Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 94 of 190
Found at i:28050160 original size:23 final size:26
Alignment explanation
Indices: 28050106--28050175 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 26
28050096 GAGCTATGAT
*
28050106 CGGTAAGCTCATTTCGAGCTGAAGAA
1 CGGTAAGCTCATATCGAGCTGAAGAA
*
28050132 CGGTAAGCTC-TATCGAGTTG-A-AA
1 CGGTAAGCTCATATCGAGCTGAAGAA
*
28050155 CGGTAAGCTCATA-AGAGCTGA
1 CGGTAAGCTCATATCGAGCTGA
28050176 TATATTGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 17 0.45
24 3 0.08
25 8 0.21
26 10 0.26
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (26 bp):
CGGTAAGCTCATATCGAGCTGAAGAA
Found at i:28062691 original size:215 final size:215
Alignment explanation
Indices: 28062314--28062744 Score: 792
Period size: 215 Copynumber: 2.0 Consensus size: 215
28062304 GCTTTTGCAA
* *
28062314 AAACTTCATCACAACCTTAGCATCGCTCTTCAGATATGCCTTGGCCTCAACCCACTTAGACACGT
1 AAACTTCATCACAACCTTAGCATCGCTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
* *
28062379 AATCTACTGCTACCAATATGTACTTGTGATCGAAAGACGGAGGGAAAGGACCAAGGAAGTAAATA
66 AATCTACTACTACCAATATGTACTTGTGATCGAAAGACAGAGGGAAAGGACCAAGGAAGTAAATA
*
28062444 CCCAAAACATCGACTAATTCTGCCTTAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGACG
131 CCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGACG
28062509 TTTCCAACCTTTTGGCATCG
196 TTTCCAACCTTTTGGCATCG
*
28062529 AAACTTCATCACAACCTTAGCATCGTTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
1 AAACTTCATCACAACCTTAGCATCGCTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
28062594 AATCTACTACTACCAATATGTACTTGTGA-CTGAAAGACAGAGGGAAAGGACCAAGGAAGTAAAT
66 AATCTACTACTACCAATATGTACTTGTGATC-GAAAGACAGAGGGAAAGGACCAAGGAAGTAAAT
28062658 ACCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGAC
130 ACCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGAC
28062723 GTTTCCAACCTTTTGGCATCG
195 GTTTCCAACCTTTTGGCATCG
28062744 A
1 A
28062745 TCACAACCCT
Statistics
Matches: 209, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
214 1 0.00
215 208 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (215 bp):
AAACTTCATCACAACCTTAGCATCGCTCGTCAGATATGCCTTGGCCTCAACCCACTTAGAAACGT
AATCTACTACTACCAATATGTACTTGTGATCGAAAGACAGAGGGAAAGGACCAAGGAAGTAAATA
CCCAAAACATCGACTAATTCTGCCTCAATGATGTTTGTCTGGGGTATTTCATTTCTTTGGTGACG
TTTCCAACCTTTTGGCATCG
Found at i:28077494 original size:106 final size:106
Alignment explanation
Indices: 28077309--28077520 Score: 415
Period size: 106 Copynumber: 2.0 Consensus size: 106
28077299 CAATAAAGTG
*
28077309 AGTTGTAAACTCAGTGCACAAATAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
1 AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
28077374 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
66 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
28077415 AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
1 AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
28077480 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
66 TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
28077521 CCAAGACAGA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (106 bp):
AGTTGTAAACTCAGTGCACAAAGAAGCTTGTTCACATAAACACATTTACCAAATAGTGTCCATAT
TCAAAGATTCGATCTGATAACAGAACATTTCTAGTTCAGAT
Found at i:28079556 original size:69 final size:71
Alignment explanation
Indices: 28079426--28079560 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 71
28079416 ACTCATTCAT
* * *
28079426 GGTTCCTAAGTGCTGATTCCACCGTATCCTTGAATATAAAAAGGGGTTGCTAAGTGTTGATTCCC
1 GGTTCCTAAGTGCTGATCCCACCGTATCCTTAAATATAAAAAGGGGTTGCTAAGTGCTGATTCCC
28079491 CCAAGG
66 CCAAGG
* * * *
28079497 GGTTGCTAAGTGCTGATCCCACCGTAT-TTTAAATGT-GAAAGGGGTTGCTAAGTGCTGATTCCC
1 GGTTCCTAAGTGCTGATCCCACCGTATCCTTAAATATAAAAAGGGGTTGCTAAGTGCTGATTCCC
28079560 C
66 C
28079561 GAATTACTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 26 0.46
70 6 0.11
71 25 0.44
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (71 bp):
GGTTCCTAAGTGCTGATCCCACCGTATCCTTAAATATAAAAAGGGGTTGCTAAGTGCTGATTCCC
CCAAGG
Found at i:28079581 original size:33 final size:33
Alignment explanation
Indices: 28079539--28079690 Score: 169
Period size: 33 Copynumber: 4.4 Consensus size: 33
28079529 ATGTGAAAGG
28079539 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
28079572 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
* ** * *
28079605 GGTTGCTAAGTGCTGATCCCACCATGTCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CC--GAATT--A-CTG--GT
* *
28079646 GGTTGCTAAGTGCTAATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
28079679 GGTTGCTAAGTG
1 GGTTGCTAAGTG
28079691 TTGAATCCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
33 65 0.66
34 2 0.02
35 2 0.02
36 4 0.04
38 3 0.03
39 2 0.02
40 2 0.02
41 19 0.19
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
Found at i:28079677 original size:107 final size:108
Alignment explanation
Indices: 28079497--28079690 Score: 336
Period size: 107 Copynumber: 1.8 Consensus size: 108
28079487 TCCCCCAAGG
* * *
28079497 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
1 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTAATTCCCCG
*
28079562 AATTACTGGTGGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
66 AATCACTGGTGGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
*
28079605 GGTTGCTAAGTGCTGATCCCACCATGTCTTAAATGTG-AAGGGGTTGCTAAGTGCTAATTCCCCG
1 GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTAATTCCCCG
28079669 AATCACTGGTGGTTGCTAAGTG
66 AATCACTGGTGGTTGCTAAGTG
28079691 TTGAATCCAC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 47 0.58
108 34 0.42
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (108 bp):
GGTTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTAATTCCCCG
AATCACTGGTGGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
Found at i:28086338 original size:27 final size:27
Alignment explanation
Indices: 28086308--28086360 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
28086298 TTGAATACAA
*
28086308 AAGGGGCTGCTAAGTGTTGATTCCCCC
1 AAGGGGCTGCTAAGTGCTGATTCCCCC
*
28086335 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGCTGCTAAGTGCTGATTCCCC
28086361 GACTCATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.26
Consensus pattern (27 bp):
AAGGGGCTGCTAAGTGCTGATTCCCCC
Found at i:28086381 original size:33 final size:33
Alignment explanation
Indices: 28086339--28086582 Score: 148
Period size: 33 Copynumber: 6.9 Consensus size: 33
28086329 TCCCCCAAGG
* * *
28086339 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATAACTGGT
* * * *
28086372 GGTTGCTAAGTGCTGATCCCACCGTATTTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--AT-AA-CTG---GT
* *
28086414 GGTTGCTAAGTGCTGATTCACCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATAACTGGT
* * *
28086447 GGTTGCTAAGTGTTGATTCCCCGAATTACTAGT
1 GGTTGCTAAGTGCTGATTCCCCGAATAACTGGT
* * * *
28086480 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--AT-AA-CTG--GT
*
28086521 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATAACTGGT
* *
28086554 GGTTGCTAAGTGTTGAATCCACCG-ATAAC
1 GGTTGCTAAGTGCTGATTCC-CCGAATAAC
28086583 GGATAATATT
Statistics
Matches: 164, Mismatches: 29, Indels: 36
0.72 0.13 0.16
Matches are distributed among these distances:
33 91 0.55
34 9 0.05
35 4 0.02
36 3 0.02
37 4 0.02
38 3 0.02
39 4 0.02
40 4 0.02
41 23 0.14
42 19 0.12
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATAACTGGT
Found at i:28086569 original size:107 final size:108
Alignment explanation
Indices: 28086339--28086578 Score: 383
Period size: 108 Copynumber: 2.2 Consensus size: 108
28086329 TCCCCCAAGG
* * * * *
28086339 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTTAA
1 GGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
*
28086404 ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATTACTGGT
66 ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATCACTGGT
*
28086447 GGTTGCTAAGTGTTGATTCCCCGAATTACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
1 GGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
*
28086512 ATGTG-AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
66 ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATCACTGGT
*
28086554 GGTTGCTAAGTGTTGAATCCACCGA
1 GGTTGCTAAGTGTTGATTCC-CCGA
28086579 TAACGGATAA
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
107 54 0.44
108 68 0.56
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (108 bp):
GGTTGCTAAGTGTTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTAA
ATGTGAAAGGGGTTGCTAAGTGCTGATTCACCGAATCACTGGT
Found at i:28086632 original size:2 final size:2
Alignment explanation
Indices: 28086625--28086659 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28086615 GGAAAGGTGA
28086625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28086660 GATGGTGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28094432 original size:22 final size:22
Alignment explanation
Indices: 28094373--28094434 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
28094363 TATGAAATAT
*
28094373 GAAAATAAATATATAAAAATTCA
1 GAAAAAAAATATAT-AAAATTCA
* * *
28094396 GAAAACATATGTATAAAA-TCTA
1 GAAAAAAAATATATAAAATTC-A
28094418 GAAAAAAAATATATAAA
1 GAAAAAAAATATATAAA
28094435 TTATAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 2 0.06
22 19 0.59
23 11 0.34
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (22 bp):
GAAAAAAAATATATAAAATTCA
Found at i:28094832 original size:15 final size:15
Alignment explanation
Indices: 28094812--28094840 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28094802 GTCAATGGTC
28094812 AGTCAACAACTAGTT
1 AGTCAACAACTAGTT
28094827 AGTCAACAACTAGT
1 AGTCAACAACTAGT
28094841 CAAAGTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (15 bp):
AGTCAACAACTAGTT
Found at i:28094881 original size:21 final size:20
Alignment explanation
Indices: 28094857--28094908 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
28094847 CAATAGTATT
28094857 TTTTAATATTTAAATATTTAA
1 TTTTAATATTT-AATATTTAA
**
28094878 TTTT-ATAATTTTTTATTTAA
1 TTTTAAT-ATTTAATATTTAA
*
28094898 ATTTAATATTT
1 TTTTAATATTT
28094909 TTATTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATATTTAATATTTAA
Found at i:28094910 original size:21 final size:20
Alignment explanation
Indices: 28094871--28094914 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
28094861 AATATTTAAA
*
28094871 TATTTAATTTTATAATTTTT
1 TATTTAATTTAATAATTTTT
28094891 TATTTAAATTTAAT-A-TTTT
1 TATTT-AATTTAATAATTTTT
28094910 TATTT
1 TATTT
28094915 TAAGTAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 6 0.27
21 7 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTAATTTAATAATTTTT
Found at i:28115321 original size:61 final size:61
Alignment explanation
Indices: 28115247--28115386 Score: 147
Period size: 61 Copynumber: 2.3 Consensus size: 61
28115237 ATCAATTTGA
* * * * ** * *
28115247 TCCTAAATATAAAAAGTTCAACAAATTTAGCTCTTAA-AGTTTACAAAATTTGTCATTTTAG
1 TCCTAACTCTAAAAAGTTCAACAAATTTAGCCCTCAATA-TTTACAAAATTAATAAATTTAG
* * * * *
28115308 TTCTAATTCTAAAAAATTCAATAAATTTGGCCCTCAATATTTACAAAATTAATAAATTTAG
1 TCCTAACTCTAAAAAGTTCAACAAATTTAGCCCTCAATATTTACAAAATTAATAAATTTAG
28115369 TCCTAACTCTAAAAAGTT
1 TCCTAACTCTAAAAAGTT
28115387 AAAAATATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
61 62 0.98
62 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.37
Consensus pattern (61 bp):
TCCTAACTCTAAAAAGTTCAACAAATTTAGCCCTCAATATTTACAAAATTAATAAATTTAG
Found at i:28117725 original size:26 final size:26
Alignment explanation
Indices: 28117690--28117742 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28117680 TTACCACCCT
28117690 TTTATGATCACAAGCATATTTCCATC
1 TTTATGATCACAAGCATATTTCCATC
28117716 TTTATGATCACAAGCATATTTCCATC
1 TTTATGATCACAAGCATATTTCCATC
28117742 T
1 T
28117743 AGGCATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (26 bp):
TTTATGATCACAAGCATATTTCCATC
Found at i:28119019 original size:45 final size:45
Alignment explanation
Indices: 28118955--28119048 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
28118945 AACAGATACT
* * * *
28118955 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATCATGTC
*
28119000 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATCATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATCATGTC
28119045 CGGT
1 CGGT
28119049 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATCATGTC
Found at i:28119112 original size:51 final size:51
Alignment explanation
Indices: 28119054--28119240 Score: 202
Period size: 51 Copynumber: 3.7 Consensus size: 51
28119044 TCGGTTCACA
* * *
28119054 TAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCTGGTACACG
* * * * ** *
28119105 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATTACCATCTGGTACACG
* * *
28119156 TAGTAGCCTGCACATAGTACT--ACACTTG-CGATCTATCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT-TACCA-TCTGGTACACG
28119206 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
28119241 CACTTTCACT
Statistics
Matches: 109, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
47 3 0.03
49 8 0.07
50 28 0.26
51 59 0.54
52 8 0.07
53 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATCTGGTACACG
Found at i:28119228 original size:101 final size:102
Alignment explanation
Indices: 28119052--28119236 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 102
28119042 GTTCGGTTCA
*
28119052 CATAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
28119117 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* * *
28119154 CATAGTAGCCTGCACATAGTACTACAC-T-TG-CGATCTATCATTCTGGTACACGTAGTAGCCTG
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCAT-TACCA-TCTGATACACGTAGTAGCCTG
28119216 CACATAGTACTACACACGTGA
64 CACATAGTACTACACACGTGA
28119237 CCATCACTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
99 3 0.04
100 6 0.08
101 42 0.55
102 26 0.34
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:28123445 original size:18 final size:18
Alignment explanation
Indices: 28123424--28123458 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28123414 CTATTATAAT
28123424 TATTAGTATTAT-TGTTTG
1 TATTAGT-TTATATGTTTG
28123442 TATTAGTTTATATGTTT
1 TATTAGTTTATATGTTT
28123459 ATTTACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
TATTAGTTTATATGTTTG
Found at i:28128215 original size:9 final size:9
Alignment explanation
Indices: 28128201--28128238 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
28128191 TGAGTTTCAA
28128201 AAAAAAATC
1 AAAAAAATC
28128210 AAAAAAATC
1 AAAAAAATC
28128219 --AAAAATC
1 AAAAAAATC
*
28128226 AAACAAATC
1 AAAAAAATC
28128235 AAAA
1 AAAA
28128239 TGAAAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.76, C:0.13, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:28128224 original size:16 final size:16
Alignment explanation
Indices: 28128203--28128238 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28128193 AGTTTCAAAA
28128203 AAAAATCAAAAAAATC
1 AAAAATCAAAAAAATC
*
28128219 AAAAATCAAACAAATC
1 AAAAATCAAAAAAATC
28128235 AAAA
1 AAAA
28128239 TGAAAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.75, C:0.14, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAAATCAAAAAAATC
Found at i:28129178 original size:46 final size:45
Alignment explanation
Indices: 28129109--28129197 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 45
28129099 AAGGAGAGGG
** * *
28129109 GACCAAGGTGAAAACCCGTAAAGGGCGCTTTGATTCCTAAAAAAAA
1 GACCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCC-AAAAAAAA
* *
28129155 GACCAAGGTGAAAACTCACAAAGGGCATTTTGAGTCCAAAAAA
1 GACCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAA
28129198 TAATAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (45 bp):
GACCAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAAAA
Found at i:28130569 original size:45 final size:45
Alignment explanation
Indices: 28130502--28130838 Score: 512
Period size: 45 Copynumber: 7.5 Consensus size: 45
28130492 GCAGCAGTGG
* * * * *
28130502 AGTAGGTTGAAAACAGCAGATCTTGTCTTCCTGTATTGGTAGTGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
28130547 AGTAGATCGAAGATATCAGATCTTGTCTTCTTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
** *
28130592 AGTAGATCAAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
**
28130637 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAATGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
28130682 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
28130727 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
28130772 AGAAGATCGAAGTTAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* *
28130817 AATAGATTAAAGATAGCAGATC
1 AGTAGATTGAAGATAGCAGATC
28130839 CGCGAGGTGT
Statistics
Matches: 265, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 265 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (45 bp):
AGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
Found at i:28131284 original size:18 final size:18
Alignment explanation
Indices: 28131263--28131297 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28131253 CTATTATAAT
28131263 TATTAGTATTAT-TGTTTG
1 TATTAGT-TTATATGTTTG
28131281 TATTAGTTTATATGTTT
1 TATTAGTTTATATGTTT
28131298 ATTTACCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
TATTAGTTTATATGTTTG
Found at i:28133120 original size:28 final size:29
Alignment explanation
Indices: 28133028--28133120 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
28133018 GCACTAGGTG
28133028 CCGGTGATTACAGTTTCTAGGTACTATGTA
1 CCGGTGA-TACAGTTTCTAGGTACTATGTA
* * * * * *
28133058 CCAGTGTTACAGTTTCCAGGCACTCTGTG
1 CCGGTGATACAGTTTCTAGGTACTATGTA
*
28133087 CCGGTGATATA-TTTCTAGGTACTATGTA
1 CCGGTGATACAGTTTCTAGGTACTATGTA
*
28133115 TCGGTG
1 CCGGTG
28133121 GTGGATACCA
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
28 18 0.37
29 26 0.53
30 5 0.10
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (29 bp):
CCGGTGATACAGTTTCTAGGTACTATGTA
Found at i:28136606 original size:14 final size:14
Alignment explanation
Indices: 28136576--28136615 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
28136566 TGAGAGATGA
28136576 GAGGGATGATAGGAT
1 GAGGGATGAT-GGAT
28136591 GAGGGATGATGGAT
1 GAGGGATGATGGAT
*
28136605 GATGGATGATG
1 GAGGGATGATG
28136616 AGAAATGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (14 bp):
GAGGGATGATGGAT
Found at i:28136614 original size:7 final size:7
Alignment explanation
Indices: 28136579--28136615 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
28136569 GAGATGAGAG
28136579 GGATGAT
1 GGATGAT
*
28136586 AGGATGAG
1 -GGATGAT
28136594 GGATGAT
1 GGATGAT
28136601 GGATGAT
1 GGATGAT
28136608 GGATGAT
1 GGATGAT
28136615 G
1 G
28136616 AGAAATGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (7 bp):
GGATGAT
Found at i:28147023 original size:7 final size:7
Alignment explanation
Indices: 28147013--28147041 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28147003 GAGATGAGAG
28147013 GGATGAT
1 GGATGAT
28147020 GGATGAT
1 GGATGAT
28147027 GGATGAT
1 GGATGAT
28147034 GGATGAT
1 GGATGAT
28147041 G
1 G
28147042 AGAAATGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (7 bp):
GGATGAT
Found at i:28151057 original size:68 final size:69
Alignment explanation
Indices: 28150937--28151065 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 69
28150927 AACTTAACCG
* *
28150937 CTTTAATATTAAATTAATATAATATTTATCAAGATAAATATGAAATTCAATTTAATATTAAGATA
1 CTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATGAAATTCAATTTAATATTAAGATA
28151002 ATCA
66 ATCA
* * *
28151006 CTTTAATATTAAATTAATAAAATA-CTATTAAGATAAATATTAAATTTAATTTAATATTAA
1 CTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATGAAATTCAATTTAATATTAA
28151066 ACTATTAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 32 0.58
69 23 0.42
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (69 bp):
CTTTAATATTAAATTAATAAAATATCTATCAAGATAAATATGAAATTCAATTTAATATTAAGATA
ATCA
Found at i:28160513 original size:20 final size:22
Alignment explanation
Indices: 28160486--28160541 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
28160476 CCTAATCAGT
*
28160486 ATACGACACATAAGTGCCT-GA
1 ATACGACACATAAGTGCCTAAA
*
28160507 A-ACGACACACGAAGTGCCTAAA
1 ATACGACACA-TAAGTGCCTAAA
28160529 ATACGACACATAA
1 ATACGACACATAA
28160542 AGTGTCTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
22 4 0.14
23 8 0.28
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTAAA
Found at i:28160904 original size:26 final size:25
Alignment explanation
Indices: 28160873--28160922 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28160863 TAGTTCAATA
28160873 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
28160899 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
28160923 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:28161271 original size:11 final size:11
Alignment explanation
Indices: 28161255--28161288 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28161245 AAACCCTAGT
28161255 TTTTCCTTTTC
1 TTTTCCTTTTC
28161266 TTTTCCTTTTC
1 TTTTCCTTTTC
*
28161277 TTCTTTCTTTTC
1 TT-TTCCTTTTC
28161289 CCCTGTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCCTTTTC
Found at i:28168926 original size:17 final size:17
Alignment explanation
Indices: 28168900--28168953 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
28168890 TAAACCATAT
28168900 ATTT-ATTCTATAATTA
1 ATTTAATTCTATAATTA
28168916 ATTTAATTC--T-A-TA
1 ATTTAATTCTATAATTA
28168929 A-TTAATTCTATAATTA
1 ATTTAATTCTATAATTA
28168945 ATTTAATTC
1 ATTTAATTC
28168954 AAGCGACCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 2 0.06
15 2 0.06
16 7 0.22
17 11 0.34
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATTCTATAATTA
Found at i:28168935 original size:12 final size:12
Alignment explanation
Indices: 28168918--28168947 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28168908 TATAATTAAT
28168918 TTAATTCTATAA
1 TTAATTCTATAA
28168930 TTAATTCTATAA
1 TTAATTCTATAA
28168942 TTAATT
1 TTAATT
28168948 TAATTCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAATTCTATAA
Found at i:28181956 original size:17 final size:17
Alignment explanation
Indices: 28181934--28181968 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28181924 TGATCCTGTC
28181934 TCACTAAAATTCAAATA
1 TCACTAAAATTCAAATA
28181951 TCACTAAAATTCAAATA
1 TCACTAAAATTCAAATA
28181968 T
1 T
28181969 TACAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (17 bp):
TCACTAAAATTCAAATA
Found at i:28182541 original size:16 final size:16
Alignment explanation
Indices: 28182516--28182552 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
28182506 ATCACGATCT
*
28182516 TTACTTTCTTCTTTAC
1 TTACTCTCTTCTTTAC
*
28182532 TTACTCTCTTGTTTAC
1 TTACTCTCTTCTTTAC
28182548 TTACT
1 TTACT
28182553 TGCTTACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.03, T:0.59
Consensus pattern (16 bp):
TTACTCTCTTCTTTAC
Found at i:28184586 original size:11 final size:11
Alignment explanation
Indices: 28184563--28184591 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28184553 TGAAGATGGT
28184563 TGTTTTG-GCA
1 TGTTTTGAGCA
28184573 TGTTTTGAGCA
1 TGTTTTGAGCA
28184584 TGTTTTGA
1 TGTTTTGA
28184592 ATAGGTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (11 bp):
TGTTTTGAGCA
Found at i:28191125 original size:17 final size:17
Alignment explanation
Indices: 28191103--28191135 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28191093 ACATATATGG
*
28191103 ATTGAATCCCAAAATTT
1 ATTGAAACCCAAAATTT
28191120 ATTGAAACCCAAAATT
1 ATTGAAACCCAAAATT
28191136 AACAAATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.30
Consensus pattern (17 bp):
ATTGAAACCCAAAATTT
Found at i:28191592 original size:22 final size:22
Alignment explanation
Indices: 28191551--28191593 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28191541 ACAACAGAAC
* *
28191551 AGGTTTTTAGCGGCATTTTTTT
1 AGGTCTTTAGCGGCACTTTTTT
*
28191573 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCACTTTTT
28191594 AACGCCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCACTTTTTT
Found at i:28191736 original size:43 final size:42
Alignment explanation
Indices: 28191683--28191851 Score: 234
Period size: 43 Copynumber: 4.0 Consensus size: 42
28191673 GCGCTTACAT
28191683 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCGTTGA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTGA
*
28191726 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTGAA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-CTTG-A
* *
28191770 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGA
**
28191812 TCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTT
1 AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTT
28191852 ATTTCACAAA
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
41 2 0.02
42 33 0.29
43 43 0.37
44 37 0.32
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGA
Found at i:28191786 original size:87 final size:86
Alignment explanation
Indices: 28191683--28191848 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 86
28191673 GCGCTTACAT
*
28191683 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCGTTGAAAAAAAACGCCGCT-AAAGATC
1 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGC-TTGAAAAAAAACGCCGCTAAAAG-T-
28191747 A-TGTTCTTTAGCGGCGTTTTGAA
63 AGTGTTCTTTAGCGGCGTTTTGAA
***
28191770 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGTTCAAAAACGCCGCTAAAAGTAGT
1 AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGAAAAAAAACGCCGCTAAAAGTAGT
28191835 GTTCTTTAGCGGCG
66 GTTCTTTAGCGGCG
28191849 CTTATTTCAC
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
85 1 0.01
86 31 0.42
87 41 0.56
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (86 bp):
AAAAAAACGCCCCTAAAGATCATGTTCTTTAGCGGCGCTTGAAAAAAAACGCCGCTAAAAGTAGT
GTTCTTTAGCGGCGTTTTGAA
Found at i:28192289 original size:12 final size:12
Alignment explanation
Indices: 28192272--28192311 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28192262 TTTTGAACCT
*
28192272 CTGCTTCTATTG
1 CTGCTTCTATCG
*
28192284 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
28192296 CTGCTTCTCTCG
1 CTGCTTCTATCG
28192308 CTGC
1 CTGC
28192312 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:28192322 original size:21 final size:21
Alignment explanation
Indices: 28192296--28192364 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
28192286 GCTTCTCTCG
*
28192296 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
28192317 CTGCTTGTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
28192338 CTGCTTCCCTCGCTGCCGTCT
1 CTGCTTCTCTCGCTGCAGCCT
28192359 CTGCTT
1 CTGCTT
28192365 TAAGTTGCTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.01, C:0.41, G:0.22, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:28195033 original size:9 final size:9
Alignment explanation
Indices: 28195019--28195268 Score: 140
Period size: 9 Copynumber: 28.0 Consensus size: 9
28195009 TTTTTCTGTA
28195019 TTATGTAAG
1 TTATGTAAG
28195028 TTATGTAAG
1 TTATGTAAG
*
28195037 TTCTGT-A-
1 TTATGTAAG
28195044 TTATGT-A-
1 TTATGTAAG
*
28195051 TTATGTATG
1 TTATGTAAG
**
28195060 CCACATGTAAG
1 --TTATGTAAG
*
28195071 TAATGTAAG
1 TTATGTAAG
*
28195080 CTATGTAAG
1 TTATGTAAG
*
28195089 TAATGTAAG
1 TTATGTAAG
* * *
28195098 ATATTTAAT
1 TTATGTAAG
28195107 TTATGTAAG
1 TTATGTAAG
28195116 TTATGTAAG
1 TTATGTAAG
* * *
28195125 ATATTTAAT
1 TTATGTAAG
*
28195134 TTATGTAAA
1 TTATGTAAG
*
28195143 TTATGCAAG
1 TTATGTAAG
* * *
28195152 ATATTTAAT
1 TTATGTAAG
*
28195161 TTACT-TAAT
1 TTA-TGTAAG
28195170 TTATGTAAG
1 TTATGTAAG
*
28195179 TTATTTAA-
1 TTATGTAAG
*
28195187 TTAACT-TAAT
1 TT-A-TGTAAG
28195197 TTATGTAAG
1 TTATGTAAG
*
28195206 TTATGCAA-
1 TTATGTAAG
* *
28195214 TATATTTAAT
1 T-TATGTAAG
28195224 TTATGTAAG
1 TTATGTAAG
*
28195233 TTATGTAAA
1 TTATGTAAG
*
28195242 TTACT-TAAT
1 TTA-TGTAAG
28195251 TTATGTAAG
1 TTATGTAAG
28195260 TTATGTAAG
1 TTATGTAAG
28195269 ATATTTNNNN
Statistics
Matches: 184, Mismatches: 43, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
7 12 0.07
8 7 0.04
9 153 0.83
10 6 0.03
11 6 0.03
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28195156 original size:27 final size:27
Alignment explanation
Indices: 28195081--28195274 Score: 212
Period size: 27 Copynumber: 6.9 Consensus size: 27
28195071 TAATGTAAGC
*
28195081 TATGTAAGTAATGTAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
28195108 TATGTAAGTTATGTAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
* *
28195135 TATGTAAATTATGCAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
28195162 TACT-TAATTTATGTAAGTTATTTAATTAACTTAATT
1 TA-TGTAAGTTATGTAAG--A--T-A-T---TTAATT
* *
28195198 TATGTAAGTTATGCAATATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
28195225 TATGTAAGTTATGTAA-ATTACTTAATT
1 TATGTAAGTTATGTAAGA-TATTTAATT
28195252 TATGTAAGTTATGTAAGATATTT
1 TATGTAAGTTATGTAAGATATTT
28195275 NNNNNNNNNN
Statistics
Matches: 143, Mismatches: 11, Indels: 26
0.79 0.06 0.14
Matches are distributed among these distances:
26 1 0.01
27 113 0.79
28 2 0.01
29 1 0.01
30 1 0.01
31 2 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 18 0.13
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.48
Consensus pattern (27 bp):
TATGTAAGTTATGTAAGATATTTAATT
Found at i:28195451 original size:17 final size:16
Alignment explanation
Indices: 28195392--28195451 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
28195382 TTAATTTATG
28195392 TTAAGTTATGTAAGATAT
1 TTAAGTTAT-T-AGATAT
* *
28195410 TTAATTTACTTAGTTAT
1 TTAAGTTA-TTAGATAT
*
28195427 GT-AGTTATTCAGATAT
1 TTAAGTTATT-AGATAT
28195443 TTAAGTTAT
1 TTAAGTTAT
28195452 GTAAGTTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 2 0.06
16 10 0.30
17 12 0.36
18 8 0.24
19 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (16 bp):
TTAAGTTATTAGATAT
Found at i:28195458 original size:9 final size:9
Alignment explanation
Indices: 28195387--28195663 Score: 153
Period size: 9 Copynumber: 30.9 Consensus size: 9
28195377 ATTACTTAAT
28195387 TTATGTTAAG
1 TTATG-TAAG
28195397 TTATGTAAG
1 TTATGTAAG
* * *
28195406 ATATTTAAT
1 TTATGTAAG
28195415 TTACT-T-AG
1 TTA-TGTAAG
28195423 TTATGT-AG
1 TTATGTAAG
*
28195431 TTAT-TCAG
1 TTATGTAAG
* *
28195439 ATATTTAAG
1 TTATGTAAG
28195448 TTATGTAAG
1 TTATGTAAG
*
28195457 TTATGTAAA
1 TTATGTAAG
*
28195466 TTACT-TAAT
1 TTA-TGTAAG
28195475 TTATGTAAG
1 TTATGTAAG
28195484 TTATGTAAG
1 TTATGTAAG
* *
28195493 TTATTTAAT
1 TTATGTAAG
*
28195502 TTACT-TAAT
1 TTA-TGTAAG
28195511 TTATGTAAG
1 TTATGTAAG
* *
28195520 TTATTTAAT
1 TTATGTAAG
*
28195529 TTACT-TAAT
1 TTA-TGTAAG
28195538 TTATGTAAG
1 TTATGTAAG
*
28195547 TTATTTAA-
1 TTATGTAAG
*
28195555 TTAACT-TAAT
1 TT-A-TGTAAG
28195565 TTATGTAAG
1 TTATGTAAG
*
28195574 TTATGCAAG
1 TTATGTAAG
* * *
28195583 ATATTTAAT
1 TTATGTAAG
28195592 TTATGTAAG
1 TTATGTAAG
**
28195601 TTA-CCAAG
1 TTATGTAAG
*
28195609 AATTACT-TAAT
1 --TTA-TGTAAG
28195620 TTATGTAAG
1 TTATGTAAG
28195629 TTATGTAAG
1 TTATGTAAG
* *
28195638 TTATTTAAT
1 TTATGTAAG
*
28195647 TTCTGTAAG
1 TTATGTAAG
28195656 TTATGTAA
1 TTATGTAA
28195664 TTAACCAAAT
Statistics
Matches: 209, Mismatches: 39, Indels: 39
0.73 0.14 0.14
Matches are distributed among these distances:
7 2 0.01
8 26 0.12
9 164 0.78
10 15 0.07
11 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28195479 original size:27 final size:27
Alignment explanation
Indices: 28195392--28195663 Score: 214
Period size: 27 Copynumber: 9.8 Consensus size: 27
28195382 TTAATTTATG
* * * *
28195392 TTAAGTTATGTAAGATATTTAATTTAC
1 TTAATTTATGTAAGTTATGTAAATTAC
* * *
28195419 TT-AGTTATGT-AGTTAT-TCAGA-TAT
1 TTAATTTATGTAAGTTATGT-AAATTAC
*
28195443 TTAAGTTATGTAAGTTATGTAAATTAC
1 TTAATTTATGTAAGTTATGTAAATTAC
28195470 TTAATTTATGTAAGTTATGTAAGTTATTTAATTTAC
1 TTAATTTATGTAAGTTA--T--G-TA---AA-TTAC
* *
28195506 TTAATTTATGTAAGTTATTTAATTTAC
1 TTAATTTATGTAAGTTATGTAAATTAC
*
28195533 TTAATTTATGTAAGTTAT-TTAATTAAC
1 TTAATTTATGTAAGTTATGTAAATT-AC
* *
28195560 TTAATTTATGTAAGTTATGCAAGA-TAT
1 TTAATTTATGTAAGTTATGTAA-ATTAC
***
28195587 TTAATTTATGTAAGTTACCAAGAATTAC
1 TTAATTTATGTAAGTTATGTA-AATTAC
* *
28195615 TTAATTTATGTAAGTTATGTAAGTTAT
1 TTAATTTATGTAAGTTATGTAAATTAC
*
28195642 TTAATTTCTGTAAGTTATGTAA
1 TTAATTTATGTAAGTTATGTAA
28195664 TTAACCAAAT
Statistics
Matches: 202, Mismatches: 24, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
24 5 0.02
25 14 0.07
26 20 0.10
27 108 0.53
28 24 0.12
29 2 0.01
31 3 0.01
32 2 0.01
34 1 0.00
35 2 0.01
36 21 0.10
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (27 bp):
TTAATTTATGTAAGTTATGTAAATTAC
Found at i:28196310 original size:13 final size:13
Alignment explanation
Indices: 28196288--28196324 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
28196278 CTCCATGGAA
28196288 ACAT-TTTTAATT
1 ACATATTTTAATT
*
28196300 AGATATTTTAATT
1 ACATATTTTAATT
28196313 ACATATTTTAAT
1 ACATATTTTAAT
28196325 AAACATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (13 bp):
ACATATTTTAATT
Found at i:28199342 original size:39 final size:38
Alignment explanation
Indices: 28199287--28199364 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
28199277 GCGTTTTTGT
* * *
28199287 TAATATCTTTTGCGGCGCTTAT-AAAAAAGCGCCGCTAA
1 TAATATCTTTAGCGGCG-ATATCAAAAAAGCGCCACTAA
*
28199325 TAATATACTTTAGCGGCGATATCCAAAAAGCGCCACTAA
1 TAATAT-CTTTAGCGGCGATATCAAAAAAGCGCCACTAA
28199364 T
1 T
28199365 TCTAATATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 9 0.26
39 25 0.74
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (38 bp):
TAATATCTTTAGCGGCGATATCAAAAAAGCGCCACTAA
Found at i:28199451 original size:114 final size:114
Alignment explanation
Indices: 28199162--28199456 Score: 299
Period size: 115 Copynumber: 2.6 Consensus size: 114
28199152 CCAAAACTCT
* * * * * * *
28199162 GCGTTTTGGTTAATACATTTTCCGACGCTTATCAAAAAGCGCCGCTAATACAATGCTTTAGCGGC
1 GCGTTTTGGTGAATATATTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACTATGATTTAGCGGC
* *** * * * *
28199227 GATTTCTCGTGAACGCCACTAATTCTAGTATACATCAAGCCTTAAGCGCT
66 GATATCTCAAAAACGCCACTAATTCTAATATACATCAAG-CTAAAACGCA
* * * *
28199277 GCGTTTTTGTTAATATCTTTTGCGGCGCTTATAAAAAAGCGCCGCTAATAATAT-ACTTTAGCGG
1 GCGTTTTGGTGAATATATTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACTATGA-TTTAGCGG
* *
28199341 CGATATC-CAAAAAGCGCCACTAATTCTAATATACCTCATG-TAAAAACGCA
65 CGATATCTCAAAAA-CGCCACTAATTCTAATATACATCAAGCT-AAAACGCA
* * ** *
28199391 GCGTTTTGGTGAGTATATTTTGCGGCGCTTCTGCACAAGCGCCGCTAATACTATGATTTAGCGGC
1 GCGTTTTGGTGAATATATTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACTATGATTTAGCGGC
28199456 G
66 G
28199457 TTTCTTTATA
Statistics
Matches: 148, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
113 1 0.01
114 63 0.43
115 84 0.57
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (114 bp):
GCGTTTTGGTGAATATATTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACTATGATTTAGCGGC
GATATCTCAAAAACGCCACTAATTCTAATATACATCAAGCTAAAACGCA
Found at i:28201343 original size:25 final size:25
Alignment explanation
Indices: 28201315--28201363 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28201305 TAGGAAAGAA
28201315 AAAAATAAGTTAGGGATTTAGGGAT
1 AAAAATAAGTTAGGGATTTAGGGAT
* *
28201340 AAAACTAAGTTAGGGATTTGGGGA
1 AAAAATAAGTTAGGGATTTAGGGA
28201364 AAATGATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.27
Consensus pattern (25 bp):
AAAAATAAGTTAGGGATTTAGGGAT
Found at i:28202495 original size:14 final size:14
Alignment explanation
Indices: 28202476--28202505 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28202466 AGTGAGAGAC
*
28202476 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
28202490 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
28202504 GA
1 GA
28202506 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:28203081 original size:20 final size:22
Alignment explanation
Indices: 28203056--28203103 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
28203046 CGAATCTCTA
28203056 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
28203076 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
28203098 AAAAAT
1 AAAAAT
28203104 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:28203329 original size:24 final size:25
Alignment explanation
Indices: 28203288--28203334 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
28203278 AAATTTTGGA
*
28203288 AAGAATTTTTCAGAAAC-ACTTTTG
1 AAGAATTCTTCAGAAACAACTTTTG
28203312 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATT-CTTCAGAAACAACTTT
28203335 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (25 bp):
AAGAATTCTTCAGAAACAACTTTTG
Found at i:28214278 original size:19 final size:19
Alignment explanation
Indices: 28214254--28214296 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28214244 CATGTTCAAA
* *
28214254 ATTTTAATACAATTTAATT
1 ATTTTAATAAAAATTAATT
28214273 ATTTT-ATAAAAATTAATT
1 ATTTTAATAAAAATTAATT
28214291 ATTTTA
1 ATTTTA
28214297 TGACAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATAAAAATTAATT
Found at i:28225461 original size:6 final size:6
Alignment explanation
Indices: 28225438--28225472 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
28225428 TTTCAAATAA
28225438 TTTCAT TTCTCTAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TT-TC-AT TTTCAT TTTCAT TTTCAT TTT
28225473 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCAT
Found at i:28226395 original size:30 final size:30
Alignment explanation
Indices: 28226361--28226423 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28226351 ACTTAACAAG
28226361 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
28226391 CAAATGCCTTTAAAATAATATCAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
28226421 CAA
1 CAA
28226424 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:28226476 original size:14 final size:14
Alignment explanation
Indices: 28226457--28226483 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28226447 CAAACAATAA
28226457 CAACATAATAGTAG
1 CAACATAATAGTAG
28226471 CAACATAATAGTA
1 CAACATAATAGTA
28226484 AAATGGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:28232124 original size:37 final size:37
Alignment explanation
Indices: 28232072--28232162 Score: 137
Period size: 37 Copynumber: 2.5 Consensus size: 37
28232062 CGAAGTTTCC
** *
28232072 AGCTTAACTTGGCTAACTCAAATAACTGGAGGTTGCG
1 AGCTTAACTCAGCTAACTCAAATAACTGGAGGTTGCA
*
28232109 AGCTTAACTCAGCTAACTCAAATAACTGGATGTTGCA
1 AGCTTAACTCAGCTAACTCAAATAACTGGAGGTTGCA
*
28232146 AGCTTAACTCAACTAAC
1 AGCTTAACTCAGCTAAC
28232163 CTTTAATCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (37 bp):
AGCTTAACTCAGCTAACTCAAATAACTGGAGGTTGCA
Found at i:28232287 original size:104 final size:105
Alignment explanation
Indices: 28232098--28232287 Score: 310
Period size: 104 Copynumber: 1.8 Consensus size: 105
28232088 CTCAAATAAC
* * *
28232098 TGGAGGTTGCGAGCTTAACTCAGCTAACTCAAATAACTGGATGTTGCAAGCTTAACTCAACTAAC
1 TGGAGGTTACGAGCTTAACTCAACTAACTCAAATAACTGGAGGTTGCAAGCTTAACTCAACTAAC
28232163 CTTTAATCATCAGTTGGGAACATAGGTCCGCAAGCTATTT
66 CTTTAATCATCAGTTGGGAACATAGGTCCGCAAGCTATTT
* * *
28232203 TGGA-GTTACGAGCTTAACTCAACTAACTCAAATAATTGGAGGTTGCGAGCTTAACTCATCTAAC
1 TGGAGGTTACGAGCTTAACTCAACTAACTCAAATAACTGGAGGTTGCAAGCTTAACTCAACTAAC
*
28232267 CTTTAATCATTAGTTGGGAAC
66 CTTTAATCATCAGTTGGGAAC
28232288 GTAAGTGTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
104 74 0.95
105 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (105 bp):
TGGAGGTTACGAGCTTAACTCAACTAACTCAAATAACTGGAGGTTGCAAGCTTAACTCAACTAAC
CTTTAATCATCAGTTGGGAACATAGGTCCGCAAGCTATTT
Found at i:28233007 original size:17 final size:17
Alignment explanation
Indices: 28232968--28233002 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28232958 TATGCAAATT
28232968 AAAA-AGAAAAGAAAGA
1 AAAAGAGAAAAGAAAGA
28232984 AAAAGAGAAAGAGAAAGA
1 AAAAGAGAAA-AGAAAGA
28233002 A
1 A
28233003 GAGAGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAGA
Found at i:28237721 original size:24 final size:23
Alignment explanation
Indices: 28237661--28237733 Score: 74
Period size: 24 Copynumber: 3.1 Consensus size: 23
28237651 TCCGGGCTGT
28237661 ATAATGGGAAGCTCATAAGAGCC
1 ATAATGGGAAGCTCATAAGAGCC
* **
28237684 ATAATTGGAAAGCTCATGCGAGCC
1 ATAA-TGGGAAGCTCATAAGAGCC
* **
28237708 AATAATGGGTAGCTCCGAAGAGCC
1 -ATAATGGGAAGCTCATAAGAGCC
28237732 AT
1 AT
28237734 TAACGGAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 6 0.15
24 29 0.74
25 4 0.10
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (23 bp):
ATAATGGGAAGCTCATAAGAGCC
Found at i:28237834 original size:26 final size:26
Alignment explanation
Indices: 28237798--28237855 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
28237788 GTAGCTTCGG
28237798 AGAGCCGTTAATCGAGAAGCTCACAA
1 AGAGCCGTTAATCGAGAAGCTCACAA
* *
28237824 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCGTTAATCGAGAAGCTCACAA
28237850 AGAGCC
1 AGAGCC
28237856 ATATATCGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (26 bp):
AGAGCCGTTAATCGAGAAGCTCACAA
Found at i:28239515 original size:20 final size:20
Alignment explanation
Indices: 28239490--28239528 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28239480 TGAGTTATTT
28239490 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
28239510 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
28239529 AAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:28244393 original size:12 final size:12
Alignment explanation
Indices: 28244378--28244404 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28244368 TAAAACTAAT
28244378 AATGTTTGATCG
1 AATGTTTGATCG
28244390 AATGTTTGATCG
1 AATGTTTGATCG
28244402 AAT
1 AAT
28244405 CAAGGCAGTA
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:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (12 bp):
AATGTTTGATCG
Found at i:28258557 original size:18 final size:18
Alignment explanation
Indices: 28258524--28258562 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
28258514 TTAATTAAAC
28258524 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
28258543 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
28258560 AAA
1 AAA
28258563 GATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:28259639 original size:16 final size:15
Alignment explanation
Indices: 28259565--28259639 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 15
28259555 TGGAAAATTT
*
28259565 ATTGAATTGAATTGTG
1 ATTGAATTGAA-AGTG
* *
28259581 ATTAAATTGGAA-TG
1 ATTGAATTGAAAGTG
28259595 ATTTGAATTGAAAGT-
1 A-TTGAATTGAAAGTG
28259610 A-TG-A--GAAAGTG
1 ATTGAATTGAAAGTG
28259621 ATTGAATTGAAATGTG
1 ATTGAATTGAAA-GTG
28259637 ATT
1 ATT
28259640 CAGAAACCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
10 6 0.13
11 1 0.02
12 3 0.07
13 3 0.07
14 3 0.07
15 14 0.30
16 16 0.35
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (15 bp):
ATTGAATTGAAAGTG
Found at i:28268638 original size:25 final size:27
Alignment explanation
Indices: 28268610--28268659 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
28268600 ATAAATAATT
28268610 AAATAT-ATATGTTTA-A-TAATATTAA
1 AAATATAATAT-TTTATATTAATATTAA
28268635 AAATATAATATTTTATATTAATATT
1 AAATATAATATTTTATATTAATATT
28268660 TTAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 5 0.23
27 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AAATATAATATTTTATATTAATATTAA
Found at i:28268652 original size:21 final size:22
Alignment explanation
Indices: 28268626--28268675 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
28268616 ATATGTTTAA
28268626 TAATATTAAAAATATAATATTT
1 TAATATTAAAAATATAATATTT
* * *
28268648 T-ATATTAATATTTTAATATTT
1 TAATATTAAAAATATAATATTT
28268669 TAATATT
1 TAATATT
28268676 TTAATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTAAAAATATAATATTT
Found at i:28268665 original size:8 final size:8
Alignment explanation
Indices: 28268640--28268687 Score: 75
Period size: 8 Copynumber: 6.4 Consensus size: 8
28268630 ATTAAAAATA
28268640 TAATATTT
1 TAATATTT
28268648 T-ATA--T
1 TAATATTT
28268653 TAATATTT
1 TAATATTT
28268661 TAATATTT
1 TAATATTT
28268669 TAATATTT
1 TAATATTT
28268677 TAATATTT
1 TAATATTT
28268685 TAA
1 TAA
28268688 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 3 0.08
8 29 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TAATATTT
Found at i:28271079 original size:70 final size:70
Alignment explanation
Indices: 28270721--28271968 Score: 719
Period size: 70 Copynumber: 17.6 Consensus size: 70
28270711 TAACAAGTTC
* * * * * *
28270721 AATACCGCAGCCTCCAAACAGTTAGTGAGAGTTTAAAGGTCTCAACTGTAATATTAAGGCTCGCA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
**
28270786 TATAA
66 GGTAA
* * ** * * * * * * ***
28270791 AGTACCACAGCCCCCAAACGGTTAGCGAGAGTTCAAAGCTCCCTGTTATTAGATTAAGGCTTATA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
28270856 GGTAA
66 GGTAA
* * * * * ** * * * * * * *
28270861 AGTACTGTAGCCCCCCAAACATTTAGAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCA
1 AATACCGCAG-CCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
* * **
28270926 TAAGTTC
64 CAGGTAA
* ** ** * * * * * *
28270933 AATACCGCAACCCTCCAAATAGCCAGTAAAAGTTAAAAGCTCTTAGTTGTCATTATTAAGGCTCA
1 AATACCGCAGCCC-CCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
**
28270998 CAGGTTT
64 CAGGTAA
* * * * * * * *
28271005 AATATCGCAGCCCCCAAATAGTTAGCAAAATTTTAAAGCTCTCAGTTATAATGTTAAGGCTCGCA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
28271070 GGTAA
66 GGTAA
** * * * * * ** * *
28271075 AATATTGCAGCCTCCAAAACAGTTAACGAGAGCT-AAAGCTCCCAAATGTAATCTTAAGGCTCGT
1 AATACCGCAGCC-CCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGC
* **
28271139 AGATTT
65 AGGTAA
** * * * * * * *
28271145 AATACTACAGCCCCCGAAACAGTTATCAAAAGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCG
1 AATACCGCAGCCCCC-AAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
**
28271210 CAGGTGC
64 CAGGTAA
* * *
28271217 AATACCGCAGCCCCCCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCG
1 AATACCGCAG-CCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
**
28271282 CAGGTTT
64 CAGGTAA
** * ** ** *
28271289 AATAATGCAGCCCCCAAAGAGTTATTGAGAGTTCAAAGCTC-CTAATTGTAATGTTAAGGCTCGC
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTC-AGCTGTAATATTAAGGCTCGC
*
28271353 AAGTAA
65 AGGTAA
** ** * * * * ** *
28271359 AATACTACAGCCTCTAAAATAGTTAGCGAGGGCT-GAAGCTC-CTAGCTATAA-CCTCAGGCTCG
1 AATACCGCAGCC-CCCAAATAGTTAGCGAGAGTTCAAAGCTCTC-AGCTGTAATATTAAGGCTCG
**
28271421 CAGGTTC
64 CAGGTAA
* * * * * * *
28271428 AATACCGTAGCCCCCAAATAGTTAGCGAGATTTCAAAGCTTTCATCTGTAATATTAATGTTCACA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
*
28271493 AGTAA
66 GGTAA
* ** * * *
28271498 ATTACCTTAGCCCCCAAATAGTTAGCAAGAGTTCAAAACT-TCCAGCTGTAATATTAAGGCTCAC
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCT-CAGCTGTAATATTAAGGCTCGC
28271562 AGGTAA
65 AGGTAA
* * * * *
28271568 AGTATCACAGCCCCCAAACAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCACA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
28271633 GGTAA
66 GGTAA
* * * * * * *
28271638 AGTACCGCAGACCCCAAATAGTTACCAAGAGTTCAAAGCTCCCAGCTGTAATATTAAGGATCACA
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
28271703 GGTAA
66 GGTAA
* ** * * ** * *
28271708 AGTACCGCAGCCCCCAAATAGTTAATGAGAGTTAAAAGCTCCCAATTGTCATTATTAAGGCTCAC
1 AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCGC
**
28271773 AGGTTT
65 AGGTAA
** * * * * *
28271779 AAGGCCACAGCCCCCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCG
1 AATACCGCAG-CCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTCG
* **
28271844 CAGATTC
64 CAGGTAA
** * * * *
28271851 AATACTACAGTCCCTCAAATAGTTAG-GTAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTC
1 AATACCGCAG-CCCCCAAATAGTTAGCG-AGAGTTCAAAGCTCTCAGCTGT-AATATTAAGGCTC
* * **
28271915 ACAGATTC
63 GCAGGTAA
* * *
28271923 AATACCGCAGCCCCTCAAATAGTTACCGAGAGTTAAAAGATCTCAG
1 AATACCGCAGCCCC-CAAATAGTTAGCGAGAGTTCAAAGCTCTCAG
28271969 TTGTCTCCCT
Statistics
Matches: 934, Mismatches: 224, Indels: 38
0.78 0.19 0.03
Matches are distributed among these distances:
68 16 0.02
69 35 0.04
70 410 0.44
71 162 0.17
72 305 0.33
73 6 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (70 bp):
AATACCGCAGCCCCCAAATAGTTAGCGAGAGTTCAAAGCTCTCAGCTGTAATATTAAGGCTCGCA
GGTAA
Found at i:28271222 original size:284 final size:284
Alignment explanation
Indices: 28270869--28271400 Score: 674
Period size: 284 Copynumber: 1.9 Consensus size: 284
28270859 AAAGTACTGT
* * * *
28270869 AGCCCCCCAAACATTTAGAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCATAAGTTCA
1 AGCCCCCCAAACAGTTACAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCACAAGTGCA
* * * * *
28270934 ATACCGCAACCCTCCAAATAGCCAGTAAAAGTTAAAAGCTCTTAGTTGTCATTATTAAGGCTCAC
66 ATACCGCAACCCCCCAAACAGCCAGCAAAAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCAC
* * * *
28270999 AGGTTTAAT-ATCGCAGCCCCCAAATAGTTAGCAAAATTTTAAAGCT-CTCAGTTATAATGTTAA
131 AGGTTTAATAAT-GCAGCCCCCAAAGAGTTAGCAAAAGTTCAAAGCTCCT-AATTATAATGTTAA
* * *
28271062 GGCTCGCAGGTAAAATATTGCAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCCCAAATGTAAT
194 GGCTCGCAAGTAAAATACTACAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCCCAAATGTAAT
28271127 CTTAAGGCTCGTAGATTTAATACTAC
259 CTTAAGGCTCGTAGATTTAATACTAC
* * * * * *
28271153 AGCCCCCGAAACAGTTATCAAA-AGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCGCAGGTGC
1 AGCCCCCCAAACAGTTA-CAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCACAAGTGC
* ** * * *
28271217 AATACCGCAGCCCCCCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCG
65 AATACCGCAACCCCCCAAACAGCCAGCAAAAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCA
*** * *
28271282 CAGGTTTAATAATGCAGCCCCCAAAGAGTTATTGAGAGTTCAAAGCTCCTAATTGTAATGTTAAG
130 CAGGTTTAATAATGCAGCCCCCAAAGAGTTAGCAAAAGTTCAAAGCTCCTAATTATAATGTTAAG
* * * * *
28271347 GCTCGCAAGTAAAATACTACAGCCTCTAAAATAGTTAGCGAGGGCTGAAGCTCC
195 GCTCGCAAGTAAAATACTACAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCC
28271401 TAGCTATAAC
Statistics
Matches: 207, Mismatches: 38, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
284 200 0.97
285 7 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (284 bp):
AGCCCCCCAAACAGTTACAAAGAGTTAAAAGCTCCCAACTGTCATTATCAAGACTCACAAGTGCA
ATACCGCAACCCCCCAAACAGCCAGCAAAAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCAC
AGGTTTAATAATGCAGCCCCCAAAGAGTTAGCAAAAGTTCAAAGCTCCTAATTATAATGTTAAGG
CTCGCAAGTAAAATACTACAGCCTCCAAAACAGTTAACGAGAGCTAAAGCTCCCAAATGTAATCT
TAAGGCTCGTAGATTTAATACTAC
Found at i:28272105 original size:58 final size:58
Alignment explanation
Indices: 28272037--28272215 Score: 166
Period size: 58 Copynumber: 3.1 Consensus size: 58
28272027 AAAAACTCCC
* *
28272037 AGCTATTGATTTTAGAAAATTTTCTTAAGCTTAAAAAAGCTCGCAAACTAATATTCTT
1 AGCTATTGATTTTAGAAAATTTTCTTAAGCTCAAAAAAGCTCGCAAACTAATATTCCT
* * * * * * * * *
28272095 AGCTGTTGATTTTCGACAA-TTTCTTTAAAG-TCCAAAATAGCTCACGAACAAATCTTCCC
1 AGCTATTGATTTTAGAAAATTTTC-TT-AAGCT-CAAAAAAGCTCGCAAACTAATATTCCT
* * * *
28272154 AACTATTAAATTTAGAAAATTTCCTTAAGCTCAAAATAA-CTCGCAAACTAATATTCCT
1 AGCTATTGATTTTAGAAAATTTTCTTAAGCTCAAAA-AAGCTCGCAAACTAATATTCCT
28272212 AGCT
1 AGCT
28272216 GACAAATCTT
Statistics
Matches: 90, Mismatches: 25, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
57 4 0.04
58 44 0.49
59 39 0.43
60 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (58 bp):
AGCTATTGATTTTAGAAAATTTTCTTAAGCTCAAAAAAGCTCGCAAACTAATATTCCT
Found at i:28272411 original size:27 final size:27
Alignment explanation
Indices: 28272370--28272427 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
28272360 TTGGCCCGCG
*
28272370 TTGTCATTCTTAGCAAGAGGGACCACA
1 TTGTCATTCTCAGCAAGAGGGACCACA
* *
28272397 TTGTCATTCTCAGCAGGAGGGTCCACA
1 TTGTCATTCTCAGCAAGAGGGACCACA
28272424 TTGT
1 TTGT
28272428 TGTTCACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (27 bp):
TTGTCATTCTCAGCAAGAGGGACCACA
Found at i:28272440 original size:27 final size:27
Alignment explanation
Indices: 28272386--28272441 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
28272376 TTCTTAGCAA
* *
28272386 GAGGGACCACATTGTCATTCTCAGCAG
1 GAGGGACCACATTGTCATTCACAACAG
* **
28272413 GAGGGTCCACATTGTTGTTCACAACAG
1 GAGGGACCACATTGTCATTCACAACAG
28272440 GA
1 GA
28272442 TGAGTCATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (27 bp):
GAGGGACCACATTGTCATTCACAACAG
Found at i:28272566 original size:110 final size:110
Alignment explanation
Indices: 28272373--28272702 Score: 516
Period size: 110 Copynumber: 3.0 Consensus size: 110
28272363 GCCCGCGTTG
* * *
28272373 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGCAGGAGGGTCCACATTGTTGTTCACAAC
1 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
*
28272438 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCATCATCTAAGTA
66 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
** * * * *
28272483 TCATTCTTAGCGGGAGGGACCACATTGTCATTCCCAGTAGGAAGGTCCACATTGTCGTTCATGAC
1 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
*
28272548 AGGATGAGTCATGTTGTCATTCTCAACTAGGTCCTCATCTAAGTA
66 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
* * * * *
28272593 TCATTCTTAGCAAGAGAGATCATATTGTCATTCTCAGAATGAGGGTCTACATTGTCGTTCACGAC
1 TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
28272658 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
66 AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
28272703 GGAATCCTGT
Statistics
Matches: 198, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 198 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (110 bp):
TCATTCTTAGCAAGAGGGACCACATTGTCATTCTCAGAAGGAGGGTCCACATTGTCGTTCACGAC
AGGATGAGTCATGTTGTCATTCTCAACTGGGTCCTCATCTAAGTA
Found at i:28282396 original size:24 final size:24
Alignment explanation
Indices: 28282354--28282410 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
28282344 ACTGGCCATG
*
28282354 TTATATTAAATATGCTTATGTATA
1 TTATATTAAATATGCTTATATATA
*
28282378 TTATATTCATATATG-TTATATATA
1 TTATATT-AAATATGCTTATATATA
*
28282402 TTAAATTAA
1 TTATATTAA
28282411 CTAATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.04
24 21 0.75
25 6 0.21
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (24 bp):
TTATATTAAATATGCTTATATATA
Found at i:28287975 original size:40 final size:40
Alignment explanation
Indices: 28287922--28288016 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
28287912 GCGTTTAGAT
*
28287922 AAAAAACGCCGCTAAAAATCAAGCATTAGCGTCACTTTTA
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
* * * * *
28287962 AAAAAACGCCGCTAAAGATTAAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
*
28288002 TAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
28288017 TGCTTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCACTTTTA
Found at i:28288155 original size:41 final size:41
Alignment explanation
Indices: 28288103--28288292 Score: 211
Period size: 41 Copynumber: 4.6 Consensus size: 41
28288093 AGGCTTTAGT
* *
28288103 GTTTTTTAAAAAGTGCCGCTAATGCTCAGGGT-TTTAGCGGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTC-GGGTCTTTAGCGGC
** *
28288144 GTTTTTAAAAAAGCATCGCTAATGATCGGGTCTTTAGCGGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
** * *
28288185 GTTTTTCGAAAAGCGCCGCTAATGATCGGGTCTTTAGCAGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
* * * *
28288226 GCTTTTGAGAAAGCGCCGCTAATGCTCGGGTCTTTAGTGGC
1 GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
* ** *
28288267 GGTTTTAATGAAGCGTCGCTAATGCT
1 GTTTTTAAAAAAGCGCCGCTAATGCT
28288293 TAGGGCAATA
Statistics
Matches: 126, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
40 4 0.03
41 122 0.97
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (41 bp):
GTTTTTAAAAAAGCGCCGCTAATGCTCGGGTCTTTAGCGGC
Found at i:28292036 original size:16 final size:16
Alignment explanation
Indices: 28292011--28292041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28292001 TGTAACCTAT
28292011 CTGATGTTTACAATAA
1 CTGATGTTTACAATAA
*
28292027 CTGATTTTTACAATA
1 CTGATGTTTACAATA
28292042 GTTTGGGACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
CTGATGTTTACAATAA
Found at i:28293263 original size:43 final size:43
Alignment explanation
Indices: 28293213--28293482 Score: 416
Period size: 43 Copynumber: 6.3 Consensus size: 43
28293203 AGATTATGTT
* ** * *
28293213 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
*
28293256 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
*
28293299 TTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
* * *
28293342 TTTAGTGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
*
28293385 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
* *
28293427 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
28293470 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
28293483 TTTTCTAAAA
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 41 0.20
43 168 0.80
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
Found at i:28293455 original size:128 final size:129
Alignment explanation
Indices: 28293213--28293482 Score: 436
Period size: 128 Copynumber: 2.1 Consensus size: 129
28293203 AGATTATGTT
* *
28293213 TTTAGCGGCGTTTTTGCT-AGAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTATG-TGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAA
28293277 AGCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
65 AGCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
* * *
28293342 TTTAGTGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGG-AAA
1 TTTAGCGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA
* * * *
28293406 GCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGTC
66 GCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
28293470 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
28293483 TTTTCTAAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
128 76 0.58
129 54 0.42
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (129 bp):
TTTAGCGGCGTTTATGTGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGGAAAA
GCGCCGCTAAAGGTCCTGGTCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
Found at i:28296247 original size:129 final size:130
Alignment explanation
Indices: 28296083--28296359 Score: 398
Period size: 130 Copynumber: 2.2 Consensus size: 130
28296073 GATTTAGATA
* * *
28296083 TTCTTAGTTCTTT--AAACTACGGTCTTTGCTTTTGTGTTTTTTCAGTTC-AATTAAAATGGGTT
1 TTCTTAGCTCTTTGCAAACTACAGTCTTTACTTTTGTGTTTTTTCAGTTCAAATTAAAATGGGTT
* **
28296145 TGTTTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTGTTG
66 TGTCTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTG
* * * *
28296210 TTCTTAGCTCTTTGCAAATTACAGTCTTTACTTTTGTGTTTTTTCGGTTCAAATTTAAATTGGTT
1 TTCTTAGCTCTTTGCAAACTACAGTCTTTACTTTTGTGTTTTTTCAGTTCAAATTAAAATGGGTT
* * *
28296275 TGTCTGTTTTTACTTTTTTTGTACTGTTTGATTCTTATTGATTGCTCCTTTTGTTGATTTTACTG
66 TGTCTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTG
* *
28296340 TTCTTAGCTATTGGCAAACT
1 TTCTTAGCTCTTTGCAAACT
28296360 GCACAACATT
Statistics
Matches: 131, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
127 12 0.09
129 31 0.24
130 88 0.67
ACGTcount: A:0.16, C:0.13, G:0.15, T:0.56
Consensus pattern (130 bp):
TTCTTAGCTCTTTGCAAACTACAGTCTTTACTTTTGTGTTTTTTCAGTTCAAATTAAAATGGGTT
TGTCTGTTTTTACTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTG
Found at i:28296742 original size:32 final size:30
Alignment explanation
Indices: 28296656--28296752 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 30
28296646 GGATTGAAGT
28296656 TTTATATGAGCATGCTGGGAAGGGTATAGG
1 TTTATATGAGCATGCTGGGAAGGGTATAGG
* * *
28296686 TTTATATGAGCCTGCTGGGAAGGGTGTAAG
1 TTTATATGAGCATGCTGGGAAGGGTATAGG
*
28296716 TTTATATGAGCATATGTTGGGAAGGGTATAGG
1 TTTATATGAGC--ATGCTGGGAAGGGTATAGG
28296748 TTTAT
1 TTTAT
28296753 GTATTTAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 38 0.66
32 20 0.34
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.34
Consensus pattern (30 bp):
TTTATATGAGCATGCTGGGAAGGGTATAGG
Found at i:28298189 original size:30 final size:30
Alignment explanation
Indices: 28298155--28298213 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
28298145 CAGTAGTAGT
*
28298155 GTGTGGGCCATAGCCCAACATAGTAACAGA
1 GTGTGGGCCATAGCCCAACACAGTAACAGA
* *
28298185 GTGTGGGCCTTAGCCCAATACAGTAACAG
1 GTGTGGGCCATAGCCCAACACAGTAACAG
28298214 TGCAAATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (30 bp):
GTGTGGGCCATAGCCCAACACAGTAACAGA
Found at i:28298350 original size:26 final size:26
Alignment explanation
Indices: 28298321--28298371 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
28298311 ACACCAATAC
* *
28298321 CGCAGCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTACCAGTAACAGTAA
28298347 CGCAGCAAAGCTACCAGTAACAGTA
1 CGCAGCAAAGCTACCAGTAACAGTA
28298372 TTTGTGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (26 bp):
CGCAGCAAAGCTACCAGTAACAGTAA
Found at i:28298610 original size:27 final size:27
Alignment explanation
Indices: 28298580--28298734 Score: 240
Period size: 27 Copynumber: 5.7 Consensus size: 27
28298570 TTATCTTATA
28298580 AGGGTATTTC-AGTAATTTTACCCATCG
1 AGGGTATTTCGA-TAATTTTACCCATCG
* *
28298607 AGGGTATTTCGATCATTTTACCTATCG
1 AGGGTATTTCGATAATTTTACCCATCG
* *
28298634 GGGGTATTTCGATAATTTTACCCATCA
1 AGGGTATTTCGATAATTTTACCCATCG
28298661 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
28298688 AGGGTATTTCGATAATTTTACCCATCG
1 AGGGTATTTCGATAATTTTACCCATCG
* *
28298715 AGGGTATTTCGGTAGTTTTA
1 AGGGTATTTCGATAATTTTA
28298735 TCCTATTTCG
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
27 116 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACCCATCG
Found at i:28299632 original size:2 final size:2
Alignment explanation
Indices: 28299625--28299681 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
28299615 ATGCCAATGC
28299625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28299667 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
28299682 CACATGTATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28299745 original size:2 final size:2
Alignment explanation
Indices: 28299738--28299776 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
28299728 CGTGTATGTT
* *
28299738 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28299777 TTGTAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28300542 original size:6 final size:6
Alignment explanation
Indices: 28300531--28300556 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28300521 CTCAGGTAAG
28300531 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
28300557 GTTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:28301631 original size:45 final size:45
Alignment explanation
Indices: 28301529--28301636 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
28301519 ATAAGACTTG
* * *
28301529 TATCTTCGATCTACTTCACCACCAGTATGGGAAAACAAGATCAGT
1 TATCTTTGATCTACTTCAACACCAGTATGGGAAAACAAGATCAGC
* * *
28301574 TTTCTTCT-ATCTACTTCAACACCAGTATGGGAAGACAAGATCTGC
1 TATCTT-TGATCTACTTCAACACCAGTATGGGAAAACAAGATCAGC
28301619 TATCTTTGATCTACTTCA
1 TATCTTTGATCTACTTCA
28301637 CGCCAATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 1 0.02
45 53 0.98
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (45 bp):
TATCTTTGATCTACTTCAACACCAGTATGGGAAAACAAGATCAGC
Found at i:28307957 original size:75 final size:69
Alignment explanation
Indices: 28307872--28308035 Score: 256
Period size: 69 Copynumber: 2.3 Consensus size: 69
28307862 AAGGTATGAA
*
28307872 AAGAAAAATGTAAAATATGTACGTGTATGTTTATATATATATATGTATGTATAAATATATTTGTA
1 AAGAATAATGTAAAATATGTACGTGTATG--T-T-TATATATA--TATGTATAAATATATTTGTA
28307937 AGAAAACATG
60 AGAAAACATG
28307947 AAGAATAATGTAAAATATGTACGTGTATGTTTATATATATATGTATAAATATATTTGTAAGAAAA
1 AAGAATAATGTAAAATATGTACGTGTATGTTTATATATATATGTATAAATATATTTGTAAGAAAA
28308012 CATG
66 CATG
*
28308016 AAGAATAATATAAAATATGT
1 AAGAATAATGTAAAATATGT
28308036 GGAAACATAC
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
69 49 0.56
71 8 0.09
72 1 0.01
73 1 0.01
75 28 0.32
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (69 bp):
AAGAATAATGTAAAATATGTACGTGTATGTTTATATATATATGTATAAATATATTTGTAAGAAAA
CATG
Found at i:28308056 original size:69 final size:69
Alignment explanation
Indices: 28307917--28308057 Score: 178
Period size: 69 Copynumber: 2.0 Consensus size: 69
28307907 TATATATATG
* **** * *
28307917 TATGTATAAATATATTTGTAAGAAAACATGAAGAATAATGTAAAATATGTACGTGTATGTTTATA
1 TATGTATAAATATATTTGTAAGAAAACATGAAGAATAATATAAAATATGTAAACATACGTTGATA
*
28307982 TATA
66 GATA
28307986 TATGTATAAATATATTTGTAAGAAAACATGAAGAATAATATAAAATATGTGGAAACATACG-TGA
1 TATGTATAAATATATTTGTAAGAAAACATGAAGAATAATATAAAATATGT--AAACATACGTTGA
28308050 -AGATA
64 TAGATA
28308055 TAT
1 TAT
28308058 TTACAAAAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
69 56 0.90
70 2 0.03
71 4 0.06
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.34
Consensus pattern (69 bp):
TATGTATAAATATATTTGTAAGAAAACATGAAGAATAATATAAAATATGTAAACATACGTTGATA
GATA
Found at i:28310016 original size:16 final size:16
Alignment explanation
Indices: 28309987--28310037 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
28309977 ACAACTAAAT
*
28309987 TATTA-ATTATAGTTC
1 TATTACATTACAGTTC
*
28310002 TATTTCATTACAGTTC
1 TATTACATTACAGTTC
*
28310018 TATTACATTACAGTTT
1 TATTACATTACAGTTC
28310034 TATT
1 TATT
28310038 CTATTCCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 4 0.13
16 27 0.87
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (16 bp):
TATTACATTACAGTTC
Found at i:28313162 original size:16 final size:17
Alignment explanation
Indices: 28313138--28313184 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
28313128 TGCCAAGTTC
28313138 ATGCATATCATAACAAA
1 ATGCATATCATAACAAA
* **
28313155 AT-CATATC-TAAGATT
1 ATGCATATCATAACAAA
28313170 ATGCATATCATAACA
1 ATGCATATCATAACA
28313185 CATGCATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (17 bp):
ATGCATATCATAACAAA
Found at i:28313189 original size:16 final size:16
Alignment explanation
Indices: 28313137--28313191 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
28313127 TTGCCAAGTT
28313137 CATGCATATCATAACAA
1 CATGCATATCATAAC-A
* *
28313154 AAT-CATATC-TAAGA
1 CATGCATATCATAACA
*
28313168 TTATGCATATCATAACA
1 -CATGCATATCATAACA
28313185 CATGCAT
1 CATGCAT
28313192 TGATTAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 18 0.60
17 6 0.20
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (16 bp):
CATGCATATCATAACA
Found at i:28319893 original size:4 final size:4
Alignment explanation
Indices: 28319886--28320301 Score: 660
Period size: 4 Copynumber: 105.0 Consensus size: 4
28319876 ACTTGCTTGA
28319886 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* **
28319934 TATG TAAG TACA T-TG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
28319981 TATG TATG TATT TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* **
28320029 TATG TATG TAAG TACA T-TG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
28320076 TATG TATT TATG TATG TATG TATG TATG TATG TATG TATG TATG TAAG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
** *
28320124 TACA T-TG TATG TATG TATG TATG TATG TATG TATT TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
28320171 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* ** *
28320219 TATG TAAG TACA T-TG TATG TATG TATG TATG TATG TATG TATG TATT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
28320266 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
28320302 ATGCATGATG
Statistics
Matches: 380, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
3 4 0.01
4 376 0.99
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:28329352 original size:2 final size:2
Alignment explanation
Indices: 28329347--28329375 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28329337 ATATATGAGT
28329347 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
28329376 GGGTTAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28331187 original size:9 final size:9
Alignment explanation
Indices: 28331173--28331205 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28331163 CTTAAAGAAC
28331173 AAAAAAAA-
1 AAAAAAAAG
28331181 AAAAAAAAG
1 AAAAAAAAG
*
28331190 AAAAAGAAG
1 AAAAAAAAG
28331199 AAAAAAA
1 AAAAAAA
28331206 GGTAAAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:28337448 original size:13 final size:13
Alignment explanation
Indices: 28337430--28337454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28337420 TAAACTCTAT
28337430 TTTCAAGTTATGG
1 TTTCAAGTTATGG
28337443 TTTCAAGTTATG
1 TTTCAAGTTATG
28337455 TTCTATACGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TTTCAAGTTATGG
Found at i:28343745 original size:20 final size:20
Alignment explanation
Indices: 28343720--28343757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28343710 GCAGAAAAGT
28343720 AGCTTGTCTACAATACTGAC
1 AGCTTGTCTACAATACTGAC
* *
28343740 AGCTTGTTTGCAATACTG
1 AGCTTGTCTACAATACTG
28343758 GTGGCTTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGCTTGTCTACAATACTGAC
Found at i:28343811 original size:21 final size:20
Alignment explanation
Indices: 28343750--28343813 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
28343740 AGCTTGTTTG
* *
28343750 CAATACTGGTGGCTTGTCCA
1 CAATACTGGTGGTTTGACCA
* **
28343770 TAATACTGGCAGTTT-ATCCA
1 CAATACTGGTGGTTTGA-CCA
28343790 CAATTACTGGTGGTTTGACCA
1 CAA-TACTGGTGGTTTGACCA
28343811 CAA
1 CAA
28343814 ACTAGTGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 16 0.48
21 16 0.48
22 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
CAATACTGGTGGTTTGACCA
Found at i:28347652 original size:22 final size:22
Alignment explanation
Indices: 28347627--28347675 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28347617 ACAAAACAAA
* *
28347627 AAGAAAGAAA-AAAATGAAACT
1 AAGAAAGAAATAAAAAGAAAAT
28347648 CAAG-AAGAAATAAAAAGAAAAT
1 -AAGAAAGAAATAAAAAGAAAAT
28347670 AAGAAA
1 AAGAAA
28347676 AGAAGTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.73, C:0.04, G:0.14, T:0.08
Consensus pattern (22 bp):
AAGAAAGAAATAAAAAGAAAAT
Found at i:28347673 original size:21 final size:21
Alignment explanation
Indices: 28347631--28347674 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28347621 AACAAAAAGA
* *
28347631 AAGAAAAAAATGAAACTCAAG
1 AAGAAAAAAAAGAAAATCAAG
28347652 AAGAAATAAAAAGAAAAT-AAG
1 AAGAAA-AAAAAGAAAATCAAG
28347673 AA
1 AA
28347675 AAGAAGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.09
Consensus pattern (21 bp):
AAGAAAAAAAAGAAAATCAAG
Found at i:28352853 original size:30 final size:30
Alignment explanation
Indices: 28352819--28352875 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28352809 GTAGGCCTAT
**
28352819 CAACAGCGTCCATACAATCACCAGGCCCAG
1 CAACAGCACCCATACAATCACCAGGCCCAG
* *
28352849 CAACAGTACCCATACAATCACCGGGCC
1 CAACAGCACCCATACAATCACCAGGCC
28352876 GAACACTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.16, T:0.11
Consensus pattern (30 bp):
CAACAGCACCCATACAATCACCAGGCCCAG
Found at i:28366175 original size:13 final size:13
Alignment explanation
Indices: 28366159--28366198 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
28366149 GGTAATATCA
*
28366159 TAAAGTAAAAAAC
1 TAAAATAAAAAAC
28366172 TAAAATAAATAAAC
1 TAAAATAAA-AAAC
*
28366186 AAAAATAAAAAAC
1 TAAAATAAAAAAC
28366199 AAACAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAAATAAAAAAC
Found at i:28366199 original size:13 final size:13
Alignment explanation
Indices: 28366164--28366201 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
28366154 TATCATAAAG
*
28366164 TAAAAAACTAAAA
1 TAAAAAACAAAAA
28366177 TAAATAAACAAAAA
1 TAAA-AAACAAAAA
28366191 TAAAAAACAAA
1 TAAAAAACAAA
28366202 CAACTAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (13 bp):
TAAAAAACAAAAA
Found at i:28368433 original size:103 final size:102
Alignment explanation
Indices: 28368180--28368547 Score: 619
Period size: 102 Copynumber: 3.6 Consensus size: 102
28368170 ATTGCATATA
28368180 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
28368245 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
28368282 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
28368347 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * *
28368385 GAGGGGTTGCTAAGTGTTGATTCCTCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
*
28368450 TGAAATGTGAAGGGGGTTGCTAAGTGTTGATTCCCCC
66 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
28368487 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCGGAATCCACCG
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
28368548 ATAACGATTA
Statistics
Matches: 244, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
102 151 0.62
103 93 0.38
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (102 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:28374186 original size:50 final size:50
Alignment explanation
Indices: 28374108--28374220 Score: 154
Period size: 50 Copynumber: 2.2 Consensus size: 50
28374098 TGATGGATTA
* * **
28374108 TATGGGATAGAAATGCATCAAATGGATTTGCGGAGGAAAGTTTGGTTAAGC
1 TATGGGA-AGAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGC
* *
28374159 TATGGGAATAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGT
1 TATGGGAAGAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGC
*
28374209 TATAGGAAGAAA
1 TATGGGAAGAAA
28374221 GGAGTTTCGC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
50 47 0.87
51 7 0.13
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.26
Consensus pattern (50 bp):
TATGGGAAGAAATGAATCAAATAGATTTGCGGAGGAAAGGCTGGTTAAGC
Found at i:28380289 original size:22 final size:22
Alignment explanation
Indices: 28380261--28380303 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28380251 TTTATTGTTC
28380261 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
28380283 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
28380304 TAGCCGTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:28385523 original size:19 final size:21
Alignment explanation
Indices: 28385482--28385526 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
28385472 TATAAATACC
28385482 CCCCTTTTTATGTGTAATTTG
1 CCCCTTTTTATGTGTAATTTG
*
28385503 CCCCTTTTT-TG-GTATTTTG
1 CCCCTTTTTATGTGTAATTTG
28385522 CCCCT
1 CCCCT
28385527 AATAATACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 2 0.09
21 9 0.39
ACGTcount: A:0.09, C:0.27, G:0.13, T:0.51
Consensus pattern (21 bp):
CCCCTTTTTATGTGTAATTTG
Found at i:28387769 original size:21 final size:20
Alignment explanation
Indices: 28387740--28387780 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
28387730 AAGAATTAGT
*
28387740 AAAAATTATAAAAATTGTAA
1 AAAAATTATAAAAAATGTAA
28387760 AAAAATTTATAAAAAATGTAA
1 AAAAA-TTATAAAAAATGTAA
28387781 CATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAAATGTAA
Found at i:28387870 original size:11 final size:11
Alignment explanation
Indices: 28387854--28387888 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
28387844 TTTTATAAAG
28387854 TTGTAAGAAAA
1 TTGTAAGAAAA
28387865 TTGTAAGAAAA
1 TTGTAAGAAAA
*
28387876 TTGTAAAAAAA
1 TTGTAAGAAAA
28387887 TT
1 TT
28387889 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (11 bp):
TTGTAAGAAAA
Found at i:28387892 original size:10 final size:11
Alignment explanation
Indices: 28387854--28387894 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
28387844 TTTTATAAAG
*
28387854 TTGTAAGAAAA
1 TTGTAAAAAAA
*
28387865 TTGTAAGAAAA
1 TTGTAAAAAAA
28387876 TTGTAAAAAAA
1 TTGTAAAAAAA
28387887 TT-TAAAAA
1 TTGTAAAAA
28387895 TATAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 6 0.21
11 23 0.79
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (11 bp):
TTGTAAAAAAA
Found at i:28387901 original size:26 final size:28
Alignment explanation
Indices: 28387872--28387923 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
28387862 AAATTGTAAG
28387872 AAAA-TTGTAAAAAAATT-TAAAAATAT
1 AAAATTTGTAAAAAAATTATAAAAATAT
28387898 AAAATTTGTAAAAAAATTATAAAAAT
1 AAAATTTGTAAAAAAATTATAAAAAT
28387924 TATCATGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATTTGTAAAAAAATTATAAAAATAT
Found at i:28389434 original size:11 final size:10
Alignment explanation
Indices: 28389419--28389476 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
28389409 TCTTAAACTT
28389419 TTTTTTATAA
1 TTTTTTATAA
28389429 TTTTTTATAA
1 TTTTTTATAA
* *
28389439 ATTTATAT-A
1 TTTTTTATAA
28389448 -TTTTTATAA
1 TTTTTTATAA
28389457 -TTTTTATAA
1 TTTTTTATAA
28389466 TTATTTTATAA
1 TT-TTTTATAA
28389477 CATATAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
8 6 0.14
9 11 0.26
10 17 0.40
11 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:28389452 original size:28 final size:28
Alignment explanation
Indices: 28389420--28389523 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 28
28389410 CTTAAACTTT
28389420 TTTTTATAATTTTTTATAAATTTATATA
1 TTTTTATAATTTTTTATAAATTTATATA
28389448 TTTTTATAA-TTTTTATAATTATTTTATAACATA
1 TTTTTATAATTTTTTATAA--A-TTTAT---ATA
* *
28389481 TAAAATTTATAATTATTTTATATATTTATA-A
1 T---TTTTATAATT-TTTTATAAATTTATATA
28389512 TTTTTATAATTT
1 TTTTTATAATTT
28389524 ATATTTCATA
Statistics
Matches: 62, Mismatches: 3, Indels: 23
0.70 0.03 0.26
Matches are distributed among these distances:
27 10 0.16
28 18 0.29
29 1 0.02
30 5 0.08
31 2 0.03
32 1 0.02
33 4 0.06
35 5 0.08
36 8 0.13
37 1 0.02
38 7 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTATAATTTTTTATAAATTTATATA
Found at i:28389461 original size:9 final size:9
Alignment explanation
Indices: 28389420--28389523 Score: 72
Period size: 9 Copynumber: 11.3 Consensus size: 9
28389410 CTTAAACTTT
28389420 TTTTTATAA
1 TTTTTATAA
28389429 TTTTTTATAA
1 -TTTTTATAA
*
28389439 -ATTTATATA
1 TTTTTATA-A
28389448 TTTTTATAA
1 TTTTTATAA
28389457 TTTTTATAA
1 TTTTTATAA
28389466 TTATTTTATAA
1 -T-TTTTATAA
**
28389477 --CATATAA
1 TTTTTATAA
**
28389484 AATTTATAA
1 TTTTTATAA
28389493 TTATTT-TATA
1 TT-TTTATA-A
*
28389503 TATTTATAA
1 TTTTTATAA
28389512 TTTTTATAA
1 TTTTTATAA
28389521 TTT
1 TTT
28389524 ATATTTCATA
Statistics
Matches: 75, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 5 0.07
8 6 0.08
9 33 0.44
10 23 0.31
11 8 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Done.