Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 17 of 79
Found at i:5556891 original size:17 final size:17
Alignment explanation
Indices: 5556871--5556907 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5556861 AATTTTTGAA
5556871 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
5556888 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
5556905 TTA
1 TTA
5556908 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:5557682 original size:24 final size:24
Alignment explanation
Indices: 5557655--5557725 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 24
5557645 ATGGAAAACT
5557655 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
* ** *
5557679 GTGAATAA--AGCTATACTGAGTT--
1 GTGAA-AAGTAGGTATGGTG-TTTCA
5557701 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
5557725 G
1 G
5557726 CGAAGAAAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
21 2 0.06
22 7 0.21
23 14 0.42
24 8 0.24
25 2 0.06
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (24 bp):
GTGAAAAGTAGGTATGGTGTTTCA
Found at i:5557706 original size:46 final size:45
Alignment explanation
Indices: 5557654--5557792 Score: 206
Period size: 46 Copynumber: 3.0 Consensus size: 45
5557644 CATGGAAAAC
* *
5557654 TGTGAAAAGTAGGTATGGTGTTTCAGTGAATAAAGCTATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAGT
*
5557700 TGTGAAAAGTAGGTATGGTGTTTCAGCGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAG-AAACCATACTGAGT
* *
5557746 TGTGAAAAGTAGGTATGGTATTTCAATGAAGGAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAA-GAAACCATACTGAGT
5557792 T
1 T
5557793 ATAGCATTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
46 81 0.95
47 4 0.05
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (45 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACCATACTGAGT
Found at i:5575328 original size:209 final size:208
Alignment explanation
Indices: 5574968--5575388 Score: 833
Period size: 209 Copynumber: 2.0 Consensus size: 208
5574958 NNNAATTTAT
5574968 AATTTATTGGCATAGTTCTCTGCTTGCCATTTGTCATAGTAAAAAGATGACACATGTAATGGAAA
1 AATTTATTGGCATAGTTCTCTGCTTGCCATTTGTCATAGTAAAAAGATGACACATGTAATGGAAA
5575033 TCCTTTACCAATTTGCTAAATGTATTTAACTTAGAATTTGCTGAACATAATAAATGATCAATATG
66 TCCTTTACCAATTTGCTAAATGTATTTAACTTAGAATTTGCTGAACATAATAAATGATCAATATG
5575098 AAATATTTTCAACAGTGTATACACAAAATTGACAAGTAGGCTTAGGTGGCATAGTTTAAATGTTT
131 AAATATTTTCAACAGTGTATACACAAAATTGACAAGTAGGCTTAGGTGGCATAGTTTAAATGTTT
5575163 AAAAATATATATA
196 AAAAATATATATA
5575176 CAATTTATTGGCATAGTTCTCTGCTTGCCATTTGTCATAGTAAAAAGATGACACATGTAATGGAA
1 -AATTTATTGGCATAGTTCTCTGCTTGCCATTTGTCATAGTAAAAAGATGACACATGTAATGGAA
5575241 ATCCTTTACCAATTTGCTAAATGTATTTAACTTAGAATTTGCTGAACATAATAAATGATCAATAT
65 ATCCTTTACCAATTTGCTAAATGTATTTAACTTAGAATTTGCTGAACATAATAAATGATCAATAT
5575306 GAAATATTTTCAACAGTGTATACACAAAATTGACAAGTAGGCTTAGGTGGCATAGTTTAAATGTT
130 GAAATATTTTCAACAGTGTATACACAAAATTGACAAGTAGGCTTAGGTGGCATAGTTTAAATGTT
5575371 TAAAAATATATATA
195 TAAAAATATATATA
5575385 AATT
1 AATT
5575389 GGCATAAATA
Statistics
Matches: 212, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
208 4 0.02
209 208 0.98
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (208 bp):
AATTTATTGGCATAGTTCTCTGCTTGCCATTTGTCATAGTAAAAAGATGACACATGTAATGGAAA
TCCTTTACCAATTTGCTAAATGTATTTAACTTAGAATTTGCTGAACATAATAAATGATCAATATG
AAATATTTTCAACAGTGTATACACAAAATTGACAAGTAGGCTTAGGTGGCATAGTTTAAATGTTT
AAAAATATATATA
Found at i:5581285 original size:5 final size:5
Alignment explanation
Indices: 5581275--5581310 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
5581265 GAAATTAAAC
5581275 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
5581311 ACTTTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:5581660 original size:27 final size:27
Alignment explanation
Indices: 5581628--5581683 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5581618 ATGATGGGTT
5581628 ATGCACTAAAAAGATGATTAGTGATTA
1 ATGCACTAAAAAGATGATTAGTGATTA
5581655 ATGCACTAAAAAGATGATTAGTGATTA
1 ATGCACTAAAAAGATGATTAGTGATTA
5581682 AT
1 AT
5581684 TAAGTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (27 bp):
ATGCACTAAAAAGATGATTAGTGATTA
Found at i:5585655 original size:27 final size:27
Alignment explanation
Indices: 5585617--5585688 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
5585607 AACACTATCG
5585617 GGAAGCTCACAAAGAGCCAATTTAACA
1 GGAAGCTCACAAAGAGCCAATTTAACA
5585644 GGAAGCTCACAAAGAGCCAATTTAACA
1 GGAAGCTCACAAAGAGCCAATTTAACA
*
5585671 GGAAGCTCACGAAGAGCC
1 GGAAGCTCACAAAGAGCC
5585689 TATAATCGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.12
Consensus pattern (27 bp):
GGAAGCTCACAAAGAGCCAATTTAACA
Found at i:5590218 original size:13 final size:12
Alignment explanation
Indices: 5590159--5590245 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 12
5590149 TTTTTAATTA
*
5590159 CAAGTTTTTTAT
1 CAAGTTTTTCAT
* *
5590171 CAAGTTTTGCAG
1 CAAGTTTTTCAT
5590183 CAAGTTCCTTT--T
1 CAAGTT--TTTCAT
*
5590195 AAAGTTTTTCAT
1 CAAGTTTTTCAT
5590207 CAAGTCTTTTCAT
1 CAAGT-TTTTCAT
* * *
5590220 AAAATTTTCCAT
1 CAAGTTTTTCAT
* *
5590232 CAAATTTTTAAT
1 CAAGTTTTTCAT
5590244 CA
1 CA
5590246 TTTCGTTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
10 3 0.05
12 42 0.74
13 10 0.18
14 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (12 bp):
CAAGTTTTTCAT
Found at i:5595208 original size:22 final size:21
Alignment explanation
Indices: 5595183--5595224 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5595173 AAAAAAACAT
*
5595183 TTTAATTTTCCTATTATTATTA
1 TTTAATTTTACTATT-TTATTA
*
5595205 TTTATTTTTACTATTTTATT
1 TTTAATTTTACTATTTTATT
5595225 TTATTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATTTTACTATTTTATTA
Found at i:5603354 original size:15 final size:15
Alignment explanation
Indices: 5603309--5603374 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
5603299 ATAACTTAAA
* *
5603309 TTCAATACTTAAATT
1 TTCAACACTTAATTT
* *
5603324 TTCAATATTTAATTT
1 TTCAACACTTAATTT
*
5603339 TTCAACACTTATTTTTT
1 TTCAACACTTA--ATTT
*
5603356 TTCGACACTTAATTT
1 TTCAACACTTAATTT
5603371 TTCA
1 TTCA
5603375 GTTTATCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 28 0.68
17 13 0.32
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.53
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:5603358 original size:17 final size:18
Alignment explanation
Indices: 5603336--5603372 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5603326 CAATATTTAA
5603336 TTTTTCAACACTT-ATTT
1 TTTTTCAACACTTAATTT
*
5603353 TTTTTCGACACTTAATTT
1 TTTTTCAACACTTAATTT
5603371 TT
1 TT
5603373 CAGTTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTCAACACTTAATTT
Found at i:5606730 original size:130 final size:131
Alignment explanation
Indices: 5606573--5606833 Score: 515
Period size: 130 Copynumber: 2.0 Consensus size: 131
5606563 TGGGTTTGGG
5606573 CAAAAAACGAGACTCATTTAGAAAATGGGTCGGGCCTCAGGTAAAACTATTTTGGCCTAGCCCGA
1 CAAAAAACGAGACTCATTTAGAAAATGGGTCGGGCCTCAGGTAAAACTATTTTGGCCTAGCCCGA
5606638 ATTATATATTAAATACATACTATTTTTAATCAAATATATATTTTTATTTTTAATCAAATATATAT
66 ATTATATATTAAATACATACTATTTTTAATCAAATATATATTTTTATTTTTAATCAAATATATAT
5606703 A
131 A
5606704 CAAAAAACGA-ACTCATTTAGAAAATGGGTCGGGCCTCAGGTAAAACTATTTTGGCCTAGCCCGA
1 CAAAAAACGAGACTCATTTAGAAAATGGGTCGGGCCTCAGGTAAAACTATTTTGGCCTAGCCCGA
5606768 ATTATATATTAAATACATACTATTTTTAATCAAATATATATTTTTATTTTTAATCAAATATATAT
66 ATTATATATTAAATACATACTATTTTTAATCAAATATATATTTTTATTTTTAATCAAATATATAT
5606833 A
131 A
5606834 TATTTTATAC
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
130 120 0.92
131 10 0.08
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (131 bp):
CAAAAAACGAGACTCATTTAGAAAATGGGTCGGGCCTCAGGTAAAACTATTTTGGCCTAGCCCGA
ATTATATATTAAATACATACTATTTTTAATCAAATATATATTTTTATTTTTAATCAAATATATAT
A
Found at i:5610216 original size:18 final size:17
Alignment explanation
Indices: 5610195--5610248 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
5610185 TTATAAAAAA
5610195 ATTATATTAATTATATAT
1 ATTATATT-ATTATATAT
*
5610213 ATTAAATTATT-TATAT
1 ATTATATTATTATATAT
*
5610229 -TTATATT-TATATTTAT
1 ATTATATTAT-TATATAT
5610245 ATTA
1 ATTA
5610249 AATCACTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 1 0.03
15 7 0.23
16 9 0.30
17 6 0.20
18 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATATTATTATATAT
Found at i:5610231 original size:6 final size:6
Alignment explanation
Indices: 5610220--5610247 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5610210 TATATTAAAT
5610220 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
5610248 AAATCACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:5610425 original size:38 final size:39
Alignment explanation
Indices: 5610355--5610434 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
5610345 TATTTAACAC
* * * *
5610355 AATAAAATATTTATTATATTTATTTGT-GTTTTTAATAT
1 AATAAAACATTTATTATAATTATTGGTATTTTTTAATAT
5610393 AATAAAACATTTATTATAATTA-TGGTAATTTTTTTAATAT
1 AATAAAACATTTATTATAATTATTGGT-A-TTTTTTAATAT
5610433 AA
1 AA
5610435 ATACTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
37 3 0.09
38 20 0.57
40 12 0.34
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (39 bp):
AATAAAACATTTATTATAATTATTGGTATTTTTTAATAT
Found at i:5610536 original size:17 final size:16
Alignment explanation
Indices: 5610503--5610551 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
5610493 ATTTAGTGTG
5610503 TTATATTTAAAAAAAA
1 TTATATTTAAAAAAAA
*
5610519 TTATTTTTAAATAAAAA
1 TTATATTTAAA-AAAAA
*
5610536 TTA-ATCTAAAAAAAA
1 TTATATTTAAAAAAAA
5610551 T
1 T
5610552 CAAATATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 8 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATATTTAAAAAAAA
Found at i:5619985 original size:42 final size:41
Alignment explanation
Indices: 5619924--5620008 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 41
5619914 CTATACTTCA
* *
5619924 CGTCAACAGGCTAGAAAGCTTGGGTTCGGTTCGAATGGGAAT
1 CGTCAACAGGCTAGAAAGCTTAGGTTCGG-TCGAATGGAAAT
* * *
5619966 CGTCAACAGGCTGGGAAGCTTATGTTCGGTCGAATGGAAAT
1 CGTCAACAGGCTAGAAAGCTTAGGTTCGGTCGAATGGAAAT
5620007 CG
1 CG
5620009 GCCCCAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 13 0.34
42 25 0.66
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.24
Consensus pattern (41 bp):
CGTCAACAGGCTAGAAAGCTTAGGTTCGGTCGAATGGAAAT
Found at i:5632105 original size:105 final size:105
Alignment explanation
Indices: 5631923--5632132 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
5631913 CTTCACTGTG
* *
5631923 GAATAAGTCAAAAAGTTTCATTCTCAGTTTTAAATCCTGACCAACTACCACTTTTCCTTTTCTCC
1 GAATAAGTCAAAAAGTTTCATTCTCAGTTCTAAATCCTGACCAACTACCACTTTCCCTTTTCTCC
5631988 TTAAAACTTTGCCATCCCATGAGTACTTCGAATGAAACTA
66 TTAAAACTTTGCCATCCCATGAGTACTTCGAATGAAACTA
5632028 GAATAAGTCAAAAAGTTTCATTCTCAGTTCTAAATCCTGACCAACTACCACTTTCCCTTTTCTCC
1 GAATAAGTCAAAAAGTTTCATTCTCAGTTCTAAATCCTGACCAACTACCACTTTCCCTTTTCTCC
5632093 TTAAAACTTTGCCATCCCATGAGTACTTCGAATGAAACTA
66 TTAAAACTTTGCCATCCCATGAGTACTTCGAATGAAACTA
5632133 AGGGTTTTTT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (105 bp):
GAATAAGTCAAAAAGTTTCATTCTCAGTTCTAAATCCTGACCAACTACCACTTTCCCTTTTCTCC
TTAAAACTTTGCCATCCCATGAGTACTTCGAATGAAACTA
Found at i:5637542 original size:16 final size:16
Alignment explanation
Indices: 5637521--5637553 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5637511 CCACTACTAG
5637521 CTCAGATTCTCATAAC
1 CTCAGATTCTCATAAC
5637537 CTCAGATTCTCATAAC
1 CTCAGATTCTCATAAC
5637553 C
1 C
5637554 CTTTTGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.30
Consensus pattern (16 bp):
CTCAGATTCTCATAAC
Found at i:5650139 original size:15 final size:15
Alignment explanation
Indices: 5650121--5650167 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5650111 GTTTTAGATA
*
5650121 ATTTTTATTTTGGTC
1 ATTTATATTTTGGTC
*
5650136 ATTTATATTTTAGATC
1 ATTTATATTTT-GGTC
*
5650152 GTTTATATTTTGGTC
1 ATTTATATTTTGGTC
5650167 A
1 A
5650168 CTCTTTGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (15 bp):
ATTTATATTTTGGTC
Found at i:5651472 original size:15 final size:16
Alignment explanation
Indices: 5651441--5651474 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5651431 CTAAATACAA
*
5651441 GTTGTTCCAAACAATG
1 GTTGTTCAAAACAATG
5651457 GTTGTTCAAAAC-ATG
1 GTTGTTCAAAACAATG
5651472 GTT
1 GTT
5651475 ATTCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (16 bp):
GTTGTTCAAAACAATG
Found at i:5652357 original size:7 final size:7
Alignment explanation
Indices: 5652347--5652376 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5652337 TTTACACTTG
5652347 AAAATTT
1 AAAATTT
5652354 AAAATTT
1 AAAATTT
5652361 AAAATTT
1 AAAATTT
5652368 AAAATTT
1 AAAATTT
5652375 AA
1 AA
5652377 TAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAAATTT
Found at i:5654697 original size:17 final size:18
Alignment explanation
Indices: 5654675--5654717 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
5654665 TAATAAGAGT
5654675 TAATATTAAAT-TTAATC
1 TAATATTAAATATTAATC
* *
5654692 TAATATT-TATATTAATT
1 TAATATTAAATATTAATC
5654709 TAATATTAA
1 TAATATTAA
5654718 TGTGATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATATTAAATATTAATC
Found at i:5655636 original size:14 final size:14
Alignment explanation
Indices: 5655617--5655643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5655607 ATAATCTATC
5655617 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
5655631 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
5655644 AGTTCCATTT
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:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:5655693 original size:59 final size:59
Alignment explanation
Indices: 5655601--5655719 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
5655591 GTTCAAAACC
5655601 TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
1 TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
*
5655660 TTGTTTATAATCTGTCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
1 TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
5655719 T
1 T
5655720 CGTTCAAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (59 bp):
TTGTTTATAATCTATCGTTGTTGCCTTACTGTTGTTGCCTTACAGTTCCATTTGTTTAG
Found at i:5655695 original size:14 final size:14
Alignment explanation
Indices: 5655676--5655702 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5655666 ATAATCTGTC
5655676 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
5655690 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
5655703 AGTTCCATTT
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:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:5662480 original size:42 final size:42
Alignment explanation
Indices: 5662420--5662521 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
5662410 GAGACGTTAA
* * *
5662420 ATTGGTGGATGGTATTGTGGT-GGGATCCATAGGAAT-GAGAAG
1 ATTGGTGGGTGGTGTTGTGATAGGG-TCCATAGGAATAG-GAAG
*
5662462 ATTGGTGGGTGGTGTTGTGATAGGGTCCATAGGAGTAGGAAG
1 ATTGGTGGGTGGTGTTGTGATAGGGTCCATAGGAATAGGAAG
*
5662504 ATTGGTAGGTGGTGTTGT
1 ATTGGTGGGTGGTGTTGT
5662522 AGTGTGACCC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
42 49 0.92
43 4 0.08
ACGTcount: A:0.22, C:0.04, G:0.43, T:0.31
Consensus pattern (42 bp):
ATTGGTGGGTGGTGTTGTGATAGGGTCCATAGGAATAGGAAG
Found at i:5675411 original size:22 final size:22
Alignment explanation
Indices: 5675386--5675427 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5675376 GAGTAAATTA
5675386 ACTCAATTT-AATACAATTTAAT
1 ACTC-ATTTCAATACAATTTAAT
*
5675408 ACTCATTTCAATCCAATTTA
1 ACTCATTTCAATACAATTTA
5675428 TATCTTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
ACTCATTTCAATACAATTTAAT
Found at i:5687807 original size:27 final size:27
Alignment explanation
Indices: 5687776--5687828 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5687766 TTTAGCTTCG
*
5687776 AAATACACTTTAAATCATTTTATTTCT
1 AAATACACTTTAAATCATTTGATTTCT
5687803 AAATACACTTTAAATCATTTGATTTC
1 AAATACACTTTAAATCATTTGATTTC
5687829 AAGTCCGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (27 bp):
AAATACACTTTAAATCATTTGATTTCT
Found at i:5690823 original size:46 final size:46
Alignment explanation
Indices: 5690743--5690973 Score: 363
Period size: 46 Copynumber: 5.0 Consensus size: 46
5690733 ACATTACTAT
* *
5690743 AACTCAGTATGGTTTGCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
5690789 AACTCAGTATGGTTTTCTTTACTGAAACATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
5690835 AACTCAGTATCGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
5690881 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
5690927 AACTCAGTATGGTTTTCTTCATTGAAATATCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
5690973 A
1 A
5690974 CTTTGCCATG
Statistics
Matches: 172, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 172 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:5696973 original size:19 final size:19
Alignment explanation
Indices: 5696935--5696997 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
5696925 AAATTTAATC
***
5696935 ATATATTTATTTTGGATAA
1 ATATATTTATTTTATTTAA
5696954 ATATATTTATTTTATTTAAA
1 ATATATTTATTTTATTT-AA
* ** *
5696974 ATAAATAAATATTATTTAA
1 ATATATTTATTTTATTTAA
5696993 ATATA
1 ATATA
5696998 AATAGATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATATATTTATTTTATTTAA
Found at i:5698078 original size:46 final size:46
Alignment explanation
Indices: 5698022--5698123 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
5698012 TATTACAAAT
* **
5698022 TAGTAGTACACCACATGATAACTACAATATTTTCCAAGTGCATAAC
1 TAGTATTACACCACATGATAACTACAATATCGTCCAAGTGCATAAC
* *
5698068 TAGTATTACACCACATGTTAACTACAATATCGTCGAAGTGCATAAC
1 TAGTATTACACCACATGATAACTACAATATCGTCCAAGTGCATAAC
*
5698114 TAATATTACA
1 TAGTATTACA
5698124 AATTAGTAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (46 bp):
TAGTATTACACCACATGATAACTACAATATCGTCCAAGTGCATAAC
Found at i:5699552 original size:14 final size:14
Alignment explanation
Indices: 5699533--5699563 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5699523 AAATTTCAAA
*
5699533 TTTAATTTTTATAT
1 TTTAATTTTGATAT
5699547 TTTAATTTTGATAT
1 TTTAATTTTGATAT
5699561 TTT
1 TTT
5699564 GAGTCCTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTAATTTTGATAT
Found at i:5699813 original size:13 final size:13
Alignment explanation
Indices: 5699795--5699819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5699785 AAAATAAAAA
5699795 ATTTAAAAAATTC
1 ATTTAAAAAATTC
5699808 ATTTAAAAAATT
1 ATTTAAAAAATT
5699820 ATTAAATTAT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTAAAAAATTC
Found at i:5711882 original size:3 final size:3
Alignment explanation
Indices: 5711874--5711952 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
5711864 CATGTTATAC
5711874 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5711922 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5711953 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5712115 original size:19 final size:19
Alignment explanation
Indices: 5712091--5712131 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5712081 TTTTTATATA
5712091 TAATATATACACATTTTTT
1 TAATATATACACATTTTTT
*
5712110 TAATATATATACATTTTTT
1 TAATATATACACATTTTTT
5712129 TAA
1 TAA
5712132 AGCTTTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATATACACATTTTTT
Found at i:5716393 original size:31 final size:31
Alignment explanation
Indices: 5716356--5716418 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
5716346 TAACAGTTCG
*
5716356 ATAACTTAAATAAAAACTTTCAAATAATTCA
1 ATAACTTAAATAAAAACTCTCAAATAATTCA
* * *
5716387 ATAACTTAAATGAAACCTCTCAAATAGTTCA
1 ATAACTTAAATAAAAACTCTCAAATAATTCA
5716418 A
1 A
5716419 GGATTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (31 bp):
ATAACTTAAATAAAAACTCTCAAATAATTCA
Found at i:5729988 original size:54 final size:53
Alignment explanation
Indices: 5729882--5730024 Score: 153
Period size: 54 Copynumber: 2.6 Consensus size: 53
5729872 GGCCTAAGAC
* *
5729882 ACGATTGTGTGTATCAAGTCAGAGAGTTACACGGTCTAACACACGGCCTGTGAA
1 ACGATCGTGTG-ACCAAGTCAGAGAGTTACACGGTCTAACACACGGCCTGTGAA
* * * ** *
5729936 AC-AGTCGTGTGACACAAGTTAGAGAGTTACACGGTCTGACACATGGTTTGTGAC
1 ACGA-TCGTGTGAC-CAAGTCAGAGAGTTACACGGTCTAACACACGGCCTGTGAA
* *
5729990 ACGATCGTGTGACCTAACTCAGTGAGTTACACGGT
1 ACGATCGTGTGACC-AAGTCAGAGAGTTACACGGT
5730025 TGAAGACATG
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
53 3 0.04
54 70 0.95
55 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (53 bp):
ACGATCGTGTGACCAAGTCAGAGAGTTACACGGTCTAACACACGGCCTGTGAA
Found at i:5731176 original size:15 final size:15
Alignment explanation
Indices: 5731152--5731187 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5731142 CACTCGGTTT
*
5731152 GAAGATGGTTTAAAC
1 GAAGACGGTTTAAAC
5731167 GAAGACGGTTTAAAC
1 GAAGACGGTTTAAAC
5731182 GAAGAC
1 GAAGAC
5731188 ATCAAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.19
Consensus pattern (15 bp):
GAAGACGGTTTAAAC
Found at i:5734861 original size:92 final size:92
Alignment explanation
Indices: 5734715--5734931 Score: 285
Period size: 92 Copynumber: 2.4 Consensus size: 92
5734705 TAACTACAAA
* * * * * *
5734715 CACTGGTGGTTTATCCACAAATTAT--TGGCAACTTCCATCTACAAAAACCGTTGTGTATTCATA
1 CACTCGTGGTTTATCCACAACTTATACTGGTAGCTTCCATCTACAAAAACCATTGTGTATTCACA
* *
5734778 ACTACTGGCAACGTATTAACCTGCAAG
66 ACTAATGACAACGTATTAACCTGCAAG
* * * *
5734805 CACTCGTGGTTTATCCACAACTTATACTAGTAGCTTTCATCTGCAAAAATCATTGTGTATTCACA
1 CACTCGTGGTTTATCCACAACTTATACTGGTAGCTTCCATCTACAAAAACCATTGTGTATTCACA
*
5734870 ACTAATGACAACGTATTAACTTGCAAG
66 ACTAATGACAACGTATTAACCTGCAAG
* *
5734897 CACTCATGGTTTATACACAACTTATACTGGTAGCT
1 CACTCGTGGTTTATCCACAACTTATACTGGTAGCT
5734932 ATTATTTGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
90 23 0.21
92 86 0.79
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (92 bp):
CACTCGTGGTTTATCCACAACTTATACTGGTAGCTTCCATCTACAAAAACCATTGTGTATTCACA
ACTAATGACAACGTATTAACCTGCAAG
Found at i:5735193 original size:92 final size:90
Alignment explanation
Indices: 5735079--5735300 Score: 284
Period size: 92 Copynumber: 2.4 Consensus size: 90
5735069 TTTTAGCTGC
*
5735079 AAAAATCGTTGTGTATTTACAACTATTGGCAGTGTATTAACCTGCAAGCACTCATGGTTTAGCCA
1 AAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCTGCAAGCACTCATGGTTTAGCCA
* *
5735144 CAACTTATATTGACAACT-TTCTTCT
66 CAACTTATACTGACAACTATT-ATCT
** * *
5735169 GGAAAAATCGTTGTGTATTCACAACTACAGGCTGTGTATTAACCTGCAAGCACTCATGGTTTATC
1 --AAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCTGCAAGCACTCATGGTTTAGC
* *
5735234 CACAACTTATACTGGCAGCTATTATCT
64 CACAACTTATACTGACAACTATTATCT
** * *
5735261 ATAAACCCATTGTGTATTCACAACTATTGGCAGCGTATTA
1 A-AAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTA
5735301 GCCTAAAACA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
90 1 0.01
91 31 0.28
92 78 0.70
93 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (90 bp):
AAAAATCGTTGTGTATTCACAACTATTGGCAGTGTATTAACCTGCAAGCACTCATGGTTTAGCCA
CAACTTATACTGACAACTATTATCT
Found at i:5735211 original size:322 final size:322
Alignment explanation
Indices: 5734626--5735273 Score: 825
Period size: 322 Copynumber: 2.0 Consensus size: 322
5734616 TTTACTATTT
* * * * *
5734626 TTGTATTGTATTGATGCTCTCATGTCATACTACGTTGCACGGGGCGGGACGCGTTGAAAGGAGGA
1 TTGTATTATATTGATGCTCTCATGTCATACTACATTGCACGGGGCGAGACGCATTGAAAGGAAGA
* * * * *
5734691 AGCATTGGCAGTTTTAACTACAAACACTGGTGGTTTATCCACAAATTATTGGCAACTTCCATCTA
66 AGCACTGACAGTTTTAACTACAAACACTGGTGGTTTATCCACAAATTACTAGCAACTTCCAGCTA
* * *
5734756 CAAAAACCGTTGTGTATTCATAACTACTGGCAACGTATTAACCTGCAAGCACTCGTGGTTTATCC
131 CAAAAACCGTTGTGTATTCACAACTACTGGCAACGTATTAACCTGCAAGCACTCATGGTTTAGCC
* *
5734821 ACAACTTATACTAGTAGCTTTCATCTGCAAAAATCATTGTGTATTCACAACTAATGACAACGTAT
196 ACAACTTATACTAGCAACTTTCATCTGCAAAAATCATTGTGTATTCACAACTAATGACAACGTAT
* * * * *
5734886 TAACTTGCAAGCACTCATGGTTTATACACAACTTATACTGGTAGCTATTATTTGTAAACTCA
261 TAACCTGCAAGCACTCATGGTTTATACACAACTTATACTGGCAGCTATTATCTATAAACCCA
* * * * * *
5734948 TTGTATTATATTGATGC-CTGCATGTCATATTACATTGTATGGGGTGAGATGTATTGAAAGGAAG
1 TTGTATTATATTGATGCTCT-CATGTCATACTACATTGCACGGGGCGAGACGCATTGAAAGGAAG
* * * * **
5735012 AAGTACTGACAGTTTTAACTACAAGCACTGGTGGTTTATCCACAGATTACTAGCAGCTTTTAGCT
65 AAGCACTGACAGTTTTAACTACAAACACTGGTGGTTTATCCACAAATTACTAGCAACTTCCAGCT
* * * * **
5735077 GCAAAAATCGTTGTGTATTTACAACTATTGGCAGTGTATTAACCTGCAAGCACTCATGGTTTAGC
130 ACAAAAACCGTTGTGTATTCACAACTACTGGCAACGTATTAACCTGCAAGCACTCATGGTTTAGC
* * * * * ***
5735142 CACAACTTATA-TTGACAACTTTCTTCTGGAAAAATCGTTGTGTATTCACAACTACA-GGCTGTG
195 CACAACTTATACTAG-CAACTTTCATCTGCAAAAATCATTGTGTATTCACAACTA-ATGACAACG
*
5735205 TATTAACCTGCAAGCACTCATGGTTTATCCACAACTTATACTGGCAGCTATTATCTATAAACCCA
258 TATTAACCTGCAAGCACTCATGGTTTATACACAACTTATACTGGCAGCTATTATCTATAAACCCA
5735270 TTGT
1 TTGT
5735274 GTATTCACAA
Statistics
Matches: 276, Mismatches: 47, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
321 4 0.01
322 271 0.98
323 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (322 bp):
TTGTATTATATTGATGCTCTCATGTCATACTACATTGCACGGGGCGAGACGCATTGAAAGGAAGA
AGCACTGACAGTTTTAACTACAAACACTGGTGGTTTATCCACAAATTACTAGCAACTTCCAGCTA
CAAAAACCGTTGTGTATTCACAACTACTGGCAACGTATTAACCTGCAAGCACTCATGGTTTAGCC
ACAACTTATACTAGCAACTTTCATCTGCAAAAATCATTGTGTATTCACAACTAATGACAACGTAT
TAACCTGCAAGCACTCATGGTTTATACACAACTTATACTGGCAGCTATTATCTATAAACCCA
Found at i:5737455 original size:24 final size:24
Alignment explanation
Indices: 5737421--5737470 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
5737411 TTTCTAGAAG
* *
5737421 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
5737445 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
5737469 AT
1 AT
5737471 GTGACTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:5741013 original size:27 final size:27
Alignment explanation
Indices: 5740982--5741034 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5740972 CCATTTTACC
5740982 CTTATTTCACCAATTCTCCTGATTTTG
1 CTTATTTCACCAATTCTCCTGATTTTG
5741009 CTTATTTCACCAATTCTCCTGATTTT
1 CTTATTTCACCAATTCTCCTGATTTT
5741035 TCTCAGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.06, T:0.49
Consensus pattern (27 bp):
CTTATTTCACCAATTCTCCTGATTTTG
Found at i:5744976 original size:24 final size:24
Alignment explanation
Indices: 5744913--5744964 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5744903 TTTCTAGAAG
* * *
5744913 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
5744937 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
5744961 ATTT
1 ATTT
5744965 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:5757916 original size:25 final size:25
Alignment explanation
Indices: 5757888--5757939 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5757878 AAACAAGGGA
5757888 AGAATAAACTCAATTTCATGTCGGC
1 AGAATAAACTCAATTTCATGTCGGC
5757913 AGAATAAACTCAATTTCATGTCGGC
1 AGAATAAACTCAATTTCATGTCGGC
5757938 AG
1 AG
5757940 TCTCGCGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (25 bp):
AGAATAAACTCAATTTCATGTCGGC
Found at i:5780280 original size:17 final size:17
Alignment explanation
Indices: 5780248--5780279 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5780238 ATTGATATAC
5780248 GAAAAAGAAGAAAAAAA
1 GAAAAAGAAGAAAAAAA
5780265 GAAAAAG--GAAAAAAA
1 GAAAAAGAAGAAAAAAA
5780280 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.53
17 7 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAAAAAAA
Found at i:5780461 original size:7 final size:7
Alignment explanation
Indices: 5780444--5780474 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5780434 TTTTTTCGTG
5780444 TCAGA-A
1 TCAGATA
5780450 TCAGATA
1 TCAGATA
5780457 TCAGATA
1 TCAGATA
5780464 TCAGATA
1 TCAGATA
5780471 TCAG
1 TCAG
5780475 TATACGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (7 bp):
TCAGATA
Found at i:5783554 original size:51 final size:53
Alignment explanation
Indices: 5783452--5783595 Score: 195
Period size: 52 Copynumber: 2.7 Consensus size: 53
5783442 TATTCTTGTA
* *
5783452 AAATTAAATGAGATTTAATGAAAAAAAAGGTGTTAGGTGTAGGAAAAAAAATTG
1 AAATT-AATGAGATTTAATGAAAAAAAAGGTGTTAGATGTAAGAAAAAAAATTG
5783506 AAA-TAGATGAGATTTAAT-AAAAAAAAGGTGTTAGATGTAAG-AAAAAAATTG
1 AAATTA-ATGAGATTTAATGAAAAAAAAGGTGTTAGATGTAAGAAAAAAAATTG
* * *
5783557 AAATTAATGAGACTGAATGAAAAAAAAGAGTGTCAGATG
1 AAATTAATGAGATTTAATGAAAAAAAAG-GTGTTAGATG
5783596 GATTTGTCAA
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
51 23 0.28
52 33 0.41
53 22 0.27
54 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.22, T:0.24
Consensus pattern (53 bp):
AAATTAATGAGATTTAATGAAAAAAAAGGTGTTAGATGTAAGAAAAAAAATTG
Found at i:5783737 original size:43 final size:44
Alignment explanation
Indices: 5783675--5783786 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
5783665 GAATTGAATT
*
5783675 AAATGAAATTCTGAAAAGTGAGTTAAA-ATAAATTGGATAGAAAC
1 AAATGAAATT-TGAAAAGTGAGTTAAAGATAAATGGGATAGAAAC
* * ** *
5783719 AAATGAGATTTGAAAAGTGAGTCAAAGATGGATGGGATAGAAAT
1 AAATGAAATTTGAAAAGTGAGTTAAAGATAAATGGGATAGAAAC
*
5783763 AAATGAAATTTGAAAAGTTAGTTA
1 AAATGAAATTTGAAAAGTGAGTTA
5783787 GAACAATTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 15 0.26
44 43 0.74
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (44 bp):
AAATGAAATTTGAAAAGTGAGTTAAAGATAAATGGGATAGAAAC
Found at i:5784204 original size:44 final size:43
Alignment explanation
Indices: 5784156--5784279 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
5784146 TCTGACTAAT
*
5784156 TTTTCAAATTTCATTTATTTCTATCCTATCCATCTTTGACTCAC
1 TTTTCAAATTTCATTTATTTCTATCCAATCCAT-TTTGACTCAC
* **
5784200 TTTTCAAATTTCATTTGTTTCTATCCAATTTATTTTGACTCAC
1 TTTTCAAATTTCATTTATTTCTATCCAATCCATTTTGACTCAC
* * * *
5784243 TTTTCAGAATTTTATTTAATTCAATTCAATCTCATTT
1 TTTTCA-AATTTCATTTATTTCTATCCAATC-CATTT
5784280 ATTTACTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
43 16 0.24
44 47 0.70
45 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.52
Consensus pattern (43 bp):
TTTTCAAATTTCATTTATTTCTATCCAATCCATTTTGACTCAC
Found at i:5787447 original size:96 final size:95
Alignment explanation
Indices: 5787333--5787506 Score: 253
Period size: 96 Copynumber: 1.8 Consensus size: 95
5787323 GCCAGCATCT
*
5787333 AAATTTTTTTTTACTTTTTTCGTATACTGATATCTGAGTCTGACGCG-AAAAAAAAGAAATTTTT
1 AAATTTTTTTTTACTTTTTTCGTATACTGATATCTGAGTCTGACACGAAAAAAAAAG-AATTTTT
5787397 TTTAAAAATTGTACTCAGGCCAACACCCAAAA
65 TTT-AAAATTGTACTCAGGCCAACACCCAAAA
* * * *
5787429 AAATTTTATTTTTA-TTTTTTTGTGTACTGATATCTGATTCTGACATGAAAAAAAAAGAATTTTT
1 AAATTTT-TTTTTACTTTTTTCGTATACTGATATCTGAGTCTGACACGAAAAAAAAAGAATTTTT
*
5787493 TTTTAAATTGTACT
65 TTTAAAATTGTACT
5787507 GGGTGCCGGC
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
95 10 0.14
96 45 0.64
97 15 0.21
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (95 bp):
AAATTTTTTTTTACTTTTTTCGTATACTGATATCTGAGTCTGACACGAAAAAAAAAGAATTTTTT
TTAAAATTGTACTCAGGCCAACACCCAAAA
Found at i:5787603 original size:111 final size:111
Alignment explanation
Indices: 5787432--5787670 Score: 349
Period size: 110 Copynumber: 2.2 Consensus size: 111
5787422 CCCAAAAAAA
* * * * *
5787432 TTTTATTTTTA-TTTTTTTGTGTACTGATATCTGATTCTGACATGAAAAAAAAAGAATTTTTTTT
1 TTTTCTTTTTACTTTTTTCGTATACTGATATCTCATTCTGACACGAAAAAAAAAGAA-TTTTTTT
5787496 TAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAA-TTTT
65 TAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAATTTTT
* **
5787542 TTTTCTTTTTACTTTTTTCGTATATTGATATCTCATTCTGACACGAAAAAAAAATTATTTTTTTT
1 TTTTCTTTTTACTTTTTTCGTATACTGATATCTCATTCTGACACGAAAAAAAAAGAATTTTTTTT
* *
5787607 AAATTGTTCTGGGTGCCGGTCATTGACAGGCCAGCACCAAATTTTT
66 AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAATTTTT
5787653 TTTTCCTTTTT-CTTTTTT
1 TTTT-CTTTTTACTTTTTT
5787671 TTTTTCCTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
110 57 0.49
111 53 0.46
112 6 0.05
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (111 bp):
TTTTCTTTTTACTTTTTTCGTATACTGATATCTCATTCTGACACGAAAAAAAAAGAATTTTTTTT
AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAATTTTT
Found at i:5793008 original size:25 final size:25
Alignment explanation
Indices: 5792974--5793061 Score: 122
Period size: 25 Copynumber: 3.5 Consensus size: 25
5792964 TTTATGTGGT
*
5792974 GCCTTTGTGGTGAGTCACTTGTAAA
1 GCCTTTGTGGCGAGTCACTTGTAAA
* * * *
5792999 GCCTTTGTGGCGATTTATTTGGAAA
1 GCCTTTGTGGCGAGTCACTTGTAAA
*
5793024 GCCTTTGTGGCAAGTCACTTGTAAA
1 GCCTTTGTGGCGAGTCACTTGTAAA
5793049 GCCTTTGTGGCGA
1 GCCTTTGTGGCGA
5793062 TTTATTTAGG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.35
Consensus pattern (25 bp):
GCCTTTGTGGCGAGTCACTTGTAAA
Found at i:5793040 original size:50 final size:50
Alignment explanation
Indices: 5792974--5793105 Score: 194
Period size: 50 Copynumber: 2.6 Consensus size: 50
5792964 TTTATGTGGT
**
5792974 GCCTTTGTGGTGAGTCACTTGTAAAGCCTTTGTGGCGATTTATTT-GGAAA
1 GCCTTTGTGGCAAGTCACTTGTAAAGCCTTTGTGGCGATTTATTTAGG-AA
5793024 GCCTTTGTGGCAAGTCACTTGTAAAGCCTTTGTGGCGATTTATTTAGGAA
1 GCCTTTGTGGCAAGTCACTTGTAAAGCCTTTGTGGCGATTTATTTAGGAA
* * * *
5793074 GCCTTTGTGGCAGGTTACCTGTAAAGTCTTTG
1 GCCTTTGTGGCAAGTCACTTGTAAAGCCTTTG
5793106 AGGAAGGTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
50 73 0.97
51 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (50 bp):
GCCTTTGTGGCAAGTCACTTGTAAAGCCTTTGTGGCGATTTATTTAGGAA
Found at i:5793075 original size:25 final size:25
Alignment explanation
Indices: 5792997--5793084 Score: 101
Period size: 25 Copynumber: 3.5 Consensus size: 25
5792987 GTCACTTGTA
5792997 AAGCCTTTGTGGCGATTTATTT-GG
1 AAGCCTTTGTGGCGATTTATTTAGG
* * *
5793021 AAAGCCTTTGTGGCAAGTCACTTGTA--
1 -AAGCCTTTGTGGCGATTTA-TT-TAGG
5793047 AAGCCTTTGTGGCGATTTATTTAGG
1 AAGCCTTTGTGGCGATTTATTTAGG
5793072 AAGCCTTTGTGGC
1 AAGCCTTTGTGGC
5793085 AGGTTACCTG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 45 0.87
26 2 0.04
27 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (25 bp):
AAGCCTTTGTGGCGATTTATTTAGG
Found at i:5793104 original size:25 final size:25
Alignment explanation
Indices: 5793076--5793135 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
5793066 TTTAGGAAGC
* *
5793076 CTTTGTGGCAGGTTACCTGTAAAGT
1 CTTTGTGGCAGGTTACCTATAAAGG
* *
5793101 CTTTGAGGAAGGTTACCTATAAAGG
1 CTTTGTGGCAGGTTACCTATAAAGG
*
5793126 CTATGTGGCA
1 CTTTGTGGCA
5793136 TAATGACTAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (25 bp):
CTTTGTGGCAGGTTACCTATAAAGG
Found at i:5805885 original size:15 final size:16
Alignment explanation
Indices: 5805865--5805897 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5805855 TGATACTGAT
5805865 TTGAGACAGGC-CATA
1 TTGAGACAGGCGCATA
*
5805880 TTGAGAGAGGCGCATA
1 TTGAGACAGGCGCATA
5805896 TT
1 TT
5805898 AGCCCTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (16 bp):
TTGAGACAGGCGCATA
Found at i:5810136 original size:12 final size:13
Alignment explanation
Indices: 5810106--5810138 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5810096 GTTACATTCC
5810106 CAAAAAGGTGAAT
1 CAAAAAGGTGAAT
5810119 CAAAAAGGTGAAT
1 CAAAAAGGTGAAT
*
5810132 TAAAAAG
1 CAAAAAG
5810139 ATGAGTTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (13 bp):
CAAAAAGGTGAAT
Found at i:5818618 original size:10 final size:10
Alignment explanation
Indices: 5818603--5818627 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5818593 TAATCTAAGC
5818603 TTAATTTCTA
1 TTAATTTCTA
5818613 TTAATTTCTA
1 TTAATTTCTA
5818623 TTAAT
1 TTAAT
5818628 ATTAAGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAATTTCTA
Found at i:5821726 original size:2 final size:2
Alignment explanation
Indices: 5821719--5821755 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5821709 TAAAAGATTC
* *
5821719 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5821756 AACATTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5821736 original size:12 final size:12
Alignment explanation
Indices: 5821719--5821755 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
5821709 TAAAAGATTC
*
5821719 ATATATATATAT
1 ATATATACATAT
5821731 ATATATACATAT
1 ATATATACATAT
5821743 ATATATACATAT
1 ATATATACATAT
5821755 A
1 A
5821756 AACATTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATACATAT
Found at i:5825055 original size:20 final size:21
Alignment explanation
Indices: 5825023--5825061 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5825013 ATCCAAGCTT
5825023 AATTTCTATCAATTTCACACC
1 AATTTCTATCAATTTCACACC
5825044 AATTTC-ATCAATTTCACA
1 AATTTCTATCAATTTCACA
5825062 ATCATGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTCTATCAATTTCACACC
Found at i:5825332 original size:21 final size:19
Alignment explanation
Indices: 5825305--5825354 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
5825295 TATTATTATA
* *
5825305 ACTTAATTAATTATGTTTTT
1 ACTTAATTAATCAT-ATTTT
5825325 ATCTTAATTAATCATATTTT
1 A-CTTAATTAATCATATTTT
5825345 ACTTAATTAA
1 ACTTAATTAA
5825355 CAAAACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 6 0.22
21 12 0.44
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (19 bp):
ACTTAATTAATCATATTTT
Found at i:5826924 original size:24 final size:25
Alignment explanation
Indices: 5826897--5826944 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5826887 TGAAAATAAC
* *
5826897 AATTCTATCAA-TTCTATTGAGAGA
1 AATTCTACCAATTTCTATCGAGAGA
5826921 AATTCTACCAATTTCTATCGAGAG
1 AATTCTACCAATTTCTATCGAGAG
5826945 GGATTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (25 bp):
AATTCTACCAATTTCTATCGAGAGA
Found at i:5837965 original size:34 final size:35
Alignment explanation
Indices: 5837907--5837976 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
5837897 AGTTGTTTTC
*
5837907 TGATTATTTGATTTTTATAGAAATTTTACAGAAAT
1 TGATTATTTGATTTTTACAGAAATTTTACAGAAAT
* * *
5837942 TGATTGTTTGA-TTTTACATAAATTTTATAGAAAT
1 TGATTATTTGATTTTTACAGAAATTTTACAGAAAT
5837976 T
1 T
5837977 TTAATACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (35 bp):
TGATTATTTGATTTTTACAGAAATTTTACAGAAAT
Found at i:5842674 original size:31 final size:31
Alignment explanation
Indices: 5842636--5842694 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5842626 TTTAAAATGC
5842636 TCAAACATTTTCAAAAGTGATCAAATAAATA
1 TCAAACATTTTCAAAAGTGATCAAATAAATA
* *
5842667 TCAAACATTTTTAAAAGTGCTCAAATAA
1 TCAAACATTTTCAAAAGTGATCAAATAA
5842695 GGGTTTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (31 bp):
TCAAACATTTTCAAAAGTGATCAAATAAATA
Found at i:5844677 original size:6 final size:6
Alignment explanation
Indices: 5844666--5844692 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5844656 TCTATTTATC
5844666 TATCTA TATCTA TATCTA TATCTA TAT
1 TATCTA TATCTA TATCTA TATCTA TAT
5844693 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:5844681 original size:16 final size:16
Alignment explanation
Indices: 5844646--5844695 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
5844636 TTTCTCATGT
* *
5844646 TATCTATCTATCTATT
1 TATCTATCTATATATA
*
5844662 TATCTATCTATATCTA
1 TATCTATCTATATATA
5844678 TATCTATATCTATATATA
1 TATC--TATCTATATATA
5844696 ATAATAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 17 0.61
18 11 0.39
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (16 bp):
TATCTATCTATATATA
Found at i:5844946 original size:6 final size:6
Alignment explanation
Indices: 5844937--5844962 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5844927 GTTTTTAAAG
5844937 ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT AT
5844963 ATATTATATA
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:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:5848953 original size:40 final size:40
Alignment explanation
Indices: 5848893--5848972 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
5848883 CGTCCTAACC
*
5848893 TTGTAAGTTATCTGAAAAGAAGGAAAAATAAGGGGGTGAG
1 TTGTAAGTTATCTCAAAAGAAGGAAAAATAAGGGGGTGAG
* *
5848933 TTGTGAGTTATCTCAAAAGAAGTAAAAATAAGGGGGTGAG
1 TTGTAAGTTATCTCAAAAGAAGGAAAAATAAGGGGGTGAG
5848973 CTATGAAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.04, G:0.31, T:0.24
Consensus pattern (40 bp):
TTGTAAGTTATCTCAAAAGAAGGAAAAATAAGGGGGTGAG
Found at i:5855227 original size:39 final size:41
Alignment explanation
Indices: 5855183--5855264 Score: 141
Period size: 39 Copynumber: 2.0 Consensus size: 41
5855173 GGTGCATATG
5855183 TCAACCAAATATTCAATCATGCATTTTCA-T-AACCAACTA
1 TCAACCAAATATTCAATCATGCATTTTCATTAAACCAACTA
*
5855222 TCAACCAAATATTTAATCATGCATTTTCATTAAACCAACTA
1 TCAACCAAATATTCAATCATGCATTTTCATTAAACCAACTA
5855263 TC
1 TC
5855265 CATACAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 28 0.70
40 1 0.03
41 11 0.28
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.33
Consensus pattern (41 bp):
TCAACCAAATATTCAATCATGCATTTTCATTAAACCAACTA
Found at i:5859572 original size:59 final size:59
Alignment explanation
Indices: 5859530--5859654 Score: 205
Period size: 59 Copynumber: 2.1 Consensus size: 59
5859520 AAGAGACAAG
* *
5859530 TTTTAAAGCAAATCAACTAGTTTTTTTTAATTAAATAAAAGCTAACTTACTGTAACAGT
1 TTTTAAAGCAAATCAACTAGTTTTTTTTAATTAAATAAAAGCTAACCTACAGTAACAGT
* * *
5859589 TTTTAAAGCAAATCAACTAGTTTTTTTTAATTAAATAAAAGCTAACTTACTGTAACGGT
1 TTTTAAAGCAAATCAACTAGTTTTTTTTAATTAAATAAAAGCTAACCTACAGTAACAGT
5859648 TTTTAAA
1 TTTTAAA
5859655 CTCGACAATC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (59 bp):
TTTTAAAGCAAATCAACTAGTTTTTTTTAATTAAATAAAAGCTAACCTACAGTAACAGT
Found at i:5866912 original size:2 final size:2
Alignment explanation
Indices: 5866907--5866931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5866897 GTATATGTAG
5866907 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
5866932 GAAGACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:5876017 original size:40 final size:40
Alignment explanation
Indices: 5875973--5876105 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 40
5875963 ACTATGTTTA
* *
5875973 GCACTTAGTATGTGATTCTAGATAGCTTCGGCTATTTATG
1 GCACTTAGTGTGCGATTCTAGATAGCTTCGGCTATTTATG
** * *
5876013 GCACTTAGTGTGCGATT-GGGAATAGCTTTGACTATTTATG
1 GCACTTAGTGTGCGATTCTAG-ATAGCTTCGGCTATTTATG
* * ** * * *
5876053 GTACTTAGTGTACGAAACTGAGATTGCTTCGGCTATGTAAG
1 GCACTTAGTGTGCGATTCT-AGATAGCTTCGGCTATTTATG
5876094 GCACTTAGTGTG
1 GCACTTAGTGTG
5876106 TAGGATGAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
39 1 0.01
40 45 0.63
41 24 0.34
42 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.36
Consensus pattern (40 bp):
GCACTTAGTGTGCGATTCTAGATAGCTTCGGCTATTTATG
Found at i:5876924 original size:23 final size:23
Alignment explanation
Indices: 5876850--5876929 Score: 124
Period size: 23 Copynumber: 3.5 Consensus size: 23
5876840 ACATGTTATG
5876850 ATGCTGTCCAATTTGGTGTATAA
1 ATGCTGTCCAATTTGGTGTATAA
* *
5876873 ATGATATCCAATTTGGTGTATAA
1 ATGCTGTCCAATTTGGTGTATAA
*
5876896 ATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGGTGTATAA
*
5876919 AAGCTGTCCAA
1 ATGCTGTCCAA
5876930 AACAGGGTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (23 bp):
ATGCTGTCCAATTTGGTGTATAA
Found at i:5883351 original size:40 final size:40
Alignment explanation
Indices: 5883304--5883420 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 40
5883294 TATGTGATTC
* * *
5883304 GAGATAGCTTCGGCTATTTATGGCATTTAGTGTGCG-ATT
1 GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAACT
*
5883343 GGGAATAGCTTCGGCTATATATGGCACTTAGTGTGCGAAACT
1 GAG-ATAGCTTCGGCTATATATGGCACTTAGTGTGCG-AACT
* * *
5883385 GAGATAACTTCGGCTATGTAAGGCACTTAGTGTGCG
1 GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCG
5883421 GGATTGATAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.03
40 31 0.46
41 30 0.45
42 4 0.06
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (40 bp):
GAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGAACT
Found at i:5883410 original size:41 final size:39
Alignment explanation
Indices: 5883286--5883420 Score: 144
Period size: 40 Copynumber: 3.4 Consensus size: 39
5883276 ACTATGTTTA
* * * *
5883286 GCACTTAGTATGTGATTCGAGATAGCTTCGGCTATTTATG
1 GCACTTAGTGTGCGACT-GAGATAGCTTCGGCTATATATG
* * *
5883326 GCATTTAGTGTGCGATTGGGAATAGCTTCGGCTATATATG
1 GCACTTAGTGTGCGACTGAG-ATAGCTTCGGCTATATATG
* * *
5883366 GCACTTAGTGTGCGAAACTGAGATAACTTCGGCTATGTAAG
1 GCACTTAGTGTGCG--ACTGAGATAGCTTCGGCTATATATG
5883407 GCACTTAGTGTGCG
1 GCACTTAGTGTGCG
5883421 GGATTGATAT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.02
40 45 0.56
41 30 0.37
42 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (39 bp):
GCACTTAGTGTGCGACTGAGATAGCTTCGGCTATATATG
Found at i:5884200 original size:23 final size:23
Alignment explanation
Indices: 5884172--5884413 Score: 394
Period size: 23 Copynumber: 10.5 Consensus size: 23
5884162 TACATGTTAT
*
5884172 AATGCTGTCCAATTTGGTTTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884195 AATGCTGTCCAATTTGATGTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884218 AACGCTGTCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATA
5884241 AATGCTGTCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884264 AATGCTGTCCAATTTGATGTATA
1 AATGCTGTCCAATTTGGTGTATA
5884287 AATGCTGTCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884310 AATACTGTCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884333 AATGCTGTCCAATTTGATGTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884356 AATGCTATCCAATTTGGTGTATA
1 AATGCTGTCCAATTTGGTGTATA
* *
5884379 AATGTTGTCCAATTTGATGTATA
1 AATGCTGTCCAATTTGGTGTATA
*
5884402 AAAGCTGTCCAA
1 AATGCTGTCCAA
5884414 AACAGGGTAG
Statistics
Matches: 202, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 202 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (23 bp):
AATGCTGTCCAATTTGGTGTATA
Found at i:5885646 original size:27 final size:27
Alignment explanation
Indices: 5885616--5885731 Score: 101
Period size: 27 Copynumber: 4.3 Consensus size: 27
5885606 AGTGAAGTGA
* * *
5885616 TGTTTATTATCTTGGTGGACTCTCTCG
1 TGTTTACTATCTTGATGGACTATCTCG
*
5885643 TGTTTACTATCCTGATGGACTATCTCG
1 TGTTTACTATCTTGATGGACTATCTCG
* * *
5885670 TGTTTACTATC-TCA-GCAGACTATCCCA
1 TGTTTACTATCTTGATG--GACTATCTCG
* * * *
5885697 TGTTTACTATCTCGAAGGACCATCCCG
1 TGTTTACTATCTTGATGGACTATCTCG
5885724 TGTTTACT
1 TGTTTACT
5885732 GACTCCAAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 69 0.93
28 1 0.01
29 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (27 bp):
TGTTTACTATCTTGATGGACTATCTCG
Found at i:5904136 original size:12 final size:12
Alignment explanation
Indices: 5904119--5904145 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5904109 AGTAAGTTTA
5904119 TTTATTTATTTC
1 TTTATTTATTTC
5904131 TTTATTTATTTC
1 TTTATTTATTTC
5904143 TTT
1 TTT
5904146 CTATGTTTTA
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTATTTC
Found at i:5904136 original size:16 final size:16
Alignment explanation
Indices: 5904115--5904147 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5904105 GTTAAGTAAG
5904115 TTTATTTATTTATTTC
1 TTTATTTATTTATTTC
*
5904131 TTTATTTATTTCTTTC
1 TTTATTTATTTATTTC
5904147 T
1 T
5904148 ATGTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTATTTATTTC
Found at i:5904686 original size:10 final size:10
Alignment explanation
Indices: 5904671--5904702 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
5904661 TCTCTCATAT
5904671 TTCCTCTCAA
1 TTCCTCTCAA
5904681 TTCCTCTCAA
1 TTCCTCTCAA
5904691 TTCCTCTCAA
1 TTCCTCTCAA
5904701 TT
1 TT
5904703 TCCTTCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.44
Consensus pattern (10 bp):
TTCCTCTCAA
Found at i:5904765 original size:51 final size:51
Alignment explanation
Indices: 5904687--5904809 Score: 187
Period size: 51 Copynumber: 2.4 Consensus size: 51
5904677 TCAATTCCTC
* * *
5904687 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTTTC-AATCTATATTTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATA-TTTAATT
5904737 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
*
5904788 TCAATTTCTTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
5904810 TTTTAAAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
50 4 0.06
51 56 0.84
52 7 0.10
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
Found at i:5905963 original size:7 final size:7
Alignment explanation
Indices: 5905951--5905975 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5905941 ATTTGATTGA
5905951 TATTTAG
1 TATTTAG
5905958 TATTTAG
1 TATTTAG
5905965 TATTTAG
1 TATTTAG
5905972 TATT
1 TATT
5905976 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:5906644 original size:18 final size:18
Alignment explanation
Indices: 5906618--5906652 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5906608 AAGTGCGTTT
*
5906618 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
5906636 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
5906653 TCCTTTTCCG
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:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:5907128 original size:43 final size:45
Alignment explanation
Indices: 5907075--5907160 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
5907065 ATATTTTGAA
*
5907075 TATTTTGATATTATTTTATGTAA-AAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
*
5907118 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
5907161 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:5907218 original size:23 final size:23
Alignment explanation
Indices: 5907166--5907776 Score: 473
Period size: 23 Copynumber: 26.3 Consensus size: 23
5907156 TTTGATGTAA
*
5907166 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
*** **
5907189 CCTAAACCCTAACCTAAAATAAT
1 TAAAAACCCTAACCTAATTTAAT
5907212 TAAAAACTCAAAACCATAACCTAATTTAAT
1 TAAAAA--C----CC-TAACCTAATTTAAT
* *
5907242 TTAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
5907265 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
5907288 TAAAAACCCTAAATCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
5907312 -AAACTCTAACCCTAACCTAATTCAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
5907338 T-AAAACCCTAAACC--A-TTAACA
1 TAAAAACCCT-AACCTAATTTAA-T
5907359 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
5907382 TAAAAACCCTAGCCTAACCAAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
5907410 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
5907433 TAAAAATCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
5907457 -AAACCCTAACCCTAACCTAATTCAAT
1 TAAA----AACCCTAACCTAATTTAAT
5907483 T-AAAACCCTAAACC--A-TTACCA-
1 TAAAAACCCT-AACCTAATTTA--AT
*
5907504 TAAAATCCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907527 TAAAAACCCTAAACT--CTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
5907548 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907571 T-AAAACCATGACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907593 TAAAAACCCTAAACT--CTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
5907614 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907637 T-AAAACCATGACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907659 TAAAAACCCTAAACT--CTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
5907680 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907703 T-AAAACCATGACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
5907725 TAAAAACCCTAAACT--CTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
5907746 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
5907769 TAAAAACC
1 TAAAAACC
5907777 TTAAACCCTT
Statistics
Matches: 469, Mismatches: 62, Indels: 114
0.73 0.10 0.18
Matches are distributed among these distances:
20 5 0.01
21 84 0.18
22 86 0.18
23 184 0.39
24 19 0.04
25 24 0.05
26 15 0.03
27 11 0.02
28 22 0.05
29 2 0.00
30 17 0.04
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:5907249 original size:53 final size:50
Alignment explanation
Indices: 5907169--5907493 Score: 197
Period size: 50 Copynumber: 6.6 Consensus size: 50
5907159 GATGTAATAA
**
5907169 AAACCCTAACCTAATTTAACCCT-AAACCCTAACCTAAAATAATTAAAAACTC
1 AAACCCTAACCTAATTTAA-TTTAAAACCCTAACCT--AATAATTAAAAACTC
* * *
5907221 AAAACCATAACCTAATTTAATTTAAAACCCTAGCCTAAT--TTAATTAA---
1 -AAACCCTAACCTAATTTAATTTAAAACCCTAACCTAATAATTAA-AAACTC
*
5907268 AAACCCTAACCTAATTTAATTAAAAACCCTAAATCCT--TAATTAAAAACTC
1 AAACCCTAACCTAATTTAATTTAAAACCCT-AA-CCTAATAATTAAAAACTC
* * * * *
5907318 TAACCCTAACCTAATTCAA-TTAAAACCCTAAACC-ATTAA--CATAA---
1 AAACCCTAACCTAATTTAATTTAAAACCCT-AACCTAATAATTAAAAACTC
* * * *
5907362 AAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACCAAATTTAATTAA---
1 AAACCCTAACCTAATTTAATTTAAAACCCTAACCTAA--TAA-TTAA-AAACTC
* * *
5907413 AAACCCTAACCTAATTTAATTAAAAATCCTAAACCCT--TAATTAAAAACCC
1 AAACCCTAACCTAATTTAATTTAAAACCCT-AA-CCTAATAATTAAAAACTC
* *
5907463 TAACCCTAACCTAATTCAA-TTAAAACCCTAA
1 AAACCCTAACCTAATTTAATTTAAAACCCTAA
5907494 ACCATTACCA
Statistics
Matches: 219, Mismatches: 29, Indels: 53
0.73 0.10 0.18
Matches are distributed among these distances:
44 20 0.09
45 10 0.05
46 29 0.13
47 10 0.05
48 15 0.07
49 29 0.13
50 37 0.17
51 35 0.16
52 2 0.01
53 32 0.15
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (50 bp):
AAACCCTAACCTAATTTAATTTAAAACCCTAACCTAATAATTAAAAACTC
Found at i:5907339 original size:50 final size:47
Alignment explanation
Indices: 5907208--5907707 Score: 307
Period size: 44 Copynumber: 10.8 Consensus size: 47
5907198 TAACCTAAAA
* * *
5907208 TAATTAAAAACTCAAAACCATAACCTAATTTAATTTAAAACCCT-AGCC-
1 TAATTAAAAACT---AACCCTAACCTAATTTAATTAAAAACCCTAAACCT
5907256 TAATTTAATTAAA--AACCCTAACCTAATTTAATTAAAAACCCTAAATCCT
1 TAA-TTAA--AAACTAACCCTAACCTAATTTAATTAAAAACCCTAAA-CCT
*
5907305 TAATTAAAAACTCTAACCCTAACCTAATTCAATT-AAAACCCTAAACCAT
1 TAATTAAAAA--CTAACCCTAACCTAATTTAATTAAAAACCCTAAACC-T
* *
5907354 TAA-CATAAA--AACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACC-
1 TAATTAAAAACTAACCCTAACCTAATTTAATTAAAAACCCTA----AACCT
* *
5907401 AAATTTAATTAAA--AACCCTAACCTAATTTAATTAAAAATCCTAAACCCT
1 TAA-TTAA--AAACTAACCCTAACCTAATTTAATTAAAAACCCTAAA-CCT
*
5907450 TAATTAAAAACCCTAACCCTAACCTAATTCAATT-AAAACCCTAAACCAT
1 TAATTAAAAA--CTAACCCTAACCTAATTTAATTAAAAACCCTAAACC-T
5907499 TACCA-T-AAAA-T--CCCTAACCTAATTTAATTAAAAACCCTAAACTCT
1 TA--ATTAAAAACTAACCCTAACCTAATTTAATTAAAAACCCTAAAC-CT
* * *
5907544 TAATT--AAA--AACCCTAGCCTAATTTAATT-AAAACCAT-GACC-
1 TAATTAAAAACTAACCCTAACCTAATTTAATTAAAAACCCTAAACCT
* * *
5907584 TAATTTAATTAAA--AACCCTAAACT--CTTAATTAAAAACCCT-AGCC-
1 TAA-TTAA--AAACTAACCCTAACCTAATTTAATTAAAAACCCTAAACCT
* * *
5907628 TAATTTAATTAA--AACCATGACCTAATTTAATTAAAAACCCTAAACTCT
1 TAA-TTAA-AAACTAACCCTAACCTAATTTAATTAAAAACCCTAAAC-CT
*
5907676 TAATT--AAA--AACCCTAGCCTAATTTAATTAAAA
1 TAATTAAAAACTAACCCTAACCTAATTTAATTAAAA
5907708 CCATGACCTA
Statistics
Matches: 373, Mismatches: 34, Indels: 94
0.74 0.07 0.19
Matches are distributed among these distances:
40 3 0.01
41 3 0.01
42 2 0.01
43 28 0.08
44 94 0.25
45 51 0.14
46 37 0.10
47 8 0.02
48 26 0.07
49 46 0.12
50 39 0.10
51 36 0.10
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.29
Consensus pattern (47 bp):
TAATTAAAAACTAACCCTAACCTAATTTAATTAAAAACCCTAAACCT
Found at i:5907381 original size:73 final size:73
Alignment explanation
Indices: 5907304--5907538 Score: 302
Period size: 73 Copynumber: 3.2 Consensus size: 73
5907294 CCCTAAATCC
*
5907304 TTAATTAAAAACTCTAACCCTAACCTAATTCAATTAAAACCCTAAACCATTAACATAAAAACCCT
1 TTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCATTAACATAAAAACCCT
5907369 AACCTAAT
66 AACCTAAT
* * * *
5907377 TTAATTAAAAACCCT-AGCCTAACCAAATTTAATTAAAAACCCT-AACCTAATTTAA-TTAAAAA
1 TTAATTAAAAACCCTAACCCTAACCTAATTCAATT-AAAACCCTAAACC--A-TTAACATAAAAA
* *
5907439 TCCTAAACC---C
62 CCCT-AACCTAAT
* *
5907449 TTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCATTACCATAAAATCCCT
1 TTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCATTAACATAAAAACCCT
5907514 AACCTAAT
66 AACCTAAT
5907522 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
5907539 ACTCTTAATT
Statistics
Matches: 136, Mismatches: 15, Indels: 22
0.79 0.09 0.13
Matches are distributed among these distances:
70 7 0.05
71 9 0.07
72 43 0.32
73 59 0.43
74 10 0.07
75 8 0.06
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (73 bp):
TTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTAAACCATTAACATAAAAACCCT
AACCTAAT
Found at i:5907385 original size:94 final size:92
Alignment explanation
Indices: 5907166--5907686 Score: 369
Period size: 94 Copynumber: 5.5 Consensus size: 92
5907156 TTTGATGTAA
**** *
5907166 TAAAAACCCTAACCTAATTTAACCCTAAACCCTAACCTAAAATAATTAAAAACTCAAAACCATAA
1 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCT----TAATTAAAAACTC-AAACCCTAA
* *
5907231 CCTAATTTAATTTAAAACCCT-AGCCTAATTTAAT
61 CCTAATTTAATTAAAAACCCTAAACC--A-TTAAT
*
5907265 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAAATCCTTAATTAAAAACTCTAACCCTAACCT
1 TAAAAACCCTAACCTAATTTAATTAAAAACCCT-AA-CCTTAATTAAAAACTCAAACCCTAACCT
* *
5907330 AATTCAATT-AAAACCCTAAACCATTAACA
64 AATTTAATTAAAAACCCTAAACCATTAA-T
* ** * *
5907359 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCC-TAACCAAATTTAATTAAAAACCCTAAC
1 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTAAA---AACT-CAAACCCTAAC
* *
5907423 CTAATTTAATTAAAAATCCTAAACCCTTAAT
62 CTAATTTAATTAAAAACCCTAAACCATTAAT
** *
5907454 TAAAAACCCTAACCCTAACCTAATTCAATT-AAAACCCTAAACC---ATT-ACCA-TAAAATCCC
1 TAAAAACCCTAA-CCTAA--T--TT-AATTAAAAACCCT-AACCTTAATTAAAAACTCAAA-CCC
5907513 TAACCTAATTTAATTAAAAACCCTAAACTC-TTAAT
58 TAACCTAATTTAATTAAAAACCCTAAAC-CATTAAT
* * * * *
5907548 TAAAAACCCTAGCCTAATTTAATT-AAAACCATGACC-TAATTTAATTAA---AAACCCTAAACT
1 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAA-TTAA-AAACTCAAACCCTAACCT
* *
5907608 --CTTAATTAAAAACCCT-AGCCTAATTTAAT
64 AATTTAATTAAAAACCCTAAACC--A-TTAAT
* *
5907637 T-AAAACCATGACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAAC
1 TAAAAACCCTAACCTAATTTAATTAAAAACCCT-AAC-CTTAATTAAAAAC
5907687 CCTAGCCTAA
Statistics
Matches: 351, Mismatches: 39, Indels: 72
0.76 0.08 0.16
Matches are distributed among these distances:
85 1 0.00
86 2 0.01
87 18 0.05
88 30 0.09
89 24 0.07
90 9 0.03
91 13 0.04
92 6 0.02
93 14 0.04
94 84 0.24
95 41 0.12
96 42 0.12
97 13 0.04
98 2 0.01
99 30 0.09
100 12 0.03
101 10 0.03
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (92 bp):
TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAATTAAAAACTCAAACCCTAACCTAA
TTTAATTAAAAACCCTAAACCATTAAT
Found at i:5907444 original size:145 final size:143
Alignment explanation
Indices: 5907221--5907575 Score: 548
Period size: 145 Copynumber: 2.5 Consensus size: 143
5907211 TTAAAAACTC
* *
5907221 AAAACCATAACCTAATTTAATTTAAAACCCTAGCCT---AATTTAATTAAAAACCCTAACCTAAT
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACAATTTAATTAAAAACCCTAACCTAAT
* *
5907283 TTAATTAAAAACCCTAAATCCTTAATTAAAAACTCTAACCCTAACCTAATTCAATTAAAACCCTA
66 TTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTA
5907348 AACCATTAACATA
131 AACCATTAACATA
5907361 AAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACCAAATTTAATTAAAAACCCTAACCTA
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAA-C-AATTTAATTAAAAACCCTAACCTA
*
5907426 ATTTAATTAAAAATCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCC
64 ATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCC
*
5907491 TAAACCATTACCATA
129 TAAACCATTAACATA
* *
5907506 AAATCCCTAACCTAATTTAATTAAAAACCCTA----AAC--TCTTAATTAAAAACCCTAGCCTAA
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACAAT-TTAATTAAAAACCCTAACCTAA
5907565 TTTAATTAAAA
65 TTTAATTAAAA
5907576 CCATGACCTA
Statistics
Matches: 201, Mismatches: 8, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
137 1 0.00
138 32 0.16
140 35 0.17
141 2 0.01
145 131 0.65
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (143 bp):
AAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAACAATTTAATTAAAAACCCTAACCTAAT
TTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAACCCTA
AACCATTAACATA
Found at i:5907585 original size:66 final size:66
Alignment explanation
Indices: 5907515--5907773 Score: 518
Period size: 66 Copynumber: 3.9 Consensus size: 66
5907505 AAAATCCCTA
5907515 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
1 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
5907580 G
66 G
5907581 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
1 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
5907646 G
66 G
5907647 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
1 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
5907712 G
66 G
5907713 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAA
1 ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAA
5907774 ACCTTAAACC
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 193 1.00
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (66 bp):
ACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAGCCTAATTTAATTAAAACCAT
G
Found at i:5907762 original size:44 final size:45
Alignment explanation
Indices: 5907237--5907802 Score: 257
Period size: 44 Copynumber: 12.4 Consensus size: 45
5907227 ATAACCTAAT
* * *
5907237 TTAATTTAAAACCCTAGCCTAATTTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTAAACT-AC
* *
5907283 TTAATTAAAAACCCTA----AATCCTTAATTAAAAACTCTAACCCTAAC
1 TTAATTAAAAACCCTAGCCTAAT--TTAATTAAAAACCCTAA-ACT-AC
* * * * *
5907328 CTAATTCAATTAAAACCCTAAACC--A-TTAACATAAAAACCCTAACCTAAT
1 TTAATT--A--AAAACCCT-AGCCTAATTTAA-TTAAAAACCCTAAACT-AC
* *
5907377 TTAATTAAAAACCCTAGCCTAACCAAATTTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAGCCT-----AATTTAATTAAAAACCCTAAACT-AC
* * * *
5907428 TTAATTAAAAATCCTAAACC---CTTAATTAAAAACCCTAACCCTAAC
1 TTAATTAAAAACCCT-AGCCTAATTTAATTAAAAACCCTAA-ACT-AC
* * * * *
5907473 CTAATTCAATTAAAACCCTAAACC--A-TTACCA-TAAAATCCCTAACCTAAT
1 TTAATT--A--AAAACCCT-AGCCTAATTTA--ATTAAAAACCCTAAACT-AC
** * ** *
5907522 TTAATTAAAAACCCTAAACT--CTTAATTAAAAACCCTAGCCTAAT
1 TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTAAACT-AC
*
5907566 TTAATT-AAAACCAT-GACCTAATTTAATTAAAAACCCTAAACT-C
1 TTAATTAAAAACCCTAG-CCTAATTTAATTAAAAACCCTAAACTAC
* * * *
5907609 TTAATTAAAAACCCTAGCCTAATTTAATT-AAAACCATGACCTAAT
1 TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTAAACT-AC
** * ** *
5907654 TTAATTAAAAACCCTAAACT--CTTAATTAAAAACCCTAGCCTAAT
1 TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTAAACT-AC
*
5907698 TTAATT-AAAACCAT-GACCTAATTTAATTAAAAACCCTAAACT-C
1 TTAATTAAAAACCCTAG-CCTAATTTAATTAAAAACCCTAAACTAC
* *
5907741 TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCTTAAAC-CC
1 TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTAAACTAC
5907785 TTAACTTTAAAAACCCTA
1 TTAA--TTAAAAACCCTA
5907803 ACCTTAACGT
Statistics
Matches: 423, Mismatches: 49, Indels: 96
0.74 0.09 0.17
Matches are distributed among these distances:
42 3 0.01
43 47 0.11
44 135 0.32
45 95 0.22
46 27 0.06
47 4 0.01
49 47 0.11
50 23 0.05
51 34 0.08
52 8 0.02
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (45 bp):
TTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTAAACTAC
Found at i:5907807 original size:21 final size:22
Alignment explanation
Indices: 5907724--5907810 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 22
5907714 CCTAATTTAA
5907724 TTAAAAACCCTAAACTCTTAA--
1 TTAAAAACCCTAAAC-CTTAACT
* *
5907745 TTAAAAACCCT-AGCC-TAATTT
1 TTAAAAACCCTAAACCTTAA-CT
*
5907766 AATTAAAAACCTTAAACCCTTAACT
1 --TTAAAAACCCTAAA-CCTTAACT
5907791 TTAAAAACCCT-AACCTTAAC
1 TTAAAAACCCTAAACCTTAAC
5907811 GTAATGTTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
18 3 0.06
19 1 0.02
20 2 0.04
21 18 0.34
22 2 0.04
23 20 0.38
24 1 0.02
25 3 0.06
26 3 0.06
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.29
Consensus pattern (22 bp):
TTAAAAACCCTAAACCTTAACT
Found at i:5911165 original size:126 final size:125
Alignment explanation
Indices: 5910854--5911231 Score: 528
Period size: 126 Copynumber: 3.0 Consensus size: 125
5910844 CCCAAACATG
*
5910854 CTACTGTAGCAAAAGTGCGCTGACGAGGCCGCAATTTTACAAATTTTTCTCAAATAGCATCATGC
1 CTACTGTAGCAAAAGTGCGCTGACGAGGCCGCAATTTTACAAATTTTTCTCAAATAGCATCCTGC
* *
5910919 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTCACAGGAC
5910978 CTACTGTAGCAAAAGTGCGCTGACGAGGCCGCAATTTTACAAATTTTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGTGCGCTGACGAGGCCGCAATTTTACAAATTTTTCTCAAATAGCATCCTGC
* * *
5911043 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTCCCGGGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTCACAGGAC
* * * * * * * *
5911104 CTACTGTAGAAAAAGCGCG-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATACCATCCTG
1 CTACTGTAGCAAAAGTGCGCT-GACGAGGCCGCAATTTTACAAATTTTTCTCAAATAGCATCCTG
** ****
5911168 CTAGAAGCGATTTTATATTATTTTATCAGAAACGTCAACTCGAAATTATTTCTTC-CAGGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTC-TCACAGGAC
5911229 CTA
1 CTA
5911232 AAAACCCTTA
Statistics
Matches: 228, Mismatches: 22, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
124 98 0.43
125 24 0.11
126 106 0.46
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGTGCGCTGACGAGGCCGCAATTTTACAAATTTTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTCACAGGAC
Found at i:5917702 original size:13 final size:13
Alignment explanation
Indices: 5917684--5917710 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5917674 CACAAAAAAG
5917684 TGAATTTTTTAAT
1 TGAATTTTTTAAT
5917697 TGAATTTTTTAAT
1 TGAATTTTTTAAT
5917710 T
1 T
5917711 ATAACAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TGAATTTTTTAAT
Found at i:5927222 original size:9 final size:9
Alignment explanation
Indices: 5927208--5927233 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5927198 GAACGCTTTA
5927208 GAAACATTT
1 GAAACATTT
5927217 GAAACATTT
1 GAAACATTT
5927226 GAAACATT
1 GAAACATT
5927234 GAGGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (9 bp):
GAAACATTT
Found at i:5928648 original size:41 final size:41
Alignment explanation
Indices: 5928603--5928698 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
5928593 GAAATGGGCA
5928603 TGCTCACACAAGCTGTGGGTCAGAATGTAAGCTACACATGT
1 TGCTCACACAAGCTGTGGGTCAGAATGTAAGCTACACATGT
5928644 TGCTCACACAAGCTGTGGGTCAGAATGTAAGCTACACATGT
1 TGCTCACACAAGCTGTGGGTCAGAATGTAAGCTACACATGT
*
5928685 TGCTCACACGAGCT
1 TGCTCACACAAGCT
5928699 ATGGAGTATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (41 bp):
TGCTCACACAAGCTGTGGGTCAGAATGTAAGCTACACATGT
Found at i:5933673 original size:17 final size:17
Alignment explanation
Indices: 5933651--5933683 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5933641 GGATCAAATT
5933651 CAAGTTCTTTTTCTTGC
1 CAAGTTCTTTTTCTTGC
*
5933668 CAAGTTTTTTTTCTTG
1 CAAGTTCTTTTTCTTG
5933684 GAGGGGAAAT
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:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (17 bp):
CAAGTTCTTTTTCTTGC
Found at i:5935807 original size:29 final size:29
Alignment explanation
Indices: 5935775--5935848 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
5935765 GATGACCATA
* *
5935775 TTATCAGGTACTTTGTGTCAGTGTTATAT
1 TTATCAGGTACTATGTCTCAGTGTTATAT
* *
5935804 TTATCAGGCACTATGTCTCGGTGTTATAT
1 TTATCAGGTACTATGTCTCAGTGTTATAT
*
5935833 TTATTAGGTACTATGT
1 TTATCAGGTACTATGT
5935849 ACTGATGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (29 bp):
TTATCAGGTACTATGTCTCAGTGTTATAT
Found at i:5939381 original size:16 final size:16
Alignment explanation
Indices: 5939348--5939387 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5939338 GCATCTATGT
5939348 TTGTATATATAGTCGA
1 TTGTATATATAGTCGA
* * *
5939364 TTGTGTATATATTTGA
1 TTGTATATATAGTCGA
5939380 TTGTATAT
1 TTGTATAT
5939388 GAAGATTCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (16 bp):
TTGTATATATAGTCGA
Found at i:5952456 original size:27 final size:28
Alignment explanation
Indices: 5952402--5952475 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
5952392 GTTTTGTTTG
*
5952402 ATTTTTCGTATTTCATAATTTAATTATA-A
1 ATTTTTC-TATTT-ATATTTTAATTATATA
*
5952431 ATTTTTCTATTTATATTTTATTTATATA
1 ATTTTTCTATTTATATTTTAATTATATA
* *
5952459 AATATT-TATTTATATTT
1 ATTTTTCTATTTATATTT
5952476 ATCTATTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 23 0.57
28 10 0.25
29 7 0.17
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (28 bp):
ATTTTTCTATTTATATTTTAATTATATA
Found at i:5952840 original size:88 final size:86
Alignment explanation
Indices: 5952672--5953139 Score: 374
Period size: 79 Copynumber: 5.5 Consensus size: 86
5952662 TTTTGTTTCC
* * * * *
5952672 AAATTAAAAGTAAATAAAATCTGTTTCAGGATTTATTTCCACCGTTCAATGGATTTTATTCCAAA
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCCGCCGTTCAA-GGATTTTATTCCAAA
* *
5952737 TTTTGGTTTTATTTCCGAACGGG
65 TTTT-GTTTTATTTCCAAACAGG
* *
5952760 AAATTAAAGGTAAAT-AAATCTGTTTCGGGATTAATTCCCGCCGTTCGACGGATTTTATTCCATT
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCCGCCGTTC-AAGGATTTTATTCCA-A
5952824 ATTTTGATTTTATTTCCAAACAGG
64 ATTTTG-TTTTATTTCCAAACAGG
* * * *
5952848 ATATTAAAGGTAAAATAAAATTTGTTTCGGGATTGATTCCCGCCGTTCAAAGATTTTATTCCAAA
1 AAATTAAAGGT-AAATAAAATCTGTTTCGGGATTAATTCCCGCCGTTCAAGGATTTTATTCCAAA
* *
5952913 TTTTGTTTTATTTCCAAAAACG
65 TTTTGTTTTATTTCCAAACAGG
* * * * * * *
5952935 --AGT--A---AAATAAAATCCGTTTTGGGATTGATTCCCGTCGTGCAACGATTTTATTCCAAAT
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCCGCCGTTCAAGGATTTTATTCCAAAT
* * *
5952993 TTTGTTTTATTTCTAAAAACG
66 TTTGTTTTATTTCCAAACAGG
* * * * * * * * *
5953014 --AGT--A---AAATAAAATCTGTTTCGGGATTTATTCTCGTCATTCAACGAATTTATTAC-ATT
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCCGCCGTTCAAGGATTTTATTCCAAAT
* * * *
5953071 TTTATTTTGTTGCCAAAAACAAG
66 TTTGTTTTATTTCC--AAACAGG
** * *
5953094 AAATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTT
1 AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCCGCCGTT
5953140 TAACAAGATT
Statistics
Matches: 321, Mismatches: 45, Indels: 29
0.81 0.11 0.07
Matches are distributed among these distances:
78 12 0.04
79 114 0.36
80 5 0.02
82 2 0.01
83 1 0.00
84 1 0.00
85 2 0.01
87 87 0.27
88 51 0.16
89 17 0.05
90 29 0.09
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (86 bp):
AAATTAAAGGTAAATAAAATCTGTTTCGGGATTAATTCCCGCCGTTCAAGGATTTTATTCCAAAT
TTTGTTTTATTTCCAAACAGG
Found at i:5953349 original size:83 final size:83
Alignment explanation
Indices: 5953095--5953321 Score: 269
Period size: 83 Copynumber: 2.7 Consensus size: 83
5953085 AAAAACAAGA
* *
5953095 AATTAAAATTAAATAAAATCTGTTTTGGGATTTATTCCCGCCGTTTAACAAGATTTTATTTTATT
1 AATTAAAATTAAATAAAATATGTTTT-GGATTTATTCCCGCCGTTTAACAAGATTTTATTTAATT
5953160 TGATTTTATTTCCAAATCAG
65 T-ATTTTATTTCCAAATCAG
* ** * * * *
5953180 AATT-AAATTAAATAAAAAAAATTTAGGATTTATTCCCGCCATTTAA-AAAATTTTATTTGATTT
1 AATTAAAATTAAATAAAATATGTTTTGGATTTATTCCCGCCGTTTAACAAGATTTTATTT-AATT
* *
5953243 TATTTTGTTTCCAAATTAG
65 TATTTTATTTCCAAATCAG
* * * *
5953262 AATTAAAATTAAATAAAATTTGTTTCTGGATTTATTCCCACTGTCTAACAAGATTTTATT
1 AATTAAAATTAAATAAAATATGTTT-TGGATTTATTCCCGCCGTTTAACAAGATTTTATT
5953322 CAATATTCTT
Statistics
Matches: 117, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
82 31 0.26
83 39 0.33
84 33 0.28
85 14 0.12
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (83 bp):
AATTAAAATTAAATAAAATATGTTTTGGATTTATTCCCGCCGTTTAACAAGATTTTATTTAATTT
ATTTTATTTCCAAATCAG
Found at i:5953423 original size:51 final size:51
Alignment explanation
Indices: 5953359--5953497 Score: 233
Period size: 51 Copynumber: 2.7 Consensus size: 51
5953349 ATGTAATCAA
* *
5953359 ATAATTTTTTTTCGAGATTTATTCCCACCGTTTAACATATTTTATTTTAAT
1 ATAATTTTGTTTCGGGATTTATTCCCACCGTTTAACATATTTTATTTTAAT
5953410 ATAATTTTGTTTCGGGATTTATTCCCACCGTTTAACATATTTTATTTTAAT
1 ATAATTTTGTTTCGGGATTTATTCCCACCGTTTAACATATTTTATTTTAAT
* **
5953461 ATAATTTTGTTTCGGGATTTAATCCTGCCGTTTAACA
1 ATAATTTTGTTTCGGGATTTATTCCCACCGTTTAACA
5953498 AAATTATTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 83 1.00
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (51 bp):
ATAATTTTGTTTCGGGATTTATTCCCACCGTTTAACATATTTTATTTTAAT
Found at i:5957252 original size:27 final size:27
Alignment explanation
Indices: 5957217--5957283 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
5957207 TATTTCACAA
*
5957217 TTTAATTATA-AATTATTCTATTTATAT
1 TTTAATTATATAAATATT-TATTTATAT
*
5957244 TTTAGTTATATAAATATTTATTTATAT
1 TTTAATTATATAAATATTTATTTATAT
*
5957271 TTATATTTATATA
1 TT-TAATTATATA
5957284 TTTTATTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTAATTATATAAATATTTATTTATAT
Found at i:5957283 original size:14 final size:13
Alignment explanation
Indices: 5957239--5957291 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 13
5957229 TTATTCTATT
5957239 TATATTTTAGTTATA
1 TATATTTTA-TT-TA
*
5957254 TAAATATTTATTTA
1 TATAT-TTTATTTA
*
5957268 TAT-TTATATTTA
1 TATATTTTATTTA
5957280 TATATTTTATTT
1 TATATTTTATTT
5957292 CACTAACGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 10 0.31
13 8 0.25
14 4 0.12
15 6 0.19
16 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
TATATTTTATTTA
Found at i:5969525 original size:299 final size:302
Alignment explanation
Indices: 5968412--5969594 Score: 2176
Period size: 302 Copynumber: 3.9 Consensus size: 302
5968402 ATTGATACTC
*
5968412 GGAGAAGAGCCCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
*
5968477 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATAGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
* *
5968542 GCAATAGAAGTAAAAAGAGAAAGAAAATTGCTTGATTGGTCACCCTAAGTTTTCAATTAATTTCA
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATAGGTCACCCTAAGTTTTCAATTAATTTCA
* *
5968607 AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACAGGTATCGTTAACAGAGACCACATC
196 AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
*
5968672 AGGATAATTAGTTTCAGCATATAGACTGCACTACATAAACAT
261 AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
5968714 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
5968779 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
5968844 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATAGGTCACCCTAAGTTTTCAATTAATTTCA
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATAGGTCACCCTAAGTTTTCAATTAATTTCA
* * *
5968909 AGAGACCAACAGAACTTTAGATGAATCATATTGGTGTCACGGATATTGCTAACAGAGACCACATC
196 AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
*
5968974 GGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
261 AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
5969016 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
5969081 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
5969146 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATAGGTCACCCTAAGTTTTCAATTAATTTCA
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATAGGTCACCCTAAGTTTTCAATTAATTTCA
5969211 AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
196 AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
*
5969276 GGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
261 AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
5969318 -G-G-AGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
1 GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
* *
5969380 GGGAACTTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
66 GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
*
5969445 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTCACT-GGTCACCCTAAGTTTTCAATTAATTTC
131 GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGA-TAGGTCACCCTAAGTTTTCAATTAATTTC
* *
5969509 AAGAGATCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACGACAT
195 AAGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACAT
5969574 CAGGATAATTAGTTTCAGCAT
260 CAGGATAATTAGTTTCAGCAT
5969595 GGTGGAGAAT
Statistics
Matches: 860, Mismatches: 20, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
299 267 0.31
300 2 0.00
301 1 0.00
302 590 0.69
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (302 bp):
GGAGAAGAGCTCTACCATGTCGCATTGCCTTCAAGCAGAACATTTGATTAAATGATATAGCTTGA
GGTAAATTTGTTGTGCGCTTGAATGAGATCTTTTATGCAGTGCAGTCTATATGATAAATCGTAAA
GCAATAGAAGTAAAAAGAGAAAGAAAACTGCTTGATAGGTCACCCTAAGTTTTCAATTAATTTCA
AGAGACCAACAGACCTTTAGATGAATCATATTGGTGTCACGGGTATTGTTAACAGAGACCACATC
AGGATAATTAGTTTCAGCATATAGACTGCACTGCATAAACAT
Found at i:5972243 original size:20 final size:20
Alignment explanation
Indices: 5972220--5972277 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 20
5972210 CACAAGAAAA
5972220 TGTCTCCATTCACCACAAAC
1 TGTCTCCATTCACCACAAAC
** * * *
5972240 TG--TCCACCCACAAGAAAA
1 TGTCTCCATTCACCACAAAC
5972258 TGTCTCCATTCACCACAAAC
1 TGTCTCCATTCACCACAAAC
5972278 CAAATCTGTT
Statistics
Matches: 26, Mismatches: 10, Indels: 4
0.65 0.25 0.10
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.34, C:0.38, G:0.07, T:0.21
Consensus pattern (20 bp):
TGTCTCCATTCACCACAAAC
Found at i:5972253 original size:38 final size:38
Alignment explanation
Indices: 5972202--5972277 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5972192 CACTCAACAG
5972202 TGTCCACCCACAAGAAAATGTCTCCATTCACCACAAAC
1 TGTCCACCCACAAGAAAATGTCTCCATTCACCACAAAC
5972240 TGTCCACCCACAAGAAAATGTCTCCATTCACCACAAAC
1 TGTCCACCCACAAGAAAATGTCTCCATTCACCACAAAC
5972278 CAAATCTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.37, G:0.08, T:0.18
Consensus pattern (38 bp):
TGTCCACCCACAAGAAAATGTCTCCATTCACCACAAAC
Found at i:5972261 original size:18 final size:18
Alignment explanation
Indices: 5972202--5972261 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
5972192 CACTCAACAG
5972202 TGTCCACCCACAAGAAAA
1 TGTCCACCCACAAGAAAA
** * * *
5972220 TGTCTCCATTCACCACAAAC
1 TG--TCCACCCACAAGAAAA
5972240 TGTCCACCCACAAGAAAA
1 TGTCCACCCACAAGAAAA
5972258 TGTC
1 TGTC
5972262 TCCATTCACC
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.35, G:0.10, T:0.18
Consensus pattern (18 bp):
TGTCCACCCACAAGAAAA
Found at i:5982096 original size:16 final size:16
Alignment explanation
Indices: 5982071--5982101 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5982061 GTTCACTCCA
*
5982071 TTCCCGGTTTTCCGAG
1 TTCCCAGTTTTCCGAG
5982087 TTCCCAGTTTTCCGA
1 TTCCCAGTTTTCCGA
5982102 TAATCAAATA
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:0.10, C:0.32, G:0.19, T:0.39
Consensus pattern (16 bp):
TTCCCAGTTTTCCGAG
Found at i:5983828 original size:22 final size:22
Alignment explanation
Indices: 5983744--5983812 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
5983734 TGTATATGAT
* * *
5983744 TCTAATATGTTTTGCATTTGTA
1 TCTATTATGTTCTGCATCTGTA
*
5983766 TATGATT-TGTTCTGCATCTGTA
1 TCT-ATTATGTTCTGCATCTGTA
5983788 TCTATTATGTTCTGCATCTGTA
1 TCTATTATGTTCTGCATCTGTA
5983810 TCT
1 TCT
5983813 GGTCTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.08
22 35 0.88
23 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (22 bp):
TCTATTATGTTCTGCATCTGTA
Found at i:5986513 original size:45 final size:46
Alignment explanation
Indices: 5986464--5986561 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
5986454 AGATAGAAAC
*
5986464 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
5986509 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
5986555 GAAAATA
1 CAAAATA
5986562 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:5990859 original size:45 final size:46
Alignment explanation
Indices: 5990795--5990892 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
5990785 AGATAGAAAT
*
5990795 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
5990840 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
5990886 GAAAATA
1 CAAAATA
5990893 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:5994985 original size:3 final size:3
Alignment explanation
Indices: 5994977--5995011 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
5994967 ATTAATCTTG
*
5994977 TAT TAT TAT TGAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT T
5995012 TATTCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6004238 original size:24 final size:25
Alignment explanation
Indices: 6004176--6004238 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
6004166 TACGAATACT
*
6004176 CAGCTCGCATGAGCTTACCGTTATT
1 CAGCTCGCATGAGCTTACCGTTATA
* *
6004201 CAGCTCGGAGGAGCTTACCGTT-TA
1 CAGCTCGCATGAGCTTACCGTTATA
*
6004225 CAGCTCGTATGAGC
1 CAGCTCGCATGAGC
6004239 ATACATGTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (25 bp):
CAGCTCGCATGAGCTTACCGTTATA
Found at i:6007686 original size:19 final size:17
Alignment explanation
Indices: 6007630--6007684 Score: 85
Period size: 17 Copynumber: 3.3 Consensus size: 17
6007620 AATAAACGAC
* *
6007630 AGAGAAT-AAAGAACAA
1 AGAGAATGAGAGAGCAA
6007646 AGAGAATGAGAGAGCAA
1 AGAGAATGAGAGAGCAA
6007663 AGAGAATGAGAGAGCAA
1 AGAGAATGAGAGAGCAA
6007680 AGAGA
1 AGAGA
6007685 GAGAGTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 7 0.19
17 29 0.81
ACGTcount: A:0.58, C:0.05, G:0.31, T:0.05
Consensus pattern (17 bp):
AGAGAATGAGAGAGCAA
Done.