Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 1 of 126
Found at i:4023 original size:26 final size:26
Alignment explanation
Indices: 3990--4062 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
3980 TGCTAATACA
* *
3990 ACACCAGCACAAAGCCTTCTAAATGT
1 ACACCAGCACAAAGCCTACTAAATAT
* *
4016 ACATCAGCTA-GAAGCCTACTAAATAT
1 ACACCAGC-ACAAAGCCTACTAAATAT
4042 ACACCAGCACAAAGCCTACTA
1 ACACCAGCACAAAGCCTACTA
4063 CGCCCTAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.03
26 37 0.95
27 1 0.03
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.18
Consensus pattern (26 bp):
ACACCAGCACAAAGCCTACTAAATAT
Found at i:4658 original size:42 final size:42
Alignment explanation
Indices: 4612--4701 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
4602 AAAATTAACT
*
4612 AAAATCACTTTACAAAATAGTCCTATTTAACCATCAGGCTTA
1 AAAATCACTTTACAAAATAGTACTATTTAACCATCAGGCTTA
4654 AAAATCACTTTACAAAATAGTACTATTTAACCATCAGGCTTA
1 AAAATCACTTTACAAAATAGTACTATTTAACCATCAGGCTTA
*
4696 ATAATC
1 AAAATC
4702 CATCATAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (42 bp):
AAAATCACTTTACAAAATAGTACTATTTAACCATCAGGCTTA
Found at i:21176 original size:16 final size:17
Alignment explanation
Indices: 21149--21183 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
21139 AGAGACTTGA
21149 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
21166 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
21182 GA
1 GA
21184 TTGAAGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:25040 original size:20 final size:20
Alignment explanation
Indices: 25015--25054 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
25005 ACCCCCTTTA
25015 TTAACATAAA-AATTTAAATT
1 TTAACA-AAATAATTTAAATT
25035 TTAACAAAATAATTTAAATT
1 TTAACAAAATAATTTAAATT
25055 AGAAAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAACAAAATAATTTAAATT
Found at i:31294 original size:16 final size:16
Alignment explanation
Indices: 31273--31304 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31263 TGATTGAAAG
*
31273 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
31289 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
31305 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:34315 original size:16 final size:17
Alignment explanation
Indices: 34288--34323 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
34278 AGAAAGTTGA
34288 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
34305 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
34321 GAG
1 GAG
34324 GGATGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.53, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:36899 original size:45 final size:45
Alignment explanation
Indices: 36820--37033 Score: 222
Period size: 45 Copynumber: 4.8 Consensus size: 45
36810 CAGTTACACA
* * *
36820 GTGG-ATCAACACATAGC-ACCACCCTTATAATCAATTATATTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTCG
* ** * *
36863 GTGGAATCAGCACATAACAACCACCTTTATTTTCAATGA-CTTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTCG
* **
36907 GTGGAGTCAGCACATAGCAACCACCTTTATAATCAA-AAGTACCCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAA-TATTCG
** * *
36952 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTA-CCAA
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTC-G
* *
36997 ATGGAATCAGCACATAGCAACCACATTTATAATCAAT
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
37034 GATACTCAGT
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
43 5 0.03
44 49 0.34
45 90 0.62
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTCG
Found at i:36988 original size:89 final size:89
Alignment explanation
Indices: 36819--37038 Score: 252
Period size: 89 Copynumber: 2.5 Consensus size: 89
36809 ACAGTTACAC
* * * **
36819 AGTGGATCAACACATAGC-ACCACCCTTATAATCAATTATATTCGGTGGAATCAGCACATAACAA
1 AGTGGATCAGCACATAGCAACCACCTTTATAATCAATAATACCCGGTGGAATCAGCACATAACAA
**
36883 CCACCTTTATTTTCAAT-G-ACTTC-
66 CCACCTTTATAATCAATGGTAC--CA
* *
36906 GGTGGAGTCAGCACATAGCAACCACCTTTATAATCAA-AAGTACCCGGTGGAATCAGCACATAGC
1 AGTGGA-TCAGCACATAGCAACCACCTTTATAATCAATAA-TACCCGGTGGAATCAGCACATAAC
36970 AACCACCTTTATAATCAATGGTACCA
64 AACCACCTTTATAATCAATGGTACCA
* * *
36996 AATGGAATCAGCACATAGCAACCACATTTATAATCAATGATAC
1 AGTGG-ATCAGCACATAGCAACCACCTTTATAATCAATAATAC
37039 TCAGTACACG
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
87 5 0.04
88 12 0.11
89 55 0.49
90 36 0.32
91 4 0.04
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (89 bp):
AGTGGATCAGCACATAGCAACCACCTTTATAATCAATAATACCCGGTGGAATCAGCACATAACAA
CCACCTTTATAATCAATGGTACCA
Found at i:45375 original size:45 final size:45
Alignment explanation
Indices: 45296--45509 Score: 222
Period size: 45 Copynumber: 4.8 Consensus size: 45
45286 CAGTTACACA
* * *
45296 GTGG-ATCAACACATAGC-ACCACCCTTATAATCAATTATATTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTCG
* ** * *
45339 GTGGAATCAGCACATAACAACCACCTTTATTTTCAATGA-CTTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTCG
* **
45383 GTGGAGTCAGCACATAGCAACCACCTTTATAATCAA-AAGTACCCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAA-TATTCG
** * *
45428 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTA-CCAA
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTC-G
* *
45473 ATGGAATCAGCACATAGCAACCACATTTATAATCAAT
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
45510 GATACTCAGT
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
43 5 0.03
44 49 0.34
45 90 0.62
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTTATAATCAATAATATTCG
Found at i:45464 original size:89 final size:89
Alignment explanation
Indices: 45295--45514 Score: 252
Period size: 89 Copynumber: 2.5 Consensus size: 89
45285 ACAGTTACAC
* * * **
45295 AGTGGATCAACACATAGC-ACCACCCTTATAATCAATTATATTCGGTGGAATCAGCACATAACAA
1 AGTGGATCAGCACATAGCAACCACCTTTATAATCAATAATACCCGGTGGAATCAGCACATAACAA
**
45359 CCACCTTTATTTTCAAT-G-ACTTC-
66 CCACCTTTATAATCAATGGTAC--CA
* *
45382 GGTGGAGTCAGCACATAGCAACCACCTTTATAATCAA-AAGTACCCGGTGGAATCAGCACATAGC
1 AGTGGA-TCAGCACATAGCAACCACCTTTATAATCAATAA-TACCCGGTGGAATCAGCACATAAC
45446 AACCACCTTTATAATCAATGGTACCA
64 AACCACCTTTATAATCAATGGTACCA
* * *
45472 AATGGAATCAGCACATAGCAACCACATTTATAATCAATGATAC
1 AGTGG-ATCAGCACATAGCAACCACCTTTATAATCAATAATAC
45515 TCAGTACACG
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
87 5 0.04
88 12 0.11
89 55 0.49
90 36 0.32
91 4 0.04
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (89 bp):
AGTGGATCAGCACATAGCAACCACCTTTATAATCAATAATACCCGGTGGAATCAGCACATAACAA
CCACCTTTATAATCAATGGTACCA
Found at i:48290 original size:36 final size:36
Alignment explanation
Indices: 48243--48316 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
48233 ATTTAATCGG
48243 GTCAGGATCTAAATAGAGCATGCACATTTCAATTAT
1 GTCAGGATCTAAATAGAGCATGCACATTTCAATTAT
*
48279 GTCAGGATCTAACTAGAGCATGCACATTTCAATTAT
1 GTCAGGATCTAAATAGAGCATGCACATTTCAATTAT
48315 GT
1 GT
48317 GTCCATTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (36 bp):
GTCAGGATCTAAATAGAGCATGCACATTTCAATTAT
Found at i:49819 original size:88 final size:87
Alignment explanation
Indices: 49658--49833 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 87
49648 GGAAATAATA
49658 AAAAGAAATACTAAGGATAATAAAAGAAGTAACAAAAAAAGGGGTCATTACCTTGTTCTTCTTAG
1 AAAAGAAATACTAAGGATAATAAAAGAAGTAACAAAAAAAGGGGTCATTACCTTGTTCTTCTTAG
*
49723 CTGTACAAGAAGAAGCAAAAGG
66 CCGTACAAGAAGAAGCAAAAGG
49745 AAAAGAAATACTAAGGATAATAAAAGAAGTAACAAAAAAAAGGGGTCATTACCTTGTTCTTCTTA
1 AAAAGAAATACTAAGGATAATAAAAGAAGTAAC-AAAAAAAGGGGTCATTACCTTGTTCTTCTTA
49810 GCCGTACAAGAAGAAGCAAAAGG
65 GCCGTACAAGAAGAAGCAAAAGG
49833 A
1 A
49834 GGGGGGGGAG
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 33 0.38
88 54 0.62
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (87 bp):
AAAAGAAATACTAAGGATAATAAAAGAAGTAACAAAAAAAGGGGTCATTACCTTGTTCTTCTTAG
CCGTACAAGAAGAAGCAAAAGG
Found at i:51015 original size:27 final size:27
Alignment explanation
Indices: 50984--51161 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
50974 TAAATTGTAC
50984 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
51011 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
51037 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
51065 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
51093 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * * *
51120 AGCACTAAGTGTGCGAGTTAATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
51147 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
51162 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:51098 original size:82 final size:81
Alignment explanation
Indices: 50985--51135 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
50975 AAATTGTACA
* *
50985 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
51049 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
51066 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
51131 TGCGA
65 TGCGA
51136 GTTAATTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.24
82 47 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:51152 original size:82 final size:81
Alignment explanation
Indices: 50981--51161 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
50971 GATTAAATTG
* *
50981 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
*
51046 GTGTGCGAATTGACCA
66 GTGTGCGAATTAACCA
* * ** *
51062 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
51126 AAGTGTGCGAGTTAATTA
64 AAGTGTGCGAATTAACCA
* *
51144 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
51162 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTAACCA
Found at i:51172 original size:27 final size:27
Alignment explanation
Indices: 51092--51169 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
51082 TTTGACTATG
* ** **
51092 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGACTCAATTATA
* *
51119 TAGCACTAAGTGTGCGAGTTAATTATA
1 TAGCACTAAGTGTGCGACTCAATTATA
*
51146 TAGCACTGAGTGTGCGGACTCAAT
1 TAGCACTAAGTGTGC-GACTCAAT
51170 ATACATTCGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 37 0.86
28 6 0.14
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGACTCAATTATA
Found at i:67203 original size:5 final size:5
Alignment explanation
Indices: 67195--67242 Score: 60
Period size: 5 Copynumber: 8.8 Consensus size: 5
67185 GGGTTAGGGT
67195 TTTTC TTTTC TTTTC TTTTCCC TTTTC TTTTC TTTTTC TTTTC ATTTT
1 TTTTC TTTTC TTTTC TTTT--C TTTTC TTTTC -TTTTC TTTTC -TTTT
67243 TAGTTTAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 25 0.64
6 9 0.23
7 5 0.13
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:67223 original size:22 final size:23
Alignment explanation
Indices: 67195--67237 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
67185 GGGTTAGGGT
67195 TTTTCTTTTC-TTTTCTTTTCCC
1 TTTTCTTTTCTTTTTCTTTTCCC
67217 TTTTCTTTTCTTTTTCTTTTC
1 TTTTCTTTTCTTTTTCTTTTC
67238 ATTTTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTCTTTTTCTTTTCCC
Found at i:67242 original size:17 final size:16
Alignment explanation
Indices: 67194--67242 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
67184 AGGGTTAGGG
67194 TTTTTCTTTTCTTTTC
1 TTTTTCTTTTCTTTTC
*
67210 TTTTCCCTTTTCTTTTC
1 TTTT-TCTTTTCTTTTC
67227 TTTTTCTTTTCATTTT
1 TTTTTCTTTTC-TTTT
67243 TAGTTTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTC
Found at i:67242 original size:22 final size:22
Alignment explanation
Indices: 67195--67242 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
67185 GGGTTAGGGT
*
67195 TTTTCTTTTCTTTTCTTTTCCC
1 TTTTCTTTTCTTTTCTTTTCCA
67217 TTTTCTTTTCTTTTTCTTTT-CA
1 TTTTCTTTTC-TTTTCTTTTCCA
67239 TTTT
1 TTTT
67243 TAGTTTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTCTTTTCTTTTCTTTTCCA
Found at i:70710 original size:50 final size:50
Alignment explanation
Indices: 70646--70743 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
70636 AATACAATCA
*
70646 CAAGATATAATTTCATAATTTAAACAAATCTAATACATTTACAAACATCT
1 CAAGATATAATTTCATAATTTAAACAAATCCAATACATTTACAAACATCT
70696 CAAGATATAATTTCATAATTTAAACAAATCCAATACATTTACAAACAT
1 CAAGATATAATTTCATAATTTAAACAAATCCAATACATTTACAAACAT
70744 AACTATAGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (50 bp):
CAAGATATAATTTCATAATTTAAACAAATCCAATACATTTACAAACATCT
Found at i:91452 original size:24 final size:24
Alignment explanation
Indices: 91425--91510 Score: 109
Period size: 24 Copynumber: 3.5 Consensus size: 24
91415 AATGACAAAT
* ** *
91425 AATTAATATATTAAATTTTAGAAA
1 AATTAATATATTAATTTTTCTAGA
*
91449 AATTTATATATTAATTTTTCTAGA
1 AATTAATATATTAATTTTTCTAGA
91473 AATTAATATATATAATTTTTTCTAGA
1 AATTAATATAT-TAA-TTTTTCTAGA
91499 AATTAATATATT
1 AATTAATATATT
91511 TTGAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
24 29 0.54
25 4 0.07
26 21 0.39
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (24 bp):
AATTAATATATTAATTTTTCTAGA
Found at i:91841 original size:12 final size:11
Alignment explanation
Indices: 91826--91885 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
91816 AAATTAAAAA
91826 AAAAAGTATTTT
1 AAAAA-TATTTT
91838 AAAAATATTTT
1 AAAAATATTTT
*
91849 AAAAATA---A
1 AAAAATATTTT
91857 AAAAATATTTT
1 AAAAATATTTT
*
91868 -TAAATATTTTT
1 AAAAATA-TTTT
91879 AAAAATA
1 AAAAATA
91886 AAATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
8 7 0.18
10 5 0.13
11 17 0.44
12 10 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:91866 original size:30 final size:31
Alignment explanation
Indices: 91824--91888 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
91814 GAAAATTAAA
91824 AAAAAAAGTATTTTAAAA-ATATTTTAAAAAT
1 AAAAAAAGTATTTTAAAATAT-TTTTAAAAAT
*
91855 AAAAAAA-TATTTTTAAATATTTTTAAAAAT
1 AAAAAAAGTATTTTAAAATATTTTTAAAAAT
91885 AAAA
1 AAAA
91889 TATATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAAAAAGTATTTTAAAATATTTTTAAAAAT
Found at i:91893 original size:29 final size:29
Alignment explanation
Indices: 91819--91893 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
91809 TTTTAGAAAA
91819 TTAAAAA-AAAAAGTA-TTTTAAAAATATT
1 TTAAAAATAAAAA-TATTTTTAAAAATATT
*
91847 TTAAAAATAAAAAAATATTTTTAAATAT-TT
1 TTAAAAAT--AAAAATATTTTTAAAAATATT
91877 TTAAAAATAAAATATAT
1 TTAAAAATAAAA-ATAT
91894 ATATTTATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 11 0.27
29 4 0.10
30 12 0.29
31 14 0.34
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
TTAAAAATAAAAATATTTTTAAAAATATT
Found at i:97055 original size:13 final size:13
Alignment explanation
Indices: 97039--97083 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
97029 AATAGTAGGT
97039 GATGATCAATTGA
1 GATGATCAATTGA
*
97052 GATGAT-TATATGA
1 GATGATCAAT-TGA
*
97065 GATAATCAATTGA
1 GATGATCAATTGA
97078 GATGAT
1 GATGAT
97084 TGTAAAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (13 bp):
GATGATCAATTGA
Found at i:97093 original size:26 final size:26
Alignment explanation
Indices: 97043--97099 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
97033 GTAGGTGATG
**
97043 ATCAATTGAGATGATTATATGAGATA
1 ATCAATTGAGATGATTATAAAAGATA
* *
97069 ATCAATTGAGATGATTGTAAAAGATG
1 ATCAATTGAGATGATTATAAAAGATA
97095 ATCAA
1 ATCAA
97100 CTAGGGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (26 bp):
ATCAATTGAGATGATTATAAAAGATA
Found at i:101144 original size:51 final size:51
Alignment explanation
Indices: 101080--101422 Score: 276
Period size: 51 Copynumber: 6.8 Consensus size: 51
101070 TATCGATGAA
* *
101080 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGT
* * * * * * *
101131 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAATAAGTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTG-GT
* * * *
101182 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTACACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATA-AATATTGGT
* * * * * *
101233 TACATGTGTGGTACTAAGTGAAGGCTACTA--TAGATACCAGA-AAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGT-G-TATC-GATAA-ATATTGGT
* * * *
101284 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCATAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-TTGGT
* * * *
101334 CACGTGTGTAGTACTATGTGAAGGCTACTAGGTG-AACTG-TAAA-ACTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GATAAATATTGGT
* *
101383 CATGTGTGTAGTACTATGTGAATGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
101423 ATGATAAAAA
Statistics
Matches: 231, Mismatches: 45, Indels: 33
0.75 0.15 0.11
Matches are distributed among these distances:
49 38 0.16
50 52 0.23
51 135 0.58
52 5 0.02
53 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGT
Found at i:101256 original size:102 final size:102
Alignment explanation
Indices: 101080--101422 Score: 348
Period size: 102 Copynumber: 3.4 Consensus size: 102
101070 TATCGATGAA
101080 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
* *
101145 TAAGTGAAGGCTACTAT-GTGTACCA-ATAAGTTTTGAG-
66 TAAGTGAAGGCTACTATAG-ATACCAGA-AAGCTTTG-GT
* * * * *
101182 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTACACT-ATGGTTACATGTGTGGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATA-AATAATGGTCACATGTGTAGTA
101246 CTAAGTGAAGGCTACTATAGATACCAGAAAGCTTTGGT
65 CTAAGTGAAGGCTACTATAGATACCAGAAAGCTTTGGT
* * * * * * *
101284 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCATAAA-ACTTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGTA
* * * *
101347 CTATGTGAAGGCTACTAGGT-GA-A-CTGTAAAAC--TGAT
65 CTAAGTGAAGGCTACTA--TAGATACCAG-AAAGCTTTGGT
* * *
101383 CATGTGTGTAGTACTATGTGAATGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
101423 ATGATAAAAA
Statistics
Matches: 203, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
99 34 0.17
100 6 0.03
101 39 0.19
102 119 0.59
103 5 0.02
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATAGATACCAGAAAGCTTTGGT
Found at i:104978 original size:114 final size:114
Alignment explanation
Indices: 104773--105127 Score: 539
Period size: 114 Copynumber: 3.1 Consensus size: 114
104763 TAAATGATTT
** * * *
104773 AGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAAGGATTTAGCGGCGTT
1 AGCGCCGCAAAATCACCTAAGTCCAACGACGCCGTTTTATGAGCTTTCGAGGATTTAGCGGCGTT
* *
104838 TTTAAGAAAGCGCCGCTAATGTTCAGGGCTTTAGCGGCGTTTTTGGGAA
66 TTTATGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAA
* * * *
104887 AGCGCCGCAAAATCACCTCAGTCCAACGACGCCATTTTTTGAGCTTTCGGGGATTTAGCGGCGTT
1 AGCGCCGCAAAATCACCTAAGTCCAACGACGCCGTTTTATGAGCTTTCGAGGATTTAGCGGCGTT
* *
104952 TTTATGAAAGCGCCGCAAATGCTCAGGGCTTTAGCGGCATTTTTGGGAA
66 TTTATGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAA
* *
105001 AGCGCCGCAAAATCACCTTAGTCCAACGACGTCGTTTTATGAGCTTTCGAGGATTTAGCGGCGTT
1 AGCGCCGCAAAATCACCTAAGTCCAACGACGCCGTTTTATGAGCTTTCGAGGATTTAGCGGCGTT
* * *
105066 TTTATGAAAGCGCCGCTAATGCACAGGTCTTTAGCGGCGTTTTTCGGAA
66 TTTATGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAA
105115 AGCGCCGCTAAAA
1 AGCGCCGC-AAAA
105128 ATATTTTATC
Statistics
Matches: 218, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
114 214 0.98
115 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (114 bp):
AGCGCCGCAAAATCACCTAAGTCCAACGACGCCGTTTTATGAGCTTTCGAGGATTTAGCGGCGTT
TTTATGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAA
Found at i:105379 original size:15 final size:15
Alignment explanation
Indices: 105359--105389 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
105349 CATATTTTAA
105359 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
105374 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
105389 G
1 G
105390 ATTAGGGGTT
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:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:107673 original size:13 final size:13
Alignment explanation
Indices: 107655--107680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
107645 ACCTCGCAGG
107655 TAATTTAACCAAA
1 TAATTTAACCAAA
107668 TAATTTAACCAAA
1 TAATTTAACCAAA
107681 AAGCAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATTTAACCAAA
Found at i:109850 original size:43 final size:43
Alignment explanation
Indices: 109789--109873 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
109779 CAATGATGTA
* * *
109789 CAAGATTTTCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* *
109832 CAAGATTTACTTGATTAAGAAAATGCATTTTATGTTTTATTA
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTA
109874 TCTTGCATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:110182 original size:43 final size:43
Alignment explanation
Indices: 110135--110403 Score: 317
Period size: 43 Copynumber: 6.3 Consensus size: 43
110125 GATATGTTTT
*
110135 TAGCGGCGTTTGTGTAAAAAGTGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* *
110178 TAGCGGCGTTTGTAG-AGAAAGCGCCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGT-GTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* ** *
110221 TAACGGCGTTTGTGTGGAAAGCGCCGCT-AAGGTTATTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGG-TCTTGATCTA
* * * *
110264 TAGCGGTGTTTGTGTGAAAAGTGCCGCTAAAGGTATTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * *
110307 TTGCGGCATTTGTGGAAAAATCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * *
110350 TAGCGGCGTTTATGGAAAAAGCGCCACTAAAGATCATGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
110393 TAGCGGCGTTT
1 TAGCGGCGTTT
110404 ATAGAAATAA
Statistics
Matches: 195, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
42 5 0.03
43 185 0.95
44 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:110371 original size:129 final size:129
Alignment explanation
Indices: 110135--110403 Score: 362
Period size: 129 Copynumber: 2.1 Consensus size: 129
110125 GATATGTTTT
* * *
110135 TAGCGGCGTTTGTGTAAAAAGTGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTAGAGAAAGC
1 TAGCGGCGTTTGTGTAAAAAGTGCCGCTAAAGGTATTGATCTATAGCGGCATTTGTAGAAAAAGC
* * * * * *
110200 GCCGCTAAAGGTCTTGAGCTATAACGGCGTTTGTGTGGAAAGCGCCGCT-AAGGTTATTGATCTA
66 GCCGCTAAAGGTCCTGAGCTATAACGGCGTTTATGTGAAAAGCGCCACTAAAGATCA-TGATCTA
* * * * *
110264 TAGCGGTGTTTGTGTGAAAAGTGCCGCTAAAGGTATTGATCTATTGCGGCATTTGTGGAAAAATC
1 TAGCGGCGTTTGTGTAAAAAGTGCCGCTAAAGGTATTGATCTATAGCGGCATTTGTAGAAAAAGC
* *
110329 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTATG-GAAAAAGCGCCACTAAAGATCATGATCTA
66 GCCGCTAAAGGTCCTGAGCTATAACGGCGTTTATGTG-AAAAGCGCCACTAAAGATCATGATCTA
110393 TAGCGGCGTTT
1 TAGCGGCGTTT
110404 ATAGAAATAA
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 1 0.01
129 115 0.95
130 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (129 bp):
TAGCGGCGTTTGTGTAAAAAGTGCCGCTAAAGGTATTGATCTATAGCGGCATTTGTAGAAAAAGC
GCCGCTAAAGGTCCTGAGCTATAACGGCGTTTATGTGAAAAGCGCCACTAAAGATCATGATCTA
Found at i:110884 original size:26 final size:26
Alignment explanation
Indices: 110804--110886 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
110794 GATGAACACG
**
110804 TGTGTAGTACTGTGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
110830 CGTGTATTGA-TAAAT-AATGG-TCAC-A
1 TGTGTAGT-ACTAAGTGAA-GGCT-ACTA
110855 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
110881 TGTGTA
1 TGTGTA
110887 CCGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:110931 original size:102 final size:102
Alignment explanation
Indices: 110800--111142 Score: 346
Period size: 102 Copynumber: 3.4 Consensus size: 102
110790 TAAGGATGAA
* *
110800 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAACT-ATGGTCACATATGTAGTA
*
110864 CTAAGTGAAGGCTACTATGTG-TACCGAAAAGTTTTGAG-
65 CTAAGTGAAGGCTACTATG-GATACCGAAAAGCTTTG-GT
* * * *
110902 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTACATATGTGGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAACTATGGTCACATATGTAGTAC
*
110967 TAAGTGAAGGCTACTATGGATACCGGAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGGATACCGAAAAGCTTTGGT
* * * * * * *
111004 CACGTATGTAGTACTATGTGAAGGCTATTACGTG-AGCCG-TAAAACT-TGATCACGTGTGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTA-TCGAT-AAACTATGGTCACATATGTAGT
* * * *
111066 ACTATGTGAAGGCTACTACGTGA-ACTGTAAAA-C--TGAT
64 ACTAAGTGAAGGCTACTATG-GATACCG-AAAAGCTTTGGT
* * * *
111103 CATGTGTGTAGTATTATGTGGAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGA
111143 ATGATAAAAA
Statistics
Matches: 203, Mismatches: 29, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
99 34 0.17
100 1 0.00
101 37 0.18
102 130 0.64
103 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAACTATGGTCACATATGTAGTAC
TAAGTGAAGGCTACTATGGATACCGAAAAGCTTTGGT
Found at i:111122 original size:49 final size:50
Alignment explanation
Indices: 110800--111136 Score: 270
Period size: 51 Copynumber: 6.7 Consensus size: 50
110790 TAAGGATGAA
* * ** * *
110800 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * * *
110851 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGTTTTGAG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA--CTTGAT
* * * * *
110902 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGT-AAACTATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AACCGTAAAACT-TGAT
* * * * * * * * *
110953 TACATATGTGGTACTAAGTGAAGGCTACTATG-GATACCGGAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGA-ACCGTAAAAC-TTGAT
* * *
111004 CACGTATGTAGTACTATGTGAAGGCTATTACGTGAGCCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
111054 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAAC-TGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
* * *
111103 CATGTGTGTAGTATTATGTGGAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
111137 TATCGAATGA
Statistics
Matches: 227, Mismatches: 49, Indels: 22
0.76 0.16 0.07
Matches are distributed among these distances:
48 1 0.00
49 39 0.17
50 49 0.22
51 130 0.57
52 8 0.04
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:112369 original size:47 final size:47
Alignment explanation
Indices: 112318--112410 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
112308 TAAAAATAAG
*
112318 CAGAAATGTTGCCGAAATTTTTACAAAAAAAAATTTAAATGTTTGAA
1 CAGAAATGCTGCCGAAATTTTTACAAAAAAAAATTTAAATGTTTGAA
*
112365 CAGAAATGCTGCCGAAATTTTTACAAAAAAAAATTTAAGTGTTTGA
1 CAGAAATGCTGCCGAAATTTTTACAAAAAAAAATTTAAATGTTTGA
112411 GTTCTAGTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (47 bp):
CAGAAATGCTGCCGAAATTTTTACAAAAAAAAATTTAAATGTTTGAA
Found at i:118545 original size:51 final size:51
Alignment explanation
Indices: 118465--118803 Score: 293
Period size: 51 Copynumber: 6.7 Consensus size: 51
118455 TATCGATGAA
* * *
118465 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* * * * * *
118516 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTG-GT
* * * * * *
118567 CACGTGCGTAGTACTGTGTGAAAGCTACTATGTGTATCGGTAAACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATTGGT
* * * * *
118618 CACATATGTGGTACTATGTGAAGGCTACTATG-GATACCGGA-AAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-TACC-GATAA-ATATTGGT
* *
118669 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGATAAATA-TTGGT
* * * *
118719 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ACTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
* *
118768 CACGTGTGTGGTACTATGTGAATGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
118804 TCGAATGATA
Statistics
Matches: 236, Mismatches: 39, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
49 37 0.16
50 50 0.21
51 145 0.61
52 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGGT
Found at i:118641 original size:102 final size:102
Alignment explanation
Indices: 118465--118806 Score: 369
Period size: 102 Copynumber: 3.4 Consensus size: 102
118455 TATCGATGAA
*
118465 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTA
* *
118529 CTAAGTGAAGGCTACTATGTG-TACC-GAGAAGTTTTGAG-
65 CTATGTGAAGGCTACTATG-GATACCGGA-AAGCTTTG-GT
* * * * *
118567 CACGTGCGTAGTACTGTGTGAAAGCTACTATGTGTATCGGTAAACTATGGTCACATATGTGGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
118632 TATGTGAAGGCTACTATGGATACCGGAAAGCTTTGGT
66 TATGTGAAGGCTACTATGGATACCGGAAAGCTTTGGT
* * * * * *
118669 CACGTATGTAGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGTA
* * * * *
118732 CTATGTGAAGGCTACTACGTGA-ACTGTAAAAC--TGAT
65 CTATGTGAAGGCTACTATG-GATACCGGAAAGCTTTGGT
* * *
118768 CACGTGTGTGGTACTATGTGAATGCTACTACGTGTATCG
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCG
118807 AATGATAAAA
Statistics
Matches: 204, Mismatches: 29, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
99 34 0.17
100 2 0.01
101 44 0.22
102 121 0.59
103 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TATGTGAAGGCTACTATGGATACCGGAAAGCTTTGGT
Found at i:120952 original size:357 final size:357
Alignment explanation
Indices: 120297--121030 Score: 1105
Period size: 357 Copynumber: 2.1 Consensus size: 357
120287 AACCTCAAGT
** * *
120297 TCCTTTTTAAATCTGTATATGATTTCTTTCAGTCCTGTGTAGTTTTTAATTGACTATGGATGATG
1 TCCTTTTTAAATCTGTATATGATTTCCGTCAGTCCTGTGCAGTTTTTAAGTGACTATGGATGATG
* ** *
120362 GCAAATTTCTCTTCTATTTCACGTACCAAGTTTGGACCCACTATCTTTTTTTGCTTAATTACATC
66 GCAAATTTCTCCTCTATTTCACGTACCAAGTTTGGACCCACTATCTTTTTTCACTCAATTACATC
* *
120427 CAACAGGTCGGTATCCTACACGTTCTACCATACAAGGCTTCGAATGGAGACATCTTGAGGCTGAC
131 CAACAGGTCGGTATCCTACACCTTCTACCATACAAGGCTTCGAATGGAGACATCTTCAGGCTGAC
*
120492 GTGGTAACTATTATTATAGGAGAATTCAACCAGAGGGACATACTTCTCCTAGGTTATTCCAAAAT
196 GTGGTAACTATTATTATAGGAGAATTCAACCAGAGGGACATACTTCTCCCAGGTTATTCCAAAAT
* *
120557 CACTCACAGAGAAACGCATTATATCCTCTAAGACCTGAATAACCTTTTCTGATTGGCCATCAATA
261 CAATCACACAGAAACGCATTATATCCTCTAAGACCTGAATAACCTTTTCTGATTGGCCATCAATA
*
120622 GAGGGTGAAA-TGCAATGCTAAAATTTTATTGG
326 GAGGGTGAAACT-CAATGCTAAAATTTTATCGG
* *
120654 TCCTTTTTAAATCTATATATGATTTCCGTCGGTCCTGTGCA-TTTTTAAGTGACTATGGATGATG
1 TCCTTTTTAAATCTGTATATGATTTCCGTCAGTCCTGTGCAGTTTTTAAGTGACTATGGATGATG
* *
120718 GCAACTTTCTCCTCTGTTTCACGTACCAAGTTTGGACCCACTATCTTTCTTTCACTCAATTACAT
66 GCAAATTTCTCCTCTATTTCACGTACCAAGTTTGGACCCACTATCTTT-TTTCACTCAATTACAT
* *
120783 CCAGCAGG-CAGGTGTCCTACACCTTCTACCATACAAGGCTTCGAATGGAGACATCTTCAGGCTG
130 CCAACAGGTC-GGTATCCTACACCTTCTACCATACAAGGCTTCGAATGGAGACATCTTCAGGCTG
* * * * * *
120847 ATGTGGTAACTATTATTATAGGAGAATTCAACTAGAGGGACTTTCTTTTCCCAGTTTATTCCAAA
194 ACGTGGTAACTATTATTATAGGAGAATTCAACCAGAGGGACATACTTCTCCCAGGTTATTCCAAA
* * * * *
120912 ATCAATCACACAGAAACGCATTATATCTTCTAAGACCTGAATAACTTTTTTTGATTGGCCATTAG
259 ATCAATCACACAGAAACGCATTATATCCTCTAAGACCTGAATAACCTTTTCTGATTGGCCATCAA
* * * *
120977 TCGAGGGTGAAACTCAGTGCTAAATTTTTGTCGG
324 TAGAGGGTGAAACTCAATGCTAAAATTTTATCGG
121011 TCCTTTTTAAATCTGTATAT
1 TCCTTTTTAAATCTGTATAT
121031 TATTGAACCA
Statistics
Matches: 338, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
356 68 0.20
357 269 0.80
358 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (357 bp):
TCCTTTTTAAATCTGTATATGATTTCCGTCAGTCCTGTGCAGTTTTTAAGTGACTATGGATGATG
GCAAATTTCTCCTCTATTTCACGTACCAAGTTTGGACCCACTATCTTTTTTCACTCAATTACATC
CAACAGGTCGGTATCCTACACCTTCTACCATACAAGGCTTCGAATGGAGACATCTTCAGGCTGAC
GTGGTAACTATTATTATAGGAGAATTCAACCAGAGGGACATACTTCTCCCAGGTTATTCCAAAAT
CAATCACACAGAAACGCATTATATCCTCTAAGACCTGAATAACCTTTTCTGATTGGCCATCAATA
GAGGGTGAAACTCAATGCTAAAATTTTATCGG
Found at i:122888 original size:18 final size:18
Alignment explanation
Indices: 122867--122912 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
122857 TTTATAAGTT
122867 GTTTAAATTTGATTTTTA
1 GTTTAAATTTGATTTTTA
122885 GTTTAAATTTGATTTTTA
1 GTTTAAATTTGATTTTTA
*
122903 GTTTATATTT
1 GTTTAAATTT
122913 TTTAGGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
GTTTAAATTTGATTTTTA
Found at i:124167 original size:35 final size:35
Alignment explanation
Indices: 124122--124258 Score: 157
Period size: 35 Copynumber: 3.9 Consensus size: 35
124112 TAGCACAGTG
* * * * * *
124122 GCATGTTTAACATGCGAATCAGAATCAGATTTATG
1 GCATGCTTAACATGCGAATCATAAGCAGAATAATA
* *
124157 GCATGCTTAACATGCGAATCATAGGCAGAACAATA
1 GCATGCTTAACATGCGAATCATAAGCAGAATAATA
* *
124192 GCATGCTTAACATGTGAGTCATAAGCAGAATAATA
1 GCATGCTTAACATGCGAATCATAAGCAGAATAATA
* * *
124227 ACACGCTTAACATGCGAATCATAATCAGAATA
1 GCATGCTTAACATGCGAATCATAAGCAGAATA
124259 TTCATAATCA
Statistics
Matches: 85, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 85 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (35 bp):
GCATGCTTAACATGCGAATCATAAGCAGAATAATA
Found at i:124950 original size:37 final size:37
Alignment explanation
Indices: 124893--125044 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
124883 TATGATCACT
*
124893 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
124928 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
124965 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
125010 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
125045 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:125028 original size:46 final size:46
Alignment explanation
Indices: 124961--125229 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
124951 TAAGTGTAGC
* **
124961 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
125007 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
125053 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
125105 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
125151 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
125203 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
125230 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:125080 original size:52 final size:52
Alignment explanation
Indices: 125004--125223 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
124994 TAGCTAAAGC
* *
125004 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
125057 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
125109 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
125155 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
125207 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
125224 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:125126 original size:98 final size:98
Alignment explanation
Indices: 124961--125229 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
124951 TAAGTGTAGC
* * *
124961 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
125026 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
125060 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
125125 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
125158 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
125223 GATCAGA
66 GATCAGA
125230 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:129360 original size:79 final size:81
Alignment explanation
Indices: 129259--129443 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
129249 GCTACTCGTT
* *
129259 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
129322 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
129339 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
129403 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
129419 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
129444 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:129443 original size:40 final size:40
Alignment explanation
Indices: 129259--129443 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
129249 GCTACTCGTT
* *
129259 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
129299 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
129339 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
129378 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
129419 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
129444 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:138481 original size:18 final size:17
Alignment explanation
Indices: 138412--138486 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 17
138402 AAGTCATTCC
*
138412 AAATTAAAAATTAATATA
1 AAATTAAATATTAATA-A
* *
138430 AAGATAATAATATCAATAA
1 AA-ATTA-AATATTAATAA
* *
138449 AAATTTAACATTAATAA
1 AAATTAAATATTAATAA
138466 AACATTAAATATTAATAA
1 AA-ATTAAATATTAATAA
138484 AAA
1 AAA
138487 ACTAAAAGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
17 12 0.27
18 19 0.42
19 6 0.13
20 8 0.18
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (17 bp):
AAATTAAATATTAATAA
Found at i:138492 original size:18 final size:18
Alignment explanation
Indices: 138458--138492 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
138448 AAAATTTAAC
* *
138458 ATTAATAAAACATTAAAT
1 ATTAATAAAAAACTAAAT
138476 ATTAATAAAAAACTAAA
1 ATTAATAAAAAACTAAA
138493 AGTAGAACCT
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:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATTAATAAAAAACTAAAT
Found at i:139035 original size:19 final size:20
Alignment explanation
Indices: 138993--139061 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
138983 GTTACAAAAT
138993 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
*
139013 AATTCAAAATAATTTT-TAA
1 AATTCAAAATAATTTTCAAA
*
139032 AATTCAAAAT-ATTTACAAA
1 AATTCAAAATAATTTTCAAA
139051 AATTCTAAAAT
1 AATTC-AAAAT
139062 TTATATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 4 0.09
19 19 0.43
20 21 0.48
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:142889 original size:15 final size:15
Alignment explanation
Indices: 142869--142903 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
142859 TTCTTTTAAC
142869 GCAAATATCTAGAAT
1 GCAAATATCTAGAAT
*
142884 GCAAATATCTATAAT
1 GCAAATATCTAGAAT
142899 GCAAA
1 GCAAA
142904 GTTTGCAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (15 bp):
GCAAATATCTAGAAT
Found at i:150898 original size:27 final size:27
Alignment explanation
Indices: 150848--150899 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
150838 TATATAAAAA
* * *
150848 ATTTAAGTTTTATAAAAATGAAAAAGT
1 ATTTAAATTTTAGAAAAATAAAAAAGT
*
150875 ATTTAAATTTTAGAAAATTAAAAAA
1 ATTTAAATTTTAGAAAAATAAAAAA
150900 ATTCCATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (27 bp):
ATTTAAATTTTAGAAAAATAAAAAAGT
Found at i:150972 original size:56 final size:55
Alignment explanation
Indices: 150937--151199 Score: 490
Period size: 56 Copynumber: 4.7 Consensus size: 55
150927 AGAATAAATT
150937 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCATTATAACAAAG
1 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCA-TATAACAAAG
150993 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCATTATAACAAAG
1 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCA-TATAACAAAG
151049 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCATTATAACAAAG
1 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCA-TATAACAAAG
151105 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCATTATAACAAAG
1 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCA-TATAACAAAG
151161 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTA
1 TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTA
151200 AAGTATCACC
Statistics
Matches: 207, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 207 1.00
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.30
Consensus pattern (55 bp):
TTATAATAAAATGAATAAAACTTAAAAAGATAAAAATTACTTTCATATAACAAAG
Found at i:159108 original size:125 final size:125
Alignment explanation
Indices: 158886--159118 Score: 466
Period size: 125 Copynumber: 1.9 Consensus size: 125
158876 ATTGTTAAGT
158886 TCAAGTAGTTGTCCCTTAAAGTCAAGTGGTTTTGGAAAATAAGATTTCGGGATCTCATTTCTGTA
1 TCAAGTAGTTGTCCCTTAAAGTCAAGTGGTTTTGGAAAATAAGATTTCGGGATCTCATTTCTGTA
158951 AACCGAGCCTATAAATATTTTTATAAAATATTTACGGAGTTACAGACTTACAAGCAGATC
66 AACCGAGCCTATAAATATTTTTATAAAATATTTACGGAGTTACAGACTTACAAGCAGATC
159011 TCAAGTAGTTGTCCCTTAAAGTCAAGTGGTTTTGGAAAATAAGATTTCGGGATCTCATTTCTGTA
1 TCAAGTAGTTGTCCCTTAAAGTCAAGTGGTTTTGGAAAATAAGATTTCGGGATCTCATTTCTGTA
159076 AACCGAGCCTATAAATATTTTTATAAAATATTTACGGAGTTAC
66 AACCGAGCCTATAAATATTTTTATAAAATATTTACGGAGTTAC
159119 TCTATAGGTA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 108 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (125 bp):
TCAAGTAGTTGTCCCTTAAAGTCAAGTGGTTTTGGAAAATAAGATTTCGGGATCTCATTTCTGTA
AACCGAGCCTATAAATATTTTTATAAAATATTTACGGAGTTACAGACTTACAAGCAGATC
Found at i:163144 original size:23 final size:22
Alignment explanation
Indices: 163118--163176 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
163108 ACCTACTTTC
*
163118 TTACTATAGTATTTTTCGGGGTA
1 TTACTATAGTATTTTT-GGGATA
163141 TTAC-AGTAGTAATTTTTGGGATA
1 TTACTA-TAGT-ATTTTTGGGATA
163164 TTACCTATA-TATT
1 TTA-CTATAGTATT
163177 GATGTAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 4 0.13
23 17 0.55
24 9 0.29
25 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.47
Consensus pattern (22 bp):
TTACTATAGTATTTTTGGGATA
Found at i:164049 original size:40 final size:40
Alignment explanation
Indices: 163992--164105 Score: 129
Period size: 40 Copynumber: 2.9 Consensus size: 40
163982 AAAAACACCA
* * * * *
163992 CTATAGATCAAGCATTAGCAGCGCTTTCTGGAATACGTCG
1 CTATAGGTCAACCATTAGCGGCGCTTTCTGAAAAACGTCG
* * *
164032 CTATGGGTCAACCATTAGCGGTGCTTTTTGAAAAACGTCG
1 CTATAGGTCAACCATTAGCGGCGCTTTCTGAAAAACGTCG
** *
164072 CTATAGGTTGACCATTAGCGGCGCTTTTTGAAAA
1 CTATAGGTCAACCATTAGCGGCGCTTTCTGAAAA
164106 TTACTGCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (40 bp):
CTATAGGTCAACCATTAGCGGCGCTTTCTGAAAAACGTCG
Found at i:164564 original size:14 final size:14
Alignment explanation
Indices: 164515--164566 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
164505 TTAATTATCA
*
164515 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
*
164529 TTATTGTTTAGGGT
1 TTATGGTTTAGGGT
*
164543 ATATGGTTTAGGGT
1 TTATGGTTTAGGGT
*
164557 TTAAGGTTTA
1 TTATGGTTTA
164567 AGAGTTACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:165001 original size:14 final size:14
Alignment explanation
Indices: 164973--165020 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
164963 GTTTTTTTTA
*
164973 TTATAAAAATCTAAT
1 TTATAAAAA-ATAAT
164988 TTATAAAAAATAA-
1 TTATAAAAAATAAT
* *
165001 TAATAAAAAATATT
1 TTATAAAAAATAAT
165015 TTATAA
1 TTATAA
165021 TATCACTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.39
14 8 0.29
15 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TTATAAAAAATAAT
Found at i:165097 original size:20 final size:20
Alignment explanation
Indices: 165072--165110 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
165062 TTTAGCGGCG
**
165072 TTTTACTTTTAAAAAAATCA
1 TTTTACTTAAAAAAAAATCA
165092 TTTTACTTAAAAAAAAATC
1 TTTTACTTAAAAAAAAATC
165111 GGGCGTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTACTTAAAAAAAAATCA
Found at i:165152 original size:20 final size:21
Alignment explanation
Indices: 165127--165169 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
165117 TTTATCCCAA
*
165127 AATTTC-CCCCTGAAACTCCT
1 AATTTCTCCCCTGAAACCCCT
165147 AATTTCTCCCCTGAAACCCCT
1 AATTTCTCCCCTGAAACCCCT
165168 AA
1 AA
165170 CTTTGCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.28, C:0.40, G:0.05, T:0.28
Consensus pattern (21 bp):
AATTTCTCCCCTGAAACCCCT
Found at i:166316 original size:42 final size:42
Alignment explanation
Indices: 166269--166351 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
166259 TTGGTTTGTT
* * *
166269 GGGGGGGGGGGGG-GGGGGCTGGGTTTTTAGTTTTGAAATGG
1 GGGGGGGGGGGGGAGGGGGCTGAGATTTTAGCTTTGAAATGG
166310 GGGGGGGGGGGGGAGGGGGCTGAGATTTTAGCTTTGAAATGG
1 GGGGGGGGGGGGGAGGGGGCTGAGATTTTAGCTTTGAAATGG
166352 ATCGTAAGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 13 0.34
42 25 0.66
ACGTcount: A:0.13, C:0.04, G:0.59, T:0.24
Consensus pattern (42 bp):
GGGGGGGGGGGGGAGGGGGCTGAGATTTTAGCTTTGAAATGG
Found at i:168183 original size:43 final size:43
Alignment explanation
Indices: 168122--168306 Score: 212
Period size: 43 Copynumber: 4.3 Consensus size: 43
168112 GAACGGTACT
* *
168122 TTTAGCGGTGTTTGTCATAAAAGCGCCGCTAAAGGTTATGTTC
1 TTTAGCGGCGTTTGTCATAAAAGCGCCGCTAAAGGTCATGTTC
*
168165 TTTAGCGGCGTTTGTCATAAAAGCGCCGCTAAAAGTCATGCTT-
1 TTTAGCGGCGTTTGTCATAAAAGCGCCGCTAAAGGTCATG-TTC
* * * * *
168208 TATAACGGCGTTTGTACGT-AAAGCGCTGCTAAAGGTCATGTTT
1 TTTAGCGGCGTTTGT-CATAAAAGCGCCGCTAAAGGTCATGTTC
* * * * *
168251 TTTAGCGGCATTTTTTATAAAAGTGCCGCTAAAGCTCATGTTC
1 TTTAGCGGCGTTTGTCATAAAAGCGCCGCTAAAGGTCATGTTC
*
168294 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
168307 TTTCACATAA
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.03
43 111 0.94
44 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTCATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:169778 original size:96 final size:95
Alignment explanation
Indices: 169603--169922 Score: 327
Period size: 96 Copynumber: 3.3 Consensus size: 95
169593 ATATGTGAGC
* *** * * * * * *
169603 TCTTTGCAAAGAATATGTGAACTGTCAATGTATTATATGCGTGAATTATCTCTACAAAGTATGTA
1 TCTTTACAAAGAATATACAAACTGTCAATGTATTGTATGTGTGAACTGTCTCTGCAAAGTATGTG
*
169668 CGAACTGTCCTTGTATTGTATGCATGAGTTG
66 CGAACTGTCATTGTATTGTATGCATGA-TTG
** *
169699 TCTTTATGAAGAATATACAAACTGTCAATGTATTGTATGTGTGAACCGTCTCTGCAAAGTATGTG
1 TCTTTACAAAGAATATACAAACTGTCAATGTATTGTATGTGTGAACTGTCTCTGCAAAGTATGTG
* *
169764 CGAATTGTCATTGTATTGTATGCATGATCTA
66 CGAACTGTCATTGTATTGTATGCATGAT-TG
* * * * * *
169795 TCTTTGCAAAGAATATGCAAATTGTCAATGTATTGTATATGTCAACTGTCT-TAGCGAAGTATGT
1 TCTTTACAAAGAATATACAAACTGTCAATGTATTGTATGTGTGAACTGTCTCT-GCAAAGTATGT
* * *
169859 GTGAACTGTCACTGTATTGTATGCATGAACTG
65 GCGAACTGTCATTGTATTGTATGCATG-ATTG
* * * * *
169891 TCTTTGCACAGAATATGCAAATTGTCATTGTA
1 TCTTTACAAAGAATATACAAACTGTCAATGTA
169923 AAGTATGAGT
Statistics
Matches: 189, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
95 2 0.01
96 186 0.98
97 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (95 bp):
TCTTTACAAAGAATATACAAACTGTCAATGTATTGTATGTGTGAACTGTCTCTGCAAAGTATGTG
CGAACTGTCATTGTATTGTATGCATGATTG
Found at i:169894 original size:48 final size:48
Alignment explanation
Indices: 169603--169894 Score: 200
Period size: 48 Copynumber: 6.1 Consensus size: 48
169593 ATATGTGAGC
* * * * * * * *
169603 TCTTTGCAAAGAATATGTGAACTGTCAATGTATTATATGCGTGAATTA
1 TCTTAGCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATGAACTG
* ** **
169651 TCTCTA-CAAAGTATGTACGAACTGTCCTTGTATTGTATGCATGAGTTG
1 TCT-TAGCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATGAACTG
* * * * ** *
169699 TCTTTATG--AAGAATATACAAACTGTCAATGTATTGTATGTGTGAACCG
1 TC-TTA-GCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATGAACTG
* * * *
169747 TCTCT-GCAAAGTATGTGCGAATTGTCATTGTATTGTATGCATGATCTA
1 TCT-TAGCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATGAACTG
* * * * *
169795 TCTTTGCAAAGAATATGCAAATTGTCAATGTATTGTAT--ATGTCAACTG
1 TCTTAGCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATG--AACTG
* * *
169843 TCTTAGCGAAGTATGTGTGAACTGTCACTGTATTGTATGCATGAACTG
1 TCTTAGCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATGAACTG
169891 TCTT
1 TCTT
169895 TGCACAGAAT
Statistics
Matches: 186, Mismatches: 46, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
46 4 0.02
47 2 0.01
48 175 0.94
49 2 0.01
50 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (48 bp):
TCTTAGCAAAGTATGTGCGAACTGTCAATGTATTGTATGCATGAACTG
Found at i:169929 original size:48 final size:47
Alignment explanation
Indices: 169673--169922 Score: 200
Period size: 48 Copynumber: 5.2 Consensus size: 47
169663 ATGTACGAAC
* ** * *
169673 TGTCCTTGTATTGTATGCATGAGTTGTCTTTATG-AAGAATATACAAAC
1 TGTCATTGTATTGTATGCATGAACTGTC-TT-TGCAAGAATATGCAAAT
* ** * * * * *
169721 TGTCAATGTATTGTATGTGTGAACCGTCTCTGCAAAGTATGTGCGAAT
1 TGTCATTGTATTGTATGCATGAACTGTCTTTGC-AAGAATATGCAAAT
* *
169769 TGTCATTGTATTGTATGCATGATCTATCTTTGCAAAGAATATGCAAAT
1 TGTCATTGTATTGTATGCATGAACTGTCTTTGC-AAGAATATGCAAAT
* * * * ** *
169817 TGTCAATGTATTGTAT--ATGTCAACTGTCTTAGCGAAGTATGTGTGAAC
1 TGTCATTGTATTGTATGCATG--AACTGTCTTTGC-AAGAATATGCAAAT
*
169865 TGTCACTGTATTGTATGCATGAACTGTCTTTGCACAGAATATGCAAAT
1 TGTCATTGTATTGTATGCATGAACTGTCTTTGCA-AGAATATGCAAAT
169913 TGTCATTGTA
1 TGTCATTGTA
169923 AAGTATGAGT
Statistics
Matches: 154, Mismatches: 41, Indels: 14
0.74 0.20 0.07
Matches are distributed among these distances:
46 5 0.03
47 2 0.01
48 144 0.94
50 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (47 bp):
TGTCATTGTATTGTATGCATGAACTGTCTTTGCAAGAATATGCAAAT
Found at i:174349 original size:12 final size:12
Alignment explanation
Indices: 174332--174358 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
174322 CGTTGTAACT
174332 TAGTTTATCTAG
1 TAGTTTATCTAG
174344 TAGTTTATCTAG
1 TAGTTTATCTAG
174356 TAG
1 TAG
174359 CCTAGAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (12 bp):
TAGTTTATCTAG
Found at i:176266 original size:57 final size:59
Alignment explanation
Indices: 176202--176317 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 59
176192 TCACTTTAAT
* * * * *
176202 ATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATC
1 ATTAAATTAATAAAATACTTACTACAAAATAAACATTAAAATAAATTTAATATTAAATC
* *
176259 ATTAAATTAATAAAATATTTATCTACAAAATAAGCATTAAAATAAATTTAATATTAAAT
1 ATTAAATTAATAAAATACTTA-CTACAAAATAAACATTAAAATAAATTTAATATTAAAT
176318 TTATTAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
57 19 0.39
59 1 0.02
60 29 0.59
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (59 bp):
ATTAAATTAATAAAATACTTACTACAAAATAAACATTAAAATAAATTTAATATTAAATC
Found at i:180795 original size:19 final size:19
Alignment explanation
Indices: 180771--180843 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
180761 AATCTTCAAG
180771 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
180790 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
180809 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
180828 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
180844 AGATATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:180869 original size:22 final size:21
Alignment explanation
Indices: 180771--180869 Score: 84
Period size: 19 Copynumber: 4.9 Consensus size: 21
180761 AATCTTCAAG
*
180771 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
180790 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
180809 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
180828 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
180850 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
180870 TAATTTGTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 45 0.66
22 12 0.18
23 11 0.16
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:189650 original size:72 final size:72
Alignment explanation
Indices: 189533--189675 Score: 277
Period size: 72 Copynumber: 2.0 Consensus size: 72
189523 AATTTCGTGG
189533 GGCAAACTCGTTGTTTTAATAAAATTAAATTGTTTATTAAAAACAACCATCTTTTCAAGGTGACC
1 GGCAAACTCGTTGTTTTAATAAAATTAAATTGTTTATTAAAAACAACCATCTTTTCAAGGTGACC
189598 CAATCAA
66 CAATCAA
*
189605 GGCAAACTTGTTGTTTTAATAAAATTAAATTGTTTATTAAAAACAACCATCTTTTCAAGGTGACC
1 GGCAAACTCGTTGTTTTAATAAAATTAAATTGTTTATTAAAAACAACCATCTTTTCAAGGTGACC
189670 CAATCA
66 CAATCA
189676 CACCTTATCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (72 bp):
GGCAAACTCGTTGTTTTAATAAAATTAAATTGTTTATTAAAAACAACCATCTTTTCAAGGTGACC
CAATCAA
Found at i:192662 original size:14 final size:14
Alignment explanation
Indices: 192645--192693 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
192635 TCATACTCAA
192645 AAAATAAATAAATC
1 AAAATAAATAAATC
192659 AAAATCAAA-AAATC
1 AAAAT-AAATAAATC
192673 AAAA-AAATCAAAGTC
1 AAAATAAAT-AAA-TC
192688 AAAATA
1 AAAATA
192694 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.10
14 17 0.57
15 9 0.30
16 1 0.03
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAATAAATC
Found at i:192680 original size:23 final size:22
Alignment explanation
Indices: 192641--192701 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
192631 GAGTTCATAC
*
192641 TCAAAAAATAAATAAATCAAAA
1 TCAAAAAATAAAAAAATCAAAA
*
192663 TCAAAAAATCAAAAAAATCAAAG
1 TCAAAAAAT-AAAAAAATCAAAA
* *
192686 TCAAAATAGAAAAAAA
1 TCAAAAAATAAAAAAA
192702 AAAGAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (22 bp):
TCAAAAAATAAAAAAATCAAAA
Found at i:192704 original size:6 final size:6
Alignment explanation
Indices: 192688--192729 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
192678 AATCAAAGTC
*
192688 AAAATAG AAAAA- AAAAAG AAAAAG AAAAAG AAAAAG TAAAAG
1 AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
192730 GAGAGGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 5 0.15
6 24 0.73
7 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:192707 original size:11 final size:11
Alignment explanation
Indices: 192688--192722 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
192678 AATCAAAGTC
*
192688 AAAATAGAAAA
1 AAAAAAGAAAA
192699 AAAAAAGAAAA
1 AAAAAAGAAAA
192710 AGAAAAAGAAAA
1 A-AAAAAGAAAA
192722 A
1 A
192723 GTAAAAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:194211 original size:53 final size:53
Alignment explanation
Indices: 194131--194236 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
194121 GAAAAGGTAG
*
194131 GCGACATCTTGGAGTATCGACAAAGTCCCGAAGATCTCCTAAACACATGTCAA
1 GCGACATCTTGGAGCATCGACAAAGTCCCGAAGATCTCCTAAACACATGTCAA
*
194184 GCGACATCTTGGAGCATCGACAAAGTCCTGAAGATCTCCTAAACACATGTCAA
1 GCGACATCTTGGAGCATCGACAAAGTCCCGAAGATCTCCTAAACACATGTCAA
194237 ACTCAGAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (53 bp):
GCGACATCTTGGAGCATCGACAAAGTCCCGAAGATCTCCTAAACACATGTCAA
Found at i:195435 original size:50 final size:49
Alignment explanation
Indices: 195274--195883 Score: 529
Period size: 50 Copynumber: 12.4 Consensus size: 49
195264 GTCTTCAATT
* * * *
195274 AAAAGATTGAAGCCACAAC-GACGAATCTTACCTTTCCAGGCAG-TGCAGTGG
1 AAAAGATTGAAGCTACAACAG-CGGATCTTA-CTTTCC-TGC-GTTGCAGTGA
* * * *
195325 AACAGATTGAAGCTACAACAGCGGATCTTGC-TTCC--C-TGGCAGTTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGCGTTGCAGTGA
* * *
195370 AAAAGATTGAAGCTACAACAGTGGATCTTACTTTCTTAGCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-GCGTTGCAGTGA
* * * * * *
195420 AACAGATTGAAGCTACAGCAGCGGATCTTACTTCCCTGACATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTG-CGTTGCAGTGA
* *
195470 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-GCGTTGCAGTGA
* * * ** * *
195520 AACAGATTGAAGCTATAACAGCGGATCTTACTTCCCTGATATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTG-CGTTGCAGTGA
* * * * *
195570 AAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTG-CGTTGCAGTGA
* * * * *
195620 AAAAGATTGAAGCTACAACAACGGATTTTACTTTCTTAGCGTTACAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-GCGTTGCAGTGA
* * ** * *
195670 AACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGATATTGCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTG-CGTTGCAGTGA
* * *
195720 AAAAGATTGAAGCTACAACAGCAGATCTTACTTTCTTAGCGTTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCT-GCGTTGCAGTGA
* * * * *
195770 AACAGATTGAAGCTACAACAGCGGATCTTGC-TTCC-CCG--GCAATTA
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGCGTTGCAGTGA
** * * *
195815 AAAAGATTGAAGCTACAACAGCAAATCTTACTTTCCAGGCGGTGCAGTGG
1 AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCC-TGCGTTGCAGTGA
*
195865 AATAGATTGAAGCTACAAC
1 AAAAGATTGAAGCTACAAC
195884 GGCAAATCTT
Statistics
Matches: 450, Mismatches: 91, Indels: 37
0.78 0.16 0.06
Matches are distributed among these distances:
45 64 0.14
46 8 0.02
47 2 0.00
48 2 0.00
49 11 0.02
50 335 0.74
51 27 0.06
52 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (49 bp):
AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTGCGTTGCAGTGA
Found at i:195546 original size:150 final size:148
Alignment explanation
Indices: 195328--196010 Score: 598
Period size: 150 Copynumber: 4.6 Consensus size: 148
195318 GCAGTGGAAC
* * * *
195328 AGATTGAAGCTACAACAGCGGATCTTGC-TTC--CCTGGCAGTTAAAAAGATTGAAGCTACAACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCAGCGTTGCAGTGAAAAAGATTGAAGCTACAACA
* * * * * * * * *
195390 GTGGATCTTACTT-TCTTAGCGTTGCAGTGGAACAGATTGAAGCTACAGCAGCGGATCTTACTTC
66 GCGGATCTTACTTCCCTGA-CATTGCAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTTC
195454 CCTGACATTGCAATTAAAA
130 CCTGACATTGCAATTAAAA
* * *
195473 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCTATAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTC--AGCGTTGCAGTGAAAAAGATTGAAGCTACAA
* * *
195538 CAGCGGATCTTACTTCCCTGATATTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTT
64 CAGCGGATCTTACTTCCCTGACATTGCAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTT
*
195603 CCCTGACATTGTAATTAAAA
129 CCCTGACATTGCAATTAAAA
* * * * *
195623 AGATTGAAGCTACAACAACGGATTTTACTTTCTTAGCGTTACAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTC--AGCGTTGCAGTGAAAAAGATTGAAGCTACAA
* *
195688 CAGCGGATCTTACTTCCCTGATATTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCTTACTT
64 CAGCGGATCTTACTTCCCTGACATTGCAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTT
* * * * ** *
195753 -TCTTAGCGTTGCAGTGGAAC
129 CCCTGA-CATTGCAATTAAAA
* ** * *
195773 AGATTGAAGCTACAACAGCGGATCTTGC-TTCCCCG--GCAATTAAAAAGATTGAAGCTACAACA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCAGCGTTGCAGTGAAAAAGATTGAAGCTACAACA
** * * * ** * * * * *
195835 GCAAATCTTACTTTCCAGGCGGTGCAGTGGAATAGATTGAAGCTACAACGGCAAATCTT-CTTTC
66 GCGGATCTTACTTCCCTGACATTGCAATGAAAAAGATTGAAGCTACAACAGCAGATCTTAC-TTC
*
195899 ACC-AACATTGCAATTAAAA
130 -CCTGACATTGCAATTAAAA
* * * * * * *
195918 AGATTGAAG-TCACAACGGCGAATCTTACTTCCCAGGCGGTGTAAT-AGAATAGATTGAAGCTAC
1 AGATTGAAGCT-ACAACAGCGGATCTTACTT-TCA-GCGTTGCAGTGA-AAAAGATTGAAGCTAC
* * * **
195981 GACGGCGAATCTTACTTCCCCAACATTGCA
62 AACAGCGGATCTTACTTCCCTGACATTGCA
196011 GTTAAACAGA
Statistics
Matches: 442, Mismatches: 79, Indels: 29
0.80 0.14 0.05
Matches are distributed among these distances:
144 2 0.00
145 128 0.29
146 5 0.01
147 4 0.01
148 2 0.00
149 7 0.02
150 291 0.66
151 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (148 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCAGCGTTGCAGTGAAAAAGATTGAAGCTACAACA
GCGGATCTTACTTCCCTGACATTGCAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTTCC
CTGACATTGCAATTAAAA
Found at i:195893 original size:50 final size:49
Alignment explanation
Indices: 195269--196023 Score: 528
Period size: 50 Copynumber: 15.3 Consensus size: 49
195259 CTATAGTCTT
* * *
195269 CAATT-AAAAGATTGAAGCCACAAC-GACGAATCTTACCTTTCCAGGCAGTG
1 CAATTAAAAAGATTGAAGCTACAACAG-CGGATCTTA-CTTTCCA-GCATTG
* ** * * *
195319 CAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGC-TTCC--C-TGG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGCATTG
* * * *
195364 CAGTTAAAAAGATTGAAGCTACAACAGTGGATCTTACTTTCTTAGCGTTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGCATTG
* ** * * * *
195414 CAGTGGAACAGATTGAAGCTACAGCAGCGGATCTTACTTCCCTGACATTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAG-CATTG
* *
195464 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGCATTG
* ** * * * * *
195514 CAGTGGAACAGATTGAAGCTATAACAGCGGATCTTACTTCCCTGATATTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAG-CATTG
* *
195564 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAG-CATTG
* * * * * *
195614 TAATTAAAAAGATTGAAGCTACAACAACGGATTTTACTTTCTTAGCGTTA
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGCATTG
* ** * * * *
195664 CAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTGATATTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAG-CATTG
* * *
195714 CAATTAAAAAGATTGAAGCTACAACAGCAGATCTTACTTTCTTAGCGTTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CAGCATTG
* ** * * **
195764 CAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGC-TTCC--C-CGG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGCATTG
** **
195809 CAATTAAAAAGATTGAAGCTACAACAGCAAATCTTACTTTCCAGGCGGTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCA-GCATTG
* ** * * ** *
195859 CAGTGGAATAGATTGAAGCTACAACGGCAAATCTT-CTTTCACCAACATTG
1 CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTT--CCAGCATTG
* * * **
195909 CAATTAAAAAGATTGAAG-TCACAACGGCGAATCTTACTTCCCAGGCGGTG
1 CAATTAAAAAGATTGAAGCT-ACAACAGCGGATCTTACTTTCCA-GCATTG
* * * * * * *
195959 TAA-TAGAATAGATTGAAGCTACGACGGCGAATCTTACTTCCCCAACATTG
1 CAATTA-AAAAGATTGAAGCTACAACAGCGGATCTTACTT-TCCAGCATTG
* *
196009 CAGTTAAACAGATTG
1 CAATTAAAAAGATTG
196024 GAGATGGCAG
Statistics
Matches: 554, Mismatches: 124, Indels: 54
0.76 0.17 0.07
Matches are distributed among these distances:
45 64 0.12
46 9 0.02
49 22 0.04
50 418 0.75
51 40 0.07
52 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (49 bp):
CAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCAGCATTG
Found at i:196001 original size:195 final size:195
Alignment explanation
Indices: 195473--196001 Score: 480
Period size: 195 Copynumber: 2.7 Consensus size: 195
195463 GCAATTAAAA
** * * * * * ** * *
195473 AGATTGAAGCTACAACAGCGGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCTATAA
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAGCTACAA
* * *** * *
195538 CAGCGGATCTTAC-TTCCCTGATATTGCAATTA-AAAAGATTGAAGCTACAACAGCGGATCTTAC
66 CAGCAGATCTTACTTTCCCAG-CGGTGCAA-TAGAACAGATTGAAGCTACAACAGCGAATCTTAC
* * ** * * *
195601 TTCCCTGACATTGTAATTAAAAAGATTGAAGCTACAACAACGGATTTTACTTTCTTAGCGTTACA
129 TTCCC---C--GGCAATTAAAAAGATTGAAGCTACAACAACAAATCTTACTTTCTCAGCGGTACA
195666 GTGGAAC
189 GTGGAAC
** * *
195673 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGATATTGCAATTAAAAAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAGCTACAA
** * * * * *
195738 CAGCAGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTGCTT
66 CAGCAGATCTTACTTTCCCAGCGGTGCAATAGAACAGATTGAAGCTACAACAGCGAATCTTACTT
* *
195803 CCCCGGCAATTAAAAAGATTGAAGCTACAACAGCAAATCTTACTTTC-CAGGCGGTGCAGTGGAA
131 CCCCGGCAATTAAAAAGATTGAAGCTACAACAACAAATCTTACTTTCTCA-GCGGTACAGTGGAA
*
195867 T
195 C
*
195868 AGATTGAAGCTACAACGGCAAATCTT-CTTTCACC-AACATTGCAATTAAAAAGATTGAAG-TCA
1 AGATTGAAGCTACAACAGCAAATCTTAC-TTC-CCTAACATTGCAATTAAAAAGATTGAAGCT-A
* * * * *
195930 CAACGGC-GAATCTTAC-TTCCCAGGCGGTGTAATAGAATAGATTGAAGCTACGACGGCGAATCT
63 CAACAGCAG-ATCTTACTTTCCCA-GCGGTGCAATAGAACAGATTGAAGCTACAACAGCGAATCT
195993 TACTTCCCC
126 TACTTCCCC
196002 AACATTGCAG
Statistics
Matches: 273, Mismatches: 48, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
194 8 0.03
195 152 0.56
196 2 0.01
197 1 0.00
199 1 0.00
200 105 0.38
201 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (195 bp):
AGATTGAAGCTACAACAGCAAATCTTACTTCCCTAACATTGCAATTAAAAAGATTGAAGCTACAA
CAGCAGATCTTACTTTCCCAGCGGTGCAATAGAACAGATTGAAGCTACAACAGCGAATCTTACTT
CCCCGGCAATTAAAAAGATTGAAGCTACAACAACAAATCTTACTTTCTCAGCGGTACAGTGGAAC
Found at i:196097 original size:18 final size:18
Alignment explanation
Indices: 196074--196108 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
196064 GATCGCATCT
*
196074 AGTCCTATCTCCCTAAGC
1 AGTCCTATCACCCTAAGC
196092 AGTCCTATCACCCTAAG
1 AGTCCTATCACCCTAAG
196109 TAGTAGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.11, T:0.26
Consensus pattern (18 bp):
AGTCCTATCACCCTAAGC
Found at i:196335 original size:132 final size:132
Alignment explanation
Indices: 196092--196723 Score: 1012
Period size: 132 Copynumber: 4.8 Consensus size: 132
196082 CTCCCTAAGC
* *
196092 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAAATTTTGTCACCCTAAGCAGT
1 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
196157 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCTCAATACAGTGGAGAAGCAAATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
196222 TT
131 TT
*
196224 TGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
*
196289 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATATAGTGGAGAAGCAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
196354 TT
131 TT
* ** * * * * *
196356 AGTCTTATCACCCTAAACAATAGTGGAATAGGTCGAAGATTGTAGATTCTGTCACCCTAAACAGT
1 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
*
196421 AGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
196486 TT
131 TT
* * *
196488 AGTCCTATCACCCTAAATAGTAGTGGAATAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGT
1 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* * * *
196553 AGTGGAGCAGATCGAATATGGTGAATCTTATCTTTCCAATACAGTGGAGAAGCAGATTTAAGTCG
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
196618 TT
131 TT
* * * *
196620 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAATATTGCAGATTCTGTCTCCCTAAGCAGT
1 AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
* *
196685 AGTAGAACAGATCGAAGATGGTGAATCTTATCTTCCCAA
66 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
196724 GTGGAATGGA
Statistics
Matches: 462, Mismatches: 38, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 462 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (132 bp):
AGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCA
TT
Found at i:196439 original size:44 final size:44
Alignment explanation
Indices: 196228--196568 Score: 155
Period size: 44 Copynumber: 7.8 Consensus size: 44
196218 GCCATTTGTC
** * * * *
196228 CTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGTAGATT
* * * *
196272 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT-GAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGTAGATT
* * * * * **
196315 CTTATCTTCCC-AATATAGTGGAGAAGCAGATTTAAGCCA-T-TAG--T
1 C-TATC-ACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGTAGATT
* ** *
196359 CTTATCACCCTAAACAATAGTGGAATAGGTCGAAGATTGTAGATT
1 C-TATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGTAGATT
* * * *
196404 CTGTCACCCTAAACAGTAGTGGAGCAGATCAAAGATGGT-GAAT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGTAGATT
* * * * ** *
196447 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATC-ACCCTAA-ACAGTAGTGGAGCAGATCGAAG--ATTGTAGATT
* ** * *
196492 CTATCACCCTAAATAGTAGTGGAATAGGTCGAAGATTGCAGATT
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGTAGATT
* *
196536 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAA
1 CTATCACCCTAAACAGTAGTGGAGCAGATCGAA
196569 TATGGTGAAT
Statistics
Matches: 211, Mismatches: 65, Indels: 42
0.66 0.20 0.13
Matches are distributed among these distances:
41 2 0.01
42 2 0.01
43 44 0.21
44 116 0.55
45 43 0.20
46 2 0.01
47 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (44 bp):
CTATCACCCTAAACAGTAGTGGAGCAGATCGAAGATTGTAGATT
Found at i:196927 original size:17 final size:18
Alignment explanation
Indices: 196905--196946 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
196895 TTTTCCTGGG
196905 CCCAAAACCAAT-ACAAA
1 CCCAAAACCAATAACAAA
* *
196922 CCC-AAACTATTAACAAA
1 CCCAAAACCAATAACAAA
196939 CCCAAAAC
1 CCCAAAAC
196947 AAATTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.55, C:0.36, G:0.00, T:0.10
Consensus pattern (18 bp):
CCCAAAACCAATAACAAA
Found at i:200422 original size:12 final size:12
Alignment explanation
Indices: 200400--200434 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
200390 AATATAAATA
200400 AATAGGTAATAAT
1 AATA-GTAATAAT
200413 AATAGTAATAAT
1 AATAGTAATAAT
*
200425 AATAATAATA
1 AATAGTAATA
200435 GGACTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:202199 original size:44 final size:44
Alignment explanation
Indices: 202131--202558 Score: 243
Period size: 44 Copynumber: 9.8 Consensus size: 44
202121 CCTTTATTTT
* * * *
202131 AATCCGCTCCATTATAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
202175 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTC
* * * * * * *
202221 AGTCTGTTCCACTGTAATCTCAGGGAAATAGGA--CCT-GGTGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * * ***
202262 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTTATTC
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTACTAGCTTC
* * *
202305 TAATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTC
1 -AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
202350 AATCTGCTCCGCGGTAATCTCAGGGAGATAAGATTTGA-AATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTA-GCTTC
** * * *
202396 GGTCTGTTCCACTGTAATCTCAGGG-GAATAAGA--CCTAG-TGC
1 AATCTGCTCCACTGTAATCTCAGGGAG-ATAAGATTACTAGCTTC
* * * * * * * *
202437 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTGGTTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTAC-TAGCTTC
* * *
202481 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
202525 AATCTACTCCGCTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
202559 CTGAAATTCT
Statistics
Matches: 286, Mismatches: 76, Indels: 44
0.70 0.19 0.11
Matches are distributed among these distances:
40 2 0.01
41 51 0.18
42 6 0.02
43 5 0.02
44 142 0.50
45 16 0.06
46 64 0.22
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:202571 original size:175 final size:175
Alignment explanation
Indices: 202086--202571 Score: 819
Period size: 175 Copynumber: 2.8 Consensus size: 175
202076 AGATCTGAAA
* * * * *
202086 CGATCTACTCTACTGTAACCTCAAAGAAATAAGATCCTTTATTTTAATCCGCTCCATTATAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
202151 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
* * *
202216 TCTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAGGACCTGGTG
131 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
*
202261 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTCTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* * *
202326 CAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCGGTAATCTCAGGGAGATAAGATTTGAAAT
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
*
202391 TCTTCGGTCTGTTCCACTGTAATCTCAGGGGAATAAGACCTAGTG
131 TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
**
202436 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGGTTTTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* *
202501 CAGGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
202566 TCTTCG
131 TCTTCG
202572 ATCTACTTCG
Statistics
Matches: 290, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 290 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (175 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
TCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTAGTG
Found at i:203894 original size:1 final size:1
Alignment explanation
Indices: 203888--203957 Score: 77
Period size: 1 Copynumber: 70.0 Consensus size: 1
203878 CTCTCCAAAG
* * * * * * *
203888 TTTTTTTGTTTTTTTTTGTTTTTTTTTTTATTTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
203953 TTTTT
1 TTTTT
203958 AGGAAGCAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.00, G:0.09, T:0.90
Consensus pattern (1 bp):
T
Found at i:203903 original size:10 final size:10
Alignment explanation
Indices: 203888--203957 Score: 88
Period size: 10 Copynumber: 6.7 Consensus size: 10
203878 CTCTCCAAAG
203888 TTTTTTTGTT
1 TTTTTTTGTT
203898 TTTTTTTGTTTT
1 TTTTTTTG--TT
*
203910 TTTTTTTATT
1 TTTTTTTGTT
203920 TTTTTTTGTT
1 TTTTTTTGTT
203930 TTTTTTTGTT
1 TTTTTTTGTT
203940 TTTTTGTT-TT
1 TTTTT-TTGTT
203950 GTTTTTTT
1 -TTTTTTT
203958 AGGAAGCAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
10 38 0.70
11 7 0.13
12 9 0.17
ACGTcount: A:0.01, C:0.00, G:0.09, T:0.90
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:203916 original size:22 final size:21
Alignment explanation
Indices: 203888--203957 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 21
203878 CTCTCCAAAG
*
203888 TTTTTTTGTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTGTTT
203909 TTTTTTTTATTTTTTTTTGTTT
1 TTTTTTTT-TTTTTTTTTGTTT
203931 TTTTTTGTTTTTTTGTTTTGTTT
1 TTTTTT-TTTTTTT-TTTTGTTT
203954 TTTT
1 TTTT
203958 AGGAAGCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 7 0.16
22 24 0.53
23 14 0.31
ACGTcount: A:0.01, C:0.00, G:0.09, T:0.90
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTTGTTT
Found at i:203929 original size:32 final size:33
Alignment explanation
Indices: 203888--203957 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 33
203878 CTCTCCAAAG
203888 TTTTTTTGTTTTTTTTTGTTTTTTT-TTTTATT
1 TTTTTTTGTTTTTTTTTGTTTTTTTGTTTTATT
*
203920 TTTTTTTGTTTTTTTTTGTTTTTTTGTTTTGTT
1 TTTTTTTGTTTTTTTTTGTTTTTTTGTTTTATT
203953 TTTTT
1 TTTTT
203958 AGGAAGCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.01, C:0.00, G:0.09, T:0.90
Consensus pattern (33 bp):
TTTTTTTGTTTTTTTTTGTTTTTTTGTTTTATT
Found at i:215405 original size:12 final size:12
Alignment explanation
Indices: 215383--215417 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
215373 AATATAAATA
215383 AATAGGTAATAAT
1 AATA-GTAATAAT
215396 AATAGTAATAAT
1 AATAGTAATAAT
*
215408 AATAATAATA
1 AATAGTAATA
215418 GGACTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:218351 original size:16 final size:18
Alignment explanation
Indices: 218332--218376 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
218322 AAAATTCTTT
218332 AAAATTCAAAAATA-G-A
1 AAAATTCAAAAATATGAA
**
218348 AAAATAGAAAAATATGAA
1 AAAATTCAAAAATATGAA
218366 AAAATTCAAAA
1 AAAATTCAAAA
218377 TTCAATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 12 0.52
17 1 0.04
18 10 0.43
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (18 bp):
AAAATTCAAAAATATGAA
Found at i:218359 original size:9 final size:8
Alignment explanation
Indices: 218339--218368 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
218329 TTTAAAATTC
218339 AAAAATAG
1 AAAAATAG
218347 AAAAATAG
1 AAAAATAG
218355 AAAAATATG
1 AAAAATA-G
218364 AAAAA
1 AAAAA
218369 ATTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (8 bp):
AAAAATAG
Found at i:218788 original size:18 final size:19
Alignment explanation
Indices: 218765--218809 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
218755 CTAACATTGA
*
218765 ATTTTAGAATT-TTTTTAT
1 ATTTTAAAATTATTTTTAT
218783 ATTTTAAAATTATTTTTAT
1 ATTTTAAAATTATTTTTAT
218802 A-TTTAAAA
1 ATTTTAAAA
218810 AAATTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTAAAATTATTTTTAT
Found at i:218810 original size:19 final size:18
Alignment explanation
Indices: 218772--218810 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
218762 TGAATTTTAG
*
218772 AATTTTTTTATATTTTAA
1 AATTTTTTTATATTTAAA
218790 AATTATTTTTATATTTAAA
1 AATT-TTTTTATATTTAAA
218809 AA
1 AA
218811 AATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTTTTATATTTAAA
Found at i:226734 original size:22 final size:22
Alignment explanation
Indices: 226709--226754 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
226699 GTTTTGAGAA
*
226709 TACT-CAAATACAGTAACAATGC
1 TACTACAAATACA-TAACAAAGC
*
226731 TACTACAAATCCATAACAAAGC
1 TACTACAAATACATAACAAAGC
226753 TA
1 TA
226755 GTTTACCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (22 bp):
TACTACAAATACATAACAAAGC
Found at i:229986 original size:20 final size:20
Alignment explanation
Indices: 229963--230028 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
229953 GTAACTCTAT
229963 ACAGAGGCACTGTAGTGCAA
1 ACAGAGGCACTGTAGTGCAA
*
229983 ACAGAGGCA-TGCTTGTGCAA
1 ACAGAGGCACTG-TAGTGCAA
** * *
230003 TTAGAGGCACAGAAGTGCAA
1 ACAGAGGCACTGTAGTGCAA
230023 ACAGAG
1 ACAGAG
230029 ACATCGTAGC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.06
20 33 0.92
21 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.15
Consensus pattern (20 bp):
ACAGAGGCACTGTAGTGCAA
Found at i:232803 original size:11 final size:11
Alignment explanation
Indices: 232789--233009 Score: 158
Period size: 11 Copynumber: 22.4 Consensus size: 11
232779 TTTTTTTTAA
232789 TTTTAAAATAT
1 TTTTAAAATAT
232800 TTTTAAAATACT
1 TTTTAAAATA-T
* *
232812 TTTT-TATTAT
1 TTTTAAAATAT
*
232822 TTTT----TAA
1 TTTTAAAATAT
232829 TTTTAAAATAT
1 TTTTAAAATAT
232840 TTTTAAAATACT
1 TTTTAAAATA-T
*
232852 TTTT--ATTAT
1 TTTTAAAATAT
232861 TTTT---A-A-
1 TTTTAAAATAT
232867 TTTTAAAATAT
1 TTTTAAAATAT
232878 TTTTAAAATAT
1 TTTTAAAATAT
232889 TTTTAAAATAT
1 TTTTAAAATAT
232900 TTTT---A-A-
1 TTTTAAAATAT
232906 TTTTAAAATAT
1 TTTTAAAATAT
232917 TTTTAAAATACT
1 TTTTAAAATA-T
*
232929 TTTT--ATTAT
1 TTTTAAAATAT
232938 TTTT---A-A-
1 TTTTAAAATAT
232944 TTTTAAAATAT
1 TTTTAAAATAT
232955 TTTTAAAATAT
1 TTTTAAAATAT
232966 TTTTAAAATAT
1 TTTTAAAATAT
232977 TTTT---A-A-
1 TTTTAAAATAT
232983 TTTTAAAATAT
1 TTTTAAAATAT
232994 TTTTAAAATACT
1 TTTTAAAATA-T
233006 TTTT
1 TTTT
233010 TAATTTTTAA
Statistics
Matches: 174, Mismatches: 8, Indels: 55
0.73 0.03 0.23
Matches are distributed among these distances:
6 16 0.09
7 10 0.06
8 2 0.01
9 14 0.08
10 15 0.09
11 97 0.56
12 20 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:232815 original size:39 final size:39
Alignment explanation
Indices: 232772--233014 Score: 386
Period size: 39 Copynumber: 6.2 Consensus size: 39
232762 TTATCTCTAT
*
232772 TTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
*
232811 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTAATTA-TTTTTAATTTTAAAATATTTTTAAAATAC
232851 TTTTT-ATTATTTTTAATTTTAAAATATTTTTAAAATA-
1 TTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
*
232888 TTTTTAAAATATTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTT-AATTATTTTTAATTTTAAAATATTTTTAAAATAC
232928 TTTTT-ATTATTTTTAATTTTAAAATATTTTTAAAATA-
1 TTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
*
232965 TTTTTAAAATATTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTT-AATTATTTTTAATTTTAAAATATTTTTAAAATAC
233005 TTTTTTAATT
1 -TTTTTAATT
233015 TTTAAAATAA
Statistics
Matches: 190, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
37 10 0.05
38 59 0.31
39 74 0.39
40 42 0.22
41 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (39 bp):
TTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:232928 original size:77 final size:77
Alignment explanation
Indices: 232772--233019 Score: 419
Period size: 77 Copynumber: 3.2 Consensus size: 77
232762 TTATCTCTAT
* * *
232772 TTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT-TATTATTTTTTAATTTTAAA
1 TTTTT-ATTATTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAAAATA-TTTTTAATTTTAAA
232836 ATATTTTTAAAATAC
63 ATATTTTTAAAATAC
232851 TTTTTATTATTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATATTTTTAATTTTAAAATA
1 TTTTTATTATTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATATTTTTAATTTTAAAATA
232916 TTTTTAAAATAC
66 TTTTTAAAATAC
232928 TTTTTATTATTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATATTTTTAATTTTAAAATA
1 TTTTTATTATTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATATTTTTAATTTTAAAATA
232993 TTTTTAAAATAC
66 TTTTTAAAATAC
*
233005 TTTTT-TAATTTTTAA
1 TTTTTATTATTTTTAA
233020 AATAAATTTT
Statistics
Matches: 164, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
76 9 0.05
77 116 0.71
78 34 0.21
79 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (77 bp):
TTTTTATTATTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATATTTTTAATTTTAAAATA
TTTTTAAAATAC
Found at i:233029 original size:20 final size:20
Alignment explanation
Indices: 232992--233030 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
232982 ATTTTAAAAT
**
232992 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
233012 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
233031 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:233037 original size:22 final size:20
Alignment explanation
Indices: 232991--233048 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
232981 AATTTTAAAA
*
232991 TATTTTTAAAAT-ACTTTTT
1 TATTTTTAAAATAAATTTTT
233010 TAATTTTTAAAATAAATTTTT
1 T-ATTTTTAAAATAAATTTTT
233031 GGTATTTATTAAAA-AAAT
1 --TATTT-TTAAAATAAAT
233049 GAGCCGGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 6 0.18
22 8 0.24
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTTTAAAATAAATTTTT
Found at i:233394 original size:26 final size:26
Alignment explanation
Indices: 233339--233414 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
233329 TCTCATCCCT
* **
233339 ATTTTACCC-TCAACAAAATTTTGATG
1 ATTTTACCCAT-AATAAAATTTTGACA
**
233365 ATTTTACCCATTGTAAAATTTTGACA
1 ATTTTACCCATAATAAAATTTTGACA
* *
233391 ATTTTGCCCCTAATAAAATTTTGA
1 ATTTTACCCATAATAAAATTTTGA
233415 GAAAATATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTTTACCCATAATAAAATTTTGACA
Found at i:233598 original size:18 final size:18
Alignment explanation
Indices: 233577--233614 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
233567 ATTTTCTTTA
233577 TTATTTCCATTTCCAATT
1 TTATTTCCATTTCCAATT
*
233595 TTATTTCTATTTCCAATT
1 TTATTTCCATTTCCAATT
233613 TT
1 TT
233615 GGAAACTTAC
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:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTTCCATTTCCAATT
Found at i:235376 original size:17 final size:17
Alignment explanation
Indices: 235356--235389 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
235346 TCGTATCCGC
235356 TAGGCAATCCTATTCGT
1 TAGGCAATCCTATTCGT
* *
235373 TAGGTAATTCTATTCGT
1 TAGGCAATCCTATTCGT
235390 CAAGTAATTC
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:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
TAGGCAATCCTATTCGT
Found at i:235396 original size:17 final size:17
Alignment explanation
Indices: 235365--235402 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
235355 CTAGGCAATC
* *
235365 CTATTCGTTAGGTAATT
1 CTATTCGTCAAGTAATT
235382 CTATTCGTCAAGTAATT
1 CTATTCGTCAAGTAATT
235399 CTAT
1 CTAT
235403 CCGCCAGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (17 bp):
CTATTCGTCAAGTAATT
Found at i:235419 original size:17 final size:17
Alignment explanation
Indices: 235399--235442 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
235389 TCAAGTAATT
*
235399 CTATCCGCCAGGCAATA
1 CTATCTGCCAGGCAATA
* *
235416 CTATTTTCCAGGCAATA
1 CTATCTGCCAGGCAATA
235433 CTATCTGCCA
1 CTATCTGCCA
235443 CGCGATACTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (17 bp):
CTATCTGCCAGGCAATA
Found at i:243884 original size:40 final size:40
Alignment explanation
Indices: 243840--243915 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
243830 ATTCACATGT
*
243840 ACTAATAATCGTGTAACATTTGGCCATCATTCTAACACGA
1 ACTAATAATCGTGTAACATTTGACCATCATTCTAACACGA
243880 ACTAATAATCGTGTAACATTTGACCATCATTCTAAC
1 ACTAATAATCGTGTAACATTTGACCATCATTCTAAC
243916 TTAATTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (40 bp):
ACTAATAATCGTGTAACATTTGACCATCATTCTAACACGA
Found at i:248043 original size:3 final size:3
Alignment explanation
Indices: 248037--248095 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
248027 AAAAAAAACA
248037 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
248085 TCT TCT TCT TC
1 TCT TCT TCT TC
248096 ATGAGAGGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:249178 original size:15 final size:16
Alignment explanation
Indices: 249158--249187 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
249148 TAATTAAATA
249158 TAATT-AATTATTTTT
1 TAATTAAATTATTTTT
249173 TAATTAAATTATTTT
1 TAATTAAATTATTTT
249188 CTCAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTAAATTATTTTT
Found at i:257259 original size:26 final size:25
Alignment explanation
Indices: 257224--257272 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
257214 GCCTAAACCC
257224 CTACTCTAAATTTTGAGTGTAAGGG
1 CTACTCTAAATTTTGAGTGTAAGGG
*
257249 CTACTACTAAATTTTGGGTGTAAG
1 CTACT-CTAAATTTTGAGTGTAAG
257273 CTTTCTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (25 bp):
CTACTCTAAATTTTGAGTGTAAGGG
Found at i:266604 original size:11 final size:11
Alignment explanation
Indices: 266588--266612 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
266578 GCTCATTTCC
266588 AACCTTAATAT
1 AACCTTAATAT
266599 AACCTTAATAT
1 AACCTTAATAT
266610 AAC
1 AAC
266613 TAGGGGGTTG
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (11 bp):
AACCTTAATAT
Found at i:268400 original size:233 final size:233
Alignment explanation
Indices: 267991--268689 Score: 1317
Period size: 233 Copynumber: 3.0 Consensus size: 233
267981 CAAATCAAAC
* *
267991 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAACAGTAAACAAATTGA
1 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAATAGTAAAAAAATTGA
* * *
268056 ATCTTCAGGGACTAATCGATAATTTTTATTTTTCCTTGATTATCTCCAGTTTGATTCAATTCTTG
66 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTTCTTGATTATCTCCAATTTGATTCAATTCTTG
** * *
268121 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAACCTTTTTTATGTTATGCCATGATTTTT
131 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATCTTATGCCATGATATTT
268186 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
196 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
268224 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAATAGTAAAAAAATTGA
1 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAATAGTAAAAAAATTGA
268289 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTTCTTGATTATCTCCAATTTGATTCAATTCTTG
66 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTTCTTGATTATCTCCAATTTGATTCAATTCTTG
268354 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATCTTATGCCATGATATTT
131 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATCTTATGCCATGATATTT
268419 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
196 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
268457 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAATAGTAAAAAAATTGA
1 ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAATAGTAAAAAAATTGA
268522 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTTCTTGATTATCTCCAATTTGATTCAATTCTTG
66 ATCTTCAGGGACTAATCGATAATTTTTGTTTTTTCTTGATTATCTCCAATTTGATTCAATTCTTG
268587 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATCTTATGCCATGATATTT
131 ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATCTTATGCCATGATATTT
268652 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
196 TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
268690 TTTTGCATTT
Statistics
Matches: 457, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 457 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (233 bp):
ACATAATTATTTAAACACATATATATACCATATGAACTTATCTGGAAAAATAGTAAAAAAATTGA
ATCTTCAGGGACTAATCGATAATTTTTGTTTTTTCTTGATTATCTCCAATTTGATTCAATTCTTG
ATCTAATTAATTATTTTAAATAATTTATCAATACCAAATATTTTTTATCTTATGCCATGATATTT
TTGAACCTATGAAATTTTATTTTTCAATACCCCTAAAG
Found at i:272951 original size:50 final size:50
Alignment explanation
Indices: 272785--272974 Score: 175
Period size: 50 Copynumber: 3.7 Consensus size: 50
272775 GGCAAAGAGA
* *
272785 TCCCATGTAAGACCATGTCTAGGACATGACATTGGCATCATTGAGATTATGAGATG
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-C--T--GA-TATGAGAAG
* * * * * *
272841 TCTCATGTAAGAACATGTCTAGGACATGGCCTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACTGATATGAGAAG
* * * *
272891 TCCC-TCGTAAGACCATGTGTGGGACATGGCATGGGCACTGATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTAGGACATGGCATTGGCACTGATATGAGAAG
* * *
272941 TCCCATGTAAGACCATATCTGGGATATGGCATTG
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTG
272975 ATAGTACAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 73 0.66
51 3 0.03
55 1 0.01
56 33 0.30
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACTGATATGAGAAG
Found at i:280548 original size:50 final size:49
Alignment explanation
Indices: 280481--280600 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 49
280471 GAGGTCCCTC
* * *
280481 GTAAGACCATGTATGGGACATAGCATGGGCACAG-ATATGAGAAC-TCCCAT
1 GTAAGACCATGTCTGGGACATAGCATGGG--CAGTACAAGA-AACATCCCAT
* * * *
280531 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACATCCCAT
1 GTAAGACCATGTCTGGGACATAGCATGGGCAGTACAAGAAACATCCCAT
*
280580 CTAAGACCATGTCTGGGACAT
1 GTAAGACCATGTCTGGGACAT
280601 GGATTTGCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
48 6 0.10
49 28 0.48
50 24 0.41
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATAGCATGGGCAGTACAAGAAACATCCCAT
Found at i:286772 original size:49 final size:49
Alignment explanation
Indices: 286713--286841 Score: 213
Period size: 49 Copynumber: 2.6 Consensus size: 49
286703 AGAAAGAATA
286713 TTTTATTTTTTATGTAATTTATTTGTCATGTGTGTTTTAGGTTTATTAG
1 TTTTATTTTTTATGTAATTTATTTGTCATGTGTGTTTTAGGTTTATTAG
* * *
286762 TTTTAATTTTTATGTAATTTATTTTTCATATGTGTTTTAGGTTTATTAG
1 TTTTATTTTTTATGTAATTTATTTGTCATGTGTGTTTTAGGTTTATTAG
* *
286811 ATTTATTTTTTATGTAATTTATTTGGCATGT
1 TTTTATTTTTTATGTAATTTATTTGTCATGT
286842 TATTTTTATT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 72 1.00
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (49 bp):
TTTTATTTTTTATGTAATTTATTTGTCATGTGTGTTTTAGGTTTATTAG
Found at i:286830 original size:16 final size:16
Alignment explanation
Indices: 286763--286834 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
286753 GTTTATTAGT
*
286763 TTTAATTTTTATGTAA
1 TTTATTTTTTATGTAA
**
286779 TTTATTTTTCATATGTGT
1 TTTATTTTT--TATGTAA
**
286797 TTTA-GGTTTAT-TAGA
1 TTTATTTTTTATGTA-A
286812 TTTATTTTTTATGTAA
1 TTTATTTTTTATGTAA
286828 TTTATTT
1 TTTATTT
286835 GGCATGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
14 1 0.02
15 7 0.17
16 21 0.50
17 4 0.10
18 9 0.21
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.65
Consensus pattern (16 bp):
TTTATTTTTTATGTAA
Done.