Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold305
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: 679795
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 27416 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2181 original size:9 final size:10
Alignment explanation
Indices: 2141--2178 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2131 CCAAACCACC
2141 TTTTTAATAA
1 TTTTTAATAA
2151 TTTTT-ATAA
1 TTTTTAATAA
* *
2160 TTTTAAAGAA
1 TTTTTAATAA
2170 TTTTTAATA
1 TTTTTAATA
2179 TTTGTCGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:9751 original size:131 final size:130
Alignment explanation
Indices: 9599--9869 Score: 380
Period size: 131 Copynumber: 2.1 Consensus size: 130
9589 CAAGATTTTA
* * *
9599 CACCACAATTTTGCATCAATTAAAAGATTTTCCATTAATTAATTTTTATTTTGATTACTCATGCA
1 CACCACAATTTTGCATCAATTAAAAGATTTTCCATTAATTAATATTTATTGTAATTACTCATGCA
* * * *
9664 ATTTAATTAATTCACCACAATTACTGTTATCATTTTATTGTAATTACCCATGCAATTTAATTGAT
66 ATTTAATTAATGCACCACAATTACTATTATCATTTTATTATAATTACCCATACAATTT-ATTGAT
9729 G
130 G
* * * *
9730 CACCACAATTTTGCATTAATTAAAAGATTTTTCATTAATTAATATTTATTGTAATTACTCATTCG
1 CACCACAATTTTGCATCAATTAAAAGATTTTCCATTAATTAATATTTATTGTAATTACTCATGCA
* * * **
9795 ATTTAATTGATGCATCACAATTACTATTATCATTTTATTATCATTGTCCATACAATTTATTGATG
66 ATTTAATTAATGCACCACAATTACTATTATCATTTTATTATAATTACCCATACAATTTATTGATG
*
9860 CGCCACAATT
1 CACCACAATT
9870 GAATTAAAAG
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 16 0.13
131 107 0.87
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.44
Consensus pattern (130 bp):
CACCACAATTTTGCATCAATTAAAAGATTTTCCATTAATTAATATTTATTGTAATTACTCATGCA
ATTTAATTAATGCACCACAATTACTATTATCATTTTATTATAATTACCCATACAATTTATTGATG
Found at i:17842 original size:20 final size:19
Alignment explanation
Indices: 17817--17885 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
17807 GTTACAAAAT
17817 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
* *
17837 AATTCAAACTAATTTTTAA
1 AATTCAAAATAATTTTAAA
17856 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
17875 AATTCCAAAAT
1 AATT-CAAAAT
17886 TTATATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.09
19 18 0.42
20 21 0.49
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:17892 original size:20 final size:19
Alignment explanation
Indices: 17817--17890 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
17807 GTTACAAAAT
17817 AATTCAAAATAATTT-TCAAA
1 AATTCAAAAT-ATTTAT-AAA
* *
17837 AATTCAAACTAATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
17856 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
17875 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
17891 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 11 0.23
19 22 0.46
20 15 0.31
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:17931 original size:18 final size:18
Alignment explanation
Indices: 17896--17930 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17886 TTATATATTT
*
17896 TTTAAAAAATTCTAAAAA
1 TTTAAAAAATACTAAAAA
17914 TTTAAAAAA-ACTAAAAA
1 TTTAAAAAATACTAAAAA
17931 AATACAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTAAAAAATACTAAAAA
Found at i:18091 original size:16 final size:16
Alignment explanation
Indices: 18072--18102 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18062 TTGAAAGAGT
18072 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
18088 TTTCAAATTTATATG
1 TTTCAAATATATATG
18103 CTTTAACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:21033 original size:20 final size:20
Alignment explanation
Indices: 20991--21035 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
20981 ATTTAATAAA
20991 TAAAAATAAAATTCTAAAAC
1 TAAAAATAAAATTCTAAAAC
*
21011 TAAAACTAAAA-TCTAAAATC
1 TAAAAATAAAATTCTAAAA-C
21031 TAAAA
1 TAAAA
21036 GTCTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAATAAAATTCTAAAAC
Found at i:21042 original size:8 final size:7
Alignment explanation
Indices: 20997--21043 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
20987 TAAATAAAAA
20997 TAAAATTC
1 TAAAA-TC
21005 TAAAA-C
1 TAAAATC
21011 TAAAA-C
1 TAAAATC
21017 TAAAATC
1 TAAAATC
21024 TAAAATC
1 TAAAATC
21031 TAAAAGTC
1 TAAAA-TC
21039 TAAAA
1 TAAAA
21044 ATAATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.32
7 13 0.35
8 12 0.32
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (7 bp):
TAAAATC
Found at i:21085 original size:9 final size:9
Alignment explanation
Indices: 21067--21113 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
21057 GTAGTGATTC
21067 AATTCGGTT
1 AATTCGGTT
*
21076 AATTCTGTT
1 AATTCGGTT
* *
21085 AATTTGGGT
1 AATTCGGTT
21094 AATTCGGTT
1 AATTCGGTT
21103 AATTCGGTT
1 AATTCGGTT
21112 AA
1 AA
21114 CCGACTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:21460 original size:16 final size:17
Alignment explanation
Indices: 21430--21462 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21420 TTCTATCAAC
21430 TAAACAATTTAAATAAA
1 TAAACAATTTAAATAAA
*
21447 TAAA-AATTTTAATAAA
1 TAAACAATTTAAATAAA
21463 AAATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAACAATTTAAATAAA
Found at i:22118 original size:17 final size:17
Alignment explanation
Indices: 22093--22130 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
22083 TAATGCATTA
22093 TTTTAACTTCT-ATCTTT
1 TTTTAACTT-TAATCTTT
*
22110 TTTTCACTTTAATCTTT
1 TTTTAACTTTAATCTTT
22127 TTTT
1 TTTT
22131 TTTCCCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAACTTTAATCTTT
Found at i:23852 original size:16 final size:16
Alignment explanation
Indices: 23831--23887 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
23821 ACTTACTTCA
*
23831 CTGTAATGGAATAGAG
1 CTGTAATAGAATAGAG
*
23847 CTGTAATTGAATAGAG
1 CTGTAATAGAATAGAG
* * * *
23863 TTATAATATAATAGAA
1 CTGTAATAGAATAGAG
23879 CTGTAATAG
1 CTGTAATAG
23888 TAATTCAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:23959 original size:44 final size:45
Alignment explanation
Indices: 23872--23959 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 45
23862 GTTATAATAT
*
23872 AATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATAGAATGG
1 AATAGAACTATAATAGTAATTCAATTGTTTGGTTGAATAGAATGG
* *
23917 AATAGAACTATAATAGT-ATTC-TTGTGTTTGGTTGAATGGAATG
1 AATAGAACTATAATAGTAATTCAAT-TGTTTGGTTGAATAGAATG
23960 ATGTTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 22 0.56
45 16 0.41
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (45 bp):
AATAGAACTATAATAGTAATTCAATTGTTTGGTTGAATAGAATGG
Found at i:24465 original size:24 final size:24
Alignment explanation
Indices: 24438--24486 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
24428 AATCTTTACA
24438 AAGCACAAAATAGAAATTAAAACT
1 AAGCACAAAATAGAAATTAAAACT
24462 AAGCACAAAATAGAAATTAAAACT
1 AAGCACAAAATAGAAATTAAAACT
24486 A
1 A
24487 TCTTTGCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.16
Consensus pattern (24 bp):
AAGCACAAAATAGAAATTAAAACT
Found at i:24779 original size:46 final size:47
Alignment explanation
Indices: 24729--24823 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 47
24719 TTTTGTAGCA
24729 TTAATTAT-ATTTTTAAATCAAAC-ATATAAGTAATATAAAACATTGT
1 TTAATTATAATTTTT-AATCAAACAATATAAGTAATATAAAACATTGT
*
24775 TTAATTATAATTTTTAATCAGACAATATAAGTAATATAAAACATTGT
1 TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAACATTGT
24822 TT
1 TT
24824 GAAGACCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
46 15 0.33
47 31 0.67
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (47 bp):
TTAATTATAATTTTTAATCAAACAATATAAGTAATATAAAACATTGT
Found at i:26532 original size:40 final size:39
Alignment explanation
Indices: 26476--26604 Score: 123
Period size: 39 Copynumber: 3.2 Consensus size: 39
26466 TCCACGTAAG
* * *
26476 CGCGATTTCCTTCCACGTCAGCAAATCGCGCTTACGTAGA
1 CGCGATTTGCTGCCACGTCAG-AAATCGCGCTGACGTAGA
* * * *
26516 CGCGATTTGTTGCCACGTAAGTAATCGCGCTGACGTGGA
1 CGCGATTTGCTGCCACGTCAGAAATCGCGCTGACGTAGA
* * * *
26555 CGCGATTTGCTGACACGTCCCCTGACATCGCGCTGACGTGGA
1 CGCGATTTGCTGCCACGT---CAGAAATCGCGCTGACGTAGA
26597 CGCGATTT
1 CGCGATTT
26605 TAGGAAAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
39 31 0.42
40 17 0.23
42 25 0.34
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.25
Consensus pattern (39 bp):
CGCGATTTGCTGCCACGTCAGAAATCGCGCTGACGTAGA
Found at i:26557 original size:39 final size:41
Alignment explanation
Indices: 26499--26604 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 41
26489 CACGTCAGCA
* * * * *
26499 AATCGCGCTTACGTAGACGCGATTTGTTGCCACGT-AAGT-
1 AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCAACTG
**
26538 AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCCCCTG
1 AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCAACTG
26579 ACATCGCGCTGACGTGGACGCGATTT
1 A-ATCGCGCTGACGTGGACGCGATTT
26605 TAGGAAAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
39 31 0.54
40 1 0.02
41 1 0.02
42 24 0.42
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (41 bp):
AATCGCGCTGACGTGGACGCGATTTGCTGACACGTCAACTG
Found at i:28687 original size:140 final size:142
Alignment explanation
Indices: 28440--28871 Score: 592
Period size: 149 Copynumber: 3.0 Consensus size: 142
28430 AAAGTTGACA
* * *
28440 TCCACGTCATCGACACATATTTTAAACA---TTTTTTAAAATTTTAACCTTTTCAA-TTTTTTT-
1 TCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAACATTTTCAACTTTTTTTC
* * * * * *
28500 CC-TTTT-TCCTTTTT-TTCTTATTATTTTTCTTGTTTCTCACTACTCTCACTTGTCTCTCTCTT
66 CCTTTTTGTCCTTTTTCTTTTTATTATTATTATT-TTTCTTATTATTCTCACTTGTCTCTCTCTT
28562 CTTTCTTTTTTTC
130 CTTTCTTTTTTTC
28575 TCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAACATTTTCAACTTTTTTTC
1 TCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAACATTTTCAACTTTTTTTC
28640 CCTTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTC
66 CCTTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTA--T-T-A-T--TCTCACTTGTCTC
28705 TCTCTTCTTTCTTTTTTTC
124 TCTCTTCTTTCTTTTTTTC
28724 TCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAACATTTTCAACTTTTTTTC
1 TCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAACATTTTCAACTTTTTTTC
28789 CCTTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTC
66 CCTTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTA--T-T-A-T--TCTCACTTGTCTC
28854 TCTCTTCTTTCTTTTTTT
124 TCTCTTCTTTCTTTTTTT
28872 TCCTCTCTTC
Statistics
Matches: 273, Mismatches: 9, Indels: 16
0.92 0.03 0.05
Matches are distributed among these distances:
135 28 0.10
138 22 0.08
139 7 0.03
140 2 0.01
141 4 0.01
142 14 0.05
143 14 0.05
145 1 0.00
146 1 0.00
149 180 0.66
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.59
Consensus pattern (142 bp):
TCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAACATTTTCAACTTTTTTTC
CCTTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTATTCTCACTTGTCTCTCTCTTC
TTTCTTTTTTTC
Found at i:28735 original size:149 final size:149
Alignment explanation
Indices: 28493--28871 Score: 715
Period size: 149 Copynumber: 2.5 Consensus size: 149
28483 ACCTTTTCAA
* * *
28493 TTTTTTTCCTTTTTCCTTTTT-TTCTTATTATTTTTCTTGTTTCTCACTACTCTCACTTGTCTCT
1 TTTTTGTCCTTTTT-CTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTCT
28557 CTCTTCTTTCTTTTTTTCTCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAA
65 CTCTTCTTTCTTTTTTTCTCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAA
28622 CATTTTCAACTTTTTTTCCC
130 CATTTTCAACTTTTTTTCCC
28642 TTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTCTC
1 TTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTCTC
28707 TCTTCTTTCTTTTTTTCTCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAAC
66 TCTTCTTTCTTTTTTTCTCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAAC
28772 ATTTTCAACTTTTTTTCCC
131 ATTTTCAACTTTTTTTCCC
28791 TTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTCTC
1 TTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTCTC
28856 TCTTCTTTCTTTTTTT
66 TCTTCTTTCTTTTTTT
28872 TCCTCTCTTC
Statistics
Matches: 226, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 6 0.03
149 220 0.97
ACGTcount: A:0.15, C:0.22, G:0.03, T:0.61
Consensus pattern (149 bp):
TTTTTGTCCTTTTTCTTTTTATTATTATTATTTTTCTTATTTCTCACTACTCTCACTTGTCTCTC
TCTTCTTTCTTTTTTTCTCCACGTCATCGACACATATTTTAAACATTTTTTTTTTAATTTTTAAC
ATTTTCAACTTTTTTTCCC
Found at i:35286 original size:17 final size:18
Alignment explanation
Indices: 35264--35304 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
35254 ATGGAAAATG
35264 AATATTTGGTAGTGGTA-
1 AATATTTGGTAGTGGTAC
* *
35281 AATATTTTGTAGTTGTAC
1 AATATTTGGTAGTGGTAC
35299 AATATT
1 AATATT
35305 GAAATGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (18 bp):
AATATTTGGTAGTGGTAC
Found at i:41299 original size:51 final size:52
Alignment explanation
Indices: 41220--41401 Score: 192
Period size: 51 Copynumber: 3.6 Consensus size: 52
41210 TATCCGGTTG
** *
41220 ACATAGTAGCCTACACTTAGTACTACACATGTGACCAATAAC-ATCCAGTAC
1 ACATAGTAGCCTACACAGAGTACTACACACGTGACCAATAACTATCCAGTAC
* * * * *
41271 ACGTAGTAGCCTGCACAGAGTACTACACACGTGATCAA-AGCTATCCGGTAC
1 ACATAGTAGCCTACACAGAGTACTACACACGTGACCAATAACTATCCAGTAC
* * ** *
41322 ACATAATAGCCTGCACTTAGTACTACACACGTGACC-ATAACTATCTTA-TAC
1 ACATAGTAGCCTACACAGAGTACTACACACGTGACCAATAACTATC-CAGTAC
* *
41373 TCATAGTAGCCTACATAGAGTACTACACA
1 ACATAGTAGCCTACACAGAGTACTACACA
41402 TGAGTTCTCA
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
50 3 0.03
51 103 0.97
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (52 bp):
ACATAGTAGCCTACACAGAGTACTACACACGTGACCAATAACTATCCAGTAC
Found at i:41332 original size:102 final size:102
Alignment explanation
Indices: 41200--41401 Score: 273
Period size: 102 Copynumber: 2.0 Consensus size: 102
41190 ACCACCATTA
* ** * *
41200 TGATCAATGCTATCCGGTTGACATAGTAGCCTACACTTAGTACTACACATGTGACCAATAAC-AT
1 TGATCAAAGCTATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACC-ATAACTAT
* *
41264 C-CAGTACACGTAGTAGCCTGCACAGAGTACTACACACG
65 CTCA-TACACATAGTAGCCTACACAGAGTACTACACACG
*
41302 TGATCAAAGCTATCCGGTACACATAATAGCCTGCACTTAGTACTACACACGTGACCATAACTATC
1 TGATCAAAGCTATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACCATAACTATC
* * *
41367 TTATACTCATAGTAGCCTACATAGAGTACTACACA
66 TCATACACATAGTAGCCTACACAGAGTACTACACA
41402 TGAGTTCTCA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
101 5 0.06
102 81 0.93
103 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (102 bp):
TGATCAAAGCTATCCGGTACACATAATAGCCTACACTTAGTACTACACACGTGACCATAACTATC
TCATACACATAGTAGCCTACACAGAGTACTACACACG
Found at i:43551 original size:9 final size:9
Alignment explanation
Indices: 43537--43567 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43527 GTTAAACGAA
43537 TCGAGTTAT
1 TCGAGTTAT
*
43546 TCGAGTTAA
1 TCGAGTTAT
43555 TCGAGTTAT
1 TCGAGTTAT
43564 TCGA
1 TCGA
43568 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:44388 original size:5 final size:5
Alignment explanation
Indices: 44378--44403 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44368 GAACAAATAT
44378 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
44404 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:44503 original size:5 final size:5
Alignment explanation
Indices: 44493--44518 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44483 CTCGAAAATT
44493 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
44519 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:46799 original size:50 final size:48
Alignment explanation
Indices: 46691--46821 Score: 172
Period size: 50 Copynumber: 2.7 Consensus size: 48
46681 TCTCATATCG
* * * ** * *
46691 ATGCCATGTCCCAAATATGGTCTTACACGAAATTACATATTGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
46739 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGAT--CACATATCGATGCCA
*
46789 ATGCCATGTCCTAGACATGGTCTTACATGGGAT
1 ATGCCATGTCCCAGACATGGTCTTACATGGGAT
46822 AGCAGATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 28 0.38
50 45 0.62
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
Found at i:48261 original size:12 final size:12
Alignment explanation
Indices: 48244--48291 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
48234 TTATATGAAA
48244 ATAGAGTACTAC
1 ATAGAGTACTAC
48256 ATAGAGTACT-C
1 ATAGAGTACTAC
*
48267 ATAGTAG-CCTAC
1 ATAG-AGTACTAC
*
48279 ATAGCGTACTAC
1 ATAGAGTACTAC
48291 A
1 A
48292 CATGAGTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (12 bp):
ATAGAGTACTAC
Found at i:50254 original size:22 final size:22
Alignment explanation
Indices: 50226--50432 Score: 200
Period size: 22 Copynumber: 9.3 Consensus size: 22
50216 GATGACAAGG
*
50226 TGTTGTCTGAATGTTGTTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
**
50248 TACTGTCTGAATGTTGGTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
* *
50270 TGCTGTCCGAATGTTGGTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
* *
50292 TGCTATCTGAATGTTGGTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
** * **
50314 TGTTGT-TCGTTTTTTAGCATACTAA
1 TGTTGTCT-GAATGTT-GGTTA--AA
* *
50339 TGTTGCCTGAATGTTGTTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
* *
50361 TATTGTCTGAATGTTGTTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
*
50383 TGTTGTCCGAATGTTGGTTAAA
1 TGTTGTCTGAATGTTGGTTAAA
* *
50405 TGTTGTCCGAATGTTGATTAAA
1 TGTTGTCTGAATGTTGGTTAAA
50427 TGTTGT
1 TGTTGT
50433 TCTCTTTTTA
Statistics
Matches: 154, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.01
22 135 0.88
23 3 0.02
24 3 0.02
25 11 0.07
26 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (22 bp):
TGTTGTCTGAATGTTGGTTAAA
Found at i:50426 original size:113 final size:113
Alignment explanation
Indices: 50226--50453 Score: 350
Period size: 113 Copynumber: 2.0 Consensus size: 113
50216 GATGACAAGG
*
50226 TGTTGTCTGAATGTTGTTTAAATACTGTCTGAATGTTGGTTAAATGCTGTCCGAATGTTGGTTAA
1 TGTTGCCTGAATGTTGTTTAAATACTGTCTGAATGTTGGTTAAATGCTGTCCGAATGTTGGTTAA
* * *
50291 ATGCTATCTGAATGTTGGTTAAATGTTGTTCGT-TTTTTAGCATACTAA
66 ATGCTATCCGAATGTTGATTAAATGTTGTTC-TCTTTTTAACATACTAA
* * *
50339 TGTTGCCTGAATGTTGTTTAAATATTGTCTGAATGTTGTTTAAATGTTGTCCGAATGTTGGTTAA
1 TGTTGCCTGAATGTTGTTTAAATACTGTCTGAATGTTGGTTAAATGCTGTCCGAATGTTGGTTAA
* * *
50404 ATGTTGTCCGAATGTTGATTAAATGTTGTTCTCTTTTTAACATATTAA
66 ATGCTATCCGAATGTTGATTAAATGTTGTTCTCTTTTTAACATACTAA
50452 TG
1 TG
50454 ATGTCCAAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
112 1 0.01
113 103 0.99
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (113 bp):
TGTTGCCTGAATGTTGTTTAAATACTGTCTGAATGTTGGTTAAATGCTGTCCGAATGTTGGTTAA
ATGCTATCCGAATGTTGATTAAATGTTGTTCTCTTTTTAACATACTAA
Found at i:50428 original size:11 final size:10
Alignment explanation
Indices: 50348--50433 Score: 55
Period size: 11 Copynumber: 7.9 Consensus size: 10
50338 ATGTTGCCTG
50348 AATGTTGTTTA
1 AATGTTG-TTA
* *
50359 AATATTGTCTG
1 AATGTTGT-TA
50370 AATGTTGTTTA
1 AATGTTG-TTA
**
50381 AATGTTGTCCG
1 AATGTTGT-TA
50392 AATGTTGGTTA
1 AATGTT-GTTA
**
50403 AATGTTGTCCG
1 AATGTTGT-TA
50414 AATGTTGATTA
1 AATGTTG-TTA
50425 AATGTTGTT
1 AATGTTGTT
50434 CTCTTTTTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
10 6 0.11
11 47 0.82
12 4 0.07
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.47
Consensus pattern (10 bp):
AATGTTGTTA
Found at i:55980 original size:15 final size:15
Alignment explanation
Indices: 55960--55989 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55950 TATTTACAGT
55960 ATGTTATTTGATATG
1 ATGTTATTTGATATG
55975 ATGTTATTTGATATG
1 ATGTTATTTGATATG
55990 TGTGAAAATT
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:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
ATGTTATTTGATATG
Found at i:57851 original size:22 final size:22
Alignment explanation
Indices: 57826--58006 Score: 184
Period size: 22 Copynumber: 8.1 Consensus size: 22
57816 GACAAGGTGC
*
57826 TGTCCGAATGTTGTTTAAATGT
1 TGTCCGAATGTTGGTTAAATGT
*
57848 TGTCCGAATGTTGGTTAAATGC
1 TGTCCGAATGTTGGTTAAATGT
* *
57870 TATCCGAATGTTGGTTAATTGT
1 TGTCCGAATGTTGGTTAAATGT
* * * **
57892 TGTTC-ATTTTTTAGCATACTAATGT
1 TGTCCGA-ATGTT-GGTTA--AATGT
*
57917 TGTCCGAATGTTGTTTAAATGT
1 TGTCCGAATGTTGGTTAAATGT
* *
57939 TGTCCGGATGTTGTTTAAATGT
1 TGTCCGAATGTTGGTTAAATGT
* *
57961 TGTCTGAATGTTGGTTAAATGC
1 TGTCCGAATGTTGGTTAAATGT
*
57983 TGTCTGAATGTTGGTTAAATGT
1 TGTCCGAATGTTGGTTAAATGT
58005 TG
1 TG
58007 GTTAAATGTT
Statistics
Matches: 131, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.01
22 112 0.85
23 3 0.02
24 3 0.02
25 11 0.08
26 1 0.01
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (22 bp):
TGTCCGAATGTTGGTTAAATGT
Found at i:57928 original size:11 final size:11
Alignment explanation
Indices: 57912--57995 Score: 71
Period size: 11 Copynumber: 7.6 Consensus size: 11
57902 TTAGCATACT
*
57912 AATGTTGTCCG
1 AATGTTGTCTG
* *
57923 AATGTTGTTTA
1 AATGTTGTCTG
*
57934 AATGTTGTCCG
1 AATGTTGTCTG
* * *
57945 GATGTTGTTTA
1 AATGTTGTCTG
57956 AATGTTGTCTG
1 AATGTTGTCTG
*
57967 AATGTTGGT-TA
1 AATGTT-GTCTG
*
57978 AATGCTGTCTG
1 AATGTTGTCTG
57989 AATGTTG
1 AATGTTG
57996 GTTAAATGTT
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
10 2 0.04
11 50 0.93
12 2 0.04
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.44
Consensus pattern (11 bp):
AATGTTGTCTG
Found at i:58003 original size:11 final size:11
Alignment explanation
Indices: 57946--58017 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
57936 TGTTGTCCGG
*
57946 ATGTTGTTTAA
1 ATGTTGGTTAA
*
57957 ATGTT-GTCTGA
1 ATGTTGGT-TAA
57968 ATGTTGGTTAA
1 ATGTTGGTTAA
* *
57979 ATGCT-GTCTGA
1 ATGTTGGT-TAA
57990 ATGTTGGTTAA
1 ATGTTGGTTAA
58001 ATGTTGGTTAA
1 ATGTTGGTTAA
58012 ATGTTG
1 ATGTTG
58018 TTCATTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 3 0.06
11 43 0.86
12 4 0.08
ACGTcount: A:0.24, C:0.04, G:0.26, T:0.46
Consensus pattern (11 bp):
ATGTTGGTTAA
Found at i:58025 original size:124 final size:124
Alignment explanation
Indices: 57876--58109 Score: 396
Period size: 124 Copynumber: 1.9 Consensus size: 124
57866 ATGCTATCCG
* * *
57876 AATGTTGGTTAATTGTTGTTCATTTTTTAGCATACTAATGTTGTCCGAATGTTGTTTAAATGTTG
1 AATGTTGGTTAAATGTTGTTCATTTTTTAGCATACTAATGCTGTCCGAATGTTGTTTAAATGCTG
** * *
57941 TCCGGATGTTGTTTAAATGTTGTCTGAATGTTGGTTAAATGCTGTCTGAATGTTGGTTA
66 TCCAAATGTTGGTTAAATGCTGTCTGAATGTTGGTTAAATGCTGTCTGAATGTTGGTTA
*
58000 AATGTTGGTTAAATGTTGTTCATTTTTTAGCATACTAATGCTGTCCGACTGTTGTTTAAATGCTG
1 AATGTTGGTTAAATGTTGTTCATTTTTTAGCATACTAATGCTGTCCGAATGTTGTTTAAATGCTG
58065 TCCAAATGTTGGTTAAATGCTGTCTGAATGTTGGTTAAATGCTGT
66 TCCAAATGTTGGTTAAATGCTGTCTGAATGTTGGTTAAATGCTGT
58110 TCATTTTTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 102 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (124 bp):
AATGTTGGTTAAATGTTGTTCATTTTTTAGCATACTAATGCTGTCCGAATGTTGTTTAAATGCTG
TCCAAATGTTGGTTAAATGCTGTCTGAATGTTGGTTAAATGCTGTCTGAATGTTGGTTA
Found at i:58061 original size:22 final size:22
Alignment explanation
Indices: 58036--58109 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
58026 TTAGCATACT
* *
58036 AATGCTGTCCGACTGTTGTTTA
1 AATGCTGTCCGAATGTTGGTTA
*
58058 AATGCTGTCCAAATGTTGGTTA
1 AATGCTGTCCGAATGTTGGTTA
*
58080 AATGCTGTCTGAATGTTGGTTA
1 AATGCTGTCCGAATGTTGGTTA
58102 AATGCTGT
1 AATGCTGT
58110 TCATTTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (22 bp):
AATGCTGTCCGAATGTTGGTTA
Found at i:58142 original size:69 final size:69
Alignment explanation
Indices: 58069--58199 Score: 210
Period size: 69 Copynumber: 1.9 Consensus size: 69
58059 ATGCTGTCCA
58069 AATGTTGGTTAAATGCTG-TCTGAATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGTT
1 AATGTTGGTTAAATGCTGTTC-GAATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGTT
58133 GTCTG
65 GTCTG
** * *
58138 AATGTTGGTTAAATTTTGTTCGAATGTTGGTTAAATGTTGTTCATTTTTTAGCATATTAATG
1 AATGTTGGTTAAATGCTGTTCGAATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATG
58200 CTATCCAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
69 55 0.96
70 2 0.04
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (69 bp):
AATGTTGGTTAAATGCTGTTCGAATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGTTG
TCTG
Found at i:58150 original size:91 final size:91
Alignment explanation
Indices: 58000--58174 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 91
57990 ATGTTGGTTA
* * *
58000 AATGTTGGTTAAATGTTGTTCATTTTTTAGCATACTAATGCTGTCCGACTGTTGTTTAAATGCTG
1 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTTAAATGCTG
58065 TCCAAATGTTGGTTAAATGCTGTCTG
66 TCCAAATGTTGGTTAAATGCTGTCTG
* * **
58091 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGTTGTCTGAATGTTGGTTAAATTTTG
1 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTTAAATGCTG
* *
58156 TTCGAATGTTGGTTAAATG
66 TCCAAATGTTGGTTAAATG
58175 TTGTTCATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (91 bp):
AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCCGAATGTTGGTTAAATGCTG
TCCAAATGTTGGTTAAATGCTGTCTG
Found at i:58158 original size:47 final size:47
Alignment explanation
Indices: 58000--58151 Score: 184
Period size: 47 Copynumber: 3.3 Consensus size: 47
57990 ATGTTGGTTA
* *
58000 AATGTTGGTTAAATGTTGTTCATTTTTTAGCATACTAATGCTGTCCG
1 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCTG
* * * ** * **
58047 ACTGTTGTTTAAATGCTGTCCAAATGTT-GGTTA--AATGCTGTCTG
1 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCTG
*
58091 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGTTGTCTG
1 AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCTG
58138 AATGTTGGTTAAAT
1 AATGTTGGTTAAAT
58152 TTTGTTCGAA
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
44 32 0.39
45 3 0.04
46 3 0.04
47 45 0.54
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (47 bp):
AATGTTGGTTAAATGCTGTTCATTTTTTAGCATACTAATGCTGTCTG
Found at i:58162 original size:22 final size:22
Alignment explanation
Indices: 58127--58180 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
58117 TTAGCATACT
58127 AATGTTG-TCTGAATGTTGGTTA
1 AATGTTGTTC-GAATGTTGGTTA
*
58149 AATTTTGTTCGAATGTTGGTTA
1 AATGTTGTTCGAATGTTGGTTA
58171 AATGTTGTTC
1 AATGTTGTTC
58181 ATTTTTTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.48
Consensus pattern (22 bp):
AATGTTGTTCGAATGTTGGTTA
Found at i:59236 original size:22 final size:22
Alignment explanation
Indices: 59208--59251 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
59198 TTAGTAGCGA
*
59208 CACTAAAAACATAGGTGGTGAT
1 CACTAAAAACACAGGTGGTGAT
*
59230 CACTAAAAACACGGGTGGTGAT
1 CACTAAAAACACAGGTGGTGAT
59252 ATTATTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (22 bp):
CACTAAAAACACAGGTGGTGAT
Found at i:61588 original size:15 final size:14
Alignment explanation
Indices: 61561--61587 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61551 TTTTTCATTT
61561 AAAAAATTATTTTA
1 AAAAAATTATTTTA
61575 AAAAAATTATTTT
1 AAAAAATTATTTT
61588 TTTAATTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAAATTATTTTA
Found at i:62035 original size:20 final size:18
Alignment explanation
Indices: 62006--62056 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
61996 ATAATATTGA
*
62006 ATTTTGAAATTTTTGTTTAT
1 ATTTTTAAATTTTT-TTT-T
*
62026 ATTTTTAAATATTTTTTT
1 ATTTTTAAATTTTTTTTT
*
62044 ATTTTTGAATTTT
1 ATTTTTAAATTTT
62057 AAATAGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 3 0.11
20 12 0.44
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
ATTTTTAAATTTTTTTTT
Found at i:62663 original size:27 final size:27
Alignment explanation
Indices: 62624--62680 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
62614 TAGAATTTAT
* *
62624 AAAAATTATAAAAAAATTTA-AAAATGA
1 AAAAAATAGAAAAAAATTTAGAAAAT-A
**
62651 AAAAAATAGAAAATCATTTAGAAAATA
1 AAAAAATAGAAAAAAATTTAGAAAATA
62678 AAA
1 AAA
62681 TATAGAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (27 bp):
AAAAAATAGAAAAAAATTTAGAAAATA
Found at i:63439 original size:43 final size:43
Alignment explanation
Indices: 63375--63624 Score: 281
Period size: 43 Copynumber: 5.8 Consensus size: 43
63365 CTTTTTTAGG
* * *
63375 CCTTTAGCGGCGCTTTCCCCACAAACGCTGCTATAGACCATGA
1 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGA
63418 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGA
1 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGA
* * * **
63461 CCTTTAGTGGCAG-TTTTTCTACAAACGCCGCTAAA-AGTTATGA
1 CCTTTAGCGGC-GCTTTTCCCACAAACGCCGCTAAAGA-CCATGA
* * * *
63504 CCGTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACAACGA
1 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGA
* * *
63547 CCTTTAGCGACGCTTTTTCGCACAAACGCCGCTAAAAACCATGA
1 CCTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACCATGA
* ** *
63591 -CTTTAGCGACGCTTTTTGCAAAAACGCCGCTAAA
1 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
63625 AACATATCAT
Statistics
Matches: 179, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
42 22 0.12
43 130 0.73
44 27 0.15
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGA
Found at i:63616 original size:129 final size:129
Alignment explanation
Indices: 63378--63625 Score: 340
Period size: 129 Copynumber: 1.9 Consensus size: 129
63368 TTTTAGGCCT
* * * * *
63378 TTAGCGGCGCTTTCCCCACAAACGCTGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAA
1 TTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACAACGACCTTTAGCGACGCTTTTCCCACAAA
* * * *
63443 CGCCGCTAAAGACCATGACCTTTAGTGGCAGTTTTTCTACAAACGCCGCTAAAAGTTATGACCG
66 CGCCGCTAAAAACCATGACCTTTAGCGACAGTTTTTCTAAAAACGCCGCTAAAAGTTATGACCG
** *
63507 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACAACGACCTTTAGCGACGCTTTTTCGCACAA
1 TTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACAACGACCTTTAGCGACGC-TTTTCCCACAA
63572 ACGCCGCTAAAAACCATGA-CTTTAGCGAC-GCTTTTTGC-AAAAACGCCGCTAAAA
65 ACGCCGCTAAAAACCATGACCTTTAGCGACAG-TTTTT-CTAAAAACGCCGCTAAAA
63626 ACATATCATA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
128 1 0.01
129 74 0.71
130 29 0.28
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (129 bp):
TTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACAACGACCTTTAGCGACGCTTTTCCCACAAA
CGCCGCTAAAAACCATGACCTTTAGCGACAGTTTTTCTAAAAACGCCGCTAAAAGTTATGACCG
Found at i:63774 original size:43 final size:43
Alignment explanation
Indices: 63712--63861 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 43
63702 TTAAATATAA
*
63712 TTTCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCT
1 TTTCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGACGCT
* * * * *
63755 TTTCCCACAAACGCTGCTAAAGACAATGACCTTTAGTGACACTT
1 TTTCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGACGC-T
** * * *
63799 TTTATCACAAACGCCACTATAGAACA-AACCTTTAGCGACGCT
1 TTTCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGACGCT
* * *
63841 TCTCGCAAAAACGCCGCTAAA
1 TTTCCCACAAACGCCGCTAAA
63862 AACATATCAT
Statistics
Matches: 84, Mismatches: 22, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
42 16 0.19
43 48 0.57
44 20 0.24
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.23
Consensus pattern (43 bp):
TTTCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGACGCT
Found at i:63788 original size:237 final size:236
Alignment explanation
Indices: 63481--63943 Score: 707
Period size: 237 Copynumber: 2.0 Consensus size: 236
63471 CAGTTTTTCT
** * *
63481 ACAAACGCCGCTAAAAGTTATGACCGTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACAACG
1 ACAAACGCCGCTAAAAGCCATAACCGTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAACG
* * * * * *
63546 ACCTTTAGCGACGCTTTTTCGCACAAACGCCGCTA-AAAACCATGA-CTTTAGCGACGCTTTTTG
66 ACCTTTAGCGACACTTTTTAGCACAAACGCCACTATAAAA-CA-AACCTTTAGCGACGCTTCTCG
63609 CAAAAACGCCGCTAAAAACATATCATACAAAAAAATTATTTTAATCAAATAATATTTATTTTTAT
129 CAAAAACGCCGCTAAAAACATATCATACAAAAAAATTATTTTAATCAAATAATATTTATTTTTAT
63674 GATAAATATTATATTAGGTTTTATTTTTTTAAATATAATTTCCC
194 GATAAATATTATATTAGGTTTTA-TTTTTTAAATATAATTTCCC
* * *
63718 ACAAACGCCGCT-AAAGACCATAACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGACAAT
1 ACAAACGCCGCTAAAAG-CCATAACCGTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAAC
* * *
63782 GACCTTTAGTGACACTTTTTATCACAAACGCCACTATAGAACAAACCTTTAGCGACGCTTCTCGC
65 GACCTTTAGCGACACTTTTTAGCACAAACGCCACTATAAAACAAACCTTTAGCGACGCTTCTCGC
*
63847 AAAAACGCCGCTAAAAACATATCATGCAAAAAAATTATTTTAATCAAATAATATTTATTTTTATG
130 AAAAACGCCGCTAAAAACATATCATACAAAAAAATTATTTTAATCAAATAATATTTATTTTTATG
*
63912 ATAAATATTATATTATGTTTTATTTTTTAAAT
195 ATAAATATTATATTAGGTTTTATTTTTTAAAT
63944 TTGAACTTTA
Statistics
Matches: 205, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
236 15 0.07
237 187 0.91
238 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (236 bp):
ACAAACGCCGCTAAAAGCCATAACCGTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACAACG
ACCTTTAGCGACACTTTTTAGCACAAACGCCACTATAAAACAAACCTTTAGCGACGCTTCTCGCA
AAAACGCCGCTAAAAACATATCATACAAAAAAATTATTTTAATCAAATAATATTTATTTTTATGA
TAAATATTATATTAGGTTTTATTTTTTAAATATAATTTCCC
Found at i:65230 original size:15 final size:17
Alignment explanation
Indices: 65210--65247 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
65200 GATAAGGAAA
65210 AAAAATTAT-AAAT-AT
1 AAAAATTATAAAATAAT
*
65225 AAAAATTCTAAAATAAT
1 AAAAATTATAAAATAAT
65242 AAAAAT
1 AAAAAT
65248 AAATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATAAAATAAT
Found at i:68540 original size:74 final size:74
Alignment explanation
Indices: 68438--68772 Score: 652
Period size: 74 Copynumber: 4.5 Consensus size: 74
68428 ATAAAAGAGT
68438 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
1 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
68503 CAGATTATG
66 CAGATTATG
68512 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
1 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
68577 CAGATTATG
66 CAGATTATG
68586 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
1 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
68651 CAGATTATG
66 CAGATTATG
* *
68660 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAAGATTTTCAGCAG
1 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
68725 CAGATTATG
66 CAGATTATG
68734 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAA
1 AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAA
68773 CAGTAGATTT
Statistics
Matches: 259, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 259 1.00
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.18
Consensus pattern (74 bp):
AAGATAAACAGTACAAAAAAAAGAAAAAGAAAAGCAAAATAAATCATGCATAATATTTTCAGTAG
CAGATTATG
Found at i:71039 original size:41 final size:41
Alignment explanation
Indices: 70981--71175 Score: 302
Period size: 41 Copynumber: 4.8 Consensus size: 41
70971 GAAAATGTTT
* * *
70981 TTAGCGGCACTTCTTCAAAAACGCCGCTAAAGAATAGAGCG
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
*
71022 TTAGCGGCGCTTATTCAAAAACGCCGCTAAAGAACAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
*
71063 TTAGCGGCGCTTCTTCAAAAACACCGCTAAAGATA-AGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGA-ACAGAGCA
* *
71104 TTAGCGGCGCTTCTTCAAAAACGTCGCTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
*
71145 TTAGCGGCGCTTCTTCAAAAATGCCGCTAAA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAA
71176 TCCCCAAAAA
Statistics
Matches: 141, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 140 0.99
42 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
Found at i:72001 original size:30 final size:29
Alignment explanation
Indices: 71959--72071 Score: 145
Period size: 30 Copynumber: 3.8 Consensus size: 29
71949 CGAACTCGAA
*
71959 CACACAGGCTGACATTATAATATGATTGCT
1 CACACAAGCTGACATTATAATA-GATTGCT
* * *
71989 CACATAAACTGACATTATAATAGTTTTGCT
1 CACACAAGCTGACATTATAATAG-ATTGCT
*
72019 CACACAAGCTGACATTACAATAAGATTGCT
1 CACACAAGCTGACATTATAAT-AGATTGCT
*
72049 CACACAAGCTAACATTATAATAG
1 CACACAAGCTGACATTATAATAG
72072 GATGTAAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
29 3 0.04
30 66 0.93
31 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (29 bp):
CACACAAGCTGACATTATAATAGATTGCT
Found at i:72030 original size:60 final size:60
Alignment explanation
Indices: 71959--72071 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
71949 CGAACTCGAA
* * * * *
71959 CACACAGGCTGACATTATAATATGATTGCTCACATAAACTGACATTATAATAGTTTTGCT
1 CACACAAGCTGACATTACAATAAGATTGCTCACACAAACTAACATTATAATAGTTTTGCT
*
72019 CACACAAGCTGACATTACAATAAGATTGCTCACACAAGCTAACATTATAATAG
1 CACACAAGCTGACATTACAATAAGATTGCTCACACAAACTAACATTATAATAG
72072 GATGTAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (60 bp):
CACACAAGCTGACATTACAATAAGATTGCTCACACAAACTAACATTATAATAGTTTTGCT
Found at i:79178 original size:24 final size:24
Alignment explanation
Indices: 79146--79194 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
79136 TGAAAAAGGA
79146 AAGCTTGATATGAATTTCATAGTG
1 AAGCTTGATATGAATTTCATAGTG
79170 AAGCTTGATATGAATTTCATAGTG
1 AAGCTTGATATGAATTTCATAGTG
79194 A
1 A
79195 CTCGTTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (24 bp):
AAGCTTGATATGAATTTCATAGTG
Found at i:81196 original size:19 final size:20
Alignment explanation
Indices: 81172--81211 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
81162 ATGTGACCCC
81172 TATTTTCCAAAATTTT-TAT
1 TATTTTCCAAAATTTTCTAT
81191 TATTTTCCAAAATTTTCTAT
1 TATTTTCCAAAATTTTCTAT
81211 T
1 T
81212 TTGTTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTCCAAAATTTTCTAT
Found at i:82365 original size:15 final size:15
Alignment explanation
Indices: 82328--82376 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
82318 ATGTAATATC
82328 ATTTTTATTTTTA-A
1 ATTTTTATTTTTATA
**
82342 ATGATT-TTTTTAT-
1 ATTTTTATTTTTATA
82355 -TTTTTATTTTTATA
1 ATTTTTATTTTTATA
82369 ATTTTTAT
1 ATTTTTAT
82377 AAATTCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
12 3 0.11
13 13 0.48
14 4 0.15
15 7 0.26
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
ATTTTTATTTTTATA
Found at i:84493 original size:86 final size:84
Alignment explanation
Indices: 84287--84506 Score: 250
Period size: 84 Copynumber: 2.6 Consensus size: 84
84277 GTTTTATTTA
* * * * *
84287 TTTTTTTTACACTCAATTGAGTACTTGAACTTTCAAAATGT-ATTAAAAAGACCCTCAAACTTAA
1 TTTTTTTTACACTCAATTGGGTACTTAAACTTTCAAAAT-TCATCAAAAAGGCCCTCAAAATTAA
*
84351 AAAAGGAAAATTAAGCCCCTG
65 AAAA-GAAAATTAAGCCCATG
** * *
84372 CATTTTTT-CACTAAATTAGGTACTTAAACTTTCAAAATTCATCAAAAAGGCCCTCAAAATTAAA
1 TTTTTTTTACACTCAATTGGGTACTTAAACTTTCAAAATTCATCAAAAAGGCCCTCAAAATTAAA
*
84436 AAA-AACAATTAAGTCCCTATT
66 AAAGAA-AATTAAG-CCC-ATG
* *
84457 TTTTTTTTACACTCAATTGGGTACTTAAACTATC-AAATGCATCAAAAAGG
1 TTTTTTTTACACTCAATTGGGTACTTAAACTTTCAAAATTCATCAAAAAGG
84507 TTATTTGACC
Statistics
Matches: 113, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
82 2 0.02
83 8 0.07
84 53 0.47
85 28 0.25
86 22 0.19
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (84 bp):
TTTTTTTTACACTCAATTGGGTACTTAAACTTTCAAAATTCATCAAAAAGGCCCTCAAAATTAAA
AAAGAAAATTAAGCCCATG
Found at i:84974 original size:20 final size:21
Alignment explanation
Indices: 84927--84974 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
84917 AGATTTTATA
* *
84927 ATTTTTAATAAAATTTTAATT
1 ATTTTTATTAAAATTATAATT
84948 -TTTTTATTAAAA-TATAATT
1 ATTTTTATTAAAATTATAATT
84967 ATTTTTAT
1 ATTTTTAT
84975 AACTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTATTAAAATTATAATT
Found at i:85115 original size:14 final size:13
Alignment explanation
Indices: 85087--85111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85077 GCGGGGACTT
85087 AATTATTTTTTTG
1 AATTATTTTTTTG
85100 AATTATTTTTTT
1 AATTATTTTTTT
85112 TGAAAATCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
AATTATTTTTTTG
Found at i:86640 original size:18 final size:18
Alignment explanation
Indices: 86617--86661 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
86607 AGTGCCACAC
86617 TTTTGTTTCTTTTTTGTA
1 TTTTGTTTCTTTTTTGTA
86635 TTTTGTTTCTTTTTTGTA
1 TTTTGTTTCTTTTTTGTA
86653 TTTTGTTTC
1 TTTTGTTTC
86662 CTTCTCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.04, C:0.07, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTGTTTCTTTTTTGTA
Found at i:89532 original size:22 final size:22
Alignment explanation
Indices: 89505--89552 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
89495 CATATATTTC
** *
89505 CTCTCAATTTTTTTCTAAAATT
1 CTCTCAATTTCCTTCCAAAATT
89527 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
89549 CTCT
1 CTCT
89553 TAAATCCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.00, T:0.48
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:89603 original size:22 final size:22
Alignment explanation
Indices: 89578--89628 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
89568 TTTCAATTTC
89578 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
**
89600 CTCTTGATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
*
89622 CTTTCAA
1 CTCTCAA
89629 ATCCATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.43
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:89619 original size:73 final size:73
Alignment explanation
Indices: 89500--89664 Score: 260
Period size: 73 Copynumber: 2.3 Consensus size: 73
89490 CCTCTCATAT
** *
89500 ATTTCCTCTCAATTTTTTTCTAAAATTCTCTCAATTTCCTTCCAAAATTCTCTT-AAATCCATAT
1 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCT-TTCAAATCCATAT
89564 TTAATTTCA
65 TTAATTTCA
**
89573 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTTGATTTCCTTCCAAAATTCTTTCAAATCCATATT
1 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTTTCAAATCCATATT
*
89638 TGATTTCA
66 TAATTTCA
89646 ATTTCCTCTCAATTTCCTT
1 ATTTCCTCTCAATTTCCTT
89665 TTTTAAAATA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
72 2 0.02
73 83 0.98
ACGTcount: A:0.26, C:0.25, G:0.01, T:0.47
Consensus pattern (73 bp):
ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCCAAAATTCTTTCAAATCCATATT
TAATTTCA
Found at i:91522 original size:18 final size:18
Alignment explanation
Indices: 91499--91534 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
91489 GCGTTTCCTA
91499 ACCCTTATATGTACCCTT
1 ACCCTTATATGTACCCTT
*
91517 ACCCTTATATGTATCCTT
1 ACCCTTATATGTACCCTT
91535 TTTCGAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.42
Consensus pattern (18 bp):
ACCCTTATATGTACCCTT
Found at i:92085 original size:29 final size:29
Alignment explanation
Indices: 92036--92361 Score: 481
Period size: 29 Copynumber: 11.2 Consensus size: 29
92026 GAAGTTTATT
* *
92036 CCTAGCCCTAACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
92065 CCTAACCCTAACCAAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
92094 CCTAACCCTAACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
92123 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
*
92152 CCTAACCCCTAACCTAACTCAATTAAAAAC
1 CCTAA-CCCTAACCTAACTTAATTAAAAAC
* *
92182 CCCAACCCTAACCTAACTCAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
* * *
92211 CCCAACCCTAACCAAACTTTATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
** * *
92240 ATTAACCCTAACCAAACTCAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
92269 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
* *
92298 CATGAACCCTAACCTAATTTAATTAAAAAC
1 CCT-AACCCTAACCTAACTTAATTAAAAAC
*
92328 CCTAACCCTAACCAAACTTAATTAAAAAC
1 CCTAACCCTAACCTAACTTAATTAAAAAC
92357 CCTAA
1 CCTAA
92362 GNNNNNNNNN
Statistics
Matches: 270, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
29 216 0.80
30 54 0.20
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.23
Consensus pattern (29 bp):
CCTAACCCTAACCTAACTTAATTAAAAAC
Found at i:92247 original size:117 final size:116
Alignment explanation
Indices: 92036--92361 Score: 465
Period size: 117 Copynumber: 2.8 Consensus size: 116
92026 GAAGTTTATT
* * * *
92036 CCTAGCCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCAAACTTAATTAAAAACCCTAACC
1 CCTAACCCTAACCTAACTTAATTAAAAACCCCAACCCTAACCTAACTTAATTAAAAACCCTAACC
* * * *
92101 CTAACCTAA-TTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAAC
66 CTAACCAAACTTT-ATTAAAAACACTAACCCTAACCAAACTCAATTAAAAAC
* * *
92152 CCTAACCCCTAACCTAACTCAATTAAAAACCCCAACCCTAACCTAACTCAATTAAAAACCCCAAC
1 CCTAA-CCCTAACCTAACTTAATTAAAAACCCCAACCCTAACCTAACTTAATTAAAAACCCTAAC
*
92217 CCTAACCAAACTTTATTAAAAACATTAACCCTAACCAAACTCAATTAAAAAC
65 CCTAACCAAACTTTATTAAAAACACTAACCCTAACCAAACTCAATTAAAAAC
** *
92269 CCTAACCCTAACCTAACTTAATTAAAAACCATGAACCCTAACCTAATTTAATTAAAAACCCTAAC
1 CCTAACCCTAACCTAACTTAATTAAAAACC-CCAACCCTAACCTAACTTAATTAAAAACCCTAAC
* *
92334 CCTAACCAAACTTAATTAAAAACCCTAA
65 CCTAACCAAACTTTATTAAAAACACTAA
92362 GNNNNNNNNN
Statistics
Matches: 186, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
116 28 0.15
117 155 0.83
118 3 0.02
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.23
Consensus pattern (116 bp):
CCTAACCCTAACCTAACTTAATTAAAAACCCCAACCCTAACCTAACTTAATTAAAAACCCTAACC
CTAACCAAACTTTATTAAAAACACTAACCCTAACCAAACTCAATTAAAAAC
Found at i:92308 original size:146 final size:146
Alignment explanation
Indices: 92041--92358 Score: 494
Period size: 146 Copynumber: 2.2 Consensus size: 146
92031 TTATTCCTAG
* * *
92041 CCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCAAACTTAATTAAAAACCCTAACCCTAAC
1 CCCTAACCTAACTTAATTAAAAACCCCAACCCTAACCAAACTTAATTAAAAACACTAACCCTAAC
* * * *
92106 CTAATTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCCTAACCTAACT
66 CAAACTCAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCCCTAACCTAACT
92171 CAATTAAAAACCCCAA
131 CAATTAAAAACCCCAA
* * *
92187 CCCTAACCTAACTCAATTAAAAACCCCAACCCTAACCAAACTTTATTAAAAACATTAACCCTAAC
1 CCCTAACCTAACTTAATTAAAAACCCCAACCCTAACCAAACTTAATTAAAAACACTAACCCTAAC
*
92252 CAAACTCAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATGAA-CCCTAACCTAAT
66 CAAACTCAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCAT-AACCCCTAACCTAAC
* *
92316 TTAATTAAAAACCCTAA
130 TCAATTAAAAACCCCAA
*
92333 CCCTAACCAAACTTAATTAAAAACCC
1 CCCTAACCTAACTTAATTAAAAACCC
92359 TAAGNNNNNN
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
146 154 0.99
147 2 0.01
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (146 bp):
CCCTAACCTAACTTAATTAAAAACCCCAACCCTAACCAAACTTAATTAAAAACACTAACCCTAAC
CAAACTCAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCATAACCCCTAACCTAACT
CAATTAAAAACCCCAA
Found at i:92921 original size:18 final size:18
Alignment explanation
Indices: 92898--92953 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
92888 CTAACCATTA
92898 ATAATTTTATATAATTTG
1 ATAATTTTATATAATTTG
*
92916 ATAATTTTACTA-ACCATTAG
1 ATAATTTTA-TATA--ATTTG
92936 -TAATTTTATATAATTTG
1 ATAATTTTATATAATTTG
92953 A
1 A
92954 GTTAATACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 4 0.13
18 12 0.39
19 11 0.35
20 4 0.13
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
ATAATTTTATATAATTTG
Found at i:92929 original size:37 final size:37
Alignment explanation
Indices: 92879--92953 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
92869 NNNNNNNNNN
92879 ATAATTTCACTAACCATTAATAATTTTATATAATTTG
1 ATAATTTCACTAACCATTAATAATTTTATATAATTTG
* *
92916 ATAATTTTACTAACCATTAGTAATTTTATATAATTTG
1 ATAATTTCACTAACCATTAATAATTTTATATAATTTG
92953 A
1 A
92954 GTTAATACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (37 bp):
ATAATTTCACTAACCATTAATAATTTTATATAATTTG
Found at i:92941 original size:19 final size:19
Alignment explanation
Indices: 92880--92943 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
92870 NNNNNNNNNA
* *
92880 TAATTTCACTAACCATTAA
1 TAATTTTACTAACCATTAG
*
92899 TAATTTTA-TATA--ATTTG
1 TAATTTTACTA-ACCATTAG
92916 ATAATTTTACTAACCATTAG
1 -TAATTTTACTAACCATTAG
92936 TAATTTTA
1 TAATTTTA
92944 TATAATTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 3 0.08
18 11 0.31
19 18 0.50
20 4 0.11
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (19 bp):
TAATTTTACTAACCATTAG
Found at i:95962 original size:125 final size:125
Alignment explanation
Indices: 95727--96104 Score: 578
Period size: 125 Copynumber: 3.0 Consensus size: 125
95717 CCCAAACATG
* * *
95727 CTACTGTAGCAAAAGCGCGCCCATGAGGCCGTGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * * **** * *
95792 TAGAAGCGATTTTATACTATTTGGTCAGAAA-AGTAAAAAAAAAATTATTTCTTACATGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAACA-TCAACTCGAAATTATTTCTTCCAGGAC
* *
95852 CTACTGTAGCAAAAGCGCGTCCACAAGGCCGTGATTTCAAAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
95917 TAAAAGCAATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
* *
95977 CTACTGTAGCATAAGCGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
96042 TAAAAGCGATTTTATACCATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
96102 CTA
1 CTA
96105 AAAACCCTAA
Statistics
Matches: 231, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
125 230 1.00
126 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGCCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
Found at i:96630 original size:34 final size:35
Alignment explanation
Indices: 96591--96660 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
96581 TAATTACAAA
96591 TAAAATTTATACTAATT-ATTTTTTAATTTATATT
1 TAAAATTTATACTAATTAATTTTTTAATTTATATT
96625 TAAAATTTATACTAATTAATTTTTTAATTTATATT
1 TAAAATTTATACTAATTAATTTTTTAATTTATATT
96660 T
1 T
96661 GGTACAGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 17 0.49
35 18 0.51
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (35 bp):
TAAAATTTATACTAATTAATTTTTTAATTTATATT
Found at i:97140 original size:21 final size:19
Alignment explanation
Indices: 97109--97150 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
97099 AAAGTTTTGG
97109 ATTTAGTATTTGTA-TTTTT
1 ATTTAGTATTT-TAGTTTTT
97128 ATTTAGTTAATTTTAGTTTTT
1 ATTTAG-T-ATTTTAGTTTTT
97149 AT
1 AT
97151 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
21 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (19 bp):
ATTTAGTATTTTAGTTTTT
Found at i:98205 original size:19 final size:17
Alignment explanation
Indices: 98181--98216 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
98171 TTAGCATTGC
98181 TTTGAAGAAGTACTTTTTG
1 TTTGAA-AAGTA-TTTTTG
98200 TTTGAAAAGTATTTTTG
1 TTTGAAAAGTATTTTTG
98217 GAAGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.19, T:0.50
Consensus pattern (17 bp):
TTTGAAAAGTATTTTTG
Found at i:101797 original size:41 final size:41
Alignment explanation
Indices: 101729--101820 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
101719 TAAATTACTG
* * *
101729 AAACTGTTTCTATAAAGCATCTGCTAATAACTATTGAACTGT
1 AAACTGATTC-ATAAAACATCTGCTAATAACTATTGAACTAT
*
101771 AAATTGATTCATAAAACATCTGCTAATAACTATTGAACTAT
1 AAACTGATTCATAAAACATCTGCTAATAACTATTGAACTAT
101812 AAACTGATT
1 AAACTGATT
101821 AATACTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 37 0.82
42 8 0.18
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (41 bp):
AAACTGATTCATAAAACATCTGCTAATAACTATTGAACTAT
Found at i:119405 original size:18 final size:19
Alignment explanation
Indices: 119382--119417 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
119372 CGCTTCCGGG
119382 ATACATCC-TACCTATGTT
1 ATACATCCATACCTATGTT
119400 ATACATCCATACCTATGT
1 ATACATCCATACCTATGT
119418 CTTCGTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (19 bp):
ATACATCCATACCTATGTT
Found at i:139709 original size:21 final size:22
Alignment explanation
Indices: 139683--139739 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
139673 AAAAGTCTAG
139683 GTTGTATCGGTAGAAC-CCAAA
1 GTTGTATCGGTAGAACTCCAAA
*
139704 GTTGTATCGGTAGAACTCCCAA
1 GTTGTATCGGTAGAACTCCAAA
*
139726 -TTCTATCGGTAGAA
1 GTTGTATCGGTAGAA
139740 TTCTGTAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (22 bp):
GTTGTATCGGTAGAACTCCAAA
Found at i:162656 original size:12 final size:13
Alignment explanation
Indices: 162632--162660 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
162622 GGGTTGTAAC
162632 TATTGCATTTATT
1 TATTGCATTTATT
162645 TATTGC-TTTATT
1 TATTGCATTTATT
162657 TATT
1 TATT
162661 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:188636 original size:40 final size:40
Alignment explanation
Indices: 188592--188673 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
188582 TAAAAGTCGT
188592 CTTAAAGATATTAGCTTCCTTAACCCTAAGCTGATGATAC
1 CTTAAAGATATTAGCTTCCTTAACCCTAAGCTGATGATAC
*
188632 CTTAAAGATATTAGCTTTCTTAACCCTAAGCTGATGATAC
1 CTTAAAGATATTAGCTTCCTTAACCCTAAGCTGATGATAC
188672 CT
1 CT
188674 GGAACGAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (40 bp):
CTTAAAGATATTAGCTTCCTTAACCCTAAGCTGATGATAC
Found at i:190521 original size:24 final size:24
Alignment explanation
Indices: 190487--190542 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
190477 CCTTTAAACA
* * *
190487 GTTCAGCTCTATTGGACTGAAGTC
1 GTTCAGTTCTATTGGACCGAAGCC
*
190511 GTTTAGTTCTATTGGACCGAAGCC
1 GTTCAGTTCTATTGGACCGAAGCC
190535 GTTCAGTT
1 GTTCAGTT
190543 ACCAACCCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (24 bp):
GTTCAGTTCTATTGGACCGAAGCC
Found at i:194546 original size:17 final size:17
Alignment explanation
Indices: 194524--194556 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
194514 CAACAATCTC
194524 ATTTCTCTTCTCTTTTT
1 ATTTCTCTTCTCTTTTT
*
194541 ATTTCTCTTTTCTTTT
1 ATTTCTCTTCTCTTTT
194557 CTCTCTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTCTCTTCTCTTTTT
Found at i:194566 original size:42 final size:42
Alignment explanation
Indices: 194520--194600 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
194510 CTTACAACAA
* * *
194520 TCTCA-TTTCTCTTCTCTTTTTATTTCTCTTTTCTTTTCTCTC
1 TCTCATTTTCTCTT-TCTCTTGATTTCTATTTTCTTTTCTCTC
* *
194562 TCTCATTTTTTCTTTCTCTTGATTTTTATTTTCTTTTCT
1 TCTCATTTTCTCTTTCTCTTGATTTCTATTTTCTTTTCT
194601 TTTAAAGTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 26 0.79
43 7 0.21
ACGTcount: A:0.06, C:0.23, G:0.01, T:0.69
Consensus pattern (42 bp):
TCTCATTTTCTCTTTCTCTTGATTTCTATTTTCTTTTCTCTC
Found at i:201890 original size:58 final size:57
Alignment explanation
Indices: 201773--201893 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
201763 ATAAATGGTT
* * * *
201773 AAATGGAGAAATAGGAAACATTTGAAAATGATTAAGGTTTTCACCATAATAAAAGTGA
1 AAATGGAGAAATA-GAAACATTTGAAAATAAATAAGGTTTTCACCAAAATAAAACTGA
* ** *
201831 AAATGGAGAAAT-GAAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATGAAAACTGA
1 AAATGGAGAAATAGAAA-CATTTGAAAATAAATAAGGTTTTCACCAAAAT-AAAACTGA
201889 AAATG
1 AAATG
201894 ACCTGAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 4 0.08
57 25 0.47
58 24 0.45
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (57 bp):
AAATGGAGAAATAGAAACATTTGAAAATAAATAAGGTTTTCACCAAAATAAAACTGA
Found at i:202864 original size:19 final size:20
Alignment explanation
Indices: 202828--202870 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
202818 GATTATGTAG
* *
202828 TTAATTAATTTTAATTT-AC
1 TTAATTAACTATAATTTAAC
*
202847 TTAATTAACTATATTTTAAC
1 TTAATTAACTATAATTTAAC
202867 TTAA
1 TTAA
202871 AAAATCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTAACTATAATTTAAC
Found at i:204248 original size:15 final size:17
Alignment explanation
Indices: 204230--204277 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
204220 AGTTTGAACA
204230 TAATAAC-T-AAATTGT
1 TAATAACTTGAAATTGT
*
204245 TAATATCTTGAAATTGT
1 TAATAACTTGAAATTGT
*
204262 TAATATCTTGAAATTG
1 TAATAACTTGAAATTG
204278 AAATTTAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 23 0.77
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (17 bp):
TAATAACTTGAAATTGT
Found at i:204260 original size:17 final size:17
Alignment explanation
Indices: 204238--204277 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
204228 CATAATAACT
204238 AAATTGTTAATATCTTG
1 AAATTGTTAATATCTTG
204255 AAATTGTTAATATCTTG
1 AAATTGTTAATATCTTG
204272 AAATTG
1 AAATTG
204278 AAATTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (17 bp):
AAATTGTTAATATCTTG
Found at i:207702 original size:23 final size:23
Alignment explanation
Indices: 207674--207718 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
207664 GTTCAAAATT
*
207674 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
207697 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
207719 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:207839 original size:69 final size:66
Alignment explanation
Indices: 207764--208044 Score: 183
Period size: 69 Copynumber: 4.0 Consensus size: 66
207754 AAATGAATTG
* * * *
207764 GATAATTTACAATAAATAATATATAATAAATTTGAAATAATA-ATACATATAAAATTTAAAAATT
1 GATAATTTA-AATAAAT-ATACATGATAAATTTAAAATAATACATACA-AT-AAATTTAAAAATA
*
207828 TTGAT
62 TTAAT
* **
207833 GATAATTCTAGAAT-AATCATACGTGATAAATCCAAAATAATAGCATACAATAAATTTAAAAATA
1 GATAATT-TA-AATAAAT-ATACATGATAAATTTAAAATAATA-CATACAATAAATTTAAAAATA
207897 TTAAT
62 TTAAT
* ** *
207902 GATAAATTTGAAATAGATATACATGATAAATTTAAAATAAT-GTTAACAATGAATTTAAAATAAT
1 GAT-AATTT-AAATAAATATACATGATAAATTTAAAATAATACAT-ACAATAAATTT-AAA-AAT
* *
207966 AATATT
61 ATTAAT
* * * * * * *
207972 GATAAATTAAA-AATAGTAAAACATGATAAATCTAAAATAATAATATACAATACACTTAGATAAT
1 GATAATTTAAATAA-A-T-ATACATGATAAATTTAAAATAAT-ACATACAATAAATTTA-AAAAT
208036 ATTAAT
61 ATTAAT
208042 GAT
1 GAT
208045 TAAATTAATA
Statistics
Matches: 166, Mismatches: 31, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
67 2 0.01
68 14 0.08
69 79 0.48
70 56 0.34
71 14 0.08
72 1 0.01
ACGTcount: A:0.54, C:0.06, G:0.07, T:0.33
Consensus pattern (66 bp):
GATAATTTAAATAAATATACATGATAAATTTAAAATAATACATACAATAAATTTAAAAATATTAA
T
Found at i:207996 original size:70 final size:68
Alignment explanation
Indices: 207856--208061 Score: 175
Period size: 70 Copynumber: 3.0 Consensus size: 68
207846 TAATCATACG
* * * **
207856 TGATAAATCCAAAATAATAG-CATACAATAAATTTAAAAATATTAATGATAAATTTGAAATAGAT
1 TGATAAATCTAAAATAAT-GTTA-ACAATAAATTTAAAAATAATAATGATAAATTAAAAATAGAT
*
207920 ATACA
64 AAACA
* * *
207925 TGATAAATTTAAAATAATGTTAACAATGAATTTAAAATAATAATATTGATAAATTAAAAATAG-T
1 TGATAAATCTAAAATAATGTTAACAATAAATTT-AAA-AATAATAATGATAAATTAAAAATAGAT
207989 AAAACA
64 -AAACA
** * * * * *
207995 TGATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAAATTAATAATA-A
1 TGATAAATCTAAAATAATGTTA-ACAATAAATTTA-AAAATAATAATGA-TAAATTAAAAATAGA
208059 TAA
63 TAA
208062 GTAAAATGAG
Statistics
Matches: 110, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
68 11 0.10
69 21 0.19
70 56 0.51
71 22 0.20
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (68 bp):
TGATAAATCTAAAATAATGTTAACAATAAATTTAAAAATAATAATGATAAATTAAAAATAGATAA
ACA
Found at i:208754 original size:23 final size:22
Alignment explanation
Indices: 208724--208768 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
208714 AAATTAAATC
208724 TCTAAGATTACAAAATCTTATCT
1 TCTAAGATTAC-AAATCTTATCT
* *
208747 TCTAAGATTGCATATCTTATCT
1 TCTAAGATTACAAATCTTATCT
208769 AAGATTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTAAGATTACAAATCTTATCT
Found at i:208771 original size:19 final size:19
Alignment explanation
Indices: 208747--208800 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
208737 AATCTTATCT
*
208747 TCTAAGATTGCATATCTTA
1 TCTAAGATTGCATATCATA
*
208766 TCTAAGATTGAATATCATA
1 TCTAAGATTGCATATCATA
208785 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
208801 CTTTTTCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:217846 original size:21 final size:21
Alignment explanation
Indices: 217820--217862 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
217810 TGTATGTCCT
217820 AGTTAAGGAAATCAAAATTAA
1 AGTTAAGGAAATCAAAATTAA
217841 AGTTAAGGAAATCAAAATTAA
1 AGTTAAGGAAATCAAAATTAA
217862 A
1 A
217863 TGGATGGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (21 bp):
AGTTAAGGAAATCAAAATTAA
Found at i:221186 original size:15 final size:15
Alignment explanation
Indices: 221166--221197 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
221156 CATTTCACTA
221166 TTATGTCTTTGATAT
1 TTATGTCTTTGATAT
221181 TTATGTCTTTGATAT
1 TTATGTCTTTGATAT
221196 TT
1 TT
221198 TGCATGTATA
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:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (15 bp):
TTATGTCTTTGATAT
Found at i:222791 original size:37 final size:36
Alignment explanation
Indices: 222728--222803 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
222718 ATTTAAAAAA
222728 TAATATTATTTTAATTATATAATATTAAATTTAAT-T
1 TAATATTATTTTAATTATATAATATT-AATTTAATAT
**
222764 TAATACTTATTTTAA-TAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATTA-TATAATATTAATTTAATAT
222801 TAA
1 TAA
222804 AGTGATTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATTATATAATATTAATTTAATAT
Found at i:227543 original size:21 final size:21
Alignment explanation
Indices: 227519--227561 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
227509 ACAGAAGCTA
227519 TGTTACCTTCTGTATGATCAC
1 TGTTACCTTCTGTATGATCAC
227540 TGTTACCTTCTGTATGATCAC
1 TGTTACCTTCTGTATGATCAC
227561 T
1 T
227562 ACTCTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (21 bp):
TGTTACCTTCTGTATGATCAC
Found at i:229724 original size:25 final size:25
Alignment explanation
Indices: 229696--229746 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
229686 CAAAATTACA
*
229696 CATATCAATTACACACACAGAGTTT
1 CATATCAATTACACACACACAGTTT
* *
229721 CATATTAATTACACATACACAGTTT
1 CATATCAATTACACACACACAGTTT
229746 C
1 C
229747 TTCAAGCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (25 bp):
CATATCAATTACACACACACAGTTT
Found at i:229893 original size:18 final size:18
Alignment explanation
Indices: 229870--229965 Score: 95
Period size: 18 Copynumber: 5.2 Consensus size: 18
229860 ATACTAATTC
* *
229870 ATATAGGGTTCACATAAA
1 ATATAGGGTTCGCATAAT
*
229888 ATATAGGGTCCGCATAAT
1 ATATAGGGTTCGCATAAT
229906 ATATAGGGTTCGCATAAT
1 ATATAGGGTTCGCATAAT
* *
229924 ATATAGTAAGAGATCACATAAT
1 ATATAG---G-GTTCGCATAAT
*
229946 ATGTAGGGTTCGCAT-AT
1 ATATAGGGTTCGCATAAT
229963 ATA
1 ATA
229966 GTAAGAGATC
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
17 4 0.06
18 44 0.69
19 1 0.02
21 1 0.02
22 14 0.22
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (18 bp):
ATATAGGGTTCGCATAAT
Found at i:229972 original size:37 final size:38
Alignment explanation
Indices: 229900--229975 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 38
229890 ATAGGGTCCG
229900 CATAATATATAGGGTTCGCATAATATATAGTAAGAGATCA
1 CATAATATATAGGGTTCGC--AATATATAGTAAGAGATCA
*
229940 CATAATATGTAGGGTTCGC-ATATATAGTAAGAGATC
1 CATAATATATAGGGTTCGCAATATATAGTAAGAGATC
229976 GTATACTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 17 0.49
40 18 0.51
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (38 bp):
CATAATATATAGGGTTCGCAATATATAGTAAGAGATCA
Found at i:230006 original size:58 final size:59
Alignment explanation
Indices: 229944--230078 Score: 183
Period size: 58 Copynumber: 2.4 Consensus size: 59
229934 AGATCACATA
* * *
229944 ATATGTAGGGTTCGCAT-ATATA-GTAAGAGATCGTATACTAAATCATATAATGGTTTGC
1 ATATGT-GGGTTCACATAATATAGGTAAGAGATCGCATACTAAATCATATAAGGGTTTGC
230002 ATA--TGGGTTCACATAATATATGGTAAGAGATCGCATACTAAATCATATAAGGGTTTGC
1 ATATGTGGGTTCACATAATATA-GGTAAGAGATCGCATACTAAATCATATAAGGGTTTGC
230060 ATA--TGGGTTCACATAATAT
1 ATATGTGGGTTCACATAATAT
230079 GTAGGATTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
55 9 0.13
56 6 0.08
58 56 0.79
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (59 bp):
ATATGTGGGTTCACATAATATAGGTAAGAGATCGCATACTAAATCATATAAGGGTTTGC
Found at i:230094 original size:76 final size:76
Alignment explanation
Indices: 230012--230159 Score: 260
Period size: 76 Copynumber: 1.9 Consensus size: 76
230002 ATATGGGTTC
*
230012 ACATAATATATGGTAAGAGATCGCATACTAAATCATATAAGGGTTTGCATATGGGTTCACATAAT
1 ACATAATATATGGTAAGAGATCGCATACTAAATCATATAAGAGTTTGCATATGGGTTCACATAAT
230077 ATGTAGGATTT
66 ATGTAGGATTT
* * *
230088 ACATAATATATGGTAAGAGATCGCATATTAAATCATATAAGAGTTTGTATATGGGTTCGCATAAT
1 ACATAATATATGGTAAGAGATCGCATACTAAATCATATAAGAGTTTGCATATGGGTTCACATAAT
230153 ATGTAGG
66 ATGTAGG
230160 GTTCGCATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (76 bp):
ACATAATATATGGTAAGAGATCGCATACTAAATCATATAAGAGTTTGCATATGGGTTCACATAAT
ATGTAGGATTT
Found at i:230277 original size:16 final size:16
Alignment explanation
Indices: 230256--230350 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 16
230246 TAGTTCACCT
*
230256 AGGGTTCGCATTCATA
1 AGGGTTCGCATACATA
* *
230272 AGGGTTCACATACCTA
1 AGGGTTCGCATACATA
*
230288 AGGGTTAGCATAC--A
1 AGGGTTCGCATACATA
*
230302 AGGAGATTCACATACATA
1 AGG-G-TTCGCATACATA
** * * *
230320 ATAGTTCACATATATG
1 AGGGTTCGCATACATA
*
230336 GGGGTTCGCATACAT
1 AGGGTTCGCATACAT
230351 GGGGGTTCAC
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
14 4 0.07
15 1 0.02
16 51 0.86
17 1 0.02
18 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (16 bp):
AGGGTTCGCATACATA
Found at i:230352 original size:16 final size:16
Alignment explanation
Indices: 230323--230363 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
230313 ATACATAATA
*
230323 GTTCACATATATGGGG
1 GTTCACATACATGGGG
*
230339 GTTCGCATACATGGGG
1 GTTCACATACATGGGG
230355 GTTCACATA
1 GTTCACATA
230364 ACAAATTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (16 bp):
GTTCACATACATGGGG
Found at i:233019 original size:14 final size:15
Alignment explanation
Indices: 232982--233023 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
232972 TTTTGATTTT
232982 TTTTAATATAATTAA
1 TTTTAATATAATTAA
*
232997 TTCTT-ATAT-TTTAA
1 TT-TTAATATAATTAA
233011 TTTTAATATAATT
1 TTTTAATATAATT
233024 TGATATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
13 2 0.09
14 10 0.45
15 8 0.36
16 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAATATAATTAA
Found at i:233054 original size:31 final size:29
Alignment explanation
Indices: 233005--233082 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 29
232995 AATTCTTATA
*
233005 TTTTAATTTTAATATAATTTGATATTT-ATATT
1 TTTTAATATT-AT-TAATTT-AT-TTTAATATT
*
233037 TTTATAATGTTATTAA-TTATTTTAATATT
1 TTT-TAATATTATTAATTTATTTTAATATT
233066 TTTTAATATTATTAATT
1 TTTTAATATTATTAATT
233083 AATTAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 14 0.34
29 11 0.27
30 2 0.05
31 3 0.07
32 5 0.12
33 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTTAATATTATTAATTTATTTTAATATT
Found at i:242020 original size:23 final size:23
Alignment explanation
Indices: 241988--242328 Score: 389
Period size: 23 Copynumber: 14.6 Consensus size: 23
241978 GATTCAAGTG
* * *
241988 AATTTAGTGTATACATGCTGTCT
1 AATTTGGTGTATAAATGCTGTCC
242011 AATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
* * *
242034 AATTTGGTATATATATGCTGCCC
1 AATTTGGTGTATAAATGCTGTCC
242057 AATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
242080 AATTT-GTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
*
242102 AATTTTGGTGTATAAATGTTGTCC
1 AA-TTTGGTGTATAAATGCTGTCC
* * *
242126 AATTTGGTATATATATGCTGCCC
1 AATTTGGTGTATAAATGCTGTCC
* *
242149 AATTTGGTGTATAAATACTGTCT
1 AATTTGGTGTATAAATGCTGTCC
* *
242172 AATTTGGTGTATATATGCTGCCC
1 AATTTGGTGTATAAATGCTGTCC
*
242195 AATTTGGTGTATAAAATGTTGTCC
1 AATTTGGTGTAT-AAATGCTGTCC
* *
242219 AATTTGGTATATATATATGCTGTTC
1 AATTTGGTGTATA-A-ATGCTGTCC
242244 AATTTGGTGTATAAAATGCTGTCC
1 AATTTGGTGTAT-AAATGCTGTCC
* * *
242268 AATTTGGTATATATATATACTGTCG
1 AATTTGGTGTATA-A-ATGCTGTCC
* *
242293 AATTGGGTGTATAAATGTTGTCC
1 AATTTGGTGTATAAATGCTGTCC
* *
242316 GA-TTGATGTATAA
1 AATTTGGTGTATAA
242329 GAGTTGTCCA
Statistics
Matches: 268, Mismatches: 42, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
22 28 0.10
23 143 0.53
24 59 0.22
25 37 0.14
26 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (23 bp):
AATTTGGTGTATAAATGCTGTCC
Found at i:242145 original size:92 final size:92
Alignment explanation
Indices: 241988--242315 Score: 460
Period size: 92 Copynumber: 3.5 Consensus size: 92
241978 GATTCAAGTG
* * * *
241988 AATTTAGTGTATACATGCTGTCTAATTTGGTGTATAAATGCTGTCCAATTTGGTATATATATGCT
1 AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGTTGTCCAATTTGGTATATATATGCT
242053 GCCCAATTTGGTGTATAAATGCTGTCC
66 GCCCAATTTGGTGTATAAATGCTGTCC
242080 AATTT-GTGTATAAATGCTGTCCAATTTTGGTGTATAAATGTTGTCCAATTTGGTATATATATGC
1 AATTTGGTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGTTGTCCAATTTGGTATATATATGC
* *
242144 TGCCCAATTTGGTGTATAAATACTGTCT
65 TGCCCAATTTGGTGTATAAATGCTGTCC
* *
242172 AATTTGGTGTATATATGCTGCCCAATTTGGTGTATAAAATGTTGTCCAATTTGGTATATATATAT
1 AATTTGGTGTATAAATGCTGTCCAATTTGGTGTAT-AAATGTTGTCCAATTTGG--TATATATAT
**
242237 GCTGTTCAATTTGGTGTATAAAATGCTGTCC
63 GCTGCCCAATTTGGTGTAT-AAATGCTGTCC
* * * *
242268 AATTTGGTATATATATATACTGTCGAATTGGGTGTATAAATGTTGTCC
1 AATTTGGTGTATA-A-ATGCTGTCCAATTTGGTGTATAAATGTTGTCC
242316 GATTGATGTA
Statistics
Matches: 211, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
91 17 0.08
92 84 0.40
93 35 0.17
95 26 0.12
96 21 0.10
97 11 0.05
98 17 0.08
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (92 bp):
AATTTGGTGTATAAATGCTGTCCAATTTGGTGTATAAATGTTGTCCAATTTGGTATATATATGCT
GCCCAATTTGGTGTATAAATGCTGTCC
Found at i:250722 original size:23 final size:23
Alignment explanation
Indices: 250696--251089 Score: 439
Period size: 23 Copynumber: 16.8 Consensus size: 23
250686 AAGTGAATTA
* *
250696 GTGTATATATGCTCTCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
250719 GTGTATAAATGCTGTCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* * **
250742 GTATATATATGCTACCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
*
250765 GTGTATAAATGTTGTCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* *
250788 GTGTACATATGCTGTCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* *
250811 GTGTATAAATGCTGTCCAAAGTTA
1 GTGTATAAATGCTGTCC-AATTTG
250835 GTGTATAAATGCTGTCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* * *
250858 GTATATATATGCTGCCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* *
250881 GTGTATAAATACTGTCTAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* * *
250904 GTGTATATATGCTGCCCAATTTA
1 GTGTATAAATGCTGTCCAATTTG
*
250927 GTGTATAAAATGTTGTCCAATTTG
1 GTGTAT-AAATGCTGTCCAATTTG
* *
250951 GTATATATATATGCTGTTCAATTTG
1 GTGTATA-A-ATGCTGTCCAATTTG
*
250976 GTGTATAAAATGCTCTCCAATTTG
1 GTGTAT-AAATGCTGTCCAATTTG
*
251000 GTGTATAAATGTTGTCCAATTTG
1 GTGTATAAATGCTGTCCAATTTG
* * * *
251023 GTATATATATATACTGTCGAATTGG
1 GTGTATA-A-ATGCTGTCCAATTTG
*
251048 GTGTATAAATGCTGTCCGATTTG
1 GTGTATAAATGCTGTCCAATTTG
*
251071 ATGTATAAGA-GCTGTCCAA
1 GTGTATAA-ATGCTGTCCAA
251090 ACAAGGTAGA
Statistics
Matches: 306, Mismatches: 57, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
23 207 0.68
24 62 0.20
25 36 0.12
26 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (23 bp):
GTGTATAAATGCTGTCCAATTTG
Found at i:250851 original size:116 final size:114
Alignment explanation
Indices: 250696--251089 Score: 493
Period size: 116 Copynumber: 3.4 Consensus size: 114
250686 AAGTGAATTA
* *
250696 GTGTATATATGCTCTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTATATATATGCTACCCAA
1 GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTATATATATGCT-CCCAA
*
250761 TTTGGTGTATAAATGTTGTCCAATTTGGTGTACATATGCTGTCCAATTTG
65 TTTGGTGTATAAATGTTGTCCAATTTGGTGTATATATGCTGTCCAATTTG
* *
250811 GTGTATAAATGCTGTCCAAAGTTAGTGTATAAATGCTGTCCAATTTGGTATATATATGCTGCCCA
1 GTGTATAAATGCTGTCC-AATTTGGTGTATAAATGCTGTCCAATTTGGTATATATATGCT-CCCA
** * * *
250876 ATTTGGTGTATAAATACTGTCTAATTTGGTGTATATATGCTGCCCAATTTA
64 ATTTGGTGTATAAATGTTGTCCAATTTGGTGTATATATGCTGTCCAATTTG
* * * * *
250927 GTGTATAAAATGTTGTCCAATTTGGTATATATATATGCTGTTCAATTTGGTGTATAAAATGCTCT
1 GTGTAT-AAATGCTGTCCAATTTGGTGTATA-A-ATGCTGTCCAATTTGGTATAT-ATATGCTC-
* * * *
250992 CCAATTTGGTGTATAAATGTTGTCCAATTTGGTATATATATATACTGTCGAATTGG
61 CCAATTTGGTGTATAAATGTTGTCCAATTTGG--TGTATATATGCTGTCCAATTTG
* *
251048 GTGTATAAATGCTGTCCGATTTGATGTATAAGA-GCTGTCCAA
1 GTGTATAAATGCTGTCCAATTTGGTGTATAA-ATGCTGTCCAA
251090 ACAAGGTAGA
Statistics
Matches: 238, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
115 15 0.06
116 105 0.44
117 11 0.05
118 28 0.12
119 37 0.16
120 20 0.08
121 22 0.09
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (114 bp):
GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTGGTATATATATGCTCCCAAT
TTGGTGTATAAATGTTGTCCAATTTGGTGTATATATGCTGTCCAATTTG
Found at i:254769 original size:4 final size:4
Alignment explanation
Indices: 254760--254786 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
254750 TGAGCGACGA
254760 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
254787 AAGAAAAAAA
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:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:256549 original size:53 final size:52
Alignment explanation
Indices: 256492--256652 Score: 149
Period size: 53 Copynumber: 3.2 Consensus size: 52
256482 ACAAAACAAC
256492 CATTTAAAACAAATTTAAGATCTTTAAAAGCAATCACTTCAAGTCAAAATCAT
1 CATTTAAAACAAATTTAAGATCTTTAAAAGCAATCACTTCAAG-CAAAATCAT
* * ** * * * * *
256545 CATTTTAAAC-AATTT---ACCCATAAAA-CACTTA-TGCTA-CAAACT-AT
1 CATTTAAAACAAATTTAAGATCTTTAAAAGCAATCACTTCAAGCAAAATCAT
*
256589 CATTTAAAACAAATTTAAGATCTTCAAAAGCAATCACTTCAAGACAAAATCAT
1 CATTTAAAACAAATTTAAGATCTTTAAAAGCAATCACTTCAAG-CAAAATCAT
*
256642 CATTTTAAACA
1 CATTTAAAACA
256653 CCCTAGGTAC
Statistics
Matches: 79, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
44 11 0.14
45 10 0.13
47 3 0.04
48 10 0.13
49 11 0.14
50 3 0.04
52 10 0.13
53 21 0.27
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (52 bp):
CATTTAAAACAAATTTAAGATCTTTAAAAGCAATCACTTCAAGCAAAATCAT
Found at i:256623 original size:97 final size:98
Alignment explanation
Indices: 256453--256652 Score: 357
Period size: 97 Copynumber: 2.1 Consensus size: 98
256443 CTTTCAAACC
*
256453 AAACAATTTACCCATAAAACACTTATGCTACAAAACAACCATTTAAAACAAATTTAAGATCTTTA
1 AAACAATTTACCCATAAAACACTTATGCTACAAAACAACCATTTAAAACAAATTTAAGATCTTCA
*
256518 AAAGCAATCACTTCAAGTCAAAATCATCATTTT
66 AAAGCAATCACTTCAAGACAAAATCATCATTTT
* *
256551 AAACAATTTACCCATAAAACACTTATGCTAC-AAACTATCATTTAAAACAAATTTAAGATCTTCA
1 AAACAATTTACCCATAAAACACTTATGCTACAAAACAACCATTTAAAACAAATTTAAGATCTTCA
256615 AAAGCAATCACTTCAAGACAAAATCATCATTTT
66 AAAGCAATCACTTCAAGACAAAATCATCATTTT
256648 AAACA
1 AAACA
256653 CCCTAGGTAC
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 67 0.68
98 31 0.32
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.28
Consensus pattern (98 bp):
AAACAATTTACCCATAAAACACTTATGCTACAAAACAACCATTTAAAACAAATTTAAGATCTTCA
AAAGCAATCACTTCAAGACAAAATCATCATTTT
Found at i:258139 original size:3 final size:3
Alignment explanation
Indices: 258072--258128 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
258062 CTTTTTTCTT
*
258072 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
258120 TTA TTA TTA
1 TTA TTA TTA
258129 ACATTTATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:259132 original size:18 final size:18
Alignment explanation
Indices: 259111--259154 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
259101 GTTTTTGTCT
259111 CAAAAGTGGGTTTTATCC
1 CAAAAGTGGGTTTTATCC
* *
259129 CAAAAGTGGTTTTTGTCC
1 CAAAAGTGGGTTTTATCC
*
259147 TAAAAGTG
1 CAAAAGTG
259155 CTTCTTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (18 bp):
CAAAAGTGGGTTTTATCC
Found at i:260087 original size:16 final size:18
Alignment explanation
Indices: 260060--260092 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
260050 TAGAATAGGG
260060 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
260077 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
260093 GTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:260099 original size:9 final size:9
Alignment explanation
Indices: 260083--260121 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
260073 TTAATTGAGA
260083 AATTAATTT
1 AATTAATTT
*
260092 AGTTAATTT
1 AATTAATTT
**
260101 AATTAATCA
1 AATTAATTT
260110 AATTAATTT
1 AATTAATTT
260119 AAT
1 AAT
260122 AAATAATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (9 bp):
AATTAATTT
Found at i:262481 original size:2 final size:2
Alignment explanation
Indices: 262474--262499 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
262464 TTAATATCCT
262474 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
262500 AAAGAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:262641 original size:29 final size:30
Alignment explanation
Indices: 262606--262664 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
262596 TCTAATTCAA
262606 TGTGTAATATTATACATGA-ATTTTGATTT
1 TGTGTAATATTATACATGACATTTTGATTT
* * *
262635 TGTGTAATTTTATATATGACATTTTTATTT
1 TGTGTAATATTATACATGACATTTTGATTT
262665 GATTCAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (30 bp):
TGTGTAATATTATACATGACATTTTGATTT
Found at i:282500 original size:31 final size:31
Alignment explanation
Indices: 282465--282523 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
282455 TTTTTGTACA
282465 TAATTAAATATTTTTATTTTGAATTTTTAGT
1 TAATTAAATATTTTTATTTTGAATTTTTAGT
*
282496 TAATTAAATATTTTTATTTTTAATTTTT
1 TAATTAAATATTTTTATTTTGAATTTTT
282524 TATCTACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TAATTAAATATTTTTATTTTGAATTTTTAGT
Found at i:290753 original size:13 final size:13
Alignment explanation
Indices: 290739--290815 Score: 82
Period size: 13 Copynumber: 5.9 Consensus size: 13
290729 AGTTCTTCAT
*
290739 TGCTTTTGAAAAT
1 TGCTTTTGAAAAG
*
290752 TGATTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
290765 TGCTGTGGAGAAG
1 TGCTTTTGAAAAG
* *
290778 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
*
290791 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
290804 TGCTTTTGAAAA
1 TGCTTTTGAAAA
290816 TTTTGAGTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:298280 original size:14 final size:14
Alignment explanation
Indices: 298261--298293 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
298251 TTCATGAGCA
298261 TTCTTTTATTTCTT
1 TTCTTTTATTTCTT
298275 TTCTTTTATTTCTT
1 TTCTTTTATTTCTT
298289 TTCTT
1 TTCTT
298294 CTCTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTATTTCTT
Done.