Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 184 of 190
Found at i:31417140 original size:10 final size:10
Alignment explanation
Indices: 31417099--31417158 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
31417089 TTAAAATTTA
* *
31417099 ATTTGAATAA
1 ATTTTAATAT
31417109 ATTTTAA-A-
1 ATTTTAATAT
*
31417117 ATTTTTATATT
1 ATTTTAATA-T
31417128 ATTTTAATAT
1 ATTTTAATAT
* *
31417138 ATTTAAATAA
1 ATTTTAATAT
31417148 ATTTTAATAT
1 ATTTTAATAT
31417158 A
1 A
31417159 AAATTATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
8 6 0.15
9 2 0.05
10 24 0.60
11 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:31417153 original size:20 final size:20
Alignment explanation
Indices: 31417099--31417158 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
31417089 TTAAAATTTA
* *
31417099 ATTTGAATAAATTTTAAAAT
1 ATTTAAATAAATTTTAATAT
* * *
31417119 TTTTATAT-TATTTTAATAT
1 ATTTAAATAAATTTTAATAT
31417138 ATTTAAATAAATTTTAATAT
1 ATTTAAATAAATTTTAATAT
31417158 A
1 A
31417159 AAATTATTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTAAATAAATTTTAATAT
Found at i:31417216 original size:20 final size:19
Alignment explanation
Indices: 31417180--31417215 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31417170 TTTATTTTAT
31417180 AAAAATTTAAAATATATAC
1 AAAAATTTAAAATATATAC
31417199 AAAAATTTAAAA-ATATA
1 AAAAATTTAAAATATATA
31417216 TTTTTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTTAAAATATATAC
Found at i:31423083 original size:29 final size:29
Alignment explanation
Indices: 31423016--31423107 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
31423006 TAATTTATTT
* * *
31423016 AAATATGATACGAATAACATAAATATACAT
1 AAAT-TGATACGACTAATATAAATATACAA
** *
31423046 GCATAGATACGACTAATATAAATATACAA
1 AAATTGATACGACTAATATAAATATACAA
31423075 AAATTGATACGACT-ATCATCAAAATATACAA
1 AAATTGATACGACTAAT-AT--AAATATACAA
31423106 AA
1 AA
31423108 TGATTAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.04
29 34 0.68
30 2 0.04
31 12 0.24
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.25
Consensus pattern (29 bp):
AAATTGATACGACTAATATAAATATACAA
Found at i:31424983 original size:11 final size:12
Alignment explanation
Indices: 31424956--31424989 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
31424946 ATATGAAGAT
31424956 ATAATATAAATAA
1 ATAATAT-AATAA
31424969 ATAATATAA-AA
1 ATAATATAATAA
31424980 ATAATATAAT
1 ATAATATAAT
31424990 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 2 0.10
13 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATATAATAA
Found at i:31425002 original size:18 final size:18
Alignment explanation
Indices: 31424981--31425015 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31424971 AATATAAAAA
* *
31424981 TAATATAATTTAAAATTT
1 TAATAAAATTAAAAATTT
31424999 TAATAAAATTAAAAATT
1 TAATAAAATTAAAAATT
31425016 GTATTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAAATTAAAAATTT
Found at i:31425058 original size:31 final size:29
Alignment explanation
Indices: 31425022--31425093 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
31425012 AATTGTATTT
* *
31425022 TAATTTTTATAT-TAATATAAATTTTAATATA
1 TAATTTTTATATAAAATAT-AA-TATAA-ATA
*
31425053 TAATTTTAATATAAAATATAATATAAATA
1 TAATTTTTATATAAAATATAATATAAATA
31425082 TAATATTTTATA
1 TAAT-TTTTATA
31425094 GGATGTAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 7 0.20
30 10 0.29
31 13 0.37
32 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAATTTTTATATAAAATATAATATAAATA
Found at i:31425059 original size:13 final size:12
Alignment explanation
Indices: 31425033--31425080 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
31425023 AATTTTTATA
31425033 TTAATATAAATT
1 TTAATATAAATT
31425045 TTAATATATAATT
1 TTAATATA-AATT
*
31425058 TTAATATAAAAT
1 TTAATATAAATT
*
31425070 ATAATATAAAT
1 TTAATATAAAT
31425081 ATAATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAATATAAATT
Found at i:31425073 original size:18 final size:18
Alignment explanation
Indices: 31425034--31425084 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
31425024 ATTTTTATAT
* *
31425034 TAATATAAATTTTAATATA
1 TAATATAAA-TATAAAATA
* *
31425053 TAATTTTAATATAAAATA
1 TAATATAAATATAAAATA
31425071 TAATATAAATATAA
1 TAATATAAATATAA
31425085 TATTTTATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAAATATAAAATA
Found at i:31425736 original size:64 final size:65
Alignment explanation
Indices: 31425606--31425747 Score: 148
Period size: 64 Copynumber: 2.2 Consensus size: 65
31425596 GTTCAGTTCG
* * * *
31425606 TTTTT-GTCAAAAAAATGCTTTTAATAATTCATATAAAAATTTTTTGAAATAATTATTAAAGGTA
1 TTTTTGGT-AAAAAAATACCTTCAATAATTCATATAAAAATTTTTTGAAATAATTATTAAAGATA
31425670 -
65 T
* * * *
31425670 TTTTTGGTAAAAAAATACCTTCAATAATTCATTTTAAAAA-TTTTTG-TATAGATTATTGAATAT
1 TTTTTGGTAAAAAAATACCTTCAATAATTCA-TATAAAAATTTTTTGAAATA-ATTATTAAAGAT
31425733 AT
64 AT
*
31425735 TTTTTGATAAAAA
1 TTTTTGGTAAAAA
31425748 TATATTTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
63 3 0.05
64 41 0.63
65 21 0.32
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (65 bp):
TTTTTGGTAAAAAAATACCTTCAATAATTCATATAAAAATTTTTTGAAATAATTATTAAAGATAT
Found at i:31425959 original size:63 final size:61
Alignment explanation
Indices: 31425770--31425996 Score: 165
Period size: 62 Copynumber: 3.7 Consensus size: 61
31425760 TCCTCTCAAC
* * * * * * *
31425770 AAAATTTTAAA-AGAA-TATAGAAGACATTTTTGTTCTAAATGCCTTCAATAATTCATACAA
1 AAAATTTTAAAGA-AATTATTGAAAATATTTTTATTCAAAAAGCCTTCAATAATTCATATAA
* ** * *** * * **
31425830 AAAATTTTAAAAGATATTATTGAAGGTATTTTTTATTAAAAAAATGTTCAATAATT-TTTTTC
1 AAAATTTT-AAAGAAATTATTGAAAATA-TTTTTATTCAAAAAGCCTTCAATAATTCATATAA
* *
31425892 AAAATTTTACGAAGAAATTATTGAAAATATTTTTATTCAAAACGCCTTTAATAATTCATATAA
1 AAAATTTTA--AAGAAATTATTGAAAATATTTTTATTCAAAAAGCCTTCAATAATTCATATAA
* *
31425955 AAAATTTTAATAGAGA-TATTTGAAAATATTTTTAATCAAAAA
1 AAAATTTTAA-AGAAATTA-TTGAAAATATTTTTATTCAAAAA
31425997 TATCTTCAAT
Statistics
Matches: 126, Mismatches: 32, Indels: 16
0.72 0.18 0.09
Matches are distributed among these distances:
60 8 0.06
61 8 0.06
62 64 0.51
63 46 0.37
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (61 bp):
AAAATTTTAAAGAAATTATTGAAAATATTTTTATTCAAAAAGCCTTCAATAATTCATATAA
Found at i:31426050 original size:17 final size:16
Alignment explanation
Indices: 31426026--31426058 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
31426016 TAAATTTTTT
31426026 TTAATATTATTATTAA
1 TTAATATTATTATTAA
31426042 TTAATTATTATTATTAA
1 TTAA-TATTATTATTAA
31426059 ATAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATATTATTATTAA
Found at i:31431958 original size:23 final size:23
Alignment explanation
Indices: 31431915--31431959 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
31431905 AAATCATGTT
*
31431915 TTATTTTTTTAATATTTAAAATTC
1 TTATTTTTTTAATA-TAAAAATTC
31431939 TTATTTTTTATAATA-AAAAAT
1 TTATTTTTT-TAATATAAAAAT
31431960 ATTTTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 9 0.47
25 5 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTTTTTAATATAAAAATTC
Found at i:31432487 original size:13 final size:13
Alignment explanation
Indices: 31432469--31432493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31432459 CTATATCTAT
31432469 AAATATTATTTAA
1 AAATATTATTTAA
31432482 AAATATTATTTA
1 AAATATTATTTA
31432494 TAATAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTATTTAA
Found at i:31433243 original size:31 final size:33
Alignment explanation
Indices: 31433206--31433272 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 33
31433196 TATTAATGAA
31433206 ATTAAAA-TTT-TACATTGATAATATATTAAAT
1 ATTAAAATTTTATACATTGATAATATATTAAAT
*
31433237 ATTAAAATTTTAAATACATTGATAATGTATTAAAT
1 ATTAAAATTTT--ATACATTGATAATATATTAAAT
31433272 A
1 A
31433273 AATTTAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
32 3 0.10
35 21 0.68
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (33 bp):
ATTAAAATTTTATACATTGATAATATATTAAAT
Found at i:31440572 original size:47 final size:45
Alignment explanation
Indices: 31440506--31440593 Score: 122
Period size: 47 Copynumber: 1.9 Consensus size: 45
31440496 TTCAATGAGA
* * * *
31440506 TTACCATTAGGTTAATCCTTTTGTTTTTATATGCTCCTATTCAAG
1 TTACCATTAGGGTAATCCTTTTGGTATCATATGCTCCTATTCAAG
31440551 TTACCATTCGAGGGTAATCCTTTTGGTATCATATGCTCCTATT
1 TTACCATT--AGGGTAATCCTTTTGGTATCATATGCTCCTATT
31440594 TAAGCTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 8 0.22
47 29 0.78
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (45 bp):
TTACCATTAGGGTAATCCTTTTGGTATCATATGCTCCTATTCAAG
Found at i:31452647 original size:2 final size:2
Alignment explanation
Indices: 31452640--31452687 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
31452630 CCCATAAGAT
31452640 TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31452679 T- TA TA TA TA
1 TA TA TA TA TA
31452688 ATAATAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:31452657 original size:12 final size:12
Alignment explanation
Indices: 31452640--31452687 Score: 68
Period size: 11 Copynumber: 4.3 Consensus size: 12
31452630 CCCATAAGAT
31452640 TATATATATATA
1 TATATATATATA
31452652 TATATATAT-TA
1 TATATATATATA
31452663 TATAT-TATATA
1 TATATATATATA
31452674 T-TATAT-TATA
1 TATATATATATA
31452684 TATA
1 TATA
31452688 ATAATAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
10 11 0.33
11 13 0.39
12 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATATATATA
Found at i:31452659 original size:14 final size:13
Alignment explanation
Indices: 31452638--31452687 Score: 75
Period size: 12 Copynumber: 3.8 Consensus size: 13
31452628 ATCCCATAAG
31452638 ATTATATATATAT
1 ATTATATATATAT
31452651 ATATATATATTATAT
1 AT-TATATA-TATAT
31452666 ATTATATAT-TAT
1 ATTATATATATAT
31452678 ATTATATATA
1 ATTATATATA
31452688 ATAATAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.35
13 3 0.09
14 12 0.35
15 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:31452686 original size:7 final size:7
Alignment explanation
Indices: 31452638--31452679 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
31452628 ATCCCATAAG
31452638 ATTATAT
1 ATTATAT
31452645 A-TATAT
1 ATTATAT
31452651 ATATATAT
1 AT-TATAT
31452659 ATTATAT
1 ATTATAT
31452666 ATTATAT
1 ATTATAT
31452673 ATTATAT
1 ATTATAT
31452680 TATATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.18
7 20 0.61
8 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTATAT
Found at i:31452697 original size:28 final size:28
Alignment explanation
Indices: 31452638--31452690 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
31452628 ATCCCATAAG
*
31452638 ATTATATATATATATATATATATTATAT
1 ATTATATATATATATATATATATAATAT
31452666 ATTATATAT-TATAT-TATATATAATA
1 ATTATATATATATATATATATATAATA
31452691 ATAATTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.42
27 5 0.21
28 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTATATATATATATATATATATAATAT
Found at i:31454014 original size:18 final size:18
Alignment explanation
Indices: 31453993--31454027 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31453983 CTGTTGCTAT
31453993 TGCTGTTGCTACTGCTGG
1 TGCTGTTGCTACTGCTGG
31454011 TGCTGTTGCTACTGCTG
1 TGCTGTTGCTACTGCTG
31454028 CTACCAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.23, G:0.31, T:0.40
Consensus pattern (18 bp):
TGCTGTTGCTACTGCTGG
Found at i:31456567 original size:2 final size:2
Alignment explanation
Indices: 31456562--31456597 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31456552 CACGAGCCTT
31456562 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31456598 ATGAAATTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31463589 original size:27 final size:26
Alignment explanation
Indices: 31463541--31463594 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
31463531 TCATATAATT
31463541 ATATATAATAACATGATTAATACTAAA
1 ATATATAATAACA-GATTAATACTAAA
*
31463568 ATATATAATTAACA-ATTCAATATTAAA
1 ATATATAA-TAACAGATT-AATACTAAA
31463595 TCAAAATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.12
27 16 0.67
28 5 0.21
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (26 bp):
ATATATAATAACAGATTAATACTAAA
Found at i:31464541 original size:20 final size:21
Alignment explanation
Indices: 31464486--31464541 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
31464476 ATAATTTTCT
*
31464486 TATTATT-TTATTTAATATAA
1 TATTATTATTATATAATATAA
* *
31464506 TATTACTATTACATAATA-AA
1 TATTATTATTATATAATATAA
*
31464526 TTTTATTATTATATAA
1 TATTATTATTATATAA
31464542 AAAACAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTATTATATAATATAA
Found at i:31464780 original size:27 final size:27
Alignment explanation
Indices: 31464728--31464780 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31464718 ATATATTTTT
**
31464728 ATAATTAATTTTAATTTTATTGTTATA
1 ATAATTAATTTTAATTTTATCATTATA
31464755 ATAATTAATTTT-ATCTTTATCATTAT
1 ATAATTAATTTTAAT-TTTATCATTAT
31464781 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
ATAATTAATTTTAATTTTATCATTATA
Found at i:31465547 original size:37 final size:36
Alignment explanation
Indices: 31465487--31465558 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
31465477 TTTTATAATT
*
31465487 TAAAACATAATATAATAAAAAATATATAAATTTTATG
1 TAAAAAATAATATAATAAAAAATATA-AAATTTTATG
* *
31465524 TAAAAAATAATATAA-ATATAAATATAATATTTTAT
1 TAAAAAATAATATAATA-AAAAATATAAAATTTTAT
31465559 ATGATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (36 bp):
TAAAAAATAATATAATAAAAAATATAAAATTTTATG
Found at i:31465565 original size:23 final size:22
Alignment explanation
Indices: 31465534--31465590 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
31465524 TAAAAAATAA
* *
31465534 TATAAATATAAATATAATATTT
1 TATATATATAAATATAAGATTT
*
31465556 TATATGATATAAATATACGATTT
1 TATAT-ATATAAATATAAGATTT
*
31465579 TTTATATATAAA
1 TATATATATAAA
31465591 ATTAATGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATATATAAATATAAGATTT
Found at i:31470869 original size:22 final size:22
Alignment explanation
Indices: 31470844--31470887 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31470834 ATTTTTTGTC
*
31470844 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
31470866 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
31470888 TAAATACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:31489943 original size:3 final size:3
Alignment explanation
Indices: 31489935--31489963 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31489925 CAAAAGAATG
31489935 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
31489964 CTGAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31490816 original size:16 final size:15
Alignment explanation
Indices: 31490797--31490830 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31490787 AATATATATG
31490797 AAAAATAAATAAATTC
1 AAAAATAAATAAA-TC
*
31490813 AAAAATCAATAAATC
1 AAAAATAAATAAATC
31490828 AAA
1 AAA
31490831 TTTAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAATAAATC
Found at i:31520833 original size:20 final size:19
Alignment explanation
Indices: 31520789--31520834 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
31520779 CATAAAATAT
31520789 AATTTTTTGATTTTATTAA
1 AATTTTTTGATTTTATTAA
31520808 ACATTTTTATGATTTT-TATAA
1 A-ATTTTT-TGATTTTAT-TAA
31520829 AATTTT
1 AATTTT
31520835 ATATCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (19 bp):
AATTTTTTGATTTTATTAA
Found at i:31524021 original size:2 final size:2
Alignment explanation
Indices: 31524014--31524053 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
31524004 GCGGGTTTAT
31524014 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31524054 GAGAGGGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31529336 original size:25 final size:27
Alignment explanation
Indices: 31529278--31529337 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 27
31529268 AATAATAATT
**
31529278 ATTATTATTATAATTATGATTGAAATAA
1 ATTA-TATTATAATTAAAATTGAAATAA
31529306 A-T-TATTATAATTAAAATT-AAA-AA
1 ATTATATTATAATTAAAATTGAAATAA
31529329 ATTATATTA
1 ATTATATTA
31529338 AATAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 3 0.11
24 4 0.14
25 19 0.68
27 1 0.04
28 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
ATTATATTATAATTAAAATTGAAATAA
Found at i:31529612 original size:12 final size:13
Alignment explanation
Indices: 31529597--31529635 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
31529587 ATTTTTAATA
31529597 TAAATATA-AAAT
1 TAAATATATAAAT
31529609 TAAATATATAAAT
1 TAAATATATAAAT
*
31529622 ATATATATATAAAT
1 -TAAATATATAAAT
31529636 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.33
13 4 0.17
14 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATATAAAT
Found at i:31530455 original size:37 final size:37
Alignment explanation
Indices: 31530404--31530487 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 37
31530394 TATATTAAAT
* * * *
31530404 TAAATAAATTTATTCATAAATAGTAAATGAA-TATATA
1 TAAATAAATATATTCATAAACAATAAATAAATTATA-A
31530441 TAAATAAATATATTCATAAACAATAAATAAATTATAA
1 TAAATAAATATATTCATAAACAATAAATAAATTATAA
31530478 TCAAATAAAT
1 T-AAATAAAT
31530488 TTAAATAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
37 29 0.71
38 12 0.29
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (37 bp):
TAAATAAATATATTCATAAACAATAAATAAATTATAA
Found at i:31530467 original size:19 final size:19
Alignment explanation
Indices: 31530442--31530487 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
31530432 GAATATATAT
*
31530442 AAATAAATATATTCATAAAC
1 AAATAAATAAATT-ATAAAC
*
31530462 -AATAAATAAATTATAATC
1 AAATAAATAAATTATAAAC
31530480 AAATAAAT
1 AAATAAAT
31530488 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAAATAAATTATAAAC
Found at i:31530513 original size:15 final size:14
Alignment explanation
Indices: 31530465--31530518 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
31530455 CATAAACAAT
31530465 AAATAAATTATAATC
1 AAATAAATT-TAATC
31530480 AAATAAATTTAAAT-
1 AAATAAATTT-AATC
31530494 AAATAAATCTTAATC
1 AAATAAAT-TTAATC
31530509 GAATATAAAT
1 -AA-ATAAAT
31530519 AAACTTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.35
15 14 0.41
16 2 0.06
17 6 0.18
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATAAATTTAATC
Found at i:31530521 original size:29 final size:28
Alignment explanation
Indices: 31530462--31530518 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 28
31530452 ATTCATAAAC
31530462 AATAAATAAATTATAATCAAATAAATTTA
1 AATAAATAAATTATAATCAAATAAA-TTA
31530491 AATAAATAAATCT-TAATCGAATATAAAT
1 AATAAATAAAT-TATAATC-AA-ATAAAT
31530519 AAACTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 16 0.64
30 4 0.16
31 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (28 bp):
AATAAATAAATTATAATCAAATAAATTA
Found at i:31533776 original size:19 final size:19
Alignment explanation
Indices: 31533752--31533790 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31533742 TGAAAATATA
31533752 ATTTTT-TTTAATAATTTTT
1 ATTTTTATTT-ATAATTTTT
*
31533771 ATTTTTATTTTTAATTTTT
1 ATTTTTATTTATAATTTTT
31533790 A
1 A
31533791 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTTATTTATAATTTTT
Found at i:31534811 original size:10 final size:11
Alignment explanation
Indices: 31534779--31534812 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
31534769 ACACCACTTG
31534779 ATGACATAAAA
1 ATGACATAAAA
31534790 ATGACATAAAA
1 ATGACATAAAA
*
31534801 ATGATATAAAA
1 ATGACATAAAA
31534812 A
1 A
31534813 AATATATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (11 bp):
ATGACATAAAA
Found at i:31540307 original size:24 final size:24
Alignment explanation
Indices: 31540274--31540321 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31540264 TCAGGTGAGG
*
31540274 CTTTATTTTCAATAACTCCATTGT
1 CTTTAGTTTCAATAACTCCATTGT
* *
31540298 CTTTAGTTTCAATAATTGCATTGT
1 CTTTAGTTTCAATAACTCCATTGT
31540322 TTTCATCAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (24 bp):
CTTTAGTTTCAATAACTCCATTGT
Found at i:31555597 original size:45 final size:45
Alignment explanation
Indices: 31555530--31555619 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
31555520 ATTTTTAAAG
31555530 GTGAAGATAAGTAAGAAATATGATTTTGCTTCTGGGAAGTGAAGA
1 GTGAAGATAAGTAAGAAATATGATTTTGCTTCTGGGAAGTGAAGA
31555575 GTGAAGATAAGT-AGAAACTATGATTTTGCTTCTGGGAAGTGAAGA
1 GTGAAGATAAGTAAGAAA-TATGATTTTGCTTCTGGGAAGTGAAGA
31555620 AATCTCTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 5 0.11
45 39 0.89
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (45 bp):
GTGAAGATAAGTAAGAAATATGATTTTGCTTCTGGGAAGTGAAGA
Found at i:31562071 original size:5 final size:5
Alignment explanation
Indices: 31562061--31562131 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
31562051 GTTTCCATTT
* * * *
31562061 TTTTA TTTTA TTTTA TTTTA TTTTA CTTTTG TTTTG TTTTG TTTT- TTTATC
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTT-TA
*
31562112 TTTCTG TTTTA TTTTA TTTT
1 TTT-TA TTTTA TTTTA TTTT
31562132 TATGCTTTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
4 3 0.05
5 45 0.76
6 11 0.19
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:31562095 original size:26 final size:26
Alignment explanation
Indices: 31562061--31562132 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
31562051 GTTTCCATTT
*
31562061 TTTTATTTTATTTTATTTTATTTTA-C
1 TTTTGTTTTATTTTATTTT-TTTTATC
* *
31562087 TTTTGTTTTGTTTT-GTTTTTTTATC
1 TTTTGTTTTATTTTATTTTTTTTATC
31562112 TTTCTGTTTTATTTTATTTTT
1 TTT-TGTTTTATTTTATTTTT
31562133 ATGCTTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
24 5 0.13
25 7 0.18
26 22 0.58
27 4 0.11
ACGTcount: A:0.11, C:0.04, G:0.06, T:0.79
Consensus pattern (26 bp):
TTTTGTTTTATTTTATTTTTTTTATC
Found at i:31562126 original size:18 final size:18
Alignment explanation
Indices: 31562105--31562144 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31562095 TGTTTTGTTT
* *
31562105 TTTTATCTTTCTGTTTTA
1 TTTTATCTTTATGCTTTA
*
31562123 TTTTATTTTTATGCTTTA
1 TTTTATCTTTATGCTTTA
31562141 TTTT
1 TTTT
31562145 GCTTGTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTATCTTTATGCTTTA
Found at i:31562342 original size:20 final size:20
Alignment explanation
Indices: 31562311--31562356 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 20
31562301 TGTTTAACTG
31562311 ATTGCATGAT-TATT-TA--
1 ATTGCATGATATATTATATT
31562327 ATTGCATGATATATTATATT
1 ATTGCATGATATATTATATT
31562347 ATTGCATGAT
1 ATTGCATGAT
31562357 GATTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.38
17 4 0.15
18 2 0.08
20 10 0.38
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (20 bp):
ATTGCATGATATATTATATT
Found at i:31566409 original size:18 final size:19
Alignment explanation
Indices: 31566381--31566419 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
31566371 AGAGTGCAAA
31566381 AAAAATGAAAAAATAAAAT
1 AAAAATGAAAAAATAAAAT
*
31566400 AAAAAT-AAAAAGTAAAAT
1 AAAAATGAAAAAATAAAAT
31566418 AA
1 AA
31566420 GAGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAATGAAAAAATAAAAT
Found at i:31567455 original size:46 final size:45
Alignment explanation
Indices: 31567388--31567528 Score: 142
Period size: 45 Copynumber: 3.1 Consensus size: 45
31567378 TAAATGAGCT
* * *
31567388 TTTTGAATGAGAATCCCAAAATTTTTCGAATGAGAATATTTAAAA
1 TTTTGAATGAGAATCCTAAAATTTTTCAAATGAGAATCTTTAAAA
* *
31567433 TTTTGAAT-AGGAATTCCTAAAATTTTTCTAAT-ATGAATCTTTGAAA
1 TTTTGAATGA-GAA-TCCTAAAATTTTTCAAATGA-GAATCTTTAAAA
* * * * * *
31567479 TTTTGGATGTGAAACTTGAAATCTTTCAAATGAGAATCTTTAAAA
1 TTTTGAATGAGAATCCTAAAATTTTTCAAATGAGAATCTTTAAAA
31567524 TTTTG
1 TTTTG
31567529 GTTGTGAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
44 1 0.01
45 41 0.52
46 37 0.47
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (45 bp):
TTTTGAATGAGAATCCTAAAATTTTTCAAATGAGAATCTTTAAAA
Found at i:31567689 original size:23 final size:23
Alignment explanation
Indices: 31567663--31567737 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
31567653 AAAGTGAATT
31567663 TTTAAATTTTTTGAATGAAAATC
1 TTTAAATTTTTTGAATGAAAATC
* ** *
31567686 TTT-AA-CTTTTGGGTGTAAAT-
1 TTTAAATTTTTTGAATGAAAATC
* *
31567706 TTTCAAAATTTTTGAATAAAAATC
1 TTT-AAATTTTTTGAATGAAAATC
*
31567730 TTTGAATT
1 TTTAAATT
31567738 CTTGAAGCAA
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
20 3 0.08
21 11 0.30
22 4 0.11
23 16 0.43
24 3 0.08
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (23 bp):
TTTAAATTTTTTGAATGAAAATC
Found at i:31567975 original size:17 final size:17
Alignment explanation
Indices: 31567898--31568028 Score: 75
Period size: 17 Copynumber: 7.7 Consensus size: 17
31567888 CCTACGAACC
* * *
31567898 TAAAATTTTTGCAAATC
1 TAAAATTCTTGCGAATA
* *
31567915 TAAAATTTTTGTGAATA
1 TAAAATTCTTGCGAATA
* *
31567932 TAAAATGCTTGCTAATA
1 TAAAATTCTTGCGAATA
* * **
31567949 TGAAACTCTTGCGAACC
1 TAAAATTCTTGCGAATA
*
31567966 TAAAATTCTTGCAAACT-
1 TAAAATTCTTGCGAA-TA
* * *
31567983 TGAAACTCTTGTGAATA
1 TAAAATTCTTGCGAATA
***
31568000 TAAAATTCTTATAAATA
1 TAAAATTCTTGCGAATA
*
31568017 TAAAGTTCTTGC
1 TAAAATTCTTGC
31568029 AAATTTGAAA
Statistics
Matches: 84, Mismatches: 28, Indels: 4
0.72 0.24 0.03
Matches are distributed among these distances:
16 1 0.01
17 83 0.99
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (17 bp):
TAAAATTCTTGCGAATA
Found at i:31568004 original size:34 final size:34
Alignment explanation
Indices: 31567898--31568009 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 34
31567888 CCTACGAACC
* * * * *
31567898 TAAAATTTTTGCAAATCTAAAATTTTTGTGAATA
1 TAAAATTCTTGCAAATATGAAACTCTTGTGAATA
* * * **
31567932 TAAAATGCTTGCTAATATGAAACTCTTGCGAACC
1 TAAAATTCTTGCAAATATGAAACTCTTGTGAATA
31567966 TAAAATTCTTGCAAACT-TGAAACTCTTGTGAATA
1 TAAAATTCTTGCAAA-TATGAAACTCTTGTGAATA
31568000 TAAAATTCTT
1 TAAAATTCTT
31568010 ATAAATATAA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
34 61 0.98
35 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (34 bp):
TAAAATTCTTGCAAATATGAAACTCTTGTGAATA
Found at i:31568028 original size:68 final size:68
Alignment explanation
Indices: 31567882--31568013 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 68
31567872 TTGCGAAACA
* * * * * *
31567882 GAAACTCCTACGAACCTAAAATTTTTGCAAATCTAAAATTTTTGTGAATATAAAATGCTTGCTAA
1 GAAACTCTTGCGAACCTAAAATTCTTGCAAATCTAAAACTCTTGTGAATATAAAATGCTTGATAA
31567947 TAT
66 TAT
* *
31567950 GAAACTCTTGCGAACCTAAAATTCTTGCAAA-CTTGAAACTCTTGTGAATATAAAATTCTT-ATA
1 GAAACTCTTGCGAACCTAAAATTCTTGCAAATC-TAAAACTCTTGTGAATATAAAATGCTTGATA
31568013 A
65 A
31568014 ATATAAAGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 4 0.07
68 51 0.93
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (68 bp):
GAAACTCTTGCGAACCTAAAATTCTTGCAAATCTAAAACTCTTGTGAATATAAAATGCTTGATAA
TAT
Found at i:31568396 original size:31 final size:31
Alignment explanation
Indices: 31568361--31568469 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 31
31568351 TGGACCTGCG
*
31568361 GTTCAATCCCGATTACTCATTTTCGATCTTA
1 GTTCAATCCAGATTACTCATTTTCGATCTTA
* * * * * *
31568392 GTTCAATCAAGATCATTTATTTTTTTGA-CTTGCG
1 GTTCAATCCAGATTACTCA--TTTTCGATCTT--A
* *
31568426 GTTCAATCCTGATTACTCATTTTCGATATTA
1 GTTCAATCCAGATTACTCATTTTCGATCTTA
31568457 GTTCAATCCAGAT
1 GTTCAATCCAGAT
31568470 CATTTATTTT
Statistics
Matches: 57, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
31 26 0.46
32 9 0.16
33 8 0.14
34 14 0.25
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (31 bp):
GTTCAATCCAGATTACTCATTTTCGATCTTA
Found at i:31568461 original size:65 final size:65
Alignment explanation
Indices: 31568348--31568689 Score: 307
Period size: 65 Copynumber: 5.2 Consensus size: 65
31568338 TTAATTTTAA
* * *
31568348 TTTTGGACCTGCGGTTCAATCCCGATTACTCATTTTCGATCTTAGTTCAATCAAGATCATTTATT
1 TTTTTGACCTACGGTTCAATCCAGATTACTCATTTTCGATCTTAGTTCAATCAAGATCATTTATT
* * * * *
31568413 TTTTTGACTTGCGGTTCAATCCTGATTACTCATTTTCGATATTAGTTCAATCCAGATCATTTATT
1 TTTTTGACCTACGGTTCAATCCAGATTACTCATTTTCGATCTTAGTTCAATCAAGATCATTTATT
* * * * * * * *
31568478 TTTTTGGCCTATGATTTAATTCCAG-TTACTCACTTTCGATATTGGTTCAATCCAGATCATTTAT
1 TTTTTGACCTACGGTTCAA-TCCAGATTACTCATTTTCGATCTTAGTTCAATCAAGATCATTTAT
31568542 T
65 T
* * ** *
31568543 CTTTTGGCCTGTGGTTCAATTCCAG-TTACTCATATTT-GATCTTAATTCAATCCAA-ATCATTT
1 TTTTTGACCTACGGTTCAA-TCCAGATTACTCAT-TTTCGATCTTAGTTCAAT-CAAGATCATTT
31568605 ATT
63 ATT
** * *** * * * *
31568608 TTCCTAACCTATAATTCAATCCATATCATTCATCTTCGATCTTAGTTCAATCCAAG-TCATTTAT
1 TTTTTGACCTACGGTTCAATCCAGATTACTCATTTTCGATCTTAGTTCAAT-CAAGATCATTTAT
31568672 T
65 T
*
31568673 TTTTTCGACTTACGGTT
1 TTTTT-GACCTACGGTT
31568690 TAGTCCCAGT
Statistics
Matches: 227, Mismatches: 43, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
64 6 0.03
65 206 0.91
66 15 0.07
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (65 bp):
TTTTTGACCTACGGTTCAATCCAGATTACTCATTTTCGATCTTAGTTCAATCAAGATCATTTATT
Found at i:31568917 original size:43 final size:42
Alignment explanation
Indices: 31568856--31569698 Score: 762
Period size: 43 Copynumber: 19.5 Consensus size: 42
31568846 ATCCCAGTCA
* *
31568856 CATATTTTAAAGTTGTTTAGCCTCTACATATAAGAGCCTATTT
1 CATATTTTAAAGTTGTTTAGCCTCTA-ATAGAAGAGCCCATTT
* *
31568899 CATATTTTAAAGTTGTTTAGCCTTTGAATAG-AGAAGCCAATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAG-AGCCCATTT
* *
31568942 CATATTTTAAAGTTGTTTAGCCTATGAATAG-AGAAGACCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAG-AGCCCATTT
* *
31568985 CATATTTTAAAGTCGTTCAGCCTCTGAATAGATA-AGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGA-AGAGCCCATTT
* *
31569028 CATATTTTAAAGTTGTTTAGCATCTGAATAGAGGAGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* * ** * **
31569071 CATATTTTAAAGTGGTTTAGTCTCTGTTTAGAAAAGCTTATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
*
31569114 CATATTTTAAAGTTGTTTAGCCTCTAAATA-AAGGGCACCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAG--CCCATTT
* * * * *
31569158 CATATTTTAAAATCGTTCAACCTTTGAATAGAAGAAGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAG-AGCCCATTT
* * *
31569202 CATATTTTAAAATTATTTAGCCTCTGAATAGAAGAGCCTATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* * * *
31569245 CATATTTTAAAGTTGATTAGTCTCTATGTAGAAGAGCTCATTT
1 CATATTTTAAAGTTGTTTAGCCTCTA-ATAGAAGAGCCCATTT
* * * ** *
31569288 CATATTTTAAAATTGATTAGCTTCTGTTTAGAGGAGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* *
31569331 CATATTTTAAAATTGTTTAGCCTTTAAATA-AAGGAGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAA-GAGCCCATTT
* ** * *
31569374 TATATTTTAAAGTTGACTAGCCTTTGAATAGAAAAGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* * * * *
31569417 CATATTTTAAAGTTGATTAGCTTCTGAATAGAGGGGTCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* *
31569460 CATATTTTAAAGTTGTTTAACCTCTAAATAAAAGAGCCCATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* * * * *
31569503 TATTTTTTTAAAGTTGTTTAACCTCTAAATAGATGAGCCTATTT
1 CA-TATTTTAAAGTTGTTTAGCCTCT-AATAGAAGAGCCCATTT
* * *
31569547 CATTTTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTCATTT
1 CATATTTTAAAGTTGTTTAGCCTCTA-ATAGAAGAGCCCATTT
** ** * * *
31569590 GTTATTTTAAAGTCATTTAGCCTTTGAATA-AATAAGCCTATTT
1 CATATTTTAAAGTTGTTTAGCCTCT-AATAGAA-GAGCCCATTT
* * *
31569633 CATATTTTAAAATTATTTAGCCTCTATATAGAAGAGCTCATTT
1 CATATTTTAAAGTTGTTTAGCCTCTA-ATAGAAGAGCCCATTT
* *
31569676 CTTATTCTAAAGTTGTTTAGCCT
1 CATATTTTAAAGTTGTTTAGCCT
31569699 TTGTACAAAT
Statistics
Matches: 661, Mismatches: 120, Indels: 38
0.81 0.15 0.05
Matches are distributed among these distances:
42 10 0.02
43 537 0.81
44 109 0.16
45 4 0.01
46 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (42 bp):
CATATTTTAAAGTTGTTTAGCCTCTAATAGAAGAGCCCATTT
Found at i:31569993 original size:3 final size:3
Alignment explanation
Indices: 31569985--31570039 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
31569975 TGGCCTAACA
31569985 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
31570033 TA- TAT TA
1 TAT TAT TA
31570040 AAACAAATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:31571086 original size:5 final size:5
Alignment explanation
Indices: 31571085--31571148 Score: 58
Period size: 5 Copynumber: 11.8 Consensus size: 5
31571075 TCTTTTTATT
*
31571085 TTTTA TTGTTTA TTTTA TTTTA TTTTGC TTTT- TTTTA TCTTTCTA TTTTA
1 TTTTA TT-T-TA TTTTA TTTTA TTTT-A TTTTA TTTTA --TTT-TA TTTTA
31571135 TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT
31571149 TTGCTTTATT
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
4 4 0.08
5 29 0.57
6 9 0.18
7 7 0.14
8 2 0.04
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:31571150 original size:17 final size:17
Alignment explanation
Indices: 31571085--31571160 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
31571075 TCTTTTTATT
*
31571085 TTTTATTGTTTATTTTA
1 TTTTATTTTTTATTTTA
*
31571102 TTTTATTTTGCTTTTTTTTA
1 TTTTA-TTT--TTTATTTTA
* *
31571122 TCTTTCTATTTTATTTTA
1 T-TTTATTTTTTATTTTA
**
31571140 TTTTATTTTTTGCTTTA
1 TTTTATTTTTTATTTTA
31571157 TTTT
1 TTTT
31571161 TGCTTATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
17 21 0.46
18 11 0.24
20 11 0.24
21 3 0.07
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTTATTTTA
Found at i:31571150 original size:33 final size:32
Alignment explanation
Indices: 31571083--31571150 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
31571073 TTTCTTTTTA
*
31571083 TTTTTTATTGTTTATTTTATTTTATTTTGCTT
1 TTTTTTATTGTTTATTTTATTTTATTTTACTT
31571115 TTTTTTATCT-TTCTATTTTATTTTATTTTA-TT
1 TTTTTTAT-TGTT-TATTTTATTTTATTTTACTT
31571147 TTTT
1 TTTT
31571151 GCTTTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.13, C:0.04, G:0.03, T:0.79
Consensus pattern (32 bp):
TTTTTTATTGTTTATTTTATTTTATTTTACTT
Found at i:31572416 original size:24 final size:24
Alignment explanation
Indices: 31572382--31572432 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
31572372 CGTCAACTTG
31572382 TATTGGATATATAGCTTTCATTAA
1 TATTGGATATATAGCTTTCATTAA
*
31572406 TATTGGCTATATAGCTTTCATTAA
1 TATTGGATATATAGCTTTCATTAA
31572430 TAT
1 TAT
31572433 GAAGTTTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (24 bp):
TATTGGATATATAGCTTTCATTAA
Found at i:31572709 original size:3 final size:3
Alignment explanation
Indices: 31572701--31572736 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
31572691 TATAATTAAT
31572701 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31572737 AGTTTCCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31574357 original size:16 final size:15
Alignment explanation
Indices: 31574333--31574394 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
31574323 TATCATTAAA
31574333 ATTTTATATCATATT
1 ATTTTATATCATATT
31574348 ATTTTCATATCATA-T
1 ATTTT-ATATCATATT
*
31574363 -TTTTATAT--TA-C
1 ATTTTATATCATATT
*
31574374 A-TTTATATTATATT
1 ATTTTATATCATATT
31574388 ATTTTAT
1 ATTTTAT
31574395 CGTATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
11 9 0.23
13 6 0.15
14 5 0.13
15 11 0.28
16 8 0.21
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTATATCATATT
Found at i:31574419 original size:40 final size:40
Alignment explanation
Indices: 31574331--31574428 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 40
31574321 ATTATCATTA
*
31574331 AAATTTTATATCATATTATTTTCATATCATATTTTTATATT
1 AAATTTTATATCATATTATTTT-ATATCATATTTTAATATT
* * *
31574372 ACA-TTTATATTATATTA-TTT-TATCGTATTTTAAATTATT
1 AAATTTTATATCATATTATTTTATATCATATTTT-AA-TATT
31574411 AAATTTTATATCAATATT
1 AAATTTTATATC-ATATT
31574429 TAAATTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
37 10 0.21
38 1 0.02
39 9 0.19
40 20 0.43
41 7 0.15
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (40 bp):
AAATTTTATATCATATTATTTTATATCATATTTTAATATT
Found at i:31575252 original size:25 final size:25
Alignment explanation
Indices: 31575199--31575252 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
31575189 CCATTATTCA
* *
31575199 TTTATATATGTAAAATATATAAAAT
1 TTTATATATGTAAAAAATATAAAAC
* * *
31575224 TTTATATTTGTAAAAAATTTAAGAC
1 TTTATATATGTAAAAAATATAAAAC
31575249 TTTA
1 TTTA
31575253 AAAAATAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (25 bp):
TTTATATATGTAAAAAATATAAAAC
Found at i:31577999 original size:27 final size:25
Alignment explanation
Indices: 31577945--31578023 Score: 65
Period size: 27 Copynumber: 3.1 Consensus size: 25
31577935 ATGTTACGAA
31577945 ATAAAA-TAT-AAA-AATAATATAAT
1 ATAAAATTATAAAATAATAATAT-AT
*
31577968 TTAAAATTATAATAATAATAATTATAT
1 ATAAAATTATAA-AATAATAA-TATAT
* *
31577995 ATAAATTTAATAAAATAAAAAATATAT
1 ATAAAATT-ATAAAAT-AATAATATAT
31578022 AT
1 AT
31578024 TCTTATATCT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 5 0.11
24 3 0.07
25 1 0.02
26 2 0.04
27 23 0.51
28 11 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAAAATTATAAAATAATAATATAT
Found at i:31578005 original size:19 final size:18
Alignment explanation
Indices: 31577961--31578007 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 18
31577951 TATAAAAATA
31577961 ATATAATTTAA-AATTAT
1 ATATAATTTAATAATTAT
31577978 A-ATAA--TAATAATTAT
1 ATATAATTTAATAATTAT
31577993 ATATAAATTTAATAA
1 ATAT-AATTTAATAA
31578008 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 7 0.28
16 6 0.24
17 3 0.12
19 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAATTAT
Found at i:31578040 original size:32 final size:31
Alignment explanation
Indices: 31578003--31578062 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
31577993 ATATAAATTT
31578003 AATAAAATAAAAAATATATATTCTTATATCTA
1 AATAAAATAAAAAATATA-ATTCTTATATCTA
* * * *
31578035 AATAAATTATAATATATAATTTTTATAT
1 AATAAAATAAAAAATATAATTCTTATAT
31578063 AAAGTATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (31 bp):
AATAAAATAAAAAATATAATTCTTATATCTA
Found at i:31582220 original size:2 final size:2
Alignment explanation
Indices: 31582215--31582253 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31582205 CACACAACAA
31582215 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31582254 AGTTTAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31584679 original size:26 final size:28
Alignment explanation
Indices: 31584641--31584694 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
31584631 TTGAATCGAG
*
31584641 TTAAATTCAAATTT-TATGAATAAAAAA
1 TTAAATTCAAATTTAGATGAATAAAAAA
31584668 TTAAA-TCAAATTTAAGATGAATAAAAA
1 TTAAATTCAAATTT-AGATGAATAAAAA
31584695 TTCGATCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 5 0.21
28 11 0.46
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (28 bp):
TTAAATTCAAATTTAGATGAATAAAAAA
Found at i:31587705 original size:24 final size:24
Alignment explanation
Indices: 31587653--31587707 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
31587643 GAGTGGTGAG
*
31587653 GGAAGAGGAAGGGATACCAGAGCTA
1 GGAAGAGGAAGAGATACCAGAGC-A
31587678 -GAAGAGGAAGTAGATACCAGAG-A
1 GGAAGAGGAAG-AGATACCAGAGCA
31587701 GGAAGAG
1 GGAAGAG
31587708 AAAAAAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.59
25 10 0.37
ACGTcount: A:0.44, C:0.09, G:0.40, T:0.07
Consensus pattern (24 bp):
GGAAGAGGAAGAGATACCAGAGCA
Found at i:31600965 original size:12 final size:13
Alignment explanation
Indices: 31600933--31600975 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
31600923 AATTTTTTTA
*
31600933 ATAAAATACATAT
1 ATAAAATAAATAT
31600946 ATATAAATAAATAT
1 ATA-AAATAAATAT
31600960 -TAAAATAAATAAT
1 ATAAAATAAAT-AT
31600973 ATA
1 ATA
31600976 TATATCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 8 0.31
13 7 0.27
14 11 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAAATAAATAT
Found at i:31601168 original size:2 final size:2
Alignment explanation
Indices: 31601161--31601197 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31601151 TTAACCTAAC
31601161 AT AT AT AT AT 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 AT AT AT AT AT A
31601198 ACATGTACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31602042 original size:22 final size:23
Alignment explanation
Indices: 31602012--31602059 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
31602002 GCCAAATACA
* * *
31602012 AAATATTATTTTTTATTTTTATT
1 AAATATTATATATGATTTTTATT
31602035 AAAT-TTATATATGATTTTTATT
1 AAATATTATATATGATTTTTATT
31602057 AAA
1 AAA
31602060 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATTATATATGATTTTTATT
Found at i:31602101 original size:12 final size:11
Alignment explanation
Indices: 31602071--31602106 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
31602061 TTTTAAAATA
31602071 TATATTATTTT
1 TATATTATTTT
31602082 TATA-T-TTTT
1 TATATTATTTT
31602091 TATATTATTTT
1 TATATTATTTT
31602102 TATAT
1 TATAT
31602107 CAATCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.35
10 2 0.09
11 13 0.57
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTATTTT
Found at i:31602708 original size:33 final size:34
Alignment explanation
Indices: 31602671--31602746 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
31602661 TTGTACTGTA
* * *
31602671 TATATATATATTAAAT-TTGATAATTTATATGTT
1 TATATATATATAAAATATTAATAATTTATATATT
*
31602704 TATAT-TATATAAAATATTAATATTTTATATATT
1 TATATATATATAAAATATTAATAATTTATATATT
31602737 TATATCATAT
1 TATAT-ATAT
31602747 TTTATATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 9 0.25
33 24 0.67
35 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (34 bp):
TATATATATATAAAATATTAATAATTTATATATT
Found at i:31602810 original size:36 final size:36
Alignment explanation
Indices: 31602767--31602835 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
31602757 AATTATGTCA
31602767 TAAAATTTATATAA-AATATATTTTT-TAATTTTTTAT
1 TAAAATTT-TA-AATAATATATTTTTATAATTTTTTAT
* *
31602803 TAAAATTTTAAATTATATTTTTTTATAATTTTT
1 TAAAATTTTAAATAATATATTTTTATAATTTTT
31602836 ATTCGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.07
35 11 0.38
36 16 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (36 bp):
TAAAATTTTAAATAATATATTTTTATAATTTTTTAT
Found at i:31603239 original size:13 final size:14
Alignment explanation
Indices: 31603186--31603240 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
31603176 ATAAGATTTG
31603186 AATATTTTATTAAT
1 AATATTTTATTAAT
*
31603200 AAAATTTTAATT--T
1 AATATTTT-ATTAAT
*
31603213 TA-ATTTTATTAAT
1 AATATTTTATTAAT
31603226 AATATTTT-TTAAT
1 AATATTTTATTAAT
31603239 AA
1 AA
31603241 ATTATTTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
11 3 0.09
12 5 0.15
13 11 0.32
14 12 0.35
15 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTTTATTAAT
Found at i:31604244 original size:23 final size:23
Alignment explanation
Indices: 31604200--31604244 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31604190 TTTTATACAT
* ** *
31604200 TATTAATTTTTTTCATTGAATTA
1 TATTAATTTATTAAATTAAATTA
31604223 TATTAATTTATTAAATTAAATT
1 TATTAATTTATTAAATTAAATT
31604245 TTATAAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTAATTTATTAAATTAAATTA
Found at i:31605884 original size:148 final size:150
Alignment explanation
Indices: 31605614--31605885 Score: 392
Period size: 148 Copynumber: 1.8 Consensus size: 150
31605604 AAGGGGACTC
* *
31605614 AGGTGGACTGCCTCAGCTGCAGTATACCAGCTGCCTGACTGGCCACAGGGGTCTAGCAGCGTGCC
1 AGGTGGACTGCCTCAGCTGCAGCACACCAGC-GCCTGACTGGCCACAGGGGTCTAGCAGCGTGCC
** *
31605679 TGCCTGCTAGCCCGCGCATCCTCTCAGCTCGATGGCATCCCTCCTACATGAATACCATCGCGTGG
65 TGCCTGCTAGCCCGCGCATCCTCTCAGCTCGATGGCATCCCTCCTACACAAACACCATCGCGTGG
31605744 TCCAGTCCCACAAGGGTCCTT
130 TCCAGTCCCACAAGGGTCCTT
31605765 AGGTGGACTGCC-CTAGCTGCAGCACACCAGC-CC-GACTGGCCACAGGGGTCTAGCAGCGTGCC
1 AGGTGGACTGCCTC-AGCTGCAGCACACCAGCGCCTGACTGGCCACAGGGGTCTAGCAGCGTGCC
* * * *
31605827 TG-CTGGCTAGCCCGTGCATCC-CATTAGCTCGATGGTATCCCTCCTACGCAAACACCATC
65 TGCCT-GCTAGCCCGCGCATCCTC-TCAGCTCGATGGCATCCCTCCTACACAAACACCATC
31605886 ATATGATCCT
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
147 3 0.03
148 76 0.70
149 2 0.02
150 1 0.01
151 27 0.25
ACGTcount: A:0.19, C:0.36, G:0.26, T:0.20
Consensus pattern (150 bp):
AGGTGGACTGCCTCAGCTGCAGCACACCAGCGCCTGACTGGCCACAGGGGTCTAGCAGCGTGCCT
GCCTGCTAGCCCGCGCATCCTCTCAGCTCGATGGCATCCCTCCTACACAAACACCATCGCGTGGT
CCAGTCCCACAAGGGTCCTT
Found at i:31607298 original size:13 final size:13
Alignment explanation
Indices: 31607280--31607304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31607270 AACATATTAT
31607280 AAAAATCTTCTTC
1 AAAAATCTTCTTC
31607293 AAAAATCTTCTT
1 AAAAATCTTCTT
31607305 TTATATATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATCTTCTTC
Found at i:31608450 original size:12 final size:13
Alignment explanation
Indices: 31608433--31608482 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
31608423 GATATAAAAT
31608433 TTTAATTAAT-TA
1 TTTAATTAATATA
*
31608445 TTTAATT-TTATA
1 TTTAATTAATATA
*
31608457 TTTATTTATATATA
1 TTTAATTA-ATATA
31608471 TTTAATTAATAT
1 TTTAATTAATAT
31608483 TTATATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 1 0.03
12 15 0.48
13 4 0.13
14 11 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTAATATA
Found at i:31615042 original size:24 final size:24
Alignment explanation
Indices: 31614997--31615043 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
31614987 GACACAAAAA
* **
31614997 TATTAAATATATATTTTTTTATTT
1 TATTAAATATATATATAATTATTT
*
31615021 TATTAAATTTATATATAATTATT
1 TATTAAATATATATATAATTATT
31615044 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTAAATATATATATAATTATTT
Found at i:31615693 original size:14 final size:14
Alignment explanation
Indices: 31615667--31615708 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
31615657 ATACGATATA
*
31615667 AATATATTTAAAA-
1 AATAAATTTAAAAT
*
31615680 ATTAAATATTAAAAT
1 AATAAAT-TTAAAAT
31615695 AATAAATTTAAAAT
1 AATAAATTTAAAAT
31615709 TTTAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.21
14 13 0.54
15 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTTAAAAT
Found at i:31615703 original size:28 final size:29
Alignment explanation
Indices: 31615667--31615743 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
31615657 ATACGATATA
*
31615667 AATATATTTAAAAATTAAAT-ATTAAAAT
1 AATAAATTTAAAAATTAAATAATTAAAAT
* * **
31615695 AATAAATTTAAAATTTTAATAATTATTAT
1 AATAAATTTAAAAATTAAATAATTAAAAT
31615724 -ATAAATTTAATAAAATTAAA
1 AATAAATTT-A-AAAATTAAA
31615744 AAAATATATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 25 0.64
29 7 0.18
30 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAAATTTAAAAATTAAATAATTAAAAT
Found at i:31615762 original size:51 final size:49
Alignment explanation
Indices: 31615682--31615778 Score: 115
Period size: 51 Copynumber: 1.9 Consensus size: 49
31615672 ATTTAAAAAT
*
31615682 TAAATATTAAAATAATAAATTTAAAATTTTAATAATTATTATATAAATTTAA
1 TAAATATTAAAAAAATAAATTTAAAATTTTAAT-ATTA--ATATAAATTTAA
* * * *
31615734 TAAA-ATTAAAAAAATATATTTTATATTTTTATATTAATATAAATT
1 TAAATATTAAAAAAATAAATTTAAAATTTTAATATTAATATAAATT
31615779 ATGATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 9 0.22
50 4 0.10
51 23 0.57
52 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (49 bp):
TAAATATTAAAAAAATAAATTTAAAATTTTAATATTAATATAAATTTAA
Found at i:31619958 original size:105 final size:104
Alignment explanation
Indices: 31619754--31619959 Score: 283
Period size: 105 Copynumber: 2.0 Consensus size: 104
31619744 TTCAAAAAAA
* *
31619754 AGGTTAAGCTGATAGCATTTTGGAAGCAAACAACAATTATTGCTAAAAACCAACTTAAGAAAAAC
1 AGGTTAAGCTCATAGCATTTTGGAACCAAACAACAATTATTGCTAAAAACCAACTTAAGAAAAAC
* *
31619819 CAAGACAAATTGAAACAACCCTACAGACTGTTTTATGAT
66 CAAGACAAATTGAAACAACCCGACAGACTATTTTATGAT
*
31619858 AGGTTAAGCTCATTAGTATTTTGGAACCAAACAACAATTATTGCTAAAAAACCAACTT-AGAGAA
1 AGGTTAAGCTCA-TAGCATTTTGGAACCAAACAACAATTATTGCT-AAAAACCAACTTAAGA-AA
* **
31619922 AATCATTACAAATTGAAACAA-CCGAC-GAACTATTTTAT
63 AACCAAGACAAATTGAAACAACCCGACAG-ACTATTTTAT
31619960 CATATTAATT
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
104 12 0.13
105 46 0.51
106 32 0.36
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (104 bp):
AGGTTAAGCTCATAGCATTTTGGAACCAAACAACAATTATTGCTAAAAACCAACTTAAGAAAAAC
CAAGACAAATTGAAACAACCCGACAGACTATTTTATGAT
Found at i:31626837 original size:3 final size:3
Alignment explanation
Indices: 31626823--31626954 Score: 61
Period size: 3 Copynumber: 44.0 Consensus size: 3
31626813 ATTGTCACCG
* ** * * * *
31626823 TCA TCG TCA TCA TCA TCA TCA TTG TAA TCG TTA TCA TCA TCAA T-G
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC-A TCA
* * ** * *
31626868 TCA TCA TAA ACA TCA TTG TAA TCA TCA TCA GT-G TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA -TCA TCA TCA TCA TCA
** * * * *
31626913 TTG TCG TCC TCC TCA TCG TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
31626955 GCAGCAGCAA
Statistics
Matches: 94, Mismatches: 31, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
2 2 0.02
3 89 0.95
4 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:31626873 original size:15 final size:15
Alignment explanation
Indices: 31626855--31626954 Score: 73
Period size: 15 Copynumber: 6.7 Consensus size: 15
31626845 TGTAATCGTT
31626855 ATCATCATCAATGTC
1 ATCATCATCAATGTC
* *
31626870 ATCATAAACATCATTGTA
1 ATCAT---CATCAATGTC
*
31626888 ATCATCATCAGTGTC
1 ATCATCATCAATGTC
*
31626903 ATCATCATCATTGTC
1 ATCATCATCAATGTC
* * *
31626918 GTCCTCCTC-ATCGTC
1 ATCATCATCAAT-GTC
31626933 ATCATCATC-A--TC
1 ATCATCATCAATGTC
31626945 ATCATCATCA
1 ATCATCATCA
31626955 GCAGCAGCAA
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
12 11 0.16
14 1 0.01
15 43 0.63
18 13 0.19
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (15 bp):
ATCATCATCAATGTC
Found at i:31629437 original size:42 final size:42
Alignment explanation
Indices: 31629388--31629474 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
31629378 TTCTGTTTAA
31629388 GTACTTTGTAAACCAATGCAAGGGTTACCATAGTTTAGTTAT
1 GTACTTTGTAAACCAATGCAAGGGTTACCATAGTTTAGTTAT
31629430 GTACTTTGTAAACCAATGCAAGGGTTACCATAGTTTAGTTAT
1 GTACTTTGTAAACCAATGCAAGGGTTACCATAGTTTAGTTAT
31629472 GTA
1 GTA
31629475 AATAAATACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (42 bp):
GTACTTTGTAAACCAATGCAAGGGTTACCATAGTTTAGTTAT
Found at i:31634663 original size:22 final size:22
Alignment explanation
Indices: 31634637--31634680 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31634627 TGTATATTTA
*
31634637 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
31634659 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
31634681 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:31635220 original size:23 final size:23
Alignment explanation
Indices: 31635200--31635284 Score: 116
Period size: 23 Copynumber: 3.6 Consensus size: 23
31635190 AAAATTTTCA
*
31635200 GCCTTCATTGCTGACTTTTTTAG
1 GCCTTCATTGCCGACTTTTTTAG
31635223 GCCTTCATTGCCGACTTTTTTAG
1 GCCTTCATTGCCGACTTTTTTAG
* * *
31635246 GCCTTCATTGCCGAATCCTGTTTAA
1 GCCTTCATTGCCG-A-CTTTTTTAG
31635271 GCCTTCATTGCCGA
1 GCCTTCATTGCCGA
31635285 ACCCTTTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
23 35 0.62
24 2 0.04
25 19 0.34
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (23 bp):
GCCTTCATTGCCGACTTTTTTAG
Found at i:31638958 original size:22 final size:22
Alignment explanation
Indices: 31638932--31638975 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31638922 TGTATATTTA
* *
31638932 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
31638954 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
31638976 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:31657279 original size:5 final size:5
Alignment explanation
Indices: 31657271--31657295 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31657261 ATAAAAGCCA
31657271 AAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG
31657296 TGTGAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:31664240 original size:31 final size:31
Alignment explanation
Indices: 31664205--31664269 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
31664195 AATGGGAAAG
*
31664205 GTTACTTTTTTCATGTTCAACCCAAATTCTA
1 GTTACTTTTTTCATGATCAACCCAAATTCTA
31664236 GTTACTTTTTTCATGATCAACCCAAATTCTA
1 GTTACTTTTTTCATGATCAACCCAAATTCTA
31664267 GTT
1 GTT
31664270 GCAAACAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (31 bp):
GTTACTTTTTTCATGATCAACCCAAATTCTA
Found at i:31670410 original size:43 final size:43
Alignment explanation
Indices: 31670349--31670435 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
31670339 GAATTTTCAA
31670349 TTGGCTTGATGTTCAGTTCATTGTCATCAGTAACTCTTTCTGT
1 TTGGCTTGATGTTCAGTTCATTGTCATCAGTAACTCTTTCTGT
* * *
31670392 TTGGCTTGATGTTCAGTTCATTGTTATCATTATCTCTTTCTGT
1 TTGGCTTGATGTTCAGTTCATTGTCATCAGTAACTCTTTCTGT
31670435 T
1 T
31670436 GTCTCATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (43 bp):
TTGGCTTGATGTTCAGTTCATTGTCATCAGTAACTCTTTCTGT
Found at i:31671333 original size:22 final size:22
Alignment explanation
Indices: 31671308--31671350 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31671298 TGTGTATTTA
31671308 TATTTATATCTC-TAAAATTAAT
1 TATTTATATC-CATAAAATTAAT
31671330 TATTTATATCCATAAAATTAA
1 TATTTATATCCATAAAATTAA
31671351 AGATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTTATATCCATAAAATTAAT
Found at i:31671619 original size:26 final size:25
Alignment explanation
Indices: 31671590--31671668 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
31671580 ATTTTCAGCT
*
31671590 TTCATTGTTG-ACTTCTATTTTAGACC
1 TTCATTGTTGAAC-TCT-GTTTAGACC
**
31671616 TTCATTACTGAACTCTGTTTAGACC
1 TTCATTGTTGAACTCTGTTTAGACC
* * * *
31671641 TTCATTGTCGAACCCTGCTAAGACC
1 TTCATTGTTGAACTCTGTTTAGACC
31671666 TTC
1 TTC
31671669 GTAGCCACTC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
25 30 0.70
26 11 0.26
27 2 0.05
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.41
Consensus pattern (25 bp):
TTCATTGTTGAACTCTGTTTAGACC
Found at i:31672651 original size:21 final size:21
Alignment explanation
Indices: 31672610--31672651 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31672600 ATAATTCCTA
**
31672610 ATATTTCTAGTGCAAGTTGAT
1 ATATTTCTAGTGCAAAATGAT
31672631 ATATTTCT-GATGCAAAATGAT
1 ATATTTCTAG-TGCAAAATGAT
31672652 TTGTTTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATTTCTAGTGCAAAATGAT
Found at i:31675389 original size:22 final size:22
Alignment explanation
Indices: 31675363--31675405 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31675353 TGTGTATTTA
*
31675363 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAAAATTAAG
31675385 TATTTGTATCTCTAAAATTAA
1 TATTTGTATCTCTAAAATTAA
31675406 TGACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TATTTGTATCTCTAAAATTAAG
Found at i:31675579 original size:24 final size:26
Alignment explanation
Indices: 31675552--31675599 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
31675542 ATACATTCAA
*
31675552 TTTTACTT-TTAGTTTTT-CACACAG
1 TTTTACTTCTTAATTTTTCCACACAG
*
31675576 TTTTATTTCTTAATTTTTCCACAC
1 TTTTACTTCTTAATTTTTCCACAC
31675600 TCACTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 8 0.40
26 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (26 bp):
TTTTACTTCTTAATTTTTCCACACAG
Found at i:31678921 original size:18 final size:19
Alignment explanation
Indices: 31678875--31678923 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
31678865 TTTAAATTTT
31678875 ATTTAT-TATTTAAATAAA
1 ATTTATATATTTAAATAAA
31678893 ATTTTAAATATATTTAAAT-AA
1 A-TTT--ATATATTTAAATAAA
31678914 ATTTATATAT
1 ATTTATATAT
31678924 AAAATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 3 0.11
21 5 0.19
22 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATATATTTAAATAAA
Found at i:31679064 original size:23 final size:24
Alignment explanation
Indices: 31679024--31679078 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
31679014 TTCACATCTT
* *
31679024 AATTTAAAATTTAATTTA-ATTTA
1 AATTTAATATATAATTTATATTTA
* *
31679047 AATTTAATATATATTTTATATTTT
1 AATTTAATATATAATTTATATTTA
*
31679071 ATTTTAAT
1 AATTTAAT
31679079 TTAAATCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTAATATATAATTTATATTTA
Found at i:31692534 original size:21 final size:20
Alignment explanation
Indices: 31692511--31692550 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31692501 TGAGAAAAGA
31692511 AAAAAGA-AGAAGAAAATGAG
1 AAAAAGAGAGAAG-AAATGAG
*
31692531 AAAATGAGAGAAGAAATGAG
1 AAAAAGAGAGAAGAAATGAG
31692551 TGGTTTCGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (20 bp):
AAAAAGAGAGAAGAAATGAG
Found at i:31694619 original size:23 final size:23
Alignment explanation
Indices: 31694592--31694635 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31694582 TTTTATTAAA
31694592 ATTTTAAATT-ATATTATTTTTTT
1 ATTTT-AATTCATATTATTTTTTT
*
31694615 ATTTTTATTCATATTATTTTT
1 ATTTTAATTCATATTATTTTT
31694636 ATATAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTTAATTCATATTATTTTTTT
Found at i:31697440 original size:28 final size:28
Alignment explanation
Indices: 31697377--31697432 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
31697367 ATTTTTAATT
* *
31697377 TTTAAATAATTTTTTATTTAAATACTAA
1 TTTAAATAATTTTTCATTTAAATAATAA
31697405 TTTAAATAATTTTTCATTTAAATCAATA
1 TTTAAATAATTTTTCATTTAAAT-AATA
31697433 GATTAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTAAATAATTTTTCATTTAAATAATAA
Found at i:31697490 original size:29 final size:29
Alignment explanation
Indices: 31697435--31697493 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
31697425 AATCAATAGA
*
31697435 TTAATAGTGTATAATTGTGTTATTTGTGT
1 TTAATAGTGTATAATTATGTTATTTGTGT
*
31697464 TTAATCGTGTA-AATTATGTTATGTTGTGT
1 TTAATAGTGTATAATTATGTTAT-TTGTGT
31697493 T
1 T
31697494 ACTTGAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.54
Consensus pattern (29 bp):
TTAATAGTGTATAATTATGTTATTTGTGT
Found at i:31699259 original size:21 final size:23
Alignment explanation
Indices: 31699218--31699264 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
31699208 TTTGTTAAAA
31699218 AATTAATATGATTTATATTTAAT
1 AATTAATATGATTTATATTTAAT
*
31699241 AATT-ATATTATTT-TATTTAAT
1 AATTAATATGATTTATATTTAAT
31699262 AAT
1 AAT
31699265 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 8 0.35
23 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTAATATGATTTATATTTAAT
Found at i:31699308 original size:24 final size:24
Alignment explanation
Indices: 31699260--31699315 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
31699250 ATTTTATTTA
31699260 ATAATAATTTAAAAATTTTACGTG
1 ATAATAATTTAAAAATTTTACGTG
* *
31699284 ATAATAATTT-TAAATTATTAGGTG
1 ATAATAATTTAAAAATT-TTACGTG
31699308 ATAA-AATT
1 ATAATAATT
31699316 ATTATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (24 bp):
ATAATAATTTAAAAATTTTACGTG
Found at i:31699508 original size:16 final size:16
Alignment explanation
Indices: 31699462--31699509 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
31699452 TTAATAAAAA
* * *
31699462 TTTTCAAAAAAATATA
1 TTTTTAAAAAATTATT
* *
31699478 TTTTTAATAACTTATT
1 TTTTTAAAAAATTATT
31699494 TTTTTAAAAAATTATT
1 TTTTTAAAAAATTATT
31699510 ACAATTGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTAAAAAATTATT
Found at i:31701796 original size:14 final size:13
Alignment explanation
Indices: 31701761--31701799 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
31701751 AAGAAAATAT
31701761 TATATAGTAT-TA
1 TATATAGTATGTA
31701773 TATATA-TATGTA
1 TATATAGTATGTA
31701785 TATATATGTATGTA
1 TATATA-GTATGTA
31701799 T
1 T
31701800 GCATATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 14 0.58
14 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (13 bp):
TATATAGTATGTA
Found at i:31702934 original size:25 final size:25
Alignment explanation
Indices: 31702906--31702956 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31702896 ACTACATGAG
31702906 AGCTAAGTTTCGAGTTCAATAAGGA
1 AGCTAAGTTTCGAGTTCAATAAGGA
31702931 AGCTAAGTTTCGAGTTCAATAAGGA
1 AGCTAAGTTTCGAGTTCAATAAGGA
31702956 A
1 A
31702957 AGTGTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (25 bp):
AGCTAAGTTTCGAGTTCAATAAGGA
Found at i:31729060 original size:31 final size:31
Alignment explanation
Indices: 31729022--31729082 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
31729012 AAAAATTAAA
31729022 ATGTATAATTTGCA-CTTTAAACTTTTAAATC
1 ATGTATAATTTGCATC-TTAAACTTTTAAATC
**
31729053 ATGTATAATTTTTATCTTAAACTTTTAAAT
1 ATGTATAATTTGCATCTTAAACTTTTAAAT
31729083 TATATACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (31 bp):
ATGTATAATTTGCATCTTAAACTTTTAAATC
Found at i:31732040 original size:59 final size:57
Alignment explanation
Indices: 31731801--31732248 Score: 481
Period size: 59 Copynumber: 7.7 Consensus size: 57
31731791 TTGTGCAGAA
* *** *
31731801 AAAATTGAAACTTTCAACTTTTTTTC-AAAATA-TTTTTTAGAAATTTTAATTTTGAGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTA-AAA-TTTAATTTTGAGG
* * ** * * *
31731858 AAAATTTATACTTTCAATTTTTCCCC-AAAATATTTTTGGAAATTTTAATTTCGAGT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTAAAATTTAATTTTGAGG
* * * *
31731914 AAAATTGATACTTTCAACTTTTCCTCAAAAACT-TTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTAAAATTTAATTTTGAGG
*
31731971 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTATAAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-TAAAA-TTTAATTTTGAGG
* ** * * *
31732030 AAAATTGATACTTTCAACTTTTTCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTT-AAAATTTAATTTTGAGG
* *
31732089 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTAAAAACTTTAATTTCGAAG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT-AAAA-TTTAATTTTGAGG
* * * * *
31732148 AAAATTGATACTTTCAACTTTTCCTCAAAAAAAAACTTTTTTTGAAAATTTACTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCC-C-CAAAAATA-TTTTTTT-AAAATTTAATTTTGAGG
31732209 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
31732249 TGGATTTTAT
Statistics
Matches: 328, Mismatches: 51, Indels: 23
0.82 0.13 0.06
Matches are distributed among these distances:
56 35 0.11
57 86 0.26
58 28 0.09
59 118 0.36
60 12 0.04
61 38 0.12
62 11 0.03
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTAAAATTTAATTTTGAGG
Found at i:31732107 original size:118 final size:117
Alignment explanation
Indices: 31731801--31732248 Score: 629
Period size: 118 Copynumber: 3.8 Consensus size: 117
31731791 TTGTGCAGAA
* ** * * * * *
31731801 AAAATTGAAACTTTCAACTTTTT-TTCAAAATA-TTTTTTAGAAATTTTAATTTTGAGAAAAATT
1 AAAATTGATACTTTCAACTTTTTCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATT
* * ** * *
31731864 TATACTTTCAATTTTTCCCC-AAAATA-TTTTTGGAAATTTTAATTTCGAGT
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTTAAAACTTTAATTTCGAGG
* * *
31731914 AAAATTGATACTTTCAACTTTTCCT--CAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTTCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATT
31731977 GATACTTTCAACTTTTCCCCAAAAATATTTTTTATAAAACTTTAATTTCGAGG
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTT-TAAAACTTTAATTTCGAGG
*
31732030 AAAATTGATACTTTCAACTTTTTCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTTCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATT
*
31732095 GATACTTTCAACTTTTCCCCAAAAATATTTTTTTAAAAACTTTAATTTCGAAG
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTT-AAAACTTTAATTTCGAGG
* *
31732148 AAAATTGATACTTTCAACTTTTCCTCAAAAAAAAACTTTTTTTGAAAATTTACTTTTAAGAAAAA
1 AAAATTGATACTTTCAACTTTT--TCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAA
31732213 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
64 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
31732249 TGGATTTTAT
Statistics
Matches: 304, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
112 4 0.01
113 65 0.21
114 7 0.02
115 5 0.02
116 39 0.13
117 1 0.00
118 109 0.36
120 74 0.24
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (117 bp):
AAAATTGATACTTTCAACTTTTTCTAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTCCCCAAAAATATTTTTTTAAAACTTTAATTTCGAGG
Found at i:31732273 original size:5 final size:5
Alignment explanation
Indices: 31732265--31732339 Score: 66
Period size: 5 Copynumber: 14.4 Consensus size: 5
31732255 TTATTTAAAG
31732265 AAAAT AAAAT AAAAT --AAT AAAAT AAAAGT GAAAAT AAAAAT AAAGA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT -AAAAT AAA-AT
*
31732311 AAAGT AAAAT AAAAAT AAAAAT AAAAT AA
1 AAAAT AAAAT -AAAAT -AAAAT AAAAT AA
31732340 TATTAAACAA
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
3 3 0.05
5 34 0.57
6 19 0.32
7 4 0.07
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:31732302 original size:17 final size:16
Alignment explanation
Indices: 31732264--31732339 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 16
31732254 TTTATTTAAA
31732264 GAAAATAAAATAAAAT
1 GAAAATAAAATAAAAT
31732280 ---AATAAAATAAAAGT
1 GAAAATAAAATAAAA-T
31732294 GAAAATAAAA-ATAAA-
1 GAAAATAAAATA-AAAT
31732309 GAAAAGTAAAATAAAAAT
1 GAAAA-TAAAAT-AAAAT
*
31732327 AAAAATAAAATAA
1 GAAAATAAAATAA
31732340 TATTAAACAA
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
15 5 0.10
16 8 0.16
17 19 0.38
18 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
GAAAATAAAATAAAAT
Found at i:31732306 original size:6 final size:6
Alignment explanation
Indices: 31732265--31732336 Score: 58
Period size: 6 Copynumber: 11.5 Consensus size: 6
31732255 TTATTTAAAG
* * *
31732265 AAAAT- AAAAT- AAAATAA TAAAATA AAAGTG AAAATA AAAATA AAGAAAA
1 AAAATA AAAATA AAAAT-A -AAAATA AAAATA AAAATA AAAATA AA-AATA
31732314 GTAAAATA AAAATA AAAATA AAA
1 --AAAATA AAAATA AAAATA AAA
31732337 TAATATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
5 10 0.18
6 31 0.56
7 4 0.07
8 8 0.15
9 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:31732321 original size:21 final size:21
Alignment explanation
Indices: 31732260--31732329 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 21
31732250 GGATTTTATT
31732260 TAAAGAAAA-TAAAATAAAATAA
1 TAAAGAAAAGTAAAAT-AAA-AA
*
31732282 TAAAATAAAAGTGAAAATAAAAA
1 T-AAAGAAAAGT-AAAATAAAAA
31732305 TAAAGAAAAGTAAAATAAAAA
1 TAAAGAAAAGTAAAATAAAAA
31732326 TAAA
1 TAAA
31732330 AATAAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.33
22 10 0.23
23 10 0.23
24 4 0.09
25 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
TAAAGAAAAGTAAAATAAAAA
Found at i:31732346 original size:11 final size:11
Alignment explanation
Indices: 31732265--31732336 Score: 74
Period size: 12 Copynumber: 6.3 Consensus size: 11
31732255 TTATTTAAAG
31732265 AAAATAAAATAA
1 AAAATAAAAT-A
31732277 AATAATAAAATA
1 AA-AATAAAATA
*
31732289 AAAGTGAAAATA
1 AAAAT-AAAATA
*
31732301 AAAAT-AAAGA
1 AAAATAAAATA
*
31732311 AAAGTAAAATA
1 AAAATAAAATA
31732322 AAAATAAAAATA
1 AAAAT-AAAATA
31732334 AAA
1 AAA
31732337 TAATATTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
10 8 0.16
11 10 0.20
12 24 0.48
13 8 0.16
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Done.