Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 6 of 26
Found at i:792137 original size:15 final size:14
Alignment explanation
Indices: 792097--792130 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
792087 AATTTTTAAT
792097 AAATTTAA-ATTTA
1 AAATTTAATATTTA
792110 AAATTTAATATTTA
1 AAATTTAATATTTA
792124 TAAATTT
1 -AAATTT
792131 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 5 0.26
15 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTTAATATTTA
Found at i:792364 original size:2 final size:2
Alignment explanation
Indices: 792357--792403 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
792347 AAGGCTTCTT
792357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
792399 TA TA T
1 TA TA T
792404 TGTTGGAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:794137 original size:13 final size:14
Alignment explanation
Indices: 794110--794143 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
794100 TTGTATTAAA
794110 AATATTTTTATATT
1 AATATTTTTATATT
794124 AATATTTTTA-ATT
1 AATATTTTTATATT
794137 AA-ATTTT
1 AATATTTT
794144 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 5 0.25
14 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:795046 original size:19 final size:17
Alignment explanation
Indices: 795002--795076 Score: 51
Period size: 19 Copynumber: 3.9 Consensus size: 17
794992 TTTCAGTTAA
795002 AAAAAAAAGAAAAAAAG
1 AAAAAAAAGAAAAAAAG
795019 AAAGGAAAAAGAAAGAAAGTAG
1 AAA--AAAAAGAAA-AAA--AG
*
795041 AAAAAAAGGGAAAAGAAAAG
1 AAAAAAA-AG-AAA-AAAAG
*
795061 AAGAAAAGAGAAAAAA
1 AA-AAAAAAGAAAAAA
795077 TAATTTGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
17 3 0.06
18 3 0.06
19 12 0.26
20 12 0.26
21 5 0.11
22 12 0.26
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAG
Found at i:795048 original size:15 final size:15
Alignment explanation
Indices: 795009--795076 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
794999 TAAAAAAAAA
795009 AGAAAAAAAGAAAGG
1 AGAAAAAAAGAAAGG
*
795024 A-AAAAGAAAGAAAGT
1 AGAAAA-AAAGAAAGG
795039 AGAAAAAAAGGGAAA--
1 AGAAAAAAA--GAAAGG
* *
795054 AGAAAAGAAGAAAAG
1 AGAAAAAAAGAAAGG
795069 AGAAAAAA
1 AGAAAAAA
795077 TAATTTGTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.09
14 4 0.09
15 28 0.64
16 4 0.09
17 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (15 bp):
AGAAAAAAAGAAAGG
Found at i:795065 original size:30 final size:30
Alignment explanation
Indices: 795004--795076 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
794994 TCAGTTAAAA
* *
795004 AAAAAAGAAAAAAAGAAAGGAAAAAGAAAG
1 AAAAGAGAAAAAAAGAAAAGAAAAAGAAAG
795034 -AAAGTAGAAAAAAAGGGAAAAG-AAAAG-AAG
1 AAAAG-AGAAAAAAA--GAAAAGAAAAAGAAAG
795064 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
795077 TAATTTGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.08
30 20 0.54
31 9 0.24
32 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (30 bp):
AAAAGAGAAAAAAAGAAAAGAAAAAGAAAG
Found at i:795399 original size:20 final size:18
Alignment explanation
Indices: 795368--795419 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
795358 TTATTTTTCA
* *
795368 TATTTTATTTCAATTTTT
1 TATTATATTTCAATTTTG
*
795386 TATATATATGTTC-AGTTTG
1 TAT-TATAT-TTCAATTTTG
795405 TATTATATTTCAATT
1 TATTATATTTCAATT
795420 CATGTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
19 11 0.41
20 3 0.11
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (18 bp):
TATTATATTTCAATTTTG
Found at i:795549 original size:10 final size:9
Alignment explanation
Indices: 795533--795593 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
795523 GTAGGGTTGA
795533 AAAAAAAAG
1 AAAAAAAAG
*
795542 AAAGAAAAG
1 AAAAAAAAG
795551 AGAAAAAAAG
1 A-AAAAAAAG
795561 AAAAAAAA-
1 AAAAAAAAG
795569 ATGAAAAAAAG
1 A--AAAAAAAG
*
795580 -AAAAAGAG
1 AAAAAAAAG
795588 AAAAAA
1 AAAAAA
795594 TTTATGTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.18
9 21 0.48
10 15 0.34
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:795558 original size:19 final size:18
Alignment explanation
Indices: 795534--795593 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 18
795524 TAGGGTTGAA
795534 AAAAAAAGAAAGAAAAGAG
1 AAAAAAAGAAA-AAAAGAG
*
795553 AAAAAAAGAAAAAAAAATG
1 AAAAAAAGAAAAAAAGA-G
795572 AAAAAAAG--AAAAAGAG
1 AAAAAAAGAAAAAAAGAG
795588 AAAAAA
1 AAAAAA
795594 TTTATGTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 7 0.18
17 6 0.16
18 5 0.13
19 20 0.53
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAGAG
Found at i:795562 original size:8 final size:8
Alignment explanation
Indices: 795534--795593 Score: 57
Period size: 8 Copynumber: 6.8 Consensus size: 8
795524 TAGGGTTGAA
795534 AAAAAAAG
1 AAAAAAAG
795542 AAAGAAAAGAG
1 -AA-AAAA-AG
795553 AAAAAAAG
1 AAAAAAAG
795561 AAAAAAAAATG
1 --AAAAAAA-G
795572 AAAAAAAG
1 AAAAAAAG
*
795580 AAAAAGAG
1 AAAAAAAG
795588 AAAAAA
1 AAAAAA
795594 TTTATGTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
8 15 0.34
9 13 0.30
10 13 0.30
11 3 0.07
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:796173 original size:36 final size:36
Alignment explanation
Indices: 796105--796173 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
796095 TTCATATTAT
* *
796105 TTTTTATATGTCAAAAGTATTATGAATTTATATAAA
1 TTTTTATATGTCAAAAGTAGTATGAATATATATAAA
* *
796141 TTTTTATATGTCAATAATTAGTAT-TATATATAT
1 TTTTTATATGTCAA-AAGTAGTATGAATATATAT
796174 TTTGGTACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 21 0.75
37 7 0.25
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (36 bp):
TTTTTATATGTCAAAAGTAGTATGAATATATATAAA
Found at i:796704 original size:43 final size:45
Alignment explanation
Indices: 796657--796754 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 45
796647 TTTATCTTAC
*
796657 ATTTTATATAATTAAA-TT-TTAACTT-TAAATTTATTT-ATTAAAT
1 ATTTTATA-AATTAAATTTATTAA-TTATAAATTTATTTAATTAAAA
*
796700 ATTTT-TAAA-TAAATTTAATTAATTATAATTTTATTTAATTAAAA
1 ATTTTATAAATTAAATTT-ATTAATTATAAATTTATTTAATTAAAA
796744 ATTTTATAAAT
1 ATTTTATAAAT
796755 ATTAAAACTT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
40 4 0.09
41 4 0.09
42 4 0.09
43 19 0.41
44 11 0.24
45 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (45 bp):
ATTTTATAAATTAAATTTATTAATTATAAATTTATTTAATTAAAA
Found at i:796732 original size:16 final size:16
Alignment explanation
Indices: 796708--796747 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
796698 ATATTTTTAA
796708 ATAAATTTAATTAATT
1 ATAAATTTAATTAATT
* *
796724 ATAATTTTATTTAATT
1 ATAAATTTAATTAATT
*
796740 AAAAATTT
1 ATAAATTT
796748 TATAAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAAATTTAATTAATT
Found at i:796797 original size:3 final size:3
Alignment explanation
Indices: 796789--796830 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
796779 AAAAATTTTA
*
796789 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
796831 GTTGTTGTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:797859 original size:15 final size:15
Alignment explanation
Indices: 797835--797868 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
797825 AAAATTTTTT
*
797835 ATTA-ATTATTTAAA
1 ATTATATTATTAAAA
797849 ATTATATTATTAAAA
1 ATTATATTATTAAAA
797864 ATTAT
1 ATTAT
797869 TAAAATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATATTATTAAAA
Found at i:797861 original size:22 final size:20
Alignment explanation
Indices: 797818--797861 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
797808 GAAAAAAGTA
*
797818 AATTTTTAAAATTTTTTATT
1 AATTTTTAAAATTTATTATT
797838 AATTATTTAAAATTATATTATT
1 AATT-TTTAAAATT-TATTATT
797860 AA
1 AA
797862 AAATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTTAAAATTTATTATT
Found at i:799439 original size:13 final size:13
Alignment explanation
Indices: 799407--799454 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
799397 AAAATTTTAA
799407 ATATTTTATAT-T
1 ATATTTTATATAT
799419 A-A-TTTATATAT
1 ATATTTTATATAT
799430 ATATTTTATA-ATT
1 ATATTTTATATA-T
*
799443 AAATTTTATATA
1 ATATTTTATATA
799455 AAAATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 3 0.10
13 16 0.53
14 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATTTTATATAT
Found at i:800070 original size:19 final size:19
Alignment explanation
Indices: 800046--800084 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
800036 TGTTAAAAAA
*
800046 ATTAATATATATTTTT-ATT
1 ATTAATAAAT-TTTTTGATT
800065 ATTAATAAATTTTTTGATT
1 ATTAATAAATTTTTTGATT
800084 A
1 A
800085 AATTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTAATAAATTTTTTGATT
Found at i:800312 original size:24 final size:24
Alignment explanation
Indices: 800268--800315 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
800258 ATTTGCTATA
**
800268 TGAAAAAAATTTTAACTTTTTATT
1 TGAAAAAAATAATAACTTTTTATT
800292 TGAAAAAAATAATAA-TATTTTATT
1 TGAAAAAAATAATAACT-TTTTATT
800316 AAATTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TGAAAAAAATAATAACTTTTTATT
Found at i:800961 original size:32 final size:31
Alignment explanation
Indices: 800920--800980 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
800910 TAAATTAATC
*
800920 ATATTATATT-ATATTTATTATATTTATTAAAG
1 ATATAATATTCATA-TTATTAT-TTTATTAAAG
*
800952 ATATAATATTCATATTATTATTTTTTTAA
1 ATATAATATTCATATTATTATTTTATTAA
800981 TTATTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 16 0.62
33 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
ATATAATATTCATATTATTATTTTATTAAAG
Found at i:801298 original size:15 final size:15
Alignment explanation
Indices: 801278--801310 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
801268 AAACTCGACT
801278 TTACAAAAATAATTA
1 TTACAAAAATAATTA
*
801293 TTACAATAATAATTA
1 TTACAAAAATAATTA
801308 TTA
1 TTA
801311 TTTTAGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TTACAAAAATAATTA
Found at i:801536 original size:16 final size:14
Alignment explanation
Indices: 801498--801579 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 14
801488 GATAAATATC
*
801498 AATTCATTTAATTT
1 AATTTATTTAATTT
801512 AATTTATTTAATTT
1 AATTTATTTAATTT
*
801526 TATCATTATTTAATTAAAT
1 AAT--TTATTTAATT---T
*
801545 AATTTGATTTTAATAT
1 AATTT-A-TTTAATTT
*
801561 -ATTTA-TTAAATT
1 AATTTATTTAATTT
801573 AATTTAT
1 AATTTAT
801580 ATTTTTTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
12 5 0.09
13 5 0.09
14 16 0.30
15 4 0.08
16 11 0.21
17 2 0.04
18 1 0.02
19 9 0.17
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (14 bp):
AATTTATTTAATTT
Found at i:803002 original size:19 final size:19
Alignment explanation
Indices: 802978--803019 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
802968 TTATCTTCTA
802978 CAATTAAAGATGGATGGAC
1 CAATTAAAGATGGATGGAC
802997 CAATTAAAGATGGATGGAC
1 CAATTAAAGATGGATGGAC
803016 CAAT
1 CAAT
803020 ATAGATCAGA
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:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (19 bp):
CAATTAAAGATGGATGGAC
Found at i:806655 original size:41 final size:43
Alignment explanation
Indices: 806577--806700 Score: 118
Period size: 41 Copynumber: 3.0 Consensus size: 43
806567 ATAATATCTT
806577 ATAATTATTATTTTAATATAAGTAATATTTTTAAAATATTAAA
1 ATAATTATTATTTTAATATAAGTAATATTTTTAAAATATTAAA
*
806620 ATAATTATT-TTTATAATA-AA-TAATCTATTTT-AAATATT--A
1 ATAATTATTATTT-TAATATAAGTAATAT-TTTTAAAATATTAAA
* * * * *
806659 ATATTTATAATTTTATTATTAACT-ATATTATTAAAATATTAA
1 ATAATTATTATTTTAATA-TAAGTAATATTTTTAAAATATTAA
806701 TATTTTCATA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
39 12 0.18
40 6 0.09
41 24 0.36
42 10 0.15
43 14 0.21
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (43 bp):
ATAATTATTATTTTAATATAAGTAATATTTTTAAAATATTAAA
Found at i:806661 original size:20 final size:18
Alignment explanation
Indices: 806576--806666 Score: 53
Period size: 19 Copynumber: 4.7 Consensus size: 18
806566 AATAATATCT
*
806576 TATAATTATTATTTT-AA
1 TATAATAATTATTTTAAA
806593 TATAAGTAA-TATTTTTAAAA
1 TATAA-TAATTA-TTTT-AAA
806613 TATTAAAATAATTATTTTTATAA
1 TA-T--AATAATTA-TTTTA-AA
806636 TA-AATAATCTATTTTAAA
1 TATAATAAT-TATTTTAAA
*
806654 TATTAATATTTAT
1 TA-TAATAATTAT
806667 AATTTTATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 22
0.71 0.02 0.26
Matches are distributed among these distances:
17 7 0.12
18 10 0.17
19 14 0.23
20 11 0.18
21 1 0.02
22 4 0.07
23 13 0.22
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
TATAATAATTATTTTAAA
Found at i:806711 original size:14 final size:13
Alignment explanation
Indices: 806694--806753 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 13
806684 TATTATTAAA
806694 ATATTAATATTTT
1 ATATTAATATTTT
806707 CATATTAAATAATTTT
1 -ATATT-AAT-ATTTT
806723 GATATTTTAATA-TTT
1 -ATA--TTAATATTTT
806738 ATATTAATATTATT
1 ATATTAATATT-TT
806752 AT
1 AT
806754 TCAAAAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
12 6 0.15
13 1 0.03
14 12 0.31
15 6 0.15
16 9 0.23
17 3 0.08
18 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (13 bp):
ATATTAATATTTT
Found at i:806727 original size:16 final size:14
Alignment explanation
Indices: 806694--806748 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 14
806684 TATTATTAAA
806694 ATATTAATATTTTC
1 ATATTAATATTTTC
*
806708 ATATTAAATAATTTTG
1 ATATT-AAT-ATTTTC
806724 ATATTTTAATA-TTT-
1 ATA--TTAATATTTTC
806738 ATATTAATATT
1 ATATTAATATT
806749 ATTATTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
12 6 0.17
13 1 0.03
14 8 0.23
15 6 0.17
16 9 0.26
17 3 0.09
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (14 bp):
ATATTAATATTTTC
Found at i:807097 original size:22 final size:23
Alignment explanation
Indices: 807072--807124 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
807062 TAATTTAGTT
*
807072 TTTAATAATT-AAATTATTAAAA
1 TTTAATAATTCAAATAATTAAAA
*
807094 TTTAACT-ATTCAACTAATTAAAA
1 TTTAA-TAATTCAAATAATTAAAA
*
807117 TTCAATAA
1 TTTAATAA
807125 ATGTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAATAATTCAAATAATTAAAA
Found at i:807538 original size:2 final size:2
Alignment explanation
Indices: 807526--807559 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
807516 ATAATTTTAT
*
807526 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
807560 CTACAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:808370 original size:24 final size:24
Alignment explanation
Indices: 808341--808390 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
808331 CTTTAAACTT
808341 TATTTATCATTTTA-TTTAAATAAA
1 TATTTAT-ATTTTATTTTAAATAAA
*
808365 TATTTATATTTTATTTTAAGTAAA
1 TATTTATATTTTATTTTAAATAAA
808389 TA
1 TA
808391 AATTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TATTTATATTTTATTTTAAATAAA
Found at i:808489 original size:28 final size:29
Alignment explanation
Indices: 808428--808500 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
808418 AACTTTAAAC
*
808428 AAAATAAAAT-TTTATTTATGTATAATTA
1 AAAATAAAATATTTATTTATGTATAAGTA
808456 AAAATAAAATATTTATTTA-G-ATATAGTA
1 AAAATAAAATATTTATTTATGTATA-AGTA
808484 AGAATATAAAA-ATTTAT
1 A-AA-ATAAAATATTTAT
808501 CTTAAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 3 0.08
28 15 0.38
29 16 0.40
30 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAATAAAATATTTATTTATGTATAAGTA
Found at i:808667 original size:19 final size:19
Alignment explanation
Indices: 808624--808682 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
808614 TGGTCCTTTG
808624 AATATATTAAT-AATAT-TA
1 AATATA-TAATAAATATATA
808642 GATATATATAA-AAATAATATA
1 -A-ATATATAATAAAT-ATATA
*
808663 AATATTTAATAAATATATA
1 AATATATAATAAATATATA
808682 A
1 A
808683 TAATATAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 20 0.59
20 12 0.35
21 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AATATATAATAAATATATA
Found at i:808674 original size:11 final size:11
Alignment explanation
Indices: 808645--808689 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
808635 AATATTAGAT
808645 ATATATAA-AA
1 ATATATAATAA
808655 ATA-AT-ATAA
1 ATATATAATAA
*
808664 ATATTTAATAA
1 ATATATAATAA
808675 ATATATAAT-A
1 ATATATAATAA
808685 ATATA
1 ATATA
808690 ACAAAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 1 0.03
9 7 0.23
10 10 0.33
11 12 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATATAATAA
Found at i:808674 original size:22 final size:23
Alignment explanation
Indices: 808631--808684 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
808621 TTGAATATAT
*
808631 TAATAATATTAGATATATATAAA
1 TAATAATATTAAATATATATAAA
*
808654 -AATAATA-TAAATATTTAATAAA
1 TAATAATATTAAATATAT-ATAAA
808676 TATATAATA
1 TA-ATAATA
808685 ATATAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.27
22 12 0.46
23 1 0.04
24 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATAATATTAAATATATATAAA
Found at i:808982 original size:20 final size:20
Alignment explanation
Indices: 808959--808999 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
808949 ATCAAAATAA
808959 ATTA-ATTTAAATTATAAATT
1 ATTATATTTAAATT-TAAATT
808979 ATTATATTTAAATTTAAATT
1 ATTATATTTAAATTTAAATT
808999 A
1 A
809000 AATTTATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATATTTAAATTTAAATT
Found at i:809004 original size:17 final size:18
Alignment explanation
Indices: 808955--809005 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
808945 ATAAATCAAA
808955 ATAAATT-AATTTAAATT
1 ATAAATTAAATTTAAATT
808972 ATAAATTATTATATTTAAATT
1 ATAAATTA--A-ATTTAAATT
808993 -TAAATTAAATTTA
1 ATAAATTAAATTTA
809006 TCGACCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 12 0.40
18 1 0.03
20 8 0.27
21 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAATTAAATTTAAATT
Found at i:809321 original size:41 final size:43
Alignment explanation
Indices: 809240--809321 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 43
809230 TAATTGATTT
* ** * *
809240 AAATTAATTTAATTTATTAAATATTTTTAATTATTTAATTTGA
1 AAATTAATTTAATTTATTAAAAAAATTTAATTAATGAATTTGA
*
809283 AAATTAA-TTAA-TTATTAAAAAAATTTATTTAATGAATTT
1 AAATTAATTTAATTTATTAAAAAAATTTAATTAATGAATTT
809322 CATCAATTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
41 22 0.67
42 4 0.12
43 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (43 bp):
AAATTAATTTAATTTATTAAAAAAATTTAATTAATGAATTTGA
Found at i:810384 original size:15 final size:15
Alignment explanation
Indices: 810364--810393 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
810354 AAAAAATTTA
*
810364 AAATATTTTTATATT
1 AAATATTTATATATT
810379 AAATATTTATATATT
1 AAATATTTATATATT
810394 TTATTAATTA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATTTATATATT
Found at i:810926 original size:13 final size:14
Alignment explanation
Indices: 810908--810943 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
810898 TTTATTTATT
810908 TTTAATTAAAT-AA
1 TTTAATTAAATCAA
*
810921 TTTAATTTAATCAA
1 TTTAATTAAATCAA
810935 TTTAATTAA
1 TTTAATTAA
810944 TTGAACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAAATCAA
Found at i:811265 original size:19 final size:17
Alignment explanation
Indices: 811206--811266 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 17
811196 CTTAAATCTA
811206 TATTAAATATCATACTACTT
1 TATTAAATAT-ATA-TA-TT
* *
811226 AATTAAATATATATTTT
1 TATTAAATATATATATT
811243 TATTAAATATTATTATATT
1 TATTAAATA-TA-TATATT
811262 TATTA
1 TATTA
811267 CTTTTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 10 0.29
18 3 0.09
19 13 0.37
20 9 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATATATATATT
Found at i:812677 original size:6 final size:6
Alignment explanation
Indices: 812668--812718 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
812658 CTGGGGTTGA
* * *
812668 GGCTAG GGCTAA GACTAG GGCTAG GGCTAG GGCTAG GGCTAG GGCTGG
1 GGCTAG GGCTAG GGCTAG GGCTAG GGCTAG GGCTAG GGCTAG GGCTAG
812716 GGC
1 GGC
812719 CAGTGGCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.16
Consensus pattern (6 bp):
GGCTAG
Found at i:813276 original size:28 final size:28
Alignment explanation
Indices: 813218--813285 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 28
813208 TTTAAATTTT
813218 AATATATAATTTATATAAAAAATGATAA
1 AATATATAATTTATATAAAAAATGATAA
813246 AATATAATAATTT-TATTAAATAAAT-ATAAA
1 AATAT-ATAATTTATA-TAAA-AAATGAT-AA
813276 TAATATATAA
1 -AATATATAA
813286 AATTATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 7 0.20
29 13 0.37
30 10 0.29
31 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
AATATATAATTTATATAAAAAATGATAA
Found at i:813288 original size:22 final size:22
Alignment explanation
Indices: 813245--813288 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
813235 AAAAATGATA
* *
813245 AAATATAATAATTTTATTAAAT
1 AAATATAATAATTATATAAAAT
813267 AAATATAAATAA-TATATAAAAT
1 AAATAT-AATAATTATATAAAAT
813289 TATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATATAATAATTATATAAAAT
Found at i:813388 original size:2 final size:2
Alignment explanation
Indices: 813344--813371 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
813334 AATTTCTTAT
813344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
813372 CACTTGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:815173 original size:20 final size:22
Alignment explanation
Indices: 815148--815194 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
815138 TCAAAGCATT
* *
815148 TTTCAACCATTTAAGC-TC-AA
1 TTTCAAACATGTAAGCTTCTAA
815168 TTTCAAACATGTAAGCTTCTAA
1 TTTCAAACATGTAAGCTTCTAA
815190 TTTCA
1 TTTCA
815195 TCAAATCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (22 bp):
TTTCAAACATGTAAGCTTCTAA
Found at i:819803 original size:21 final size:22
Alignment explanation
Indices: 819768--819822 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
819758 TTAAAATATT
* *
819768 AATAATAATATATTAAATTTTT
1 AATATTAATATATTAAATTTTA
*
819790 AATTTTAATA-ATTAAATTTTA
1 AATATTAATATATTAAATTTTA
819811 AATATTAATATA
1 AATATTAATATA
819823 AATATTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTAATATATTAAATTTTA
Found at i:820800 original size:22 final size:22
Alignment explanation
Indices: 820762--820814 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
820752 TATTTCGAAT
*
820762 TAAATATTAATAAATAAAT-AAA
1 TAAATAAT-ATAAATAAATAAAA
*
820784 TAAATAATATAATATAATTAAAA
1 TAAATAATATAA-ATAAATAAAA
820807 TAAA-AATA
1 TAAATAATA
820815 CAATTGTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 16 0.59
23 7 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATAATATAAATAAATAAAA
Found at i:822039 original size:2 final size:2
Alignment explanation
Indices: 821985--822020 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
821975 ATCTTAAAAC
*
821985 AT AT CT 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
822021 GTGTGTGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:822221 original size:18 final size:19
Alignment explanation
Indices: 822198--822236 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
822188 AACTATAGTG
*
822198 TTATTAAAT-AATTTAATA
1 TTATTAAATAAATTGAATA
*
822216 TTATTAATTAAATTGAATA
1 TTATTAAATAAATTGAATA
822235 TT
1 TT
822237 TAATATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTATTAAATAAATTGAATA
Found at i:822344 original size:15 final size:15
Alignment explanation
Indices: 822326--822356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
822316 TATTAATTAA
822326 TTAAAAATTTAATAT
1 TTAAAAATTTAATAT
*
822341 TTAATAATTTAATAT
1 TTAAAAATTTAATAT
822356 T
1 T
822357 ATTAAAAGCT
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:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAAAATTTAATAT
Found at i:822353 original size:8 final size:8
Alignment explanation
Indices: 822296--822354 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
822286 CAATTTCTTA
822296 AATTTATAT
1 AATTTA-AT
*
822305 AATTTATT
1 AATTTAAT
822313 AAATATTAATT
1 -AAT-TTAA-T
*
822324 AA-TTAAA
1 AATTTAAT
822331 AATTTAAT
1 AATTTAAT
822339 -ATTTAAT
1 AATTTAAT
822346 AATTTAAT
1 AATTTAAT
822354 A
1 A
822355 TTATTAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
7 9 0.22
8 17 0.41
9 9 0.22
10 5 0.12
11 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AATTTAAT
Found at i:825779 original size:16 final size:16
Alignment explanation
Indices: 825758--825791 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
825748 AACAAATGTA
825758 TGGTCTTTCTTTAGAT
1 TGGTCTTTCTTTAGAT
*
825774 TGGTCTTTCTTTGGAT
1 TGGTCTTTCTTTAGAT
825790 TG
1 TG
825792 TAAAGCAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.56
Consensus pattern (16 bp):
TGGTCTTTCTTTAGAT
Found at i:834951 original size:10 final size:10
Alignment explanation
Indices: 834938--834970 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
834928 AAAATTTTTT
834938 ATTAATTTAA
1 ATTAATTTAA
834948 ATT-ATTTAA
1 ATTAATTTAA
*
834957 TTTAATTTAA
1 ATTAATTTAA
834967 ATTA
1 ATTA
834971 TTATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:836541 original size:15 final size:15
Alignment explanation
Indices: 836523--836560 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
836513 AAAATATATT
836523 ATTTAAAAATAAAAA
1 ATTTAAAAATAAAAA
*
836538 ATTTAAATATAAAAA
1 ATTTAAAAATAAAAA
*
836553 AATTAAAA
1 ATTTAAAA
836561 TTGATTAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTTAAAAATAAAAA
Found at i:837209 original size:16 final size:17
Alignment explanation
Indices: 837172--837215 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
837162 TTAATTTAAA
*
837172 TTAAAATAATTTTAACTG
1 TTAAAA-AAATTTAACTG
837190 TTAAAAAAATTTAA-TG
1 TTAAAAAAATTTAACTG
*
837206 TTAAATAAAT
1 TTAAAAAAAT
837216 AATAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 7 0.29
18 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (17 bp):
TTAAAAAAATTTAACTG
Found at i:837495 original size:18 final size:19
Alignment explanation
Indices: 837461--837497 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
837451 TTTATTTGAA
837461 TTTTTATATTTATAATTAT
1 TTTTTATATTTATAATTAT
*
837480 TTTTTATTTTTA-AATTAT
1 TTTTTATATTTATAATTAT
837498 GAGTTCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTATATTTATAATTAT
Found at i:837632 original size:29 final size:29
Alignment explanation
Indices: 837570--837633 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
837560 GTATTATAAA
*
837570 ATTTT-AAATAAATTATTAAAATAATATT
1 ATTTTGAAATAAATTATCAAAATAATATT
* *
837598 AATTTGAAATAAATTATCAAAATATTATT
1 ATTTTGAAATAAATTATCAAAATAATATT
837627 ATTTTGA
1 ATTTTGA
837634 CTCGTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
ATTTTGAAATAAATTATCAAAATAATATT
Found at i:837809 original size:17 final size:17
Alignment explanation
Indices: 837787--837827 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
837777 GATCATCTAC
*
837787 TATTATTAGTATAATAT
1 TATTATTAGTATAATAA
* *
837804 TATTATTTGTTTAATAA
1 TATTATTAGTATAATAA
837821 TATTATT
1 TATTATT
837828 GAAGTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTATTAGTATAATAA
Found at i:837885 original size:19 final size:18
Alignment explanation
Indices: 837858--837902 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 18
837848 ATTTTTTAAA
*
837858 ATTATAAAAGATTATATT
1 ATTATAAAAGATAATATT
837876 ATTAATAAAAGATAATATT
1 ATT-ATAAAAGATAATATT
837895 ATTATAAA
1 ATTATAAA
837903 TATAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTATAAAAGATAATATT
Found at i:837962 original size:29 final size:26
Alignment explanation
Indices: 837929--837995 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 26
837919 ATTATTAAAA
837929 AAATTATTTCATTTACGATTAATAA-CAAT
1 AAATTATTT-ATTTA-GATT-ATAATC-AT
837958 AAATTTTATTTATTTAGATTATAATCAT
1 AAA--TTATTTATTTAGATTATAATCAT
837986 ATAATTATTT
1 A-AATTATTT
837996 TAAAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
27 6 0.18
28 7 0.21
29 10 0.29
30 5 0.15
31 6 0.18
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (26 bp):
AAATTATTTATTTAGATTATAATCAT
Found at i:838168 original size:31 final size:31
Alignment explanation
Indices: 838130--838189 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
838120 TCTAATTATT
* *
838130 AAGGATTGTAATTGTCTAGTTATTTTAAATC
1 AAGGATTGTAATTATCTAATTATTTTAAATC
*
838161 AAGGATTGTAATTATTTAATTATTTTAAA
1 AAGGATTGTAATTATCTAATTATTTTAAA
838190 ATTATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (31 bp):
AAGGATTGTAATTATCTAATTATTTTAAATC
Found at i:838290 original size:13 final size:14
Alignment explanation
Indices: 838272--838304 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
838262 ATGATTATTA
838272 TTTAAATTAAA-AT
1 TTTAAATTAAATAT
838285 TTTAAATTAAATAT
1 TTTAAATTAAATAT
838299 TTTAAA
1 TTTAAA
838305 ATAATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAATTAAATAT
Found at i:838711 original size:29 final size:29
Alignment explanation
Indices: 838637--838711 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 29
838627 TTTTTATTAA
838637 TTAAAATT-ATAATATTTTAATAATATTT
1 TTAAAATTAATAATATTTTAATAATATTT
* *
838665 TT-AAATTAAT-ATTTTTTTATAAT-TTAT
1 TTAAAATTAATAATATTTTAATAATATT-T
838692 TTAAAAATTAATAATATTTT
1 TT-AAAATTAATAATATTTT
838712 GGTGAATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 2 0.05
27 19 0.49
28 4 0.10
29 8 0.21
30 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAAATTAATAATATTTTAATAATATTT
Found at i:840148 original size:16 final size:16
Alignment explanation
Indices: 840108--840171 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
840098 CTGAACTGAC
**
840108 CCGAAATGATTCGAA-
1 CCGAAATGACCCGAAT
*
840123 CCTGAAATGACTCGAAT
1 CC-GAAATGACCCGAAT
* *
840140 TCGAGATGACCCGAAT
1 CCGAAATGACCCGAAT
*
840156 CCGAAATGACCAGAAT
1 CCGAAATGACCCGAAT
840172 AATTAATCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 2 0.05
16 37 0.93
17 1 0.03
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (16 bp):
CCGAAATGACCCGAAT
Found at i:841682 original size:27 final size:27
Alignment explanation
Indices: 841647--841734 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
841637 ATCCTTAAAA
*
841647 TTTATTAAAACAATTAAAATAACAAAT
1 TTTAATAAAACAATTAAAATAACAAAT
* * *
841674 TTTAATAAAATAAAGTT--AAT-CCTTAAAG
1 TTTAATAAAA-CAA-TTAAAATAAC--AAAT
* *
841702 TTTACTAAAACAATTAAAATAATAAAT
1 TTTAATAAAACAATTAAAATAACAAAT
841729 TTTAAT
1 TTTAAT
841735 TTACTTATAA
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
26 3 0.07
27 22 0.50
28 17 0.39
29 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (27 bp):
TTTAATAAAACAATTAAAATAACAAAT
Found at i:841694 original size:55 final size:55
Alignment explanation
Indices: 841622--841734 Score: 181
Period size: 55 Copynumber: 2.1 Consensus size: 55
841612 AAGTAAAATG
* *
841622 AATAAAATGAAGCTAATCCTTAAAATTTATTAAAACAATTAAAATAACAAATTTT
1 AATAAAATAAAGCTAATCCTTAAAATTTACTAAAACAATTAAAATAACAAATTTT
* * *
841677 AATAAAATAAAGTTAATCCTTAAAGTTTACTAAAACAATTAAAATAATAAATTTT
1 AATAAAATAAAGCTAATCCTTAAAATTTACTAAAACAATTAAAATAACAAATTTT
841732 AAT
1 AAT
841735 TTACTTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (55 bp):
AATAAAATAAAGCTAATCCTTAAAATTTACTAAAACAATTAAAATAACAAATTTT
Found at i:849698 original size:2 final size:2
Alignment explanation
Indices: 849693--849735 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
849683 AAGGATTTTT
* *
849693 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
849735 T
1 T
849736 GATGTTTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:849716 original size:14 final size:14
Alignment explanation
Indices: 849693--849735 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
849683 AAGGATTTTT
*
849693 TATATATATATATA
1 TATATGTATATATA
849707 TATATGTATATATA
1 TATATGTATATATA
849721 TATATGTATATATA
1 TATATGTATATATA
849735 T
1 T
849736 GATGTTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:852315 original size:24 final size:24
Alignment explanation
Indices: 852288--852337 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
852278 TTGATGGAAG
*
852288 ATGAAATGTTAAACAAATATAGAA
1 ATGAAATGTTAAACAAACATAGAA
* *
852312 ATGAACTGTTAAACACACATAGAA
1 ATGAAATGTTAAACAAACATAGAA
852336 AT
1 AT
852338 AACTTACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
ATGAAATGTTAAACAAACATAGAA
Found at i:854113 original size:22 final size:23
Alignment explanation
Indices: 854071--854114 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
854061 ATCTTTTTAG
*
854071 TAAAAAAAATCACAATTTTAAAT
1 TAAAAAAAATCACAATATTAAAT
854094 TAAAAAAATAT-A-AATATTAAA
1 TAAAAAAA-ATCACAATATTAAA
854115 ATTTAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAAAAATCACAATATTAAAT
Found at i:854121 original size:14 final size:15
Alignment explanation
Indices: 854087--854133 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
854077 AAATCACAAT
* *
854087 TTTAAATTAAAAAAA
1 TTTAAACTATAAAAA
* *
854102 TATAAA-TATTAAAA
1 TTTAAACTATAAAAA
854116 TTTAAACTATAAAAA
1 TTTAAACTATAAAAA
854131 TTT
1 TTT
854134 GTTAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAACTATAAAAA
Found at i:856081 original size:2 final size:2
Alignment explanation
Indices: 856074--856104 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
856064 TAATCTTCAC
856074 AT 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 AT A
856105 ACAAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:856594 original size:5 final size:5
Alignment explanation
Indices: 856584--856610 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
856574 TCCCCCATTT
856584 TCAGA TCAGA TCAGA TCAGA TCAGA TC
1 TCAGA TCAGA TCAGA TCAGA TCAGA TC
856611 TCTTTTTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (5 bp):
TCAGA
Found at i:857748 original size:31 final size:31
Alignment explanation
Indices: 857706--857785 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
857696 TATAATTTTT
857706 AAAA-AATAATATAAAATTTAA-TTTTATTA
1 AAAATAATAATATAAAATTTAATTTTTATTA
*
857735 AATAATAATAATAT---ATTTAAATTTTTATTT
1 AA-AATAATAATATAAAATTT-AATTTTTATTA
857765 AAAATAA-AATATAAAATTTAA
1 AAAATAATAATATAAAATTTAA
857786 ATTAATATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
28 9 0.21
29 9 0.21
30 13 0.30
31 12 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AAAATAATAATATAAAATTTAATTTTTATTA
Found at i:857785 original size:19 final size:18
Alignment explanation
Indices: 857761--857800 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
857751 TTAAATTTTT
857761 ATTTAAAATAAAATATAAA
1 ATTTAAAATAAAATA-AAA
* *
857780 ATTTAAATTAATATAAAA
1 ATTTAAAATAAAATAAAA
857798 ATT
1 ATT
857801 AATGTCGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTAAAATAAAATAAAA
Found at i:857786 original size:31 final size:32
Alignment explanation
Indices: 857703--857788 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 32
857693 TTTTATAATT
857703 TTTAAAA-AATAATATAAAATTT-AA-TTTTA
1 TTTAAAATAATAATATAAAATTTAAATTTTTA
*
857732 -TT-AAATAATAATA-ATATATTTAAATTTTTA
1 TTTAAAATAATAATATA-AAATTTAAATTTTTA
857762 TTTAAAATAA-AATATAAAATTTAAATT
1 TTTAAAATAATAATATAAAATTTAAATT
857789 AATATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
27 4 0.08
28 14 0.29
29 2 0.04
30 5 0.10
31 16 0.33
32 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTAAAATAATAATATAAAATTTAAATTTTTA
Found at i:858092 original size:15 final size:14
Alignment explanation
Indices: 858072--858101 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
858062 AATAAAGATT
858072 AAAATTTAAATATAA
1 AAAATTTAAA-ATAA
858087 AAAATTTAAAATAA
1 AAAATTTAAAATAA
858101 A
1 A
858102 TTTTTTAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATTTAAAATAA
Found at i:859157 original size:2 final size:2
Alignment explanation
Indices: 859150--859180 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
859140 TGTATGTAAA
859150 AT 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 AT A
859181 CAATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:861656 original size:79 final size:79
Alignment explanation
Indices: 861551--861757 Score: 299
Period size: 79 Copynumber: 2.6 Consensus size: 79
861541 GAGATAATAA
* * * * *
861551 CGGGGTTGGAGTGTCCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCGAT-A
861616 -TTAGCAAAAAAAAT
65 TTTAGCAAAAAAAAT
* *
861630 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCGATAT
* * * *
861695 TTTGGAAATAAAGT
66 TTAGCAAAAAAAAT
861709 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
861758 GATCAACGGG
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 1 0.01
79 113 0.99
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCGATAT
TTAGCAAAAAAAAT
Found at i:861743 original size:28 final size:28
Alignment explanation
Indices: 861709--861779 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
861699 GAAATAAAGT
861709 CGGGGTTGGAGTATCCCCTCGAAAAT-AA
1 CGGGGTTGGAGTATCCCC-CGAAAATCAA
**
861737 CGGGGTTGGAGTAT-CCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCCGAAAATCAA
*
861764 CGGGGTTAGAGTATCC
1 CGGGGTTGGAGTATCC
861780 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 5 0.13
27 18 0.47
28 15 0.39
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGAAAATCAA
Found at i:861824 original size:107 final size:105
Alignment explanation
Indices: 861630--862046 Score: 366
Period size: 107 Copynumber: 3.9 Consensus size: 105
861620 CAAAAAAAAT
* * * * *
861630 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCGATA-
1 CGGGATTGGAGTAT-CCC-CGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTAT
* *
861694 TTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGAAAATAA
64 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCG-AAATAA
* ** * *
861737 CGGGGTTGGAGTATCCCCGATGATCAACGGGGTTAGAGTATCCTCGATTGTGAAAAATTGGTATT
1 CGGGATTGGAGTATCCCCGAAAAT-AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATT
*
861802 TTTGGAAATAAAATCGGAGTTGGAGTAT-CCC-CG-ATTAA
65 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGAAATAA
* * * ** * * *
861840 AGGAAAATTGGCGT-T--TTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTA
1 CGG--GATTGGAGTATCCCCGAAAAT--AA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTG
* * *
861902 GTGTTTTAGCG--ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAA
60 GTATTTTTG-GAAATAAAATCGGAGTTGGAGTATCCCCTC-GAAATAA
* * * *
861948 CGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGT
1 CGGGATTGGAGTATCCCCGA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-A
* *
862013 TTTTTGGAAATAAAATCGGAATTAGAGTATCCCC
63 TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
862047 GATTATAGAA
Statistics
Matches: 243, Mismatches: 47, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
102 4 0.02
103 8 0.03
104 41 0.17
105 31 0.13
106 48 0.20
107 72 0.30
108 13 0.05
109 24 0.10
110 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (105 bp):
CGGGATTGGAGTATCCCCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTT
TTGGAAATAAAATCGGAGTTGGAGTATCCCCTCGAAATAA
Found at i:861831 original size:52 final size:52
Alignment explanation
Indices: 861772--862103 Score: 175
Period size: 52 Copynumber: 6.3 Consensus size: 52
861762 AACGGGGTTA
* *
861772 GAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCGGAGTTG
** * ** *
861824 GAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA-TTG
1 GAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAACC-GGAGTTG
* * *
861876 GAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGAGTTG
1 GAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAACCGGAGTTG
* **** * * *
861928 GAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGGGTTG
1 GAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAACCGGAGTTG
* * * *
861983 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAATTA
1 GAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAACCGGAGTTG
* * * * *
862037 GAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAACCGGAGTTG
*
862088 GAATATCCCCGATTGT
1 GAGTATCCCCGATTGT
862104 AGAGAATTGA
Statistics
Matches: 210, Mismatches: 44, Indels: 53
0.68 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 37 0.18
52 75 0.36
53 33 0.16
54 27 0.13
55 18 0.09
56 2 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (52 bp):
GAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCGGAGTTG
Found at i:861964 original size:28 final size:27
Alignment explanation
Indices: 861924--861994 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
861914 TAAAACCGGA
**
861924 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
861952 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
861979 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
861995 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:862079 original size:51 final size:52
Alignment explanation
Indices: 861983--862111 Score: 154
Period size: 51 Copynumber: 2.5 Consensus size: 52
861973 AACGGGGTTG
* *
861983 GAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAATTA
1 GAGTATCCCCGATTGTAG-A-AAATTAGTG-TTTTTGAAAATAAAATCGGAATTA
* * *
862037 GAGTATCCCCGATTATAGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTAGAAAATTAGTGTTTTTGAAAATAAAATCGGAATTA
* *
862088 GAATATCCCCGATTGTAGAGAATT
1 GAGTATCCCCGATTGTAGAAAATT
862112 GATAAACTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
51 41 0.62
53 8 0.12
54 16 0.24
55 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (52 bp):
GAGTATCCCCGATTGTAGAAAATTAGTGTTTTTGAAAATAAAATCGGAATTA
Found at i:864485 original size:13 final size:13
Alignment explanation
Indices: 864467--864492 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
864457 ACAAAGATCC
864467 ATGTATCGATACA
1 ATGTATCGATACA
864480 ATGTATCGATACA
1 ATGTATCGATACA
864493 CAGAAAAATG
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:864488 original size:33 final size:33
Alignment explanation
Indices: 864446--864512 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
864436 AAAATTTCCA
***
864446 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
864479 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
864512 A
1 A
864513 TTTTCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:864556 original size:19 final size:18
Alignment explanation
Indices: 864532--864631 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
864522 CAGTAGCTAA
864532 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
864551 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
864566 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
864583 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
864598 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
864615 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
864632 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:864572 original size:13 final size:13
Alignment explanation
Indices: 864554--864610 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
864544 ACAATACTTA
864554 TGTATCGATACAT
1 TGTATCGATACAT
864567 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
864585 ATGTATCGATACAT
1 -TGTATCGATACAT
864599 TGTATCGATACA
1 TGTATCGATACA
864611 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:864576 original size:32 final size:32
Alignment explanation
Indices: 864535--864629 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
864525 TAGCTAATTA
*
864535 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
864567 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
864599 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
864630 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:864711 original size:21 final size:21
Alignment explanation
Indices: 864687--864764 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
864677 CATTTGTAGG
864687 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
864708 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
**
864729 ATGTATCGATACATTATACAA
1 ATGTATCGATACATTCCACAA
864750 ATGTATCGATACATT
1 ATGTATCGATACATT
864765 TGGATAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:865563 original size:28 final size:28
Alignment explanation
Indices: 865532--865616 Score: 66
Period size: 28 Copynumber: 3.1 Consensus size: 28
865522 TTGAGGAGTA
865532 AAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGTGCCACCAACTTGTGTGGGCTTT
** ** * * * *
865560 AAAAG-GCGTCCTGCTCTTTGAGGAC-TG
1 AAAAGTGCCACCAACT-TGTGTGGGCTTT
*
865587 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGTGCCACCAACTTGTGTGGGCTTT
865615 AA
1 AA
865617 GAGGTGTCCT
Statistics
Matches: 37, Mismatches: 17, Indels: 6
0.62 0.28 0.10
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (28 bp):
AAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:865978 original size:59 final size:58
Alignment explanation
Indices: 865513--866220 Score: 757
Period size: 55 Copynumber: 12.3 Consensus size: 58
865503 ATAAAGTGTA
* * * *
865513 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTTGTGTGGGCTTT---AAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGA-TGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
*
865568 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
*
865623 TCCTGCTTTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT---AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
* * * * *
865678 TCCTGCTCTTTGGGGACTGAAAAATGACACCAACTTGTGTGGGC-TT-CG-AAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
* * * **
865733 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT---AAGAAAAGGTG
* * *
865794 TCTTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTT---AAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
865849 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT--G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
* *
865904 TCCTGCTCTTTGAGGA-TTAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT-A-AGAAAAGGTG
* **
865963 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAATG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT-A-AGAAAAGGTG
* * * *
866022 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGCG
1 TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTT-A-AGAAAAGGTG
*
866081 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTT--AAGAAAAGGTG
* **
866141 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGC-TTT--AA-GAAAAGGTG
*
866203 TCCTGCTCTCTGAGGACT
1 TCCTGCTCTTTGAGGACT
866221 AAAAAGCGGA
Statistics
Matches: 579, Mismatches: 43, Indels: 55
0.86 0.06 0.08
Matches are distributed among these distances:
53 3 0.01
54 30 0.05
55 239 0.41
56 13 0.02
58 1 0.00
59 134 0.23
60 77 0.13
61 57 0.10
62 25 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (58 bp):
TCCTGCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAAAAGGTG
Found at i:867222 original size:17 final size:16
Alignment explanation
Indices: 867202--867262 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
867192 CTTTTCTCTC
*
867202 TTTTTCTTTGTTTTGT
1 TTTTTTTTTGTTTTGT
*
867218 TTTTTTGTTTTTTTTCCGT
1 TTTTTT-TTTGTTTT--GT
*
867237 TTTTTTTTTCTTTTGCT
1 TTTTTTTTTGTTTTG-T
867254 TTTTTTTTT
1 TTTTTTTTT
867263 TGAAGAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.16
17 17 0.45
18 7 0.18
19 8 0.21
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTGTTTTGT
Found at i:867239 original size:18 final size:16
Alignment explanation
Indices: 867186--867263 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 16
867176 CTTAAGTAGG
* *
867186 TTTTTTCTTTTCTCTCT
1 TTTTTTTTTTTTTC-CT
* * **
867203 TTTTCTTTGTTTTGTT
1 TTTTTTTTTTTTTCCT
867219 TTTTTGTTTTTTTTCCGT
1 TTTTT-TTTTTTTTCC-T
*
867237 TTTTTTTTTCTTTTGCT
1 TTTTTTTTT-TTTTCCT
867254 TTTTTTTTTT
1 TTTTTTTTTT
867264 GAAGAGAAGG
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
16 6 0.13
17 30 0.64
18 11 0.23
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTTTCCT
Found at i:867240 original size:19 final size:18
Alignment explanation
Indices: 867216--867263 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
867206 TCTTTGTTTT
867216 GTTTTTTTGTTTTTTTTCC
1 GTTTTTTT-TTTTTTTTCC
* *
867235 GTTTTTTTTTTCTTTTGC
1 GTTTTTTTTTTTTTTTCC
867253 -TTTTTTTTTTT
1 GTTTTTTTTTTT
867264 GAAGAGAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 10 0.38
18 8 0.31
19 8 0.31
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (18 bp):
GTTTTTTTTTTTTTTTCC
Found at i:879129 original size:16 final size:17
Alignment explanation
Indices: 879098--879130 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
879088 TTTAATATTT
*
879098 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
879115 ATAAAA-TTATAATTAA
1 ATAAAATTTATAATTAA
879131 TGAAGTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:879213 original size:11 final size:11
Alignment explanation
Indices: 879183--879212 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
879173 AAATTTAATC
879183 ATATAAAATAT
1 ATATAAAATAT
879194 ATATAAAATAT
1 ATATAAAATAT
879205 ATAATAAA
1 AT-ATAAA
879213 TTAAGATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAAATAT
Found at i:882999 original size:32 final size:33
Alignment explanation
Indices: 882958--883023 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
882948 AAAATTTCCA
**
882958 AATGTATCGATACAAAGATCCATGTA-CGATAC
1 AATGTATCGATACAAAGAAACATGTATCGATAC
*
882990 AATGTATCGATACACAGAAACATGTATCGATAC
1 AATGTATCGATACAAAGAAACATGTATCGATAC
883023 A
1 A
883024 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAACATGTATCGATAC
Found at i:884357 original size:190 final size:191
Alignment explanation
Indices: 884140--884516 Score: 625
Period size: 190 Copynumber: 2.0 Consensus size: 191
884130 AAATTAAAAA
*
884140 TTTATATAATTGAATTTAAAATTAAAATTGAATCATTATAATAAACTATAAAAATATAAAAAATT
1 TTTATATAATTGAATTTAAAATTAAAATTAAATCATTATAATAAACTATAAAAATATAAAAAATT
* * *
884205 CGAGGCATGAT-ATAAATATAATACGATACAAAAACAATATGACATGAATATATAAACATATCAA
66 C-AAGCATGATGATAAATATAATACGATACAAAAACAACATAACATGAATATATAAACATATCAA
* *
884269 ATCTATAAAAAA-ATAAATTATTAACGT-TTAAAAGTTTATATAAATTTATAATACTTTCAAT
130 ATCTATAAAAAATA-AAATTATTAACATCTAAAAAGTTTATATAAATTTATAATACTTTCAAT
*
884330 TTTATATAATTGAATTTAAAGTTAAAATTAAATCATTATAATAAACTATAAAAATATAAAAAATT
1 TTTATATAATTGAATTTAAAATTAAAATTAAATCATTATAATAAACTATAAAAATATAAAAAATT
* * *
884395 CAAGCATGATGATAAATATAATACGATACAAAAATAACATAACATGAATATATAAACATGTTAAA
66 CAAGCATGATGATAAATATAATACGATACAAAAACAACATAACATGAATATATAAACATATCAAA
884460 TCTATAAAAAATAAAATTATTAACATCTAAAAAGTTTATATAAATTTATAATACTTT
131 TCTATAAAAAATAAAATTATTAACATCTAAAAAGTTTATATAAATTTATAATACTTT
884517 GAACAAAAAA
Statistics
Matches: 174, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
189 8 0.05
190 136 0.78
191 30 0.17
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (191 bp):
TTTATATAATTGAATTTAAAATTAAAATTAAATCATTATAATAAACTATAAAAATATAAAAAATT
CAAGCATGATGATAAATATAATACGATACAAAAACAACATAACATGAATATATAAACATATCAAA
TCTATAAAAAATAAAATTATTAACATCTAAAAAGTTTATATAAATTTATAATACTTTCAAT
Found at i:885474 original size:40 final size:40
Alignment explanation
Indices: 885426--885527 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 40
885416 ATTTATATAT
*
885426 ATAAAAATATAAATATGATATAAAAAT--T-AATTAAAAA
1 ATAAAAATATAAATATGATATAAAAATAATAAAATAAAAA
* ** *
885463 ATAATAAAAATAAATATGACGTAAATATAATAAAATAAAAA
1 ATAA-AAATATAAATATGATATAAAAATAATAAAATAAAAA
** *
885504 ATAAATTTATAAATATTATATAAA
1 ATAAAAATATAAATATGATATAAA
885528 GTTATAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
37 4 0.08
38 19 0.38
40 15 0.30
41 12 0.24
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (40 bp):
ATAAAAATATAAATATGATATAAAAATAATAAAATAAAAA
Found at i:885745 original size:24 final size:25
Alignment explanation
Indices: 885711--885763 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
885701 GTACAGATAG
* *
885711 AAAATATAATTATTCGACCATGTTT
1 AAAATATAATTATTCAACCATGTGT
*
885736 AAAA-ATAATTATTCAATCATGTGT
1 AAAATATAATTATTCAACCATGTGT
885760 AAAA
1 AAAA
885764 GTTACGTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (25 bp):
AAAATATAATTATTCAACCATGTGT
Found at i:886013 original size:17 final size:17
Alignment explanation
Indices: 885991--886030 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
885981 TTTATTTAAT
*
885991 TTAATTAATTTTTAAAA
1 TTAATTAATTTTAAAAA
886008 TTAATTAATTTTAAAAA
1 TTAATTAATTTTAAAAA
886025 TTAATT
1 TTAATT
886031 TACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATTAATTTTAAAAA
Found at i:886174 original size:20 final size:20
Alignment explanation
Indices: 886151--886200 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
886141 AAATTCATAG
886151 TATATA-ATAATTTAACATT
1 TATATATATAATTTAACATT
*
886170 CTATA-ATATAATTTATCATT
1 -TATATATATAATTTAACATT
886190 TATATAGTATA
1 TATATA-TATA
886201 TTATATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATATATAATTTAACATT
Found at i:886258 original size:28 final size:27
Alignment explanation
Indices: 886197--886259 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 27
886187 ATTTATATAG
*
886197 TATATTATATAATACATAATATAAAAT
1 TATATTTTATAATACATAATATAAAAT
886224 TAT-TTTTAT-ATA-ATAATATAAATAATT
1 TATATTTTATAATACATAATAT-AA-AA-T
886251 TATATTTTA
1 TATATTTTA
886260 AAACTTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 7 0.23
25 5 0.16
26 7 0.23
27 7 0.23
28 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TATATTTTATAATACATAATATAAAAT
Found at i:886733 original size:26 final size:27
Alignment explanation
Indices: 886698--886751 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
886688 TTTCACACTA
* *
886698 AATTATATTTA-TTTCTTTTTACCTTTT
1 AATTATATTTACTTT-TTTATACATTTT
886725 AATTA-ATTTACTTTTTTATACATTTT
1 AATTATATTTACTTTTTTATACATTTT
886751 A
1 A
886752 TAATCCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (27 bp):
AATTATATTTACTTTTTTATACATTTT
Found at i:887369 original size:2 final size:2
Alignment explanation
Indices: 887362--887417 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
887352 GTTTTACTTC
* * *
887362 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AC AT AT GT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
887403 AT AT GAA AT AT AT AT
1 AT AT -AT AT AT AT AT
887418 CTAATTAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:887387 original size:20 final size:20
Alignment explanation
Indices: 887362--887417 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
887352 GTTTTACTTC
887362 ATATATATATATATATGTAT
1 ATATATATATATATATGTAT
*
887382 ATATATATATACATATGTAT
1 ATATATATATATATATGTAT
*
887402 -TATATGAAATATATAT
1 ATATAT-ATATATATAT
887418 CTAATTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATATATATATATATGTAT
Found at i:887817 original size:3 final size:3
Alignment explanation
Indices: 887809--887842 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
887799 ATGCACGGTG
887809 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
887843 GATATTGAGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:888955 original size:15 final size:15
Alignment explanation
Indices: 888935--888974 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
888925 TATTATATGG
888935 AATTAGGTTTA-GAGT
1 AATTA-GTTTAGGAGT
*
888950 AATTAGTTTAGGGGT
1 AATTAGTTTAGGAGT
888965 AATTAGTTTA
1 AATTAGTTTA
888975 AAGTCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (15 bp):
AATTAGTTTAGGAGT
Found at i:903058 original size:13 final size:13
Alignment explanation
Indices: 903040--903064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
903030 TTTTACAATT
903040 TGTATCGATACAA
1 TGTATCGATACAA
903053 TGTATCGATACA
1 TGTATCGATACA
903065 TAAGTTTTGT
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:904095 original size:20 final size:21
Alignment explanation
Indices: 904056--904096 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
904046 TCAGCCCATG
904056 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAGCTATGT
*
904077 TTCATGCATTTTTAG-TATGT
1 TTCATGCATTTTGAGCTATGT
904097 CCAATGCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (21 bp):
TTCATGCATTTTGAGCTATGT
Found at i:912045 original size:24 final size:24
Alignment explanation
Indices: 912001--912092 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 24
911991 TTATTTAATT
* * *
912001 TTTATTTTAAAATAA-AATAATTTA
1 TTTA-TTTAATATAATATTAATTAA
*
912025 TTTATTTAATATAATATTAATAAA
1 TTTATTTAATATAATATTAATTAA
*
912049 TTTATTATTATATAATA--AATTAAA
1 TTTATT-TAATATAATATTAATT-AA
*
912073 ATT-TTTAATATAATATTAAT
1 TTTATTTAATATAATATTAAT
912093 ATGATTAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
22 9 0.16
23 14 0.25
24 23 0.42
25 9 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTATTTAATATAATATTAATTAA
Found at i:912046 original size:27 final size:25
Alignment explanation
Indices: 912024--912093 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
912014 AAAATAATTT
*
912024 ATTTATT-TAATATAATATTAATAA
1 ATTTATTATTATATAATATTAATAA
912048 ATTTATTATTATATAATA--AATTAAA
1 ATTTATTATTATATAATATTAA-T-AA
912073 ATTT-TTA--ATATAATATTAATA
1 ATTTATTATTATATAATATTAATA
912094 TGATTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
22 9 0.22
23 3 0.08
24 13 0.32
25 15 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTATTATTATATAATATTAATAA
Found at i:912061 original size:20 final size:19
Alignment explanation
Indices: 912028--912069 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
912018 TAATTTATTT
912028 ATTTAATATAATATTAATAA
1 ATTTAATATAATA-TAATAA
* *
912048 ATTTATTATTATATAATAA
1 ATTTAATATAATATAATAA
912067 ATT
1 ATT
912070 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAATATAATATAATAA
Found at i:913011 original size:2 final size:2
Alignment explanation
Indices: 913004--913038 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
912994 TCAACTGGCA
913004 AT AT AT 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 AT AT AT A
913039 ACAAAAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:913378 original size:28 final size:28
Alignment explanation
Indices: 913338--913419 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
913328 CCTTTTGTTT
913338 AATTTAATAATAATTAA-ATATATAAAAA
1 AATTTAATAATAATTAATA-ATATAAAAA
913366 AATTT-ATATATAATTAATAATATAAAAA
1 AATTTAATA-ATAATTAATAATATAAAAA
*
913394 AA---AATAATTATTAATAAATGATAAAA
1 AATTTAATAATAATTAAT-AAT-ATAAAA
913420 CATAAAAGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
25 8 0.17
26 6 0.12
27 9 0.19
28 24 0.50
29 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
AATTTAATAATAATTAATAATATAAAAA
Found at i:913476 original size:16 final size:15
Alignment explanation
Indices: 913430--913472 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
913420 CATAAAAGTA
913430 AAATATATAATTATAT
1 AAATATATAATTAT-T
* *
913446 AAATAAATTATTATT
1 AAATATATAATTATT
913461 AAATATATAATT
1 AAATATATAATT
913473 TATTTTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATATAATTATT
Found at i:913480 original size:18 final size:18
Alignment explanation
Indices: 913448--913498 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
913438 AATTATATAA
*
913448 ATAAATTATTATTAAATAT
1 ATAATTTATT-TTAAATAT
913467 ATAATTTATTTT-AATAT
1 ATAATTTATTTTAAATAT
* *
913484 AAAATAATATTTTAA
1 ATAAT-TTATTTTAA
913499 TATTTTGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.33
18 8 0.30
19 10 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATTTATTTTAAATAT
Found at i:913564 original size:17 final size:18
Alignment explanation
Indices: 913527--913581 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
913517 TTTTTTAAAT
*
913527 TTTATAATATTAAATAAAA
1 TTTATAATATTATA-AAAA
913546 TTTA-AATATTATAAAAA
1 TTTATAATATTATAAAAA
*
913563 TTCATAA-ATTATAATAAA
1 TTTATAATATTATAA-AAA
913581 T
1 T
913582 AATTAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 14 0.44
18 14 0.44
19 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTATAATATTATAAAAA
Found at i:913656 original size:17 final size:17
Alignment explanation
Indices: 913618--913658 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
913608 AATTTATGTA
913618 AATATATAATGATTATAT
1 AATATATAAT-ATTATAT
913636 -ATATATAAT-TTAATAT
1 AATATATAATATT-ATAT
913652 AATATAT
1 AATATAT
913659 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 4 0.19
17 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATATAATATTATAT
Done.