Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012782.1 Kokia drynarioides strain JFW-HI SEQ_127794, 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: 188170
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 86 characters in sequence are not A, C, G, or T
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--43 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 AAA
* *
4 AT AT AT AT AT AT AT AT AT AT AT AT AT GT -T AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44 AGATTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:590 original size:14 final size:14
Alignment explanation
Indices: 542--593 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
532 AAAGCCTCTC
*
542 CCCCATTTC-CCTTC
1 CCCC-TTTCTCCTTT
* *
556 CCCCTTCCTTCTTT
1 CCCCTTTCTCCTTT
*
570 CTCCTTTCTCCTTT
1 CCCCTTTCTCCTTT
584 CCCCTTTCTC
1 CCCCTTTCTC
594 GTTTTCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 3 0.10
14 27 0.90
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.46
Consensus pattern (14 bp):
CCCCTTTCTCCTTT
Found at i:679 original size:14 final size:14
Alignment explanation
Indices: 646--686 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
636 CAGAGACGAT
646 CCTTTCTTCTTTCC
1 CCTTTCTTCTTTCC
** *
660 AGTTTCTCCTTTCC
1 CCTTTCTTCTTTCC
674 CCTTTCTTCTTTC
1 CCTTTCTTCTTTC
687 GATAAGCACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.02, T:0.56
Consensus pattern (14 bp):
CCTTTCTTCTTTCC
Found at i:19918 original size:31 final size:31
Alignment explanation
Indices: 19876--19943 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
19866 TTAATCCACA
*
19876 ATACATGAAACTTTGAA-TATGATTCAAATGT
1 ATACATAAAACTTT-AATTATGATTCAAATGT
* *
19907 ATACATAAAACTTTAATTTTGATTCAATTGT
1 ATACATAAAACTTTAATTATGATTCAAATGT
*
19938 ACACAT
1 ATACAT
19944 TTAAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (31 bp):
ATACATAAAACTTTAATTATGATTCAAATGT
Found at i:26130 original size:16 final size:16
Alignment explanation
Indices: 26109--26143 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
26099 CTCATTTCAA
26109 CATACATGTGAATATT
1 CATACATGTGAATATT
26125 CATACATGTGAATATT
1 CATACATGTGAATATT
26141 CAT
1 CAT
26144 TCATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (16 bp):
CATACATGTGAATATT
Found at i:26542 original size:23 final size:23
Alignment explanation
Indices: 26511--26637 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
26501 AGTGCTGGGT
26511 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
26534 AACAAAGAGTACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
26557 ATCAGAGAGCACACAAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* * *
26581 TAACAGATAGCACGAGACA-TGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
26605 AACAGAGAGCACACATAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
**
26628 CTCAGAGAGC
1 AACAGAGAGC
26638 GCGCTAGTGT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.03
23 64 0.74
24 2 0.02
25 14 0.16
26 3 0.03
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:35174 original size:12 final size:12
Alignment explanation
Indices: 35157--35183 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35147 TTTATGCAAG
35157 ATTTATTTTTTT
1 ATTTATTTTTTT
35169 ATTTATTTTTTT
1 ATTTATTTTTTT
35181 ATT
1 ATT
35184 GAATGATTTT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:35838 original size:95 final size:96
Alignment explanation
Indices: 35654--35849 Score: 270
Period size: 95 Copynumber: 2.1 Consensus size: 96
35644 CGTTGAGTTG
* * *
35654 AACT-TTGAAAACCTTCTGATAAATTTAAAATTGAGAATTAAGATTACATATTATCATCCAAATG
1 AACTCTTGAAAACCTTCTGACAAATTTAAAATTGAGAATTAAGATTACAGATTACCATCCAAATG
* * * *
35718 ATAAAGATAATATAAGAGGACATACAATCAC
66 ATAAAAATAATACAAAAGGACATACAACCAC
* ** *
35749 AACTCTTGAAAACCTTCTGACAGATTTAGGATTGAGAA-TAATATTACAGATTACCATCCAAATG
1 AACTCTTGAAAACCTTCTGACAAATTTAAAATTGAGAATTAAGATTACAGATTACCATCCAAATG
*
35813 ATAAAAATAATACAAAAGGATATACAACCAC
66 ATAAAAATAATACAAAAGGACATACAACCAC
35844 AACTCT
1 AACTCT
35850 CCCCAAGAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 59 0.67
96 29 0.33
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (96 bp):
AACTCTTGAAAACCTTCTGACAAATTTAAAATTGAGAATTAAGATTACAGATTACCATCCAAATG
ATAAAAATAATACAAAAGGACATACAACCAC
Found at i:41473 original size:14 final size:16
Alignment explanation
Indices: 41441--41471 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41431 TTATAAAAAT
41441 ATATATTTAACTTGAA
1 ATATATTTAACTTGAA
41457 ATATATTTAA-TTGAA
1 ATATATTTAACTTGAA
41472 TAACAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (16 bp):
ATATATTTAACTTGAA
Found at i:49542 original size:80 final size:80
Alignment explanation
Indices: 49399--49551 Score: 243
Period size: 80 Copynumber: 1.9 Consensus size: 80
49389 AAAAAAAAAA
* * * * *
49399 ATCTGATTAACAATTTTATTATCTAAATTTGAATAACTGATAATGATGAATTTATGCCTTTCAAA
1 ATCTAATTAACAATTTTATTATCTAAATCTGAAAAACTGATAATAATGAATTTATGCCCTTCAAA
49464 TAGAATCAATCAAAT
66 TAGAATCAATCAAAT
* *
49479 ATCTAATTAATAATTTTATTATCTAAATCTGAAAAATTGATAATAATGAATTTATGCCCTTCAAA
1 ATCTAATTAACAATTTTATTATCTAAATCTGAAAAACTGATAATAATGAATTTATGCCCTTCAAA
49544 TAGAATCA
66 TAGAATCA
49552 CATGATATAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (80 bp):
ATCTAATTAACAATTTTATTATCTAAATCTGAAAAACTGATAATAATGAATTTATGCCCTTCAAA
TAGAATCAATCAAAT
Found at i:52937 original size:12 final size:12
Alignment explanation
Indices: 52922--52946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52912 ACTAAAGTTT
52922 TATTTTGATATA
1 TATTTTGATATA
52934 TATTTTGATATA
1 TATTTTGATATA
52946 T
1 T
52947 TTTAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TATTTTGATATA
Found at i:56805 original size:20 final size:21
Alignment explanation
Indices: 56780--56848 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
56770 GAATACATAG
56780 AAAAGA-ATGCCACTTTATGC
1 AAAAGAGATGCCACTTTATGC
**
56800 AAAAGAGATG-CACAGTA-G-
1 AAAAGAGATGCCACTTTATGC
56818 AAAAGA-ATGCCACTTTATGC
1 AAAAGAGATGCCACTTTATGC
*
56838 AAAAGATATGC
1 AAAAGAGATGC
56849 ACAGTACACA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.08
18 11 0.28
19 2 0.05
20 17 0.43
21 7 0.17
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (21 bp):
AAAAGAGATGCCACTTTATGC
Found at i:56828 original size:38 final size:38
Alignment explanation
Indices: 56777--56854 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
56767 GTTGAATACA
56777 TAGAAAAGAATGCCACTTTATGCAAAAGAGATGCACAG
1 TAGAAAAGAATGCCACTTTATGCAAAAGAGATGCACAG
*
56815 TAGAAAAGAATGCCACTTTATGCAAAAGATATGCACAG
1 TAGAAAAGAATGCCACTTTATGCAAAAGAGATGCACAG
56853 TA
1 TA
56855 CACACTCAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (38 bp):
TAGAAAAGAATGCCACTTTATGCAAAAGAGATGCACAG
Found at i:65706 original size:67 final size:61
Alignment explanation
Indices: 65597--65780 Score: 187
Period size: 59 Copynumber: 3.0 Consensus size: 61
65587 AAATTTATAA
* * *
65597 TAAT-TTAATTTAATAATTATCTTAAT-AGTATTTTATTAATTTAATATTAATGTGATTAT
1 TAATATTAATTTAATATTTATCTTGATAAATATTTTATTAATTTAATATTAATGTGATTAT
* * * *
65656 CTCAATATTAAATTTAATGTTTATCTTGTAGATAAATATTTTATTAATTTAATA-TGAT-TTAAT
1 -T-AATATT-AATTTAATATTTATC-T-T-GATAAATATTTTATTAATTTAATATTAATGTGATT
65719 AT
60 AT
* * * *
65721 TAATATTAATTTAATATTTATCTTGATAAGTATTATAGTAATTTAATATTAAAGTGATTA
1 TAATATTAATTTAATATTTATCTTGATAAATATTTTATTAATTTAATATTAATGTGATTA
65781 AGTTTAATTA
Statistics
Matches: 100, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
59 21 0.21
60 4 0.04
61 8 0.08
62 16 0.16
63 19 0.19
64 2 0.02
65 6 0.06
66 5 0.05
67 19 0.19
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.51
Consensus pattern (61 bp):
TAATATTAATTTAATATTTATCTTGATAAATATTTTATTAATTTAATATTAATGTGATTAT
Found at i:65915 original size:21 final size:20
Alignment explanation
Indices: 65891--65932 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
65881 ATTTTTGTAC
*
65891 TTATGTTGCATTTGAAGACAT
1 TTATGATGCATTT-AAGACAT
*
65912 TTATGATGTATTTAAGACAT
1 TTATGATGCATTTAAGACAT
65932 T
1 T
65933 GTTTGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (20 bp):
TTATGATGCATTTAAGACAT
Found at i:67474 original size:2 final size:2
Alignment explanation
Indices: 67467--67491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67457 ATTTCTGCTA
67467 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
67492 ATTTTAACTT
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:68052 original size:21 final size:21
Alignment explanation
Indices: 68028--68075 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
68018 TTTTTTATTC
*
68028 TTGTTTGCTA-CTATTTTGCTG
1 TTGTTTGCTATC-ATTTTGATG
68049 TTGTTTGCTATCATTTTGATG
1 TTGTTTGCTATCATTTTGATG
68070 TTGTTT
1 TTGTTT
68076 TATTGTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (21 bp):
TTGTTTGCTATCATTTTGATG
Found at i:73062 original size:30 final size:31
Alignment explanation
Indices: 73028--73099 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
73018 GTTATATTTA
* *
73028 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAATAGTCACTAAACTTATCGAAAA-GTG
*
73058 ACAAAATAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAATAGTCACTAAACTTATCGAAAAGTG
73089 ACAAAATAGTC
1 ACAAAATAGTC
73100 CTCTTGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.46
31 15 0.41
32 5 0.14
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (31 bp):
ACAAAATAGTCACTAAACTTATCGAAAAGTG
Found at i:74040 original size:25 final size:24
Alignment explanation
Indices: 74013--74139 Score: 140
Period size: 22 Copynumber: 5.3 Consensus size: 24
74003 GAAACGCATA
*
74013 AGTGCTGGAGAAACAGAAGCACA-AA
1 AGTGCTGG-G-AACAGAAGCACACAC
74038 AGTGCTGGGAA-ACGATAGGCACACAC
1 AGTGCTGGGAACA-GA-A-GCACACAC
74064 AGTGCT--GAACAGAAGCACACAC
1 AGTGCTGGGAACAGAAGCACACAC
74086 AGTGCT--GAACAGAAGCACACAC
1 AGTGCTGGGAACAGAAGCACACAC
*
74108 AGTGCTGGGTAATAGAAGCACACAC
1 AGTGCTGGG-AACAGAAGCACACAC
74133 AGTGCTG
1 AGTGCTG
74140 AACAAAAGCG
Statistics
Matches: 92, Mismatches: 2, Indels: 16
0.84 0.02 0.15
Matches are distributed among these distances:
22 37 0.40
23 5 0.05
24 8 0.09
25 35 0.38
26 7 0.08
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.12
Consensus pattern (24 bp):
AGTGCTGGGAACAGAAGCACACAC
Found at i:74082 original size:22 final size:22
Alignment explanation
Indices: 74056--74148 Score: 141
Period size: 22 Copynumber: 4.1 Consensus size: 22
74046 GAAACGATAG
74056 GCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAA
74078 GCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAA
*
74100 GCACACACAGTGCTGGGTAATAGAA
1 GCACACACAGTGCT--G-AACAGAA
*
74125 GCACACACAGTGCTGAACAAAA
1 GCACACACAGTGCTGAACAGAA
74147 GC
1 GC
74149 GCACTAGCGT
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
22 43 0.66
23 1 0.02
24 1 0.02
25 20 0.31
ACGTcount: A:0.40, C:0.26, G:0.24, T:0.11
Consensus pattern (22 bp):
GCACACACAGTGCTGAACAGAA
Found at i:74125 original size:47 final size:44
Alignment explanation
Indices: 74056--74148 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 44
74046 GAAACGATAG
*
74056 GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAAAA
*
74100 GCACACACAGTGCTGGGTAATAGAAGCACACACAGTGCTGAACAAAA
1 GCACACACAGTGCT--G-AACAGAAGCACACACAGTGCTGAACAAAA
74147 GC
1 GC
74149 GCACTAGCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 14 0.32
46 1 0.02
47 29 0.66
ACGTcount: A:0.40, C:0.26, G:0.24, T:0.11
Consensus pattern (44 bp):
GCACACACAGTGCTGAACAGAAGCACACACAGTGCTGAACAAAA
Found at i:74356 original size:21 final size:21
Alignment explanation
Indices: 74332--74372 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
74322 TGTCACCAAT
*
74332 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
74353 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
74373 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Found at i:76930 original size:21 final size:21
Alignment explanation
Indices: 76906--76951 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
76896 TTTCATGTAT
* *
76906 TATTATAT-TAATTTATTTAAA
1 TATTATATATAACTTAATT-AA
76927 TATTATATATAACTTAATTAA
1 TATTATATATAACTTAATTAA
76948 TATT
1 TATT
76952 TAACTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATATATAACTTAATTAA
Found at i:86868 original size:11 final size:12
Alignment explanation
Indices: 86844--86873 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
86834 CAATTCAAAT
86844 TTTATTATTTTA
1 TTTATTATTTTA
86856 TTTATTA-TTTA
1 TTTATTATTTTA
86867 TTTATTA
1 TTTATTA
86874 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:88623 original size:20 final size:19
Alignment explanation
Indices: 88586--88623 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
88576 AACAAATTTT
*
88586 TATTTTTATTTACCAAATG
1 TATTTTTATTCACCAAATG
88605 TATTTTTATTCACCTAAAT
1 TATTTTTATTCACC-AAAT
88624 TCCAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (19 bp):
TATTTTTATTCACCAAATG
Found at i:91025 original size:87 final size:86
Alignment explanation
Indices: 90856--91025 Score: 277
Period size: 86 Copynumber: 2.0 Consensus size: 86
90846 AGTCCTTGAC
* *
90856 TGAGTTGGTGTCACGAGTCAGTGCTATTTAATTCATCACTAAAAAAAACTTTATTTTAGCATAAT
1 TGAGTTGGTATCACGAGTCAGTGCTATTTAATTCACCACTAAAAAAAACTTTATTTTAGCATAAT
90921 ACTTACATATTTGTGTTTAAT
66 ACTTACATATTTGTGTTTAAT
* * *
90942 TGAGTTGGTATCACGAGTTAGTGCTATTTAATTTACCACTAAATCAAAACTTTATTTTAGCATAA
1 TGAGTTGGTATCACGAGTCAGTGCTATTTAATTCACCACTAAA-AAAAACTTTATTTTAGCATAA
*
91007 TATTTACATATTTGTGTTT
65 TACTTACATATTTGTGTTT
91026 TTTTCTTTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 39 0.51
87 38 0.49
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (86 bp):
TGAGTTGGTATCACGAGTCAGTGCTATTTAATTCACCACTAAAAAAAACTTTATTTTAGCATAAT
ACTTACATATTTGTGTTTAAT
Found at i:91146 original size:11 final size:12
Alignment explanation
Indices: 91104--91146 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
91094 AATATGTAGC
* *
91104 AAAAAATAACAA
1 AAAAAAAAACTA
91116 AAAAAGAGAAACTA
1 AAAAA-A-AAACTA
91130 AAAAAAAAACTA
1 AAAAAAAAACTA
91142 AAAAA
1 AAAAA
91147 CGAAACATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 2 0.07
14 9 0.33
ACGTcount: A:0.81, C:0.07, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAAAAAAACTA
Found at i:93134 original size:101 final size:101
Alignment explanation
Indices: 92959--93158 Score: 400
Period size: 101 Copynumber: 2.0 Consensus size: 101
92949 TCCCATATGA
92959 CTGTGTTTGGCCCATTCTATTTAATCCTCTGTAATGCACCGGTTTTAGTCCAGAAACGTCTCTCT
1 CTGTGTTTGGCCCATTCTATTTAATCCTCTGTAATGCACCGGTTTTAGTCCAGAAACGTCTCTCT
93024 CCTCTCTTTTTTACCTCCACTTCACTACAAACTCTT
66 CCTCTCTTTTTTACCTCCACTTCACTACAAACTCTT
93060 CTGTGTTTGGCCCATTCTATTTAATCCTCTGTAATGCACCGGTTTTAGTCCAGAAACGTCTCTCT
1 CTGTGTTTGGCCCATTCTATTTAATCCTCTGTAATGCACCGGTTTTAGTCCAGAAACGTCTCTCT
93125 CCTCTCTTTTTTACCTCCACTTCACTACAAACTC
66 CCTCTCTTTTTTACCTCCACTTCACTACAAACTC
93159 CACAACTATT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.19, C:0.31, G:0.11, T:0.39
Consensus pattern (101 bp):
CTGTGTTTGGCCCATTCTATTTAATCCTCTGTAATGCACCGGTTTTAGTCCAGAAACGTCTCTCT
CCTCTCTTTTTTACCTCCACTTCACTACAAACTCTT
Found at i:98121 original size:29 final size:29
Alignment explanation
Indices: 98089--98249 Score: 99
Period size: 28 Copynumber: 5.7 Consensus size: 29
98079 GGATATAACC
*
98089 TTTCCATTGACAT-CTTTACGGATATCCCT
1 TTTCCATTGATATCCTTT-CGGATATCCCT
* * *
98118 TTT-CA-TAATTATCCTTTCAGATATACCT
1 TTTCCATTGA-TATCCTTTCGGATATCCCT
*
98146 TTTTCATTGATATCCTTTCGGATATCCCT
1 TTTCCATTGATATCCTTTCGGATATCCCT
* *
98175 TTT-CA-TAATTATCCTTAT-GGATATAACCT
1 TTTCCATTGA-TATCCTT-TCGGATAT-CCCT
* *
98204 TTT-CATTTATAT-CTTACGGATAGGT-CCT
1 TTTCCATTGATATCCTTTCGGATA--TCCCT
*
98232 TTT-CATCGATATCCTTTC
1 TTTCCATTGATATCCTTTC
98250 AGACATCCGT
Statistics
Matches: 106, Mismatches: 14, Indels: 24
0.74 0.10 0.17
Matches are distributed among these distances:
27 4 0.04
28 52 0.49
29 45 0.42
30 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTCCATTGATATCCTTTCGGATATCCCT
Found at i:98196 original size:28 final size:29
Alignment explanation
Indices: 98102--98209 Score: 125
Period size: 29 Copynumber: 3.8 Consensus size: 29
98092 CCATTGACAT
98102 CTTTACGGATAT-CCCTTTTCATAATTATC
1 CTTT-CGGATATACCCTTTTCATAATTATC
* * *
98131 CTTTCAGATATACCTTTTTCATTGA-TATC
1 CTTTCGGATATACCCTTTTCA-TAATTATC
98160 CTTTCGGATAT-CCCTTTTCATAATTATC
1 CTTTCGGATATACCCTTTTCATAATTATC
*
98188 CTTAT-GGATATAACCTTTTCAT
1 CTT-TCGGATATACCCTTTTCAT
98210 TTATATCTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.03
28 27 0.40
29 36 0.54
30 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (29 bp):
CTTTCGGATATACCCTTTTCATAATTATC
Found at i:98219 original size:28 final size:26
Alignment explanation
Indices: 98069--98225 Score: 75
Period size: 28 Copynumber: 5.6 Consensus size: 26
98059 CTTCTCACAG
*
98069 TTATTCTTATGGATATAACCTTTCCAT
1 TTATTCTTATGGATAT-ACCTTTTCAT
* * * *
98096 TGACATCTTTACGGATATCCCTTTTCAT
1 TTA-TTC-TTATGGATATACCTTTTCAT
* *
98124 AATTATCCTT-TCAGATATACCTTTTTCAT
1 --TTATTCTTAT-GGATATACC-TTTTCAT
* *
98153 TGATATCCTT-TCGGATATCCCTTTTCAT
1 T--TATTCTTAT-GGATATACCTTTTCAT
*
98181 AATTATCCTTATGGATATAACCTTTTCAT
1 --TTATTCTTATGGATAT-ACCTTTTCAT
*
98210 TTATATCTTACGGATA
1 TTAT-TCTTATGGATA
98226 GGTCCTTTTC
Statistics
Matches: 101, Mismatches: 16, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
27 7 0.07
28 48 0.48
29 43 0.43
30 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.46
Consensus pattern (26 bp):
TTATTCTTATGGATATACCTTTTCAT
Found at i:98233 original size:114 final size:114
Alignment explanation
Indices: 98032--98283 Score: 289
Period size: 114 Copynumber: 2.2 Consensus size: 114
98022 GGAGTAAACC
* * * * * *
98032 TTTTCCTTGATGTCCTTACAGATATCCCTTCTCACAGTTATTCTTATGGATATAACCTTTCCATT
1 TTTTCATTGATATCCTTTCGGATATCCCTTCTCACAATTATCCTTATGGATATAACCTTTCCATT
*
98097 GACATCTTTACGGATATCCCTTTTCAT-AATTATCCTTTCAGATATACC-T
66 GACATCTTTACGGATATCCCTTTTCATCAA-TATCCTTTCAGACAT-CCGT
* * *
98146 TTTTCATTGATATCCTTTCGGATATCCCTTTTCATAATTATCCTTATGGATATAACCTTTTCATT
1 TTTTCATTGATATCCTTTCGGATATCCCTTCTCACAATTATCCTTATGGATATAACCTTTCCATT
* * *
98211 TATATC-TTACGGATAGGT-CCTTTTCATCGATATCCTTTCAGACATCCGT
66 GACATCTTTACGGATA--TCCCTTTTCATCAATATCCTTTCAGACATCCGT
* **
98260 TTTTGA-AAATATCCTTTCGGATAT
1 TTTTCATTGATATCCTTTCGGATAT
98284 AACCTTTACA
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
113 27 0.23
114 89 0.75
115 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (114 bp):
TTTTCATTGATATCCTTTCGGATATCCCTTCTCACAATTATCCTTATGGATATAACCTTTCCATT
GACATCTTTACGGATATCCCTTTTCATCAATATCCTTTCAGACATCCGT
Found at i:98247 original size:57 final size:56
Alignment explanation
Indices: 98016--98225 Score: 237
Period size: 57 Copynumber: 3.7 Consensus size: 56
98006 CCACCAACAC
* * * * * *
98016 CCTTATGGAGTA-AACCTTTTCCTTGATGTCCTTACAGATATCCCTTCTCACAGTTAT
1 CCTTATGGA-TATAACCTTTTCATTGATAT-CTTACGGATATCCCTTTTCATAATTAT
* * *
98073 TCTTATGGATATAACCTTTCCATTGACATCTTTACGGATATCCCTTTTCATAATTAT
1 CCTTATGGATATAACCTTTTCATTGATATC-TTACGGATATCCCTTTTCATAATTAT
* *
98130 CCTT-TCAGATAT-ACCTTTTTCATTGATATCCTTTCGGATATCCCTTTTCATAATTAT
1 CCTTAT-GGATATAACC-TTTTCATTGATAT-CTTACGGATATCCCTTTTCATAATTAT
*
98187 CCTTATGGATATAACCTTTTCATTTATATCTTACGGATA
1 CCTTATGGATATAACCTTTTCATTGATATCTTACGGATA
98226 GGTCCTTTTC
Statistics
Matches: 129, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
56 16 0.12
57 108 0.84
58 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (56 bp):
CCTTATGGATATAACCTTTTCATTGATATCTTACGGATATCCCTTTTCATAATTAT
Found at i:99305 original size:3 final size:3
Alignment explanation
Indices: 99297--99336 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
99287 CCTCAATTTG
*
99297 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
99337 CACCACTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:106302 original size:24 final size:24
Alignment explanation
Indices: 106253--106302 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
106243 TATATGTGAA
*
106253 AAATAATAAAATAAATAAATATAT
1 AAATAATAAAATAAATAAATAAAT
* *
106277 AAATAATACATTAAATTAAA-AAAT
1 AAATAATAAAATAAA-TAAATAAAT
106301 AA
1 AA
106303 CTCTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAATAAAATAAATAAATAAAT
Found at i:106350 original size:20 final size:20
Alignment explanation
Indices: 106293--106351 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
106283 TACATTAAAT
* *
106293 TAAAAAATAACTC-TTAATT
1 TAAAAAATAACTCAATAATC
*
106312 TAAAGAAAATAAACACAATAATC
1 T-AA-AAAAT-AACTCAATAATC
106335 TAAAAAATAACTCAATA
1 TAAAAAATAACTCAATA
106352 GAAAAACTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 1 0.03
20 10 0.31
21 10 0.31
22 6 0.19
23 5 0.16
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.25
Consensus pattern (20 bp):
TAAAAAATAACTCAATAATC
Found at i:108199 original size:18 final size:17
Alignment explanation
Indices: 108114--108199 Score: 84
Period size: 17 Copynumber: 4.9 Consensus size: 17
108104 TCCGGGCCCA
*
108114 ATAAGATTTAAATTCATT
1 ATAA-ATTTAAATTTATT
* *
108132 TTAAAATTAAATTTATT
1 ATAAATTTAAATTTATT
* *
108149 TTAAGTTTAAATTTACTT
1 ATAAATTTAAATTTA-TT
108167 A-AAATTTTAAATTTATT
1 ATAAA-TTTAAATTTATT
108184 ATAAATTTAAAGTTTA
1 ATAAATTTAAA-TTTA
108200 AATCTATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
17 35 0.61
18 22 0.39
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:108875 original size:9 final size:9
Alignment explanation
Indices: 108861--108928 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
108851 TTTTACTAAC
108861 TATTAATAA
1 TATTAATAA
108870 TATTAATAA
1 TATTAATAA
*
108879 CTGTTTTAATAA
1 ---TATTAATAA
**
108891 TAACAATAA
1 TATTAATAA
*
108900 TAATAATAA
1 TATTAATAA
*
108909 TATTAATGA
1 TATTAATAA
*
108918 CATTAATAA
1 TATTAATAA
108927 TA
1 TA
108929 ATAAATGCTT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 38 0.83
12 8 0.17
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (9 bp):
TATTAATAA
Found at i:108893 original size:3 final size:3
Alignment explanation
Indices: 108885--108960 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
108875 ATAACTGTTT
* * * * *
108885 TAA TAA TAA CAA TAA TAA TAA TAA TAT TAA TGA CAT TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
** * *
108934 TGC T-T TAA TGA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
108961 TATTATTATT
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
2 1 0.02
3 51 0.93
4 3 0.05
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:109410 original size:65 final size:66
Alignment explanation
Indices: 109280--109413 Score: 173
Period size: 65 Copynumber: 2.0 Consensus size: 66
109270 CGTGTACTAG
*** * *
109280 CGGGTGACGGACGTCAAAGCATGGTGGTCACGCACGGCAGCCGACGAGGCGTGTGCAGCGGAGCC
1 CGGGTGACGGACGTCAAAGCATGGTGGTCACGCACGGCAGCCGACGAGGCACATGCAACGAAGCC
109345 A
66 A
* * *
109346 CGGG-GACGGACGTCGAAGCATGGTGGTCACGCGCGTC-GACCGACGAGGCACATGCAACGAAGC
1 CGGGTGACGGACGTCAAAGCATGGTGGTCACGCACGGCAG-CCGACGAGGCACATGCAACGAAGC
109409 CA
65 CA
109411 CGG
1 CGG
109414 TGGCAGGACG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
64 1 0.02
65 54 0.92
66 4 0.07
ACGTcount: A:0.22, C:0.28, G:0.40, T:0.10
Consensus pattern (66 bp):
CGGGTGACGGACGTCAAAGCATGGTGGTCACGCACGGCAGCCGACGAGGCACATGCAACGAAGCC
A
Found at i:110060 original size:30 final size:30
Alignment explanation
Indices: 110017--110101 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
110007 GGAGGTCCCT
*
110017 AAACTGTCTGAAAATTCCATTTTCAAACTCG
1 AAACTTTC-GAAAATTCCATTTTCAAACTCG
* * **
110048 AAACTTTCGAAAATTACATTTTTACCCTCG
1 AAACTTTCGAAAATTCCATTTTCAAACTCG
* *
110078 -AACTTCCAAAAATTCCATTTTCAA
1 AAACTTTCGAAAATTCCATTTTCAA
110102 CCCTTGAGCT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 19 0.43
30 18 0.41
31 7 0.16
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (30 bp):
AAACTTTCGAAAATTCCATTTTCAAACTCG
Found at i:110091 original size:29 final size:29
Alignment explanation
Indices: 110027--110216 Score: 154
Period size: 30 Copynumber: 6.4 Consensus size: 29
110017 AAACTGTCTG
* ** * *
110027 AAAATTCCATTTTCAAACTCGAAACTTTCG
1 AAAATTCCATTTTTACCCTCG-AACTTCCA
*
110057 AAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* * *
110086 AAAATTCCATTTTCAACCCTTGAGCTTCCA
1 AAAATTCCATTTT-TACCCTCGAACTTCCA
*
110116 AAAATTCCATTTTTACCC-CTGAACCTCCA
1 AAAATTCCATTTTTACCCTC-GAACTTCCA
* * *
110145 AAATTTCCATTTTTGATCCT-GAAACTTTCA
1 AAAATTCCATTTTT-ACCCTCG-AACTTCCA
*
110175 AAAATTACCA-TTTTACCCTCGGA-TGTCCA
1 AAAATT-CCATTTTTACCCTCGAACT-TCCA
*
110204 AAAACTCCATTTT
1 AAAATTCCATTTT
110217 CGACCTTGAA
Statistics
Matches: 128, Mismatches: 23, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
28 4 0.03
29 59 0.46
30 62 0.48
31 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTCCA
Found at i:110227 original size:59 final size:60
Alignment explanation
Indices: 110027--110304 Score: 222
Period size: 59 Copynumber: 4.8 Consensus size: 60
110017 AAACTGTCTG
* * *
110027 AAAATTCCATTTTCAA-ACTCGAAACTTTCGAAAATTA-CATTTTTACCCTCGAACT-TCCA
1 AAAATTCCATTTTCAACCCTTGAAACTTTCAAAAATTACCATTTTTACCC-CGAA-TGTCCA
* * **
110086 AAAATTCCATTTTCAACCCTTG-AGCTTCCAAAAATT-CCATTTTTACCCCTGAACCTCCA
1 AAAATTCCATTTTCAACCCTTGAAACTTTCAAAAATTACCATTTTTACCCC-GAATGTCCA
* ** * *
110145 AAATTTCCATTTTTGATCC-TGAAACTTTCAAAAATTACCA-TTTTACCCTCGGATGTCCA
1 AAAATTCCATTTTCAACCCTTGAAACTTTCAAAAATTACCATTTTTACCC-CGAATGTCCA
* * * * *
110204 AAAACTCCATTTTCGA-CCTTGAAACTTT-TAAAATTACC-CTTTTACCCCGAATGTCAA
1 AAAATTCCATTTTCAACCCTTGAAACTTTCAAAAATTACCATTTTTACCCCGAATGTCCA
* * * *
110261 AAAATTTCC-TTTTTAA-CCTCGAATA-TTCCCAAAATTACCATTTT
1 AAAA-TTCCATTTTCAACCCTTGAA-ACTTTCAAAAATTACCATTTT
110305 GCCCCAAAAA
Statistics
Matches: 178, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
57 25 0.14
58 35 0.20
59 111 0.62
60 7 0.04
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (60 bp):
AAAATTCCATTTTCAACCCTTGAAACTTTCAAAAATTACCATTTTTACCCCGAATGTCCA
Found at i:117910 original size:6 final size:6
Alignment explanation
Indices: 117901--117925 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
117891 AAAAAAACAA
117901 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
117926 GGGGGTTCAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:118970 original size:123 final size:123
Alignment explanation
Indices: 118742--119013 Score: 357
Period size: 123 Copynumber: 2.2 Consensus size: 123
118732 CATCTTCTTA
* * *
118742 ATGAGATACTGAGAAG-AGGACCAAATCAATGAAACGAGGCTTGATGTGAACAAATCTTCGAACC
1 ATGAGATACTGAGAAGTA-GACCAAATCAATGAAACAAGGCTTAAAGTGAACAAATCTTCGAACC
* * * * *
118806 CCAGCTTCCTGATGAGATATTGAGAAACAGGTCGAAATAATAAAATGGTTAGCTTCCTG
65 CCAGCTTCCTGATAAGACACTGAGAAACAGGTAGAAATAATAAAAAGGTTAGCTTCCTG
* * * * *
118865 ATGAGAAACTGAGAAGTAGACCAAATCAATGAAATAAGGTTTAAAGTGAGCAAATCTTCTAACCC
1 ATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTTAAAGTGAACAAATCTTCGAACCC
** * *
118930 CAGCTTCCTGATAAGACACTGAGAAGTAGGTAGAAGTAATAAAAAGGTTAGTTTCCTG
66 CAGCTTCCTGATAAGACACTGAGAAACAGGTAGAAATAATAAAAAGGTTAGCTTCCTG
* *
118988 ATGAGATACTGAAAAGTGGACCAAAT
1 ATGAGATACTGAGAAGTAGACCAAAT
119014 TCGTCTTCCT
Statistics
Matches: 128, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
123 127 0.99
124 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (123 bp):
ATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAGGCTTAAAGTGAACAAATCTTCGAACCC
CAGCTTCCTGATAAGACACTGAGAAACAGGTAGAAATAATAAAAAGGTTAGCTTCCTG
Found at i:119193 original size:201 final size:204
Alignment explanation
Indices: 118912--119504 Score: 592
Period size: 201 Copynumber: 2.9 Consensus size: 204
118902 GGTTTAAAGT
* * * * *
118912 GAGCAAATCTTCTAACCCCAGCTTCCTGATAAGACACTGAGAAGTAGGTAGAAGTAATAAAAAGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGG
* * * *
118977 TTAGTTTCCTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATAAGGTATAGAGAAAC
66 TTAGCTTCCTGATGAGATACTGAAAAGTCGACCAAATTCGTCTTCCTGATAAGATACAGAGAAAC
* *** * * * * * *
119042 GGATTAAAACAAGTGAGGTGGTCATCTTCCTGTTGAGATACAGAGAAGTATACC-AA-C-TCGAG
131 GGATTAAAACAAATGACACGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCACCCAC
*
119104 GCTCAACGC
196 GCTCAACAC
* * * * * *
119113 GAGCAAATCTTCGAACCCCAACTTCTTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGG
* * *
119178 TTAGCTTCTTGATGAGATACTGAGAAGTCGACCAAATTCGTCTTCCTGATGAGATACAGAGAAAC
66 TTAGCTTCCTGATGAGATACTGAAAAGTCGACCAAATTCGTCTTCCTGATAAGATACAGAGAAAC
* * *
119243 GGATTGAAACAAATGACACGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
131 GGATTAAAACAAATGACACGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATC--ACCC
* * *
119308 ACGCTCGATAT
194 ACGCTCAACAC
*
119319 GAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACA-
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAA-AG
* * * ** * *
119383 GTTATCTCCCTGATGA-AGTAC-GAGGAAGT-GAACCAAAACCATCTTCCTGATGAA-ACACAGA
65 GTTAGCTTCCTGATGAGA-TACTGA-AAAGTCG-ACCAAATTCGTCTTCCTGAT-AAGATACAGA
** * * * * * *
119444 GAAGTGGACTAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTA-AGAAGAAGGCCAA
126 GAAACGGATTAAAACAAATGACACGGTCATCTTCCTGATGAGATAC-AGAGAAGAAGACCAA
119505 GTCAATGAAA
Statistics
Matches: 320, Mismatches: 61, Indels: 17
0.80 0.15 0.04
Matches are distributed among these distances:
201 156 0.49
202 2 0.01
203 1 0.00
205 4 0.01
206 156 0.49
207 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (204 bp):
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAGG
TTAGCTTCCTGATGAGATACTGAAAAGTCGACCAAATTCGTCTTCCTGATAAGATACAGAGAAAC
GGATTAAAACAAATGACACGGTCATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCACCCAC
GCTCAACAC
Found at i:119430 original size:206 final size:203
Alignment explanation
Indices: 118911--119509 Score: 611
Period size: 206 Copynumber: 2.9 Consensus size: 203
118901 AGGTTTAAAG
* * * *
118911 TGAGCAAATCTTCT-AACCCCAGCTTCCTGATAAGACACTGAGAAGTAGGTAGAAGTAATAAAAA
1 TGAGCAAATCTT-TGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAA
* * * *
118975 GGTTAGT-TTCCTGATGAGATACTGAAAAGTGGACCAAATTCGTCTTCCTGATAAGGTATAGAGA
65 -GTTA-TCTTCCTGATGAGATACTGAGAAGT-GACCAAATTCGTCTTCCTGATGAGATACAGAGA
** * * * * *
119039 AACGGATTAAAACAAGTGAGGTGGTCATCTTCCTGTTGAGATACAGAGAAGTATACC-AA-C--T
127 AACGGATTAAAACAAGTGACATGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAC
* * *
119100 CGAGGCTCAACG
192 CCACGCTCAACA
* * * * * * * *
119112 CGAGCAAATCTTCGAACCCCAACTTCTTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAAATG
1 TGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAA-A
* *
119177 GTTAGCTTCTTGATGAGATACTGAGAAGTCGACCAAATTCGTCTTCCTGATGAGATACAGAGAAA
65 GTTATCTTCCTGATGAGATACTGAGAAGT-GACCAAATTCGTCTTCCTGATGAGATACAGAGAAA
* * * *
119242 CGGATTGAAACAAATGACACGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACC
129 CGGATTAAAACAAGTGACATGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATC-AACC
* *
119307 CACGCTCGATA
193 CACGCTCAACA
119318 TGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACA
1 TGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAA-A
* ** * * *
119383 GTTATCTCCCTGATGA-AGTAC-GAGGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGA
65 GTTATCTTCCTGATGAGA-TACTGA-GAAGTG-ACCAAATTCGTCTTCCTGATGAGATACAGAGA
** * * * * * *
119446 AGTGGACTAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTAAGAAGAAGGCCAAGTCAA
127 AACGGATTAAAACAAGTGACATGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
119510 TGAAACCAGA
Statistics
Matches: 323, Mismatches: 64, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
201 153 0.47
202 2 0.01
203 1 0.00
205 6 0.02
206 161 0.50
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (203 bp):
TGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAAAG
TTATCTTCCTGATGAGATACTGAGAAGTGACCAAATTCGTCTTCCTGATGAGATACAGAGAAACG
GATTAAAACAAGTGACATGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAACCCAC
GCTCAACA
Found at i:119798 original size:17 final size:17
Alignment explanation
Indices: 119776--119821 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
119766 CCAACAGGAT
*
119776 TTAAATTCATTTTAAAA
1 TTAAATTTATTTTAAAA
**
119793 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
119810 TTAAATTTATTT
1 TTAAATTTATTT
119822 AAATCAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:120489 original size:9 final size:9
Alignment explanation
Indices: 120467--120542 Score: 62
Period size: 9 Copynumber: 8.0 Consensus size: 9
120457 TCAAAATGTT
120467 TTAATAACTA
1 TTAATAA-TA
120477 TTAATAATA
1 TTAATAATA
*
120486 TTAATAACTGTT
1 TTAATAA---TA
120498 TTAATAATA
1 TTAATAATA
**
120507 ACAATAATA
1 TTAATAATA
*
120516 ATAATAATA
1 TTAATAATA
* *
120525 TTAATGACA
1 TTAATAATA
120534 TTAATAATA
1 TTAATAATA
120543 ATAAACAGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
9 38 0.72
10 7 0.13
12 8 0.15
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (9 bp):
TTAATAATA
Found at i:120563 original size:3 final size:3
Alignment explanation
Indices: 120499--120546 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
120489 ATAACTGTTT
* * * * *
120499 TAA TAA TAA CAA TAA TAA TAA TAA TAT TAA TGA CAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
120547 ACAGTTTTCT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:120601 original size:3 final size:3
Alignment explanation
Indices: 120593--120622 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
120583 TTTAATGATA
120593 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
120623 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:121708 original size:30 final size:30
Alignment explanation
Indices: 121673--121864 Score: 169
Period size: 30 Copynumber: 6.4 Consensus size: 30
121663 AAATTGTCTG
*
121673 AAAATTCCATTTTCAACCTCGAAACCTCTA
1 AAAATTCCATTTTCAACCTCGAAACTTCTA
* * * *
121703 AAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTCAACCTCGAAACTTCTA
* *
121733 AAAATTCCATTTTTACCCTCG-AACTTCTA
1 AAAATTCCATTTTCAACCTCGAAACTTCTA
*
121762 AAAATTCCATTTTCGACCTCGAAGA-TTCTA
1 AAAATTCCATTTTCAACCTCGAA-ACTTCTA
* * * * *
121792 AAAATTCCATTTT-TACCCCCAAACCTCCA
1 AAAATTCCATTTTCAACCTCGAAACTTCTA
* * *
121821 AAATTTCCATTTTTAGTCC-CGAAACTT-TCA
1 AAAATTCCATTTTCA-ACCTCGAAACTTCT-A
121851 AAAATTACCATTTT
1 AAAATT-CCATTTT
121865 ACCCTCGTAT
Statistics
Matches: 131, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.01
29 46 0.35
30 74 0.56
31 10 0.08
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTCAACCTCGAAACTTCTA
Found at i:121795 original size:59 final size:58
Alignment explanation
Indices: 121673--121955 Score: 217
Period size: 59 Copynumber: 4.8 Consensus size: 58
121663 AAATTGTCTG
* * * * * *
121673 AAAATTCCATTTTCAACCTCGAAACCTCTAAAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTACCCTCG-AACTTCTAAAAATTCCATTTTTGA-CCCGAAACTTCTA
*
121733 AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTCCATTTTCGACCTCGAAGA-TTCTA
1 AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACC-CGAA-ACTTCTA
* * * * * *
121792 AAAATTCCATTTTTACCCCCAAACCTCCAAAATTTCCATTTTTAGTCCCGAAACTT-TCA
1 AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTCCATTTTT-GACCCGAAACTTCT-A
* * *
121851 AAAATTACCA-TTTTACCCTCGTA-TGTCCAAAAACTT-CATTTTTGACCTCGAAAC-TCTC
1 AAAATT-CCATTTTTACCCTCGAACT-TCTAAAAA-TTCCATTTTTGACC-CGAAACTTCTA
* *
121909 AAAATTACC-CTTTTACCC-CGAA-TATCTAAAAATTTCC-TTTTTAACCC
1 AAAATT-CCATTTTTACCCTCGAACT-TCTAAAAA-TTCCATTTTTGACCC
121956 CGAATATTCC
Statistics
Matches: 185, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
56 1 0.01
57 21 0.11
58 26 0.14
59 109 0.59
60 28 0.15
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCGAAACTTCTA
Found at i:121871 original size:89 final size:88
Alignment explanation
Indices: 121673--121871 Score: 237
Period size: 89 Copynumber: 2.2 Consensus size: 88
121663 AAATTGTCTG
* *
121673 AAAATTCCATTTTCAACCTCGAAACCTCTAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAT
1 AAAATTCCATTTT-ACCCTCGAAACCTCTAAAAATTCCATTTTTAACCCCAAAACCTCCAAAAAT
121738 TCCATTTTTACCCTCGAACTTCTA
65 TCCATTTTTACCCTCGAACTTCTA
* *
121762 AAAATTCCATTTT-CGACCTCGAAGA-TTCTAAAAATTCCATTTTT-ACCCCCAAACCTCCAAAA
1 AAAATTCCATTTTAC--CCTCGAA-ACCTCTAAAAATTCCATTTTTAACCCCAAAACCTCCAAAA
* *
121824 TTTCCATTTTTAGTCC-CGAAACTT-TCA
63 ATTCCATTTTTA-CCCTCG-AACTTCT-A
121851 AAAATTACCATTTTACCCTCG
1 AAAATT-CCATTTTACCCTCG
121872 TATGTCCAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
88 30 0.31
89 57 0.59
90 8 0.08
91 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (88 bp):
AAAATTCCATTTTACCCTCGAAACCTCTAAAAATTCCATTTTTAACCCCAAAACCTCCAAAAATT
CCATTTTTACCCTCGAACTTCTA
Found at i:121922 original size:29 final size:29
Alignment explanation
Indices: 121890--122015 Score: 114
Period size: 28 Copynumber: 4.4 Consensus size: 29
121880 AAAACTTCAT
* *
121890 TTTTGACCTCGAA-ACTCTCAAAATTACCC
1 TTTTGACCCCGAATA-TCTCAAAATTACCA
* * *
121919 TTTT-ACCCCGAATATCTAAAAATTTCCT
1 TTTTGACCCCGAATATCTCAAAATTACCA
* *
121947 TTTTAACCCCGAATATTCCCAAAATTACCA
1 TTTTGACCCCGAATA-TCTCAAAATTACCA
* * *
121977 TTTTGCCCCCAAAAATC-CAAAATTACCA
1 TTTTGACCCCGAATATCTCAAAATTACCA
*
122005 TTTTGCCCCCG
1 TTTTGACCCCG
122016 GGTATCCGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
28 43 0.53
29 17 0.21
30 21 0.26
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (29 bp):
TTTTGACCCCGAATATCTCAAAATTACCA
Found at i:121999 original size:58 final size:57
Alignment explanation
Indices: 121702--122000 Score: 165
Period size: 59 Copynumber: 5.1 Consensus size: 57
121692 CGAAACCTCT
* * * * * *
121702 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCT
1 AAAATTTCC-TTTTTAACCCCGAAA-TTCCCAAAATTACCA-TTTTACCC-CCAAATATCC
* ** * ** **
121761 AAAAATTCCATTTTCGACCTCGAAGATTCTAAAAATT-CCATTTTTACCCCCAAACCTCC
1 AAAATTTCC-TTTTTAACCCCGAA-ATTCCCAAAATTACCA-TTTTACCCCCAAATATCC
** * * * ** *
121820 AAAATTTCCATTTTTAGTCCCGAAACTTTCAAAAATTACCATTTTACCCTCGTATGTCC
1 AAAATTTCC-TTTTTAACCCCGAAA-TTCCCAAAATTACCATTTTACCCCCAAATATCC
* * * * * * * * *
121879 AAAAACTTCATTTTTGACCTCGAAACTCTCAAAATTACCCTTTTA-CCCCGAATATCTA
1 -AAAATTTCCTTTTTAACCCCGAAATTCCCAAAATTACCATTTTACCCCCAAATATC-C
* *
121937 AAAATTTCCTTTTTAACCCCGAATATTCCCAAAATTACCATTTTGCCCCCAAAAATCC
1 AAAATTTCCTTTTTAACCCCGAA-ATTCCCAAAATTACCATTTTACCCCCAAATATCC
121995 AAAATT
1 AAAATT
122001 ACCATTTTGC
Statistics
Matches: 184, Mismatches: 48, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
57 27 0.15
58 42 0.23
59 104 0.57
60 11 0.06
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (57 bp):
AAAATTTCCTTTTTAACCCCGAAATTCCCAAAATTACCATTTTACCCCCAAATATCC
Found at i:125610 original size:14 final size:15
Alignment explanation
Indices: 125580--125613 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
125570 CACGAGGGTT
125580 TTTCACTGTTAAATA
1 TTTCACTGTTAAATA
*
125595 TTTCACT-TTTAATA
1 TTTCACTGTTAAATA
125609 TTTCA
1 TTTCA
125614 TGTAGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTCACTGTTAAATA
Found at i:131312 original size:28 final size:30
Alignment explanation
Indices: 131277--131342 Score: 109
Period size: 28 Copynumber: 2.3 Consensus size: 30
131267 ATGATATTTT
131277 AAAATAATTTTAATAATTTTA-AATTT-AA
1 AAAATAATTTTAATAATTTTATAATTTAAA
*
131305 AAAATAATTTTAATAATTTTATATTTTAAA
1 AAAATAATTTTAATAATTTTATAATTTAAA
131335 AAAATAAT
1 AAAATAAT
131343 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 21 0.60
29 4 0.11
30 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
AAAATAATTTTAATAATTTTATAATTTAAA
Found at i:131332 original size:16 final size:15
Alignment explanation
Indices: 131281--131333 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
131271 TATTTTAAAA
131281 TAATTTTAATAATTT
1 TAATTTTAATAATTT
* **
131296 TAAATTTAA-AA-AA
1 TAATTTTAATAATTT
131309 TAATTTTAATAATTT
1 TAATTTTAATAATTT
131324 TATATTTTAA
1 TA-ATTTTAA
131334 AAAAATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 8 0.28
14 4 0.14
15 10 0.34
16 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTTTAATAATTT
Found at i:136794 original size:22 final size:22
Alignment explanation
Indices: 136743--136822 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 22
136733 GCTAGGGAAA
*
136743 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
136765 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
136788 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
136811 CAGTAGGCACAC
1 CAGTAGGCACAC
136823 GAGGTGCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.36, C:0.29, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:136837 original size:23 final size:23
Alignment explanation
Indices: 136715--136887 Score: 94
Period size: 23 Copynumber: 7.4 Consensus size: 23
136705 TGAAGTACTT
136715 AACAGTAAGCACAC-AAGTGCTAGGGA
1 AACAGTAAGCACACGAAGTGC----GA
136741 AACAGTAAGCACAC-ACAGTGC-A
1 AACAGTAAGCACACGA-AGTGCGA
* *
136763 ATCCAGTAGGCACAC-ACAGTGC-A
1 A-ACAGTAAGCACACGA-AGTGCGA
* * * *
136786 ATCAGTAGGCGCAC-ATAGCGC-A
1 AACAGTAAGCACACGA-AGTGCGA
* *
136808 AATCAGTAGGCACACGAGGTGCGA
1 AA-CAGTAAGCACACGAAGTGCGA
* *
136832 AACAGTAAGCTCACGAAGTGTGA
1 AACAGTAAGCACACGAAGTGCGA
136855 AACAGTAAGCACAC-ACAGTGCTG-
1 AACAGTAAGCACACGA-AGTGC-GA
136878 AACAGTAAGC
1 AACAGTAAGC
136888 GCGCTAGCGT
Statistics
Matches: 124, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
22 21 0.17
23 78 0.63
24 5 0.04
26 15 0.12
27 5 0.04
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.13
Consensus pattern (23 bp):
AACAGTAAGCACACGAAGTGCGA
Found at i:138927 original size:24 final size:24
Alignment explanation
Indices: 138899--138965 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
138889 AGAAATAATC
138899 TTTCAGTTAAACTTTATTTATTTG
1 TTTCAGTTAAACTTTATTTATTTG
* *
138923 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTTTATTTATTTG
* *
138947 TTTGAGTCAAACTCTTATT
1 TTTCAGTTAAACT-TTATT
138966 AGTCTAGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 32 0.89
25 4 0.11
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTCAGTTAAACTTTATTTATTTG
Found at i:139695 original size:22 final size:22
Alignment explanation
Indices: 139659--139700 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
139649 AAGCTTTGAT
139659 TTTAAAATTAGTTTTAAATTGG
1 TTTAAAATTAGTTTTAAATTGG
* *
139681 TTTAAATTTATTTTTAAATT
1 TTTAAAATTAGTTTTAAATT
139701 TAAATTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTAAAATTAGTTTTAAATTGG
Found at i:139702 original size:6 final size:6
Alignment explanation
Indices: 139681--139746 Score: 62
Period size: 6 Copynumber: 10.8 Consensus size: 6
139671 TTTAAATTGG
** ** *
139681 TTTAAA TTTATT TTTAAA TTTAAA TTTATCT TTTAAAA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTT-AAA TTTAAA TTTAAA
139730 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
139747 TCAAATTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 4 0.09
6 36 0.77
7 6 0.13
8 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:139704 original size:18 final size:18
Alignment explanation
Indices: 139681--139745 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
139671 TTTAAATTGG
139681 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
139699 TTTAAATTTATCTTTTAAAA
1 TTTAAATTTAT-TTTT-AAA
*
139719 TTTAAATTTA-CTTTAAA
1 TTTAAATTTATTTTTAAA
139736 TTTAAATTTA
1 TTTAAATTTA
139746 ATCAAATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 13 0.30
18 14 0.32
19 4 0.09
20 13 0.30
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:140547 original size:12 final size:12
Alignment explanation
Indices: 140527--140561 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
140517 TACTTTTTAA
*
140527 TAATAATAATGT
1 TAATAATAATAT
*
140539 TAGTAATAATAT
1 TAATAATAATAT
140551 TAATAATAATA
1 TAATAATAATA
140562 AACATTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:140571 original size:27 final size:27
Alignment explanation
Indices: 140523--140575 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
140513 TAACTACTTT
**
140523 TTAATAATAATAATGTTAGTAATAATA
1 TTAATAATAATAACATTAGTAATAATA
140550 TTAATAATAATAAACATT-GTAATAAT
1 TTAATAATAAT-AACATTAGTAATAAT
140576 GATAGTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (27 bp):
TTAATAATAATAACATTAGTAATAATA
Found at i:141667 original size:29 final size:29
Alignment explanation
Indices: 141610--141923 Score: 194
Period size: 28 Copynumber: 11.0 Consensus size: 29
141600 GAAGGTCCTT
141610 AAACTGTCCAAAAATT-CTATTTTTGACCCCG
1 AAACT-TCCAAAAATTAC-ATTTTT-ACCCCG
141641 AAACTTCCAAAAATTACATTTTTA--CC-
1 AAACTTCCAAAAATTACATTTTTACCCCG
* *
141667 ---C--CCAAAAATTGCATTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCCG
* ***
141691 AAACTTCCAAAAATTCCA-TTTTACCTTA
1 AAACTTCCAAAAATTACATTTTTACCCCG
*
141719 AAACTTCCAAAAATTACA-TTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCG
* * * * *
141747 AAATTTCCAAAAATTCCATTCTTAAACTCG
1 AAACTTCCAAAAATTACATT-TTTACCCCG
*** *
141777 AAACTTCTTGAAATTACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTTACCCCG
*
141806 AAACTTCCAAAAAAATTCCATTTTTGACTCCCG
1 AAACTTCC--AAAAATTACATTTTT-AC-CCCG
*
141839 AAACTTTCAAAAATTACCA-TTTTACCCCTG
1 AAACTTCCAAAAATTA-CATTTTTACCCC-G
* *
141869 -AA-TGTCCAAAAACTCCATTTTTTACCCC-
1 AAACT-TCCAAAAATTACA-TTTTTACCCCG
* *
141897 -AACTTTCAAAAGTTACCA-TTTTACCCC
1 AAACTTCCAAAAATTA-CATTTTTACCCC
141924 CGAATGTCCA
Statistics
Matches: 223, Mismatches: 38, Indels: 48
0.72 0.12 0.16
Matches are distributed among these distances:
21 17 0.08
23 3 0.01
27 12 0.05
28 59 0.26
29 41 0.18
30 48 0.22
31 29 0.13
32 4 0.02
33 10 0.04
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCG
Found at i:141683 original size:20 final size:21
Alignment explanation
Indices: 141647--141689 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
141637 CCCGAAACTT
141647 CCAAAAATTACATTTTTACCC
1 CCAAAAATTACATTTTTACCC
*
141668 CCAAAAATTGCATTTTTACCC
1 CCAAAAATTACATTTTTACCC
141689 C
1 C
141690 TAAACTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (21 bp):
CCAAAAATTACATTTTTACCC
Found at i:141700 original size:50 final size:51
Alignment explanation
Indices: 141617--141712 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 51
141607 CTTAAACTGT
141617 CCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCC
1 CCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCC
* *
141668 CCAAAAATTGC-ATTTTT-ACCCCTAAACTTCCAAAAATTCCATTTT
1 CCAAAAATT-CTATTTTTGACCCCGAAACTTCCAAAAATTACATTTT
141713 ACCTTAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
50 26 0.62
51 15 0.36
52 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (51 bp):
CCAAAAATTCTATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCC
Found at i:141917 original size:57 final size:59
Alignment explanation
Indices: 141719--142041 Score: 207
Period size: 57 Copynumber: 5.5 Consensus size: 59
141709 TTTTACCTTA
* * * * ** *
141719 AAACTTCCAAAAATTA-CATTTTACCCCCAAATTTCCAAAAATTCCATTCTTAAACT-CG
1 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATT-TTTGACTCCC
** * *
141777 AAAC-TTCTTGAAATTA-CATTTTTACCCCCAAACT-TCCAAAAAAATTCCATTTTTGACTCCC
1 AAACTTTC-AAAAATTACCA-TTTTACCCCCGAA-TGTCC--AAAAACTCCATTTTTGACTCCC
* *
141838 GAAACTTTCAAAAATTACCATTTTACCCCTGAATGTCCAAAAACTCCATTTTTTAC-CCC
1 -AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACTCCC
* ** *
141897 -AACTTTCAAAAGTTACCATTTTACCCCCGAATGTCCAAAATTTCTATTTTTGA-TCCC
1 AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACTCCC
*** * * ** * * * * *
141954 GATTTTTTTAAAAATTACCGTTTTACCTACGAATAT-CTAAAATTTCATTTTTAAC-CCC
1 -AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACTCCC
* * *
142012 AAAATTTCCCAAAATTACCATTTTGCCCCC
1 AAACTTT-CAAAAATTACCATTTTACCCCC
142042 AAGAGTCTAA
Statistics
Matches: 209, Mismatches: 41, Indels: 30
0.75 0.15 0.11
Matches are distributed among these distances:
57 56 0.27
58 44 0.21
59 44 0.21
60 22 0.11
61 14 0.07
62 24 0.11
63 5 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTTGACTCCC
Found at i:141935 original size:29 final size:29
Alignment explanation
Indices: 141846--141936 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
141836 CCGAAACTTT
*
141846 CAAAAATTACCATTTTACCCCTGAATGTC
1 CAAAAATTACCATTTTACCCCCGAATGTC
* *
141875 CAAAAACT-CCATTTTTTA-CCCC-AACT-TT
1 CAAAAATTACCA--TTTTACCCCCGAA-TGTC
*
141903 CAAAAGTTACCATTTTACCCCCGAATGTC
1 CAAAAATTACCATTTTACCCCCGAATGTC
141932 CAAAA
1 CAAAA
141937 TTTCTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
27 5 0.10
28 17 0.35
29 22 0.45
30 5 0.10
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGAATGTC
Found at i:142480 original size:96 final size:97
Alignment explanation
Indices: 142299--142491 Score: 216
Period size: 96 Copynumber: 2.0 Consensus size: 97
142289 AAAAACTTTA
* * * * *
142299 AAATCGAGGCAATATTCTTTTATTTCGAATTTTGAAAATTTGTGTCTTAACTTACTAGGCACGAT
1 AAATCAAGGCAATATTCTTTTATCTCGAATTCTGAAAATTTGTATCTAAACTTACTAGGCACGAT
* *
142364 TTTTCTTCAAATCGGAATAATCGAATATCCTT
66 TTTTCTCCAAATCGGAATAATCGAACATCCTT
* **
142396 AAATCAAGGCAATGTT-TTTTATCTCTG-ATTCTGAAAATTTGTATCTAAACTTACTAGGTGCGA
1 AAATCAAGGCAATATTCTTTTATCTC-GAATTCTGAAAATTTGTATCTAAACTTACTAGGCACGA
*
142459 CTTTTT-TCCGAAA-C-GAGATAATCTAACATCCTT
65 -TTTTTCTCC-AAATCGGA-ATAATCGAACATCCTT
142492 TTCCAAAGTT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
95 2 0.02
96 56 0.69
97 23 0.28
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (97 bp):
AAATCAAGGCAATATTCTTTTATCTCGAATTCTGAAAATTTGTATCTAAACTTACTAGGCACGAT
TTTTCTCCAAATCGGAATAATCGAACATCCTT
Found at i:143168 original size:18 final size:18
Alignment explanation
Indices: 143136--143174 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
143126 AATATCGCTT
143136 TAAACAAATTAATTATAAA
1 TAAACAAATTAATTA-AAA
*
143155 TAAA-AAATTTATTAAAA
1 TAAACAAATTAATTAAAA
143172 TAA
1 TAA
143175 TAATTACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAACAAATTAATTAAAA
Found at i:149045 original size:28 final size:27
Alignment explanation
Indices: 148997--149050 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
148987 TCATAAATAA
148997 ATATATTACAATATTAGTAAAAGATTAT
1 ATATATTACAATATTAGTAAAA-ATTAT
* **
149025 ATATATTACAATTTTTTTAAAAATTA
1 ATATATTACAATATTAGTAAAAATTA
149051 AACAAATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
ATATATTACAATATTAGTAAAAATTAT
Found at i:155742 original size:78 final size:78
Alignment explanation
Indices: 155613--155762 Score: 291
Period size: 78 Copynumber: 1.9 Consensus size: 78
155603 GAGTGGGTGG
*
155613 GGTTTGTCCATATTCTGGAACCATACCCTTTCACAAGTTTAAGGTGTGGTTGGGATGCAATGCAT
1 GGTTTGTCCACATTCTGGAACCATACCCTTTCACAAGTTTAAGGTGTGGTTGGGATGCAATGCAT
155678 ATTCCAAGTTTAA
66 ATTCCAAGTTTAA
155691 GGTTTGTCCACATTCTGGAACCATACCCTTTCACAAGTTTAAGGTGTGGTTGGGATGCAATGCAT
1 GGTTTGTCCACATTCTGGAACCATACCCTTTCACAAGTTTAAGGTGTGGTTGGGATGCAATGCAT
155756 ATTCCAA
66 ATTCCAA
155763 TATATGGACT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (78 bp):
GGTTTGTCCACATTCTGGAACCATACCCTTTCACAAGTTTAAGGTGTGGTTGGGATGCAATGCAT
ATTCCAAGTTTAA
Found at i:165503 original size:20 final size:20
Alignment explanation
Indices: 165478--165516 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
165468 TTAATGCGTT
* *
165478 ATTTTAGTCTTTCTTTTTTC
1 ATTTTAATCTTTATTTTTTC
165498 ATTTTAATCTTTATTTTTT
1 ATTTTAATCTTTATTTTTT
165517 TACCCATATC
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:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTTAATCTTTATTTTTTC
Found at i:166178 original size:28 final size:29
Alignment explanation
Indices: 166137--166199 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
166127 AAATACATCG
166137 TAAATCTTGTACTTTTATT-TTT-AATAATT
1 TAAATCTTGTACTTTT-TTATTTCAA-AATT
*
166166 TAAAT-TTTTACTTTTTTATTTCAAAATT
1 TAAATCTTGTACTTTTTTATTTCAAAATT
166194 TAAATC
1 TAAATC
166200 AATTTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 2 0.07
28 21 0.70
29 7 0.23
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (29 bp):
TAAATCTTGTACTTTTTTATTTCAAAATT
Found at i:168123 original size:13 final size:13
Alignment explanation
Indices: 168105--168129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168095 TTAGATATGT
168105 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
168118 TTTTTTTCTTTT
1 TTTTTTTCTTTT
168130 TGGTTATTGG
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:173077 original size:2 final size:2
Alignment explanation
Indices: 173070--173098 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
173060 TTTTGTTTCG
173070 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
173099 CTATTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:173661 original size:15 final size:15
Alignment explanation
Indices: 173643--173677 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
173633 GCAGATTTCG
173643 TATTTTTCAATTTTA
1 TATTTTTCAATTTTA
*
173658 TATTTTTGAATTTTA
1 TATTTTTCAATTTTA
*
173673 AATTT
1 TATTT
173678 GTTTTAGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TATTTTTCAATTTTA
Found at i:177064 original size:30 final size:29
Alignment explanation
Indices: 177028--177462 Score: 208
Period size: 30 Copynumber: 14.9 Consensus size: 29
177018 ACACGGGGGT
* *
177028 AAAATGGTAGTTTTGGAAGGTTCGGAGTAA
1 AAAATGGGATTTTTGGAAGGTTCGGAGT-A
*
177058 AAAATGGGATTTTTGGAA-GTTCGAGGGT-
1 AAAATGGGATTTTTGGAAGGTTCG-GAGTA
* * *
177086 AAAATGGTAATTTTCGAAAGGTTC-GAGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGA-GT-A
*
177117 AAAATGGGATTTTTGGAA-GTT-TGATGGT-
1 AAAATGGGATTTTTGGAAGGTTCGGA--GTA
* * *
177145 AAAATGGTAATTTTCGGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGAGT-A
*
177176 AAAATGGGATTTTTGGAA-GTTTGGAGGT-
1 AAAATGGGATTTTTGGAAGGTTCGGA-GTA
* *
177204 AAAATGGTAATTTTTGGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTTGGAAGGTTCGGAGT-A
* * *
177235 AAAAGGGGATTTTTGGAA-GTTAAGGGGT-
1 AAAATGGGATTTTTGGAAGGTT-CGGAGTA
** ** *
177263 AAAATGATATTTTTAAAAGGTTCGGGGTCA
1 AAAATGGGATTTTTGGAAGGTTCGGAGT-A
* *
177293 AAAATGGGATTTTTGGAA-GTTAGGGGGT-
1 AAAATGGGATTTTTGGAAGGTT-CGGAGTA
** * *
177321 AAAATGATAATTTTTAGAAGATTCGGAGTTA
1 AAAATG-GGATTTTTGGAAGGTTCGGAG-TA
* *
177352 AAAATGAGATTTTTGGAA-GTTCGAGGGT-
1 AAAATGGGATTTTTGGAAGGTTCG-GAGTA
* * *
177380 -AAATGGTATTTTTTGAAAGGTTCATG-GTCA
1 AAAATGGGA-TTTTTGGAAGGTTC-GGAGT-A
*
177410 AAAAGGGGATTTTTGGAA-GTTC-GATGGT-
1 AAAATGGGATTTTTGGAAGGTTCGGA--GTA
*
177438 AAAATGGTAATTTTTGGAA-GTTCGG
1 AAAATGG-GATTTTTGGAAGGTTCGG
177463 GGGTAAAATG
Statistics
Matches: 311, Mismatches: 55, Indels: 78
0.70 0.12 0.18
Matches are distributed among these distances:
27 7 0.02
28 62 0.20
29 97 0.31
30 112 0.36
31 33 0.11
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGGTTCGGAGTA
Found at i:177335 original size:117 final size:116
Alignment explanation
Indices: 177023--177756 Score: 751
Period size: 117 Copynumber: 6.2 Consensus size: 116
177013 CGGATACACG
* * * * * *
177023 GGGGTAAAATGGTAGTTTTGGAAGGTTCGGAGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAA
1 GGGGTAAAATGGTATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
* * *
177088 AATGGTAA-TTTTCGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTT
66 AATGGTAATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTA
* ** *
177139 GATGGTAAAATGGTAATTTTCGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGAGGT
1 G-GGGTAAAATGGT-ATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
177204 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAGGGGATTTTTGGAAGTTAA
64 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT-A
* * *
177258 GGGGTAAAATGATATTTTTAAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTAGGGGGTAA
1 GGGGTAAAATGGTATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
* * * * * *
177323 AATGATAATTTTTAGAAGATTCGGAGTTAAAAATGAGATTTTTGGAAGTTC
66 AATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTA
* ** * * **
177374 GAGGGT-AAATGGTATTTTTTGAAAGGTTCATGGTCAAAAAGGGGATTTTTGGAAGTTCGATGGT
1 G-GGGTAAAATGGTATTTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
177438 AAAATGGTAATTTTTGGAA-GTTCGGGGGTAAAATGGTAATTTTAGAATGGGATTTTTGGAAGTT
64 AAAATGGTAATTTTTAGAAGGTTC-GGGG-----T--CAA----A-AATGGGATTTTTGGAAGTT
*
177502 CG
116 -A
* * * **
177504 GGGGTAAAAAGGTAATTTTAGAAGGTTCGAGGTCAAAAATAAGATTTTTGGAAGTTTGGGGGTAA
1 GGGGTAAAATGGTATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
* * * *
177569 AATGGTAATTTTTAGAAGGTTTGGGGTTAAAAATTGGATTTTTGGAAGTTT
66 AATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTA
* * *
177620 GAGGGTAAAATGGTAATTTTAGAAGGTTCGGGATCAAAAAT-GAATTTTTTGGAAGTTTGGGGGT
1 G-GGGTAAAATGGTATTTTTAGAAGGTTCGGGGTCAAAAATGGGA-TTTTTGGAAGTTTGGGGGT
* * *
177684 AAAATGGTAA-TTTTAGAAGATTCGGGGTCAAAAATGAGTTTTTTGGAAGTTTA
64 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTA
*
177737 -GGGTCGAAAATGGGATTTTT
1 GGGGT--AAAATGGTATTTTT
177757 GGATAGTTTA
Statistics
Matches: 520, Mismatches: 71, Indels: 53
0.81 0.11 0.08
Matches are distributed among these distances:
115 4 0.01
116 52 0.10
117 258 0.50
118 97 0.19
119 6 0.01
122 4 0.01
124 4 0.01
128 1 0.00
129 78 0.15
130 16 0.03
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.34
Consensus pattern (116 bp):
GGGGTAAAATGGTATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
AATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTA
Found at i:177480 original size:58 final size:58
Alignment explanation
Indices: 177024--177759 Score: 587
Period size: 59 Copynumber: 12.4 Consensus size: 58
177014 GGATACACGG
* *
177024 GGGTAAAATGGT-AGTTTTGGAAGGTTCGGAGTAAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* * * *
177082 GGGTAAAATGGTAATTTTCGAAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* * *
177141 TGGTAAAATGGTAATTTTCGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTG-
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* *
177199 GAGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAGGGGATTTTTGGAAGTT-AA
1 G-GGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* ** * *
177258 GGGGTAAAATGAT-ATTTTTAAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTAGG
1 -GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* * * * *
177317 GGGTAAAATGATAATTTTTAGAAGATTCGGAGTTAAAAATGAGATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGG-GGTAAAAATGGGATTTTTGGAAGTTCGA
* * ** *
177376 GGGT-AAATGGTATTTTTTGAAAGGTTCATGGTCAAAAAGGGGATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* * ** *
177434 TGGTAAAATGGTAATTTTTGGAA-GTTCGGGGGT-AAAATGGTAATTTTAGAATGGGATTTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGGTTC-GGGGTAAAAATGG-GATTTT----T-GGA-AGTTCG
177497 AA
58 -A
** ** ** * * * ** * *
177499 GTTCGGGGGTAAAAAGGTAATTTTAGAAGGTTCGAGGTCAAAAATAAGATTTTTGGAAGTTTGG
1 -----GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
* * * *
177563 GGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTTAAAAATTGGATTTTTGGAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGG-TAAAAATGGGATTTTTGGAAGTTCGA
* * * * *
177622 GGGTAAAATGGTAA-TTTTAGAAGGTTCGGGATCAAAAAT-GAATTTTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGA-TTTTTGGAAGTTCGA
* * * * *
177680 GGGTAAAATGGTAA-TTTTAGAAGATTCGGGGTCAAAAATGAGTTTTTTGGAAGTT-TA
1 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-AAAAATGGGATTTTTGGAAGTTCGA
*
177737 GGGTCGAAAATGG-GATTTTTGGA
1 GGGT--AAAATGGTAATTTTTGGA
177760 TAGTTTAGGG
Statistics
Matches: 557, Mismatches: 88, Indels: 65
0.78 0.12 0.09
Matches are distributed among these distances:
57 15 0.03
58 202 0.36
59 289 0.52
60 4 0.01
62 1 0.00
63 3 0.01
64 3 0.01
65 4 0.01
66 3 0.01
67 1 0.00
70 18 0.03
71 9 0.02
72 5 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAATGGGATTTTTGGAAGTTCGA
Found at i:177500 original size:42 final size:42
Alignment explanation
Indices: 177447--177526 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
177437 TAAAATGGTA
*
177447 ATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTAGAATGGG
1 ATTTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTAGAATGGG
177489 ATTTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTAGAA
1 ATTTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTAGAA
177527 GGTTCGAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (42 bp):
ATTTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTAGAATGGG
Found at i:177552 original size:246 final size:246
Alignment explanation
Indices: 177240--177710 Score: 646
Period size: 246 Copynumber: 1.9 Consensus size: 246
177230 GGTCAAAAAG
* * * **
177240 GGGATTTTTGGAAGTTAAGGGGTAAAATGATATTTTTAAAAGGTTCGGGGTCAAAAATGGGATTT
1 GGGATTTTTGGAAGTTAAGGGGTAAAAAGATAATTTTAAAAGGTTCGAGGTCAAAAATAAGATTT
177305 TTGGAAGTTAGGGGGTAAAATGATAATTTTTAGAAGATTCGGAGTTAAAAA-TGAGATTTTTGGA
66 TTGGAAGTTAGGGGGTAAAATGATAATTTTTAGAAGATTCGGAGTTAAAAATTG-GATTTTTGGA
* * * *
177369 AGTTCGAGGGT-AAATGGTATTTTTTGAAAGGTTCATGG-TCAAAAAGGGGA-TTTTTGGAAGTT
130 AGTTCGAGGGTAAAATGGTAATTTTAG-AAGGTTC-GGGATCAAAAA-GGAATTTTTTGGAAGTT
* *
177431 CGATGGTAAAATGGTAATTTTTGGAAG-TTCGGGGGTAAAATGGTAATTTTAGAAT
192 CGAGGGTAAAATGGTAA-TTTTAGAAGATTCGGGGGTAAAATGGTAATTTTAGAAT
** * *
177486 GGGATTTTTGGAAGTTCGGGGGTAAAAAGGTAATTTTAGAAGGTTCGAGGTCAAAAATAAGATTT
1 GGGATTTTTGGAAGTTAAGGGGTAAAAAGATAATTTTAAAAGGTTCGAGGTCAAAAATAAGATTT
* * * * *
177551 TTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTTGGGGTTAAAAATTGGATTTTTGGAA
66 TTGGAAGTTAGGGGGTAAAATGATAATTTTTAGAAGATTCGGAGTTAAAAATTGGATTTTTGGAA
* * * *
177616 GTTTGAGGGTAAAATGGTAATTTTAGAAGGTTCGGGATCAAAAATGAATTTTTTGGAAGTTTGGG
131 GTTCGAGGGTAAAATGGTAATTTTAGAAGGTTCGGGATCAAAAAGGAATTTTTTGGAAGTTCGAG
177681 GGTAAAATGGTAATTTTAGAAGATTCGGGG
196 GGTAAAATGGTAATTTTAGAAGATTCGGGG
177711 TCAAAAATGA
Statistics
Matches: 196, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
245 12 0.06
246 169 0.86
247 15 0.08
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (246 bp):
GGGATTTTTGGAAGTTAAGGGGTAAAAAGATAATTTTAAAAGGTTCGAGGTCAAAAATAAGATTT
TTGGAAGTTAGGGGGTAAAATGATAATTTTTAGAAGATTCGGAGTTAAAAATTGGATTTTTGGAA
GTTCGAGGGTAAAATGGTAATTTTAGAAGGTTCGGGATCAAAAAGGAATTTTTTGGAAGTTCGAG
GGTAAAATGGTAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTTAGAAT
Found at i:177740 original size:29 final size:28
Alignment explanation
Indices: 177490--177765 Score: 136
Period size: 30 Copynumber: 9.5 Consensus size: 28
177480 TAGAATGGGA
*
177490 TTTTTGGAAGTTCGGGGGT-AAAAA-GGT
1 TTTTTGGAAGTT-TGGGGTCAAAAATGGT
* * * * * *
177517 AATTTTAGAAGGTTCGAGGTCAAAAATAAGA
1 -TTTTTGGAA-GTTTGGGGTCAAAAAT-GGT
177548 TTTTTGGAAGTTTGGGGGT--AAAATGGT
1 TTTTTGGAAGTTT-GGGGTCAAAAATGGT
* * *
177575 AATTTTTAGAAGGTTTGGGGTTAAAAATTGGA
1 --TTTTTGGAA-GTTTGGGGTCAAAAA-TGGT
177607 TTTTTGGAAGTTTGAGGGT--AAAATGGT
1 TTTTTGGAAGTTTG-GGGTCAAAAATGGT
* * * * *
177634 AATTTTAGAAGGTTCGGGATCAAAAATGAAT
1 -TTTTTGGAA-GTTTGGGGTCAAAAATG-GT
177665 TTTTTGGAAGTTTGGGGGT--AAAATGGT
1 TTTTTGGAAGTTT-GGGGTCAAAAATGGT
* * *
177692 AATTTTAGAAGATTCGGGGTCAAAAATGAGT
1 -TTTTTGGAAG-TTTGGGGTCAAAAATG-GT
* * *
177723 TTTTTGGAAGTTTAGGGTCGAAAATGGGA
1 TTTTTGGAAGTTTGGGGTCAAAAAT-GGT
177752 TTTTTGGATAGTTT
1 TTTTTGGA-AGTTT
177766 AGGGACCTCC
Statistics
Matches: 188, Mismatches: 35, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
27 5 0.03
28 49 0.26
29 59 0.31
30 64 0.34
31 8 0.04
32 3 0.02
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (28 bp):
TTTTTGGAAGTTTGGGGTCAAAAATGGT
Found at i:179664 original size:17 final size:17
Alignment explanation
Indices: 179635--179715 Score: 81
Period size: 17 Copynumber: 4.8 Consensus size: 17
179625 TTAAATTTGG
*
179635 AAATAATTTTAAACTTA
1 AAATAAATTTAAACTTA
** *
179652 ATTTAAATTTAAATTTA
1 AAATAAATTTAAACTTA
* *
179669 AAATAAATTTAAATTTT
1 AAATAAATTTAAACTTA
* **
179686 AAACAAATTTAATTTTA
1 AAATAAATTTAAACTTA
179703 AAATAAATTTAAA
1 AAATAAATTTAAA
179716 GGGAGTATGG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTAAACTTA
Found at i:179673 original size:34 final size:35
Alignment explanation
Indices: 179617--179715 Score: 112
Period size: 34 Copynumber: 2.8 Consensus size: 35
179607 TTTTATTTAT
* *
179617 TTTAAATTTTAAATTTGGAAATAATTTTAAA-CTTAA
1 TTTAAA-TTTAAATTT-AAAATAAATTTAAATCTTAA
*
179653 TTTAAATTTAAATTTAAAATAAATTTAAATTTTAA
1 TTTAAATTTAAATTTAAAATAAATTTAAATCTTAA
** *
179688 -ACAAATTTAATTTTAAAATAAATTTAAA
1 TTTAAATTTAAATTTAAAATAAATTTAAA
179716 GGGAGTATGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 37 0.66
35 13 0.23
36 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (35 bp):
TTTAAATTTAAATTTAAAATAAATTTAAATCTTAA
Found at i:184577 original size:30 final size:30
Alignment explanation
Indices: 184536--184598 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
184526 CCTTCTGGTT
*
184536 TCTACGGAGATATTTGTCCCGATTTTCACC
1 TCTACGGAGATACTTGTCCCGATTTTCACC
*
184566 TCTATGGAGATACTTGTCCCGATTTTCACC
1 TCTACGGAGATACTTGTCCCGATTTTCACC
184596 TCT
1 TCT
184599 TTCTCTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (30 bp):
TCTACGGAGATACTTGTCCCGATTTTCACC
Done.