Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold37
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: 836391
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:600887 original size:17 final size:17
Alignment explanation
Indices: 600865--600897 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
600855 TGTTCTTCCT
600865 TTATTATTATTATTATA
1 TTATTATTATTATTATA
600882 TTATTATTATTATTAT
1 TTATTATTATTATTAT
600898 TATTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTATTATTATA
Found at i:604820 original size:6 final size:6
Alignment explanation
Indices: 604811--604857 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
604801 TTAAAATATT
604811 AATAAA AATAATA ATATAAA AAT--A AATAAA TAATAAA AATAAA AATA
1 AATAAA AATAA-A A-ATAAA AATAAA AATAAA -AATAAA AATAAA AATA
604858 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.11
6 18 0.50
7 10 0.28
8 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:604831 original size:14 final size:14
Alignment explanation
Indices: 604812--604858 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
604802 TAAAATATTA
604812 ATAAAAATAATAAT
1 ATAAAAATAATAAT
604826 ATAAAAATAAATAAAT
1 ATAAAAAT-AAT-AAT
*
604842 AATAAAAATAAAAAT
1 -ATAAAAATAATAAT
604857 AT
1 AT
604859 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 10 0.34
15 6 0.21
16 5 0.17
17 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:604848 original size:17 final size:16
Alignment explanation
Indices: 604804--604857 Score: 69
Period size: 15 Copynumber: 3.5 Consensus size: 16
604794 AAAATAATTA
*
604804 AAATATTAATAAAAAT
1 AAATAATAATAAAAAT
604820 -AATAAT-ATAAAAAT
1 AAATAATAATAAAAAT
604834 AAATAAATAATAAAAAT
1 AAAT-AATAATAAAAAT
604851 AAA-AATA
1 AAATAATA
604858 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 8 0.24
15 12 0.35
16 3 0.09
17 11 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATAATAAAAAT
Found at i:605983 original size:2 final size:2
Alignment explanation
Indices: 605976--606009 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
605966 TCAATGGAGA
605976 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
606010 GTCATGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:606719 original size:3 final size:3
Alignment explanation
Indices: 606706--606751 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
606696 ACCATTCACC
606706 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
606752 AAGCAGGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:609471 original size:22 final size:22
Alignment explanation
Indices: 609403--609476 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
609393 GTATCAATGT
*
609403 TTATTTA-AT-AAAAAATTTAT
1 TTATTTATATAAAAAAATTTAA
* * *
609423 TTAAATTTAATTATAACAATATATAA
1 TT--ATTT-A-TATAAAAAAATTTAA
609449 TTATTTATATAAAAAAATTTAA
1 TTATTTATATAAAAAAATTTAA
*
609471 TAATTT
1 TTATTT
609477 TAATGAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 2 0.05
22 21 0.52
23 2 0.05
24 4 0.10
25 2 0.05
26 9 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTTATATAAAAAAATTTAA
Found at i:610365 original size:15 final size:14
Alignment explanation
Indices: 610313--610358 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
610303 ATATAAAAGA
*
610313 TAATATTTAATAAATT
1 TAATATTT-A-AATTT
610329 TAATATTTAAATTT
1 TAATATTTAAATTT
610343 TAATATTTATAATTT
1 TAATATTTA-AATTT
610358 T
1 T
610359 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.46
15 7 0.25
16 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTAAATTT
Found at i:611023 original size:23 final size:22
Alignment explanation
Indices: 610997--611057 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
610987 ATTTATTCGC
*
610997 TAACATTAAATAAATATGTTTAT
1 TAACA-TAAATAAATATGTTCAT
611020 TAACATATAATCAAATATGTTCAT
1 TAACATA-AAT-AAATATGTTCAT
*
611044 GAACAATAAATAAA
1 TAAC-ATAAATAAA
611058 CAAATCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 11 0.33
24 17 0.52
25 3 0.09
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.34
Consensus pattern (22 bp):
TAACATAAATAAATATGTTCAT
Found at i:611152 original size:36 final size:34
Alignment explanation
Indices: 611108--611178 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 34
611098 TTTAAATATA
* * *
611108 AAATAATAAAACATAAATATTATTAATTATATTAT
1 AAATAATAAAACACAAATAATAGTAA-TATATTAT
611143 AAATGAATAAAACACAAATAATAGTAATATATTAT
1 AAAT-AATAAAACACAAATAATAGTAATATATTAT
611178 A
1 A
611179 TTTGAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (34 bp):
AAATAATAAAACACAAATAATAGTAATATATTAT
Found at i:611213 original size:22 final size:22
Alignment explanation
Indices: 611188--611236 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
611178 ATTTGAACAA
* *
611188 TAAATAAATT-TTAAATGAGCTT
1 TAAACAAATTATTAAAAG-GCTT
*
611210 TAAACAATTTATTAAAAGGCTT
1 TAAACAAATTATTAAAAGGCTT
611232 TAAAC
1 TAAAC
611237 GATTTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (22 bp):
TAAACAAATTATTAAAAGGCTT
Found at i:611218 original size:21 final size:20
Alignment explanation
Indices: 611194--611246 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
611184 ACAATAAATA
*
611194 AATTTTAAATGAGCTTTAAAC
1 AATTTTAAAAG-GCTTTAAAC
611215 AATTTATTAAAAGGCTTTAAAC
1 AA-TT-TTAAAAGGCTTTAAAC
*
611237 GATTTATAAA
1 AATTT-TAAA
611247 CGAGTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 12 0.44
23 6 0.22
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (20 bp):
AATTTTAAAAGGCTTTAAAC
Found at i:612858 original size:25 final size:25
Alignment explanation
Indices: 612824--612873 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
612814 CTGGTTGATT
*
612824 CTCATCACACCACTAACAATAATAA
1 CTCATCACACCAATAACAATAATAA
*
612849 CTCATCACACCAATAATAATAATAA
1 CTCATCACACCAATAACAATAATAA
612874 TAATAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (25 bp):
CTCATCACACCAATAACAATAATAA
Found at i:615689 original size:2 final size:2
Alignment explanation
Indices: 615682--615719 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
615672 TATGGTTGTT
615682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
615720 CTTTAATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:616658 original size:19 final size:19
Alignment explanation
Indices: 616611--616664 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
616601 TAAATATTAA
*
616611 AATAAAATAATTTTTTAAAT
1 AATAAAAT-ATATTTTAAAT
* **
616631 ATTTTAATATATTTTAAAT
1 AATAAAATATATTTTAAAT
*
616650 AATAAAATAAATTTT
1 AATAAAATATATTTT
616665 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAAAATATATTTTAAAT
Found at i:616684 original size:27 final size:31
Alignment explanation
Indices: 616626--616684 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 31
616616 AATAATTTTT
616626 TAAATATTTTAATATATTTTAAATAATAAAA
1 TAAATATTTTAATATATTTTAAATAATAAAA
*
616657 TAAAT-TTTTAA-A-ATTTTAAA-AATTAAA
1 TAAATATTTTAATATATTTTAAATAATAAAA
616684 T
1 T
616685 TATAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
28 8 0.30
29 1 0.04
30 6 0.22
31 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAATATTTTAATATATTTTAAATAATAAAA
Found at i:616690 original size:38 final size:41
Alignment explanation
Indices: 616606--616700 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 41
616596 ATATATAAAT
* * * *
616606 ATTAAAATAAAATAATTTTTTAAATATTTTAATATATTTTA
1 ATTATAATAAAATAAATTTTTAAATATTTTAATATAATTAA
616647 A--ATAATAAAATAAATTTTTAAA-ATTTTAA-A-AATTAA
1 ATTATAATAAAATAAATTTTTAAATATTTTAATATAATTAA
616683 ATTATAATAAAATGAAAT
1 ATTATAATAAAAT-AAAT
616701 AAATAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
36 5 0.11
37 1 0.02
38 17 0.36
39 23 0.49
41 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (41 bp):
ATTATAATAAAATAAATTTTTAAATATTTTAATATAATTAA
Found at i:618916 original size:15 final size:15
Alignment explanation
Indices: 618898--618928 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
618888 ATTGAAAACT
618898 TAAGTAATGAATTTA
1 TAAGTAATGAATTTA
*
618913 TAAGTATTGAATTTA
1 TAAGTAATGAATTTA
618928 T
1 T
618929 TATTTTAAAA
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:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (15 bp):
TAAGTAATGAATTTA
Found at i:619235 original size:2 final size:2
Alignment explanation
Indices: 619228--619264 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
619218 TTGGGGATTT
619228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
619265 TCTTAACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:621034 original size:22 final size:22
Alignment explanation
Indices: 621009--621083 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 22
620999 TCGAATTATT
621009 ATTTAATAATAAATTTTTTTAA
1 ATTTAATAATAAATTTTTTTAA
* * ** * *
621031 ATTTATTTATAAAAATATATAA
1 ATTTAATAATAAATTTTTTTAA
621053 ATATTAAT-AT-AATTTTTTTAA
1 AT-TTAATAATAAATTTTTTTAA
621074 TAGTTTAATA
1 -A-TTTAATA
621084 TTATTTAAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
21 7 0.18
22 26 0.68
23 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTTAATAATAAATTTTTTTAA
Found at i:621375 original size:2 final size:2
Alignment explanation
Indices: 621368--621400 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
621358 TACTAAATGC
621368 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 A
621401 AAGTGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:623787 original size:26 final size:26
Alignment explanation
Indices: 623724--623777 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
623714 AATATATTAG
* * *
623724 TATAAAATTAATTATTTTTGTATACT
1 TATATAATTAATTATTATTGTATAAT
*
623750 TTTATAATTAATTATTATTGTATAAT
1 TATATAATTAATTATTATTGTATAAT
623776 TA
1 TA
623778 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (26 bp):
TATATAATTAATTATTATTGTATAAT
Found at i:624804 original size:5 final size:5
Alignment explanation
Indices: 624778--624828 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
624768 CTCATCAAAC
* * * *
624778 TTAAC TTAAT TCAAT TCAAT TTAAT TT--T TTTAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
624826 TTA
1 TTA
624829 TGAATATCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
3 3 0.08
5 37 0.93
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:625647 original size:2 final size:2
Alignment explanation
Indices: 625640--625679 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
625630 ACTTGGCAAT
625640 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
625680 AAGTCAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:626408 original size:2 final size:2
Alignment explanation
Indices: 626401--626426 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
626391 TAATAATTTG
626401 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
626427 TGCATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:628482 original size:24 final size:26
Alignment explanation
Indices: 628455--628503 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
628445 TTATGTTTTT
628455 TTAAAAAATTA-TTTTATT-ATATTA
1 TTAAAAAATTATTTTTATTAATATTA
*
628479 TTAAAATATTATTTTTATTAATATT
1 TTAAAAAATTATTTTTATTAATATT
628504 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTAAAAAATTATTTTTATTAATATTA
Found at i:628498 original size:17 final size:17
Alignment explanation
Indices: 628476--628545 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 17
628466 TTTTATTATA
628476 TTATTAAAATATTATTT
1 TTATTAAAATATTATTT
*
628493 TTATTAATAT-TTATTT
1 TTATTAAAATATTATTT
* *
628509 TT-TT-ATA-ATTAATT
1 TTATTAAAATATTATTT
* *
628523 TAAATAAAATATTATTT
1 TTATTAAAATATTATTT
628540 TTATTA
1 TTATTA
628546 TTAAACTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 9 0.22
15 3 0.07
16 10 0.24
17 19 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTAAAATATTATTT
Found at i:629425 original size:16 final size:18
Alignment explanation
Indices: 629404--629439 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
629394 GACATAAAAA
629404 ATAAT-AAAAATA-TAAT
1 ATAATAAAAAATATTAAT
629420 ATAATAAAAAATATTAAT
1 ATAATAAAAAATATTAAT
629438 AT
1 AT
629440 GACATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATAAAAAATATTAAT
Found at i:629446 original size:23 final size:23
Alignment explanation
Indices: 629392--629447 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
629382 AATTTTGAAC
629392 ATGACATAAAAAATAATAAAAAT
1 ATGACATAAAAAATAATAAAAAT
* * **
629415 ATAATATAATAAAA-AATATTAAT
1 ATGACATAA-AAAATAATAAAAAT
629438 ATGACATAAA
1 ATGACATAAA
629448 TACTCAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
22 1 0.04
23 21 0.81
24 4 0.15
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
ATGACATAAAAAATAATAAAAAT
Found at i:630038 original size:22 final size:20
Alignment explanation
Indices: 629998--630039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
629988 ACTTTAATTT
*
629998 ATTTTATACATTTTAATTAC
1 ATTTTATAAATTTTAATTAC
630018 ATTTTGATAAATTTTCAATTAC
1 ATTTT-ATAAATTTT-AATTAC
630040 CATTGCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 8 0.42
22 6 0.32
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTATAAATTTTAATTAC
Found at i:632626 original size:19 final size:19
Alignment explanation
Indices: 632592--632637 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
632582 AAAATTATAG
*
632592 TTTTTTT-TACT-TTTAAT
1 TTTTTTTATACTCTTAAAT
632609 TTTTTTTATAACTCTTAAAT
1 TTTTTTTAT-ACTCTTAAAT
632629 TTTTATTTA
1 TTTT-TTTA
632638 ATAAACTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 3 0.12
20 9 0.38
21 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTTATACTCTTAAAT
Found at i:635876 original size:2 final size:2
Alignment explanation
Indices: 635863--635903 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
635853 TTATATTTTC
* * *
635863 AT AT AA AT AT AT AT AT AT AT AT AT AT AT GT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
635904 ATAGAGGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:638504 original size:16 final size:17
Alignment explanation
Indices: 638477--638508 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
638467 ACTTTTAAAA
638477 TAAAAGAAATTAATAAT
1 TAAAAGAAATTAATAAT
638494 TAAAA-AAATTAATAA
1 TAAAAGAAATTAATAA
638509 AAAAGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
TAAAAGAAATTAATAAT
Found at i:638989 original size:21 final size:19
Alignment explanation
Indices: 638950--638996 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
638940 TATTTTTAAA
*
638950 ATAAATAAAAAATTATATT
1 ATAAATAAAAAAATATATT
*
638969 ATTAATAAAAGAAATATTATT
1 ATAAATAAAA-AAATA-TATT
638990 ATAAATA
1 ATAAATA
638997 TAATAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.39
20 4 0.17
21 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAATAAAAAAATATATT
Found at i:639426 original size:25 final size:26
Alignment explanation
Indices: 639398--639447 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
639388 AAAAATATAT
* *
639398 AATTACAACCTAAATTAAA-ATTTTC
1 AATTAAAAACTAAATTAAATATTTTC
*
639423 AATTAAAAATTAAATTAAATATTTT
1 AATTAAAAACTAAATTAAATATTTT
639448 AAAATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (26 bp):
AATTAAAAACTAAATTAAATATTTTC
Found at i:639805 original size:11 final size:12
Alignment explanation
Indices: 639789--639837 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
639779 CATGTCAAAA
639789 TAATAA-TATTT
1 TAATAATTATTT
639800 TAATAATTTATTT
1 TAATAA-TTATTT
639813 TAAATTAA-TATTT
1 T-AA-TAATTATTT
639826 TAATAATTATTT
1 TAATAATTATTT
639838 AAAAAATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 9 0.27
12 7 0.21
13 12 0.36
14 2 0.06
15 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAATAATTATTT
Found at i:640702 original size:80 final size:79
Alignment explanation
Indices: 640547--640694 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 79
640537 CCACCCATGT
* * *
640547 AATAGGTGTAACAATTTTAGTATAAATAAAGATATTATAAATAGGAATATTAAAATAAAAAAGTA
1 AATAAGTGTAACAATTTTAATATAAATAAAGATATTATAAATAAGAATATTAAAATAAAAAAG-A
640612 AAAATAAAAAAATGC
65 AAAATAAAAAAATGC
* *
640627 AATAAGTGTACCAATTTTAATATAGATAAAGATATTATAAATAAGAATATTAAAATTAAAAAA-A
1 AATAAGTGTAACAATTTTAATATAAATAAAGATATTATAAATAAGAATATTAAAA-TAAAAAAGA
640691 AAAA
65 AAAA
640695 GGTAAAAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
79 5 0.08
80 50 0.81
81 7 0.11
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.28
Consensus pattern (79 bp):
AATAAGTGTAACAATTTTAATATAAATAAAGATATTATAAATAAGAATATTAAAATAAAAAAGAA
AAATAAAAAAATGC
Found at i:643587 original size:13 final size:13
Alignment explanation
Indices: 643560--643594 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
643550 AAGTTTTTAT
643560 TTAAAAATAGAAAA
1 TTAAAAA-AGAAAA
*
643574 TTAAAAAAGGAAA
1 TTAAAAAAGAAAA
643587 TTAAAAAA
1 TTAAAAAA
643595 ATAATAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (13 bp):
TTAAAAAAGAAAA
Found at i:647344 original size:2 final size:2
Alignment explanation
Indices: 647339--647366 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
647329 ATACTTCGCT
647339 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
647367 AAAAAAAAAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:652230 original size:15 final size:17
Alignment explanation
Indices: 652196--652235 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
652186 CAAAAGTAAG
652196 TATTTAATATGAATATA
1 TATTTAATATGAATATA
652213 TATTTAATAT-AA-ATA
1 TATTTAATATGAATATA
652228 TATTTAAT
1 TATTTAAT
652236 TTTGTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTTAATATGAATATA
Found at i:655645 original size:18 final size:18
Alignment explanation
Indices: 655596--655645 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
655586 GAAAATATTA
*
655596 TATTTAAAAAA-TAAGTT
1 TATTTAAAAAATTAAATT
* * *
655613 TATATAAATATTTAAATT
1 TATTTAAAAAATTAAATT
655631 TATTTAAAAAATTAA
1 TATTTAAAAAATTAA
655646 CTTAATCTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTTAAAAAATTAAATT
Found at i:655716 original size:6 final size:6
Alignment explanation
Indices: 655705--655734 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
655695 ATACAATATA
655705 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
655735 ATATTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:655746 original size:18 final size:18
Alignment explanation
Indices: 655703--655748 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
655693 TTATACAATA
*
655703 TATT-TTATTTTTATTTT
1 TATTATTATTTTTATTAT
*
655720 TATTTTTATTTTTATATAT
1 TATTATTATTTTTAT-TAT
655739 TA-TATTATTT
1 TATTATTATTT
655749 ATATCATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTATTATTTTTATTAT
Found at i:656568 original size:30 final size:31
Alignment explanation
Indices: 656532--656614 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 31
656522 TTTTTATTTT
656532 AAATAAACTCTTAATCTTTAATTG-ATACT-C
1 AAATAAACTCTTAATCTTTAATTGTATA-TAC
*
656562 AAATAAACTCTTAA-CTTTTAA-TGTTTATAC
1 AAATAAACTCTTAATC-TTTAATTGTATATAC
656592 AAATAAACTCTTAAT-TTATAATT
1 AAATAAACTCTTAATCTT-TAATT
656615 TATTCTTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
29 6 0.13
30 39 0.85
31 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.42
Consensus pattern (31 bp):
AAATAAACTCTTAATCTTTAATTGTATATAC
Found at i:657741 original size:20 final size:19
Alignment explanation
Indices: 657700--657741 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
657690 TATAAATTAT
*
657700 AATATTTGAAATTTATAGA
1 AATATTTGAAATTTATACA
657719 AATATTTAGAAA-TTATTACA
1 AATATTT-GAAATTTA-TACA
657739 AAT
1 AAT
657742 TTAAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (19 bp):
AATATTTGAAATTTATACA
Found at i:660632 original size:17 final size:17
Alignment explanation
Indices: 660578--660651 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 17
660568 ATATAATAAA
*
660578 TAAAATTATAATATGTT
1 TAAAATTATAATATATT
* *
660595 TAAATATCATATATTTATT
1 TAAA-ATTATA-ATATATT
*
660614 TAAAATTTTAATATATT
1 TAAAATTATAATATATT
*
660631 TAATAATTAATATTATATT
1 TAA-AATT-ATAATATATT
660650 TA
1 TA
660652 TATTTATGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 13 0.29
18 13 0.29
19 19 0.42
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TAAAATTATAATATATT
Found at i:663257 original size:5 final size:5
Alignment explanation
Indices: 663247--663273 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
663237 ACTTAAACAA
663247 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
663274 CAACACCTTC
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:664201 original size:28 final size:28
Alignment explanation
Indices: 664165--664227 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
664155 TCATCAATTT
* *
664165 TTTATTACATTTAAATAAATCTATCATC
1 TTTAATACATTTAAATAAATCTATAATC
*
664193 TTTAATACATTTAAATAAATCTATAATT
1 TTTAATACATTTAAATAAATCTATAATC
664221 TTTAATA
1 TTTAATA
664228 ATCTCCTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAATACATTTAAATAAATCTATAATC
Found at i:664901 original size:3 final size:3
Alignment explanation
Indices: 664893--664918 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
664883 AAGCTTAATT
664893 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
664919 TTTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:666249 original size:3 final size:3
Alignment explanation
Indices: 666241--666281 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
666231 CTCCAACCAG
666241 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
666282 ATCTTCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:668213 original size:13 final size:13
Alignment explanation
Indices: 668189--668222 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
668179 TATAAATAAA
668189 AAAACA-AGAAAT
1 AAAACAGAGAAAT
*
668201 TAAACAGAGAAAT
1 AAAACAGAGAAAT
668214 AAAACAGAG
1 AAAACAGAG
668223 TGAGAGAGAG
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:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAACAGAGAAAT
Found at i:668662 original size:20 final size:20
Alignment explanation
Indices: 668619--668662 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
668609 TATAATTATT
* *
668619 TTAAATAAATATATTTTTAA
1 TTAAATAAAAATATATTTAA
668639 TTAAATAAAAATA-ATTTAA
1 TTAAATAAAAATATATTTAA
668658 GTTAA
1 -TTAA
668663 GTTATTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAATAAAAATATATTTAA
Found at i:668834 original size:16 final size:16
Alignment explanation
Indices: 668808--668892 Score: 91
Period size: 16 Copynumber: 5.3 Consensus size: 16
668798 AAAGTTAATG
*
668808 AATTT-AATTATTTTG
1 AATTTAAATTATTTTA
*
668823 AGTTTAAATTATTTTA
1 AATTTAAATTATTTTA
*
668839 AATTTAAATTATTTTT
1 AATTTAAATTATTTTA
* * *
668855 AATTTGAATCATTTAA
1 AATTTAAATTATTTTA
*
668871 AATTTAAATTGTATTTA
1 AATTTAAATTAT-TTTA
668888 AATTT
1 AATTT
668893 TGATATCTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 4 0.07
16 44 0.79
17 8 0.14
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:669303 original size:23 final size:21
Alignment explanation
Indices: 669264--669311 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
669254 AATTTATGAA
669264 TTTTTATTATAATAATAATAATT
1 TTTTTATTATAATAAT-AT-ATT
*
669287 TTTTTATTCCTAA-AATATATT
1 TTTTTATT-ATAATAATATATT
669308 TTTT
1 TTTT
669312 GAGAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 11 0.48
24 3 0.13
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTATTATAATAATATATT
Found at i:671064 original size:16 final size:17
Alignment explanation
Indices: 671032--671068 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
671022 AAATAATATT
671032 ATTTGTTAAATATTTAA
1 ATTTGTTAAATATTTAA
*
671049 ATTTTTTAAA-ATTTAA
1 ATTTGTTAAATATTTAA
671065 ATTT
1 ATTT
671069 AATAAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTGTTAAATATTTAA
Found at i:673204 original size:3 final size:3
Alignment explanation
Indices: 673198--673236 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
673188 ATAATAATAA
*
673198 TAT TAT TA- TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
673237 TCTTTTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:674696 original size:2 final size:2
Alignment explanation
Indices: 674689--674750 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
674679 TTTCATATGA
* *
674689 AT AT AT AT AT AT AT AT AT AT AT -T AA AT AT A- AT -T GA- AG A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
674727 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
674751 GTACTTATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
1 5 0.10
2 47 0.90
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:675210 original size:19 final size:21
Alignment explanation
Indices: 675159--675205 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
675149 ATGTATTTTT
675159 TATATGATAAAAATTACTTAA
1 TATATGATAAAAATTACTTAA
675180 TATATGATAAAAATTACTTAA
1 TATATGATAAAAATTACTTAA
675201 TATAT
1 TATAT
675206 AAAAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (21 bp):
TATATGATAAAAATTACTTAA
Found at i:675313 original size:17 final size:17
Alignment explanation
Indices: 675287--675350 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
675277 TCAAGGCTCG
*
675287 ATTTATTTTTTTAATAA
1 ATTTAATTTTTTAATAA
*
675304 ATTTAATTTTTTATTAAA
1 ATTTAATTTTTTAAT-AA
675322 ATTT-A-TTTTT--TAA
1 ATTTAATTTTTTAATAA
675335 ATTTAATATTTTTAAT
1 ATTTAAT-TTTTTAAT
675351 TATATTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 6 0.15
14 2 0.05
16 10 0.26
17 14 0.36
18 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTAATTTTTTAATAA
Found at i:675314 original size:18 final size:18
Alignment explanation
Indices: 675287--675332 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
675277 TCAAGGCTCG
675287 ATTTATTTTTTTAAT-AA
1 ATTTATTTTTTTAATAAA
* *
675304 ATTTAATTTTTTATTAAA
1 ATTTATTTTTTTAATAAA
675322 ATTTATTTTTT
1 ATTTATTTTTT
675333 AAATTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTTTTTTAATAAA
Found at i:676687 original size:15 final size:15
Alignment explanation
Indices: 676627--676692 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 15
676617 GCTCCGTAGT
*
676627 TAAAT-TATATTAATT
1 TAAATATAT-TTAATA
*
676642 TAAATAAATATTAAATA
1 TAAAT--ATATTTAATA
676659 TAAATATTTATTTAATA
1 TAAATA--TATTTAATA
676676 TAAATATATTTAATA
1 TAAATATATTTAATA
676691 TA
1 TA
676693 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 17 0.40
17 23 0.53
18 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATATATTTAATA
Found at i:676880 original size:11 final size:11
Alignment explanation
Indices: 676864--676894 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
676854 TTTATATTCA
676864 AATATAAATTG
1 AATATAAATTG
*
676875 AATATAAATTT
1 AATATAAATTG
676886 AATATAAAT
1 AATATAAAT
676895 ATCAAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AATATAAATTG
Found at i:678304 original size:19 final size:19
Alignment explanation
Indices: 678282--678319 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
678272 TTAAATAAAT
678282 AAAATAATA-TAAAATATTA
1 AAAAT-ATAGTAAAATATTA
*
678301 AAAATATAGTAAATTATTA
1 AAAATATAGTAAAATATTA
678320 TTAAATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AAAATATAGTAAAATATTA
Found at i:679281 original size:2 final size:2
Alignment explanation
Indices: 679276--679303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
679266 TATACGTGTG
679276 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
679304 CACTTTAGCC
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:680223 original size:21 final size:22
Alignment explanation
Indices: 680199--680263 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
680189 TTCAACAACC
680199 AAAATTAAATTT-TAAATTTTA
1 AAAATTAAATTTATAAATTTTA
*
680220 AAAAATAATATTTAATAAA-TTT-
1 AAAATTAA-ATTT-ATAAATTTTA
* *
680242 AAATTTAAATTTATTAATTTTA
1 AAAATTAAATTTATAAATTTTA
680264 CGAGTAGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 10 0.29
23 3 0.09
24 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATTAAATTTATAAATTTTA
Found at i:682582 original size:24 final size:23
Alignment explanation
Indices: 682539--682584 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
682529 TACAATAAAG
* *
682539 TATTTTTATCTTTTTTTTTTGGA
1 TATTTTTAACTTTTTGTTTTGGA
682562 TATTTATTAACTTTTTGTTTTGG
1 TATTT-TTAACTTTTTGTTTTGG
682585 GGATTTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.15, C:0.04, G:0.11, T:0.70
Consensus pattern (23 bp):
TATTTTTAACTTTTTGTTTTGGA
Found at i:682590 original size:24 final size:23
Alignment explanation
Indices: 682540--682590 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
682530 ACAATAAAGT
* * *
682540 ATTTTTATCTTTTTTTTTTGGAT
1 ATTTTTAACTTTTTGTTTTGGAG
*
682563 ATTTATTAACTTTTTGTTTTGGGG
1 ATTT-TTAACTTTTTGTTTTGGAG
682587 ATTT
1 ATTT
682591 CTTGGTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.67
Consensus pattern (23 bp):
ATTTTTAACTTTTTGTTTTGGAG
Found at i:682982 original size:16 final size:18
Alignment explanation
Indices: 682961--682996 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
682951 TAATATGATT
682961 AATTGATTA-AAT-TAAA
1 AATTGATTATAATCTAAA
682977 AATTGATTATAATCTAAA
1 AATTGATTATAATCTAAA
682995 AA
1 AA
682997 GTGACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.36
Consensus pattern (18 bp):
AATTGATTATAATCTAAA
Found at i:684666 original size:25 final size:25
Alignment explanation
Indices: 684633--684680 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
684623 GGTATTGTCT
684633 TTTTATTATAATTCTTATAAATTTAA
1 TTTTATTATAATT-TTATAAATTTAA
* *
684659 TTTT-TTATTATTTTTTAAATTT
1 TTTTATTATAATTTTATAAATTT
684681 TTTAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 7 0.35
26 4 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTATTATAATTTTATAAATTTAA
Found at i:685825 original size:24 final size:22
Alignment explanation
Indices: 685786--685863 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 22
685776 ATAAGGTTTG
**
685786 TTAATATATTAATT-AATATTT
1 TTAATATATTTTTTAAATATTT
685807 TTAGTATGATATTTTTTAAAAATATTT
1 TTA--AT-ATATTTTTT--AAATATTT
685834 TTAATATATTTTTTAAATTATTTT
1 TTAATATATTTTTTAAA-TA-TTT
685858 TTAATA
1 TTAATA
685864 ATTAATAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 4 0.09
24 25 0.53
25 2 0.04
27 10 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
TTAATATATTTTTTAAATATTT
Found at i:685842 original size:11 final size:12
Alignment explanation
Indices: 685815--685863 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
685805 TTTTAGTATG
685815 ATAT-TTTTTAA
1 ATATATTTTTAA
*
685826 AAATATTTTT-A
1 ATATATTTTTAA
685837 ATATATTTTTTAA
1 ATATA-TTTTTAA
*
685850 AT-TATTTTTTA
1 ATATATTTTTAA
685861 ATA
1 ATA
685864 ATTAATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 16 0.52
12 12 0.39
13 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATATTTTTAA
Found at i:685859 original size:12 final size:12
Alignment explanation
Indices: 685816--685861 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
685806 TTTAGTATGA
685816 TATTTTTTAAA-
1 TATTTTTTAAAT
*
685827 AATATTTTT-AAT
1 TAT-TTTTTAAAT
685839 ATATTTTTTAAAT
1 -TATTTTTTAAAT
685852 TATTTTTTAA
1 TATTTTTTAA
685862 TAATTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 4 0.14
12 20 0.69
13 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTTTTAAAT
Found at i:690215 original size:2 final size:2
Alignment explanation
Indices: 690208--690234 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
690198 TGTCTGCTGA
690208 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 A
690235 AGCCAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:691725 original size:21 final size:20
Alignment explanation
Indices: 691701--691743 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
691691 AGATTCTCTA
*
691701 ATAATAGATAAGATAATTTTT
1 ATAATAGAT-AGATAAATTTT
**
691722 ATAATTTATAGATAAATTTT
1 ATAATAGATAGATAAATTTT
691742 AT
1 AT
691744 TAACGAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
ATAATAGATAGATAAATTTT
Found at i:692328 original size:20 final size:21
Alignment explanation
Indices: 692292--692342 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
692282 TATTTGTGTG
692292 AATATTAAAA-A--TAAAATT
1 AATATTAAAATATTTAAAATT
692310 AATA-TAAAATATTTAAAATT
1 AATATTAAAATATTTAAAATT
*
692330 TATATTAAAATAT
1 AATATTAAAATAT
692343 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
20 10 0.36
21 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATTAAAATATTTAAAATT
Found at i:693168 original size:3 final size:3
Alignment explanation
Indices: 693160--693186 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
693150 GTAATATGAG
693160 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
693187 TATTACCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:693459 original size:15 final size:16
Alignment explanation
Indices: 693439--693469 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
693429 AATAAATTAC
693439 ATTTAAAA-AATTTTT
1 ATTTAAAATAATTTTT
693454 ATTTAAAATAATTTTT
1 ATTTAAAATAATTTTT
693470 TAAAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAAAATAATTTTT
Found at i:695800 original size:17 final size:17
Alignment explanation
Indices: 695778--695820 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
695768 TTGTTTCTTA
* *
695778 CTTTTTTTTTTATCTTTT
1 CTTTTTCTTTT-TCCTTT
695796 CTTTTTCTTTTTCCTTT
1 CTTTTTCTTTTTCCTTT
695813 CTTCTTTC
1 CTT-TTTC
695821 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTTTCTTTTTCCTTT
Found at i:696611 original size:22 final size:23
Alignment explanation
Indices: 696568--696611 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
696558 AATTGAATTT
*
696568 TAAAAATTTAATATTAAATATAA
1 TAAAAATTTAATATAAAATATAA
*
696591 TAAATATTTAAT-TAAAATATA
1 TAAAAATTTAATATAAAATATA
696612 TATTTAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAATTTAATATAAAATATAA
Found at i:696932 original size:13 final size:14
Alignment explanation
Indices: 696909--696937 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
696899 CTATAAAATT
696909 TTAATTTTATTTAA
1 TTAATTTTATTTAA
696923 TTAA-TTTATTTAA
1 TTAATTTTATTTAA
696936 TT
1 TT
696938 CGATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTAATTTTATTTAA
Found at i:697289 original size:29 final size:28
Alignment explanation
Indices: 697256--697320 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
697246 AATATGAAAA
*
697256 TAATATAATAAATATAATATAAAATATT
1 TAATATAATAAAAATAATATAAAATATT
* * *
697284 TAAATATTATAAAAATAATATGACATATT
1 T-AATATAATAAAAATAATATAAAATATT
697313 TAATATAA
1 TAATATAA
697321 ATGTTGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
TAATATAATAAAAATAATATAAAATATT
Found at i:699147 original size:22 final size:20
Alignment explanation
Indices: 699110--699149 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
699100 GCCCGCCCAT
*
699110 TCCTCATGTCTTCTTCTCTG
1 TCCTCATGTCTCCTTCTCTG
699130 TCCTCATTCGTCTCCTTCTC
1 TCCTCA-T-GTCTCCTTCTC
699150 ACCTCATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.05, C:0.40, G:0.07, T:0.47
Consensus pattern (20 bp):
TCCTCATGTCTCCTTCTCTG
Found at i:699532 original size:16 final size:16
Alignment explanation
Indices: 699511--699543 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
699501 TAATTCTATA
699511 ATTA-TTTATAATAAAT
1 ATTATTTTA-AATAAAT
699527 ATTATTTTAAATAAAT
1 ATTATTTTAAATAAAT
699543 A
1 A
699544 ATTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATTTTAAATAAAT
Found at i:699797 original size:20 final size:20
Alignment explanation
Indices: 699747--699802 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
699737 AAATTTAAAC
699747 ATATATTTTATATTAATTTTA
1 ATAT-TTTTATATTAATTTTA
* *
699768 ATATTATTATTTTAATATTTA
1 ATATTTTTATATTAAT-TTTA
699789 AT-TTTTTATCATTA
1 ATATTTTTAT-ATTA
699803 TTATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTTTATATTAATTTTA
Found at i:699802 original size:26 final size:25
Alignment explanation
Indices: 699750--699819 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
699740 TTTAAACATA
*
699750 TATTTTATATTAATTTTAATATTAT
1 TATTTTATATTAATTTTAATATCAT
*
699775 TATTTTAATATTTAATTTT-TTATCAT
1 TATTTT-ATA-TTAATTTTAATATCAT
699801 TATTATT-T-TT-ATTTTAATA
1 TATT-TTATATTAATTTTAATA
699820 AAATAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
22 5 0.13
23 4 0.11
25 7 0.18
26 12 0.32
27 10 0.26
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTTTATATTAATTTTAATATCAT
Found at i:699812 original size:15 final size:14
Alignment explanation
Indices: 699750--699809 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
699740 TTTAAACATA
699750 TATTTT-ATATTA-
1 TATTTTAATATTAT
699762 -ATTTTAATATTAT
1 TATTTTAATATTAT
699775 TATTTTAATATTTAAT
1 TATTTTAATA-TT-AT
699791 T-TTTT-ATCATTAT
1 TATTTTAAT-ATTAT
699804 TATTTT
1 TATTTT
699810 TATTTTAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
11 5 0.12
12 6 0.15
13 3 0.07
14 17 0.41
15 7 0.17
16 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTAATATTAT
Found at i:700154 original size:15 final size:15
Alignment explanation
Indices: 700130--700210 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
700120 GATTTAATAT
700130 TTTAATATTTATTTTA
1 TTTAA-ATTTATTTTA
*
700146 TTTAAATTTAATTTA
1 TTTAAATTTATTTTA
* * *
700161 TATAATATCTGA--TAA
1 TTTAA-AT-TTATTTTA
*
700176 TTT-AATTTATTAT-
1 TTTAAATTTATTTTA
*
700189 TTTGAATTTATTTTA
1 TTTAAATTTATTTTA
700204 TTTAAAT
1 TTTAAAT
700211 AAATATTATT
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
12 2 0.04
13 5 0.10
14 10 0.20
15 23 0.47
16 7 0.14
17 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTAAATTTATTTTA
Found at i:701136 original size:13 final size:13
Alignment explanation
Indices: 701085--701137 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
701075 AAATCAAGCA
701085 TTTTAATT-TTAT
1 TTTTAATTATTAT
701097 TTTTAATTATTAAT
1 TTTTAATTATT-AT
*
701111 TTTTTA-TATTTAT
1 TTTTAATTA-TTAT
*
701124 TTTCAATTATTAT
1 TTTTAATTATTAT
701137 T
1 T
701138 ATTTTATTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 8 0.24
13 15 0.44
14 11 0.32
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAATTATTAT
Found at i:701144 original size:27 final size:29
Alignment explanation
Indices: 701084--701144 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
701074 TAAATCAAGC
*
701084 ATTTTA-ATTTTATTTTTAATTATTAATT
1 ATTTTATATTTTATTTTCAATTATTAATT
701112 -TTTTATA-TTTATTTTCAATTATT-ATT
1 ATTTTATATTTTATTTTCAATTATTAATT
701138 ATTTTAT
1 ATTTTAT
701145 TAGCTTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 26 0.87
28 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (29 bp):
ATTTTATATTTTATTTTCAATTATTAATT
Found at i:701145 original size:21 final size:19
Alignment explanation
Indices: 701084--701145 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
701074 TAAATCAAGC
*
701084 ATTTTAATTTTATT-TTTA
1 ATTTTAATTTTATTATTTT
701102 ATTATTAATTTT-TTATATTT
1 ATT-TTAATTTTATTAT-TTT
701122 ATTTTCAATTATTATTATTTT
1 ATTTT-AATT-TTATTATTTT
701143 ATT
1 ATT
701146 AGCTTTAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.14
19 11 0.30
20 9 0.24
21 8 0.22
22 4 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTAATTTTATTATTTT
Found at i:701633 original size:18 final size:18
Alignment explanation
Indices: 701591--701638 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
701581 AAAATTAAAT
*
701591 TAATTTTACATAATTTTA
1 TAATTTTAAATAATTTTA
701609 TAATTTTAAATAA-TTTA
1 TAATTTTAAATAATTTTA
*
701626 TATTTTTTAAATA
1 TA-ATTTTAAATA
701639 TGACTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTTTAAATAATTTTA
Found at i:701782 original size:16 final size:16
Alignment explanation
Indices: 701763--701815 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
701753 ATATCAAATA
701763 ATTAATTAATTATAAT
1 ATTAATTAATTATAAT
*
701779 ATTAATT-ATATATAAA
1 ATTAATTAAT-TATAAT
*
701795 ATTAATTAATT-TTAT
1 ATTAATTAATTATAAT
701810 ATTAAT
1 ATTAAT
701816 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 10 0.31
16 20 0.62
17 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAATTAATTATAAT
Found at i:701827 original size:25 final size:26
Alignment explanation
Indices: 701775--701832 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
701765 TAATTAATTA
*
701775 TAATATTAATTATATATAAAATTAAT
1 TAATATTAATTATATATAAAATAAAT
*
701801 TAATTTTATATTA-ATAT-AAATAAAT
1 TAATATTA-ATTATATATAAAATAAAT
701826 TAATATT
1 TAATATT
701833 TTACTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 13 0.46
26 11 0.39
27 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATATTAATTATATATAAAATAAAT
Found at i:701968 original size:83 final size:84
Alignment explanation
Indices: 701786--702037 Score: 347
Period size: 83 Copynumber: 3.1 Consensus size: 84
701776 AATATTAATT
* *
701786 ATATATAAAATTAATTAATTTTATATTAATATAAATAAATTAATATTTTACTTTTTTT--AA-A-
1 ATATATAAAATTAATTAATTTTATATTAATATAAATAAATTATTATTTTATTTTTTTTCGAAGAT
* *
701847 --AATATATTGCAGCAATG
66 GTAATACATGGCAGCAATG
*
701864 TTATATAAAATTAATTAATTTTATATTAATATAAATAAATTATTATTTTA-TTTTTTTCGAAGAT
1 ATATATAAAATTAATTAATTTTATATTAATATAAATAAATTATTATTTTATTTTTTTTCGAAGAT
*
701928 GTGATACATGGCAGCAATG
66 GTAATACATGGCAGCAATG
701947 ATATATAAAATTAATTAATTTTATATTAATATAAATAAATTATTATTTTAATTTTTTTTTCGAAG
1 ATATATAAAATTAATTAATTTTATATTAATATAAATAAATTATTATTTT-A-TTTTTTTTCGAAG
* **
702012 ATGTAATATACAGCAGCAATG
64 ATGTAATACATGGCAGCAATG
*
702033 CTATA
1 ATATA
702038 AATAGGAATA
Statistics
Matches: 154, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
77 7 0.05
78 48 0.31
79 2 0.01
80 1 0.01
83 62 0.40
84 1 0.01
86 33 0.21
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (84 bp):
ATATATAAAATTAATTAATTTTATATTAATATAAATAAATTATTATTTTATTTTTTTTCGAAGAT
GTAATACATGGCAGCAATG
Found at i:702901 original size:2 final size:2
Alignment explanation
Indices: 702896--702926 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
702886 TCTGTATTCC
702896 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
702927 AAGGGTGCTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:708748 original size:16 final size:16
Alignment explanation
Indices: 708727--708757 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
708717 TTTGGGAAGG
*
708727 AGATTCAACCTAAAGT
1 AGATTCAAACTAAAGT
708743 AGATTCAAACTAAAG
1 AGATTCAAACTAAAG
708758 CTATTTCCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (16 bp):
AGATTCAAACTAAAGT
Found at i:722307 original size:40 final size:40
Alignment explanation
Indices: 722252--722332 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
722242 AGTTTTTCTG
*
722252 TTCTTCTTTTCTTCATCAATTTTCCGTGGGAGAAAATTTA
1 TTCTTCTTTTCTTCATCAATTTTCCGTGGAAGAAAATTTA
722292 TTCTTCTTTTCTTCATCAATTTTCCGTGGAAGAAAATTTA
1 TTCTTCTTTTCTTCATCAATTTTCCGTGGAAGAAAATTTA
722332 T
1 T
722333 CTCGCTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.48
Consensus pattern (40 bp):
TTCTTCTTTTCTTCATCAATTTTCCGTGGAAGAAAATTTA
Found at i:728351 original size:2 final size:2
Alignment explanation
Indices: 728344--728381 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
728334 GTGCCCTCCA
728344 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
728382 TAACGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:728500 original size:4 final size:4
Alignment explanation
Indices: 728491--728517 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
728481 AAAAAGCAAC
728491 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
728518 AACATCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:730853 original size:2 final size:2
Alignment explanation
Indices: 730846--730873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
730836 TTTTTCAAAT
730846 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
730874 ATTAACAAGT
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:731953 original size:2 final size:2
Alignment explanation
Indices: 731946--731974 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
731936 AAATAATTTC
731946 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
731975 AAAAGTCACC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:732917 original size:12 final size:12
Alignment explanation
Indices: 732897--732957 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
732887 TAAACTCTAC
*
732897 ATATATATATAT
1 ATATGTATATAT
*
732909 ATATGTATATGT
1 ATATGTATATAT
*
732921 ATATGTATATGT
1 ATATGTATATAT
732933 ATATG--TATAT
1 ATATGTATATAT
*
732943 GTATGTATATAT
1 ATATGTATATAT
732955 ATA
1 ATA
732958 ACACAAATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 8 0.19
12 34 0.81
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:732923 original size:18 final size:18
Alignment explanation
Indices: 732897--732957 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
732887 TAAACTCTAC
*
732897 ATATATATATATATATGT
1 ATATATATATGTATATGT
*
732915 ATATGTATATGTATATGT
1 ATATATATATGTATATGT
*
732933 ATATGTATATG--TATGT
1 ATATATATATGTATATGT
732949 ATATATATA
1 ATATATATA
732958 ACACAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.32
18 27 0.68
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
ATATATATATGTATATGT
Found at i:732957 original size:6 final size:6
Alignment explanation
Indices: 732897--732946 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
732887 TAAACTCTAC
* *
732897 ATATAT ATATAT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
732945 AT
1 AT
732947 GTATATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:733885 original size:6 final size:6
Alignment explanation
Indices: 733874--733924 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
733864 ATAATTAAAT
* *
733874 TTTATA TTTATA -TTATA TTT-TA ATTAT- TTTATT TTTAT- TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
733918 TTTATA T
1 TTTATA T
733925 CGTATTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTATA
Found at i:733946 original size:38 final size:38
Alignment explanation
Indices: 733872--733946 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
733862 AAATAATTAA
* * * *
733872 ATTTTATATTTATATTATATTTTAATTATTTTATTTTT
1 ATTTTATATTTATATCATATTTAAATTATATAATTTTT
*
733910 ATTTTATATTTATATCGTATTTAAATT-TAATAATTTT
1 ATTTTATATTTATATCATATTTAAATTAT-ATAATTTT
733947 GAACTATTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (38 bp):
ATTTTATATTTATATCATATTTAAATTATATAATTTTT
Found at i:734189 original size:2 final size:2
Alignment explanation
Indices: 734148--734181 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
734138 TTTAAAAGTA
734148 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
734182 TCATATATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:735451 original size:19 final size:18
Alignment explanation
Indices: 735429--735464 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
735419 TGTTTGTACG
735429 ATATACAATTATCTATTTA
1 ATATACAATTAT-TATTTA
*
735448 ATATATAATTATTATTT
1 ATATACAATTATTATTT
735465 TTTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATACAATTATTATTTA
Found at i:736462 original size:3 final size:3
Alignment explanation
Indices: 736456--736497 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
736446 TCTGCTTATT
736456 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
736498 TAGTGAAAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:736766 original size:22 final size:22
Alignment explanation
Indices: 736723--736767 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
736713 CATAAATATT
** *
736723 ATAAAACAATAAATTTTTAAAA
1 ATAAAACAATAAATAATAAAAA
*
736745 ATAAAATAATAAATAATAAAAA
1 ATAAAACAATAAATAATAAAAA
736767 A
1 A
736768 ACATTCTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAAAACAATAAATAATAAAAA
Found at i:737652 original size:74 final size:73
Alignment explanation
Indices: 737570--737706 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 73
737560 AAAACAAAGT
* *
737570 AAAAAAAAAAATCCTTAGAGGTTATTCAACAC-TTCTTCT-AAGAATCAGACAAAAACAAAATAA
1 AAAAAAAAAAATCCTTAAAGGTTATTCAACACACTC-TCTGAA-AATCAGACAAAAACAAAATAA
737633 TGTGAAGCTC
64 TGTGAAGCTC
* * *
737643 AAAAGAAAAAAATCTTTAAAGTTTATTCAACACACTCTCTGAAAATCCGACAAAAACAAAATAA
1 AAAA-AAAAAAATCCTTAAAGGTTATTCAACACACTCTCTGAAAATCAGACAAAAACAAAATAA
737707 AGTCAAATTG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
73 4 0.07
74 48 0.86
75 4 0.07
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.23
Consensus pattern (73 bp):
AAAAAAAAAAATCCTTAAAGGTTATTCAACACACTCTCTGAAAATCAGACAAAAACAAAATAATG
TGAAGCTC
Found at i:738699 original size:2 final size:2
Alignment explanation
Indices: 738694--738722 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
738684 TTTTAGAAGC
738694 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
738723 CACACAAAAA
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:739526 original size:2 final size:2
Alignment explanation
Indices: 739519--739558 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
739509 ATATAGCTAT
739519 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
739559 CTCTTTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:740802 original size:2 final size:2
Alignment explanation
Indices: 740795--740824 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
740785 TAAAATAAGA
740795 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
740825 TGTTTTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:742341 original size:3 final size:3
Alignment explanation
Indices: 742333--742371 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
742323 ATAAGTTTTA
742333 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
742372 TTCTCTAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:745624 original size:16 final size:17
Alignment explanation
Indices: 745572--745624 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
745562 TTTAGATTAC
745572 AAATATAATATTTATAT
1 AAATATAATATTTATAT
** **
745589 ATTTATACGA-TTATAT
1 AAATATAATATTTATAT
745605 AAATATAATATTTATA-
1 AAATATAATATTTATAT
745621 AAAT
1 AAAT
745625 TATTAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATATAATATTTATAT
Found at i:754665 original size:24 final size:25
Alignment explanation
Indices: 754628--754677 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
754618 TGATTAATTT
754628 ATTTTGAATAATAACAT-AATACACTC
1 ATTTTGAATAATAA-ATAAATA-ACTC
754654 ATTTT-AA-AATAAATAAATAACTC
1 ATTTTGAATAATAAATAAATAACTC
754677 A
1 A
754678 GCTAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.30
24 9 0.39
25 2 0.09
26 5 0.22
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (25 bp):
ATTTTGAATAATAAATAAATAACTC
Found at i:755093 original size:19 final size:19
Alignment explanation
Indices: 755041--755100 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
755031 GTAAACATTA
* *
755041 AAAAATATATTAAGTTATTT
1 AAAAAT-TATTAAATTAATT
**
755061 AAATTTTA-TAAATTAATT
1 AAAAATTATTAAATTAATT
755079 AAAAATTATTAAATT-ATT
1 AAAAATTATTAAATTAATT
755097 AAAA
1 AAAA
755101 TTAAATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 21 0.64
19 8 0.24
20 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAATTATTAAATTAATT
Found at i:755113 original size:15 final size:15
Alignment explanation
Indices: 755086--755130 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
755076 ATTAAAAATT
*
755086 ATTAAA-TTATTAAA
1 ATTAAATTTTTTAAA
755100 ATTAAATTTTTTAAA
1 ATTAAATTTTTTAAA
* *
755115 AATATATTTTTTAAA
1 ATTAAATTTTTTAAA
755130 A
1 A
755131 AAATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATTTTTTAAA
Found at i:757112 original size:2 final size:2
Alignment explanation
Indices: 757107--757147 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
757097 TTTTCATACG
*
757107 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
757148 TCTGGTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.