Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 31 of 129
Found at i:6314402 original size:4 final size:4
Alignment explanation
Indices: 6314310--6314465 Score: 59
Period size: 4 Copynumber: 41.2 Consensus size: 4
6314300 AAAAAGATAA
* * * * * *
6314310 AAAT AAA- AAAT -AAT AGAT AAAT ATAT TAAT AGAT AACT AAA- AGA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
6314354 AAAT AATT AGAT AAAT AAAA AAAT ATTAAT AGAT AAAT -AAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT
* * *
6314402 -AAT AAA- ATAA- AAAT AGAT AAAT -AAT AAA- AATAT TAAT AGAT AAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT
*
6314447 -AAT AAAA AAAT AAA- AAAT A
1 AAAT AAAT AAAT AAAT AAAT A
6314466 TATATTAATG
Statistics
Matches: 110, Mismatches: 28, Indels: 28
0.66 0.17 0.17
Matches are distributed among these distances:
3 33 0.30
4 72 0.65
5 1 0.01
6 4 0.04
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:6314402 original size:32 final size:32
Alignment explanation
Indices: 6314354--6314433 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
6314344 AACTAAAAGA
**
6314354 AAATAATTAGATAAATAAAAAAATATTAATAGAT
1 AAATAA-TA-ATAAATAAAAAAATAAAAATAGAT
*
6314388 AAATAATAATAAATAATAAAATAAAAATAGAT
1 AAATAATAATAAATAAAAAAATAAAAATAGAT
6314420 AAATAATAA-AAATA
1 AAATAATAATAAATA
6314434 TTAATAGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.12
32 30 0.70
33 2 0.05
34 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (32 bp):
AAATAATAATAAATAAAAAAATAAAAATAGAT
Found at i:6314411 original size:22 final size:23
Alignment explanation
Indices: 6314304--6314459 Score: 118
Period size: 22 Copynumber: 7.0 Consensus size: 23
6314294 AAGAAAAAAA
6314304 AGATAAA-AAT-AAA-AAATAAT
1 AGATAAATAATAAAATAAATAAT
* *
6314324 AGATAAATATATTAATAGATAACTAAA
1 AGATAAATA-A-TAA-A-ATAAATAAT
* *
6314351 AGA-AAATAATTAGATAAATAA-
1 AGATAAATAATAAAATAAATAAT
*
6314372 A-A-AAATATTAATAGATAAATAAT
1 AGATAAATAATAA-A-ATAAATAAT
6314395 A-ATAAATAATAAAATAAA-AAT
1 AGATAAATAATAAAATAAATAAT
*
6314416 AGATAAATAATAAAA-ATATTAAT
1 AGATAAATAATAAAATA-AATAAT
6314439 AGATAAATAATAAAA-AAATAA
1 AGATAAATAATAAAATAAATAA
6314460 AAAATATATA
Statistics
Matches: 111, Mismatches: 11, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
20 15 0.14
21 7 0.06
22 39 0.35
23 23 0.21
24 11 0.10
25 2 0.02
26 6 0.05
27 8 0.07
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.26
Consensus pattern (23 bp):
AGATAAATAATAAAATAAATAAT
Found at i:6314435 original size:55 final size:56
Alignment explanation
Indices: 6314294--6314461 Score: 215
Period size: 55 Copynumber: 3.0 Consensus size: 56
6314284 AAAATTAATC
* *
6314294 AAGAAAAAAAAGATAAA-AATAAAAA-A-TAATAGATAAATATATTAATAGATAACTAA
1 AAGAAAAAATAGATAAATAATAAAAATATTAATAGATAAATA-A-TAATAAATAA-TAA
6314350 AAGAAAATAATTAGATAAATAA-AAAAATATTAATAGATAAATAATAATAAATAATAA
1 AAGAAAA-AA-TAGATAAATAATAAAAATATTAATAGATAAATAATAATAAATAATAA
*
6314407 AA-TAAAAATAGATAAATAATAAAAATATTAATAGATAAATAATAA-AAA-AATAA
1 AAGAAAAAATAGATAAATAATAAAAATATTAATAGATAAATAATAATAAATAATAA
6314460 AA
1 AA
6314462 AATATATATT
Statistics
Matches: 103, Mismatches: 3, Indels: 15
0.85 0.02 0.12
Matches are distributed among these distances:
53 7 0.07
54 14 0.14
55 27 0.26
56 10 0.10
57 7 0.07
58 21 0.20
59 4 0.04
60 13 0.13
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (56 bp):
AAGAAAAAATAGATAAATAATAAAAATATTAATAGATAAATAATAATAAATAATAA
Found at i:6314439 original size:15 final size:15
Alignment explanation
Indices: 6314389--6314450 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 15
6314379 TTAATAGATA
*
6314389 AATAATAATAAATAAT
1 AATAATAA-AAATATT
*
6314405 AA-AATAAAAATAGATA
1 AATAATAAAAAT--ATT
6314421 AATAATAAAAATATT
1 AATAATAAAAATATT
6314436 AATAGATAAATAATA
1 AATA-ATAAA-AATA
6314451 AAAAAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.11
15 11 0.29
16 10 0.26
17 13 0.34
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATAATAAAAATATT
Found at i:6314439 original size:23 final size:23
Alignment explanation
Indices: 6314389--6314459 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
6314379 TTAATAGATA
6314389 AATAATA-ATAAATAAT-AAAAT
1 AATAATAGATAAATAATAAAAAT
*
6314410 AAAAATAGATAAATAATAAAAAT
1 AATAATAGATAAATAATAAAAAT
*
6314433 ATTAATAGATAAATAATAAAAA-
1 AATAATAGATAAATAATAAAAAT
6314455 AATAA
1 AATAA
6314460 AAAATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 6 0.14
22 13 0.30
23 25 0.57
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (23 bp):
AATAATAGATAAATAATAAAAAT
Found at i:6314491 original size:32 final size:32
Alignment explanation
Indices: 6314366--6314501 Score: 113
Period size: 32 Copynumber: 4.3 Consensus size: 32
6314356 ATAATTAGAT
* * * *
6314366 AAATAAAAAAATATTAATAGATAAATAATAAT
1 AAATAATAAATTAATAATAGATAAATAATAAA
* *
6314398 AAATAATAAAATAAAAATAGATAAATAATAAA
1 AAATAATAAATTAATAATAGATAAATAATAAA
* *
6314430 AATATTAATAGATAAATAATA-A-AAA-AATAAA
1 AA-A-TAATAAATTAATAATAGATAAATAATAAA
* *
6314461 AAAT-ATATATTAATGAATAGACAAATAAT-AA
1 AAATAATAAATTAAT-AATAGATAAATAATAAA
6314492 AAATAA-AAAT
1 AAATAATAAAT
6314502 AAAAATAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
28 8 0.09
29 5 0.06
30 2 0.02
31 20 0.23
32 37 0.43
33 2 0.02
34 12 0.14
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.26
Consensus pattern (32 bp):
AAATAATAAATTAATAATAGATAAATAATAAA
Found at i:6314505 original size:5 final size:6
Alignment explanation
Indices: 6314388--6314511 Score: 51
Period size: 6 Copynumber: 20.3 Consensus size: 6
6314378 ATTAATAGAT
* * *
6314388 AAATAA TAATAA ATAAT-A AAATAA AAAT-- AGATAA ATAATAA AAATAT
1 AAATAA AAATAA A-AATAA AAATAA AAATAA AAATAA A-AATAA AAATAA
* * * * * * *
6314435 TAATAGA TAAATAA TAA-AA AAATAAA AAATATA TATTAA TGAATAG ACA-AA
1 AAATA-A -AAATAA AAATAA AAAT-AA AAATA-A AAATAA -AAATAA AAATAA
*
6314486 TAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
6314512 GCCAATTGGG
Statistics
Matches: 85, Mismatches: 21, Indels: 24
0.65 0.16 0.18
Matches are distributed among these distances:
4 3 0.04
5 9 0.11
6 47 0.55
7 22 0.26
8 4 0.05
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (6 bp):
AAATAA
Found at i:6314888 original size:43 final size:41
Alignment explanation
Indices: 6314764--6315187 Score: 385
Period size: 43 Copynumber: 10.0 Consensus size: 41
6314754 TTTTAAGTAA
* *
6314764 AGGCTCAACGACTTTGAAAAAATAAAAAAAGCTCCTCTAAACAG
1 AGGCTCAACGACTTTG-AAAAAT--AAATAGCTCCTCTAATCAG
* * * * *
6314808 AGGCTCCATGACCTTG-AAAATAAATGGTTCCTCTAATCAG
1 AGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATCAG
* *
6314848 ACGCTCAACGACTTTGGAAAATAAATAAAGCTCCTCTAATCAG
1 AGGCTCAACGACTTTGAAAAATAAAT--AGCTCCTCTAATCAG
* * * * * *
6314891 AAGCTTAAAGACTTTGAAAAATAAATGGCTCCTTTAATTAG
1 AGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATCAG
*
6314932 AGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAG
1 AGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATCAG
* *
6314973 AGG--CAACAGAACTTTTGGGAAAATAAATAGCTCATCTAAGT-AG
1 AGGCTCAAC-G-AC-TTT-GAAAAATAAATAGCTCCTCTAA-TCAG
*
6315016 AGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAG
1 AGGCTCAACGACTTTG-AAAAATAAAT--AGCTCCTCTAATCAG
* * *
6315060 AGGCTCAACAACTTTAAAAAATAAATGGCTCCTCTAATCAG
1 AGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATCAG
* * *
6315101 AGG--CAACAGAACTTTGGAAAAAATAAATAGCTCATCTAAACAA
1 AGGCTCAAC-G-ACTTT-G-AAAAATAAATAGCTCCTCTAATCAG
*
6315144 AGGCTCAACAAACTTTGAAAAAATAAA-AGGCTCCTCTAATCAG
1 AGGCTCAAC-GACTTTG-AAAAATAAATA-GCTCCTCTAATCAG
6315187 A
1 A
6315188 TACAACAAAC
Statistics
Matches: 316, Mismatches: 43, Indels: 43
0.79 0.11 0.11
Matches are distributed among these distances:
39 8 0.03
40 28 0.09
41 85 0.27
42 21 0.07
43 119 0.38
44 46 0.15
45 9 0.03
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (41 bp):
AGGCTCAACGACTTTGAAAAATAAATAGCTCCTCTAATCAG
Found at i:6314938 original size:84 final size:85
Alignment explanation
Indices: 6314764--6315183 Score: 443
Period size: 84 Copynumber: 5.0 Consensus size: 85
6314754 TTTTAAGTAA
* * *
6314764 AGGCTCAACGACTTTGAAAAAATAAAAAAAGCTCCTCTAAACAGAGGCTC--CATGACCTTG-AA
1 AGGCTCAACGACTTTG-AAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACA-GACTTTGAAA
* *
6314826 AATAAATGGTTCCTCTAATCAG
64 AATAAATGGCTCCTCTAATTAG
* * * *
6314848 ACGCTCAACGACTTTGGAAAATAAATAAAGCTCCTCTAATCAGAAGCTTAA-AGACTTTGAAAAA
1 AGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACAGACTTTGAAAAA
*
6314912 TAAATGGCTCCTTTAATTAG
66 TAAATGGCTCCTCTAATTAG
* *
6314932 AGGCTCAACGACTTTGAAAAATAAAT--GGCTCCTCTAATCAGAGG--CAACAGAACTTTTGGGA
1 AGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACAG-AC-TTT-GAA
* * *
6314993 AAATAAATAGCTCATCTAAGTAG
63 AAATAAATGGCTCCTCTAATTAG
* *
6315016 AGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACA-ACTTTAAAAA
1 AGGCTCAACGACTTTG-AAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACAGACTTTGAAAA
*
6315080 ATAAATGGCTCCTCTAATCAG
65 ATAAATGGCTCCTCTAATTAG
* * * *
6315101 AGG--CAACAGAACTTTGGAAAAAATAAAT--AGCTCATCTAAACAAAGGCTCAACAAACTTTGA
1 AGGCTCAAC-G-ACTTT-G-AAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACAGACTTTG-
*
6315162 AAAAATAAAAGGCTCCTCTAAT
61 AAAAATAAATGGCTCCTCTAAT
6315184 CAGATACAAC
Statistics
Matches: 285, Mismatches: 34, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
80 2 0.01
81 2 0.01
82 18 0.06
83 41 0.14
84 119 0.42
85 43 0.15
86 36 0.13
87 19 0.07
89 5 0.02
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (85 bp):
AGGCTCAACGACTTTGAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACAGACTTTGAAAAA
TAAATGGCTCCTCTAATTAG
Found at i:6315092 original size:128 final size:126
Alignment explanation
Indices: 6314757--6315187 Score: 497
Period size: 128 Copynumber: 3.4 Consensus size: 126
6314747 AAAGCTCTTT
* * * * * *
6314757 TAAGTAAAGGCTCAACGACTTTGAAAAAATAAAAAAAGCTCCTCTAAACAGAGGCTCCATGACCT
1 TAAGTAAAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACGACTT
* * * *
6314822 TGAAAATAAATGGTTCCTCTAATCAGACGCTCAAC-G-ACTTT-GGAAAATAAATAAAGCTCCTC
66 TAAAAATAAATGGCTCCTCTAATCAGA-G-GCAACAGAACTTTGGGAAAATAAAT--AGCTCATC
* * * *
6314884 TAA-TCAGAA-GCTTAA-AGACTTTG-AAAAATAAAT--GGCTCCTTTAATTAGAGGCTCAACGA
1 TAAGT-A-AAGGCTCAACA-ACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACGA
6314943 CTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCAACAGAACTTTTGGGAAAATAAATAGCTCAT
63 CTTT-AAAAATAAATGGCTCCTCTAATCAGAGGCAACAGAAC-TTTGGGAAAATAAATAGCTCAT
6315008 C
126 C
* *
6315009 TAAGTAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACAACTT
1 TAAGTAAAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACGACTT
*
6315074 TAAAAAATAAATGGCTCCTCTAATCAGAGGCAACAGAACTTTGGAAAAAATAAATAGCTCATC
66 T-AAAAATAAATGGCTCCTCTAATCAGAGGCAACAGAACTTTGG-GAAAATAAATAGCTCATC
** *
6315137 TAAACAAAGGCTCAACAAACTTTGAAAAAAT-AA-AAGGCTCCTCTAATCAGA
1 TAAGTAAAGGCTCAAC-AACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGA
6315188 TACAACAAAC
Statistics
Matches: 262, Mismatches: 26, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
123 4 0.02
124 26 0.10
125 48 0.18
126 25 0.10
127 48 0.18
128 97 0.37
129 14 0.05
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (126 bp):
TAAGTAAAGGCTCAACAACTTTGAAAAAATAAATAAAGCTCCTCTAATCAGAGGCTCAACGACTT
TAAAAATAAATGGCTCCTCTAATCAGAGGCAACAGAACTTTGGGAAAATAAATAGCTCATC
Found at i:6316083 original size:63 final size:63
Alignment explanation
Indices: 6315984--6316104 Score: 206
Period size: 63 Copynumber: 1.9 Consensus size: 63
6315974 AGCACTAATC
* *
6315984 ATTTCAAAATAAATTTCATCATCTGTCATTTGGTCATCATTCATAAGCTTCTCAGTACTAGCT
1 ATTTCAAAAAAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTCTCAGTACTAGCT
* *
6316047 ATTTCAAAAAAAATTTCATCTTCTGTCACTTGGTCATCGTTCATAAGCTTCTCAGTAC
1 ATTTCAAAAAAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTCTCAGTAC
6316105 CAGTTTCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (63 bp):
ATTTCAAAAAAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTTCTCAGTACTAGCT
Found at i:6316794 original size:18 final size:18
Alignment explanation
Indices: 6316773--6316813 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6316763 AATTTAAATC
6316773 TTTTTTTCATTT-TTTCAT
1 TTTTTTTC-TTTCTTTCAT
*
6316791 TTTTTTTCTTTCTTTCCT
1 TTTTTTTCTTTCTTTCAT
6316809 TTTTT
1 TTTTT
6316814 CCTCTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTCTTTCTTTCAT
Found at i:6316823 original size:26 final size:26
Alignment explanation
Indices: 6316771--6316839 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
6316761 TCAATTTAAA
* * *
6316771 TCTTTTTTTCATTTTTTCATTTTTTT
1 TCTTTCTTTCATTTTTTCATCTATTT
* *
6316797 TCTTTCTTTCCTTTTTTCCTCTATTT
1 TCTTTCTTTCATTTTTTCATCTATTT
* *
6316823 TTTTTCTTTAATTTTTT
1 TCTTTCTTTCATTTTTT
6316840 TTTCATCATC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (26 bp):
TCTTTCTTTCATTTTTTCATCTATTT
Found at i:6321074 original size:16 final size:15
Alignment explanation
Indices: 6321044--6321076 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6321034 TATTTTCAAC
*
6321044 TTTTTTCAAAATTTT
1 TTTTTTGAAAATTTT
6321059 TTTTTTGAAAATTTT
1 TTTTTTGAAAATTTT
6321074 TTT
1 TTT
6321077 ATTTTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTTGAAAATTTT
Found at i:6322057 original size:22 final size:20
Alignment explanation
Indices: 6322029--6322093 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 20
6322019 ATAAATATAT
*
6322029 TAATAGATAACTAAAAGAAAA
1 TAATAGATAAATAAAA-AAAA
6322050 TAATTAGATAAATAAAAAAATA
1 TAA-TAGATAAATAAAAAAA-A
6322072 TTAATAGATAAATAATAAAAAA
1 -TAATAGATAAATAA-AAAAAA
6322094 ATAAAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 6 0.15
22 25 0.64
23 8 0.21
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
TAATAGATAAATAAAAAAAA
Found at i:6322106 original size:29 final size:30
Alignment explanation
Indices: 6322057--6322129 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
6322047 AAATAATTAG
* *
6322057 ATAAATAAA-AAAATATTAATAGATAAATA
1 ATAAAAAAATAAAATATAAATAGATAAATA
6322086 ATAAAAAAATAAAATA-AAATAGATAAATA
1 ATAAAAAAATAAAATATAAATAGATAAATA
6322115 ATAAAAAAAATAAAA
1 AT-AAAAAAATAAAA
6322130 AATATATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 22 0.55
30 18 0.45
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (30 bp):
ATAAAAAAATAAAATATAAATAGATAAATA
Found at i:6322117 original size:21 final size:21
Alignment explanation
Indices: 6322088--6322167 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
6322078 GATAAATAAT
6322088 AAAAA-AATAAAATAAAATAG
1 AAAAATAATAAAATAAAATAG
*
6322108 ATAAATAATAAAA-AAAATA-
1 AAAAATAATAAAATAAAATAG
*
6322127 AAAAATATATATTAAT-AAATAG
1 AAAAATA-ATA-AAATAAAATAG
*
6322149 ACAAATAATAAAAATAAAA
1 AAAAATAAT-AAAATAAAA
6322168 GCCAATTGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.12
20 13 0.27
21 19 0.40
22 10 0.21
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (21 bp):
AAAAATAATAAAATAAAATAG
Found at i:6322126 original size:9 final size:9
Alignment explanation
Indices: 6322088--6322131 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
6322078 GATAAATAAT
6322088 AAAAAAATA
1 AAAAAAATA
6322097 AAATAAAATA
1 AAA-AAAATA
*
6322107 GATAAATAATA
1 -A-AAAAAATA
6322118 AAAAAAATA
1 AAAAAAATA
6322127 AAAAA
1 AAAAA
6322132 TATATATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 15 0.50
10 7 0.23
11 6 0.20
12 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (9 bp):
AAAAAAATA
Found at i:6322147 original size:4 final size:4
Alignment explanation
Indices: 6322003--6322166 Score: 54
Period size: 4 Copynumber: 40.8 Consensus size: 4
6321993 AAAAAGATAA
* * * * * *
6322003 AAAT AAA- AAAT -AAT AGAT AAAT ATAT TAAT AGAT AACT AAA- AGA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * *
6322047 AAAT AATT AGAT AAAT AAAA AAAT ATTAAT AGAT AAAT -AAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT AAAT
* * *
6322096 AAAAT AAAAT AGAT AAAT -AAT AAAAA AAAT AAA- AAAT ATATAT TAAT
1 -AAAT -AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A-A-AT AAAT
* * *
6322143 AAAT AGAC AAAT AATAA AAAT AAA
1 AAAT AAAT AAAT AA-AT AAAT AAA
6322167 AGCCAATTGG
Statistics
Matches: 113, Mismatches: 34, Indels: 26
0.65 0.20 0.15
Matches are distributed among these distances:
3 19 0.17
4 72 0.64
5 16 0.14
6 6 0.05
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:6322251 original size:21 final size:21
Alignment explanation
Indices: 6322222--6322262 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6322212 CTTAGGCCCA
6322222 AATGACCTTGGGCCCAGACCC
1 AATGACCTTGGGCCCAGACCC
*
6322243 AATGGCCTTGGGCCCAGACC
1 AATGACCTTGGGCCCAGACC
6322263 AAATAGGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.37, G:0.27, T:0.15
Consensus pattern (21 bp):
AATGACCTTGGGCCCAGACCC
Found at i:6325185 original size:10 final size:10
Alignment explanation
Indices: 6325172--6325218 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
6325162 AAAAATTAAT
6325172 AAAAAAGGAA
1 AAAAAAGGAA
*
6325182 AAAAAAAGAA
1 AAAAAAGGAA
* *
6325192 AAGAAAGAAA
1 AAAAAAGGAA
6325202 AAAAAAGGAA
1 AAAAAAGGAA
6325212 AAAAAAG
1 AAAAAAG
6325219 AATTGATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAGGAA
Found at i:6325219 original size:20 final size:19
Alignment explanation
Indices: 6325172--6325220 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
6325162 AAAAATTAAT
*
6325172 AAAAAAGGAAAAAAAAAGA
1 AAAAAAAGAAAAAAAAAGA
*
6325191 AAAGAAAGAAAAAAAAAGGA
1 AAAAAAAGAAAAAAAAA-GA
6325211 AAAAAAAGAA
1 AAAAAAAGAA
6325221 TTGATATAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAGA
Found at i:6325498 original size:13 final size:12
Alignment explanation
Indices: 6325480--6325518 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
6325470 GGGAAAAGAG
6325480 AAATGAGAAGAAA
1 AAATGAGAA-AAA
6325493 AAATGAGAAAAA
1 AAATGAGAAAAA
6325505 AAAGTGA-AAAAA
1 AAA-TGAGAAAAA
6325517 AA
1 AA
6325519 GCAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (12 bp):
AAATGAGAAAAA
Found at i:6325506 original size:11 final size:10
Alignment explanation
Indices: 6325488--6325545 Score: 66
Period size: 10 Copynumber: 5.8 Consensus size: 10
6325478 AGAAATGAGA
*
6325488 AGAAAAAATG
1 AGAAAAAAAG
6325498 AGAAAAAAAAG
1 AG-AAAAAAAG
*
6325509 TGAAAAAAA-
1 AGAAAAAAAG
6325518 AGCAAAAAAAG
1 AG-AAAAAAAG
6325529 A-AAAAAAAG
1 AGAAAAAAAG
6325538 AGAAAAAA
1 AGAAAAAA
6325546 TGAAGACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 10 0.24
10 22 0.54
11 9 0.22
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:6325524 original size:9 final size:9
Alignment explanation
Indices: 6325487--6325545 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
6325477 GAGAAATGAG
6325487 AAGAAAAAA
1 AAGAAAAAA
*
6325496 TGAGAAAAAA
1 -AAGAAAAAA
6325506 AAGTGAAAAAA
1 AA--GAAAAAA
*
6325517 AAGCAAAAA
1 AAGAAAAAA
6325526 AAGAAAAAA
1 AAGAAAAAA
6325535 AAGAGAAAAA
1 AAGA-AAAAA
6325545 A
1 A
6325546 TGAAGACTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 19 0.45
10 14 0.33
11 9 0.21
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:6326628 original size:46 final size:45
Alignment explanation
Indices: 6326578--6326721 Score: 130
Period size: 46 Copynumber: 3.1 Consensus size: 45
6326568 AAAAAAGACC
** *
6326578 TTTGAAACCTTGGATATGAATCTCTAAAATTTTTTAAATGAGAATA
1 TTTGAAAATTTGGAT-TGAATCTCTAAAATTTTTCAAATGAGAATA
* * * *
6326624 TTTGAAAATTTGGATGGAAATTTCTAAAATTTTTCAAATGTGAATC
1 TTTGAAAATTTGGATTG-AATCTCTAAAATTTTTCAAATGAGAATA
* * * *
6326670 TTT-AAAATTTTGGATGTGAAAC-CTTGAAATTATTCAAATGAGAATT
1 TTTGAAAA-TTTGGAT-TGAATCTC-TAAAATTTTTCAAATGAGAATA
6326716 TTTGAA
1 TTTGAA
6326722 TTCTAGAAGT
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
45 6 0.08
46 70 0.89
47 3 0.04
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (45 bp):
TTTGAAAATTTGGATTGAATCTCTAAAATTTTTCAAATGAGAATA
Found at i:6327001 original size:34 final size:33
Alignment explanation
Indices: 6326875--6327005 Score: 84
Period size: 34 Copynumber: 3.8 Consensus size: 33
6326865 ATGATGAAAT
* **
6326875 TGAATTTCTTGCAAATTTGAAAATTCTTGTGAACC
1 TGAAATTCTTGCAAACCTG-AAATTCTTG-GAACC
* * **
6326910 AT-AGATTCTTGCAAACCTTAAATTCTTTTAAACC
1 -TGAAATTCTTGCAAACCTGAAATTC-TTGGAACC
** *** * *
6326944 AAAAATTCTTATGAACTTAAAATTCTTAGGAACC
1 TGAAATTCTTGCAAACCTGAAATTCTT-GGAACC
6326978 TGAAATTCTTGCAAACCTGAAATTCTTG
1 TGAAATTCTTGCAAACCTGAAATTCTTG
6327006 AGAATATGAA
Statistics
Matches: 69, Mismatches: 23, Indels: 9
0.68 0.23 0.09
Matches are distributed among these distances:
33 3 0.04
34 51 0.74
35 14 0.20
36 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (33 bp):
TGAAATTCTTGCAAACCTGAAATTCTTGGAACC
Found at i:6327005 original size:17 final size:17
Alignment explanation
Indices: 6326914--6327005 Score: 69
Period size: 17 Copynumber: 5.4 Consensus size: 17
6326904 TGAACCATAG
*
6326914 ATTCTTGCAAACCTTAA
1 ATTCTTGCAAACCTAAA
** *
6326931 ATTCTTTTAAACCAAAA
1 ATTCTTGCAAACCTAAA
*** *
6326948 ATTCTTATGAACTTAAA
1 ATTCTTGCAAACCTAAA
* *
6326965 ATTCTTAG-GAACCTGAA
1 ATTCTT-GCAAACCTAAA
*
6326982 ATTCTTGCAAACCTGAA
1 ATTCTTGCAAACCTAAA
6326999 ATTCTTG
1 ATTCTTG
6327006 AGAATATGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
16 1 0.02
17 60 0.98
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (17 bp):
ATTCTTGCAAACCTAAA
Found at i:6327327 original size:35 final size:35
Alignment explanation
Indices: 6327264--6327341 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
6327254 AACCTTTGCG
* *
6327264 AATC-TGAAATCTTTTTGAATTTGAAACCTCTGTAA
1 AATCTTGAAATCTTTGTGAATTAGAAACCTCTG-AA
*
6327299 AA-CTTGAAATCTTTGTGAATCTAG-AACCTTTGAA
1 AATCTTGAAATCTTTGTGAAT-TAGAAACCTCTGAA
6327333 AATCTTGAA
1 AATCTTGAA
6327342 TCATTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 5 0.14
35 30 0.81
36 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (35 bp):
AATCTTGAAATCTTTGTGAATTAGAAACCTCTGAA
Found at i:6327721 original size:43 final size:43
Alignment explanation
Indices: 6327649--6327755 Score: 162
Period size: 43 Copynumber: 2.5 Consensus size: 43
6327639 TATTTTTTAA
* * *
6327649 TTTAAAATTGTTTTAG-CTTCTATATAGAAGAGTCAATTTCGTAT
1 TTTAAAGTTG-TTTAGCCTT-TATACAGAAGAGTCAATTTCCTAT
6327693 TTTAAAGTTGTTTAGCCTTTATACAGAAGAGTCAATTTCCTAT
1 TTTAAAGTTGTTTAGCCTTTATACAGAAGAGTCAATTTCCTAT
6327736 TTTAAAGTTGTTTAGCCTTT
1 TTTAAAGTTGTTTAGCCTTT
6327756 GTATAGAGGA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
43 47 0.80
44 12 0.20
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (43 bp):
TTTAAAGTTGTTTAGCCTTTATACAGAAGAGTCAATTTCCTAT
Found at i:6328764 original size:102 final size:101
Alignment explanation
Indices: 6328658--6328863 Score: 226
Period size: 102 Copynumber: 2.0 Consensus size: 101
6328648 AAACATATTT
* * * *
6328658 AAATAAAAACT-TTACCAATAGATTGAAATGT-AAT-TTTT-TTTT-AAATAAGATTTTACC-AT
1 AAAT-AAAACTCTTACCAACAGATTAAAAAGTCAATATTTTATTTTAAAATAAAATTTTACCAAT
6328717 CATATTGAAAAAACTTATAACATTTTTTTATTTAAAAAAATAA
65 -ATATTGAAAAAACTTAT-A-ATTTTTTTA---AAAAAAATAA
*
6328760 AAATAAAAGTCTTACCAACAGATTAAAAAGTCAATATTTTATTTTCAAAATAAAATTTTACCAAT
1 AAATAAAACTCTTACCAACAGATTAAAAAGTCAATATTTTATTTT-AAAATAAAATTTTACCAAT
* **
6328825 ATATTGGAAAGCCTTATAATTTTTTTAAAAAAAATAA
65 ATATTGAAAAAACTTATAATTTTTTTAAAAAAAATAA
6328862 AA
1 AA
6328864 TCAAGTTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
101 5 0.06
102 33 0.37
103 3 0.03
104 4 0.04
105 13 0.15
106 1 0.01
107 28 0.31
108 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (101 bp):
AAATAAAACTCTTACCAACAGATTAAAAAGTCAATATTTTATTTTAAAATAAAATTTTACCAATA
TATTGAAAAAACTTATAATTTTTTTAAAAAAAATAA
Found at i:6332239 original size:13 final size:13
Alignment explanation
Indices: 6332218--6332250 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
6332208 TACAACATGC
6332218 GACAAATATTTTA
1 GACAAATATTTTA
*
6332231 GATAAATATTTTA
1 GACAAATATTTTA
6332244 GACAAAT
1 GACAAAT
6332251 GAAAAATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (13 bp):
GACAAATATTTTA
Found at i:6333104 original size:22 final size:22
Alignment explanation
Indices: 6333052--6333107 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
6333042 TATAAGCTAC
*
6333052 TCGAATTTAACTTGAATAAAAT
1 TCGAATTTGACTTGAATAAAAT
6333074 TCGAATTTGACTTGAATAAAAT
1 TCGAATTTGACTTGAATAAAAT
6333096 TCGAATTTGACT
1 TCGAATTTGACT
6333108 CGATTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (22 bp):
TCGAATTTGACTTGAATAAAAT
Found at i:6336849 original size:11 final size:11
Alignment explanation
Indices: 6336833--6336863 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
6336823 ATTTGTTAAA
6336833 TTTATTTTTTG
1 TTTATTTTTTG
6336844 TTTA-TTTTTG
1 TTTATTTTTTG
6336854 TTTATTTTTT
1 TTTATTTTTT
6336864 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTG
Found at i:6336853 original size:10 final size:10
Alignment explanation
Indices: 6336833--6336871 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
6336823 ATTTGTTAAA
6336833 TTTATTTTTTG
1 TTTA-TTTTTG
6336844 TTTATTTTTG
1 TTTATTTTTG
6336854 TTTATTTTT-
1 TTTATTTTTG
*
6336863 TTAATTTTT
1 TTTATTTTT
6336872 TAATTTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 8 0.30
10 15 0.56
11 4 0.15
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTATTTTTG
Found at i:6336872 original size:10 final size:9
Alignment explanation
Indices: 6336833--6336888 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
6336823 ATTTGTTAAA
6336833 TTTATTTTTT
1 TTTA-TTTTT
6336843 GTTTATTTTT
1 -TTTATTTTT
6336853 GTTTA-TTTT
1 -TTTATTTTT
*
6336862 TTTAATTTT
1 TTTATTTTT
* *
6336871 TTAATTTGT
1 TTTATTTTT
6336880 TTTATTTTT
1 TTTATTTTT
6336889 AATTTTACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
8 4 0.10
9 21 0.54
10 10 0.26
11 4 0.10
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.80
Consensus pattern (9 bp):
TTTATTTTT
Found at i:6336886 original size:17 final size:16
Alignment explanation
Indices: 6336857--6336894 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
6336847 ATTTTTGTTT
6336857 ATTTTTTTAATTTTTTA
1 ATTTTTTTAA-TTTTTA
6336874 ATTTGTTTT-ATTTTTA
1 ATTT-TTTTAATTTTTA
6336890 ATTTT
1 ATTTT
6336895 ACTTTTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 10 0.50
17 5 0.25
18 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
ATTTTTTTAATTTTTA
Found at i:6337429 original size:2 final size:2
Alignment explanation
Indices: 6337422--6337446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6337412 TACCTTTTTC
6337422 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
6337447 GTAACTCTCA
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:6338163 original size:16 final size:16
Alignment explanation
Indices: 6338142--6338172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6338132 TATTTAAGTT
6338142 ATTTAAAATATAAAAA
1 ATTTAAAATATAAAAA
*
6338158 ATTTAAAATTTAAAA
1 ATTTAAAATATAAAA
6338173 TATAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTTAAAATATAAAAA
Found at i:6338204 original size:17 final size:16
Alignment explanation
Indices: 6338164--6338196 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6338154 AAAAATTTAA
6338164 AATTTAAAATATAATTT
1 AATTT-AAATATAATTT
6338181 AATTTAAATAT-ATTT
1 AATTTAAATATAATTT
6338196 A
1 A
6338197 TTATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTAAATATAATTT
Found at i:6338286 original size:42 final size:42
Alignment explanation
Indices: 6338199--6338290 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
6338189 TATATTTATT
* * * * *
6338199 ATTTAATTAATAAAAATTAATTAAACTGATTGAATTAATTCA
1 ATTTAATTAATAAAAATAAAATAAAATAATAGAATTAATTCA
6338241 ATTTAATTAATAAAAATAAAATAAAATAAAATAGAA-TAATT-A
1 ATTTAATTAATAAAAATAAAATAAAAT--AATAGAATTAATTCA
6338283 ATTTAATT
1 ATTTAATT
6338291 TTAAATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
42 33 0.77
43 5 0.12
44 5 0.12
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (42 bp):
ATTTAATTAATAAAAATAAAATAAAATAATAGAATTAATTCA
Found at i:6348471 original size:14 final size:14
Alignment explanation
Indices: 6348452--6348491 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
6348442 TAATACGATA
6348452 ATTTATATATTTAT
1 ATTTATATATTTAT
*
6348466 ATTTATTTATTTTAT
1 ATTTATATA-TTTAT
6348481 ATTTGATATAT
1 ATTT-ATATAT
6348492 ATAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
ATTTATATATTTAT
Found at i:6349084 original size:3 final size:3
Alignment explanation
Indices: 6349076--6349103 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6349066 TACCAAGGAA
6349076 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6349104 CGGTGTCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6352587 original size:2 final size:2
Alignment explanation
Indices: 6352580--6352613 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6352570 AGGAAATGAA
6352580 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6352614 CACTTGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6362957 original size:2 final size:2
Alignment explanation
Indices: 6362952--6362978 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6362942 ACCTATATAT
6362952 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
6362979 GAATTATAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6363286 original size:36 final size:36
Alignment explanation
Indices: 6363246--6363317 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
6363236 GAAGAACGAG
* *
6363246 AGAATTTTATTGCAGACCAGTACTAATATGATAATC
1 AGAATTTTACTGCAGACCAGTACTAATACGATAATC
6363282 AGAATTTTACTGCAGACCAGTACTAATACGATAATC
1 AGAATTTTACTGCAGACCAGTACTAATACGATAATC
6363318 TTACAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (36 bp):
AGAATTTTACTGCAGACCAGTACTAATACGATAATC
Found at i:6364855 original size:27 final size:27
Alignment explanation
Indices: 6364825--6364879 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6364815 CTGTAGAAAG
6364825 TAAACTCAGAGAAACACTACATCTAGC
1 TAAACTCAGAGAAACACTACATCTAGC
6364852 TAAACTCAGAGAAACACTACATCTAGC
1 TAAACTCAGAGAAACACTACATCTAGC
6364879 T
1 T
6364880 TTCTCAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.20
Consensus pattern (27 bp):
TAAACTCAGAGAAACACTACATCTAGC
Found at i:6370207 original size:33 final size:34
Alignment explanation
Indices: 6370168--6370237 Score: 124
Period size: 35 Copynumber: 2.1 Consensus size: 34
6370158 GATAAATAAA
6370168 AATATGCCATTTATAT-AAAAAAAATTGTCTAAT
1 AATATGCCATTTATATAAAAAAAAATTGTCTAAT
6370201 AATATGCCATTTATATAAAAAAAAAATTGTCTAAT
1 AATATGCCATTTATAT-AAAAAAAAATTGTCTAAT
6370236 AA
1 AA
6370238 ATTTTACAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 16 0.46
35 19 0.54
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (34 bp):
AATATGCCATTTATATAAAAAAAAATTGTCTAAT
Found at i:6370806 original size:15 final size:15
Alignment explanation
Indices: 6370786--6370832 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
6370776 TGTCGTAAAC
6370786 CAAAAAAATAAAAAA
1 CAAAAAAATAAAAAA
6370801 CAAAAAAA-AATAAAGA
1 CAAAAAAATAA-AAA-A
*
6370817 GAAAAGAAATAAAAAA
1 CAAAA-AAATAAAAAA
6370833 AAATTGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 6 0.22
17 6 0.22
18 2 0.07
ACGTcount: A:0.83, C:0.04, G:0.06, T:0.06
Consensus pattern (15 bp):
CAAAAAAATAAAAAA
Found at i:6375123 original size:18 final size:18
Alignment explanation
Indices: 6375100--6375138 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6375090 ATTGCTTCAA
* *
6375100 ATCCAATAGTAATAAGTC
1 ATCCAACAGTAACAAGTC
6375118 ATCCAACAGTAACAAGTC
1 ATCCAACAGTAACAAGTC
6375136 ATC
1 ATC
6375139 AAAATTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (18 bp):
ATCCAACAGTAACAAGTC
Found at i:6376017 original size:30 final size:30
Alignment explanation
Indices: 6375981--6376042 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
6375971 TCCAACAAAG
6375981 TTTGAAAAATACTAATTTTTACGTAATACA
1 TTTGAAAAATACTAATTTTTACGTAATACA
6376011 TTTGAAAAATACTAATTTTTACGTAATACA
1 TTTGAAAAATACTAATTTTTACGTAATACA
6376041 TT
1 TT
6376043 ATAATCATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (30 bp):
TTTGAAAAATACTAATTTTTACGTAATACA
Found at i:6376657 original size:3 final size:3
Alignment explanation
Indices: 6376649--6376692 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6376639 ACTATCCATG
6376649 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6376693 TCTCTTTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6377879 original size:3 final size:3
Alignment explanation
Indices: 6377873--6377900 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6377863 ATAATAAAAA
6377873 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6377901 AAATAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:6379869 original size:14 final size:16
Alignment explanation
Indices: 6379840--6379893 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 16
6379830 CTAAAATTAA
*
6379840 TAAA-ATATTATT-TT
1 TAAATATATAATTATT
6379854 TAAATATA-AA-TATT
1 TAAATATATAATTATT
*
6379868 TAAATATATAATTATA
1 TAAATATATAATTATT
6379884 TAAATATATA
1 TAAATATATA
6379894 TAAATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 1 0.03
14 15 0.44
15 5 0.15
16 13 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATATATAATTATT
Found at i:6379873 original size:8 final size:8
Alignment explanation
Indices: 6379857--6379893 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
6379847 TTATTTTTAA
6379857 ATATAAAT
1 ATATAAAT
*
6379865 ATTTAAAT
1 ATATAAAT
*
6379873 ATATAATT
1 ATATAAAT
6379881 ATATAAAT
1 ATATAAAT
6379889 ATATA
1 ATATA
6379894 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:6379900 original size:14 final size:14
Alignment explanation
Indices: 6379854--6379901 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
6379844 ATATTATTTT
* *
6379854 TAAATATAAATATT
1 TAAATATATATATA
6379868 TAAATATATAATTATA
1 TAAATATAT-A-TATA
*
6379884 TAAATATATATAAA
1 TAAATATATATATA
6379898 TAAA
1 TAAA
6379902 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.52
15 2 0.07
16 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:6379906 original size:26 final size:24
Alignment explanation
Indices: 6379857--6379907 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
6379847 TTATTTTTAA
* *
6379857 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
6379881 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
6379907 A
1 A
6379908 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:6380558 original size:22 final size:24
Alignment explanation
Indices: 6380507--6380562 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
6380497 GATTGTATAG
*
6380507 ATAATATAAA-TATATATTTATTT
1 ATAATATAAATTATATATTTAATT
*
6380530 TTAATATAAATTATA-ATTTAATT
1 ATAATATAAATTATATATTTAATT
6380553 AT-ATATAAAT
1 ATAATATAAAT
6380563 GTAATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.28
23 17 0.59
24 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATAATATAAATTATATATTTAATT
Found at i:6380575 original size:21 final size:22
Alignment explanation
Indices: 6380510--6380575 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
6380500 TGTATAGATA
*
6380510 ATATAAATATATATTTATTTTTA-
1 ATATAAAT-TATAATT-TTTTTAT
**
6380533 ATATAAATTATAATTTAATTAT
1 ATATAAATTATAATTTTTTTAT
*
6380555 ATATAAA-TGTAATTTTTTTAT
1 ATATAAATTATAATTTTTTTAT
6380576 TAAATTAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 15 0.42
22 13 0.36
23 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATAAATTATAATTTTTTTAT
Found at i:6380632 original size:16 final size:17
Alignment explanation
Indices: 6380606--6380638 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6380596 TATTTTTATT
*
6380606 AATATAATAATATAATA
1 AATATAATAATAAAATA
6380623 AATA-AATAATAAAATA
1 AATATAATAATAAAATA
6380639 TATTTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATAATAATAAAATA
Found at i:6380913 original size:26 final size:26
Alignment explanation
Indices: 6380884--6380956 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
6380874 ATCTCACGTG
* *
6380884 ATTTATTAATTAAATTAT-TAAATAAT
1 ATTTATTAATAAAAATATATAAA-AAT
*
6380910 ATTTTTTAATAAAAATATATAAAAAT
1 ATTTATTAATAAAAATATATAAAAAT
* *
6380936 ATATAAATAATAAAAATATAT
1 AT-TTATTAATAAAAATATAT
6380957 TTTTATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTTATTAATAAAAATATATAAAAAT
Found at i:6380931 original size:10 final size:10
Alignment explanation
Indices: 6380918--6380956 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
6380908 ATATTTTTTA
6380918 ATAAAAATAT
1 ATAAAAATAT
6380928 ATAAAAATAT
1 ATAAAAATAT
6380938 AT--AAATA-
1 ATAAAAATAT
6380945 ATAAAAATAT
1 ATAAAAATAT
6380955 AT
1 AT
6380957 TTTTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.08
8 5 0.19
9 5 0.19
10 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:6380950 original size:17 final size:18
Alignment explanation
Indices: 6380922--6380956 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6380912 TTTTTAATAA
6380922 AAATATATAAAAATATAT
1 AAATATATAAAAATATAT
6380940 AAATA-ATAAAAATATAT
1 AAATATATAAAAATATAT
6380957 TTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATATAAAAATATAT
Found at i:6381821 original size:20 final size:20
Alignment explanation
Indices: 6381798--6381836 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6381788 ATGACCCCTA
* *
6381798 AATTATTAAAATTTTAATAT
1 AATTACTAAAATTTGAATAT
6381818 AATTACTAAAATTTGAATA
1 AATTACTAAAATTTGAATA
6381837 ATTGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTACTAAAATTTGAATAT
Found at i:6381955 original size:19 final size:18
Alignment explanation
Indices: 6381931--6381974 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
6381921 TATTTGAAAA
*
6381931 TTTTTAATTTTTCATACAT
1 TTTTTAATTTTT-ATAAAT
6381950 TTTTTAAATTTTTATAAAT
1 TTTTT-AATTTTTATAAAT
6381969 TTTTTA
1 TTTTTA
6381975 TTTAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAATTTTTATAAAT
Found at i:6389176 original size:58 final size:59
Alignment explanation
Indices: 6389081--6389744 Score: 709
Period size: 60 Copynumber: 11.0 Consensus size: 59
6389071 TGTTCTTGTG
* * *
6389081 TAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATATTTTTGAAAATTT-ATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTT
* * *
6389139 TAAGGAAAATTGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTTTGAAACTTTGATTTC
1 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATA---TTTTTTTGAAAATTTGATTTT
* * * *
6389201 CAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTCTTCTTTGAAAATTT-ATTTC
1 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-AT-TTTTTTGAAAATTTGATTTT
* *
6389261 TAAGGAAAACTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTGAAAATTTATTTTATTATT
1 TAAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTG-AAA---A--TT-TGA--
6389325 TTTTTT
56 --TTTT
*
6389331 TAAGGAAAATTGATACTTTCAACTTTT-CTCTAAAAATATTTTTTTGAAAATTTTGATCTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAAA-TTTGATTTT
** *** *
6389391 TAAAAAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTG-AAATTTTATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTT
6389449 TAAGGAAAATTGATACTTTCAACTTTT-CTCTAAAAATA-TTTTTTGAAAATTTCGATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAAATTT-GATTTT
* * *
6389508 CAAAGAAAATTGATACTTTCAACTTTT-CTCCAAAAATAATTTTTTGAAAATTTCGATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCT-CAAAAATATTTTTTTGAAAATTT-GATTTT
* * * *
6389568 CAAAGAAAATTGATACTTTCAACTTTTCC-CTAAAAATAATTTTTTGAAAATTTTGATCTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAAA-TTTGATTTT
*** *
6389628 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTG-AAATTTTATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTT
* * * * * *
6389686 TAAGAAAAATTGATACTTTAAACTTTTCCCCAAAAATATTTTTTGGAAACTTGGATTTT
1 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTT
6389745 CATTTAAAGA
Statistics
Matches: 522, Mismatches: 53, Indels: 61
0.82 0.08 0.10
Matches are distributed among these distances:
57 10 0.02
58 129 0.25
59 61 0.12
60 189 0.36
61 33 0.06
62 40 0.08
64 4 0.01
65 4 0.01
66 2 0.00
69 4 0.01
70 46 0.09
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (59 bp):
TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTGATTTT
Found at i:6389345 original size:70 final size:70
Alignment explanation
Indices: 6389252--6389383 Score: 228
Period size: 70 Copynumber: 1.9 Consensus size: 70
6389242 TTCTTTGAAA
6389252 ATTTATTTCTAAGGAAAACTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAATTTATT
1 ATTTATTTCTAAGGAAAACTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAATTTATT
6389317 TTATT
66 TTATT
* * * *
6389322 ATTTTTTTTTAAGGAAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTTGAAAATTT
1 ATTTATTTCTAAGGAAAACTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAATTT
6389384 TGATCTTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (70 bp):
ATTTATTTCTAAGGAAAACTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAATTTATT
TTATT
Found at i:6389459 original size:118 final size:118
Alignment explanation
Indices: 6389322--6389734 Score: 609
Period size: 118 Copynumber: 3.5 Consensus size: 118
6389312 TTATTTTATT
*
6389322 ATTTT-TTTTTAAGGAAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTTGAAAATTTTG
1 ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTG
*
6389386 ATCTTTAAAAAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAA
66 ATCTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAA
* *
6389439 ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCTCTAAAAATA-TTTTTTGAAAATTTCG
1 ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTG
****
6389503 AT-TTTCAAAGAAAATTGATACTTTCAACTTTT-CTCCAAAAATAATTTTTTGAAA
66 ATCTTT-AAAGAAAATTGATACTTTCAACTTTTCCT-CAAAACCCTTTTTTTG-AA
* * * *
6389557 ATTTCGATTTTCAAAGAAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTGAAAATTTT
1 ATTT-TATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTT
*
6389622 GATCTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAA
65 GATCTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAA
* * * *
6389676 ATTTTATTTTTAAGAAAAATTGATACTTTAAACTTTTCCCCAAAAATATTTTTTGGAAA
1 ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAA
6389735 CTTGGATTTT
Statistics
Matches: 264, Mismatches: 24, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
116 5 0.02
117 59 0.22
118 95 0.36
119 46 0.17
120 54 0.20
121 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (118 bp):
ATTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTG
ATCTTTAAAGAAAATTGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAA
Found at i:6389520 original size:26 final size:26
Alignment explanation
Indices: 6389491--6389580 Score: 65
Period size: 26 Copynumber: 3.2 Consensus size: 26
6389481 AAAATATTTT
6389491 TTGAAAATTTCGATTTTCAAAGAAAA
1 TTGAAAATTTCGATTTTCAAAGAAAA
* * *
6389517 TTGATACTTTCAACTTTTCTCCAAA-AATAA
1 TTGAAAATTTCGA--TTT-T-CAAAGAA-AA
6389547 TTTTTTGAAAATTTCGATTTTCAAAGAAAA
1 ----TTGAAAATTTCGATTTTCAAAGAAAA
6389577 TTGA
1 TTGA
6389581 TACTTTCAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 20
0.65 0.08 0.27
Matches are distributed among these distances:
26 14 0.29
28 3 0.06
29 3 0.06
30 12 0.25
31 3 0.06
32 3 0.06
34 10 0.21
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (26 bp):
TTGAAAATTTCGATTTTCAAAGAAAA
Found at i:6389615 original size:237 final size:240
Alignment explanation
Indices: 6389086--6389746 Score: 847
Period size: 237 Copynumber: 2.7 Consensus size: 240
6389076 TTGTGTAAGA
* *
6389086 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATATTTTTGAAAA-TTT-ATTTTTAAGGAAAA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATAAT-TTTTTGAAAATTTTGATCTTTAAGGAAAA
* *** * **
6389148 TTGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTTTGAAACTTTGATTTCCAAGGAAAATTG
65 TTGATACTTTCAACTTTTCCTC--AAA-ACCCTTTTTTTGAAA-TTTTATTTTTAAGGAAAATTG
* *
6389213 ATACTTTCAACTTTTCCTCAAAAATCCTCTTCTTTGAAAATTT-A-TTTCTAAGGAAAACTGATA
126 ATACTTTCAACTTTTCCT-AAAAAT-AT-TT-TTTGAAAATTTGATTTTC-AAAGAAAACTGATA
* ** * *
6389276 CTTTCAACTTTTCTCCAAAAATATTTTTTTGAAAATTTATTTTATTATTTTTTTTTAAGG
186 CTTTCAACTTTTCTCCAAAAATAATTTTTTGAAAA--TATTTTACGA---TTTTTCAAAG
* * **
6389336 AAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTTGAAAATTTTGATCTTTAAAAAAAAT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTGAAAATTTTGATCTTTAAGGAAAAT
6389401 TGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACT
66 TGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACT
*
6389466 TTCAACTTTTCTCTAAAAATATTTTTTGAAAATTTCGATTTTCAAAGAAAATTGATACTTTCAAC
131 TTCAACTTTTC-CTAAAAATATTTTTTGAAAATTT-GATTTTCAAAGAAAACTGATACTTTCAAC
6389531 TTTTCTCCAAAAATAATTTTTTG-AAA-A-TTT-CGA-TTTTCAAAG
194 TTTTCTCCAAAAATAATTTTTTGAAAATATTTTACGATTTTTCAAAG
6389573 AAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTGAAAATTTTGATCTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTGAAAATTTTGATCTTTAAGGAAAAT
*
6389638 TGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAAATTTTATTTTTAAGAAAAATTGATACT
66 TGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACT
* * * *
6389703 TTAAACTTTTCCCCAAAAATATTTTTTGGAAACTTGGATTTTCA
131 TTCAACTTTT-CCTAAAAATATTTTTT-GAAAATTTGATTTTCA
6389747 TTTAAAGAAA
Statistics
Matches: 372, Mismatches: 30, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
237 163 0.44
238 7 0.02
241 1 0.00
242 3 0.01
243 1 0.00
245 11 0.03
246 5 0.01
247 44 0.12
248 44 0.12
249 14 0.04
250 43 0.12
251 4 0.01
252 32 0.09
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (240 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATAATTTTTTGAAAATTTTGATCTTTAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAACCCTTTTTTTGAAATTTTATTTTTAAGGAAAATTGATACT
TTCAACTTTTCCTAAAAATATTTTTTGAAAATTTGATTTTCAAAGAAAACTGATACTTTCAACTT
TTCTCCAAAAATAATTTTTTGAAAATATTTTACGATTTTTCAAAG
Found at i:6389896 original size:25 final size:25
Alignment explanation
Indices: 6389861--6389908 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6389851 AACCTAATCT
*
6389861 AATAAATAAATAAAAT-AAAAAAACA
1 AATAAACAAAT-AAATGAAAAAAACA
6389886 AATAAACAAATAAATGAAAAAAA
1 AATAAACAAATAAATGAAAAAAA
6389909 AAAACCTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (25 bp):
AATAAACAAATAAATGAAAAAAACA
Found at i:6391047 original size:34 final size:35
Alignment explanation
Indices: 6390987--6391054 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
6390977 ATTCAATTGG
*
6390987 GCCTTACCCATTTGGACCAGGCCCAATTGATCTGA
1 GCCTGACCCATTTGGACCAGGCCCAATTGATCTGA
*
6391022 GCCTGACCCATTTGG-TCAGGCCCAATTGATCTG
1 GCCTGACCCATTTGGACCAGGCCCAATTGATCTG
6391055 GACTTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (35 bp):
GCCTGACCCATTTGGACCAGGCCCAATTGATCTGA
Found at i:6391574 original size:23 final size:23
Alignment explanation
Indices: 6391543--6391587 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6391533 AAATTATACG
*
6391543 TATTGAAATTTAAATTTTAAATT
1 TATTAAAATTTAAATTTTAAATT
**
6391566 TATTAAAATTTATTTTTTAAAT
1 TATTAAAATTTAAATTTTAAAT
6391588 ATAATTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTAAAATTTAAATTTTAAATT
Found at i:6394117 original size:371 final size:370
Alignment explanation
Indices: 6393170--6394453 Score: 1660
Period size: 370 Copynumber: 3.5 Consensus size: 370
6393160 GTCTGATCGT
* * * * * *
6393170 CACGGTTCACACCTTTGTGAGGTATTATCTGTTTTGACCCCCCTGACCTCATGGTTTTATCCTAC
1 CACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGACCCCCCTGACCTCACGATTTTATCCTAC
** * * *
6393235 AAAAGGTACCTCACAAAGC-GAAGGTGATGTGAATCATTTTATACCCCAGTAACCCTCTTATTAT
66 AAAAGACACCTCACAAGGCGGAA-GTGATGTGAACCATTTTATACCCCAGTGACCCTCTTATTAT
* *
6393299 ATTCGATGTGAGATTCATGACTCTTTCTTAAGTCCGTGACATTCTCCTGCACCCAACCTCGTGAC
130 GTTCGATGTGAGATTCAGGACTCTTTCTTAAGTCCGTGACATTCTCC-GCACCCAACCTCGTGAC
* * * *
6393364 GCCCTCGTCACGGAAGCTGGCCACCTTGCCTACCTCCCTCGAGGTGCTTGGCGTGGATTGAACGG
194 GCCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCTCGAGGCGCTTGGCGTAGATTGAACGG
* *
6393429 TTTAGGGCTGGCTCTGATACCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCACGCGGCTTC
259 TTTAGGGCTGGCTCTGATACCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCC
* * *
6393494 GGGACCC-GGACATTCACCCTTCCGACATCCCAGATCAGCCTTCTTGC
324 GGGACCCGGGA-ATTCACCCTTCCGACGTCCCAAATCAGCCTTCCTGC
* * *
6393541 CACGGTTCACACCCTTGTGAGGTATTATCCGCTTTGA-CCTCCTGACCTCACGATTTTGTCCTAC
1 CACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGACCCCCCTGACCTCACGATTTTATCCTAC
* * ** * * * * *
6393605 AAAAGACGCTTCACAAGGAAGAGGTGGTGTGAACCATTCTATACCCCAGTGAACCTCCTATTATG
66 AAAAGACACCTCACAAGGCGGAAGTGATGTGAACCATTTTATACCCCAGTGACCCTCTTATTATG
*
6393670 TTCGATGTGGGATTCAGGACTCTTTCTTAAGTCCGTGACATTCTCCCGCACCCAACCTCGTGACG
131 TTCGATGTGAGATTCAGGACTCTTTCTTAAGTCCGTGACATTCT-CCGCACCCAACCTCGTGACG
* * * *
6393735 CCCTCGTCACGGAGGCTGGTCACCCTGCCTACCTCCCTTGAGGCGCTTGGCGTAGATCGAACAGT
195 CCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCTCGAGGCGCTTGGCGTAGATTGAACGGT
* * * *
6393800 TTAGGACTGACTCTGATACTACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCA
260 TTAGGGCTGGCTCTGATACCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCG
* * *
6393865 GGACCCGGGAATTCACCCTTCCGGCGTCTCAAATCAGCCTTCCTGT
325 GGACCCGGGAATTCACCCTTCCGACGTCCCAAATCAGCCTTCCTGC
* * * * * * *
6393911 CACGGTTCACATCCTTGTGAGGTATTGTCCGCTCTGGCCCCCTTGACCTCACGGTTTTGTCCTAT
1 CACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGACCCCCCTGACCTCACGATTTTATCCTAC
* * * * *
6393976 AAAAGACGCCTCACAAGGCGGAAGTGGTGTGAACCCTTTTATACCCCAGGGACCCTCATATTATG
66 AAAAGACACCTCACAAGGCGGAAGTGATGTGAACCATTTTATACCCCAGTGACCCTCTTATTATG
* * *
6394041 TTCGATGTGGGATTC-GAGACTCTTCCTTAAGTCCGTGACATTCTCTCGTACCCAACCTCGTGAC
131 TTCGATGTGAGATTCAG-GACTCTTTCTTAAGTCCGTGACATTCTC-CGCACCCAACCTCGTGAC
* * * *
6394105 GCCTTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCTCGAGACGCTTGACGTAAATTGAACGG
194 GCCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCTCGAGGCGCTTGGCGTAGATTGAACGG
* * * * *
6394170 TTTAGGGCTGGCTCTGATACCACTTGTCACGGTGGTCGAGACTCAAGCTTCAAACCCGCACGGTT
259 TTTAGGGCTGGCTCTGATACCACTTGTCAC-G-GGTCGAGACTTAAGCTCCGAACCCGCGCGGCT
* * * * *
6394235 CCGGGACCCGGGCATTCACCCTTTCGACGTCCCGAATTAGCCTGACC-GC
322 CCGGGACCCGGGAATTCACCCTTCCGACGTCCCAAATCAGCCT-TCCTGC
* * * * *
6394284 CACGGTTCACACCCTTGTGAGGTATTGTCCGTTCTGGCCCCCCTGGCCTCACGATTTTATCTTAC
1 CACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGACCCCCCTGACCTCACGATTTTATCCTAC
* * * * * *
6394349 AAAAGGCATCTCACAAGACGGAGGTGATGTGAATCATTTTATACCCCAATGACCCTCTTATTATG
66 AAAAGACACCTCACAAGGCGGAAGTGATGTGAACCATTTTATACCCCAGTGACCCTCTTATTATG
* *
6394414 TTCGATGTGAGATTCAAGACTCTTTTTTAAGTCCGTGACA
131 TTCGATGTGAGATTCAGGACTCTTTCTTAAGTCCGTGACA
6394454 CATGGACCTC
Statistics
Matches: 793, Mismatches: 110, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
370 318 0.40
371 262 0.33
372 1 0.00
373 210 0.26
374 2 0.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (370 bp):
CACGGTTCACACCCTTGTGAGGTATTATCCGCTCTGACCCCCCTGACCTCACGATTTTATCCTAC
AAAAGACACCTCACAAGGCGGAAGTGATGTGAACCATTTTATACCCCAGTGACCCTCTTATTATG
TTCGATGTGAGATTCAGGACTCTTTCTTAAGTCCGTGACATTCTCCGCACCCAACCTCGTGACGC
CCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCCTCGAGGCGCTTGGCGTAGATTGAACGGTT
TAGGGCTGGCTCTGATACCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGG
GACCCGGGAATTCACCCTTCCGACGTCCCAAATCAGCCTTCCTGC
Found at i:6394822 original size:30 final size:30
Alignment explanation
Indices: 6394786--6394871 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 30
6394776 TATTATATTT
* *
6394786 AAATAAATTTTTAATTTTTAATTTGCAT-A
1 AAATAAATCTTTAACTTTTAATTTGCATCA
*
6394815 CAAATAAATCTTTAACTTTTAATTTGTATCA
1 -AAATAAATCTTTAACTTTTAATTTGCATCA
*
6394846 AAATAAACTCTTAAACTTTTAATTTG
1 AAATAAA-TCTTTAACTTTTAATTTG
6394872 TACTTAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 32 0.64
31 18 0.36
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (30 bp):
AAATAAATCTTTAACTTTTAATTTGCATCA
Found at i:6394866 original size:31 final size:31
Alignment explanation
Indices: 6394801--6394890 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
6394791 AATTTTTAAT
* *
6394801 TTTTAATTTGCAT-ACAAATAAA-TCTTTAAC
1 TTTTAATTTGTATCA-AAATAAACTCTTAAAC
6394831 TTTTAATTTGTATCAAAATAAACTCTTAAAC
1 TTTTAATTTGTATCAAAATAAACTCTTAAAC
* *
6394862 TTTTAATTTGTA-CTTAAATAAACTATTAA
1 TTTTAATTTGTATC-AAAATAAACTCTTAA
6394891 CATAAATTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
30 20 0.38
31 33 0.62
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTTAATTTGTATCAAAATAAACTCTTAAAC
Found at i:6394982 original size:29 final size:29
Alignment explanation
Indices: 6394917--6394984 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
6394907 ATTTGAAATA
6394917 AGATTTATTTAGATACAAATCAAAATATG
1 AGATTTATTTAGATACAAATCAAAATATG
*
6394946 AGAGTTTATTTGGATA-AAAT-AAAAGTATAG
1 AGA-TTTATTTAGATACAAATCAAAA-TAT-G
6394976 AGATTTATT
1 AGATTTATT
6394985 AAAAAATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 4 0.11
29 16 0.46
30 15 0.43
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.37
Consensus pattern (29 bp):
AGATTTATTTAGATACAAATCAAAATATG
Found at i:6401102 original size:31 final size:30
Alignment explanation
Indices: 6401067--6401288 Score: 133
Period size: 31 Copynumber: 7.1 Consensus size: 30
6401057 TTACGCTGAG
* *
6401067 GTGAATTTGTGCCAAGGTGATTTACATAGAA
1 GTGAATTTATGCTAAGGTGATTTACAT-GAA
** * ** *
6401098 GTGAATCCATGCCAAGGTGAATTTATGTTAAA
1 GTGAATTTATGCTAAGGTG-ATTTA-CATGAA
** *
6401130 GTGAATTTATGCTAAGACGATTTTCACTGAA
1 GTGAATTTATGCTAAGGTGATTTACA-TGAA
* * * *
6401161 GTGAATCTGTGCTGATGTGATTTACATTG-A
1 GTGAATTTATGCTAAGGTGATTTACA-TGAA
* * *
6401191 GATAAATTTACGCTAAGGTAATTTACATTGAA
1 G-TGAATTTATGCTAAGGTGATTTACA-TGAA
* *
6401223 GTTAATTTATGTTAAGGTGATTTACACTGAA
1 GTGAATTTATGCTAAGGTGATTTACA-TGAA
* * *
6401254 GTGAATATATG-TCAAGATGATTTTCATCGAA
1 GTGAATTTATGCT-AAGGTGATTTACAT-GAA
6401285 GTGA
1 GTGA
6401289 GCTGTTTTGC
Statistics
Matches: 145, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
30 4 0.03
31 117 0.81
32 23 0.16
33 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (30 bp):
GTGAATTTATGCTAAGGTGATTTACATGAA
Found at i:6401381 original size:30 final size:30
Alignment explanation
Indices: 6401339--6401395 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
6401329 GCTCATTGCT
*
6401339 GAGCTCAACCTTTATGAAGGTAATTTTGTA
1 GAGCTCAACCTTTATGAAAGTAATTTTGTA
* *
6401369 GAGCT-AAGCCTTTTTGAAAGTATTTTT
1 GAGCTCAA-CCTTTATGAAAGTAATTTT
6401396 CTTAAACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (30 bp):
GAGCTCAACCTTTATGAAAGTAATTTTGTA
Found at i:6404442 original size:30 final size:30
Alignment explanation
Indices: 6404408--6404468 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
6404398 AATTAATTAA
* * *
6404408 TTAAATATATATATTTATATAATGATATTT
1 TTAAATATATATATTTAAAAAATCATATTT
*
6404438 TTAAATATTTATATTTAAAAAATCATATTT
1 TTAAATATATATATTTAAAAAATCATATTT
6404468 T
1 T
6404469 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TTAAATATATATATTTAAAAAATCATATTT
Found at i:6404454 original size:14 final size:14
Alignment explanation
Indices: 6404408--6404456 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6404398 AATTAATTAA
6404408 TTAAATATATATAT
1 TTAAATATATATAT
* *
6404422 TTATATAATGATATTT
1 TTAAAT-AT-ATATAT
*
6404438 TTAAATATTTATAT
1 TTAAATATATATAT
6404452 TTAAA
1 TTAAA
6404457 AAATCATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 14 0.50
15 4 0.14
16 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TTAAATATATATAT
Found at i:6404471 original size:21 final size:22
Alignment explanation
Indices: 6404445--6404492 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
6404435 TTTTTAAATA
6404445 TTTATA-TTTAAAAAAT-CATAT
1 TTTATATTTTAAAAAATAC-TAT
6404466 TTTATATTTTAAAAAATACTAT
1 TTTATATTTTAAAAAATACTAT
6404488 TTTAT
1 TTTAT
6404493 TAATTTCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTATATTTTAAAAAATACTAT
Found at i:6405669 original size:18 final size:18
Alignment explanation
Indices: 6405646--6405680 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6405636 TTGAAATGAG
*
6405646 GTAATATATAAAAAAAAT
1 GTAATATACAAAAAAAAT
6405664 GTAATATACAAAAAAAA
1 GTAATATACAAAAAAAA
6405681 AAACTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (18 bp):
GTAATATACAAAAAAAAT
Found at i:6405708 original size:2 final size:2
Alignment explanation
Indices: 6405703--6405732 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6405693 AGTTGTTTTG
6405703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6405733 TTACATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6406347 original size:24 final size:25
Alignment explanation
Indices: 6406320--6406374 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
6406310 TGTTTATATT
6406320 TATTTGATATT-TAAAATTTTGATA
1 TATTTGATATTATAAAATTTTGATA
* * *
6406344 TATTTAATATTATAAATTTTTGTTA
1 TATTTGATATTATAAAATTTTGATA
6406369 TATTTG
1 TATTTG
6406375 TGTTAATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (25 bp):
TATTTGATATTATAAAATTTTGATA
Found at i:6410483 original size:25 final size:25
Alignment explanation
Indices: 6410449--6410510 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
6410439 ATAATCTCAC
* *
6410449 ATTTTGGATGGTTTCAGTGAGCCTA
1 ATTTTGGATGGTTTCAATAAGCCTA
6410474 ATTTTGGATGGTTTCAATAAGCCTA
1 ATTTTGGATGGTTTCAATAAGCCTA
6410499 ATTTTGGATGGT
1 ATTTTGGATGGT
6410511 CTTACGTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (25 bp):
ATTTTGGATGGTTTCAATAAGCCTA
Found at i:6413008 original size:3 final size:3
Alignment explanation
Indices: 6413002--6413121 Score: 129
Period size: 3 Copynumber: 41.0 Consensus size: 3
6412992 GTAATAGTAG
*
6413002 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -CA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * *
6413049 TCC TAG TAA TAA TAA CAA TAA TAA TAG GAA TAA TAA -AA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
6413095 TAA TAC TAA TAA TAA CAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
6413122 AAGTACTAGT
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
2 5 0.05
3 95 0.95
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:6414124 original size:24 final size:25
Alignment explanation
Indices: 6414097--6414151 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
6414087 TTATTGACTC
6414097 TATTTTGATCCATGTCATT-CATCT
1 TATTTTGATCCATGTCATTCCATCT
* * * *
6414121 TA-TTTGTTCCTTTTCATTCCATTT
1 TATTTTGATCCATGTCATTCCATCT
6414145 TATTTTG
1 TATTTTG
6414152 CACTTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 13 0.52
24 8 0.32
25 4 0.16
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.58
Consensus pattern (25 bp):
TATTTTGATCCATGTCATTCCATCT
Found at i:6419114 original size:33 final size:33
Alignment explanation
Indices: 6419077--6419143 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
6419067 TGGACTACAA
6419077 ATAGCACTCAGAGTTTCTATTAATTACCAAATG
1 ATAGCACTCAGAGTTTCTATTAATTACCAAATG
*
6419110 ATAGCACTTAGAGTTTCTATTAATTACCAAATG
1 ATAGCACTCAGAGTTTCTATTAATTACCAAATG
6419143 A
1 A
6419144 CTCTGATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
ATAGCACTCAGAGTTTCTATTAATTACCAAATG
Found at i:6420710 original size:24 final size:24
Alignment explanation
Indices: 6420663--6420710 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6420653 ACAAGTACTT
* **
6420663 ATATATATTTATTTATATTTTCAA
1 ATATATATTTATTAATATAATCAA
*
6420687 ATATATATTTATTAATGTAATCAA
1 ATATATATTTATTAATATAATCAA
6420711 TTATGTCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
ATATATATTTATTAATATAATCAA
Found at i:6424589 original size:97 final size:98
Alignment explanation
Indices: 6424395--6424578 Score: 289
Period size: 97 Copynumber: 1.9 Consensus size: 98
6424385 GTATAAGTTG
*
6424395 CTATGTGCTGATTGTTGATATGGTTGCCCTTTTCTGGACTATGAAATAGTTCCTGTTAGCACAAA
1 CTATGTGCTGATTGTTGATATGCTTGCCCTTTTCTGGACTATGAAATAGTTCCTGTTAGCACAAA
6424460 GGAGTGCAGGTTTATAAGTGATCCATTAATGAA
66 GGAGTGCAGGTTTATAAGTGATCCATTAATGAA
* * * * *
6424493 CTATGTGCTGGTTGTTGATATGCTTGTCCTTTT-TGTACTATGAAATAGTTCCTGTTAGGACACA
1 CTATGTGCTGATTGTTGATATGCTTGCCCTTTTCTGGACTATGAAATAGTTCCTGTTAGCACAAA
* *
6424557 GGAGTTCATGTTTATAAGTGAT
66 GGAGTGCAGGTTTATAAGTGAT
6424579 TCTTTGATGA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 48 0.62
98 30 0.38
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (98 bp):
CTATGTGCTGATTGTTGATATGCTTGCCCTTTTCTGGACTATGAAATAGTTCCTGTTAGCACAAA
GGAGTGCAGGTTTATAAGTGATCCATTAATGAA
Found at i:6431314 original size:6 final size:6
Alignment explanation
Indices: 6431303--6431331 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6431293 CTTCAAATTC
6431303 GCTTCT GCTTCT GCTTCT GCTTCT G-TTCT
1 GCTTCT GCTTCT GCTTCT GCTTCT GCTTCT
6431332 TCATTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.00, C:0.31, G:0.17, T:0.52
Consensus pattern (6 bp):
GCTTCT
Found at i:6431377 original size:13 final size:13
Alignment explanation
Indices: 6431335--6431377 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
6431325 CTGTTCTTCA
*
6431335 TTTCTTCTTGTTC
1 TTTCTTCTTTTTC
*
6431348 -TTCTTCTTTTCC
1 TTTCTTCTTTTTC
*
6431360 CTTCTTCTTTTTC
1 TTTCTTCTTTTTC
6431373 TTTCT
1 TTTCT
6431378 CGCTCTCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTCTTCTTTTTC
Found at i:6435824 original size:24 final size:24
Alignment explanation
Indices: 6435779--6435825 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6435769 TTATTTTCAG
*
6435779 TATATTTAATATTTTTTATAAAAA
1 TATATTTAATATTTTCTATAAAAA
*
6435803 TATATTTATTATTTATCT-TAAAA
1 TATATTTAATATTT-TCTATAAAA
6435826 TAATAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATTTAATATTTTCTATAAAAA
Found at i:6436529 original size:22 final size:20
Alignment explanation
Indices: 6436472--6436531 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 20
6436462 AGTTTATTTA
6436472 GTAATTTAATATATAATTAATT
1 GTAATTTAATA-A-AATTAATT
*
6436494 GTACATTATGATAAAATTTAATAT
1 GTA-ATT-TAATAAAA-TTAAT-T
6436518 GTAATTTAATAAAA
1 GTAATTTAATAAAA
6436532 ATATTATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
22 12 0.38
23 12 0.38
24 8 0.25
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
GTAATTTAATAAAATTAATT
Found at i:6441344 original size:63 final size:62
Alignment explanation
Indices: 6441241--6441594 Score: 170
Period size: 62 Copynumber: 5.7 Consensus size: 62
6441231 AAAAAATATT
* * * *** * * **
6441241 GGAGATTATTTAAAACGTTTCTGATGGGAAATATCTTAAATAATCATTTTTATGTTTATAAAA
1 GGAGATTATTTAAAGCATTTTTGATCAAAAATACCTTAAATAATC-TCTAAATGTTTATAAAA
* * * * *
6441304 -GAGATTATTTAAGGTATTTTTGGTCTAAAAATACCTTAAATAATCTCTAAATTTTTTTAAAA
1 GGAGATTATTTAAAGCATTTTTGATC-AAAAATACCTTAAATAATCTCTAAATGTTTATAAAA
* * * * *
6441366 GGAGATTATTTAAAGCGTTTTTGATCAAAAACACCTTATATAATATCTAATAT-TTTTTAAAA
1 GGAGATTATTTAAAGCATTTTTGATCAAAAATACCTTAAATAATCTCTAA-ATGTTTATAAAA
** * **** * * **
6441428 AAAGATTATTT-AAGACGTTTTTTG-TCAAAAACGTTTTAAATAATACCCTTCAAT-TTT-TTGA
1 GGAGATTATTTAAAG-C-ATTTTTGATCAAAAATACCTTAAATAAT-CTC-TAAATGTTTATAAA
6441489 A
62 A
** * * * * * *
6441490 GG-GTATTATTTAAAGTGTTTATAATCAAAAACACCTTAAATAATTTTTAACAT-TTT-TTAAA
1 GGAG-ATTATTTAAAGCATTTTTGATCAAAAATACCTTAAATAATCTCTAA-ATGTTTATAAAA
* * *
6441551 -GAGGATTATTTAATGCGTTTTTGATCAAAAATGCCTTAAATAAT
1 GGA-GATTATTTAAAGCATTTTTGATCAAAAATACCTTAAATAAT
6441595 ATTTTTCATT
Statistics
Matches: 224, Mismatches: 54, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
60 3 0.01
61 51 0.23
62 114 0.51
63 54 0.24
64 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (62 bp):
GGAGATTATTTAAAGCATTTTTGATCAAAAATACCTTAAATAATCTCTAAATGTTTATAAAA
Found at i:6441504 original size:124 final size:123
Alignment explanation
Indices: 6441370--6441595 Score: 303
Period size: 124 Copynumber: 1.8 Consensus size: 123
6441360 TTAAAAGGAG
* * * *
6441370 ATTATTTAAAGCGTTTTTGATCAAAAACACCTTATATAATATCTAATATTTTTTAAAAAAAGATT
1 ATTATTTAAAGCGTTTATAATCAAAAACACCTTAAATAATATCTAACATTTTTT-AAAAAAGATT
**
6441435 ATTTAA-GACGTTTTTTG-TCAAAAACGTTTTAAATAATACCCTTCAATTTTTTGAAGGGT
65 ATTTAATG-CG-TTTTTGATCAAAAACGCCTTAAATAATACCCTTCAATTTTTTGAAGGGT
* * * * *
6441494 ATTATTTAAAGTGTTTATAATCAAAAACACCTTAAATAATTTTTAACATTTTTTAAAGAGGATTA
1 ATTATTTAAAGCGTTTATAATCAAAAACACCTTAAATAATATCTAACATTTTTTAAAAAAGATTA
*
6441559 TTTAATGCGTTTTTGATCAAAAATGCCTTAAATAATA
66 TTTAATGCGTTTTTGATCAAAAACGCCTTAAATAATA
6441596 TTTTTCATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
122 6 0.07
123 34 0.39
124 48 0.55
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (123 bp):
ATTATTTAAAGCGTTTATAATCAAAAACACCTTAAATAATATCTAACATTTTTTAAAAAAGATTA
TTTAATGCGTTTTTGATCAAAAACGCCTTAAATAATACCCTTCAATTTTTTGAAGGGT
Found at i:6441578 original size:61 final size:60
Alignment explanation
Indices: 6441301--6441594 Score: 229
Period size: 62 Copynumber: 4.8 Consensus size: 60
6441291 TATGTTTATA
* ** * * *
6441301 AAAGA-GATTATTTAAGGTATTTTTGGTCTAAAAATACCTTAAATAATCTCTAAATTTTTTT
1 AAAGAGGATTATTTAAAGCGTTTTTGATC-AAAAACACCTTAAATAATCTTTAAA-TTTTTT
* * *
6441362 AAA-AGGAGATTATTTAAAGCGTTTTTGATCAAAAACACCTTATATAATATCTAATATTTTTT
1 AAAGA-G-GATTATTTAAAGCGTTTTTGATCAAAAACACCTTAAATAATCTTTAA-ATTTTTT
* * *** * *
6441424 AAAAAAAGATTATTT-AAGACGTTTTTTG-TCAAAAACGTTTTAAATAATACCCTTCAATTTTTT
1 -AAAGAGGATTATTTAAAG-CG-TTTTTGATCAAAAACACCTTAAATAAT--CTTTAAATTTTTT
* * * * *
6441487 GAAG-GGTATTATTTAAAGTGTTTATAATCAAAAACACCTTAAATAATTTTTAACATTTTTT
1 AAAGAGG-ATTATTTAAAGCGTTTTTGATCAAAAACACCTTAAATAATCTTTAA-ATTTTTT
* **
6441548 AAAGAGGATTATTTAATGCGTTTTTGATCAAAAATGCCTTAAATAAT
1 AAAGAGGATTATTTAAAGCGTTTTTGATCAAAAACACCTTAAATAAT
6441595 ATTTTTCATT
Statistics
Matches: 183, Mismatches: 35, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
60 4 0.02
61 55 0.30
62 82 0.45
63 39 0.21
64 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (60 bp):
AAAGAGGATTATTTAAAGCGTTTTTGATCAAAAACACCTTAAATAATCTTTAAATTTTTT
Found at i:6441924 original size:61 final size:60
Alignment explanation
Indices: 6441801--6441927 Score: 166
Period size: 61 Copynumber: 2.1 Consensus size: 60
6441791 TTTATAAGAT
** * **
6441801 TTTTTTATAGATTATTTAAGGTGTTTTTGGCTATAAAATACCTTAAATAATGCTGATTAA
1 TTTTTTATAGATTATTTAAAATGTTTTTGGCTAGAAAATACCTTAAATAATGCCCATTAA
* *
6441861 TTTTTTATGGGATTATTTAAAATGTTTTTTGCTAGAAAATACCTTAAATAAT-CCCATTCAA
1 TTTTTTAT-AGATTATTTAAAATGTTTTTGGCTAGAAAATACCTTAAATAATGCCCATT-AA
6441922 TTTTTT
1 TTTTTT
6441928 GTAAAAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
60 12 0.21
61 46 0.79
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (60 bp):
TTTTTTATAGATTATTTAAAATGTTTTTGGCTAGAAAATACCTTAAATAATGCCCATTAA
Found at i:6445581 original size:2 final size:2
Alignment explanation
Indices: 6445574--6445606 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6445564 CCAGGCCCTG
*
6445574 AT AT AT AT AC AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6445607 TAATATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6453571 original size:16 final size:18
Alignment explanation
Indices: 6453550--6453590 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
6453540 AATAAAATTA
6453550 TTTAATTATTT-TC-TTT
1 TTTAATTATTTCTCATTT
*
6453566 TTTAATTCTTTCTCATTT
1 TTTAATTATTTCTCATTT
6453584 TTTAATT
1 TTTAATT
6453591 TTGAATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.45
17 2 0.09
18 10 0.45
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAATTATTTCTCATTT
Found at i:6459996 original size:15 final size:16
Alignment explanation
Indices: 6459976--6460013 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
6459966 TAAAATCACA
6459976 TTATTTA-ATATAATT
1 TTATTTAGATATAATT
*
6459991 TTATTTATGATATTATT
1 TTATTTA-GATATAATT
6460008 TTATTT
1 TTATTT
6460014 TATCTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
17 13 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTATTTAGATATAATT
Found at i:6464005 original size:26 final size:26
Alignment explanation
Indices: 6463969--6464020 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6463959 GGAGCCTTAG
6463969 CTGTTAGGTTTTTCCTTTTAATAATA
1 CTGTTAGGTTTTTCCTTTTAATAATA
6463995 CTGTTAGGTTTTTCCTTTTAATAATA
1 CTGTTAGGTTTTTCCTTTTAATAATA
6464021 GACATTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (26 bp):
CTGTTAGGTTTTTCCTTTTAATAATA
Found at i:6469012 original size:27 final size:28
Alignment explanation
Indices: 6468965--6469033 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
6468955 ATATAAATTT
* **
6468965 TATAATATTAAAAAATATTTTATAT-TTA
1 TATAATA-TAAATAATATTTTATATAAAA
6468993 TATTAATATAAATAAT-TTTTATATAAAA
1 TA-TAATATAAATAATATTTTATATAAAA
6469021 TATAATATAAATA
1 TATAATATAAATA
6469034 TATAAACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 19 0.53
28 12 0.33
29 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATATAAATAATATTTTATATAAAA
Found at i:6469015 original size:21 final size:23
Alignment explanation
Indices: 6468989--6469030 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
6468979 ATATTTTATA
*
6468989 TTTATAT-TAATATAA-ATAATT
1 TTTATATAAAATATAATATAATT
6469010 TTTATATAAAATATAATATAA
1 TTTATATAAAATATAATATAA
6469031 ATATATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTATATAAAATATAATATAATT
Found at i:6477953 original size:17 final size:19
Alignment explanation
Indices: 6477921--6477958 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
6477911 GTATGTTTAT
*
6477921 ATAATTATATATTTTATAA
1 ATAATTATATATTTTAAAA
6477940 ATAATTAT-TA-TTTAAAA
1 ATAATTATATATTTTAAAA
6477957 AT
1 AT
6477959 TTTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAATTATATATTTTAAAA
Found at i:6488480 original size:20 final size:20
Alignment explanation
Indices: 6488444--6488481 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6488434 ACATATTTTT
**
6488444 TTATTATTTTATTTATAAAA
1 TTATTATTTTACCTATAAAA
6488464 TTATTATTTTACCTATAA
1 TTATTATTTTACCTATAA
6488482 TCTAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTTTACCTATAAAA
Found at i:6490835 original size:16 final size:16
Alignment explanation
Indices: 6490811--6490844 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6490801 TTAGTTTCTG
*
6490811 GATATAAAAATGGAAA
1 GATAGAAAAATGGAAA
*
6490827 GATAGAAAATTGGAAA
1 GATAGAAAAATGGAAA
6490843 GA
1 GA
6490845 AATTGAAAAG
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:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (16 bp):
GATAGAAAAATGGAAA
Found at i:6490859 original size:12 final size:12
Alignment explanation
Indices: 6490830--6490875 Score: 62
Period size: 11 Copynumber: 4.1 Consensus size: 12
6490820 ATGGAAAGAT
*
6490830 AGAAAATTGGAA
1 AGAAAATTGAAA
6490842 AG-AAATTGAAA
1 AGAAAATTGAAA
6490853 AGAAAATTG-AA
1 AGAAAATTGAAA
6490864 A-AAAATTGAAA
1 AGAAAATTGAAA
6490875 A
1 A
6490876 AAATGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 7 0.23
11 16 0.52
12 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (12 bp):
AGAAAATTGAAA
Found at i:6490868 original size:10 final size:10
Alignment explanation
Indices: 6490832--6490885 Score: 65
Period size: 10 Copynumber: 5.2 Consensus size: 10
6490822 GGAAAGATAG
6490832 AAAATTGGAAA
1 AAAATT-GAAA
*
6490843 GAAATTGAAAA
1 AAAATTG-AAA
6490854 GAAAATTGAAA
1 -AAAATTGAAA
6490865 AAAATTGAAA
1 AAAATTGAAA
6490875 AAAA-TGAAA
1 AAAATTGAAA
6490884 AA
1 AA
6490886 CATGTGTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 7 0.18
10 15 0.38
11 11 0.28
12 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.17
Consensus pattern (10 bp):
AAAATTGAAA
Found at i:6490869 original size:22 final size:23
Alignment explanation
Indices: 6490830--6490875 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
6490820 ATGGAAAGAT
*
6490830 AGAAAATTGGAAAGAAATTGAAA
1 AGAAAATTGGAAAAAAATTGAAA
6490853 AGAAAATT-GAAAAAAATTGAAA
1 AGAAAATTGGAAAAAAATTGAAA
6490875 A
1 A
6490876 AAATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (23 bp):
AGAAAATTGGAAAAAAATTGAAA
Found at i:6490876 original size:23 final size:24
Alignment explanation
Indices: 6490816--6490876 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
6490806 TTCTGGATAT
*
6490816 AAAAATGGAAAGATAGAAAATTGGAA
1 AAAAATTGAAA-A-AGAAAATTGGAA
*
6490842 AGAAATTG-AAAAGAAAATT-GAA
1 AAAAATTGAAAAAGAAAATTGGAA
6490864 AAAAATTGAAAAA
1 AAAAATTGAAAAA
6490877 AATGAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 10 0.32
23 12 0.39
24 1 0.03
25 2 0.06
26 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (24 bp):
AAAAATTGAAAAAGAAAATTGGAA
Found at i:6492143 original size:14 final size:14
Alignment explanation
Indices: 6492124--6492151 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6492114 ATATTATATA
6492124 CATTACATATATTT
1 CATTACATATATTT
6492138 CATTACATATATTT
1 CATTACATATATTT
6492152 AATTGATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
CATTACATATATTT
Found at i:6500619 original size:6 final size:6
Alignment explanation
Indices: 6500610--6500641 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6500600 CCGCGGTGCT
*
6500610 GGTGGA GGTGGA GGTGGA GGTGGA GGAGGA GG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GG
6500642 GGCAACTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.69, T:0.12
Consensus pattern (6 bp):
GGTGGA
Found at i:6501260 original size:46 final size:46
Alignment explanation
Indices: 6501193--6501284 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
6501183 CTAAACTTAT
*
6501193 AAATTTGTAATGATATAGATGGTAGAAGTAGTTAATTGTTAGACAC
1 AAATTTGTAATGATATAGATGGTAGAAGTAGTTAATTGTCAGACAC
* *
6501239 AAATTTGTAATGATATAGATGGTTGAGGTAGTTAATTGTCAGACAC
1 AAATTTGTAATGATATAGATGGTAGAAGTAGTTAATTGTCAGACAC
6501285 GCAGCTTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (46 bp):
AAATTTGTAATGATATAGATGGTAGAAGTAGTTAATTGTCAGACAC
Found at i:6511511 original size:2 final size:2
Alignment explanation
Indices: 6511462--6511500 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
6511452 TATTGAAAGA
*
6511462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
6511501 TGCAGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6517069 original size:23 final size:23
Alignment explanation
Indices: 6517042--6517090 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6517032 AAATAATAAT
*
6517042 AAAATTATTGTAATTAAAATTAA
1 AAAATTATTATAATTAAAATTAA
**
6517065 AAAATTATTATAATTATGATTAA
1 AAAATTATTATAATTAAAATTAA
6517088 AAA
1 AAA
6517091 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
AAAATTATTATAATTAAAATTAA
Found at i:6517164 original size:21 final size:22
Alignment explanation
Indices: 6517139--6517186 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
6517129 AATAAATATT
6517139 TAAATTTAATTA-ATGATATAA
1 TAAATTTAATTATATGATATAA
*
6517160 TAAATTTAATTATATTATATAA
1 TAAATTTAATTATATGATATAA
*
6517182 AAAAT
1 TAAAT
6517187 ACGATTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAATTTAATTATATGATATAA
Found at i:6524167 original size:21 final size:21
Alignment explanation
Indices: 6524126--6524168 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6524116 TTCAAATTTT
* *
6524126 ATTTTAAAATTATTTTTATAA
1 ATTTTAAAATTATATTAATAA
6524147 ATTTTAAATATTA-ATTAATAA
1 ATTTTAAA-ATTATATTAATAA
6524168 A
1 A
6524169 AAAATAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAAAATTATATTAATAA
Done.