Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014928.1 Kokia drynarioides strain JFW-HI SEQ_129971, 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: 294720
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
Found at i:3341 original size:27 final size:27
Alignment explanation
Indices: 3303--3367 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
3293 TGCAAGTTGT
* *
3303 GTTCACTAGTTGGTTTGGAGAGCTAGA
1 GTTCACCAGTTGGTGTGGAGAGCTAGA
* *
3330 GTTCACCAGTT-GTGTGGAGCGCTAGG
1 GTTCACCAGTTGGTGTGGAGAGCTAGA
*
3356 GTTCTCCAGTTG
1 GTTCACCAGTTG
3368 AGTTGCGAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (27 bp):
GTTCACCAGTTGGTGTGGAGAGCTAGA
Found at i:6338 original size:32 final size:32
Alignment explanation
Indices: 6302--6391 Score: 76
Period size: 32 Copynumber: 3.1 Consensus size: 32
6292 AATTTAAGTG
6302 TTAATGGAGTGGTTAGTTAAGGCTAAAGGTGA
1 TTAATGGAGTGGTTAGTTAAGGCTAAAGGTGA
* *
6334 TTAATGTCA-TGG--AATT-----T-AA-GTG-
1 TTAATG-GAGTGGTTAGTTAAGGCTAAAGGTGA
6356 TTAATGGAGTGGTTAGTTAAGGCTAAAGGTGA
1 TTAATGGAGTGGTTAGTTAAGGCTAAAGGTGA
6388 TTAA
1 TTAA
6392 GGAAGCTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 24
0.60 0.06 0.34
Matches are distributed among these distances:
21 1 0.02
22 9 0.21
23 3 0.07
24 5 0.12
25 1 0.02
29 1 0.02
30 5 0.12
31 3 0.07
32 13 0.31
33 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (32 bp):
TTAATGGAGTGGTTAGTTAAGGCTAAAGGTGA
Found at i:6346 original size:54 final size:54
Alignment explanation
Indices: 6282--6391 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
6272 AAGATAGTGG
6282 AATGTCATGGAATTTAAGTGTTAATGGAGTGGTTAGTTAAGGCTAAAGGTGATT
1 AATGTCATGGAATTTAAGTGTTAATGGAGTGGTTAGTTAAGGCTAAAGGTGATT
6336 AATGTCATGGAATTTAAGTGTTAATGGAGTGGTTAGTTAAGGCTAAAGGTGATT
1 AATGTCATGGAATTTAAGTGTTAATGGAGTGGTTAGTTAAGGCTAAAGGTGATT
6390 AA
1 AA
6392 GGAAGCTTAA
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:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (54 bp):
AATGTCATGGAATTTAAGTGTTAATGGAGTGGTTAGTTAAGGCTAAAGGTGATT
Found at i:10724 original size:26 final size:26
Alignment explanation
Indices: 10695--10753 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
10685 TTTAGCTCAA
*
10695 ACGAGCCCAAACAGATTATCTCTCTT
1 ACGAGCCCAAACAGATTATCGCTCTT
10721 ACGAGCCCAAACAGATTATCGCTCTT
1 ACGAGCCCAAACAGATTATCGCTCTT
*
10747 ATGAGCC
1 ACGAGCC
10754 AGACAGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.24
Consensus pattern (26 bp):
ACGAGCCCAAACAGATTATCGCTCTT
Found at i:10769 original size:25 final size:25
Alignment explanation
Indices: 10741--10804 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
10731 ACAGATTATC
*
10741 GCTCTTATGAGCCAGACAGAATAA-T
1 GCTCTTATGAGCCAGACA-AAAAATT
* * *
10766 GCTCTTGTGAACCAGTCAAAAAATT
1 GCTCTTATGAGCCAGACAAAAAATT
10791 GCTCTTATGAGCCA
1 GCTCTTATGAGCCA
10805 AAATTCAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (25 bp):
GCTCTTATGAGCCAGACAAAAAATT
Found at i:12198 original size:24 final size:24
Alignment explanation
Indices: 12140--12192 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
12130 TGTACTTTGT
* *
12140 TATGAGAACCTATGTTATATGATG
1 TATGCGAACCTATGCTATATGATG
*
12164 TTTGCGAACCTATGCTATATGATG
1 TATGCGAACCTATGCTATATGATG
12188 TATGC
1 TATGC
12193 AGACCTTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (24 bp):
TATGCGAACCTATGCTATATGATG
Found at i:17107 original size:15 final size:16
Alignment explanation
Indices: 17082--17115 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17072 AGTGAGATGA
17082 AATTCGAATCGAATCG
1 AATTCGAATCGAATCG
*
17098 AATT-GAATCGAGTCG
1 AATTCGAATCGAATCG
17113 AAT
1 AAT
17116 ACTTTTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (16 bp):
AATTCGAATCGAATCG
Found at i:17261 original size:43 final size:43
Alignment explanation
Indices: 17190--17291 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 43
17180 GAACTAATGT
*
17190 AGAAGAAGAA-GAA--TGGAGGATTTTATTTAAGGA-TTTTGGA
1 AGAAGAAGAATGAATTTGGAGGATTTAATTT-AGGACTTTTGGA
*
17230 AGAAGAATGAATGAATTTGGA-GATTTAATTTAGGACTTTTTGA
1 AGAAGAA-GAATGAATTTGGAGGATTTAATTTAGGACTTTTGGA
*
17273 AGAAGAAGCATGAATTTGG
1 AGAAGAAGAATGAATTTGG
17292 GGGTTTGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
40 7 0.13
41 3 0.06
42 18 0.33
43 22 0.41
44 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.31
Consensus pattern (43 bp):
AGAAGAAGAATGAATTTGGAGGATTTAATTTAGGACTTTTGGA
Found at i:29493 original size:24 final size:24
Alignment explanation
Indices: 29466--29626 Score: 97
Period size: 24 Copynumber: 6.7 Consensus size: 24
29456 AAACGTATAT
*
29466 AAGCTAACGAGTGTAAATGTGTGC
1 AAGCTAACGAGCGTAAATGTGTGC
* * ** * **
29490 AAGCTGACGAGTGTAAACATATAT
1 AAGCTAACGAGCGTAAATGTGTGC
* *
29514 AAGCTAACAAGCGTAAAAGTGTGC
1 AAGCTAACGAGCGTAAATGTGTGC
* * **
29538 AAGCTGACGAGCGTAAATGTATAT
1 AAGCTAACGAGCGTAAATGTGTGC
* * * **
29562 AAGCTGACGAGCGTAAACGTATAT
1 AAGCTAACGAGCGTAAATGTGTGC
* * * * * *
29586 AAGATGACGAGAGTAAACGTATAC
1 AAGCTAACGAGCGTAAATGTGTGC
29610 AAGCTAACGAGCGTAAA
1 AAGCTAACGAGCGTAAA
29627 AAGTATACAA
Statistics
Matches: 110, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 110 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.20
Consensus pattern (24 bp):
AAGCTAACGAGCGTAAATGTGTGC
Found at i:29513 original size:48 final size:48
Alignment explanation
Indices: 29453--29641 Score: 225
Period size: 48 Copynumber: 3.9 Consensus size: 48
29443 ATATGTAAAA
* *
29453 TGTAAACGTATATAAGCTAACGAGTGTAAATGTGTGCAAGCTGACGAG
1 TGTAAACGTATATAAGCTAACGAGCGTAAAAGTGTGCAAGCTGACGAG
* *
29501 TGTAAACATATATAAGCTAACAAGCGTAAAAGTGTGCAAGCTGACGAG
1 TGTAAACGTATATAAGCTAACGAGCGTAAAAGTGTGCAAGCTGACGAG
* * * * * ** *
29549 CGTAAATGTATATAAGCTGACGAGCGTAAACGTATATAAGATGACGAG
1 TGTAAACGTATATAAGCTAACGAGCGTAAAAGTGTGCAAGCTGACGAG
* * * *
29597 AGTAAACGTATACAAGCTAACGAGCGTAAAAAGTATACAAGCTGA
1 TGTAAACGTATATAAGCTAACGAGCGT-AAAAGTGTGCAAGCTGA
29642 TAACAGTAAA
Statistics
Matches: 119, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 105 0.88
49 14 0.12
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22
Consensus pattern (48 bp):
TGTAAACGTATATAAGCTAACGAGCGTAAAAGTGTGCAAGCTGACGAG
Found at i:29571 original size:72 final size:72
Alignment explanation
Indices: 29454--29641 Score: 214
Period size: 72 Copynumber: 2.6 Consensus size: 72
29444 TATGTAAAAT
* * * * * * *
29454 GTAAACGTATATAAGCTAACGAGTGTAAATGTGTGCAAGCTGACGAGTGTAAACATATATAAGCT
1 GTAAAAGTATACAAGCTAACGAGCGTAAATGTATACAAGCTGACGAGCGTAAACATATATAAGAT
*
29519 AACAAGC
66 AACAAGA
* * * * *
29526 GTAAAAGTGTGCAAGCTGACGAGCGTAAATGTATATAAGCTGACGAGCGTAAACGTATATAAGAT
1 GTAAAAGTATACAAGCTAACGAGCGTAAATGTATACAAGCTGACGAGCGTAAACATATATAAGAT
* *
29591 GACGAGA
66 AACAAGA
* *
29598 GTAAACGTATACAAGCTAACGAGCGTAAAAAGTATACAAGCTGA
1 GTAAAAGTATACAAGCTAACGAGCGT-AAATGTATACAAGCTGA
29642 TAACAGTAAA
Statistics
Matches: 94, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
72 79 0.84
73 15 0.16
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (72 bp):
GTAAAAGTATACAAGCTAACGAGCGTAAATGTATACAAGCTGACGAGCGTAAACATATATAAGAT
AACAAGA
Found at i:30326 original size:21 final size:21
Alignment explanation
Indices: 30302--30355 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
30292 GAAGTATGGG
30302 TTGTATCGGTAGTACCTATAC
1 TTGTATCGGTAGTACCTATAC
30323 TTGTATCGGTAGTACCTATAC
1 TTGTATCGGTAGTACCTATAC
*
30344 TTGTATCAGTAG
1 TTGTATCGGTAG
30356 AACTTCCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGTATCGGTAGTACCTATAC
Found at i:40940 original size:13 final size:13
Alignment explanation
Indices: 40922--40947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40912 CCATTTAATT
40922 CTATATTGTTCAA
1 CTATATTGTTCAA
40935 CTATATTGTTCAA
1 CTATATTGTTCAA
40948 GCATTTGTGG
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:0.08, T:0.46
Consensus pattern (13 bp):
CTATATTGTTCAA
Found at i:46191 original size:45 final size:45
Alignment explanation
Indices: 46127--46252 Score: 191
Period size: 44 Copynumber: 2.8 Consensus size: 45
46117 CTAGTTACAA
* *
46127 ACAAGCAGCCATGTAGGTTGTGGACGAAGCAACCAATATTCGTAG
1 ACAAGCAGCCATGTAGGTTGTGGACGAAGCCACCAATATTCGCAG
* *
46172 ACAAGCAGCCATGTAGGTTGTGGA-TAAACCACCAATATTCGCAG
1 ACAAGCAGCCATGTAGGTTGTGGACGAAGCCACCAATATTCGCAG
* *
46216 ACAAGCTGCCATGTAGGTTGTGAACGAAGCCACCAAT
1 ACAAGCAGCCATGTAGGTTGTGGACGAAGCCACCAAT
46253 TCTTCCTCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 38 0.53
45 34 0.47
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (45 bp):
ACAAGCAGCCATGTAGGTTGTGGACGAAGCCACCAATATTCGCAG
Found at i:56153 original size:21 final size:22
Alignment explanation
Indices: 56109--56156 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
56099 TCAGCATTTG
* *
56109 GTATCGATACTTCTTTTGAAAA
1 GTATCGATACTTCATTTAAAAA
56131 GTATCGATA-TTCATTTAAAAA
1 GTATCGATACTTCATTTAAAAA
56152 GTATC
1 GTATC
56157 AAAAATTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
GTATCGATACTTCATTTAAAAA
Found at i:62706 original size:27 final size:27
Alignment explanation
Indices: 62676--62731 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
62666 GGAGAGAAGA
62676 TAGAACCATTATTAAATTGTAAAAGTT
1 TAGAACCATTATTAAATTGTAAAAGTT
62703 TAGAACCATTATTAAATTGTAAAAGTT
1 TAGAACCATTATTAAATTGTAAAAGTT
62730 TA
1 TA
62732 TTTTAAGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (27 bp):
TAGAACCATTATTAAATTGTAAAAGTT
Found at i:63215 original size:57 final size:58
Alignment explanation
Indices: 63143--63269 Score: 168
Period size: 57 Copynumber: 2.2 Consensus size: 58
63133 TTTTAGGACG
* * *
63143 TTTTCATTTTTATTTTGGAGAAAACCATATTAATTTTCAAAT-TATTC-CATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCATAATAATTTCCAAATGT-TTCTCATTTCTCCA
* *
63200 TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTTATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCATAATAATTTCCAAATGTTTCTCATTTCTCCA
*
63258 TTTCTCCTTTTC
1 TTT-TCATTTTC
63270 TATTCATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
57 41 0.67
58 13 0.21
59 7 0.11
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.50
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGGAGAAAACCATAATAATTTCCAAATGTTTCTCATTTCTCCA
Found at i:65375 original size:26 final size:26
Alignment explanation
Indices: 65345--65399 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
65335 ACAAATATCA
* *
65345 ATTTCGTATATTTATTTCATATAAAC
1 ATTTCGTATAATAATTTCATATAAAC
* *
65371 ATTTCGTATAATAATTTTATCTAAAC
1 ATTTCGTATAATAATTTCATATAAAC
65397 ATT
1 ATT
65400 ACATTTTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (26 bp):
ATTTCGTATAATAATTTCATATAAAC
Found at i:65817 original size:2 final size:2
Alignment explanation
Indices: 65810--65835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65800 ATCTCAATTC
65810 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
65836 TAAATAATCA
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:72991 original size:15 final size:15
Alignment explanation
Indices: 72971--73000 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
72961 AAGGGGATTT
*
72971 GTAAAATAAAAGGGA
1 GTAAAAAAAAAGGGA
72986 GTAAAAAAAAAGGGA
1 GTAAAAAAAAAGGGA
73001 CATAAAAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (15 bp):
GTAAAAAAAAAGGGA
Found at i:75889 original size:30 final size:30
Alignment explanation
Indices: 75853--75913 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
75843 GAGGTAGCTC
75853 AACTTTCATCTCTTCAAACCACATAAGATG
1 AACTTTCATCTCTTCAAACCACATAAGATG
75883 AACTTTCATCTCTTCAAACCACATAAGATG
1 AACTTTCATCTCTTCAAACCACATAAGATG
75913 A
1 A
75914 CGTCTACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.30
Consensus pattern (30 bp):
AACTTTCATCTCTTCAAACCACATAAGATG
Found at i:84870 original size:9 final size:9
Alignment explanation
Indices: 84856--84897 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
84846 GAATAGCATA
84856 AAAAGAAAT
1 AAAAGAAAT
*
84865 AAAAGAAGT
1 AAAAGAAAT
84874 AAAAAGAAAT
1 -AAAAGAAAT
*
84884 AAAAGAAGT
1 AAAAGAAAT
84893 AAAAG
1 AAAAG
84898 TTGAGATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (9 bp):
AAAAGAAAT
Found at i:84878 original size:19 final size:19
Alignment explanation
Indices: 84854--84896 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
84844 GTGAATAGCA
84854 TAAAAAGAAATAAAAGAAG
1 TAAAAAGAAATAAAAGAAG
84873 TAAAAAGAAATAAAAGAAG
1 TAAAAAGAAATAAAAGAAG
84892 TAAAA
1 TAAAA
84897 GTTGAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (19 bp):
TAAAAAGAAATAAAAGAAG
Found at i:88918 original size:53 final size:53
Alignment explanation
Indices: 88861--89104 Score: 210
Period size: 53 Copynumber: 4.6 Consensus size: 53
88851 ATCCATGTAT
* * *
88861 CTCACGATGACACAAAGTCATCGGACCCTTAATCCGT-AGTAGGATCCATATAA
1 CTCACGATGACACAAAGTCATCGGACCTTTAATCCATGA-TAGGATTCATATAA
* * *
88914 CTCAC-AGTGACACATAGTTATCGAACCTTTAATCCATGATAGGATTCATATAA
1 CTCACGA-TGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCATATAA
** * * * * *** **
88967 CTCAAAATAAAATAGAGTCATCGGACCTTTAATATGTGATACAATTCATATAA
1 CTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCATATAA
* * * ** *
89020 CTGATGATGGCACAAGAGTCATCAAACC-TTAATCCATGATAAGATTCATATAA
1 CTCACGATGACACAA-AGTCATCGGACCTTTAATCCATGATAGGATTCATATAA
*
89073 CTCACGATGACAC--AGTCATCAGACCTTTAATC
1 CTCACGATGACACAAAGTCATCGGACCTTTAATC
89105 TTTGGCACAA
Statistics
Matches: 149, Mismatches: 37, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
50 11 0.07
51 6 0.04
52 1 0.01
53 119 0.80
54 12 0.08
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (53 bp):
CTCACGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCATATAA
Found at i:95980 original size:18 final size:18
Alignment explanation
Indices: 95959--95993 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
95949 ACACCTTCGG
*
95959 TAAGGCCTCCACCTCCTA
1 TAAGACCTCCACCTCCTA
*
95977 TAAGACCTTCACCTCCT
1 TAAGACCTCCACCTCCT
95994 CCTGTGATAG
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:0.23, C:0.43, G:0.09, T:0.26
Consensus pattern (18 bp):
TAAGACCTCCACCTCCTA
Found at i:98922 original size:24 final size:24
Alignment explanation
Indices: 98890--98988 Score: 108
Period size: 24 Copynumber: 4.1 Consensus size: 24
98880 GTATACTAGT
*
98890 TAACTATTCTAGGCTCATAAGAGC
1 TAACCATTCTAGGCTCATAAGAGC
* * *
98914 TAACCATTCTGGGCTCGTAAGAGG
1 TAACCATTCTAGGCTCATAAGAGC
* * * *
98938 TAACCATTTTGGGCACGTAAGAGC
1 TAACCATTCTAGGCTCATAAGAGC
* *
98962 TAACCATCCTAGGCTCATCAGAGC
1 TAACCATTCTAGGCTCATAAGAGC
98986 TAA
1 TAA
98989 TGTTATCTGT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (24 bp):
TAACCATTCTAGGCTCATAAGAGC
Found at i:101746 original size:50 final size:50
Alignment explanation
Indices: 101654--101788 Score: 130
Period size: 50 Copynumber: 2.7 Consensus size: 50
101644 TAAGGAGGAA
* * *
101654 GTATCTGGCAGTAAATCT-TCAAATATTTAGTGGCATGCCCACA-TATTTCT
1 GTATCTGGCAGTAAATCTAT-AAATATTTGGTGGCATGACCACACTA-ATCT
* ** *
101704 GTATCTGGCAGTAGATCTATAAATATTTGGTGGTTTTACCACACTAATCT
1 GTATCTGGCAGTAAATCTATAAATATTTGGTGGCATGACCACACTAATCT
* * * * *
101754 ATTTCTGGCAGTAAATATACAATTATTTGGTGGCA
1 GTATCTGGCAGTAAATCTATAAATATTTGGTGGCA
101789 ATCCCGCAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
50 65 0.96
51 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (50 bp):
GTATCTGGCAGTAAATCTATAAATATTTGGTGGCATGACCACACTAATCT
Found at i:117117 original size:3 final size:3
Alignment explanation
Indices: 117109--117143 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
117099 AAAATTCAAA
117109 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
117144 AAGAGAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:136039 original size:24 final size:23
Alignment explanation
Indices: 136009--136084 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
135999 GACTTTCAAT
136009 TTCTTCACTGATAGCTTATCTGAA
1 TTCTTCACTG-TAGCTTATCTGAA
* * *
136033 TTCTTCA--G--GCATTTTGTCAA
1 TTCTTCACTGTAGC-TTATCTGAA
136053 TTTCTTCACTGGTAGCTTATCTGAA
1 -TTCTTCACT-GTAGCTTATCTGAA
136078 TTCTTCA
1 TTCTTCA
136085 GGCATTTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 7 0.18
22 1 0.03
24 15 0.38
25 6 0.15
26 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (23 bp):
TTCTTCACTGTAGCTTATCTGAA
Found at i:136069 original size:45 final size:45
Alignment explanation
Indices: 136004--136094 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
135994 TACAGGACTT
136004 TCAATTTCTTCACTGATAGCTTATCTGAATTCTTCAGGCATTTTG
1 TCAATTTCTTCACTGATAGCTTATCTGAATTCTTCAGGCATTTTG
*
136049 TCAATTTCTTCACTGGTAGCTTATCTGAATTCTTCAGGCATTTTG
1 TCAATTTCTTCACTGATAGCTTATCTGAATTCTTCAGGCATTTTG
136094 T
1 T
136095 TAACACTACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (45 bp):
TCAATTTCTTCACTGATAGCTTATCTGAATTCTTCAGGCATTTTG
Found at i:140697 original size:2 final size:2
Alignment explanation
Indices: 140690--140721 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
140680 CTATACATAC
140690 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
140722 TCTTTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151707 original size:17 final size:17
Alignment explanation
Indices: 151677--151717 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
151667 AAACTAAAAG
151677 GAATGCAGTGACAATTAA
1 GAATGCAGTGACAA-TAA
151695 -AATGCAG-GCACAATAA
1 GAATGCAGTG-ACAATAA
151711 GAATGCA
1 GAATGCA
151718 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (17 bp):
GAATGCAGTGACAATAA
Found at i:158875 original size:6 final size:6
Alignment explanation
Indices: 158864--159002 Score: 153
Period size: 6 Copynumber: 23.3 Consensus size: 6
158854 AATTAGTACA
* *
158864 TTTATT TTTATT TTCATT TTCA-T TTTATT TTTCATT TTTATT TTTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTT-ATT TTTATT TTT-ATT
* *
158913 TTTCA-T TTT-TT TTCATT TTTCTT TTTATT TTTATT TTTATT TTTATT
1 TTT-ATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
158960 TTTATT TTTATT TTT-TGT TTTA-T TTTATT TATAAT TTTATT TT
1 TTTATT TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TT
159003 ATTATGCACT
Statistics
Matches: 115, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
5 13 0.11
6 88 0.77
7 14 0.12
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:165256 original size:8 final size:8
Alignment explanation
Indices: 165245--165269 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
165235 TACATGTACG
165245 TATGTATA
1 TATGTATA
165253 TATGTATA
1 TATGTATA
165261 TATGTATA
1 TATGTATA
165269 T
1 T
165270 TTATTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:166815 original size:20 final size:20
Alignment explanation
Indices: 166792--166840 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
166782 TGAGTTTTAC
166792 TATCAAAATATGCATTTTGA
1 TATCAAAATATGCATTTTGA
166812 TATCAAAATATGCATTTTGA
1 TATCAAAATATGCATTTTGA
166832 TATCAAAAT
1 TATCAAAAT
166841 TGTAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (20 bp):
TATCAAAATATGCATTTTGA
Found at i:176121 original size:11 final size:11
Alignment explanation
Indices: 176102--176142 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
176092 TGATGATTTT
*
176102 AATACTTTTAA
1 AATAATTTTAA
176113 AATAATTTTAA
1 AATAATTTTAA
176124 AATAATTTT--
1 AATAATTTTAA
176133 AATAATTTTA
1 AATAATTTTA
176143 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.32
11 19 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
AATAATTTTAA
Found at i:184892 original size:12 final size:13
Alignment explanation
Indices: 184875--184907 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
184865 ATCTTTTGCC
184875 TTTATTTTCTA-T
1 TTTATTTTCTATT
184887 TTTATTTTCTATT
1 TTTATTTTCTATT
184900 TTTATTTT
1 TTTATTTT
184908 TATGCTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTCTATT
Found at i:191025 original size:7 final size:7
Alignment explanation
Indices: 191013--191093 Score: 64
Period size: 7 Copynumber: 12.1 Consensus size: 7
191003 AAAAGTGAAC
191013 GGTCAAT
1 GGTCAAT
191020 GGTCAA-
1 GGTCAAT
*
191026 GGTCAAC
1 GGTCAAT
191033 GGTCAAT
1 GGTCAAT
191040 GGTCAA-
1 GGTCAAT
*
191046 AGTC-AT
1 GGTCAAT
191052 GGTCAA-
1 GGTCAAT
*
191058 GGTCAAC
1 GGTCAAT
* *
191065 GATCAAC
1 GGTCAAT
191072 GAGTCAA-
1 G-GTCAAT
*
191079 AGTCAAT
1 GGTCAAT
191086 GGTCAAT
1 GGTCAAT
191093 G
1 G
191094 AGTCGGTAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
5 1 0.02
6 23 0.38
7 33 0.54
8 4 0.07
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (7 bp):
GGTCAAT
Found at i:191059 original size:32 final size:34
Alignment explanation
Indices: 191014--191091 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 34
191004 AAAGTGAACG
* *
191014 GTCAATGGTCAAGGTCAACGGTCAATG-GTCAAA
1 GTCAATGGTCAAGGTCAACGATCAACGAGTCAAA
191047 GTC-ATGGTCAAGGTCAACGATCAACGAGTCAAA
1 GTCAATGGTCAAGGTCAACGATCAACGAGTCAAA
191080 GTCAATGGTCAA
1 GTCAATGGTCAA
191092 TGAGTCGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 21 0.51
33 12 0.29
34 8 0.20
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (34 bp):
GTCAATGGTCAAGGTCAACGATCAACGAGTCAAA
Found at i:192533 original size:16 final size:16
Alignment explanation
Indices: 192504--192550 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
192494 ATCTTCTTCG
192504 AATCCCTAAAATATTAA
1 AATCCCT-AAATATTAA
*
192521 AATCCCTAAATATCAA
1 AATCCCTAAATATTAA
*
192537 AATCCCCAAATATT
1 AATCCCTAAATATT
192551 TGAATCCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (16 bp):
AATCCCTAAATATTAA
Found at i:193491 original size:32 final size:32
Alignment explanation
Indices: 193425--193568 Score: 121
Period size: 33 Copynumber: 4.4 Consensus size: 32
193415 AGTTAACTGC
* **
193425 TGGGGAGGGTGATGATGAAGTTATAGAAGTTGA
1 TGGGGAAGGTGATGATGAAG-GGTAGAAGTTGA
*
193458 TGGGGAGGGTGATGATGAAGGGTAGAA-TCTGA
1 TGGGGAAGGTGATGATGAAGGGTAGAAGT-TGA
* ** *
193490 TGGTGAAGGTGATTTTGAAAGGGTAGAAGTTGT
1 TGGGGAAGGTGATGATG-AAGGGTAGAAGTTGA
* * * *
193523 TGAGGAAGGTGATGTAGGAGGGGTAGAAGCTGA
1 TGGGGAAGGTGATG-ATGAAGGGTAGAAGTTGA
*
193556 TGTGG-AGGTGATG
1 TGGGGAAGGTGATG
193569 TAGGAGGGTT
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
31 1 0.01
32 29 0.32
33 59 0.65
34 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.45, T:0.26
Consensus pattern (32 bp):
TGGGGAAGGTGATGATGAAGGGTAGAAGTTGA
Found at i:193738 original size:51 final size:51
Alignment explanation
Indices: 193615--193730 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
193605 AAGTTGCTGT
* * * *
193615 TGATGAATATGCTGCTGATTTTGCATCATTAGATGGAGGGCATAATATTGC
1 TGATGAATATGCTGCTAATTTTGCATCATCAGATAGAGGGCATAATATTAC
* * * *
193666 TAATGAATATGATGCTAATTTTGCATCCTCAGATAGAGTGG-ATAATGTTAC
1 TGATGAATATGCTGCTAATTTTGCATCATCAGATAGAG-GGCATAATATTAC
193717 TGATGAATATGCTG
1 TGATGAATATGCTG
193731 TTTATTTTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 52 0.96
52 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (51 bp):
TGATGAATATGCTGCTAATTTTGCATCATCAGATAGAGGGCATAATATTAC
Found at i:198056 original size:15 final size:15
Alignment explanation
Indices: 198036--198069 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
198026 TTTTTGGAAT
*
198036 GATTAGGGATTTCAC
1 GATTAGAGATTTCAC
*
198051 GATTAGAGATTTCAT
1 GATTAGAGATTTCAC
198066 GATT
1 GATT
198070 TTAGTTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (15 bp):
GATTAGAGATTTCAC
Found at i:204217 original size:32 final size:31
Alignment explanation
Indices: 204117--204222 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 31
204107 CATAAAAGAG
* * *
204117 GATTCGTAGATATGACGAACATCATACATGC
1 GATTCATAGATATGGCAAACATCATACATGC
* *
204148 GAATTCATAGATAAGG-AAGACATCATACATGTG
1 G-ATTCATAGATATGGCAA-ACATCATACATG-C
*
204181 GATTCATAGATATGGCAAACATCATGCATGC
1 GATTCATAGATATGGCAAACATCATACATGC
*
204212 AGATTCGTAGA
1 -GATTCATAGA
204223 AGAGGATTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
31 2 0.03
32 56 0.92
33 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (31 bp):
GATTCATAGATATGGCAAACATCATACATGC
Found at i:204233 original size:46 final size:46
Alignment explanation
Indices: 204180--204268 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
204170 TCATACATGT
* *
204180 GGATTCATAGATATGGCAAACATCATGCATGCAGATTCGTAGAAGA
1 GGATTCATAGATATGGCAAACATCATACATGCAGATTCATAGAAGA
* *
204226 GGATTCATAGATGTGGCGAACATCATACATGCAGATTCATAGA
1 GGATTCATAGATATGGCAAACATCATACATGCAGATTCATAGA
204269 TAAGGCAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (46 bp):
GGATTCATAGATATGGCAAACATCATACATGCAGATTCATAGAAGA
Found at i:212950 original size:6 final size:6
Alignment explanation
Indices: 212939--212977 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
212929 TGATCAAAAT
* * *
212939 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
212978 TATGAATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:218912 original size:5 final size:5
Alignment explanation
Indices: 218902--218954 Score: 78
Period size: 5 Copynumber: 11.4 Consensus size: 5
218892 CTCAAGTAGT
218902 AAATA AAATA AAATA AAAT- AAAT- AAATA AAATA AAAT- AAAT- AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
218948 AAATA AA
1 AAATA AA
218955 GAAAGAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 16 0.35
5 30 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:218927 original size:23 final size:22
Alignment explanation
Indices: 218901--218954 Score: 90
Period size: 23 Copynumber: 2.4 Consensus size: 22
218891 TCTCAAGTAG
218901 TAAATAAAATAAAATAAAATAAA
1 TAAATAAAATAAAAT-AAATAAA
218924 TAAATAAAATAAAATAAATAAA
1 TAAATAAAATAAAATAAATAAA
218946 TAAAATAAA
1 T-AAATAAA
218955 GAAAGAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAATAAAATAAAATAAATAAA
Found at i:218930 original size:18 final size:18
Alignment explanation
Indices: 218901--218954 Score: 99
Period size: 18 Copynumber: 2.9 Consensus size: 18
218891 TCTCAAGTAG
218901 TAAATAAAATAAAATAAAA
1 TAAAT-AAATAAAATAAAA
218920 TAAATAAATAAAATAAAA
1 TAAATAAATAAAATAAAA
218938 TAAATAAATAAAATAAA
1 TAAATAAATAAAATAAA
218955 GAAAGAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 30 0.86
19 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAATAAATAAAATAAAA
Found at i:223652 original size:15 final size:15
Alignment explanation
Indices: 223626--223665 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
223616 TTTTCTTTTC
223626 TTTTCTTCTTTTCCCT
1 TTTTCTT-TTTTCCCT
*
223642 TTTTCTTTTTTCTCT
1 TTTTCTTTTTTCCCT
223657 TTTT-TTTTT
1 TTTTCTTTTT
223666 ATATATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 11 0.48
16 7 0.30
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTCCCT
Found at i:223665 original size:13 final size:13
Alignment explanation
Indices: 223615--223664 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
223605 TATATATATA
223615 TTTTTCTTTTCT-
1 TTTTTCTTTTCTC
*
223627 TTTCTTCTTTTCCC
1 TTT-TTCTTTTCTC
223641 TTTTTCTTTTTTCTC
1 TTTTTC--TTTTCTC
223656 TTTTT-TTTT
1 TTTTTCTTTT
223665 TATATATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 7 0.22
13 11 0.34
14 3 0.09
15 11 0.34
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:224071 original size:22 final size:22
Alignment explanation
Indices: 224044--224087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
224034 CATATGATTC
224044 AAAAATT-AAGCATCAAATGCAA
1 AAAAATTCAAGCA-CAAATGCAA
*
224066 AAAAATTCAAGCACAATTGCAA
1 AAAAATTCAAGCACAAATGCAA
224088 TAATCTGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.16, G:0.09, T:0.18
Consensus pattern (22 bp):
AAAAATTCAAGCACAAATGCAA
Found at i:224252 original size:17 final size:17
Alignment explanation
Indices: 224222--224279 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
224212 TAATTTACAG
*
224222 TGACAAATGGAAATGCAA
1 TGAC-AATGAAAATGCAA
* *
224240 TGACAATGCAAATGCAG
1 TGACAATGAAAATGCAA
224257 TGACAACT-AAAATGCAA
1 TGACAA-TGAAAATGCAA
224274 TGACAA
1 TGACAA
224280 AGGGGATGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 30 0.86
18 5 0.14
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (17 bp):
TGACAATGAAAATGCAA
Found at i:224823 original size:37 final size:37
Alignment explanation
Indices: 224779--224858 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
224769 AATATTCTGG
* * *
224779 AATGCATCCAAGATTTTCCCTGCATAAATATTCTTCA
1 AATGCATCCAAGACTATCACTGCATAAATATTCTTCA
* *
224816 AATGCATCCAGGACTATCACTGCATAAGTATTCTTCA
1 AATGCATCCAAGACTATCACTGCATAAATATTCTTCA
*
224853 ATTGCA
1 AATGCA
224859 CCTATGAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (37 bp):
AATGCATCCAAGACTATCACTGCATAAATATTCTTCA
Found at i:225734 original size:16 final size:16
Alignment explanation
Indices: 225713--225743 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
225703 TTGTGGATCC
225713 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
225729 CATTTTATCTTTATT
1 CATTTTACCTTTATT
225744 TTCACATAAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:228590 original size:17 final size:17
Alignment explanation
Indices: 228576--228623 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
228566 CACATTTTTT
228576 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTTAA
* *
228593 TTGTCACTGCA-TCTACA
1 TTGTCATTGCATTTTA-A
228610 TTGTCATTGCATTT
1 TTGTCATTGCATTT
228624 CTAGATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 3 0.12
17 21 0.84
18 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (17 bp):
TTGTCATTGCATTTTAA
Found at i:234139 original size:289 final size:289
Alignment explanation
Indices: 233625--234348 Score: 966
Period size: 289 Copynumber: 2.5 Consensus size: 289
233615 ACCGCGCGAG
* * * * * * *
233625 TCATTTATATTCGATCACTACCTCCCTTGACGGAATCCAACAAGCTTTTTCCAATTAAACATGCC
1 TCATTTAAATTCAATCATTACCTCCCTTGATGGAATCCAACTAGCTTTTTCCAATTGAACACGCC
* *
233690 AATTTGTTTGTGAGAATTTGAACTTGGTAGACGATCGTCTCATTTTCCTAACTATACACCAAACA
66 AATTTGTTCGTGAGAATTCGAACTTGGTAGACGATCGTCTCATTTTCCTAACTATACACCAAACA
* **
233755 ACTCCAACCCAACTTTTCCTTATGTAGTCGATTCTTGTACGACCTGCAAACCGACCCTTGATGAA
131 ACTCCAACCCAACTTTTCCTTATGTAGTCGATTCTTGTACGACCTACAAACCGACCCTTGACAAA
*
233820 TTTCTAACCACATAACTTGTGTTCGTAATTTAAGATTTCGGTAGCCTTGCGATCTTGAAAGCCCA
196 TTTCTAACCACATAACTTGTGTTCGTAATTTAAGATTTCGGTAGCCTTGCGATCTGGAAAGCCCA
* * ***
233885 ACTCGAATTAACGGCCACAACCGCGTTGA
261 ACTCAAATTAACAGCCACAACCGCACAGA
* *
233914 TCATTTAAATTCAATTATTACCTCCCTTGATTGAATCCAACTAGCTTTTTCCAATTGAACACGCC
1 TCATTTAAATTCAATCATTACCTCCCTTGATGGAATCCAACTAGCTTTTTCCAATTGAACACGCC
* * * * * * * *
233979 AATTTGTTCATGGGAATTCGAACTCGGTAGACGATCGTCAT-GTTTTCCTGACTGTACGCCAAAT
66 AATTTGTTCGTGAGAATTCGAACTTGGTAGACGATCGTC-TCATTTTCCTAACTATACACCAAAC
* * * *
234043 AACTCCAACCCAACTTTTCCTTGTGTAGTCGATTCTTGTACGACCTACAAGCTGACCCTTGGCAA
130 AACTCCAACCCAACTTTTCCTTATGTAGTCGATTCTTGTACGACCTACAAACCGACCCTTGACAA
* *
234108 ATTTCTAACCACGTAACTTGTG-TCTGTAATTTAAGATTTTGGTAGCCTTGCGATCTGGAAAGCC
195 ATTTCTAACCACATAACTTGTGTTC-GTAATTTAAGATTTCGGTAGCCTTGCGATCTGGAAAGCC
* *
234172 CAACTCAAATTAACAGCCTCAACCGCACAGG
259 CAACTCAAATTAACAGCCACAACCGCACAGA
* * *
234203 TCATTTAAATTCAATCATTACCTCCCTTGATGGAATCGAACTAGATTTTTCCAATTGAACACGCA
1 TCATTTAAATTCAATCATTACCTCCCTTGATGGAATCCAACTAGCTTTTTCCAATTGAACACGCC
** * * * * * * **
234268 AATTTGTTCGCAAGAATTCGAACTTGGTAGACGACCATCTCAATTTCCCAATTGTACGTCAAACA
66 AATTTGTTCGTGAGAATTCGAACTTGGTAGACGATCGTCTCATTTTCCTAACTATACACCAAACA
*
234333 ACTCCAACCTAACTTT
131 ACTCCAACCCAACTTT
234349 CAAAGCAAAT
Statistics
Matches: 376, Mismatches: 56, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
288 3 0.01
289 372 0.99
290 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (289 bp):
TCATTTAAATTCAATCATTACCTCCCTTGATGGAATCCAACTAGCTTTTTCCAATTGAACACGCC
AATTTGTTCGTGAGAATTCGAACTTGGTAGACGATCGTCTCATTTTCCTAACTATACACCAAACA
ACTCCAACCCAACTTTTCCTTATGTAGTCGATTCTTGTACGACCTACAAACCGACCCTTGACAAA
TTTCTAACCACATAACTTGTGTTCGTAATTTAAGATTTCGGTAGCCTTGCGATCTGGAAAGCCCA
ACTCAAATTAACAGCCACAACCGCACAGA
Found at i:243909 original size:21 final size:21
Alignment explanation
Indices: 243880--243919 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
243870 GGAGGAAATG
*
243880 CAAGTGGAA-GAAGAAGAAGAA
1 CAAGAGGAAGGAA-AAGAAGAA
243901 CAAGAGGAAGGAAAAGAAG
1 CAAGAGGAAGGAAAAGAAG
243920 TTGAGGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.57, C:0.05, G:0.35, T:0.03
Consensus pattern (21 bp):
CAAGAGGAAGGAAAAGAAGAA
Found at i:244225 original size:21 final size:19
Alignment explanation
Indices: 244175--244225 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
244165 AAAAAAGAAA
* *
244175 AAGGAAGCGCACCAAGGAT
1 AAGGAAGCGCAACAAGGAG
*
244194 AA-GAAGAGCAACAAGGAAG
1 AAGGAAGCGCAACAAGG-AG
244213 AGAGGAAGCGCAA
1 A-AGGAAGCGCAA
244226 GAAGCAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 12 0.48
19 4 0.16
20 1 0.04
21 8 0.32
ACGTcount: A:0.49, C:0.16, G:0.33, T:0.02
Consensus pattern (19 bp):
AAGGAAGCGCAACAAGGAG
Found at i:244372 original size:17 final size:17
Alignment explanation
Indices: 244340--244406 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
244330 CTGTTAGTAA
**
244340 TCATTGTCATCACATTC
1 TCATTGTCATTGCATTC
244357 TCATTGTCATTGCATT-
1 TCATTGTCATTGCATTC
* *
244373 TTATTTGTCACTGCATTC
1 TCA-TTGTCATTGCATTC
*
244391 GCATTGTCATTGCATT
1 TCATTGTCATTGCATT
244407 TCCATTTGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
16 2 0.05
17 38 0.93
18 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.46
Consensus pattern (17 bp):
TCATTGTCATTGCATTC
Found at i:244381 original size:34 final size:35
Alignment explanation
Indices: 244343--244416 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
244333 TTAGTAATCA
* *
244343 TTGTCA-TCACATTCTCATTGTCATTGCATTT-TAT
1 TTGTCACT-ACATTCGCATTGTCATTGCATTTCCAT
*
244377 TTGTCACTGCATTCGCATTGTCATTGCATTTCCAT
1 TTGTCACTACATTCGCATTGTCATTGCATTTCCAT
244412 TTGTC
1 TTGTC
244417 TTTGTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 27 0.77
35 8 0.23
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (35 bp):
TTGTCACTACATTCGCATTGTCATTGCATTTCCAT
Found at i:244412 original size:17 final size:17
Alignment explanation
Indices: 244358--244412 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
244348 ATCACATTCT
244358 CATTGTCATTGCATTT-
1 CATTGTCATTGCATTTC
* *
244374 TATTTGTCACTGCA-TTC
1 CA-TTGTCATTGCATTTC
244391 GCATTGTCATTGCATTTC
1 -CATTGTCATTGCATTTC
244409 CATT
1 CATT
244413 TGTCTTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
16 3 0.10
17 24 0.77
18 4 0.13
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:249478 original size:21 final size:22
Alignment explanation
Indices: 249452--249493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
249442 AATCAAAAAG
249452 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
249473 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
249494 ACATATAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:254025 original size:26 final size:26
Alignment explanation
Indices: 253995--254044 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
253985 AACACATAAG
*
253995 TATGAATAACTAAGATTGCAACTTAA
1 TATGAATAACTAAAATTGCAACTTAA
254021 TATGAATAACTAAAATTGCAACTT
1 TATGAATAACTAAAATTGCAACTT
254045 CATCAAAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (26 bp):
TATGAATAACTAAAATTGCAACTTAA
Found at i:255120 original size:15 final size:15
Alignment explanation
Indices: 255072--255121 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
255062 CTTCAGCTAA
*
255072 TTCTTTCTTAACATC
1 TTCTTTCTCAACATC
* *
255087 TTTTTTCTCAACATT
1 TTCTTTCTCAACATC
*
255102 TTCTTTCTCGACATC
1 TTCTTTCTCAACATC
255117 TTCTT
1 TTCTT
255122 CTTTATCGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.16, C:0.26, G:0.02, T:0.56
Consensus pattern (15 bp):
TTCTTTCTCAACATC
Found at i:255813 original size:24 final size:24
Alignment explanation
Indices: 255780--255825 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
255770 GTTAAGAGTA
*
255780 AAAATTGTTAGTGCAAATGTAATAT
1 AAAATTGTTAGAGCAAAT-TAATAT
255805 AAAA-TGTTAGAGCAAATTAAT
1 AAAATTGTTAGAGCAAATTAAT
255826 GAAAGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (24 bp):
AAAATTGTTAGAGCAAATTAATAT
Found at i:257377 original size:2 final size:2
Alignment explanation
Indices: 257364--257393 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
257354 TTGTATAATA
*
257364 AT AT AC 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
257394 TTCATAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:258041 original size:16 final size:16
Alignment explanation
Indices: 258020--258054 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
258010 TATGAAAACA
258020 AATAAAATGCAAGGAC
1 AATAAAATGCAAGGAC
*
258036 AATAAAATGCAATGAC
1 AATAAAATGCAAGGAC
258052 AAT
1 AAT
258055 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.17
Consensus pattern (16 bp):
AATAAAATGCAAGGAC
Found at i:258991 original size:7 final size:7
Alignment explanation
Indices: 258979--259005 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
258969 GGGTGGCTTT
258979 CTTTTCC
1 CTTTTCC
258986 CTTTTCC
1 CTTTTCC
258993 CTTTTCC
1 CTTTTCC
259000 CTTTTC
1 CTTTTC
259006 TTTCTTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTTTCC
Found at i:261806 original size:22 final size:22
Alignment explanation
Indices: 261781--261825 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
261771 GCCTGGGTTT
261781 TGCATCTTTCTTAGTAAAAAGG
1 TGCATCTTTCTTAGTAAAAAGG
261803 TGCATCTTTCTTAGTAAAAAGG
1 TGCATCTTTCTTAGTAAAAAGG
261825 T
1 T
261826 ATCTTAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (22 bp):
TGCATCTTTCTTAGTAAAAAGG
Found at i:264585 original size:19 final size:19
Alignment explanation
Indices: 264541--264605 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
264531 TTTCTCGAAA
* **
264541 AAGTCAATGGTCAACCCAAA
1 AAGTCAATGGTCAA-CGATC
**
264561 AAGTCAATGGTCAATTATC
1 AAGTCAATGGTCAACGATC
264580 AAGTCAATGGTCAACGATC
1 AAGTCAATGGTCAACGATC
264599 AAGTCAA
1 AAGTCAA
264606 CAATCAATGG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 25 0.64
20 14 0.36
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (19 bp):
AAGTCAATGGTCAACGATC
Found at i:265751 original size:309 final size:309
Alignment explanation
Indices: 265192--265813 Score: 1208
Period size: 309 Copynumber: 2.0 Consensus size: 309
265182 GTTCTATTTG
*
265192 TAAAGAAGAAAGATAGAACCCTTCGACTATGCATCAATTATCAGAAGCTGAATAGTTGATGATTA
1 TAAAGAAGAAAGATAGAACCCTTCGACTATGCATCAATTATCAGAAGCTAAATAGTTGATGATTA
* *
265257 AGAACAAATACCCTTTACCTCGTATTGATGACCTATTCGATCAGTTTCGAGGAGCAATTGTTTTC
66 AGAACAAATACCCTTTACCTCGTATTGATGACCTATTCGATCAGTTTCGAGGAGCAACTGTGTTC
265322 TCAAAGATAAATTTGAGATCTAGGTATTATCAGCTTACGGTCAAAGATTTTGATGTGTTCAAGAC
131 TCAAAGATAAATTTGAGATCTAGGTATTATCAGCTTACGGTCAAAGATTTTGATGTGTTCAAGAC
265387 AGCTTTTCAAACTCGTTATAGGCACTATGAGTTTCTGGTGATGTTGTTCGGGTCAACTAATGCTC
196 AGCTTTTCAAACTCGTTATAGGCACTATGAGTTTCTGGTGATGTTGTTCGGGTCAACTAATGCTC
265452 CTACTGCATTTATGGACATGATGAATAGGGTGTTTCAACCTTACTTGGA
261 CTACTGCATTTATGGACATGATGAATAGGGTGTTTCAACCTTACTTGGA
265501 TAAAGAAGAAAGATAGAACCCTTCGACTATGCATCAATTATCAGAAGCTAAATAGTTGATGATTA
1 TAAAGAAGAAAGATAGAACCCTTCGACTATGCATCAATTATCAGAAGCTAAATAGTTGATGATTA
265566 AGAACAAATACCCTTTACCTCGTATTGATGACCTATTCGATCAGTTTCGAGGAGCAACTGTGTTC
66 AGAACAAATACCCTTTACCTCGTATTGATGACCTATTCGATCAGTTTCGAGGAGCAACTGTGTTC
*
265631 TCTAAGATAAATTTGAGATCTAGGTATTATCAGCTTACGGTCAAAGATTTTGATGTGTTCAAGAC
131 TCAAAGATAAATTTGAGATCTAGGTATTATCAGCTTACGGTCAAAGATTTTGATGTGTTCAAGAC
265696 AGCTTTTCAAACTCGTTATAGGCACTATGAGTTTCTGGTGATGTTGTTCGGGTCAACTAATGCTC
196 AGCTTTTCAAACTCGTTATAGGCACTATGAGTTTCTGGTGATGTTGTTCGGGTCAACTAATGCTC
265761 CTACTGCATTTATGGACATGATGAATAGGGTGTTTCAACCTTACTTGGA
261 CTACTGCATTTATGGACATGATGAATAGGGTGTTTCAACCTTACTTGGA
265810 TAAA
1 TAAA
265814 TTTGTGGTGG
Statistics
Matches: 309, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
309 309 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (309 bp):
TAAAGAAGAAAGATAGAACCCTTCGACTATGCATCAATTATCAGAAGCTAAATAGTTGATGATTA
AGAACAAATACCCTTTACCTCGTATTGATGACCTATTCGATCAGTTTCGAGGAGCAACTGTGTTC
TCAAAGATAAATTTGAGATCTAGGTATTATCAGCTTACGGTCAAAGATTTTGATGTGTTCAAGAC
AGCTTTTCAAACTCGTTATAGGCACTATGAGTTTCTGGTGATGTTGTTCGGGTCAACTAATGCTC
CTACTGCATTTATGGACATGATGAATAGGGTGTTTCAACCTTACTTGGA
Found at i:269010 original size:19 final size:19
Alignment explanation
Indices: 268986--269025 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
268976 CGTTAACCCA
*
268986 TTGACCATTGATCATTGAC
1 TTGACCACTGATCATTGAC
*
269005 TTGACCACTGATCGTTGAC
1 TTGACCACTGATCATTGAC
269024 TT
1 TT
269026 TTTGGGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGACCACTGATCATTGAC
Found at i:286859 original size:37 final size:37
Alignment explanation
Indices: 286748--286889 Score: 153
Period size: 37 Copynumber: 3.9 Consensus size: 37
286738 GGATCATTGA
* * * *
286748 CACAAAGCCTGCTATGCACATAGCTTGAATAC-ACTGG
1 CACAAAGCCTGCTAGGAACACAGCCTGAATACAAC-GG
* * *
286785 CACGAAGCCTGCT-GGAACACAACCTGAATACACCGG
1 CACAAAGCCTGCTAGGAACACAGCCTGAATACAACGG
* * * *
286821 CACTAAGCCTGTTAGGTACACAGCCTGAATGCAACGG
1 CACAAAGCCTGCTAGGAACACAGCCTGAATACAACGG
*
286858 CACAAAGCCTGCTAGGCACACAGCCTGAATAC
1 CACAAAGCCTGCTAGGAACACAGCCTGAATAC
286890 TGTGCAAACA
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
36 26 0.30
37 60 0.70
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.16
Consensus pattern (37 bp):
CACAAAGCCTGCTAGGAACACAGCCTGAATACAACGG
Found at i:294157 original size:37 final size:37
Alignment explanation
Indices: 294101--294323 Score: 248
Period size: 37 Copynumber: 6.0 Consensus size: 37
294091 ATTCTTGGAT
** * * *
294101 CACCGGCATAAAGCTTGCTAGGCACATAGCCCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
*
294138 CACCGGCACGAAGCCTGCTAGGCACACAACCTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
* * * *
294175 GACCGTCACGAAGCCTACTAGGCACACAGCTTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
* ** *
294212 CACTGATACGAAGCCTGCTAGGCACACAGCTTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
* * *
294249 CATCGGCACGAAGCCTGCTCGGCACACAGCCTGAGTA
1 CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
* * * * *
294286 TACCAGCACGAAGCTTGCTAGGCACACCGCTTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
294323 C
1 C
294324 TGTGCAAACA
Statistics
Matches: 154, Mismatches: 32, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 154 1.00
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.16
Consensus pattern (37 bp):
CACCGGCACGAAGCCTGCTAGGCACACAGCCTGAATA
Found at i:294310 original size:111 final size:111
Alignment explanation
Indices: 294111--294323 Score: 302
Period size: 111 Copynumber: 1.9 Consensus size: 111
294101 CACCGGCATA
* *
294111 AAGCTTGCTAGGCACATAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAACCTGAATAG
1 AAGCCTGCTAGGCACACAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAACCTGAATAG
294176 ACCGTCACGAAGCCTACTAGGCACACAGCTTGAATACACTGATACG
66 ACCGTCACGAAGCCTACTAGGCACACAGCTTGAATACACTGATACG
** * * * * *
294222 AAGCCTGCTAGGCACACAGCTTGAATACATCGGCACGAAGCCTGCTCGGCACACAGCCTGAGTAT
1 AAGCCTGCTAGGCACACAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAACCTGAATAG
* * *
294287 ACCAG-CACGAAGCTTGCTAGGCACACCGCTTGAATAC
66 ACC-GTCACGAAGCCTACTAGGCACACAGCTTGAATAC
294324 TGTGCAAACA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 88 0.99
112 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.16
Consensus pattern (111 bp):
AAGCCTGCTAGGCACACAGCCCGAATACACCGGCACGAAGCCTGCTAGGCACACAACCTGAATAG
ACCGTCACGAAGCCTACTAGGCACACAGCTTGAATACACTGATACG
Done.