Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold58
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: 1582273
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 125418 characters in sequence are not A, C, G, or T
File 10 of 10
Found at i:1500927 original size:13 final size:13
Alignment explanation
Indices: 1500909--1500934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1500899 ACAAAGATCC
1500909 ATGTATCGATACA
1 ATGTATCGATACA
1500922 ATGTATCGATACA
1 ATGTATCGATACA
1500935 TAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1500930 original size:33 final size:33
Alignment explanation
Indices: 1500888--1500954 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1500878 AAAATTTCCA
***
1500888 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1500921 AATGTATCGATACATAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1500954 A
1 A
1500955 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1501089 original size:21 final size:21
Alignment explanation
Indices: 1501065--1501121 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1501055 CATTTGTAGG
1501065 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1501086 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1501107 ATGTATCGATACATT
1 ATGTATCGATACATT
1501122 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1505507 original size:2 final size:2
Alignment explanation
Indices: 1505502--1505529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1505492 ACGAATAGAA
1505502 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
1505530 GGTAGAAAAG
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:1507159 original size:13 final size:13
Alignment explanation
Indices: 1507141--1507166 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1507131 ATTATAATTA
1507141 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1507154 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1507167 ATTATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAATTTAAAT
Found at i:1508841 original size:17 final size:17
Alignment explanation
Indices: 1508819--1508853 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1508809 AAATTTTGTC
*
1508819 TAAAATATTAAAAAAAT
1 TAAAATATCAAAAAAAT
*
1508836 TAAAATATCATAAAAAT
1 TAAAATATCAAAAAAAT
1508853 T
1 T
1508854 TTATAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAATATCAAAAAAAT
Found at i:1508939 original size:17 final size:18
Alignment explanation
Indices: 1508917--1508954 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1508907 TTAATTTGTA
*
1508917 TTTAAATAAATT-ATTAT
1 TTTAAAAAAATTAATTAT
1508934 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
1508952 TTT
1 TTT
1508955 TAAACTTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:1509481 original size:29 final size:29
Alignment explanation
Indices: 1509407--1509483 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
1509397 TTTTATTGAG
*
1509407 ATAAATTTTATATTTTT-A-TTATACTAAA
1 ATAAATATTA-ATTTTTAATTTATACTAAA
* *
1509435 ATAAA-ATTTAATTATTAATTTATATTAAA
1 ATAAATA-TTAATTTTTAATTTATACTAAA
1509464 ATAAATATTAATTTTTAATT
1 ATAAATATTAATTTTTAATT
1509484 AAGTTAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.12
28 9 0.22
29 26 0.63
30 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
ATAAATATTAATTTTTAATTTATACTAAA
Found at i:1510374 original size:20 final size:20
Alignment explanation
Indices: 1510336--1510375 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1510326 TAATTCGACT
*
1510336 TAAAAATTTATTTTATTATA
1 TAAAAATTTATATTATTATA
1510356 TAAAATATTTATATT-TTATA
1 TAAAA-ATTTATATTATTATA
1510376 ATTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAAATTTATATTATTATA
Found at i:1510382 original size:21 final size:21
Alignment explanation
Indices: 1510335--1510382 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1510325 TTAATTCGAC
* *
1510335 TTAAAAATTTATTTTATTATA
1 TTAAATATTTATATTATTATA
*
1510356 TAAAATATTTATATT-TTATAA
1 TTAAATATTTATATTATTAT-A
1510377 TTAAAT
1 TTAAAT
1510383 TTATAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAAATATTTATATTATTATA
Found at i:1516586 original size:18 final size:18
Alignment explanation
Indices: 1516564--1516613 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
1516554 TCTAAAAATA
*
1516564 ATATAAAAATAATTAATATT
1 ATATAAAAATAA-T-ATAAT
1516584 ATATAAAACATAATATAAT
1 ATATAAAA-ATAATATAAT
*
1516603 ATAAAAAAATA
1 ATATAAAAATA
1516614 TGAACACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 11 0.41
20 9 0.33
21 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATAAAAATAATATAAT
Found at i:1516589 original size:20 final size:22
Alignment explanation
Indices: 1516564--1516604 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1516554 TCTAAAAATA
1516564 ATATAAAA-ATAAT-TAATATT
1 ATATAAAACATAATATAATATT
1516584 ATATAAAACATAATATAATAT
1 ATATAAAACATAATATAATAT
1516605 AAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATAAAACATAATATAATATT
Found at i:1516601 original size:12 final size:11
Alignment explanation
Indices: 1516556--1516601 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1516546 TTTTATGATC
1516556 TAAAAATAATA
1 TAAAAATAATA
1516567 TAAAAATAAT-
1 TAAAAATAATA
* *
1516577 T-AATATTATA
1 TAAAAATAATA
1516587 TAAAACATAATA
1 TAAAA-ATAATA
1516599 TAA
1 TAA
1516602 TATAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 12 0.43
12 8 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:1516903 original size:23 final size:24
Alignment explanation
Indices: 1516872--1516923 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1516862 ATTATAACAT
* * *
1516872 AATACAAATATAATATAATAA-AA
1 AATAAAAATATAACATAAAAATAA
*
1516895 AATAAAAATATTACATAAAAATAA
1 AATAAAAATATAACATAAAAATAA
1516919 AATAA
1 AATAA
1516924 TATGATATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (24 bp):
AATAAAAATATAACATAAAAATAA
Found at i:1517640 original size:14 final size:14
Alignment explanation
Indices: 1517598--1517649 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
1517588 ATTTAATATT
*
1517598 AAAAATTATTTAAA
1 AAAAATTATATAAA
1517612 TAAATAATTTAATATAAA
1 -AAA-AA-TT-ATATAAA
1517630 AAAAATTATATAAA
1 AAAAATTATATAAA
1517644 AAAAAT
1 AAAAAT
1517650 CCAAACCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 13 0.39
15 5 0.15
16 4 0.12
17 5 0.15
18 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTATATAAA
Found at i:1518855 original size:21 final size:21
Alignment explanation
Indices: 1518796--1519022 Score: 166
Period size: 21 Copynumber: 11.0 Consensus size: 21
1518786 TTAAAGTTAG
* *
1518796 CAAAAGTTAAGAAAATCATAT
1 CAAAAGTTAACAAAATTATAT
* * *
1518817 CAAAGACTAAACAAAATTATTT
1 CAAA-AGTTAACAAAATTATAT
*
1518839 CAAAAGTTAATAAAATTATAT
1 CAAAAGTTAACAAAATTATAT
* * *
1518860 -AAAACTTAGCAAATTTATAT
1 CAAAAGTTAACAAAATTATAT
* **
1518880 TAAAAGTTTTCAAAATTATAT
1 CAAAAGTTAACAAAATTATAT
* *
1518901 -AAAATGGTAACAAAACTATAT
1 CAAAA-GTTAACAAAATTATAT
1518922 C-AAA-TTATA-AAAATTATAT
1 CAAAAGTTA-ACAAAATTATAT
* *
1518941 -AAAATGTTATCAAAATCATAT
1 CAAAA-GTTAACAAAATTATAT
1518962 -AAAA-TTATA-AAAATTATAT
1 CAAAAGTTA-ACAAAATTATAT
* *
1518981 AAAAAGTTATCAAAATTATAT
1 CAAAAGTTAACAAAATTATAT
* *
1519002 CAAAAGTTATCAAAACTATAT
1 CAAAAGTTAACAAAATTATAT
1519023 ATAAAATTAT
Statistics
Matches: 163, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
19 26 0.16
20 25 0.15
21 96 0.59
22 16 0.10
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (21 bp):
CAAAAGTTAACAAAATTATAT
Found at i:1518944 original size:40 final size:39
Alignment explanation
Indices: 1518891--1519036 Score: 170
Period size: 40 Copynumber: 3.6 Consensus size: 39
1518881 AAAAGTTTTC
* *
1518891 AAAATTATATAAAATGGTAACAAAACTATATCAAATTATA
1 AAAATTATATAAAATGTTATCAAAA-TATATCAAATTATA
*
1518931 AAAATTATATAAAATGTTATCAAAATCATATAAAATTATA
1 AAAATTATATAAAATGTTATCAAAAT-ATATCAAATTATA
*
1518971 AAAATTATATAAAAAGTTATCAAAATTATATCAAAAGTTATCA
1 AAAATTATATAAAATGTTATCAAAA-TATATC-AAA-TTAT-A
*
1519014 AAACTATATATAAAA--TTATCAAA
1 AAAAT-TATATAAAATGTTATCAAA
1519037 CTATTATAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 10
0.85 0.05 0.09
Matches are distributed among these distances:
39 1 0.01
40 63 0.67
41 4 0.04
42 12 0.13
43 5 0.05
44 9 0.10
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (39 bp):
AAAATTATATAAAATGTTATCAAAATATATCAAATTATA
Found at i:1518962 original size:61 final size:60
Alignment explanation
Indices: 1518874--1519046 Score: 174
Period size: 61 Copynumber: 2.8 Consensus size: 60
1518864 CTTAGCAAAT
* * *
1518874 TTATATTAAAAGTTTTCAAAATTATATAAAATGGTA-ACAAAACTATAT-CAAA-TTATAAAAA
1 TTATA-TAAAAGTTATCAAAATCATATAAAAT--TATA-AAAACTATATAAAAAGTTATAAAAA
* *
1518935 TTATATAAAATGTTATCAAAATCATATAAAATTATAAAAATTATATAAAAAGTTATCAAAA
1 TTATATAAAA-GTTATCAAAATCATATAAAATTATAAAAACTATATAAAAAGTTATAAAAA
* *
1518996 TTATATCAAAAGTTATCAAAACTATATATAAAATTAT-CAAACTATTATAAA
1 TTATAT-AAAAGTTATCAAAA-T-CATATAAAATTATAAAAACTA-TATAAA
1519047 TATTATCAGA
Statistics
Matches: 96, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
59 11 0.11
60 9 0.09
61 48 0.50
62 10 0.10
63 18 0.19
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (60 bp):
TTATATAAAAGTTATCAAAATCATATAAAATTATAAAAACTATATAAAAAGTTATAAAAA
Found at i:1518990 original size:12 final size:11
Alignment explanation
Indices: 1518927--1519032 Score: 73
Period size: 11 Copynumber: 10.1 Consensus size: 11
1518917 TATATCAAAT
1518927 TATAAAAATTA
1 TATAAAAATTA
1518938 TAT-AAAATGT-
1 TATAAAAAT-TA
* *
1518948 TATCAAAATCA
1 TATAAAAATTA
1518959 TAT-AAAA-T-
1 TATAAAAATTA
1518967 TATAAAAATTA
1 TATAAAAATTA
*
1518978 TATAAAAAGT-
1 TATAAAAATTA
*
1518988 TATCAAAATTA
1 TATAAAAATTA
* *
1518999 TATCAAAAGT-
1 TATAAAAATTA
* *
1519009 TATCAAAACTA
1 TATAAAAATTA
1519020 TATATAAAATTA
1 TATA-AAAATTA
1519032 T
1 T
1519033 CAAACTATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 30 0.39
11 33 0.43
12 7 0.09
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.35
Consensus pattern (11 bp):
TATAAAAATTA
Found at i:1519044 original size:21 final size:20
Alignment explanation
Indices: 1518828--1519152 Score: 231
Period size: 21 Copynumber: 15.9 Consensus size: 20
1518818 AAAGACTAAA
*
1518828 CAAAATTATTTCAAAAGTTAAT
1 CAAAATTATAT-AAAAGTT-AT
* *
1518850 -AAAATTATATAAAACTTAG
1 CAAAATTATATAAAAGTTAT
* *
1518869 CAAATTTATATTAAAAGTTTT
1 CAAAATTATA-TAAAAGTTAT
* *
1518890 CAAAATTATATAAAATGGTAA
1 CAAAATTATATAAAA-GTTAT
* *
1518911 CAAAACTATATCAAA-TTAT
1 CAAAATTATATAAAAGTTAT
*
1518930 AAAAATTATATAAAATGTTAT
1 CAAAATTATATAAAA-GTTAT
*
1518951 CAAAATCATATAAAA-TTAT
1 CAAAATTATATAAAAGTTAT
*
1518970 AAAAATTATATAAAAAGTTAT
1 CAAAATTATAT-AAAAGTTAT
1518991 CAAAATTATATCAAAAGTTAT
1 CAAAATTATAT-AAAAGTTAT
1519012 CAAAACTATATATAAAA-TTAT
1 CAAAA-T-TATATAAAAGTTAT
*
1519033 CAAACTATTATA-AATA-TTAT
1 CAAA--ATTATATAAAAGTTAT
*
1519053 CAGAAATCTAT-CAAAAGTTA-
1 CA-AAAT-TATATAAAAGTTAT
* *
1519073 CTAAATTAT-TAGAAATATTAT
1 CAAAATTATATA-AAA-GTTAT
* * *
1519094 CAAAATTTTTTTAAA-TT-T
1 CAAAATTATATAAAAGTTAT
* *
1519112 CAAAATTATATAAAAGCATAC
1 CAAAATTATATAAAAG-TTAT
1519133 CAAAATTATATTAAAAGTTA
1 CAAAATTATA-TAAAAGTTA
1519153 CGACAATTAT
Statistics
Matches: 242, Mismatches: 38, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
18 17 0.07
19 39 0.16
20 43 0.18
21 124 0.51
22 13 0.05
23 6 0.02
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (20 bp):
CAAAATTATATAAAAGTTAT
Found at i:1520518 original size:39 final size:38
Alignment explanation
Indices: 1520475--1520549 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
1520465 ACAAATGCTG
1520475 TCAAAATCATATTATATA-TTACAAAATAATAAAATCATA
1 TCAAAATCATATT-TA-AGTTACAAAATAATAAAATCATA
*
1520514 TCAAAATTATATTTAAGGTTACAAAATAATAAAATC
1 TCAAAATCATATTTAA-GTTACAAAATAATAAAATC
1520550 TTATTAAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
37 1 0.03
38 2 0.06
39 30 0.91
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (38 bp):
TCAAAATCATATTTAAGTTACAAAATAATAAAATCATA
Found at i:1525487 original size:18 final size:19
Alignment explanation
Indices: 1525460--1525497 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1525450 TAAAATAAAA
*
1525460 TTTTATTAAT-TTTAATAT
1 TTTTAATAATATTTAATAT
*
1525478 TTTTAATAATATTTATTAT
1 TTTTAATAATATTTAATAT
1525497 T
1 T
1525498 AATAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAATAATATTTAATAT
Found at i:1525518 original size:17 final size:17
Alignment explanation
Indices: 1525475--1525515 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1525465 TTAATTTTAA
*
1525475 TATTTTTAAT-AATATT
1 TATTATTAATAAATATT
1525491 TATTATTAATAAATATT
1 TATTATTAATAAATATT
1525508 TA-TATTAA
1 TATTATTAA
1525516 ATATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATTAATAAATATT
Found at i:1526598 original size:15 final size:16
Alignment explanation
Indices: 1526571--1526600 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1526561 ATTTTCACAA
1526571 AAAAAATTCAAAAGAT
1 AAAAAATTCAAAAGAT
1526587 AAAAAATT-AAAAGA
1 AAAAAATTCAAAAGA
1526601 GAAGAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAAAATTCAAAAGAT
Found at i:1526608 original size:16 final size:16
Alignment explanation
Indices: 1526571--1526608 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1526561 ATTTTCACAA
*
1526571 AAAAAATTCAAAAGAT
1 AAAAAATTCAAAAGAG
1526587 AAAAAATT-AAAAGAG
1 AAAAAATTCAAAAGAG
1526602 AAGAAAA
1 AA-AAAA
1526609 GTGAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAAATTCAAAAGAG
Found at i:1529000 original size:15 final size:16
Alignment explanation
Indices: 1528980--1529017 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1528970 GATGCAGTGT
1528980 TCCTTGGC-GCAACGC
1 TCCTTGGCAGCAACGC
*
1528995 TCCTTGACAGCAACGC
1 TCCTTGGCAGCAACGC
*
1529011 TCTTTGG
1 TCCTTGG
1529018 TCATTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.16, C:0.34, G:0.24, T:0.26
Consensus pattern (16 bp):
TCCTTGGCAGCAACGC
Found at i:1537504 original size:16 final size:16
Alignment explanation
Indices: 1537483--1537514 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1537473 GTTTGGATAA
1537483 GTTCGGGTTCGAATTT
1 GTTCGGGTTCGAATTT
*
1537499 GTTCGGGTTCGGATTT
1 GTTCGGGTTCGAATTT
1537515 AAATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.12, G:0.34, T:0.44
Consensus pattern (16 bp):
GTTCGGGTTCGAATTT
Found at i:1537683 original size:20 final size:19
Alignment explanation
Indices: 1537658--1537712 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1537648 TATATTTAAT
*
1537658 TATTTATTTATTAAAATTTA
1 TATTTATATA-TAAAATTTA
1537678 TATTTATATATAAAA-TTA
1 TATTTATATATAAAATTTA
*
1537696 -ATTTGTTATATAAAATT
1 TATTT-ATATATAAAATT
1537713 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 4 0.13
18 12 0.39
19 6 0.19
20 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTTATATATAAAATTTA
Found at i:1537726 original size:18 final size:18
Alignment explanation
Indices: 1537687--1537726 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1537677 ATATTTATAT
*
1537687 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
*
1537705 ATAAAATTAATTTTTTAA
1 ATAAAATTAATTTGTTAA
1537723 ATAA
1 ATAA
1537727 TTTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:1539757 original size:32 final size:36
Alignment explanation
Indices: 1539699--1539790 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 36
1539689 ATATTATAAT
1539699 TATATTTAATATATTATATATTTATATAAATTTTGA
1 TATATTTAATATATTATATATTTATATAAATTTTGA
*
1539735 TATA-TTAATA-ATT-TAT-TTTATATAAATTTTAA
1 TATATTTAATATATTATATATTTATATAAATTTTGA
**
1539767 TACGTTT-ATATATT-TATA-TTATAT
1 TATATTTAATATATTATATATTTATAT
1539791 TTGTATTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
32 20 0.40
33 17 0.34
34 3 0.06
35 6 0.12
36 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (36 bp):
TATATTTAATATATTATATATTTATATAAATTTTGA
Found at i:1540101 original size:9 final size:9
Alignment explanation
Indices: 1540087--1540111 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1540077 AAATTAATTA
1540087 AAAAATTTT
1 AAAAATTTT
1540096 AAAAATTTT
1 AAAAATTTT
1540105 AAAAATT
1 AAAAATT
1540112 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAAAATTTT
Found at i:1540117 original size:9 final size:8
Alignment explanation
Indices: 1540082--1540130 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
1540072 AAATAAAATT
1540082 AATTAAAA
1 AATTAAAA
1540090 AATTTTAAAA
1 AA--TTAAAA
* *
1540100 ATTTTAAA
1 AATTAAAA
1540108 AATTAAAA
1 AATTAAAA
1540116 AATTAAAA
1 AATTAAAA
*
1540124 AAATAAA
1 AATTAAA
1540131 TAATATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 27 0.79
10 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AATTAAAA
Found at i:1542521 original size:20 final size:20
Alignment explanation
Indices: 1542475--1542531 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
1542465 TTGTATCGAC
*
1542475 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
1542494 TC-ATTGTATTGATACATGG
1 ACAATTGTATCGATACATGG
1542513 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
1542532 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:1542585 original size:20 final size:20
Alignment explanation
Indices: 1542560--1542610 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1542550 TTACCACTGT
*
1542560 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
1542580 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
1542600 TTGTATCGATA
1 TTGTATCGATA
1542611 TATTGCTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:1544445 original size:18 final size:17
Alignment explanation
Indices: 1544419--1544475 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 17
1544409 ATAATTTACT
1544419 TAAAAATTAATTTTATA
1 TAAAAATTAATTTTATA
1544436 TAACAAATTAATTTTATA
1 TAA-AAATTAATTTTATA
1544454 TAAAAATATAAATTTTA-A
1 TAAAAAT-T-AATTTTATA
1544472 TAAA
1 TAAA
1544476 TAATGTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.19
18 23 0.62
19 7 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAATTAATTTTATA
Found at i:1544639 original size:6 final size:6
Alignment explanation
Indices: 1544628--1544664 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1544618 CTCAAAATTG
* *
1544628 ACTTGA ACTTGA ACTTGA ACTTGA ACCTGA ACCTGA A
1 ACTTGA ACTTGA ACTTGA ACTTGA ACTTGA ACTTGA A
1544665 TCCAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (6 bp):
ACTTGA
Found at i:1544814 original size:16 final size:16
Alignment explanation
Indices: 1544780--1544814 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1544770 ATTGAAATTC
*
1544780 AAAATAATCCAAATCT
1 AAAATAATCCAAATAT
*
1544796 AAAATAATTCAAATAT
1 AAAATAATCCAAATAT
1544812 AAA
1 AAA
1544815 TTAACCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAATCCAAATAT
Found at i:1544918 original size:2 final size:2
Alignment explanation
Indices: 1544911--1544942 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1544901 TAAAAGCATC
1544911 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
1544943 ACTAATTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1545099 original size:12 final size:12
Alignment explanation
Indices: 1545069--1545093 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1545059 AATATTTATG
1545069 TATTTATATTTT
1 TATTTATATTTT
1545081 TATTTATATTTT
1 TATTTATATTTT
1545093 T
1 T
1545094 TATTATTTAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:1545102 original size:20 final size:20
Alignment explanation
Indices: 1545061--1545102 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1545051 AAAAGAAAAA
*
1545061 TATTTATGTATTTATATTTT
1 TATTTATATATTTATATTTT
*
1545081 TATTTATAT-TTTTTATTATT
1 TATTTATATATTTATATT-TT
1545101 TA
1 TA
1545103 AAATATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTATATATTTATATTTT
Found at i:1545270 original size:31 final size:32
Alignment explanation
Indices: 1545232--1545296 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
1545222 AAATATTAAA
*
1545232 ATTTATATAAATTTTTATACTTTAAT-TATTC
1 ATTTATATAAATTTTGATACTTTAATATATTC
* * *
1545263 ATTTATATACATTTTGATATTTTCATATATTC
1 ATTTATATAAATTTTGATACTTTAATATATTC
1545295 AT
1 AT
1545297 GTCATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.57
Consensus pattern (32 bp):
ATTTATATAAATTTTGATACTTTAATATATTC
Found at i:1545468 original size:21 final size:22
Alignment explanation
Indices: 1545442--1545484 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1545432 TATCATGTTT
*
1545442 ATATTTTGTTTAA-ATTTATAA
1 ATATTTTATTTAATATTTATAA
*
1545463 ATATTTTATTTAATTTTTATAA
1 ATATTTTATTTAATATTTATAA
1545485 TGATTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATTTTATTTAATATTTATAA
Found at i:1548450 original size:5 final size:5
Alignment explanation
Indices: 1548440--1548478 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
1548430 GGGCCAACTG
1548440 TGACC TGACC TGACC TGACC TGACC TGACC TGA-C TGACC
1 TGACC TGACC TGACC TGACC TGACC TGACC TGACC TGACC
1548479 CCACACTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (5 bp):
TGACC
Found at i:1549304 original size:5 final size:5
Alignment explanation
Indices: 1549294--1549324 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1549284 TATATCTAGC
*
1549294 ATATT ATATT ATATT GTATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT ATATT A
1549325 AAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:1550552 original size:12 final size:12
Alignment explanation
Indices: 1550535--1550575 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
1550525 TCATCTCAAA
1550535 TAATAATTTTAT
1 TAATAATTTTAT
1550547 TAATAA-TTTAT
1 TAATAATTTTAT
*
1550558 TAA-AATTTAAT
1 TAATAATTTTAT
*
1550569 AAATAAT
1 TAATAAT
1550576 ATTTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 2 0.08
11 14 0.56
12 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TAATAATTTTAT
Found at i:1554609 original size:2 final size:2
Alignment explanation
Indices: 1554602--1554626 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1554592 AACTATTTTC
1554602 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 A
1554627 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1555126 original size:16 final size:16
Alignment explanation
Indices: 1555107--1555160 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
1555097 AAATTTAAAA
1555107 AATATTAAAATATTTT
1 AATATTAAAATATTTT
1555123 AATA-TAAAATTATTTT
1 AATATTAAAA-TATTTT
* *
1555139 AATAATATAAT-TTTT
1 AATATTAAAATATTTT
1555154 AATATTA
1 AATATTA
1555161 TTAAACATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 15 0.44
16 15 0.44
17 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTAAAATATTTT
Found at i:1555132 original size:15 final size:15
Alignment explanation
Indices: 1555107--1555158 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
1555097 AAATTTAAAA
1555107 AATATTAAAATATTTT
1 AATA-TAAAATATTTT
1555123 AATATAAAATTATTTT
1 AATATAAAA-TATTTT
*
1555139 AATAATATAAT-TTTT
1 AAT-ATAAAATATTTT
1555154 AATAT
1 AATAT
1555159 TATTAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.06
15 12 0.36
16 14 0.42
17 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATAAAATATTTT
Found at i:1555196 original size:22 final size:23
Alignment explanation
Indices: 1555133--1555197 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
1555123 AATATAAAAT
* *
1555133 TATTTTAATAATATAATTTTTAA
1 TATTTTAAAAATATAATATTTAA
* *
1555156 TATTATTAAACATA-CATATTT-A
1 TATT-TTAAAAATATAATATTTAA
1555178 TATTTTAAAAATATAATATT
1 TATTTTAAAAATATAATATT
1555198 ATTTTAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 8 0.24
22 10 0.29
23 9 0.26
24 7 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAAAATATAATATTTAA
Found at i:1555264 original size:47 final size:50
Alignment explanation
Indices: 1555171--1555272 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 50
1555161 TTAAACATAC
* *
1555171 ATATTT-ATATTTTAAAAATATAATATTATTTTAATAATAAATTATTAAT
1 ATATTTAATATTTTAAAAATATAATAGTATTTTAATAATAAAATATTAAT
* *
1555220 ATATTTAATATTTTAATAA-A-AATAGTA-TTTAATAA-AACAATATTATT
1 ATATTTAATATTTTAAAAATATAATAGTATTTTAATAATAA-AATATTAAT
1555267 AT-TTTA
1 ATATTTA
1555273 GTAATAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
46 6 0.13
47 17 0.36
48 6 0.13
49 7 0.15
50 11 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (50 bp):
ATATTTAATATTTTAAAAATATAATAGTATTTTAATAATAAAATATTAAT
Found at i:1555493 original size:16 final size:17
Alignment explanation
Indices: 1555461--1555495 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1555451 TAGAAATAAC
1555461 ATTTTAATAATTATTAT
1 ATTTTAATAATTATTAT
*
1555478 ATTTTAA-AATTTTTAT
1 ATTTTAATAATTATTAT
1555494 AT
1 AT
1555496 AATTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTAATAATTATTAT
Found at i:1555733 original size:20 final size:21
Alignment explanation
Indices: 1555698--1555736 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1555688 ATAATATTTT
*
1555698 AATAATAATTATATTTATATA
1 AATAATAATAATATTTATATA
1555719 AATAATAA-AATATTTATA
1 AATAATAATAATATTTATA
1555737 CAATTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATAATAATATTTATATA
Found at i:1556013 original size:15 final size:16
Alignment explanation
Indices: 1555988--1556024 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1555978 AATTTCTACT
1555988 TTTTTTAAAAAAATT-A
1 TTTTTT-AAAAAATTAA
1556004 TTTTTT-AAAAATTAA
1 TTTTTTAAAAAATTAA
1556019 TTTTTT
1 TTTTTT
1556025 GTGAAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTTAAAAAATTAA
Found at i:1557271 original size:172 final size:173
Alignment explanation
Indices: 1556970--1557687 Score: 607
Period size: 173 Copynumber: 4.1 Consensus size: 173
1556960 AATTATTAGG
* *
1556970 TAATTTTAGATATTTT-ATAATAAAATGAATTTACCGGATTAAAAATTAAGAAATATTAAGTCTA
1 TAATTTTAGATATTTTAATAATAAAAGGAATTTACCAGATTAAAAATTAAGAAATATTAAGTCTA
* * *
1557034 AAGAAAAACATAAATTGAAACTTTCATATTAAAATATAATAATTTCTCAAGCCAAAAAATTTTTT
66 AAGAAAAACATAAATTAAAACTTTCATATTAAAATAGAACAATTTCTCAAGCC-AAAAATTTTTT
* * *
1557099 TTTACATAATTTTAGATTTTAAAAATTTTTAAAAATTTATTACA
130 TTTACATAATTTTAAATTTTAAAAATTTTTAAAAATTTATCAAA
* *
1557143 TAATTTTAGATATTTTAATAATAAAAGGCATTTACCATATTAAAAATTAA-AAATATTAAGTCTA
1 TAATTTTAGATATTTTAATAATAAAAGGAATTTACCAGATTAAAAATTAAGAAATATTAAGTCTA
** * * * *
1557207 AA-AAAAACATAAATTAAAACTTTTGTGTTAACAAT-GAACAGTTTCTCAAGCCCAAATTTTTTT
66 AAGAAAAACATAAATTAAAACTTTCATATTAA-AATAGAACAATTTCTCAAGCCAAAAATTTTTT
* *
1557270 TTTACATAATTTTAAATTTTGAAAATTTTTAAATATTTATCAAA
130 TTTACATAATTTTAAATTTTAAAAATTTTTAAAAATTTATCAAA
* *** * *
1557314 TAATTTTAGATATTTTAATAATAAAA-TATATTTATTGGATTAAAAAATTATGAAATAATAAGTC
1 TAATTTTAGATATTTTAATAATAAAAGGA-ATTTACCAGATT-AAAAATTAAGAAATATTAAGTC
* * * * * **** * ** **
1557378 TGAA-AAAAATATAAATTGATACTTTCGTATTAAAATATGATTTTGTTTCTTAAGTGTAAAAAAA
64 TAAAGAAAAACATAAATTAAAACTTTCATATTAAAATA-GA-ACAATTTCTCAAG-CCAAAAATT
*** * * *
1557442 TCGCTTTACATAATTTTAGATTTTTGAAAATTTTTAAATATTTA-CAAGA
126 TTTTTTTACATAATTTTA-AATTTTAAAAATTTTTAAAAATTTATCAA-A
* * ** * * * *
1557491 TTATTTTAGATATTTTAATAATAAAA-TACATTTATTAGGTTAAAAAATTATGAAATAATAACTC
1 TAATTTTAGATATTTTAATAATAAAAGGA-ATTTACCAGATT-AAAAATTAAGAAATATTAAGTC
** * * * * * * * * * *
1557555 T-AA-AAAAGTATATATTGATATTTTCATATTAAAATACAATAGTTTCTTAA-ACATAAAAATTT
64 TAAAGAAAAACATAAATTAAAACTTTCATATTAAAATAGAACAATTTCTCAAGCCA-AAAATTTT
* * *
1557617 ATTTT-CTATAATTTTAAATTTT-AATATTTTTAAAATATTAATCAAA
128 TTTTTAC-ATAATTTTAAATTTTAAAAATTTTTAAAA-ATTTATCAAA
*
1557663 TAATTTTAAATATTTTAATAATAAA
1 TAATTTTAGATATTTTAATAATAAA
1557688 TATATTTAAA
Statistics
Matches: 460, Mismatches: 70, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
171 93 0.20
172 85 0.18
173 94 0.20
174 41 0.09
175 10 0.02
176 52 0.11
177 85 0.18
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (173 bp):
TAATTTTAGATATTTTAATAATAAAAGGAATTTACCAGATTAAAAATTAAGAAATATTAAGTCTA
AAGAAAAACATAAATTAAAACTTTCATATTAAAATAGAACAATTTCTCAAGCCAAAAATTTTTTT
TTACATAATTTTAAATTTTAAAAATTTTTAAAAATTTATCAAA
Found at i:1557320 original size:171 final size:173
Alignment explanation
Indices: 1556970--1557695 Score: 713
Period size: 171 Copynumber: 4.2 Consensus size: 173
1556960 AATTATTAGG
* *
1556970 TAATTTTAGATATTTT-ATAATAAAATGA-ATTTACCGGATT-AAAAATTA-AGAAATATTAAGT
1 TAATTTTAGATATTTTAATAATAAAAT-ACATTTACCAGATTAAAAAATTATA-AAATAATAAGT
* *
1557031 CTAAAGAAAAACATAAATTGAAACTTTCATATTAAAATATAATAATTTCTCAAGCCAAAAAATTT
64 CTAAA-AAAAACATAAATTGAAACTTTCATATTAAAATAGAATAGTTTCTCAAGCCAAAAAA-TT
* * * * *
1557096 TTTTTTACATAATTTTAGATTTTAAAAATTTTTAAAAATTTATTACA
127 TTTTTTACATAATTTTAAATTTTGAAAATTTTTAAATATTTATCAAA
** * *
1557143 TAATTTTAGATATTTTAATAATAAAAGGCATTTACCATATT-AAAAATTA-AAAATATTAAGTCT
1 TAATTTTAGATATTTTAATAATAAAATACATTTACCAGATTAAAAAATTATAAAATAATAAGTCT
* ** * * * **
1557206 AAAAAAAACATAAATTAAAACTTTTGTGTTAACAAT-GAACAGTTTCTCAAGCCCAAATTTTTTT
66 AAAAAAAACATAAATTGAAACTTTCATATTAA-AATAGAATAGTTTCTCAAGCCAAAAAATTTTT
1557270 TTTACATAATTTTAAATTTTGAAAATTTTTAAATATTTATCAAA
130 TTTACATAATTTTAAATTTTGAAAATTTTTAAATATTTATCAAA
* *** *
1557314 TAATTTTAGATATTTTAATAATAAAATATATTTATTGGATTAAAAAATTATGAAATAATAAGTCT
1 TAATTTTAGATATTTTAATAATAAAATACATTTACCAGATTAAAAAATTATAAAATAATAAGTCT
* * * * * * * ** * *
1557379 GAAAAAAATATAAATTGATACTTTCGTATTAAAATATGATTTTGTTTCTTAAGTGTAAAAAAATC
66 AAAAAAAACATAAATTGAAACTTTCATATTAAAATA-GA-ATAGTTTCTCAAG-CCAAAAAATTT
** *
1557444 GCTTTACATAATTTTAGATTTTTGAAAATTTTTAAATATTTA-CAAGA
128 TTTTTACATAATTTTA-AATTTTGAAAATTTTTAAATATTTATCAA-A
* ** * * *
1557491 TTATTTTAGATATTTTAATAATAAAATACATTTATTAGGTTAAAAAATTATGAAATAATAACTCT
1 TAATTTTAGATATTTTAATAATAAAATACATTTACCAGATTAAAAAATTATAAAATAATAAGTCT
** * * * * * * *
1557556 -AAAAAAGTATATATTGATATTTTCATATTAAAATACAATAGTTTCTTAA-ACATAAAAATTTAT
66 AAAAAAAACATAAATTGAAACTTTCATATTAAAATAGAATAGTTTCTCAAGCCA-AAAAATTTTT
* *
1557619 TTT-CTATAATTTTAAATTTT-AATATTTTTAAAATATTAATCAAA
130 TTTAC-ATAATTTTAAATTTTGAAAATTTTT-AAATATTTATCAAA
* *
1557663 TAATTTTAAATATTTTAATAAT-AAATATATTTA
1 TAATTTTAGATATTTTAATAATAAAATACATTTA
1557696 AAAAGTAAAT
Statistics
Matches: 466, Mismatches: 72, Indels: 32
0.82 0.13 0.06
Matches are distributed among these distances:
171 96 0.21
172 89 0.19
173 94 0.20
174 40 0.09
175 10 0.02
176 52 0.11
177 85 0.18
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (173 bp):
TAATTTTAGATATTTTAATAATAAAATACATTTACCAGATTAAAAAATTATAAAATAATAAGTCT
AAAAAAAACATAAATTGAAACTTTCATATTAAAATAGAATAGTTTCTCAAGCCAAAAAATTTTTT
TTACATAATTTTAAATTTTGAAAATTTTTAAATATTTATCAAA
Found at i:1557664 original size:349 final size:345
Alignment explanation
Indices: 1556970--1557695 Score: 806
Period size: 349 Copynumber: 2.1 Consensus size: 345
1556960 AATTATTAGG
*
1556970 TAATTTTAGATATTTT-ATAATAAAATGA-ATTTACCGGATTAAAAATTAAGAAATATTAAGTCT
1 TAATTTTAGATATTTTAATAATAAAAT-ATATTTACCGGATTAAAAATTAAGAAATAATAAGTCT
* **
1557033 AAAGAAAAACATAAATTGAAACTTTCATATTAAAATATAATAATTTCTCAAGCCAAAAAATTTTT
65 AAAGAAAAACATAAATTGAAACTTTCATATTAAAATATAATAATTTCTCAAGCCAAAAAATATCG
* **
1557098 TTTTACATAATTTTAGATTTTAAAAATTTTTAAAAATTTATTACATAATTTTAGATATTTTAATA
130 CTTTACATAATTTTAGATTTTAAAAATTTTTAAAAATTTACAACATAATTTTAGATATTTTAATA
* * * *
1557163 ATAAAAGGCATTTACCATATTAAAAATTAAAAATATTAAGTCTAAAAAAAACATAAATTAAAACT
195 ATAAAAGACATTTACCAGATTAAAAATTAAAAATAATAACTCTAAAAAAAACATAAATTAAAACT
* * * * * ** *
1557228 TTTGTGTTAACAATGAACAGTTTCTCAAGCCCAAATTTTTTTTTTACATAATTTTAAATTTTGAA
260 TTTATATTAACAATCAACAGTTTCTCAAACACAAAAATTTATTTTACATAATTTTAAATTTTGAA
*
1557293 AATTTTTAAATATTTATCAAA
325 AATTTTTAAATATTAATCAAA
** *
1557314 TAATTTTAGATATTTTAATAATAAAATATATTTATTGGATTAAAAAATTATGAAATAATAAGTCT
1 TAATTTTAGATATTTTAATAATAAAATATATTTACCGGATT-AAAAATTAAGAAATAATAAGTCT
* * * * * ** * **
1557379 GAA-AAAAATATAAATTGATACTTTCGTATTAAAATATGATTTTGTTTCTTAAGTGTAAAAAA-A
65 AAAGAAAAACATAAATTGAAACTTTCATATTAAAATAT-A-ATAATTTCTCAAG-CCAAAAAATA
* * * *
1557442 TCGCTTTACATAATTTTAGATTTTTGAAAATTTTTAAATATTTACAAGATTATTTTAGATATTTT
127 TCGCTTTACATAATTTTAGA-TTTTAAAAATTTTTAAAAATTTACAACATAATTTTAGATATTTT
* ** * * ** *
1557507 AATAATAAAATACATTTATTAGGTTAAAAAATTATGAAATAATAACTCT-AAAAAAGTATATATT
191 AATAATAAAAGACATTTACCAGATT-AAAAATTA-AAAATAATAACTCTAAAAAAAACATAAATT
* * * * *
1557571 GATA-TTTTCATATTAA-AATACAATAGTTTCTTAAACATAAAAATTTATTTT-CTATAATTTTA
254 AAAACTTTT-ATATTAACAAT-CAACAGTTTCTCAAACACAAAAATTTATTTTAC-ATAATTTTA
*
1557633 AATTTT-AATATTTTTAAAATATTAATCAAA
316 AATTTTGAAAATTTTT-AAATATTAATCAAA
*
1557663 TAATTTTAAATATTTTAATAAT-AAATATATTTA
1 TAATTTTAGATATTTTAATAATAAAATATATTTA
1557696 AAAAGTAAAT
Statistics
Matches: 317, Mismatches: 52, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
344 17 0.05
345 51 0.16
346 24 0.08
347 26 0.08
348 90 0.28
349 98 0.31
350 11 0.03
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (345 bp):
TAATTTTAGATATTTTAATAATAAAATATATTTACCGGATTAAAAATTAAGAAATAATAAGTCTA
AAGAAAAACATAAATTGAAACTTTCATATTAAAATATAATAATTTCTCAAGCCAAAAAATATCGC
TTTACATAATTTTAGATTTTAAAAATTTTTAAAAATTTACAACATAATTTTAGATATTTTAATAA
TAAAAGACATTTACCAGATTAAAAATTAAAAATAATAACTCTAAAAAAAACATAAATTAAAACTT
TTATATTAACAATCAACAGTTTCTCAAACACAAAAATTTATTTTACATAATTTTAAATTTTGAAA
ATTTTTAAATATTAATCAAA
Found at i:1557864 original size:29 final size:29
Alignment explanation
Indices: 1557820--1557897 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
1557810 AGTGTCAAGT
* * *
1557820 AAAATAATAGTGTTTTAATAAATAGTTTC
1 AAAATAATATTATTTTAATAAATAGTATC
* * *
1557849 AAAATAATATTATTTTGATAATTTGTATC
1 AAAATAATATTATTTTAATAAATAGTATC
* *
1557878 AAAATTAAGATTACTTTAAT
1 AAAA-TAATATTATTTTAAT
1557898 TAATCTAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (29 bp):
AAAATAATATTATTTTAATAAATAGTATC
Found at i:1559199 original size:2 final size:2
Alignment explanation
Indices: 1559192--1559230 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1559182 TATGGTGTCT
1559192 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 T
1559231 TCATTTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1559645 original size:23 final size:23
Alignment explanation
Indices: 1559602--1559645 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1559592 AGGAAACAAC
**
1559602 ATAAAATTAAAGTGCGGATATAA
1 ATAAAATTAAAGTGCCCATATAA
1559625 ATAAAATTATAAGT-CCCATAT
1 ATAAAATTA-AAGTGCCCATAT
1559646 GAACTATGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (23 bp):
ATAAAATTAAAGTGCCCATATAA
Found at i:1562527 original size:22 final size:22
Alignment explanation
Indices: 1562502--1562548 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1562492 CTGATTTTCA
* * *
1562502 TTTTAAATTTGAATAATTTATT
1 TTTTAAATTTAAATAAATAATT
*
1562524 TTTTTAATTTAAATAAATAATT
1 TTTTAAATTTAAATAAATAATT
1562546 TTT
1 TTT
1562549 ACTTAACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAAATTTAAATAAATAATT
Found at i:1563393 original size:17 final size:16
Alignment explanation
Indices: 1563371--1563429 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
1563361 GTCACATAAA
1563371 TTAAATTATTTCAAAAT
1 TTAAATTATTT-AAAAT
*
1563388 TTAAA-TACTTAATAAT
1 TTAAATTATTTAA-AAT
*
1563404 TT-AGTTATTTTAAAAT
1 TTAAATTA-TTTAAAAT
*
1563420 TTGAATTATT
1 TTAAATTATT
1563430 ATGAGTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.09
16 18 0.53
17 13 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAAATTATTTAAAAT
Found at i:1564764 original size:6 final size:6
Alignment explanation
Indices: 1564755--1564793 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1564745 ATAAAAATTT
* *
1564755 TAAATT TAAATA TAAATA TAAATA TTAATA TAAATA TAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAA
1564794 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATA
Found at i:1564801 original size:12 final size:11
Alignment explanation
Indices: 1564761--1564799 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1564751 ATTTTAAATT
1564761 TAAATATAAATA
1 TAAATAT-AATA
1564773 TAAATATTAATA
1 TAAATA-TAATA
*
1564785 TAAATATAATT
1 TAAATATAATA
1564796 TAAA
1 TAAA
1564800 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 16 0.64
13 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1567105 original size:21 final size:21
Alignment explanation
Indices: 1567081--1567129 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
1567071 AATATTATAG
1567081 TTTAAATAAAAATTATATAAA
1 TTTAAATAAAAATTATATAAA
*
1567102 TTTAAATTAAAAGTTATATAAA
1 TTTAAA-TAAAAATTATATAAA
1567124 -TTAAAT
1 TTTAAAT
1567130 TAATCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 11 0.42
22 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTAAATAAAAATTATATAAA
Found at i:1567130 original size:21 final size:22
Alignment explanation
Indices: 1567081--1567132 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1567071 AATATTATAG
1567081 TTTAAA-TAAAAATTATATAAA
1 TTTAAATTAAAAATTATATAAA
*
1567102 TTTAAATTAAAAGTTATATAAA
1 TTTAAATTAAAAATTATATAAA
1567124 -TTAAATTAA
1 TTTAAATTAA
1567133 TCTAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTAAATTAAAAATTATATAAA
Found at i:1567707 original size:26 final size:26
Alignment explanation
Indices: 1567658--1567726 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
1567648 TTTCTCTCTC
**
1567658 TATTATCATAAATTTATTTTAAAAAA
1 TATTATCATAAATTTATTGAAAAAAA
*
1567684 TATTATTCAT-AATTTATTGAAAAATA
1 TATTA-TCATAAATTTATTGAAAAAAA
*
1567710 TA-TATCAAAAATTTATT
1 TATTATCATAAATTTATT
1567727 ATTAAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.08
25 10 0.27
26 20 0.54
27 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (26 bp):
TATTATCATAAATTTATTGAAAAAAA
Found at i:1567890 original size:18 final size:17
Alignment explanation
Indices: 1567867--1567910 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1567857 AATAATGTGA
1567867 ATTTTTTATTAATTTAAT
1 ATTTTTTATTAA-TTAAT
*
1567885 ATTTTTAAATTAATTAAT
1 ATTTTT-TATTAATTAAT
1567903 ATTTTTTA
1 ATTTTTTA
1567911 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTTATTAATTAAT
Found at i:1568125 original size:26 final size:26
Alignment explanation
Indices: 1568096--1568152 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1568086 GTGATAAAAA
1568096 TTTAA-TAAAAATAATT-TTGTAAAATT
1 TTTAACTAAAAAT--TTATTGTAAAATT
* *
1568122 TTTAACTTAAAATTTATTTTAAAATT
1 TTTAACTAAAAATTTATTGTAAAATT
1568148 TTTAA
1 TTTAA
1568153 ATAATGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 19 0.70
27 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTAACTAAAAATTTATTGTAAAATT
Found at i:1568693 original size:18 final size:18
Alignment explanation
Indices: 1568666--1568709 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1568656 TTATATATCT
*
1568666 AAATAATATATGAATAGA
1 AAATATTATATGAATAGA
* *
1568684 AAATATTATATGTATATA
1 AAATATTATATGAATAGA
1568702 AAA-ATTAT
1 AAATATTAT
1568710 GTAATTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
AAATATTATATGAATAGA
Found at i:1569554 original size:27 final size:27
Alignment explanation
Indices: 1569524--1569576 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1569514 TTCAAAAATG
*
1569524 AAACA-AATACAATATGAAAAATAACTA
1 AAACATAATACAATA-AAAAAATAACTA
*
1569551 AAACATTATACAATAAAAAAATAACT
1 AAACATAATACAATAAAAAAATAACT
1569577 CTAACATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.21
Consensus pattern (27 bp):
AAACATAATACAATAAAAAAATAACTA
Found at i:1570077 original size:8 final size:8
Alignment explanation
Indices: 1570064--1570124 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 8
1570054 AAATATAATA
1570064 ATTTATAT
1 ATTTATAT
1570072 ATTTATAT
1 ATTTATAT
*
1570080 ATTGATTAT
1 ATTTA-TAT
1570089 ATTATAATTAT
1 ATT-T-A-TAT
*
1570100 ATTTAAAAT
1 ATTT-ATAT
1570109 ATTT-TAT
1 ATTTATAT
1570116 ATTTATAT
1 ATTTATAT
1570124 A
1 A
1570125 AATTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 6 0.13
8 16 0.36
9 12 0.27
10 3 0.07
11 8 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:1570094 original size:22 final size:23
Alignment explanation
Indices: 1570069--1570124 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1570059 TAATAATTTA
* *
1570069 TATATTTATATATT-GATTATAT
1 TATATTTATATATTAAAATATAT
* *
1570091 TATAATTATAT-TTAAAATATTT
1 TATATTTATATATTAAAATATAT
1570113 TATATTTATATA
1 TATATTTATATA
1570125 AATTTTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATTTATATATTAAAATATAT
Found at i:1570143 original size:18 final size:17
Alignment explanation
Indices: 1570096--1570161 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
1570086 TATATTATAA
1570096 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
1570112 TTATATTTATATAAATT
1 TTATATTTATATAAATT
1570129 TTAATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
1570145 TTATA-TTATA-AAATT
1 TTATATTTATATAAATT
1570160 TT
1 TT
1570162 TAAATACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.07
14 3 0.07
15 6 0.14
16 12 0.28
17 8 0.19
18 8 0.19
19 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:1575133 original size:4 final size:4
Alignment explanation
Indices: 1575124--1575148 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1575114 CTGAAAAACC
1575124 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1575149 TATCCTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1576083 original size:14 final size:16
Alignment explanation
Indices: 1576056--1576100 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
1576046 TATTTAATTA
1576056 TAATATATATAAATAT
1 TAATATATATAAATAT
*
1576072 TAATAT-TA-AAATTT
1 TAATATATATAAATAT
*
1576086 TAATATATCTAAATA
1 TAATATATATAAATA
1576101 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 11 0.46
15 3 0.12
16 10 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATATATAAATAT
Found at i:1576092 original size:30 final size:29
Alignment explanation
Indices: 1576051--1576117 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 29
1576041 ATTTATATTT
* * *
1576051 AATTATAATATATATAAATATTAATATTAA
1 AATTTTAATATATATAAATAATAA-AATAA
*
1576081 AATTTTAATATATCTAAATAATAAAATAA
1 AATTTTAATATATATAAATAATAAAATAA
1576110 AATTTTAA
1 AATTTTAA
1576118 AACAATGTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTTTAATATATATAAATAATAAAATAA
Found at i:1576454 original size:6 final size:6
Alignment explanation
Indices: 1576443--1576467 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1576433 GTAACAGTGC
1576443 AGCTGT AGCTGT AGCTGT AGCTGT A
1 AGCTGT AGCTGT AGCTGT AGCTGT A
1576468 CCTGCACCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
AGCTGT
Found at i:1577528 original size:11 final size:11
Alignment explanation
Indices: 1577495--1577533 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1577485 ATCAAGTATC
*
1577495 AATATAAATTT
1 AATATAAATTA
1577506 AATAATATAATTA
1 AAT-ATA-AATTA
1577519 AATATAAATTA
1 AATATAAATTA
1577530 AATA
1 AATA
1577534 ATATTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 12 0.48
12 6 0.24
13 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATATAAATTA
Found at i:1579704 original size:13 final size:13
Alignment explanation
Indices: 1579686--1579713 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1579676 TATTTTAAAT
1579686 AATAAAAAATATA
1 AATAAAAAATATA
1579699 AATAAAAAATATA
1 AATAAAAAATATA
1579712 AA
1 AA
1579714 CACTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAAAATATA
Found at i:1579771 original size:23 final size:24
Alignment explanation
Indices: 1579734--1579809 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
1579724 TTGTTCTCTC
1579734 ATATATAAAATAAAATAAAATATTA
1 ATATAT-AAATAAAATAAAATATTA
*
1579759 ATATATAAA-AAAATACAAAAATATA
1 ATATATAAATAAAATA-AAATAT-TA
* * *
1579784 ATATTTAAATACAA-AAAATATAA
1 ATATATAAATAAAATAAAATATTA
1579807 ATA
1 ATA
1579810 CAAACACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 10 0.23
24 13 0.30
25 17 0.40
26 3 0.07
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
ATATATAAATAAAATAAAATATTA
Found at i:1579891 original size:17 final size:17
Alignment explanation
Indices: 1579870--1579903 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
1579860 AAAAGTGTGA
1579870 AAAAAAAAGAAAAAAGCC
1 AAAAAAAA-AAAAAAGCC
1579888 AAAAAAAAAAAAAAGC
1 AAAAAAAAAAAAAAGC
1579904 ACTACGTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAGCC
Found at i:1580405 original size:11 final size:11
Alignment explanation
Indices: 1580372--1580405 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1580362 AAAAAATATG
1580372 ATATAAAAATA
1 ATATAAAAATA
1580383 AT-TAAAACATA
1 ATATAAAA-ATA
1580394 ATATAAAAATA
1 ATATAAAAATA
1580405 A
1 A
1580406 GTATGACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:1580414 original size:22 final size:23
Alignment explanation
Indices: 1580364--1580421 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
1580354 ATAAACGAAA
* *
1580364 AAAATATG-ATATAAAAATAATT
1 AAAACATGAATATAAAAATAAGT
1580386 AAAACAT-AATATAAAAATAAGT
1 AAAACATGAATATAAAAATAAGT
**
1580408 ATGACATGAATATA
1 AAAACATGAATATA
1580422 TGAACATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (23 bp):
AAAACATGAATATAAAAATAAGT
Found at i:1580700 original size:18 final size:20
Alignment explanation
Indices: 1580657--1580701 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
1580647 TTATGTAATT
1580657 AATTTTATATTATTAATAAA
1 AATTTTATATTATTAATAAA
1580677 AA-TTTA-ATTA-TAA-AATA
1 AATTTTATATTATTAATAA-A
1580694 AATTTTAT
1 AATTTTAT
1580702 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.09
17 6 0.27
18 8 0.36
19 4 0.18
20 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTATATTATTAATAAA
Found at i:1580710 original size:17 final size:17
Alignment explanation
Indices: 1580666--1580711 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1580656 TAATTTTATA
1580666 TTATT-AATAA-AAATT
1 TTATTAAATAATAAATT
*
1580681 TAATTATAA-AATAAATT
1 TTATTA-AATAATAAATT
1580698 TTATTAAATAATAA
1 TTATTAAATAATAA
1580712 TTATGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.16
16 4 0.16
17 17 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATTAAATAATAAATT
Found at i:1581111 original size:23 final size:23
Alignment explanation
Indices: 1581060--1581114 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1581050 TACTATTTTA
*
1581060 AATATACAAAAAATAAAAACATG
1 AATATAAAAAAAATAAAAACATG
*
1581083 AA-ATAAAAAATAATTAAAACAT-
1 AATATAAAAAA-AATAAAAACATG
1581105 AATATAAAAA
1 AATATAAAAA
1581115 TGAATATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (23 bp):
AATATAAAAAAAATAAAAACATG
Found at i:1581264 original size:13 final size:13
Alignment explanation
Indices: 1581224--1581257 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1581214 TATATTAAAA
*
1581224 TTTCTTTTATTTC
1 TTTCTTTTATTTT
1581237 TTTCTTTTATTTT
1 TTTCTTTTATTTT
1581250 TTTCTTTT
1 TTTCTTTT
1581258 TTCTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTATTTT
Found at i:1581584 original size:21 final size:22
Alignment explanation
Indices: 1581545--1581585 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1581535 TAAAACATAA
*
1581545 CATAAAAATGATATGCATATGG
1 CATAAAAATGATATACATATGG
*
1581567 CATAAATAT-ATATACATAT
1 CATAAAAATGATATACATAT
1581586 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (22 bp):
CATAAAAATGATATACATATGG
Done.