Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 120 of 131
Found at i:21547084 original size:14 final size:14
Alignment explanation
Indices: 21547065--21547112 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
21547055 GCCTTAATGT
21547065 TTAGATGGAGAGGC
1 TTAGATGGAGAGGC
* * *
21547079 TTAGATTGAAAAGGT
1 TTAGA-TGGAGAGGC
*
21547094 TTGGATGGAGAGGC
1 TTAGATGGAGAGGC
21547108 TTAGA
1 TTAGA
21547113 GAGAAGCCAA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.31, C:0.04, G:0.38, T:0.27
Consensus pattern (14 bp):
TTAGATGGAGAGGC
Found at i:21549907 original size:30 final size:30
Alignment explanation
Indices: 21549871--21549973 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
21549861 CACTCTATTT
21549871 AAATAAATTCTTATAATTTAATTTATACTC
1 AAATAAATTCTTATAATTTAATTTATACTC
* * *
21549901 AAATAAATTTTTATATTTTATTTTATA-TCC
1 AAATAAATTCTTATAATTTAATTTATACT-C
* * * *
21549931 AAATAAATTTTTA-ATATTTAATTCACACTT
1 AAATAAATTCTTATA-ATTTAATTTATACTC
*
21549961 AAATAAATCCTTA
1 AAATAAATTCTTA
21549974 ATATAAATCA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 2 0.03
30 57 0.95
31 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATAAATTCTTATAATTTAATTTATACTC
Found at i:21556642 original size:15 final size:15
Alignment explanation
Indices: 21556622--21556651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21556612 TTCAACCTTA
*
21556622 AAAGAAATTATATTT
1 AAAGAAAATATATTT
21556637 AAAGAAAATATATTT
1 AAAGAAAATATATTT
21556652 GTAGGCATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAGAAAATATATTT
Found at i:21558268 original size:22 final size:22
Alignment explanation
Indices: 21558238--21558289 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
21558228 ATTAATAAAA
*
21558238 TATATTTTAT-ATCGATATGAAT
1 TATAATTTATAAT-GATATGAAT
**
21558260 TATAATTTATAATTTTATGAAT
1 TATAATTTATAATGATATGAAT
21558282 TATAATTT
1 TATAATTT
21558290 TTATGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (22 bp):
TATAATTTATAATGATATGAAT
Found at i:21558807 original size:3 final size:3
Alignment explanation
Indices: 21558799--21558831 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21558789 CGTATCTTTC
21558799 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21558832 TTACATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:21559102 original size:20 final size:22
Alignment explanation
Indices: 21559067--21559117 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
21559057 CTTGAAATTA
21559067 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
21559089 ATAAAATA-TATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
21559109 AT-AAATATT
1 ATAAAATATT
21559118 TAAAAATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.18
20 7 0.25
21 8 0.29
22 8 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:21559140 original size:30 final size:29
Alignment explanation
Indices: 21559091--21559151 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
21559081 TTTAAAATAT
* * *
21559091 AAAATATATTTTTTAAATATAAATATTTA
1 AAAATATATTATATAAATATAAATAATTA
*
21559120 AAAATATCATTATATAAATATATATAATTA
1 AAAATAT-ATTATATAAATATAAATAATTA
21559150 AA
1 AA
21559152 TAATTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
AAAATATATTATATAAATATAAATAATTA
Found at i:21559159 original size:12 final size:14
Alignment explanation
Indices: 21559103--21559163 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
21559093 AATATATTTT
* *
21559103 TTAAATATAAATAT
1 TTAAATATATATAA
* *
21559117 TTAAAAATATCATTA
1 TTAAATATAT-ATAA
21559132 TATAAATATATATAA
1 T-TAAATATATATAA
21559147 TTAAATA-AT-TAA
1 TTAAATATATATAA
21559159 TTAAA
1 TTAAA
21559164 ATTAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 14 0.36
15 7 0.18
16 8 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAATATATATAA
Found at i:21560286 original size:32 final size:32
Alignment explanation
Indices: 21560250--21560315 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
21560240 ATAAGAAAAA
*
21560250 ATGGTGACCAAAGCTTAACCCAGCTTAAGCCC
1 ATGGTAACCAAAGCTTAACCCAGCTTAAGCCC
21560282 ATGGTAACCAAAGCTTAACCCAGCTTAAGCCC
1 ATGGTAACCAAAGCTTAACCCAGCTTAAGCCC
21560314 AT
1 AT
21560316 CACATGGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (32 bp):
ATGGTAACCAAAGCTTAACCCAGCTTAAGCCC
Found at i:21567983 original size:21 final size:20
Alignment explanation
Indices: 21567939--21567980 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
21567929 TCATTGGAAT
21567939 ATTTTTTATTTATTTTCAAA
1 ATTTTTTATTTATTTTCAAA
*
21567959 ATTTTATTACTTTTTTTTCAAA
1 ATTTT-TTA-TTTATTTTCAAA
21567981 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 3 0.16
22 11 0.58
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTTATTTATTTTCAAA
Found at i:21569500 original size:14 final size:15
Alignment explanation
Indices: 21569476--21569504 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21569466 AAACTTATAG
21569476 TAAATAATTAATAAT
1 TAAATAATTAATAAT
21569491 TAAA-AATTAATAAT
1 TAAATAATTAATAAT
21569505 GCAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATAATTAATAAT
Found at i:21575079 original size:2 final size:2
Alignment explanation
Indices: 21575067--21575104 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
21575057 AGAAAATCAT
21575067 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21575105 TACATAGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21591071 original size:21 final size:20
Alignment explanation
Indices: 21591024--21591071 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
21591014 TCTCTGCTTT
21591024 TTCT-CTCTTTGTTATCTTC
1 TTCTCCTCTTTGTTATCTTC
*
21591043 TTCACCTCTTTGCTTAAT-TTC
1 TTCTCCTCTTTG-TT-ATCTTC
21591064 TTCTCCTC
1 TTCTCCTC
21591072 ATATAACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 7 0.29
21 12 0.50
22 2 0.08
ACGTcount: A:0.08, C:0.31, G:0.04, T:0.56
Consensus pattern (20 bp):
TTCTCCTCTTTGTTATCTTC
Found at i:21594605 original size:1 final size:1
Alignment explanation
Indices: 21594599--21594640 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
21594589 TTTCAATCAG
* * *
21594599 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21594641 CAAACCACTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21597268 original size:27 final size:26
Alignment explanation
Indices: 21597237--21597298 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
21597227 ACCAGTCACC
21597237 TCTTTCTATTTTTAATTT-TTTATTTTT
1 TCTTTCTATTTTT-ATTTCTTTA-TTTT
* *
21597264 TCTTTCTCTTTTTGTTTCTTTATTTT
1 TCTTTCTATTTTTATTTCTTTATTTT
21597290 T-TTTCTATT
1 TCTTTCTATT
21597299 CTTTGTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 7 0.23
26 8 0.26
27 16 0.52
ACGTcount: A:0.10, C:0.11, G:0.02, T:0.77
Consensus pattern (26 bp):
TCTTTCTATTTTTATTTCTTTATTTT
Found at i:21600892 original size:16 final size:17
Alignment explanation
Indices: 21600860--21600902 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
21600850 TATAATTTAA
21600860 AATATAATATGATGATAT
1 AATATAA-ATGATGATAT
21600878 AATATAAAT-ATGATAT
1 AATATAAATGATGATAT
21600894 AATAATAAA
1 AAT-ATAAA
21600903 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (17 bp):
AATATAAATGATGATAT
Found at i:21600893 original size:24 final size:24
Alignment explanation
Indices: 21600850--21600915 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
21600840 ACTTAAATTT
* * *
21600850 TATAATTTAAAATATAATATGATGA
1 TATAATAT-AAATATAATATAATAA
*
21600875 TATAATATAAATATGATATAATAA
1 TATAATATAAATATAATATAATAA
* *
21600899 TAAAATATAAAAATAAT
1 TATAATATAAATATAAT
21600916 TATATATGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 27 0.79
25 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
TATAATATAAATATAATATAATAA
Found at i:21601010 original size:31 final size:32
Alignment explanation
Indices: 21600967--21601026 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
21600957 TTTTATATTG
*
21600967 ATATAAATTAAATATAT-AATTTTCATATAAA
1 ATATAAATTAAATATATAAATTTTAATATAAA
21600998 ATAT-AATATAAATATATAAATTTTAATAT
1 ATATAAAT-TAAATATATAAATTTTAATAT
21601027 TTTACATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.12
31 13 0.50
32 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAAATTAAATATATAAATTTTAATATAAA
Found at i:21601483 original size:7 final size:7
Alignment explanation
Indices: 21601455--21601491 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
21601445 TTTTATATTT
21601455 ATATATA
1 ATATATA
21601462 ATATA-A
1 ATATATA
*
21601468 AAATA-A
1 ATATATA
21601474 ATATATA
1 ATATATA
21601481 ATATATA
1 ATATATA
21601488 ATAT
1 ATAT
21601492 TTCAGCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 10 0.37
7 17 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATATATA
Found at i:21602906 original size:145 final size:143
Alignment explanation
Indices: 21602515--21603084 Score: 624
Period size: 145 Copynumber: 4.1 Consensus size: 143
21602505 TTAGTTTTAT
* * *
21602515 ATCAAAATATGAATTATATTTTTTTAATTTTATTAAATTTATATATAATTTTTATTAAAATTTTA
1 ATCAAAATATGAAATATA-TTTTTTAATTTTGTTAAACTTATATATAATTTTTATTAAAATTTTA
* * * *
21602580 AATTTTATTATTTTTATATTTTTTATATCA---TCG--------TATTATATTTTAAATTATCAT
65 AACTTTATCATTTTCATATTTTTTATATCATTTTCGTATTATCATATTATATTTTAAATTACCAT
*
21602634 ATTTAATTTTATTTA
130 ATTT-ATTTTATCTA
*
21602649 ATCAAAATAT--AATATATATTTTAATTTTGTTAAACTTATATATAA-TTTTATTAAAA-TTTAA
1 ATCAAAATATGAAATATATTTTTTAATTTTGTTAAACTTATATATAATTTTTATTAAAATTTTAA
* * * * * * * **
21602710 ACTTTATCAATTGCATATTCTTTTTATATAATTTTTGGATCATCGTATTATATTTTAAATTATTA
66 ACTTTATCATTTTCATA-T-TTTTTATATCATTTTCGTATTATCATATTATATTTTAAATTACCA
*
21602775 TATTTGTGTTTATCTA
129 TATTTAT-TTTATCTA
21602791 ATCAAAATATGAAATATATTTCTTTAATTTTGTTAAACTTATATATAATTTTTATTAAAATTTTA
1 ATCAAAATATGAAATATATTT-TTTAATTTTGTTAAACTTATATATAATTTTTATTAAAATTTTA
*
21602856 AACTTTATCATTTTCATATTTTTTATATCATTTTCGTATTATCATATTATAATTTAAATTACCAT
65 AACTTTATCATTTTCATATTTTTTATATCATTTTCGTATTATCATATTATATTTTAAATTACCAT
21602921 ATTTATTTTTATCTA
130 ATTTA-TTTTATCTA
* *
21602936 ATCAAAATATGAAATCTATTTTTTAATTTT-ATAAA-TTATAT-T--TTTTTATTAAAATTTTAA
1 ATCAAAATATGAAATATATTTTTTAATTTTGTTAAACTTATATATAATTTTTATTAAAATTTTAA
* ** * * *
21602996 TCCGTATTATTTTTC-TATTCTTTTCATATCATTTTTGTATTATCATATTATATTTGAAATTACC
66 ACTTTATCA-TTTTCATATT-TTTT-ATATCATTTTCGTATTATCATATTATATTTTAAATTACC
* *
21603060 GTATTTGCTTTTATCTA
128 ATATTT-ATTTTATCTA
21603077 ATCAAAAT
1 ATCAAAAT
21603085 CACTCATCCA
Statistics
Matches: 375, Mismatches: 37, Indels: 41
0.83 0.08 0.09
Matches are distributed among these distances:
129 17 0.05
130 12 0.03
131 36 0.10
132 5 0.01
134 12 0.03
139 27 0.07
140 9 0.02
141 60 0.16
142 47 0.13
143 4 0.01
144 17 0.05
145 96 0.26
146 13 0.03
147 20 0.05
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (143 bp):
ATCAAAATATGAAATATATTTTTTAATTTTGTTAAACTTATATATAATTTTTATTAAAATTTTAA
ACTTTATCATTTTCATATTTTTTATATCATTTTCGTATTATCATATTATATTTTAAATTACCATA
TTTATTTTATCTA
Found at i:21604355 original size:24 final size:25
Alignment explanation
Indices: 21604328--21604377 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
21604318 AATAATTATT
* *
21604328 ATTATTATAACTATGATT-AAAAAA
1 ATTACTATAACTATAATTGAAAAAA
*
21604352 ATTACTATAATTATAATTGAAAAAA
1 ATTACTATAACTATAATTGAAAAAA
21604377 A
1 A
21604378 AATTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
ATTACTATAACTATAATTGAAAAAA
Found at i:21610087 original size:61 final size:61
Alignment explanation
Indices: 21609992--21610113 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
21609982 GCTCTACTTC
* * *
21609992 AACATATATAAAGAATAAATGAGCACAACAGCAAAAGGTATGATTGTTTTGAAAAATCCAT
1 AACATATACAAAGAATAAACGAGCACAACAGCAAAAGGTATGATTGTTTTAAAAAATCCAT
21610053 AACATATACAAAGAATAAACGAGCACAACAGCAAAAGGTATGATTGTTTTAAAAAATCCAT
1 AACATATACAAAGAATAAACGAGCACAACAGCAAAAGGTATGATTGTTTTAAAAAATCCAT
21610114 TGGATCAACA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (61 bp):
AACATATACAAAGAATAAACGAGCACAACAGCAAAAGGTATGATTGTTTTAAAAAATCCAT
Found at i:21613120 original size:18 final size:19
Alignment explanation
Indices: 21613099--21613146 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
21613089 TAATTCATAA
21613099 ATTTAATTAAATTTTTA-T
1 ATTTAATTAAATTTTTATT
* *
21613117 ATTTAAATATATTTTTATT
1 ATTTAATTAAATTTTTATT
21613136 ATTTTAATTAA
1 A-TTTAATTAA
21613147 TAAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.62
19 2 0.08
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAATTAAATTTTTATT
Found at i:21613230 original size:25 final size:25
Alignment explanation
Indices: 21613172--21613230 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
21613162 TAAGCTTAAA
21613172 TTTAAATATAAATAATTAAATTTTT
1 TTTAAATATAAATAATTAAATTTTT
* *
21613197 ATCAAATATAAA-AATTAAATTTATT
1 TTTAAATATAAATAATTAAATTT-TT
*
21613222 TTTATATAT
1 TTTAAATAT
21613231 TAATCGAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAAATATAAATAATTAAATTTTT
Found at i:21613667 original size:24 final size:24
Alignment explanation
Indices: 21613640--21613689 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
21613630 ATAGAACACG
*
21613640 AAAATAT-TATTTAAATATAATATA
1 AAAATATATAATT-AATATAATATA
*
21613664 AAAATATATAATTAATATAATTTA
1 AAAATATATAATTAATATAATATA
21613688 AA
1 AA
21613690 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATATATAATTAATATAATATA
Found at i:21614283 original size:16 final size:16
Alignment explanation
Indices: 21614230--21614306 Score: 67
Period size: 16 Copynumber: 5.1 Consensus size: 16
21614220 TTTGATTCAA
21614230 AATTA-ATAAA-ATAT
1 AATTATATAAATATAT
* *
21614244 TATT-TTTAAA-ATAT
1 AATTATATAAATATAT
*
21614258 AA-TATTTAAATATAT
1 AATTATATAAATATAT
21614273 AATTATATAAATATAT
1 AATTATATAAATATAT
*
21614289 -ATATATATAAATAAAT
1 AAT-TATATAAATATAT
21614305 AA
1 AA
21614307 ATAATTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
13 1 0.02
14 18 0.35
15 8 0.15
16 24 0.46
17 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTATATAAATATAT
Found at i:21614310 original size:8 final size:8
Alignment explanation
Indices: 21614250--21614309 Score: 70
Period size: 8 Copynumber: 7.8 Consensus size: 8
21614240 ATATTATTTT
21614250 TAAA-ATA
1 TAAATATA
*
21614257 T-AATATT
1 TAAATATA
21614264 TAAATATA
1 TAAATATA
*
21614272 TAATTATA
1 TAAATATA
21614280 TAAATATA
1 TAAATATA
*
21614288 TATATATA
1 TAAATATA
*
21614296 TAAATAAA
1 TAAATATA
21614304 TAAATA
1 TAAATA
21614310 ATTAATTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
6 2 0.05
7 4 0.09
8 38 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAATATA
Found at i:21616621 original size:35 final size:35
Alignment explanation
Indices: 21616575--21616644 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
21616565 ACATATCCTT
21616575 AGTCAGATTTACTTAGGTTATAGTATTAATTGTTC
1 AGTCAGATTTACTTAGGTTATAGTATTAATTGTTC
21616610 AGTCAGATTTACTTAGGTTATAGTATTAATTGTTC
1 AGTCAGATTTACTTAGGTTATAGTATTAATTGTTC
21616645 TGTTACTAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.46
Consensus pattern (35 bp):
AGTCAGATTTACTTAGGTTATAGTATTAATTGTTC
Found at i:21620539 original size:25 final size:23
Alignment explanation
Indices: 21620511--21620559 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
21620501 TTTTATGTTA
*
21620511 ATATAAATTATAATACGTAATTTTT
1 ATATAAAATATAATA--TAATTTTT
21620536 ATATAAAATATAATATAATTTTT
1 ATATAAAATATAATATAATTTTT
21620559 A
1 A
21620560 ATATTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
25 14 0.61
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATAAAATATAATATAATTTTT
Found at i:21620575 original size:155 final size:159
Alignment explanation
Indices: 21620319--21620628 Score: 468
Period size: 163 Copynumber: 1.9 Consensus size: 159
21620309 TTAACAAAAC
*
21620319 AAAAAGTATATATTTTATATTTTATGTTGACATAAATTATAATACGTAATTTTTATATAAAATAC
1 AAAAAGTATATATTTTATATTTTATGTTAACATAAATTATAATACGTAATTTTTATATAAAATA-
21620384 GATACAAATATATAATTTTTAATATTTAATTCGACACAAAATCTATAC-AAAAGCCATAATTTTT
65 -AT---AATATATAATTTTTAATATTTAATTCGACACAAAATCTATACAAAAAGCCATAATTTTT
**
21620448 ATCTATATTTATATTTTCTTTAAAAAGAAAATCT
126 ATCTATAAATATATTTTCTTTAAAAAGAAAATCT
*
21620482 AAAAA-TATATATTTTATATTTTTATGTTAATATAAATTATAATACGTAATTTTTATATAAAAT-
1 AAAAAGTATATATTTTATA-TTTTATGTTAACATAAATTATAATACGTAATTTTTATATAAAATA
*
21620545 AT-A-ATATAATTTTTAATATTTGATTCGACACAAAATCTATACAAAAAAGCCATAATTTTTATC
65 ATAATATATAATTTTTAATATTTAATTCGACACAAAATCTATAC-AAAAAGCCATAATTTTTATC
*
21620608 TATAAATATCTTTTCTTTAAA
129 TATAAATATATTTTCTTTAAA
21620629 GGGGGAATCT
Statistics
Matches: 138, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
155 38 0.28
156 1 0.01
157 37 0.27
160 2 0.01
162 13 0.09
163 47 0.34
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (159 bp):
AAAAAGTATATATTTTATATTTTATGTTAACATAAATTATAATACGTAATTTTTATATAAAATAA
TAATATATAATTTTTAATATTTAATTCGACACAAAATCTATACAAAAAGCCATAATTTTTATCTA
TAAATATATTTTCTTTAAAAAGAAAATCT
Found at i:21622054 original size:26 final size:28
Alignment explanation
Indices: 21621996--21622055 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
21621986 GTAATTGAAT
* *
21621996 AGATAGAAGATAGATATATAATATTATA
1 AGATATAAGATAGATATATAAGATTATA
*
21622024 A-ATATAA-ATAGATATAT-AGATTGTA
1 AGATATAAGATAGATATATAAGATTATA
21622049 AGATATA
1 AGATATA
21622056 GTTTTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 15 0.54
27 5 0.18
28 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (28 bp):
AGATATAAGATAGATATATAAGATTATA
Found at i:21637324 original size:24 final size:24
Alignment explanation
Indices: 21637262--21637350 Score: 60
Period size: 24 Copynumber: 3.7 Consensus size: 24
21637252 GAACCCATAA
* *
21637262 ATTTTAAT-ATTTATATTTAATAT
1 ATTTTAATAAATTAAATTTAATAT
* * *
21637285 ATTATCAATATA-TAAATTTTATAT
1 ATT-TTAATAAATTAAATTTAATAT
*
21637309 ATTTTAATAAATTAAATAATAATAT
1 ATTTTAATAAATTAAAT-TTAATAT
21637334 -TTCATTAATAAA-TAAAT
1 ATT--TTAATAAATTAAAT
21637351 ATACATAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
23 9 0.18
24 24 0.47
25 10 0.20
26 8 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTAATAAATTAAATTTAATAT
Found at i:21637419 original size:31 final size:31
Alignment explanation
Indices: 21637376--21637444 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
21637366 TTTTTAAAAA
* *
21637376 AATTTA-TTCATTAATAAAATATTATTATTT
1 AATTTATTTCATTAATAAAATATCATCATTT
* *
21637406 GATTTATTTCATTAATAAATTATCATCATTT
1 AATTTATTTCATTAATAAAATATCATCATTT
21637437 AATTTATT
1 AATTTATT
21637445 AACGATGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (31 bp):
AATTTATTTCATTAATAAAATATCATCATTT
Found at i:21638557 original size:14 final size:14
Alignment explanation
Indices: 21638516--21638559 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
21638506 AAAATATTTA
* *
21638516 ATAAATAAATTACT
1 ATAAATAAATAAAT
*
21638530 ATAAATTGAATAAAT
1 ATAAA-TAAATAAAT
21638545 ATAAATAAATAAAT
1 ATAAATAAATAAAT
21638559 A
1 A
21638560 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
ATAAATAAATAAAT
Found at i:21639170 original size:23 final size:23
Alignment explanation
Indices: 21639137--21639182 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21639127 TTTTTATCTT
* *
21639137 TTTTTTTATTTTTAATTAATTAA
1 TTTTTTAATTTTTAATAAATTAA
*
21639160 TTTTTTAATTTTTTATAAATTAA
1 TTTTTTAATTTTTAATAAATTAA
21639183 ACATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTAATTTTTAATAAATTAA
Found at i:21639238 original size:16 final size:17
Alignment explanation
Indices: 21639217--21639264 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
21639207 TTATTATTTT
*
21639217 TTATTATTTATTAATAAAA
1 TTATTATTTAAT-AT-AAA
21639236 TTATTATTTAATATAAA
1 TTATTATTTAATATAAA
*
21639253 -TATAATTTAATA
1 TTATTATTTAATA
21639265 ATTTTTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 2 0.07
19 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATTATTTAATATAAA
Found at i:21644581 original size:193 final size:195
Alignment explanation
Indices: 21644239--21644601 Score: 570
Period size: 193 Copynumber: 1.9 Consensus size: 195
21644229 TTCATTTATA
* *
21644239 AAATTAAAAATTATGAAGATAATATATTTGATACTTTTCAAATATAATTTTTTTAATTTCTACCA
1 AAATTAAAAATTATGAAGATAATATATTTGATAATTTTCAAATATAATTTTTTTAATTCCTACCA
* *
21644304 AATGTTTGGATTTTTTAAATATGCCAATTCTCTTGGTATGGAAGAAATCTCTACCAATTCTTTGG
66 AATGTTTGGATTTTTTAAATATGCCAATTCTCTAGGTATGGAAGAAATCTCTACCAATTATTTGG
21644369 TTTTTTAGATATACCAATTCACACATCTTATCATGTAAAATATTGATATTATATATATATATATG
131 TTTTTTAGATATACCAATTCACACATCTTATCATGTAAAATATTGATATTATATATATATATATG
*
21644434 AAATTAAAAATTAT-ATTGATAATATATTTGATAATTTTC-AA-ATAATTTTTTTAATTCCTACC
1 AAATTAAAAATTATGA-AGATAATATATTTGATAATTTTCAAATATAATTTTTTTAATTCCTACC
* * * *
21644496 AAATGTTTGGTTTTTTTAGATATTCCAATTCTCTAGGTATGGAGGAAATCTCTACCAATTATTTG
65 AAATGTTTGGATTTTTTAAATATGCCAATTCTCTAGGTATGGAAGAAATCTCTACCAATTATTTG
* * ** *
21644561 GTTTTTTAGGTATGCCAATTCATGCATTTTATCATGTAAAA
130 GTTTTTTAGATATACCAATTCACACATCTTATCATGTAAAA
21644602 CGTTAATAAT
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
193 115 0.75
194 3 0.02
195 35 0.23
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (195 bp):
AAATTAAAAATTATGAAGATAATATATTTGATAATTTTCAAATATAATTTTTTTAATTCCTACCA
AATGTTTGGATTTTTTAAATATGCCAATTCTCTAGGTATGGAAGAAATCTCTACCAATTATTTGG
TTTTTTAGATATACCAATTCACACATCTTATCATGTAAAATATTGATATTATATATATATATATG
Found at i:21647727 original size:18 final size:18
Alignment explanation
Indices: 21647683--21647730 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
21647673 GACTCGATTA
* *
21647683 TATATATTTAAATTATTTT
1 TATATATTT-ATTTAATTT
21647702 TA-ATTATTTATTTAATTT
1 TATA-TATTTATTTAATTT
21647720 TATATATTTAT
1 TATATATTTAT
21647731 ATTTATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATTTATTTAATTT
Found at i:21650217 original size:29 final size:28
Alignment explanation
Indices: 21650165--21650222 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
21650155 TCAATTAATT
21650165 TCGAATTAAATTATCTAAAATTTAATTAA
1 TCGAATTAAATTATCTAAAATTT-ATTAA
* * **
21650194 TCGAATTATATTATTTAATTTTTATTAA
1 TCGAATTAAATTATCTAAAATTTATTAA
21650222 T
1 T
21650223 ATAATTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (28 bp):
TCGAATTAAATTATCTAAAATTTATTAA
Found at i:21650470 original size:16 final size:16
Alignment explanation
Indices: 21650451--21650485 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21650441 TAATATATTT
*
21650451 TTATTTTATATTTGAA
1 TTATATTATATTTGAA
*
21650467 TTATATTATATTTTAA
1 TTATATTATATTTGAA
21650483 TTA
1 TTA
21650486 AAATTTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTATATTATATTTGAA
Found at i:21652149 original size:30 final size:28
Alignment explanation
Indices: 21652095--21652161 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 28
21652085 TTTATTTATA
21652095 AAATAAATTTTATATTTTTATTATATTT
1 AAATAAATTTTATATTTTTATTATATTT
*
21652123 TAATAAATTTT-TATTATTTAATTTATATTT
1 AAATAAATTTTATATT-TTT-A-TTATATTT
21652153 AAATAAATT
1 AAATAAATT
21652162 ATTGATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 4 0.12
28 13 0.38
29 1 0.03
30 16 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
AAATAAATTTTATATTTTTATTATATTT
Found at i:21652153 original size:29 final size:29
Alignment explanation
Indices: 21652080--21652161 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
21652070 AAGTTATTGA
*
21652080 ATTATTTTATTTATA--AAATAAATTTTAT
1 ATTA-TTTATTTATATTTAATAAATTTTAT
21652108 ATT-TTTA-TTATATTTTAATAAATTTT-T
1 ATTATTTATTTATA-TTTAATAAATTTTAT
21652135 ATTATTTAATTTATATTTAAATAAATT
1 ATTATTT-ATTTATATTT-AATAAATT
21652162 ATTGATTTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
25 5 0.11
26 4 0.09
27 4 0.09
28 16 0.35
29 4 0.09
30 13 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTATTTATTTATATTTAATAAATTTTAT
Found at i:21652212 original size:30 final size:30
Alignment explanation
Indices: 21652173--21652245 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
21652163 TTGATTTATG
*
21652173 TTAAAGGTTTAATTAGG-TACCAATAAAAAA
1 TTAAAGGTTT-ATTAGGATACAAATAAAAAA
* * *
21652203 TTAAGGGTTTATTTGGATGCAAATAAAAAA
1 TTAAAGGTTTATTAGGATACAAATAAAAAA
*
21652233 TTAAAGATTTATT
1 TTAAAGGTTTATT
21652246 TAAATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (30 bp):
TTAAAGGTTTATTAGGATACAAATAAAAAA
Found at i:21659144 original size:22 final size:20
Alignment explanation
Indices: 21659103--21659157 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
21659093 AAATCATATA
21659103 AATGTATAAT-AATAAATTAT
1 AATG-ATAATAAATAAATTAT
*
21659123 ATTGATAATAAATAACATTTAT
1 AATGATAATAAATAA-A-TTAT
*
21659145 AATGATAAGAAAT
1 AATGATAATAAAT
21659158 TATATGATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 1 0.03
22 15 0.52
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
AATGATAATAAATAAATTAT
Found at i:21659743 original size:27 final size:28
Alignment explanation
Indices: 21659704--21659762 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
21659694 TCAATAATTT
* *
21659704 TAATAAGTCATTTAATATAA-TATAATA
1 TAATAAATAATTTAATATAATTATAATA
* * *
21659731 TAATAAATAATTTATTTTAATTATATTA
1 TAATAAATAATTTAATATAATTATAATA
21659759 TAAT
1 TAAT
21659763 GTATAAATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TAATAAATAATTTAATATAATTATAATA
Found at i:21660170 original size:22 final size:23
Alignment explanation
Indices: 21660134--21660192 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
21660124 ATAAATATAC
*
21660134 AATAATTTATTATAATGATAATA
1 AATAATATATTATAATGATAATA
21660157 AATAATAT-TTATAATGATAA-A
1 AATAATATATTATAATGATAATA
* *
21660178 AA-AATTTATGATAAT
1 AATAATATATTATAAT
21660193 ATTAATAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 9 0.28
22 12 0.38
23 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AATAATATATTATAATGATAATA
Found at i:21661349 original size:18 final size:18
Alignment explanation
Indices: 21661320--21661370 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
21661310 TATTTTGTTC
21661320 ATATTTTA-AATTTAAAT
1 ATATTTTATAATTTAAAT
*
21661337 ATATTTTATAATTTATAT
1 ATATTTTATAATTTAAAT
*
21661355 -TATGTTTATATTTTAA
1 ATAT-TTTATAATTTAA
21661371 TAATTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATATTTTATAATTTAAAT
Found at i:21663880 original size:15 final size:16
Alignment explanation
Indices: 21663860--21663899 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
21663850 AAAATTTTAT
21663860 AAATATT-TTTATTAA
1 AAATATTATTTATTAA
21663875 AAATATTTATTTATTAA
1 AAATA-TTATTTATTAA
*
21663892 ATATATTA
1 AAATATTA
21663900 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTATTTATTAA
Found at i:21664819 original size:24 final size:23
Alignment explanation
Indices: 21664774--21664819 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21664764 GATTTTTTTT
* *
21664774 ATAAAAGAAATCATAGTCTTAAA
1 ATAAAAAAAATCATAGTATTAAA
*
21664797 ATAAAAAAAATTATAAGTATTAA
1 ATAAAAAAAATCAT-AGTATTAA
21664820 GATTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (23 bp):
ATAAAAAAAATCATAGTATTAAA
Found at i:21668786 original size:3 final size:3
Alignment explanation
Indices: 21668769--21668811 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
21668759 ATACACACAT
*
21668769 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
21668812 TTTTGGTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21671569 original size:21 final size:24
Alignment explanation
Indices: 21671544--21671590 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
21671534 TCATTAAATA
21671544 TTATTAAAAT-ATTTT-ATAT-TT
1 TTATTAAAATAATTTTAATATGTT
*
21671565 TTATTAATATAATTTTAATATGTT
1 TTATTAAAATAATTTTAATATGTT
21671589 TT
1 TT
21671591 TATCTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 5 0.23
23 4 0.18
24 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTAAAATAATTTTAATATGTT
Found at i:21672984 original size:6 final size:6
Alignment explanation
Indices: 21672975--21673010 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
21672965 ATATTTGCGG
21672975 TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA
1 TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA
21673011 CTTCTTCGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
TGACGA
Found at i:21675820 original size:3 final size:3
Alignment explanation
Indices: 21675812--21675836 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21675802 CAGAAAAAAC
21675812 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
21675837 AAAGCCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:21680853 original size:18 final size:18
Alignment explanation
Indices: 21680830--21680865 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21680820 GGACTGATTT
*
21680830 ATTATAATATATTTTTTA
1 ATTATAAAATATTTTTTA
*
21680848 ATTATAAAATTTTTTTTA
1 ATTATAAAATATTTTTTA
21680866 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATAAAATATTTTTTA
Found at i:21683545 original size:37 final size:38
Alignment explanation
Indices: 21683499--21683578 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
21683489 GTACTTTAAC
* * *
21683499 TTTTCTTTTTCTGGATAACATGAGT-CTGAACTTTTTTT
1 TTTTTTTTTTCT-GATAACATGAGTCCGGAACTTTTTAT
21683537 TTTTTTTTTTCTGATAACATGAGTCCGGAAC-TTTTAT
1 TTTTTTTTTTCTGATAACATGAGTCCGGAACTTTTTAT
21683574 TTTTT
1 TTTTT
21683579 CATGATAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 22 0.58
38 16 0.42
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (38 bp):
TTTTTTTTTTCTGATAACATGAGTCCGGAACTTTTTAT
Found at i:21683568 original size:38 final size:38
Alignment explanation
Indices: 21683499--21683579 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
21683489 GTACTTTAAC
* *
21683499 TTTTCTTTTTCTGGATAACATGAGTCTGAACTTTTTTT
1 TTTTCTTTTTCTGGATAACATGAGTCGGAACTTTTATT
*
21683537 TTTTTTTTTTCT-GATAACATGAGTCCGGAACTTTTATT
1 TTTTCTTTTTCTGGATAACATGAGT-CGGAACTTTTATT
21683575 TTTTC
1 TTTTC
21683580 ATGATAACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 12 0.32
38 26 0.68
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (38 bp):
TTTTCTTTTTCTGGATAACATGAGTCGGAACTTTTATT
Found at i:21683978 original size:57 final size:57
Alignment explanation
Indices: 21683886--21684055 Score: 216
Period size: 57 Copynumber: 3.0 Consensus size: 57
21683876 AGAGAATAAG
* *
21683886 GGGGACAGACGTGACAAAGTCTCCTTCGTCTTGCATACTTCCATCCAATCCATTGAC
1 GGGGACAGACGTGACAAAGTCTCCTTCGCCATGCATACTTCCATCCAATCCATTGAC
* * * * * * *
21683943 TGGTACAGACGTGACAAAGTCTCCTTTGGCATGCATACTTCCATCCGATTCATGGAC
1 GGGGACAGACGTGACAAAGTCTCCTTCGCCATGCATACTTCCATCCAATCCATTGAC
* * *
21684000 GGGGACAGAC-TCGACAAACTTTCCTTCGCCATGCATACTTCCATCCAATCCTTTGA
1 GGGGACAGACGT-GACAAAGTCTCCTTCGCCATGCATACTTCCATCCAATCCATTGA
21684056 GGACATCTGA
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 1 0.01
57 93 0.99
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (57 bp):
GGGGACAGACGTGACAAAGTCTCCTTCGCCATGCATACTTCCATCCAATCCATTGAC
Found at i:21690091 original size:2 final size:2
Alignment explanation
Indices: 21690084--21690117 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
21690074 AATATACGTT
*
21690084 TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
21690118 TAAAATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21690929 original size:29 final size:31
Alignment explanation
Indices: 21690863--21690921 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
21690853 TTTGTTAATG
*
21690863 AAAATAAAAAAAATTACAATATAAATAATTAA
1 AAAATAAAAAAAATTA-AATATAAAAAATTAA
21690895 AAAATAAAAAAAA-T-AATATAAAAAATT
1 AAAATAAAAAAAATTAAATATAAAAAATT
21690922 TTAGAATACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
31 1 0.04
32 13 0.50
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (31 bp):
AAAATAAAAAAAATTAAATATAAAAAATTAA
Found at i:21691152 original size:16 final size:16
Alignment explanation
Indices: 21691133--21691169 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21691123 TATTTTTAAA
21691133 TAAAAATA-AAATAACT
1 TAAAAATATAAATAA-T
21691149 T-AAAATATAAATAAT
1 TAAAAATATAAATAAT
21691164 TAAAAA
1 TAAAAA
21691170 ATTAAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATATAAATAAT
Found at i:21691174 original size:23 final size:23
Alignment explanation
Indices: 21691132--21691189 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
21691122 ATATTTTTAA
21691132 ATAAAAATAAAATAACTTAAAAT
1 ATAAAAATAAAATAACTTAAAAT
21691155 ATAAATAATTAAAA-AA-TTAAAA-
1 ATAAA-AA-TAAAATAACTTAAAAT
*
21691177 AGTAAAAAAAAAA
1 A-TAAAAATAAAA
21691190 ATCGGATCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 15 0.48
24 4 0.13
25 5 0.16
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (23 bp):
ATAAAAATAAAATAACTTAAAAT
Found at i:21691175 original size:16 final size:16
Alignment explanation
Indices: 21691134--21691185 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
21691124 ATTTTTAAAT
*
21691134 AAAAATAAAATAACTTA
1 AAAAATTAAATAA-TTA
*
21691151 AAATA-TAAATAATTA
1 AAAAATTAAATAATTA
*
21691166 AAAAATTAAA-AAGTA
1 AAAAATTAAATAATTA
21691181 AAAAA
1 AAAAA
21691186 AAAAATCGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 16 0.53
16 10 0.33
17 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAATTAAATAATTA
Found at i:21696812 original size:22 final size:22
Alignment explanation
Indices: 21696776--21696818 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21696766 ATTTTTGTCT
*
21696776 TTAATTCTAGGGATATAAATAC
1 TTAATTCTAGAGATATAAATAC
*
21696798 TTAATTTTAGAGATATAAATA
1 TTAATTCTAGAGATATAAATA
21696819 TAAATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
TTAATTCTAGAGATATAAATAC
Found at i:21700516 original size:24 final size:25
Alignment explanation
Indices: 21700489--21700542 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
21700479 TAGAATGGTT
21700489 ATGAAAGCCTTAACA-GGTTCAACA
1 ATGAAAGCCTTAACAGGGTTCAACA
* *
21700513 ATGAAGGCCTTAACAGGGTTCGACA
1 ATGAAAGCCTTAACAGGGTTCAACA
21700538 ATGAA
1 ATGAA
21700543 GGTCTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (25 bp):
ATGAAAGCCTTAACAGGGTTCAACA
Found at i:21700538 original size:25 final size:24
Alignment explanation
Indices: 21700489--21700544 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
21700479 TAGAATGGTT
*
21700489 ATGAAAGCCTTAACAGGTTCAACA
1 ATGAAGGCCTTAACAGGTTCAACA
*
21700513 ATGAAGGCCTTAACAGGGTTCGACA
1 ATGAAGGCCTTAACA-GGTTCAACA
21700538 ATGAAGG
1 ATGAAGG
21700545 TCTAAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.20
Consensus pattern (24 bp):
ATGAAGGCCTTAACAGGTTCAACA
Found at i:21700832 original size:22 final size:22
Alignment explanation
Indices: 21700807--21700850 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21700797 ACTTTTTGTC
* *
21700807 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATAAAAATA
21700829 CTTAATTCTAGAGATAAAAATA
1 CTTAATTCTAGAGATAAAAATA
21700851 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATAAAAATA
Found at i:21705721 original size:240 final size:240
Alignment explanation
Indices: 21705298--21705777 Score: 933
Period size: 240 Copynumber: 2.0 Consensus size: 240
21705288 CACCGACATG
21705298 TACAAGGTTGTCTGGCTACAAAGCAAGTACAGCGATCAGATGATGACCCAACAATATTTGAGATC
1 TACAAGGTTGTCTGGCTACAAAGCAAGTACAGCGATCAGATGATGACCCAACAATATTTGAGATC
*
21705363 GCTTACCGCGGAAGGCATACTTGTACTCTAGGCTCACATGTAGTGCCTTCTCTAGGACCCTTGAA
66 ACTTACCGCGGAAGGCATACTTGTACTCTAGGCTCACATGTAGTGCCTTCTCTAGGACCCTTGAA
21705428 AAATCAAGACCAAGGAAACTTTTCTGCTTCGTCCACTACATCCGGTATTACATATTGCTCCACGA
131 AAATCAAGACCAAGGAAACTTTTCTGCTTCGTCCACTACATCCGGTATTACATATTGCTCCACGA
* *
21705493 GCCCAACTCCAAGTCCGAGCGGGATGAACCCCATCGTGCAGGAAA
196 GCCCAACTCCAAGTCCAAGCGGAATGAACCCCATCGTGCAGGAAA
21705538 TACAAGGTTGTCTGGCTACAAAGCAAGTACAGCGATCAGATGATGACCCAACAATATTTGAGATC
1 TACAAGGTTGTCTGGCTACAAAGCAAGTACAGCGATCAGATGATGACCCAACAATATTTGAGATC
21705603 ACTTACCGCGGAAGGCATACTTGTACTCTAGGCTCACATGTAGTGCCTTCTCTAGGACCCTTGAA
66 ACTTACCGCGGAAGGCATACTTGTACTCTAGGCTCACATGTAGTGCCTTCTCTAGGACCCTTGAA
21705668 AAATCAAGACCAAGGAAACTTTTCTGCTTCGTCCACTACATCCGGTATTACATATTGCTCCACGA
131 AAATCAAGACCAAGGAAACTTTTCTGCTTCGTCCACTACATCCGGTATTACATATTGCTCCACGA
21705733 GCCCAACTCCAAGTCCAAGCGGAATGAACCCCATCGTGCAGGAAA
196 GCCCAACTCCAAGTCCAAGCGGAATGAACCCCATCGTGCAGGAAA
21705778 ACATTGACTT
Statistics
Matches: 237, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
240 237 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (240 bp):
TACAAGGTTGTCTGGCTACAAAGCAAGTACAGCGATCAGATGATGACCCAACAATATTTGAGATC
ACTTACCGCGGAAGGCATACTTGTACTCTAGGCTCACATGTAGTGCCTTCTCTAGGACCCTTGAA
AAATCAAGACCAAGGAAACTTTTCTGCTTCGTCCACTACATCCGGTATTACATATTGCTCCACGA
GCCCAACTCCAAGTCCAAGCGGAATGAACCCCATCGTGCAGGAAA
Found at i:21706826 original size:20 final size:20
Alignment explanation
Indices: 21706801--21706839 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
21706791 CAGCTTCTTT
21706801 CTTTGTTTTAACTTTCTTCC
1 CTTTGTTTTAACTTTCTTCC
21706821 CTTTGTTTTAACTTTCTTC
1 CTTTGTTTTAACTTTCTTC
21706840 ATTAAAAAAT
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:0.23, G:0.05, T:0.62
Consensus pattern (20 bp):
CTTTGTTTTAACTTTCTTCC
Found at i:21711573 original size:18 final size:18
Alignment explanation
Indices: 21711546--21711580 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21711536 ATCTTTTATC
* *
21711546 TTCAATATTTCAGATCAT
1 TTCAAAATTTCAAATCAT
21711564 TTCAAAATTTCAAATCA
1 TTCAAAATTTCAAATCA
21711581 AAGTCAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (18 bp):
TTCAAAATTTCAAATCAT
Found at i:21717364 original size:17 final size:16
Alignment explanation
Indices: 21717342--21717374 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
21717332 CTCCCACTTG
21717342 TCTTTGTAATTGTTTTC
1 TCTTTGTAATT-TTTTC
21717359 TCTTTGTAATTTTTTC
1 TCTTTGTAATTTTTTC
21717375 AAATCTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.67
Consensus pattern (16 bp):
TCTTTGTAATTTTTTC
Found at i:21726333 original size:18 final size:18
Alignment explanation
Indices: 21726310--21726347 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21726300 AACAGAGGTG
21726310 CTGTAAGAACCATAATCA
1 CTGTAAGAACCATAATCA
* *
21726328 CTGTAAGGATCATAATCA
1 CTGTAAGAACCATAATCA
21726346 CT
1 CT
21726348 ATAATTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (18 bp):
CTGTAAGAACCATAATCA
Found at i:21730468 original size:24 final size:25
Alignment explanation
Indices: 21730441--21730491 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
21730431 TATTTTTATG
*
21730441 AATTTATTAATTTTAAT-AAAAATA
1 AATTTATTAATATTAATAAAAAATA
**
21730465 AATTTATTTGTATTAATAAAAAATA
1 AATTTATTAATATTAATAAAAAATA
21730490 AA
1 AA
21730492 ATATCCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AATTTATTAATATTAATAAAAAATA
Found at i:21732478 original size:30 final size:30
Alignment explanation
Indices: 21732444--21732503 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
21732434 TCTAATCAAG
* *
21732444 AATTTAATTGGATGAAAATATATATTTAAA
1 AATTTAATTGAATAAAAATATATATTTAAA
*
21732474 AATTTAATTGAATAAAAATATATGTTTAAA
1 AATTTAATTGAATAAAAATATATATTTAAA
21732504 GGTCAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (30 bp):
AATTTAATTGAATAAAAATATATATTTAAA
Found at i:21732586 original size:19 final size:21
Alignment explanation
Indices: 21732536--21732587 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
21732526 AATTGATGAT
21732536 TTAAATATTTATAATAAAATA
1 TTAAATATTTATAATAAAATA
* *
21732557 TTAAAAATTTA-AAT-AATTA
1 TTAAATATTTATAATAAAATA
*
21732576 TTAAATTTTTAT
1 TTAAATATTTAT
21732588 TTGAACGTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.50
20 3 0.12
21 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATATTTATAATAAAATA
Found at i:21734517 original size:18 final size:18
Alignment explanation
Indices: 21734464--21734518 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
21734454 ACAGAGGTAT
* *
21734464 TGTAAGAACCATAATCAA
1 TGTAAGGACCATAATCAC
*
21734482 TGTAAGGAACATAATCAC
1 TGTAAGGACCATAATCAC
21734500 TGTAAGGACCATAATCAC
1 TGTAAGGACCATAATCAC
21734518 T
1 T
21734519 AGAATTATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (18 bp):
TGTAAGGACCATAATCAC
Found at i:21740259 original size:2 final size:2
Alignment explanation
Indices: 21740252--21740282 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21740242 TCTTCTCATT
21740252 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21740283 TCCTTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21740516 original size:30 final size:30
Alignment explanation
Indices: 21740482--21740541 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
21740472 TCTAATTGAG
21740482 AATTTAATTGAAT-AACAATAAATATTTAAA
1 AATTTAATTGAATGAA-AATAAATATTTAAA
* *
21740512 AATTTAATTGAATGAAAATATATGTTTAAA
1 AATTTAATTGAATGAAAATAAATATTTAAA
21740542 GGTTAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (30 bp):
AATTTAATTGAATGAAAATAAATATTTAAA
Found at i:21749064 original size:32 final size:32
Alignment explanation
Indices: 21749021--21749083 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
21749011 CAAATGATAT
21749021 GATAAACAATAGTAATACCCATCCTAGGAAAG
1 GATAAACAATAGTAATACCCATCCTAGGAAAG
*
21749053 GATAAATAATAGTAATACCCATCCTAGGAAA
1 GATAAACAATAGTAATACCCATCCTAGGAAA
21749084 ATGTGTCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (32 bp):
GATAAACAATAGTAATACCCATCCTAGGAAAG
Found at i:21755952 original size:57 final size:55
Alignment explanation
Indices: 21755787--21756053 Score: 177
Period size: 57 Copynumber: 4.7 Consensus size: 55
21755777 AATTCTAAGG
* * * * *
21755787 AAAAATTGATACTTTCAACTTTTTCC-TCAAACA-TTTCTGAGATTTTCTTTA---A
1 AAAAATTGATA-TTTCAAC-ATTTCCTTAAAACATTTTTTGAAATTTTTTTTATTTA
* * * * * *
21755839 AGAAAATCGATACTTCAACTTTTTCTTAAAAATATTTTTTTGAAATATTGTTTTATTTGA
1 A-AAAATTGATATTTCAACATTTCCTT-AAAACA-TTTTTTGAAAT-TTTTTTTATTT-A
* *
21755899 AAAAATTGATATTTCAAAATTTCCTTACTAACATTTTTTGAAATTTTTTTTA-TTA
1 AAAAATTGATATTTCAACATTTCCTTA-AAACATTTTTTGAAATTTTTTTTATTTA
* * * * *
21755954 AAGGAAATTGATATTTCGACTTTTCCTCAAAAACATTTTCTTTTGGAATATTTTTTATTTA
1 AA--AAATTGATATTTCAACATTTCCT-TAAAACA--TT-TTTTGAAATTTTTTTTATTTA
*
21756015 AGGAAAATTGATACTTCAACATTTCCTTAAAACATTTTT
1 A--AAAATTGATATTTCAACATTTCCTTAAAACATTTTT
21756054 AAAATTATAT
Statistics
Matches: 167, Mismatches: 28, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
51 5 0.03
52 8 0.05
53 13 0.08
55 11 0.07
56 8 0.05
57 34 0.20
58 15 0.09
59 25 0.15
60 23 0.14
61 24 0.14
63 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (55 bp):
AAAAATTGATATTTCAACATTTCCTTAAAACATTTTTTGAAATTTTTTTTATTTA
Found at i:21756040 original size:61 final size:59
Alignment explanation
Indices: 21755829--21756053 Score: 226
Period size: 60 Copynumber: 3.8 Consensus size: 59
21755819 ATTTCTGAGA
* * * * * *
21755829 TTTTCTTTAAAGAAAATCGATACTTCAACTTTTTCTTAAAAATATTTTTTTGAAATATT
1 TTTTATTTAAGGAAAATTGATACTTCAACATTTCCTTAAAAACATTTTTTTGAAATATT
* * ** *
21755888 GTTTTATTTGAA--AAAATTGATATTTCAAAATTTCCTTACTAACA-TTTTTTGAAATTTT
1 -TTTTATTT-AAGGAAAATTGATACTTCAACATTTCCTTAAAAACATTTTTTTGAAATATT
* * * * * *
21755946 TTTTATTAAAGG-AAATTGATATTTCGACTTTTCCTCAAAAACATTTTCTTTTGGAATATT
1 TTTTATTTAAGGAAAATTGATACTTCAACATTTCCTTAAAAACA-TTT-TTTTGAAATATT
21756006 TTTTATTTAAGGAAAATTGATACTTCAACATTTCCTT-AAAACATTTTT
1 TTTTATTTAAGGAAAATTGATACTTCAACATTTCCTTAAAAACATTTTT
21756054 AAAATTATAT
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
56 2 0.01
57 32 0.24
58 15 0.11
59 29 0.22
60 34 0.25
61 22 0.16
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (59 bp):
TTTTATTTAAGGAAAATTGATACTTCAACATTTCCTTAAAAACATTTTTTTGAAATATT
Found at i:21756041 original size:118 final size:115
Alignment explanation
Indices: 21755835--21756053 Score: 280
Period size: 118 Copynumber: 1.9 Consensus size: 115
21755825 GAGATTTTCT
* * *
21755835 TTAAAGAAAATCGATACTTCAACTTTTTCTTAAAAATATTTTTTTGAAATATTGTTTTATTTGAA
1 TTAAAGAAAATCGATACTTCAACTTTTCCTCAAAAACATTTTTTTGAAATATTGTTTTATTTGAA
* *
21755900 AAAATTGATATTTCAAAATTTCCTTACTAACATTTTTTGAAATTTTTTTTA
66 AAAATTGATACTTCAAAATTTCCTTA-AAACATTTTTTGAAATTTTTTTTA
* * * * *
21755951 TTAAAGGAAATTGATATTTCGACTTTTCCTCAAAAACATTTTCTTTTGGAATATT-TTTTATTT-
1 TTAAAGAAAATCGATACTTCAACTTTTCCTCAAAAACA-TTT-TTTTGAAATATTGTTTTATTTG
*
21756014 AAGGAAAATTGATACTTCAACATTTCCTTAAAACATTTTT
64 AA--AAAATTGATACTTCAAAATTTCCTTAAAACATTTTT
21756054 AAAATTATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
116 33 0.38
117 20 0.23
118 35 0.40
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (115 bp):
TTAAAGAAAATCGATACTTCAACTTTTCCTCAAAAACATTTTTTTGAAATATTGTTTTATTTGAA
AAAATTGATACTTCAAAATTTCCTTAAAACATTTTTTGAAATTTTTTTTA
Found at i:21756067 original size:118 final size:116
Alignment explanation
Indices: 21755835--21756068 Score: 278
Period size: 116 Copynumber: 2.0 Consensus size: 116
21755825 GAGATTTTCT
* * *
21755835 TTAAAGAAAATCGATACTTCAACTTTTTCTTAAAAATATTTTTTTGAAATATTGTTTTATTTGAA
1 TTAAAGAAAATCGATACTTCAACTTTTCCTCAAAAACATTTTTTTGAAATATTGTTTTATTTGAA
* * *
21755900 AAAATTGATATTTCAAAATTTCCTTACTAACATTTTTTGAAATTTTTTTTA
66 AAAATTGATACTTCAAAATTTCCTTACAAACATTTTTTAAAATTTTTTTTA
* * * * *
21755951 TTAAAGGAAATTGATATTTCGACTTTTCCTCAAAAACATTTTCTTTTGGAATATT-TTTTATTT-
1 TTAAAGAAAATCGATACTTCAACTTTTCCTCAAAAACA-TTT-TTTTGAAATATTGTTTTATTTG
*
21756014 AAGGAAAATTGATACTTCAACATTTCCTTA-AAACA-TTTTTAAAATTATATTTTTA
64 AA--AAAATTGATACTTCAAAATTTCCTTACAAACATTTTTTAAAATT-T-TTTTTA
21756069 GGGAAAAATT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
116 43 0.43
117 16 0.16
118 41 0.41
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (116 bp):
TTAAAGAAAATCGATACTTCAACTTTTCCTCAAAAACATTTTTTTGAAATATTGTTTTATTTGAA
AAAATTGATACTTCAAAATTTCCTTACAAACATTTTTTAAAATTTTTTTTA
Found at i:21756964 original size:63 final size:63
Alignment explanation
Indices: 21756857--21757000 Score: 216
Period size: 63 Copynumber: 2.3 Consensus size: 63
21756847 TCACAAAAAA
* * * * *
21756857 TTTGCAAAGATTTTAATATTTGCCAAAAGTCAATATTTGCAAAGGTTTGCAAGAATTCCAAGT
1 TTTGCAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGCAAAGGTTTGCAAGAATTCCAAGG
* *
21756920 TTTGTAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGTAAAGGTTTGCAAGAATTCCAAGG
1 TTTGCAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGCAAAGGTTTGCAAGAATTCCAAGG
*
21756983 TTCGCAAAGATTTCAAAA
1 TTTGCAAAGATTTCAAAA
21757001 GTTGCAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (63 bp):
TTTGCAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGCAAAGGTTTGCAAGAATTCCAAGG
Found at i:21757432 original size:35 final size:35
Alignment explanation
Indices: 21757393--21757469 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
21757383 CATGATGCGT
*
21757393 AAGAATTCAGA-TATTCACAAG-ATTTTCAAATTTGC
1 AAGAATTCAAACT-TTCACAAGAATTTT-AAATTTGC
* *
21757428 AAGAATTCAAACTTTCGCAAGAATTTTAGATTTGC
1 AAGAATTCAAACTTTCACAAGAATTTTAAATTTGC
21757463 AAGAATT
1 AAGAATT
21757470 TTTAGATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 31 0.84
36 6 0.16
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (35 bp):
AAGAATTCAAACTTTCACAAGAATTTTAAATTTGC
Found at i:21757449 original size:18 final size:16
Alignment explanation
Indices: 21757417--21757469 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
21757407 TCACAAGATT
21757417 TTCAAATTTGCAAGAA
1 TTCAAATTTGCAAGAA
21757433 TTCAAACTTTCGCAAGAA
1 TTCAAA-TTT-GCAAGAA
* *
21757451 TTTTAGATTTGCAAGAA
1 -TTCAAATTTGCAAGAA
21757468 TT
1 TT
21757470 TTTAGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 8 0.25
17 10 0.31
18 10 0.31
19 4 0.12
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (16 bp):
TTCAAATTTGCAAGAA
Found at i:21757474 original size:18 final size:17
Alignment explanation
Indices: 21757422--21757477 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
21757412 AGATTTTCAA
* *
21757422 ATTTGCAAGAA-TTCAA
1 ATTTGCAAGAATTTTAG
21757438 ACTTTCGCAAGAATTTTAG
1 A-TTT-GCAAGAATTTTAG
21757457 ATTTGCAAGAATTTTTAG
1 ATTTGCAAGAA-TTTTAG
21757475 ATT
1 ATT
21757478 AACAGGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 1 0.03
17 10 0.29
18 19 0.56
19 4 0.12
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (17 bp):
ATTTGCAAGAATTTTAG
Found at i:21757486 original size:18 final size:18
Alignment explanation
Indices: 21757445--21757487 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21757435 CAAACTTTCG
**
21757445 CAAGAA-TTTTAGATTTG
1 CAAGAATTTTTAGATTAA
21757462 CAAGAATTTTTAGATTAA
1 CAAGAATTTTTAGATTAA
*
21757480 CAGGAATT
1 CAAGAATT
21757488 ACAAGATTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (18 bp):
CAAGAATTTTTAGATTAA
Found at i:21757825 original size:21 final size:21
Alignment explanation
Indices: 21757783--21757827 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
21757773 TTTCATATCC
21757783 AAAAATTAAAGATTTTCCTTAA
1 AAAAATTAAAGATTTT-CTTAA
21757805 AAAAACTTAAAGATTTT-TTAA
1 AAAAA-TTAAAGATTTTCTTAA
21757826 AA
1 AA
21757828 TTTCAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 11 0.50
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAAATTAAAGATTTTCTTAA
Found at i:21757850 original size:23 final size:23
Alignment explanation
Indices: 21757824--21757895 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
21757814 AAGATTTTTT
21757824 AAAATTTCAAAAATTCACATTCA
1 AAAATTTCAAAAATTCACATTCA
* * * * *
21757847 AAAACTTT-AATACTTCATA-ACC
1 AAAA-TTTCAAAAATTCACATTCA
* *
21757869 AAAATTTCAAAGATTCTCATTCA
1 AAAATTTCAAAAATTCACATTCA
21757892 AAAA
1 AAAA
21757896 ATTTTGGGAT
Statistics
Matches: 34, Mismatches: 12, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
21 3 0.09
22 11 0.32
23 17 0.50
24 3 0.09
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (23 bp):
AAAATTTCAAAAATTCACATTCA
Found at i:21757893 original size:22 final size:22
Alignment explanation
Indices: 21757867--21757930 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
21757857 TACTTCATAA
21757867 CCAAAATTTCAAAGATTCTCATT
1 CCAAAATTTCAAAGATTCTCA-T
* *** *
21757890 CAAAAAATTT-TGGGATTCACAT
1 C-CAAAATTTCAAAGATTCTCAT
21757912 CCAAAATTTCAAAGATTCT
1 CCAAAATTTCAAAGATTCT
21757931 TATTTGAAAA
Statistics
Matches: 29, Mismatches: 10, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
21 7 0.24
22 7 0.24
23 8 0.28
24 7 0.24
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.33
Consensus pattern (22 bp):
CCAAAATTTCAAAGATTCTCAT
Found at i:21760170 original size:142 final size:142
Alignment explanation
Indices: 21759914--21760196 Score: 467
Period size: 142 Copynumber: 2.0 Consensus size: 142
21759904 GTGATTAGGC
*
21759914 AAAGGGTTTTTAGTGACATTCAACTCCCCTAATTCATTAAAGCTCACTGAACCTGCTCGAATCAA
1 AAAGGATTTTTAGTGACATTCAACTCCCCTAATTCATTAAAGCTCACTGAACCTGCTCGAATCAA
*
21759979 ACTTTGCACCTTGTGCTTAAAAACTGGGTAAGTTTATATAAAGTGACCTACATTCCATTATGATA
66 ACTTTGCACCTTGTACTTAAAAACTGGGTAAGTTTATATAAAGTGACCTACATTCCATTATGATA
21760044 ATCACATGTGGA
131 ATCACATGTGGA
* * * * * * *
21760056 AAAGGATTTTTTGTGACATTTAACTCCCTTGATTCCTTGAAGCTCACTGAACCTGTTCGAATCAA
1 AAAGGATTTTTAGTGACATTCAACTCCCCTAATTCATTAAAGCTCACTGAACCTGCTCGAATCAA
* *
21760121 ACTTTGCACCTTGTACTTAAAAACTGGGTAAGTTTTTATAAAGTGACCTACATTCCATTATGTTA
66 ACTTTGCACCTTGTACTTAAAAACTGGGTAAGTTTATATAAAGTGACCTACATTCCATTATGATA
21760186 ATCACATGTGG
131 ATCACATGTGG
21760197 CATTAATATT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
142 130 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (142 bp):
AAAGGATTTTTAGTGACATTCAACTCCCCTAATTCATTAAAGCTCACTGAACCTGCTCGAATCAA
ACTTTGCACCTTGTACTTAAAAACTGGGTAAGTTTATATAAAGTGACCTACATTCCATTATGATA
ATCACATGTGGA
Found at i:21763939 original size:23 final size:21
Alignment explanation
Indices: 21763903--21763947 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
21763893 AAGCATGCAA
21763903 ATAATATCATGCAATAATAAT
1 ATAATATCATGCAATAATAAT
21763924 ATAATATACCATGCAATAATAAT
1 ATAATAT--CATGCAATAATAAT
21763947 A
1 A
21763948 ACCAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
23 15 0.68
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (21 bp):
ATAATATCATGCAATAATAAT
Found at i:21764010 original size:21 final size:21
Alignment explanation
Indices: 21763984--21764041 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
21763974 ATAATATAAT
*
21763984 ATATAAATTATCATACAATTA
1 ATATAAAATATCATACAATTA
**
21764005 ATATAAAATATCATGTAATTA
1 ATATAAAATATCATACAATTA
*
21764026 AT-TAATAT-TCATACAA
1 ATATAAAATATCATACAA
21764042 AGATATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 20 0.65
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAAAATATCATACAATTA
Found at i:21764121 original size:3 final size:3
Alignment explanation
Indices: 21764113--21764175 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
21764103 TTTTAAATTT
21764113 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21764160 -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
21764176 CAACATAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:21764594 original size:14 final size:15
Alignment explanation
Indices: 21764567--21764595 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21764557 AAATTCATCT
21764567 TTTTCCAGAAAAAAA
1 TTTTCCAGAAAAAAA
21764582 TTTTCCA-AAAAAAA
1 TTTTCCAGAAAAAAA
21764596 AACCAAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (15 bp):
TTTTCCAGAAAAAAA
Found at i:21764596 original size:15 final size:15
Alignment explanation
Indices: 21764567--21764596 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21764557 AAATTCATCT
*
21764567 TTTTCCAGAAAAAAA
1 TTTTCCAAAAAAAAA
21764582 TTTTCCAAAAAAAAA
1 TTTTCCAAAAAAAAA
21764597 ACCAAACCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (15 bp):
TTTTCCAAAAAAAAA
Found at i:21765958 original size:11 final size:11
Alignment explanation
Indices: 21765942--21765971 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
21765932 ACTAGTTCAA
21765942 TTTTTTTCTTT
1 TTTTTTTCTTT
21765953 TTTTTTTCTTT
1 TTTTTTTCTTT
21765964 TTTATTTT
1 TTT-TTTT
21765972 AATTTACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:21766130 original size:10 final size:9
Alignment explanation
Indices: 21766096--21766142 Score: 58
Period size: 9 Copynumber: 4.9 Consensus size: 9
21766086 ACTATTTCTT
21766096 TAAAAAAAA
1 TAAAAAAAA
21766105 TAAAATGAAAA
1 TAAAA--AAAA
*
21766116 TAAAAATAGA
1 TAAAAA-AAA
21766126 TAAAAAAAA
1 TAAAAAAAA
21766135 TAAAAAAA
1 TAAAAAAA
21766143 TAAGAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 16 0.48
10 8 0.24
11 9 0.27
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:21787590 original size:3 final size:3
Alignment explanation
Indices: 21787582--21787607 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21787572 ATTTTTTCGT
21787582 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
21787608 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:21787612 original size:3 final size:3
Alignment explanation
Indices: 21787606--21787646 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
21787596 AATAATAATA
21787606 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21787647 CAATTGGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21789189 original size:20 final size:20
Alignment explanation
Indices: 21789166--21789211 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21789156 TCATTAATGT
*
21789166 TTTTAATTATTATATTATAA
1 TTTTAAATATTATATTATAA
*
21789186 TTTTAAATATTTTATTAT--
1 TTTTAAATATTATATTATAA
21789204 TTTTAAAT
1 TTTTAAAT
21789212 TAAATATCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAATATTATATTATAA
Found at i:21793189 original size:112 final size:113
Alignment explanation
Indices: 21792899--21793189 Score: 278
Period size: 112 Copynumber: 2.5 Consensus size: 113
21792889 ATTTAAATTC
* * * * *
21792899 TAAGGAAAAATTGATACTTTCAACTTTTTTCTC-AAACATTTCTGAGATACTTTTTATTTAAGGA
1 TAAGG-AAAATTGATACTTTCAAC-ATTTCCTCAAAACATTT-TTA-A-A-ATTTTATTTAAGGG
*
21792963 AAATTGATACTTTAACTATTTCTTAAAAATATTTTTTTGAAATATTGTTTTATT
60 AAATTGATACTTTAACTATTTCTTAAAAACATTTTTTTGAAATATTGTTTTATT
* * * * *
21793017 TGAA--AAAATTAATA-TTGCAA-ATTTCCTTACTAACATTTTTGAAAATTTTATTTAAAGGAAA
1 T-AAGGAAAATTGATACTTTCAACATTTCCTCA-AAACATTTTT-AAAATTTTATTTAAGGGAAA
*
21793078 TTGATA-TTTCAACT-TTTCCTTAAAAACATTTTCTTTGGAATATT-TTTTATT
63 TTGATACTTT-AACTATTT-CTTAAAAACATTTT-TTTGAAATATTGTTTTATT
*
21793129 TAAGGAAAATTGATACTTTCAACGTTTCCTCAAAACATTTTTAAAATTATT-TTT-AGGGAAA
1 TAAGGAAAATTGATACTTTCAACATTTCCTCAAAACATTTTTAAAATT-TTATTTAAGGGAAA
21793190 AATTTACCAT
Statistics
Matches: 143, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
111 8 0.06
112 51 0.36
113 34 0.24
114 18 0.13
115 20 0.14
116 9 0.06
118 1 0.01
119 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (113 bp):
TAAGGAAAATTGATACTTTCAACATTTCCTCAAAACATTTTTAAAATTTTATTTAAGGGAAATTG
ATACTTTAACTATTTCTTAAAAACATTTTTTTGAAATATTGTTTTATT
Found at i:21794079 original size:63 final size:63
Alignment explanation
Indices: 21793972--21794115 Score: 207
Period size: 63 Copynumber: 2.3 Consensus size: 63
21793962 TCACAAAAAA
* * * * *
21793972 TTTGCAAAGATTTTAAGATTTGCCAAAAGTCAATATTTGCAAAGGTCTGCAAGAATTCCAAGT
1 TTTGCAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGCAAAGGTCTGCAAGAATTCCAAGG
* * *
21794035 TTTGTAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGTAAAGGTTTGCAAGAATTCCAAGG
1 TTTGCAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGCAAAGGTCTGCAAGAATTCCAAGG
*
21794098 TTCGCAAAGATTTCAAAA
1 TTTGCAAAGATTTCAAAA
21794116 GTTGCAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (63 bp):
TTTGCAAAGATTTCAAAATTCGCCAAAAGTCAAGATTTGCAAAGGTCTGCAAGAATTCCAAGG
Found at i:21794439 original size:62 final size:62
Alignment explanation
Indices: 21794320--21794442 Score: 142
Period size: 62 Copynumber: 2.0 Consensus size: 62
21794310 AGAATTTTCA
* * * *
21794320 AATTTGCAAGATTTTCAATTTTATAAGAACTTAAAGATTCACAAGACCTTTAGATTCACAAG
1 AATTTGCAAGAGTTTCAAATTTATAAGAACTTAAAGATTCACAAGAACTTTAAATTCACAAG
* * **
21794382 AATTTGTAAGAGTTTCAAATTTGTAAGAA-TTAAAAGATTCGTAA-AACTTTCAAATTCACAA
1 AATTTGCAAGAGTTTCAAATTTATAAGAACTT-AAAGATTCACAAGAACTTT-AAATTCACAA
21794443 AAACTTTAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 7 0.14
62 44 0.86
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (62 bp):
AATTTGCAAGAGTTTCAAATTTATAAGAACTTAAAGATTCACAAGAACTTTAAATTCACAAG
Found at i:21794564 original size:18 final size:17
Alignment explanation
Indices: 21794508--21794567 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
21794498 CATGATGTGT
*
21794508 AAGAATTCAAATATTCAC
1 AAGAATTCAAAT-TTCGC
*
21794526 AAGATTTTCAAATTT-GC
1 AAGA-ATTCAAATTTCGC
21794543 AAGAATTCAAACTTTCGC
1 AAGAATTCAAA-TTTCGC
21794561 AAGAATT
1 AAGAATT
21794568 TTAGATTTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.17
17 8 0.22
18 15 0.42
19 7 0.19
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (17 bp):
AAGAATTCAAATTTCGC
Found at i:21794564 original size:35 final size:35
Alignment explanation
Indices: 21794508--21794584 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
21794498 CATGATGTGT
21794508 AAGAATTCAAATATTCACAAG-ATTTTCAAATTTGC
1 AAGAATTCAAATATTCACAAGAATTTT-AAATTTGC
* *
21794543 AAGAATTCAAACT-TTCGCAAGAATTTTAGATTTGC
1 AAGAATTCAAA-TATTCACAAGAATTTTAAATTTGC
21794578 AAGAATT
1 AAGAATT
21794585 TTCAGATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
35 32 0.84
36 6 0.16
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (35 bp):
AAGAATTCAAATATTCACAAGAATTTTAAATTTGC
Found at i:21794581 original size:17 final size:17
Alignment explanation
Indices: 21794537--21794592 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
21794527 AGATTTTCAA
* *
21794537 ATTTGCAAGAA-TTCAA
1 ATTTGCAAGAATTTTAG
21794553 ACTTTCGCAAGAATTTTAG
1 A-TTT-GCAAGAATTTTAG
21794572 ATTTGCAAGAATTTTCAG
1 ATTTGCAAGAATTTT-AG
21794590 ATT
1 ATT
21794593 AATAAGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 1 0.03
17 14 0.41
18 15 0.44
19 4 0.12
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (17 bp):
ATTTGCAAGAATTTTAG
Found at i:21795101 original size:9 final size:9
Alignment explanation
Indices: 21795087--21795112 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21795077 TATAACTTTA
21795087 AAAGTTTGG
1 AAAGTTTGG
21795096 AAAGTTTGG
1 AAAGTTTGG
21795105 AAAGTTTG
1 AAAGTTTG
21795113 TCAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (9 bp):
AAAGTTTGG
Found at i:21795323 original size:24 final size:24
Alignment explanation
Indices: 21795291--21795358 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
21795281 ATGCCAATGT
*
21795291 CCAACAATGATGCAAATGCATGCC
1 CCAACAATGATGCAAATGCATACC
21795315 CCAACAATGATGCAAATGCATACC
1 CCAACAATGATGCAAATGCATACC
* *
21795339 CCAATAATGGTGCAAATGCA
1 CCAACAATGATGCAAATGCA
21795359 ATTATCAAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (24 bp):
CCAACAATGATGCAAATGCATACC
Found at i:21797354 original size:141 final size:142
Alignment explanation
Indices: 21797085--21797359 Score: 473
Period size: 142 Copynumber: 1.9 Consensus size: 142
21797075 AGGCAAAGGG
21797085 TTTTTAGTGACATTCAACTCCCCTGATTCATTGAAGCTCACTGAACCTGCTCGAATCAAACTTTG
1 TTTTTAGTGACATTCAACTCCCCTGATTCATTGAAGCTCACTGAACCTGCTCGAATCAAACTTTG
*
21797150 CACCTTATGCTTAAAAACTGGGCAAGTTTCTATAAAGTGACCTATATTCCATTATGATAATCACA
66 CACCTTATGCTTAAAAACTGGGCAAGTTTCTATAAAGTGACCTACATTCCATTATGATAATCACA
21797215 TGTGGAAAGGAT
131 TGTGGAAAGGAT
* *
21797227 TTTTTTGTGACATTCAACTCCCTTGATTCATTGAAGCTCACTGAACCTGCTCGAATCAAAC-TTG
1 TTTTTAGTGACATTCAACTCCCCTGATTCATTGAAGCTCACTGAACCTGCTCGAATCAAACTTTG
* * *
21797291 CACCTTGTGGTTAAAACCTGGGCAAGTTTCTATAAAAGTGACCTACATT-CATTATGATAATCAC
66 CACCTTATGCTTAAAAACTGGGCAAGTTTCTAT-AAAGTGACCTACATTCCATTATGATAATCAC
21797355 ATGTG
130 ATGTG
21797360 ACTTAATATA
Statistics
Matches: 126, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
141 53 0.42
142 73 0.58
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (142 bp):
TTTTTAGTGACATTCAACTCCCCTGATTCATTGAAGCTCACTGAACCTGCTCGAATCAAACTTTG
CACCTTATGCTTAAAAACTGGGCAAGTTTCTATAAAGTGACCTACATTCCATTATGATAATCACA
TGTGGAAAGGAT
Found at i:21800144 original size:13 final size:13
Alignment explanation
Indices: 21800126--21800152 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21800116 GGGCAAGGAT
21800126 ACAAAATAAATAA
1 ACAAAATAAATAA
21800139 ACAAAATAAATAA
1 ACAAAATAAATAA
21800152 A
1 A
21800153 ATACAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
ACAAAATAAATAA
Found at i:21801041 original size:23 final size:21
Alignment explanation
Indices: 21801005--21801049 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
21800995 GATCATGCAA
21801005 ATAATATCATGCAATAATAAT
1 ATAATATCATGCAATAATAAT
21801026 ATAATATACCATGCAATAATAAT
1 ATAATAT--CATGCAATAATAAT
21801049 A
1 A
21801050 ACCAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
23 15 0.68
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (21 bp):
ATAATATCATGCAATAATAAT
Found at i:21801112 original size:21 final size:21
Alignment explanation
Indices: 21801086--21801129 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
21801076 ATAATATAAT
*
21801086 ATATAAATTATCATACAATTA
1 ATATAAAATATCATACAATTA
**
21801107 ATATAAAATATCATGTAATTA
1 ATATAAAATATCATACAATTA
21801128 AT
1 AT
21801130 TAATATTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATAAAATATCATACAATTA
Found at i:21801223 original size:3 final size:3
Alignment explanation
Indices: 21801215--21801264 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
21801205 TTTTAAATTT
21801215 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21801263 TA
1 TA
21801265 CAACATAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:21802459 original size:13 final size:13
Alignment explanation
Indices: 21802441--21802466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21802431 AAGAAGCTTT
21802441 GCCAAAAAAAAAA
1 GCCAAAAAAAAAA
21802454 GCCAAAAAAAAAA
1 GCCAAAAAAAAAA
21802467 AAACTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (13 bp):
GCCAAAAAAAAAA
Found at i:21803071 original size:18 final size:18
Alignment explanation
Indices: 21803044--21803084 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
21803034 GACTAGTTCA
* **
21803044 ATTTTTTTCTTTTTTTTT
1 ATTTTGTTCTTTTAATTT
21803062 ATTTTGTTCTTTTAATTT
1 ATTTTGTTCTTTTAATTT
21803080 ATTTT
1 ATTTT
21803085 TTTTATCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.80
Consensus pattern (18 bp):
ATTTTGTTCTTTTAATTT
Found at i:21803098 original size:14 final size:13
Alignment explanation
Indices: 21803053--21803108 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 13
21803043 AATTTTTTTC
21803053 TTTTTTTTTATTT
1 TTTTTTTTTATTT
* *
21803066 TGTTCTTTTAATTT
1 T-TTTTTTTTATTT
*
21803080 ATTTTTTTTATCTT
1 TTTTTTTTTAT-TT
*
21803094 TTTTTTATTATTT
1 TTTTTTTTTATTT
21803107 TT
1 TT
21803109 CTTAGTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTATTT
Found at i:21803122 original size:38 final size:38
Alignment explanation
Indices: 21803045--21803123 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
21803035 ACTAGTTCAA
*
21803045 TTTTTTTCTTTTTTTTTATTTTGTTCTTTTAATTTATT
1 TTTTTTTCTTTTTTTTTATTTTGTTCTCTTAATTTATT
* *
21803083 TTTTTTATC-TTTTTTTTATTATT-TT-TCTTAGTTTAAT
1 TTTTTT-TCTTTTTTTTTATT-TTGTTCTCTTAATTTATT
21803120 TTTT
1 TTTT
21803124 ATGTTCCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 13 0.36
38 19 0.53
39 4 0.11
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.80
Consensus pattern (38 bp):
TTTTTTTCTTTTTTTTTATTTTGTTCTCTTAATTTATT
Found at i:21803123 original size:37 final size:37
Alignment explanation
Indices: 21803037--21803123 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
21803027 ATTAACTGAC
* * *
21803037 TAGTTCAATTTTTTTCTTTTTTTTTATTTTGTTCTTT
1 TAGTTTAATTTTTTTATTTTTTTTTATTTTGTTCTCT
* *
21803074 TAATTTATTTTTTTTATCTTTTTTTTATTATT-TT-TCT
1 TAGTTTAATTTTTTTAT-TTTTTTTTATT-TTGTTCTCT
21803111 TAGTTTAATTTTT
1 TAGTTTAATTTTT
21803124 ATGTTCCAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
37 26 0.63
38 13 0.32
39 2 0.05
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (37 bp):
TAGTTTAATTTTTTTATTTTTTTTTATTTTGTTCTCT
Found at i:21816928 original size:12 final size:12
Alignment explanation
Indices: 21816913--21816937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21816903 TCTTTTTTTG
21816913 TTTTTTTACTTT
1 TTTTTTTACTTT
21816925 TTTTTTTACTTT
1 TTTTTTTACTTT
21816937 T
1 T
21816938 GACTTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTACTTT
Done.