Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 23 of 121
Found at i:4075729 original size:12 final size:11
Alignment explanation
Indices: 4075649--4075728 Score: 76
Period size: 11 Copynumber: 7.2 Consensus size: 11
4075639 AAAATAGAAT
4075649 AATAAATAATATA
1 AATAAA-AATA-A
4075662 AATAAAAATAAA
1 AATAAAAAT-AA
4075674 AATAAAAAT-A
1 AATAAAAATAA
*
4075684 AATAAAGA-AA
1 AATAAAAATAA
*
4075694 AGTAAAACA-AA
1 AATAAAA-ATAA
4075705 AATAAAAATAA
1 AATAAAAATAA
*
4075716 AATAAAGATAA
1 AATAAAAATAA
4075727 AA
1 AA
4075729 AAGAATATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
10 15 0.26
11 23 0.40
12 13 0.22
13 7 0.12
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:4076751 original size:25 final size:25
Alignment explanation
Indices: 4076723--4076773 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4076713 AGAAAAGAAA
*
4076723 ATAATTATA-ATATAATAATAAATAT
1 ATAATTATATAAAT-ATAATAAATAT
*
4076748 ATAATTATATAAATATAATACATAT
1 ATAATTATATAAATATAATAAATAT
4076773 A
1 A
4076774 AATATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATTATATAAATATAATAAATAT
Found at i:4076763 original size:14 final size:14
Alignment explanation
Indices: 4076722--4076843 Score: 67
Period size: 14 Copynumber: 8.4 Consensus size: 14
4076712 AAGAAAAGAA
4076722 AATAAT-TATAATAT
1 AATAATATA-AATAT
4076736 AATAATA-AATATAT
1 AATAATATAA-ATAT
*
4076750 AATTATATAAATAT
1 AATAATATAAATAT
4076764 AATACATATAAATATT
1 AATA-ATATAAATA-T
* *
4076780 AACAGAGA-AAATA-
1 AATA-ATATAAATAT
4076793 AATAA-ATAAATA-
1 AATAATATAAATAT
*
4076805 AATAAAGATATACATAT
1 AAT--A-ATATAAATAT
*
4076822 ATTAATATATAATAAT
1 AATAATATA-AAT-AT
4076838 AATAAT
1 AATAAT
4076844 GAATAATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
11 1 0.01
12 9 0.11
13 4 0.05
14 30 0.35
15 20 0.24
16 19 0.22
17 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:4077074 original size:1 final size:1
Alignment explanation
Indices: 4077063--4077134 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
4077053 AACATTGTCA
* * * * * * * *
4077063 TTTTTTGTTTTTATTGTTTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTGTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
4077128 TGTTTTT
1 TTTTTTT
4077135 GACCAAAGCT
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:4077081 original size:9 final size:8
Alignment explanation
Indices: 4077063--4077134 Score: 83
Period size: 8 Copynumber: 8.5 Consensus size: 8
4077053 AACATTGTCA
4077063 TTTTTTGT
1 TTTTTTGT
4077071 TTTTATTGT
1 TTTT-TTGT
4077080 TTTTTT-T
1 TTTTTTGT
4077087 TTGTTTTGTTT
1 TT-TTTTG--T
4077098 TTTTTTGTT
1 TTTTTTG-T
4077107 TTTTTTGT
1 TTTTTTGT
*
4077115 TTTTTTAT
1 TTTTTTGT
4077123 TTTTTTGT
1 TTTTTTGT
4077131 TTTT
1 TTTT
4077135 GACCAAAGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
7 3 0.05
8 29 0.51
9 17 0.30
10 5 0.09
11 3 0.05
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (8 bp):
TTTTTTGT
Found at i:4077085 original size:19 final size:18
Alignment explanation
Indices: 4077063--4077134 Score: 87
Period size: 17 Copynumber: 4.1 Consensus size: 18
4077053 AACATTGTCA
4077063 TTTTTTGTTTTTATTG-TT
1 TTTTTTGTTTTT-TTGTTT
*
4077081 TTTTTT-TTGTTTTGTTT
1 TTTTTTGTTTTTTTGTTT
*
4077098 TTTTTTGTTTTTTT-TGT
1 TTTTTTGTTTTTTTGTTT
*
4077115 TTTTTTATTTTTTTGTTT
1 TTTTTTGTTTTTTTGTTT
4077133 TT
1 TT
4077135 GACCAAAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
16 3 0.07
17 27 0.59
18 16 0.35
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (18 bp):
TTTTTTGTTTTTTTGTTT
Found at i:4077094 original size:25 final size:25
Alignment explanation
Indices: 4077065--4077134 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 25
4077055 CATTGTCATT
4077065 TTTTGTTTTTATTGTTTTTTTT-TTG
1 TTTTGTTTTT-TTGTTTTTTTTGTTG
*
4077090 TTTTGTTTTTTTTTGTTTTTTTTGTTT
1 TTTTG--TTTTTTTGTTTTTTTTGTTG
*
4077117 TTTTATTTTTTTGTTTTT
1 TTTTGTTTTTTTGTTTTT
4077135 GACCAAAGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 18 0.45
26 11 0.28
27 11 0.28
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (25 bp):
TTTTGTTTTTTTGTTTTTTTTGTTG
Found at i:4077106 original size:35 final size:35
Alignment explanation
Indices: 4077063--4077134 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
4077053 AACATTGTCA
4077063 TTTTTTGTTTTTATTGTTTTTTT-TTTGTTTTGTTT
1 TTTTTTGTTTTTATTGTTTTTTTATTT-TTTTGTTT
*
4077098 TTTTTTGTTTTTTTTGTTTTTTTATTTTTTTGTTT
1 TTTTTTGTTTTTATTGTTTTTTTATTTTTTTGTTT
4077133 TT
1 TT
4077135 GACCAAAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 32 0.91
36 3 0.09
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.88
Consensus pattern (35 bp):
TTTTTTGTTTTTATTGTTTTTTTATTTTTTTGTTT
Found at i:4077231 original size:41 final size:41
Alignment explanation
Indices: 4077142--4077423 Score: 368
Period size: 41 Copynumber: 7.0 Consensus size: 41
4077132 TTTGACCAAA
* * *
4077142 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-G-AAAGTAAATT
* *
4077185 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
4077226 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
4077267 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGGAAAGTAAATT
*
4077308 ACTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* *
4077349 G---CTCTAAACAGAGGCAACA-AAC-TTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
4077385 GCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAGGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAA-GTAAAT
4077424 ACTCCTAGAC
Statistics
Matches: 217, Mismatches: 12, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
36 15 0.07
37 3 0.01
38 17 0.08
39 27 0.12
40 6 0.03
41 119 0.55
43 30 0.14
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:4078687 original size:22 final size:24
Alignment explanation
Indices: 4078662--4078706 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
4078652 TATTTTTTCA
4078662 TTTT-CTCATTTTTCCC-CTTTTT
1 TTTTCCTCATTTTTCCCTCTTTTT
**
4078684 TTTTCCTTTTTTTTCCCTCTTTT
1 TTTTCCTCATTTTTCCCTCTTTT
4078707 CTCATTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTCCTCATTTTTCCCTCTTTTT
Found at i:4082692 original size:61 final size:58
Alignment explanation
Indices: 4082551--4082710 Score: 248
Period size: 61 Copynumber: 2.7 Consensus size: 58
4082541 TTGTGTAGGA
*
4082551 AAAATTGATACTTTCAACTTTTCCTCAAAAATCATTTTTTTGAAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTTTGAAAATTTATTTCTAAGG
*
4082610 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTA---TTTCTAAGG
* *
4082671 AAAATTGATACTTTTAACTTTTCCCTAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
4082711 TGGAATTTTT
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
58 17 0.18
59 31 0.33
61 46 0.49
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTCTAAGG
Found at i:4082718 original size:61 final size:61
Alignment explanation
Indices: 4082551--4082728 Score: 233
Period size: 61 Copynumber: 3.0 Consensus size: 61
4082541 TTGTGTAGGA
* *
4082551 AAAATTGATACTTTCAACTTTT-CCTCAAAAATCATTTTTTT-GAA--AATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAAT-ATTTTTTTGGAATTTATTTATTTTTAAGG
* *
4082610 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTT-TTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTG-GAATTTATTTATTTTTAAGG
*
4082671 AAAATTGATACTTTTAACTTTTCCCTAAAAATATTTTTTTTGGAATTT-TTTATTTTTA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAATTTATTTATTTTTA
4082729 TTTAAAGAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
58 8 0.08
59 28 0.27
60 7 0.07
61 50 0.48
62 12 0.11
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (61 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAATTTATTTATTTTTAAGG
Found at i:4082767 original size:6 final size:6
Alignment explanation
Indices: 4082736--4082820 Score: 68
Period size: 6 Copynumber: 13.7 Consensus size: 6
4082726 TTATTTAAAG
*
4082736 AAAATA GAATAATAA AAAATA TAAATA AAAATA AAAATA AATAA-A GAAAAGT-
1 AAAATA -AA-AAT-A AAAATA AAAATA AAAATA AAAATA AA-AATA -AAAA-TA
* *
4082788 AAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
4082821 GAATATTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
5 5 0.08
6 44 0.69
7 9 0.14
8 5 0.08
9 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:4082810 original size:32 final size:33
Alignment explanation
Indices: 4082736--4082819 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
4082726 TTATTTAAAG
* *
4082736 AAAATAGAATAATA-AAAAATATAAATAAAAATA
1 AAAATAAAATAA-AGAAAAATATAAACAAAAATA
*
4082769 AAAAT-AAATAAAGAAAAGTA-AAACAAAAATA
1 AAAATAAAATAAAGAAAAATATAAACAAAAATA
4082800 AAAATAAAATAAAGATAAAA
1 AAAATAAAATAAAGA-AAAA
4082820 AGAATATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 16 0.36
32 20 0.45
33 8 0.18
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (33 bp):
AAAATAAAATAAAGAAAAATATAAACAAAAATA
Found at i:4082817 original size:11 final size:11
Alignment explanation
Indices: 4082736--4082819 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
4082726 TTATTTAAAG
*
4082736 AAAATAGAATA
1 AAAATAAAATA
*
4082747 ATAA-AAAATA
1 AAAATAAAATA
*
4082757 TAAATAAAAATA
1 AAAAT-AAAATA
4082769 AAAAT-AAATA
1 AAAATAAAATA
* *
4082779 AAGA-AAAGTA
1 AAAATAAAATA
4082789 AAACA-AAAATA
1 AAA-ATAAAATA
4082800 AAAATAAAATA
1 AAAATAAAATA
*
4082811 AAGATAAAA
1 AAAATAAAA
4082820 AGAATATTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
10 22 0.38
11 26 0.45
12 10 0.17
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:4082855 original size:11 final size:11
Alignment explanation
Indices: 4082756--4082861 Score: 53
Period size: 10 Copynumber: 9.5 Consensus size: 11
4082746 AATAAAAAAT
4082756 ATAAATAA-AA
1 ATAAATAATAA
4082766 ATAAA-AATAA
1 ATAAATAATAA
*
4082776 ATAAAGAA-AA
1 ATAAATAATAA
* *
4082786 GTAAA-ACAAAA
1 ATAAATA-ATAA
4082797 ATAAA-AATAAA
1 ATAAATAAT-AA
*
4082808 ATAAA-GATAA
1 ATAAATAATAA
* *
4082818 AAAGAATATTAA
1 ATA-AATAATAA
4082830 ATAAACCTAATATA
1 ATAAA--TAATA-A
4082844 ATAAATAAATAA
1 ATAAAT-AATAA
4082856 ATAAAT
1 ATAAAT
4082862 TAAAAAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 24 0.32
11 22 0.29
12 13 0.17
13 8 0.11
14 6 0.08
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.21
Consensus pattern (11 bp):
ATAAATAATAA
Found at i:4083880 original size:25 final size:25
Alignment explanation
Indices: 4083852--4083902 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4083842 AAGAAAAGAA
*
4083852 ATAATTATA-ATATAATAATAAATAT
1 ATAATTATATAAAT-ATAATAAATAT
*
4083877 ATAATTATATAAATATAATACATAT
1 ATAATTATATAAATATAATAAATAT
4083902 A
1 A
4083903 AATATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATTATATAAATATAATAAATAT
Found at i:4083892 original size:14 final size:14
Alignment explanation
Indices: 4083851--4083972 Score: 67
Period size: 14 Copynumber: 8.4 Consensus size: 14
4083841 AAAGAAAAGA
4083851 AATAAT-TATAATAT
1 AATAATATA-AATAT
4083865 AATAATA-AATATAT
1 AATAATATAA-ATAT
*
4083879 AATTATATAAATAT
1 AATAATATAAATAT
4083893 AATACATATAAATATT
1 AATA-ATATAAATA-T
* *
4083909 AACAGAGA-AAATA-
1 AATA-ATATAAATAT
4083922 AATAA-ATAAATA-
1 AATAATATAAATAT
*
4083934 AATAAAGATATACATAT
1 AAT--A-ATATAAATAT
*
4083951 ATTAATATATAATAAT
1 AATAATATA-AAT-AT
4083967 AATAAT
1 AATAAT
4083973 GAATAATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
11 1 0.01
12 9 0.11
13 4 0.05
14 30 0.35
15 20 0.24
16 19 0.22
17 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:4088379 original size:36 final size:35
Alignment explanation
Indices: 4088304--4088453 Score: 122
Period size: 36 Copynumber: 4.0 Consensus size: 35
4088294 TCTTTGACTC
*
4088304 GTGGTTTAATCTC-GATCATTTTTATAGTTTTTCTGACTT
1 GTGGTTTAATC-CAG-TCA-TTTT-TA-TTTTTCTCACTT
*
4088343 GTAGTTTAATCCTAGTCATTTTTATTTTTCTCACTT
1 GTGGTTTAATCC-AGTCATTTTTATTTTTCTCACTT
* ** * *
4088379 GTGGTTTAATCCCGATCATTTCTTTAGTTTCCCTGACTC
1 GTGGTTTAATCCAG-TCA-TT-TTTA-TTTTTCTCACTT
*
4088418 GTGGTTTAATCCCAGTCGTTTTTATTTTTCTCACTT
1 GTGGTTTAAT-CCAGTCATTTTTATTTTTCTCACTT
4088454 ACGATTTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
35 1 0.01
36 33 0.37
37 8 0.09
38 11 0.12
39 33 0.37
40 4 0.04
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (35 bp):
GTGGTTTAATCCAGTCATTTTTATTTTTCTCACTT
Found at i:4088398 original size:75 final size:75
Alignment explanation
Indices: 4088304--4088519 Score: 244
Period size: 75 Copynumber: 2.9 Consensus size: 75
4088294 TCTTTGACTC
* ** * *
4088304 GTGGTTTAATCTCGATCATTTTTATAGTTTTTCTGACTTGTAGTTTAATCCTAGTCATTTTTATT
1 GTGGTTTAATCCCGATCATTTTTATAGTTTCCCTGACTCGTAGTTTAATCCCAGTCATTTTTATT
4088369 TTTCTCACTT
66 TTTCTCACTT
* *
4088379 GTGGTTTAATCCCGATCATTTCTT-TAGTTTCCCTGACTCGTGGTTTAATCCCAGTCGTTTTTAT
1 GTGGTTTAATCCCGATCATTT-TTATAGTTTCCCTGACTCGTAGTTTAATCCCAGTCATTTTTAT
4088443 TTTTCTCACTT
65 TTTTCTCACTT
** * * * * *
4088454 ACGATTTAATCCTGATCATTTCTATAGTTTCCCTAACTTGCG-A-TTTAATCCCAATC-TTTTT-
1 GTGGTTTAATCCCGATCATTTTTATAGTTTCCCTGAC-T-CGTAGTTTAATCCCAGTCATTTTTA
4088515 TTTTT
64 TTTTT
4088520 ATCTTTCTAA
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
73 5 0.04
74 6 0.05
75 106 0.87
76 3 0.02
77 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (75 bp):
GTGGTTTAATCCCGATCATTTTTATAGTTTCCCTGACTCGTAGTTTAATCCCAGTCATTTTTATT
TTTCTCACTT
Found at i:4088430 original size:39 final size:38
Alignment explanation
Indices: 4088298--4088430 Score: 146
Period size: 39 Copynumber: 3.5 Consensus size: 38
4088288 CTTTAATCTT
*
4088298 TGACTCGTGGTTTAATCTCGATCATTTTTATAGTTTTTC
1 TGACTCGTGGTTTAATCCCGATCATTTTT-TAGTTTTTC
* * *
4088337 TGACTTGTAGTTTAAT-CCTAGTCA-TTTTTA-TTTTTC
1 TGACTCGTGGTTTAATCCCGA-TCATTTTTTAGTTTTTC
* * **
4088373 TCACTTGTGGTTTAATCCCGATCATTTCTTTAGTTTCCC
1 TGACTCGTGGTTTAATCCCGATCATTT-TTTAGTTTTTC
4088412 TGACTCGTGGTTTAATCCC
1 TGACTCGTGGTTTAATCCC
4088431 AGTCGTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
36 23 0.29
37 7 0.09
38 10 0.13
39 38 0.49
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (38 bp):
TGACTCGTGGTTTAATCCCGATCATTTTTTAGTTTTTC
Found at i:4088634 original size:34 final size:34
Alignment explanation
Indices: 4088620--4088695 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
4088610 TTAATTCTGG
4088620 TCTCTTTATTCTCTAATTCATGATTTAATCTCGA
1 TCTCTTTATTCTCTAATTCATGATTTAATCTCGA
* * * * * *
4088654 TCTCTTTATTCTCTGATTTACGGTTCAATTTCGA
1 TCTCTTTATTCTCTAATTCATGATTTAATCTCGA
4088688 TCTCTTTA
1 TCTCTTTA
4088696 ATTTAAAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.20, C:0.21, G:0.08, T:0.51
Consensus pattern (34 bp):
TCTCTTTATTCTCTAATTCATGATTTAATCTCGA
Found at i:4088836 original size:34 final size:34
Alignment explanation
Indices: 4088798--4088866 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
4088788 AGTTAATATC
* *
4088798 ATTTTTTGATTCGCGGTTTAATCCCGATCTCTTT
1 ATTTTTTGATTCGCGATTCAATCCCGATCTCTTT
* *
4088832 ATTTTTTGATTCGCGATTCAATCTCGATCTTTTT
1 ATTTTTTGATTCGCGATTCAATCCCGATCTCTTT
4088866 A
1 A
4088867 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (34 bp):
ATTTTTTGATTCGCGATTCAATCCCGATCTCTTT
Found at i:4088869 original size:171 final size:171
Alignment explanation
Indices: 4088641--4089381 Score: 898
Period size: 171 Copynumber: 4.3 Consensus size: 171
4088631 TCTAATTCAT
** * *
4088641 GATTTAATCTCGATCTCTTTATTCTCTGATTTACGGTTCAATTTCGATCTCTTTAATTTAAAATC
1 GATTTAATCTCGATCTCTTTATTCTCTGATTCGCGATTCAATCTCGATCTCTTTAATTTAAAATC
* * ** *
4088706 GTAGTTTAATCTTGATTGTTGTTATCCTCTGACTCGTGGTTTAATTTCGGTCTCTTTATTTTCTT
66 GTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTAATCCCAGTCTCTTTATTTTCTT
** *
4088771 ACTTGTGATTCAATTTAAGTTAATATCATTTTTTGATTCGC
131 ACTTGTGATTCAATCCAAGTTAACATCATTTTTTGATTCGC
* * * * * *
4088812 GGTTTAATCCCGATCTCTTTATTTTTTGATTCGCGATTCAATCTCGATCTTTTTAATTTAAAATT
1 GATTTAATCTCGATCTCTTTATTCTCTGATTCGCGATTCAATCTCGATCTCTTTAATTTAAAATC
4088877 GTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTAATCCC-GATCTCTTTATTTTCT
66 GTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTAATCCCAG-TCTCTTTATTTTCT
* *
4088941 TACTTGTGATTCAATCTAAGTTAACATCATTTTTTGATTCAC
130 TACTTGTGATTCAATCCAAGTTAACATCATTTTTTGATTCGC
* * * * *
4088983 GATTTAATCTCGATCTGTTTATTTTCCGATTCGCGATTCAATCCCAATCTCTTTAATTTAAAATC
1 GATTTAATCTCGATCTCTTTATTCTCTGATTCGCGATTCAATCTCGATCTCTTTAATTTAAAATC
* * * ** * * *
4089048 GTAGCTTAATCTTGATTGTTGTTAACCTCTGACTTGTGGTCTATTCCCAGTCTTTTTATTTT-TT
66 GTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTAATCCCAGTCTCTTTATTTTCTT
* * *
4089112 GACTTGTGATTCGATCCAAGTTAACGTCATTTTTTGACTCGC
131 -ACTTGTGATTCAATCCAAGTTAACATCATTTTTTGATTCGC
* * * * * * *
4089154 -AGTTTTATCTCGATCTCTTTATTCT-TCGATTCGTGTTTCAATTTTGATCTCTTTAATTCAAAG
1 GA-TTTAATCTCGATCTCTTTATTCTCT-GATTCGCGATTCAATCTCGATCTCTTTAATTTAAAA
* * *
4089217 TCGCAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGATTTAATCTCAGTCTCTCTTA-TTT
64 TCGTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTAATCCCAGTCTCT-TTATTTT
* * *
4089281 CTTTACTTTGTGATTCAATCCAAGTTAACGTCATTTTTTAATTCGT
128 C-TTAC-TTGTGATTCAATCCAAGTTAACATCATTTTTTGATTCGC
* * * * *
4089327 GATTTAATCTCGGTTTCTTTATTCTCTGATTCGCGGTTTAATCCCGATCTCTTTA
1 GATTTAATCTCGATCTCTTTATTCTCTGATTCGCGATTCAATCTCGATCTCTTTA
4089382 TTCTCTGATT
Statistics
Matches: 484, Mismatches: 75, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
170 4 0.01
171 393 0.81
172 6 0.01
173 79 0.16
174 2 0.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (171 bp):
GATTTAATCTCGATCTCTTTATTCTCTGATTCGCGATTCAATCTCGATCTCTTTAATTTAAAATC
GTAGTTTAATCTCGATTGTTGTTATCCTCTGACTCATGGTTTAATCCCAGTCTCTTTATTTTCTT
ACTTGTGATTCAATCCAAGTTAACATCATTTTTTGATTCGC
Found at i:4089772 original size:3 final size:3
Alignment explanation
Indices: 4089752--4089800 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
4089742 CATTTTAGTC
* *
4089752 TAA TAT TAA TAA T-T TAA TAA TAA TAA TAA TATA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
4089796 -AA TAA
1 TAA TAA
4089801 ATAAAAGGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.13
3 30 0.79
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4089775 original size:14 final size:12
Alignment explanation
Indices: 4089752--4089800 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
4089742 CATTTTAGTC
*
4089752 TAATATTAATAA
1 TAATAATAATAA
*
4089764 T-TTAATAATAA
1 TAATAATAATAA
4089775 TAATAATATATAA
1 TAATAATA-ATAA
4089788 TAA-AATAA-AA
1 TAATAATAATAA
4089798 TAA
1 TAA
4089801 ATAAAAGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.16
11 10 0.31
12 10 0.31
13 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:4089778 original size:17 final size:16
Alignment explanation
Indices: 4089752--4089804 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 16
4089742 CATTTTAGTC
* *
4089752 TAATATTAATAATTTAA
1 TAATAATAATAATAT-A
4089769 TAATAATAATAATATA
1 TAATAATAATAATATA
*
4089785 TAATAA-AATAAAATA
1 TAATAATAATAATATA
4089800 -AATAA
1 TAATAA
4089805 AAGGAGACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 7 0.21
17 13 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAATAATAATATA
Found at i:4098972 original size:27 final size:27
Alignment explanation
Indices: 4098943--4098995 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4098933 GCATGCAATT
4098943 TTTTTGG-ATTTATTAATTTTCAAAAG
1 TTTTTGGTATTTATTAATTTTCAAAAG
* *
4098969 TTTTTGGTATTTTTTTATTTTCAAAAG
1 TTTTTGGTATTTATTAATTTTCAAAAG
4098996 CATTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.58
Consensus pattern (27 bp):
TTTTTGGTATTTATTAATTTTCAAAAG
Found at i:4101251 original size:18 final size:19
Alignment explanation
Indices: 4101212--4101251 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4101202 ACTGATCTTT
*
4101212 TGTGCTTCTTTTAGAGCATG
1 TGTGCTTCTTTTACAG-ATG
4101232 TGTGCTTCTTTTACAG-TG
1 TGTGCTTCTTTTACAGATG
4101250 TG
1 TG
4101252 ATGCCAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
20 15 0.79
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.47
Consensus pattern (19 bp):
TGTGCTTCTTTTACAGATG
Found at i:4108049 original size:210 final size:210
Alignment explanation
Indices: 4107523--4108160 Score: 871
Period size: 210 Copynumber: 3.0 Consensus size: 210
4107513 TCCTAAATAT
*
4107523 TTTCAAAATTTTATTTTATGAAAAAAATTAATATTTAAACTTTTGGTTAGCATTTTTCTAAATTT
1 TTTCAAAATTTTATTTTAAGAAAAAAATTAATATTTAAACTTTTGGTTAGCATTTTTCTAAATTT
4107588 ATTTTGTTTATTTTATTTTTTATTTTTCAAAGAATTTAGGAAAAATGATATTTCAACTTTTTCTT
66 ATTTTGTTTATTTTATTTTTTATTTTTCAAAGAATTTAGGAAAAATGATATTTCAACTTTTTCTT
* * * *
4107653 AAATATTTTCAAAATTTTATTC--T-AAAGAAAATAGATATTTCAACTT-TTT-TTTAGAGTTGT
131 AAATATTTTCAAAATTTTATTCTATGAAAAAAAAT-GATATTTCAA-TTATTTCCTTAGTGTTTT
*
4107713 TGAAACGAAGATTTTTA
194 TGAAACAAAGATTTTTA
*** * * ** **
4107730 TTTGTTTTATTTTTATTTTTAAAGAATTGAAAAATTGATATTTCAATTTTTTTCTTTAGC--TTT
1 -TT-TCAAAATTTTA-TTTT-AAGAA---AAAAATTAATATTT-AA-ACTTTTGGTTAGCATTTT
* * *
4107793 T-TAAATTTTTTTTTGTTTATTTTATTTTTTATATTTCAAAGAATTTAAGAAAAATTGATATTTC
57 TCTAAA-TTTATTTTGTTTATTTTATTTTTTATTTTTCAAAGAATTTAGGAAAAA-TGATATTTC
** *
4107857 AGTTTTTTCTTAAATATTTTCAAAATTTGATTCTATGAAAAAAAATGATATTTCAATTATTTCCT
120 AACTTTTTCTTAAATATTTTCAAAATTTTATTCTATGAAAAAAAATGATATTTCAATTATTTCCT
4107922 TAGTGTTTTTGAAACAAAGATTTTTA
185 TAGTGTTTTTGAAACAAAGATTTTTA
*
4107948 TTTCAAAATTTTATTTTAAG-AAAAAATTAATATTTAAACTTTTGGTTAGCATTTTTCTAAAATT
1 TTTCAAAATTTTATTTTAAGAAAAAAATTAATATTTAAACTTTTGGTTAGCATTTTTCTAAATTT
*
4108012 GTTTTGTTTATTTTATTTTTTATTTTTCAAAGAATTTAGGAAAAATGATATTTCAACTTTTTCTT
66 ATTTTGTTTATTTTATTTTTTATTTTTCAAAGAATTTAGGAAAAATGATATTTCAACTTTTTCTT
*
4108077 AAATGTTTTCAAAATTTTATTCTATGAAAAAAAAATGATATTTCAATTATTTCCTTAGTGTTTTT
131 AAATATTTTCAAAATTTTATTCTATG-AAAAAAAATGATATTTCAATTATTTCCTTAGTGTTTTT
4108142 GAAACAAAGATTTTTA
195 GAAACAAAGATTTTTA
4108158 TTT
1 TTT
4108161 ATTTTGTTTT
Statistics
Matches: 373, Mismatches: 38, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
208 11 0.03
209 51 0.14
210 122 0.33
211 8 0.02
213 5 0.01
214 65 0.17
215 45 0.12
216 18 0.05
217 16 0.04
218 32 0.09
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (210 bp):
TTTCAAAATTTTATTTTAAGAAAAAAATTAATATTTAAACTTTTGGTTAGCATTTTTCTAAATTT
ATTTTGTTTATTTTATTTTTTATTTTTCAAAGAATTTAGGAAAAATGATATTTCAACTTTTTCTT
AAATATTTTCAAAATTTTATTCTATGAAAAAAAATGATATTTCAATTATTTCCTTAGTGTTTTTG
AAACAAAGATTTTTA
Found at i:4110011 original size:10 final size:11
Alignment explanation
Indices: 4109984--4110012 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4109974 TAATTTTAAT
4109984 TTTAAAATCTA
1 TTTAAAATCTA
4109995 TTTAAAATCTA
1 TTTAAAATCTA
4110006 -TTAAAAT
1 TTTAAAAT
4110013 ATTAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAAATCTA
Found at i:4113069 original size:18 final size:19
Alignment explanation
Indices: 4113036--4113119 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 19
4113026 GCTAGAGCAG
* *
4113036 AAAATTTTATTTTATTAT-
1 AAAATTTTAATATATTATA
4113054 AAAATTTTAATATATT-TA
1 AAAATTTTAATATATTATA
* **
4113072 AATAGTTTTAGATATAAAATA
1 AA-AATTTTA-ATATATTATA
*
4113093 AAAATTTT--TATTTTATA
1 AAAATTTTAATATATTATA
4113110 AAAATTTTAA
1 AAAATTTTAA
4113120 AAATATATAG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
17 15 0.29
18 16 0.31
19 6 0.12
20 10 0.20
21 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AAAATTTTAATATATTATA
Found at i:4113244 original size:24 final size:23
Alignment explanation
Indices: 4113190--4113245 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
4113180 TTTACTATCT
4113190 AAATTT-AATCAAAATTAAATAA
1 AAATTTCAATCAAAATTAAATAA
** *
4113212 AAAAATCAATCCAAATTAAATTAA
1 AAATTTCAATCAAAATTAAA-TAA
*
4113236 ACATTTCAAT
1 AAATTTCAAT
4113246 TTTTTCATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 4 0.15
23 12 0.46
24 10 0.38
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATTTCAATCAAAATTAAATAA
Found at i:4115026 original size:2 final size:2
Alignment explanation
Indices: 4115019--4115045 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4115009 GTTGCAAGAC
4115019 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4115046 AGTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4116209 original size:29 final size:28
Alignment explanation
Indices: 4116150--4116220 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
4116140 TTTTGTTGAT
* *
4116150 ATAAAATAATAAATAATTTTATTATATA
1 ATAAATTAATAAATAATTATATTATATA
4116178 ATAAATTAATAAATAAATTATATGTAT-TA
1 ATAAATTAATAAAT-AATTATAT-TATATA
*
4116207 ATATATTAATAAAT
1 ATAAATTAATAAAT
4116221 GTTATAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.34
29 22 0.58
30 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
ATAAATTAATAAATAATTATATTATATA
Found at i:4121474 original size:3 final size:3
Alignment explanation
Indices: 4121466--4121515 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
4121456 AAATTTTTTA
4121466 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4121514 TA
1 TA
4121516 ATCTTTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4122347 original size:3 final size:3
Alignment explanation
Indices: 4122334--4122383 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
4122324 TTGTTTATGA
* *
4122334 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT T-T ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
4122379 TAT TA
1 TAT TA
4122384 CTAGTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 39 0.95
4 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4122445 original size:22 final size:22
Alignment explanation
Indices: 4122410--4122470 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
4122400 TAGAAACAAT
*
4122410 AAAT-AAATATAATAAAAATAA
1 AAATAAAATAAAATAAAAATAA
*
4122431 AAATAAAATAAAATAAAGACTAA
1 AAATAAAATAAAATAAA-AATAA
*
4122454 AAA-AATAT-AAATAAAAA
1 AAATAAAATAAAATAAAAA
4122471 ATTTAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.03
21 11 0.32
22 15 0.44
23 7 0.21
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
AAATAAAATAAAATAAAAATAA
Found at i:4122445 original size:31 final size:31
Alignment explanation
Indices: 4122410--4122469 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4122400 TAGAAACAAT
*
4122410 AAATAAATA-TAATAAAAATAAAAATAAAATA
1 AAATAAAGACTAA-AAAAATAAAAATAAAATA
*
4122441 AAATAAAGACTAAAAAAATATAAATAAAA
1 AAATAAAGACTAAAAAAATAAAAATAAAA
4122470 AATTTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (31 bp):
AAATAAAGACTAAAAAAATAAAAATAAAATA
Found at i:4122953 original size:15 final size:15
Alignment explanation
Indices: 4122935--4122988 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
4122925 AAAAACTTTT
4122935 TAACATAAATGTTTG
1 TAACATAAATGTTTG
* *
4122950 TAACAAAGAAAAATGTTTT
1 TAAC----ATAAATGTTTG
4122969 TAACATAAATGTTTG
1 TAACATAAATGTTTG
4122984 TAACA
1 TAACA
4122989 AAGAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 18 0.58
19 13 0.42
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (15 bp):
TAACATAAATGTTTG
Found at i:4122965 original size:19 final size:19
Alignment explanation
Indices: 4122941--4123001 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
4122931 TTTTTAACAT
4122941 AAATGTTTGTAACAAAGAA
1 AAATGTTTGTAACAAAGAA
* *
4122960 AAATGTTTTTAAC----AT
1 AAATGTTTGTAACAAAGAA
4122975 AAATGTTTGTAACAAAGAA
1 AAATGTTTGTAACAAAGAA
4122994 AAATGTTT
1 AAATGTTT
4123002 TAGCATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 13 0.38
19 21 0.62
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (19 bp):
AAATGTTTGTAACAAAGAA
Found at i:4122969 original size:34 final size:34
Alignment explanation
Indices: 4122931--4123011 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
4122921 TTTTAAAAAC
4122931 TTTTTAACATAAATGTTTGTAACAAAGAAAAATG
1 TTTTTAACATAAATGTTTGTAACAAAGAAAAATG
4122965 TTTTTAACATAAATGTTTGTAACAAAGAAAAATG
1 TTTTTAACATAAATGTTTGTAACAAAGAAAAATG
*
4122999 -TTTTAGCATAAAT
1 TTTTTAACATAAAT
4123012 TTTAGGAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 12 0.26
34 34 0.74
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (34 bp):
TTTTTAACATAAATGTTTGTAACAAAGAAAAATG
Found at i:4131284 original size:39 final size:38
Alignment explanation
Indices: 4131230--4131631 Score: 347
Period size: 39 Copynumber: 10.3 Consensus size: 38
4131220 TAAAAGAGCC
*
4131230 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGGA
1 ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGCTTTT-GA
* * *
4131269 ATTTAATGTTTGTTGCCTTTGGTTAAATGAGCTTTTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGC-TTTTGA
* * * *
4131308 ATTTAAAGTTTGTTGCCTTTGGTTAAATGAACTTTTTGG
1 ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGC-TTTTGA
* * ** * *
4131347 ATTTAAAGTTTGTTACCTCTGGTGGGAGGAACTTTTTAA
1 ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGC-TTTTGA
* * * *
4131386 CATTTAAAGTTTGTTGCCTCTGGTTAAAGAAGCTTTTTA
1 -ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGCTTTTGA
* * * * * *
4131425 GATTTAAAGTTTGTTACCTCTAGTGAGATGAGCTTTTTAA
1 -ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGC-TTTTGA
* * * * * *
4131465 CAATTAAAGTTAGTTACCTCTGGTGAGAGAAGCCTTTTGA
1 -ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAG-CTTTTGA
* * *
4131505 ATTTAAAGTTTGTTG-CTTCTGATGAAATGACCCTTTTGA
1 ATTTAAAGTTTGTTGCCTT-TGGTGAAAGGA-GCTTTTGA
*
4131544 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGCTTTTGA
* * * *
4131582 ATTTAAAGTTTGTTGCCTATGATGAGATGAGCTTTTTGA
1 ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGC-TTTTGA
4131621 ATTTAAAGTTT
1 ATTTAAAGTTT
4131632 TATAACCTCT
Statistics
Matches: 302, Mismatches: 53, Indels: 16
0.81 0.14 0.04
Matches are distributed among these distances:
38 36 0.12
39 196 0.65
40 69 0.23
41 1 0.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (38 bp):
ATTTAAAGTTTGTTGCCTTTGGTGAAAGGAGCTTTTGA
Found at i:4131410 original size:79 final size:76
Alignment explanation
Indices: 4131230--4131631 Score: 426
Period size: 79 Copynumber: 5.1 Consensus size: 76
4131220 TAAAAGAGCC
* * * * *
4131230 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGGAATTTAATGTTTGTTGCCTTTGGTTAA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAA-GAACTTTTGG-ATTTAAAGTTTGTTGCCTCTGGTGAG
4131295 ATGAGCTTTTTGA
64 ATGAGCTTTTTGA
* *
4131308 ATTTAAAGTTTGTTGCCTTTGGTTAAATGAACTTTTTGGATTTAAAGTTTGTTACCTCTGGTGGG
1 ATTTAAAGTTTGTTGCCTTTGGTTAAA-GAAC-TTTTGGATTTAAAGTTTGTTGCCTCTGGTGAG
* * *
4131373 AGGAACTTTTTAA
64 ATGAGCTTTTTGA
* * * *
4131386 CATTTAAAGTTTGTTGCCTCTGGTTAAAGAAGCTTTTTAGATTTAAAGTTTGTTACCTCTAGTGA
1 -ATTTAAAGTTTGTTGCCTTTGGTTAAAGAA-C-TTTTGGATTTAAAGTTTGTTGCCTCTGGTGA
*
4131451 GATGAGCTTTTTAA
63 GATGAGCTTTTTGA
* * * * * * * * *
4131465 CAATTAAAGTTAGTTACCTCTGGTGAGAGAAGCCTTTTGAATTTAAAGTTTGTTGCTTCTGATGA
1 -ATTTAAAGTTTGTTGCCTTTGGTTAAAGAA--CTTTTGGATTTAAAGTTTGTTGCCTCTGGTGA
* * *
4131530 AATGACCCTTTTGA
63 GATGAGCTTTTTGA
* * * *
4131544 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGAATTTAAAGTTTGTTGCCTATGATGAGA
1 ATTTAAAGTTTGTTGCCTTTGGTTAAA-GAACTTTTGGATTTAAAGTTTGTTGCCTCTGGTGAGA
4131609 TGAGCTTTTTGA
65 TGAGCTTTTTGA
4131621 ATTTAAAGTTT
1 ATTTAAAGTTT
4131632 TATAACCTCT
Statistics
Matches: 274, Mismatches: 45, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
77 52 0.19
78 84 0.31
79 137 0.50
80 1 0.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (76 bp):
ATTTAAAGTTTGTTGCCTTTGGTTAAAGAACTTTTGGATTTAAAGTTTGTTGCCTCTGGTGAGAT
GAGCTTTTTGA
Found at i:4131420 original size:118 final size:116
Alignment explanation
Indices: 4131230--4131631 Score: 432
Period size: 118 Copynumber: 3.4 Consensus size: 116
4131220 TAAAAGAGCC
* * * * * * * *
4131230 ATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGGAATTTAATGTTTGTTGCCTTTGGTTAA
1 ATTTAAAGTTTGTTACCTCTGGTGAGA-GAACTTTTTGAATTTAAAGTTTGTTGCCTCTGGTTAA
* *
4131295 ATGAGCTTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAATGAACTTTTTGG
65 ATGAGCTTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTTGA
* *
4131347 ATTTAAAGTTTGTTACCTCTGGTGGGAGGAACTTTTTAACATTTAAAGTTTGTTGCCTCTGGTTA
1 ATTTAAAGTTTGTTACCTCTGGTGAGA-GAACTTTTTGA-ATTTAAAGTTTGTTGCCTCTGGTTA
* * * * * *
4131412 AA-GAAGCTTTTT-AGATTTAAAGTTTGTTACCTCTAGTGAGATGAGCTTTTTAA
64 AATG-AGCTTTTTGA-ATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTTGA
* * * * * *
4131465 CAATTAAAGTTAGTTACCTCTGGTGAGAGAAGCCTTTTGAATTTAAAGTTTGTTGCTTCTGATGA
1 -ATTTAAAGTTTGTTACCTCTGGTGAGAGAA-CTTTTTGAATTTAAAGTTTGTTGCCTCTGGTTA
* * *
4131530 AATGACCCTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGC-TTTTGA
64 AATGAGCTTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTTGA
* * * *
4131582 ATTTAAAGTTTGTTGCCTATGATGAGATGAGCTTTTTGAATTTAAAGTTT
1 ATTTAAAGTTTGTTACCTCTGGTGAGA-GAACTTTTTGAATTTAAAGTTT
4131632 TATAACCTCT
Statistics
Matches: 235, Mismatches: 42, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
116 40 0.17
117 40 0.17
118 123 0.52
119 32 0.14
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (116 bp):
ATTTAAAGTTTGTTACCTCTGGTGAGAGAACTTTTTGAATTTAAAGTTTGTTGCCTCTGGTTAAA
TGAGCTTTTTGAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTTGA
Found at i:4133693 original size:3 final size:3
Alignment explanation
Indices: 4133685--4133714 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4133675 AATATGAAAG
4133685 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4133715 GTTAATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4135959 original size:23 final size:22
Alignment explanation
Indices: 4135925--4135967 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4135915 ATATTTATAT
*
4135925 ATAAATTTTAATTTTAAAAATA
1 ATAAATTTTAATATTAAAAATA
4135947 ATAAATATTTAATATTAAAAA
1 ATAAAT-TTTAATATTAAAAA
4135968 ATATTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAATTTTAATATTAAAAATA
Found at i:4135967 original size:24 final size:22
Alignment explanation
Indices: 4135925--4135970 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
4135915 ATATTTATAT
*
4135925 ATAAATTTTAATTTTAAAAATA
1 ATAAATTTTAATTTAAAAAATA
4135947 ATAAATATTTAATATTAAAAAATA
1 ATAAAT-TTTAAT-TTAAAAAATA
4135971 TTATGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 6 0.29
24 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATTTTAATTTAAAAAATA
Found at i:4137050 original size:35 final size:33
Alignment explanation
Indices: 4136985--4137061 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 33
4136975 TTGCTGATAA
4136985 AATATAATAAATAACTTTTAATATATAATAAATT
1 AATA-AATAAATAACTTTTAATATATAATAAATT
* *
4137019 AATAAATAAATAATTTTTGTATTATATAATAAATT
1 AATAAATAAATAA-CTTT-TAATATATAATAAATT
4137054 AATAAATA
1 AATAAATA
4137062 TTATAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 9 0.23
34 7 0.18
35 23 0.59
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
AATAAATAAATAACTTTTAATATATAATAAATT
Found at i:4137084 original size:22 final size:21
Alignment explanation
Indices: 4137038--4137091 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
4137028 ATAATTTTTG
4137038 TATTATATAATAAATTAATAAA
1 TATTATA-AATAAATTAATAAA
4137060 TATTATAAATAACATT-A-AAA
1 TATTATAAATAA-ATTAATAAA
4137080 TA-TATAAA-AAAT
1 TATTATAAATAAAT
4137092 AATTTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 6 0.19
20 5 0.16
21 6 0.19
22 10 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TATTATAAATAAATTAATAAA
Found at i:4141612 original size:5 final size:5
Alignment explanation
Indices: 4141602--4141647 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
4141592 GTTTGTTTAC
*
4141602 TTGTT TTGTT TT-TT TCTGTT TTGTTT TTTTT TTGTT TTGTT TTGTT
1 TTGTT TTGTT TTGTT T-TGTT TTG-TT TTGTT TTGTT TTGTT TTGTT
4141648 AAATATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 3 0.08
5 26 0.72
6 7 0.19
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (5 bp):
TTGTT
Found at i:4141631 original size:16 final size:16
Alignment explanation
Indices: 4141580--4141644 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
4141570 CCTTGACTTC
*
4141580 TTTCTTTTTTGTGTTTGT
1 TTTCTGTTTTGT-TTT-T
*
4141598 TTACTTGTTTTG-TTTT
1 TTTC-TGTTTTGTTTTT
4141614 TTTCTGTTTTGTTTTT
1 TTTCTGTTTTGTTTTT
*
4141630 TTTTTGTTTTGTTTT
1 TTTCTGTTTTGTTTT
4141645 GTTAAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.17
16 22 0.54
17 3 0.07
18 3 0.07
19 6 0.15
ACGTcount: A:0.02, C:0.05, G:0.14, T:0.80
Consensus pattern (16 bp):
TTTCTGTTTTGTTTTT
Found at i:4141634 original size:21 final size:21
Alignment explanation
Indices: 4141602--4141647 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
4141592 GTTTGTTTAC
*
4141602 TTGTTTTGTTTTT-TTCTGTT
1 TTGTTTTGTTTTTGTTTTGTT
*
4141622 TTGTTTTTTTTTTGTTTTGTT
1 TTGTTTTGTTTTTGTTTTGTT
4141643 TTGTT
1 TTGTT
4141648 AAATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (21 bp):
TTGTTTTGTTTTTGTTTTGTT
Found at i:4141636 original size:11 final size:12
Alignment explanation
Indices: 4141584--4141647 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
4141574 GACTTCTTTC
4141584 TTTTTTGTGTTTG
1 TTTTTTGT-TTTG
*
4141597 TTTACTTGTTTTG
1 TTT-TTTGTTTTG
4141610 TTTTTTTCTGTTTTG
1 --TTTTT-TGTTTTG
4141625 TTTTTT-TTTTG
1 TTTTTTGTTTTG
4141636 --TTTTGTTTTG
1 TTTTTTGTTTTG
4141646 TT
1 TT
4141648 AAATATTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
9 4 0.10
10 5 0.12
11 5 0.12
12 1 0.02
13 12 0.29
14 5 0.12
15 10 0.24
ACGTcount: A:0.02, C:0.03, G:0.16, T:0.80
Consensus pattern (12 bp):
TTTTTTGTTTTG
Found at i:4141973 original size:49 final size:49
Alignment explanation
Indices: 4141813--4143362 Score: 1883
Period size: 49 Copynumber: 31.7 Consensus size: 49
4141803 ACAGAAAAGG
* * *
4141813 GCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTTC-TTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * *
4141861 CCTCCTCTCAACAGAGGTTCCACAACTTTAAAATTT-TATT-TCGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
* * *
4141909 GCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * *
4141958 GCTCGTCTCAACAGAGGCTTCACAACTTTAAAATTT-TTATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTT-TCTTGAAAAA
4142007 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* *
4142055 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTTC--GGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TC-TTTCTTGAAAAA
* * *
4142104 GCTCCTCTTAACAGAGGCTCCACAACTTTAAAA-TTCTCATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
*
4142153 GCTCCCCTGCTCTCAGCAGAGGCTCCACAACTTTAAAATTTC-TTCTTGAAAAA
1 GCT---C--CTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * * *
4142206 GCTCCTCTCAATAGA-GTTCCACAACTTTAAAATTT-TATT-TCGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
* * *
4142253 GCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * * *
4142302 GCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTT-TCATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
4142351 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* *
4142399 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTTC--GGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TC-TTTCTTGAAAAA
* * *
4142448 GCTCCTCTTAACAGAGGCTCCACAACTTTAAAA-TTCTCATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
*
4142497 GCTCCCCTGCTCTCAGCAGAGGCTCCACAACTTTAAAATTTC-TTCTTGAAAAA
1 GCT---C--CTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * * *
4142550 GCTCCTCTCAATAGAGGTTCCACAACTTTAAAATTT-TATT-TCGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
* * *
4142598 GCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * * *
4142647 GCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTT-TCATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
4142696 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* *
4142744 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTTC--GGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TC-TTTCTTGAAAAA
* * *
4142793 GCTCCTCTTAACAGAGGCTCCACAACTTTAAAA-TTCTCATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
*
4142842 GCTCCCCTGCTCTTAGCAGAGGCTCCACAAC-TTAAAATTTC-TTCTTGAAAAA
1 GCT--CCT-CTC--AACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * *
4142894 GCTCCTCTCAACAGAGGTTCCACAACTTTAAAATTT-TATT-TCGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
* * *
4142942 GCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * *
4142991 GCTCCTCTCAACAGAGGCTTCACAACTTTAAAATTT-TCATCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCT-TTCTTGAAAAA
*
4143040 GCTCCTCTCAACAGAGGCTTCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
*
4143088 GCTCCTCTCAATAGAGGCTCCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * * *
4143136 GCTACTCTCAACAGAGGCTCAACGACTTTAAAATCT-TTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
*
4143184 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
* * * *
4143232 GCTCTTCTCAACAAAGGTTCCACAACTTTAAAAATTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
*
4143281 GCTCCTCTCAACAGAGGCTCAACAACTTTAAAA-TTCTTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTC-TTTCTTGAAAAA
* *
4143330 GCTCCTTTCAACAGAGGCTCAACAACTTTAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA
4143363 ATCTCATTTA
Statistics
Matches: 1304, Mismatches: 132, Indels: 131
0.83 0.08 0.08
Matches are distributed among these distances:
46 3 0.00
47 66 0.05
48 527 0.40
49 557 0.43
50 11 0.01
51 15 0.01
52 16 0.01
53 30 0.02
54 73 0.06
55 6 0.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (49 bp):
GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
Found at i:4142450 original size:344 final size:345
Alignment explanation
Indices: 4141817--4143362 Score: 2638
Period size: 344 Copynumber: 4.5 Consensus size: 345
4141807 AAAAGGGCTC
* * *
4141817 CTCTTAGCAGAGGCTCAACAACTTTAAAATTTCTTCTTGAAAAACCTCCTCTCAACAGAGGTTCC
1 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGTTCC
*
4141882 ACAACTTTAAAATTTTATTTCGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
66 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
* * *
4141947 TTCTTGAAAAAGCTCGTCTCAACAGAGGCTTCACAACTTTAAAATTTTTATCTTGGAAAAGCTCC
131 TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
4142012 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
196 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
4142077 CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
261 CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
4142142 ATCTTGGAAAAGCTCCCCTG
326 ATCTTGGAAAAGCTCCCCTG
*
4142162 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAATAGA-GTTCC
1 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGTTCC
4142226 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
66 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
4142291 TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
131 TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
4142356 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
196 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
4142421 CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
261 CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
4142486 ATCTTGGAAAAGCTCCCCTG
326 ATCTTGGAAAAGCTCCCCTG
*
4142506 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAATAGAGGTTCC
1 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGTTCC
4142571 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
66 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
4142636 TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
131 TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
4142701 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
196 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
4142766 CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
261 CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
4142831 ATCTTGGAAAAGCTCCCCTG
326 ATCTTGGAAAAGCTCCCCTG
*
4142851 CTCTTAGCAGAGGCTCCACAAC-TTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGTTCC
1 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGTTCC
4142915 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
66 ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
*
4142980 TTCTTGAAAAAGCTCCTCTCAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
131 TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
* * *
4143045 TCTCAACAGAGGCTTCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAATAGAGGCTCCA
196 TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
* * * * * *
4143110 CAACTTTAAAATTCT--TTCTTGAAAAAGCTACTCTCAACAGAGGCTCAACGACTTTAAAA-TCT
261 CAACTTTAAAATTCTCATT-TCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCT
** *
4143172 TTTCTTGAAAAAGCT---C--
325 CATCTTGGAAAAGCTCCCCTG
* * * *
4143188 CTCTCAACAGAGGCTCTACAACTTTAAAA-TTCTTTCTTGAAAAAGCTCTTCTCAACAAAGGTTC
1 CTCTCAGCAGAGGCTCCACAACTTTAAAATTTC-TTCTTGAAAAAGCTCCTCTCAACAGAGGTTC
* * *
4143252 CACAACTTTAAAAATTCTT-TCTT-GAAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAA-
65 CACAACTTT-AAAATT-TTAT-TTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAAT
4143314 TTCTTTTCTTGAAAAAGCTCCT-TTCAACAGAGGC-TCAACAACTTTAAAA
127 TTC-TTTCTTGAAAAAGCTCCTCTT-AACAGAGGCTTC-ACAACTTTAAAA
4143363 ATCTCATTTA
Statistics
Matches: 1159, Mismatches: 32, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
337 22 0.02
338 50 0.04
339 83 0.07
340 4 0.00
342 17 0.01
343 35 0.03
344 587 0.51
345 361 0.31
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (345 bp):
CTCTCAGCAGAGGCTCCACAACTTTAAAATTTCTTCTTGAAAAAGCTCCTCTCAACAGAGGTTCC
ACAACTTTAAAATTTTATTTCGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTCAAAATTTCT
TTCTTGAAAAAGCTCCTCTTAACAGAGGCTTCACAACTTTAAAATTTTCATCTTGGAAAAGCTCC
TCTCAACAGAGGCTCCACAACTTTAAAATTCTTTCTTGAAAAAGCTCCTCTCAACAGAGGCTCTA
CAACTTTAAAATTCTCATTTCGGAAAAGCTCCTCTTAACAGAGGCTCCACAACTTTAAAATTCTC
ATCTTGGAAAAGCTCCCCTG
Found at i:4156585 original size:15 final size:15
Alignment explanation
Indices: 4156565--4156605 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 15
4156555 TGTTTACTTG
4156565 TTTTGTTTTTTTCTA
1 TTTTGTTTTTTTCTA
*
4156580 TTTTGTTTTTTTTTCTT
1 TTTTG--TTTTTTTCTA
4156597 TTTTGTTTT
1 TTTTGTTTT
4156606 GTTTTGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
17 14 0.61
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (15 bp):
TTTTGTTTTTTTCTA
Found at i:4156590 original size:17 final size:17
Alignment explanation
Indices: 4156570--4156610 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4156560 ACTTGTTTTG
4156570 TTTTTTTCTATTTTGTT
1 TTTTTTTCTATTTTGTT
*
4156587 TTTTTTTCTTTTTTGTT
1 TTTTTTTCTATTTTGTT
4156604 TTGTTTT
1 TT-TTTT
4156611 GTTAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTATTTTGTT
Found at i:4156598 original size:22 final size:21
Alignment explanation
Indices: 4156565--4156610 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4156555 TGTTTACTTG
4156565 TTTTGTTTTTTTCTATTTTGT
1 TTTTGTTTTTTTCTATTTTGT
* * *
4156586 TTTTTTTTCTTTTTTGTTTTGT
1 TTTTGTTT-TTTTCTATTTTGT
4156608 TTT
1 TTT
4156611 GTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (21 bp):
TTTTGTTTTTTTCTATTTTGT
Found at i:4158404 original size:19 final size:21
Alignment explanation
Indices: 4158368--4158415 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
4158358 ATTCCAATTA
*
4158368 AAAACAAAATCGTAAAAAAC-
1 AAAACAAAAACGTAAAAAACT
4158388 AAAACAAAAAC-TAAAAAACT
1 AAAACAAAAACGTAAAAAACT
4158408 AAAA-AAAA
1 AAAACAAAA
4158416 GTTAAACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAACAAAAACGTAAAAAACT
Found at i:4159579 original size:30 final size:30
Alignment explanation
Indices: 4159513--4159575 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
4159503 TCTATAAAAT
4159513 AAAATAAAAATTAACTAAAAATTATTAATA
1 AAAATAAAAATTAACTAAAAATTATTAATA
**
4159543 AAAATAAATTTTAACT-AAAATTATTAATA
1 AAAATAAAAATTAACTAAAAATTATTAATA
4159572 AAAA
1 AAAA
4159576 ATAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATAAAAATTAACTAAAAATTATTAATA
Found at i:4160281 original size:19 final size:18
Alignment explanation
Indices: 4160237--4160285 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
4160227 TATCTTTTTA
*
4160237 GTAAATTTTAA-TAAATT
1 GTAAATTTTAATTAAATG
*
4160254 TTAAGATTTTAATTAAAATG
1 GTAA-ATTTTAATT-AAATG
4160274 GTAAATTTTAAT
1 GTAAATTTTAAT
4160286 AGGTGGTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 7 0.27
19 9 0.35
20 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
GTAAATTTTAATTAAATG
Found at i:4169956 original size:35 final size:35
Alignment explanation
Indices: 4169917--4169986 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
4169907 TAGAAGATGC
4169917 CTTAAATGTCATATTTATTCTGATAAGATTCATGT
1 CTTAAATGTCATATTTATTCTGATAAGATTCATGT
*
4169952 CTTAAATGTCATATTTATTTTGATAAGATTCATGT
1 CTTAAATGTCATATTTATTCTGATAAGATTCATGT
4169987 TCTTTCATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.47
Consensus pattern (35 bp):
CTTAAATGTCATATTTATTCTGATAAGATTCATGT
Found at i:4171892 original size:51 final size:50
Alignment explanation
Indices: 4171775--4171896 Score: 111
Period size: 51 Copynumber: 2.4 Consensus size: 50
4171765 AATTGTTAAA
* * * * *
4171775 CCTCTGCTTAGATGAACTTTTTTAAAAATGAAAATTTTTAAAGTTATTGAG
1 CCTCTGCTTAAAGGAGC-TTTTTAAAAATGAAAATTGTTAAAGTTAATGAG
* * * *
4171826 TCTCTGCTTAAAGGAGTCTTTTTCAAGATGAGAATTGTTAAAGTTAATGAG
1 CCTCTGCTTAAAGGAG-CTTTTTAAAAATGAAAATTGTTAAAGTTAATGAG
* *
4171877 CCTTTG-TTCAGAGGAGCTTT
1 CCTCTGCTT-AAAGGAGCTTT
4171897 CCTTATCAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
50 6 0.11
51 50 0.88
52 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (50 bp):
CCTCTGCTTAAAGGAGCTTTTTAAAAATGAAAATTGTTAAAGTTAATGAG
Found at i:4172473 original size:6 final size:6
Alignment explanation
Indices: 4172462--4172521 Score: 84
Period size: 6 Copynumber: 9.7 Consensus size: 6
4172452 CCTGAACCCA
* *
4172462 TTATTT TTATTT TTATTT TTATTT TCATTT TTACTT TTATTT TTATTCT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATT-T
4172511 ATTATTT TTAT
1 -TTATTT TTAT
4172522 AGTTTTATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 41 0.85
7 2 0.04
8 5 0.10
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:4173748 original size:8 final size:8
Alignment explanation
Indices: 4173735--4173768 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4173725 AATTTAGATT
4173735 TTTTTTTA
1 TTTTTTTA
4173743 TTTTTTTA
1 TTTTTTTA
*
4173751 TTTTTTGA
1 TTTTTTTA
4173759 TTTTCTTTA
1 TTTT-TTTA
4173768 T
1 T
4173769 CATTTTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:4173924 original size:14 final size:15
Alignment explanation
Indices: 4173907--4173952 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
4173897 TAAACTTTAT
4173907 AAAATAATA-AAATA
1 AAAATAATATAAATA
4173921 AAAATAA-ATAAATA
1 AAAATAATATAAATA
*
4173935 ATAATAATGATAAA-A
1 AAAATAAT-ATAAATA
4173950 AAA
1 AAA
4173953 TAGAAGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 3 0.11
16 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAATATAAATA
Found at i:4174299 original size:30 final size:30
Alignment explanation
Indices: 4174225--4174295 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
4174215 TCCTTTTTTC
* *
4174225 TATTAA-ATAAAATAAAATTTATCTAAAAAT
1 TATTAATA-AAAATAAAAATTAACTAAAAAT
*
4174255 TATTAATAAAAATAAAAATTAACT-AAAGT
1 TATTAATAAAAATAAAAATTAACTAAAAAT
*
4174284 TATTTATAAAAA
1 TATTAATAAAAA
4174296 ATAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 15 0.42
30 20 0.56
31 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (30 bp):
TATTAATAAAAATAAAAATTAACTAAAAAT
Found at i:4176409 original size:9 final size:8
Alignment explanation
Indices: 4176397--4176428 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4176387 TTCTTTTTTC
4176397 TTTTTTAT
1 TTTTTTAT
4176405 TTTTTTAT
1 TTTTTTAT
4176413 TTTTTTAT
1 TTTTTTAT
*
4176421 TATTTTAT
1 TTTTTTAT
4176429 AAGATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:4176580 original size:21 final size:20
Alignment explanation
Indices: 4176556--4176617 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
4176546 TAACATGCAT
4176556 AAATATTAATAATAAAATTTA
1 AAATATTAA-AATAAAATTTA
** *
4176577 AAATAACAAAAATAATATTTA
1 AAAT-ATTAAAATAAAATTTA
* *
4176598 AAAAATTCAAAAAAAAATTT
1 AAATATT-AAAATAAAATTT
4176618 TTTTTTACCT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.03
21 27 0.87
22 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATTAAAATAAAATTTA
Found at i:4177636 original size:9 final size:8
Alignment explanation
Indices: 4177608--4177687 Score: 52
Period size: 9 Copynumber: 9.0 Consensus size: 8
4177598 AGCCCCCTCC
4177608 TTTTTATT
1 TTTTTATT
*
4177616 TCTTCTATTT
1 T-TTTTA-TT
4177626 TTTTGTATT
1 TTTT-TATT
4177635 TTTTTAGTAT
1 TTTTTA-T-T
*
4177645 TTATTATT
1 TTTTTATT
*
4177653 TTTGTATT
1 TTTTTATT
4177661 TTTTTAATAT
1 TTTTT-AT-T
*
4177671 TTTGTATT
1 TTTTTATT
4177679 TTTTATATT
1 TTTT-TATT
4177688 CTGTATTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 18 0.32
9 22 0.39
10 16 0.29
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (8 bp):
TTTTTATT
Found at i:4177654 original size:26 final size:26
Alignment explanation
Indices: 4177621--4177681 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
4177611 TTATTTCTTC
*
4177621 TATT-TTTTTGTATTTTTTTAGTATT
1 TATTATTTTTGTATTTTTTTAATATT
4177646 TATTATTTTTGTATTTTTTTAATATT
1 TATTATTTTTGTATTTTTTTAATATT
4177672 T-TGTATTTTT
1 TAT-TATTTTT
4177682 TATATTCTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 5 0.15
26 28 0.85
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (26 bp):
TATTATTTTTGTATTTTTTTAATATT
Found at i:4177673 original size:18 final size:17
Alignment explanation
Indices: 4177608--4177697 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 17
4177598 AGCCCCCTCC
*
4177608 TTTTTAT-TTCTTCTATT
1 TTTTTATATT-TTGTATT
* *
4177625 TTTTTGTATTTTTTTAGTAT
1 TTTTTATA-TTTTGTA-T-T
*
4177645 TTATTAT-TTTTGTATT
1 TTTTTATATTTTGTATT
4177661 TTTTTAATATTTTGTA-T
1 TTTTT-ATATTTTGTATT
*
4177678 TTTTTATATTCTGTATT
1 TTTTTATATTTTGTATT
4177695 TTT
1 TTT
4177698 GTTTAATTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
16 14 0.24
17 19 0.32
18 17 0.29
19 3 0.05
20 6 0.10
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTTATATTTTGTATT
Found at i:4177686 original size:16 final size:16
Alignment explanation
Indices: 4177636--4177697 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
4177626 TTTTGTATTT
*
4177636 TTTTAGTATTTATTAT-
1 TTTT-GTATTTTTTATA
4177652 TTTTGTATTTTTTTAATA
1 TTTTGTA-TTTTTT-ATA
4177670 TTTTGTATTTTTTATA
1 TTTTGTATTTTTTATA
*
4177686 TTCTGTATTTTT
1 TTTTGTATTTTT
4177698 GTTTAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.07
16 23 0.56
17 8 0.20
18 7 0.17
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (16 bp):
TTTTGTATTTTTTATA
Found at i:4178127 original size:48 final size:49
Alignment explanation
Indices: 4178058--4178279 Score: 218
Period size: 48 Copynumber: 4.6 Consensus size: 49
4178048 TCTTCTCAGC
* ** * *
4178058 AGAGGCTCAACAAATTT-AAAATTTTGTCTTGAAAAAGTTCCTTTAAGT
1 AGAGGCTCAACAAATTTAAAAATCTCATCTAGAAAAAGTTCCTCTAAGT
* *
4178106 AGAGGCTCAA-AACTTTAAAAATCTCATCTAGAAAAAGTTCCTCTCAGT
1 AGAGGCTCAACAAATTTAAAAATCTCATCTAGAAAAAGTTCCTCTAAGT
* * * * * * *
4178154 AGAGGCTCAACAATTTTAAAAATCCTCATTTTGAAAAAGCTCTTCTCAGC
1 AGAGGCTCAACAAATTTAAAAAT-CTCATCTAGAAAAAGTTCCTCTAAGT
* * * * *
4178204 AGAGGCTTAACAACTTT-AAAATCTCATCTGGAAAAAGCTCATCTCAA-T
1 AGAGGCTCAACAAATTTAAAAATCTCATCTAGAAAAAGTTCCTCT-AAGT
*
4178252 AGAGGCTCAACAACTTTAAAAATCTCAT
1 AGAGGCTCAACAAATTTAAAAATCTCAT
4178280 ATGTTCTCCA
Statistics
Matches: 148, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
47 5 0.03
48 80 0.54
49 27 0.18
50 36 0.24
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (49 bp):
AGAGGCTCAACAAATTTAAAAATCTCATCTAGAAAAAGTTCCTCTAAGT
Found at i:4190112 original size:10 final size:10
Alignment explanation
Indices: 4190097--4190127 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
4190087 TTTTATTTGA
4190097 AAATTTTATT
1 AAATTTTATT
4190107 AAATTTTATT
1 AAATTTTATT
4190117 AAATTTTATT
1 AAATTTTATT
4190127 A
1 A
4190128 TTTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
AAATTTTATT
Found at i:4191763 original size:27 final size:26
Alignment explanation
Indices: 4191724--4191804 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
4191714 CCCCTTTTGG
*
4191724 TTTTTTTTTGTATTTTATATTTTTATA
1 TTTTTTTTGGTATTTTATATTTTT-TA
*
4191751 TTTTTTTTGGTATTTTTTATTTTTTA
1 TTTTTTTTGGTATTTTATATTTTTTA
* *
4191777 -TTATTTTGGTGTTTGTAT-TTTTTGTA
1 TTTTTTTTGGTATTT-TATATTTTT-TA
4191803 TT
1 TT
4191805 CTATATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
25 17 0.37
26 6 0.13
27 23 0.50
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.77
Consensus pattern (26 bp):
TTTTTTTTGGTATTTTATATTTTTTA
Found at i:4195420 original size:19 final size:19
Alignment explanation
Indices: 4195373--4195421 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
4195363 TTTTCGTGTT
* * *
4195373 TCATTGTAACAGTCTACTA
1 TCATTGTAGCAATCTACGA
*
4195392 TCATTATAGCAATCTACGA
1 TCATTGTAGCAATCTACGA
*
4195411 TTATTGTAGCA
1 TCATTGTAGCA
4195422 GTAATAGTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (19 bp):
TCATTGTAGCAATCTACGA
Found at i:4198151 original size:11 final size:11
Alignment explanation
Indices: 4198137--4198259 Score: 51
Period size: 11 Copynumber: 10.5 Consensus size: 11
4198127 TAGAATAATA
4198137 AAAAAATAAAT
1 AAAAAATAAAT
4198148 AAAATAA-AAAT
1 AAAA-AATAAAT
4198159 AAAAAGA-AAAGT
1 AAAAA-ATAAA-T
4198171 AAAACAA-AAAT
1 AAAA-AATAAAT
4198182 -AAAAATAAAT
1 AAAAAATAAAT
*
4198192 AAGATAAAAAGAAT
1 AA-A-AAATA-AAT
**
4198206 ATTAAATAAACCT
1 AAAAAATAAA--T
*
4198219 AATATAATAAAT
1 AA-AAAATAAAT
4198231 AAATAAAATAAAT
1 -AA-AAAATAAAT
4198244 ATAAAAA-AAA-
1 A-AAAAATAAAT
4198254 AAAAAA
1 AAAAAA
4198260 ACCTGGAGCG
Statistics
Matches: 90, Mismatches: 8, Indels: 30
0.70 0.06 0.23
Matches are distributed among these distances:
9 7 0.08
10 9 0.10
11 23 0.26
12 22 0.24
13 19 0.21
14 10 0.11
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:4198159 original size:6 final size:6
Alignment explanation
Indices: 4198123--4198190 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
4198113 TTATTTAAAG
* *
4198123 AAAATA GAATAATA AAAA-A ATAAAT- AAAATA AAAATA AAAAGA AAAGT-
1 AAAATA -AA-AATA AAAATA A-AAATA AAAATA AAAATA AAAATA AAAATA
*
4198171 AAAACA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AA
4198191 TAAGATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
5 9 0.18
6 33 0.66
7 4 0.08
8 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:4198251 original size:13 final size:13
Alignment explanation
Indices: 4198118--4198244 Score: 62
Period size: 12 Copynumber: 10.2 Consensus size: 13
4198108 TATTTTTATT
*
4198118 TAAAGAAAATAGAA
1 TAAATAAAATA-AA
4198132 T-AATAAAA-AAA
1 TAAATAAAATAAA
4198143 TAAATAAAAT-AA
1 TAAATAAAATAAA
4198155 -AAATAAAA-AGAA
1 TAAATAAAATA-AA
* *
4198167 -AAGTAAAA-CAA
1 TAAATAAAATAAA
4198178 -AAATAAAAATAAA
1 TAAAT-AAAATAAA
4198191 TAAGATAAAA-AGAA
1 TAA-ATAAAATA-AA
*
4198205 T--ATTAAATAAA
1 TAAATAAAATAAA
*
4198216 CCT-AATATAATAAA
1 --TAAATAAAATAAA
4198230 TAAATAAAATAAA
1 TAAATAAAATAAA
4198243 TA
1 TA
4198245 TAAAAAAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.26
12 25 0.28
13 22 0.24
14 18 0.20
15 2 0.02
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:4199240 original size:14 final size:14
Alignment explanation
Indices: 4199199--4199320 Score: 67
Period size: 14 Copynumber: 8.4 Consensus size: 14
4199189 AAAAGAAAAA
4199199 AATAAT-TATAATAT
1 AATAATATA-AATAT
4199213 AATAATA-AATATAT
1 AATAATATAA-ATAT
*
4199227 AATTATATAAATAT
1 AATAATATAAATAT
4199241 AATACATATAAATATT
1 AATA-ATATAAATA-T
* *
4199257 AACAGAGA-AAATA-
1 AATA-ATATAAATAT
4199270 AATAA-ATAAATA-
1 AATAATATAAATAT
*
4199282 AATAAAGATATACATAT
1 AAT--A-ATATAAATAT
*
4199299 ATTAATATATAATAAT
1 AATAATATA-AAT-AT
4199315 AATAAT
1 AATAAT
4199321 GAATAATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
11 1 0.01
12 9 0.11
13 4 0.05
14 30 0.35
15 20 0.24
16 19 0.22
17 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:4199242 original size:25 final size:25
Alignment explanation
Indices: 4199200--4199250 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
4199190 AAAGAAAAAA
*
4199200 ATAATTATAATATAATAATAAATAT
1 ATAATTATAAAATAATAATAAATAT
*
4199225 ATAATTATATAAAT-ATAATACATAT
1 ATAATTATA-AAATAATAATAAATAT
4199250 A
1 A
4199251 AATATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATTATAAAATAATAATAAATAT
Found at i:4203913 original size:18 final size:17
Alignment explanation
Indices: 4203892--4203939 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
4203882 TTTTTTTGTA
4203892 TTTTATATTTTTATATTT
1 TTTTATATTTTT-TATTT
*
4203910 TTTTGGTATTTTTTATTT
1 TTTT-ATATTTTTTATTT
4203928 TTTTATTATTTT
1 TTTTA-TATTTT
4203940 GGTGTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (17 bp):
TTTTATATTTTTTATTT
Found at i:4203918 original size:26 final size:26
Alignment explanation
Indices: 4203881--4203960 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
4203871 AGCCTCCCCC
*
4203881 TTTTTTTTGTATTTTATATTTTTATA
1 TTTTTTTGGTATTTTATATTTTTATA
* *
4203907 TTTTTTTGGTATTTTTTATTTTTTTA
1 TTTTTTTGGTATTTTATATTTTTATA
* * *
4203933 TTATTTTGGTGTTTGTAT-TTTTTGTA
1 TTTTTTTGGTATTT-TATATTTTTATA
4203959 TT
1 TT
4203961 CTATATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
26 44 0.96
27 2 0.04
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (26 bp):
TTTTTTTGGTATTTTATATTTTTATA
Found at i:4207593 original size:19 final size:19
Alignment explanation
Indices: 4207546--4207594 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
4207536 TTTTCGTGTT
* *
4207546 TCATTGTAGCAGTCTACTA
1 TCATTGTAGCAATCTACGA
* *
4207565 TCACTATAGCAATCTACGA
1 TCATTGTAGCAATCTACGA
*
4207584 TTATTGTAGCA
1 TCATTGTAGCA
4207595 GCAATAGTAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (19 bp):
TCATTGTAGCAATCTACGA
Found at i:4209564 original size:31 final size:30
Alignment explanation
Indices: 4209528--4209592 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
4209518 TAAAAATAGG
4209528 AAAACCCTA-AAAAAAAAAACCCATCTAAGAA
1 AAAACCCTACAAAAAAAAAACCCA-CTAA-AA
* **
4209559 AAAACCCTACAAACAAAAGCCCCACTAAAA
1 AAAACCCTACAAAAAAAAAACCCACTAAAA
4209589 AAAA
1 AAAA
4209593 GGTTTTGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.20
31 13 0.43
32 11 0.37
ACGTcount: A:0.63, C:0.26, G:0.03, T:0.08
Consensus pattern (30 bp):
AAAACCCTACAAAAAAAAAACCCACTAAAA
Found at i:4209788 original size:23 final size:23
Alignment explanation
Indices: 4209755--4209808 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
4209745 ACTTTGGGCT
*
4209755 TTGATCTAAGCTATTTTAGGTCA
1 TTGATCCAAGCTATTTTAGGTCA
4209778 TTGATCCAAGCTATTTTAGGTCA
1 TTGATCCAAGCTATTTTAGGTCA
4209801 TTGATCCA
1 TTGATCCA
4209809 TATTCAGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (23 bp):
TTGATCCAAGCTATTTTAGGTCA
Found at i:4210794 original size:130 final size:130
Alignment explanation
Indices: 4210554--4210794 Score: 335
Period size: 130 Copynumber: 1.9 Consensus size: 130
4210544 TAAATAATAA
4210554 AATAACAATAAAGTCACGAGTGGTGATTTTATTAAGAATATTCTCACAAAGAAACTTTCTAAAAT
1 AATAACAATAAAGTCACGAGTGGTGATTTTATTAAGAATATTCTCACAAAGAAACTTTCTAAAAT
* **
4210619 ATTCTAAAAGTGTTAGAAGTATTTTAGAATTTTTCAAGGAAAAAAAAGAATTAAAAAAAATTACT
66 ATTCTAAAAGTGTTAGAAATATTTTAGAATTTTTCAAACAAAAAAAAGAATTAAAAAAAATTACT
* * * *
4210684 AATAACAATAAAGTTACTAGTGGTGATTTTATTGAA-AATATTCAT-ACAAATAAATTTTCTAAA
1 AATAACAATAAAGTCACGAGTGGTGATTTTATT-AAGAATATTC-TCACAAAGAAACTTTCTAAA
* * * *
4210747 ATGCTT-TAAAAGTGTTGGAAATGTTTTAGAATTTTTCAAACATAAAAA
64 AT-ATTCTAAAAGTGTTAGAAATATTTTAGAATTTTTCAAACAAAAAAA
4210795 TAATAAAAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
130 92 0.95
131 5 0.05
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (130 bp):
AATAACAATAAAGTCACGAGTGGTGATTTTATTAAGAATATTCTCACAAAGAAACTTTCTAAAAT
ATTCTAAAAGTGTTAGAAATATTTTAGAATTTTTCAAACAAAAAAAAGAATTAAAAAAAATTACT
Found at i:4211725 original size:18 final size:18
Alignment explanation
Indices: 4211702--4211737 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4211692 CTACCATTCT
*
4211702 TTGTATACGTGAATAGTA
1 TTGTATACGTAAATAGTA
*
4211720 TTGTATATGTAAATAGTA
1 TTGTATACGTAAATAGTA
4211738 CCATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (18 bp):
TTGTATACGTAAATAGTA
Found at i:4212197 original size:19 final size:19
Alignment explanation
Indices: 4212156--4212203 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4212146 ATTTTCACAT
* *
4212156 TTACTGTAGCAGTCTATTA
1 TTACTGTAGCAGTCAATGA
*
4212175 TTACTGTAGCAGTCAATGG
1 TTACTGTAGCAGTCAATGA
*
4212194 TTACTATAGC
1 TTACTGTAGC
4212204 GATGGCGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (19 bp):
TTACTGTAGCAGTCAATGA
Found at i:4213522 original size:23 final size:25
Alignment explanation
Indices: 4213496--4213560 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
4213486 TAAATTAATA
*
4213496 AATAAATAAATT-T-TGTATTATAT
1 AATAAATAAATTATATGTATCATAT
4213519 AATAAATAAATTATATGTATCATAT
1 AATAAATAAATTATATGTATCATAT
* *
4213544 ATATATATATATTATAT
1 A-ATAAATAAATTATAT
4213561 TACAACATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.33
24 1 0.03
25 10 0.28
26 13 0.36
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (25 bp):
AATAAATAAATTATATGTATCATAT
Found at i:4216780 original size:30 final size:30
Alignment explanation
Indices: 4216746--4216818 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
4216736 ATCATTTTTC
*
4216746 TTGAAATCAAATCATTTTGAATTTTG-AATT
1 TTGAAAACAAATCATTTT-AATTTTGAAATT
* *
4216776 TTGAAAACAAACCATTTTATTTTTGAAATT
1 TTGAAAACAAATCATTTTAATTTTGAAATT
*
4216806 TTAAAAACAAATC
1 TTGAAAACAAATC
4216819 TAATTATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.16
30 31 0.84
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (30 bp):
TTGAAAACAAATCATTTTAATTTTGAAATT
Found at i:4216828 original size:29 final size:28
Alignment explanation
Indices: 4216766--4216829 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
4216756 ATCATTTTGA
* *
4216766 ATTTTGAATTTTGAAAACAAACCATTTT
1 ATTTTGAATTTTAAAAACAAACCATATT
*
4216794 ATTTTTGAAATTTTAAAAACAAATC-TAATT
1 A-TTTTG-AATTTTAAAAACAAACCAT-ATT
4216824 ATTTTG
1 ATTTTG
4216830 GATCAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (28 bp):
ATTTTGAATTTTAAAAACAAACCATATT
Found at i:4217284 original size:12 final size:12
Alignment explanation
Indices: 4217269--4217293 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4217259 TAGGTTTTTG
4217269 GTTTAAGGTTTA
1 GTTTAAGGTTTA
4217281 GTTTAAGGTTTA
1 GTTTAAGGTTTA
4217293 G
1 G
4217294 GGTTTAATTT
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:0.28, T:0.48
Consensus pattern (12 bp):
GTTTAAGGTTTA
Found at i:4217284 original size:19 final size:19
Alignment explanation
Indices: 4217268--4217310 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
4217258 TTAGGTTTTT
4217268 GGTTTAAGGTTTAGTTTAA
1 GGTTTAAGGTTTAGTTTAA
* * *
4217287 GGTTTAGGGTTTAATTTAG
1 GGTTTAAGGTTTAGTTTAA
4217306 GGTTT
1 GGTTT
4217311 GGGGCTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (19 bp):
GGTTTAAGGTTTAGTTTAA
Found at i:4217310 original size:26 final size:26
Alignment explanation
Indices: 4217281--4217345 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
4217271 TTAAGGTTTA
4217281 GTTTAAGGTTTAGGGTTTAATTTAGG
1 GTTTAAGGTTTAGGGTTTAATTTAGG
** * * **
4217307 GTTTGGGGCTTAAGGTTTGGTTTAGG
1 GTTTAAGGTTTAGGGTTTAATTTAGG
*
4217333 GTCTAAGGTTTAG
1 GTTTAAGGTTTAG
4217346 ATGTAATTAA
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.43
Consensus pattern (26 bp):
GTTTAAGGTTTAGGGTTTAATTTAGG
Found at i:4217319 original size:19 final size:19
Alignment explanation
Indices: 4217268--4217319 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
4217258 TTAGGTTTTT
* * *
4217268 GGTTTAAGGTTTAGTTTAA
1 GGTTTAGGGCTTAATTTAA
* *
4217287 GGTTTAGGGTTTAATTTAG
1 GGTTTAGGGCTTAATTTAA
*
4217306 GGTTTGGGGCTTAA
1 GGTTTAGGGCTTAA
4217320 GGTTTGGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (19 bp):
GGTTTAGGGCTTAATTTAA
Found at i:4219909 original size:19 final size:17
Alignment explanation
Indices: 4219865--4219919 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
4219855 AAAAAGAGAG
*
4219865 AAACAAAAAAC-ATAAA
1 AAACAAAAAACAAAAAA
*
4219881 AAACATAAAAGCAAAAAA
1 AAACA-AAAAACAAAAAA
4219899 AATACAAAAAACAAAAAA
1 AA-ACAAAAAACAAAAAA
4219917 AAA
1 AAA
4219920 AACTTTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 19 0.58
19 3 0.09
ACGTcount: A:0.82, C:0.11, G:0.02, T:0.05
Consensus pattern (17 bp):
AAACAAAAAACAAAAAA
Found at i:4219914 original size:24 final size:23
Alignment explanation
Indices: 4219865--4219921 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
4219855 AAAAAGAGAG
* *
4219865 AAACAAAAAACATAAAAAACATA
1 AAACAAAAAAAATAAAAAACACA
4219888 AAAGCAAAAAAAATACAAAAA-ACA
1 AAA-CAAAAAAAATA-AAAAACACA
4219912 AAA-AAAAAAA
1 AAACAAAAAAA
4219922 CTTTGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 7 0.23
23 3 0.10
24 15 0.50
25 5 0.17
ACGTcount: A:0.82, C:0.11, G:0.02, T:0.05
Consensus pattern (23 bp):
AAACAAAAAAAATAAAAAACACA
Found at i:4228329 original size:12 final size:12
Alignment explanation
Indices: 4228314--4228366 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
4228304 TCTATTTTCT
*
4228314 ATTTTGATTTTG
1 ATTTTGATGTTG
4228326 ATTTT-AT-TT-
1 ATTTTGATGTTG
4228335 ATTTTG-TGTTG
1 ATTTTGATGTTG
*
4228346 ATTTTTATGTTG
1 ATTTTGATGTTG
*
4228358 ACTTTGATG
1 ATTTTGATG
4228367 ATTTTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
9 6 0.18
10 4 0.12
11 7 0.21
12 17 0.50
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.64
Consensus pattern (12 bp):
ATTTTGATGTTG
Found at i:4228383 original size:3 final size:3
Alignment explanation
Indices: 4228377--4228418 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
4228367 ATTTTTTTGA
* *
4228377 TAT TAT TGT TAT TAT TAT TAT TGT TAT T-T TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4228419 GCAATAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4240915 original size:40 final size:40
Alignment explanation
Indices: 4240873--4240963 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
4240863 CCTCTTAGCT
* **
4240873 TTTTAAATTTAAAGTTT-GTTGCCTCT-GTTCAGAGGAGCC
1 TTTTAAATTTAAAGTTTCATAACCTCTGGTT-AGAGGAGCC
*
4240912 TTTTGAATTTAAAGTTTCATAACCTCTGGTTAGAGGAGCC
1 TTTTAAATTTAAAGTTTCATAACCTCTGGTTAGAGGAGCC
*
4240952 TTTTAATTTTAA
1 TTTTAAATTTAA
4240964 GAGCCTTTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 16 0.36
40 25 0.57
41 3 0.07
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (40 bp):
TTTTAAATTTAAAGTTTCATAACCTCTGGTTAGAGGAGCC
Found at i:4241135 original size:40 final size:39
Alignment explanation
Indices: 4241044--4241481 Score: 315
Period size: 40 Copynumber: 11.3 Consensus size: 39
4241034 CCTCTTAGAT
* * *
4241044 TTTTAATATTTAAAGTTTGTTGCATTTGGTTAAAGAAGCAC
1 TTTTAA-ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGC-C
* * * * *
4241085 TTTTGAATTTAAAATTTGTTACCTCTGGTGAGAGGAGCC
1 TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
*
4241124 TTTTAATATTTAAAGTTTGTTATCTTTGGTTAAAGGAGCAC
1 TTTTAA-ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGC-C
* * ** *
4241165 TTTTGAATTTAAAGTTTGTTGCCTTTAATGAAAGGAG-C
1 TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
* *
4241203 TATTTAAATTTAAAGCTTT-TTACCTTTGGTTAAATGAGCT
1 T-TTTAAATTTAAAG-TTTGTTACCTTTGGTTAAAGGAGCC
** * *
4241243 TTTTGACCTTTAAAGTTTGTTACCTCTGGTTAAAGGAGGC
1 TTTT-AAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
* * * * *
4241283 ------ATTTAAAGTTCGTTATCTCTGGTCAGAGGAG-C
1 TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
* *
4241315 TTTT-AATTTAAAGTTTAG-TGCTTTTGGTTAAAGGAG-C
1 TTTTAAATTTAAAGTTT-GTTACCTTTGGTTAAAGGAGCC
* *
4241352 TTTTCAACATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCC
1 TTTT-AA-ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
* * * * * * *
4241393 TTTTGAATTTAAAGTTCGTTGCCTCTAGTGAGAGGAGCC
1 TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
** * * *
4241432 TTTTAAATTTAAAGTTTCATAACTTATGTTTAAAAGAGCC
1 TTTTAAATTTAAAGTTTGTTACCTT-TGGTTAAAGGAGCC
*
4241472 TTTCAAATTT
1 TTTTAAATTT
4241482 TCTTTAAAAA
Statistics
Matches: 311, Mismatches: 67, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
32 1 0.00
33 26 0.08
37 27 0.09
38 3 0.01
39 85 0.27
40 153 0.49
41 16 0.05
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (39 bp):
TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCC
Found at i:4241177 original size:80 final size:77
Alignment explanation
Indices: 4241044--4241448 Score: 371
Period size: 80 Copynumber: 5.2 Consensus size: 77
4241034 CCTCTTAGAT
* * * * *
4241044 TTTTAATATTTAAAGTTTGTTGCATTTGGTTAAAGAAGCACTTTTGAATTTAAAATTTGTTACCT
1 TTTTAA-ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGC-CTTTTGAATTTAAAGTTTGTTGCCT
*
4241109 CTGGTGAGAGGAGCC
64 CTGGTGAAAGGAG-C
*
4241124 TTTTAATATTTAAAGTTTGTTATCTTTGGTTAAAGGAGCACTTTTGAATTTAAAGTTTGTTGCCT
1 TTTTAA-ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGC-CTTTTGAATTTAAAGTTTGTTGCCT
* **
4241189 TTAATGAAAGGAGC
64 CTGGTGAAAGGAGC
* * * *
4241203 TATTTAAATTTAAAGCTTT-TTACCTTTGGTTAAATGAGCTTTTTGACCTTTAAAGTTTGTTACC
1 T-TTTAAATTTAAAG-TTTGTTACCTTTGGTTAAAGGAGCCTTTTGA-ATTTAAAGTTTGTTGCC
*
4241267 TCTGGTTAAAGGAGGC
63 TCTGGTGAAAGGA-GC
* * * * * * *
4241283 ------ATTTAAAGTTCGTTATCTCTGGTCAGAGGAG-CTTTT-AATTTAAAGTTTAG-TGCTTT
1 TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCCTTTTGAATTTAAAGTTT-GTTGCCTC
*
4241339 TGGTTAAAGGAGC
65 TGGTGAAAGGAGC
* * *
4241352 TTTTCAACATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCCTTTTGAATTTAAAGTTCGTTGCCT
1 TTTT-AA-ATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCCTTTTGAATTTAAAGTTTGTTGCCT
* *
4241417 CTAGTGAGAGGAGCC
64 CTGGTGAAAGGAG-C
4241432 TTTTAAATTTAAAGTTT
1 TTTTAAATTTAAAGTTT
4241449 CATAACTTAT
Statistics
Matches: 264, Mismatches: 43, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
69 2 0.01
70 24 0.09
71 2 0.01
72 6 0.02
73 22 0.08
77 24 0.09
78 23 0.09
79 78 0.30
80 83 0.31
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (77 bp):
TTTTAAATTTAAAGTTTGTTACCTTTGGTTAAAGGAGCCTTTTGAATTTAAAGTTTGTTGCCTCT
GGTGAAAGGAGC
Found at i:4241313 original size:33 final size:33
Alignment explanation
Indices: 4241251--4241313 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
4241241 CTTTTTGACC
* *
4241251 TTTAAAGTTTGTTACCTCTGGTTAAAGGAGGCA
1 TTTAAAGTTCGTTACCTCTGGTCAAAGGAGGCA
* *
4241284 TTTAAAGTTCGTTATCTCTGGTCAGAGGAG
1 TTTAAAGTTCGTTACCTCTGGTCAAAGGAG
4241314 CTTTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (33 bp):
TTTAAAGTTCGTTACCTCTGGTCAAAGGAGGCA
Found at i:4241471 original size:79 final size:76
Alignment explanation
Indices: 4241044--4241474 Score: 324
Period size: 79 Copynumber: 5.5 Consensus size: 76
4241034 CCTCTTAGAT
* * * *
4241044 TTTTAATATTTAAAGTTTGTTGCATTTGGTT-AAAGAAGCACTTTTGAATTTAAAATTTGTTACC
1 TTTTAA-ATTTAAAGTTT-TTACCTTTGGTTAAAAG-AGC-CTTTTGAATTTAAAGTTTGTTGCC
*
4241108 TCTGGTGAGAGGAGCC
62 TCTGGTGAAAGGAG-C
* *
4241124 TTTTAATATTTAAAGTTTGTTATCTTTGGTTAAAGGAGCACTTTTGAATTTAAAGTTTGTTGCCT
1 TTTTAA-ATTTAAAGTTT-TTACCTTTGGTTAAAAGAGC-CTTTTGAATTTAAAGTTTGTTGCCT
* **
4241189 TTAATGAAAGGAGC
63 CTGGTGAAAGGAGC
* * * *
4241203 TATTTAAATTTAAAGCTTTTTACCTTTGGTTAAATGAGCTTTTTGACCTTTAAAGTTTGTTACCT
1 T-TTTAAATTTAAAG-TTTTTACCTTTGGTTAAAAGAGCCTTTTGA-ATTTAAAGTTTGTTGCCT
*
4241268 CTGGTTAAAGGAGGC
63 CTGGTGAAAGGA-GC
* * * * * * * *
4241283 ------ATTTAAAGTTCGTTATCTCTGGTCAGAGGAG-CTTTT-AATTTAAAGTTTAG-TGCTTT
1 TTTTAAATTTAAAGTT-TTTACCTTTGGTTAAAAGAGCCTTTTGAATTTAAAGTTT-GTTGCCTC
*
4241339 TGGTTAAAGGAGC
64 TGGTGAAAGGAGC
* * *
4241352 TTTTCAACATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCCTTTTGAATTTAAAGTTCGTTGCCT
1 TTTT-AA-ATTTAAAGTTT-TTACCTTTGGTTAAAAGAGCCTTTTGAATTTAAAGTTTGTTGCCT
* *
4241417 CTAGTGAGAGGAGCC
63 CTGGTGAAAGGAG-C
* * *
4241432 TTTTAAATTTAAAGTTTCATAACTTATGTTTAAAAGAGCCTTT
1 TTTTAAATTTAAAGTTT-TTACCTT-TGGTTAAAAGAGCCTTT
4241475 CAAATTTTCT
Statistics
Matches: 281, Mismatches: 49, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
69 2 0.01
70 24 0.09
71 2 0.01
72 6 0.02
73 22 0.08
77 23 0.08
78 27 0.10
79 93 0.33
80 79 0.28
81 3 0.01
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (76 bp):
TTTTAAATTTAAAGTTTTTACCTTTGGTTAAAAGAGCCTTTTGAATTTAAAGTTTGTTGCCTCTG
GTGAAAGGAGC
Found at i:4242545 original size:17 final size:18
Alignment explanation
Indices: 4242525--4242558 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4242515 TTTCACAGGT
*
4242525 TTTTTCTTTTCT-TTTTC
1 TTTTTATTTTCTATTTTC
4242542 TTTTTATTTTCTATTTT
1 TTTTTATTTTCTATTTT
4242559 GATTTTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTCTATTTTC
Found at i:4242580 original size:9 final size:10
Alignment explanation
Indices: 4242566--4242639 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 10
4242556 TTTGATTTTG
4242566 ATTTTAT-TT
1 ATTTTATATT
*
4242575 ATTTTATGTT
1 ATTTTATATT
*
4242585 GATTTTTTTATT
1 -A-TTTTATATT
4242597 -TTTTATATT
1 ATTTTATATT
*
4242606 ATTGT-TATT
1 ATTTTATATT
*
4242615 ATTATTATTGTT
1 ATT-TTA-TATT
4242627 ATTTTATATT
1 ATTTTATATT
4242637 ATT
1 ATT
4242640 ATTAACAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
9 22 0.43
10 12 0.24
11 4 0.08
12 13 0.25
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (10 bp):
ATTTTATATT
Found at i:4242588 original size:20 final size:20
Alignment explanation
Indices: 4242548--4242598 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
4242538 TTTCTTTTTA
* *
4242548 TTTTCTATTTTGATTTTGAT
1 TTTTTTATTTTGATGTTGAT
4242568 TTTATTTATTTT-ATGTTGAT
1 TTT-TTTATTTTGATGTTGAT
4242588 TTTTTTATTTT
1 TTTTTTATTTT
4242599 TTATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.29
20 13 0.46
21 7 0.25
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.75
Consensus pattern (20 bp):
TTTTTTATTTTGATGTTGAT
Found at i:4242607 original size:12 final size:15
Alignment explanation
Indices: 4242602--4242643 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4242592 TTATTTTTTA
4242602 TATTATTGTTATTAT
1 TATTATTGTTATTAT
4242617 TATTATTGTTATT-T
1 TATTATTGTTATTAT
*
4242631 TA-TATTATTATTA
1 TATTATTGTTATTA
4242644 ACAATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
15 13 0.52
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TATTATTGTTATTAT
Found at i:4242608 original size:3 final size:3
Alignment explanation
Indices: 4242602--4242643 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
4242592 TTATTTTTTA
* *
4242602 TAT TAT TGT TAT TAT TAT TAT TGT TAT T-T TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4242644 ACAATAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4243055 original size:16 final size:14
Alignment explanation
Indices: 4243015--4243054 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
4243005 TAAACAATGT
*
4243015 AAAACAATAATAAA
1 AAAATAATAATAAA
*
4243029 AAAATAATAAT-GA
1 AAAATAATAATAAA
4243042 AAAATAATAATAA
1 AAAATAATAATAA
4243055 TTGATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAATAATAATAAA
Found at i:4243551 original size:3 final size:3
Alignment explanation
Indices: 4243543--4243572 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4243533 TAGAATATGA
4243543 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4243573 TTCACAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4245012 original size:23 final size:24
Alignment explanation
Indices: 4245003--4245052 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
4244993 CTTTTATATA
*
4245003 ATTTTT-ATTTTTAATTTATATAT
1 ATTTTTAATTTTTATTTTATATAT
*
4245026 ATTTTTAATTTTAATTTTTATATAT
1 ATTTTTAATTTTTA-TTTTATATAT
4245051 AT
1 AT
4245053 GTGAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 6 0.26
25 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTAATTTTTATTTTATATAT
Found at i:4245267 original size:11 final size:11
Alignment explanation
Indices: 4245251--4245281 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4245241 CATGAGTCTA
4245251 GCCTGAACTTG
1 GCCTGAACTTG
4245262 GCCTGAACTTG
1 GCCTGAACTTG
*
4245273 GCCTAAACT
1 GCCTGAACT
4245282 CAGCTTGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (11 bp):
GCCTGAACTTG
Found at i:4247708 original size:2 final size:2
Alignment explanation
Indices: 4247701--4247725 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4247691 GATTCCTCAT
4247701 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4247726 GACCATTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4249397 original size:43 final size:42
Alignment explanation
Indices: 4249349--4249431 Score: 148
Period size: 43 Copynumber: 2.0 Consensus size: 42
4249339 TAAAAAAAAA
*
4249349 GTATATGTTTTTATCCTTTTACTTTTTTCTTCCAATTTTTTGT
1 GTATATGTTTTTATCCTTTTAC-ATTTTCTTCCAATTTTTTGT
4249392 GTATATGTTTTTATCCTTTTACATTTTCTTCCAATTTTTT
1 GTATATGTTTTTATCCTTTTACATTTTCTTCCAATTTTTT
4249432 ATCTGTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 17 0.44
43 22 0.56
ACGTcount: A:0.16, C:0.14, G:0.06, T:0.64
Consensus pattern (42 bp):
GTATATGTTTTTATCCTTTTACATTTTCTTCCAATTTTTTGT
Found at i:4249445 original size:42 final size:43
Alignment explanation
Indices: 4249350--4249445 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 43
4249340 AAAAAAAAAG
* * * *
4249350 TATATGTTTTTATCCTTTTACTTTTTTCTTCCAATTTTTTGTG
1 TATATATTTTTATCCTTTTACTATTTTCTTCCAATTTTTTATC
*
4249393 TATATGTTTTTATCCTTTTAC-ATTTTCTTCCAATTTTTTATC
1 TATATATTTTTATCCTTTTACTATTTTCTTCCAATTTTTTATC
* *
4249435 TGTTTATTTTT
1 TATATATTTTT
4249446 TTTATGTCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 26 0.55
43 21 0.45
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.66
Consensus pattern (43 bp):
TATATATTTTTATCCTTTTACTATTTTCTTCCAATTTTTTATC
Found at i:4252898 original size:16 final size:16
Alignment explanation
Indices: 4252869--4252902 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4252859 TAAAGGTTTT
*
4252869 AATTTTAATATTATTA
1 AATTTAAATATTATTA
*
4252885 AATTTAAATTTTATTA
1 AATTTAAATATTATTA
4252901 AA
1 AA
4252903 AACCTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTAAATATTATTA
Done.