Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 60 of 208
Found at i:17191820 original size:24 final size:24
Alignment explanation
Indices: 17191788--17191921 Score: 142
Period size: 24 Copynumber: 5.6 Consensus size: 24
17191778 TCGTGTACGG
** *
17191788 AATCAGTCATACAAATCACATACA
1 AATCAGTCATTTAAATCACAGACA
*
17191812 AATCAGTCATTTAAGTCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
17191836 AATCAATCATTTAAATCAAAGACA
1 AATCAGTCATTTAAATCACAGACA
* * * *
17191860 AATCAGTCATTTACATCTCGGATA
1 AATCAGTCATTTAAATCACAGACA
* * *
17191884 AATCATTCATTTACATCACAGAAA
1 AATCAGTCATTTAAATCACAGACA
*
17191908 AATCAATCATTTAA
1 AATCAGTCATTTAA
17191922 CCTCGAGGGC
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:17191969 original size:27 final size:27
Alignment explanation
Indices: 17191939--17192103 Score: 213
Period size: 27 Copynumber: 6.1 Consensus size: 27
17191929 GGCAAAAATA
17191939 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
17191966 GTCATTTTGCCGTACAGAGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
17191993 GTTATTTTACCCCATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
17192020 GTCATTTTACCCTACAGGAGTATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
*
17192047 GTCATTTTACCCTACATGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
17192074 GTCATTTTACCTTACAGGGGTACTACG
1 GTCATTTTACCCTACAGGGGCATTACG
17192101 GTC
1 GTC
17192104 TACAGTCGCC
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:17201520 original size:29 final size:30
Alignment explanation
Indices: 17201487--17201548 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
17201477 CCTTTCCTTT
* *
17201487 ATTCGATAGCCGAGGCTA-CCGTTTTCATA
1 ATTCGATAGCCAAAGCTATCCGTTTTCATA
* *
17201516 ATTCGATGGCCAAAGCTATCCTTTTTCATA
1 ATTCGATAGCCAAAGCTATCCGTTTTCATA
17201546 ATT
1 ATT
17201549 TGATGATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (30 bp):
ATTCGATAGCCAAAGCTATCCGTTTTCATA
Found at i:17201572 original size:30 final size:30
Alignment explanation
Indices: 17201533--17201729 Score: 122
Period size: 30 Copynumber: 6.7 Consensus size: 30
17201523 GGCCAAAGCT
* *
17201533 ATCCTTTTTCATAATTTGATGATCTTCACC
1 ATCCCTTTTCATAATTCGATGATCTTCACC
** * *
17201563 ATCCCTTTTCATTGTTCGAGGGT-TGTCACC
1 ATCCCTTTTCATAATTCGATGATCT-TCACC
* * * ***
17201593 ATCTCTTTTCATAATTTGAT-AGCGAAAGCC
1 ATCCCTTTTCATAATTCGATGATCTTCA-CC
* **
17201623 ATCCCTTTTCATGA-TCGAT-AGTC-GAAGCC
1 ATCCCTTTTCATAATTCGATGA-TCTTCA-CC
* * *
17201652 ATCCCTTTTCATAGTTCGATGGTCATCACC
1 ATCCCTTTTCATAATTCGATGATCTTCACC
*
17201682 ATCCCTTTTCATAATT-GATGGT-TGTCACC
1 ATCCCTTTTCATAATTCGATGATCT-TCACC
17201711 ATCCCTTTTCATAA-TCGAT
1 ATCCCTTTTCATAATTCGAT
17201730 AGCCGAAGTT
Statistics
Matches: 130, Mismatches: 28, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.01
29 52 0.40
30 76 0.58
31 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATGATCTTCACC
Found at i:17201652 original size:29 final size:29
Alignment explanation
Indices: 17201591--17201766 Score: 135
Period size: 29 Copynumber: 6.0 Consensus size: 29
17201581 AGGGTTGTCA
* *
17201591 CCATCTCTTTTCATAATTTGATAG-CGAAAG
1 CCATCCCTTTTCATAA-TCGATAGTCG-AAG
*
17201621 CCATCCCTTTTCATGATCGATAGTCGAAG
1 CCATCCCTTTTCATAATCGATAGTCGAAG
* *
17201650 CCATCCCTTTTCATAGTTCGATGGTC-ATCA-
1 CCATCCCTTTTCATA-ATCGATAGTCGA--AG
* * * *
17201680 CCATCCCTTTTCATAATTGATGGTTGTCA-
1 CCATCCCTTTTCATAATCGATAGTCG-AAG
*
17201709 CCATCCCTTTTCATAATCGATAGCCGAAG
1 CCATCCCTTTTCATAATCGATAGTCGAAG
** * * *
17201738 TTATCCCTTTTCATAGTCTATAGCCGAAG
1 CCATCCCTTTTCATAATCGATAGTCGAAG
17201767 TTATCCCATT
Statistics
Matches: 120, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.01
29 79 0.66
30 39 0.32
31 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.35
Consensus pattern (29 bp):
CCATCCCTTTTCATAATCGATAGTCGAAG
Found at i:17201713 original size:59 final size:59
Alignment explanation
Indices: 17201533--17201725 Score: 185
Period size: 59 Copynumber: 3.3 Consensus size: 59
17201523 GGCCAAAGCT
* * * ** *
17201533 ATCCTTTTTCATAATTTGATGATCTTCACCATCCCTTTTCATTGTTCGAGGGTTGTCACC
1 ATCCCTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAATT-GATGGTTGTCACC
* * * * * * * *
17201593 ATCTCTTTTCATAATTTGATAG-CGA-AAGCCATCCCTTTTCATGATCGATAGTCG-AAGCC
1 ATCCCTTTTCATAATTTGATGGTC-ATCA-CCATCCCTTTTCATAATTGATGGTTGTCA-CC
* *
17201652 ATCCCTTTTCATAGTTCGATGGTCATCACCATCCCTTTTCATAATTGATGGTTGTCACC
1 ATCCCTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAATTGATGGTTGTCACC
17201711 ATCCCTTTTCATAAT
1 ATCCCTTTTCATAAT
17201726 CGATAGCCGA
Statistics
Matches: 103, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
58 1 0.01
59 66 0.64
60 36 0.35
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (59 bp):
ATCCCTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAATTGATGGTTGTCACC
Found at i:17201767 original size:29 final size:29
Alignment explanation
Indices: 17201711--17201779 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
17201701 GGTTGTCACC
17201711 ATCCCTTTTCATAATCGATAGCCGAAGTT
1 ATCCCTTTTCATAATCGATAGCCGAAGTT
* *
17201740 ATCCCTTTTCATAGTCTATAGCCGAAGTT
1 ATCCCTTTTCATAATCGATAGCCGAAGTT
*
17201769 ATCCCATTTCA
1 ATCCCTTTTCA
17201780 CCCGTCAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAGTT
Found at i:17221931 original size:100 final size:100
Alignment explanation
Indices: 17221758--17221959 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 100
17221748 TTAGGATAAT
*
17221758 TTGCATTAGGGATCATTGCATTTAGTTTAATATATTTTAATCACAACTTCTCAACTATATTGTGT
1 TTGCATTAGGGATCATTGCATTCAGTTTAATATATTTTAATCACAACTTCTCAACTATATTGTGT
17221823 TTTTATTTACCAAATTGTTAATATAATTTTAAAAA
66 TTTTATTTACCAAATTGTTAATATAATTTTAAAAA
17221858 TTGCATTAGGGATCATTGCATTCAGTTTAATATATTTTAATCACAACTTCTCAACTATATTGTGT
1 TTGCATTAGGGATCATTGCATTCAGTTTAATATATTTTAATCACAACTTCTCAACTATATTGTGT
17221923 TTTTATTTACCAAATTGTTAATATAATTTTAAAAA
66 TTTTATTTACCAAATTGTTAATATAATTTTAAAAA
17221958 TT
1 TT
17221960 AAGTGACTTA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (100 bp):
TTGCATTAGGGATCATTGCATTCAGTTTAATATATTTTAATCACAACTTCTCAACTATATTGTGT
TTTTATTTACCAAATTGTTAATATAATTTTAAAAA
Found at i:17225015 original size:50 final size:50
Alignment explanation
Indices: 17224956--17225100 Score: 146
Period size: 50 Copynumber: 2.9 Consensus size: 50
17224946 CATTGAGATT
* * *
17224956 ATGAGAGGTCTCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCACCGAG
*** * * * *
17225006 ATGAGAGGTCCCCCAAAAGACCATGTCTGGGACATGACATGGGCACCGAT
1 ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCACCGAG
** * * * *
17225056 ATGAGAACTCCCATGAAAGACCATATCTAGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCA
17225101 GTATAGAAAA
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGAAAGACCATGTTTGGGACATGGCATTGGCACCGAG
Found at i:17232563 original size:50 final size:50
Alignment explanation
Indices: 17232460--17232652 Score: 165
Period size: 50 Copynumber: 3.7 Consensus size: 50
17232450 GAGAATGAGA
* * *
17232460 TCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGAATATGAGAGG
1 TCCCATGTAAGACCATTTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* * *
17232516 TCCCATGTAACACTATTTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATTTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
17232566 TCTCC-CGTAAGACCATGTCTGGGACATGACATGGGCACCGATACGAGAAC
1 TC-CCATGTAAGACCATTTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
17232616 TCCCATGTAAGACCATATT-TGGGATATGGCATTGGCA
1 TCCCATGTAAGACCAT-TTCTGGGACATGGCATTGGCA
17232653 GTATAGAAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 2 0.02
50 71 0.63
51 3 0.03
53 3 0.03
55 1 0.01
56 32 0.29
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATTTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:17232652 original size:100 final size:103
Alignment explanation
Indices: 17232466--17232652 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 103
17232456 GAGATCCCAT
* * ** *
17232466 GTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGAATATGAGAGGTCCCATGTAACACTA
1 GTAAGACCATGTCTGGGACATGACATGGGCATC--T-AGAATACGAGAACTCCCATGTAACACCA
*
17232531 TTTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCCC
63 TTTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCTCCC
* *
17232572 GTAAGACCATGTCTGGGACATGACATGGGCA-C-CG-ATACGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGACATGGGCATCTAGAATACGAGAACTCCCATGTAACACCAT-T
*
17232634 T-TGGGATATGGCATTGGCA
65 TCTGGGACATGGCATTGGCA
17232653 GTATAGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
100 37 0.52
101 3 0.04
105 1 0.01
106 30 0.42
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGACATGGGCATCTAGAATACGAGAACTCCCATGTAACACCATTT
CTGGGACATGGCATTGGCACCGAGATGAGAGGTCTCCC
Found at i:17232688 original size:49 final size:50
Alignment explanation
Indices: 17232572--17232706 Score: 141
Period size: 49 Copynumber: 2.7 Consensus size: 50
17232562 GAGGTCTCCC
* * *
17232572 GTAAGACCATGTCTGGGACATGACATGGGCACCG-ATACGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGTATACGAAAACTCCCAT
* * *
17232622 GTAAGACCATATTTGGGATATGGCATTGGCA-GTATA-GAAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACGTATACGAAAAC-TCCCAT
* * * *
17232671 GTAAGACTATGTCTGGGACATAGCTTTGGCATGTAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACGTAT
17232707 TATCAGATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
48 6 0.09
49 34 0.49
50 30 0.43
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGTATACGAAAACTCCCAT
Found at i:17232949 original size:20 final size:20
Alignment explanation
Indices: 17232911--17232949 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17232901 TAAGTAAGTA
*
17232911 AGTAAGTAAACAAGTGAGTG
1 AGTAAGTAAACAAGCGAGTG
*
17232931 AGTAAGTAAAGAAGCGAGT
1 AGTAAGTAAACAAGCGAGT
17232950 AAAGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.31, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGCGAGTG
Found at i:17243810 original size:22 final size:22
Alignment explanation
Indices: 17243785--17243829 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
17243775 TGATAAACTT
17243785 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATTATTTA
* *
17243807 TAATTTATATATTAATTTTTTA
1 TAATATATATATTAATTATTTA
17243829 T
1 T
17243830 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATATATATATTAATTATTTA
Found at i:17249047 original size:17 final size:17
Alignment explanation
Indices: 17249027--17249060 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17249017 AGGAATTTAC
17249027 TTATGCTATG-CATGAAT
1 TTATG-TATGTCATGAAT
17249044 TTATGTATGTCATGAAT
1 TTATGTATGTCATGAAT
17249061 AAACACGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (17 bp):
TTATGTATGTCATGAAT
Found at i:17249130 original size:20 final size:20
Alignment explanation
Indices: 17249105--17249159 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
17249095 AATCTTATGT
17249105 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
* *
17249125 TAAGTATATGAAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
17249145 TAAGTAAATGGAATG
1 TAAGTAAATGGAATG
17249160 TTATGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:17256493 original size:25 final size:25
Alignment explanation
Indices: 17256443--17256506 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
17256433 CCGGTTTCAA
*
17256443 CTCGTATGAG-TTACCGATACTCAG
1 CTCGCATGAGCTTACCGATACTCAG
* * *
17256467 CTCGCATGAGCTTACCGTTATTTAG
1 CTCGCATGAGCTTACCGATACTCAG
* *
17256492 CTCGGAGGAGCTTAC
1 CTCGCATGAGCTTAC
17256507 TATTATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 9 0.27
25 24 0.73
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (25 bp):
CTCGCATGAGCTTACCGATACTCAG
Found at i:17256512 original size:25 final size:25
Alignment explanation
Indices: 17256463--17256529 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
17256453 TTACCGATAC
* * *
17256463 TCAGCTCGCATGAGCTTACCGTTAT
1 TCAGCTCGGAGGAGCTTACCATTAT
* *
17256488 TTAGCTCGGAGGAGCTTACTATTAT
1 TCAGCTCGGAGGAGCTTACCATTAT
* *
17256513 TCAACTCAGAGGAGCTT
1 TCAGCTCGGAGGAGCTT
17256530 GCTGTTTATA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (25 bp):
TCAGCTCGGAGGAGCTTACCATTAT
Found at i:17266982 original size:27 final size:27
Alignment explanation
Indices: 17266952--17267028 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
17266942 ATTTTAGGAC
17266952 AAGGTCTTGTGGTGAAACCATGGAGTT
1 AAGGTCTTGTGGTGAAACCATGGAGTT
** **
17266979 AA-G----GAAGTGAATACC-TTTAGTT
1 AAGGTCTTGTGGTGAA-ACCATGGAGTT
17267001 AAGGTCTTGTGGTGAAACCATGGAGTT
1 AAGGTCTTGTGGTGAAACCATGGAGTT
17267028 A
1 A
17267029 GGGAGGCCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
22 13 0.37
23 4 0.11
26 4 0.11
27 14 0.40
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (27 bp):
AAGGTCTTGTGGTGAAACCATGGAGTT
Found at i:17270457 original size:19 final size:18
Alignment explanation
Indices: 17270416--17270464 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
17270406 TAAAAATAAA
* *
17270416 ATAAAATAAATTTAAATT
1 ATAAAATAAATTAAAAAT
*
17270434 TTAAAATGAAATTAAAAAT
1 ATAAAAT-AAATTAAAAAT
17270453 ATAAATATAAAT
1 ATAAA-ATAAAT
17270465 AAGCCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATTAAAAAT
Found at i:17270946 original size:24 final size:24
Alignment explanation
Indices: 17270917--17270964 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17270907 TATCGATTTA
*
17270917 TTTTTATATTAGATAAATATAATT
1 TTTTTACATTAGATAAATATAATT
* *
17270941 TTTTTACATTGGATAGATATAATT
1 TTTTTACATTAGATAAATATAATT
17270965 ATTTCTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTTTACATTAGATAAATATAATT
Found at i:17271721 original size:15 final size:15
Alignment explanation
Indices: 17271701--17271731 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17271691 ATAATTTATT
17271701 ATATAAAATTTTTTG
1 ATATAAAATTTTTTG
17271716 ATATAAAATTTTTTG
1 ATATAAAATTTTTTG
17271731 A
1 A
17271732 AAGAGTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATATAAAATTTTTTG
Found at i:17272564 original size:10 final size:11
Alignment explanation
Indices: 17272520--17272566 Score: 53
Period size: 10 Copynumber: 4.3 Consensus size: 11
17272510 CATGCTTTTT
*
17272520 AAATAATTATAA
1 AAAT-ATTATTA
17272532 AAATATTA-TA
1 AAATATTATTA
17272542 AAATATTATTTA
1 AAATATTA-TTA
17272554 AAAT-TTATTA
1 AAATATTATTA
17272564 AAA
1 AAA
17272567 CTGACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATTATTA
Found at i:17278820 original size:71 final size:71
Alignment explanation
Indices: 17278704--17278846 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
17278694 TGCAATTACA
17278704 AACTCAATCAAACATCCATACTATCAAACTAGCAATTTGCCAACATGTCAATCTTTTAAGGCTTG
1 AACTCAATCAAACATCCATACTATCAAACTAGCAATTTGCCAACATGTCAATCTTTTAAGGCTTG
17278769 AAACAT
66 AAACAT
17278775 AACTCAATCAAACATCCATACTATCAAACTAGCAATTTGCCAACATGTCAATCTTTTAAGGCTTG
1 AACTCAATCAAACATCCATACTATCAAACTAGCAATTTGCCAACATGTCAATCTTTTAAGGCTTG
17278840 AAACAT
66 AAACAT
17278846 A
1 A
17278847 CCTGGTTCGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (71 bp):
AACTCAATCAAACATCCATACTATCAAACTAGCAATTTGCCAACATGTCAATCTTTTAAGGCTTG
AAACAT
Found at i:17290483 original size:2 final size:2
Alignment explanation
Indices: 17290478--17290504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17290468 TTATTGATAC
17290478 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 A
17290505 ATCATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17291352 original size:25 final size:25
Alignment explanation
Indices: 17291323--17291372 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
17291313 GAAGAAATGG
17291323 TTAAAAACTCAAGAAAGCAACACTT
1 TTAAAAACTCAAGAAAGCAACACTT
17291348 TTAAAAACTCAAGAAAGCAACACTT
1 TTAAAAACTCAAGAAAGCAACACTT
17291373 ACACTAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (25 bp):
TTAAAAACTCAAGAAAGCAACACTT
Found at i:17291966 original size:21 final size:21
Alignment explanation
Indices: 17291942--17291988 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
17291932 GCCTAGTAAA
17291942 AAGTCTTGAGAACTTAGGTTC
1 AAGTCTTGAGAACTTAGGTTC
17291963 AAGTCTTGAGAACTTAGGTTC
1 AAGTCTTGAGAACTTAGGTTC
17291984 AAGTC
1 AAGTC
17291989 ACATTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (21 bp):
AAGTCTTGAGAACTTAGGTTC
Found at i:17317814 original size:27 final size:27
Alignment explanation
Indices: 17317784--17317839 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
17317774 GTAACCAATA
* *
17317784 TATTCCACTAGGACAGTAAACACAGGG
1 TATTCCACCAGGACAGTAAACACAAGG
* *
17317811 TATTCCTCCAGGATAGTAAACACAAGG
1 TATTCCACCAGGACAGTAAACACAAGG
17317838 TA
1 TA
17317840 GACCTTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (27 bp):
TATTCCACCAGGACAGTAAACACAAGG
Found at i:17317879 original size:27 final size:27
Alignment explanation
Indices: 17317821--17317889 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
17317811 TATTCCTCCA
*
17317821 GGATAGTAAACACAAGGTAGACCTTTG
1 GGATAGTAAACACAAGGTAGACCGTTG
* * * **
17317848 AGATAATAAACACAGGGTAGTTCGTTG
1 GGATAGTAAACACAAGGTAGACCGTTG
*
17317875 GGATAGTAAGCACAA
1 GGATAGTAAACACAA
17317890 AGAACTCTGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (27 bp):
GGATAGTAAACACAAGGTAGACCGTTG
Found at i:17322538 original size:21 final size:22
Alignment explanation
Indices: 17322512--17322567 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
17322502 GAGCACTCAA
*
17322512 ATGCATCCACAACAAG-GCTAG
1 ATGCATCCACAACAAGACCTAG
* *
17322533 ATGCATGCAC-ACCAGACCTAG
1 ATGCATCCACAACAAGACCTAG
*
17322554 ACGCATCCACAACA
1 ATGCATCCACAACA
17322568 TTCTTCAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 4 0.15
21 21 0.78
22 2 0.07
ACGTcount: A:0.38, C:0.34, G:0.16, T:0.12
Consensus pattern (22 bp):
ATGCATCCACAACAAGACCTAG
Found at i:17326876 original size:6 final size:6
Alignment explanation
Indices: 17326865--17326890 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17326855 GATTGTTTTA
17326865 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
17326891 GCAGAATAAT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:17332632 original size:21 final size:21
Alignment explanation
Indices: 17332608--17332649 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17332598 AAATGTGGGA
* *
17332608 ATGTTCGCCAGAGTTAAACGT
1 ATGTTCACCAGAGCTAAACGT
17332629 ATGTTCACCAGAGCTAAACGT
1 ATGTTCACCAGAGCTAAACGT
17332650 TTATTGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (21 bp):
ATGTTCACCAGAGCTAAACGT
Found at i:17333833 original size:17 final size:17
Alignment explanation
Indices: 17333811--17333850 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
17333801 ATGGTAAATA
17333811 ATGATACATAATCTAGC
1 ATGATACATAATCTAGC
17333828 ATGATACATAATCTAGC
1 ATGATACATAATCTAGC
17333845 ATGATA
1 ATGATA
17333851 ATTTCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (17 bp):
ATGATACATAATCTAGC
Found at i:17334294 original size:27 final size:27
Alignment explanation
Indices: 17334264--17334325 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
17334254 CTATCGGGAC
*
17334264 AGTAAACATGGGGCAGTCTACCAAGAT
1 AGTAAACATGGAGCAGTCTACCAAGAT
* * *
17334291 AGTAAACATGGAGTAGTCTACTAGGAT
1 AGTAAACATGGAGCAGTCTACCAAGAT
*
17334318 AATAAACA
1 AGTAAACA
17334326 CGGGATAGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (27 bp):
AGTAAACATGGAGCAGTCTACCAAGAT
Found at i:17334334 original size:27 final size:27
Alignment explanation
Indices: 17334278--17334335 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
17334268 AACATGGGGC
* *
17334278 AGTCTACCAAGATAGTAAACATGGAGT
1 AGTCTACCAAGATAATAAACAGGGAGT
* *
17334305 AGTCTACTAGGATAATAAACACGGGA-T
1 AGTCTACCAAGATAATAAACA-GGGAGT
17334332 AGTC
1 AGTC
17334336 CACCGGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (27 bp):
AGTCTACCAAGATAATAAACAGGGAGT
Found at i:17334423 original size:27 final size:27
Alignment explanation
Indices: 17334366--17334443 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 27
17334356 TGTAGTCCAT
* *
17334366 CGAGACAATAATCACAGGGTAGTCTGC
1 CGAGACAATAAACACAGGGTAGTCTGA
* * * *
17334393 CGAGACAATAAACACTGGTTTGTTTGA
1 CGAGACAATAAACACAGGGTAGTCTGA
** * *
17334420 CGAGGTAGTAAACACAAGGTAGTC
1 CGAGACAATAAACACAGGGTAGTC
17334444 CACTGGGACA
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (27 bp):
CGAGACAATAAACACAGGGTAGTCTGA
Found at i:17339363 original size:39 final size:40
Alignment explanation
Indices: 17339295--17339395 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 40
17339285 TAGTATAGAA
* *
17339295 GGCATGTTTCAACATGCAATCAGTTTAGTAG-AAATA-GTT-
1 GGCATGTTT-AACATGCAATCAGTATAGTAGCAAA-ACATTG
*
17339334 GGCATGTTTAACATGCAATTAGTAATAGTAGCAAAACATTG
1 GGCATGTTTAACATGCAATCAGT-ATAGTAGCAAAACATTG
* *
17339375 GGCATGCTTAACATGCGATCA
1 GGCATGTTTAACATGCAATCA
17339396 ATTTCAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
38 13 0.25
39 16 0.31
40 5 0.10
41 18 0.35
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (40 bp):
GGCATGTTTAACATGCAATCAGTATAGTAGCAAAACATTG
Found at i:17342192 original size:14 final size:15
Alignment explanation
Indices: 17342173--17342201 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17342163 AAAAATATTT
17342173 TAACATTT-AAAACC
1 TAACATTTGAAAACC
17342187 TAACATTTGAAAACC
1 TAACATTTGAAAACC
17342202 CTTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
TAACATTTGAAAACC
Found at i:17343249 original size:19 final size:19
Alignment explanation
Indices: 17343219--17343274 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
17343209 TTTTTTAAAA
17343219 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
17343237 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
17343256 T-TAAATTATTTTGAATTTT
1 TATAAA-TATTTAGAATTTT
17343275 CTTTTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 10 0.29
19 25 0.71
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:17352674 original size:21 final size:23
Alignment explanation
Indices: 17352642--17352688 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 23
17352632 TTAATTATTG
*
17352642 ATTTAATGCACATCTT-TAT-CA
1 ATTTAATGCACAACTTGTATACA
17352663 ATTTACAT-CACAACTTGTATACA
1 ATTTA-ATGCACAACTTGTATACA
17352686 ATT
1 ATT
17352689 CATGCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTTAATGCACAACTTGTATACA
Found at i:17354603 original size:14 final size:14
Alignment explanation
Indices: 17354584--17354614 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17354574 AAGGTATAAG
*
17354584 TGATTAATTTTCAC
1 TGATTAATTCTCAC
17354598 TGATTAATTCTCAC
1 TGATTAATTCTCAC
17354612 TGA
1 TGA
17354615 GTTTTTTCGA
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:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (14 bp):
TGATTAATTCTCAC
Found at i:17355727 original size:18 final size:18
Alignment explanation
Indices: 17355704--17355781 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
17355694 AGCTGTACCA
17355704 TAAAATGGCGAACTATAT
1 TAAAATGGCGAACTATAT
* *
17355722 TAAAATGGCGGACTGTAT
1 TAAAATGGCGAACTATAT
* *
17355740 TAAAATGGCAAACAATAT
1 TAAAATGGCGAACTATAT
* * *
17355758 AAAAATGGTGGACTATAT
1 TAAAATGGCGAACTATAT
17355776 TAAAAT
1 TAAAAT
17355782 TGTGAATTGT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (18 bp):
TAAAATGGCGAACTATAT
Found at i:17355745 original size:36 final size:36
Alignment explanation
Indices: 17355704--17355781 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
17355694 AGCTGTACCA
* * * *
17355704 TAAAATGGCGAACTATATTAAAATGGCGGACTGTAT
1 TAAAATGGCAAACAATATAAAAATGGCGGACTATAT
*
17355740 TAAAATGGCAAACAATATAAAAATGGTGGACTATAT
1 TAAAATGGCAAACAATATAAAAATGGCGGACTATAT
17355776 TAAAAT
1 TAAAAT
17355782 TGTGAATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (36 bp):
TAAAATGGCAAACAATATAAAAATGGCGGACTATAT
Found at i:17355814 original size:18 final size:18
Alignment explanation
Indices: 17355793--17355831 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
17355783 GTGAATTGTA
*
17355793 TTAATTTGGAAAACTTTG
1 TTAATTTGGAAAACTATG
*
17355811 TTAATTTGGCAAACTATG
1 TTAATTTGGAAAACTATG
17355829 TTA
1 TTA
17355832 TTTATGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (18 bp):
TTAATTTGGAAAACTATG
Found at i:17362183 original size:21 final size:19
Alignment explanation
Indices: 17362151--17362194 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
17362141 GATGTAGTTC
17362151 AAAAAATTTTAAAAATTATT
1 AAAAAATTTTAAAAATTA-T
* *
17362171 AAAAAGTTGTTAAATATTAT
1 AAAAAATT-TTAAAAATTAT
17362191 AAAA
1 AAAA
17362195 TAACTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAAAATTTTAAAAATTAT
Found at i:17362300 original size:19 final size:19
Alignment explanation
Indices: 17362277--17362326 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
17362267 TAAAAATGCT
17362277 ATAAAATGTTA-AAATATA
1 ATAAAATGTTATAAATATA
* *
17362295 AGTAAATTATTATAAATATA
1 A-TAAAATGTTATAAATATA
*
17362315 ATAAAAAGTTAT
1 ATAAAATGTTAT
17362327 TCAAATTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
ATAAAATGTTATAAATATA
Found at i:17362622 original size:21 final size:22
Alignment explanation
Indices: 17362598--17362664 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
17362588 CTTTAAGTTT
* *
17362598 AATTTAAT-TTTCATATCATTA
1 AATTTAATATATCACATCATTA
17362619 AA-TTAATATATCACATCATTA
1 AATTTAATATATCACATCATTA
*
17362640 TATTT--TATAT-A-ATCATTA
1 AATTTAATATATCACATCATTA
*
17362658 ATTTTAA
1 AATTTAA
17362665 ATGTTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 10 0.27
19 1 0.03
20 10 0.27
21 14 0.38
22 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTAATATATCACATCATTA
Found at i:17367108 original size:13 final size:12
Alignment explanation
Indices: 17367078--17367105 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17367068 AACTTAAATA
17367078 TTTTAATTTAGT
1 TTTTAATTTAGT
17367090 TTTTAATTTAGT
1 TTTTAATTTAGT
17367102 TTTT
1 TTTT
17367106 TAACATAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTAATTTAGT
Found at i:17369649 original size:13 final size:15
Alignment explanation
Indices: 17369628--17369659 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17369618 TGACAAAATC
*
17369628 AAAATATATTTTAAA
1 AAAATATATGTTAAA
17369643 AAAATATATGTTAAA
1 AAAATATATGTTAAA
17369658 AA
1 AA
17369660 TGTTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATGTTAAA
Found at i:17370143 original size:14 final size:14
Alignment explanation
Indices: 17370104--17370211 Score: 65
Period size: 13 Copynumber: 8.2 Consensus size: 14
17370094 GCATATATGC
17370104 ATATATAA-ATA-A
1 ATATATAATATATA
*
17370116 GTATAATAAT-TATA
1 ATAT-ATAATATATA
17370130 ATATATAATATATA
1 ATATATAATATATA
17370144 ATATAATAATA-ATA
1 ATAT-ATAATATATA
*
17370158 A-A-CTAATA-ATA
1 ATATATAATATATA
*
17370169 ATACAATAATA-ATA
1 ATA-TATAATATATA
*
17370183 ATATA-AATAAATA
1 ATATATAATATATA
* *
17370196 GTAT-TAAAATATA
1 ATATATAATATATA
17370209 ATA
1 ATA
17370212 AAAAACTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
11 9 0.12
12 8 0.10
13 27 0.35
14 27 0.35
15 6 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATATAATATATA
Found at i:17370154 original size:3 final size:3
Alignment explanation
Indices: 17370118--17370185 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
17370108 ATAAATAAGT
* *
17370118 ATA ATA ATT ATA ATA TATA ATA TATA AT- ATA ATA ATA ATA A-A CTA
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
*
17370163 ATA ATA AT- ACA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
17370186 TAAATAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:17370157 original size:11 final size:11
Alignment explanation
Indices: 17370118--17370212 Score: 65
Period size: 11 Copynumber: 8.4 Consensus size: 11
17370108 ATAAATAAGT
17370118 ATAATAAT-T-
1 ATAATAATATA
17370127 ATAAT-ATATA
1 ATAATAATATA
17370137 ATATATAATATA
1 ATA-ATAATATA
17370149 ATAATAATAAACTA
1 ATAATAAT--A-TA
*
17370163 ATAATAATACA
1 ATAATAATATA
17370174 ATAATAATA-A
1 ATAATAATATA
17370184 TATAAATAAATAGTA
1 -AT-AAT-AATA-TA
*
17370199 TTAA-AATATA
1 ATAATAATATA
17370209 ATAA
1 ATAA
17370213 AAAACTAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 9 0.13
11 23 0.32
12 12 0.17
13 7 0.10
14 11 0.15
15 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (11 bp):
ATAATAATATA
Found at i:17377954 original size:26 final size:26
Alignment explanation
Indices: 17377925--17378030 Score: 88
Period size: 26 Copynumber: 4.1 Consensus size: 26
17377915 ATCCACTCAT
* *
17377925 GGTCCTCCAACTAACTCAAACTCCAG
1 GGTCCTCCAACCAACTCAAACTCAAG
*** * *
17377951 GGTCCTTGGACCCATTCAAACTCAAG
1 GGTCCTCCAACCAACTCAAACTCAAG
* * *
17377977 GGACCTCCAACCAACCCAAACTCAAA
1 GGTCCTCCAACCAACTCAAACTCAAG
* *
17378003 GGTCCT-CAGACTAACTCAAACTTAAG
1 GGTCCTCCA-ACCAACTCAAACTCAAG
17378029 GG
1 GG
17378031 ATCATCTTGA
Statistics
Matches: 59, Mismatches: 20, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
25 2 0.03
26 57 0.97
ACGTcount: A:0.33, C:0.34, G:0.15, T:0.18
Consensus pattern (26 bp):
GGTCCTCCAACCAACTCAAACTCAAG
Found at i:17379555 original size:29 final size:29
Alignment explanation
Indices: 17379523--17379582 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
17379513 TTATTTATAT
17379523 TTTCAATTGTAACT-ATTTAATTTTTAAAG
1 TTTCAATTGTAA-TGATTTAATTTTTAAAG
17379552 TTTCAATTGTAATGATTTAATTTTTAAAG
1 TTTCAATTGTAATGATTTAATTTTTAAAG
17379581 TT
1 TT
17379583 AAATTTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (29 bp):
TTTCAATTGTAATGATTTAATTTTTAAAG
Found at i:17383688 original size:25 final size:25
Alignment explanation
Indices: 17383660--17383728 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
17383650 AAGAGAATGG
* *
17383660 AAAATAAAGAAAA-AAAAGAAAGTT
1 AAAAAAAAGAAAAGAAAAAAAAGTT
* *
17383684 AAAAAACATAAAAGAAAAAAAAGTT
1 AAAAAAAAGAAAAGAAAAAAAAGTT
* *
17383709 AAAAAACATAAAAGAAAAAA
1 AAAAAAAAGAAAAGAAAAAA
17383729 TTAAATTGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 10 0.25
25 30 0.75
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.10
Consensus pattern (25 bp):
AAAAAAAAGAAAAGAAAAAAAAGTT
Found at i:17386426 original size:24 final size:24
Alignment explanation
Indices: 17386399--17386457 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
17386389 TTATATGATA
17386399 TGAATATAATATGACAAAATTTAT
1 TGAATATAATATGACAAAATTTAT
** *
17386423 TGAA-ATATATATGTTAAATTTTAT
1 TGAATATA-ATATGACAAAATTTAT
*
17386447 T-TATATAATAT
1 TGAATATAATAT
17386458 ATAATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
TGAATATAATATGACAAAATTTAT
Found at i:17387940 original size:3 final size:3
Alignment explanation
Indices: 17387915--17387975 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
17387905 GTTATCTTTG
*
17387915 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA -TA TTA CTTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
17387960 TTT TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
17387976 ATATATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17387982 original size:15 final size:15
Alignment explanation
Indices: 17387921--17387982 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
17387911 TTTGTTATTA
17387921 TATTA-TATATTACTAT
1 TATTATTATA-TA-TAT
17387937 TATTATTATAT-TACT
1 TATTATTATATATA-T
* *
17387952 TATTATTATTTTTAT
1 TATTATTATATATAT
17387967 TATTATTATATATAT
1 TATTATTATATATAT
17387982 T
1 T
17387983 TATGCGCATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.05
15 26 0.65
16 8 0.20
17 4 0.10
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTATATATAT
Found at i:17387982 original size:24 final size:24
Alignment explanation
Indices: 17387915--17387979 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
17387905 GTTATCTTTG
*
17387915 TTATTATATTATATATTACTATTA
1 TTATTATATTATATATTATTATTA
*
17387939 TTATTATATTACT-TATTATTATTT
1 TTATTATATTA-TATATTATTATTA
17387963 TTATTATTATTATATAT
1 TTATTA-TATTATATAT
17387980 ATTTATGCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 27 0.75
25 9 0.25
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTATATTATATATTATTATTA
Found at i:17388006 original size:2 final size:2
Alignment explanation
Indices: 17387999--17388023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17387989 CATATGTATC
17387999 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17388024 TGTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17388043 original size:26 final size:24
Alignment explanation
Indices: 17388014--17388076 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
17388004 ATATATATAT
17388014 ATATATATATTGTTTTATTTTTATTA
1 ATATATATATT-TTTTA-TTTTATTA
17388040 ATATATATACATTTTTTATTTTATTA
1 ATATATAT--ATTTTTTATTTTATTA
*
17388066 TTAT-TATATTT
1 ATATATATATTT
17388077 ATGCATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
23 4 0.12
25 3 0.09
26 19 0.56
27 5 0.15
28 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
ATATATATATTTTTTATTTTATTA
Found at i:17388044 original size:32 final size:32
Alignment explanation
Indices: 17388008--17388086 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
17387998 CTATATATAT
* * *
17388008 ATATATATATATATATTGTTTTATTTTTATTA
1 ATATATATACATATATTATTTTATTATTATTA
* *
17388040 ATATATATACATTTTTTATTTTATTATTATT-
1 ATATATATACATATATTATTTTATTATTATTA
* *
17388071 ATATTTATGCATATAT
1 ATATATATACATATAT
17388087 ACGCATATGT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 12 0.32
32 26 0.68
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (32 bp):
ATATATATACATATATTATTTTATTATTATTA
Found at i:17392219 original size:2 final size:2
Alignment explanation
Indices: 17392202--17392256 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
17392192 TTCTGAGATG
* *
17392202 AC AC AC AA AC AG AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
17392244 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
17392257 TATGGATGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.53, C:0.45, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17394694 original size:18 final size:18
Alignment explanation
Indices: 17394657--17394694 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17394647 AAAAAATGAC
*
17394657 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAAAAT
17394675 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTACATTT-AAAAT
17394693 AT
1 AT
17394695 ATAGTGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:17394827 original size:19 final size:19
Alignment explanation
Indices: 17394803--17394851 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
17394793 AGTTAATAAT
17394803 AAATTTGATTATGGTGGGC
1 AAATTTGATTATGGTGGGC
17394822 AAATTTGATTATGGTGGGC
1 AAATTTGATTATGGTGGGC
17394841 AAATTTGATTA
1 AAATTTGATTA
17394852 CAATGACTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (19 bp):
AAATTTGATTATGGTGGGC
Found at i:17395535 original size:15 final size:15
Alignment explanation
Indices: 17395515--17395544 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17395505 ACTTAGCCTT
17395515 AATTACATGTAACAA
1 AATTACATGTAACAA
*
17395530 AATTACATGTGACAA
1 AATTACATGTAACAA
17395545 TTATTCGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
AATTACATGTAACAA
Found at i:17400443 original size:23 final size:23
Alignment explanation
Indices: 17400416--17400460 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17400406 TTCAATATCA
*
17400416 TTCATAT-AATTTAATCATCATAT
1 TTCATATGAATGTAATC-TCATAT
*
17400439 TTCATTTGAATGTAATCTCATA
1 TTCATATGAATGTAATCTCATA
17400461 ACAATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
TTCATATGAATGTAATCTCATAT
Found at i:17400602 original size:20 final size:20
Alignment explanation
Indices: 17400572--17400997 Score: 415
Period size: 20 Copynumber: 21.3 Consensus size: 20
17400562 CATAGTGCTG
* *
17400572 AACAAAGGCACCAAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
17400592 TATAGAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* ** * *
17400612 AATAGAGGTGCTGGAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
17400632 AACAGAGACATCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
17400652 AATAGAGGCACC-AGAGTGCA
1 AACAGAGGCACCGA-AGTGCA
*
17400672 AACAAAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
17400692 AACAAAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
17400712 TACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
17400732 AACAGAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* **
17400752 TACAGAGGCATTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
*
17400772 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
17400792 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
17400812 TACAGAGGCATCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* ** * *
17400832 TACAGAGATATCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
17400852 AATAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
17400872 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
17400892 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
17400912 TACAGAGGCATCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
17400932 TACAGAGGCACCGAACTGCA
1 AACAGAGGCACCGAAGTGCA
* * * ** *
17400952 AATAAAGGCATCGTGGTACA
1 AACAGAGGCACCGAAGTGCA
*
17400972 AATAGAGGCACCGAAGTAG-A
1 AACAGAGGCACCGAAGT-GCA
17400992 AACAGA
1 AACAGA
17400998 TACATTTCAA
Statistics
Matches: 337, Mismatches: 66, Indels: 6
0.82 0.16 0.01
Matches are distributed among these distances:
19 1 0.00
20 335 0.99
21 1 0.00
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.11
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:17400997 original size:80 final size:80
Alignment explanation
Indices: 17400572--17400988 Score: 487
Period size: 80 Copynumber: 5.2 Consensus size: 80
17400562 CATAGTGCTG
* * * * ** * * *
17400572 AACAAAGGCACCAAAGTGCATATAGAGGCA-CTGAAGTGCAAATAGAGGTGCTGGAGTGCAAACA
1 AACAGAGGCACCGAAGTGCATACAGAGGCATC-GAAGTGCAAACAGAGGCACCGAAGTACAAACA
* *
17400636 GAGACATCGAAGTACA
65 GAGGCACCGAAGTACA
* * * * * *
17400652 AATAGAGGCACC-AGAGTGCAAACAAAGGCACCGAAGTGCAAACAAAGGCACCGAAGTACATACA
1 AACAGAGGCACCGA-AGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACA
17400716 GAGGCACCGAAGTACA
65 GAGGCACCGAAGTACA
* *
17400732 AACAGAGGCACTGAAGTGCATACAGAGGCATTGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
1 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
*
17400797 AGGCACCGAAGTGCA
66 AGGCACCGAAGTACA
* * ** * *
17400812 TACAGAGGCATCGAAGTGCATACAGAGATATCGAAGTACAAATAGAGGCACCGAAGTACAAACAG
1 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
17400877 AGGCACCGAAGTACA
66 AGGCACCGAAGTACA
* * * * *
17400892 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCATACAGAGGCACCGAACTGCAAATAA
1 AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
* **
17400957 AGGCATCGTGGTACA
66 AGGCACCGAAGTACA
*
17400972 AATAGAGGCACCGAAGT
1 AACAGAGGCACCGAAGT
17400989 AGAAACAGAT
Statistics
Matches: 286, Mismatches: 48, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
79 1 0.00
80 283 0.99
81 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.27, T:0.11
Consensus pattern (80 bp):
AACAGAGGCACCGAAGTGCATACAGAGGCATCGAAGTGCAAACAGAGGCACCGAAGTACAAACAG
AGGCACCGAAGTACA
Found at i:17403543 original size:12 final size:12
Alignment explanation
Indices: 17403505--17403543 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
17403495 ACTAAAATGA
17403505 TTTAATAAAATT
1 TTTAATAAAATT
*
17403517 CTTAATAACATATT
1 TTTAATAA-A-ATT
17403531 TTTAATAAAATT
1 TTTAATAAAATT
17403543 T
1 T
17403544 CTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAATAAAATT
Found at i:17403789 original size:16 final size:17
Alignment explanation
Indices: 17403770--17403807 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17403760 TGAAGTTTTT
17403770 TTTTAAATTT-TGAAAA
1 TTTTAAATTTCTGAAAA
* *
17403786 TTTTAATTTTCTGAAAT
1 TTTTAAATTTCTGAAAA
17403803 TTTTA
1 TTTTA
17403808 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTCTGAAAA
Found at i:17403789 original size:20 final size:19
Alignment explanation
Indices: 17403750--17403789 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
17403740 AAGTTGATAG
**
17403750 TTTTTAATTTTGAAGTTTT
1 TTTTTAATTTTGAAAATTT
17403769 TTTTTAAATTTTGAAAATTT
1 TTTTT-AATTTTGAAAATTT
17403789 T
1 T
17403790 AATTTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TTTTTAATTTTGAAAATTT
Found at i:17403815 original size:37 final size:35
Alignment explanation
Indices: 17403751--17403822 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 35
17403741 AGTTGATAGT
* * *
17403751 TTTTAATTTTGAAGTTTTTTTTTAAATTTTGAAAA
1 TTTTAATTTTGAAATTTTTATTAAAATTTTGAAAA
17403786 TTTTAATTTTCTGAAATTTTTATTAAAATTTTGAAAA
1 TTTTAA-TTT-TGAAATTTTTATTAAAATTTTGAAAA
17403823 AGTTTAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 6 0.19
36 3 0.09
37 23 0.72
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (35 bp):
TTTTAATTTTGAAATTTTTATTAAAATTTTGAAAA
Found at i:17403820 original size:20 final size:19
Alignment explanation
Indices: 17403755--17403821 Score: 50
Period size: 20 Copynumber: 3.5 Consensus size: 19
17403745 GATAGTTTTT
* *
17403755 AATTTTGAAGTTTTTTTTTA
1 AATTTTGAA-ATTTTTATTA
*
17403775 AATTTTGAAAATTTTAATT-
1 AATTTTG-AAATTTTTATTA
*
17403794 --TTCTGAAATTTTTATTAA
1 AATTTTGAAATTTTTATT-A
17403812 AATTTTGAAA
1 AATTTTGAAA
17403822 AAGTTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
16 10 0.28
17 4 0.11
20 20 0.56
21 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (19 bp):
AATTTTGAAATTTTTATTA
Found at i:17410068 original size:123 final size:125
Alignment explanation
Indices: 17409762--17410112 Score: 555
Period size: 126 Copynumber: 2.8 Consensus size: 125
17409752 TAATTTCGAG
**
17409762 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
17409827 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCACGGAAGAAATAA-TATTTTT
* *
17409888 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGCAGGATGCTATTTGTGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * *
17409953 AAATCGCGGCCTCGT-TAGCGCACTTTTGCTATAGTAGGTCATGTAAGAAAT-A-ATTTTT
66 AAATCGCGCCCTCGTGGA-CGCGCTTTTGCTATAGTAGGTCACGGAAGAAATAATATTTTT
*
17410011 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
17410076 AAATCGTGCCCTCGTGGACGCGCTTTTGCTATAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAG
17410113 CATGTTTGGG
Statistics
Matches: 206, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
123 99 0.48
124 1 0.00
125 2 0.01
126 104 0.50
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGTAGGTCACGGAAGAAATAATATTTTT
Found at i:17413396 original size:116 final size:116
Alignment explanation
Indices: 17413192--17413522 Score: 599
Period size: 116 Copynumber: 2.9 Consensus size: 116
17413182 ATTAATTGAT
*
17413192 AAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCTGTCA
1 AAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCAGTCA
*
17413257 AAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTGAGTCAAA
66 AAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAA
*
17413308 AAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCAGTTA
1 AAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCAGTCA
17413373 AAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAA
66 AAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAA
* *
17413424 AAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGTTAGTACCAGTCA
1 AAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCAGTCA
* *
17413489 AAACATTTTTCCAAATCTAACATTACGTTAATGT
66 AAACATTTTTCCAAATCTAACATTATGTGAATGT
17413523 TAGGGTTTTT
Statistics
Matches: 207, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 207 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (116 bp):
AAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCAGTCA
AAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAA
Found at i:17413629 original size:29 final size:29
Alignment explanation
Indices: 17413590--17413778 Score: 306
Period size: 29 Copynumber: 6.4 Consensus size: 29
17413580 TTTTAAGTTA
17413590 AGGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
* *
17413620 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
17413649 AGGGGTTAGGGTTTTTAATTAAATTAGGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
17413679 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
17413708 AGGATTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
17413737 AGGGTTAGGGTTTTTATTTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
17413766 AGGGTTTAGGGTT
1 AGGG-TTAGGGTT
17413779 AAATTAGGTG
Statistics
Matches: 149, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
29 110 0.74
30 39 0.26
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:17413665 original size:59 final size:59
Alignment explanation
Indices: 17413581--17413778 Score: 326
Period size: 59 Copynumber: 3.4 Consensus size: 59
17413571 GGTTAGGGTT
* *
17413581 TTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAA
1 TTTAGGTT-AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
*
17413641 TTTAGGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
1 TTTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
* * *
17413700 ATTAGGTTA-GGATTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTATTTAA
1 TTTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
17413758 TTTAGGTTAGGGTTTAGGGTT
1 TTTAGGTTAGGGTTTAGGGTT
17413779 AAATTAGGTG
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
58 55 0.43
59 67 0.52
60 7 0.05
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (59 bp):
TTTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
Found at i:17413766 original size:23 final size:23
Alignment explanation
Indices: 17413739--17413800 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
17413729 ATTAGGTTAG
*
17413739 GGTTAGGGTTTTTATTTAATTTA
1 GGTTAGGGTTTTTATTTAAATTA
****
17413762 GGTTAGGGTTTAGGGTTAAATTA
1 GGTTAGGGTTTTTATTTAAATTA
*
17413785 GGTGAGGGTTTTTATT
1 GGTTAGGGTTTTTATT
17413801 ACATCAAATA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (23 bp):
GGTTAGGGTTTTTATTTAAATTA
Found at i:17413822 original size:25 final size:25
Alignment explanation
Indices: 17413794--17413906 Score: 94
Period size: 25 Copynumber: 4.7 Consensus size: 25
17413784 AGGTGAGGGT
17413794 TTTTATTACATCAAATAAATTTCTA
1 TTTTATTACATCAAATAAATTTCTA
*
17413819 TTTTATTACATCAAAT-AATATC-A
1 TTTTATTACATCAAATAAATTTCTA
** * * ** *
17413842 --AAATAAC-TCGAAT-TTTTTATTA
1 TTTTATTACATCAAATAAATTT-CTA
*
17413864 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAATTTCTA
17413889 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
17413907 TATCAAAATA
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
20 7 0.11
21 4 0.06
22 1 0.02
23 1 0.02
24 9 0.14
25 41 0.63
26 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (25 bp):
TTTTATTACATCAAATAAATTTCTA
Found at i:17413920 original size:35 final size:35
Alignment explanation
Indices: 17413814--17413920 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 35
17413804 TCAAATAAAT
17413814 TTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TTCTATTTTATTACATCAAATAATATCAAAATAAC
* * *** * *
17413849 -TCGAATTTT-TTATTATTTTATTACATC-AAATAAAC
1 TTC-TATTTTATTA-CATCAAATAATATCAAAAT-AAC
17413884 TTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TTCTATTTTATTACATCAAATAATATCAAAATAAC
17413919 TT
1 TT
17413921 AAAAAATTTC
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
34 9 0.17
35 34 0.65
36 9 0.17
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (35 bp):
TTCTATTTTATTACATCAAATAATATCAAAATAAC
Found at i:17415063 original size:7 final size:7
Alignment explanation
Indices: 17415053--17415077 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17415043 TTATATACAT
17415053 AATACTA
1 AATACTA
17415060 AATACTA
1 AATACTA
17415067 AATACTA
1 AATACTA
17415074 AATA
1 AATA
17415078 TCAATCGAAT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:17416281 original size:22 final size:22
Alignment explanation
Indices: 17416256--17416311 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
17416246 AAATATGGAT
17416256 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
17416278 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
17416300 TTGAGAGGAATT
1 TTGAGA-GAATT
17416312 GAGAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:17416328 original size:12 final size:11
Alignment explanation
Indices: 17416272--17416328 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
17416262 GAATTTTGGA
17416272 AGGAAATTGAG
1 AGGAAATTGAG
*
17416283 A-GAATTTTG-G
1 AGGAA-ATTGAG
17416293 AAGGAAATTGAG
1 -AGGAAATTGAG
17416305 AGG-AATTGAG
1 AGGAAATTGAG
17416315 AGGAAATATGAG
1 AGGAAAT-TGAG
17416327 AG
1 AG
17416329 AGGATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:17423597 original size:19 final size:19
Alignment explanation
Indices: 17423573--17423645 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
17423563 AATCTTCAAG
17423573 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
17423592 GATATGTAATCTTAGACAT
1 GATATGCAATCTTAGATAT
*
17423611 GATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
17423630 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
17423646 AGATATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:17423897 original size:23 final size:23
Alignment explanation
Indices: 17423853--17423897 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
17423843 TTTTATTTTG
* *
17423853 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
17423876 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
17423898 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:17425730 original size:23 final size:23
Alignment explanation
Indices: 17425695--17425738 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17425685 AAGTATGTAT
17425695 ATATATTAATTACAAATGTATAC
1 ATATATTAATTACAAATGTATAC
** *
17425718 ATATATTTGTTACACATGTAT
1 ATATATTAATTACAAATGTAT
17425739 TTATAATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (23 bp):
ATATATTAATTACAAATGTATAC
Found at i:17427419 original size:12 final size:12
Alignment explanation
Indices: 17427404--17427430 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17427394 TAATTAATTA
17427404 ATTAATATTATC
1 ATTAATATTATC
17427416 ATTAATATTATC
1 ATTAATATTATC
17427428 ATT
1 ATT
17427431 TTTCCTTTTA
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:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTAATATTATC
Found at i:17427595 original size:3 final size:3
Alignment explanation
Indices: 17427580--17427663 Score: 96
Period size: 3 Copynumber: 28.0 Consensus size: 3
17427570 TAAACCTTAG
* * * *
17427580 ATT ATT TTT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT AAT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
17427628 ATT ATT ATT ATT ATC ATT ATC ATT ATC ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17427664 TTTAATGTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:17431007 original size:19 final size:19
Alignment explanation
Indices: 17430983--17431030 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
17430973 TAATACCTCT
17430983 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTTCAT-CA
17431002 TTTGCATTACATTTCATCA
1 TTTGCATTACATTTCATCA
*
17431021 TATGCATTAC
1 TTTGCATTAC
17431031 GTTTTACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (19 bp):
TTTGCATTACATTTCATCA
Found at i:17439244 original size:45 final size:45
Alignment explanation
Indices: 17439178--17439263 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
17439168 GTCATCATGG
*
17439178 CGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAA
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAGATAA
* * *
17439223 CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAG
1 CGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAG
17439264 CTATAGATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (45 bp):
CGAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTGAAGATAA
Found at i:17444303 original size:58 final size:58
Alignment explanation
Indices: 17444212--17444325 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 58
17444202 ATGGATTAAT
* *
17444212 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCTTGTTCACCATTTTTGTGCTAG
1 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCTAG
*
17444270 TTGAAATTCACCGGACAGTTCGAGTATTGCTATCCCCTGTTCACCATTTTCGTGCT
1 TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCT
17444326 GCTGGCTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (58 bp):
TTGAAATTCACCGGACAGTTCGAGTATTCCTATCCCCTGTTCACCATTTTCGTGCTAG
Found at i:17445147 original size:40 final size:40
Alignment explanation
Indices: 17445092--17445172 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
17445082 ATTCGTATAT
*
17445092 TGATCCAATTATTATTCTTTCTTCTTTTGAAAGGAATTAC
1 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
17445132 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
1 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
17445172 T
1 T
17445173 ATGATTCTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (40 bp):
TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
Found at i:17446026 original size:15 final size:15
Alignment explanation
Indices: 17446006--17446035 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17445996 GTTATGTAAG
17446006 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
17446021 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
17446036 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:17450373 original size:15 final size:15
Alignment explanation
Indices: 17450350--17450380 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17450340 GCTATGTAAG
*
17450350 TGAATGGTCAAGAGT
1 TGAAAGGTCAAGAGT
17450365 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
17450380 T
1 T
17450381 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:17451402 original size:13 final size:13
Alignment explanation
Indices: 17451386--17451412 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17451376 CTTAAAACTC
17451386 ATGCCATATTCAT
1 ATGCCATATTCAT
17451399 ATGCCATATTCAT
1 ATGCCATATTCAT
17451412 A
1 A
17451413 CTTAGTCAAC
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:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATGCCATATTCAT
Found at i:17451677 original size:25 final size:25
Alignment explanation
Indices: 17451648--17451702 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
17451638 TTGTTTGATT
17451648 AATATTAATATTATGATTAATTAAA
1 AATATTAATATTATGATTAATTAAA
* * *
17451673 AATATTGATATTTTGATTAATTAGA
1 AATATTAATATTATGATTAATTAAA
17451698 AATAT
1 AATAT
17451703 ATGAAAACGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (25 bp):
AATATTAATATTATGATTAATTAAA
Found at i:17455316 original size:50 final size:50
Alignment explanation
Indices: 17455191--17455482 Score: 264
Period size: 50 Copynumber: 5.7 Consensus size: 50
17455181 GAATATAACA
* * * * * * *
17455191 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGA-TGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTCATATAGG
* * * * *
17455240 TACCAATTCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATAGG
* ** * * *
17455290 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATAGG
* * * * *
17455340 TGCCAACGCCATGTCCTAGACATTGTCTTACATGGGACTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATAGG
* * *
17455390 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--T--A-GG
*
17455446 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
17455483 TCTCTTTACC
Statistics
Matches: 198, Mismatches: 37, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
49 36 0.18
50 125 0.63
53 1 0.01
56 36 0.18
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATAGG
Found at i:17458067 original size:15 final size:16
Alignment explanation
Indices: 17458032--17458074 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
17458022 ATATTGCGAC
*
17458032 AAATCATAAAAAGATT
1 AAATAATAAAAAGATT
*
17458048 TAATAATAAAAA-ATT
1 AAATAATAAAAAGATT
17458063 AAATAACTAAAA
1 AAATAA-TAAAA
17458075 TAAATGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAATAAAAAGATT
Found at i:17468516 original size:26 final size:25
Alignment explanation
Indices: 17468478--17468536 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
17468468 ATAGATACTA
*
17468478 TATTTTTAGTTTTTTTATTTAATTTT
1 TATTTTTAGTTTTTTAATTT-ATTTT
* *
17468504 TATTTTTATTTTTTTAATTTCTTTT
1 TATTTTTAGTTTTTTAATTTATTTT
17468529 TAATTTTT
1 T-ATTTTT
17468537 TAGGTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (25 bp):
TATTTTTAGTTTTTTAATTTATTTT
Found at i:17470611 original size:26 final size:26
Alignment explanation
Indices: 17470575--17470627 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17470565 TTAGTTGTTC
17470575 TATGCTTTGAGAATTTTTAAAGTAAA
1 TATGCTTTGAGAATTTTTAAAGTAAA
17470601 TATGCTTTGAGAATTTTTAAAGTAAA
1 TATGCTTTGAGAATTTTTAAAGTAAA
17470627 T
1 T
17470628 CAGTATTAGT
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:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (26 bp):
TATGCTTTGAGAATTTTTAAAGTAAA
Found at i:17477422 original size:21 final size:20
Alignment explanation
Indices: 17477389--17477428 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
17477379 CTAATCTGAT
*
17477389 CAATAGAAAATTTTAATTTA
1 CAATAGAAAATTTGAATTTA
*
17477409 CAATATGATAATTTGAATTT
1 CAATA-GAAAATTTGAATTT
17477429 TGTTATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
CAATAGAAAATTTGAATTTA
Found at i:17479696 original size:17 final size:17
Alignment explanation
Indices: 17479674--17479709 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
17479664 GATGGCAGAC
17479674 TATGCATGTGTAACTCG
1 TATGCATGTGTAACTCG
17479691 TATGCATGTGTAACTCG
1 TATGCATGTGTAACTCG
17479708 TA
1 TA
17479710 GCTCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (17 bp):
TATGCATGTGTAACTCG
Found at i:17484089 original size:27 final size:27
Alignment explanation
Indices: 17484051--17484104 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17484041 TTGCCACATA
17484051 ACCGTGTGACCCCTATTTTCAAAATTT
1 ACCGTGTGACCCCTATTTTCAAAATTT
17484078 ACCGTGTGACCCCTATTTTCAAAATTT
1 ACCGTGTGACCCCTATTTTCAAAATTT
17484105 TCAACTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (27 bp):
ACCGTGTGACCCCTATTTTCAAAATTT
Found at i:17484664 original size:7 final size:8
Alignment explanation
Indices: 17484634--17484664 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
17484624 TTTTTAAGGG
17484634 GTAAAATA
1 GTAAAATA
17484642 GTAAAATA
1 GTAAAATA
17484650 GTAAAATA
1 GTAAAATA
17484658 G-AAAATA
1 GTAAAATA
17484665 AATGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (8 bp):
GTAAAATA
Found at i:17485878 original size:25 final size:25
Alignment explanation
Indices: 17485846--17485931 Score: 172
Period size: 25 Copynumber: 3.4 Consensus size: 25
17485836 TAATATATAT
17485846 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
17485871 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
17485896 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
17485921 AATATATATTT
1 AATATATATTT
17485932 AATATATAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
AATATATATTTGATTAAAAATAAAA
Found at i:17488976 original size:28 final size:28
Alignment explanation
Indices: 17488940--17489027 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
17488930 GGGTGTCTTG
* **
17488940 TTTAA-AGGTTCGCCACTCAGGCATTCC
1 TTTAAGAGGTTTGCCACAAAGGCATTCC
*
17488967 TTTAAGAGGTTTGCCACAAAGGCGTTCC
1 TTTAAGAGGTTTGCCACAAAGGCATTCC
*
17488995 TTTCAGAGGTTTGCCACAAAGGC-TATCC
1 TTTAAGAGGTTTGCCACAAAGGCAT-TCC
17489023 TTTAA
1 TTTAA
17489028 TTGAGTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 6 0.11
28 47 0.89
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (28 bp):
TTTAAGAGGTTTGCCACAAAGGCATTCC
Found at i:17497142 original size:25 final size:25
Alignment explanation
Indices: 17497107--17497154 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
17497097 ACATGTATGT
*
17497107 TCATACGAGCTGAATAACAGTAAGC
1 TCATACAAGCTGAATAACAGTAAGC
* *
17497132 TCATACAAGCTGAGTATCAGTAA
1 TCATACAAGCTGAATAACAGTAA
17497155 ATTTATAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (25 bp):
TCATACAAGCTGAATAACAGTAAGC
Found at i:17500583 original size:13 final size:13
Alignment explanation
Indices: 17500567--17500591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17500557 TAACCACTTC
17500567 AATTAATTAATTT
1 AATTAATTAATTT
17500580 AATTAATTAATT
1 AATTAATTAATT
17500592 AAAACCCAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:17501961 original size:28 final size:27
Alignment explanation
Indices: 17501928--17501994 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
17501918 CTTCCTTTAC
* *
17501928 GTTCGCCACAAGGGCA-TCTTGTTTAGAG
1 GTTCGCCACAA-GGCATTCCT-TTAAGAG
17501956 GTTCGCCACTAAGGCATTCCTTTAAGAG
1 GTTCGCCAC-AAGGCATTCCTTTAAGAG
*
17501984 GTTTGCCACAA
1 GTTCGCCACAA
17501995 AAAGCTCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 27 0.79
29 5 0.15
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (27 bp):
GTTCGCCACAAGGCATTCCTTTAAGAG
Found at i:17503551 original size:20 final size:20
Alignment explanation
Indices: 17503526--17503563 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17503516 GTTAGCCATA
*
17503526 TTCATATATATATATGTATT
1 TTCATACATATATATGTATT
17503546 TTCATACATATATATGTA
1 TTCATACATATATATGTA
17503564 CATACGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCATACATATATATGTATT
Found at i:17507561 original size:14 final size:14
Alignment explanation
Indices: 17507542--17507582 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
17507532 GATGCTCCAG
17507542 ACGTCATCACGGGT
1 ACGTCATCACGGGT
*
17507556 ACGTCATCACTGGT
1 ACGTCATCACGGGT
*
17507570 ACTTCATCACGGG
1 ACGTCATCACGGG
17507583 ACTGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (14 bp):
ACGTCATCACGGGT
Found at i:17516782 original size:43 final size:43
Alignment explanation
Indices: 17516728--17516815 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
17516718 ATATGGATAA
17516728 CATTAAAAAAAAATTAACTAAAGGAAGAGGCGAATGGAAATAT
1 CATTAAAAAAAAATTAACTAAAGGAAGAGGCGAATGGAAATAT
*
17516771 CATTAAAAAAAATTTAACTAAAGGAAGAGGCGAATGGAAATAT
1 CATTAAAAAAAAATTAACTAAAGGAAGAGGCGAATGGAAATAT
17516814 CA
1 CA
17516816 CCTAGGTACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.19
Consensus pattern (43 bp):
CATTAAAAAAAAATTAACTAAAGGAAGAGGCGAATGGAAATAT
Found at i:17539483 original size:14 final size:14
Alignment explanation
Indices: 17539464--17539491 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17539454 ATGACATTTT
17539464 GACATTTAAAAATC
1 GACATTTAAAAATC
17539478 GACATTTAAAAATC
1 GACATTTAAAAATC
17539492 AATAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
GACATTTAAAAATC
Found at i:17541799 original size:28 final size:28
Alignment explanation
Indices: 17541755--17541814 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
17541745 ATATTTATAT
*
17541755 TATATTATTTTAATATTTAATAA-TTTTA
1 TATATTATTTTAATATTGAA-AATTTTTA
*
17541783 TATATT-TTTTATCTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAATTTTTA
17541811 TATA
1 TATA
17541815 GTCATCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAATTTTTA
Found at i:17541812 original size:26 final size:27
Alignment explanation
Indices: 17541754--17541813 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
17541744 AATATTTATA
*
17541754 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
17541781 TATATATT-TTTTATCTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
17541808 TTATAT
1 TTATAT
17541814 AGTCATCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 5 0.17
27 12 0.41
28 12 0.41
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:17542221 original size:19 final size:19
Alignment explanation
Indices: 17542186--17542258 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
17542176 ATTCAATTTA
17542186 AAATAAA-TAT-TTA-ATT
1 AAATAAATTATATTAGATT
17542202 AAATAAATTATATTAGATT
1 AAATAAATTATATTAGATT
* * * * *
17542221 ATATGAATAATATTTTGTTTT
1 AAATAAATTATA-TTAG-ATT
17542242 AAATAAATTATA-TAGAT
1 AAATAAATTATATTAGAT
17542259 ATTTAATTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 7 0.17
17 3 0.07
18 4 0.10
19 14 0.33
20 3 0.07
21 11 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AAATAAATTATATTAGATT
Found at i:17542371 original size:23 final size:23
Alignment explanation
Indices: 17542336--17542382 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
17542326 TACACAATTT
17542336 ATCTATTTCATTTAACTTAAAGA
1 ATCTATTTCATTTAACTTAAAGA
* * *
17542359 ATCTTTTTTATTTAAGTTAAAGA
1 ATCTATTTCATTTAACTTAAAGA
17542382 A
1 A
17542383 ATTATCACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (23 bp):
ATCTATTTCATTTAACTTAAAGA
Found at i:17542510 original size:173 final size:168
Alignment explanation
Indices: 17542284--17542624 Score: 475
Period size: 173 Copynumber: 2.0 Consensus size: 168
17542274 AGAAATTTAA
*
17542284 AAAAAAAGATTAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
1 AAAAAAAGATAAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
* *
17542349 AACTTAAAGAATCTTTTTTATTTAAGTTAAAGAAATTATCACATTTAAAAAACAAGTATGTTTTT
66 AACATAAAGAA--TTTTTTATTTAACTTAAAGAAATTATCACA--TAAAAAA-AAGTATGTTTTT
17542414 CATATTAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
126 CATATTAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
* * * * * * * *
17542457 AAAAATAGATAAATATTTAATTAAATATATTAATTAATCTATTAGATAATTTATCTATTTGATTT
1 AAAAAAAGATAAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
* * *
17542522 AACATAAATAATTTTTTATTTAACTTAAAGAAATTATCACATATAAAAAAGTATTTTTTTCATAT
66 AACATAAAGAATTTTTTATTTAACTTAAAGAAATTATCACATAAAAAAAAGTATGTTTTTCATAT
* * * *
17542587 TAGATCAATTTTCTATTTAATAAAATTAATTTTTATTT
131 TAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
17542625 TCAGATTACT
Statistics
Matches: 150, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
168 50 0.33
169 6 0.04
171 29 0.19
173 65 0.43
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (168 bp):
AAAAAAAGATAAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
AACATAAAGAATTTTTTATTTAACTTAAAGAAATTATCACATAAAAAAAAGTATGTTTTTCATAT
TAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
Found at i:17542784 original size:19 final size:19
Alignment explanation
Indices: 17542756--17542797 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
17542746 AAAGTAGAAC
17542756 AAAAATAAATACAAA-ATTA
1 AAAAATAAAT-CAAATATTA
17542775 TAAAAA-AAATCAAATATTA
1 -AAAAATAAATCAAATATTA
17542794 AAAA
1 AAAA
17542798 TTTTACTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATAAATCAAATATTA
Done.