Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold435
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: 524057
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 3
Found at i:2414 original size:14 final size:14
Alignment explanation
Indices: 2395--2430 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
2385 TAATTTAGGT
2395 GGGGGGGGGGAGGG
1 GGGGGGGGGGAGGG
2409 GGGGGGGGGGAGGG
1 GGGGGGGGGGAGGG
2423 GCGGGGGG
1 G-GGGGGG
2431 ATGGGGGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.06, C:0.03, G:0.92, T:0.00
Consensus pattern (14 bp):
GGGGGGGGGGAGGG
Found at i:2437 original size:14 final size:12
Alignment explanation
Indices: 2395--2440 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
2385 TAATTTAGGT
*
2395 GGGGGGGGGGAGG
1 GGGGGGGGGG-GA
2408 GGGGGGGGGGGA
1 GGGGGGGGGGGA
*
2420 GGGGCGGGGGGA
1 GGGGGGGGGGGA
2432 TGGGGGGGG
1 -GGGGGGGG
2441 TGTACAAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.07, C:0.02, G:0.89, T:0.02
Consensus pattern (12 bp):
GGGGGGGGGGGA
Found at i:12887 original size:17 final size:17
Alignment explanation
Indices: 12846--12886 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
12836 CATATATGTA
12846 TTTATTTTATTTATTAC
1 TTTATTTTATTTATTAC
*
12863 TTTATTTTATTTA-TAT
1 TTTATTTTATTTATTAC
12879 TTTATTTT
1 TTTATTTT
12887 TTTGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTATTTATTAC
Found at i:13299 original size:157 final size:156
Alignment explanation
Indices: 13086--13479 Score: 494
Period size: 158 Copynumber: 2.5 Consensus size: 156
13076 ATTAGACCCA
* * * *
13086 AAAAGAT-TAAAAAGTTTTTAAGATCCTTTATACTCC-GACAGACACCCATAGGAATATAAAAGA
1 AAAAGATATAAAAAGTTTTTAA-ATCTTTTATAC-CCTTACAGATACCCATA-AAATATAAAAGA
* * * *
13149 TTAAAAACG-CTAATATTTATTTTAATTATGAGAGTGTTAATTCAA-TTTTATTTATTTTTGAAA
63 TTAAAAACGAATAATATTTATTTTAATAATGAGAGTGCTAATTCAATTTTTATTTA-TTTTAAAA
* *
13212 AATATCATTTCGTA-CTTTAATAGAAGCTCG
127 AATATCATTTCATATC-TTAATAGAAACTCG
* *
13242 AAAAGATATAAAAAGTTTTTGAAATCTTTTATACCCTTACGGATACCCATACAAATATCAAAGAT
1 AAAAGATATAAAAAGTTTTT-AAATCTTTTATACCCTTACAGATACCCATA-AAATATAAAAGAT
* * *
13307 TAAAAATGAATAATATTTATTTTAATAATTAGAGTGCTAATTTAATTTTTATTTATTTTAAAAAA
64 TAAAAACGAATAATATTTATTTTAATAATGAGAGTGCTAATTCAATTTTTATTTATTTTAAAAAA
*
13372 TATCATTTCATATCTTAATGGAAACTCG
129 TATCATTTCATATCTTAATAGAAACTCG
* *
13400 AAAAGATATAAAAAATTTTCAGAATCTTTTATACCCTTACAGATACCCATAAGAATATAAAAGAT
1 AAAAGATATAAAAAGTTTTTA-AATCTTTTATACCCTTACAGATACCCATAA-AATATAAAAGAT
*
13465 TAAAAA-AAATAATAT
64 TAAAAACGAATAATAT
13480 AAAATATCTT
Statistics
Matches: 208, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
156 9 0.04
157 61 0.29
158 128 0.62
159 10 0.05
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (156 bp):
AAAAGATATAAAAAGTTTTTAAATCTTTTATACCCTTACAGATACCCATAAAATATAAAAGATTA
AAAACGAATAATATTTATTTTAATAATGAGAGTGCTAATTCAATTTTTATTTATTTTAAAAAATA
TCATTTCATATCTTAATAGAAACTCG
Found at i:13566 original size:28 final size:29
Alignment explanation
Indices: 13534--13592 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
13524 CTTTTGCCTT
*
13534 ATTTACAATTTAACC-CTAAATTTTCAAA
1 ATTTACAATTTAACCTCTAAATATTCAAA
*
13562 ATTTACAATTTCACCTCTAAATATTCAAA
1 ATTTACAATTTAACCTCTAAATATTCAAA
13591 AT
1 AT
13593 AACACTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTTACAATTTAACCTCTAAATATTCAAA
Found at i:17186 original size:16 final size:19
Alignment explanation
Indices: 17149--17189 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17139 ACAAATTTTA
17149 TATATAATATATACTAAAT
1 TATATAATATATACTAAAT
17168 TATATAATAT-TA-T-AAT
1 TATATAATATATACTAAAT
17184 TATATA
1 TATATA
17190 TGAATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 2 0.09
19 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATAATATATACTAAAT
Found at i:17216 original size:10 final size:9
Alignment explanation
Indices: 17149--17235 Score: 54
Period size: 10 Copynumber: 9.3 Consensus size: 9
17139 ACAAATTTTA
*
17149 TATATAATA
1 TATATAATT
*
17158 TATACTAAAT
1 TATA-TAATT
*
17168 TATATAATA
1 TATATAATT
17177 T-TATAATT
1 TATATAATT
17185 ATATATGAATT
1 -TATAT-AATT
*
17196 TTTATATATT
1 TATATA-ATT
17206 TATATTAATT
1 TATA-TAATT
*
17216 T-TAATAAAT
1 TAT-ATAATT
17225 TA-ATAATT
1 TATATAATT
17233 TAT
1 TAT
17236 TTATTATCAT
Statistics
Matches: 60, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
8 13 0.22
9 16 0.27
10 25 0.42
11 6 0.10
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (9 bp):
TATATAATT
Found at i:17742 original size:17 final size:17
Alignment explanation
Indices: 17693--17748 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
17683 TATGATTATG
*
17693 TTTAAA-ATTTAA-TAA
1 TTTAAATATATAATTAA
17708 TATTAAATATAAATAATTAA
1 T-TTAAATAT--ATAATTAA
*
17728 TTTAAATATATAATTAC
1 TTTAAATATATAATTAA
17745 TTTA
1 TTTA
17749 TTATTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 13 0.38
19 11 0.32
20 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATATATAATTAA
Found at i:19576 original size:19 final size:19
Alignment explanation
Indices: 19552--19590 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
19542 AAATTTGTCT
19552 ACCTCTTCTTCACTTTCCG
1 ACCTCTTCTTCACTTTCCG
19571 ACCTCTTCTTCACTTTCCG
1 ACCTCTTCTTCACTTTCCG
19590 A
1 A
19591 ACTAGGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.13, C:0.41, G:0.05, T:0.41
Consensus pattern (19 bp):
ACCTCTTCTTCACTTTCCG
Found at i:26719 original size:12 final size:12
Alignment explanation
Indices: 26706--26750 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 12
26696 ATTTATTATA
26706 ATTATAAATA-T
1 ATTATAAATATT
26717 A--ATAAATATT
1 ATTATAAATATT
26727 ATTATAAATAATT
1 ATTATAAAT-ATT
*
26740 ATAATAAATAT
1 ATTATAAATAT
26751 CATTTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
9 7 0.24
10 2 0.07
11 1 0.03
12 8 0.28
13 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTATAAATATT
Found at i:26743 original size:25 final size:26
Alignment explanation
Indices: 26698--26750 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
26688 CACACCACAT
26698 TTATTATAATTATAAATATAATAAATA
1 TTATTATAA-TATAAATATAATAAATA
*
26725 TTATTATAA-ATAATTATAATAAATA
1 TTATTATAATATAAATATAATAAATA
26750 T
1 T
26751 CATTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.64
27 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTATTATAATATAAATATAATAAATA
Found at i:27101 original size:28 final size:28
Alignment explanation
Indices: 27069--27152 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
27059 TTAACAATAA
*
27069 ATTTTATATATAATATAAATATTTTAAT
1 ATTTTATATATATTATAAATATTTTAAT
* * *
27097 ATTTTATA-ATATTATAATTATATTAAAA
1 ATTTTATATATATTATAAATAT-TTTAAT
27125 ATTTTATATAT-TTATATAA-ATTTTAAT
1 ATTTTATATATATTATA-AATATTTTAAT
27152 A
1 A
27153 AATTAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
27 16 0.35
28 27 0.59
29 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTTATATATATTATAAATATTTTAAT
Found at i:27112 original size:36 final size:38
Alignment explanation
Indices: 27072--27164 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 38
27062 ACAATAAATT
*
27072 TTATATATAATA-TAAATATTTTA-ATATTT-TATAATA
1 TTATA-ATAATATTAAAAATTTTATATATTTATATAATA
*
27108 TTATAATTATATTAAAAATTTTATATATTTATATAA-A
1 TTATAATAATATTAAAAATTTTATATATTTATATAATA
* *
27145 TTTTAATAA-ATTAATAATTT
1 TTATAATAATATTAAAAATTT
27165 ATTTATTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.10
36 25 0.51
37 14 0.29
38 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TTATAATAATATTAAAAATTTTATATATTTATATAATA
Found at i:27147 original size:19 final size:19
Alignment explanation
Indices: 27065--27149 Score: 72
Period size: 19 Copynumber: 4.5 Consensus size: 19
27055 AAATTTAACA
*
27065 ATAAATTTTATATA-TAAT
1 ATAAATTTTATATATTTAT
27083 ATAAATATTT-TAATATTT-T
1 ATAAAT-TTTAT-ATATTTAT
*
27102 AT-AATATTATA-ATTATATT
1 ATAAATTTTATATATT-TA-T
*
27121 AAAAATTTTATATATTTAT
1 ATAAATTTTATATATTTAT
27140 ATAAATTTTA
1 ATAAATTTTA
27150 ATAAATTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
16 3 0.06
17 4 0.08
18 11 0.21
19 21 0.40
20 11 0.21
21 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAAATTTTATATATTTAT
Found at i:30533 original size:14 final size:14
Alignment explanation
Indices: 30514--30543 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30504 ATCTGCAATT
30514 TGATTTTTCACTGA
1 TGATTTTTCACTGA
*
30528 TGATTTTTCATTGA
1 TGATTTTTCACTGA
30542 TG
1 TG
30544 GAAGCCCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (14 bp):
TGATTTTTCACTGA
Found at i:34213 original size:18 final size:18
Alignment explanation
Indices: 34190--34226 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34180 GTGATTCTGA
*
34190 TTTCTAGCCATTATTACT
1 TTTCTAGCCAGTATTACT
34208 TTTCTAGCCAGTATTACT
1 TTTCTAGCCAGTATTACT
34226 T
1 T
34227 ACTGCCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTCTAGCCAGTATTACT
Found at i:37039 original size:17 final size:17
Alignment explanation
Indices: 36998--37040 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
36988 AAAAATAAAA
* *
36998 ATATTTAACTTCATTTT
1 ATATTTAACTTCAATTG
*
37015 ATTATTTAACTTGAATTG
1 A-TATTTAACTTCAATTG
37033 ATATTTAA
1 ATATTTAA
37041 GTAATTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (17 bp):
ATATTTAACTTCAATTG
Found at i:51964 original size:2 final size:2
Alignment explanation
Indices: 51957--51981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51947 CATACCTAAG
51957 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
51982 AACTAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52085 original size:7 final size:7
Alignment explanation
Indices: 52073--52100 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
52063 ATCCTAATTT
52073 TATAATA
1 TATAATA
52080 TATAATA
1 TATAATA
52087 TATAATA
1 TATAATA
52094 TATAATA
1 TATAATA
52101 AAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATAATA
Found at i:52287 original size:15 final size:16
Alignment explanation
Indices: 52255--52293 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
52245 TGGGTATTAG
52255 TAATAAAATATTAATAA
1 TAATAAAATA-TAATAA
52272 TAATAAAATA-AATAA
1 TAATAAAATATAATAA
52287 TAATAAA
1 TAATAAA
52294 TTTCTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 12 0.55
17 10 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATAAAATATAATAA
Found at i:56525 original size:127 final size:127
Alignment explanation
Indices: 56295--56549 Score: 323
Period size: 127 Copynumber: 2.0 Consensus size: 127
56285 ATATTTGAGC
* * ** **
56295 AAGCTTAGGTTATAACATTATTAATCTTGATAAAACTGAATAAGATTTGTGAGTGATAATGTAAG
1 AAGCTTAGGTTATAACATTATTAATCTTGACAAAACTGAATAAAATTTGTGAACGATAAAATAAG
* * * * * * * *
56360 ATGTTGATATAAGCTTAAGCTTAGTTTAACCTTTTTGATTAACATTACTATTGCAAAATCTT
66 ATGTTGATATAAACTTAAACTGAGTCTAACCTTATTGATAAACACTACTATTACAAAATCTT
* *
56422 AAGCTTAGGTTATAATATTATTAATCTTGACAAAATTGAATAAAATTTGTGAACGATAAAATAAG
1 AAGCTTAGGTTATAACATTATTAATCTTGACAAAACTGAATAAAATTTGTGAACGATAAAATAAG
* * *
56487 ATGTTGATATAAATTTAAACTCGA-TCTGACCTTATTGATAAACACTACTATTACATAATCTT
66 ATGTTGATATAAACTTAAACT-GAGTCTAACCTTATTGATAAACACTACTATTACAAAATCTT
56549 A
1 A
56550 TAATTAGCAT
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
127 107 0.99
128 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (127 bp):
AAGCTTAGGTTATAACATTATTAATCTTGACAAAACTGAATAAAATTTGTGAACGATAAAATAAG
ATGTTGATATAAACTTAAACTGAGTCTAACCTTATTGATAAACACTACTATTACAAAATCTT
Found at i:62423 original size:21 final size:22
Alignment explanation
Indices: 62397--62449 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
62387 CTATATTATT
62397 TTTTAAATTTAATTTTTAAT-A
1 TTTTAAATTTAATTTTTAATAA
* * *
62418 TTTTAAAATTATTTTTTATTAA
1 TTTTAAATTTAATTTTTAATAA
62440 TTTTAAATTT
1 TTTTAAATTT
62450 TAAATAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTAAATTTAATTTTTAATAA
Found at i:62452 original size:37 final size:35
Alignment explanation
Indices: 62391--62479 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 35
62381 ACTCCTCTAT
* *
62391 ATTATTTTTTAAATTT-AATTTTTAATATTTTAAA
1 ATTATTTTTTAAATTTAAATTTTAAATAATTTAAA
*
62425 ATTATTTTTTATTAATTTTAAATTTTAAATAATTTAAT
1 ATTATTTTTTA--AA-TTTAAATTTTAAATAATTTAAA
*
62463 A-TATCTTTTAATATTTA
1 ATTATTTTTTAA-ATTTA
62480 TATTATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
34 11 0.24
35 5 0.11
36 3 0.07
37 11 0.24
38 16 0.35
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (35 bp):
ATTATTTTTTAAATTTAAATTTTAAATAATTTAAA
Found at i:62498 original size:15 final size:14
Alignment explanation
Indices: 62471--62500 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
62461 ATATATCTTT
62471 TAATATTTATATTA
1 TAATATTTATATTA
62485 TAATATTATATATTA
1 TAATATT-TATATTA
62500 T
1 T
62501 TTATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:62633 original size:18 final size:18
Alignment explanation
Indices: 62608--62655 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
62598 AAAGTTTAAT
62608 TTATTTTTTAAAT-AAAC
1 TTATTTTTTAAATCAAAC
*
62625 TTAATTTTTT-ACTCAAAC
1 TT-ATTTTTTAAATCAAAC
62643 TTATTTTTTAAAT
1 TTATTTTTTAAAT
62656 TAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTTTTTAAATCAAAC
Found at i:62710 original size:18 final size:19
Alignment explanation
Indices: 62676--62711 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62666 TATTTAAATT
62676 TTTTAAATATCAAATAAAA
1 TTTTAAATATCAAATAAAA
*
62695 TTTTAAAT-TTAAATAAA
1 TTTTAAATATCAAATAAA
62712 TAATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTAAATATCAAATAAAA
Found at i:71033 original size:15 final size:16
Alignment explanation
Indices: 70997--71036 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
70987 TTAAATTTTT
*
70997 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
71014 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
71029 ATAAAATT
1 ATAAAATT
71037 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:71039 original size:16 final size:17
Alignment explanation
Indices: 70997--71039 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
70987 TTAAATTTTT
*
70997 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
71014 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
71029 ATAAAATTTAT
1 ATAAAATTTAT
71040 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:71098 original size:18 final size:18
Alignment explanation
Indices: 71072--71107 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
71062 ATTGATATAT
* *
71072 AAATTTTATATTAAATTA
1 AAATATTATAATAAATTA
71090 AAATATTATAATAAATTA
1 AAATATTATAATAAATTA
71108 TGTAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATTATAATAAATTA
Found at i:72444 original size:16 final size:16
Alignment explanation
Indices: 72415--72488 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
72405 CGAACCCGAT
* *
72415 TGACCCGAATCTGAAA
1 TGACTCGAACCTGAAA
*
72431 TTACTCGAACCTGAAA
1 TGACTCGAACCTGAAA
*
72447 TGA-TCTGAACCCGAAA
1 TGACTC-GAACCTGAAA
*
72463 CGACTCGAACCTGAAA
1 TGACTCGAACCTGAAA
*
72479 TGACCCGAAC
1 TGACTCGAAC
72489 TCAAAACGAC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
15 2 0.04
16 43 0.91
17 2 0.04
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (16 bp):
TGACTCGAACCTGAAA
Found at i:72496 original size:32 final size:32
Alignment explanation
Indices: 72433--72498 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
72423 ATCTGAAATT
* * *
72433 ACTCGAACCTGAAATGATCTGAACCCGAAACG
1 ACTCGAACCTGAAATGACCCGAACCCAAAACG
*
72465 ACTCGAACCTGAAATGACCCGAACTCAAAACG
1 ACTCGAACCTGAAATGACCCGAACCCAAAACG
72497 AC
1 AC
72499 CAATGACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.30, G:0.17, T:0.14
Consensus pattern (32 bp):
ACTCGAACCTGAAATGACCCGAACCCAAAACG
Found at i:73172 original size:11 final size:12
Alignment explanation
Indices: 73151--73207 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 12
73141 AAAATATGAC
*
73151 ATAAAAAATAAT
1 ATAAAACATAAT
73163 -TAAAACATAAT
1 ATAAAACATAAT
73174 ATAAAA-ATAA-
1 ATAAAACATAAT
*
73184 ATATAACATGAAT
1 ATAAAACAT-AAT
73197 ATAAGAACATA
1 ATAA-AACATA
73208 TAAATATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 5 0.14
11 16 0.43
12 7 0.19
13 4 0.11
14 5 0.14
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.25
Consensus pattern (12 bp):
ATAAAACATAAT
Found at i:73179 original size:22 final size:23
Alignment explanation
Indices: 73141--73200 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
73131 ATCAAATATA
* *
73141 AAAATATGACATA-AAAAATAATT
1 AAAACATGA-ATATAAAAATAAAT
73164 AAAACAT-AATATAAAAATAAAT
1 AAAACATGAATATAAAAATAAAT
*
73186 ATAACATGAATATAA
1 AAAACATGAATATAA
73201 GAACATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
23 13 0.41
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (23 bp):
AAAACATGAATATAAAAATAAAT
Found at i:73680 original size:12 final size:12
Alignment explanation
Indices: 73628--73687 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 12
73618 CAAATACATA
73628 TTTTTTTCTTTC
1 TTTTTTTCTTTC
*
73640 TTTCTTTCTTTTC
1 TTTTTTTC-TTTC
*
73653 TTTTTTT-TCTCC
1 TTTTTTTCT-TTC
73665 TTTTTTTCTTTC
1 TTTTTTTCTTTC
*
73677 TTTTTCTCTTT
1 TTTTTTTCTTT
73688 TCCCTCCTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 1 0.03
12 28 0.70
13 11 0.28
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:73695 original size:30 final size:29
Alignment explanation
Indices: 73635--73695 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
73625 ATATTTTTTT
* **
73635 CTTTCTTTCTTTCTTTTCTTTTTTTTCTC
1 CTTTCTTTCTTTCTTTTCTCTTTTCCCTC
*
73664 CTTTTTTTCTTTCTTTTTCTCTTTTCCCTC
1 CTTTCTTTCTTTC-TTTTCTCTTTTCCCTC
73694 CT
1 CT
73696 GAACGTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (29 bp):
CTTTCTTTCTTTCTTTTCTCTTTTCCCTC
Found at i:73941 original size:13 final size:13
Alignment explanation
Indices: 73923--73963 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
73913 TATAAACATG
73923 ATATTTATAAAA-A
1 ATATTTA-AAAATA
73936 ATATTTAAAAATA
1 ATATTTAAAAATA
73949 ATA--TAAAAATA
1 ATATTTAAAAATA
73960 ATAT
1 ATAT
73964 GCATATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 11 0.42
12 4 0.15
13 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATTTAAAAATA
Found at i:74120 original size:24 final size:25
Alignment explanation
Indices: 74088--74141 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
74078 AACACAATTT
74088 TTTTTCTTTTTT-TACGTTCTTTCC
1 TTTTTCTTTTTTCTACGTTCTTTCC
* * *
74112 TTTTTCTTTTTTCTCCTTTCTTTCT
1 TTTTTCTTTTTTCTACGTTCTTTCC
74137 TTTTT
1 TTTTT
74142 TAGTCAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTTCTTTTTTCTACGTTCTTTCC
Found at i:75099 original size:2 final size:2
Alignment explanation
Indices: 75092--75133 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
75082 GAGATTTGTA
75092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75134 GATGGATAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75515 original size:2 final size:2
Alignment explanation
Indices: 75508--75537 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75498 AACATCCTAG
75508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75538 AGGTTTGTTG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80886 original size:2 final size:2
Alignment explanation
Indices: 80879--80917 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
80869 AAGCTGTCCT
*
80879 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
80918 GGGCTTGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:86223 original size:25 final size:26
Alignment explanation
Indices: 86195--86250 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
86185 AAATTATACA
*
86195 TTATTAATAAATTAAATAATTT-TAT
1 TTATTAATAAATAAAATAATTTATAT
*
86220 TTATTAATAAATAAAATTATTTATAT
1 TTATTAATAAATAAAATAATTTATAT
86246 TTATT
1 TTATT
86251 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATTAATAAATAAAATAATTTATAT
Found at i:86322 original size:8 final size:8
Alignment explanation
Indices: 86309--86347 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
86299 TTTAATAACC
86309 ATTTATAA
1 ATTTATAA
86317 ATTTATAA
1 ATTTATAA
*
86325 ATTAATAA
1 ATTTATAA
*
86333 TATATATAA
1 -ATTTATAA
86342 ATTTAT
1 ATTTAT
86348 TATTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
ATTTATAA
Found at i:86451 original size:13 final size:13
Alignment explanation
Indices: 86433--86457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
86423 TAACAAATAT
86433 TAAATTAATCGAC
1 TAAATTAATCGAC
86446 TAAATTAATCGA
1 TAAATTAATCGA
86458 GAATCCGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
TAAATTAATCGAC
Found at i:92056 original size:2 final size:2
Alignment explanation
Indices: 92044--92077 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
92034 CTATTTGAAA
*
92044 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92078 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92082 original size:2 final size:2
Alignment explanation
Indices: 92077--92114 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
92067 TATATATATA
92077 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
92115 CAGATGGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:92400 original size:48 final size:50
Alignment explanation
Indices: 92325--92448 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 50
92315 ATTAGATAAG
* * *
92325 TTATATTTTATAATGCATTGAAAATATAGTAT-TTATA-ATCATTCCCATA
1 TTATAATTTATAATGCATTGAAAATATAGT-TGTAAGATATCATTCCCATA
*
92374 TTATAATTTATAAT-CATTGAAAATATAGTTGGGTAAGATATCTTTCCCATA
1 TTATAATTTATAATGCATTGAAAATATAGTT--GTAAGATATCATTCCCATA
92425 TTATAATTTATAATGCATTGAAAA
1 TTATAATTTATAATGCATTGAAAA
92449 CAGTCAAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
47 1 0.02
48 15 0.23
49 13 0.20
50 3 0.05
51 25 0.38
52 9 0.14
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (50 bp):
TTATAATTTATAATGCATTGAAAATATAGTTGTAAGATATCATTCCCATA
Found at i:92825 original size:2 final size:2
Alignment explanation
Indices: 92818--92852 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
92808 GGAAAAGATT
*
92818 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92853 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:92857 original size:2 final size:2
Alignment explanation
Indices: 92852--92885 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
92842 TATATATATA
92852 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
92886 AGAGACATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:93958 original size:2 final size:2
Alignment explanation
Indices: 93945--93979 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
93935 GTTATATGCT
*
93945 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
93980 TTTTCTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:94966 original size:6 final size:6
Alignment explanation
Indices: 94955--94982 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
94945 CTGTTAAGAT
94955 TTCTTG TTCTTG TTCTTG TTCTTG TTCT
1 TTCTTG TTCTTG TTCTTG TTCTTG TTCT
94983 GGACATGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.14, T:0.68
Consensus pattern (6 bp):
TTCTTG
Found at i:96830 original size:2 final size:2
Alignment explanation
Indices: 96823--96860 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
96813 TGGAAAAGAA
96823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96861 TCATTGCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97237 original size:15 final size:13
Alignment explanation
Indices: 97211--97245 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
97201 GTTTTGTAAT
97211 TTATATTTTTATA
1 TTATATTTTTATA
97224 TTATATTTAATTATA
1 TTATATTT--TTATA
97239 TTATATT
1 TTATATT
97246 GATATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
15 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:97260 original size:20 final size:19
Alignment explanation
Indices: 97219--97278 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
97209 ATTTATATTT
97219 TTATATTATATTTAATTATA
1 TTATATTATATTTAA-TATA
97239 TTATATTGATATTTAA-AGTA
1 TTATATT-ATATTTAATA-TA
*
97259 TTATAATTAT-TTTCATATA
1 TTAT-ATTATATTTAATATA
97278 T
1 T
97279 ATTTTGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 8 0.23
20 16 0.46
21 11 0.31
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATATTATATTTAATATA
Found at i:97744 original size:19 final size:18
Alignment explanation
Indices: 97701--97744 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
97691 GTAAGCAAAG
* *
97701 TAATAATATATATATATA
1 TAATATTATATATATACA
97719 TATATATTATATATATAGCA
1 TA-ATATTATATATATA-CA
97739 TAATAT
1 TAATAT
97745 ATACAGAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.77
20 3 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATATTATATATATACA
Found at i:97744 original size:21 final size:21
Alignment explanation
Indices: 97706--97747 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
97696 CAAAGTAATA
*
97706 ATATATATATATATATATATT
1 ATATATATACATATATATATT
97727 ATATATATAGCATAATATATA
1 ATATATATA-CAT-ATATATA
97748 CAGAGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATATATACATATATATATT
Found at i:97747 original size:2 final size:2
Alignment explanation
Indices: 97706--97735 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
97696 CAAAGTAATA
97706 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
97736 GCATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98314 original size:129 final size:129
Alignment explanation
Indices: 98155--98406 Score: 414
Period size: 129 Copynumber: 2.0 Consensus size: 129
98145 GAATATGTGA
* * ** *
98155 TTTTATGGCCGCAGGCAGGATCTTCATTTCTCACGGTTGTCACTATATGTAGCTGCTGTAATATA
1 TTTTATGGCCGCAGGCAGGATCTGCATTTCTCACGGTTGTCACTATATATAGCTGCCATAAAATA
*
98220 TACATAGCCTAACATTATCTGCATTTTTTAATTGTTCCATATATATATATATATATATGCACAG
66 TACATAGCCTAACATTATCTGCATTTTTTAATTGTTACATATATATATATATATATATGCACAG
** *
98284 TTTTATGGTTGCAGGCAGGATCTGCATTTCTCATGGTTGTCACTATATATAGCTGCCATAAAATA
1 TTTTATGGCCGCAGGCAGGATCTGCATTTCTCACGGTTGTCACTATATATAGCTGCCATAAAATA
*
98349 TACATAGCCTAACATTATCTGCATTTTTTAATTGTTATATATATATATATATATATAT
66 TACATAGCCTAACATTATCTGCATTTTTTAATTGTTACATATATATATATATATATAT
98407 ATAAACAACT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 113 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (129 bp):
TTTTATGGCCGCAGGCAGGATCTGCATTTCTCACGGTTGTCACTATATATAGCTGCCATAAAATA
TACATAGCCTAACATTATCTGCATTTTTTAATTGTTACATATATATATATATATATATGCACAG
Found at i:98389 original size:2 final size:2
Alignment explanation
Indices: 98384--98409 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98374 TTTTAATTGT
98384 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
98410 AACAACTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98642 original size:5 final size:5
Alignment explanation
Indices: 98632--98669 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
98622 GATACAGGAA
*
98632 ATAAT ATAAT AAAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
98670 TTCACCTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:102484 original size:13 final size:13
Alignment explanation
Indices: 102466--102491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
102456 CAATTTTTTG
102466 TGTATCGATACAT
1 TGTATCGATACAT
102479 TGTATCGATACAT
1 TGTATCGATACAT
102492 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:102576 original size:20 final size:20
Alignment explanation
Indices: 102551--102623 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
102541 CATCCTTTTT
102551 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
102571 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
102592 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
102612 ATGTATCGATAC
1 ATGTATCGATAC
102624 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:102596 original size:21 final size:21
Alignment explanation
Indices: 102530--102606 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
102520 CTGCCAAGAA
*
102530 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
102551 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
102571 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
102592 ATGTATCGATACATT
1 ATGTATCGATACATT
102607 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:102596 original size:41 final size:41
Alignment explanation
Indices: 102530--102623 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
102520 CTGCCAAGAA
102530 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
102571 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
102612 ATGTATCGATAC
1 ATGTATCGATAC
102624 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:103718 original size:27 final size:27
Alignment explanation
Indices: 103688--103740 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
103678 CCTTTAATAC
103688 AAAATTTATACAAACTCTCCCCCTTAG
1 AAAATTTATACAAACTCTCCCCCTTAG
103715 AAAATTTATACAAACTCTCCCCCTTA
1 AAAATTTATACAAACTCTCCCCCTTA
103741 ATACGTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAATTTATACAAACTCTCCCCCTTAG
Found at i:104594 original size:13 final size:13
Alignment explanation
Indices: 104576--104600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104566 ACTGAAGCAA
104576 TGTATCGATACAT
1 TGTATCGATACAT
104589 TGTATCGATACA
1 TGTATCGATACA
104601 ATCTGGAAAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:106164 original size:84 final size:84
Alignment explanation
Indices: 106009--106173 Score: 194
Period size: 84 Copynumber: 2.0 Consensus size: 84
105999 CATTTTCCAC
* * *
106009 TTGCAACTCATTTCTTTGCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTTTGCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
106074 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
106093 TTGCAACTC-TTTCATATT-CTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCT
1 TTGCAACTCATTTC-T-TTGCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCT
* * *
106154 ACACTTATTGATTTATTTTC
62 AAACTCATTGATTTACTTTC
106174 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 52 0.75
85 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTTTGCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:108224 original size:13 final size:13
Alignment explanation
Indices: 108206--108231 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108196 CAATTTTTTG
108206 TGTATCGATACAT
1 TGTATCGATACAT
108219 TGTATCGATACAT
1 TGTATCGATACAT
108232 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:108316 original size:20 final size:20
Alignment explanation
Indices: 108291--108363 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
108281 CATCCTTTTT
108291 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
108311 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
108332 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
108352 ATGTATCGATAC
1 ATGTATCGATAC
108364 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:108336 original size:21 final size:21
Alignment explanation
Indices: 108270--108346 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
108260 CTGCCAAGAA
*
108270 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
108291 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
108311 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
108332 ATGTATCGATACATT
1 ATGTATCGATACATT
108347 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:108336 original size:41 final size:41
Alignment explanation
Indices: 108270--108363 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
108260 CTGCCAAGAA
108270 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
108311 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
108352 ATGTATCGATAC
1 ATGTATCGATAC
108364 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:109732 original size:2 final size:2
Alignment explanation
Indices: 109725--109750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
109715 CTGTAAATAG
109725 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
109751 AGGCAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:114035 original size:2 final size:2
Alignment explanation
Indices: 114028--114055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
114018 GTTCAATCAA
114028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
114056 GTTTCATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114393 original size:61 final size:61
Alignment explanation
Indices: 114321--114444 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
114311 AAGTGCTCAC
*
114321 CATGCAATGCAACAAAAGAAAATCTATTTTTGAGTGCCTTAGATCAGCACATAATCACTTT
1 CATGCAATGCAACAAAAGAAAATCTATTTTTGAGTGCCTCAGATCAGCACATAATCACTTT
*
114382 CATGCAATGCAACAAAAGAATATCTATTTTTGAGTGCCTCAGATCAGCACATAATCACTTT
1 CATGCAATGCAACAAAAGAAAATCTATTTTTGAGTGCCTCAGATCAGCACATAATCACTTT
114443 CA
1 CA
114445 AAACTAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (61 bp):
CATGCAATGCAACAAAAGAAAATCTATTTTTGAGTGCCTCAGATCAGCACATAATCACTTT
Found at i:114797 original size:34 final size:33
Alignment explanation
Indices: 114729--114804 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
114719 TCACAATATC
* * *
114729 TAAATAAAATACTGCGAACTGCTTATCGAGAAA
1 TAAATAAAATACTGCGAACTACATATAGAGAAA
*
114762 TAAACTAAAATACTGCGAA-TACATGTAGAGAAAA
1 TAAA-TAAAATACTGCGAACTACATATAGAG-AAA
114796 TAAAATAAA
1 T-AAATAAA
114805 GAATTATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 11 0.31
34 22 0.61
35 3 0.08
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.22
Consensus pattern (33 bp):
TAAATAAAATACTGCGAACTACATATAGAGAAA
Found at i:117026 original size:67 final size:67
Alignment explanation
Indices: 116947--117080 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
116937 TAAACTCGAC
116947 TCATTGAATGGCTTTAACAAAAGCTATAATATTTTAAAATAAAATAAGAGAGAGTTCATCTCAAA
1 TCATTGAATGGCTTTAACAAAAGCTATAATATTTTAAAATAAAATAAGAGAGAGTTCATCTCAAA
117012 AG
66 AG
117014 TCATTGAATGGCTTTAACAAAAGCTATAATATTTTAAAATAAAATAAGAGAGAGTTCATCTCAAA
1 TCATTGAATGGCTTTAACAAAAGCTATAATATTTTAAAATAAAATAAGAGAGAGTTCATCTCAAA
117079 AG
66 AG
117081 CTTTCTTCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (67 bp):
TCATTGAATGGCTTTAACAAAAGCTATAATATTTTAAAATAAAATAAGAGAGAGTTCATCTCAAA
AG
Found at i:123818 original size:32 final size:32
Alignment explanation
Indices: 123764--123826 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
123754 ATTTTTTTGA
* *
123764 ATTTTTATATTTTATAAATATTTTAAATTTAC
1 ATTTTTATAATTTAAAAATATTTTAAATTTAC
123796 ATTTTT-TAATTTAAAAATTATTTTAAATTTA
1 ATTTTTATAATTTAAAAA-TATTTTAAATTTA
123827 TATATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTTTATAATTTAAAAATATTTTAAATTTAC
Found at i:123853 original size:18 final size:18
Alignment explanation
Indices: 123796--123854 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 18
123786 TTAAATTTAC
123796 ATTTTTT-AATTTA-AAA
1 ATTTTTTAAATTTATAAA
*
123812 ATTATTTTAAATTTATATAT
1 ATT-TTTTAAATTTATA-AA
123832 ATTTTTTAAATTTATAAA
1 ATTTTTTAAATTTATAAA
123850 ATTTT
1 ATTTT
123855 ATTGGCATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 12 0.32
19 14 0.38
20 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTTAAATTTATAAA
Found at i:135010 original size:2 final size:2
Alignment explanation
Indices: 135003--135041 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
134993 TTGGAGGTGT
135003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
135042 CAGGCAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:148424 original size:3 final size:3
Alignment explanation
Indices: 148418--148446 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
148408 GATGATGATT
148418 ACA ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA AC
148447 GGAGAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:155820 original size:2 final size:2
Alignment explanation
Indices: 155813--155840 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
155803 CTTGTTTTAT
155813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
155841 AAAGATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:156995 original size:10 final size:9
Alignment explanation
Indices: 156979--157011 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
156969 TGTTGCAACC
156979 CTAGCTTAG
1 CTAGCTTAG
156988 CTTAGCTTAG
1 C-TAGCTTAG
156998 CTAGC-TAG
1 CTAGCTTAG
157006 CTAGCT
1 CTAGCT
157012 GGCCTCTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (9 bp):
CTAGCTTAG
Found at i:160102 original size:2 final size:2
Alignment explanation
Indices: 160095--160140 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
160085 CCAGTCGACG
*
160095 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160136 AT AT A
1 AT AT A
160141 AAGAAAAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:162668 original size:14 final size:14
Alignment explanation
Indices: 162651--162680 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
162641 TTAAAATAAA
*
162651 AAAATTATAATTAT
1 AAAATAATAATTAT
162665 AAAATAATAATTAT
1 AAAATAATAATTAT
162679 AA
1 AA
162681 TATAGCTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATAATAATTAT
Found at i:163174 original size:23 final size:24
Alignment explanation
Indices: 163134--163180 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
163124 TGCTTATATC
163134 TATATTTTTTATAATATACAAATA
1 TATATTTTTTATAATATACAAATA
* *
163158 TATATTTTTT-TATTATATAAATA
1 TATATTTTTTATAATATACAAATA
163181 GATTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTTTTTATAATATACAAATA
Found at i:163467 original size:20 final size:17
Alignment explanation
Indices: 163424--163468 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 17
163414 ATATTTAAAA
163424 TATTATATATATAATTT
1 TATTATATATATAATTT
163441 T-TTATATATTAATAATTTT
1 TATTATATA-T-ATAA-TTT
163460 TATTATATA
1 TATTATATA
163469 AATATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 4 0.17
19 4 0.17
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATATATAATTT
Found at i:163472 original size:18 final size:18
Alignment explanation
Indices: 163424--163472 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
163414 ATATTTAAAA
*
163424 TATTATATATATAATTTT
1 TATTATATAAATAATTTT
*
163442 T-TATATATTAATAATTTT
1 TAT-TATATAAATAATTTT
163460 TATTATATAAATA
1 TATTATATAAATA
163473 TATTAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATAAATAATTTT
Found at i:164908 original size:18 final size:18
Alignment explanation
Indices: 164874--164914 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
164864 AAAAGGAGTC
164874 ATTTTTAAGTAAATAATT
1 ATTTTTAAGTAAATAATT
*
164892 AGTTTTTAA-TAAGTAATT
1 A-TTTTTAAGTAAATAATT
164910 ATTTT
1 ATTTT
164915 CAAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (18 bp):
ATTTTTAAGTAAATAATT
Found at i:165839 original size:28 final size:28
Alignment explanation
Indices: 165807--165892 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 28
165797 TATAAATATG
165807 ATATAATATAAATAAAAAAATATTTTAA
1 ATATAATATAAATAAAAAAATATTTTAA
* *
165835 ATATAATTATAATATAATAAAATA-TATAA
1 ATATAA-TATAA-ATAAAAAAATATTTTAA
* * *
165864 ATATAATATTAATAAATAAAT-TATTAA
1 ATATAATATAAATAAAAAAATATTTTAA
165891 AT
1 AT
165893 TTATGCTCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
27 13 0.27
28 10 0.21
29 15 0.31
30 10 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAATATAAATAAAAAAATATTTTAA
Found at i:165861 original size:23 final size:24
Alignment explanation
Indices: 165835--165879 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
165825 AATATTTTAA
*
165835 ATATAATTATAATA-TAATAAAAT
1 ATATAAATATAATATTAATAAAAT
165858 ATATAAATATAATATTAATAAA
1 ATATAAATATAATATTAATAAA
165880 TAAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAAATATAATATTAATAAAAT
Found at i:166375 original size:18 final size:18
Alignment explanation
Indices: 166334--166375 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
166324 CATCATATTT
*
166334 TATGAAAAGATATTTTTA
1 TATGAAAAGATATCTTTA
*
166352 -ATGAAAATATATCTTTA
1 TATGAAAAGATATCTTTA
166369 TATGAAA
1 TATGAAA
166376 TGATGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (18 bp):
TATGAAAAGATATCTTTA
Found at i:166430 original size:21 final size:21
Alignment explanation
Indices: 166390--166432 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
166380 GTAATAATTG
**
166390 AATGAAAAAATATATTTTTTA
1 AATGAAAAAATATAACTTTTA
166411 AATGAAAAAATATAACTTTTA
1 AATGAAAAAATATAACTTTTA
166432 A
1 A
166433 TAATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
AATGAAAAAATATAACTTTTA
Found at i:166441 original size:23 final size:21
Alignment explanation
Indices: 166394--166442 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
166384 TAATTGAATG
* * *
166394 AAAAAATATATTTTTTAAATG
1 AAAAAATATACTTTTAAAATC
166415 AAAAAATATAACTTTTAATAATC
1 AAAAAATAT-ACTTTTAA-AATC
166438 AAAAA
1 AAAAA
166443 TTATTATGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 6 0.26
23 8 0.35
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAAAATATACTTTTAAAATC
Found at i:170747 original size:20 final size:18
Alignment explanation
Indices: 170721--170758 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
170711 AGATTAAAAA
170721 AATA-AAAAATAAAAAATC
1 AATATAAAAA-AAAAAATC
170739 AATATAAAAAAAAAAATC
1 AATATAAAAAAAAAAATC
170757 AA
1 AA
170759 GCAGAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (18 bp):
AATATAAAAAAAAAAATC
Found at i:172266 original size:22 final size:22
Alignment explanation
Indices: 172223--172274 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
172213 TCAATTATGA
* * *
172223 ATATG-TTAAAATATTTTTTTT
1 ATATGTTTAAAAAATTATATTT
172244 ATATGTTTAAAAAATTATATTT
1 ATATGTTTAAAAAATTATATTT
*
172266 ATATATTTA
1 ATATGTTTA
172275 TACTCGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATATGTTTAAAAAATTATATTT
Found at i:173893 original size:3 final size:3
Alignment explanation
Indices: 173885--173923 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
173875 TACATGCTCA
173885 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
173924 TTGGATTTGG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:178191 original size:17 final size:17
Alignment explanation
Indices: 178169--178202 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
178159 GAAAAATATA
*
178169 TAAAAATTAAATCAAAT
1 TAAAAATAAAATCAAAT
*
178186 TAAAAATAAAATTAAAT
1 TAAAAATAAAATCAAAT
178203 ATGTAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATAAAATCAAAT
Found at i:178931 original size:28 final size:28
Alignment explanation
Indices: 178897--178955 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
178887 AATCATGTAA
*
178897 ATAAAAATAT-AATATAAATTATTAAATAT
1 ATAAAAATATCAA-ATAAA-AATTAAATAT
178926 ATAAAAATATCAAATAAAAATTAAATAT
1 ATAAAAATATCAAATAAAAATTAAATAT
178954 AT
1 AT
178956 TATATCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 11 0.39
29 15 0.54
30 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAAAAATATCAAATAAAAATTAAATAT
Found at i:178990 original size:19 final size:21
Alignment explanation
Indices: 178951--178997 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
178941 AAAAATTAAA
178951 TATATTATATCATATTAATTT
1 TATATTATATCATATTAATTT
*
178972 TATATT-TATTATA-TAATTT
1 TATATTATATCATATTAATTT
*
178991 TTTATTA
1 TATATTA
178998 AATACATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.48
20 6 0.26
21 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTATATCATATTAATTT
Found at i:194927 original size:33 final size:32
Alignment explanation
Indices: 194884--194962 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
194874 ATAATATAAT
* * *
194884 TATAATATAAA-TATTTAAACATATTAAATTTTA
1 TATAAAATAAATTA-TT-AACATATCAAAATTTA
*
194917 TATAAAATAAATTATTAATATATCAAAATTTA
1 TATAAAATAAATTATTAACATATCAAAATTTA
*
194949 TAT-AAATATATTAT
1 TATAAAATAAATTAT
194963 AAAACAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 10 0.25
32 16 0.40
33 12 0.30
34 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (32 bp):
TATAAAATAAATTATTAACATATCAAAATTTA
Found at i:196060 original size:2 final size:2
Alignment explanation
Indices: 196055--196079 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
196045 TATATATATA
196055 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
196080 TTCTCCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:197044 original size:2 final size:2
Alignment explanation
Indices: 197037--197080 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
197027 CATAGCTTAT
*
197037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
197078 TA T
1 TA T
197081 TTGATTCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:199331 original size:2 final size:2
Alignment explanation
Indices: 199326--199351 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
199316 TAAAAAAAAC
199326 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
199352 CTTAACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203554 original size:17 final size:17
Alignment explanation
Indices: 203532--203583 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
203522 AAATTATTAT
203532 TATTATTATTATAATAA
1 TATTATTATTATAATAA
*
203549 TCTTATTA--ATAATATA
1 TATTATTATTATAATA-A
203565 TATT-TTATT-TAATAA
1 TATTATTATTATAATAA
203580 TATT
1 TATT
203584 TTTTTGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATTATTATAATAA
Found at i:203895 original size:14 final size:14
Alignment explanation
Indices: 203864--203910 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
203854 GTTTCTTCAA
203864 ATATTTAGATTTTATT
1 ATATTTA-ATTTT-TT
203880 AT-TTTAAGTTTTTT
1 ATATTTAA-TTTTTT
*
203894 ATATTTTATTTTTT
1 ATATTTAATTTTTT
203908 ATA
1 ATA
203911 ATACTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 14 0.50
15 12 0.43
16 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (14 bp):
ATATTTAATTTTTT
Found at i:204348 original size:18 final size:19
Alignment explanation
Indices: 204327--204383 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
204317 CTTTAAATGT
204327 AATTATATAAAATATTA-A
1 AATTATATAAAATATTATA
*
204345 AATTATATATAAATATTATT
1 AATTATATA-AAATATTATA
*
204365 AATTACATAAAAATATTAT
1 AATTATAT-AAAATATTAT
204384 CTTAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.26
19 8 0.24
20 16 0.47
21 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATATAAAATATTATA
Found at i:204397 original size:67 final size:67
Alignment explanation
Indices: 204264--204397 Score: 157
Period size: 66 Copynumber: 2.0 Consensus size: 67
204254 TATTTTTTAA
* * * * *
204264 ATATAATATTATTACAATTACATACATATATTTTAACTTACATATAATATTATCTTTAAATGTAA
1 ATATAATAATATTAAAATTACATACAAATATTTTAACTTACATAAAATATTATCTTTAAATATAA
204329 TT
66 TT
* *
204331 ATATAA-AATATTAAAATTATATATAAATATTATTAA-TTACATAAAAATATTATC-TTAATATA
1 ATATAATAATATTAAAATTACATACAAATATT-TTAACTTACAT-AAAATATTATCTTTAA-ATA
204393 TAATT
63 TAATT
204398 TCTATTCAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
66 30 0.53
67 27 0.47
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.45
Consensus pattern (67 bp):
ATATAATAATATTAAAATTACATACAAATATTTTAACTTACATAAAATATTATCTTTAAATATAA
TT
Found at i:211350 original size:18 final size:18
Alignment explanation
Indices: 211327--211363 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
211317 ACAGCTATCG
211327 GGTGTTGGTACACGTCTA
1 GGTGTTGGTACACGTCTA
*
211345 GGTGTTGGTACATGTCTA
1 GGTGTTGGTACACGTCTA
211363 G
1 G
211364 ATGTCTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.35
Consensus pattern (18 bp):
GGTGTTGGTACACGTCTA
Found at i:213295 original size:64 final size:64
Alignment explanation
Indices: 213227--213369 Score: 216
Period size: 64 Copynumber: 2.2 Consensus size: 64
213217 TAACCGATTA
* *
213227 TAATAGTTAGCATAGTTTTTTAGCATAGGCCCTGTTAACGGGTAAGAAGAGTTAG-ATTAGGCCC
1 TAATAGTTAGCATAGTTTTTTAGCATAGGCCCTGGTAACAGGTAAGAAGAGTTAGCA-TAGGCCC
* * *
213291 TAATAGTTAGAATAGTTTTTTAGCATAGGCCTTGGTAACAGGTAAGAATAGTTAGCATAGGCCC
1 TAATAGTTAGCATAGTTTTTTAGCATAGGCCCTGGTAACAGGTAAGAAGAGTTAGCATAGGCCC
*
213355 TAATACTTAGCATAG
1 TAATAGTTAGCATAG
213370 GGACTGCTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
64 70 0.99
65 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (64 bp):
TAATAGTTAGCATAGTTTTTTAGCATAGGCCCTGGTAACAGGTAAGAAGAGTTAGCATAGGCCC
Found at i:217586 original size:3 final size:3
Alignment explanation
Indices: 217580--217608 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
217570 TTGTTGTTGT
217580 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
217609 TTCTTTGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:218289 original size:20 final size:21
Alignment explanation
Indices: 218260--218299 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
218250 AATTTAAATT
218260 AAAATAATTTTAAATATTTAA
1 AAAATAATTTTAAATATTTAA
*
218281 AAAAT-ATTTTTAATATTTA
1 AAAATAATTTTAAATATTTA
218300 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATAATTTTAAATATTTAA
Found at i:221114 original size:20 final size:19
Alignment explanation
Indices: 221088--221132 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
221078 AAAATTTTAA
221088 ATATTATATTTAATATAATAT
1 ATATTAT-TTTAA-ATAATAT
221109 -TATTATTTTAAATAATAT
1 ATATTATTTTAAATAATAT
221127 ATATTA
1 ATATTA
221133 ATTAATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 10 0.43
20 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTATTTTAAATAATAT
Found at i:221124 original size:23 final size:24
Alignment explanation
Indices: 221098--221150 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
221088 ATATTATATT
*
221098 TAATATAATATT-ATT-ATTTTAAA
1 TAATAT-ATATTAATTAATCTTAAA
221121 TAATATATATTAATTAATCTTAAA
1 TAATATATATTAATTAATCTTAAA
*
221145 AAATAT
1 TAATAT
221151 GCTAATGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 9 0.35
24 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATATATATTAATTAATCTTAAA
Found at i:221137 original size:18 final size:19
Alignment explanation
Indices: 221089--221138 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
221079 AAATTTTAAA
221089 TATTATATTTAATATAATAT
1 TATTATA-TTAATATAATAT
*
221109 TATTATTTTAA-ATAATAT
1 TATTATATTAATATAATAT
221127 ATATTA-ATTAAT
1 -TATTATATTAAT
221139 CTTAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
20 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATTAATATAATAT
Found at i:221399 original size:13 final size:13
Alignment explanation
Indices: 221383--221428 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
221373 ATTCAGTTGA
221383 AAAAATTATGTTT
1 AAAAATTATGTTT
* *
221396 AAAAATTATGGTG
1 AAAAATTATGTTT
221409 AAAAA-TATAGTTT
1 AAAAATTAT-GTTT
221422 AAAAATT
1 AAAAATT
221429 TGTAAGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 3 0.11
13 23 0.85
14 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
AAAAATTATGTTT
Found at i:222052 original size:16 final size:16
Alignment explanation
Indices: 222021--222064 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
222011 GAGTTAGAAT
*
222021 ATAAAAAAATATTTAAA
1 ATAATAAAA-ATTTAAA
222038 ATAATAAAAATTTAAA
1 ATAATAAAAATTTAAA
222054 A-ACATAAAAAT
1 ATA-ATAAAAAT
222065 AATAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 16 0.64
17 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAATAAAAATTTAAA
Found at i:227228 original size:82 final size:82
Alignment explanation
Indices: 227091--227252 Score: 261
Period size: 82 Copynumber: 2.0 Consensus size: 82
227081 CTGAAAAATG
* **
227091 GGGCTACCCTTTGAGTAAAATATTCGGCCAAAATCAGTTTTGGATCGCTTTTATGTAAACCAAAC
1 GGGCTACCCTCTGAGTAAAATATTCCACCAAAATCAGTTTTGGATCGCTTTTATGTAAACCAAAC
227156 CAGACCAGAAGGAACTC
66 CAGACCAGAAGGAACTC
* * *
227173 GGGCTGCCCTCTGAGTAATATATTCCACCAAAATCGGTTTTGGATCGCTTTTATGTAAACCAAAC
1 GGGCTACCCTCTGAGTAAAATATTCCACCAAAATCAGTTTTGGATCGCTTTTATGTAAACCAAAC
*
227238 CAGACCAGTAGGAAC
66 CAGACCAGAAGGAAC
227253 CTTTCATGAC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (82 bp):
GGGCTACCCTCTGAGTAAAATATTCCACCAAAATCAGTTTTGGATCGCTTTTATGTAAACCAAAC
CAGACCAGAAGGAACTC
Found at i:229535 original size:28 final size:28
Alignment explanation
Indices: 229491--229547 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
229481 TGAAACAAAA
* *
229491 TTGCTTATGGAAGCAAATTTAGTTTGGG
1 TTGCTTATGGAAACAAATTTACTTTGGG
229519 TTGCTTATGGAAACAAATTTACTTTGGG
1 TTGCTTATGGAAACAAATTTACTTTGGG
229547 T
1 T
229548 GCGGTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (28 bp):
TTGCTTATGGAAACAAATTTACTTTGGG
Found at i:240779 original size:23 final size:21
Alignment explanation
Indices: 240753--240801 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
240743 TTTGATATAT
*
240753 ATTTTTTCAACTCTTTTAAAAAA
1 ATTTTTT-AA-TCTTTGAAAAAA
* *
240776 ATTTGTTAATCTTTGATAAAA
1 ATTTTTTAATCTTTGAAAAAA
240797 ATTTT
1 ATTTT
240802 ATATAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.64
22 2 0.09
23 6 0.27
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTTTAATCTTTGAAAAAA
Found at i:240902 original size:21 final size:21
Alignment explanation
Indices: 240876--240929 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
240866 ATAACCTTTT
240876 AATATAATTTTGAT-AATAATC
1 AATATAATTTTGATAAAT-ATC
* *
240897 AATATAATTTTGATAAATTTT
1 AATATAATTTTGATAAATATC
240918 AATATAATTTTG
1 AATATAATTTTG
240930 GTGGCCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (21 bp):
AATATAATTTTGATAAATATC
Found at i:240917 original size:10 final size:11
Alignment explanation
Indices: 240872--240929 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
240862 TTTGATAACC
*
240872 TTTTAATATAA
1 TTTTGATATAA
240883 TTTTGATAATAA
1 TTTTGAT-ATAA
**
240895 --TCAATATAA
1 TTTTGATATAA
240904 TTTTGATA-AA
1 TTTTGATATAA
*
240914 TTTTAATATAA
1 TTTTGATATAA
240925 TTTTG
1 TTTTG
240930 GTGGCCTTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
9 4 0.11
10 12 0.33
11 16 0.44
12 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (11 bp):
TTTTGATATAA
Done.