Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010829.1 Kokia drynarioides strain JFW-HI SEQ_125796, 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: 380201
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:622 original size:18 final size:18
Alignment explanation
Indices: 599--633 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
589 ATTCGAGTTG
*
599 ACTCAAATAACTTGATTA
1 ACTCAAATAACTCGATTA
617 ACTCAAATAACTCGATT
1 ACTCAAATAACTCGATT
634 CGTTTAACTC
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:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (18 bp):
ACTCAAATAACTCGATTA
Found at i:1734 original size:17 final size:16
Alignment explanation
Indices: 1686--1734 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1676 TATGTTCATA
*
1686 TTATTTTATTCAATAT
1 TTATTTTATTCATTAT
*
1702 TTATTTTTATTTATTATT
1 TTA-TTTTATTCATTA-T
*
1720 TTATTTCATTCATTA
1 TTATTTTATTCATTA
1735 AATTTGCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.11
17 20 0.74
18 4 0.15
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTATTCATTAT
Found at i:5721 original size:21 final size:20
Alignment explanation
Indices: 5697--5735 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5687 AATGTCATAT
*
5697 TTCAAGAAATTTATTATATCC
1 TTCAA-AAATTCATTATATCC
*
5718 TTCAATAATTCATTATAT
1 TTCAAAAATTCATTATAT
5736 ACATAAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
TTCAAAAATTCATTATATCC
Found at i:6184 original size:145 final size:145
Alignment explanation
Indices: 5908--6186 Score: 337
Period size: 145 Copynumber: 1.9 Consensus size: 145
5898 ATATCAAATG
* * * * * *
5908 TGAGCTCAACTCTAGTTGGATATACCAACGATATTTTGCACCTAGCGCTAGTCGGATAACCGATA
1 TGAGCTCAACTCTAATTGGATATACCAACGAAATTTTACACCCAACGCTAGTCGGATAACCGACA
* * * * * * * ** * *
5973 AGTTGTGTGCCCAGCACTAGTCAGATAAATTGACGGAGATTGCGTCCAGCGCTAGTCGAATAAAC
66 AGTTATGTGCCCAACACTAATCAAATAAATAGACGAAGATTACACCCAACGCTAATCGAATAAAC
6038 CGACAATTTCAAAGA
131 CGACAATTTCAAAGA
6053 TGAGCTCAACTCTAATTGGATATACCAAC-AAATGTTTACACCCAACGCTAGTCGGATAAACCGA
1 TGAGCTCAACTCTAATTGGATATACCAACGAAAT-TTTACACCCAACGCTAGTCGGAT-AACCGA
* * * *
6117 CGATTTATGTGCCCAACACTAATCAAATAAATAGATGAAGGTTACACCCAACGCTAATCGAAT-A
64 CAAGTTATGTGCCCAACACTAATCAAATAAATAGACGAAGATTACACCCAACGCTAATCGAATAA
6181 ACCGAC
129 ACCGAC
6187 GAATATAATT
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
144 3 0.03
145 55 0.50
146 53 0.48
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (145 bp):
TGAGCTCAACTCTAATTGGATATACCAACGAAATTTTACACCCAACGCTAGTCGGATAACCGACA
AGTTATGTGCCCAACACTAATCAAATAAATAGACGAAGATTACACCCAACGCTAATCGAATAAAC
CGACAATTTCAAAGA
Found at i:12165 original size:20 final size:20
Alignment explanation
Indices: 12140--12186 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
12130 TCTTTTAAGA
12140 AAAAATTTGAAATGGAAAAC
1 AAAAATTTGAAATGGAAAAC
12160 AAAAATTTGAAATGGAAAAC
1 AAAAATTTGAAATGGAAAAC
12180 AAGAAAT
1 AA-AAAT
12187 GTTATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.62, C:0.04, G:0.15, T:0.19
Consensus pattern (20 bp):
AAAAATTTGAAATGGAAAAC
Found at i:12691 original size:30 final size:30
Alignment explanation
Indices: 12655--12712 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12645 TTAATAAAGG
*
12655 TAAAATTGT-ATTTTGATCCTCTAAAAATGA
1 TAAAATTGTGATTTT-ATCCTATAAAAATGA
*
12685 TAAAATTTTGATTTTATCCTATAAAAAT
1 TAAAATTGTGATTTTATCCTATAAAAAT
12713 TGCACTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (30 bp):
TAAAATTGTGATTTTATCCTATAAAAATGA
Found at i:18541 original size:30 final size:29
Alignment explanation
Indices: 18477--18542 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
18467 AAATGATTTT
* *
18477 AATTTTATTTTGAATTTTTTTTTAACTATC
1 AATTTTATTTTCAATTTTTTTTT-ACTAAC
*
18507 AATTTTTTTTTCAATTTGTTTTTT-CTAAC
1 AATTTTATTTTCAATTT-TTTTTTACTAAC
*
18536 AAATTTA
1 AATTTTA
18543 ATGAATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.30
30 15 0.50
31 6 0.20
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (29 bp):
AATTTTATTTTCAATTTTTTTTTACTAAC
Found at i:19235 original size:19 final size:19
Alignment explanation
Indices: 19179--19250 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
19169 TATTTAGTCA
*
19179 AATAATAAA-ATATTAATAT
1 AATAATAAATAT-TTATTAT
* *
19198 AATTAATATAATTTATTATTTT
1 AA-TAATA-AATAT-TTATTAT
19220 AATAATAAATATTTATTAT
1 AATAATAAATATTTATTAT
*
19239 AATTATAAATAT
1 AATAATAAATAT
19251 GTTAATAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 19 0.43
20 9 0.20
21 7 0.16
22 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAATAAATATTTATTAT
Found at i:19246 original size:22 final size:21
Alignment explanation
Indices: 19180--19246 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
19170 ATTTAGTCAA
*
19180 ATAATAAAATATTAATATAA-T
1 ATAATAAAAT-TTATTATAATT
* *
19201 -TAATATAATTTATTAT-TTT
1 ATAATAAAATTTATTATAATT
19220 AATAATAAATATTTATTATAATT
1 -ATAATAAA-ATTTATTATAATT
19243 ATAA
1 ATAA
19247 ATATGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 6 0.17
22 13 0.36
23 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATAAAATTTATTATAATT
Found at i:25419 original size:17 final size:17
Alignment explanation
Indices: 25334--25422 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
25324 CAATATAAAC
25334 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
25351 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAA--A-TTTAAT
25371 ATTAAATTAAA---AAT
1 ATTAAATTAAATTTAAT
*
25385 ATT--ATTAAA-ATAAGT
1 ATTAAATTAAATTTAA-T
25400 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
25417 ATTAAA
1 ATTAAA
25423 CTATTAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 22
0.72 0.01 0.27
Matches are distributed among these distances:
12 6 0.10
14 8 0.13
15 4 0.07
17 21 0.35
18 5 0.08
19 2 0.03
20 14 0.23
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:30133 original size:18 final size:18
Alignment explanation
Indices: 30102--30136 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30092 CCTTAATCAA
* *
30102 TTTCTTCTTTCCCTTAGC
1 TTTCTACTTCCCCTTAGC
30120 TTTCTACTTCCCCTTAG
1 TTTCTACTTCCCCTTAG
30137 AGGATGAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.34, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTCTACTTCCCCTTAGC
Found at i:38035 original size:38 final size:39
Alignment explanation
Indices: 37967--38040 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
37957 TACAACTGAT
*
37967 CATGTCAACTAATTGCAAAAGACAAAACATGTTGGTCAC
1 CATGTCAACTAACTGCAAAAGACAAAACATGTTGGTCAC
* *
38006 CATGTCACCTAACTGC-AAAGACCAAACATGTTGGT
1 CATGTCAACTAACTGCAAAAGACAAAACATGTTGGT
38041 GAACTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 18 0.56
39 14 0.44
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (39 bp):
CATGTCAACTAACTGCAAAAGACAAAACATGTTGGTCAC
Found at i:43663 original size:23 final size:23
Alignment explanation
Indices: 43637--43773 Score: 186
Period size: 23 Copynumber: 6.0 Consensus size: 23
43627 TTTACACATT
* *
43637 AATCACATTAACTATTAAGCCTA
1 AATCACATTAACTTTTAAGCATA
43660 AATCACATTAACTTTTAAGCATA
1 AATCACATTAACTTTTAAGCATA
* * *
43683 AATAACATTAAATTTTAAGCACA
1 AATCACATTAACTTTTAAGCATA
* *
43706 GATCACATTATCTTTTAAGCATA
1 AATCACATTAACTTTTAAGCATA
*
43729 AATCACATTAACTCTTAAGCATA
1 AATCACATTAACTTTTAAGCATA
*
43752 AATCACATTATCTTTTAA-CATA
1 AATCACATTAACTTTTAAGCATA
43774 TAACGCATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 4 0.04
23 95 0.96
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.34
Consensus pattern (23 bp):
AATCACATTAACTTTTAAGCATA
Found at i:44900 original size:18 final size:19
Alignment explanation
Indices: 44871--44909 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
44861 AAAATATCAT
*
44871 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
44890 ATTAA-TTTAATTTACTTG
1 ATTAATTTTAATTTACTTG
44908 AT
1 AT
44910 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:44933 original size:13 final size:13
Alignment explanation
Indices: 44915--44939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44905 TTGATCAAAA
44915 TTAATTTTTCAAC
1 TTAATTTTTCAAC
44928 TTAATTTTTCAA
1 TTAATTTTTCAA
44940 GAAAATTCTT
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:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTTTCAAC
Found at i:50893 original size:13 final size:13
Alignment explanation
Indices: 50875--50900 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50865 CAATCATCAA
50875 AACAAACAATTTT
1 AACAAACAATTTT
50888 AACAAACAATTTT
1 AACAAACAATTTT
50901 GACTCTCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AACAAACAATTTT
Found at i:52228 original size:43 final size:43
Alignment explanation
Indices: 52179--52309 Score: 101
Period size: 45 Copynumber: 3.0 Consensus size: 43
52169 TTATTAAGAT
*
52179 AAATATTAGATTAAATTTAATATTAAATCTTATTAAAATAATA
1 AAATATTAAATTAAATTTAATATTAAATCTTATTAAAATAATA
* * * * *
52222 AAATATT-TATCTACAAGATAAATACTTTAATATTAAATTAATAA-AAT-
1 AAATATTAAAT-TA-AA-TTTAATA-TTAAATCTT--ATTAA-AATAATA
*
52269 AAGTATTAAATTAAATTTAATATTAAA-C-TATTAAAATAATA
1 AAATATTAAATTAAATTTAATATTAAATCTTATTAAAATAATA
52310 TTATTTTTGG
Statistics
Matches: 67, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
39 2 0.03
40 8 0.12
42 3 0.04
43 9 0.13
44 6 0.09
45 10 0.15
46 9 0.13
47 8 0.12
48 10 0.15
49 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (43 bp):
AAATATTAAATTAAATTTAATATTAAATCTTATTAAAATAATA
Found at i:55651 original size:15 final size:16
Alignment explanation
Indices: 55625--55654 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55615 TCAAATCATG
55625 CAAAACAATCCAAAAA
1 CAAAACAATCCAAAAA
55641 CAAAA-AATCCAAAA
1 CAAAACAATCCAAAA
55655 GAAAGTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.23, G:0.00, T:0.07
Consensus pattern (16 bp):
CAAAACAATCCAAAAA
Found at i:61661 original size:19 final size:19
Alignment explanation
Indices: 61637--61676 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
61627 ATTAATTTTC
61637 ATCAAATAAAATAAAATTA
1 ATCAAATAAAATAAAATTA
* *
61656 ATCAAATTAATTAAAATTA
1 ATCAAATAAAATAAAATTA
61675 AT
1 AT
61677 ATGATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAAATAAAATAAAATTA
Found at i:61807 original size:37 final size:36
Alignment explanation
Indices: 61759--61834 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
61749 ATTCAAAAAA
61759 TAATATTATTTTAATAGT-TTAATATTAACTTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATTAA-TTTAATAT
*
61795 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAATAT
61832 TAA
1 TAA
61835 AGTGATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:61832 original size:11 final size:11
Alignment explanation
Indices: 61759--61834 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
61749 ATTCAAAAAA
*
61759 TAATATTATTT
1 TAATATTAATT
61770 TAATAGTTTAATAT
1 TAATA--TTAAT-T
61784 TAACT-TTAATT
1 TAA-TATTAATT
*
61795 TAATACTTATTT
1 TAATA-TTAATT
*
61807 TAATAGT-ATT
1 TAATATTAATT
61817 T--TATTAATT
1 TAATATTAATT
61826 TAATATTAA
1 TAATATTAA
61835 AGTGATTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 4 0.08
11 16 0.31
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:64441 original size:15 final size:14
Alignment explanation
Indices: 64421--64463 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
64411 TAGTTTCGTC
64421 ACTATAGTTTTAGA
1 ACTATAGTTTTAGA
64435 GACTATAGTTTCTAGA
1 -ACTATAGTTT-TAGA
*
64451 ATCTAAAGTTTTA
1 A-CTATAGTTTTA
64464 CAGCCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (14 bp):
ACTATAGTTTTAGA
Found at i:73682 original size:20 final size:20
Alignment explanation
Indices: 73660--73744 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
73650 TGCGTTTAGC
*
73660 ATTTTTGACCAAAGTTTGCCA
1 ATTTTTGACCAATGTTTG-CA
* * * *
73681 TTTTTTTATCAATGTTCGCA
1 ATTTTTGACCAATGTTTGCA
*
73701 ATTATTGACCAATGTTTGCA
1 ATTTTTGACCAATGTTTGCA
* * *
73721 ATTTTTAACCAATATTTGCT
1 ATTTTTGACCAATGTTTGCA
73741 ATTT
1 ATTT
73745 CTAATCTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
20 37 0.74
21 13 0.26
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (20 bp):
ATTTTTGACCAATGTTTGCA
Found at i:74615 original size:96 final size:95
Alignment explanation
Indices: 74497--75034 Score: 364
Period size: 96 Copynumber: 5.5 Consensus size: 95
74487 GAAGCTATAG
* *
74497 AAGCAAATCTTATCTC-CTTGAAGTTGCAGTGGAGTAAGATGAAGCTACGACAATCCTACATCCT
1 AAGCAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAAGATGAAGCTACGACAATCCTACATCCT
* * *
74561 TGAAGTTGCGAGGATCTGATTAAAACTACGA
65 TGAAGTTGCAAGGGTCAGATTAAAACTACGA
* * ** * * *
74592 AAGCGAATCTTTATCTCTCTGAAGATATAGTAGAGCAAGATTAAAGCTAC-AAAATCAAATACTA
1 AAGCAAATC-TTATCTCTCTGAAGTTGCAGTAGAGCAAGA-TGAAGCTACGACAATC--CTAC-A
* * * * * * *
74656 TACCCCTAAAGTTGTAGAGGGGCAAATTAAAGCTA-TA
61 T--CCTTGAAGTTGCA-AGGGTCAGATTAAAACTACGA
* * * * *
74693 GAAGCAAATCTTATCTC-CTTGAAGTTACAATGGAGCAAGATAAAGCTACGACAATCTTACATCC
1 -AAGCAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAAGATGAAGCTACGACAATCCTACATCC
* * *
74757 TTGATGTTGCAAGGGTTATATTAAAACTACGA
64 TTGAAGTTGCAAGGGTCAGATTAAAACTACGA
* * * * * ** *
74789 AAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGTAAGATTAATGCTGCAAAATCAAATCCTAT
1 AAGCAAATC-TTATCTCTCTGAAGTTGCAGTAGAGCAAGATGAA-GCT--ACGA-C-AATCCTAC
* * * * * * * * **
74854 ACCCCTAAATTTGTAAAGGGGCAGATTGAAGCTATAA
60 ATCCTTGAAGTTG-CAAGGGTCAGATTAAAACTACGA
* * * * * **
74891 AAGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAGCTGAATCTACGACAATCCTATGTCCTT
1 AAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAGATGAAGCTACGACAATCCTACATCCTT
* * *
74956 GAAGTTGCAAGGATCGGATTAAAACTACCA
66 GAAGTTGCAAGGGTCAGATTAAAACTACGA
* *
74986 AAGCAAATCTTTATCTCTTTGAAGTTGCAGTAGAGCAAGATGAAACTAC
1 AAGCAAATC-TTATCTCTCTGAAGTTGCAGTAGAGCAAGATGAAGCTAC
75035 CTTATTAAAT
Statistics
Matches: 332, Mismatches: 89, Indels: 43
0.72 0.19 0.09
Matches are distributed among these distances:
95 55 0.17
96 112 0.34
97 13 0.04
98 7 0.02
99 7 0.02
100 13 0.04
101 80 0.24
102 45 0.14
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (95 bp):
AAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAGATGAAGCTACGACAATCCTACATCCTT
GAAGTTGCAAGGGTCAGATTAAAACTACGA
Found at i:74691 original size:197 final size:197
Alignment explanation
Indices: 74449--75117 Score: 829
Period size: 197 Copynumber: 3.4 Consensus size: 197
74439 AGCAACAACC
* * *
74449 TCAAATCCTATACTCTTAAAGTTGTAGAGGGGCGAATTGAAGCTATAGAAGCAAATCTTATCTCC
1 TCAAATCCTATACCCCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAGAAGCAAATCTTATCTCC
* *
74514 TTGAAGTTGCAGTGGAGTAAGATGAAGCTACGACAATCCTACATCCTTGAAGTTGCGAGGATCTG
66 TTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACAATCCTACATCCTTGAAGTTGCAAGGATCTG
* * *
74579 ATTAAAACTACGAAAGCGAATCTTTATCTCTCTGAAGATATAGTAGAGCAAGATTAAAGCTACAA
131 ATTAAAACTACGAAAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGCAAGATTAAAGCTACAA
74644 AA
196 AA
* *
74646 TCAAATACTATACCCCTAAAGTTGTAGAGGGGCAAATTAAAGCTATAGAAGCAAATCTTATCTCC
1 TCAAATCCTATACCCCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAGAAGCAAATCTTATCTCC
* * * * * *
74711 TTGAAGTTACAATGGAGCAAGATAAAGCTACGACAATCTTACATCCTTGATGTTGCAAGGGT-TA
66 TTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACAATCCTACATCCTTGAAGTTGCAAGGATCT-
* * * *
74775 TATTAAAACTACGAAAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGTAAGATTAATGCTGCA
130 GATTAAAACTACGAAAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGCAAGATTAAAGCTACA
74840 AAA
195 AAA
* * * *
74843 TCAAATCCTATACCCCTAAATTTGTAAAGGGGCAGATTGAAGCTATAAAAGCAAATCTTATCTCC
1 TCAAATCCTATACCCCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAGAAGCAAATCTTATCTCC
* * * * ** *
74908 CTGAAGTTGTAGTGGAGCAAGCTGAATCTACGACAATCCTATGTCCTTGAAGTTGCAAGGATCGG
66 TTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACAATCCTACATCCTTGAAGTTGCAAGGATCTG
* * * * * **
74973 ATTAAAACTACCAAAGCAAATCTTTATCTCTTTGAAGTTGCAGTAGAGCAAGATGAAA-CTACCT
131 ATTAAAACTACGAAAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGCAAGATTAAAGCTACAA
*
75037 TA
196 AA
* * * * * * ** * * * * *
75039 TTAAATTCTATCCCCCTGAAGTTGTAGTGGGTCGGATTGAAGTTACAAAAGCAAATCCTATCTTC
1 TCAAATCCTATACCCCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAGAAGCAAATCTTATCTCC
* *
75104 ATGAAGTTGTAGTG
66 TTGAAGTTGCAGTG
75118 AAATGGATAA
Statistics
Matches: 405, Mismatches: 65, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
196 70 0.17
197 335 0.83
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (197 bp):
TCAAATCCTATACCCCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAGAAGCAAATCTTATCTCC
TTGAAGTTGCAGTGGAGCAAGATGAAGCTACGACAATCCTACATCCTTGAAGTTGCAAGGATCTG
ATTAAAACTACGAAAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGCAAGATTAAAGCTACAA
AA
Found at i:74708 original size:101 final size:101
Alignment explanation
Indices: 74592--74928 Score: 289
Period size: 101 Copynumber: 3.4 Consensus size: 101
74582 AAAACTACGA
*
74592 AAGCGAATCTTTATCTCTCTGAAGATATAGTAGAGCAAGATTAAAGCTACAAAATCAAATACTAT
1 AAGCAAATCTTTATCTCTCTGAAGATATAGTAGAGCAAGATTAAAGCTACAAAATCAAATACTAT
74657 ACCCCTAAAGTTGTAGAGGGGCAAATTAAAGCTATAG
66 ACCCCTAAAGTTGTA-AGGGGCAAATTAAAGCTATAG
* * * * * *
74694 AAGCAAATC-TTATCTC-CTTGAAGTTACAATGGAGCAAGA-TAAAGCTACGACAATC--TTAC-
1 AAGCAAATCTTTATCTCTC-TGAAGATATAGTAGAGCAAGATTAAAGCTAC-AAAATCAAATACT
* * * * ** * * *
74753 AT--CCTTGATGTTGCAAGGGTTATATTAAAACTA-CG
64 ATACCCCTAAAGTTGTAAGGGGCAAATTAAAGCTATAG
* * * * * *
74788 AAAGCAAATCTTTATCTCTATGAAGATGTAGTAGAGTAAGATTAATGCTGCAAAATCAAATCCTA
1 -AAGCAAATCTTTATCTCTCTGAAGATATAGTAGAGCAAGATTAAAGCTACAAAATCAAATACTA
* * * *
74853 TACCCCTAAATTTGTAAAGGGGCAGATTGAAGCTATAA
65 TACCCCTAAAGTTGT-AAGGGGCAAATTAAAGCTATAG
* * * *
74891 AAGCAAATC-TTATCTCCCTGAAGTTGTAGTGGAGCAAG
1 AAGCAAATCTTTATCTCTCTGAAGATATAGTAGAGCAAG
74929 CTGAATCTAC
Statistics
Matches: 177, Mismatches: 45, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
94 1 0.01
95 23 0.13
96 36 0.20
97 7 0.04
98 4 0.02
99 5 0.03
100 10 0.06
101 60 0.34
102 31 0.18
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (101 bp):
AAGCAAATCTTTATCTCTCTGAAGATATAGTAGAGCAAGATTAAAGCTACAAAATCAAATACTAT
ACCCCTAAAGTTGTAAGGGGCAAATTAAAGCTATAG
Found at i:74718 original size:50 final size:49
Alignment explanation
Indices: 74450--74927 Score: 120
Period size: 50 Copynumber: 9.7 Consensus size: 49
74440 GCAACAACCT
* * * * *
74450 CAAATCCTATACT-CTTAAAGTTGTAGAGGGGCGAATTGAAGCTATAGAAG
1 CAAATCTTAT-CTCCTTGAAGTTGTAGAGGAGCAAATTAAAGCTA-AGAAG
* * * * *
74500 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAAGA-TGAAGCTACG-A-
1 CAAATCTTATCTCCTTGAAGTTGTAGAGGAGCAA-ATTAAAGCTAAGAAG
* * * ** * *
74547 C-AATCCTA-CATCCTTGAAGTTG-CGAGGATCTGATTAAAACTACGAAAG
1 CAAATCTTATC-TCCTTGAAGTTGTAGAGGAGCAAATTAAAGCTAAG-AAG
* * * * *
74595 CGAATCTTTATCT-CTCTGAAGATATAGTA-GAGCAAGATTAAAGCTACAAAAT
1 CAAATC-TTATCTCCT-TGAAGTTGTAG-AGGAGCAA-ATTAAAGCTA-AGAAG
* * *
74647 CAAATAC-TATAC-CCCTAAAGTTGTAGAGGGGCAAATTAAAGCTATAGAAG
1 CAAAT-CTTAT-CTCCTTGAAGTTGTAGAGGAGCAAATTAAAGCTA-AGAAG
** *
74697 CAAATCTTATCTCCTTGAAGTTACA-ATGGAGCAAGA-TAAAGCTACG-A-
1 CAAATCTTATCTCCTTGAAGTTGTAGA-GGAGCAA-ATTAAAGCTAAGAAG
* * * * * *
74744 C-AATCTTA-CATCCTTGATGTTGCA-AGG-GTTATATTAAAACTACGAAAG
1 CAAATCTTATC-TCCTTGAAGTTGTAGAGGAG-CAAATTAAAGCTAAG-AAG
* * * *
74792 CAAATCTTTATCT-CTATGAAGATGTAGTA-GAGTAAGATTAATGCTGCAA-AAT
1 CAAATC-TTATCTCCT-TGAAGTTGTAG-AGGAGCAA-ATTAAAGCT--AAGAAG
* * * * * * * * *
74844 CAAATCCTATAC-CCCTAAATTTGTAAAGGGGCAGATTGAAGCTATAAAAG
1 CAAATCTTAT-CTCCTTGAAGTTGTAGAGGAGCAAATTAAAGCTA-AGAAG
* *
74894 CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAA
1 CAAATCTTATCTCCTTGAAGTTGTAGAGGAGCAA
74928 GCTGAATCTA
Statistics
Matches: 308, Mismatches: 75, Indels: 90
0.65 0.16 0.19
Matches are distributed among these distances:
44 3 0.01
45 26 0.08
46 38 0.12
47 4 0.01
48 5 0.02
49 21 0.07
50 132 0.43
51 40 0.13
52 37 0.12
53 1 0.00
54 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (49 bp):
CAAATCTTATCTCCTTGAAGTTGTAGAGGAGCAAATTAAAGCTAAGAAG
Found at i:76820 original size:16 final size:15
Alignment explanation
Indices: 76791--76839 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
76781 CATTCCATAA
76791 TTTTTTACTTTTTAT
1 TTTTTTACTTTTTAT
76806 TTTTTTACTTATTTAT
1 TTTTTTACTT-TTTAT
* *
76822 TTTATTATTTTATTAT
1 TTTTTTACTTT-TTAT
76838 TT
1 TT
76840 AGCATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTACTTTTTAT
Found at i:76840 original size:15 final size:15
Alignment explanation
Indices: 76790--76839 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
76780 CCATTCCATA
76790 ATTTTTTACTTT-TT
1 ATTTTTTACTTTATT
76804 ATTTTTTTAC-TTATTT
1 A-TTTTTTACTTTA-TT
*
76820 ATTTTATTATTTTATT
1 ATTTT-TTACTTTATT
76836 ATTT
1 ATTT
76840 AGCATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 3 0.10
15 12 0.40
16 12 0.40
17 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTACTTTATT
Found at i:76952 original size:43 final size:41
Alignment explanation
Indices: 76885--76972 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 41
76875 TTTATTCTAT
* ** *
76885 TTATTTTTGTTTATTTTATTTTATTGTGTAGTATGTACATATTA
1 TTATTTATGTTTATTTTACATTATTAT-TAGTAT-TACAT-TTA
*
76929 TTATTTAT-TTTATTTTACATTATTATTTGTATTACATTTA
1 TTATTTATGTTTATTTTACATTATTATTAGTATTACATTTA
76969 TTAT
1 TTAT
76973 ATTTACATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 7 0.18
41 5 0.13
42 5 0.13
43 15 0.38
44 7 0.18
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (41 bp):
TTATTTATGTTTATTTTACATTATTATTAGTATTACATTTA
Found at i:76955 original size:28 final size:27
Alignment explanation
Indices: 76924--77023 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 27
76914 AGTATGTACA
76924 TATTATTATTTATTTTATTTTACATTAT
1 TATT-TTATTTATTTTATTTTACATTAT
*
76952 TATTTGTATTACATTTATTATATTTACA-T-T
1 TATTT-TATT-TA-TT-TTAT-TTTACATTAT
76982 TA-TTTATTTATTTTATTTTATCATTTAT
1 TATTTTATTTATTTTATTTTA-CA-TTAT
77010 T-TTGTT-TTTATTTT
1 TATT-TTATTTATTTT
77024 CCTTTAGTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
24 4 0.07
25 6 0.10
26 2 0.03
27 3 0.05
28 23 0.39
29 5 0.08
30 5 0.08
31 5 0.08
32 6 0.10
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (27 bp):
TATTTTATTTATTTTATTTTACATTAT
Found at i:78729 original size:17 final size:17
Alignment explanation
Indices: 78707--78739 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
78697 TTGGGAAGCA
78707 TAAAATA-AAAGATAAAC
1 TAAAATAGAAAG-TAAAC
78724 TAAAATAGAAAGTAAA
1 TAAAATAGAAAGTAAA
78740 AGCAAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAGTAAAC
Found at i:80507 original size:21 final size:21
Alignment explanation
Indices: 80460--80516 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
80450 TCTTCACACT
* *
80460 TTTTCTTACTC-TTTCCTTTTG
1 TTTT-TTACTCATTTTCTTTTA
80481 TGTTTTTACTCATTTTCTTTTA
1 T-TTTTTACTCATTTTCTTTTA
*
80503 TTTTTCACT-ATTTT
1 TTTTTTACTCATTTT
80517 TCTCTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.16
21 14 0.45
22 12 0.39
ACGTcount: A:0.11, C:0.18, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTTTACTCATTTTCTTTTA
Found at i:92209 original size:17 final size:17
Alignment explanation
Indices: 92187--92219 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
92177 TTGGAAAGCA
92187 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
92204 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
92220 AGCAAAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:93889 original size:64 final size:64
Alignment explanation
Indices: 93815--93939 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 64
93805 CAAGTGCAGC
* *
93815 AGCAATGATAGTAGA-AGCAACAGGTTAGTCTCTAACCAAAAATTCTCTCCTAGAACAATCACTA
1 AGCAATGATAGCA-ATAGCAACAGGTTAGTCTCTAACCAAAAATTCTCTCATAGAACAATCACTA
* *
93879 AGCAATGATAGCAATAGCAACAGGTTAGTCTCTAACCACAAATTCTCTCATAGGACAATCA
1 AGCAATGATAGCAATAGCAACAGGTTAGTCTCTAACCAAAAATTCTCTCATAGAACAATCA
93940 TTGACACGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
63 1 0.02
64 55 0.98
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (64 bp):
AGCAATGATAGCAATAGCAACAGGTTAGTCTCTAACCAAAAATTCTCTCATAGAACAATCACTA
Found at i:94405 original size:10 final size:10
Alignment explanation
Indices: 94390--94420 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
94380 TTTGTCGAAG
94390 AAATTTAAGA
1 AAATTTAAGA
94400 AAATTTAAGA
1 AAATTTAAGA
94410 AAATTTAAGA
1 AAATTTAAGA
94420 A
1 A
94421 GTAAAAACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (10 bp):
AAATTTAAGA
Found at i:96345 original size:37 final size:37
Alignment explanation
Indices: 96295--96368 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
96285 AGTATTTTTA
96295 ACTTAGTTTTACATTTTCTAACTTAATGAAGCTTAGT
1 ACTTAGTTTTACATTTTCTAACTTAATGAAGCTTAGT
96332 ACTTAGTTTTACATTTTCTAACTTAATGAAGCTTAGT
1 ACTTAGTTTTACATTTTCTAACTTAATGAAGCTTAGT
96369 CTAATTTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (37 bp):
ACTTAGTTTTACATTTTCTAACTTAATGAAGCTTAGT
Found at i:105221 original size:17 final size:16
Alignment explanation
Indices: 105201--105257 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
105191 GTTATCATCA
105201 CATTTCGTTTGTCATTG
1 CATTTC-TTTGTCATTG
*
105218 CATTTTTCTTGTCATTG
1 CATTTCT-TTGTCATTG
* *
105235 CATCTTCATTGCCATTG
1 CAT-TTCTTTGTCATTG
105252 CATTTC
1 CATTTC
105258 CATATATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.12
17 28 0.82
18 2 0.06
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (16 bp):
CATTTCTTTGTCATTG
Found at i:106579 original size:10 final size:10
Alignment explanation
Indices: 106564--106589 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
106554 TAAATACTGA
106564 AGAGAAGGAG
1 AGAGAAGGAG
106574 AGAGAAGGAG
1 AGAGAAGGAG
106584 AGAGAA
1 AGAGAA
106590 AGGGTGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (10 bp):
AGAGAAGGAG
Found at i:111669 original size:21 final size:21
Alignment explanation
Indices: 111643--111692 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
111633 CAAAGTTGCC
111643 TGGAAATTATGCATATTCTTG
1 TGGAAATTATGCATATTCTTG
111664 TGGAAATTATGCATATTCTTG
1 TGGAAATTATGCATATTCTTG
*
111685 TAGAAATT
1 TGGAAATT
111693 TGACAGTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (21 bp):
TGGAAATTATGCATATTCTTG
Found at i:112042 original size:17 final size:18
Alignment explanation
Indices: 112012--112046 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
112002 AGTTACATAG
*
112012 TTTATAATTTATAAAAAT
1 TTTATAATTAATAAAAAT
112030 TTTA-AATTAATAAAAAT
1 TTTATAATTAATAAAAAT
112047 AAAATTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTATAATTAATAAAAAT
Found at i:112100 original size:30 final size:29
Alignment explanation
Indices: 112044--112108 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
112034 AATTAATAAA
112044 AATAAAATTATACTTTAATCTCTTAAATAT
1 AATAAAATTATACTTTAATCTCTTAAA-AT
* * *
112074 AATAAAATTTTGA-TTTAATTTTTTAAAAT
1 AATAAAATTAT-ACTTTAATCTCTTAAAAT
*
112103 TATAAA
1 AATAAA
112109 GCTATAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 7 0.23
30 22 0.73
31 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (29 bp):
AATAAAATTATACTTTAATCTCTTAAAAT
Found at i:112598 original size:19 final size:19
Alignment explanation
Indices: 112574--112610 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
112564 GAATTTTACA
112574 TTTTTTTTTAATTTGATAT
1 TTTTTTTTTAATTTGATAT
112593 TTTTTTTTTAATTTGATA
1 TTTTTTTTTAATTTGATA
112611 CTTTAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTTTTTTAATTTGATAT
Found at i:112992 original size:60 final size:58
Alignment explanation
Indices: 112886--113059 Score: 190
Period size: 59 Copynumber: 2.9 Consensus size: 58
112876 ATAAATTTAG
* *
112886 ATACCAAATTGAATCTAAAAAAAATTTAGGTACCAAATTAGAAAAAAATGTTAAGTTCAA
1 ATACCAAATCG-ATCTAAAAAAAATTTAGGTATCAAATTA-AAAAAAATGTTAAGTTCAA
* * * *
112946 ATACTAAATCGAGTCTAAAAAAAATTTAGGTATCAAATTAAAAAAAATGTCAAATTTAA
1 ATACCAAATCGA-TCTAAAAAAAATTTAGGTATCAAATTAAAAAAAATGTTAAGTTCAA
* * * * *
113005 ATACCATATTGA-ATAAAAAAATTATTTAGATATC-AATTAAAAAAAATATTAAGTT
1 ATACCAAATCGATCTAAAAAAA--ATTTAGGTATCAAATTAAAAAAAATGTTAAGTT
113060 ACTAAATATT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
57 8 0.08
58 18 0.19
59 36 0.37
60 35 0.36
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (58 bp):
ATACCAAATCGATCTAAAAAAAATTTAGGTATCAAATTAAAAAAAATGTTAAGTTCAA
Found at i:113007 original size:59 final size:58
Alignment explanation
Indices: 112878--113051 Score: 199
Period size: 60 Copynumber: 2.9 Consensus size: 58
112868 AATATTTAAT
* * *
112878 AAATTTAGATACCAAATTGAATCTAAAAAAAATTTAGGTACCAAATTAGAAAAAAATGTT
1 AAATTTAAATACCAAATTG-ATCTAAAAAAAATTTAGGTATCAAATTA-AAAAAAATGTC
* * * *
112938 AAGTTCAAATACTAAATCGAGTCTAAAAAAAATTTAGGTATCAAATTAAAAAAAATGTC
1 AAATTTAAATACCAAATTGA-TCTAAAAAAAATTTAGGTATCAAATTAAAAAAAATGTC
* * *
112997 AAATTTAAATACCATATTGA-ATAAAAAAATTATTTAGATATC-AATTAAAAAAAAT
1 AAATTTAAATACCAAATTGATCTAAAAAAA--ATTTAGGTATCAAATTAAAAAAAAT
113052 ATTAAGTTAC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
57 8 0.08
58 13 0.13
59 36 0.37
60 40 0.41
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (58 bp):
AAATTTAAATACCAAATTGATCTAAAAAAAATTTAGGTATCAAATTAAAAAAAATGTC
Found at i:113154 original size:9 final size:9
Alignment explanation
Indices: 113140--113165 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
113130 GTGATGTATA
113140 ACTGATGGT
1 ACTGATGGT
113149 ACTGATGGT
1 ACTGATGGT
113158 ACTGATGG
1 ACTGATGG
113166 CAATGCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.31
Consensus pattern (9 bp):
ACTGATGGT
Found at i:115631 original size:148 final size:150
Alignment explanation
Indices: 115431--115721 Score: 426
Period size: 148 Copynumber: 2.0 Consensus size: 150
115421 CTCAAATTAA
* * * * *
115431 TGTTAAAGAAATAAAATATATAAGTGACAAGATAAGAGGATTTGTGGGGGTTGCACAAGTGAAAT
1 TGTTAAAAAAATAAAATATATAAGTGACAAGATAAAAAGATATGTGAGGGTTGCACAAGTGAAAT
* * * * *
115496 CTGTATAGGAGTATA-TTTCTTTTATTTGATATTATTTAGAATAAGTTGTTTCAACCTTTTTACA
66 CCGTATAAGAGTATACTTT-TTCTATTTGATATTATTTAGAATAAGGTGTTTCAACCTTCTTACA
*
115560 TTACTTCTATTAGAAAATTCT
130 TTACATCTATTAGAAAATTCT
* *
115581 TGTTAAAAAAAT-AAA-ATATAAGTGACAAGATAAAAAGATATGTGAGGGTTGTACAAGTGGAAT
1 TGTTAAAAAAATAAAATATATAAGTGACAAGATAAAAAGATATGTGAGGGTTGCACAAGTGAAAT
*
115644 CCGTATAAGAGTATACTTTTTCTATTTGATATTGTTTAGAATAAGGTGTTTCAACCTTCTTACAT
66 CCGTATAAGAGTATACTTTTTCTATTTGATATTATTTAGAATAAGGTGTTTCAACCTTCTTACAT
115709 TACATCTATTAGA
131 TACATCTATTAGA
115722 GATTAATTAG
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
148 109 0.87
149 6 0.05
150 11 0.09
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (150 bp):
TGTTAAAAAAATAAAATATATAAGTGACAAGATAAAAAGATATGTGAGGGTTGCACAAGTGAAAT
CCGTATAAGAGTATACTTTTTCTATTTGATATTATTTAGAATAAGGTGTTTCAACCTTCTTACAT
TACATCTATTAGAAAATTCT
Found at i:119399 original size:52 final size:51
Alignment explanation
Indices: 119316--119502 Score: 230
Period size: 52 Copynumber: 3.6 Consensus size: 51
119306 ATTTCATTTA
* * **** *
119316 ATACTCACAATGACACATAGTCATCGAACCTCTTGTTCCATAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCAAAATCCATAAA-GATTCAT
*
119368 ATACTCACGATGACACATAGTCACCGGACCTCAAAATCCATAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCAAAATCCAT-AAAGATTCAT
* * *
119420 ATACTCACGATGGCACATAATCATCAGACCTCAAAATCCATGAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCAAAATCCAT-AAAGATTCAT
* *
119472 ATACTCACGATGACACATTGTCATCAGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
119503 TTTTCATTTA
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 115 0.97
53 3 0.03
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTCAAAATCCATAAAGATTCAT
Found at i:126520 original size:52 final size:52
Alignment explanation
Indices: 126428--126614 Score: 196
Period size: 52 Copynumber: 3.6 Consensus size: 52
126418 ATTTCATTTA
* **** * *
126428 ATACTCACAATGACACATAGTCATCAGACCTCTTGTTCTATAAAGAAATCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCAAAATCTATAAAGGATTCAT
*
126480 ATACTCACGATGACACATAGTCA-CCGAACCTCAAAATCTATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCTCAAAATCTATAAAGGATTCAT
* * * * * * * *
126532 ATACTAATGATGGCACATAATCATCATACCTTAAAATCCATGAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCAAAATCTATAAAGGATTCAT
* *
126584 ATACTCACGATGACACATTGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
126615 TTTTCATTTA
Statistics
Matches: 109, Mismatches: 24, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
51 2 0.02
52 106 0.97
53 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCAAAATCTATAAAGGATTCAT
Found at i:130987 original size:23 final size:23
Alignment explanation
Indices: 130944--130987 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
130934 CAAACCTGAA
*
130944 TTGGTTTAGGGTATGGTTTGGGC
1 TTGGTTTAGGGTATGGCTTGGGC
*
130967 TTGGTTT-GGGTGTGGGCTTGG
1 TTGGTTTAGGGTAT-GGCTTGG
130988 TTTGATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.05, C:0.05, G:0.48, T:0.43
Consensus pattern (23 bp):
TTGGTTTAGGGTATGGCTTGGGC
Found at i:137940 original size:21 final size:21
Alignment explanation
Indices: 137895--137949 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
137885 TTTCGAAAAT
* *
137895 AGTCAATGGTCAA-ATTTAAT
1 AGTCAATGGTCAACAGTTAAC
*
137915 GGTCAATGGTCAACAGTTAAC
1 AGTCAATGGTCAACAGTTAAC
137936 AGTCAATGGTCAAC
1 AGTCAATGGTCAAC
137950 GATCAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (21 bp):
AGTCAATGGTCAACAGTTAAC
Found at i:138062 original size:18 final size:18
Alignment explanation
Indices: 138039--138073 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
138029 GTTTGGGCTT
138039 GGTTTGATTTGAGTTTAG
1 GGTTTGATTTGAGTTTAG
138057 GGTTTGATTTGAGTTTA
1 GGTTTGATTTGAGTTTA
138074 AAAGGTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (18 bp):
GGTTTGATTTGAGTTTAG
Found at i:139673 original size:15 final size:16
Alignment explanation
Indices: 139655--139688 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
139645 AAGGAAGAGG
139655 AGAAAGAAGAAGA-AA
1 AGAAAGAAGAAGAGAA
*
139670 AGAAAGAAGGAGAGAA
1 AGAAAGAAGAAGAGAA
139686 AGA
1 AGA
139689 GGAAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AGAAAGAAGAAGAGAA
Found at i:161443 original size:25 final size:25
Alignment explanation
Indices: 161415--161468 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
161405 ATCTAAATTA
* *
161415 ATTTAAAGGTGAAGAGATTATGCAC
1 ATTTAAAGGTGAAAAGATGATGCAC
*
161440 ATTTCAAGGTGAAAAGATGATGCAC
1 ATTTAAAGGTGAAAAGATGATGCAC
161465 ATTT
1 ATTT
161469 TAATTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (25 bp):
ATTTAAAGGTGAAAAGATGATGCAC
Found at i:162063 original size:23 final size:22
Alignment explanation
Indices: 162032--162075 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
162022 AAAGAAATAA
*
162032 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
162054 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
162076 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:166449 original size:3 final size:3
Alignment explanation
Indices: 166441--166475 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
166431 GAAGGAAAAT
166441 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
166476 GCATGAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:167574 original size:12 final size:12
Alignment explanation
Indices: 167557--167596 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
167547 GGAAAATGGG
167557 AAAAAGAAAGAA
1 AAAAAGAAAGAA
*
167569 AAAAAGAGAGAA
1 AAAAAGAAAGAA
167581 AGAAAAG-AAGAA
1 A-AAAAGAAAGAA
167593 AAAA
1 AAAA
167597 TGTTTGCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.12
12 17 0.68
13 5 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:167580 original size:16 final size:16
Alignment explanation
Indices: 167561--167591 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
167551 AATGGGAAAA
167561 AGAAAGAAAAAAAGAG
1 AGAAAGAAAAAAAGAG
*
167577 AGAAAGAAAAGAAGA
1 AGAAAGAAAAAAAGA
167592 AAAAATGTTT
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAAAGAG
Found at i:181804 original size:21 final size:21
Alignment explanation
Indices: 181765--181805 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
181755 TGGCTGTACA
* **
181765 TGATTTTGATGTGGCTGCATT
1 TGATCTTGATGTGAATGCATT
181786 TGATCTTGATGTGAATGCAT
1 TGATCTTGATGTGAATGCAT
181806 CTGAGTACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (21 bp):
TGATCTTGATGTGAATGCATT
Found at i:186665 original size:12 final size:12
Alignment explanation
Indices: 186650--186679 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
186640 AAGAAGTGGT
*
186650 AAAAGAGGAAGG
1 AAAAGAGGAAGA
186662 AAAAGAGGAAGA
1 AAAAGAGGAAGA
186674 AAAAGA
1 AAAAGA
186680 TGCTGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
AAAAGAGGAAGA
Found at i:201846 original size:21 final size:20
Alignment explanation
Indices: 201808--201846 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
201798 GCAAGGAATT
*
201808 TGAAACAACAAAATTAAAAG
1 TGAAACAACAAAAGTAAAAG
*
201828 TGAAACAGATAAAAGTAAA
1 TGAAACA-ACAAAAGTAAA
201847 TAAAAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (20 bp):
TGAAACAACAAAAGTAAAAG
Found at i:223270 original size:37 final size:37
Alignment explanation
Indices: 223139--223270 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
223129 GCACTTCTAG
** * *
223139 ATTGCACCCAAAACTGTCG-TCGCATGAATATT-TTCGA
1 ATTGCACCCAGGACTGTCGCT-GTATAAATATTCTTC-A
* *
223176 AATGCACCCAAGACTGTCGCTGTATAAATATTCTTCA
1 ATTGCACCCAGGACTGTCGCTGTATAAATATTCTTCA
* * * * *
223213 ATTACATCCAGGACTATCGCT-TCATAAGTTTTCTTCA
1 ATTGCACCCAGGACTGTCGCTGT-ATAAATATTCTTCA
*
223250 ATTGCACCCAGGAATGTCGCT
1 ATTGCACCCAGGACTGTCGCT
223271 ACATGAACAT
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
36 1 0.01
37 72 0.94
38 4 0.05
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (37 bp):
ATTGCACCCAGGACTGTCGCTGTATAAATATTCTTCA
Found at i:223298 original size:26 final size:26
Alignment explanation
Indices: 223264--223317 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
223254 CACCCAGGAA
*
223264 TGTCGCTACATGAACATGTCTAGAAT
1 TGTCACTACATGAACATGTCTAGAAT
*
223290 TGTCACTACATGAACGTGTCTAGAAT
1 TGTCACTACATGAACATGTCTAGAAT
223316 TG
1 TG
223318 CACCCAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (26 bp):
TGTCACTACATGAACATGTCTAGAAT
Found at i:225302 original size:12 final size:12
Alignment explanation
Indices: 225282--225319 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
225272 CTGTGGAGAC
225282 AGAAGAGGAAAA
1 AGAAGAGGAAAA
*
225294 AGAATAGGAAGAA
1 AGAAGAGGAA-AA
225307 A-AAGAGGAAAA
1 AGAAGAGGAAAA
225318 AG
1 AG
225320 GAGGAGGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.14
12 16 0.73
13 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (12 bp):
AGAAGAGGAAAA
Found at i:229562 original size:26 final size:27
Alignment explanation
Indices: 229533--229609 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
229523 TTTTGAACGA
* *
229533 GTTCCTGCAGCGACAATTCTGGGCAT-
1 GTTCATGCAGCGACAATTTTGGGCATC
* *
229559 GTTCATGCAGCGACATTTTTGGACATC
1 GTTCATGCAGCGACAATTTTGGGCATC
*
229586 G-TCATGCAGTGACAATTTTGGGCA
1 GTTCATGCAGCGACAATTTTGGGCA
229610 CAATTCTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 42 0.98
27 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (27 bp):
GTTCATGCAGCGACAATTTTGGGCATC
Found at i:241033 original size:18 final size:17
Alignment explanation
Indices: 241002--241048 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
240992 TCAGTCACCT
241002 GAAAAAGAAAAAAATGA
1 GAAAAAGAAAAAAATGA
*
241019 GAAAAAGGAAGAAAAT--
1 GAAAAA-GAAAAAAATGA
241035 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
241049 AATTGTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 6 0.22
18 8 0.30
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
GAAAAAGAAAAAAATGA
Found at i:241050 original size:17 final size:17
Alignment explanation
Indices: 241001--241051 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
240991 CTCAGTCACC
*
241001 TGAAAAAGAAAAAAATGA
1 TGAAAAAGAAAAAAA-AA
* *
241019 -GAAAAAG-GAAGAAAA
1 TGAAAAAGAAAAAAAAA
241034 TGAAAAAGAAAAAAAAA
1 TGAAAAAGAAAAAAAAA
241051 T
1 T
241052 TGTGTATTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
15 1 0.04
16 11 0.42
17 14 0.54
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.08
Consensus pattern (17 bp):
TGAAAAAGAAAAAAAAA
Found at i:244641 original size:21 final size:21
Alignment explanation
Indices: 244615--244663 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
244605 AGGGTGTTTG
*
244615 TTGCAACATTTACATGATATA
1 TTGCAACATATACATGATATA
*
244636 TTGCAACATATACATGATATG
1 TTGCAACATATACATGATATA
244657 TTGCAAC
1 TTGCAAC
244664 GAAGAAGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (21 bp):
TTGCAACATATACATGATATA
Found at i:248282 original size:13 final size:13
Alignment explanation
Indices: 248264--248288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
248254 TTTCATCATA
248264 TAGTTTTTATTTT
1 TAGTTTTTATTTT
248277 TAGTTTTTATTT
1 TAGTTTTTATTT
248289 GCTTTTTGAT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TAGTTTTTATTTT
Found at i:250187 original size:20 final size:21
Alignment explanation
Indices: 250146--250195 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
250136 GTATCGATCC
*
250146 GGTATCGATACCTTTTGATAA
1 GGTATCGATACATTTTGATAA
*
250167 GGTATCGATA-ATTTTGTTAA
1 GGTATCGATACATTTTGATAA
250187 GGTATCGAT
1 GGTATCGAT
250196 TTTTAAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (21 bp):
GGTATCGATACATTTTGATAA
Found at i:264501 original size:16 final size:16
Alignment explanation
Indices: 264467--264501 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
264457 CTATTTTCTA
*
264467 TTTCTTTTAATTATGT
1 TTTCTTTTAATTATAT
*
264483 TTTCTTTTAATTTTAT
1 TTTCTTTTAATTATAT
264499 TTT
1 TTT
264502 TCCTCAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTCTTTTAATTATAT
Found at i:282415 original size:18 final size:20
Alignment explanation
Indices: 282379--282416 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
282369 TAACACTAGA
282379 CTCATAGAGTTGAAACATAT
1 CTCATAGAGTTGAAACATAT
*
282399 CTCATA-AG-TGAAGCATAT
1 CTCATAGAGTTGAAACATAT
282417 AGCTAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATAGAGTTGAAACATAT
Found at i:282608 original size:21 final size:21
Alignment explanation
Indices: 282579--282633 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
282569 CAGTTCACTT
* *
282579 GGTTCGGGTTTGGATCAAAAG
1 GGTTTGGGTTAGGATCAAAAG
** *
282600 GGTTTGGGTTAGTTTTAAAAG
1 GGTTTGGGTTAGGATCAAAAG
282621 GGTTTGGGTTAGG
1 GGTTTGGGTTAGG
282634 TTGGCTTCTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.40, T:0.36
Consensus pattern (21 bp):
GGTTTGGGTTAGGATCAAAAG
Found at i:282884 original size:82 final size:81
Alignment explanation
Indices: 282789--282952 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 81
282779 AAGACTTAAT
*
282789 CGGCCTCAATACAAGAAACACCACTCACCCAAAATTAAGAACGACCACCAACACGATAGAGAAAG
1 CGGCCTCAATACAAGAAACACCACTCACCCAAAATTAAGAACAACCACCAACACGATAGAGAAAG
282854 GGGCGACGATGCAAAA
66 GGGCGACGATGCAAAA
*
282870 NCGGCCTCAATACAAGAAACACCACTCACCCAAAATTAAGAACAACCACTAACACGATAGAGAAA
1 -CGGCCTCAATACAAGAAACACCACTCACCCAAAATTAAGAACAACCACCAACACGATAGAGAAA
282935 GGGGCGACGATGCAAAA
65 GGGGCGACGATGCAAAA
282952 C
1 C
282953 TGAAAGGTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
81 1 0.01
82 79 0.99
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (81 bp):
CGGCCTCAATACAAGAAACACCACTCACCCAAAATTAAGAACAACCACCAACACGATAGAGAAAG
GGGCGACGATGCAAAA
Found at i:284057 original size:13 final size:13
Alignment explanation
Indices: 284039--284065 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
284029 AATAGGGGTG
284039 CGACACTTGCGCC
1 CGACACTTGCGCC
284052 CGACACTTGCGCC
1 CGACACTTGCGCC
284065 C
1 C
284066 ATACAAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.48, G:0.22, T:0.15
Consensus pattern (13 bp):
CGACACTTGCGCC
Found at i:285534 original size:434 final size:434
Alignment explanation
Indices: 284696--286000 Score: 2045
Period size: 434 Copynumber: 3.0 Consensus size: 434
284686 GGCCAGGATG
* *
284696 CATGGAATAAGGGCTATCATGCGCCTCACAGAGAATAGTCTGTTTAATTCCAGAATCCTTCGGAA
1 CATGGAATAAGGGCTATCATGTG-CTCACGGAGAATAGTCTGTTTAATTCCAGAATCCTTCGGAA
* *
284761 CATAGTATCGACCTCGGAAGCATATTATACCATTTTGATCCATGGAGAAGTCCACAGATTTACCT
65 CACAGTATCGACCTCGGAAGCATATTATACCATTTTGATCCATGGAGAAGTCCACAGATATACCT
* * * *
284826 TCTTCCACCTCTCTCATACGGTGCACTAGTTACGAATCATTAGACTGCTCCGCCTTAATCTCCAA
130 TCTTCCACCTCTCTCATACAGTGCACTAGATACGGATCATTAGACTGCTCCGCCTTAATCTCCGA
* *
284891 GAGTAAAGTGGGAATAACTCAAAGTTCAGCTAAAAGACTGTCATCCTCAAACAAACTCATTTTGG
195 GAGTAAAGTGGGAATAACTCGAAGTTTAGCTAAAAGACTGTCATCCTCAAACAAACTCATTTTGG
* * * ** *
284956 AAAATAAAGCCCTTAGTTCAGTCACAGCACTACGACTTAAGGTGTCGGCAACCACATTAGCCTTT
260 AAAATAAAGCCCTCAATTCAGTCACAACACTACGACTTAAGGCCTCGGCAACCACATTAGCCTTG
* * * * *
285021 CCAAGGTGATACTTAATCTCACAGTCGTAGTCCTTCAATAGTTCCAACCAACGTCATTGTCTTAA
325 CCAGGGTGATACTCAATCTCACAGTCGTAGTCCTTCAGTAGTTCCAACCAACGACGTTGTCTTAA
285086 ATTAAGCTCTCTCTGAGTAAGCAAATACTTTAAGCTTTTATGATC
390 ATTAAGCTCTCTCTGAGTAAGCAAATACTTTAAGCTTTTATGATC
* * *
285131 CATGGAATAAGAGCTATCATGTGCTCACGGAGAATAGTTTGTTTAATTCCAGAATCCTTCGAAAC
1 CATGGAATAAGGGCTATCATGTGCTCACGGAGAATAGTCTGTTTAATTCCAGAATCCTTCGGAAC
* * * *
285196 ACAGTAACGACCTCAGAAGCATATTATACCATTTTGATCCATGGAAAAGTCCACAGATGTACCTT
66 ACAGTATCGACCTCGGAAGCATATTATACCATTTTGATCCATGGAGAAGTCCACAGATATACCTT
* *
285261 CTTCCACCTCTCTCATACAATGCACTAGATACGGATCATTAGACTGCTCCGCCTTAATCTTCGAG
131 CTTCCACCTCTCTCATACAGTGCACTAGATACGGATCATTAGACTGCTCCGCCTTAATCTCCGAG
* *
285326 AGTAAAGTAGGAATAACTCGAAGTTTAGCTAAAAGACTGTCATCCTCAAACAAACTCATTTTAGA
196 AGTAAAGTGGGAATAACTCGAAGTTTAGCTAAAAGACTGTCATCCTCAAACAAACTCATTTTGGA
*
285391 AAATAAAGCCCTCAATTCAGTCACAACACTATGACTTAAGGCCTCGGCAACCACATTAGCCTTGC
261 AAATAAAGCCCTCAATTCAGTCACAACACTACGACTTAAGGCCTCGGCAACCACATTAGCCTTGC
*
285456 CAGGGTGATACTCAATCTCACAGTCATAGTCCTTCAGTAGTTCCAACCAACGACGTTGTCTTAAA
326 CAGGGTGATACTCAATCTCACAGTCGTAGTCCTTCAGTAGTTCCAACCAACGACGTTGTCTTAAA
* *
285521 TTAAGCTCTCTCTGAGTAAGCAAATACTTTAAGATTTTATGATT
391 TTAAGCTCTCTCTGAGTAAGCAAATACTTTAAGCTTTTATGATC
* * * * * *
285565 CAAGGAATAAGGGCTATCATGCAT-CTCATGGAGAATAGTCTGTTTAATTTCAAAATCTTTTGGA
1 CATGGAATAAGGGCTATCATG--TGCTCACGGAGAATAGTCTGTTTAATTCCAGAATCCTTCGGA
* *
285629 GCACAGTATCGACCTCGGAAGCATATTATACCATTTTGATCCATGGAGAAGTCCACAAATATACC
64 ACACAGTATCGACCTCGGAAGCATATTATACCATTTTGATCCATGGAGAAGTCCACAGATATACC
* * * *
285694 TTCTTCCACCTCTCTCATGCAGTGCACTAGATACGGATCATTAGATTGCTCTGCTTTAATCTCCG
129 TTCTTCCACCTCTCTCATACAGTGCACTAGATACGGATCATTAGACTGCTCCGCCTTAATCTCCG
*
285759 AGAGTAAAGTGGGAATAACTCGAAGTTTAGCTAAAAGACTGTCATCCTCAAACAAACTCATTCTG
194 AGAGTAAAGTGGGAATAACTCGAAGTTTAGCTAAAAGACTGTCATCCTCAAACAAACTCATTTTG
* * *
285824 GCAAATAAAGCCCTCAATTCAGTCACAACACTACGACTTAAGGCCTCGACAAGCACATTAGCCTT
259 GAAAATAAAGCCCTCAATTCAGTCACAACACTACGACTTAAGGCCTCGGCAACCACATTAGCCTT
* * * * *
285889 GCCAGGGAGATACTCAGTCTCACAGTCGCAATCCTTCAGTAGTTCTAACCAACGACGTTGTCTTA
324 GCCAGGGTGATACTCAATCTCACAGTCGTAGTCCTTCAGTAGTTCCAACCAACGACGTTGTCTTA
* *
285954 AATTAAGTTCTCTCTAAGTAAGCAAATACTTTAAGCTTTTATGATC
389 AATTAAGCTCTCTCTGAGTAAGCAAATACTTTAAGCTTTTATGATC
286000 C
1 C
286001 GTGAAAATGT
Statistics
Matches: 795, Mismatches: 73, Indels: 4
0.91 0.08 0.00
Matches are distributed among these distances:
434 397 0.50
435 397 0.50
436 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (434 bp):
CATGGAATAAGGGCTATCATGTGCTCACGGAGAATAGTCTGTTTAATTCCAGAATCCTTCGGAAC
ACAGTATCGACCTCGGAAGCATATTATACCATTTTGATCCATGGAGAAGTCCACAGATATACCTT
CTTCCACCTCTCTCATACAGTGCACTAGATACGGATCATTAGACTGCTCCGCCTTAATCTCCGAG
AGTAAAGTGGGAATAACTCGAAGTTTAGCTAAAAGACTGTCATCCTCAAACAAACTCATTTTGGA
AAATAAAGCCCTCAATTCAGTCACAACACTACGACTTAAGGCCTCGGCAACCACATTAGCCTTGC
CAGGGTGATACTCAATCTCACAGTCGTAGTCCTTCAGTAGTTCCAACCAACGACGTTGTCTTAAA
TTAAGCTCTCTCTGAGTAAGCAAATACTTTAAGCTTTTATGATC
Found at i:289892 original size:16 final size:17
Alignment explanation
Indices: 289871--289918 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
289861 TTATCAAAAA
289871 TTTCTTTCTTTTTCT-T
1 TTTCTTTCTTTTTCTAT
*
289887 TTTCTTCCTTTTTCTCAT
1 TTTCTTTCTTTTTCT-AT
*
289905 TTTGTTTCTTTTTC
1 TTTCTTTCTTTTTC
289919 AAATGATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTAT
Found at i:292857 original size:20 final size:21
Alignment explanation
Indices: 292832--292870 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
292822 GCAAGGAATT
292832 TGAAACAAA-AAAAGTAAAAG
1 TGAAACAAATAAAAGTAAAAG
292852 TGAAACAAATAAAAGTAAA
1 TGAAACAAATAAAAGTAAA
292871 TAAAAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.69, C:0.05, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAATAAAAGTAAAAG
Found at i:301013 original size:2 final size:2
Alignment explanation
Indices: 301006--301038 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
300996 ACAATCATTC
301006 AT AT AT AT -T CAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
301039 ATCTATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.93
3 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:301164 original size:6 final size:6
Alignment explanation
Indices: 301153--301185 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
301143 ATGAAAACCC
301153 AAAAAT AAAAAT AAAAGAT AAAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAA
301186 TATATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:301173 original size:13 final size:12
Alignment explanation
Indices: 301153--301185 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
301143 ATGAAAACCC
301153 AAAAATAAAAAT
1 AAAAATAAAAAT
301165 AAAAGATAAAAAT
1 AAAA-ATAAAAAT
301178 -AAAATAAA
1 AAAAATAAA
301186 TATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 7 0.35
13 8 0.40
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:302255 original size:14 final size:14
Alignment explanation
Indices: 302232--302266 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
302222 CAACCCAAAA
*
302232 GTCAACGATCAATG
1 GTCAACGATCAACG
*
302246 GTCAATGATCAACG
1 GTCAACGATCAACG
302260 GTCAACG
1 GTCAACG
302267 GGTTCAGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (14 bp):
GTCAACGATCAACG
Found at i:302323 original size:20 final size:21
Alignment explanation
Indices: 302300--302344 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
302290 CGGTTCACTT
302300 GGTTTGGGTCAAAA-GGTTTG
1 GGTTTGGGTCAAAAGGGTTTG
*
302320 GGTTTGGTTCAAAAGGGTTTG
1 GGTTTGGGTCAAAAGGGTTTG
302341 GGTT
1 GGTT
302345 AGGTTGGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.18, C:0.04, G:0.40, T:0.38
Consensus pattern (21 bp):
GGTTTGGGTCAAAAGGGTTTG
Found at i:302340 original size:21 final size:20
Alignment explanation
Indices: 302300--302349 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
302290 CGGTTCACTT
*
302300 GGTTTGGGTCAAAAGGTTTG
1 GGTTTGGTTCAAAAGGTTTG
302320 GGTTTGGTTCAAAAGGGTTTG
1 GGTTTGGTTCAAAA-GGTTTG
*
302341 GGTTAGGTT
1 GGTTTGGTT
302350 GGCTTGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.18, C:0.04, G:0.40, T:0.38
Consensus pattern (20 bp):
GGTTTGGTTCAAAAGGTTTG
Found at i:308705 original size:6 final size:6
Alignment explanation
Indices: 308696--308728 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
308686 ATGAAAACCA
308696 AAAAAT AAAAAT AAAAGAT AAAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT AAA
308729 TATATAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:308711 original size:13 final size:13
Alignment explanation
Indices: 308695--308724 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
308685 GATGAAAACC
308695 AAAAAATAAAAAT
1 AAAAAATAAAAAT
*
308708 AAAAGATAAAAAT
1 AAAAAATAAAAAT
308721 AAAA
1 AAAA
308725 TAAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:309845 original size:19 final size:19
Alignment explanation
Indices: 309796--309847 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
309786 ACAATCAACA
** *
309796 GTCAACGGGTTCAGGTTGG
1 GTCAACGGGTTTGGGTCGG
309815 GTCAACGGGTTTGGGTCGG
1 GTCAACGGGTTTGGGTCGG
309834 GTCAACGGGTTTGG
1 GTCAACGGGTTTGG
309848 TTCACTTGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.13, C:0.15, G:0.44, T:0.27
Consensus pattern (19 bp):
GTCAACGGGTTTGGGTCGG
Found at i:309890 original size:20 final size:21
Alignment explanation
Indices: 309855--309908 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
309845 TGGTTCACTT
*
309855 GGTTTGGGTTTGGTT-CAAAAG
1 GGTTTGGG-TTAGTTCCAAAAG
309876 GGTTTGGGTTAGTTCCAAAAG
1 GGTTTGGGTTAGTTCCAAAAG
*
309897 GGTTTGGATTAG
1 GGTTTGGGTTAG
309909 GTTGGCTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.20, C:0.06, G:0.37, T:0.37
Consensus pattern (21 bp):
GGTTTGGGTTAGTTCCAAAAG
Found at i:314858 original size:21 final size:20
Alignment explanation
Indices: 314824--314863 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
314814 ATTTTTAATT
* *
314824 ATTTTTTTATTTTTTAAAAC
1 ATTTTTTTAATTTTAAAAAC
314844 ATTTTTTATAATTTTAAAAA
1 ATTTTTT-TAATTTTAAAAA
314864 ATAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTTAATTTTAAAAAC
Found at i:315691 original size:29 final size:29
Alignment explanation
Indices: 315658--315730 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
315648 ATTCTGATTG
* *
315658 ATTGAATAAATTATTCTTATTGATTTTAA
1 ATTGAATAAATTATTCTGACTGATTTTAA
315687 ATTGAATAAAATT-TTCTGACTGATTTTAA
1 ATTGAAT-AAATTATTCTGACTGATTTTAA
315716 ATTGAATAAATTATT
1 ATTGAATAAATTATT
315731 TCGTTTTCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 5 0.12
29 30 0.75
30 5 0.12
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (29 bp):
ATTGAATAAATTATTCTGACTGATTTTAA
Found at i:319475 original size:22 final size:22
Alignment explanation
Indices: 319430--319488 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
319420 TAAAAAGTAT
** **
319430 TCAATTAAATTGGTGCAATGAA
1 TCAATTAAATTGGCACAACCAA
319452 TCAATTAAATTGGCACAACCAA
1 TCAATTAAATTGGCACAACCAA
*
319474 TCAATTATATTGGCA
1 TCAATTAAATTGGCA
319489 TATTACATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (22 bp):
TCAATTAAATTGGCACAACCAA
Found at i:325408 original size:19 final size:19
Alignment explanation
Indices: 325384--325428 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
325374 AATAAATATA
325384 AATAAAATT-TAAATTTAAT
1 AATAAAATTGTAAA-TTAAT
325403 AAT-AAATTGTAAATTAAT
1 AATAAAATTGTAAATTAAT
*
325421 AAAAAAAT
1 AATAAAAT
325429 AAATGAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATAAAATTGTAAATTAAT
Found at i:325834 original size:17 final size:17
Alignment explanation
Indices: 325812--325855 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
325802 GGTTTTAAGC
325812 ACCATTTTTCCTCAACA
1 ACCATTTTTCCTCAACA
325829 ACCATTTTTCCTCAACA
1 ACCATTTTTCCTCAACA
325846 ACCATTTTTC
1 ACCATTTTTC
325856 ATGGAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (17 bp):
ACCATTTTTCCTCAACA
Found at i:328712 original size:21 final size:21
Alignment explanation
Indices: 328688--328727 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
328678 TAATACCATG
328688 TTGTGCATA-ATATTCACCAAA
1 TTGTGCA-ACATATTCACCAAA
*
328709 TTGTTCAACATATTCACCA
1 TTGTGCAACATATTCACCA
328728 CCACTGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
TTGTGCAACATATTCACCAAA
Found at i:332431 original size:24 final size:21
Alignment explanation
Indices: 332379--332432 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
332369 TAACAAAAAC
332379 TTCCTCTTTCTCTCCTTTCAT
1 TTCCTCTTTCTCTCCTTTCAT
* * *
332400 TTCTTCTTCTTTCTCCTCTTCCT
1 TTCCTCTT-TCTCTCCT-TTCAT
332423 TCTCCTCTTT
1 T-TCCTCTTT
332433 GATACCCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.27
22 7 0.27
23 6 0.23
24 6 0.23
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (21 bp):
TTCCTCTTTCTCTCCTTTCAT
Found at i:338502 original size:18 final size:18
Alignment explanation
Indices: 338481--338536 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
338471 TAAAGTCTGT
*
338481 TGTGGCTGCATAC-GAGCA
1 TGTGACTGCAT-CTGAGCA
*
338499 TGTGATTGCATCTGAGCA
1 TGTGACTGCATCTGAGCA
* *
338517 TGTGATTGCATCTGATCA
1 TGTGACTGCATCTGAGCA
338535 TG
1 TG
338537 ATGTACCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (18 bp):
TGTGACTGCATCTGAGCA
Found at i:346576 original size:23 final size:21
Alignment explanation
Indices: 346550--346595 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
346540 AATAACTTGA
346550 TTAACTCAAATAACTTGAATTAT
1 TTAACTC-AA-AACTTGAATTAT
* *
346573 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAACTTGAATTAT
346594 TT
1 TT
346596 TTCAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAACTTGAATTAT
Found at i:350771 original size:3 final size:3
Alignment explanation
Indices: 350763--350801 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
350753 TTTTCATCCT
350763 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
350802 ACAATCGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:351765 original size:28 final size:28
Alignment explanation
Indices: 351725--351778 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
351715 GGTAACAGGA
*
351725 ATGACCTTTGGGTCAACAGGGAGTAAGC
1 ATGACCTTTGGGTCAACAAGGAGTAAGC
*
351753 ATGACCTTTGGGTCAATAAGGAGTAA
1 ATGACCTTTGGGTCAACAAGGAGTAA
351779 ATCGGATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACAAGGAGTAAGC
Found at i:356716 original size:30 final size:30
Alignment explanation
Indices: 356621--356785 Score: 161
Period size: 30 Copynumber: 5.5 Consensus size: 30
356611 ATACAAGATC
* * * *
356621 AAAACGTAAATTTGGAAAAGCTTAGGTGGTG
1 AAAATGTAATTTTGGAAAAGTTTAGG-GGTT
* * * * * * *
356652 AAAATGTAATTTAGGGAAAG-CTCGAGATC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
356681 AAAATGTGATTTTGGAGAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
356711 AAAATGCAATTTTAGAAAAATTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
*
356741 AAAATGTAATTTTGGACAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
356771 AAAATGTAATTTTGG
1 AAAATGTAATTTTGG
356786 GGACATTCGG
Statistics
Matches: 106, Mismatches: 27, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
29 18 0.17
30 72 0.68
31 16 0.15
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTT
Found at i:356814 original size:60 final size:60
Alignment explanation
Indices: 356689--356821 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
356679 TCAAAATGTG
* * **
356689 ATTTTGGAGAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAATTTAGGGGTTAAAATGTA
1 ATTTTGGACAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAATTTAGGGGTCAAAACATA
* * ** * *
356749 ATTTTGGACAAGTTTAGGGGTTAAAATGTAATTTTGGGGACA-TTCGGGGTCAAAACATA
1 ATTTTGGACAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAATTTAGGGGTCAAAACATA
* *
356808 ATTTTTGAAAAGTT
1 ATTTTGGACAAGTT
356822 CGAGGGTCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 25 0.41
60 36 0.59
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (60 bp):
ATTTTGGACAAGTTTAGGGGTTAAAATGCAATTTTAGAAAAATTTAGGGGTCAAAACATA
Found at i:357958 original size:16 final size:14
Alignment explanation
Indices: 357919--357952 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
357909 TAATAATGGT
*
357919 AATATA-ATAAATA
1 AATATATATTAATA
357932 AATATATATTAATA
1 AATATATATTAATA
357946 AATATAT
1 AATATAT
357953 GTATTAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:358522 original size:24 final size:25
Alignment explanation
Indices: 358495--358548 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
358485 TGGATTTGTT
*
358495 TGTAAATGGAC-TTTTAAATTTAAA
1 TGTAAATGGACATTTTAAATGTAAA
*
358519 TGT-ATTGGACATTTTAAATGTAAA
1 TGTAAATGGACATTTTAAATGTAAA
358543 -GTAAAT
1 TGTAAAT
358549 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.41
Consensus pattern (25 bp):
TGTAAATGGACATTTTAAATGTAAA
Found at i:359091 original size:39 final size:38
Alignment explanation
Indices: 359060--359268 Score: 156
Period size: 39 Copynumber: 5.4 Consensus size: 38
359050 TGCCTCTAGT
*
359060 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC
* * * *
359099 TCGGGGTAAGAGATAGGATAGCT-GCGATCTGTCCCAAGC
1 TCGGGGTAAGAGATTGGCT-GATGGTGATCTG-CCCAAGC
* * * * *
359138 TTGGGTTAAGAGAGTGACTGATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC
* * * * *
359177 TCGGGGTAAGAGA-T--CAGACGGTTGCAATCTTCCTTAAGT
1 TCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCC-CAAGC
* *
359216 TCGGGGTAACAGATTGGCTGATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC
359255 TCGGGGTAAGAGAT
1 TCGGGGTAAGAGAT
359269 CCCAAGATCG
Statistics
Matches: 129, Mismatches: 31, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
36 5 0.04
37 2 0.02
38 5 0.04
39 105 0.81
40 5 0.04
41 2 0.02
42 5 0.04
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (38 bp):
TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGC
Found at i:359179 original size:78 final size:78
Alignment explanation
Indices: 359043--359269 Score: 262
Period size: 78 Copynumber: 2.9 Consensus size: 78
359033 TTTGGATGGT
* * * * ** *
359043 TGCAATCTGCCTCTAGTTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAA
1 TGCAATCTTCCTCAAGTTCGGGGTAACAGAGTGACTGATGGTGATCTGCCCCAGGCTCGGGGTAA
*
359108 GAGAT-AGGATAGC
66 GAGATCA-GACAGC
* * *
359121 TGCGATCTGTCC-CAAGCTT-GGGTTAAGAGAGTGACTGATGGTGATCTGCCCCAGGCTCGGGGT
1 TGCAATCT-TCCTCAAG-TTCGGGGTAACAGAGTGACTGATGGTGATCTGCCCCAGGCTCGGGGT
* *
359184 AAGAGATCAGACGGT
64 AAGAGATCAGACAGC
* * *
359199 TGCAATCTTCCTTAAGTTCGGGGTAACAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
1 TGCAATCTTCCTCAAGTTCGGGGTAACAGAGTGACTGATGGTGATCTGCCCCAGGCTCGGGGTAA
359264 GAGATC
66 GAGATC
359270 CCAAGATCGG
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
77 5 0.04
78 117 0.92
79 5 0.04
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (78 bp):
TGCAATCTTCCTCAAGTTCGGGGTAACAGAGTGACTGATGGTGATCTGCCCCAGGCTCGGGGTAA
GAGATCAGACAGC
Found at i:359309 original size:60 final size:60
Alignment explanation
Indices: 359216--359329 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
359206 TTCCTTAAGT
* *
359216 TCGGGGTAACAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAGAGATCCCAAGA
1 TCGGGGTAACAGATTAGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCCCAAGA
* * *
359276 TCGGGGTAAGAGATTAGCTGATGGTGATTTGCCCCAGGCTTGGGGTAAAAGATC
1 TCGGGGTAACAGATTAGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATC
359330 GGATGACTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (60 bp):
TCGGGGTAACAGATTAGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCCCAAGA
Found at i:359345 original size:39 final size:39
Alignment explanation
Indices: 359302--359405 Score: 147
Period size: 39 Copynumber: 2.7 Consensus size: 39
359292 GCTGATGGTG
* *
359302 ATTTGCCCCAGGCTTGGGGTAAAAGATCGGATGACTACA
1 ATTTGCCCCAGGCTTGGGGTAAGAGATCAGATGACTACA
* * *
359341 ATTTGCCCCAGGCTCGGGGTAAGAGATCAGATGGCTGCA
1 ATTTGCCCCAGGCTTGGGGTAAGAGATCAGATGACTACA
*
359380 ATTTGCCCCAGTCTT-GGGTAAGAGAT
1 ATTTGCCCCAGGCTTGGGGTAAGAGAT
359406 TGGTTGATGG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 11 0.19
39 47 0.81
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (39 bp):
ATTTGCCCCAGGCTTGGGGTAAGAGATCAGATGACTACA
Found at i:359487 original size:116 final size:115
Alignment explanation
Indices: 359279--359599 Score: 369
Period size: 116 Copynumber: 2.8 Consensus size: 115
359269 CCCAAGATCG
* * * * * * *
359279 GGGTAAGAGATTAGCTGATGGTGATTTGCCCCAGGCTTGGGGTAAAAGATCGGATGACTACAATT
1 GGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGC-TCGGGTTAAAGATCGGATGGCTACAATC
* * * * *
359344 TGCCCCAGGCTCGGGGTAAGAGATCAGATGGCTGCAATTTGCCCCAGTCTT-
64 TGCCCCAAGCTCAGGGTAAGAGATCAGATGGCTGCAATCTACCCCAGGCTTA
* * *
359395 GGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCAGGGTTAAAGATCAGATGGCTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTC-GGGTTAAAGATCGGATGGCTACAATC
* *
359460 TACCCCAAGCTCAAGGTTAA-AGATCAGATGGCTGCAATCTACCCCAGGCTTA
64 TGCCCCAAGCTC-AGGGTAAGAGATCAGATGGCTGCAATCTACCCCAGGCTTA
*
359512 GGGTAAGAGATTGGCTGATGGTGATCTACCCAAGCTCGGAG-TAAGAGATCGGATGGCTACAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCTCGG-GTTAA-AGATCGGATGGCTACAATC
* **
359576 TGCCCCAGGCTTGGGGTAAGAGAT
64 TGCCCCAAGCTCAGGGTAAGAGAT
359600 TGGCTGATGG
Statistics
Matches: 172, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
115 14 0.08
116 124 0.72
117 34 0.20
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (115 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCTCGGGTTAAAGATCGGATGGCTACAATCTG
CCCCAAGCTCAGGGTAAGAGATCAGATGGCTGCAATCTACCCCAGGCTTA
Found at i:359561 original size:77 final size:78
Alignment explanation
Indices: 359457--359677 Score: 311
Period size: 77 Copynumber: 2.8 Consensus size: 78
359447 GATGGCTGCA
* * * * *
359457 ATCTACCCCAAGCTCAAGGTTAAAGATCAGATGGCTGCAATCTACCCCAGGCTTAGGGTAAGAGA
1 ATCTACCCTAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTACCCCAGGCTTGGGGTAAGAGA
359522 TTGGCTGATGGTG
66 TTGGCTGATGGTG
* * *
359535 ATCTACCC-AAGCTC-GGAGTAAGAGATCGGATGGCTACAATCTGCCCCAGGCTTGGGGTAAGAG
1 ATCTACCCTAAGCTCAGG-GTAAAAGATCGGATGGCTGCAATCTACCCCAGGCTTGGGGTAAGAG
359598 ATTGGCTGATGGTG
65 ATTGGCTGATGGTG
* * **
359612 ATCTGCCCTAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTACCCTAGGCGCGGGGTAAGAGA
1 ATCTACCCTAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTACCCCAGGCTTGGGGTAAGAGA
359677 T
66 T
359678 CGAAATTTTC
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
76 1 0.01
77 67 0.53
78 56 0.44
79 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (78 bp):
ATCTACCCTAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTACCCCAGGCTTGGGGTAAGAGA
TTGGCTGATGGTG
Found at i:359631 original size:116 final size:112
Alignment explanation
Indices: 359269--359638 Score: 316
Period size: 116 Copynumber: 3.2 Consensus size: 112
359259 GGTAAGAGAT
* * * * * * *
359269 CCCAAGATCGGGGTAAGAGATTAGCTGATGGTGATTTGCCCCAGGCTTGGGGTAAAAGATCGGAT
1 CCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCT-ACCCAAGC-TCGGGT-AAAGATCGGAT
* * * *
359334 GACTACAATTTGCCCCAGGCTCGGGGTAAGAGATCAGATGGCTGCAATTTG
63 GGCTACAATCTGCCCCAGGCTAGGGGTAAGAGATCAGATGGCTG-AATCTG
* * * * *
359385 CCCCAG-TCTTGGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCAGGGTTAAAGATCAGA
1 CCCAAGCTC-AGGGTAAGAGATTGGCTGATGGTGATCTACCC-AAGCTC-GGG-TAAAGATCGGA
* * * * * *
359449 TGGCTGCAATCTACCCCAAGCTCAAGGTTAA-AGATCAGATGGCTGCAATCTAC
62 TGGCTACAATCTGCCCCAGGCT-AGGGGTAAGAGATCAGATGGCTG-AATCT-G
* *
359502 CCCAGGCTTAGGGTAAGAGATTGGCTGATGGTGATCTACCCAAGCTCGGAGTAAGAGATCGGATG
1 CCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCAAGCTCGG-GTAA-AGATCGGATG
* *
359567 GCTACAATCTGCCCCAGGCTTGGGGTAAGAGATTGGCTGATGG-TG-ATCTG
64 GCTACAATCTGCCCCAGGCTAGGGGTAAGAGA-T--CAGATGGCTGAATCTG
*
359617 CCCTAAGCTCAGGGTAAAAGAT
1 CCC-AAGCTCAGGGTAAGAGAT
359639 CGGATGGCTG
Statistics
Matches: 203, Mismatches: 37, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
115 19 0.09
116 135 0.67
117 40 0.20
118 3 0.01
119 6 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (112 bp):
CCCAAGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCAAGCTCGGGTAAAGATCGGATGGC
TACAATCTGCCCCAGGCTAGGGGTAAGAGATCAGATGGCTGAATCTG
Found at i:359660 original size:39 final size:39
Alignment explanation
Indices: 359318--359679 Score: 205
Period size: 39 Copynumber: 9.3 Consensus size: 39
359308 CCCAGGCTTG
* * * * * * *
359318 GGGTAAAAGATCGGATGACTACAATTTGCCCCAGGCTCG
1 GGGTAAGAGATCGGATGGCTGCAATCTACCCCAAGCTCA
* * * *
359357 GGGTAAGAGATCAGATGGCTGCAATTTGCCCC-AG-TCTT
1 GGGTAAGAGATCGGATGGCTGCAATCTACCCCAAGCTC-A
* * *
359395 GGGTAAGAGATTGGTTGATGG-TG--ATCTGCCCTAAGCTCA
1 GGGTAAGAGA-TCG--GATGGCTGCAATCTACCCCAAGCTCA
*
359434 GGGTTAA-AGATCAGATGGCTGCAATCTACCCCAAGCTCAA
1 GGG-TAAGAGATCGGATGGCTGCAATCTACCCCAAGCTC-A
* * * *
359474 GGTTAA-AGATCAGATGGCTGCAATCTACCCCAGGCTTA
1 GGGTAAGAGATCGGATGGCTGCAATCTACCCCAAGCTCA
*
359512 GGGTAAGAGATTGGCTGATGG-TG--ATCTA-CCCAAGCTC-
1 GGGTAAGAGA-T--CGGATGGCTGCAATCTACCCCAAGCTCA
* * * **
359549 GGAGTAAGAGATCGGATGGCTACAATCTGCCCCAGGCTTG
1 GG-GTAAGAGATCGGATGGCTGCAATCTACCCCAAGCTCA
* * *
359589 GGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCTAAGCTCA
1 GGGTAAGAGA-T--CGGATGGCTGCAATCTACCCCAAGCTCA
* * * * *
359628 GGGTAAAAGATCGGATGGCTGCAATCTACCCTAGGCGCG
1 GGGTAAGAGATCGGATGGCTGCAATCTACCCCAAGCTCA
359667 GGGTAAGAGATCG
1 GGGTAAGAGATCG
359680 AAATTTTCAA
Statistics
Matches: 256, Mismatches: 40, Indels: 54
0.73 0.11 0.15
Matches are distributed among these distances:
35 6 0.02
36 12 0.05
37 9 0.04
38 45 0.18
39 150 0.59
40 14 0.05
41 8 0.03
42 12 0.05
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GGGTAAGAGATCGGATGGCTGCAATCTACCCCAAGCTCA
Found at i:366839 original size:7 final size:6
Alignment explanation
Indices: 366767--366889 Score: 138
Period size: 6 Copynumber: 19.0 Consensus size: 6
366757 TTACAATTGA
*
366767 GAAAGA GAAAGG GAAAGG AGAAAGAG GAAAGG GAAAGG GAAAGG GAAAGG
1 GAAAGG GAAAGG GAAAGG -GAAAG-G GAAAGG GAAAGG GAAAGG GAAAGG
* *
366817 GAAAGG GAAAAG GAAAGG AGAAAGG AGAAAGGG GGAAGG GAAAGG AGAAAGG
1 GAAAGG GAAAGG GAAAGG -GAAAGG -GAAA-GG GAAAGG GAAAGG -GAAAGG
366869 GAGAAGG GAAATGGG GAAAGG
1 GA-AAGG GAAA--GG GAAAGG
366890 CTTCGAAAGA
Statistics
Matches: 104, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
6 59 0.57
7 36 0.35
8 9 0.09
ACGTcount: A:0.51, C:0.00, G:0.48, T:0.01
Consensus pattern (6 bp):
GAAAGG
Found at i:377473 original size:11 final size:11
Alignment explanation
Indices: 377454--377484 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
377444 TAAAAAGATT
377454 AATATAAATTA
1 AATATAAATTA
*
377465 AATACAAATTA
1 AATATAAATTA
377476 AATATAAAT
1 AATATAAAT
377485 AATATTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
AATATAAATTA
Found at i:378297 original size:110 final size:109
Alignment explanation
Indices: 378056--378252 Score: 254
Period size: 110 Copynumber: 1.8 Consensus size: 109
378046 TATTTTCTCA
* * * * * * * *
378056 ATTTTCTCTTT-TTCTTTCTTTAAGAATATATTGGACCTTTTGAGGCGAAATGAAATGACACCAA
1 ATTTTCTCTTTCTTTTTTTTTTTAGAATGTGTTAGCCCTTTTGACGCGAAATGAAATGACACCAA
**
378120 AGCACTCCATCCCGATTACTCAGCCCAACATGCTCTCAATCATTT
66 AGCACTCCATCCCGATTACTCAGCCCAACACACTCTCAAT-ATTT
*
378165 ATTTTCTCTTTCTTTTTTTTTTTAGAATGTGTTAGCCCTTTTGACGCGAAATGAAATGACAATC-
1 ATTTTCTCTTTCTTTTTTTTTTTAGAATGTGTTAGCCCTTTTGACGCGAAATGAAATGAC-ACCA
*
378229 AAGCACTCCATCCCGGTTACTCAG
65 AAGCACTCCATCCCGATTACTCAG
378253 TCTATCACAC
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
109 11 0.14
110 63 0.83
111 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.37
Consensus pattern (109 bp):
ATTTTCTCTTTCTTTTTTTTTTTAGAATGTGTTAGCCCTTTTGACGCGAAATGAAATGACACCAA
AGCACTCCATCCCGATTACTCAGCCCAACACACTCTCAATATTT
Done.