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 24 of 131
Found at i:5813167 original size:19 final size:19
Alignment explanation
Indices: 5813127--5813168 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5813117 GGGTATTTTT
*
5813127 TATTTTTTTAATATATAAA
1 TATTTTTATAATATATAAA
*
5813146 TATTTTTATATTAT-TAATA
1 TATTTTTATAATATATAA-A
5813165 TATT
1 TATT
5813169 AAGTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTATAATATATAAA
Found at i:5813302 original size:29 final size:29
Alignment explanation
Indices: 5813229--5813303 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
5813219 ATTGTGTTCT
* **
5813229 TTTATATATATTTATGTTAATTATATTTA
1 TTTATATATATTTATATTAATTATACCTA
* * * *
5813258 TTTTTAAATATCTATATTAGTTATACCTA
1 TTTATATATATTTATATTAATTATACCTA
*
5813287 TTTATATTTATTTATAT
1 TTTATATATATTTATAT
5813304 CGTGTTTAAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTATATATATTTATATTAATTATACCTA
Found at i:5814264 original size:12 final size:12
Alignment explanation
Indices: 5814249--5814325 Score: 75
Period size: 12 Copynumber: 6.4 Consensus size: 12
5814239 TAAAGAAGCG
* *
5814249 AAGAAAGAAGAT
1 AAGAAAGAGGAA
5814261 AAGACAA-AGGAA
1 AAGA-AAGAGGAA
*
5814273 AAGAAAGAGGAG
1 AAGAAAGAGGAA
** *
5814285 AAGAAAGAACAG
1 AAGAAAGAGGAA
5814297 AAGAAAGAGGAA
1 AAGAAAGAGGAA
*
5814309 AAGAAAGATGAA
1 AAGAAAGAGGAA
5814321 AAGAA
1 AAGAA
5814326 GGAACAGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
11 2 0.04
12 50 0.93
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (12 bp):
AAGAAAGAGGAA
Found at i:5814288 original size:36 final size:36
Alignment explanation
Indices: 5814248--5814334 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
5814238 CTAAAGAAGC
* *
5814248 GAAGAAAGAAGATAAGACAA-AGGAAAAGAAAGAGGA
1 GAAGAAAGAACAGAAGA-AAGAGGAAAAGAAAGAGGA
*
5814284 GAAGAAAGAACAGAAGAAAGAGGAAAAGAAAGATGA
1 GAAGAAAGAACAGAAGAAAGAGGAAAAGAAAGAGGA
* *
5814320 AAAGAAGGAACAGAA
1 GAAGAAAGAACAGAA
5814335 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.64, C:0.03, G:0.30, T:0.02
Consensus pattern (36 bp):
GAAGAAAGAACAGAAGAAAGAGGAAAAGAAAGAGGA
Found at i:5820653 original size:3 final size:3
Alignment explanation
Indices: 5820647--5820694 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
5820637 TTATTAGATA
* *
5820647 TAT TAT TAT TAAT TAT TAAT TAT TAT TAA TAT AAT TAT TATT TAT TAT
1 TAT TAT TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
5820695 AAAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 29 0.76
4 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5820655 original size:15 final size:15
Alignment explanation
Indices: 5820635--5820688 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
5820625 AATATAAAAA
5820635 TATTATTAGATAT-AT
1 TATTATTA-ATATAAT
5820650 TATTATTAATTATTAAT
1 TATTATTAA-TA-TAAT
5820667 TATTATTAATATAAT
1 TATTATTAATATAAT
5820682 TATTATT
1 TATTATT
5820689 TATTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.03
15 21 0.58
16 3 0.08
17 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATTATTAATATAAT
Found at i:5820659 original size:32 final size:33
Alignment explanation
Indices: 5820600--5820710 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 33
5820590 GTTTTTATTT
*
5820600 AAAAT-TT-TTAA-ATAATTTTTAATTTAATATA
1 AAAATATTATTAATATAATTATT-ATTTAATATA
5820631 AAAATATTATTAGATAT-ATTATTA-TTAAT-TA
1 AAAATATTATTA-ATATAATTATTATTTAATATA
* * *
5820662 TTAATTATTATTAATATAATTATTATTTATTATA
1 -AAAATATTATTAATATAATTATTATTTAATATA
*
5820696 AAAATAATTTTTAAT
1 AAAAT-ATTATTAAT
5820711 TTTTATTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
31 11 0.17
32 24 0.38
33 11 0.17
34 16 0.25
35 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
AAAATATTATTAATATAATTATTATTTAATATA
Found at i:5820661 original size:22 final size:22
Alignment explanation
Indices: 5820649--5820720 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
5820639 ATTAGATATA
5820649 TTATT-AT-TAATTATTAATTA
1 TTATTAATATAATTATTAATTA
*
5820669 TTATTAATATAATTATTATTTA
1 TTATTAATATAATTATTAATTA
* * * *
5820691 TTATAAAAATAATTTTTAATTT
1 TTATTAATATAATTATTAATTA
5820713 TTATTAAT
1 TTATTAAT
5820721 TTTATAAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.12
21 2 0.05
22 35 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTAATATAATTATTAATTA
Found at i:5820694 original size:7 final size:7
Alignment explanation
Indices: 5820636--5820693 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
5820626 ATATAAAAAT
5820636 ATTATTA
1 ATTATTA
5820643 GATATATT-
1 -AT-TATTA
5820651 ATTATTA
1 ATTATTA
5820658 ATTATTA
1 ATTATTA
5820665 ATTATT-
1 ATTATTA
5820671 ATTAATATA
1 ATT-AT-TA
5820680 ATTATTA
1 ATTATTA
*
5820687 TTTATTA
1 ATTATTA
5820694 TAAAAATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
6 7 0.16
7 25 0.57
8 5 0.11
9 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (7 bp):
ATTATTA
Found at i:5820740 original size:18 final size:17
Alignment explanation
Indices: 5820698--5820740 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5820688 TTATTATAAA
* *
5820698 AATAATTTTTAATTTTT
1 AATAATTTTTAAATATT
*
5820715 ATTAATTTTATAAATATT
1 AATAATTTT-TAAATATT
5820733 AATAATTT
1 AATAATTT
5820741 AAATTTGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATAATTTTTAAATATT
Found at i:5828061 original size:18 final size:19
Alignment explanation
Indices: 5828038--5828078 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5828028 TTTATTGCAC
* *
5828038 TTAAATAAGTTTTTAAT-T
1 TTAAATAAATTCTTAATCT
5828056 TTAAATAAATTCTTAATCT
1 TTAAATAAATTCTTAATCT
5828075 TTAA
1 TTAA
5828079 TTTGTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAATAAATTCTTAATCT
Found at i:5829048 original size:28 final size:27
Alignment explanation
Indices: 5829016--5829078 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
5829006 TTTTTGTTGC
*
5829016 ATTTATCTATGTATATATATGTTTATTT
1 ATTTATCTATGTATATATAT-TTTAATT
* * *
5829044 ATTTATCTATTTTTATCTATTTTAATT
1 ATTTATCTATGTATATATATTTTAATT
5829071 ATTTATCT
1 ATTTATCT
5829079 TTGTTTATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 14 0.45
28 17 0.55
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.63
Consensus pattern (27 bp):
ATTTATCTATGTATATATATTTTAATT
Found at i:5829094 original size:27 final size:27
Alignment explanation
Indices: 5829016--5829092 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
5829006 TTTTTGTTGC
* * * *
5829016 ATTTATCTATGTATATATATGTTTATTT
1 ATTTATCTATTTTTATCTAT-TTTAATT
5829044 ATTTATCTATTTTTATCTATTTTAATT
1 ATTTATCTATTTTTATCTATTTTAATT
5829071 ATTTATCT-TTGTTTATC-ATTTT
1 ATTTATCTATT-TTTATCTATTTT
5829093 TATGGTTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.16
27 20 0.45
28 17 0.39
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (27 bp):
ATTTATCTATTTTTATCTATTTTAATT
Found at i:5829577 original size:9 final size:10
Alignment explanation
Indices: 5829553--5829597 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
5829543 GAATTATCAT
5829553 TTTTTTGTGAA
1 TTTTTTG-GAA
5829564 TTTTTTGGAA
1 TTTTTTGGAA
*
5829574 TTTTTTGAAA
1 TTTTTTGGAA
*
5829584 TTTTTTGAAA
1 TTTTTTGGAA
5829594 TTTT
1 TTTT
5829598 CATCTTTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.64
Consensus pattern (10 bp):
TTTTTTGGAA
Found at i:5833154 original size:30 final size:30
Alignment explanation
Indices: 5833120--5833178 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
5833110 TTACTAAGCT
5833120 CCTAATATGAGATACAAGATAAACTCTTAC
1 CCTAATATGAGATACAAGATAAACTCTTAC
*
5833150 CCTAATGTGAGATACAAGATAAACTCTTA
1 CCTAATATGAGATACAAGATAAACTCTTA
5833179 ACTCCTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (30 bp):
CCTAATATGAGATACAAGATAAACTCTTAC
Found at i:5835741 original size:3 final size:3
Alignment explanation
Indices: 5835733--5835779 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5835723 TCATAAATGG
5835733 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5835780 CTATAATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5841995 original size:3 final size:3
Alignment explanation
Indices: 5841982--5842036 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
5841972 AATATTCTGA
5841982 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5842029 AAT AAT AA
1 AAT AAT AA
5842037 AAAGATTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5845744 original size:23 final size:20
Alignment explanation
Indices: 5845714--5845757 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
5845704 AAAAAAATAT
5845714 ATATTTTAAAATTTAATATTATA
1 ATATTTT-AAATTT-AT-TTATA
5845737 ATATTTTAAATTTATTTATA
1 ATATTTTAAATTTATTTATA
5845757 A
1 A
5845758 ATGAGATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 6 0.29
23 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTAAATTTATTTATA
Found at i:5848375 original size:17 final size:18
Alignment explanation
Indices: 5848340--5848381 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
5848330 AAGCTTATGG
5848340 TAAATATTAATATTAATT
1 TAAATATTAATATTAATT
* *
5848358 TAAAT-TTAATTTTTATT
1 TAAATATTAATATTAATT
5848375 TAAATAT
1 TAAATAT
5848382 ATTTAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATATTAATATTAATT
Found at i:5848704 original size:15 final size:14
Alignment explanation
Indices: 5848676--5848709 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5848666 AGATAATTTA
5848676 ATAATTTTTAAAAT
1 ATAATTTTTAAAAT
*
5848690 ATAATTTTTATAA-
1 ATAATTTTTAAAAT
5848703 ATAATTT
1 ATAATTT
5848710 AAAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATTTTTAAAAT
Found at i:5852085 original size:26 final size:26
Alignment explanation
Indices: 5852035--5852085 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5852025 AAAAATTACA
* *
5852035 AAATAATATTATTAATTTATTATAAT
1 AAATAATATTATTAATATATAATAAT
* *
5852061 AAATAATTTTATTACTATATAATAA
1 AAATAATATTATTAATATATAATAA
5852086 ATTAATAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATAATATTATTAATATATAATAAT
Found at i:5859242 original size:68 final size:68
Alignment explanation
Indices: 5859120--5859257 Score: 177
Period size: 68 Copynumber: 2.0 Consensus size: 68
5859110 TTGCTGGGGG
*
5859120 GGAGATTGTTGGCAAATTGGAGATTGGCCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
1 GGAGATTGTTGGCAAATTGGAGATTGACCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
5859185 AAA
66 AAA
* * * * * * * * **
5859188 GGAGATTGTTGGTAGATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATT
1 GGAGATTGTTGGCAAATTGGAGATTGACCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
5859253 AAA
66 AAA
5859256 GG
1 GG
5859258 TTTGACTTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (68 bp):
GGAGATTGTTGGCAAATTGGAGATTGACCGTATCCATCAACTCTATGTACTCGAACACCAGTATT
AAA
Found at i:5859320 original size:42 final size:42
Alignment explanation
Indices: 5859261--5859343 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
5859251 TTAAAGGTTT
*
5859261 GACTTGAATGCTGCGAGTATATAATAATATGTAAAAATGGAC
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
5859303 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
5859344 TTTGAGGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (42 bp):
GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
Found at i:5859454 original size:140 final size:140
Alignment explanation
Indices: 5859202--5859483 Score: 564
Period size: 140 Copynumber: 2.0 Consensus size: 140
5859192 ATTGTTGGTA
5859202 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
1 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
5859267 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
66 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
5859332 TGCAAAAATG
131 TGCAAAAATG
5859342 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
1 GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
5859407 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
66 AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
5859472 TGCAAAAATG
131 TGCAAAAATG
5859482 GA
1 GA
5859484 ATACCTAAGT
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (140 bp):
GATTTGAGGTTGACTGTGTCCATCAACTTTGTGTGTTCGAACACCAGTATTAAAGGTTTGACTTG
AATGCTGCGAGTATATAATAATATGTAAAAATGGACGACTTGAATGCTGCGAGTATATAATAATA
TGCAAAAATG
Found at i:5859460 original size:42 final size:42
Alignment explanation
Indices: 5859401--5859483 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
5859391 TTAAAGGTTT
*
5859401 GACTTGAATGCTGCGAGTATATAATAATATGTAAAAATGGAC
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
5859443 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
1 GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGA
5859484 ATACCTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (42 bp):
GACTTGAATGCTGCGAGTATATAATAATATGCAAAAATGGAC
Found at i:5859725 original size:19 final size:19
Alignment explanation
Indices: 5859692--5859738 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
5859682 CACATGTGAG
*
5859692 TAAAGAATC-TCACATCAT
1 TAAAAAATCTTCACATCAT
5859710 TAAAAAATCTTCACATCAT
1 TAAAAAATCTTCACATCAT
5859729 TAAAAAATCT
1 TAAAAAATCT
5859739 AAATGAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAAATCTTCACATCAT
Found at i:5867854 original size:20 final size:20
Alignment explanation
Indices: 5867829--5867871 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5867819 TTCAATTAAC
*
5867829 TCTATTTTT-TATCTTTTCTT
1 TCTATTTTTCTAGCTTTT-TT
5867849 TCTATTTTTCTAGCTTTTTT
1 TCTATTTTTCTAGCTTTTTT
5867869 TCT
1 TCT
5867872 TTCTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.72
Consensus pattern (20 bp):
TCTATTTTTCTAGCTTTTTT
Found at i:5868091 original size:2 final size:2
Alignment explanation
Indices: 5868084--5868123 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5868074 GTTCGTACCA
5868084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5868124 GATTATGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5869065 original size:16 final size:16
Alignment explanation
Indices: 5869025--5869078 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5869015 TGAAATTATC
* *
5869025 AATATTCAAGAATAAT
1 AATATTTAATAATAAT
*
5869041 TATATTTTAATAATAAT
1 AATA-TTTAATAATAAT
*
5869058 AATATTTAATACTAA-
1 AATATTTAATAATAAT
5869073 AATATT
1 AATATT
5869079 ATATTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 6 0.19
16 13 0.41
17 13 0.41
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (16 bp):
AATATTTAATAATAAT
Found at i:5869186 original size:21 final size:21
Alignment explanation
Indices: 5869162--5869210 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
5869152 ACTATTCTTG
* * *
5869162 AAATATTATTTTTTAATATTA
1 AAATATTAATATTTAATACTA
* *
5869183 AAATAGTAATATTTATTACTA
1 AAATATTAATATTTAATACTA
5869204 AAATATT
1 AAATATT
5869211 TATACTATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTAATATTTAATACTA
Found at i:5869597 original size:17 final size:19
Alignment explanation
Indices: 5869577--5869611 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5869567 TTAATTAAAA
5869577 TTAA-ATAA-AATATTTTT
1 TTAATATAATAATATTTTT
5869594 TTAATATAATAATATTTT
1 TTAATATAATAATATTTT
5869612 AAGTCGAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATATAATAATATTTTT
Found at i:5870051 original size:15 final size:14
Alignment explanation
Indices: 5870019--5870054 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5870009 TGAAAATATA
*
5870019 AAAATAATTTTTTT
1 AAAATAATTTTTTC
5870033 AAAATAATTTTTTAC
1 AAAATAATTTTTT-C
5870048 AAAATAA
1 AAAATAA
5870055 ATAGAGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATAATTTTTTC
Found at i:5870204 original size:26 final size:27
Alignment explanation
Indices: 5870175--5870226 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
5870165 GAATGAAAAA
*
5870175 AATTTCATCTAATTA-TTAG-AATTCAC
1 AATTACAT-TAATTATTTAGCAATTCAC
*
5870201 AATTACATTTATTATTTAGCAATTCA
1 AATTACATTAATTATTTAGCAATTCA
5870227 AACTTTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTACATTAATTATTTAGCAATTCAC
Found at i:5870848 original size:24 final size:25
Alignment explanation
Indices: 5870803--5870863 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
5870793 AATATAAATT
* **
5870803 TATTTAATAATTTTTACTTTTTAAA
1 TATTTAATAATTATTAAATTTTAAA
5870828 TATTTAA-AATTATTAAATTTTAAA
1 TATTTAATAATTATTAAATTTTAAA
5870852 T-TTTAATAATTA
1 TATTTAATAATTA
5870864 AAAGTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.16
24 20 0.62
25 7 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTAATAATTATTAAATTTTAAA
Found at i:5872029 original size:2 final size:2
Alignment explanation
Indices: 5872022--5872050 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5872012 AATGATTCTA
5872022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5872051 GACATCCCAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5872343 original size:2 final size:2
Alignment explanation
Indices: 5872336--5872360 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5872326 AATTAGGGTG
5872336 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 T
5872361 CTAAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5873545 original size:21 final size:21
Alignment explanation
Indices: 5873521--5873574 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
5873511 ACATAAAGAT
5873521 TAATTATTATATATTAATAAA
1 TAATTATTATATATTAATAAA
*
5873542 TAA-TATTTATATTTTAATAAA
1 TAATTA-TTATATATTAATAAA
*
5873563 TAATAATT-TATA
1 TAATTATTATATA
5873575 ATTTATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTATTATATATTAATAAA
Found at i:5876684 original size:56 final size:55
Alignment explanation
Indices: 5876598--5876708 Score: 170
Period size: 56 Copynumber: 2.0 Consensus size: 55
5876588 GTTCATGGTA
5876598 GTAGATATCTCATCTGCCTATAATATGATATTAGACAAACCTAACCAGTATGTTAT
1 GTAGATATCTCATCTGCCTATAATATGATATTAGACAAA-CTAACCAGTATGTTAT
* * *
5876654 GTAGATATCCTC-TCTGCCTATAATATGATATTAGATAGACTAACCAGTCTGTTAT
1 GTAGATAT-CTCATCTGCCTATAATATGATATTAGACAAACTAACCAGTATGTTAT
5876709 ATGGCTTATA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
55 15 0.29
56 33 0.65
57 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (55 bp):
GTAGATATCTCATCTGCCTATAATATGATATTAGACAAACTAACCAGTATGTTAT
Found at i:5878941 original size:19 final size:21
Alignment explanation
Indices: 5878903--5878951 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
5878893 ATTCATACTT
*
5878903 TCTCTAAAAATTTATATTCTG
1 TCTCTAAAAATTTATATTCTC
5878924 TCTCTAAAAA-TT-TATTCTC
1 TCTCTAAAAATTTATATTCTC
5878943 TCTCTAAAA
1 TCTCTAAAA
5878952 TCATAGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.56
20 2 0.07
21 10 0.37
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (21 bp):
TCTCTAAAAATTTATATTCTC
Found at i:5879093 original size:22 final size:21
Alignment explanation
Indices: 5879046--5879117 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
5879036 TTAATTGAAT
* * *
5879046 TCATACTCTCTCTCTAATATAT
1 TCATACTTTCTCTCTAA-AAAC
*
5879068 TCATACTTTCTCTTTAAAAAAC
1 TCATACTTTCTCTCT-AAAAAC
** *
5879090 TCATTGTTTCTCTCTAAAAAT
1 TCATACTTTCTCTCTAAAAAC
5879111 TCATACT
1 TCATACT
5879118 CTTTGCTTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 10 0.26
22 27 0.69
23 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.44
Consensus pattern (21 bp):
TCATACTTTCTCTCTAAAAAC
Found at i:5880154 original size:9 final size:9
Alignment explanation
Indices: 5880142--5880171 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5880132 AATATTTTAT
5880142 TAATTAAAA
1 TAATTAAAA
5880151 TAATTAAAA
1 TAATTAAAA
5880160 TATATTAAAA
1 TA-ATTAAAA
5880170 TA
1 TA
5880172 TAAAACTTGA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:5880168 original size:10 final size:10
Alignment explanation
Indices: 5880144--5880173 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5880134 TATTTTATTA
5880144 ATTAAAATA-
1 ATTAAAATAT
5880153 ATTAAAATAT
1 ATTAAAATAT
5880163 ATTAAAATAT
1 ATTAAAATAT
5880173 A
1 A
5880174 AAACTTGATT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:5883051 original size:2 final size:2
Alignment explanation
Indices: 5883039--5883068 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5883029 AGCGGTCTCC
*
5883039 TA TA GA 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
5883069 AAATCCCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5888156 original size:2 final size:2
Alignment explanation
Indices: 5888149--5888178 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5888139 AGAGAAATAA
*
5888149 AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5888179 CCAAAAGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5888591 original size:15 final size:17
Alignment explanation
Indices: 5888571--5888605 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5888561 ATTTGATGAG
5888571 ATAAAA-AAAA-TAATT
1 ATAAAAGAAAATTAATT
5888586 ATAAAAGAAAATTAATT
1 ATAAAAGAAAATTAATT
5888603 ATA
1 ATA
5888606 TTAAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 4 0.22
17 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAAAGAAAATTAATT
Found at i:5888611 original size:19 final size:18
Alignment explanation
Indices: 5888571--5888617 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
5888561 ATTTGATGAG
5888571 ATAAA-AAAAATAATTAT
1 ATAAAGAAAAATAATTAT
*
5888588 A-AAAGAAAATTAATTAT
1 ATAAAGAAAAATAATTAT
5888605 ATTAAAGATAAAA
1 A-TAAAGA-AAAA
5888618 AATACATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 3 0.12
17 13 0.54
19 5 0.21
20 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAAAGAAAAATAATTAT
Found at i:5889316 original size:19 final size:19
Alignment explanation
Indices: 5889279--5889315 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5889269 AATTAAAGAA
*
5889279 AATTTTTTTTAATACTTTT
1 AATTTTTTTTAAAACTTTT
5889298 AATTTTTTTTAAAA-TTTT
1 AATTTTTTTTAAAACTTTT
5889316 TTTATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
AATTTTTTTTAAAACTTTT
Found at i:5889774 original size:68 final size:69
Alignment explanation
Indices: 5889660--5889795 Score: 204
Period size: 68 Copynumber: 2.0 Consensus size: 69
5889650 GCTGTAAGAT
* * *
5889660 ATGACATATCTTACTCTGACTTAAAAAATTAAACAGTCCATCTACCC-AAATTTTTTTTACCTAA
1 ATGACATATCTTACCCTAACTTAAAAAATTAAACAATCCATCTACCCTAAATTTTTTTTACCTAA
5889724 AAAG
66 AAAG
* *
5889728 ATGACATATCTTACCCTAA-TCTAAAAAATTAAACAATCTATTTACCCTAAATTTTTTTTACCTA
1 ATGACATATCTTACCCTAACT-TAAAAAATTAAACAATCCATCTACCCTAAATTTTTTTTACCTA
5889792 AAAA
65 AAAA
5889796 AATAAAACGC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
67 1 0.02
68 40 0.66
69 20 0.33
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (69 bp):
ATGACATATCTTACCCTAACTTAAAAAATTAAACAATCCATCTACCCTAAATTTTTTTTACCTAA
AAAG
Found at i:5898200 original size:11 final size:11
Alignment explanation
Indices: 5898186--5898218 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5898176 TAACTTGTGA
5898186 ATTTTTTTATT
1 ATTTTTTTATT
5898197 ATTTTTTTATT
1 ATTTTTTTATT
*
5898208 ATTATTTTATT
1 ATTTTTTTATT
5898219 TATAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:5898209 original size:14 final size:14
Alignment explanation
Indices: 5898187--5898221 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5898177 AACTTGTGAA
5898187 TTTTT-TTATTATT
1 TTTTTATTATTATT
5898200 TTTTTATTATTATT
1 TTTTTATTATTATT
5898214 TTATTTAT
1 TT-TTTAT
5898222 AAAATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTATTATTATT
Found at i:5899208 original size:23 final size:23
Alignment explanation
Indices: 5899182--5899250 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
5899172 ACTAAGGCCT
5899182 GAAAAGTG-AGATAAAGTAAGAAA
1 GAAAA-TGAAGATAAAGTAAGAAA
5899205 GAAAATGAAGATAAAGTAAGAAA
1 GAAAATGAAGATAAAGTAAGAAA
* *
5899228 GAAAACGAAGAGAAAG--AGAAA
1 GAAAATGAAGATAAAGTAAGAAA
5899249 GA
1 GA
5899251 GAAAGTGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.16
22 2 0.05
23 34 0.79
ACGTcount: A:0.64, C:0.01, G:0.26, T:0.09
Consensus pattern (23 bp):
GAAAATGAAGATAAAGTAAGAAA
Found at i:5903568 original size:102 final size:101
Alignment explanation
Indices: 5903438--5903622 Score: 275
Period size: 102 Copynumber: 1.8 Consensus size: 101
5903428 ACATTAGACC
* *
5903438 AAAAAAAAAAAAAAGATACCGTATAAATTTTTACAAAAATCATAAATTAATTTGATAAAAATTAA
1 AAAAAAAAAAAAAAGACACCGTATAAATTTTAACAAAAATCATAAATTAATTTGATAAAAATTAA
*
5903503 AGGTATATTTTAAATTTGTTGGTGATACTAAGCAAA
66 AAGTATATTTTAAATTTGTTGGTGATACTAAGCAAA
* *
5903539 AAAAAAAAAAAAACAGACACC-TCGA-AAATTTTAACAAAAATTATAAATTGATTTGATAAAAAT
1 AAAAAAAAAAAAA-AGACACCGT--ATAAATTTTAACAAAAATCATAAATTAATTTGATAAAAAT
*
5903602 TAAAAGTATGTTTTAAATTTG
63 TAAAAGTATATTTTAAATTTG
5903623 ATGTATTAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 14 0.19
102 60 0.80
103 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (101 bp):
AAAAAAAAAAAAAAGACACCGTATAAATTTTAACAAAAATCATAAATTAATTTGATAAAAATTAA
AAGTATATTTTAAATTTGTTGGTGATACTAAGCAAA
Found at i:5926942 original size:3 final size:3
Alignment explanation
Indices: 5926934--5926978 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5926924 TAACACCTTC
5926934 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5926979 TATTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5926983 original size:3 final size:3
Alignment explanation
Indices: 5926977--5927012 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5926967 AATAATAATA
5926977 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5927013 TAGTTTTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5934564 original size:14 final size:14
Alignment explanation
Indices: 5934545--5934571 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5934535 CAAAACAGGA
5934545 GATAGAAGAAAATT
1 GATAGAAGAAAATT
5934559 GATAGAAGAAAAT
1 GATAGAAGAAAAT
5934572 CTTGACCATA
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:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (14 bp):
GATAGAAGAAAATT
Found at i:5935329 original size:19 final size:19
Alignment explanation
Indices: 5935305--5935346 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
5935295 CAAACATTGC
5935305 AACTGCATATTGTCAGTTT
1 AACTGCATATTGTCAGTTT
5935324 AACTGCATATTGTCAGTTT
1 AACTGCATATTGTCAGTTT
5935343 AACT
1 AACT
5935347 CCCTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (19 bp):
AACTGCATATTGTCAGTTT
Found at i:5941383 original size:6 final size:6
Alignment explanation
Indices: 5941372--5941425 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
5941362 AATTTTTTTC
* ** * *
5941372 AATTAT AATTAT AATAAT TTTTTT AATTAT AATTAT AATAAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
*
5941420 TATTAT
1 AATTAT
5941426 TTTTAATATT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
AATTAT
Found at i:5941399 original size:24 final size:25
Alignment explanation
Indices: 5941361--5941413 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
5941351 AATTTTTTGT
5941361 TAATTTTTTTCAATTATAATTATAA
1 TAATTTTTTTCAATTATAATTATAA
5941386 TAATTTTTTT-AATTATAATTATAA
1 TAATTTTTTTCAATTATAATTATAA
5941410 TAAT
1 TAAT
5941414 AATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATTTTTTTCAATTATAATTATAA
Found at i:5941424 original size:24 final size:24
Alignment explanation
Indices: 5941372--5941425 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
5941362 AATTTTTTTC
* *
5941372 AATTATAATTATAATAATTTTTTT
1 AATTATAATTATAATAATATTATT
5941396 AATTATAATTATAATAATAATTATT
1 AATTATAATTATAATAAT-ATTATT
5941421 -ATTAT
1 AATTAT
5941426 TTTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATAATTATAATAATATTATT
Found at i:5945175 original size:24 final size:24
Alignment explanation
Indices: 5945123--5945177 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
5945113 TAATGATTTT
*
5945123 ATGTAATAATGATCTTGAATCATC
1 ATGTGATAATGATCTTGAATCATC
*
5945147 ATGTGATAGTGATCTTGAATCATC
1 ATGTGATAATGATCTTGAATCATC
5945171 ATGTGAT
1 ATGTGAT
5945178 TAGATCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (24 bp):
ATGTGATAATGATCTTGAATCATC
Found at i:5945452 original size:19 final size:20
Alignment explanation
Indices: 5945402--5945453 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
5945392 TTTTATTTTT
*
5945402 TTAAATTTATTTATAATATAA
1 TTAATTTTATTT-TAATATAA
* *
5945423 TT-GTTTGATTTTAATAT-A
1 TTAATTTTATTTTAATATAA
5945441 TTAATTTTATTTT
1 TTAATTTTATTTT
5945454 TAATTTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 6 0.24
21 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTAATTTTATTTTAATATAA
Found at i:5945658 original size:24 final size:25
Alignment explanation
Indices: 5945631--5945679 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5945621 AACAAACAGG
*
5945631 GTAAT-TTTGATATTTTTA-AATAAC
1 GTAATATTTGAT-TTTTAATAATAAC
5945655 GTAATATTTGATTTTTAATAATAAC
1 GTAATATTTGATTTTTAATAATAAC
5945680 AAATACAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (25 bp):
GTAATATTTGATTTTTAATAATAAC
Found at i:5949781 original size:22 final size:22
Alignment explanation
Indices: 5949756--5949797 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5949746 TTGTTTATCC
* *
5949756 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
5949778 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
5949798 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:5953725 original size:22 final size:22
Alignment explanation
Indices: 5953700--5953741 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5953690 TTGTCTATCC
* * *
5953700 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATAAAAATACT
5953722 TAATTCTAGAGATAAAAATA
1 TAATTCTAGAGATAAAAATA
5953742 TAAATATACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATAAAAATACT
Found at i:5958016 original size:24 final size:27
Alignment explanation
Indices: 5957981--5958041 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
5957971 TGGGATAAAA
*
5957981 AATTATTATATTA-T-TATATATTTTT
1 AATTATTTTATTATTGTATATATTTTT
5958006 AA-TATTTTATTATTGTATATATTTTT
1 AATTATTTTATTATTGTATATATTTTT
5958032 AATTATTTTA
1 AATTATTTTA
5958042 ATTACTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 9 0.28
25 3 0.09
26 13 0.41
27 7 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
AATTATTTTATTATTGTATATATTTTT
Found at i:5958055 original size:26 final size:26
Alignment explanation
Indices: 5957996--5958057 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
5957986 TTATATTATT
* *
5957996 ATATATTTTTAATATTTTATTATTGT
1 ATATATTTTTAATATTTTATTACTGC
5958022 ATATATTTTTAATTATTTTAATTACT-C
1 ATATATTTTTAA-TATTTT-ATTACTGC
5958049 ATA-ATTTTT
1 ATATATTTTT
5958058 TTATAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 18 0.56
27 9 0.28
28 5 0.16
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (26 bp):
ATATATTTTTAATATTTTATTACTGC
Found at i:5970832 original size:7 final size:6
Alignment explanation
Indices: 5970804--5970874 Score: 63
Period size: 6 Copynumber: 11.8 Consensus size: 6
5970794 CAATGTTGAT
* * * * * *
5970804 TTTTAA TTTTAA TTTTGA TTTTAA TTTTTTA TTTTAG TTTTGA TTATAT
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTTTAA TTTTAA TTTTAA
*
5970853 TTTTAA TTTTAA TGTT-A TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTA
5970875 GTCAAAAGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
5 4 0.08
6 40 0.82
7 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:5970832 original size:19 final size:20
Alignment explanation
Indices: 5970788--5970862 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 20
5970778 AAAAGTTCAA
* *
5970788 AATTTTCAATGTTGATTTTT
1 AATTTTTAATTTTGATTTTT
5970808 AA-TTTTAATTTTGA-TTTT
1 AATTTTTAATTTTGATTTTT
* *
5970826 AATTTTTTATTTTAGTTTTGATT
1 AATTTTTAATTTT-GATTT--TT
5970849 ATATTTTTAATTTT
1 A-ATTTTTAATTTT
5970863 AATGTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.14
19 19 0.43
20 3 0.07
21 2 0.05
23 3 0.07
24 11 0.25
ACGTcount: A:0.25, C:0.01, G:0.07, T:0.67
Consensus pattern (20 bp):
AATTTTTAATTTTGATTTTT
Found at i:5970832 original size:25 final size:25
Alignment explanation
Indices: 5970802--5970874 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
5970792 TTCAATGTTG
5970802 ATTTTTAATTTTAATTTTGATTTTA
1 ATTTTTAATTTTAATTTTGATTTTA
* * *
5970827 ATTTTTTATTTTAGTTTTGATTAT-
1 ATTTTTAATTTTAATTTTGATTTTA
*
5970851 ATTTTTAATTTTAATGTT-ATTTTA
1 ATTTTTAATTTTAATTTTGATTTTA
5970875 GTCAAAAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 4 0.10
24 15 0.38
25 21 0.52
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (25 bp):
ATTTTTAATTTTAATTTTGATTTTA
Found at i:5971709 original size:19 final size:18
Alignment explanation
Indices: 5971687--5971789 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 18
5971677 CGGTTTTGCT
5971687 TTTTTTATTTATTTTTTA
1 TTTTTTATTTATTTTTTA
* *
5971705 ATTTTGATTTTATTTTTTA
1 TTTTTTA-TTTATTTTTTA
**
5971724 TTTCCTATTTATGTTTTTA
1 TTTTTTATTTAT-TTTTTA
* *
5971743 TCTATTTTCTATT-TTTTTCA
1 T-T-TTTTAT-TTATTTTTTA
*
5971763 TATTTTTATTTTTATTTTTA
1 T-TTTTTATTTAT-TTTTTA
5971783 TTTTTTA
1 TTTTTTA
5971790 ATTGCATGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
18 12 0.18
19 33 0.51
20 14 0.22
21 4 0.06
22 2 0.03
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTATTTATTTTTTA
Found at i:5971780 original size:5 final size:6
Alignment explanation
Indices: 5971688--5971787 Score: 57
Period size: 6 Copynumber: 16.8 Consensus size: 6
5971678 GGTTTTGCTT
* * * * *
5971688 TTTTTA TTTATT- TTTTAA TTTTGA -TTTTA TTTTTTA TTTCCTA TTTATG
1 TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA -TTTTTA TTT-TTA TTTTTA
* **
5971737 TTTTTA --TCTA TTTTCTA TTTTT- TTCATA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5971783 TTTTT
1 TTTTT
5971788 TAATTGCATG
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
4 3 0.04
5 8 0.11
6 42 0.59
7 18 0.25
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:5971963 original size:18 final size:18
Alignment explanation
Indices: 5971940--5971990 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
5971930 TTACTACTTG
5971940 ATATTTTGCATGATTAAT
1 ATATTTTGCATGATTAAT
5971958 ATA-TTTGCATGGAAATTAAT
1 ATATTTTGCAT-G--ATTAAT
5971978 AT-TTTTGCATGAT
1 ATATTTTGCATGAT
5971991 GTATTGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 9 0.31
18 4 0.14
19 1 0.03
20 15 0.52
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (18 bp):
ATATTTTGCATGATTAAT
Found at i:5976224 original size:11 final size:11
Alignment explanation
Indices: 5976210--5976251 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
5976200 GGAAAGTATG
5976210 AAGAAAAAATA
1 AAGAAAAAATA
**
5976221 AAGAAATGA-A
1 AAGAAAAAATA
5976231 AAGAAAAAATA
1 AAGAAAAAATA
5976242 AAGAAAAAAT
1 AAGAAAAAAT
5976252 GGAAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (11 bp):
AAGAAAAAATA
Found at i:5976258 original size:21 final size:19
Alignment explanation
Indices: 5976210--5976271 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 19
5976200 GGAAAGTATG
5976210 AAGAAAAAATAAAGAAATGAA
1 AAGAAAAAATAAAGAAA--AA
5976231 AAGAAAAAATAAAGAAAAA
1 AAGAAAAAATAAAGAAAAA
*
5976250 ATGGAAAAAA-AAAGGAAAAA
1 A-AGAAAAAATAAA-GAAAAA
5976270 AA
1 AA
5976272 AAGTTAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 6 0.16
20 14 0.38
21 17 0.46
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
AAGAAAAAATAAAGAAAAA
Found at i:5976259 original size:11 final size:11
Alignment explanation
Indices: 5976245--5976274 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5976235 AAAAATAAAG
*
5976245 AAAAAATGGAA
1 AAAAAAAGGAA
5976256 AAAAAAAGGAA
1 AAAAAAAGGAA
5976267 AAAAAAAG
1 AAAAAAAG
5976275 TTAACAGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (11 bp):
AAAAAAAGGAA
Found at i:5977121 original size:124 final size:124
Alignment explanation
Indices: 5976978--5977214 Score: 343
Period size: 124 Copynumber: 1.9 Consensus size: 124
5976968 GACTCTTTTA
* * *
5976978 TTCCTTTGAAAAGAAATCCAGAATGATAGGGGTAAGAAA-AAAATGAAATAAGTGAAAAAGCTTG
1 TTCCTTTGAAAAGAAATCCAGAATGACAGAGGCAA-AAAGAAAATGAAATAAGTGAAAAAGCTTG
* * * * *
5977042 ATCCAGAATGACAACGACAAGGAGGAAATGACACAAGAAAGGTGAAAAAGCTTGATTATG
65 ATCCAAAATGACAACGACAAGAAGAAAATGAAACAAGAAAGCTGAAAAAGCTTGATTATG
5977102 TTCCTTTG-AAAGAAAATCCAGAATGACAGAGGCAAAAAGAAAATGAAATAAGTGAAAAAGCTTG
1 TTCCTTTGAAAAG-AAATCCAGAATGACAGAGGCAAAAAGAAAATGAAATAAGTGAAAAAGCTTG
* * *
5977166 ATCCAAAATGACAAGGGCAAGAAGAAAATGAAATAAGAAAGCTGAAAAA
65 ATCCAAAATGACAACGACAAGAAGAAAATGAAACAAGAAAGCTGAAAAA
5977215 AACTTGAAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
123 7 0.07
124 93 0.93
ACGTcount: A:0.51, C:0.11, G:0.22, T:0.17
Consensus pattern (124 bp):
TTCCTTTGAAAAGAAATCCAGAATGACAGAGGCAAAAAGAAAATGAAATAAGTGAAAAAGCTTGA
TCCAAAATGACAACGACAAGAAGAAAATGAAACAAGAAAGCTGAAAAAGCTTGATTATG
Found at i:5977501 original size:21 final size:21
Alignment explanation
Indices: 5977475--5977517 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5977465 TTCGTGATAG
5977475 TTGTTTGATGGATA-AGAAATT
1 TTGTTT-ATGGATATAGAAATT
*
5977496 TTGTTTATGGATATTGAAATT
1 TTGTTTATGGATATAGAAATT
5977517 T
1 T
5977518 AAAAGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (21 bp):
TTGTTTATGGATATAGAAATT
Found at i:5977625 original size:18 final size:18
Alignment explanation
Indices: 5977599--5978121 Score: 198
Period size: 18 Copynumber: 29.2 Consensus size: 18
5977589 GATTACAAAC
*
5977599 CTTTACGAATCTTGAAAT
1 CTTTGCGAATCTTGAAAT
* *
5977617 CTTTGCGAACCTTGAAAC
1 CTTTGCGAATCTTGAAAT
*
5977635 CTTTGGGAATCTTGAAAT
1 CTTTGCGAATCTTGAAAT
* * * *
5977653 TTTTACAAATCTTGAAAC
1 CTTTGCGAATCTTGAAAT
**
5977671 CTTTATGAATCTTGAAAT
1 CTTTGCGAATCTTGAAAT
* * *
5977689 CTTTGCAAATCTTGGAAC
1 CTTTGCGAATCTTGAAAT
* * *
5977707 CTTTACGAATATTGGAAT
1 CTTTGCGAATCTTGAAAT
*
5977725 CTTTTC-AAGTCTT-AGAAT
1 CTTTGCGAA-TCTTGA-AAT
** *
5977743 CTTTATGAATCTT-AGAAC
1 CTTTGCGAATCTTGA-AAT
* *
5977761 CTTTGCGAACCTTGGAATT
1 CTTTGCGAATCTT-GAAAT
* ** * *
5977780 TTTTATGAACCTTGAAAC
1 CTTTGCGAATCTTGAAAT
* * * *
5977798 CTATGTGAATCATGAAAC
1 CTTTGCGAATCTTGAAAT
* * *
5977816 CTTTGCCAATCATGAAAC
1 CTTTGCGAATCTTGAAAT
*
5977834 CTTTGCGAAT-TTTAGAAT
1 CTTTGCGAATCTTGA-AAT
* * *
5977852 CCTTTAC-AATTATTGAAAC
1 -CTTTGCGAA-TCTTGAAAT
* *
5977871 CTTGGCGAATCTTAGAACT
1 CTTTGCGAATCTT-GAAAT
* * *
5977890 -TTTACAAATCTTGAAAA
1 CTTTGCGAATCTTGAAAT
* *
5977907 CTTTGCAAATCTTAAAAT
1 CTTTGCGAATCTTGAAAT
* * *
5977925 CTTTGTGAATCTAGGAAT
1 CTTTGCGAATCTTGAAAT
*
5977943 CTTAT--GAACCTTGAAAT
1 CTT-TGCGAATCTTGAAAT
* *
5977960 CTTTGCAAATCTTGGAAT
1 CTTTGCGAATCTTGAAAT
**
5977978 CAATGCGAATCTT-AGAAT
1 CTTTGCGAATCTTGA-AAT
* *
5977996 CTTAGC-ACAACTTG-AAT
1 CTTTGCGA-ATCTTGAAAT
* *
5978013 CTTTTGAGAATCTT-AGAAC
1 C-TTTGCGAATCTTGA-AAT
* *
5978032 CTTTACGAATCTTG-AAC
1 CTTTGCGAATCTTGAAAT
* * *
5978049 CTTTGTGAAT-TTTAAAC
1 CTTTGCGAATCTTGAAAT
* *
5978066 CTTTACGAAACTTG-AAT
1 CTTTGCGAATCTTGAAAT
* *
5978083 CTTTTGCGAATTTTG-AAC
1 C-TTTGCGAATCTTGAAAT
*
5978101 CTTTGCGAAACTT-AAAT
1 CTTTGCGAATCTTGAAAT
5978118 CTTT
1 CTTT
5978122 TACTAATTTT
Statistics
Matches: 370, Mismatches: 108, Indels: 55
0.69 0.20 0.10
Matches are distributed among these distances:
16 3 0.01
17 64 0.17
18 268 0.72
19 31 0.08
20 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (18 bp):
CTTTGCGAATCTTGAAAT
Found at i:5978014 original size:53 final size:53
Alignment explanation
Indices: 5977875--5978016 Score: 139
Period size: 53 Copynumber: 2.7 Consensus size: 53
5977865 TGAAACCTTG
* * **
5977875 GCGAATCTTAGAACTTTTA-CAAATCTTGAAAACTTTGCAAATCTTAAAATCTTT
1 GCGAATCTTAGAA-TCTTAGCAAA-CTTGAAATCTTTGCAAATCTTAAAATCAAT
* * **
5977929 GTGAATC-TAGGAATCTTATG-AACCTTGAAATCTTTGCAAATCTTGGAATCAAT
1 GCGAATCTTA-GAATCTTA-GCAAACTTGAAATCTTTGCAAATCTTAAAATCAAT
5977982 GCGAATCTTAGAATCTTAGCACAACTTG-AATCTTT
1 GCGAATCTTAGAATCTTAGCA-AACTTGAAATCTTT
5978017 TGAGAATCTT
Statistics
Matches: 72, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
52 1 0.01
53 53 0.74
54 18 0.25
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (53 bp):
GCGAATCTTAGAATCTTAGCAAACTTGAAATCTTTGCAAATCTTAAAATCAAT
Found at i:5978102 original size:35 final size:35
Alignment explanation
Indices: 5978004--5978139 Score: 157
Period size: 35 Copynumber: 3.9 Consensus size: 35
5977994 ATCTTAGCAC
* *
5978004 AACTTGAATCTTTTGAGAATCTTAGAACCTTTACGA
1 AACTTGAATCTTTTGCGAAT-TTTGAACCTTTACGA
* * * *
5978040 ATCTTGAA-CCTTTGTGAATTTTAAACCTTTACGA
1 AACTTGAATCTTTTGCGAATTTTGAACCTTTACGA
*
5978074 AACTTGAATCTTTTGCGAATTTTGAACCTTTGCGA
1 AACTTGAATCTTTTGCGAATTTTGAACCTTTACGA
* * * *
5978109 AACTTAAATCTTTTACTAATTTTGAATCTTT
1 AACTTGAATCTTTTGCGAATTTTGAACCTTT
5978140 TGATTCTTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
34 20 0.24
35 58 0.68
36 7 0.08
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (35 bp):
AACTTGAATCTTTTGCGAATTTTGAACCTTTACGA
Found at i:5978116 original size:52 final size:53
Alignment explanation
Indices: 5978037--5978141 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 53
5978027 AGAACCTTTA
* **
5978037 CGAATCTTGAACCTTTGTGAATTTTAAA-CCTTTACGAAACTTGAATCTTTTG
1 CGAATCTTGAACCTTTGCGAAACTTAAATCCTTTACGAAACTTGAATCTTTTG
* * * **
5978089 CGAATTTTGAACCTTTGCGAAACTTAAATCTTTTACTAATTTTGAATCTTTTG
1 CGAATCTTGAACCTTTGCGAAACTTAAATCCTTTACGAAACTTGAATCTTTTG
5978142 ATTCTTTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 24 0.55
53 20 0.45
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (53 bp):
CGAATCTTGAACCTTTGCGAAACTTAAATCCTTTACGAAACTTGAATCTTTTG
Found at i:5978121 original size:17 final size:17
Alignment explanation
Indices: 5978024--5978121 Score: 61
Period size: 17 Copynumber: 5.6 Consensus size: 17
5978014 TTTTGAGAAT
* *
5978024 CTTAGAACCTTTACGAAT
1 CTTA-AACCTTTGCGAAA
* * *
5978042 CTTGAACCTTTGTGAAT
1 CTTAAACCTTTGCGAAA
* *
5978059 TTTAAACCTTTACGAAA
1 CTTAAACCTTTGCGAAA
* * *
5978076 CTTGAATCTTTTGCGAAT
1 CTT-AAACCTTTGCGAAA
* *
5978094 TTTGAACCTTTGCGAAA
1 CTTAAACCTTTGCGAAA
*
5978111 CTTAAATCTTT
1 CTTAAACCTTT
5978122 TACTAATTTT
Statistics
Matches: 58, Mismatches: 21, Indels: 3
0.71 0.26 0.04
Matches are distributed among these distances:
17 43 0.74
18 15 0.26
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (17 bp):
CTTAAACCTTTGCGAAA
Found at i:5978254 original size:34 final size:35
Alignment explanation
Indices: 5978193--5978272 Score: 117
Period size: 34 Copynumber: 2.3 Consensus size: 35
5978183 TTGTGAATCT
5978193 TAAATATTTTGCAAATTTTGAACCTTTGCAAAACC
1 TAAATATTTTGCAAATTTTGAACCTTTGCAAAACC
** *
5978228 TAAATATTTTGCAAA-TTTGAGTCTTTGCAAAACT
1 TAAATATTTTGCAAATTTTGAACCTTTGCAAAACC
*
5978262 TGAATATTTTG
1 TAAATATTTTG
5978273 GGAATTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 26 0.63
35 15 0.37
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.41
Consensus pattern (35 bp):
TAAATATTTTGCAAATTTTGAACCTTTGCAAAACC
Found at i:5978279 original size:34 final size:35
Alignment explanation
Indices: 5978137--5978307 Score: 146
Period size: 36 Copynumber: 4.9 Consensus size: 35
5978127 ATTTTGAATC
* ** * * *
5978137 TTTTGATTCTTTGTTAAACTTGAATATTTTGTGAAT
1 TTTTGAATCTTTGCAAAACTTAAATATTTTG-CAAA
* ** *
5978173 TTTTTAATCTTTGTGAATCTTAAATATTTTGCAAA
1 TTTTGAATCTTTGCAAAACTTAAATATTTTGCAAA
* *
5978208 TTTTGAACCTTTGCAAAACCTAAATATTTTGCAAA
1 TTTTGAATCTTTGCAAAACTTAAATATTTTGCAAA
* * * *
5978243 -TTTGAGTCTTTGCAAAACTTGAATATTTTGGGAAT
1 TTTTGAATCTTTGCAAAACTTAAATATTTT-GCAAA
* * *
5978278 TTTTGTATCTTTGCAAATCTTAAATTTTTT
1 TTTTGAATCTTTGCAAAACTTAAATATTTT
5978308 TATGAATTTT
Statistics
Matches: 109, Mismatches: 24, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
34 25 0.23
35 34 0.31
36 50 0.46
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (35 bp):
TTTTGAATCTTTGCAAAACTTAAATATTTTGCAAA
Found at i:5978647 original size:6 final size:6
Alignment explanation
Indices: 5978632--5978730 Score: 123
Period size: 6 Copynumber: 16.8 Consensus size: 6
5978622 CAATGTTGAT
* * * *
5978632 TTTTAA TTTTAC TTTTGA TTTTAA TTTTTGA TTTT-A GTTT-A TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTTTAA TTTTAA TTTTAA
*
5978679 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TGTT-A
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
5978726 TTTTA
1 TTTTA
5978731 GTCATAAGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
5 12 0.15
6 64 0.79
7 5 0.06
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:5979656 original size:15 final size:14
Alignment explanation
Indices: 5979636--5979702 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 14
5979626 ATTTTGATTT
5979636 TATTTTTTATTTTCC
1 TATTTTTTATTTT-C
5979651 TATTTTTTA-TTT-
1 TATTTTTTATTTTC
* *
5979663 TATCTTTT-TTTCC
1 TATTTTTTATTTTC
5979676 TA-TTTTTATTTTC
1 TATTTTTTATTTTC
*
5979689 GATGTTTTTATTTT
1 TAT-TTTTTATTTT
5979703 TTAATTACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 13 0.31
13 7 0.17
14 3 0.07
15 19 0.45
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (14 bp):
TATTTTTTATTTTC
Found at i:5979679 original size:25 final size:26
Alignment explanation
Indices: 5979626--5979687 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 26
5979616 TTCAATTTTG
* *
5979626 ATTTTGATTTTATTTTTTATTTTCCT
1 ATTTTTATTTTATTCTTTATTTTCCT
5979652 ATTTTTTATTTTA-TCTTT-TTTTCCT
1 A-TTTTTATTTTATTCTTTATTTTCCT
5979677 ATTTTTATTTT
1 ATTTTTATTTT
5979688 CGATGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 10 0.30
25 8 0.24
26 5 0.15
27 10 0.30
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.76
Consensus pattern (26 bp):
ATTTTTATTTTATTCTTTATTTTCCT
Found at i:5979696 original size:24 final size:25
Alignment explanation
Indices: 5979645--5979697 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
5979635 TTATTTTTTA
** *
5979645 TTTTCCTATTTTTTATTTTATCTTT
1 TTTTCCTATTTTTTATTTTAGATGT
*
5979670 TTTTCCTA-TTTTTATTTTCGATGT
1 TTTTCCTATTTTTTATTTTAGATGT
5979694 TTTT
1 TTTT
5979698 ATTTTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTCCTATTTTTTATTTTAGATGT
Found at i:5979817 original size:14 final size:15
Alignment explanation
Indices: 5979786--5979815 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5979776 ATTTTTTTTC
*
5979786 TATTTTTGCATTATT
1 TATTTTTGCATGATT
5979801 TATTTTTGCATGATT
1 TATTTTTGCATGATT
5979816 ATATATTTAA
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:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (15 bp):
TATTTTTGCATGATT
Found at i:5979829 original size:38 final size:38
Alignment explanation
Indices: 5979757--5979829 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
5979747 AATTGGTAAG
* * *
5979757 ATTATTTATTATTTGCGTGATTTTTTTTCTATTTTTGC
1 ATTATTTATTATTTGCATGATTTTATTTCAATTTTTGC
5979795 ATTATTTATT-TTTGCATGATTATATATTT-AATTTT
1 ATTATTTATTATTTGCATGATT-T-TATTTCAATTTT
5979830 ATTATTTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
37 10 0.33
38 16 0.53
39 4 0.13
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.64
Consensus pattern (38 bp):
ATTATTTATTATTTGCATGATTTTATTTCAATTTTTGC
Found at i:5979900 original size:18 final size:18
Alignment explanation
Indices: 5979877--5979928 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
5979867 TCATTGCATG
5979877 ATATTTTGCATGATTAAT
1 ATATTTTGCATGATTAAT
*
5979895 ATA-TTTGCTTGGTAATTAAT
1 ATATTTTGCAT-G--ATTAAT
5979915 AT-TTTTGCATGATT
1 ATATTTTGCATGATT
5979929 TATTGCATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 1 0.04
20 14 0.50
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (18 bp):
ATATTTTGCATGATTAAT
Found at i:5979970 original size:13 final size:13
Alignment explanation
Indices: 5979952--5979991 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5979942 GATATTATAT
5979952 TTATTGCATGATA
1 TTATTGCATGATA
5979965 TTATTGCATGATAA
1 TTATTGCATGAT-A
* *
5979979 TTTTTACATGATA
1 TTATTGCATGATA
5979992 ATTTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (13 bp):
TTATTGCATGATA
Found at i:5979999 original size:15 final size:14
Alignment explanation
Indices: 5979958--5979997 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5979948 ATATTTATTG
* *
5979958 CATGAT-ATTATTG
1 CATGATAATTTTTA
5979971 CATGATAATTTTTA
1 CATGATAATTTTTA
5979985 CATGATAATTTTT
1 CATGATAATTTTT
5979998 TATATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (14 bp):
CATGATAATTTTTA
Found at i:5987775 original size:40 final size:37
Alignment explanation
Indices: 5987700--5987842 Score: 105
Period size: 40 Copynumber: 3.7 Consensus size: 37
5987690 TAACAAAATC
* * *
5987700 TAATTTAAATATAT-TATTTTAAAAAAATGCATTTTCAAA
1 TAATCTAAATATATATCTTTTAAAATAA-G--TTTTCAAA
*
5987739 TAATCTAAATATATATCTTTTACAATTTAAAGTTTTCAAA
1 TAATCTAAATATATATCTTTTA-AA-AT-AAGTTTTCAAA
* *
5987779 T-A-C-AATGATATATTATCTTTTAAAATAGGTTTTCTAA
1 TAATCTAA--ATATA-TATCTTTTAAAATAAGTTTTCAAA
*
5987816 TAATATAAATATATATCTTTTTAAAAT
1 TAATCTAAATATATATC-TTTTAAAAT
5987843 TAAAAATATC
Statistics
Matches: 85, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
37 16 0.19
38 17 0.20
39 21 0.25
40 26 0.31
41 2 0.02
42 1 0.01
43 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
TAATCTAAATATATATCTTTTAAAATAAGTTTTCAAA
Found at i:5987811 original size:37 final size:38
Alignment explanation
Indices: 5987731--5987842 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 38
5987721 AAAAAATGCA
* * *
5987731 TTTTCAAATAATCTAAATATATATC-TTTTACAATTTAAAG
1 TTTTCAAATAATATAAATATATATCTTTTTA-AA-AT-AGG
*
5987771 TTTTCAAATACA-AT-GATATATTATC-TTTTAAAATAGG
1 TTTTCAAATA-ATATAAATATA-TATCTTTTTAAAATAGG
*
5987808 TTTTCTAATAATATAAATATATATCTTTTTAAAAT
1 TTTTCAAATAATATAAATATATATCTTTTTAAAAT
5987843 TAAAAATATC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
36 1 0.02
37 17 0.28
38 15 0.25
39 7 0.11
40 20 0.33
41 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTCAAATAATATAAATATATATCTTTTTAAAATAGG
Found at i:5988219 original size:18 final size:18
Alignment explanation
Indices: 5988182--5988220 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5988172 AAATCAATGG
**
5988182 TTTTTTGTTTTTGATTTT
1 TTTTTTGTTTTTGAAATT
5988200 TTTTTTGTTTTTGAAATT
1 TTTTTTGTTTTTGAAATT
5988218 TTT
1 TTT
5988221 ATAAAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTTTTGTTTTTGAAATT
Found at i:5991615 original size:2 final size:2
Alignment explanation
Indices: 5991608--5991643 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5991598 TTAGCATCTA
5991608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5991644 ACATATAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5991777 original size:18 final size:18
Alignment explanation
Indices: 5991754--5991788 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5991744 AATAAATTTC
5991754 TTTAATAAATTATTTAAA
1 TTTAATAAATTATTTAAA
**
5991772 TTTAATATTTTATTTAA
1 TTTAATAAATTATTTAA
5991789 TTATTTAAAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATAAATTATTTAAA
Found at i:5991780 original size:13 final size:14
Alignment explanation
Indices: 5991761--5991799 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
5991751 TTCTTTAATA
5991761 AATTATTTAAATTT
1 AATTATTTAAATTT
*
5991775 AA-TATTT-TATTT
1 AATTATTTAAATTT
5991787 AATTATTTAAATT
1 AATTATTTAAATT
5991800 CAAATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATTTAAATTT
Found at i:5992114 original size:2 final size:2
Alignment explanation
Indices: 5992109--5992134 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5992099 TATATATATA
5992109 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
5992135 CTTAATAAAT
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:5994653 original size:18 final size:19
Alignment explanation
Indices: 5994630--5994672 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
5994620 TATTTTATTT
5994630 TATAAAAATT-TAAAAATA
1 TATAAAAATTATAAAAATA
*
5994648 TATAAAAATTAATAAGAATA
1 TATAAAAATT-ATAAAAATA
5994668 TATAA
1 TATAA
5994673 TTAGATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
20 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TATAAAAATTATAAAAATA
Found at i:5996416 original size:14 final size:14
Alignment explanation
Indices: 5996396--5996433 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
5996386 CCTACATCTC
5996396 GAAAAACAAGAGC-
1 GAAAAACAAGAGCA
5996409 GAAAAA-ACAGAGCA
1 GAAAAACA-AGAGCA
5996423 GAAAAACAAGA
1 GAAAAACAAGA
5996434 TCGGCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 11 0.50
14 9 0.41
15 1 0.05
ACGTcount: A:0.66, C:0.13, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAACAAGAGCA
Found at i:6000194 original size:30 final size:30
Alignment explanation
Indices: 6000158--6000214 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
6000148 AATTATGTGT
*
6000158 TTAGATATAAAATTAAATAGTTTTTTATCA
1 TTAGATATAAAATTAAACAGTTTTTTATCA
*
6000188 TTAGATATAAAATTAAACATTTTTTTA
1 TTAGATATAAAATTAAACAGTTTTTTA
6000215 ATTATATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (30 bp):
TTAGATATAAAATTAAACAGTTTTTTATCA
Found at i:6002374 original size:24 final size:23
Alignment explanation
Indices: 6002342--6002399 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
6002332 TTATAGTTTG
* *
6002342 TTTATTGTTCATGAATATATTC-
1 TTTAATGTTCATAAATATATTCA
*
6002364 TTTATACTGTTCGTAAATATATTCA
1 TTTA-A-TGTTCATAAATATATTCA
6002389 TTTAATGTTCA
1 TTTAATGTTCA
6002400 CGAACGAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 16 0.55
25 4 0.14
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (23 bp):
TTTAATGTTCATAAATATATTCA
Found at i:6003006 original size:27 final size:25
Alignment explanation
Indices: 6002976--6003025 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
6002966 ATTAATTAAA
* *
6002976 ATTAATTTATTTTTATTGAAAAAATAT
1 ATTAATATATATTTA-T-AAAAAATAT
6003003 ATTAATATATATTTATAAAAAAT
1 ATTAATATATATTTATAAAAAAT
6003026 TACCCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 1 0.05
27 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTAATATATATTTATAAAAAATAT
Found at i:6006796 original size:3 final size:3
Alignment explanation
Indices: 6006784--6006840 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
6006774 AATAAACCTT
6006784 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6006831 ATA ATA ATA A
1 ATA ATA ATA A
6006841 ATGGTTTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6006949 original size:25 final size:24
Alignment explanation
Indices: 6006901--6006951 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
6006891 CAAAAAATTT
*
6006901 AATAAAATTAATAAAAATAGTAAA
1 AATAAAATTAATAAAAAGAGTAAA
6006925 AATAATAATTAATAAAAACGA-TAAA
1 AATAA-AATTAATAAAAA-GAGTAAA
6006950 AA
1 AA
6006952 AATTAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (24 bp):
AATAAAATTAATAAAAAGAGTAAA
Found at i:6010444 original size:21 final size:21
Alignment explanation
Indices: 6010418--6010457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6010408 GGTTTTTTTT
*
6010418 TTTTTTCTTTCTTTCTTTGAA
1 TTTTTTCTTTATTTCTTTGAA
*
6010439 TTTTTTTTTTATTTCTTTG
1 TTTTTTCTTTATTTCTTTG
6010458 TTTATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTTCTTTATTTCTTTGAA
Found at i:6010448 original size:25 final size:23
Alignment explanation
Indices: 6010414--6010476 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 23
6010404 TCCAGGTTTT
*
6010414 TTTTTTTTTTCTTTCTTTCTTTGAA
1 TTTTTTTTTTATTTCTTTCTTT--A
*
6010439 TTTTTTTTTTATTTCTTTGTTTA
1 TTTTTTTTTTATTTCTTTCTTTA
6010462 TTTTATTTTTTATTT
1 TTTT-TTTTTTATTT
6010477 ATTAGATTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 5 0.14
24 10 0.29
25 20 0.57
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (23 bp):
TTTTTTTTTTATTTCTTTCTTTA
Found at i:6010469 original size:28 final size:29
Alignment explanation
Indices: 6010410--6010479 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
6010400 CCGCTCCAGG
* *
6010410 TTTTTTTTTTTTTTCTTTCTTTCTTTGAA
1 TTTTTTTTTTATTTCTTTCTTTATTTGAA
* *
6010439 TTTTTTTTTTATTTCTTTGTTTATTT-TA
1 TTTTTTTTTTATTTCTTTCTTTATTTGAA
*
6010467 TTTTTTATTTATT
1 TTTTTTTTTTATT
6010480 AGATTAGGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (29 bp):
TTTTTTTTTTATTTCTTTCTTTATTTGAA
Found at i:6010473 original size:12 final size:11
Alignment explanation
Indices: 6010410--6010476 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 11
6010400 CCGCTCCAGG
6010410 TTTT-TTTTTT
1 TTTTATTTTTT
*
6010420 TTTTCTTTCTTT
1 TTTTATTT-TTT
*
6010432 CTTTGAATTTTTT
1 -TTT-TATTTTTT
6010445 TTTTATTTCTTT
1 TTTTATTT-TTT
*
6010457 GTTTATTTTATT
1 TTTTATTTT-TT
6010469 TTTTATTT
1 TTTTATTT
6010477 ATTAGATTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
10 4 0.09
11 8 0.17
12 25 0.54
13 6 0.13
14 3 0.07
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:6010619 original size:59 final size:59
Alignment explanation
Indices: 6010550--6010901 Score: 432
Period size: 59 Copynumber: 5.9 Consensus size: 59
6010540 TAAAAATAAA
* *
6010550 AAATTT-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAGGAAT
1 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* * *
6010608 AAATTTCC--AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCATAAAT
1 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
6010665 AAATTTCGAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
1 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAAT
* *
6010729 AAATTTCCAAAAAAAAATACATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTTCC-AAAAAAAAT--ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
6010791 CAAAATTT-CAAAAAAAATATTTTT-GGGAAAAAATTGAAAGTATCAATTTTCCTT-GAAAAT
1 --AAATTTCCAAAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
*
6010851 CGAAATTTCC--AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCC
1 --AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
6010902 CTACAAAAAA
Statistics
Matches: 260, Mismatches: 17, Indels: 33
0.84 0.05 0.11
Matches are distributed among these distances:
57 51 0.20
58 6 0.02
59 81 0.31
60 44 0.17
61 1 0.00
62 14 0.05
63 1 0.00
64 18 0.07
65 9 0.03
67 35 0.13
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.34
Consensus pattern (59 bp):
AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:6010867 original size:186 final size:177
Alignment explanation
Indices: 6010541--6010917 Score: 508
Period size: 186 Copynumber: 2.1 Consensus size: 177
6010531 CTCTTTAAAT
* **
6010541 AAAAATAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAGGA
1 AAAAA-AAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
* * *
6010606 ATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCATAAATAAATTT
65 ATAAATTTCAAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTCATAAATAAATTT
* *
6010671 CGAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-
130 C-AAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCCTAC
*
6010719 AAAGAAAAATAAATTTCCAAAAAAAAATACATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 AAA-AAAAA-AAATTT-C-AAAAAAAAT--ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
*
6010784 TAAAAATCAAAATTTCAAAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTGA-A
60 TAAAAAT--AAATTTC-AAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCC-TCATA
*
6010848 AATCGAAATTTC-CAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCCTAC
121 AAT--AAATTTCAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCCTAC
6010906 AAAAAAAAAAAT
1 AAAAAAAAAAAT
6010918 CATTCTTTCC
Statistics
Matches: 175, Mismatches: 11, Indels: 19
0.85 0.05 0.09
Matches are distributed among these distances:
178 6 0.03
179 8 0.05
180 1 0.01
181 9 0.05
183 38 0.22
185 11 0.06
186 90 0.51
187 5 0.03
188 7 0.04
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.32
Consensus pattern (177 bp):
AAAAAAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
TAAATTTCAAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTCATAAATAAATTTC
AAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCCTAC
Found at i:6014704 original size:21 final size:22
Alignment explanation
Indices: 6014679--6014722 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6014669 ACACTGGATG
*
6014679 AAAAATGAGAAAAAA-GAAAAA
1 AAAAAGGAGAAAAAATGAAAAA
*
6014700 AAAAAGGGGAAAAAATGAAAAA
1 AAAAAGGAGAAAAAATGAAAAA
6014722 A
1 A
6014723 GAGATCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (22 bp):
AAAAAGGAGAAAAAATGAAAAA
Found at i:6016081 original size:41 final size:41
Alignment explanation
Indices: 6015957--6016568 Score: 948
Period size: 40 Copynumber: 15.0 Consensus size: 41
6015947 ATGATTGTCA
6015957 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
6015997 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
6016037 AGGAGCAATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
6016078 AGGAGCAATTTACTTTTCAAAGT--TGGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGG-TGCCTCTGTTTAG
*
6016118 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
6016159 AGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
6016201 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
*
6016241 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
6016282 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
6016323 AGGAGCAATTTACTTTTCAAAGT-TTGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
6016363 AGGAGCAATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
6016404 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
6016444 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
* *
6016484 AGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
6016525 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
6016567 AG
1 AG
6016569 AAGCTTTGGT
Statistics
Matches: 539, Mismatches: 15, Indels: 34
0.92 0.03 0.06
Matches are distributed among these distances:
39 23 0.04
40 232 0.43
41 201 0.37
42 83 0.15
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:6016088 original size:81 final size:81
Alignment explanation
Indices: 6015957--6016568 Score: 933
Period size: 81 Copynumber: 7.5 Consensus size: 81
6015947 ATGATTGTCA
6015957 AGGAGCAATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG
1 AGGAGCAATTTA-TTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG
6016019 TTCGTTGCCTCTGTTTAG
64 TTCGTTGCCTCTGTTTAG
6016037 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
1 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
*
6016102 GGTTGCCTCTGTTTAG
66 CGTTGCCTCTGTTTAG
*
6016118 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAG-
1 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGT
*
6016182 TCGTGGTACCTCTGTTTAG
65 TCGT--TGCCTCTGTTTAG
*
6016201 AGGAGCAATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG
1 AGGAGCAATTTA-TTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG
6016263 -TCGTGGTGCCTCTGTTTAG
64 TTCGT--TGCCTCTGTTTAG
*
6016282 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
1 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
*
6016347 TGTTGCCTCTGTTTAG
66 CGTTGCCTCTGTTTAG
6016363 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
1 AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
6016428 CGTTGCCTCTGTTTAG
66 CGTTGCCTCTGTTTAG
*
6016444 AGGAGCAATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG
1 AGGAGCAATTTA-TTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG
*
6016506 -TCGTGGTACCTCTGTTTAG
64 TTCGT--TGCCTCTGTTTAG
*
6016525 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAG
1 AGGAGCAATTTATTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAG
6016569 AAGCTTTGGT
Statistics
Matches: 498, Mismatches: 14, Indels: 37
0.91 0.03 0.07
Matches are distributed among these distances:
79 12 0.02
80 62 0.12
81 290 0.58
82 80 0.16
83 47 0.09
84 7 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (81 bp):
AGGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
CGTTGCCTCTGTTTAG
Found at i:6016592 original size:8 final size:8
Alignment explanation
Indices: 6016579--6016645 Score: 95
Period size: 8 Copynumber: 8.6 Consensus size: 8
6016569 AAGCTTTGGT
6016579 AAAAAACA
1 AAAAAACA
6016587 AAAAAA-A
1 AAAAAACA
*
6016594 AACAAA-A
1 AAAAAACA
6016601 AAAAAACA
1 AAAAAACA
6016609 AAAAAAC-
1 AAAAAACA
6016616 AAAAAACA
1 AAAAAACA
6016624 AAAAAACA
1 AAAAAACA
6016632 AAAAAACCA
1 AAAAAA-CA
6016641 AAAAA
1 AAAAA
6016646 TGTTGAGTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
7 19 0.35
8 28 0.52
9 7 0.13
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:6016595 original size:11 final size:11
Alignment explanation
Indices: 6016579--6016637 Score: 93
Period size: 11 Copynumber: 5.3 Consensus size: 11
6016569 AAGCTTTGGT
6016579 AAAAAACAAAA
1 AAAAAACAAAA
6016590 AAAAAACAAAA
1 AAAAAACAAAA
6016601 AAAAAACAAAA
1 AAAAAACAAAA
6016612 AAACAAA-AAACA
1 AAA-AAACAAA-A
6016624 AAAAAACAAAA
1 AAAAAACAAAA
6016635 AAA
1 AAA
6016638 CCAAAAAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 35 0.78
12 10 0.22
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:6016606 original size:15 final size:15
Alignment explanation
Indices: 6016579--6016637 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
6016569 AAGCTTTGGT
6016579 AAAAAACAAAAAAAA
1 AAAAAACAAAAAAAA
*
6016594 AACAAAA-AAAAAACA
1 AA-AAAACAAAAAAAA
*
6016609 AAAAAACAAAAAACA
1 AAAAAACAAAAAAAA
6016624 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
6016638 CCAAAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
14 4 0.10
15 32 0.80
16 4 0.10
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAAAAA
Found at i:6016638 original size:23 final size:22
Alignment explanation
Indices: 6016579--6016645 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 22
6016569 AAGCTTTGGT
6016579 AAAAAACAAAAAAA-AAACAAAA
1 AAAAAACAAAAAAACAAA-AAAA
6016601 AAAAAACAAAAAAACAAAAAACA
1 AAAAAACAAAAAAACAAAAAA-A
*
6016624 AAAAAACAAAAAAACCAAAAAA
1 AAAAAACAAAAAAACAAAAAAA
6016646 TGTTGAGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 18 0.43
23 24 0.57
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAACAAAAAAACAAAAAAA
Done.