Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015237.1 Kokia drynarioides strain JFW-HI SEQ_130282, 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: 810367
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 195 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:223904 original size:21 final size:20
Alignment explanation
Indices: 223878--223916 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
223868 GGGGGAAAGT
223878 GAGAAAGAGAAAAAGTTTTTG
1 GAGAAA-AGAAAAAGTTTTTG
*
223899 GAGAAAATAAAAAGTTTT
1 GAGAAAAGAAAAAGTTTT
223917 GAGGGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (20 bp):
GAGAAAAGAAAAAGTTTTTG
Found at i:224076 original size:164 final size:169
Alignment explanation
Indices: 223750--224081 Score: 405
Period size: 164 Copynumber: 2.0 Consensus size: 169
223740 GGAAGTAAAA
* * * *
223750 TTTTGAGGGAAAGTAATTAGGGGAGTAAAATTTTGGAGGGAAAATATTCAAAAAAATTGGGAGGG
1 TTTTGAGGGAAAATAAATAGGGGAGTAAAATTTTGGAAGAAAAATATT-AAAAAAATT--GAGGG
* * * *
223815 GGGAATGGGTTTGGGTAGATGGAGGGTTGGATAGGAAGGGAGTAAATGTTTTAGGGGGAAAGTGA
63 GGAAATGGGTTTGGGTAGAT-GAGGGGTGAATAGGAAGGGAGTAAAAGTTTTAGGGGGAAAGTGA
*
223880 GAAAGAGAAAAAGTTTTTGGAGAAAATAAAAAGTTTTGAGGGT
127 GAAAGAGAAAAAGTTTTTGGAGAAAATAAAAAGGTTTGAGGGT
223923 TTTTGA-GGAAAATAAAT-GGGGAGTAAAATTTTGGAAGAAAAATATT-AAAAAATT-AGGGGGA
1 TTTTGAGGGAAAATAAATAGGGGAGTAAAATTTTGGAAGAAAAATATTAAAAAAATTGAGGGGGA
*
223984 AATGGGTTTGGGGTA-AT-AGGGGTGAA-ATGTGAGGGGAGTAAAAGTTTT-GGGGGAAAGTGA-
66 AATGGGTTT-GGGTAGATGAGGGGTGAATA-G-GAAGGGAGTAAAAGTTTTAGGGGGAAAGTGAG
* *
224044 AGAAGAGTAAAAG-TTTTGGGGAAAAGTAAAAAGGTTTG
128 A-AAGAGAAAAAGTTTTTGGAGAAAA-TAAAAAGGTTTG
224082 GAGTTTGGGG
Statistics
Matches: 142, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
163 13 0.09
164 41 0.29
165 16 0.11
166 17 0.12
167 5 0.04
169 8 0.06
171 27 0.19
172 9 0.06
173 6 0.04
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (169 bp):
TTTTGAGGGAAAATAAATAGGGGAGTAAAATTTTGGAAGAAAAATATTAAAAAAATTGAGGGGGA
AATGGGTTTGGGTAGATGAGGGGTGAATAGGAAGGGAGTAAAAGTTTTAGGGGGAAAGTGAGAAA
GAGAAAAAGTTTTTGGAGAAAATAAAAAGGTTTGAGGGT
Found at i:224132 original size:9 final size:9
Alignment explanation
Indices: 224118--224154 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
224108 TATAGTTTAA
*
224118 TATTCGATT
1 TATTCGAAT
224127 TATTCGAAT
1 TATTCGAAT
*
224136 TATTCGAGT
1 TATTCGAAT
224145 TATTCGAAT
1 TATTCGAAT
224154 T
1 T
224155 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:224141 original size:18 final size:18
Alignment explanation
Indices: 224118--224154 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
224108 TATAGTTTAA
*
224118 TATTCGATTTATTCGAAT
1 TATTCGAGTTATTCGAAT
224136 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCGAAT
224154 T
1 T
224155 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCGAAT
Found at i:225933 original size:21 final size:21
Alignment explanation
Indices: 225908--225947 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
225898 AGTCGAAACT
*
225908 ACTTTTGTATTATCGAATTTA
1 ACTTTTGTATCATCGAATTTA
*
225929 ACTTTTGTATCATTGAATT
1 ACTTTTGTATCATCGAATT
225948 CAACATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (21 bp):
ACTTTTGTATCATCGAATTTA
Found at i:232647 original size:19 final size:19
Alignment explanation
Indices: 232612--232649 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
232602 ATTTAAATTA
*
232612 CTATGTTGAGATAGATTTT
1 CTATGTTGAGAAAGATTTT
232631 CTATGTT-AGAAAGGATTTT
1 CTATGTTGAGAAA-GATTTT
232650 TTAAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (19 bp):
CTATGTTGAGAAAGATTTT
Found at i:233885 original size:21 final size:21
Alignment explanation
Indices: 233839--233890 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
233829 ACAGAGAGTC
233839 ATGGGAGAA-AAAGGGAAGGA
1 ATGGGAGAATAAAGGGAAGGA
*
233859 ATTGGGAGAATAACGAGG-AGGA
1 A-TGGGAGAATAAAG-GGAAGGA
*
233881 ATGGGTGAAT
1 ATGGGAGAAT
233891 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 16 0.59
22 8 0.30
23 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.42, T:0.13
Consensus pattern (21 bp):
ATGGGAGAATAAAGGGAAGGA
Found at i:236464 original size:34 final size:34
Alignment explanation
Indices: 236421--236489 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
236411 TTAAACCAAA
236421 AACGATTCAAGTCGTTGTTTACTTTGATGATTTG
1 AACGATTCAAGTCGTTGTTTACTTTGATGATTTG
*
236455 AACGATTCAAGTCGTTGTTTGCTTTGATGATTTG
1 AACGATTCAAGTCGTTGTTTACTTTGATGATTTG
236489 A
1 A
236490 TACAAGCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (34 bp):
AACGATTCAAGTCGTTGTTTACTTTGATGATTTG
Found at i:236779 original size:12 final size:12
Alignment explanation
Indices: 236764--236801 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
236754 ACATTTTGCA
236764 TGTTGTTTTTGG
1 TGTTGTTTTTGG
236776 TGTTG-TTTTGG
1 TGTTGTTTTTGG
*
236787 CTATTGTTTTTGG
1 -TGTTGTTTTTGG
236800 TG
1 TG
236802 CTATTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 6 0.27
12 10 0.45
13 6 0.27
ACGTcount: A:0.03, C:0.03, G:0.32, T:0.63
Consensus pattern (12 bp):
TGTTGTTTTTGG
Found at i:236784 original size:24 final size:23
Alignment explanation
Indices: 236756--236818 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
236746 GGTTGATTAC
*
236756 ATTTTGCATGTTGTTTTTGGTGTT
1 ATTTTGC-TGTTGTTTTTGGTGCT
* *
236780 GTTTTGGCTATTGTTTTTGGTGCT
1 ATTTT-GCTGTTGTTTTTGGTGCT
*
236804 ATTTTACTGTTGTTT
1 ATTTTGCTGTTGTTT
236819 CGCTGTGGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 8 0.25
24 22 0.69
25 2 0.06
ACGTcount: A:0.08, C:0.06, G:0.24, T:0.62
Consensus pattern (23 bp):
ATTTTGCTGTTGTTTTTGGTGCT
Found at i:236957 original size:24 final size:26
Alignment explanation
Indices: 236930--236977 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
236920 TATTGAGAAA
*
236930 TATTTGAT-T-TAATGTTTTTAAATG
1 TATTTGATATATAATATTTTTAAATG
236954 TATTTGATATATAATATTTTTAAA
1 TATTTGATATATAATATTTTTAAA
236978 ATTTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (26 bp):
TATTTGATATATAATATTTTTAAATG
Found at i:240531 original size:14 final size:16
Alignment explanation
Indices: 240512--240545 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
240502 GAATAAAGTG
240512 TTTTTGAGAC-T-TAA
1 TTTTTGAGACATGTAA
240526 TTTTTGAGACATGTAA
1 TTTTTGAGACATGTAA
240542 TTTT
1 TTTT
240546 GGTATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 1 0.06
16 7 0.39
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (16 bp):
TTTTTGAGACATGTAA
Found at i:242669 original size:13 final size:13
Alignment explanation
Indices: 242651--242684 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
242641 TTGATTAGAC
242651 TTTAGTTTTTAAG
1 TTTAGTTTTTAAG
**
242664 TTTAGTTTTTATT
1 TTTAGTTTTTAAG
242677 TTTAGTTT
1 TTTAGTTT
242685 CGAAACGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (13 bp):
TTTAGTTTTTAAG
Found at i:250629 original size:81 final size:81
Alignment explanation
Indices: 250522--250698 Score: 291
Period size: 81 Copynumber: 2.2 Consensus size: 81
250512 AGCCAAAAAA
* ** *
250522 ATTTTTAGGGGGGCCGAAGTTAAATTGTAATTTTAATGATAGTAAAAATGTAATTTTTAAAGGAT
1 ATTTTTA-GGGGGTCGAAAATAAATTGTAATTTTAATGATAGTAAAAAAGTAATTTTTAAAGGAT
250587 TAAATCAAAATTTTATC
65 TAAATCAAAATTTTATC
*
250604 ATTTTTAGGGGGTCGAAAATAAATTGTAATTTTTATGATAGTAAAAAAGTAATTTTTAAAGGATT
1 ATTTTTAGGGGGTCGAAAATAAATTGTAATTTTAATGATAGTAAAAAAGTAATTTTTAAAGGATT
250669 AAATCAAAATTTTATC
66 AAATCAAAATTTTATC
*
250685 AATTTTAGGGGGTC
1 ATTTTTAGGGGGTC
250699 AAAGTGGAAT
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
81 82 0.92
82 7 0.08
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (81 bp):
ATTTTTAGGGGGTCGAAAATAAATTGTAATTTTAATGATAGTAAAAAAGTAATTTTTAAAGGATT
AAATCAAAATTTTATC
Found at i:252924 original size:23 final size:23
Alignment explanation
Indices: 252894--253023 Score: 188
Period size: 23 Copynumber: 5.7 Consensus size: 23
252884 TATATCTATA
252894 CTTAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
*
252917 CTTAAATATTAATATGATTTATG
1 CTTAAATATTAATGTGATTTATG
* * *
252940 ATTAAATATTAATGTGACTTGTG
1 CTTAAATATTAATGTGATTTATG
*
252963 CTTAAGTATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
* *
252986 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTATG
*
253009 CTCAAATATTAATGT
1 CTTAAATATTAATGT
253024 TAAATATTAA
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 93 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.46
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTATG
Found at i:252965 original size:46 final size:46
Alignment explanation
Indices: 252894--253234 Score: 407
Period size: 46 Copynumber: 7.6 Consensus size: 46
252884 TATATCTATA
*
252894 CTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTATG
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
* * * *
252940 ATTAAATATTAATGTGACTTGTGCTTAAGTATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
* *
252986 CTTAAATATTAATATGATTTGTGC-TCAA-A-T-AT-T-A---ATG
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
* * * *
253023 -TTAAATATTAATATGATTTGTG-TTCATATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTGCTT-AAATATTAATATGATTTATG
* * *
253068 CTTAAATATTAATGTGATTTGTGCTCAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
* * * *
253114 CCTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
* *
253160 CTCAAATATTAATGTGACTTGTGCTTAAATATTAATATGATTTATG
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
*
253206 ATTAAATATTAATGTGATTTGTGCTTAAA
1 CTTAAATATTAATGTGATTTGTGCTTAAA
253235 GAATTAGAAT
Statistics
Matches: 255, Mismatches: 28, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
36 23 0.09
37 4 0.02
38 1 0.00
39 1 0.00
40 3 0.01
41 2 0.01
42 3 0.01
43 1 0.00
44 1 0.00
45 4 0.02
46 211 0.83
47 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (46 bp):
CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTATG
Found at i:253005 original size:69 final size:69
Alignment explanation
Indices: 252894--253234 Score: 434
Period size: 69 Copynumber: 5.1 Consensus size: 69
252884 TATATCTATA
* * * *
252894 CTTAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGACT
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAATGTGATT
252959 TGTG
66 TGTG
* * *
252963 CTTAAGTATTAATGTGATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATT-A----A--
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAATGTGATT
253021 --TG
66 TGTG
* * *
253023 -TTAAATATTAATATGATTTGTG-TTCATATATTAATGTGATTTGTGCTTAAATATTAATGTGAT
1 CTTAAATATTAATGTGATTTGTGCTT-AAATATTAATATGATTTGTGCTTAAATATTAATGTGAT
253086 TTGTG
65 TTGTG
* * * *
253091 CTCAAATATTAATGTGATTTGTGCCTAAATATTAATATGATTTGTGCTCAAATATTAATATGATT
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAATGTGATT
253156 TGTG
66 TGTG
* * * *
253160 CTCAAATATTAATGTGACTTGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATT
1 CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAATGTGATT
253225 TGTG
66 TGTG
253229 CTTAAA
1 CTTAAA
253235 GAATTAGAAT
Statistics
Matches: 236, Mismatches: 24, Indels: 24
0.83 0.08 0.08
Matches are distributed among these distances:
58 2 0.01
59 46 0.19
60 3 0.01
64 2 0.01
68 3 0.01
69 179 0.76
70 1 0.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (69 bp):
CTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTTAAATATTAATGTGATT
TGTG
Found at i:253034 original size:36 final size:36
Alignment explanation
Indices: 252987--253059 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
252977 TGATTTATGC
252987 TTAAATATTAATATGATTTGTGCTCAAATATTAATG
1 TTAAATATTAATATGATTTGTGCTCAAATATTAATG
* *
253023 TTAAATATTAATATGATTTGTGTTCATATATTAATG
1 TTAAATATTAATATGATTTGTGCTCAAATATTAATG
253059 T
1 T
253060 GATTTGTGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (36 bp):
TTAAATATTAATATGATTTGTGCTCAAATATTAATG
Found at i:253233 original size:23 final size:23
Alignment explanation
Indices: 253023--253234 Score: 300
Period size: 23 Copynumber: 9.2 Consensus size: 23
253013 AATATTAATG
*
253023 TTAAATATTAATATGATTTGTG-
1 TTAAATATTAATGTGATTTGTGC
*
253045 TTCATATATTAATGTGATTTGTGC
1 TT-AAATATTAATGTGATTTGTGC
253069 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
*
253092 TCAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
* *
253115 CTAAATATTAATATGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
* *
253138 TCAAATATTAATATGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
* *
253161 TCAAATATTAATGTGACTTGTGC
1 TTAAATATTAATGTGATTTGTGC
* * *
253184 TTAAATATTAATATGATTTATGA
1 TTAAATATTAATGTGATTTGTGC
253207 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
253230 TTAAA
1 TTAAA
253235 GAATTAGAAT
Statistics
Matches: 169, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
22 2 0.01
23 165 0.98
24 2 0.01
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTGTGC
Found at i:257418 original size:15 final size:15
Alignment explanation
Indices: 257386--257427 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
257376 CGAGGCAACG
257386 TCTTCTTCTTCTTCCT
1 TCTT-TTCTTCTTCCT
257402 TCTTTTCTT-TTCTCT
1 TCTTTTCTTCTTC-CT
257417 TCTTTTACTTC
1 TCTTTT-CTTC
257428 AATACCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTTTTCTTCTTCCT
Found at i:266400 original size:28 final size:28
Alignment explanation
Indices: 266347--266413 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
266337 GTTAGCTTCT
* *
266347 ATATATGGTCGGCTCTGTCCCCTGAATG
1 ATATATGGTCAGCTCTGTCCCCTGAATA
* *
266375 ATATATGGTCAGCTTTG-CCACTTGAATA
1 ATATATGGTCAGCTCTGTCC-CCTGAATA
*
266403 ACATATGGTCA
1 ATATATGGTCA
266414 ACCCTGTCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 2 0.06
28 31 0.94
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (28 bp):
ATATATGGTCAGCTCTGTCCCCTGAATA
Found at i:270159 original size:10 final size:10
Alignment explanation
Indices: 270089--270160 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 10
270079 AATTTAAAAA
*
270089 TATATATATT
1 TATATATTTT
*
270099 TATATATTTA
1 TATATATTTT
270109 TAT-TATTTT
1 TATATATTTT
*
270118 TA-ATAATTT
1 TATATATTTT
*
270127 TA-ATTTTTT
1 TATATATTTT
*
270136 TAAAAATAATTTT
1 T--ATAT-ATTTT
270149 TATATATTTT
1 TATATATTTT
270159 TA
1 TA
270161 AGTTTTTAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 20 0.41
10 18 0.37
11 4 0.08
12 2 0.04
13 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATATTTT
Found at i:270175 original size:41 final size:43
Alignment explanation
Indices: 270105--270190 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 43
270095 TATTTATATA
270105 TTTATATTATTTTTAATAATTTTAATTTTTTTAAA-AA-TAATT
1 TTTATATTATTTTTAAT-ATTTTAATTTTTTTAAATAATTAATT
270147 TTTATA-TATTTTTAAGT-TTTTAATTTTTTTTAAATAATTAATT
1 TTTATATTATTTTTAA-TATTTTAA-TTTTTTTAAATAATTAATT
270190 T
1 T
270191 CTAACGTGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
40 6 0.15
41 19 0.47
42 9 0.22
43 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (43 bp):
TTTATATTATTTTTAATATTTTAATTTTTTTAAATAATTAATT
Found at i:270185 original size:39 final size:41
Alignment explanation
Indices: 270105--270185 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
270095 TATTTATATA
270105 TTTATATTATTTTTAATAATTTTAATTTTTTTAAAAATAATT
1 TTTATATTATTTTTAAT-ATTTTAATTTTTTTAAAAATAATT
*
270147 TTTATA-TATTTTTAAGT-TTTTAATTTTTTT-TAAATAATT
1 TTTATATTATTTTTAA-TATTTTAATTTTTTTAAAAATAATT
270186 AATTTCTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 8 0.22
40 13 0.35
41 9 0.24
42 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (41 bp):
TTTATATTATTTTTAATATTTTAATTTTTTTAAAAATAATT
Found at i:274334 original size:17 final size:17
Alignment explanation
Indices: 274314--274350 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
274304 TTTTAAGTAC
*
274314 TTATTTTGAGTTTAAAT
1 TTATTTTGAATTTAAAT
274331 TTATTTTGAATTTAAAT
1 TTATTTTGAATTTAAAT
274348 TTA
1 TTA
274351 AAATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (17 bp):
TTATTTTGAATTTAAAT
Found at i:274958 original size:7 final size:7
Alignment explanation
Indices: 274938--275005 Score: 56
Period size: 7 Copynumber: 10.4 Consensus size: 7
274928 ATGATTTCAT
*
274938 TAAATGA
1 TAAATAA
274945 TAAATAA
1 TAAATAA
*
274952 TACATAA
1 TAAATAA
274959 TAAATAA
1 TAAATAA
*
274966 T-TATAA
1 TAAATAA
*
274972 T-ATTAA
1 TAAATAA
274978 T-AATAA
1 TAAATAA
274984 TAAAT-A
1 TAAATAA
274990 -AAATAA
1 TAAATAA
*
274996 TAAAAAA
1 TAAATAA
275003 TAA
1 TAA
275006 GTTTAAGGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 4 0.08
6 16 0.32
7 30 0.60
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (7 bp):
TAAATAA
Found at i:274961 original size:3 final size:3
Alignment explanation
Indices: 274947--274998 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
274937 TTAAATGATA
* *
274947 AAT AAT ACAT AAT AAAT AAT TAT AAT ATT AAT AAT AAT AAAT AA- AAT
1 AAT AAT A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
274994 AAT AA
1 AAT AA
274999 AAAATAAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:275003 original size:15 final size:15
Alignment explanation
Indices: 274976--275005 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
274966 TTATAATATT
*
274976 AATAATAATAAATAA
1 AATAATAAAAAATAA
274991 AATAATAAAAAATAA
1 AATAATAAAAAATAA
275006 GTTTAAGGGA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAATAAAAAATAA
Found at i:281741 original size:6 final size:6
Alignment explanation
Indices: 281730--281757 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
281720 ATTTGACAAA
281730 CATACT CATACT CATACT CATACT CATA
1 CATACT CATACT CATACT CATACT CATA
281758 ACATGTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
CATACT
Found at i:284008 original size:3 final size:3
Alignment explanation
Indices: 284002--284040 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
283992 TTATGATATT
284002 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
284041 AGGGATGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:286349 original size:39 final size:39
Alignment explanation
Indices: 286295--286616 Score: 276
Period size: 39 Copynumber: 8.3 Consensus size: 39
286285 CAGTCATTCG
* *
286295 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
* *** ** *
286334 ATCTCTTACCCCGAGCCTGGTGTAGAT-TGTAGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCA-TCAGCCA
* *
286373 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
* *
286412 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
* * *
286451 ATCTCTTACCCTGAGCCTAGGGTAGATTGCAGCCAT---TCA
1 ATCTCTTACCCCGAGCCTGGGGTAGA-T-CA-CCATCAGCCA
* * *
286490 ATCTCTTACCCCGAGCCTGGGGTAGATCACAATTAGTCA
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
* * * * * * ** *
286529 ATCTCTTACCCCGAACCTGGAGCAGATTA-TAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCA-TCAGCCA
* * *
286568 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
*
286607 ATTTCTTACC
1 ATCTCTTACC
286617 TTGATCATGG
Statistics
Matches: 229, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
36 3 0.01
37 2 0.01
38 3 0.01
39 213 0.93
40 3 0.01
41 2 0.01
42 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGTAGATCACCATCAGCCA
Found at i:286501 original size:117 final size:117
Alignment explanation
Indices: 286295--286555 Score: 373
Period size: 117 Copynumber: 2.2 Consensus size: 117
286285 CAGTCATTCG
* * *
286295 ATCTCTTACCCCGAGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCCTGGTGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGTGTAGA
* * *
286360 TTGTAGTCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAGCCA
66 TTGCAGCCATTCAATCTCTTACCCCGAGCCTGGGGCAGATCA-CAATCAGCCA
* *
286412 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCAATCTCTTACCCTGAGCCTAGG-GTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCT-GGTGTAG
* * *
286476 ATTGCAGCCATTCAATCTCTTACCCCGAGCCTGGGGTAGATCACAATTAGTCA
65 ATTGCAGCCATTCAATCTCTTACCCCGAGCCTGGGGCAGATCACAATCAGCCA
* *
286529 ATCTCTTACCCCGAACCTGGAGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
286556 TATAGCCATT
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
116 1 0.01
117 126 0.98
118 2 0.02
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (117 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGTGTAGA
TTGCAGCCATTCAATCTCTTACCCCGAGCCTGGGGCAGATCACAATCAGCCA
Found at i:286616 original size:117 final size:117
Alignment explanation
Indices: 286295--286594 Score: 311
Period size: 117 Copynumber: 2.6 Consensus size: 117
286285 CAGTCATTCG
* * * * * *
286295 ATCTCTTACCCCGAGCCTAGG-GTAAATCACCATCAGCCAATCTCTTACCCCGAGCCT-GGTGTA
1 ATCTCTTACCCCGAACCT-GGAGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTAGG-GCA
* * * *
286358 GATTGTAGTCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
64 GATTGCAGCCATCCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
* * * * *
286412 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCAATCTCTTACCCTGAGCCTAGGGTAGA
1 ATCTCTTACCCCGAACCTGGAGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
* * * *
286477 TTGCAGCCATTCAATCTCTTACCCCGAGCCTGGGGTAGATCA-CAATTAGTCA
66 TTGCAGCCATCCAATCTCTTACCCCGAGCCTGGGGCAGATCATC-ATCAGCCA
* ** * * *
286529 ATCTCTTACCCCGAACCTGGAGCAGATTAT-AGCCATTCGATCTCTTACCCCGAGCTTGGGGCAG
1 ATCTCTTACCCCGAACCTGGAGCAGATCATCA-CCAGCCAATCTCTTACCCCGAGCCTAGGGCAG
286593 AT
65 AT
286595 CACCATCAAC
Statistics
Matches: 158, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
116 4 0.03
117 152 0.96
118 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (117 bp):
ATCTCTTACCCCGAACCTGGAGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
TTGCAGCCATCCAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCA
Found at i:286644 original size:78 final size:78
Alignment explanation
Indices: 286412--286646 Score: 281
Period size: 78 Copynumber: 3.0 Consensus size: 78
286402 TCATCAGCCA
* * * *
286412 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAGCCAATCTCTTACCCTGAGCCTAGGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCTGAACCTGGGGCAGA
*
286477 TTGCAGCCATTCA
66 TTGCAGCCATTCG
* * * * * *
286490 ATCTCTTACCCCGAGCCTGGGGTAGATCACAATTAGTCAATCTCTTACCCCGAACCTGGAGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCTGAACCTGGGGCAGA
**
286555 TTATAGCCATTCG
66 TTGCAGCCATTCG
* * * * * *
286568 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAACCAATTTCTTACCTTGATCATGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCTGAACCTGGGGCAGA
* *
286633 TGGCAGTCATTCG
66 TTGCAGCCATTCG
286646 A
1 A
286647 AGCAATAAAG
Statistics
Matches: 128, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 128 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCTGAACCTGGGGCAGA
TTGCAGCCATTCG
Found at i:287026 original size:17 final size:17
Alignment explanation
Indices: 287006--287091 Score: 109
Period size: 17 Copynumber: 5.1 Consensus size: 17
286996 CCAATTTTAA
*
287006 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
287023 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* *
287040 ACTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
287057 ATTCTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
287074 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
287091 A
1 A
287092 AAATTTAATT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:287034 original size:6 final size:6
Alignment explanation
Indices: 287001--287099 Score: 64
Period size: 6 Copynumber: 16.8 Consensus size: 6
286991 TGAACCCAAT
* * * *
287001 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AC TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
287048 TTTAAA CTT--A TTCTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTTAAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
287095 TTTAA
1 TTTAA
287100 TTAAAAGTCC
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
4 2 0.03
5 13 0.18
6 43 0.60
7 14 0.19
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:287050 original size:34 final size:34
Alignment explanation
Indices: 287008--287091 Score: 123
Period size: 34 Copynumber: 2.5 Consensus size: 34
286998 AATTTTAAAT
* *
287008 TTTAAATTTTAATTTATTTTAAGTTTAAATTTAC
1 TTTAAATTTAAATTTATTCTAAGTTTAAATTTAC
* * *
287042 TTTAAATTTAAACTTATTCTGAGTTTAAATTTAT
1 TTTAAATTTAAATTTATTCTAAGTTTAAATTTAC
287076 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
287092 AAATTTAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTAAATTTAAATTTATTCTAAGTTTAAATTTAC
Found at i:287714 original size:7 final size:7
Alignment explanation
Indices: 287694--287755 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
287684 ACAATTTCAT
*
287694 TAAATGA
1 TAAATAA
287701 TAAATAA
1 TAAATAA
*
287708 TACATAA
1 TAAATAA
287715 TAAATAA
1 TAAATAA
*
287722 T-TATAA
1 TAAATAA
*
287728 T-ATTAA
1 TAAATAA
287734 T-AATAA
1 TAAATAA
287740 TAAAT-A
1 TAAATAA
287746 -AAATAA
1 TAAATAA
287752 TAAA
1 TAAA
287756 AAAGAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 4 0.09
6 16 0.36
7 25 0.56
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (7 bp):
TAAATAA
Found at i:287717 original size:3 final size:3
Alignment explanation
Indices: 287703--287754 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
287693 TTAAATGATA
* *
287703 AAT AAT ACAT AAT AAAT AAT TAT AAT ATT AAT AAT AAT AAAT AA- AAT
1 AAT AAT A-AT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
287750 AAT AA
1 AAT AA
287755 AAAAGAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:288661 original size:29 final size:29
Alignment explanation
Indices: 288629--288906 Score: 144
Period size: 29 Copynumber: 9.6 Consensus size: 29
288619 AAAATTTTCC
288629 AAAATTACATTTTTACCCTTGAACTCCTA
1 AAAATTACATTTTTACCCTTGAACTCCTA
* * * *
288658 AAAATTATATTTTTGCCCTCGAACTTCTA
1 AAAATTACATTTTTACCCTTGAACTCCTA
* * * * *
288687 AAAATTACA-TTTTGCCCCTAAATTTCTA
1 AAAATTACATTTTTACCCTTGAACTCCTA
* *
288715 AAAATTGCTTTTTTACCCCTTGAACTTCC-A
1 AAAATTACATTTTTA-CCCTTGAAC-TCCTA
* * *** *
288745 AAAATCATATTTTTACCCCCAAACTTCTCA
1 AAAATTACATTTTTACCCTTGAACTCCT-A
* * *
288775 AAAATTAAAATTTTACCC-TAAACTTCC-A
1 AAAATTACATTTTTACCCTTGAAC-TCCTA
* * *
288803 AAAATCACA-TTTTA-CCTTGAATTTCCCA
1 AAAATTACATTTTTACCCTTGAA-CTCCTA
* * **
288831 AAAATGATATTTTTATCCCTAAAACTTCC--
1 AAAATTACATTTTTA-CCCTTGAAC-TCCTA
*
288860 AAAATTACATTTTTA-CCTCGAACTTTCCT-
1 AAAATTACATTTTTACCCTTGAAC--TCCTA
*
288889 AAAATGACATTTTTACCC
1 AAAATTACATTTTTACCC
288907 CTAAATCTTT
Statistics
Matches: 190, Mismatches: 43, Indels: 31
0.72 0.16 0.12
Matches are distributed among these distances:
26 2 0.01
27 17 0.09
28 44 0.23
29 79 0.42
30 38 0.20
31 10 0.05
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTTGAACTCCTA
Found at i:288693 original size:58 final size:58
Alignment explanation
Indices: 288625--288943 Score: 183
Period size: 58 Copynumber: 5.5 Consensus size: 58
288615 CCCTAAAATT
* * * *
288625 TTCC-AAAATTACATTTTTACCCTTGAACTCCTAAAAATTATATTTTT-GCCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCCTAAACTCCTAAAAATTATATTTTTAACCCT-AAAC
* * * * * * *
288682 TTCTAAAAATTACA-TTTTGCCCCTAAATTTCTAAAAATTGCT-TTTTTACCCCTTGAAC
1 TTCCAAAAATTACATTTTTACCCCTAAACTCCTAAAAATT-ATATTTTTAACCC-TAAAC
* * * * * *
288740 TTCCAAAAATCATATTTTTACCCCCAAACTTCTCAAAAATTAAAATTTT-ACCCTAAAC
1 TTCCAAAAATTACATTTTTACCCCTAAACTCCT-AAAAATTATATTTTTAACCCTAAAC
* * ** * * *
288798 TTCCAAAAATCACA-TTTTA-CCTTGAATTTCCCAAAAATGATATTTTTATCCCTAAAAC
1 TTCCAAAAATTACATTTTTACCCCT-AAACTCCTAAAAATTATATTTTTAACCCT-AAAC
* * * * *
288856 TTCC-AAAATTACATTTTTACCTC-GAACTTTCCT-AAAATGACATTTTTACCCCTAAATC
1 TTCCAAAAATTACATTTTTACCCCTAAAC--TCCTAAAAATTATATTTTTAACCCTAAA-C
*** *
288914 TTTTTAAAATTACATTTTAACCCC-AAACTC
1 TTCCAAAAATTACATTTTTACCCCTAAACTC
288944 TCCGAAACTT
Statistics
Matches: 202, Mismatches: 44, Indels: 32
0.73 0.16 0.12
Matches are distributed among these distances:
56 14 0.07
57 55 0.27
58 79 0.39
59 43 0.21
60 11 0.05
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (58 bp):
TTCCAAAAATTACATTTTTACCCCTAAACTCCTAAAAATTATATTTTTAACCCTAAAC
Found at i:288700 original size:28 final size:28
Alignment explanation
Indices: 288629--288942 Score: 131
Period size: 29 Copynumber: 10.9 Consensus size: 28
288619 AAAATTTTCC
** *
288629 AAAATTACATTTTTACCCTTGAACTCCTA
1 AAAATTACA-TTTTACCCTCAAACTTCTA
* * *
288658 AAAATTATATTTTTGCCCTCGAACTTCTA
1 AAAATTACA-TTTTACCCTCAAACTTCTA
* *
288687 AAAATTACATTTTGCCC-CTAAATTTCTA
1 AAAATTACATTTTACCCTC-AAACTTCTA
* * ** *
288715 AAAATTGCTTTTTTACCCCTTGAACTTCCA
1 AAAATTAC-ATTTTA-CCCTCAAACTTCTA
* * *
288745 AAAATCATATTTTTACCCCCAAACTTCTCA
1 AAAATTACA-TTTTACCCTCAAACTTCT-A
* *
288775 AAAATTAAAATTTTACCCT-AAACTTCCA
1 AAAATT-ACATTTTACCCTCAAACTTCTA
* ** * *
288803 AAAATCACATTTTA-CCTTGAATTTCCCA
1 AAAATTACATTTTACCCTCAAACTT-CTA
* * * *
288831 AAAATGATATTTTTATCCCTAAAACTTC-C
1 AAAATTACA-TTTTA-CCCTCAAACTTCTA
*
288860 AAAATTACATTTTTA-CCTCGAACTTTCCT-
1 AAAATTACA-TTTTACCCTCAAAC-TT-CTA
* * *
288889 AAAATGACATTTTTACCC-CTAAATCTTTTT
1 AAAATTACA-TTTTACCCTC-AAA-CTTCTA
288919 AAAATTACATTTTAACCC-CAAACT
1 AAAATTACATTTT-ACCCTCAAACT
288943 CTCCGAAACT
Statistics
Matches: 221, Mismatches: 44, Indels: 41
0.72 0.14 0.13
Matches are distributed among these distances:
26 3 0.01
27 18 0.08
28 42 0.19
29 95 0.43
30 53 0.24
31 10 0.05
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAATTACATTTTACCCTCAAACTTCTA
Found at i:288901 original size:86 final size:85
Alignment explanation
Indices: 288625--288876 Score: 212
Period size: 87 Copynumber: 2.9 Consensus size: 85
288615 CCCTAAAATT
* * * *
288625 TTCC-AAAATTACATTTTTACCCTTGAAC-TCCTAAAAATTATATTTTTGCCCTC-GAACTTCT-
1 TTCCAAAAATCACA-TTTTA-CCTTGAACTTCC-AAAAATCATATTTTTACCC-CAAAACTTCTC
* * *
288686 AAAAATT-ACATTTTGCCCCTAAAT
62 AAAAATTAAAATTTT-ACCCTAAAC
* ** * *
288710 TTCTAAAAATTGCTTTTTTACCCCTTGAACTTCCAAAAATCATATTTTTACCCCCAAACTTCTCA
1 TTCCAAAAATCAC-ATTTTA--CCTTGAACTTCCAAAAATCATATTTTTACCCCAAAACTTCTCA
288775 AAAATTAAAATTTTACCCTAAAC
63 AAAATTAAAATTTTACCCTAAAC
* * *
288798 TTCCAAAAATCACATTTTACCTTGAATTTCCCAAAAATGATATTTTTATCCCTAAAACTTC-C-A
1 TTCCAAAAATCACATTTTACCTTGAACTT-CCAAAAATCATATTTTTA-CCCCAAAACTTCTCAA
* *
288861 AAATTACATTTTTACC
64 AAATTAAAATTTTACC
288877 TCGAACTTTC
Statistics
Matches: 139, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
85 27 0.19
86 31 0.22
87 48 0.35
88 27 0.19
89 6 0.04
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (85 bp):
TTCCAAAAATCACATTTTACCTTGAACTTCCAAAAATCATATTTTTACCCCAAAACTTCTCAAAA
ATTAAAATTTTACCCTAAAC
Found at i:295849 original size:51 final size:51
Alignment explanation
Indices: 295789--295891 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
295779 TTAACATCGA
*
295789 AATGAAAAGAGGAAATCATGTACTTGAATGCCAAAAGAGATGGGTGATAAT
1 AATGAAAAGAGGAAATCATGTACTTGAATGCCAAAAGAGATGGATGATAAT
295840 AATGAAAAGAGGAAATCATGTACTTGAATGCCAAAAGAGATGGATGATAAT
1 AATGAAAAGAGGAAATCATGTACTTGAATGCCAAAAGAGATGGATGATAAT
295891 A
1 A
295892 CCAGGAAGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (51 bp):
AATGAAAAGAGGAAATCATGTACTTGAATGCCAAAAGAGATGGATGATAAT
Found at i:301618 original size:15 final size:15
Alignment explanation
Indices: 301598--301627 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
301588 ATATTAAAGA
301598 AAGACTTGATAGAGG
1 AAGACTTGATAGAGG
301613 AAGACTTGATAGAGG
1 AAGACTTGATAGAGG
301628 CGTTGCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
AAGACTTGATAGAGG
Found at i:316771 original size:3 final size:3
Alignment explanation
Indices: 316763--316800 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
316753 AATTCTTCCC
316763 ATT ATT ATT AATT ATT ATT ATT ATT ATT -TT ATT -TT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
316801 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:316784 original size:16 final size:14
Alignment explanation
Indices: 316763--316800 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
316753 AATTCTTCCC
316763 ATTATTATTAATTATT
1 ATTATTATT-ATT-TT
316779 ATTATTATTATTTT
1 ATTATTATTATTTT
316793 ATT-TTATT
1 ATTATTATT
316801 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 5 0.23
15 3 0.14
16 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTATTATTTT
Found at i:317747 original size:24 final size:24
Alignment explanation
Indices: 317714--317788 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
317704 AGAAATAATC
*
317714 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
317738 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
317762 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
317786 TTT
1 TTT
317789 GAGTCAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:319762 original size:24 final size:24
Alignment explanation
Indices: 319729--319779 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
319719 AGAAATAATT
*
319729 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
319753 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
319777 TTT
1 TTT
319780 GAGTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:323395 original size:140 final size:142
Alignment explanation
Indices: 322951--323491 Score: 468
Period size: 134 Copynumber: 3.9 Consensus size: 142
322941 TAGGTGTACA
* * * ** *
322951 CTGTTGTGTTTATTATACTGTTTTCATGCTTGATAAACATGTGCCA--TGTCAAGTTTTTATATG
1 CTGTTGTGTTTATTATACTGTTTTCATGTTTAATAAACA--TG-CATTTGACTTGTTTTCATATG
* * **
323014 GTGTTCATGAATTTCAGTAAT-GCCATATATAATTCACATTTAGG-TTTTGAAATTTAGCTCAAT
63 GTGTTCATGAATTTCAATAATAG-CATATACAATTCACATTTAGGCTTTACAAATTTAGCTCAAT
*
323077 TGTACTTAAAACGTA--
127 TGTAATT-AAACGTATT
** * *
323092 ---TTGTG----TTATACTGTTTTTGTGTTTAATAAACATGCATTTTGACTTGTGTCCATATGGT
1 CTGTTGTGTTTATTATACTGTTTTCATGTTTAATAAACATGCA-TTTGACTTGTTTTCATATGGT
* * * * ** * *
323150 GTTCATGAATTTCTGA-AATGGCACATACACTTTGCATTTA-GATTTAGAAATTTAGCTC-----
65 GTTCATGAATTTC-AATAATAGCATATACAATTCACATTTAGGCTTTACAAATTTAGCTCAATTG
*
323208 -AATTAAACGTTTT
129 TAATTAAACGTATT
* * * * * *
323221 CTGTTGTATTTATTATACCGCTTTCGTGTTTAATAGACATGCATTTGACTTGTTTTCATAGGGTG
1 CTGTTGTGTTTATTATACTGTTTTCATGTTTAATAAACATGCATTTGACTTGTTTTCATATGGTG
* *
323286 TTCATGAAATTCAATAATAGCATATACAATTCACATTTAGG-TTT-CAAATTTAACTCAATTGTA
66 TTCATGAATTTCAATAATAGCATATACAATTCACATTTAGGCTTTACAAATTTAGCTCAATTGTA
323349 ATTAAACGTATT
131 ATTAAACGTATT
* * * *
323361 CTGTTGTGTTTATTCTACTGTTTTCATGTTTAATAAACATGCATGATGTCTTGTTTTCACATGGT
1 CTGTTGTGTTTATTATACTGTTTTCATGTTTAATAAACATGCAT-TTGACTTGTTTTCATATGGT
* * * *
323426 GATCATGAATTTCAATAATAGC--ATACAATTCACATTTAGGCTTTGC-AATTGAGCTCGATTGT
65 GTTCATGAATTTCAATAATAGCATATACAATTCACATTTAGGCTTTACAAATTTAGCTCAATTGT
323488 AATT
130 AATT
323492 TTAGTACATA
Statistics
Matches: 321, Mismatches: 53, Indels: 53
0.75 0.12 0.12
Matches are distributed among these distances:
127 6 0.02
128 3 0.01
131 2 0.01
132 6 0.02
133 1 0.00
134 92 0.29
135 53 0.17
136 28 0.09
138 5 0.02
139 18 0.06
140 70 0.22
141 37 0.12
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (142 bp):
CTGTTGTGTTTATTATACTGTTTTCATGTTTAATAAACATGCATTTGACTTGTTTTCATATGGTG
TTCATGAATTTCAATAATAGCATATACAATTCACATTTAGGCTTTACAAATTTAGCTCAATTGTA
ATTAAACGTATT
Found at i:326505 original size:17 final size:17
Alignment explanation
Indices: 326483--326516 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
326473 TTCCCTCTAC
326483 CTGGATGGGATATATAG
1 CTGGATGGGATATATAG
326500 CTGGATGGGATATATAG
1 CTGGATGGGATATATAG
326517 TTGTATGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (17 bp):
CTGGATGGGATATATAG
Found at i:327025 original size:87 final size:86
Alignment explanation
Indices: 326864--327046 Score: 192
Period size: 87 Copynumber: 2.1 Consensus size: 86
326854 TACAACAAAA
* *
326864 TTTTAAAAATCAATGAAGACTTTGTTTTTATTTTGCACTCATTTGGATAATTAAAATTTCAAAAT
1 TTTTAAAAAGCAATGAAGACTTTGTTTTTATTTTGCACTCAATTGGATAATTAAAATTTCAAAAT
*
326929 GCATTAAAAA-TCCCTTCAAACT
66 GCATAAAAAAGT--CTTCAAACT
* * * * * ** *
326951 TTTTAAAAAGCAATTAAG-TTTCTGTTTTTATTTTGCATTCAATT-GATACTTGATTTTTTAAAA
1 TTTTAAAAAGCAATGAAGACTT-TGTTTTTATTTTGCACTCAATTGGATAATTAAAATTTCAAAA
*
327014 TGCATAAAAAAAGTTTTCAAACT
65 TGCAT-AAAAAAGTCTTCAAACT
327037 TTTTCAAAAA
1 TTTT-AAAAA
327047 AAAAAATTAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
86 33 0.41
87 46 0.57
88 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (86 bp):
TTTTAAAAAGCAATGAAGACTTTGTTTTTATTTTGCACTCAATTGGATAATTAAAATTTCAAAAT
GCATAAAAAAGTCTTCAAACT
Found at i:327234 original size:18 final size:17
Alignment explanation
Indices: 327188--327244 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
327178 ATGCATCTTA
*
327188 TATTTTTTCTAATTTTT
1 TATTTTTTATAATTTTT
*
327205 AATAAATTTTTATTAATTTTT
1 --T-ATTTTTTA-TAATTTTT
327226 TATTTTTTATAATTTTT
1 TATTTTTTATAATTTTT
327243 TA
1 TA
327245 CCTCTTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.30
18 7 0.21
19 2 0.06
20 6 0.18
21 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTTATAATTTTT
Found at i:327244 original size:10 final size:10
Alignment explanation
Indices: 327185--327244 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
327175 TTTATGCATC
327185 TTAT-ATTTT
1 TTATAATTTT
*
327194 TTCTAATTTT
1 TTATAATTTT
* *
327204 TAATAAATTT
1 TTATAATTTT
327214 TTATTAA-TTT
1 TTA-TAATTTT
327224 TT-T-ATTTT
1 TTATAATTTT
327232 TTATAATTTT
1 TTATAATTTT
327242 TTA
1 TTA
327245 CCTCTTATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 1 0.02
8 6 0.15
9 4 0.10
10 27 0.66
11 3 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATAATTTT
Found at i:327539 original size:89 final size:85
Alignment explanation
Indices: 327439--327602 Score: 204
Period size: 86 Copynumber: 1.9 Consensus size: 85
327429 GTTTTTTTTT
* * * *
327439 ATGTATTTTGAAAGTTTAAGTATCTAATTGATTGCAAAATAAAAATAGTGA-CTTAATTTTTTTT
1 ATGTATTTTGAAAG-TT-AGCATCCAAGTGAGTGCAAAA-AAAAATAG-GAGCTTAATTTTTTTT
327503 TTTAAATAGTTTGAGAGCTTATTTG
62 TTTAAA-AGTTTGAGAGCTTATTTG
** *
327528 ATGTATTTTGAAAGTTAGCATCCAAGTGAGTGCAAAAAAACTTAGGAGTTTAATTTTTTTTTTTA
1 ATGTATTTTGAAAGTTAGCATCCAAGTGAGTGCAAAAAAAAATAGGAGCTTAATTTTTTTTTTTA
*
327593 TAAGTTTGAG
66 AAAGTTTGAG
327603 GATCTTTTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 10 0.15
86 23 0.35
87 17 0.26
88 2 0.03
89 14 0.21
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (85 bp):
ATGTATTTTGAAAGTTAGCATCCAAGTGAGTGCAAAAAAAAATAGGAGCTTAATTTTTTTTTTTA
AAAGTTTGAGAGCTTATTTG
Found at i:327791 original size:18 final size:18
Alignment explanation
Indices: 327768--327806 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
327758 TTCTCTAAAC
327768 TTGTCCATATGTATTTAA
1 TTGTCCATATGTATTTAA
*
327786 TTGTCCATTTGTATTTAA
1 TTGTCCATATGTATTTAA
327804 TTG
1 TTG
327807 GATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (18 bp):
TTGTCCATATGTATTTAA
Found at i:342078 original size:21 final size:23
Alignment explanation
Indices: 342038--342082 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
342028 ATTTGGGTTG
*
342038 TTTTCTAGATACGTTTTATTTAA
1 TTTTCTAGATACGATTTATTTAA
342061 TTTTCTAGAT-C-ATTTATTTAA
1 TTTTCTAGATACGATTTATTTAA
342082 T
1 T
342083 AAATGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTTCTAGATACGATTTATTTAA
Found at i:344938 original size:29 final size:29
Alignment explanation
Indices: 344905--344995 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
344895 TAAATCACTA
*
344905 AGAAATGACAACCTTTATGGCAAAACTCT
1 AGAAAGGACAACCTTTATGGCAAAACTCT
* * * * *
344934 AGAAAGGTA-AGCCTTTTTGACAAACCTGT
1 AGAAAGG-ACAACCTTTATGGCAAAACTCT
* *
344963 -TAAAGGACAACCTTTACGGCAAAACTCT
1 AGAAAGGACAACCTTTATGGCAAAACTCT
*
344991 GGAAA
1 AGAAA
344996 AGGTATGCCT
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
27 1 0.02
28 19 0.42
29 24 0.53
30 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.23
Consensus pattern (29 bp):
AGAAAGGACAACCTTTATGGCAAAACTCT
Found at i:345024 original size:58 final size:57
Alignment explanation
Indices: 344911--345124 Score: 252
Period size: 57 Copynumber: 3.8 Consensus size: 57
344901 ACTAAGAAAT
* *
344911 GACAACCTTTATGGCAAAACTCT-AGAAAGGTAAGCCTTTTTGACAAACCTGTTAAAG
1 GACAACCTTTATGGCAAAACTCTGA-AAAGGTAAGCCTTTGTGGCAAACCTGTTAAAG
* * *
344968 GACAACCTTTACGGCAAAACTCTGGAAAAGGTATGCCTTTGTGGCAAACCTATTAAAG
1 GACAACCTTTATGGCAAAACTCT-GAAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAG
* * * * * * *
345026 GATAGCTTTTGTGGAAAAACTCTGAAAAGGTAAGCCTTTGTAGCGAACCTGTTAAAG
1 GACAACCTTTATGGCAAAACTCTGAAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAG
* * * *
345083 GACAACCTTTGTGGAAAAACTCT-AAAAGGAAAGCTTTTGTGG
1 GACAACCTTTATGGCAAAACTCTGAAAAGGTAAGCCTTTGTGG
345125 TTGTTTCTAG
Statistics
Matches: 134, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
56 16 0.12
57 72 0.54
58 45 0.34
59 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (57 bp):
GACAACCTTTATGGCAAAACTCTGAAAAGGTAAGCCTTTGTGGCAAACCTGTTAAAG
Found at i:345036 original size:28 final size:28
Alignment explanation
Indices: 344983--345124 Score: 90
Period size: 28 Copynumber: 5.0 Consensus size: 28
344973 CCTTTACGGC
*
344983 AAAACTCTGGAAAAGG-TATGCCTTTGTGGC
1 AAAACTCT--AAAAGGATA-GCCTTTGTGGA
* * * *
345013 AAACCTATTAAAGGATAGCTTTTGTGGA
1 AAAACTCTAAAAGGATAGCCTTTGTGGA
* *
345041 AAAACTCTGAAAAGG-TAAGCCTTTGTAGC
1 AAAACTCT-AAAAGGAT-AGCCTTTGTGGA
* * * * * *
345070 GAACCTGTTAAAGGACAACCTTTGTGGA
1 AAAACTCTAAAAGGATAGCCTTTGTGGA
* *
345098 AAAACTCTAAAAGGAAAGCTTTTGTGG
1 AAAACTCTAAAAGGATAGCCTTTGTGG
345125 TTGTTTCTAG
Statistics
Matches: 82, Mismatches: 26, Indels: 10
0.69 0.22 0.08
Matches are distributed among these distances:
28 55 0.67
29 21 0.26
30 6 0.07
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (28 bp):
AAAACTCTAAAAGGATAGCCTTTGTGGA
Found at i:351999 original size:18 final size:18
Alignment explanation
Indices: 351978--352015 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
351968 TAATAAAATA
*
351978 TTAATATATTTAATGTTT
1 TTAATATATTTAATATTT
351996 TTAATATATTTAATATTT
1 TTAATATATTTAATATTT
352014 TT
1 TT
352016 TACTAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTAATATATTTAATATTT
Found at i:353485 original size:149 final size:146
Alignment explanation
Indices: 353322--353721 Score: 450
Period size: 149 Copynumber: 2.7 Consensus size: 146
353312 GTCAAAAGAG
353322 AGGTAAATT-TTGTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTA-TAAAT
1 AGGTAAATTGTT-TTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTACTAAAT
* *
353385 TATTTATTTAGTTTAATGTTTATGTGATTTTTTATAATTATTTTTTGTTTAGTAGGGTAGATTAA
65 TATTTATTTAGTTTAATGTTTATGTGATTTTTTATAA-T-TTTTTTATTTAGTAGAGTAGATTAA
**
353450 --AGAGAAGAAATTTAA-GAA
128 GTAGA-AAGAAA-GGAATGAA
* ***
353468 AGGTATATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATCATACTTGT
1 AGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTAT--TACTAAA
* * * * *
353533 TTAGTTATTTTGTTTAATTTTTATGTTATTTGTTATTAATTTTTTTATTTAGTAGAGTAGATTAA
64 TTATTTATTTAGTTTAATGTTTATGTGATTTTTTA-TAATTTTTTTATTTAGTAGAGTAGATTAA
* *
353598 GTGGAAAGAAAGGAATGTA
128 GTAGAAAGAAAGGAATGAA
* * *** *
353617 AGGTAAATTGTTTTGTTGTTTTAAATTGAATTTACTTTTATTTTGTTAGTAATTAATTATTAGAA
1 AGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATT-ATTACT--AA
* *
353682 ATTATTTGTTCAGTTTAATGTTTATGTGATTTTTTTATAA
63 ATTATTTATTTAGTTTAATGTTTATGTGA-TTTTTTATAA
353722 ATGTAATTTG
Statistics
Matches: 210, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
146 52 0.25
147 2 0.01
148 30 0.14
149 88 0.42
150 32 0.15
151 6 0.03
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (146 bp):
AGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTACTAAATT
ATTTATTTAGTTTAATGTTTATGTGATTTTTTATAATTTTTTTATTTAGTAGAGTAGATTAAGTA
GAAAGAAAGGAATGAA
Found at i:353560 original size:21 final size:21
Alignment explanation
Indices: 353532--353576 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
353522 ATCATACTTG
353532 TTTAGTTATTT-TGT-TTAATT
1 TTTAGTTATTTGT-TATTAATT
353552 TTTATGTTATTTGTTATTAATT
1 TTTA-GTTATTTGTTATTAATT
353574 TTT
1 TTT
353577 TTATTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 10 0.45
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (21 bp):
TTTAGTTATTTGTTATTAATT
Found at i:354003 original size:21 final size:21
Alignment explanation
Indices: 353962--354003 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
353952 GATTATCATT
* **
353962 ACATATCAGACACGGTGAATA
1 ACATATCAAACACGGACAATA
353983 ACATATCAAACACGGACAATA
1 ACATATCAAACACGGACAATA
354004 TCATGGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (21 bp):
ACATATCAAACACGGACAATA
Found at i:360286 original size:18 final size:18
Alignment explanation
Indices: 360263--360308 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
360253 CTATTTATAT
*
360263 TATTGAATTTTTTAATAA
1 TATTGAATTTTATAATAA
*
360281 TATTGAATATTTATATTAA
1 TATTGAAT-TTTATAATAA
*
360300 AATTGAATT
1 TATTGAATT
360309 ATTAATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATTGAATTTTATAATAA
Found at i:364645 original size:4 final size:4
Alignment explanation
Indices: 364636--364662 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
364626 ATTAGTGATT
364636 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
364663 TTCCTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:377894 original size:23 final size:23
Alignment explanation
Indices: 377868--377920 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
377858 ATGTTGAAGC
*
377868 GGACATCGCCTCTACATGCTCGA
1 GGACATCACCTCTACATGCTCGA
*
377891 GGACATCACCTCTATATGCTCGA
1 GGACATCACCTCTACATGCTCGA
377914 GGACATC
1 GGACATC
377921 CGAGGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (23 bp):
GGACATCACCTCTACATGCTCGA
Found at i:392979 original size:145 final size:145
Alignment explanation
Indices: 392716--393011 Score: 583
Period size: 145 Copynumber: 2.0 Consensus size: 145
392706 CTTGGGGCTT
*
392716 CCTATGGTCGTTGGGCGAAACAAGAAGGTAGCTTTCCATACTATTTAAGATCACATCCTAAGTAA
1 CCTATGGTCGTTGGACGAAACAAGAAGGTAGCTTTCCATACTATTTAAGATCACATCCTAAGTAA
392781 GATTAGGGGATGGTGTAATTGTCGGCTATCTCAAGAGAGTAAAATGGTGTTCATAAAGTTTGTTT
66 GATTAGGGGATGGTGTAATTGTCGGCTATCTCAAGAGAGTAAAATGGTGTTCATAAAGTTTGTTT
392846 GACAAGCTTTACCGA
131 GACAAGCTTTACCGA
392861 CCTATGGTCGTTGGACGAAACAAGAAGGTAGCTTTCCATACTATTTAAGATCACATCCTAAGTAA
1 CCTATGGTCGTTGGACGAAACAAGAAGGTAGCTTTCCATACTATTTAAGATCACATCCTAAGTAA
392926 GATTAGGGGATGGTGTAATTGTCGGCTATCTCAAGAGAGTAAAATGGTGTTCATAAAGTTTGTTT
66 GATTAGGGGATGGTGTAATTGTCGGCTATCTCAAGAGAGTAAAATGGTGTTCATAAAGTTTGTTT
392991 GACAAGCTTTACCGA
131 GACAAGCTTTACCGA
393006 CCTATG
1 CCTATG
393012 CGAAAACGAT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 150 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (145 bp):
CCTATGGTCGTTGGACGAAACAAGAAGGTAGCTTTCCATACTATTTAAGATCACATCCTAAGTAA
GATTAGGGGATGGTGTAATTGTCGGCTATCTCAAGAGAGTAAAATGGTGTTCATAAAGTTTGTTT
GACAAGCTTTACCGA
Found at i:396058 original size:20 final size:18
Alignment explanation
Indices: 396042--396082 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
396032 GGTAAAAGAC
396042 AAAAATATTTACAAAAAA
1 AAAAATATTTACAAAAAA
*
396060 ACAAATATTTACAAAAAA
1 AAAAATATTTACAAAAAA
396078 AAAAA
1 AAAAA
396083 AAAGACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATATTTACAAAAAA
Found at i:396385 original size:21 final size:23
Alignment explanation
Indices: 396359--396403 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
396349 TTAAAATTAA
*
396359 AAAACAAA-TTAAAT-TATGAAT
1 AAAACAAATTTAAATACATGAAT
396380 AAAACAAATTTAAATACATGAAT
1 AAAACAAATTTAAATACATGAAT
396403 A
1 A
396404 CATCATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAACAAATTTAAATACATGAAT
Found at i:401815 original size:9 final size:8
Alignment explanation
Indices: 401800--401826 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
401790 AGCAACACTT
401800 TAAAAAAA
1 TAAAAAAA
401808 TAAAAAAA
1 TAAAAAAA
401816 TAAAAAAA
1 TAAAAAAA
401824 TAA
1 TAA
401827 TCATTTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:403973 original size:21 final size:19
Alignment explanation
Indices: 403949--404100 Score: 112
Period size: 20 Copynumber: 7.5 Consensus size: 19
403939 TTCCTCGCAT
403949 TTTTTTGGTATTCCATCATA
1 TTTTTTGGTATTCC-TCATA
* *
403969 GTTTTTT-GTATTGCTTATA
1 -TTTTTTGGTATTCCTCATA
403988 TATTTTTGGTACTTCCTCATA
1 T-TTTTTGGTA-TTCCTCATA
404009 TTTTTTGGTATATCACTCATAA
1 TTTTTTGGTAT-TC-CTCAT-A
*
404031 TTTTTT-GTATTTCCTCACA
1 TTTTTTGGTA-TTCCTCATA
* * *
404050 TTTTTTGATATTCAATCACAA
1 TTTTTTGGTATTC-CTCA-TA
*
404071 TTTTTT-ATATTGCCTCATA
1 TTTTTTGGTATT-CCTCATA
404090 TTTTTTTGGTA
1 -TTTTTTGGTA
404101 CTCTTTCGGG
Statistics
Matches: 107, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.01
19 21 0.20
20 43 0.40
21 34 0.32
22 8 0.07
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (19 bp):
TTTTTTGGTATTCCTCATA
Found at i:404042 original size:102 final size:103
Alignment explanation
Indices: 403894--404102 Score: 269
Period size: 102 Copynumber: 2.0 Consensus size: 103
403884 TTTTTTTTTA
* *** * *
403894 TACTTACTCATATTTTTTTGGTATTTTTTTCATAATTTTTTATATTTCCTCGCATTTTTTTGGTA
1 TACTTACTCATATTTTTTTGGTATATCACTCATAATTTTTTATATTTCCTCACA-TTTTTTGATA
* * * * *
403959 TTCCATCATAGTTTTTTGTATTG-CTTATATATTTTTGG
65 TTCAATCACAATTTTTTATATTGCCTCATATATTTTTGG
* *
403997 TACTTCCTCATA-TTTTTTGGTATATCACTCATAATTTTTTGTATTTCCTCACATTTTTTGATAT
1 TACTTACTCATATTTTTTTGGTATATCACTCATAATTTTTTATATTTCCTCACATTTTTTGATAT
*
404061 TCAATCACAATTTTTTATATTGCCTCATATTTTTTTGG
66 TCAATCACAATTTTTTATATTGCCTCATATATTTTTGG
404099 TACT
1 TACT
404103 CTTTCGGGTT
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
101 28 0.31
102 52 0.57
103 11 0.12
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (103 bp):
TACTTACTCATATTTTTTTGGTATATCACTCATAATTTTTTATATTTCCTCACATTTTTTGATAT
TCAATCACAATTTTTTATATTGCCTCATATATTTTTGG
Found at i:404073 original size:40 final size:41
Alignment explanation
Indices: 403989--404095 Score: 135
Period size: 40 Copynumber: 2.6 Consensus size: 41
403979 TTGCTTATAT
* * * * *
403989 ATTTTTGGTACTTCCTCATATTTTTTGGTATATCACTCATA
1 ATTTTTTGTATTTCCTCATATTTTTTGATATATCAATCACA
*
404030 ATTTTTTGTATTTCCTCACATTTTTTGATAT-TCAATCACA
1 ATTTTTTGTATTTCCTCATATTTTTTGATATATCAATCACA
* *
404070 ATTTTTTATATTGCCTCATATTTTTT
1 ATTTTTTGTATTTCCTCATATTTTTT
404096 TGGTACTCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
40 30 0.53
41 27 0.47
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.55
Consensus pattern (41 bp):
ATTTTTTGTATTTCCTCATATTTTTTGATATATCAATCACA
Found at i:404095 original size:20 final size:19
Alignment explanation
Indices: 403886--404096 Score: 93
Period size: 20 Copynumber: 10.4 Consensus size: 19
403876 TCTTATATTT
*
403886 TTTTTTTATACTTACTCATA
1 TTTTTTTATA-TTCCTCATA
* **
403906 TTTTTTTGGTATTTTTTTCATA
1 -TTTTTT--TATATTCCTCATA
* **
403928 ATTTTTTATATTTCCTCGCA
1 TTTTTTTATA-TTCCTCATA
*
403948 TTTTTTTGGTATTCCATCATA
1 TTTTTTT-ATATTCC-TCATA
* * * *
403969 GTTTTTTGTATTGCTTATA
1 TTTTTTTATATTCCTCATA
**
403988 TATTTTTGGTACTTCCTCATA
1 T-TTTTTTATA-TTCCTCATA
404009 TTTTTTGGTATA-TCACTCATAA
1 TTTTTT--TATATTC-CTCAT-A
*
404031 TTTTTTGTAT-TTCCTCACA
1 TTTTTT-TATATTCCTCATA
* * *
404050 TTTTTTGATATTCAATCACA
1 TTTTTTTATATTC-CTCATA
*
404070 ATTTTTTATATTGCCTCATA
1 TTTTTTTATATT-CCTCATA
404090 TTTTTTT
1 TTTTTTT
404097 GGTACTCTTT
Statistics
Matches: 145, Mismatches: 30, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
18 2 0.01
19 17 0.12
20 65 0.45
21 42 0.29
22 16 0.11
23 3 0.02
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTTTTATATTCCTCATA
Found at i:405194 original size:24 final size:24
Alignment explanation
Indices: 405166--405222 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
405156 TAGACTAATA
*
405166 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
405190 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
405214 AGAATTTAA
1 AGAGTTTAA
405223 TTGAAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:405223 original size:24 final size:24
Alignment explanation
Indices: 405178--405228 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
405168 AGTTTGACTC
*
405178 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAATTG
*
405202 AAACAATTAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAATTG
405226 AAA
1 AAA
405229 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAATTG
Found at i:407439 original size:60 final size:59
Alignment explanation
Indices: 407362--407492 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 59
407352 ATTTTTAACA
* * * * **
407362 CTTAGAATTTTTGGTACTTCTTTAG-GTTTTATGGTATTCTTTTTTTTTTTTTTGTATTCC
1 CTTATAATTTTTGGTACTTCTTTAGAATTTT-TGATATT-TTCTCATTTTTTTTGTATTCC
* *
407422 CTTATAATTTTTGGTACTTTTTTAGAATTTTTGATATTTTCTCATTTTTTTTGTATTCT
1 CTTATAATTTTTGGTACTTCTTTAGAATTTTTGATATTTTCTCATTTTTTTTGTATTCC
*
407481 CTCATAATTTTT
1 CTTATAATTTTT
407493 ATACATCCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 28 0.46
60 29 0.48
61 4 0.07
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63
Consensus pattern (59 bp):
CTTATAATTTTTGGTACTTCTTTAGAATTTTTGATATTTTCTCATTTTTTTTGTATTCC
Found at i:407491 original size:19 final size:19
Alignment explanation
Indices: 407410--407749 Score: 62
Period size: 20 Copynumber: 17.2 Consensus size: 19
407400 CTTTTTTTTT
* *
407410 TTTTTGTATTCCCTTATAA
1 TTTTTGTATTCTCTCATAA
* * *
407429 TTTTTGGTACTT-TTTTAGAA
1 TTTTT-GTA-TTCTCTCATAA
* **
407449 TTTTTGATATTTTCTCATTT
1 TTTTTG-TATTCTCTCATAA
407469 TTTTTGTATTCTCTCATAA
1 TTTTTGTATTCTCTCATAA
* * *
407488 TTTTTATACATC-CTCGTAA
1 TTTTTGTA-TTCTCTCATAA
* * *
407507 TTTCT-AATACATCCTCAT-A
1 TTTTTGTATTC-T-CTCATAA
*
407526 TTTTTGATAAATT-T-TCATATT
1 TTTTTG-T--ATTCTCTCATA-A
*
407547 TTTTTGTATTCCCTCATAA
1 TTTTTGTATTCTCTCATAA
* * *
407566 TTTTTGGTACATCTTTAATAA
1 TTTTT-GTA-TTCTCTCATAA
*
407587 TTTTT-TATACATCTTCAT-A
1 TTTTTGTATTC-TC-TCATAA
*
407606 TTTTTGGTAATT-TTTCAT-A
1 TTTTT-GT-ATTCTCTCATAA
*
407625 TTTTCTATATT-TCCTCATAA
1 TTTT-TGTATTCT-CTCATAA
* * *
407645 TTTTTGGTACTT-TTTCAGAG
1 TTTTT-GTA-TTCTCTCATAA
407665 TTTTTAGTATTAC-CTCATAA
1 TTTTT-GTATT-CTCTCATAA
*
407685 TTTTTTAGTATTCTCTCACAA
1 -TTTTT-GTATTCTCTCATAA
* *
407706 TTTTT-TATACATCTTCTTAA
1 TTTTTGTATTC-TC-TCATAA
*
407726 TATTTGGTACTTC-CTCATAA
1 T-TTTTGTA-TTCTCTCATAA
407746 TTTT
1 TTTT
407750 AGGTATTCAT
Statistics
Matches: 232, Mismatches: 52, Indels: 74
0.65 0.15 0.21
Matches are distributed among these distances:
17 1 0.00
18 13 0.06
19 80 0.34
20 84 0.36
21 46 0.20
22 4 0.02
23 4 0.02
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTTGTATTCTCTCATAA
Found at i:407540 original size:79 final size:79
Alignment explanation
Indices: 407448--407650 Score: 234
Period size: 80 Copynumber: 2.6 Consensus size: 79
407438 CTTTTTTAGA
**
407448 ATTTTTGAT-ATTTTCTCATTTTTTTTGTATTCTCTCATAATTTTT-ATACATC-CTCGTAATTT
1 ATTTTTGATAATTTT-TCATTTTTTTTGTATTCTCTCATAATTTTTGATACATCTCTAATAATTT
407510 CTAATACATCCTCAT
65 CTAATACATCCTCAT
* * * *
407525 ATTTTTGATAAATTTTCATATTTTTTTGTATTCCCTCATAATTTTTGGTACATCTTTAATAATTT
1 ATTTTTGATAATTTTTCAT-TTTTTTTGTATTCTCTCATAATTTTTGATACATCTCTAATAATTT
* * *
407590 TTTATACATCTTCAT
65 CTAATACATCCTCAT
* * * *
407605 ATTTTTGGTAATTTTTCATATTTTCTATATT-TCCTCATAATTTTTG
1 ATTTTTGATAATTTTTCATTTTTTTTGTATTCT-CTCATAATTTTTG
407651 GTACTTTTTC
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
77 13 0.12
78 29 0.27
79 28 0.26
80 36 0.34
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57
Consensus pattern (79 bp):
ATTTTTGATAATTTTTCATTTTTTTTGTATTCTCTCATAATTTTTGATACATCTCTAATAATTTC
TAATACATCCTCAT
Found at i:407562 original size:39 final size:38
Alignment explanation
Indices: 407518--407689 Score: 150
Period size: 40 Copynumber: 4.4 Consensus size: 38
407508 TTCTAATACA
* *
407518 TCCTCAT-ATTTTTGATAAATTTTCATATTTTTTTGTAT
1 TCCTCATAATTTTTGGTAAATTTTCATA-TTTTTTATAT
* * *
407556 TCCCTCATAATTTTTGGTACATCTTTAATAATTTTTTATACA
1 T-CCTCATAATTTTTGGTAAAT-TTTCAT-ATTTTTTATA-T
* * *
407598 TCTTCAT-ATTTTTGGTAATTTTTCATATTTTCTATATT
1 TCCTCATAATTTTTGGTAAATTTTCATATTTTTTATA-T
** * *
407636 TCCTCATAATTTTTGGTACTTTTTCAGAGTTTTTAGTAT
1 TCCTCATAATTTTTGGTAAATTTTCATATTTTTTA-TAT
407675 TACCTCATAATTTTT
1 T-CCTCATAATTTTT
407690 TAGTATTCTC
Statistics
Matches: 109, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
38 16 0.15
39 36 0.33
40 37 0.34
41 18 0.17
42 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.56
Consensus pattern (38 bp):
TCCTCATAATTTTTGGTAAATTTTCATATTTTTTATAT
Found at i:407586 original size:21 final size:20
Alignment explanation
Indices: 407562--407614 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
407552 GTATTCCCTC
407562 ATAATTTTTGGTACATCTTTA
1 ATAATTTTTGGTACATC-TTA
** *
407583 ATAATTTTTTATACATCTTC
1 ATAATTTTTGGTACATCTTA
407603 AT-ATTTTTGGTA
1 ATAATTTTTGGTA
407615 ATTTTTCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 8 0.30
20 4 0.15
21 15 0.56
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.55
Consensus pattern (20 bp):
ATAATTTTTGGTACATCTTA
Found at i:407631 original size:119 final size:119
Alignment explanation
Indices: 407507--407721 Score: 272
Period size: 119 Copynumber: 1.8 Consensus size: 119
407497 ATCCTCGTAA
* * * *
407507 TTTCTAATACATCCTCAT-ATTTTTGATAAATTTTCATATTTTTTTGTATTCCCTCATAA-TTTT
1 TTTCT-ATACATCCTCATAATTTTTGATAAATTTTCAGAGTTTTTAGTATTACCTCATAATTTTT
* * *
407570 TGGTACATCTTTAATAATTTTTTATACATCTTCATATTTTTGGTAATTTTTCATAT
65 TAGTA-ATCTCTAACAATTTTTTATACATCTTCATATTTTTGGTAATTTTTCATAT
** * **
407626 TTTCTATATTTCCTCATAATTTTTGGTACTTTTTCAGAGTTTTTAGTATTACCTCATAATTTTTT
1 TTTCTATACATCCTCATAATTTTTGATAAATTTTCAGAGTTTTTAGTATTACCTCATAATTTTTT
* *
407691 AGTATTCTCTCACAATTTTTTATACATCTTC
66 AGTAATCTCTAACAATTTTTTATACATCTTC
407722 TTAATATTTG
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
118 10 0.12
119 62 0.77
120 8 0.10
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.55
Consensus pattern (119 bp):
TTTCTATACATCCTCATAATTTTTGATAAATTTTCAGAGTTTTTAGTATTACCTCATAATTTTTT
AGTAATCTCTAACAATTTTTTATACATCTTCATATTTTTGGTAATTTTTCATAT
Found at i:407688 original size:79 final size:77
Alignment explanation
Indices: 407519--407689 Score: 184
Period size: 79 Copynumber: 2.2 Consensus size: 77
407509 TCTAATACAT
* *
407519 CCTCATATTTTTGATAAATTTTCATATTTTTTTGTATTCCCTCATAATTTTTGGTACATCTTTAA
1 CCTCATATTTTTGATAAATTTTCATATTTTTCTATATTCCCTCATAATTTTTGGTACATCTTTAA
*
407584 TAATTTTTTATA
66 GAATTTTTTATA
* * * *
407596 CATCTTCATATTTTTGGTAATTTTTCATA-TTTTCTATATTTCCTCATAATTTTTGGTAC-TTTT
1 C--C-TCATATTTTTGATAAATTTTCATATTTTTCTATATTCCCTCATAATTTTTGGTACATCTT
* *
407659 TCAGAGTTTTTAGTATTA
63 TAAGAATTTTT--TA-TA
407677 CCTCATAATTTTT
1 CCTCAT-ATTTTT
407690 TAGTATTCTC
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
77 1 0.01
78 15 0.19
79 35 0.45
80 24 0.31
81 3 0.04
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.56
Consensus pattern (77 bp):
CCTCATATTTTTGATAAATTTTCATATTTTTCTATATTCCCTCATAATTTTTGGTACATCTTTAA
GAATTTTTTATA
Found at i:407689 original size:21 final size:21
Alignment explanation
Indices: 407665--407712 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
407655 TTTTTCAGAG
*
407665 TTTTTAGTATTAC-CTCATAAT
1 TTTTTAGTATT-CTCTCACAAT
407686 TTTTTAGTATTCTCTCACAAT
1 TTTTTAGTATTCTCTCACAAT
407707 TTTTTA
1 TTTTTA
407713 TACATCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTTAGTATTCTCTCACAAT
Found at i:408095 original size:20 final size:20
Alignment explanation
Indices: 408070--408126 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
408060 TTTCGTATTC
* **
408070 TTTTTGTGTGTCCTCATTTT
1 TTTTTGTATGTCCTCAAGTT
*
408090 TTTTTGTATTTCCTCAAGTT
1 TTTTTGTATGTCCTCAAGTT
*
408110 TTTTTGGTATTTCCTCA
1 TTTTT-GTATGTCCTCA
408127 TACTTTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (20 bp):
TTTTTGTATGTCCTCAAGTT
Found at i:408111 original size:21 final size:21
Alignment explanation
Indices: 408070--408126 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
408060 TTTCGTATTC
* * *
408070 TTTTTGTGTGTCCTC-ATTTT
1 TTTTTGTATTTCCTCAAGTTT
408090 TTTTTGTATTTCCTCAAGTTT
1 TTTTTGTATTTCCTCAAGTTT
*
408111 TTTTGGTATTTCCTCA
1 TTTTTGTATTTCCTCA
408127 TACTTTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (21 bp):
TTTTTGTATTTCCTCAAGTTT
Found at i:408133 original size:21 final size:21
Alignment explanation
Indices: 408080--408315 Score: 86
Period size: 20 Copynumber: 11.7 Consensus size: 21
408070 TTTTTGTGTG
* *
408080 TCCTCAT-TTTTTTTTGTATT
1 TCCTCATAATTTTTTGGTATT
*
408100 TCCTCA-AGTTTTTTTGGTATT
1 TCCTCATA-ATTTTTTGGTATT
* *
408121 TCCTCAT-ACTTTTTGGTATGC
1 TCCTCATAATTTTTTGGTAT-T
**
408142 TCC-CATAATTTTTT-GTGCT
1 TCCTCATAATTTTTTGGTATT
* * *
408161 CCCTCGTAATTTTTT-GTACT
1 TCCTCATAATTTTTTGGTATT
* *
408181 TCCTCGT-ATTTTTTGGTATA
1 TCCTCATAATTTTTTGGTATT
* * **
408201 ACCTCCTAA-TTTTTGGTGCT
1 TCCTCATAATTTTTTGGTATT
* **
408221 CCCTCATGTTTTTTTTTGGTACTT
1 TCCTCA--TAATTTTTTGGTA-TT
*
408245 T-CTTAT-ATTTTTTGGTATT
1 TCCTCATAATTTTTTGGTATT
* * *
408264 CCCTCA-AAATTTTTGGTACT
1 TCCTCATAATTTTTTGGTATT
* * *
408284 TCTTCGT-ATATTTTGGTATT
1 TCCTCATAATTTTTTGGTATT
*
408304 ACCT-A-AATTTTT
1 TCCTCATAATTTTT
408316 ATTTTTATGA
Statistics
Matches: 158, Mismatches: 42, Indels: 33
0.68 0.18 0.14
Matches are distributed among these distances:
19 16 0.10
20 100 0.63
21 29 0.18
22 1 0.01
23 11 0.07
24 1 0.01
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (21 bp):
TCCTCATAATTTTTTGGTATT
Found at i:408174 original size:60 final size:60
Alignment explanation
Indices: 408110--408280 Score: 148
Period size: 60 Copynumber: 2.8 Consensus size: 60
408100 TCCTCAAGTT
* * *
408110 TTTTTGGTATTTCCTCATACTTTTTGGTAT--GCTCCCATAATTTTTTGTGCTCCCTCGTAA
1 TTTTTGGTACTTCCTCATACTTTTTGGTATAACCT-CC-TAATTTTTGGTGCTCCCTCGTAA
* * * **
408170 TTTTTTGTACTTCCTCGTATTTTTTGGTATAACCTCCTAATTTTTGGTGCTCCCTCATGTTTT
1 TTTTTGGTACTTCCTCATACTTTTTGGTATAACCTCCTAATTTTTGGTGCTCCCTC--G-TAA
* * * ** **
408233 TTTTTGGTACTTTCTTATATTTTTTGGTATTCCCTCAAAATTTTTGGT
1 TTTTTGGTACTTCCTCATACTTTTTGGTATAACCTCCTAATTTTTGGT
408281 ACTTCTTCGT
Statistics
Matches: 90, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
60 44 0.49
61 2 0.02
62 3 0.03
63 41 0.46
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.54
Consensus pattern (60 bp):
TTTTTGGTACTTCCTCATACTTTTTGGTATAACCTCCTAATTTTTGGTGCTCCCTCGTAA
Found at i:408298 original size:40 final size:38
Alignment explanation
Indices: 408233--408315 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 38
408223 CTCATGTTTT
* *
408233 TTTTTGGTACTTTCTTATATTTTTTGGTATTCCCTCAAAA
1 TTTTTGGTACTTTCTTATATATTTTGGTATTACCT--AAA
*
408273 TTTTTGGTAC-TTCTTCGTATATTTTGGTATTACCTAAA
1 TTTTTGGTACTTTCTT-ATATATTTTGGTATTACCTAAA
408311 TTTTT
1 TTTTT
408316 ATTTTTATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 8 0.21
39 5 0.13
40 26 0.67
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (38 bp):
TTTTTGGTACTTTCTTATATATTTTGGTATTACCTAAA
Found at i:409171 original size:17 final size:17
Alignment explanation
Indices: 409151--409184 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
409141 ATTTATTAGA
409151 GATTA-CGAATAATTATG
1 GATTACCGAA-AATTATG
409168 GATTACCGAAAATTATG
1 GATTACCGAAAATTATG
409185 AGGGAGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (17 bp):
GATTACCGAAAATTATG
Found at i:409271 original size:18 final size:20
Alignment explanation
Indices: 409235--409272 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
409225 GGAAATACCG
*
409235 AAAATATTGTTTTTTTTTAT
1 AAAATATTGTTTTTATTTAT
409255 AAAAT-TTG-TTTTATTTAT
1 AAAATATTGTTTTTATTTAT
409273 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
AAAATATTGTTTTTATTTAT
Found at i:409469 original size:19 final size:19
Alignment explanation
Indices: 409445--409492 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
409435 AGCTGTATCC
* *
409445 AAAATTATGAGGAAATATA
1 AAAATTATAAGAAAATATA
409464 AAAATTATAAGAAAATATA
1 AAAATTATAAGAAAATATA
*
409483 AAAAATATAA
1 AAAATTATAA
409493 AGGAATTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AAAATTATAAGAAAATATA
Found at i:409487 original size:9 final size:9
Alignment explanation
Indices: 409457--409493 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
409447 AATTATGAGG
409457 AAATATAAA
1 AAATATAAA
*
409466 AATTATAAGA
1 AAATATAA-A
409476 AAATATAAA
1 AAATATAAA
409485 AAATATAAA
1 AAATATAAA
409494 GGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
AAATATAAA
Found at i:414249 original size:16 final size:18
Alignment explanation
Indices: 414205--414262 Score: 75
Period size: 17 Copynumber: 3.3 Consensus size: 18
414195 ATGTTATTTA
* *
414205 TAAATTAAATTGATCAAA
1 TAAATTAAATTTATCAAT
414223 TAAATTAAATTT-TCAAT
1 TAAATTAAATTTATCAAT
414240 TAAA-TAAATTTATCAAT
1 TAAATTAAATTTATCAAT
*
414257 TTAATT
1 TAAATT
414263 CTAATTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.20
17 16 0.46
18 12 0.34
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAATTAAATTTATCAAT
Found at i:415636 original size:29 final size:29
Alignment explanation
Indices: 415594--415653 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
415584 TTAAAAAGAA
415594 ACGCATAAAGTTAGTGAAAGAAATATAAG
1 ACGCATAAAGTTAGTGAAAGAAATATAAG
415623 ACGCATAAAGTTAGTGAAAGAAATATAAG
1 ACGCATAAAGTTAGTGAAAGAAATATAAG
415652 AC
1 AC
415654 TAGAAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (29 bp):
ACGCATAAAGTTAGTGAAAGAAATATAAG
Found at i:416148 original size:12 final size:12
Alignment explanation
Indices: 416133--416165 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
416123 TTATACGGTT
416133 TGGGACACGGGC
1 TGGGACACGGGC
416145 TGGGACACGGGC
1 TGGGACACGGGC
416157 TGGGACACG
1 TGGGACACG
416166 ACTATGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.48, T:0.09
Consensus pattern (12 bp):
TGGGACACGGGC
Found at i:419141 original size:51 final size:51
Alignment explanation
Indices: 419025--419262 Score: 264
Period size: 51 Copynumber: 4.6 Consensus size: 51
419015 TTTCATTTAA
* ** * *
419025 TACTCACGATGTCA-TATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
** * *
419078 TACTCACGATGACACAAAGTCATCGGACCTTTAATCCATTATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * *
419129 TACTCATGATGACACCTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* * * * *
419180 TAATCATGATGACATTTAGTCATCAGG-CATTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATC-GGACCTTTAATCCATAAAGGATTCATT
*
419231 TACTCACGATGACACTTAGTCATCGAACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
419263 TCGTTTATAG
Statistics
Matches: 158, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.01
51 120 0.76
52 11 0.07
53 26 0.16
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:422421 original size:51 final size:50
Alignment explanation
Indices: 422326--422529 Score: 223
Period size: 51 Copynumber: 4.0 Consensus size: 50
422316 TGATGTCATA
** * * *
422326 TAGTCATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGATGACACA
1 TAGTCATCGGACCT-TTAATCCTTA-AGG-ATTCATTTACTCACGATGACACT
* * * * *
422379 AAGTCATCGGACCCTTAATCCATTATGGGTTCATTTACTCACGATTACACT
1 TAGTCATCGGACCTTTAATCC-TTAAGGATTCATTTACTCACGATGACACT
* *
422430 TATTCATCGGACCTTTAATCCGTAAAGGATTCA--TACTCACGATGACACT
1 TAGTCATCGGACCTTTAATCC-TTAAGGATTCATTTACTCACGATGACACT
*
422479 TAGTCATCGAACCTTTAATCCTTAAAGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCTTTAATCCTT-AAGGATTCATTTACTCACGATGACACT
422530 CATCGGACCT
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
48 1 0.01
49 43 0.34
51 61 0.48
52 7 0.06
53 14 0.11
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (50 bp):
TAGTCATCGGACCTTTAATCCTTAAGGATTCATTTACTCACGATGACACT
Found at i:423828 original size:71 final size:70
Alignment explanation
Indices: 423696--423864 Score: 232
Period size: 71 Copynumber: 2.4 Consensus size: 70
423686 AGGCTGTTAC
* * ** *
423696 ACAAATGCAAGATCTCAACCATCAGACCAGTTCACTTTATAGTGACTCACGATGCTGTAGAGAAT
1 ACAAATGCAAGATCTCATCCATCAGACCAGTTCACTTTACAGCAACTCACGATACTGTAGAGAAT
423761 CCACA
66 CCACA
* * *
423766 ACAAATGTAAGATCTCATCCATTAGACCAGTTTCACTTTACAGCAACTCACGATATTGTAGAGAA
1 ACAAATGCAAGATCTCATCCATCAGACCAG-TTCACTTTACAGCAACTCACGATACTGTAGAGAA
*
423831 TCCGCA
65 TCCACA
423837 ACAAATGCAAGATTCTCAT-CATCAGACC
1 ACAAATGCAAGA-TCTCATCCATCAGACC
423865 TTTAATCCGC
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
70 27 0.31
71 53 0.62
72 6 0.07
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (70 bp):
ACAAATGCAAGATCTCATCCATCAGACCAGTTCACTTTACAGCAACTCACGATACTGTAGAGAAT
CCACA
Found at i:427295 original size:101 final size:101
Alignment explanation
Indices: 427165--427381 Score: 314
Period size: 101 Copynumber: 2.2 Consensus size: 101
427155 CGAATCTTCG
* *
427165 AAAATA-AAGAACATTTATCAATTTTAAATAGGATATTCAATTACTTAGGTTTAAAGAAAAATCA
1 AAAATATAAGAACATTTATCAATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCA
* *
427229 TACTCAATA-TGTTAGGGCACAATTTCTCGAGTTCCCT
66 TAC-CAATACT-TTAGGACACAATTTCTCAAGTTCCCT
* *
427266 AAAATAT-TGAACATTTATCGATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCA
1 AAAATATAAGAACATTTATCAATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCA
* *
427330 TACCAGTACTTTAGGACACAATTTCTCAAGTTTCCT
66 TACCAATACTTTAGGACACAATTTCTCAAGTTCCCT
*
427366 GAAATATAAGAACATT
1 AAAATATAAGAACATT
427382 ACCTTGATTT
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
100 33 0.32
101 70 0.68
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (101 bp):
AAAATATAAGAACATTTATCAATTTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAACCA
TACCAATACTTTAGGACACAATTTCTCAAGTTCCCT
Found at i:435108 original size:27 final size:27
Alignment explanation
Indices: 435057--435120 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
435047 AAATATTCTC
*
435057 TAAATTAAT-AAATGTTAATTCATCGA
1 TAAATTAATAAAATATTAATTCATCGA
* *
435083 TAAATTAATAAAATATTCATTTATCGA
1 TAAATTAATAAAATATTAATTCATCGA
*
435110 TAAACTAATAA
1 TAAATTAATAA
435121 TCTAGATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTCATCGA
Found at i:439797 original size:28 final size:28
Alignment explanation
Indices: 439757--439810 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
439747 AATGAGCATC
*
439757 ATGACCTTTGGGTTAACAGGGAGTAAGT
1 ATGACCTTTGGGTCAACAGGGAGTAAGT
439785 ATGACCTTTGGGTCAACAGGGAGTAA
1 ATGACCTTTGGGTCAACAGGGAGTAA
439811 ATCAGATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACAGGGAGTAAGT
Found at i:447034 original size:15 final size:15
Alignment explanation
Indices: 447014--447043 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
447004 GTAGAACTAC
447014 TCGATAAATTTTAAA
1 TCGATAAATTTTAAA
*
447029 TCGATATATTTTAAA
1 TCGATAAATTTTAAA
447044 AGGAGTGGTT
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
TCGATAAATTTTAAA
Found at i:449638 original size:41 final size:41
Alignment explanation
Indices: 449576--449671 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
449566 GAATTTTATT
*
449576 TTAAGAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* *
449617 TTAACAAGAATTTTAGTCACCCAATTCTAACAGTCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
449658 TTGACAAGAATTCT
1 TTAACAAGAATTCT
449672 CTACGAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:449683 original size:17 final size:17
Alignment explanation
Indices: 449661--449699 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
449651 CTCCACCTTG
* *
449661 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
*
449678 ACAAGAACTCTCAATGA
1 ACAAGAACTCTCAACGA
449695 ACAAG
1 ACAAG
449700 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:456115 original size:32 final size:29
Alignment explanation
Indices: 456078--456159 Score: 76
Period size: 32 Copynumber: 2.7 Consensus size: 29
456068 TCCACACGCT
456078 CATGTGGCCCACACGACCCAACTAGTCCAT-CC
1 CATGTGGCCCACACGACCCAAC-A---CATGCC
* * *
456110 CATGTGACTCACACGACCTAACACATGCC
1 CATGTGGCCCACACGACCCAACACATGCC
**
456139 TGTGTGGCCCACACGACCCAA
1 CATGTGGCCCACACGACCCAA
456160 ATAGCCCAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 3 0.07
29 18 0.44
31 1 0.02
32 19 0.46
ACGTcount: A:0.27, C:0.40, G:0.17, T:0.16
Consensus pattern (29 bp):
CATGTGGCCCACACGACCCAACACATGCC
Found at i:462823 original size:8 final size:9
Alignment explanation
Indices: 462804--462859 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 9
462794 CTTTGATAGC
*
462804 AATATTATT
1 AATATAATT
462813 AATA-AATT
1 AATATAATT
462821 AATATAATTAT
1 AATATAA-T-T
462832 AATATAATAT
1 AATATAAT-T
*
462842 AATACAATAT
1 AATATAAT-T
462852 AATATAAT
1 AATATAAT
462860 ATATTCAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.17
9 6 0.15
10 20 0.49
11 8 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATAATT
Found at i:462837 original size:5 final size:5
Alignment explanation
Indices: 462812--462862 Score: 70
Period size: 5 Copynumber: 10.4 Consensus size: 5
462802 GCAATATTAT
*
462812 TAATA -AAT- TAATA TAATTA TAATA TAATA TAATA CAATA TAATA TAATA
1 TAATA TAATA TAATA TAA-TA TAATA TAATA TAATA TAATA TAATA TAATA
462861 TA
1 TA
462863 TTCAACATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 6 0.15
5 30 0.73
6 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:473709 original size:35 final size:34
Alignment explanation
Indices: 473604--473714 Score: 116
Period size: 34 Copynumber: 3.2 Consensus size: 34
473594 ATATGAGAGT
*
473604 CTATATGTTATGCGATCCCTAGGAACATGCGA-C
1 CTATATGTTATGCGAACCCTAGGAACATGCGAGC
* *** * *
473637 CTTATATGTTATGCAAACCCTAGGTGTATGTGGGC
1 C-TATATGTTATGCGAACCCTAGGAACATGCGAGC
* *
473672 CTATATGATTATGCGAACCCGAGGCACATGCGAGC
1 CTATATG-TTATGCGAACCCTAGGAACATGCGAGC
473707 CTATATGT
1 CTATATGT
473715 AGTTCAAATA
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
33 1 0.02
34 31 0.51
35 29 0.48
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (34 bp):
CTATATGTTATGCGAACCCTAGGAACATGCGAGC
Found at i:474659 original size:19 final size:20
Alignment explanation
Indices: 474622--474659 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
474612 AAAAATTTCC
* *
474622 TTTTATTTTCTCCTTAAAAT
1 TTTTATTTTCCCCTCAAAAT
474642 TTTTA-TTTCCCCTCAAAA
1 TTTTATTTTCCCCTCAAAA
474660 CCCTCAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTATTTTCCCCTCAAAAT
Found at i:474836 original size:53 final size:51
Alignment explanation
Indices: 474725--474901 Score: 176
Period size: 53 Copynumber: 3.3 Consensus size: 51
474715 CGTAAAAAAA
** *
474725 TTTACTTCACCCCAAACCCCCAAAAATTTTCCCCTTTTACTTTCTCCTCAAAAAT
1 TTTACTTC-CCCCAAA-CCCCAAAAATTTT-TTCTTTTACTTTCTCC-CAAAACT
* *
474780 TTTACTTCCCCCAAATTCCCAAAACTTTTTTCTTTTACTTTCTTCCCAAAACT
1 TTTACTTCCCCCAAA-CCCCAAAAATTTTTTCTTTTACTTTC-TCCCAAAACT
* * **
474833 TTTACTTCCTCCAAACCCCTAAAATTTTTTTCTTTTTGGTTTC-CCCTAAAACT
1 TTTACTTCCCCCAAACCCC-AAAAATTTTTTC-TTTTACTTTCTCCC-AAAACT
*
474886 GTTACTTCCCCCAAAC
1 TTTACTTCCCCCAAAC
474902 TCTAAAAACT
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
52 6 0.06
53 62 0.59
54 29 0.28
55 8 0.08
ACGTcount: A:0.25, C:0.33, G:0.02, T:0.40
Consensus pattern (51 bp):
TTTACTTCCCCCAAACCCCAAAAATTTTTTCTTTTACTTTCTCCCAAAACT
Found at i:477908 original size:17 final size:17
Alignment explanation
Indices: 477886--477924 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
477876 CTCCACCTTG
* *
477886 ACAAGAATTCTTTACAA
1 ACAAGAACTCTTAACAA
*
477903 ACAAGAACTCTTAACGA
1 ACAAGAACTCTTAACAA
477920 ACAAG
1 ACAAG
477925 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (17 bp):
ACAAGAACTCTTAACAA
Found at i:487581 original size:45 final size:45
Alignment explanation
Indices: 487530--487641 Score: 117
Period size: 45 Copynumber: 2.5 Consensus size: 45
487520 GAATTTGAGT
487530 CGCCCTTTACGGGTTTTCAACTCA-CAA-T-TCTTTTTGTTTTCAAGA
1 CGCCCTTTACGGGTTTTCAACTCATCAACTCTCTTTTT-TTTT--AGA
* * * *
487575 TGCCCTTTGCAGGTTTTC-A-TCATGAACTCTCTTTTTTTTTAGA
1 CGCCCTTTACGGGTTTTCAACTCATCAACTCTCTTTTTTTTTAGA
*
487618 CGCCCTTTACGGGTTTTCATCTCA
1 CGCCCTTTACGGGTTTTCAACTCA
487642 ATTTTAGGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
43 21 0.39
44 3 0.06
45 23 0.43
46 7 0.13
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (45 bp):
CGCCCTTTACGGGTTTTCAACTCATCAACTCTCTTTTTTTTTAGA
Found at i:487633 original size:43 final size:42
Alignment explanation
Indices: 487530--487644 Score: 117
Period size: 43 Copynumber: 2.6 Consensus size: 42
487520 GAATTTGAGT
487530 CGCCCTTTACGGGTTTTCAACTCACAATTCTTTTTGTTTTCAAGA
1 CGCCCTTTACGGGTTTTC-A-TCACAATTCTTTTTGTTTT-AAGA
* * * *
487575 TGCCCTTTGCAGGTTTTCATCATGAACTCTCTTTTT-TTTT-AGA
1 CGCCCTTTACGGGTTTTCATCA-CAA-T-TCTTTTTGTTTTAAGA
*
487618 CGCCCTTTACGGGTTTTCATCTCAATT
1 CGCCCTTTACGGGTTTTCATCACAATT
487645 TTAGGCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 2 0.03
43 24 0.41
44 3 0.05
45 20 0.34
46 7 0.12
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.44
Consensus pattern (42 bp):
CGCCCTTTACGGGTTTTCATCACAATTCTTTTTGTTTTAAGA
Found at i:498987 original size:29 final size:28
Alignment explanation
Indices: 498950--499203 Score: 176
Period size: 29 Copynumber: 8.8 Consensus size: 28
498940 AATGGTGATA
498950 TTTGA-AAGTTCGAGGG-AAAATATAAGTT
1 TTTGAGAAGTTCG-GGGTAAAATATAA-TT
*
498978 TTTGAGAAGTTCTGGGGTAAAAATATGATT
1 TTTGAGAAGTTC-GGGGT-AAAATATAATT
* * *
499008 TTTG-GAAGTACGGGAGTAAAAATGTGATT
1 TTTGAGAAGTTCGGG-GT-AAAATATAATT
* *
499037 TTTG-GAAGTTCGGAGGCAAAAGTGTAATT
1 TTTGAGAAGTTCGG-GGTAAAA-TATAATT
* *
499066 TTTGAGAAGTTCGGGGCAAAATGTAATT
1 TTTGAGAAGTTCGGGGTAAAATATAATT
* *
499094 TTTGAGAAGTTTGAGGGTTAAAATGTAATT
1 TTTGAGAAGTTCG-GGG-TAAAATATAATT
* * *
499124 TTTG-GAAAGTTCAGGATCAAAATGTAATT
1 TTTGAG-AAGTTCGGGGT-AAAATATAATT
* * * * *
499153 TTTGGAAAATTTAGGGTTAAAATGTAATT
1 TTT-GAGAAGTTCGGGGTAAAATATAATT
*
499182 TTTGAGAAGTTTAGGGGTAAAA
1 TTTGAGAAG-TTCGGGGTAAAA
499204 ATGTGATTTC
Statistics
Matches: 192, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
28 36 0.19
29 103 0.54
30 45 0.23
31 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTGAGAAGTTCGGGGTAAAATATAATT
Found at i:499045 original size:58 final size:58
Alignment explanation
Indices: 498966--499212 Score: 209
Period size: 58 Copynumber: 4.2 Consensus size: 58
498956 AGTTCGAGGG
* * *
498966 AAAATATAAGTTTTTGAGAAGTTCTGGGGTAAAAATATGATTTTTG-GAAGTACGGGAGTA
1 AAAATGTAA-TTTTTGAGAAGTT-TGGGGTAAAAATGTAATTTTTGAGAAGTACGGG-GTA
* * * * * *
499026 AAAATGTGATTTTTG-GAAGTTCGGAGGCAAAAGTGTAATTTTTGAGAAGTTCGGGG-C
1 AAAATGTAATTTTTGAGAAGTTTGG-GGTAAAAATGTAATTTTTGAGAAGTACGGGGTA
* * * * *
499083 AAAATGTAATTTTTGAGAAGTTTGAGGGTTAAAATGTAATTTTTG-GAAAGTTCAGGATC
1 AAAATGTAATTTTTGAGAAGTTTG-GGGTAAAAATGTAATTTTTGAG-AAGTACGGGGTA
* * *
499142 AAAATGTAATTTTTG-GAAAATTTAGGGTTAAAATGTAATTTTTGAGAAGTTTA-GGGGTA
1 AAAATGTAATTTTTGAG-AAGTTTGGGGTAAAAATGTAATTTTTGAGAAG--TACGGGGTA
*
499201 AAAATGTGATTT
1 AAAATGTAATTT
499213 CTAGAAAATT
Statistics
Matches: 154, Mismatches: 23, Indels: 21
0.78 0.12 0.11
Matches are distributed among these distances:
57 17 0.11
58 77 0.50
59 52 0.34
60 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTTGAGAAGTTTGGGGTAAAAATGTAATTTTTGAGAAGTACGGGGTA
Found at i:499075 original size:88 final size:86
Alignment explanation
Indices: 498934--499212 Score: 268
Period size: 88 Copynumber: 3.2 Consensus size: 86
498924 TGGAAATTGA
* * * *
498934 GGGT-AAAATGGTGATATTTGAAAGTTC-GAGGGAAAATATAAGTTTTTGAGAAGTTCTGGGGTA
1 GGGTAAAAAT-GTGATTTTTGGAAGTTCGGAGGCAAAATGTAA-TTTTTGAGAAGTTCTGGGGTA
* *
498997 AAAATATGATTTTTG-GAAGTACG
64 AAAATGTAATTTTTGAGAAGTA-G
*
499020 GGAGTAAAAATGTGATTTTTGGAAGTTCGGAGGCAAAAGTGTAATTTTTGAGAAGTTC-GGGG-C
1 GG-GTAAAAATGTGATTTTTGGAAGTTCGGAGGCAAAA-TGTAATTTTTGAGAAGTTCTGGGGTA
*
499083 AAAATGTAATTTTTGAGAAGTTTG
64 AAAATGTAATTTTTGAGAAG-TAG
* * * * *
499107 AGGGTTAAAATGTAATTTTTGGAAAGTTCAGGA-TCAAAATGTAATTTTTG-GAAAATT-TAGGG
1 -GGGTAAAAATGTGATTTTTGG-AAGTTC-GGAGGCAAAATGTAATTTTTGAG-AAGTTCTGGGG
*
499169 TTAAAATGTAATTTTTGAGAAGTTTAG
62 TAAAAATGTAATTTTTGAGAAG--TAG
499196 GGGTAAAAATGTGATTT
1 GGGTAAAAATGTGATTT
499213 CTAGAAAATT
Statistics
Matches: 163, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
86 16 0.10
87 61 0.37
88 76 0.47
89 10 0.06
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (86 bp):
GGGTAAAAATGTGATTTTTGGAAGTTCGGAGGCAAAATGTAATTTTTGAGAAGTTCTGGGGTAAA
AATGTAATTTTTGAGAAGTAG
Found at i:499179 original size:116 final size:115
Alignment explanation
Indices: 498922--499192 Score: 300
Period size: 116 Copynumber: 2.3 Consensus size: 115
498912 AAGTCGAACG
* * *
498922 TTTGGAAATTGAGGGTAAAATGGTGATATTTGA-AAGTTCGAGGGAAAATATAAGTTTTTGAGAA
1 TTTGGAAATTTAGGGTAAAAT-GTAATTTTTGAGAAGTTCGAGGGAAAATATAAGTTTTTGAGAA
* * *
498986 GTTCTGGGGTAAAAATATGATTTTTGGAAGTACGGGAGTAAAAATGTGATT
65 GTTCTGGGGTAAAAATATAATTTTTGGAAGTACAGGAGTAAAAATGTAATT
* ** * *
499037 TTTGGAAGTTCGGAGGCAAAAGTGTAATTTTTGAGAAGTTCG-GGGCAAAATGTAA-TTTTTGAG
1 TTTGGAAATTTAG-GGTAAAA-TGTAATTTTTGAGAAGTTCGAGGG-AAAATATAAGTTTTTGAG
* * * *
499100 AAGTT-TGAGGGTTAAAATGTAATTTTTGGAAAGTTCAGGA-TCAAAATGTAATT
63 AAGTTCTG-GGGTAAAAATATAATTTTTGG-AAGTACAGGAGTAAAAATGTAATT
499153 TTTGGAAAATTTAGGGTTAAAATGTAATTTTTGAGAAGTT
1 TTTGG-AAATTTAGGG-TAAAATGTAATTTTTGAGAAGTT
499193 TAGGGGTAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
115 12 0.09
116 85 0.65
117 33 0.25
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (115 bp):
TTTGGAAATTTAGGGTAAAATGTAATTTTTGAGAAGTTCGAGGGAAAATATAAGTTTTTGAGAAG
TTCTGGGGTAAAAATATAATTTTTGGAAGTACAGGAGTAAAAATGTAATT
Found at i:500934 original size:6 final size:6
Alignment explanation
Indices: 500925--501009 Score: 58
Period size: 6 Copynumber: 15.0 Consensus size: 6
500915 TGGACATTAG
* * *
500925 TAAATT TAAA-- TAATTT TAAACT TAAATT TACAA-- AAAATT TAAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAA-TT
* *
500971 TAAA-- TAGATT TAAATT TAAA-A TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
501010 CTGTTTGTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
4 8 0.13
5 5 0.08
6 39 0.65
7 8 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
TAAATT
Done.