Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 26 of 29
Found at i:4367045 original size:29 final size:26
Alignment explanation
Indices: 4366995--4367056 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 26
4366985 TTCAAATAAT
4366995 ATAAAATTAATATTTAAATAATCAAA
1 ATAAAATTAATATTTAAATAATCAAA
4367021 ATAAAATTAATCTAATTTAAATAATCAAA
1 ATAAAATTAA--T-ATTTAAATAATCAAA
4367050 ATAAAAT
1 ATAAAAT
4367057 CATTTCGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.30
28 1 0.03
29 22 0.67
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAAAATTAATATTTAAATAATCAAA
Found at i:4371694 original size:23 final size:24
Alignment explanation
Indices: 4371658--4371708 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
4371648 TCACTAAATT
*
4371658 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAATAATATATTAATAAA
*
4371681 TTTAAATACA-AATATTTTAATAAA
1 TTTAAATA-ATAATATATTAATAAA
4371705 TTTA
1 TTTA
4371709 TTTCAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAATAATAATATATTAATAAA
Found at i:4372016 original size:31 final size:31
Alignment explanation
Indices: 4371981--4372062 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
4371971 ATCAAATCTT
* *
4371981 AAAAAATAAGTAAATATTTTTTA-AATAATAA
1 AAAAAATAAATAAAT-TTTTTTATAAAAATAA
* **
4372012 AAAAAATAAATATATTTTTTTATAAAAATTT
1 AAAAAATAAATAAATTTTTTTATAAAAATAA
4372043 AAAAAATAACACTAAATTTT
1 AAAAAATAA-A-TAAATTTT
4372063 CCCCAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 7 0.17
31 27 0.64
32 1 0.02
33 7 0.17
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (31 bp):
AAAAAATAAATAAATTTTTTTATAAAAATAA
Found at i:4372031 original size:29 final size:29
Alignment explanation
Indices: 4371951--4372031 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
4371941 ATAATAAGTT
* * **
4371951 AAAAAAATAAGTATATTTTAATCAAATCTTA
1 AAAAAAATAAATATATTTT--TTAAATAATA
4371982 AAAAATAAGT-AA-ATATTTTTTAAATAATA
1 AAAAA-AA-TAAATATATTTTTTAAATAATA
4372011 AAAAAAATAAATATATTTTTT
1 AAAAAAATAAATATATTTTTT
4372032 TATAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 1 0.02
28 4 0.10
29 21 0.50
31 12 0.29
32 3 0.07
33 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAAAAATAAATATATTTTTTAAATAATA
Found at i:4373437 original size:9 final size:9
Alignment explanation
Indices: 4373423--4373456 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
4373413 AGAAAGAAAG
4373423 AAAAATAAA
1 AAAAATAAA
4373432 AAAAATAAA
1 AAAAATAAA
*
4373441 AGAAATAAA
1 AAAAATAAA
4373450 AAAAATA
1 AAAAATA
4373457 TTTATGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:4373821 original size:11 final size:12
Alignment explanation
Indices: 4373786--4373836 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 12
4373776 TATTCGTGTC
4373786 ATATTCATTTTTT
1 ATATT-ATTTTTT
*
4373799 ATATTATGTTTT
1 ATATTATTTTTT
4373811 A-ATTATTTTTT
1 ATATTATTTTTT
*
4373822 ATATCATATTTTT
1 ATATTAT-TTTTT
4373835 AT
1 AT
4373837 TTTTCATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 10 0.30
12 11 0.33
13 12 0.36
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:4374323 original size:37 final size:39
Alignment explanation
Indices: 4374281--4374359 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 39
4374271 ATTATTTTTC
*
4374281 ATATTAAAAATATTATATT-TTT-ATATA-ATTTTTTTAT
1 ATATTAAAAAT-TTATATTATTTCATATATATTTTTATAT
* *
4374318 ATATTAATAATTTATTTTATTTCATATATATTTTTATAT
1 ATATTAAAAATTTATATTATTTCATATATATTTTTATAT
4374357 ATA
1 ATA
4374360 CGTGTATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 6 0.17
37 13 0.36
38 5 0.14
39 12 0.33
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (39 bp):
ATATTAAAAATTTATATTATTTCATATATATTTTTATAT
Found at i:4374790 original size:16 final size:15
Alignment explanation
Indices: 4374744--4374787 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
4374734 ATTATATTAT
*
4374744 TTTAAATAAATTTTA
1 TTTAATTAAATTTTA
4374759 -TTAATTATAATTTTA
1 TTTAATTA-AATTTTA
4374774 TTTAATTAAATTTT
1 TTTAATTAAATTTT
4374788 TATAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 6 0.23
15 13 0.50
16 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATTAAATTTTA
Found at i:4382014 original size:19 final size:20
Alignment explanation
Indices: 4381990--4382028 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4381980 TTCTTTAAAT
*
4381990 ATATTTTAAAGA-TTAAAAG
1 ATATTTTAAAAATTTAAAAG
4382009 ATATTTTAAAAATTTAAAAG
1 ATATTTTAAAAATTTAAAAG
4382029 CAAACGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
ATATTTTAAAAATTTAAAAG
Found at i:4382768 original size:4 final size:4
Alignment explanation
Indices: 4382759--4382784 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4382749 GTAGAAGAAG
4382759 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
4382785 AGAAGCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:4386574 original size:2 final size:2
Alignment explanation
Indices: 4386567--4386594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4386557 TTTTATACAA
4386567 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
4386595 TGATTTAAAA
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):
AT
Found at i:4386851 original size:29 final size:29
Alignment explanation
Indices: 4386809--4386881 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 29
4386799 TTTTATGCTT
4386809 AATAATATTGATTAATATGATATTTATAA-AAA
1 AATAATA-T-ATTAATATGATA-TTA-AATAAA
* **
4386841 AATAA-ATATTATTATTTTATTAAATAAA
1 AATAATATATTAATATGATATTAAATAAA
4386869 AATAATATATTAA
1 AATAATATATTAA
4386882 ACATTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 2 0.06
28 11 0.31
29 15 0.43
30 1 0.03
31 1 0.03
32 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
AATAATATATTAATATGATATTAAATAAA
Found at i:4388516 original size:3 final size:3
Alignment explanation
Indices: 4388508--4388535 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4388498 TCTATTGCTT
4388508 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4388536 ATTCTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4389019 original size:11 final size:11
Alignment explanation
Indices: 4389003--4389061 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
4388993 ACATAATTAT
4389003 ATAAAAATATA
1 ATAAAAATATA
4389014 AT-AAAAT-T-
1 ATAAAAATATA
4389022 -T-AAAATATA
1 ATAAAAATATA
*
4389031 ATATAAATATA
1 ATAAAAATATA
*
4389042 ATATAAATA-A
1 ATAAAAATATA
4389052 ATAAAAATAT
1 ATAAAAATAT
4389062 TAAAATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 6 0.15
8 1 0.02
9 1 0.02
10 15 0.37
11 18 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:4389028 original size:17 final size:17
Alignment explanation
Indices: 4389001--4389061 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
4388991 CAACATAATT
4389001 ATATAAAAATATAATAAA
1 ATAT-AAAATATAATAAA
*
4389019 ATTTAAAATATAATATAA
1 ATATAAAATATAATA-AA
*
4389037 ATATAATATA-AAT-AA
1 ATATAAAATATAATAAA
4389052 ATA-AAAATAT
1 ATATAAAATAT
4389062 TAAAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.14
15 5 0.14
17 14 0.38
18 13 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATAAA
Found at i:4389046 original size:16 final size:15
Alignment explanation
Indices: 4389025--4389054 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
4389015 TAAAATTTAA
4389025 AATATAATATAAATAT
1 AATATAA-ATAAATAT
4389041 AATATAAATAAATA
1 AATATAAATAAATA
4389055 AAAATATTAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAATAAATAT
Found at i:4391595 original size:2 final size:2
Alignment explanation
Indices: 4391588--4391613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4391578 TTTCTCTGGG
4391588 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
4391614 ATATCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:4392337 original size:3 final size:3
Alignment explanation
Indices: 4392329--4392354 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4392319 TGAGAAATGC
4392329 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
4392355 CAGGTGGACT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4394853 original size:2 final size:2
Alignment explanation
Indices: 4394846--4394875 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4394836 AACAACTATG
4394846 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
4394876 GCAGAAGGCT
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):
TA
Found at i:4398931 original size:11 final size:10
Alignment explanation
Indices: 4398910--4399067 Score: 60
Period size: 11 Copynumber: 15.2 Consensus size: 10
4398900 TGCTCACCCC
4398910 TAATATTTTAA
1 TAAT-TTTTAA
4398921 TATATTTTTAA
1 TA-ATTTTTAA
** *
4398932 TAACGTGTAA
1 TAATTTTTAA
4398942 -AATAATTTTAA
1 TAAT--TTTTAA
4398953 TAATTTTTGAAA
1 TAATTTTT--AA
*
4398965 TAA-TTTTGA
1 TAATTTTTAA
4398974 TAATTTTTGATA
1 TAATTTTT-A-A
* *
4398986 AAATTTTATGA
1 TAATTTT-TAA
4398997 TAA-TTTTAA
1 TAATTTTTAA
*
4399006 TACATTTATAA
1 TA-ATTTTTAA
*
4399017 TAA-TTTTGA
1 TAATTTTTAA
*
4399026 -ACTTTTT-A
1 TAATTTTTAA
*
4399034 TACAATTTTAA
1 TA-ATTTTTAA
4399045 TAATATTTATAA
1 TAAT-TTT-TAA
4399057 TAA-TTTTAA
1 TAATTTTTAA
4399066 TA
1 TA
4399068 TCATTTTATA
Statistics
Matches: 110, Mismatches: 19, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
8 2 0.02
9 24 0.22
10 26 0.24
11 34 0.31
12 23 0.21
13 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:4398956 original size:9 final size:9
Alignment explanation
Indices: 4398942--4399067 Score: 67
Period size: 10 Copynumber: 12.4 Consensus size: 9
4398932 TAACGTGTAA
4398942 AATAATTTT
1 AATAATTTT
4398951 AATAATTTTT
1 AATAA-TTTT
4398961 GAAATAATTTT
1 --AATAATTTT
*
4398972 GATAATTTTT
1 AATAA-TTTT
*
4398982 GATAAAATTTT
1 -A-ATAATTTT
4398993 ATGATAATTTT
1 A--ATAATTTT
4399004 AATACATTTAT
1 AATA-ATTT-T
4399015 AATAATTTT
1 AATAATTTT
4399024 GAACT--TTTT
1 -AA-TAATTTT
*
4399033 ATACAATTTT
1 A-ATAATTTT
4399043 AATAATATTTAT
1 AAT-A-ATTT-T
4399055 AATAATTTT
1 AATAATTTT
4399064 AATA
1 AATA
4399068 TCATTTTATA
Statistics
Matches: 93, Mismatches: 7, Indels: 34
0.69 0.05 0.25
Matches are distributed among these distances:
8 1 0.01
9 24 0.26
10 29 0.31
11 27 0.29
12 12 0.13
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (9 bp):
AATAATTTT
Found at i:4399063 original size:21 final size:21
Alignment explanation
Indices: 4398910--4399067 Score: 84
Period size: 21 Copynumber: 7.7 Consensus size: 21
4398900 TGCTCACCCC
*
4398910 TAAT-ATTTTAAT-ATATTTT
1 TAATAATTTTAATAATATTTA
* *
4398929 TAATAACGTGTAA-AATAATTT-
1 TAATAA-TTTTAATAAT-ATTTA
4398950 TAATAATTTTTGAAATAAT-TTTGA
1 TAATAA-TTTT--AATAATATTT-A
* *
4398974 TAAT--TTTTGATAAAATTTTA
1 TAATAATTTTAATAATA-TTTA
* *
4398994 TGATAATTTTAAT-ACATTTA
1 TAATAATTTTAATAATATTTA
* * *
4399014 TAATAATTTTGA-ACTTTTTA
1 TAATAATTTTAATAATATTTA
*
4399034 T-ACAATTTTAATAATATTTA
1 TAATAATTTTAATAATATTTA
4399054 TAATAATTTTAATA
1 TAATAATTTTAATA
4399068 TCATTTTATA
Statistics
Matches: 103, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
19 16 0.16
20 31 0.30
21 34 0.33
22 13 0.13
23 2 0.02
24 7 0.07
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (21 bp):
TAATAATTTTAATAATATTTA
Found at i:4399080 original size:21 final size:21
Alignment explanation
Indices: 4398988--4399085 Score: 98
Period size: 20 Copynumber: 4.8 Consensus size: 21
4398978 TTTTGATAAA
*
4398988 ATTTTATGATAATTTTAATAC
1 ATTTTATAATAATTTTAATAC
*
4399009 A-TTTATAATAATTTTGA-AC
1 ATTTTATAATAATTTTAATAC
* *
4399028 TTTTTAT-ACAATTTTAATA-
1 ATTTTATAATAATTTTAATAC
4399047 ATATTTATAATAATTTTAATATC
1 AT-TTTATAATAATTTTAATA-C
*
4399070 ATTTTAT-ATAAGTTTA
1 ATTTTATAATAATTTTA
4399086 TACTAAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
19 11 0.17
20 25 0.40
21 20 0.32
22 5 0.08
23 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTTATAATAATTTTAATAC
Found at i:4400411 original size:33 final size:36
Alignment explanation
Indices: 4400333--4400413 Score: 89
Period size: 38 Copynumber: 2.3 Consensus size: 36
4400323 TAATAAATTT
*
4400333 AATAATT-TTAAATATAATATAAAAATATGATTTATAA
1 AATAATTAATAAATATAATAT--AAATATGATTTATAA
*
4400370 AATTATTAATAAATATAATAT-AATAT-ATTTA-AA
1 AATAATTAATAAATATAATATAAATATGATTTATAA
*
4400403 TATAATTAATA
1 AATAATTAATA
4400414 TAAATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
33 11 0.28
34 5 0.13
35 5 0.13
37 6 0.15
38 12 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
AATAATTAATAAATATAATATAAATATGATTTATAA
Found at i:4400417 original size:15 final size:15
Alignment explanation
Indices: 4400341--4400420 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
4400331 TTAATAATTT
4400341 TAAATATAA-T-ATA
1 TAAATATAATTAATA
* * *
4400354 AAAATATGATTTATA
1 TAAATATAATTAATA
*
4400369 -AAATTATTAATAAATA
1 TAAA-TA-TAATTAATA
*
4400385 T-AATATAA-TATATT
1 TAAATATAATTA-ATA
4400399 TAAATATAATTAATA
1 TAAATATAATTAATA
4400414 TAAATAT
1 TAAATAT
4400421 TTAAAATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
13 8 0.16
14 10 0.20
15 23 0.45
16 10 0.20
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (15 bp):
TAAATATAATTAATA
Found at i:4400427 original size:24 final size:24
Alignment explanation
Indices: 4400377--4400425 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4400367 TAAAATTATT
4400377 AATAAATATAATATAATATATTTA
1 AATAAATATAATATAATATATTTA
4400401 AATATAAT-TAATATAA-ATATTTA
1 AATA-AATATAATATAATATATTTA
4400424 AA
1 AA
4400426 ATTTTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 9 0.38
24 12 0.50
25 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAAATATAATATAATATATTTA
Found at i:4400434 original size:45 final size:43
Alignment explanation
Indices: 4400329--4400436 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 43
4400319 AAGTTAATAA
* *
4400329 ATTTAATAATTTTAAATATAATATAAAAATATGATTTATAAAAT
1 ATTTAATAATTTT-AATATAATATAAAAATATAATTAATAAAAT
* * *
4400373 -TATTAATAAATATAATATAATATATTTAAATATAATTAATATAAAT
1 AT-TTAATAATTTTAATATAATATA--AAAATATAATTAATA-AAAT
4400419 ATTTAA-AATTTTAATATA
1 ATTTAATAATTTTAATATA
4400437 TTTAATTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
43 12 0.23
44 9 0.17
45 22 0.42
46 8 0.15
47 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (43 bp):
ATTTAATAATTTTAATATAATATAAAAATATAATTAATAAAAT
Found at i:4401018 original size:25 final size:26
Alignment explanation
Indices: 4400989--4401040 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
4400979 AAAATAAAAA
*
4400989 AATAAATTAATCGATATTTTA-TAAT
1 AATAAATTAATCAATATTTTATTAAT
* *
4401014 AATAAATTTATTAATATTTTATTAAT
1 AATAAATTAATCAATATTTTATTAAT
4401040 A
1 A
4401041 TTTTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
AATAAATTAATCAATATTTTATTAAT
Found at i:4401036 original size:11 final size:11
Alignment explanation
Indices: 4401020--4401047 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4401010 TAATAATAAA
4401020 TTTATTAATAT
1 TTTATTAATAT
4401031 TTTATTAATAT
1 TTTATTAATAT
4401042 TTTATT
1 TTTATT
4401048 TAAATAAATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:4401220 original size:11 final size:11
Alignment explanation
Indices: 4401197--4401266 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
4401187 AAAATTTTTA
*
4401197 ATAAAAA-ATT
1 ATAAAAATAAT
4401207 ATAAAAATAAT
1 ATAAAAATAAT
4401218 ATAAAAATAAT
1 ATAAAAATAAT
* *
4401229 TTAAATATAAT
1 ATAAAAATAAT
4401240 ATAATAAA-AAT
1 ATAA-AAATAAT
*
4401251 ATATAAAATTAT
1 ATA-AAAATAAT
4401263 ATAA
1 ATAA
4401267 CATAATTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
10 7 0.14
11 35 0.70
12 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:4401271 original size:25 final size:26
Alignment explanation
Indices: 4401213--4401271 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
4401203 AATTATAAAA
*
4401213 ATAATATAAAAATAATTTAAATATAAT
1 ATAA-ATAAAAATAATATAAATATAAT
*
4401240 AT-AATAAAAAT-ATATAAA-ATTAT
1 ATAAATAAAAATAATATAAATATAAT
4401263 ATAACATAA
1 ATAA-ATAA
4401272 TTTATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 6 0.21
24 7 0.25
25 12 0.43
26 1 0.04
27 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAAATAAAAATAATATAAATATAAT
Found at i:4401335 original size:17 final size:17
Alignment explanation
Indices: 4401294--4401339 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
4401284 TTTAAATTTA
4401294 TATAAATATAAATAATATT
1 TATAAATA-AAA-AATATT
4401313 T-T-AATAAAAAATATT
1 TATAAATAAAAAATATT
4401328 TATAAATAAAAA
1 TATAAATAAAAA
4401340 GGAAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
16 4 0.16
17 12 0.48
18 1 0.04
19 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAAATAAAAAATATT
Found at i:4401338 original size:15 final size:15
Alignment explanation
Indices: 4401301--4401339 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4401291 TTATATAAAT
*
4401301 ATAAATAATATTTTA
1 ATAAAAAATATTTTA
4401316 ATAAAAAATATTTATAA
1 ATAAAAAATATTT-T-A
4401333 ATAAAAA
1 ATAAAAA
4401340 GGAAAGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 1 0.05
17 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAAAAATATTTTA
Found at i:4401917 original size:32 final size:33
Alignment explanation
Indices: 4401859--4401936 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 33
4401849 TTAAATTATG
*
4401859 ATATAAAATATATAAATATTTGAAATTTTATATA
1 ATATAAAATAT-TAAATATTTGAAATTTTATAAA
*
4401893 ATATAAATTATT-AATATATT-AAATTTTATAAA
1 ATATAAAATATTAAATAT-TTGAAATTTTATAAA
4401925 ATATAAAATATT
1 ATATAAAATATT
4401937 TTATGATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 27 0.68
33 3 0.08
34 10 0.25
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATATAAAATATTAAATATTTGAAATTTTATAAA
Found at i:4401931 original size:16 final size:16
Alignment explanation
Indices: 4401881--4401931 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
4401871 TAAATATTTG
*
4401881 AAATTTTATATAATAT
1 AAATTTTATAAAATAT
* *
4401897 AAATTAT-TAATATATT
1 AAATTTTATAAAATA-T
4401913 AAATTTTATAAAATAT
1 AAATTTTATAAAATAT
4401929 AAA
1 AAA
4401932 ATATTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 5 0.18
16 17 0.61
17 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTTATAAAATAT
Found at i:4402321 original size:2 final size:2
Alignment explanation
Indices: 4402314--4402350 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4402304 AATAAAATAA
4402314 AG AG AG 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 AG AG AG A
4402351 AGAACGTAAC
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4419148 original size:23 final size:22
Alignment explanation
Indices: 4419103--4419148 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
4419093 AAAATAAATT
* *
4419103 TTATAGTATTAAATATGATATA
1 TTATAGAATTAAATATAATATA
*
4419125 TTATAGAATATAATTATAATATA
1 TTATAGAAT-TAAATATAATATA
4419148 T
1 T
4419149 ATGTGTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
TTATAGAATTAAATATAATATA
Found at i:4419242 original size:21 final size:21
Alignment explanation
Indices: 4419216--4419259 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4419206 AAGATAATTT
4419216 TATAAATGTAATA-ATTTTAAA
1 TATAAATGTAATATA-TTTAAA
*
4419237 TATAAATTTAATATATTTAAA
1 TATAAATGTAATATATTTAAA
4419258 TA
1 TA
4419260 AAAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TATAAATGTAATATATTTAAA
Found at i:4419274 original size:15 final size:17
Alignment explanation
Indices: 4419246--4419277 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
4419236 ATATAAATTT
4419246 AATATATTTAAATAAAA
1 AATATATTTAAATAAAA
4419263 AATA-ATTT-AATAAAA
1 AATATATTTAAATAAAA
4419278 TGATAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATATTTAAATAAAA
Found at i:4419808 original size:8 final size:8
Alignment explanation
Indices: 4419795--4419827 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4419785 ACCCACACCC
4419795 TTTGTTTT
1 TTTGTTTT
4419803 TTTGTTTT
1 TTTGTTTT
4419811 TTT-TTTT
1 TTTGTTTT
4419818 TTTGTCTTT
1 TTTGT-TTT
4419827 T
1 T
4419828 GACTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 12 0.52
9 4 0.17
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (8 bp):
TTTGTTTT
Found at i:4423013 original size:2 final size:2
Alignment explanation
Indices: 4423006--4423037 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4422996 TTTAGTTGCA
4423006 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4423038 GCAAACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4429166 original size:12 final size:12
Alignment explanation
Indices: 4429145--4429174 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4429135 GCTATATATA
*
4429145 AAAAAACAAAAC
1 AAAAACCAAAAC
4429157 AAAAACCAAAAC
1 AAAAACCAAAAC
4429169 AAAAAC
1 AAAAAC
4429175 TGCCTGCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAACCAAAAC
Found at i:4434046 original size:20 final size:20
Alignment explanation
Indices: 4434021--4434058 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4434011 ATATATTTTA
*
4434021 TTAATTTTTATTTAAAATTT
1 TTAATTTTTAATTAAAATTT
4434041 TTAATTTTTAATTAAAAT
1 TTAATTTTTAATTAAAAT
4434059 CAACAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTTTTAATTAAAATTT
Found at i:4435120 original size:21 final size:21
Alignment explanation
Indices: 4435096--4435135 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4435086 GATTTAAGAG
*
4435096 TTTAAAAGATAAAAAAATAAT
1 TTTAAAACATAAAAAAATAAT
*
4435117 TTTAAAACATTAAAAAATA
1 TTTAAAACATAAAAAAATA
4435136 TATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (21 bp):
TTTAAAACATAAAAAAATAAT
Found at i:4435141 original size:11 final size:11
Alignment explanation
Indices: 4435127--4435152 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4435117 TTTAAAACAT
4435127 TAAAAAATATA
1 TAAAAAATATA
4435138 TAAAAAATATA
1 TAAAAAATATA
4435149 TAAA
1 TAAA
4435153 TTTAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:4437887 original size:2 final size:2
Alignment explanation
Indices: 4437880--4437915 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4437870 AAATTATCTT
* *
4437880 TA TA TA TA TA TA TA TA TA TA TA TA AA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4437916 ACTATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4437916 original size:12 final size:12
Alignment explanation
Indices: 4437881--4437922 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
4437871 AATTATCTTT
*
4437881 ATATATATATAT
1 ATATATATATAA
4437893 ATATATATATAA
1 ATATATATATAA
*
4437905 ATTTATATATAA
1 ATATATATATAA
*
4437917 CTATAT
1 ATATAT
4437923 TTTTAGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATATATAA
Found at i:4439954 original size:2 final size:2
Alignment explanation
Indices: 4439947--4439980 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4439937 AAATGGAATT
*
4439947 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4439981 AAGAAATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4443392 original size:16 final size:17
Alignment explanation
Indices: 4443371--4443405 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4443361 TTACATTAAA
4443371 TTTTAA-ATATATTTTT
1 TTTTAACATATATTTTT
*
4443387 TTTTAACATTTATTTTT
1 TTTTAACATATATTTTT
4443404 TT
1 TT
4443406 ACTCATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAACATATATTTTT
Found at i:4445229 original size:3 final size:3
Alignment explanation
Indices: 4445221--4445245 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4445211 TGAATATGTG
4445221 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
4445246 TGTATGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4445924 original size:22 final size:23
Alignment explanation
Indices: 4445879--4445943 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
4445869 TCTTGCATGT
*
4445879 ATAAAATTATAAATTTTTTTCACA-
1 ATAAAATTAT-AA-TTTTTACACAG
* *
4445903 ATTAACTTATAATTTTTACACAG
1 ATAAAATTATAATTTTTACACAG
*
4445926 ATAAAATTATAAATTTTA
1 ATAAAATTATAATTTTTA
4445944 TTCATAATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 9 0.26
23 17 0.50
24 8 0.24
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAATTATAATTTTTACACAG
Found at i:4445940 original size:24 final size:23
Alignment explanation
Indices: 4445879--4445942 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
4445869 TCTTGCATGT
*
4445879 ATAAAATTATAAATTTTTTTCACA
1 ATAAAATTATAAA-TTTTTACACA
* *
4445903 ATTAACTTAT-AATTTTTACACA
1 ATAAAATTATAAATTTTTACACA
4445925 GATAAAATTATAAATTTT
1 -ATAAAATTATAAATTTT
4445943 ATTCATAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 9 0.27
23 10 0.30
24 14 0.42
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAATTATAAATTTTTACACA
Found at i:4445987 original size:51 final size:47
Alignment explanation
Indices: 4445879--4445991 Score: 127
Period size: 51 Copynumber: 2.3 Consensus size: 47
4445869 TCTTGCATGT
* *
4445879 ATAAAATTATAAATTTTTTTCACAATTAACTTATAATTTTTACACAG
1 ATAAAATTATAAATTTTATTCACAATCAACTTATAATTTTTACACAG
* * * **
4445926 ATAAAATTATAAATTTTATTCATAATCATTCTATAAATAATTTTTATATGG
1 ATAAAATTATAAATTTTATTCACAATCA-ACT-T--ATAATTTTTACACAG
4445977 ATAAAATTATAAATT
1 ATAAAATTATAAATT
4445992 ATCCAACATA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 25 0.45
48 2 0.04
49 1 0.02
51 27 0.49
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (47 bp):
ATAAAATTATAAATTTTATTCACAATCAACTTATAATTTTTACACAG
Found at i:4446271 original size:16 final size:16
Alignment explanation
Indices: 4446223--4446273 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
4446213 TATTTATAAA
*
4446223 AAAT-ATTTACTTATT
1 AAATAATTTACTTATC
* *
4446238 AAATAAATTTAATAATC
1 AAAT-AATTTACTTATC
4446255 AAATAATTTACTTATC
1 AAATAATTTACTTATC
4446271 AAA
1 AAA
4446274 ATATAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 4 0.14
16 13 0.45
17 12 0.41
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAATTTACTTATC
Found at i:4446275 original size:17 final size:17
Alignment explanation
Indices: 4446222--4446276 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
4446212 TTATTTATAA
4446222 AAAAT-ATTTACTTAT-
1 AAAATAATTTACTTATC
* * *
4446237 TAAATAAATTTAATAATC
1 AAAAT-AATTTACTTATC
4446255 -AAATAATTTACTTATC
1 AAAATAATTTACTTATC
4446271 AAAATA
1 AAAATA
4446277 TAAATATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 17 0.55
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATAATTTACTTATC
Found at i:4450003 original size:2 final size:2
Alignment explanation
Indices: 4449996--4450021 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4449986 AATATAAAGG
4449996 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
4450022 GCATGCTACA
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:4456134 original size:23 final size:25
Alignment explanation
Indices: 4456107--4456167 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
4456097 GTATTCTTAC
4456107 TGTGTTTATATTATTTT-T-TATGT
1 TGTGTTTATATTATTTTATATATGT
4456130 TGTGTTT-TAATT-TTTTATATATGT
1 TGTGTTTAT-ATTATTTTATATATGT
* *
4456154 TGAGTTTATGTTAT
1 TGTGTTTATATTAT
4456168 ATCTCAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 13 0.42
25 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (25 bp):
TGTGTTTATATTATTTTATATATGT
Found at i:4456901 original size:17 final size:17
Alignment explanation
Indices: 4456858--4456903 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
4456848 TGAATATTTT
4456858 TTAATAAATTTTA-TTAA
1 TTAA-AAATTTTATTTAA
*
4456875 TT-ATAATTTTATTTAA
1 TTAAAAATTTTATTTAA
4456891 TTAAAAATTTTAT
1 TTAAAAATTTTAT
4456904 AAATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 11 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAAAATTTTATTTAA
Found at i:4465739 original size:50 final size:50
Alignment explanation
Indices: 4465680--4465917 Score: 404
Period size: 50 Copynumber: 4.8 Consensus size: 50
4465670 TATACTTAGA
* * *
4465680 GTCAACAATTATAGCCATCTTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
4465730 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
4465780 GTCAACAATTATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
4465830 GTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
4465880 GTCAATAATTATGGCCACCTCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
4465918 ACTTTTCACC
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 177 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:4470367 original size:50 final size:50
Alignment explanation
Indices: 4470290--4470525 Score: 269
Period size: 50 Copynumber: 4.7 Consensus size: 50
4470280 TATACTTAGA
* * * * * * *
4470290 GTCAACAATTATGGCTACCTTTCTCTATTGTTAAAGGTTGGTAAAAAATC
1 GTCAACAATTATGACAACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
* * *
4470340 GTCAACAAGTAT-AGCAACCGCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGA-CAACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
* * *
4470390 GTCAACAATTATGACAATCTCTCTCTATTGTCAAAGATTGACGAAGAATC
1 GTCAACAATTATGACAACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
*
4470440 GTCAACAATTATGGTC-ACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
1 GTCAACAATTAT-GACAACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
* ** * *
4470490 GTCAACAACTATGACCGCCTTTCTCTATTATCAAAG
1 GTCAACAATTATGACAACCTCTCTCTATTGTCAAAG
4470526 ATATTTTCCG
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.01
50 154 0.97
51 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGACAACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
Found at i:4470464 original size:100 final size:100
Alignment explanation
Indices: 4470290--4470527 Score: 298
Period size: 100 Copynumber: 2.4 Consensus size: 100
4470280 TATACTTAGA
* * * * **
4470290 GTCAACAATTATGGCTACCTTTCTCTATTGTTAAAGGTTGGTAAAAAATCGTCAACAAGTATAGC
1 GTCAACAATTATGACAACCTTTCTCTATTGTCAAAGATTGACAAAAAATCGTCAACAAGTATAGC
*
4470355 AACCGCTCTCTATTGTCAAAGGTTGGTGAAGAATC
66 AACCGCTCTCTATTGTCAAAGGTTGATGAAGAATC
* * * * * *
4470390 GTCAACAATTATGACAATCTCTCTCTATTGTCAAAGATTGACGAAGAATCGTCAACAATTATGGT
1 GTCAACAATTATGACAACCTTTCTCTATTGTCAAAGATTGACAAAAAATCGTCAACAAGTATAG-
*
4470455 C-ACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
65 CAACCGCTCTCTATTGTCAAAGGTTGATGAAGAATC
* ** *
4470490 GTCAACAACTATGACCGCCTTTCTCTATTATCAAAGAT
1 GTCAACAATTATGACAACCTTTCTCTATTGTCAAAGAT
4470528 ATTTTCCGGT
Statistics
Matches: 117, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
100 116 0.99
101 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (100 bp):
GTCAACAATTATGACAACCTTTCTCTATTGTCAAAGATTGACAAAAAATCGTCAACAAGTATAGC
AACCGCTCTCTATTGTCAAAGGTTGATGAAGAATC
Found at i:4477219 original size:1 final size:1
Alignment explanation
Indices: 4477215--4477239 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4477205 GATTTTTTTT
4477215 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
4477240 ATGTTACAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4482424 original size:16 final size:17
Alignment explanation
Indices: 4482403--4482435 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4482393 TTATAATTTT
4482403 AATT-AATTTTAGTAAA
1 AATTAAATTTTAGTAAA
*
4482419 AATTAAATTTTATTAAA
1 AATTAAATTTTAGTAAA
4482436 TAATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTAAATTTTAGTAAA
Found at i:4482920 original size:10 final size:11
Alignment explanation
Indices: 4482904--4482936 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
4482894 CATTTAATAA
4482904 AATAAAAAATT
1 AATAAAAAATT
4482915 -ATAAAAAATT
1 AATAAAAAATT
4482925 AATAAAATAATT
1 AATAAAA-AATT
4482937 TTATTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 6 0.30
12 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AATAAAAAATT
Found at i:4483943 original size:18 final size:20
Alignment explanation
Indices: 4483908--4483947 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
4483898 ACACAACATA
4483908 AAAAAATTAAAATATAACAC
1 AAAAAATTAAAATATAACAC
*
4483928 AAAAAA-TAATAT-TAACAC
1 AAAAAATTAAAATATAACAC
4483946 AA
1 AA
4483948 CTTAAAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAATTAAAATATAACAC
Found at i:4484054 original size:11 final size:10
Alignment explanation
Indices: 4484022--4484118 Score: 50
Period size: 8 Copynumber: 10.1 Consensus size: 10
4484012 TTTAATATTT
4484022 TAAATATACAA
1 TAAATATA-AA
*
4484033 -AAATA-ATA
1 TAAATATAAA
4484041 TAAATATAACA
1 TAAATATAA-A
* *
4484052 TAAAAATAAT
1 TAAATATAAA
4484062 TAAAATATAACA
1 T-AAATATAA-A
*
4484074 -AAAAATAAA
1 TAAATATAAA
4484083 TACAATA-AAA
1 TA-AATATAAA
4484093 -AAATAT-AA
1 TAAATATAAA
4484101 -AAATAT-AA
1 TAAATATAAA
4484109 -AAATATAAA
1 TAAATATAAA
4484118 T
1 T
4484119 TTATAATACT
Statistics
Matches: 68, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
8 21 0.31
9 10 0.15
10 18 0.26
11 19 0.28
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (10 bp):
TAAATATAAA
Found at i:4484056 original size:22 final size:21
Alignment explanation
Indices: 4484022--4484108 Score: 82
Period size: 22 Copynumber: 4.4 Consensus size: 21
4484012 TTTAATATTT
4484022 TAAATAT-AC-AAAAATAATA
1 TAAATATAACAAAAAATAATA
4484041 TAAATATAACATAAAAATAAT-
1 TAAATATAACA-AAAAATAATA
4484062 TAAAATATAACAAAAAATAA-A
1 T-AAATATAACAAAAAATAATA
*
4484083 TACA-AT-A-AAAAAAT-ATA
1 TAAATATAACAAAAAATAATA
*
4484100 AAAATATAA
1 TAAATATAA
4484109 AAATATAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
16 1 0.02
17 10 0.18
18 3 0.05
19 10 0.18
20 4 0.07
21 10 0.18
22 19 0.33
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAATATAACAAAAAATAATA
Found at i:4484076 original size:10 final size:9
Alignment explanation
Indices: 4484063--4484117 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 9
4484053 AAAAATAATT
4484063 AAAATATAA
1 AAAATATAA
*
4484072 CAAAAAATAA
1 -AAAATATAA
4484082 ATACAATA-AA
1 A-A-AATATAA
4484092 AAAATAT-A
1 AAAATATAA
4484100 AAAATAT-A
1 AAAATATAA
4484108 AAAATATAA
1 AAAATATAA
4484117 A
1 A
4484118 TTTATAATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 20 0.51
9 4 0.10
10 12 0.31
11 3 0.08
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATATAA
Found at i:4484102 original size:8 final size:8
Alignment explanation
Indices: 4484086--4484117 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4484076 AAATAAATAC
*
4484086 AATAAAAA
1 AATATAAA
4484094 AATATAAA
1 AATATAAA
4484102 AATATAAA
1 AATATAAA
4484110 AATATAAA
1 AATATAAA
4484118 TTTATAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AATATAAA
Found at i:4484105 original size:16 final size:16
Alignment explanation
Indices: 4484031--4484117 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 16
4484021 TTAAATATAC
*
4484031 AAAAATAATATAAATAT
1 AAAAATAA-AAAAATAT
*
4484048 -AACATAAAAATAAT-T
1 AAAAATAAAAA-AATAT
4484063 AAAATATAACAAAAA-AT
1 AAAA-ATAA-AAAAATAT
4484080 AAATACAATAAAAAAATAT
1 -AA-A-AATAAAAAAATAT
*
4484099 AAAAATATAAAAATAT
1 AAAAATAAAAAAATAT
4484115 AAA
1 AAA
4484118 TTTATAATAC
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
15 3 0.05
16 26 0.46
17 8 0.14
18 12 0.21
19 7 0.12
20 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAAAAAATAT
Found at i:4484178 original size:21 final size:20
Alignment explanation
Indices: 4484141--4484179 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4484131 AAGTAATAAA
* *
4484141 AAATAACATAAATAAAATAT
1 AAATAACAAAAAAAAAATAT
4484161 AAATACACAAAAAAAAAAT
1 AAATA-ACAAAAAAAAAAT
4484180 TCTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAACAAAAAAAAAATAT
Found at i:4493993 original size:6 final size:6
Alignment explanation
Indices: 4493982--4494016 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4493972 AGGCTCCGAT
4493982 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
4494017 ACAAGGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:4494027 original size:18 final size:18
Alignment explanation
Indices: 4493983--4494021 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4493973 GGCTCCGATG
**
4493983 AAGAGGAAGAGGAAGAGG
1 AAGAGGAAGAGGAAGAAC
4494001 AAGAGGAAGAGGAAGAAC
1 AAGAGGAAGAGGAAGAAC
4494019 AAG
1 AAG
4494022 GAGAAGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.44, T:0.00
Consensus pattern (18 bp):
AAGAGGAAGAGGAAGAAC
Found at i:4501746 original size:16 final size:17
Alignment explanation
Indices: 4501727--4501759 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4501717 TTATAATTTT
4501727 AATT-AATTTTAATAAA
1 AATTAAATTTTAATAAA
*
4501743 AATTAAATTTTATTAAA
1 AATTAAATTTTAATAAA
4501760 TAATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATTTTAATAAA
Found at i:4503280 original size:18 final size:20
Alignment explanation
Indices: 4503240--4503284 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
4503230 ATAAGAACAC
*
4503240 AACATAAAAAATTAAAATAT
1 AACACAAAAAATTAAAATAT
*
4503260 AACACAAAAAA-TAATAT-T
1 AACACAAAAAATTAAAATAT
4503278 AACACAA
1 AACACAA
4503285 CTTAAAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (20 bp):
AACACAAAAAATTAAAATAT
Found at i:4503392 original size:11 final size:10
Alignment explanation
Indices: 4503360--4503457 Score: 59
Period size: 9 Copynumber: 10.1 Consensus size: 10
4503350 TTTAATATTT
4503360 TAAATATACAA
1 TAAATATA-AA
*
4503371 -AAATA-ATA
1 TAAATATAAA
4503379 TAAATATAACA
1 TAAATATAA-A
* *
4503390 TAAAAATAAT
1 TAAATATAAA
4503400 TAAAATATAACA
1 T-AAATATAA-A
*
4503412 -AAAAATAAA
1 TAAATATAAA
4503421 TACAATA-AAA
1 TA-AATATAAA
4503431 -AAATAT-AA
1 TAAATATAAA
4503439 -AAATATAAA
1 TAAATATAAA
4503448 -AAATATAAA
1 TAAATATAAA
4503457 T
1 T
4503458 TTATAATACT
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
8 13 0.19
9 19 0.28
10 18 0.26
11 19 0.28
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAATATAAA
Found at i:4503394 original size:22 final size:21
Alignment explanation
Indices: 4503360--4503455 Score: 84
Period size: 22 Copynumber: 4.9 Consensus size: 21
4503350 TTTAATATTT
4503360 TAAATAT-AC-AAAAATAATA
1 TAAATATAACAAAAAATAATA
4503379 TAAATATAACATAAAAATAAT-
1 TAAATATAACA-AAAAATAATA
4503400 TAAAATATAACAAAAAATAA-A
1 T-AAATATAACAAAAAATAATA
*
4503421 TACA-AT-A-AAAAAAT-ATA
1 TAAATATAACAAAAAATAATA
* *
4503438 AAAATATAA-AAAATATAA
1 TAAATATAACAAAAAATAA
4503456 ATTTATAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
16 1 0.02
17 10 0.16
18 3 0.05
19 16 0.25
20 5 0.08
21 10 0.16
22 19 0.30
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAATATAACAAAAAATAATA
Found at i:4503463 original size:17 final size:17
Alignment explanation
Indices: 4503391--4503456 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
4503381 AATATAACAT
*
4503391 AAAAATAATTAAAATATA
1 AAAAAT-ATAAAAATATA
*
4503409 ACAAAAAATAAATACA-ATAA
1 A-AAAATATAAA-A-ATAT-A
4503429 AAAAATATAAAAATATA
1 AAAAATATAAAAATATA
4503446 AAAAATATAAA
1 AAAAATATAAA
4503457 TTTATAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
17 13 0.32
18 8 0.20
19 16 0.40
20 3 0.08
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATATAAAAATATA
Found at i:4503516 original size:20 final size:20
Alignment explanation
Indices: 4503480--4503517 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4503470 AAGTAATAAA
*
4503480 AAATAACATAAATAAAATAT
1 AAATAACATAAAAAAAATAT
4503500 AAATACACA-AAAAAAAAT
1 AAATA-ACATAAAAAAAAT
4503518 TCTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAACATAAAAAAAATAT
Found at i:4513314 original size:6 final size:6
Alignment explanation
Indices: 4513303--4513337 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4513293 AGGCTCCGAT
4513303 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
4513338 ACAAGGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:4513348 original size:18 final size:18
Alignment explanation
Indices: 4513304--4513342 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4513294 GGCTCCGATG
**
4513304 AAGAGGAAGAGGAAGAGG
1 AAGAGGAAGAGGAAGAAC
4513322 AAGAGGAAGAGGAAGAAC
1 AAGAGGAAGAGGAAGAAC
4513340 AAG
1 AAG
4513343 GAGAAGTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.44, T:0.00
Consensus pattern (18 bp):
AAGAGGAAGAGGAAGAAC
Found at i:4517829 original size:2 final size:2
Alignment explanation
Indices: 4517822--4517861 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4517812 TGTTTTACGA
4517822 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4517862 CCCTTTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4517970 original size:15 final size:15
Alignment explanation
Indices: 4517948--4517987 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4517938 TTTCATCAAA
4517948 TATTATTTTAAA-AT
1 TATTATTTTAAATAT
*
4517962 TATTTATTTAAAATAT
1 TA-TTATTTTAAATAT
4517978 TATTATTTTA
1 TATTATTTTA
4517988 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 16 0.73
16 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTTTAAATAT
Found at i:4518300 original size:19 final size:18
Alignment explanation
Indices: 4518276--4518321 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4518266 AGTATGAATT
*
4518276 AATTAAATTTTATTTTTAA
1 AATTAAATTTTA-ATTTAA
*
4518295 AATTAAAATTTAATTTAA
1 AATTAAATTTTAATTTAA
*
4518313 AATTTAATT
1 AATTAAATT
4518322 AAATTATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAAATTTTAATTTAA
Found at i:4518323 original size:11 final size:11
Alignment explanation
Indices: 4518295--4518324 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
4518285 TTATTTTTAA
4518295 AATTAAAATTT
1 AATTAAAATTT
4518306 AATTTAAAATTT
1 AA-TTAAAATTT
4518318 AATTAAA
1 AATTAAA
4518325 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTAAAATTT
Found at i:4521502 original size:6 final size:6
Alignment explanation
Indices: 4521493--4521526 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
4521483 TGTCCATGGA
4521493 GTATAT GTATAT GTATAT GTATAT GTATAT GTAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTAT
4521527 GTACTTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:4529900 original size:18 final size:19
Alignment explanation
Indices: 4529877--4529914 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4529867 AAGTCGAGTT
*
4529877 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATATAAAA
4529895 ATTTATTTAATATATAAAA
1 ATTTATTTAATATATAAAA
4529914 A
1 A
4529915 AATTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTTAATATATAAAA
Found at i:4530194 original size:15 final size:16
Alignment explanation
Indices: 4530169--4530206 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4530159 TAGTAAAAGA
4530169 AAAATATT-AAATTATT
1 AAAATATTAAAATT-TT
4530185 AAAA-ATTAAAATTTT
1 AAAATATTAAAATTTT
4530200 AAAATAT
1 AAAATAT
4530207 ATATTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATTAAAATTTT
Found at i:4531008 original size:12 final size:13
Alignment explanation
Indices: 4530991--4531019 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4530981 ATTATTACAG
4530991 TTAAATTTTTT-A
1 TTAAATTTTTTGA
4531003 TTAAATTTTTTGA
1 TTAAATTTTTTGA
4531016 TTAA
1 TTAA
4531020 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TTAAATTTTTTGA
Found at i:4535706 original size:21 final size:22
Alignment explanation
Indices: 4535669--4535713 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4535659 AAATAAAATT
*
4535669 ATTTATATTTTATATAAA-TAA
1 ATTTATATTTCATATAAATTAA
4535690 ATTTATATTATCA-ATAAATTAA
1 ATTTATATT-TCATATAAATTAA
4535712 AT
1 AT
4535714 AATATCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTATATTTCATATAAATTAA
Found at i:4537144 original size:11 final size:11
Alignment explanation
Indices: 4537112--4537148 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4537102 TTTAGATATA
4537112 ATAAAAA-AAT
1 ATAAAAATAAT
4537122 -TAAAATATAAT
1 ATAAAA-ATAAT
4537133 ATAAAAATAAT
1 ATAAAAATAAT
4537144 ATAAA
1 ATAAA
4537149 TATTTCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.21
10 1 0.04
11 13 0.54
12 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:4537149 original size:22 final size:19
Alignment explanation
Indices: 4537107--4537151 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
4537097 ATAATTTTAG
*
4537107 ATATAATAAAAAAATTAAA
1 ATATAATAAAAAAAATAAA
4537126 ATATAATATAAAAATAATATAA
1 ATATAATA-AAAAA-AATA-AA
4537148 ATAT
1 ATAT
4537152 TTCATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 5 0.23
21 3 0.14
22 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATAATAAAAAAAATAAA
Found at i:4537917 original size:2 final size:2
Alignment explanation
Indices: 4537910--4537938 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4537900 TTAATCTTCT
4537910 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 T
4537939 TCATAGTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4538872 original size:6 final size:6
Alignment explanation
Indices: 4538861--4538892 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4538851 TTTAAATAAT
*
4538861 TTTATA TTTATA TTTATA TTTATA TATATA TT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TT
4538893 AAATATCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:4548808 original size:2 final size:2
Alignment explanation
Indices: 4548803--4548845 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4548793 CCCCTGCCCC
4548803 AT AT AT AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4548843 AT A
1 AT A
4548846 AATCCCAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4561664 original size:16 final size:16
Alignment explanation
Indices: 4561634--4561663 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4561624 AAATTATTTG
4561634 TTTATTTAATTTTTTA
1 TTTATTTAATTTTTTA
4561650 TTTATTT-ATTTTTT
1 TTTATTTAATTTTTT
4561664 TGGGCAAACT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTAATTTTTTA
Found at i:4562850 original size:2 final size:2
Alignment explanation
Indices: 4562843--4562870 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4562833 ATGGAAATTG
4562843 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4562871 TTAGGAATAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4567212 original size:2 final size:2
Alignment explanation
Indices: 4567200--4567234 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4567190 TAATAAATGC
*
4567200 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4567235 TATCATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4567858 original size:29 final size:28
Alignment explanation
Indices: 4567826--4567886 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
4567816 TATTTTATTT
4567826 AAAAT-AAAATTTATTTAAATATACATATA
1 AAAATAAAAATTTATTTAAATATA-ATA-A
*
4567855 AAAATAAAAAATTTATTTAGATATAATAA
1 AAAAT-AAAAATTTATTTAAATATAATAA
4567884 AAA
1 AAA
4567887 TATAGTGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 9 0.31
30 3 0.10
31 17 0.59
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATAAAAATTTATTTAAATATAATAA
Found at i:4568779 original size:13 final size:16
Alignment explanation
Indices: 4568746--4568800 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 16
4568736 ATCGTAATAT
*
4568746 AATTTAA-TTATTTTAA
1 AATTTAATTTATATT-A
4568762 AATTT-A-TTATA-TA
1 AATTTAATTTATATTA
4568775 AATTTAATTTATATTA
1 AATTTAATTTATATTA
4568791 AA-TTAATTTA
1 AATTTAATTTA
4568801 AATTTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
13 6 0.17
14 2 0.06
15 18 0.51
16 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTAATTTATATTA
Found at i:4568789 original size:20 final size:21
Alignment explanation
Indices: 4568757--4568808 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
4568747 ATTTAATTAT
* *
4568757 TTTAAAATT-TATTATATAAA
1 TTTAAATTTATATTAAATAAA
*
4568777 TTT-AATTTATATTAAATTAA
1 TTTAAATTTATATTAAATAAA
4568797 TTTAAATTTATA
1 TTTAAATTTATA
4568809 AATTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 15 0.56
21 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAATTTATATTAAATAAA
Found at i:4576331 original size:27 final size:28
Alignment explanation
Indices: 4576266--4576336 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
4576256 AAACAAGCCT
*
4576266 CCATATTTGACAAATC-CAAAGAAAACCA
1 CCATTTTTGACAAA-CACAAAGAAAACCA
* *
4576294 CCATTTTTGACAAACACAAA-ATAACTA
1 CCATTTTTGACAAACACAAAGAAAACCA
4576321 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
4576337 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Found at i:4578240 original size:21 final size:22
Alignment explanation
Indices: 4578216--4578261 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
4578206 ATTTGTTGAA
**
4578216 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGTCGTGGAGTACT
4578237 ACTCCACCTGTCGTGGAGTACT
1 ACTCCACCTGTCGTGGAGTACT
4578259 ACT
1 ACT
4578262 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGTCGTGGAGTACT
Found at i:4581482 original size:2 final size:2
Alignment explanation
Indices: 4581477--4581505 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4581467 GTTCCAAAAA
4581477 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
4581506 AAAAGAGCAG
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:4584444 original size:32 final size:34
Alignment explanation
Indices: 4584408--4584477 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 34
4584398 ACATTATTAG
**
4584408 TAAATTAA-ATTA-TACTATTTTATTAAA-AAATA
1 TAAATTAATATTATTAAAATTTT-TTAAATAAATA
4584440 TAAA-TAATATTATTAAAATTTTTTAAATAAATA
1 TAAATTAATATTATTAAAATTTTTTAAATAAATA
4584473 TAAAT
1 TAAAT
4584478 ATTTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
31 3 0.09
32 13 0.41
33 16 0.50
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATTAATATTATTAAAATTTTTTAAATAAATA
Found at i:4585693 original size:2 final size:2
Alignment explanation
Indices: 4585686--4585720 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4585676 AAATTCCAAC
*
4585686 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4585721 GACACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4587155 original size:39 final size:39
Alignment explanation
Indices: 4587101--4587193 Score: 186
Period size: 39 Copynumber: 2.4 Consensus size: 39
4587091 TAAAGATATA
4587101 TGCTCCCCCATGTGTTGATAAGTTGTTGCGGGTTGTAAT
1 TGCTCCCCCATGTGTTGATAAGTTGTTGCGGGTTGTAAT
4587140 TGCTCCCCCATGTGTTGATAAGTTGTTGCGGGTTGTAAT
1 TGCTCCCCCATGTGTTGATAAGTTGTTGCGGGTTGTAAT
4587179 TGCTCCCCCATGTGT
1 TGCTCCCCCATGTGT
4587194 GCCATTATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (39 bp):
TGCTCCCCCATGTGTTGATAAGTTGTTGCGGGTTGTAAT
Found at i:4589484 original size:2 final size:2
Alignment explanation
Indices: 4589477--4589506 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4589467 CCATACGTTG
4589477 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
4589507 GTCGGTAGGG
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:4591797 original size:2 final size:2
Alignment explanation
Indices: 4591790--4591840 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4591780 CATCCAGGCC
4591790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4591832 TA TA TA TA T
1 TA TA TA TA T
4591841 CTAATTAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4593374 original size:32 final size:32
Alignment explanation
Indices: 4593338--4593400 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
4593328 TGAAGTATGA
4593338 CTTGGTATCTAACGATGTTTGAATGACCTAAT
1 CTTGGTATCTAACGATGTTTGAATGACCTAAT
4593370 CTTGGTATCTAACGATGTTTGAATGACCTAA
1 CTTGGTATCTAACGATGTTTGAATGACCTAA
4593401 CCTTCCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (32 bp):
CTTGGTATCTAACGATGTTTGAATGACCTAAT
Found at i:4593482 original size:2 final size:2
Alignment explanation
Indices: 4593475--4593507 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4593465 TTTTACCTTT
4593475 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 T
4593508 TTGAGGGTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4593658 original size:15 final size:15
Alignment explanation
Indices: 4593640--4593678 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
4593630 TGCAAATTAA
4593640 ACTTGAT-TGAATTCT
1 ACTTGATCT-AATTCT
*
4593655 ACTTAATCTAATTCT
1 ACTTGATCTAATTCT
4593670 ACTTGATCT
1 ACTTGATCT
4593679 CGACCTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (15 bp):
ACTTGATCTAATTCT
Found at i:4598685 original size:5 final size:5
Alignment explanation
Indices: 4598675--4598704 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
4598665 TTAAGAATTG
*
4598675 AAGAA AAGAA AAGAA AAGAA AAGGA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
4598705 GCAAGGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:4599277 original size:5 final size:5
Alignment explanation
Indices: 4599269--4599294 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4599259 ATTAAATTTT
4599269 TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA T
4599295 AAAAAAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:4599939 original size:23 final size:21
Alignment explanation
Indices: 4599893--4599948 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 21
4599883 CATCTTTGAG
4599893 ATATTTATAA-TT-TTTTAAA
1 ATATTTATAATTTATTTTAAA
4599912 ATATTTATAATTTATTTTATATA
1 ATATTTATAATTTATTTTA-A-A
*
4599935 TTATTTA-AATTTAT
1 ATATTTATAATTTAT
4599949 ATTTTTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.31
20 2 0.06
21 5 0.16
22 8 0.25
23 7 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTATAATTTATTTTAAA
Found at i:4599952 original size:35 final size:36
Alignment explanation
Indices: 4599912--4599988 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
4599902 ATTTTTTAAA
* * *
4599912 ATATTTATAATTTATTT-TATA-TATTATTTAAATTT
1 ATATTTATAA-TGATTTAAATATTATTAATTAAATTT
*
4599947 ATATTT-TTATGATTTAAATATTATTAATTAAATTT
1 ATATTTATAATGATTTAAATATTATTAATTAAATTT
4599982 ATATTTA
1 ATATTTA
4599989 AAAATAGTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 5 0.14
34 5 0.14
35 25 0.71
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (36 bp):
ATATTTATAATGATTTAAATATTATTAATTAAATTT
Found at i:4599970 original size:14 final size:12
Alignment explanation
Indices: 4599912--4599990 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
4599902 ATTTTTTAAA
4599912 ATATTTATAATTT
1 ATATTTA-AATTT
* *
4599925 AT-TTTATATAT
1 ATATTTAAATTT
4599936 -TATTTAAATTT
1 ATATTTAAATTT
4599947 ATA-TT---TTT
1 ATATTTAAATTT
4599955 ATGATTTAAATATT
1 AT-ATTTAAAT-TT
*
4599969 ATTAATTAAATTT
1 A-TATTTAAATTT
4599982 ATATTTAAA
1 ATATTTAAA
4599991 AATAGTCGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 19
0.67 0.08 0.25
Matches are distributed among these distances:
8 5 0.10
9 1 0.02
10 3 0.06
11 12 0.24
12 13 0.25
13 6 0.12
14 10 0.20
15 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
ATATTTAAATTT
Found at i:4600179 original size:37 final size:39
Alignment explanation
Indices: 4600127--4600199 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
4600117 ATTAATATAT
*
4600127 TTTAAATCATAAATATA-ATATTTAAATTTA-AAAATTA
1 TTTAAATCATAAATATATATATATAAATTTACAAAATTA
*
4600164 TTTAAATC-TATAATATATATATATATATTTACAAAA
1 TTTAAATCATA-AATATATATATATAAATTTACAAAA
4600200 ATAAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 2 0.06
37 14 0.45
38 11 0.35
39 4 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (39 bp):
TTTAAATCATAAATATATATATATAAATTTACAAAATTA
Found at i:4605258 original size:59 final size:60
Alignment explanation
Indices: 4605188--4605306 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 60
4605178 GCATAAGCTA
4605188 CCATTCCATTACAATCTTAGGAATAGTCGTTAAATTTTCTTATAC-TTTTTTTTTCCTTT
1 CCATTCCATTACAATCTTAGGAATAGTCGTTAAATTTTCTTATACTTTTTTTTTTCCTTT
**
4605247 CCATTCCATTACAATCTTAGGAATAGTTTTTAAATTTTCTTATACTTTTTTTTTTCCTTT
1 CCATTCCATTACAATCTTAGGAATAGTCGTTAAATTTTCTTATACTTTTTTTTTTCCTTT
4605307 TGACATATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 43 0.75
60 14 0.25
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (60 bp):
CCATTCCATTACAATCTTAGGAATAGTCGTTAAATTTTCTTATACTTTTTTTTTTCCTTT
Found at i:4608492 original size:2 final size:2
Alignment explanation
Indices: 4608485--4608513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4608475 TATTTGTATG
4608485 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 T
4608514 TCTGAAAGGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.