Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006678.1 Hibiscus syriacus cultivar Beakdansim tig00016563_pilon, whole genome shotgun sequence
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: 1086949
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 3 of 5
Found at i:430021 original size:21 final size:22
Alignment explanation
Indices: 429991--430159 Score: 151
Period size: 21 Copynumber: 8.0 Consensus size: 22
429981 GATTTACATA
*
429991 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATTAGTCCAAG
*
430012 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTAGTCCAAG
**
430035 TT--CGTTGCGA-TAGTTGAAG
1 TTCGCGTTGCGATTAGTCCAAG
* *
430054 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTAGTCCAAG
*
430077 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTAGTCCAAG
*
430098 TTCGCGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATTAGTCCAAG
*
430119 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTAGTCCAAG
430142 TT--CGTTGCGA-TAGTCCAA
1 TTCGCGTTGCGATTAGTCCAA
430160 AATCGCAACG
Statistics
Matches: 123, Mismatches: 15, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.12
21 74 0.60
23 34 0.28
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (22 bp):
TTCGCGTTGCGATTAGTCCAAG
Found at i:430055 original size:42 final size:42
Alignment explanation
Indices: 429997--430110 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
429987 CATATTCGCA
* *
429997 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTTCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
430039 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTTCAAGTTCGCGTTGCGATTTATTCCAAATTCG
430081 TTGCGATTTA-TTCCAAGTTCGCGTTGCGAT
1 TTGCGA--TAGTT-CAAGTTCGCGTTGCGAT
430111 AGTCGAAGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
42 45 0.69
43 2 0.03
44 18 0.28
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTTCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:430119 original size:65 final size:63
Alignment explanation
Indices: 430016--430152 Score: 238
Period size: 65 Copynumber: 2.1 Consensus size: 63
430006 TCCAAGTTCG
*
430016 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
430079 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
430144 CGTTGCGAT
1 CGTTGCGAT
430153 AGTCCAAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
63 21 0.30
65 49 0.70
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (63 bp):
CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:430911 original size:21 final size:21
Alignment explanation
Indices: 430887--430927 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
430877 CGTTGCGATT
430887 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
430908 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
430928 TATGTAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:430956 original size:41 final size:41
Alignment explanation
Indices: 430911--431031 Score: 140
Period size: 41 Copynumber: 3.0 Consensus size: 41
430901 TGCGAACTTG
*
430911 GACTATCGCAATGCGAATATGTA-A-A-TCGTAATGCGATAGCC
1 GACTATCGCAATGCG-AT-T-TACATATTCGCAATGCGATAGCC
* *
430952 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGCC
1 GACTATCGCAATGCGATTTACATATTCGCAATGCGATAGCC
* * *
430993 GACTATCGCATTACGATTTACATATTCGCATTGCGATAG
1 GACTATCGCAATGCGATTTACATATTCGCAATGCGATAG
431032 TCCAAGTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 3 0.04
41 66 0.90
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (41 bp):
GACTATCGCAATGCGATTTACATATTCGCAATGCGATAGCC
Found at i:430966 original size:21 final size:19
Alignment explanation
Indices: 430942--431070 Score: 73
Period size: 21 Copynumber: 6.3 Consensus size: 19
430932 TAAATCGTAA
430942 TGCGATAGCCGACTATCGCAT
1 TGCGATAGCC-A-TATCGCAT
***
430963 TGCGATTTACATATTCGCAT
1 TGCGATAGCCATA-TCGCAT
430983 TGCGATAGCCGACTATCGCAT
1 TGCGATAGCC-A-TATCGCAT
* ***
431004 TACGATTTACATATTCGCAT
1 TGCGATAGCCATA-TCGCAT
431024 TGCGATAGTCCA-AGTTCGCAT
1 TGCGATAG-CCATA--TCGCAT
431045 TGCGATAGTCCA-AGTTCGCAT
1 TGCGATAG-CCATA--TCGCAT
431066 TGCGA
1 TGCGA
431071 ATCTGGAAAC
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
19 4 0.05
20 27 0.31
21 55 0.62
22 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (19 bp):
TGCGATAGCCATATCGCAT
Found at i:430982 original size:20 final size:20
Alignment explanation
Indices: 430957--431029 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
430947 TAGCCGACTA
430957 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
***
430977 TCGCATTGCGATAGCCGACTA-
1 TCGCATTGCGATTTAC-A-TAT
*
430998 TCGCATTACGATTTACATAT
1 TCGCATTGCGATTTACATAT
431018 TCGCATTGCGAT
1 TCGCATTGCGAT
431030 AGTCCAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.60
21 13 0.31
22 2 0.05
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:431043 original size:41 final size:41
Alignment explanation
Indices: 430942--431050 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
430932 TAAATCGTAA
*
430942 TGCGATAGCCGACTATCGCATTGCGATTTACATATTCGCAT
1 TGCGATAGCCAACTATCGCATTGCGATTTACATATTCGCAT
* *
430983 TGCGATAGCCGACTATCGCATTACGATTTACATATTCGCAT
1 TGCGATAGCCAACTATCGCATTGCGATTTACATATTCGCAT
*
431024 TGCGATAGTCCAAGT-TCGCATTGCGAT
1 TGCGATAG-CCAACTATCGCATTGCGAT
431051 AGTCCAAGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 59 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (41 bp):
TGCGATAGCCAACTATCGCATTGCGATTTACATATTCGCAT
Found at i:432712 original size:14 final size:14
Alignment explanation
Indices: 432695--432727 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
432685 ATTTCTATGT
*
432695 AGGGAATTATTTGC
1 AGGGAATTATTTAC
432709 AGGGAATTATTTAC
1 AGGGAATTATTTAC
432723 AGGGA
1 AGGGA
432728 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:436231 original size:113 final size:112
Alignment explanation
Indices: 436081--436303 Score: 367
Period size: 113 Copynumber: 2.0 Consensus size: 112
436071 TTATTGTTCA
* * *
436081 TTTGTTTGGGGAAATTTGGTGACTTGGAGAATCAAGAAACAAGCTGTAGTTTCTAGAAGTAGTGC
1 TTTGTTTAGGGAAATTTGGTGACTTGGAGAATCAAGAAACAAGCTATAGTTTCCAGAAGTAGTGC
*
436146 AGAAGCAGAATATCGGGGCAATGGCACTTGGAATTTGTGAAGGCATCG
66 AGAAGCAGAATATC-GGGCAATGACACTTGGAATTTGTGAAGGCATCG
436194 TTTGTTTAGGGAAATTTGGTGACTTGGAGAAGT-AAGAAACAAGCTATAGTTTCCAGAAGTAGTG
1 TTTGTTTAGGGAAATTTGGTGACTTGGAGAA-TCAAGAAACAAGCTATAGTTTCCAGAAGTAGTG
* *
436258 CAGAAGCATAATATCGGGCAATGACATTTGGAATTTGTGAAGGCAT
65 CAGAAGCAGAATATCGGGCAATGACACTTGGAATTTGTGAAGGCAT
436304 TTGGTTACGA
Statistics
Matches: 103, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
112 29 0.28
113 73 0.71
114 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (112 bp):
TTTGTTTAGGGAAATTTGGTGACTTGGAGAATCAAGAAACAAGCTATAGTTTCCAGAAGTAGTGC
AGAAGCAGAATATCGGGCAATGACACTTGGAATTTGTGAAGGCATCG
Found at i:443260 original size:39 final size:39
Alignment explanation
Indices: 443214--443298 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
443204 TTTTAAAAAT
443214 AATTTAGAATGCTAAT-GT-AAAATAATTTAAGAAATTAAG
1 AATTTAGAATG-TAATAGTGAAAA-AATTTAAGAAATTAAG
* ** *
443253 AATTTAGAATGTTATAGTGGCAAAATTTAAGAAATTAGG
1 AATTTAGAATGTAATAGTGAAAAAATTTAAGAAATTAAG
443292 AATTTAG
1 AATTTAG
443299 GACTTAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 3 0.08
39 35 0.88
40 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.34
Consensus pattern (39 bp):
AATTTAGAATGTAATAGTGAAAAAATTTAAGAAATTAAG
Found at i:450620 original size:28 final size:28
Alignment explanation
Indices: 450582--450666 Score: 161
Period size: 28 Copynumber: 3.0 Consensus size: 28
450572 TACATACTTA
*
450582 TTAATAAAATGTATTTAAGTATAATCAC
1 TTAATAAAATGTATTCAAGTATAATCAC
450610 TTAATAAAATGTATTCAAGTATAATCAC
1 TTAATAAAATGTATTCAAGTATAATCAC
450638 TTAATAAAATGTATTCAAGTATAATCAC
1 TTAATAAAATGTATTCAAGTATAATCAC
450666 T
1 T
450667 CTTTCCCTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (28 bp):
TTAATAAAATGTATTCAAGTATAATCAC
Found at i:451672 original size:24 final size:24
Alignment explanation
Indices: 451644--451692 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
451634 ATGCTTTTGT
*
451644 GTCATGCAGGGGTGGATGTATGTG
1 GTCATGCAGGGGCGGATGTATGTG
451668 GTCATGCAGGGGCGGATGTATGTG
1 GTCATGCAGGGGCGGATGTATGTG
451692 G
1 G
451693 CTCCCTATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.10, G:0.47, T:0.27
Consensus pattern (24 bp):
GTCATGCAGGGGCGGATGTATGTG
Found at i:453603 original size:30 final size:31
Alignment explanation
Indices: 453567--453658 Score: 111
Period size: 30 Copynumber: 3.0 Consensus size: 31
453557 AAAAAATTTG
*
453567 AATACTTTAGATACCTATTTTGAT-TAAAAA
1 AATACTTTAGATACCTATTTTGATCCAAAAA
453597 AATACTTTA-AGTACCTATTTTGATCCAAAAA
1 AATACTTTAGA-TACCTATTTTGATCCAAAAA
*
453628 AATAACTTTAGGA-ACTTATTTTGA-CCAAAAA
1 AAT-ACTTTA-GATACCTATTTTGATCCAAAAA
453659 TTCCTTTAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
29 1 0.02
30 22 0.40
31 15 0.27
32 16 0.29
34 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (31 bp):
AATACTTTAGATACCTATTTTGATCCAAAAA
Found at i:460805 original size:14 final size:14
Alignment explanation
Indices: 460786--460812 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
460776 ATTTTTTAAA
460786 AATATTTTAATTTG
1 AATATTTTAATTTG
460800 AATATTTTAATTT
1 AATATTTTAATTT
460813 TTGGTCAAAA
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:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
AATATTTTAATTTG
Found at i:461884 original size:48 final size:48
Alignment explanation
Indices: 461810--461950 Score: 165
Period size: 48 Copynumber: 2.9 Consensus size: 48
461800 TTTATACAAC
* *
461810 AAAAAAATATAGCACTTAACATATACTTACACCGGTGTAAGTGAATAA
1 AAAAAAATATAGCACTTAACACATACTTACACCGGTGTAAGTAAATAA
* * * ** *
461858 AAAAAAGTGTAGTACTTAACACATACTTACACCTCTGTAATTAAATAAA
1 AAAAAAATATAGCACTTAACACATACTTACACCGGTGTAAGTAAAT-AA
* * *
461907 ATAAAAAATATAACACTTAACACATACTTACAACGGTATAAGTA
1 A-AAAAAATATAGCACTTAACACATACTTACACCGGTGTAAGTA
461951 TTTACATCTC
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
48 38 0.51
49 3 0.04
50 33 0.45
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (48 bp):
AAAAAAATATAGCACTTAACACATACTTACACCGGTGTAAGTAAATAA
Found at i:465152 original size:35 final size:35
Alignment explanation
Indices: 465101--465177 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
465091 TGTAACCAAT
465101 AAATAAGAGTTGGATTAGGACTCAAATACTAGTCTA
1 AAAT-AGAGTTGGATTAGGACTCAAATACTAGTCTA
*
465137 GAATAGAGTTGGATTAGGACTCAAATACTAGTCTA
1 AAATAGAGTTGGATTAGGACTCAAATACTAGTCTA
465172 AAATAG
1 AAATAG
465178 GATTTTTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 36 0.92
36 3 0.08
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (35 bp):
AAATAGAGTTGGATTAGGACTCAAATACTAGTCTA
Found at i:465707 original size:18 final size:18
Alignment explanation
Indices: 465657--465707 Score: 50
Period size: 23 Copynumber: 2.6 Consensus size: 18
465647 TATATTTCCA
465657 TTAT-TATTATTTTTTAT
1 TTATATATTATTTTTTAT
465674 TTCATTTATACTTTATTTTTTAT
1 TT-A--TATA--TTATTTTTTAT
465697 TTATATATTAT
1 TTATATATTAT
465708 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 11
0.72 0.00 0.28
Matches are distributed among these distances:
17 2 0.07
18 5 0.18
20 5 0.18
21 2 0.07
22 1 0.04
23 13 0.46
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATATTATTTTTTAT
Found at i:465783 original size:27 final size:27
Alignment explanation
Indices: 465753--465819 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
465743 TTATAATTTC
465753 TTTTATTTTTTTTAATTA-TTACTATTA
1 TTTTATTTTTTTTAA-TACTTACTATTA
*
465780 TTTT-TTTTATTTTAATACTTATTATTA
1 TTTTATTTT-TTTTAATACTTACTATTA
*
465807 TTATTATATTTTT
1 TT-TTATTTTTTT
465820 ATACATTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 6 0.18
27 20 0.59
28 5 0.15
29 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTATTTTTTTTAATACTTACTATTA
Found at i:465847 original size:2 final size:2
Alignment explanation
Indices: 465840--465874 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
465830 TATAAATTGT
465840 TA TA TA TA TA 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 TA TA TA TA TA T
465875 TCATATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:466030 original size:18 final size:17
Alignment explanation
Indices: 466005--466043 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
465995 TATGTGATTG
466005 TTTTTTTTTCATT-TAT
1 TTTTTTTTTCATTGTAT
*
466021 TTTTTATTTTCTTTGTAT
1 TTTTT-TTTTCATTGTAT
466039 TTTTT
1 TTTTT
466044 CTCATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 8 0.40
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTCATTGTAT
Found at i:474175 original size:48 final size:48
Alignment explanation
Indices: 474099--474192 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
474089 TCAAGATCAG
*
474099 TATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCAAA
1 TATGCCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCAAA
* * *
474147 TATGCCATACGAATCCATGGAGAAAATAACAGAACTCACATGTTCA
1 TATGCCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCA
474193 CTTCCATTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.21
Consensus pattern (48 bp):
TATGCCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCAAA
Found at i:474727 original size:21 final size:21
Alignment explanation
Indices: 474676--474719 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
474666 TCCTAATCCT
474676 ATACCACTGACTTATATATCG
1 ATACCACTGACTTATATATCG
*
474697 ATACCACTGACTTATATCTCG
1 ATACCACTGACTTATATATCG
474718 AT
1 AT
474720 CACTCTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (21 bp):
ATACCACTGACTTATATATCG
Found at i:475691 original size:5 final size:5
Alignment explanation
Indices: 475681--475715 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
475671 GTATACAAAA
475681 ATATT ATATT ATATT ATATT ATATT -TATT -TATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
475716 TGTTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
ATATT
Found at i:475701 original size:15 final size:14
Alignment explanation
Indices: 475681--475735 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
475671 GTATACAAAA
475681 ATATTATATTATATT
1 ATATTATATT-TATT
475696 ATATTATATTTATT
1 ATATTATATTTATT
475710 -TATTAT-TGTTATT
1 ATATTATAT-TTATT
475723 ATTATTAATATTT
1 A-TATT-ATATTT
475736 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 11 0.31
14 4 0.11
15 14 0.40
16 4 0.11
17 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATATTATATTTATT
Found at i:476250 original size:4 final size:4
Alignment explanation
Indices: 476243--476304 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
476233 TAAATATATA
* * * *
476243 TATT TATT TATC TATT TATT TATT T-TT TATT AATAT TATT ATATT AATA
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT -TATT TATT
*
476292 TATT TTTT TATT T
1 TATT TATT TATT T
476305 TTTTCTCATG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
3 3 0.07
4 35 0.78
5 7 0.16
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:480873 original size:3 final size:3
Alignment explanation
Indices: 480865--480940 Score: 86
Period size: 3 Copynumber: 26.0 Consensus size: 3
480855 TATTTTTATT
480865 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
** **
480908 TAA TAA TAA TAA TTT TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
480941 AAGTAAAACA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 6 0.10
3 52 0.85
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:483500 original size:387 final size:388
Alignment explanation
Indices: 482752--483527 Score: 1502
Period size: 387 Copynumber: 2.0 Consensus size: 388
482742 TTCATAGTAA
482752 TTTTGAATATGAAATCGAATTATTAATAGTATGTTTTATTGTATAATTCTAATGTATGTCAATGT
1 TTTTGAATATGAAATCGAATTATTAATAGTATGTTTTATTGTATAATTCTAATGTATGTCAATGT
482817 CGTTGTATGCATGTATGTACCATATCACCATACTTTATTTTAGGATTAAGTCCATTATATTTATG
66 CGTTGTATGCATGTATGTACCATATCACCATACTTTATTTTAGGATTAAGTCCATTATATTTATG
482882 TTTGTTTTTCTTTAATTAGTTGTTTAATTTTATGTGTATTTGAATTTAGTCATTATATTTATGTA
131 TTTGTTTTTCTTTAATTAGTTGTTTAATTTTATGTGTATTTGAATTTAGTCATTATATTTATGTA
482947 TATATATATATATACTTTTTTTTAATTTATAGTTTAGCATGCTATGATTTTGTTTTTATATTTTA
196 TATATATATATATACTTTTTTTTAATTTATAGTTTAGCATGCTATGATTTTGTTTTTATATTTTA
*
483012 GGTCACATGTATACATAATATGTTAATATGCATGGTTTATGATTTTTTTAGTTAAAATATGTGTA
261 GGTCACATGTATACATAATATGTTAATATGCATGGTTTAAGATTTTTTTAGTTAAAATATGTGTA
*
483077 TATGATTTTTTGTATGTCACGTTGAACGATTTTTTTT-AATTTTGTTTAATCAATTTTGACAT
326 TATGATTTTTTGTATGTCACGTTGAACGATTTTTTTTAAATTTTGTTTAATCAAATTTGACAT
483139 TTTTGAATATGAAATCGAATTATTAATAGTATGTTTTATTGTATAATTCTAATGTATGTCAATGT
1 TTTTGAATATGAAATCGAATTATTAATAGTATGTTTTATTGTATAATTCTAATGTATGTCAATGT
483204 CGTTGTATGCATGTATGTACCATATCACCATACTTTATTTTAGGATTAAGTCCATTATATTTATG
66 CGTTGTATGCATGTATGTACCATATCACCATACTTTATTTTAGGATTAAGTCCATTATATTTATG
483269 TTTGTTTTTCTTTAATTAGTTGTTTAATTTTATGTGTATTTGAATTTAGTCATTATATTTATGTA
131 TTTGTTTTTCTTTAATTAGTTGTTTAATTTTATGTGTATTTGAATTTAGTCATTATATTTATGTA
483334 TATATATATATACT-CTTTTTTTTAATTTATAGTTTAGCATGCTATGATTTTGTTTTTATATTTT
196 TATATATATATA-TACTTTTTTTTAATTTATAGTTTAGCATGCTATGATTTTGTTTTTATATTTT
483398 AGGTCACATGTATACATAATATGTTAATATGCATGGTTTAAGATTTTTTTTAGTTAAAATATGTG
260 AGGTCACATGTATACATAATATGTTAATATGCATGGTTTAAGA-TTTTTTTAGTTAAAATATGTG
483463 TATATGATTTTTTGTATGTCACGTTGAACGATTTTTTTTAAATTTTGTTTAATCAAATTTGACAT
324 TATATGATTTTTTGTATGTCACGTTGAACGATTTTTTTTAAATTTTGTTTAATCAAATTTGACAT
483528 GACATTTTTT
Statistics
Matches: 384, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
387 299 0.78
388 61 0.16
389 24 0.06
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (388 bp):
TTTTGAATATGAAATCGAATTATTAATAGTATGTTTTATTGTATAATTCTAATGTATGTCAATGT
CGTTGTATGCATGTATGTACCATATCACCATACTTTATTTTAGGATTAAGTCCATTATATTTATG
TTTGTTTTTCTTTAATTAGTTGTTTAATTTTATGTGTATTTGAATTTAGTCATTATATTTATGTA
TATATATATATATACTTTTTTTTAATTTATAGTTTAGCATGCTATGATTTTGTTTTTATATTTTA
GGTCACATGTATACATAATATGTTAATATGCATGGTTTAAGATTTTTTTAGTTAAAATATGTGTA
TATGATTTTTTGTATGTCACGTTGAACGATTTTTTTTAAATTTTGTTTAATCAAATTTGACAT
Found at i:485074 original size:46 final size:49
Alignment explanation
Indices: 484998--485098 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 49
484988 ATTTATTTTC
484998 ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTT
* *
485046 ATTTTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTT
1 ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTT
*
485093 CTTTTT
1 ATTTTT
485099 GTGGATAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
46 28 0.57
47 10 0.20
48 11 0.22
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.42
Consensus pattern (49 bp):
ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTT
Found at i:494663 original size:27 final size:27
Alignment explanation
Indices: 494633--494691 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
494623 AAATAATAAT
494633 AAAAAATG-AGAAAAAGAAAAAGGAG-
1 AAAAAATGAAGAAAAAGAAAAAGGAGA
* * *
494658 GAAAAATGAAAGAAAATGAAAAATGAGA
1 AAAAAATG-AAGAAAAAGAAAAAGGAGA
494686 AAAAAA
1 AAAAAA
494692 ATATAAAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.26
27 15 0.56
28 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (27 bp):
AAAAAATGAAGAAAAAGAAAAAGGAGA
Found at i:494745 original size:21 final size:21
Alignment explanation
Indices: 494703--494745 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
494693 TATAAAACGT
*
494703 ATGAAAAACAAAAAGAGAAAA
1 ATGAAAAACAAAAAGAAAAAA
*
494724 ATGAAAAA-AAAGAGAAATAAA
1 ATGAAAAACAAAAAGAAA-AAA
494745 A
1 A
494746 GGAGGGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (21 bp):
ATGAAAAACAAAAAGAAAAAA
Found at i:496124 original size:51 final size:51
Alignment explanation
Indices: 496063--496320 Score: 284
Period size: 51 Copynumber: 4.9 Consensus size: 51
496053 AAATTCGTTT
*
496063 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAACGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
496114 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* ** *
496165 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTC
* * ** *
496217 GTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCTGTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACAAGTTC
* * * *
496272 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGAGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
496321 CCGTTTTATT
Statistics
Matches: 184, Mismatches: 16, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
51 93 0.51
52 10 0.05
54 2 0.01
55 46 0.25
56 31 0.17
57 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:496295 original size:55 final size:56
Alignment explanation
Indices: 496073--496427 Score: 301
Period size: 55 Copynumber: 6.6 Consensus size: 56
496063 GTTGAAGATT
* * * ** **
496073 GAGTCCTATACTCTCTGAAGGAATAGGGAACGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
496124 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* *
496175 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
496231 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
496286 GAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * * *
496342 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TAAATATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
496397 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
496428 AGGCTCGTCA
Statistics
Matches: 265, Mismatches: 29, Indels: 16
0.85 0.09 0.05
Matches are distributed among these distances:
51 83 0.31
52 10 0.04
54 3 0.01
55 86 0.32
56 81 0.31
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (56 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:496326 original size:111 final size:107
Alignment explanation
Indices: 496064--496377 Score: 354
Period size: 111 Copynumber: 2.9 Consensus size: 107
496054 AATTCGTTTG
* ** *
496064 TTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGA-ACGGACAAG-TTCGTTGAAGA---TT
1 TTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGA-GGACCCGTTTTGTTGAAGATTGTT
* * *
496124 -GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
65 CGAGTTCTATACTCTCTGAACGAATAGGGAGCGGACAAGTTCA
*
496166 TTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 TTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTGTTGAAGATTGTTC
* * ** *
496231 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCTGTTTA
66 GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACAAGTTCA
* *
496273 TTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTATTGAAGATT
1 TTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTGTTGAAGATT
* * * *
496338 GTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACA
62 GTTCGAGTTC-TATACTCTCTGAACGAATAGGGAGCGGACA
496378 CATTTTATAA
Statistics
Matches: 178, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
102 42 0.24
103 10 0.06
106 2 0.01
107 41 0.23
110 4 0.02
111 79 0.44
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (107 bp):
TTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTGTTGAAGATTGTTC
GAGTTCTATACTCTCTGAACGAATAGGGAGCGGACAAGTTCA
Found at i:496398 original size:111 final size:111
Alignment explanation
Indices: 496175--496456 Score: 308
Period size: 111 Copynumber: 2.5 Consensus size: 111
496165 GTTGAAGATT
* * * *
496175 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTATTGAAGATTGTTCAAGTTCTAT
* * * * *
496240 ACTCCCTGAACGGATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
66 ACTCCCTGAACGAATAGAGAGCAGACCTGTTTATTAAAGATTGTTC
496286 GAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTATTGAAGATTGTTCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTATTGAAGATTGTTCAAGTTC-TA
* * *
496350 TACTCTCTGAATGAATAGAGAGCAGACACAT-TTTA-TAAATATTGTTC
65 TACTCCCTGAACGAATAGAGAGCAGAC-C-TGTTTATTAAAGATTGTTC
* * ** *
496397 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGCAGG-CTCGTCAT-TTGAAGATTTTTCAAGTT
1 GAGTTC-TATACTCT-CTGAAGGAATAGAGAG-AGGACCCGTTTTATTGAAGATTGTTCAAGTT
496457 TTATTTATCC
Statistics
Matches: 147, Mismatches: 17, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
110 20 0.14
111 118 0.80
112 8 0.05
113 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (111 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGAGGACCCGTTTTATTGAAGATTGTTCAAGTTCTAT
ACTCCCTGAACGAATAGAGAGCAGACCTGTTTATTAAAGATTGTTC
Found at i:505000 original size:16 final size:16
Alignment explanation
Indices: 504979--505009 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
504969 CAGTTTTTAG
504979 TGCATTATATATATAA
1 TGCATTATATATATAA
*
504995 TGCATTATCTATATA
1 TGCATTATATATATA
505010 TTGAGCGGAT
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:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (16 bp):
TGCATTATATATATAA
Found at i:508788 original size:21 final size:21
Alignment explanation
Indices: 508762--508801 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
508752 AGACAAGTAG
* *
508762 TACTCCACAGCAGGTGGAGCA
1 TACTCCAAAACAGGTGGAGCA
508783 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
508802 TTTCAGCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.25, G:0.28, T:0.15
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCA
Found at i:511293 original size:36 final size:36
Alignment explanation
Indices: 511252--511327 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
511242 ATTTTCGGGA
511252 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
511288 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
511324 TTTT
1 TTTT
511328 TTGCTATAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:520596 original size:21 final size:22
Alignment explanation
Indices: 520548--520598 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
520538 TTTTTTTTGG
*
520548 AATAAAAACAGTTAGATCTATTAA
1 AATAAAAACACTTAGA--TATTAA
*
520572 AATAAAAACACTTAGA-ATTAC
1 AATAAAAACACTTAGATATTAA
520593 AATAAA
1 AATAAA
520599 TATTTAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
24 15 0.60
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.25
Consensus pattern (22 bp):
AATAAAAACACTTAGATATTAA
Found at i:520999 original size:24 final size:24
Alignment explanation
Indices: 520946--521010 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
520936 ATTTAATATT
* *
520946 ATTTATGTCAATATTGTTATTTAAA
1 ATTTATGTCAATATTATTA-TGAAA
520971 A-TTATGTCAATATTATTA-GAATA
1 ATTTATGTCAATATTATTATGAA-A
*
520994 ATTTAT-TTAATATTATT
1 ATTTATGTCAATATTATT
521011 TATGTCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 12 0.34
24 20 0.57
25 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTATGTCAATATTATTATGAAA
Found at i:521099 original size:33 final size:32
Alignment explanation
Indices: 521046--521155 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 32
521036 TATATCCATA
*
521046 ATTTTA-T-AAATAAAAATATTATGATTATTAT
1 ATTTTATTAAAATAAAATTATTAT-ATTATTAT
521077 ATTTTATTAAAATAAAATTATTATA--ATT-T
1 ATTTTATTAAAATAAAATTATTATATTATTAT
* * *
521106 A-TTTATTAAAATTATATTAATATATTATTA-
1 ATTTTATTAAAATAAAATTATTATATTATTAT
521136 ATTATGTATTAAAAATAAAA
1 ATT-T-TATT-AAAATAAAA
521156 AATATTATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
28 20 0.31
29 2 0.03
30 7 0.11
31 7 0.11
32 3 0.05
33 18 0.28
34 7 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
ATTTTATTAAAATAAAATTATTATATTATTAT
Found at i:521111 original size:14 final size:15
Alignment explanation
Indices: 521072--521123 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
521062 TATTATGATT
521072 ATTATATTTTATTAAA
1 ATTATA-TTTATTAAA
* * *
521088 A-TAAAATTATTATA
1 ATTATATTTATTAAA
521102 ATT-TATTTATTAAA
1 ATTATATTTATTAAA
521116 ATTATATT
1 ATTATATT
521124 AATATATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
14 19 0.68
15 8 0.29
16 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTATATTTATTAAA
Found at i:521165 original size:33 final size:33
Alignment explanation
Indices: 521084--521165 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
521074 TATATTTTAT
* * *
521084 TAAAATAAAATTATTATAATTTATTTATTAAAAT
1 TAAAA-AATATTATTATAATTTATGTATTAAAAA
**
521118 TATATTAATA-TATTATTAA-TTATGTATTAAAAA
1 TA-AAAAATATTATTA-TAATTTATGTATTAAAAA
521151 TAAAAAATATTATTA
1 TAAAAAATATTATTA
521166 AAATATTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
32 5 0.13
33 24 0.63
34 8 0.21
35 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
TAAAAAATATTATTATAATTTATGTATTAAAAA
Found at i:521166 original size:19 final size:19
Alignment explanation
Indices: 521142--521202 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
521132 ATTAATTATG
521142 TATTAAAAATAAAAAATAT
1 TATTAAAAATAAAAAATAT
* *
521161 TATTAAAATATTAAAATTATAA
1 TATTAAAA-A-TAAAA-AATAT
521183 TATT-AAAAT-AAAAATAT
1 TATTAAAAATAAAAAATAT
521200 TAT
1 TAT
521203 ATTATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.17
18 3 0.09
19 9 0.26
20 2 0.06
21 8 0.23
22 7 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTAAAAATAAAAAATAT
Found at i:521166 original size:41 final size:40
Alignment explanation
Indices: 521112--521214 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 40
521102 ATTTATTTAT
* *
521112 TAAAATTA-TATTAATATATTATTAATTAT-GTATTAAAAA
1 TAAAAATATTATTAATATATTATTAATTATAATATT-AAAA
* *
521151 TAAAAAATATTATTAAAATATTA-AAATTATAATATTAAAA
1 T-AAAAATATTATTAATATATTATTAATTATAATATTAAAA
*
521191 TAAAAATATTA-TATTATATT-TTAA
1 TAAAAATATTATTAATATATTATTAA
521215 GGAGCATATA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
38 9 0.17
39 11 0.21
40 17 0.32
41 16 0.30
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (40 bp):
TAAAAATATTATTAATATATTATTAATTATAATATTAAAA
Found at i:521170 original size:11 final size:11
Alignment explanation
Indices: 521108--521173 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
521098 TATAATTTAT
521108 TTATTAAAAT-
1 TTATTAAAATA
*
521118 TATATTAATATA
1 T-TATTAAAATA
*
521130 TTATT-AATTA
1 TTATTAAAATA
521140 TGTATTAAAA-A
1 T-TATTAAAATA
*
521151 -TA-AAAAATA
1 TTATTAAAATA
521160 TTATTAAAATA
1 TTATTAAAATA
521171 TTA
1 TTA
521174 AAATTATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 7 0.16
11 26 0.60
12 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:521184 original size:14 final size:14
Alignment explanation
Indices: 521162--521201 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
521152 AAAAAATATT
521162 ATTAAAATATTAAA
1 ATTAAAATATTAAA
*
521176 ATTATAATATTAAA
1 ATTAAAATATTAAA
*
521190 ATAAAAATATTA
1 ATTAAAATATTA
521202 TATTATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTAAAATATTAAA
Found at i:521323 original size:29 final size:30
Alignment explanation
Indices: 521286--521348 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 30
521276 AATTTCATTA
521286 ATAATTATTATATATTATTAA-AATAAAATT
1 ATAATTATTATATATTA-TAATAATAAAATT
*
521316 ATAA-TATTATATATTATAATAATATAATT
1 ATAATTATTATATATTATAATAATAAAATT
521345 ATAA
1 ATAA
521349 CAATACAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 3 0.10
29 24 0.77
30 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATAATTATTATATATTATAATAATAAAATT
Found at i:521324 original size:8 final size:8
Alignment explanation
Indices: 521308--521372 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 8
521298 TATTATTAAA
*
521308 ATAAAATT
1 ATAATATT
521316 ATAATATT
1 ATAATATT
521324 AT-ATATT
1 ATAATATT
*
521331 ATAATAAT
1 ATAATATT
*
521339 ATAATTATA
1 ATAA-TATT
* *
521348 ACAATACAGT
1 ATAAT--ATT
521358 ATAATATT
1 ATAATATT
521366 ATAATAT
1 ATAATAT
521373 AAAATTATCA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
7 7 0.16
8 27 0.61
9 5 0.11
10 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (8 bp):
ATAATATT
Found at i:524571 original size:36 final size:36
Alignment explanation
Indices: 524531--524663 Score: 221
Period size: 36 Copynumber: 3.7 Consensus size: 36
524521 ATCCATTATT
524531 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
*
524567 AGCTTTGATACATTCGTGTATCAATATTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* *
524603 AGCTTTGGTACATTCATGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* *
524639 AGCTTTGGTAGATTCGTGTATCAAT
1 AGCTTTGATACATTCGTGTATCAAT
524664 ATCCAACACC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
AGCTTTGATACATTCGTGTATCAATGTTATCATATC
Found at i:527679 original size:2 final size:2
Alignment explanation
Indices: 527629--527664 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
527619 CCAAACATAA
* *
527629 AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
527665 TGCATTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:528080 original size:23 final size:23
Alignment explanation
Indices: 528044--528104 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
528034 CAACTCGTAT
528044 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * * *
528067 AATTGCACCTAAGTACCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
528090 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
528105 TCATATGAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:531385 original size:197 final size:197
Alignment explanation
Indices: 531050--531443 Score: 761
Period size: 197 Copynumber: 2.0 Consensus size: 197
531040 CGAAATGTAA
531050 GGGAGGCTTGACTTAGCGATGTGGGTCCTTTGATTTATTTTGTTGCTAATCAGCCCGATAGAGAG
1 GGGAGGCTTGACTTAGCGATGTGGGTCCTTTGATTTATTTTGTTGCTAATCAGCCCGATAGAGAG
* *
531115 GCACTCCCAAGTCGATCGGTAGCTTCAATGGTGGACGTAAATGGAGTTTGGCGCTGGGAGTTAAT
66 GCACTCCCAAGTCGATCAGTAGCTTCAATGGTGGACGTAAATGGAGTTTGGCGCGGGGAGTTAAT
531180 CATCCATCTATTACCGAGCAATATTATACAGAGGATGGTACCAACGATGCCCCTATGGCAGTGCA
131 CATCCATCTATTACCGAGCAATATTATACAGAGGATGGTACCAACGATGCCCCTATGGCAGTGCA
531245 TG
196 TG
*
531247 GGGAGGCTTGGCTTAGCGATGTGGGTCCTTTGATTTATTTTGTTGCTAATCAGCCCGATAGAGAG
1 GGGAGGCTTGACTTAGCGATGTGGGTCCTTTGATTTATTTTGTTGCTAATCAGCCCGATAGAGAG
531312 GCACTCCCAAGTCGATCAGTAGCTTCAATGGTGGACGTAAATGGAGTTTGGCGCGGGGAGTTAAT
66 GCACTCCCAAGTCGATCAGTAGCTTCAATGGTGGACGTAAATGGAGTTTGGCGCGGGGAGTTAAT
531377 CATCCATCTATTACCGAGCAATATTATACAGAGGATGGTACCAACGATGCCCCTATGGCAGTGCA
131 CATCCATCTATTACCGAGCAATATTATACAGAGGATGGTACCAACGATGCCCCTATGGCAGTGCA
531442 TG
196 TG
531444 AAGCTCGATG
Statistics
Matches: 194, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 194 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (197 bp):
GGGAGGCTTGACTTAGCGATGTGGGTCCTTTGATTTATTTTGTTGCTAATCAGCCCGATAGAGAG
GCACTCCCAAGTCGATCAGTAGCTTCAATGGTGGACGTAAATGGAGTTTGGCGCGGGGAGTTAAT
CATCCATCTATTACCGAGCAATATTATACAGAGGATGGTACCAACGATGCCCCTATGGCAGTGCA
TG
Found at i:534394 original size:26 final size:23
Alignment explanation
Indices: 534365--534418 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
534355 TATTTTAAAA
*
534365 TATTTATGTACTTTTTAGAATCATAT
1 TATTTATGTA--TTTTA-AATAATAT
*
534391 TATTTATTTATTTTAAATAATAT
1 TATTTATGTATTTTAAATAATAT
534414 TATTT
1 TATTT
534419 TTAAATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.46
24 5 0.19
26 9 0.35
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (23 bp):
TATTTATGTATTTTAAATAATAT
Found at i:534416 original size:19 final size:19
Alignment explanation
Indices: 534394--534446 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
534384 ATCATATTAT
534394 TTATTTATTTTAAATAATA
1 TTATTTATTTTAAATAATA
534413 TTA--T-TTTTAAAT--TA
1 TTATTTATTTTAAATAATA
534427 TCTATTTAATTTTAAATAAT
1 T-TATTT-ATTTTAAATAAT
534447 GTTGTACGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 8 0.30
17 2 0.07
19 11 0.41
21 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTTATTTTAAATAATA
Found at i:535078 original size:26 final size:26
Alignment explanation
Indices: 535044--535096 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
535034 CCTAATTTAT
** * *
535044 ATTAATGGTGTATTTTAATGTATGTC
1 ATTAATGGTACATTTCAATGGATGTC
*
535070 ATTAGTGGTACATTTCAATGGATGTC
1 ATTAATGGTACATTTCAATGGATGTC
535096 A
1 A
535097 CTCATTGACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (26 bp):
ATTAATGGTACATTTCAATGGATGTC
Found at i:557151 original size:29 final size:30
Alignment explanation
Indices: 557095--557152 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
557085 AAAATAGATT
**
557095 ATCAATAGAAAAATATGTGAAAACATATCA
1 ATCAATAGAAAAATATACGAAAACATATCA
557125 ATCAATAG-AAAATATAACGAAAA-ATATC
1 ATCAATAGAAAAATAT-ACGAAAACATATC
557153 TAAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.22
Consensus pattern (30 bp):
ATCAATAGAAAAATATACGAAAACATATCA
Found at i:558018 original size:17 final size:17
Alignment explanation
Indices: 557996--558052 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
557986 CGGGTCTGAT
557996 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
* *
558013 ATATATAAATATTATATATAT
1 ATATAT--AT-TTAAAT-TAA
558034 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
558051 AT
1 AT
558053 TAAATTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 10 0.31
18 5 0.16
19 4 0.12
20 5 0.16
21 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:560307 original size:15 final size:15
Alignment explanation
Indices: 560287--560341 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
560277 AGAGATAATG
560287 AAAGAAGAAAAAGAT
1 AAAGAAGAAAAAGAT
*
560302 AAAGAAGAAGAAA-TT
1 AAAGAAGAA-AAAGAT
*
560317 AGTAGAAGAAAAAGAT
1 A-AAGAAGAAAAAGAT
*
560333 ACAGAAGAA
1 AAAGAAGAA
560342 GACAGAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.67, C:0.02, G:0.22, T:0.09
Consensus pattern (15 bp):
AAAGAAGAAAAAGAT
Found at i:560314 original size:25 final size:25
Alignment explanation
Indices: 560286--560363 Score: 68
Period size: 31 Copynumber: 2.9 Consensus size: 25
560276 GAGAGATAAT
560286 GAAAGAAGAAAAAGATAAAGAAGAA
1 GAAAGAAGAAAAAGATAAAGAAGAA
*
560311 GAAATTAGTAGAAGAAAAAGATACAGAAGAA
1 G--A--A--AGAAGAAAAAGATAAAGAAGAA
*
560342 GACAGAAGAAAAAAGA-AAAGAA
1 GAAAGAAG-AAAAAGATAAAGAA
560364 AATAAAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
25 11 0.26
26 7 0.16
27 1 0.02
29 2 0.05
31 22 0.51
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.06
Consensus pattern (25 bp):
GAAAGAAGAAAAAGATAAAGAAGAA
Found at i:561363 original size:20 final size:20
Alignment explanation
Indices: 561331--561374 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
561321 TAAACTTTTG
561331 AAAA-TTATAAAATAATTAT
1 AAAATTTATAAAATAATTAT
* *
561350 TAAATTTATTAAATAATTAT
1 AAAATTTATAAAATAATTAT
561370 AAAAT
1 AAAAT
561375 AATCATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTATAAAATAATTAT
Found at i:561368 original size:31 final size:30
Alignment explanation
Indices: 561333--561400 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 30
561323 AACTTTTGAA
*
561333 AATTATAAAATAATTATTAAATTTATTAAAT
1 AATTATAAAATAATCATTAAATTTA-TAAAT
*
561364 AATTATAAAATAATCATTAAATTTATAATT
1 AATTATAAAATAATCATTAAATTTATAAAT
561394 AATTATA
1 AATTATA
561401 GTATTGACGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AATTATAAAATAATCATTAAATTTATAAAT
Found at i:561385 original size:11 final size:11
Alignment explanation
Indices: 561333--561385 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
561323 AACTTTTGAA
*
561333 AATTATAAAAT
1 AATTATTAAAT
561344 AATTATTAAAT
1 AATTATTAAAT
561355 --TTATTAAAT
1 AATTATTAAAT
*
561364 AATTATAAAAT
1 AATTATTAAAT
*
561375 AATCATTAAAT
1 AATTATTAAAT
561386 TTATAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 9 0.25
11 27 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTATTAAAT
Found at i:561755 original size:22 final size:23
Alignment explanation
Indices: 561710--561767 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
561700 TTAGTTGGCA
*
561710 GATATTTAGTTA-GTTAAGCTGTT
1 GATAATTAGTTAGGTT-AGCTGTT
561733 GATAATTAGTTAGGTT-GCTGTT
1 GATAATTAGTTAGGTTAGCTGTT
* *
561755 GTTAATAAGTTAG
1 GATAATTAGTTAG
561768 TTTGTTAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.55
23 11 0.35
24 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.24, T:0.45
Consensus pattern (23 bp):
GATAATTAGTTAGGTTAGCTGTT
Found at i:568403 original size:6 final size:6
Alignment explanation
Indices: 568392--568451 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
568382 TGGCACCAGC
* * *
568392 GATGGG GATGGG GATGGG AATGGG AATGGG GATGGG CATGGG GATGGG
1 GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG GATGGG
*
568440 GATGGG CATGGG
1 GATGGG GATGGG
568452 TGTGATGGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.20, C:0.03, G:0.60, T:0.17
Consensus pattern (6 bp):
GATGGG
Found at i:568414 original size:18 final size:18
Alignment explanation
Indices: 568393--568451 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
568383 GGCACCAGCG
*
568393 ATGGGGATGGGGATGGGA
1 ATGGGGATGGGGATGGGC
*
568411 ATGGGAATGGGGATGGGC
1 ATGGGGATGGGGATGGGC
568429 ATGGGGATGGGGATGGGC
1 ATGGGGATGGGGATGGGC
568447 ATGGG
1 ATGGG
568452 TGTGATGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.20, C:0.03, G:0.59, T:0.17
Consensus pattern (18 bp):
ATGGGGATGGGGATGGGC
Found at i:574567 original size:19 final size:19
Alignment explanation
Indices: 574545--574586 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
574535 GTGGTTTACG
574545 GTTTTTT-TCCGTTGTTTAT
1 GTTTTTTAT-CGTTGTTTAT
*
574564 GTTTTTTATCGTTGTTTTT
1 GTTTTTTATCGTTGTTTAT
574583 GTTT
1 GTTT
574587 ATCTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.71
Consensus pattern (19 bp):
GTTTTTTATCGTTGTTTAT
Found at i:580039 original size:20 final size:20
Alignment explanation
Indices: 580014--580058 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
580004 ATATTGGTAC
580014 CGATACTGACCT-TTCAGTAT
1 CGATACTGACCTCTT-AGTAT
580034 CGATACTGACCTCTTAGTAT
1 CGATACTGACCTCTTAGTAT
*
580054 AGATA
1 CGATA
580059 TTTTTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (20 bp):
CGATACTGACCTCTTAGTAT
Found at i:581277 original size:29 final size:31
Alignment explanation
Indices: 581229--581297 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
581219 ATTACAGTTC
*
581229 ATAAAATAATTAGTATTTA-TT-AATATTAT
1 ATAAAATAATTAATATTTATTTAAATATTAT
*
581258 ATCAAATAA-TAATATATTATTTAAATATTAT
1 ATAAAATAATTAATAT-TTATTTAAATATTAT
*
581289 GTAAAATAA
1 ATAAAATAA
581298 GTTATAGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.15
29 11 0.33
30 2 0.06
31 15 0.45
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (31 bp):
ATAAAATAATTAATATTTATTTAAATATTAT
Found at i:581695 original size:139 final size:139
Alignment explanation
Indices: 581445--581723 Score: 558
Period size: 139 Copynumber: 2.0 Consensus size: 139
581435 CCCACTGTTA
581445 AAAACTTAACAGTGCTTTAAACTTCTCACCATAAGTTAATATCACTTCATCATTGTAAAGATAAA
1 AAAACTTAACAGTGCTTTAAACTTCTCACCATAAGTTAATATCACTTCATCATTGTAAAGATAAA
581510 AAATGTCACGTCAACAACTCTGTTAATTTTTTAACGGTATGATACCAAATTGAAACTTAAACTAA
66 AAATGTCACGTCAACAACTCTGTTAATTTTTTAACGGTATGATACCAAATTGAAACTTAAACTAA
581575 ACATTAGGT
131 ACATTAGGT
581584 AAAACTTAACAGTGCTTTAAACTTCTCACCATAAGTTAATATCACTTCATCATTGTAAAGATAAA
1 AAAACTTAACAGTGCTTTAAACTTCTCACCATAAGTTAATATCACTTCATCATTGTAAAGATAAA
581649 AAATGTCACGTCAACAACTCTGTTAATTTTTTAACGGTATGATACCAAATTGAAACTTAAACTAA
66 AAATGTCACGTCAACAACTCTGTTAATTTTTTAACGGTATGATACCAAATTGAAACTTAAACTAA
581714 ACATTAGGT
131 ACATTAGGT
581723 A
1 A
581724 TGGTTTTGAA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (139 bp):
AAAACTTAACAGTGCTTTAAACTTCTCACCATAAGTTAATATCACTTCATCATTGTAAAGATAAA
AAATGTCACGTCAACAACTCTGTTAATTTTTTAACGGTATGATACCAAATTGAAACTTAAACTAA
ACATTAGGT
Found at i:582035 original size:17 final size:17
Alignment explanation
Indices: 582013--582054 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
582003 TTTGATAATT
582013 TTTAAAAATAATTTAAA
1 TTTAAAAATAATTTAAA
* **
582030 TTTAAAAATATTTTCTA
1 TTTAAAAATAATTTAAA
582047 TTTAAAAA
1 TTTAAAAA
582055 GCCCAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAAAATAATTTAAA
Found at i:582869 original size:29 final size:29
Alignment explanation
Indices: 582818--582875 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
582808 TTAGATTTAG
* *
582818 GATTTTTCAAAATTTA-GTTTTTTTAAAA
1 GATTTTTCAAAATTTAGGGTTTTCTAAAA
*
582846 GATTTTTGAAAACTTTAGGGTTTTCTAAAA
1 GATTTTTCAAAA-TTTAGGGTTTTCTAAAA
582876 ATATAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.44
29 4 0.16
30 10 0.40
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (29 bp):
GATTTTTCAAAATTTAGGGTTTTCTAAAA
Found at i:591336 original size:16 final size:16
Alignment explanation
Indices: 591315--591345 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
591305 ACTATTCAAA
591315 TGAATAGTAAATTTTG
1 TGAATAGTAAATTTTG
591331 TGAATAGTAAATTTT
1 TGAATAGTAAATTTT
591346 TTTTCGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
TGAATAGTAAATTTTG
Found at i:598432 original size:552 final size:552
Alignment explanation
Indices: 597389--599045 Score: 3260
Period size: 552 Copynumber: 3.0 Consensus size: 552
597379 GCAGCTAACG
* *
597389 AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAAAATGGATGATGCACACAATCAGGGGATT
1 AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAGAATGGATGATGCACACTATCAGGGGATT
597454 GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
66 GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
** *
597519 AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCTCCAGCTGATGCTTGATTCTAATAGCCATTGGTA
131 AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCAACAACTGATGCTTGATTCTAATAGCCATTGGTA
597584 CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
196 CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
597649 TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
261 TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
597714 AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
326 AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
597779 AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
391 AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
597844 GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
456 GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
597909 ATTTGCCTTGAGCCTTTTTTTTCTATTATCAA
521 ATTTGCCTTGAGCCTTTTTTTTCTATTATCAA
597941 AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAGAATGGATGATGCACACTATCAGGGGATT
1 AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAGAATGGATGATGCACACTATCAGGGGATT
598006 GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
66 GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
598071 AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCAACAACTGATGCTTGATTCTAATAGCCATTGGTA
131 AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCAACAACTGATGCTTGATTCTAATAGCCATTGGTA
598136 CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
196 CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
598201 TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
261 TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
598266 AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
326 AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
598331 AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
391 AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
598396 GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
456 GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
598461 ATTTGCCTTGAGCCTTTTTTTTCTATTATCAA
521 ATTTGCCTTGAGCCTTTTTTTTCTATTATCAA
598493 AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAGAATGGATGATGCACACTATCAGGGGATT
1 AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAGAATGGATGATGCACACTATCAGGGGATT
598558 GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
66 GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
598623 AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCAACAACTGATGCTTGATTCTAATAGCCATTGGTA
131 AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCAACAACTGATGCTTGATTCTAATAGCCATTGGTA
598688 CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
196 CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
598753 TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
261 TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
598818 AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
326 AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
598883 AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
391 AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
598948 GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
456 GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
*
599013 ATTTGCCTTAAGCCTTTTTTTTCTATTATCAA
521 ATTTGCCTTGAGCCTTTTTTTTCTATTATCAA
599045 A
1 A
599046 TTATACATAG
Statistics
Matches: 1099, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
552 1099 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (552 bp):
AGGGGGTTGAAACTAGGGGTTGAACTCAATGCACCAGAATGGATGATGCACACTATCAGGGGATT
GGTGTGTTGGTGGGTACTGATTCTTGGTGTGCAACTCATGAGGGTTTCTTGGTTTGCTGTTTTTA
AGGCTCGAGCTCGTCGACAGCAGTCTTCCGCAACAACTGATGCTTGATTCTAATAGCCATTGGTA
CGTAAACCGAAATAATAGAGTTATATATCTTGATATAAGCAAAAATCTACTAAAACGTCTACATT
TTGTTTTATAAGCAGTCAACATACATGTAAGAAAAGTTGTTTTACAGTTACATGAATAGCTTTAT
AGAAATGCTACTTGTTTTGAATGATAAAAGTAGGTATGCTATATGCTTGAATGTTTTGTGGCTCA
AAGTGTTTAGCTTCCCGGATGACGGGTAAGAAGCAACTATTGTCCATCTCTTACCCTGCATGATA
GTAGTGTTGGTTCCTGTGCATTCCAATTGCTTTGGGTATTTGTGTTTTTGATAGGTTAAGATGAG
ATTTGCCTTGAGCCTTTTTTTTCTATTATCAA
Found at i:609117 original size:69 final size:69
Alignment explanation
Indices: 609006--609143 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
608996 TTATTTTGCC
609006 CTTTAGAATTTTAGTTCACCCCTTAAGTTTAAGTTTGCCCCTCTAACATAAAATCATGTATCCGT
1 CTTTAGAATTTTAGTTCACCCCTTAAGTTTAAGTTTGCCCCTCTAACATAAAATCATGTATCCGT
609071 CCCT
66 CCCT
609075 CTTTAGAATTTTAGTTCACCCCTTAAGTTTAAGTTTGCCCCTCTAACATAAAATCATGTATCCGT
1 CTTTAGAATTTTAGTTCACCCCTTAAGTTTAAGTTTGCCCCTCTAACATAAAATCATGTATCCGT
609140 CCCT
66 CCCT
609144 GGGTAGAGCT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (69 bp):
CTTTAGAATTTTAGTTCACCCCTTAAGTTTAAGTTTGCCCCTCTAACATAAAATCATGTATCCGT
CCCT
Found at i:613994 original size:3 final size:3
Alignment explanation
Indices: 613988--614042 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
613978 ACACATAAAC
* * *
613988 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA AT- ATA TTA A-A ATT A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
614033 ATA ATA ATA A
1 ATA ATA ATA A
614043 AAAAGACCCG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:633735 original size:36 final size:36
Alignment explanation
Indices: 633695--633863 Score: 221
Period size: 36 Copynumber: 4.7 Consensus size: 36
633685 AAAGTATTGG
*
633695 CACTTTCGATTCAAGTCGAACGGAATAAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAATAAAGCATCGA
* * ** *
633731 CACTTCCGATTCAAGTCAAATGGAAGGAGGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAATAAAGCATCGA
* * *
633767 CACTTCCGATTCAAGTCGAACGGAATGAGGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAATAAAGCATCGA
* * *
633803 TACTTCCGATTCAAGTCGAACAGAAAAAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAATAAAGCATCGA
*
633839 CACTTCCGATTCAAGTCGAATGGAA
1 CACTTCCGATTCAAGTCGAACGGAA
633864 AGATGTATCG
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 114 1.00
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAATAAAGCATCGA
Found at i:653201 original size:2 final size:2
Alignment explanation
Indices: 653194--653219 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
653184 TCTTGGAATT
653194 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
653220 GGGTTAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:653293 original size:2 final size:2
Alignment explanation
Indices: 653282--653323 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
653272 TTTATAATCT
653282 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
653323 T
1 T
653324 GATAAGCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:653930 original size:15 final size:15
Alignment explanation
Indices: 653910--653945 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
653900 TGAGACATTA
* *
653910 CCCGCCCCGCATCCT
1 CCCGCCCCACATCCG
653925 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
653940 CCCGCC
1 CCCGCC
653946 TAGCTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.69, G:0.14, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:654856 original size:9 final size:9
Alignment explanation
Indices: 654842--654901 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
654832 AGGGCTGGAA
654842 ACCGGTTTG
1 ACCGGTTTG
*
654851 ACCGGTTCG
1 ACCGGTTTG
654860 AACCGGTTTCG
1 -ACCGGTTT-G
*
654871 ACCGGTATG
1 ACCGGTTTG
654880 AACCGGTTTG
1 -ACCGGTTTG
*
654890 ACCGGTCTG
1 ACCGGTTTG
654899 ACC
1 ACC
654902 CGACCCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 20 0.47
10 22 0.51
11 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:654875 original size:20 final size:19
Alignment explanation
Indices: 654841--654895 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
654831 GAGGGCTGGA
654841 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTAT-G
654860 AACCGGTTTCGACCGGTATG
1 AACCGGTTT-GACCGGTATG
654880 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
654896 CTGACCCGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.47
20 17 0.50
21 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTATG
Found at i:654913 original size:14 final size:14
Alignment explanation
Indices: 654896--654924 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
654886 TTTGACCGGT
654896 CTGACCCGACCCGA
1 CTGACCCGACCCGA
654910 CTGACCCGACCCGA
1 CTGACCCGACCCGA
654924 C
1 C
654925 CGTTGACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:661216 original size:20 final size:20
Alignment explanation
Indices: 661177--661235 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
661167 GAGGACTGGA
*
661177 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACC-GATTTC
661197 AACCGGTTCTGACCGATTTC
1 AACCGGTTCTGACCGATTTC
* *
661217 GATCGGTTC-GAACCGATTT
1 AACCGGTTCTG-ACCGATTT
661236 GACCGATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.82
21 5 0.15
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (20 bp):
AACCGGTTCTGACCGATTTC
Found at i:668399 original size:31 final size:31
Alignment explanation
Indices: 668361--668421 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
668351 AAAACACAAT
*
668361 ATATGATCACTTTTGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAG
668392 ATATGATCACTTTCGTTTTTATTTAATTAA
1 ATATGATCACTTTCGTTTTTATTTAATTAA
668422 AATGTGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAG
Found at i:682872 original size:18 final size:17
Alignment explanation
Indices: 682849--682893 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
682839 CAACATTCCA
*
682849 GTAATCTTATTCCTGCCG
1 GTAATCTTATTCC-ACCG
* *
682867 GTAATCATATTCCACTG
1 GTAATCTTATTCCACCG
682884 GTAATCTTAT
1 GTAATCTTAT
682894 ATTCCGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.40
Consensus pattern (17 bp):
GTAATCTTATTCCACCG
Found at i:686780 original size:24 final size:23
Alignment explanation
Indices: 686753--686797 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
686743 TTCGATCGTC
686753 GATTAAATTAAATTATTCTTAATT
1 GATTAAATTAAA-TATTCTTAATT
* *
686777 GATTTAATTAAATATTTTTAA
1 GATTAAATTAAATATTCTTAA
686798 CTGTTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
GATTAAATTAAATATTCTTAATT
Found at i:690000 original size:12 final size:12
Alignment explanation
Indices: 689983--690010 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
689973 GATTAACTCC
689983 CTCTCTCTCGCT
1 CTCTCTCTCGCT
689995 CTCTCTCTCGCT
1 CTCTCTCTCGCT
690007 CTCT
1 CTCT
690011 GCCTTTCAGG
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:0.00, C:0.50, G:0.07, T:0.43
Consensus pattern (12 bp):
CTCTCTCTCGCT
Found at i:692549 original size:29 final size:29
Alignment explanation
Indices: 692507--692564 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
692497 ACCTGTCCTG
*
692507 ATACTTCCTTTTCCTGAATTTAAGAATTT
1 ATACTTCCGTTTCCTGAATTTAAGAATTT
692536 ATACTTCCGTTTCCTGAATTTAAGAATTT
1 ATACTTCCGTTTCCTGAATTTAAGAATTT
692565 TCTTCTGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (29 bp):
ATACTTCCGTTTCCTGAATTTAAGAATTT
Found at i:695104 original size:4 final size:4
Alignment explanation
Indices: 695095--695121 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
695085 CAAGAACCCC
695095 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
695122 TCATTTTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:700629 original size:102 final size:98
Alignment explanation
Indices: 700488--700682 Score: 300
Period size: 102 Copynumber: 1.9 Consensus size: 98
700478 TCATGTTTAC
***
700488 ACTAAAATCCCGACTACGTCCCTGGGTCAATGGACGTGGACTTTCTTTTCTTGATATTAAATTTA
1 ACTAAAATCCCGACTACGTCCCTACATCAATGGACGTGGACTTTCTTTT-TT-ATATTAAATTTA
700553 CAAATCTCCAAGTTCTCATCTATCAAAACTCCTTTGA
64 CAAATCTCCAAGTT-TCATCTA-CAAAACTCCTTTGA
* * *
700590 ACTAAAATCCTGACTCCGTCCCTACATTAATGGACGTGGACTTTCTTTTTTATATTAAATTTACA
1 ACTAAAATCCCGACTACGTCCCTACATCAATGGACGTGGACTTTCTTTTTTATATTAAATTTACA
700655 AATCTCCAAGTTTCATCTACAAAACTCC
66 AATCTCCAAGTTTCATCTACAAAACTCC
700683 AAAAATATTA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
98 9 0.10
99 7 0.08
100 26 0.30
101 2 0.02
102 43 0.49
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (98 bp):
ACTAAAATCCCGACTACGTCCCTACATCAATGGACGTGGACTTTCTTTTTTATATTAAATTTACA
AATCTCCAAGTTTCATCTACAAAACTCCTTTGA
Found at i:704413 original size:77 final size:78
Alignment explanation
Indices: 704195--704434 Score: 224
Period size: 77 Copynumber: 3.1 Consensus size: 78
704185 TAAATGTATA
* * * * *
704195 TAATAAATTGTGTTGTGTCCAAGAATGTCATGGTTCA-TTAAAAA-AAGTTTGCGATCTGGAATG
1 TAATAAAATGGGTTGTGTCCAATAATGTCATGGTTCACTAAAAAATAAGATTGCGATCTGGAATG
*
704258 TTAATATATATTTCT
66 TTAATAT-T-TTTAT
* ** * * * * *
704273 CTAAATAAGATGGGTTGAATCCAATAATGTCATGGTTCACTAAGAAATAGGATAG-AATTTGGAA
1 -T-AATAAAATGGGTTGTGTCCAATAATGTCATGGTTCACTAAAAAATAAGATTGCGATCTGGAA
*
704337 CGTTAATATTTTTAT
64 TGTTAATATTTTTAT
* *
704352 TAATAAAATGGGTTGTGCCCAATAATATCATGGTTCACTAAAAATATAAG-TTGCGA-CTGGAAT
1 TAATAAAATGGGTTGTGTCCAATAATGTCATGGTTCACTAAAAA-ATAAGATTGCGATCTGGAAT
*
704415 GTTAA-AATTTTAT
65 GTTAATATTTTTAT
704428 T-ATAAAA
1 TAATAAAA
704435 AAATTCGAAA
Statistics
Matches: 129, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
75 6 0.05
76 8 0.06
77 49 0.38
78 6 0.05
79 5 0.04
80 31 0.24
81 20 0.16
82 4 0.03
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (78 bp):
TAATAAAATGGGTTGTGTCCAATAATGTCATGGTTCACTAAAAAATAAGATTGCGATCTGGAATG
TTAATATTTTTAT
Found at i:704449 original size:18 final size:18
Alignment explanation
Indices: 704426--704462 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
704416 TTAAAATTTT
*
704426 ATTATAAAAAAATTCGAA
1 ATTATAAAAAAAATCGAA
704444 ATTATAAAAAAAATCGAA
1 ATTATAAAAAAAATCGAA
704462 A
1 A
704463 GCATGTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (18 bp):
ATTATAAAAAAAATCGAA
Found at i:705258 original size:77 final size:77
Alignment explanation
Indices: 704970--705261 Score: 291
Period size: 77 Copynumber: 3.8 Consensus size: 77
704960 ACTTTTGAAT
* ** * ** * * * *
704970 TTTTA-TAATAAAAATTTTAACATTTTAGGTCGCAACTTATTTTTTAGTGAACCAAT-ACATTCT
1 TTTTATTAATAAAAATATTAACATTCCAGATCATAACATATTTCTTAATGAACC-ATGATATTCT
* *
705033 TGGGCATAACTCA
65 TGGGCACAACACA
* * * *
705046 TTTTATTAATAAAAATATTAACATTTCAGATCATAACATATTTCTTAGTAAACCATGACATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCATAACATATTTCTTAATGAACCATGATATTCTT
* *
705111 GGGCTCAACATA
66 GGGCACAACACA
* * * *
705123 TTTTATTAATAAAAATATTAACATTCAAGATCATAACCTATATCTTAATGAACTATGATATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCATAACATATTTCTTAATGAACCATGATATTCTT
* *
705188 GGACACAACCCA
66 GGGCACAACACA
* * ** * *
705200 TTTTATTAATAAAAGTATTAACATTCCATATCGCATCATATTTCTTATTGAACCATGATATT
1 TTTTATTAATAAAAATATTAACATTCCAGATCATAACATATTTCTTAATGAACCATGATATT
705262 TTTAGACGTA
Statistics
Matches: 180, Mismatches: 34, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
76 7 0.04
77 173 0.96
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCATAACATATTTCTTAATGAACCATGATATTCTT
GGGCACAACACA
Found at i:709091 original size:23 final size:23
Alignment explanation
Indices: 709059--709107 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
709049 AATTTGGTTC
*
709059 GTTTAGTTTGTGTTCATTCGTTT
1 GTTTAATTTGTGTTCATTCGTTT
709082 GTTTAATTTGTGTTCATTCGTTT
1 GTTTAATTTGTGTTCATTCGTTT
709105 GTT
1 GTT
709108 CGGTTAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.08, G:0.20, T:0.61
Consensus pattern (23 bp):
GTTTAATTTGTGTTCATTCGTTT
Found at i:709119 original size:17 final size:17
Alignment explanation
Indices: 709097--709131 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
709087 ATTTGTGTTC
709097 ATTCGTTTGTTCGGTTA
1 ATTCGTTTGTTCGGTTA
709114 ATTCGTTTGTTCGGTTA
1 ATTCGTTTGTTCGGTTA
709131 A
1 A
709132 AATTAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.51
Consensus pattern (17 bp):
ATTCGTTTGTTCGGTTA
Found at i:729228 original size:21 final size:21
Alignment explanation
Indices: 729188--729241 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
729178 ACCGTGATTG
* *
729188 CGGCCGTCGCGGGCGTTATTA
1 CGGCCGTCGCGGACGCTATTA
* *
729209 CGGCTGTCGCGGACGCTATTG
1 CGGCCGTCGCGGACGCTATTA
*
729230 CGGCCATCGCGG
1 CGGCCGTCGCGG
729242 GTAACTTGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.09, C:0.31, G:0.39, T:0.20
Consensus pattern (21 bp):
CGGCCGTCGCGGACGCTATTA
Found at i:729986 original size:24 final size:25
Alignment explanation
Indices: 729935--729995 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
729925 TTTAAATTAG
* * *
729935 AAATATAAAATTATTCAAATATTCA
1 AAATATAAAATTATACAAATACTAA
*
729960 AAATATTAAA-TATACAAATACTAA
1 AAATATAAAATTATACAAATACTAA
729984 AAATA-AAAATTA
1 AAATATAAAATTA
729996 AATTATTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.10
24 18 0.60
25 9 0.30
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATATAAAATTATACAAATACTAA
Found at i:730380 original size:25 final size:23
Alignment explanation
Indices: 730352--730409 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
730342 AAACATTGTT
730352 TCGACTAATCCAAATTTTGTAAGTC
1 TCGACTAATCCAAA-TTT-TAAGTC
*
730377 TCGACTAAAT-TAAATTTTAAGTC
1 TCGACT-AATCCAAATTTTAAGTC
*
730400 TCGATTAATC
1 TCGACTAATC
730410 TAGTAAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 3 0.10
23 11 0.38
24 3 0.10
25 9 0.31
26 3 0.10
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
TCGACTAATCCAAATTTTAAGTC
Found at i:737675 original size:36 final size:37
Alignment explanation
Indices: 737622--737693 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 37
737612 GAGATAAAGA
* *
737622 TGGATATTTTCCATGGTTATGTTCAAATGGTACAAGG
1 TGGATATTTCCCATGGTTAAGTTCAAATGGTACAAGG
737659 TGGATA-TTCCCATGGTTAAGTTCAAATGGTACAAG
1 TGGATATTTCCCATGGTTAAGTTCAAATGGTACAAG
737694 AAGGGAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 27 0.82
37 6 0.18
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (37 bp):
TGGATATTTCCCATGGTTAAGTTCAAATGGTACAAGG
Found at i:739297 original size:14 final size:14
Alignment explanation
Indices: 739274--739334 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 14
739264 TTAACTTAAA
*
739274 TTTAACTTAAAATT
1 TTTAATTTAAAATT
*
739288 TTTAATTT-AATTAT
1 TTTAATTTAAAAT-T
739302 TTTAATTTAAACATT
1 TTTAATTTAAA-ATT
739317 TGTTAATTTCAAAATT
1 T-TTAATTT-AAAATT
739333 TT
1 TT
739335 GATCCAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.08
14 16 0.41
15 5 0.13
16 12 0.31
17 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (14 bp):
TTTAATTTAAAATT
Found at i:743455 original size:52 final size:52
Alignment explanation
Indices: 743391--743489 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
743381 TAATAAAATG
*
743391 ATAAAATGAAATTAAAAATAAT-AAATTAAATTAATCAACATCTAAAAATAAT
1 ATAAAATGAAATTAAAAATAATGAAA-TAAATTAATCAACATATAAAAATAAT
* * *
743443 ATAAAATTAAATTAAAAATAATGAAATAAATTCATTAACATATAAAA
1 ATAAAATGAAATTAAAAATAATGAAATAAATTAATCAACATATAAAA
743490 TAGAAAAGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 39 0.93
53 3 0.07
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (52 bp):
ATAAAATGAAATTAAAAATAATGAAATAAATTAATCAACATATAAAAATAAT
Found at i:743992 original size:2 final size:2
Alignment explanation
Indices: 743985--744049 Score: 70
Period size: 2 Copynumber: 35.5 Consensus size: 2
743975 CCACCCCAAT
* *
743985 TA TA TA TA TA TA TA TA TA TA -A TA TT TT TA TA T- TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
744023 TA TA TA TA -A TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
744050 TTTTGGATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:744015 original size:15 final size:15
Alignment explanation
Indices: 743985--744051 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
743975 CCACCCCAAT
*
743985 TATAT-ATATATATA
1 TATATAATATTTATA
743999 TATATAATATTT-T-
1 TATATAATATTTATA
*
744012 TATAT--TAATTATA
1 TATATAATATTTATA
*
744025 TATATAATATATATA
1 TATATAATATTTATA
744040 TATATAATATTT
1 TATATAATATTT
744052 TTGGATTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 4 0.09
12 1 0.02
13 10 0.23
14 6 0.14
15 22 0.51
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATAATATTTATA
Found at i:744041 original size:26 final size:27
Alignment explanation
Indices: 743985--744047 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
743975 CCACCCCAAT
*
743985 TATATATAT-A-TATATATATAATATT
1 TATATATATAATTATATATATAATATA
*
744010 TTTATAT-TAATTATATATATAATATA
1 TATATATATAATTATATATATAATATA
744036 TATATATATAAT
1 TATATATATAAT
744048 ATTTTTGGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.03
25 7 0.22
26 20 0.62
27 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATATATATAATTATATATATAATATA
Found at i:748841 original size:30 final size:30
Alignment explanation
Indices: 748807--748867 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
748797 CATCGAGTTG
* *
748807 GGCGACGATGACGACGGTAGTGTGTTGCAT
1 GGCGACGACGACGACGGTAGTGTGTCGCAT
*
748837 GGCGACGACGACGACGGTGGTGTGTCGCAT
1 GGCGACGACGACGACGGTAGTGTGTCGCAT
748867 G
1 G
748868 CCGGTAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.20
Consensus pattern (30 bp):
GGCGACGACGACGACGGTAGTGTGTCGCAT
Found at i:766956 original size:22 final size:22
Alignment explanation
Indices: 766914--766956 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
766904 TTAATTTTTA
* *
766914 TGATATGTTTTCTTCTATCTTC
1 TGATATATTTTCATCTATCTTC
766936 TGATATATTTTCAATCT-TCTT
1 TGATATATTTTC-ATCTATCTT
766957 TATTTATCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.19, C:0.16, G:0.07, T:0.58
Consensus pattern (22 bp):
TGATATATTTTCATCTATCTTC
Found at i:771572 original size:21 final size:21
Alignment explanation
Indices: 771546--771604 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
771536 GAGTTACCCG
771546 CGATGGCCTCAATAGCGTCCA
1 CGATGGCCTCAATAGCGTCCA
*
771567 CGATGGCCTCAATAGCGTCCG
1 CGATGGCCTCAATAGCGTCCA
** *
771588 CGACAGCCGCAATAGCG
1 CGATGGCCTCAATAGCG
771605 CCAGCGACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.34, G:0.27, T:0.15
Consensus pattern (21 bp):
CGATGGCCTCAATAGCGTCCA
Found at i:771611 original size:21 final size:20
Alignment explanation
Indices: 771576--771642 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 20
771566 ACGATGGCCT
771576 CAATAGCGTCCGCGACAGCCG
1 CAATAGCG-CCGCGACAGCCG
771597 CAATAGCGCCAGCGACAGCCG
1 CAATAGCGCC-GCGACAGCCG
* *
771618 CAATTGCGCCCGCGACGGCCG
1 CAATAGCG-CCGCGACAGCCG
771639 CAAT
1 CAAT
771643 CACGGTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.24, C:0.39, G:0.28, T:0.09
Consensus pattern (20 bp):
CAATAGCGCCGCGACAGCCG
Found at i:772225 original size:38 final size:39
Alignment explanation
Indices: 772156--772235 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 39
772146 ACAAAGGCAC
* * *
772156 AAAGATCAGCAATCGAAGATGAAGTAGAAATTAGAGAGG
1 AAAGATCAACAATCGAAGATGAAGTAAAAATTAAAGAGG
* *
772195 AAAG-TCAACAATTGAAGATGAAGTAAAAATTAAATAGG
1 AAAGATCAACAATCGAAGATGAAGTAAAAATTAAAGAGG
772233 AAA
1 AAA
772236 ACAATTGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 32 0.89
39 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.23, T:0.17
Consensus pattern (39 bp):
AAAGATCAACAATCGAAGATGAAGTAAAAATTAAAGAGG
Found at i:775677 original size:19 final size:19
Alignment explanation
Indices: 775629--775683 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
775619 TATTAGTATT
775629 TTATTAACA-TAATATTAAA
1 TTATTAA-ATTAATATTAAA
*
775648 TTATTATATTAATATTAAA
1 TTATTAAATTAATATTAAA
775667 TGTA-TAAATTAATATTA
1 T-TATTAAATTAATATTA
775684 CTCATTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 1 0.03
19 29 0.91
20 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TTATTAAATTAATATTAAA
Found at i:775847 original size:39 final size:38
Alignment explanation
Indices: 775804--775917 Score: 94
Period size: 39 Copynumber: 3.0 Consensus size: 38
775794 TATCTATGTA
*
775804 TATATTAATTTAATATTAAAAATATAATATAATTAA-ATT
1 TATATTAATGT-ATATTAAAAATATAA-ATAATTAATATT
* * *
775843 TATATTATATGTATATTAAATATTTTAATAATTAATATT
1 TATATTA-ATGTATATTAAAAATATAAATAATTAATATT
* *
775882 TTTATTAAAATG-ATATT-AAAATATTAAT--TTAATATT
1 TATATT--AATGTATATTAAAAATATAAATAATTAATATT
775918 AAATGTAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
36 8 0.12
38 17 0.27
39 32 0.50
40 6 0.09
41 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (38 bp):
TATATTAATGTATATTAAAAATATAAATAATTAATATT
Found at i:782304 original size:2 final size:2
Alignment explanation
Indices: 782297--782321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
782287 AATTTAACAC
782297 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 A
782322 ATTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:784616 original size:27 final size:28
Alignment explanation
Indices: 784586--784659 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 28
784576 ACTAAGGTGA
784586 GATAAAACA-TAAAAATATCATAAATAT
1 GATAAAACATTAAAAATATCATAAATAT
784613 GATAAAACATTAAAAAATATCATAAATAT
1 GATAAAACATT-AAAAATATCATAAATAT
784642 GATAAAACATTAAAAATA
1 GATAAAACATTAAAAATA
784660 ATTCTAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 9 0.20
28 8 0.18
29 28 0.62
ACGTcount: A:0.64, C:0.07, G:0.04, T:0.26
Consensus pattern (28 bp):
GATAAAACATTAAAAATATCATAAATAT
Found at i:788564 original size:17 final size:17
Alignment explanation
Indices: 788544--788583 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
788534 TTTACTAATT
* *
788544 AAATAATTTAATTATAA
1 AAATAACTTAATAATAA
788561 AAATAACTTAATAATAA
1 AAATAACTTAATAATAA
*
788578 GAATAA
1 AAATAA
788584 AATTAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATAACTTAATAATAA
Found at i:798103 original size:8 final size:9
Alignment explanation
Indices: 798056--798129 Score: 51
Period size: 10 Copynumber: 7.8 Consensus size: 9
798046 TATAAGTTTT
798056 ATTTTTATA
1 ATTTTTATA
* *
798065 GTTTTTACA
1 ATTTTTATA
*
798074 TTTTTTTAATA
1 -ATTTTT-ATA
**
798085 ATTTAAATA
1 ATTTTTATA
798094 TATTTTTATA
1 -ATTTTTATA
798104 ATTTTT-TA
1 ATTTTTATA
798112 ATATTTTATA
1 AT-TTTTATA
798122 ATTATTTA
1 ATT-TTTA
798130 ATGTTCATCG
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
8 4 0.08
9 21 0.42
10 23 0.46
11 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:798109 original size:30 final size:31
Alignment explanation
Indices: 798061--798128 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
798051 GTTTTATTTT
*
798061 TATAGTTTTTACATTTTTTTAATAATTTA-AA
1 TATA-TTTTTACAATTTTTTAATAATTTATAA
* *
798092 TATATTTTTATAATTTTTTAATATTTTATAA
1 TATATTTTTACAATTTTTTAATAATTTATAA
798123 T-TATTT
1 TATATTT
798129 AATGTTCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (31 bp):
TATATTTTTACAATTTTTTAATAATTTATAA
Found at i:798120 original size:18 final size:18
Alignment explanation
Indices: 798097--798131 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
798087 TTAAATATAT
*
798097 TTTTATAATTTTTTAATA
1 TTTTATAATTATTTAATA
798115 TTTTATAATTATTTAAT
1 TTTTATAATTATTTAAT
798132 GTTCATCGTA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAATTATTTAATA
Found at i:804762 original size:31 final size:32
Alignment explanation
Indices: 804727--804787 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
804717 ATAATTTTTA
*
804727 AATTTAA-TTGTTAAACTTTAGATAAAATACT
1 AATTTAACTTGTTAAACTTTAAATAAAATACT
* * *
804758 AATTTAACTTTTTGAAGTTTAAATAAAATA
1 AATTTAACTTGTTAAACTTTAAATAAAATA
804788 TCATTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (32 bp):
AATTTAACTTGTTAAACTTTAAATAAAATACT
Found at i:805300 original size:6 final size:6
Alignment explanation
Indices: 805291--805315 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
805281 GGGATGATAA
805291 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
805316 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Done.