Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 202 of 211
Found at i:62474763 original size:13 final size:13
Alignment explanation
Indices: 62474745--62474776 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
62474735 TTTCCAGCAA
62474745 TTATGAATTTATT
1 TTATGAATTTATT
62474758 TTATGAATTTATT
1 TTATGAATTTATT
*
62474771 TGATGA
1 TTATGA
62474777 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:62474984 original size:50 final size:50
Alignment explanation
Indices: 62474871--62475111 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
62474861 ATTTGGGTAA
* * *
62474871 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
62474927 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
62474977 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
62475027 AGAGGTCCC-TATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
62475076 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
62475112 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.21
50 61 0.37
51 24 0.14
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:62475077 original size:99 final size:103
Alignment explanation
Indices: 62474871--62475119 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
62474861 ATTTGGGTAA
62474871 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
62474936 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* * *
62474977 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGT-CCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
62475038 TAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGA-CACG
* *
62475076 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
62475120 GTTATTATCA
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
98 1 0.01
99 41 0.31
100 46 0.35
101 2 0.02
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
Found at i:62476604 original size:29 final size:30
Alignment explanation
Indices: 62476562--62476636 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
62476552 TAATCCCAAT
* * *
62476562 TAGTTAGGAGACTAAATTTAAAAAAA-TAA
1 TAGTTAGGTGACTAAACTAAAAAAAATTAA
* *
62476591 TAGTTGGGTGACTAAACTAAAAAAAATTGA
1 TAGTTAGGTGACTAAACTAAAAAAAATTAA
*
62476621 TAATTAGGTGACTAAA
1 TAGTTAGGTGACTAAA
62476637 AAAAGAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.28
Consensus pattern (30 bp):
TAGTTAGGTGACTAAACTAAAAAAAATTAA
Found at i:62484658 original size:18 final size:17
Alignment explanation
Indices: 62484632--62484667 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
62484622 CCTGCCCATG
*
62484632 GGCCGGACGGCCCGGCCC
1 GGCCCGACGGCCC-GCCC
62484650 GGCCCGACGGCCCGCCC
1 GGCCCGACGGCCCGCCC
62484667 G
1 G
62484668 AAATATGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.06, C:0.53, G:0.42, T:0.00
Consensus pattern (17 bp):
GGCCCGACGGCCCGCCC
Found at i:62484815 original size:29 final size:29
Alignment explanation
Indices: 62484774--62484838 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
62484764 TATTTTTTAA
*
62484774 TTTTTTAATTTTAAAATACTTTAAAAATAT
1 TTTTTTTATTTT-AAATACTTTAAAAATAT
** * *
62484804 TTTTTTTA-TTTATTTATTTTTAAAATAT
1 TTTTTTTATTTTAAATACTTTAAAAATAT
62484832 TTTTTTT
1 TTTTTTT
62484839 GTGTTTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 20 0.67
29 3 0.10
30 7 0.23
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTTTTATTTTAAATACTTTAAAAATAT
Found at i:62489073 original size:5 final size:5
Alignment explanation
Indices: 62489063--62489087 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62489053 CCATTAAGTC
62489063 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
62489088 TTACAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:62490480 original size:37 final size:40
Alignment explanation
Indices: 62490428--62490524 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 40
62490418 TAATAATTTA
*
62490428 ACACCCAGTGTCTCATCG-GTTAAAACGAAGT-G-AATTG
1 ACACCCAGTGTCTCATCGAATTAAAACGAAGTAGAAATTG
* * **
62490465 GCACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTG
1 ACACCCAGTGTCTCATCGAATTAAAACGAAGTAG-AAATTG
62490506 ACACCCAGTGTCTCATCGA
1 ACACCCAGTGTCTCATCGA
62490525 CTCAAAGTCG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
37 16 0.33
38 10 0.20
39 1 0.02
41 22 0.45
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (40 bp):
ACACCCAGTGTCTCATCGAATTAAAACGAAGTAGAAATTG
Found at i:62490511 original size:41 final size:41
Alignment explanation
Indices: 62490389--62490524 Score: 129
Period size: 40 Copynumber: 3.4 Consensus size: 41
62490379 ACCAGTTTGG
* * * * * *
62490389 CACCCAGTGCCTCATTGGA-TAATTCGAAGTAATAATTTAA
1 CACCCAGTGCCTCATCGAATTAATACGAAGTAGTAAATTGA
* * * *
62490429 CACCCAGTGTCTCATCG-GTTAAAACGAAGT-G--AATTGG
1 CACCCAGTGCCTCATCGAATTAATACGAAGTAGTAAATTGA
*
62490466 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAATACGAAGTAGTAAATTGA
*
62490507 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
62490525 CTCAAAGTCG
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 19 0.25
38 10 0.13
39 1 0.01
40 24 0.32
41 22 0.29
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAATTAATACGAAGTAGTAAATTGA
Found at i:62496717 original size:11 final size:11
Alignment explanation
Indices: 62496701--62496725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62496691 TTCAATTCAA
62496701 ATAATCAATAT
1 ATAATCAATAT
62496712 ATAATCAATAT
1 ATAATCAATAT
62496723 ATA
1 ATA
62496726 TACCAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:62496750 original size:15 final size:16
Alignment explanation
Indices: 62496703--62496752 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
62496693 CAATTCAAAT
*
62496703 AATCAATATATAA-TC
1 AATCAATATACAATTC
62496718 AAT-ATATATACCAATTC
1 AATCA-ATATA-CAATTC
62496735 AATCAATATA-AATTC
1 AATCAATATACAATTC
62496750 AAT
1 AAT
62496753 AAATTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 2 0.07
17 10 0.33
18 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (16 bp):
AATCAATATACAATTC
Found at i:62497723 original size:25 final size:27
Alignment explanation
Indices: 62497681--62497733 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
62497671 TTTGTTTTAT
62497681 TATACATTAATATATTAT-TATAATATA
1 TATACATTAATATATTATGTA-AATATA
*
62497708 TATAC-TTAA-ATGTTATGTAAATATA
1 TATACATTAATATATTATGTAAATATA
62497733 T
1 T
62497734 TTCATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 13 0.54
26 6 0.25
27 5 0.21
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
TATACATTAATATATTATGTAAATATA
Found at i:62505219 original size:85 final size:81
Alignment explanation
Indices: 62505077--62505305 Score: 244
Period size: 85 Copynumber: 2.7 Consensus size: 81
62505067 AGCAAGGGAC
*
62505077 TTGGT-CCCTTGGTTTGGTAAATATTCCTCTTTTAGTCCTCTAAATTTATAAACTTGTCATTAAA
1 TTGGTCCCCTTGGTTTGGTAAA-ATTCCTC-TTTAGTCCTCTAAATTTGT-AACTTGTCATT-AA
*
62505141 TTAAATGGTAAAAATAAAAA
62 TTAAATGGAAAAAATAAAAA
* *
62505161 TTGGTCCCCTTGATTTGGTAAAATTCCTCATTTAGGTCCTCTAAATTTGTAATCTTGTCAGCTAA
1 TTGGTCCCCTTGGTTTGGTAAAATTCCTC-TTTA-GTCCTCTAAATTTGTAA-CTTGTCA-TTAA
** **
62505226 TTAAATGGAAAAAATGTACC
62 TTAAATGGAAAAAATAAAAA
** * * *
62505246 TTGAACCCATTGGTTTGGTAAAATGCCTCTTGTAGTCCTCCAAATTTGTGAACTTGTCAT
1 TTGGTCCCCTTGGTTTGGTAAAATTCCTCTT-TAGTCCTCTAAATTTGT-AACTTGTCAT
62505306 ATAAGTACTT
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
84 41 0.33
85 81 0.66
86 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (81 bp):
TTGGTCCCCTTGGTTTGGTAAAATTCCTCTTTAGTCCTCTAAATTTGTAACTTGTCATTAATTAA
ATGGAAAAAATAAAAA
Found at i:62506291 original size:28 final size:29
Alignment explanation
Indices: 62506236--62506297 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
62506226 TTGAATCGAT
*
62506236 TTTATAATTTTTTTAATAATTTTAAATTG
1 TTTATAATTTTTTTAATAATTTTAAATTA
*
62506265 TTTATATTTTTTTTCAAT-ATTTT-AATTA
1 TTTATAATTTTTTT-AATAATTTTAAATTA
62506293 TTTAT
1 TTTAT
62506298 GTAATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 18 0.60
30 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTATAATTTTTTTAATAATTTTAAATTA
Found at i:62513917 original size:13 final size:13
Alignment explanation
Indices: 62513891--62513930 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
62513881 TGTTTTATTT
62513891 AATTAAATAATTA
1 AATTAAATAATTA
62513904 AAGTTAAA-AATTA
1 AA-TTAAATAATTA
62513917 AATTAAATTAATTA
1 AATTAAA-TAATTA
62513931 GTCGAATCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
13 9 0.38
14 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AATTAAATAATTA
Found at i:62522824 original size:24 final size:25
Alignment explanation
Indices: 62522789--62522836 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
62522779 TTATGAAATT
62522789 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
62522813 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
62522837 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:62522881 original size:92 final size:92
Alignment explanation
Indices: 62522670--62522861 Score: 264
Period size: 92 Copynumber: 2.1 Consensus size: 92
62522660 AATTGTTATG
* * * *
62522670 AATTTATTATTAAGAATTTTATGAAA-TT-ATATATCACTATTAAATTATATTTAATATTAATTA
1 AATTTATTATCAAGAATTTTATGAAATTTAATAT-TAATTATTAAATTATATGTAATATTAATTA
* * *
62522733 TTTTAAATTGTATAAATTCATATAAGAA
65 TTTTAAATTATACAAATTCATAAAAGAA
62522761 AATTTATTATCAAGAATTTTATGAAATTTAATATTAATTATTAAATTATATGTAATAATT-ATTA
1 AATTTATTATCAAGAATTTTATGAAATTTAATATTAATTATTAAATTATATGTAAT-ATTAATTA
* *
62522825 TTTTAAATTATACAAATTCATAAAATAT
65 TTTTAAATTATACAAATTCATAAAAGAA
62522853 AATTTATTA
1 AATTTATTA
62522862 GTTATAATTA
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
91 25 0.28
92 57 0.64
93 7 0.08
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (92 bp):
AATTTATTATCAAGAATTTTATGAAATTTAATATTAATTATTAAATTATATGTAATATTAATTAT
TTTAAATTATACAAATTCATAAAAGAA
Found at i:62522895 original size:28 final size:27
Alignment explanation
Indices: 62522864--62522936 Score: 62
Period size: 28 Copynumber: 2.7 Consensus size: 27
62522854 ATTTATTAGT
62522864 TATAATTATTTTAAATTTTATTAAATA
1 TATAATTATTTTAAATTTTATTAAATA
* * *
62522891 -ATATATT-TTAATTAAAATATATTTAATA
1 TATA-ATTATT--TTAAATTTTATTAAATA
*
62522919 T-TAATTATTTCAAATTTT
1 TATAATTATTTTAAATTTT
62522937 CATTTATAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 11
0.67 0.12 0.21
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 18 0.51
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
TATAATTATTTTAAATTTTATTAAATA
Found at i:62522924 original size:54 final size:54
Alignment explanation
Indices: 62522866--62523059 Score: 158
Period size: 54 Copynumber: 3.4 Consensus size: 54
62522856 TTATTAGTTA
62522866 TAATTATTTTAAATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTTAAATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAT
* * * **
62522920 TAATTATTTCAAATTTTCATTTATAGTATCATATATTATAATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTTAAATTTT-A-TTA-A--ATAATATATTTTAA-TT-A--AAA-T-ATAT-TTAATA
62522985 T
54 T
* * * *
62522986 TAATTA-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTTA-AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAT
*
62523040 TAATTATGTT-AATTTGTATT
1 TAATTATTTTAAATTT-TATT
62523060 TACAGTATCA
Statistics
Matches: 111, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
53 5 0.05
54 30 0.27
55 6 0.05
56 4 0.04
57 3 0.03
59 13 0.12
60 4 0.04
61 13 0.12
63 4 0.04
64 4 0.04
65 8 0.07
66 17 0.15
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (54 bp):
TAATTATTTTAAATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAT
Found at i:62523015 original size:37 final size:38
Alignment explanation
Indices: 62522950--62523134 Score: 94
Period size: 38 Copynumber: 4.8 Consensus size: 38
62522940 TTATAGTATC
* * *
62522950 ATATATT-ATAATTTGAGTAAATTCATATAAGAATATTA
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATATTA
**
62522988 AT-TATTAAGAATTTTATTAAATTATATATTTTAAT-TATA
1 ATATATTAAGAATTTTATTAAATTATATA--AGAATAT-TA
* * * * * * * *
62523027 ATATATTTAATAATAATTATGTTAATTTGTATTTACAGTA-TC
1 ATATA-TTAAGAAT--TT-TATTAAATTATA-TAAGAATATTA
* * *
62523069 ATATATTATG-ATTTGAGTAAATTCATATAAGAATATTA
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATATTA
62523107 AT-TATTAAGAATTTTATTAAATTATATA
1 ATATATTAAGAATTTTATTAAATTATATA
62523135 TTTTAATTAT
Statistics
Matches: 105, Mismatches: 28, Indels: 29
0.65 0.17 0.18
Matches are distributed among these distances:
37 30 0.29
38 34 0.32
39 7 0.07
40 4 0.04
41 10 0.10
42 6 0.06
43 4 0.04
44 9 0.09
45 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (38 bp):
ATATATTAAGAATTTTATTAAATTATATAAGAATATTA
Found at i:62523037 original size:15 final size:15
Alignment explanation
Indices: 62523002--62523053 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
62522992 TTAAGAATTT
*
62523002 TATTAAATTAT-ATA
1 TATTTAATTATAATA
62523016 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
62523030 TATTTAATAATAAT-
1 TATTTAATTATAATA
62523044 TATGTTAATT
1 TAT-TTAATT
62523054 TGTATTTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:62523108 original size:119 final size:119
Alignment explanation
Indices: 62522877--62523144 Score: 450
Period size: 119 Copynumber: 2.2 Consensus size: 119
62522867 AATTATTTTA
* * *
62522877 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTTTCATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTT-AAATTTTCATTT
*
62522942 ATAGTATCATATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 ACAGTATCATATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
62522997 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTGT-ATT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT-TTAAATTT-TCATT
*
62523060 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TACAGTATCATATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
62523116 AATTTTATTAAATTATATATTTTAATTAT
1 AATTTTATTAAATTATATATTTTAATTAT
62523145 CTTATTAAAA
Statistics
Matches: 141, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
119 91 0.65
120 48 0.34
121 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTAAATTTTCATTTA
CAGTATCATATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:62523240 original size:18 final size:17
Alignment explanation
Indices: 62523212--62523246 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62523202 ATTATTAAGA
*
62523212 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
62523229 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
62523247 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:62523491 original size:45 final size:43
Alignment explanation
Indices: 62523392--62523501 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
62523382 TTTTCCATTA
62523392 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* ***
62523431 TACTATTACACCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
*
62523476 TGCTATTACACCTCTAATCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
62523502 CCTCTAATCT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
39 17 0.29
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.32
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:62523503 original size:16 final size:16
Alignment explanation
Indices: 62523482--62523517 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
62523472 GATTTGCTAT
62523482 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
62523498 TACACCTCTAATCTAA
1 TACACCTCTAATCCAA
62523514 TACA
1 TACA
62523518 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:62523908 original size:27 final size:25
Alignment explanation
Indices: 62523857--62523905 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
62523847 AAATTATATG
* *
62523857 TTATATACATGTAAATATATCTTAA
1 TTATATACATATAAATATAGCTTAA
62523882 TTATATACATATAAATATAAGCTT
1 TTATATACATATAAATAT-AGCTT
62523906 TAAGATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (25 bp):
TTATATACATATAAATATAGCTTAA
Found at i:62524663 original size:46 final size:46
Alignment explanation
Indices: 62524610--62524767 Score: 182
Period size: 46 Copynumber: 3.5 Consensus size: 46
62524600 AATGATCATT
62524610 TAATTATTAA-TATTTTATTATCATATAATTATGAAAAGTTACAAAA
1 TAATTATTAACTATTTTATT-TCATATAATTATGAAAAGTTACAAAA
* * * * **
62524656 TAATTATTAACTATTTAATTTTATAAAATATAT-AAAATGGT-C-ATT
1 TAATTATTAACTATTTTATTTCATATAAT-TATGAAAA-GTTACAAAA
62524701 TAATTATTAA-TATTTTATTGTCATATAATTATGAAAAGTTACAAAA
1 TAATTATTAACTATTTTATT-TCATATAATTATGAAAAGTTACAAAA
*
62524747 TAATTATTAACTATTTAATTT
1 TAATTATTAACTATTTTATTT
62524768 TATCTTTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
44 13 0.14
45 23 0.25
46 34 0.37
47 21 0.23
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (46 bp):
TAATTATTAACTATTTTATTTCATATAATTATGAAAAGTTACAAAA
Found at i:62524700 original size:91 final size:92
Alignment explanation
Indices: 62524584--62524770 Score: 349
Period size: 91 Copynumber: 2.0 Consensus size: 92
62524574 TCTCACCTAA
62524584 TTATAAAAATATATAAAATGATCATTTAATTATTAATATTTTATTATCATATAATTATGAAAAGT
1 TTATAAAAATATATAAAATGATCATTTAATTATTAATATTTTATTATCATATAATTATGAAAAGT
62524649 TACAAAATAATTATTAACTATTTAATT
66 TACAAAATAATTATTAACTATTTAATT
* *
62524676 TTAT-AAAATATATAAAATGGTCATTTAATTATTAATATTTTATTGTCATATAATTATGAAAAGT
1 TTATAAAAATATATAAAATGATCATTTAATTATTAATATTTTATTATCATATAATTATGAAAAGT
62524740 TACAAAATAATTATTAACTATTTAATT
66 TACAAAATAATTATTAACTATTTAATT
62524767 TTAT
1 TTAT
62524771 CTTTTTTGTT
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
91 89 0.96
92 4 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TTATAAAAATATATAAAATGATCATTTAATTATTAATATTTTATTATCATATAATTATGAAAAGT
TACAAAATAATTATTAACTATTTAATT
Found at i:62528929 original size:6 final size:6
Alignment explanation
Indices: 62528913--62528944 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
62528903 GGGGTTTAGT
62528913 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA T
62528945 GAACTTCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTAA
Found at i:62539427 original size:13 final size:14
Alignment explanation
Indices: 62539409--62539442 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
62539399 AAATAGGTTA
62539409 AATTTTGCT-TTTT
1 AATTTTGCTATTTT
62539422 AATTTTGCTATTTT
1 AATTTTGCTATTTT
62539436 AATTTTG
1 AATTTTG
62539443 TCATGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (14 bp):
AATTTTGCTATTTT
Found at i:62541541 original size:15 final size:15
Alignment explanation
Indices: 62541521--62541628 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
62541511 TTTATGGAAA
62541521 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
62541536 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
62541550 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
62541566 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
62541580 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* * **
62541596 ATCAAATAT-TAGAA
1 ATCAAAGATATGGGT
62541610 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
62541626 ATC
1 ATC
62541629 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:62541550 original size:30 final size:30
Alignment explanation
Indices: 62541514--62541628 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
62541504 ATCCATATTT
*
62541514 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
62541544 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
62541574 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
62541604 TTAGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
62541629 GAGATATTGG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 82 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:62546223 original size:15 final size:15
Alignment explanation
Indices: 62546203--62546310 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
62546193 TTTATGGAAA
62546203 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
62546218 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
62546232 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
62546248 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
62546262 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
62546278 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
62546292 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
62546308 ATC
1 ATC
62546311 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:62546232 original size:30 final size:30
Alignment explanation
Indices: 62546196--62546310 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
62546186 ATCCATATTT
*
62546196 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
62546226 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
62546256 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
62546286 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
62546311 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:62553068 original size:16 final size:16
Alignment explanation
Indices: 62553047--62553085 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
62553037 GTTTGATAGA
62553047 AATTTTTTAA-AATATT
1 AATTTTTTAACAAT-TT
62553063 AA-TTTTTAACAATTT
1 AATTTTTTAACAATTT
62553078 AATTTTTT
1 AATTTTTT
62553086 TCGCATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTTTAACAATTT
Found at i:62554958 original size:15 final size:15
Alignment explanation
Indices: 62554940--62555008 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
62554930 TATATGTGAA
62554940 ATTAATATATATTAT
1 ATTAATATATATTAT
*
62554955 ATTAAAATA-AGTT-T
1 ATTAATATATA-TTAT
*
62554969 ACTTAATATATAAGTAT
1 A-TTAATATAT-ATTAT
*
62554986 ATATATTATATATTAT
1 AT-TAATATATATTAT
*
62555002 AATAATA
1 ATTAATA
62555009 AAACAAACAA
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
14 3 0.07
15 21 0.51
16 7 0.17
17 10 0.24
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (15 bp):
ATTAATATATATTAT
Found at i:62556060 original size:37 final size:41
Alignment explanation
Indices: 62555957--62556070 Score: 121
Period size: 37 Copynumber: 2.9 Consensus size: 41
62555947 TTCGACTTCG
*
62555957 AGTCGATGAGACACTGGGTGTAAATTTACTTCTTCGGATTA
1 AGTCGATGAGACACTGGGTGTCAATTTACTTCTTCGGATTA
* * * * * *
62555998 ATTTGATAAGGCACTGGGTGCCAATTTAC-T-TT-GG-TTT
1 AGTCGATGAGACACTGGGTGTCAATTTACTTCTTCGGATTA
62556035 AGTCGATGAGACACTGGGTGTCAATTTA-TTACTTCG
1 AGTCGATGAGACACTGGGTGTCAATTTACTT-CTTCG
62556071 AGTTATCCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
37 26 0.46
38 2 0.04
39 4 0.07
40 2 0.04
41 23 0.40
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (41 bp):
AGTCGATGAGACACTGGGTGTCAATTTACTTCTTCGGATTA
Found at i:62558117 original size:26 final size:26
Alignment explanation
Indices: 62558088--62558145 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
62558078 ATAAGAGCCA
* *
62558088 TAATTAGGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACTTT
* *
62558114 TAATCAGGAAGCTCACGAAGAGCTTT
1 TAATCAGGAAGCTCACAAAGAACTTT
62558140 TAATCA
1 TAATCA
62558146 AGAGCTTCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACTTT
Found at i:62560707 original size:23 final size:22
Alignment explanation
Indices: 62560681--62560725 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
62560671 AAAATTTGTT
* *
62560681 GGCTTTGTAATTTTGTTTATTTA
1 GGCTTGGT-ATTTTATTTATTTA
*
62560704 GGCTTGGTTTTTTATTTATTTA
1 GGCTTGGTATTTTATTTATTTA
62560726 TAAATTTAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (22 bp):
GGCTTGGTATTTTATTTATTTA
Found at i:62563128 original size:6 final size:6
Alignment explanation
Indices: 62563117--62563141 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62563107 CCCCAGTCTC
62563117 CCATTA CCATTA CCATTA CCATTA C
1 CCATTA CCATTA CCATTA CCATTA C
62563142 AACCTTCATA
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (6 bp):
CCATTA
Found at i:62563614 original size:2 final size:2
Alignment explanation
Indices: 62563602--62563630 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
62563592 ATTTGGTAAC
62563602 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
62563631 TCACGTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:62568057 original size:6 final size:6
Alignment explanation
Indices: 62568046--62568078 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
62568036 TATATCATAT
62568046 CCACAA CCACAA CCACAA CCACAA CCACAA CCA
1 CCACAA CCACAA CCACAA CCACAA CCACAA CCA
62568079 TCTACAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CCACAA
Found at i:62570022 original size:6 final size:6
Alignment explanation
Indices: 62570011--62570039 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
62570001 AAATGTTGTG
62570011 ATAATT ATAATT ATAATT ATAATT -TAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT
62570040 TAAATTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATAATT
Found at i:62571576 original size:27 final size:28
Alignment explanation
Indices: 62571524--62571582 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
62571514 AGAATAAATT
*
62571524 TAAAATTTATGTATAAAGCAACTAAAAA
1 TAAAATTTATATATAAAGCAACTAAAAA
*
62571552 TAAAA-TTATATATAAA-TAACTTAAAAA
1 TAAAATTTATATATAAAGCAAC-TAAAAA
62571579 TAAA
1 TAAA
62571583 TCATTTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 3 0.11
27 20 0.71
28 5 0.18
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (28 bp):
TAAAATTTATATATAAAGCAACTAAAAA
Found at i:62571748 original size:38 final size:38
Alignment explanation
Indices: 62571697--62571776 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
62571687 TAACACATAT
62571697 AAAAAATTTAAACTAAATAATATAT-ATACATATATAA
1 AAAAAATTTAAACTAAATAATATATAATACATATATAA
*
62571734 AAAACAATTTAAACTAAATAATATATACATACATATATTA
1 AAAA-AATTTAAACTAAATAATATATA-ATACATATATAA
62571774 AAA
1 AAA
62571777 TAGATGCTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 4 0.10
38 21 0.54
40 14 0.36
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (38 bp):
AAAAAATTTAAACTAAATAATATATAATACATATATAA
Found at i:62572637 original size:5 final size:5
Alignment explanation
Indices: 62572580--62572630 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
62572570 ATGTGTTAAA
* *
62572580 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATT ATATT ATAT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATAT
62572631 ATTATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
5 32 0.80
6 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:62573973 original size:18 final size:19
Alignment explanation
Indices: 62573950--62573988 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
62573940 ATATATAGAT
62573950 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
62573968 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
62573987 AT
1 AT
62573989 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:62574338 original size:39 final size:39
Alignment explanation
Indices: 62574228--62574362 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
62574218 GACCTCGAGT
* * * *
62574228 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
62574269 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
62574307 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
62574346 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
62574363 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:62574506 original size:18 final size:19
Alignment explanation
Indices: 62574485--62574525 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
62574475 AATGAAATGA
62574485 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
62574503 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
62574522 GAAA
1 GAAA
62574526 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:62579047 original size:5 final size:5
Alignment explanation
Indices: 62579021--62579077 Score: 69
Period size: 5 Copynumber: 10.8 Consensus size: 5
62579011 ATGTGTTAAA
* *
62579021 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATT ATATAT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATATT ATAT-T
62579069 ATATT ATAT
1 ATATT ATAT
62579078 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
5 32 0.71
6 13 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (5 bp):
ATATT
Found at i:62579055 original size:26 final size:25
Alignment explanation
Indices: 62579022--62579078 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
62579012 TGTGTTAAAA
62579022 TATATATATTAAATTAT-TATTATAT
1 TATATATATTAAATTATATA-TATAT
*
62579047 TATAGTATATTATATTATATATATAT
1 TATA-TATATTAAATTATATATATAT
62579073 TATATA
1 TATATA
62579079 AATAAGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 6 0.21
26 21 0.72
27 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATATATATTAAATTATATATATAT
Found at i:62580416 original size:18 final size:19
Alignment explanation
Indices: 62580393--62580431 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
62580383 ATATATAGAT
62580393 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
62580411 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
62580430 AT
1 AT
62580432 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:62580781 original size:39 final size:39
Alignment explanation
Indices: 62580671--62580805 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
62580661 GACCTCGAGT
* * * *
62580671 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
62580712 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
62580750 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
62580789 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
62580806 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:62580949 original size:18 final size:19
Alignment explanation
Indices: 62580928--62580968 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
62580918 AATGAAATGA
62580928 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
62580946 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
62580965 GAAA
1 GAAA
62580969 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:62582572 original size:15 final size:15
Alignment explanation
Indices: 62582554--62582585 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
62582544 GGCTAGGGGT
62582554 ATTGGGCTTAGGCTA
1 ATTGGGCTTAGGCTA
*
62582569 ATTGGGTTTAGGCTA
1 ATTGGGCTTAGGCTA
62582584 AT
1 AT
62582586 AGAGTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (15 bp):
ATTGGGCTTAGGCTA
Found at i:62582592 original size:15 final size:15
Alignment explanation
Indices: 62582561--62582594 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
62582551 GGTATTGGGC
* *
62582561 TTAGGCTAATTGGGT
1 TTAGGCTAATAGAGT
62582576 TTAGGCTAATAGAGT
1 TTAGGCTAATAGAGT
62582591 TTAG
1 TTAG
62582595 TTTACTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (15 bp):
TTAGGCTAATAGAGT
Found at i:62583316 original size:44 final size:44
Alignment explanation
Indices: 62583266--62583356 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
62583256 ATTGAAGTAA
* *
62583266 AATAGAAATTGTGGTAA-CTATACATTTAAAAATAATTATAATTT
1 AATAGAAATTGTGGTAATC-ACACATTTAAAAATAATTATAACTT
* *
62583310 AATAGAAGTTGTGGTAATCACACGTTTAAAAATAATTATAACTT
1 AATAGAAATTGTGGTAATCACACATTTAAAAATAATTATAACTT
62583354 AAT
1 AAT
62583357 TTACAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (44 bp):
AATAGAAATTGTGGTAATCACACATTTAAAAATAATTATAACTT
Found at i:62590513 original size:19 final size:21
Alignment explanation
Indices: 62590473--62590514 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
62590463 GGTATAGAAG
62590473 AAATATTTTTACATATTAATA
1 AAATATTTTTACATATTAATA
*
62590494 AAATA-TTTTATATA-TAATA
1 AAATATTTTTACATATTAATA
62590513 AA
1 AA
62590515 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 8 0.40
21 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATTTTTACATATTAATA
Found at i:62593471 original size:31 final size:27
Alignment explanation
Indices: 62593406--62593475 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 27
62593396 TATAATTAAA
*
62593406 TTATCATTTTGGTATATGTACTTTTTT
1 TTATCAATTTGGTATATGTACTTTTTT
*
62593433 TTATCAATTTGGTATTTGTACTCTATTTT
1 TTATCAATTTGGTATATGTACT-T-TTTT
62593462 GGTTATCAATTTGG
1 --TTATCAATTTGG
62593476 CCATTGTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 20 0.54
28 1 0.03
29 4 0.11
31 12 0.32
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (27 bp):
TTATCAATTTGGTATATGTACTTTTTT
Found at i:62593483 original size:31 final size:32
Alignment explanation
Indices: 62593433--62593494 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
62593423 GTACTTTTTT
*
62593433 TTATCAATTTGGTATTTGTACTCT-ATTTTGG
1 TTATCAATTTGGCATTTGTACTCTCATTTTGG
*
62593464 TTATCAATTTGGCCA-TTGTACTTTCATTTTG
1 TTATCAATTTGG-CATTTGTACTCTCATTTTG
62593495 TATACCCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.53
Consensus pattern (32 bp):
TTATCAATTTGGCATTTGTACTCTCATTTTGG
Found at i:62594961 original size:2 final size:2
Alignment explanation
Indices: 62594954--62594983 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
62594944 CTACTCATTG
62594954 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
62594984 GGGGTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:62609884 original size:6 final size:6
Alignment explanation
Indices: 62609875--62609900 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
62609865 CTTAGGCTTA
62609875 GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GG
62609901 TGTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:62610137 original size:3 final size:3
Alignment explanation
Indices: 62610124--62610157 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
62610114 CGGTGGCTGC
* *
62610124 GGA GAA GGA GGA GGA GGA GGA GGA AGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
62610158 ATTTTTGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:62610575 original size:3 final size:3
Alignment explanation
Indices: 62610567--62610596 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
62610557 TTAGTTTTAA
62610567 ATT ATT ATT ATTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT
62610597 AAAACCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:62610799 original size:17 final size:17
Alignment explanation
Indices: 62610773--62610805 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
62610763 TACTTTTAAA
62610773 TTTTAATTATTTTATAT
1 TTTTAATTATTTTATAT
*
62610790 TTTTATTTATTTTATA
1 TTTTAATTATTTTATA
62610806 AAAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAATTATTTTATAT
Found at i:62611198 original size:18 final size:21
Alignment explanation
Indices: 62611165--62611219 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
62611155 TTTAAATTTT
* *
62611165 ATTTTTAAAAAAATTA-T-AA
1 ATTTATAAAAATATTATTAAA
*
62611184 ATTTGT-AAAATATTATTAAA
1 ATTTATAAAAATATTATTAAA
62611204 ATTTATAAAAATATTA
1 ATTTATAAAAATATTA
62611220 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.27
19 6 0.20
20 7 0.23
21 9 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTATAAAAATATTATTAAA
Found at i:62611220 original size:18 final size:18
Alignment explanation
Indices: 62611165--62611222 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
62611155 TTTAAATTTT
* *
62611165 ATTTTTAAAAAAATTATAA
1 ATTTATAAAAATATTA-AA
*
62611184 ATTTGTAAAATATTATTAAA
1 ATTTATAAAA-A-TATTAAA
62611204 ATTTATAAAAATATTAAA
1 ATTTATAAAAATATTAAA
62611222 A
1 A
62611223 AAATTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 8 0.24
19 10 0.29
20 12 0.35
21 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTTATAAAAATATTAAA
Found at i:62611224 original size:11 final size:11
Alignment explanation
Indices: 62611190--62611234 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
62611180 ATAAATTTGT
*
62611190 AAAATATTATT
1 AAAATATTATA
62611201 AAAAT-TTATA
1 AAAATATTATA
62611211 AAAATATTA-A
1 AAAATATTATA
62611221 AAAA-ATTA-A
1 AAAATATTATA
62611230 AAAAT
1 AAAAT
62611235 CAAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 9 0.29
10 14 0.45
11 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATATTATA
Found at i:62611225 original size:21 final size:21
Alignment explanation
Indices: 62611182--62611234 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
62611172 AAAAAATTAT
* **
62611182 AAATTTGT-AAAATATTATTA
1 AAATTTATAAAAATATTAAAA
62611202 AAATTTATAAAAATATTAAAA
1 AAATTTATAAAAATATTAAAA
62611223 AAA-TTA-AAAAAT
1 AAATTTATAAAAAT
62611235 CAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.21
20 10 0.34
21 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTTATAAAAATATTAAAA
Found at i:62611436 original size:10 final size:10
Alignment explanation
Indices: 62611421--62611486 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
62611411 CAACTTAAAC
*
62611421 TTTTTAATGA
1 TTTTTAATAA
62611431 TTTTTAATAA
1 TTTTTAATAA
**
62611441 -TTTT-ATTG
1 TTTTTAATAA
*
62611449 TTTTGAATAA
1 TTTTTAATAA
62611459 TATTTTAATAA
1 T-TTTTAATAA
*
62611470 ATTTTAATAA
1 TTTTTAATAA
62611480 TATTTTA
1 T-TTTTA
62611487 CTTATTTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
8 2 0.05
9 7 0.16
10 21 0.49
11 13 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:62611484 original size:11 final size:11
Alignment explanation
Indices: 62611449--62611486 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
62611439 AATTTTATTG
62611449 TTTTGAATAATA
1 TTTT-AATAATA
62611461 TTTTAATAA-A
1 TTTTAATAATA
62611471 TTTTAATAATA
1 TTTTAATAATA
62611482 TTTTA
1 TTTTA
62611487 CTTATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.40
11 11 0.44
12 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTTAATAATA
Found at i:62611509 original size:20 final size:21
Alignment explanation
Indices: 62611486--62611528 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
62611476 ATAATATTTT
62611486 ACTTA-TTTATAAATTAAAAA
1 ACTTATTTTATAAATTAAAAA
*
62611506 ACTTATTTTTATAATTTAAAAA
1 ACTTA-TTTTATAAATTAAAAA
62611528 A
1 A
62611529 AATAAGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ACTTATTTTATAAATTAAAAA
Found at i:62613056 original size:18 final size:18
Alignment explanation
Indices: 62613031--62613073 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
62613021 TGGATGTGAT
* *
62613031 TTTA-ATTCTTTTATATA
1 TTTATATTCTTTCATAAA
62613048 TTTATATTCTTTCATAAA
1 TTTATATTCTTTCATAAA
62613066 TTTATATT
1 TTTATATT
62613074 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATTCTTTCATAAA
Found at i:62613444 original size:23 final size:22
Alignment explanation
Indices: 62613395--62613445 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
62613385 AAATGGGAAA
62613395 ATAAAAACTAAAATACACCATT
1 ATAAAAACTAAAATACACCATT
*
62613417 A-AAAATCTAGAAA-ACACCATT
1 ATAAAAACTA-AAATACACCATT
62613438 AGTAAAAA
1 A-TAAAAA
62613446 AATGGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 16 0.67
22 4 0.17
23 4 0.17
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.20
Consensus pattern (22 bp):
ATAAAAACTAAAATACACCATT
Found at i:62613541 original size:23 final size:21
Alignment explanation
Indices: 62613495--62613543 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
62613485 ATCCAATTCT
*
62613495 AAAATTTGATTAAAAATTAAA
1 AAAATTTGAATAAAAATTAAA
*
62613516 AAAATTTGAAATAGAAAATTAGA
1 AAAATTTG-AATA-AAAATTAAA
62613539 AAAAT
1 AAAAT
62613544 AAAGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (21 bp):
AAAATTTGAATAAAAATTAAA
Found at i:62613584 original size:24 final size:25
Alignment explanation
Indices: 62613538--62613596 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
62613528 AGAAAATTAG
* *
62613538 AAAAATAAAGAAAAATGACTTGCCT
1 AAAAATAAAAAAAAATGACTTGCAT
*
62613563 AGAAATAAAAAAAAATGA-TTGCAT
1 AAAAATAAAAAAAAATGACTTGCAT
62613587 AAAAATAAAA
1 AAAAATAAAA
62613597 CATGTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (25 bp):
AAAAATAAAAAAAAATGACTTGCAT
Found at i:62616289 original size:11 final size:12
Alignment explanation
Indices: 62616255--62616317 Score: 72
Period size: 12 Copynumber: 5.0 Consensus size: 12
62616245 AAGATGAAAG
*
62616255 CTTGATTGAAAA
1 CTTGATTAAAAA
62616267 CTTGATTAAAAA
1 CTTGATTAAAAA
62616279 CTTGATTAAAAACA
1 CTTGATT-AAAA-A
*
62616293 CTTGATGAAAAAA
1 CTTGAT-TAAAAA
*
62616306 CTTGATGAAAAA
1 CTTGATTAAAAA
62616318 GTGAACATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
12 23 0.51
13 11 0.24
14 11 0.24
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.29
Consensus pattern (12 bp):
CTTGATTAAAAA
Found at i:62616316 original size:27 final size:26
Alignment explanation
Indices: 62616266--62616317 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
62616256 TTGATTGAAA
* *
62616266 ACTTGATTAAAAACTTGATTAAAAAC
1 ACTTGATAAAAAACTTGATGAAAAAC
62616292 ACTTGATGAAAAAACTTGATGAAAAA
1 ACTTGAT-AAAAAACTTGATGAAAAA
62616318 GTGAACATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.27
Consensus pattern (26 bp):
ACTTGATAAAAAACTTGATGAAAAAC
Found at i:62621816 original size:31 final size:31
Alignment explanation
Indices: 62621774--62621845 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
62621764 TTAAATGAAA
*
62621774 AAGT-ATTGAACTAGTCGAAAGTT-TTCATTT
1 AAGTCATTGAACTAGTCAAAAGTTGTT-ATTT
*
62621804 AAGTCATTGAACTATTCAAAAGTTGTTATTT
1 AAGTCATTGAACTAGTCAAAAGTTGTTATTT
*
62621835 AATTCATTGAA
1 AAGTCATTGAA
62621846 TTGTTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 31 0.84
32 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (31 bp):
AAGTCATTGAACTAGTCAAAAGTTGTTATTT
Found at i:62622460 original size:16 final size:16
Alignment explanation
Indices: 62622439--62622497 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
62622429 TAGTTCAACA
62622439 ATTTAAAATTAAAAAT
1 ATTTAAAATTAAAAAT
*
62622455 ATTT--AACTAAAAAT
1 ATTTAAAATTAAAAAT
* *
62622469 -TAATAAAAATAAAAAT
1 AT-TTAAAATTAAAAAT
*
62622485 ATTAAAAATTAAA
1 ATTTAAAATTAAA
62622498 TTTAATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
13 1 0.03
14 10 0.30
16 21 0.64
17 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTTAAAATTAAAAAT
Found at i:62632748 original size:83 final size:83
Alignment explanation
Indices: 62632659--62632825 Score: 262
Period size: 83 Copynumber: 2.0 Consensus size: 83
62632649 AAGTTACATT
*
62632659 AGTTTTGATTATTTTAGGTTTTAGTTGTATCAAGTTTAACTCACTTCAAACTATGATAATTATGG
1 AGTTTTGATTATTTTAGGTTTTAATTGTATCAAGTTTAACTCACTTCAAACTATGATAATTATGG
*
62632724 TTTACCATGTGTCCTTTG
66 TTTACCATGGGTCCTTTG
* ** * * *
62632742 AGTTTTGATTATTTTAGGTTTTAATTGTTTTGAGTTTAACTCACTTCGAACTATGCTAGTTATGG
1 AGTTTTGATTATTTTAGGTTTTAATTGTATCAAGTTTAACTCACTTCAAACTATGATAATTATGG
62632807 TTTACCATGGGTCCTTTG
66 TTTACCATGGGTCCTTTG
62632825 A
1 A
62632826 ATTCGAGCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (83 bp):
AGTTTTGATTATTTTAGGTTTTAATTGTATCAAGTTTAACTCACTTCAAACTATGATAATTATGG
TTTACCATGGGTCCTTTG
Found at i:62633082 original size:7 final size:7
Alignment explanation
Indices: 62633070--62633100 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
62633060 TATAAGGTGT
62633070 AATAAAA
1 AATAAAA
62633077 AAT-AAA
1 AATAAAA
62633083 AATAAAA
1 AATAAAA
62633090 AATAAAA
1 AATAAAA
62633097 AATA
1 AATA
62633101 TAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:62633088 original size:13 final size:13
Alignment explanation
Indices: 62633070--62633097 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
62633060 TATAAGGTGT
62633070 AATAAAAAATAAA
1 AATAAAAAATAAA
62633083 AATAAAAAATAAA
1 AATAAAAAATAAA
62633096 AA
1 AA
62633098 ATATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:62633095 original size:20 final size:20
Alignment explanation
Indices: 62633070--62633108 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62633060 TATAAGGTGT
62633070 AATAAAAAATAAAAATAAAA
1 AATAAAAAATAAAAATAAAA
*
62633090 AATAAAAAATATAAATAAA
1 AATAAAAAATAAAAATAAA
62633109 TATATTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (20 bp):
AATAAAAAATAAAAATAAAA
Found at i:62633547 original size:16 final size:16
Alignment explanation
Indices: 62633507--62633547 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
62633497 TAATTTATTA
62633507 AATAAAAT-TTATCTT
1 AATAAAATATTATCTT
* *
62633522 AAT-TAATATTATTTT
1 AATAAAATATTATCTT
62633537 AATAAAATATT
1 AATAAAATATT
62633548 TAAATTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAAAATATTATCTT
Found at i:62639989 original size:21 final size:21
Alignment explanation
Indices: 62639963--62640003 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62639953 AGACGAGCAA
* *
62639963 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
62639984 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
62640004 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:62644673 original size:21 final size:20
Alignment explanation
Indices: 62644647--62644719 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
62644637 ACATATATGT
62644647 ATAATAATGATGAAAATAATA
1 ATAATAAT-ATGAAAATAATA
62644668 ATAATAATAGTGAAAATAAATA
1 ATAATAATA-TGAAAAT-AATA
62644690 AT-ATAATAAT-AAATATAATA
1 ATAATAAT-ATGAAA-ATAATA
* *
62644710 GTAACAATAT
1 ATAATAATAT
62644720 TAGTAATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.24
21 27 0.60
22 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAATATGAAAATAATA
Found at i:62644691 original size:16 final size:15
Alignment explanation
Indices: 62644662--62644704 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
62644652 AATGATGAAA
62644662 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
62644676 AGTGAA-AATAAATAAT
1 A-T-AATAATAAATAAT
62644692 ATAATAATAAATA
1 ATAATAATAAATA
62644705 TAATAGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 13 0.52
16 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:62645208 original size:20 final size:20
Alignment explanation
Indices: 62645173--62645218 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
62645163 GAAAGAAAAA
*
62645173 AAAAGA-AGAGGAGGGAGAG
1 AAAAGAGAGAGGAGGGAAAG
62645192 AAAAGAGAGAGCG-GGGAAAG
1 AAAAGAGAGAG-GAGGGAAAG
*
62645212 AAGAGAG
1 AAAAGAG
62645219 GGGAGGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.46, T:0.00
Consensus pattern (20 bp):
AAAAGAGAGAGGAGGGAAAG
Found at i:62645215 original size:18 final size:17
Alignment explanation
Indices: 62645174--62645223 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
62645164 AAAGAAAAAA
62645174 AAAGAAGAG-GAGGGAG
1 AAAGAAGAGAGAGGGAG
*
62645190 AGAA-AAGAGAGAGCGGGG
1 A-AAGAAGAGAGAG-GGAG
62645208 AAAGAAGAGAG-GGGAG
1 AAAGAAGAGAGAGGGAG
62645224 GGGGGAGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 9 0.32
17 8 0.29
18 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (17 bp):
AAAGAAGAGAGAGGGAG
Found at i:62645344 original size:22 final size:23
Alignment explanation
Indices: 62645317--62645364 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
62645307 ACTCTAATTT
* * *
62645317 TTTTTATTTTTTA-TTTCTTATA
1 TTTTTATATTATATTTTCGTATA
62645339 TTTTTATATTATATTTTCGTATA
1 TTTTTATATTATATTTTCGTATA
62645362 TTT
1 TTT
62645365 GTCGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTTATATTATATTTTCGTATA
Found at i:62645904 original size:16 final size:16
Alignment explanation
Indices: 62645883--62645914 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
62645873 TTTTGTGTAA
*
62645883 TGGGCTGTTAGTTTAG
1 TGGGCTGGTAGTTTAG
62645899 TGGGCTGGTAGTTTAG
1 TGGGCTGGTAGTTTAG
62645915 GTTATTGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (16 bp):
TGGGCTGGTAGTTTAG
Found at i:62651925 original size:21 final size:21
Alignment explanation
Indices: 62651881--62651918 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
62651871 TAATTTGTAA
62651881 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
62651902 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
62651919 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:62652264 original size:19 final size:20
Alignment explanation
Indices: 62652240--62652277 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62652230 GTAAAGATAT
62652240 AATA-TTAGTTTTTAATTTA
1 AATATTTAGTTTTTAATTTA
*
62652259 AATATTTATTTTTTAATTT
1 AATATTTAGTTTTTAATTT
62652278 TTTTTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
AATATTTAGTTTTTAATTTA
Found at i:62653813 original size:16 final size:17
Alignment explanation
Indices: 62653784--62653826 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
62653774 TCACTTTTAA
62653784 TATTAAAT--TAATATT
1 TATTAAATAATAATATT
62653799 TATTAAA-AATAATATT
1 TATTAAATAATAATATT
*
62653815 TTTTAAATAATA
1 TATTAAATAATA
62653827 TTGGTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 13 0.54
17 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTAAATAATAATATT
Found at i:62653824 original size:14 final size:15
Alignment explanation
Indices: 62653786--62653828 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
62653776 ACTTTTAATA
62653786 TTAAATTAATATTTAT
1 TTAAA-TAATATTTAT
*
62653802 TAAAAATAATATTT-T
1 T-TAAATAATATTTAT
62653817 TTAAATAATATT
1 TTAAATAATATT
62653829 GGTTAACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 9 0.38
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATAATATTTAT
Found at i:62656784 original size:24 final size:24
Alignment explanation
Indices: 62656757--62656803 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
62656747 CTATAACAGG
*
62656757 TAGCTCCGCAGAGCAATTAACGGC
1 TAGCTCCGAAGAGCAATTAACGGC
* *
62656781 TAGCTTCGAAGAGCACTTAACGG
1 TAGCTCCGAAGAGCAATTAACGG
62656804 GAATCACCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (24 bp):
TAGCTCCGAAGAGCAATTAACGGC
Found at i:62660337 original size:22 final size:21
Alignment explanation
Indices: 62660273--62660338 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
62660263 ATTTTTAACA
* *
62660273 TTTAAAAATATTTTTTATAAAT
1 TTTAAAAATA-ATTTTATAATT
*
62660295 TTT-ATAATAATTTT-TAATT
1 TTTAAAAATAATTTTATAATT
*
62660314 TTTAAAAATAGTGTTTATAATT
1 TTTAAAAATAAT-TTTATAATT
62660336 TTT
1 TTT
62660339 TGAATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 7 0.19
20 10 0.28
21 8 0.22
22 11 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTAAAAATAATTTTATAATT
Found at i:62662244 original size:11 final size:11
Alignment explanation
Indices: 62662209--62662329 Score: 70
Period size: 11 Copynumber: 11.9 Consensus size: 11
62662199 ACCAAAAATT
62662209 TATTTTAAAAA
1 TATTTTAAAAA
*
62662220 -A-ATTAAAAA
1 TATTTTAAAAA
62662229 GTATTTTAAAAA
1 -TATTTTAAAAA
62662241 TATTTTAAAAA
1 TATTTTAAAAA
62662252 TA----AAAAA
1 TATTTTAAAAA
*
62662259 -A-TGTAAAAA
1 TATTTTAAAAA
62662268 GTATTTTAAAAA
1 -TATTTTAAAAA
*
62662280 AATTTT--AAA
1 TATTTTAAAAA
*
62662289 -A-TTAAAAAA
1 TATTTTAAAAA
* *
62662298 TA-ATAAAAAA
1 TATTTTAAAAA
62662308 GTATTTTAAAAA
1 -TATTTTAAAAA
62662320 TATTTTAAAA
1 TATTTTAAAA
62662330 TTAAAAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
6 1 0.01
7 7 0.08
8 1 0.01
9 18 0.20
10 9 0.10
11 32 0.36
12 20 0.23
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:62662280 original size:40 final size:38
Alignment explanation
Indices: 62662213--62662340 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 38
62662203 AAAATTTATT
62662213 TTAAAAAAATTAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAGTATTTTAAAAATATTTTAAAA
* *
62662251 ATAAAAAAATGTAAAAAGTATTTTAAAAAAATTTTAAAA
1 TTAAAAAAAT-TAAAAAGTATTTTAAAAATATTTTAAAA
*
62662290 TTAAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
1 TT-AAAAA-AATTAAAAAGTATTTTAAAAATATTTTAAAA
62662330 TTAAAAAAATT
1 TTAAAAAAATT
62662341 TTAAAAATAA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
38 12 0.15
39 33 0.41
40 33 0.41
41 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (38 bp):
TTAAAAAAATTAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:62662347 original size:40 final size:39
Alignment explanation
Indices: 62662213--62662347 Score: 200
Period size: 40 Copynumber: 3.4 Consensus size: 39
62662203 AAAATTTATT
62662213 TTAAAAAAA-TTAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAAGTATTTTAAAAATATTTTAAAA
* * *
62662251 ATAAAAAAATGTAAAAAGTATTTTAAAAAAATTTTAAAA
1 TTAAAAAAATTTAAAAAGTATTTTAAAAATATTTTAAAA
* *
62662290 TTAAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAA-ATTTAAAAAGTATTTTAAAAATATTTTAAAA
62662330 TTAAAAAAATTTTAAAAA
1 TTAAAAAAA-TTTAAAAA
62662348 TAAATATATT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
38 8 0.10
39 35 0.42
40 41 0.49
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (39 bp):
TTAAAAAAATTTAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:62662358 original size:17 final size:17
Alignment explanation
Indices: 62662314--62662358 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
62662304 AAAAGTATTT
*
62662314 TAAAAATATTTTAAAAT
1 TAAAAATATTTTAAAAA
*
62662331 TAAAAAAATTTTAAAAA
1 TAAAAATATTTTAAAAA
*
62662348 TAAATATATTT
1 TAAAAATATTT
62662359 ATTATATCGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAAATATTTTAAAAA
Found at i:62666515 original size:26 final size:26
Alignment explanation
Indices: 62666479--62666531 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
62666469 TATATATGTA
**
62666479 GAAAATGTTTCATTCATTTTCTAATT
1 GAAAATGTTTCATTCATCGTCTAATT
62666505 GAAAATGTTTCATTCATCGTCTAATT
1 GAAAATGTTTCATTCATCGTCTAATT
62666531 G
1 G
62666532 CGCTCTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (26 bp):
GAAAATGTTTCATTCATCGTCTAATT
Found at i:62674974 original size:12 final size:12
Alignment explanation
Indices: 62674957--62675008 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
62674947 TCAAAGGAAA
62674957 AAAATAAATAAT
1 AAAATAAATAAT
62674969 AAAATAAATAAT
1 AAAATAAATAAT
*
62674981 AGCAATGATAATAAT
1 A-AAAT-A-AATAAT
62674996 AATAAT-AATAAT
1 AA-AATAAATAAT
62675008 A
1 A
62675009 GTGACAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 20 0.59
13 3 0.09
14 1 0.03
15 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:62675183 original size:3 final size:3
Alignment explanation
Indices: 62675158--62675207 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
62675148 GTGCAATTTG
*
62675158 TAA TAA -AA TAGA TAA TGA TAA TAA TAA TAA TAGA TAA -AA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
62675203 TAA TA
1 TAA TA
62675208 GTGAGGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:62675187 original size:15 final size:15
Alignment explanation
Indices: 62675160--62675204 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
62675150 GCAATTTGTA
62675160 ATAAAATAGATAAT-G
1 ATAAAATA-ATAATAG
62675175 ATAATAATAATAATAG
1 ATAA-AATAATAATAG
62675191 ATAAAATAATAATA
1 ATAAAATAATAATA
62675205 ATAGTGAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (15 bp):
ATAAAATAATAATAG
Found at i:62675206 original size:21 final size:22
Alignment explanation
Indices: 62675158--62675207 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
62675148 GTGCAATTTG
*
62675158 TAATAA-AATAGATAATGATAA
1 TAATAATAATAGATAATAATAA
62675179 TAATAATAATAGATAA-AATAA
1 TAATAATAATAGATAATAATAA
62675200 TAATAATA
1 TAATAATA
62675208 GTGAGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (22 bp):
TAATAATAATAGATAATAATAA
Found at i:62689679 original size:44 final size:43
Alignment explanation
Indices: 62689623--62689736 Score: 192
Period size: 44 Copynumber: 2.6 Consensus size: 43
62689613 AAGTACCAAG
62689623 TACCAACCCAATAAACTAAAGTCTACCCAAACCCAATTACCATT
1 TACCAA-CCAATAAACTAAAGTCTACCCAAACCCAATTACCATT
62689667 TACCAACGCAATAAACTAAAGTCTACCCAAACCCAATTACCATT
1 TACCAAC-CAATAAACTAAAGTCTACCCAAACCCAATTACCATT
62689711 TACCAATCCAATAAAACTAAAGTCTA
1 TACCAA-CCAAT-AAACTAAAGTCTA
62689737 AAACTAAAGA
Statistics
Matches: 67, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
43 1 0.01
44 52 0.78
45 14 0.21
ACGTcount: A:0.45, C:0.31, G:0.04, T:0.21
Consensus pattern (43 bp):
TACCAACCAATAAACTAAAGTCTACCCAAACCCAATTACCATT
Found at i:62689740 original size:13 final size:13
Alignment explanation
Indices: 62689722--62689751 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
62689712 ACCAATCCAA
*
62689722 TAAAACTAAAGTC
1 TAAAACTAAAGAC
62689735 TAAAACTAAAGAC
1 TAAAACTAAAGAC
62689748 TAAA
1 TAAA
62689752 TCTCTAATAA
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:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
TAAAACTAAAGAC
Found at i:62690393 original size:21 final size:21
Alignment explanation
Indices: 62690369--62690408 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
62690359 TTAATCAGTT
*
62690369 AAATATCATTATATAGCAATA
1 AAATAACATTATATAGCAATA
62690390 AAATAACATTATATAGCAA
1 AAATAACATTATATAGCAA
62690409 ATCGATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (21 bp):
AAATAACATTATATAGCAATA
Found at i:62690443 original size:8 final size:9
Alignment explanation
Indices: 62690407--62690461 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
62690397 ATTATATAGC
*
62690407 AAATCGATT
1 AAATCGGTT
**
62690416 AAATTAGTT
1 AAATCGGTT
*
62690425 AAATCGATT
1 AAATCGGTT
*
62690434 -AATCAGTT
1 AAATCGGTT
62690442 AAATCGGTT
1 AAATCGGTT
62690451 AAATCGGTT
1 AAATCGGTT
62690460 AA
1 AA
62690462 TTTTTAACCA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
8 6 0.17
9 30 0.83
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (9 bp):
AAATCGGTT
Found at i:62690443 original size:17 final size:17
Alignment explanation
Indices: 62690407--62690452 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
62690397 ATTATATAGC
*
62690407 AAATCGATTAAATTAGTT
1 AAATCGATT-AATCAGTT
62690425 AAATCGATTAATCAGTT
1 AAATCGATTAATCAGTT
*
62690442 AAATCGGTTAA
1 AAATCGATTAA
62690453 ATCGGTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (17 bp):
AAATCGATTAATCAGTT
Found at i:62690460 original size:18 final size:18
Alignment explanation
Indices: 62690407--62690461 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
62690397 ATTATATAGC
*
62690407 AAATCGATTAAATTAGTT
1 AAATCGATTAAATCAGTT
62690425 AAATCGATT-AATCAGTT
1 AAATCGATTAAATCAGTT
* *
62690442 AAATCGGTTAAATCGGTT
1 AAATCGATTAAATCAGTT
62690460 AA
1 AA
62690462 TTTTTAACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
AAATCGATTAAATCAGTT
Found at i:62691865 original size:10 final size:10
Alignment explanation
Indices: 62691827--62691865 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
62691817 TAAAAAATAC
62691827 CTTTTTTTCT
1 CTTTTTTTCT
*
62691837 CTTCTCTTTCT
1 CTT-TTTTTCT
*
62691848 CTCTTTTTCT
1 CTTTTTTTCT
62691858 CTTTTTTT
1 CTTTTTTT
62691866 TTCTGCAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:62691985 original size:27 final size:26
Alignment explanation
Indices: 62691955--62692043 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 26
62691945 GAGTAGTCCT
62691955 GCCAATCAGTATGACACCATTGGTGCC
1 GCCAATCAGTATG-CACCATTGGTGCC
* *
62691982 GCCAACCTCATTA-GCACCATCGGTGCC
1 GCCAA--TCAGTATGCACCATTGGTGCC
* *
62692009 GCCACTCAGTATGGCACCTTTGGTGCC
1 GCCAATCAGTAT-GCACCATTGGTGCC
62692036 GCCAATCA
1 GCCAATCA
62692044 CAATTCCTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
25 5 0.10
27 40 0.78
28 1 0.02
29 5 0.10
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (26 bp):
GCCAATCAGTATGCACCATTGGTGCC
Found at i:62768768 original size:11 final size:11
Alignment explanation
Indices: 62768749--62768793 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
62768739 CCGAATATAA
62768749 TAAATATATTTT
1 TAAA-ATATTTT
62768761 TAAAATA--TT
1 TAAAATATTTT
62768770 TAAAATATTTTT
1 TAAAATA-TTTT
62768782 TAAAAT-TTTT
1 TAAAATATTTT
62768792 TA
1 TA
62768794 TTTTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.30
10 6 0.20
11 3 0.10
12 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TAAAATATTTT
Found at i:62774770 original size:17 final size:18
Alignment explanation
Indices: 62774741--62774774 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
62774731 TGTCAGATAT
62774741 TTTTATAAATTTCTTAAA
1 TTTTATAAATTTCTTAAA
62774759 TTTTAT-AATTTCTTAA
1 TTTTATAAATTTCTTAA
62774775 TAATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATAAATTTCTTAAA
Found at i:62775179 original size:21 final size:22
Alignment explanation
Indices: 62775149--62775197 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
62775139 AATATCAAAG
62775149 ATATAATTTTAT-ATTAATATTT
1 ATATAATTTTATAATTAA-ATTT
62775171 ATAT-ATTTTATAATTAAATTT
1 ATATAATTTTATAATTAAATTT
*
62775192 AAATAA
1 ATATAA
62775198 AAATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATAATTTTATAATTAAATTT
Found at i:62777233 original size:16 final size:16
Alignment explanation
Indices: 62777212--62777247 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
62777202 TTTGGTTCGC
62777212 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62777228 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
62777244 TGTA
1 TGTA
62777248 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:62777505 original size:18 final size:17
Alignment explanation
Indices: 62777484--62777518 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62777474 TTATTATTTA
*
62777484 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
62777502 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
62777519 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Done.