Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1108
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: 130252
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:6339 original size:1 final size:1
Alignment explanation
Indices: 6333--6423 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
6323 AAATCTTCAC
* * ** * * * **
6333 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
6398 TTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
6424 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:6369 original size:30 final size:31
Alignment explanation
Indices: 6333--6425 Score: 134
Period size: 34 Copynumber: 2.9 Consensus size: 31
6323 AAATCTTCAC
6333 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTT
1 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTT
6364 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTT
1 TTTTTT-TTTTG--TTTTTTTTTTCTTTTTCCTT
* *
6398 TTTTTTTGTT-TTGTTTTTTTCTTTTTCC
1 TTTTTTTTTTGTTTTTTTTTTCTTTTTCC
6426 AATTGCCATG
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
30 17 0.30
31 6 0.11
32 5 0.09
33 3 0.05
34 26 0.46
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (31 bp):
TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTT
Found at i:6387 original size:34 final size:35
Alignment explanation
Indices: 6333--6424 Score: 147
Period size: 35 Copynumber: 2.7 Consensus size: 35
6323 AAATCTTCAC
6333 TTTTTT-TTTTG--TTTTTTTTTTCTTTTTCC-TT
1 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
6364 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
1 TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
6399 TTTTTTGTTTTGTTTTTTTCTTTTTC
1 TTTTTTGTTTTGTTTTTTT-TTTTTC
6425 CAATTGCCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
31 6 0.11
32 5 0.09
34 18 0.32
35 21 0.38
36 6 0.11
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (35 bp):
TTTTTTGTTTTGTTTTTTTTTTTTCTTTTTCCTTT
Found at i:18201 original size:14 final size:13
Alignment explanation
Indices: 18179--18213 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
18169 GATAGATTGC
18179 AATTTAAGATACA
1 AATTTAAGATACA
*
18192 AATATTAAGATTCA
1 AAT-TTAAGATACA
18206 AATTTAAG
1 AATTTAAG
18214 TGAGGATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (13 bp):
AATTTAAGATACA
Found at i:19355 original size:28 final size:26
Alignment explanation
Indices: 19326--19380 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
19316 ATTCAACGAT
19326 AATTAAAAATATAATGATAAAATTTAATAA
1 AATT-AAAATAT-ATGAT-AAATTTAAT-A
*
19356 AATTATAATATATGATAAATTTAAT
1 AATTAAAATATATGATAAATTTAAT
19381 TTTAGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
28 5 0.21
29 6 0.25
30 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (26 bp):
AATTAAAATATATGATAAATTTAATA
Found at i:27473 original size:5 final size:5
Alignment explanation
Indices: 27463--27519 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
27453 ACTATACGAT
*
27463 ATATA ATATA A-A-A AT-TA ATTAAA ATATA ATATA ATATA A-A-A ATATAA
1 ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA ATAT-A
27510 ATATA ATATA
1 ATATA ATATA
27520 TATGTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
3 4 0.09
4 5 0.12
5 27 0.63
6 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:27498 original size:28 final size:29
Alignment explanation
Indices: 27463--27519 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
27453 ACTATACGAT
*
27463 ATATAATATAAAAAT-TAATTAAAATATA
1 ATATAATATAAAAATATAAATAAAATATA
*
27491 ATATAATATAAAAATATAAATATAATATA
1 ATATAATATAAAAATATAAATAAAATATA
27520 TATGTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
ATATAATATAAAAATATAAATAAAATATA
Found at i:27514 original size:19 final size:18
Alignment explanation
Indices: 27483--27519 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
27473 AAAATTAATT
27483 AAAATATAATATAATATA
1 AAAATATAATATAATATA
27501 AAAATATAAATATAATATA
1 AAAATAT-AATATAATATA
27520 TATGTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATATAATATAATATA
Found at i:27585 original size:17 final size:17
Alignment explanation
Indices: 27504--27587 Score: 50
Period size: 17 Copynumber: 4.9 Consensus size: 17
27494 TAATATAAAA
* *
27504 ATATAAATATAATATAT
1 ATATAAATATAAAATTT
*
27521 ATGTAAATATTTTAAAATTT
1 ATATAAATA---TAAAATTT
* *
27541 ATAT-AATCT-GAA-TT
1 ATATAAATATAAAATTT
27555 AT-TAATATATTAAAATTT
1 ATATAA-ATA-TAAAATTT
27573 ATATAAATATAAAAT
1 ATATAAATATAAAAT
27588 ATTTTTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 18
0.66 0.11 0.24
Matches are distributed among these distances:
13 1 0.02
14 5 0.10
15 4 0.08
16 2 0.04
17 16 0.32
18 7 0.14
19 6 0.12
20 9 0.18
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:27619 original size:37 final size:37
Alignment explanation
Indices: 27556--27627 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
27546 ATCTGAATTA
27556 TTAATATATTAAAATTTATATAAATATA-AAATATTT
1 TTAATATATTAAAATTTATATAAATATATAAATATTT
**
27592 TTAATATGATTACGATTTA-ATAAAATATATAAATAT
1 TTAATAT-ATTAAAATTTATAT-AAATATATAAATAT
27628 AATACGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 9 0.29
37 16 0.52
38 6 0.19
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (37 bp):
TTAATATATTAAAATTTATATAAATATATAAATATTT
Found at i:32624 original size:46 final size:47
Alignment explanation
Indices: 32571--32665 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
32561 TTACCTTTTC
32571 TTTTATAGGAGCAAGTATTA-TTTAGATTATAGACTTTATATGGATA
1 TTTTATAGGAGCAAGTATTATTTTAGATTATAGACTTTATATGGATA
* *
32617 TTTTATAGGAGCATGTATTATTTTAGATTATAGACTTTATCTGGATA
1 TTTTATAGGAGCAAGTATTATTTTAGATTATAGACTTTATATGGATA
32664 TT
1 TT
32666 CTCATATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 19 0.41
47 27 0.59
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (47 bp):
TTTTATAGGAGCAAGTATTATTTTAGATTATAGACTTTATATGGATA
Found at i:41066 original size:15 final size:15
Alignment explanation
Indices: 41046--41082 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
41036 GCTTTATATA
41046 TGTGATTAACATGTG
1 TGTGATTAACATGTG
**
41061 TGTGATTAATTTGTG
1 TGTGATTAACATGTG
41076 TGTGATT
1 TGTGATT
41083 CCTTGATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.49
Consensus pattern (15 bp):
TGTGATTAACATGTG
Found at i:43379 original size:2 final size:2
Alignment explanation
Indices: 43372--43404 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43362 TTTGGCTCTT
43372 TA TA TA 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 TA TA TA T
43405 CATGCTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44069 original size:3 final size:3
Alignment explanation
Indices: 44061--44103 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
44051 TGAACAATGA
* * *
44061 GTG GTG GTG GTG GTG GAG GTG GTG GTG GTG GTA GTG GTA GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
44104 AGAACTGGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.07, C:0.00, G:0.63, T:0.30
Consensus pattern (3 bp):
GTG
Found at i:44408 original size:3 final size:3
Alignment explanation
Indices: 44400--44436 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
44390 ATTAACGGAC
44400 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44437 GAGATGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:46521 original size:5 final size:5
Alignment explanation
Indices: 46502--46549 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
46492 GGGTTTCTAG
* * * *
46502 TTTCT CTTCT CTTTCT TTTCG TTTCT TTTCT TTACT TTTCT TTCCT TT
1 TTTCT TTTCT -TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
46550 GGTTTTGGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (5 bp):
TTTCT
Found at i:47524 original size:2 final size:2
Alignment explanation
Indices: 47517--47555 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
47507 GTTTATAAAT
47517 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
47556 TACATATAGA
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:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:52845 original size:19 final size:19
Alignment explanation
Indices: 52807--52844 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
52797 TATTATATAT
*
52807 ATTTATTTTATATAATAAA
1 ATTTATTTAATATAATAAA
52826 ATTTATTTAATAT-ATAAA
1 ATTTATTTAATATAATAAA
52844 A
1 A
52845 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTAATATAATAAA
Found at i:52957 original size:22 final size:21
Alignment explanation
Indices: 52915--52961 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
52905 GAGAGTTAAA
* *
52915 ATTTAATTTATTATTTGAATT
1 ATTTAATTTATTACTTAAATT
52936 GATTTAATCTT-TTACTTAAATT
1 -ATTTAAT-TTATTACTTAAATT
52958 ATTT
1 ATTT
52962 TTTAGATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (21 bp):
ATTTAATTTATTACTTAAATT
Found at i:54988 original size:2 final size:2
Alignment explanation
Indices: 54981--55017 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54971 CTTGGACTAC
54981 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
55018 CTTATCACTT
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:56507 original size:127 final size:127
Alignment explanation
Indices: 56292--56530 Score: 313
Period size: 127 Copynumber: 1.9 Consensus size: 127
56282 AGTTGGCCGA
* * * *
56292 GACGAAACCATACGATCTAACAAGTCAGGAAGGTTAACCAGGATAAAACCATATGTGTCAACGAG
1 GACGAAACCATACGATCCAACAAGTCAGGAAAGTTAACCAGGATAAAACCATACGAGTCAACGAG
* * *
56357 TTAGAAAAGAGTTGGCTGGGACAAAA-TCATATGAACTAACAAGTTAGAAAAGTGTTGATTGG
66 TTAGAAAAGAGTTAGCTGAGACAAAACT-ATATGAACCAACAAGTTAGAAAAGTGTTGATTGG
* * * *
56419 GACGAAACCATACG-TACCAATAAGTCAGGAAAGTTGATC-GAGATGAAACCATACGAGTCAACG
1 GACGAAACCATACGAT-CCAACAAGTCAGGAAAGTTAACCAG-GATAAAACCATACGAGTCAACG
* *
56482 AGTTAGAAAAGGGTTAGTTGAGACAAAACTATATGAACCAACAAGTTAG
64 AGTTAGAAAAGAGTTAGCTGAGACAAAACTATATGAACCAACAAGTTAG
56531 GAGGGTTCAT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
126 2 0.02
127 93 0.97
128 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (127 bp):
GACGAAACCATACGATCCAACAAGTCAGGAAAGTTAACCAGGATAAAACCATACGAGTCAACGAG
TTAGAAAAGAGTTAGCTGAGACAAAACTATATGAACCAACAAGTTAGAAAAGTGTTGATTGG
Found at i:56570 original size:41 final size:42
Alignment explanation
Indices: 56458--56576 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 42
56448 AAAGTTGATC
* * *
56458 GAGATGAAACCATACGAGTCAACGAGTTAGAAAAGGGTTAGTT
1 GAGACGAAACTATATGAGTCAACGAGTTAG-AAAGGGTTAGTT
* ** * *
56501 GAGACAAAACTATATGAACCAACAAGTTAG-GAGGGTTCA-TT
1 GAGACGAAACTATATGAGTCAACGAGTTAGAAAGGGTT-AGTT
56542 -AGGACGAAACTATATGAGTCAACGAGTTAGAAAGG
1 GA-GACGAAACTATATGAGTCAACGAGTTAGAAAGG
56577 AGTTGGACGA
Statistics
Matches: 60, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
40 1 0.02
41 32 0.53
42 4 0.07
43 23 0.38
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (42 bp):
GAGACGAAACTATATGAGTCAACGAGTTAGAAAGGGTTAGTT
Found at i:56581 original size:127 final size:126
Alignment explanation
Indices: 56292--56599 Score: 286
Period size: 127 Copynumber: 2.4 Consensus size: 126
56282 AGTTGGCCGA
* * * * * * * *
56292 GACGAAACCATACG-ATCTAACAAGTCAGGAAGGTT-AACCAGGATAAAACCATATGTGTCAACG
1 GACGAAACCATACGTA-CCAACAAGTCAGAAAAGTTGGACGA-GATGAAACCATACGAGTCAACG
* * * * * *
56355 AGTTAGAAAAGAGTTGGCTGGGACAAAATCATATGAACTAACAAGTTAGAAAAGTGTTGATTGG
64 AGTTAGAAAAGAGTTAGCTGAGACAAAATCATATGAACCAACAAGTTAG-AAAGGGTTCATTAG
* *
56419 GACGAAACCATACGTACCAATAAGTCAGGAAAGTT-GATCGAGATGAAACCATACGAGTCAACGA
1 GACGAAACCATACGTACCAACAAGTCAGAAAAGTTGGA-CGAGATGAAACCATACGAGTCAACGA
* * *
56483 GTTAGAAAAGGGTTAGTTGAGACAAAA-CTATATGAACCAACAAGTTAG-GAGGGTTCATTAG
65 GTTAGAAAAGAGTTAGCTGAGACAAAATC-ATATGAACCAACAAGTTAGAAAGGGTTCATTAG
* * * * *
56544 GACGAAACTATATG-AGTCAACGAGTTAGAAAGGAGTTGGACGAGATGAAACCATAC
1 GACGAAACCATACGTA-CCAACAAGTCAGAAA--AGTTGGACGAGATGAAACCATAC
56600 AAACTAATAA
Statistics
Matches: 150, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
124 1 0.01
125 31 0.21
126 1 0.01
127 112 0.75
128 5 0.03
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (126 bp):
GACGAAACCATACGTACCAACAAGTCAGAAAAGTTGGACGAGATGAAACCATACGAGTCAACGAG
TTAGAAAAGAGTTAGCTGAGACAAAATCATATGAACCAACAAGTTAGAAAGGGTTCATTAG
Found at i:56613 original size:43 final size:43
Alignment explanation
Indices: 56561--57262 Score: 343
Period size: 43 Copynumber: 16.3 Consensus size: 43
56551 CTATATGAGT
* *
56561 CAACGAGTTAGAAAGGAGTTGGACGAGATGAAACCATACAAAC
1 CAACAAGTTAGAAAGGAGTTGGTCGAGATGAAACCATACAAAC
* * * * **
56604 TAATAAGTTA-AAAGGGTGTTGGTCGGGATGAAACCATACGTAC
1 CAACAAGTTAGAAA-GGAGTTGGTCGAGATGAAACCATACAAAC
* * **
56647 CAACAAGTTAGAAAAGAGTTGG-CTAGGACAAAACCATACAAAC
1 CAACAAGTTAGAAAGGAGTTGGTCGA-GATGAAACCATACAAAC
* * * * * * * ***
56690 TAGCAAGTTAGAAGGGTGTTAGCCAAGATGAAACCATATGTAC
1 CAACAAGTTAGAAAGGAGTTGGTCGAGATGAAACCATACAAAC
* * * ** * ** *
56733 CAACAATTTAG-AAGAATATTGGTTAAGATGAAACCACACGTAG
1 CAACAAGTTAGAAAGGA-GTTGGTCGAGATGAAACCATACAAAC
* * * *
56776 CAACGAGTTAGAAAGAAGTTGG-CTAAGATGAAACCATACAAAA
1 CAACAAGTTAGAAAGGAGTTGGTC-GAGATGAAACCATACAAAC
* * ***
56819 CAACAAGTTAGAAAGGTGTTGGTCGGGATGAAACCATATGCAC
1 CAACAAGTTAGAAAGGAGTTGGTCGAGATGAAACCATACAAAC
** * ** *
56862 CAATGAGATAGAAAGGAGTTGGTCGAGACAAAACCATACGAAC
1 CAACAAGTTAGAAAGGAGTTGGTCGAGATGAAACCATACAAAC
* * * ***
56905 CAACAAGTTAGAAAGGTGTTGGTTG-GAATGAAACCACATGTAC
1 CAACAAGTTAGAAAGGAGTTGGTCGAG-ATGAAACCATACAAAC
* ** *
56948 CAATAAGTTAGAAAGGAGTTGG-AAAGGATAAAACCATACAAAC
1 CAACAAGTTAGAAAGGAGTTGGTCGA-GATGAAACCATACAAAC
* * * * *
56991 CAACAAGTTAGAAGGGTA-TTGG-CTAGGACGAAACAATACATAC
1 CAACAAGTTAGAAAGG-AGTTGGTCGA-GATGAAACCATACAAAC
** * * ** *
57034 CAATGAGTTATGAGAGTA-TTGGTCGAGACAAAACCATACATAC
1 CAACAAGTTA-GAAAGGAGTTGGTCGAGATGAAACCATACAAAC
** * * *
57077 CAATGAGTTAGAAA-AAGGTTGG-CCAGGATGAAACCATACAAAG
1 CAACAAGTTAGAAAGGA-GTTGGTCGA-GATGAAACCATACAAAC
* * * * *
57120 CAATAAGTTAGAAA-GATATTGGTCGAGATGTAACAATACATAC
1 CAACAAGTTAGAAAGGA-GTTGGTCGAGATGAAACCATACAAAC
* * * * * **
57163 CAACGAGTTAGAAAAGAATTGG-CCATGATGAAATCATATGAAC
1 CAACAAGTTAGAAAGGAGTTGGTCGA-GATGAAACCATACAAAC
* * * ** * *
57206 CAACAAGTTAGAATGGTGTTAGGTAG-GACAAAACTATACATAC
1 CAACAAGTTAGAAAGGAGTT-GGTCGAGATGAAACCATACAAAC
*
57249 CAACGAGTTAGAAA
1 CAACAAGTTAGAAA
57263 AGTTGACTAA
Statistics
Matches: 492, Mismatches: 145, Indels: 44
0.72 0.21 0.06
Matches are distributed among these distances:
41 1 0.00
42 14 0.03
43 453 0.92
44 24 0.05
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.20
Consensus pattern (43 bp):
CAACAAGTTAGAAAGGAGTTGGTCGAGATGAAACCATACAAAC
Found at i:56658 original size:86 final size:85
Alignment explanation
Indices: 56561--57262 Score: 389
Period size: 86 Copynumber: 8.2 Consensus size: 85
56551 CTATATGAGT
* *
56561 CAACGAGTTAGAAAGGAGTTGGACGAGATGAAACCATACAAACTAATAAGTTA-AAAGGGTGTTG
1 CAACAAGTTAGAAAGGAGTTGG-CGAGATGAAACCATACAAACCAATAAGTTAGAAA-GGTGTTG
* *
56625 GTCGGGATGAAACCATACGTAC
64 GTCGAGATGAAACCATACATAC
* * ** * ** * *
56647 CAACAAGTTAGAAAAGAGTTGGCTAGGACAAAACCATACAAACTAGCAAGTTAGAAGGGTGTTAG
1 CAACAAGTTAGAAAGGAGTTGGCGA-GATGAAACCATACAAACCAATAAGTTAGAAAGGTGTTGG
* * **
56712 CCAAGATGAAACCATATGTAC
65 TCGAGATGAAACCATACATAC
* * * ** * ** * ** **
56733 CAACAATTTAG-AAGAATATTGGTTAAGATGAAACCACACGTAGCAACGAGTTAGAAAGAAGTTG
1 CAACAAGTTAGAAAGGA-GTTGG-CGAGATGAAACCATACAAACCAATAAGTTAGAAAGGTGTTG
* * *
56797 G-CTAAGATGAAACCATACAAAA
64 GTC-GAGATGAAACCATACATAC
* * *** * * *
56819 CAACAAGTTAGAAAGGTGTTGGTCGGGATGAAACCATATGCACCAATGAGATAGAAAGGAGTTGG
1 CAACAAGTTAGAAAGGAGTTGG-CGAGATGAAACCATACAAACCAATAAGTTAGAAAGGTGTTGG
**
56884 TCGAGACAAAACCATACGA-AC
65 TCGAGATGAAACCATAC-ATAC
* * * *** *
56905 CAACAAGTTAGAAAGGTGTTGGTTG-GAATGAAACCACATGTACCAATAAGTTAGAAAGGAGTTG
1 CAACAAGTTAGAAAGGAGTTGG-CGAG-ATGAAACCATACAAACCAATAAGTTAGAAAGGTGTTG
** * *
56969 G-AAAGGATAAAACCATACAAAC
64 GTCGA-GATGAAACCATACATAC
* * * * * * * *
56991 CAACAAGTTAGAAGGGTA-TTGGCTAGGACGAAACAATACATACCAATGAGTTATGAGA-GTATT
1 CAACAAGTTAGAAAGG-AGTTGGCGA-GATGAAACCATACAAACCAATAAGTTA-GAAAGGTGTT
**
57054 GGTCGAGACAAAACCATACATAC
63 GGTCGAGATGAAACCATACATAC
** * * * * *
57077 CAATGAGTTAGAAA-AAGGTTGGCCAGGATGAAACCATACAAAGCAATAAGTTAGAAAGATATTG
1 CAACAAGTTAGAAAGGA-GTTGGCGA-GATGAAACCATACAAACCAATAAGTTAGAAAGGTGTTG
* *
57141 GTCGAGATGTAACAATACATAC
64 GTCGAGATGAAACCATACATAC
* * * * * ** * *
57163 CAACGAGTTAGAAAAGAATTGGCCATGATGAAATCATATGAACCAACAAGTTAGAATGGTGTTAG
1 CAACAAGTTAGAAAGGAGTTGGCGA-GATGAAACCATACAAACCAATAAGTTAGAAAGGTGTT-G
* ** *
57228 GTAG-GACAAAACTATACATAC
64 GTCGAGATGAAACCATACATAC
*
57249 CAACGAGTTAGAAA
1 CAACAAGTTAGAAA
57263 AGTTGACTAA
Statistics
Matches: 483, Mismatches: 112, Indels: 42
0.76 0.18 0.07
Matches are distributed among these distances:
84 1 0.00
85 12 0.02
86 452 0.94
87 18 0.04
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.20
Consensus pattern (85 bp):
CAACAAGTTAGAAAGGAGTTGGCGAGATGAAACCATACAAACCAATAAGTTAGAAAGGTGTTGGT
CGAGATGAAACCATACATAC
Found at i:56936 original size:129 final size:128
Alignment explanation
Indices: 56350--57003 Score: 346
Period size: 129 Copynumber: 5.1 Consensus size: 128
56340 CCATATGTGT
* * * * * * * *
56350 CAACGAGTTAGAAAAGAGTTGG-CTGGGACAAAATCATATGAACTAACAAGTTAGAAAAGTGTTG
1 CAACAAGTTAGAAAGGAGTTGGTC-GAGACAAAACCATACGAACCAACAAGTTAGAAAGGAGTTG
* * * * * * *
56414 ATTGGGACGAAACCATACGTACCAATAAGTCAGGAAA---GTTGATCGAGATGAAACCATACGAG
65 GTTGGAACGAAACCATACGAAACAACAAGTTA-GAAAGGTGTTGGTCGAGATGAAACCATACGA-
*
56476 T
128 C
* * * * * * *
56477 CAACGAGTTAGAAAAGG-GTTAGTTGAGACAAAACTATATGAACCAACAAGTTAG-GAGG-GTTC
1 CAACAAGTTAG-AAAGGAGTTGGTCGAGACAAAACCATACGAACCAACAAGTTAGAAAGGAGTTG
* * * ** * * * *
56539 ATTAGG-ACGAAACTATATGAGTCAACGAGTTAGAAAGGAGTTGGACGAGATGAAACCATACAAA
65 GTT-GGAACGAAACCATACGAAACAACAAGTTAGAAAGGTGTTGGTCGAGATGAAACCATAC-GA
56603 C
128 C
* * * * ** * *
56604 TAATAAGTTA-AAAGGGTGTTGGTCGGGATGAAACCATACGTACCAACAAGTTAGAAAAGAGTTG
1 CAACAAGTTAGAAA-GGAGTTGGTCGAGACAAAACCATACGAACCAACAAGTTAGAAAGGAGTTG
* * * * * * * *
56668 GCTAGG-ACAAAACCATAC-AAACTAGCAAGTTAGAAGGGTGTTAGCCAAGATGAAACCATATGT
65 G-TTGGAACGAAACCATACGAAAC-AACAAGTTAGAAAGGTGTTGGTCGAGATGAAACCATACG-
56731 AC
127 AC
* * * ** ** * * * * *
56733 CAACAATTTAG-AAGAATATTGGTTAAGATGAAACCACACGTAGCAACGAGTTAGAAAGAAGTTG
1 CAACAAGTTAGAAAGGA-GTTGGTCGAGACAAAACCATACGAACCAACAAGTTAGAAAGGAGTTG
* * * * * *
56797 GCT-AAGATGAAACCATACAAAACAACAAGTTAGAAAGGTGTTGGTCGGGATGAAACCATATGCA
65 GTTGGA-ACGAAACCATACGAAACAACAAGTTAGAAAGGTGTTGGTCGAGATGAAACCATACG-A
56861 C
128 C
** * *
56862 CAATGAGATAGAAAGGAGTTGGTCGAGACAAAACCATACGAACCAACAAGTTAGAAAGGTGTTGG
1 CAACAAGTTAGAAAGGAGTTGGTCGAGACAAAACCATACGAACCAACAAGTTAGAAAGGAGTTGG
* * * * * * * ** * *
56927 TTGGAATGAAACCACATGTACCAATAAGTTAGAAAGGAGTTGG-AAAGGATAAAACCATACAAAC
66 TTGGAACGAAACCATACGAAACAACAAGTTAGAAAGGTGTTGGTCGA-GATGAAACCATAC-GAC
56991 CAACAAGTTAGAA
1 CAACAAGTTAGAA
57004 GGGTATTGGC
Statistics
Matches: 392, Mismatches: 112, Indels: 44
0.72 0.20 0.08
Matches are distributed among these distances:
124 4 0.01
125 27 0.07
126 6 0.02
127 97 0.25
128 10 0.03
129 238 0.61
130 10 0.03
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (128 bp):
CAACAAGTTAGAAAGGAGTTGGTCGAGACAAAACCATACGAACCAACAAGTTAGAAAGGAGTTGG
TTGGAACGAAACCATACGAAACAACAAGTTAGAAAGGTGTTGGTCGAGATGAAACCATACGAC
Found at i:57401 original size:42 final size:41
Alignment explanation
Indices: 57333--57436 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 41
57323 ATAAACTAAT
* * *
57333 AAGTTGACTAGGATGAAACCATATGAGTCAAC-AAAGAAAA
1 AAGTTGGCTAGGACGAAACCAAATGAGTCAACGAAAGAAAA
*
57373 AAGGGTTGGCTAGGACGAAACCAAATGAGTCAACGAAGGAAAA
1 AA--GTTGGCTAGGACGAAACCAAATGAGTCAACGAAAGAAAA
*
57416 AAGTTAGCTAGGACGAAACCA
1 AAGTTGGCTAGGACGAAACCA
57437 TACGAATCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
40 2 0.04
41 18 0.32
42 27 0.48
43 9 0.16
ACGTcount: A:0.46, C:0.14, G:0.25, T:0.14
Consensus pattern (41 bp):
AAGTTGGCTAGGACGAAACCAAATGAGTCAACGAAAGAAAA
Found at i:57447 original size:41 final size:41
Alignment explanation
Indices: 57340--57449 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
57330 AATAAGTTGA
* *
57340 CTAGGATGAAACCATATGAGTCAACAAAGAAAAAAGGGTTGG
1 CTAGGACGAAACCATATGAGTCAACAAAGAAAAAA-GGTTAG
* *
57382 CTAGGACGAAACCAAATGAGTCAACGAAGGAAAAAA-GTTAG
1 CTAGGACGAAACCATATGAGTCAAC-AAAGAAAAAAGGTTAG
* *
57423 CTAGGACGAAACCATACGAATCAACAA
1 CTAGGACGAAACCATATGAGTCAACAA
57450 GTTAATCAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
40 2 0.03
41 26 0.43
42 23 0.38
43 9 0.15
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (41 bp):
CTAGGACGAAACCATATGAGTCAACAAAGAAAAAAGGTTAG
Found at i:57521 original size:73 final size:73
Alignment explanation
Indices: 57384--57671 Score: 263
Period size: 73 Copynumber: 3.9 Consensus size: 73
57374 AGGGTTGGCT
* * * * * *
57384 AGGACGAAACCAAATGAGTCAACGAAGGAAAAAAGTTAGCTAGGACGAAACCATACGAATCAACA
1 AGGATGAAACCATACGAGTCAACGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
57449 AGTTAATC
66 AGTTAATC
** * * * * * * *
57457 AGGACAAAACTATACGAGTCAATGAAAGAAAGGAGTTGGCTAGGACAAAACTATATGAACCAACA
1 AGGATGAAACCATACGAGTCAACGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
*
57522 AGTTGATC
66 AGTTAATC
* * * * ** * * *
57530 AGGATGAAACCATACAAGTCAACGAAGGAAAATAATTAGCCAAAACAAAAACATACGAATCAAGA
1 AGGATGAAACCATACGAGTCAACGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
57595 AGTTAA-C
66 AGTTAATC
* * * * ** * *
57602 CGAGATGAAACCATACGAGTTAATGAAGGAAAGGAGTTAGCTAGGATGAAACCATATGAACCAAT
1 AG-GATGAAACCATACGAGTCAACGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAAC
57667 AAGTT
65 AAGTT
57672 GACTGAAACA
Statistics
Matches: 165, Mismatches: 49, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
72 2 0.01
73 163 0.99
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (73 bp):
AGGATGAAACCATACGAGTCAACGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
AGTTAATC
Found at i:57659 original size:146 final size:145
Alignment explanation
Indices: 57400--57709 Score: 372
Period size: 146 Copynumber: 2.1 Consensus size: 145
57390 AAACCAAATG
* ** * * *
57400 AGTCAACGAAGGAAAAAAGTTAGCTAGGACGAAACCATACGAATCAACAAGTTAATCAGGACAAA
1 AGTCAACGAAGGAAAAAA-TTAGCCAAAACAAAAACATACGAATCAACAAGTTAACCAGGACAAA
* * *
57465 ACTATACGAGTCAATGAAAGAAAGGAGTTGGCTAGGACAAAACTATATGAACCAACAAGTTGATC
65 ACCATACGAGTCAATGAAAGAAAGGAGTTAGCTAGGACAAAACCATATGAACCAACAAGTTGA-C
* **
57530 AG-GATGAAACCATACA
129 AGAAACAAAACCATACA
* **
57546 AGTCAACGAAGGAAAATAATTAGCCAAAACAAAAACATACGAATCAAGAAGTTAACC-GAGATGA
1 AGTCAACGAAGGAAAA-AATTAGCCAAAACAAAAACATACGAATCAACAAGTTAACCAG-GACAA
* * ** *
57610 AACCATACGAGTTAATGAAGGAAAGGAGTTAGCTAGGATGAAACCATATGAACCAATAAGTTGAC
64 AACCATACGAGTCAATGAAAGAAAGGAGTTAGCTAGGACAAAACCATATGAACCAACAAGTTGAC
*
57675 TGAAACAAAACCATACA
129 AGAAACAAAACCATACA
*
57692 AGTCAACTAAGGAAAAAA
1 AGTCAACGAAGGAAAAAA
57710 ATTGATGAAA
Statistics
Matches: 139, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
145 5 0.04
146 132 0.95
147 2 0.01
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (145 bp):
AGTCAACGAAGGAAAAAATTAGCCAAAACAAAAACATACGAATCAACAAGTTAACCAGGACAAAA
CCATACGAGTCAATGAAAGAAAGGAGTTAGCTAGGACAAAACCATATGAACCAACAAGTTGACAG
AAACAAAACCATACA
Found at i:57686 original size:73 final size:74
Alignment explanation
Indices: 57384--57707 Score: 246
Period size: 73 Copynumber: 4.4 Consensus size: 74
57374 AGGGTTGGCT
* * * * * * *
57384 AGGACGAAACCAAATGAGTCAACGAAGGAAAAAAGTTAGCTAGGACGAAACCATACGAATCAACA
1 AGGACAAAACCATACGAGTCAATGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
*
57449 AGTT-AATC
66 AGTTGACTC
* * * * * *
57457 AGGACAAAACTATACGAGTCAATGAAAGAAAGGAGTTGGCTAGGACAAAACTATATGAACCAACA
1 AGGACAAAACCATACGAGTCAATGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
57522 AGTTGA-TC
66 AGTTGACTC
** * * * * * ** * * *
57530 AGGATGAAACCATACAAGTCAACGAAGGAAAATAATTAGCCAAAACAAAAACATACGAATCAAGA
1 AGGACAAAACCATACGAGTCAATGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
*
57595 AGTTAAC-C
66 AGTTGACTC
** * * ** * *
57603 -GAGATGAAACCATACGAGTTAATGAAGGAAAGGAGTTAGCTAGGATGAAACCATATGAACCAAT
1 AG-GACAAAACCATACGAGTCAATGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAAC
*
57667 AAGTTGACTG
65 AAGTTGACTC
* *
57677 A-AACAAAACCATACAAGTCAACT-AAGGAAAA
1 AGGACAAAACCATACGAGTCAA-TGAAGGAAAA
57708 AAATTGATGA
Statistics
Matches: 190, Mismatches: 55, Indels: 12
0.74 0.21 0.05
Matches are distributed among these distances:
72 1 0.01
73 187 0.98
74 2 0.01
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (74 bp):
AGGACAAAACCATACGAGTCAATGAAGGAAAAGAGTTAGCTAGGACAAAACCATACGAACCAACA
AGTTGACTC
Found at i:59051 original size:17 final size:17
Alignment explanation
Indices: 59031--59072 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
59021 TTCTTGTTTA
59031 TTGTTTTTTTTTCTATT
1 TTGTTTTTTTTTCTATT
*
59048 TTGTTTTTTTTTCTCTT
1 TTGTTTTTTTTTCTATT
59065 TT-TTTTTT
1 TTGTTTTTT
59073 ATTTTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (17 bp):
TTGTTTTTTTTTCTATT
Found at i:59070 original size:30 final size:29
Alignment explanation
Indices: 59034--59100 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
59024 TTGTTTATTG
59034 TTTTTTTTTCTATTTTGTT-TTTTTTTCTC
1 TTTTTTTTT-TATTTTGTTATTTTTTTCTC
*
59063 TTTTTTTTTTATTTTTTTCATTTTTTTCTC
1 TTTTTTTTTTATTTTGTT-ATTTTTTTCTC
*
59093 TCTTTTTT
1 TTTTTTTT
59101 GGGCATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.24
29 9 0.26
30 17 0.50
ACGTcount: A:0.04, C:0.10, G:0.01, T:0.84
Consensus pattern (29 bp):
TTTTTTTTTTATTTTGTTATTTTTTTCTC
Found at i:59087 original size:19 final size:18
Alignment explanation
Indices: 59034--59089 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
59024 TTGTTTATTG
*
59034 TTTTTTTTTCTATTTTGTT
1 TTTTTTTTTC-ATTTTTTT
* *
59053 TTTTTTTCTCTTTTTTTT
1 TTTTTTTTTCATTTTTTT
59071 TTATTTTTTTCATTTTTTT
1 TT-TTTTTTTCATTTTTTT
59090 CTCTCTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 8 0.26
19 23 0.74
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTCATTTTTTT
Found at i:67959 original size:13 final size:13
Alignment explanation
Indices: 67941--67966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67931 TTGCTCACTA
67941 TATCGATACATTG
1 TATCGATACATTG
67954 TATCGATACATTG
1 TATCGATACATTG
67967 CTCTTTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:67961 original size:33 final size:33
Alignment explanation
Indices: 67919--67985 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
67909 TTTACCCAGA
67919 TGTATCGATACATTGCTCACTATATCGATACAT
1 TGTATCGATACATTGCTCACTATATCGATACAT
** *
67952 TGTATCGATACATTGCTCTTTGTATCGATACAT
1 TGTATCGATACATTGCTCACTATATCGATACAT
67985 T
1 T
67986 TTACAATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTGCTCACTATATCGATACAT
Found at i:70381 original size:51 final size:51
Alignment explanation
Indices: 70326--70464 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 51
70316 CCTCGGTTCG
**
70326 ATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCTAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCTAACTCCGATTTT
* * * ** * *
70377 ATTTCTAAAGCATCGATTTACCGCAATCGGGGATACTCTAACTCTGATTTT
1 ATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCTAACTCCGATTTT
* * *
70428 ATTTTCAAAACACCAATTTTTCACAATTGGGGATACT
1 ATTTCCAAAACATCAATTTTTCACAATCGGGGATACT
70465 TCAACCCCGT
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCTAACTCCGATTTT
Found at i:70574 original size:28 final size:28
Alignment explanation
Indices: 70535--70590 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
70525 TTTTTTCATA
*
70535 ATCGGGGGTACTCCAA-CTCCGTTATTTC
1 ATCGGGGATACTCCAATC-CCGTTATTTC
70563 ATCGGGGATACTCCAATCCCGTTATTTC
1 ATCGGGGATACTCCAATCCCGTTATTTC
70591 CGAAAAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (28 bp):
ATCGGGGATACTCCAATCCCGTTATTTC
Found at i:70656 original size:51 final size:52
Alignment explanation
Indices: 70597--70809 Score: 184
Period size: 51 Copynumber: 4.2 Consensus size: 52
70587 TTTCCGAAAA
* * *
70597 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATC-GGT
1 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAGGG
* * * *** * *
70648 GATACTCCAACTCTGATTTTATTTCCAAAATATTGATTTCTCATAATCGGGG
1 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAGGG
* ** * *
70700 GATAC-CTTAACCCCGACCTTATTTCT-AAATCATCGATTTTTCATAATCA-GG
1 GATACTC-CAACCCCGATTTTATTTCTAAAAT-ACCAATTTTTCATAATCAGGG
* ** * *
70751 GATACTCCAACCCCGGTTTTATTTCTGGAAGACCAATTTTCCATAATC-GGG
1 GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAGGG
70802 GATACTCC
1 GATACTCC
70810 GGCCCTGTTG
Statistics
Matches: 130, Mismatches: 26, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
51 92 0.71
52 38 0.29
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (52 bp):
GATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATCAGGG
Found at i:70672 original size:110 final size:109
Alignment explanation
Indices: 70456--70660 Score: 252
Period size: 110 Copynumber: 1.9 Consensus size: 109
70446 TTTCACAATT
* ** * * * *
70456 GGGGATACTTCAACCCCGTTATTTTTGAGAGGATACTCCAACCCCGGCTTTATATCTAAAAATAT
1 GGGGATACTCCAACCCCGTTATTTCCGAAAAGATACTCCAACCCCGACTTTATATCTAAAAATAC
* * *
70521 TAATTTTTTTCATAATCGGGGGTACTCCAACTCCGTTATTTCATC
66 CAA-TTTTTTCACAATCGGGGATACTCCAACTCCGTTATTTCATC
* * * *
70566 GGGGATACTCCAATCCCGTTATTTCCGAAAAGATACTCCAACCCTGATTTTATTTCT-AAAATAC
1 GGGGATACTCCAACCCCGTTATTTCCGAAAAGATACTCCAACCCCGACTTTATATCTAAAAATAC
*
70630 CAA-TTTTTCACAATCGGTGATACTCCAACTC
66 CAATTTTTTCACAATCGGGGATACTCCAACTC
70661 TGATTTTATT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
107 25 0.31
109 8 0.10
110 47 0.59
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (109 bp):
GGGGATACTCCAACCCCGTTATTTCCGAAAAGATACTCCAACCCCGACTTTATATCTAAAAATAC
CAATTTTTTCACAATCGGGGATACTCCAACTCCGTTATTTCATC
Found at i:71877 original size:51 final size:51
Alignment explanation
Indices: 71785--71915 Score: 201
Period size: 51 Copynumber: 2.6 Consensus size: 51
71775 CGTAGCGACA
* *
71785 GTATCGATACATTGAAAAAT-TATCGATACATCTAGAAAAAAAGACAGAAT
1 GTATCGATACATTGAAGAATGTATCGATACATCTAGAAAAAAAAACAGAAT
* **
71835 GTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAAACAGAAT
1 GTATCGATACATTGAAGAATGTATCGATACATCTAGAAAAAAAAACAGAAT
*
71886 GTATCGATACATTGAAGAATGTTTCGATAC
1 GTATCGATACATTGAAGAATGTATCGATAC
71916 TTTCATACAT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
50 19 0.26
51 55 0.74
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.27
Consensus pattern (51 bp):
GTATCGATACATTGAAGAATGTATCGATACATCTAGAAAAAAAAACAGAAT
Found at i:71906 original size:20 final size:21
Alignment explanation
Indices: 71881--71937 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
71871 GTAAAAAAAC
*
71881 AGAATGTATCGATACATTGA-
1 AGAATGTATCGATACATTCAT
* *
71901 AGAATGTTTCGATACTTTCAT
1 AGAATGTATCGATACATTCAT
*
71922 A-CATGTATCGATACAT
1 AGAATGTATCGATACAT
71938 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (21 bp):
AGAATGTATCGATACATTCAT
Found at i:75303 original size:52 final size:52
Alignment explanation
Indices: 75221--75347 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
75211 CGAAATATGA
75221 AAATTTGCCTGCATG--TCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
75271 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
75323 AAATTTTCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
75348 AAGATCGGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
50 15 0.21
52 58 0.79
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:75359 original size:52 final size:52
Alignment explanation
Indices: 75221--75368 Score: 194
Period size: 52 Copynumber: 2.9 Consensus size: 52
75211 CGAAATATGA
**
75221 AAATTTGCCTGCATG--TCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
** *
75271 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* * *
75323 AAATTTTCCTGCATGTATCGATACA-AAGATCGGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATAACAT-AGTGTATCGATACAT
75369 TTGAGTAATG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
50 15 0.17
51 2 0.02
52 72 0.81
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
Found at i:75430 original size:13 final size:13
Alignment explanation
Indices: 75412--75495 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
75402 AGCTTCGTAG
75412 CGATACATTGTAT
1 CGATACATTGTAT
75425 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
75444 CGATACATTGTAT
1 CGATACATTGTAT
75457 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
75476 CGATACATTGTAT
1 CGATACATTGTAT
75489 CGATACA
1 CGATACA
75496 ACCCTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:75444 original size:19 final size:18
Alignment explanation
Indices: 75420--75516 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 18
75410 AGCGATACAT
75420 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
75439 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
75452 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
75471 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
75484 TGTATCGATACAACCCTTA
1 TGTATCGATACAA-ACTTA
75503 TGTATCGATACAAA
1 TGTATCGATACAAA
75517 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 25
0.70 0.02 0.27
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 3 0.05
18 2 0.03
19 35 0.55
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:75453 original size:32 final size:32
Alignment explanation
Indices: 75412--75514 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
75402 AGCTTCGTAG
*
75412 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
75444 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
75476 CGATACATTGTATCGATACAACCCTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
75508 CGATACA
1 CGATACA
75515 AATCGTTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:76462 original size:102 final size:101
Alignment explanation
Indices: 76285--76780 Score: 449
Period size: 102 Copynumber: 4.9 Consensus size: 101
76275 GAGAAGAATG
** * *
76285 CCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAATATGACGAAGGCGCCAATATGCTGA
1 CCAATGTGCTGATTCAAGGCCAACGACATT-GGACTTAAAGATGACAAAGGCGCCAATATGCTGA
76350 TTCAAGGCCAGCGATACT-AATCTTTAAAGATGAAGGTA
65 TTCAAGGCCAGCGATACTGAA-C-TTAAAGATGAAGGTA
** * *
76388 CCAATGTGCTGATTCCCGGCCAACGACATTGGACTTAAAGATGACAAAGGCACCAATATGATGAT
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGAT
* * *
76453 TCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
66 TCAAGGCCAGCGATACTGAACTTAAAGATGAAGGTA
* * *
76489 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---AAAGGTGCCAATGTGCTGAT
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGAT
* * * ** **
76551 TCAAGGCCAACGACATTGGGCTTAAAAGATGACAAAGGCG
66 TCAAGGCCAGCGATACTGAACTT-AAAGATG---AAGGTA
* * * * * * *
76591 CCAATATGCTGATTCAAGGCCAGCGATACT-AATCTTTAAAGATG---AAGGTGCCAATGTGCTG
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGA-C-TTAAAGATGACAAAGGCGCCAATATGCTG
* * * * * *
76652 ATTTC-AGGCCAACGACATTGGACTTAAAGATGAAGATG
64 A-TTCAAGGCCAGCGATACTGAACTTAAAGATGAAGGTA
* * *
76690 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGAT---AAAGGTGCCAATATGCTAAT
1 CCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGAT
* * *
76752 TCAAGGTCAGCGATATTGGACTTAGAAGA
66 TCAAGGCCAGCGATACTGAACTTA-AAGA
76781 AGACGCCACC
Statistics
Matches: 340, Mismatches: 40, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
97 3 0.01
98 78 0.23
99 42 0.12
101 54 0.16
102 86 0.25
103 74 0.22
104 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (101 bp):
CCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGAT
TCAAGGCCAGCGATACTGAACTTAAAGATGAAGGTA
Found at i:76512 original size:49 final size:49
Alignment explanation
Indices: 76283--76780 Score: 507
Period size: 49 Copynumber: 9.9 Consensus size: 49
76273 ATGAGAAGAA
** *
76283 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAATATGACGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATT-GGACTT-AA-A-GATGAAGG
* * * * * *
76336 CGCCAATATGCTGATTCAAGGCCAGCGATACT-AATCTTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGA-C-TTAAAGATGAAGG
* **
76386 TACCAATGTGCTGATTCCCGGCCAACGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATG---AAGG
** * * * *
76438 CACCAATATGATGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* *
76487 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
*
76536 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGCTTAAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT-AAAGATG---AAGG
* * * * * *
76589 CGCCAATATGCTGATTCAAGGCCAGCGATACT-AATCTTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGA-C-TTAAAGATGAAGG
*
76639 TGCCAATGTGCTGATTTC-AGGCCAACGACATTGGACTTAAAGATGAAGA
1 TGCCAATGTGCTGA-TTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* *
76688 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
* * * * *
76737 TGCCAATATGCTAATTCAAGGTCAGCGATATTGGACTTAGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTA-AAGA
76781 AGACGCCACC
Statistics
Matches: 372, Mismatches: 57, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
48 3 0.01
49 179 0.48
50 70 0.19
51 6 0.02
52 44 0.12
53 68 0.18
54 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (49 bp):
TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGG
Found at i:76677 original size:152 final size:150
Alignment explanation
Indices: 76331--76780 Score: 588
Period size: 152 Copynumber: 3.0 Consensus size: 150
76321 TAAATATGAC
* * * * * * *
76331 GAAGGCGCCAATATGCTGATTCAAGGCCAGCGATACT-AATCTTTAAAGATGAAGGTACCAATGT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGA-C-TTAAAGATGAAGGTGCCAATGT
** * *
76395 GCTGATTCCCGGCCAACGACATTGGACTTAAAGATGACAAAGGCACCAATATGATGATTCAAGGC
64 GCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGC
* *
76460 CAGCGATATTGGACTTAAAGAT
129 CAGCGATACTGAACTTAAAGAT
* *
76482 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATGTGC
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
76547 TGATTCAAGGCCAACGACATTGGGCTTAAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCC
66 TGATTCAAGGCCAACGACATTGGACTT-AAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCC
76612 AGCGATACT-AATCTTTAAAGAT
130 AGCGATACTGAA-C-TTAAAGAT
*
76634 GAAGGTGCCAATGTGCTGATTTC-AGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATGTG
1 GAAGGTGCCAATGTGCTGA-TTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTG
* * * *
76698 CTGATTCAAGGCCAACGACATTGGTCTTAAAGAT---AAAGGTGCCAATATGCTAATTCAAGGTC
65 CTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCC
* *
76760 AGCGATATTGGACTTAGAAGA
130 AGCGATACTGAACTTA-AAGA
76781 AGACGCCACC
Statistics
Matches: 269, Mismatches: 23, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
147 3 0.01
148 38 0.14
149 1 0.00
150 47 0.17
151 84 0.31
152 93 0.35
153 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (150 bp):
GAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCA
GCGATACTGAACTTAAAGAT
Found at i:76878 original size:34 final size:34
Alignment explanation
Indices: 76834--76947 Score: 126
Period size: 34 Copynumber: 3.4 Consensus size: 34
76824 TGGGCTTTTG
* * *
76834 AAAAGGGTGCCACTGACTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACTGAGTTGTGGGCTTAAAAAGA
76868 AAAAGAGTGCCA-TGGAGTTGTGGGCTTACAAAAGA
1 AAAAGAGTGCCACT-GAGTTGTGGGCTTA-AAAAGA
* * *
76903 AAAGGAGTGCCACGGAGTTGTGGACTTAAAAA-A
1 AAAAGAGTGCCACTGAGTTGTGGGCTTAAAAAGA
76936 GAAAAG-GTGCCA
1 -AAAAGAGTGCCA
76948 ATATGTTGAC
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
33 8 0.12
34 32 0.46
35 29 0.42
ACGTcount: A:0.37, C:0.13, G:0.32, T:0.18
Consensus pattern (34 bp):
AAAAGAGTGCCACTGAGTTGTGGGCTTAAAAAGA
Found at i:76912 original size:35 final size:34
Alignment explanation
Indices: 76833--76942 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
76823 ATGGGCTTTT
* *
76833 GAAAAGG-GTGCCACT-GACTTGTGGGCTTAAAAG
1 GAAAAGGAGTGCCA-TGGAGTTGTGGGCTTAAAAA
*
76866 GAAAAAGAGTGCCATGGAGTTGTGGGCTTACAAAA
1 GAAAAGGAGTGCCATGGAGTTGTGGGCTTA-AAAA
* *
76901 GAAAAGGAGTGCCACGGAGTTGTGGACTTAAAAAA
1 GAAAAGGAGTGCCATGGAGTTGTGGGCTT-AAAAA
76936 GAAAAGG
1 GAAAAGG
76943 TGCCAATATG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.10
34 19 0.28
35 40 0.60
36 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.33, T:0.18
Consensus pattern (34 bp):
GAAAAGGAGTGCCATGGAGTTGTGGGCTTAAAAA
Found at i:77055 original size:33 final size:31
Alignment explanation
Indices: 76981--77069 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 31
76971 TATTGGGCTT
*
76981 AAAGGTGCCACGGAGTTGTGGACTTAAAAGA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGA
*
77012 AAAGGCGCCACGGAGTTGTGGGCTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-G-A
* *
77045 AAAGATGCCACGGACTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
77070 TTAAAGGTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 27 0.53
32 1 0.02
33 23 0.45
ACGTcount: A:0.31, C:0.16, G:0.34, T:0.19
Consensus pattern (31 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGA
Found at i:77123 original size:58 final size:58
Alignment explanation
Indices: 77042--77220 Score: 197
Period size: 58 Copynumber: 3.1 Consensus size: 58
77032 GGCTTAAAAG
* *
77042 GAAAAA-GATGCCACGGACTTGTGGGCTTTTAAAGGTTGCCACTGATTTGTGGGCTTT
1 GAAAAAGGATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTAATTTGTGGGCTTT
* * *
77099 GAAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCGCTAATTTGTGGGCTTT
1 GAAAAAGGATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTAATTTGTGGGCTTT
* * * *
77157 G---AAGGTTGCCACTGATTTGTGGGCTTTGAAAAATAGG-TGCCACTAACTTGTGGGCTTTT
1 GAAAAAGGATGCCACTGACTTGTGGGCTTT---TAA-AGGTTGCCACTAATTTGTGGGC-TTT
77216 GAAAA
1 GAAAA
77221 GGGTGAGGAA
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
55 24 0.24
57 6 0.06
58 64 0.63
59 7 0.07
62 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (58 bp):
GAAAAAGGATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTAATTTGTGGGCTTT
Found at i:77165 original size:27 final size:27
Alignment explanation
Indices: 77050--77186 Score: 166
Period size: 28 Copynumber: 4.9 Consensus size: 27
77040 AGGAAAAAGA
* * *
77050 TGCCACGGACTTGTGGGCTTTTAAAGGT
1 TGCCACTGATTTGTGGGC-TTTGAAGGT
*
77078 TGCCACTGATTTGTGGGCTTTGAAAAAGGG
1 TGCCACTGATTTGTGGGCTTTG---AAGGT
*
77108 TGCCACTGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGATTTGTGGGC-TTTGAAGGT
* *
77136 TGCCGCTAATTTGTGGGCTTTGAAGGT
1 TGCCACTGATTTGTGGGCTTTGAAGGT
77163 TGCCACTGATTTGTGGGCTTTGAA
1 TGCCACTGATTTGTGGGCTTTGAA
77187 AAATAGGTGC
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
27 34 0.36
28 35 0.37
30 21 0.22
31 4 0.04
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (27 bp):
TGCCACTGATTTGTGGGCTTTGAAGGT
Found at i:77172 original size:85 final size:87
Alignment explanation
Indices: 77060--77218 Score: 277
Period size: 85 Copynumber: 1.9 Consensus size: 87
77050 TGCCACGGAC
* *
77060 TTGTGGGCTTTTAAAGGTTGCCACTGATTTGTGGGCTTTGAAAAA-GGGTGCCACTGACTTGTGG
1 TTGTGGGCTTTTAAAGGTTGCCACTGATTTGTGGGCTTTGAAAAATAGGTGCCACTAACTTGTGG
77124 GCTTTTGAAGGTTGCCGCTAAT
66 GCTTTTGAAGGTTGCCGCTAAT
*
77146 TTGTGGGC-TTTGAAGGTTGCCACTGATTTGTGGGCTTTGAAAAATAGGTGCCACTAACTTGTGG
1 TTGTGGGCTTTTAAAGGTTGCCACTGATTTGTGGGCTTTGAAAAATAGGTGCCACTAACTTGTGG
77210 GCTTTTGAA
66 GCTTTTGAA
77219 AAGGGTGAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
85 35 0.51
86 34 0.49
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.35
Consensus pattern (87 bp):
TTGTGGGCTTTTAAAGGTTGCCACTGATTTGTGGGCTTTGAAAAATAGGTGCCACTAACTTGTGG
GCTTTTGAAGGTTGCCGCTAAT
Found at i:78590 original size:21 final size:21
Alignment explanation
Indices: 78566--78642 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
78556 AATTTATCCA
78566 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
78587 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
78608 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
78629 AATGTATCGATACA
1 AATGTATCGATACA
78643 AGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:78704 original size:19 final size:18
Alignment explanation
Indices: 78680--78745 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
78670 TTCAACAATT
78680 TGTATCGATACATAAGTTA
1 TGTATCGATACATAAG-TA
78699 TGTATCGATAC---A--A
1 TGTATCGATACATAAGTA
78712 TGTATCGATACATAAGTA
1 TGTATCGATACATAAGTA
78730 TTGTATCGATACATAA
1 -TGTATCGATACATAA
78746 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 12 0.29
16 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAAGTA
Found at i:78716 original size:13 final size:13
Alignment explanation
Indices: 78698--78723 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78688 TACATAAGTT
78698 ATGTATCGATACA
1 ATGTATCGATACA
78711 ATGTATCGATACA
1 ATGTATCGATACA
78724 TAAGTATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:78717 original size:32 final size:32
Alignment explanation
Indices: 78680--78742 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
78670 TTCAACAATT
78680 TGTATCGATACATAAGT-TATGTATCGATACAA
1 TGTATCGATACATAAGTAT-TGTATCGATACAA
78712 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
78743 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:78803 original size:13 final size:13
Alignment explanation
Indices: 78785--78810 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78775 CATTTTTCTG
78785 TGTATCGATACAT
1 TGTATCGATACAT
78798 TGTATCGATACAT
1 TGTATCGATACAT
78811 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:80550 original size:1 final size:1
Alignment explanation
Indices: 80544--80624 Score: 81
Period size: 1 Copynumber: 81.0 Consensus size: 1
80534 GTTGTTGTTG
* * * * * * * *
80544 TTTTTTTGTTTTTTTTTCTTTGTTTTTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTTTGTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
80609 TGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTT
80625 GTGGAGGATG
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.01, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:80572 original size:25 final size:24
Alignment explanation
Indices: 80538--80626 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 24
80528 GTTGTTGTTG
*
80538 TTGTTGTTTTTTTGTTTTTTTTTCT
1 TTGTTTTTTTTTTGTTTTTTTTT-T
80563 TTGTTTTTTTTTTGTTTTTTGTTTT
1 TTGTTTTTTTTTTGTTTTTT-TTTT
* * *
80588 TTTTTGTTTTTTTTGTTTGTTTGTT
1 TTGTT-TTTTTTTTGTTTTTTTTTT
80613 TT-TTTTTTTTTTGT
1 TTGTTTTTTTTTTGT
80627 GGAGGATGCC
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
23 10 0.17
24 2 0.03
25 29 0.50
26 17 0.29
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.87
Consensus pattern (24 bp):
TTGTTTTTTTTTTGTTTTTTTTTT
Found at i:80575 original size:18 final size:17
Alignment explanation
Indices: 80541--80624 Score: 107
Period size: 17 Copynumber: 5.0 Consensus size: 17
80531 GTTGTTGTTG
*
80541 TTGTTTTTTTGTTTTTT
1 TTGTTTTTTTTTTTTTT
* *
80558 TT-TCTTTGTTTTTTTT
1 TTGTTTTTTTTTTTTTT
*
80574 TTGTTTTTTGTTTTTTT
1 TTGTTTTTTTTTTTTTT
* *
80591 TTGTTTTTTTTGTTTGT
1 TTGTTTTTTTTTTTTTT
80608 TTGTTTTTTTTTTTTTT
1 TTGTTTTTTTTTTTTTT
80625 GTGGAGGATG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
16 13 0.24
17 42 0.76
ACGTcount: A:0.00, C:0.01, G:0.11, T:0.88
Consensus pattern (17 bp):
TTGTTTTTTTTTTTTTT
Found at i:80591 original size:42 final size:42
Alignment explanation
Indices: 80523--80626 Score: 138
Period size: 42 Copynumber: 2.4 Consensus size: 42
80513 ATCCGAACCC
*
80523 TTTTTGTTGTTGTTGTTGTTGTTTTTTTGTTTTTTTTTCTTTGTT
1 TTTTTTTTGTT-TT-TTGTTGTTTTTTTG-TTTTTTTTCTTTGTT
*
80568 TTTTTTTTGTTTTTTGTT-TTTTTTTGTTTTTTTTGTTTGTT
1 TTTTTTTTGTTTTTTGTTGTTTTTTTGTTTTTTTTCTTTGTT
*
80609 TGTTTTTTTTTTTTTTGT
1 T-TTTTTTTGTTTTTTGT
80627 GGAGGATGCC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
41 15 0.27
42 23 0.42
43 5 0.09
44 2 0.04
45 10 0.18
ACGTcount: A:0.00, C:0.01, G:0.14, T:0.85
Consensus pattern (42 bp):
TTTTTTTTGTTTTTTGTTGTTTTTTTGTTTTTTTTCTTTGTT
Found at i:94538 original size:52 final size:52
Alignment explanation
Indices: 94458--94586 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
94448 CGAAATATGA
* *
94458 AAATTTGCCTGCATGTATCAATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
94510 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
94562 AAATTTTCCTGAATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
94587 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:94597 original size:52 final size:52
Alignment explanation
Indices: 94458--94606 Score: 192
Period size: 52 Copynumber: 2.9 Consensus size: 52
94448 CGAAATATGA
* * * **
94458 AAATTTGCCTGCATGTATCAATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGAATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* **
94510 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGAATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* *
94562 AAATTTTCCTGAATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGAATGTATCGATACATAACAT-AGTGTATCGATACA
94607 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGAATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
Found at i:94613 original size:13 final size:13
Alignment explanation
Indices: 94595--94619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
94585 CAAAGATCAG
94595 TGTATCGATACAA
1 TGTATCGATACAA
94608 TGTATCGATACA
1 TGTATCGATACA
94620 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:94696 original size:19 final size:18
Alignment explanation
Indices: 94672--94768 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
94662 AGCGATATAT
94672 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
94691 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
94704 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
94723 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
94736 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
94755 TGTATCGATACAAA
1 TGTATCGATACAAA
94769 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:94706 original size:32 final size:32
Alignment explanation
Indices: 94664--94766 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
94654 AGCTTCGTAG
* *
94664 CGATATATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
94696 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
94728 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
94760 CGATACA
1 CGATACA
94767 AATCGTTGAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:94709 original size:13 final size:13
Alignment explanation
Indices: 94691--94747 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
94681 ACAAAACTTA
94691 TGTATCGATACAT
1 TGTATCGATACAT
94704 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
94722 ATGTATCGATACAT
1 -TGTATCGATACAT
94736 TGTATCGATACA
1 TGTATCGATACA
94748 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:99638 original size:13 final size:13
Alignment explanation
Indices: 99620--99649 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
99610 TTTGGAGGCT
99620 TAAATAAAGAAAG
1 TAAATAAAGAAAG
*
99633 TAAATAAAGAAAT
1 TAAATAAAGAAAG
99646 TAAA
1 TAAA
99650 AATAAAAAGA
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:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
TAAATAAAGAAAG
Found at i:99777 original size:14 final size:14
Alignment explanation
Indices: 99760--99808 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
99750 AGAAAAACTT
99760 GAAAGAAAAAGAGA
1 GAAAGAAAAAGAGA
* *
99774 GAAAAAAAAAGAAA
1 GAAAGAAAAAGAGA
99788 G-AAG-AAAAGAGA
1 GAAAGAAAAAGAGA
*
99800 AAAAGAAAA
1 GAAAGAAAA
99809 GATTCAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 7 0.25
13 5 0.18
14 16 0.57
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAGA
Found at i:99779 original size:24 final size:24
Alignment explanation
Indices: 99760--99810 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
99750 AGAAAAACTT
99760 GAAAGAA-AAAGAGAGAAAAAAAAA
1 GAAAGAAGAAA-AGAGAAAAAAAAA
99784 GAAAGAAGAAAAGAGAAAAAGAAAA
1 GAAAGAAGAAAAGAGAAAAA-AAAA
99809 GA
1 GA
99811 TTCAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (24 bp):
GAAAGAAGAAAAGAGAAAAAAAAA
Found at i:99781 original size:13 final size:13
Alignment explanation
Indices: 99761--99810 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
99751 GAAAAACTTG
99761 AAAGAAAAAGAGAGA
1 AAAG-AAAAGAGA-A
99776 AAA-AAAA-AGAA
1 AAAGAAAAGAGAA
99787 AGAAGAAAAGAGAA
1 A-AAGAAAAGAGAA
99801 AAAGAAAAGA
1 AAAGAAAAGA
99811 TTCAAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.06
12 5 0.16
13 17 0.53
14 5 0.16
15 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAGAA
Found at i:100174 original size:136 final size:135
Alignment explanation
Indices: 99929--100181 Score: 368
Period size: 136 Copynumber: 1.9 Consensus size: 135
99919 TGAAAGCTTA
* *
99929 ATGATCCTAGGTCATTAACTTAGGTGTAGCTTGAGCTTAATGGTTTCCTAACTATTTTGGTGGCC
1 ATGATCCTAAGTCATTAACTTAGGTGTAGCTTGAGCTTAATGGTTTCCTAACTATTTTAGTGGCC
* * * *
99994 AAGCAACAGCTAAAATCCAGTTTATTTAATTTCTTGTTAGTTATTTAGTTTATATGTAATTAAAG
66 AAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATATGTAATTAAAG
100059 GTTTG
131 GTTTG
* *
100064 ATGATCCTAAGTCATTAACTTAGGTGATAGCTTGATCTTAATGGTTTTCTAA-TCATTTTAGTGG
1 ATGATCCTAAGTCATTAACTTAGGTG-TAGCTTGAGCTTAATGGTTTCCTAACT-ATTTTAGTGG
*
100128 CCAAACAAGAGCTAAAATCC-CTTCCATTTAATTT-TTGTTAGTTTATTTAATTTA
64 CCAAACAACAGCTAAAATCCACTT-CATTTAATTTCTTGTTAG-TTATTTAATTTA
100182 AGGCAACACT
Statistics
Matches: 105, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
135 35 0.33
136 70 0.67
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (135 bp):
ATGATCCTAAGTCATTAACTTAGGTGTAGCTTGAGCTTAATGGTTTCCTAACTATTTTAGTGGCC
AAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATATGTAATTAAAG
GTTTG
Found at i:100201 original size:136 final size:136
Alignment explanation
Indices: 99921--100236 Score: 353
Period size: 136 Copynumber: 2.3 Consensus size: 136
99911 TGTTTTCATG
* *
99921 AAAG-CTTAATGATCCTAGGTCATTAACTTAGGTG-TAGCTTGAGCTTAATGGTTTCCTAACTAT
1 AAAGACTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGAGCTTAATGGTTTCCTAACTAT
* * * * * *
99984 TTTGGTGGCCAAGCAACAGCTAAAATCCAGTTTATTTAATTTCTTGTTAGTTATTTAGTTTATAT
66 TTTAGTGGCCAAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATAG
* *
100049 GTAATT
131 GAAACT
** * *
100055 AAAGGTTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGATCTTAATGGTTTTCTAA-TCA
1 AAAGACTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGAGCTTAATGGTTTCCTAACT-A
*
100119 TTTTAGTGGCCAAACAAGAGCTAAAATCC-CTTCCATTTAATTT-TTGTTAGTTTATTTAATTTA
65 TTTTAGTGGCCAAACAACAGCTAAAATCCACTT-CATTTAATTTCTTGTTAG-TTATTTAATTTA
100182 -AGGCAACACT
128 TAGG-AA-ACT
* * *
100192 -AAGACTTGATGGTCCTAAGT--TTAATATTAGATGATAGCTTGAGCT
1 AAAGACTTGATGATCCTAAGTCATTAA-CTTAGGTGATAGCTTGAGCT
100237 AGGTTTCCCA
Statistics
Matches: 154, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
134 8 0.05
135 56 0.36
136 88 0.57
137 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (136 bp):
AAAGACTTGATGATCCTAAGTCATTAACTTAGGTGATAGCTTGAGCTTAATGGTTTCCTAACTAT
TTTAGTGGCCAAACAACAGCTAAAATCCACTTCATTTAATTTCTTGTTAGTTATTTAATTTATAG
GAAACT
Found at i:100561 original size:8 final size:8
Alignment explanation
Indices: 100548--100788 Score: 77
Period size: 8 Copynumber: 28.4 Consensus size: 8
100538 TTTTTATTCA
100548 AAAAAATT
1 AAAAAATT
100556 AAAAAA--
1 AAAAAATT
100562 AAGAAAATCT
1 AA-AAAAT-T
100572 AAAAAA-T
1 AAAAAATT
*
100579 AAAAATTTT
1 AAAAA-ATT
100588 AAAAAATT
1 AAAAAATT
**
100596 TTAAAA-T
1 AAAAAATT
100603 ATAAAAA-T
1 A-AAAAATT
100611 -AAAAATT
1 AAAAAATT
*
100618 CAAAAATT
1 AAAAAATT
100626 ATAAAAATT
1 A-AAAAATT
* *
100635 CTATAAATT
1 -AAAAAATT
100644 CAAAAGAATT
1 -AAAA-AATT
*
100654 AAAAAGTTTTT
1 AAAAA---ATT
**
100665 AAAATTTT
1 AAAAAATT
100673 AAAAAATT
1 AAAAAATT
100681 ATTAAAAATCT
1 A--AAAAAT-T
* *
100692 TAAAATTT
1 AAAAAATT
*
100700 AAAAAAAT
1 AAAAAATT
100708 ATAAAAA-T
1 A-AAAAATT
100716 AAAAAATAT
1 AAAAAAT-T
*
100725 CAAAAATTT
1 -AAAAAATT
*
100734 AAAAAACT
1 AAAAAATT
100742 AAAAATATAT
1 AAAAA-AT-T
100752 AATTAAATATGT
1 AA--AAA-AT-T
*
100764 AGAAAA-T
1 AAAAAATT
100771 -AAAAATT
1 AAAAAATT
100778 AAAAAATT
1 AAAAAATT
100786 AAA
1 AAA
100789 TTTGAAAAAT
Statistics
Matches: 178, Mismatches: 27, Indels: 56
0.68 0.10 0.21
Matches are distributed among these distances:
6 11 0.06
7 19 0.11
8 65 0.37
9 44 0.25
10 24 0.13
11 7 0.04
12 8 0.04
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:100590 original size:9 final size:9
Alignment explanation
Indices: 100578--100715 Score: 60
Period size: 9 Copynumber: 15.8 Consensus size: 9
100568 ATCTAAAAAA
100578 TAAAAATTT
1 TAAAAATTT
100587 TAAAAAATTT
1 T-AAAAATTT
*
100597 T-AAAA-TA
1 TAAAAATTT
100604 TAAAAA---
1 TAAAAATTT
100610 TAAAAA-TT
1 TAAAAATTT
* *
100618 CAAAAATTA
1 TAAAAATTT
*
100627 TAAAAATTC
1 TAAAAATTT
*
100636 TATAAA-TT
1 TAAAAATTT
* *
100644 CAAAAGA-AT
1 TAAAA-ATTT
100653 TAAAAAGTTT
1 TAAAAA-TTT
*
100663 TTAAAATTT
1 TAAAAATTT
100672 TAAAAAATTAT
1 T-AAAAATT-T
*
100683 TAAAAATCT
1 TAAAAATTT
100692 T-AAAATTT
1 TAAAAATTT
* * *
100700 AAAAAAATA
1 TAAAAATTT
100709 TAAAAAT
1 TAAAAAT
100716 AAAAAATATC
Statistics
Matches: 97, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
6 6 0.06
7 2 0.02
8 24 0.25
9 36 0.37
10 27 0.28
11 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (9 bp):
TAAAAATTT
Found at i:100617 original size:22 final size:23
Alignment explanation
Indices: 100589--100633 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
100579 AAAAATTTTA
**
100589 AAAAATTTTAAAA-TATAAAAAT
1 AAAAATTCAAAAATTATAAAAAT
100611 AAAAATTCAAAAATTATAAAAAT
1 AAAAATTCAAAAATTATAAAAAT
100634 TCTATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATTCAAAAATTATAAAAAT
Found at i:100695 original size:28 final size:26
Alignment explanation
Indices: 100598--100715 Score: 84
Period size: 27 Copynumber: 4.5 Consensus size: 26
100588 AAAAAATTTT
* *
100598 AAAATATAAAAA---TAAAAATTCAA
1 AAAATATAAAAATCTTAAAATTTAAA
* *
100621 AAATTATAAAAAT-TCTATAAATTCAAA
1 AAAATATAAAAATCT-TA-AAATTTAAA
* *
100648 AGAAT-TAAAAAGTTTTTAAAATTTTAAA
1 AAAATATAAAAA--TCTTAAAA-TTTAAA
*
100676 AAATTATTAAAAATCTTAAAATTTAAA
1 AAAATA-TAAAAATCTTAAAATTTAAA
100703 AAAATATAAAAAT
1 AAAATATAAAAAT
100716 AAAAAATATC
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
23 11 0.15
26 15 0.20
27 23 0.31
28 18 0.24
29 1 0.01
30 6 0.08
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATATAAAAATCTTAAAATTTAAA
Found at i:100719 original size:15 final size:16
Alignment explanation
Indices: 100701--100731 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
100691 TTAAAATTTA
100701 AAAAAATAT-AAAAAT
1 AAAAAATATCAAAAAT
100716 AAAAAATATCAAAAAT
1 AAAAAATATCAAAAAT
100732 TTAAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAAATATCAAAAAT
Found at i:100745 original size:42 final size:43
Alignment explanation
Indices: 100672--100753 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
100662 TTTAAAATTT
* **
100672 TAAAAAATTATTAAAAATCTTAAAATTTAAAAAAATATAAAAA
1 TAAAAAATTATCAAAAATCTTAAAAACTAAAAAAATATAAAAA
*
100715 TAAAAAA-TATCAAAAAT-TTAAAAAACTAAAAATATATAA
1 TAAAAAATTATCAAAAATCTT-AAAAACTAAAAAAATATAA
100754 TTAAATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.06
42 25 0.74
43 7 0.21
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (43 bp):
TAAAAAATTATCAAAAATCTTAAAAACTAAAAAAATATAAAAA
Found at i:101206 original size:13 final size:15
Alignment explanation
Indices: 101177--101212 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
101167 TTCTGCCCAT
101177 TTTCCTCTTTCTTCC
1 TTTCCTCTTTCTTCC
101192 TTTCC-CTTT-TTCC
1 TTTCCTCTTTCTTCC
101205 TTTCCTCT
1 TTTCCTCT
101213 ATCTGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCCTCTTTCTTCC
Found at i:101331 original size:28 final size:28
Alignment explanation
Indices: 101276--101337 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
101266 TGTTTTTAAG
*
101276 TTTTTT-AAATTTTAAGTTTTTGATATA
1 TTTTTTAAAATTTAAAGTTTTTGATATA
101303 TATTTTTAAAATTTAAAAGTTTTT-A-ATA
1 T-TTTTTAAAATTT-AAAGTTTTTGATATA
101331 TTTTTTA
1 TTTTTTA
101338 GATATTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 7 0.23
28 9 0.29
29 7 0.23
30 8 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTTTAAAATTTAAAGTTTTTGATATA
Found at i:101344 original size:28 final size:30
Alignment explanation
Indices: 101276--101337 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
101266 TGTTTTTAAG
* *
101276 TTTTTTAAATTT-TAAGTTTTTGATATATA
1 TTTTTAAAATTTAAAAGTTTTTGATATATA
101305 TTTTTAAAATTTAAAAGTTTTT-A-ATAT-
1 TTTTTAAAATTTAAAAGTTTTTGATATATA
101332 TTTTTA
1 TTTTTA
101338 GATATTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.20
28 4 0.13
29 12 0.40
30 8 0.27
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTTAAAATTTAAAAGTTTTTGATATATA
Found at i:101434 original size:13 final size:14
Alignment explanation
Indices: 101416--101452 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
101406 AAAAATATTC
101416 TTATATTTTTAA-T
1 TTATATTTTTAATT
101429 TTATA-TTTTAATTT
1 TTATATTTTTAA-TT
101443 TTATATTTTT
1 TTATATTTTT
101453 TGCAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 5 0.24
14 6 0.29
15 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATATTTTTAATT
Found at i:101723 original size:30 final size:30
Alignment explanation
Indices: 101682--101778 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
101672 TTTATTGTAG
* *
101682 TTTATTTTTTTAAAATTTAAATTTATGCAT
1 TTTACTTTTTTAAAATTTAAATTTATGCAA
* *
101712 TTTACTTTTTTACAATTTAAATTCATGCAA
1 TTTACTTTTTTAAAATTTAAATTTATGCAA
* ** *
101742 TTT--TTTCTT-GCATTTAGAATTTATGCAC
1 TTTACTTTTTTAAAATTTA-AATTTATGCAA
101770 TTTACTTTT
1 TTTACTTTT
101779 GTTGCAAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.09
28 17 0.31
30 32 0.59
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (30 bp):
TTTACTTTTTTAAAATTTAAATTTATGCAA
Found at i:101893 original size:2 final size:2
Alignment explanation
Indices: 101886--101917 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
101876 GACATACTTT
101886 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
101918 GATAGATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101922 original size:4 final size:4
Alignment explanation
Indices: 101915--101953 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
101905 ATATATATAT
101915 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
101954 CAACTACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:111443 original size:32 final size:32
Alignment explanation
Indices: 111402--111465 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
111392 CTTGGATGAC
111402 ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
1 ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
* *
111434 ATTCTCAGCAGCTGATTTGGAAACTAATGGCA
1 ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
111466 CCCCTTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (32 bp):
ATTCTCAGCAGCTGATTTCGAAACTAACGGCA
Found at i:119347 original size:13 final size:13
Alignment explanation
Indices: 119329--119354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
119319 TACAGCAAGT
119329 ATGTATCGATACA
1 ATGTATCGATACA
119342 ATGTATCGATACA
1 ATGTATCGATACA
119355 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:121552 original size:21 final size:21
Alignment explanation
Indices: 121519--121563 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
121509 TTGCAAGTTG
*
121519 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
121541 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
121561 AAA
1 AAA
121564 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:125647 original size:20 final size:20
Alignment explanation
Indices: 125604--125649 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
125594 AAATCTTTTG
125604 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
125625 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
125645 CAAAA
1 CAAAA
125650 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:127412 original size:21 final size:23
Alignment explanation
Indices: 127364--127412 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
127354 AAATTGCTAC
*
127364 AATTACTTTGTTAAGGGGATATG
1 AATTACTTTGTTAAGGGGAGATG
127387 AATTAC-TTGATTAAGGGG-GA-G
1 AATTACTTTG-TTAAGGGGAGATG
127408 AATTA
1 AATTA
127413 TATAACGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 4 0.17
23 14 0.58
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (23 bp):
AATTACTTTGTTAAGGGGAGATG
Found at i:127473 original size:91 final size:91
Alignment explanation
Indices: 127290--127471 Score: 316
Period size: 90 Copynumber: 2.0 Consensus size: 91
127280 AATAAATTTT
127290 GATATGAATTACTTGATTAAGGGGGAGAATATTAATAAACGGGGAGATAAAGGGGAGAATGCGTA
1 GATATGAATTACTTGATTAAGGGGGAGAATATTAATAAACGGGGAGATAAAGGGGAGAATGCGTA
*
127355 AATTGCTACAATTACTTTGTTAAGGG
66 AATTGCTACAATTACTTTATTAAGGG
127381 GATATGAATTACTTGATTAAGGGGGAG-A-ATT-ATATAACGGGGGAGATAAAGGGGAGAATGCG
1 GATATGAATTACTTGATTAAGGGGGAGAATATTAATA-AAC-GGGGAGATAAAGGGGAGAATGCG
127443 TAAATTGCTACAATTACTTTATTAAGGG
64 TAAATTGCTACAATTACTTTATTAAGGG
127471 G
1 G
127472 GAGAATGTAC
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
88 3 0.03
89 6 0.07
90 52 0.59
91 27 0.31
ACGTcount: A:0.37, C:0.07, G:0.29, T:0.27
Consensus pattern (91 bp):
GATATGAATTACTTGATTAAGGGGGAGAATATTAATAAACGGGGAGATAAAGGGGAGAATGCGTA
AATTGCTACAATTACTTTATTAAGGG
Found at i:128147 original size:13 final size:13
Alignment explanation
Indices: 128129--128154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128119 TACAGCAAGT
128129 ATGTATCGATACA
1 ATGTATCGATACA
128142 ATGTATCGATACA
1 ATGTATCGATACA
128155 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:128152 original size:32 final size:32
Alignment explanation
Indices: 128111--128173 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
128101 TAGCCAAACT
**
128111 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
128143 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
128174 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:129984 original size:13 final size:13
Alignment explanation
Indices: 129966--129997 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
129956 TTGTTTTCAA
129966 CCACCTTGCTCAG
1 CCACCTTGCTCAG
129979 CCACCTTGCTCAG
1 CCACCTTGCTCAG
129992 CCACCT
1 CCACCT
129998 CTGTCGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.50, G:0.12, T:0.22
Consensus pattern (13 bp):
CCACCTTGCTCAG
Done.