Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 75 of 189
Found at i:20883872 original size:10 final size:10
Alignment explanation
Indices: 20883857--20883897 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
20883847 ATGAAATTTT
20883857 TAAATAATAA
1 TAAATAATAA
20883867 TAAATAATAA
1 TAAATAATAA
20883877 -ATAATAAATAA
1 TA-AAT-AATAA
20883888 TAAATAATAA
1 TAAATAATAA
20883898 ATAATTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 18 0.64
11 8 0.29
12 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAATAATAA
Found at i:20883920 original size:7 final size:7
Alignment explanation
Indices: 20883862--20883902 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
20883852 ATTTTTAAAT
20883862 AATAATA
1 AATAATA
20883869 AATAATA
1 AATAATA
20883876 AATAATA
1 AATAATA
20883883 AATAATA
1 AATAATA
20883890 AATAATA
1 AATAATA
20883897 AATAAT
1 AATAAT
20883903 TATCATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:20885310 original size:9 final size:9
Alignment explanation
Indices: 20885298--20885419 Score: 67
Period size: 9 Copynumber: 13.6 Consensus size: 9
20885288 CAAAAAAGGT
20885298 TAAAAATTA
1 TAAAAATTA
20885307 T-AAAATTGA
1 TAAAAATT-A
*
20885316 TAGAAAATCA
1 TA-AAAATTA
20885326 TAAAAATTA
1 TAAAAATTA
* *
20885335 CAAATA-TA
1 TAAAAATTA
* *
20885343 TATAATTTA
1 TAAAAATTA
20885352 TTAAAAA-T-
1 -TAAAAATTA
20885360 TAAAAA-TA
1 TAAAAATTA
** *
20885368 TAGAAACGTG
1 TA-AAAATTA
20885378 TAAAAATTA
1 TAAAAATTA
*
20885387 TAAAAAGTA
1 TAAAAATTA
20885396 TAGAAAATTA
1 TA-AAAATTA
20885406 T-AAAATATA
1 TAAAAAT-TA
20885415 TAAAA
1 TAAAA
20885420 GTTTAAATTC
Statistics
Matches: 85, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
7 7 0.08
8 17 0.20
9 36 0.42
10 20 0.24
11 5 0.06
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:20885410 original size:27 final size:26
Alignment explanation
Indices: 20885300--20885419 Score: 84
Period size: 28 Copynumber: 4.5 Consensus size: 26
20885290 AAAAAGGTTA
* *
20885300 AAAATTATAAAATTGATAGAAAATCAT
1 AAAATTATAAAAAT-ATAGAAAATTAT
* * * *
20885327 AAAAATTACAAATATATA-TAATTTATT
1 -AAAATTATAAAAATATAGAAAATTA-T
* *
20885354 AAAAAT-TAAAAATATAGAAACGTGTA-
1 AAAATTATAAAAATATAGAAA-AT-TAT
20885380 AAAATTATAAAAAGTATAGAAAATTAT
1 AAAATTATAAAAA-TATAGAAAATTAT
20885407 AAAATATATAAAA
1 AAAAT-TATAAAA
20885420 GTTTAAATTC
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
25 8 0.11
26 18 0.25
27 17 0.24
28 28 0.39
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (26 bp):
AAAATTATAAAAATATAGAAAATTAT
Found at i:20885458 original size:22 final size:23
Alignment explanation
Indices: 20885421--20885466 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
20885411 TATATAAAAG
20885421 TTTAAATTCTTTTTAATTTTATA
1 TTTAAATTCTTTTTAATTTTATA
20885444 TTTAAATT-TTTTTAATTTTATA
1 TTTAAATTCTTTTTAATTTTATA
20885466 T
1 T
20885467 AACCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAAATTCTTTTTAATTTTATA
Found at i:20886183 original size:22 final size:22
Alignment explanation
Indices: 20886154--20886205 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
20886144 ATTGTTTAAT
*
20886154 TAGGGTTTAAGGTTTATTAAAG
1 TAGGGTTTAAGGTTAATTAAAG
* * *
20886176 TATGGTTTAGGGTTAATTAAAT
1 TAGGGTTTAAGGTTAATTAAAG
20886198 TAGGGTTT
1 TAGGGTTT
20886206 TAGCATTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (22 bp):
TAGGGTTTAAGGTTAATTAAAG
Found at i:20886385 original size:29 final size:29
Alignment explanation
Indices: 20886352--20886419 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
20886342 TTAAGTGTTC
* *
20886352 TGAAAAAATAATTTTGACGAGATGGGTTT
1 TGAAAAAATAATTTTGACAAGATGAGTTT
20886381 TGAAAAAATAATTTTGACAAGATGAGTTT
1 TGAAAAAATAATTTTGACAAGATGAGTTT
20886410 TGAAAAAATA
1 TGAAAAAATA
20886420 TCCCAGGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.32
Consensus pattern (29 bp):
TGAAAAAATAATTTTGACAAGATGAGTTT
Found at i:20889749 original size:20 final size:19
Alignment explanation
Indices: 20889706--20889747 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
20889696 ATACTAAGTT
20889706 AAAATATAACAGTAAAATA
1 AAAATATAACAGTAAAATA
*
20889725 AAAATATAACAGTGAAATA
1 AAAATATAACAGTAAAATA
20889744 AAAA
1 AAAA
20889748 ATTTAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAATATAACAGTAAAATA
Found at i:20889945 original size:18 final size:17
Alignment explanation
Indices: 20889907--20889947 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20889897 ATAAAAAAAT
*
20889907 AAAAATAGAATGTAGAT
1 AAAAATAGAATGTAGAA
*
20889924 AAAAATAGAATTTAGGAA
1 AAAAATAGAATGTA-GAA
20889942 AAAAAT
1 AAAAAT
20889948 TATTAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (17 bp):
AAAAATAGAATGTAGAA
Found at i:20889972 original size:11 final size:11
Alignment explanation
Indices: 20889958--20889999 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
20889948 TATTAGAGAA
20889958 TTTGAGAGATT
1 TTTGAGAGATT
20889969 TTTGAGAG-TT
1 TTTGAGAGATT
* *
20889979 GATTGAGAAATT
1 -TTTGAGAGATT
20889991 TTTGAGAGA
1 TTTGAGAGA
20890000 ATTGTGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (11 bp):
TTTGAGAGATT
Found at i:20890007 original size:22 final size:22
Alignment explanation
Indices: 20889944--20890011 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
20889934 TTTAGGAAAA
*
20889944 AAATTATT-AGAGAATT-TGAG
1 AAATTTTTGAGAGAATTGTGAG
*
20889964 AGATTTTTGAGAG--TTGATTGAG
1 AAATTTTTGAGAGAATTG--TGAG
20889986 AAATTTTTGAGAGAATTGTGAG
1 AAATTTTTGAGAGAATTGTGAG
20890008 AAAT
1 AAAT
20890012 GTGAGTGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 4 0.10
22 24 0.62
24 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (22 bp):
AAATTTTTGAGAGAATTGTGAG
Found at i:20890526 original size:27 final size:28
Alignment explanation
Indices: 20890485--20890537 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
20890475 AGTATAATGA
20890485 TAAAATTATACTTT-ACCCCTTAAAGTT
1 TAAAATTATACTTTAACCCCTTAAAGTT
*
20890512 TAAAATT-TACTTTTAACCCTTTAAAG
1 TAAAATTATAC-TTTAACCCCTTAAAG
20890538 CAGTTTTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 10 0.43
28 10 0.43
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (28 bp):
TAAAATTATACTTTAACCCCTTAAAGTT
Found at i:20891007 original size:24 final size:23
Alignment explanation
Indices: 20890980--20891034 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
20890970 ACCCTTAAAA
20890980 ATAAACATATATATAA-TTAATTTT
1 ATAAACAT-TAT-TAACTTAATTTT
* *
20891004 ATAATAAATTATTAACTTATTTTT
1 ATAA-ACATTATTAACTTAATTTT
20891028 ATAAACA
1 ATAAACA
20891035 AATTCATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 5 0.19
24 18 0.69
25 3 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAACATTATTAACTTAATTTT
Found at i:20898795 original size:20 final size:18
Alignment explanation
Indices: 20898770--20898812 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
20898760 TAATACATCA
20898770 AATAATTAATACATATTACC
1 AATAATTAATACA-ATT-CC
*
20898790 AATAA-TAATTCAATTCC
1 AATAATTAATACAATTCC
20898807 AATAAT
1 AATAAT
20898813 AAAACACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 6 0.29
20 5 0.24
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAATTAATACAATTCC
Found at i:20905519 original size:3 final size:3
Alignment explanation
Indices: 20905511--20905556 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
20905501 CCTCTGAAAT
20905511 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
20905557 CTTTCCGTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:20909010 original size:25 final size:25
Alignment explanation
Indices: 20908964--20909011 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
20908954 AATTTAGCCA
* * * *
20908964 TTTTTATTTTATTTTTATATTTTTC
1 TTTTAATTTAATTTTCACATTTTTC
20908989 TTTTAATTTAATTTTCACATTTT
1 TTTTAATTTAATTTTCACATTTT
20909012 AATTTTTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTAATTTAATTTTCACATTTTTC
Found at i:20918361 original size:25 final size:27
Alignment explanation
Indices: 20918332--20918395 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
20918322 TATATTTGTT
20918332 TTTTTATACATATAA-TTAATTT-TATA
1 TTTTTATA-ATATAAGTTAATTTATATA
20918358 TTTTTATAA-A-AAGTTAATTTATATA
1 TTTTTATAATATAAGTTAATTTATATA
20918383 TTTTTATATATAT
1 TTTTTATA-ATAT
20918396 GTATGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 13 0.39
26 9 0.27
27 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTATAATATAAGTTAATTTATATA
Found at i:20930977 original size:44 final size:44
Alignment explanation
Indices: 20930864--20931105 Score: 199
Period size: 44 Copynumber: 5.5 Consensus size: 44
20930854 AGTAAATAGG
* * * **
20930864 TCTTATCCCCCTGAAGTTGTAGTGG-GACAGATTGAAGATGGCA-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-TAGATTGAA-ACCG-ATAA
*
20930909 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAACCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAACCGATAA
* * * * ***
20930953 TCTGATCTCCTTGAAGTTGTAGTGGAGCAGATT-AAATTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAACCGATA-A
* * * * * *
20930997 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAA-C-A-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAACCGATAA
* *
20931038 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAACCGATAA
* *
20931082 TCCTATCTCCCTGAAGTTGTAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
20931106 AAGCGGATTA
Statistics
Matches: 154, Mismatches: 36, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
41 30 0.19
42 2 0.01
43 9 0.06
44 80 0.52
45 32 0.21
46 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAACCGATAA
Found at i:20931057 original size:41 final size:41
Alignment explanation
Indices: 20930997--20931233 Score: 136
Period size: 44 Copynumber: 5.6 Consensus size: 41
20930987 AATTAATAGA
*
20930997 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAA-CAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCG-AAGCAAG
* * * * *
20931038 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCGAAG-C-A-AG
* * * ** *
20931082 TCCTATCTCCCTGAAGTTGTAGT-GAAGCGGATTAAAGTAATGG
1 TCTTATCTCCCTGAAGTTGCAGTAG-AGTGGATCGAAGCAA--G
* * * * *
20931125 ATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGTATCAGG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCGAAGCAAG
* ** ** * *
20931167 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGTGGA-T-CG-AAGCAAG
*
20931211 TCTTATCCCCCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGT
20931234 GAGACAGATC
Statistics
Matches: 146, Mismatches: 38, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
40 2 0.01
41 54 0.37
42 4 0.03
43 3 0.02
44 82 0.56
45 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGTGGATCGAAGCAAG
Found at i:20931090 original size:129 final size:129
Alignment explanation
Indices: 20930909--20931193 Score: 455
Period size: 129 Copynumber: 2.2 Consensus size: 129
20930899 AGATGGCAAA
*
20930909 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAACCGATAATCTGATCTCCTTGAAGTTGTA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAACCGATAATCTGATCTCCCTGAAGTTGTA
* * *
20930974 GTGGAGCAGATTAAATTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAACAAG
66 GTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
*
20931038 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATAATCCT-ATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAACCGATAAT-CTGATCTCCCTGAAGTTGT
* * * * *
20931102 AGTGAAGCGGATTAAAGTAATGGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGTATCAGG
65 AGTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
*
20931167 TCTTATCTCCCTGAGGTTGCAGCGGAG
1 TCTTATCTCCCTGAGGTTGCAGTGGAG
20931194 CAGACTGAGT
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
129 142 0.99
130 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (129 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAACCGATAATCTGATCTCCCTGAAGTTGTA
GTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
Found at i:20931452 original size:45 final size:44
Alignment explanation
Indices: 20931384--20931535 Score: 121
Period size: 44 Copynumber: 3.4 Consensus size: 44
20931374 GCTACAATCC
* * *
20931384 CCCTGAAGTTACAGTGG-GACAGATCGAAGATGGCAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAG-CAGATCGAAGACGACAAATC-TATCT
* * * * * *
20931429 CCCTGAGGTTGTAGTGGAGCAGATTGAAGCCGATAATTCTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAAATCTATCT
* *
20931473 CCCTGAAGTTGCAGTGGAGCAGA-CAGAAGA-AACCAATCCTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATC-GAAGACGACAAAT-CTATCT
* * *
20931517 CCCTAAAGTTACAATGGAG
1 CCCTGAAGTTGCAGTGGAG
20931536 TGGATTAAAA
Statistics
Matches: 84, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
43 3 0.04
44 52 0.62
45 28 0.33
46 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGATCGAAGACGACAAATCTATCT
Found at i:20933125 original size:25 final size:27
Alignment explanation
Indices: 20933096--20933159 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
20933086 TATATTTGTT
20933096 TTTTTATACATATAA-TTAATTT-TATA
1 TTTTTATA-ATATAAGTTAATTTATATA
20933122 TTTTTATAA-A-AAGTTAATTTATATA
1 TTTTTATAATATAAGTTAATTTATATA
20933147 TTTTTATATATAT
1 TTTTTATA-ATAT
20933160 GTATGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 13 0.39
26 9 0.27
27 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTATAATATAAGTTAATTTATATA
Found at i:20933193 original size:30 final size:27
Alignment explanation
Indices: 20933142--20933201 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 27
20933132 AAGTTAATTT
20933142 ATATATTTTTATATATATGTATGA-ATA
1 ATATATTTTTATATATATGTAT-ATATA
*
20933169 ATATTTTTTTACTATACGTATGTATATATA
1 ATATATTTTTA-TATA--TATGTATATATA
20933199 ATA
1 ATA
20933202 ATACATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.36
28 4 0.14
29 1 0.04
30 13 0.46
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
ATATATTTTTATATATATGTATATATA
Found at i:20934707 original size:29 final size:29
Alignment explanation
Indices: 20934663--20934841 Score: 211
Period size: 29 Copynumber: 6.2 Consensus size: 29
20934653 GAGGTCTCGA
20934663 GCCACTGGTTTTCCAAATTTTACAATTTT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
* * * *
20934692 GTCACTGATTTTCCAAATTTTATAGTTTT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
* * *
20934721 GCCACT-GTTATTCCAGATTTT-CAGTTCT
1 GCCACTGGTT-TTCCAAATTTTACAATTTT
*
20934749 GCCACTGGTTTTCCAAATTTTACAATTCT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
* *
20934778 ACCACT-GTTATTCCAGATTTTACAATTTT
1 GCCACTGGTT-TTCCAAATTTTACAATTTT
* *
20934807 GCCACTGGTTTTCCAGATTTTACAGTTTT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
20934836 GCCACT
1 GCCACT
20934842 CTTCTTCAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
28 26 0.20
29 100 0.78
30 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (29 bp):
GCCACTGGTTTTCCAAATTTTACAATTTT
Found at i:20934808 original size:86 final size:87
Alignment explanation
Indices: 20934663--20934841 Score: 256
Period size: 86 Copynumber: 2.1 Consensus size: 87
20934653 GAGGTCTCGA
* ** * *
20934663 GCCACTGGTTTTCCAAATTTTACAATTTTGTCACTGATTTTCCAAATTTTATAGTTTTGCCACT-
1 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTGATTTTCCAAATTTTACAATTTTGCCACTG
20934727 GTTATTCCAGATTTT-CAGTTCT
66 GTT-TTCCAGATTTTACAGTTCT
*
20934749 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTG-TTATTCCAGATTTTACAATTTTGCCACT
1 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTGATT-TTCCAAATTTTACAATTTTGCCACT
*
20934813 GGTTTTCCAGATTTTACAGTTTT
65 GGTTTTCCAGATTTTACAGTTCT
20934836 GCCACT
1 GCCACT
20934842 CTTCTTCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
85 2 0.02
86 66 0.80
87 15 0.18
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (87 bp):
GCCACTGGTTTTCCAAATTTTACAATTCTACCACTGATTTTCCAAATTTTACAATTTTGCCACTG
GTTTTCCAGATTTTACAGTTCT
Found at i:20938134 original size:12 final size:12
Alignment explanation
Indices: 20938117--20938142 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20938107 TTCATGAATC
20938117 AAATTACATATT
1 AAATTACATATT
20938129 AAATTACATATT
1 AAATTACATATT
20938141 AA
1 AA
20938143 CTTTAAAAGG
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:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTACATATT
Found at i:20938331 original size:19 final size:19
Alignment explanation
Indices: 20938309--20938355 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
20938299 TAAAATTCAT
20938309 ATTTATTTATTGGA-TATA
1 ATTTATTTATTGGAGTATA
*
20938327 GATTTATGTA-TGGAGTATA
1 -ATTTATTTATTGGAGTATA
*
20938346 ATTTTTTTAT
1 ATTTATTTAT
20938356 AAAACATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (19 bp):
ATTTATTTATTGGAGTATA
Found at i:20938789 original size:14 final size:14
Alignment explanation
Indices: 20938751--20938779 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20938741 TAATAACATA
20938751 ATAAATTA-TTAAT
1 ATAAATTATTTAAT
20938764 ATAAATTATTTAAT
1 ATAAATTATTTAAT
20938778 AT
1 AT
20938780 TATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATTATTTAAT
Found at i:20941825 original size:77 final size:77
Alignment explanation
Indices: 20941730--20941894 Score: 323
Period size: 77 Copynumber: 2.2 Consensus size: 77
20941720 ATAAATTTTA
20941730 AAAAT-AAAAAAAGTAAAAATTCAAAATAAAAATTTAAAAATTATACAAGTTCATTTTTATAATA
1 AAAATAAAAAAAAGTAAAAATTCAAAATAAAAATTTAAAAATTATACAAGTTCATTTTTATAATA
20941794 TTTAAACTATAT
66 TTTAAACTATAT
20941806 AAAATAAAAAAAAGTAAAAATTCAAAATAAAAATTTAAAAATTATACAAGTTCATTTTTATAATA
1 AAAATAAAAAAAAGTAAAAATTCAAAATAAAAATTTAAAAATTATACAAGTTCATTTTTATAATA
20941871 TTTAAACTATAT
66 TTTAAACTATAT
20941883 AAAATAAAAAAA
1 AAAATAAAAAAA
20941895 TTATATAAAA
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 5 0.06
77 83 0.94
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (77 bp):
AAAATAAAAAAAAGTAAAAATTCAAAATAAAAATTTAAAAATTATACAAGTTCATTTTTATAATA
TTTAAACTATAT
Found at i:20942237 original size:21 final size:21
Alignment explanation
Indices: 20942213--20942254 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
20942203 ATTTTTTCTA
20942213 AAGTTAAAA-GTCAAAACTATT
1 AAGTTAAAAGGT-AAAACTATT
20942234 AAGTTAAAAGGTAAAACTATT
1 AAGTTAAAAGGTAAAACTATT
20942255 TCGTTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATT
Found at i:20974999 original size:22 final size:22
Alignment explanation
Indices: 20974954--20974999 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
20974944 ACTGATCGAC
* **
20974954 ATGTTGCAACACGGGGAGTTGA
1 ATGTTGCAACACAGGGAGCAGA
*
20974976 ATGTTGCAACATAGGGAGCAGA
1 ATGTTGCAACACAGGGAGCAGA
20974998 AT
1 AT
20975000 AGCATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.22
Consensus pattern (22 bp):
ATGTTGCAACACAGGGAGCAGA
Found at i:20977317 original size:31 final size:31
Alignment explanation
Indices: 20977282--20977343 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
20977272 TATATGGAGG
* *
20977282 AGACAAACCTCTCTTCTACTATATTAACAAT
1 AGACAAACCTCTCTTCCACTAAATTAACAAT
20977313 AGACAAACCTCTCTTCCACTAAATTAACAAT
1 AGACAAACCTCTCTTCCACTAAATTAACAAT
20977344 CCCACTGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.29
Consensus pattern (31 bp):
AGACAAACCTCTCTTCCACTAAATTAACAAT
Found at i:20981201 original size:5 final size:5
Alignment explanation
Indices: 20981185--20981231 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
20981175 AAATTTTTTG
* *
20981185 GGCCC GGGCCC GGCCC GGCCC GGCCC GGCCC GCCCC GGCCC GCCCC G
1 GGCCC -GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC GGCCC G
20981232 AATATAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
5 33 0.87
6 5 0.13
ACGTcount: A:0.00, C:0.62, G:0.38, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:20981567 original size:20 final size:20
Alignment explanation
Indices: 20981542--20981582 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20981532 AAGTTTGTTT
20981542 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
20981562 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
20981582 T
1 T
20981583 CCCAGTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTCTTTCTCTGATA
Found at i:20982693 original size:13 final size:13
Alignment explanation
Indices: 20982677--20982726 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
20982667 ATAGCCATTA
*
20982677 TTTCTTACATTTG
1 TTTCTTACATTTC
20982690 TTTCTGTA-ATTTC
1 TTTCT-TACATTTC
20982703 TTTCTTACA-TTC
1 TTTCTTACATTTC
20982715 TTTCTTACATTT
1 TTTCTTACATTT
20982727 GTATTTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 14 0.42
13 17 0.52
14 2 0.06
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (13 bp):
TTTCTTACATTTC
Found at i:20982717 original size:12 final size:12
Alignment explanation
Indices: 20982672--20982725 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
20982662 TATGCATAGC
*
20982672 CATTATTTCTTA
1 CATTCTTTCTTA
*
20982684 CATTTGTTTCTGTA
1 CA-TTCTTTCT-TA
20982698 -ATTTCTTTCTTA
1 CA-TTCTTTCTTA
20982710 CATTCTTTCTTA
1 CATTCTTTCTTA
20982722 CATT
1 CATT
20982726 TGTATTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 18 0.49
13 17 0.46
14 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.59
Consensus pattern (12 bp):
CATTCTTTCTTA
Found at i:20985713 original size:18 final size:18
Alignment explanation
Indices: 20985690--20985735 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
20985680 GGTTGCAAAA
20985690 AGGACGATGACGATGATG
1 AGGACGATGACGATGATG
*
20985708 AGGACGATGAGGATGATG
1 AGGACGATGACGATGATG
*
20985726 AGGATGATGA
1 AGGACGATGA
20985736 TGTTTCTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.41, T:0.17
Consensus pattern (18 bp):
AGGACGATGACGATGATG
Found at i:20985716 original size:9 final size:9
Alignment explanation
Indices: 20985690--20985735 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
20985680 GGTTGCAAAA
*
20985690 AGGACGATG
1 AGGATGATG
*
20985699 ACGATGATG
1 AGGATGATG
*
20985708 AGGACGATG
1 AGGATGATG
20985717 AGGATGATG
1 AGGATGATG
20985726 AGGATGATG
1 AGGATGATG
20985735 A
1 A
20985736 TGTTTCTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.41, T:0.17
Consensus pattern (9 bp):
AGGATGATG
Found at i:20985936 original size:11 final size:11
Alignment explanation
Indices: 20985910--20985944 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
20985900 TGTGTACTTG
20985910 TGGATGTGCTTA
1 TGGATGTGC-TA
20985922 TGGATGTGCTA
1 TGGATGTGCTA
*
20985933 TGGATGTACTA
1 TGGATGTGCTA
20985944 T
1 T
20985945 CTATATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.20, C:0.09, G:0.31, T:0.40
Consensus pattern (11 bp):
TGGATGTGCTA
Found at i:20994744 original size:22 final size:21
Alignment explanation
Indices: 20994719--20994762 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
20994709 TGATAAACTT
20994719 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
20994741 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
20994762 T
1 T
20994763 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:21000267 original size:18 final size:17
Alignment explanation
Indices: 21000240--21000273 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21000230 TAACAGACTT
21000240 ATTCACCAAGCATTTAG
1 ATTCACCAAGCATTTAG
*
21000257 ATTCAACCAAGCCTTTA
1 ATTC-ACCAAGCATTTA
21000274 AATTTGGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.29
Consensus pattern (17 bp):
ATTCACCAAGCATTTAG
Found at i:21005653 original size:20 final size:19
Alignment explanation
Indices: 21005625--21005664 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21005615 TTTATTTGAG
*
21005625 AGTAAAGGGTGAGAAATAAA
1 AGTAAAGGG-GAAAAATAAA
*
21005645 AGTATAGGGGAAAAATAAA
1 AGTAAAGGGGAAAAATAAA
21005664 A
1 A
21005665 AGTTTTGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (19 bp):
AGTAAAGGGGAAAAATAAA
Found at i:21005817 original size:30 final size:31
Alignment explanation
Indices: 21005778--21005837 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
21005768 GGAGGTGGAA
*
21005778 TGGGAAGGGAATAAAAGTTTT-AGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTGA-GGGAAAAG
*
21005809 TGGG-AGGGAGTAAAAATTTTGAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
21005838 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:21006149 original size:9 final size:9
Alignment explanation
Indices: 21006132--21006162 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
21006122 TCGAGTTGAT
21006132 TCGAATAAC
1 TCGAATAAC
*
21006141 TCGATTAAC
1 TCGAATAAC
21006150 TCGAATAAC
1 TCGAATAAC
21006159 TCGA
1 TCGA
21006163 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:21009875 original size:44 final size:44
Alignment explanation
Indices: 21009825--21009914 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
21009815 GTTAAAATAA
* * * * * *
21009825 AATAGAAGTTGTGATAATTATACATTTAAAAATAATTATAATTT
1 AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
21009869 AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
1 AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
21009913 AA
1 AA
21009915 ATTAAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (44 bp):
AATAGAAATAGTGAAAATTACACATTTAAAAATAAATAGAATTT
Found at i:21010179 original size:44 final size:45
Alignment explanation
Indices: 21010107--21010197 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 45
21010097 AAAGTTGGAA
* * *
21010107 AATAGAAGTTTGTCATAATTATAAATTTAAAAATAATTATAATTT
1 AATAGAAGTTTATAATAATTATAAATTTAAAAATAATTAGAATTT
21010152 AATAGAAG-TTATAATAATTA-AACATTTAAAAATAATTAGAATTT
1 AATAGAAGTTTATAATAATTATAA-ATTTAAAAATAATTAGAATTT
21010196 AA
1 AA
21010198 ATTATTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 2 0.05
44 32 0.76
45 8 0.19
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (45 bp):
AATAGAAGTTTATAATAATTATAAATTTAAAAATAATTAGAATTT
Found at i:21010197 original size:17 final size:18
Alignment explanation
Indices: 21010164--21010198 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21010154 TAGAAGTTAT
21010164 AATAATTAAACATTTAAA
1 AATAATTAAACATTTAAA
*
21010182 AATAATTAGA-ATTTAAA
1 AATAATTAAACATTTAAA
21010199 TTATTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AATAATTAAACATTTAAA
Found at i:21010285 original size:283 final size:281
Alignment explanation
Indices: 21009766--21010285 Score: 690
Period size: 283 Copynumber: 1.8 Consensus size: 281
21009756 CATATTACTG
* *
21009766 ACATTTAAAATTAATTATAATATTTAATTTAGAACTATTTATTAAAAAAGTTAAAATAAAATAGA
1 ACATTTAAAATTAATTATAATATTTAATTTAGAACTATTAATTAAAAAAGTT--AAGAAAATAGA
* * *
21009831 AGTTGTGATAATTATACATTTAAAAATAATTATAATTTAATAGAAATAGTGAAAATTACACATTT
64 AGTTGTCATAATTATAAATTTAAAAATAATTATAATTTAATAGAAATAGTGAAAATTAAACATTT
*
21009896 AAAAATAAATAGAATTTAAATTAAAATTATTAGTTTAAAAAGTTATGCTAATTTAAATAGAATTA
129 AAAAATAAATAGAATTTAAATTAAAATTATTAGTTAAAAAAGTTATGCTAATTTAAATAGAATTA
* * * *
21009961 CTATTTGATTAAAACACTAAGCATAAAATATAGGAGAAAATTTTGAAAAGATAGAATACTTTTTA
194 CTACTTAAATAAAACACTAAGAATAAAATATAGGAGAAAATTTTGAAAAGATAGAATACTTTTTA
21010026 TTTTTCATCATATTACTAAATTC
259 TTTTTCATCATATTACTAAATTC
* * * *
21010049 ACATTTAAAAATTATTTATAATATTTAATTTATAATTATTAATTAAAAAAAGTT-GGAAAATAGA
1 ACATTT-AAAATTAATTATAATATTTAATTTAGAACTATTAATT-AAAAAAGTTAAGAAAATAGA
*
21010113 AGTTTGTCATAATTATAAATTTAAAAATAATTATAATTTAATAGAAGTTA-T-AATAATTAAACA
64 AG-TTGTCATAATTATAAATTTAAAAATAATTATAATTTAATAGAA-ATAGTGAA-AATTAAACA
* ** * * *
21010176 TTTAAAAATAATTAGAATTTAAATTATTATTATTAGTTAAAAAAGTTGTGTTAATTTTAAAATAT
126 TTTAAAAATAAATAGAATTTAAATTAAAATTATTAGTTAAAAAAGTTATGCTAA-TTT-AAATAG
* * ** *
21010241 AGTTATTACTTAAATACTACTCTAAGAATAAAATAT-GG-GAAAATT
189 AATTACTACTTAAATAAAACACTAAGAATAAAATATAGGAGAAAATT
21010286 GTGATAATTA
Statistics
Matches: 204, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
282 12 0.06
283 111 0.54
284 40 0.20
285 41 0.20
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (281 bp):
ACATTTAAAATTAATTATAATATTTAATTTAGAACTATTAATTAAAAAAGTTAAGAAAATAGAAG
TTGTCATAATTATAAATTTAAAAATAATTATAATTTAATAGAAATAGTGAAAATTAAACATTTAA
AAATAAATAGAATTTAAATTAAAATTATTAGTTAAAAAAGTTATGCTAATTTAAATAGAATTACT
ACTTAAATAAAACACTAAGAATAAAATATAGGAGAAAATTTTGAAAAGATAGAATACTTTTTATT
TTTCATCATATTACTAAATTC
Found at i:21010539 original size:20 final size:21
Alignment explanation
Indices: 21010511--21010555 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
21010501 AATAAGTTAA
21010511 AAAAATTTTAATTAT-TATTT
1 AAAAATTTTAATTATATATTT
* *
21010531 AAAATTTTTTATTATAATATTT
1 AAAAATTTTAATTAT-ATATTT
21010553 AAA
1 AAA
21010556 TTTATAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAAATTTTAATTATATATTT
Found at i:21011227 original size:20 final size:20
Alignment explanation
Indices: 21011194--21011245 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
21011184 TTGCTATAAA
* * *
21011194 TATTTTAAAATTTTGAAAAT
1 TATTTTGAATTTTTGAAAAC
*
21011214 TATTTTGAATTTTTTTAAAAC
1 TATTTTGAA-TTTTTGAAAAC
21011235 TATTTTGAATT
1 TATTTTGAATT
21011246 GGTTTGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (20 bp):
TATTTTGAATTTTTGAAAAC
Found at i:21011233 original size:21 final size:21
Alignment explanation
Indices: 21011204--21011245 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21011194 TATTTTAAAA
*
21011204 TTTTGAAAATTATTTTGAATT
1 TTTTGAAAACTATTTTGAATT
*
21011225 TTTTTAAAACTATTTTGAATT
1 TTTTGAAAACTATTTTGAATT
21011246 GGTTTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTGAAAACTATTTTGAATT
Found at i:21012852 original size:17 final size:17
Alignment explanation
Indices: 21012830--21012868 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21012820 ACTTTATTGT
21012830 ATTTATTAATT-AATATA
1 ATTTATT-ATTAAATATA
*
21012847 ATTTATTATTAAATTTA
1 ATTTATTATTAAATATA
21012864 ATTTA
1 ATTTA
21012869 ATAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATTATTAAATATA
Found at i:21023182 original size:15 final size:15
Alignment explanation
Indices: 21023161--21023201 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
21023151 AACTAAACAC
21023161 AAATAAAATTAATA-
1 AAATAAAATTAATAG
*
21023175 ATAATAAAATAAATAG
1 A-AATAAAATTAATAG
21023191 AAA-AAAATTAA
1 AAATAAAATTAA
21023202 GAAGGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.35
15 14 0.61
16 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAAAATTAATAG
Found at i:21026794 original size:16 final size:15
Alignment explanation
Indices: 21026769--21026798 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21026759 ATTAAGTTAA
21026769 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
21026784 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
21026799 ATGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:21053928 original size:6 final size:6
Alignment explanation
Indices: 21053917--21053943 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21053907 TCATGTATCC
21053917 GTCCGA GTCCGA GTCCGA GTCCGA GTC
1 GTCCGA GTCCGA GTCCGA GTCCGA GTC
21053944 GTGTTAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.19
Consensus pattern (6 bp):
GTCCGA
Found at i:21062106 original size:11 final size:11
Alignment explanation
Indices: 21062090--21062132 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
21062080 GTTTTAATTA
21062090 AATAAAATATT
1 AATAAAATATT
21062101 AAT-AAATATCT
1 AATAAAATAT-T
21062112 AATTAAAATATT
1 AA-TAAAATATT
21062124 AATAAAATA
1 AATAAAATA
21062133 ATATTTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.21
11 13 0.45
12 4 0.14
13 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAAATATT
Found at i:21063558 original size:22 final size:24
Alignment explanation
Indices: 21063532--21063575 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
21063522 ATTTTGTTCA
21063532 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
21063554 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
21063576 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:21069021 original size:18 final size:17
Alignment explanation
Indices: 21068989--21069023 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21068979 TTTACAAACT
*
21068989 TAAAAAATATATTAAAA
1 TAAAAAATAAATTAAAA
21069006 TAAAAAATAAATTTAAAA
1 TAAAAAATAAA-TTAAAA
21069024 AAGGAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATAAATTAAAA
Found at i:21074827 original size:25 final size:25
Alignment explanation
Indices: 21074780--21074827 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21074770 TAGGCTAACT
* *
21074780 AGAGTTTAAGTGAGAAACTAAAAAC
1 AGAGTTTAACTGAGAAACGAAAAAC
21074805 AGAGTTTAACTGAGAGAA-GAAAA
1 AGAGTTTAACTGAGA-AACGAAAA
21074828 CCAAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (25 bp):
AGAGTTTAACTGAGAAACGAAAAAC
Found at i:21095068 original size:4 final size:4
Alignment explanation
Indices: 21095061--21095088 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21095051 TACTAGTCTC
21095061 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
21095089 CCATTTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:21096830 original size:45 final size:45
Alignment explanation
Indices: 21096766--21096858 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
21096756 AATTTGTTCA
21096766 CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
1 CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
*
21096811 CTCAAATACACTCACAAAATACGTTCCACAATGAACAGACAAGTG
1 CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
21096856 CTC
1 CTC
21096859 TCAATACTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (45 bp):
CTCAAATACACTCACAAAATACATTCCACAATGAACAGACAAGTG
Found at i:21098347 original size:20 final size:21
Alignment explanation
Indices: 21098324--21098362 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
21098314 ATAGGTGTAT
*
21098324 AATAATTAGTGTT-TAAATGA
1 AATAAATAGTGTTATAAATGA
*
21098344 AATAAATATTGTTATAAAT
1 AATAAATAGTGTTATAAAT
21098363 TTATTGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
AATAAATAGTGTTATAAATGA
Found at i:21100402 original size:17 final size:17
Alignment explanation
Indices: 21100380--21100412 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21100370 GATGAATGAC
21100380 TTAATT-ACTATTTCATA
1 TTAATTGACT-TTTCATA
21100397 TTAATTGACTTTTCAT
1 TTAATTGACTTTTCAT
21100413 GAAGGAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAATTGACTTTTCATA
Found at i:21103243 original size:26 final size:26
Alignment explanation
Indices: 21103205--21103310 Score: 124
Period size: 26 Copynumber: 4.1 Consensus size: 26
21103195 TGTACCTAAA
*
21103205 TAGCAGGCCTTGAGCCGGTGTTTATT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
* * * *
21103231 TAGCAAGCTTTGAGCTGGTGATTACT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
* * *
21103257 T-GCAGGCTATGAGCTGGTGCTTATT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
*
21103282 TAGCAGGCTTTGAGCCAGTGTTTATT
1 TAGCAGGCTTTGAGCCGGTGTTTATT
21103308 TAG
1 TAG
21103311 TAGGTACTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
25 21 0.32
26 45 0.68
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (26 bp):
TAGCAGGCTTTGAGCCGGTGTTTATT
Found at i:21115454 original size:26 final size:26
Alignment explanation
Indices: 21115423--21115475 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
21115413 CCCAAATCAT
*
21115423 ATAAATAAACAAAATATAA-AAAAATA
1 ATAAATAAA-AAAATAAAACAAAAATA
21115449 ATAAATAAAAAAATAAAACAAAAATA
1 ATAAATAAAAAAATAAAACAAAAATA
21115475 A
1 A
21115476 AGTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (26 bp):
ATAAATAAAAAAATAAAACAAAAATA
Found at i:21115472 original size:11 final size:11
Alignment explanation
Indices: 21115425--21115476 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
21115415 CAAATCATAT
21115425 AAAT-AAACAA
1 AAATAAAACAA
21115435 AATATAAAA-AA
1 AA-ATAAAACAA
*
21115446 ATAATAAATAAAA
1 A-AATAAA-ACAA
21115459 AAATAAAACAA
1 AAATAAAACAA
21115470 AAATAAA
1 AAATAAA
21115477 GTAATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 2 0.06
11 20 0.56
12 11 0.31
13 3 0.08
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (11 bp):
AAATAAAACAA
Found at i:21115599 original size:26 final size:27
Alignment explanation
Indices: 21115558--21115609 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
21115548 CAAACAGATC
*
21115558 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
21115585 CCAAA-ACCCAATTAACCTAGCCCAA
1 CCAAATACCCAATTAACCTAGCCCAA
21115610 CTAATGTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.42, C:0.40, G:0.04, T:0.13
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:21117038 original size:14 final size:14
Alignment explanation
Indices: 21117019--21117045 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21117009 ATATAGATAT
21117019 ACTATTTTTATTAA
1 ACTATTTTTATTAA
21117033 ACTATTTTTATTA
1 ACTATTTTTATTA
21117046 TACATATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
ACTATTTTTATTAA
Found at i:21117234 original size:18 final size:18
Alignment explanation
Indices: 21117206--21117246 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21117196 TGATGTGAGC
21117206 TTATTGTCTTATGTGTAT
1 TTATTGTCTTATGTGTAT
*
21117224 TGTATTG-CTTATTTGTAT
1 T-TATTGTCTTATGTGTAT
21117242 TTATT
1 TTATT
21117247 AATTATTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (18 bp):
TTATTGTCTTATGTGTAT
Found at i:21122846 original size:23 final size:23
Alignment explanation
Indices: 21122820--21122917 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
21122810 ATAAGTGCCA
21122820 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21122843 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
21122866 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21122888 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21122911 CACTGAT
1 CACTGAT
21122918 CAATAACACT
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:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:21122885 original size:45 final size:45
Alignment explanation
Indices: 21122827--21122915 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
21122817 CCACACTGAT
* *
21122827 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
21122872 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
21122916 ATCAATAACA
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:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:21130209 original size:23 final size:23
Alignment explanation
Indices: 21130183--21130256 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
21130173 ATAAGTGCCA
21130183 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21130206 CACTG--ATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
21130227 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
21130250 CACTGAT
1 CACTGAT
21130257 CAATAACACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
21 20 0.43
23 26 0.57
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:21130216 original size:21 final size:21
Alignment explanation
Indices: 21130190--21130256 Score: 107
Period size: 21 Copynumber: 3.1 Consensus size: 21
21130180 CCACACTGAT
21130190 ATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTG
*
21130211 ATGTAGCCAAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTG
21130232 AAATGTAGCCGAAGCTACCACTG
1 --ATGTAGCCGAAGCTACCACTG
21130255 AT
1 AT
21130257 CAATAACACT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.52
23 20 0.48
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (21 bp):
ATGTAGCCGAAGCTACCACTG
Found at i:21138846 original size:44 final size:44
Alignment explanation
Indices: 21138774--21138871 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
21138764 CAAGAGTGAG
* *
21138774 GGAGCAGATTGAAGCCAGAAATCTTATCTCCCTG-AGATTACAGT
1 GGAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAAG-TTACAAT
* *
21138818 GGAGCAGATTGAAGTC-GATAATCCTATCTCCTTGAAGTTACAAT
1 GGAGCAGATTGAAGCCAGA-AATCCTATCTCCCTGAAGTTACAAT
*
21138862 AGAGCAGATT
1 GGAGCAGATT
21138872 AAAATAAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 2 0.04
44 43 0.91
45 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (44 bp):
GGAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAAGTTACAAT
Found at i:21138890 original size:44 final size:44
Alignment explanation
Indices: 21138793--21138891 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
21138783 TGAAGCCAGA
* * * * ** *
21138793 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTGAGATTACAATAGAGCAGATTAAAATAAAG
* *
21138837 AATCCTATCTCCTTGA-AGTTACAATAGAGCAGATTAAAATAAAG
1 AATCTTATCTCCCTGAGA-TTACAATAGAGCAGATTAAAATAAAG
21138881 AATCTTATCTC
1 AATCTTATCTC
21138892 TCTAAAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
43 1 0.02
44 43 0.98
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAATAGAGCAGATTAAAATAAAG
Found at i:21139103 original size:145 final size:145
Alignment explanation
Indices: 21138837--21139161 Score: 535
Period size: 145 Copynumber: 2.2 Consensus size: 145
21138827 TGAAGTCGAT
* *
21138837 AATCCTATCTCCTTGAAGTTACAATAGAGCAGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
* *
21138902 CAGTAGAATAGATCGCATCATGTCTTATCTCCCTGAGATTATAGTGGAATAAACCGAAGAATTCC
66 CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAGAATTCC
21138967 TAATCGAAAATGGTG
131 TAATCGAAAATGGTG
* *
21138982 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAATG-ATCTTATTTCTCTAAAATT
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAA-GAATCTTATCTCTCTAAAATT
* *
21139046 ACAGTAGAATAGATTGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTC
65 ACAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAGAATTC
21139111 CTAATCGAAAATGGTG
130 CTAATCGAAAATGGTG
* * *
21139127 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATT
21139162 GAAGCTAGAA
Statistics
Matches: 167, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
145 166 0.99
146 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (145 bp):
AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAAGAATCTTATCTCTCTAAAATTA
CAGTAGAATAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAAACCGAAGAATTCC
TAATCGAAAATGGTG
Found at i:21139193 original size:44 final size:44
Alignment explanation
Indices: 21139127--21139249 Score: 176
Period size: 44 Copynumber: 2.8 Consensus size: 44
21139117 GAAAATGGTG
21139127 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGA-
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-AGAT
* *
21139171 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAGAT
** * *
21139215 AATCCAATCTCCTTGAGGTTACAGTGGAGCGGATT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT
21139250 AAAATAAAGG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
43 2 0.03
44 69 0.97
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAGAT
Found at i:21139269 original size:44 final size:42
Alignment explanation
Indices: 21139127--21139269 Score: 133
Period size: 44 Copynumber: 3.3 Consensus size: 42
21139117 GAAAATGGTG
**
21139127 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGA
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-AAAATA-A
* *** *
21139171 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-AA-AATAA
** * *
21139215 AATCCAATCTCCTTGAGGTTACAGTGGAGCGGATTAAAATAA
1 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAA
21139257 AGGATCTTATCTC
1 A--ATCTTATCTC
21139270 TCTAAAATTA
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 75 0.93
45 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (42 bp):
AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTAAAATAA
Found at i:21139278 original size:233 final size:232
Alignment explanation
Indices: 21138982--21139647 Score: 1131
Period size: 233 Copynumber: 2.9 Consensus size: 232
21138972 GAAAATGGTG
*
21138982 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAATGATCTTATTTCTCTAAAATTA
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTA-TTCTCTAAAATTA
* *
21139047 CAGTAGAATAGATTGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
65 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
*
21139112 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGAAATCTT
130 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTT
21139177 ATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
195 ATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
* * *
21139215 AATCCAATCTCCTTGAGGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAATTA
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTAT-TCTCTAAAATTA
* * *
21139280 CAGTAGAGTAGATCACATCAGGTCTTATCTCCCTAAGATTACAATGGAATAGACCGAAGAATTCC
65 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCC
*
21139345 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAAAATCTT
130 TAATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTT
*
21139410 ATCTCTCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
195 ATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
* *
21139448 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAATAAAAGATCTTA---TCTGAAATTAC
1 AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATTCTCTAAAATTAC
* * *
21139510 AGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGATTACAGTGGAATAGATCGAAGAACTCCT
66 AGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCT
*
21139575 AATCGAAAATGGTGAATCTTATCTCCTTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTA
131 AATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTA
21139640 TCTCCCTG
196 TCTCCCTG
21139648 CGGTATAGTG
Statistics
Matches: 407, Mismatches: 25, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
229 139 0.34
232 1 0.00
233 267 0.66
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (232 bp):
AATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATTCTCTAAAATTAC
AGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTCCT
AATCGAAAATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTA
TCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGAT
Found at i:21139501 original size:44 final size:44
Alignment explanation
Indices: 21139360--21139482 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
21139350 GAAAATGGTG
* *
21139360 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAA
1 AATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCCAAA
* *
21139404 AATCTTATCT-CTCTG-AGATTACAGTGGAGCAGATTGAAGCCGAT
1 AATCTTATCTCCT-TGAAG-TTACAGTGGAGCAGATTGAAGCCAAA
*
21139448 AATCCTATCTCCTTGAAGTTACAGTGGAGCAGATT
1 AATCTTATCTCCTTGAAGTTACAGTGGAGCAGATT
21139483 AAAATAAAAG
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
43 2 0.03
44 64 0.91
45 4 0.06
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTGAAGCCAAA
Found at i:21139805 original size:50 final size:49
Alignment explanation
Indices: 21139686--21139806 Score: 111
Period size: 50 Copynumber: 2.4 Consensus size: 49
21139676 ACGACAGATA
* * *
21139686 TTGCTTCCCCAACATTGCAGTTAGAAAGATTGAAGCTGCAATAGTGAATC
1 TTGCTTCCCCGACATTGCAG-TAGAAAGATTGAAGCTACAAAAGTGAATC
* * * ** *
21139736 TTACTGCCCAGTA-GGTGCAGTGGAACAGATTGAAGCTACAACAAG-GAATC
1 TTGCTTCCCCG-ACATTGCAGTAGAA-AGATTGAAGCTACAA-AAGTGAATC
21139786 TTGCTTCCCCGACATTGCAGT
1 TTGCTTCCCCGACATTGCAGT
21139807 TAAACGGATT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
49 5 0.09
50 45 0.85
51 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (49 bp):
TTGCTTCCCCGACATTGCAGTAGAAAGATTGAAGCTACAAAAGTGAATC
Found at i:21140089 original size:15 final size:14
Alignment explanation
Indices: 21140054--21140104 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
21140044 GGCCCAAATC
* *
21140054 AAATAAATAAACAA
1 AAATAAAAAAATAA
21140068 AATATAAAAAAATAA
1 AA-ATAAAAAAATAA
21140083 TAAATAAAAAAATAA
1 -AAATAAAAAAATAA
21140098 AAATAAA
1 AAATAAA
21140105 GTTATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 9 0.27
15 22 0.67
16 2 0.06
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:21141901 original size:18 final size:18
Alignment explanation
Indices: 21141873--21141913 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
21141863 TGATGTGAGC
21141873 TTATTGTCTTATGTGTAT
1 TTATTGTCTTATGTGTAT
*
21141891 TGTATTG-CTTATTTGTAT
1 T-TATTGTCTTATGTGTAT
21141909 TTATT
1 TTATT
21141914 AATTATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 12 0.57
19 5 0.24
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (18 bp):
TTATTGTCTTATGTGTAT
Found at i:21145023 original size:18 final size:20
Alignment explanation
Indices: 21144983--21145027 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
21144973 AATATGATAA
21144983 ATTTATAAACGATAAAATAT
1 ATTTATAAACGATAAAATAT
*
21145003 ATTTA-AAATGATAAAAT-T
1 ATTTATAAACGATAAAATAT
21145021 ATTTATA
1 ATTTATA
21145028 TAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTTATAAACGATAAAATAT
Found at i:21146394 original size:22 final size:22
Alignment explanation
Indices: 21146360--21146401 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21146350 GATTTTTCAC
*
21146360 ATCATTTAAATAAAATAAAATT
1 ATCATTTAAATAAAAAAAAATT
**
21146382 ATCATTTTTATAAAAAAAAA
1 ATCATTTAAATAAAAAAAAA
21146402 AAGGTTTAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
ATCATTTAAATAAAAAAAAATT
Found at i:21155068 original size:12 final size:12
Alignment explanation
Indices: 21155031--21155080 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
21155021 ATCGTTGTAC
21155031 AAATCTAACATAA
1 AAATCTAA-ATAA
21155044 AAA---AAACTAA
1 AAATCTAAA-TAA
21155054 AAATCTAAATAA
1 AAATCTAAATAA
*
21155066 AAATCAAAATAA
1 AAATCTAAATAA
21155078 AAA
1 AAA
21155081 ATTACTTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
9 1 0.03
10 8 0.25
12 17 0.53
13 6 0.19
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATCTAAATAA
Found at i:21155079 original size:23 final size:23
Alignment explanation
Indices: 21155031--21155080 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
21155021 ATCGTTGTAC
*
21155031 AAATCTAACATAAAAAAAACTAA
1 AAATCTAACATAAAAAAAAATAA
21155054 AAATCTAA-ATAAAAATCAAAATAA
1 AAATCTAACATAAAAA--AAAATAA
21155078 AAA
1 AAA
21155081 ATTACTTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 9 0.38
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (23 bp):
AAATCTAACATAAAAAAAAATAA
Found at i:21156834 original size:25 final size:25
Alignment explanation
Indices: 21156788--21156835 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21156778 AAATACTATC
*
21156788 AAAAATTTTAAAAATATTTTTTCGT
1 AAAAATTTTAAAAATATCTTTTCGT
*
21156813 AAAACTTTTCAAAAATA-CTTTTC
1 AAAAATTTT-AAAAATATCTTTTC
21156836 AACTTCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAATTTTAAAAATATCTTTTCGT
Found at i:21158812 original size:24 final size:22
Alignment explanation
Indices: 21158764--21158813 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
21158754 ATACTTATTC
*
21158764 TTTATATATAAATATATTTTCT
1 TTTATATATAAATAAATTTTCT
21158786 TTTATATGAATAAATAAAGTTTT-T
1 TTTATAT--ATAAATAAA-TTTTCT
21158810 TTTA
1 TTTA
21158814 AGATCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTATATATAAATAAATTTTCT
Found at i:21161661 original size:24 final size:24
Alignment explanation
Indices: 21161634--21161679 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
21161624 TTCATTATAA
*
21161634 TCAATTTTTCACCTTTCATCTTCT
1 TCAACTTTTCACCTTTCATCTTCT
*
21161658 TCAACTTTTCATCTTTCATCTT
1 TCAACTTTTCACCTTTCATCTT
21161680 TTTGTAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.54
Consensus pattern (24 bp):
TCAACTTTTCACCTTTCATCTTCT
Found at i:21161835 original size:3 final size:3
Alignment explanation
Indices: 21161827--21161904 Score: 111
Period size: 3 Copynumber: 26.0 Consensus size: 3
21161817 TTCTTTGTAG
* * * * *
21161827 TAT TAT TAT TGT TGT AAT TAT TAT TAC TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21161875 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21161905 ATAAAACAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:21162239 original size:14 final size:14
Alignment explanation
Indices: 21162220--21162249 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21162210 TACCATTTTA
21162220 TTGCTAATTCTTCT
1 TTGCTAATTCTTCT
21162234 TTGCTAATTCTTCT
1 TTGCTAATTCTTCT
21162248 TT
1 TT
21162250 TACCATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (14 bp):
TTGCTAATTCTTCT
Found at i:21162400 original size:20 final size:20
Alignment explanation
Indices: 21162375--21162413 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
21162365 ATTTAATTTT
21162375 TCTTTTTATCTGAACCGGTA
1 TCTTTTTATCTGAACCGGTA
21162395 TCTTTTTATCTGAACCGGT
1 TCTTTTTATCTGAACCGGT
21162414 TTAAGCAAAA
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:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (20 bp):
TCTTTTTATCTGAACCGGTA
Found at i:21166594 original size:20 final size:20
Alignment explanation
Indices: 21166569--21166608 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21166559 CGTAAAATGA
*
21166569 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
21166589 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
21166609 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:21166598 original size:34 final size:35
Alignment explanation
Indices: 21166554--21166620 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21166544 CAGTAAAATA
* *
21166554 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
21166588 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
21166621 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:21167286 original size:9 final size:9
Alignment explanation
Indices: 21167274--21167350 Score: 66
Period size: 9 Copynumber: 8.4 Consensus size: 9
21167264 AAATAAAAAA
21167274 AATTCGGGT
1 AATTCGGGT
21167283 AATTCGGGCAT
1 AATTCGGG--T
**
21167294 TTTTC-GGT
1 AATTCGGGT
* *
21167302 AATTCAGTT
1 AATTCGGGT
*
21167311 AATTCGGTT
1 AATTCGGGT
*
21167320 AATTCGGTT
1 AATTCGGGT
21167329 AATTCGGGT
1 AATTCGGGT
*
21167338 AATTCGGAT
1 AATTCGGGT
21167347 AATT
1 AATT
21167351 TTTAACCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
8 4 0.07
9 47 0.82
10 2 0.04
11 4 0.07
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:21167340 original size:27 final size:26
Alignment explanation
Indices: 21167274--21167350 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
21167264 AAATAAAAAA
*
21167274 AATTCGGGTAATTCGGGCATT-TTTCGGT
1 AATTCGGGTAATTC-GG--TTAATTCGGT
* *
21167302 AATTCAGTTAATTCGGTTAATTCGGTT
1 AATTCGGGTAATTCGGTTAATTCGG-T
*
21167329 AATTCGGGTAATTCGGATAATT
1 AATTCGGGTAATTCGGTTAATT
21167351 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 22 0.54
28 12 0.29
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (26 bp):
AATTCGGGTAATTCGGTTAATTCGGT
Found at i:21167343 original size:18 final size:18
Alignment explanation
Indices: 21167299--21167350 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
21167289 GGCATTTTTC
*
21167299 GGTAATTCAGTTAATTCG
1 GGTAATTCGGTTAATTCG
*
21167317 GTTAATTCGGTTAATTCG
1 GGTAATTCGGTTAATTCG
*
21167335 GGTAATTCGGATAATT
1 GGTAATTCGGTTAATT
21167351 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (18 bp):
GGTAATTCGGTTAATTCG
Found at i:21172756 original size:11 final size:11
Alignment explanation
Indices: 21172720--21172758 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
21172710 TAAATAGTAA
*
21172720 TTTATTAATAT
1 TTTAATAATAT
21172731 TTTAATGAGATAT
1 TTTAAT-A-ATAT
21172744 TTTAATAATAT
1 TTTAATAATAT
21172755 TTTA
1 TTTA
21172759 TTTAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.52
12 2 0.08
13 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:21175982 original size:14 final size:14
Alignment explanation
Indices: 21175959--21176017 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 14
21175949 TATGAATAAT
21175959 AATATAATAAAACAA
1 AATATAATAAAAC-A
21175974 ATATCATAATAAAA-A
1 A-AT-ATAATAAAACA
*
21175989 AATATGATAATAA-A
1 AATATAATAA-AACA
21176003 AATA-AATAAAACA
1 AATATAATAAAACA
21176016 AA
1 AA
21176018 AAAGAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 13 0.34
14 9 0.24
15 3 0.08
16 2 0.05
17 9 0.24
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (14 bp):
AATATAATAAAACA
Found at i:21175993 original size:16 final size:16
Alignment explanation
Indices: 21175962--21176004 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
21175952 GAATAATAAT
21175962 ATAATAAAACAAATATC
1 ATAATAAAA-AAATATC
*
21175979 ATAATAAAAAAATATG
1 ATAATAAAAAAATATC
21175995 ATAATAAAAA
1 ATAATAAAAA
21176005 TAAATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAATAAAAAAATATC
Found at i:21176004 original size:17 final size:17
Alignment explanation
Indices: 21175962--21176010 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
21175952 GAATAATAAT
*
21175962 ATAATAAAACAAATATC
1 ATAATAAAAAAAATATC
*
21175979 ATAAT-AAAAAAATATG
1 ATAATAAAAAAAATATC
21175995 ATAATAAAAATAAATA
1 ATAATAAAAA-AAATA
21176011 AAACAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 9 0.32
18 5 0.18
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
ATAATAAAAAAAATATC
Found at i:21178132 original size:27 final size:30
Alignment explanation
Indices: 21178098--21178152 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
21178088 TCTTTATTGA
21178098 TATATTTTTC-TCTTTT-TTT-ATTTTAAT
1 TATATTTTTCATCTTTTCTTTCATTTTAAT
*
21178125 TATATTTTTCATTTTTTCTTTCATTTTA
1 TATATTTTTCATCTTTTCTTTCATTTTA
21178153 TTTTTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 5 0.21
29 3 0.12
30 6 0.25
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (30 bp):
TATATTTTTCATCTTTTCTTTCATTTTAAT
Found at i:21178158 original size:12 final size:12
Alignment explanation
Indices: 21178113--21178158 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
21178103 TTTTCTCTTT
*
21178113 TTTTA-TTTTAA
1 TTTTATTTTTCA
*
21178124 TTATATTTTTCA
1 TTTTATTTTTCA
21178136 TTTT-TTCTTTCA
1 TTTTATT-TTTCA
21178148 TTTTATTTTTC
1 TTTTATTTTTC
21178159 CAATTTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.21
12 21 0.72
13 2 0.07
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:21188337 original size:2 final size:2
Alignment explanation
Indices: 21188330--21188358 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21188320 TTCCAATAGC
21188330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21188359 TTAAAATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21189520 original size:19 final size:18
Alignment explanation
Indices: 21189494--21189544 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
21189484 CGTTTCTAGG
21189494 TTTTTTTTTCCTTATTCC
1 TTTTTTTTTCCTTATTCC
* *
21189512 TTCTTTTTTTCAATAATTCC
1 TT-TTTTTTTC-CTTATTCC
*
21189532 TTTTTTCTTCCTT
1 TTTTTTTTTCCTT
21189545 CTTTCTCTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 3 0.12
19 15 0.58
20 8 0.31
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTTTTTCCTTATTCC
Found at i:21189807 original size:30 final size:31
Alignment explanation
Indices: 21189771--21189828 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
21189761 AAAAATCAAG
*
21189771 AAAATTAACATCACAAAC-AAAATCCATTAA
1 AAAATTAACATAACAAACAAAAATCCATTAA
21189801 AAAATTAACATAACAAACAAAAATCCAT
1 AAAATTAACATAACAAACAAAAATCCAT
21189829 CAATCTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (31 bp):
AAAATTAACATAACAAACAAAAATCCATTAA
Found at i:21190452 original size:25 final size:27
Alignment explanation
Indices: 21190387--21190460 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 27
21190377 GAAAATAAAT
*
21190387 AATAAAAGAAAATGGAAACTGGAAACTGG
1 AATAAAAGAAAAGGGAAACTGGAAAC--G
21190416 AATAGGAAAGAAAAGGGAAA-TGGAAA-G
1 AATA--AAAGAAAAGGGAAACTGGAAACG
21190443 AATAAAAGAAAAGGGAAA
1 AATAAAAGAAAAGGGAAA
21190461 AGAAAAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 14 0.33
27 5 0.12
29 4 0.10
30 6 0.14
31 13 0.31
ACGTcount: A:0.61, C:0.03, G:0.27, T:0.09
Consensus pattern (27 bp):
AATAAAAGAAAAGGGAAACTGGAAACG
Found at i:21191642 original size:21 final size:21
Alignment explanation
Indices: 21191618--21191657 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21191608 CAATAAAAAA
21191618 AAAGCCTTTACCAAGAATACT
1 AAAGCCTTTACCAAGAATACT
* *
21191639 AAAGGCTTTTCCAAGAATA
1 AAAGCCTTTACCAAGAATA
21191658 GCAAGAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAGCCTTTACCAAGAATACT
Found at i:21192307 original size:58 final size:59
Alignment explanation
Indices: 21192195--21192313 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
21192185 ATAAAACAAA
21192195 AGAAAGAATCATCAGCTTCTTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTCTTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
21192254 AGAAAGAATCATCAGCTTCTTCATTTT-TTTTAACTCCCATCGAAAATCCATTGTTGTT
1 AGAAAGAATCATCAGCTTCTTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
21192312 AG
1 AG
21192314 TCTCCAAGGT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 33 0.55
59 27 0.45
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (59 bp):
AGAAAGAATCATCAGCTTCTTCATTTTGTTTTAACTCCCATCGAAAATCCATTGTTGTT
Found at i:21194276 original size:10 final size:11
Alignment explanation
Indices: 21194255--21194437 Score: 87
Period size: 11 Copynumber: 17.9 Consensus size: 11
21194245 GGCCCATTTT
21194255 TATTTT-AAAA
1 TATTTTAAAAA
21194265 -ATTTTAAAAA
1 TATTTTAAAAA
*
21194275 -A-TTAAAAAA
1 TATTTTAAAAA
21194284 GTATTTTAAAAA
1 -TATTTTAAAAA
21194296 TATTTTAAAAA
1 TATTTTAAAAA
21194307 TATTTT--AAA
1 TATTTTAAAAA
**
21194316 -ATTAAAAAAA
1 TATTTTAAAAA
* **
21194326 AATTAAAAAAA
1 TATTTTAAAAA
*
21194337 GTATTTTAAAAT
1 -TATTTTAAAAA
21194349 TATTTT--AAA
1 TATTTTAAAAA
21194358 -A--TTAAAAA
1 TATTTTAAAAA
* *
21194366 -AATTAAAAAA
1 TATTTTAAAAA
21194376 GTATTTTAAAAA
1 -TATTTTAAAAA
21194388 TA-TTT-AAAA
1 TATTTTAAAAA
21194397 -A-TTTAAAAA
1 TATTTTAAAAA
* *
21194406 -AATTAAAAAA
1 TATTTTAAAAA
* *
21194416 GTATGTAAAAAA
1 -TATTTTAAAAA
21194428 TATTTTAAAA
1 TATTTTAAAA
21194438 TTAAAAAAAT
Statistics
Matches: 138, Mismatches: 17, Indels: 35
0.73 0.09 0.18
Matches are distributed among these distances:
6 2 0.01
8 12 0.09
9 26 0.19
10 24 0.17
11 44 0.32
12 30 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:21194359 original size:31 final size:30
Alignment explanation
Indices: 21194302--21194368 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
21194292 AAAATATTTT
21194302 AAAAATATTTTAAAATTAAAAAAAAATTAA
1 AAAAATATTTTAAAATTAAAAAAAAATTAA
****
21194332 AAAAAGTATTTTAAAATTATTTTAAAATTAA
1 AAAAA-TATTTTAAAATTAAAAAAAAATTAA
21194363 AAAAAT
1 AAAAAT
21194369 TAAAAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAAATATTTTAAAATTAAAAAAAAATTAA
Found at i:21194365 original size:39 final size:39
Alignment explanation
Indices: 21194255--21194447 Score: 246
Period size: 40 Copynumber: 4.8 Consensus size: 39
21194245 GGCCCATTTT
* *
21194255 TATTTTAAAAAT-TTTAAAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTT-TAAAATTAAAAAA--A-TTAAAAAAG
21194296 TATTTTAAAAATATTTTAAAATTAAAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATT--AAAAAAATT-AAAAAAG
*
21194338 TATTTTAAAATTATTTTAAAATTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
*
21194377 TATTTTAAAAATATTTAAAAATTTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAAAAAG
* *
21194417 TATGTAAAAAATATTTTAAAATTAAAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAAAT
21194448 AAATATATTT
Statistics
Matches: 138, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
39 36 0.26
40 47 0.34
41 24 0.17
42 25 0.18
43 6 0.04
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (39 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
Found at i:21194373 original size:8 final size:9
Alignment explanation
Indices: 21194355--21194447 Score: 62
Period size: 9 Copynumber: 9.6 Consensus size: 9
21194345 AAATTATTTT
21194355 AAAATTAAA
1 AAAATTAAA
21194364 AAAATTAAA
1 AAAATTAAA
21194373 AAAGTATTTTAAA
1 AAA--A--TTAAA
* *
21194386 AATATTTAA
1 AAAATTAAA
*
21194395 AAATTTAAA
1 AAAATTAAA
21194404 AAAATTAAA
1 AAAATTAAA
21194413 AAAGTATGTAAA
1 AAA--AT-TAAA
**
21194425 AAATATT-TT
1 AAA-ATTAAA
21194434 AAAATTAAA
1 AAAATTAAA
21194443 AAAAT
1 AAAAT
21194448 AAATATATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
8 3 0.05
9 41 0.62
10 1 0.02
11 7 0.11
12 7 0.11
13 7 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAATTAAA
Found at i:21194386 original size:11 final size:10
Alignment explanation
Indices: 21194359--21194438 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
21194349 TATTTTAAAA
*
21194359 TTAAAAAAAT
1 TTAAAAATAT
*
21194369 TAAAAAAGTATT
1 TTAAAAA-TA-T
21194381 TTAAAAATAT
1 TTAAAAATAT
21194391 TT-AAAA-AT
1 TTAAAAATAT
*
21194399 TTAAAAAAAT
1 TTAAAAATAT
*
21194409 TAAAAAAGTAT
1 TTAAAAA-TAT
*
21194420 GTAAAAAATAT
1 -TTAAAAATAT
*
21194431 TTTAAAAT
1 TTAAAAAT
21194439 TAAAAAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
8 4 0.07
9 8 0.14
10 23 0.40
11 8 0.14
12 14 0.25
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:21194397 original size:31 final size:31
Alignment explanation
Indices: 21194255--21194406 Score: 111
Period size: 30 Copynumber: 5.0 Consensus size: 31
21194245 GGCCCATTTT
21194255 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTAAAAAATTAAAAAAG
**
21194285 TATTTTAAAAATATTTTAAAAATATT-TTAAA-
1 TATTTTAAAAATA-TTTAAAAA-ATTAAAAAAG
** * * ** *
21194316 -ATTAAAAAAAAATTAAAAAAAGTATTTTAAAAT
1 TATTTTAAAAATATT-TAAAAA--ATTAAAAAAG
*
21194349 TATTTT--AAA-ATTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTAAAAAATTAAAAAAG
*
21194377 TATTTTAAAAATATTTAAAAATTTAAAAAA
1 TATTTTAAAAATATTTAAAAAATTAAAAAA
21194407 ATTAAAAAAG
Statistics
Matches: 97, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
28 13 0.13
29 2 0.02
30 35 0.36
31 23 0.24
32 18 0.19
33 3 0.03
34 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAAATTAAAAAAG
Found at i:21201779 original size:15 final size:17
Alignment explanation
Indices: 21201744--21201782 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21201734 AGTTGATTTT
*
21201744 TTTTTTTAGATTTGAGC
1 TTTTTTAAGATTTGAGC
21201761 TTTTTTAAG-TTTGAG-
1 TTTTTTAAGATTTGAGC
21201776 TTTTTTA
1 TTTTTTA
21201783 TATTCGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 6 0.29
17 8 0.38
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (17 bp):
TTTTTTAAGATTTGAGC
Found at i:21205450 original size:3 final size:3
Alignment explanation
Indices: 21205442--21205469 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
21205432 TCAGCTTCTT
21205442 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21205470 ATAATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21209674 original size:16 final size:16
Alignment explanation
Indices: 21209655--21209687 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21209645 ATTTTAGAGC
*
21209655 ACATATATATATATAT
1 ACATAAATATATATAT
21209671 ACATAAATATATATAT
1 ACATAAATATATATAT
21209687 A
1 A
21209688 ATACAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ACATAAATATATATAT
Found at i:21210849 original size:4 final size:4
Alignment explanation
Indices: 21210786--21210833 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
21210776 TTATTCTATT
* * * * *
21210786 TTTA TTTA TCTA TTTA TTTA TGTA TTCA TTCA TTTA TTTA TTTC TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
21210834 CTCTTTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (4 bp):
TTTA
Done.