTTCCGTG
16395197 AAACCA AAACCA AAACCA AAACCA AA
1 AAACCA AAACCA AAACCA AAACCA AA
16395223 CAGAATACAA
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCA
Found at i:16396198 original size:18 final size:17
Alignment explanation
Indices: 16396158--16396191 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16396148 AAAGTTTAGG
16396158 GGGAAAATAAAAAGTTT
1 GGGAAAATAAAAAGTTT
*
16396175 TGGAAAATAAAAA-TTT
1 GGGAAAATAAAAAGTTT
16396191 G
1 G
16396192 AGGGAAAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 1
0.83 0.11 0.06
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (17 bp):
GGGAAAATAAAAAGTTT
Found at i:16402219 original size:17 final size:16
Alignment explanation
Indices: 16402188--16402221 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16402178 ATGAAAATCT
*
16402188 ATAAAATATGTTAATA
1 ATAAAATATGATAATA
16402204 ATAAAGATATGATAATA
1 ATAAA-ATATGATAATA
16402221 A
1 A
16402222 ATGTCCCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (16 bp):
ATAAAATATGATAATA
Found at i:16412337 original size:18 final size:17
Alignment explanation
Indices: 16412304--16412342 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16412294 TTGTATAAAT
16412304 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
16412322 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
16412339 TGTG
1 TGTG
16412343 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:16412595 original size:23 final size:23
Alignment explanation
Indices: 16412568--16412665 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
16412558 AGTGTTATTG
16412568 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
16412591 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16412614 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16412636 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16412659 ATCAGTG
1 ATCAGTG
16412666 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16412634 original size:45 final size:45
Alignment explanation
Indices: 16412570--16412658 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
16412560 TGTTATTGAT
* *
16412570 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
16412615 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
16412659 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:16421598 original size:23 final size:23
Alignment explanation
Indices: 16421567--16421626 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
16421557 CGGGGTAGAG
16421567 CACACGGGCGTGTGTATTGTCTC
1 CACACGGGCGTGTGTATTGTCTC
** *
16421590 TGCACGGGCATGTGTATTGTCTC
1 CACACGGGCGTGTGTATTGTCTC
16421613 CACACGGGCGTGTG
1 CACACGGGCGTGTG
16421627 AAACATTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.28
Consensus pattern (23 bp):
CACACGGGCGTGTGTATTGTCTC
Found at i:16423160 original size:23 final size:23
Alignment explanation
Indices: 16423130--16423175 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16423120 CATGAAGTAT
16423130 ACGTAGATTATCATGTAGGATAC
1 ACGTAGATTATCATGTAGGATAC
16423153 ACGTAGATTATCATGTAGGATAC
1 ACGTAGATTATCATGTAGGATAC
16423176 CATGTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (23 bp):
ACGTAGATTATCATGTAGGATAC
Found at i:16425304 original size:12 final size:12
Alignment explanation
Indices: 16425287--16425326 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
16425277 ATATTAAAAA
16425287 AAAAAGAAAATG
1 AAAAAGAAAATG
16425299 AAAAAGAAAATG
1 AAAAAGAAAATG
16425311 AAGAAAAGAAAA-G
1 -A-AAAAGAAAATG
16425324 AAA
1 AAA
16425327 CCAAGTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.08
12 13 0.50
13 2 0.08
14 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:16428399 original size:35 final size:35
Alignment explanation
Indices: 16428359--16428436 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
16428349 TGACAAAAAA
16428359 AAATTTAACAATATCAACAGTTAGACTTAATTTTC
1 AAATTTAACAATATCAACAGTTAGACTTAATTTTC
16428394 AAATTTAACAATATCAACAGTTAGACTTAATTTTC
1 AAATTTAACAATATCAACAGTTAGACTTAATTTTC
16428429 AAATTTAA
1 AAATTTAA
16428437 AAAGTATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (35 bp):
AAATTTAACAATATCAACAGTTAGACTTAATTTTC
Found at i:16430699 original size:19 final size:17
Alignment explanation
Indices: 16430677--16430726 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
16430667 TTTTTTTGCT
16430677 TTTTAATAAAATTTTAATA
1 TTTTAATAAAATTTT--TA
16430696 TTTTAA-AGAAATTTTTA
1 TTTTAATA-AAATTTTTA
16430713 TTTT-ATAAAATTTT
1 TTTTAATAAAATTTT
16430727 GTTAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.28
17 7 0.24
18 1 0.03
19 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTAATAAAATTTTTA
Found at i:16430734 original size:19 final size:20
Alignment explanation
Indices: 16430712--16430755 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
16430702 AGAAATTTTT
16430712 ATTTTATAA-AA-TTTTGTTA
1 ATTTTATAATAATTTTTG-TA
16430731 ATTTT-TAATAATTTTTGTA
1 ATTTTATAATAATTTTTGTA
16430750 ATTTTA
1 ATTTTA
16430756 ACAATTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTATAATAATTTTTGTA
Found at i:16430756 original size:18 final size:20
Alignment explanation
Indices: 16430723--16430763 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
16430713 TTTTATAAAA
*
16430723 TTTTGTTAATTTTTAATAAT
1 TTTTGTTAATTTTTAACAAT
16430743 TTTTG-TAA-TTTTAACAAT
1 TTTTGTTAATTTTTAACAAT
16430761 TTT
1 TTT
16430764 CTTTAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 3 0.15
20 5 0.25
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTGTTAATTTTTAACAAT
Found at i:16430785 original size:22 final size:21
Alignment explanation
Indices: 16430760--16430800 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16430750 ATTTTAACAA
*
16430760 TTTTCTTTAACTTATTTATAG
1 TTTTTTTTAACTTATTTATAG
* *
16430781 TTTTTTTTTACTTTTTTATA
1 TTTTTTTTAACTTATTTATA
16430801 ATAAAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTTTTAACTTATTTATAG
Found at i:16431955 original size:161 final size:161
Alignment explanation
Indices: 16431682--16432656 Score: 1925
Period size: 161 Copynumber: 6.1 Consensus size: 161
16431672 AATTACTTTT
*
16431682 AAGGCGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGC-TGTATT
1 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
*
16431746 GAATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
66 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
16431811 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
131 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
16431842 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
1 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
16431907 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
66 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
16431972 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
131 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
16432003 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
1 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
16432068 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
66 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
16432133 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
131 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
16432164 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
1 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
16432229 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
66 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
16432294 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
131 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
16432325 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
1 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
16432390 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
66 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
16432455 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
131 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
16432486 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
1 AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
16432551 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
66 GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
16432616 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
131 TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
16432647 AAGGTGTTTT
1 AAGGTGTTTT
16432657 TTTTTTTTTT
Statistics
Matches: 812, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
160 57 0.07
161 755 0.93
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.40
Consensus pattern (161 bp):
AAGGTGTTTTGTTATTTTGAGAGATTTTGAGGAAAATTAAACGTTTTTGAGTTGGTGCTTGTATT
GGATTGGTAGAATCGCTATTTAGGAAATTTGAGGAAAATGAAGCGTTTTTTTATTTTCGGGTTAG
TCTCAAAACTTTTGAGAGATTAGAGGAAGTG
Found at i:16433080 original size:19 final size:19
Alignment explanation
Indices: 16433056--16433114 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
16433046 GTAAAGTAAA
16433056 CCTACTTTTTCTTAAAACT
1 CCTACTTTTTCTTAAAACT
***
16433075 CCTAC--TTGAAT-AAA--
1 CCTACTTTTTCTTAAAACT
16433089 CCTACTTTTTCTTAAAACT
1 CCTACTTTTTCTTAAAACT
16433108 CCTACTT
1 CCTACTT
16433115 GAATCATCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
14 5 0.17
16 6 0.21
17 6 0.21
19 12 0.41
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (19 bp):
CCTACTTTTTCTTAAAACT
Found at i:16433094 original size:33 final size:33
Alignment explanation
Indices: 16433052--16433118 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
16433042 AAAGGTAAAG
16433052 TAAACCTACTTTTTCTTAAAACTCCTACTTGAA
1 TAAACCTACTTTTTCTTAAAACTCCTACTTGAA
16433085 TAAACCTACTTTTTCTTAAAACTCCTACTTGAA
1 TAAACCTACTTTTTCTTAAAACTCCTACTTGAA
16433118 T
1 T
16433119 CATCAAGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (33 bp):
TAAACCTACTTTTTCTTAAAACTCCTACTTGAA
Found at i:16438300 original size:3 final size:3
Alignment explanation
Indices: 16438292--16438411 Score: 240
Period size: 3 Copynumber: 40.0 Consensus size: 3
16438282 ATCTCTCCCT
16438292 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16438340 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16438388 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
16438412 CAATGCCATG
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16451316 original size:31 final size:32
Alignment explanation
Indices: 16451259--16451341 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
16451249 CTTTATATAC
*
16451259 TAATAAAATAATAAAATATCTTATTAAAGT-AT
1 TAATAAAATAATAAAATATCTAATTAAA-TAAT
**
16451291 TAATAAAATAAT-ATTTATCTAATTAAATAAT
1 TAATAAAATAATAAAATATCTAATTAAATAAT
16451322 T-ATAAAAT-ATCAAAATATCT
1 TAATAAAATAAT-AAAATATCT
16451342 CTAGCATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 2 0.05
30 8 0.19
31 21 0.49
32 12 0.28
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (32 bp):
TAATAAAATAATAAAATATCTAATTAAATAAT
Found at i:16456420 original size:36 final size:36
Alignment explanation
Indices: 16456321--16456448 Score: 152
Period size: 36 Copynumber: 3.5 Consensus size: 36
16456311 CTCCCTATTT
16456321 TGGTGTGATTTCGGTTGGACTAGCTCTT-TAGAGCCAT-
1 TGGTGTG-TTTCGGTTGGACTAGCTCTTAT-GAG-CATC
* * *
16456358 TGGTGTGTTATTGGGTGGACTGGCTCTTATGAGCATC
1 TGGTGTGTT-TCGGTTGGACTAGCTCTTATGAGCATC
* *
16456395 TGTTGTGTTTCAGTTGGACTAGCTCTTATGAGCATC
1 TGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCATC
*
16456431 TGGTGTGTTTCGATTGGA
1 TGGTGTGTTTCGGTTGGA
16456449 ATATCGATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
36 43 0.56
37 33 0.43
38 1 0.01
ACGTcount: A:0.15, C:0.14, G:0.31, T:0.40
Consensus pattern (36 bp):
TGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCATC
Found at i:16458894 original size:35 final size:37
Alignment explanation
Indices: 16458818--16458942 Score: 123
Period size: 35 Copynumber: 3.5 Consensus size: 37
16458808 ATGTTCTGGT
* * * * *
16458818 TCGCATGTTAAACATGTTAATATTCTGATATTTTGAT
1 TCGCATGTTAAGCATGCTATTAATCTGATATTTTGAC
16458855 TCGCATGTTAAGCATGCTATTAATCT-A-ATTTTGAC
1 TCGCATGTTAAGCATGCTATTAATCTGATATTTTGAC
* * * * *
16458890 TCGCATGTTAAGCATGCCATT-ATTTG-TGATTCTAAT
1 TCGCATGTTAAGCATGCTATTAATCTGAT-ATTTTGAC
16458926 TCGCATGTTAAGCATGC
1 TCGCATGTTAAGCATGC
16458943 CACTGTGTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
34 3 0.04
35 27 0.36
36 23 0.31
37 22 0.29
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (37 bp):
TCGCATGTTAAGCATGCTATTAATCTGATATTTTGAC
Found at i:16458937 original size:36 final size:35
Alignment explanation
Indices: 16458853--16458944 Score: 112
Period size: 36 Copynumber: 2.6 Consensus size: 35
16458843 TGATATTTTG
* * *
16458853 ATTCGCATGTTAAGCATGCTATTAATCTAATTTTG
1 ATTCGCATGTTAAGCATGCCATTAATCTAATTCTA
* * * *
16458888 ACTCGCATGTTAAGCATGCCATTATTTGTGATTCTA
1 ATTCGCATGTTAAGCATGCCATTA-ATCTAATTCTA
16458924 ATTCGCATGTTAAGCATGCCA
1 ATTCGCATGTTAAGCATGCCA
16458945 CTGTGTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 22 0.46
36 26 0.54
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (35 bp):
ATTCGCATGTTAAGCATGCCATTAATCTAATTCTA
Found at i:16461165 original size:36 final size:36
Alignment explanation
Indices: 16461124--16461196 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
16461114 CTCGCTCGGC
16461124 TAGCTTTCCTTACAGTCCCATGGGTCTCCATCTACT
1 TAGCTTTCCTTACAGTCCCATGGGTCTCCATCTACT
*
16461160 TAGCTTTCCTTGCAGTCCCATGGGTCTCCATCTACT
1 TAGCTTTCCTTACAGTCCCATGGGTCTCCATCTACT
16461196 T
1 T
16461197 CTTTTAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (36 bp):
TAGCTTTCCTTACAGTCCCATGGGTCTCCATCTACT
Found at i:16465960 original size:17 final size:16
Alignment explanation
Indices: 16465910--16465965 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
16465900 ACAGGCATAA
16465910 ATAAAAACATCCAATC
1 ATAAAAACATCCAATC
* * *
16465926 ATAAATAAAAACCCATC
1 ATAAA-AACATCCAATC
16465943 ATCAAAAACATCCAATC
1 AT-AAAAACATCCAATC
16465960 A-AAAAA
1 ATAAAAA
16465966 ATGACCCATG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 5 0.16
16 5 0.16
17 19 0.59
18 3 0.09
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAAAACATCCAATC
Found at i:16467688 original size:47 final size:47
Alignment explanation
Indices: 16467629--16467721 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 47
16467619 TGCTTCGATC
* *
16467629 CCCCTTCCAAAAGATAGTTTAGGGCTTGATTAATGCATATGGAGGTA
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTA
* * *
16467676 CCCCTTCTAAAAGATAATTTAGGATTTGATTAATGCGTATGGAGGT
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGT
16467722 GGTCTAGCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (47 bp):
CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTA
Found at i:16470517 original size:17 final size:17
Alignment explanation
Indices: 16470497--16470537 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
16470487 ATTTTAATAG
16470497 ATTTAATA-TTAAATTTA
1 ATTTAATACTT-AATTTA
16470514 ATTTAATACTTAATTTA
1 ATTTAATACTTAATTTA
16470531 ATATTAA
1 AT-TTAA
16470538 AATGATTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATACTTAATTTA
Found at i:16471234 original size:9 final size:9
Alignment explanation
Indices: 16471220--16471269 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
16471210 ATAAGTATAA
*
16471220 AATTAACTG
1 AATTAACCG
16471229 AATTAACCG
1 AATTAACCG
*
16471238 ACTTAACCG
1 AATTAACCG
* *
16471247 AATTACCCA
1 AATTAACCG
16471256 AATTAACCG
1 AATTAACCG
16471265 AATTA
1 AATTA
16471270 TTTGTATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:16472790 original size:28 final size:25
Alignment explanation
Indices: 16472725--16472781 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
16472715 CTCCTTGAAT
*
16472725 AAAATCAAGAAGAAAATTACTTCTA
1 AAAATCAAGAAGAAAACTACTTCTA
*
16472750 AAAATCAAGAAGAAAACTATTTCTA
1 AAAATCAAGAAGAAAACTACTTCTA
16472775 AAAATCA
1 AAAATCA
16472782 CAAGAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.58, C:0.12, G:0.07, T:0.23
Consensus pattern (25 bp):
AAAATCAAGAAGAAAACTACTTCTA
Found at i:16474265 original size:71 final size:71
Alignment explanation
Indices: 16474149--16474316 Score: 205
Period size: 71 Copynumber: 2.4 Consensus size: 71
16474139 TTGAGTAATC
* * * ** *
16474149 TTGCAGATTCTTGACAGCTTGAGTGAACAATATCGAATCATTATTTAATCG-TGGTTGAGATCCA
1 TTGCAGATTCTCGACAGCTTGAGTGAACAACATCGAATCATTATTT-AGCGATGACTAAGATCCA
16474213 ACATAAG
65 ACATAAG
*
16474220 TTGCAGATTCTCGACAGCTTGAGTGAA-AAGCATTGAATCATTATTTAGCGATGACTAAGATCCA
1 TTGCAGATTCTCGACAGCTTGAGTGAACAA-CATCGAATCATTATTTAGCGATGACTAAGATCCA
16474284 ACATAAG
65 ACATAAG
** * *
16474291 TTATAGATTTTCGACAACTTGAGTGA
1 TTGCAGATTCTCGACAGCTTGAGTGA
16474317 GTAGCATCAA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
70 5 0.06
71 79 0.94
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (71 bp):
TTGCAGATTCTCGACAGCTTGAGTGAACAACATCGAATCATTATTTAGCGATGACTAAGATCCAA
CATAAG
Found at i:16476430 original size:26 final size:22
Alignment explanation
Indices: 16476380--16476448 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 22
16476370 TTAAGTGTTG
*
16476380 TTTGTTTGATATATATGTTATCA
1 TTTGTTTTATATATAT-TTATCA
*
16476403 TTATTTTTTATATATATATTATCACA
1 TT-TGTTTTATATATAT-TTAT--CA
*
16476429 TTTGTTTTGTATATATTTAT
1 TTTGTTTTATATATATTTAT
16476449 ATGTCTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 2 0.05
24 20 0.53
25 12 0.32
26 4 0.11
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTGTTTTATATATATTTATCA
Found at i:16484345 original size:59 final size:62
Alignment explanation
Indices: 16484280--16484397 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 62
16484270 ATCACTATAA
* * *
16484280 TATTAAATTAATATAATA-TT-TAT-CAATATAAAAATTAGATTAAATTTAATATTAAATAT
1 TATTAAATTAATAGAATATTTGTATACAAGATAAAAATTAAATTAAATTTAATATTAAATAT
* * * *
16484339 TATTAAATTAATGGAATATTTGTCTACAAGATAAACATTAAATTTAATTTAATATTAAA
1 TATTAAATTAATAGAATATTTGTATACAAGATAAAAATTAAATTAAATTTAATATTAAA
16484398 ATAATCACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 16 0.33
60 2 0.04
61 2 0.04
62 29 0.59
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (62 bp):
TATTAAATTAATAGAATATTTGTATACAAGATAAAAATTAAATTAAATTTAATATTAAATAT
Found at i:16484458 original size:18 final size:17
Alignment explanation
Indices: 16484432--16484466 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16484422 TAAAATACTA
16484432 TTAAGTTAAGTATTAAAT
1 TTAAGTTAA-TATTAAAT
*
16484450 TTAATTTAATATTAAAT
1 TTAAGTTAATATTAAAT
16484467 CTATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTAAGTTAATATTAAAT
Found at i:16488475 original size:20 final size:21
Alignment explanation
Indices: 16488445--16488495 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
16488435 GGGAATAAAC
16488445 GGAATTGAGCTCAAACGAGCT
1 GGAATTGAGCTCAAACGAGCT
*
16488466 GGAA-TGAGCTCAAATGAGCT
1 GGAATTGAGCTCAAACGAGCT
*
16488486 GG-TTTGAGCT
1 GGAATTGAGCT
16488496 GAACGGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (21 bp):
GGAATTGAGCTCAAACGAGCT
Found at i:16495063 original size:26 final size:27
Alignment explanation
Indices: 16495014--16495079 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
16495004 CAATGAGTCC
*
16495014 TTTTTTTTCGTTTTGAGCAATTTAA-T
1 TTTTTTTTCTTTTTGAGCAATTTAACT
*
16495040 TTTTTTTTCTTTTATGAGC-TTTTAACT
1 TTTTTTTTCTTTT-TGAGCAATTTAACT
16495067 TTTCATTTTTCTT
1 TTT--TTTTTCTT
16495080 CTTTATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 17 0.50
27 9 0.26
29 8 0.24
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.67
Consensus pattern (27 bp):
TTTTTTTTCTTTTTGAGCAATTTAACT
Found at i:16496665 original size:44 final size:44
Alignment explanation
Indices: 16496617--16496717 Score: 175
Period size: 44 Copynumber: 2.2 Consensus size: 44
16496607 GTGTGCAAAC
16496617 ATGTTCATGGTAGCTTCAGCTATTTGAATTCACCAGCGAGGTCT
1 ATGTTCATGGTAGCTTCAGCTATTTGAATTCACCAGCGAGGTCT
*
16496661 ATGTTCATGGTAGCTTTAGCTATTTGAATTCACCAGCGAGGTCT
1 ATGTTCATGGTAGCTTCAGCTATTTGAATTCACCAGCGAGGTCT
16496705 ATTGTTCGATGGT
1 A-TGTTC-ATGGT
16496718 TGAAAATTGA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
44 44 0.81
45 5 0.09
46 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (44 bp):
ATGTTCATGGTAGCTTCAGCTATTTGAATTCACCAGCGAGGTCT
Found at i:16498278 original size:9 final size:9
Alignment explanation
Indices: 16498259--16498332 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
16498249 AGTTCATTTA
16498259 TTTAA-GTG
1 TTTAATGTG
16498267 TTTAATGTG
1 TTTAATGTG
16498276 TTT--TGTG
1 TTTAATGTG
16498283 TTTAATAAGTG
1 TTTAAT--GTG
16498294 TTTAAATGTG
1 TTT-AATGTG
*
16498304 TTTAATATG
1 TTTAATGTG
16498313 -TT--TGT-
1 TTTAATGTG
16498318 TTTAATGTG
1 TTTAATGTG
16498327 TTTAAT
1 TTTAAT
16498333 TGCAGGTGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
6 4 0.07
7 7 0.13
8 10 0.19
9 18 0.33
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (9 bp):
TTTAATGTG
Found at i:16498305 original size:21 final size:22
Alignment explanation
Indices: 16498279--16498332 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
16498269 TAATGTGTTT
16498279 TGTGTTTAATAAG-TGTTTAAA
1 TGTGTTTAATAAGTTGTTTAAA
* *
16498300 TGTGTTTAATATGTTTGTTTTAA
1 TGTGTTTAATAAG-TTGTTTAAA
16498323 TGTGTTTAAT
1 TGTGTTTAAT
16498333 TGCAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TGTGTTTAATAAGTTGTTTAAA
Found at i:16502888 original size:18 final size:18
Alignment explanation
Indices: 16502849--16502911 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
16502839 TTTAATATAT
16502849 TTAATATTTAATATTAAA
1 TTAATATTTAATATTAAA
**
16502867 TTAA-ATTTAATACTTATC
1 TTAATATTTAATA-TTAAA
** *
16502885 TTAATAATTTTTTATTAAT
1 TTAAT-ATTTAATATTAAA
16502904 TTAATATT
1 TTAATATT
16502912 AAAGTGATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 8 0.22
18 14 0.39
19 8 0.22
20 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATATTTAATATTAAA
Found at i:16503012 original size:26 final size:25
Alignment explanation
Indices: 16502964--16503053 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 25
16502954 ATAAATATTC
16502964 TATTAA-TTTAA-TAATATT-T-AA
1 TATTAAGTTTAATTAATATTATAAA
16502985 TATTAAGTTTAATGTAATATTATAAA
1 TATTAAGTTTAAT-TAATATTATAAA
* *
16503011 TATT-AGATTAAATTTAATATTA-AAG
1 TATTAAG-TTTAA-TTAATATTATAAA
16503036 TGATTAAGTTTAA-TAATA
1 T-ATTAAGTTTAATTAATA
16503054 GTTGAACTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
21 6 0.11
22 5 0.09
24 12 0.21
25 6 0.11
26 25 0.44
27 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
TATTAAGTTTAATTAATATTATAAA
Found at i:16506300 original size:16 final size:16
Alignment explanation
Indices: 16506264--16506316 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
16506254 GTTATATACT
* *
16506264 CATGAATTGAGTATGG
1 CATGAAATGAGTATTG
*
16506280 TATGAAATGATGTATT-
1 CATGAAATGA-GTATTG
*
16506296 CATGAATTGAGTATTG
1 CATGAAATGAGTATTG
16506312 CATGA
1 CATGA
16506317 CTAATGCCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (16 bp):
CATGAAATGAGTATTG
Found at i:16506853 original size:16 final size:16
Alignment explanation
Indices: 16506828--16506858 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16506818 TTGTACCCCC
16506828 TATTTAAATAATATAT
1 TATTTAAATAATATAT
*
16506844 TATTTTAATAATATA
1 TATTTAAATAATATA
16506859 ATAATGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTTAAATAATATAT
Found at i:16508381 original size:26 final size:25
Alignment explanation
Indices: 16508349--16508418 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
16508339 CTCGATATAT
16508349 GGCTCTTCATGAGCTTCCCAATTAAA
1 GGCTCTTC-TGAGCTTCCCAATTAAA
* * ** *
16508375 GGTTCTTTGTGAGCTTCCTGATTAAT
1 GGCTC-TTCTGAGCTTCCCAATTAAA
*
16508401 GGCTCTTCGGAGCTTCCC
1 GGCTCTTCTGAGCTTCCC
16508419 GATATGGCTC
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
25 10 0.29
26 22 0.65
27 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (25 bp):
GGCTCTTCTGAGCTTCCCAATTAAA
Found at i:16508464 original size:25 final size:25
Alignment explanation
Indices: 16508385--16508464 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
16508375 GGTTCTTTGT
* *
16508385 GAGCTTCCTGAT-TAATGGCTCTTCG
1 GAGCTTCCCGATAT-ATGGCTCTCCG
* **
16508410 GAGCTTCCCG--ATATGGCTCGCTT
1 GAGCTTCCCGATATATGGCTCTCCG
* *
16508433 GAACTTCCCGATATATGGCTATCCG
1 GAGCTTCCCGATATATGGCTCTCCG
16508458 GAGCTTC
1 GAGCTTC
16508465 TTGATTAATG
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
23 16 0.39
24 1 0.02
25 24 0.59
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTCTCCG
Found at i:16508522 original size:73 final size:73
Alignment explanation
Indices: 16508385--16508525 Score: 178
Period size: 73 Copynumber: 1.9 Consensus size: 73
16508375 GGTTCTTTGT
* * *
16508385 GAGCTTCCTGATTAATGGCTCTTCGGAGCTTCCCGATATGGCTCGCTTGAACTTCCCGATATATG
1 GAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGATATGGCTCGCATGAACTTCCCGAAATATG
16508450 GCTATCCG
66 GCTATCCG
* * * * *
16508458 GAGCTTCTTGATTAATGGTTCTTCGGAGCTACCC-ATTATTGGCTTGCATGAGCTT-CCTAAATA
1 GAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGA-TA-TGGCTCGCATGAACTTCCCGAAATA
16508521 TGGCT
64 TGGCT
16508526 CTTATGAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
72 1 0.02
73 44 0.76
74 13 0.22
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (73 bp):
GAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGATATGGCTCGCATGAACTTCCCGAAATATG
GCTATCCG
Found at i:16511709 original size:31 final size:31
Alignment explanation
Indices: 16511648--16511709 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
16511638 GATTATACCT
*
16511648 ATGAAACTTGAATTGTGATTCATATGTATAA
1 ATGAAACTTGAATTGTGATTCATATATATAA
* * *
16511679 ATGAAGCTTTAATTTTGATTCA-ATTATATAA
1 ATGAAACTTGAATTGTGATTCATA-TATATAA
16511710 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (31 bp):
ATGAAACTTGAATTGTGATTCATATATATAA
Found at i:16512919 original size:29 final size:31
Alignment explanation
Indices: 16512870--16512948 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
16512860 TTTGAACCAT
16512870 AATCAAA-TTTACATGTA-TAAAATT-CAC-TA
1 AATCAAAGTTTA-A-GTATTAAAATTACACATA
16512899 AATCAAAGTTTAAGTATT-AAATTACACATTA
1 AATCAAAGTTTAAGTATTAAAATTACACA-TA
* *
16512930 AATCAAAGTTCATGTATTA
1 AATCAAAGTTTAAGTATTA
16512949 TTTTGAGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 8 0.19
29 12 0.29
30 4 0.10
31 18 0.43
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.35
Consensus pattern (31 bp):
AATCAAAGTTTAAGTATTAAAATTACACATA
Done.