Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 23 of 109
Found at i:3952928 original size:24 final size:23
Alignment explanation
Indices: 3952877--3952921 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3952867 AAAATTAAGA
*
3952877 AAAAAGGAAAAAAATAAGCAAAG
1 AAAAAGGAAAAAAATAAGAAAAG
3952900 AAAAAGGAGAAAAAAT-AGAAAA
1 AAAAAGGA-AAAAAATAAGAAAA
3952922 AGGAAAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (23 bp):
AAAAAGGAAAAAAATAAGAAAAG
Found at i:3953682 original size:20 final size:18
Alignment explanation
Indices: 3953659--3953711 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
3953649 TAAAATTTTC
3953659 AAAAATTTTGAAAAAATCT
1 AAAAATTTT-AAAAAATCT
**
3953678 AAAAATCTAAAAAAAAATCT
1 AAAAAT-T-TTAAAAAATCT
3953698 AAAAATTTTAAAAA
1 AAAAATTTTAAAAA
3953712 GAAAAAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 5 0.18
19 7 0.25
20 16 0.57
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATTTTAAAAAATCT
Found at i:3953693 original size:12 final size:12
Alignment explanation
Indices: 3953678--3953702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3953668 GAAAAAATCT
3953678 AAAAATCTAAAA
1 AAAAATCTAAAA
3953690 AAAAATCTAAAA
1 AAAAATCTAAAA
3953702 A
1 A
3953703 TTTTAAAAAG
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATCTAAAA
Found at i:3957461 original size:46 final size:46
Alignment explanation
Indices: 3957359--3957463 Score: 110
Period size: 47 Copynumber: 2.2 Consensus size: 46
3957349 TTATTTGACA
* *
3957359 TTTATAAAAATAATTTAAAAATATTAAAATTATACAAATAATAAATT
1 TTTAT-AAAATAATTTAAAAATAGTAAAATAATACAAATAATAAATT
3957406 TTTAATAAAATAA-TTAAAAATTAGTAAAATAATA-ATATATAA-AATATT
1 TTT-ATAAAATAATTTAAAAA-TAGTAAAATAATACA-A-ATAATAA-ATT
3957454 TTT-TAAAATA
1 TTTATAAAATA
3957464 TATATTGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
46 15 0.29
47 24 0.47
48 12 0.24
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (46 bp):
TTTATAAAATAATTTAAAAATAGTAAAATAATACAAATAATAAATT
Found at i:3958987 original size:12 final size:13
Alignment explanation
Indices: 3958962--3958995 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3958952 GCTTTAGAAT
3958962 AAAATAAAAGTAA
1 AAAATAAAAGTAA
3958975 AAAATAAAA-TAA
1 AAAATAAAAGTAA
*
3958987 AAAACAAAA
1 AAAATAAAA
3958996 ACCAAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAATAAAAGTAA
Found at i:3959302 original size:2 final size:2
Alignment explanation
Indices: 3959295--3959323 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3959285 TTTAGAAAGA
3959295 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3959324 ATGGCCATTG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3961123 original size:21 final size:21
Alignment explanation
Indices: 3961073--3961124 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3961063 ACGATATAAA
* *
3961073 AATAATATAATATAAAATTTT
1 AATAAAATTATATAAAATTTT
3961094 AATAAAATTATATATAAA-TTT
1 AATAAAATTATATA-AAATTTT
3961115 AATAAAATTA
1 AATAAAATTA
3961125 AAAAATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAAAATTATATAAAATTTT
Found at i:3966650 original size:26 final size:26
Alignment explanation
Indices: 3966611--3966678 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
3966601 AAATTTTTTT
3966611 TAAAAATCTA-AAAAAAATTAAAATTA
1 TAAAAAT-TATAAAAAAATTAAAATTA
* * *
3966637 TAAAAATTATAAAAAATTTATAATTT
1 TAAAAATTATAAAAAAATTAAAATTA
* *
3966663 TTATAATT-TAAAAAAA
1 TAAAAATTATAAAAAAA
3966679 ATCATAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
25 9 0.26
26 26 0.74
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAAATTATAAAAAAATTAAAATTA
Found at i:3966767 original size:20 final size:20
Alignment explanation
Indices: 3966735--3966790 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
3966725 TCAAAAAATA
3966735 TTTA-AAAAATTCTAAATTT
1 TTTATAAAAATTCTAAATTT
* *
3966754 TTTTTAAAATTTCTAAATTT
1 TTTATAAAAATTCTAAATTT
3966774 TTTATAAAAATTCTAAA
1 TTTATAAAAATTCTAAA
3966791 AAAATTAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTATAAAAATTCTAAATTT
Found at i:3966910 original size:17 final size:17
Alignment explanation
Indices: 3966866--3966909 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3966856 AAAATATTCA
*
3966866 AAAAATGAAGATTTTAAT
1 AAAAAT-AAAATTTTAAT
3966884 AAAAATAAAATTTT-AT
1 AAAAATAAAATTTTAAT
*
3966900 TAAAATAAAA
1 AAAAATAAAA
3966910 AAATCACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 7 0.29
18 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAAATAAAATTTTAAT
Found at i:3967599 original size:31 final size:30
Alignment explanation
Indices: 3967546--3967605 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
3967536 TTTTAGTGAC
*
3967546 TTTTATAAAATTTTAATATTTTAATATTTG
1 TTTTATAAAATTTTAATATTTTAAAATTTG
*
3967576 TTTT-TAAAATTTTTAAATCTTTTAAAATTT
1 TTTTATAAAA-TTTT-AATATTTTAAAATTT
3967606 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 8 0.31
31 13 0.50
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
TTTTATAAAATTTTAATATTTTAAAATTTG
Found at i:3967650 original size:20 final size:20
Alignment explanation
Indices: 3967621--3967677 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3967611 AAAATTGCAA
3967621 TTTTTAAATTTTTTA-ACATT
1 TTTTTAAATTTTTTACA-ATT
*
3967641 TTTTTGAATTTTTTACAATTT
1 TTTTTAAATTTTTTACAA-TT
3967662 TTTTTCAAATTTTTTA
1 TTTTT-AAATTTTTTA
3967678 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
21 8 0.25
22 9 0.28
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAAATTTTTTACAATT
Found at i:3967663 original size:21 final size:20
Alignment explanation
Indices: 3967621--3967695 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
3967611 AAAATTGCAA
3967621 TTTTTAAATTTTTTAACA-TT
1 TTTTTAAATTTTTTAA-ATTT
*
3967641 TTTTTGAATTTTTTACAATTT
1 TTTTTAAATTTTTTA-AATTT
**
3967662 TTTTTCAAATTTTTTATTTTT
1 TTTTT-AAATTTTTTAAATTT
3967683 TTTTTGAAATTTT
1 TTTTT-AAATTTT
3967696 CTTTTTATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.32
21 23 0.49
22 9 0.19
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTAAATTTTTTAAATTT
Found at i:3967664 original size:22 final size:20
Alignment explanation
Indices: 3967621--3967695 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
3967611 AAAATTGCAA
* **
3967621 TTTTTAAATTTTTTAACATT
1 TTTTTGAATTTTTTAATTTT
3967641 TTTTTGAATTTTTTACAATTTT
1 TTTTTGAATTTTTT--AATTTT
** *
3967663 TTTTCAAATTTTTTATTTTT
1 TTTTTGAATTTTTTAATTTT
3967683 TTTTTGAAATTTT
1 TTTTTG-AATTTT
3967696 CTTTTTATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 22 0.50
21 6 0.14
22 16 0.36
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTGAATTTTTTAATTTT
Found at i:3967695 original size:10 final size:9
Alignment explanation
Indices: 3967621--3967664 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
3967611 AAAATTGCAA
3967621 TTTTTAAAT
1 TTTTTAAAT
3967630 TTTTTAACATT
1 TTTTTAA-A-T
*
3967641 TTTTTGAAT
1 TTTTTAAAT
3967650 TTTTTACAAT
1 TTTTTA-AAT
3967660 TTTTT
1 TTTTT
3967665 TTCAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 13 0.43
10 10 0.33
11 7 0.23
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:3967701 original size:20 final size:21
Alignment explanation
Indices: 3967659--3967701 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3967649 TTTTTTACAA
*
3967659 TTTTTTTTCAAATTTTTTATT
1 TTTTTTTTCAAATTTTCTATT
*
3967680 TTTTTTTTGAAATTTTCT-TT
1 TTTTTTTTCAAATTTTCTATT
3967700 TT
1 TT
3967702 ATGTTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTTCAAATTTTCTATT
Found at i:3968659 original size:17 final size:17
Alignment explanation
Indices: 3968637--3968677 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3968627 TTACTGACAT
3968637 AATATTTATCT-ATTATC
1 AATATTTAT-TAATTATC
*
3968654 AATATTAATTAATTATC
1 AATATTTATTAATTATC
3968671 AA-ATTTA
1 AATATTTA
3968678 AATCATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTATTAATTATC
Found at i:3969301 original size:60 final size:59
Alignment explanation
Indices: 3969190--3969309 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 59
3969180 TTTCGTAATT
*
3969190 ATAATAAAAATATTATAATTATTTTGATTAATTTTAATGAAATGATATTTTTATAATTATG
1 ATAATAAAAATATTATAATAATTTT-ATT-ATTTTAATGAAATGATATTTTTATAATTATG
*
3969251 ATAA-AAAAATATTATAATAATTTT-TT-TTTATAATGATAATAGGTAGTTTTTATAATTAT
1 ATAATAAAAATATTATAATAATTTTATTATTT-TAATGA-AAT-GATA-TTTTTATAATTAT
3969310 AGTTGAAGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
56 3 0.06
57 6 0.11
58 5 0.09
59 3 0.06
60 32 0.60
61 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (59 bp):
ATAATAAAAATATTATAATAATTTTATTATTTTAATGAAATGATATTTTTATAATTATG
Found at i:3969769 original size:13 final size:13
Alignment explanation
Indices: 3969751--3969776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3969741 ATTTTTTTTA
3969751 AAAAAAATAATAT
1 AAAAAAATAATAT
3969764 AAAAAAATAATAT
1 AAAAAAATAATAT
3969777 GAGGATAAAA
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:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAATAATAT
Found at i:3970056 original size:20 final size:21
Alignment explanation
Indices: 3970033--3970086 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
3970023 GTAATAAATA
* *
3970033 AAAAAATTAAAAAATAAT-TT
1 AAAATATTAAAAAAGAATATT
*
3970053 AAAATATAAAAAAAGAATATT
1 AAAATATTAAAAAAGAATATT
3970074 -AAATATTAAAAAA
1 AAAATATTAAAAAA
3970087 ATATATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAATATTAAAAAAGAATATT
Found at i:3970065 original size:21 final size:19
Alignment explanation
Indices: 3970041--3970094 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 19
3970031 TAAAAAAATT
3970041 AAAAAATAATTTAAAATATA
1 AAAAAATAATTT-AAATATA
*
3970061 AAAAAAGAATATTAAATATTA
1 AAAAAATAAT-TTAAATA-TA
3970082 AAAAAATATATTT
1 AAAAAATA-ATTT
3970095 TGAGATACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 14 0.48
21 13 0.45
22 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATAATTTAAATATA
Found at i:3977383 original size:20 final size:21
Alignment explanation
Indices: 3977355--3977402 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
3977345 ATCTGTAATG
* *
3977355 AAAAGAAAACCAAA-AAAA-A
1 AAAAAAAAAACAAACAAAAGA
3977374 AAAAAAAAAACAAACAAAAGA
1 AAAAAAAAAACAAACAAAAGA
*
3977395 AAGAAAAA
1 AAAAAAAA
3977403 TAAGGCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.50
20 4 0.17
21 8 0.33
ACGTcount: A:0.85, C:0.08, G:0.06, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAACAAAAGA
Found at i:3978415 original size:23 final size:22
Alignment explanation
Indices: 3978371--3978424 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
3978361 TTTGTTTATA
*
3978371 ATAATTATATAATAAAAATAATT
1 ATAATTATTTAATAAAAATAA-T
*
3978394 ATAATTATTTAA-ATAAACTAAT
1 ATAATTATTTAATA-AAAATAAT
*
3978416 ATGATTATT
1 ATAATTATT
3978425 CATTAAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAATTATTTAATAAAAATAAT
Found at i:3982428 original size:2 final size:2
Alignment explanation
Indices: 3982423--3982448 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3982413 CATATATATA
3982423 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3982449 GTCATGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3983811 original size:17 final size:18
Alignment explanation
Indices: 3983789--3983822 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3983779 CAGTTTATTC
3983789 AATTGTACTAAA-AAAAT
1 AATTGTACTAAATAAAAT
*
3983806 AATTGTATTAAATAAAA
1 AATTGTACTAAATAAAA
3983823 ATAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (18 bp):
AATTGTACTAAATAAAAT
Found at i:3990199 original size:19 final size:18
Alignment explanation
Indices: 3990160--3990237 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 18
3990150 ATTCCTTCTT
3990160 TTTAATTCTTTTTTTATA
1 TTTAATTCTTTTTTTATA
3990178 TTTAATTCCTTTTTTT-TAA
1 TTTAATT-CTTTTTTTAT-A
* * *
3990197 TTT-TTTATTTTTTTTCTA
1 TTTAATT-CTTTTTTTATA
*
3990215 TTTAATTTTTCTCTTTTATA
1 TTTAATTCTT-T-TTTTATA
3990235 TTT
1 TTT
3990238 TTATATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
18 24 0.49
19 16 0.33
20 9 0.18
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTAATTCTTTTTTTATA
Found at i:3990232 original size:37 final size:38
Alignment explanation
Indices: 3990168--3990245 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
3990158 TTTTTAATTC
3990168 TTTTTTTATATTTAATTCCTTTTTTTTA-ATTTTT-TAT
1 TTTTTTTATATTTAATT-CTTTTTTTTATATTTTTATAT
*
3990205 TTTTTTTCTATTTAATT-TTTCTCTTTTATATTTTTATAT
1 TTTTTTTATATTTAATTCTTT-T-TTTTATATTTTTATAT
3990244 TT
1 TT
3990246 AATAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 3 0.08
36 1 0.03
37 21 0.58
38 6 0.17
39 5 0.14
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (38 bp):
TTTTTTTATATTTAATTCTTTTTTTTATATTTTTATAT
Found at i:3991779 original size:65 final size:65
Alignment explanation
Indices: 3991709--3991851 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 65
3991699 TTTCCAAAAA
*
3991709 CAAAAAAAAAAGATAAGAAAAAAAGAATTTCTAAATTA-ACCCAAATGGTGAAAAATTTAGAAA-
1 CAAAAAAAAAAGATAA-AAAAAAAGAATTTCTAAA-TAGACCCAAATGATGAAAAATTTAGAAAT
3991772 TC
64 TC
* * * * **
3991774 CAAAAAAATATATATAAATAAAGAGAATTTCTAAATAGGTCCAAATGATGAAAAATTTAGAAATT
1 CAAAAAAA-AAAGATAAAAAAAAAGAATTTCTAAATAGACCCAAATGATGAAAAATTTAGAAATT
*
3991839 T
65 C
3991840 CAAAAAAGAAAA
1 CAAAAAA-AAAA
3991852 TATTTCTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
64 2 0.03
65 46 0.71
66 16 0.25
67 1 0.02
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.22
Consensus pattern (65 bp):
CAAAAAAAAAAGATAAAAAAAAAGAATTTCTAAATAGACCCAAATGATGAAAAATTTAGAAATTC
Found at i:3995874 original size:37 final size:36
Alignment explanation
Indices: 3995827--3995904 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
3995817 TGAAAGAATG
* *
3995827 AAATAAAAAAAAAATAAAAAAAAATGAAAAAAGAGAGA
1 AAATGAAAAAAGAA-AAAAAAAAATG-AAAAAGAGAGA
*
3995865 AAATGAAAAAATGAAAAAAAAAAATGAAAAGGAGAGA
1 AAATGAAAAAA-GAAAAAAAAAAATGAAAAAGAGAGA
3995902 AAA
1 AAA
3995905 AGAAGACTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 13 0.36
38 21 0.58
39 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (36 bp):
AAATGAAAAAAGAAAAAAAAAAATGAAAAAGAGAGA
Found at i:3995894 original size:8 final size:8
Alignment explanation
Indices: 3995845--3995894 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
3995835 AAAAAATAAA
3995845 AAAAAATG
1 AAAAAATG
3995853 AAAAAA-G
1 AAAAAATG
3995860 AGAGAAAATG
1 A-A-AAAATG
3995870 AAAAAATG
1 AAAAAATG
3995878 -AAAAA--
1 AAAAAATG
3995883 AAAAAATG
1 AAAAAATG
3995891 AAAA
1 AAAA
3995895 GGAGAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
6 5 0.14
7 7 0.19
8 17 0.47
9 5 0.14
10 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAAAATG
Found at i:3996680 original size:63 final size:61
Alignment explanation
Indices: 3996588--3996854 Score: 273
Period size: 63 Copynumber: 4.2 Consensus size: 61
3996578 AAACGTCTAG
* * * * * * * *
3996588 TGCTAAGAAACTTGTGATTGGTGACCAAATGATAGAGGTCGAAACTTGTTTTGAAATGGCTAG
1 TGCTAAGAAGCCTATGAGTGGTGA-CAAATGAT-GAGGCCAAAACTTGTTTTGAAATAGCTAA
*
3996651 TGCTAAGAAGCCTATGAGTGGTGATCAAATGATGCAGGCCAAAACTTGTTTTGAAACAGCTAA
1 TGCTAAGAAGCCTATGAGTGGTGA-CAAATGATG-AGGCCAAAACTTGTTTTGAAATAGCTAA
* * * *
3996714 TGCTAAGAAGCCTATGAGTGGTGAACAAATAATGGATGCCAAAATTTGTTCTGAAATAGCTAA
1 TGCTAAGAAGCCTATGAGTGGTG-ACAAATGAT-GAGGCCAAAACTTGTTTTGAAATAGCTAA
* * * * * * *
3996777 TGCTAAGAAGCTTATGAGTGGTGACTAAATGATGAAGGGCAAAATTTGTTCTGAACTTGTTAA
1 TGCTAAGAAGCCTATGAGTGGTGAC-AAATGATG-AGGCCAAAACTTGTTTTGAAATAGCTAA
*
3996840 TGCTGAGAAGCCTAT
1 TGCTAAGAAGCCTAT
3996855 AAATGATAAT
Statistics
Matches: 175, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
62 4 0.02
63 169 0.97
64 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (61 bp):
TGCTAAGAAGCCTATGAGTGGTGACAAATGATGAGGCCAAAACTTGTTTTGAAATAGCTAA
Found at i:3997346 original size:17 final size:17
Alignment explanation
Indices: 3997324--3997363 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3997314 CCTACTCCAC
3997324 CTAGCTAATTAAAGCAT
1 CTAGCTAATTAAAGCAT
**
3997341 CTAGCTCCTTAAAGCAT
1 CTAGCTAATTAAAGCAT
3997358 CTAGCT
1 CTAGCT
3997364 CTCTCTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (17 bp):
CTAGCTAATTAAAGCAT
Found at i:3997364 original size:17 final size:17
Alignment explanation
Indices: 3997332--3997364 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3997322 ACCTAGCTAA
3997332 TTAAAGCATCTAGCTCC
1 TTAAAGCATCTAGCTCC
3997349 TTAAAGCATCTAGCTC
1 TTAAAGCATCTAGCTC
3997365 TCTCTCTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (17 bp):
TTAAAGCATCTAGCTCC
Found at i:3998701 original size:14 final size:14
Alignment explanation
Indices: 3998636--3998690 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3998626 CGTTTTCTTT
**
3998636 AAACCCTAAAATCC
1 AAACCCTAAAATTG
* * *
3998650 AAACCTTAAATTTTA
1 AAACCCTAAA-ATTG
3998665 AAACCCTAAAATTG
1 AAACCCTAAAATTG
3998679 AAACCCTAAAAT
1 AAACCCTAAAAT
3998691 CTAATCCCTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.24
Consensus pattern (14 bp):
AAACCCTAAAATTG
Found at i:3998714 original size:30 final size:30
Alignment explanation
Indices: 3998679--3998765 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
3998669 CCTAAAATTG
* * * * *
3998679 AAACCCTAAAATCTAATCCCTAATCCTTTC
1 AAACCCTAAAATCAAAACCCTAAACCCTCC
*
3998709 AAACCCTAAAAACAAAACCCTAAACCCTCC
1 AAACCCTAAAATCAAAACCCTAAACCCTCC
* *
3998739 AAACCCTAAAAT-TAAACTCTAAACCCT
1 AAACCCTAAAATCAAAACCCTAAACCCT
3998766 AAAAATGAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
29 13 0.27
30 35 0.73
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (30 bp):
AAACCCTAAAATCAAAACCCTAAACCCTCC
Found at i:3998760 original size:29 final size:29
Alignment explanation
Indices: 3998679--3998827 Score: 98
Period size: 29 Copynumber: 5.3 Consensus size: 29
3998669 CCTAAAATTG
* * * *
3998679 AAACCCTAAAATCTAATCCCTAATCCTTTC
1 AAACCCTAAAAT-TAAACCCTAAACCCTCC
**
3998709 AAACCCTAAAAACAAAACCCTAAACCCTCC
1 AAACCCT-AAAATTAAACCCTAAACCCTCC
*
3998739 AAACCCTAAAATTAAACTCTAAACCCT--
1 AAACCCTAAAATTAAACCCTAAACCCTCC
* ** * *
3998766 --A----AAAATGAAACTTTAAACTCTCT
1 AAACCCTAAAATTAAACCCTAAACCCTCC
* *
3998789 AAACCCTAAAATTAAACCTTAAACCTTCC
1 AAACCCTAAAATTAAACCCTAAACCCTCC
3998818 AAACCCTAAA
1 AAACCCTAAA
3998828 CCTCCAAACC
Statistics
Matches: 93, Mismatches: 17, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
21 17 0.18
25 2 0.02
29 44 0.47
30 26 0.28
31 4 0.04
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (29 bp):
AAACCCTAAAATTAAACCCTAAACCCTCC
Found at i:3998764 original size:20 final size:21
Alignment explanation
Indices: 3998739--3998783 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3998729 TAAACCCTCC
*
3998739 AAACCCT-AAAATTAAACTCT
1 AAACCCTAAAAATGAAACTCT
*
3998759 AAACCCTAAAAATGAAACTTT
1 AAACCCTAAAAATGAAACTCT
3998780 AAAC
1 AAAC
3998784 TCTCTAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.53, C:0.22, G:0.02, T:0.22
Consensus pattern (21 bp):
AAACCCTAAAAATGAAACTCT
Found at i:3998765 original size:50 final size:49
Alignment explanation
Indices: 3998709--3998858 Score: 159
Period size: 50 Copynumber: 3.1 Consensus size: 49
3998699 TAATCCTTTC
3998709 AAACCCTAAAAACAAAACCCTAAACCCTCCAAACCCTAAAATTAAACTCT
1 AAACCCTAAAAACAAAACCCTAAACCCTCCAAACCCTAAAATTAAAC-CT
** ** * *
3998759 AAACCCTAAAAATGAAACTTTAAACTCTCTAAACCCTAAAATTAAACCTT
1 AAACCCTAAAAACAAAACCCTAAACCCTCCAAACCCTAAAATTAAACC-T
* *
3998809 AAA-CCT----TCCAAACCCTAAA-CCTCCAAACCCTAAAATTAAACCCT
1 AAACCCTAAAAACAAAACCCTAAACCCTCCAAACCCTAAAATTAAA-CCT
3998853 AAACCC
1 AAACCC
3998859 CCTAAACCTT
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
44 23 0.27
45 12 0.14
49 4 0.05
50 45 0.54
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (49 bp):
AAACCCTAAAAACAAAACCCTAAACCCTCCAAACCCTAAAATTAAACCT
Found at i:3998765 original size:94 final size:92
Alignment explanation
Indices: 3998665--3998858 Score: 212
Period size: 94 Copynumber: 2.1 Consensus size: 92
3998655 TTAAATTTTA
* * **
3998665 AAACCCTAAAATTGAAACCCTAAA-ATCTAATCCCTAATCCTTTCAAACCCTAAA-AACAAAACC
1 AAACCCTAAAAATGAAACCCTAAACATCTAAACCCTAA--AATT-AAACCCTAAACAACAAAACC
*
3998728 CTAAACCCTCCAAACCCTAAAATTAAACTCT
63 CTAAA-CCTCCAAACCCTAAAATTAAACCCT
** * * ** *
3998759 AAACCCTAAAAATGAAACTTTAAACTCTCTAAACCCTAAAATTAAACCTTAAACCTTCCAAACCC
1 AAACCCTAAAAATGAAACCCTAAAC-ATCTAAACCCTAAAATTAAACCCTAAA-CAACAAAACCC
3998824 TAAACCTCCAAACCCTAAAATTAAACCCT
64 TAAACCTCCAAACCCTAAAATTAAACCCT
3998853 AAACCC
1 AAACCC
3998859 CCTAAACCTT
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
93 9 0.11
94 53 0.63
95 11 0.13
96 11 0.13
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (92 bp):
AAACCCTAAAAATGAAACCCTAAACATCTAAACCCTAAAATTAAACCCTAAACAACAAAACCCTA
AACCTCCAAACCCTAAAATTAAACCCT
Found at i:3998806 original size:13 final size:14
Alignment explanation
Indices: 3998788--3998856 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 14
3998778 TTAAACTCTC
3998788 TAAACCCTAAA-AT
1 TAAACCCTAAACAT
* *
3998801 TAAACCTTAAACCT
1 TAAACCCTAAACAT
*
3998815 TCCAAACCCTAAACCT
1 T--AAACCCTAAACAT
*
3998831 CCAAACCCTAAA-AT
1 -TAAACCCTAAACAT
3998845 TAAACCCTAAAC
1 TAAACCCTAAAC
3998857 CCCCTAAACC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 20 0.44
14 3 0.07
15 10 0.22
16 12 0.27
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACAT
Found at i:3998835 original size:15 final size:16
Alignment explanation
Indices: 3998802--3998842 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
3998792 CCCTAAAATT
*
3998802 AAACCTTAAACCTTCC
1 AAACCCTAAACCTTCC
3998818 AAACCCTAAACC-TCC
1 AAACCCTAAACCTTCC
3998833 AAACCCTAAA
1 AAACCCTAAA
3998843 ATTAAACCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (16 bp):
AAACCCTAAACCTTCC
Found at i:3998866 original size:44 final size:45
Alignment explanation
Indices: 3998779--3998871 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 45
3998769 AATGAAACTT
* * *
3998779 TAAACTCTCTAAACCCTAAAATTAAACCTTAAACCTTCCAAACCC
1 TAAACTCTCCAAACCCTAAAATTAAACCCTAAACCTCCCAAACCC
*
3998824 TAAAC-CTCCAAACCCTAAAATTAAACCCTAAACC-CCCTAAACCT
1 TAAACTCTCCAAACCCTAAAATTAAACCCTAAACCTCCC-AAACCC
3998868 TAAA
1 TAAA
3998872 TCAAAACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 2 0.05
44 36 0.84
45 5 0.12
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (45 bp):
TAAACTCTCCAAACCCTAAAATTAAACCCTAAACCTCCCAAACCC
Found at i:3998990 original size:17 final size:16
Alignment explanation
Indices: 3998947--3999020 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 16
3998937 AACCTAATCC
3998947 CCAAACCCTAAAA--T
1 CCAAACCCTAAAATTT
* * *
3998961 CAAAACTCTAAATTTT
1 CCAAACCCTAAAATTT
3998977 CCAAACCCTAAAA-TT
1 CCAAACCCTAAAATTT
* *
3998992 -CAAGCCCTAAAATCCT
1 CCAAACCCTAAAAT-TT
*
3999008 CTAAACCCTAAAA
1 CCAAACCCTAAAA
3999021 CCAAACACTA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
14 21 0.47
15 2 0.04
16 12 0.27
17 10 0.22
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (16 bp):
CCAAACCCTAAAATTT
Found at i:3999002 original size:30 final size:31
Alignment explanation
Indices: 3998818--3999033 Score: 129
Period size: 30 Copynumber: 7.4 Consensus size: 31
3998808 TAAACCTTCC
*
3998818 AAACCCT-AAA-CCTCCAAACCCTAAAAT-T
1 AAACCCTAAAATCCTCCAAACCCTAAAATCA
* *
3998846 AAACCCT-AAA-CCCCCTAAA-CCTTAAATCA
1 AAACCCTAAAATCCTCC-AAACCCTAAAATCA
* * *
3998875 AAACCCT-ACATCCTCAAAACCATAAAA-CTA
1 AAACCCTAAAATCCTCCAAACCCTAAAATC-A
* * ** *
3998905 AAA-CCTTAAACCCTTTAAACCCTAAAATAA
1 AAACCCTAAAATCCTCCAAACCCTAAAATCA
*
3998935 AAAACCT--AATCC-CCAAACCCTAAAATCA
1 AAACCCTAAAATCCTCCAAACCCTAAAATCA
* **
3998963 AAACTCT-AAATTTTCCAAACCCTAAAATTC-
1 AAACCCTAAAATCCTCCAAACCCTAAAA-TCA
* * *
3998993 AAGCCCTAAAATCCTCTAAACCCTAAAA-CC
1 AAACCCTAAAATCCTCCAAACCCTAAAATCA
*
3999023 AAACACTAAAA
1 AAACCCTAAAA
3999034 CTCTTGAGAC
Statistics
Matches: 146, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
28 39 0.27
29 27 0.18
30 58 0.40
31 22 0.15
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (31 bp):
AAACCCTAAAATCCTCCAAACCCTAAAATCA
Found at i:3999067 original size:15 final size:15
Alignment explanation
Indices: 3999049--3999078 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3999039 GAGACTTAAA
3999049 CCAAAACCCCAAAAT
1 CCAAAACCCCAAAAT
*
3999064 CCAAAACTCCAAAAT
1 CCAAAACCCCAAAAT
3999079 ATTGAAGTCA
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:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (15 bp):
CCAAAACCCCAAAAT
Found at i:4003300 original size:49 final size:49
Alignment explanation
Indices: 4003228--4003325 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
4003218 TAAGCTAATG
* *
4003228 TACTTATAGCATTCAAGTCAGTACCAGAATCATGAAAAATAAAAATGCA
1 TACTTATAGCATTAAACTCAGTACCAGAATCATGAAAAATAAAAATGCA
* * *
4003277 TACTTATAGCATTTAAACT-AGTACTAGAATTATGAAAAATAAAGATGCA
1 TACTTATAGCA-TTAAACTCAGTACCAGAATCATGAAAAATAAAAATGCA
4003326 AGTCAGGTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 38 0.88
50 5 0.12
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (49 bp):
TACTTATAGCATTAAACTCAGTACCAGAATCATGAAAAATAAAAATGCA
Found at i:4007336 original size:105 final size:105
Alignment explanation
Indices: 4007213--4007458 Score: 440
Period size: 105 Copynumber: 2.4 Consensus size: 105
4007203 GAAAGGGACA
4007213 TTTGCATTTGCATCATTTGCATCTGCACCATAAGAAAGATATTCGCATTTACATCACTTGTATTT
1 TTTGCATTTGCATCATTTGCATCTGCACCATAAGAAAGATATTCGCATTTACATCACTTGTATTT
4007278 GCACTTGTACAAGATATTTGCATTCGCATCATAAGAAAAG
66 GCACTTGTACAAGATATTTGCATTCGCATCATAAGAAAAG
* *
4007318 TTTGCATTTGTATCATTTGCATCTGCACCGTAAGAAAGATATTCGCATTTACATCACTTGTATTT
1 TTTGCATTTGCATCATTTGCATCTGCACCATAAGAAAGATATTCGCATTTACATCACTTGTATTT
4007383 GCACTTGTACAAGATATTTGCATTCGCATCATAAGAAAAG
66 GCACTTGTACAAGATATTTGCATTCGCATCATAAGAAAAG
* * *
4007423 TTTGCATTTGCATCA-TGGCATCTGCATCTTAAGAAA
1 TTTGCATTTGCATCATTTGCATCTGCACCATAAGAAA
4007459 AGGTATTTGT
Statistics
Matches: 135, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 18 0.13
105 117 0.87
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (105 bp):
TTTGCATTTGCATCATTTGCATCTGCACCATAAGAAAGATATTCGCATTTACATCACTTGTATTT
GCACTTGTACAAGATATTTGCATTCGCATCATAAGAAAAG
Found at i:4007828 original size:22 final size:22
Alignment explanation
Indices: 4007803--4007865 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
4007793 GTCGATTCTG
* *
4007803 TAAGACCTTC-GAGCATGATTTT
1 TAAGACCTTCAG-GCATAATCTT
4007825 TAAGACCTTCAGGCATAATCTT
1 TAAGACCTTCAGGCATAATCTT
* *
4007847 TAAGACTTTTAGGCATAAT
1 TAAGACCTTCAGGCATAAT
4007866 TTCAATTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (22 bp):
TAAGACCTTCAGGCATAATCTT
Found at i:4008087 original size:131 final size:132
Alignment explanation
Indices: 4007765--4008071 Score: 391
Period size: 132 Copynumber: 2.3 Consensus size: 132
4007755 GATTGATTTC
* *
4007765 TTATTTTTTAACTTGCAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGAGCATGATTTTTAAGA
1 TTATTTTTTGACTTGCAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGAGCATGATTTCTAAGA
* * ** * * ****
4007830 CCTTCAGGCATAATCTTTAAGACTTTTAGGCATAATTTCAATTCACATTATTGTTTTGATCAATT
66 CCTCCAGGCATAATATTTAAGACTTCCAAGCATAATTTCAATTCACAGTATTGTCCCAATCAATT
4007895 CT
131 CT
* * *
4007897 TTATTTTTTGACTTGCGGTGTTGTCTCAGTCGATTCTATAAGACCTTCGAGCATGATTTCTAAGA
1 TTATTTTTTGACTTGCAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGAGCATGATTTCTAAGA
* ** * * *
4007962 CCTCCAGGTATAATATTTAAGAC-TCCAAGCATAATTTTGATTCGCAGTGTTGTCCCAATCGATT
66 CCTCCAGGCATAATATTTAAGACTTCCAAGCATAATTTCAATTCACAGTATTGTCCCAATCAATT
4008026 CT
131 CT
* * *
4008028 TTATTTTTTGATTTACAGTGTTGTCCCAGTCGATTTTGTAAGAC
1 TTATTTTTTGACTTGCAGTGTTGTCCCAGTCGATTCTGTAAGAC
4008072 ATCCAGATAT
Statistics
Matches: 148, Mismatches: 27, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
131 68 0.46
132 80 0.54
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (132 bp):
TTATTTTTTGACTTGCAGTGTTGTCCCAGTCGATTCTGTAAGACCTTCGAGCATGATTTCTAAGA
CCTCCAGGCATAATATTTAAGACTTCCAAGCATAATTTCAATTCACAGTATTGTCCCAATCAATT
CT
Found at i:4008574 original size:107 final size:107
Alignment explanation
Indices: 4008388--4008591 Score: 282
Period size: 107 Copynumber: 1.9 Consensus size: 107
4008378 ACCTCTGGAT
* * * * *
4008388 ATAATTTTGACTTATGGTGTTGTCTCGATCGATTTTATAATTTTGACTTGCGATGTTGTCCCAGT
1 ATAATTTTGACTTATAGTGTTGTCTCGATCAATTTCATAATTTTGACTTACGATGTTATCCCAGT
* *
4008453 CAATTCCATAATTTTGACTTGCGGTGTTGTCCCGATCGATCC
66 CAATTCCATAATTTTGACTTACAGTGTTGTCCCGATCGATCC
* * * *
4008495 ATAATTTTGACTTGTAGTGTTGTCTTGGTCAATTTCATAATTTTGACTTACGATGTTATCCCGGT
1 ATAATTTTGACTTATAGTGTTGTCTCGATCAATTTCATAATTTTGACTTACGATGTTATCCCAGT
** *
4008560 TGATTTCATAATTTTGACTTACAGTGTTGTCC
66 CAATTCCATAATTTTGACTTACAGTGTTGTCC
4008592 TAGTCATTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
107 83 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.44
Consensus pattern (107 bp):
ATAATTTTGACTTATAGTGTTGTCTCGATCAATTTCATAATTTTGACTTACGATGTTATCCCAGT
CAATTCCATAATTTTGACTTACAGTGTTGTCCCGATCGATCC
Found at i:4008645 original size:74 final size:73
Alignment explanation
Indices: 4008392--4008712 Score: 285
Period size: 74 Copynumber: 4.4 Consensus size: 73
4008382 CTGGATATAA
* * * * *
4008392 TTTTGACTTATGGTGTTGTCTCGATCGATTTTATAATTTTGACTTGC-GATGTTGTCCCAGTCA-
1 TTTTGACTTACGATGTTGTCCCGATCGATTTCATAATTTTGACTTGCAG-TGTTGTCCTAGTCAT
* *** *
4008455 ATTCCATAA
65 TTTTTTTAC
* * * * * * *
4008464 TTTTGACTTGCGGTGTTGTCCCGATCGA-TCCATAATTTTGACTTGTAGTGTTGTCTTGGTCA-A
1 TTTTGACTTACGATGTTGTCCCGATCGATTTCATAATTTTGACTTGCAGTGTTGTCCTAGTCATT
** *
4008527 TTTCATAA
66 TTTTTTAC
* * * *
4008535 TTTTGACTTACGATGTTATCCCGGTTGATTTCATAATTTTGACTTACAGTGTTGTCCTAGTCATT
1 TTTTGACTTACGATGTTGTCCCGATCGATTTCATAATTTTGACTTGCAGTGTTGTCCTAGTCATT
4008600 TTTTTTAC
66 TTTTTTAC
* *
4008608 TTTTCGA-TTGACGATGTTGTCCCGATCAATTTCATAATTTTGACTTGCGGTGTTGT-CTAGATC
1 TTTT-GACTT-ACGATGTTGTCCCGATCGATTTCATAATTTTGACTTGCAGTGTTGTCCTAG-TC
4008671 ATTTTTTTTAC
63 ATTTTTTTTAC
** * *
4008682 TATTAAACTTACGGTGTTGTCCTGATCGATT
1 T-TTTGACTTACGATGTTGTCCCGATCGATT
4008713 CTTTATTTCT
Statistics
Matches: 206, Mismatches: 35, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
71 57 0.28
72 55 0.27
73 15 0.07
74 75 0.36
75 4 0.02
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.46
Consensus pattern (73 bp):
TTTTGACTTACGATGTTGTCCCGATCGATTTCATAATTTTGACTTGCAGTGTTGTCCTAGTCATT
TTTTTTAC
Found at i:4008671 original size:36 final size:36
Alignment explanation
Indices: 4008388--4008664 Score: 229
Period size: 36 Copynumber: 7.7 Consensus size: 36
4008378 ACCTCTGGAT
** * * *
4008388 ATAATTTTGACTTATGGTGTTGTCTCGATCGATTTT
1 ATAATTTTGACTTGCGGTGTTGTCCCGATCAATTTC
* *
4008424 ATAATTTTGACTTGCGATGTTGTCCC-AGTCAATTCC
1 ATAATTTTGACTTGCGGTGTTGTCCCGA-TCAATTTC
* *
4008460 ATAATTTTGACTTGCGGTGTTGTCCCGATCGA-TCC
1 ATAATTTTGACTTGCGGTGTTGTCCCGATCAATTTC
** ** *
4008495 ATAATTTTGACTTGTAGTGTTGTCTTGGTCAATTTC
1 ATAATTTTGACTTGCGGTGTTGTCCCGATCAATTTC
* * * * **
4008531 ATAATTTTGACTTACGATGTTATCCCGGTTGATTTC
1 ATAATTTTGACTTGCGGTGTTGTCCCGATCAATTTC
* * * * *
4008567 ATAATTTTGACTTACAGTGTTGT-CCTAGTCATTTTTT
1 ATAATTTTGACTTGCGGTGTTGTCCCGA-TCA-ATTTC
* * *
4008604 TTACTTTTCGA-TTGACGATGTTGTCCCGATCAATTTC
1 ATAATTTT-GACTTG-CGGTGTTGTCCCGATCAATTTC
4008641 ATAATTTTGACTTGCGGTGTTGTC
1 ATAATTTTGACTTGCGGTGTTGTC
4008665 TAGATCATTT
Statistics
Matches: 187, Mismatches: 45, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
35 32 0.17
36 116 0.62
37 24 0.13
38 12 0.06
39 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (36 bp):
ATAATTTTGACTTGCGGTGTTGTCCCGATCAATTTC
Found at i:4009134 original size:27 final size:27
Alignment explanation
Indices: 4009082--4009134 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4009072 TATCATTTAT
*
4009082 TAATTAAATATTAAAAAAATATAAAAA
1 TAATTAAATATTAAAAAAAGATAAAAA
4009109 TAATTAAATAATTAAAAAAAGA-AAAA
1 TAATTAAAT-ATTAAAAAAAGATAAAA
4009135 TAAAAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (27 bp):
TAATTAAATATTAAAAAAAGATAAAAA
Found at i:4010553 original size:29 final size:29
Alignment explanation
Indices: 4010520--4010603 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
4010510 CATTTTCTTT
*
4010520 AAACCCTAAATTTCAAAACTCTAAAATTG
1 AAACCCTAAATTTCAAAACCCTAAAATTG
* * *
4010549 AAACCCTAAAATT-GAAACCCTAAAATTT
1 AAACCCTAAATTTCAAAACCCTAAAATTG
* * *
4010577 AATCCATAAACTTTCCAAACCCTAAAA
1 AAACCCTAAA-TTTCAAAACCCTAAAA
4010604 ACGAAACGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
28 20 0.44
29 14 0.31
30 11 0.24
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.25
Consensus pattern (29 bp):
AAACCCTAAATTTCAAAACCCTAAAATTG
Found at i:4010586 original size:14 final size:14
Alignment explanation
Indices: 4010520--4010575 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
4010510 CATTTTCTTT
* *
4010520 AAACCCTAAATTTCA
1 AAACCCTAAAATT-G
*
4010535 AAACTCTAAAATTG
1 AAACCCTAAAATTG
4010549 AAACCCTAAAATTG
1 AAACCCTAAAATTG
4010563 AAACCCTAAAATT
1 AAACCCTAAAATT
4010576 TAATCCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (14 bp):
AAACCCTAAAATTG
Found at i:4010679 original size:29 final size:29
Alignment explanation
Indices: 4010590--4010763 Score: 163
Period size: 30 Copynumber: 5.9 Consensus size: 29
4010580 CCATAAACTT
* *
4010590 TCCAAACCCTAAAAACGAAACGCTAAACCC
1 TCCAAACCCT-AAAACAAAACCCTAAACCC
* *
4010620 TCCAAACCCCAAAA-ATGAAACCTTAAACCC
1 TCCAAACCCTAAAACA--AAACCCTAAACCC
* *
4010650 TCCAAACCTTGAAACAAAACCCTAAACCC
1 TCCAAACCCTAAAACAAAACCCTAAACCC
** * * *
4010679 TTTAAACCTTAAAAACAAAATCATAAACCC
1 TCCAAACCCT-AAAACAAAACCCTAAACCC
*
4010709 TCCAAACCCTAAAATCAAAACCCCAAA-CC
1 TCCAAACCCTAAAA-CAAAACCCTAAACCC
**
4010738 TCCAAACCCTAAAATTAAACCCTAAA
1 TCCAAACCCTAAAACAAAACCCTAAA
4010764 AACGAACCTC
Statistics
Matches: 117, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
28 9 0.08
29 44 0.38
30 63 0.54
31 1 0.01
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.15
Consensus pattern (29 bp):
TCCAAACCCTAAAACAAAACCCTAAACCC
Found at i:4010693 original size:59 final size:59
Alignment explanation
Indices: 4010580--4010751 Score: 175
Period size: 59 Copynumber: 2.9 Consensus size: 59
4010570 AAAATTTAAT
** * * **
4010580 CCATAAACTTTCCAAACCCTAAAAACGAAACGCTAAACCCTCCAAACCCCAAAAATGAAA
1 CCATAAACCCTCCAAACCCT-AAAACAAAACCCTAAACCCTCCAAACCCCAAAAACAAAA
* * * ** **
4010640 CCTTAAACCCTCCAAACCTTGAAACAAAACCCTAAACCCTTTAAACCTTAAAAACAAAA
1 CCATAAACCCTCCAAACCCTAAAACAAAACCCTAAACCCTCCAAACCCCAAAAACAAAA
* * *
4010699 TCATAAACCCTCCAAACCCTAAAATCAAAACCCCAAA-CCTCCAAACCCTAAAA
1 CCATAAACCCTCCAAACCCTAAAA-CAAAACCCTAAACCCTCCAAACCCCAAAA
4010752 TTAAACCCTA
Statistics
Matches: 90, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 63 0.70
60 27 0.30
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.15
Consensus pattern (59 bp):
CCATAAACCCTCCAAACCCTAAAACAAAACCCTAAACCCTCCAAACCCCAAAAACAAAA
Found at i:4010787 original size:29 final size:28
Alignment explanation
Indices: 4010754--4010849 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 28
4010744 CCCTAAAATT
*
4010754 AAACCCTAAAAACGAACCTCTAAACTTTC
1 AAACCCTAAAAAC-AACCTCTAAACCTTC
* * *
4010783 AAACCTTAAATTA-AACCT-TAAACCCTC
1 AAACCCTAAA-AACAACCTCTAAACCTTC
* * *
4010810 TAAACCCTAAAATCAAAACTCCAAACCTTC
1 -AAACCCTAAAAAC-AACCTCTAAACCTTC
4010840 AAACCCTAAA
1 AAACCCTAAA
4010850 CCCCCTAAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
27 7 0.13
28 14 0.27
29 23 0.44
30 8 0.15
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (28 bp):
AAACCCTAAAAACAACCTCTAAACCTTC
Found at i:4010876 original size:30 final size:30
Alignment explanation
Indices: 4010840--4010911 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
4010830 CCAAACCTTC
*
4010840 AAACCCTAAACCCCCTAAACTCTAAAA-TCA
1 AAACCCTAAACCCCCAAAACTCTAAAACT-A
* * *
4010870 AAACCCTAAATCCTCAAAACTGTAAAACTA
1 AAACCCTAAACCCCCAAAACTCTAAAACTA
*
4010900 AAACCTTAAACC
1 AAACCCTAAACC
4010912 TTAAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (30 bp):
AAACCCTAAACCCCCAAAACTCTAAAACTA
Found at i:4011023 original size:15 final size:15
Alignment explanation
Indices: 4011005--4011035 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4010995 GAGACTTAAA
4011005 CCAAAACCCCAAAAT
1 CCAAAACCCCAAAAT
*
4011020 CCAAAACTCCAAAAT
1 CCAAAACCCCAAAAT
4011035 C
1 C
4011036 TTGAAGTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.10
Consensus pattern (15 bp):
CCAAAACCCCAAAAT
Found at i:4012341 original size:22 final size:21
Alignment explanation
Indices: 4012312--4012373 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
4012302 TCTTGAATCC
*
4012312 TCAAATGAGAATATTTGAGTTT
1 TCAAATGAGAATCTTTGAG-TT
* * *
4012334 TTAGATGAGAATCTTCGAGTT
1 TCAAATGAGAATCTTTGAGTT
4012355 TCAAATGAGAATCTTTGAG
1 TCAAATGAGAATCTTTGAG
4012374 ATGTGAAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (21 bp):
TCAAATGAGAATCTTTGAGTT
Found at i:4012485 original size:44 final size:43
Alignment explanation
Indices: 4012430--4012554 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
4012420 AAGAATATTC
4012430 AAACTTTTGGATGTGAATCTCCAAAATTTGAACAT-AAAAG-ATT
1 AAACTTTTGGATGTGAA-CTCCAAAATTTGAA-ATGAAAAGCATT
* * ** *
4012473 AAACTTTTTGGATGTGAACTCCAAAGTTCTCAAATGCGAAGCTTT
1 AAAC-TTTTGGATGTGAACTCCAAAATT-TGAAATGAAAAGCATT
*
4012518 GAACTTTTGGATGTGAACTCCAAAATTTG-AATGAAAA
1 AAACTTTTGGATGTGAACTCCAAAATTTGAAATGAAAA
4012555 TCTTTAAATG
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
42 6 0.09
43 16 0.24
44 41 0.60
45 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (43 bp):
AAACTTTTGGATGTGAACTCCAAAATTTGAAATGAAAAGCATT
Found at i:4012968 original size:42 final size:42
Alignment explanation
Indices: 4012813--4012996 Score: 187
Period size: 42 Copynumber: 4.5 Consensus size: 42
4012803 GATTGTCAAT
*** * *
4012813 GAGCATTTTATTTTTCAAAAGTTATGGCACCTCTATTTATAG
1 GAGCATTTTATTTTTCAAAAGTTATGATGCCTCTGTTTAGAG
* * * *
4012855 GAGCATTTTA-TTTTCTAAAGTTATGGTGCTTATGTTTAGAG
1 GAGCATTTTATTTTTCAAAAGTTATGATGCCTCTGTTTAGAG
* * *
4012896 GGGCA-TTTATTTTT--TAAGTTGTGATGCCTCTGTTTAGAG
1 GAGCATTTTATTTTTCAAAAGTTATGATGCCTCTGTTTAGAG
* * *
4012935 GAGTATTTTATTTTTCAAAAGTTGTTATGCCTCTGTTTAGAG
1 GAGCATTTTATTTTTCAAAAGTTATGATGCCTCTGTTTAGAG
*
4012977 GAGCATTTATTTTTTTCAAA
1 GAGCATTT-TATTTTTCAAA
4012997 GTCGTTGAGT
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 23 0.19
40 13 0.11
41 32 0.27
42 40 0.34
43 10 0.08
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.46
Consensus pattern (42 bp):
GAGCATTTTATTTTTCAAAAGTTATGATGCCTCTGTTTAGAG
Found at i:4012983 original size:81 final size:80
Alignment explanation
Indices: 4012842--4012991 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 80
4012832 AGTTATGGCA
* * * * *
4012842 CCTCTATTTATAGGAGCATTTTATTTTCTAAAGTTATGGTGCTTATGTTTAGAGGGGCATTTATT
1 CCTCTATTTAGAGGAGCATTTTATTTTCAAAAGTTATGATGCCTATGTTTAGAGGAGCATTTATT
4012907 TTTTAAGTTGTGATG
66 TTTTAAGTTGTGATG
* * * * *
4012922 CCTCTGTTTAGAGGAGTATTTTATTTTTCAAAAGTTGTTATGCCTCTGTTTAGAGGAGCATTTAT
1 CCTCTATTTAGAGGAGCATTTTA-TTTTCAAAAGTTATGATGCCTATGTTTAGAGGAGCATTTAT
4012987 TTTTT
65 TTTTT
4012992 TCAAAGTCGT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
80 20 0.34
81 39 0.66
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (80 bp):
CCTCTATTTAGAGGAGCATTTTATTTTCAAAAGTTATGATGCCTATGTTTAGAGGAGCATTTATT
TTTTAAGTTGTGATG
Found at i:4013466 original size:17 final size:17
Alignment explanation
Indices: 4013437--4013491 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
4013427 TTTATCTTCA
*
4013437 ATTTTTT-TATTTATCT
1 ATTTTTTATTTTTATCT
*
4013453 ATTTTTTATTTTTATGT
1 ATTTTTTATTTTTATCT
*
4013470 -TGTTTTTA-TTTTATTT
1 AT-TTTTTATTTTTATCT
4013486 ATTTTT
1 ATTTTT
4013492 AGATTTACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (17 bp):
ATTTTTTATTTTTATCT
Found at i:4013492 original size:15 final size:15
Alignment explanation
Indices: 4013440--4013492 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
4013430 ATCTTCAATT
*
4013440 TTTTTA-TTTATCTA
1 TTTTTATTTTATTTA
*
4013454 TTTTTTATTTTTATGTTG
1 -TTTTTA-TTTTAT-TTA
4013472 TTTTTATTTTATTTA
1 TTTTTATTTTATTTA
4013487 TTTTTA
1 TTTTTA
4013493 GATTTACCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 14 0.44
16 6 0.19
17 11 0.34
18 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTATTTA
Found at i:4014793 original size:48 final size:51
Alignment explanation
Indices: 4014711--4014805 Score: 133
Period size: 48 Copynumber: 1.9 Consensus size: 51
4014701 GAGAAAAAAG
* * * *
4014711 AAAAGAAGAATTTCTAAATTGACCTAAATGGTGAAATTTTTA-AAATTTTC
1 AAAAGAAGAAATTCTAAATTGACCCAAATAGTGAAAATTTTAGAAATTTTC
4014761 AAAA-AAGAAATT-TAAATTGACCCAAATAGTGAAAATTTTAGAAAT
1 AAAAGAAGAAATTCTAAATTGACCCAAATAGTGAAAATTTTAGAAAT
4014806 CCAACAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 25 0.62
49 11 0.28
50 4 0.10
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (51 bp):
AAAAGAAGAAATTCTAAATTGACCCAAATAGTGAAAATTTTAGAAATTTTC
Found at i:4014825 original size:48 final size:47
Alignment explanation
Indices: 4014725--4014825 Score: 105
Period size: 48 Copynumber: 2.1 Consensus size: 47
4014715 GAAGAATTTC
* * * ***
4014725 TAAATTGACCTAAATGGTGAAATTTTTAAAATTTTCAAAAAAGAAATT
1 TAAATTGACCCAAATAGTGAAAATTTTAAAATCAACAAAAAAGAAA-T
*
4014773 TAAATTGACCCAAATAGTGAAAATTTTAGAAATCCAACAAAAAATAAA-
1 TAAATTGACCCAAATAGTGAAAATTTTA-AAAT-CAACAAAAAAGAAAT
4014821 TAAAT
1 TAAAT
4014826 AAAGAGAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
48 30 0.68
49 4 0.09
50 10 0.23
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (47 bp):
TAAATTGACCCAAATAGTGAAAATTTTAAAATCAACAAAAAAGAAAT
Found at i:4016964 original size:12 final size:12
Alignment explanation
Indices: 4016930--4016964 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4016920 CATATTTTGT
*
4016930 TTTTTGTTTTCA
1 TTTTTGTTTTTA
4016942 TTTTTGTTTTTA
1 TTTTTGTTTTTA
*
4016954 TTTTTATTTTT
1 TTTTTGTTTTT
4016965 TAATTAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.83
Consensus pattern (12 bp):
TTTTTGTTTTTA
Found at i:4031051 original size:14 final size:14
Alignment explanation
Indices: 4031034--4031060 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4031024 TTTATAAAAT
4031034 AAATTTATTTTTTA
1 AAATTTATTTTTTA
4031048 AAATTTATTTTTT
1 AAATTTATTTTTT
4031061 CGTTTATAAA
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:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AAATTTATTTTTTA
Found at i:4033359 original size:21 final size:23
Alignment explanation
Indices: 4033326--4033371 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
4033316 TTTTTTTTTT
*
4033326 AATTTGAAGTTATCAAAATTTAA
1 AATTTGAAGTTATCAAAATTAAA
*
4033349 AATTTG-A-TTATTAAAATTAAA
1 AATTTGAAGTTATCAAAATTAAA
4033370 AA
1 AA
4033372 ATCTAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 1 0.05
23 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (23 bp):
AATTTGAAGTTATCAAAATTAAA
Found at i:4034042 original size:94 final size:94
Alignment explanation
Indices: 4033879--4034070 Score: 348
Period size: 94 Copynumber: 2.0 Consensus size: 94
4033869 TCAGTCACTG
4033879 CTTTAGTTGTCCTTTGTCACTGGTTTCCTTATTCAACCACGTCACCTTCAGTCTTAAATTTGCAA
1 CTTTAGTTGTCCTTTGTCACTGGTTTCCTTATTCAACCACGTCACCTTCAGTCTTAAATTTGCAA
4033944 TCGGTAACTTATTACAATAAGTTAATGGA
66 TCGGTAACTTATTACAATAAGTTAATGGA
* *
4033973 CTTTAGTTGTCCTTTGTCACTGGTTTCCTTATTCAACCACGTCATCTTCAGTCTTAAATTTGCAG
1 CTTTAGTTGTCCTTTGTCACTGGTTTCCTTATTCAACCACGTCACCTTCAGTCTTAAATTTGCAA
* *
4034038 TCGGTAACTTATTACATTAAGTTTATGGA
66 TCGGTAACTTATTACAATAAGTTAATGGA
4034067 CTTT
1 CTTT
4034071 TTACTTCCTC
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (94 bp):
CTTTAGTTGTCCTTTGTCACTGGTTTCCTTATTCAACCACGTCACCTTCAGTCTTAAATTTGCAA
TCGGTAACTTATTACAATAAGTTAATGGA
Found at i:4034330 original size:12 final size:13
Alignment explanation
Indices: 4034310--4034368 Score: 61
Period size: 12 Copynumber: 4.6 Consensus size: 13
4034300 ATATTATTTT
4034310 TAATATAAATATAA
1 TAAT-TAAATATAA
4034324 -AATTAAATATATA
1 TAATTAAATATA-A
* *
4034337 TAAATAATTATAA
1 TAATTAAATATAA
4034350 -AATTAAATA-AA
1 TAATTAAATATAA
4034361 TAATTAAA
1 TAATTAAA
4034369 AAAATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 2 0.05
12 22 0.58
13 5 0.13
14 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAATATAA
Found at i:4034348 original size:14 final size:14
Alignment explanation
Indices: 4034318--4034363 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
4034308 TTTAATATAA
4034318 ATATAAAATTAAAT
1 ATATAAAATTAAAT
4034332 ATATATAAA-T-AAT
1 ATATA-AAATTAAAT
4034345 -TATAAAATTAAAT
1 ATATAAAATTAAAT
*
4034358 AAATAA
1 ATATAA
4034364 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
11 3 0.11
12 5 0.19
13 6 0.22
14 10 0.37
15 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATAAAATTAAAT
Found at i:4037624 original size:17 final size:18
Alignment explanation
Indices: 4037596--4037629 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4037586 ATAAATATAT
*
4037596 AAAAATTAATTTTTTAAA
1 AAAAATTAATTTATTAAA
4037614 AAAAATT-ATTTATTAA
1 AAAAATTAATTTATTAA
4037630 TAAAGTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATTAATTTATTAAA
Found at i:4039739 original size:29 final size:29
Alignment explanation
Indices: 4039668--4039739 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
4039658 GGAATGATTT
* * *
4039668 TTAAATTATAATAAAATGTTTGATTTGATAT
1 TTAAATTAT-A-AAAATGTTTAATTTAATAA
* *
4039699 TTAAATTTTAAAAATTTTTAATTTAATAA
1 TTAAATTATAAAAATGTTTAATTTAATAA
*
4039728 TTATATTATAAA
1 TTAAATTATAAA
4039740 TTTATTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 25 0.74
30 1 0.03
31 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
TTAAATTATAAAAATGTTTAATTTAATAA
Found at i:4040195 original size:30 final size:29
Alignment explanation
Indices: 4040159--4040259 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 29
4040149 TTACGACATC
* *
4040159 TAAATAAATTTTTAATTTTTAATTTATATT
1 TAAATAAA-TATTAACTTTTAATTTATATT
*
4040189 TAAATAAGACATTAACTTTT-ATTTCATATT
1 TAAATAA-ATATTAACTTTTAATTT-ATATT
* * *
4040219 CAAATAAATCTTAACTTTTAATTTGTATT
1 TAAATAAATATTAACTTTTAATTTATATT
4040248 TAAATAAATATT
1 TAAATAAATATT
4040260 CAAAATATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 28 0.47
30 30 0.51
31 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (29 bp):
TAAATAAATATTAACTTTTAATTTATATT
Found at i:4040519 original size:15 final size:15
Alignment explanation
Indices: 4040474--4040521 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
4040464 AAAAATATGT
*
4040474 TTTAAAATTTTCAAA
1 TTTAAAATTTACAAA
*
4040489 TTTCAAAATTCA-AAA
1 TTT-AAAATTTACAAA
4040504 TTTAAAATTTACAAA
1 TTTAAAATTTACAAA
4040519 TTT
1 TTT
4040522 TATTTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.25
15 15 0.54
16 6 0.21
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAAATTTACAAA
Found at i:4042948 original size:24 final size:24
Alignment explanation
Indices: 4042893--4042966 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
4042883 GGTAGGAAGG
*
4042893 AGAACAAGAAA-GAAAAGAA-AAATA
1 AGAA-AAGAAAGGAAAA-AAGAAAAA
*
4042917 AGATAAAGAAAGGAAATAAGAAAAA
1 AGA-AAAGAAAGGAAAAAAGAAAAA
4042942 AGAAAAG-AAGGAAAAAAAGAAAAA
1 AGAAAAGAAAGG-AAAAAAGAAAAA
4042966 A
1 A
4042967 ACAAATTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
23 4 0.09
24 27 0.63
25 12 0.28
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (24 bp):
AGAAAAGAAAGGAAAAAAGAAAAA
Found at i:4043661 original size:24 final size:24
Alignment explanation
Indices: 4043625--4043679 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
4043615 TTTTTTTATG
*
4043625 TTTTTTCACTTTTAT-CTTTTAATT
1 TTTTTTTACTTTT-TGCTTTTAATT
* *
4043649 TTTTTTTATTTTTTGTTTTTAATT
1 TTTTTTTACTTTTTGCTTTTAATT
4043673 TTTTTTT
1 TTTTTTT
4043680 TAATTAGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTTTTACTTTTTGCTTTTAATT
Found at i:4043662 original size:18 final size:19
Alignment explanation
Indices: 4043634--4043684 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
4043624 GTTTTTTCAC
*
4043634 TTTTATCTTTTAATTTTT-
1 TTTTATTTTTTAATTTTTA
*
4043652 TTTTATTTTTT-GTTTTTAA
1 TTTTATTTTTTAATTTTT-A
4043671 TTTT-TTTTTTAATT
1 TTTTATTTTTTAATT
4043685 AGGGAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.19
18 16 0.59
19 6 0.22
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTTAATTTTTA
Found at i:4043682 original size:12 final size:12
Alignment explanation
Indices: 4043641--4043684 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
4043631 CACTTTTATC
4043641 TTTTAA-TTTTT
1 TTTTAATTTTTT
*
4043652 TTTTATTTTTTGT
1 TTTTAATTTTT-T
4043665 TTTTAATTTTTT
1 TTTTAATTTTTT
4043677 TTTTAATT
1 TTTTAATT
4043685 AGGGAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 5 0.17
12 13 0.45
13 11 0.38
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:4046031 original size:16 final size:16
Alignment explanation
Indices: 4046012--4046069 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
4046002 TGTCAACAAA
4046012 TAATTTTTATGGAGTT
1 TAATTTTTATGGAGTT
*
4046028 TAATTTTTAT--ATTT
1 TAATTTTTATGGAGTT
4046042 TAATTTTTATGGAGTT
1 TAATTTTTATGGAGTT
*
4046058 TAATTTATATGG
1 TAATTTTTATGG
4046070 TTGTCAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 13 0.35
16 24 0.65
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (16 bp):
TAATTTTTATGGAGTT
Found at i:4057275 original size:2 final size:2
Alignment explanation
Indices: 4057268--4057304 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4057258 GTAGTACGTT
4057268 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4057305 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4057309 original size:2 final size:2
Alignment explanation
Indices: 4057304--4057337 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4057294 TCTCTCTCTC
4057304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4057338 CGTCCGTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4062699 original size:20 final size:20
Alignment explanation
Indices: 4062665--4062704 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4062655 ATCTTAAATC
** *
4062665 CAAATTAATTGTAAATTTAT
1 CAAATTAATCCTAAAATTAT
4062685 CAAATTAATCCTAAAATTAT
1 CAAATTAATCCTAAAATTAT
4062705 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (20 bp):
CAAATTAATCCTAAAATTAT
Found at i:4063555 original size:21 final size:21
Alignment explanation
Indices: 4063529--4063589 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
4063519 GATTCAATCA
4063529 AATTTAAATATTTTTATATTT
1 AATTTAAATATTTTTATATTT
*
4063550 AATTTAAAT-TATTTATGAATTT
1 AATTTAAATATTTTTAT--ATTT
4063572 AATTT--A-ATTTTTATATTT
1 AATTTAAATATTTTTATATTT
4063590 TAATATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 4 0.11
20 13 0.37
21 9 0.26
22 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
AATTTAAATATTTTTATATTT
Found at i:4063571 original size:22 final size:21
Alignment explanation
Indices: 4063529--4063593 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
4063519 GATTCAATCA
*
4063529 AATTTAAA-TATTTTTATATTT
1 AATTTAAATTATTTATA-ATTT
4063550 AATTTAAATTATTTATGAATTT
1 AATTTAAATTATTTAT-AATTT
*
4063572 AATTT-AATT-TTTATATTTT
1 AATTTAAATTATTTATAATTT
4063591 AAT
1 AAT
4063594 ATATTTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
21 12 0.30
22 15 0.38
23 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
AATTTAAATTATTTATAATTT
Found at i:4063593 original size:19 final size:19
Alignment explanation
Indices: 4063538--4063613 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
4063528 AAATTTAAAT
4063538 ATTTTTATA-TTTAATTTAA
1 ATTTTTATATTTTAATTT-A
*
4063557 ATTATTTATGAATTTAATTTA
1 ATT-TTTAT-ATTTTAATTTA
*
4063578 ATTTTTATATTTTAATAT-
1 ATTTTTATATTTTAATTTA
*
4063596 ATTTTAATTATTTTAATT
1 ATTTTTA-TATTTTAATT
4063614 AATAAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.12
19 20 0.41
20 10 0.20
21 5 0.10
22 8 0.16
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (19 bp):
ATTTTTATATTTTAATTTA
Found at i:4063596 original size:10 final size:10
Alignment explanation
Indices: 4063583--4063612 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4063573 ATTTAATTTT
4063583 TATATTTTAA
1 TATATTTTAA
4063593 TATATTTTAA
1 TATATTTTAA
4063603 T-TATTTTAA
1 TATATTTTAA
4063612 T
1 T
4063613 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:4063609 original size:9 final size:9
Alignment explanation
Indices: 4063585--4063614 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
4063575 TTAATTTTTA
4063585 TATTTTAAT
1 TATTTTAAT
4063594 ATATTTTAAT
1 -TATTTTAAT
4063604 TATTTTAAT
1 TATTTTAAT
4063613 TA
1 TA
4063615 ATAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:4063764 original size:5 final size:5
Alignment explanation
Indices: 4063747--4063784 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
4063737 TTTTTATTTC
*
4063747 AAATT AAATTT AAATT AAA-A AAATT AAATT AAATT AAA
1 AAATT AAA-TT AAATT AAATT AAATT AAATT AAATT AAA
4063785 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.10
5 21 0.72
6 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AAATT
Found at i:4063780 original size:19 final size:20
Alignment explanation
Indices: 4063747--4063785 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
4063737 TTTTTATTTC
4063747 AAATTAAATTTAAATTAAAA
1 AAATTAAATTTAAATTAAAA
4063767 AAATTAAA-TTAAATTAAAA
1 AAATTAAATTTAAATTAAAA
4063786 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTAAATTTAAATTAAAA
Found at i:4077462 original size:18 final size:19
Alignment explanation
Indices: 4077428--4077469 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
4077418 AAATTTAAAT
4077428 TATAA-ATTTATTAATTAA
1 TATAATATTTATTAATTAA
4077446 TATAATATTTATT-ATTAA
1 TATAATATTTATTAATTAA
4077464 TATAAT
1 TATAAT
4077470 TAATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATAATATTTATTAATTAA
Found at i:4077463 original size:22 final size:21
Alignment explanation
Indices: 4077435--4077477 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4077425 AATTATAAAT
4077435 TTATTAAT-TAATATAATATTTA
1 TTATTAATATAAT-TAAT-TTTA
4077457 TTATTAATATAATTAATTTTA
1 TTATTAATATAATTAATTTTA
4077478 AATAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTAATATAATTAATTTTA
Found at i:4078167 original size:21 final size:20
Alignment explanation
Indices: 4078137--4078208 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
4078127 ATTTCAACAT
* *
4078137 TAATTTTAATTTTATTATTA
1 TAATTTTAATCTTATCATTA
*
4078157 TAATATTTAATCTCATCATTA
1 TAAT-TTTAATCTTATCATTA
*
4078178 TAATAATTAATCTTATCATTA
1 TAAT-TTTAATCTTATCATTA
*
4078199 TTATTTTAAT
1 TAATTTTAAT
4078209 TTCATCAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.20
21 35 0.80
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTAATCTTATCATTA
Found at i:4086648 original size:52 final size:51
Alignment explanation
Indices: 4086541--4086695 Score: 177
Period size: 52 Copynumber: 3.0 Consensus size: 51
4086531 ATAACCATAA
* * * * * * *
4086541 AAACTTACCCATTAAGAATCCCTATCCCTTAGAATTTTTCTCCTGTAAGTT
1 AAACTTACCTATTAAGAATTCATTTCCCTTAGAATTCTTCTCTTGTAAGTC
*
4086592 AAACTTACCTATTAAGAATTCATTTCCCCTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTACCTATTAAGAATTCATTT-CCCTTAGAATTCTTCTCTTGTAAGTC
** *
4086644 AAACTTACCTATTAAGAA-TCATCTTTCTTTTAGAATTCTTCTTTTGTAAGTC
1 AAACTTACCTATTAAGAATTCA--TTTCCCTTAGAATTCTTCTCTTGTAAGTC
4086696 TTCTTATCCA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
51 24 0.27
52 62 0.70
53 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (51 bp):
AAACTTACCTATTAAGAATTCATTTCCCTTAGAATTCTTCTCTTGTAAGTC
Found at i:4086736 original size:11 final size:11
Alignment explanation
Indices: 4086720--4086761 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
4086710 GCAATATCTG
4086720 ACAAATCTCAA
1 ACAAATCTCAA
*
4086731 ACAAATCTCTA
1 ACAAATCTCAA
*
4086742 ACAAATCCCAA
1 ACAAATCTCAA
4086753 ACAAATCTC
1 ACAAATCTC
4086762 TTATGGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:4086745 original size:22 final size:22
Alignment explanation
Indices: 4086720--4086762 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4086710 GCAATATCTG
*
4086720 ACAAATCTCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
4086742 ACAAATCCCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
4086763 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:4087688 original size:52 final size:51
Alignment explanation
Indices: 4087607--4087752 Score: 143
Period size: 52 Copynumber: 2.8 Consensus size: 51
4087597 TATAACTATA
* * *
4087607 CAAACTTGACC-ATTAAGAATCCCTATCCCCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTG-CCTATTAAGAAT-TCTTTCCCCTTAGAATTCTTCTCCTGAAAGT
* *
4087659 CAAACTTGCCTATTAAGAATTCATTTCCCCTTAAAATTCTTCTCTTGAAAGT
1 CAAACTTGCCTATTAAGAATTC-TTTCCCCTTAGAATTCTTCTCCTGAAAGT
* * * * **
4087711 TAAACTTACATATTAAAAATCTCTTT-CTTTTAGAATTCTTCT
1 CAAACTTGCCTATTAAGAAT-TCTTTCCCCTTAGAATTCTTCT
4087753 TTTGCAAGTC
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
51 16 0.20
52 61 0.77
53 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATTCTTTCCCCTTAGAATTCTTCTCCTGAAAGT
Found at i:4087803 original size:11 final size:11
Alignment explanation
Indices: 4087787--4087828 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
4087777 GCAATATCTG
4087787 ACAAATCTCAA
1 ACAAATCTCAA
*
4087798 ACAAATCTCTA
1 ACAAATCTCAA
*
4087809 ACAAATCCCAA
1 ACAAATCTCAA
4087820 ACAAATCTC
1 ACAAATCTC
4087829 TTATGAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:4087812 original size:22 final size:22
Alignment explanation
Indices: 4087787--4087829 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4087777 GCAATATCTG
*
4087787 ACAAATCTCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
4087809 ACAAATCCCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
4087830 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:4088768 original size:52 final size:52
Alignment explanation
Indices: 4088678--4088802 Score: 142
Period size: 52 Copynumber: 2.4 Consensus size: 52
4088668 TATAACTATA
* * * * * *
4088678 CAAACTTGCCCATTAAAAATCCCTATCCTCTTAGAATTCTTCTCCTGTAAAT
1 CAAACTTGCCAATTAAGAATCCATATCCCCTTAAAATTCTTCTCCTGCAAAT
* * * *
4088730 CAAACTTGCCAATTAAGAATTCATTTCCCCTTAAAATTCTTCTCTTGCAAGT
1 CAAACTTGCCAATTAAGAATCCATATCCCCTTAAAATTCTTCTCCTGCAAAT
* *
4088782 CAAACTTACCTATTAAGAATC
1 CAAACTTGCCAATTAAGAATC
4088803 ATCTTTCTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.34
Consensus pattern (52 bp):
CAAACTTGCCAATTAAGAATCCATATCCCCTTAAAATTCTTCTCCTGCAAAT
Found at i:4088820 original size:52 final size:52
Alignment explanation
Indices: 4088707--4088832 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 52
4088697 TCCCTATCCT
* * * *
4088707 CTTAGAATTCTTCTCCTGTAAATCAAACTTGCCAATTAAGAATTCATTTCCC
1 CTTAGAATTCTTCTCTTGCAAGTCAAACTTACCAATTAAGAATTCATTTCCC
* * * *
4088759 CTTAAAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAGAA-TCATCTTTCT
1 CTTAGAATTCTTCTCTTGCAAGTCAAACTTACCAATTAAGAATTCAT-TTCCC
* *
4088811 TTTAGAATTCTT-TTTTGCAAGT
1 CTTAGAATTCTTCTCTTGCAAGT
4088833 TTTCTTATCC
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 13 0.21
52 49 0.79
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (52 bp):
CTTAGAATTCTTCTCTTGCAAGTCAAACTTACCAATTAAGAATTCATTTCCC
Found at i:4088874 original size:11 final size:11
Alignment explanation
Indices: 4088858--4088899 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
4088848 GTAATATCTG
4088858 ACAAATCTCAA
1 ACAAATCTCAA
*
4088869 ACAAATCTCTA
1 ACAAATCTCAA
*
4088880 ACAAATCCCAA
1 ACAAATCTCAA
4088891 ACAAATCTC
1 ACAAATCTC
4088900 TTATGAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:4088883 original size:22 final size:22
Alignment explanation
Indices: 4088858--4088900 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4088848 GTAATATCTG
*
4088858 ACAAATCTCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
4088880 ACAAATCCCAAACAAATCTCT
1 ACAAATCCCAAACAAATCTCT
4088901 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:4090337 original size:20 final size:21
Alignment explanation
Indices: 4090304--4090342 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4090294 TTTTCAAAGT
*
4090304 GATTTTGAA-TTTTTTTTAGA
1 GATTTTGAAGTTTTATTTAGA
*
4090324 GATTTTTAAGTTTTATTTA
1 GATTTTGAAGTTTTATTTA
4090343 ATATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (21 bp):
GATTTTGAAGTTTTATTTAGA
Found at i:4090894 original size:2 final size:2
Alignment explanation
Indices: 4090889--4090918 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4090879 AAAAAGAGTT
4090889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4090919 AATTCTTCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4099690 original size:16 final size:17
Alignment explanation
Indices: 4099658--4099691 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4099648 CATTTGGTGA
*
4099658 TTAAATTTTTATGAAAT
1 TTAAATTTTCATGAAAT
4099675 TTAAATTTTCAT-AAAT
1 TTAAATTTTCATGAAAT
4099691 T
1 T
4099692 AGCTAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTTCATGAAAT
Found at i:4102194 original size:27 final size:28
Alignment explanation
Indices: 4102135--4102208 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 28
4102125 GAATAGTTGA
* * *
4102135 TAAATTATTTGATTATATT-TTATTTAT
1 TAAATTATTTAATTAAATTATGATTTAT
*
4102162 TTAATTATTTAATTAAATTATGATTT-T
1 TAAATTATTTAATTAAATTATGATTTAT
*
4102189 TAAATTA-ATAATTAAGATTA
1 TAAATTATTTAATTAA-ATTA
4102209 AAATTATCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 7 0.18
27 27 0.69
28 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TAAATTATTTAATTAAATTATGATTTAT
Found at i:4107602 original size:28 final size:28
Alignment explanation
Indices: 4107561--4107643 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
4107551 AATATTATAT
**
4107561 AATTAATAAATTTATAATTAAAATATTA
1 AATTAATATTTTTATAATTAAAATATTA
* * *
4107589 TATTAATATTTTTAAAATTTAAATATTA
1 AATTAATATTTTTATAATTAAAATATTA
4107617 AATTAAATATTTTATTATAATTTAAAA
1 AATT-AATA-TTT-TTATAA-TTAAAA
4107644 ATTTTGCATC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 26 0.60
29 4 0.09
30 3 0.07
31 5 0.12
32 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTAATATTTTTATAATTAAAATATTA
Found at i:4107633 original size:40 final size:40
Alignment explanation
Indices: 4107567--4107647 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 40
4107557 ATATAATTAA
* *
4107567 TAAATTTATAATTAAAATATTATATTAATATTTTTAAAATT
1 TAAATTTATAATTAAAATATTATATT-ATAATTTAAAAATT
*
4107608 TAAATATTA-AATT-AAATATTTTATTATAATTTAAAAATT
1 TAAAT-TTATAATTAAAATATTATATTATAATTTAAAAATT
4107647 T
1 T
4107648 TGCATCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 13 0.36
40 11 0.31
41 9 0.25
42 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
TAAATTTATAATTAAAATATTATATTATAATTTAAAAATT
Found at i:4107641 original size:19 final size:19
Alignment explanation
Indices: 4107572--4107648 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
4107562 ATTAATAAAT
* *
4107572 TTATAATTAAAATATTATA
1 TTATAATTTAAATATTTTA
* *
4107591 TTAATATTTTTAAA-ATTTAA
1 TT-ATA-ATTTAAATATTTTA
* *
4107611 ATATTAAATTAAATATTTTA
1 TTA-TAATTTAAATATTTTA
*
4107631 TTATAATTTAAAAATTTT
1 TTATAATTTAAATATTTT
4107649 GCATCATTCT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 21 0.49
20 17 0.40
21 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATAATTTAAATATTTTA
Found at i:4108919 original size:24 final size:23
Alignment explanation
Indices: 4108870--4108931 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 23
4108860 CCTTATCAAC
*
4108870 AAAAAATGAAAATTTTGGATTCTA
1 AAAAAAT-AAAATTTTGGAATCTA
4108894 AAAAAATAATAATTTTGGGAAT-TA
1 AAAAAATAA-AATTTT-GGAATCTA
4108918 AAATAAATATAAAT
1 AAA-AAATA-AAAT
4108932 AAAATTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 2 0.06
24 18 0.55
25 12 0.36
26 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (23 bp):
AAAAAATAAAATTTTGGAATCTA
Found at i:4111314 original size:20 final size:20
Alignment explanation
Indices: 4111276--4111316 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4111266 CAAACATTGT
*
4111276 AATATCTAATACCGTTTTTG
1 AATATCTAATACCGCTTTTG
4111296 AATATCTAAT-CCTGCTTTTG
1 AATATCTAATACC-GCTTTTG
4111316 A
1 A
4111317 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (20 bp):
AATATCTAATACCGCTTTTG
Found at i:4113606 original size:32 final size:32
Alignment explanation
Indices: 4113546--4113607 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
4113536 AAAAAATCTA
4113546 AAATATTTTAAAATATGCAAAAAATTAAAACTG
1 AAATATTTTAAAATAT-CAAAAAATTAAAACTG
*
4113579 AAATATTTTAAAAATAT-AAAAATTTAAAA
1 AAATATTTT-AAAATATCAAAAAATTAAAA
4113608 AATCTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 11 0.41
33 9 0.33
34 7 0.26
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (32 bp):
AAATATTTTAAAATATCAAAAAATTAAAACTG
Found at i:4113671 original size:55 final size:55
Alignment explanation
Indices: 4113612--4113715 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 55
4113602 TTAAAAAATC
4113612 TAAAAA-TTTTAATAAAAATCCAAAAAATTCAAAAAAATGAAAATTTTAATAAAAA
1 TAAAAATTTTTAA-AAAAATCCAAAAAATTCAAAAAAATGAAAATTTTAATAAAAA
* * * * * *
4113667 TAAAAATTTTTGAAAAAATCTAAAAATTTGAAAAAAGTTAAAATTTTAA
1 TAAAAATTTTTAAAAAAATCCAAAAAATTCAAAAAAATGAAAATTTTAA
4113716 AAATTTTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 37 0.88
56 5 0.12
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (55 bp):
TAAAAATTTTTAAAAAAATCCAAAAAATTCAAAAAAATGAAAATTTTAATAAAAA
Found at i:4113709 original size:26 final size:25
Alignment explanation
Indices: 4113680--4113737 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
4113670 AAATTTTTGA
4113680 AAAAATCTAAAAA-TTTGAAAAAAGTT
1 AAAAATCTAAAAATTTTG-AAAAA-TT
* *
4113706 AAAATTTTAAAAATTTTTGAAAAATT
1 AAAAATCTAAAAA-TTTTGAAAAATT
4113732 AAAAAT
1 AAAAAT
4113738 TTTCAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 18 0.67
27 5 0.19
28 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (25 bp):
AAAAATCTAAAAATTTTGAAAAATT
Found at i:4113710 original size:37 final size:35
Alignment explanation
Indices: 4113662--4113781 Score: 105
Period size: 37 Copynumber: 3.5 Consensus size: 35
4113652 AAATTTTAAT
*
4113662 AAAAATAAAAATTTTTGAAAAAATCTAAAAATTTGA
1 AAAAATTAAAATTTTT-AAAAAATCTAAAAATTTGA
4113698 AAAAAGTTAAAA-TTTT-AAAAAT-T-----TTTG-
1 AAAAA-TTAAAATTTTTAAAAAATCTAAAAATTTGA
* *
4113725 AAAAATTAAAAATTTTCAAAAAATCTAAAATATTTTA
1 AAAAATT-AAAATTTTTAAAAAATCTAAAA-ATTTGA
4113762 AAAAATTAAAAATTTTTAAA
1 AAAAATT-AAAATTTTTAAA
4113782 TAAAAATAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
26 2 0.03
27 9 0.13
28 7 0.10
29 6 0.09
30 1 0.01
33 1 0.01
34 6 0.09
36 12 0.18
37 24 0.35
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (35 bp):
AAAAATTAAAATTTTTAAAAAATCTAAAAATTTGA
Found at i:4113725 original size:28 final size:28
Alignment explanation
Indices: 4113693--4113746 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 28
4113683 AATCTAAAAA
4113693 TTTGAAAAAAGTT-AAAATTTT-AAAAATT
1 TTTG-AAAAA-TTAAAAATTTTCAAAAATT
4113721 TTTGAAAAATTAAAAATTTTCAAAAA
1 TTTGAAAAATTAAAAATTTTCAAAAA
4113747 ATCTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.08
27 13 0.54
28 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (28 bp):
TTTGAAAAATTAAAAATTTTCAAAAATT
Done.