Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 15 of 33
Found at i:2344002 original size:22 final size:21
Alignment explanation
Indices: 2343977--2344044 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 21
2343967 CTATTCAAAA
2343977 TAATATTAAAAATATTTTATAT
1 TAATATTAAAAATATTTT-TAT
* *
2343999 TAATATT-TATATATTTTTATT
1 TAATATTAAAAATATTTTTA-T
2344020 TAA-A-TAAAAATATTTTTAAT
1 TAATATTAAAAATATTTTT-AT
2344040 TAATA
1 TAATA
2344045 AATAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 16 0.42
21 14 0.37
22 7 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATATTAAAAATATTTTTAT
Found at i:2344032 original size:20 final size:20
Alignment explanation
Indices: 2343983--2344051 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2343973 AAAATAATAT
2343983 TAAA-AATA-TTTTATATTAA
1 TAAATAATATTTTTA-ATTAA
** *
2344002 TATTTATATATTTTTATTTAAA
1 TAAATA-ATATTTTTAATT-AA
2344024 TAAA-AATATTTTTAATTAA
1 TAAATAATATTTTTAATTAA
2344043 TAAATAATA
1 TAAATAATA
2344052 ATTCAAGTCG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 8 0.21
20 16 0.41
21 6 0.15
22 9 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATAATATTTTTAATTAA
Found at i:2352269 original size:3 final size:3
Alignment explanation
Indices: 2352261--2352293 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2352251 ACTCTCAAAT
2352261 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2352294 CAAACAAATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2354587 original size:30 final size:33
Alignment explanation
Indices: 2354551--2354615 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
2354541 CAAAATAATT
*
2354551 AAAATAAA-A-TATAAA-ACATAAATA-ATGTAA
1 AAAATAAACATTATAAATAAATAAATATAT-TAA
2354581 AAAATAAACATTATAAATAAATAAATATATTAA
1 AAAATAAACATTATAAATAAATAAATATATTAA
2354614 AA
1 AA
2354616 TTTATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 8 0.27
31 1 0.03
32 6 0.20
33 13 0.43
34 2 0.07
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (33 bp):
AAAATAAACATTATAAATAAATAAATATATTAA
Found at i:2354614 original size:17 final size:17
Alignment explanation
Indices: 2354559--2354615 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
2354549 TTAAAATAAA
*
2354559 ATATAAAACATAAATA-
1 ATATAAAAAATAAATAT
* *
2354575 ATGTAAAAAATAAACAT
1 ATATAAAAAATAAATAT
2354592 -TATAAATAAATAAATAT
1 ATATAAA-AAATAAATAT
2354609 AT-TAAAA
1 ATATAAAA
2354616 TTTATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 19 0.58
17 13 0.39
18 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (17 bp):
ATATAAAAAATAAATAT
Found at i:2355931 original size:24 final size:24
Alignment explanation
Indices: 2355904--2355950 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2355894 AATTAATTCA
* *
2355904 ATAAAAATTAAATTTTAATTTTTT
1 ATAAAAATAAAATTTAAATTTTTT
*
2355928 ATAATAATAAAATTTAAATTTTT
1 ATAAAAATAAAATTTAAATTTTT
2355951 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAAAATAAAATTTAAATTTTTT
Found at i:2355937 original size:30 final size:31
Alignment explanation
Indices: 2355903--2355963 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2355893 AAATTAATTC
2355903 AATAAAAATTAAA-TTTTAATTTTTTATAAT
1 AATAAAAATTAAATTTTTAATTTTTTATAAT
* *
2355933 AATAAAATTTAAATTTTTAATTTTTTTTAAT
1 AATAAAAATTAAATTTTTAATTTTTTATAAT
2355964 TTTATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
AATAAAAATTAAATTTTTAATTTTTTATAAT
Found at i:2357297 original size:18 final size:18
Alignment explanation
Indices: 2357274--2357319 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
2357264 ATGTTGAAAA
2357274 TTATACTTGTAATGATAT
1 TTATACTTGTAATGATAT
2357292 TTATACTCTTGTAATGATAT
1 TTATA--CTTGTAATGATAT
*
2357312 TTAAACTT
1 TTATACTT
2357320 ACATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (18 bp):
TTATACTTGTAATGATAT
Found at i:2360045 original size:20 final size:19
Alignment explanation
Indices: 2360020--2360057 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2360010 AAAGAATTGA
2360020 AGAGGGACGAGGGATGCTTG
1 AGAGGGACGAGGGA-GCTTG
*
2360040 AGAGGGAGGAGGGAGCTT
1 AGAGGGACGAGGGAGCTT
2360058 CTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.08, G:0.53, T:0.13
Consensus pattern (19 bp):
AGAGGGACGAGGGAGCTTG
Found at i:2361349 original size:31 final size:31
Alignment explanation
Indices: 2361313--2361414 Score: 80
Period size: 41 Copynumber: 3.0 Consensus size: 31
2361303 TAATAAAAAA
2361313 TATATTTAAATTTTTATAAATTAAAATAAAT
1 TATATTTAAATTTTTATAAATTAAAATAAAT
*
2361344 TATATTTTAAAAGTTTAAATTCATATAATTAAATAAAAAAT
1 TATA-TTT-AAA-TTT---TT-ATA-AATT-AA-AATAAAT
* *
2361385 TA-ATTTAAATTTTTACAAATAAAAATAAAT
1 TATATTTAAATTTTTATAAATTAAAATAAAT
2361415 AATAACTCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
30 6 0.11
31 6 0.11
32 6 0.11
33 5 0.09
34 5 0.09
37 5 0.09
38 6 0.11
39 7 0.12
40 3 0.05
41 8 0.14
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (31 bp):
TATATTTAAATTTTTATAAATTAAAATAAAT
Found at i:2361464 original size:22 final size:24
Alignment explanation
Indices: 2361428--2361471 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2361418 AACTCTAATC
*
2361428 AAATTAATAT-TTTAAATAAAAAT
1 AAATTAATATCTTAAAATAAAAAT
2361451 AAATT-ATATCTTAAAATAAAA
1 AAATTAATATCTTAAAATAAAA
2361472 TAACTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATTAATATCTTAAAATAAAAAT
Found at i:2361757 original size:16 final size:15
Alignment explanation
Indices: 2361733--2361771 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2361723 AAATTCATAT
2361733 AATTAAATAAAAAATA
1 AATTAAAT-AAAAATA
*
2361749 AATTTAATAAAAATA
1 AATTAAATAAAAATA
*
2361764 AATCAAAT
1 AATTAAAT
2361772 TTATTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTAAATAAAAATA
Found at i:2368899 original size:15 final size:15
Alignment explanation
Indices: 2368875--2368916 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2368865 GATAAGTAGT
* *
2368875 TGGATAAACATGTGA
1 TGGATGAACAAGTGA
2368890 TGGATGAACAAGTGA
1 TGGATGAACAAGTGA
2368905 TGGATGAA-AAGT
1 TGGATGAACAAGT
2368917 AGTGCATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.40, C:0.05, G:0.31, T:0.24
Consensus pattern (15 bp):
TGGATGAACAAGTGA
Found at i:2373077 original size:5 final size:5
Alignment explanation
Indices: 2373067--2373091 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2373057 AATGAAGATC
2373067 GGTTG GGTTG GGTTG GGTTG GGTTG
1 GGTTG GGTTG GGTTG GGTTG GGTTG
2373092 CTGTCAGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGTTG
Found at i:2374139 original size:37 final size:32
Alignment explanation
Indices: 2374075--2374148 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
2374065 TATTATAATT
*
2374075 AAATTTAAATAAAATTTTTTATTATTAAATAA
1 AAATTTAAATAAAATTTTTGATTATTAAATAA
*
2374107 TAATTTAAATAAAATTAATTTGATTTAAATTAAATAA
1 AAATTTAAATAAAATT--TTTGA-TT--ATTAAATAA
2374144 AAATT
1 AAATT
2374149 ATATTCAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 15 0.44
34 4 0.12
35 2 0.06
37 13 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
AAATTTAAATAAAATTTTTGATTATTAAATAA
Found at i:2374869 original size:10 final size:10
Alignment explanation
Indices: 2374854--2374960 Score: 59
Period size: 10 Copynumber: 11.1 Consensus size: 10
2374844 CATAATAATT
2374854 TATATATTTA
1 TATATATTTA
2374864 TATATATTTA
1 TATATATTTA
2374874 TATAT-TTTA
1 TATATATTTA
*
2374883 -ATGTA-TTA
1 TATATATTTA
2374891 TA-AT-TTTA
1 TATATATTTA
* **
2374899 TTTA-ATAAA
1 TATATATTTA
2374908 TTATATATTTA
1 -TATATATTTA
*
2374919 TATAAATTT-
1 TATATATTTA
*
2374928 TA-ATAAATTA
1 TATAT-ATTTA
*
2374938 TAAATATTAATA
1 TATATATT--TA
2374950 TATATATTTA
1 TATATATTTA
2374960 T
1 T
2374961 TTCTTTTATT
Statistics
Matches: 72, Mismatches: 13, Indels: 24
0.66 0.12 0.22
Matches are distributed among these distances:
8 12 0.17
9 13 0.18
10 33 0.46
11 5 0.07
12 9 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
TATATATTTA
Found at i:2375663 original size:33 final size:32
Alignment explanation
Indices: 2375626--2375701 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
2375616 TTTTAATGGA
2375626 TTTATTTTTAAAAAATAAAT-AATTATTTAAATT
1 TTTATTTTTAAAAAATAAATAAATT-TTTAAA-T
* * * *
2375659 TTTATTTTTGTACAATTAAGTAAATTTTTAAAT
1 TTTATTTTT-AAAAAATAAATAAATTTTTAAAT
2375692 TTTATTTTTA
1 TTTATTTTTA
2375702 TTTAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
33 19 0.53
34 13 0.36
35 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (32 bp):
TTTATTTTTAAAAAATAAATAAATTTTTAAAT
Found at i:2375705 original size:17 final size:17
Alignment explanation
Indices: 2375685--2375725 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
2375675 TAAGTAAATT
2375685 TTTAAATT-TTATTTTTA
1 TTTAAATTATT-TTTTTA
2375702 TTT-AATTAATTTTTTTA
1 TTTAAATT-ATTTTTTTA
2375719 TTTAAAT
1 TTTAAAT
2375726 AAAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 12 0.57
18 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAAATTATTTTTTTA
Found at i:2378329 original size:18 final size:18
Alignment explanation
Indices: 2378306--2378340 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2378296 GCTCCAGTTG
*
2378306 ATGTGGTTGGAGGTGCAC
1 ATGTGGTCGGAGGTGCAC
*
2378324 ATGTGGTCGGTGGTGCA
1 ATGTGGTCGGAGGTGCA
2378341 ACAATGTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.11, G:0.46, T:0.29
Consensus pattern (18 bp):
ATGTGGTCGGAGGTGCAC
Found at i:2381042 original size:23 final size:23
Alignment explanation
Indices: 2381022--2381066 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2381012 TTAATTTAGA
2381022 TTAAATTATTTTTAAATTTTAAAT
1 TTAAATT-TTTTTAAATTTTAAAT
* *
2381046 TTTAATTTTTTTTAATTTTAA
1 TTAAATTTTTTTAAATTTTAA
2381067 GTGATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTAAATTTTTTTAAATTTTAAAT
Found at i:2381087 original size:26 final size:28
Alignment explanation
Indices: 2381057--2381115 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
2381047 TTAATTTTTT
* *
2381057 TTAATTTTAAG-TGATTTTATATTTAAA
1 TTAATTTTAAGATAATTTTAAATTTAAA
*
2381084 -TAA-TTTCAGATAATTTTAAATTTAAA
1 TTAATTTTAAGATAATTTTAAATTTAAA
2381110 TTAATT
1 TTAATT
2381116 AAATTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
27 3 0.12
28 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (28 bp):
TTAATTTTAAGATAATTTTAAATTTAAA
Found at i:2381119 original size:15 final size:16
Alignment explanation
Indices: 2381099--2381129 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2381089 TCAGATAATT
2381099 TTAAATTT-AAATTAA
1 TTAAATTTAAAATTAA
2381114 TTAAATTTAAAATTAA
1 TTAAATTTAAAATTAA
2381130 GGTTCATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAAATTAA
Found at i:2381715 original size:16 final size:15
Alignment explanation
Indices: 2381694--2381736 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
2381684 AACTCGCATT
2381694 TTAAAATAATCTAAA
1 TTAAAATAATCTAAA
*
2381709 CTTAAAATAATTTAAA
1 -TTAAAATAATCTAAA
2381725 TTCAAAATAATC
1 TT-AAAATAATC
2381737 AATTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAATAATCTAAA
Found at i:2381927 original size:15 final size:15
Alignment explanation
Indices: 2381907--2381947 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2381897 AAAATTATCT
2381907 AAAATTTAAATAATA
1 AAAATTTAAATAATA
* *
2381922 AAAATTAAAATAATT
1 AAAATTTAAATAATA
*
2381937 TAAATTTAAAT
1 AAAATTTAAAT
2381948 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATTTAAATAATA
Found at i:2381952 original size:15 final size:15
Alignment explanation
Indices: 2381898--2381986 Score: 54
Period size: 15 Copynumber: 5.7 Consensus size: 15
2381888 ATTAAACATA
*
2381898 AAATTATCTAAAATTT
1 AAATTAT-TTAAATTT
* ** *
2381914 AAATAATAAAAATTA
1 AAATTATTTAAATTT
*
2381929 AAATAATTTAAATTT
1 AAATTATTTAAATTT
*
2381944 AAATTATTTAAAAATCT
1 AAATTATTT--AAATTT
* *
2381961 AAATCAATT-AATTT
1 AAATTATTTAAATTT
2381975 AAATTAATTTAA
1 AAATT-ATTTAA
2381987 TTAAAAATTA
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
14 8 0.14
15 29 0.52
16 7 0.12
17 12 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTATTTAAATTT
Found at i:2381964 original size:47 final size:46
Alignment explanation
Indices: 2381898--2381986 Score: 108
Period size: 47 Copynumber: 1.9 Consensus size: 46
2381888 ATTAAACATA
*
2381898 AAATTATCTAAAATTTAAAT-AATAAAAATTAAAATAATTTAAATTT
1 AAATTATCTAAAATCTAAATCAAT-AAAATTAAAATAATTTAAATTT
* * * *
2381944 AAATTATTTAAAAATCTAAATCAATTAATTTAAATTAATTTAA
1 AAATTATCT-AAAATCTAAATCAATAAAATTAAAATAATTTAA
2381987 TTAAAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 8 0.22
47 25 0.69
48 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (46 bp):
AAATTATCTAAAATCTAAATCAATAAAATTAAAATAATTTAAATTT
Found at i:2381975 original size:37 final size:35
Alignment explanation
Indices: 2381932--2382004 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
2381922 AAAATTAAAA
*
2381932 TAATTTAAATTTAAATTATTTAAAAATCTAAATCAAT
1 TAATTTAAA-TTAAATTAATTAAAAAT-TAAATCAAT
* *
2381969 TAATTTAAATTAATTTAATTAAAAATTAATTCAAT
1 TAATTTAAATTAAATTAATTAAAAATTAAATCAAT
2382004 T
1 T
2382005 CGCCTAGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 9 0.27
36 15 0.45
37 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (35 bp):
TAATTTAAATTAAATTAATTAAAAATTAAATCAAT
Found at i:2382224 original size:12 final size:12
Alignment explanation
Indices: 2382207--2382231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2382197 GAAGTACATT
2382207 TATATTATTTTA
1 TATATTATTTTA
2382219 TATATTATTTTA
1 TATATTATTTTA
2382231 T
1 T
2382232 TTTAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTATTTTA
Found at i:2382245 original size:16 final size:17
Alignment explanation
Indices: 2382206--2382258 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2382196 AGAAGTACAT
*
2382206 TTATATTATTTTATATA
1 TTATTTTATTTTATATA
2382223 TTATTTTATTTTA-AT-
1 TTATTTTATTTTATATA
*
2382238 TATATTTTAATATTATATA
1 T-TATTTT-ATTTTATATA
2382257 TT
1 TT
2382259 TATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 8 0.27
17 17 0.57
18 3 0.10
19 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTTTATTTTATATA
Found at i:2382254 original size:13 final size:12
Alignment explanation
Indices: 2382205--2382264 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 12
2382195 TAGAAGTACA
2382205 TTTATATTAT-T
1 TTTATATTATAT
2382216 TTATATATTATTTTAT
1 TT-TATATTA---TAT
2382232 TTTA-ATTATAT
1 TTTATATTATAT
2382243 TTTAATATTATAT
1 TTT-ATATTATAT
2382256 ATTTATATT
1 -TTTATATT
2382265 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
11 8 0.20
12 8 0.20
13 12 0.29
14 7 0.17
15 3 0.07
16 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:2382278 original size:32 final size:34
Alignment explanation
Indices: 2382216--2382280 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
2382206 TTATATTATT
* *
2382216 TTATATATTATTTTATTTTAATTATATTTTAATA
1 TTATATATTATATTATTTTAATAATATTTTAATA
2382250 TTATATATTTATATT-TTTTAA-AAT-TTTTAAT
1 TTATATA-TTATATTATTTTAATAATATTTTAAT
2382281 TTTTATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.25
33 2 0.07
34 13 0.46
35 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (34 bp):
TTATATATTATATTATTTTAATAATATTTTAATA
Found at i:2382301 original size:18 final size:17
Alignment explanation
Indices: 2382280--2382340 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
2382270 AAATTTTTAA
2382280 TTTTTATTAATTGAATAT
1 TTTTTATTAATT-AATAT
*
2382298 TTTTTATTTATTAA-A-
1 TTTTTATTAATTAATAT
* *
2382313 TTTTAAATAATTTAATAT
1 TTTTTATTAA-TTAATAT
2382331 TTTTT-TTAAT
1 TTTTTATTAAT
2382341 ATTTTATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 6 0.18
18 15 0.44
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTATTAATTAATAT
Found at i:2382306 original size:47 final size:52
Alignment explanation
Indices: 2382204--2382308 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 52
2382194 CTAGAAGTAC
* * *
2382204 ATTTATATTATTTTATATATTATTTTATTTTAATTATATTTTAATATTATAT
1 ATTTATATTATTTTATAAATTATTTAATTTTAATTATATTTGAATATTATAT
* * *
2382256 ATTTATATT-TTTTA-AAATT-TTTAATTTTTATTA-A-TTGAATATTTTTT
1 ATTTATATTATTTTATAAATTATTTAATTTTAATTATATTTGAATATTATAT
2382303 ATTTAT
1 ATTTAT
2382309 TAAATTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
47 16 0.34
48 1 0.02
49 12 0.26
50 4 0.09
51 5 0.11
52 9 0.19
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (52 bp):
ATTTATATTATTTTATAAATTATTTAATTTTAATTATATTTGAATATTATAT
Found at i:2382382 original size:19 final size:21
Alignment explanation
Indices: 2382353--2382403 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2382343 TTTATATTAT
2382353 AAATTACATATAT-AAAATA-A
1 AAATTA-ATATATAAAAATATA
*
2382373 AATTTAATATATAAAAATATA
1 AAATTAATATATAAAAATATA
2382394 AAATTAATAT
1 AAATTAATAT
2382404 TTATTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 11 0.41
21 10 0.37
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATTAATATATAAAAATATA
Found at i:2382411 original size:28 final size:27
Alignment explanation
Indices: 2382362--2382414 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2382352 TAAATTACAT
2382362 ATATAAAATAAAATTTAATATATAAAA
1 ATATAAAATAAAATTTAATATATAAAA
* *
2382389 ATATAAAATTAATATTTATTATATAA
1 ATATAAAA-TAAAATTTAATATATAA
2382415 TTATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATATAAAATAAAATTTAATATATAAAA
Found at i:2382439 original size:16 final size:17
Alignment explanation
Indices: 2382413--2382444 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2382403 TTTATTATAT
2382413 AATTATAAATTAAATTA
1 AATTATAAATTAAATTA
2382430 AATT-TAAATTAAATT
1 AATTATAAATTAAATT
2382445 TTATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATAAATTAAATTA
Found at i:2382521 original size:31 final size:31
Alignment explanation
Indices: 2382483--2382563 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
2382473 GTTTATAATT
*
2382483 AATTTAATA-TTTTATTTAAATTTATTTTTAA
1 AATTTAATATTTTTAATTAAATTT-TTTTTAA
2382514 AATTTAATATTTTTAATTAAA-TTTTTTTAA
1 AATTTAATATTTTTAATTAAATTTTTTTTAA
**
2382544 ATATAAAATAATTTTTAATT
1 A-ATTTAAT-ATTTTTAATT
2382564 TTAAATTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
30 8 0.18
31 16 0.36
32 20 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
AATTTAATATTTTTAATTAAATTTTTTTTAA
Found at i:2383430 original size:13 final size:13
Alignment explanation
Indices: 2383402--2383445 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
2383392 TTTCAAAATT
2383402 TTTTAGAGATATAA
1 TTTTAGAGA-ATAA
2383416 TTTTAGAGAATAA
1 TTTTAGAGAATAA
*
2383429 TTATTA-AAAATAA
1 TT-TTAGAGAATAA
2383442 TTTT
1 TTTT
2383446 TTATCTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 12 0.43
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (13 bp):
TTTTAGAGAATAA
Found at i:2383799 original size:27 final size:27
Alignment explanation
Indices: 2383748--2383799 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2383738 TGAACATATG
**
2383748 AAATTTATATAAAATAAACTTGATACA
1 AAATTTATATAAAATAAACACGATACA
*
2383775 AAATTTATATAAAATGAACACGATA
1 AAATTTATATAAAATAAACACGATA
2383800 TGAACTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (27 bp):
AAATTTATATAAAATAAACACGATACA
Found at i:2385773 original size:13 final size:14
Alignment explanation
Indices: 2385766--2385794 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2385756 TTAATCAATT
2385766 TTTTTAATATATTA
1 TTTTTAATATATTA
2385780 TTTTTAAT-TATTA
1 TTTTTAATATATTA
2385793 TT
1 TT
2385795 AAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAATATATTA
Found at i:2387113 original size:10 final size:10
Alignment explanation
Indices: 2387093--2387145 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
2387083 ATATTAATTT
2387093 AATTA-ATAA
1 AATTATATAA
2387102 AATTATATAA
1 AATTATATAA
* *
2387112 AATTTTAAATTA
1 AA--TTATATAA
2387124 AATTATATAA
1 AATTATATAA
*
2387134 AATTTTATAA
1 AATTATATAA
2387144 AA
1 AA
2387146 ATAAAGATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.14
10 23 0.64
12 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTATATAA
Found at i:2387916 original size:3 final size:3
Alignment explanation
Indices: 2387908--2387945 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2387898 TCATTTGGCC
2387908 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2387946 AGGGTTGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2389174 original size:2 final size:2
Alignment explanation
Indices: 2389167--2389201 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2389157 CTAGACTCAA
2389167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2389202 ATAACTAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2389402 original size:3 final size:3
Alignment explanation
Indices: 2389396--2389424 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2389386 CAACAACAAC
2389396 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2389425 AGCCAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2391806 original size:20 final size:20
Alignment explanation
Indices: 2391774--2391811 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2391764 ATTATATTAA
2391774 TATTAATTTAATATTAAACT
1 TATTAATTTAATATTAAACT
2391794 TATT-ATTTAAATATTAAA
1 TATTAATTT-AATATTAAA
2391812 AAAACTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAATTTAATATTAAACT
Found at i:2393035 original size:14 final size:14
Alignment explanation
Indices: 2393012--2393042 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2393002 AATAAATAAT
*
2393012 TTAATTTTTATTTA
1 TTAATATTTATTTA
2393026 TTAATATTTATTTA
1 TTAATATTTATTTA
2393040 TTA
1 TTA
2393043 TATAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTAATATTTATTTA
Found at i:2394731 original size:15 final size:17
Alignment explanation
Indices: 2394691--2394726 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2394681 TTTGAAATGA
*
2394691 ATATCAAATATAAATAT
1 ATATCTAATATAAATAT
*
2394708 ATATCTAATATAATTAT
1 ATATCTAATATAAATAT
2394725 AT
1 AT
2394727 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATCTAATATAAATAT
Found at i:2394973 original size:2 final size:2
Alignment explanation
Indices: 2394968--2394992 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2394958 TACGTGTGTG
2394968 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 T
2394993 CCAGCTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2401500 original size:24 final size:25
Alignment explanation
Indices: 2401473--2401530 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
2401463 GATAATTTAT
2401473 TTAATTTAATAA-ATTTAAATTAAA
1 TTAATTTAATAATATTTAAATTAAA
* * *
2401497 TTAAATTAA-AATTTTTAATTTAAA
1 TTAATTTAATAATATTTAAATTAAA
2401521 TTAATTTAAT
1 TTAATTTAAT
2401531 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATTTAATAATATTTAAATTAAA
Found at i:2404369 original size:24 final size:25
Alignment explanation
Indices: 2404336--2404390 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2404326 TATATTTATT
* * *
2404336 TATTTATAATTTAAT-TAAATTAAA
1 TATTTTTAATTTAATAAAAATAAAA
*
2404360 TATTTTTAATTTTATAAAAATAAAA
1 TATTTTTAATTTAATAAAAATAAAA
2404385 TATTTT
1 TATTTT
2404391 AATAAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTTTAATTTAATAAAAATAAAA
Found at i:2404688 original size:14 final size:15
Alignment explanation
Indices: 2404662--2404690 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2404652 TTAATGTAAA
2404662 TTTTAAAATTAATTT
1 TTTTAAAATTAATTT
2404677 TTTTAAAA-TAATTT
1 TTTTAAAATTAATTT
2404691 AAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTAAAATTAATTT
Found at i:2406004 original size:15 final size:15
Alignment explanation
Indices: 2405986--2406016 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2405976 CTCTAATAAC
2405986 TTTATCTGAGACTGA
1 TTTATCTGAGACTGA
2406001 TTTATCTGAGACTGA
1 TTTATCTGAGACTGA
2406016 T
1 T
2406017 AATGGTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (15 bp):
TTTATCTGAGACTGA
Found at i:2407966 original size:79 final size:79
Alignment explanation
Indices: 2407856--2408114 Score: 281
Period size: 79 Copynumber: 3.3 Consensus size: 79
2407846 TAGCTTAACT
* * *
2407856 AAAATCAAACTTTT-AGAGTCGTATTAGTGATTTCATGCCTAAACCGGACCTTTTAGGGTCATTT
1 AAAACCAAACTTTTAAG-GTCGTATTAGTGATTTCATGCCTAAACTGAACCTTTTAGGGTCATTT
* *
2407920 TAGATTTTTTCCACC
65 TAGACTTTTCCCACC
* * * * * *
2407935 AAAATCAAACTTTTAAGGTTGTATTAGTGATTTTACGCCTAAATTGAACCTTTTAGGGTTATTTT
1 AAAACCAAACTTTTAAGGTCGTATTAGTGATTTCATGCCTAAACTGAACCTTTTAGGGTCATTTT
*
2408000 AGACTTTTCCCACT
66 AGACTTTTCCCACC
* * * * * * * *
2408014 AAAACCAAACCTTCAAGGTCGTATTAG-CACTTTCATGCATAAACTGAACTTTTTTAAGATCCTT
1 AAAACCAAACTTTTAAGGTCGTATTAGTGA-TTTCATGCCTAAACTGAAC-CTTTTAGGGTCATT
2408078 TTAGACTTTTCCCACC
64 TTAGACTTTTCCCACC
2408094 AAAACCAAA-TCTTTAAGGTCG
1 AAAACCAAACT-TTTAAGGTCG
2408115 CGTTAGCACT
Statistics
Matches: 149, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
78 1 0.01
79 104 0.70
80 44 0.30
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (79 bp):
AAAACCAAACTTTTAAGGTCGTATTAGTGATTTCATGCCTAAACTGAACCTTTTAGGGTCATTTT
AGACTTTTCCCACC
Found at i:2411860 original size:13 final size:13
Alignment explanation
Indices: 2411842--2411867 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2411832 ACATTTTGGG
2411842 ATGTATCGATACA
1 ATGTATCGATACA
2411855 ATGTATCGATACA
1 ATGTATCGATACA
2411868 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2411966 original size:20 final size:21
Alignment explanation
Indices: 2411919--2411971 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
2411909 GCCAATGACC
**
2411919 TGTATCGATACATTTTTTTCA
1 TGTATCGATACATTTTAGTCA
*
2411940 AGTATCGATACA-TTTAGTCA
1 TGTATCGATACATTTTAGTCA
2411960 TGTATCGATACA
1 TGTATCGATACA
2411972 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTTAGTCA
Found at i:2411977 original size:13 final size:13
Alignment explanation
Indices: 2411959--2411983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2411949 ACATTTAGTC
2411959 ATGTATCGATACA
1 ATGTATCGATACA
2411972 ATGTATCGATAC
1 ATGTATCGATAC
2411984 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2413075 original size:12 final size:12
Alignment explanation
Indices: 2413060--2413084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2413050 TTACACTAAT
2413060 TTTTGTTTTCAC
1 TTTTGTTTTCAC
2413072 TTTTGTTTTCAC
1 TTTTGTTTTCAC
2413084 T
1 T
2413085 CTCATCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTGTTTTCAC
Found at i:2414049 original size:13 final size:13
Alignment explanation
Indices: 2414031--2414056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2414021 TACAGCAAGT
2414031 ATGTATCGATACA
1 ATGTATCGATACA
2414044 ATGTATCGATACA
1 ATGTATCGATACA
2414057 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2419953 original size:12 final size:12
Alignment explanation
Indices: 2419936--2419965 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2419926 CGTGGACATA
2419936 AATATTGTGGAT
1 AATATTGTGGAT
2419948 AATATTGTGGAT
1 AATATTGTGGAT
*
2419960 GATATT
1 AATATT
2419966 ATGTCAATAA
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:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (12 bp):
AATATTGTGGAT
Found at i:2420617 original size:21 final size:21
Alignment explanation
Indices: 2420567--2420619 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
2420557 ATACATCACT
*
2420567 TTAAAGTATCAATACTTTACA
1 TTAAAGTATCAATACCTTACA
* *
2420588 TAAAAAGTATCAATACCTTATA
1 T-TAAAGTATCAATACCTTACA
2420610 TTAAAGTATC
1 TTAAAGTATC
2420620 GATGCCTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (21 bp):
TTAAAGTATCAATACCTTACA
Found at i:2424665 original size:26 final size:26
Alignment explanation
Indices: 2424612--2424666 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
2424602 TTAAATAATA
*
2424612 AAATATATATTAAAATTATATATGTT
1 AAATATATATTAAAATTATAAATGTT
2424638 AAATA-ATACTTAAAATTATTAAAT-TT
1 AAATATATA-TTAAAATTA-TAAATGTT
2424664 AAA
1 AAA
2424667 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 19 0.73
27 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
AAATATATATTAAAATTATAAATGTT
Found at i:2424714 original size:16 final size:15
Alignment explanation
Indices: 2424693--2424732 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 15
2424683 AATTATAAAC
2424693 TATTAAATTATATTTA
1 TATT-AATTATATTTA
2424709 TATTAA-T-T-TTTA
1 TATTAATTATATTTA
2424721 TATTAATTATAT
1 TATTAATTATAT
2424733 AAGTTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 2 0.10
15 3 0.14
16 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATTATATTTA
Found at i:2424951 original size:16 final size:16
Alignment explanation
Indices: 2424930--2424969 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2424920 TTGTTGAAGG
2424930 ATTAAATTCTATTTTA
1 ATTAAATTCTATTTTA
2424946 ATTAAATTCTATTTTA
1 ATTAAATTCTATTTTA
*
2424962 ATTTAATT
1 ATTAAATT
2424970 TTGGATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTAAATTCTATTTTA
Found at i:2433964 original size:2 final size:2
Alignment explanation
Indices: 2433957--2433995 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2433947 ATGAGATCAC
2433957 AG 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 AG A
2433996 ACTTGCCTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2434596 original size:25 final size:26
Alignment explanation
Indices: 2434567--2434623 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
2434557 TATATGTTTA
*
2434567 AATTATATTAA-ATTATTATAAAAATT
1 AATTATATTAATATTAATAT-AAAATT
*
2434593 -ATTATTTTAATATTAATATAAAATT
1 AATTATATTAATATTAATATAAAATT
2434618 AATTAT
1 AATTAT
2434624 GAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTATATTAATATTAATATAAAATT
Found at i:2434920 original size:20 final size:20
Alignment explanation
Indices: 2434895--2434934 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2434885 TGAGCTTTTA
2434895 TATATATATATTATAATAAT
1 TATATATATATTATAATAAT
2434915 TATATATATATTATAATAAT
1 TATATATATATTATAATAAT
2434935 AATTATTTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATATATATTATAATAAT
Found at i:2434936 original size:26 final size:25
Alignment explanation
Indices: 2434891--2434953 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2434881 CATTTGAGCT
*
2434891 TTTATATATA-TAT-ATTATAATAA
1 TTTATATATATTATAATAATAATAA
*
2434914 TTATATATATATTATAATAATAATTA
1 TT-TATATATATTATAATAATAATAA
*
2434940 TTTAT-TAGATTATA
1 TTTATATATATTATA
2434954 GCACAATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 16 0.47
25 6 0.18
26 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTATATATATTATAATAATAATAA
Found at i:2435204 original size:12 final size:13
Alignment explanation
Indices: 2435174--2435207 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
2435164 GCTTGAGTTC
2435174 AATTCAAAATTCGT
1 AATTCAAAATTC-T
2435188 AATTCAAAATT-T
1 AATTCAAAATTCT
2435200 AATTCAAA
1 AATTCAAA
2435208 CTCTATCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
14 11 0.55
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (13 bp):
AATTCAAAATTCT
Found at i:2435777 original size:22 final size:21
Alignment explanation
Indices: 2435752--2435792 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2435742 TTTATCATAA
*
2435752 TATATTATTAAATAAATTTTAT
1 TATATAATTAAA-AAATTTTAT
*
2435774 TATATAATTTAAAAATTTT
1 TATATAATTAAAAAATTTT
2435793 TAAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATAATTAAAAAATTTTAT
Found at i:2438291 original size:2 final size:2
Alignment explanation
Indices: 2438284--2438309 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2438274 ACATAAAGCA
2438284 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
2438310 TGTTATTGAC
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:2450841 original size:14 final size:14
Alignment explanation
Indices: 2450822--2450857 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2450812 TATGGATAAA
2450822 AATCTATTTAATAT
1 AATCTATTTAATAT
2450836 AATCTATTTAATAT
1 AATCTATTTAATAT
*
2450850 AATATATT
1 AATCTATT
2450858 AAAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
AATCTATTTAATAT
Found at i:2455640 original size:2 final size:2
Alignment explanation
Indices: 2455635--2455662 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2455625 ACACACACAC
2455635 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
2455663 TCCATATGGG
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:2456482 original size:22 final size:22
Alignment explanation
Indices: 2456439--2456500 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 22
2456429 TAAAAGAAGA
2456439 TTTTATTATTTTCACATATATAAAT
1 TTTTATTATTTT-A-AT-TATAAAT
**
2456464 TTTTATTATTTTAATTATATTT
1 TTTTATTATTTTAATTATAAAT
2456486 TTTTA-TATTTTAATT
1 TTTTATTATTTTAATT
2456501 TTTTACAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.29
22 10 0.29
23 2 0.06
24 1 0.03
25 12 0.34
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTTAATTATAAAT
Found at i:2457696 original size:2 final size:2
Alignment explanation
Indices: 2457691--2457723 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2457681 GAATATATGC
2457691 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2457724 CTCACAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2460018 original size:17 final size:17
Alignment explanation
Indices: 2459976--2460018 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2459966 TACTCAAATC
**
2459976 ATATTAAAAATATTTTT
1 ATATTAAATTTATTTTT
2459993 ATATTAAATTTATTTTT
1 ATATTAAATTTATTTTT
*
2460010 TTATTAAAT
1 ATATTAAAT
2460019 GAATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTAAATTTATTTTT
Found at i:2463300 original size:24 final size:23
Alignment explanation
Indices: 2463254--2463300 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2463244 TTTAAACTAA
*
2463254 TATTAAAATATTAAAAATTATTT
1 TATTAAAATATTAAAAATAATTT
* *
2463277 TATTAATAATATTACATATAATTT
1 TATTAA-AATATTAAAAATAATTT
2463301 AAGATTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAAAATATTAAAAATAATTT
Found at i:2464448 original size:14 final size:14
Alignment explanation
Indices: 2464431--2464457 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2464421 TATATATATG
2464431 TATGTATATTAGAA
1 TATGTATATTAGAA
2464445 TATGTATATTAGA
1 TATGTATATTAGA
2464458 TTTTGGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
TATGTATATTAGAA
Found at i:2466214 original size:23 final size:24
Alignment explanation
Indices: 2466183--2466228 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2466173 AAATTAAACA
*
2466183 TCAAGTAAT-CCACTATTTATGGC
1 TCAAGTAATACCACTAGTTATGGC
*
2466206 TCAATTAATAGCCACTAGTTATG
1 TCAAGTAATA-CCACTAGTTATG
2466229 TTATCAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
25 11 0.58
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (24 bp):
TCAAGTAATACCACTAGTTATGGC
Found at i:2468981 original size:15 final size:14
Alignment explanation
Indices: 2468947--2468982 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2468937 TAAAAAGTTG
2468947 AAAAA-TAATTTTA
1 AAAAATTAATTTTA
2468960 AAAAATTAATTTTA
1 AAAAATTAATTTTA
2468974 ATAAAATTA
1 A-AAAATTA
2468983 GAGAATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 9 0.43
15 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAATTAATTTTA
Found at i:2469096 original size:23 final size:23
Alignment explanation
Indices: 2469070--2469122 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
2469060 GCCTATTTAA
2469070 AATATTTAAAATCTTTTTA-TATT
1 AATATTTAAAAT-TTTTTATTATT
2469093 AATATTT--AATTTTTTATTATT
1 AATATTTAAAATTTTTTATTATT
2469114 AA-ATTTAAA
1 AATATTTAAA
2469123 TAAATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 10 0.37
21 9 0.33
22 1 0.04
23 7 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATTTAAAATTTTTTATTATT
Found at i:2469895 original size:49 final size:44
Alignment explanation
Indices: 2469805--2469898 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 44
2469795 TATATTTATA
* *
2469805 TTATATTAATATATTTTATTACATTAAAATTATAATTAAAATAT
1 TTATATTAATAAATTTTAATACATTAAAATTATAATTAAAATAT
*
2469849 TTATATTATATAAATTTTAATATATTAATAATTCATAATATAAAAATAT
1 TTATATTA-ATAAATTTTAATACATTAA-AATT-ATAAT-T-AAAATAT
2469898 T
1 T
2469899 AAAAAATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 8 0.19
45 16 0.38
46 4 0.10
47 5 0.12
48 1 0.02
49 8 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (44 bp):
TTATATTAATAAATTTTAATACATTAAAATTATAATTAAAATAT
Found at i:2470458 original size:2 final size:2
Alignment explanation
Indices: 2470451--2470475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2470441 GGTGACAAAC
2470451 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 A
2470476 ACGCGCGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2471272 original size:18 final size:18
Alignment explanation
Indices: 2471249--2471289 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2471239 TCAGCCTGGT
*
2471249 CAGTTCCGTAGCCACCAG
1 CAGTTCCATAGCCACCAG
*
2471267 CAGTTCCATAGCCACCGG
1 CAGTTCCATAGCCACCAG
2471285 CAGTT
1 CAGTT
2471290 GTATTATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.20
Consensus pattern (18 bp):
CAGTTCCATAGCCACCAG
Found at i:2471419 original size:57 final size:57
Alignment explanation
Indices: 2471267--2471454 Score: 245
Period size: 57 Copynumber: 3.3 Consensus size: 57
2471257 TAGCCACCAG
** * *
2471267 CAGTTCCATAGCCACCGGCAGTTGTATTATAAGTAGAGTAACGAGTTTCAGCCTGGC
1 CAGTTCCATAGCCACCACCAGGTGTATTATAAGAAGAGTAACGAGTTTCAGCCTGGC
** * *
2471324 CAGTTCCATAGCCACCGGCAGGTGTATTATAAGTAGAGTAATGAGTTTCAGCCTGGC
1 CAGTTCCATAGCCACCACCAGGTGTATTATAAGAAGAGTAACGAGTTTCAGCCTGGC
* * *
2471381 CAGTTCCGTAGCCACCACCAGCAG-GT-TTATTAGAAGAGTAACGAGTTTCAGCTTGGC
1 CAGTTCCATAGCCACCACCAG--GTGTATTATAAGAAGAGTAACGAGTTTCAGCCTGGC
2471438 CAGTTCCATAGCCACCA
1 CAGTTCCATAGCCACCA
2471455 GCAGTTCCAT
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
57 116 0.97
58 2 0.02
59 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (57 bp):
CAGTTCCATAGCCACCACCAGGTGTATTATAAGAAGAGTAACGAGTTTCAGCCTGGC
Found at i:2471518 original size:18 final size:18
Alignment explanation
Indices: 2471497--2471538 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2471487 AGAGTAGGGA
* *
2471497 GTTTCAGAGAAGGCGGTG
1 GTTTCAGAGAAGGCAGAG
2471515 GTTTCAGAGAAGGCAGAG
1 GTTTCAGAGAAGGCAGAG
2471533 GTTTCA
1 GTTTCA
2471539 ACAGGCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.12, G:0.38, T:0.24
Consensus pattern (18 bp):
GTTTCAGAGAAGGCAGAG
Found at i:2471855 original size:15 final size:14
Alignment explanation
Indices: 2471831--2471868 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
2471821 ATTTAATATA
2471831 TTTTTGAAAAAATTG
1 TTTTT-AAAAAATTG
2471846 TTTTTAAAAAATTG
1 TTTTTAAAAAATTG
2471860 TTTTTAAAA
1 TTTTTAAAA
2471869 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
TTTTTAAAAAATTG
Found at i:2473300 original size:2 final size:2
Alignment explanation
Indices: 2473250--2473280 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2473240 TCATACATAC
2473250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2473281 GAGTTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2473570 original size:22 final size:23
Alignment explanation
Indices: 2473542--2473585 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2473532 ATTTTTAAGC
2473542 AAAAAGTG-GATTTTTTAAAAGT
1 AAAAAGTGAGATTTTTTAAAAGT
*
2473564 AAAAAGTGAATATTTTTTAAAA
1 AAAAAGTG-AGATTTTTTAAAA
2473586 AGATAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (23 bp):
AAAAAGTGAGATTTTTTAAAAGT
Found at i:2474113 original size:12 final size:12
Alignment explanation
Indices: 2474096--2474125 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2474086 ACATCACACG
2474096 TATTACATGTGA
1 TATTACATGTGA
2474108 TATTACATGTGA
1 TATTACATGTGA
2474120 TATTAC
1 TATTAC
2474126 GTATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (12 bp):
TATTACATGTGA
Found at i:2475473 original size:13 final size:13
Alignment explanation
Indices: 2475455--2475479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2475445 CATTTTATGG
2475455 TGTATCGATACAA
1 TGTATCGATACAA
2475468 TGTATCGATACA
1 TGTATCGATACA
2475480 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2475495 original size:32 final size:33
Alignment explanation
Indices: 2475432--2475499 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
2475422 CGTTACAAAC
**
2475432 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
2475465 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
2475497 CAA
1 CAA
2475500 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:2476038 original size:18 final size:18
Alignment explanation
Indices: 2476017--2476054 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2476007 TGATATAAAA
2476017 ATTTAATAA-AAATATAAT
1 ATTTAA-AATAAATATAAT
2476035 ATTTAAAATAAATATAAT
1 ATTTAAAATAAATATAAT
2476053 AT
1 AT
2476055 AACATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTAAAATAAATATAAT
Found at i:2476768 original size:179 final size:172
Alignment explanation
Indices: 2476441--2476768 Score: 374
Period size: 179 Copynumber: 1.9 Consensus size: 172
2476431 AAATTTTAAT
* * * **
2476441 TTAATTGGTATATAATTGTAATATTAATTAATTAAGAATTAATCTAAAATTAAAGGTTTTGCTCA
1 TTAATTGGCATATAACTGTAATACTAATTAATTAAGAATTAATCTAAAATTAAAAATTTTGCTCA
* * *
2476506 TTGAGTAGTATAAATAATTTAAATCTAAAAGTGTAATTTAATATAAATATGAAGTATATAATTTC
66 TTGAGTAATATAAATAATTTAAATCTAAAAGTGTAATTCAATATAAATATGAAGTATAT-ATTTA
** *
2476571 ATAAATTTTATTATATAATTAATAAAATGCATTGAAAGTTTAG
130 ATAAATTAGATAATATAATTAATAAAATGCATTGAAAGTTTAG
* * *
2476614 TTAATTTGCATATAACTGTTAATACTAATTAATTGAGAATTAATTTAAAATTAAAAATCTTTGCT
1 TTAATTGGCATATAACTG-TAATACTAATTAATTAAGAATTAATCTAAAATTAAAAAT-TTTGCT
* * **
2476679 CATTGAGTAAT-TCAACTAATTTAAATTACTGTAAAAGTGTAATTCAATCTGGATATGAAGTAT-
64 CATTGAGTAATAT-AAATAATTTAAA-T-C--TAAAAGTGTAATTCAATATAAATATGAAGTATA
2476742 T-TTTAAATTAGAATTAGATAATATAAT
124 TATTT-AA-TA-AATTAGATAATATAAT
2476769 CTTATAAATT
Statistics
Matches: 127, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
173 15 0.12
174 35 0.28
175 27 0.21
176 4 0.03
177 2 0.02
178 3 0.02
179 41 0.32
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.41
Consensus pattern (172 bp):
TTAATTGGCATATAACTGTAATACTAATTAATTAAGAATTAATCTAAAATTAAAAATTTTGCTCA
TTGAGTAATATAAATAATTTAAATCTAAAAGTGTAATTCAATATAAATATGAAGTATATATTTAA
TAAATTAGATAATATAATTAATAAAATGCATTGAAAGTTTAG
Found at i:2477882 original size:2 final size:2
Alignment explanation
Indices: 2477875--2477908 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2477865 GAAATTGGTG
2477875 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
2477909 GTAATTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2479011 original size:18 final size:17
Alignment explanation
Indices: 2478988--2479029 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
2478978 TTAAAATAAA
2478988 TAAAAAATCAATATTTTT
1 TAAAAAATCAAT-TTTTT
*
2479006 TAAAAAAATTAATTTTTT
1 T-AAAAAATCAATTTTTT
2479024 TAAAAA
1 TAAAAA
2479030 TGAAAAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAAAATCAATTTTTT
Found at i:2479013 original size:19 final size:18
Alignment explanation
Indices: 2478989--2479029 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
2478979 TAAAATAAAT
2478989 AAAAAATCAATATTTTTTA
1 AAAAAATCAAT-TTTTTTA
*
2479008 AAAAAATTAATTTTTTTA
1 AAAAAATCAATTTTTTTA
2479026 AAAA
1 AAAA
2479030 TGAAAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAAATCAATTTTTTTA
Found at i:2479411 original size:2 final size:2
Alignment explanation
Indices: 2479404--2479435 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2479394 AAAATCCTTG
*
2479404 TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2479436 CCAAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2479506 original size:38 final size:37
Alignment explanation
Indices: 2479463--2479538 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
2479453 ATAGAAGATA
*
2479463 ATATATATCTA-ATTTAGTTTAATATATTTTTATAATTTTT
1 ATATA-ATCTATATTTA-TTTAAT-TATTATTAT-ATTTTT
*
2479503 ATATAATTTATATTTATTTAATTATTATTATATTTT
1 ATATAATCTATATTTATTTAATTATTATTATATTTT
2479539 ATTTTTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 5 0.15
38 8 0.24
39 10 0.30
40 10 0.30
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (37 bp):
ATATAATCTATATTTATTTAATTATTATTATATTTTT
Found at i:2479524 original size:26 final size:28
Alignment explanation
Indices: 2479485--2479560 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 28
2479475 TTTAGTTTAA
*
2479485 TATATTT-TTATAATTTTTA-TATAATT
1 TATATTTATTATAATTATTATTATAATT
*
2479511 TATATTTATT-TAATTATTATTATATTT
1 TATATTTATTATAATTATTATTATAATT
*
2479538 TATTTTTATGTA-AATTATATATT
1 TATATTTAT-TATAATTAT-TATT
2479561 TTAAATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 15 0.36
27 16 0.38
28 7 0.17
29 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TATATTTATTATAATTATTATTATAATT
Found at i:2479554 original size:25 final size:25
Alignment explanation
Indices: 2479526--2479618 Score: 75
Period size: 25 Copynumber: 3.6 Consensus size: 25
2479516 TTATTTAATT
* *
2479526 ATTATTATATTTT-ATTTTTATGTAA
1 ATTA-TATATTTTAAATTTTAAGTAA
2479551 ATTATATATTTTAAATTTTAAGTAA
1 ATTATATATTTTAAATTTTAAGTAA
* *
2479576 ATTAAAAATATTTAATATGTTTAA-TAA
1 ATTATATAT-TTTAA-AT-TTTAAGTAA
*
2479603 ATT-TTTATTTTTAAAT
1 ATTATATA-TTTTAAAT
2479619 ATATATAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
24 8 0.14
25 23 0.41
26 11 0.20
27 9 0.16
28 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
ATTATATATTTTAAATTTTAAGTAA
Found at i:2479652 original size:23 final size:22
Alignment explanation
Indices: 2479608--2479649 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2479598 AATAAATTTT
2479608 TATTTTTAAATATATATAATAA
1 TATTTTTAAATATATATAATAA
*
2479630 TATTTTTAATTA-ATATAATA
1 TATTTTTAAATATATATAATA
2479650 TAAATATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTTTAAATATATATAATAA
Found at i:2479758 original size:19 final size:19
Alignment explanation
Indices: 2479736--2479773 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2479726 AAAATATTAA
2479736 TATT-ATATAAAATTATTTT
1 TATTAATATAAAATT-TTTT
2479755 TATTAATATAAAATTTTTT
1 TATTAATATAAAATTTTTT
2479774 AATTTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAATATAAAATTTTTT
Found at i:2480196 original size:27 final size:30
Alignment explanation
Indices: 2480166--2480235 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 30
2480156 ATTAATTGTA
*
2480166 TTATATTTTATTTATATTT-T-A-ATAATT
1 TTATATTTTATTTAAATTTATCATATAATT
* *
2480193 TTATACTATATTTAAATTTATCATATAATT
1 TTATATTTTATTTAAATTTATCATATAATT
2480223 TATATAATTTTAT
1 T-TAT-ATTTTAT
2480236 AATAATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 16 0.48
28 1 0.03
29 1 0.03
30 7 0.21
31 3 0.09
32 5 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATATTTTATTTAAATTTATCATATAATT
Found at i:2481479 original size:3 final size:3
Alignment explanation
Indices: 2481471--2481502 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2481461 ATAACTCCTA
*
2481471 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2481503 ACATAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2491370 original size:25 final size:25
Alignment explanation
Indices: 2491339--2491393 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
2491329 GGAGTGGGAG
2491339 GAGGAGCAGGCGGGGGAGCAATAGA
1 GAGGAGCAGGCGGGGGAGCAATAGA
* ** *
2491364 GAGGAGCATGCTTGGGAGGAATAGA
1 GAGGAGCAGGCGGGGGAGCAATAGA
2491389 GAGGA
1 GAGGA
2491394 AAGGAGAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.49, T:0.09
Consensus pattern (25 bp):
GAGGAGCAGGCGGGGGAGCAATAGA
Found at i:2495042 original size:2 final size:2
Alignment explanation
Indices: 2495035--2495059 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2495025 CATGCCTGAA
2495035 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 A
2495060 ATTCTCACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2496252 original size:74 final size:74
Alignment explanation
Indices: 2496128--2496351 Score: 281
Period size: 74 Copynumber: 3.0 Consensus size: 74
2496118 AGTTTTCATG
*
2496128 TCAGACCCAGACCCAGATCCACGACGACAAGACCCATCGCA-TAGATCTGTCTCAAGCAATTCAT
1 TCAGACCCAGACCCAGATCCACGACGACACGACCCATCG-AGTAGATCTGTCTCAAGCAATTCAT
*
2496192 TCGGTTTGATC
65 TCGATTT-ATC
* * * * *
2496203 TC-GACCCAGACCAAGATTCACGGCGACACGACCCATCGAGTAGAGCTGTCTCAAGCAACTCATT
1 TCAGACCCAGACCCAGATCCACGACGACACGACCCATCGAGTAGATCTGTCTCAAGCAATTCATT
*
2496267 CCATTTTATC
66 CGA-TTTATC
* * * ** *
2496277 TCAGACCCAGACCCAGATCCACAACGACACGACCCACCCAGTAGATCCATATCAAGCAATTCATT
1 TCAGACCCAGACCCAGATCCACGACGACACGACCCATCGAGTAGATCTGTCTCAAGCAATTCATT
2496342 CGATTTATC
66 CGATTTATC
2496351 T
1 T
2496352 GTATTGAGTG
Statistics
Matches: 126, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 67 0.53
75 58 0.46
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (74 bp):
TCAGACCCAGACCCAGATCCACGACGACACGACCCATCGAGTAGATCTGTCTCAAGCAATTCATT
CGATTTATC
Found at i:2496414 original size:19 final size:22
Alignment explanation
Indices: 2496378--2496425 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 22
2496368 AAATTTTATT
2496378 TTTATTATTTATATAATAAAAA
1 TTTATTATTTATATAATAAAAA
2496400 TTTATT-TTT-TA-AAT-AAAA
1 TTTATTATTTATATAATAAAAA
*
2496418 TTAATTAT
1 TTTATTAT
2496426 AAAAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.38
19 4 0.17
20 2 0.08
21 3 0.12
22 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTATTATTTATATAATAAAAA
Found at i:2496437 original size:22 final size:22
Alignment explanation
Indices: 2496412--2496454 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2496402 TATTTTTTAA
2496412 ATAAA-ATTAATTATAAAAATAT
1 ATAAATATTAA-TATAAAAATAT
2496434 ATAAATATTAATATAAAAATA
1 ATAAATATTAATATAAAAATA
2496455 AATTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAATATTAATATAAAAATAT
Found at i:2496871 original size:2 final size:2
Alignment explanation
Indices: 2496860--2496899 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2496850 ATATATATAT
*
2496860 AG AG AT AG 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 AG AG AG AG
2496900 TGGAGACTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:2501404 original size:11 final size:11
Alignment explanation
Indices: 2501388--2501566 Score: 110
Period size: 11 Copynumber: 16.6 Consensus size: 11
2501378 ATAATATATG
2501388 TATTTATATTA
1 TATTTATATTA
2501399 TATTTATA-TA
1 TATTTATATTA
* *
2501409 T-TTTTTATAA
1 TATTTATATTA
*
2501419 T-TTTATTTTA
1 TATTTATATTA
*
2501429 AATTT-TA-TA
1 TATTTATATTA
2501438 TATTTATA-TA
1 TATTTATATTA
*
2501448 AATTTTAATATTAA
1 TA-TTT-ATATT-A
2501462 TATTTATACATTA
1 TATTTAT--ATTA
*
2501475 -ATTT-TAATA
1 TATTTATATTA
*
2501484 TAATTATA--A
1 TATTTATATTA
2501493 TATTTATATTA
1 TATTTATATTA
*
2501504 TATTCATATTA
1 TATTTATATTA
2501515 TATTTATATTA
1 TATTTATATTA
* **
2501526 TTTTTATCCTA
1 TATTTATATTA
2501537 -ATTTATATTA
1 TATTTATATTA
*
2501547 AATTTATTATATA
1 TATTTA-TAT-TA
2501560 TATTTAT
1 TATTTAT
2501567 TTTCACAATG
Statistics
Matches: 130, Mismatches: 22, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
9 22 0.17
10 27 0.21
11 51 0.39
12 13 0.10
13 12 0.09
14 5 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2501405 original size:6 final size:6
Alignment explanation
Indices: 2501388--2501566 Score: 52
Period size: 6 Copynumber: 31.2 Consensus size: 6
2501378 ATAATATATG
*
2501388 TATTTA TA-TTA TATTTA TATATT- T-TTTA TAATTT- TATTTTA AATTT-
1 TATTTA TATTTA TATTTA TAT-TTA TATTTA T-ATTTA TA-TTTA TATTTA
** * *
2501434 TA--TA TATTTA TATAAA T-TTTAA TATTAA TATTTA TACATTA -ATTT-
1 TATTTA TATTTA TATTTA TATTT-A TATTTA TATTTA TA-TTTA TATTTA
* *
2501479 TA-ATA TAATTATAA TATTTA TA-TTA TATTCA TA-TTA TATTTA TA-TTA
1 TATTTA T-ATT-T-A TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
* * *
2501526 T-TTT- TATCCTA -ATTTA TA-TTA AATTTA TTATATA TATTTA T
1 TATTTA TAT-TTA TATTTA TATTTA TATTTA -TATTTA TATTTA T
2501567 TTTCACAATG
Statistics
Matches: 125, Mismatches: 20, Indels: 56
0.62 0.10 0.28
Matches are distributed among these distances:
3 1 0.01
4 6 0.05
5 36 0.29
6 60 0.48
7 16 0.13
8 4 0.03
9 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (6 bp):
TATTTA
Found at i:2501436 original size:20 final size:19
Alignment explanation
Indices: 2501397--2501464 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
2501387 GTATTTATAT
**
2501397 TATATTTATATATTTTTTA
1 TATATTTATATAAATTTTA
*
2501416 TA-ATTTTATTTTAAATTTTA
1 TATA-TTTA-TATAAATTTTA
2501436 TATATTTATATAAATTTTA
1 TATATTTATATAAATTTTA
*
2501455 -ATATTAATAT
1 TATATTTATAT
2501465 TTATACATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 10 0.24
19 16 0.39
20 14 0.34
21 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTTATATAAATTTTA
Found at i:2501454 original size:26 final size:26
Alignment explanation
Indices: 2501423--2501501 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 26
2501413 TTATAATTTT
*
2501423 ATTTTAAATTTTATATATTTATATAA
1 ATTTTAAATATTATATATTTATATAA
*
2501449 ATTTT-AATATTA-ATATTTATACATTA
1 ATTTTAAATATTATATATTTAT--ATAA
2501475 ATTTTAATATAATTATAATATTTATAT
1 ATTTTAA-AT-ATTAT-ATATTTATAT
2501502 TATATTCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
24 8 0.18
25 6 0.14
26 13 0.30
27 1 0.02
28 2 0.05
29 6 0.14
31 8 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTTAAATATTATATATTTATATAA
Found at i:2501464 original size:18 final size:19
Alignment explanation
Indices: 2501427--2501464 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2501417 AATTTTATTT
*
2501427 TAAATTTTATATATTTATA
1 TAAATTTTATATATTAATA
2501446 TAAATTTTA-ATATTAATA
1 TAAATTTTATATATTAATA
2501464 T
1 T
2501465 TTATACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAAATTTTATATATTAATA
Found at i:2502978 original size:16 final size:16
Alignment explanation
Indices: 2502957--2503004 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
2502947 GATAATTAAA
*
2502957 AATTTAAATTTAAAAT
1 AATTTAAACTTAAAAT
*
2502973 AATTTAAACTTAAATT
1 AATTTAAACTTAAAAT
**
2502989 AATCAAAACTTAAAAT
1 AATTTAAACTTAAAAT
2503005 GACTTGAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTTAAACTTAAAAT
Found at i:2517086 original size:48 final size:47
Alignment explanation
Indices: 2516994--2517086 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 47
2516984 ATTAAAAATT
* *
2516994 ATAAAAATTATAATTTTTGCAAGTTATAAGTTTAAATAATAATAATA
1 ATAAAAATTATAATTTTTGCAAGTTATAAGTTTAAAGAAAAATAATA
* **
2517041 ATAATAAATTATAATTTTTGCAAGTTATAATTTTTTAGAAAAATAA
1 ATAA-AAATTATAATTTTTGCAAGTTATAAGTTTAAAGAAAAATAA
2517087 AAAAATTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.42
Consensus pattern (47 bp):
ATAAAAATTATAATTTTTGCAAGTTATAAGTTTAAAGAAAAATAATA
Found at i:2518312 original size:14 final size:14
Alignment explanation
Indices: 2518293--2518321 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2518283 AAAATTGGTT
2518293 AATATTTTATAAAA
1 AATATTTTATAAAA
2518307 AATATTTTATAAAA
1 AATATTTTATAAAA
2518321 A
1 A
2518322 TTTAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTTATAAAA
Found at i:2518553 original size:16 final size:16
Alignment explanation
Indices: 2518529--2518590 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
2518519 CTCTAATCTT
*
2518529 TATAATTTTATTTAAA
1 TATATTTTTATTTAAA
2518545 TATATTTTTATGTT---
1 TATATTTTTAT-TTAAA
*
2518559 TATATTTATATTTAAA
1 TATATTTTTATTTAAA
* *
2518575 TAAATTTTTATATAAA
1 TATATTTTTATTTAAA
2518591 ATAAAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 2 0.05
14 10 0.27
16 23 0.62
17 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATATTTTTATTTAAA
Found at i:2518561 original size:30 final size:30
Alignment explanation
Indices: 2518527--2518585 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2518517 TTCTCTAATC
*
2518527 TTTATAATTT-TATTTAAATATATTTTTATG
1 TTTAT-ATTTATATTTAAATAAATTTTTATG
2518557 TTTATATTTATATTTAAATAAATTTTTAT
1 TTTATATTTATATTTAAATAAATTTTTAT
2518586 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTATATTTATATTTAAATAAATTTTTATG
Done.