Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2094.1
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: 300585
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 19302 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4119 original size:21 final size:21
Alignment explanation
Indices: 4094--4162 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4084 TATAATGATT
4094 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
4115 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
4135 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
4155 ATTATTAT
1 ATTATTAT
4163 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:4175 original size:15 final size:14
Alignment explanation
Indices: 4149--4179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4139 TATGGTTTTA
4149 TATTAGATTATTAT
1 TATTAGATTATTAT
4163 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
4178 TA
1 TA
4180 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:7249 original size:30 final size:30
Alignment explanation
Indices: 7192--7257 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
7182 AATCTATATT
*
7192 TTTATT-TTAATTTCAAAATATTGCATTTG
1 TTTATTATTAATTTCAAAATATTACATTTG
*
7221 TATTATTATTAATTTTAAAAT-TTACATTTG
1 T-TTATTATTAATTTCAAAATATTACATTTG
7251 TTTATTA
1 TTTATTA
7258 ATGTATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 7 0.21
30 14 0.42
31 12 0.36
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (30 bp):
TTTATTATTAATTTCAAAATATTACATTTG
Found at i:8541 original size:2 final size:2
Alignment explanation
Indices: 8534--8562 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8524 CAAACATCTT
8534 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
8563 CTAAATTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9921 original size:20 final size:19
Alignment explanation
Indices: 9866--9921 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
9856 TGATCCAAAG
*
9866 AATAATATAAATATATTTA
1 AATAATATAAATATATTAA
* *
9885 AATAATAAAGAAAATATTAA
1 AATAATATA-AATATATTAA
*
9905 AATTGATATAAATATAT
1 AA-TAATATAAATATAT
9922 GTTCGCTCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.28
20 16 0.55
21 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
AATAATATAAATATATTAA
Found at i:21095 original size:24 final size:24
Alignment explanation
Indices: 21062--21132 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 24
21052 TTAGCTTTTA
21062 TGAGCTTTCCGATTATGACTCTTCG
1 TGAG-TTTCCGATTATGACTCTTCG
* * *
21087 TGAGTTTCCCATTAATTGGCTCTTTG
1 TGAGTTTCCGATT-A-TGACTCTTCG
*
21113 TGAGCTTCCTGA-TATGACTC
1 TGAGTTTCC-GATTATGACTC
21133 ACTTGAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
24 13 0.35
25 6 0.16
26 17 0.46
27 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (24 bp):
TGAGTTTCCGATTATGACTCTTCG
Found at i:21768 original size:60 final size:60
Alignment explanation
Indices: 21675--21793 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
21665 TTAAAAGCTT
* *
21675 ATTTTGTTTTATTTCCTCTGTTCTATAGTGCTCGGAAGCTCATAAAGGTTGGAATCGGTA
1 ATTTTATTTTATTTCCTCTGTTCTATAGTGCTCGAAAGCTCATAAAGGTTGGAATCGGTA
*
21735 ATTTTATTTTATTTCCTCTGTTTTATAGTGCTCGAAAGCTCATAAAGGTTGGAATCGGT
1 ATTTTATTTTATTTCCTCTGTTCTATAGTGCTCGAAAGCTCATAAAGGTTGGAATCGGT
21794 TGGAACATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (60 bp):
ATTTTATTTTATTTCCTCTGTTCTATAGTGCTCGAAAGCTCATAAAGGTTGGAATCGGTA
Found at i:23220 original size:74 final size:74
Alignment explanation
Indices: 23101--23259 Score: 295
Period size: 74 Copynumber: 2.2 Consensus size: 74
23091 GTAAGTTAAA
23101 TTCTTGA-T-TATTTCTTGAATTCTTTCTGTTTTTGTGACTTTTACAACTAGGTCCATTTGTTGA
1 TTCTTGATTCTATTTCTTGAATTCTTTCTGTTTTTGTGACTTTTACAACTAGGTCCATTTGTTGA
23164 ATTCATTAG
66 ATTCATTAG
*
23173 TTCTTGATTCTATTTCTTGAATTTTTTCTGTTTTTGTGACTTTTACAACTAGGTCCATTTGTTGA
1 TTCTTGATTCTATTTCTTGAATTCTTTCTGTTTTTGTGACTTTTACAACTAGGTCCATTTGTTGA
23238 ATTCATTAG
66 ATTCATTAG
23247 TTCTTGATTCTAT
1 TTCTTGATTCTAT
23260 GAAAGAAATT
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
72 7 0.08
73 1 0.01
74 76 0.90
ACGTcount: A:0.19, C:0.14, G:0.13, T:0.54
Consensus pattern (74 bp):
TTCTTGATTCTATTTCTTGAATTCTTTCTGTTTTTGTGACTTTTACAACTAGGTCCATTTGTTGA
ATTCATTAG
Found at i:35007 original size:14 final size:14
Alignment explanation
Indices: 34988--35015 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34978 ACAATGTAAG
34988 TCAATTTTCGATTC
1 TCAATTTTCGATTC
35002 TCAATTTTCGATTC
1 TCAATTTTCGATTC
35016 AAAATTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
TCAATTTTCGATTC
Found at i:42899 original size:28 final size:28
Alignment explanation
Indices: 42867--42932 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
42857 ATTTATTTGA
42867 GTATTTTCTTTGAATCAACAATAG-TTG
1 GTATTTTCTTTGAATCAACAATAGCTTG
* *
42894 TGTATTTTCTTTGAATCAATAGTAGCTTG
1 -GTATTTTCTTTGAATCAACAATAGCTTG
42923 GTATTTTCTT
1 GTATTTTCTT
42933 CTTGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 32 0.91
29 3 0.09
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (28 bp):
GTATTTTCTTTGAATCAACAATAGCTTG
Found at i:44196 original size:14 final size:15
Alignment explanation
Indices: 44177--44205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44167 AATAAGTTAG
44177 AGAGTA-TGTTTATT
1 AGAGTATTGTTTATT
44191 AGAGTATTGTTTATT
1 AGAGTATTGTTTATT
44206 TTAAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
AGAGTATTGTTTATT
Found at i:48039 original size:19 final size:20
Alignment explanation
Indices: 48017--48067 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
48007 TTAATCTTAG
48017 TTAATTAAGTTAATTAGGT-
1 TTAATTAAGTTAATTAGGTA
* * *
48036 TTAATTATAATAAATTAGTTA
1 TTAATTA-AGTTAATTAGGTA
48057 TTAATTAAGTT
1 TTAATTAAGTT
48068 TAATGGGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 7 0.28
20 11 0.44
21 7 0.28
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TTAATTAAGTTAATTAGGTA
Found at i:50877 original size:117 final size:117
Alignment explanation
Indices: 50739--50975 Score: 411
Period size: 117 Copynumber: 2.0 Consensus size: 117
50729 ATTAATTTGA
* *
50739 AAAAAAAATTAGATTAAGCAACATGCAAGGATCATAATAATAGTTCATGATAAATATGAAATATG
1 AAAAAAAATTAGATTAAGCAACATCCAAGGATCATAATAATAGTTCATGATAAATACGAAATATG
*
50804 TTACACTAAATTAATAAACACATTTAATAATAATGATTAAAAATAATTGTTG
66 TTACACTAAATTAATAAAAACATTTAATAATAATGATTAAAAATAATTGTTG
*
50856 AAAAAAAATTAGATTAAGCAACATCCAAGGATCATAATAATAGTTCATGATAAATACGAAATATT
1 AAAAAAAATTAGATTAAGCAACATCCAAGGATCATAATAATAGTTCATGATAAATACGAAATATG
* * *
50921 TTATATTAAATTAATAAAAATATTTAATAATAATGATTAAAAATAATTGTTG
66 TTACACTAAATTAATAAAAACATTTAATAATAATGATTAAAAATAATTGTTG
50973 AAA
1 AAA
50976 TGTGACTTTC
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 113 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (117 bp):
AAAAAAAATTAGATTAAGCAACATCCAAGGATCATAATAATAGTTCATGATAAATACGAAATATG
TTACACTAAATTAATAAAAACATTTAATAATAATGATTAAAAATAATTGTTG
Found at i:51257 original size:12 final size:12
Alignment explanation
Indices: 51240--51273 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
51230 CGGCCAACCC
51240 ATATTAATTTTT
1 ATATTAATTTTT
*
51252 ATATTATTTTTT
1 ATATTAATTTTT
51264 ATA-TAATTTT
1 ATATTAATTTT
51274 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:51431 original size:30 final size:29
Alignment explanation
Indices: 51395--51458 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 29
51385 CAATTTAACA
51395 AACAAATGC-TTCTAAAATAATAACAAAATT
1 AACAAATGCGTT-TAAAATAATAA-AAAATT
51425 AACAAATGCGTTTAAAATAATAAAAAATT
1 AACAAATGCGTTTAAAATAATAAAAAATT
51454 AACAA
1 AACAA
51459 TAAAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 11 0.33
30 20 0.61
31 2 0.06
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (29 bp):
AACAAATGCGTTTAAAATAATAAAAAATT
Found at i:51513 original size:22 final size:22
Alignment explanation
Indices: 51488--51530 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51478 TATCCAAATA
51488 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
51510 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
51531 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:51534 original size:11 final size:11
Alignment explanation
Indices: 51495--51535 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
51485 ATAATAACAA
51495 CAAAATAGTAG
1 CAAAATAGTAG
* *
51506 CAACATAATAG
1 CAAAATAGTAG
*
51517 TAAAATAGTAG
1 CAAAATAGTAG
51528 CAAAATAG
1 CAAAATAG
51536 AGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:51543 original size:22 final size:22
Alignment explanation
Indices: 51496--51543 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
51486 TAATAACAAC
* *
51496 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
51518 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
51540 AAAA
1 AAAA
51544 CAATAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:53211 original size:18 final size:18
Alignment explanation
Indices: 53179--53236 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
53169 ATGAAAACCC
* *
53179 TATAGTAAGTGAACCCCT
1 TATAGTATGTAAACCCCT
*
53197 TATAGTATGTAAACCACT
1 TATAGTATGTAAACCCCT
* * *
53215 GATATTGTGTAAA-CCCT
1 TATAGTATGTAAACCCCT
53232 TATAG
1 TATAG
53237 GTGAGCCCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 6 0.19
18 25 0.81
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (18 bp):
TATAGTATGTAAACCCCT
Found at i:53527 original size:27 final size:26
Alignment explanation
Indices: 53496--53555 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
53486 ATTTAATATG
*
53496 CGAACCCTAGGTGCGAACCCATATGTA
1 CGAACCCTAGGTACGAA-CCATATGTA
* *
53523 CGAACCCCTAGGTACGAACCATATTTG
1 CGAA-CCCTAGGTACGAACCATATGTA
53550 CGAACC
1 CGAACC
53556 TCTGTACGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 15 0.52
28 12 0.41
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (26 bp):
CGAACCCTAGGTACGAACCATATGTA
Found at i:53528 original size:14 final size:14
Alignment explanation
Indices: 53496--53542 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
53486 ATTTAATATG
*
53496 CGAACCC-TAGGTG
1 CGAACCCATAGGTA
*
53509 CGAACCCATATGTA
1 CGAACCCATAGGTA
*
53523 CGAACCCCTAGGTA
1 CGAACCCATAGGTA
53537 CGAACC
1 CGAACC
53543 ATATTTGCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 7 0.24
14 22 0.76
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (14 bp):
CGAACCCATAGGTA
Found at i:58055 original size:44 final size:44
Alignment explanation
Indices: 57967--58057 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
57957 ATAATTATAA
* * * *
57967 ATTAAATTATAATTATTTTTAAATGCATAATTATAAGAATTTCT
1 ATTAAATTATAATAATTATTAAATGCATAATTATAACAACTTCT
* * *
58011 ATTAACTTATAATAATTATTAAATGTATAATTATCACAACTTCT
1 ATTAAATTATAATAATTATTAAATGCATAATTATAACAACTTCT
58055 ATT
1 ATT
58058 TTAGTTTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (44 bp):
ATTAAATTATAATAATTATTAAATGCATAATTATAACAACTTCT
Found at i:59407 original size:15 final size:16
Alignment explanation
Indices: 59387--59425 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
59377 CTAGAACCCT
59387 CTTTCACTTTGTATC-
1 CTTTCACTTTGTATCA
59402 CTTTCACTTTGTATCA
1 CTTTCACTTTGTATCA
59418 C-TTCACTT
1 CTTTCACTT
59426 CTATATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 22 0.96
16 1 0.04
ACGTcount: A:0.15, C:0.28, G:0.05, T:0.51
Consensus pattern (16 bp):
CTTTCACTTTGTATCA
Found at i:68886 original size:5 final size:5
Alignment explanation
Indices: 68871--68927 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
68861 TTTGACATTT
* *
68871 TTAAA TT-AA TTAAA TTAAAA TTAAA TTAAA TTATAA --AAA TCAAA CTAAA
1 TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTA-AA TTAAA TTAAA TTAAA
68920 TTAAA TTA
1 TTAAA TTA
68928 TTTTTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
3 2 0.05
4 5 0.11
5 30 0.68
6 7 0.16
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (5 bp):
TTAAA
Found at i:68899 original size:16 final size:15
Alignment explanation
Indices: 68873--68903 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
68863 TGACATTTTT
68873 AAATTAATTAAATTA
1 AAATTAATTAAATTA
68888 AAATTAAATTAAATTA
1 AAATT-AATTAAATTA
68904 TAAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTAATTAAATTA
Found at i:69241 original size:24 final size:24
Alignment explanation
Indices: 69197--69246 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
69187 ATTTGATGTT
*
69197 TTATTAAAAATGAAAATATATAAAA
1 TTATTAAAAA-GAAAACATATAAAA
*
69222 TTATTAAAAA-AAACACATATCAAA
1 TTATTAAAAAGAAA-ACATATAAAA
69246 T
1 T
69247 GAATTTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 3 0.14
24 9 0.41
25 10 0.45
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (24 bp):
TTATTAAAAAGAAAACATATAAAA
Found at i:69811 original size:25 final size:25
Alignment explanation
Indices: 69782--69831 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
69772 CATGATTGGA
*
69782 ATATTAGATATAATTATTAAATTGT
1 ATATTAAATATAATTATTAAATTGT
* *
69807 ATATTAAATATGATTGTTAAATTGT
1 ATATTAAATATAATTATTAAATTGT
69832 TAAAATATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (25 bp):
ATATTAAATATAATTATTAAATTGT
Found at i:73926 original size:13 final size:13
Alignment explanation
Indices: 73910--73974 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
73900 TATTAATAAT
73910 ATATTTTATTTAA
1 ATATTTTATTTAA
*
73923 ATATTTT-TATTAT
1 ATATTTTAT-TTAA
*
73936 ATA-TTAATTTAATA
1 ATATTTTATTT-A-A
73950 TATATTTTATTTAA
1 -ATATTTTATTTAA
73964 ATACTTTTATT
1 ATA-TTTTATT
73975 ATATATTGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
12 5 0.12
13 18 0.44
14 8 0.20
15 4 0.10
16 6 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTTATTTAA
Found at i:73964 original size:41 final size:44
Alignment explanation
Indices: 73893--73996 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 44
73883 AAAAAATATT
*
73893 TATTATATATTAATAATATATTTTATTTAAATATTTTTATTATA
1 TATTATATATTAATAATATATTTTATTTAAATACTTTTATTATA
73937 TATTA-AT-TTAAT-ATATATTTTATTTAAATACTTTTATTATA
1 TATTATATATTAATAATATATTTTATTTAAATACTTTTATTATA
*
73978 TATTGATAATATAAATAAT
1 TATT-AT-ATATTAATAAT
73997 TTTTTTTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
41 32 0.60
42 6 0.11
43 2 0.04
44 7 0.13
45 4 0.08
46 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (44 bp):
TATTATATATTAATAATATATTTTATTTAAATACTTTTATTATA
Found at i:87493 original size:24 final size:24
Alignment explanation
Indices: 87465--87646 Score: 85
Period size: 24 Copynumber: 7.4 Consensus size: 24
87455 GAAATGAAGT
87465 AATAATATAAAACAA-CTTAAATCA
1 AATAATATAAAACAATCTTAAAT-A
* * *
87489 AATAATATAAGATAATTTTAAATA
1 AATAATATAAAACAATCTTAAATA
87513 AATAATATATGTATAA-AAGGT-TTAAAATA
1 AATAATATA---A-AACAA--TCTT-AAATA
*
87542 AATACTATAAAAGCAAT-TTAAAGTA
1 AATAATATAAAA-CAATCTTAAA-TA
*
87567 AATAATAGAAAACAAT-TTAAA-A
1 AATAATATAAAACAATCTTAAATA
* * * *
87589 TCATCA-ATAAAA-AGTCTAAAATA
1 -AATAATATAAAACAATCTTAAATA
*
87612 AATAATACGTAAAAAAAT-TTAAAATA
1 AATAATA--TAAAACAATCTT-AAATA
87638 AATAATATA
1 AATAATATA
87647 CATAAAATAA
Statistics
Matches: 123, Mismatches: 16, Indels: 38
0.69 0.09 0.21
Matches are distributed among these distances:
21 2 0.02
22 13 0.11
23 5 0.04
24 37 0.30
25 29 0.24
26 15 0.12
27 5 0.04
28 3 0.02
29 14 0.11
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (24 bp):
AATAATATAAAACAATCTTAAATA
Found at i:87561 original size:25 final size:24
Alignment explanation
Indices: 87533--87644 Score: 97
Period size: 25 Copynumber: 4.7 Consensus size: 24
87523 GTATAAAAGG
* *
87533 TTTAAAATAAATACTATAAAAGCAA
1 TTTAAAATAAATAATAGAAAA-CAA
*
87558 TTTAAAGTAAATAATAGAAAACAA
1 TTTAAAATAAATAATAGAAAACAA
* *
87582 TTTAAAAT-CATCAAT--AAAA-AG
1 TTTAAAATAAAT-AATAGAAAACAA
* *
87603 TCTAAAATAAATAATACGTAAAAAAA
1 TTTAAAATAAATAATA-G-AAAACAA
87629 TTTAAAATAAATAATA
1 TTTAAAATAAATAATA
87645 TACATAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
21 11 0.16
22 6 0.09
23 2 0.03
24 13 0.19
25 22 0.31
26 16 0.23
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (24 bp):
TTTAAAATAAATAATAGAAAACAA
Found at i:87653 original size:26 final size:27
Alignment explanation
Indices: 87594--87653 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
87584 TAAAATCATC
87594 AATAAAAAGTCTAAAATAAATAATACGT
1 AATAAAAAGTCTAAAATAAATAATAC-T
*
87622 AA-AAAAA-TTTAAAATAAATAATA-T
1 AATAAAAAGTCTAAAATAAATAATACT
87646 ACATAAAA
1 A-ATAAAA
87654 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 2 0.07
25 1 0.03
26 19 0.66
27 5 0.17
28 2 0.07
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (27 bp):
AATAAAAAGTCTAAAATAAATAATACT
Found at i:87691 original size:46 final size:43
Alignment explanation
Indices: 87622--87707 Score: 109
Period size: 46 Copynumber: 1.9 Consensus size: 43
87612 AATAATACGT
*
87622 AAAAAAATTTAAAATAAATAATATACATAAAATAAAAAAAAAAC
1 AAAAAAATTTAAAATAAAAAATATACATAAAA-AAAAAAAAAAC
* * *
87666 AAAAAACAGTTTAACATAAAAAATATATATAAAAAAATAAAA
1 AAAAAA-A-TTTAAAATAAAAAATATACATAAAAAAAAAAAA
87708 TAAATAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 6 0.17
45 8 0.22
46 22 0.61
ACGTcount: A:0.73, C:0.05, G:0.01, T:0.21
Consensus pattern (43 bp):
AAAAAAATTTAAAATAAAAAATATACATAAAAAAAAAAAAAAC
Found at i:87948 original size:26 final size:25
Alignment explanation
Indices: 87919--88046 Score: 88
Period size: 24 Copynumber: 5.2 Consensus size: 25
87909 ACATGTATTA
*
87919 AAAACAGTTTAAAATGAATATTATAT
1 AAAA-AGTTTAAAATGAATAATATAT
* *
87945 AAAAAATTTAAAGTGAATAATATAT
1 AAAAAGTTTAAAATGAATAATATAT
* *
87970 AAAATAGTTTAAACTATG--TATTGTAT
1 AAAA-AGTTTAAA--ATGAATAATATAT
* *
87996 ATAAA-TTTAAAAT-ACATAATATGT
1 AAAAAGTTTAAAATGA-ATAATATAT
* *
88020 -AAAAGTTTAAAATAAATAACA-AT
1 AAAAAGTTTAAAATGAATAATATAT
88043 AAAA
1 AAAA
88047 GGAATTTAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
22 2 0.03
23 4 0.05
24 27 0.34
25 24 0.30
26 20 0.25
28 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (25 bp):
AAAAAGTTTAAAATGAATAATATAT
Found at i:87961 original size:25 final size:25
Alignment explanation
Indices: 87917--88072 Score: 81
Period size: 24 Copynumber: 6.0 Consensus size: 25
87907 TGACATGTAT
*
87917 TAAAAACAGTTTAAAATGAATATTATA
1 TAAAAA-A-TTTAAAATGAATAATATA
*
87944 TAAAAAATTTAAAGTGAATAATATA
1 TAAAAAATTTAAAATGAATAATATA
* * *
87969 TAAAATAGTTTAAACTATG--TATTGTA
1 TAAAA-AATTTAAA--ATGAATAATATA
* *
87995 T-ATAAATTTAAAAT-ACATAATATG
1 TAAAAAATTTAAAATGA-ATAATATA
* * *
88019 T-AAAAGTTTAAAATAAATAACA-A
1 TAAAAAATTTAAAATGAATAATATA
88042 TAAAAGGAATTTAACATATAGAATAATATA
1 TAAAA--AATTTAA-A-AT-GAATAATATA
88072 T
1 T
88073 CTAAATAACA
Statistics
Matches: 97, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
22 2 0.02
23 1 0.01
24 31 0.32
25 24 0.25
26 20 0.21
27 7 0.07
28 4 0.04
29 6 0.06
30 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (25 bp):
TAAAAAATTTAAAATGAATAATATA
Found at i:87973 original size:23 final size:24
Alignment explanation
Indices: 87887--87982 Score: 70
Period size: 25 Copynumber: 3.8 Consensus size: 24
87877 AGTAATTAAC
* **
87887 ATATATAT-AATAATTCGAAATGA
1 ATATATATAAAAAATTTAAAATGA
*
87910 CATGTAT-TAAAAACAGTTTAAAATGA
1 -ATATATATAAAAA-A-TTTAAAATGA
*
87936 ATATTATATAAAAAATTTAAAGTGA
1 ATA-TATATAAAAAATTTAAAATGA
*
87961 ATAATATATAAAATAGTTTAAA
1 AT-ATATATAAAA-AATTTAAA
87983 CTATGTATTG
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.02
24 8 0.14
25 23 0.40
26 20 0.34
27 6 0.10
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (24 bp):
ATATATATAAAAAATTTAAAATGA
Found at i:88112 original size:41 final size:41
Alignment explanation
Indices: 88032--88112 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
88022 AAGTTTAAAA
*
88032 TAAATAACAATAAAAGGAATTTAACATATAGAATAATATATC
1 TAAATAACAATAAAA-GAATTTAACATAGAGAATAATATATC
*
88074 TAAATAACATATAAAA-AATTTAA-ATAGATAATATATATA
1 TAAATAACA-ATAAAAGAATTTAACATAGAGAATA-ATATA
88113 AAATAGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 8 0.23
41 12 0.34
42 9 0.26
43 6 0.17
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (41 bp):
TAAATAACAATAAAAGAATTTAACATAGAGAATAATATATC
Found at i:88333 original size:9 final size:8
Alignment explanation
Indices: 88311--88353 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 8
88301 AAAAGAACTG
88311 AAATAA-T
1 AAATAATT
88318 AAATAATT
1 AAATAATT
88326 ATAATAATT
1 A-AATAATT
88335 AAATAAATT
1 AAAT-AATT
88344 AAATAGATT
1 AAATA-ATT
88353 A
1 A
88354 GGACTAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.19
8 6 0.19
9 20 0.62
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (8 bp):
AAATAATT
Found at i:89821 original size:3 final size:3
Alignment explanation
Indices: 89813--89842 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
89803 GTCAAATGCC
89813 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
89843 GTTGTAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:89903 original size:15 final size:16
Alignment explanation
Indices: 89883--89921 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
89873 CATAAACCCA
89883 AAATAAAAAT-AAAAT
1 AAATAAAAATAAAAAT
*
89898 AAATAAAACTAAAAAT
1 AAATAAAAATAAAAAT
89914 AAATAAAA
1 AAATAAAA
89922 GTCCATTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:89912 original size:21 final size:19
Alignment explanation
Indices: 89882--89920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
89872 CCATAAACCC
89882 AAAATAAAAATAAAATAAAT
1 AAAATAAAAAT-AAATAAAT
89902 AAAACTAAAAATAAATAAA
1 AAAA-TAAAAATAAATAAA
89921 AGTCCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAATAAAAATAAATAAAT
Found at i:92780 original size:30 final size:30
Alignment explanation
Indices: 92746--92808 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
92736 ATTTATTTTA
92746 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
92776 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
92806 TTG
1 TTG
92809 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:111184 original size:14 final size:14
Alignment explanation
Indices: 111167--111202 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
111157 CAGAGCTAAT
111167 CAAACACAGCTACA
1 CAAACACAGCTACA
111181 CAAACACAGCTACA
1 CAAACACAGCTACA
111195 CAAACACA
1 CAAACACA
111203 ATGCTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.36, G:0.06, T:0.06
Consensus pattern (14 bp):
CAAACACAGCTACA
Found at i:113349 original size:21 final size:21
Alignment explanation
Indices: 113325--113369 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
113315 GGAGAATATG
* **
113325 AAAACAGAAAAGCTAAAAATA
1 AAAAAAGAAAAGAGAAAAATA
*
113346 AAAAAATAAAAGAGAAAAATA
1 AAAAAAGAAAAGAGAAAAATA
113367 AAA
1 AAA
113370 TAGTTTTAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAAAGAAAAGAGAAAAATA
Found at i:118478 original size:24 final size:25
Alignment explanation
Indices: 118446--118528 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 25
118436 AAAAATAGTG
*
118446 TATATATTATTTTTATTTATA-TAT
1 TATACATTATTTTTATTTATATTAT
* *
118470 TATTCATTA-TATTATTTATATTAT
1 TATACATTATTTTTATTTATATTAT
** *
118494 TATACATT-TTATTTATAAATTTTAT
1 TATACATTATT-TTTATTTATATTAT
*
118519 TATATATTAT
1 TATACATTAT
118529 ATATTTTACT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 10 0.22
24 18 0.39
25 17 0.37
26 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TATACATTATTTTTATTTATATTAT
Found at i:118482 original size:29 final size:28
Alignment explanation
Indices: 118448--118533 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
118438 AAATAGTGTA
118448 TATATTATTTTTATTTATATATTATTCAT
1 TATATTATTTTTATTTATATATTATT-AT
* *
118477 TATATTATTTATATTATTATACATT-TTAT
1 TATATTATTTTTA-T-TTATATATTATTAT
* *
118506 T-TATAAATTTTA-TTATATATTATATAT
1 TATATTATTTTTATTTATATATTAT-TAT
118533 T
1 T
118534 TTACTATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
25 8 0.17
26 1 0.02
27 4 0.09
28 8 0.17
29 15 0.32
30 3 0.06
31 8 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TATATTATTTTTATTTATATATTATTAT
Found at i:118494 original size:12 final size:12
Alignment explanation
Indices: 118453--118534 Score: 50
Period size: 12 Copynumber: 6.9 Consensus size: 12
118443 GTGTATATAT
*
118453 TATTTTTATTTA
1 TATTATTATTTA
*
118465 TA-TATTATTCA
1 TATTATTATTTA
118476 T-TATATTATTTA
1 TAT-TATTATTTA
118488 TATTATTA--TA
1 TATTATTATTTA
*
118498 CATT-TTATTTA
1 TATTATTATTTA
118509 TAAATT-TTATTATA
1 T--ATTATTATT-TA
118523 TATTATATATTT
1 TATTAT-TATTT
118535 TACTATATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
9 3 0.05
10 5 0.09
11 10 0.18
12 19 0.35
13 11 0.20
14 7 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:118505 original size:21 final size:21
Alignment explanation
Indices: 118454--118510 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
118444 TGTATATATT
*
118454 ATTTTTATTTATATATTATTC
1 ATTTTTATTTATATATTATAC
118475 ATTATATTATTTATATTATTATAC
1 ATT-T-TTATTTATA-TATTATAC
118499 A-TTTTATTTATA
1 ATTTTTATTTATA
118511 AATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 10 0.31
24 8 0.25
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTATTTATATATTATAC
Found at i:121927 original size:550 final size:551
Alignment explanation
Indices: 120887--121986 Score: 1767
Period size: 550 Copynumber: 2.0 Consensus size: 551
120877 TACATTCGGT
*** *
120887 GGGCAAGTTTGAGGGATTTAATATTGGTGTACCCAGATGTGAAGAAGAGGGTTGATGTTTTGGCC
1 GGGCAAGTTTGAGGGATTTAATATTGGCACACCCAGATGTGAAGAAGAGGGTTGATGTTCTGGCC
*
120952 TTAAGTATTTATGGTTTGGTGACTTTCCCTAAAGCTATTGGGCACATAGATGAGGCAATTACGGA
66 TTAAGTATTTATGGTTTGGTGACTTTCCCTAAAGCTATTGGGCACATAGATGAGGCAATTACCGA
* * *
121017 TTTATTCGATCAACTTGGTAAATAGAACACACTTGTGCCTGCAATCTTAGCTGAGACGTTTAGAT
131 TTTATTCGATCAACTTGGTAAACAGAACACACCTGTGCCTGCAATCCTAGCTGAGACGTTTAGAT
**
121082 CCTTGAGCGCACGTCGGAGAGCTGGTGAAGGTAGATTAATTTGATGTGCACAGTTGTTATAAGTA
196 CCTTGAGCGCACGTCAAAGAGCTGGTGAAGGTAGATTAATTTGATGTGCACAGTTGTTATAAGTA
* *
121147 TGGTTCCATAGTCACTTTTAGAAGGTTGATAAGGTTCCTTGTCGAGTGTCCTTTGAGGATTATTC
261 TGGTTCCATAGTCACTTTTAGAAGGTTGATAAGATTCCTTGCCGAGTGTCCTTTGAGGATTATTC
* * *
121212 TCCCTTAAGGGAAGCTGCAGCTACGACGAGGAGGGACGAAATTACAGAAGAAATATGGACAGAAA
326 TCCCTTAACGGAAGCTGCAGCTACGACAAGGAGGGACGAAATTACAGAAGAAAGATGGACAGAAA
* * *
121277 TACTTTAGAATCTCCGAGAGGAAGATATAATGTGGAAAGCTCATTAGATGGCTCCTAATGAAGTC
391 TACTTCAGAATCTCCAAGAGAAAGATATAATGTGGAAAGCTCATTAGATGGCTCCTAATGAAGTC
*
121342 CTTTATCATTGTGGAAGTTTTGATTGGGTACCTCTTCATGGAATTT-GGGAGTCGTTGGTTATGC
456 CTTTATCATTGTGGAAGTTTTGATTGGGTACCTCTTCATGGAATTTGGGGAGTCATTGGTTATGC
*
121406 ACCATTACTCGTCTTAAGGCAATACAAAGCA
521 ACCATTACTCGTCCTAAGGCAATACAAAGCA
* *
121437 GGGCAAGTTTGAGGGATTTGATATTGGCACACCTAGATGTGAAGAAGAGGGTTGATGTTCTGGCC
1 GGGCAAGTTTGAGGGATTTAATATTGGCACACCCAGATGTGAAGAAGAGGGTTGATGTTCTGGCC
* * ** *
121502 TTAAGTATTTATGGTTTGGTGATTTTCCCTAAAGCTATTGGGCATATAGATGAGGCGGTTGCCGA
66 TTAAGTATTTATGGTTTGGTGACTTTCCCTAAAGCTATTGGGCACATAGATGAGGCAATTACCGA
*
121567 TTTATTCGATCGACTTGGTAAACAGAACACACCTGTGCCTGCAATCCTAGCTGAGACGTTTAGAT
131 TTTATTCGATCAACTTGGTAAACAGAACACACCTGTGCCTGCAATCCTAGCTGAGACGTTTAGAT
* * *
121632 TCTTGAGCGCACGTCAAAGAGCTGGTGAAGGTAGATTCA-TTGTATGTGCACAGTTGTTATTAGT
196 CCTTGAGCGCACGTCAAAGAGCTGGTGAAGGTAGATTAATTTG-ATGTGCACAGTTGTTATAAGT
* * *
121696 GTGGTTCCATAGTCACTTTTGGAATGTTGATAAGATTCCTTGCCGAGTGTCCTTTGAGGATTATT
260 ATGGTTCCATAGTCACTTTTAGAAGGTTGATAAGATTCCTTGCCGAGTGTCCTTTGAGGATTATT
* * *
121761 CTCCCTTAACGGAAGCTGCAGCTAC-ACCAAGGAGGGACGACATTACAGAGGAAAGATGGACGGA
325 CTCCCTTAACGGAAGCTGCAGCTACGA-CAAGGAGGGACGAAATTACAGAAGAAAGATGGACAGA
*
121825 AATACTTCAGAATCTCCAAGAGAAAGATATAATGTGGAAAGCTTC-TTGGATGGCTCCTAATGAA
389 AATACTTCAGAATCTCCAAGAGAAAGATATAATGTGGAAAGC-TCATTAGATGGCTCCTAATGAA
* *
121889 GTCCTTTATCGTTGTGGAAGTTTTGATTGGGTACCTCTTCTTGGAATTTGGGGAGTCATTGGTTA
453 GTCCTTTATCATTGTGGAAGTTTTGATTGGGTACCTCTTCATGGAATTTGGGGAGTCATTGGTTA
* *
121954 TGCATCATTACTCTTCCTAAGGCAATACAAAGC
518 TGCACCATTACTCGTCCTAAGGCAATACAAAGC
121987 GGGGTAGTTT
Statistics
Matches: 504, Mismatches: 42, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
549 4 0.01
550 454 0.90
551 46 0.09
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (551 bp):
GGGCAAGTTTGAGGGATTTAATATTGGCACACCCAGATGTGAAGAAGAGGGTTGATGTTCTGGCC
TTAAGTATTTATGGTTTGGTGACTTTCCCTAAAGCTATTGGGCACATAGATGAGGCAATTACCGA
TTTATTCGATCAACTTGGTAAACAGAACACACCTGTGCCTGCAATCCTAGCTGAGACGTTTAGAT
CCTTGAGCGCACGTCAAAGAGCTGGTGAAGGTAGATTAATTTGATGTGCACAGTTGTTATAAGTA
TGGTTCCATAGTCACTTTTAGAAGGTTGATAAGATTCCTTGCCGAGTGTCCTTTGAGGATTATTC
TCCCTTAACGGAAGCTGCAGCTACGACAAGGAGGGACGAAATTACAGAAGAAAGATGGACAGAAA
TACTTCAGAATCTCCAAGAGAAAGATATAATGTGGAAAGCTCATTAGATGGCTCCTAATGAAGTC
CTTTATCATTGTGGAAGTTTTGATTGGGTACCTCTTCATGGAATTTGGGGAGTCATTGGTTATGC
ACCATTACTCGTCCTAAGGCAATACAAAGCA
Found at i:131199 original size:44 final size:44
Alignment explanation
Indices: 131144--131901 Score: 1043
Period size: 44 Copynumber: 17.2 Consensus size: 44
131134 ATAGATCACC
* **
131144 GATAGCAGATTTGGCATCTCTGTATTAACAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* *
131188 GATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * * *
131232 TATAGTAGATTTGACGTCTCTGTATTGGCAGAGAGCGGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * * *
131276 GATAGTAGATTTGACATCTCTATATTGGT-AGAGAGCAGATTGAA
1 GATAGCAGATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCGAA
* * *
131320 GATAGCAGATTTGGCATCTCTGTATTGACAGTGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * *
131364 GATAACAGATTTGGTGTCTCTGTATTGACAGAGAGCAGATCAAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * * *
131408 GATAGTAGATTTGGCGTCTCTGTCTTGACAGAGAGCATATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* *
131452 GATAGCCGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * *
131496 GATAGTAGATTTGACGTCTCTGTATTGTTAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
*
131540 GATAGCAGATTTAGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * *
131584 GATAGTAGATTTGACGTCTCTGTATTGTTAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
*
131628 GATAGCAGATTTAGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* * *
131672 GATAGTAGATTTGACGTCTCTGTATTGTTAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
*
131716 GATAGCAGATTTAGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
** *
131760 GATAGCAGATTTAACCTCTCTGTATTGGT-AGAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCGAA
* * *
131804 AATAGCAGATTTGGCGTCTCTGTATTGACAGAGAACAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
* *
131848 GATAGCAGATTTGGCGTCTCTGTATTGACAAAGAGCAGATCGAA
1 GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
*
131892 GATAGTAGAT
1 GATAGCAGAT
131902 CTGACATTTG
Statistics
Matches: 632, Mismatches: 78, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
43 2 0.00
44 627 0.99
45 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (44 bp):
GATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAA
Found at i:132200 original size:13 final size:14
Alignment explanation
Indices: 132174--132204 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
132164 CCGGCCCATG
132174 AAATAAATAAATAA
1 AAATAAATAAATAA
132188 AAATAAA-AAATAA
1 AAATAAATAAATAA
132201 AAAT
1 AAAT
132205 TAAGGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:132695 original size:25 final size:25
Alignment explanation
Indices: 132648--132695 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
132638 TGATATACAT
* *
132648 ACATACAATAAAATATAGGCAGTTG
1 ACATACAATAAAAAATAGCCAGTTG
132673 ACATACACATAAAAAATA-CCAGT
1 ACATACA-ATAAAAAATAGCCAGT
132696 AGATTATCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (25 bp):
ACATACAATAAAAAATAGCCAGTTG
Found at i:133212 original size:24 final size:25
Alignment explanation
Indices: 133180--133261 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 25
133170 AAAAATAGTG
*
133180 TATATATTATTTTTATTTATA-TAT
1 TATACATTATTTTTATTTATATTAT
* *
133204 TATTCATTA-TATTATTTATATTAT
1 TATACATTATTTTTATTTATATTAT
** *
133228 TATACATT-TTATTTATAAATTTTAT
1 TATACATTATT-TTTATTTATATTAT
*
133253 TATATATTA
1 TATACATTA
133262 GTTAAATGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 10 0.22
24 18 0.40
25 17 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATACATTATTTTTATTTATATTAT
Found at i:133239 original size:21 final size:21
Alignment explanation
Indices: 133188--133244 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
133178 TGTATATATT
*
133188 ATTTTTATTTATATATTATTC
1 ATTTTTATTTATATATTATAC
133209 ATTATATTATTTATATTATTATAC
1 ATT-T-TTATTTATA-TATTATAC
133233 A-TTTTATTTATA
1 ATTTTTATTTATA
133245 AATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 10 0.31
24 8 0.25
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTATTTATATATTATAC
Found at i:134679 original size:19 final size:19
Alignment explanation
Indices: 134655--134693 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
134645 AGGAAGCTTC
134655 GTCTTCAGATGTTATAACT
1 GTCTTCAGATGTTATAACT
134674 GTCTTCAGATGTTATAACT
1 GTCTTCAGATGTTATAACT
134693 G
1 G
134694 GTAGTTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (19 bp):
GTCTTCAGATGTTATAACT
Found at i:139359 original size:44 final size:41
Alignment explanation
Indices: 139296--139411 Score: 133
Period size: 44 Copynumber: 2.7 Consensus size: 41
139286 TGAGTTCATG
*
139296 TAAGACCATGTCTGGGACATTGGCCTCGACTTATGATTTACGTA
1 TAAGACCATGTCTGGGACATTGGCATCGA-TT-TGATTT-CGTA
* * *
139340 TAAGACCATGTTTGGGACATCGGCATCGTATTTGATTTCGTG
1 TAAGACCATGTCTGGGACATTGGCATCG-ATTTGATTTCGTA
* * *
139382 TAAGAACTTGTCTGGGACAGTGGCATCGAT
1 TAAGACCATGTCTGGGACATTGGCATCGAT
139412 ATTTTATTAC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
41 2 0.03
42 26 0.42
43 6 0.10
44 27 0.44
45 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
TAAGACCATGTCTGGGACATTGGCATCGATTTGATTTCGTA
Found at i:139398 original size:42 final size:42
Alignment explanation
Indices: 139294--139431 Score: 131
Period size: 42 Copynumber: 3.2 Consensus size: 42
139284 TGTGAGTTCA
*
139294 TGTAAGACCATGTCTGGGACATTGGCCTCG-ACTTATGATTTACG
1 TGTAAGACCATGTCTGGGACA-TGGCATCGTA-TT-TGATTTACG
* *
139338 TATAAGACCATGTTTGGGACATCGGCATCGTATTTGATTT-CG
1 TGTAAGACCATGTCTGGGACAT-GGCATCGTATTTGATTTACG
* * * *
139380 TGTAAGAACTTGTCTGGGACAGTGGCATCGATATTTTA-TTACA
1 TGTAAGACCATGTCTGGGACA-TGGCATCG-TATTTGATTTACG
139423 TGTAA-ACCA
1 TGTAAGACCA
139432 CATCTGAGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
42 30 0.38
43 20 0.26
44 27 0.35
45 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATGGCATCGTATTTGATTTACG
Found at i:143139 original size:9 final size:9
Alignment explanation
Indices: 143125--143206 Score: 64
Period size: 9 Copynumber: 9.4 Consensus size: 9
143115 ATTATTTTAG
143125 AAAATTTTT
1 AAAATTTTT
143134 AAAA-TTTT
1 AAAATTTTT
*
143142 -AACTTTTT
1 AAAATTTTT
**
143150 ATATTTTTTT
1 A-AAATTTTT
*
143160 AGAATTTTT
1 AAAATTTTT
*
143169 AAAATTTTC
1 AAAATTTTT
* *
143178 AAAA-ATAT
1 AAAATTTTT
143186 -AAATTTTT
1 AAAATTTTT
143194 AAAATTTTT
1 AAAATTTTT
143203 AAAA
1 AAAA
143207 ATTAATTTGA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
7 5 0.09
8 11 0.20
9 32 0.58
10 7 0.13
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (9 bp):
AAAATTTTT
Found at i:145046 original size:6 final size:6
Alignment explanation
Indices: 145035--145067 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
145025 AAAATTGCTA
145035 AGCCCG AGCCCG AGCCCG AGCCCG A-CCC- AGCCC
1 AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCC
145068 ATATTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 1 0.04
5 6 0.23
6 19 0.73
ACGTcount: A:0.18, C:0.55, G:0.27, T:0.00
Consensus pattern (6 bp):
AGCCCG
Found at i:146904 original size:5 final size:5
Alignment explanation
Indices: 146894--146920 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
146884 TTATGTTTTA
146894 ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT AT
146921 AAACTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:147263 original size:15 final size:15
Alignment explanation
Indices: 147243--147299 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
147233 CGATGAATTT
*
147243 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
147258 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
147273 ATTGAAATTATATTG
1 ATTGAAATTATATTG
147288 ATTG-AATTATAT
1 ATTGAAATTATAT
147300 AATATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:147703 original size:23 final size:22
Alignment explanation
Indices: 147673--147780 Score: 114
Period size: 21 Copynumber: 5.0 Consensus size: 22
147663 GCTTTACTGA
* *
147673 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTA-T
*
147696 TCAGGCACCTCGTGTGTCGTA-
1 TCAGGCACCTCATGTGTCGTAT
147717 TCAGGCACCTCATGTGTCGTA-
1 TCAGGCACCTCATGTGTCGTAT
* *
147738 TCAGGCACCTCGTGTGTCAT-T
1 TCAGGCACCTCATGTGTCGTAT
* * *
147759 TTAGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
147781 ACTGATCAGG
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
21 53 0.74
22 1 0.01
23 18 0.25
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (22 bp):
TCAGGCACCTCATGTGTCGTAT
Found at i:147720 original size:21 final size:21
Alignment explanation
Indices: 147685--147755 Score: 115
Period size: 21 Copynumber: 3.3 Consensus size: 21
147675 AGGCACTTTA
147685 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
*
147708 TGTGTCGTATCAGGCACCTCA
1 TGTGTCGTATCAGGCACCTCG
147729 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
147750 TGTGTC
1 TGTGTC
147756 ATTTTAGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 37 0.80
23 9 0.20
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.32
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:147755 original size:42 final size:42
Alignment explanation
Indices: 147672--147780 Score: 155
Period size: 42 Copynumber: 2.5 Consensus size: 42
147662 GGCTTTACTG
*
147672 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGTA--TCAGGCACCTCGTGTGTCAT
* *
147716 ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCAT
1 ATCAGGCACTTTATGTGTCGTATCAGGCACCTCGTGTGTCAT
* *
147758 TTTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
147781 ACTGATCAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 38 0.66
44 20 0.34
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (42 bp):
ATCAGGCACTTTATGTGTCGTATCAGGCACCTCGTGTGTCAT
Found at i:164854 original size:21 final size:20
Alignment explanation
Indices: 164825--164863 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
164815 TTTCCCTTTT
164825 TATAGTTTAGTAATTTTGTCA
1 TATAGTTTA-TAATTTTGTCA
* *
164846 TATATTTTATTATTTTGT
1 TATAGTTTATAATTTTGT
164864 TTTTTAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (20 bp):
TATAGTTTATAATTTTGTCA
Found at i:165537 original size:17 final size:18
Alignment explanation
Indices: 165515--165552 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
165505 CGTGATCCGA
165515 TTGAAAA-AC-AAGAATTT
1 TTGAAAACACGAA-AATTT
165532 TTGAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
165550 TTG
1 TTG
165553 GGATCCGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 10 0.53
19 2 0.11
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:165994 original size:29 final size:30
Alignment explanation
Indices: 165962--166018 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
165952 ATTAGCAGCG
* *
165962 TGAAAATGATAA-AATAACAAATATTTAAA
1 TGAAAATAATAAGAACAACAAATATTTAAA
*
165991 TGAAGATAATAAGAACAACAAATATTTA
1 TGAAAATAATAAGAACAACAAATATTTA
166019 GAAAGTAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (30 bp):
TGAAAATAATAAGAACAACAAATATTTAAA
Found at i:167409 original size:21 final size:21
Alignment explanation
Indices: 167384--167433 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
167374 TAGGATCTGT
**
167384 AACTTCAATGTGCTCCACTGC
1 AACTTCAATCAGCTCCACTGC
* * *
167405 AACTTCGATCAGCTCCATTGT
1 AACTTCAATCAGCTCCACTGC
167426 AACTTCAA
1 AACTTCAA
167434 GGCTCTGCTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (21 bp):
AACTTCAATCAGCTCCACTGC
Found at i:167827 original size:72 final size:72
Alignment explanation
Indices: 167727--167870 Score: 213
Period size: 72 Copynumber: 2.0 Consensus size: 72
167717 CGGCATGTAA
*
167727 CCCTAGGCTCAACTCACCTCTAGTAATATGAGTTGATTTTT-G-AAA-AGCATAATTGAAAATAC
1 CCCTAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGGCAAACAG-A-AATTGAAAATAC
167789 CTCAGCGTG
64 CTCAGCGTG
* *
167798 CCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGCAAACAGAAATTGAAATTACC
1 CCCT-AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGGCAAACAGAAATTGAAAATACC
167863 TCAGCGTG
65 TCAGCGTG
167871 TAACACCCCG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
71 4 0.06
72 35 0.53
73 21 0.32
74 4 0.06
75 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (72 bp):
CCCTAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGGCAAACAGAAATTGAAAATACCT
CAGCGTG
Found at i:169253 original size:37 final size:37
Alignment explanation
Indices: 169203--169282 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
169193 CTTATTACGA
* *
169203 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
169240 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
169277 GGTCTT
1 AGTCTT
169283 TAGAGTCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:169472 original size:47 final size:47
Alignment explanation
Indices: 169413--169663 Score: 337
Period size: 47 Copynumber: 5.4 Consensus size: 47
169403 TATCACATTT
* *
169413 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
* * *
169458 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
* * *
169505 ATACACCTGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
*
169552 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
** * *
169599 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTA-TCTCAC
*
169647 ATATACACT-TTCACATT
1 ATACACA-TGTTCACATT
169664 TATTCAATTA
Statistics
Matches: 183, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
45 6 0.03
46 1 0.01
47 157 0.86
48 18 0.10
49 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.31
Consensus pattern (47 bp):
ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCAC
Found at i:169702 original size:94 final size:93
Alignment explanation
Indices: 169420--169693 Score: 250
Period size: 94 Copynumber: 2.9 Consensus size: 93
169410 TTTATACACT
* * * * * *
169420 TTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
* * * * * * ** *
169485 GCCACTCGGCCTTATCACACATACACCTG
66 GACATTC-GACATACCACATATATGCATG
* * *
169514 TTCACTTTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTG
1 TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
* * * * *
169579 GCCATTCGGCCTTATCTCATATATGCATG
66 GACATTC-GACATACCACATATATGCATG
* *
169608 TTCACATTCATCACATTGGCCATTCGGCCCTATTCACACATATACACT-TTCACATTTATTCA-A
1 TTCACATTCATCACATTGGCCATTCGGCCCTA-TCACACATACACA-TGTTCACATTCA-TCACA
169671 TTAGAC-TTC-ACATACCACATATA
63 TTAGACATTCGACATACCACATATA
169694 CTATCATGTA
Statistics
Matches: 156, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
92 10 0.06
94 116 0.74
95 26 0.17
96 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.32
Consensus pattern (93 bp):
TTCACATTCATCACATTGGCCATTCGGCCCTATCACACATACACATGTTCACATTCATCACATTA
GACATTCGACATACCACATATATGCATG
Found at i:169702 original size:141 final size:140
Alignment explanation
Indices: 169413--169694 Score: 335
Period size: 141 Copynumber: 2.0 Consensus size: 140
169403 TATCACATTT
169413 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
1 ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
* * *
169476 ATCACATTGGCCACTCGGCCTTATCACACATACACCTGTTCACTTTCATCACATTGGCCATTCGG
66 ATCACATTGGCCACTCGGCCCTATCACACATACACCTGTTCACTTTCATCACATTAGACATTC-G
* * *
169541 CCTTATCACAC
130 ACATACCACAC
* * * ** *
169552 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTC
1 ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
* *
169617 ATCACATTGGCCATTCGGCCCTATTCACACATATACACT-TTCACATTT-ATTCA-ATTAGAC-T
66 ATCACATTGGCCACTCGGCCCTA-TCACACATACAC-CTGTTCAC-TTTCA-TCACATTAGACAT
*
169678 TC-ACATACCACAT
127 TCGACATACCACAC
169691 ATAC
1 ATAC
169695 TATCATGTAC
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
139 17 0.14
140 1 0.01
141 74 0.61
142 22 0.18
143 8 0.07
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (140 bp):
ATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACATGCTCACATTC
ATCACATTGGCCACTCGGCCCTATCACACATACACCTGTTCACTTTCATCACATTAGACATTCGA
CATACCACAC
Found at i:173037 original size:76 final size:76
Alignment explanation
Indices: 172886--173308 Score: 635
Period size: 76 Copynumber: 5.6 Consensus size: 76
172876 GGGTGTCACA
* * * * * * *
172886 CAGCGTGTCTTGAGGCCCAACTCACCTCT--CAATGTAAGTTGA-TATTTTTGAAAACCAGAAAT
1 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
172948 TGAAAATACCT
66 TGAAAATACCT
*
172959 CAGCGTGCCCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
1 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
173024 TGAAAATACCT
66 TGAAAATACCT
*
173035 CAGCGTGCCCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
1 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
173100 TGAAAATACCT
66 TGAAAATACCT
*
173111 CAGCGTGCCCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
1 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
173176 TGAAAATACCT
66 TGAAAATACCT
* * *
173187 CAGCGTGCCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA---TTTTTGACAAA-CAAAAA
1 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTA-AAACCAGAAA
*
173248 TTGAAATTACCT
65 TTGAAAATACCT
* * *
173260 CAGCATACCCTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
173309 GAAAACAGAA
Statistics
Matches: 326, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
73 87 0.27
74 3 0.01
75 11 0.03
76 225 0.69
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (76 bp):
CAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAACCAGAAAT
TGAAAATACCT
Found at i:185021 original size:18 final size:17
Alignment explanation
Indices: 184991--185024 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
184981 GATCCGATTG
*
184991 AAAAACGAGAATTTTTT
1 AAAAACGAAAATTTTTT
185008 AAAACACGAAAATTTTT
1 AAAA-ACGAAAATTTTT
185025 GGGATCCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (17 bp):
AAAAACGAAAATTTTTT
Found at i:185390 original size:17 final size:17
Alignment explanation
Indices: 185368--185400 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
185358 TTGTATAAAA
185368 TTTATT-TTATTGTTAAT
1 TTTATTATTATT-TTAAT
185385 TTTATTATTATTTTAA
1 TTTATTATTATTTTAA
185401 AGGCATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTATTATTTTAAT
Found at i:187250 original size:16 final size:16
Alignment explanation
Indices: 187214--187257 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
187204 CCCGAAGACA
* *
187214 ATTTTATTTATTTTTT
1 ATTTTAATTCTTTTTT
187230 A-TTTAATTCTTTTTT
1 ATTTTAATTCTTTTTT
187245 ATTTTATATTCTT
1 ATTTTA-ATTCTT
187258 CAAATTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 5 0.21
17 6 0.25
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTAATTCTTTTTT
Found at i:187407 original size:6 final size:7
Alignment explanation
Indices: 187390--187415 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
187380 CTTAAATTCT
187390 TTTTTTA
1 TTTTTTA
187397 TTTTTTA
1 TTTTTTA
187404 TTTTTTA
1 TTTTTTA
187411 TTTTT
1 TTTTT
187416 GTTTATTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:193103 original size:18 final size:19
Alignment explanation
Indices: 193080--193122 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
193070 TTTTAAAAAA
*
193080 TAAATTTTATAAAT-ATTT
1 TAAATTTTAAAAATAATTT
193098 TAAATTTTAAAAATAATTT
1 TAAATTTTAAAAATAATTT
*
193117 TGAATT
1 TAAATT
193123 ATTTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAAATTTTAAAAATAATTT
Found at i:193113 original size:31 final size:30
Alignment explanation
Indices: 193062--193135 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
193052 TTTTAGAATT
*
193062 TTTTAAATTTTTAAAAAATAAATTTTATAAATA
1 TTTTAAA-TTTTAAAAAAT-AATTTT-GAAATA
*
193095 TTTTAAATTTT-AAAAATAATTTTGAATTA
1 TTTTAAATTTTAAAAAATAATTTTGAAATA
193124 TTTTATAATTTT
1 TTTTA-AATTTT
193136 TGTTGAGAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 9 0.24
30 12 0.32
31 6 0.16
32 4 0.11
33 7 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTTAAATTTTAAAAAATAATTTTGAAATA
Found at i:199198 original size:21 final size:21
Alignment explanation
Indices: 199147--199199 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
199137 GACACATATG
199147 CATGGTATAT-ATAAAAATGT
1 CATGGTATATAATAAAAATGT
* *
199167 -ATAAGTAATATAATAAAAATTT
1 CAT-GGT-ATATAATAAAAATGT
199189 CATGGTATATA
1 CATGGTATATA
199200 TACATGTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 9 0.35
22 11 0.42
23 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (21 bp):
CATGGTATATAATAAAAATGT
Found at i:200043 original size:22 final size:20
Alignment explanation
Indices: 200018--200060 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
200008 TATTAATCTA
200018 AAAAAAATGCCTAAATAATAAT
1 AAAAAAATG-CTAAA-AATAAT
*
200040 -AAAATATGCTAAAAATAAT
1 AAAAAAATGCTAAAAATAAT
200059 AA
1 AA
200061 TACAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 7 0.37
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAAAATGCTAAAAATAAT
Found at i:202077 original size:43 final size:43
Alignment explanation
Indices: 201553--202064 Score: 997
Period size: 43 Copynumber: 11.9 Consensus size: 43
201543 TCAAATCTGC
201553 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201596 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201639 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201682 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201725 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201768 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201811 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201854 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201897 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201940 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
201983 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
* * *
202026 GACTTTTAGCGGCATTTATTGGAAAAACGCCGCTAAAAG
1 GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAG
202065 TCACGGCTTT
Statistics
Matches: 466, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 466 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (43 bp):
GACTTTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGCCTT
Found at i:202197 original size:31 final size:32
Alignment explanation
Indices: 202159--202231 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
202149 CATTAAATTC
* * *
202159 CAACCAAATACAACAAATATAGTAT-AAAATG
1 CAACCAAAAACAACAAATATAGCATAAAAATA
* *
202190 CAACCAAAAACAGCAAATTTAGCATAAAAATA
1 CAACCAAAAACAACAAATATAGCATAAAAATA
202222 CAACCAAAAA
1 CAACCAAAAA
202232 ATTAATTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 21 0.58
32 15 0.42
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.15
Consensus pattern (32 bp):
CAACCAAAAACAACAAATATAGCATAAAAATA
Found at i:202962 original size:241 final size:241
Alignment explanation
Indices: 202539--203254 Score: 1396
Period size: 241 Copynumber: 3.0 Consensus size: 241
202529 TTGTTGCACC
202539 TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
1 TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
202604 GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
66 GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
202669 TCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAAGGTTGGAGAGAAGGTTAGCTATTG
131 TCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAAGGTTGGAGAGAAGGTTAGCTATTG
202734 TTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATATTCAA
196 TTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATATTCAA
202780 TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
1 TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
202845 GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
66 GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
*
202910 TCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAGAAAGGTTGGAGAGAAGGTTAGCTATTG
131 TCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAAGGTTGGAGAGAAGGTTAGCTATTG
*
202975 TTGTAATTTTAATGGACAAGCAAGCTCCATGGTAATAAATATTCAA
196 TTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATATTCAA
203021 TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
1 TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
203086 GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
66 GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
* *
203151 CCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAAGGTTGGAGAGAAGGTCAGCTATTG
131 TCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAAGGTTGGAGAGAAGGTTAGCTATTG
203216 TTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAA
196 TTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAA
203255 ATTTATTCAT
Statistics
Matches: 469, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
241 469 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (241 bp):
TAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTTTTTGAATTTTTTAAGATTCATCATACGTG
GCGTTGTTACACCTAGGGAGGATCCATTATATCTTACAGCTCGATATAAGGCAACCCGTCAGGTT
TCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAAAAGGTTGGAGAGAAGGTTAGCTATTG
TTGTAATTTTAATGGACAAGCAAGCTACATGGTAATAAATATTCAA
Found at i:206938 original size:20 final size:18
Alignment explanation
Indices: 206893--206930 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
206883 GAAAGGCTGA
*
206893 GAAAGAAAAGGGAATTGG
1 GAAAGAAAAGGGAATGGG
206911 GAAAGAAAAGGGAATCGGG
1 GAAAGAAAAGGGAAT-GGG
206930 G
1 G
206931 GAGAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.47, C:0.03, G:0.42, T:0.08
Consensus pattern (18 bp):
GAAAGAAAAGGGAATGGG
Found at i:207196 original size:22 final size:21
Alignment explanation
Indices: 207171--207228 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
207161 ATTTTTTACT
207171 TTTTTATAATTTTTATATTGAA
1 TTTTTATAATTTTTATATT-AA
207193 TTTTTAT-ATCTTTTATATTAA
1 TTTTTATAAT-TTTTATATTAA
*
207214 TTTTAAATAATTTTT
1 TTTT-TATAATTTTT
207229 TTTAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.25
22 22 0.69
23 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTTATAATTTTTATATTAA
Found at i:207798 original size:14 final size:14
Alignment explanation
Indices: 207780--207846 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
207770 CCAGAAAAGT
*
207780 AAATCATTTTCCAT
1 AAATCATTTTCCAG
*
207794 AAATCATTTTTCAAG
1 AAATCA-TTTTCCAG
*
207809 AAATTATTTTCCAG
1 AAATCATTTTCCAG
207823 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
207837 AAAACATTTT
1 AAATCATTTT
207847 ACCTGCAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 35 0.76
15 11 0.24
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.40
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:208013 original size:7 final size:7
Alignment explanation
Indices: 207987--208119 Score: 56
Period size: 7 Copynumber: 18.7 Consensus size: 7
207977 AATCATACAA
207987 CATAACC
1 CATAACC
* *
207994 CTTAAATC
1 CAT-AACC
208002 CATAACC
1 CATAACC
208009 CATAACC
1 CATAACC
*
208016 CCTAACC
1 CATAACC
208023 CATAACC
1 CATAACC
*
208030 CCTAACTC
1 CATAAC-C
208038 C-TAACAC
1 CATAAC-C
*
208045 C-TAAAC
1 CATAACC
*
208051 CTTAAACC
1 CAT-AACC
*
208059 C-CAACC
1 CATAACC
* *
208065 CTTAAAC
1 CATAACC
*
208072 CATAAAC
1 CATAACC
** *
208079 TGTAAAC
1 CATAACC
*
208086 CATAATC
1 CATAACC
208093 CATAAACC
1 CAT-AACC
*
208101 CATAATC
1 CATAACC
*
208108 CATAATC
1 CATAACC
208115 CATAA
1 CATAA
208120 ACCTTAAAAT
Statistics
Matches: 99, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
6 7 0.07
7 75 0.76
8 17 0.17
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (7 bp):
CATAACC
Found at i:208023 original size:14 final size:14
Alignment explanation
Indices: 208004--208048 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
207994 CTTAAATCCA
208004 TAACCCATAACCCC
1 TAACCCATAACCCC
208018 TAACCCATAACCCC
1 TAACCCATAACCCC
*
208032 TAACTCC-TAACACC
1 TAAC-CCATAACCCC
208046 TAA
1 TAA
208049 ACCTTAAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 27 0.93
15 2 0.07
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (14 bp):
TAACCCATAACCCC
Found at i:208027 original size:21 final size:21
Alignment explanation
Indices: 207987--208119 Score: 72
Period size: 21 Copynumber: 6.2 Consensus size: 21
207977 AATCATACAA
* * *
207987 CATAACCCTTAAATCCATAACC
1 CATAACCCCT-AACCCATAAAC
*
208009 CATAACCCCTAACCCATAACC
1 CATAACCCCTAACCCATAAAC
* *
208030 CCTAACTCCTAACACC-TAAAC
1 CATAACCCCTAAC-CCATAAAC
* *
208051 CTTAAACCCC-AACCCTTAAAC
1 CAT-AACCCCTAACCCATAAAC
* ** * *
208072 CATAAACTGTAAACCATAATC
1 CATAACCCCTAACCCATAAAC
* * *
208093 CATAAACCCATAATCCATAATC
1 CAT-AACCCCTAACCCATAAAC
208115 CATAA
1 CATAA
208120 ACCTTAAAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
20 5 0.06
21 50 0.57
22 33 0.38
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (21 bp):
CATAACCCCTAACCCATAAAC
Found at i:208127 original size:7 final size:7
Alignment explanation
Indices: 208067--208127 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
208057 CCCCAACCCT
208067 TAAACCA
1 TAAACCA
**
208074 TAAACTG
1 TAAACCA
208081 TAAACCA
1 TAAACCA
*
208088 TAATCCA
1 TAAACCA
208095 TAAACCCA
1 TAAA-CCA
*
208103 TAATCCA
1 TAAACCA
*
208110 TAATCCA
1 TAAACCA
*
208117 TAAACCT
1 TAAACCA
208124 TAAA
1 TAAA
208128 ATAGTAACTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 38 0.86
8 6 0.14
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:208432 original size:24 final size:24
Alignment explanation
Indices: 208405--208453 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
208395 TTAAAATAAC
*
208405 AATTAATTTTTATATAGACTTTTA
1 AATTAATTTTTATATAAACTTTTA
208429 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
208453 A
1 A
208454 TAAATATACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTATATAAACTTTTA
Found at i:209127 original size:41 final size:41
Alignment explanation
Indices: 209070--209279 Score: 309
Period size: 41 Copynumber: 5.1 Consensus size: 41
209060 AGTTATATGA
209070 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
* *
209111 CTTTTAGCGGCGTTTTACCAAAAGCGCCACTACTGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
** *
209152 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAAAGCTCTAT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
*
209193 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCAGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
*
209234 -TTTTAGCGGCGTTTTTGA-TAAAA-CGCCGCTATTGCTCTGT
1 CTTTTAGCGGCG-TTTT-ACCAAAAGCGCCGCTATTGCTCTGT
*
209274 GTTTTA
1 CTTTTA
209280 TAATTTTTGC
Statistics
Matches: 154, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
40 27 0.18
41 126 0.82
42 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (41 bp):
CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTCTGT
Found at i:209318 original size:12 final size:12
Alignment explanation
Indices: 209303--209328 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
209293 ATTTTTTGAT
209303 AAAACGCCGCTA
1 AAAACGCCGCTA
209315 AAAACGCCGCTA
1 AAAACGCCGCTA
209327 AA
1 AA
209329 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:210183 original size:18 final size:18
Alignment explanation
Indices: 210142--210184 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
210132 TTCTTATCCG
*
210142 AACTCTCCAACTCTCTCA
1 AACTCTCAAACTCTCTCA
*
210160 AGCTCTCAAACTCTC-CA
1 AACTCTCAAACTCTCTCA
210177 CAACTCTC
1 -AACTCTC
210185 TAAAAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.28, C:0.44, G:0.02, T:0.26
Consensus pattern (18 bp):
AACTCTCAAACTCTCTCA
Found at i:210305 original size:12 final size:11
Alignment explanation
Indices: 210284--210310 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
210274 TAATTCTTTC
210284 TTTTTCTTTTT
1 TTTTTCTTTTT
210295 TTTTTCTTTTT
1 TTTTTCTTTTT
210306 TTTTT
1 TTTTT
210311 GCAAAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:211686 original size:48 final size:47
Alignment explanation
Indices: 211615--211710 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 47
211605 GAAAATTGAC
*
211615 GAATTAAGGGCAAAATTGGAATATTGCAAAATTTACTTAATAAACTA
1 GAATTAAGGGAAAAATTGGAATATTGCAAAATTTACTTAATAAACTA
211662 NGAATTAAGGGAAAAATTGGAATATTGCAAAATTTACTTAATAAACTA
1 -GAATTAAGGGAAAAATTGGAATATTGCAAAATTTACTTAATAAACTA
211710 G
1 G
211711 GACTAAAGTG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (47 bp):
GAATTAAGGGAAAAATTGGAATATTGCAAAATTTACTTAATAAACTA
Found at i:213213 original size:7 final size:7
Alignment explanation
Indices: 213183--213221 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
213173 TTATCTGAGC
*
213183 AGTGATA
1 AGTGACA
213190 AGTGACA
1 AGTGACA
*
213197 AGCGACA
1 AGTGACA
213204 AGTGACA
1 AGTGACA
*
213211 AGTGATA
1 AGTGACA
213218 AGTG
1 AGTG
213222 GTAGCTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.18
Consensus pattern (7 bp):
AGTGACA
Found at i:213220 original size:14 final size:14
Alignment explanation
Indices: 213183--213221 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
213173 TTATCTGAGC
213183 AGTGATAAGTGACA
1 AGTGATAAGTGACA
* *
213197 AGCGACAAGTGACA
1 AGTGATAAGTGACA
213211 AGTGATAAGTG
1 AGTGATAAGTG
213222 GTAGCTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.18
Consensus pattern (14 bp):
AGTGATAAGTGACA
Found at i:213282 original size:51 final size:51
Alignment explanation
Indices: 213200--213310 Score: 177
Period size: 51 Copynumber: 2.2 Consensus size: 51
213190 AGTGACAAGC
* *
213200 GACAAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGATTAGT
1 GACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATTAGT
** *
213251 GACAAGTGGTAAGTGATAAGTAGTAGTTTTAGCTACACTTATCTGATTAGT
1 GACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATTAGT
213302 GACAAGTGA
1 GACAAGTGA
213311 TACATGTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATTAGT
Found at i:217144 original size:13 final size:13
Alignment explanation
Indices: 217126--217151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
217116 GCTCGGCAGG
217126 GACACGCCCGTGT
1 GACACGCCCGTGT
217139 GACACGCCCGTGT
1 GACACGCCCGTGT
217152 ACGATTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:228698 original size:21 final size:20
Alignment explanation
Indices: 228666--228714 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
228656 AGCCTGTAAT
228666 ATAAACAATAATAATAATAG
1 ATAAACAATAATAATAATAG
228686 ATAAACGAATAATAATAATAG
1 ATAAAC-AATAATAATAATAG
*
228707 GTAAACAA
1 ATAAACAA
228715 ATTCGAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.22
Consensus pattern (20 bp):
ATAAACAATAATAATAATAG
Found at i:235314 original size:32 final size:32
Alignment explanation
Indices: 235259--235328 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
235249 TAAAAAAAAA
* *
235259 AACAAATATCTCAGCACAATCAAATAACAAAT
1 AACAAATATCTCAACACAATCAAACAACAAAT
* *
235291 AACAAATAAT-TCAACACATTCAAACAATAAAT
1 AACAAAT-ATCTCAACACAATCAAACAACAAAT
235323 AACAAA
1 AACAAA
235329 AAAAAAACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.60, C:0.20, G:0.01, T:0.19
Consensus pattern (32 bp):
AACAAATATCTCAACACAATCAAACAACAAAT
Found at i:236994 original size:20 final size:20
Alignment explanation
Indices: 236969--237011 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
236959 ACTTTTTTCT
236969 CTTGCGTATTATTTATTATA
1 CTTGCGTATTATTTATTATA
236989 CTTGCGTATTATTTATTATA
1 CTTGCGTATTATTTATTATA
237009 CTT
1 CTT
237012 TCTCCCTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (20 bp):
CTTGCGTATTATTTATTATA
Found at i:242010 original size:20 final size:19
Alignment explanation
Indices: 241979--242016 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
241969 TGGTCTCATA
241979 TTATTATAATTATAATTAT
1 TTATTATAATTATAATTAT
241998 TTATTACTAATTATAATTA
1 TTATTA-TAATTATAATTA
242017 ATAAGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTATAATTATAATTAT
Found at i:242717 original size:18 final size:18
Alignment explanation
Indices: 242694--242728 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
242684 TATAAATTAT
242694 ATAAAATATTAA-TATGAA
1 ATAAAAT-TTAACTATGAA
242712 ATAAAATTTAACTATGA
1 ATAAAATTTAACTATGA
242729 TAGAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
ATAAAATTTAACTATGAA
Found at i:243032 original size:17 final size:18
Alignment explanation
Indices: 243010--243043 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
243000 TAAATAACAA
243010 AAAAATTTT-TATTTTTG
1 AAAAATTTTATATTTTTG
243027 AAAAATTTTATATTTTT
1 AAAAATTTTATATTTTT
243044 CATATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AAAAATTTTATATTTTTG
Found at i:257387 original size:206 final size:206
Alignment explanation
Indices: 257024--257774 Score: 1261
Period size: 206 Copynumber: 3.6 Consensus size: 206
257014 GCAGATCTGG
* *
257024 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTCTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCT
* *
257089 GATTTAGCTTTCATGTGCTTACGATGAAGCAAATCTAAGACGATTTGGCATCTCTGTATTGTCAG
65 GATTTAGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * *
257154 AGAGTAGATCGAAGTTTGGCTTCTCCATATTCGATGGAGGGCAGACACGTAGCAGATCTAACCTT
130 AGAGCAGATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
257219 CAGATGATTAGA
195 CAGATGATTAGA
257231 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
* * *
257296 ATTTGGCTTTCACGTGCTTACGATGAAACAAATCTAAGATAATTTGGCATCTCTGTATTGTCAGA
66 ATTTAGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
257361 GAGCAGATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
131 GAGCAGATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
257426 AGATGATTAGA
196 AGATGATTAGA
257437 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAA-ATCATAGCT
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGA-CATAGCT
* *
257501 GATTTAGCTTTTACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTAGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
257566 AGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
130 AGAGCAGATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
*
257631 TAGATGATTAGA
195 CAGATGATTAGA
* * *
257643 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGTTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
* * ** *
257708 ATTTGGTTTTTGCGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
66 ATTTAGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
257773 GA
131 GA
257775 ACAAATTGAA
Statistics
Matches: 517, Mismatches: 25, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
205 1 0.00
206 508 0.98
207 8 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (206 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTG
ATTTAGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAGCAGATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTC
AGATGATTAGA
Found at i:259338 original size:28 final size:28
Alignment explanation
Indices: 259307--259362 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
259297 TTTCTAATTA
* * *
259307 AATTTAATTTTAATCCTTTTTATATTTT
1 AATTTAATTTAAATACTTTATATATTTT
**
259335 AATTTGCTTTAAATACTTTATATATTTT
1 AATTTAATTTAAATACTTTATATATTTT
259363 TAAATATTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (28 bp):
AATTTAATTTAAATACTTTATATATTTT
Found at i:259406 original size:17 final size:17
Alignment explanation
Indices: 259386--259419 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
259376 TATATTACTA
259386 TTATTATCCAT-TATTTT
1 TTATTAT-CATATATTTT
259403 TTATTATCATATATTTT
1 TTATTATCATATATTTT
259420 ATCTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATCATATATTTT
Found at i:259453 original size:16 final size:16
Alignment explanation
Indices: 259397--259459 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
259387 TATTATCCAT
* *
259397 TATTTTTTATTATCATA
1 TATTTTATATTAT-AAA
*
259414 TATTTTAT-CTATAAA
1 TATTTTATATTATAAA
*
259429 TTATATTATATTATAAA
1 -TATTTTATATTATAAA
*
259446 TATTTTATTTTATA
1 TATTTTATATTATA
259460 TATTTCTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.05
16 22 0.59
17 13 0.35
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTATATTATAAA
Found at i:259469 original size:12 final size:11
Alignment explanation
Indices: 259453--259482 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
259443 AAATATTTTA
259453 TTTTATATATT
1 TTTTATATATT
259464 TCTTTATATATT
1 T-TTTATATATT
259476 TTTTATA
1 TTTTATA
259483 AAATTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATATATT
Found at i:259500 original size:20 final size:21
Alignment explanation
Indices: 259472--259511 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
259462 TTTCTTTATA
*
259472 TATTTTTTA-TAAAATTGTAT
1 TATTATTTACTAAAATTGTAT
*
259492 TATTATTTACTAAATTTGTA
1 TATTATTTACTAAAATTGTA
259512 AATGGCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTATTTACTAAAATTGTAT
Found at i:259853 original size:18 final size:18
Alignment explanation
Indices: 259827--259867 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
259817 TACCATATTA
*
259827 TATTTCATACTATATTTT
1 TATTACATACTATATTTT
259845 TATTACATACTATATTTT
1 TATTACATACTATATTTT
259863 TATTA
1 TATTA
259868 TTCAATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTACATACTATATTTT
Found at i:259940 original size:22 final size:23
Alignment explanation
Indices: 259902--259952 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
259892 CTTTCTCATA
* *
259902 TATTTT-TTTATTATATATTATT
1 TATTTTATTTATTATATAGTACT
*
259924 TATTTTATTT-TTTTATAGTACT
1 TATTTTATTTATTATATAGTACT
259946 TATTTTA
1 TATTTTA
259953 CCATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTTATTTATTATATAGTACT
Found at i:260003 original size:21 final size:22
Alignment explanation
Indices: 259977--260037 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
259967 GCAAAATACT
259977 TATTATATTT-TTATTATTTTA
1 TATTATATTTCTTATTATTTTA
259998 TATTATATTTCCTTA-TATTTTA
1 TATTATATTT-CTTATTATTTTA
* *
260020 T-TCATATTATATTATTAT
1 TATTATATT-TCTTATTAT
260038 ACATAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 19 0.56
22 12 0.35
23 3 0.09
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATATTTCTTATTATTTTA
Found at i:265676 original size:17 final size:18
Alignment explanation
Indices: 265651--265684 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
265641 TATGAATTGA
*
265651 TTTATTGTATGATTAATG
1 TTTATTGTATGAATAATG
265669 TTTA-TGTATGAATAAT
1 TTTATTGTATGAATAAT
265685 TTATGAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
TTTATTGTATGAATAATG
Found at i:272057 original size:3 final size:3
Alignment explanation
Indices: 272051--272214 Score: 328
Period size: 3 Copynumber: 54.7 Consensus size: 3
272041 ATAGGAGGAA
272051 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
272099 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
272147 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
272195 AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
272215 TATAAAATAA
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 161 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:272259 original size:22 final size:22
Alignment explanation
Indices: 272218--272260 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
272208 AGAAGAATAT
*
272218 AAAATAAAGAAAATGAGAAAGA
1 AAAATAAAGAAAAGGAGAAAGA
*
272240 AAAATAAAGAAAAGGGGAAAG
1 AAAATAAAGAAAAGGAGAAAG
272261 GAGAAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (22 bp):
AAAATAAAGAAAAGGAGAAAGA
Done.