Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 14 of 20
Found at i:2183392 original size:2 final size:2
Alignment explanation
Indices: 2183387--2183426 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2183377 GTTTGGCCAA
2183387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2183427 GCATGCTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2192560 original size:2 final size:2
Alignment explanation
Indices: 2192545--2192648 Score: 109
Period size: 2 Copynumber: 52.0 Consensus size: 2
2192535 GATAAATTCT
* * * * * * *
2192545 TA TA TA TG TG TA TA TA TG TA TC TA TA TG TA TG TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2192587 TG TG TG TG 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
2192629 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
2192649 GACACATCAT
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2194007 original size:17 final size:17
Alignment explanation
Indices: 2193982--2194015 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2193972 TGCTCCTGGT
* *
2193982 CATGTGATATTTACTGC
1 CATGCGATATTAACTGC
2193999 CATGCGATATTAACTGC
1 CATGCGATATTAACTGC
2194016 AAGGATGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (17 bp):
CATGCGATATTAACTGC
Found at i:2200884 original size:3 final size:3
Alignment explanation
Indices: 2200878--2200903 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2200868 TCCTTCCTCC
2200878 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
2200904 ATTATCTTGA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2200989 original size:12 final size:12
Alignment explanation
Indices: 2200974--2201017 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2200964 GGTTTTTAGT
2200974 TTGGTTTTGTTC
1 TTGGTTTTGTTC
* *
2200986 TTGGTCTTGGTC
1 TTGGTTTTGTTC
*
2200998 TTGCTTTTGTTC
1 TTGGTTTTGTTC
2201010 TTGGTTTT
1 TTGGTTTT
2201018 TCTTCTTACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.11, G:0.25, T:0.64
Consensus pattern (12 bp):
TTGGTTTTGTTC
Found at i:2200989 original size:24 final size:25
Alignment explanation
Indices: 2200962--2201018 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
2200952 AACATGTTTG
*
2200962 TTGGTTTTTAGT-TTGGTTTTGTTC
1 TTGGTTTTTAGTCTTGCTTTTGTTC
* *
2200986 TTGG-TCTTGGTCTTGCTTTTGTTC
1 TTGGTTTTTAGTCTTGCTTTTGTTC
2201010 TTGGTTTTT
1 TTGGTTTTT
2201019 CTTCTTACGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 19 0.70
25 3 0.11
ACGTcount: A:0.02, C:0.09, G:0.25, T:0.65
Consensus pattern (25 bp):
TTGGTTTTTAGTCTTGCTTTTGTTC
Found at i:2201814 original size:23 final size:23
Alignment explanation
Indices: 2201788--2201831 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2201778 ATTTTATAGT
*
2201788 TTATT-TTTTTAATATATAATTAA
1 TTATTATTTATAA-ATATAATTAA
2201811 TTATTATTTATAAATATAATT
1 TTATTATTTATAAATATAATT
2201832 TTTTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATTATTTATAAATATAATTAA
Found at i:2202629 original size:18 final size:18
Alignment explanation
Indices: 2202590--2202629 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2202580 ATATATTATG
*
2202590 ATATGATATTTTTATCAC
1 ATATGATATTTTTATCAA
*
2202608 ATATGATATTTTTATTAA
1 ATATGATATTTTTATCAA
2202626 ATAT
1 ATAT
2202630 TTATTATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (18 bp):
ATATGATATTTTTATCAA
Found at i:2202885 original size:15 final size:15
Alignment explanation
Indices: 2202865--2202897 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2202855 AGATATTTAA
2202865 AAATTAATATAAAAT
1 AAATTAATATAAAAT
*
2202880 AAATTAATATAATAT
1 AAATTAATATAAAAT
2202895 AAA
1 AAA
2202898 AATTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTAATATAAAAT
Found at i:2203065 original size:20 final size:20
Alignment explanation
Indices: 2203037--2203075 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2203027 TCAATAATTT
*
2203037 ATTTTTTTTAAAAAAATAAA
1 ATTTATTTTAAAAAAATAAA
*
2203057 ATTTATTTTTAAAAAATAA
1 ATTTATTTTAAAAAAATAA
2203076 TTTTCTACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTATTTTAAAAAAATAAA
Found at i:2203159 original size:3 final size:3
Alignment explanation
Indices: 2203151--2203184 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2203141 ACAAAAGGCG
2203151 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2203185 TACGGTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2205897 original size:20 final size:20
Alignment explanation
Indices: 2205872--2205912 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2205862 TCGTGCCAAC
2205872 GATTTAAGATTTATTTGGAT
1 GATTTAAGATTTATTTGGAT
2205892 GATTTAAGATTTATTTGGAT
1 GATTTAAGATTTATTTGGAT
2205912 G
1 G
2205913 TACAGTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
GATTTAAGATTTATTTGGAT
Found at i:2206151 original size:35 final size:35
Alignment explanation
Indices: 2206112--2206237 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
2206102 TTATTAACAA
*
2206112 TATATTTATATTAAATAATAAAATATAAATAAAAT
1 TATATTTATTTTAAATAATAAAATATAAATAAAAT
* * ** *
2206147 TATATTTATTTTGAATAATAATTAAAATTTATTAAA-
1 TATATTTATTTTAAATAATAA--AATATAAATAAAAT
* *
2206183 TGTAGTTATTTTAAATAATAAAATATAAATAAAAT
1 TATATTTATTTTAAATAATAAAATATAAATAAAAT
*
2206218 AATATTTATTTTAAATAATA
1 TATATTTATTTTAAATAATA
2206238 TTAAAATTTA
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
34 9 0.12
35 36 0.50
36 18 0.25
37 9 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (35 bp):
TATATTTATTTTAAATAATAAAATATAAATAAAAT
Found at i:2206508 original size:41 final size:41
Alignment explanation
Indices: 2206451--2206533 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
2206441 GCACCCACTT
2206451 CATGGACGAACACGACTAGCTTTTTCGCCAAATTACATAAA
1 CATGGACGAACACGACTAGCTTTTTCGCCAAATTACATAAA
2206492 CATGGACGAACACGACTAGCTTTTTCGCCAAATTACATAAA
1 CATGGACGAACACGACTAGCTTTTTCGCCAAATTACATAAA
2206533 C
1 C
2206534 CCAAAATGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (41 bp):
CATGGACGAACACGACTAGCTTTTTCGCCAAATTACATAAA
Found at i:2206667 original size:28 final size:27
Alignment explanation
Indices: 2206607--2206677 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
2206597 GCCACCCATT
2206607 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
* *
2206634 TGTTTGTAAAAAATGGTGGTT-TTTTT
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
2206660 TGGATTTGTCAAATATGG
1 T-G-TTTGTCAAAAATGG
2206678 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.13
27 21 0.55
28 12 0.32
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:2206780 original size:20 final size:20
Alignment explanation
Indices: 2206755--2206800 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2206745 AAATAGAGGC
*
2206755 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
2206775 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
2206795 TCCCTC
1 TCCCTC
2206801 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:2210933 original size:27 final size:28
Alignment explanation
Indices: 2210899--2210964 Score: 100
Period size: 27 Copynumber: 2.4 Consensus size: 28
2210889 GCCACCCATT
2210899 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
*
2210926 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
2210954 -GATTTGTCAAA
1 TG-TTTGTCAAA
2210965 TATGAAGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.47
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTATCTTTG
Found at i:2211072 original size:20 final size:20
Alignment explanation
Indices: 2211047--2211092 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2211037 AAATAGAGGC
*
2211047 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
2211067 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
2211087 TCCCTC
1 TCCCTC
2211093 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:2212018 original size:15 final size:16
Alignment explanation
Indices: 2212000--2212039 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2211990 TTTTAAATTT
2212000 TTATATATTTA-AAAA
1 TTATATATTTATAAAA
*
2212015 TTATATATTTATATAA
1 TTATATATTTATAAAA
*
2212031 TAATATATT
1 TTATATATT
2212040 AAATATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATATTTATAAAA
Found at i:2212414 original size:18 final size:17
Alignment explanation
Indices: 2212364--2212419 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
2212354 TTATATAAAA
2212364 ATAATTAATATAAAATAT
1 ATAATTAAT-TAAAATAT
* *
2212382 GA-AAATAATTTAAATAT
1 -ATAATTAATTAAAATAT
*
2212399 ATAATTATATTAAAATTT
1 ATAATTA-ATTAAAATAT
2212417 ATA
1 ATA
2212420 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 11 0.37
18 17 0.57
19 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATAATTAATTAAAATAT
Found at i:2212419 original size:61 final size:60
Alignment explanation
Indices: 2212342--2212470 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 60
2212332 ATTATATCCG
2212342 ATTATA-T-AAATATTATATAAAA-ATAATTAATATAAAATATGAAAA-TAATTTAAATATATA
1 ATTATATTAAAATATTATATAAAATA-AATT-AT-T-AAATATGAAAATTAATTTAAATATATA
* * *
2212402 ATTATATTAAAAT-TTATATAAAATAAATTATTATATATTAAAATTTATTTAAATATATA
1 ATTATATTAAAATATTATATAAAATAAATTATTAAATATGAAAATTAATTTAAATATATA
*
2212461 A-TATTTTAAA
1 ATTATATTAAA
2212471 TATAGTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
58 17 0.28
59 16 0.26
60 8 0.13
61 15 0.25
62 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (60 bp):
ATTATATTAAAATATTATATAAAATAAATTATTAAATATGAAAATTAATTTAAATATATA
Found at i:2212449 original size:17 final size:17
Alignment explanation
Indices: 2212404--2212450 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
2212394 AATATATAAT
2212404 TATATTAAAATTTA-TA
1 TATATTAAAATTTATTA
* *
2212420 TAAAAT-AAA-TTATTA
1 TATATTAAAATTTATTA
2212435 TATATTAAAATTTATT
1 TATATTAAAATTTATT
2212451 TAAATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 7 0.29
17 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTAAAATTTATTA
Found at i:2220368 original size:2 final size:2
Alignment explanation
Indices: 2220361--2220387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2220351 TCTTTTTCTT
2220361 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 T
2220388 TGTGTAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2220640 original size:2 final size:2
Alignment explanation
Indices: 2220633--2220681 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
2220623 CAACAAAAAC
2220633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
2220674 TA TCA TA T
1 TA T-A TA T
2220682 CCTACAAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.05
2 37 0.86
3 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2232077 original size:6 final size:6
Alignment explanation
Indices: 2232066--2232093 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2232056 CCAGCTCAAA
2232066 ATTATC ATTATC ATTATC ATTATC ATTA
1 ATTATC ATTATC ATTATC ATTATC ATTA
2232094 AAACCTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTATC
Found at i:2233865 original size:11 final size:12
Alignment explanation
Indices: 2233851--2233892 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2233841 CTTTTATTAA
2233851 TATATTAT-ATT
1 TATATTATAATT
2233862 TATATTATAATT
1 TATATTATAATT
2233874 TA-ATTTATAATT
1 TATA-TTATAATT
2233886 TAATATT
1 T-ATATT
2233893 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.33
12 14 0.52
13 3 0.11
14 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTATAATT
Found at i:2234257 original size:17 final size:17
Alignment explanation
Indices: 2234237--2234269 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2234227 TATTAACTTT
2234237 TTTTATTTAA-AAATTAC
1 TTTT-TTTAATAAATTAC
2234254 TTTTTTTAATAAATTA
1 TTTTTTTAATAAATTA
2234270 AAGACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTTTAATAAATTAC
Found at i:2235023 original size:28 final size:30
Alignment explanation
Indices: 2234952--2235032 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 30
2234942 TTTTATATAA
*
2234952 ATATAATAAGTATG-TTAAAATTTTATTAAATT
1 ATATAATAA-TATGAAT-AAATTTTATT-AATT
* *
2234984 ATATAATTATAT-AATGAATTTTATT-ATT
1 ATATAATAATATGAATAAATTTTATTAATT
*
2235012 ATGTAATAATATGAATAAATT
1 ATATAATAATATGAATAAATT
2235033 AAAAAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
28 13 0.32
29 7 0.17
30 9 0.22
31 4 0.10
32 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATAATAATATGAATAAATTTTATTAATT
Found at i:2235257 original size:21 final size:21
Alignment explanation
Indices: 2235214--2235257 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2235204 TTTAATATAA
*
2235214 ATAATTTATGATCATTTTGTT
1 ATAATTTATGATCATTTTATT
*
2235235 ATAATTTAT-CTCATTGTTATT
1 ATAATTTATGATCATT-TTATT
2235256 AT
1 AT
2235258 TATATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
ATAATTTATGATCATTTTATT
Found at i:2236163 original size:14 final size:14
Alignment explanation
Indices: 2236129--2236181 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
2236119 TTTATTTATA
* *
2236129 TTAATATTTATATT
1 TTAATAATTAAATT
*
2236143 TTTATAATTAAATT
1 TTAATAATTAAATT
2236157 TTAATAA--AAATT
1 TTAATAATTAAATT
*
2236169 TTAATTATTAAAT
1 TTAATAATTAAAT
2236182 AATAATTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 11 0.34
14 21 0.66
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATAATTAAATT
Found at i:2238268 original size:14 final size:15
Alignment explanation
Indices: 2238249--2238277 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2238239 TATTTTGTGA
2238249 ATCTGCC-AATTTGC
1 ATCTGCCTAATTTGC
2238263 ATCTGCCTAATTTGC
1 ATCTGCCTAATTTGC
2238278 TAAAATGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.38
Consensus pattern (15 bp):
ATCTGCCTAATTTGC
Found at i:2238511 original size:22 final size:22
Alignment explanation
Indices: 2238476--2238518 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2238466 ACAAATTATT
2238476 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
2238498 TAAATATTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
2238519 TTCTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:2238750 original size:31 final size:30
Alignment explanation
Indices: 2238698--2238769 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
2238688 AGTAGCTGAT
*
2238698 TAAATTTAATAATATCAAATTAAATTACGTAA
1 TAAATTTAA-AATATCAAATTAAAATA-GTAA
* *
2238730 TAAATTTAAAATAT-ATAATTAAAATATTAT
1 TAAATTTAAAATATCA-AATTAAAATAGTAA
2238760 TAAATTTAAA
1 TAAATTTAAA
2238770 CATTTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 13 0.36
31 14 0.39
32 9 0.25
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
TAAATTTAAAATATCAAATTAAAATAGTAA
Found at i:2239696 original size:13 final size:13
Alignment explanation
Indices: 2239678--2239716 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2239668 TAAATTTCAA
2239678 TATATTTATTTTT
1 TATATTTATTTTT
*
2239691 TATATTTATAATTT
1 TATATTTAT-TTTT
2239705 TAT-TTTATTTTT
1 TATATTTATTTTT
2239717 AAAATTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATATTTATTTTT
Found at i:2240241 original size:21 final size:22
Alignment explanation
Indices: 2240217--2240263 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2240207 TATTTACTTT
* *
2240217 TATTTATTTTC-TATTTAAAAA
1 TATTTATTTACATATTAAAAAA
2240238 TATTT-TTTACATATTAAAAAA
1 TATTTATTTACATATTAAAAAA
2240259 T-TTTA
1 TATTTA
2240264 AAATTTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTATTTACATATTAAAAAA
Found at i:2241166 original size:2 final size:2
Alignment explanation
Indices: 2241161--2241185 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2241151 ATCAAAAAAT
2241161 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
2241186 TTGGATTTGG
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:2244797 original size:12 final size:12
Alignment explanation
Indices: 2244776--2244810 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2244766 AAATCATATC
2244776 TTAAAA-TATTT
1 TTAAAATTATTT
2244787 TTAAAATTATTT
1 TTAAAATTATTT
2244799 TTAAAATT-TTT
1 TTAAAATTATTT
2244810 T
1 T
2244811 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAAAATTATTT
Found at i:2244836 original size:16 final size:16
Alignment explanation
Indices: 2244792--2244848 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
2244782 TATTTTTAAA
*
2244792 ATTATTTTTAAAATTT
1 ATTATTTTTAAAAATT
* **
2244808 TTTATAATT-AAAATT
1 ATTATTTTTAAAAATT
*
2244823 ATTATTTTTAAAAATA
1 ATTATTTTTAAAAATT
*
2244839 AATATTTTTA
1 ATTATTTTTA
2244849 TAATTAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTTTTAAAAATT
Found at i:2244849 original size:22 final size:21
Alignment explanation
Indices: 2244806--2244849 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2244796 TTTTTAAAAT
* *
2244806 TTTTTATAATTAAAATTATTA
1 TTTTTAAAAATAAAATTATTA
*
2244827 TTTTTAAAAATAAATATTTTTA
1 TTTTTAAAAATAAA-ATTATTA
2244849 T
1 T
2244850 AATTAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTAAAAATAAAATTATTA
Found at i:2247040 original size:8 final size:8
Alignment explanation
Indices: 2247027--2247052 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2247017 TATAACAAAG
2247027 TTAACTGC
1 TTAACTGC
2247035 TTAACTGC
1 TTAACTGC
2247043 TTAACTGC
1 TTAACTGC
2247051 TT
1 TT
2247053 TAGTAAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (8 bp):
TTAACTGC
Found at i:2252040 original size:25 final size:26
Alignment explanation
Indices: 2251987--2252041 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
2251977 TTATGTATTT
* * *
2251987 TTAAAATTTTTATTCTCATTTAAAGA
1 TTAAAATTTTAATTCTCATTAAAAAA
*
2252013 TTAAAATTTTAATT-TTATTAAAAAA
1 TTAAAATTTTAATTCTCATTAAAAAA
2252038 TTAA
1 TTAA
2252042 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAAAATTTTAATTCTCATTAAAAAA
Found at i:2252058 original size:29 final size:31
Alignment explanation
Indices: 2252015--2252073 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
2252005 TTTAAAGATT
*
2252015 AAAATTTTAATTTTATTAAAAAATTAATTAA
1 AAAATTTTAATTTTAATAAAAAATTAATTAA
*
2252046 AAAATTTT-A-TTTAATAAAAAATTTATTA
1 AAAATTTTAATTTTAATAAAAAATTAATTA
2252074 TATTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 1 0.04
31 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAATTTTAATTTTAATAAAAAATTAATTAA
Found at i:2252095 original size:21 final size:19
Alignment explanation
Indices: 2252037--2252096 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
2252027 TTATTAAAAA
*
2252037 ATTAATTAAAAAATTTTAT
1 ATTAATAAAAAAATTTTAT
*
2252056 -TTAATAAAAAATTTATTAT
1 ATTAATAAAAAAATT-TTAT
*
2252075 ATTTATAAATAAAAATTTTAT
1 ATTAAT-AA-AAAAATTTTAT
2252096 A
1 A
2252097 AAATTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
20 4 0.12
21 7 0.21
22 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATAAAAAAATTTTAT
Found at i:2252107 original size:23 final size:24
Alignment explanation
Indices: 2252058--2252108 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2252048 AATTTTATTT
* * *
2252058 AATAAAAAATTTATTATATTTATA
1 AATAAAAAATTTATTAAAATTAAA
*
2252082 AATAAAAATTTTA-TAAAATTAAA
1 AATAAAAAATTTATTAAAATTAAA
2252105 AATA
1 AATA
2252109 CTTTAATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAAAAATTTATTAAAATTAAA
Found at i:2252761 original size:14 final size:14
Alignment explanation
Indices: 2252744--2252798 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
2252734 TATTTATTTT
*
2252744 TTATATGATATAAA
1 TTATATAATATAAA
* *
2252758 TTATTTAGTATAAA
1 TTATATAATATAAA
*
2252772 -TATAATAATATATA
1 TTAT-ATAATATAAA
2252786 TTATATAAT-TAAA
1 TTATATAATATAAA
2252799 AAAATGATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 6 0.19
14 23 0.72
15 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:2255347 original size:22 final size:23
Alignment explanation
Indices: 2255322--2255365 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2255312 TTAAATTACT
2255322 ATATAAAATATTAA-AAATTTTA
1 ATATAAAATATTAATAAATTTTA
*
2255344 ATATTAAATATTAATAAATTTT
1 ATATAAAATATTAATAAATTTT
2255366 TATAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATAAAATATTAATAAATTTTA
Found at i:2255373 original size:24 final size:22
Alignment explanation
Indices: 2255322--2255374 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
2255312 TTAAATTACT
*
2255322 ATATAAAATATTAAAAATTTTA
1 ATATTAAATATTAAAAATTTTA
*
2255344 ATATTAAATATTAATAAATTTTT
1 ATATTAAATATTAA-AAATTTTA
2255367 ATAATTAA
1 AT-ATTAA
2255375 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 13 0.48
23 9 0.33
24 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTAAATATTAAAAATTTTA
Found at i:2255658 original size:29 final size:27
Alignment explanation
Indices: 2255586--2255658 Score: 65
Period size: 29 Copynumber: 2.6 Consensus size: 27
2255576 ACTTTTTATC
* * *
2255586 AATATTTTATTTTTATTTATAATTTTT
1 AATATTTTATTTTCATTCAAAATTTTT
* * *
2255613 AAAATGTTAATTATCATTCACAAATTTTTT
1 AATAT-TTTATTTTCATTCA-AAA-TTTTT
2255643 AATATTTTATTTTCAT
1 AATATTTTATTTTCAT
2255659 CGATTAGTGT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
27 4 0.12
28 10 0.29
29 11 0.32
30 9 0.26
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (27 bp):
AATATTTTATTTTCATTCAAAATTTTT
Found at i:2259021 original size:17 final size:17
Alignment explanation
Indices: 2258999--2259054 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
2258989 TTTATTTTAA
2258999 TTTTAATTTTTTATATT
1 TTTTAATTTTTTATATT
*** *
2259016 TTTTAAAAGTTTAT-GT
1 TTTTAATTTTTTATATT
2259032 TTTTAATTATTTT-TATT
1 TTTTAATT-TTTTATATT
2259049 TTTTAA
1 TTTTAA
2259055 AAATTTTTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (17 bp):
TTTTAATTTTTTATATT
Found at i:2259060 original size:17 final size:18
Alignment explanation
Indices: 2259006--2259063 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
2258996 TAATTTTAAT
*
2259006 TTTTTATATTTTTTAAAA
1 TTTTTATATTTTTAAAAA
* * **
2259024 -GTTTATGTTTTTAATTA
1 TTTTTATATTTTTAAAAA
2259041 TTTTTAT-TTTTTAAAAA
1 TTTTTATATTTTTAAAAA
2259058 TTTTTA
1 TTTTTA
2259064 AAATTTGACC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 26 0.84
18 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTATATTTTTAAAAA
Found at i:2263688 original size:11 final size:12
Alignment explanation
Indices: 2263663--2263707 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2263653 AAATTTAATT
2263663 AATTTAATTTAA
1 AATTTAATTTAA
*
2263675 AATTTATTTTAA
1 AATTTAATTTAA
* *
2263687 ATTTTAAATATAA
1 AATTT-AATTTAA
2263700 AATTTAAT
1 AATTTAAT
2263708 CAAAAACTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTTAATTTAA
Found at i:2263915 original size:12 final size:12
Alignment explanation
Indices: 2263898--2263922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2263888 TTGTACTACA
2263898 TAAATTTAAGGT
1 TAAATTTAAGGT
2263910 TAAATTTAAGGT
1 TAAATTTAAGGT
2263922 T
1 T
2263923 CAGAAACCTT
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAATTTAAGGT
Found at i:2264736 original size:16 final size:16
Alignment explanation
Indices: 2264686--2264728 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2264676 ATCAAAAGTT
*
2264686 AAAATATAAAATAATA
1 AAAATTTAAAATAATA
* *
2264702 TATATTTAAAATAATA
1 AAAATTTAAAATAATA
2264718 AAAATTTAAAA
1 AAAATTTAAAA
2264729 ATATAAAATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTTAAAATAATA
Found at i:2265961 original size:2 final size:2
Alignment explanation
Indices: 2265954--2265985 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2265944 TAACAATCTT
2265954 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2265986 GTTCTCCTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2267972 original size:32 final size:34
Alignment explanation
Indices: 2267897--2267974 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
2267887 TTATTGAAAG
*
2267897 TGTTGAAGACACCAATGAAGCAATAAGAGTACTG
1 TGTTGAAGACACCAATGAAGCAATAAGAGTACTC
*
2267931 TGTTGAAGACACCAATGAAG-TAT-AGAGTACTC
1 TGTTGAAGACACCAATGAAGCAATAAGAGTACTC
*
2267963 TGTTCAAGACAC
1 TGTTGAAGACAC
2267975 TTCAAGTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 19 0.46
33 2 0.05
34 20 0.49
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (34 bp):
TGTTGAAGACACCAATGAAGCAATAAGAGTACTC
Found at i:2271344 original size:19 final size:20
Alignment explanation
Indices: 2271322--2271359 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2271312 GGTATTTTAT
*
2271322 ATAAAATAGAT-TTTTTTTG
1 ATAAAATAAATATTTTTTTG
*
2271341 ATAAATTAAATATTTTTTT
1 ATAAAATAAATATTTTTTT
2271360 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATAAAATAAATATTTTTTTG
Found at i:2271586 original size:172 final size:175
Alignment explanation
Indices: 2271242--2271599 Score: 677
Period size: 174 Copynumber: 2.1 Consensus size: 175
2271232 CTTTTCTAGG
2271242 TTTTTCATTTTGCACTAAAATTCGACATACTGAATAAAAAAAAATTCAAGCAAAAAAAAATTTAT
1 TTTTTCATTTTGCACTAAAATTCGACATACTGAATAAAAAAAAATTCAAGCAAAAAAAAATTTAT
*
2271307 GAATGGGTATTTTATATAAAATAGATTTTTTTTGATAAATTAAATATTTTTTTTAAAAAATATGT
66 GAATGGGTATTTTATATAAAATAGATTTTTTTTGATAAATTAAATAATTTTTTTAAAAAATATGT
2271372 AATATATATTTACATAAAATTTGAAGTATAAAAATATAAAAATAA
131 AATATATATTTACATAAAATTTGAAGTATAAAAATATAAAAATAA
2271417 TTTTTCATTTTGCACTAAAATTCGACATACTGAAT-AAAAAAAATTCAAGCAAAAAAAAATTTAT
1 TTTTTCATTTTGCACTAAAATTCGACATACTGAATAAAAAAAAATTCAAGCAAAAAAAAATTTAT
2271481 GAATGGGTATTTTATATAAAATAGATTTTTTTTGATAAATTAAATAATTTTTTTAAAAAATATGT
66 GAATGGGTATTTTATATAAAATAGATTTTTTTTGATAAATTAAATAATTTTTTTAAAAAATATGT
2271546 -A-ATATATTTACATAAAATTTGAAGTATAAAAATATAAAAATAA
131 AATATATATTTACATAAAATTTGAAGTATAAAAATATAAAAATAA
*
2271589 TTTTTTATTTT
1 TTTTTCATTTT
2271600 TATTTTTAAT
Statistics
Matches: 181, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
172 52 0.29
173 1 0.01
174 93 0.51
175 35 0.19
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (175 bp):
TTTTTCATTTTGCACTAAAATTCGACATACTGAATAAAAAAAAATTCAAGCAAAAAAAAATTTAT
GAATGGGTATTTTATATAAAATAGATTTTTTTTGATAAATTAAATAATTTTTTTAAAAAATATGT
AATATATATTTACATAAAATTTGAAGTATAAAAATATAAAAATAA
Found at i:2272183 original size:23 final size:23
Alignment explanation
Indices: 2272153--2272196 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2272143 TAATACGTTG
2272153 AAAATATCTTAAAAATATTCTGA
1 AAAATATCTTAAAAATATTCTGA
2272176 AAAATATCTTAAAAATATTCT
1 AAAATATCTTAAAAATATTCT
2272197 TCAACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAATATCTTAAAAATATTCTGA
Found at i:2272197 original size:12 final size:11
Alignment explanation
Indices: 2272153--2272193 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
2272143 TAATACGTTG
2272153 AAAATATCTTA
1 AAAATATCTTA
*
2272164 AAAATATTCTGA
1 AAAATA-TCTTA
2272176 AAAATATCTTA
1 AAAATATCTTA
2272187 AAAATAT
1 AAAATAT
2272194 TCTTCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (11 bp):
AAAATATCTTA
Found at i:2272725 original size:18 final size:17
Alignment explanation
Indices: 2272697--2272730 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2272687 CTCATATAAA
2272697 AAATAATAAATTAAACG
1 AAATAATAAATTAAACG
2272714 AAATAGATAAATTAAAC
1 AAATA-ATAAATTAAAC
2272731 AAAAAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATAATAAATTAAACG
Found at i:2273035 original size:22 final size:22
Alignment explanation
Indices: 2273008--2273051 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2272998 TTTTTCTTTT
*
2273008 ATTTTAAAATT-AAAATTTAAA
1 ATTTTTAAATTAAAAATTTAAA
*
2273029 ATTTTTATATTAAAAATTTAAA
1 ATTTTTAAATTAAAAATTTAAA
2273051 A
1 A
2273052 ATAAGACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTTAAATTAAAAATTTAAA
Found at i:2280827 original size:2 final size:2
Alignment explanation
Indices: 2280820--2280846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2280810 TTCATACATT
2280820 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 T
2280847 GCCCGTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2283354 original size:12 final size:14
Alignment explanation
Indices: 2283327--2283363 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
2283317 AATTTTAAAC
2283327 ATAAAATAATTAAT
1 ATAAAATAATTAAT
2283341 ATAAAAT-A-TAAT
1 ATAAAATAATTAAT
2283353 ATAAAA-AATTA
1 ATAAAATAATTA
2283364 TTATTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.52
13 3 0.14
14 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAAAATAATTAAT
Found at i:2283859 original size:26 final size:26
Alignment explanation
Indices: 2283829--2283878 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2283819 TATACTAAAT
2283829 AATTAATTTA-TATATATAAATATACA
1 AATT-ATTTAGTATATATAAATATACA
*
2283855 AATTATTTAGTATATATATATATA
1 AATTATTTAGTATATATAAATATA
2283879 AGAATGCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTATTTAGTATATATAAATATACA
Found at i:2286132 original size:29 final size:29
Alignment explanation
Indices: 2286099--2286167 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
2286089 TTAAAATTAA
*
2286099 ATTAAAAAATATAAATATTTATATTTATTT
1 ATTAAAAAATATAAA-ATTTATAATTATTT
*
2286129 -TTAAAAATATTTAAAATTTATAATTATTT
1 ATTAAAAA-ATATAAAATTTATAATTATTT
*
2286158 ATTAATAAAT
1 ATTAAAAAAT
2286168 GTTATCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTAAAAAATATAAAATTTATAATTATTT
Found at i:2295616 original size:16 final size:15
Alignment explanation
Indices: 2295582--2295638 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
2295572 ATGATCTAAT
*
2295582 ATAAAA-AATAAATA
1 ATAAAATAATAATTA
*
2295596 TTAAATATAATAATTA
1 ATAAA-ATAATAATTA
**
2295612 ATAAAATATATTTTTA
1 ATAAAATA-ATAATTA
2295628 ATAAAATAATA
1 ATAAAATAATA
2295639 TAATTTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 24 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATAATAATTA
Found at i:2295617 original size:28 final size:29
Alignment explanation
Indices: 2295578--2295642 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
2295568 TTGAATGATC
*
2295578 TAATATAA-AAAATAAATATTAAATATAA
1 TAATATAATAAAATAAATATTAAATAAAA
* * *
2295606 TAAT-TAATAAAATATATTTTTAATAAAA
1 TAATATAATAAAATAAATATTAAATAAAA
2295634 TAATATAAT
1 TAATATAAT
2295643 TTTTAATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 24 0.77
29 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
TAATATAATAAAATAAATATTAAATAAAA
Found at i:2295620 original size:17 final size:16
Alignment explanation
Indices: 2295598--2295643 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2295588 AATAAATATT
2295598 AAATATAATAATTAATA
1 AAATAT-ATAATTAATA
**
2295615 AAATATATTTTTAATA
1 AAATATATAATTAATA
2295631 AAATAATATAATT
1 AAAT-ATATAATT
2295644 TTTAATATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATATATAATTAATA
Found at i:2301211 original size:11 final size:11
Alignment explanation
Indices: 2301195--2301224 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2301185 ATATATAAAA
2301195 TAATATTTTTT
1 TAATATTTTTT
2301206 TAATATTTTTT
1 TAATATTTTTT
2301217 TATATATT
1 TA-ATATT
2301225 GTATATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TAATATTTTTT
Found at i:2301221 original size:21 final size:21
Alignment explanation
Indices: 2301203--2301269 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
2301193 AATAATATTT
2301203 TTTTA-ATATTTTTTTATATA
1 TTTTATATATTTTTTTATATA
* *
2301223 TTGTATATATTATTTTATATA
1 TTTTATATATTTTTTTATATA
* *
2301244 TTTTATATATTTATTTAAATA
1 TTTTATATATTTTTTTATATA
2301265 TTTTA
1 TTTTA
2301270 ATTAATTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 4 0.10
21 36 0.90
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (21 bp):
TTTTATATATTTTTTTATATA
Found at i:2301245 original size:9 final size:9
Alignment explanation
Indices: 2301214--2301255 Score: 57
Period size: 9 Copynumber: 4.3 Consensus size: 9
2301204 TTTAATATTT
2301214 TTTTATATA
1 TTTTATATA
2301223 TTGTATATATTA
1 TT-T-TATA-TA
2301235 TTTTATATA
1 TTTTATATA
2301244 TTTTATATA
1 TTTTATATA
2301253 TTT
1 TTT
2301256 ATTTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 16 0.53
10 5 0.17
11 5 0.17
12 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTATATA
Found at i:2301285 original size:15 final size:16
Alignment explanation
Indices: 2301265--2301298 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2301255 TATTTAAATA
2301265 TTTTAATTAAT-TAAT
1 TTTTAATTAATATAAT
*
2301280 TTTTAATTTATATAAT
1 TTTTAATTAATATAAT
2301296 TTT
1 TTT
2301299 ACCTAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATTAATATAAT
Found at i:2303923 original size:8 final size:8
Alignment explanation
Indices: 2303910--2303942 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2303900 TTCGGGTAGA
2303910 TTTTGTTT
1 TTTTGTTT
2303918 TTTTGTTT
1 TTTTGTTT
*
2303926 TGTT-TTT
1 TTTTGTTT
2303933 TTTTGTTT
1 TTTTGTTT
2303941 TT
1 TT
2303943 ACTTTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTGTTT
Found at i:2303928 original size:13 final size:13
Alignment explanation
Indices: 2303910--2303934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2303900 TTCGGGTAGA
2303910 TTTTGTTTTTTTG
1 TTTTGTTTTTTTG
2303923 TTTTGTTTTTTT
1 TTTTGTTTTTTT
2303935 TTGTTTTTAC
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTGTTTTTTTG
Found at i:2303948 original size:15 final size:15
Alignment explanation
Indices: 2303915--2303952 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2303905 GTAGATTTTG
*
2303915 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTC
2303930 TTTTTTTGTTTT-TAC
1 TTTTTTTGTTTTGT-C
2303945 TTTTTTTG
1 TTTTTTTG
2303953 GGCAGTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.84
Consensus pattern (15 bp):
TTTTTTTGTTTTGTC
Found at i:2304670 original size:22 final size:22
Alignment explanation
Indices: 2304645--2304706 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
2304635 AAAAAATTAC
*
2304645 AATAAGAAAATATTTTTATATT
1 AATAATAAAATATTTTTATATT
* * *
2304667 AATATTTAAATATTTTTAAATT
1 AATAATAAAATATTTTTATATT
*
2304689 TA-AATAAAATATTTTTAT
1 AATAATAAAATATTTTTAT
2304707 TAAAATATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AATAATAAAATATTTTTATATT
Found at i:2304718 original size:22 final size:22
Alignment explanation
Indices: 2304651--2304718 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
2304641 TTACAATAAG
2304651 AAAATATTTTTA-TATTAATATT
1 AAAATATTTTTATTA-TAATATT
*
2304673 TAAATATTTTTAAATT-TAA-A-T
1 AAAATATTTTT--ATTATAATATT
*
2304694 AAAATATTTTTATTAAAATATT
1 AAAATATTTTTATTATAATATT
2304716 AAA
1 AAA
2304719 TAAATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 12 0.32
22 15 0.41
23 3 0.08
24 1 0.03
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAATATTTTTATTATAATATT
Found at i:2304808 original size:47 final size:45
Alignment explanation
Indices: 2304715--2304827 Score: 109
Period size: 47 Copynumber: 2.4 Consensus size: 45
2304705 ATTAAAATAT
* * * *
2304715 TAAATAAATATAAAAATAATTTTAAAAATATAATTTTTTATGAAA
1 TAAATAAATATAAAAATAAGTTTAAAAATATAATATATTATAAAA
* * *
2304760 TAAATAAATTTAAAAAATTAAGTTTAATAATATTATATATTATAAAATA
1 TAAATAAATAT-AAAAA-TAAGTTTAAAAATATAATATATTAT-AAA-A
*
2304809 TAATATAAATATATAAATA
1 TAA-ATAAATATAAAAATA
2304828 TTTTAAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
45 10 0.19
46 5 0.09
47 20 0.37
48 4 0.07
49 8 0.15
50 7 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (45 bp):
TAAATAAATATAAAAATAAGTTTAAAAATATAATATATTATAAAA
Found at i:2304815 original size:12 final size:13
Alignment explanation
Indices: 2304793--2304916 Score: 55
Period size: 12 Copynumber: 9.4 Consensus size: 13
2304783 TTAATAATAT
*
2304793 TATATATTATAAA
1 TATATAATATAAA
2304806 -ATATAATATAAA
1 TATATAATATAAA
2304818 TATATAAATATTTTAAA
1 TATAT-AATA---TAAA
2304835 TTTTATATAATATAAA
1 ---TATATAATATAAA
*
2304851 T-TATTAT-TAAA
1 TATATAATATAAA
* * *
2304862 AATATAAAAT-AT
1 TATATAATATAAA
*
2304874 TTTA-AATAT-AA
1 TATATAATATAAA
2304885 T-TATAATATAATAA
1 TATATAATAT-A-AA
*
2304899 AATATAATATAAA
1 TATATAATATAAA
2304912 TATAT
1 TATAT
2304917 GAATTTAGTT
Statistics
Matches: 84, Mismatches: 12, Indels: 30
0.67 0.10 0.24
Matches are distributed among these distances:
10 2 0.02
11 15 0.18
12 23 0.27
13 12 0.14
14 7 0.08
15 8 0.10
16 4 0.05
17 4 0.05
19 4 0.05
20 5 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATAATATAAA
Found at i:2304849 original size:45 final size:48
Alignment explanation
Indices: 2304789--2304916 Score: 158
Period size: 45 Copynumber: 2.7 Consensus size: 48
2304779 AAGTTTAATA
*
2304789 ATATTATATATTATAAAATATAATATAAATATAT-AAATATTTTAAAT
1 ATATTATATAATATAAAATATAATATAAATATATAAAATATTTTAAAT
* * *
2304836 -T-TTATATAATATAAATTATTAT-TAAAAATATAAAATATTTTAAAT
1 ATATTATATAATATAAAATATAATATAAATATATAAAATATTTTAAAT
2304881 ATAATTATA-ATATAATAAAATATAATATAAATATAT
1 AT-ATTATATA-AT-ATAAAATATAATATAAATATAT
2304917 GAATTTAGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
44 8 0.12
45 31 0.46
46 2 0.03
47 1 0.01
48 7 0.10
49 10 0.15
50 8 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (48 bp):
ATATTATATAATATAAAATATAATATAAATATATAAAATATTTTAAAT
Found at i:2305279 original size:3 final size:3
Alignment explanation
Indices: 2305271--2305298 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2305261 AACAATACCC
2305271 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2305299 GAGTCACCCG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2307335 original size:2 final size:2
Alignment explanation
Indices: 2307328--2307360 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2307318 ATTTTCATTG
2307328 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2307361 TTTGGTTTAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2311558 original size:13 final size:13
Alignment explanation
Indices: 2311517--2311565 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2311507 TAATGAAATG
*
2311517 AATAATTTAATTT
1 AATATTTTAATTT
**
2311530 TGTATTCTTAAATTT
1 AATATT-TT-AATTT
2311545 AATATTTTAATTT
1 AATATTTTAATTT
2311558 AATATTTT
1 AATATTTT
2311566 TTGAATTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 16 0.55
14 4 0.14
15 9 0.31
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (13 bp):
AATATTTTAATTT
Found at i:2327296 original size:24 final size:24
Alignment explanation
Indices: 2327190--2327297 Score: 80
Period size: 24 Copynumber: 4.3 Consensus size: 24
2327180 ACAACGGGAG
2327190 ATTAGATATTTT-TATTTTTTAAAA
1 ATTA-ATATTTTATATTTTTTAAAA
*
2327214 ATAAGATATTATTCAACTATTTTTTAAAAAA
1 ATTA-ATATT-TT--A-TATTTTTT--AAAA
* *
2327245 ATTAA-ATATTA-ATTTTAT-AAA
1 ATTAATATTTTATATTTTTTAAAA
2327266 ATATAATATTTTATATTTTTTAAAA
1 AT-TAATATTTTATATTTTTTAAAA
2327291 ATTAATA
1 ATTAATA
2327298 AATAAATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
21 5 0.07
22 3 0.04
23 5 0.07
24 26 0.39
25 7 0.10
26 1 0.01
28 2 0.03
29 10 0.15
30 1 0.01
31 7 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAATATTTTATATTTTTTAAAA
Found at i:2327503 original size:21 final size:21
Alignment explanation
Indices: 2327473--2327520 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2327463 AAAAATGGTA
* *
2327473 TAATTCTTTTACAAGTTATTT
1 TAATTCTTTTAAAAGTAATTT
*
2327494 TAATTTTTTTAAAAGTAATTT
1 TAATTCTTTTAAAAGTAATTT
2327515 TAATTC
1 TAATTC
2327521 AATTTTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
TAATTCTTTTAAAAGTAATTT
Found at i:2331812 original size:22 final size:24
Alignment explanation
Indices: 2331787--2331830 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2331777 TTTATTATAT
2331787 TTTTTAATTATAT-TA-TATATTA
1 TTTTTAATTATATATAGTATATTA
*
2331809 TTTTTATTTATATATAGTATAT
1 TTTTTAATTATATATAGTATAT
2331831 ATATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTAATTATATATAGTATATTA
Found at i:2331829 original size:26 final size:25
Alignment explanation
Indices: 2331779--2331836 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
2331769 AAATTTAATT
*
2331779 TATTATATTTTTTAATTATATTATA
1 TATTATATTTTTTAATTATAGTATA
*
2331804 TATTAT-TTTTATTTATATATAGTATA
1 TATTATATTTT-TTAAT-TATAGTATA
2331830 TA-TATAT
1 TATTATAT
2331837 CATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 13 0.46
26 11 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TATTATATTTTTTAATTATAGTATA
Found at i:2331874 original size:20 final size:20
Alignment explanation
Indices: 2331838--2331876 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2331828 TATATATATC
*
2331838 ATATAAATAATATAAACATA
1 ATATAAATAATAAAAACATA
2331858 ATAT-AATAATTAAAAACAT
1 ATATAAATAA-TAAAAACAT
2331877 TAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATAAATAATAAAAACATA
Found at i:2331935 original size:10 final size:10
Alignment explanation
Indices: 2331922--2331952 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2331912 TAATAAAAAT
*
2331922 TAAATATAAA
1 TAAATTTAAA
2331932 TAAATTTAAA
1 TAAATTTAAA
2331942 TAAATTTAAA
1 TAAATTTAAA
2331952 T
1 T
2331953 TTTATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:2331980 original size:41 final size:43
Alignment explanation
Indices: 2331923--2332005 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 43
2331913 AATAAAAATT
* *
2331923 AAATATAAATAAATTTAAAT-AAATT-TAAATTTTATATTTAC
1 AAATAAAAATAAATTTAAATAAAATTAAAAATTTTATATTTAC
*
2331964 AAATAAAAATAGATTTAAATAAAAATTAAAAATTTTATATTT
1 AAATAAAAATAAATTTAAAT-AAAATTAAAAATTTTATATTT
2332006 TATATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 18 0.50
43 5 0.14
44 13 0.36
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (43 bp):
AAATAAAAATAAATTTAAATAAAATTAAAAATTTTATATTTAC
Found at i:2332027 original size:53 final size:52
Alignment explanation
Indices: 2331913--2332038 Score: 148
Period size: 51 Copynumber: 2.4 Consensus size: 52
2331903 TTTAAAATTT
* *
2331913 AATAAAAATTAAATATAAAT-AAATTTAAATAAATTTAAATTTTATATTTACA
1 AATAAAAA-TAAATATAAATAAAAATTAAATAAATTTAAATTTTATATTAACA
* * * *
2331965 AATAAAAATAGATTTAAATAAAAATTAAA-AATTTTATATTTTATATTAAATCA
1 AATAAAAATAAATATAAATAAAAATTAAATAAATTTAAATTTTATATT-AA-CA
*
2332018 AATATAAATAAATATAAATAA
1 AATAAAAATAAATATAAATAA
2332039 TATTAATATC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
51 25 0.40
52 17 0.27
53 20 0.32
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (52 bp):
AATAAAAATAAATATAAATAAAAATTAAATAAATTTAAATTTTATATTAACA
Found at i:2333627 original size:16 final size:16
Alignment explanation
Indices: 2333608--2333650 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
2333598 ACATGCATAC
2333608 ATACATACATACAAAT
1 ATACATACATACAAAT
*
2333624 ATACAT--ATACACAT
1 ATACATACATACAAAT
*
2333638 ATATATACATACA
1 ATACATACATACA
2333651 CACAGAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.52
16 11 0.48
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (16 bp):
ATACATACATACAAAT
Found at i:2334564 original size:26 final size:27
Alignment explanation
Indices: 2334533--2334583 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2334523 TATATAATAA
2334533 AAATA-TAAAAT-TAATATTTTTGAATT
1 AAATATTAAAATGTAAT-TTTTTGAATT
*
2334559 AAATATTAATATGTAATTTTTTGAA
1 AAATATTAAAATGTAATTTTTTGAA
2334584 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 13 0.59
28 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (27 bp):
AAATATTAAAATGTAATTTTTTGAATT
Found at i:2334593 original size:27 final size:27
Alignment explanation
Indices: 2334531--2334593 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2334521 AATATATAAT
**
2334531 AAAAATATAAAATTAATATTTTTGAATT
1 AAAAAT-TAAAATTAATATTTTTGAAAA
* *
2334559 AAATATTAATATGTAAT-TTTTTGAAAA
1 AAAAATTAAAAT-TAATATTTTTGAAAA
2334586 AAAAATTA
1 AAAAATTA
2334594 TTTTTGAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 20 0.69
28 9 0.31
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (27 bp):
AAAAATTAAAATTAATATTTTTGAAAA
Found at i:2335176 original size:12 final size:12
Alignment explanation
Indices: 2335159--2335193 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2335149 CCAACTCCGC
2335159 AAAAAAA-AAAA
1 AAAAAAAGAAAA
2335170 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
2335182 AAGAAAAGAAAA
1 AAAAAAAGAAAA
2335194 TCATATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:2335367 original size:38 final size:38
Alignment explanation
Indices: 2335312--2335387 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
2335302 ATATATACAC
*
2335312 ATATATATATATGTATATAGTAATGTGACACTCAACTT
1 ATATATATATATATATATAGTAATGTGACACTCAACTT
*
2335350 ATATATATATATATATATTGTAATGTGACACTCAACTT
1 ATATATATATATATATATAGTAATGTGACACTCAACTT
2335388 TCATATTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (38 bp):
ATATATATATATATATATAGTAATGTGACACTCAACTT
Found at i:2338975 original size:6 final size:6
Alignment explanation
Indices: 2338967--2339053 Score: 65
Period size: 6 Copynumber: 15.0 Consensus size: 6
2338957 AACAGTGTAT
* * * * *
2338967 TTATAT TTATCA TTATTAA TTATAA TAATAA TTATTA TTATAT TTATAA
1 TTATAA TTATAA TTA-TAA TTATAA TTATAA TTATAA TTATAA TTATAA
* * *
2339016 TTATAA -TAAAA TTA-AA -AATAT TTATAA TTATAA -TATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
2339054 ATGATGCAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
4 1 0.02
5 12 0.19
6 45 0.71
7 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
TTATAA
Found at i:2339036 original size:27 final size:28
Alignment explanation
Indices: 2338983--2339055 Score: 94
Period size: 27 Copynumber: 2.5 Consensus size: 28
2338973 TTATCATTAT
**
2338983 TAATTATAATAATAATTATTATTATATTTA
1 TAATTATAATAA-AATTA-TAAAATATTTA
2339013 TAATTATAATAAAATTA-AAAATATTTA
1 TAATTATAATAAAATTATAAAATATTTA
2339040 TAATTATAATATAAAT
1 TAATTATAATA-AAAT
2339056 GATGCAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 19 0.47
28 4 0.10
29 5 0.12
30 12 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATTATAATAAAATTATAAAATATTTA
Found at i:2347094 original size:28 final size:28
Alignment explanation
Indices: 2347063--2347145 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 28
2347053 AAATAACACA
*
2347063 ATAT-AAATATATGAATATGTTAAAATTT
1 ATATAAAATATAT-AATATATTAAAATTT
2347091 ATATAAAATAATTATTAATATATTAAAATTT
1 ATATAAAAT-A-TA-TAATATATTAAAATTT
* *
2347122 ATTTAAAATATATAATATTTTAAA
1 ATATAAAATATATAATATATTAAA
2347146 TATAATTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 15 0.31
29 6 0.12
30 2 0.04
31 24 0.50
32 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
ATATAAAATATATAATATATTAAAATTT
Found at i:2347856 original size:33 final size:34
Alignment explanation
Indices: 2347834--2347897 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
2347824 TAATTATTTA
*
2347834 TAATGATATATAAAATTAAAAAATCGATAAAATT
1 TAATGATATATAAAATTAAAAAATCAATAAAATT
*
2347868 TAATGATATAT-AAATTAAAATATCAATAAA
1 TAATGATATATAAAATTAAAAAATCAATAAA
2347898 GCTTACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (34 bp):
TAATGATATATAAAATTAAAAAATCAATAAAATT
Found at i:2347880 original size:17 final size:17
Alignment explanation
Indices: 2347834--2347881 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2347824 TAATTATTTA
2347834 TAATGATATATAAAATT
1 TAATGATATATAAAATT
* ** **
2347851 AAAAAATCGATAAAATT
1 TAATGATATATAAAATT
2347868 TAATGATATATAAA
1 TAATGATATATAAA
2347882 TTAAAATATC
Statistics
Matches: 21, Mismatches: 10, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (17 bp):
TAATGATATATAAAATT
Found at i:2351386 original size:20 final size:19
Alignment explanation
Indices: 2351361--2351402 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2351351 TTCGATGATT
* *
2351361 TTTAATATATTATAACTTTA
1 TTTAATATAATA-AACTTAA
2351381 TTTAATATAATAAACTTAA
1 TTTAATATAATAAACTTAA
2351400 TTT
1 TTT
2351403 GATTTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATATAATAAACTTAA
Found at i:2352192 original size:25 final size:23
Alignment explanation
Indices: 2352164--2352239 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 23
2352154 TTTAAAAATA
2352164 TTAAATTTAAAGTATTTTATATATT
1 TTAAATTTAAA-TA-TTTATATATT
*
2352189 TTAATATATT-AATAATTTATATTATA
1 TTAA-AT-TTAAAT-ATTTATA-TATT
*
2352215 TAAAATTTAAAATATTTATATATT
1 TTAAATTT-AAATATTTATATATT
2352239 T
1 T
2352240 ATATTATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
24 6 0.14
25 20 0.48
26 14 0.33
27 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TTAAATTTAAATATTTATATATT
Found at i:2355718 original size:15 final size:15
Alignment explanation
Indices: 2355673--2355724 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
2355663 GAAAAGACAA
2355673 TTAATTAA-AAAATAT
1 TTAATTAATAAAA-AT
* * *
2355688 TTACTTATTAAGAAT
1 TTAATTAATAAAAAT
2355703 TTAATTAATAAAAAT
1 TTAATTAATAAAAAT
2355718 TTAATTA
1 TTAATTA
2355725 CATTTTGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
TTAATTAATAAAAAT
Found at i:2358260 original size:31 final size:32
Alignment explanation
Indices: 2358215--2358284 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
2358205 ATAACACAAT
*
2358215 ATAATATATGAATATGTTAAAATTTATATAAA
1 ATAATATATGAATATATTAAAATTTATATAAA
* *
2358247 ATAAT-TATTAATATATTAAAATTTATTTAAA
1 ATAATATATGAATATATTAAAATTTATATAAA
2358278 AT-ATATA
1 ATAATATA
2358285 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 2 0.06
31 27 0.79
32 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
ATAATATATGAATATATTAAAATTTATATAAA
Found at i:2358669 original size:46 final size:46
Alignment explanation
Indices: 2358583--2358671 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
2358573 GAATCGAAAG
* *** * *
2358583 TTAAATTAATTAATTTTTTTATTTTTTATTTAATTATAATATTTAA
1 TTAAATTAATCAATTTTTTTATTTAAAAATTAAATATAATATTTAA
2358629 TTAAATTAATCAATTTTTTATATTTAAAAATTAAAT-TAATATT
1 TTAAATTAATCAATTTTTT-TATTTAAAAATTAAATATAATATT
2358672 AAAAATGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 25 0.69
47 11 0.31
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (46 bp):
TTAAATTAATCAATTTTTTTATTTAAAAATTAAATATAATATTTAA
Found at i:2361350 original size:15 final size:15
Alignment explanation
Indices: 2361302--2361353 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
2361292 GAAAAGACAA
2361302 TTAATTAA-AAAATAT
1 TTAATTAATAAAA-AT
* * *
2361317 TTACTTTATTAAGAAT
1 TTA-ATTAATAAAAAT
2361333 TTAATTAATAAAAAT
1 TTAATTAATAAAAAT
2361348 TTAATT
1 TTAATT
2361354 TACATATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 18 0.62
16 8 0.28
17 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAATTAATAAAAAT
Found at i:2362589 original size:20 final size:19
Alignment explanation
Indices: 2362564--2362605 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2362554 TTCGATGATT
* *
2362564 TTTAATATATTATAACTTTA
1 TTTAATATAATA-AACTTAA
2362584 TTTAATATAATAAACTTAA
1 TTTAATATAATAAACTTAA
2362603 TTT
1 TTT
2362606 GATTTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATATAATAAACTTAA
Found at i:2372588 original size:2 final size:2
Alignment explanation
Indices: 2372581--2372607 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2372571 TTTGTCACTG
2372581 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2372608 ACTCAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2373991 original size:2 final size:2
Alignment explanation
Indices: 2373984--2374018 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2373974 CCGTATTACA
2373984 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
2374019 CACACGTGAT
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:2374715 original size:17 final size:17
Alignment explanation
Indices: 2374684--2374750 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
2374674 TATTTTAATT
* *
2374684 TTTTTAAATTAATTTTTA
1 TTTTTAAAAT-ATTTATA
2374702 TTTTTAAAATATTTATA
1 TTTTTAAAATATTTATA
*
2374719 -TTTAATAAATATTTATA
1 TTTTTA-AAATATTTATA
2374736 TTTATT-AAATATTTA
1 TTT-TTAAAATATTTA
2374751 AATATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.10
17 26 0.62
18 11 0.26
19 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTAAAATATTTATA
Found at i:2374738 original size:34 final size:35
Alignment explanation
Indices: 2374694--2374799 Score: 96
Period size: 34 Copynumber: 3.1 Consensus size: 35
2374684 TTTTTAAATT
* * *
2374694 AATTTTTATTTTTAAAATATTTATAT-TTAATAAA
1 AATTTATATTTTTAAAATATTTAAATATAAATAAA
*
2374728 TATTTATATTTATT-AAATATTTAAATATAAATAAA
1 AATTTATATTT-TTAAAATATTTAAATATAAATAAA
* * *
2374763 AATATA-ATCTTTTAAAAAATTTAAA-A-ACATAAA
1 AATTTATAT-TTTTAAAATATTTAAATATAAATAAA
2374796 AATT
1 AATT
2374800 AAAAAAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
33 9 0.15
34 25 0.42
35 25 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (35 bp):
AATTTATATTTTTAAAATATTTAAATATAAATAAA
Found at i:2375396 original size:2 final size:2
Alignment explanation
Indices: 2375389--2375419 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2375379 TTGGTTTTAG
*
2375389 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2375420 AATCATGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2378879 original size:4 final size:4
Alignment explanation
Indices: 2378858--2378901 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
2378848 TTTTTTATTA
* * * *
2378858 ATAT CTAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT TTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2378902 CCAAAAGATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:2378885 original size:10 final size:10
Alignment explanation
Indices: 2378858--2378901 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
2378848 TTTTTTATTA
* *
2378858 ATATCTATAC
1 ATATATATAT
*
2378868 ATACATATAT
1 ATATATATAT
2378878 ATATATATAT
1 ATATATATAT
*
2378888 ATATATTTAT
1 ATATATATAT
2378898 ATAT
1 ATAT
2378902 CCAAAAGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:2382849 original size:6 final size:7
Alignment explanation
Indices: 2382834--2382858 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2382824 TTTTCCTTTC
2382834 TTTTATT
1 TTTTATT
2382841 TTTTATT
1 TTTTATT
2382848 TTTTATT
1 TTTTATT
2382855 TTTT
1 TTTT
2382859 TTAACTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:2383013 original size:2 final size:2
Alignment explanation
Indices: 2383008--2383045 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2382998 AACAACCCAC
*
2383008 AT AT AT -T AT AT A- AT AT AT GT 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
2383046 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2383702 original size:2 final size:2
Alignment explanation
Indices: 2383697--2383721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2383687 CTTGAATAAA
2383697 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
2383722 CTTATTTTAA
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:2383869 original size:16 final size:18
Alignment explanation
Indices: 2383848--2383880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2383838 TTTTTTTTAA
2383848 TTTTTT-CT-CCTTATTC
1 TTTTTTCCTACCTTATTC
2383864 TTTTTTCCTACCTTATT
1 TTTTTTCCTACCTTATT
2383881 ATGGATGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTCCTACCTTATTC
Found at i:2387287 original size:2 final size:2
Alignment explanation
Indices: 2387282--2387319 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2387272 TTTGTAAATG
*
2387282 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2387320 TATTTAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Done.