Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold403
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: 416698
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:292057 original size:28 final size:28
Alignment explanation
Indices: 292017--292076 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
292007 AAATACTAGA
* *
292017 TTAATGGGATAAAGGGTATTTCATATAT
1 TTAATGGGATAAAAGATATTTCATATAT
292045 TTAATGGGATAAAAGATATTTCATATAT
1 TTAATGGGATAAAAGATATTTCATATAT
292073 TTAA
1 TTAA
292077 ACCTTAGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (28 bp):
TTAATGGGATAAAAGATATTTCATATAT
Found at i:293037 original size:2 final size:2
Alignment explanation
Indices: 293030--293067 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
293020 TAGAATTTTG
*
293030 AT AT AT AT AT AT AT CT 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
293068 TAGAGTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:293859 original size:9 final size:9
Alignment explanation
Indices: 293845--293874 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
293835 AATTATCATA
293845 TTTTTTATT
1 TTTTTTATT
293854 TTTTTTA-T
1 TTTTTTATT
293862 TTTTTTATT
1 TTTTTTATT
293871 TTTT
1 TTTT
293875 AAAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:293875 original size:7 final size:8
Alignment explanation
Indices: 293845--293874 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
293835 AATTATCATA
293845 TTTTTTATT
1 TTTTTTA-T
293854 TTTTTTAT
1 TTTTTTAT
293862 TTTTTTAT
1 TTTTTTAT
293870 TTTTT
1 TTTTT
293875 AAAATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:294125 original size:28 final size:27
Alignment explanation
Indices: 294065--294126 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
294055 TTTATTATAA
294065 TTTTTAAAGTACAAAGATTAAAATATT
1 TTTTTAAAGTACAAAGATTAAAATATT
*
294092 TATTTTAATAGTATAAA-ATTTAAAATATT
1 T-TTTTAA-AGTACAAAGA-TTAAAATATT
294121 TTTTTA
1 TTTTTA
294127 TTATAATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 1 0.03
28 12 0.39
29 18 0.58
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTTTAAAGTACAAAGATTAAAATATT
Found at i:297000 original size:147 final size:147
Alignment explanation
Indices: 296834--297129 Score: 520
Period size: 147 Copynumber: 2.0 Consensus size: 147
296824 AGATAGTTTA
*
296834 TACCCATTTAGATTTATGCATATTTTATTTTTTAATTTATTTTTAAAAAATATATATTTTAAATT
1 TACCCATTTAGATTGATGCATATTTTATTTTTTAATTTATTTTTAAAAAATATATATTTTAAATT
** *
296899 TAATATTTAATAATTTGTTTTTATTAAGTCTAATATATAAATAACCAGACATTTTTTATATTTAA
66 TAATATTTAATAATTTACTTTTATTAAGTCTAATATATAAATAACCAGACATTTTTTAAATTTAA
296964 CTATAATATTATATATT
131 CTATAATATTATATATT
*
296981 TACCCATTTAGATTGATGCATATTTTATTTTTTAATTTATTTTTGAAAAATATATATTTTAAATT
1 TACCCATTTAGATTGATGCATATTTTATTTTTTAATTTATTTTTAAAAAATATATATTTTAAATT
**
297046 TAATATTTAATAATTTACTTTTATTAAGTCTAATATATAAATAACTTGACATTTTTTAAATTTAA
66 TAATATTTAATAATTTACTTTTATTAAGTCTAATATATAAATAACCAGACATTTTTTAAATTTAA
*
297111 TTATAATATTATATATT
131 CTATAATATTATATATT
297128 TA
1 TA
297130 TTCTTTATAT
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 141 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (147 bp):
TACCCATTTAGATTGATGCATATTTTATTTTTTAATTTATTTTTAAAAAATATATATTTTAAATT
TAATATTTAATAATTTACTTTTATTAAGTCTAATATATAAATAACCAGACATTTTTTAAATTTAA
CTATAATATTATATATT
Found at i:300498 original size:21 final size:20
Alignment explanation
Indices: 300474--300512 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
300464 GCTGGGACCT
*
300474 TGTATCGATTCATTCTAAAAA
1 TGTATCGATGCATT-TAAAAA
300495 TGTATCGATGCATTTAAA
1 TGTATCGATGCATTTAAA
300513 CAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATGCATTTAAAAA
Found at i:300865 original size:27 final size:27
Alignment explanation
Indices: 300806--300862 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
300796 TGTTAAGATT
*
300806 AATTTTTAAAATTAATAATTTTAATTAA
1 AATTTTTAAAATTAATAAATTT-ATTAA
300834 AATTTTTAAATATTAAATAAATTT-TTAA
1 AATTTTTAAA-ATT-AATAAATTTATTAA
300862 A
1 A
300863 TTTAAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 15 0.58
29 3 0.12
30 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTTTTAAAATTAATAAATTTATTAA
Found at i:300867 original size:18 final size:19
Alignment explanation
Indices: 300833--300868 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
300823 ATTTTAATTA
300833 AAATTTTTAAATATTAAAT
1 AAATTTTTAAATATTAAAT
300852 AAATTTTTAAAT-TTAAA
1 AAATTTTTAAATATTAAA
300869 CGAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTTTAAATATTAAAT
Found at i:303275 original size:24 final size:25
Alignment explanation
Indices: 303233--303293 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
303223 TATTATTTAA
303233 AATATTTAAAATATATTTTTAT-ATT
1 AATATTT-AAATATATTTTTATAATT
*
303258 AATATTTATATATATTTTTATAATT
1 AATATTTAAATATATTTTTATAATT
303283 AAT-TTTAAATA
1 AATATTTAAATA
303294 AAAATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATATTTAAATATATTTTTATAATT
Found at i:303698 original size:14 final size:13
Alignment explanation
Indices: 303679--303708 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
303669 TAAGAAGCTT
303679 TTTGTTTTTGTTTG
1 TTTGTTTTT-TTTG
303693 TTTGTTTTTTTTG
1 TTTGTTTTTTTTG
303706 TTT
1 TTT
303709 AAAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (13 bp):
TTTGTTTTTTTTG
Found at i:307659 original size:11 final size:11
Alignment explanation
Indices: 307643--307746 Score: 66
Period size: 11 Copynumber: 10.0 Consensus size: 11
307633 ATCTTGAACC
307643 AGAAAAGAAAG
1 AGAAAAGAAAG
307654 AGAAAAGAAAG
1 AGAAAAGAAAG
*
307665 A-AGAAG-AAG
1 AGAAAAGAAAG
307674 AGAGAAA-AAAG
1 AGA-AAAGAAAG
*
307685 AAAAAAG-AA-
1 AGAAAAGAAAG
307694 AGAAAAG-AAG
1 AGAAAAGAAAG
*
307704 AAGAAGAAAAAAG
1 -AGAA-AAGAAAG
*
307717 A-AAAAGAGAG
1 AGAAAAGAAAG
307727 -GAAAAAGAAAG
1 AG-AAAAGAAAG
307738 -GAAAA-AAAG
1 AGAAAAGAAAG
307747 TAGCTTGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
9 16 0.21
10 19 0.25
11 34 0.45
12 3 0.04
13 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AGAAAAGAAAG
Found at i:307668 original size:7 final size:7
Alignment explanation
Indices: 307647--307723 Score: 58
Period size: 7 Copynumber: 11.6 Consensus size: 7
307637 TGAACCAGAA
307647 AAGAAAG
1 AAGAAAG
307654 -AG-AA-
1 AAGAAAG
307658 AAGAAAG
1 AAGAAAG
307665 AAG-AAG
1 AAGAAAG
*
307671 AAGAGAG
1 AAGAAAG
*
307678 AAAAAAG
1 AAGAAAG
*
307685 AAAAAAG
1 AAGAAAG
307692 AAAGAAAAG
1 -AAG-AAAG
307701 AAG-AAG
1 AAGAAAG
*
307707 AAGAAAA
1 AAGAAAG
307714 AAGAAA-
1 AAGAAAG
307720 AAGA
1 AAGA
307724 GAGGAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
5 4 0.07
6 20 0.34
7 25 0.43
8 5 0.09
9 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:307708 original size:42 final size:41
Alignment explanation
Indices: 307651--307744 Score: 104
Period size: 42 Copynumber: 2.2 Consensus size: 41
307641 CCAGAAAAGA
*
307651 AAGAGAAAAGAAAGAAGAAGAAGAGAGAAAAA-AGA-AAAAAGA
1 AAGAAAAAAGAAAGAAGAA-AA-A-AGAAAAAGAGAGAAAAAGA
307693 AAGAAAAGAAG-AAGAAGAAAAAAGAAAAAGAGAGGAAAAAGA
1 AAGAAAA-AAGAAAGAAGAAAAAAGAAAAAGAGA-GAAAAAGA
307735 AAGGAAAAAA
1 AA-GAAAAAA
307745 AGTAGCTTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
39 7 0.15
40 4 0.09
41 2 0.04
42 25 0.54
43 8 0.17
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (41 bp):
AAGAAAAAAGAAAGAAGAAAAAAGAAAAAGAGAGAAAAAGA
Found at i:307731 original size:32 final size:33
Alignment explanation
Indices: 307650--307744 Score: 114
Period size: 31 Copynumber: 3.1 Consensus size: 33
307640 ACCAGAAAAG
*
307650 AAAGAGAAAAGAAAG--AAGAAGAAGAGAGAAA
1 AAAGAAAAAAGAAAGAAAAGAAGAAGAGAGAAA
307681 AAAGAAAAAAGAAAGAAAAGAAGAAGA-AGAAA
1 AAAGAAAAAAGAAAGAAAAGAAGAAGAGAGAAA
* *
307713 AAAG-AAAAAGAGAGGAAA-AAGAA-AG-GAAA
1 AAAGAAAAAAGAAAGAAAAGAAGAAGAGAGAAA
307742 AAA
1 AAA
307745 AGTAGCTTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
29 8 0.14
30 5 0.09
31 26 0.45
32 9 0.16
33 10 0.17
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (33 bp):
AAAGAAAAAAGAAAGAAAAGAAGAAGAGAGAAA
Found at i:307744 original size:24 final size:24
Alignment explanation
Indices: 307656--307746 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
307646 AAAGAAAGAG
* *
307656 AAAAGAAAGAAGAAGAAGAGAGAA
1 AAAAGAAAGAAGAAAAAGAGAGGA
* * *
307680 AAAAGAAAAAAGAAAGAAAAGAAGA
1 AAAAGAAAGAAGAAA-AAGAGAGGA
* *
307705 AGAAGAAAAAAGAAAAAGAGAGGA
1 AAAAGAAAGAAGAAAAAGAGAGGA
307729 AAAAGAAAGGAA-AAAAAG
1 AAAAGAAA-GAAGAAAAAG
307747 TAGCTTGGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 33 0.60
25 22 0.40
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (24 bp):
AAAAGAAAGAAGAAAAAGAGAGGA
Found at i:308558 original size:13 final size:13
Alignment explanation
Indices: 308540--308566 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
308530 ACATGCTGCT
308540 TTGTATCGATACA
1 TTGTATCGATACA
308553 TTGTATCGATACA
1 TTGTATCGATACA
308566 T
1 T
308567 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:308563 original size:33 final size:32
Alignment explanation
Indices: 308521--308585 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
308511 CACACCCAGA
*
308521 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
308554 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
308586 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:308596 original size:20 final size:19
Alignment explanation
Indices: 308550--308606 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
308540 TTGTATCGAT
*
308550 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
308569 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
308588 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
308607 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:308672 original size:13 final size:13
Alignment explanation
Indices: 308651--308681 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
308641 CGATACATGG
*
308651 TACAATGTATCGA
1 TACATTGTATCGA
308664 TACATTGTATCGA
1 TACATTGTATCGA
308677 TACAT
1 TACAT
308682 GAAGAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:310278 original size:3 final size:3
Alignment explanation
Indices: 310270--310307 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
310260 GAGGAAGATA
*
310270 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
310308 TCGGATGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:316907 original size:107 final size:107
Alignment explanation
Indices: 316695--316907 Score: 376
Period size: 109 Copynumber: 2.0 Consensus size: 107
316685 AAAGGGGGAG
316695 AAGTATGTGAAAATAAATTTTTTTATTTATAAAAGGGGGAGAAGATAATCGTTTAAGGGGGAGAA
1 AAGTATGTGAAAATAAATTTTTTTATTTATAAAAGGGGGAGAAGATAATCGTTTAAGGGGGAGAA
*
316760 TTTTTTTTTTAAAGGAGGAGATAATTGTTTAAAGGGGAGAAAT
66 -TTTTTTTTTAAAGGAGGAGATAATCGTTTAAAGGGGAGAAAT
316803 AAGTATGTGAAAATAAATTTTTTTTATTTATAAAAGGGGGAGAAGATAATCGTTTAAGGGGGAGA
1 AAGTATGTGAAAATAAA-TTTTTTTATTTATAAAAGGGGGAGAAGATAATCGTTTAAGGGGGAGA
316868 A-TTTTTTTTAAAGGAGGAGATAATCGTTT-AAGCGGGAGAA
65 ATTTTTTTTTAAAGGAGGAGATAATCGTTTAAAG-GGGAGAA
316908 TTTTTAAGGG
Statistics
Matches: 102, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
106 3 0.03
107 34 0.33
108 17 0.17
109 48 0.47
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (107 bp):
AAGTATGTGAAAATAAATTTTTTTATTTATAAAAGGGGGAGAAGATAATCGTTTAAGGGGGAGAA
TTTTTTTTTAAAGGAGGAGATAATCGTTTAAAGGGGAGAAAT
Found at i:317461 original size:13 final size:13
Alignment explanation
Indices: 317443--317469 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
317433 ACATGCTGCT
317443 TTGTATCGATACA
1 TTGTATCGATACA
317456 TTGTATCGATACA
1 TTGTATCGATACA
317469 T
1 T
317470 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:317466 original size:33 final size:32
Alignment explanation
Indices: 317424--317488 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
317414 CACACCCAGA
*
317424 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
317457 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
317489 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:317499 original size:20 final size:19
Alignment explanation
Indices: 317453--317509 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
317443 TTGTATCGAT
*
317453 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
317472 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
317491 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
317510 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:317947 original size:11 final size:11
Alignment explanation
Indices: 317931--317955 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
317921 GCGCTATAAG
317931 TAGCAAGGTAT
1 TAGCAAGGTAT
317942 TAGCAAGGTAT
1 TAGCAAGGTAT
317953 TAG
1 TAG
317956 TATTATGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCAAGGTAT
Found at i:318528 original size:47 final size:47
Alignment explanation
Indices: 318454--318545 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 47
318444 AAAGTCAACA
*
318454 ACCTGAAACCGAACTGACCCGAACTCAAAATGACTCGAACCCGAATG
1 ACCTGAAACCGAACTGACCCGAACTCAAAATGACCCGAACCCGAATG
* * * *
318501 ACCTGAATCCAGAA-TGACTCGCACTCAAAATGACCCGAATCCGAA
1 ACCTGAAACC-GAACTGACCCGAACTCAAAATGACCCGAACCCGAA
318546 ATAACCCGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 36 0.92
48 3 0.08
ACGTcount: A:0.38, C:0.32, G:0.16, T:0.14
Consensus pattern (47 bp):
ACCTGAAACCGAACTGACCCGAACTCAAAATGACCCGAACCCGAATG
Found at i:318600 original size:16 final size:16
Alignment explanation
Indices: 318463--318597 Score: 98
Period size: 16 Copynumber: 8.5 Consensus size: 16
318453 AACCTGAAAC
*
318463 CGAACTGACCCGAACT
1 CGAAATGACCCGAACT
* * *
318479 CAAAATGACTCGAACC
1 CGAAATGACCCGAACT
*
318495 CG-AATGACCTGAA-T
1 CGAAATGACCCGAACT
* * *
318509 CCAGAATGACTCGCACT
1 CGA-AATGACCCGAACT
*
318526 CAAAATGACCCGAA-T
1 CGAAATGACCCGAACT
* *
318541 CCGAAATAACCCGAACC
1 -CGAAATGACCCGAACT
*
318558 CGAAATAACCCGAA-T
1 CGAAATGACCCGAACT
*
318573 CTGAAATGATCCGAACT
1 C-GAAATGACCCGAACT
318590 CGAAATGA
1 CGAAATGA
318598 TCCAAATAAT
Statistics
Matches: 91, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
14 1 0.01
15 11 0.12
16 74 0.81
17 5 0.05
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (16 bp):
CGAAATGACCCGAACT
Found at i:318700 original size:21 final size:22
Alignment explanation
Indices: 318659--318700 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
318649 TTAAAAAAAT
*
318659 TAAGTTATTAAAATAATATTTA
1 TAAGTTATTAAAATAAAATTTA
*
318681 TAAGTTA-TAATATAAAATTT
1 TAAGTTATTAAAATAAAATTT
318701 TGAATTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TAAGTTATTAAAATAAAATTTA
Found at i:318707 original size:47 final size:45
Alignment explanation
Indices: 318656--318744 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
318646 TATTTAAAAA
318656 AATTAAGTTAT-TAAAATAATATTTATAAGTTATAATATAAAATTTTG
1 AATT-AGTTATATAAAATAATA-TTATAAGTT-TAATATAAAATTTTG
* * * *
318703 AATTAGTTATATAATATATTATTATATGTTTAATATATAATT
1 AATTAGTTATATAAAATAATATTATAAGTTTAATATAAAATT
318745 ATTATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 11 0.30
46 14 0.38
47 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (45 bp):
AATTAGTTATATAAAATAATATTATAAGTTTAATATAAAATTTTG
Found at i:319093 original size:16 final size:16
Alignment explanation
Indices: 319060--319093 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
319050 TTATAACAAT
*
319060 TTTAATTTTTTATCAA
1 TTTAATTTTTTATAAA
*
319076 TTTAATTTTTTTTAAA
1 TTTAATTTTTTATAAA
319092 TT
1 TT
319094 GTTATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATTTTTTATAAA
Found at i:319665 original size:53 final size:53
Alignment explanation
Indices: 319553--319676 Score: 126
Period size: 53 Copynumber: 2.3 Consensus size: 53
319543 TCTAAACTTA
* * * * * * *
319553 AAATGACTTGAACCTAATTTAACCCGAATTTTAAACTCGATTAACCCGAATCT
1 AAATGACTCGAACCTGATTTAACCCGAATATTAAACCCAATTAACCCGAACCG
* *
319606 AGAATGACTCGAACCTGA-TTAACCTGAATATTAAACCCAATTAACCCAGACCCG
1 A-AATGACTCGAACCTGATTTAACCCGAATATTAAACCCAATTAACCC-GAACCG
319660 AAATGA-TACGAACCTGA
1 AAATGACT-CGAACCTGA
319677 AAACAACCTA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
52 1 0.02
53 40 0.68
54 18 0.31
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (53 bp):
AAATGACTCGAACCTGATTTAACCCGAATATTAAACCCAATTAACCCGAACCG
Found at i:320051 original size:22 final size:19
Alignment explanation
Indices: 320022--320061 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
320012 ATTTTACATA
320022 ATTAAATTAAAATAAAAAATT
1 ATTAAATT--AATAAAAAATT
320043 ATTATAATTAATAAAAAAT
1 ATTA-AATTAATAAAAAAT
320062 ATAATTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAATTAATAAAAAATT
Found at i:320207 original size:20 final size:21
Alignment explanation
Indices: 320167--320205 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
320157 ACATATATAC
320167 AAAAATATATATGTAACAAAT
1 AAAAATATATATGTAACAAAT
320188 AAAAAT-TATAT-TAACAAA
1 AAAAATATATATGTAACAAA
320206 ATCATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAAATATATATGTAACAAAT
Found at i:321555 original size:2 final size:2
Alignment explanation
Indices: 321548--321590 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
321538 TATTAATGCA
321548 AT 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 AT
321590 A
1 A
321591 ATGGTATGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:322018 original size:20 final size:21
Alignment explanation
Indices: 321993--322037 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
321983 GTCCATTTGA
321993 AAAAAAAATAGATTTAGA-TT
1 AAAAAAAATAGATTTAGATTT
**
322013 AAAAAATTTAGATTTAGATTT
1 AAAAAAAATAGATTTAGATTT
322034 AAAA
1 AAAA
322038 TCTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAAAAAATAGATTTAGATTT
Found at i:322802 original size:23 final size:25
Alignment explanation
Indices: 322761--322807 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
322751 TATTTTTTAA
*
322761 TTAAAAAATAATATCTAATTAATTT
1 TTAAAAAATAATATCTAATAAATTT
322786 TTAAAAAAT-ATAT-TAATAAATT
1 TTAAAAAATAATATCTAATAAATT
322808 AAAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
25 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTAAAAAATAATATCTAATAAATTT
Found at i:322841 original size:40 final size:40
Alignment explanation
Indices: 322770--322957 Score: 131
Period size: 39 Copynumber: 4.8 Consensus size: 40
322760 ATTAAAAAAT
* * *
322770 AATATCTAATTAATTTTTAAAA-AATATATTAATAAATTAA
1 AATAT-TAATTATTTTTTAAAATAAAAAATTAATAAATTAA
322810 AATATTAATTATTTTTTAAAATAAAAAA-T--TAAATTGAA
1 AATATTAATTATTTTTTAAAATAAAAAATTAATAAATT-AA
* * ****
322848 AAAATTTATTATTATTTTTTGTTAATAAAATTAA-AAA-TAA
1 AATATTAATTATT-TTTTAAAATAA-AAAATTAATAAATTAA
* ** * ** *
322888 TAT-TTAATTAACTTTAAAAAT-TTACATTAATAAATTAA
1 AATATTAATTATTTTTTAAAATAAAAAATTAATAAATTAA
*
322926 AATATTGATTATTTTTTAAAATAAAAAATTAA
1 AATATTAATTATTTTTTAAAATAAAAAATTAA
322958 ATTAAAAAGC
Statistics
Matches: 107, Mismatches: 30, Indels: 22
0.67 0.19 0.14
Matches are distributed among these distances:
36 6 0.06
37 9 0.08
38 22 0.21
39 43 0.40
40 22 0.21
41 2 0.02
42 3 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (40 bp):
AATATTAATTATTTTTTAAAATAAAAAATTAATAAATTAA
Found at i:322917 original size:116 final size:113
Alignment explanation
Indices: 322759--322995 Score: 343
Period size: 116 Copynumber: 2.1 Consensus size: 113
322749 ATTATTTTTT
* *
322759 AATTAAAAAATAATATCTAATTAATTTTTAAAAAATATATTAATAAATTAAAATATTAATTATTT
1 AATT-AAAAATAATATCTAATTAATCTTTAAAAAATACATTAATAAATTAAAATATTAATTATTT
*
322824 TTTAAAATAAAAAATTAAATTGAAAAA-ATTTATTATTATTTTTTGTTAATAA
65 TTTAAAATAAAAAATTAAATT-AAAAACATTTATTATTA--TATT-TTAATAA
* * *
322876 AATTAAAAATAATATTTAATTAA-CTTTAAAAATTTACATTAATAAATTAAAATATTGATTATTT
1 AATTAAAAATAATATCTAATTAATCTTTAAAAA-ATACATTAATAAATTAAAATATTAATTATTT
322940 TTTAAAATAAAAAATTAAATTAAAAAGCATTTATTATTATATTTTAATAA
65 TTTAAAATAAAAAATTAAATTAAAAA-CATTTATTATTATATTTTAATAA
322990 AATTAA
1 AATTAA
322996 TTAAATTTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
114 13 0.12
115 16 0.14
116 67 0.60
117 15 0.14
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (113 bp):
AATTAAAAATAATATCTAATTAATCTTTAAAAAATACATTAATAAATTAAAATATTAATTATTTT
TTAAAATAAAAAATTAAATTAAAAACATTTATTATTATATTTTAATAA
Found at i:323018 original size:18 final size:20
Alignment explanation
Indices: 322975--323019 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
322965 AGCATTTATT
*
322975 ATTATATTTTAATAAAATTA
1 ATTAAATTTTAATAAAATTA
*
322995 ATTAAATTTTAA-AAATTTA
1 ATTAAATTTTAATAAAATTA
323014 A-TAAAT
1 ATTAAAT
323020 AATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 7 0.30
20 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAATTTTAATAAAATTA
Found at i:323449 original size:19 final size:19
Alignment explanation
Indices: 323425--323489 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
323415 TAGCCAAACT
323425 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
323444 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
323457 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
323478 TGTATCGATACA
1 TGTATCGATACA
323490 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:323461 original size:13 final size:13
Alignment explanation
Indices: 323443--323468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
323433 TACACAAAAT
323443 ATGTATCGATACA
1 ATGTATCGATACA
323456 ATGTATCGATACA
1 ATGTATCGATACA
323469 CAAAAAATAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:323466 original size:32 final size:33
Alignment explanation
Indices: 323425--323489 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
323415 TAGCCAAACT
323425 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
323457 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
323490 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:325723 original size:21 final size:21
Alignment explanation
Indices: 325690--325739 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
325680 TTGCAAGTTG
*
325690 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
325712 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
325733 AAATAAA
1 AAATAAA
325740 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:327557 original size:15 final size:15
Alignment explanation
Indices: 327537--327567 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
327527 TAAAAATATC
*
327537 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
327552 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
327567 C
1 C
327568 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:329645 original size:13 final size:13
Alignment explanation
Indices: 329627--329651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329617 GGAAATTCAA
329627 TGTATCGATACAC
1 TGTATCGATACAC
329640 TGTATCGATACA
1 TGTATCGATACA
329652 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:329806 original size:20 final size:20
Alignment explanation
Indices: 329763--329808 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
329753 AAATCTTTTG
329763 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
329784 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
329804 CAAAA
1 CAAAA
329809 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:332215 original size:13 final size:13
Alignment explanation
Indices: 332197--332222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
332187 TACACAAAAT
332197 ATGTATCGATACA
1 ATGTATCGATACA
332210 ATGTATCGATACA
1 ATGTATCGATACA
332223 CAAAAAATAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:332235 original size:34 final size:34
Alignment explanation
Indices: 332179--332277 Score: 184
Period size: 34 Copynumber: 3.0 Consensus size: 34
332169 TAGCCAAACT
332179 TGTATCGATACAC--AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATATGTATCGATACAA
332211 TGTATCGATACACAAAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATATGTATCGATACAA
332245 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACACAAAAAATATGTATCGATACA
332278 TTCACACGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
32 13 0.20
34 52 0.80
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (34 bp):
TGTATCGATACACAAAAAATATGTATCGATACAA
Found at i:332249 original size:13 final size:13
Alignment explanation
Indices: 332231--332256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
332221 CACAAAAAAT
332231 ATGTATCGATACA
1 ATGTATCGATACA
332244 ATGTATCGATACA
1 ATGTATCGATACA
332257 CAAAAAATAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:333128 original size:15 final size:15
Alignment explanation
Indices: 333108--333138 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
333098 TATAAAATTA
333108 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
333123 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
333138 A
1 A
333139 CATGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTAATTTATTTTT
Found at i:333277 original size:11 final size:11
Alignment explanation
Indices: 333261--333297 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
333251 TTATTACTTT
333261 TTATTTATAAA
1 TTATTTATAAA
* *
333272 TTATTTTTAAT
1 TTATTTATAAA
333283 TTATTTATAAA
1 TTATTTATAAA
333294 TTAT
1 TTAT
333298 ACAAATTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:333574 original size:11 final size:11
Alignment explanation
Indices: 333558--333594 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
333548 TTATTACTTT
333558 TTATTTATAAA
1 TTATTTATAAA
* *
333569 TTATTTTTAAT
1 TTATTTATAAA
333580 TTATTTATAAA
1 TTATTTATAAA
333591 TTAT
1 TTAT
333595 GCAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:333743 original size:290 final size:286
Alignment explanation
Indices: 333149--333790 Score: 873
Period size: 290 Copynumber: 2.2 Consensus size: 286
333139 CATGTATTAT
* *
333149 TTTTCGATAACTACTTAAATACGAG-TTTTTTTAATCTATAAAATGACCAAGAAAAAATTTATTA
1 TTTTCGATAACGACTTAAATACGAGCTTTTTTT-ATCTGTAAAATGACCAAG-AAAAATTTATTA
** *
333213 TACATGTATTTTTAAAATTAATTAATATTGTACATGTATTATTACTTTTTATTTATAAATTATTT
64 TACATGTATTTTTAAAATTAATTAATATAATACATGAATTATTACTTTTTATTTATAAATTATTT
*
333278 TTAATTTATTTATAAATTATACAAATTTAGTTTTATTAAAATTAATTAATATTGTACATGTATTA
129 TTAATTTATTTATAAATTATACAAATTTAGTTTTATTAAAATTAATTAATATTATAC---TATTA
* * **
333343 GTTTTATAATTGATAAAACTTAAATTTATGTTAGCCAACAATATCTTACTTTTTTCAATAACGAC
191 G-TTTATAATTGATAAAACTTAAATTTATGTTAACAAACAATAAATTACTTTTTTCAATAACGAC
** * *
333408 TTATTTTGGATTTACAGACGCACACATTTTAT
255 TTATTTCAGATTTACAGACGCACACATTTCAG
** *
333440 TTTTTAATAACGACTTAAATACGAGCTTTCTTTTATCTGTAAAATGACCAAGTAAAAATTTATTG
1 TTTTCGATAACGACTTAAATACGAGCTTT-TTTTATCTGTAAAATGACCAAG-AAAAATTTATTA
*
333505 TACATGTATTTTTTTATTAAAATTAATTAATATAATGCATGAATTATTACTTTTTATTTATAAAT
64 TACATGTA----TTT-TTAAAATTAATTAATATAATACATGAATTATTACTTTTTATTTATAAAT
*
333570 TATTTTTAATTTATTTATAAATTATGCAAATTTA-TTTT-TTAAAAAATTAATTAATATTATAC-
124 TATTTTTAATTTATTTATAAATTATACAAATTTAGTTTTATT--AAAATTAATTAATATTATACT
* *
333632 A-TA-TTTATAATTGATAGAACTTAAATTTATGTTAACAAACAATAAATTACTTTTTTCAATAAT
187 ATTAGTTTATAATTGATAAAACTTAAATTTATGTTAACAAACAATAAATTACTTTTTTCAATAAC
*
333695 GACTTATTTCAGATTTACAGATGCACACATTTCAG
252 GACTTATTTCAGATTTACAGACGCACACATTTCAG
* *
333730 TTTTCGGTAACGACTTAAATACGAGCTTTTTTTTATTTGTAAAATGACCAAGAAAACATTT
1 TTTTCGATAACGACTTAAATACGAGC-TTTTTTTATCTGTAAAATGACCAAGAAAA-ATTT
333791 TCCTCAACTT
Statistics
Matches: 313, Mismatches: 27, Indels: 23
0.86 0.07 0.06
Matches are distributed among these distances:
289 4 0.01
290 132 0.42
291 25 0.08
292 41 0.13
293 5 0.02
295 2 0.01
296 7 0.02
297 97 0.31
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (286 bp):
TTTTCGATAACGACTTAAATACGAGCTTTTTTTATCTGTAAAATGACCAAGAAAAATTTATTATA
CATGTATTTTTAAAATTAATTAATATAATACATGAATTATTACTTTTTATTTATAAATTATTTTT
AATTTATTTATAAATTATACAAATTTAGTTTTATTAAAATTAATTAATATTATACTATTAGTTTA
TAATTGATAAAACTTAAATTTATGTTAACAAACAATAAATTACTTTTTTCAATAACGACTTATTT
CAGATTTACAGACGCACACATTTCAG
Found at i:337532 original size:90 final size:84
Alignment explanation
Indices: 337378--337626 Score: 250
Period size: 83 Copynumber: 2.9 Consensus size: 84
337368 AAAGGAATTT
* * * * * * * * * *
337378 GATTCTCAAATATAATTTATGCATTAGTTTAATCTTTGCAGTGTCATACTCATAATCAACCAACT
1 GATTCTC-AGTATAATTCATGCATTAGTCTAATCTTTGCAGTCTAACATTTACAATCAATCAACT
337443 TTTCTTTTTTTACCAAATGAAATCC
65 TTTCTTTTTTTA--AAA--AAAT-C
*
337468 GATTCTCATGTATAATTCATGCATTAGTCTAATCTTTGCAGTCTGACATTTACAATCAATCAAC-
1 GATTCTCA-GTATAATTCATGCATTAGTCTAATCTTTGCAGTCTAACATTTACAATCAATCAACT
* *
337532 TTT-TTTTATTAAAAAAATT
65 TTTCTTTTTTTAAAAAAATC
* * * * *
337551 AATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCTAACATTTACAATCAATCAACT
1 GATTCTCAG-TATAATTCATGCATTAGTCTAATCTTTGCAGTCTAACATTTACAATCAATCAACT
337616 TTTCTTTTTTT
65 TTTCTTTTTTT
337627 TTTCATAAAA
Statistics
Matches: 136, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
82 1 0.01
83 56 0.41
84 7 0.05
85 6 0.04
86 3 0.02
88 7 0.05
89 4 0.03
90 52 0.38
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.43
Consensus pattern (84 bp):
GATTCTCAGTATAATTCATGCATTAGTCTAATCTTTGCAGTCTAACATTTACAATCAATCAACTT
TTCTTTTTTTAAAAAAATC
Found at i:341707 original size:167 final size:167
Alignment explanation
Indices: 341395--341706 Score: 425
Period size: 167 Copynumber: 1.9 Consensus size: 167
341385 TCAGATTTTT
*
341395 GAAAAACCAAGTTTTCTATTCCATAAATGTTTTTAAGAGGATTTTCATTAGTTTCTAAATTTTAA
1 GAAAAACCAAGTTTTCTATTCCATAAATGTTTTTAAGAGGATTTTCATTAGTTTATAAATTTTAA
* * *
341460 AATTCACTAAATATTATTATTTAATTGCGATTAAATCAGTTTTCAAAAAATCATTTATTTTCATG
66 AATTCACTAAATATCATTATTTAATTGAGAATAAATCAGTTTTCAAAAAATCATTTATTTTCATG
*
341525 AGTTTTTCATTTTTTTCCTTAAAAGTTTTCTATTCCC
131 AGTTTGTCATTTTTTTCCTTAAAAGTTTTCTATTCCC
* * * * *
341562 GAAAAATCGAGTTTTCTATTCCATAAATGTTTTT-AGGGGAATTTTTC-TTGGTTTATAATTTTT
1 GAAAAACCAAGTTTTCTATTCCATAAATGTTTTTAAGAGG-A-TTTTCATTAGTTTATAAATTTT
* * * ***
341625 AAAATTCA-TCAAATATCATTATTTAATT-ATAATAAATTAGTTTTGAAATTTTCATTTATTTTC
64 AAAATTCACT-AAATATCATTATTTAATTGAGAATAAATCAGTTTTCAAAAAATCATTTATTTTC
341688 ATGAGTTTGTCATTTTTTT
128 ATGAGTTTGTCATTTTTTT
341707 TTGAAATGCC
Statistics
Matches: 126, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
166 50 0.40
167 71 0.56
168 5 0.04
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (167 bp):
GAAAAACCAAGTTTTCTATTCCATAAATGTTTTTAAGAGGATTTTCATTAGTTTATAAATTTTAA
AATTCACTAAATATCATTATTTAATTGAGAATAAATCAGTTTTCAAAAAATCATTTATTTTCATG
AGTTTGTCATTTTTTTCCTTAAAAGTTTTCTATTCCC
Found at i:341788 original size:164 final size:166
Alignment explanation
Indices: 341454--341804 Score: 372
Period size: 164 Copynumber: 2.1 Consensus size: 166
341444 AGTTTCTAAA
* * *
341454 TTTTAAAATTCA-CTAAATATTATTATTTAATTGCGATTAAATCAGTTTTCAAAAAATCATTTAT
1 TTTTAAAATTCATC-AAATATCATTATTTAATTGAGAATAAATCAGTTTTCAAAAAATCATTTAT
* * * * *
341518 TTTCATGAGTTTTTCATTTTTTTCCTTAAAAGTTTTCTATTCCCGAAAAATCGAGTTTTCTATTC
65 TTTCATGAGTTTGTCATTTTTTT-CTTAAAAGCTTTCTATTCCCGAAAAATAGAATTTCCTATTC
* * * * ** *
341583 CATAAATGTTTTTAGGGGAATTTTTCTTGGTTTATAAT
129 CACAAAGGTTTTGAAGGGAATTTTTCTAAGTTTAAAAT
* * * ***
341621 TTTTAAAATTCATCAAATATCATTATTTAATT-ATAATAAATTAGTTTTGAAATTTTCATTTATT
1 TTTTAAAATTCATCAAATATCATTATTTAATTGAGAATAAATCAGTTTTCAAAAAATCATTTATT
* * *
341685 TTCATGAGTTTGTCATTTTTTT-TTGAAATGCCTTTGT-TT-TCGAAAAATAGAATTTCCTATTC
66 TTCATGAGTTTGTCATTTTTTTCTT-AAAAG-CTTTCTATTCCCGAAAAATAGAATTTCCTATTC
*
341747 CACAAAGGTTTTCGAATGG-ATTTTTCTAAGTTTAAAAT
129 CACAAAGGTTTT-GAAGGGAATTTTTCTAAGTTTAAAAT
* *
341785 TTTTATAATTCATCTAATAT
1 TTTTAAAATTCATCAAATAT
341805 TGTCATTAAA
Statistics
Matches: 153, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
164 65 0.42
165 9 0.06
166 49 0.32
167 29 0.19
168 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (166 bp):
TTTTAAAATTCATCAAATATCATTATTTAATTGAGAATAAATCAGTTTTCAAAAAATCATTTATT
TTCATGAGTTTGTCATTTTTTTCTTAAAAGCTTTCTATTCCCGAAAAATAGAATTTCCTATTCCA
CAAAGGTTTTGAAGGGAATTTTTCTAAGTTTAAAAT
Found at i:341833 original size:164 final size:165
Alignment explanation
Indices: 341454--341848 Score: 350
Period size: 164 Copynumber: 2.4 Consensus size: 165
341444 AGTTTCTAAA
* * * * * *
341454 TTTTAAAATTCA-CTAAATATTATTATTTAATTGCGATTAAATCAGTTTTCAAAAAATCATTTAT
1 TTTTAAAATTCATC-AAATATCATCATTAAACTAC-ATTAAATCAGTTTTGAAAAAATCATTTAT
* * * * *
341518 TTTCATGAGTTTTTCATTTTTTTCCTTAAAAGTTTTCTATTCCCGAAAAATCGAGTTTTCTATTC
64 TTTCATGAGTTTGTCATTTTTTT-CTTAAAAGCTTTCTATTCCCGAAAAATAGAATTTCCTATTC
* * * * ** *
341583 CATAAATGTTTTTAGGGGAATTTTTCTTGGTTTATAAT
128 CACAAAGGTTTTGAAGGGAATTTTTCTAAGTTTAAAAT
* * * * * * ***
341621 TTTTAAAATTCATCAAATATCATTATTTAATTATAATAAATTAGTTTTGAAATTTTCATTTATTT
1 TTTTAAAATTCATCAAATATCATCATTAAACTACATTAAATCAGTTTTGAAAAAATCATTTATTT
* * *
341686 TCATGAGTTTGTCATTTTTTT-TTGAAATGCCTTTGT-TT-TCGAAAAATAGAATTTCCTATTCC
66 TCATGAGTTTGTCATTTTTTTCTT-AAAAG-CTTTCTATTCCCGAAAAATAGAATTTCCTATTCC
*
341748 ACAAAGGTTTTCGAATGG-ATTTTTCTAAGTTTAAAAT
129 ACAAAGGTTTT-GAAGGGAATTTTTCTAAGTTTAAAAT
* * ** * * *
341785 TTTTATAATTCATCTAATATTGTCATTAAACTCCATTAAATCAGTTTTGAGAAATTCAATTTAT
1 TTTTAAAATTCATCAAATATCATCATTAAACTACATTAAATCAGTTTTGAAAAAATC-ATTTAT
341849 GTCATGAATT
Statistics
Matches: 184, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
164 90 0.49
165 15 0.08
166 49 0.27
167 29 0.16
168 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (165 bp):
TTTTAAAATTCATCAAATATCATCATTAAACTACATTAAATCAGTTTTGAAAAAATCATTTATTT
TCATGAGTTTGTCATTTTTTTCTTAAAAGCTTTCTATTCCCGAAAAATAGAATTTCCTATTCCAC
AAAGGTTTTGAAGGGAATTTTTCTAAGTTTAAAAT
Found at i:342377 original size:13 final size:13
Alignment explanation
Indices: 342356--342389 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
342346 TTGGGCAAGT
342356 GAGAAAAAAAAAA
1 GAGAAAAAAAAAA
*
342369 GAGAGAAAAAAAA
1 GAGAAAAAAAAAA
342382 GA-AAAAAA
1 GAGAAAAAA
342390 TAGAAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
GAGAAAAAAAAAA
Found at i:342386 original size:19 final size:18
Alignment explanation
Indices: 342359--342397 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
342349 GGCAAGTGAG
*
342359 AAAAAAAAAAGAGAGAAA
1 AAAAAAAAAAAAGAGAAA
*
342377 AAAAAGAAAAAAATAGAAA
1 AAAAA-AAAAAAAGAGAAA
342396 AA
1 AA
342398 CTAGTAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAAAGAGAAA
Found at i:342696 original size:24 final size:24
Alignment explanation
Indices: 342669--342714 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
342659 TGTATGGATG
342669 ATGATGTTGGTTGTCTATTTAAAA
1 ATGATGTTGGTTGTCTATTTAAAA
*
342693 ATGATGTTGGTTGTCTGTTTAA
1 ATGATGTTGGTTGTCTATTTAA
342715 GCTTAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (24 bp):
ATGATGTTGGTTGTCTATTTAAAA
Found at i:343281 original size:17 final size:16
Alignment explanation
Indices: 343256--343287 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
343246 TAAAATTTTT
343256 TAAAAAATAAATAAAA
1 TAAAAAATAAATAAAA
343272 TAAAATAATAAATAAA
1 TAAAA-AATAAATAAA
343288 TATTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAAATAAATAAAA
Found at i:343529 original size:140 final size:142
Alignment explanation
Indices: 343301--343566 Score: 356
Period size: 140 Copynumber: 1.9 Consensus size: 142
343291 TATTTTATCC
* * * *
343301 AATAAAAATTATTATCTTAATTTTTCTAGATTTTTAATATTCCTATGATTTTTTGTAAGGGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTTCAATATTCCTATGATTTTCTATAAGGGTATA
** * * * *
343366 AAAATCTTCAAAAGTTTTTGTATCTTTTCGGTTTTTCATTAAGGTACAAAATGA-ATTTTTTGAA
66 AAAATCTTCAAAACATTTCGTATCTTTTCGGTTCTTAATTAAGATACAAAATGAGATTTTTTGAA
343430 ATTAAAAAATTA
131 ATTAAAAAATTA
* * * *
343442 AATAAAAATTATTGTCTTAATTTTTCAAGA-TTTCATTATTCCTATGGTTTTCTATAGGGGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTTCAATATTCCTATGATTTTCTATAAGGGTATA
* * * *
343506 GAAATCTTTAAAACATTTCGTATCTTTTTGGTTCTTAATTAAGATACGAAATGAGATTTTT
66 AAAATCTTCAAAACATTTCGTATCTTTTCGGTTCTTAATTAAGATACAAAATGAGATTTTT
343567 GTAATTTACA
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
140 72 0.68
141 34 0.32
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (142 bp):
AATAAAAATTATTATCTTAATTTTTCAAGATTTTCAATATTCCTATGATTTTCTATAAGGGTATA
AAAATCTTCAAAACATTTCGTATCTTTTCGGTTCTTAATTAAGATACAAAATGAGATTTTTTGAA
ATTAAAAAATTA
Found at i:344134 original size:155 final size:154
Alignment explanation
Indices: 343663--344186 Score: 465
Period size: 155 Copynumber: 3.4 Consensus size: 154
343653 CAGGTGCTTT
* * ** *
343663 TAAGTCGAAGGCATCCGCTAAGGGTATTTTTGGT-ATTTTTTAGAATCGAGTCTTAGGTTATCAT
1 TAAGTCGAAGGTATCCGCTAAGGGCA-TTTTCATAATTTTTTAGAATCGAGTCTTAGGTTATCAC
* * * * * *
343727 CAGGTCCGTTTTTATGCTGAAGTTGGGTATTTAGGATAAGTTAATCCCATCTATAATCCTTTTTA
65 CAGGTTCGCTTTTATGCCGAAGCT-GGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTA
* *
343792 AGTACTTTAGGAGTATTGGGCACTTC
129 AGTACTTTAAGAGTATTGAGCACTTC
** * *
343818 TAAGTCGAAGGTATCTC-CTAAGGGCATTTTCATAATTTTTTTTAGGTTCAAGTCCTAGGTTATC
1 TAAGTCGAAGGTATC-CGCTAAGGGCATTTTCATAA--TTTTTTAGAATCGAGTCTTAGGTTATC
* * * ** * * * *
343882 ACCAGG-TCGCTTCTATGCCAAAGGT-GTACACATAGGATAGATTCAAT--CTTTTCT-ATCCTT
63 ACCAGGTTCGCTTTTATGCCGAAGCTGGT--ATTTAGGATAGGTTC-ATCCCATCTATAATCCTT
* * *
343942 TTTAAGTCCTTGATAG-GTATTGAACACTTC
125 TTTAAGTACTTTA-AGAGTATTGAGCACTTC
* * * **
343972 TACGTCGAAGTTATCC-CTTAAGGGTATTTTTGTAATTTTTTAGAATCGAGTCTTAGGTTATCAC
1 TAAGTCGAAGGTATCCGC-TAAGGGCATTTTCATAATTTTTTAGAATCGAGTCTTAGGTTATCAC
* * *
344036 CAGGTTTGCTTTTATGCCGAAGCTAGGTATTTAGGATAGGCTCATCCCATCTATAATCATTTTTA
65 CAGGTTCGCTTTTATGCCGAAGCT-GGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTA
* * *
344101 AGTTCTTTAAGAGTATTGAGTACTTT
129 AGTACTTTAAGAGTATTGAGCACTTC
* * * *
344127 TACGTCGAAGGTA-CCTCGTAGGGGCATTTTCATAATTTTTCTAGACTCGAGTCTTAGGTT
1 TAAGTCGAAGGTATCCGC-TAAGGGCATTTTCATAATTTTT-TAGAATCGAGTCTTAGGTT
344187 GTCATTCTTA
Statistics
Matches: 290, Mismatches: 61, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
152 31 0.11
153 28 0.10
154 71 0.24
155 88 0.30
156 42 0.14
157 30 0.10
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (154 bp):
TAAGTCGAAGGTATCCGCTAAGGGCATTTTCATAATTTTTTAGAATCGAGTCTTAGGTTATCACC
AGGTTCGCTTTTATGCCGAAGCTGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAG
TACTTTAAGAGTATTGAGCACTTC
Found at i:349535 original size:14 final size:14
Alignment explanation
Indices: 349512--349564 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
349502 AATATGATAT
*
349512 ATATTTAAATATAA
1 ATATTAAAATATAA
349526 ATATTAAAATATAA
1 ATATTAAAATATAA
* *
349540 TTTTTTAAATATATAA
1 -ATATTAAA-ATATAA
*
349556 AAATTAAAA
1 ATATTAAAA
349565 AAATTAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 14 0.45
15 11 0.35
16 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:349537 original size:24 final size:24
Alignment explanation
Indices: 349488--349538 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
349478 TTTTTAATTC
* * *
349488 ATATTTAATATTTAAATATGATAT
1 ATATTTAATATATAAATATAAAAT
349512 ATATTTAA-ATATAAATATTAAAAT
1 ATATTTAATATATAAATA-TAAAAT
349536 ATA
1 ATA
349539 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
ATATTTAATATATAAATATAAAAT
Found at i:350039 original size:25 final size:26
Alignment explanation
Indices: 349997--350047 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
349987 TATTTTATTT
*
349997 ATTTAATTAAATTTATTTTAAATATAA
1 ATTTAATTAAATTTA-TTTAAAAATAA
350024 ATTTAA-T-AATTTATTTAAAAATAA
1 ATTTAATTAAATTTATTTAAAAATAA
350048 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 6 0.26
26 1 0.04
27 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAATTAAATTTATTTAAAAATAA
Found at i:350051 original size:27 final size:27
Alignment explanation
Indices: 349997--350047 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
349987 TATTTTATTT
*
349997 ATTTAATTAAATTTATTTTAAATATAA
1 ATTTAATTAAATTTATTTAAAATATAA
350024 ATTTAA-T-AATTTATTTAAAA-ATAA
1 ATTTAATTAAATTTATTTAAAATATAA
350048 TAAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 1 0.04
27 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTAATTAAATTTATTTAAAATATAA
Found at i:350165 original size:69 final size:65
Alignment explanation
Indices: 349976--350174 Score: 165
Period size: 65 Copynumber: 3.0 Consensus size: 65
349966 TAGATCTCAT
* * *
349976 ATATTAATAAATATTTTATTTATTTAATTAAATTTATTTTAAATATAAATTTAATAATTT-ATTT
1 ATATTAATAAATATTTTATTTATTTAATTAAATATATTCTAAATATAAA-TTAAAAATTTAATTT
350040 A
65 A
* * * * * * * *
350041 AAAATAATAAAAATTTTA-TTAATTAAATATATTAAAATC-AAAT-TAAATTTAAAAAAATTTAA
1 ATATTAATAAATATTTTATTTATTTAATTA-AATATATTCTAAATATAAA-TT--AAAAATTT-A
350103 ATCTCTA
61 AT-T-TA
* * *
350110 ATATTAATAAATATTTTATTTATTTAATTAAGTCTATTCTAAATATGAATTAAAAATTT-ATTTA
1 ATATTAATAAATATTTTATTTATTTAATTAAATATATTCTAAATATAAATTAAAAATTTAATTTA
350174 A
1 A
350175 ACTGACAAAA
Statistics
Matches: 103, Mismatches: 21, Indels: 21
0.71 0.14 0.14
Matches are distributed among these distances:
63 7 0.07
64 16 0.16
65 27 0.26
66 2 0.02
67 2 0.02
68 9 0.09
69 22 0.21
70 15 0.15
71 3 0.03
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (65 bp):
ATATTAATAAATATTTTATTTATTTAATTAAATATATTCTAAATATAAATTAAAAATTTAATTTA
Found at i:350587 original size:3 final size:3
Alignment explanation
Indices: 350581--350605 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
350571 AAAAAAAAAA
350581 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
350606 GCAAAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:350753 original size:2 final size:2
Alignment explanation
Indices: 350746--350774 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
350736 AAACCTGTAA
350746 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
350775 CACATATAAA
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:350837 original size:2 final size:2
Alignment explanation
Indices: 350830--350858 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
350820 AGTTTAGAAC
350830 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
350859 ATTTATGTAT
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:354622 original size:22 final size:19
Alignment explanation
Indices: 354585--354626 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
354575 GAACCTGAAA
354585 AACCCAACCAATCAACCCG
1 AACCCAACCAATCAACCCG
354604 AACCCTAATCCAATCCAACCCG
1 AACCC-AA-CCAAT-CAACCCG
354626 A
1 A
354627 TTTGACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 5 0.25
22 8 0.40
ACGTcount: A:0.40, C:0.45, G:0.05, T:0.10
Consensus pattern (19 bp):
AACCCAACCAATCAACCCG
Found at i:354718 original size:16 final size:16
Alignment explanation
Indices: 354647--354798 Score: 117
Period size: 16 Copynumber: 9.5 Consensus size: 16
354637 AAAGTCAACA
*
354647 ACCCGAATCCAAACTG
1 ACCCGAATCCAAAATG
* * *
354663 ACCC-AAACTCGAAATA
1 ACCCGAATC-CAAAATG
* *
354679 ACTCGAACCCAAAATG
1 ACCCGAATCCAAAATG
** *
354695 ACTTGAATCCAGAATG
1 ACCCGAATCCAAAATG
* *
354711 CCCCGAATTCAAAATG
1 ACCCGAATCCAAAATG
354727 ACCCGAATCCAAAATG
1 ACCCGAATCCAAAATG
* *
354743 ACCCGAATCCGAAATA
1 ACCCGAATCCAAAATG
**
354759 ACCCGAATCTGAAATG
1 ACCCGAATCCAAAATG
* * *
354775 ACCTGAACCCGAAATG
1 ACCCGAATCCAAAATG
*
354791 ATCCGAAT
1 ACCCGAAT
354799 AATTAACTCG
Statistics
Matches: 106, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
15 3 0.03
16 100 0.94
17 3 0.03
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.16
Consensus pattern (16 bp):
ACCCGAATCCAAAATG
Found at i:355910 original size:16 final size:16
Alignment explanation
Indices: 355891--355957 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 16
355881 TCCGAACTTG
*
355891 AAATGGCCCGAACCCA
1 AAATGACCCGAACCCA
* * *
355907 AAATGATCCGAATCTA
1 AAATGACCCGAACCCA
* *
355923 AAATGACCGGAACCCG
1 AAATGACCCGAACCCA
*
355939 AAATGACCAGAACCCA
1 AAATGACCCGAACCCA
355955 AAA
1 AAA
355958 ACAACCCGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.45, C:0.28, G:0.16, T:0.10
Consensus pattern (16 bp):
AAATGACCCGAACCCA
Found at i:357698 original size:30 final size:33
Alignment explanation
Indices: 357639--357699 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
357629 ATTCACAAAA
* *
357639 ATATTATATAGATCAATTTCCGGCCATAATTGT
1 ATATTATATAGAGCAATTTCCGACCATAATTGT
357672 ATATTATATAGAGC-ATTT-C-ACCATAATT
1 ATATTATATAGAGCAATTTCCGACCATAATT
357700 AAACAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 1 0.04
32 4 0.15
33 13 0.50
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (33 bp):
ATATTATATAGAGCAATTTCCGACCATAATTGT
Found at i:358189 original size:3 final size:3
Alignment explanation
Indices: 358138--358171 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
358128 ATATTAAAAT
358138 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
358172 CTTACGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:358852 original size:2 final size:2
Alignment explanation
Indices: 358845--358875 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
358835 TATTAATGCA
*
358845 AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
358876 ATGGTATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:359740 original size:32 final size:32
Alignment explanation
Indices: 359704--359765 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
359694 GTTGAAAATT
*
359704 TTTAATGACT-ATCAAATTTACAAGTAATTACC
1 TTTAAT-ACTCATCAAATTTACAAATAATTACC
*
359736 TTTAATATTCATCAAATTTACAAATAATTA
1 TTTAATACTCATCAAATTTACAAATAATTA
359766 TGGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (32 bp):
TTTAATACTCATCAAATTTACAAATAATTACC
Found at i:360168 original size:110 final size:114
Alignment explanation
Indices: 360026--360257 Score: 391
Period size: 112 Copynumber: 2.1 Consensus size: 114
360016 ATTATTTTTT
*
360026 AATTAAAAAATAGTATTTAATTAACTTTAAAAAAA-CACATTAATAAATTAAAATATTAATTATT
1 AATT-AAAAATAATATTTAATTAACTTTAAAAAAATCACATTAATAAATTAAAATATTAATTATT
*
360090 TTTTAAAATAAAAAATTAAATTAAAAA-CATTTATTA-T-TTTTTAATAA
65 TTTTAAAATAAAAAATTAAATTAAAAAGAATTTATTATTATTTTTAATAA
*
360137 AATTAAAAATAATATTTAATTAACTTTAAAAAAATTTACATTAATAAATTAAAATATTAATTATT
1 AATTAAAAATAATATTTAATTAACTTTAAAAAAA-TCACATTAATAAATTAAAATATTAATTATT
360202 TTTTAAAATAAAAAATTAAATTAAAAAGAATTTATTATTATTTTTAATAA
65 TTTTAAAATAAAAAATTAAATTAAAAAGAATTTATTATTATTTTTAATAA
360252 AATTAA
1 AATTAA
360258 TTAAATTTAA
Statistics
Matches: 113, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
110 29 0.26
111 4 0.04
112 55 0.49
113 8 0.07
114 1 0.01
115 16 0.14
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (114 bp):
AATTAAAAATAATATTTAATTAACTTTAAAAAAATCACATTAATAAATTAAAATATTAATTATTT
TTTAAAATAAAAAATTAAATTAAAAAGAATTTATTATTATTTTTAATAA
Found at i:360260 original size:41 final size:39
Alignment explanation
Indices: 360064--360275 Score: 148
Period size: 38 Copynumber: 5.6 Consensus size: 39
360054 AAAAAAACAC
* *
360064 ATTAA-TAAATTAAAATATTAATTATTTTTTAAAATAAA
1 ATTAATTAAATTAAAAAATTTATTATTTTTTAAAATAAA
360102 A--AATTAAATTAAAAACATTTATTATTTTTT--AATAAA
1 ATTAATTAAATTAAAAA-ATTTATTATTTTTTAAAATAAA
* **
360138 ATTAA--AAA-T--AATATTTAATTA-ACTTTAAAA-AAA
1 ATTAATTAAATTAAAAAATTT-ATTATTTTTTAAAATAAA
* * *
360171 TTTACATTAATAAATTAAAATATTAATTATTTTTTAAAATAAA
1 ATTA-A-T--TAAATTAAAAAATTTATTATTTTTTAAAATAAA
*
360214 A--AATTAAATTAAAAAGAATTTATTATTATTTT-TAATAAA
1 ATTAATTAAATT-AAAA-AATTTATTATT-TTTTAAAATAAA
360253 ATTAATTAAATTTAAAAAATTTA
1 ATTAATTAAA-TTAAAAAATTTA
360276 ATAAATAATA
Statistics
Matches: 137, Mismatches: 13, Indels: 46
0.70 0.07 0.23
Matches are distributed among these distances:
32 7 0.05
33 12 0.09
34 3 0.02
35 1 0.01
36 12 0.09
37 16 0.12
38 20 0.15
39 20 0.15
40 12 0.09
41 16 0.12
42 15 0.11
43 3 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (39 bp):
ATTAATTAAATTAAAAAATTTATTATTTTTTAAAATAAA
Found at i:360326 original size:59 final size:55
Alignment explanation
Indices: 360210--360314 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 55
360200 TTTTTTAAAA
* *
360210 TAAAAAATTAAATTAAAAAGAATTTATTATTATTTTTAATAAAATTAATTAAATT
1 TAAAAAATTAAATTAAAAAGAATTAATTATTATTTTTAATAAAATTAAATAAATT
* * *
360265 TAAAAAATTTAA-TAAATAATATATTAATTATTATTTTTTATAAAATTAAA
1 TAAAAAATTAAATTAAA-AAGA-ATTAATTATTATTTTTAATAAAATTAAA
360315 AATAATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
54 4 0.09
55 14 0.33
56 25 0.58
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (55 bp):
TAAAAAATTAAATTAAAAAGAATTAATTATTATTTTTAATAAAATTAAATAAATT
Found at i:360641 original size:11 final size:11
Alignment explanation
Indices: 360625--360661 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
360615 TTATTACTTT
360625 TTATTTATAAA
1 TTATTTATAAA
* *
360636 TTATTTTTAAT
1 TTATTTATAAA
360647 TTATTTATAAA
1 TTATTTATAAA
360658 TTAT
1 TTAT
360662 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:360938 original size:11 final size:11
Alignment explanation
Indices: 360922--360958 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
360912 TTATTACTTT
360922 TTATTTATAAA
1 TTATTTATAAA
* *
360933 TTATTTTTAAT
1 TTATTTATAAA
360944 TTATTTATAAA
1 TTATTTATAAA
360955 TTAT
1 TTAT
360959 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:361138 original size:291 final size:292
Alignment explanation
Indices: 360514--361150 Score: 931
Period size: 291 Copynumber: 2.2 Consensus size: 292
360504 TATTTTTCAG
* * *
360514 TAACGACTTAAATATGAGTTTTTCTTTAATTGTAAAATGACCAAGACAAAATTTATTATACATGT
1 TAACGACTTAAATATGAGCTTTTCTTTATTTGTAAAATGACCAA-AAAAAATTTATTATACATGT
** *
360579 ATTTTTTTATTAAAATTAATTAATATTGTACATGTATTATTACTTTTTATTTATAAATTATTTTT
65 ATTTTTTTATTAAAATTAATTAATATAATACATGAATTATTACTTTTTATTTATAAATTATTTTT
**
360644 AATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTACATATATTAGT
130 AATTTATTTATAAATTATACAAATTTATTTTTAAAAAAATTAATTAATATTGTAC--A-ATTAG-
* ** * * *
360709 TTTATAATTGATAGAACTTAAATTTATGTTAGCCAACAATATTTTACTTTTTTCAATAGCGACTT
191 TTTATAATTGATAGAACTTAAATTTATGTTAGCAAACAATAAATTACCTCTTTCAATAACGACTT
* * * *
360774 ATTTCGGATTTATAGATGCACACAGTTTATTTTTCGA
256 ATTTCAGATTTACAAATGCACACAGTTTAGTTTTCGA
* * * *
360811 TAATGACTTAAATATAAGCTTTTCTTTATCTGTAAAATGACCAAAAAAAATTTATTGTACATGTA
1 TAACGACTTAAATATGAGCTTTTCTTTATTTGTAAAATGACCAAAAAAAATTTATTATACATGTA
*
360876 TTATTTTTATTAAAATTAATTAATATAATGCATGAATTATTACTTTTTATTTATAAATTATTTTT
66 TT-TTTTTATTAAAATTAATTAATATAATACATGAATTATTACTTTTTATTTATAAATTATTTTT
360941 AATTTATTTATAAATTATACAAATTTATTTTTTAAAAAAATTAATTAATATTGTAC-A-TA-TTT
130 AATTTATTTATAAATTATACAAATTTA-TTTTTAAAAAAATTAATTAATATTGTACAATTAGTTT
* *
361003 ATAATTGATAGAACTTAAATTTATGTTAGCAAACAATAAATTGCCTCTTTCGATAACGACTTATT
194 ATAATTGATAGAACTTAAATTTATGTTAGCAAACAATAAATTACCTCTTTCAATAACGACTTATT
361068 TCAGATTTACAAATGCACACA-TTTCAGTTTTCGA
259 TCAGATTTACAAATGCACACAGTTT-AGTTTTCGA
* *
361102 TAACGACTTAAATACGAGCTTTTCTTTATTTGTAAAATGACCAAGAAAA
1 TAACGACTTAAATATGAGCTTTTCTTTATTTGTAAAATGACCAAAAAAA
361151 CATTGCCCTC
Statistics
Matches: 307, Mismatches: 30, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
290 3 0.01
291 130 0.42
293 2 0.01
294 1 0.00
296 21 0.07
297 124 0.40
298 26 0.08
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (292 bp):
TAACGACTTAAATATGAGCTTTTCTTTATTTGTAAAATGACCAAAAAAAATTTATTATACATGTA
TTTTTTTATTAAAATTAATTAATATAATACATGAATTATTACTTTTTATTTATAAATTATTTTTA
ATTTATTTATAAATTATACAAATTTATTTTTAAAAAAATTAATTAATATTGTACAATTAGTTTAT
AATTGATAGAACTTAAATTTATGTTAGCAAACAATAAATTACCTCTTTCAATAACGACTTATTTC
AGATTTACAAATGCACACAGTTTAGTTTTCGA
Found at i:362208 original size:13 final size:13
Alignment explanation
Indices: 362190--362214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362180 TTGTTTATTG
362190 TATCGATACATTA
1 TATCGATACATTA
362203 TATCGATACATT
1 TATCGATACATT
362215 TTGGGTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:364700 original size:51 final size:52
Alignment explanation
Indices: 364638--364752 Score: 135
Period size: 51 Copynumber: 2.2 Consensus size: 52
364628 TTCCGAGGGA
* ** * * *
364638 ATACTCTAACCCTAG-TTTTATTTCTGAAATACCAATTTTTCACAATTGGAG
1 ATACTCCAACCCTAGATTTTATTTCCAAAACACCAATTTTTCACAATCGAAG
* *
364689 ATACTCCAACCC-CGATTTTATTTCCAAAACACTAATTTTTCACAATCGAAG
1 ATACTCCAACCCTAGATTTTATTTCCAAAACACCAATTTTTCACAATCGAAG
*
364740 GTACTCCAACCCT
1 ATACTCCAACCCT
364753 GTTATTTCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (52 bp):
ATACTCCAACCCTAGATTTTATTTCCAAAACACCAATTTTTCACAATCGAAG
Found at i:364772 original size:28 final size:28
Alignment explanation
Indices: 364741--364809 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
364731 CAATCGAAGG
**
364741 TACTCCAACCCTGTTATTTCATCGGGGA
1 TACTCCAACCCTGTTATTTCAGAGGGGA
** *
364769 TACTCCAACCCCATTATTTCCGAGGGGA
1 TACTCCAACCCTGTTATTTCAGAGGGGA
364797 TACTCCAACCCTG
1 TACTCCAACCCTG
364810 GCTTTATTCC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (28 bp):
TACTCCAACCCTGTTATTTCAGAGGGGA
Found at i:365054 original size:158 final size:158
Alignment explanation
Indices: 364761--365095 Score: 424
Period size: 158 Copynumber: 2.1 Consensus size: 158
364751 CTGTTATTTC
* *
364761 ATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
* * * * *
364826 ATTGATTTCCCACAATCGGGGATACTCCAACCCTGTTATTTTCGCGGAGATACTCCAACCCTGGC
66 ACTGATTTCCCACAATCAGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGAC
**
364891 CTTA-TTTCTA-AAGCATCGATTTTTTATA
131 CTTATTTTC-AGAA-CATCGATTTTCCATA
* * * * * *
364919 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATT-TTCAAAA
1 ATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCT-AAAA
* * * *
364983 TACTGATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGA
65 TACTGATTTCCCACAATCAGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGA
**
365048 TTTTATTTTCAGAACATCGATTTTCCATA
130 CCTTATTTTCAGAACATCGATTTTCCATA
*
365077 GTCGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
365096 TGTTGTTATC
Statistics
Matches: 151, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
157 1 0.01
158 144 0.95
159 6 0.04
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (158 bp):
ATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
ACTGATTTCCCACAATCAGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCCAACCCCGAC
CTTATTTTCAGAACATCGATTTTCCATA
Found at i:365096 original size:79 final size:78
Alignment explanation
Indices: 364761--365099 Score: 369
Period size: 79 Copynumber: 4.3 Consensus size: 78
364751 CTGTTATTTC
** * * * * *
364761 ATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCT-AAAC
* * *
364826 ATTGATTTCCCACA
65 ATCGATTTTCCATA
* * * * *
364840 ATCGGGGATACTCCAACCCTGTTATTTTCGCGGAGATACTCCAACCCTGGCCTTATTTCTAAAGC
1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCTAAA-C
**
364905 ATCGATTTTTTATA
65 ATCGATTTTCCATA
* * * *
364919 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTT-TCAAA-
1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCT-AAAC
*
364982 ATACTGATTTTCTATA
65 AT-C-GATTTTCCATA
* *
364998 ATCAGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTT-TCAGAA
1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCT-A-AA
365062 CATCGATTTTCCATA
64 CATCGATTTTCCATA
*
365077 GTCGGGGATACTCCAACCCTGTT
1 ATCGGGGATACTCCAACCCTGTT
365100 GTTATCCCCA
Statistics
Matches: 224, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
77 2 0.01
78 5 0.02
79 212 0.95
80 3 0.01
81 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCTAAACA
TCGATTTTCCATA
Found at i:368932 original size:91 final size:91
Alignment explanation
Indices: 368591--369300 Score: 757
Period size: 92 Copynumber: 7.8 Consensus size: 91
368581 AACTGTGATG
* ** * * * *
368591 TTTACAATCGATCAACTTTTCAGTTTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTATG
1 TTTACAATCAATCAACTTTTCTTTTTTTC-ATAAAAAAGAATCTGATTCTCAGATATAATTCATG
* * *
368656 CATTAGTCTAATCTTTGCAGTGTCATA
65 CATTAGTCTAATCTTTGCAGTCTGACA
* * * * *
368683 CTTATAATCAACCAACTTTTCTTTTTTT-TTACCAAAAGAAATCTGATTCTCATG-TATAATTCA
1 TTTACAATCAATCAACTTTTCTTTTTTTCATA-AAAAAG-AATCTGATTCTCA-GATATAATTCA
* * **
368746 TGCATTAGTCAAATCCTTATAGTCTGACA
63 TGCATTAGTCTAATCTTTGCAGTCTGACA
* * *
368775 TTTACAATCAATCAAC---T-TTTTTTT-A-ATAAAA-AAT-TGATTTTCATATATAATTCATGC
1 TTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
** *
368832 ATTAGTCTAATCTTTATACTCTGACA
66 ATTAGTCTAATCTTTGCAGTCTGACA
*
368858 TTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTATGC
1 TTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
* * *
368923 ATTAATCTAATATTTGCAGTTTGACA
66 ATTAGTCTAATCTTTGCAGTCTGACA
* * * *
368949 TTTAGAGTCACTCAACTTTTCTTTTTTTTTTCTATAAAAAA-AAT-TGATTTTCAGATATAATTC
1 TTTACAATCAATCAACTTTTC---TTTTTTTC-ATAAAAAAGAATCTGATTCTCAGATATAATTC
* * *
369012 ATGCATTAGTCTAATCCTTACACTCTGACA
62 ATGCATTAGTCTAATCTTTGCAGTCTGACA
*
369042 TTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTATGC
1 TTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
* * *
369107 ATTAATCTAATATTTGCAGTTTGACA
66 ATTAGTCTAATCTTTGCAGTCTGACA
*** * * *
369133 TTTAGGGTCACTCAACTTTTCTTTTTTTTTCTATAAAAAA-AAT-TAATTTTCAGATATAATTCA
1 TTTACAATCAATCAACTTTTC--TTTTTTTC-ATAAAAAAGAATCTGATTCTCAGATATAATTCA
*
369196 TGCATTAGTCTAATCCTTGCAGTCTGACA
63 TGCATTAGTCTAATCTTTGCAGTCTGACA
*
369225 TTTATC-ATCAATCAACTTTTCTTTTTTTTCATAAAAAAAGAATCTGATTCTCAGATATAATCCA
1 TTTA-CAATCAATCAACTTTTC-TTTTTTTCAT-AAAAAAGAATCTGATTCTCAGATATAATTCA
369289 TGCATTAGTCTA
63 TGCATTAGTCTA
369301 TTTCTTACAA
Statistics
Matches: 515, Mismatches: 78, Indels: 49
0.80 0.12 0.08
Matches are distributed among these distances:
83 59 0.11
84 3 0.01
86 5 0.01
87 8 0.02
88 8 0.02
89 14 0.03
90 17 0.03
91 135 0.26
92 140 0.27
93 99 0.19
94 19 0.04
95 8 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (91 bp):
TTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATGC
ATTAGTCTAATCTTTGCAGTCTGACA
Found at i:369019 original size:93 final size:92
Alignment explanation
Indices: 368591--369300 Score: 758
Period size: 91 Copynumber: 7.8 Consensus size: 92
368581 AACTGTGATG
* ** * * * *
368591 TTTACAATCGATCAACTTTTC-AGTTTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTAT
1 TTTACAATCAATCAACTTTTCTTTTTTTTC-ATAAAAAAGAATCTGATTCTCAGATATAATTCAT
* * *
368655 GCATTAGTCTAATCTTTGCAGTGTCATA
65 GCATTAGTCTAATCTTTGCAGTCTGACA
* * * *
368683 CTTATAATCAACCAACTTTTCTTTTTTTT--TACCAAAAGAAATCTGATTCTCATG-TATAATTC
1 TTTACAATCAATCAACTTTTCTTTTTTTTCATA-AAAAAG-AATCTGATTCTCA-GATATAATTC
* * **
368745 ATGCATTAGTCAAATCCTTATAGTCTGACA
63 ATGCATTAGTCTAATCTTTGCAGTCTGACA
* * *
368775 TTTACAATCAATCAA-----CTTTTTTTT-A-ATAAAA-AAT-TGATTTTCATATATAATTCATG
1 TTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATG
** *
368831 CATTAGTCTAATCTTTATACTCTGACA
66 CATTAGTCTAATCTTTGCAGTCTGACA
*
368858 TTTACAATCAATCAACTTTTC-TTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTATG
1 TTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATG
* * *
368922 CATTAATCTAATATTTGCAGTTTGACA
66 CATTAGTCTAATCTTTGCAGTCTGACA
* * * *
368949 TTTAGAGTCACTCAACTTTTCTTTTTTTTTTCTATAAAAAA-AAT-TGATTTTCAGATATAATTC
1 TTTACAATCAATCAACTTTTC--TTTTTTTTC-ATAAAAAAGAATCTGATTCTCAGATATAATTC
* * *
369012 ATGCATTAGTCTAATCCTTACACTCTGACA
63 ATGCATTAGTCTAATCTTTGCAGTCTGACA
*
369042 TTTACAATCAATCAACTTTTC-TTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTATG
1 TTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATG
* * *
369106 CATTAATCTAATATTTGCAGTTTGACA
66 CATTAGTCTAATCTTTGCAGTCTGACA
*** * * *
369133 TTTAGGGTCACTCAACTTTTCTTTTTTTTTCTATAAAAAA-AAT-TAATTTTCAGATATAATTCA
1 TTTACAATCAATCAACTTTTC-TTTTTTTTC-ATAAAAAAGAATCTGATTCTCAGATATAATTCA
*
369196 TGCATTAGTCTAATCCTTGCAGTCTGACA
64 TGCATTAGTCTAATCTTTGCAGTCTGACA
*
369225 TTTATC-ATCAATCAACTTTTCTTTTTTTTCATAAAAAAAGAATCTGATTCTCAGATATAATCCA
1 TTTA-CAATCAATCAACTTTTCTTTTTTTTCAT-AAAAAAGAATCTGATTCTCAGATATAATTCA
369289 TGCATTAGTCTA
64 TGCATTAGTCTA
369301 TTTCTTACAA
Statistics
Matches: 514, Mismatches: 76, Indels: 55
0.80 0.12 0.09
Matches are distributed among these distances:
83 58 0.11
84 3 0.01
86 4 0.01
87 17 0.03
88 2 0.00
89 13 0.03
90 17 0.03
91 135 0.26
92 134 0.26
93 104 0.20
94 19 0.04
95 8 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (92 bp):
TTTACAATCAATCAACTTTTCTTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTCATG
CATTAGTCTAATCTTTGCAGTCTGACA
Found at i:369021 original size:184 final size:183
Alignment explanation
Indices: 368614--369300 Score: 867
Period size: 184 Copynumber: 3.8 Consensus size: 183
368604 AACTTTTCAG
** * * * * * * *
368614 TTTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTATGCATTAGTCTAATCTTTGCAGTGT
1 TTTTTCTAT-AAAAAAAAT-TGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCT
* * * * * * *
368679 CATACTTATAATCAACCAACTTTTCTTTTTTT-TTACCAAAAGAAATCTGATTCTCATG-TATAA
64 GACATTTACAATCAATCAACTTTTCTTTTTTTCATA-AAAAAG-AATCTGATTCTCA-GATATAA
* * * ** ** * * * *
368742 TTCATGCATTAGTCAAATCCTTATAGTCTGACATTTACAATCAATCAA-----C--TT
126 TTTATGCATTAATCTAATATTTGCAGTTTGACATTTAGAGTCACTCAACTTTTCTTTT
* * * *
368793 TTTTT-TA-ATAAAAAATTGATTTTCATATATAATTCATGCATTAGTCTAATCTTTATACTCTGA
1 TTTTTCTATAAAAAAAATTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCTGA
368856 CATTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTAT
66 CATTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTAT
368921 GCATTAATCTAATATTTGCAGTTTGACATTTAGAGTCACTCAACTTTTCTTTTT
131 GCATTAATCTAATATTTGCAGTTTGACATTTAGAGTCACTCAACTTTTC-TTTT
368975 TTTTTCTATAAAAAAAATTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCTGA
1 TTTTTCTATAAAAAAAATTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCTGA
369040 CATTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTAT
66 CATTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTAT
*
369105 GCATTAATCTAATATTTGCAGTTTGACATTTAGGGTCACTCAACTTTTCTTTT
131 GCATTAATCTAATATTTGCAGTTTGACATTTAGAGTCACTCAACTTTTCTTTT
* * *
369158 TTTTTCTATAAAAAAAATTAATTTTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTCTGA
1 TTTTTCTATAAAAAAAATTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCTGA
*
369223 CATTTATC-ATCAATCAACTTTTCTTTTTTTTCATAAAAAAAGAATCTGATTCTCAGATATAATC
66 CATTTA-CAATCAATCAACTTTTC-TTTTTTTCAT-AAAAAAGAATCTGATTCTCAGATATAATT
* *
369287 CATGCATTAGTCTA
128 TATGCATTAATCTA
369301 TTTCTTACAA
Statistics
Matches: 454, Mismatches: 39, Indels: 24
0.88 0.08 0.05
Matches are distributed among these distances:
173 1 0.00
174 55 0.12
175 70 0.15
176 8 0.02
178 2 0.00
179 6 0.01
182 7 0.02
183 89 0.20
184 176 0.39
185 40 0.09
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (183 bp):
TTTTTCTATAAAAAAAATTGATTTTCAGATATAATTCATGCATTAGTCTAATCCTTACACTCTGA
CATTTACAATCAATCAACTTTTCTTTTTTTCATAAAAAAGAATCTGATTCTCAGATATAATTTAT
GCATTAATCTAATATTTGCAGTTTGACATTTAGAGTCACTCAACTTTTCTTTT
Found at i:369802 original size:20 final size:21
Alignment explanation
Indices: 369777--369816 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
369767 TATTATTTTT
*
369777 TTTAAAAATATTTA-ATTAAC
1 TTTAAAAAAATTTATATTAAC
369797 TTTAAAAAAATTTATATTAA
1 TTTAAAAAAATTTATATTAA
369817 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAAAAAATTTATATTAAC
Found at i:369917 original size:23 final size:22
Alignment explanation
Indices: 369888--369941 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
369878 TTTTTTCATA
369888 AAATTAAAAATAA-TAT-TTAATT
1 AAATTAAAAA-AATTATATTAA-T
369910 AAATTTAAAAAAATTATATTAAT
1 AAA-TTAAAAAAATTATATTAAT
369933 AAATTAAAA
1 AAATTAAAA
369942 TATTAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.38
23 14 0.48
24 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATTAAAAAAATTATATTAAT
Found at i:369919 original size:22 final size:23
Alignment explanation
Indices: 369888--369943 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
369878 TTTTTTCATA
*
369888 AAATTAAAAATAA-TAT-TTAATT
1 AAATTTAAAATAATTATATTAA-T
*
369910 AAATTTAAAAAAATTATATTAAT
1 AAATTTAAAATAATTATATTAAT
369933 AAA-TTAAAATA
1 AAATTTAAAATA
369944 TTAAAACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 18 0.62
23 7 0.24
24 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAAATAATTATATTAAT
Found at i:370207 original size:15 final size:15
Alignment explanation
Indices: 370163--370214 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
370153 AAAAATTTTT
*
370163 AAATTTAAAAATC-A
1 AAATTTTAAAATCTA
*
370177 TAAATTTT-ATATCTA
1 -AAATTTTAAAATCTA
370192 AAATTTTAAAATCT-
1 AAATTTTAAAATCTA
370206 AAATTTTAA
1 AAATTTTAA
370215 TTTTATAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTTAAAATCTA
Found at i:375330 original size:49 final size:49
Alignment explanation
Indices: 375266--375692 Score: 400
Period size: 49 Copynumber: 8.8 Consensus size: 49
375256 ATGTTAAAAA
* *
375266 TGCCAATATGCTGATTTAAGGCCAACGATATCGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
* * *** * * *
375315 TGCCAATGTACTGATTCAAGGCTGGCGACATTGGTCATAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
* * * * * * *
375364 TGCCAATATGTTGATTCAAGACTAATGATATCGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
* * * * *
375413 TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAA-G
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
375461 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT---AAAGG
** * * *
375513 CACCAATATGCTGATTCAAGGTCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
* * * * * *
375562 GGCCAATGTGCTAATTCAAGACCATCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
* * * * **
375611 TGCCAATGTGCTAATTCAAGGCCAGC-A-A---CA-TTAAACTTAAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
* * *
375654 TGTCAATATGCTGATTCAAGGCCAGCAATATTGGACTTA
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA
375693 GAAAAAGATG
Statistics
Matches: 305, Mismatches: 63, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
43 33 0.11
44 2 0.01
45 1 0.00
47 1 0.00
48 41 0.13
49 183 0.60
51 3 0.01
52 41 0.13
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATAAAGG
Found at i:375395 original size:98 final size:98
Alignment explanation
Indices: 375218--375642 Score: 449
Period size: 98 Copynumber: 4.3 Consensus size: 98
375208 GAAGAATGCT
** * * * ** *
375218 AATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAAATGCCAATATGCTGATTT
1 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTA--AA-GATAAAGGTGCCAATATGCTGATTC
*
375283 AAGGCCAACGATATCGGACTTAAAGATAAAGGTGCC
63 AAGACCAACGATATCGGACTTAAAGATAAAGGTGCC
* * * *
375319 AATGTACTGATTCAAGGCTGGCGACATTGGTCATAAAGATAAAGGTGCCAATATGTTGATTCAAG
1 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAG
* * * * *
375384 ACTAATGATATCGGACTTAAAGATGAAGATGCT
66 ACCAACGATATCGGACTTAAAGATAAAGGTGCC
*
375417 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAA-GTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAG
* * **
375481 GCCAACGATATTGGACTTAAAGATGACAAAGGCACC
66 ACCAACGATATCGGACTTAAAGAT---AAAGGTGCC
* * * * * * *
375517 AATATGCTGATTCAAGG-TCAGCGATATTGGACTTAAAGATGAAGGGGCCAATGTGCTAATTCAA
1 AATGTGCTGATTCAAGGCT-AGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* * *
375581 GACCATCGATATTGGACTTAAAGATGAAGGTGCC
65 GACCAACGATATCGGACTTAAAGATAAAGGTGCC
* * *
375615 AATGTGCTAATTCAAGGCCAGCAACATT
1 AATGTGCTGATTCAAGGCTAGCGACATT
375643 AAACTTAAAG
Statistics
Matches: 268, Mismatches: 50, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
97 40 0.15
98 117 0.44
99 2 0.01
100 41 0.15
101 68 0.25
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (98 bp):
AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAG
ACCAACGATATCGGACTTAAAGATAAAGGTGCC
Found at i:375779 original size:29 final size:29
Alignment explanation
Indices: 375737--376033 Score: 275
Period size: 28 Copynumber: 10.4 Consensus size: 29
375727 AAGGGCATCA
* *
375737 ACTTGTGTGCTTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* * *
375766 ACTTATGGGCTTTTG-AAGGTTGCCATTG
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* *
375794 ACTTGTGGGCTTCTG-AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* * * *
375822 ACTTGTGGGCTTCTG-AAGGTTGTCACTA
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* * * *
375850 ACTTGTAGGC-TTTGAAAAGGTGCCAGTA
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* * *
375878 ACTTGAGGGCTTTTG-AAGGTTGCCATTG
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* **
375906 ACTTGTGGGC-TTTGAAAAGTTACTGCTG
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* *
375934 ACTTGTGGGCTTTTGAAAAGATGCCAATG
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
* * *
375963 ACTTATGGGC-TTTAAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAA-GTTGCCACTG
** *
375992 ACTTGTGGGCTTTTGAAAAAATGCCACTA
1 ACTTGTGGGCTTTTGAAAAGTTGCCACTG
376021 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
376034 GGAAGGTGAG
Statistics
Matches: 220, Mismatches: 42, Indels: 12
0.80 0.15 0.04
Matches are distributed among these distances:
27 7 0.03
28 130 0.59
29 76 0.35
30 7 0.03
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (29 bp):
ACTTGTGGGCTTTTGAAAAGTTGCCACTG
Found at i:376448 original size:37 final size:37
Alignment explanation
Indices: 376398--376479 Score: 164
Period size: 37 Copynumber: 2.2 Consensus size: 37
376388 AAAGACGAAG
376398 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
376435 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
376472 CACAAATG
1 CACAAATG
376480 TATGATTGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
Found at i:384633 original size:52 final size:52
Alignment explanation
Indices: 384555--384683 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
384545 CGAAATATGA
* *
384555 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
384607 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
384659 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
384684 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:384696 original size:52 final size:51
Alignment explanation
Indices: 384555--384703 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
384545 CGAAATATGA
*
384555 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
384607 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
384659 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
384704 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:384710 original size:13 final size:13
Alignment explanation
Indices: 384692--384716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
384682 CAAAGATCAG
384692 TGTATCGATACAA
1 TGTATCGATACAA
384705 TGTATCGATACA
1 TGTATCGATACA
384717 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:384794 original size:33 final size:33
Alignment explanation
Indices: 384757--384823 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
384747 AGTAGCTTAA
384757 ATTGTATCAATACAAAAAAATATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
* * ***
384790 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAAAAATATGTATCGATAC
384823 A
1 A
384824 AATCATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCAATACAAAAAAATATGTATCGATAC
Found at i:384797 original size:13 final size:13
Alignment explanation
Indices: 384779--384803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
384769 CAAAAAAATA
384779 TGTATCGATACAT
1 TGTATCGATACAT
384792 TGTATCGATACA
1 TGTATCGATACA
384804 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:388408 original size:14 final size:14
Alignment explanation
Indices: 388353--388411 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
388343 ATTCATATTT
388353 AATATTTAAATATGA
1 AATATTTAAATAT-A
388368 TACATATTTAAATATA
1 -A-ATATTTAAATATA
*
388384 AATATTAAAATATA
1 AATATTTAAATATA
* *
388398 ATTTTTTAAATATA
1 AATATTTAAATATA
388412 TAAAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 2 0.05
17 12 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
AATATTTAAATATA
Found at i:389454 original size:3 final size:3
Alignment explanation
Indices: 389448--389472 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
389438 ACAGAAAAAA
389448 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
389473 GCAAAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:390207 original size:20 final size:20
Alignment explanation
Indices: 390171--390211 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
390161 GATTACCATG
390171 ATTTCTAAATATAAATTATAT
1 ATTTCTAAATATAAATT-TAT
*
390192 ATTTCT-AATATTAATTTAT
1 ATTTCTAAATATAAATTTAT
390211 A
1 A
390212 GTTAAAACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTCTAAATATAAATTTAT
Found at i:390430 original size:2 final size:2
Alignment explanation
Indices: 390423--390458 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
390413 AAGAAAGCAT
390423 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
390459 ATTATCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:391420 original size:42 final size:42
Alignment explanation
Indices: 391368--391452 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
391358 ATGTTATATT
391368 TCAACCTTTTATTTAAAATAGCATTAATCATAGAGAAGACAA
1 TCAACCTTTTATTTAAAATAGCATTAATCATAGAGAAGACAA
* *
391410 TCAATCTTTTATTTAAAGTAGCATTAATCATAGAGAAGACAA
1 TCAACCTTTTATTTAAAATAGCATTAATCATAGAGAAGACAA
391452 T
1 T
391453 TGACAAGCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (42 bp):
TCAACCTTTTATTTAAAATAGCATTAATCATAGAGAAGACAA
Found at i:392411 original size:32 final size:34
Alignment explanation
Indices: 392373--392447 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 34
392363 GTAATGAAAC
392373 TTTTGTTGAAAAAAG-TTTACTTTTGGT-AAAAT-
1 TTTTGTTGAAAAAAGATTTA-TTTTGGTCAAAATA
*
392405 TTTTGTTGAAAAAAGATTTATTTTTGTCCAAAATA
1 TTTTGTTGAAAAAAGATTTATTTTGGT-CAAAATA
392440 TTTTGTTG
1 TTTTGTTG
392448 GAGTATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
32 21 0.55
33 4 0.11
34 5 0.13
35 8 0.21
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (34 bp):
TTTTGTTGAAAAAAGATTTATTTTGGTCAAAATA
Found at i:392808 original size:21 final size:21
Alignment explanation
Indices: 392765--392809 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
392755 TTATTGAGTT
*
392765 AAAATTAAATTAAATTAAATA
1 AAAATTAAAATAAATTAAATA
*
392786 AAAATATAAAATAAA-TAAGTA
1 AAAAT-TAAAATAAATTAAATA
392807 AAA
1 AAA
392810 TAATATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTAAAATAAATTAAATA
Found at i:393109 original size:11 final size:11
Alignment explanation
Indices: 393093--393117 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
393083 GCACTATAAG
393093 TAGCAAGGTAT
1 TAGCAAGGTAT
393104 TAGCAAGGTAT
1 TAGCAAGGTAT
393115 TAG
1 TAG
393118 TATTCTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCAAGGTAT
Found at i:393591 original size:22 final size:19
Alignment explanation
Indices: 393554--393595 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
393544 GAACCTGAAA
393554 AACCCAACCAATCAACCCG
1 AACCCAACCAATCAACCCG
393573 AACCCTAATCCAATCCAACCCG
1 AACCC-AA-CCAAT-CAACCCG
393595 A
1 A
393596 TTTGACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 5 0.25
22 8 0.40
ACGTcount: A:0.40, C:0.45, G:0.05, T:0.10
Consensus pattern (19 bp):
AACCCAACCAATCAACCCG
Found at i:393767 original size:16 final size:16
Alignment explanation
Indices: 393616--393766 Score: 108
Period size: 16 Copynumber: 9.4 Consensus size: 16
393606 AAAGTCAACA
* *
393616 ACCCGAATCTGAACTG
1 ACCCGAATCCGAAATG
*
393632 ACCC-AAACTCGAAATG
1 ACCCGAATC-CGAAATG
* * *
393648 ACTCGAACCCAAAATG
1 ACCCGAATCCGAAATG
**
393664 ACTTGAATCC-AGAATG
1 ACCCGAATCCGA-AATG
* * * * *
393680 CCCCAAATTCAAAATA
1 ACCCGAATCCGAAATG
393696 ACCCGAATCCGAAATG
1 ACCCGAATCCGAAATG
*
393712 ACCCGAATCCGAAATA
1 ACCCGAATCCGAAATG
*
393728 ACCCGAATCTGAAATG
1 ACCCGAATCCGAAATG
* *
393744 ATCCGAACCCGAAATG
1 ACCCGAATCCGAAATG
*
393760 ATCCGAA
1 ACCCGAA
393767 CTTAAATTAA
Statistics
Matches: 106, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
15 4 0.04
16 98 0.92
17 4 0.04
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.16
Consensus pattern (16 bp):
ACCCGAATCCGAAATG
Found at i:394817 original size:16 final size:16
Alignment explanation
Indices: 394786--394849 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
394776 TAAACCCGAT
*
394786 TGATCCGAACCTGAAA
1 TGATCCGAACCCGAAA
*
394802 TGATCCGAATCCGAAA
1 TGATCCGAACCCGAAA
** **
394818 CAATCTAAACCCGAAA
1 TGATCCGAACCCGAAA
*
394834 TGATCTGAACCCGAAA
1 TGATCCGAACCCGAAA
394850 ACAATCTGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.17
Consensus pattern (16 bp):
TGATCCGAACCCGAAA
Found at i:394848 original size:32 final size:33
Alignment explanation
Indices: 394793--394856 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
394783 GATTGATCCG
* *
394793 AACCTGAAATGATCCGAATCCG-AAACAATCTA
1 AACCCGAAATGATCCGAACCCGAAAACAATCTA
*
394825 AACCCGAAATGATCTGAACCCGAAAACAATCT
1 AACCCGAAATGATCCGAACCCGAAAACAATCT
394857 GAAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 19 0.68
33 9 0.32
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.17
Consensus pattern (33 bp):
AACCCGAAATGATCCGAACCCGAAAACAATCTA
Found at i:394858 original size:17 final size:16
Alignment explanation
Indices: 394812--394859 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
394802 TGATCCGAAT
*
394812 CCGAAACAATCTAAAC
1 CCGAAACAATCTGAAC
**
394828 CCGAAATGATCTGAAC
1 CCGAAACAATCTGAAC
394844 CCGAAAACAATCTGAA
1 CCG-AAACAATCTGAA
394860 AAATTTACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (16 bp):
CCGAAACAATCTGAAC
Found at i:395375 original size:20 final size:21
Alignment explanation
Indices: 395333--395375 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
395323 AAACATATAT
*
395333 ATAAAAATATATATGTAACAA
1 ATAAAAATATATATGTAAAAA
395354 ATAAAAAT-TATAT-TAATAAA
1 ATAAAAATATATATGTAA-AAA
395374 AT
1 AT
395376 CATTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 9 0.45
21 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAAAATATATATGTAAAAA
Done.