Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold324
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: 2336777
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 1 of 16
Found at i:450 original size:3 final size:3
Alignment explanation
Indices: 444--483 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
434 CACCACAAGG
444 CAA CAA C-A CAA CAA CAA CAA CAA CAA C-A CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
484 AACTTGGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:466 original size:17 final size:17
Alignment explanation
Indices: 444--483 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
434 CACCACAAGG
444 CAACAAC-ACAACAACAA
1 CAACAACAAC-ACAACAA
461 CAACAACAACACAACAA
1 CAACAACAACACAACAA
478 CAACAA
1 CAACAA
484 AACTTGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (17 bp):
CAACAACAACACAACAA
Found at i:469 original size:20 final size:20
Alignment explanation
Indices: 444--483 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
434 CACCACAAGG
444 CAACAACACAACAACAACAA
1 CAACAACACAACAACAACAA
464 CAACAACACAACAACAACAA
1 CAACAACACAACAACAACAA
484 AACTTGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (20 bp):
CAACAACACAACAACAACAA
Found at i:974 original size:14 final size:15
Alignment explanation
Indices: 957--985 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
947 TATTTTTATT
957 TTAATAAAAT-TAAA
1 TTAATAAAATATAAA
971 TTAATAAAATATAAA
1 TTAATAAAATATAAA
986 CTTTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATAAAATATAAA
Found at i:1787 original size:23 final size:25
Alignment explanation
Indices: 1757--1802 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1747 TAAATAATTA
1757 AAAAAATA-TA-AAATATATTATCT
1 AAAAAATAGTATAAATATATTATCT
*
1780 AAAAAATAGTATAAATATTTTAT
1 AAAAAATAGTATAAATATATTAT
1803 ATATAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAAAATAGTATAAATATATTATCT
Found at i:1841 original size:13 final size:15
Alignment explanation
Indices: 1815--1846 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1805 ATAAATATTT
1815 TAAATTTATATAATA
1 TAAATTTATATAATA
1830 TAAA-TTAT-TAATA
1 TAAATTTATATAATA
1843 TAAA
1 TAAA
1847 AATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTATATAATA
Found at i:6241 original size:30 final size:30
Alignment explanation
Indices: 6205--6275 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
6195 GAAAGGCAAT
6205 TCCAATGTGCTGGAGTAGCTGCACTAAGAG
1 TCCAATGTGCTGGAGTAGCTGCACTAAGAG
6235 TCCAATGTGCTGGAGTAGCTGCACTAAGAG
1 TCCAATGTGCTGGAGTAGCTGCACTAAGAG
6265 TCCAATGTGCT
1 TCCAATGTGCT
6276 ATGTCCTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (30 bp):
TCCAATGTGCTGGAGTAGCTGCACTAAGAG
Found at i:7914 original size:45 final size:45
Alignment explanation
Indices: 7862--7952 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
7852 CAAAACTCCC
* * *
7862 CAAGCTTTTGATCTTCAAAAGCCTTCAGTTCAGTGACATTTTCTG
1 CAAGCTTTCGATCTTCAAAAACCTTCAGCTCAGTGACATTTTCTG
7907 CAAGCTTTCGATCTTCAAAAACCTTCAGCTCAGTGACATTTTCTG
1 CAAGCTTTCGATCTTCAAAAACCTTCAGCTCAGTGACATTTTCTG
7952 C
1 C
7953 TTGCTTGTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (45 bp):
CAAGCTTTCGATCTTCAAAAACCTTCAGCTCAGTGACATTTTCTG
Found at i:8934 original size:61 final size:61
Alignment explanation
Indices: 8839--8960 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
8829 TTCAAATTAC
8839 TGTAGTTAATTTCATACATAATTTAACCTAGCAGCATCCATACAGAAACAAAATATGATAT
1 TGTAGTTAATTTCATACATAATTTAACCTAGCAGCATCCATACAGAAACAAAATATGATAT
8900 TGTAGTTAATTTCATACATAATTTAACCTAGCAGCATCCATACAGAAACAAAATATGATAT
1 TGTAGTTAATTTCATACATAATTTAACCTAGCAGCATCCATACAGAAACAAAATATGATAT
8961 ATACATGATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (61 bp):
TGTAGTTAATTTCATACATAATTTAACCTAGCAGCATCCATACAGAAACAAAATATGATAT
Found at i:14082 original size:50 final size:50
Alignment explanation
Indices: 14023--14379 Score: 560
Period size: 50 Copynumber: 7.2 Consensus size: 50
14013 AGTTGCTTAG
* * * * *
14023 AGTCAACAATTATGG-CTACCTTTCTCTATTATCAAATGTTGGTGAAGAAT
1 AGTCAACAATTACGGTC-ACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
14073 AGTCAACAATTACGGTCACCTCTCTCGATTGTC-AAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
14122 AGTCAACAATTACGGCCATCTCTCTCGATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
14172 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
14222 CGTCAACAATTACGGTCACCTCTCTCGATTGTC-AAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
14271 AGTCAACAATTATGGACATCTCTCTCGATTGTCAAAGGTTGGTGAA-AAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
14320 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
14370 AGTCAACAAT
1 AGTCAACAAT
14380 GGCAACACAT
Statistics
Matches: 283, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
49 136 0.48
50 146 0.52
51 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:14194 original size:99 final size:100
Alignment explanation
Indices: 14023--14379 Score: 558
Period size: 99 Copynumber: 3.6 Consensus size: 100
14013 AGTTGCTTAG
* * * * * *
14023 AGTCAACAATTATGGCTACCTTTCTCTATTATCAAATGTTGGTGAAGAATAGTCAACAATTACGG
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGG
14088 TCACCTCTCTCGATTGTC-AAGGTTGGTGAAGAAT
66 TCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
14122 AGTCAACAATTACGGCCATCTCTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAACAATTACGG
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGG
14187 TCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
66 TCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
14222 CGTCAACAATTACGGTCACCTCTCTCGATTGTC-AAGGTTGGTGAAGAATAGTCAACAATTATGG
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGG
* *
14286 ACATCTCTCTCGATTGTCAAAGGTTGGTGAA-AAT
66 TCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
14320 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTCAACAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAACAAT
14380 GGCAACACAT
Statistics
Matches: 239, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
98 35 0.15
99 158 0.66
100 46 0.19
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (100 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAACAATTACGG
TCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:14293 original size:149 final size:148
Alignment explanation
Indices: 14023--14379 Score: 608
Period size: 149 Copynumber: 2.4 Consensus size: 148
14013 AGTTGCTTAG
* * * * *
14023 AGTCAACAATTATGG-CTACCTTTCTCTATTATCAAATGTTGGTGAAGAATAGTCAACAATTACG
1 AGTCAACAATTACGGTC-ACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTCAACAATTACG
*
14087 GTCACCTCTCTCGATTGTCAAGGTTGGTGAAGAATAGTCAACAATTACGGCCATCTCTCTCGATT
65 GTCACCTCTCTCGATTGTCAAGGTTGGTGAAGAATAGTCAACAATTACGGACATCTCTCTCGATT
14152 GTCAAAGGTTGGTGAAAAAT
130 GTCAAAGGTTGGTG-AAAAT
* *
14172 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGG
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTCAACAATTACGG
*
14237 TCACCTCTCTCGATTGTCAAGGTTGGTGAAGAATAGTCAACAATTATGGACATCTCTCTCGATTG
66 TCACCTCTCTCGATTGTCAAGGTTGGTGAAGAATAGTCAACAATTACGGACATCTCTCTCGATTG
14302 TCAAAGGTTGGTGAAAAT
131 TCAAAGGTTGGTGAAAAT
14320 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTCAACAAT
1 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTCAACAAT
14380 GGCAACACAT
Statistics
Matches: 197, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
148 63 0.32
149 133 0.68
150 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (148 bp):
AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTCAACAATTACGG
TCACCTCTCTCGATTGTCAAGGTTGGTGAAGAATAGTCAACAATTACGGACATCTCTCTCGATTG
TCAAAGGTTGGTGAAAAT
Found at i:18781 original size:46 final size:50
Alignment explanation
Indices: 18731--18840 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 50
18721 AGTTACTTAG
* * *
18731 AGTCAACAATTACGGTTA-CT-TCTCTATTATCAAA-GTTGGTGAA-AAT
1 AGTCAACAATTACGGTCACCTCTCTCAATTATCAAAGGTCGGTGAAGAAT
* * *
18777 AGTCAATAATTATGGTCACCTCTCTCAATTGTCAAAGGTCGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCAATTATCAAAGGTCGGTGAAGAAT
*
18827 CGTCAACAATTACG
1 AGTCAACAATTACG
18841 ACTACTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.29
47 2 0.04
48 12 0.24
49 8 0.16
50 14 0.27
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCAATTATCAAAGGTCGGTGAAGAAT
Found at i:26395 original size:3 final size:3
Alignment explanation
Indices: 26387--26412 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26377 CTAATGCAAG
26387 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
26413 GAATTTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28490 original size:2 final size:2
Alignment explanation
Indices: 28483--28515 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28473 TATAAGCACT
28483 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28516 TATTGCTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29886 original size:2 final size:2
Alignment explanation
Indices: 29879--29919 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29869 ATGCCCACAG
29879 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29920 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:29924 original size:2 final size:2
Alignment explanation
Indices: 29919--29960 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
29909 TCTCTCTCTC
29919 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
29961 ACTGCACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36796 original size:18 final size:18
Alignment explanation
Indices: 36775--36810 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36765 ATCTGAGGCT
36775 GAGCCTGAGCCAGAGTCA
1 GAGCCTGAGCCAGAGTCA
* *
36793 GAGCTTGAGCCTGAGTCA
1 GAGCCTGAGCCAGAGTCA
36811 ATCTATCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (18 bp):
GAGCCTGAGCCAGAGTCA
Found at i:38856 original size:2 final size:2
Alignment explanation
Indices: 38843--38904 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
38833 GACTAATTCT
*
38843 TA TA TT TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
38885 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
38905 CACACACACA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40538 original size:21 final size:21
Alignment explanation
Indices: 40513--40563 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40503 TATTTTATTT
*
40513 TTTAAATTTTTTTATTGTATA
1 TTTAAATTTTTATATTGTATA
* * *
40534 TTTAAAATATTATATTTTATA
1 TTTAAATTTTTATATTGTATA
*
40555 TTTATATTT
1 TTTAAATTT
40564 AAATAAATAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTAAATTTTTATATTGTATA
Found at i:40582 original size:13 final size:13
Alignment explanation
Indices: 40566--40598 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40556 TTATATTTAA
*
40566 ATAAATATTAAAT
1 ATAAATATCAAAT
40579 ATAAATATCAAAT
1 ATAAATATCAAAT
40592 ATAAATA
1 ATAAATA
40599 ATATCTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAATATCAAAT
Found at i:42415 original size:36 final size:37
Alignment explanation
Indices: 42365--42446 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
42355 TTTTAAATAT
* * **
42365 AATAATATAAAAATA-TTATATATTTTAAAATTTTTA
1 AATAAAATAAAAATATTTAAATAAATTAAAATTTTTA
*
42401 AATAAAATATAAATATTTAAATAAATTAAAATTTTT-
1 AATAAAATAAAAATATTTAAATAAATTAAAATTTTTA
42437 AA-AAAATAAA
1 AATAAAATAAA
42447 TCATTAATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 7 0.18
36 15 0.38
37 17 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (37 bp):
AATAAAATAAAAATATTTAAATAAATTAAAATTTTTA
Found at i:42419 original size:19 final size:18
Alignment explanation
Indices: 42390--42439 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
42380 TTATATATTT
42390 TAAAATTTTTAAATAAAA
1 TAAAATTTTTAAATAAAA
* *
42408 TATAAATATTTAAATAAAT
1 TA-AAATTTTTAAATAAAA
42427 TAAAATTTTTAAA
1 TAAAATTTTTAAA
42440 AAATAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTTTAAATAAAA
Found at i:44728 original size:2 final size:2
Alignment explanation
Indices: 44716--44751 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
44706 ATGGGCTTGC
*
44716 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44752 GTAATAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45229 original size:26 final size:27
Alignment explanation
Indices: 45198--45251 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
45188 TTAAAATATT
*
45198 ATTTATAATTAAAT-TTAAATAAAAAA
1 ATTTATAATTAAATAATAAATAAAAAA
* *
45224 ATTTATTATTAAATAATAATTAAAAAA
1 ATTTATAATTAAATAATAAATAAAAAA
45251 A
1 A
45252 ATTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTTATAATTAAATAATAAATAAAAAA
Found at i:47462 original size:2 final size:2
Alignment explanation
Indices: 47457--47494 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
47447 TGTGTGTGTG
47457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47495 TCTAGTTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:48355 original size:2 final size:2
Alignment explanation
Indices: 48343--48381 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
48333 CGAGATGATC
*
48343 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48382 GTGAATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:50116 original size:29 final size:29
Alignment explanation
Indices: 50084--50140 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
50074 AAATTGGGTG
*
50084 TTTAGTTTGAATTCAGACCACATACTTCA
1 TTTAGTTTGAATTCAGACCACAAACTTCA
50113 TTTAGTTTGAATTCAGACCACAAACTTC
1 TTTAGTTTGAATTCAGACCACAAACTTC
50141 TTTTTATCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTAGTTTGAATTCAGACCACAAACTTCA
Found at i:50849 original size:2 final size:2
Alignment explanation
Indices: 50842--50879 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
50832 TGATTAGATC
*
50842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50880 GTAAGGCAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51904 original size:20 final size:21
Alignment explanation
Indices: 51881--51926 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
51871 AAATAAAGCT
* *
51881 TTTTTATTATA-AATTTTATA
1 TTTTTATAATATAATTATATA
51901 TTTTTATAATATAATTATATA
1 TTTTTATAATATAATTATATA
51922 TTTTT
1 TTTTT
51927 TACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATAATATAATTATATA
Found at i:51927 original size:22 final size:21
Alignment explanation
Indices: 51880--51928 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
51870 CAAATAAAGC
* *
51880 TTTTTTATTATAAATTTTATA
1 TTTTTTATAATAAATTATATA
51901 -TTTTTATAATATAATTATATA
1 TTTTTTATAATA-AATTATATA
51922 TTTTTTA
1 TTTTTTA
51929 CAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 8 0.33
22 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTATAATAAATTATATA
Found at i:52095 original size:18 final size:18
Alignment explanation
Indices: 52055--52096 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
52045 TATTAAAAAT
* *
52055 TAAATTAAAAATATACTA
1 TAAATAAAAAATATAATA
*
52073 AAAATAAAAAATATAATA
1 TAAATAAAAAATATAATA
52091 TAAATA
1 TAAATA
52097 TATCTAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATAAAAAATATAATA
Found at i:53159 original size:107 final size:107
Alignment explanation
Indices: 52973--53185 Score: 318
Period size: 107 Copynumber: 2.0 Consensus size: 107
52963 TATTTTAAGG
* * * * *
52973 CGTAGGTTCGTCACGTTGTCTAGATCACAGGGGTTGGCTGATCATTAGCGAGCGCGCGGTGGTCC
1 CGTAGGTTCGTCACATCGTCTAAAGCACAGGGGTTGGCAGATCATTAGCGAGCGCGCGGTGGTCC
* * *
53038 TCACTCTACTCACTGCTGCTATCTCACTGGTTATTTAGTGCA
66 TCACTCTACCCACTGCTACTATCTCACTAGTTATTTAGTGCA
* *
53080 CGTAGGTTCGTCACATCGTCTAAAGCTCAGGGGTTGGCAGATCATTAGCTAGCGCGCGGTGGTCC
1 CGTAGGTTCGTCACATCGTCTAAAGCACAGGGGTTGGCAGATCATTAGCGAGCGCGCGGTGGTCC
* *
53145 TCACTCTACCCACTGCTACTATGTCACTATTTATTTAGTGC
66 TCACTCTACCCACTGCTACTATCTCACTAGTTATTTAGTGC
53186 CCTGCTATCC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 94 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (107 bp):
CGTAGGTTCGTCACATCGTCTAAAGCACAGGGGTTGGCAGATCATTAGCGAGCGCGCGGTGGTCC
TCACTCTACCCACTGCTACTATCTCACTAGTTATTTAGTGCA
Found at i:53616 original size:2 final size:2
Alignment explanation
Indices: 53609--53646 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
53599 CCTTTCAGTA
53609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53647 ATTGTTATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54118 original size:3 final size:3
Alignment explanation
Indices: 54110--54144 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
54100 ATTAAAAAGC
54110 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54145 CTTTAAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55414 original size:3 final size:3
Alignment explanation
Indices: 55406--55442 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
55396 CAGTTACAAG
55406 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55443 GATATGACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:58470 original size:21 final size:21
Alignment explanation
Indices: 58422--58470 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
58412 AAATATTTTT
*
58422 ATAATTATATATAAATAAAAA
1 ATAATTTTATATAAATAAAAA
* * *
58443 ATAATTTTTTATAATTAAATA
1 ATAATTTTATATAAATAAAAA
58464 ATAATTT
1 ATAATTT
58471 AAGTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATTTTATATAAATAAAAA
Found at i:58657 original size:19 final size:17
Alignment explanation
Indices: 58629--58672 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
58619 AATTATAAAC
*
58629 TAAAATATTACTTTTTCAA
1 TAAAAAATTA-TTTTT-AA
*
58648 TAAAAAATTATTTTTTA
1 TAAAAAATTATTTTTAA
58665 TAAAAAAT
1 TAAAAAAT
58673 AGCTTGAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 5 0.22
19 9 0.39
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAAATTATTTTTAA
Found at i:60186 original size:20 final size:22
Alignment explanation
Indices: 60163--60204 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
60153 ATGTAATTAT
60163 ATTTTAA-AAA-TAATATTTAA
1 ATTTTAATAAATTAATATTTAA
60183 ATTTTAATAAATTTAATATTTA
1 ATTTTAATAAA-TTAATATTTA
60205 TATTCTCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
23 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTAATAAATTAATATTTAA
Found at i:60191 original size:17 final size:17
Alignment explanation
Indices: 60171--60203 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
60161 ATATTTTAAA
60171 AATAATATTTAA-ATTTT
1 AATAA-ATTTAATATTTT
60188 AATAAATTTAATATTT
1 AATAAATTTAATATTT
60204 ATATTCTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATAAATTTAATATTTT
Found at i:61740 original size:20 final size:22
Alignment explanation
Indices: 61694--61740 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
61684 AAATAATGAG
61694 TAAATATAATAATTTAATAAAT
1 TAAATATAATAATTTAATAAAT
* * *
61716 CAAATA-AAT-ATTTAATTATT
1 TAAATATAATAATTTAATAAAT
61736 TAAAT
1 TAAAT
61741 GTTATTATCT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 13 0.62
21 3 0.14
22 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATAATAATTTAATAAAT
Found at i:62094 original size:2 final size:2
Alignment explanation
Indices: 62089--62148 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
62079 ACACATAAGA
62089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62131 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
62149 GCATTGCATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62933 original size:32 final size:32
Alignment explanation
Indices: 62892--62962 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
62882 CGTTTTTGTG
62892 CATGTGCGAGTAGAAATACTCTAAGATAATTT
1 CATGTGCGAGTAGAAATACTCTAAGATAATTT
62924 CATGTGCGAGTAGAAATACTCTAAGATAATTT
1 CATGTGCGAGTAGAAATACTCTAAGATAATTT
62956 CATGTGC
1 CATGTGC
62963 TTCCTTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (32 bp):
CATGTGCGAGTAGAAATACTCTAAGATAATTT
Found at i:63738 original size:37 final size:37
Alignment explanation
Indices: 63688--63763 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
63678 AGGTATTGGT
*
63688 ATGATTTTTTTTGATAATTAGGACTCAAAAAATTGAA
1 ATGATTTTCTTTGATAATTAGGACTCAAAAAATTGAA
* **
63725 ATGATTTTCTTTGATAATTAGTACTTGAAAAATTGAA
1 ATGATTTTCTTTGATAATTAGGACTCAAAAAATTGAA
63762 AT
1 AT
63764 ATTATATGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (37 bp):
ATGATTTTCTTTGATAATTAGGACTCAAAAAATTGAA
Found at i:64299 original size:11 final size:12
Alignment explanation
Indices: 64277--64305 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
64267 GCGAAATTAG
64277 TAAAATAATATT
1 TAAAATAATATT
64289 TAAAA-AATATT
1 TAAAATAATATT
64300 TAAAAT
1 TAAAAT
64306 TATAATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATAATATT
Found at i:65190 original size:14 final size:15
Alignment explanation
Indices: 65154--65204 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
65144 AAAATAACAC
* *
65154 ATTAAACAAAAAATT
1 ATTAAATAATAAATT
65169 A-T-AATAAT-AATT
1 ATTAAATAATAAATT
65181 ATTAAATAATAAATT
1 ATTAAATAATAAATT
65196 -TTAAATAAT
1 ATTAAATAAT
65205 TTTATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 16 0.52
15 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAATAATAAATT
Found at i:65528 original size:17 final size:18
Alignment explanation
Indices: 65492--65528 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
65482 TTTATAAAAA
65492 TTTAATTAAATATAATTT
1 TTTAATTAAATATAATTT
65510 TTTAATTCAAATA-AATTT
1 TTTAATT-AAATATAATTT
65528 T
1 T
65529 AAAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATTAAATATAATTT
Found at i:65580 original size:12 final size:13
Alignment explanation
Indices: 65544--65582 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
65534 TTTATGATAT
65544 ATAATCATTTAATA
1 ATAATCA-TTAATA
65558 ATAATCA-TAATA
1 ATAATCATTAATA
65570 ATAAT-ATTAATA
1 ATAATCATTAATA
65582 A
1 A
65583 CAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 16 0.67
14 7 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATCATTAATA
Found at i:65889 original size:17 final size:18
Alignment explanation
Indices: 65850--65901 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
65840 ATTCAGATAT
65850 ATAAATA-ATTAAAATTA
1 ATAAATATATTAAAATTA
65867 ATAAATATATTAAAATGT-
1 ATAAATATATTAAAAT-TA
65885 A-AAATATATTCAAAATT
1 ATAAATATATT-AAAATT
65902 TATTAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 17 0.53
18 14 0.44
19 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAAATATATTAAAATTA
Found at i:66090 original size:25 final size:25
Alignment explanation
Indices: 66062--66112 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
66052 TTGGTGAAAA
66062 AAATTATAATAAAATTAAAATTCTT
1 AAATTATAATAAAATTAAAATTCTT
66087 AAATTATAATAAAATTAAAATTCTT
1 AAATTATAATAAAATTAAAATTCTT
66112 A
1 A
66113 CGTATAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATTATAATAAAATTAAAATTCTT
Found at i:66125 original size:24 final size:25
Alignment explanation
Indices: 66066--66129 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
66056 TGAAAAAAAT
*
66066 TATAATAAAATTAAAATTCTTAAAT
1 TATAATAAAATTAAAATTCTTAAAG
*
66091 TATAATAAAATTAAAATTCTT-ACG
1 TATAATAAAATTAAAATTCTTAAAG
66115 TATAGATAAATATTA
1 TATA-ATAAA-ATTA
66130 CTAATTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 5 0.14
25 26 0.74
26 4 0.11
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (25 bp):
TATAATAAAATTAAAATTCTTAAAG
Found at i:66632 original size:7 final size:7
Alignment explanation
Indices: 66617--66648 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
66607 TTGCAACCAA
*
66617 TAATTAT
1 TAATAAT
66624 TAATAAT
1 TAATAAT
66631 TAATAAT
1 TAATAAT
66638 TAATAAT
1 TAATAAT
66645 TAAT
1 TAAT
66649 TTCATTGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAATAAT
Found at i:67336 original size:19 final size:20
Alignment explanation
Indices: 67296--67339 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
67286 TATTGAATTC
67296 AATAAAAATATTATATTAAA
1 AATAAAAATATTATATTAAA
* *
67316 AATAAATATATT-TATTTAA
1 AATAAAAATATTATATTAAA
67335 AATAA
1 AATAA
67340 TAATTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAAAAATATTATATTAAA
Found at i:68599 original size:22 final size:22
Alignment explanation
Indices: 68558--68600 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
68548 TGAGATCATT
*
68558 ATAAAATAAACAAATTTTAAAG
1 ATAAAATAAACAAATATTAAAG
68580 ATAAAATAAA-AAATAATTAAA
1 ATAAAATAAACAAAT-ATTAAA
68601 TTATTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAAAATAAACAAATATTAAAG
Found at i:70345 original size:19 final size:20
Alignment explanation
Indices: 70313--70356 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
70303 TTAAAAATGT
* *
70313 TATTTAATTTTATTA-ATCA
1 TATTTAAATATATTATATCA
*
70332 TATTTAAATATATTATATTA
1 TATTTAAATATATTATATCA
70352 TATTT
1 TATTT
70357 TTATCGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTAAATATATTATATCA
Found at i:70890 original size:3 final size:3
Alignment explanation
Indices: 70882--70910 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
70872 TGGAGGGCTT
70882 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
70911 GAAGAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:73408 original size:3 final size:3
Alignment explanation
Indices: 73400--73436 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
73390 AGCTAAACTT
73400 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
73437 AATATTCCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:74334 original size:4 final size:4
Alignment explanation
Indices: 74309--74350 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
74299 ATTTGGGGAA
* * *
74309 ATAT ATAC ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
74351 CTGACTTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:74342 original size:10 final size:10
Alignment explanation
Indices: 74309--74350 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
74299 ATTTGGGGAA
74309 ATATATACAT
1 ATATATACAT
*
74319 ATACATACAT
1 ATATATACAT
*
74329 ATATATATAT
1 ATATATACAT
*
74339 ATATATATAT
1 ATATATACAT
74349 AT
1 AT
74351 CTGACTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATACAT
Found at i:74350 original size:6 final size:6
Alignment explanation
Indices: 74309--74350 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
74299 ATTTGGGGAA
* * *
74309 ATATAT ACATAT ACATAC ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
74351 CTGACTTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:75507 original size:19 final size:19
Alignment explanation
Indices: 75483--75523 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
75473 ATGGCAATTC
*
75483 GATTGATGTGACAATATCA
1 GATTGATGTAACAATATCA
75502 GATTGATGTAACAATATCA
1 GATTGATGTAACAATATCA
75521 GAT
1 GAT
75524 ACACAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (19 bp):
GATTGATGTAACAATATCA
Found at i:75863 original size:40 final size:40
Alignment explanation
Indices: 75808--75888 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
75798 CTGCATTTAT
75808 TTCTTATAGAAGGTTCATATAGTTACTTCTGACCAAATGG
1 TTCTTATAGAAGGTTCATATAGTTACTTCTGACCAAATGG
75848 TTCTTATAGAAGGTTCATATAGTTACTTCTGACCAAATGG
1 TTCTTATAGAAGGTTCATATAGTTACTTCTGACCAAATGG
75888 T
1 T
75889 CATGTCACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (40 bp):
TTCTTATAGAAGGTTCATATAGTTACTTCTGACCAAATGG
Found at i:79887 original size:1 final size:1
Alignment explanation
Indices: 79881--79910 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
79871 AGAACACATT
79881 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
79911 AAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:81728 original size:16 final size:18
Alignment explanation
Indices: 81689--81732 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
81679 ATTTGATAGT
81689 TTTAAATATACTAATAAA
1 TTTAAATATACTAATAAA
* *
81707 TATAAAT-TA-TAATATA
1 TTTAAATATACTAATAAA
81723 TTTAAATATA
1 TTTAAATATA
81733 TTTAACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 12 0.55
17 4 0.18
18 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAATATACTAATAAA
Found at i:81793 original size:49 final size:50
Alignment explanation
Indices: 81723--81817 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 50
81713 TTATAATATA
81723 TTTAAATATATTTAACATAATTAATATAATAATTATATTTATATTTAAAAT
1 TTTAAATATATTTAACATAATTAATATAATAATTATATTTAT-TTTAAAAT
* * * **
81774 TTTAAA-ATATTTTA-ATAATTTATATTATGTTTATATTTATTTTA
1 TTTAAATATATTTAACATAATTAATATAATAATTATATTTATTTTA
81818 CTAAAAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.10
49 22 0.56
50 7 0.18
51 6 0.15
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (50 bp):
TTTAAATATATTTAACATAATTAATATAATAATTATATTTATTTTAAAAT
Found at i:82197 original size:1 final size:1
Alignment explanation
Indices: 82191--82216 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
82181 TCTACCGTTG
82191 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
82217 TCTCCTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:88684 original size:23 final size:25
Alignment explanation
Indices: 88636--88693 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
88626 AAATTAATTT
88636 TAATTTTAATTTTATTAAATTATAA
1 TAATTTTAATTTTATTAAATTATAA
* *
88661 TAATTTTTA-TTT-TTAAATTGTAA
1 TAATTTTAATTTTATTAAATTATAA
*
88684 TAATGTTAAT
1 TAATTTTAAT
88694 ATTAACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 17 0.61
24 3 0.11
25 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (25 bp):
TAATTTTAATTTTATTAAATTATAA
Found at i:89433 original size:11 final size:10
Alignment explanation
Indices: 89413--89442 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
89403 AAAAAACATA
89413 AAATATATAT
1 AAATATATAT
89423 AAATATGATAT
1 AAATAT-ATAT
89434 AAATATATA
1 AAATATATA
89443 GCATTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
AAATATATAT
Found at i:89546 original size:15 final size:15
Alignment explanation
Indices: 89524--89559 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
89514 AAAAATACAA
89524 TTTTTTTTTCTT-TT
1 TTTTTTTTTCTTCTT
89538 TTCTTTTTTTCTTCTT
1 TT-TTTTTTTCTTCTT
89554 TTTTTT
1 TTTTTT
89560 CCCAACATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 14 0.70
16 4 0.20
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTCTTCTT
Found at i:90322 original size:14 final size:14
Alignment explanation
Indices: 90303--90330 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
90293 TAATTATAAA
90303 ATATAAAAATATTT
1 ATATAAAAATATTT
90317 ATATAAAAATATTT
1 ATATAAAAATATTT
90331 TTTTATTTTT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAAAAATATTT
Found at i:91083 original size:3 final size:3
Alignment explanation
Indices: 91075--91099 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
91065 CGGTGAAGGT
91075 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
91100 AAGGGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:96986 original size:19 final size:17
Alignment explanation
Indices: 96942--96991 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
96932 TATTATTTAC
96942 TAATTATATTTTT-TAA
1 TAATTATATTTTTATAA
96958 -AATTTATATTTTTATATA
1 TAA-TTATATTTTTATA-A
*
96976 TAATATATATTGTTAT
1 TAAT-TATATTTTTAT
96992 GCTCATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
17 2 0.07
18 2 0.07
19 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTATATTTTTATAA
Found at i:97589 original size:16 final size:16
Alignment explanation
Indices: 97547--97595 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
97537 ATAAAAATCG
97547 ATTAAAATT-ATTTTA
1 ATTAAAATTAATTTTA
97562 ATT-AAA--AA-TTTA
1 ATTAAAATTAATTTTA
97574 ATTAAAATTAATTTTA
1 ATTAAAATTAATTTTA
*
97590 TTTAAA
1 ATTAAA
97596 TTTTAATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 3 0.11
15 5 0.18
16 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAAATTAATTTTA
Found at i:97776 original size:27 final size:27
Alignment explanation
Indices: 97746--97829 Score: 71
Period size: 31 Copynumber: 3.0 Consensus size: 27
97736 TAATATCGAT
*
97746 TTAATTATTTTAATTTTTAAATTAATA
1 TTAATTATTTTAATTTTTAAATTAAAA
*
97773 TTAATTAATTCGATCAA-TTTTAATATTAAAA
1 TTAATT-ATT---TTAATTTTTAA-ATTAAAA
** *
97804 TTAATTAAATTAATTTTTAATTTAAA
1 TTAATTATTTTAATTTTTAAATTAAA
97830 TAAATAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 14 0.31
28 9 0.20
30 7 0.16
31 15 0.33
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (27 bp):
TTAATTATTTTAATTTTTAAATTAAAA
Found at i:98480 original size:26 final size:28
Alignment explanation
Indices: 98428--98497 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
98418 AGTAGCTATT
*
98428 AAATATTAATATTTATTTAATATTTTAA
1 AAATATTAATATATATTTAATATTTTAA
98456 AAATATGT-ATATATATTT-ATA-TTTAA
1 AAATAT-TAATATATATTTAATATTTTAA
*
98482 AAATATTTAAAATATA
1 AAATA-TTAATATATA
98498 AATATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 11 0.30
27 10 0.27
28 15 0.41
29 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
AAATATTAATATATATTTAATATTTTAA
Found at i:98852 original size:19 final size:19
Alignment explanation
Indices: 98811--98853 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
98801 CAAAACTACT
98811 ATTTTTCTTTAATATTTTG
1 ATTTTTCTTTAATATTTTG
*
98830 -TTTTTTTTCTAA-ATTTTG
1 ATTTTTCTT-TAATATTTTG
98848 ATTTTT
1 ATTTTT
98854 AACCCGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (19 bp):
ATTTTTCTTTAATATTTTG
Found at i:99384 original size:158 final size:159
Alignment explanation
Indices: 99022--99487 Score: 523
Period size: 158 Copynumber: 2.9 Consensus size: 159
99012 CCCCCCCCGG
* * **
99022 CCAAAACTAGGGCTTCCGTTTCG-AATTTTGGGGATTTCGCTATCAAATTATGTAGTTAAGGAAG
1 CCAAAACTAGGGTTTCC-TTTTGAAATTTTGGGGATTTTACTATCAAATTATGTAGTTAA-G--G
*
99086 AAGCTGGAGCCTTTCTAATAATTATTG-TAATAAAATTTTACCTTTCCTGGGCTTAGATTGAAAT
62 AA-CTGGAGCCTTTCTAATTATTA-TGATAAT-AAATTTTACCTTTCCTGGGCTTAGATTGAAA-
* *
99150 CTCCAATTATTTTTCTCTGATTTTTAGCTCTATGTTTCTC
123 CTCC-A-T-TTTTTCTTTGATTTTTAGCTTTATGTTTCTC
* * *
99190 CCAAAACTAGGGTTTCCGTTTGAAAATTTGGGGATTTTTCTATCAAATTATGTAGTTAAGGAATC
1 CCAAAACTAGGGTTTCCTTTTGAAATTTTGGGGATTTTACTATCAAATTATGTAGTTAAGGAA-C
99255 TGGAGCCTTTCTAATTATTATGATAATAAATTTTACCTTTCCTGGGCTTAGATTGAAA-TCC-TT
65 TGGAGCCTTTCTAATTATTATGATAATAAATTTTACCTTTCCTGGGCTTAGATTGAAACTCCATT
* * *
99318 TTTTCTTTGATTGTTAGCTTTAT-TTTTTAT
130 TTTTCTTTGATTTTTAGCTTTATGTTTCT-C
* * *
99348 CCAAAACTAGGTTTTCCTTTTGAAATTTTGGGGATTTTACTGTCAAATTATGTAGTTGAGGAA--
1 CCAAAACTAGGGTTTCCTTTTGAAATTTTGGGGATTTTACTATCAAATTATGTAGTTAAGGAACT
* *
99411 -GA-----T-T-ATTATAAT-ATAGTAAATTTTACCTTTCCTGGGCTTAGATTGAAATCTCCAAT
66 GGAGCCTTTCTAATTATTATGATAATAAATTTTACCTTTCCTGGGCTTAGATTGAAA-CTCC-AT
99467 TTTTTCTTTGATTTTTAGCTT
129 TTTTTCTTTGATTTTTAGCTT
99488 CATTCTTCCA
Statistics
Matches: 269, Mismatches: 22, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
146 35 0.13
147 7 0.03
148 4 0.01
149 1 0.00
150 21 0.08
154 2 0.01
157 4 0.01
158 78 0.29
159 1 0.00
162 3 0.01
164 33 0.12
165 27 0.10
167 4 0.01
168 49 0.18
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (159 bp):
CCAAAACTAGGGTTTCCTTTTGAAATTTTGGGGATTTTACTATCAAATTATGTAGTTAAGGAACT
GGAGCCTTTCTAATTATTATGATAATAAATTTTACCTTTCCTGGGCTTAGATTGAAACTCCATTT
TTTCTTTGATTTTTAGCTTTATGTTTCTC
Found at i:101061 original size:6 final size:6
Alignment explanation
Indices: 101050--101076 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
101040 GAAGTAAGTT
101050 TCTATC TCTATC TCTATC TCTATC TCT
1 TCTATC TCTATC TCTATC TCTATC TCT
101077 GATTGTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTATC
Found at i:106882 original size:14 final size:15
Alignment explanation
Indices: 106851--106883 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
106841 AAATTTAATT
106851 ATAATTATTAATATA
1 ATAATTATTAATATA
*
106866 ATAATTTTTAA-ATA
1 ATAATTATTAATATA
106880 ATAA
1 ATAA
106884 AATATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTATTAATATA
Found at i:114003 original size:16 final size:16
Alignment explanation
Indices: 113979--114015 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
113969 GTATATGGAA
* *
113979 CTATTAGCTTTTTTAT
1 CTATGAGCTTTTTTAG
113995 CTATGAGCTTTTTTAG
1 CTATGAGCTTTTTTAG
114011 CTATG
1 CTATG
114016 GTTAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.54
Consensus pattern (16 bp):
CTATGAGCTTTTTTAG
Found at i:114277 original size:16 final size:16
Alignment explanation
Indices: 114256--114305 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
114246 ATATAAAATC
*
114256 ATTTTTTCTCAATTTA
1 ATTTTTTATCAATTTA
* *
114272 ATTTTTTAT-TATATTG
1 ATTTTTTATCAAT-TTA
114288 ATTTTTTATCAATTTA
1 ATTTTTTATCAATTTA
114304 AT
1 AT
114306 AAATACTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (16 bp):
ATTTTTTATCAATTTA
Found at i:116248 original size:3 final size:3
Alignment explanation
Indices: 116240--116281 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
116230 ATTATGCCTT
116240 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
116282 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:116286 original size:2 final size:2
Alignment explanation
Indices: 116279--116305 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
116269 ATTATTATTT
116279 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
116306 TTCTGCAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117803 original size:26 final size:25
Alignment explanation
Indices: 117766--117815 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
117756 CAGATCCAAG
117766 ATATATTATATTTTATATTTATATAT
1 ATATATTATATTTTAT-TTTATATAT
117792 ATATATCT-TATTTTATTTTATATA
1 ATATAT-TATATTTTATTTTATATA
117816 ATGTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 14 0.61
27 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATATTATATTTTATTTTATATAT
Found at i:117813 original size:19 final size:21
Alignment explanation
Indices: 117766--117815 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
117756 CAGATCCAAG
*
117766 ATATAT-TATATTTTATATTT
1 ATATATATATATCTTATATTT
117786 ATATATATATATCTTAT-TTT
1 ATATATATATATCTTATATTT
*
117806 AT-TTTATATA
1 ATATATATATA
117816 ATGTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 11 0.41
21 9 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATATATATCTTATATTT
Found at i:117872 original size:17 final size:18
Alignment explanation
Indices: 117839--117872 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
117829 ATTTGAAATA
117839 AATAAATTTTAATATAAT
1 AATAAATTTTAATATAAT
*
117857 AATATATTTT-ATATAA
1 AATAAATTTTAATATAA
117873 ATTTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAATTTTAATATAAT
Found at i:119851 original size:18 final size:16
Alignment explanation
Indices: 119830--119874 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
119820 AAAAAAAAAA
119830 AAAAAGGTAAAAAAGGGT
1 AAAAA-GTAAAAAA-GGT
*
119848 AAAACAGTAGAAAAGGT
1 AAAA-AGTAAAAAAGGT
119865 AAAAAGTAAA
1 AAAAAGTAAA
119875 TATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.21
17 7 0.29
18 11 0.46
19 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.22, T:0.11
Consensus pattern (16 bp):
AAAAAGTAAAAAAGGT
Found at i:120338 original size:61 final size:60
Alignment explanation
Indices: 120272--120390 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
120262 TTTTATTTAG
* * * *
120272 ATAATTTTATAATTTT-A-TTATATTTAATTAAGTTTTGTAATCTTTAATTTGTATTTAAAAT
1 ATAA-TTTA-AATTTTAATTTATATTTAAATAAATTTT-TAATCTTTAATTTATATCTAAAAT
*
120333 ATAATTTAATTTTTAATTTATATTTAAATAAATTTTTAATCTTTAATTTATATCTAAA
1 ATAATTTAAATTTTAATTTATATTTAAATAAATTTTTAATCTTTAATTTATATCTAAA
120391 TAAACTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 5 0.10
60 25 0.49
61 21 0.41
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (60 bp):
ATAATTTAAATTTTAATTTATATTTAAATAAATTTTTAATCTTTAATTTATATCTAAAAT
Found at i:120350 original size:30 final size:30
Alignment explanation
Indices: 120309--120402 Score: 113
Period size: 30 Copynumber: 3.1 Consensus size: 30
120299 TTAAGTTTTG
*
120309 TAATCTTTAATTTGTATTTAAAATATAA-TT
1 TAATCTTTAATTTATATTTAAAATA-AATTT
*
120339 TAATTTTTAATTTATATTT-AAATAAATTTT
1 TAATCTTTAATTTATATTTAAAATAAA-TTT
*
120369 TAATCTTTAATTTATATCT-AAATAAACTTT
1 TAATCTTTAATTTATATTTAAAATAAA-TTT
120399 TAAT
1 TAAT
120403 ATAAATAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 2 0.04
29 5 0.09
30 50 0.88
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (30 bp):
TAATCTTTAATTTATATTTAAAATAAATTT
Found at i:120439 original size:22 final size:21
Alignment explanation
Indices: 120403--120455 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
120393 AACTTTTAAT
*
120403 ATAAATAAATTTTTTATTAAAA
1 ATAAA-AAATTTTTTAATAAAA
*
120425 ATAAAAAATTATTTTAATACAA
1 ATAAAAAATT-TTTTAATAAAA
120447 ATAAAAAAT
1 ATAAAAAAT
120456 ACATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAAAAATTTTTTAATAAAA
Found at i:120468 original size:25 final size:22
Alignment explanation
Indices: 120423--120499 Score: 59
Period size: 25 Copynumber: 3.3 Consensus size: 22
120413 TTTTTATTAA
*
120423 AAATAAAAAATTATTTTAATAC
1 AAATAAAAAATTATTTAAATAC
120445 AAATAAAAAATACATATTTAAATA-
1 AAATAAAAAAT---TATTTAAATAC
*
120469 AAAGTATAAAATTTTATTTAAAATA-
1 AAA-TA-AAAA-ATTATTT-AAATAC
120494 AAATAA
1 AAATAA
120500 TTTAAATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
22 11 0.24
23 1 0.02
24 10 0.22
25 19 0.41
26 4 0.09
27 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (22 bp):
AAATAAAAAATTATTTAAATAC
Found at i:121199 original size:19 final size:18
Alignment explanation
Indices: 121177--121224 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
121167 TATTAATTAA
*
121177 TAATAAAAATATTTAAATT
1 TAATAAAAATATATAAA-T
* *
121196 TAATTATAATATATAAAT
1 TAATAAAAATATATAAAT
121214 TAATATAAAAT
1 TAATA-AAAAT
121225 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAAAAATATATAAAT
Found at i:122882 original size:18 final size:18
Alignment explanation
Indices: 122854--122902 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
122844 AAGATCAAAT
**
122854 TAAATAAATATAAATCGTA
1 TAAA-AAATATAAATAATA
122873 TAAAAAATATAAA-AATA
1 TAAAAAATATAAATAATA
122890 TAAAAAAT-TAAAT
1 TAAAAAATATAAAT
122903 TAAATTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 9 0.33
19 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAAATATAAATAATA
Found at i:123148 original size:14 final size:15
Alignment explanation
Indices: 123129--123167 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
123119 TAAAGTAAAT
123129 TTTTTTATTTGTG-A
1 TTTTTTATTTGTGTA
*
123143 TTTTTTATTTTTGTA
1 TTTTTTATTTGTGTA
*
123158 TTTTTAATTT
1 TTTTTTATTT
123168 TAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTTTATTTGTGTA
Found at i:123167 original size:15 final size:16
Alignment explanation
Indices: 123136--123168 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
123126 AATTTTTTTA
*
123136 TTTGTGATTTTTTATT
1 TTTGTGATTTTTAATT
123152 TTTGT-ATTTTTAATT
1 TTTGTGATTTTTAATT
123167 TT
1 TT
123169 AAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTGTGATTTTTAATT
Found at i:123167 original size:22 final size:22
Alignment explanation
Indices: 123127--123168 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
123117 CGTAAAGTAA
* *
123127 ATTTTTTTATTTGTGATTTTTT
1 ATTTTTGTATTTGTAATTTTTT
*
123149 ATTTTTGTATTTTTAATTTT
1 ATTTTTGTATTTGTAATTTT
123169 AAAAATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (22 bp):
ATTTTTGTATTTGTAATTTTTT
Found at i:123548 original size:24 final size:24
Alignment explanation
Indices: 123516--123573 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
123506 GGAGCCAAAG
* * *
123516 GGTAAGTGGTGGCTCATACAGGTT
1 GGTATGTGGCGGCTCATACAGGTC
*
123540 GGTATGTGGCGGTTCATACAGGTC
1 GGTATGTGGCGGCTCATACAGGTC
123564 GGTATGTGGC
1 GGTATGTGGC
123574 TGTCCAGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (24 bp):
GGTATGTGGCGGCTCATACAGGTC
Found at i:123953 original size:24 final size:23
Alignment explanation
Indices: 123921--123968 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
123911 GAAATTTAAT
*
123921 TAATTTATATAATTATTTAAATTA
1 TAATATATATAA-TATTTAAATTA
* *
123945 TAATATATATTATATTTTAATTA
1 TAATATATATAATATTTAAATTA
123968 T
1 T
123969 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATATATATAATATTTAAATTA
Found at i:123981 original size:20 final size:20
Alignment explanation
Indices: 123956--124007 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
123946 AATATATATT
123956 ATATTTTAATTATTTTAAAA
1 ATATTTTAATTATTTTAAAA
*
123976 ATATTTT-A-TATTTTTAAA
1 ATATTTTAATTATTTTAAAA
123994 A-ATTTTAATATATT
1 ATATTTTAAT-TATT
124008 AATAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.18
18 11 0.39
19 1 0.04
20 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTAATTATTTTAAAA
Found at i:124004 original size:18 final size:19
Alignment explanation
Indices: 123958--124007 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
123948 TATATATTAT
123958 ATTTTAAT-TATTTTAAAA
1 ATTTTAATATATTTTAAAA
*
123976 ATATTTTATAT-TTTTAAAA
1 AT-TTTAATATATTTTAAAA
123995 ATTTTAATATATT
1 ATTTTAATATATT
124008 AATAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTAATATATTTTAAAA
Found at i:124006 original size:27 final size:26
Alignment explanation
Indices: 123939--124007 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
123929 ATAATTATTT
* *
123939 AAATTATAATATATATTATATTTTAA
1 AAATTTTAATATATTTTATATTTTAA
** *
123965 TTATTTTAAAAATATTTTATATTTTTAA
1 AAATTTT-AATATATTTTATA-TTTTAA
123993 AAATTTTAATATATT
1 AAATTTTAATATATT
124008 AATAATTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
26 4 0.12
27 18 0.55
28 11 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATTTTAATATATTTTATATTTTAA
Found at i:124020 original size:33 final size:32
Alignment explanation
Indices: 123975--124066 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
123965 TTATTTTAAA
* * *
123975 AATATTTTATATTTTTAAAAATTTTAATATATT
1 AATAATTTATA-TTATAAAAATTTTAAAATATT
*
124008 AATAATTTATATTATATAAATTTTAAAATATT
1 AATAATTTATATTATAAAAATTTTAAAATATT
* *
124040 CATATATTCT-TATTATAATATATTTTA
1 AATA-ATT-TATATTATAA-AAATTTTA
124067 TATTATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
32 21 0.43
33 20 0.41
34 8 0.16
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (32 bp):
AATAATTTATATTATAAAAATTTTAAAATATT
Found at i:124023 original size:18 final size:18
Alignment explanation
Indices: 123975--124024 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
123965 TTATTTTAAA
*
123975 AATATTTTATATT-T-TT
1 AATAATTTATATTATATT
* *
123991 AAAAATTT-TAATATATT
1 AATAATTTATATTATATT
124008 AATAATTTATATTATAT
1 AATAATTTATATTATAT
124025 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.12
16 7 0.27
17 9 0.35
18 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATAATTTATATTATATT
Found at i:124203 original size:21 final size:22
Alignment explanation
Indices: 124169--124217 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
124159 ATAGATTTAA
* *
124169 ATTTTAATATTTATAATTTTTT
1 ATTTTAATAATTATAATATTTT
124191 ATTTTAA-AATTATAATATTTT
1 ATTTTAATAATTATAATATTTT
124212 ATTTTA
1 ATTTTA
124218 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTAATAATTATAATATTTT
Found at i:124228 original size:23 final size:21
Alignment explanation
Indices: 124181--124229 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
124171 TTTAATATTT
* **
124181 ATAATTTTTTATTTTAAAATT
1 ATAATATTTTATTTTAAAAAA
124202 ATAATATTTTATTTTATTAAAAA
1 ATAATATTTTATTTTA--AAAAA
124225 ATAAT
1 ATAAT
124230 TAATTAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAATATTTTATTTTAAAAAA
Found at i:124939 original size:21 final size:21
Alignment explanation
Indices: 124915--124954 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
124905 TATTTTTATT
124915 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
124936 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
124955 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:125004 original size:51 final size:48
Alignment explanation
Indices: 124893--125004 Score: 111
Period size: 51 Copynumber: 2.3 Consensus size: 48
124883 TTAATATTTA
* * *
124893 ATAAATAAAAAATATTTTTATTTAAATTTAATTATAAAATATATAAAT
1 ATAAATAAAAAATATTTTTATTTAAATTGAATGATAAAATAAATAAAT
* *
124941 ATTAATATAAAATAATTTTTATTAATAAA-TGAATCGAGTAAAA-AAATAAAT
1 ATAAATAAAAAAT-ATTTTTATT--TAAATTGAAT-GA-TAAAATAAATAAAT
*
124992 CTAAATAAAAAAT
1 ATAAATAAAAAAT
125005 TTAAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
48 11 0.22
49 9 0.18
50 4 0.08
51 22 0.43
52 5 0.10
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (48 bp):
ATAAATAAAAAATATTTTTATTTAAATTGAATGATAAAATAAATAAAT
Found at i:125530 original size:3 final size:3
Alignment explanation
Indices: 125522--125549 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
125512 CAATTGTTTG
125522 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
125550 ATTTCTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:126656 original size:20 final size:20
Alignment explanation
Indices: 126631--126692 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
126621 AATTATTAAC
*
126631 ATATAATAATTTACATAAAT
1 ATATAATAATTTAAATAAAT
*
126651 ATATAATATTTTAAATATAAT
1 ATATAATAATTTAAATA-AAT
*
126672 -TATAAT-ATTTATATAAAT
1 ATATAATAATTTAAATAAAT
126690 ATA
1 ATA
126693 ATATAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.08
19 9 0.25
20 21 0.58
21 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAATAATTTAAATAAAT
Found at i:126696 original size:11 final size:11
Alignment explanation
Indices: 126662--126703 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
126652 TATAATATTT
126662 TAAATATAAT-
1 TAAATATAATA
*
126672 TATAATATTTATA
1 TA-AATA-TAATA
126685 TAAATATAATA
1 TAAATATAATA
126696 TAAATATA
1 TAAATATA
126704 TAAATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 16 0.59
12 7 0.26
13 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAATATAATA
Found at i:126702 original size:17 final size:17
Alignment explanation
Indices: 126645--126703 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
126635 AATAATTTAC
126645 ATAAATATATAATAT--T
1 ATAAATATA-AATATAAT
* *
126661 TTAAATATAATTATAAT
1 ATAAATATAAATATAAT
**
126678 ATTTATATAAATATAAT
1 ATAAATATAAATATAAT
126695 ATAAATATA
1 ATAAATATA
126704 TAAATTTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 21 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATATAAATATAAT
Found at i:133311 original size:2 final size:2
Alignment explanation
Indices: 133290--133338 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
133280 CAGTTCGAAG
* * *
133290 AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133331 AT AT AT AT
1 AT AT AT AT
133339 GATGACAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:133428 original size:2 final size:2
Alignment explanation
Indices: 133421--133448 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
133411 TGTTTCATCC
133421 TA 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 TA
133449 CATGTTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139225 original size:9 final size:10
Alignment explanation
Indices: 139195--139227 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
139185 ATTTATACGC
139195 AAAATAAAAG
1 AAAATAAAAG
139205 AAAATAAAAG
1 AAAATAAAAG
139215 AAAAT-AAAG
1 AAAATAAAAG
139224 AAAA
1 AAAA
139228 CTTCATACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:148932 original size:232 final size:232
Alignment explanation
Indices: 148494--149082 Score: 959
Period size: 232 Copynumber: 2.5 Consensus size: 232
148484 GAAATATATC
* * * *
148494 GCTATTAGCTTGTTTCTTTTATTAATTACTAGGGTGCATTTTTTAACGTAAATGAAAAGTTGAAC
1 GCTATTAGTTTGTTTCTTTTATTAATTACCAGGGTGCATTTTTTAACTTAAATGAAAAGTTGAAT
* *
148559 TCGAAATTTATTTAGTTTATGTAAAACTGTTAAAAAAATTGAATTAAATTGATTAGAACTGATTG
66 TCGAAATTTAATTAGTTTATGTAATACTGTTAAAAAAATTGAATTAAATTGATTAGAACTGATTG
* *
148624 GGTTAAAAATTAATGCTAGTCCAATTAAGTTTAAGGCATGTTATAAAATCAAAATTTTTTTTAAA
131 GATCAAAAATTAATGCTAGTCCAATTAAGTTTAAGGCATGTTATAAAATCAAAATTTTTTTTAAA
* *
148689 AAAAATTATTAATTTTAATAACTTTTAATATTTTAAT
196 AAAAATTATTAATTTTAATAACCTTTAAAATTTTAAT
* *
148726 GCTATTGGTTTGTTTCTTTTATTAATTACCAGGGTGCATTTTTCAACTTAAATGAAAAGTTTGAA
1 GCTATTAGTTTGTTTCTTTTATTAATTACCAGGGTGCATTTTTTAACTTAAATGAAAAG-TTGAA
* *
148791 TTTGAAATTTAATTAGTTTATGTAATACTGTTAAAAAAATTGAATTAAATTGATTAAAACTGATT
65 TTCGAAATTTAATTAGTTTATGTAATACTGTTAAAAAAATTGAATTAAATTGATTAGAACTGATT
*
148856 GGATCAAAAATTAATGCTAGTCCAATTAAGTTTAAGGCATGTTATAAAAT-TAAA-TTTTTTTAA
130 GGATCAAAAATTAATGCTAGTCCAATTAAGTTTAAGGCATGTTATAAAATCAAAATTTTTTTTAA
148919 AAAAAATTTATTAATTTTAATAACCTTTAAAATTTTAAT
195 AAAAAA-TTATTAATTTTAATAACCTTTAAAATTTTAAT
* *
148958 GCTATTTGTTTGTTTCTTTTATTAATTACCAGGGTGCATTTTTTAA-TGTAAATAAAAAGTTGAA
1 GCTATTAGTTTGTTTCTTTTATTAATTACCAGGGTGCATTTTTTAACT-TAAATGAAAAGTTGAA
* *
149022 TTCAAAATTTAATTAATTTATGTAATACTGTTAAAAAAATTGAATTAAATTGATTAGAACT
65 TTCGAAATTTAATTAGTTTATGTAATACTGTTAAAAAAATTGAATTAAATTGATTAGAACT
149083 TATTAAGTTT
Statistics
Matches: 332, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
231 78 0.23
232 141 0.42
233 113 0.34
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.43
Consensus pattern (232 bp):
GCTATTAGTTTGTTTCTTTTATTAATTACCAGGGTGCATTTTTTAACTTAAATGAAAAGTTGAAT
TCGAAATTTAATTAGTTTATGTAATACTGTTAAAAAAATTGAATTAAATTGATTAGAACTGATTG
GATCAAAAATTAATGCTAGTCCAATTAAGTTTAAGGCATGTTATAAAATCAAAATTTTTTTTAAA
AAAAATTATTAATTTTAATAACCTTTAAAATTTTAAT
Found at i:155030 original size:2 final size:2
Alignment explanation
Indices: 155018--155048 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
155008 ATGTTTGTCC
155018 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155049 GATGATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:161853 original size:29 final size:29
Alignment explanation
Indices: 161820--161925 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 29
161810 TTAATTGACT
161820 TTAAATATATTACATTATATTTAAAATTA
1 TTAAATATATTACATTATATTTAAAATTA
* *
161849 TTAAATTTATTACGAGTTA-ATTGTATTAATTGA
1 TTAAATATATTAC-A-TTATATT-TA-AAATT-A
*
161882 CTTTAAATATATTACATCATATTTAAAATTA
1 --TTAAATATATTACATTATATTTAAAATTA
*
161913 TTAAATTTATTAC
1 TTAAATATATTAC
161926 GAGTCTCTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
29 24 0.38
30 4 0.06
31 6 0.10
32 8 0.13
33 5 0.08
34 4 0.06
35 12 0.19
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (29 bp):
TTAAATATATTACATTATATTTAAAATTA
Found at i:161884 original size:64 final size:64
Alignment explanation
Indices: 161800--161929 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
161790 AATGTACAAT
*
161800 GTTAATTGTATTAATTGACTTTAAATATATTACATTATATTTAAAATTATTAAATTTATTACGA
1 GTTAATTGTATTAATTGACTTTAAATATATTACATCATATTTAAAATTATTAAATTTATTACGA
161864 GTTAATTGTATTAATTGACTTTAAATATATTACATCATATTTAAAATTATTAAATTTATTACGA
1 GTTAATTGTATTAATTGACTTTAAATATATTACATCATATTTAAAATTATTAAATTTATTACGA
161928 GT
1 GT
161930 CTCTGCGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (64 bp):
GTTAATTGTATTAATTGACTTTAAATATATTACATCATATTTAAAATTATTAAATTTATTACGA
Found at i:161889 original size:35 final size:34
Alignment explanation
Indices: 161800--161897 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 34
161790 AATGTACAAT
161800 GTTAATTGTATTAATTGACTTTAAATATATTACA
1 GTTAATTGTATTAATTGACTTTAAATATATTACA
* *
161834 -TTATATT-TA-AAATT-A--TTAAATTTATTACGA
1 GTTA-ATTGTATTAATTGACTTTAAATATATTAC-A
161864 GTTAATTGTATTAATTGACTTTAAATATATTACA
1 GTTAATTGTATTAATTGACTTTAAATATATTACA
161898 TCATATTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
29 12 0.23
30 4 0.08
31 6 0.12
32 8 0.15
33 6 0.12
34 4 0.08
35 12 0.23
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (34 bp):
GTTAATTGTATTAATTGACTTTAAATATATTACA
Found at i:163003 original size:17 final size:19
Alignment explanation
Indices: 162970--163006 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
162960 TTTTAAATAT
162970 TATATATTATATAAATTTA
1 TATATATTATATAAATTTA
162989 TATATATTA-AT-AATTTA
1 TATATATTATATAAATTTA
163006 T
1 T
163007 GTTATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 2 0.11
19 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATTATATAAATTTA
Done.