Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 5 of 345
Found at i:1535466 original size:75 final size:74
Alignment explanation
Indices: 1535345--1535517 Score: 207
Period size: 75 Copynumber: 2.4 Consensus size: 74
1535335 TCCATGGCAA
** *
1535345 AGTGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTA
1 AGTGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-
*
1535405 T-CCATACTG
65 TCCCATACCG
1535414 AGCTGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT
1 AG-TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT
1535479 TCCCATACCG
65 TCCCATACCG
***
1535489 AGTAAAAAAATGTAGGTATGGTATT-TCAA
1 AGT-GTGAAATGTAGGTATGGTATTATCAA
1535518 TGAGGAAAAC
Statistics
Matches: 89, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
69 2 0.02
70 18 0.20
73 4 0.04
74 6 0.07
75 59 0.66
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (74 bp):
AGTGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTT
CCCATACCG
Found at i:1535485 original size:35 final size:35
Alignment explanation
Indices: 1535350--1535515 Score: 165
Period size: 35 Copynumber: 4.6 Consensus size: 35
1535340 GGCAAAGTGT
* **
1535350 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
1535385 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
1535420 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* * *
1535460 GAAATGTAGGTATGGCATTTCCCATACCGAGTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
1535495 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
1535516 AATGAGGAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
35 84 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:1544742 original size:39 final size:39
Alignment explanation
Indices: 1544697--1544774 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
1544687 TATAATCGAG
*
1544697 TTAAGTCCGGTTCAATCAATACAATAAAAGTTTAAACTT
1 TTAAGTCCGGTTCAATCAATACAATAAAAGTTCAAACTT
*
1544736 TTAAGTCTGGTTCAATCAATACAATAAAAGTTCAAACTT
1 TTAAGTCCGGTTCAATCAATACAATAAAAGTTCAAACTT
1544775 AAATTACTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (39 bp):
TTAAGTCCGGTTCAATCAATACAATAAAAGTTCAAACTT
Found at i:1551881 original size:2 final size:2
Alignment explanation
Indices: 1551874--1551911 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1551864 CCTTAAATTC
1551874 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
1551912 AAGAGATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1561446 original size:29 final size:30
Alignment explanation
Indices: 1561404--1561484 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
1561394 TAAATGAACC
* *
1561404 AAATCAAACTTTCATGTATAAAATTGCATA-
1 AAATCAAA-GTTCATGTATAAAATTACATAT
*
1561434 AAATCAAAGTTCATGTATACAATTACATATT
1 AAATCAAAGTTCATGTATAAAATTACATA-T
* *
1561465 AAACCATAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
1561485 TTTTGGGATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 18 0.42
30 8 0.19
31 17 0.40
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACATAT
Found at i:1561861 original size:31 final size:31
Alignment explanation
Indices: 1561826--1561885 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1561816 ATTTAATAGA
*
1561826 GAGTGATCAAAATAAAAATAATCTAAAATAT
1 GAGTGATCAAAATAAAAATAACCTAAAATAT
* *
1561857 GAGTGATCAAAATAGAAATTACCTAAAAT
1 GAGTGATCAAAATAAAAATAACCTAAAAT
1561886 GTTATGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (31 bp):
GAGTGATCAAAATAAAAATAACCTAAAATAT
Found at i:1562319 original size:20 final size:20
Alignment explanation
Indices: 1562294--1562346 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
1562284 CCCAACCCGA
1562294 ATATTATATTAATTATATAT
1 ATATTATATTAATTATATAT
*
1562314 ATATTAAATAATAATTATATAT
1 ATATT--ATATTAATTATATAT
1562336 AT-TTATATTAA
1 ATATTATATTAA
1562347 ATCACTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 6 0.21
20 5 0.17
21 2 0.07
22 16 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTATATTAATTATATAT
Found at i:1577761 original size:91 final size:90
Alignment explanation
Indices: 1577648--1577826 Score: 236
Period size: 95 Copynumber: 1.9 Consensus size: 90
1577638 GCTGAGGTAA
* *
1577648 TTTCAATTTCTGTTGTCAAAAAAA-ATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCA
1 TTTCAATTTCTGTTGTCAAAAAAACATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAAG--A
*
1577712 CACACCGAGGTATTTTCAATTTCCGTT
64 CACACCGAGGTAATTTCAATTTCCGTT
*
1577739 TTTCAATTTCTGCCTT-TCAAAAAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA
1 TTTCAATTTCTG--TTGTC--AAAAAAACATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAA
* *
1577803 GACACGCTGAGGTAATTTCAATTT
62 GACACACCGAGGTAATTTCAATTT
1577827 TTGTTGTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
91 12 0.16
92 2 0.03
93 22 0.29
94 7 0.09
95 34 0.44
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (90 bp):
TTTCAATTTCTGTTGTCAAAAAAACATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAAGACA
CACCGAGGTAATTTCAATTTCCGTT
Found at i:1577867 original size:74 final size:76
Alignment explanation
Indices: 1577760--1577902 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 76
1577750 GCCTTTCAAA
* *
1577760 AAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACGCTGAGGTAATTTCAA
1 AAAAAACATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAAGCACACGCCGAGGTAATTTCAA
1577824 TTTTTGTTGTC
66 TTTTTGTTGTC
* * * *
1577835 AAAAAA-ATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCA
1 AAAAAACATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAAG-CACACGCCGAGGTAATTTCA
1577899 ATTT
65 ATTT
1577903 CCGTTTTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
74 33 0.55
75 6 0.10
76 21 0.35
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (76 bp):
AAAAAACATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAAGCACACGCCGAGGTAATTTCAA
TTTTTGTTGTC
Found at i:1577905 original size:169 final size:167
Alignment explanation
Indices: 1577591--1578088 Score: 835
Period size: 169 Copynumber: 3.0 Consensus size: 167
1577581 AGGTATTTTC
* * *
1577591 AAAAAAATCAACTTATATTGCGAGAGATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
1577656 TCTGTTGTCAAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACACCGAG
66 T-TGTTGTC-AAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
1577721 GTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
129 GTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
*
1577760 AAAAAACATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
1 AAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-
*
1577825 TTTTGTTGTCAAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
64 TTTTGTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
1577890 GTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
129 GTATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
*
1577929 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGACACGCTGAGGTAATTTC----
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* * *
1577990 -TGTTGTCAAAAAAATCAACTCGTATTGCGAGCGGCGGGTTAAGCCTCAGGTCACACGCCGAGGT
66 TTGTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGT
1578054 ATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCA
131 ATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCA
1578089 CGTAGACCTA
Statistics
Matches: 315, Mismatches: 12, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
162 95 0.30
168 53 0.17
169 104 0.33
170 60 0.19
171 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (167 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
TTGTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGT
ATTTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
Found at i:1578039 original size:68 final size:69
Alignment explanation
Indices: 1577929--1578059 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 69
1577919 GCCTTTCAAA
* * * *
1577929 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGG-ACACGCTGAGGTAATTTCTGT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAGCCTCAGGCACACGCCGAGGTAATTTCTGT
1577993 TGTC
66 TGTC
* * * *
1577997 AAAAAAATCAACTCGTATTGCGAGCGGCGGGTTAAGCCTCAGGTCACACGCCGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAGCCTCAGG-CACACGCCGAGGTAATTTC
1578060 AATTTCCGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 37 0.70
70 16 0.30
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (69 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAGCCTCAGGCACACGCCGAGGTAATTTCTGT
TGTC
Found at i:1590092 original size:21 final size:21
Alignment explanation
Indices: 1590066--1590106 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1590056 AGACGAGCGA
* *
1590066 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1590087 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1590107 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1594785 original size:31 final size:31
Alignment explanation
Indices: 1594747--1594806 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1594737 ATACTAAAAA
*
1594747 AATTTTAATTTTAATTCAATTGTATATATAC
1 AATTTTAATTTTAATTCAATTATATATATAC
*
1594778 AATTTTAATTTTTATTCAATTATATATAT
1 AATTTTAATTTTAATTCAATTATATATAT
1594807 TTAAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (31 bp):
AATTTTAATTTTAATTCAATTATATATATAC
Found at i:1595444 original size:8 final size:8
Alignment explanation
Indices: 1595431--1595465 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1595421 TTTCAATTAT
1595431 GTTGCCAC
1 GTTGCCAC
1595439 GTTGCCAC
1 GTTGCCAC
*
1595447 GTTGCCAT
1 GTTGCCAC
*
1595455 GTTGTCAC
1 GTTGCCAC
1595463 GTT
1 GTT
1595466 TCCTGCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.11, C:0.29, G:0.26, T:0.34
Consensus pattern (8 bp):
GTTGCCAC
Found at i:1599105 original size:29 final size:29
Alignment explanation
Indices: 1599046--1599105 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1599036 AACTTATATC
*
1599046 TTTATAATTTCTAGAGGACTAAATCATTT
1 TTTATAATTTCTAGAGGACTAAATCAATT
*
1599075 TTTATAATTT-TTGA-GACTAAAATACAATT
1 TTTATAATTTCTAGAGGACT-AAAT-CAATT
1599104 TT
1 TT
1599106 ACCAATACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 7 0.26
29 16 0.59
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTATAATTTCTAGAGGACTAAATCAATT
Found at i:1599804 original size:30 final size:30
Alignment explanation
Indices: 1599770--1599839 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
1599760 TTTTGATACC
*
1599770 AAAACTTTGATTTGGGGTAATTATACTCAT
1 AAAACTTTGATTTGGGGCAATTATACTCAT
* * *
1599800 AAAACTTTTTTTATTTGGTGCAATTATATTCAT
1 AAAAC---TTTGATTTGGGGCAATTATACTCAT
1599833 AAAACTT
1 AAAACTT
1599840 AAATCATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 7 0.21
33 26 0.79
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (30 bp):
AAAACTTTGATTTGGGGCAATTATACTCAT
Found at i:1606456 original size:42 final size:42
Alignment explanation
Indices: 1606393--1606519 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
1606383 CTTCGTTTTC
* * *
1606393 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCTCAGCTATGGTCTTACACATATTCACAT-A
* *
1606436 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCTCAGCTATGGTCTTACACATATTCACATA
*
1606477 TCGATGCCATAGCTTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCTCAGCTATGGTCTTACAC-ATATTCACATA
1606518 TC
1 TC
1606520 TCACTGATGC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 10 0.14
42 62 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCTCAGCTATGGTCTTACACATATTCACATA
Found at i:1608133 original size:28 final size:28
Alignment explanation
Indices: 1608064--1608164 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
1608054 GACAAGATTG
* * * *
1608064 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
1608094 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
1608122 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
1608151 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
1608165 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:1608158 original size:29 final size:28
Alignment explanation
Indices: 1608093--1608164 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
1608083 AAAATTGTAC
*
1608093 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
1608121 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
1608150 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
1608165 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:1615941 original size:28 final size:28
Alignment explanation
Indices: 1615872--1615972 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
1615862 GACAAGATTG
* * * *
1615872 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
1615902 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
1615930 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
1615959 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
1615973 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:1615966 original size:29 final size:28
Alignment explanation
Indices: 1615901--1615972 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
1615891 AAAATTGTAC
*
1615901 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
1615929 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
1615958 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
1615973 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:1617482 original size:31 final size:31
Alignment explanation
Indices: 1617447--1617626 Score: 274
Period size: 31 Copynumber: 5.8 Consensus size: 31
1617437 CTTGTCACTT
*
1617447 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
1617478 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1617509 GTAGCCGGAA-CTACCACTTTTTACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
1617540 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
1617571 GTAGCTGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1617602 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
1617627 TGTCATTTGT
Statistics
Matches: 139, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
30 3 0.02
31 134 0.96
32 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:1617708 original size:50 final size:51
Alignment explanation
Indices: 1617602--1617730 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
1617592 CACTGATCAG
* * *
1617602 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
1617653 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
1617703 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
1617731 TTCCGTGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:1628158 original size:18 final size:17
Alignment explanation
Indices: 1628137--1628194 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
1628127 TAATATTACA
1628137 ATAAATCATTTAATTATT
1 ATAAAT-ATTTAATTATT
1628155 AT-AATATTTAAATTTAATT
1 ATAAATATTT-AA-TT-ATT
1628174 A-AAA-ATTTACATTATT
1 ATAAATATTTA-ATTATT
1628190 ATAAA
1 ATAAA
1628195 AAATAATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
16 8 0.24
17 11 0.32
18 9 0.26
19 6 0.18
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATATTTAATTATT
Found at i:1634599 original size:12 final size:12
Alignment explanation
Indices: 1634574--1634612 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
1634564 TGGTTACTAG
1634574 TCTTCTTTTCTTTT
1 TCTT-TTTT-TTTT
1634588 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1634600 TCTTTTTTTTTT
1 TCTTTTTTTTTT
1634612 T
1 T
1634613 GTCTAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 17 0.68
13 4 0.16
14 4 0.16
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:1634602 original size:18 final size:17
Alignment explanation
Indices: 1634579--1634612 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1634569 ACTAGTCTTC
1634579 TTTTCTTTTTCTTTTTTT
1 TTTTCTTTTT-TTTTTTT
1634597 TTTTCTTTTTTTTTTT
1 TTTTCTTTTTTTTTTT
1634613 GTCTAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTCTTTTTTTTTTTT
Found at i:1634611 original size:11 final size:11
Alignment explanation
Indices: 1634576--1634611 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1634566 GTTACTAGTC
*
1634576 TTCTTTTCTTT
1 TTCTTTTTTTT
1634587 TTCTTTTTTTTT
1 TTC-TTTTTTTT
1634599 TTCTTTTTTTT
1 TTCTTTTTTTT
1634610 TT
1 TT
1634612 TGTCTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:1634612 original size:6 final size:6
Alignment explanation
Indices: 1634579--1634611 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1634569 ACTAGTCTTC
*
1634579 TTTTCT TTTTCT TTTTTT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1634612 TGTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTCT
Found at i:1640647 original size:23 final size:23
Alignment explanation
Indices: 1640596--1640649 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1640586 TTTATAATTT
*
1640596 TATAA-TTTTTCAAGGGATTAAA
1 TATAATTTTTTCAAGGGATCAAA
* *
1640618 TAGAATTTTTTTAA-GGATCAAA
1 TATAATTTTTTCAAGGGATCAAA
1640640 GTATAATTTT
1 -TATAATTTT
1640650 ATCATTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
TATAATTTTTTCAAGGGATCAAA
Found at i:1642496 original size:32 final size:32
Alignment explanation
Indices: 1642460--1642528 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1642450 TAAAAAATAA
1642460 AGTTTATAGTTGTTTTTAGAACAAAACTGATG
1 AGTTTATAGTTGTTTTTAGAACAAAACTGATG
1642492 AGTTTATAGTTGTTTTTAGAACAAAACTGATG
1 AGTTTATAGTTGTTTTTAGAACAAAACTGATG
1642524 A-TTTA
1 AGTTTA
1642529 AAGGATCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (32 bp):
AGTTTATAGTTGTTTTTAGAACAAAACTGATG
Found at i:1646050 original size:2 final size:2
Alignment explanation
Indices: 1646043--1646086 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1646033 AATTCAAGGA
1646043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1646084 AT A
1 AT A
1646087 ATAATAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1646661 original size:14 final size:13
Alignment explanation
Indices: 1646642--1646684 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1646632 TTTTTGCACG
1646642 AATTTTGTAAAATA
1 AATTTT-TAAAATA
**
1646656 AATTTTTTTAATA
1 AATTTTTAAAATA
1646669 AATTTTTAAAGATA
1 AATTTTTAAA-ATA
1646683 AA
1 AA
1646685 CTACATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (13 bp):
AATTTTTAAAATA
Found at i:1656630 original size:16 final size:17
Alignment explanation
Indices: 1656592--1656631 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1656582 AAAATTTTAA
1656592 CTTTTGCTCAAAAGTACT
1 CTTTTGCTCAAAAG-ACT
*
1656610 TTTTTGCTCAAAA-ACT
1 CTTTTGCTCAAAAGACT
1656626 CTTTTG
1 CTTTTG
1656632 AGAAGCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (17 bp):
CTTTTGCTCAAAAGACT
Found at i:1662437 original size:37 final size:37
Alignment explanation
Indices: 1662396--1662469 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1662386 CAAAGGTTAA
1662396 ATCTCAATGTTTTATTTTATTTTAACAGGCAAACTTT
1 ATCTCAATGTTTTATTTTATTTTAACAGGCAAACTTT
1662433 ATCTCAATGTTTTATTTTATTTTAACAGGCAAACTTT
1 ATCTCAATGTTTTATTTTATTTTAACAGGCAAACTTT
1662470 CTTTGTTAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (37 bp):
ATCTCAATGTTTTATTTTATTTTAACAGGCAAACTTT
Found at i:1662765 original size:11 final size:11
Alignment explanation
Indices: 1662749--1662773 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1662739 ACACCATAAA
1662749 AATTTTAAATT
1 AATTTTAAATT
1662760 AATTTTAAATT
1 AATTTTAAATT
1662771 AAT
1 AAT
1662774 AAAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:1663477 original size:30 final size:31
Alignment explanation
Indices: 1663426--1663489 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
1663416 AACCATCCAC
*
1663426 ATCTTAACATGTTACTTTTTTTGATAACGGGA
1 ATCTTAACATGTTA-TTTTTTTAATAACGGGA
1663458 ATCTTAACATGTT-TTTTTTTAATAACGGGA
1 ATCTTAACATGTTATTTTTTTAATAACGGGA
1663488 AT
1 AT
1663490 GATGTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 18 0.58
32 13 0.42
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (31 bp):
ATCTTAACATGTTATTTTTTTAATAACGGGA
Found at i:1669698 original size:4 final size:4
Alignment explanation
Indices: 1669689--1669724 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1669679 AACAACACTT
*
1669689 TATG TATG TATG TATG TATG TTTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1669725 GAACTAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:1691241 original size:156 final size:154
Alignment explanation
Indices: 1690776--1691243 Score: 614
Period size: 156 Copynumber: 3.0 Consensus size: 154
1690766 CTGCTGCAAT
*
1690776 GGTAGACCCGTGGATGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAGACCT
1 GGTAGACCAGTGGATGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAG-CCT
* * *
1690841 TGGGTTGAATGACATGGCCGCAGGTCCAGCATTATCTCTAGTGCTACTTTTCTGGGGATTCAAGA
65 TTGGTTGAA-GACATGGCCGCAGGTCCAGCATTTTCTCTAGCGCTACTTTTCTGGGGATTCAAGA
*
1690906 AAAAATCAAGATCATTGACTTGTAAC
129 AAAAATCAAGATCATTGACTTGTGAC
* * * * * * *
1690932 GGTAGCCCAGTGTAAGCACGTACTTCAACTAAATGACCAGAT-AAACCATTGGGTGATTCAGCCT
1 GGTAGACCAGTGGATGCACATGCTTCAACTGAATGACCAGATGAAA-CATTGGGTAATTCAGCCT
* * * * **
1690996 TTCGGTTAAAAGACCTGGCCGCAGGTGCAGCATCTTCTCTAGCAATACTTTTCTGGGGATTCAAG
65 TT-GGTT-GAAGACATGGCCGCAGGTCCAGCATTTTCTCTAGCGCTACTTTTCTGGGGATTCAAG
** *
1691061 AAAAAATCTGGACCATTGACTTGTGAC
128 AAAAAATCAAGATCATTGACTTGTGAC
* * *
1691088 TGTAGACCAGTGGATTCACATGCTTCAACTGAACGACCAGATGAAACATTGGGTAATTCAGCCTT
1 GGTAGACCAGTGGATGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAGCCTT
* *
1691153 TGGATTGGAAGAGATGGCCTCAGGTCCAGCATTTTCTCTAGCGCTACTTTTCTGGGGATTCAAGA
66 TGG-TT-GAAGACATGGCCGCAGGTCCAGCATTTTCTCTAGCGCTACTTTTCTGGGGATTCAAGA
* *
1691218 AAAAAGCAAGATCATTGAATTGTGAC
129 AAAAATCAAGATCATTGACTTGTGAC
1691244 ATAGTCTTGA
Statistics
Matches: 262, Mismatches: 45, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
155 9 0.03
156 248 0.95
157 5 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (154 bp):
GGTAGACCAGTGGATGCACATGCTTCAACTGAATGACCAGATGAAACATTGGGTAATTCAGCCTT
TGGTTGAAGACATGGCCGCAGGTCCAGCATTTTCTCTAGCGCTACTTTTCTGGGGATTCAAGAAA
AAATCAAGATCATTGACTTGTGAC
Found at i:1703082 original size:41 final size:42
Alignment explanation
Indices: 1703013--1703092 Score: 137
Period size: 41 Copynumber: 1.9 Consensus size: 42
1703003 TTTTTTAGGG
1703013 GTTAAATTGAGAAAAAATTGTTAAGTTTTGAGATTAATACAA
1 GTTAAATTGAGAAAAAATTGTTAAGTTTTGAGATTAATACAA
1703055 GTTAAATTGAG-AAAAATT-TTCAAGTTTTGAGATTAATA
1 GTTAAATTGAGAAAAAATTGTT-AAGTTTTGAGATTAATA
1703093 TGAATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
40 2 0.05
41 24 0.65
42 11 0.30
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (42 bp):
GTTAAATTGAGAAAAAATTGTTAAGTTTTGAGATTAATACAA
Found at i:1703994 original size:12 final size:12
Alignment explanation
Indices: 1703976--1704098 Score: 140
Period size: 12 Copynumber: 10.2 Consensus size: 12
1703966 TTTAAATTTA
1703976 TTTCTTTTCTTC
1 TTTCTTTTCTTC
*
1703988 CTTCTTTTCTTC
1 TTTCTTTTCTTC
*
1704000 TTTCTTTTCCTC
1 TTTCTTTTCTTC
*
1704012 TTTCTTCTCTTC
1 TTTCTTTTCTTC
* *
1704024 CTTCTTCTCTTC
1 TTTCTTTTCTTC
* *
1704036 TTTCTTCTCCTC
1 TTTCTTTTCTTC
*
1704048 TTTCTTTTCCTC
1 TTTCTTTTCTTC
1704060 TTTCTTTTCTTCC
1 TTTCTTTTCTT-C
1704073 TTT-TTTTCTTC
1 TTTCTTTTCTTC
* *
1704084 CTTCTTCTCTTC
1 TTTCTTTTCTTC
1704096 TTT
1 TTT
1704099 AGCAGGTCCT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
11 3 0.03
12 89 0.93
13 4 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCTTTTCTTC
Found at i:1704035 original size:48 final size:48
Alignment explanation
Indices: 1703977--1704098 Score: 190
Period size: 48 Copynumber: 2.5 Consensus size: 48
1703967 TTAAATTTAT
*
1703977 TTCTTTTCTTCCTTCTTTTCTTCTTTCTTTTCCTCTTTCTTCTCTTCC
1 TTCTTTTCTTCCTTCTTCTCTTCTTTCTTTTCCTCTTTCTTCTCTTCC
* * * *
1704025 TTCTTCTCTTCTTTCTTCTCCTCTTTCTTTTCCTCTTTCTTTTCTTCC
1 TTCTTTTCTTCCTTCTTCTCTTCTTTCTTTTCCTCTTTCTTCTCTTCC
*
1704073 TTTTTTTCTTCCTTCTTCTCTTCTTT
1 TTCTTTTCTTCCTTCTTCTCTTCTTT
1704099 AGCAGGTCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (48 bp):
TTCTTTTCTTCCTTCTTCTCTTCTTTCTTTTCCTCTTTCTTCTCTTCC
Found at i:1707366 original size:44 final size:45
Alignment explanation
Indices: 1707276--1707404 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1707266 GACAGAACGA
*
1707276 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1707322 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1707366 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1707405 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1718649 original size:22 final size:21
Alignment explanation
Indices: 1718600--1718653 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1718590 GATATGTATT
1718600 AAAAATATAAAATAAATATATA
1 AAAAATA-AAAATAAATATATA
1718622 AAAAATAAAAATACAATA-ATA
1 AAAAATAAAAATA-AATATATA
*
1718643 CATAAATAAAA
1 -AAAAATAAAA
1718654 TTCCAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAATAAAAATAAATATATA
Found at i:1718932 original size:17 final size:18
Alignment explanation
Indices: 1718912--1718946 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1718902 ACTAAAGGGA
1718912 TAATC-TATAAATAAAAT
1 TAATCATATAAATAAAAT
*
1718929 TAATCATTTAAATAAAAT
1 TAATCATATAAATAAAAT
1718947 AAAACGCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATCATATAAATAAAAT
Found at i:1722732 original size:28 final size:28
Alignment explanation
Indices: 1722678--1722733 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1722668 ACTTATAAAG
* ***
1722678 TAAATATTAAAATTCCAAATTTTAAATT
1 TAAAAATTAAAATTCCAAATAAAAAATT
*
1722706 TAAAAATTAAAATTCTAAATAAAAAATT
1 TAAAAATTAAAATTCCAAATAAAAAATT
1722734 ATCAATATTT
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:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAAATTAAAATTCCAAATAAAAAATT
Found at i:1723492 original size:29 final size:29
Alignment explanation
Indices: 1723433--1723492 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1723423 TTTAGTCTAA
* *
1723433 TGTGTAATTTTATACATAAAATTTGATTT
1 TGTGTAATTTTATACATAAAATTTCAATT
* *
1723462 TGTGTATTTTTATACATGAAATTTCAATT
1 TGTGTAATTTTATACATAAAATTTCAATT
1723491 TG
1 TG
1723493 ATCCAATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.52
Consensus pattern (29 bp):
TGTGTAATTTTATACATAAAATTTCAATT
Found at i:1728525 original size:1 final size:1
Alignment explanation
Indices: 1728519--1728544 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1728509 GTATAACATG
1728519 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1728545 GTATTACTCC
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:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1729520 original size:56 final size:56
Alignment explanation
Indices: 1729434--1729547 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
1729424 TAAATGATAG
1729434 AATGAATCCCATCATCAACATCTTCCTCGTGCACTCCACAATGATGACAAGTACTC
1 AATGAATCCCATCATCAACATCTTCCTCGTGCACTCCACAATGATGACAAGTACTC
1729490 AATGAATCCCATCATCAACATCTTCCTCGTGCACTCCACAATGATGACAAGTACTC
1 AATGAATCCCATCATCAACATCTTCCTCGTGCACTCCACAATGATGACAAGTACTC
1729546 AA
1 AA
1729548 AGCACGGAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.25
Consensus pattern (56 bp):
AATGAATCCCATCATCAACATCTTCCTCGTGCACTCCACAATGATGACAAGTACTC
Found at i:1730981 original size:17 final size:17
Alignment explanation
Indices: 1730961--1731002 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1730951 TTTATGTTAT
1730961 AAATTATATAATATAAA
1 AAATTATATAATATAAA
*
1730978 AAATAATATAATATAAA
1 AAATTATATAATATAAA
*
1730995 ACATTATA
1 AAATTATA
1731003 AACGGGCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:1732961 original size:103 final size:104
Alignment explanation
Indices: 1732799--1733005 Score: 353
Period size: 103 Copynumber: 2.0 Consensus size: 104
1732789 AATCTTGACC
* *
1732799 ATTAGTTCAAAAAGTATACTAATTTTTTTATTAAAAAATTATTTAATTTAAACTGTTAAAAATCA
1 ATTAGATCAAAAAGTATACTAATTTTTTTATTAAAAAATTATTTAATTTAAACTGTTAAAAACCA
* *
1732864 CCATAACTAATAAAATAATTAAATAATGACACATAACAT
66 ACATAACTAACAAAATAATTAAATAATGACACATAACAT
* *
1732903 ATTAGATCAAAGAGTATACTAA-TTTTTTGTTAAAAAATTATTTAATTTAAACTGTTAAAAACCA
1 ATTAGATCAAAAAGTATACTAATTTTTTTATTAAAAAATTATTTAATTTAAACTGTTAAAAACCA
1732967 ACATAACTAACAAAATAATTAAATAATGACACATAACAT
66 ACATAACTAACAAAATAATTAAATAATGACACATAACAT
1733006 GTCACATGAA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 77 0.79
104 20 0.21
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (104 bp):
ATTAGATCAAAAAGTATACTAATTTTTTTATTAAAAAATTATTTAATTTAAACTGTTAAAAACCA
ACATAACTAACAAAATAATTAAATAATGACACATAACAT
Found at i:1740817 original size:20 final size:18
Alignment explanation
Indices: 1740792--1740832 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
1740782 AAAACTTTAA
1740792 TTTTATCATTTTAATTAATT
1 TTTTATCATTTT-A-TAATT
*
1740812 TTTTATTATTTTATAATT
1 TTTTATCATTTTATAATT
1740830 TTT
1 TTT
1740833 ATAAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATCATTTTATAATT
Found at i:1744599 original size:18 final size:18
Alignment explanation
Indices: 1744568--1744608 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1744558 ATTATAAAGA
*
1744568 CTTTGATTTTTCAAATTAT
1 CTTT-ATTTCTCAAATTAT
1744587 CTTTATTTCTCAAATTAT
1 CTTTATTTCTCAAATTAT
1744605 -TTTA
1 CTTTA
1744609 GGTGTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (18 bp):
CTTTATTTCTCAAATTAT
Found at i:1745063 original size:13 final size:13
Alignment explanation
Indices: 1745040--1745073 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1745030 TGTATTACAA
1745040 AAAACATTTAAAAT
1 AAAA-ATTTAAAAT
1745054 AAAAATTTAAAAT
1 AAAAATTTAAAAT
*
1745067 ATAAATT
1 AAAAATT
1745074 AAATTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTTAAAAT
Found at i:1747062 original size:17 final size:18
Alignment explanation
Indices: 1747025--1747063 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1747015 AGAATTTATA
*
1747025 AATTATATTTTAAATATT
1 AATTATATTTTAAATAAT
*
1747043 AATTAT-TTTTAATTAAT
1 AATTATATTTTAAATAAT
1747060 AATT
1 AATT
1747064 TTAACACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTATATTTTAAATAAT
Found at i:1755342 original size:20 final size:20
Alignment explanation
Indices: 1755313--1755352 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1755303 GATTCACTAA
*
1755313 ATATACGTATCTTATAAGAG
1 ATATAAGTATCTTATAAGAG
1755333 ATATAAGTATCTTATAAGAG
1 ATATAAGTATCTTATAAGAG
1755353 TGGATCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (20 bp):
ATATAAGTATCTTATAAGAG
Found at i:1761536 original size:25 final size:25
Alignment explanation
Indices: 1761508--1761556 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1761498 GCTGGATCTT
*
1761508 GGGTTGTCGTTTTCCAGAGGATAAA
1 GGGTTGTCGTTTTCCAAAGGATAAA
1761533 GGGTTGTCGTTTTCCAAAGGATAA
1 GGGTTGTCGTTTTCCAAAGGATAA
1761557 TATAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.31, T:0.33
Consensus pattern (25 bp):
GGGTTGTCGTTTTCCAAAGGATAAA
Found at i:1763912 original size:21 final size:23
Alignment explanation
Indices: 1763886--1763933 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
1763876 AATTTGATGC
1763886 TTTTTGCTGTT-GTTT-TCACTA
1 TTTTTGCTGTTCGTTTGTCACTA
* *
1763907 TTTTTGCTTTTCTTTTGTCACTA
1 TTTTTGCTGTTCGTTTGTCACTA
1763930 TTTT
1 TTTT
1763934 GGTGTCGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 3 0.13
23 10 0.43
ACGTcount: A:0.08, C:0.15, G:0.10, T:0.67
Consensus pattern (23 bp):
TTTTTGCTGTTCGTTTGTCACTA
Found at i:1768447 original size:6 final size:6
Alignment explanation
Indices: 1768438--1768463 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1768428 TTTTAATCAT
1768438 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
1768464 ATAATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:1768544 original size:39 final size:41
Alignment explanation
Indices: 1768473--1768558 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 41
1768463 TATAATCAAT
*
1768473 TTTTATTATATTTTTTAATTTGTGTAATGTTTTAAGAATTG
1 TTTTAATATATTTTTTAATTTGTGTAATGTTTTAAGAATTG
* ** * *
1768514 TTTTAATATA-TTTTT-ATTTGTTTCTTGTTTTAATATTTG
1 TTTTAATATATTTTTTAATTTGTGTAATGTTTTAAGAATTG
1768553 TTTTAA
1 TTTTAA
1768559 ATGTATTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 25 0.64
40 5 0.13
41 9 0.23
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.65
Consensus pattern (41 bp):
TTTTAATATATTTTTTAATTTGTGTAATGTTTTAAGAATTG
Found at i:1781353 original size:22 final size:21
Alignment explanation
Indices: 1781327--1781368 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1781317 CTAAATTTGA
1781327 AAATT-TGAAAAGTACAAAAATT
1 AAATTATGAAAA-TA-AAAAATT
1781349 AAATTATGAAAATAAAAAAT
1 AAATTATGAAAATAAAAAAT
1781369 ATAGGACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (21 bp):
AAATTATGAAAATAAAAAATT
Found at i:1782139 original size:28 final size:28
Alignment explanation
Indices: 1782108--1782170 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
1782098 ATATATATAC
* *
1782108 TAAAATTGACCAAAATAAATGTT-AAAAA
1 TAAAATTGA-AAAAATAAATATTGAAAAA
*
1782136 TAAATGTTGAAAAAATAAATATTGAAAAA
1 TAAA-ATTGAAAAAATAAATATTGAAAAA
*
1782165 TTAAAT
1 TAAAAT
1782171 GCTAAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (28 bp):
TAAAATTGAAAAAATAAATATTGAAAAA
Found at i:1782151 original size:15 final size:15
Alignment explanation
Indices: 1782119--1782171 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
1782109 AAAATTGACC
1782119 AAAATAAATGTT--A
1 AAAATAAATGTTGAA
1782132 AAAATAAATGTTGAA
1 AAAATAAATGTTGAA
*
1782147 AAAATAAATATTGAA
1 AAAATAAATGTTGAA
*
1782162 AAATTAAATG
1 AAAATAAATG
1782172 CTAAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
13 12 0.34
15 23 0.66
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (15 bp):
AAAATAAATGTTGAA
Found at i:1805119 original size:18 final size:16
Alignment explanation
Indices: 1805086--1805125 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1805076 TCGTGTCAAC
1805086 AAAAAAATTAAAAATA
1 AAAAAAATTAAAAATA
*
1805102 AAAAAAA-TAATAATA
1 AAAAAAATTAAAAATA
1805117 ATAAAAAAT
1 A-AAAAAAT
1805126 CATAAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAAAATTAAAAATA
Found at i:1805130 original size:16 final size:15
Alignment explanation
Indices: 1805086--1805130 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1805076 TCGTGTCAAC
* *
1805086 AAAAAAATTAAAAAT
1 AAAAAAAATAATAAT
1805101 AAAAAAAATAATAAT
1 AAAAAAAATAATAAT
*
1805116 AATAAAAAATCATAA
1 AA-AAAAAATAATAA
1805131 ATCATAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAAAATAATAAT
Found at i:1805619 original size:23 final size:23
Alignment explanation
Indices: 1805599--1805641 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1805589 TTTTATTAGG
1805599 GTAAATTT-TA-TTAAATTATTA
1 GTAAATTTATATTTAAATTATTA
*
1805620 GTAAATTTATATTTTAATTATT
1 GTAAATTTATATTTAAATTATT
1805642 CAACTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (23 bp):
GTAAATTTATATTTAAATTATTA
Found at i:1805703 original size:31 final size:31
Alignment explanation
Indices: 1805665--1805726 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1805655 TTCTAAAATG
* *
1805665 ATCATTAAATTATT-TGAAAATTTTTATTTAA
1 ATCATTAAACTATTCAG-AAATTTTTATTTAA
*
1805696 ATCATTAAACTATTCAGAAGTTTTTATTTAA
1 ATCATTAAACTATTCAGAAATTTTTATTTAA
1805727 GTCCATCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (31 bp):
ATCATTAAACTATTCAGAAATTTTTATTTAA
Found at i:1810940 original size:15 final size:15
Alignment explanation
Indices: 1810922--1810960 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1810912 TTCATATATA
1810922 TTTTAATTTG-GTTAT
1 TTTTAATTTGTGTT-T
1810937 TTTTAATTTGTGTTT
1 TTTTAATTTGTGTTT
*
1810952 TTTAAATTT
1 TTTTAATTT
1810961 TAGAATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTTAATTTGTGTTT
Found at i:1812061 original size:20 final size:20
Alignment explanation
Indices: 1812023--1812062 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1812013 ACCATTGAAG
* **
1812023 GTTAGGTTAAAGAGTAAATT
1 GTTAGATTAAAGAACAAATT
1812043 GTTAGATTAAAGAACAAATT
1 GTTAGATTAAAGAACAAATT
1812063 AATCCTTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (20 bp):
GTTAGATTAAAGAACAAATT
Found at i:1815066 original size:1 final size:1
Alignment explanation
Indices: 1815062--1815094 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
1815052 TTTTGGTTGG
1815062 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1815095 GCATTTACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1817249 original size:230 final size:230
Alignment explanation
Indices: 1816657--1817578 Score: 1756
Period size: 230 Copynumber: 4.0 Consensus size: 230
1816647 ACTAGATTAC
* *
1816657 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTCTTTCTTTTCAGAAGCATTTTCCCT
1 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
** *
1816722 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCAAAATA
66 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
*
1816787 CTAGACGAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
131 CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
1816852 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
196 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
1816887 AATATCAATGATA-TTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
1 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
*
1816951 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAAACACGACA
66 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
1817016 CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
131 CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
1817081 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
196 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
1817116 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
1 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
1817181 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
66 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
* *
1817246 CTAGACAAGGTGATTAAATTTAAATTGCGTTGAAACATTTATTCAAATATACTCAAGGAGATTAG
131 CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
1817311 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
196 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
1817346 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
1 AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
1817411 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
66 TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
1817476 CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
131 CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
1817541 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
196 TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
1817576 AAT
1 AAT
1817579 GTGACTGATG
Statistics
Matches: 679, Mismatches: 12, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
229 222 0.33
230 457 0.67
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (230 bp):
AATATCAATGATATTTTTTTCCATGCTTATTGGTTTTATTTTTTCTTTTCAGGAGCATTTTCCCT
TGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAAGAAACCACGACA
CTAGACAAGGTGATTAAATTTAAATTGTGTTGAAACACTTATTCAAATATACTCAAGGAGATTAG
TTACTATTAAAATTTGTTATTTGATTCTCAAGGTT
Found at i:1818931 original size:20 final size:22
Alignment explanation
Indices: 1818906--1818946 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1818896 CATATTTCGA
1818906 AAATCTAAT-TCA-ATTTTTTC
1 AAATCTAATCTCACATTTTTTC
1818926 AAATCTAATCTCACATTTTTT
1 AAATCTAATCTCACATTTTTT
1818947 GTTTGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATCTAATCTCACATTTTTTC
Found at i:1819919 original size:21 final size:21
Alignment explanation
Indices: 1819894--1819945 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
1819884 TAACTTATTT
1819894 ATATATTATAATAA-AATGTAA
1 ATATATTATAATAATAAT-TAA
1819915 ATATATT-TAA-AATAATTAA
1 ATATATTATAATAATAATTAA
*
1819934 AAATATTA-AATA
1 ATATATTATAATA
1819946 TTAAATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 13 0.48
20 7 0.26
21 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATATTATAATAATAATTAA
Found at i:1825652 original size:31 final size:30
Alignment explanation
Indices: 1825592--1825651 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
1825582 ACTATGAAGT
1825592 CAAGTTCATATACTAATTTGAACCAAAAAA
1 CAAGTTCATATACTAATTTGAACCAAAAAA
1825622 CAAGTTCAGGTAT-CTAATTTG-ACCAAAAAA
1 CAAGTTCA--TATACTAATTTGAACCAAAAAA
1825652 ATTTAGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 17 0.61
31 8 0.29
32 3 0.11
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (30 bp):
CAAGTTCATATACTAATTTGAACCAAAAAA
Found at i:1825667 original size:27 final size:31
Alignment explanation
Indices: 1825606--1825672 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 31
1825596 TTCATATACT
*
1825606 AATTTGAACCAAAAAACAAGTTCAGGTATCT
1 AATTTGAACCAAAAAACAAGTTCAGGTATCA
*
1825637 AATTTG-ACC-AAAAA-AA-TTTAGGTATCA
1 AATTTGAACCAAAAAACAAGTTCAGGTATCA
1825664 AA-TTGAACC
1 AATTTGAACC
1825673 TTGAGGCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 3 0.09
27 14 0.42
28 2 0.06
29 5 0.15
30 3 0.09
31 6 0.18
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (31 bp):
AATTTGAACCAAAAAACAAGTTCAGGTATCA
Found at i:1827092 original size:21 final size:21
Alignment explanation
Indices: 1827041--1827095 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1827031 GATTTGATTT
* * *
1827041 TAATTTTTATTA-CTTGCTTA
1 TAATTTTTTTTATCATGCTAA
*
1827061 TAAATTATTTTTATCATGCTAA
1 T-AATTTTTTTTATCATGCTAA
1827083 TAATTTTTTTTAT
1 TAATTTTTTTTAT
1827096 AATAATTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 20 0.71
22 7 0.25
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (21 bp):
TAATTTTTTTTATCATGCTAA
Found at i:1834974 original size:29 final size:31
Alignment explanation
Indices: 1834931--1835001 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
1834921 AAATTTATAT
* *
1834931 ATGAATTTTGTTTTAATGTGTACTT-T-GAC
1 ATGAATTTTGATTTAATGTGTAATTATAGAC
* * *
1834960 ATGAATTTTGATTTAGTGTTTAATTATATAC
1 ATGAATTTTGATTTAATGTGTAATTATAGAC
1834991 ATGAATTTTGA
1 ATGAATTTTGA
1835002 ATTGTATTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 21 0.60
30 1 0.03
31 13 0.37
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (31 bp):
ATGAATTTTGATTTAATGTGTAATTATAGAC
Found at i:1845709 original size:30 final size:33
Alignment explanation
Indices: 1845673--1845733 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1845663 AGATAGAACT
*
1845673 TGTAACAGA-AGG-ACTAGTTTGCTC-TTTTGA
1 TGTAACAGACAGGAACTAATTTGCTCATTTTGA
*
1845703 TGTAACATACAGGAACTAATTTGCTCATTTT
1 TGTAACAGACAGGAACTAATTTGCTCATTTT
1845734 TTTTAGTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 3 0.12
32 11 0.42
33 4 0.15
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (33 bp):
TGTAACAGACAGGAACTAATTTGCTCATTTTGA
Found at i:1850794 original size:34 final size:31
Alignment explanation
Indices: 1850743--1850805 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 31
1850733 AAAAATAAAC
1850743 ATTTTTATAGTTATTAAATTTTCTAGAATTTT
1 ATTTTTATAGTTATTAAATTTTCTA-AATTTT
*
1850775 ATTTATTATATGTTTTTAAATTTTCTAAATT
1 ATTT-TTATA-GTTATTAAATTTTCTAAATT
1850806 CAAATGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 4 0.14
33 9 0.32
34 15 0.54
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (31 bp):
ATTTTTATAGTTATTAAATTTTCTAAATTTT
Found at i:1852400 original size:21 final size:21
Alignment explanation
Indices: 1852371--1852413 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1852361 AATATTGATA
1852371 ATTTAAAAATATAA-TTAAAAT
1 ATTTAAAAAT-TAATTTAAAAT
*
1852392 ATTTTAAAATTAATTTAAAAT
1 ATTTAAAAATTAATTTAAAAT
1852413 A
1 A
1852414 AGAGCCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAAAAATTAATTTAAAAT
Found at i:1853098 original size:31 final size:28
Alignment explanation
Indices: 1853042--1853108 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
1853032 TCATAAAATT
1853042 AAAATTTAGTCCTTATACTTTTAATTCTA
1 AAAATTTAGTCCTTATACTTTTAATT-TA
* * *
1853071 AAAATTTAGTCTTTCTACTTTTTTAATTTC
1 AAAATTTAGTCCTTATAC--TTTTAATTTA
1853101 AAAATTTA
1 AAAATTTA
1853109 AGACTAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 16 0.48
30 9 0.27
31 8 0.24
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (28 bp):
AAAATTTAGTCCTTATACTTTTAATTTA
Found at i:1854234 original size:2 final size:2
Alignment explanation
Indices: 1854223--1854259 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1854213 CCATCATTCA
*
1854223 AT AT -T AT AT AT AT AT AT AT AT AT GT 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
1854260 TTTTAAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1855515 original size:2 final size:2
Alignment explanation
Indices: 1855508--1855535 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1855498 CTCCAAACAA
1855508 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
1855536 TTGCGAAGAT
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):
AT
Found at i:1857063 original size:22 final size:22
Alignment explanation
Indices: 1857037--1857099 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
1857027 ATATTATAAC
1857037 ATAGAATCAAATCAATATAAAA
1 ATAGAATCAAATCAATATAAAA
*
1857059 ATAGAATC--AT---TAT-AAC
1 ATAGAATCAAATCAATATAAAA
1857075 ATAGAATCAAATCAATATAAAA
1 ATAGAATCAAATCAATATAAAA
1857097 ATA
1 ATA
1857100 CAACTGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 10 0.30
17 3 0.09
18 2 0.06
20 2 0.06
21 3 0.09
22 13 0.39
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.25
Consensus pattern (22 bp):
ATAGAATCAAATCAATATAAAA
Found at i:1857071 original size:38 final size:37
Alignment explanation
Indices: 1857025--1857099 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 37
1857015 ATTTTTCTAT
1857025 GAATATTATAACATAGAATCAAATCAATATAAAAATA
1 GAATATTATAACATAGAATCAAATCAATATAAAAATA
1857062 GAATCATTATAACATAGAATCAAATCAATATAAAAATA
1 GAAT-ATTATAACATAGAATCAAATCAATATAAAAATA
1857100 CAACTGCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 4 0.11
38 33 0.89
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (37 bp):
GAATATTATAACATAGAATCAAATCAATATAAAAATA
Found at i:1857072 original size:17 final size:16
Alignment explanation
Indices: 1857046--1857084 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1857036 CATAGAATCA
1857046 AATCAATATAAAAATAG
1 AATCAATAT-AAAATAG
* *
1857063 AATCATTATAACATAG
1 AATCAATATAAAATAG
1857079 AATCAA
1 AATCAA
1857085 ATCAATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (16 bp):
AATCAATATAAAATAG
Found at i:1860112 original size:21 final size:21
Alignment explanation
Indices: 1860086--1860128 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1860076 GGGATAATTC
1860086 AATTTCAGCCAATTTAGTAGT
1 AATTTCAGCCAATTTAGTAGT
1860107 AATTTCAGCCAATTTAGTAGT
1 AATTTCAGCCAATTTAGTAGT
1860128 A
1 A
1860129 TCGTGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (21 bp):
AATTTCAGCCAATTTAGTAGT
Found at i:1862119 original size:30 final size:29
Alignment explanation
Indices: 1862069--1862127 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1862059 AATTAGGATA
* *
1862069 AATATTAATTTTATATATAAATTTTGATT
1 AATATTAATTTAATACATAAATTTTGATT
1862098 AATATATAATTTAATACATAAATTTTGATT
1 AATAT-TAATTTAATACATAAATTTTGATT
1862128 TAATGTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (29 bp):
AATATTAATTTAATACATAAATTTTGATT
Found at i:1864130 original size:20 final size:20
Alignment explanation
Indices: 1864089--1864135 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1864079 ATAATTTAAT
1864089 AAATAAAAATAAAAATCTAA
1 AAATAAAAATAAAAATCTAA
** *
1864109 ATCTAAAACTAAAAA--TAA
1 AAATAAAAATAAAAATCTAA
1864127 AAATAAAAA
1 AAATAAAAA
1864136 ACATATAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAAATAAAAATCTAA
Found at i:1865755 original size:35 final size:36
Alignment explanation
Indices: 1865686--1865761 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 36
1865676 TAAGTGAATG
1865686 AAAACTTT-TATAAAAATATATAAAAATATATTTATT
1 AAAA-TTTATATAAAAATATATAAAAATATATTTATT
*
1865722 ATAAATTTATATAAAAATA-ATTAAAACT-T-TTTATT
1 A-AAATTTATATAAAAATATA-TAAAAATATATTTATT
1865757 AAAAT
1 AAAAT
1865762 GAAAAAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
34 4 0.11
35 7 0.19
36 6 0.17
37 19 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (36 bp):
AAAATTTATATAAAAATATATAAAAATATATTTATT
Found at i:1876744 original size:16 final size:15
Alignment explanation
Indices: 1876723--1876752 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1876713 CGTTTGGATT
1876723 TTGGTGGGTCTCGTTG
1 TTGGTGGGT-TCGTTG
1876739 TTGGTGGGTTCGTT
1 TTGGTGGGTTCGTT
1876753 ATCGTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.43, T:0.47
Consensus pattern (15 bp):
TTGGTGGGTTCGTTG
Found at i:1881788 original size:29 final size:30
Alignment explanation
Indices: 1881756--1881821 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
1881746 ATTTATTATT
*
1881756 TTATTTAAGTTTT-AAAATTATTT-TATGT-A
1 TTATTTAA-TTTTAAAAATAATTTATAT-TAA
1881785 TTA-TTAATTTTAAAAATAATTTATATTAA
1 TTATTTAATTTTAAAAATAATTTATATTAA
1881814 TTATTTAA
1 TTATTTAA
1881822 AAATATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
27 4 0.12
28 14 0.44
29 10 0.31
30 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
TTATTTAATTTTAAAAATAATTTATATTAA
Found at i:1881811 original size:22 final size:23
Alignment explanation
Indices: 1881786--1881830 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1881776 TTTTATGTAT
1881786 TATTAA-T-TTTAAAAATAATTTA
1 TATTAATTATTTAAAAAT-ATTTA
1881808 TATTAATTATTTAAAAATATTTA
1 TATTAATTATTTAAAAATATTTA
1881831 AAATTTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 6 0.29
24 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATTATTTAAAAATATTTA
Found at i:1881819 original size:25 final size:26
Alignment explanation
Indices: 1881760--1881830 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
1881750 ATTATTTTAT
* *
1881760 TTAAGTTTTAAAATTATTTTATGTATTA
1 TTAA-TTTTAAAAATAATTTA-GTATTA
1881788 TTAATTTTAAAAATAATTTA-TATTAA
1 TTAATTTTAAAAATAATTTAGTATT-A
1881814 TT-A-TTTAAAAAT-ATTTA
1 TTAATTTTAAAAATAATTTA
1881831 AAATTTATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.12
24 9 0.22
25 5 0.12
26 3 0.08
27 14 0.35
28 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
TTAATTTTAAAAATAATTTAGTATTA
Found at i:1888984 original size:19 final size:19
Alignment explanation
Indices: 1888947--1888984 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1888937 ATTGAAATGA
*
1888947 TTATTTTATTTTATGATAT
1 TTATTTTATTTTATAATAT
1888966 TTATTTTATTATT-TAATAT
1 TTATTTTATT-TTATAATAT
1888985 ATAAGCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTTATTTTATAATAT
Found at i:1890570 original size:30 final size:30
Alignment explanation
Indices: 1890529--1890619 Score: 146
Period size: 30 Copynumber: 3.0 Consensus size: 30
1890519 CTAATCTTAG
*
1890529 CCTTTTCCACCACCAACTCCACTAGCCACT
1 CCTTTTCCACCACCAACTCCACTAGCCACA
*
1890559 CCTTTTTCACCACCAACTCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
* *
1890589 CATTTTCCACCACCAAATCCACTAGCCACA
1 CCTTTTCCACCACCAACTCCACTAGCCACA
1890619 C
1 C
1890620 TTGCTCCATT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.27, C:0.47, G:0.03, T:0.22
Consensus pattern (30 bp):
CCTTTTCCACCACCAACTCCACTAGCCACA
Found at i:1890640 original size:30 final size:30
Alignment explanation
Indices: 1890534--1890661 Score: 143
Period size: 30 Copynumber: 4.3 Consensus size: 30
1890524 CTTAGCCTTT
* *
1890534 TCCACCACCAACTCCACTAGCCACTCCTT-T
1 TCCACCACCAACTCCACTAGCCAC-ACTTGC
* *
1890564 TTCACCACCAACTCCACTAGCCACACATT-T
1 TCCACCACCAACTCCACTAGCCACAC-TTGC
*
1890594 TCCACCACCAAATCCACTAGCCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
** * *
1890624 TCCATTACCTACTCCACTAACCACACTTGC
1 TCCACCACCAACTCCACTAGCCACACTTGC
1890654 TCCACCAC
1 TCCACCAC
1890662 ATTTGTACCT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
29 3 0.04
30 81 0.96
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.22
Consensus pattern (30 bp):
TCCACCACCAACTCCACTAGCCACACTTGC
Found at i:1891240 original size:27 final size:25
Alignment explanation
Indices: 1891159--1891280 Score: 74
Period size: 25 Copynumber: 5.0 Consensus size: 25
1891149 ATTATATTTC
* *
1891159 TTAATATTATATTATATATAT-TCT
1 TTAATACTATATTATATATATATAT
* **
1891183 TT--TAATATATTAGGTATAT-T-T
1 TTAATACTATATTATATATATATAT
* *
1891204 TAAATTCTATATTACGTATATATATAT
1 TTAATACTATATTA--TATATATATAT
* * * *
1891231 TTTATACTATTTTATTTATATATCT
1 TTAATACTATATTATATATATATAT
* *
1891256 TTAATATTATATTATTTATATATAT
1 TTAATACTATATTATATATATATAT
1891281 AAATTTTTTC
Statistics
Matches: 74, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.03
22 15 0.20
23 8 0.11
24 2 0.03
25 35 0.47
26 1 0.01
27 11 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATACTATATTATATATATATAT
Found at i:1891250 original size:25 final size:25
Alignment explanation
Indices: 1891222--1891280 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
1891212 ATATTACGTA
* *
1891222 TATATATATTTTATACTATTTTATT
1 TATATATATTTAATACTATATTATT
* *
1891247 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATT
1891272 TATATATAT
1 TATATATAT
1891281 AAATTTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATT
Found at i:1891331 original size:22 final size:24
Alignment explanation
Indices: 1891303--1891361 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
1891293 ACATGTTATC
1891303 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
1891325 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
1891350 TTATGTACATAT
1 TTATGTATATAT
1891362 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:1891351 original size:25 final size:25
Alignment explanation
Indices: 1891319--1891367 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1891309 ATATATCTTA
**
1891319 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
1891344 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
1891368 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:1891543 original size:16 final size:15
Alignment explanation
Indices: 1891519--1891566 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
1891509 TAATTATTAT
*
1891519 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
1891535 TATTTTAATATTTTA
1 TATTTTAATATTTTA
1891550 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
1891566 T
1 T
1891567 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:1891554 original size:7 final size:8
Alignment explanation
Indices: 1891519--1891570 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
1891509 TAATTATTAT
*
1891519 TATTCTAA
1 TATTTTAA
*
1891527 TATTTTGA
1 TATTTTAA
1891535 TATTTTAA
1 TATTTTAA
1891543 TATTTT-A
1 TATTTTAA
1891550 TATTTTATA
1 TATTTTA-A
*
1891559 TATTTTAT
1 TATTTTAA
1891567 TATT
1 TATT
1891571 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:1899885 original size:23 final size:20
Alignment explanation
Indices: 1899831--1899885 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
1899821 GAATTTGATT
*
1899831 AATATAATATTAATATTTTA
1 AATATAAAATTAATATTTTA
*
1899851 AATATTAGAATTAAATTATTTTAA
1 AATA-TAAAATT-AA-TATTTT-A
1899875 AATATAAAATT
1 AATATAAAATT
1899886 CAGAAGTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 5 0.18
22 2 0.07
23 12 0.43
24 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATATAAAATTAATATTTTA
Found at i:1906262 original size:25 final size:25
Alignment explanation
Indices: 1906214--1906264 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1906204 TAAATTGTTT
1906214 AAAAATAATAATAAAACATTAATTAA
1 AAAAATAATAATAAAACA-TAATTAA
*
1906240 AAAAATAATATATACAACA-AATTAA
1 AAAAATAATA-ATAAAACATAATTAA
1906265 GTCAAGTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 10 0.43
27 7 0.30
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAAATAATAATAAAACATAATTAA
Found at i:1907244 original size:13 final size:13
Alignment explanation
Indices: 1907226--1907250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1907216 ATAATATTGA
1907226 AATTAATTTAATT
1 AATTAATTTAATT
1907239 AATTAATTTAAT
1 AATTAATTTAAT
1907251 CTTTTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:1908978 original size:25 final size:26
Alignment explanation
Indices: 1908950--1909000 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1908940 TTTTTTTTAT
*
1908950 ATTTTTATTTT-TATTTTAAAAAATA
1 ATTTTTATTTTCAATTTTAAAAAATA
1908975 ATTTTTATTTTCGAATTTTAAAAAAT
1 ATTTTTATTTTC-AATTTTAAAAAAT
1909001 TTTAAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
27 12 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTTTATTTTCAATTTTAAAAAATA
Found at i:1909385 original size:15 final size:15
Alignment explanation
Indices: 1909357--1909399 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1909347 TAGATTTGAT
* *
1909357 TATTTTTACTTTTTG
1 TATTTTTATTTTTTA
1909372 TATTTTTATTTTTTA
1 TATTTTTATTTTTTA
* *
1909387 AATTTTAATTTTT
1 TATTTTTATTTTT
1909400 ACTGAACGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (15 bp):
TATTTTTATTTTTTA
Found at i:1911991 original size:17 final size:18
Alignment explanation
Indices: 1911971--1912008 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1911961 ATTTTTTGAT
*
1911971 TAAT-TTTTAATTTTATA
1 TAATGTTTTAATTTTAAA
*
1911988 TAATGTTTTATTTTTAAA
1 TAATGTTTTAATTTTAAA
1912006 TAA
1 TAA
1912009 CAAAAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TAATGTTTTAATTTTAAA
Found at i:1919391 original size:12 final size:12
Alignment explanation
Indices: 1919374--1919398 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1919364 AGTGTAAAAA
1919374 ACATATATATAT
1 ACATATATATAT
1919386 ACATATATATAT
1 ACATATATATAT
1919398 A
1 A
1919399 TGGAAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:1922562 original size:16 final size:16
Alignment explanation
Indices: 1922541--1922573 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1922531 AACCTTGACT
1922541 CCTAAGGGGTCACTGC
1 CCTAAGGGGTCACTGC
1922557 CCTAAGGGGTCACTGC
1 CCTAAGGGGTCACTGC
1922573 C
1 C
1922574 ACCATAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18
Consensus pattern (16 bp):
CCTAAGGGGTCACTGC
Found at i:1923307 original size:79 final size:80
Alignment explanation
Indices: 1923166--1923328 Score: 265
Period size: 79 Copynumber: 2.0 Consensus size: 80
1923156 AGAGATTACT
* * *
1923166 AACTACGATTGAAAGGAATAAAAGATACCCTTCATTCCTCAACCACCCTCCCGCTTCTTTCCTTT
1 AACTACGACTGAAAGGAATAAAAGATACCCTTCATTCCTCAACCACCCTCCCGCCTCATTCCTTT
1923231 CAAACTGCAAAACGA
66 CAAACTGCAAAACGA
* *
1923246 AACT-CGACTGAAAGGAATAAAAGATATCCTTCATTCCTCAACCACCCTCCTGCCTCATTCCTTT
1 AACTACGACTGAAAGGAATAAAAGATACCCTTCATTCCTCAACCACCCTCCCGCCTCATTCCTTT
*
1923310 CAAACTGCAAAACGG
66 CAAACTGCAAAACGA
1923325 AACT
1 AACT
1923329 TGTCTAAAGT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 73 0.95
80 4 0.05
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (80 bp):
AACTACGACTGAAAGGAATAAAAGATACCCTTCATTCCTCAACCACCCTCCCGCCTCATTCCTTT
CAAACTGCAAAACGA
Found at i:1925970 original size:6 final size:6
Alignment explanation
Indices: 1925963--1925992 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1925953 GGAATATCCC
*
1925963 TCTCCC TCTCCA TCTCCA TCTCCA TCTCCA
1 TCTCCA TCTCCA TCTCCA TCTCCA TCTCCA
1925993 AATCATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.53, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCCA
Found at i:1926784 original size:19 final size:19
Alignment explanation
Indices: 1926752--1926814 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1926742 TTTTAAATTG
1926752 ATAT-AAAT-TTATAAAAA
1 ATATAAAATATTATAAAAA
*
1926769 ATATAAAATATTATAAATA
1 ATATAAAATATTATAAAAA
* * *
1926788 TTACAAAATAATAT-AAAA
1 ATATAAAATATTATAAAAA
1926806 ATATAAAAT
1 ATATAAAAT
1926815 TAAATAAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 4 0.11
18 14 0.38
19 19 0.51
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAAAATATTATAAAAA
Found at i:1926809 original size:21 final size:20
Alignment explanation
Indices: 1926783--1926842 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
1926773 AAAATATTAT
1926783 AAATATTACAAAATAATATAA
1 AAATATTA-AAAATAATATAA
*
1926804 AAATA-TAAAATTAA-ATAA
1 AAATATTAAAAATAATATAA
* *
1926822 AACATATTTAAAATTATATAA
1 AA-ATATTAAAAATAATATAA
1926843 GTGCGTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 6 0.19
19 9 0.28
20 8 0.25
21 9 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATATTAAAAATAATATAA
Found at i:1926895 original size:19 final size:19
Alignment explanation
Indices: 1926869--1926923 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1926859 TATAAAAATC
1926869 ATAAAAATTATTTAAA-TT
1 ATAAAAATTATTTAAAGTT
*
1926887 ATCAAAAATTGATATAAAGTT
1 AT-AAAAATT-ATTTAAAGTT
*
1926908 ATAAATATTATTTAAA
1 ATAAAAATTATTTAAA
1926924 AATAATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 12 0.39
21 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
ATAAAAATTATTTAAAGTT
Found at i:1927715 original size:3 final size:3
Alignment explanation
Indices: 1927707--1927745 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1927697 CTTATGAGCG
1927707 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1927746 GGGTAGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1928529 original size:31 final size:30
Alignment explanation
Indices: 1928493--1928563 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
1928483 AGGTTTTAGT
*
1928493 AAAATTTTAAAAGTTTAACGA-GATTTTTTAA
1 AAAATTTTAAAA--TTAACGACAATTTTTTAA
* * *
1928524 AAAATTATGAAATTAATGACAATTTTTTAA
1 AAAATTTTAAAATTAACGACAATTTTTTAA
*
1928554 AAAAATTTAA
1 AAAATTTTAA
1928564 GAGGTTCTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 6 0.19
30 16 0.50
31 10 0.31
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (30 bp):
AAAATTTTAAAATTAACGACAATTTTTTAA
Found at i:1928647 original size:2 final size:2
Alignment explanation
Indices: 1928640--1928679 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1928630 CCGCGTTTGA
1928640 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
1928680 TTATCAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1938083 original size:17 final size:18
Alignment explanation
Indices: 1938063--1938109 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1938053 TTTTTTGCTC
1938063 TTTGTTTTCTGCTTCTT-
1 TTTGTTTTCTGCTTCTTG
* *
1938080 TTTGTTTTTTGCTTGTTG
1 TTTGTTTTCTGCTTCTTG
1938098 TTTGTTTGTCTG
1 TTTGTTT-TCTG
1938110 TTGCTTGCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 7 0.28
19 3 0.12
ACGTcount: A:0.00, C:0.11, G:0.19, T:0.70
Consensus pattern (18 bp):
TTTGTTTTCTGCTTCTTG
Found at i:1938938 original size:43 final size:42
Alignment explanation
Indices: 1938877--1939002 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 42
1938867 GATTTCAATC
* * *
1938877 CTGTTACCCTATTGCTTAGGGGGTTAAGCCCATCATCTTCGAT
1 CTGTTACCCTACTACTTAGGGGGTTAAGCCCATCATCTTCG-G
* * * * ** *
1938920 CTGTTTCCCTACTACTTAGGGGGTTAGGATCTAT-AAATGCGG
1 CTGTTACCCTACTACTTAGGGGGTTAAG-CCCATCATCTTCGG
1938962 CTTGTTACCCTACTACTTAGGGGGTTAAAGCCCATCATCTT
1 C-TGTTACCCTACTACTTAGGGGGTT-AAGCCCATCATCTT
1939003 TGATTTGCTC
Statistics
Matches: 62, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
42 1 0.02
43 54 0.87
44 7 0.11
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (42 bp):
CTGTTACCCTACTACTTAGGGGGTTAAGCCCATCATCTTCGG
Done.