Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 66 of 199
Found at i:19431064 original size:21 final size:20
Alignment explanation
Indices: 19431050--19431105 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
19431040 TTGAGGATTG
19431050 AAAATTGGAAATTGAAAATT
1 AAAATTGGAAATTGAAAATT
*
19431070 AAAATTTGGAGATTGAAAATAT
1 AAAA-TTGGAAATTGAAAAT-T
*
19431092 AAAATTGAAAATTG
1 AAAATTGGAAATTG
19431106 GGGATTGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 22 0.71
22 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (20 bp):
AAAATTGGAAATTGAAAATT
Found at i:19431089 original size:28 final size:28
Alignment explanation
Indices: 19431053--19431125 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
19431043 AGGATTGAAA
*
19431053 ATTGGAAATTGAAAATT-AAAATTTGGAG
1 ATTGAAAATTGAAAATTGAAAA-TTGGAG
*
19431081 ATTGAAAATAT-AAAATTGAAAATTGGGG
1 ATTGAAAAT-TGAAAATTGAAAATTGGAG
* *
19431109 ATTGAAGATTGAGAATT
1 ATTGAAAATTGAAAATT
19431126 TAGGAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 32 0.84
29 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.32
Consensus pattern (28 bp):
ATTGAAAATTGAAAATTGAAAATTGGAG
Found at i:19431120 original size:7 final size:7
Alignment explanation
Indices: 19431046--19431105 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
19431036 AGGATTGAGG
19431046 ATTGAAA
1 ATTGAAA
*
19431053 ATTGGAA
1 ATTGAAA
19431060 ATTGAAA
1 ATTGAAA
19431067 ATT-AAA
1 ATTGAAA
* *
19431073 ATTTGGAG
1 A-TTGAAA
19431081 ATTGAAA
1 ATTGAAA
19431088 ATAT-AAA
1 AT-TGAAA
19431095 ATTGAAA
1 ATTGAAA
19431102 ATTG
1 ATTG
19431106 GGGATTGAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 5 0.12
7 35 0.81
8 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.32
Consensus pattern (7 bp):
ATTGAAA
Found at i:19431880 original size:17 final size:18
Alignment explanation
Indices: 19431853--19431888 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
19431843 AAAAATATAA
19431853 AAAAGTTATAAAAATTTT
1 AAAAGTTATAAAAATTTT
*
19431871 AAAA-TTATAAAATTTTT
1 AAAAGTTATAAAAATTTT
19431888 A
1 A
19431889 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAAGTTATAAAAATTTT
Found at i:19432794 original size:30 final size:29
Alignment explanation
Indices: 19432760--19432816 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
19432750 GTCCTAAATA
19432760 ATATTATTTTAGAATTTTTAA-ATTTTTTAT
1 ATATTA-TTTA-AATTTTTAATATTTTTTAT
*
19432790 ATATTATTTACATTTTTAATATTTTTT
1 ATATTATTTAAATTTTTAATATTTTTT
19432817 TAAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATATTATTTAAATTTTTAATATTTTTTAT
Found at i:19433725 original size:21 final size:22
Alignment explanation
Indices: 19433674--19433726 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
19433664 TTGTTTGAAT
* * *
19433674 TTTTAATTAATTAATTAATTAA
1 TTTTATTTAATTAATAAATAAA
19433696 TTTGT-TTTAATT-ATAAATAAA
1 TTT-TATTTAATTAATAAATAAA
19433717 TTTTATTTAA
1 TTTTATTTAA
19433727 AATTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 15 0.58
22 9 0.35
23 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTATTTAATTAATAAATAAA
Found at i:19433734 original size:16 final size:18
Alignment explanation
Indices: 19433700--19433741 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
19433690 AATTAATTTG
*
19433700 TTTTAATTATAAATAAA-
1 TTTTATTTATAAATAAAT
*
19433717 TTTTATTTA-AAATTAAT
1 TTTTATTTATAAATAAAT
19433734 TTTTATTT
1 TTTTATTT
19433742 GATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTATTTATAAATAAAT
Found at i:19434422 original size:16 final size:17
Alignment explanation
Indices: 19434393--19434425 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19434383 AAATGTTTTT
19434393 TAAAAAATTATTTAATA
1 TAAAAAATTATTTAATA
*
19434410 TAAAATATT-TTTAATA
1 TAAAAAATTATTTAATA
19434426 CTATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAAATTATTTAATA
Found at i:19434475 original size:16 final size:17
Alignment explanation
Indices: 19434444--19434511 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 17
19434434 ATATATGTAA
19434444 AATAAATATATAAAATT
1 AATAAATATATAAAATT
*
19434461 AATAATTAT-TAAAATCT
1 AATAAATATATAAAAT-T
19434478 -ATAAA-AT-TAAAATTT
1 AATAAATATATAAAA-TT
19434493 AATGATAATATAATAAAAT
1 AAT-A-AATAT-ATAAAAT
19434512 ATATTATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
15 8 0.20
16 13 0.32
17 10 0.24
18 2 0.05
19 2 0.05
20 1 0.02
21 5 0.12
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (17 bp):
AATAAATATATAAAATT
Found at i:19434521 original size:15 final size:15
Alignment explanation
Indices: 19434501--19434530 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19434491 TTAATGATAA
19434501 TATAATAAAATATAT
1 TATAATAAAATATAT
*
19434516 TATAATAATATATAT
1 TATAATAAAATATAT
19434531 AGTATTACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAATAAAATATAT
Found at i:19434764 original size:20 final size:20
Alignment explanation
Indices: 19434701--19434764 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 20
19434691 TAAACAATAA
*
19434701 TATATAAT-AATTAATATAT
1 TATATAATGAAATAATATAT
* *
19434720 TATGTAATGATAT-A-ATAT
1 TATATAATGAAATAATATAT
*
19434738 TACATAATGAAATAATATAT
1 TATATAATGAAATAATATAT
*
19434758 TTTATAA
1 TATATAA
19434765 GTATTAATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
18 14 0.41
19 9 0.26
20 11 0.32
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATAATGAAATAATATAT
Found at i:19449198 original size:44 final size:44
Alignment explanation
Indices: 19449134--19449224 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
19449124 GTAGGTCAAA
* *
19449134 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTGAAGTGAGAAAC
* * *
19449178 TAATATTAAAATAACTTACACTTATCAAAGTTGAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAAAGTTGAAGTGAGAAAC
19449222 TAA
1 TAA
19449225 AAAAAAAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTGAAGTGAGAAAC
Found at i:19449427 original size:26 final size:27
Alignment explanation
Indices: 19449398--19449453 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
19449388 TGGGAATTGA
*
19449398 TAATTAT-AAATAAAATTATTGTATTC
1 TAATTATAAAAAAAAATTATTGTATTC
*
19449424 TAATTGTAAAAAAAAATTATTGTATTC
1 TAATTATAAAAAAAAATTATTGTATTC
19449451 TAA
1 TAA
19449454 AAAAAAGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (27 bp):
TAATTATAAAAAAAAATTATTGTATTC
Found at i:19449444 original size:22 final size:21
Alignment explanation
Indices: 19449419--19449459 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19449409 AAAATTATTG
*
19449419 TATTCTAATTGTAAAAAAAAAT
1 TATTCT-ATTCTAAAAAAAAAT
*
19449441 TATTGTATTCTAAAAAAAA
1 TATTCTATTCTAAAAAAAA
19449460 GCCTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
TATTCTATTCTAAAAAAAAAT
Found at i:19450010 original size:58 final size:59
Alignment explanation
Indices: 19449899--19450010 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 59
19449889 AGGATTGACA
** *
19449899 TTGATTTTTTAAAAATACAACTCTTTCACTATTTACTTTTTTAACTTAAAAAAATTACT
1 TTGATTTTTTAAAAATACAACTCTACCACTATTTACTTTTATAACTTAAAAAAATTACT
* * *
19449958 TTGATTTTTT-TAAATACAACTCTACCACTATTTACTCTTTATGACTTCAAAAA
1 TTGATTTTTTAAAAATACAACTCTACCACTATTTACT-TTTATAACTTAAAAAA
19450011 GGTAATATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 23 0.50
59 23 0.50
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.46
Consensus pattern (59 bp):
TTGATTTTTTAAAAATACAACTCTACCACTATTTACTTTTATAACTTAAAAAAATTACT
Found at i:19453849 original size:43 final size:43
Alignment explanation
Indices: 19453769--19453912 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
19453759 TATGTGAAAA
* * * * * *
19453769 AAACACCGCTAAAGAAC-TCGACATTTAACAGCGCTTTACCCGC
1 AAACACTGCTAAAGAACAT-GACCTTTAGCGGCACTTTACCCAC
*
19453812 AAACACTGCTAAAGAATATGACCTTTAGCGGCACTTTACCCAC
1 AAACACTGCTAAAGAACATGACCTTTAGCGGCACTTTACCCAC
* * * *
19453855 AAACGCTGCTAAAGAACATGACCTTTAGCGGCGCTTGACCCAT
1 AAACACTGCTAAAGAACATGACCTTTAGCGGCACTTTACCCAC
* *
19453898 AAACGCCGCTAAAGA
1 AAACACTGCTAAAGA
19453913 GCATAATATT
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 86 0.99
44 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (43 bp):
AAACACTGCTAAAGAACATGACCTTTAGCGGCACTTTACCCAC
Found at i:19453945 original size:43 final size:41
Alignment explanation
Indices: 19453898--19454031 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 41
19453888 CTTGACCCAT
*
19453898 AAACGCCGCTAAAGAGCATAATATTTAGCAACACTTTTATCAC
1 AAACGCCGCTAAAGAGCATAAT-TTTAGCAGC-CTTTTATCAC
* * * * *
19453941 AAACGTCGCTATAA-AGAATGACTTTTAG-AGGCTTTTTTTCAC
1 AAACGCCGCTA-AAGAGCAT-AATTTTAGCA-GCCTTTTATCAC
* * *
19453983 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAGCATAAT-TTTAGCAGC-CTTTTATCAC
19454026 AAACGC
1 AAACGC
19454032 TAAAAGTACC
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
41 3 0.04
42 29 0.41
43 34 0.49
44 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (41 bp):
AAACGCCGCTAAAGAGCATAATTTTAGCAGCCTTTTATCAC
Found at i:19459540 original size:14 final size:14
Alignment explanation
Indices: 19459523--19459748 Score: 113
Period size: 14 Copynumber: 15.9 Consensus size: 14
19459513 ACTAATTAAT
*
19459523 CTAAACCCTAACCC
1 CTAAACCCTAAACC
*
19459537 CT-AACCCTTAACC
1 CTAAACCCTAAACC
*
19459550 CTTAAACCCTAAATC
1 C-TAAACCCTAAACC
* * *
19459565 ATAAATCCTAACCCC
1 CTAAACCCTAA-ACC
*
19459580 CT-AACCCTTAACC
1 CTAAACCCTAAACC
* * *
19459593 TTTAACCCTTAACCC
1 CTAAACCC-TAAACC
*
19459608 CT-AACCCTTAACTC
1 CTAAACCCTAAAC-C
*
19459622 CTAACCCCTAAACC
1 CTAAACCCTAAACC
*
19459636 TTAAATCCC--AACC
1 CTAAA-CCCTAAACC
*
19459649 CTTAAACCATAAACC
1 C-TAAACCCTAAACC
* * *
19459664 ATAAACCATAATCC
1 CTAAACCCTAAACC
* *
19459678 CTAAATCCATAATCC
1 CTAAA-CCCTAAACC
* * *
19459693 ATAAACCTTAAAATC
1 CTAAACCCT-AAACC
*
19459708 GT-AACTCCTAAACC
1 CTAAAC-CCTAAACC
*
19459722 TTAAACCCTAAACC
1 CTAAACCCTAAACC
19459736 CTAAACCCTAAAC
1 CTAAACCCTAAAC
19459749 TATAATGATA
Statistics
Matches: 161, Mismatches: 36, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
13 22 0.14
14 86 0.53
15 53 0.33
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:19459559 original size:8 final size:7
Alignment explanation
Indices: 19459526--19459639 Score: 81
Period size: 7 Copynumber: 16.3 Consensus size: 7
19459516 AATTAATCTA
19459526 AACCC-T
1 AACCCTT
*
19459532 AACCCCT
1 AACCCTT
19459539 AACCCTT
1 AACCCTT
19459546 AACCCTT
1 AACCCTT
*
19459553 AAACCCTA
1 -AACCCTT
* * *
19459561 AATCATA
1 AACCCTT
*
19459568 AATCC-T
1 AACCCTT
*
19459574 AACCCCCT
1 AA-CCCTT
19459582 AACCCTT
1 AACCCTT
*
19459589 AACCTTT
1 AACCCTT
19459596 AACCCTT
1 AACCCTT
*
19459603 AACCCCT
1 AACCCTT
19459610 AACCCTT
1 AACCCTT
19459617 AACTCC-T
1 AAC-CCTT
*
19459624 AACCCCT
1 AACCCTT
*
19459631 AAACCTT
1 AACCCTT
19459638 AA
1 AA
19459640 ATCCCAACCC
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
6 9 0.10
7 68 0.77
8 11 0.12
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCCTT
Found at i:19459561 original size:21 final size:21
Alignment explanation
Indices: 19459526--19459748 Score: 93
Period size: 21 Copynumber: 10.5 Consensus size: 21
19459516 AATTAATCTA
*
19459526 AACCC-TAACCCCTAACCCTT
1 AACCCTTAAACCCTAACCCTT
* * *
19459546 AACCCTTAAACCCTAAATCATA
1 AACCCTTAAACCCT-AACCCTT
* *
19459568 AATCC-TAACCCCCTAACCCTT
1 AACCCTTAA-ACCCTAACCCTT
* *
19459589 AA-CCTTTAACCCTTAACCCCT
1 AACCCTTAAACCC-TAACCCTT
*
19459610 AACCCTT-AACTCCTAACCCCT
1 AACCCTTAAAC-CCTAACCCTT
*
19459631 AAACCTTAAATCCC-AACCCTT
1 AACCCTTAAA-CCCTAACCCTT
* * * * *
19459652 AAACCATAAACCATAAACCAT
1 AACCCTTAAACCCTAACCCTT
* * *
19459673 AATCCC-TAAATCCATAATCCAT
1 AA-CCCTTAAA-CCCTAACCCTT
* * *
19459695 AAACCTTAAAATCGTAACTCC-T
1 AACCCTT-AAACCCTAAC-CCTT
* *
19459717 AAACCTTAAACCCTAAACCCTA
1 AACCCTTAAACCCT-AACCCTT
19459739 AACCC-TAAAC
1 AACCCTTAAAC
19459749 TATAATGATA
Statistics
Matches: 158, Mismatches: 28, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
20 12 0.08
21 84 0.53
22 56 0.35
23 6 0.04
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCCTTAAACCCTAACCCTT
Found at i:19459663 original size:7 final size:7
Alignment explanation
Indices: 19459651--19459753 Score: 64
Period size: 7 Copynumber: 14.4 Consensus size: 7
19459641 TCCCAACCCT
19459651 TAAACCA
1 TAAACCA
19459658 TAAACCA
1 TAAACCA
19459665 TAAACCA
1 TAAACCA
* *
19459672 TAATCCC
1 TAAACCA
19459679 TAAATCCA
1 TAAA-CCA
*
19459687 TAATCCA
1 TAAACCA
*
19459694 TAAACCT
1 TAAACCA
* *
19459701 TAAAATCG
1 T-AAACCA
*
19459709 T-AACTCC
1 TAAAC-CA
*
19459716 TAAACCT
1 TAAACCA
*
19459723 TAAACCC
1 TAAACCA
*
19459730 TAAACCC
1 TAAACCA
*
19459737 TAAACCC
1 TAAACCA
*
19459744 TAAACTA
1 TAAACCA
19459751 TAA
1 TAA
19459754 TGATAGTTAA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
6 2 0.03
7 62 0.81
8 13 0.17
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:19459704 original size:22 final size:21
Alignment explanation
Indices: 19459579--19459747 Score: 103
Period size: 21 Copynumber: 8.0 Consensus size: 21
19459569 ATCCTAACCC
* * *
19459579 CCTAACCC-TTAACCTTTAAC
1 CCTAACCCATAAACCTTAAAT
* * *
19459599 CCTTAACCCCTAACCCTTAACT
1 CC-TAACCCATAAACCTTAAAT
*
19459621 CCTAACCCCTAAACCTTAAAT
1 CCTAACCCATAAACCTTAAAT
* * *
19459642 CCCAACCCTTAAACCATAAA-
1 CCTAACCCATAAACCTTAAAT
* * *
19459662 CCATAAACCATAATCCCTAAAT
1 CC-TAACCCATAAACCTTAAAT
*
19459684 CCATAATCCATAAACCTTAAAAT
1 CC-TAACCCATAAACCTT-AAAT
* *
19459707 CGTAACTCC-TAAACCTTAAAC
1 CCTAAC-CCATAAACCTTAAAT
*
19459728 CCTAAACCC-TAAACCCTAAA
1 CCT-AACCCATAAACCTTAAA
19459748 CTATAATGAT
Statistics
Matches: 119, Mismatches: 23, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.03
21 70 0.59
22 38 0.32
23 7 0.06
ACGTcount: A:0.40, C:0.37, G:0.01, T:0.23
Consensus pattern (21 bp):
CCTAACCCATAAACCTTAAAT
Found at i:19460288 original size:40 final size:40
Alignment explanation
Indices: 19460154--19460318 Score: 163
Period size: 40 Copynumber: 4.1 Consensus size: 40
19460144 TGAATTTTTT
* * * * *
19460154 GCGGCGTTTTTCAAGAAGCACTGCTCATGCTTGATCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
* ** *
19460194 ACGGTGTTTTTCAAGAAGAGCA--GCTAATGCTCGACCTATA
1 GCGGCATTTTTCAA-AA-AGCACCGCTAATGCTTGACCTATA
* * *
19460234 ACGGCATTTTTCAAAAAGCGCCGCTAATGGTTGACCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
* * *
19460274 GCGGCATTTTTCAAAAACCACCGTTAATGCTTGATCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
19460314 GCGGC
1 GCGGC
19460319 GCTTTTTGAT
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 94 0.90
41 1 0.01
42 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
GCGGCATTTTTCAAAAAGCACCGCTAATGCTTGACCTATA
Found at i:19460340 original size:27 final size:26
Alignment explanation
Indices: 19460300--19460351 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
19460290 ACCACCGTTA
* * *
19460300 ATGCTTGATCTATAGCGGCGCTTTTTG
1 ATGCTCGATATATAGCAGCG-TTTTTG
19460327 ATGCTCGATATATAGCAGCGTTTTT
1 ATGCTCGATATATAGCAGCGTTTTT
19460352 CAAAAAGCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATGCTCGATATATAGCAGCGTTTTTG
Found at i:19461703 original size:32 final size:32
Alignment explanation
Indices: 19461665--19461728 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
19461655 AATAAGTACT
19461665 AAACATGCATTAGGACCATTTAAAAAAATATC
1 AAACATGCATTAGGACCATTTAAAAAAATATC
*
19461697 AAACATGCATTAGGACCATTTAACAAAATATC
1 AAACATGCATTAGGACCATTTAAAAAAATATC
19461729 CCAAAACTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.25
Consensus pattern (32 bp):
AAACATGCATTAGGACCATTTAAAAAAATATC
Found at i:19465190 original size:12 final size:12
Alignment explanation
Indices: 19465173--19465220 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
19465163 GTTCACGAAC
*
19465173 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
19465185 AAGCTCATTTAT
1 AAGCTCGTTTAT
* *
19465197 TAGCTTGTTTAT
1 AAGCTCGTTTAT
19465209 AAGCTCGTTTAT
1 AAGCTCGTTTAT
19465221 TGACTCGTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:19465206 original size:24 final size:24
Alignment explanation
Indices: 19465174--19465244 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
19465164 TTCACGAACA
19465174 AGCTCGTTTAAAAGCTCATTTATT
1 AGCTCGTTTAAAAGCTCATTTATT
* * *
19465198 AGCTTGTTTATAAGCTCGTTTATT
1 AGCTCGTTTAAAAGCTCATTTATT
**
19465222 -GACTCGTTTATGA-CTCATTTATT
1 AG-CTCGTTTAAAAGCTCATTTATT
19465245 TATTCATGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 10 0.25
24 30 0.75
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.46
Consensus pattern (24 bp):
AGCTCGTTTAAAAGCTCATTTATT
Found at i:19465227 original size:12 final size:12
Alignment explanation
Indices: 19465212--19465244 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
19465202 TGTTTATAAG
19465212 CTCGTTTATTGA
1 CTCGTTTATTGA
19465224 CTCGTTTA-TGA
1 CTCGTTTATTGA
*
19465235 CTCATTTATT
1 CTCGTTTATT
19465245 TATTCATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:19465435 original size:12 final size:12
Alignment explanation
Indices: 19465413--19465459 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
19465403 ATTATTTTTT
19465413 AACATTGTTCATG
1 AACA-TGTTCATG
19465426 AACATGTTCACT-
1 AACATGTTCA-TG
* *
19465438 TATATGTTCATG
1 AACATGTTCATG
19465450 AACATGTTCA
1 AACATGTTCA
19465460 ATTAAGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.79
13 5 0.18
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (12 bp):
AACATGTTCATG
Found at i:19465450 original size:24 final size:23
Alignment explanation
Indices: 19465418--19465480 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
19465408 TTTTTAACAT
*
19465418 TGTTCATGAACATGTTCACTTATA
1 TGTTCATGAACATGTTCAATTA-A
19465442 TGTTCATGAACATGTTCAATTAA
1 TGTTCATGAACATGTTCAATTAA
*
19465465 -GTTAAATGAACATGTT
1 TGTT-CATGAACATGTT
19465481 TGTGAACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.08
23 12 0.33
24 21 0.58
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:19469849 original size:134 final size:133
Alignment explanation
Indices: 19469609--19470056 Score: 513
Period size: 134 Copynumber: 3.4 Consensus size: 133
19469599 GGCTATAATG
* * * * * * *
19469609 GGGTATAACATGTAAGATCATAACTCGACTATGATAATATAGAGAGTCCACCATGACGTTAAACA
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
* *
19469674 TGTGGTATTATGTGTAAGACCATAGCTCATCTATGGAAACATAGAGAGTCTGCCAGGACATTAAA
66 TGTGGTATAATGTGTAAGACCATAGCTCA-CTATGGAAACATAGAGAGTCTACCAGGACATTAAA
19469739 CATA
130 CATA
* * * *
19469743 GGGTATAATGTGTAAGACCATAGCTCGACAATGACAACATAGAGAGTTCACCAGGACATTAAACA
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
* * * * *
19469808 TGTGGTATAATGTGTAAGACCATAGCTCGACTATGGTAACATAAAAAGTCCACTAGGACATTAAA
66 TGTGGTATAATGTGTAAGACCATAGCTC-ACTATGGAAACATAGAGAGTCTACCAGGACATTAAA
19469873 CATA
130 CATA
* * * * * * *
19469877 GGGTATAATATGTAAAAACATAGTTCG-CTATGACAACTTAAAGAGTCCGCCAAGATATTAAACA
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
* * * * *
19469941 TATGGTATATTGTGTAAGACCATAGCTTAACTATGGCAACATAGAGAGT-TTCCTAGGACATTAA
66 TGTGGTATAATGTGTAAGACCATAGC-TCACTATGGAAACATAGAGAGTCTACC-AGGACATTAA
*
19470005 ACATG
129 ACATA
* * * * * *
19470010 GGGTATGATGTGTAAGACCACAGCTCAACTATGACAGCATATAGAGT
1 GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGT
19470057 TTGTCGGGAT
Statistics
Matches: 262, Mismatches: 48, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
132 1 0.00
133 105 0.40
134 155 0.59
135 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (133 bp):
GGGTATAATATGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCCACCAAGACATTAAACA
TGTGGTATAATGTGTAAGACCATAGCTCACTATGGAAACATAGAGAGTCTACCAGGACATTAAAC
ATA
Found at i:19469988 original size:200 final size:201
Alignment explanation
Indices: 19469606--19470043 Score: 524
Period size: 200 Copynumber: 2.2 Consensus size: 201
19469596 ATGGGCTATA
** * * * * * * *
19469606 ATGGGGTATAACATGTAAGATCATAACTCGACTATGATAATATAGAGAGTCCACCATGACGTTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGATAACATAAAAAGTCCACCAGGACATTAA
* * * * * * * *
19469671 ACATGTGGTATTATGTGTAAGACCATAGCTCATCTATGGAAACATAGAGAGTCTGCCAGGACATT
66 ACATGTGGTATAATATGTAAAAACATAGCTCAGCTATGGAAACATAAAGAGTCCGCCAAGACATT
*
19469736 AAACATAGGGTATAATGTGTAAGACCATAGCTCGACAATGACAACATAGAGAG-TTCACCAGGAC
131 AAACATAGGGTATAATGTGTAAGACCATAGCTCAACAATGACAACATAGAGAGTTTC-CCAGGAC
19469800 ATTAAAC
195 ATTAAAC
* * *
19469807 ATGTGGTATAATGTGTAAGACCATAGCTCGACTATGGTAACATAAAAAGTCCACTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGATAACATAAAAAGTCCACCAGGACATTAA
* * *
19469872 ACATAG-GGTATAATATGTAAAAACATAGTTC-GCTAT-GACAACTTAAAGAGTCCGCCAAGATA
66 ACAT-GTGGTATAATATGTAAAAACATAGCTCAGCTATGGA-AACATAAAGAGTCCGCCAAGACA
* * * * * *
19469934 TTAAACATATGGTATATTGTGTAAGACCATAGCTTAACTATGGCAACATAGAGAGTTTCCTAGGA
129 TTAAACATAGGGTATAATGTGTAAGACCATAGCTCAACAATGACAACATAGAGAGTTTCCCAGGA
19469999 CATTAAAC
194 CATTAAAC
* * *
19470007 ATGGGGTATGATGTGTAAGACCACAGCTCAACTATGA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGA
19470044 CAGCATATAG
Statistics
Matches: 199, Mismatches: 35, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
199 2 0.01
200 116 0.58
201 80 0.40
202 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (201 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCGACTATGATAACATAAAAAGTCCACCAGGACATTAA
ACATGTGGTATAATATGTAAAAACATAGCTCAGCTATGGAAACATAAAGAGTCCGCCAAGACATT
AAACATAGGGTATAATGTGTAAGACCATAGCTCAACAATGACAACATAGAGAGTTTCCCAGGACA
TTAAAC
Found at i:19470058 original size:67 final size:67
Alignment explanation
Indices: 19469609--19470057 Score: 424
Period size: 67 Copynumber: 6.7 Consensus size: 67
19469599 GGCTATAATG
** * * * * * * * *
19469609 GGGTATAACATGTAAGATCATAACTCGACTATGATAATATAGAGAGTCCACCATGACGTTAAACA
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
19469674 T-
66 TA
* * *
19469675 GTGGTATTATGTGTAAGACCATAGCTCATCTATGGA-AACATAGAGAG-TCTGCCAGGACATTAA
1 G-GGTATAATGTGTAAGACCATAGCTCAACTAT-GACAACATAGAGAGTTC-ACCAGGACATTAA
19469738 ACATA
63 ACATA
* *
19469743 GGGTATAATGTGTAAGACCATAGCTCGACAATGACAACATAGAGAGTTCACCAGGACATTAAACA
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
19469808 T-
66 TA
* ** * * * *
19469809 GTGGTATAATGTGTAAGACCATAGCTCGACTATGGTAACATAAAAAGTCCACTAGGACATTAAAC
1 G-GGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAAC
19469874 ATA
65 ATA
* * * * * * * * * * *
19469877 GGGTATAATATGTAAAAACATAGTTC-GCTATGACAACTTAAAGAGTCCGCCAAGATATTAAACA
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
19469941 TA
66 TA
* * * * *
19469943 TGGTATATTGTGTAAGACCATAGCTTAACTATGGCAACATAGAGAGTTTC-CTAGGACATTAAAC
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAG-TTCACCAGGACATTAAAC
*
19470007 ATG
65 ATA
* * * *
19470010 GGGTATGATGTGTAAGACCACAGCTCAACTATGACAGCATATAGAGTT
1 GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTT
19470058 TGTCGGGATA
Statistics
Matches: 312, Mismatches: 61, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
66 57 0.18
67 247 0.79
68 8 0.03
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (67 bp):
GGGTATAATGTGTAAGACCATAGCTCAACTATGACAACATAGAGAGTTCACCAGGACATTAAACA
TA
Found at i:19484439 original size:21 final size:20
Alignment explanation
Indices: 19484401--19484451 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
19484391 CAAATACGTC
*
19484401 AACAGAAGCT-TGAAAGCTG
1 AACAGAAGCTCTAAAAGCTG
19484420 AACAGAAGCTCGTAAAAGCTG
1 AACAGAAGCTC-TAAAAGCTG
*
19484441 AACAAAAGCTC
1 AACAGAAGCTC
19484452 ATAAGAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (20 bp):
AACAGAAGCTCTAAAAGCTG
Found at i:19485002 original size:17 final size:18
Alignment explanation
Indices: 19484972--19485013 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
19484962 AGTTAATTCA
*
19484972 TCAAATTAACTAATTT-TC
1 TCAAA-TAAATAATTTATC
19484990 TCAAATAAATAATTTATC
1 TCAAATAAATAATTTATC
19485008 -CAAATA
1 TCAAATA
19485014 TTCTAAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAAATAAATAATTTATC
Found at i:19487462 original size:16 final size:16
Alignment explanation
Indices: 19487441--19487471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19487431 TGTTTCATTT
*
19487441 GTATTTGTATCAATTG
1 GTATTTGGATCAATTG
19487457 GTATTTGGATCAATT
1 GTATTTGGATCAATT
19487472 TGTAGTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.48
Consensus pattern (16 bp):
GTATTTGGATCAATTG
Found at i:19489464 original size:30 final size:31
Alignment explanation
Indices: 19489409--19489476 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
19489399 ACCGTTAAAA
** * **
19489409 TATTTACACTATTGGTCCTTCAAATTTTTCG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
19489440 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
19489470 TATTTAC
1 TATTTAC
19489477 TCTTGAGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:19492669 original size:3 final size:3
Alignment explanation
Indices: 19492649--19492689 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
19492639 TTAAGATATG
* *
19492649 ATA AGA ATA ATGA ATA ATA ATA ATA ATT ATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19492690 ACACCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19494462 original size:51 final size:51
Alignment explanation
Indices: 19494338--19494522 Score: 160
Period size: 51 Copynumber: 3.6 Consensus size: 51
19494328 AGTTGCTAGG
* * * * * * *
19494338 TCACGTGTGTAGTACTATGTGCAGGTTACTACGTGTATCGGAATG-ATA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATGAAAATGA
* * ***
19494388 TCGCATGTGTAGTACCATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAAT-GA
* * * * * *
19494439 TCACGTGTGTAGTACTATTTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGA
*
19494490 TCACATGTGTAGTACTATGTGCAGGATACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
19494523 TGAACCAGGT
Statistics
Matches: 105, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 2 0.02
50 34 0.32
51 67 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGA
Found at i:19500883 original size:124 final size:126
Alignment explanation
Indices: 19500662--19500919 Score: 344
Period size: 125 Copynumber: 2.1 Consensus size: 126
19500652 CGTGGACGCA
* * *
19500662 AAGAATTTGTGAAATCGCGCCCTCCTGGACGCGATTTTGCTAAAGTTGGTCCTGGAAGAAATAAT
1 AAGAATTTGTGAAATCGCGCCCACCTGGACGCGATTTTGCTAAAGTTGATCCTGGAAAAAATAAT
* * *
19500727 TTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCT-TTATGAG
66 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAACCAAGATGCTATT-TGAG
* * * * * * *
19500787 AAGAATTTGTTAAATCGCGCCCACGTGGATGCGCTTTTGCTACA-TTATATCCT-GAAAAAATTA
1 AAGAATTTGTGAAATCGCGCCCACCTGGACGCGATTTTGCTAAAGTT-GATCCTGGAAAAAATAA
*
19500850 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTATTTGAG
65 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAACCAAGATGCTATTTGAG
19500912 AAGAATTT
1 AAGAATTT
19500920 TTGNNNNNNN
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
124 41 0.35
125 73 0.63
126 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (126 bp):
AAGAATTTGTGAAATCGCGCCCACCTGGACGCGATTTTGCTAAAGTTGATCCTGGAAAAAATAAT
TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAACCAAGATGCTATTTGAG
Found at i:19504324 original size:60 final size:60
Alignment explanation
Indices: 19504260--19504397 Score: 267
Period size: 60 Copynumber: 2.3 Consensus size: 60
19504250 AGTAGAATTC
19504260 TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
1 TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
19504320 TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
1 TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
*
19504380 CCAAATAATATCAAAATA
1 TCAAATAATATCAAAATA
19504398 ACTCAAAAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 77 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (60 bp):
TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
Found at i:19504440 original size:25 final size:25
Alignment explanation
Indices: 19504411--19504458 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
19504401 CAAAAAATTT
*
19504411 TTCTATTTTATTATATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
*
19504436 TTCTATTTTATTACATTAAATAA
1 TTCTATTTTATTACATCAAATAA
19504459 TATCAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:19504490 original size:45 final size:45
Alignment explanation
Indices: 19504426--19504511 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
19504416 TTTTATTATA
* * *
19504426 TCAAATAAACTTCTATTTTATTACATTAAATAATATCAAAATAAC
1 TCAAAAAAACTTCTATTTTACTACATAAAATAATATCAAAATAAC
*
19504471 TCAAAAAAATTTCTATTTTACTACATAAAATAATATCAAAA
1 TCAAAAAAACTTCTATTTTACTACATAAAATAATATCAAAA
19504512 CATTCAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (45 bp):
TCAAAAAAACTTCTATTTTACTACATAAAATAATATCAAAATAAC
Found at i:19505141 original size:8 final size:8
Alignment explanation
Indices: 19505130--19505154 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19505120 GGTTGCCTTC
19505130 GTCGTCTT
1 GTCGTCTT
19505138 GTCGTCTT
1 GTCGTCTT
19505146 GTCGTCTT
1 GTCGTCTT
19505154 G
1 G
19505155 GATTTAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.28, T:0.48
Consensus pattern (8 bp):
GTCGTCTT
Found at i:19506857 original size:51 final size:51
Alignment explanation
Indices: 19506796--19506893 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
19506786 AATAATATAA
*
19506796 AAATAGGGATTTAAGAGAAAT-TT-AAGAAGAACTTGAGAGCAAGTTGAAATT
1 AAATAGGGATTTAAGAGAAATATTGAAG--GAACTTGAGAGCAAATTGAAATT
* * *
19506847 AAATATGGATTTGAGAGAAATATTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATATTGAAGGAACTTGAGAGCAAATTGA
19506894 GAGGAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 36 0.88
52 2 0.05
53 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATATTGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:19506891 original size:12 final size:11
Alignment explanation
Indices: 19506855--19506909 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
19506845 TTAAATATGG
19506855 ATTTGAGAGAA
1 ATTTGAGAGAA
*
19506866 ATATTGA-AGGA
1 AT-TTGAGAGAA
19506877 ATTTGAGAGCAA
1 ATTTGAGAG-AA
19506889 A-TTGAGAGGAA
1 ATTTGAGA-GAA
19506900 ATTTGAGAGA
1 ATTTGAGAGA
19506910 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 4 0.11
11 20 0.54
12 13 0.35
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:19506902 original size:23 final size:22
Alignment explanation
Indices: 19506855--19506909 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
19506845 TTAAATATGG
19506855 ATTTGAGAGAAATATTGAAGGA
1 ATTTGAGAGAAATATTGAAGGA
*
19506877 ATTTGAGAGCAA-ATTGAGAGGAA
1 ATTTGAGAGAAATATTGA-AGG-A
19506900 ATTTGAGAGA
1 ATTTGAGAGA
19506910 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 14 0.48
23 10 0.34
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATATTGAAGGA
Found at i:19507709 original size:20 final size:18
Alignment explanation
Indices: 19507695--19507743 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
19507685 TAAATATTAT
*
19507695 AAAAATATAAAAAATCTA
1 AAAAATATAAAAAATTTA
*
19507713 ACAAAATATAATAAATTATAA
1 A-AAAATATAAAAAATT-T-A
19507734 AAAAATATAA
1 AAAAATATAA
19507744 CATTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 10 0.38
21 2 0.08
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATATAAAAAATTTA
Found at i:19507718 original size:10 final size:9
Alignment explanation
Indices: 19507695--19507743 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 9
19507685 TAAATATTAT
19507695 AAAAATATA
1 AAAAATATA
*
19507704 AAAAATCTA
1 AAAAATATA
19507713 ACAAAATATA
1 A-AAAATATA
*
19507723 ATAAATTATAA
1 A-AAAATAT-A
19507734 AAAAATATA
1 AAAAATATA
19507743 A
1 A
19507744 CATTAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 11 0.33
10 20 0.61
11 2 0.06
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATATA
Found at i:19507720 original size:19 final size:20
Alignment explanation
Indices: 19507695--19507743 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
19507685 TAAATATTAT
*
19507695 AAAAATATAA-AAAATCTAA
1 AAAAATATAATAAAATATAA
* *
19507714 CAAAATATAATAAATTATAA
1 AAAAATATAATAAAATATAA
19507734 AAAAATATAA
1 AAAAATATAA
19507744 CATTAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATAATAAAATATAA
Found at i:19507853 original size:32 final size:33
Alignment explanation
Indices: 19507791--19507853 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
19507781 AAAGTATTAG
* *
19507791 AATTCTTAAAAAGATAATAAAAATTGTAAAACA
1 AATTATTAAAAAGATAATAAAAATTATAAAACA
* *
19507824 AATTATTAAAAA-ATATTAAAATTTATAAAA
1 AATTATTAAAAAGATAATAAAAATTATAAAA
19507854 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (33 bp):
AATTATTAAAAAGATAATAAAAATTATAAAACA
Found at i:19507878 original size:9 final size:10
Alignment explanation
Indices: 19507809--19507884 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 10
19507799 AAAAGATAAT
*
19507809 AAAAATTGTAA
1 AAAAATTAT-A
19507820 AACAAATTATTA
1 AA-AAATTA-TA
*
19507832 AAAAA-TATT
1 AAAAATTATA
*
19507841 AAAATTTAT-
1 AAAAATTATA
*
19507850 AAAATTTAT-
1 AAAAATTATA
19507859 AAAAATTATTAA
1 AAAAATTA-T-A
19507871 AAAAATTATA
1 AAAAATTATA
19507881 AAAA
1 AAAA
19507885 CTTGAACTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
9 21 0.38
10 11 0.20
11 6 0.11
12 16 0.29
13 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:19508420 original size:19 final size:20
Alignment explanation
Indices: 19508398--19508437 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19508388 AAATTATTAA
*
19508398 TTTTATAT-TTTTATAAAAT
1 TTTTATATATTTTAAAAAAT
19508417 TTTTATATATTTTAAAAAAT
1 TTTTATATATTTTAAAAAAT
19508437 T
1 T
19508438 ATATTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATATTTTAAAAAAT
Found at i:19515690 original size:51 final size:51
Alignment explanation
Indices: 19515555--19515745 Score: 235
Period size: 51 Copynumber: 3.8 Consensus size: 51
19515545 GTTGAAAGTG
* * *
19515555 ATGGTCACTTGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* *
19515604 ATAGGTCCCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * ** * * *
19515655 TTCGATCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATTGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
19515707 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
19515746 AACTGAACAT
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 75 0.63
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.34
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
Found at i:19515745 original size:26 final size:26
Alignment explanation
Indices: 19515665--19515745 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
19515655 TTCGATCATG
19515665 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
19515691 CGTGTA-T-CGGAT-TGTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
19515716 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
19515742 TGTG
1 TGTG
19515746 AACTGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:19515838 original size:45 final size:45
Alignment explanation
Indices: 19515752--19515840 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
19515742 TGTGAACTGA
* * * *
19515752 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCGG
19515797 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCG
19515841 AGCATCTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCGG
Found at i:19526215 original size:14 final size:14
Alignment explanation
Indices: 19526198--19526224 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19526188 CCTATTTTCC
19526198 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
19526212 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
19526225 CGCTGCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (14 bp):
TTTTTTGTTTTTTT
Found at i:19529765 original size:20 final size:20
Alignment explanation
Indices: 19529736--19529791 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
19529726 ATTTTAAAAT
* *
19529736 CAAGTGAAAATGATTTTAAC
1 CAAGTAAAAATGATTTCAAC
*
19529756 CAAGTAAAAATGATTTCAAT
1 CAAGTAAAAATGATTTCAAC
* *
19529776 CAAGTTAAAATCATTT
1 CAAGTAAAAATGATTT
19529792 AACACATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (20 bp):
CAAGTAAAAATGATTTCAAC
Found at i:19544345 original size:23 final size:23
Alignment explanation
Indices: 19544298--19544346 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19544288 ACCTACTTTC
* * **
19544298 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTTAGAATA
19544321 TTACAGTAGTAATTTTTAGAATA
1 TTACAGTAGTAATTTTTAGAATA
19544344 TTA
1 TTA
19544347 TAGTTTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (23 bp):
TTACAGTAGTAATTTTTAGAATA
Found at i:19561043 original size:44 final size:43
Alignment explanation
Indices: 19560970--19561100 Score: 183
Period size: 43 Copynumber: 3.0 Consensus size: 43
19560960 TTTTATCCTA
*
19560970 GAAAAAAAAATTTAGAAAA-AGGAGAAGATAATCTTGGGTTGTT
1 GAAAAAAGAATTTA-AAAAGAGGAGAAGATAATCTTGGGTTGTT
* * *
19561013 GAAAAAAGATTTTATAAAAGAGGAGGAGATAATCTTGAGTTGTT
1 GAAAAAAGAATTTA-AAAAGAGGAGAAGATAATCTTGGGTTGTT
* *
19561057 GAAAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT
19561100 G
1 G
19561101 GTTTTACCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 42 0.55
44 35 0.45
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.25
Consensus pattern (43 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT
Found at i:19565318 original size:30 final size:30
Alignment explanation
Indices: 19565273--19565350 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
19565263 ATATGGATAT
*
19565273 ATTGATTCATGTATGGTTATACATTGCCGA
1 ATTGATTCATATATGGTTATACATTGCCGA
* ** * ** *
19565303 ATTGTTTGGTATATGGATATAGGTTGCTGA
1 ATTGATTCATATATGGTTATACATTGCCGA
19565333 ATTGATTCATATATGGTT
1 ATTGATTCATATATGGTT
19565351 GTTCATTGTT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (30 bp):
ATTGATTCATATATGGTTATACATTGCCGA
Found at i:19567073 original size:78 final size:78
Alignment explanation
Indices: 19566991--19567160 Score: 331
Period size: 78 Copynumber: 2.2 Consensus size: 78
19566981 CATACTCAAT
19566991 TTTAAGCATATATCCTATTACACATATAATCACCTAACGCTCAAGCATATATCATAATACACATA
1 TTTAAGCATATATCCTATTACACATATAATCACCTAACGCTCAAGCATATATCATAATACACATA
19567056 TAATCTCATAACA
66 TAATCTCATAACA
*
19567069 TTTAAGCATATATCCTATTACACATATAATCACCTAATGCTCAAGCATATATCATAATACACATA
1 TTTAAGCATATATCCTATTACACATATAATCACCTAACGCTCAAGCATATATCATAATACACATA
19567134 TAATCTCATAACA
66 TAATCTCATAACA
19567147 TTTAAGCATATATC
1 TTTAAGCATATATC
19567161 TCAATACTCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 91 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (78 bp):
TTTAAGCATATATCCTATTACACATATAATCACCTAACGCTCAAGCATATATCATAATACACATA
TAATCTCATAACA
Found at i:19567154 original size:39 final size:39
Alignment explanation
Indices: 19566991--19567160 Score: 205
Period size: 39 Copynumber: 4.4 Consensus size: 39
19566981 CATACTCAAT
* * * *
19566991 TTTAAGCATATATCCTATTACACATATAATCACCTAACG
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
* * *
19567030 CTCAAGCATATATCATAATACACATATAATCTCATAACA
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
* * * **
19567069 TTTAAGCATATATCCTATTACACATATAATCACCTAATG
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
* * *
19567108 CTCAAGCATATATCATAATACACATATAATCTCATAACA
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
19567147 TTTAAGCATATATC
1 TTTAAGCATATATC
19567161 TCAATACTCA
Statistics
Matches: 106, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 106 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCATAATACACATATAATCACATAACA
Found at i:19568884 original size:50 final size:50
Alignment explanation
Indices: 19568795--19569080 Score: 286
Period size: 50 Copynumber: 5.6 Consensus size: 50
19568785 TTGTACTGCT
* * * * ** *
19568795 AATGCCATATCCCAGATATGGTCTTACAAGAGAGTTCTCATATAGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
* ** * *
19568845 CATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCT
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
*** * *
19568895 AACATCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCT
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
** * * * *
19568945 AACACTATGTCCCAGACATGGTCTT-CAATGGGACCCCTTATCTCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTAGGTGCC
*
19568995 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCT--A-GGTGCC
19569051 AATGCCATGTCCCAGACATGGTCTTACATG
1 AATGCCATGTCCCAGACATGGTCTTACATG
19569081 AGATCTCTTT
Statistics
Matches: 198, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 157 0.79
51 1 0.01
53 4 0.02
56 35 0.18
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
Found at i:19581564 original size:43 final size:44
Alignment explanation
Indices: 19581414--19581588 Score: 273
Period size: 44 Copynumber: 4.0 Consensus size: 44
19581404 TTTTATACTA
* *
19581414 GAAAAAAGAATTT-AAAAAGAGGAGAAGATAATATTGGATTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
*
19581457 GAAAAAATAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
*
19581501 GAAAAAAGAATTTCAAAAAGAGGAGAAGATATTCTTGGGTTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
* * *
19581545 GAAAAAATAATTT-AAAAAGAGGAGAAGATAAACATGGGTTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
19581588 G
1 G
19581589 GGTTGTTGGT
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
43 40 0.33
44 82 0.67
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (44 bp):
GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
Found at i:19581571 original size:87 final size:87
Alignment explanation
Indices: 19581414--19581588 Score: 289
Period size: 87 Copynumber: 2.0 Consensus size: 87
19581404 TTTTATACTA
19581414 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGAG
1 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGAG
* *
19581479 GAGAAGATAATCTTGGGTTGTT
66 GAGAAGATAAACATGGGTTGTT
* * *
19581501 GAAAAAAGAATTTCAAAAAGAGGAGAAGATATTCTTGGGTTGTTGAAAAAATAATTT-AAAAAGA
1 GAAAAAAGAATTT-AAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGA
19581565 GGAGAAGATAAACATGGGTTGTT
65 GGAGAAGATAAACATGGGTTGTT
19581588 G
1 G
19581589 GGTTGTTGGT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 42 0.51
88 40 0.49
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (87 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGAG
GAGAAGATAAACATGGGTTGTT
Found at i:19592100 original size:48 final size:48
Alignment explanation
Indices: 19592020--19592177 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
19592010 GGGAAGGATA
* * *
19592020 TGAAAAGAGTAAGTTAATATGACTCTTTATGTGATATATGTTACGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
* * *
19592068 TGAAATGAGTAAGTTAATATGACCCTGCATGTGATATTTGTTATGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
* *
19592116 TGAAATGAGTAAGTTAAAATGACTTTGTATGTGATATATGTTATGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
*
19592164 TGAAATAAGTAAGT
1 TGAAATGAGTAAGT
19592178 GATAACTCTT
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.39
Consensus pattern (48 bp):
TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
Found at i:19603418 original size:19 final size:20
Alignment explanation
Indices: 19603370--19603418 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
19603360 ATTCATCATG
19603370 TTAA-TATTTTTAAGATAAT
1 TTAATTATTTTTAAGATAAT
19603389 TTAATTA-TTTTATA-AT-AT
1 TTAATTATTTTTA-AGATAAT
19603407 TTAATTATTTTT
1 TTAATTATTTTT
19603419 TTGACAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTAATTATTTTTAAGATAAT
Found at i:19609286 original size:27 final size:27
Alignment explanation
Indices: 19609239--19609308 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
19609229 CATTTGACAC
* *
19609239 ATTTTACATCAGATTATAGAGCTTCAA
1 ATTTTACATCAGATTAGAGAGATTCAA
** *
19609266 ATTTTACATCATTTTAGAGAGATTTAA
1 ATTTTACATCAGATTAGAGAGATTCAA
19609293 ATTTTACATCAAGATT
1 ATTTTACATC-AGATT
19609309 TTCAATCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (27 bp):
ATTTTACATCAGATTAGAGAGATTCAA
Found at i:19621141 original size:18 final size:17
Alignment explanation
Indices: 19621108--19621143 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19621098 CTCTGCATGA
19621108 GTTTCTTTGTTTTATTT
1 GTTTCTTTGTTTTATTT
*
19621125 GTTTCTTTTTCTTTATTT
1 GTTTCTTTGT-TTTATTT
19621143 G
1 G
19621144 ATTCGGGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.06, C:0.08, G:0.11, T:0.75
Consensus pattern (17 bp):
GTTTCTTTGTTTTATTT
Found at i:19631304 original size:106 final size:104
Alignment explanation
Indices: 19631112--19631319 Score: 296
Period size: 106 Copynumber: 2.0 Consensus size: 104
19631102 GTTACTCCAT
* *
19631112 CCCCTACCCTCAATATTGTATTAAAAAATTAAAAATATTATTAATGAGATCATTACTTATGGAAG
1 CCCCTACCCTCAATATTGTATTAAAAAATTAAAAATATTATTAATGAGATCATTACTAATAGAAG
*
19631177 ATATTATTAACTATTTCAACAAACTTTTATATACCAACA
66 ATATTATTAACTATTTCAACAAACTTTTACATACCAACA
* *
19631216 CCCCTACCC-CAATATTTTA-TAAAAAATGATACAAATTTATTATTAATGAGATCATTA-TAAAT
1 CCCCTACCCTCAATATTGTATTAAAAAAT--TA-AAA-ATATTATTAATGAGATCATTACT-AAT
*
19631278 ATAAGATATTATTAACTATTTCAACAAACTTTTACATACCAA
61 AGAAGATATTATTAACTATTTCAACAAACTTTTACATACCAA
19631320 TAGGTGTTGG
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
102 8 0.09
103 9 0.10
104 11 0.12
105 4 0.04
106 61 0.66
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (104 bp):
CCCCTACCCTCAATATTGTATTAAAAAATTAAAAATATTATTAATGAGATCATTACTAATAGAAG
ATATTATTAACTATTTCAACAAACTTTTACATACCAACA
Found at i:19648174 original size:18 final size:17
Alignment explanation
Indices: 19648146--19648179 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19648136 GACAAAGAAT
19648146 CAATAAATACAAATAAA
1 CAATAAATACAAATAAA
*
19648163 CAATACAATACACATAA
1 CAATA-AATACAAATAA
19648180 GAGCAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAATAAATACAAATAAA
Found at i:19648891 original size:3 final size:3
Alignment explanation
Indices: 19648877--19648939 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
19648867 AAACAAACCT
*
19648877 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19648925 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
19648940 AGTTAAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19652829 original size:19 final size:19
Alignment explanation
Indices: 19652791--19652830 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19652781 CATTTGTTTG
*
19652791 CACTTTGGTGCTTCTTTTA
1 CACTTTGGTGCTTCTATTA
19652810 CACTTTGGTG-TCTCTATTA
1 CACTTTGGTGCT-TCTATTA
19652829 CA
1 CA
19652831 GTTCAGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (19 bp):
CACTTTGGTGCTTCTATTA
Found at i:19656580 original size:25 final size:24
Alignment explanation
Indices: 19656547--19656601 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
19656537 TTGGTTTATT
*
19656547 TTTAATTATA-TTTAAAATATTTTAA
1 TTTATTTATACTTT-AAA-ATTTTAA
*
19656572 TTTATTTATACTTTTAAATTTTAA
1 TTTATTTATACTTTAAAATTTTAA
19656596 TTTATT
1 TTTATT
19656602 AACATTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTATACTTTAAAATTTTAA
Found at i:19657518 original size:20 final size:20
Alignment explanation
Indices: 19657482--19657548 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
19657472 ATAAATTTAA
*
19657482 AAATAAATCTAAGTTTTTATT
1 AAATAAATATAA-TTTTTATT
* *
19657503 AAATAAATATAATTTTAAAT
1 AAATAAATATAATTTTTATT
* *
19657523 ATATAAATATAATTTTATTTT
1 AAATAAATATAATTTT-TATT
19657544 AAATA
1 AAATA
19657549 TGATAATAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
AAATAAATATAATTTTTATT
Found at i:19657520 original size:39 final size:41
Alignment explanation
Indices: 19657472--19657548 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
19657462 ATATAATTGG
*
19657472 ATAAATTTAAA-A-ATAAATCTAAGTTTT-TATTAAATAAAT
1 ATAAATTTAAATATATAAATATAA-TTTTATATTAAATAAAT
* *
19657511 ATAATTTTAAATATATAAATATAATTTTATTTTAAATA
1 ATAAATTTAAATATATAAATATAATTTTATATTAAATA
19657549 TGATAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 10 0.31
40 5 0.16
41 17 0.53
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (41 bp):
ATAAATTTAAATATATAAATATAATTTTATATTAAATAAAT
Found at i:19657918 original size:21 final size:23
Alignment explanation
Indices: 19657894--19657936 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19657884 AAACATAAAA
19657894 TAAA-TAAATATATTTT-ATAAT
1 TAAATTAAATATATTTTCATAAT
*
19657915 TAAATTAAATATTTTTTCATAA
1 TAAATTAAATATATTTTCATAA
19657937 ATACTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATTAAATATATTTTCATAAT
Found at i:19658947 original size:6 final size:6
Alignment explanation
Indices: 19658936--19658973 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
19658926 TACGTTCTTC
*
19658936 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTCCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
19658974 CTTCACTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:19659978 original size:14 final size:14
Alignment explanation
Indices: 19659959--19659985 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19659949 GTATGCTTAT
19659959 ATCTATATCTGTAC
1 ATCTATATCTGTAC
19659973 ATCTATATCTGTA
1 ATCTATATCTGTA
19659986 TTGGGGCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (14 bp):
ATCTATATCTGTAC
Found at i:19668409 original size:56 final size:56
Alignment explanation
Indices: 19668318--19668516 Score: 277
Period size: 56 Copynumber: 3.7 Consensus size: 56
19668308 ATTTGGGTAA
*
19668318 AGAGATCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
19668374 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
* *
19668430 AGAGGTCCCATGTAAGACCATGTC-TAGGACACGGCATTGGCA-C--CGAG---ATG
1 AGAGGTCCCATGTAAGACCATGTCTTA-GACATGGCATTGGCATCATTGAGATTATG
* * **
19668480 AGAGGTCCCCTGTAAGACCATATCTGGGACATGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCAT
19668517 GGCCACCGAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
50 34 0.26
53 3 0.02
55 3 0.02
56 93 0.70
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (56 bp):
AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
Found at i:19668481 original size:50 final size:53
Alignment explanation
Indices: 19668318--19668572 Score: 258
Period size: 56 Copynumber: 4.8 Consensus size: 53
19668308 ATTTGGGTAA
* *
19668318 AGAGATCCCATGTAAGACCATGTCTTA-GACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTC-TAGGACATGGCATTGGCATCA-CGAG--TATG
*
19668374 AGAGGTCCCATGTAAGACCATGTCTTA-GACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTC-TAGGACATGGCATTGGCATCA-CGAG--TATG
*
19668430 AGAGGTCCCATGTAAGACCATGTCTAGGACACGGCATTGGCA-C-CGAG-ATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCACGAGTATG
* * *
19668480 AGAGGTCCCCTGTAAGACCATATCTGGGACATGGCA-TGGC--CACCGA-TATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCA-CGAGTATG
** * * *
19668530 AGAACTCCCATGTAAGACCATATCTGGGACATGGCTTTGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCAT
19668573 GTTATTATCA
Statistics
Matches: 181, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
48 1 0.01
49 4 0.02
50 73 0.40
51 4 0.02
53 3 0.02
55 3 0.02
56 93 0.51
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (53 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCACGAGTATG
Found at i:19668570 original size:100 final size:104
Alignment explanation
Indices: 19668371--19668571 Score: 248
Period size: 100 Copynumber: 2.0 Consensus size: 104
19668361 CATTGAGATT
* * * **
19668371 ATGAGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATGAGAGGT
1 ATGAGAGGTCCCATGTAAGACCATATCTGAGACATGGCATTGGCA-CA-TCAGATTATGAGAACT
*
19668436 CCCATGTAAGACCATGTCTAGGACACGGCATTGGCACCGAG
64 CCCATGTAAGACCATATCTAGGACACGGCATTGGCACCGAG
* * *
19668477 ATGAGAGGTCCCCTGTAAGACCATATCTGGGACATGGCA-TGGC-CA-CCGA-TATGAGAACTCC
1 ATGAGAGGTCCCATGTAAGACCATATCTGAGACATGGCATTGGCACATCAGATTATGAGAACTCC
* * *
19668538 CATGTAAGACCATATCTGGGACATGGCTTTGGCA
66 CATGTAAGACCATATCTAGGACACGGCATTGGCA
19668572 TGTTATTATC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
100 40 0.48
101 2 0.02
103 2 0.02
105 4 0.05
106 35 0.42
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (104 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGAGACATGGCATTGGCACATCAGATTATGAGAACTCC
CATGTAAGACCATATCTAGGACACGGCATTGGCACCGAG
Found at i:19674427 original size:302 final size:302
Alignment explanation
Indices: 19673880--19674489 Score: 1150
Period size: 302 Copynumber: 2.0 Consensus size: 302
19673870 AGAACCGGTA
19673880 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
1 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
19673945 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
66 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
*
19674010 ATCTCTTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTA
131 ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTA
*
19674075 GATTTTGGGCCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGATGAGGAAAAATTTATCTTT
196 GATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATCCGATGAGGAAAAATTTATCTTT
19674140 ACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
261 ACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
*
19674182 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTGTTCTG
1 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
*
19674247 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACCCAA
66 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
19674312 ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTC
131 ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCT-
**
19674377 A-ATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATTTGATGAGGAAAAATTTATCTT
195 AGATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATCCGATGAGGAAAAATTTATCTT
19674441 TACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
260 TACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
19674484 AAAATT
1 AAAATT
19674490 TCGACGTTTG
Statistics
Matches: 301, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
302 300 1.00
303 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (302 bp):
AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTA
GATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATCCGATGAGGAAAAATTTATCTTT
ACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
Found at i:19675635 original size:56 final size:53
Alignment explanation
Indices: 19675544--19675847 Score: 322
Period size: 50 Copynumber: 5.8 Consensus size: 53
19675534 ATATGGGTAA
* * *
19675544 AGAGATCCCATGTAAGACTATGTCTAGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA--GAGA-TATG
*
19675600 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
* * * *
19675650 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGACATTGGAATCATTGACATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA--GAGA-TATG
* * * *
19675706 AGAGGTCCCATGTAAAACCATGTGTGGGACATGGCGTTGGCA-CCGAG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
* *
19675756 AGAGGTTCCC-TCTAAGACCATGTCTGGGACATGGCATGGGCATC---GATATG
1 AGAGG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
* * *
19675806 AGAAGTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19675848 GTACAAGAAT
Statistics
Matches: 210, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
48 1 0.00
49 4 0.02
50 114 0.54
51 5 0.02
53 5 0.02
55 1 0.00
56 80 0.38
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (53 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
Found at i:19675739 original size:106 final size:104
Alignment explanation
Indices: 19675544--19675847 Score: 400
Period size: 106 Copynumber: 2.9 Consensus size: 104
19675534 ATATGGGTAA
* * * *
19675544 AGAGATCCCATGTAAGACTATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGG-ATCATTGA-ATTATGAGAGGTCCC
19675609 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
64 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
*
19675650 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGACATTGGAATCATTGACATTATGAGAGGTCCC
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGG-ATCATTGA-ATTATGAGAGGTCCC
* * * *
19675715 ATGTAAAACCATGTGTGGGACATGGCGTTGGCACCGAGATG
64 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * * *
19675756 AGAGGTTCCCTCTAAGACCATGTCTGGGACATGGCA-TGG-GCATCG-A-TATGAGAAGTCCCAT
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGGATCATTGAATTATGAGAGGTCCCAT
* *
19675817 GTAAGACCATATCTGGGATATGGCATTGGCA
66 GTAAGACCATGTCTGGGACATGGCATTGGCA
19675848 GTACAAGAAT
Statistics
Matches: 176, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 40 0.23
101 1 0.01
103 4 0.02
105 3 0.02
106 128 0.73
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (104 bp):
AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGGATCATTGAATTATGAGAGGTCCCAT
GTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:19679844 original size:61 final size:61
Alignment explanation
Indices: 19679749--19679876 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
19679739 GAGTCCAGTC
* * *
19679749 CGTGTGGCTCCAAACAAGGTCGTGTGGTTAACCTACACACCGATGTGCGACCTCACATGCA
1 CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTACACACCCATGTACGACCTCACATGCA
* * * *
19679810 CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTATACGCCCATGTACGACCTTACATGCC
1 CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTACACACCCATGTACGACCTCACATGCA
19679871 CGTGTG
1 CGTGTG
19679877 CATGGATTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (61 bp):
CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTACACACCCATGTACGACCTCACATGCA
Found at i:19689067 original size:12 final size:12
Alignment explanation
Indices: 19689050--19689079 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19689040 CCATACACAC
19689050 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
19689062 CCGTGTGCTAGG
1 CCGTGTGCCAGG
19689074 CCGTGT
1 CCGTGT
19689080 AACAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:19690158 original size:25 final size:25
Alignment explanation
Indices: 19690130--19690209 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
19690120 ATGCTCATGT
*
19690130 GAGCTATGGATCGGTATGCTCTCAC
1 GAGCTATGGATCGGTAAGCTCTCAC
19690155 GAGC--TGGAAATCGGTAAGCTCAT-AC
1 GAGCTATGG--ATCGGTAAGCTC-TCAC
* * *
19690180 GAGCTAAGAATCGGTAAGCTCTCAT
1 GAGCTATGGATCGGTAAGCTCTCAC
19690205 GAGCT
1 GAGCT
19690210 GGTGTGTCTG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
23 3 0.07
24 1 0.02
25 39 0.87
26 1 0.02
27 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (25 bp):
GAGCTATGGATCGGTAAGCTCTCAC
Found at i:19694110 original size:13 final size:13
Alignment explanation
Indices: 19694079--19694163 Score: 63
Period size: 13 Copynumber: 6.4 Consensus size: 13
19694069 AGGCAACCCA
19694079 ATTT-TTATT-TT
1 ATTTATTATTATT
*
19694090 AGTTATTATTATT
1 ATTTATTATTATT
19694103 ATTTATTATT-TT
1 ATTTATTATTATT
19694115 ATTTTATT-TTATTT
1 A-TTTATTATTA-TT
19694129 ACTTTATTTATTACTTT
1 A-TTTA-TTATTA--TT
19694146 ATTTTATT-TTATT
1 A-TTTATTATTATT
19694159 ATTTA
1 ATTTA
19694164 CTACTTATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
11 3 0.05
12 14 0.23
13 20 0.32
14 7 0.11
15 5 0.08
16 5 0.08
17 8 0.13
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:19694118 original size:5 final size:5
Alignment explanation
Indices: 19694081--19694158 Score: 68
Period size: 5 Copynumber: 14.4 Consensus size: 5
19694071 GCAACCCAAT
19694081 TTTTA TTTTA GTTATTA TTATTA TTTATTA TTTTA TTTTA TTTTA -TTTA
1 TTTTA TTTTA -TT-TTA TT-TTA -TT-TTA TTTTA TTTTA TTTTA TTTTA
* *
19694130 CTTTA TTTATTA CTTTA TTTTA TTTTA TT
1 TTTTA -TT-TTA TTTTA TTTTA TTTTA TT
19694159 ATTTACTACT
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 4 0.06
5 36 0.56
6 12 0.19
7 12 0.19
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:19694127 original size:31 final size:30
Alignment explanation
Indices: 19694081--19694162 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
19694071 GCAACCCAAT
*
19694081 TTTTATTTTA-GTTATTATTATTATTTATTA
1 TTTTATTTTATTTTATTATT-TTATTTATTA
*
19694111 TTTTATTTTATTTTATTTACTTTATTTATTA
1 TTTTATTTTATTTTA-TTATTTTATTTATTA
*
19694142 CTTTATTTTATTTTATTATTT
1 TTTTATTTTATTTTATTATTT
19694163 ACTACTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 15 0.33
31 27 0.59
32 4 0.09
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (30 bp):
TTTTATTTTATTTTATTATTTTATTTATTA
Found at i:19695389 original size:101 final size:100
Alignment explanation
Indices: 19695201--19695389 Score: 231
Period size: 101 Copynumber: 1.9 Consensus size: 100
19695191 GAACATGTTA
* ** * * *
19695201 GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTTTCTTCGTGTGAAAAGGTTCGATGTGTT
1 GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATGTC
*
19695266 CTTAAGAAAAAATTATAGTAAATTAGGAGTGTGCTG
66 CTAAAGAAAAAA-TATAGTAAATTAGGAGTGTGCTG
* *
19695302 GGCTGAGTAATCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCAGTATAT-
1 GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTC-G-ATATG
19695366 TCCTAAAGCATAAAAA-ATA-TAAAT
64 TCCTAAAG-A-AAAAATATAGTAAAT
19695390 AATAAATAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
101 56 0.75
102 10 0.13
103 4 0.05
104 5 0.07
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (100 bp):
GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATGTC
CTAAAGAAAAAATATAGTAAATTAGGAGTGTGCTG
Found at i:19696006 original size:15 final size:15
Alignment explanation
Indices: 19695981--19696015 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19695971 AACTCTATTT
*
19695981 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
19695995 TAATTAATATTAAGA
1 TAATTAATATTAAGA
19696010 TAATTA
1 TAATTA
19696016 TTAATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:19697562 original size:22 final size:22
Alignment explanation
Indices: 19697537--19697583 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
19697527 AATCACAAGC
19697537 AAAGTAGAACTATTACCAAGAT
1 AAAGTAGAACTATTACCAAGAT
19697559 AAAGTAGAACTATTACCAAGAT
1 AAAGTAGAACTATTACCAAGAT
19697581 AAA
1 AAA
19697584 CATATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (22 bp):
AAAGTAGAACTATTACCAAGAT
Found at i:19699886 original size:12 final size:12
Alignment explanation
Indices: 19699869--19699893 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19699859 CTGTGTCAGA
19699869 GGCTTCATCAAT
1 GGCTTCATCAAT
19699881 GGCTTCATCAAT
1 GGCTTCATCAAT
19699893 G
1 G
19699894 ATTTCTCAAA
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:0.24, G:0.20, T:0.32
Consensus pattern (12 bp):
GGCTTCATCAAT
Found at i:19705103 original size:21 final size:22
Alignment explanation
Indices: 19705066--19705106 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19705056 GCACCCTAGG
*
19705066 CTTTTATTTTATGATTCCTTTC
1 CTTTTATTTAATGATTCCTTTC
19705088 CTTTTATTTAAT-ATTCCTT
1 CTTTTATTTAATGATTCCTT
19705107 AAAAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (22 bp):
CTTTTATTTAATGATTCCTTTC
Found at i:19707061 original size:41 final size:41
Alignment explanation
Indices: 19707004--19707123 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
19706994 TGATCGAATG
* * * *
19707004 TAATTCAGACTTATTGTCCAGGAGGCTTGATGCCGGTGATA
1 TAATTCAGACTCATTGTCCAGCAGGCTTAATGCCAGTGATA
* *
19707045 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACTCATTGTCCAGCAGGCTTAATGCCAGTGATA
* * * * * *
19707086 TTATTCGGACT-ATAAGTCTAGCAGGCTAAAAGCCAGTG
1 TAATTCAGACTCAT-TGTCCAGCAGGCTTAATGCCAGTG
19707124 TATTAAATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (41 bp):
TAATTCAGACTCATTGTCCAGCAGGCTTAATGCCAGTGATA
Found at i:19711060 original size:12 final size:13
Alignment explanation
Indices: 19711043--19711074 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19711033 GTGGCTATGC
19711043 AAGGGAAA-GGAA
1 AAGGGAAATGGAA
19711055 AAGGGAAATGGAA
1 AAGGGAAATGGAA
19711068 AAGGGAA
1 AAGGGAA
19711075 TGATAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (13 bp):
AAGGGAAATGGAA
Found at i:19711588 original size:21 final size:22
Alignment explanation
Indices: 19711550--19711597 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
19711540 ATTATGAATA
*
19711550 TTAATTCATAATATAATTAATT
1 TTAATTCATAATACAATTAATT
* *
19711572 TTAATT-ATAATCCAATTTATT
1 TTAATTCATAATACAATTAATT
19711593 TTAAT
1 TTAAT
19711598 CCAATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTCATAATACAATTAATT
Found at i:19717862 original size:106 final size:106
Alignment explanation
Indices: 19717677--19717869 Score: 305
Period size: 106 Copynumber: 1.8 Consensus size: 106
19717667 ATACATACGA
* * * * *
19717677 ATAGGTTTATCCCGGATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
1 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAAAGATAGAAAAACTACCAGTAA
*
19717742 TAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
66 AAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
*
19717783 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAAAGATAGAAAAACTCCCAGTAA
1 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAAAGATAGAAAAACTACCAGTAA
* *
19717848 AAATATTTGGAGCAGAAGCTTC
66 AAACATCTGGAGCAGAAGCTTC
19717870 ATCTTGTGCA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 78 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (106 bp):
ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAAAGATAGAAAAACTACCAGTAA
AAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
Found at i:19722476 original size:45 final size:45
Alignment explanation
Indices: 19722427--19722547 Score: 154
Period size: 45 Copynumber: 2.7 Consensus size: 45
19722417 ACCGGAAATG
* * *
19722427 AATAAGAACATAGTTGAAAGACACTATGGCACTAT-TATAGAAACA
1 AATAAGACCATAGTTGAAAGACACTATGGCAATATGT-CAGAAACA
* *
19722472 AATAAGACCATAGTTGAAAGACACTATGGCAATATGTCGGAAATA
1 AATAAGACCATAGTTGAAAGACACTATGGCAATATGTCAGAAACA
* * *
19722517 AATAAGACCATGGCTAAAAGACACTATGGCA
1 AATAAGACCATAGTTGAAAGACACTATGGCA
19722548 TACTTAAACA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 66 0.99
46 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (45 bp):
AATAAGACCATAGTTGAAAGACACTATGGCAATATGTCAGAAACA
Found at i:19738488 original size:45 final size:45
Alignment explanation
Indices: 19738437--19738522 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
19738427 TATGAACCGA
* * * *
19738437 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCAGCGG
1 ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCAGCGG
19738482 ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCA
1 ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCA
19738523 CCGAGTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCAGCGG
Found at i:19749777 original size:22 final size:23
Alignment explanation
Indices: 19749749--19749805 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
19749739 CTGTGGTGTA
19749749 GTGGCAAGG-TGGCGTCACAGGT
1 GTGGCAAGGATGGCGTCACAGGT
*
19749771 GTGGCAAGGATATGGTGTCACAGGT
1 GTGGCAAGG--ATGGCGTCACAGGT
*
19749796 GTGGTAAGGA
1 GTGGCAAGGA
19749806 GAGGTTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 9 0.30
23 1 0.03
25 20 0.67
ACGTcount: A:0.23, C:0.12, G:0.44, T:0.21
Consensus pattern (23 bp):
GTGGCAAGGATGGCGTCACAGGT
Found at i:19750994 original size:19 final size:19
Alignment explanation
Indices: 19750965--19751007 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
19750955 TGTTATGAGC
19750965 CTCGT-TGGGCCGAAATGGG
1 CTCGTGTGGGCC-AAATGGG
*
19750984 C-CGTGTGGGCCTAATGGG
1 CTCGTGTGGGCCAAATGGG
19751002 CTCGTG
1 CTCGTG
19751008 AGCCCCTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (19 bp):
CTCGTGTGGGCCAAATGGG
Found at i:19751599 original size:161 final size:160
Alignment explanation
Indices: 19751218--19751718 Score: 480
Period size: 161 Copynumber: 3.1 Consensus size: 160
19751208 AAAAGGTAGT
* * * * * * * *
19751218 TAAATTTACCGAAACACCCTCGATGGGTAAGATTATCGAAATACTCCCGATGGGTAATATTACCG
1 TAAAATTACTGAAATACCCTCGATGGGTAAAATTATTGAAATAC-CCCAATGGGTAAAATTACTG
* ** ** * * *
19751283 AAATACCCCCGAAGGGTAAAATTATTGAAATACCCCCAAAGGGTAAAACTATTGAAATACCCCCG
65 AAATA-CCCTGAAGGGTAAAATTACCGAAATACCCCTGATGGGTAAAATTACTGAAATACCCCCG
* *
19751348 ATGGGTAAAATTACTAAAATACCCTTGATGGG
129 AAGGGTAAAATTACTAAAATACCCTTGAAGGG
* * * *
19751380 TTAAATTACTGAAATACCCTCGATGGGTAAAATTATTAAAATACCCCGAA-GCGTAAAATTACTA
1 TAAAATTACTGAAATACCCTCGATGGGTAAAATTATTGAAATACCCC-AATGGGTAAAATTACTG
* * *
19751444 AAATACCTCTGAAGCGTAAAATTACCAAAATACCCCTGATGGGTAATATTACTGAAATACCCCCG
65 AAATACC-CTGAAGGGTAAAATTACCGAAATACCCCTGATGGGTAAAATTACTGAAATACCCCCG
* *
19751509 AAGGGTAAAATTACTGACATA-CC-TGCACAGGG
129 AAGGGTAAAATTACTAAAATACCCTTG-A-AGGG
* * *
19751541 TAAAATTAC-GAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCTAATGGGTAAAATTA-TC
1 TAAAATTACTG-AAATACCCTCGATGGGTAAAATTATTGAAATACCCCAATGGGTAAAATTACT-
* * ** *
19751604 GAAATACCCTCGATGGGTAAAATTACCGAAATA-CTCTCGATGGGTAAAATTACCAAAATA--TC
64 GAAATACCCT-GAAGGGTAAAATTACCGAAATACCCCT-GATGGGTAAAATTACTGAAATACCCC
* * * **
19751666 TGATGGGTAAAATTA-TCGAAATACCCCCGAAGGG
127 CGAAGGGTAAAATTACT-AAAATACCCTTGAAGGG
19751700 TAAAATTACTGAAATACCC
1 TAAAATTACTGAAATACCC
19751719 CCATAGGGTA
Statistics
Matches: 280, Mismatches: 46, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
158 1 0.00
159 42 0.15
160 18 0.06
161 181 0.65
162 38 0.14
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (160 bp):
TAAAATTACTGAAATACCCTCGATGGGTAAAATTATTGAAATACCCCAATGGGTAAAATTACTGA
AATACCCTGAAGGGTAAAATTACCGAAATACCCCTGATGGGTAAAATTACTGAAATACCCCCGAA
GGGTAAAATTACTAAAATACCCTTGAAGGG
Found at i:19751719 original size:27 final size:27
Alignment explanation
Indices: 19751218--19751730 Score: 436
Period size: 27 Copynumber: 19.1 Consensus size: 27
19751208 AAAAGGTAGT
* * * *
19751218 TAAATTTACCGAAACACCCTCGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* *
19751245 TAAGATTA-TCGAAATACTCCCGATGGG
1 TAAAATTACT-GAAATACCCCCGATGGG
* * *
19751272 TAATATTACCGAAATACCCCCGAAGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* * *
19751299 TAAAATTATTGAAATACCCCCAAAGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* *
19751326 TAAAACTATTGAAATACCCCCGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* **
19751353 TAAAATTACTAAAATACCCTTGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* *
19751380 TTAAATTACTGAAATACCCTCGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* * * *
19751407 TAAAATTATTAAAATA-CCCCGAAGCG
1 TAAAATTACTGAAATACCCCCGATGGG
* * * * *
19751433 TAAAATTACTAAAATACCTCTGAAGCG
1 TAAAATTACTGAAATACCCCCGATGGG
** *
19751460 TAAAATTACCAAAATACCCCTGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* *
19751487 TAATATTACTGAAATACCCCCGAAGGG
1 TAAAATTACTGAAATACCCCCGATGGG
* *
19751514 TAAAATTACTGACATACCTGCAC-A-GGG
1 TAAAATTACTGAAATACC--CCCGATGGG
*
19751541 TAAAATTAC-GAAAATACCCTCGATGGG
1 TAAAATTACTG-AAATACCCCCGATGGG
* * * **
19751568 TAAAATGATTGAAAT-GCCCTAATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
*
19751594 TAAAATTA-TCGAAATACCCTCGATGGG
1 TAAAATTACT-GAAATACCCCCGATGGG
* * *
19751621 TAAAATTACCGAAATACTCTCGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
** * *
19751648 TAAAATTACCAAAATA--TCTGATGGG
1 TAAAATTACTGAAATACCCCCGATGGG
*
19751673 TAAAATTA-TCGAAATACCCCCGAAGGG
1 TAAAATTACT-GAAATACCCCCGATGGG
19751700 TAAAATTACTGAAATACCCCC-ATAGGG
1 TAAAATTACTGAAATACCCCCGAT-GGG
19751727 TAAA
1 TAAA
19751731 CTGTCTGTTA
Statistics
Matches: 398, Mismatches: 71, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
25 22 0.06
26 44 0.11
27 327 0.82
28 3 0.01
29 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (27 bp):
TAAAATTACTGAAATACCCCCGATGGG
Found at i:19753458 original size:25 final size:25
Alignment explanation
Indices: 19753430--19753483 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
19753420 TGTAGTGGCA
* *
19753430 AGGTGGCGTCACAGGTGTGGCAAGG
1 AGGTGGCGTCACAAGTGTGGCAAAG
* *
19753455 AGGTGGTGTCACAAGTGTGGTAAAG
1 AGGTGGCGTCACAAGTGTGGCAAAG
19753480 AGGT
1 AGGT
19753484 TAGAGGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.44, T:0.20
Consensus pattern (25 bp):
AGGTGGCGTCACAAGTGTGGCAAAG
Found at i:19755274 original size:10 final size:10
Alignment explanation
Indices: 19755259--19755285 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19755249 CTAAGGTATT
19755259 GAAGAGATGC
1 GAAGAGATGC
19755269 GAAGAGATGC
1 GAAGAGATGC
19755279 GAAGAGA
1 GAAGAGA
19755286 CGAATCTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.41, T:0.07
Consensus pattern (10 bp):
GAAGAGATGC
Found at i:19765006 original size:32 final size:32
Alignment explanation
Indices: 19764970--19765033 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
19764960 TTAAGCCGAA
19764970 AATCTTTGTTTGCTCTACGTGCAATGAATACT
1 AATCTTTGTTTGCTCTACGTGCAATGAATACT
19765002 AATCTTTGTTTGCTCTACGTGCAATGAATACT
1 AATCTTTGTTTGCTCTACGTGCAATGAATACT
19765034 CAGTTGACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (32 bp):
AATCTTTGTTTGCTCTACGTGCAATGAATACT
Found at i:19767709 original size:50 final size:49
Alignment explanation
Indices: 19767591--19767719 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 49
19767581 GATAATAACA
* * *
19767591 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTCTAGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATGTTTCTAGTAC
* * *
19767640 TGCCAATGCCATATCCCAGATATGGTCTTAAATGGG-TGTTCTCATA-TTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATGTT-TC-TAGTAC
*
19767689 GTGCCCATGCCATGTCCCAGACATGGTCTTA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTA
19767720 CGGGGGACCT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.06
49 35 0.51
50 29 0.43
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATGTTTCTAGTAC
Found at i:19767733 original size:50 final size:52
Alignment explanation
Indices: 19767591--19767837 Score: 229
Period size: 50 Copynumber: 4.8 Consensus size: 52
19767581 GATAATAACA
* * ** * * *
19767591 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTC-TA-GT-AC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTTCAG
* * * ***
19767640 TGCCAATGCCATATCCCAGATATGGTCTTAAATGGGTGTTCTCATA-TTC-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTTCAG
* ** *
19767690 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT-C-TCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTTCAG
* *
19767740 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATAACTTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ACTTC-A-G
*
19767795 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
19767838 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
49 36 0.23
50 80 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 39 0.25
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACTTCAG
Found at i:19784542 original size:13 final size:13
Alignment explanation
Indices: 19784524--19784559 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19784514 CCATTTGTTA
*
19784524 TGTCACCATACTT
1 TGTCACCAAACTT
19784537 TGTCACCAAACTT
1 TGTCACCAAACTT
*
19784550 TGCCACCAAA
1 TGTCACCAAA
19784560 TCATTCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.28
Consensus pattern (13 bp):
TGTCACCAAACTT
Found at i:19800563 original size:30 final size:30
Alignment explanation
Indices: 19800504--19800565 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
19800494 TTTTTTTGAA
* * * *
19800504 AATATTTACAAAAAGAGGCATCTAGTTTTT
1 AATATTTACAAAAAGAGGAACCAAATTTTT
*
19800534 AATATTTACAAAAAGAGTAACCAAATTTTT
1 AATATTTACAAAAAGAGGAACCAAATTTTT
19800564 AA
1 AA
19800566 AAATAATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGAACCAAATTTTT
Found at i:19809415 original size:22 final size:22
Alignment explanation
Indices: 19809390--19809446 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
19809380 AATTTAGCCA
19809390 TTTTT-TATTTTAATTTTAATAT
1 TTTTTATATTTTAATTTTAAT-T
*
19809412 TTTTTGT-TTTTAA-TTTAATT
1 TTTTTATATTTTAATTTTAATT
*
19809432 TTTTTATATTCTAAT
1 TTTTTATATTTTAAT
19809447 ATTCTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 7 0.23
21 11 0.37
22 11 0.37
23 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTATATTTTAATTTTAATT
Found at i:19816276 original size:3 final size:3
Alignment explanation
Indices: 19816270--19816346 Score: 52
Period size: 3 Copynumber: 25.7 Consensus size: 3
19816260 CTCCCCTTAT
* * *
19816270 TTA TTA TTA TATA TT- TT- TTA TTA TTA CTA TTA TTA CTA ATA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
19816314 TTA TT- CTA TTTA TTA TATG TTG TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA TT
19816347 TGTTTAGTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.08
3 48 0.80
4 7 0.12
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:19817366 original size:37 final size:37
Alignment explanation
Indices: 19817317--19817393 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
19817307 ATGATGCACA
*
19817317 CTTTCTTTGGAGCACGGCGATGCGACCCCAATTTGAT
1 CTTTCTTTGGAGCACAGCGATGCGACCCCAATTTGAT
*
19817354 CTTTCTTTGGAGCACAGCGATGCGGCCCCAATTTGAT
1 CTTTCTTTGGAGCACAGCGATGCGACCCCAATTTGAT
19817391 CTT
1 CTT
19817394 GCATATTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.31
Consensus pattern (37 bp):
CTTTCTTTGGAGCACAGCGATGCGACCCCAATTTGAT
Found at i:19830294 original size:42 final size:42
Alignment explanation
Indices: 19830232--19830330 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
19830222 CCACATGCCT
* *
19830232 GTGTGCCAGGCCATGTACCCTTCGAAGTAGTCTCACACGCTC
1 GTGTGCCAGGCCATGCACCCTTCGAAGTAGCCTCACACGCTC
** *
19830274 GTGTGCCAGGCTGTGCACCCTTCGAAGTAGCCTTACACGC-C
1 GTGTGCCAGGCCATGCACCCTTCGAAGTAGCCTCACACGCTC
* *
19830315 TATGTGCTAGGCCATG
1 -GTGTGCCAGGCCATG
19830331 TACTAGGCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.24
Consensus pattern (42 bp):
GTGTGCCAGGCCATGCACCCTTCGAAGTAGCCTCACACGCTC
Found at i:19831600 original size:43 final size:43
Alignment explanation
Indices: 19831353--19831615 Score: 294
Period size: 43 Copynumber: 6.1 Consensus size: 43
19831343 TAAAAAAATA
* * *
19831353 CCGCTAAAGATAATGGCCTTTAGCGGCGCTTCTTCCACAAACG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* * ** * *
19831396 CCGCTAAAGATCATGGCCTTTAGTGGCGCTTCTTTCGCAAACA
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* *
19831439 CCGCTAAAGATTATGAGCTTTAGCGGCGCTTCTACCACAAACG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
** *
19831482 CCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTACCACAAACG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* * * * ** *
19831525 TCGCTAAAAAT-ATGACCTTTAGTGACATTTCTACCACAAATG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* ** *
19831567 CCGCTAAAGATCATGACCTTTAGCGGTGCTTCTATTACAAATG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
19831610 CCGCTA
1 CCGCTA
19831616 TAAAAATGAA
Statistics
Matches: 183, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 32 0.17
43 151 0.83
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
Found at i:19848765 original size:7 final size:7
Alignment explanation
Indices: 19848753--19848779 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19848743 ATTTTGATAT
19848753 TTTAAAA
1 TTTAAAA
19848760 TTTAAAA
1 TTTAAAA
19848767 TTTAAAA
1 TTTAAAA
19848774 TTTAAA
1 TTTAAA
19848780 TATAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Done.