Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 26 of 402
Found at i:5830325 original size:24 final size:24
Alignment explanation
Indices: 5830306--5830352 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5830296 ATATAATTAT
*
5830306 GCAAATAAATATATTAATAATCAA
1 GCAAATAAATACATTAATAATCAA
* *
5830330 GCAATTAAATACGTTAATAATCA
1 GCAAATAAATACATTAATAATCA
5830353 TGTAATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (24 bp):
GCAAATAAATACATTAATAATCAA
Found at i:5830395 original size:23 final size:23
Alignment explanation
Indices: 5830369--5830434 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
5830359 CAAATTAAGT
*
5830369 ATAATCGCACAAATAAATATATA
1 ATAATCACACAAATAAATATATA
**
5830392 ATAATCATGCAAAT--ATAT-TA
1 ATAATCACACAAATAAATATATA
5830412 ATAAATCACACAAATAAATATAT
1 AT-AATCACACAAATAAATATAT
5830435 TAATCAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.12
21 14 0.41
23 15 0.44
24 1 0.03
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (23 bp):
ATAATCACACAAATAAATATATA
Found at i:5830412 original size:46 final size:44
Alignment explanation
Indices: 5830344--5830434 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
5830334 TTAAATACGT
* *
5830344 TAATAATCATGTAATCAAATTAAGTATAATCGCACAAATAAATATA
1 TAATAATCATGAAATCAAATTAA-TA-AATCACACAAATAAATATA
*
5830390 TAATAATCATGCAAAT-ATATTAATAAATCACACAAATAAATATA
1 TAATAATCATG-AAATCAAATTAATAAATCACACAAATAAATATA
5830434 T
1 T
5830435 TAATCAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 19 0.46
45 2 0.05
46 17 0.41
47 3 0.07
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.31
Consensus pattern (44 bp):
TAATAATCATGAAATCAAATTAATAAATCACACAAATAAATATA
Found at i:5830439 original size:21 final size:21
Alignment explanation
Indices: 5830370--5830440 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
5830360 AAATTAAGTA
*
5830370 TAATCGCACAAATAAATATAT
1 TAATCACACAAATAAATATAT
** *
5830391 AATAATCATGCAAATATAT-TAAT
1 --TAATCACACAAATAAATAT-AT
*
5830414 AAATCACACAAATAAATATAT
1 TAATCACACAAATAAATATAT
5830435 TAATCA
1 TAATCA
5830441 AATATATTAC
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 20 0.54
22 2 0.05
23 15 0.41
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.30
Consensus pattern (21 bp):
TAATCACACAAATAAATATAT
Found at i:5830443 original size:13 final size:12
Alignment explanation
Indices: 5830402--5830449 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5830392 ATAATCATGC
5830402 AAATATATTAAT
1 AAATATATTAAT
* **
5830414 AAATCACACAAAT
1 AAAT-ATATTAAT
5830427 AAATATATTAAT
1 AAATATATTAAT
5830439 CAAATATATTA
1 -AAATATATTA
5830450 CGCAAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATATTAAT
Found at i:5830455 original size:13 final size:13
Alignment explanation
Indices: 5830427--5830478 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
5830417 TCACACAAAT
**
5830427 AAATATATTAATC
1 AAATATATTACGC
5830440 AAATATATTACGC
1 AAATATATTACGC
*
5830453 AAATAAATTATCTAGC
1 AAATATATTA-C--GC
5830469 AAATATATTA
1 AAATATATTA
5830479 TTAGTCATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 20 0.62
14 1 0.03
16 11 0.34
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (13 bp):
AAATATATTACGC
Found at i:5830476 original size:29 final size:30
Alignment explanation
Indices: 5830422--5830478 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
5830412 ATAAATCACA
*
5830422 CAAATAAATATATTAATCAAATATATTACG
1 CAAATAAATATATTAAGCAAATATATTACG
5830452 CAAATAAAT-TATCT-AGCAAATATATTA
1 CAAATAAATATAT-TAAGCAAATATATTA
5830479 TTAGTCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (30 bp):
CAAATAAATATATTAAGCAAATATATTACG
Found at i:5835014 original size:25 final size:27
Alignment explanation
Indices: 5834986--5835061 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 27
5834976 CCTTTTCTTC
5834986 TTTATTTTATTTTT-TA-A-TTTACATT
1 TTTATTTTATTTTTATATATTTTACA-T
* *
5835011 TTTATTTATGTTATTTATATATTTTCCAT
1 TTTATTT-TATT-TTTATATATTTTACAT
*
5835040 TTTATTTTA-TTTTATAGATTTT
1 TTTATTTTATTTTTATATATTTT
5835062 TTTTCTAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
25 7 0.17
26 14 0.33
27 4 0.10
28 3 0.07
29 9 0.21
30 5 0.12
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (27 bp):
TTTATTTTATTTTTATATATTTTACAT
Found at i:5835019 original size:29 final size:30
Alignment explanation
Indices: 5834986--5835054 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
5834976 CCTTTTCTTC
*
5834986 TTTATTTTATTT-TTTAATTTACATTTT-T
1 TTTATTTTATTTATATAATTTACATTTTAT
* * *
5835014 ATTTATGTTATTTATATATTTTCCATTTTAT
1 -TTTATTTTATTTATATAATTTACATTTTAT
5835045 TTTATTTTAT
1 TTTATTTTAT
5835055 AGATTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 11 0.33
30 21 0.64
31 1 0.03
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.71
Consensus pattern (30 bp):
TTTATTTTATTTATATAATTTACATTTTAT
Found at i:5835140 original size:20 final size:20
Alignment explanation
Indices: 5835115--5835152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5835105 TATAAATTTC
5835115 TTTTAA-AAAATAATAAAAAA
1 TTTTAACAAAATAA-AAAAAA
5835135 TTTTAACAAAATAAAAAA
1 TTTTAACAAAATAAAAAA
5835153 TGTTTCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
TTTTAACAAAATAAAAAAAA
Found at i:5838982 original size:21 final size:21
Alignment explanation
Indices: 5838934--5838982 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5838924 TAGTTAACAT
*
5838934 AATATAACATATACAAGGAAT
1 AATATAACATATACAAGGAAC
* * *
5838955 AACATAATATATACAATGAAC
1 AATATAACATATACAAGGAAC
5838976 AATATAA
1 AATATAA
5838983 AAGGTTAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.06, T:0.24
Consensus pattern (21 bp):
AATATAACATATACAAGGAAC
Found at i:5840395 original size:32 final size:32
Alignment explanation
Indices: 5840324--5840396 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
5840314 ATAAATAACT
* *
5840324 ATGCAAATAAATATATTAATAATTATACAATC
1 ATGCAAATAAATAAATTAATAATTATACAATA
** *
5840356 ACACAAATAAATAAATTAATTAATTA-ATAATA
1 ATGCAAATAAATAAATTAA-TAATTATACAATA
5840388 ATGCAAATA
1 ATGCAAATA
5840397 GACATGCAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
32 27 0.82
33 6 0.18
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (32 bp):
ATGCAAATAAATAAATTAATAATTATACAATA
Found at i:5840486 original size:21 final size:19
Alignment explanation
Indices: 5840461--5840548 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 19
5840451 AATAAGCAAT
5840461 TAAATATATAATCATACAAA
1 TAAATATA-AATCATACAAA
* *
5840481 TAAAATACAAATCATGCAAA
1 T-AAATATAAATCATACAAA
* * *
5840501 TAAACATACAATTAAACAAA
1 TAAATATA-AATCATACAAA
*
5840521 TAGTAATATAAATCATGCAAA
1 TA--AATATAAATCATACAAA
5840542 TAAATAT
1 TAAATAT
5840549 GTAATTAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
19 10 0.19
20 22 0.42
21 16 0.30
22 5 0.09
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.26
Consensus pattern (19 bp):
TAAATATAAATCATACAAA
Found at i:5840555 original size:41 final size:40
Alignment explanation
Indices: 5840456--5840557 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 40
5840446 AAATGAATAA
* * *
5840456 GCAATTAAATATATAATCATACAAATAAAATACAAATCAT
1 GCAAATAAATATATAATTAAACAAATAAAATACAAATCAT
* * * *
5840496 GCAAATAAACATACAATTAAACAAATAGTAATATAAATCAT
1 GCAAATAAATATATAATTAAACAAATA-AAATACAAATCAT
*
5840537 GCAAATAAATATGTAATTAAA
1 GCAAATAAATATATAATTAAA
5840558 TATATAATCA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 22 0.43
41 29 0.57
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (40 bp):
GCAAATAAATATATAATTAAACAAATAAAATACAAATCAT
Found at i:5840558 original size:93 final size:95
Alignment explanation
Indices: 5840437--5840612 Score: 248
Period size: 93 Copynumber: 1.9 Consensus size: 95
5840427 TAATAATGTA
* * *
5840437 AAATCATGTAAATGAATAAGCAATTAAATATATAATCA-TACA-AATAAAATACAAATCATGCAA
1 AAATCATGCAAATAAATAAGCAATTAAATATATAATCAGTAAATAATAAAATACAAATCATGCAA
*
5840500 ATAAACATACAATTAAACAAATAGTAATAT
66 AAAAACATACAATTAAACAAATAGTAATAT
* * * *
5840530 AAATCATGCAAATAAATATGTAATTAAATATATAATCAGGTAAATAATAATATATAAATCATGCA
1 AAATCATGCAAATAAATAAGCAATTAAATATATAATCA-GTAAATAATAAAATACAAATCATGCA
*
5840595 AAAAAACATGCAATTAAA
65 AAAAAACATACAATTAAA
5840613 TATATAATCA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
93 34 0.48
95 3 0.04
96 34 0.48
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (95 bp):
AAATCATGCAAATAAATAAGCAATTAAATATATAATCAGTAAATAATAAAATACAAATCATGCAA
AAAAACATACAATTAAACAAATAGTAATAT
Found at i:5840592 original size:55 final size:55
Alignment explanation
Indices: 5840526--5840631 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
5840516 ACAAATAGTA
* * * *
5840526 ATATAAATCATGCAAATAAATATGTAATTAAATATATAATCAGGTAAATAATAAT
1 ATATAAATCATGCAAAAAAACATGCAATTAAATATATAATCAGGCAAATAATAAT
*
5840581 ATATAAATCATGCAAAAAAACATGCAATTAAATATATAATCATGCAAATAA
1 ATATAAATCATGCAAAAAAACATGCAATTAAATATATAATCAGGCAAATAA
5840632 ATATATTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (55 bp):
ATATAAATCATGCAAAAAAACATGCAATTAAATATATAATCAGGCAAATAATAAT
Found at i:5840643 original size:24 final size:24
Alignment explanation
Indices: 5840616--5840756 Score: 100
Period size: 24 Copynumber: 6.1 Consensus size: 24
5840606 AATTAAATAT
5840616 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* * **
5840640 ATAATCAAGCAATTAAATACGTTA
1 ATAATCATGCAAATAAATATATTA
* *
5840664 ATAATCATG-TAATCAAAT-TA-AA
1 ATAATCATGCAAAT-AAATATATTA
***
5840686 TATAATCGCACAAATAAATATA-TA
1 -ATAATCATGCAAATAAATATATTA
5840710 ATAATCATGC----AAATATATTA
1 ATAATCATGCAAATAAATATATTA
**
5840730 ATAAATCACACAAATAAATATATTA
1 AT-AATCATGCAAATAAATATATTA
5840755 AT
1 AT
5840757 CAAATATATT
Statistics
Matches: 87, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
19 7 0.08
20 4 0.05
21 6 0.07
22 1 0.01
23 19 0.22
24 38 0.44
25 12 0.14
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:5840704 original size:23 final size:23
Alignment explanation
Indices: 5840678--5840748 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
5840668 TCATGTAATC
*
5840678 AAATTAAATATAATCGCACAAAT
1 AAATTAAATATAATCACACAAAT
* **
5840701 AAA-TATATAATAATCATGCAAAT
1 AAATTAAAT-ATAATCACACAAAT
*
5840724 ATATT-AATA-AATCACACAAAT
1 AAATTAAATATAATCACACAAAT
5840745 AAAT
1 AAAT
5840749 ATATTAATCA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 13 0.35
22 5 0.14
23 18 0.49
24 1 0.03
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (23 bp):
AAATTAAATATAATCACACAAAT
Found at i:5840730 original size:46 final size:44
Alignment explanation
Indices: 5840662--5840752 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
5840652 TTAAATACGT
* *
5840662 TAATAATCATGTAATCAAATTAAATATAATCGCACAAATAAATATA
1 TAATAATCATGAAATCAAATT-AATA-AATCACACAAATAAATATA
*
5840708 TAATAATCATGCAAAT-ATATTAATAAATCACACAAATAAATATA
1 TAATAATCATG-AAATCAAATTAATAAATCACACAAATAAATATA
5840752 T
1 T
5840753 TAATCAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 19 0.46
45 4 0.10
46 15 0.37
47 3 0.07
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (44 bp):
TAATAATCATGAAATCAAATTAATAAATCACACAAATAAATATA
Found at i:5840750 original size:23 final size:24
Alignment explanation
Indices: 5840684--5840761 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 24
5840674 AATCAAATTA
*
5840684 AATATAATCGCACAAATAAATATAT
1 AATA-AATCACACAAATAAATATAT
**
5840709 AAT-AATCATGCAAAT--ATAT-T
1 AATAAATCACACAAATAAATATAT
5840729 AATAAATCACACAAATAAATATATT
1 AATAAATCACACAAATAAATATA-T
5840754 AATCAAAT
1 AAT-AAAT
5840762 ATATTACGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
20 4 0.10
21 14 0.33
23 13 0.31
25 7 0.17
26 4 0.10
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (24 bp):
AATAAATCACACAAATAAATATAT
Found at i:5840761 original size:13 final size:12
Alignment explanation
Indices: 5840720--5840767 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5840710 ATAATCATGC
5840720 AAATATATTAAT
1 AAATATATTAAT
* **
5840732 AAATCACACAAAT
1 AAAT-ATATTAAT
5840745 AAATATATTAAT
1 AAATATATTAAT
5840757 CAAATATATTA
1 -AAATATATTA
5840768 CGCAAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATATTAAT
Found at i:5840773 original size:13 final size:13
Alignment explanation
Indices: 5840745--5840796 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
5840735 TCACACAAAT
**
5840745 AAATATATTAATC
1 AAATATATTACGC
5840758 AAATATATTACGC
1 AAATATATTACGC
*
5840771 AAATAAATTATCTAGC
1 AAATATATTA-C--GC
5840787 AAATATATTA
1 AAATATATTA
5840797 TTAGTCATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 20 0.62
14 1 0.03
16 11 0.34
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (13 bp):
AAATATATTACGC
Found at i:5840794 original size:29 final size:30
Alignment explanation
Indices: 5840740--5840796 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
5840730 ATAAATCACA
*
5840740 CAAATAAATATATTAATCAAATATATTACG
1 CAAATAAATATATTAAGCAAATATATTACG
5840770 CAAATAAAT-TATCT-AGCAAATATATTA
1 CAAATAAATATAT-TAAGCAAATATATTA
5840797 TTAGTCATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.33
Consensus pattern (30 bp):
CAAATAAATATATTAAGCAAATATATTACG
Found at i:5841142 original size:26 final size:26
Alignment explanation
Indices: 5841106--5841164 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
5841096 AATTACTGTG
*
5841106 AGGTCCCCATTTTGATCACAGATTCA
1 AGGTCCTCATTTTGATCACAGATTCA
5841132 AGGTCCTCATTTTGATCACAGATTCA
1 AGGTCCTCATTTTGATCACAGATTCA
5841158 AGGTCCT
1 AGGTCCT
5841165 TATATAGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (26 bp):
AGGTCCTCATTTTGATCACAGATTCA
Found at i:5842763 original size:15 final size:15
Alignment explanation
Indices: 5842745--5842773 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5842735 TATAATAGTA
5842745 AATAATTAATAATTT
1 AATAATTAATAATTT
5842760 AATAATTAATAATT
1 AATAATTAATAATT
5842774 GAAAACTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATTAATAATTT
Found at i:5842934 original size:15 final size:15
Alignment explanation
Indices: 5842880--5842938 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
5842870 AATAAATTAG
5842880 TGATAACTTAATAAT
1 TGATAACTTAATAAT
** *
5842895 AAATAA-ATAATAAT
1 TGATAACTTAATAAT
* *
5842909 TTA-ATAGTTAATAAT
1 TGATA-ACTTAATAAT
5842924 TGATAACTTAATAAT
1 TGATAACTTAATAAT
5842939 AAATCAGTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
13 1 0.03
14 9 0.27
15 22 0.67
16 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (15 bp):
TGATAACTTAATAAT
Found at i:5842950 original size:44 final size:42
Alignment explanation
Indices: 5842795--5842962 Score: 160
Period size: 44 Copynumber: 3.9 Consensus size: 42
5842785 AATAATCAGT
* * *
5842795 ATAACTTAGTAGT-AATCATTAATAATTTAATAATTAACCAATG
1 ATAACTTAATAATAAATCA-TAATAATTTAATAATTAA-TAATG
* * * * *
5842838 ATAACTTAATAGTAAATTATAAATAGTTTAATAATAAATTAGTG
1 ATAACTTAATAATAAATCAT-AATAATTTAATAATTAA-TAATG
* *
5842882 ATAACTTAATAATAAATAAATAATAATTTAATAGTTAATAATTG
1 ATAACTTAATAATAAAT-CATAATAATTTAATAATTAATAA-TG
*
5842926 ATAACTTAATAATAAATCAGTAATAATATAAT-ATTAA
1 ATAACTTAATAATAAATCA-TAATAATTTAATAATTAA
5842963 ATACACAATA
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
43 20 0.19
44 82 0.79
45 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.38
Consensus pattern (42 bp):
ATAACTTAATAATAAATCATAATAATTTAATAATTAATAATG
Found at i:5842951 original size:22 final size:22
Alignment explanation
Indices: 5842729--5842988 Score: 129
Period size: 22 Copynumber: 12.0 Consensus size: 22
5842719 CACAAATTAA
* *
5842729 TAATAA-TATAATAGTAAATAAT
1 TAATAACT-TAATAATAAATCAT
* * *
5842751 TAATAATTTAATAATTAATAAT
1 TAATAACTTAATAATAAATCAT
* *
5842773 TGAA-AACTTAAAAAT-AATCAG
1 T-AATAACTTAATAATAAATCAT
* *
5842794 T-ATAACTTAGTAGT-AATCAT
1 TAATAACTTAATAATAAATCAT
* * * *
5842814 TAATAATTTAATAATTAACCAA
1 TAATAACTTAATAATAAATCAT
* * *
5842836 TGATAACTTAATAGTAAATTAT
1 TAATAACTTAATAATAAATCAT
* ** * *
5842858 AAATAGTTTAATAATAAATTAG
1 TAATAACTTAATAATAAATCAT
* * *
5842880 TGATAACTTAATAATAAATAAA
1 TAATAACTTAATAATAAATCAT
* * * *
5842902 TAATAATTTAATAGTTAATAAT
1 TAATAACTTAATAATAAATCAT
* *
5842924 TGATAACTTAATAATAAATCAG
1 TAATAACTTAATAATAAATCAT
*
5842946 TAATAA-TATAATATTAAATACA-
1 TAATAACT-TAATAATAAAT-CAT
* * *
5842968 CAATAACTTAGTAGTAAATCA
1 TAATAACTTAATAATAAATCA
5842989 ATTATAATAT
Statistics
Matches: 180, Mismatches: 50, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.01
20 14 0.08
21 18 0.10
22 141 0.78
23 6 0.03
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (22 bp):
TAATAACTTAATAATAAATCAT
Found at i:5842958 original size:88 final size:86
Alignment explanation
Indices: 5842722--5842996 Score: 209
Period size: 88 Copynumber: 3.2 Consensus size: 86
5842712 GGATATACAC
* * * * * * * *
5842722 AAATTAATAATAATATAATAGTAAATAATTAATAATTTAATAATTAATAATTGAAA-ACTTAAAA
1 AAATAAATAATAATTTAATAGTTAATAATTGATAACTTAATAATAAATAA-T-AAATAATTAATA
* *
5842786 AT-AATCAGTATAACTTAGTAGT
64 ATAAATCAGTATAACTTAATAAT
* * * * * * *
5842808 -AATCATTAATAATTTAATAATTAACCAA-TGATAACTTAATAGTAAATTATAAATAGTTTAATA
1 AAATAAATAATAATTTAATAGTTAA-TAATTGATAACTTAATAATAAATAATAAATA-ATTAATA
*
5842871 ATAAATTAGTGATAACTTAATAAT
64 ATAAATCAGT-ATAACTTAATAAT
*
5842895 AAATAAATAATAATTTAATAGTTAATAATTGATAACTTAATAATAAATCAGT-AATAATATAATA
1 AAATAAATAATAATTTAATAGTTAATAATTGATAACTTAATAATAAAT-AATAAATAAT-TAATA
* ** * *
5842959 TTAAATACACAATAACTTAGTAGT
64 ATAAAT-CAGTATAACTTAATAAT
* *
5842983 AAATCAATTATAAT
1 AAATAAATAATAAT
5842997 ATAGTTGTAA
Statistics
Matches: 147, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
83 3 0.02
84 2 0.01
85 42 0.29
86 8 0.05
87 14 0.10
88 76 0.52
89 2 0.01
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (86 bp):
AAATAAATAATAATTTAATAGTTAATAATTGATAACTTAATAATAAATAATAAATAATTAATAAT
AAATCAGTATAACTTAATAAT
Found at i:5842973 original size:66 final size:66
Alignment explanation
Indices: 5842794--5842995 Score: 160
Period size: 66 Copynumber: 3.1 Consensus size: 66
5842784 AAATAATCAG
* * * * * ** ** *
5842794 TATAACTTAGTAGT-AATCATTAATAATTTAATAATTAACCAATGATAACTTAATAGTAAAT-TA
1 TATAACTTAATAATAAATCAGTAATAACTTAATAATAAATAAACAATAACTTAATAGTAAATCAA
5842857 T
66 T
* ** * * * * *
5842858 AAATAGTTTAATAATAAATTAGTGATAACTTAATAATAAATAAATAATAATTTAATAGTTAAT-A
1 -TATAACTTAATAATAAATCAGTAATAACTTAATAATAAATAAACAATAACTTAATAGTAAATCA
5842922 AT
65 AT
* * *
5842924 TGATAACTTAATAATAAATCAGTAATAA-TATAATATTAAATACACAATAACTTAGTAGTAAATC
1 T-ATAACTTAATAATAAATCAGTAATAACT-TAATAATAAATAAACAATAACTTAATAGTAAATC
5842988 AAT
64 AAT
5842991 TATAA
1 TATAA
5842996 TATAGTTGTA
Statistics
Matches: 106, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
65 10 0.09
66 92 0.87
67 4 0.04
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (66 bp):
TATAACTTAATAATAAATCAGTAATAACTTAATAATAAATAAACAATAACTTAATAGTAAATCAA
T
Found at i:5842974 original size:44 final size:44
Alignment explanation
Indices: 5842882--5843039 Score: 135
Period size: 44 Copynumber: 3.6 Consensus size: 44
5842872 TAAATTAGTG
* * **
5842882 ATAACTTAATAATAAATAAATAATAATTTAATAGTTAATAATTG
1 ATAACTTAATAATAAATCAATAATAATATAATAGTTAATAATCA
*
5842926 ATAACTTAATAATAAATCAGTAATAATATAATA-TTAAATACA-CA
1 ATAACTTAATAATAAATCAATAATAATATAATAGTT-AATA-ATCA
* * * * * * *
5842970 ATAACTTAGTAGTAAATCAATTATAATATAGTTGTAAATTTAT-A
1 ATAACTTAATAATAAATCAATAATAATATAATAGTTAA-TAATCA
*
5843014 ATAA-TATAATAATAAATCAATTATAA
1 ATAACT-TAATAATAAATCAATAATAA
5843040 CTTACTAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
43 3 0.03
44 87 0.94
45 3 0.03
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (44 bp):
ATAACTTAATAATAAATCAATAATAATATAATAGTTAATAATCA
Found at i:5842995 original size:22 final size:22
Alignment explanation
Indices: 5842976--5843039 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
5842966 CACAATAACT
5842976 TAGTAGTAAATCAATTATAATA
1 TAGTAGTAAATCAATTATAATA
* ** *
5842998 TAGTTGTAAATTTATAATAATA
1 TAGTAGTAAATCAATTATAATA
* *
5843020 TAATAATAAATCAATTATAA
1 TAGTAGTAAATCAATTATAA
5843040 CTTACTAAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (22 bp):
TAGTAGTAAATCAATTATAATA
Found at i:5843104 original size:22 final size:22
Alignment explanation
Indices: 5843063--5843209 Score: 69
Period size: 21 Copynumber: 6.9 Consensus size: 22
5843053 AAGTGATAAC
* *
5843063 TTATCAAAATTATGTTAAAAGG
1 TTATCAAAATTATATAAAAAGG
*
5843085 TTATCAAAATTTTATAAAAA--
1 TTATCAAAATTATATAAAAAGG
* *
5843105 TTAT-AAAAGTTATAT-TAATGG
1 TTATCAAAA-TTATATAAAAAGG
* * *
5843126 CTA-CAAAAATTATATCATAA-G
1 TTATC-AAAATTATATAAAAAGG
* *
5843147 TTA-CTAAATTAATATAAAAA-A
1 TTATCAAAATT-ATATAAAAAGG
* * *
5843168 TTTTTAAAATTATATAAAAA-A
1 TTATCAAAATTATATAAAAAGG
*
5843189 TTATCAAAATTTTATTAAAAA
1 TTATCAAAATTATA-TAAAAA
5843210 TTTTCAATCT
Statistics
Matches: 95, Mismatches: 21, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
19 6 0.06
20 14 0.15
21 42 0.44
22 33 0.35
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTATATAAAAAGG
Found at i:5843216 original size:21 final size:21
Alignment explanation
Indices: 5843152--5843216 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
5843142 ATAAGTTACT
*
5843152 AAATTAATATAAAAAATTTTTA
1 AAATT-ATATAAAAAATTTTCA
*
5843174 AAATTATATAAAAAATTATCA
1 AAATTATATAAAAAATTTTCA
* *
5843195 AAATTTTATTAAAAATTTTCA
1 AAATTATATAAAAAATTTTCA
5843216 A
1 A
5843217 TCTTTTAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTATATAAAAAATTTTCA
Found at i:5847668 original size:19 final size:19
Alignment explanation
Indices: 5847644--5847683 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5847634 ATATTTGATT
*
5847644 TTAACTGGCATCATCAATG
1 TTAACTGACATCATCAATG
* *
5847663 TTAACTTATATCATCAATG
1 TTAACTGACATCATCAATG
5847682 TT
1 TT
5847684 GATTGATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (19 bp):
TTAACTGACATCATCAATG
Found at i:5849050 original size:2 final size:2
Alignment explanation
Indices: 5849039--5849076 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5849029 TTTTTTGTAG
*
5849039 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5849077 AAAGAGCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5849290 original size:25 final size:23
Alignment explanation
Indices: 5849244--5849293 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
5849234 TTTTTTTTTT
* *
5849244 AAAATTAATTAATTTTTTAAATA
1 AAAATTAATTAATTATTGAAATA
5849267 AAAATATATATTAATTATTGAAATA
1 AAAAT-TA-ATTAATTATTGAAATA
5849292 AA
1 AA
5849294 TATCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 2 0.09
25 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATTAATTAATTATTGAAATA
Found at i:5850152 original size:20 final size:20
Alignment explanation
Indices: 5850127--5850164 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5850117 TAATTAATTT
5850127 TAATTTTATTATTATTATAA
1 TAATTTTATTATTATTATAA
*
5850147 TAATTTTATTTTTATTAT
1 TAATTTTATTATTATTAT
5850165 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TAATTTTATTATTATTATAA
Found at i:5850173 original size:26 final size:26
Alignment explanation
Indices: 5850112--5850173 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
5850102 AAATATATAA
5850112 TTTTTTAATTAATTTTAATTTTATTAT
1 TTTTTTAA-TAATTTTAATTTTATTAT
* * *
5850139 TATTATAATAATTTTATTTTTATTAT
1 TTTTTTAATAATTTTAATTTTATTAT
5850165 TTTTTTAAT
1 TTTTTTAAT
5850174 TTTATTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTTTAATAATTTTAATTTTATTAT
Found at i:5854639 original size:19 final size:20
Alignment explanation
Indices: 5854604--5854641 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5854594 GTCTCATTAT
5854604 CATAATTAGGTTTTTAAATG
1 CATAATTAGGTTTTTAAATG
5854624 CATAATTAGG-TTTTAAAT
1 CATAATTAGGTTTTTAAAT
5854642 ATTATACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
CATAATTAGGTTTTTAAATG
Found at i:5855492 original size:3 final size:3
Alignment explanation
Indices: 5855484--5855535 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5855474 TAGTTGGGTA
5855484 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
5855532 TAT T
1 TAT T
5855536 TTCTTTCTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5856305 original size:25 final size:24
Alignment explanation
Indices: 5856277--5856328 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
5856267 AAGGTTTTCC
**
5856277 TTTTTCATTTTCATTTTCATTTTAT
1 TTTTTCATTTGAATTTTCA-TTTAT
* *
5856302 TTTTTGATTTGAATTTTGATTTAT
1 TTTTTCATTTGAATTTTCATTTAT
5856326 TTT
1 TTT
5856329 ATTATCTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (24 bp):
TTTTTCATTTGAATTTTCATTTAT
Found at i:5859941 original size:115 final size:115
Alignment explanation
Indices: 5859724--5859942 Score: 264
Period size: 115 Copynumber: 1.9 Consensus size: 115
5859714 TACGATCTTG
* * *
5859724 ACTTAGTCTTGGTCACTTTCAGACTCGTAACATGATCTTAATCATCCATTCTTGACCCAAGCTAG
1 ACTTAGTCTTGGTCACTTTCAGACTCATAACATGATCTCAATCATCCAATCTTGACCCAAGCTAG
*
5859789 ATCATTTTATTGATTCATGATTTCATCTCGGTCAGTCATTTTTAACCTTC
66 ATCATTTTATTGATTCATGATTTCATCTCAGTCAGTCATTTTTAACCTTC
* * * * * * *
5859839 ACTTAGTCTTGGTCGCTTTTAGACTTATGACATCG-TCTCAATCATTCAATCTTG-CCCTAGGTT
1 ACTTAGTCTTGGTCACTTTCAGACTCATAACAT-GATCTCAATCATCCAATCTTGACCC-AAGCT
* * *
5859902 AGATCATTTTCTTGATTCATGGTTTCAT-TCTAGTTAGTCAT
64 AGATCATTTTATTGATTCATGATTTCATCTC-AGTCAGTCAT
5859943 CTTCGACCTC
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
114 5 0.06
115 81 0.93
116 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (115 bp):
ACTTAGTCTTGGTCACTTTCAGACTCATAACATGATCTCAATCATCCAATCTTGACCCAAGCTAG
ATCATTTTATTGATTCATGATTTCATCTCAGTCAGTCATTTTTAACCTTC
Found at i:5860709 original size:119 final size:119
Alignment explanation
Indices: 5860493--5860710 Score: 258
Period size: 119 Copynumber: 1.8 Consensus size: 119
5860483 ATTTCGGTTC
* * * * * * * *
5860493 TATCTAGATCATCTTCTTGATTCATGATTTTATCTCAATCAGTCATATTCGACCTTGACTTAATC
1 TATCCAGATCATCTTCTTAATTCATGATTTCATCCCAATCAGCCATACTCGACCTCGACTCAATC
* * *
5860558 CGATCGCTTTATCTTTAAACTCATAGTTTTATCTTGATCATTTAATCTCGGCTT
66 CGATCACTTTATCTCTAAACTCATAATTTTATCTTGATCATTTAATCTCGGCTT
* *
5860612 TATCCAGATCATTTTTTTAATTCATGATTTCATCCCAATCAGCCAT-CTCGACCTCGACTCAATC
1 TATCCAGATCATCTTCTTAATTCATGATTTCATCCCAATCAGCCATACTCGACCTCGACTCAATC
* * * * *
5860676 CTAGTCATTTTATCTCTAGATTTATAATTTTATCT
66 CGA-TCACTTTATCTCTAAACTCATAATTTTATCT
5860711 CAGTCATTTA
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
118 17 0.21
119 63 0.79
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (119 bp):
TATCCAGATCATCTTCTTAATTCATGATTTCATCCCAATCAGCCATACTCGACCTCGACTCAATC
CGATCACTTTATCTCTAAACTCATAATTTTATCTTGATCATTTAATCTCGGCTT
Found at i:5861739 original size:6 final size:6
Alignment explanation
Indices: 5861728--5861756 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5861718 TAGACACCGT
5861728 TTTATA TTTATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTAT
5861757 TTTTCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:5861781 original size:6 final size:7
Alignment explanation
Indices: 5861756--5861780 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5861746 TTTATATTTA
5861756 TTTTTCC
1 TTTTTCC
5861763 TTTTTCC
1 TTTTTCC
5861770 TTTTTCC
1 TTTTTCC
5861777 TTTT
1 TTTT
5861781 CTAGCAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCC
Found at i:5863349 original size:13 final size:12
Alignment explanation
Indices: 5863325--5863400 Score: 54
Period size: 13 Copynumber: 6.5 Consensus size: 12
5863315 ATGAACAAGA
*
5863325 ATAAAGAAAAAT
1 ATAAATAAAAAT
5863337 ATACAATAAAAAT
1 ATA-AATAAAAAT
*
5863350 A-ATAATGAAAA-
1 ATA-AATAAAAAT
5863361 ATAAAT-AAAAT
1 ATAAATAAAAAT
*
5863372 AT-GATAAAAAT
1 ATAAATAAAAAT
*
5863383 AAAAAATAAAAAT
1 -ATAAATAAAAAT
5863396 A-AAAT
1 ATAAAT
5863401 CACAAGTGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
10 6 0.12
11 15 0.29
12 14 0.27
13 17 0.33
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (12 bp):
ATAAATAAAAAT
Found at i:5863365 original size:19 final size:18
Alignment explanation
Indices: 5863341--5863388 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 18
5863331 AAAAATATAC
5863341 AATAAAAATAATAATG-AAA
1 AATAAAAA-AAT-ATGAAAA
5863360 AATAAATAAAATATGATAAA
1 AATAAA-AAAATATGA-AAA
5863380 AATAAAAAA
1 AATAAAAAA
5863389 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 11 0.42
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (18 bp):
AATAAAAAAATATGAAAA
Found at i:5872685 original size:17 final size:17
Alignment explanation
Indices: 5872659--5872698 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5872649 AAGGTTTAAA
*
5872659 GTTTTTGGGTTTGGAAG
1 GTTTTAGGGTTTGGAAG
* *
5872676 GTTTTAGGGTTTTGATG
1 GTTTTAGGGTTTGGAAG
5872693 GTTTTA
1 GTTTTA
5872699 AGACTTAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (17 bp):
GTTTTAGGGTTTGGAAG
Found at i:5873223 original size:10 final size:10
Alignment explanation
Indices: 5873208--5873251 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
5873198 AACTTAGATT
5873208 TTATTTATTA
1 TTATTTATTA
*
5873218 TTATTTATTG
1 TTATTTATTA
*
5873228 TTATTTACTA
1 TTATTTATTA
5873238 TTA-TTATTA
1 TTATTTATTA
*
5873247 ATATT
1 TTATT
5873252 GACAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:5876538 original size:1 final size:1
Alignment explanation
Indices: 5876534--5876569 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
5876524 GGGCTAACAG
* *
5876534 TTTTTTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5876570 GGGGGGGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:5876556 original size:19 final size:18
Alignment explanation
Indices: 5876534--5876569 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5876524 GGGCTAACAG
5876534 TTTTTTTTTTCTTTTTTTC
1 TTTTTTTTTT-TTTTTTTC
5876553 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
5876570 GGGGGGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTTC
Found at i:5881521 original size:34 final size:33
Alignment explanation
Indices: 5881470--5881538 Score: 111
Period size: 34 Copynumber: 2.1 Consensus size: 33
5881460 TAGACATGAT
* *
5881470 CATACGGCCCTGCTAACGGGTTATAGTAGTTAG
1 CATAAGGCCCTGCTAACGGGTTATAATAGTTAG
5881503 CATAAGGCCCTGGCTAACGGGTTATAATAGTTAG
1 CATAAGGCCCT-GCTAACGGGTTATAATAGTTAG
5881537 CA
1 CA
5881539 ATGATCATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 10 0.30
34 23 0.70
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (33 bp):
CATAAGGCCCTGCTAACGGGTTATAATAGTTAG
Found at i:5881674 original size:21 final size:21
Alignment explanation
Indices: 5881649--5881723 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
5881639 ATGATTTACG
5881649 ATGATTTTTAAAGACTGATTC
1 ATGATTTTTAAAGACTGATTC
*
5881670 ATGATTTGTATATAAAGA-TGATTATG
1 ATGA-TT-T-T-TAAAGACTGA-T-TC
* *
5881696 ATGATTTTTAATGACTGATAC
1 ATGATTTTTAAAGACTGATTC
5881717 ATGATTT
1 ATGATTT
5881724 GGTTTGATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
21 11 0.26
22 8 0.19
23 5 0.12
24 5 0.12
25 9 0.21
26 5 0.12
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (21 bp):
ATGATTTTTAAAGACTGATTC
Found at i:5883442 original size:56 final size:58
Alignment explanation
Indices: 5883328--5883480 Score: 170
Period size: 56 Copynumber: 2.6 Consensus size: 58
5883318 ATTTTGAAAT
*
5883328 ATATTTTTTTGAAAT-TTTTTTATTTTTTAAGAAAAATTAATACTTTCAACTATTCCTTAA
1 ATATTTTTTAGAAATATTTTTTA---TTTAAGAAAAATTAATACTTTCAACTATTCCTTAA
* *
5883388 ATATTTTTTGGAAATATTTTTTATTTAA-AAAAATTAATAC-TTCAACTTTTCCTTAA
1 ATATTTTTTAGAAATATTTTTTATTTAAGAAAAATTAATACTTTCAACTATTCCTTAA
** * *
5883444 A-AAATTTTAAAAATTATTTTTTATTTAGGAAGAAATT
1 ATATTTTTTAGAAA-TATTTTTTATTTAAGAA-AAATT
5883481 TAACCTCCAT
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
55 8 0.10
56 29 0.35
57 14 0.17
58 10 0.12
60 14 0.17
61 7 0.09
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (58 bp):
ATATTTTTTAGAAATATTTTTTATTTAAGAAAAATTAATACTTTCAACTATTCCTTAA
Found at i:5885290 original size:15 final size:15
Alignment explanation
Indices: 5885270--5885318 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
5885260 AAAAAATAGA
*
5885270 AATTCAAAGGTTCGT
1 AATTCAAAGATTCGT
*
5885285 AATTCAAAGATTCCT
1 AATTCAAAGATTCGT
5885300 AATGTTCAAAGATTCGT
1 AA--TTCAAAGATTCGT
5885317 AA
1 AA
5885319 GATTTTCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 15 0.52
17 14 0.48
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (15 bp):
AATTCAAAGATTCGT
Found at i:5885367 original size:35 final size:35
Alignment explanation
Indices: 5885311--5885384 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
5885301 ATGTTCAAAG
* *
5885311 ATTCGTAAGATTTTCAGATTCGCAAGAA-TTTCAT
1 ATTCGCAAGATTTTCAAATTCGCAAGAATTTTCAT
5885345 ATTCGCAAGAATTTTCAAATTCGCAAGAATTTTCAT
1 ATTCGCAAG-ATTTTCAAATTCGCAAGAATTTTCAT
5885381 ATTC
1 ATTC
5885385 ATAATAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 8 0.22
35 18 0.50
36 10 0.28
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (35 bp):
ATTCGCAAGATTTTCAAATTCGCAAGAATTTTCAT
Found at i:5885393 original size:18 final size:18
Alignment explanation
Indices: 5885311--5885384 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
5885301 ATGTTCAAAG
* *
5885311 ATTCGTAAG-ATTTTCAG
1 ATTCGCAAGAATTTTCAT
5885328 ATTCGCAAGAA-TTTCAT
1 ATTCGCAAGAATTTTCAT
*
5885345 ATTCGCAAGAATTTTCAA
1 ATTCGCAAGAATTTTCAT
5885363 ATTCGCAAGAATTTTCAT
1 ATTCGCAAGAATTTTCAT
5885381 ATTC
1 ATTC
5885385 ATAATAATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
17 24 0.47
18 27 0.53
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTCGCAAGAATTTTCAT
Found at i:5885692 original size:18 final size:18
Alignment explanation
Indices: 5885671--5885709 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5885661 AGATTTTCAT
*
5885671 ATTCGTAAGAATTTAAAA
1 ATTCATAAGAATTTAAAA
*
5885689 ATTCATAAGATTTTAAAA
1 ATTCATAAGAATTTAAAA
5885707 ATT
1 ATT
5885710 TGCCAAAATT
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:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
ATTCATAAGAATTTAAAA
Found at i:5885706 original size:17 final size:17
Alignment explanation
Indices: 5885654--5885706 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5885644 AAGACTTCAG
* * *
5885654 ATTCTTAAGATTTTCAT
1 ATTCATAAGATTTTAAA
* *
5885671 ATTCGTAAGAATTTAAAA
1 ATTCATAAG-ATTTTAAA
5885689 ATTCATAAGATTTTAAA
1 ATTCATAAGATTTTAAA
5885706 A
1 A
5885707 ATTTGCCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (17 bp):
ATTCATAAGATTTTAAA
Found at i:5885767 original size:17 final size:17
Alignment explanation
Indices: 5885747--5885799 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
5885737 AAAGATTTGC
*
5885747 AAGAATTGAAGATTCAT
1 AAGAATTAAAGATTCAT
* *
5885764 AAGAACTCAA-ATTCAT
1 AAGAATTAAAGATTCAT
*
5885780 AAGAATTAAAGATTCGT
1 AAGAATTAAAGATTCAT
5885797 AAG
1 AAG
5885800 GTTTTTTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.26
Consensus pattern (17 bp):
AAGAATTAAAGATTCAT
Found at i:5887282 original size:26 final size:26
Alignment explanation
Indices: 5887229--5887284 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
5887219 TATTTTCACA
* *
5887229 TTTTCATTTTTTTCATTTTTCACCTT
1 TTTTCATTTTCTTCATTTTGCACCTT
*
5887255 TTTTTATTTTCTTCATTTTGCA--TT
1 TTTTCATTTTCTTCATTTTGCACCTT
5887279 TTTTCA
1 TTTTCA
5887285 CTTCATCCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 7 0.27
26 19 0.73
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTCATTTTCTTCATTTTGCACCTT
Found at i:5890627 original size:4 final size:4
Alignment explanation
Indices: 5890620--5890648 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5890610 ATAATAAGCA
5890620 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
5890649 TCTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5891018 original size:86 final size:86
Alignment explanation
Indices: 5890873--5891030 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 86
5890863 ACTCATACAA
* * * *
5890873 TAATTTTAATCAATTATAATATGAGAGGTATTTTTGTAATTATGGTATGAGAGCATTTTCATAAT
1 TAATTTTAATCAATTATAATATGACAAGTATTTTTGCAATTATGGTAAGAGAGCATTTTCATAAT
5890938 TATGGTTATAGAGTATTAAAG
66 TATGGTTATAGAGTATTAAAG
* *
5890959 TAATTTTAA-CAAATTATAATATGACAAGTGTTTTTGCAATTATGGTAAGA-AGGCATTTTCGTA
1 TAATTTTAATC-AATTATAATATGACAAGTATTTTTGCAATTATGGTAAGAGA-GCATTTTCATA
5891022 ATTATGGTT
64 ATTATGGTT
5891031 GTTGAGGGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
85 2 0.03
86 62 0.97
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (86 bp):
TAATTTTAATCAATTATAATATGACAAGTATTTTTGCAATTATGGTAAGAGAGCATTTTCATAAT
TATGGTTATAGAGTATTAAAG
Found at i:5892017 original size:16 final size:16
Alignment explanation
Indices: 5891996--5892026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5891986 AATAAAGTGG
5891996 ATCAAAAAAAATTTAA
1 ATCAAAAAAAATTTAA
*
5892012 ATCAAAAAATATTTA
1 ATCAAAAAAAATTTA
5892027 TCAATTATGT
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:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
ATCAAAAAAAATTTAA
Found at i:5892159 original size:21 final size:21
Alignment explanation
Indices: 5892135--5892174 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5892125 GAAAAAACTT
5892135 AAAAA-AAAAAAGTAAAAAAGC
1 AAAAATAAAAAA-TAAAAAAGC
5892156 AAAAATAAAAAATAAAAAA
1 AAAAATAAAAAATAAAAAA
5892175 AATTTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAATAAAAAATAAAAAAGC
Found at i:5892725 original size:24 final size:24
Alignment explanation
Indices: 5892698--5892746 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5892688 TATATTTTTT
*
5892698 ATAATTATAATTAAAAATATTATA
1 ATAATTATAATTAAAAATAATATA
* *
5892722 ATAATTTTAATTAAATATAATATA
1 ATAATTATAATTAAAAATAATATA
5892746 A
1 A
5892747 AAATATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTATAATTAAAAATAATATA
Found at i:5892761 original size:35 final size:34
Alignment explanation
Indices: 5892703--5892771 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
5892693 TTTTTATAAT
*
5892703 TATAATTAAAAATATTATAATAATTTTAATTAAA
1 TATAATTAAAAATATTATAATAATTATAATTAAA
* * *
5892737 TATAATATAAAAATATTTTCATAATTATGATTAAA
1 TATAAT-TAAAAATATTATAATAATTATAATTAAA
5892772 AAGTTTGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 6 0.20
35 24 0.80
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (34 bp):
TATAATTAAAAATATTATAATAATTATAATTAAA
Found at i:5893081 original size:19 final size:18
Alignment explanation
Indices: 5893053--5893088 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5893043 AATATATTTT
5893053 TTTATAATTTTTTAAAAA
1 TTTATAATTTTTTAAAAA
5893071 TTTATTAATTTTTTAAAA
1 TTTA-TAATTTTTTAAAA
5893089 GGAAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATAATTTTTTAAAAA
Found at i:5893632 original size:15 final size:15
Alignment explanation
Indices: 5893600--5893639 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5893590 CATAAATATA
* *
5893600 AAAATAAATATAATAT
1 AAAA-AAATAAAAAAT
5893616 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
5893631 AAAAAAATA
1 AAAAAAATA
5893640 CTTTATCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:5894964 original size:104 final size:104
Alignment explanation
Indices: 5894782--5894992 Score: 377
Period size: 104 Copynumber: 2.0 Consensus size: 104
5894772 TGGACTTGTT
* * *
5894782 TAAACATGTTCTTCCTTCAACATGAATTAAACTTACCGAACCATGCTGTCAATGATTTAAAAATT
1 TAAACATGTTCTTCCTTCAACATGAATTAAACTTACCAAACCATGCTGTCAATGAATTAAAAAAT
*
5894847 TTCCCAAGGAGCATGCATGAACATGCAGTAAAATGCAGA
66 TTCCCAAGAAGCATGCATGAACATGCAGTAAAATGCAGA
*
5894886 TAAACATGTTTTTCCTTCAACATGAATTAAACTTACCAAACCATGCTGTCAATGAATTAAAAAAT
1 TAAACATGTTCTTCCTTCAACATGAATTAAACTTACCAAACCATGCTGTCAATGAATTAAAAAAT
5894951 TTCCCAAGAAGCATGCATGAACATGCAGTAAAATGCAGA
66 TTCCCAAGAAGCATGCATGAACATGCAGTAAAATGCAGA
5894990 TAA
1 TAA
5894993 TGAGGTCACA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (104 bp):
TAAACATGTTCTTCCTTCAACATGAATTAAACTTACCAAACCATGCTGTCAATGAATTAAAAAAT
TTCCCAAGAAGCATGCATGAACATGCAGTAAAATGCAGA
Found at i:5901673 original size:26 final size:24
Alignment explanation
Indices: 5901637--5901695 Score: 91
Period size: 26 Copynumber: 2.4 Consensus size: 24
5901627 TTAATATCAC
5901637 TATTAAAATATTAAAATTATTTAT
1 TATTAAAATATTAAAATTATTTAT
*
5901661 TATTAAAGTATATTGAAATTATTTAT
1 TATTAAA--ATATTAAAATTATTTAT
5901687 TATTAAAAT
1 TATTAAAAT
5901696 TACTAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 9 0.28
26 23 0.72
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
TATTAAAATATTAAAATTATTTAT
Found at i:5901832 original size:13 final size:13
Alignment explanation
Indices: 5901781--5901844 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
5901771 TAAAATAAAA
*
5901781 TTATTTATTATTC
1 TTATTTATTAATC
*
5901794 TTTATATTATTCAT-
1 -TTAT-TTATTAATC
*
5901808 TAATATTA-TAATC
1 TTAT-TTATTAATC
*
5901821 TTATTTATTAATA
1 TTATTTATTAATC
5901834 TTATTTATTAA
1 TTATTTATTAA
5901845 CAATATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
12 6 0.15
13 25 0.61
14 4 0.10
15 6 0.15
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTTATTAATC
Found at i:5901874 original size:41 final size:42
Alignment explanation
Indices: 5901823--5901912 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 42
5901813 TTATAATCTT
*
5901823 ATTTATTAATATTATTTATTAACAAT-ATATAATTTATCAAT-A
1 ATTTA-TAATATTATTTATTAA-AATAATATAATTTATAAATAA
* *
5901865 ATTTATAATATTATTTATTAATATAATATTATTTATAAATAA
1 ATTTATAATATTATTTATTAAAATAATATAATTTATAAATAA
5901907 ATTTAT
1 ATTTAT
5901913 GCTCAAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 2 0.05
41 29 0.67
42 12 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (42 bp):
ATTTATAATATTATTTATTAAAATAATATAATTTATAAATAA
Found at i:5901888 original size:13 final size:13
Alignment explanation
Indices: 5901816--5901888 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
5901806 ATTAATATTA
*
5901816 TAATCTTATTTAT
1 TAATATTATTTAT
5901829 TAATATTATTTAT
1 TAATATTATTTAT
5901842 TAACAATATATAATTTAT
1 T---AATAT-T-ATTTAT
*
5901860 CAATA--ATTTA-
1 TAATATTATTTAT
5901870 TAATATTATTTAT
1 TAATATTATTTAT
5901883 TAATAT
1 TAATAT
5901889 AATATTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
10 4 0.08
11 5 0.10
12 5 0.10
13 19 0.39
15 4 0.08
16 5 0.10
17 1 0.02
18 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (13 bp):
TAATATTATTTAT
Found at i:5901889 original size:18 final size:18
Alignment explanation
Indices: 5901797--5901905 Score: 73
Period size: 18 Copynumber: 5.9 Consensus size: 18
5901787 ATTATTCTTT
*
5901797 ATATTATTCATTAATAT-
1 ATATTATTTATTAATATA
* *
5901814 -TATAATCTTATTTAT-TA
1 ATATTAT-TTATTAATATA
*
5901831 ATATTATTTATTAACA-A
1 ATATTATTTATTAATATA
*
5901848 TATATAATTTATCAATAATTTATA
1 -ATATTATTTAT---TAA--TATA
5901872 ATATTATTTATTAATATA
1 ATATTATTTATTAATATA
*
5901890 ATATTATTTATAAATA
1 ATATTATTTATTAATA
5901906 AATTTATGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
16 6 0.08
17 13 0.18
18 34 0.48
20 3 0.04
21 3 0.04
23 11 0.15
24 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTATTTATTAATATA
Found at i:5914062 original size:2 final size:2
Alignment explanation
Indices: 5914055--5914081 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5914045 ATGTTTTAGC
5914055 TA 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 TA T
5914082 TTTCTTTCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5915545 original size:13 final size:13
Alignment explanation
Indices: 5915527--5915556 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5915517 GGGTTGAGGG
*
5915527 AATTCCCTTCTTC
1 AATTCCATTCTTC
5915540 AATTCCATTCTTC
1 AATTCCATTCTTC
5915553 AATT
1 AATT
5915557 GTGTGATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTCCATTCTTC
Found at i:5916395 original size:17 final size:17
Alignment explanation
Indices: 5916375--5916427 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
5916365 ATTTCAAAAA
5916375 TAAAATCTTAAATACAC
1 TAAAATCTTAAATACAC
* *
5916392 TAAAATATTTAAA-A-AA
1 TAAAAT-CTTAAATACAC
*
5916408 TAAAACCTTAAATACAC
1 TAAAATCTTAAATACAC
5916425 TAA
1 TAA
5916428 CCCGATGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 11 0.39
18 5 0.18
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAATCTTAAATACAC
Found at i:5916407 original size:33 final size:33
Alignment explanation
Indices: 5916360--5916427 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
5916350 CGTGAAGAAA
* *
5916360 AAAATATTTCAAAAATAAAATCTTAAATACACT
1 AAAATATTTAAAAAATAAAACCTTAAATACACT
5916393 AAAATATTTAAAAAATAAAACCTTAAATACACT
1 AAAATATTTAAAAAATAAAACCTTAAATACACT
5916426 AA
1 AA
5916428 CCCGATGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (33 bp):
AAAATATTTAAAAAATAAAACCTTAAATACACT
Found at i:5916440 original size:33 final size:33
Alignment explanation
Indices: 5916370--5916443 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
5916360 AAAATATTTC
* * *
5916370 AAAAATAAAATCTTAAATACACTAAAATATTTA
1 AAAAATAAAACCTTAAATACACTAAAAGATGTA
**
5916403 AAAAATAAAACCTTAAATACACTAACCCGATGTA
1 AAAAATAAAACCTTAAATACACTAA-AAGATGTA
5916437 AAAAATA
1 AAAAATA
5916444 CACTAACTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (33 bp):
AAAAATAAAACCTTAAATACACTAAAAGATGTA
Found at i:5919307 original size:2 final size:2
Alignment explanation
Indices: 5919300--5919326 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5919290 GTGAGAGGGC
5919300 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
5919327 TAAAACAAAC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5932459 original size:22 final size:23
Alignment explanation
Indices: 5932416--5932464 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
5932406 CAAAGTTTCT
*
5932416 CTAAAATTATTTTCGATAACTAA
1 CTAAAATTATATTCGATAACTAA
*
5932439 CTAAAATTA-ATTCGATGACTAA
1 CTAAAATTATATTCGATAACTAA
5932461 CTAA
1 CTAA
5932465 TTAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (23 bp):
CTAAAATTATATTCGATAACTAA
Found at i:5933553 original size:13 final size:13
Alignment explanation
Indices: 5933535--5933563 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5933525 GGTCAGAAGT
5933535 ACAAATTTAACCA
1 ACAAATTTAACCA
5933548 ACAAATTTAACCA
1 ACAAATTTAACCA
5933561 ACA
1 ACA
5933564 TACCATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (13 bp):
ACAAATTTAACCA
Found at i:5936874 original size:84 final size:86
Alignment explanation
Indices: 5936697--5936875 Score: 195
Period size: 84 Copynumber: 2.1 Consensus size: 86
5936687 GTTTTGACAG
* * * *
5936697 CACAGTTTGTTTGGAAGAAAATCAGGGTGAAATTGCTGCTGATGTTTCTTGTTCAAAAGAATTAA
1 CACAGTTTGTTTGGAAGAAAATCAGGGTCAAAGTGCTGC-GATGGTTCTAGTTCAAAAGAATTAA
* * *
5936762 TGGGTGATATGCATGGTGATAG
65 TGGGTGATATGCATGGTAACAA
** * * *
5936784 TGCAGTTTTTTTGGAAGAAAATCAGGGTCAAAGTG-TG-GATGGTTCTAGTTCAAAGGAATTGAT
1 CACAGTTTGTTTGGAAGAAAATCAGGGTCAAAGTGCTGCGATGGTTCTAGTTCAAAAGAATTAAT
5936847 GGGTGATAGGTGCA-GG-AACAA
66 GGGTGATA--TGCATGGTAACAA
5936868 CACAGTTT
1 CACAGTTT
5936876 ACTCAAATGG
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
84 38 0.50
85 2 0.03
86 6 0.08
87 30 0.39
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.31
Consensus pattern (86 bp):
CACAGTTTGTTTGGAAGAAAATCAGGGTCAAAGTGCTGCGATGGTTCTAGTTCAAAAGAATTAAT
GGGTGATATGCATGGTAACAA
Found at i:5957290 original size:25 final size:25
Alignment explanation
Indices: 5957229--5957291 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
5957219 TTATATATTT
* *
5957229 ATATTGTATTTTATATAAAAATAAT
1 ATATTATATTTTATATAAAAATAAA
**
5957254 ATATTATAATTTATATATAATTATAAA
1 ATATTAT-ATTT-TATATAAAAATAAA
5957281 ATATT-TATTTT
1 ATATTATATTTT
5957292 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 1 0.03
25 10 0.31
26 5 0.16
27 16 0.50
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
ATATTATATTTTATATAAAAATAAA
Found at i:5964601 original size:24 final size:24
Alignment explanation
Indices: 5964574--5964620 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5964564 CTTTATAGTG
*
5964574 ATTAAAGCAGTACCTGGTAGTTGC
1 ATTAAAGCAGTACATGGTAGTTGC
* * *
5964598 ATTAAGGGAGTGCATGGTAGTTG
1 ATTAAAGCAGTACATGGTAGTTG
5964621 AATCTTAACC
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:0.28, C:0.11, G:0.32, T:0.30
Consensus pattern (24 bp):
ATTAAAGCAGTACATGGTAGTTGC
Found at i:5965029 original size:20 final size:19
Alignment explanation
Indices: 5965004--5965045 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5964994 AATTTTTCTG
*
5965004 TTATTTGTTGATTTTCTTAT
1 TTATTTATTGATTTT-TTAT
*
5965024 TTATTTATTTATTTTTTAT
1 TTATTTATTGATTTTTTAT
5965043 TTA
1 TTA
5965046 CATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (19 bp):
TTATTTATTGATTTTTTAT
Found at i:5966554 original size:25 final size:25
Alignment explanation
Indices: 5966526--5966575 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5966516 CTATCACTTT
*
5966526 TCAAAGAAAACA-TAAACAAAAAAAA
1 TCAAAGAAAAAATTAAA-AAAAAAAA
5966551 TCAAAGAAAAAATTAAAAAAAAAAA
1 TCAAAGAAAAAATTAAAAAAAAAAA
5966576 CACAATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.78, C:0.08, G:0.04, T:0.10
Consensus pattern (25 bp):
TCAAAGAAAAAATTAAAAAAAAAAA
Found at i:5974686 original size:32 final size:32
Alignment explanation
Indices: 5974635--5974696 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5974625 GCATCACTTG
* *
5974635 CATCTGCATCATGAGAAAGACATTTGCATTCA
1 CATCTACATCATGAAAAAGACATTTGCATTCA
*
5974667 CATCTACATTATGAAAAAGACATTTGCATT
1 CATCTACATCATGAAAAAGACATTTGCATT
5974697 TTCATCACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
CATCTACATCATGAAAAAGACATTTGCATTCA
Found at i:5975352 original size:22 final size:22
Alignment explanation
Indices: 5975265--5975368 Score: 61
Period size: 22 Copynumber: 4.8 Consensus size: 22
5975255 CAACTAGTAC
*
5975265 TTAAGCCTAGATTAGCTGACACT
1 TTAAGCCCAGATTAGCTGACA-T
* *
5975288 TTAAGCCCA-AATA--TGGCAT
1 TTAAGCCCAGATTAGCTGACAT
* * * * **
5975307 TTAAACCCATATCAACTGGTAT
1 TTAAGCCCAGATTAGCTGACAT
*
5975329 TTAAGCCTAGATTAGCTGACAT
1 TTAAGCCCAGATTAGCTGACAT
* *
5975351 TTGAAACCCAAATTAGCT
1 TT-AAGCCCAGATTAGCT
5975369 AGCACTCTAA
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 9 0.15
20 6 0.10
22 25 0.42
23 20 0.33
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (22 bp):
TTAAGCCCAGATTAGCTGACAT
Found at i:5975384 original size:23 final size:22
Alignment explanation
Indices: 5975358--5975419 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
5975348 CATTTGAAAC
*
5975358 CCAAATTAGCTAGCACTCTAAAT
1 CCAAATTAGCTAGCACT-TAAAG
* * *
5975381 CCAAATTAACTAACACTTTAAG
1 CCAAATTAGCTAGCACTTAAAG
*
5975403 CCTAAATTAGCTGGCAC
1 CC-AAATTAGCTAGCAC
5975420 ATTTGAGATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26
Consensus pattern (22 bp):
CCAAATTAGCTAGCACTTAAAG
Found at i:5975526 original size:23 final size:24
Alignment explanation
Indices: 5975471--5975528 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
5975461 AAATTGGCTA
*
5975471 GCACTTTAA-ACTCAGTTTAGTTG
1 GCACTTTAAGCCTCAGTTTAGTTG
* *
5975494 GCATTTTAAGCCT-AGTTTAGTTT
1 GCACTTTAAGCCTCAGTTTAGTTG
5975517 GCACTTTAAGCC
1 GCACTTTAAGCC
5975529 CAGATCAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (24 bp):
GCACTTTAAGCCTCAGTTTAGTTG
Found at i:5987663 original size:47 final size:47
Alignment explanation
Indices: 5987559--5987830 Score: 314
Period size: 47 Copynumber: 5.7 Consensus size: 47
5987549 AGAACTCAAT
* *
5987559 AGTTGTTGAGCCTCTGCTGAGACGAGCTCTTTCTAAAATGAGATTTTAA
1 AGTTGTTGAGCCTCTGCTGAGAAGAGCT-TTT-TCAAATGAGATTTTAA
* **
5987608 AGTTGTTGAGCCTCTACTGAGATTAGCTTTTTCAAATG-GATTTTTAA
1 AGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTCAAATGAGA-TTTTAA
*
5987655 AGTTGTTGAGCCTTTGCTGAGAAGAGCTTTTTCAAATGAGATTTTAA
1 AGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTCAAATGAGATTTTAA
* * *
5987702 AGTAGTTGAGCCTCTGTTGAGAAAAGCTTTTTCTAAGATGAGATTTTAA
1 AGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTC-AA-ATGAGATTTTAA
* * * * *
5987751 AGTTGTTGAGCCTCTACTTA-AAGAAACTTTTTTCAAATAAAATTTTAA
1 AGTTGTTGAGCCTCTGCTGAGAAG-AGC-TTTTTCAAATGAGATTTTAA
* * *
5987799 AGTTGTTGAACCTCCGCTGAGAGGAGCTTTTT
1 AGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTT
5987831 TTTTTCAGAT
Statistics
Matches: 190, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
46 2 0.01
47 86 0.45
48 37 0.19
49 59 0.31
50 6 0.03
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (47 bp):
AGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTCAAATGAGATTTTAA
Found at i:5987743 original size:143 final size:144
Alignment explanation
Indices: 5987563--5987830 Score: 376
Period size: 143 Copynumber: 1.9 Consensus size: 144
5987553 CTCAATAGTT
**
5987563 GTTGAGCCTCTGCTGAGACGAGCTCTTTCTAAAATGAGATTTTAAAGTTGTTGAGCCTCTACTGA
1 GTTGAGCCTCTGCTGAGAAAAGCTCTTTCTAAAATGAGATTTTAAAGTTGTTGAGCCTCTACTGA
* ** * ** * * **
5987628 GATTAGC-TTTTTCAAATGGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAAGAGCTTTTTCAAAT
66 AAGAAACTTTTTTCAAATAAAATTTTAAAGTTGTTGAACCTCCGCTGAGAAGAGCTTTTTCAAAT
5987692 GAGATTTTAAAGTA
131 GAGATTTTAAAGTA
* * * *
5987706 GTTGAGCCTCTGTTGAGAAAAGCTTTTTCTAAGATGAGATTTTAAAGTTGTTGAGCCTCTACTTA
1 GTTGAGCCTCTGCTGAGAAAAGCTCTTTCTAAAATGAGATTTTAAAGTTGTTGAGCCTCTACTGA
*
5987771 AAGAAACTTTTTTCAAATAAAATTTTAAAGTTGTTGAACCTCCGCTGAGAGGAGCTTTTT
66 AAGAAACTTTTTTCAAATAAAATTTTAAAGTTGTTGAACCTCCGCTGAGAAGAGCTTTTT
5987831 TTTTTCAGAT
Statistics
Matches: 107, Mismatches: 17, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
143 62 0.58
144 45 0.42
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (144 bp):
GTTGAGCCTCTGCTGAGAAAAGCTCTTTCTAAAATGAGATTTTAAAGTTGTTGAGCCTCTACTGA
AAGAAACTTTTTTCAAATAAAATTTTAAAGTTGTTGAACCTCCGCTGAGAAGAGCTTTTTCAAAT
GAGATTTTAAAGTA
Found at i:5987798 original size:97 final size:94
Alignment explanation
Indices: 5987559--5987830 Score: 278
Period size: 96 Copynumber: 2.8 Consensus size: 94
5987549 AGAACTCAAT
* * * * * * *
5987559 AGTTGTTGAGCCTCTGCTGAGACGAGCTCTTTCTAAAATGAGATTTTAAAGTTGTTGAGCCTCTA
1 AGTTGTTGAGCCTCTACTGAGAAGAACT-TTT-TCAAATAAAATTTTAAAGTTGTTGAGCCTCTG
**
5987624 CTGAGATTAGCTTTTTCAAATGGATTTTTAA
64 CTGAGAAAAGCTTTTTCAAATGGATTTTTAA
* * * * * * *
5987655 AGTTGTTGAGCCTTTGCTGAGAAGAGCTTTTTCAAATGAGATTTTAAAGTAGTTGAGCCTCTGTT
1 AGTTGTTGAGCCTCTACTGAGAAGAACTTTTTCAAATAAAATTTTAAAGTTGTTGAGCCTCTGCT
5987720 GAGAAAAGCTTTTTCTAAGATGAGA-TTTTAA
66 GAGAAAAGCTTTTTC-AA-ATG-GATTTTTAA
* * *
5987751 AGTTGTTGAGCCTCTACTTA-AAGAAACTTTTTTCAAATAAAATTTTAAAGTTGTTGAACCTCCG
1 AGTTGTTGAGCCTCTACTGAGAAG-AAC-TTTTTCAAATAAAATTTTAAAGTTGTTGAGCCTCTG
**
5987815 CTGAGAGGAGCTTTTT
64 CTGAGAAAAGCTTTTT
5987831 TTTTTCAGAT
Statistics
Matches: 151, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
94 43 0.28
95 8 0.05
96 54 0.36
97 46 0.30
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (94 bp):
AGTTGTTGAGCCTCTACTGAGAAGAACTTTTTCAAATAAAATTTTAAAGTTGTTGAGCCTCTGCT
GAGAAAAGCTTTTTCAAATGGATTTTTAA
Found at i:5988129 original size:10 final size:9
Alignment explanation
Indices: 5988125--5988166 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
5988115 CAAAAAATAC
5988125 AAAAACAAA
1 AAAAACAAA
5988134 ATAAAACAAA
1 A-AAAACAAA
5988144 ATAAAACAAA
1 A-AAAACAAA
5988154 AAAATA-AAA
1 AAAA-ACAAA
5988163 AAAA
1 AAAA
5988167 GAATATTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 11 0.35
10 20 0.65
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAAACAAA
Found at i:5988132 original size:15 final size:16
Alignment explanation
Indices: 5988112--5988144 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5988102 AATAAAAATT
*
5988112 AAACAAAA-AATACAA
1 AAACAAAATAAAACAA
5988127 AAACAAAATAAAACAA
1 AAACAAAATAAAACAA
5988143 AA
1 AA
5988145 TAAAACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (16 bp):
AAACAAAATAAAACAA
Found at i:5988157 original size:23 final size:22
Alignment explanation
Indices: 5988116--5988166 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
5988106 AAAATTAAAC
*
5988116 AAAAAATACAAAAACAAAATAA
1 AAAAAATACAAAAAAAAAATAA
5988138 AACAAAATA-AAACAAAAAAATAA
1 AA-AAAATACAAA-AAAAAAATAA
5988161 AAAAAA
1 AAAAAA
5988167 GAATATTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (22 bp):
AAAAAATACAAAAAAAAAATAA
Found at i:5991144 original size:3 final size:3
Alignment explanation
Indices: 5991040--5991126 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
5991030 CGGATTAGTC
5991040 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5991088 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5991127 TATCATTTAG
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5994126 original size:25 final size:25
Alignment explanation
Indices: 5994094--5994165 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
5994084 TTTTTTTATT
5994094 TATAATAAAATAAAAATTAAAAATA
1 TATAATAAAATAAAAATTAAAAATA
* *
5994119 TATAAT-AAATATAAATATAAAAAAA
1 TATAATAAAATAAAAAT-TAAAAATA
5994144 TATAA-AAACA-AAAAA-TAAAAAT
1 TATAATAAA-ATAAAAATTAAAAAT
5994166 TACGTTACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.15
24 9 0.22
25 24 0.60
26 1 0.03
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (25 bp):
TATAATAAAATAAAAATTAAAAATA
Found at i:5994146 original size:16 final size:17
Alignment explanation
Indices: 5994103--5994149 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5994093 TTATAATAAA
* *
5994103 ATAAAAATTAAAAATAT
1 ATAAAAAATATAAATAT
*
5994120 ATAATAAATATAAATAT
1 ATAAAAAATATAAATAT
5994137 A-AAAAAATATAAA
1 ATAAAAAATATAAA
5994150 AACAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAAATATAAATAT
Found at i:5994156 original size:16 final size:16
Alignment explanation
Indices: 5994125--5994158 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5994115 AATATATAAT
* *
5994125 AAATATAAATATAAAA
1 AAATATAAAAACAAAA
5994141 AAATATAAAAACAAAA
1 AAATATAAAAACAAAA
5994157 AA
1 AA
5994159 TAAAAATTAC
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:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATATAAAAACAAAA
Found at i:5995354 original size:13 final size:13
Alignment explanation
Indices: 5995331--5995355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5995321 AAAAAATTGA
5995331 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
5995344 AAAAAAAAAAAG
1 AAAAAAAAAAAG
5995356 AAAGAAGTGT
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:5996004 original size:3 final size:3
Alignment explanation
Indices: 5995996--5996022 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5995986 ATCATCTAAG
5995996 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
5996023 ATGTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5997113 original size:4 final size:4
Alignment explanation
Indices: 5997104--5997130 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5997094 TCTTATAAGG
5997104 CCCT CCCT CCCT CCCT CCCT CCCT CCC
1 CCCT CCCT CCCT CCCT CCCT CCCT CCC
5997131 CCTTTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (4 bp):
CCCT
Found at i:6000728 original size:31 final size:30
Alignment explanation
Indices: 6000693--6000769 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
6000683 AATAATAAAA
6000693 AATTTTAAATATTAT-TTTTAATTAATTATTT
1 AATTTTAAAT-TTATATTTT-ATTAATTATTT
* *
6000724 AATTTTATATTTATAATTTTATTATTTATTT
1 AATTTTAAATTTAT-ATTTTATTAATTATTT
* *
6000755 AA-ATTATATTTATAT
1 AATTTTAAATTTATAT
6000770 AAAAATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 14 0.34
31 21 0.51
32 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
AATTTTAAATTTATATTTTATTAATTATTT
Found at i:6000740 original size:14 final size:15
Alignment explanation
Indices: 6000702--6000752 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
6000692 AAATTTTAAA
*
6000702 TATTATTTTTAA-TT
1 TATTATTTATAATTT
*
6000716 AATTA-TT-TAATTT
1 TATTATTTATAATTT
6000729 TA-TATTTATAATTT
1 TATTATTTATAATTT
6000743 TATTATTTAT
1 TATTATTTAT
6000753 TTAAATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 7 0.23
14 12 0.39
15 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTTATAATTT
Found at i:6000771 original size:32 final size:32
Alignment explanation
Indices: 6000708--6000768 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
6000698 TAAATATTAT
*
6000708 TTTTAATTAATTATTTAATTTTATATTTATAA
1 TTTTAATTAATTATTTAATTATATATTTATAA
* *
6000740 TTTT-ATTATTTATTTAAAT-TATATTTATA
1 TTTTAATTAATTATTTAATTATATATTTATA
6000769 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 10 0.37
31 13 0.48
32 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTTTAATTAATTATTTAATTATATATTTATAA
Found at i:6000862 original size:37 final size:37
Alignment explanation
Indices: 6000799--6000871 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
6000789 AAAAAATAAT
* *
6000799 ATTTTATTAATTTCGAATTAAATTAGATT-GGATATG
1 ATTTTATTAATATCAAATTAAATTAGATTCGGATATG
*
6000835 ATTTTATATAATATCAAATTAAGTTAGATTCGGATAT
1 ATTTTAT-TAATATCAAATTAAATTAGATTCGGATAT
6000872 AAAAAATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 7 0.22
37 19 0.59
38 6 0.19
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.45
Consensus pattern (37 bp):
ATTTTATTAATATCAAATTAAATTAGATTCGGATATG
Found at i:6003630 original size:23 final size:21
Alignment explanation
Indices: 6003586--6003630 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
6003576 TATATATATA
**
6003586 TATATATATTATTAATTTAAT
1 TATATATATTATTAATAAAAT
6003607 TATATATATTATGTTAATAAAAT
1 TATATATATTA--TTAATAAAAT
6003630 T
1 T
6003631 TTTATGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATATATATTATTAATAAAAT
Found at i:6003687 original size:33 final size:33
Alignment explanation
Indices: 6003650--6003718 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
6003640 TACTTTAATT
*
6003650 TTATATATTA-ATTTAATAAAAATATTATATT-TA
1 TTATAT-TTATATATAATAAAAATATTAT-TTATA
*
6003683 TTATATTTATATATAATTAAAATATTATTTATA
1 TTATATTTATATATAATAAAAATATTATTTATA
6003716 TTA
1 TTA
6003719 AAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTATATTTATATATAATAAAAATATTATTTATA
Found at i:6010195 original size:2 final size:2
Alignment explanation
Indices: 6010188--6010215 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6010178 TTCTAGATGC
6010188 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
6010216 CAAATTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6011868 original size:28 final size:28
Alignment explanation
Indices: 6011829--6011885 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
6011819 AAGATCAATA
6011829 AAAGTGCTATGTTTTTAAAATGAAAGTT
1 AAAGTGCTATGTTTTTAAAATGAAAGTT
6011857 AAAGTGCTATGTTTTTAAAATGAAAGTT
1 AAAGTGCTATGTTTTTAAAATGAAAGTT
6011885 A
1 A
6011886 TGTATGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.39
Consensus pattern (28 bp):
AAAGTGCTATGTTTTTAAAATGAAAGTT
Found at i:6016824 original size:10 final size:10
Alignment explanation
Indices: 6016809--6016833 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6016799 AAGATTGGAT
6016809 TTTTTTTTTC
1 TTTTTTTTTC
6016819 TTTTTTTTTC
1 TTTTTTTTTC
6016829 TTTTT
1 TTTTT
6016834 AAGTAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:6017241 original size:13 final size:13
Alignment explanation
Indices: 6017225--6017256 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6017215 AATTATTTTC
6017225 TAAAAAATAAAAA
1 TAAAAAATAAAAA
6017238 TAAAAAATAAAAA
1 TAAAAAATAAAAA
*
6017251 CAAAAA
1 TAAAAA
6017257 TTATTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:6021511 original size:27 final size:27
Alignment explanation
Indices: 6021453--6021511 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
6021443 AGGTTGGATA
*
6021453 GGTTGAGAATCTGATTGTAAAGGGACT
1 GGTTGAGAATATGATTGTAAAGGGACT
* * * * *
6021480 AGTTGAGAATATGGTTTTGAAGGGGCT
1 GGTTGAGAATATGATTGTAAAGGGACT
6021507 GGTTG
1 GGTTG
6021512 GGAAATTGGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.37, T:0.32
Consensus pattern (27 bp):
GGTTGAGAATATGATTGTAAAGGGACT
Found at i:6021526 original size:21 final size:21
Alignment explanation
Indices: 6021500--6021541 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6021490 ATGGTTTTGA
*
6021500 AGGGGCTGGTTGGGAAATTGG
1 AGGGGCTAGTTGGGAAATTGG
*
6021521 AGGGGCTAGTTGGGAAGTTGG
1 AGGGGCTAGTTGGGAAATTGG
6021542 CAAGTCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.52, T:0.24
Consensus pattern (21 bp):
AGGGGCTAGTTGGGAAATTGG
Found at i:6026725 original size:33 final size:33
Alignment explanation
Indices: 6026683--6026748 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6026673 CACTTAAAAA
6026683 ATGTATTTTGTTCCTAGAATTTTCCTGTTGTAG
1 ATGTATTTTGTTCCTAGAATTTTCCTGTTGTAG
6026716 ATGTATTTTGTTCCTAGAATTTTCCTGTTGTAG
1 ATGTATTTTGTTCCTAGAATTTTCCTGTTGTAG
6026749 GAAATGTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (33 bp):
ATGTATTTTGTTCCTAGAATTTTCCTGTTGTAG
Found at i:6026744 original size:17 final size:17
Alignment explanation
Indices: 6026691--6026744 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
6026681 AAATGTATTT
6026691 TGTTCCTAGAATTTTCC
1 TGTTCCTAGAATTTTCC
* *
6026708 TGTT-GTAG-ATGTATT-T
1 TGTTCCTAGAAT-T-TTCC
6026724 TGTTCCTAGAATTTTCC
1 TGTTCCTAGAATTTTCC
6026741 TGTT
1 TGTT
6026745 GTAGGAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
17 14 0.50
18 2 0.07
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.52
Consensus pattern (17 bp):
TGTTCCTAGAATTTTCC
Done.