Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 190 of 210
Found at i:55946990 original size:72 final size:72
Alignment explanation
Indices: 55946873--55947015 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
55946863 CTCAGATTTA
*
55946873 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAA
55946938 CTTGAGG
66 CTTGAGG
* *
55946945 AAAAAAGGGATCAT-CTCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATTGTTTAAA
1 AAAAAAGGGATCATGC-CCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAA
55947009 ACTTGAG
65 ACTTGAG
55947016 TTTGAAAAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 1 0.01
72 66 0.99
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (72 bp):
AAAAAAGGGATCATGCCCAGTAAGTTAGGACACAATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGAGG
Found at i:55947458 original size:10 final size:10
Alignment explanation
Indices: 55947429--55947459 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
55947419 ATATGTAAGT
*
55947429 ATGTATATAT
1 ATGTATATAA
55947439 ATGTATATAA
1 ATGTATATAA
55947449 ATGTATATAA
1 ATGTATATAA
55947459 A
1 A
55947460 AATTATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (10 bp):
ATGTATATAA
Found at i:55947527 original size:33 final size:35
Alignment explanation
Indices: 55947483--55947550 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
55947473 AAATAATATA
55947483 AAAATATGTGTA-TATATATATATT-TACAAAAGTT
1 AAAATATGTGTACTATATATATATTATA-AAAAGTT
55947517 AAAA-ATGTGTACGTATATATATATTATAAAAAGT
1 AAAATATGTGTAC-TATATATATATTATAAAAAGT
55947551 ATGTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 7 0.23
34 4 0.13
35 18 0.58
36 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (35 bp):
AAAATATGTGTACTATATATATATTATAAAAAGTT
Found at i:55947557 original size:20 final size:18
Alignment explanation
Indices: 55947532--55947571 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
55947522 TGTGTACGTA
55947532 TATATATATTATAAAAAG
1 TATATATATTATAAAAAG
*
55947550 TATGTATATTATAAAAA-
1 TATATATATTATAAAAAG
55947567 TATAT
1 TATAT
55947572 GCATGTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TATATATATTATAAAAAG
Found at i:55948828 original size:21 final size:21
Alignment explanation
Indices: 55948804--55948861 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
55948794 CTACACGCTT
*
55948804 ATGTGAAGGCCACACATGCCC
1 ATGTGAAGGCCACACAGGCCC
55948825 ATGTGAAGGCCACACAGGCCC
1 ATGTGAAGGCCACACAGGCCC
* *
55948846 TTATGAAGGCCACACA
1 ATGTGAAGGCCACACA
55948862 CACTCGTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (21 bp):
ATGTGAAGGCCACACAGGCCC
Found at i:55956842 original size:11 final size:10
Alignment explanation
Indices: 55956822--55956865 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
55956812 TAATAACATA
*
55956822 AAATATATTT
1 AAATAAATTT
55956832 AAATCAAATTT
1 AAAT-AAATTT
55956843 AAAATAAATTT
1 -AAATAAATTT
55956854 AAATAAGATTT
1 AAATAA-ATTT
55956865 A
1 A
55956866 CATATGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 10 0.33
11 16 0.53
12 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAATAAATTT
Found at i:55956846 original size:22 final size:22
Alignment explanation
Indices: 55956820--55956865 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
55956810 AATAATAACA
*
55956820 TAAAATATATTTAAATCAA-ATT
1 TAAAATAAATTTAAAT-AAGATT
55956842 TAAAATAAATTTAAATAAGATT
1 TAAAATAAATTTAAATAAGATT
55956864 TA
1 TA
55956866 CATATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAAATAAATTTAAATAAGATT
Found at i:55962074 original size:31 final size:31
Alignment explanation
Indices: 55962039--55962102 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
55962029 AAATAATCAC
*
55962039 TGAACTATTCAAAAGTTTCCATTTAAGTCAT
1 TGAACCATTCAAAAGTTTCCATTTAAGTCAT
** ** *
55962070 TGAACCATTTGAAAGTTTTTATTTAAGTTAT
1 TGAACCATTCAAAAGTTTCCATTTAAGTCAT
55962101 TG
1 TG
55962103 GGCTGTTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (31 bp):
TGAACCATTCAAAAGTTTCCATTTAAGTCAT
Found at i:55975944 original size:9 final size:9
Alignment explanation
Indices: 55975930--55975966 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55975920 TATAGTTTGA
55975930 TATTCGAAT
1 TATTCGAAT
55975939 TATTCGAAT
1 TATTCGAAT
*
55975948 TATTCGAGT
1 TATTCGAAT
55975957 TATTCGAAT
1 TATTCGAAT
55975966 T
1 T
55975967 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55976036 original size:9 final size:9
Alignment explanation
Indices: 55976019--55976058 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
55976009 TCGAGTTGAT
55976019 TCGAATAAC
1 TCGAATAAC
*
55976028 TCGATTAAC
1 TCGAATAAC
55976037 TCGAATAAC
1 TCGAATAAC
55976046 TCGAATAAC
1 TCGAATAAC
55976055 TCGA
1 TCGA
55976059 TTCGTTTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:55976415 original size:27 final size:27
Alignment explanation
Indices: 55976377--55976430 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
55976367 GGATCGGATG
55976377 AATCGGTAAAAGAATCGGTTTTCTACA
1 AATCGGTAAAAGAATCGGTTTTCTACA
*
55976404 AATCGGTAAAAGAATCGGTTTTTTACA
1 AATCGGTAAAAGAATCGGTTTTCTACA
55976431 TTTTGGGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (27 bp):
AATCGGTAAAAGAATCGGTTTTCTACA
Found at i:55980707 original size:21 final size:21
Alignment explanation
Indices: 55980679--55980736 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
55980669 GCTTCTGTTT
*
55980679 AACCCTTATGGGTTTTCGTTA
1 AACCCTTATGGGTTTCCGTTA
* * * * *
55980700 AACTCTTACGAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTA
55980721 AACCCTTATGGGTTTC
1 AACCCTTATGGGTTTC
55980737 TGTTTATCTC
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTA
Found at i:55980713 original size:42 final size:42
Alignment explanation
Indices: 55980607--55980735 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 42
55980597 TCGTGTTTAC
* * * * * * *
55980607 TTTTCGTTTACCTCTCACGAACTTCTGTTTAACTCATATGAG
1 TTTTCGTTAAACTCTTACGAGCTTCTGTTTAACCCTTATGGG
* * * *
55980649 TTTCCGTTCAGCTC-TATTGAGCTTCTGTTTAACCCTTATGGG
1 TTTTCGTTAAACTCTTA-CGAGCTTCTGTTTAACCCTTATGGG
* *
55980691 TTTTCGTTAAACTCTTACGAGCTTCCGTTCAACCCTTATGGG
1 TTTTCGTTAAACTCTTACGAGCTTCTGTTTAACCCTTATGGG
55980733 TTT
1 TTT
55980736 CTGTTTATCT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 1 0.01
42 67 0.96
43 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (42 bp):
TTTTCGTTAAACTCTTACGAGCTTCTGTTTAACCCTTATGGG
Found at i:55980755 original size:42 final size:42
Alignment explanation
Indices: 55980666--55980757 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
55980656 TCAGCTCTAT
* * *
55980666 TGAGCTTCTGTTTAACCCTTATGGGTTTTCGTTAAACTCTTA
1 TGAGCTTCCGTTCAACCCTTATGGGTTTTCGTTAAACTCTCA
* * *
55980708 CGAGCTTCCGTTCAACCCTTATGGG-TTTCTGTTTATCTCTCA
1 TGAGCTTCCGTTCAACCCTTATGGGTTTTC-GTTAAACTCTCA
55980750 TGAGCTTC
1 TGAGCTTC
55980758 TATTCAGCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.42
Consensus pattern (42 bp):
TGAGCTTCCGTTCAACCCTTATGGGTTTTCGTTAAACTCTCA
Found at i:55983044 original size:51 final size:52
Alignment explanation
Indices: 55982967--55983094 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 52
55982957 TGGATACCCG
* *
55982967 GTGGCCTGCACATAGTACCACCCTTGT-AGCCAAAGCTA-CCTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCCTTCTTCACAAA
* *
55983018 GTGGCCTTCACATAGTACCACACTTGTGATCAAAGCTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCCTTCTTCACAAA
*
55983070 GTGGCATTCACATAGTACCACACTT
1 GTGGCCTTCACATAGTACCACACTT
55983095 AAGTCACTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 33 0.47
52 37 0.53
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCCTTCTTCACAAA
Found at i:55987357 original size:32 final size:32
Alignment explanation
Indices: 55987320--55987384 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
55987310 CTACCTCTGC
*
55987320 TGGCAGTATTACTCGGTCTAACACTCTGAAAT
1 TGGCAGTATTACCCGGTCTAACACTCTGAAAT
55987352 TGGCAGTATTACCCGGTCTAACACTCTGAAAT
1 TGGCAGTATTACCCGGTCTAACACTCTGAAAT
55987384 T
1 T
55987385 TTTCTTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (32 bp):
TGGCAGTATTACCCGGTCTAACACTCTGAAAT
Found at i:55988915 original size:45 final size:46
Alignment explanation
Indices: 55988861--55988971 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
55988851 ATCACTTGTC
*
55988861 CTTGATCAGATAAGTGTAGC-TAGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCACTTTACCA
*
55988906 CTTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCACTTTACCA
55988952 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
55988972 CACTTATCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 20 0.32
46 43 0.68
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTTAAGCTACCACTTATCACTTTACCA
Found at i:55988954 original size:46 final size:45
Alignment explanation
Indices: 55988848--55989118 Score: 216
Period size: 37 Copynumber: 6.6 Consensus size: 45
55988838 CATATGACCT
* *
55988848 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
55988891 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTTAAGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC-TAAGCTACCA
55988937 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* **
55988974 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* **
55989011 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* ** *
55989048 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
55989094 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTATCACTTGATCAGA
55989119 AGTACTCAAA
Statistics
Matches: 206, Mismatches: 9, Indels: 23
0.87 0.04 0.10
Matches are distributed among these distances:
37 101 0.49
39 2 0.01
40 3 0.01
41 2 0.01
43 10 0.05
44 5 0.02
45 20 0.10
46 63 0.31
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (45 bp):
CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:55988975 original size:37 final size:37
Alignment explanation
Indices: 55988933--55989080 Score: 260
Period size: 37 Copynumber: 4.0 Consensus size: 37
55988923 AGCTTAAGCT
* **
55988933 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
55988970 GCCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
55989007 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
55989044 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
55989081 GCTAAAACTA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:55990339 original size:11 final size:11
Alignment explanation
Indices: 55990323--55990354 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
55990313 TTCCTAACTT
55990323 CACCATTCCGA
1 CACCATTCCGA
55990334 CACCATTCCGA
1 CACCATTCCGA
55990345 CACCATTCCG
1 CACCATTCCG
55990355 TTTGTCAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.47, G:0.09, T:0.19
Consensus pattern (11 bp):
CACCATTCCGA
Found at i:56008525 original size:23 final size:25
Alignment explanation
Indices: 56008513--56008564 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
56008503 AAGTTCAAGT
56008513 GAGCC-ATATCAGGAAGCTCACAAA
1 GAGCCTATATCAGGAAGCTCACAAA
* *
56008537 GAGCCTATATCAGGACGCTCATAAA
1 GAGCCTATATCAGGAAGCTCACAAA
56008562 GAG
1 GAG
56008565 TTGCGGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (25 bp):
GAGCCTATATCAGGAAGCTCACAAA
Found at i:56018032 original size:14 final size:14
Alignment explanation
Indices: 56017994--56018033 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
56017984 ATCTATGAGC
56017994 ATCTCTTTCTTT-T
1 ATCTCTTTCTTTAT
56018007 AT-TCTATTCTTTAT
1 ATCTCT-TTCTTTAT
56018021 ATCTCTTTCTTTA
1 ATCTCTTTCTTTA
56018034 ACATTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 10 0.42
15 3 0.12
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (14 bp):
ATCTCTTTCTTTAT
Found at i:56020287 original size:33 final size:33
Alignment explanation
Indices: 56020236--56020299 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
56020226 ACAAGCAATG
56020236 ACAGTCTAGGACTGAGCCCTATT-CAGTAACAGT
1 ACAGTCTAGGACTGAGCCC-ATTACAGTAACAGT
* * *
56020269 ACAGTGTAGGCCTTAGCCCATTACAGTAACA
1 ACAGTCTAGGACTGAGCCCATTACAGTAACA
56020300 ATGTGGGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (33 bp):
ACAGTCTAGGACTGAGCCCATTACAGTAACAGT
Found at i:56020310 original size:28 final size:28
Alignment explanation
Indices: 56020264--56020325 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
56020254 CTATTCAGTA
* *
56020264 ACAGT-ACAGTGTAGGCCTTAGCCCATT
1 ACAGTAACAATGTAGGCCTTAGCCCAAT
*
56020291 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTAGGCCTTAGCCCAAT
56020319 ACAGTAA
1 ACAGTAA
56020326 TGGTACGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (28 bp):
ACAGTAACAATGTAGGCCTTAGCCCAAT
Found at i:56020722 original size:27 final size:27
Alignment explanation
Indices: 56020692--56020912 Score: 307
Period size: 27 Copynumber: 8.1 Consensus size: 27
56020682 CATAACAGTA
* *
56020692 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
* *
56020719 ATTTTACCCTATGAGGGTAATTCGGTC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
*
56020746 ATTTTACCCTGTGAGGGTAATTCGGTC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
* *
56020773 ATTTTACCATGTGGGGGTGATTCGGTC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
* *
56020800 ATTTTACCCTGTGGGGGTGATTCGATC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
* *
56020827 ATTTTACCCTCTGGGGGTAATTCGATC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
*
56020854 ATTTTACCCTGTGGGAGGTAATTCAGTC
1 ATTTTACCCTGTGGG-GGTAATTCGGTC
* *
56020882 ATTTTATCCGGTGGGGGTAATTCGGTC
1 ATTTTACCCTGTGGGGGTAATTCGGTC
56020909 ATTT
1 ATTT
56020913 ATTGATCTCT
Statistics
Matches: 177, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
27 154 0.87
28 23 0.13
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (27 bp):
ATTTTACCCTGTGGGGGTAATTCGGTC
Found at i:56036168 original size:3 final size:3
Alignment explanation
Indices: 56036160--56036193 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56036150 TAATCTCCCT
56036160 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
56036194 GATGATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:56036418 original size:36 final size:38
Alignment explanation
Indices: 56036378--56036450 Score: 107
Period size: 36 Copynumber: 2.0 Consensus size: 38
56036368 CGAATATAAT
56036378 AAATATATTTTTTA-TTTTTTA-TTTTAAAAT-ATTTTA
1 AAATA-ATTTTTTATTTTTTTATTTTTAAAATAATTTTA
*
56036414 AAATACTTTTTTATTTTTTTATTTTTAAAATAATTTT
1 AAATAATTTTTTATTTTTTTATTTTTAAAATAATTTT
56036451 TTGTGTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
35 7 0.21
36 12 0.36
37 9 0.27
38 5 0.15
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (38 bp):
AAATAATTTTTTATTTTTTTATTTTTAAAATAATTTTA
Found at i:56036429 original size:28 final size:27
Alignment explanation
Indices: 56036391--56036452 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
56036381 TATATTTTTT
56036391 ATTTTTTATTTTAAAATATTTTAAAATA
1 ATTTTTTATTTTAAAAT-TTTTAAAATA
* ***
56036419 CTTTTTTATTTTTTTATTTTTAAAATA
1 ATTTTTTATTTTAAAATTTTTAAAATA
56036446 ATTTTTT
1 ATTTTTT
56036453 GTGTTTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTTTATTTTAAAATTTTTAAAATA
Found at i:56036749 original size:33 final size:33
Alignment explanation
Indices: 56036711--56036815 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
56036701 AAATTGTCAG
*
56036711 ATAATTACAGCTTAGATACATTGTTTTCGTATT
1 ATAATTACAGCTTACATACATTGTTTTCGTATT
*
56036744 ATAATTGCAGCTTACATACATTGTTTTCGTATT
1 ATAATTACAGCTTACATACATTGTTTTCGTATT
* *
56036777 ATAATTACAGCTTATATACATTGTTTTCATATT
1 ATAATTACAGCTTACATACATTGTTTTCGTATT
56036810 ATAATT
1 ATAATT
56036816 TTTTTTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (33 bp):
ATAATTACAGCTTACATACATTGTTTTCGTATT
Found at i:56039993 original size:5 final size:5
Alignment explanation
Indices: 56039983--56040007 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56039973 TAGTCTTTTC
56039983 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
56040008 CTTTTTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:56040013 original size:15 final size:15
Alignment explanation
Indices: 56039976--56040013 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
56039966 ATACTTCTAG
56039976 TCTTTTCTATTTTATT
1 TCTTTT-TATTTTATT
56039992 T-TATTTTATTTTATT
1 TCT-TTTTATTTTATT
56040007 TCTTTTT
1 TCTTTTT
56040014 GTAACAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (15 bp):
TCTTTTTATTTTATT
Found at i:56046712 original size:22 final size:22
Alignment explanation
Indices: 56046684--56046745 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
56046674 CGTAGCTTAC
56046684 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
56046706 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * *
56046728 ACGAACTAAACCCTCATG
1 ACGTACTAAGCTCTCATG
56046746 GAAATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:56047012 original size:20 final size:23
Alignment explanation
Indices: 56046967--56047015 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
56046957 TAATTATATT
56046967 AATTTTTAATAATATAAAGTGATG
1 AATTTTTAATAATATAAAG-GATG
56046991 AATTTTTAATAA-A-AAA-GATG
1 AATTTTTAATAATATAAAGGATG
56047011 AATTT
1 AATTT
56047016 ATTCTTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
22 3 0.12
23 1 0.04
24 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (23 bp):
AATTTTTAATAATATAAAGGATG
Found at i:56050221 original size:15 final size:15
Alignment explanation
Indices: 56050201--56050230 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56050191 AAGTAGTTTG
56050201 GAGCTAGTTTGTGTT
1 GAGCTAGTTTGTGTT
56050216 GAGCTAGTTTGTGTT
1 GAGCTAGTTTGTGTT
56050231 TGAGGCTTGG
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:0.13, C:0.07, G:0.33, T:0.47
Consensus pattern (15 bp):
GAGCTAGTTTGTGTT
Found at i:56054112 original size:37 final size:36
Alignment explanation
Indices: 56054009--56054132 Score: 205
Period size: 36 Copynumber: 3.4 Consensus size: 36
56053999 TACGTATGAT
**
56054009 CACTTATCAC-TTGTCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTGATCAGATAAGTGTAGC
*
56054044 CACCTATCACTTTGTTTCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTGATCAGATAAGTGTAGC
56054080 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTC-TGATCAGATAAGTGTAGC
56054117 CACTTATCACTTTGTT
1 CACTTATCACTTTGTT
56054133 ANNNNNNNNN
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
35 9 0.11
36 40 0.48
37 34 0.41
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTTTCTGATCAGATAAGTGTAGC
Found at i:56058856 original size:17 final size:18
Alignment explanation
Indices: 56058822--56058856 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
56058812 ACTAAGATTG
*
56058822 TTGCATAGTTATACTATT
1 TTGCATAGTTATAATATT
56058840 TTGCATAG-TATAATATT
1 TTGCATAGTTATAATATT
56058857 AAGTTAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (18 bp):
TTGCATAGTTATAATATT
Found at i:56062751 original size:9 final size:9
Alignment explanation
Indices: 56062737--56062761 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
56062727 AGGAAATTTA
56062737 TTTTAATAT
1 TTTTAATAT
56062746 TTTTAATAT
1 TTTTAATAT
56062755 TTTTAAT
1 TTTTAAT
56062762 GTAATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:56063295 original size:26 final size:28
Alignment explanation
Indices: 56063242--56063304 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
56063232 TTTATACAGG
56063242 TTAAAATATTTCATAAATTTATATACTA-
1 TTAAAA-ATTTCATAAATTTATATACTAT
*
56063270 TTAAAAATTTTA-AAATTTA-ATCACTAT
1 TTAAAAATTTCATAAATTTATAT-ACTAT
56063297 TTAAAAAT
1 TTAAAAAT
56063305 AATAATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.06
26 11 0.34
27 13 0.41
28 6 0.19
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.44
Consensus pattern (28 bp):
TTAAAAATTTCATAAATTTATATACTAT
Found at i:56064931 original size:15 final size:16
Alignment explanation
Indices: 56064908--56064941 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56064898 ATAATGGGCT
*
56064908 AAAACTGAA-TTTTAA
1 AAAAATGAATTTTTAA
56064923 AAAAATGAATTTTTAA
1 AAAAATGAATTTTTAA
56064939 AAA
1 AAA
56064942 TTTCAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
AAAAATGAATTTTTAA
Found at i:56065026 original size:60 final size:60
Alignment explanation
Indices: 56064950--56065063 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
56064940 AATTTCAAAG
* * * **
56064950 TTAGGACTAAATTGAAAGATTTTGTAAATGTTGAGGGCTAAATTTATTGAATTTTTATAA
1 TTAGAACTAAAATGAAAAATTTTGTAAACATTGAGGGCTAAATTTATTGAATTTTTATAA
*
56065010 TTAGAACTAAAATGAAAAATTTTGTAAACATTGAGGGCTAAATTTGTTGAATTT
1 TTAGAACTAAAATGAAAAATTTTGTAAACATTGAGGGCTAAATTTATTGAATTT
56065064 CCTATATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (60 bp):
TTAGAACTAAAATGAAAAATTTTGTAAACATTGAGGGCTAAATTTATTGAATTTTTATAA
Found at i:56065964 original size:7 final size:7
Alignment explanation
Indices: 56065952--56065981 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
56065942 TTCGTATGGG
56065952 ATTTAGA
1 ATTTAGA
56065959 ATTTAGA
1 ATTTAGA
56065966 ATTTAGA
1 ATTTAGA
56065973 ATTTAGA
1 ATTTAGA
56065980 AT
1 AT
56065982 CTAATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (7 bp):
ATTTAGA
Found at i:56071545 original size:46 final size:46
Alignment explanation
Indices: 56071473--56071562 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
56071463 CCTTAGTTTT
* * * *
56071473 GAATAAGTTGTGCTTTAGGAACAACTTATTCGTACGAATAAGTTCC
1 GAATAAGTTGTGCTTAACGAACAACTTACTCGTACAAATAAGTTCC
*
56071519 GAATAAGTTGATGCTTAACG-AGAACTTACTCGTACAAATAAGTT
1 GAATAAGTTG-TGCTTAACGAACAACTTACTCGTACAAATAAGTT
56071563 TCCATGATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 31 0.82
47 7 0.18
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (46 bp):
GAATAAGTTGTGCTTAACGAACAACTTACTCGTACAAATAAGTTCC
Found at i:56078004 original size:2 final size:2
Alignment explanation
Indices: 56077999--56078023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56077989 ATATATATAT
56077999 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
56078024 AATGTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56078804 original size:14 final size:15
Alignment explanation
Indices: 56078785--56078813 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56078775 ATCAAATTTG
56078785 TTATTAA-CTTTTAT
1 TTATTAATCTTTTAT
56078799 TTATTAATCTTTTAT
1 TTATTAATCTTTTAT
56078814 ATACGGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTAATCTTTTAT
Found at i:56083812 original size:21 final size:19
Alignment explanation
Indices: 56083767--56083813 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
56083757 TCAAGTGATT
56083767 TAAAAATTTATAAAAAAGA
1 TAAAAATTTATAAAAAAGA
*
56083786 TTAAAATATATATAAAAATAGA
1 -TAAAA-ATTTATAAAAA-AGA
56083808 -AAAAAT
1 TAAAAAT
56083814 CAATTTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 9 0.38
21 10 0.42
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAAAATTTATAAAAAAGA
Found at i:56085350 original size:32 final size:33
Alignment explanation
Indices: 56085305--56085368 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
56085295 GAATTATAAA
* *
56085305 TTTTACAAGGGTCAAATAGCAGTTTTACCAATC
1 TTTTACAAAGGTCAAATAGCAATTTTACCAATC
*
56085338 TTTTA-AAAGGTCATATAGCAATTTTACCAAT
1 TTTTACAAAGGTCAAATAGCAATTTTACCAAT
56085369 AATGGAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (33 bp):
TTTTACAAAGGTCAAATAGCAATTTTACCAATC
Found at i:56089712 original size:29 final size:29
Alignment explanation
Indices: 56089670--56089728 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
56089660 GTATTGGGAC
56089670 TGATGCATTTGATTATGATTTGCGTTTGT
1 TGATGCATTTGATTATGATTTGCGTTTGT
56089699 TGATGCATTTGATTATGATTTGCGTTTGT
1 TGATGCATTTGATTATGATTTGCGTTTGT
56089728 T
1 T
56089729 CTGTTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.53
Consensus pattern (29 bp):
TGATGCATTTGATTATGATTTGCGTTTGT
Found at i:56092952 original size:15 final size:16
Alignment explanation
Indices: 56092931--56092977 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
56092921 TAATACTAAT
56092931 TAAATAATAATAAGAA
1 TAAATAATAATAAGAA
*
56092947 -AAATAAATAATAATAA
1 TAAAT-AATAATAAGAA
*
56092963 TGAA-AATAATAAGAA
1 TAAATAATAATAAGAA
56092978 GAAGAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 14 0.54
16 10 0.38
17 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAATAATAATAAGAA
Found at i:56092955 original size:19 final size:20
Alignment explanation
Indices: 56092931--56092968 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
56092921 TAATACTAAT
56092931 TAAATAATAATAA-GAAAAA
1 TAAATAATAATAATGAAAAA
56092950 TAAATAATAATAATGAAAA
1 TAAATAATAATAATGAAAA
56092969 TAATAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
TAAATAATAATAATGAAAAA
Found at i:56094238 original size:21 final size:21
Alignment explanation
Indices: 56094214--56094253 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56094204 GCCATGTACT
*
56094214 TCAGTCACACAGACGTGTCTC
1 TCAGCCACACAGACGTGTCTC
* *
56094235 TCAGCCACACGGCCGTGTC
1 TCAGCCACACAGACGTGTC
56094254 CCTTTGCCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.38, G:0.23, T:0.20
Consensus pattern (21 bp):
TCAGCCACACAGACGTGTCTC
Found at i:56097562 original size:24 final size:23
Alignment explanation
Indices: 56097534--56097578 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
56097524 TTTTAATACA
*
56097534 ATCAAATTTGTATTATTAATTTAT
1 ATCAAATTTGTA-TATAAATTTAT
56097558 ATCAAATTTGTATATAAATTT
1 ATCAAATTTGTATATAAATTT
56097579 TGATTTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
ATCAAATTTGTATATAAATTTAT
Found at i:56102019 original size:21 final size:20
Alignment explanation
Indices: 56101986--56102025 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
56101976 TGGATAATTA
*
56101986 ATTAATTAATTATTTTATTTT
1 ATTAAATAATTA-TTTATTTT
*
56102007 ATTAAATAGTTATTTATTT
1 ATTAAATAATTATTTATTT
56102026 AATGGATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTAAATAATTATTTATTTT
Found at i:56104484 original size:18 final size:18
Alignment explanation
Indices: 56104457--56104491 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56104447 ATTATAAACG
*
56104457 TAAATTACAAATTGTATA
1 TAAATAACAAATTGTATA
*
56104475 TAAATAACAATTTGTAT
1 TAAATAACAAATTGTAT
56104492 CAATTGTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
TAAATAACAAATTGTATA
Found at i:56105215 original size:5 final size:5
Alignment explanation
Indices: 56105207--56105231 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56105197 AAAAATAAAA
56105207 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
56105232 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:56111148 original size:6 final size:6
Alignment explanation
Indices: 56111133--56111181 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
56111123 TGAAAACAAA
* * * *
56111133 ATATGT ATATAG ATATAT AGATAT GTATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
56111181 A
1 A
56111182 ATTAGATCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:56111167 original size:4 final size:4
Alignment explanation
Indices: 56111133--56111181 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
56111123 TGAAAACAAA
* * * *
56111133 ATAT GTAT ATAG ATAT ATAG ATAT GTAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
56111181 A
1 A
56111182 ATTAGATCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:56113077 original size:17 final size:17
Alignment explanation
Indices: 56113055--56113091 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
56113045 CGCATATGGT
56113055 TTTTTTATTTTATT-TTA
1 TTTTTTATTTT-TTATTA
56113072 TTTTTTATTTTTTATTA
1 TTTTTTATTTTTTATTA
56113089 TTT
1 TTT
56113092 ATTCAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTATTTTTTATTA
Found at i:56113086 original size:14 final size:14
Alignment explanation
Indices: 56113054--56113094 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
56113044 TCGCATATGG
56113054 TTTTT-TTATTT-T
1 TTTTTATTATTTAT
* *
56113066 ATTTTATTTTTTAT
1 TTTTTATTATTTAT
56113080 TTTTTATTATTTAT
1 TTTTTATTATTTAT
56113094 T
1 T
56113095 CAAGATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 4 0.17
13 5 0.22
14 14 0.61
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTATTTAT
Found at i:56118318 original size:16 final size:16
Alignment explanation
Indices: 56118297--56118328 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56118287 ATTCATTTCA
56118297 GGGAATGAAGCAAAAC
1 GGGAATGAAGCAAAAC
56118313 GGGAATGAAGCAAAAC
1 GGGAATGAAGCAAAAC
56118329 TAGTGGGAAG
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:0.50, C:0.12, G:0.31, T:0.06
Consensus pattern (16 bp):
GGGAATGAAGCAAAAC
Found at i:56126540 original size:6 final size:6
Alignment explanation
Indices: 56126531--56126560 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
56126521 TTACATCAAT
56126531 AAATTC AAATTC AAATTC AAATTC AAATTC
1 AAATTC AAATTC AAATTC AAATTC AAATTC
56126561 CGCCACAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTC
Found at i:56128977 original size:3 final size:3
Alignment explanation
Indices: 56128928--56128957 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
56128918 GACATCAATG
*
56128928 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56128958 GTAATAGCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:56137521 original size:26 final size:25
Alignment explanation
Indices: 56137472--56137539 Score: 93
Period size: 25 Copynumber: 2.6 Consensus size: 25
56137462 AAAAATAAAA
56137472 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAAC-TTTTTT
*
56137499 ATTTACCAAATATATATTA-TTTTTT
1 ATTTACCAAA-ATATATAACTTTTTT
56137524 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
56137540 CAAAAAAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
24 6 0.15
25 16 0.41
27 14 0.36
28 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTACCAAAATATATAACTTTTTT
Found at i:56137636 original size:27 final size:27
Alignment explanation
Indices: 56137614--56137681 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
56137604 ACGCCAATGG
*
56137614 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAATAC
*
56137641 CATTGGCGGCACCAATGGTGCCAATAC
1 CATTGGCGGCACCAAAGGTGCCAATAC
*
56137668 CATTGGCAGCACCA
1 CATTGGCGGCACCA
56137682 CTTAATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAATAC
Found at i:56137733 original size:4 final size:4
Alignment explanation
Indices: 56137724--56137853 Score: 85
Period size: 4 Copynumber: 32.0 Consensus size: 4
56137714 GAAGGAGAGG
* *
56137724 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
* *
56137773 GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA G-AA GAAAA GGAAAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -G-AAA
*
56137822 GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
56137854 AGGAAAGGAG
Statistics
Matches: 103, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
3 18 0.17
4 57 0.55
5 21 0.20
6 7 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:56137749 original size:18 final size:19
Alignment explanation
Indices: 56137728--56137866 Score: 106
Period size: 18 Copynumber: 7.0 Consensus size: 19
56137718 GAGAGGGAAA
56137728 GAAAGAAAGAAAGGAG-AG
1 GAAAGAAAGAAAGGAGAAG
*
56137746 GAAAGAAAGAAA-AAGAAG
1 GAAAGAAAGAAAGGAGAAG
56137764 GAAAGAAAAGGAAAGGAGAAG
1 GAAAG-AAA-GAAAGGAGAAG
* *
56137785 AGAAAAAAAGAAAGAAAGAAG
1 -GAAAGAAAGAAAG-GAGAAG
* *
56137806 AAGAAGAAAAGGAAAAGAGAA-
1 GA-AAG-AAA-GAAAGGAGAAG
*
56137827 GAAA-AAAGAAAGAAAGAAG
1 GAAAGAAAGAAAG-GAGAAG
56137846 GAAAGAAAAGGAAAGGAGAAG
1 GAAAG-AAA-GAAAGGAGAAG
56137867 AGAGAAAAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
17 6 0.06
18 26 0.27
19 7 0.07
20 12 0.13
21 24 0.25
22 16 0.17
23 4 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAAGGAGAAG
Found at i:56137789 original size:22 final size:21
Alignment explanation
Indices: 56137724--56137880 Score: 102
Period size: 22 Copynumber: 7.7 Consensus size: 21
56137714 GAAGGAGAGG
* * *
56137724 GAAAGAAAGAAAGAAAGGAGA
1 GAAAAAAAGAAAGAGAGAAGA
*
56137745 GGAAAGAAAGAAA-A-AGAAG-
1 -GAAAAAAAGAAAGAGAGAAGA
56137764 GAAAGAAAAGGAAAG-GAGAAGA
1 GAAA-AAAA-GAAAGAGAGAAGA
*
56137786 GAAAAAAAGAAAGAAAGAAGAA
1 GAAAAAAAGAAAGAGAGAAG-A
*
56137808 GAAGAAAAGGAAA-AGAG-A-A
1 GAA-AAAAAGAAAGAGAGAAGA
*
56137827 G-AAAAAAGAAAGAAAGAAG-
1 GAAAAAAAGAAAGAGAGAAGA
56137846 GAAAGAAAAGGAAAG-GAGAAGA
1 GAAA-AAAA-GAAAGAGAGAAGA
*
56137868 GAGAAAAA-AAAGA
1 GAAAAAAAGAAAGA
56137881 ACAAGAGGGA
Statistics
Matches: 110, Mismatches: 9, Indels: 34
0.72 0.06 0.22
Matches are distributed among these distances:
17 8 0.07
18 8 0.07
19 11 0.10
20 15 0.14
21 29 0.26
22 31 0.28
23 8 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
GAAAAAAAGAAAGAGAGAAGA
Found at i:56137810 original size:48 final size:46
Alignment explanation
Indices: 56137746--56137881 Score: 137
Period size: 45 Copynumber: 3.1 Consensus size: 46
56137736 GAAAGGAGAG
*
56137746 GAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAA
1 GAAAGAAAGAAGAAGAAGGAAAGAAAAGGAAA-GAG-AGAGAAAAAAA
56137794 GAAAG--A-AAGAAGAA-G-AAGAAAAGGAAA-AGAGA-AGAAAAAA
1 GAAAGAAAGAAGAAGAAGGAAAGAAAAGGAAAGAGAGAGA-AAAAAA
* * *
56137834 GAAAGAAAGAAGGA-AAGAAAAGGAAAGGAGAAGAGAGA-AAAAAAA
1 GAAAGAAAGAAGAAGAAGGAAAGAAAAGGA-AAGAGAGAGAAAAAAA
56137879 GAA
1 GAA
56137882 CAAGAGGGAA
Statistics
Matches: 76, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
39 1 0.01
40 14 0.18
41 2 0.03
42 3 0.04
43 16 0.21
44 10 0.13
45 18 0.24
46 7 0.09
48 5 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (46 bp):
GAAAGAAAGAAGAAGAAGGAAAGAAAAGGAAAGAGAGAGAAAAAAA
Found at i:56137821 original size:29 final size:29
Alignment explanation
Indices: 56137789--56137874 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
56137779 GAGAAGAGAA
56137789 AAAAAGAAAGAAAGAAGAAGAAGAAAAGG
1 AAAAAGAAAGAAAGAAGAAGAAGAAAAGG
* *
56137818 -AAAAGAGAAGAAAAAAGAAAGAA-AGAAGG
1 AAAAAGA-AAGAAAGAAG-AAGAAGAAAAGG
* *
56137847 AAAGAA-AAGGAAAGGAGAAGAGAGAAAA
1 AAA-AAGAAAGAAAGAAGAAGA-AGAAAA
56137875 AAAAGAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
28 10 0.22
29 22 0.49
30 11 0.24
31 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAGAAAGAAGAAGAAGAAAAGG
Found at i:56137839 original size:44 final size:44
Alignment explanation
Indices: 56137746--56137881 Score: 163
Period size: 44 Copynumber: 3.1 Consensus size: 44
56137736 GAAAGGAGAG
* *
56137746 GAAAGAAAGAAA-AAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 GAAAGAAAGAAAGAAGAA-G-AAGAAAAGGAAAAGAGAAGAAAAAA
56137791 -AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAA
1 GAAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAA
* *
56137834 GAAAGAAAGAAGGAAAGAA-AAGGAAAGGAGAAGAGAGAA-AAAAAA
1 GAAAGAAAGAAAG-AAGAAGAAGAAAAGGA-AA-AGAGAAGAAAAAA
56137879 GAA
1 GAA
56137882 CAAGAGGGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
43 23 0.28
44 32 0.39
45 21 0.26
46 6 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (44 bp):
GAAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAA
Found at i:56137916 original size:82 final size:83
Alignment explanation
Indices: 56137747--56137914 Score: 236
Period size: 82 Copynumber: 2.0 Consensus size: 83
56137737 AAAGGAGAGG
*
56137747 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAG
1 AAAGAAAG-AAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAACAAGAAGAAG
* *
56137812 AAAAGGAAAAGAGAAGAAA
65 AAAAGGAAAAAAAAAGAAA
* *
56137831 AAAGAAAG-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAGAAAAA-AAAG-AACAAGAGGGAAG
1 AAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAACAAGA-AGAAG
56137893 -AAAGGAAAAAAAAAAGAAA
65 AAAAGG-AAAAAAAAAGAAA
56137912 AAA
1 AAA
56137915 AGGTAATTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
80 11 0.14
81 22 0.29
82 36 0.47
84 8 0.10
ACGTcount: A:0.71, C:0.01, G:0.28, T:0.00
Consensus pattern (83 bp):
AAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAACAAGAAGAAGA
AAAGGAAAAAAAAAGAAA
Found at i:56144252 original size:19 final size:21
Alignment explanation
Indices: 56144228--56144266 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
56144218 ACTAAAACAA
*
56144228 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
56144247 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
56144267 ATCAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:56144511 original size:27 final size:27
Alignment explanation
Indices: 56144412--56144512 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
56144402 AATACGAATA
*
56144412 GTGCCGCCAAT-CAATATGGAACCATTG
1 GTGCCGCCAATGCAAT-TGGCACCATTG
*
56144439 GTGCCGCCAATGGAATTGGCACCATTG
1 GTGCCGCCAATGCAATTGGCACCATTG
*** *
56144466 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGCAATTGGCACCATTG
*
56144493 GTGCCGCCAATGCCATTGGC
1 GTGCCGCCAATGCAATTGGC
56144513 GTGACTAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
27 62 0.95
28 3 0.05
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAATGCAATTGGCACCATTG
Found at i:56144637 original size:28 final size:27
Alignment explanation
Indices: 56144577--56144647 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
56144567 TTTGTTTTTG
56144577 ATATATTTTGGTAAATAAAAAAATAAT
1 ATATATTTTGGTAAATAAAAAAATAAT
*
56144604 ATATATTTTGGTAAATAAAAAAA-AGTT
1 ATATATTTTGGTAAATAAAAAAATA-AT
56144631 ATAATATTTTGGTAAAT
1 AT-ATATTTTGGTAAAT
56144648 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 1 0.02
27 26 0.63
28 14 0.34
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAATAAT
Found at i:56147470 original size:50 final size:46
Alignment explanation
Indices: 56147413--56147617 Score: 122
Period size: 44 Copynumber: 4.4 Consensus size: 46
56147403 GATCCTATAC
56147413 CCCTGAAGTTGCAGTGGGTCGAATTAAAGTCACCATAGTGAATCTTATCT
1 CCCTGAAGTTGCAGTGGG-CGAATTAAA-TCA-CATA-TGAATCTTATCT
* *
56147463 CCCTGAAGTTGCAGTAGAGCAAATTAAAT---ATATGAATCTTATCT
1 CCCTGAAGTTGCAGT-GGGCGAATTAAATCACATATGAATCTTATCT
* * * * *
56147507 CCTTAAAGTTGCAGTGGAGC-AGATTGAAGCTAC--A--AATCCTATAC-
1 CCCTGAAGTTGCAGTGG-GCGA-ATTAAATC-ACATATGAATCTTAT-CT
* * * * *
56147551 CCCTGAAGTTGCAATGGGTCGGATTAAATCCACCATAGCGAACCGTATCT
1 CCCTGAAGTTGCAGTGGG-CGAATTAAAT-CA-CATA-TGAATCTTATCT
56147601 CCCTGAAGTTGCAGTGG
1 CCCTGAAGTTGCAGTGG
56147618 AGCAGATTGA
Statistics
Matches: 120, Mismatches: 17, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
43 3 0.03
44 60 0.50
45 6 0.05
46 1 0.01
47 1 0.01
49 2 0.02
50 45 0.38
51 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (46 bp):
CCCTGAAGTTGCAGTGGGCGAATTAAATCACATATGAATCTTATCT
Found at i:56147560 original size:44 final size:44
Alignment explanation
Indices: 56147453--56147906 Score: 269
Period size: 44 Copynumber: 10.0 Consensus size: 44
56147443 CACCATAGTG
* * * * ** **
56147453 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAATATATG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * *
56147497 AATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTGAAGCTACA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * *
56147541 AATCCTATAC-CCCTGAAGTTGCAATGG-GTCGGATTAAATCCACCA
1 AATCCTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCTA-CA
* *
56147586 TAGCGAACCGTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACG
1 -A---ATCC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * *
56147635 AA-CCTCATCTCCCTGAAATTGCAGTGGAGTAGATTGAAGTTACA
1 AATCCT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * ** * *
56147679 AATCATATAC-CCTTAAAGTTGCAGTGG-GTTGGATT-AATTCCACCA
1 AATCCTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAA-GCTA-CA
* * * * *
56147724 CAGCGAACCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTATA
1 -A---ATCC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* *
56147773 AA-CCTCATCTCCCTAAAGTTGCAGGGGAGCAGATTGAAGCTACA
1 AATCCT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * * * *
56147817 AATCTTATCTCCCTGAAGTTGCAGTGAAACAAATTGACGCTACA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
* * *
56147861 ATTCCTATAC-CCCTAAAGTTGCAGTGG-GCTAGAATGAAGCTACA
1 AATCCTAT-CTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGCTACA
56147905 AA
1 AA
56147907 AACAAATCTT
Statistics
Matches: 313, Mismatches: 69, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
43 7 0.02
44 226 0.72
45 13 0.04
46 2 0.01
48 2 0.01
49 9 0.03
50 50 0.16
51 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACA
Found at i:56147657 original size:138 final size:138
Alignment explanation
Indices: 56147404--56147842 Score: 605
Period size: 138 Copynumber: 3.2 Consensus size: 138
56147394 GAAACCATAG
* * *
56147404 ATCCTATACCCCTGAAGTTGCAGTGGGTCGAATTAAAGT-CACCATAGTGAATCTTATCTCCCTG
1 ATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAA-TCCACCATAGCGAACCTTATCTCCCTG
** * * *
56147468 AAGTTGCAGTAGAGCAAATTAAATATATGAATCTTATCTCCTTAAAGTTGCAGTGGAGCAGATTG
65 AAGTTGCAGTAGAGCAAATTAAAGCTATGAACCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTG
56147533 AAGCTACAA
130 AAGCTACAA
* *
56147542 ATCCTATACCCCTGAAGTTGCAATGGGTCGGATTAAATCCACCATAGCGAACCGTATCTCCCTGA
1 ATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAATCCACCATAGCGAACCTTATCTCCCTGA
* * * * *
56147607 AGTTGCAGTGGAGCAGATTGAAGCTACGAACCTCATCTCCCTGAAA-TTGCAGTGGAGTAGATTG
66 AGTTGCAGTAGAGCAAATTAAAGCTATGAACCTCATCTCCCT-AAAGTTGCAGTGGAGCAGATTG
*
56147671 AAGTTACAA
130 AAGCTACAA
* * * * * *
56147680 ATCATATACCCTTAAAGTTGCAGTGGGTTGGATTAATTCCACCACAGCGAACCTTATCTCCCTGA
1 ATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAATCCACCATAGCGAACCTTATCTCCCTGA
* *
56147745 AGTTGCAGTAGAGCAAATTAAAGCTATAAACCTCATCTCCCTAAAGTTGCAGGGGAGCAGATTGA
66 AGTTGCAGTAGAGCAAATTAAAGCTATGAACCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTGA
56147810 AGCTACAA
131 AGCTACAA
*
56147818 ATCTTAT-CTCCCTGAAGTTGCAGTG
1 ATCCTATAC-CCCTGAAGTTGCAGTG
56147843 AAACAAATTG
Statistics
Matches: 262, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
137 5 0.02
138 254 0.97
139 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (138 bp):
ATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTAAATCCACCATAGCGAACCTTATCTCCCTGA
AGTTGCAGTAGAGCAAATTAAAGCTATGAACCTCATCTCCCTAAAGTTGCAGTGGAGCAGATTGA
AGCTACAA
Found at i:56147920 original size:182 final size:182
Alignment explanation
Indices: 56147597--56147939 Score: 427
Period size: 182 Copynumber: 1.9 Consensus size: 182
56147587 AGCGAACCGT
* * * *
56147597 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACGAACCTCATCTCCCTGAAATTGCAGTGG
1 ATCTCCCTAAAGTTGCAGGGGAGCAGATTGAAGCTACAAACCTCATCTCCCTGAAATTGCAGTGA
** * * * * * * * * * *
56147662 AGTAGATTGAAGTTACAAATCATATACCCTTAAAGTTGCAGTGGGTTGGATTAATTCCACCACAG
66 AACAAATTGAAGCTACAAATCATATACCCCTAAAGTTGCAGTGGGTAGAATGAATGCCACAAAAA
* *
56147727 CGAACCTTATCTCCCTGAAGTTGCAGTAGAGCAAATTAAAGCTATAAACCTC
131 CAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAATTAAAGCTATAAACCTC
* * *
56147779 ATCTCCCTAAAGTTGCAGGGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGA
1 ATCTCCCTAAAGTTGCAGGGGAGCAGATTGAAGCTACAAACCTCATCTCCCTGAAATTGCAGTGA
* * * *
56147844 AACAAATTGACGCTACAATTCCTATACCCCTAAAGTTGCAGTGGGCTAGAATGAA-GCTACAAAA
66 AACAAATTGAAGCTACAAATCATATACCCCTAAAGTTGCAGTGGG-TAGAATGAATGCCACAAAA
* *
56147908 ACAAATCTTATCTCCTTGAAGTTGCAATAGAG
130 ACAAACCTTATCTCCCTGAAGTTGCAATAGAG
56147940 TAAGATGAAG
Statistics
Matches: 133, Mismatches: 27, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
182 127 0.95
183 6 0.05
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (182 bp):
ATCTCCCTAAAGTTGCAGGGGAGCAGATTGAAGCTACAAACCTCATCTCCCTGAAATTGCAGTGA
AACAAATTGAAGCTACAAATCATATACCCCTAAAGTTGCAGTGGGTAGAATGAATGCCACAAAAA
CAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAATTAAAGCTATAAACCTC
Found at i:56150030 original size:105 final size:105
Alignment explanation
Indices: 56149846--56150044 Score: 303
Period size: 105 Copynumber: 1.9 Consensus size: 105
56149836 TTATTTTCGA
* *
56149846 GAATTCGAGACATCATGCCCTAACTTATGAGGCATGATTTTCTTCCCGATTAACTCGAAATACAA
1 GAATTCGAGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTAACTCGAAATACAA
56149911 AGACATTCTGCATAAAATTTGATTTAATTTCTTTTTTTGG
66 AGACATTCTGCATAAAATTTGATTTAATTTCTTTTTTTGG
* *
56149951 GAATTCGAGACATCGTGCCCTAACTTACGAGACATGATTTTCTTCTCGATTAACTC-AAA-ACAT
1 GAATTCGAGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTAACTCGAAATACA-
* * *
56150014 GAAGGCATTTTTCATAAAATTTGATTTAATT
65 -AAGACATTCTGCATAAAATTTGATTTAATT
56150045 AGCGATATTT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
103 3 0.04
104 3 0.04
105 79 0.93
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (105 bp):
GAATTCGAGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTAACTCGAAATACAA
AGACATTCTGCATAAAATTTGATTTAATTTCTTTTTTTGG
Found at i:56150069 original size:105 final size:104
Alignment explanation
Indices: 56149853--56150073 Score: 234
Period size: 105 Copynumber: 2.1 Consensus size: 104
56149843 CGAGAATTCG
* *
56149853 AGACATCATGCCCTAACTTATGAGGCATGATTTTCTTCCCGATTAACTCGAAATACAAAGACATT
1 AGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTAACTCGAAATACAAAGACATT
* * **** *
56149918 CTGCATAAAATTTGATTTAATTTCTTTTTTTGGGAATTC
66 CTGCATAAAATTTGATTTAATTGCTATTTTAAAAAAATC
* * *
56149957 GAGACATCGTGCCCTAACTTACGAGACATGATTTTCTTCTCGATTAACTC-AAA-ACATGAAGGC
1 -AGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTAACTCGAAATACA--AAGAC
* *
56150020 ATTTTTCATAAAATTTGATTTAATTAGCGATATTTTAAAAAAAT-
63 ATTCTGCATAAAATTTGATTTAATT-GC--TATTTTAAAAAAATC
56150064 A-ACATCATGC
1 AGACATCATGC
56150074 AAAAAAAAGG
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
103 3 0.03
104 3 0.03
105 80 0.83
106 2 0.02
108 8 0.08
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (104 bp):
AGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTAACTCGAAATACAAAGACATT
CTGCATAAAATTTGATTTAATTGCTATTTTAAAAAAATC
Found at i:56153911 original size:20 final size:21
Alignment explanation
Indices: 56153886--56153946 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
56153876 TGTTTGTATC
56153886 TAAAATTTTAATAAATA-AAT
1 TAAAATTTTAATAAATATAAT
**
56153906 TAAAATCGT-ATAAATATAAT
1 TAAAATTTTAATAAATATAAT
*
56153926 TTAAATTTTAAATAATATATA
1 TAAAATTTT-AATAA-ATATA
56153947 TAGGCCTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.22
20 16 0.50
22 4 0.12
23 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAATTTTAATAAATATAAT
Found at i:56155429 original size:2 final size:2
Alignment explanation
Indices: 56155422--56155462 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
56155412 GCTAAATTTA
*
56155422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56155463 GAATGAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56155516 original size:10 final size:10
Alignment explanation
Indices: 56155501--56155526 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56155491 TATTAATCAT
56155501 AAAAAATATA
1 AAAAAATATA
56155511 AAAAAATATA
1 AAAAAATATA
56155521 AAAAAA
1 AAAAAA
56155527 CCACTTTATT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATATA
Found at i:56160993 original size:20 final size:20
Alignment explanation
Indices: 56160957--56160995 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
56160947 TAGTTAATTA
*
56160957 ATTTAATTATAGTTTATTTT
1 ATTTAATTATAGATTATTTT
56160977 ATTTAATTATTA-ATTATTT
1 ATTTAATTA-TAGATTATTT
56160996 AAACTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTAATTATAGATTATTTT
Found at i:56164624 original size:22 final size:22
Alignment explanation
Indices: 56164578--56164621 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
56164568 TTTTGGATTA
*
56164578 TTATAATTTTTGAAAAATATTT
1 TTATAATTTTAGAAAAATATTT
56164600 TTATAA-TTTAG-AAAATATTT
1 TTATAATTTTAGAAAAATATTT
56164620 TT
1 TT
56164622 TTAGTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TTATAATTTTAGAAAAATATTT
Found at i:56165898 original size:27 final size:27
Alignment explanation
Indices: 56165813--56165892 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 27
56165803 GCCAACAAGA
*
56165813 CTGGCAAGATAGTGTACGCTAGTAGGT
1 CTGGCAAGATAGTGTTCGCTAGTAGGT
* * * *
56165840 CTGGCGAGCTAGTGTTCGATAGTTGGT
1 CTGGCAAGATAGTGTTCGCTAGTAGGT
* *
56165867 CTGGCAAGTTAGTGTTCGCCAGTAGG
1 CTGGCAAGATAGTGTTCGCTAGTAGG
56165893 CTTGGCGAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.20, C:0.16, G:0.35, T:0.29
Consensus pattern (27 bp):
CTGGCAAGATAGTGTTCGCTAGTAGGT
Found at i:56167048 original size:18 final size:17
Alignment explanation
Indices: 56167016--56167049 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56167006 AGACAGATTT
*
56167016 ATTATTTTGTTTATATA
1 ATTATTTTATTTATATA
56167033 ATTATTTATATTTATAT
1 ATTATTT-TATTTATAT
56167050 TTATATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTATTTTATTTATATA
Found at i:56167311 original size:21 final size:21
Alignment explanation
Indices: 56167285--56167340 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
56167275 TAATTCTGTT
56167285 TCGGGATTTATTCCTATTAAA
1 TCGGGATTTATTCCTATTAAA
*
56167306 TCGGGATTT-TTACTATTAAA
1 TCGGGATTTATTCCTATTAAA
*
56167326 CCGGGATTTATTCCT
1 TCGGGATTTATTCCT
56167341 GTCGTTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (21 bp):
TCGGGATTTATTCCTATTAAA
Found at i:56167539 original size:81 final size:83
Alignment explanation
Indices: 56167330--56167728 Score: 393
Period size: 82 Copynumber: 5.0 Consensus size: 83
56167320 ATTAAACCGG
* * *
56167330 GATTTATTCCTGTCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTGCAAACA-AGAATTAAT
1 GATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAACAGAGAATTAAT
* * **
56167394 TGAATAATTCT-ATTCCC
66 TAAATAATTCTGTTTCAA
** *
56167411 GAATTTATTCTTGCCGTTTAACAAATTTTATTCGATTTTGATTTTGTTTCCAAA-AGAGAATTAA
1 G-ATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAACAGAGAATTAA
*
56167475 TTGAATAA-TCTGTTTCAA
65 TTAAATAATTCTGTTTCAA
* * *
56167493 GATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTAATTTTGTTTCCAAATGAGAAGATTTA
1 GATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAA-CAG-AGAATTA
*
56167558 ATTAAATAATTTTGTTTCAA
64 ATTAAATAATTCTGTTTCAA
* *
56167578 GATTTATT-CCGCCGCTTAACAGA--TT-TT--ATTTTGATTTTGTTTCCAAACAG-GATTTAAT
1 GATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAACAGAGAATTAAT
* ***
56167636 CAAATAATTCTGTTTTGG
66 TAAATAATTCTGTTTCAA
* * * * * *
56167654 GATTTGTTCCCGCCATTTAAC--ATATT-TT--ATTTTAATTTTGTTTTCAAACA-AGATTTAAT
1 GATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAACAGAGAATTAAT
56167713 TAAATAACTT-TGTTTC
66 TAAATAA-TTCTGTTTC
56167729 GGAATTTAAT
Statistics
Matches: 277, Mismatches: 29, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
75 1 0.00
76 28 0.10
77 53 0.19
78 4 0.01
79 19 0.07
81 55 0.20
82 70 0.25
83 2 0.01
84 28 0.10
85 17 0.06
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (83 bp):
GATTTATTCCCGCCGTTTAACAGATTTTATTCGATTTTGATTTTGTTTCCAAACAGAGAATTAAT
TAAATAATTCTGTTTCAA
Found at i:56167692 original size:77 final size:78
Alignment explanation
Indices: 56167363--56167728 Score: 316
Period size: 77 Copynumber: 4.6 Consensus size: 78
56167353 ATTTTATTCG
* * * * * ** **
56167363 ATTTTGATTTTGTTTGCAAACA-AGAATTAATTGAATAATTCT-ATTCCCGAATTTATTCTTGCC
1 ATTTTAATTTTGTTTCCAAACAGAGATTTAATTAAATAATTCTGTTTCAAG-ATTTATTCCCGCC
*
56167426 GTTTAACAAATTTTATT
65 GTTTAAC--ATATT-TT
* * *
56167443 CGATTTTGATTTTGTTTCCAAA-AGAGAATTAATTGAATAA-TCTGTTTCAAGATTTATTCCCGC
1 --ATTTTAATTTTGTTTCCAAACAGAGATTTAATTAAATAATTCTGTTTCAAGATTTATTCCCGC
*
56167506 CGTTTAACAGATTTTATT
64 CGTTTAAC--ATATT-TT
* *
56167524 CGATTTTAATTTTGTTTCCAAATGAGAAGATTTAATTAAATAATTTTGTTTCAAGATTTATT-CC
1 --ATTTTAATTTTGTTTCCAAA-CAG-AGATTTAATTAAATAATTCTGTTTCAAGATTTATTCCC
* *
56167588 GCCGCTTAACAGATTTT
62 GCCGTTTAACATATTTT
* * *** * *
56167605 ATTTTGATTTTGTTTCCAAACAG-GATTTAATCAAATAATTCTGTTTTGGGATTTGTTCCCGCCA
1 ATTTTAATTTTGTTTCCAAACAGAGATTTAATTAAATAATTCTGTTTCAAGATTTATTCCCGCCG
56167669 TTTAACATATTTT
66 TTTAACATATTTT
*
56167682 ATTTTAATTTTGTTTTCAAACA-AGATTTAATTAAATAACTT-TGTTTC
1 ATTTTAATTTTGTTTCCAAACAGAGATTTAATTAAATAA-TTCTGTTTC
56167729 GGAATTTAAT
Statistics
Matches: 246, Mismatches: 29, Indels: 23
0.83 0.10 0.08
Matches are distributed among these distances:
76 28 0.11
77 55 0.22
78 4 0.02
79 19 0.08
81 54 0.22
82 42 0.17
83 2 0.01
84 25 0.10
85 17 0.07
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (78 bp):
ATTTTAATTTTGTTTCCAAACAGAGATTTAATTAAATAATTCTGTTTCAAGATTTATTCCCGCCG
TTTAACATATTTT
Found at i:56167746 original size:77 final size:75
Alignment explanation
Indices: 56167363--56167769 Score: 280
Period size: 77 Copynumber: 5.1 Consensus size: 75
56167353 ATTTTATTCG
* * * * * * * * *
56167363 ATTTTGATTTTGTTTGCAAACAAGAATTAATTGAATAATTCTATTCCCGAATTTATTCTTGCCGT
1 ATTTTAATTTTGTTTCCAAACAAGATTTAATTAAATAATT-TGTTTCGGAATTTATTC-CGCCAT
*
56167428 TTAACAAATTTTATT
64 TTAACAGA--TT-TT
* * * * *
56167443 CGATTTTGATTTTGTTTCCAAA-AGAGAATTAATTGAATAATCTGTTTC-AAGATTTATTCCCGC
1 --ATTTTAATTTTGTTTCCAAACA-AGATTTAATTAAATAATTTGTTTCGGA-ATTTATT-CCGC
*
56167506 CGTTTAACAGATTTTATT
61 CATTTAACAGA--TT-TT
* *
56167524 CGATTTTAATTTTGTTTCCAAATGAGAAGATTTAATTAAATAATTTTGTTTC-AAGATTTATTCC
1 --ATTTTAATTTTGTTTCC-AA--ACAAGATTTAATTAAATAA-TTTGTTTCGGA-ATTTATTCC
**
56167588 GCCGCTTAACAGATTTT
59 GCCATTTAACAGATTTT
* * * * * *
56167605 ATTTTGATTTTGTTTCCAAACAGGATTTAATCAAATAATTCTGTTTTGGGATTTGTTCCCGCCAT
1 ATTTTAATTTTGTTTCCAAACAAGATTTAATTAAATAATT-TGTTTCGGAATTTATT-CCGCCAT
*
56167670 TTAACATATTTT
64 TTAACAGATTTT
* *
56167682 ATTTTAATTTTGTTTTCAAACAAGATTTAATTAAATAACTTTGTTTCGGAATTTAATCCTGCCAT
1 ATTTTAATTTTGTTTCCAAACAAGATTTAATTAAATAA-TTTGTTTCGGAATTTATTCC-GCCAT
* * * *
56167747 TCAATAGAATTG
64 TTAACAGATTTT
56167759 ATTTTAATTTT
1 ATTTTAATTTT
56167770 ATTTTGTTTC
Statistics
Matches: 276, Mismatches: 36, Indels: 31
0.80 0.10 0.09
Matches are distributed among these distances:
75 2 0.01
76 29 0.11
77 85 0.31
78 4 0.01
79 16 0.06
80 1 0.00
81 51 0.18
82 41 0.15
84 29 0.11
85 18 0.07
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.46
Consensus pattern (75 bp):
ATTTTAATTTTGTTTCCAAACAAGATTTAATTAAATAATTTGTTTCGGAATTTATTCCGCCATTT
AACAGATTTT
Found at i:56170096 original size:16 final size:16
Alignment explanation
Indices: 56170063--56170096 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56170053 TTTTACATAA
**
56170063 ATATAAATATTTGTTT
1 ATATAAATATTTACTT
56170079 ATATAAATATTTACTT
1 ATATAAATATTTACTT
56170095 AT
1 AT
56170097 GTTAAGTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATAAATATTTACTT
Found at i:56173683 original size:15 final size:15
Alignment explanation
Indices: 56173663--56173695 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
56173653 AAGAATTAAA
56173663 CCTACCCTTTTTGCC
1 CCTACCCTTTTTGCC
56173678 CCTACCCTTTTTGCC
1 CCTACCCTTTTTGCC
56173693 CCT
1 CCT
56173696 TTTGTCCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.48, G:0.06, T:0.39
Consensus pattern (15 bp):
CCTACCCTTTTTGCC
Found at i:56186529 original size:3 final size:3
Alignment explanation
Indices: 56186521--56186551 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56186511 TTCATTTGTA
56186521 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
56186552 GTCGGGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:56197699 original size:29 final size:27
Alignment explanation
Indices: 56197634--56197699 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 27
56197624 AATTTAATGC
*
56197634 GTATAATTACACCAAATTAAAATCTAT
1 GTATAATTACACCAAATTAAAATCCAT
*
56197661 ATATCAAATTACA-CATTAATTCAAAATCCAT
1 GTAT--AATTACACCA--AATT-AAAATCCAT
56197692 GTATAATT
1 GTATAATT
56197700 TTGAGGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 3 0.10
28 2 0.06
29 11 0.35
30 4 0.13
31 11 0.35
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (27 bp):
GTATAATTACACCAAATTAAAATCCAT
Found at i:56209183 original size:16 final size:16
Alignment explanation
Indices: 56209147--56209177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56209137 CCCCTCAACA
*
56209147 AATTTTAATCTAAAAG
1 AATTTGAATCTAAAAG
56209163 AATTTGAATCTAAAA
1 AATTTGAATCTAAAA
56209178 TGATTTTAAA
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:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
AATTTGAATCTAAAAG
Found at i:56209455 original size:17 final size:17
Alignment explanation
Indices: 56209433--56209466 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56209423 TTTATTGTTC
56209433 AATTATTATATAATTAA
1 AATTATTATATAATTAA
* *
56209450 AATTATTTTATTATTAA
1 AATTATTATATAATTAA
56209467 TATAATCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTATTATATAATTAA
Found at i:56213130 original size:51 final size:51
Alignment explanation
Indices: 56213069--56213284 Score: 317
Period size: 51 Copynumber: 4.3 Consensus size: 51
56213059 GCTTCTGATC
* * *
56213069 AGTGGCAAGTGATAAGTGATTGCTTCAGCTACACTTATTTGATCAATGACA
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
56213120 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* * * *
56213171 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
56213222 AATGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAGGGACA
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
**
56213272 AGTGATAAGTGAT
1 AGTGGCAAGTGAT
56213285 CATACGCAAG
Statistics
Matches: 151, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 33 0.22
51 118 0.78
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:56221710 original size:126 final size:126
Alignment explanation
Indices: 56221520--56221763 Score: 348
Period size: 126 Copynumber: 1.9 Consensus size: 126
56221510 ACGAAATTTA
* * * *
56221520 TTTCATTTTTGAAAATTTTAAAAGGATACTTTGCTATTTAGGTTTAACGACAAAATCGAGACCCC
1 TTTCATTTTTGAAAATCTTAAAAGGATACTTCGCTATTTAGGTATAACGACAAAATCGAAACCCC
*
56221585 GTAAGTTAGGGTACGATCTCTCGAATCACCAAAACGCAAAGATATTGTCTTATTGAGATTCC
66 GTAAGTTAGGGTACAATCTCTCGAATCACCAAAACGCAAA-ATATTGTCTTATTGAGATTCC
* * *
56221647 TTTCATTTTTG-AAATCTTAAAAGGATACTTCGTTATCTT-GGTATAACGAGAAAATTGAAACCC
1 TTTCATTTTTGAAAATCTTAAAAGGATACTTCGCTAT-TTAGGTATAACGACAAAATCGAAACCC
* ** *
56221710 CGTAAGTTAGGGTACAATTTCTCGAATTTCCAAAACGCGAAATATTGTCTTATT
65 CGTAAGTTAGGGTACAATCTCTCGAATCACCAAAACGCAAAATATTGTCTTATT
56221764 TTAAAATTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
125 13 0.12
126 78 0.75
127 13 0.12
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (126 bp):
TTTCATTTTTGAAAATCTTAAAAGGATACTTCGCTATTTAGGTATAACGACAAAATCGAAACCCC
GTAAGTTAGGGTACAATCTCTCGAATCACCAAAACGCAAAATATTGTCTTATTGAGATTCC
Found at i:56222225 original size:16 final size:17
Alignment explanation
Indices: 56222192--56222227 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
56222182 CGGGCCCAAT
56222192 AAACTAAACCTAAGCCC
1 AAACTAAACCTAAGCCC
56222209 AAACTAAACCT-AGCCC
1 AAACTAAACCTAAGCCC
56222225 AAA
1 AAA
56222228 AAACAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.50, C:0.33, G:0.06, T:0.11
Consensus pattern (17 bp):
AAACTAAACCTAAGCCC
Found at i:56223318 original size:2 final size:2
Alignment explanation
Indices: 56223311--56223341 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
56223301 TGCATATTTA
56223311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56223342 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56227035 original size:63 final size:63
Alignment explanation
Indices: 56226936--56227061 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
56226926 AGTGCGGTGT
56226936 AATTTATAAATCCTGAATTTTCAAAGACCAACATCAAAAAGTTTAAAGCATATACTTCTTTCA
1 AATTTATAAATCCTGAATTTTCAAAGACCAACATCAAAAAGTTTAAAGCATATACTTCTTTCA
56226999 AATTTATAAATCCTGAATTTTCAAAGACCAACATCAAAAAGTTTAAAGCATATACTTCTTTCA
1 AATTTATAAATCCTGAATTTTCAAAGACCAACATCAAAAAGTTTAAAGCATATACTTCTTTCA
56227062 CTAAATCATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.33
Consensus pattern (63 bp):
AATTTATAAATCCTGAATTTTCAAAGACCAACATCAAAAAGTTTAAAGCATATACTTCTTTCA
Found at i:56229390 original size:88 final size:89
Alignment explanation
Indices: 56229220--56229424 Score: 279
Period size: 88 Copynumber: 2.3 Consensus size: 89
56229210 TTGATTTTAG
* * *
56229220 TAAATTCATATAATACCATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAATA-AAATTTATTATCAAGAATTTTATGAAATTATATAT--CTATTAAATTAT
* *
56229285 ATTTAATATTAATTATTTTAAATTGTA
63 ATGTAATATTAATTATTTTAAATTATA
*
56229312 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATAT-TATTAAATTATATG
1 TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCTATTAAATTATATG
56229376 TAATAATT-ATTATTTTAAATTATA
66 TAAT-ATTAATTATTTTAAATTATA
* * *
56229400 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAATAAAATTTATTA
56229425 GTTATAATTA
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
88 53 0.52
89 3 0.03
91 32 0.31
92 14 0.14
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (89 bp):
TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCTATTAAATTATATG
TAATATTAATTATTTTAAATTATA
Found at i:56229458 original size:28 final size:27
Alignment explanation
Indices: 56229427--56229502 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
56229417 ATTTATTAGT
56229427 TATAATTATTTTAAATTTTATTAAATCA
1 TATAATTATTTTAAATTTTATTAAAT-A
* * *
56229455 TAT-ATT-TTAATTAAAATATATTTAATA
1 TATAATTATT--TTAAATTTTATTAAATA
*
56229482 T-TAATTATTTCAAATTTTATT
1 TATAATTATTTTAAATTTTATT
56229503 TTATAGTATC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
26 12 0.32
27 8 0.21
28 18 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
TATAATTATTTTAAATTTTATTAAATA
Found at i:56229466 original size:47 final size:49
Alignment explanation
Indices: 56229342--56229467 Score: 114
Period size: 47 Copynumber: 2.6 Consensus size: 49
56229332 TATTATCAAG
* * *
56229342 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATTATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* * * * * *
56229393 AATTATA-CAAATTCATAAAATATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
56229440 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
56229468 AAATATATTT
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
47 32 0.55
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:56229487 original size:54 final size:54
Alignment explanation
Indices: 56229429--56229755 Score: 183
Period size: 54 Copynumber: 5.6 Consensus size: 54
56229419 TTATTAGTTA
*
56229429 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTTAAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAT
* * * * **
56229483 TAATTATTTCAAATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTTAAATTTTA--TTA-A--AT--TATA-TAT--TTTAATTAAAAT-ATAT-TTAATA
56229548 T
54 T
* * *
56229549 TAATTA-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTTA-AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAT
* * * * **
56229603 TAATTATGTT-AATTTATATTTTACAGTATTATATATTATGGTTTGAGTAAATTCATATAAGAAT
1 TAATTATTTTAAATTT-TA--TTA-A--A-T-TATA-TAT--TTTAATTAAAAT-ATAT-TTAAT
56229667 AT
53 AT
* *
56229669 TAATTA-TTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAA
1 TAATTATTTTA-AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAT
* * * *
56229723 TAATTATGTTAAAATATGATTAAATTATTTATT
1 TAATTAT-TTTAAATTTTATTAAATTATATATT
56229756 ATTGATATTA
Statistics
Matches: 207, Mismatches: 35, Indels: 61
0.68 0.12 0.20
Matches are distributed among these distances:
53 5 0.02
54 39 0.19
55 27 0.13
56 27 0.13
57 2 0.01
58 6 0.03
59 11 0.05
60 2 0.01
61 10 0.05
62 6 0.03
63 2 0.01
64 23 0.11
65 12 0.06
66 30 0.14
67 5 0.02
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (54 bp):
TAATTATTTTAAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAT
Found at i:56229564 original size:66 final size:64
Alignment explanation
Indices: 56229478--56229688 Score: 194
Period size: 66 Copynumber: 3.4 Consensus size: 64
56229468 AAATATATTT
* *
56229478 AATATTAATTATTTCAAATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTA-TTAAAATTTTATTTTA-AGTATTATATATTATGATTTGAGTAAATTCATATAA
56229543 G
64 G
* * **
56229544 AATATTAATTATTAAGAATTTTA--TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTAA-AATTTTATTTTAAGTATTATATATTATGATTTGAGTAAATTCATATAAG
* * *
56229598 AATAATAATTATGT-TAATTTATATTTTACAGTATTATATATTATGGTTTGAGTAAATTCATATA
1 AATATTAATTAT-TAAAATTT-TATTTTA-AGTATTATATATTATGATTTGAGTAAATTCATATA
56229662 AG
63 AG
56229664 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTAA-AATTTTATT
56229689 AAATTATATA
Statistics
Matches: 113, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 11 0.10
60 7 0.06
61 10 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 8 0.07
66 33 0.29
67 5 0.04
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTAAAATTTTATTTTAAGTATTATATATTATGATTTGAGTAAATTCATATAAG
Found at i:56229564 original size:120 final size:120
Alignment explanation
Indices: 56229440--56229734 Score: 504
Period size: 120 Copynumber: 2.5 Consensus size: 120
56229430 AATTATTTTA
* *
56229440 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
56229503 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
56229560 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
56229625 ACAGTATTATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
56229680 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAA
56229735 AATATGATTA
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 5 0.03
120 159 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:56229577 original size:59 final size:58
Alignment explanation
Indices: 56229514--56229697 Score: 162
Period size: 59 Copynumber: 3.1 Consensus size: 58
56229504 TATAGTATCA
56229514 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATG-TTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * * * * * * * *
56229573 TATA-TAT-TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-CAGTATT
1 TATATTATGTTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA--AAT
56229633 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 -TATATTAT-GTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
56229693 TATAT
1 TATAT
56229698 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
56 6 0.06
57 11 0.12
58 9 0.10
59 17 0.18
60 12 0.13
61 12 0.13
62 9 0.10
63 11 0.12
64 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (58 bp):
TATATTATGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:56229600 original size:15 final size:15
Alignment explanation
Indices: 56229565--56229616 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
56229555 TTAAGAATTT
*
56229565 TATTAAATTAT-ATA
1 TATTTAATTATAATA
56229579 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
56229593 TATTTAATAATAAT-
1 TATTTAATTATAATA
56229607 TATGTTAATT
1 TAT-TTAATT
56229617 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:56229709 original size:18 final size:17
Alignment explanation
Indices: 56229681--56229715 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56229671 ATTATTAAGA
*
56229681 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56229698 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56229716 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:56229963 original size:45 final size:44
Alignment explanation
Indices: 56229874--56229968 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
56229864 TTACACCTCT
*
56229874 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
56229918 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
56229963 ATTACA
1 ATTACA
56229969 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.44
45 25 0.56
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:56229968 original size:16 final size:16
Alignment explanation
Indices: 56229947--56229984 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
56229937 TTGATTTGCT
*
56229947 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
56229963 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
56229979 AATACA
1 ATTACA
56229985 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:56232035 original size:3 final size:3
Alignment explanation
Indices: 56232027--56232060 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56232017 ATGAATTTAG
56232027 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
56232061 GGGCAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:56243271 original size:15 final size:17
Alignment explanation
Indices: 56243239--56243275 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
56243229 CTTTTAATCT
*
56243239 TTTTTTTTATGTGTTTA
1 TTTTTGTTATGTGTTTA
56243256 TTTTTGTTAT-TG-TTA
1 TTTTTGTTATGTGTTTA
56243271 TTTTT
1 TTTTT
56243276 CTCTTTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (17 bp):
TTTTTGTTATGTGTTTA
Found at i:56246060 original size:22 final size:22
Alignment explanation
Indices: 56246026--56246081 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
56246016 ACAATATCCA
56246026 AATAATAACAACAAAAT-AGTAGC
1 AATAA-AACAACAAAATGA-TAGC
*
56246049 AATAAAATAACAAAATGATAGC
1 AATAAAACAACAAAATGATAGC
*
56246071 AAAAAAACAAC
1 AATAAAACAAC
56246082 GAAACAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.14
Consensus pattern (22 bp):
AATAAAACAACAAAATGATAGC
Found at i:56252105 original size:22 final size:22
Alignment explanation
Indices: 56252045--56252102 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 22
56252035 AATCTTCAAG
56252045 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
56252064 GATATGCAATTTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
56252086 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
56252103 GATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.39
22 8 0.26
23 11 0.35
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:56253600 original size:13 final size:13
Alignment explanation
Indices: 56253584--56253608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56253574 ATTTTAATAA
56253584 ATTAAAATGTTTT
1 ATTAAAATGTTTT
56253597 ATTAAAATGTTT
1 ATTAAAATGTTT
56253609 AATCTCAAGG
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
ATTAAAATGTTTT
Found at i:56260788 original size:18 final size:18
Alignment explanation
Indices: 56260765--56260818 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
56260755 AATTTTTATG
56260765 ATTGGGTTGGGTTGAGTA
1 ATTGGGTTGGGTTGAGTA
56260783 ATTGGGTTGGGTTG-GATA
1 ATTGGGTTGGGTTGAG-TA
* *
56260801 CTTGGGTTTGGATTGAGT
1 ATTGGG-TTGGGTTGAGT
56260819 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 1 0.03
18 21 0.68
19 8 0.26
20 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAGTA
Found at i:56261846 original size:22 final size:22
Alignment explanation
Indices: 56261818--56261867 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
56261808 CAAACAAATG
56261818 TTCTCTCAA-TTTCTTTCCAAAA
1 TTCTCTCAATTTTC-TTCCAAAA
56261840 TTCTCTCAATTTTCTTCCAAAA
1 TTCTCTCAATTTTCTTCCAAAA
56261862 TTCTCT
1 TTCTCT
56261868 TAAACTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (22 bp):
TTCTCTCAATTTTCTTCCAAAA
Found at i:56261877 original size:52 final size:52
Alignment explanation
Indices: 56261820--56261919 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
56261810 AACAAATGTT
* * * * * *
56261820 CTCTCAATTTCTTTCCAAAATTCTCTCAATTTTCTTCCAAAATTCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
56261872 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCT
56261920 CAAATCCATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (52 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCTTAAA
Done.