Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 167 of 187
Found at i:49285341 original size:15 final size:15
Alignment explanation
Indices: 49285321--49285352 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49285311 ATGTATATTT
49285321 CTGTAGAACTGGAAA
1 CTGTAGAACTGGAAA
*
49285336 CTGTAGAATTGGAAA
1 CTGTAGAACTGGAAA
49285351 CT
1 CT
49285353 ATGTTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (15 bp):
CTGTAGAACTGGAAA
Found at i:49289738 original size:15 final size:13
Alignment explanation
Indices: 49289702--49289736 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
49289692 TTAATCAAAG
49289702 ATATGTATAAGAT
1 ATATGTATAAGAT
49289715 ATATGTATAAGAT
1 ATATGTATAAGAT
49289728 ATATGTATA
1 ATATGTATA
49289737 TATATAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (13 bp):
ATATGTATAAGAT
Found at i:49290284 original size:2 final size:2
Alignment explanation
Indices: 49290277--49290317 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
49290267 TAATACAAAT
49290277 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49290318 CCATGTGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49290511 original size:41 final size:41
Alignment explanation
Indices: 49290450--49290565 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
49290440 GAAGACTTAT
* * *
49290450 TGCCAGTGAGATAATTCAGACTCTATGTCTAGCAAGCTGGA
1 TGCCAGTGAAACAATTCAGACTCTAAGTCTAGCAAGCTGGA
* * *
49290491 TGCTAGTGAAACAATTCAGACTCTACGTCTAGCAAGTTGGA
1 TGCCAGTGAAACAATTCAGACTCTAAGTCTAGCAAGCTGGA
* * * *
49290532 TGCCGGTGAAACATTTCGGACTTTAAGTCTAGCA
1 TGCCAGTGAAACAATTCAGACTCTAAGTCTAGCA
49290566 GGCCAAAAGC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
TGCCAGTGAAACAATTCAGACTCTAAGTCTAGCAAGCTGGA
Found at i:49292152 original size:24 final size:23
Alignment explanation
Indices: 49292096--49292179 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 23
49292086 AAAATAATAA
* **
49292096 AGTAGATTATATATTATTTTTAT
1 AGTAAATTATATATTATAATTAT
*
49292119 AGT--ATTATATATTATAATTTT
1 AGTAAATTATATATTATAATTAT
*
49292140 AGTAAATTCATATAATAATAATTAT
1 AGTAAATT-ATAT-ATTATAATTAT
*
49292165 ATTAAATTATATATT
1 AGTAAATTATATATT
49292180 TTTTTATTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 18 0.36
23 8 0.16
24 8 0.16
25 16 0.32
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (23 bp):
AGTAAATTATATATTATAATTAT
Found at i:49292216 original size:46 final size:47
Alignment explanation
Indices: 49292122--49292216 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 47
49292112 TTTTTATAGT
49292122 ATTATATATTATAATTTTAGTAAATTCATATAATAATAATTATATTAA
1 ATTATATATTAT-ATTTTAGTAAATTCATATAATAATAATTATATTAA
* *
49292170 ATTATATATT-T-TTTTATTAAATT-ATATTTAATAATAATTATGTTAA
1 ATTATATATTATATTTTAGTAAATTCATA--TAATAATAATTATATTAA
49292216 A
1 A
49292217 ATATGGTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 3 0.07
45 11 0.26
46 18 0.42
47 1 0.02
48 10 0.23
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (47 bp):
ATTATATATTATATTTTAGTAAATTCATATAATAATAATTATATTAA
Found at i:49292274 original size:58 final size:57
Alignment explanation
Indices: 49292166--49292276 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
49292156 AATAATTATA
*
49292166 TTAAATTATATATTTTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGG
1 TTAAATTATATATTTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGG
* * *
49292223 TTAAATTATTTATTATTTTTATTAAATTATTTTTAATATTAATCT-TATTAAAAT
1 TTAAATTATATATT-TTTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
49292277 TTAATAACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
57 13 0.27
58 34 0.71
59 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (57 bp):
TTAAATTATATATTTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGG
Found at i:49292480 original size:16 final size:16
Alignment explanation
Indices: 49292450--49292481 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49292440 TGATTACAAC
49292450 TCTATTCAATTACAGT
1 TCTATTCAATTACAGT
*
49292466 TCTATTCCATTACAGT
1 TCTATTCAATTACAGT
49292482 GAACCAAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (16 bp):
TCTATTCAATTACAGT
Found at i:49295106 original size:26 final size:26
Alignment explanation
Indices: 49295077--49295126 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
49295067 TTTGGTATAG
49295077 ACTAGTCTTGTCCATGTAAAGTTTTC
1 ACTAGTCTTGTCCATGTAAAGTTTTC
49295103 ACTAGTCTTGTCCATGTAAAGTTT
1 ACTAGTCTTGTCCATGTAAAGTTT
49295127 CCTTTCAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (26 bp):
ACTAGTCTTGTCCATGTAAAGTTTTC
Found at i:49304379 original size:18 final size:18
Alignment explanation
Indices: 49304352--49304391 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
49304342 TAGGAAGCTG
* *
49304352 AACCATCAGCTTCCACTA
1 AACCAGCAGCTCCCACTA
*
49304370 AACCAGCAGCTCCCACTG
1 AACCAGCAGCTCCCACTA
49304388 AACC
1 AACC
49304392 GGCACCTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.42, G:0.10, T:0.15
Consensus pattern (18 bp):
AACCAGCAGCTCCCACTA
Found at i:49307961 original size:16 final size:14
Alignment explanation
Indices: 49307934--49307970 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
49307924 ATTACGTTTG
49307934 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
*
49307948 AAAAAAATAAAAAA
1 AAAAAAATAAAAAT
49307962 ATAAAAAAT
1 A-AAAAAAT
49307971 TATATAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:49307970 original size:7 final size:8
Alignment explanation
Indices: 49307934--49307969 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
49307924 ATTACGTTTG
49307934 AAAAAAAT
1 AAAAAAAT
49307942 --AAAAAT
1 AAAAAAAT
49307948 AAAAAAAT
1 AAAAAAAT
49307956 AAAAAAAT
1 AAAAAAAT
49307964 AAAAAA
1 AAAAAA
49307970 TTATATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:49308583 original size:13 final size:13
Alignment explanation
Indices: 49308565--49308620 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
49308555 AATTTAGAAT
49308565 TATTTAGTGATAA
1 TATTTAGTGATAA
49308578 TATTTAGTGATAA
1 TATTTAGTGATAA
* *
49308591 TGTTTA--GA-AT
1 TATTTAGTGATAA
*
49308601 TATTTAGTGATTA
1 TATTTAGTGATAA
49308614 TATTTAG
1 TATTTAG
49308621 GAAAAATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 25 0.71
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:49309301 original size:9 final size:9
Alignment explanation
Indices: 49309287--49309312 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
49309277 ATATTAAGGG
49309287 AAAATGGAT
1 AAAATGGAT
49309296 AAAATGGAT
1 AAAATGGAT
49309305 AAAATGGA
1 AAAATGGA
49309313 AGTGTTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (9 bp):
AAAATGGAT
Found at i:49312119 original size:43 final size:43
Alignment explanation
Indices: 49312055--49312139 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
49312045 TGGAGACAAT
* *
49312055 TAATTCTAATGCCAAAAGTTATAGTCTATATTGACTAACAAGC
1 TAATTCTAATACCAAAAGTTATAGACTATATTGACTAACAAGC
* * *
49312098 TAATTCTAATACCAAATGTTATAGACTATTTTGACTTACAAG
1 TAATTCTAATACCAAAAGTTATAGACTATATTGACTAACAAG
49312140 GTACTATCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (43 bp):
TAATTCTAATACCAAAAGTTATAGACTATATTGACTAACAAGC
Found at i:49316121 original size:13 final size:13
Alignment explanation
Indices: 49316103--49316127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49316093 ATCATGTCAC
49316103 TTTTTATTTTTAT
1 TTTTTATTTTTAT
49316116 TTTTTATTTTTA
1 TTTTTATTTTTA
49316128 AGGTTTTATA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:49316935 original size:16 final size:17
Alignment explanation
Indices: 49316884--49316942 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
49316874 TATAAAAATA
*
49316884 TAATAAAAATAAAATAAG
1 TAATAAAAA-AACATAAG
* *
49316902 T-ATAATAAAACATTAG
1 TAATAAAAAAACATAAG
49316918 TAATAAAAAAACA-AAG
1 TAATAAAAAAACATAAG
49316934 TAATGAAAA
1 TAAT-AAAA
49316943 GAAAGAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 13 0.38
17 20 0.59
18 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (17 bp):
TAATAAAAAAACATAAG
Found at i:49324274 original size:22 final size:23
Alignment explanation
Indices: 49324248--49324292 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
49324238 CCAGGTTAGA
49324248 TAAAACAATTAAAATA-AATAAT
1 TAAAACAATTAAAATAGAATAAT
*
49324270 TAAAATAATTAAAATAGAATAAT
1 TAAAACAATTAAAATAGAATAAT
49324293 AAATCTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAACAATTAAAATAGAATAAT
Found at i:49324778 original size:8 final size:8
Alignment explanation
Indices: 49324765--49324796 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
49324755 AAAAATTTAG
49324765 AATAATAA
1 AATAATAA
49324773 AATAATAA
1 AATAATAA
49324781 AATAATAA
1 AATAATAA
49324789 AATAATAA
1 AATAATAA
49324797 GAGTTGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:49328868 original size:8 final size:8
Alignment explanation
Indices: 49328855--49328879 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
49328845 TAAAAATTTG
49328855 AAATAATA
1 AAATAATA
49328863 AAATAATA
1 AAATAATA
49328871 AAATAATA
1 AAATAATA
49328879 A
1 A
49328880 GAGCTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:49338006 original size:56 final size:58
Alignment explanation
Indices: 49337858--49338020 Score: 197
Period size: 57 Copynumber: 2.9 Consensus size: 58
49337848 TTTTTCAAGT
* * * * ***
49337858 CATTGTCATTTTCATTTCGGTGAAAACCACGTTCATTTCCAAATGATTT-CATCACTC
1 CATTTTCATTTTAATTTAGGAGAAAACCATAATCATTTCCAAATGATTTCCATCACTC
* * **
49337915 CATTTTCATTTTAATTTTGGAGAAAACCATAATCATTTTCAAATG-TTTCCATTTCTC
1 CATTTTCATTTTAATTTAGGAGAAAACCATAATCATTTCCAAATGATTTCCATCACTC
*
49337972 CATTTTCA-TTTAATTTAGGAGAAAACCATAATCATTTCCAAATGCTTTC
1 CATTTTCATTTTAATTTAGGAGAAAACCATAATCATTTCCAAATGATTTC
49338021 TTGTTTCTCT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 37 0.40
57 55 0.60
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (58 bp):
CATTTTCATTTTAATTTAGGAGAAAACCATAATCATTTCCAAATGATTTCCATCACTC
Found at i:49339262 original size:66 final size:69
Alignment explanation
Indices: 49339138--49339272 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 69
49339128 TGTTTGAAAT
* * * * *
49339138 TTGACAATTTTATTGTTAAAATGGCTACTGTTTAGTTGTGTGTGAAAGGCATTTAAACTGTCCAA
1 TTGACAAATTTATTGCTAAAATGGCTACTGTTCAGTCGTGTGTGAAAGACATTTAAACTGTCCAA
49339203 ATTG
66 ATTG
49339207 TTGACAAATTTATTGCT-AAATGGCTACTGTTCAG-CG-GTGTGAAAGACATTTAAACTGTCCAA
1 TTGACAAATTTATTGCTAAAATGGCTACTGTTCAGTCGTGTGTGAAAGACATTTAAACTGTCCAA
49339269 ATTG
66 ATTG
49339273 ATGATAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
66 29 0.48
67 1 0.02
68 16 0.26
69 15 0.25
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (69 bp):
TTGACAAATTTATTGCTAAAATGGCTACTGTTCAGTCGTGTGTGAAAGACATTTAAACTGTCCAA
ATTG
Found at i:49363622 original size:16 final size:16
Alignment explanation
Indices: 49363601--49363632 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49363591 GTTTTGTTGC
*
49363601 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
49363617 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
49363633 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:49363952 original size:51 final size:50
Alignment explanation
Indices: 49363858--49363998 Score: 153
Period size: 51 Copynumber: 2.8 Consensus size: 50
49363848 TACCGGTTCA
* * *
49363858 CATAGTAGCCTGCACATAGTACTACAGATGTGACCATCACTATCCGATACC
1 CATAGTAGCCTCCACATAGTACTACACACGTGACCA-CACTATCCGATACC
* * * *
49363909 CGTAGTAGCCTCCACATAGTACTACACACGTGATCGA-AGCTATCCGGTACG
1 CATAGTAGCCTCCACATAGTACTACACACGTGA-CCACA-CTATCCGATACC
*
49363960 CATAGTAGCCTCTACATAGTACTAC-C-CGTGACCATCACT
1 CATAGTAGCCTCCACATAGTACTACACACGTGACCA-CACT
49363999 TTCACTTTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
48 2 0.03
49 7 0.09
50 3 0.04
51 62 0.82
52 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (50 bp):
CATAGTAGCCTCCACATAGTACTACACACGTGACCACACTATCCGATACC
Found at i:49377647 original size:69 final size:67
Alignment explanation
Indices: 49377519--49377657 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 67
49377509 TTATTTTATT
* * *
49377519 TTATTTAATATTAAATTAAATTTAATACTTATGTTAATAGTATTTTATTAATTTAATATTAAAGT
1 TTATTTAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGT
49377584 GA
66 GA
* * * *
49377586 TTATATTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAT
1 TTAT-TTAATATTAAATTAAATCTAATACTTATCTTAAT-AGTATTATATTAATTTAATATTAAA
49377651 GTGA
64 GTGA
49377655 TTA
1 TTA
49377658 AGTTTAATCA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
67 4 0.06
68 29 0.46
69 30 0.48
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (67 bp):
TTATTTAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAATATTAAAGT
GA
Found at i:49387494 original size:23 final size:22
Alignment explanation
Indices: 49387451--49387496 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
49387441 ATTTTGTTCA
*
49387451 ACTTTAACTTTTATTTAAAAAC
1 ACTTTAACTTTTATATAAAAAC
* *
49387473 ACTTTAATTTGTTATATCAAAAC
1 ACTTTAACTT-TTATATAAAAAC
49387496 A
1 A
49387497 TATTATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (22 bp):
ACTTTAACTTTTATATAAAAAC
Found at i:49389119 original size:42 final size:42
Alignment explanation
Indices: 49389054--49389138 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
49389044 GTTACTAGAC
* *
49389054 TTCGTCAGTAATTATACTCAGTTATCATAGAATATTGAAATT
1 TTCGTCAGTAATTATAATCAGTTATCATAAAATATTGAAATT
*
49389096 TTCGTCAGTAATTATAATTAGTTATCATAAAATATTGAAATT
1 TTCGTCAGTAATTATAATCAGTTATCATAAAATATTGAAATT
49389138 T
1 T
49389139 ATCTTTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (42 bp):
TTCGTCAGTAATTATAATCAGTTATCATAAAATATTGAAATT
Found at i:49389441 original size:4 final size:4
Alignment explanation
Indices: 49389432--49389457 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
49389422 TAACATATGT
49389432 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
49389458 GCATTTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:49394139 original size:16 final size:17
Alignment explanation
Indices: 49394098--49394138 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
49394088 CATTTAGTTT
49394098 TTTTTA-TTTAATTTAG
1 TTTTTATTTTAATTTAG
*
49394114 TTTTTATTTTATTTTA-
1 TTTTTATTTTAATTTAG
49394130 -TTTTATTTT
1 TTTTTATTTT
49394139 TCACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 9 0.39
16 6 0.26
17 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTAATTTAG
Found at i:49406722 original size:3 final size:3
Alignment explanation
Indices: 49406714--49406758 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
49406704 ATTCGATCTT
49406714 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49406759 AAAGATTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49407513 original size:16 final size:16
Alignment explanation
Indices: 49407492--49407532 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
49407482 ATAAAAAAAT
* *
49407492 ATAAATAGACATGAAA
1 ATAAATAAAAATGAAA
49407508 ATAAATAAAAATG-AA
1 ATAAATAAAAATGAAA
49407523 A-AAATAAAAA
1 ATAAATAAAAA
49407533 AAATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 9 0.39
15 3 0.13
16 11 0.48
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (16 bp):
ATAAATAAAAATGAAA
Found at i:49408299 original size:149 final size:152
Alignment explanation
Indices: 49408139--49408500 Score: 509
Period size: 152 Copynumber: 2.4 Consensus size: 152
49408129 CGAAATAGTT
* * *** *
49408139 AAAAAAATCAAAATTTTATTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAATTTTCTTTT
1 AAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAAAAATATTTT
* * * *
49408204 TATTTTTCAAAATCTAAATTTTCTC-CTTTT-AA-AAAAAACACTATTTTTCTTAAAAATTAAAG
66 TATTTTTCAAAAGCTAAACTTACTCACTTTTAAAGAAAAAACACTATTTTTCTTAAAAATTAAAA
* *
49408266 CTTTTATTTTGAAGTAGTTGAA
131 CTTTTACTTTGAAATAGTTGAA
*
49408288 AAAAAAATCAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGAC-TAAAAAAATATTTT
1 AAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAAAAATATTTT
* *
49408352 TATTTTTCAAAAGCTAAACTTACTCATTTTTTAAAGAAAAAACACTATTTTTCTTAAAGATTAAA
66 TATTTTTCAAAAGCTAAACTTACTCA-CTTTTAAAGAAAAAACACTATTTTTCTTAAAAATTAAA
*
49408417 ATTTTTACTTTGAAATAGTTGAA
130 ACTTTTACTTTGAAATAGTTGAA
* *
49408440 AAAAAAAT-AAAAGCTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATAACTAAAAAAAATA
1 AAAAAAATCAAAA-CTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAAAAATA
49408501 GATTTTTTCC
Statistics
Matches: 188, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
148 32 0.17
149 47 0.25
150 4 0.02
151 6 0.03
152 90 0.48
153 9 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (152 bp):
AAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAAAAATATTTT
TATTTTTCAAAAGCTAAACTTACTCACTTTTAAAGAAAAAACACTATTTTTCTTAAAAATTAAAA
CTTTTACTTTGAAATAGTTGAA
Found at i:49414876 original size:27 final size:27
Alignment explanation
Indices: 49414820--49414876 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
49414810 TTATCCTAGC
* *
49414820 AAAATTTTAACAATTTTACCCTTGGAA
1 AAAATTTTAACAATTTTACCCCTAGAA
** *
49414847 AAAATTTTGCCAATTTTACCCCTAGTA
1 AAAATTTTAACAATTTTACCCCTAGAA
49414874 AAA
1 AAA
49414877 TTTCGAGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (27 bp):
AAAATTTTAACAATTTTACCCCTAGAA
Found at i:49416305 original size:14 final size:14
Alignment explanation
Indices: 49416280--49416316 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
49416270 TGGTGACTCT
49416280 ACGTTAATGTAGGCA
1 ACGTT-ATGTAGGCA
49416295 ACGTTATGTAGGCA
1 ACGTTATGTAGGCA
49416309 ACGTTATG
1 ACGTTATG
49416317 ACAGCTTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (14 bp):
ACGTTATGTAGGCA
Found at i:49419233 original size:4 final size:4
Alignment explanation
Indices: 49419219--49419276 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
49419209 GTGCCCCAAT
* * * * *
49419219 TTCA ATCA TTCA TTCA TTCG TTCA TTCA TTCA TCCA TTCA TTAA CTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
*
49419267 TTCA CTCA TT
1 TTCA TTCA TT
49419277 TGTTTATTTA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.45
Consensus pattern (4 bp):
TTCA
Found at i:49430142 original size:31 final size:32
Alignment explanation
Indices: 49430107--49430168 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
49430097 CACAAATTCT
49430107 GGTGAAAACTCT-ATATTTTTTTTCACTAACC
1 GGTGAAAACTCTAATATTTTTTTTCACTAACC
* *
49430138 GGTGAAAACTGTAATATTTTTTTTCTCTAAC
1 GGTGAAAACTCTAATATTTTTTTTCACTAAC
49430169 TTTTTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (32 bp):
GGTGAAAACTCTAATATTTTTTTTCACTAACC
Found at i:49433505 original size:469 final size:468
Alignment explanation
Indices: 49432626--49433536 Score: 1404
Period size: 469 Copynumber: 1.9 Consensus size: 468
49432616 CGCCACAATC
* * *
49432626 TCAATTCACATATACCCAATAGCTCGCAAGAAGGACAAGCTCACAGATCCAGCTCGCTAAAGTTT
1 TCAATTCACATATACCCAATAGCTCGCAAGAAGGACAAGCTCACAGAGCCAGCTCGCCAAAGCTT
* *
49432691 CAGTTCGCCTATACCCACGAAGCGCACAGTCACCCAGACACATGTGTACCACACCTAATCTGTAT
66 CAATTCGCCTATACCCACGAAGCGCACAGTCACCCAGACACATGTGTAACACACCTAATCTGTAT
* *
49432756 CATTCATCGAAATAGGTTACGGAGCATTACCGTAAAATCGTAACTTAAAACATTCATTTTCAAAC
131 CATTCATCGAAATAGGTTACGGAGCATTACCGTAAAATCATAACTTAAAACATTCATTTCCAAAC
* *
49432821 ATTTCATTAATCATAGTATAATTCATTCATACACATGCATATCGTCCCTTATTCAAGCCCTCGAG
196 ATTTCATTAATCATAGAATAATTCATTCATACACATGCATATCATCCCTTATTCAAGCCCTCGAG
*
49432886 GCCTTAGAAACACTTTAGAAACGATTCAGGACTAAATCGGGAACATTTGAAACATTGAGAAAAAA
261 GCCTTAGAAACACTTTAGAAACGATTCAGGACTAAATCAGGAACATTTGAAACATTGAGAAAAAA
* * **
49432951 GTTAGATAAATTCACACAGCAGGAGTCACATGACTGTGTGACTCACATGGCCGAGACACATGCCC
326 GTTAGAAAAATTCACACAGCAGGAGTCACACGACTGTGTGACTCACACAGCCGAGACACATGCCC
49433016 ATGTCTCAAGCCATGTAACATTCGAAATAGGGACACACAGCCGTGTCCCACCGCGTGTCCCTTCA
391 ATGTCTCAAGCCATGTAACATTCGAAATAGGGACACACAGCCGTGTCCCACCGCGTGTCCCTTCA
49433081 ACCTGCCATAGTA
456 ACCTGCCATAGTA
* * *
49433094 TCAATTCATATATACCCAATAGCTCGCAAGAAGGACAAGCTCACGGAGCCAGCTCGCCACAGCTT
1 TCAATTCACATATACCCAATAGCTCGCAAGAAGGACAAGCTCACAGAGCCAGCTCGCCAAAGCTT
* * **
49433159 CAATTCGCTTATACCCACGAAGTGCGTAGTCACCCAGACACATGTGTAACAC-CCTTAA-CTCGT
66 CAATTCGCCTATACCCACGAAGCGCACAGTCACCCAGACACATGTGTAACACACC-TAATCT-GT
** *
49433222 ATCATTTGTC-AGAATAGGGTTACGGAGCATTACCGTAAAAAT-ATAACTTAAAGCATTCATTTC
129 ATCATTCATCGA-AATA-GGTTACGGAGCATTACCGT-AAAATCATAACTTAAAACATTCATTTC
*
49433285 CAAACATTTCATTAATCATAGAATAATTCATTCATACACATGCATATCATCCCTTATTCGAGCCC
191 CAAACATTTCATTAATCATAGAATAATTCATTCATACACATGCATATCATCCCTTATTCAAGCCC
* * *
49433350 TCGAGGTCTTAGAAACACTTTAGAAACGATTCGGGACTAAATCAGGAACATTTGAAACATTGAGG
256 TCGAGGCCTTAGAAACACTTTAGAAACGATTCAGGACTAAATCAGGAACATTTGAAACATTGAGA
* *
49433415 AAAAAGTTAGAAAAATTCACACTA-CAAGG-GTCACACGATTGTGTGACTCACACAGCTGAGACA
321 AAAAAGTTAGAAAAATTCACAC-AGC-AGGAGTCACACGACTGTGTGACTCACACAGCCGAGACA
* * *
49433478 CATGTCCGTGTCTCAGGCCGA-GTAACATTCGAAATAGGGACACACAGCCGTGTCCCACC
384 CATGCCCATGTCTCAAGCC-ATGTAACATTCGAAATAGGGACACACAGCCGTGTCCCACC
49433537 CCATGTCTGT
Statistics
Matches: 402, Mismatches: 33, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
467 5 0.01
468 122 0.30
469 265 0.66
470 10 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (468 bp):
TCAATTCACATATACCCAATAGCTCGCAAGAAGGACAAGCTCACAGAGCCAGCTCGCCAAAGCTT
CAATTCGCCTATACCCACGAAGCGCACAGTCACCCAGACACATGTGTAACACACCTAATCTGTAT
CATTCATCGAAATAGGTTACGGAGCATTACCGTAAAATCATAACTTAAAACATTCATTTCCAAAC
ATTTCATTAATCATAGAATAATTCATTCATACACATGCATATCATCCCTTATTCAAGCCCTCGAG
GCCTTAGAAACACTTTAGAAACGATTCAGGACTAAATCAGGAACATTTGAAACATTGAGAAAAAA
GTTAGAAAAATTCACACAGCAGGAGTCACACGACTGTGTGACTCACACAGCCGAGACACATGCCC
ATGTCTCAAGCCATGTAACATTCGAAATAGGGACACACAGCCGTGTCCCACCGCGTGTCCCTTCA
ACCTGCCATAGTA
Found at i:49438210 original size:137 final size:137
Alignment explanation
Indices: 49437952--49438217 Score: 324
Period size: 137 Copynumber: 1.9 Consensus size: 137
49437942 ATGTCATTAG
* * * *
49437952 GGTTACCATGTTTCAGGTGCTAGTCCTAAATGTCCTACTAGTGGCTGAGTTCCAGCATATGTTGC
1 GGTTACCATGGTTCAGGTGCTAGTCCTAAATGTCCTACCAATGGCTGAGTTCCAACATATGTTGC
* * *
49438017 GGATACTTGATAGCTTGTGTGAGCAACACCATGTAGCTACGTTCTGACCGACAACTTGTGTGAGA
66 GGATACTTGACAGCTTGTGTGAGCAACACCATGTAGCTACGTTCTGACCAAAAACTTGTGTGAGA
49438082 AGACTCA
131 AGACTCA
* * * *
49438089 GGTTACTATGGTTCAGGTGCTGGTCTTGAATGTCCTACCAATGGCTGAAG-TCCAACAT-TAGTT
1 GGTTACCATGGTTCAGGTGCTAGTCCTAAATGTCCTACCAATGGCTG-AGTTCCAACATAT-GTT
* * ** *
49438152 G-TGATACTTGACAGCTTGTGTGAGCGACATTATGTAGCTTACATT-TCGACCAAAAACTTGTGT
64 GCGGATACTTGACAGCTTGTGTGAGCAACACCATGTAGC-TACGTTCT-GACCAAAAACTTGTGT
49438215 GAG
127 GAG
49438218 CAGGCCCATT
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
136 34 0.31
137 73 0.67
138 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (137 bp):
GGTTACCATGGTTCAGGTGCTAGTCCTAAATGTCCTACCAATGGCTGAGTTCCAACATATGTTGC
GGATACTTGACAGCTTGTGTGAGCAACACCATGTAGCTACGTTCTGACCAAAAACTTGTGTGAGA
AGACTCA
Found at i:49446370 original size:6 final size:6
Alignment explanation
Indices: 49446359--49446383 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49446349 TGCTAACACA
49446359 TTCCTT TTCCTT TTCCTT TTCCTT T
1 TTCCTT TTCCTT TTCCTT TTCCTT T
49446384 ACATTATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCCTT
Found at i:49454405 original size:45 final size:45
Alignment explanation
Indices: 49454341--49454518 Score: 211
Period size: 45 Copynumber: 4.0 Consensus size: 45
49454331 ATCGGGTACA
* *
49454341 ATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCCACTATGTATC
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTATGTATC
* * * *
49454386 ATTGATTATAAAGGTGGTTGTTATGTACTGATTCCACCAGGTA-C
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTATGTATC
* * *
49454430 TATTGATTATGAAGGTGGTTGCTATGTGTTGATTCCACCGA-GTATC
1 -ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCA-CTATGTATC
* *
49454476 ATTGACTATAAGGGTGG-TGCTATGTGCTGA-TCCACTATGTATC
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTATGTATC
49454519 TGTTATTATT
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
42 2 0.02
43 9 0.08
44 13 0.12
45 86 0.76
46 3 0.03
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (45 bp):
ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTATGTATC
Found at i:49454492 original size:90 final size:88
Alignment explanation
Indices: 49454335--49454510 Score: 246
Period size: 90 Copynumber: 2.0 Consensus size: 88
49454325 ACGTGTATCG
* * *
49454335 GGTACAATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCCACTATGTATCATTGATTATAAAGG
1 GGTACAATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACGATGTATCATTGACTATAAAGG
*
49454400 TGGTTGTTATGTACTGATTCCACCA
66 TGG-TGCTATGTACTGA-TCCACCA
* * *
49454425 GGTACTATTGATTATGAAGGTGGTTGCTATGTGTTGATTCCACCGA-GTATCATTGACTATAAGG
1 GGTACAATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCA-CGATGTATCATTGACTATAAAG
*
49454489 GTGGTGCTATGTGCTGATCCAC
65 GTGGTGCTATGTACTGATCCAC
49454511 TATGTATCTG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 5 0.06
89 11 0.14
90 59 0.77
91 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.37
Consensus pattern (88 bp):
GGTACAATTGATTATAAAGGTGGTTGCTATGTGTTGATTCCACGATGTATCATTGACTATAAAGG
TGGTGCTATGTACTGATCCACCA
Found at i:49457141 original size:69 final size:69
Alignment explanation
Indices: 49456861--49457441 Score: 324
Period size: 69 Copynumber: 8.4 Consensus size: 69
49456851 TTACAAGATT
* * * * * *** * * * *
49456861 AAAACCGCAGCCTCTAATACTGTTAGAGAGAGCAAAGCTCTTTACTGTCACACTAAGACTCGCAA
1 AAAACCACAGCCTCCAACACAGTTAGAGAGAACAAAGCTCCCAACTGTCATACTAAGGCTCGTAG
49456926 GTGA
66 GTGA
** * * *
49456930 AAAACTGCAACCTCCAACACAGTTAGAGAGAACAAAGCTCTCAACTGTCATATTAAGGCTCGTAG
1 AAAACCACAGCCTCCAACACAGTTAGAGAGAACAAAGCTCCCAACTGTCATACTAAGGCTCGTAG
49456995 GTGA
66 GTGA
* * * * * * * * * *
49456999 AAAATCATAGCC-ACGACACAGCTAACAAGAGTTAA-AAA-CACTCAGCTGTCATACTAAGGCTT
1 AAAACCACAGCCTCCAACACAG-TTA-GAGAG--AACAAAGCTCCCAACTGTCATACTAAGGCTC
49457061 GTAGGTGA
62 GTAGGTGA
* * *
49457069 AAAACCACAACCTCCAACACAGTTAGAGAGAACAAAGCTCCCAACTGCCAT-CATAGGGCTCGTA
1 AAAACCACAGCCTCCAACACAGTTAGAGAGAACAAAGCTCCCAACTGTCATAC-TAAGGCTCGTA
49457133 GGTGA
65 GGTGA
** ** * * * *
49457138 AAAACCGTAGCCTTTAACATAATTAGCGAGAGTTACAAA-CTCCCAAATGTC--A-TAAGGCTCG
1 AAAACCACAGCCTCCAACACAGTTA--GAGAG-AACAAAGCTCCCAACTGTCATACTAAGGCTCG
*
49457199 CAGGTGA
63 TAGGTGA
* * *** * **
49457206 AAAATCACAGCCTCCAACACAGTTAGCA-AGAGCAAAGCTATTAGCTGTCATACTAAGGCTCACA
1 AAAACCACAGCCTCCAACACAGTTAG-AGAGAACAAAGCTCCCAACTGTCATACTAAGGCTCGTA
49457270 GGTGA
65 GGTGA
** * * * ** * * *
49457275 AAATTCGCAGCCTCCAGCACAGTTAGCGAGAGTTAA-AAA-CTCTCAGGTGTAATATTAATGCTC
1 AAAACCACAGCCTCCAACACAGTTA--GAGAG--AACAAAGCTCCCAACTGTCATACTAAGGCTC
*
49457338 GTAGGTTA
62 GTAGGTGA
* * * * *
49457346 AAAATCACAACCTCCAACACAGTTAGAGAGAGTTA-AAAACTCCCAGCTATCATACTAAGGCTCG
1 AAAACCACAGCCTCCAACACAGTTAGAGAGA---ACAAAGCTCCCAACTGTCATACTAAGGCTCG
* *
49457410 CAGGAGA
63 TAGGTGA
* *
49457417 AAAACCACAGCC-ACGACACAGTTAG
1 AAAACCACAGCCTCCAACACAGTTAG
49457442 CAAGAATTAA
Statistics
Matches: 390, Mismatches: 96, Indels: 51
0.73 0.18 0.09
Matches are distributed among these distances:
65 4 0.01
66 10 0.03
67 4 0.01
68 44 0.11
69 153 0.39
70 59 0.15
71 105 0.27
72 10 0.03
73 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (69 bp):
AAAACCACAGCCTCCAACACAGTTAGAGAGAACAAAGCTCCCAACTGTCATACTAAGGCTCGTAG
GTGA
Found at i:49457266 original size:137 final size:139
Alignment explanation
Indices: 49456937--49457376 Score: 365
Period size: 137 Copynumber: 3.2 Consensus size: 139
49456927 TGAAAAACTG
* **
49456937 CAACCTCCAACACAGTTAGAGAGAACAAAGCT-CTCAACTGTCAT-ATTAAGGCTCGTAGGTGAA
1 CAACCTCCAACACAGTTAGAGAGAACAAAGCTAC-CAACTGCCATCA-TAAGGCTCACAGGTGAA
* ** * * ** * * * * ** *
49457000 AAATCATAGCC-ACGACACAGCTAACAAGAGTTAAAAACACTCAGCTGT-CATACTAAGGCTTGT
64 AAACCGCAGCCTCCAACACAATTAGCGAGAGTTAAAAACTCCCAAATGTACAT--TAAGGCTCGT
*
49457063 AGGTGAAAAACCA
127 AGGTGAAAAATCA
* * **
49457076 CAACCTCCAACACAGTTAGAGAGAACAAAGCTCCCAACTGCCATCATAGGGCTCGTAGGTGAAAA
1 CAACCTCCAACACAGTTAGAGAGAACAAAGCTACCAACTGCCATCATAAGGCTCACAGGTGAAAA
* ** * * *
49457141 ACCGTAGCCTTTAACATAATTAGCGAGAGTTACAAACTCCCAAATGT-CA-TAAGGCTCGCAGGT
66 ACCGCAGCCTCCAACACAATTAGCGAGAGTTAAAAACTCCCAAATGTACATTAAGGCTCGTAGGT
49457204 GAAAAATCA
131 GAAAAATCA
* * ** * *
49457213 CAGCCTCCAACACAGTTAGCA-AGAGCAAAGCTATTAGCTGTCAT-ACTAAGGCTCACAGGTGAA
1 CAACCTCCAACACAGTTAG-AGAGAACAAAGCTACCAACTGCCATCA-TAAGGCTCACAGGTGAA
** * * * ** * *
49457276 AATTCGCAGCCTCCAGCACAGTTAGCGAGAGTTAAAAACTCTCAGGTGTAATATTAATGCTCGTA
64 AAACCGCAGCCTCCAACACAATTAGCGAGAGTTAAAAACTCCCAAATGT-ACATTAAGGCTCGTA
*
49457341 GGTTAAAAATCA
128 GGTGAAAAATCA
49457353 CAACCTCCAACACAGTTAGAGAGA
1 CAACCTCCAACACAGTTAGAGAGA
49457377 GTTAAAAACT
Statistics
Matches: 245, Mismatches: 47, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
136 1 0.00
137 106 0.43
138 1 0.00
139 68 0.28
140 69 0.28
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (139 bp):
CAACCTCCAACACAGTTAGAGAGAACAAAGCTACCAACTGCCATCATAAGGCTCACAGGTGAAAA
ACCGCAGCCTCCAACACAATTAGCGAGAGTTAAAAACTCCCAAATGTACATTAAGGCTCGTAGGT
GAAAAATCA
Found at i:49457409 original size:71 final size:71
Alignment explanation
Indices: 49456905--49457479 Score: 378
Period size: 71 Copynumber: 8.3 Consensus size: 71
49456895 AAGCTCTTTA
* * * *
49456905 CTGTCACACTAAGACTCGCAAGTGAAAAACTGCA-A-CCTCCAACACAGTTAGAGAGA---ACAA
1 CTGTCATACTAAGGCTCGTAGGTGAAAAA-T-CACAGCCTCCAACACAGTTAGAGAGAGTTA-AA
* * *
49456965 AGCTCTCAA
63 AACTCCCAG
* * * * * *
49456974 CTGTCATATTAAGGCTCGTAGGTGAAAAATCATAGCC-ACGACACAGCTA-ACAAGAGTTAAAAA
1 CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAGA-GAGAGTTAAAAA
* *
49457037 CACTCAG
65 CTCCCAG
* * * *
49457044 CTGTCATACTAAGGCTTGTAGGTGAAAAACCACAACCTCCAACACAGTTAGAGAGA---ACAAAG
1 CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAGAGAGAGTTA-AAAA
*
49457106 CTCCCAA
65 CTCCCAG
* * * ** ** * * * *
49457113 CTGCCAT-CATAGGGCTCGTAGGTGAAAAACCGTAGCCTTTAACATAATTAGCGAGAGTTACAAA
1 CTGTCATAC-TAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAGAGAGAGTTAAAAA
*
49457177 CTCCCAA
65 CTCCCAG
* * * *
49457184 ATGTC--A-TAAGGCTCGCAGGTGAAAAATCACAGCCTCCAACACAGTTAGCA-AGAG--CAAAG
1 CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAG-AGAGAGTTAAAAA
***
49457243 CTATTAG
65 CTCCCAG
** * * * *
49457250 CTGTCATACTAAGGCTCACAGGTGAAAATTCGCAGCCTCCAGCACAGTTAGCGAGAGTTAAAAAC
1 CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAGAGAGAGTTAAAAAC
*
49457315 TCTCAG
66 TCCCAG
* * * * * *
49457321 GTGTAATATTAATGCTCGTAGGTTAAAAATCACAACCTCCAACACAGTTAGAGAGAGTTAAAAAC
1 CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAGAGAGAGTTAAAAAC
49457386 TCCCAG
66 TCCCAG
* * * * * * *
49457392 CTATCATACTAAGGCTCGCAGGAGAAAAACCACAGCC-ACGACACAGTTAGCA-AGAATTAAAAA
1 CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAG-AGAGAGTTAAAAA
*
49457455 CTCCTAG
65 CTCCCAG
* * *
49457462 TTGTCGTATTAAGGCTCG
1 CTGTCATACTAAGGCTCG
49457480 CAAGTGCAAA
Statistics
Matches: 386, Mismatches: 98, Indels: 43
0.73 0.19 0.08
Matches are distributed among these distances:
66 9 0.02
67 3 0.01
68 54 0.14
69 118 0.31
70 81 0.21
71 119 0.31
72 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (71 bp):
CTGTCATACTAAGGCTCGTAGGTGAAAAATCACAGCCTCCAACACAGTTAGAGAGAGTTAAAAAC
TCCCAG
Found at i:49465243 original size:16 final size:15
Alignment explanation
Indices: 49465215--49465250 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
49465205 CACACACTCT
49465215 CTCTCCCCCCTCCCC
1 CTCTCCCCCCTCCCC
*
49465230 TTCTCCCTCCCTCCCC
1 CTCTCCC-CCCTCCCC
49465246 CTCTC
1 CTCTC
49465251 TCTCTCTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (15 bp):
CTCTCCCCCCTCCCC
Found at i:49471360 original size:11 final size:13
Alignment explanation
Indices: 49471323--49471364 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
49471313 GGCTCGACCC
*
49471323 ATATTATTT-TTT
1 ATATTATTTATAT
49471335 ATATTATTTATAT
1 ATATTATTTATAT
49471348 ATATT-TTTAATAT
1 ATATTATTT-ATAT
49471361 ATAT
1 ATAT
49471365 AATATATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTATTTATAT
Found at i:49471369 original size:22 final size:22
Alignment explanation
Indices: 49471323--49471371 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
49471313 GGCTCGACCC
* *
49471323 ATAT-TATTTTTTATATTATTT
1 ATATATATTTTTAATATTATTA
49471344 ATATATATTTTTAATA-TATATA
1 ATATATATTTTTAATATTAT-TA
49471366 ATATAT
1 ATATAT
49471372 CAAAAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATATATTTTTAATATTATTA
Found at i:49471521 original size:20 final size:18
Alignment explanation
Indices: 49471486--49471531 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 18
49471476 CTAAAATAGT
49471486 AACAAAATTAACAATAAC
1 AACAAAATTAACAATAAC
49471504 AACAAGAATTATACAATAAC
1 AACAA-AATTA-ACAATAAC
49471524 AACAAAAT
1 AACAAAAT
49471532 AGTAGCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.19
19 8 0.31
20 13 0.50
ACGTcount: A:0.65, C:0.15, G:0.02, T:0.17
Consensus pattern (18 bp):
AACAAAATTAACAATAAC
Found at i:49475396 original size:16 final size:16
Alignment explanation
Indices: 49475372--49475422 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
49475362 TAATAAAATA
*
49475372 ATTATAATTATTTTAT
1 ATTAAAATTATTTTAT
49475388 ATTAAAATT-TTTT-T
1 ATTAAAATTATTTTAT
* * *
49475402 ATGAACATAATTTTAT
1 ATTAAAATTATTTTAT
49475418 ATTAA
1 ATTAA
49475423 GATTTAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
16 13 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTAAAATTATTTTAT
Found at i:49475826 original size:11 final size:10
Alignment explanation
Indices: 49475807--49475836 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
49475797 ATATACTATC
49475807 ATATTAATTA
1 ATATTAATTA
49475817 ATATTTAATTA
1 ATA-TTAATTA
49475828 ATATTAATT
1 ATATTAATT
49475837 TTATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATATTAATTA
Found at i:49476030 original size:33 final size:33
Alignment explanation
Indices: 49475978--49476051 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
49475968 TCACACACGT
* * *
49475978 ATGTGTG-TGGAAATCACGTATCTATAACATAG
1 ATGTGTGTTGAAAATCACGTATCTATAACACAA
*
49476010 ATGTGTGTTGAAAATCACGTATTTATAACACAA
1 ATGTGTGTTGAAAATCACGTATCTATAACACAA
49476043 ATGTGTGTT
1 ATGTGTGTT
49476052 TAAATGTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 7 0.19
33 30 0.81
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (33 bp):
ATGTGTGTTGAAAATCACGTATCTATAACACAA
Found at i:49478203 original size:22 final size:23
Alignment explanation
Indices: 49478166--49478213 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
49478156 TTAAGGAAAT
49478166 TTTAGCGCACTTATCGTCTT-GCAC
1 TTTAGCG-ACTTATCGT-TTCGCAC
49478190 TTTAGCG-CTTATCGTTTCGCAC
1 TTTAGCGACTTATCGTTTCGCAC
49478212 TT
1 TT
49478214 CGGTGCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 14 0.61
24 7 0.30
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.42
Consensus pattern (23 bp):
TTTAGCGACTTATCGTTTCGCAC
Found at i:49478221 original size:22 final size:22
Alignment explanation
Indices: 49478196--49478285 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 22
49478186 GCACTTTAGC
49478196 GCTTATCGTTTCGCACTTCGGT
1 GCTTATCGTTTCGCACTTCGGT
* * *
49478218 GCTTATCGTTCCGTACTTCAGT
1 GCTTATCGTTTCGCACTTCGGT
* * *
49478240 GCCTATTGTTTTGCACTTCGGT
1 GCTTATCGTTTCGCACTTCGGT
49478262 GCTTAGT-GATTT-GCACTTCGGT
1 GCTTA-TCG-TTTCGCACTTCGGT
49478284 GC
1 GC
49478286 CTATTGTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 52 0.93
23 4 0.07
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.41
Consensus pattern (22 bp):
GCTTATCGTTTCGCACTTCGGT
Found at i:49478280 original size:44 final size:43
Alignment explanation
Indices: 49478175--49478293 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 43
49478165 TTTTAGCGCA
* * * *
49478175 CTTATCGTCTTGCACTTTAGCGCTTATCGTTTCGCACTTCGGTG
1 CTTATCGT-TTGCACTTCAGTGCCTATTGTTTCGCACTTCGGTG
* * *
49478219 CTTATCGTTCCGTACTTCAGTGCCTATTGTTTTGCACTTCGGTG
1 CTTATCGTT-TGCACTTCAGTGCCTATTGTTTCGCACTTCGGTG
*
49478263 CTTAGT-GATTTGCACTTCGGTGCCTATTGTT
1 CTTA-TCG-TTTGCACTTCAGTGCCTATTGTT
49478294 ATATTAGTGC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
43 1 0.02
44 58 0.94
45 3 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (43 bp):
CTTATCGTTTGCACTTCAGTGCCTATTGTTTCGCACTTCGGTG
Found at i:49479574 original size:23 final size:24
Alignment explanation
Indices: 49479496--49479583 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
49479486 ACACATGTTT
* * * *
49479496 TGTAAGTGCCCTTATGGCGTCTTC
1 TGTAAGTGCCTTTGTGGCATATTC
* *
49479520 TATAAGTGCCTTTGTGGCTTATTC
1 TGTAAGTGCCTTTGTGGCATATTC
* *
49479544 TGTTAGTGCCTTTGTTGCAT-TTC
1 TGTAAGTGCCTTTGTGGCATATTC
49479567 TGTAAGTGCCTTTGTGG
1 TGTAAGTGCCTTTGTGG
49479584 AGTATTAGAG
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.44
Consensus pattern (24 bp):
TGTAAGTGCCTTTGTGGCATATTC
Found at i:49503131 original size:20 final size:21
Alignment explanation
Indices: 49503094--49503139 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
49503084 CGAAATGCAA
49503094 TCAACCTAAAATGAATTAAAT
1 TCAACCTAAAATGAATTAAAT
* *
49503115 TCAAGCTAAATTG-ATTAAAT
1 TCAACCTAAAATGAATTAAAT
49503135 T-AACC
1 TCAACC
49503140 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 3 0.14
20 8 0.36
21 11 0.50
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
TCAACCTAAAATGAATTAAAT
Found at i:49506005 original size:25 final size:25
Alignment explanation
Indices: 49505963--49506016 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
49505953 TTTTCTCAAA
*
49505963 AATTTAATTAATATAAAATATTA-AT
1 AATTTAATAAATATAAAA-ATTAGAT
49505988 AATTTAATAAAT-TGAAAAATTAGAT
1 AATTTAATAAATAT-AAAAATTAGAT
49506013 AATT
1 AATT
49506017 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
AATTTAATAAATATAAAAATTAGAT
Found at i:49506732 original size:30 final size:30
Alignment explanation
Indices: 49506678--49506736 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
49506668 TTTTGAAAAC
* *
49506678 ATTTACAAAAAGAGGCATCTAATTTTTAAT
1 ATTTACAAAAAGAGGCACCAAATTTTTAAT
49506708 ATTTACAAAAAGA-GCAACCAAATTTTTAA
1 ATTTACAAAAAGAGGC-ACCAAATTTTTAA
49506737 AAAATAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (30 bp):
ATTTACAAAAAGAGGCACCAAATTTTTAAT
Found at i:49522217 original size:24 final size:24
Alignment explanation
Indices: 49522162--49522209 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
49522152 AAATGCAAGG
49522162 AAAGGTAAAAGTATTAAGGGTTCT
1 AAAGGTAAAAGTATTAAGGGTTCT
49522186 AAAGGTAAAAGTATTAAGGGTTCT
1 AAAGGTAAAAGTATTAAGGGTTCT
49522210 TTGGGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (24 bp):
AAAGGTAAAAGTATTAAGGGTTCT
Found at i:49524501 original size:20 final size:20
Alignment explanation
Indices: 49524476--49524544 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
49524466 CCAGAGCCAT
49524476 CGAAGTACATACAAAGGCAC
1 CGAAGTACATACAAAGGCAC
*
49524496 CGAAGTGCATACAAAGGCAC
1 CGAAGTACATACAAAGGCAC
* *
49524516 CAAAGTACAAACAAAGGCAC
1 CGAAGTACATACAAAGGCAC
49524536 CGAAGTACA
1 CGAAGTACA
49524545 ATCCTGTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.46, C:0.25, G:0.20, T:0.09
Consensus pattern (20 bp):
CGAAGTACATACAAAGGCAC
Found at i:49526059 original size:50 final size:50
Alignment explanation
Indices: 49525984--49526084 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
49525974 GGTCCATGGC
* * *
49525984 ACCATATTGTGTAAGACCATAGCTGGTGGGCTATAGCATCATATGGAAAG
1 ACCATATCGTATAAGACCATAGCTGGTAGGCTATAGCATCATATGGAAAG
* *
49526034 ACCATATCGTATAAGACCATAGCTGGTAGGTTATGGCATCATATGGAAAG
1 ACCATATCGTATAAGACCATAGCTGGTAGGCTATAGCATCATATGGAAAG
49526084 A
1 A
49526085 ACTAAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (50 bp):
ACCATATCGTATAAGACCATAGCTGGTAGGCTATAGCATCATATGGAAAG
Found at i:49526213 original size:27 final size:27
Alignment explanation
Indices: 49526164--49526224 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
49526154 CACGCCAAAA
49526164 AAAGGAAGCCTTTCTAGCAATCTAT-G
1 AAAGGAAGCCTTTCTAGCAATCTATGG
* * *
49526190 AAATGGAAGCCTTTGTGGCTATCTATGG
1 AAA-GGAAGCCTTTCTAGCAATCTATGG
49526218 AAAGGAA
1 AAAGGAA
49526225 CTATGAAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 23 0.77
28 4 0.13
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (27 bp):
AAAGGAAGCCTTTCTAGCAATCTATGG
Found at i:49526332 original size:27 final size:27
Alignment explanation
Indices: 49526314--49526380 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
49526304 TGGTAAACTA
49526314 TGAAGGAATAGTAGCTATGGCAAACAC
1 TGAAGGAATAGTAGCTATGGCAAACAC
49526341 TGAAGGAATAGTAGCTATGGCAAACAC
1 TGAAGGAATAGTAGCTATGGCAAACAC
49526368 TGAAGGAATAGTA
1 TGAAGGAATAGTA
49526381 TATGTTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (27 bp):
TGAAGGAATAGTAGCTATGGCAAACAC
Found at i:49526452 original size:27 final size:27
Alignment explanation
Indices: 49526299--49526453 Score: 123
Period size: 27 Copynumber: 5.7 Consensus size: 27
49526289 GAAGAATTAC
*
49526299 ATATATGGTAAACTATGAAGGAATAGT
1 ATATATGGTAAACTCTGAAGGAATAGT
** * *
49526326 AGCTATGGCAAACACTGAAGGAATAGT
1 ATATATGGTAAACTCTGAAGGAATAGT
** * *
49526353 AGCTATGGCAAACACTGAAGGAATAGT
1 ATATATGGTAAACTCTGAAGGAATAGT
* * ** * * *
49526380 ATATGTTGTGTACTCTAAATGAATAAT
1 ATATATGGTAAACTCTGAAGGAATAGT
*
49526407 ATATATGGTGAA-TACTGAAGGAATAGT
1 ATATATGGTAAACT-CTGAAGGAATAGT
* *
49526434 ATATATGGTGAACTTTGAAG
1 ATATATGGTAAACTCTGAAG
49526454 AAACGATTCT
Statistics
Matches: 103, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
26 1 0.01
27 101 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
ATATATGGTAAACTCTGAAGGAATAGT
Found at i:49527912 original size:26 final size:25
Alignment explanation
Indices: 49527878--49527958 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
49527868 AATATGTGAT
*
49527878 TTAATTTGGTCTTAGTTTAGAACAAA
1 TTAAATTGGTCTTAGTTTAG-ACAAA
*
49527904 TTAAATTGGTCTTA-TTTCAGACACA
1 TTAAATTGGTCTTAGTTT-AGACAAA
*
49527929 TT-AATTGTGTCTATTGTTTAGACAAA
1 TTAAATTG-GTCT-TAGTTTAGACAAA
49527955 TTAA
1 TTAA
49527959 TTGTGTCCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
24 5 0.11
25 13 0.28
26 24 0.52
27 4 0.09
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:49527959 original size:26 final size:26
Alignment explanation
Indices: 49527892--49527974 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
49527882 TTTGGTCTTA
49527892 GTTTAGAACAAATTAAATTG-GTCT-TAT
1 GTTTAG-ACAAATT-AATTGTGTCTAT-T
* *
49527919 -TTCAGACACATTAATTGTGTCTATT
1 GTTTAGACAAATTAATTGTGTCTATT
*
49527944 GTTTAGACAAATTAATTGTGTCCAGTT
1 GTTTAGACAAATTAATTGTGTCTA-TT
49527971 GTTT
1 GTTT
49527975 GTTTTAACCA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
24 5 0.11
25 11 0.23
26 25 0.53
27 6 0.13
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (26 bp):
GTTTAGACAAATTAATTGTGTCTATT
Found at i:49530858 original size:20 final size:20
Alignment explanation
Indices: 49530835--49530883 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
49530825 TAGCTCCTTT
49530835 AGCTCGTTTCAGCTCCAA-TC
1 AGCTCGTTTCAGCT-CAATTC
* *
49530855 AGCTCATTTGAGCTCAATTC
1 AGCTCGTTTCAGCTCAATTC
49530875 AGCTCGTTT
1 AGCTCGTTT
49530884 AAGCCTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (20 bp):
AGCTCGTTTCAGCTCAATTC
Found at i:49530893 original size:20 final size:20
Alignment explanation
Indices: 49530835--49530898 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
49530825 TAGCTCCTTT
* *
49530835 AGCTCGTTTCAGCTCCAA-TC
1 AGCTCGTTTAAGC-CTAATTC
* *
49530855 AGCTCATTTGAG-CTCAATTC
1 AGCTCGTTTAAGCCT-AATTC
*
49530875 AGCTCGTTTAAGCCTAATTT
1 AGCTCGTTTAAGCCTAATTC
49530895 AGCT
1 AGCT
49530899 TTCTTTCAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 30 0.86
21 2 0.06
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (20 bp):
AGCTCGTTTAAGCCTAATTC
Found at i:49546199 original size:25 final size:25
Alignment explanation
Indices: 49546149--49546199 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
49546139 AGATAAAATC
* *
49546149 AGAAACCATGCTTGCATTTTATCTA
1 AGAAACCATGCTTGCATTTGAGCTA
49546174 AGAAACCATGCTTGCATTTGAGCTA
1 AGAAACCATGCTTGCATTTGAGCTA
49546199 A
1 A
49546200 CTTATGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (25 bp):
AGAAACCATGCTTGCATTTGAGCTA
Found at i:49546634 original size:16 final size:14
Alignment explanation
Indices: 49546599--49546639 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
49546589 ACTAATAATA
*
49546599 TAAATATAAATACT
1 TAAAAATAAATACT
49546613 TAAAAATAAATACT
1 TAAAAATAAATACT
49546627 TAAGAAAATAAAT
1 T-A-AAAATAAAT
49546640 TTCCCCCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.58
15 1 0.04
16 9 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (14 bp):
TAAAAATAAATACT
Found at i:49547683 original size:36 final size:36
Alignment explanation
Indices: 49547636--49547708 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
49547626 TATTGGTTTG
49547636 ATGGTTAAACATTAGTAAATTTATCATTGAGGCCCT
1 ATGGTTAAACATTAGTAAATTTATCATTGAGGCCCT
49547672 ATGGTTAAACATTAGTAAATTTATCATTGAGGCCCT
1 ATGGTTAAACATTAGTAAATTTATCATTGAGGCCCT
49547708 A
1 A
49547709 ACTTCAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (36 bp):
ATGGTTAAACATTAGTAAATTTATCATTGAGGCCCT
Found at i:49553624 original size:21 final size:22
Alignment explanation
Indices: 49553599--49553642 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
49553589 ACATATTAAT
*
49553599 AATTA-ACATGAAAATAATATA
1 AATTATACATAAAAATAATATA
* *
49553620 AATTATGCATAAAAATCATATA
1 AATTATACATAAAAATAATATA
49553642 A
1 A
49553643 TACAACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
AATTATACATAAAAATAATATA
Found at i:49554062 original size:23 final size:24
Alignment explanation
Indices: 49554018--49554062 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
49554008 AATCATGTTA
* * *
49554018 TAAAACTTAATTAAATTTATAAGC
1 TAAAACATAATTAAAATAATAAGC
49554042 TAAAACATAA-TAAAATAATAA
1 TAAAACATAATTAAAATAATAA
49554063 TGTAACGCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (24 bp):
TAAAACATAATTAAAATAATAAGC
Found at i:49555804 original size:27 final size:27
Alignment explanation
Indices: 49555707--49555794 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
49555697 GAGGTCAATT
* *
49555707 AAATGATCGAAATACCCTCGTAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
* *
49555734 AAATGACCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCTCATAGGGTA
49555761 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
49555788 AAATGAC
1 AAATGAC
49555795 TATTATACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCATAGGGTA
Found at i:49555997 original size:26 final size:26
Alignment explanation
Indices: 49555968--49556022 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
49555958 TCTGCCACAT
* *
49555968 ATACTGTTACTGGCAGCTTTGTTGCG
1 ATACTATTACTAGCAGCTTTGTTGCG
*
49555994 ATACTATTACTAGTAGCTTTGTTGCG
1 ATACTATTACTAGCAGCTTTGTTGCG
49556020 ATA
1 ATA
49556023 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (26 bp):
ATACTATTACTAGCAGCTTTGTTGCG
Found at i:49557368 original size:27 final size:27
Alignment explanation
Indices: 49557348--49557575 Score: 280
Period size: 27 Copynumber: 8.4 Consensus size: 27
49557338 GGGGTGTAAT
49557348 AGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
49557375 -GATCATTTTACCCTATGGGGGTATTTC
1 AG-TCATTTTACCCTATGGGGGTATTTC
*
49557402 GGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* *
49557429 AGTCATTCTACCCTATAGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
49557456 GGTCATTTTACCTTATGAGGGTATTT-
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
49557482 TGATCATTTTACCCTATGAGGGTATTTT
1 AG-TCATTTTACCCTATGGGGGTATTTC
* * *
49557510 GGTCATTTTACACTATTGGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTC
* * *
49557537 GGTCATTTTACCCTATTGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTC
*
49557564 TGTCATTTTACC
1 AGTCATTTTACC
49557576 TATTTTACGG
Statistics
Matches: 179, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
26 2 0.01
27 175 0.98
28 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTC
Found at i:49557396 original size:54 final size:54
Alignment explanation
Indices: 49557349--49557575 Score: 321
Period size: 54 Copynumber: 4.2 Consensus size: 54
49557339 GGGTGTAATA
49557349 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCG
* *
49557403 GTCATTTTACCCTATGGGGGTATTTC-AGTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCGA-TCATTTTACCCTATGGGGGTATTTCG
* * * * *
49557457 GTCATTTTACCTTATGAGGGTATTTTGATCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCG
* * * * **
49557511 GTCATTTTACACTATTGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTTT
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCG
49557565 GTCATTTTACC
1 GTCATTTTACC
49557576 TATTTTACGG
Statistics
Matches: 152, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 150 0.99
55 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (54 bp):
GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCG
Found at i:49557462 original size:81 final size:81
Alignment explanation
Indices: 49557348--49557575 Score: 330
Period size: 81 Copynumber: 2.8 Consensus size: 81
49557338 GGGGTGTAAT
* * *
49557348 AGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTAC
1 AGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
*
49557413 CCTATGGGGGTATTTC
66 CCTATGAGGGTATTTC
* * * *
49557429 AGTCATTCTACCCTATAGGGGTATTTCGGTCATTTTACCTTATGAGGGTATTTTGATCATTTTAC
1 AGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
*
49557494 CCTATGAGGGTATTTT
66 CCTATGAGGGTATTTC
* * * * *
49557510 GGTCATTTTACACTATTGGGGTATTTCGGTCATTTTACCCTATTGGGGTATTTTTGTCATTTTAC
1 AGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
49557575 C
66 C
49557576 TATTTTACGG
Statistics
Matches: 129, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 129 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (81 bp):
AGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
CCTATGAGGGTATTTC
Found at i:49565514 original size:23 final size:23
Alignment explanation
Indices: 49565495--49565539 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
49565485 GCACACTAAT
49565495 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
49565518 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
49565540 TCAATAACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:49565792 original size:18 final size:17
Alignment explanation
Indices: 49565766--49565804 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
49565756 ATTTTCCTTC
49565766 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
49565783 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
49565801 CACA
1 CACA
49565805 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:49572889 original size:23 final size:23
Alignment explanation
Indices: 49572863--49572961 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
49572853 ATAAGTGCCA
*
49572863 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
49572886 CACTGATATATAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
49572909 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
49572932 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
49572955 CACTGAT
1 CACTGAT
49572962 CAATAACACA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:49573212 original size:18 final size:17
Alignment explanation
Indices: 49573186--49573224 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
49573176 ATTTTCCTTC
49573186 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
49573203 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
49573221 CACA
1 CACA
49573225 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:49592799 original size:15 final size:16
Alignment explanation
Indices: 49592779--49592809 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49592769 GATTTGGCGA
49592779 TATAAAT-TATAATTT
1 TATAAATATATAATTT
49592794 TATAAATATATAATTT
1 TATAAATATATAATTT
49592810 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAAATATATAATTT
Found at i:49592830 original size:22 final size:22
Alignment explanation
Indices: 49592778--49592823 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
49592768 AGATTTGGCG
*
49592778 ATATAAATTATAATTTTATAAAT
1 ATATAATTTA-AATTTTATAAAT
49592801 ATATAATTTAAATTTTA-AAAT
1 ATATAATTTAAATTTTATAAAT
49592822 AT
1 AT
49592824 GGTAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATAATTTAAATTTTATAAAT
Found at i:49599274 original size:41 final size:41
Alignment explanation
Indices: 49599229--49599308 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
49599219 TGCACACACA
*
49599229 TGCCCTCGTTTGTACTTCGGTACCCCTGAATTACACATATG
1 TGCCCCCGTTTGTACTTCGGTACCCCTGAATTACACATATG
* * *
49599270 TGCCCCCGTTTGTACTTCGTTACCCTTGAATTGCACATA
1 TGCCCCCGTTTGTACTTCGGTACCCCTGAATTACACATA
49599309 CATACCCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (41 bp):
TGCCCCCGTTTGTACTTCGGTACCCCTGAATTACACATATG
Found at i:49604562 original size:45 final size:45
Alignment explanation
Indices: 49604494--49604587 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
49604484 AACAGATACT
* * * *
49604494 CGGTGGATTTAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATACCAACCACCTTACTAATCAATGATGTC
* *
49604539 CGGTGGAATCAGCACATACCAACCACCTTACTAATCTATGATGTT
1 CGGTGGAATCAGCACATACCAACCACCTTACTAATCAATGATGTC
49604584 CGGT
1 CGGT
49604588 TCACATAGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (45 bp):
CGGTGGAATCAGCACATACCAACCACCTTACTAATCAATGATGTC
Found at i:49604652 original size:51 final size:51
Alignment explanation
Indices: 49604589--49604729 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 51
49604579 ATGTTCGGTT
* * * * *
49604589 CACATAGTAGCCTGCACATGGTACTACACATGTGACCATTACCATTCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACAATCCGATA
* * *
49604640 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACAATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACAATCCGATA
*
49604691 CACATAATAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
49604730 CACTTTCACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.03
51 73 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACAATCCGATA
Found at i:49608195 original size:9 final size:10
Alignment explanation
Indices: 49608168--49608193 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
49608158 TTATTTTAAC
49608168 AAAAAAATTT
1 AAAAAAATTT
49608178 AAAAAAATTT
1 AAAAAAATTT
49608188 AAAAAA
1 AAAAAA
49608194 TTCTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:49608635 original size:12 final size:12
Alignment explanation
Indices: 49608607--49608640 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
49608597 GTATTAGCAA
49608607 AAATAACAAAATT
1 AAATAA-AAAATT
*
49608620 AAATAAAAAGTT
1 AAATAAAAAATT
49608632 AAATAAAAA
1 AAATAAAAA
49608641 TATTTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (12 bp):
AAATAAAAAATT
Found at i:49608755 original size:19 final size:20
Alignment explanation
Indices: 49608733--49608780 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
49608723 AAAAATATTT
*
49608733 TTTTAAAAAAATTA-TAAAC
1 TTTTAAAAAAATTATTAAAA
*
49608752 TTTT-GAAAAATTATTAAAA
1 TTTTAAAAAAATTATTAAAA
49608771 TTTATAAAAA
1 TTT-TAAAAA
49608781 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 1 0.04
21 3 0.13
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TTTTAAAAAAATTATTAAAA
Found at i:49609980 original size:103 final size:103
Alignment explanation
Indices: 49609693--49610333 Score: 864
Period size: 103 Copynumber: 6.3 Consensus size: 103
49609683 AATTGTTGTT
* * * * * *
49609693 TTTTATGATTTTTTAGTAATGTAAATTAAAAAATAATTATTTTATAATTATTTTGTTAGTAGTTT
1 TTTTGTGATTTTTTAGTAATGTAATTTTAAAAA-AATAATTTTATAGTTATTTTGTTAGTAATTT
49609758 ATGATTAGG-T-TATAAATTGTTAGTG--T--TTT-GTG
65 ATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
* * * *
49609790 TTTTGTTATTTTTTAGTAATGTAATTTCTTTTAAAAAATGTTATATTTAT--TTATTTTCTTAGT
1 TTTTGTGATTTTTTAGTAATGTAA----TTTTAAAAAA-ATAAT-TTTATAGTTATTTTGTTAGT
*
49609853 AATTTATGGGATTAGG-T-TATAAATTGTTAGTGTTTAGTTTAGGG
60 AATTTAT--GATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
49609897 TTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTA
1 TTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTA
* *
49609962 TGATTGGGTTATATAAATTGTTAGTGTTTAGTTTAGAG
66 TGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
* *
49610000 TTTTGTGATTTTTTAGTAATGTAATTTAAAAAAAATAATTTTATAGTTATTTTTTTAGTAATTTA
1 TTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTA
** *
49610065 CAATTAGGTTATATAAATTGTTAGTGTTTATTTTAGTG
66 TGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
* *
49610103 TTTTATGATTTTTTAGTAATGTAAATTTTTAAAAGAATAATTTTATAGTTATTTTGTTAGTAATT
1 TTTTGTGATTTTTTAGTAATGT-AA-TTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTAATT
49610168 TATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
64 TATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
* *
49610208 TTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAA-AA-ATTATAGTTATTTTGTTAGTAGTTTA
1 TTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTA
*
49610271 TGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTT
66 TGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
49610309 TTTTGTGATTTTTT--TAATG-AATTTT
1 TTTTGTGATTTTTTAGTAATGTAATTTT
49610334 TTATATAATG
Statistics
Matches: 492, Mismatches: 33, Indels: 37
0.88 0.06 0.07
Matches are distributed among these distances:
97 22 0.04
98 6 0.01
99 5 0.01
100 19 0.04
101 97 0.20
102 34 0.07
103 182 0.37
104 5 0.01
105 94 0.19
106 3 0.01
107 25 0.05
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (103 bp):
TTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAATAATTTTATAGTTATTTTGTTAGTAATTTA
TGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTG
Found at i:49612719 original size:71 final size:73
Alignment explanation
Indices: 49612633--49612790 Score: 203
Period size: 75 Copynumber: 2.2 Consensus size: 73
49612623 GTAATTTAAA
* ** *
49612633 TAACTTTATATTTATGT-ATTTCTTTGT-CATTTTAATTATTAATTTTAGGGGTTTTTTGCAATT
1 TAACTTTGTATTTATGTAATGACTTTGTCCATTTTAATTATTAATTTTAGGGGTTTTATGCAATT
*
49612696 TAAATAGT
66 TAAATAAT
* * *
49612704 TAACTTTGTATTTATGTAATGACTTTTTCACCATTTTAGTTATTAATTTTAGGGGTTTTATGTAA
1 TAACTTTGTATTTATGTAATGACTTTGT--CCATTTTAATTATTAATTTTAGGGGTTTTATGCAA
49612769 TTTAAATAAT
64 TTTAAATAAT
*
49612779 AAACTTTGTATT
1 TAACTTTGTATT
49612791 ATTTACATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
71 16 0.22
72 7 0.09
75 51 0.69
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.54
Consensus pattern (73 bp):
TAACTTTGTATTTATGTAATGACTTTGTCCATTTTAATTATTAATTTTAGGGGTTTTATGCAATT
TAAATAAT
Found at i:49625428 original size:121 final size:121
Alignment explanation
Indices: 49625214--49625434 Score: 433
Period size: 121 Copynumber: 1.8 Consensus size: 121
49625204 CCATTGAACT
*
49625214 AAAACTTCTGTTATTGCTTGATTACCCCTTTGCCCAAGTGTAAATCAAGAATTTTAAGGGGTTCT
1 AAAACTTCTATTATTGCTTGATTACCCCTTTGCCCAAGTGTAAATCAAGAATTTTAAGGGGTTCT
49625279 TTTACCAATGTACTATAACACCCTTCACCTGTTCTTAATTACCCCTTCACCTGTTC
66 TTTACCAATGTACTATAACACCCTTCACCTGTTCTTAATTACCCCTTCACCTGTTC
49625335 AAAACTTCTATTATTGCTTGATTACCCCTTTGCCCAAGTGTAAATCAAGAATTTTAAGGGGTTCT
1 AAAACTTCTATTATTGCTTGATTACCCCTTTGCCCAAGTGTAAATCAAGAATTTTAAGGGGTTCT
49625400 TTTACCAATGTACTATAACACCCTTCACCTGTTCT
66 TTTACCAATGTACTATAACACCCTTCACCTGTTCT
49625435 GACAACTGAT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 99 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (121 bp):
AAAACTTCTATTATTGCTTGATTACCCCTTTGCCCAAGTGTAAATCAAGAATTTTAAGGGGTTCT
TTTACCAATGTACTATAACACCCTTCACCTGTTCTTAATTACCCCTTCACCTGTTC
Found at i:49628742 original size:43 final size:43
Alignment explanation
Indices: 49628695--49628797 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
49628685 TCTCAGACGT
* * * *
49628695 GGTCTTACATGT-AATCAAATAACGATGCCACTGTCCCAGATAG
1 GGTCTTACACGTAAATCAAAT-ACAATGCCAATGTCCCAGACAG
* * *
49628738 GGTCTTACACGTAAATCATATACAATGCCAATGTTCCAGACAT
1 GGTCTTACACGTAAATCAAATACAATGCCAATGTCCCAGACAG
*
49628781 GGTCTTACACATAAATC
1 GGTCTTACACGTAAATC
49628798 TCAAATTGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 44 0.86
44 7 0.14
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAAATACAATGCCAATGTCCCAGACAG
Found at i:49639174 original size:17 final size:17
Alignment explanation
Indices: 49639152--49639193 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
49639142 CTGTCACATG
*
49639152 AATTAAATTGATTATA-A
1 AATTAAATTAATT-TAGA
*
49639169 AATTAATTTAATTTAGA
1 AATTAAATTAATTTAGA
49639186 AATTAAAT
1 AATTAAAT
49639194 ATTGAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
AATTAAATTAATTTAGA
Found at i:49655587 original size:33 final size:33
Alignment explanation
Indices: 49655550--49655628 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
49655540 CAAATACTAT
49655550 CATTCAATCATACCTAAGCATGTATACTTACCG
1 CATTCAATCATACCTAAGCATGTATACTTACCG
49655583 CATTCAATCATACCTAAGCATGTATACTTACCG
1 CATTCAATCATACCTAAGCATGTATACTTACCG
49655616 CATTCAATCATAC
1 CATTCAATCATAC
49655629 TCATATAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (33 bp):
CATTCAATCATACCTAAGCATGTATACTTACCG
Found at i:49655936 original size:17 final size:16
Alignment explanation
Indices: 49655910--49655941 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
49655900 TCGTAGATCT
49655910 CTGACAAGCTTCCAAA
1 CTGACAAGCTTCCAAA
49655926 CTGATCAAGCTTCCAA
1 CTGA-CAAGCTTCCAA
49655942 TTATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.22
Consensus pattern (16 bp):
CTGACAAGCTTCCAAA
Found at i:49659978 original size:50 final size:49
Alignment explanation
Indices: 49659923--49660115 Score: 192
Period size: 50 Copynumber: 3.9 Consensus size: 49
49659913 CATTGAAGTT
* *
49659923 ATGAGAGGTTCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAC
* * * * * *
49659973 ATGAGAGGTCCCCTTTAAGACCATGTCTGGGATATGACATGGGCACTGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-GAC
** * *
49660023 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACG-AC
* * ** *
49660072 AAGAAACATCCCATGTAAGA-CATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
49660116 TGTTATTATC
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
48 22 0.18
49 18 0.15
50 79 0.66
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAC
Found at i:49661904 original size:20 final size:20
Alignment explanation
Indices: 49661830--49661906 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 20
49661820 ACTAATGTGT
*
49661830 CAGACAAGCTACCAGTATTG
1 CAGACAAGCTACCAGTAATG
* * **
49661850 CAGATAAACTGTCAGTAATG
1 CAGACAAGCTACCAGTAATG
** ** *
49661870 TGGATTAGCCACCAGTAATG
1 CAGACAAGCTACCAGTAATG
*
49661890 CAGACAAGCTGCCAGTA
1 CAGACAAGCTACCAGTA
49661907 CTTTCTCCTT
Statistics
Matches: 39, Mismatches: 18, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (20 bp):
CAGACAAGCTACCAGTAATG
Found at i:49684948 original size:21 final size:21
Alignment explanation
Indices: 49684922--49684961 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49684912 ACCATATAAG
49684922 TATTGTGTC-AATTAATTAAAA
1 TATTGT-TCGAATTAATTAAAA
*
49684943 TATTGTTCGGATTAATTAA
1 TATTGTTCGAATTAATTAA
49684962 TTAATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
TATTGTTCGAATTAATTAAAA
Found at i:49692478 original size:28 final size:30
Alignment explanation
Indices: 49692446--49692508 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
49692436 ATTGATAGGC
* *
49692446 ATGAGAGCTAAGAGAGTTGAGGGA-GA-GG
1 ATGAGAGATAAGAGAGATGAGGGATGAGGG
* *
49692474 ATGAGAGATGAGAGGGATGAGGGATGAGGG
1 ATGAGAGATAAGAGAGATGAGGGATGAGGG
49692504 ATGAG
1 ATGAG
49692509 GGATGATTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 20 0.69
29 2 0.07
30 7 0.24
ACGTcount: A:0.35, C:0.02, G:0.49, T:0.14
Consensus pattern (30 bp):
ATGAGAGATAAGAGAGATGAGGGATGAGGG
Found at i:49692494 original size:9 final size:8
Alignment explanation
Indices: 49692468--49692514 Score: 57
Period size: 7 Copynumber: 6.2 Consensus size: 8
49692458 AGAGTTGAGG
49692468 GAGAGGAT
1 GAGAGGAT
49692476 GAGA-GAT
1 GAGAGGAT
49692483 GAGAGGGAT
1 GAGA-GGAT
49692492 GAG-GGAT
1 GAGAGGAT
49692499 GAG-GGAT
1 GAGAGGAT
49692506 GAG-GGAT
1 GAGAGGAT
49692513 GA
1 GA
49692515 TTGAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 27 0.73
8 4 0.11
9 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.53, T:0.13
Consensus pattern (8 bp):
GAGAGGAT
Found at i:49692504 original size:14 final size:14
Alignment explanation
Indices: 49692463--49692514 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
49692453 CTAAGAGAGT
49692463 TGAGGGA-GA-GGA
1 TGAGGGATGAGGGA
*
49692475 TGAGAGATGAGAGGGA
1 TGAGGGAT--GAGGGA
49692491 TGAGGGATGAGGGA
1 TGAGGGATGAGGGA
49692505 TGAGGGATGA
1 TGAGGGATGA
49692515 TTGAAAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 6 0.18
14 16 0.47
15 2 0.06
16 10 0.29
ACGTcount: A:0.33, C:0.00, G:0.54, T:0.13
Consensus pattern (14 bp):
TGAGGGATGAGGGA
Found at i:49692506 original size:23 final size:21
Alignment explanation
Indices: 49692464--49692508 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
49692454 TAAGAGAGTT
49692464 GAGGGAGAGGATGAGAGATGA
1 GAGGGAGAGGATGAGAGATGA
*
49692485 GAGGGATGAGGGATGAGGGATGA
1 GAGGGA-GA-GGATGAGAGATGA
49692508 G
1 G
49692509 GGATGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.56, T:0.11
Consensus pattern (21 bp):
GAGGGAGAGGATGAGAGATGA
Found at i:49692509 original size:21 final size:20
Alignment explanation
Indices: 49692457--49692514 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
49692447 TGAGAGCTAA
*
49692457 GAGAGTTGAGGGA-GAGGAT
1 GAGAGATGAGGGATGAGGAT
49692476 GAGAGATGAGAGGGATGAGGGAT
1 GAGAGAT--GAGGGATGA-GGAT
*
49692499 GAGGGATGAGGGATGA
1 GAGAGATGAGGGATGA
49692515 TTGAAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 6 0.18
21 15 0.45
22 2 0.06
23 10 0.30
ACGTcount: A:0.33, C:0.00, G:0.53, T:0.14
Consensus pattern (20 bp):
GAGAGATGAGGGATGAGGAT
Found at i:49693950 original size:22 final size:22
Alignment explanation
Indices: 49693922--49694074 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
49693912 TGTTGATAGT
*
49693922 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
49693944 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
49693966 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
49693988 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
49694010 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
49694032 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
49694054 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
49694075 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:49695118 original size:20 final size:20
Alignment explanation
Indices: 49695093--49695130 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49695083 ACCCCTTTTA
49695093 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
49695113 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
49695131 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:49703309 original size:14 final size:14
Alignment explanation
Indices: 49703290--49703317 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49703280 CTAATTTATT
49703290 AATGAATTATTAAA
1 AATGAATTATTAAA
49703304 AATGAATTATTAAA
1 AATGAATTATTAAA
49703318 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:49703684 original size:20 final size:19
Alignment explanation
Indices: 49703661--49703721 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 19
49703651 ATTGCCTAAA
49703661 AAAATGAAAAAAATAAAACT
1 AAAATGAAAAAAATAAAA-T
49703681 AAAATGAAAAACAAT-AAAT
1 AAAATGAAAAA-AATAAAAT
49703700 AAACATGCAAGAAAAATAAAAT
1 AAA-ATG-AA-AAAAATAAAAT
49703722 GTACTTGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 8 0.22
22 7 0.19
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAATGAAAAAAATAAAAT
Found at i:49719378 original size:47 final size:47
Alignment explanation
Indices: 49719324--49719414 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
49719314 ATCAATAAAT
49719324 GATAATTTAAGGATCAAGTCAAGAGAACAAGGCATAATGTAGCAAAG
1 GATAATTTAAGGATCAAGTCAAGAGAACAAGGCATAATGTAGCAAAG
*
49719371 GATAATTTAAGGATCAAGTCAAGAGAACTAGGCATAATGTAGCA
1 GATAATTTAAGGATCAAGTCAAGAGAACAAGGCATAATGTAGCA
49719415 TAACAATTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (47 bp):
GATAATTTAAGGATCAAGTCAAGAGAACAAGGCATAATGTAGCAAAG
Found at i:49722228 original size:31 final size:29
Alignment explanation
Indices: 49722184--49722241 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
49722174 GTATATCTAC
*
49722184 AAGATAAACATTAA-ATTTAATTTAATATT
1 AAGATAAACATTAATA-TTAAATTAATATT
49722213 AAGATAATCACATTAATATTAAATTAATA
1 AAGATAA--ACATTAATATTAAATTAATA
49722242 AAAGACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
31 17 0.68
32 1 0.04
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (29 bp):
AAGATAAACATTAATATTAAATTAATATT
Found at i:49724215 original size:27 final size:27
Alignment explanation
Indices: 49724185--49724344 Score: 126
Period size: 27 Copynumber: 5.9 Consensus size: 27
49724175 TGTGTTGGAG
* * *
49724185 GACTACCCCGTGTTTAGTATCCTACCA
1 GACTACCCTGTGTTTAGTGTCCTAACA
* *
49724212 GACTACCTTGTGTTTAGTGTCCCAAC-
1 GACTACCCTGTGTTTAGTGTCCTAACA
* * **
49724238 GAGCTACCCCGTGTTTAGTGTCCCAATG
1 GA-CTACCCTGTGTTTAGTGTCCTAACA
* *
49724266 GGCTACCCTGTGTTTAGTGTCCCTACCA
1 GACTACCCTGTGTTTAGTGT-CCTAACA
*** * *
49724294 -ACTATTATGTGTTTAGTCTCCTAGCA
1 GACTACCCTGTGTTTAGTGTCCTAACA
* *
49724320 CACTACCCTGTGTTTAGTGCCCTAA
1 GACTACCCTGTGTTTAGTGTCCTAA
49724345 TGGACTCCAT
Statistics
Matches: 103, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
26 8 0.08
27 91 0.88
28 4 0.04
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (27 bp):
GACTACCCTGTGTTTAGTGTCCTAACA
Found at i:49724245 original size:54 final size:54
Alignment explanation
Indices: 49724186--49724338 Score: 153
Period size: 54 Copynumber: 2.8 Consensus size: 54
49724176 GTGTTGGAGG
* * *
49724186 ACTACCCCGTGTTTAGTATCCTACCAGACTACCTTGTGTTTAGTGTCCCAACGA
1 ACTACCCCGTGTTTAGTATCCTAACAGACTACCCTGTGTTTAGTGTCCCAACCA
* * * ** * *
49724240 GCTACCCCGTGTTTAGTGTCCCAATGGGCTACCCTGTGTTTAGTGTCCCTACCA
1 ACTACCCCGTGTTTAGTATCCTAACAGACTACCCTGTGTTTAGTGTCCCAACCA
**** * * *
49724294 ACTATTATGTGTTTAGTCTCCTAGCACACTACCCTGTGTTTAGTG
1 ACTACCCCGTGTTTAGTATCCTAACAGACTACCCTGTGTTTAGTG
49724339 CCCTAATGGA
Statistics
Matches: 77, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (54 bp):
ACTACCCCGTGTTTAGTATCCTAACAGACTACCCTGTGTTTAGTGTCCCAACCA
Found at i:49731428 original size:128 final size:128
Alignment explanation
Indices: 49731190--49731949 Score: 1153
Period size: 128 Copynumber: 5.9 Consensus size: 128
49731180 ATAGATTTGT
* * * * * *
49731190 GGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTCGTCGTGTTCGATATGCTCCACTACTGC
1 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
* *
49731255 TTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGGGAGATAGGACTAGC
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTAGC
* * * *
49731318 GGCTTAAATCTACTTCCCTACTCTTGAAAATAAGATTCGCCATATTCGATCTGCTCCGCTACTGC
1 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
* * * * *
49731383 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCTACTGTTGACCAGAGAGATAGGACTTGT
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTAGC
* *
49731446 GGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCACCATCTTCGATCTGCTCCGCTACTGC
1 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
* *
49731511 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGT
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTAGC
* *
49731574 GGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
1 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
* * *
49731639 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGTTGACCCGAGAGATAGGACTAGC
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTAGC
* * *
49731702 GGCTTAAATCTGCTTCCCTACCCCTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTAC
1 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
* *
49731767 TTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGGACTAGC
66 TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTAGC
* * *
49731830 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATT-GCTCGTTTTCGATTTGCTCCGCTACTG
1 GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGC-CATCTTCGATCTGCTCCGCTACTG
* * * **
49731894 CTTAGCGAGATAAGATCTGTAATTTCCAATCTATTCCACTGCCAACCAGGGAGATA
65 CTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATA
49731950 AAATTACTGG
Statistics
Matches: 586, Mismatches: 45, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
127 2 0.00
128 584 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (128 bp):
GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGC
TTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTAGC
Found at i:49731895 original size:384 final size:383
Alignment explanation
Indices: 49731177--49732061 Score: 1182
Period size: 384 Copynumber: 2.3 Consensus size: 383
49731167 TAACGTCGAA
* * * *
49731177 GAGATAGATTTGTGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTCGTCGTGTTCGATAT
1 GAGATAGACTTGTGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATAT
* *
49731242 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGGGAG
66 GCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGAGAG
* *
49731307 ATAGGACTAGCGGCTTAAATCTACTTCCCTACTCTTGAAAATAAGATTCGCCATATTCGATCTGC
131 ATAGGACTAGCGGCTTAAATCTACTTCCCTACCCCTGAAAATAAGATTCGCCATATTCGATCTGC
* * * *
49731372 TCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCTACTGTTGACCAGAGAGAT
196 TCCGCTACTACTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGAGAGAT
* * *
49731437 AGGACTTGTGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCACCATCTTCGATCTGCTC
261 AGGACTAGCGGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCACCATCTTCGATCTGCTC
* **
49731502 CGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGG
326 CGCTACTGCTTAGCGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCCAACCAGG
* * * *
49731560 GAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCATCTTCGATC
1 GAGATA-GACTTGTGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATA
* ** *
49731625 TGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGTTGACCCGAGA
65 TGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGAGA
* * * *
49731690 GATAGGACTAGCGGCTTAAATCTGCTTCCCTACCCCTGAAGATAAGATTCGCCGTCTTCGATCTG
130 GATAGGACTAGCGGCTTAAATCTACTTCCCTACCCCTGAAAATAAGATTCGCCATATTCGATCTG
* *
49731755 CTCCGCTACTACTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGA
195 CTCCGCTACTACTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGAGAGA
* * * *
49731820 TAGGACTAGCGGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTGC-TCGTTTTCGATTTGC
260 TAGGACTAGCGGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATT-CACCATCTTCGATCTGC
* *
49731884 TCCGCTACTGCTTAGCGAGATAAGATCTGTAATTTCCAATCTATTCCACTGCCAACCAGG
324 TCCGCTACTGCTTAGCGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCCAACCAGG
* * * * * * ** * * * *
49731944 GAGATAAAATTACTGGCTTTAATGTAC-TCCATTGTAACCATAGGGAGGTAAAATCCGCCATCTT
1 GAGATAGACTT-GTGGCTTAAATCTACTTCCCTACT--CC-T--GAAGATAAGATTCGCCATCTT
* * * *
49732008 CGATGTGCTCCACTACAGCTTAGGGAGATAAGATCTGTAATCTT-CAATCTATTC
60 CGATATGCTCCACTACTGCTTAGGGAGACAAGATCTGTAAT-TTCCAACCTATTC
49732062 AGCTGTCAAC
Statistics
Matches: 436, Mismatches: 57, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
383 14 0.03
384 354 0.81
385 2 0.00
386 1 0.00
388 63 0.14
389 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (383 bp):
GAGATAGACTTGTGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTCGCCATCTTCGATAT
GCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGAGAG
ATAGGACTAGCGGCTTAAATCTACTTCCCTACCCCTGAAAATAAGATTCGCCATATTCGATCTGC
TCCGCTACTACTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGAGAGAT
AGGACTAGCGGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTCACCATCTTCGATCTGCTC
CGCTACTGCTTAGCGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCCAACCAGG
Found at i:49731962 original size:128 final size:127
Alignment explanation
Indices: 49731189--49732226 Score: 1067
Period size: 128 Copynumber: 8.0 Consensus size: 127
49731179 GATAGATTTG
* * * * *
49731189 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTCGTCGTGTTCGATATGCTCCACTACTG
1 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATT-GCCATCTTCGATCTGCTCCGCTACTG
* * * *
49731254 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTACTGACCAGGGAGATAGGACTAGC
65 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGAATTA-C
* * *
49731318 -GGCTTAAATCTACTTCCCTACTCTTGAAAATAAGATTCGCCATATTCGATCTGCTCCGCTACTG
1 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATT-GCCATCTTCGATCTGCTCCGCTACTG
* * * * * * *
49731382 CTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCTACTGTTGACCAGAGAGATAGGACTT-G
65 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATA-GAATTAC
* * *
49731445 TGGCTTAAATCTGCTTCCCTACTCTTGAAGATAAGATTCACCATCTTCGATCTGCTCCGCTACTG
1 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATT-GCCATCTTCGATCTGCTCCGCTACTG
* * * *
49731510 CTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT-G
65 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATA-GAATTAC
* * *
49731573 TGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTG
1 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATT-GCCATCTTCGATCTGCTCCGCTACTG
* * * * * * *
49731638 CTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGTTGACCCGAGAGATAGGACTAGC
65 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGAATTA-C
* * * *
49731702 -GGCTTAAATCTGCTTCCCTACCCCTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTA
1 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATT-GCCATCTTCGATCTGCTCCGCTACTG
* *
49731766 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGGACTAGC
65 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGAATTA-C
* * * *
49731830 -GGCTTAAATCTGCTTCCCTACTCCTGAAGATAAGATTGCTCGTTTTCGATTTGCTCCGCTACTG
1 TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTGC-CATCTTCGATCTGCTCCGCTACTG
* * * *
49731894 CTTAGCGAGATAAGATCTGTAATTTCCAATCTATTCCACTGCCAACCAGGGAGATAAAATTAC
65 CTTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGAATTAC
* * * ** * * * * * *
49731957 TGGCTTTAATGTAC-TCCATTGTAACCATAGGGAGGTAAAATCCGCCATCTTCGATGTGCTCCAC
1 TGGCTTAAATCTACTTCCCTACT--CC-T--GAAGATAAGAT-TGCCATCTTCGATCTGCTCCGC
* *
49732021 TACAGCTTAGGGAGATAAGATCTGTAATCTT-CAATCTATT-CAGCTG-TCAACCAGGGAGATAG
60 TACTGCTTAGGGAGATAAGATCTGTAAT-TTCCAACCTATTCCA-CTGCT-AACCAGGGAGATAG
49732083 AATTAC
122 AATTAC
* * * * * *
49732089 TAGCTTCAA-CGTAC-TCCACTGTAAC-CATAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCC
1 TGGCTTAAATC-TACTTCC-C--T-ACTCCT--GAAGATAAGAT-TGCCATCTTCGATCTGCTCC
* * * *
49732151 ACTACTGCTTAGGGAGATAAGATCTGTAATCTT-CAATCTATTCCACTGCCAACCAAGGAGATAG
58 GCTACTGCTTAGGGAGATAAGATCTGTAAT-TTCCAACCTATTCCACTGCTAACCAGGGAGATAG
49732215 AATTAC
122 AATTAC
49732221 TGGCTT
1 TGGCTT
49732227 TAATGTAATC
Statistics
Matches: 804, Mismatches: 83, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
127 10 0.01
128 585 0.73
129 4 0.00
130 1 0.00
131 2 0.00
132 194 0.24
133 7 0.01
135 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (127 bp):
TGGCTTAAATCTACTTCCCTACTCCTGAAGATAAGATTGCCATCTTCGATCTGCTCCGCTACTGC
TTAGGGAGATAAGATCTGTAATTTCCAACCTATTCCACTGCTAACCAGGGAGATAGAATTAC
Found at i:49733637 original size:13 final size:14
Alignment explanation
Indices: 49733600--49733646 Score: 69
Period size: 13 Copynumber: 3.4 Consensus size: 14
49733590 GGCCTCTCCA
*
49733600 TTTCCTTTTTCATTT
1 TTTCATTTTTCA-TT
49733615 TTTCATTTTTCATT
1 TTTCATTTTTCATT
49733629 TTTCA-TTTTCATT
1 TTTCATTTTTCATT
49733642 TTTCA
1 TTTCA
49733647 CATTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 13 0.42
14 7 0.23
15 11 0.35
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCATTTTTCATT
Found at i:49733650 original size:15 final size:15
Alignment explanation
Indices: 49733606--49733652 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
49733596 TCCATTTCCT
*
49733606 TTTTCATTTTTTCA-T
1 TTTTCA-TTTTTCACA
49733621 TTTTCATTTTT--CA
1 TTTTCATTTTTCACA
49733634 TTTTCATTTTTCACA
1 TTTTCATTTTTCACA
49733649 TTTT
1 TTTT
49733653 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 5 0.18
15 12 0.43
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTTTCACA
Found at i:49733653 original size:22 final size:21
Alignment explanation
Indices: 49733600--49733646 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
49733590 GGCCTCTCCA
*
49733600 TTTCCTTTTTCATTTTTTCATT
1 TTTCATTTTTCA-TTTTTCATT
49733622 TTTCATTTTTCA-TTTTCATT
1 TTTCATTTTTCATTTTTCATT
49733642 TTTCA
1 TTTCA
49733647 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCATTTTTCATTTTTCATT
Found at i:49733663 original size:7 final size:7
Alignment explanation
Indices: 49733600--49733646 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
49733590 GGCCTCTCCA
*
49733600 TTTCCTT
1 TTTCATT
49733607 TTTCATTT
1 TTTCA-TT
49733615 TTTCATT
1 TTTCATT
49733622 TTTCATT
1 TTTCATT
49733629 TTTCA-T
1 TTTCATT
49733635 TTTCATT
1 TTTCATT
49733642 TTTCA
1 TTTCA
49733647 CATTTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 6 0.16
7 24 0.65
8 7 0.19
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTCATT
Done.