Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 28 of 135
Found at i:11091215 original size:21 final size:21
Alignment explanation
Indices: 11091181--11091236 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
11091171 AAATTTTGAT
11091181 TAAATTAATAAAATAAAAAATTA
1 TAAATT-AT-AAATAAAAAATTA
* *
11091204 TAAATTATAAATTATAAATTA
1 TAAATTATAAATAAAAAATTA
11091225 TAAATTATAAAT
1 TAAATTATAAAT
11091237 TTAAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 23 0.74
22 2 0.06
23 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTATAAATAAAAAATTA
Found at i:11091556 original size:14 final size:14
Alignment explanation
Indices: 11091539--11091566 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11091529 CTCACATTTC
11091539 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
11091553 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
11091567 GATTTCTGCT
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:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:11091557 original size:19 final size:18
Alignment explanation
Indices: 11091519--11091563 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
11091509 TACGGTACGC
11091519 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
11091536 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
11091555 TTCTTTTCT
1 TTCTTTTCT
11091564 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:11094203 original size:17 final size:18
Alignment explanation
Indices: 11094178--11094219 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
11094168 TATAAGAATA
*
11094178 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
11094195 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
11094213 ATTAAAT
1 ATTAAAT
11094220 GATATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:11094763 original size:19 final size:20
Alignment explanation
Indices: 11094736--11094781 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
11094726 TATTTTTAAA
* *
11094736 ATTTTAAAAATTAAAAAA-C
1 ATTTAAAAAAATAAAAAATC
11094755 ATTTAAAAAAATAAAAAATC
1 ATTTAAAAAAATAAAAAATC
11094775 A-TTAAAA
1 ATTTAAAA
11094782 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
ATTTAAAAAAATAAAAAATC
Found at i:11095773 original size:74 final size:74
Alignment explanation
Indices: 11095667--11095889 Score: 446
Period size: 74 Copynumber: 3.0 Consensus size: 74
11095657 TAAAAATAGG
11095667 AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
1 AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
11095732 GTATATTCT
66 GTATATTCT
11095741 AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
1 AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
11095806 GTATATTCT
66 GTATATTCT
11095815 AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
1 AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
11095880 GTATATTCT
66 GTATATTCT
11095889 A
1 A
11095890 AGTTTCGATT
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 149 1.00
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.24
Consensus pattern (74 bp):
AGTAAATTCTTTACAGGAAAAGAAGAAGAAAAAAATCCTCCACGTCATTAACAAAATCCAACGTG
GTATATTCT
Found at i:11097348 original size:14 final size:14
Alignment explanation
Indices: 11097306--11097335 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11097296 AGGTTGATTA
11097306 TTTTCTTCATATTC
1 TTTTCTTCATATTC
11097320 TTTTCTTCATATTC
1 TTTTCTTCATATTC
11097334 TT
1 TT
11097336 CATATTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTCTTCATATTC
Found at i:11102432 original size:324 final size:324
Alignment explanation
Indices: 11101843--11102490 Score: 1296
Period size: 324 Copynumber: 2.0 Consensus size: 324
11101833 ATATAAATAA
11101843 ATTAGTAACTTTGACTCAGATAGACAACTTGAATTTACATATAGGAAAATAATGATAGTATGGAA
1 ATTAGTAACTTTGACTCAGATAGACAACTTGAATTTACATATAGGAAAATAATGATAGTATGGAA
11101908 AATGTTGTTTAAATGTGTTATACACATTAAGGATATGAAATGGAGAGGAGGAGGTGGAAAATTGG
66 AATGTTGTTTAAATGTGTTATACACATTAAGGATATGAAATGGAGAGGAGGAGGTGGAAAATTGG
11101973 GAAAATATATGAATGATTTGTGTATAATTGGTCATATGCTTGATTATAATTGATAAACGATGAAA
131 GAAAATATATGAATGATTTGTGTATAATTGGTCATATGCTTGATTATAATTGATAAACGATGAAA
11102038 TAGAAATGATGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATGTGTGAAAATAAAGTT
196 TAGAAATGATGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATGTGTGAAAATAAAGTT
11102103 TCATAATATGTATGTATGGTATATTCGGTATATGATTTGACATGAAGTAATGTCATGAATGGTT
261 TCATAATATGTATGTATGGTATATTCGGTATATGATTTGACATGAAGTAATGTCATGAATGGTT
11102167 ATTAGTAACTTTGACTCAGATAGACAACTTGAATTTACATATAGGAAAATAATGATAGTATGGAA
1 ATTAGTAACTTTGACTCAGATAGACAACTTGAATTTACATATAGGAAAATAATGATAGTATGGAA
11102232 AATGTTGTTTAAATGTGTTATACACATTAAGGATATGAAATGGAGAGGAGGAGGTGGAAAATTGG
66 AATGTTGTTTAAATGTGTTATACACATTAAGGATATGAAATGGAGAGGAGGAGGTGGAAAATTGG
11102297 GAAAATATATGAATGATTTGTGTATAATTGGTCATATGCTTGATTATAATTGATAAACGATGAAA
131 GAAAATATATGAATGATTTGTGTATAATTGGTCATATGCTTGATTATAATTGATAAACGATGAAA
11102362 TAGAAATGATGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATGTGTGAAAATAAAGTT
196 TAGAAATGATGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATGTGTGAAAATAAAGTT
11102427 TCATAATATGTATGTATGGTATATTCGGTATATGATTTGACATGAAGTAATGTCATGAATGGTT
261 TCATAATATGTATGTATGGTATATTCGGTATATGATTTGACATGAAGTAATGTCATGAATGGTT
11102491 CATGAATTAA
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
324 324 1.00
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.35
Consensus pattern (324 bp):
ATTAGTAACTTTGACTCAGATAGACAACTTGAATTTACATATAGGAAAATAATGATAGTATGGAA
AATGTTGTTTAAATGTGTTATACACATTAAGGATATGAAATGGAGAGGAGGAGGTGGAAAATTGG
GAAAATATATGAATGATTTGTGTATAATTGGTCATATGCTTGATTATAATTGATAAACGATGAAA
TAGAAATGATGCTTATATTTGTGCATTATTGGTCATGGTTTAAGCTCATGTGTGAAAATAAAGTT
TCATAATATGTATGTATGGTATATTCGGTATATGATTTGACATGAAGTAATGTCATGAATGGTT
Found at i:11103061 original size:36 final size:37
Alignment explanation
Indices: 11103014--11103094 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
11103004 ATCAGTGACA
*
11103014 AGTGATAAGTGGTAG-TTTAGCTACATTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
*
11103050 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
11103087 AGTGATAA
1 AGTGATAA
11103095 CTGACAAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:11103158 original size:87 final size:88
Alignment explanation
Indices: 11103009--11103229 Score: 338
Period size: 87 Copynumber: 2.5 Consensus size: 88
11102999 TTCTAATCAG
*
11103009 TGACAAGTGATAAGTGGTAG-TTTAGCTACATTTATCTGATCAGTGATAAGTGGTAGCTTTAGCT
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGCTTTAGCT
*
11103073 GCACTTATCTGATCAGTGATAAC
66 GCACTTATCTGATCAGTGACAAC
* * * *
11103096 TGACAAGTGATAAGTGGTAGCTTTAGTTGCACTTATTTGATCAGTGATAAGTGGTGGC-TTAGCT
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGCTTTAGCT
* *
11103160 GCACTTATCTGATCGGTGACAAG
66 GCACTTATCTGATCAGTGACAAC
* *
11103183 TGACAAGTGATAAGTGGTAGCTTTACCTACACTTATCTAATCAGTGA
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGA
11103230 CAACTGATAA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
87 88 0.73
88 32 0.27
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (88 bp):
TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGCTTTAGCT
GCACTTATCTGATCAGTGACAAC
Found at i:11103173 original size:36 final size:37
Alignment explanation
Indices: 11103101--11103184 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 37
11103091 ATAACTGACA
* *
11103101 AGTGATAAGTGGTAGCTTTAGTTGCACTTATTTGATC
1 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
*
11103138 AGTGATAAGTGGTGGC-TTAGCTGCACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
* *
11103174 GGTGACAAGTG
1 AGTGATAAGTG
11103185 ACAAGTGATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 27 0.64
37 15 0.36
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.35
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
Found at i:11107895 original size:15 final size:15
Alignment explanation
Indices: 11107870--11107907 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
11107860 AGACCATGGA
*
11107870 AGAAGAGGTGGA-GT
1 AGAAGAAGTGGAGGT
11107884 ATGAAGAAGTGGAGGT
1 A-GAAGAAGTGGAGGT
11107900 AGAAGAAG
1 AGAAGAAG
11107908 AAGGAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.81
16 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (15 bp):
AGAAGAAGTGGAGGT
Found at i:11107906 original size:3 final size:3
Alignment explanation
Indices: 11107900--11107947 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
11107890 AAGTGGAGGT
* * *
11107900 AGA AGA AGA AGG AGA GGA AGA A-A TAGA AGA AGA AGA GGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA
11107945 AGA
1 AGA
11107948 CCTGGATGTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.95
4 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:11107916 original size:18 final size:18
Alignment explanation
Indices: 11107886--11107947 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
11107876 GGTGGAGTAT
*
11107886 GAAGAAGTG-GAGGTAGAA
1 GAAGAAG-GAGAGGAAGAA
11107904 GAAGAAGGAGAGGAAGAAATA
1 GAAGAAGGAGAGGAAG--A-A
*
11107925 GAAGAAGAAGAGGAAGAA
1 GAAGAAGGAGAGGAAGAA
11107943 GAAGA
1 GAAGA
11107948 CCTGGATGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 1 0.03
18 19 0.50
19 1 0.03
20 1 0.03
21 16 0.42
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (18 bp):
GAAGAAGGAGAGGAAGAA
Found at i:11107927 original size:21 final size:21
Alignment explanation
Indices: 11107903--11107942 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11107893 TGGAGGTAGA
*
11107903 AGAAGAAGGAGAGGAAGAAAT
1 AGAAGAAGAAGAGGAAGAAAT
11107924 AGAAGAAGAAGAGGAAGAA
1 AGAAGAAGAAGAGGAAGAA
11107943 GAAGACCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.03
Consensus pattern (21 bp):
AGAAGAAGAAGAGGAAGAAAT
Found at i:11112327 original size:21 final size:21
Alignment explanation
Indices: 11112301--11112349 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
11112291 TTCTTCATTA
*
11112301 TCTTCTTCTTCGTCTTGCTCT
1 TCTTCTTCTTCGACTTGCTCT
* * *
11112322 TGTTCTCCTTCGACTTGTTCT
1 TCTTCTTCTTCGACTTGCTCT
11112343 TCTTCTT
1 TCTTCTT
11112350 TATGATTATC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.31, G:0.10, T:0.57
Consensus pattern (21 bp):
TCTTCTTCTTCGACTTGCTCT
Found at i:11118643 original size:146 final size:147
Alignment explanation
Indices: 11118377--11118670 Score: 556
Period size: 146 Copynumber: 2.0 Consensus size: 147
11118367 TACGTTAACG
11118377 CAATGATGGAAATATAATTACGAATAATAATTTTACATATGAAAATATATATCTTTTTAGTCGTA
1 CAATGATGG-AATATAATTACGAATAATAATTTTACATATGAAAATATATATCTTTTTAGTCGTA
11118442 TTAGTTGAAAGAAAATACTTATATGATAATTTTTTACCTCGTATTTAATAGTATAATTATATAAT
65 TTAGTTGAAAGAAAATACTTATATGATAATTTTTTACCTCGTATTTAATAGTATAATTATATAAT
11118507 TATATCATTTTAAATTTT
130 TATATCATTTTAAATTTT
11118525 CAATGATGG-ATATAATTACGAATAATAATTTTACATATGAAAATATATATCTTTTTAGTCGTAT
1 CAATGATGGAATATAATTACGAATAATAATTTTACATATGAAAATATATATCTTTTTAGTCGTAT
11118589 TAGTTGAAAGAAAATACTTATATGAT-ATTATTTTACCTCGTATTTAATAGTATAATTATATAAT
66 TAGTTGAAAGAAAATACTTATATGATAATT-TTTTACCTCGTATTTAATAGTATAATTATATAAT
11118653 TATATCATTTTAAATTTT
130 TATATCATTTTAAATTTT
11118671 AAAATATTAA
Statistics
Matches: 145, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
145 3 0.02
146 133 0.92
148 9 0.06
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (147 bp):
CAATGATGGAATATAATTACGAATAATAATTTTACATATGAAAATATATATCTTTTTAGTCGTAT
TAGTTGAAAGAAAATACTTATATGATAATTTTTTACCTCGTATTTAATAGTATAATTATATAATT
ATATCATTTTAAATTTT
Found at i:11133029 original size:28 final size:28
Alignment explanation
Indices: 11132976--11133029 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
11132966 CTTTTTATTT
*
11132976 TTCCCTCAAAACTTTTACTCCTTCCCAC
1 TTCCCTCAAAACTTTTACTCCCTCCCAC
11133004 TTCCC-CAAAACTTTTACTCTCCTCCC
1 TTCCCTCAAAACTTTTACTC-CCTCCC
11133030 CTCCCAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.35
Consensus pattern (28 bp):
TTCCCTCAAAACTTTTACTCCCTCCCAC
Found at i:11141947 original size:63 final size:63
Alignment explanation
Indices: 11141838--11141964 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 63
11141828 AAGTATGGTG
* * * *
11141838 CTTTAGTGCCATATGGTATATCTATCTGGACCATTATAAACATGCCATGCTTGGCACAATAGA
1 CTTTAGTGCCATATGGTATAGCTATCTGCACCATTATAAACATGCCATACTTGGCACAAAAGA
* * * * *
11141901 CTTTGGTGCCATATGGTATAGCTATCTTCACCATTATAACCCTGCCATATTTGGCACAAAAGA
1 CTTTAGTGCCATATGGTATAGCTATCTGCACCATTATAAACATGCCATACTTGGCACAAAAGA
11141964 C
1 C
11141965 AGATTCACAG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (63 bp):
CTTTAGTGCCATATGGTATAGCTATCTGCACCATTATAAACATGCCATACTTGGCACAAAAGA
Found at i:11144556 original size:24 final size:22
Alignment explanation
Indices: 11144522--11144568 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
11144512 ATCAACTCAT
11144522 ATTATTATTATTTTTTAAAATATA
1 ATTATTATTA-TTTTT-AAATATA
*
11144546 ATTATTTTTATTTTTAAATATA
1 ATTATTATTATTTTTAAATATA
11144568 A
1 A
11144569 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATTATTATTTTTAAATATA
Found at i:11150743 original size:140 final size:140
Alignment explanation
Indices: 11150498--11150754 Score: 349
Period size: 140 Copynumber: 1.8 Consensus size: 140
11150488 TTCAAAGGTT
* * *
11150498 AAAGTACCTAACAGATTATCCTATAAAACACAAATGAAAGAAGGAACCAACTCTTCTAATTCGAG
1 AAAGCACCCAACAGATTATCCTATAAAACACAAATGAAAGAAGGAACCAACTCTCCTAATTCGAG
* *
11150563 TCCAGTAAATCAATCATCAATAGCAAAATTAAAATGACCTCAACTCTGAATCAACAACTGATTAT
66 TCCAGTAAATCAATAATCAATAGCAAAATTAAAATCACCTCAACTCTGAATCAACAACTGATTAT
11150628 TTCACCGATG
131 TTCACCGATG
* * **
11150638 AAAGCACCCAACAGATTATCCTATAAAATACAAAT-AACGAAAGGGTCCAAACTCTCCTAATTCG
1 AAAGCACCCAACAGATTATCCTATAAAACACAAATGAAAG-AAGGAACC-AACTCTCCTAATTCG
* * * *
11150702 ATTCCA-TAAATCAATAATCAATAGCAAAA-TATACATCACCTCATCTTTGAATC
64 AGTCCAGTAAATCAATAATCAATAGCAAAATTA-AAATCACCTCAACTCTGAATC
11150755 TTTGTTCTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
139 5 0.05
140 77 0.76
141 19 0.19
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.25
Consensus pattern (140 bp):
AAAGCACCCAACAGATTATCCTATAAAACACAAATGAAAGAAGGAACCAACTCTCCTAATTCGAG
TCCAGTAAATCAATAATCAATAGCAAAATTAAAATCACCTCAACTCTGAATCAACAACTGATTAT
TTCACCGATG
Found at i:11152635 original size:2 final size:2
Alignment explanation
Indices: 11152628--11152657 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11152618 TGCTTAGAAT
11152628 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11152658 TCAGTGTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11160034 original size:2 final size:2
Alignment explanation
Indices: 11160027--11160051 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11160017 AAGTATAGTT
11160027 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
11160052 CTTGTGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11163236 original size:120 final size:120
Alignment explanation
Indices: 11163023--11163270 Score: 496
Period size: 120 Copynumber: 2.1 Consensus size: 120
11163013 CACCTCACCT
11163023 GCAATCAAGACAAATTCAAACAGAATATGTAATCAGCATCGGGAAAATAATAGCAAAATCACATA
1 GCAATCAAGACAAATTCAAACAGAATATGTAATCAGCATCGGGAAAATAATAGCAAAATCACATA
11163088 TTTATGCTCTACCAAGAACACGCGTGTGTATGTTATATGCAGTATGCTGAAAGGA
66 TTTATGCTCTACCAAGAACACGCGTGTGTATGTTATATGCAGTATGCTGAAAGGA
11163143 GCAATCAAGACAAATTCAAACAGAATATGTAATCAGCATCGGGAAAATAATAGCAAAATCACATA
1 GCAATCAAGACAAATTCAAACAGAATATGTAATCAGCATCGGGAAAATAATAGCAAAATCACATA
11163208 TTTATGCTCTACCAAGAACACGCGTGTGTATGTTATATGCAGTATGCTGAAAGGA
66 TTTATGCTCTACCAAGAACACGCGTGTGTATGTTATATGCAGTATGCTGAAAGGA
11163263 GCAATCAA
1 GCAATCAA
11163271 CCTAAACAAA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 128 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (120 bp):
GCAATCAAGACAAATTCAAACAGAATATGTAATCAGCATCGGGAAAATAATAGCAAAATCACATA
TTTATGCTCTACCAAGAACACGCGTGTGTATGTTATATGCAGTATGCTGAAAGGA
Found at i:11165703 original size:2 final size:2
Alignment explanation
Indices: 11165696--11165727 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11165686 TGCTTAGAAT
11165696 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11165728 TCAGTGTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11169991 original size:16 final size:15
Alignment explanation
Indices: 11169953--11169982 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11169943 CATTCTTCAC
11169953 AATCTTTCCATGTCT
1 AATCTTTCCATGTCT
11169968 AATCTTTCCATGTCT
1 AATCTTTCCATGTCT
11169983 TCTTCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (15 bp):
AATCTTTCCATGTCT
Found at i:11186873 original size:31 final size:30
Alignment explanation
Indices: 11186827--11186884 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
11186817 TCTAGTTTAT
11186827 ATTTTTTATA-ATTTTTAAAGAATTAAAACA
1 ATTTTTTATATATTTTTAAA-AATTAAAACA
*
11186857 ATTTTTTATTATTTTTTTAAAAATTAAA
1 ATTTTTTA-TATATTTTTAAAAATTAAA
11186885 GTATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 9 0.36
32 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTTTTTATATATTTTTAAAAATTAAAACA
Found at i:11195029 original size:27 final size:27
Alignment explanation
Indices: 11194999--11195135 Score: 267
Period size: 27 Copynumber: 5.1 Consensus size: 27
11194989 AATGCATATT
11194999 CAGCCGAAATCATAGATAAGATTACCA
1 CAGCCGAAATCATAGATAAGATTACCA
11195026 CAGCCGAAATCATAGATAAGATTACCA
1 CAGCCGAAATCATAGATAAGATTACCA
11195053 CAGCCGAAATCATAGATAAGATTACCA
1 CAGCCGAAATCATAGATAAGATTACCA
11195080 CAGCCGAAATCATAGATAAGATTACCA
1 CAGCCGAAATCATAGATAAGATTACCA
11195107 CAGCCGAAATCATAGAT-AGATTACCA
1 CAGCCGAAATCATAGATAAGATTACCA
11195133 CAG
1 CAG
11195136 GTGGGAACCT
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
26 12 0.11
27 98 0.89
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (27 bp):
CAGCCGAAATCATAGATAAGATTACCA
Found at i:11202318 original size:15 final size:15
Alignment explanation
Indices: 11202298--11202337 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
11202288 TATCATAAGG
11202298 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
11202313 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
*
11202327 ACAT-TTTAAAA
1 AAATATTTAAAA
11202338 TTACTTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:11207191 original size:21 final size:21
Alignment explanation
Indices: 11207165--11207204 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11207155 TTGGGTCATC
11207165 TTCTTCTTCCTCTTGTTCTGG
1 TTCTTCTTCCTCTTGTTCTGG
*
11207186 TTCTTCTTCTTCTTGTTCT
1 TTCTTCTTCCTCTTGTTCT
11207205 TCTTCAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.10, T:0.62
Consensus pattern (21 bp):
TTCTTCTTCCTCTTGTTCTGG
Found at i:11222917 original size:211 final size:212
Alignment explanation
Indices: 11222552--11222974 Score: 830
Period size: 211 Copynumber: 2.0 Consensus size: 212
11222542 AAGGGCAGCC
11222552 TCCAATGATGTATCTTTTTTTTTTTTTTTTGGGGGCATGTAACCTTAGAATCTCACTTGTTAGTT
1 TCCAATGATGTATCTTTTTTTTTTTTTTTTGGGGGCATGTAACCTTAGAATCTCACTTGTTAGTT
11222617 GAAAGTAAATTGAAGTCTCTCACCATTGATAGAGATGATCATTCTCTTGTAACAATTAATTGAAG
66 GAAAGTAAATTGAAGTCTCTCACCATTGATAGAGATGATCATTCTCTTGTAACAATTAATTGAAG
11222682 CTTAATATTATTAGTAGAATCTTACTACAAGGAAAACAGGCTCTCAGTGAGGCTTATATCCCACT
131 CTTAATATTATTAGTAGAATCTTACTACAAGGAAAACAGGCTCTCAGTGAGGCTTATATCCCACT
11222747 TGGTTAAAAAAAAGTTA
196 TGGTTAAAAAAAAGTTA
*
11222764 TCCAATGATG-ATCTTTTTTTTTTTTTTTTGGGTGCATGTAACCTTAGAATCTCACTTGTTAGTT
1 TCCAATGATGTATCTTTTTTTTTTTTTTTTGGGGGCATGTAACCTTAGAATCTCACTTGTTAGTT
11222828 GAAAGTAAATTGAAGTCTCTCACCATTGATAGAGATGATCATTCTCTTGTAACAATTAATTGAAG
66 GAAAGTAAATTGAAGTCTCTCACCATTGATAGAGATGATCATTCTCTTGTAACAATTAATTGAAG
11222893 CTTAATATTATTAGTAGAATCTTACTACAAGGAAAACAGGCTCTCAGTGAGGCTTATATCCCACT
131 CTTAATATTATTAGTAGAATCTTACTACAAGGAAAACAGGCTCTCAGTGAGGCTTATATCCCACT
11222958 TGGTTAAAAAAAAGTTA
196 TGGTTAAAAAAAAGTTA
11222975 ATTACTTTGA
Statistics
Matches: 210, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
211 200 0.95
212 10 0.05
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (212 bp):
TCCAATGATGTATCTTTTTTTTTTTTTTTTGGGGGCATGTAACCTTAGAATCTCACTTGTTAGTT
GAAAGTAAATTGAAGTCTCTCACCATTGATAGAGATGATCATTCTCTTGTAACAATTAATTGAAG
CTTAATATTATTAGTAGAATCTTACTACAAGGAAAACAGGCTCTCAGTGAGGCTTATATCCCACT
TGGTTAAAAAAAAGTTA
Found at i:11226714 original size:31 final size:29
Alignment explanation
Indices: 11226646--11226717 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
11226636 AACGTGTTAC
* *
11226646 ATTTTAGTCACTTATGTTTGAAATGTTAT
1 ATTTTAGTCACTTATGTTTCAAATGTAAT
* **
11226675 GTTTTAGTCACTTATGTTATCATGTTGTAAT
1 ATTTTAGTCACTTATGTT-TCA-AATGTAAT
11226706 ATTTTAGTCACT
1 ATTTTAGTCACT
11226718 GAGCCGTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.49
30 2 0.06
31 16 0.46
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTCAAATGTAAT
Found at i:11229461 original size:18 final size:18
Alignment explanation
Indices: 11229435--11229472 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11229425 CATATTCTAA
11229435 TAAACATATAATTTATAT
1 TAAACATATAATTTATAT
*
11229453 TAAATATATAATTTATAT
1 TAAACATATAATTTATAT
11229471 TA
1 TA
11229473 CATAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAACATATAATTTATAT
Found at i:11232281 original size:24 final size:25
Alignment explanation
Indices: 11232254--11232301 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
11232244 AGAGGAAAGT
11232254 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAATGAAAAAAAA
** *
11232278 TTAAATTACTTAAAATGAAAAAAA
1 TTAAAGAACATAAAATGAAAAAAA
11232302 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (25 bp):
TTAAAGAACATAAAATGAAAAAAAA
Found at i:11233735 original size:20 final size:21
Alignment explanation
Indices: 11233712--11233767 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
11233702 CTACGTAAAC
11233712 TTAAATTATTTTTTAAATAA-
1 TTAAATTATTTTTTAAATAAG
* *
11233732 TTAAAATCA-TTTTTACATAAG
1 TT-AAATTATTTTTTAAATAAG
11233753 TTTAAATTATTTTTT
1 -TTAAATTATTTTTT
11233768 TATTGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 12 0.41
21 10 0.34
22 7 0.24
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAAATTATTTTTTAAATAAG
Found at i:11233738 original size:21 final size:22
Alignment explanation
Indices: 11233714--11233767 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
11233704 ACGTAAACTT
11233714 AAATTATTTTTTAAATAA-TTA
1 AAATTATTTTTTAAATAAGTTA
* * *
11233735 AAATCA-TTTTTACATAAGTTT
1 AAATTATTTTTTAAATAAGTTA
11233756 AAATTATTTTTT
1 AAATTATTTTTT
11233768 TATTGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
AAATTATTTTTTAAATAAGTTA
Found at i:11234664 original size:11 final size:11
Alignment explanation
Indices: 11234650--11234694 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
11234640 ATCTTTTTAA
11234650 TTTTAAAATAT
1 TTTTAAAATAT
11234661 TTTTAAAATAT
1 TTTTAAAATAT
*
11234672 TTTT---TTAT
1 TTTTAAAATAT
11234680 TTTTAAAATAT
1 TTTTAAAATAT
11234691 TTTT
1 TTTT
11234695 TTGTGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 7 0.24
11 22 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:11234682 original size:19 final size:19
Alignment explanation
Indices: 11234658--11234696 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11234648 AATTTTAAAA
11234658 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATATTTTTT
11234677 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATATTTTTT
11234696 T
1 T
11234697 GTGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTAAAATATTTTTT
Found at i:11234703 original size:19 final size:19
Alignment explanation
Indices: 11234662--11234703 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
11234652 TTAAAATATT
*
11234662 TTTAAAATATTTTTTTATT
1 TTTAAAATATTTTTTTATG
*
11234681 TTTAAAATATTTTTTTGTG
1 TTTAAAATATTTTTTTATG
11234700 TTTA
1 TTTA
11234704 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTAAAATATTTTTTTATG
Found at i:11246267 original size:33 final size:33
Alignment explanation
Indices: 11246220--11246286 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
11246210 CCATTTTCAG
*
11246220 TTGTTTTCATTTAATTAGCATCAGAAATGGCTT
1 TTGTGTTCATTTAATTAGCATCAGAAATGGCTT
11246253 TTGTGTTCATTTAATTAGCATCAGAAATGGCTT
1 TTGTGTTCATTTAATTAGCATCAGAAATGGCTT
11246286 T
1 T
11246287 GTCTATTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (33 bp):
TTGTGTTCATTTAATTAGCATCAGAAATGGCTT
Found at i:11253841 original size:2 final size:2
Alignment explanation
Indices: 11253834--11253876 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11253824 TGATAACGTT
11253834 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
11253876 T
1 T
11253877 ATACATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11254935 original size:16 final size:16
Alignment explanation
Indices: 11254914--11254945 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11254904 AATTTATGCC
11254914 ATGTTCGTGATGTTAT
1 ATGTTCGTGATGTTAT
11254930 ATGTTCGTGATGTTAT
1 ATGTTCGTGATGTTAT
11254946 TTTTCCTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (16 bp):
ATGTTCGTGATGTTAT
Found at i:11277648 original size:15 final size:15
Alignment explanation
Indices: 11277628--11277658 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11277618 ACCGCGGAAA
*
11277628 GCTCTGATTCAAGGG
1 GCTCTGATCCAAGGG
11277643 GCTCTGATCCAAGGG
1 GCTCTGATCCAAGGG
11277658 G
1 G
11277659 TTGTGACCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (15 bp):
GCTCTGATCCAAGGG
Found at i:11296159 original size:16 final size:16
Alignment explanation
Indices: 11296138--11296168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11296128 TTAGAATGTT
11296138 TGTATTATTTTGTATC
1 TGTATTATTTTGTATC
*
11296154 TGTATTTTTTTGTAT
1 TGTATTATTTTGTAT
11296169 TTTTTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (16 bp):
TGTATTATTTTGTATC
Found at i:11296545 original size:13 final size:13
Alignment explanation
Indices: 11296527--11296563 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
11296517 TTCTTTATTA
11296527 CTTTTGAGAAACG
1 CTTTTGAGAAACG
**
11296540 CTTTTGAGAAGTG
1 CTTTTGAGAAACG
11296553 CTTTTGAGAAA
1 CTTTTGAGAAA
11296564 TTTGGTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (13 bp):
CTTTTGAGAAACG
Found at i:11296954 original size:22 final size:21
Alignment explanation
Indices: 11296929--11296972 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
11296919 AAGCATATGA
*
11296929 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
11296951 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
11296972 A
1 A
11296973 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:11296999 original size:44 final size:44
Alignment explanation
Indices: 11296951--11297088 Score: 276
Period size: 44 Copynumber: 3.1 Consensus size: 44
11296941 TATATTCAAT
11296951 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
11296995 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
11297039 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
11297083 AAATGA
1 AAATGA
11297089 AAGCCGAGAC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 94 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (44 bp):
AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:11299601 original size:26 final size:26
Alignment explanation
Indices: 11299565--11299617 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
11299555 GTAAACGGCG
11299565 ATGCTAATCAATTGGGGCTCATCTGT
1 ATGCTAATCAATTGGGGCTCATCTGT
*
11299591 ATGCTAATCAATTTGGGCTCATCTGT
1 ATGCTAATCAATTGGGGCTCATCTGT
11299617 A
1 A
11299618 ATTACTGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
ATGCTAATCAATTGGGGCTCATCTGT
Found at i:11300087 original size:17 final size:17
Alignment explanation
Indices: 11300067--11300437 Score: 108
Period size: 16 Copynumber: 21.6 Consensus size: 17
11300057 AGAAAAGGAC
11300067 TTTTCATTTCAATTTATT
1 TTTTCATTTCAATTTA-T
* * *
11300085 TTTTAATTTCAATTCAA
1 TTTTCATTTCAATTTAT
*
11300102 ATTTCATTT-AATTT-T
1 TTTTCATTTCAATTTAT
*
11300117 ATATTCATTTCACATTTCAT
1 -TTTTCATTTCA-ATTT-AT
** *
11300137 TTTATTTTTTC-ATTTAA
1 TTT-TCATTTCAATTTAT
11300154 TTTT--TTTCATATTTTATT
1 TTTTCATTTCA-A-TTTA-T
* *
11300172 TTTTCATTTAAAATT-T
1 TTTTCATTTCAATTTAT
11300188 TTTTCATATTC-ATTT-T
1 TTTTCAT-TTCAATTTAT
* *
11300204 TTTTCTTTTCCA-TT-T
1 TTTTCATTTCAATTTAT
11300219 TTTTCATTTC-ATTTCA-
1 TTTTCATTTCAATTT-AT
* *
11300235 TATTCATTTCAACGTTA-
1 TTTTCATTTCAA-TTTAT
*
11300252 TTTTCATTTCATATTCAT
1 TTTTCATTTCA-ATTTAT
11300270 TACAACTTTCATTTC-ATTTCAT
1 T-----TTTCATTTCAATTT-AT
* *
11300292 ATTTCATTTC-A--CA-
1 TTTTCATTTCAATTTAT
* *
11300305 -TTTCATTTC-TTTTTT
1 TTTTCATTTCAATTTAT
11300320 TTTTCATTTCAATTTATTT
1 TTTTCATTTCAATTTA--T
*
11300339 TTTTCATATTC-ATCT-T
1 TTTTCAT-TTCAATTTAT
*
11300355 TTCTCATTTCAATTT-T
1 TTTTCATTTCAATTTAT
*
11300371 TTTTAATATTC-ATTT-T
1 TTTTCAT-TTCAATTTAT
11300387 TTTCTCATTTCAATTTATTTAT
1 TTT-TCATTTC-A---ATTTAT
11300409 TTTTCATTTCAATTTAT
1 TTTTCATTTCAATTTAT
*
11300426 ATTTTAATTTCA
1 -TTTTCATTTCA
11300438 TTTCAAATTT
Statistics
Matches: 268, Mismatches: 40, Indels: 90
0.67 0.10 0.23
Matches are distributed among these distances:
12 9 0.03
14 6 0.02
15 20 0.07
16 77 0.29
17 57 0.21
18 42 0.16
19 14 0.05
20 14 0.05
21 14 0.05
22 6 0.02
23 9 0.03
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTCATTTCAATTTAT
Found at i:11300152 original size:12 final size:13
Alignment explanation
Indices: 11300131--11300180 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
11300121 TCATTTCACA
11300131 TTTCATTTTATTT
1 TTTCATTTTATTT
*
11300144 TTTCATTTAATTTT
1 TTTCATTTTA-TTT
11300158 TTTCATATTTTATTT
1 TTTC--ATTTTATTT
11300173 TTTCATTT
1 TTTCATTT
11300181 AAAATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 13 0.41
14 7 0.22
15 7 0.22
16 5 0.16
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCATTTTATTT
Found at i:11300156 original size:23 final size:24
Alignment explanation
Indices: 11300067--11300156 Score: 78
Period size: 28 Copynumber: 3.6 Consensus size: 24
11300057 AGAAAAGGAC
11300067 TTTTCATTTCAATTT-ATTTT-TT
1 TTTTCATTTCAATTTCATTTTATT
* * *
11300089 AATTTCAATTCAAATTTCATTTAATTT
1 -TTTTCATTTC-AATTTCATTTTA-TT
11300116 TATATTCATTTCACATTTCATTTTATT
1 T-T-TTCATTTCA-ATTTCATTTTATT
11300143 TTTTCATTT-AATTT
1 TTTTCATTTCAATTT
11300157 TTTTCATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
23 12 0.22
24 6 0.11
25 11 0.20
26 1 0.02
27 7 0.13
28 17 0.31
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTCATTTCAATTTCATTTTATT
Found at i:11300167 original size:29 final size:30
Alignment explanation
Indices: 11300135--11300225 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 30
11300125 TTCACATTTC
11300135 ATTTTATTTTTTCATTT-AATTTTTTTCAT
1 ATTTTATTTTTTCATTTAAATTTTTTTCAT
11300164 ATTTTATTTTTTCATTTAAAATTTTTTTCAT
1 ATTTTATTTTTTCATTT-AAATTTTTTTCAT
* **
11300195 ATTCATT-TTTTTTCTTTTCCATTTTTTTCAT
1 ATT--TTATTTTTTCATTTAAATTTTTTTCAT
11300226 TTCATTTCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
29 17 0.31
31 26 0.47
32 10 0.18
33 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (30 bp):
ATTTTATTTTTTCATTTAAATTTTTTTCAT
Found at i:11300202 original size:15 final size:14
Alignment explanation
Indices: 11300131--11300232 Score: 82
Period size: 15 Copynumber: 6.9 Consensus size: 14
11300121 TCATTTCACA
*
11300131 TTTCATTTTA-TTT
1 TTTCATTTCATTTT
*
11300144 TTTCATTTAATTTT
1 TTTCATTTCATTTT
*
11300158 TTTCATATT-TTATTT
1 TTTCAT-TTCAT-TTT
*
11300173 TTTCATTTAAAATTTT
1 TTTCATTT--CATTTT
11300189 TTTCATATTCATTTTT
1 TTTCAT-TTCA-TTTT
*
11300205 TTTCTTTTCCATTTT
1 TTTCATTT-CATTTT
11300220 TTTCATTTCATTT
1 TTTCATTTCATTT
11300233 CATATTCATT
Statistics
Matches: 74, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
13 9 0.12
14 17 0.23
15 25 0.34
16 20 0.27
17 3 0.04
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCATTTCATTTT
Found at i:11300228 original size:5 final size:5
Alignment explanation
Indices: 11300220--11300459 Score: 71
Period size: 5 Copynumber: 44.0 Consensus size: 5
11300210 TTTCCATTTT
*
11300220 TTTCA TTTCA TTTCA TATTCA TTTCAA CGTT-A TTTTCA TTTCA TATTCA
1 TTTCA TTTCA TTTCA T-TTCA TTTC-A -TTTCA -TTTCA TTTCA T-TTCA
* * **
11300269 TTACAA CTTTCA TTTCA TTTCATA TTTCA TTTCACA TTTCA TTTCTT TTTTT
1 TTTC-A -TTTCA TTTCA TTTC--A TTTCA TTT--CA TTTCA TTTC-A TTTCA
*
11300321 TTTCA TTTCAA TTT-A TTT-T TTTCA TATTCA TCTT-- TTCTCA TTTCAA
1 TTTCA TTTC-A TTTCA TTTCA TTTCA T-TTCA T-TTCA TT-TCA TTTC-A
** * **
11300367 TTTTT TTTAA TATTCA TTTTT TTCTCA TTTCAA TTT-A TTT-A TTTTTCA
1 TTTCA TTTCA T-TTCA TTTCA TT-TCA TTTC-A TTTCA TTTCA --TTTCA
* *
11300415 TTTCAA TTTATA TTTTAA TTTCA TTTCAAA TTTCA TTTCA TTTCA
1 TTTC-A TTT-CA -TTTCA TTTCA TTTC--A TTTCA TTTCA TTTCA
11300460 AATATTTTCT
Statistics
Matches: 181, Mismatches: 24, Indels: 60
0.68 0.09 0.23
Matches are distributed among these distances:
3 1 0.01
4 14 0.08
5 88 0.49
6 54 0.30
7 24 0.13
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCA
Found at i:11300259 original size:28 final size:28
Alignment explanation
Indices: 11300221--11300302 Score: 121
Period size: 28 Copynumber: 2.9 Consensus size: 28
11300211 TTCCATTTTT
11300221 TTCATTTCATTTCATATTCATTTCAACG
1 TTCATTTCATTTCATATTCATTTCAACG
* *
11300249 TT-ATTTTCATTTCATATTCATTACAACT
1 TTCA-TTTCATTTCATATTCATTTCAACG
11300277 TTCATTTCATTTCATATTTCATTTCA
1 TTCATTTCATTTCATA-TTCATTTCA
11300303 CATTTCATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
27 1 0.02
28 38 0.79
29 9 0.19
ACGTcount: A:0.26, C:0.20, G:0.01, T:0.54
Consensus pattern (28 bp):
TTCATTTCATTTCATATTCATTTCAACG
Found at i:11300295 original size:12 final size:12
Alignment explanation
Indices: 11300279--11300313 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
11300269 TTACAACTTT
11300279 CATTTCATTTCA
1 CATTTCATTTCA
*
11300291 TATTTCATTTCA
1 CATTTCATTTCA
11300303 CATTTCATTTC
1 CATTTCATTTC
11300314 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (12 bp):
CATTTCATTTCA
Found at i:11300357 original size:33 final size:36
Alignment explanation
Indices: 11300305--11300419 Score: 125
Period size: 35 Copynumber: 3.3 Consensus size: 36
11300295 TCATTTCACA
* * *
11300305 TTTCAT-TTCTTTTTTTTTTCATTTCAATTTATTTT
1 TTTCATATTCATTCTTTTCTCATTTCAATTTATTTT
11300340 TTTCATATTCA-TCTTTTCTCATTTCAA--T-TTTT
1 TTTCATATTCATTCTTTTCTCATTTCAATTTATTTT
* *
11300372 TTTAATATTCATTTTTTTCTCATTTCAATTTATTTATT
1 TTTCATATTCATTCTTTTCTCATTTCAATTTA-TT-TT
11300410 TTTCAT-TTCA
1 TTTCATATTCA
11300420 ATTTATATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
32 14 0.21
33 16 0.24
35 21 0.31
36 3 0.04
37 6 0.09
38 7 0.10
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (36 bp):
TTTCATATTCATTCTTTTCTCATTTCAATTTATTTT
Found at i:11300364 original size:68 final size:72
Alignment explanation
Indices: 11300292--11300457 Score: 175
Period size: 68 Copynumber: 2.4 Consensus size: 72
11300282 TTCATTTCAT
* * *
11300292 ATTTCATTTCACATTTCATTTCTTTTTTTTTTCATTTCAATTTA-TT-TTTTTCATATTC-ATCT
1 ATTTCATTTCAAATTTCATTTCATTTTTTTCTCATTTCAATTTATTTATTTTTCAT-TTCAATCT
*
11300354 -T-TTCTC
65 ATATTCTA
** * *
11300360 ATTTCAATTT--TTTTTAATATTCATTTTTTTCTCATTTCAATTTATTTATTTTTCATTTCAATT
1 ATTTC-ATTTCAAATTTCAT-TTCATTTTTTTCTCATTTCAATTTATTTATTTTTCATTTCAATC
*
11300423 TATATTTTA
64 TATATTCTA
11300432 ATTTCATTTCAAATTTCATTTCATTT
1 ATTTCATTTCAAATTTCATTTCATTT
11300458 CAAATATTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
67 5 0.06
68 28 0.36
69 9 0.12
70 11 0.14
71 5 0.06
72 15 0.19
73 5 0.06
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (72 bp):
ATTTCATTTCAAATTTCATTTCATTTTTTTCTCATTTCAATTTATTTATTTTTCATTTCAATCTA
TATTCTA
Found at i:11300428 original size:23 final size:20
Alignment explanation
Indices: 11300316--11300443 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 20
11300306 TTCATTTCTT
11300316 TTTTTTTTCATTTCAATTTA
1 TTTTTTTTCATTTCAATTTA
*
11300336 -TTTTTTTCA--T--ATTCA
1 TTTTTTTTCATTTCAATTTA
* *
11300351 TCTTTTCTCATTTCAATTT-
1 TTTTTTTTCATTTCAATTTA
**
11300370 TTTTTAAT-A-TTC-A--T-
1 TTTTTTTTCATTTCAATTTA
*
11300384 TTTTTTCTCATTTCAATTTA
1 TTTTTTTTCATTTCAATTTA
11300404 TTTATTTTTCATTTCAATTTA
1 TTT-TTTTTCATTTCAATTTA
11300425 TATTTTAATTTCATTTCAA
1 T-TTTT--TTTCATTTCAA
11300444 ATTTCATTTC
Statistics
Matches: 83, Mismatches: 10, Indels: 27
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.08
15 5 0.06
16 11 0.13
17 5 0.06
18 2 0.02
19 15 0.18
20 6 0.07
21 19 0.23
22 2 0.02
23 11 0.13
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTTTCATTTCAATTTA
Found at i:11300452 original size:17 final size:17
Alignment explanation
Indices: 11300410--11300462 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
11300400 TTTATTTATT
*
11300410 TTTCATTTCAATTT-ATAT
1 TTTCATTTC-ATTTCA-AA
*
11300428 TTTAATTTCATTTCAAA
1 TTTCATTTCATTTCAAA
11300445 TTTCATTTCATTTCAAA
1 TTTCATTTCATTTCAAA
11300462 T
1 T
11300463 ATTTTCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTCATTTCATTTCAAA
Found at i:11300457 original size:28 final size:28
Alignment explanation
Indices: 11300220--11300457 Score: 77
Period size: 28 Copynumber: 8.5 Consensus size: 28
11300210 TTTCCATTTT
* *
11300220 TTTCATTTCA-TTTCATATTCATTTCAAC
1 TTTCATTTCATTTTAAT-TTCATTTCAAA
* * * *
11300248 GTT-ATTTTCA-TTTCATATTCATTACAAC
1 TTTCA-TTTCATTTTAAT-TTCATTTCAAA
* *
11300276 TTTCATTTCATTTCATATTTCATTTCACA
1 TTTCATTTCATTTTA-ATTTCATTTCAAA
* **
11300305 TTTCATTTCTTTTTTTTTTCATTTC-AA
1 TTTCATTTCATTTTAATTTCATTTCAAA
* **
11300332 TTT-ATTT--TTTTCATATTCATCTTTTCTCA
1 TTTCATTTCATTTT-A-ATT--TCATTTCAAA
* **
11300361 TTTCAATTT-TTTTTAATATTCATTT--TT
1 TTTC-ATTTCATTTTAAT-TTCATTTCAAA
* ***
11300388 TTCTCATTTCAATTT-ATTT-ATTTTTCA
1 TT-TCATTTCATTTTAATTTCATTTCAAA
*
11300415 TTTCAATTTATATTTTAATTTCATTTCAAA
1 TTTC-ATTT-CATTTTAATTTCATTTCAAA
11300445 TTTCATTTCATTT
1 TTTCATTTCATTT
11300458 CAAATATTTT
Statistics
Matches: 159, Mismatches: 30, Indels: 42
0.69 0.13 0.18
Matches are distributed among these distances:
24 4 0.03
25 4 0.03
26 10 0.06
27 19 0.12
28 59 0.37
29 40 0.25
30 13 0.08
31 6 0.04
32 4 0.03
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTCATTTCATTTTAATTTCATTTCAAA
Found at i:11300514 original size:33 final size:35
Alignment explanation
Indices: 11300434--11300536 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 35
11300424 ATATTTTAAT
* *
11300434 TTCATTTCAAATTTCATTTCATTTCAAATATTTTC
1 TTCATTTTAAATTTCATTTTATTTCAAATATTTTC
* * *
11300469 TTCTTTAATTAAATTTCATTTTATTT-AATTTTTTTC
1 TTCATT--TTAAATTTCATTTTATTTCAAATATTTTC
*
11300505 -TCATTTTAAATTTCATGTTATTTCAAA-ATTTT
1 TTCATTTTAAATTTCATTTTATTTCAAATATTTT
11300537 AAATTTCATT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
33 21 0.38
34 2 0.04
35 9 0.16
36 8 0.14
37 16 0.29
ACGTcount: A:0.28, C:0.12, G:0.01, T:0.59
Consensus pattern (35 bp):
TTCATTTTAAATTTCATTTTATTTCAAATATTTTC
Found at i:11300539 original size:25 final size:25
Alignment explanation
Indices: 11300507--11300561 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
11300497 TTTTTTTCTC
*
11300507 ATTTTAAATTTCATGTT-ATTTCAAA
1 ATTTTAAATTTCAT-TTAAATTCAAA
11300532 ATTTTAAATTTCATTTAAATTCAAA
1 ATTTTAAATTTCATTTAAATTCAAA
11300557 ATTTT
1 ATTTT
11300562 TCTCATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (25 bp):
ATTTTAAATTTCATTTAAATTCAAA
Found at i:11302385 original size:5 final size:5
Alignment explanation
Indices: 11302367--11302413 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
11302357 TCAATTTTTT
* *
11302367 TTTCA TTTAAA TTTCA TTTCA TTTCA TTTCA TTTCAA CTTCA TTTCA
1 TTTCA TTT-CA TTTCA TTTCA TTTCA TTTCA TTTC-A TTTCA TTTCA
11302414 ATAAAAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 28 0.78
6 8 0.22
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (5 bp):
TTTCA
Found at i:11302567 original size:101 final size:101
Alignment explanation
Indices: 11302405--11302598 Score: 304
Period size: 101 Copynumber: 1.9 Consensus size: 101
11302395 TCATTTCAAC
11302405 TTCATTTCAATAAAAAAGCTTAATTTATTTTTTAAATTTTACTCATATATCTTTTTTAAATATAA
1 TTCATTTCAATAAAAAA-CTTAATTTATTTTTTAAA-TTTACTCATATATCTTTTTTAAATATAA
11302470 TTTCATTTCATTCCCAATTTTAATATAATTTTATTTCAT
64 TTTCATTTCATTCCCAATTTTAAT-TAATTTTATTTCAT
*
11302509 TTCATTTCAA-AATAAAA-TTCAATTTCTTTTTTAAA-TTACTCATATATCTTTTTTAAATATAA
1 TTCATTTCAATAA-AAAACTT-AATTTATTTTTTAAATTTACTCATATATCTTTTTTAAATATAA
*
11302571 TTTCATTTCATTCCTAATTTTAATTAAT
64 TTTCATTTCATTCCCAATTTTAATTAAT
11302599 ATATTTAAAG
Statistics
Matches: 86, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
100 4 0.05
101 50 0.58
102 2 0.02
103 16 0.19
104 14 0.16
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.53
Consensus pattern (101 bp):
TTCATTTCAATAAAAAACTTAATTTATTTTTTAAATTTACTCATATATCTTTTTTAAATATAATT
TCATTTCATTCCCAATTTTAATTAATTTTATTTCAT
Found at i:11305535 original size:12 final size:11
Alignment explanation
Indices: 11305505--11305529 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11305495 TTCAACTAAT
11305505 AAAGCAAACAA
1 AAAGCAAACAA
11305516 AAAGCAAACAA
1 AAAGCAAACAA
11305527 AAA
1 AAA
11305530 TTCAAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAGCAAACAA
Found at i:11309608 original size:19 final size:18
Alignment explanation
Indices: 11309551--11309610 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
11309541 ATTGGAATAT
11309551 AATATTTAATTATTATATTTA
1 AATATTTAATTA--A-ATTTA
* *
11309572 AATATTTAAATATCATTTA
1 AATATTTAATTA-AATTTA
11309591 AATATTCTAATTAAATTTA
1 AATATT-TAATTAAATTTA
11309610 A
1 A
11309611 TAAATAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
20 6 0.18
21 11 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTTAATTAAATTTA
Found at i:11310353 original size:6 final size:6
Alignment explanation
Indices: 11310344--11310369 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11310334 AAAAATATTA
11310344 AATTTT AATTTT AATTTT AATTTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
11310370 AAAATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:11314393 original size:30 final size:31
Alignment explanation
Indices: 11314358--11314417 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
11314348 TTTAGCAAAT
11314358 AATAATGTGATTATTTAGATAACTA-AATTA
1 AATAATGTGATTATTTAGATAACTATAATTA
11314388 AATAATGTGATTATTTAGATAACTATAATT
1 AATAATGTGATTATTTAGATAACTATAATT
11314418 TAGAACACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (31 bp):
AATAATGTGATTATTTAGATAACTATAATTA
Found at i:11323249 original size:22 final size:23
Alignment explanation
Indices: 11323202--11323251 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
11323192 GGCCCGGGTT
* * *
11323202 ATTAAAATTATATTTTTATTAAA
1 ATTAAAACTATATTGTTAGTAAA
11323225 ATTAAAACTA-ATTGTTAGTAAA
1 ATTAAAACTATATTGTTAGTAAA
11323247 ATTAA
1 ATTAA
11323252 TTGTTATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTAAAACTATATTGTTAGTAAA
Found at i:11323252 original size:16 final size:16
Alignment explanation
Indices: 11323227--11323266 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
11323217 TTATTAAAAT
*
11323227 TAAAACTAATTGTTAG
1 TAAAATTAATTGTTAG
*
11323243 TAAAATTAATTGTTAT
1 TAAAATTAATTGTTAG
11323259 TAAAATTA
1 TAAAATTA
11323267 TATCAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:11323367 original size:35 final size:35
Alignment explanation
Indices: 11323321--11323601 Score: 134
Period size: 35 Copynumber: 7.6 Consensus size: 35
11323311 ATCTAACATT
* * *
11323321 TTGTTAGTAAAATTATTAATTGTTAATTGTAATAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
*
11323356 TTGTTAGTAAAATTATCAAATTATATCAAAT-TATTAA
1 TTGTTAGTAAAATTAT-AAATTGT-T-AAATGTATTAA
* * * * * * ** *
11323393 TTGTTAGTACTAGTCAAAACATTTTGTAAAATCTAACATT
1 TTGTTAGTA-AAATTATAA-A--TTGTTAAATGTATTA-A
* * *
11323433 TTGTTAGTCAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
*
11323468 TTGTTAGTAAAATTATCAAATTATATCAAAT-TATTAA
1 TTGTTAGTAAAATTAT-AAATTGT-T-AAATGTATTAA
* * * * * * ** *
11323505 TTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATT
1 TTGTTAGTA-AAATTATAA-A--TTGTTAAATGTATTA-A
* * *
11323545 TTGTTAGTCAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
11323580 TTGTTAGTAAAATTATCAAATT
1 TTGTTAGTAAAATTAT-AAATT
11323602 ATATCAGATT
Statistics
Matches: 175, Mismatches: 52, Indels: 37
0.66 0.20 0.14
Matches are distributed among these distances:
35 46 0.26
36 34 0.19
37 35 0.20
38 24 0.14
39 14 0.08
40 22 0.13
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (35 bp):
TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
Found at i:11323413 original size:112 final size:112
Alignment explanation
Indices: 11323261--11323612 Score: 616
Period size: 112 Copynumber: 3.1 Consensus size: 112
11323251 ATTGTTATTA
* * * *
11323261 AAATTATATCAAATTA-TATTTTTTTTGTACCAATCAAAACATTTTGTAAAATCTAACATTTTGT
1 AAATTATATCAAATTATTA-ATTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGT
* *
11323325 TAGTAAAATTATTAATTGTTAATTGTAATAATTGTTAGTAAAATTATC
65 TAGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
*
11323373 AAATTATATCAAATTATTAATTGTTAGTACTAGTCAAAACATTTTGTAAAATCTAACATTTTGTT
1 AAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTT
11323438 AGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
66 AGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
11323485 AAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTT
1 AAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTT
11323550 AGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
66 AGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
*
11323597 AAATTATATCAGATTA
1 AAATTATATCAAATTA
11323613 GGGTTAGGGT
Statistics
Matches: 230, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
112 228 0.99
113 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (112 bp):
AAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTT
AGTCAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
Found at i:11323510 original size:37 final size:38
Alignment explanation
Indices: 11323353--11323513 Score: 118
Period size: 37 Copynumber: 4.3 Consensus size: 38
11323343 TTAATTGTAA
11323353 TAATTGTTAGTAAAATTATCAAATTATATCAAAT-TAT
1 TAATTGTTAGTAAAATTATCAAATTATATCAAATCTAT
* * * * * * * *
11323390 TAATTGTTAGTACTAGTCA-AAACATTTTGTAAAATCTAA
1 TAATTGTTAGTA-AAATTATCAA-ATTATATCAAATCTAT
* * * * * * *
11323429 CATTTTGTTAGTCAAATTAT-TAATTGT-T-AATTGTAT
1 TA-ATTGTTAGTAAAATTATCAAATTATATCAAATCTAT
11323465 TAATTGTTAGTAAAATTATCAAATTATATCAAAT-TAT
1 TAATTGTTAGTAAAATTATCAAATTATATCAAATCTAT
11323502 TAATTGTTAGTA
1 TAATTGTTAGTA
11323514 CCAGTCAAAA
Statistics
Matches: 91, Mismatches: 25, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
35 15 0.16
36 11 0.12
37 31 0.34
38 19 0.21
39 7 0.08
40 8 0.09
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (38 bp):
TAATTGTTAGTAAAATTATCAAATTATATCAAATCTAT
Found at i:11323760 original size:15 final size:15
Alignment explanation
Indices: 11323740--11323771 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11323730 GGTTTTGGTA
11323740 TTTTTAAGTTAAGGG
1 TTTTTAAGTTAAGGG
*
11323755 TTTTTAAGTTTAGGG
1 TTTTTAAGTTAAGGG
11323770 TT
1 TT
11323772 AGGGTTAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (15 bp):
TTTTTAAGTTAAGGG
Found at i:11323760 original size:68 final size:68
Alignment explanation
Indices: 11323683--11323930 Score: 248
Period size: 68 Copynumber: 3.5 Consensus size: 68
11323673 GGTTATGGTT
* * *
11323683 AGGGGTTTTAAGTTAAGGATTAAGGTTAGGGCTAAGGTTTTTGTTAGGGTTTTGGTATTTTTAAG
1 AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAAGGTTTTTGTTAGGGTTTTGGTATTTTTAAG
11323748 TTA
66 TTA
* * *
11323751 AGGGTTTTTAAGTTTAGGGTTAGGGTTAGGGTTAGGGTTAGGATTTTTAAGTTAAGGG-TTAGAG
1 AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGCTA-----AGG-TTTTT--GTT-AGGGTTTTG-G
*
11323815 TTTTTAAGTTAAGGGTT-
56 TATTT---TTAA--GTTA
* * * *
11323832 AGGGTTTTTATGTTAAGGGTTAGGGTTAGGGCTAGGGTTTTTGTTAGGGTTTTGGTGTTATTAAG
1 AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAAGGTTTTTGTTAGGGTTTTGGTATTTTTAAG
11323897 TTA
66 TTA
11323900 AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGG
1 AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGG
11323931 TTTTTAAGTT
Statistics
Matches: 148, Mismatches: 15, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
67 3 0.02
68 59 0.40
69 4 0.03
72 8 0.05
73 9 0.06
74 5 0.03
75 5 0.03
76 8 0.05
77 9 0.06
80 4 0.03
81 31 0.21
82 3 0.02
ACGTcount: A:0.22, C:0.01, G:0.35, T:0.43
Consensus pattern (68 bp):
AGGGTTTTTAAGTTAAGGGTTAGGGTTAGGGCTAAGGTTTTTGTTAGGGTTTTGGTATTTTTAAG
TTA
Found at i:11323773 original size:6 final size:6
Alignment explanation
Indices: 11323764--11323792 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11323754 GTTTTTAAGT
11323764 TTAGGG TTAGGG TTAGGG TTAGGG TTAGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGG
11323793 ATTTTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (6 bp):
TTAGGG
Found at i:11323808 original size:27 final size:25
Alignment explanation
Indices: 11323778--11323860 Score: 83
Period size: 21 Copynumber: 3.6 Consensus size: 25
11323768 GGTTAGGGTT
11323778 AGGGTTAGGGTTAGGATTTTTAAGTTA
1 AGGGTTAGGGTTA-G-TTTTTAAGTTA
11323805 AGGGTTA--G--AGTTTTTAAGTTA
1 AGGGTTAGGGTTAGTTTTTAAGTTA
*
11323826 AGGGTTA-GG---GTTTTTATGTTA
1 AGGGTTAGGGTTAGTTTTTAAGTTA
11323847 AGGGTTAGGGTTAG
1 AGGGTTAGGGTTAG
11323861 GGCTAGGGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
21 36 0.72
22 4 0.08
23 1 0.02
25 2 0.04
27 7 0.14
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (25 bp):
AGGGTTAGGGTTAGTTTTTAAGTTA
Found at i:11323810 original size:21 final size:21
Alignment explanation
Indices: 11323784--11323855 Score: 110
Period size: 21 Copynumber: 3.4 Consensus size: 21
11323774 GGTTAGGGTT
11323784 AGGGTTAGGATTTTTAAGTTA
1 AGGGTTAGGATTTTTAAGTTA
11323805 AGGGTTA-GAGTTTTTAAGTTA
1 AGGGTTAGGA-TTTTTAAGTTA
* *
11323826 AGGGTTAGGGTTTTTATGTTA
1 AGGGTTAGGATTTTTAAGTTA
11323847 AGGGTTAGG
1 AGGGTTAGG
11323856 GTTAGGGCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
22 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (21 bp):
AGGGTTAGGATTTTTAAGTTA
Found at i:11323856 original size:21 final size:21
Alignment explanation
Indices: 11323794--11323858 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
11323784 AGGGTTAGGA
*
11323794 TTTTTAAGTTAAGGGTTAGAG
1 TTTTTAAGTTAAGGGTTAGGG
11323815 TTTTTAAGTTAAGGGTTAGGG
1 TTTTTAAGTTAAGGGTTAGGG
*
11323836 TTTTTATGTTAAGGGTTAGGG
1 TTTTTAAGTTAAGGGTTAGGG
11323857 TT
1 TT
11323859 AGGGCTAGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
TTTTTAAGTTAAGGGTTAGGG
Found at i:11323912 original size:15 final size:15
Alignment explanation
Indices: 11323892--11323947 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
11323882 TTTGGTGTTA
11323892 TTAAGTTAAGGGTTT
1 TTAAGTTAAGGGTTT
11323907 TTAAGTTAAGGG---
1 TTAAGTTAAGGGTTT
*
11323919 TTAGGGTT-AGGGTTT
1 TTA-AGTTAAGGGTTT
11323934 TTAAGTTAAGGGTT
1 TTAAGTTAAGGGTT
11323948 AGGTTATGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 3 0.09
15 21 0.62
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (15 bp):
TTAAGTTAAGGGTTT
Found at i:11333907 original size:21 final size:21
Alignment explanation
Indices: 11333877--11333926 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
11333867 CGCTGTTTCT
* *
11333877 AATCTTACTGCTACAGTACCC
1 AATCTCACTGCTACAGTAACC
*
11333898 AATCTCACTGCTACAGTAACT
1 AATCTCACTGCTACAGTAACC
11333919 AATCTCAC
1 AATCTCAC
11333927 CGCCACCGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (21 bp):
AATCTCACTGCTACAGTAACC
Found at i:11334076 original size:29 final size:29
Alignment explanation
Indices: 11334044--11334109 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
11334034 ATAGGGATAT
* *
11334044 GATTAAATTAATCTCTCTACTATTAAATA
1 GATTAAATTAATCCCTCTACTATTAAAAA
* * *
11334073 GATTAATTTAGTCCCTGTACTATTAAAAA
1 GATTAAATTAATCCCTCTACTATTAAAAA
*
11334102 AATTAAAT
1 GATTAAAT
11334110 AAGGCCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (29 bp):
GATTAAATTAATCCCTCTACTATTAAAAA
Found at i:11335097 original size:13 final size:13
Alignment explanation
Indices: 11335081--11335107 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11335071 AAATAATTAA
11335081 AAAATTTAAACTT
1 AAAATTTAAACTT
11335094 AAAATTTAAACTT
1 AAAATTTAAACTT
11335107 A
1 A
11335108 TATTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTTAAACTT
Found at i:11339002 original size:2 final size:2
Alignment explanation
Indices: 11338995--11339026 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
11338985 CTTACAGCAA
*
11338995 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11339027 TTGATCGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11342139 original size:15 final size:16
Alignment explanation
Indices: 11342109--11342140 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11342099 TTATATTATA
11342109 AAAATATTATTAAATT
1 AAAATATTATTAAATT
11342125 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
11342140 A
1 A
11342141 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:11342144 original size:25 final size:26
Alignment explanation
Indices: 11342101--11342154 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 26
11342091 TTCTTGATTT
11342101 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATT-AATTAAA
*
11342128 ATATTAT-AAATTA-TATTAATTAAA
1 ATATTATAAAAATATTATTAATTAAA
11342152 ATA
1 ATA
11342155 AAAATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.38
25 4 0.15
26 5 0.19
27 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAATTAAA
Found at i:11342168 original size:28 final size:28
Alignment explanation
Indices: 11342112--11342170 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11342102 TATTATAAAA
* *
11342112 ATATTATTAAATTAAAATATTATAAATT
1 ATATTATTAAAATAAAATATAATAAATT
*
11342140 ATATTAATTAAAATAAAA-ATAATATATT
1 ATATT-ATTAAAATAAAATATAATAAATT
11342168 ATA
1 ATA
11342171 GGAAACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATTATTAAAATAAAATATAATAAATT
Found at i:11342335 original size:19 final size:22
Alignment explanation
Indices: 11342297--11342339 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11342287 TGTGAAAAAA
11342297 AATATTATTATATGATTATTAT
1 AATATTATTATATGATTATTAT
*
11342319 AATA-TATTATTATTATTATTA
1 AATATTATTA-TATGATTATTA
11342340 ACTAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATTATTATATGATTATTAT
Found at i:11342387 original size:17 final size:18
Alignment explanation
Indices: 11342365--11342400 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
11342355 GGAATAAAAT
*
11342365 AAAAGAATAAA-AGAAAC
1 AAAAGAAGAAATAGAAAC
11342382 AAAAGAAGAAATAGAAAC
1 AAAAGAAGAAATAGAAAC
11342400 A
1 A
11342401 GAATAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAGAAGAAATAGAAAC
Found at i:11346926 original size:18 final size:17
Alignment explanation
Indices: 11346900--11346938 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11346890 ATTTTCCTTC
11346900 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
11346917 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
11346935 CACA
1 CACA
11346939 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:11358527 original size:28 final size:28
Alignment explanation
Indices: 11358495--11358579 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
11358485 TTTTTTTGTT
11358495 TAAACATCTACGATCATGTATATTTCCC
1 TAAACATCTACGATCATGTATATTTCCC
* * * ***
11358523 TAAACA-CTA-G--C-TTTTTTTTTGTT
1 TAAACATCTACGATCATGTATATTTCCC
*
11358546 TAAACATCCACGATCATGTATATTTCCC
1 TAAACATCTACGATCATGTATATTTCCC
11358574 TAAACA
1 TAAACA
11358580 CTAGCTTATT
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
23 12 0.31
24 3 0.08
25 1 0.03
26 1 0.03
27 4 0.10
28 18 0.46
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAACATCTACGATCATGTATATTTCCC
Found at i:11358559 original size:51 final size:51
Alignment explanation
Indices: 11358484--11358586 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
11358474 ATCCTATTCA
*
11358484 TTTTTTTTGTTTAAACATCTACGATCATGTATATTTCCCTAAACACTAGCT
1 TTTTTTTTGTTTAAACATCCACGATCATGTATATTTCCCTAAACACTAGCT
11358535 TTTTTTTTGTTTAAACATCCACGATCATGTATATTTCCCTAAACACTAGCT
1 TTTTTTTTGTTTAAACATCCACGATCATGTATATTTCCCTAAACACTAGCT
11358586 T
1 T
11358587 ATTAAGGCGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (51 bp):
TTTTTTTTGTTTAAACATCCACGATCATGTATATTTCCCTAAACACTAGCT
Found at i:11361120 original size:11 final size:11
Alignment explanation
Indices: 11361104--11361130 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11361094 TGCCTAAACC
11361104 GAAAATTGTAA
1 GAAAATTGTAA
11361115 GAAAATTGTAA
1 GAAAATTGTAA
11361126 GAAAA
1 GAAAA
11361131 AACAAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (11 bp):
GAAAATTGTAA
Found at i:11366964 original size:128 final size:128
Alignment explanation
Indices: 11366810--11367065 Score: 512
Period size: 128 Copynumber: 2.0 Consensus size: 128
11366800 TTCGAATTTT
11366810 AAGGGGTCAAAGTGTAATTTTATTTTTACTAATTTAAAATTTTAAAAATTCTTAAAGAGCTTAGA
1 AAGGGGTCAAAGTGTAATTTTATTTTTACTAATTTAAAATTTTAAAAATTCTTAAAGAGCTTAGA
11366875 TAGCAATTTTTCATTTTAGGAGGGCCGGGCTCATCCATCAATCTTTATCATCTTGAGTTGACA
66 TAGCAATTTTTCATTTTAGGAGGGCCGGGCTCATCCATCAATCTTTATCATCTTGAGTTGACA
11366938 AAGGGGTCAAAGTGTAATTTTATTTTTACTAATTTAAAATTTTAAAAATTCTTAAAGAGCTTAGA
1 AAGGGGTCAAAGTGTAATTTTATTTTTACTAATTTAAAATTTTAAAAATTCTTAAAGAGCTTAGA
11367003 TAGCAATTTTTCATTTTAGGAGGGCCGGGCTCATCCATCAATCTTTATCATCTTGAGTTGACA
66 TAGCAATTTTTCATTTTAGGAGGGCCGGGCTCATCCATCAATCTTTATCATCTTGAGTTGACA
11367066 TATTCATAGA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (128 bp):
AAGGGGTCAAAGTGTAATTTTATTTTTACTAATTTAAAATTTTAAAAATTCTTAAAGAGCTTAGA
TAGCAATTTTTCATTTTAGGAGGGCCGGGCTCATCCATCAATCTTTATCATCTTGAGTTGACA
Found at i:11369003 original size:62 final size:62
Alignment explanation
Indices: 11368930--11369046 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
11368920 CAGAAAAAAC
* * *
11368930 AATAAACTGTTTTAAATA-CTCACCACGTGTCTATCAAGGATCAAAATACATGTCGACTGTCG
1 AATAAACTGTTTTAAATACCT-ACCACGTGCCAATCAAGGAACAAAATACATGTCGACTGTCG
* * *
11368992 AATAAATTGTTTTAAATACCTACTACGTGCCAATCAAGGAACTAAATACATGTCG
1 AATAAACTGTTTTAAATACCTACCACGTGCCAATCAAGGAACAAAATACATGTCG
11369047 TTTTTTAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
62 46 0.96
63 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (62 bp):
AATAAACTGTTTTAAATACCTACCACGTGCCAATCAAGGAACAAAATACATGTCGACTGTCG
Found at i:11369439 original size:17 final size:18
Alignment explanation
Indices: 11369404--11369454 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
11369394 GATTCACCTG
11369404 TTTTAGAAAAAAA-AA-A
1 TTTTAGAAAAAAATAATA
11369420 TTTTA-AAAAAAATAATA
1 TTTTAGAAAAAAATAATA
11369437 TTTTATGAAAAAAATAAT
1 TTTTA-GAAAAAAATAAT
11369455 TTTATTCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.23
16 7 0.23
17 6 0.19
19 11 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
TTTTAGAAAAAAATAATA
Found at i:11369459 original size:17 final size:16
Alignment explanation
Indices: 11369404--11369458 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
11369394 GATTCACCTG
*
11369404 TTTTAGAAAAAAAAAA
1 TTTTAGAAAAAAATAA
11369420 TTTTA-AAAAAAATAATA
1 TTTTAGAAAAAAAT-A-A
11369437 TTTTATGAAAAAAATAA
1 TTTTA-GAAAAAAATAA
11369454 TTTTA
1 TTTTA
11369459 TTCACTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
17 12 0.35
18 1 0.03
19 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (16 bp):
TTTTAGAAAAAAATAA
Found at i:11369601 original size:75 final size:78
Alignment explanation
Indices: 11369490--11369634 Score: 215
Period size: 75 Copynumber: 1.9 Consensus size: 78
11369480 ACAAAACAAG
* *
11369490 TTTTATAAGCAGAAATTATAAATTTTTACAAACAAATTATGTTAA-TTTTT-TTATATAAATATT
1 TTTTATAAACAAAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAAATATT
11369553 ATTTATCTCAAAT
66 ATTTATCTCAAAT
* * * *
11369566 TTTTATAAACAAAAATTAT-TATTTTTACGAACAAATTATTTTAATTTTTTATTATATAATTATT
1 TTTTATAAACAAAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAAATATT
11369630 ATTTA
66 ATTTA
11369635 CCTCTCAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 22 0.36
76 22 0.36
77 17 0.28
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (78 bp):
TTTTATAAACAAAAATTATAAATTTTTACAAACAAATTATGTTAATTTTTTATTATATAAATATT
ATTTATCTCAAAT
Found at i:11369793 original size:22 final size:22
Alignment explanation
Indices: 11369765--11369818 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
11369755 AAAAACAAAT
11369765 AATATATAATAAAAATT-ATATA
1 AATATATAATAAAAATTAAT-TA
** *
11369787 AATATATTTTAAAATTTAATTA
1 AATATATAATAAAAATTAATTA
11369809 AATATA-AATA
1 AATATATAATA
11369819 TATTTATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATATAATAAAAATTAATTA
Found at i:11371439 original size:21 final size:21
Alignment explanation
Indices: 11371415--11371454 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11371405 TCAACAATTT
*
11371415 AATATTGATATTAAAATTAAA
1 AATATTAATATTAAAATTAAA
*
11371436 AATATTAATATTATAATTA
1 AATATTAATATTAAAATTA
11371455 CAAAGAATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AATATTAATATTAAAATTAAA
Found at i:11373981 original size:87 final size:87
Alignment explanation
Indices: 11373835--11374228 Score: 375
Period size: 87 Copynumber: 4.6 Consensus size: 87
11373825 CGCTTTCTCT
* * *
11373835 TGCCAGTAATAAGGA-TATCAGTTTCCAATACTTTGATCTCCCTCATTGCTGATAGATCCATCTT
1 TGCCAGTAAT-CGGAGTATCAGTTTCCAATACTTCGATCTCCCTCATTGCTGATATATCCATCTT
11373899 -TCCAGTGACACAAAGGTTATCAG
65 AT-CAGTGACACAAAGGTTATCAG
* *
11373922 TGCCAGTAATCGGAGTATCAGTTTCCAATACTTCAATCTCTCTCATTGCTGATATATCCATCTTA
1 TGCCAGTAATCGGAGTATCAGTTTCCAATACTTCGATCTCCCTCATTGCTGATATATCCATCTTA
*
11373987 TCAGTGACACAAAGGTTATCTG
66 TCAGTGACACAAAGGTTATCAG
* * * * *
11374009 TGCCAGTAATCAGAGCATCAGTTTCCCATTCTTCGATCTCCCCCA---CTG-------C-T-TTA
1 TGCCAGTAATCGGAGTATCAGTTTCCAATACTTCGATCTCCCTCATTGCTGATATATCCATCTTA
*
11374062 TCAGTGACACAAAGATTATCAG
66 TCAGTGACACAAAGGTTATCAG
* * * * * *
11374084 TGCCAGTAATTGGGGCATAAGTTTCTAATACTTTGATCTCCCTCATTGCTGACAGATCCATATCC
1 TGCCAGTAATCGGAGTATCAGTTTCCAATACTTCGATCTCCCTCATTGCT----GAT--ATATCC
* * *
11374149 ATCTTATCAGTGACATAAAGGTCACCAG
60 ATCTTATCAGTGACACAAAGGTTATCAG
* * * * * *
11374177 TGCCAGCAACCGGAGTATCACTTTCCAATCCTTCGATCTCCATCACTGCTGA
1 TGCCAGTAATCGGAGTATCAGTTTCCAATACTTCGATCTCCCTCATTGCTGA
11374229 GAGATCCTTA
Statistics
Matches: 247, Mismatches: 40, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
75 59 0.24
76 1 0.00
77 1 0.00
78 2 0.01
82 1 0.00
84 3 0.01
86 3 0.01
87 113 0.46
88 1 0.00
89 2 0.01
91 1 0.00
92 1 0.00
93 59 0.24
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (87 bp):
TGCCAGTAATCGGAGTATCAGTTTCCAATACTTCGATCTCCCTCATTGCTGATATATCCATCTTA
TCAGTGACACAAAGGTTATCAG
Found at i:11374122 original size:75 final size:75
Alignment explanation
Indices: 11373984--11374125 Score: 194
Period size: 75 Copynumber: 1.9 Consensus size: 75
11373974 TATATCCATC
* * * * *
11373984 TTATCAGTGACACAAAGGTTATCTGTGCCAGTAATCAGAGCATCAGTTTCCCATTCTTCGATCTC
1 TTATCAGTGACACAAAGATTATCAGTGCCAGTAATCAGAGCATAAGTTTCCAATACTTCGATCTC
11374049 CCCCACTGCT
66 CCCCACTGCT
** * * *
11374059 TTATCAGTGACACAAAGATTATCAGTGCCAGTAATTGGGGCATAAGTTTCTAATACTTTGATCTC
1 TTATCAGTGACACAAAGATTATCAGTGCCAGTAATCAGAGCATAAGTTTCCAATACTTCGATCTC
11374124 CC
66 CC
11374126 TCATTGCTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (75 bp):
TTATCAGTGACACAAAGATTATCAGTGCCAGTAATCAGAGCATAAGTTTCCAATACTTCGATCTC
CCCCACTGCT
Found at i:11375021 original size:39 final size:39
Alignment explanation
Indices: 11374978--11375062 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
11374968 TTCGCAGCTA
*
11374978 CAAGCTTTGGTTTCTTTT-CCTTGACTAGCTTTGGAGTTG
1 CAAGCTTTGGTTTCTTTTCCCTT-ACTAGATTTGGAGTTG
* *
11375017 CAAGCCTTGGTTTCTTTTCCCTTACTTGATTTGGAGTTG
1 CAAGCTTTGGTTTCTTTTCCCTTACTAGATTTGGAGTTG
11375056 CAAGCTT
1 CAAGCTT
11375063 CAGTGTGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.90
40 4 0.10
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (39 bp):
CAAGCTTTGGTTTCTTTTCCCTTACTAGATTTGGAGTTG
Found at i:11375846 original size:213 final size:213
Alignment explanation
Indices: 11375587--11376023 Score: 766
Period size: 213 Copynumber: 2.0 Consensus size: 213
11375577 CCCATTGAAA
11375587 CCATCTTCTTTTTGCTTGCTTGTGACGGTGCAGACTGTGGACTCCAAGCATAAGTCTTCGATTCC
1 CCAT-TTCTTTTTGCTTGCTTGTGACGGTGCAGACTGTGGACTCCAAGCATAAGTCTTCGATTCC
* * *
11375652 ATCAAAATTTCTGCCTGGACAAAAGTTCTGTTCCTTGCCTTCACCAGCACTCAACAAATCCGCCG
65 ATCAAAATTTCTGCCTGGACAAAAATTCTGTTCCTTGCCTTCACCAGCACTCAACAAATCCCCCA
11375717 TGCCTAGAGAATCCAAGCTCATCTTCAAATCTAATTTGCCTACAAATCCCAAACTTATGCACTCT
130 TGCCTAGAGAATCCAAGCTCATCTTCAAATCTAATTTGCCTACAAATCCCAAACTTATGCACTCT
11375782 GTTCTGTTGGAACTTTGCT
195 GTTCTGTTGGAACTTTGCT
11375801 CCATTTCTTTTTGCTTGCTTGTGACGGTGCAGACTGTGGACTCCAAGCATAAGTCTTCGATTCCA
1 CCATTTCTTTTTGCTTGCTTGTGACGGTGCAGACTGTGGACTCCAAGCATAAGTCTTCGATTCCA
*
11375866 TCAAAATTTCTGCCTGGACAAAAATTCTGTTCCTTGCTTTCACCAGCACTCAACAAATCCCCCAT
66 TCAAAATTTCTGCCTGGACAAAAATTCTGTTCCTTGCCTTCACCAGCACTCAACAAATCCCCCAT
* *** **
11375931 GCCTAGAGAATCCAAGCTCATCTTCAAATCTATTTTGCCTACCGGTCCCAAACTTATGCTGTCTG
131 GCCTAGAGAATCCAAGCTCATCTTCAAATCTAATTTGCCTACAAATCCCAAACTTATGCACTCTG
11375996 TTCTGTTGGAACTTTGCT
196 TTCTGTTGGAACTTTGCT
*
11376014 CCTTTTCTTT
1 CCATTTCTTT
11376024 GTCTGACAAT
Statistics
Matches: 212, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
213 208 0.98
214 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (213 bp):
CCATTTCTTTTTGCTTGCTTGTGACGGTGCAGACTGTGGACTCCAAGCATAAGTCTTCGATTCCA
TCAAAATTTCTGCCTGGACAAAAATTCTGTTCCTTGCCTTCACCAGCACTCAACAAATCCCCCAT
GCCTAGAGAATCCAAGCTCATCTTCAAATCTAATTTGCCTACAAATCCCAAACTTATGCACTCTG
TTCTGTTGGAACTTTGCT
Found at i:11385465 original size:24 final size:24
Alignment explanation
Indices: 11385438--11385486 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
11385428 GCAGCTTCAG
11385438 CAGGCCTCTTCTTGCTTGACTCGA
1 CAGGCCTCTTCTTGCTTGACTCGA
*
11385462 CAGGTCTCTTCTTGCTTGACTCGA
1 CAGGCCTCTTCTTGCTTGACTCGA
11385486 C
1 C
11385487 CTAGAAGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (24 bp):
CAGGCCTCTTCTTGCTTGACTCGA
Found at i:11385748 original size:18 final size:18
Alignment explanation
Indices: 11385723--11385769 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
11385713 TGAAAAGAAA
*
11385723 CCTCATCAGACTCATCAT
1 CCTCATCAGAATCATCAT
* *
11385741 CGTCATCAGAATCATCTT
1 CCTCATCAGAATCATCAT
11385759 CCTCATCAGAA
1 CCTCATCAGAA
11385770 CCACTCTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.28
Consensus pattern (18 bp):
CCTCATCAGAATCATCAT
Found at i:11397500 original size:17 final size:17
Alignment explanation
Indices: 11397478--11397536 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
11397468 GAAAGTTTTA
11397478 AAAATATTAAAAAAATG
1 AAAATATTAAAAAAATG
* ** *
11397495 AAAATATATAACAATTTA
1 AAAATAT-TAAAAAAATG
*
11397513 AAAATAATAAAAAAATG
1 AAAATATTAAAAAAATG
11397530 AAAATAT
1 AAAATAT
11397537 ATAACAATTT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAATATTAAAAAAATG
Found at i:11397513 original size:35 final size:35
Alignment explanation
Indices: 11397474--11397561 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
11397464 GACTGAAAGT
*
11397474 TTTAAAAATATTAAAAAAATGAAAATATATAACAA
1 TTTAAAAATAATAAAAAAATGAAAATATATAACAA
11397509 TTTAAAAATAATAAAAAAATGAAAATATATAACAA
1 TTTAAAAATAATAAAAAAATGAAAATATATAACAA
*
11397544 TTTAAAAACAATAAAAAA
1 TTTAAAAATAATAAAAAA
11397562 TAGGAGGATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.26
Consensus pattern (35 bp):
TTTAAAAATAATAAAAAAATGAAAATATATAACAA
Found at i:11397516 original size:18 final size:18
Alignment explanation
Indices: 11397495--11397551 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
11397485 TAAAAAAATG
11397495 AAAATATATAACAATTTA
1 AAAATATATAACAATTTA
* ** *
11397513 AAAATA-ATAAAAAAATG
1 AAAATATATAACAATTTA
11397530 AAAATATATAACAATTTA
1 AAAATATATAACAATTTA
11397548 AAAA
1 AAAA
11397552 CAATAAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATATATAACAATTTA
Found at i:11397550 original size:17 final size:17
Alignment explanation
Indices: 11397495--11397550 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
11397485 TAAAAAAATG
11397495 AAAATATATAACAATTT
1 AAAATATATAACAATTT
* * *
11397512 AAAA-ATAATAAAAAAATG
1 AAAATAT-AT-AACAATTT
11397530 AAAATATATAACAATTT
1 AAAATATATAACAATTT
11397547 AAAA
1 AAAA
11397551 ACAATAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.50
18 11 0.37
19 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATATATAACAATTT
Found at i:11422716 original size:6 final size:6
Alignment explanation
Indices: 11422702--11422732 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11422692 TGAAGGATGA
11422702 TTTTT- TTTTTC TTTTTC TTTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
11422733 GCTTAATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:11431219 original size:24 final size:23
Alignment explanation
Indices: 11431187--11431232 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11431177 AAATTAAAAT
* *
11431187 AAATCATTAATTATTATATTTTTA
1 AAATAATT-ATTATTAAATTTTTA
*
11431211 AAATAATTATTTTTAAATTTTT
1 AAATAATTATTATTAAATTTTT
11431233 TGAACTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATAATTATTATTAAATTTTTA
Found at i:11451256 original size:2 final size:2
Alignment explanation
Indices: 11451213--11451242 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11451203 CTGGAAAGCA
11451213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11451243 GCTTTATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11451440 original size:231 final size:231
Alignment explanation
Indices: 11451037--11451499 Score: 908
Period size: 231 Copynumber: 2.0 Consensus size: 231
11451027 TTATAATAAG
11451037 GGCATGGTTTCATCTTCCCATTCTGAGGCCAACTTTCTTGTTCATTGCCTTCTCTGGTGATCTTC
1 GGCATGGTTTCATCTTCCCATTCTGAGGCCAACTTTCTTGTTCATTGCCTTCTCTGGTGATCTTC
11451102 ACATGACATATCAAAACCTGCCTAAATTTTAATTCAAAATCATGCATTGCGCCATTAATTAGATG
66 ACATGACATATCAAAACCTGCCTAAATTTTAATTCAAAATCATGCATTGCGCCATTAATTAGATG
11451167 GAACTTCTACTTGGCATCTTCCCTTTTTCAATAACACTGGAAAGCAATATATATATATATATATA
131 GAACTTCTACTTGGCATCTTCCCTTTTTCAATAACACTGGAAAGCAATATATATATATATATATA
* *
11451232 TATATATATATGCTTTATCTATATAACTAATGGGGA
196 TATATATATATGCTTTAGCTAAATAACTAATGGGGA
11451268 GGCATGGTTTCATCTTCCCATTCTGAGGCCAACTTTCTTGTTCATTGCCTTCTCTGGTGATCTTC
1 GGCATGGTTTCATCTTCCCATTCTGAGGCCAACTTTCTTGTTCATTGCCTTCTCTGGTGATCTTC
11451333 ACATGACATATCAAAACCTGCCTAAATTTTAATTCAAAATCATGCATTGCGCCATTAATTAGATG
66 ACATGACATATCAAAACCTGCCTAAATTTTAATTCAAAATCATGCATTGCGCCATTAATTAGATG
11451398 GAACTTCTACTTGGCATCTTCCCTTTTTCAATAACACTGGAAAGCAATATATATATATATATATA
131 GAACTTCTACTTGGCATCTTCCCTTTTTCAATAACACTGGAAAGCAATATATATATATATATATA
11451463 TATATATATATGCTTTAGCTAAATAACTAATGGGGA
196 TATATATATATGCTTTAGCTAAATAACTAATGGGGA
11451499 G
1 G
11451500 AAAGTAGAAT
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
231 230 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (231 bp):
GGCATGGTTTCATCTTCCCATTCTGAGGCCAACTTTCTTGTTCATTGCCTTCTCTGGTGATCTTC
ACATGACATATCAAAACCTGCCTAAATTTTAATTCAAAATCATGCATTGCGCCATTAATTAGATG
GAACTTCTACTTGGCATCTTCCCTTTTTCAATAACACTGGAAAGCAATATATATATATATATATA
TATATATATATGCTTTAGCTAAATAACTAATGGGGA
Found at i:11451451 original size:2 final size:2
Alignment explanation
Indices: 11451444--11451473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11451434 CTGGAAAGCA
11451444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11451474 GCTTTAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11457597 original size:28 final size:27
Alignment explanation
Indices: 11457537--11457597 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
11457527 TTATATTTTC
*
11457537 TTATAAAATTTATTAAAAATTAAAATTA
1 TTAT-AAATTTATAAAAAATTAAAATTA
*
11457565 ATATAAATTTATAAAAAACTTATAAA-TA
1 TTATAAATTTATAAAAAA-TTA-AAATTA
11457593 TTATA
1 TTATA
11457598 CAAATACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 13 0.46
28 12 0.43
29 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TTATAAATTTATAAAAAATTAAAATTA
Found at i:11457611 original size:21 final size:19
Alignment explanation
Indices: 11457567--11457613 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
11457557 TAAAATTAAT
*
11457567 ATAAATTTATAAAAAACTT
1 ATAAATTTATAAAAAACTA
*
11457586 ATAAATATTATACAAATACTA
1 ATAAAT-TTATA-AAAAACTA
11457607 ATAAATT
1 ATAAATT
11457614 AGTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATTTATAAAAAACTA
Found at i:11458480 original size:9 final size:9
Alignment explanation
Indices: 11458393--11458623 Score: 58
Period size: 9 Copynumber: 23.9 Consensus size: 9
11458383 GAGGAACCAC
11458393 ATTTTTAT-
1 ATTTTTATA
11458401 ATATTTT-TA
1 AT-TTTTATA
*
11458410 ATATTTTAGA
1 AT-TTTTATA
*
11458420 ACTTTTATAGA
1 A-TTTT-TATA
11458431 ATTTTTATA
1 ATTTTTATA
11458440 ATTTTTATA
1 ATTTTTATA
*
11458449 AGTATTTATGA
1 A-TTTTTAT-A
*
11458460 TTTTTTTAATA
1 -ATTTTT-ATA
11458471 ATTTTTATA
1 ATTTTTATA
* *
11458480 AGTTTATAGGA
1 A-TTTTTA-TA
* *
11458491 AGTTTTAAA
1 ATTTTTATA
11458500 TATTTTTAGTA
1 -ATTTTTA-TA
* *
11458511 TGTTTTTATT
1 -ATTTTTATA
11458521 A-TTTTATA
1 ATTTTTATA
*
11458529 ATTTATTA-G
1 ATTT-TTATA
* *
11458538 ATTTTTTTT
1 ATTTTTATA
*
11458547 GTTTTTACAATA
1 ATTTTT---ATA
11458559 AGTTTTTATGA
1 A-TTTTTAT-A
*
11458570 TTTTTTTATA
1 -ATTTTTATA
* *
11458580 AATTTTAAA
1 ATTTTTATA
*
11458589 ATTTATATA
1 ATTTTTATA
*
11458598 ATTTTTTTA
1 ATTTTTATA
*
11458607 AATTTTA-A
1 ATTTTTATA
11458615 CATTTTTAT
1 -ATTTTTAT
11458624 GAGAAAATAT
Statistics
Matches: 163, Mismatches: 36, Indels: 46
0.67 0.15 0.19
Matches are distributed among these distances:
8 13 0.08
9 70 0.43
10 42 0.26
11 30 0.18
12 3 0.02
13 5 0.03
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:11458505 original size:30 final size:29
Alignment explanation
Indices: 11458423--11458507 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 29
11458413 TTTTAGAACT
*
11458423 TTTATAGAATTTTTATA-ATTTTTATAAG
1 TTTATAGAATTTTTAAATATTTTTATAAG
* *
11458451 TATT-TATGATTTTTTTAATAATTTTTATAAG
1 T-TTATA-GAATTTTTAAAT-ATTTTTATAAG
*
11458482 TTTATAGGAAGTTTTAAATATTTTTA
1 TTTATA-GAATTTTTAAATATTTTTA
11458508 GTATGTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
28 3 0.07
29 10 0.22
30 9 0.20
31 23 0.51
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (29 bp):
TTTATAGAATTTTTAAATATTTTTATAAG
Done.