Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009133.1 Kokia drynarioides strain JFW-HI SEQ_123837, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 226359
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 135 characters in sequence are not A, C, G, or T
Found at i:2330 original size:158 final size:158
Alignment explanation
Indices: 2042--2356 Score: 432
Period size: 158 Copynumber: 2.0 Consensus size: 158
2032 TCATGTTTTA
* *
2042 CTCACACAAGCTGTGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTGGGCTACACGAT
1 CTCACACAAGCTGTGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGAT
* * * * **
2107 GCTGCTCACATGAGCTGTGGAGAATCCGCAGTAAATGTCGAATCTCAGCCATCGGTAGGACATCT
66 GCTGCTCACACGAGCTATGGAGAATCCGCAATAAATATCGAATCTCAGCCATCGGTAAAACATCT
* ** *
2172 AAGACTAGCATTCATATGACCTGTAATG
131 AAGACCAGCACGCATATAACCTGTAATG
* * * * * *
2200 CTCACACGAGCTGTGAAGTGGGCTTGCTTATACGAGCTGTGGGTCGAGATGTTAGGCTACAAGAT
1 CTCACACAAGCTGTGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGAT
** * *
2265 GCTGCTCACACGAGCTATGGAGAATTTGCAATAAATATCGGATCTCAGTCATCGGTAAAACATCT
66 GCTGCTCACACGAGCTATGGAGAATCCGCAATAAATATCGAATCTCAGCCATCGGTAAAACATCT
2330 AAGACCAGCACGCATATAACCTGTAAT
131 AAGACCAGCACGCATATAACCTGTAAT
2357 TCCTGAAATC
Statistics
Matches: 135, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
158 135 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (158 bp):
CTCACACAAGCTGTGAAATGGGCCTGCTCACACGAGCTATGGGTCGAGATGTTAGGCTACAAGAT
GCTGCTCACACGAGCTATGGAGAATCCGCAATAAATATCGAATCTCAGCCATCGGTAAAACATCT
AAGACCAGCACGCATATAACCTGTAATG
Found at i:2523 original size:2 final size:2
Alignment explanation
Indices: 2516--2541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2506 TTATGTGAAG
2516 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
2542 GATCAATTTA
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:16556 original size:141 final size:144
Alignment explanation
Indices: 16287--16645 Score: 362
Period size: 141 Copynumber: 2.6 Consensus size: 144
16277 ATTATCTTTA
* * *
16287 TATTTAT-AGGTTGTGAAGGGATTATGTGTAGTTCTAAGCATTGTATAAAAAAAATCAGATATTA
1 TATTTATGAGGTTGGGAAGGGATTATATGTAGTTCTAAGCATTGTATAAAAAAAAGCAGATATTA
* * * * * * *
16351 TTAAAACATATAATGGCATAAGTATTATTGTCAAAGCAAAAGAACGTGAGTTTGAGTGCGTTGAA
66 GTAAAACATATAATGGCATAACTATTATTGTCAAAGCAAAAGAACGTGAATTCGAATACATTGAA
16416 ACGCATTATCCTCT
131 ACGCATTATCCTCT
* * * * * *
16430 TATTTATGAGTTTGGGAA-GGATTATATGTAGTTC-AGGTATTGTAT-CAAAAGAGCATATATTA
1 TATTTATGAGGTTGGGAAGGGATTATATGTAGTTCTAAGCATTGTATAAAAAAAAGCAGATATTA
* * * *
16492 GTAAAACATTTAATGGCATGACTATTATTGTTAATGCAAGAAG-ACGTGAATTCGAATACATTGA
66 GTAAAACATATAATGGCATAACTATTATTGTCAAAGCAA-AAGAACGTGAATTCGAATACATTGA
*
16556 AACGCATTATCTTCT
130 AACGCATTATCCTCT
* * ** * *
16571 TATTTATGA-ATT--GAAGAG-TTATGGGT-GATTCTAAGCATTGTATCAAAAGAA-CAGATATT
1 TATTTATGAGGTTGGGAAGGGATTATATGTAG-TTCTAAGCATTGTATAAAAAAAAGCAGATATT
* *
16630 ATTAAAACATAAAATG
65 AGTAAAACATATAATG
16646 AGATTGTTTA
Statistics
Matches: 176, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
137 1 0.01
138 12 0.07
139 30 0.17
140 6 0.03
141 85 0.48
142 12 0.07
143 22 0.12
144 8 0.05
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (144 bp):
TATTTATGAGGTTGGGAAGGGATTATATGTAGTTCTAAGCATTGTATAAAAAAAAGCAGATATTA
GTAAAACATATAATGGCATAACTATTATTGTCAAAGCAAAAGAACGTGAATTCGAATACATTGAA
ACGCATTATCCTCT
Found at i:28505 original size:11 final size:11
Alignment explanation
Indices: 28464--28528 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 11
28454 TGTAAAGAAA
28464 ATTATTATTTT
1 ATTATTATTTT
28475 -TTATTATTTT
1 ATTATTATTTT
* *
28485 GTCATTATTTT
1 ATTATTATTTT
*
28496 ATTATCATTTT
1 ATTATTATTTT
* * *
28507 GTTATCATATT
1 ATTATTATTTT
*
28518 ACTATTATTTT
1 ATTATTATTTT
28529 GTTGTTATTA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 10 0.23
11 33 0.77
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:28527 original size:22 final size:22
Alignment explanation
Indices: 28476--28531 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
28466 TATTATTTTT
* * * *
28476 TATTATTTTGTCATTATTTTAT
1 TATTATTTTGTTATCATATTAC
*
28498 TATCATTTTGTTATCATATTAC
1 TATTATTTTGTTATCATATTAC
28520 TATTATTTTGTT
1 TATTATTTTGTT
28532 GTTATTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.64
Consensus pattern (22 bp):
TATTATTTTGTTATCATATTAC
Found at i:31859 original size:6 final size:6
Alignment explanation
Indices: 31847--31889 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
31837 TTTATTCAGC
* *
31847 ATATAA GTATAA GTATAA ATATAA ATATAA ATGAATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA AT--ATAA ATATA
31890 TTTAAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:32349 original size:18 final size:18
Alignment explanation
Indices: 32332--32380 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
32322 TAGTGTATTA
32332 TATTTTT-AA-AAAAAAT
1 TATTTTTAAATAAAAAAT
32348 TATTTTTAAATAAAAAAT
1 TATTTTTAAATAAAAAAT
* **
32366 AATTTAAAAATAAAA
1 TATTTTTAAATAAAA
32381 TATGAACGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 7 0.25
17 2 0.07
18 19 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTTTTAAATAAAAAAT
Found at i:32351 original size:16 final size:17
Alignment explanation
Indices: 32332--32363 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32322 TAGTGTATTA
32332 TATTTTTAAA-AAAAAT
1 TATTTTTAAATAAAAAT
32348 TATTTTTAAATAAAAA
1 TATTTTTAAATAAAAA
32364 ATAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTTAAATAAAAAT
Found at i:32707 original size:8 final size:8
Alignment explanation
Indices: 32694--32745 Score: 95
Period size: 8 Copynumber: 6.4 Consensus size: 8
32684 AATGAGCTCA
32694 CATGTGGG
1 CATGTGGG
32702 CATGTGGG
1 CATGTGGG
32710 CATGTGGG
1 CATGTGGG
32718 CATGTGGG
1 CATGTGGG
32726 CATGTGGG
1 CATGTGGG
32734 CATGTGGAG
1 CATGTGG-G
32743 CAT
1 CAT
32746 CGGTTTAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 39 0.91
9 4 0.09
ACGTcount: A:0.15, C:0.13, G:0.46, T:0.25
Consensus pattern (8 bp):
CATGTGGG
Found at i:39180 original size:27 final size:27
Alignment explanation
Indices: 39132--39183 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39122 GATAAATTGA
*
39132 AATTTTAAAATTAATTACTGAATTTTC
1 AATTTTAAAATTAATGACTGAATTTTC
* * *
39159 AATTTTAAATTTGATGAGTGAATTT
1 AATTTTAAAATTAATGACTGAATTT
39184 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (27 bp):
AATTTTAAAATTAATGACTGAATTTTC
Found at i:39797 original size:48 final size:48
Alignment explanation
Indices: 39725--39821 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
39715 GGTCGGGTAA
* *
39725 TGGGGTGTGTCAAGGTTTGGGGTGTTACAACATGATATGTGAATTGGT
1 TGGGGTGTGTCAAGGTCTGAGGTGTTACAACATGATATGTGAATTGGT
*
39773 TGGGGTGTGTCAAGGTCTGAGGTGTTACATCATGATATGTGAATTGGT
1 TGGGGTGTGTCAAGGTCTGAGGTGTTACAACATGATATGTGAATTGGT
39821 T
1 T
39822 TATAATATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (48 bp):
TGGGGTGTGTCAAGGTCTGAGGTGTTACAACATGATATGTGAATTGGT
Found at i:44449 original size:6 final size:6
Alignment explanation
Indices: 44438--44471 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
44428 TGATTGGCGT
* *
44438 AGGGGC AGGGGC AGGGGC AGCGGC AGGGAC AGGG
1 AGGGGC AGGGGC AGGGGC AGGGGC AGGGGC AGGG
44472 CAACATGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.18, G:0.62, T:0.00
Consensus pattern (6 bp):
AGGGGC
Found at i:47906 original size:16 final size:16
Alignment explanation
Indices: 47862--47898 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
47852 AATTAAGTTA
* *
47862 ATTTTAAAAAAATTTT
1 ATTTTTAAAATATTTT
47878 ATTTTTAAAATATTTT
1 ATTTTTAAAATATTTT
47894 ATTTT
1 ATTTT
47899 GTTAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTAAAATATTTT
Found at i:49756 original size:6 final size:6
Alignment explanation
Indices: 49739--49832 Score: 59
Period size: 6 Copynumber: 15.8 Consensus size: 6
49729 CTCAACCACA
* * * *
49739 GAAGAT GGAGAT GAAGAT -AAGGGT AAAGAT GAAGAT GGAGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAA-GAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * *
49787 GAGGTT G-GGAT GAAGAT G-AGTAT GAGGGT AAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAG-AT GAAGAT GAAGAT GAAGAT GAAGA
49833 CAATGATCAC
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
5 8 0.12
6 55 0.83
7 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (6 bp):
GAAGAT
Found at i:49800 original size:17 final size:18
Alignment explanation
Indices: 49764--49806 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
49754 GATAAGGGTA
*
49764 AAGATGAAGATGGAGATG
1 AAGATGAGGATGGAGATG
*
49782 AAGATGAGGTTGG-GATG
1 AAGATGAGGATGGAGATG
49799 AAGATGAG
1 AAGATGAG
49807 TATGAGGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.42, T:0.19
Consensus pattern (18 bp):
AAGATGAGGATGGAGATG
Found at i:51231 original size:19 final size:19
Alignment explanation
Indices: 51175--51235 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
51165 TTTGATGCTT
*
51175 TTTTTTACTGTTTTGGTTG
1 TTTTTTACTGTTTTAGTTG
*
51194 TTATTTT--TTTTTTATGTTG
1 TT-TTTTACTGTTTTA-GTTG
51213 TTTTTTACTGTTTTAGTTG
1 TTTTTTACTGTTTTAGTTG
51232 TTTT
1 TTTT
51236 CGTGTTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 9 0.26
19 16 0.46
20 10 0.29
ACGTcount: A:0.08, C:0.03, G:0.15, T:0.74
Consensus pattern (19 bp):
TTTTTTACTGTTTTAGTTG
Found at i:51446 original size:24 final size:23
Alignment explanation
Indices: 51415--51466 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
51405 TTAATATAAA
*
51415 ATTTTTTTAATGTATTTTAAATTT
1 ATTTTTTTAATGT-TTTTAAATGT
51439 ATTTTTTTTAATGTTTTTAAATGT
1 A-TTTTTTTAATGTTTTTAAATGT
51463 ATTT
1 ATTT
51467 GATATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 3 0.12
24 11 0.42
25 12 0.46
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (23 bp):
ATTTTTTTAATGTTTTTAAATGT
Found at i:51450 original size:25 final size:24
Alignment explanation
Indices: 51416--51466 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
51406 TAATATAAAA
*
51416 TTTTTTTAATGTATTTTAAATTTAT
1 TTTTTTTAATGT-TTTTAAATGTAT
51441 TTTTTTTAATGTTTTTAAATGTAT
1 TTTTTTTAATGTTTTTAAATGTAT
51465 TT
1 TT
51467 GATATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (24 bp):
TTTTTTTAATGTTTTTAAATGTAT
Found at i:52863 original size:39 final size:41
Alignment explanation
Indices: 52818--52900 Score: 125
Period size: 39 Copynumber: 2.0 Consensus size: 41
52808 TTAATACAAC
*
52818 AAATATTTATTATATTTAT-TTGTATTTTTTAATAT-AATA
1 AAATATTTATTATATTTATATTGTATTCTTTAATATAAATA
*
52857 AAATATTTATTATATTTATAGTTGTGTTCTTTAATATAAATA
1 AAATATTTATTATATTTATA-TTGTATTCTTTAATATAAATA
52899 AA
1 AA
52901 TTTTAATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
39 19 0.49
41 14 0.36
42 6 0.15
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (41 bp):
AAATATTTATTATATTTATATTGTATTCTTTAATATAAATA
Found at i:53743 original size:31 final size:31
Alignment explanation
Indices: 53708--53769 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
53698 AATAGTCATT
53708 AACTA-TTCAAAAGTTTTCATTTAAGTCACTG
1 AACTATTTCAAAA-TTTTCATTTAAGTCACTG
* *
53739 AACTATTTGAAAATTTTTATTTAAGTCACTG
1 AACTATTTCAAAATTTTCATTTAAGTCACTG
53770 GGTTGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (31 bp):
AACTATTTCAAAATTTTCATTTAAGTCACTG
Found at i:55807 original size:20 final size:19
Alignment explanation
Indices: 55773--55815 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
55763 ATAATAAAAG
55773 TAAAATATGATTTAATATTA
1 TAAAATATGATTTAA-ATTA
55793 TAAAATAT-ATATTAAATTA
1 TAAAATATGAT-TTAAATTA
55812 -AAAA
1 TAAAA
55816 AACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAAATATGATTTAAATTA
Found at i:72450 original size:14 final size:14
Alignment explanation
Indices: 72433--72462 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
72423 TTAAAAAATA
*
72433 AAAAAAAATTATTT
1 AAAAAAAATTAATT
72447 AAAAAAAATTAATT
1 AAAAAAAATTAATT
72461 AA
1 AA
72463 TTGATGACAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAAAATTAATT
Found at i:73867 original size:28 final size:31
Alignment explanation
Indices: 73799--73882 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 31
73789 TAATGTAAAC
* * *
73799 ATTAAAATAATGTTAAGATAACTATATAAAAA
1 ATTAAAATAAT-ATAATATAAATATATAAAAA
** *
73831 ATTTCAATAA-ATAA-A-AAATATATAAAAT
1 ATTAAAATAATATAATATAAATATATAAAAA
73859 ATTAAAATAATATAATATAAATAT
1 ATTAAAATAATATAATATAAATAT
73883 TTTTTTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 19 0.45
29 5 0.12
30 4 0.10
31 6 0.14
32 8 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (31 bp):
ATTAAAATAATATAATATAAATATATAAAAA
Found at i:78650 original size:22 final size:21
Alignment explanation
Indices: 78612--78662 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
78602 ATAAATTTAT
78612 TAAATATTAAAATAAAACAATA
1 TAAATATTAAAATAAAA-AATA
*
78634 TAAATATTTTAAA-AAAAAATA
1 TAAATA-TTAAAATAAAAAATA
78655 -AAAT-TTAA
1 TAAATATTAA
78663 TATGGGCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.12
20 4 0.15
21 4 0.15
22 10 0.38
23 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATATTAAAATAAAAAATA
Found at i:82020 original size:10 final size:10
Alignment explanation
Indices: 82005--82029 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
81995 ATGCAATCAC
82005 ATTAAATAAT
1 ATTAAATAAT
82015 ATTAAATAAT
1 ATTAAATAAT
82025 ATTAA
1 ATTAA
82030 TTTTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAAATAAT
Found at i:85899 original size:2 final size:2
Alignment explanation
Indices: 85894--85920 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
85884 TGTAGAAATC
85894 AT 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 AT A
85921 AAATTGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86157 original size:23 final size:24
Alignment explanation
Indices: 86115--86171 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
86105 AATTATAAAT
* *
86115 TATTTTTTTATACGATAATTTTTA
1 TATTTTTTTATACGAAAATTTATA
*
86139 TATTTTTTTTTAC-AAAATTTATA
1 TATTTTTTTATACGAAAATTTATA
*
86162 TATTTCTTTA
1 TATTTTTTTA
86172 CATTTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTTTTTTATACGAAAATTTATA
Found at i:86180 original size:21 final size:21
Alignment explanation
Indices: 86131--86186 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
86121 TTTATACGAT
* *
86131 AATTTTTATATTTTTTTTTAC
1 AATTTTTATATATTTCTTTAC
**
86152 AAAATTTATATATTTCTTTAC
1 AATTTTTATATATTTCTTTAC
*
86173 ATTTTTTATA-ATTT
1 AATTTTTATATATTT
86187 TCTTACGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTTTATATATTTCTTTAC
Found at i:86188 original size:21 final size:21
Alignment explanation
Indices: 86133--86208 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
86123 TATACGATAA
* * *
86133 TTTTTATATTTTTTTTTACAA
1 TTTTTATAATTTTCTTTACAT
**
86154 AATTTAT-ATATTTCTTTACAT
1 TTTTTATAAT-TTTCTTTACAT
86175 TTTTTATAATTTTC-TTACGAT
1 TTTTTATAATTTTCTTTAC-AT
* *
86196 TTTATAAAATTTT
1 TTTTTATAATTTT
86209 ATATTTTTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 5 0.12
21 36 0.84
22 2 0.05
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (21 bp):
TTTTTATAATTTTCTTTACAT
Found at i:86225 original size:28 final size:30
Alignment explanation
Indices: 86194--86272 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 30
86184 TTTTCTTACG
86194 ATTTTATAAAATTT-TATATTT-TTT-CTAT
1 ATTTTATAAAATTTATA-ATTTCTTTACTAT
*
86222 ATTTCTAT-ATATTTATAATTTCTTTACTAT
1 ATTT-TATAAAATTTATAATTTCTTTACTAT
*
86252 -TTTTATAAAAATTTACAATTT
1 ATTTTAT-AAAATTTATAATTT
86273 TTATAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
28 16 0.38
29 11 0.26
30 15 0.36
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTTATAAAATTTATAATTTCTTTACTAT
Found at i:86255 original size:38 final size:39
Alignment explanation
Indices: 86155--86259 Score: 96
Period size: 38 Copynumber: 2.7 Consensus size: 39
86145 TTTTTACAAA
86155 ATTTATATATTTCTTTAC-ATTTTTTATAATTTTCTTACG
1 ATTTATA-ATTTCTTTACTATTTTTTATAATTTTCTTACG
** * *
86194 ATTTTATAAAAT-TTTA-TATTTTTTCT-ATATTTCTATA-T
1 A-TTTATAATTTCTTTACTATTTTTTATAAT-TTTCT-TACG
86232 ATTTATAATTTCTTTACTA-TTTTTATAA
1 ATTTATAATTTCTTTACTATTTTTTATAA
86260 AAATTTACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
37 10 0.19
38 28 0.54
39 8 0.15
40 6 0.12
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.62
Consensus pattern (39 bp):
ATTTATAATTTCTTTACTATTTTTTATAATTTTCTTACG
Found at i:86302 original size:19 final size:18
Alignment explanation
Indices: 86156--86302 Score: 73
Period size: 19 Copynumber: 7.7 Consensus size: 18
86146 TTTTACAAAA
*
86156 TTTATATATTTCTTTACATTT
1 TTTATA-ATTT-TTTATA-TT
*
86177 TTTATAATTTTCTTACGA-T
1 TTTATAATTTT-TTA-TATT
**
86196 TTTATAAAATTTTATATT
1 TTTATAATTTTTTATATT
* * *
86214 TTT-TCTATATTTCTATATA
1 TTTAT-AAT-TTTTTATATT
86233 TTTATAATTTCTTTACTATT
1 TTTATAATTT-TTTA-TATT
*** *
86253 TTTATAAAAATTTACAATT
1 TTTATAATTTTTTA-TATT
*
86272 TTTATAAATTTTTATGATT
1 TTTATAATTTTTTAT-ATT
86291 TTTATAATTTTT
1 TTTATAATTTTT
86303 AATAAATTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
17 2 0.02
18 10 0.10
19 60 0.62
20 18 0.19
21 7 0.07
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTATAATTTTTTATATT
Found at i:86312 original size:19 final size:19
Alignment explanation
Indices: 86271--86343 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
86261 AATTTACAAT
* *
86271 TTTTATAAATTTTT-ATGAT
1 TTTTAT-AATTTTTAATAAA
86290 TTTTATAATTTTTAATAAA
1 TTTTATAATTTTTAATAAA
* *
86309 TTTTTTATATTTTTATTAAAA
1 TTTTATA-ATTTTTAAT-AAA
* *
86330 TTTAATAACTTTTA
1 TTTTATAATTTTTA
86344 GGGTGTGACA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.16
19 15 0.34
20 14 0.32
21 8 0.18
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAA
Found at i:86332 original size:21 final size:21
Alignment explanation
Indices: 86289--86328 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
86279 ATTTTTATGA
86289 TTTTTATAATTTTTAATAAAT
1 TTTTTATAATTTTTAATAAAT
*
86310 TTTTTAT-ATTTTTATTAAA
1 TTTTTATAATTTTTAATAAA
86329 ATTTAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATAATTTTTAATAAAT
Found at i:89365 original size:20 final size:20
Alignment explanation
Indices: 89333--89378 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
89323 GTTTGAGTTA
*
89333 AATTAAGAGTAAATA-GATTT
1 AATTAAGAGTAAAAATGA-TT
89353 AATTAAG-GTTAAAAATGATT
1 AATTAAGAG-TAAAAATGATT
89373 AATTAA
1 AATTAA
89379 AGCTTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (20 bp):
AATTAAGAGTAAAAATGATT
Found at i:90332 original size:51 final size:51
Alignment explanation
Indices: 90252--90428 Score: 275
Period size: 51 Copynumber: 3.5 Consensus size: 51
90242 TGAAAGAGTT
* * *
90252 CGATGACTAAGTGTCATTGTGGGCAAATGAATCCTTTAT-GAGTTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGA-TTAAAGGTC
* * *
90303 CGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAATGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
*
90354 TGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
90405 CGATGACTAAGTGTCATCGTGAGT
1 CGATGACTAAGTGTCATCGTGAGT
90429 TTATGGATTC
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
51 112 0.98
52 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTC
Found at i:97717 original size:51 final size:51
Alignment explanation
Indices: 97519--97698 Score: 265
Period size: 51 Copynumber: 3.5 Consensus size: 51
97509 TAAACGAAAG
* *
97519 GGTCCGATGACTAAGTGTCATCGTGAGCAAATGAAT-CTTTCATGGATTAAA
1 GGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTT-ATGGATTAAA
* * * *
97570 GGTCCGATGACTAAGTGTCATCGTAAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTATGGATTAAA
*
97621 GGTCCGATGACTAAGTGTCATTGTGAGTAAATTAATCCTTTATGGA-TAAA
1 GGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTATGGATTAAA
*
97671 GGTCCGATGTCTAAGTGTCATTGTGAGT
1 GGTCCGATGACTAAGTGTCATTGTGAGT
97699 TTATGGATTC
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
50 30 0.25
51 84 0.71
52 4 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTATGGATTAAA
Found at i:99153 original size:5 final size:5
Alignment explanation
Indices: 99143--99180 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
99133 AAAATTATTA
*
99143 AAAAT AAAAT AAAAT GAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
99181 TATTTTTAAA
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:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:100659 original size:22 final size:22
Alignment explanation
Indices: 100628--100669 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
100618 CGATTAGCAC
* *
100628 GACTCGAATCGAGGTGGTTCGA
1 GACTCAAATCGAGATGGTTCGA
100650 GACTCAAATCGAGATGGTTC
1 GACTCAAATCGAGATGGTTC
100670 AAGAGGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (22 bp):
GACTCAAATCGAGATGGTTCGA
Found at i:109169 original size:2 final size:2
Alignment explanation
Indices: 109164--109192 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
109154 TAATTTTTAA
109164 AT AT 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 AT AT A
109193 AAATACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:109237 original size:20 final size:20
Alignment explanation
Indices: 109214--109258 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
109204 AATAAATATT
*
109214 TTTAACAAATTAAAAATAAA
1 TTTAAAAAATTAAAAATAAA
* *
109234 TTTAAAAAATTTAAAATACA
1 TTTAAAAAATTAAAAATAAA
109254 TTTAA
1 TTTAA
109259 TATAAAATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTAAAAAATTAAAAATAAA
Found at i:109577 original size:15 final size:16
Alignment explanation
Indices: 109547--109585 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
109537 TAGTAAAAAT
109547 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
109564 ATAATTTA-TATTTTA
1 ATAATTTATTATTTTA
109579 ATAATTT
1 ATAATTT
109586 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.64
16 4 0.18
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:109619 original size:22 final size:21
Alignment explanation
Indices: 109593--109654 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
109583 TTTTTAAAAA
109593 ATTAAATTAAATTTTTATTATT
1 ATTAAATTAAA-TTTTATTATT
* * *
109615 TTTAAAGTCAAATTTTAATATT
1 ATTAAA-TTAAATTTTATTATT
*
109637 ATTAATTTAAAATTTTAT
1 ATTAAATT-AAATTTTAT
109655 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 1 0.03
22 26 0.84
23 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAAATTAAATTTTATTATT
Found at i:114349 original size:7 final size:7
Alignment explanation
Indices: 114337--114366 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
114327 GAAAGTTTGT
114337 TAAGCTA
1 TAAGCTA
114344 TAAGCTA
1 TAAGCTA
114351 TAAGCTA
1 TAAGCTA
114358 TAAGCTA
1 TAAGCTA
114365 TA
1 TA
114367 CATACTAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (7 bp):
TAAGCTA
Found at i:115375 original size:29 final size:28
Alignment explanation
Indices: 115343--115431 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
115333 AATCCAACCA
*
115343 AAATCAAAATAACCCTAAATCAAAAATAA
1 AAATCAAAATAACCCTAAAT-AAAAATCA
* *
115372 AAATCCAAAT---CC-AAATAAAAACCA
1 AAATCAAAATAACCCTAAATAAAAATCA
115396 AAATC-AAATAAACCCTAAATTAAAAATCA
1 AAATCAAAAT-AACCCTAAA-TAAAAATCA
*
115425 CAATCAA
1 AAATCAA
115432 TATCGACATC
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 4 0.08
24 11 0.23
25 4 0.08
26 2 0.04
27 2 0.04
28 3 0.06
29 21 0.44
30 1 0.02
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (28 bp):
AAATCAAAATAACCCTAAATAAAAATCA
Found at i:115389 original size:18 final size:17
Alignment explanation
Indices: 115338--115407 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 17
115328 ATCATAATCC
*
115338 AACCAAAATCAAA-ATA
1 AACCAAAATCAAATAAA
* *
115354 ACCCTAAATCAAAAATAAA
1 AACCAAAATC--AAATAAA
115373 AATCC-AAATCCAAATAAA
1 AA-CCAAAAT-CAAATAAA
115391 AACCAAAATCAAATAAA
1 AACCAAAATCAAATAAA
115408 CCCTAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
16 8 0.18
17 10 0.23
18 16 0.36
19 7 0.16
20 3 0.07
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.14
Consensus pattern (17 bp):
AACCAAAATCAAATAAA
Found at i:115520 original size:43 final size:44
Alignment explanation
Indices: 115442--115530 Score: 137
Period size: 43 Copynumber: 2.0 Consensus size: 44
115432 TATCGACATC
*
115442 AAATTCGAATAAACACAAAATAACCCTAAATACAAATATCTCAT
1 AAATTCGAATAAACACAAAATAACCCTAAATACAAATATCCCAT
*
115486 AAATTTGAATAAACAC-AAAT-ACCTCTAAATACAAATATCCCAT
1 AAATTCGAATAAACACAAAATAACC-CTAAATACAAATATCCCAT
115529 AA
1 AA
115531 CCCAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
42 3 0.07
43 24 0.57
44 15 0.36
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (44 bp):
AAATTCGAATAAACACAAAATAACCCTAAATACAAATATCCCAT
Found at i:126933 original size:61 final size:61
Alignment explanation
Indices: 126857--126982 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
126847 ACCTAAATTA
* * *
126857 TTTTTGTTCACGTTAAG-CTCTAAATTTG-ACAATTATTTTCACATTGAGACTTGAAATTTTT
1 TTTTTGTTCAAGTTAAGTCTC-AAA-TTGAACAAATATTTTCACATTGAGACTTCAAATTTTT
* *
126918 TTTTTGTTCAAGTTAAGTCTCGAATTGAACAAATATTTTCACATTGAGACTTCAACTTTTT
1 TTTTTGTTCAAGTTAAGTCTCAAATTGAACAAATATTTTCACATTGAGACTTCAAATTTTT
126979 TTTT
1 TTTT
126983 CTTCAAATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
60 3 0.05
61 52 0.90
62 3 0.05
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (61 bp):
TTTTTGTTCAAGTTAAGTCTCAAATTGAACAAATATTTTCACATTGAGACTTCAAATTTTT
Found at i:128928 original size:62 final size:62
Alignment explanation
Indices: 128852--128969 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 62
128842 ATTTTTCTCT
* *
128852 AAGTTAAGCTCTAAA-TTCGAAAATTATTTTCACATTGAGACTTAAATTTTTTTTTTTTGTTC
1 AAGTTAAGCTCTAAACTTAGAAAA-TATTTTCACATTGAGACTTAAACTTTTTTTTTTTGTTC
* * * *
128914 AAGTTAAG-TCCTAAACTTAGTAAATATTTTCATATTGGGACTTTAACTTTTTTTTT
1 AAGTTAAGCT-CTAAACTTAGAAAATATTTTCACATTGAGACTTAAACTTTTTTTTT
128970 ATCCAAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
61 1 0.02
62 41 0.85
63 6 0.12
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (62 bp):
AAGTTAAGCTCTAAACTTAGAAAATATTTTCACATTGAGACTTAAACTTTTTTTTTTTGTTC
Found at i:129454 original size:18 final size:19
Alignment explanation
Indices: 129431--129466 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
129421 ATTTTTTTTT
129431 GATAAAATATAAA-AATAG
1 GATAAAATATAAACAATAG
*
129449 GATAAAATCTAAACAATA
1 GATAAAATATAAACAATA
129467 AACACAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
GATAAAATATAAACAATAG
Found at i:130227 original size:6 final size:6
Alignment explanation
Indices: 130225--130252 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
130215 AAATTATAAT
130225 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
130253 AAATCACTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:132900 original size:214 final size:214
Alignment explanation
Indices: 132524--132953 Score: 806
Period size: 214 Copynumber: 2.0 Consensus size: 214
132514 CTCCCATTCC
*
132524 CCAGTCAAAACTGCCTCATGAATTATATGACCGAGCCTCTCCATGGCCAACACGAACAAATATAG
1 CCAGTCAAAACTACCTCATGAATTATATGACCGAGCCTCTCCATGGCCAACACGAACAAATATAG
* *
132589 AGATATTGGATCTCCCTGTCTCACTCCTTTTGAAGGGAAAAATTCGTTGATAATTTCACCATTCC
66 AGACATTGGATCTCCCTGTCTCACTCCTTTTGAAGGGAAAAATTCGTCGATAATTTCACCATTCC
132654 ATAAAAATTGCATCGAGGCTGAAGAAATGCACCGCAATAAGATTCTCACAAATTTTTTAGGCAAT
131 ATAAAAATTGCATCGAGGCTGAAGAAATGCACCGCAATAAGATTCTCACAAATTTTTTAGGCAAT
132719 TTAGCGTCCTTAAGAGTGT
196 TTAGCGTCCTTAAGAGTGT
*
132738 CCAGTCAAAACTACCTCATGAATTATATGACTGAGCCTCTCCATGGCCAACACGAACAAATATAG
1 CCAGTCAAAACTACCTCATGAATTATATGACCGAGCCTCTCCATGGCCAACACGAACAAATATAG
132803 AGACATTGGATCTCCCTGTCTCACTCCTTTTGAAGGGAAAAATTCGTCGATAATTTCACCATTCC
66 AGACATTGGATCTCCCTGTCTCACTCCTTTTGAAGGGAAAAATTCGTCGATAATTTCACCATTCC
* *
132868 ATAAAAGTTGCATCGAGGCTGAAGATATGCACCGCAATAAGATTCTCACAAATTTTTTAGGCAAT
131 ATAAAAATTGCATCGAGGCTGAAGAAATGCACCGCAATAAGATTCTCACAAATTTTTTAGGCAAT
132933 TTAGCGTCCTTAAGAGTGT
196 TTAGCGTCCTTAAGAGTGT
132952 CC
1 CC
132954 TGAATGAAGT
Statistics
Matches: 210, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
214 210 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (214 bp):
CCAGTCAAAACTACCTCATGAATTATATGACCGAGCCTCTCCATGGCCAACACGAACAAATATAG
AGACATTGGATCTCCCTGTCTCACTCCTTTTGAAGGGAAAAATTCGTCGATAATTTCACCATTCC
ATAAAAATTGCATCGAGGCTGAAGAAATGCACCGCAATAAGATTCTCACAAATTTTTTAGGCAAT
TTAGCGTCCTTAAGAGTGT
Found at i:135404 original size:15 final size:16
Alignment explanation
Indices: 135384--135413 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
135374 TAGTGTATTA
135384 TATTTTTAAA-AAAAG
1 TATTTTTAAATAAAAG
135399 TATTTTTAAATAAAA
1 TATTTTTAAATAAAA
135414 ATTAATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TATTTTTAAATAAAAG
Found at i:135902 original size:15 final size:15
Alignment explanation
Indices: 135864--135902 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
135854 TATTAAACTA
*
135864 AAAATAAAACAAAGT
1 AAAATAAAATAAAGT
*
135879 AAAAT-AAATATAGT
1 AAAATAAAATAAAGT
135893 AAAATAAAAT
1 AAAATAAAAT
135903 CTTGTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATAAAATAAAGT
Found at i:136646 original size:54 final size:54
Alignment explanation
Indices: 136564--136673 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
136554 GATGGATTAA
136564 TTGGAATTATGGAAAACTGAAATGAGAAAAGATTAGGAAAGCAATTAAATAAAT
1 TTGGAATTATGGAAAACTGAAATGAGAAAAGATTAGGAAAGCAATTAAATAAAT
136618 TTGGAATTATGGAAAACTGAAATGAGAAAAGATTAGGAAAGCAATTAAATAAAT
1 TTGGAATTATGGAAAACTGAAATGAGAAAAGATTAGGAAAGCAATTAAATAAAT
136672 TT
1 TT
136674 TGCAAAAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.25
Consensus pattern (54 bp):
TTGGAATTATGGAAAACTGAAATGAGAAAAGATTAGGAAAGCAATTAAATAAAT
Found at i:137954 original size:1 final size:1
Alignment explanation
Indices: 137950--137975 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
137940 NNNNNNNNNN
137950 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
137976 TATTGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:142084 original size:22 final size:21
Alignment explanation
Indices: 142019--142080 Score: 115
Period size: 21 Copynumber: 2.9 Consensus size: 21
142009 AAATTTTAAA
142019 TTAATAAAAATAAAATTACATT
1 TTAATAAAAA-AAAATTACATT
142041 TTAATAAAAAAAAATTACATT
1 TTAATAAAAAAAAATTACATT
142062 TTAATAAAAAAAAATTACA
1 TTAATAAAAAAAAATTACA
142081 ATTTCGATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 30 0.75
22 10 0.25
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAATAAAAAAAAATTACATT
Found at i:145920 original size:42 final size:42
Alignment explanation
Indices: 145868--145947 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
145858 AGATAGACAG
* * * *
145868 TTTCCAGACTTCTCATTTGGGAACTTGGCTGCAGAATGGGCC
1 TTTCCAGACTTCTCACTTGGAAACTTGACTGAAGAATGGGCC
* *
145910 TTTCTAGACTTCTCACTTGGAAATTTGACTGAAGAATG
1 TTTCCAGACTTCTCACTTGGAAACTTGACTGAAGAATG
145948 AGCAGGACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
TTTCCAGACTTCTCACTTGGAAACTTGACTGAAGAATGGGCC
Found at i:153692 original size:173 final size:174
Alignment explanation
Indices: 153178--153701 Score: 870
Period size: 174 Copynumber: 3.0 Consensus size: 174
153168 TAGTAGAACT
* *
153178 AGTGAATGGTAGACGATGACTCTTCCCCATGCAACATGCTTCACACAAAGGGATGTGTTGACGAA
1 AGTGAATGGTAGATGATGACTCTTCCCCATGCAACATGCTTCACACAAAGGGATGTGTTGACGTA
* *
153243 CAAATTGAGATTTGTTGCACTGCTTCATGACTTTATTTTGCATCTCGATTGAAGAATGAACAAGA
66 CAAATTGAGATTTGTTGCACTGCTTCATGACTTTATTTTGCACCTCGATTGAAGGATGAACAAGA
*
153308 CGTCAATGCCATAACCAAAATTCAAAAGACGGAGAAGATAAAGA
131 CGTCAATGCCATAACCAAAATTCAAGAGACGGAGAAGATAAAGA
* *
153352 AGTGAATGGTAGATGATGACTCTTCCTCATGCAACATGCTTCACACAAAGGGATGTGTTAACGTA
1 AGTGAATGGTAGATGATGACTCTTCCCCATGCAACATGCTTCACACAAAGGGATGTGTTGACGTA
* * * *
153417 CAAATTGGGATTTGTTGTACTGCCTCATGACTTTATTTTGCACCTTGATTGAAGGATGAACAAGA
66 CAAATTGAGATTTGTTGCACTGCTTCATGACTTTATTTTGCACCTCGATTGAAGGATGAACAAGA
*
153482 CGTCAATGCCATAACCAAAATTCAAGAGACAGAGAAGATAAAGA
131 CGTCAATGCCATAACCAAAATTCAAGAGACGGAGAAGATAAAGA
* *
153526 AGTGAATGGTAGATGATGACTCTTCCCCATGCAACATGCTTCGCACAAAAGGATGTGTTGACGTA
1 AGTGAATGGTAGATGATGACTCTTCCCCATGCAACATGCTTCACACAAAGGGATGTGTTGACGTA
* * *
153591 CAAAAT-AGATTTGTTACACTGCTTCATGACTTTATTTTGCACCTCGATTGAAGGATGAGCAAGA
66 CAAATTGAGATTTGTTGCACTGCTTCATGACTTTATTTTGCACCTCGATTGAAGGATGAACAAGA
* *
153655 TGTCAATGCCATAACCAAAATTCAAGAGACGGAGAAGACAAAGA
131 CGTCAATGCCATAACCAAAATTCAAGAGACGGAGAAGATAAAGA
153699 AGT
1 AGT
153702 ACCGGTAATG
Statistics
Matches: 324, Mismatches: 26, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
173 96 0.30
174 228 0.70
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (174 bp):
AGTGAATGGTAGATGATGACTCTTCCCCATGCAACATGCTTCACACAAAGGGATGTGTTGACGTA
CAAATTGAGATTTGTTGCACTGCTTCATGACTTTATTTTGCACCTCGATTGAAGGATGAACAAGA
CGTCAATGCCATAACCAAAATTCAAGAGACGGAGAAGATAAAGA
Found at i:155629 original size:18 final size:20
Alignment explanation
Indices: 155598--155637 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
155588 TTCTTGCTAA
155598 TATTATATTAAATAAAAATG
1 TATTATATTAAATAAAAATG
*
155618 TATTAT-TT-AATAAAAGTG
1 TATTATATTAAATAAAAATG
155636 TA
1 TA
155638 AGTTTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
TATTATATTAAATAAAAATG
Found at i:157886 original size:23 final size:23
Alignment explanation
Indices: 157859--157907 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
157849 ATCTGTTTTT
* *
157859 AATTTCTTTTTCTATTATCTGGA
1 AATTTCTTGTTCTATTATCAGGA
157882 AA--T-TTGTTCTATTATCAGGA
1 AATTTCTTGTTCTATTATCAGGA
157902 AATTTC
1 AATTTC
157908 CTTCTAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
20 17 0.81
21 1 0.05
22 1 0.05
23 2 0.10
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (23 bp):
AATTTCTTGTTCTATTATCAGGA
Found at i:157893 original size:20 final size:20
Alignment explanation
Indices: 157868--157906 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
157858 TAATTTCTTT
*
157868 TTCTATTATCTGGAAATTTG
1 TTCTATTATCAGGAAATTTG
157888 TTCTATTATCAGGAAATTT
1 TTCTATTATCAGGAAATTT
157907 CCTTCTAACT
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:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTCTATTATCAGGAAATTTG
Found at i:158280 original size:16 final size:16
Alignment explanation
Indices: 158263--158311 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
158253 GTTTTTACTT
*
158263 AATTAAATTAAAATTTAA
1 AATT-AATTAATA-TTAA
158281 AATT-A-TAATATTAA
1 AATTAATTAATATTAA
158295 AATTAATTAATATTAA
1 AATTAATTAATATTAA
158311 A
1 A
158312 TTTTTACGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 8 0.29
15 5 0.18
16 11 0.39
18 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATTAATATTAA
Found at i:159583 original size:31 final size:31
Alignment explanation
Indices: 159521--159594 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
159511 TTTTTTAATT
*
159521 AAATTTGGCTTTTAACCTTTTAAAAAATAGTC
1 AAATTT-GCTATTAACCTTTTAAAAAATAGTC
* *
159553 AAATTTGACTATTATCCTTTT-AGAAATAGTC
1 AAATTTG-CTATTAACCTTTTAAAAAATAGTC
159584 -AATTTGCTATT
1 AAATTTGCTATT
159595 TTTTTTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 5 0.13
30 6 0.16
31 10 0.26
32 17 0.45
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (31 bp):
AAATTTGCTATTAACCTTTTAAAAAATAGTC
Found at i:159736 original size:29 final size:29
Alignment explanation
Indices: 159704--159765 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
159694 ACTATTTTTT
*
159704 AAATTATTTATTGATGTGACATATATAAC
1 AAATTATTTATTGATATGACATATATAAC
* * *
159733 AAATTTTTTGTTGATATGTCATATATAAC
1 AAATTATTTATTGATATGACATATATAAC
159762 AAAT
1 AAAT
159766 GATATCTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (29 bp):
AAATTATTTATTGATATGACATATATAAC
Found at i:160118 original size:19 final size:18
Alignment explanation
Indices: 160094--160152 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
160084 AAATTTATAA
160094 TAAATTTTGAATTATATTT
1 TAAATTTT-AATTATATTT
* *
160113 TAAATTAATAATTATAATT
1 TAAATT-TTAATTATATTT
* *
160132 TAAGTTTTAATTGT-TTT
1 TAAATTTTAATTATATTT
160149 TAAA
1 TAAA
160153 GGTGGATTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 5 0.16
18 6 0.19
19 20 0.62
20 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TAAATTTTAATTATATTT
Found at i:163755 original size:40 final size:40
Alignment explanation
Indices: 163641--163763 Score: 131
Period size: 40 Copynumber: 3.1 Consensus size: 40
163631 GTTGTCTAGT
* * * **
163641 AGTGTTTACAGTGTCAC-AGCTAGTACAGTAATAACGTTGC
1 AGTGTTTACAGTGTCACTA-CCAATTCAGTAATAATATTGC
* * * * *
163681 AGCGTTTACAGTTTCACTACCAGTTCAATAATAATATTAC
1 AGTGTTTACAGTGTCACTACCAATTCAGTAATAATATTGC
*
163721 AGTGTTTACGGTGTCACTACCAATTCAGTAATAATATTGC
1 AGTGTTTACAGTGTCACTACCAATTCAGTAATAATATTGC
163761 AGT
1 AGT
163764 CGTTCCAGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 67 0.99
41 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (40 bp):
AGTGTTTACAGTGTCACTACCAATTCAGTAATAATATTGC
Found at i:164767 original size:77 final size:77
Alignment explanation
Indices: 164668--164814 Score: 258
Period size: 77 Copynumber: 1.9 Consensus size: 77
164658 CAACCTCGTA
*
164668 ACAAACAAGAAAAGAACAAAACCTTACAATTTACTAGCCCAATCTCATACCAAAGTAGCAACCGG
1 ACAAACAAGAAAAGAACAAAACCTTACAATTTACTAGCCCAATCTCATACCAAAGTAGCAACCAG
164733 TTAACAGAAGCT
66 TTAACAGAAGCT
** *
164745 ACAAACAAGAAAAGAATGAAACCTTACAATTTACTAGCTCAATCTCATACCAAAGTAGCAACCAG
1 ACAAACAAGAAAAGAACAAAACCTTACAATTTACTAGCCCAATCTCATACCAAAGTAGCAACCAG
164810 TTAAC
66 TTAAC
164815 GAATGACAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.18
Consensus pattern (77 bp):
ACAAACAAGAAAAGAACAAAACCTTACAATTTACTAGCCCAATCTCATACCAAAGTAGCAACCAG
TTAACAGAAGCT
Found at i:165245 original size:53 final size:53
Alignment explanation
Indices: 165152--165278 Score: 164
Period size: 53 Copynumber: 2.4 Consensus size: 53
165142 TGGTGTGTAT
* * * *
165152 GGCACACGGGCTGGCACATGGGCATGTGTCAGAGTGTGTGTATACTGTTTTGG
1 GGCACACGGGCTGACACATGGACATGTGTCAGAGTATGTGTATACTGTTTTAG
* * * *
165205 GGCATACGGGTTGACACATGGACGTGTGTCAGGGTATGTGTATACTGTTTTAG
1 GGCACACGGGCTGACACATGGACATGTGTCAGAGTATGTGTATACTGTTTTAG
* *
165258 GGAACATGGGCTGACACATGG
1 GGCACACGGGCTGACACATGG
165279 GTGTGGGTAC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.28
Consensus pattern (53 bp):
GGCACACGGGCTGACACATGGACATGTGTCAGAGTATGTGTATACTGTTTTAG
Found at i:166725 original size:31 final size:30
Alignment explanation
Indices: 166687--166771 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
166677 TATTAAAGGG
166687 TAATTTTAAAAGAAATAAAAATAAAAGTG-TT
1 TAATTTTAAAA-AAATAAAAATAAAAG-GATT
*
166718 TAATTTTAACAAAAATAAAAATAGAAGGATT
1 TAATTTTAA-AAAAATAAAAATAAAAGGATT
166749 T-ATTTTAAAAAAA-AAAGAATAAA
1 TAATTTTAAAAAAATAAA-AATAAA
166772 TGGGTAAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.06
29 10 0.20
30 8 0.16
31 26 0.53
32 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.29
Consensus pattern (30 bp):
TAATTTTAAAAAAATAAAAATAAAAGGATT
Found at i:169520 original size:13 final size:13
Alignment explanation
Indices: 169502--169528 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
169492 ATTCAATATC
169502 TCCGTGGCAATCT
1 TCCGTGGCAATCT
169515 TCCGTGGCAATCT
1 TCCGTGGCAATCT
169528 T
1 T
169529 AGTAATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCGTGGCAATCT
Found at i:174386 original size:24 final size:23
Alignment explanation
Indices: 174359--174405 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
174349 TCCAAACGGT
174359 TCAA-ATCAAATAAATAATTAAAAA
1 TCAATATCAAA-AAAT-ATTAAAAA
*
174383 TCAATATTAAAAAATATTAAAAA
1 TCAATATCAAAAAATATTAAAAA
174406 GTTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
TCAATATCAAAAAATATTAAAAA
Found at i:174593 original size:17 final size:17
Alignment explanation
Indices: 174573--174606 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
174563 AAAACATAAA
*
174573 TTTTAAAAATTATATAT
1 TTTTAAAAAATATATAT
174590 TTTTAAAAAATATATAT
1 TTTTAAAAAATATATAT
174607 GAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAAAAATATATAT
Found at i:174838 original size:21 final size:22
Alignment explanation
Indices: 174813--174857 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
174803 TTGAACAAAA
174813 TTTTATATTTTTTAA-AAA-TAT
1 TTTTA-ATTTTTTAATAAATTAT
*
174834 TTTTAGTTTTTTAATAAATTAT
1 TTTTAATTTTTTAATAAATTAT
174856 TT
1 TT
174858 GCTTTGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 8 0.38
22 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTAATTTTTTAATAAATTAT
Found at i:176839 original size:3 final size:3
Alignment explanation
Indices: 176796--176821 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
176786 GACATGGGAT
176796 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
176822 TTGAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:188691 original size:2 final size:2
Alignment explanation
Indices: 188684--188712 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
188674 AATTTTGCAT
188684 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
188713 TATATACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:190184 original size:22 final size:22
Alignment explanation
Indices: 190149--190204 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
190139 TTTTTTCCGT
*
190149 AAAAAA-AAATGGAAAAA-AGAA
1 AAAAAATAAAAGGAAAAACA-AA
*
190170 GAAAAATAAAAGGAAAAACAAA
1 AAAAAATAAAAGGAAAAACAAA
190192 AAAAAATTAAAAG
1 AAAAAA-TAAAAG
190205 AACATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 17 0.59
23 7 0.24
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAAATAAAAGGAAAAACAAA
Found at i:190197 original size:23 final size:22
Alignment explanation
Indices: 190149--190219 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 22
190139 TTTTTTCCGT
* *
190149 AAAAAA-AAATGGAAAAAAGAA
1 AAAAAATAAAAGGAAAAAAAAA
*
190170 GAAAAATAAAAGGAAAAACAAAA
1 AAAAAATAAAAGGAAAAA-AAAA
* * *
190193 AAAAATTAAAA-GAACATAAAA
1 AAAAAATAAAAGGAAAAAAAAA
190214 AAAAAA
1 AAAAAA
190220 CTTAAAAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 14 0.35
22 14 0.35
23 12 0.30
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAAAATAAAAGGAAAAAAAAA
Found at i:191142 original size:11 final size:11
Alignment explanation
Indices: 191126--191150 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
191116 CAACAAATAT
191126 TTGATAAAAGA
1 TTGATAAAAGA
191137 TTGATAAAAGA
1 TTGATAAAAGA
191148 TTG
1 TTG
191151 GAAAATGAGT
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (11 bp):
TTGATAAAAGA
Found at i:193683 original size:18 final size:18
Alignment explanation
Indices: 193669--193703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
193659 TAAATATGAT
*
193669 ATAATAATAAAATATAAA
1 ATAAAAATAAAATATAAA
*
193687 ATAAAAATAAAAAATAA
1 ATAAAAATAAAATATAA
193704 GTTGAAACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAATAAAATATAAA
Found at i:196444 original size:30 final size:30
Alignment explanation
Indices: 196374--196450 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
196364 ATAACAAGAA
* *
196374 GACTATTTTGTCAC-TTTTCGATAATTTTAAT
1 GACTGTTTTGTCACATTTTC-A-AATATTAAT
*
196405 GATTGTTTTGTCACATTTTC-AATATTAAGT
1 GACTGTTTTGTCACATTTTCAAATATTAA-T
196435 GACTGTTTTGTCACAT
1 GACTGTTTTGTCACAT
196451 GTAACCGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.17
30 16 0.40
31 12 0.30
32 5 0.12
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTTCAAATATTAAT
Found at i:204642 original size:10 final size:10
Alignment explanation
Indices: 204627--204659 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
204617 ATTATATGAA
204627 AAATAAATAT
1 AAATAAATAT
204637 AAAT-AATAT
1 AAATAAATAT
204646 AAAATAAATAT
1 -AAATAAATAT
204657 AAA
1 AAA
204660 ATGTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.24
10 11 0.52
11 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATAAATAT
Found at i:204657 original size:11 final size:11
Alignment explanation
Indices: 204626--204661 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
204616 TATTATATGA
204626 AAAATAAATAT
1 AAAATAAATAT
204637 -AAAT-AATAT
1 AAAATAAATAT
204646 AAAATAAATAT
1 AAAATAAATAT
204657 AAAAT
1 AAAAT
204662 GTTATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.22
10 8 0.35
11 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:215061 original size:16 final size:16
Alignment explanation
Indices: 215040--215070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
215030 GTGTGCTTTT
*
215040 TGATTGGTTGAAAATA
1 TGATTGATTGAAAATA
215056 TGATTGATTGAAAAT
1 TGATTGATTGAAAAT
215071 TCCCCTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (16 bp):
TGATTGATTGAAAATA
Found at i:217275 original size:60 final size:60
Alignment explanation
Indices: 217210--217331 Score: 172
Period size: 60 Copynumber: 2.0 Consensus size: 60
217200 GATAAAACTC
* * * * *
217210 TAATAATAATGTAATTAGTGTTGTTTGAATTCAGATTACACATAAGATAATGAATATTTT
1 TAATAATAATGCAATTAGTGTGGTTTGAACTCAGATCACACATAAGATAATGAATACTTT
* * *
217270 TAATAATAATGCGATTAGTGTGGTTTGAACTCAGGTCATACATAAGATAATGAATACTTT
1 TAATAATAATGCAATTAGTGTGGTTTGAACTCAGATCACACATAAGATAATGAATACTTT
217330 TA
1 TA
217332 CCATCAGACC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (60 bp):
TAATAATAATGCAATTAGTGTGGTTTGAACTCAGATCACACATAAGATAATGAATACTTT
Found at i:218285 original size:15 final size:16
Alignment explanation
Indices: 218265--218298 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
218255 AATTTTTTAA
218265 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
218280 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
218296 AAA
1 AAA
218299 CAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:223011 original size:28 final size:28
Alignment explanation
Indices: 222959--223024 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
222949 TTTGCCTCAG
*
222959 ATTACATCTTAGTCACTTATGTTTGAAAT
1 ATTACAT-TTAGTCACTTATATTTGAAAT
* *
222988 GTTACATTTATTCACTTATATTTGAAAT
1 ATTACATTTAGTCACTTATATTTGAAAT
223016 ATTACATTT
1 ATTACATTT
223025 TAGTTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 27 0.82
29 6 0.18
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (28 bp):
ATTACATTTAGTCACTTATATTTGAAAT
Found at i:225430 original size:9 final size:9
Alignment explanation
Indices: 225405--225447 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
225395 TTTTTTTAAA
225405 AATATTATTT
1 AATATT-TTT
225415 -ATA-TTTT
1 AATATTTTT
225422 AATATTTTT
1 AATATTTTT
*
225431 AAAATTTTT
1 AATATTTTT
225440 AATATTTT
1 AATATTTT
225448 ATTTTCAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 3 0.10
8 4 0.14
9 22 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:225630 original size:2 final size:2
Alignment explanation
Indices: 225623--225648 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
225613 TGATTATGTC
225623 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
225649 CACACACATT
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:226220 original size:21 final size:20
Alignment explanation
Indices: 226176--226220 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
226166 AACGAAAAAT
*
226176 GAAG-GAAAAAATAAAGAAA
1 GAAGAGAAAAAAGAAAGAAA
*
226195 AAAGAGAAAGAAAGAAAGAAA
1 GAAGAGAAA-AAAGAAAGAAA
226216 GAAGA
1 GAAGA
226221 AGGAAGAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.19
21 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
GAAGAGAAAAAAGAAAGAAA
Found at i:226227 original size:18 final size:17
Alignment explanation
Indices: 226188--226247 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
226178 AGGAAAAAAT
226188 AAAGAAAAAAGAGAAAG
1 AAAGAAAAAAGAGAAAG
*
226205 AAAGAAAGAA-AG-AAG
1 AAAGAAAAAAGAGAAAG
* * * *
226220 AAGGAAGAAGGAGAAGG
1 AAAGAAAAAAGAGAAAG
*
226237 AAAAAAAAAAG
1 AAAGAAAAAAG
226248 GTAATGTGTT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
15 9 0.29
16 4 0.13
17 18 0.58
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAGAAAG
Done.