Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 128 of 279
Found at i:40762962 original size:97 final size:91
Alignment explanation
Indices: 40762778--40762983 Score: 277
Period size: 97 Copynumber: 2.2 Consensus size: 91
40762768 CACTAATGAA
40762778 CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
1 CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
* *
40762843 ATATCAGAGAGCACTAGCGTGCTAGTAAT
66 ATATCAGAGAGCACAAACGTGC---TAAT
** * *
40762872 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAATCAGTGAGCACTGGCGTGC
1 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGC
*
40762937 TAAATATCAGAGAGCACAAATGTGCTAAT
63 TAAATATCAGAGAGCACAAACGTGCTAAT
40762966 CAGAGAGCATGCTGAAGT
1 CAGAGAGCA--CTGAAGT
40762984 CCCTTAACAT
Statistics
Matches: 98, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
94 30 0.31
96 8 0.08
97 60 0.61
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (91 bp):
CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
ATATCAGAGAGCACAAACGTGCTAAT
Found at i:40765389 original size:20 final size:20
Alignment explanation
Indices: 40765366--40765405 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40765356 TATAATTATT
40765366 TAATTAATAAATATCTTTTA
1 TAATTAATAAATATCTTTTA
40765386 TAATTAATAAATATCTTTTA
1 TAATTAATAAATATCTTTTA
40765406 ATACTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTAATAAATATCTTTTA
Found at i:40765940 original size:46 final size:46
Alignment explanation
Indices: 40765884--40766200 Score: 494
Period size: 46 Copynumber: 6.9 Consensus size: 46
40765874 GGTCATTACA
40765884 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
* *
40765930 TCCATGGTATCTTTCAACCATGGTCTTGCACATTTCATATCAGGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
** * *
40765976 GCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
*
40766021 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
*
40766067 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
** * *
40766113 GCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCACGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
* *
40766158 GTCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
40766201 AGAGCACACT
Statistics
Matches: 249, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
45 82 0.33
46 167 0.67
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
Found at i:40766043 original size:91 final size:92
Alignment explanation
Indices: 40765884--40766195 Score: 493
Period size: 91 Copynumber: 3.4 Consensus size: 92
40765874 GGTCATTACA
* *
40765884 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTTCCATGGTATCTTTCAACC
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACC
* *
40765949 ATGGTCTTGCACATTTCATATCAGGTT
66 ATGGTCTTACACATTTCATATCACGTT
** * *
40765976 GCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCATGTTGCCATGGTATCTTTCAACC
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACC
*
40766040 ATGGTCTTACACATTTCATATCATGTT
66 ATGGTCTTACACATTTCATATCACGTT
40766067 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACC
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACC
** *
40766132 ATGGTCTTATTC-TTTCATGTCACGTT
66 ATGGTCTTACACATTTCATATCACGTT
*
40766158 GTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
40766196 TTCAGAGAGC
Statistics
Matches: 203, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
91 133 0.66
92 70 0.34
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (92 bp):
GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACC
ATGGTCTTACACATTTCATATCACGTT
Found at i:40766130 original size:137 final size:137
Alignment explanation
Indices: 40765884--40766200 Score: 571
Period size: 137 Copynumber: 2.3 Consensus size: 137
40765874 GGTCATTACA
*
40765884 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTTCCATGGTATCTTTCAACC
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACC
* *
40765949 ATGGTCTTGCACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATG
66 ATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATG
*
40766014 TCATGTT
131 TCACGTT
*
40766021 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACC
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACC
40766086 ATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATG
66 ATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATG
40766151 TCACGTT
131 TCACGTT
* *
40766158 GTCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
40766201 AGAGCACACT
Statistics
Matches: 172, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 172 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (137 bp):
GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACC
ATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTCATG
TCACGTT
Found at i:40768313 original size:3 final size:3
Alignment explanation
Indices: 40768299--40768347 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
40768289 TTTTATACTA
*
40768299 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40768342 AA- AAT A
1 AAT AAT A
40768348 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40768321 original size:11 final size:11
Alignment explanation
Indices: 40768305--40768343 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
40768295 ACTAAATAAT
40768305 TAATAATAAAA
1 TAATAATAAAA
*
40768316 TAATAATGAAA
1 TAATAATAAAA
40768327 TAATAATAAAA
1 TAATAATAAAA
40768338 TAATAA
1 TAATAA
40768344 AATATCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:40768330 original size:19 final size:19
Alignment explanation
Indices: 40768306--40768347 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40768296 CTAAATAATT
*
40768306 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
40768325 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
40768344 AATA
1 AATA
40768348 TCTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:40768370 original size:20 final size:21
Alignment explanation
Indices: 40768317--40768381 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 21
40768307 ATAATAAAAT
* *
40768317 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
40768336 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
40768357 AATAAT-ATATATCTAATT-A
1 AATAATAAAATATCTAATTAA
40768376 AATAAT
1 AATAAT
40768382 CATAAGATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 18 0.46
20 12 0.31
21 9 0.23
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:40769121 original size:46 final size:46
Alignment explanation
Indices: 40769022--40769147 Score: 166
Period size: 46 Copynumber: 2.7 Consensus size: 46
40769012 GAGGAATCCA
* * *
40769022 AACTCGTTGAGTTGCGTTTCGAGTTCACCTATGGATGCAAGCATCTG
1 AACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGCAAGCATCTC
* *
40769069 AACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGTGAA-CA-CTC
1 AACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATG-CAAGCATCTC
40769114 AAGCTCGTTGAGTTGCGTTCCGAGTTCATTATGG
1 AA-CTCGTTGAGTTGCGTTCCGAGTTCATTATGG
40769148 GTGAGATTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
45 4 0.06
46 40 0.56
47 27 0.38
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (46 bp):
AACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGCAAGCATCTC
Found at i:40771791 original size:43 final size:42
Alignment explanation
Indices: 40771720--40771887 Score: 168
Period size: 43 Copynumber: 4.0 Consensus size: 42
40771710 ACATAAGCTT
* * * *
40771720 ATACA-ATGCC-ATATCCTAGATATGGTCTTACATGTTATC-
1 ATACACATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
* * *
40771759 ATACATCGATGCCACTGTCCCAGACAGGGTCTTACATGAAATCGA
1 ATACA-C-ATGCCAATGTCCCAGACATGGTCTTACATGTAATC-A
*
40771804 TTA-ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATATCA
1 ATACAC-ATGCCAATGTCCCAGACATGGTCTTACATGT-A-ATCA
40771848 ATACA-ATGCCAATGT-CCAGACATGGTCTTACATGTAATCA
1 ATACACATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
40771888 TATCTCAATA
Statistics
Matches: 107, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
39 5 0.05
40 4 0.04
41 1 0.01
42 25 0.23
43 61 0.57
44 5 0.05
45 6 0.06
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (42 bp):
ATACACATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
Found at i:40771879 original size:85 final size:83
Alignment explanation
Indices: 40771722--40771886 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 83
40771712 ATAAGCTTAT
* * *
40771722 ACAATGCCATATCCTAGATATGGTCTTACATGTTATCATACATCGATGCCACTGTCCCAGACAGG
1 ACAATGCCATATCCCAGACATGGTCTTACATGTTATCATACA-C-ATGCCAATGTCCCAGACAGG
40771787 GTCTTACATGAAATCGATTA
64 GTCTTACATGAAATCGATTA
*
40771807 ACAATGCCAATGTCCCAGACATGGTCTTACATGTAATATCAATACA-ATGCCAATGT-CCAGACA
1 ACAATGCC-ATATCCCAGACATGGTCTTACATGT--TATC-ATACACATGCCAATGTCCCAGACA
* *
40771870 TGGTCTTACATGTAATC
62 GGGTCTTACATGAAATC
40771887 ATATCTCAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
85 30 0.43
86 31 0.44
88 4 0.06
89 5 0.07
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (83 bp):
ACAATGCCATATCCCAGACATGGTCTTACATGTTATCATACACATGCCAATGTCCCAGACAGGGT
CTTACATGAAATCGATTA
Found at i:40772425 original size:29 final size:29
Alignment explanation
Indices: 40772361--40772426 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
40772351 ATTTCATTTA
* *
40772361 TTTCACAATTTAACCCCTCAATTTACACT
1 TTTCTCAATTTAACCCCTCAATATACACT
* * *
40772390 TTTCTCAATTTAATCCCT-AATATGCATT
1 TTTCTCAATTTAACCCCTCAATATACACT
40772418 TTTACTCAA
1 TTT-CTCAA
40772427 AATAACTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.42
Consensus pattern (29 bp):
TTTCTCAATTTAACCCCTCAATATACACT
Found at i:40776838 original size:21 final size:21
Alignment explanation
Indices: 40776809--40776860 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
40776799 ACAGCGGTGA
* *
40776809 CGGTGAGATTAGTTATTGTAG
1 CGGTGAGATTAGATACTGTAG
*
40776830 CGGTAAGATTAGATACTGTAG
1 CGGTGAGATTAGATACTGTAG
*
40776851 CAGTGAGATT
1 CGGTGAGATT
40776861 CGAAACAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.33
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGTAG
Found at i:40785603 original size:12 final size:12
Alignment explanation
Indices: 40785588--40785622 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
40785578 AAAGAGGAGA
40785588 AGAAGAAGGATG
1 AGAAGAAGGATG
*
40785600 AGAATAAGGATG
1 AGAAGAAGGATG
40785612 AGAAGAAGGAT
1 AGAAGAAGGAT
40785623 AGCCGGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.11
Consensus pattern (12 bp):
AGAAGAAGGATG
Found at i:40793996 original size:28 final size:26
Alignment explanation
Indices: 40793954--40794011 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
40793944 ATTTTTATAA
* *
40793954 TTTTTAAAAATTAAATTAAAATTTGT
1 TTTTTAAAAATTAAAATAAAATTTAT
40793980 TTTTTAGAAAGATTAAAATAAAATTTAT
1 TTTTTA-AAA-ATTAAAATAAAATTTAT
40794008 TTTT
1 TTTT
40794012 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.21
27 3 0.11
28 19 0.68
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (26 bp):
TTTTTAAAAATTAAAATAAAATTTAT
Found at i:40795034 original size:3 final size:3
Alignment explanation
Indices: 40795026--40795057 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40795016 GCTTTAACAT
40795026 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40795058 TGTTACCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40795944 original size:13 final size:13
Alignment explanation
Indices: 40795926--40795951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40795916 TGGTAAAACA
40795926 TCTGAAGCTGTGG
1 TCTGAAGCTGTGG
40795939 TCTGAAGCTGTGG
1 TCTGAAGCTGTGG
40795952 ACTGTACGGA
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:0.15, C:0.15, G:0.38, T:0.31
Consensus pattern (13 bp):
TCTGAAGCTGTGG
Found at i:40799330 original size:6 final size:6
Alignment explanation
Indices: 40799319--40799345 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40799309 CGATAATACA
40799319 AGAGGG AGAGGG AGAGGG AGAGGG AGA
1 AGAGGG AGAGGG AGAGGG AGAGGG AGA
40799346 ATGGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:40805897 original size:42 final size:45
Alignment explanation
Indices: 40805811--40805897 Score: 108
Period size: 47 Copynumber: 1.9 Consensus size: 45
40805801 TTAAATATAA
* *
40805811 TTGTTCAAAATTAAATATATATTTCACTCCAATTTAATTTTTTAATCT
1 TTGTTCAAAATTAAATATATATTTCA---CAATATAATTCTTTAATCT
40805859 TTGTT-AAAATTAAATATATATTT-A-AATATAATTCTTTAA
1 TTGTTCAAAATTAAATATATATTTCACAATATAATTCTTTAA
40805898 AAAAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 13 0.35
46 1 0.03
47 18 0.49
48 5 0.14
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.49
Consensus pattern (45 bp):
TTGTTCAAAATTAAATATATATTTCACAATATAATTCTTTAATCT
Found at i:40817688 original size:8 final size:8
Alignment explanation
Indices: 40817675--40817704 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
40817665 CTGGGACCGA
40817675 ATTTTATC
1 ATTTTATC
40817683 ATTTTATC
1 ATTTTATC
40817691 ATTTTATC
1 ATTTTATC
40817699 ATTTTA
1 ATTTTA
40817705 AGCCTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTTATC
Found at i:40827499 original size:32 final size:34
Alignment explanation
Indices: 40827428--40827536 Score: 125
Period size: 34 Copynumber: 3.3 Consensus size: 34
40827418 ATATAATTAT
* * *
40827428 TTTTATATTAAATTATATTAAAATTTTTAAAATA
1 TTTTATTTTAAATTATATTAAAATATTTCAAATA
* **
40827462 CTTTATTTTAAATTATACTTTGAA-A-TT-AAATA
1 TTTTATTTTAAATTATA-TTAAAATATTTCAAATA
*
40827494 TTTTATATTAAATTATATTAAAATATTTCAAATA
1 TTTTATTTTAAATTATATTAAAATATTTCAAATA
40827528 TTTTATTTT
1 TTTTATTTT
40827537 TATATTTACT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 4 0.07
32 21 0.34
33 4 0.07
34 28 0.46
35 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTTATTTTAAATTATATTAAAATATTTCAAATA
Found at i:40834486 original size:24 final size:24
Alignment explanation
Indices: 40834440--40834487 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40834430 TAATGGTGAA
*
40834440 ATTATATTTCAATCAGATTTAATC
1 ATTATATTTCAATCAGATATAATC
* **
40834464 ATTATATTTTAATTTGATATAATC
1 ATTATATTTCAATCAGATATAATC
40834488 TATCATCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTATATTTCAATCAGATATAATC
Found at i:40841657 original size:30 final size:31
Alignment explanation
Indices: 40841621--40841682 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
40841611 GCAAGAAGAG
40841621 AAAGAAATATCTTGG-TTTTTTTTTGCTGAT
1 AAAGAAATATCTTGGTTTTTTTTTTGCTGAT
40841651 AAAGAAATATCTTGGTTTTTTTTTTGCTGAT
1 AAAGAAATATCTTGGTTTTTTTTTTGCTGAT
40841682 A
1 A
40841683 TTATTCTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.50
Consensus pattern (31 bp):
AAAGAAATATCTTGGTTTTTTTTTTGCTGAT
Found at i:40847550 original size:39 final size:38
Alignment explanation
Indices: 40847469--40847546 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 38
40847459 CATTTAAGTA
* *
40847469 ATTTTTTAAATTTTAAAAATTCAAAAAAATTATAAAACT
1 ATTTTTTAAATATTAAAAATT-AAAAAAATTATAAAAAT
*
40847508 ATTTTTTAAATATTAAAACATT--AAAAATTCTAAAAAT
1 ATTTTTTAAATATTAAAA-ATTAAAAAAATTATAAAAAT
40847545 AT
1 AT
40847547 ATTTATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 15 0.43
39 17 0.49
40 3 0.09
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (38 bp):
ATTTTTTAAATATTAAAAATTAAAAAAATTATAAAAAT
Found at i:40850122 original size:46 final size:46
Alignment explanation
Indices: 40850062--40850283 Score: 304
Period size: 46 Copynumber: 4.8 Consensus size: 46
40850052 TTTGACATGA
* * * * *
40850062 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
**
40850108 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* **
40850154 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
* *
40850200 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
40850245 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
40850284 TTTAGAGAGC
Statistics
Matches: 155, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
45 44 0.28
46 111 0.72
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:40850275 original size:91 final size:92
Alignment explanation
Indices: 40850062--40850283 Score: 340
Period size: 92 Copynumber: 2.4 Consensus size: 92
40850052 TTTGACATGA
* * * * * **
40850062 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAAATTGCCATGGTATCTTTCAA
*
40850126 CCATGGTCTTGTTCATTTCATATCACGT
65 CCATGGTCTTATTCATTTCATATCACGT
40850154 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAATTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAATTGCCATGGTATCTTTCAAC
*
40850219 CATGGTCTTATTC-TTTCATGTCACGT
66 CATGGTCTTATTCATTTCATATCACGT
40850245 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
40850284 TTTAGAGAGC
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
91 55 0.46
92 65 0.54
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAATTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCATATCACGT
Found at i:40850389 original size:54 final size:54
Alignment explanation
Indices: 40850321--40850458 Score: 222
Period size: 54 Copynumber: 2.6 Consensus size: 54
40850311 ATCCTTACAG
*
40850321 CGGGATTACTAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
* *
40850375 CGGGATTACCAGTCCAGGCTAAATCCCCTATAATATAAACTTATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
* * *
40850429 CAGGATTACCAGTCCATGCTAAATTCCCTG
1 CGGGATTACCAGTCCAGGCTAAATCCCCTG
40850459 CAACGACAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGT
Found at i:40855205 original size:11 final size:11
Alignment explanation
Indices: 40855189--40855216 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40855179 ACTAAATAAT
40855189 TAATAATAAAA
1 TAATAATAAAA
40855200 TAATAATAAAA
1 TAATAATAAAA
40855211 TAATAA
1 TAATAA
40855217 AATATCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:40855243 original size:20 final size:21
Alignment explanation
Indices: 40855190--40855265 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
40855180 CTAAATAATT
*
40855190 AATAATAAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
40855209 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
40855230 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
40855251 TAATCATAAAATATC
1 -AATAATAAAATATC
40855266 AACATCATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.26
20 12 0.26
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:40856726 original size:3 final size:3
Alignment explanation
Indices: 40856714--40856746 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
40856704 CAATTAGTTG
40856714 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40856747 GTAAATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:40858883 original size:93 final size:93
Alignment explanation
Indices: 40858753--40858925 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
40858743 CGCCCATAAG
* * *
40858753 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
40858818 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
*
40858846 CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
40858911 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
40858926 CAAATATCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:40858921 original size:46 final size:46
Alignment explanation
Indices: 40858746--40858921 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
40858736 TGTAACCCGC
* * *
40858746 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* * *
40858792 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACG-CTCG---CAT
* *
40858842 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
* *
40858885 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
40858922 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 67 0.61
47 31 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCAT
Found at i:40859455 original size:5 final size:5
Alignment explanation
Indices: 40859445--40859474 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
40859435 AATAATTAAG
40859445 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
40859475 AAAAGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:40869271 original size:15 final size:16
Alignment explanation
Indices: 40869251--40869280 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40869241 TTATCACTAC
40869251 TTAACAT-ATATGTGG
1 TTAACATAATATGTGG
40869266 TTAACATAATATGTG
1 TTAACATAATATGTG
40869281 TAACGCCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (16 bp):
TTAACATAATATGTGG
Found at i:40871274 original size:47 final size:47
Alignment explanation
Indices: 40871141--40871347 Score: 193
Period size: 47 Copynumber: 4.3 Consensus size: 47
40871131 ATAGTAAAAC
** * *
40871141 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * * *
40871190 TATGGTCTTACAC-GGATCACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* *
40871236 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * *
40871283 TATGGTCTTATACGGAAGCACATATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA-----CCGATGCCATAGCCCAGA
40871335 TATGGTCTTATAC
1 TATGGTCTTATAC
40871348 GAAAATCACA
Statistics
Matches: 133, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
46 27 0.20
47 56 0.42
48 10 0.08
49 13 0.10
52 27 0.20
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:40873595 original size:22 final size:22
Alignment explanation
Indices: 40873570--40873612 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40873560 ACTCTAGGTG
40873570 TACAAGTCTATAATCAAGAATA
1 TACAAGTCTATAATCAAGAATA
40873592 TACAAGTCTATAATCAAGAAT
1 TACAAGTCTATAATCAAGAAT
40873613 GAACATTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (22 bp):
TACAAGTCTATAATCAAGAATA
Found at i:40876434 original size:20 final size:20
Alignment explanation
Indices: 40876409--40876448 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40876399 GGTTTGAGAA
*
40876409 ACCATTTATTTGCATTAATG
1 ACCATTTATTTACATTAATG
40876429 ACCATTTATTTACATTAATG
1 ACCATTTATTTACATTAATG
40876449 TTTGAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (20 bp):
ACCATTTATTTACATTAATG
Found at i:40882139 original size:100 final size:100
Alignment explanation
Indices: 40882022--40882221 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
40882012 GTCTACTTCT
40882022 ATCCGTTTTTTCCCAATACTGTTTTGAGTAATATAGCTACTAGTCTGTTCCCTCTATCTTGTAAT
1 ATCCGTTTTTTCCCAATACTGTTTTGAGTAATATAGCTACTAGTCTGTTCCCTCTATCTTGTAAT
40882087 TATGTTTGTGTTGTGTTTGACATTGTTTTATGTTG
66 TATGTTTGTGTTGTGTTTGACATTGTTTTATGTTG
*
40882122 ATCCTTTTTTTCCCAATACTGTTTTGAGTAATATAGCTACTAGTCTGTTCCCTCTATCTTGTAAT
1 ATCCGTTTTTTCCCAATACTGTTTTGAGTAATATAGCTACTAGTCTGTTCCCTCTATCTTGTAAT
40882187 TATGTTTGTGTTGTGTTTGACATTGTTTTATGTTG
66 TATGTTTGTGTTGTGTTTGACATTGTTTTATGTTG
40882222 TTGGTGCAGA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.51
Consensus pattern (100 bp):
ATCCGTTTTTTCCCAATACTGTTTTGAGTAATATAGCTACTAGTCTGTTCCCTCTATCTTGTAAT
TATGTTTGTGTTGTGTTTGACATTGTTTTATGTTG
Found at i:40885384 original size:45 final size:45
Alignment explanation
Indices: 40885333--40885472 Score: 217
Period size: 45 Copynumber: 3.1 Consensus size: 45
40885323 CAAATAGGTT
*
40885333 ATTGAGCTTTAATTTTTATTAGAATCTAAAGCTAGTAATCTTTTG
1 ATTGAGCTTTAATTTTTATTAGCATCTAAAGCTAGTAATCTTTTG
* *
40885378 ATTGAGCTTTAATTTTTATTAGCATCTAAACCTAGTAAACTTTTG
1 ATTGAGCTTTAATTTTTATTAGCATCTAAAGCTAGTAATCTTTTG
* * *
40885423 TTTGAGCTTCAATTTTTATTACCATCTAAAGCTAGTAATCTTTTG
1 ATTGAGCTTTAATTTTTATTAGCATCTAAAGCTAGTAATCTTTTG
*
40885468 TTTGA
1 ATTGA
40885473 AATAAAAACT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (45 bp):
ATTGAGCTTTAATTTTTATTAGCATCTAAAGCTAGTAATCTTTTG
Found at i:40885768 original size:19 final size:19
Alignment explanation
Indices: 40885744--40885780 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40885734 TACCAATGAA
*
40885744 ATAAATAAAATAGAAATAG
1 ATAAATAAAATAAAAATAG
*
40885763 ATAAATAATATAAAAATA
1 ATAAATAAAATAAAAATA
40885781 ATATTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
ATAAATAAAATAAAAATAG
Found at i:40885814 original size:22 final size:23
Alignment explanation
Indices: 40885763--40885814 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
40885753 ATAGAAATAG
40885763 ATAAATAATATAAAAATAATATT
1 ATAAATAATATAAAAATAATATT
* ***
40885786 A-ATATAATATTTTAAT-ATATT
1 ATAAATAATATAAAAATAATATT
40885807 ATAAATAA
1 ATAAATAA
40885815 AATATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAAATAATATAAAAATAATATT
Found at i:40885826 original size:24 final size:24
Alignment explanation
Indices: 40885765--40885879 Score: 63
Period size: 24 Copynumber: 4.7 Consensus size: 24
40885755 AGAAATAGAT
* * *
40885765 AAATAATATAAAAATAATATTAATA
1 AAAT-ATATAAATATATTATAAATA
* * *
40885790 TAATATTTTAATATATTATAAATA
1 AAATATATAAATATATTATAAATA
* *
40885814 AAATATATAAATAAATTCTAATACTA
1 AAATATATAAATATATTATAA-A-TA
*
40885840 ATATATATTAGAATATA-TAT-AATA
1 AAATATA-TA-AATATATTATAAATA
* * *
40885864 GATTAGATAAATATAT
1 AAATATATAAATATAT
40885880 AATAGAATTA
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
22 6 0.09
23 2 0.03
24 36 0.54
25 5 0.07
26 9 0.13
27 4 0.06
28 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.39
Consensus pattern (24 bp):
AAATATATAAATATATTATAAATA
Found at i:40896410 original size:85 final size:89
Alignment explanation
Indices: 40896295--40896654 Score: 538
Period size: 95 Copynumber: 4.0 Consensus size: 89
40896285 TAAACTGTAA
*
40896295 AATTAAGACAAACAACCAAAAACAG-C-AAAAAAAAG-AAGAAGAA-GGGTGAAACATATATTTA
1 AATTAAGACAAACAACCAAAAACAGACAAAAAAAAAGAAAAAAGAAGGGGTGAAACATATATTTA
40896356 AATCATAGAGTCAATAGGTGTATC
66 AATCATAGAGTCAATAGGTGTATC
*
40896380 AATTAAGACAAACAACCAAAAACAG-C-AAAAAAAAG-AAGAAGAA-GGGTGAAACATATATTTA
1 AATTAAGACAAACAACCAAAAACAGACAAAAAAAAAGAAAAAAGAAGGGGTGAAACATATATTTA
40896441 AATCATAGAGTCAATAGGTGTATC
66 AATCATAGAGTCAATAGGTGTATC
40896465 AATTAAGACAAACAACCAAAAACAGCAACAAAAAAAAAAGAAAAAAAAAGAAGGGGTGAAACATA
1 AATTAAGACAAACAACCAAAAACAG--AC-AAAAAAAAAG---AAAAAAGAAGGGGTGAAACATA
40896530 TATTTAAATCATAGAGTCAATAGGTGTATC
60 TATTTAAATCATAGAGTCAATAGGTGTATC
40896560 AATTAAGACAAACAACCAAAAACAGCAACAAAAAAAAAAGAAAAAAAAAGAAGGGGTGAAACATA
1 AATTAAGACAAACAACCAAAAACAG--AC-AAAAAAAAAG---AAAAAAGAAGGGGTGAAACATA
40896625 TATTTAAATCATAGAGTCAATAGGTGTATC
60 TATTTAAATCATAGAGTCAATAGGTGTATC
40896655 TGAATCCTAT
Statistics
Matches: 264, Mismatches: 1, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
85 110 0.42
88 1 0.00
90 9 0.03
94 7 0.03
95 137 0.52
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.17
Consensus pattern (89 bp):
AATTAAGACAAACAACCAAAAACAGACAAAAAAAAAGAAAAAAGAAGGGGTGAAACATATATTTA
AATCATAGAGTCAATAGGTGTATC
Found at i:40899613 original size:23 final size:23
Alignment explanation
Indices: 40899531--40899617 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
40899521 CCTGATCAGT
*
40899531 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
40899553 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
40899573 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
40899596 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
40899618 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:40901087 original size:16 final size:17
Alignment explanation
Indices: 40901052--40901087 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
40901042 CCTAATTCTC
40901052 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
40901068 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
40901083 CCTTC
1 CCTTC
40901088 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:40915840 original size:9 final size:9
Alignment explanation
Indices: 40915828--40915914 Score: 52
Period size: 9 Copynumber: 9.7 Consensus size: 9
40915818 AAAATTAAAT
40915828 GAATTAACC
1 GAATTAACC
*
40915837 GAATTAATC
1 GAATTAACC
*
40915846 AAATTAACC
1 GAATTAACC
40915855 GAATT-ACTC
1 GAATTAAC-C
* *
40915864 AAATT-ATC
1 GAATTAACC
* **
40915872 TAGATTAATT
1 GA-ATTAACC
*
40915882 AAATTAACC
1 GAATTAACC
**
40915891 GAATTAATT
1 GAATTAACC
40915900 GAATTAACC
1 GAATTAACC
40915909 GAATTA
1 GAATTA
40915915 TTTGTATAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
8 4 0.07
9 52 0.88
10 3 0.05
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (9 bp):
GAATTAACC
Found at i:40915843 original size:18 final size:18
Alignment explanation
Indices: 40915820--40915914 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
40915810 ATAAGTATAA
*
40915820 AATTAAATGAATTAACCG
1 AATTAAATAAATTAACCG
40915838 AATT-AATCAAATTAACCG
1 AATTAAAT-AAATTAACCG
* * *
40915856 AATT-ACTCAAATT-ATCT
1 AATTAAAT-AAATTAACCG
*
40915873 AGATTAATTAAATTAACCG
1 A-ATTAAATAAATTAACCG
* *
40915892 AATTAATTGAATTAACCG
1 AATTAAATAAATTAACCG
40915910 AATTA
1 AATTA
40915915 TTTGTATAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.09
18 54 0.83
19 5 0.08
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATTAAATAAATTAACCG
Found at i:40915869 original size:36 final size:36
Alignment explanation
Indices: 40915829--40915914 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
40915819 AAATTAAATG
*
40915829 AATTAACCGAATTAATCAAATTAACCGAATTACTCA
1 AATTAACCGAATTAATCAAATTAACCGAATTAATCA
* * * **
40915865 AATT-ATCTAGATTAATTAAATTAACCGAATTAATTG
1 AATTAACCGA-ATTAATCAAATTAACCGAATTAATCA
40915901 AATTAACCGAATTA
1 AATTAACCGAATTA
40915915 TTTGTATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
35 3 0.08
36 34 0.85
37 3 0.08
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.33
Consensus pattern (36 bp):
AATTAACCGAATTAATCAAATTAACCGAATTAATCA
Found at i:40920329 original size:17 final size:15
Alignment explanation
Indices: 40920300--40920333 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
40920290 CTTGCAAAAT
40920300 ATAAAATATATTTAA
1 ATAAAATATATTTAA
40920315 ATAATAATATAATTTAA
1 ATAA-AATAT-ATTTAA
40920332 AT
1 AT
40920334 TAGATCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATATATTTAA
Found at i:40923880 original size:12 final size:11
Alignment explanation
Indices: 40923864--40923897 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
40923854 GTTCTACTTG
40923864 ATTTTTCTTTT
1 ATTTTTCTTTT
40923875 ATTTTTCTTTTT
1 ATTTTTC-TTTT
40923887 ATTTTTCTTTT
1 ATTTTTCTTTT
40923898 TTGTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:40923898 original size:12 final size:12
Alignment explanation
Indices: 40923864--40923898 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
40923854 GTTCTACTTG
40923864 ATTTTTC-TTTT
1 ATTTTTCTTTTT
40923875 ATTTTTCTTTTT
1 ATTTTTCTTTTT
40923887 ATTTTTCTTTTT
1 ATTTTTCTTTTT
40923899 TGTTTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (12 bp):
ATTTTTCTTTTT
Found at i:40923904 original size:12 final size:11
Alignment explanation
Indices: 40923865--40923904 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
40923855 TTCTACTTGA
*
40923865 TTTTTCTTTTA
1 TTTTTCTTTTT
40923876 TTTTTCTTTTT
1 TTTTTCTTTTT
40923887 ATTTTTCTTTTT
1 -TTTTTCTTTTT
40923899 TGTTTT
1 T-TTTT
40923905 TTACCACACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.05, C:0.07, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:40932835 original size:6 final size:6
Alignment explanation
Indices: 40932824--40932856 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40932814 AAACCCTTTA
*
40932824 CATGCT CATGCT CATGCT CATGCT TATGCT CAT
1 CATGCT CATGCT CATGCT CATGCT CATGCT CAT
40932857 TTCATTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.36
Consensus pattern (6 bp):
CATGCT
Found at i:40934106 original size:17 final size:18
Alignment explanation
Indices: 40934078--40934111 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40934068 ATAACTTTTA
40934078 AAAGTAAAAACAAAAAAT
1 AAAGTAAAAACAAAAAAT
40934096 AAAGT-AAAACAAAAAA
1 AAAGTAAAAACAAAAAA
40934112 GAAGAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAGTAAAAACAAAAAAT
Found at i:40944809 original size:12 final size:12
Alignment explanation
Indices: 40944792--40944817 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40944782 ATGTGCCGAC
40944792 TACCGTTACTGT
1 TACCGTTACTGT
40944804 TACCGTTACTGT
1 TACCGTTACTGT
40944816 TA
1 TA
40944818 TCGATTCGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (12 bp):
TACCGTTACTGT
Found at i:40944848 original size:45 final size:45
Alignment explanation
Indices: 40944798--40944895 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
40944788 CGACTACCGT
* * *
40944798 TACTGTTACCGTTACTGTTATCGATTCGGCACTTTGTGTGTCAAA
1 TACTGTTACCGTAACCGTTATCGATTCAGCACTTTGTGTGTCAAA
* **
40944843 TACTGTTACTGTAACCGTTATCGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTAACCGTTATCGATTCAGCACTTTGTGTGTCAAA
40944888 TACTGTTA
1 TACTGTTA
40944896 TTGTTGCTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTAACCGTTATCGATTCAGCACTTTGTGTGTCAAA
Found at i:40945135 original size:18 final size:18
Alignment explanation
Indices: 40945087--40945172 Score: 109
Period size: 18 Copynumber: 4.7 Consensus size: 18
40945077 AAAGATCGAC
* *
40945087 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAA-CTGAT
40945106 TGTTACTGAATAACTGAT
1 TGTTACTGAATAACTGAT
* * *
40945124 TATTATTGAATAATTGAT
1 TGTTACTGAATAACTGAT
*
40945142 TGTTACCGAATAACTGAT
1 TGTTACTGAATAACTGAT
40945160 TGTTACTGAATAA
1 TGTTACTGAATAA
40945173 ATTATCGTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
18 44 0.77
19 13 0.23
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (18 bp):
TGTTACTGAATAACTGAT
Found at i:40945153 original size:36 final size:37
Alignment explanation
Indices: 40945089--40945172 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 37
40945079 AGATCGACTG
*
40945089 TTACTGAATAATTTAATTGTTACTGAATAACTGATTA
1 TTACTGAATAATTTAATTGTTACCGAATAACTGATTA
* * *
40945126 TTATTGAATAA-TTGATTGTTACCGAATAACTGATTG
1 TTACTGAATAATTTAATTGTTACCGAATAACTGATTA
40945162 TTACTGAATAA
1 TTACTGAATAA
40945173 ATTATCGTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 32 0.76
37 10 0.24
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (37 bp):
TTACTGAATAATTTAATTGTTACCGAATAACTGATTA
Found at i:40955712 original size:22 final size:23
Alignment explanation
Indices: 40955687--40955732 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
40955677 CAACCAAATC
40955687 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
40955709 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
40955732 A
1 A
40955733 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:40955738 original size:23 final size:23
Alignment explanation
Indices: 40955694--40955738 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40955684 ATCAATTCAA
*
40955694 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
40955717 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
40955739 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:40959300 original size:54 final size:54
Alignment explanation
Indices: 40959266--40959638 Score: 746
Period size: 54 Copynumber: 6.9 Consensus size: 54
40959256 CTCTAATGAG
40959266 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
40959320 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
40959374 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
40959428 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
40959482 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
40959536 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
40959590 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGA
1 GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGA
40959639 CTTTTTCCTT
Statistics
Matches: 319, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 319 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (54 bp):
GTCGGGATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATT
Found at i:40960053 original size:37 final size:37
Alignment explanation
Indices: 40959985--40960055 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
40959975 TTATCGTTTG
* *
40959985 TTTCTATTAAAAATAGACTCATTTATAATTCTAGCCA
1 TTTCTATTAAAAATAGACTCATTAAGAATTCTAGCCA
* *
40960022 TTTCTCTTAAAAATAGACTCATTAAGGATTCTAG
1 TTTCTATTAAAAATAGACTCATTAAGAATTCTAG
40960056 ATATATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (37 bp):
TTTCTATTAAAAATAGACTCATTAAGAATTCTAGCCA
Found at i:40962487 original size:6 final size:6
Alignment explanation
Indices: 40962478--40962507 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
40962468 GAAAAAATAT
40962478 AAATGG AAATGG AAATGG AAATGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG
40962508 GGAAGAATAA
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:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:40965431 original size:18 final size:18
Alignment explanation
Indices: 40965396--40965431 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40965386 TAAATATTTC
*
40965396 GAGTTATTTAGATTAATT
1 GAGTTATTTAGATCAATT
*
40965414 GAGTTATTTGGATCAATT
1 GAGTTATTTAGATCAATT
40965432 TGAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (18 bp):
GAGTTATTTAGATCAATT
Found at i:40969067 original size:14 final size:15
Alignment explanation
Indices: 40969038--40969071 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40969028 ATTCCATTTG
*
40969038 AATAATTTTTCGAAA
1 AATAATTTTACGAAA
*
40969053 AATAATTTTACAAAA
1 AATAATTTTACGAAA
40969068 AATA
1 AATA
40969072 TTATTTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (15 bp):
AATAATTTTACGAAA
Found at i:40979144 original size:31 final size:31
Alignment explanation
Indices: 40979106--40979169 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
40979096 TCTCTGAGTG
40979106 TTAATTTAATATGCAATT-TATAT-TATAAATT
1 TTAATTTAATAT--AATTATATATATATAAATT
* *
40979137 TTAATTTAGTATAATTATATATATATGAATT
1 TTAATTTAATATAATTATATATATATAAATT
40979168 TT
1 TT
40979170 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 5 0.17
31 20 0.69
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (31 bp):
TTAATTTAATATAATTATATATATATAAATT
Found at i:40979227 original size:29 final size:25
Alignment explanation
Indices: 40979165--40979218 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
40979155 ATATATATGA
* * *
40979165 ATTTTTTTATTAAATACATCAAATT
1 ATTTTTGTATTAAATAAATAAAATT
40979190 ATTTTTGTATTAAATAAATAAAATT
1 ATTTTTGTATTAAATAAATAAAATT
40979215 ATTT
1 ATTT
40979219 GTATATGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTTTGTATTAAATAAATAAAATT
Found at i:40987881 original size:61 final size:61
Alignment explanation
Indices: 40987768--40987895 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 61
40987758 TCCTAAATAT
* ** ** * **
40987768 TAAAAAAATTAACAAATTTAGACCTCAATGTTTACAAAATTTATCATTTTAGTTCTAGTTC
1 TAAAAAAATCAACAAATTTAGACCTCAACATTTACAAAATTTATCAAATTAGTCCTAACTC
* *
40987829 TAAAAAAATCAATAAATTTAG-CTCTCAACATTTACAAAATTTGTCAAATTAGTCCTAACTC
1 TAAAAAAATCAACAAATTTAGAC-CTCAACATTTACAAAATTTATCAAATTAGTCCTAACTC
40987890 TAAAAA
1 TAAAAA
40987896 TTTTATTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 55 0.98
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (61 bp):
TAAAAAAATCAACAAATTTAGACCTCAACATTTACAAAATTTATCAAATTAGTCCTAACTC
Found at i:40992146 original size:15 final size:15
Alignment explanation
Indices: 40992126--40992155 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40992116 TCAAATAATT
*
40992126 TTTATATTATATTAA
1 TTTATATAATATTAA
40992141 TTTATATAATATTAA
1 TTTATATAATATTAA
40992156 ATAAAATATG
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):
TTTATATAATATTAA
Found at i:40997686 original size:69 final size:69
Alignment explanation
Indices: 40997575--40997704 Score: 251
Period size: 69 Copynumber: 1.9 Consensus size: 69
40997565 CTTCAGATAT
*
40997575 GCTTCATGCAAACTTTGGTTATAGCTTGGAATCATTATTCTACATGATCATAGCATAGTTTCTAT
1 GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTTCTAT
40997640 CTCG
66 CTCG
40997644 GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTT
1 GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTT
40997705 TAGCATCCCA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (69 bp):
GCTTCATGCAAACTTTGGTTATAGCTTGAAATCATTATTCTACATGATCATAGCATAGTTTCTAT
CTCG
Found at i:41003192 original size:23 final size:23
Alignment explanation
Indices: 41003166--41003238 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
41003156 AGTGCCACAT
41003166 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
41003189 TGATATGTAGCC-ATAGCTACCAC
1 TGATATGTAGCCGA-AGCTACCAC
*
41003212 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
41003235 TGAT
1 TGAT
41003239 CAATAACACT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 44 0.96
24 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:41003338 original size:8 final size:8
Alignment explanation
Indices: 41003325--41003353 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
41003315 ACCCGGGACT
41003325 CACTGTAA
1 CACTGTAA
41003333 CACTGTAA
1 CACTGTAA
41003341 CACTGTAA
1 CACTGTAA
41003349 CACTG
1 CACTG
41003354 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:41010118 original size:58 final size:59
Alignment explanation
Indices: 41010003--41010128 Score: 164
Period size: 58 Copynumber: 2.1 Consensus size: 59
41009993 GACTTACTGA
* * *
41010003 GTAATTAGTGAGGCCGAGGAAACTTTAATTTGATTTGTTTCCAAAATTGTGGGTGTAATAAG
1 GTAATTAGTGAGGACGAGGAAAC--T-ATTTGATTTGTTTCCAAAAGTATGGGTGTAATAAG
* * *
41010065 GTAATTAGTGAGGACGAGGAAAC-CTTTGATTTGTTTCCAAAGGTATGGTTGTAATAAG
1 GTAATTAGTGAGGACGAGGAAACTATTTGATTTGTTTCCAAAAGTATGGGTGTAATAAG
41010123 GTAATT
1 GTAATT
41010129 TATTTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 36 0.62
62 22 0.38
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (59 bp):
GTAATTAGTGAGGACGAGGAAACTATTTGATTTGTTTCCAAAAGTATGGGTGTAATAAG
Found at i:41011976 original size:60 final size:62
Alignment explanation
Indices: 41011902--41012024 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 62
41011892 TTAGTCAAAT
* *
41011902 AATATAAAATAGTATATAAATATT-ATTTGGTAAAAATAAAATTT-AATAATTACAATATCTA
1 AATATAAAATAGTATATAAATATTAATTAGATAAAAAT-AAATTTAAATAATTACAATATCTA
* *
41011963 AATAT-AAATAGTATCTAAATATTAATTAGATAAAAATAAATTTAAATAATTATAATATCTA
1 AATATAAAATAGTATATAAATATTAATTAGATAAAAATAAATTTAAATAATTACAATATCTA
41012024 A
1 A
41012025 TACAAATTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
60 23 0.41
61 33 0.59
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (62 bp):
AATATAAAATAGTATATAAATATTAATTAGATAAAAATAAATTTAAATAATTACAATATCTA
Found at i:41014108 original size:22 final size:22
Alignment explanation
Indices: 41014080--41014121 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41014070 TATTTATATT
41014080 TTTTTAATGAAATTTAATAATA
1 TTTTTAATGAAATTTAATAATA
**
41014102 TTTTTAATTTAATTTAATAA
1 TTTTTAATGAAATTTAATAA
41014122 ACTAATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTTTAATGAAATTTAATAATA
Found at i:41016288 original size:75 final size:75
Alignment explanation
Indices: 41016181--41016454 Score: 514
Period size: 75 Copynumber: 3.7 Consensus size: 75
41016171 ACTAGTCGGA
* *
41016181 TTAACCGACGGTAATGAA-TGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAG
1 TTAACCTACGATAA-GAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAG
41016245 TGCTAGCCGAG
65 TGCTAGCCGAG
41016256 TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAGT
1 TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAGT
41016321 GCTAGCCGAG
66 GCTAGCCGAG
41016331 TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAGT
1 TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAGT
41016396 GCTAGCCGAG
66 GCTAGCCGAG
41016406 TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAAC
1 TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAAC
41016455 GGTGAATTGC
Statistics
Matches: 196, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
74 3 0.02
75 193 0.98
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (75 bp):
TTAACCTACGATAAGAATTGTGAGCCCAGCTCTAGTTGGATAAACCAACAATATTTGTACCCAGT
GCTAGCCGAG
Found at i:41022389 original size:38 final size:38
Alignment explanation
Indices: 41022203--41022390 Score: 191
Period size: 38 Copynumber: 4.9 Consensus size: 38
41022193 CGAGGTATAA
* * * * *
41022203 AACCCAAACATAACACCAGCACGAAGCCTACGGGACTTT
1 AACCCAGATATAATACCAGCACTAAGCCTGCGGGA-TTT
* * *
41022242 AAACTCAGATATAATACCAGCACTAGGCCTGCGAGATTT
1 -AACCCAGATATAATACCAGCACTAAGCCTGCGGGATTT
* * *
41022281 AGCCCGGATATAATACCAGCA-TGAAGCCTGCAGGATTT
1 AACCCAGATATAATACCAGCACT-AAGCCTGCGGGATTT
* * *
41022319 AACCCGGATATATTACCAGCACGAAGCCTGCGGGATTT
1 AACCCAGATATAATACCAGCACTAAGCCTGCGGGATTT
*
41022357 AACCCAGATATAATTCCAGCA-TATAGCCTGCGGG
1 AACCCAGATATAATACCAGCACTA-AGCCTGCGGG
41022391 TCTTTAAGCC
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
37 2 0.02
38 91 0.74
39 3 0.02
40 27 0.22
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (38 bp):
AACCCAGATATAATACCAGCACTAAGCCTGCGGGATTT
Found at i:41024763 original size:28 final size:28
Alignment explanation
Indices: 41024723--41024781 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
41024713 CAATCACAAT
41024723 TATTCATTCTTTAAAACTAACATTCAAC
1 TATTCATTCTTTAAAACTAACATTCAAC
41024751 TATTCATTCTTTAAAACTAACATTCAAC
1 TATTCATTCTTTAAAACTAACATTCAAC
41024779 TAT
1 TAT
41024782 CAATAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (28 bp):
TATTCATTCTTTAAAACTAACATTCAAC
Found at i:41024791 original size:28 final size:28
Alignment explanation
Indices: 41024723--41024791 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
41024713 CAATCACAAT
**
41024723 TATTCATTCTTTAAAACTAACATTCAAC
1 TATTCATAATTTAAAACTAACATTCAAC
**
41024751 TATTCATTCTTTAAAACTAACATTCAAC
1 TATTCATAATTTAAAACTAACATTCAAC
41024779 TA-TCAATAATTTA
1 TATTC-ATAATTTA
41024792 GCAAAAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 2 0.05
28 36 0.95
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (28 bp):
TATTCATAATTTAAAACTAACATTCAAC
Found at i:41025613 original size:13 final size:13
Alignment explanation
Indices: 41025595--41025621 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41025585 ACCAAAATCA
41025595 TAATTATAATAAT
1 TAATTATAATAAT
41025608 TAATTATAATAAT
1 TAATTATAATAAT
41025621 T
1 T
41025622 CCGATAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTATAATAAT
Found at i:41034087 original size:15 final size:15
Alignment explanation
Indices: 41034067--41034095 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41034057 TCATAAGTCA
41034067 ATGCCAATGTCCTAG
1 ATGCCAATGTCCTAG
41034082 ATGCCAATGTCCTA
1 ATGCCAATGTCCTA
41034096 ACTATTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (15 bp):
ATGCCAATGTCCTAG
Found at i:41040069 original size:46 final size:47
Alignment explanation
Indices: 41040004--41040152 Score: 187
Period size: 46 Copynumber: 3.2 Consensus size: 47
41039994 TTTATCTTTG
* * * * *
41040004 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
**
41040050 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
* *
41040096 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
*
41040142 CAGGTTGCCAT
1 CATGTTGCCAT
41040153 TGTAATACCC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
45 4 0.04
46 86 0.96
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
Found at i:41060529 original size:14 final size:14
Alignment explanation
Indices: 41060510--41060542 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41060500 TTAAGACCTA
*
41060510 ATATATACATATGT
1 ATATATACATATAT
41060524 ATATATACATATAT
1 ATATATACATATAT
41060538 ATATA
1 ATATA
41060543 GTTTTGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:41066442 original size:31 final size:31
Alignment explanation
Indices: 41066407--41066467 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
41066397 ATTAATATAA
* *
41066407 ATTCAAAATAGATAAAATAAATCACCTCTAC
1 ATTCAAAACAAATAAAATAAATCACCTCTAC
41066438 ATTCAAAACAAATAAAATAAATCACCTCTA
1 ATTCAAAACAAATAAAATAAATCACCTCTA
41066468 GACAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.25
Consensus pattern (31 bp):
ATTCAAAACAAATAAAATAAATCACCTCTAC
Found at i:41066789 original size:22 final size:23
Alignment explanation
Indices: 41066764--41066808 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
41066754 ATACTCACAC
41066764 AACCA-TATCAACTTCAG-AAGCA
1 AACCATTATCAAC-TCAGTAAGCA
41066786 AACCATTATCAACTCAGTAAGCA
1 AACCATTATCAACTCAGTAAGCA
41066809 TACAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.44, C:0.27, G:0.09, T:0.20
Consensus pattern (23 bp):
AACCATTATCAACTCAGTAAGCA
Found at i:41067488 original size:31 final size:30
Alignment explanation
Indices: 41067445--41067524 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
41067435 CATGTGTACT
*
41067445 TTAATATACTAAATTAAACACTAAAATTAAA
1 TTAA-ATACTAAATTAAACACTAAAATCAAA
***
41067476 CTTAAATACTAAATTAAATTTTAAAATCAAA
1 -TTAAATACTAAATTAAACACTAAAATCAAA
41067507 TTAAAATACTAAATTAAA
1 TT-AAATACTAAATTAAA
41067525 AAAATTCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.05
31 37 0.86
32 4 0.09
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (30 bp):
TTAAATACTAAATTAAACACTAAAATCAAA
Found at i:41067500 original size:19 final size:19
Alignment explanation
Indices: 41067454--41067493 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
41067444 TTTAATATAC
41067454 TAAA-TTAAACACTAAAAT
1 TAAACTTAAACACTAAAAT
*
41067472 TAAACTTAAATACT-AAAT
1 TAAACTTAAACACTAAAAT
41067490 TAAA
1 TAAA
41067494 TTTTAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAACTTAAACACTAAAAT
Found at i:41068312 original size:14 final size:14
Alignment explanation
Indices: 41068295--41068327 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41068285 ATAATATCCG
41068295 AATAATAACAATAA
1 AATAATAACAATAA
*
41068309 AATAATAACAATAT
1 AATAATAACAATAA
41068323 AATAA
1 AATAA
41068328 CAATATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAACAATAA
Found at i:41068324 original size:22 final size:22
Alignment explanation
Indices: 41068298--41068353 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
41068288 ATATCCGAAT
*
41068298 AATAACAATAAAATAATAACAA
1 AATAACAACAAAATAATAACAA
* * * *
41068320 TATAATAACAATATGATAACAA
1 AATAACAACAAAATAATAACAA
41068342 AATAACAACAAA
1 AATAACAACAAA
41068354 TAACAAGAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (22 bp):
AATAACAACAAAATAATAACAA
Found at i:41079258 original size:61 final size:61
Alignment explanation
Indices: 41079179--41079294 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 61
41079169 TAGATTAGAA
* *
41079179 ACAGCATTTTAACAAACATTGACGAAGCTA-GGGTGTAATCAAGCTGAGTTGAGTCCAAAT
1 ACAGCATTTTAACAAACATTGACAAAGCTAGGGGTGTAATCAAGCTGAGCTGAGTCCAAAT
41079239 ACAGTCATTTTAACAAACATTGACAAAGCTAGGGGTGTAATCAAGCTGAGCTGAGT
1 ACAG-CATTTTAACAAACATTGACAAAGCTAGGGGTGTAATCAAGCTGAGCTGAGT
41079295 TCGAATATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 4 0.08
61 25 0.48
62 23 0.44
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (61 bp):
ACAGCATTTTAACAAACATTGACAAAGCTAGGGGTGTAATCAAGCTGAGCTGAGTCCAAAT
Found at i:41080794 original size:53 final size:53
Alignment explanation
Indices: 41080736--41080838 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
41080726 CAGGATCCTA
41080736 CAACATTTTGAAAAAGATCACTTCGGTTAATATAGATGGAACAGGAAACCGTC
1 CAACATTTTGAAAAAGATCACTTCGGTTAATATAGATGGAACAGGAAACCGTC
41080789 CAACATTTTGAAAAAGATCACTTCGGTTAATATAGATGGAACAGGAAACC
1 CAACATTTTGAAAAAGATCACTTCGGTTAATATAGATGGAACAGGAAACC
41080839 TTCATCGAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (53 bp):
CAACATTTTGAAAAAGATCACTTCGGTTAATATAGATGGAACAGGAAACCGTC
Found at i:41082436 original size:18 final size:19
Alignment explanation
Indices: 41082403--41082443 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
41082393 ACTAAAATTC
41082403 AAATATAACCTTTTAAAAGT
1 AAATATAA-CTTTTAAAAGT
*
41082423 AAATATAA-TTTTAAAGGT
1 AAATATAACTTTTAAAAGT
41082441 AAA
1 AAA
41082444 AGTGTCGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (19 bp):
AAATATAACTTTTAAAAGT
Found at i:41090232 original size:18 final size:18
Alignment explanation
Indices: 41090209--41090246 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41090199 TGCCACGGCG
*
41090209 AGGTGAGCGAAATCTAAT
1 AGGTGAACGAAATCTAAT
*
41090227 AGGTGAACGAGATCTAAT
1 AGGTGAACGAAATCTAAT
41090245 AG
1 AG
41090247 AACATAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (18 bp):
AGGTGAACGAAATCTAAT
Found at i:41101963 original size:16 final size:16
Alignment explanation
Indices: 41101942--41101974 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41101932 AAAATTTGTG
41101942 AGTACAACAATAATTC
1 AGTACAACAATAATTC
41101958 AGTACAACAATAATTC
1 AGTACAACAATAATTC
41101974 A
1 A
41101975 ATCTAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
AGTACAACAATAATTC
Found at i:41103680 original size:16 final size:16
Alignment explanation
Indices: 41103659--41103695 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
41103649 ATATAGGACA
41103659 TGGTTCAAACTACGAT
1 TGGTTCAAACTACGAT
41103675 TGGTTCAAACTACGAT
1 TGGTTCAAACTACGAT
41103691 TGGTT
1 TGGTT
41103696 GAATGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (16 bp):
TGGTTCAAACTACGAT
Found at i:41115409 original size:87 final size:85
Alignment explanation
Indices: 41115317--41115818 Score: 316
Period size: 87 Copynumber: 5.9 Consensus size: 85
41115307 ATTTTAATTC
* * *
41115317 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
1 GCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCAATCTGCTCCACTGTAATCTCAGGGAG
41115382 ATAAGATTTCTGGCCTCAATCT
66 ATAAGA--TCTGGCCTCAATCT
* * * *
41115404 GCTCCACTGTAACCTCAGGGAGATAAGAT-CTGACATTCTTTAGTCTGTTCCACTGTAATCTCAG
1 GCTCCACTGTAACTTCAGGGAGATAAGATACTG----TCTTCAATCTGCTCCACTGTAATCTCAG
* * * *
41115468 GGAAATAAGACCTGG--TGCGATCC
62 GGAGATAAGATCTGGCCT-CAATCT
* * *** *
41115491 GCTCTACTGTAACTTCAGAGAGATACTTTA-T-T-TT-AATCCGCTCCACTGTAA-CTTCAGGGA
1 GCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCAATCTGCTCCACTGTAATC-TCAGGGA
* * * * *
41115551 GATAGGATAGTGTCTTCGATCT
65 GATAAGAT-CTGGCCTCAATCT
* * * * *
41115573 GCTCCGCTGTAA-TCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGG
1 GCTCCACTGTAACT-TCAGGGAGATAAGA-TACTGTCTTCAATCTGCTCCACTGTAATCTCAGGG
* * *
41115637 AGATAAGATCTGACATTCTTTAGTCT
64 AGATAAGATCTGGC---C-TCAATCT
* * * * * * * * *
41115663 GTTCCACTGTAA-TCTCAGGGAAATAAGA-CCTG-GTGCGATCCGCTCTACTGTAA-CTTCAGAG
1 GCTCCACTGTAACT-TCAGGGAGATAAGATACTGTCTTCAATCTGCTCCACTGTAATC-TCAGGG
* * *
41115724 AGATAAGATC---CTTTAATCC
64 AGATAAGATCTGGCCTCAATCT
* * * *
41115743 GCTCCACTGTAACTTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAACTTCAGGGAGATAAGA-TACTGTCTTCAATCTGCTCCACTGTAATCTCAGGGA
41115808 GATAAGATCTG
65 GATAAGATCTG
41115819 TAATTCTTTG
Statistics
Matches: 317, Mismatches: 69, Indels: 60
0.71 0.15 0.13
Matches are distributed among these distances:
79 1 0.00
80 54 0.17
81 6 0.02
82 28 0.09
83 32 0.10
84 3 0.01
86 8 0.03
87 115 0.36
88 8 0.03
90 62 0.20
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (85 bp):
GCTCCACTGTAACTTCAGGGAGATAAGATACTGTCTTCAATCTGCTCCACTGTAATCTCAGGGAG
ATAAGATCTGGCCTCAATCT
Found at i:41115414 original size:44 final size:42
Alignment explanation
Indices: 41115317--41115815 Score: 288
Period size: 44 Copynumber: 11.7 Consensus size: 42
41115307 ATTTTAATTC
* ** *
41115317 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCT
1 GCTCCACTGTAAC-TCAGGGAGATAAGATTCTGGCTTCAATCT
* *
41115360 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCT
1 GCTCCACTGTAA-CTCAGGGAGATAAGA-TTCTGGCTTCAATCT
* *
41115404 GCTCCACTGTAACCTCAGGGAGATAAGA-TCTGACATTCTTTAGTCT
1 GCTCCACTGTAA-CTCAGGGAGATAAGATTCTGGC-TTC---AATCT
* * * * * *
41115450 GTTCCACTGTAATCTCAGGGAAATAAGA-CCTGG-TGCGATCC
1 GCTCCACTGTAA-CTCAGGGAGATAAGATTCTGGCTTCAATCT
* * * ** * *
41115491 GCTCTACTGTAACTTCAGAGAGAT-A-CTT-T-ATTTTAATCC
1 GCTCCACTGTAAC-TCAGGGAGATAAGATTCTGGCTTCAATCT
* ** * *
41115530 GCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCT
1 GCTCCACTGTAAC-TCAGGGAGATAAGATTCTGGCTTCAATCT
* *
41115573 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCT
1 GCTCCACTGTAA-CTCAGGGAGATAAGA-TTCTGGCTTCAATCT
* *
41115617 GCTCCACTGTAACCTCAGGGAGATAAGA-TCTGACATTCTTTAGTCT
1 GCTCCACTGTAA-CTCAGGGAGATAAGATTCTGGC-TTC---AATCT
* * * * * *
41115663 GTTCCACTGTAATCTCAGGGAAATAAGA-CCTGG-TGCGATCC
1 GCTCCACTGTAA-CTCAGGGAGATAAGATTCTGGCTTCAATCT
* * * *
41115704 GCTCTACTGTAACTTCAGAGAGATAAGA-TC---CTTTAATCC
1 GCTCCACTGTAAC-TCAGGGAGATAAGATTCTGGCTTCAATCT
* ***
41115743 GCTCCACTGTAACTTCAGGGAGATAGGATTACTATATTCAATCT
1 GCTCCACTGTAAC-TCAGGGAGATAAGATT-CTGGCTTCAATCT
*
41115787 GCTCCGCTGTAATCTCAGGGAGATAAGAT
1 GCTCCACTGTAA-CTCAGGGAGATAAGAT
41115816 CTGTAATTCT
Statistics
Matches: 352, Mismatches: 77, Indels: 53
0.73 0.16 0.11
Matches are distributed among these distances:
39 58 0.16
40 4 0.01
41 47 0.13
42 11 0.03
43 57 0.16
44 110 0.31
45 1 0.00
46 64 0.18
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
GCTCCACTGTAACTCAGGGAGATAAGATTCTGGCTTCAATCT
Found at i:41115606 original size:213 final size:213
Alignment explanation
Indices: 41115298--41115815 Score: 928
Period size: 213 Copynumber: 2.4 Consensus size: 213
41115288 TAAAGAGATA
* *
41115298 AGATCCTTTATTTTAATTCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCT
1 AGATACTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCT
41115363 CCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAT
66 CCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAT
41115428 AAGATCTGACATTCTTTAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCCGC
131 AAGATCTGACATTCTTTAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCCGC
41115493 TCTACTGTAACTTCAGAG
196 TCTACTGTAACTTCAGAG
*
41115511 AGATACTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCT
1 AGATACTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCT
41115576 CCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAT
66 CCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAT
41115641 AAGATCTGACATTCTTTAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCCGC
131 AAGATCTGACATTCTTTAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCCGC
41115706 TCTACTGTAACTTCAGAG
196 TCTACTGTAACTTCAGAG
*** ** * * *
41115724 AGATAAGATCCTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTATATTCAATCTGC
1 AGATACTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCAATCTGC
41115789 TCCGCTGTAATCTCAGGGAGATAAGAT
65 TCCGCTGTAATCTCAGGGAGATAAGAT
41115816 CTGTAATTCT
Statistics
Matches: 292, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
213 252 0.86
214 40 0.14
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (213 bp):
AGATACTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCAATCTGCT
CCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCAATCTGCTCCACTGTAACCTCAGGGAGAT
AAGATCTGACATTCTTTAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCCGC
TCTACTGTAACTTCAGAG
Found at i:41117140 original size:67 final size:67
Alignment explanation
Indices: 41117006--41117132 Score: 254
Period size: 67 Copynumber: 1.9 Consensus size: 67
41116996 GGTTTTCGAC
41117006 TCAAGCCCTCTTTGGTCTCAAAGTGCCCTTTACGGGTTTTCACCTTAGCCTCTCCAAAGTCCCTT
1 TCAAGCCCTCTTTGGTCTCAAAGTGCCCTTTACGGGTTTTCACCTTAGCCTCTCCAAAGTCCCTT
41117071 TT
66 TT
41117073 TCAAGCCCTCTTTGGTCTCAAAGTGCCCTTTACGGGTTTTCACCTTAGCCTCTCCAAAGT
1 TCAAGCCCTCTTTGGTCTCAAAGTGCCCTTTACGGGTTTTCACCTTAGCCTCTCCAAAGT
41117133 TTTTTTTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.17, C:0.32, G:0.16, T:0.35
Consensus pattern (67 bp):
TCAAGCCCTCTTTGGTCTCAAAGTGCCCTTTACGGGTTTTCACCTTAGCCTCTCCAAAGTCCCTT
TT
Found at i:41137376 original size:27 final size:27
Alignment explanation
Indices: 41137341--41137401 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
41137331 AAATTATATT
* *
41137341 TTAATTTTTTATTTATAAAAT-AAATTAA
1 TTAA-TTTTTATATATAAAATCAAA-GAA
*
41137369 TTAATTTTTATATATTAAATCAAAGAA
1 TTAATTTTTATATATAAAATCAAAGAA
41137396 TTAATT
1 TTAATT
41137402 AATTATTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAATTTTTATATATAAAATCAAAGAA
Found at i:41139231 original size:26 final size:24
Alignment explanation
Indices: 41139177--41139251 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
41139167 CACTAAATCT
**
41139177 TTAAAAAAA-ACCTATTTAATTAA
1 TTAAAAAAAGACCTATTTAACCAA
41139200 TTAAAAAAAGACCTATTTAACCAA
1 TTAAAAAAAGACCTATTTAACCAA
* *
41139224 TTAAAAAAATCGACATTTTTAACCAA
1 TTAAAAAAA--GACCTATTTAACCAA
41139250 TT
1 TT
41139252 TAACCCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
23 9 0.20
24 21 0.47
26 15 0.33
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (24 bp):
TTAAAAAAAGACCTATTTAACCAA
Found at i:41155023 original size:19 final size:19
Alignment explanation
Indices: 41154993--41155064 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
41154983 AAAAAAATAA
41154993 ATTTTGGAATTTTTAAAATT
1 ATTTT-GAATTTTTAAAATT
*
41155013 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
41155032 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
*
41155052 ACTTTGAATTTTT
1 ATTTTGAATTTTT
41155065 TTTTGTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 25 0.52
20 23 0.48
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:41157391 original size:31 final size:32
Alignment explanation
Indices: 41157356--41157419 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
41157346 TTTAAAGTTG
41157356 AGTGACC-AAAATGTAAATTTACC-AATAATTT
1 AGTGACCTAAAATGT-AATTTACCAAATAATTT
*
41157387 AGTGACCTTAAATGTAATTTACCTAAATAATTT
1 AGTGACCTAAAATGTAATTTACC-AAATAATTT
41157420 TATATAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 15 0.52
32 6 0.21
33 8 0.28
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (32 bp):
AGTGACCTAAAATGTAATTTACCAAATAATTT
Found at i:41159546 original size:12 final size:12
Alignment explanation
Indices: 41159529--41159555 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41159519 GAATGATGCG
41159529 TTAAATCAAACT
1 TTAAATCAAACT
41159541 TTAAATCAAACT
1 TTAAATCAAACT
41159553 TTA
1 TTA
41159556 TTTGATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAATCAAACT
Found at i:41170203 original size:13 final size:14
Alignment explanation
Indices: 41170181--41170210 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41170171 TGAGTTTAAA
41170181 TTCAAGGTTTAGGG
1 TTCAAGGTTTAGGG
41170195 TTCAA-GTTTAGGG
1 TTCAAGGTTTAGGG
41170208 TTC
1 TTC
41170211 GAGATTCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.40
Consensus pattern (14 bp):
TTCAAGGTTTAGGG
Found at i:41171886 original size:13 final size:13
Alignment explanation
Indices: 41171868--41171892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41171858 ATGTATAATT
41171868 CAAGAACTAGTAC
1 CAAGAACTAGTAC
41171881 CAAGAACTAGTA
1 CAAGAACTAGTA
41171893 TCAATAAAAA
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (13 bp):
CAAGAACTAGTAC
Found at i:41180465 original size:21 final size:20
Alignment explanation
Indices: 41180428--41180466 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41180418 AAAGAAGATT
*
41180428 TATATTTTTCAATAATTTTA
1 TATATTTTTCAAGAATTTTA
*
41180448 TATATTTTTAGAAGAATTT
1 TATATTTTT-CAAGAATTT
41180467 AAATAGCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (20 bp):
TATATTTTTCAAGAATTTTA
Found at i:41181849 original size:24 final size:24
Alignment explanation
Indices: 41181822--41181867 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
41181812 TTTGTGTAAA
* *
41181822 TTTTGCATTAGTTTTTTTGTTTTT
1 TTTTGCATTAGATTTTATGTTTTT
* *
41181846 TTTTTCTTTAGATTTTATGTTT
1 TTTTGCATTAGATTTTATGTTT
41181868 AACAATACTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.11, C:0.04, G:0.11, T:0.74
Consensus pattern (24 bp):
TTTTGCATTAGATTTTATGTTTTT
Found at i:41182164 original size:196 final size:196
Alignment explanation
Indices: 41181490--41182387 Score: 862
Period size: 198 Copynumber: 4.6 Consensus size: 196
41181480 TATTTGATTG
** * * *
41181490 AATGGGTTTTTGTT-TTCCATTGAATTATGCTTATTTTAGATCTTTAACTTGGTGGGATTACAAG
1 AATGGGTTTTTGTTATTGTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAG
* ** * * ** ** * **
41181554 TAACTTGTGATGGGTAATCTTAATATGTTGAAGCTTGCAAAGAGACTAAAATTAATGGGGTTTTG
66 AAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTTG
* * * * * * * *** ****
41181619 TGTC-AGTTTTGCATTAGTTTTTGGTTTTTTCTCTTTACACTTCTATG-ATAGTTTATGTTATT-
131 TATCGA-ATTTGCATTAGGTTTTGGTGTTTT-TCTTTA-GCTTTTATGTTTA-ACAAAACCATTC
**
41181681 TGATT
192 AAATT
* * * * *
41181686 GAATGGGGTTTTGTTTTTTTATTGAATTATGCTTATTTAAGATCATTAACTTGGTGAGATTACAA
1 -AATGGGTTTTTGTTATTGTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAA
** * * * * *
41181751 GAAATTTATGATGGG-ACTCTTAATATGTTGAGGCTTGCAAAGAGAGTGAAATTAATGGGTTTTT
65 GAAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTT
* * * * * * * *
41181815 GTGT-AAATTTTGCATTAGTTTTTTTGTTTTTTTTTTCTTTAGATTTTATGTTTAACAATACTAT
130 GTATCGAA-TTTGCATTAG--GTTTTG--GTGTTTTTCTTTAGCTTTTATGTTTAACAAAACCAT
* *
41181879 TCGAGTT
190 TCAAATT
* * *
41181886 AATGGGTTTTTGTT-TTTTATTGAATTATGCTTATTTGAGATCTTTAACTTAGTGAGATTACAAG
1 AATGGGTTTTTGTTATTGTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAG
* * * *
41181950 AGAAATGTGATGGGTACTATTGATATGTTGCGGCTTGCAAAGAGTGTGAATTTAATGGTTTTTTG
66 AAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTTG
* * * **
41182015 TATCGAGTTTGCATTAGGTTTTGGGGGTTTTCTTTAGCTTTTATGTTTAACAAAACGGTTCAAAT
131 TATCGAATTTGCATTAGGTTTTGGTGTTTTTCTTTAGCTTTTATGTTTAACAAAACCATTCAAAT
41182080 T
196 T
*
41182081 GATGGGTTTTTGTTATTGT-TTGAATTATTGCTTATTTGAGATCCTTAACTTGGTGAGATTACAA
1 AATGGGTTTTTGTTATTGTATTGAATTA-TGCTTATTTGAGATCCTTAACTTGGTGAGATTACAA
* * * * *
41182145 GAAAAATGCGATGGGTACTATTAATATGTTGGGGCTTGTAAAGAGTGTAAAATTAGTGTTTTTTT
65 GAAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTT
* * *
41182210 GTATCGAATTCGCATTAGGTTTTGGTGTTTTTCTTTTGCTTTTATGTTTAACGAAACCATTCAAA
130 GTATCGAATTTGCATTAGGTTTTGGTGTTTTTCTTTAGCTTTTATGTTTAACAAAACCATTC---
41182275 AAATT
192 AAATT
* *
41182280 AATGGGTTTTTGTTATTG-GTTGAATTATGTTTATTTGAGATCCTTAACTTGGTGA-AGTTACAA
1 AATGGGTTTTTGTTATTGTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGA-TTACAA
* * *
41182343 GACAAATGTGATGGGTACTCTTAACATGTTGGGGCTTGCAAAGAG
65 GAAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAG
41182388 AGTTGGGGCC
Statistics
Matches: 599, Mismatches: 84, Indels: 35
0.83 0.12 0.05
Matches are distributed among these distances:
195 54 0.09
196 147 0.25
197 78 0.13
198 186 0.31
199 117 0.20
200 11 0.02
201 6 0.01
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (196 bp):
AATGGGTTTTTGTTATTGTATTGAATTATGCTTATTTGAGATCCTTAACTTGGTGAGATTACAAG
AAAAATGTGATGGGTACTATTAATATGTTGGGGCTTGCAAAGAGTGTGAAATTAATGGTTTTTTG
TATCGAATTTGCATTAGGTTTTGGTGTTTTTCTTTAGCTTTTATGTTTAACAAAACCATTCAAAT
T
Found at i:41187304 original size:16 final size:15
Alignment explanation
Indices: 41187275--41187327 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
41187265 AATCTTTGAC
* *
41187275 AATTTTTTTTATTTA
1 AATTATTTTAATTTA
*
41187290 ATTTACTTTTAATTTA
1 AATTA-TTTTAATTTA
41187306 AATTATTTTAAATTTA
1 AATTATTTT-AATTTA
41187322 AATTAT
1 AATTAT
41187328 AAATCGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 7 0.22
16 25 0.78
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTATTTTAATTTA
Found at i:41193378 original size:17 final size:17
Alignment explanation
Indices: 41193352--41193388 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
41193342 GTTGAACTAA
* *
41193352 TTTAATAAAATTTATAT
1 TTTAAAAAAATATATAT
41193369 TTTAAAAAAATATATAT
1 TTTAAAAAAATATATAT
41193386 TTT
1 TTT
41193389 TATGAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAAAAATATATAT
Found at i:41195743 original size:23 final size:22
Alignment explanation
Indices: 41195691--41195745 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
41195681 TTATTTAGAA
*
41195691 TTTGAATTA-AAATGATGAATT
1 TTTGAATTATAAATGATAAATT
* *
41195712 TTGTAAATTATAAATGCTAAATT
1 TT-TGAATTATAAATGATAAATT
41195735 TGTTGAATTAT
1 T-TTGAATTAT
41195746 TTACAGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 6 0.22
23 18 0.67
24 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (22 bp):
TTTGAATTATAAATGATAAATT
Found at i:41196603 original size:15 final size:15
Alignment explanation
Indices: 41196583--41196614 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41196573 AATAGGTAGG
41196583 GGACCGGACTAGACC
1 GGACCGGACTAGACC
*
41196598 GGACCGGACTGGACC
1 GGACCGGACTAGACC
41196613 GG
1 GG
41196615 CTAGTAGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.31, G:0.41, T:0.06
Consensus pattern (15 bp):
GGACCGGACTAGACC
Found at i:41199561 original size:6 final size:6
Alignment explanation
Indices: 41199526--41199553 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41199516 GAGGAAAAAT
41199526 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
41199554 AGAGAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
TAAAGA
Found at i:41205433 original size:76 final size:76
Alignment explanation
Indices: 41205303--41205455 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
41205293 TTAATTTAAA
41205303 ATCTTAATCATAATTTGAGATATATGATGCAATAAATCCTTTGTACTTGAGAACAATGCTCCCAA
1 ATCTTAATCATAATTTGAGATATATGATGCAATAAATCCTTTGTACTTGAGAACAATGCTCCCAA
41205368 AGTTGATCTTC
66 AGTTGATCTTC
* *
41205379 ATCTTAATCATAATTTGAGATATATGATGCAATTAATCCTTTGTACTTGGGAACAATGCTCCCAA
1 ATCTTAATCATAATTTGAGATATATGATGCAATAAATCCTTTGTACTTGAGAACAATGCTCCCAA
41205444 AGTTGATCTTC
66 AGTTGATCTTC
41205455 A
1 A
41205456 CATTGAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (76 bp):
ATCTTAATCATAATTTGAGATATATGATGCAATAAATCCTTTGTACTTGAGAACAATGCTCCCAA
AGTTGATCTTC
Found at i:41211946 original size:45 final size:45
Alignment explanation
Indices: 41211891--41212051 Score: 150
Period size: 45 Copynumber: 3.5 Consensus size: 45
41211881 AACCGTTAAC
41211891 ATTCTATCGATTTAATCTTAAATTCTATAAACCTTAACTGTTTAT
1 ATTCTATCGATTTAATCTTAAATTCTATAAACCTTAACTGTTTAT
* * * *
41211936 ATTTTATCGATTTAAT-TTTAATTCTGTTAAA--ATAA-TGTTGATTCATCT
1 ATTCTATCGATTTAATCTTAAATTCT-ATAAACCTTAACTG-T--TT-A--T
* * * *
41211984 ATTCTATCAATTTAATCTTAAATTTTATAGACCTTAACTGTTTAC
1 ATTCTATCGATTTAATCTTAAATTCTATAAACCTTAACTGTTTAT
*
41212029 ATTCTATCGATTTAATCATAAAT
1 ATTCTATCGATTTAATCTTAAAT
41212052 CCATTAATAA
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 8 0.09
45 42 0.46
46 1 0.01
47 1 0.01
48 20 0.22
49 7 0.08
50 4 0.04
51 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.48
Consensus pattern (45 bp):
ATTCTATCGATTTAATCTTAAATTCTATAAACCTTAACTGTTTAT
Found at i:41216446 original size:59 final size:59
Alignment explanation
Indices: 41216342--41216459 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
41216332 GCATGGAGCG
* * *
41216342 GCAAGAAACTCGTTGTTGATCATTTTAAGATGTTTTGATGCATTGCATATGCACATATA
1 GCAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGCATTGCATATGCACATATA
* *
41216401 GCAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGTATTGCATATGCACTTATA
1 GCAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGCATTGCATATGCACATATA
41216460 TCTAATGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37
Consensus pattern (59 bp):
GCAAGAAACCCGTTGTTGATCATTTTAAGATATTTGGATGCATTGCATATGCACATATA
Found at i:41222283 original size:122 final size:122
Alignment explanation
Indices: 41222066--41222311 Score: 411
Period size: 122 Copynumber: 2.0 Consensus size: 122
41222056 CTCGAATATT
* *
41222066 TTTTCCTTCGAAACCCTTGGATAACTTTAAATCAATCAAACAAAAAGACAAGATAGTTTATAGCA
1 TTTTCCTTCGAAACCCTTGGATAACTTTAAATCAACCAAACAAAAAGACAAGATAGCTTATAGCA
* *
41222131 TGAAAGAAAGCTATTCTAAGCTATTCATTCTTCATATAACCCAAAATTCTAACTAGG
66 TGAAAAAAAGCTATTCTAAGCTATGCATTCTTCATATAACCCAAAATTCTAACTAGG
* * *
41222188 TTTTCCTTTGAAACCCTTGGATAATTTTAAATCAACCAAACAAAAAGACAGGATAGCTTATAGCA
1 TTTTCCTTCGAAACCCTTGGATAACTTTAAATCAACCAAACAAAAAGACAAGATAGCTTATAGCA
* *
41222253 TGAAAAAAAGCTATTCTAAGCTATGCATTCTTCATATAACCCAAAGTTCTGACTAGG
66 TGAAAAAAAGCTATTCTAAGCTATGCATTCTTCATATAACCCAAAATTCTAACTAGG
41222310 TT
1 TT
41222312 CAAAATGATA
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 115 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (122 bp):
TTTTCCTTCGAAACCCTTGGATAACTTTAAATCAACCAAACAAAAAGACAAGATAGCTTATAGCA
TGAAAAAAAGCTATTCTAAGCTATGCATTCTTCATATAACCCAAAATTCTAACTAGG
Found at i:41224079 original size:21 final size:20
Alignment explanation
Indices: 41224028--41224079 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
41224018 AAATCTAAAT
* *
41224028 TAAAATACTAAAATTCAGGA
1 TAAAATACTGAAATTCAGAA
* *
41224048 TAAAATCCTGAAATTCCGAA
1 TAAAATACTGAAATTCAGAA
41224068 TAAAAATACTGA
1 T-AAAATACTGA
41224080 TGTTGGCATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (20 bp):
TAAAATACTGAAATTCAGAA
Done.