Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002141.1 Hibiscus syriacus cultivar Beakdansim tig00004375_pilon, 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: 209361
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:580 original size:24 final size:26
Alignment explanation
Indices: 553--611 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
543 TTTTAAATTC
553 TATTATTTTATTTATT-GTA-AAGTT
1 TATTATTTTATTTATTAGTATAAGTT
* *
577 TATTCA-TTTATTTTTTAGTATTAGTT
1 TATT-ATTTTATTTATTAGTATAAGTT
603 TA-TATTTTA
1 TATTATTTTA
612 ATTTGTATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 14 0.48
25 9 0.31
26 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (26 bp):
TATTATTTTATTTATTAGTATAAGTT
Found at i:889 original size:43 final size:43
Alignment explanation
Indices: 841--931 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
831 TTAGGGCTTT
*
841 TAAAATTTGGT-ACAA-AATTAAATAAATACAAATAATAGTATAA
1 TAAAATTTGGTCA-AATAATTAAATAAATACAAAT-ATAATATAA
* *
884 TAAAATTTGGTCAAATAATTAAATATATATAAATATAATATAA
1 TAAAATTTGGTCAAATAATTAAATAAATACAAATATAATATAA
927 TAAAA
1 TAAAA
932 AAATAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 26 0.60
44 17 0.40
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (43 bp):
TAAAATTTGGTCAAATAATTAAATAAATACAAATATAATATAA
Found at i:5794 original size:2 final size:2
Alignment explanation
Indices: 5789--5813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5779 GAAAAAAAAA
5789 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5814 GAACCTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12413 original size:15 final size:16
Alignment explanation
Indices: 12395--12427 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12385 AATTTGATCA
*
12395 AATAATTAAATA-AAT
1 AATAAATAAATATAAT
12410 AATAAATAAATATAAT
1 AATAAATAAATATAAT
12426 AA
1 AA
12428 AAAAGTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAATAAATATAAT
Found at i:16352 original size:55 final size:55
Alignment explanation
Indices: 16284--16409 Score: 207
Period size: 55 Copynumber: 2.3 Consensus size: 55
16274 ATCGATCGTT
* * * *
16284 AAACATCAGACATTTGCCATAAAGTTGATTGAGCAATCTCTATGTTAAAACTATA
1 AAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
*
16339 TAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
1 AAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
16394 AAACATGAGACATTTG
1 AAACATGAGACATTTG
16410 ATGTGCCTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (55 bp):
AAACATGAGACATTTGCCATAAAGTTGATCGAGCAATCACTATGTTAAAACTACA
Found at i:21110 original size:14 final size:15
Alignment explanation
Indices: 21083--21115 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
21073 AAAATAATTA
21083 AAAATATATAATTTT
1 AAAATATATAATTTT
*
21098 AAAATAT-TTATTTT
1 AAAATATATAATTTT
21112 AAAA
1 AAAA
21116 ATCAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATATAATTTT
Found at i:21116 original size:15 final size:16
Alignment explanation
Indices: 21080--21117 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
21070 CTAAAAATAA
21080 TTAAAAATATATAATT
1 TTAAAAATATATAATT
*
21096 TT-AAAATAT-TTATT
1 TTAAAAATATATAATT
21110 TTAAAAAT
1 TTAAAAAT
21118 CAGAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 12 0.60
16 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAAATATATAATT
Found at i:21156 original size:112 final size:114
Alignment explanation
Indices: 20988--21192 Score: 269
Period size: 113 Copynumber: 1.8 Consensus size: 114
20978 ATAAGATATT
* *
20988 TATTTATTTAGAAATATCAGAAAATGACTTCTAGTGCTTTAAGACAGCTCATTTCTTAATA-TAA
1 TATTTATTTAGAAATATCAGAAAATGACATCCAGTGCTTTAAGACAGCTCATTTCTTAATATTAA
21052 AAAATAATAAACATTTATCTAAAAATAATTAAAAATATATAATTTTAAAA
66 AAAATAATAAACA-TTATCTAAAAATAATTAAAAATATATAATTTTAAAA
*
21102 TATTTATTTTA-AAA-ATCAGAAAATGAACATCCAGTTGCTTT-A-ACTGC-CATTTCTTAATAT
1 TATTTA-TTTAGAAATATCAGAAAATG-ACATCCAG-TGCTTTAAGACAGCTCATTTCTTAATAT
* * * *
21162 TGAAAAATAATAAATATTATTTAAAATTAAT
63 TAAAAAATAATAAACATTATCTAAAAATAAT
21193 ATAATATTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
112 25 0.31
113 29 0.36
114 16 0.20
115 10 0.12
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (114 bp):
TATTTATTTAGAAATATCAGAAAATGACATCCAGTGCTTTAAGACAGCTCATTTCTTAATATTAA
AAAATAATAAACATTATCTAAAAATAATTAAAAATATATAATTTTAAAA
Found at i:21187 original size:20 final size:21
Alignment explanation
Indices: 21159--21200 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
21149 CATTTCTTAA
21159 TATTGAAAAATAATA-AATAT
1 TATTGAAAAATAATATAATAT
* *
21179 TATTTAAAATTAATATAATAT
1 TATTGAAAAATAATATAATAT
21200 T
1 T
21201 TAATATGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTGAAAAATAATATAATAT
Found at i:21202 original size:18 final size:19
Alignment explanation
Indices: 21156--21203 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
21146 TGCCATTTCT
*
21156 TAATATTGAAAAATAATAAA
1 TAATATTTAAAAATAAT-AA
* *
21176 TATTATTTAAAATTAAT-A
1 TAATATTTAAAAATAATAA
21194 TAATATTTAA
1 TAATATTTAA
21204 TATGACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 10 0.42
20 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATATTTAAAAATAATAA
Found at i:22649 original size:3 final size:3
Alignment explanation
Indices: 22643--22701 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
22633 TATTTTTTTA
* * * **
22643 AAT AAT ATT AAT AAT AAT ATAT AAA AAT AAT AAA AAT TTT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
*
22689 CAT AAT AAT AAT A
1 AAT AAT AAT AAT A
22702 CTATATAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:51063 original size:16 final size:16
Alignment explanation
Indices: 51044--51093 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
51034 GAGAATTTAA
51044 AATATTTTATATTTTT
1 AATATTTTATATTTTT
* *
51060 AATA-TTTA-ATATTC
1 AATATTTTATATTTTT
*
51074 AATATTTTACTATTTAT
1 AATATTTTA-TATTTTT
51091 AAT
1 AAT
51094 TTTATGGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
14 8 0.31
15 8 0.31
16 4 0.15
17 6 0.23
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATTTTATATTTTT
Found at i:51141 original size:17 final size:18
Alignment explanation
Indices: 51105--51147 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
51095 TTATGGGATG
51105 AAAAATAGTATTATTATA
1 AAAAATAGTATTATTATA
51123 AAAAAT-GTAATTATT-TA
1 AAAAATAGT-ATTATTATA
51140 AAACAATA
1 AAA-AATA
51148 TTTTACTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAAATAGTATTATTATA
Found at i:56035 original size:15 final size:15
Alignment explanation
Indices: 56015--56046 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
56005 GATAGTAGGC
56015 TGCTATAAACAAGAA
1 TGCTATAAACAAGAA
56030 TGCTATAAACAAGAA
1 TGCTATAAACAAGAA
56045 TG
1 TG
56047 GATGGTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (15 bp):
TGCTATAAACAAGAA
Found at i:56441 original size:11 final size:11
Alignment explanation
Indices: 56422--56451 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
56412 ATATTACATA
56422 TTAATTATAAAT
1 TTAA-TATAAAT
56434 TTAATATAAAT
1 TTAATATAAAT
56445 TTAATAT
1 TTAATAT
56452 TTATCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAATATAAAT
Found at i:57639 original size:20 final size:20
Alignment explanation
Indices: 57572--57639 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
57562 GTTGTGTAAT
57572 GGATCGA-TCCTTTTGAAAA
1 GGATCGATTCCTTTTGAAAA
***
57591 GGATCGATTCCTCGGGAGAAA
1 GGATCGATTCCTTTTGA-AAA
* * *
57612 GAAACGATTCCTTTTCAAAA
1 GGATCGATTCCTTTTGAAAA
57632 GGATCGAT
1 GGATCGAT
57640 CCATTGGGGA
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
19 7 0.19
20 15 0.42
21 14 0.39
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
GGATCGATTCCTTTTGAAAA
Found at i:64089 original size:23 final size:23
Alignment explanation
Indices: 64059--64106 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
64049 ACCGTTGAAC
64059 TTATAAAA-ATTTAAATAAAAAAA
1 TTATAAAATATTTAAA-AAAAAAA
* *
64082 TTATAAAATTTTTAAAAAAATAA
1 TTATAAAATATTTAAAAAAAAAA
64105 TT
1 TT
64107 TTTTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTATAAAATATTTAAAAAAAAAA
Found at i:64996 original size:27 final size:27
Alignment explanation
Indices: 64941--64995 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
64931 ATCTTAGAGG
*
64941 TGCACAAAAAATTCGAATATCTGATTT
1 TGCACAAAAAATTCGAATATCGGATTT
*
64968 TGCATAAAAAATATCCGAA-ATCGGATTT
1 TGCACAAAAAAT-T-CGAATATCGGATTT
64996 GGAAAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 9 0.38
29 4 0.17
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (27 bp):
TGCACAAAAAATTCGAATATCGGATTT
Found at i:65515 original size:19 final size:19
Alignment explanation
Indices: 65493--65535 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
65483 GCCATGAATT
*
65493 GTCATAGGCTGTCTTTACA
1 GTCAGAGGCTGTCTTTACA
*
65512 GTCAGGGGCTGTCTTTACA
1 GTCAGAGGCTGTCTTTACA
65531 GTCAG
1 GTCAG
65536 GGGCAGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (19 bp):
GTCAGAGGCTGTCTTTACA
Found at i:65536 original size:19 final size:19
Alignment explanation
Indices: 65499--65539 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
65489 AATTGTCATA
65499 GGCTGTCTTTACAGTCAGG
1 GGCTGTCTTTACAGTCAGG
65518 GGCTGTCTTTACAGTCAGG
1 GGCTGTCTTTACAGTCAGG
65537 GGC
1 GGC
65540 AGTCGGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.22, G:0.34, T:0.29
Consensus pattern (19 bp):
GGCTGTCTTTACAGTCAGG
Found at i:74038 original size:24 final size:24
Alignment explanation
Indices: 73956--74069 Score: 113
Period size: 24 Copynumber: 4.8 Consensus size: 24
73946 AAAATTTCAA
* * * * *
73956 GAGCTTGATTAAAACTCAAAACTT
1 GAGCTCGATTGAAGCTCGAAACTC
* *
73980 GAGCTTGATTAAAGCTCGAAACTC
1 GAGCTCGATTGAAGCTCGAAACTC
*
74004 GAGCTCGATTGAAGCTTGAAACTC
1 GAGCTCGATTGAAGCTCGAAACTC
** *
74028 GAGCTCGATTGAAGCTCG-ATTTT
1 GAGCTCGATTGAAGCTCGAAACTC
*
74051 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTGAAGCTCGA
74070 TTTTAAGCTC
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 19 0.24
24 59 0.76
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
GAGCTCGATTGAAGCTCGAAACTC
Found at i:74045 original size:11 final size:11
Alignment explanation
Indices: 74029--74071 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
74019 TTGAAACTCG
74029 AGCTCGATTGA
1 AGCTCGATTGA
74040 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
74052 AGCTCGATTCA
1 AGCTCGATTGA
74063 AGCTCGATT
1 AGCTCGATT
74072 TTAAGCTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:74058 original size:23 final size:23
Alignment explanation
Indices: 74004--74079 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
73994 CTCGAAACTC
* ** *
74004 GAGCTCGATTGAAGCTTGAAACTC
1 GAGCTCGATTGAAGCTCG-ATTTT
74028 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTT
*
74051 GAGCTCGATTCAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTT
*
74074 AAGCTC
1 GAGCTC
74080 AATTCGGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 29 0.63
24 17 0.37
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTTT
Found at i:74077 original size:12 final size:11
Alignment explanation
Indices: 74029--74079 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
74019 TTGAAACTCG
*
74029 AGCTCGATTGA
1 AGCTCGATTTA
*
74040 AGCTCGATTTTG
1 AGCTCGA-TTTA
*
74052 AGCTCGATTCA
1 AGCTCGATTTA
74063 AGCTCGATTTTA
1 AGCTCGA-TTTA
74075 AGCTC
1 AGCTC
74080 AATTCGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (11 bp):
AGCTCGATTTA
Found at i:75473 original size:7 final size:7
Alignment explanation
Indices: 75461--75560 Score: 121
Period size: 7 Copynumber: 14.4 Consensus size: 7
75451 TATCAGATTA
75461 AGGGTTT
1 AGGGTTT
*
75468 ATGGTTT
1 AGGGTTT
75475 AGGGTTT
1 AGGGTTT
*
75482 AGGATTT
1 AGGGTTT
*
75489 AGGTTTT
1 AGGGTTT
75496 AGGGTTT
1 AGGGTTT
75503 AGGGTTT
1 AGGGTTT
75510 A-GGTTT
1 AGGGTTT
75516 AGGGTTT
1 AGGGTTT
75523 AGGGTTT
1 AGGGTTT
*
75530 AAGGTTT
1 AGGGTTT
*
75537 AAGGTTT
1 AGGGTTT
***
75544 ATAATTT
1 AGGGTTT
75551 AGGGTTT
1 AGGGTTT
75558 AGG
1 AGG
75561 TTCATGGCTC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
6 6 0.08
7 74 0.93
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
AGGGTTT
Found at i:76056 original size:21 final size:21
Alignment explanation
Indices: 76032--76071 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
76022 ATTTTTTTAA
*
76032 ATTTTATAGAATTTT-TAATAT
1 ATTTT-TAAAATTTTATAATAT
76053 ATTTTTAAAATTTTATAAT
1 ATTTTTAAAATTTTATAAT
76072 TATCAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATTTTATAATAT
Found at i:76079 original size:28 final size:29
Alignment explanation
Indices: 76024--76079 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
76014 TTTATTTTAT
* * *
76024 TTTTTTAAATTTTATAGAATTTTTAATATA
1 TTTTTAAAATTTTATA-AATTATCAATATA
76054 TTTTTAAAATTTTAT-AATTATCAATA
1 TTTTTAAAATTTTATAAATTATCAATA
76080 ATGTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
30 14 0.61
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTAAAATTTTATAAATTATCAATATA
Found at i:76095 original size:14 final size:14
Alignment explanation
Indices: 76076--76105 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
76066 TATAATTATC
*
76076 AATAATGTATTTTT
1 AATAATGTAATTTT
76090 AATAATGTAATTTT
1 AATAATGTAATTTT
76104 AA
1 AA
76106 AAAATCTAAA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:77492 original size:20 final size:20
Alignment explanation
Indices: 77467--77535 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
77457 TTCGAGTTTG
* * *
77467 ACTCGAAAAGTTTGCAAGTA
1 ACTCGAAAAGCTTACGAGTA
*
77487 AGTCGAAAAGCTTACGAGTA
1 ACTCGAAAAGCTTACGAGTA
77507 ACTCGAAAAGCTTACGAGTA
1 ACTCGAAAAGCTTACGAGTA
77527 ACTCGAAAA
1 ACTCGAAAA
77536 TATAATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (20 bp):
ACTCGAAAAGCTTACGAGTA
Found at i:84564 original size:38 final size:38
Alignment explanation
Indices: 84507--84581 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
84497 TAACGTTAAG
*
84507 TTTTGAACAAGGGTACTAAAATTAAACAAAAACTAAAC
1 TTTTGAACAAGGGTACTAAAATGAAACAAAAACTAAAC
* * * *
84545 TTTTTAACAATGGTGCTAAAATGAAATAAAAACTAAA
1 TTTTGAACAAGGGTACTAAAATGAAACAAAAACTAAA
84582 GTTTAGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (38 bp):
TTTTGAACAAGGGTACTAAAATGAAACAAAAACTAAAC
Found at i:85315 original size:35 final size:35
Alignment explanation
Indices: 85253--85355 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 35
85243 ACATAATTAC
85253 TTGATTTGTACTTAGC-TTAAGCATTTTGAGTTCA
1 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
85287 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
1 TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
* *
85322 TTGATTTGTACTT-GTCTTTAAGCAATTCGAGTTC
1 TTGATTTGTACTTAG-CTTTAAGCATTTTGAGTTC
85356 TTCGGCAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 17 0.26
35 48 0.74
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (35 bp):
TTGATTTGTACTTAGCTTTAAGCATTTTGAGTTCA
Found at i:88059 original size:228 final size:225
Alignment explanation
Indices: 87665--88118 Score: 863
Period size: 228 Copynumber: 2.0 Consensus size: 225
87655 TCCTTAAACC
*
87665 AGACAGCTTTCATCAGAGGCAGAAACATTGGGATAATACTCTGCTTGCCTAAGATGGTTAAAGGT
1 AGACAGCTTTCATCAGAGGCAGAAACATTGGGATAATACTCTGCTTGCCAAAGATGGTTAAAGGT
87730 TATAGTAGGAACTCCATATCACCAAGGTGCACTCTGAAAATTGATCTTCATAAAGCATTTGACTT
66 TATAGTAGGAACTCCATATCACCAAGGTGCACTCTGAAAATTGATCTTCATAAAGCATTTGACTT
87795 CATTCATTGGGATTTTATTTCAGCTATTCTTAAAGCTTTAAATCTTCCTCAAAAATTCATCGATT
131 CATTCATTGGGATTTTATTTCAGCTATTCTTAAAGCTTTAAATCTTCCTCAAAAATTCATCGATT
87860 GGACTGAAGCATGTTTTACTCAAGCAAGAT
196 GGACTGAAGCATGTTTTACTCAAGCAAGAT
87890 AGACAGCTTTCATCAGAGGCAGAAACATTGTGGATAATACTCTGCTTGCCCAAGAGATGGTTAAA
1 AGACAGCTTTCATCAGAGGCAGAAACATTG-GGATAATACTCTGCTTG-CCAA-AGATGGTTAAA
87955 GGTTATAGTAGGAACTCCATATCACCAAGGTGCACTCTGAAAATTGATCTTCATAAAGCATTTGA
63 GGTTATAGTAGGAACTCCATATCACCAAGGTGCACTCTGAAAATTGATCTTCATAAAGCATTTGA
88020 CTTCATTCATTGGGATTTTATTTCAGCTATTCTTAAAGCTTTAAATCTTCCTCAAAAATTCATCG
128 CTTCATTCATTGGGATTTTATTTCAGCTATTCTTAAAGCTTTAAATCTTCCTCAAAAATTCATCG
*
88085 ATTGGACTGAAGCATGTTTTACTTAAGCAAGAT
193 ATTGGACTGAAGCATGTTTTACTCAAGCAAGAT
88118 A
1 A
88119 TTCCATATCT
Statistics
Matches: 224, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
225 30 0.13
226 17 0.08
227 3 0.01
228 174 0.78
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (225 bp):
AGACAGCTTTCATCAGAGGCAGAAACATTGGGATAATACTCTGCTTGCCAAAGATGGTTAAAGGT
TATAGTAGGAACTCCATATCACCAAGGTGCACTCTGAAAATTGATCTTCATAAAGCATTTGACTT
CATTCATTGGGATTTTATTTCAGCTATTCTTAAAGCTTTAAATCTTCCTCAAAAATTCATCGATT
GGACTGAAGCATGTTTTACTCAAGCAAGAT
Found at i:89545 original size:22 final size:22
Alignment explanation
Indices: 89503--89544 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
89493 TCCAGAATGC
89503 CAGAGGGGAACCGATACCCCCA
1 CAGAGGGGAACCGATACCCCCA
*
89525 CAGA-GGGAACCGATTCCCCC
1 CAGAGGGGAACCGATACCCCC
89545 CTAAAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.38, G:0.26, T:0.07
Consensus pattern (22 bp):
CAGAGGGGAACCGATACCCCCA
Found at i:90806 original size:30 final size:30
Alignment explanation
Indices: 90762--90885 Score: 205
Period size: 30 Copynumber: 4.1 Consensus size: 30
90752 TCGAGACATA
90762 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
90793 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
90823 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* **
90853 TGGACAGTTACCG-GGGTCTTGGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
90882 TGGA
1 TGGA
90886 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 17 0.19
30 66 0.73
31 7 0.08
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:96510 original size:162 final size:162
Alignment explanation
Indices: 96241--96570 Score: 561
Period size: 162 Copynumber: 2.0 Consensus size: 162
96231 CAGGATTTGG
* * *
96241 CAAATGGGACTGATAGCAATCAAGTTGGGTCGGAGAAAGTTACTGCTGGACAGGGATCAGAATCT
1 CAAATGGGACTGATACCAATCAAGTTGGCTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCT
* * *
96306 CAGCCTACAGACAATATGCAAAAGTCTGGGGATGTAGGTCAATCTCAATCAGCAAGTGGAAATCA
66 CAGCCTACAGACAATATGCAAAAGTCTGGGGATATAGGTCAATCTCAACCAGCAAATGGAAATCA
96371 CAGTGATATTTCTTCTTCAGTCAAGAAGGATA
131 CAGTGATATTTCTTCTTCAGTCAAGAAGGATA
*
96403 CTAATGGGACTGATACCAATCAAGTTGGCTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCT
1 CAAATGGGACTGATACCAATCAAGTTGGCTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCT
* * * *
96468 CAGCCTTCAGACAATATGCAGAAGTCTGGGGATATAGGTCAATCTCAACCAGTAAATGGAGATCA
66 CAGCCTACAGACAATATGCAAAAGTCTGGGGATATAGGTCAATCTCAACCAGCAAATGGAAATCA
96533 CAGTGATATTTCTTCTTCAGTCAAGAAGGATA
131 CAGTGATATTTCTTCTTCAGTCAAGAAGGATA
96565 CAAATG
1 CAAATG
96571 AATCGGGGAA
Statistics
Matches: 156, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 156 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (162 bp):
CAAATGGGACTGATACCAATCAAGTTGGCTCGGAGAAAGGTACTGCTGGACAGGGATCAGAATCT
CAGCCTACAGACAATATGCAAAAGTCTGGGGATATAGGTCAATCTCAACCAGCAAATGGAAATCA
CAGTGATATTTCTTCTTCAGTCAAGAAGGATA
Found at i:106431 original size:19 final size:21
Alignment explanation
Indices: 106401--106447 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
106391 TCATGGAAAG
*
106401 TATTATTTGAAATATT-ATTT
1 TATTATTGGAAATATTGATTT
106421 T-TTATTGGAAATATTGATTT
1 TATTATTGGAAATATTGATTT
106441 TATTATT
1 TATTATT
106448 TAAAAATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 6 0.25
21 5 0.21
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TATTATTGGAAATATTGATTT
Found at i:106564 original size:17 final size:18
Alignment explanation
Indices: 106536--106572 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
106526 CACACAATAT
106536 TAATATTTTTAATAAAAA
1 TAATATTTTTAATAAAAA
106554 TAATA-TTTTAATAAAAA
1 TAATATTTTTAATAAAAA
106571 TA
1 TA
106573 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATTTTTAATAAAAA
Found at i:107772 original size:14 final size:15
Alignment explanation
Indices: 107753--107781 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
107743 TTAATAAAAT
107753 TTTAATA-TAAATAA
1 TTTAATATTAAATAA
107767 TTTAATATTAAATAA
1 TTTAATATTAAATAA
107782 ATTATATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATATTAAATAA
Found at i:115548 original size:35 final size:37
Alignment explanation
Indices: 115502--115574 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 37
115492 TTCATTTAGG
115502 GGGGAATCGATA-CCCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
115537 GGGGAATCGATACCCCCCCAGGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCCA-GGGGGGAATCTGTTCCC
115575 CCCTACACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 12 0.34
36 7 0.20
38 16 0.46
ACGTcount: A:0.19, C:0.32, G:0.33, T:0.16
Consensus pattern (37 bp):
GGGGAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
Found at i:118511 original size:31 final size:32
Alignment explanation
Indices: 118473--118543 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
118463 TTAAAAAAAC
* *
118473 TGGTCACTTA-TATTATTGTTTTATTAAGTTT
1 TGGTCACTTATTATTATGGTTTTATTAAGATT
* *
118504 TGGTCAC-TATTGTTATGGTTTTATTCAGATT
1 TGGTCACTTATTATTATGGTTTTATTAAGATT
*
118535 TGGCCACTT
1 TGGTCACTT
118544 GAACGTTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 2 0.06
31 30 0.91
32 1 0.03
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (32 bp):
TGGTCACTTATTATTATGGTTTTATTAAGATT
Found at i:119775 original size:31 final size:31
Alignment explanation
Indices: 119740--119818 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
119730 ATTCAACGTC
* *
119740 TAAGTGACCAAAATTTAATAAAACGATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACG
*
119771 TAAGTGACTAAAACTTAATAAAACAATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACG
*
119802 TAAGTGATCAAAACTTA
1 TAAGTGACCAAAACTTA
119819 CTTTTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAACG
Found at i:123184 original size:23 final size:23
Alignment explanation
Indices: 123158--123204 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
123148 ATATAGGATC
*
123158 ATATTAAATTAAACATAGATGAA
1 ATATTAAATCAAACATAGATGAA
123181 ATATTAAATCAAACATAGATGAA
1 ATATTAAATCAAACATAGATGAA
123204 A
1 A
123205 GAAATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (23 bp):
ATATTAAATCAAACATAGATGAA
Found at i:127043 original size:21 final size:21
Alignment explanation
Indices: 127025--127064 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
127015 GAGTAACACA
127025 AATTTTTT-ATATAAAAACAAT
1 AATTTTTTCA-ATAAAAACAAT
127046 AATTTTTTCAATAAAAACA
1 AATTTTTTCAATAAAAACA
127065 TGTAAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTTTTCAATAAAAACAAT
Found at i:136177 original size:36 final size:34
Alignment explanation
Indices: 136125--136234 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 34
136115 TTTCAGGCAC
*
136125 TTGAATTACTTTGGAATTAGGGATTTAGAATGTAA
1 TTGAATTACTTTGGAATTAGGG-TTTAGAATGAAA
* *
136160 TTGAATTATTTTTGGAATTTAGAGTTTAGAATGAAA
1 TTGAATTA-CTTTGGAA-TTAGGGTTTAGAATGAAA
*
136196 TTGAATTACTTTGGAATTTGGGGTTTAGAATGAAA
1 TTGAATTACTTTGGAA-TTAGGGTTTAGAATGAAA
136231 TTGA
1 TTGA
136235 GGACTATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 36 0.54
36 26 0.39
37 5 0.07
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (34 bp):
TTGAATTACTTTGGAATTAGGGTTTAGAATGAAA
Found at i:138304 original size:2 final size:2
Alignment explanation
Indices: 138297--138327 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
138287 TGATTCGTGC
138297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
138328 TAAGATGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:158258 original size:6 final size:6
Alignment explanation
Indices: 158249--158275 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
158239 GATGCTGCAA
158249 GAGCTG GAGCTG GAGCTG GAGCTG GAG
1 GAGCTG GAGCTG GAGCTG GAGCTG GAG
158276 TTGGCGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.52, T:0.15
Consensus pattern (6 bp):
GAGCTG
Found at i:158408 original size:27 final size:27
Alignment explanation
Indices: 158344--158434 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
158334 AGGAGATGAA
*
158344 GATGGAGATGATGGTATTGGTTCAGGT
1 GATGGAGATGATGGTATTGGTGCAGGT
*
158371 AATGGTAGAGATGATGGTATTGGTGCAGGT
1 GAT-G--GAGATGATGGTATTGGTGCAGGT
*
158401 GATGGAGATGAAGGCT-TTGGTGCAGGT
1 GATGGAGATGATGG-TATTGGTGCAGGT
158428 GATGGAG
1 GATGGAG
158435 GTAGAGATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 29 0.52
28 2 0.04
29 1 0.02
30 24 0.43
ACGTcount: A:0.24, C:0.04, G:0.43, T:0.29
Consensus pattern (27 bp):
GATGGAGATGATGGTATTGGTGCAGGT
Found at i:158466 original size:27 final size:28
Alignment explanation
Indices: 158348--158467 Score: 102
Period size: 27 Copynumber: 4.1 Consensus size: 28
158338 GATGAAGATG
*
158348 GAGATGATGGTATTGGTTCAGGTAATGGTA
1 GAGATGATGGTATTGGTGCAGGTAA--GTA
* *
158378 GAGATGATGGTATTGGTGCAGGTGA-TG
1 GAGATGATGGTATTGGTGCAGGTAAGTA
*
158405 GAGATGAAGGCT-TTGGTGCAGGTGATGGAGGTA
1 GAGATGATGG-TATTGGTGCAGGT-A---A-GTA
*
158438 GAGATGATGGTATTCGTGCAGGTAA-TA
1 GAGATGATGGTATTGGTGCAGGTAAGTA
158465 GAG
1 GAG
158468 GTAGAGATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
27 26 0.35
28 1 0.01
29 1 0.01
30 23 0.31
31 1 0.01
32 2 0.03
33 20 0.27
ACGTcount: A:0.26, C:0.05, G:0.41, T:0.28
Consensus pattern (28 bp):
GAGATGATGGTATTGGTGCAGGTAAGTA
Found at i:158623 original size:39 final size:39
Alignment explanation
Indices: 158509--158624 Score: 187
Period size: 39 Copynumber: 3.0 Consensus size: 39
158499 AGATGAAGCT
* * * * *
158509 GGTGTAGATGATGGAGGTTTTAGAAATGGAGCCGGAACT
1 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
158548 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
1 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
158587 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGC
1 GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGC
158625 AGATGATGTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.22, C:0.09, G:0.44, T:0.26
Consensus pattern (39 bp):
GGTGTAGGTGATGGTGGTTTTGGAAATGGAGCCGGAGCC
Found at i:174093 original size:12 final size:12
Alignment explanation
Indices: 174076--174115 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
174066 GTGTCTAAAG
174076 AATGTTTTGAGA
1 AATGTTTTGAGA
174088 AATGTTTT----
1 AATGTTTTGAGA
174096 AATGTTTTGAGA
1 AATGTTTTGAGA
174108 AATGTTTT
1 AATGTTTT
174116 AATATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 8 0.33
12 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (12 bp):
AATGTTTTGAGA
Found at i:174101 original size:20 final size:20
Alignment explanation
Indices: 174076--174123 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
174066 GTGTCTAAAG
174076 AATGTTTTGAGAAATGTTTT
1 AATGTTTTGAGAAATGTTTT
174096 AATGTTTTGAGAAATGTTTT
1 AATGTTTTGAGAAATGTTTT
*
174116 AATATTTT
1 AATGTTTT
174124 AATTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (20 bp):
AATGTTTTGAGAAATGTTTT
Found at i:174571 original size:21 final size:21
Alignment explanation
Indices: 174545--174642 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
174535 ATCAGTTTCC
174545 AAAATCGCAACGCGATTATTG
1 AAAATCGCAACGCGATTATTG
* *
174566 AAAATCGCAATGCGA-TAGT-
1 AAAATCGCAACGCGATTATTG
** *
174585 ACAAATTCGCATTGCGATT-TTCC
1 A-AAA-TCGCAACGCGATTATT-G
* *
174608 AGAATCGCAACGCGAATA-TG
1 AAAATCGCAACGCGATTATTG
174628 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
174643 ACACATAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.33
21 36 0.59
22 3 0.05
23 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATTG
Found at i:174635 original size:20 final size:20
Alignment explanation
Indices: 174610--174802 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
174600 GATTTTCCAG
* ** *
174610 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
174630 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
174650 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
174670 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
174690 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
174710 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
174730 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
174750 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
174771 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
174791 AATCGCAACGCG
1 AATCGCAACGCG
174803 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:175220 original size:33 final size:33
Alignment explanation
Indices: 175181--175251 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
175171 TTCACTTAGA
175181 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
175214 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
175247 TTTCA
1 TTTCA
175252 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:175357 original size:21 final size:21
Alignment explanation
Indices: 175331--175407 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
175321 TGCAGAAGAG
175331 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
175352 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
175372 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
175394 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
175408 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:175411 original size:14 final size:14
Alignment explanation
Indices: 175392--175448 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
175382 GAAAAATGAA
175392 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
175406 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
175425 AATCGCAACGAGAG
1 AATCGCAACGAGAG
175439 AATCGCAACG
1 AATCGCAACG
175449 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:175423 original size:33 final size:33
Alignment explanation
Indices: 175385--175464 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
175375 GCAACGAGAA
175385 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
175418 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
175451 AAACCAAAATCGCA
1 AAATGAAAATCGCA
175465 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:175535 original size:21 final size:21
Alignment explanation
Indices: 175509--175573 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
175499 CGCGTTGCGA
175509 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
175530 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
175550 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
175571 TTC
1 TTC
175574 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:175570 original size:20 final size:20
Alignment explanation
Indices: 175465--175571 Score: 95
Period size: 19 Copynumber: 5.7 Consensus size: 20
175455 CAAAATCGCA
*
175465 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
*
175484 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
175503 TTGCG------ATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
175517 TTGCGATTTTCATTTCTCTCG
1 TTGCGATTTTCA-TTCTCTCG
*** *
175538 TTGCGACAGTCATTCTCTCA
1 TTGCGATTTTCATTCTCTCG
175558 TTGCGATTTTCATT
1 TTGCGATTTTCATT
175572 TCAACCAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.04
14 9 0.12
19 24 0.33
20 19 0.26
21 17 0.24
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCATTCTCTCG
Found at i:177413 original size:93 final size:93
Alignment explanation
Indices: 177254--177476 Score: 428
Period size: 93 Copynumber: 2.4 Consensus size: 93
177244 TAGATTGCTT
*
177254 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
177319 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
177347 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
177412 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
177440 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
177477 AATACCCTGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 127 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:177611 original size:14 final size:14
Alignment explanation
Indices: 177592--177647 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
177582 CGAAACTTAA
*
177592 AATCGCAACGAGAG
1 AATCGCAACGAAAG
177606 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
*
177623 AAATCGCAACGACAG
1 -AATCGCAACGAAAG
177638 AATCGCAACG
1 AATCGCAACG
177648 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:177632 original size:32 final size:33
Alignment explanation
Indices: 177574--177695 Score: 176
Period size: 32 Copynumber: 3.7 Consensus size: 33
177564 TAGTTTACTT
* * *
177574 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
177608 TCGCAACGCGAAA-TGAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
177640 TCGCAACGCGAAACCAAAATCGCAACGACA-AA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
177672 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
177696 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
32 56 0.68
33 14 0.17
34 12 0.15
ACGTcount: A:0.45, C:0.28, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:177662 original size:19 final size:19
Alignment explanation
Indices: 177638--177695 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
177628 GCAACGACAG
177638 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
177657 AATCGCAA--CG--A-C-A
1 AATCGCAACGCGAAACCAA
177670 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
177689 AATCGCA
1 AATCGCA
177696 TTGCGATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 3 0.09
17 3 0.09
18 1 0.03
19 16 0.48
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:177713 original size:19 final size:19
Alignment explanation
Indices: 177691--177849 Score: 166
Period size: 19 Copynumber: 8.6 Consensus size: 19
177681 GAAACCAAAA
*
177691 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
177710 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
177724 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
177743 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
177762 TCGCGTTGTGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
177781 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
177800 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
177819 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
177839 TCGTGTTGCGA
1 TCGCGTTGCGA
177850 AAGTAAACTA
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
14 10 0.09
16 3 0.03
17 3 0.03
19 89 0.76
20 12 0.10
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:179787 original size:14 final size:14
Alignment explanation
Indices: 179768--179803 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
179758 ATTGTTTAAT
179768 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
179782 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
179796 TGATTTGT
1 TGATTTGT
179804 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:179978 original size:20 final size:19
Alignment explanation
Indices: 179910--179988 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
179900 AAAAATGACT
179910 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
179929 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
179943 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
179962 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
179982 ATCGCAA
1 ATCGCAA
179989 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:180066 original size:53 final size:53
Alignment explanation
Indices: 180003--180293 Score: 523
Period size: 53 Copynumber: 5.5 Consensus size: 53
179993 AGAATCGCAA
*
180003 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
180056 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
180109 TGCGATTTTCATTTCGCATTGCGATTTTCATTTACGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
180162 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
180215 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
180268 TG-GTATTTTCATTTCGCATTGCGATT
1 TGCG-ATTTTCATTTCGCATTGCGATT
180294 CTCTCGTTGC
Statistics
Matches: 232, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
52 1 0.00
53 230 0.99
54 1 0.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:182605 original size:12 final size:12
Alignment explanation
Indices: 182588--182612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
182578 TCTTCGGGGA
182588 CTTTTTCTTCTT
1 CTTTTTCTTCTT
182600 CTTTTTCTTCTT
1 CTTTTTCTTCTT
182612 C
1 C
182613 AGAATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:182821 original size:24 final size:24
Alignment explanation
Indices: 182787--182833 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
182777 CTGAAACATC
182787 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
182811 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
182834 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:183553 original size:20 final size:20
Alignment explanation
Indices: 183525--183753 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
183515 AAATTTCAGT
* * *
183525 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
183545 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
183565 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
183585 GTTGTGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
183605 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
183625 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
183645 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
183665 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
183685 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
183705 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
183725 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
183745 GTTGCGATT
1 GTTGCGATT
183754 CTGGAAAATC
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 178 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:187945 original size:15 final size:16
Alignment explanation
Indices: 187925--187969 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
187915 TGTCATGTCC
187925 AGATTTTTTTTAAAT-
1 AGATTTTTTTTAAATA
187940 AGA-TTTTTTTAAATA
1 AGATTTTTTTTAAATA
*
187955 ATATTTTATTTTAAA
1 AGATTTT-TTTTAAA
187970 AAAAATCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 3 0.12
17 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
AGATTTTTTTTAAATA
Found at i:188243 original size:42 final size:42
Alignment explanation
Indices: 188184--188303 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
188174 TTTCCCCGAA
188184 TTCCCATGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCATGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
* * *
188226 TTCCCGTGTTTGTTTCACGTTATTCGTTTCCCGGAAAATGTT
1 TTCCCATGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
* *
188268 TTCCCATGTTTGTTTAACGTAATTGGTTTTCCGGAA
1 TTCCCATGTTTGTTTCACGTAATTCGTTTTCCGGAA
188304 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.45
Consensus pattern (42 bp):
TTCCCATGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
Found at i:188534 original size:24 final size:22
Alignment explanation
Indices: 188495--188542 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
188485 TTATTTATTT
*
188495 ATATTTATAATAATATAATATA
1 ATATTTATAATAATATAAAATA
*
188517 ATATTTTTAATATTATATAAAATA
1 ATATTTATAATA--ATATAAAATA
188541 AT
1 AT
188543 CAATTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
24 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTTATAATAATATAAAATA
Found at i:188677 original size:23 final size:23
Alignment explanation
Indices: 188651--188695 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
188641 AATAATATTT
188651 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
188674 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
188696 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:189058 original size:15 final size:15
Alignment explanation
Indices: 189016--189059 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
189006 TTCTAGAAAT
*
189016 GTAATTCATTTTCCA
1 GTAATTCATTTTTCA
**
189031 G-AATTCAAATTTCA
1 GTAATTCATTTTTCA
189045 GTAATTCATTTTTCA
1 GTAATTCATTTTTCA
189060 ATTCCAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:189073 original size:29 final size:28
Alignment explanation
Indices: 189016--189073 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
189006 TTCTAGAAAT
*
189016 GTAATTCATTTTCCAGAATTCAAATTTCA
1 GTAATTCATTTTCCA-AATTCAAAATTCA
*
189045 GTAATTCATTTTTC-AATTCCAATAATTCA
1 GTAATTCATTTTCCAAATT-CAA-AATTCA
189074 AATTTTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.16
28 3 0.12
29 18 0.72
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.43
Consensus pattern (28 bp):
GTAATTCATTTTCCAAATTCAAAATTCA
Found at i:190148 original size:37 final size:37
Alignment explanation
Indices: 190075--190149 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
190065 GTTGAAAAAT
* * *
190075 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAACTGAAAATCATAAA
* *
190112 ATTTATATAATTTTTTTTACAAAACTGAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAACTGAAAATCATAAA
190149 A
1 A
190150 ATGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAACTGAAAATCATAAA
Found at i:195760 original size:7 final size:7
Alignment explanation
Indices: 195750--195774 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
195740 TTTGTTTTGC
195750 TTTTTCT
1 TTTTTCT
195757 TTTTTCT
1 TTTTTCT
195764 TTTTTCT
1 TTTTTCT
195771 TTTT
1 TTTT
195775 CTTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:200582 original size:2 final size:2
Alignment explanation
Indices: 200575--200600 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
200565 TGTTCTAGAA
200575 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
200601 CTGTGTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:206464 original size:20 final size:20
Alignment explanation
Indices: 206439--206485 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
206429 TTTTAGGGTC
206439 GAATTTTAAAAAAAATTATT
1 GAATTTTAAAAAAAATTATT
206459 GAATTTT--AAAAAATTATT
1 GAATTTTAAAAAAAATTATT
206477 GAATTTTAA
1 GAATTTTAA
206486 TTTGATCCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 18 0.72
20 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
GAATTTTAAAAAAAATTATT
Found at i:207016 original size:31 final size:31
Alignment explanation
Indices: 206978--207037 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
206968 AAGTTTTTTA
206978 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
207009 TACGAGCTGTGGTGAGAGGATGAAGCTTT
1 TACGAGCTGTGGCGAGAGGATGAAGCTTT
207038 TGCATGTGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.25
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:207074 original size:22 final size:22
Alignment explanation
Indices: 207046--207088 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
207036 TTTGCATGTG
207046 CCATGCACGTCGGAAGAGGTCA
1 CCATGCACGTCGGAAGAGGTCA
*
207068 CCATGCACGTTGGAAGAGGTC
1 CCATGCACGTCGGAAGAGGTC
207089 GCCTGCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.16
Consensus pattern (22 bp):
CCATGCACGTCGGAAGAGGTCA
Done.