Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 137 of 203
Found at i:43660187 original size:54 final size:54
Alignment explanation
Indices: 43660115--43660301 Score: 189
Period size: 54 Copynumber: 3.4 Consensus size: 54
43660105 ATTTAATAAA
*
43660115 AATATATAATTTAATAAAATTCTTCATAATAAATATTCAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTCTTCATAATAAATATTCAATTTACTAAAATCAT
* * * * * * ** * *
43660169 AATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAA
1 AATATATAAT-CTAATAAAAT-T-CTTCATAATAA--A-TATTCAATTTACTAAAATCAT
*
43660228 AATATATAATTTAATAAAATTCTTCATAATAAATATTCAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTCTTCATAATAAATATTCAATTTACTAAAATCAT
43660282 AATATATAATACT-ATAAAAT
1 AATATATAAT-CTAATAAAAT
43660302 ATAATTTAAA
Statistics
Matches: 102, Mismatches: 23, Indels: 16
0.72 0.16 0.11
Matches are distributed among these distances:
54 48 0.47
55 4 0.04
56 8 0.08
57 8 0.08
58 3 0.03
59 31 0.30
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (54 bp):
AATATATAATCTAATAAAATTCTTCATAATAAATATTCAATTTACTAAAATCAT
Found at i:43660212 original size:113 final size:113
Alignment explanation
Indices: 43660089--43660479 Score: 638
Period size: 113 Copynumber: 3.4 Consensus size: 113
43660079 TTCTAACATC
43660089 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATAATAAATATTCA
1 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATAATAAATATTCA
43660154 ATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
66 ATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
43660202 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATAATAAATATTCA
1 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATAATAAATATTCA
43660267 ATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
66 ATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
* * * *
43660315 ATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTACTGTCTTAATAATAAATAT
1 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA--AAAT-TCTTCATAATAAATAT
*
43660380 TCTTATATGAATTTACTAAAATCATAATATATAATATTATAAAATATAATTTAAAATA
63 TC-------AATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
*
43660438 ATTATTATTAAATATAATTTAATAAAAATATATGATTTAATA
1 ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA
43660480 GCTATTGTCT
Statistics
Matches: 263, Mismatches: 5, Indels: 10
0.95 0.02 0.04
Matches are distributed among these distances:
113 154 0.59
115 2 0.01
116 17 0.06
123 90 0.34
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (113 bp):
ATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATAATAAATATTCA
ATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATA
Found at i:43660343 original size:16 final size:17
Alignment explanation
Indices: 43660324--43660356 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43660314 AATTATTATT
43660324 AAATATA-ATTTAATAA
1 AAATATAGATTTAATAA
43660340 AAATATATGATTTAATA
1 AAATATA-GATTTAATA
43660357 GCTACTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATATAGATTTAATAA
Found at i:43660428 original size:22 final size:24
Alignment explanation
Indices: 43660383--43660429 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
43660373 TAAATATTCT
43660383 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
43660407 TATAT-AATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
43660429 T
1 T
43660430 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:43660450 original size:26 final size:25
Alignment explanation
Indices: 43660410--43660468 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
43660400 ATCATAATAT
43660410 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
43660435 ATAATTATTATTAAATATAATTTAATA
1 ATAA-TATTATAAAATATAATTTAA-A
*
43660462 AAAATAT
1 ATAATAT
43660469 ATGATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 22 0.73
27 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:43660466 original size:16 final size:17
Alignment explanation
Indices: 43660447--43660479 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43660437 AATTATTATT
43660447 AAATATA-ATTTAATAA
1 AAATATAGATTTAATAA
43660463 AAATATATGATTTAATA
1 AAATATA-GATTTAATA
43660480 GCTATTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATATAGATTTAATAA
Found at i:43660501 original size:64 final size:64
Alignment explanation
Indices: 43660310--43660501 Score: 186
Period size: 64 Copynumber: 3.1 Consensus size: 64
43660300 ATATAATTTA
*
43660310 AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTACTGTCTTAATAAT
1 AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
* * * * * ****
43660374 AAAT-ATTCTTA-T--AT-GAATTTACT-AAAATCATAAT-ATATAATA-TTATAAAATATAAT-
1 AAATAATTATTATTAAATATAATTTAATAAAAAT-AT-ATGATTTAATAGCTATTGTCT-TAATA
*
43660430 TT
63 AT
43660432 AAAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
1 -AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
43660497 AAATA
1 AAATA
43660502 TTCTTATATG
Statistics
Matches: 94, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
58 9 0.10
59 24 0.26
60 10 0.11
61 1 0.01
62 1 0.01
63 10 0.11
64 29 0.31
65 10 0.11
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (64 bp):
AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
Found at i:43660523 original size:59 final size:58
Alignment explanation
Indices: 43660326--43660523 Score: 186
Period size: 59 Copynumber: 3.3 Consensus size: 58
43660316 TTATTATTAA
*
43660326 ATATAATTTAATAAAAATATATGATTTAATAGCTACTGTCTTAATAATAAATATTCTT
1 ATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
* * ** ** * *
43660384 ATATGAATTTACTAAAATCATAATAT-ATAATATTATAAAATATAAT-TTAA-AATAATTATTAT
1 ATAT-AATTTAATAAAA--AT-ATATGAT--T-TAAT-AGCTATTGTCTTAATAATAAATATTCT
43660446 T
58 T
43660447 AAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
1 --ATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
*
43660507 ATATGAATTTACTAAAA
1 ATAT-AATTTAATAAAA
43660524 TCATAATATA
Statistics
Matches: 108, Mismatches: 18, Indels: 27
0.71 0.12 0.18
Matches are distributed among these distances:
58 13 0.12
59 29 0.27
60 12 0.11
61 8 0.07
62 8 0.07
63 12 0.11
64 18 0.17
65 8 0.07
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (58 bp):
ATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
Found at i:43660532 original size:64 final size:64
Alignment explanation
Indices: 43660341--43660533 Score: 206
Period size: 64 Copynumber: 3.1 Consensus size: 64
43660331 ATTTAATAAA
*
43660341 AATATATGATTTAATAGCTACTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
* ** ** * * *
43660405 AATATATAATATT-ATAAAATATAAT-TTAA-AATAATTATTATTAAATAT-AATTTA--ATAA-
1 AATATATGAT-TTAAT-AGCTATTGTCTTAATAATAAATATTCTT--ATATGAATTTACTAAAAT
43660463 -A-
62 CAT
43660464 AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
43660528 AATATA
1 AATATA
43660534 ACTTGAGAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
58 11 0.11
59 21 0.21
60 12 0.12
61 3 0.03
62 3 0.03
63 12 0.12
64 27 0.27
65 10 0.10
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (64 bp):
AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:43664856 original size:41 final size:41
Alignment explanation
Indices: 43664716--43664828 Score: 217
Period size: 41 Copynumber: 2.8 Consensus size: 41
43664706 GACTTTAAGT
43664716 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
43664757 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
43664798 CTAGCAGGCTACATGCCGGTGATCTGAATCA
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCA
43664829 TGCTATAAGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:43665778 original size:49 final size:49
Alignment explanation
Indices: 43665706--43665809 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
43665696 GAAAAAAAAC
* * *
43665706 AAATTAAAATTAAGTTGAATATCATGAATCAAAAGGTGAACACTT-TATA
1 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACA-TTGTATA
43665755 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACATTGTATA
1 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACATTGTATA
43665804 AAATTA
1 AAATTA
43665810 TAACACATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 2 0.04
49 49 0.96
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACATTGTATA
Found at i:43667622 original size:33 final size:33
Alignment explanation
Indices: 43667578--43667643 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
43667568 GAATTAAAAT
43667578 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
*
43667611 TTGTTGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
43667644 AATTTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (33 bp):
TTGTAGGTATATGTATAATTGAGCTAAAATTAA
Found at i:43667877 original size:19 final size:19
Alignment explanation
Indices: 43667850--43667886 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43667840 AACAAATTAA
*
43667850 TTGTTGGTATATGTAAAAT
1 TTGTAGGTATATGTAAAAT
43667869 TTGTAGGTATATGTAAAA
1 TTGTAGGTATATGTAAAA
43667887 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGTAGGTATATGTAAAAT
Found at i:43668208 original size:18 final size:18
Alignment explanation
Indices: 43668187--43668221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43668177 TTAAATATAT
*
43668187 AATTTAATTAGTTTTATG
1 AATTTAAATAGTTTTATG
*
43668205 AATTTAAATATTTTTAT
1 AATTTAAATAGTTTTAT
43668222 TTTAACCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTTAAATAGTTTTATG
Found at i:43678451 original size:13 final size:13
Alignment explanation
Indices: 43678428--43678497 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
43678418 ACTAACTTAT
*
43678428 ATTATATATATTTG
1 ATTA-ATATATTTA
43678442 ATTAATATA-TTA
1 ATTAATATATTTA
*
43678454 ATTAACT-TAATTA
1 ATTAA-TATATTTA
* *
43678467 ATCTTATATATTTG
1 AT-TAATATATTTA
43678481 ATTAATATA-TTA
1 ATTAATATATTTA
43678493 ATTAA
1 ATTAA
43678498 CTTAATTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 16 0.35
13 18 0.39
14 12 0.26
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (13 bp):
ATTAATATATTTA
Found at i:43678452 original size:22 final size:22
Alignment explanation
Indices: 43678425--43678492 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 22
43678415 TCCACTAACT
43678425 TATATTATATATATTTGATTAA
1 TATATTATATATATTTGATTAA
* *
43678447 TATATTA-AT-TAACTTAATT-A
1 TATATTATATAT-ATTTGATTAA
*
43678467 -AT-CT-TATATATTTGATTAA
1 TATATTATATATATTTGATTAA
43678486 TATATTA
1 TATATTA
43678493 ATTAACTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
18 9 0.27
19 4 0.12
20 4 0.12
21 9 0.27
22 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (22 bp):
TATATTATATATATTTGATTAA
Found at i:43678477 original size:39 final size:39
Alignment explanation
Indices: 43678432--43678511 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
43678422 ACTTATATTA
43678432 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
1 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
43678471 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
1 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
43678510 TA
1 TA
43678512 CTTAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (39 bp):
TATATATTTGATTAATATATTAATTAACTTAATTAATCT
Found at i:43679485 original size:25 final size:26
Alignment explanation
Indices: 43679453--43679507 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
43679443 TTATTAAATT
*
43679453 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
43679478 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
43679503 A-ATAT
1 ATATAT
43679508 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:43679741 original size:16 final size:16
Alignment explanation
Indices: 43679720--43679755 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
43679710 GATTTGCTAT
43679720 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43679736 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
43679752 TACA
1 TACA
43679756 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43680028 original size:22 final size:23
Alignment explanation
Indices: 43680001--43680047 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
43679991 ATTATTGACA
43680001 TTTTATAATTAAA-AATTATTAT
1 TTTTATAATTAAACAATTATTAT
*
43680023 TTTTATAATTAAACTATTATTAT
1 TTTTATAATTAAACAATTATTAT
43680046 TT
1 TT
43680048 AATTTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATAATTAAACAATTATTAT
Found at i:43680042 original size:20 final size:21
Alignment explanation
Indices: 43680001--43680048 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
43679991 ATTATTGACA
*
43680001 TTTTATAATTAAAAATTATTAT
1 TTTTATAATT-AAAACTATTAT
43680023 TTTTATAATT-AAACTATTAT
1 TTTTATAATTAAAACTATTAT
43680043 TATTTA
1 T-TTTA
43680049 ATTTAAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
22 10 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATAATTAAAACTATTAT
Found at i:43681797 original size:23 final size:23
Alignment explanation
Indices: 43681771--43681817 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
43681761 TTTGGTGCAG
*
43681771 TGCAGTTGTACTGCCTAGGGTCT
1 TGCAGTTGTACTGCCTAAGGTCT
43681794 TGCAGTTGTACTGCCTAAGGTCT
1 TGCAGTTGTACTGCCTAAGGTCT
43681817 T
1 T
43681818 TTTTCTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (23 bp):
TGCAGTTGTACTGCCTAAGGTCT
Found at i:43681920 original size:26 final size:26
Alignment explanation
Indices: 43681891--43681941 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
43681881 CCCTTTTACT
43681891 TCTACTTCTTGTTTTAAACACTTTCC
1 TCTACTTCTTGTTTTAAACACTTTCC
*
43681917 TCTACTTCTTGTTTTAAACCCTTTC
1 TCTACTTCTTGTTTTAAACACTTTC
43681942 TTGCATGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (26 bp):
TCTACTTCTTGTTTTAAACACTTTCC
Found at i:43683154 original size:589 final size:589
Alignment explanation
Indices: 43682038--43683336 Score: 2526
Period size: 589 Copynumber: 2.2 Consensus size: 589
43682028 GTGTTGTTGC
43682038 ATGTAAATCTGGCTTTAGTGGTAATATATATTTCCATATTTCCTTTTATCTGACTTTGCAATTGC
1 ATGTAAATCTGGCTTTAGTGGTAATATATATTTCCATATTTCCTTTTATCTGACTTTGCAATTGC
43682103 ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTTTGTATTTTTCTTGAATGATCTGCT
66 ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTTTGTATTTTTCTTGAATGATCTGCT
43682168 TATATTGTGCTCTGGATTTAAAAAAAAAGAAGCAAATTTACGTGTATTGAAGTTAGCTTTGAAAA
131 TATATTGTGCTCTGGATTTAAAAAAAAAGAAGCAAATTTACGTGTATTGAAGTTAGCTTTGAAAA
43682233 TTGTCCATGAAGCATGAAGTTTAGATTGTGATCTGTTTATATTGTGCTCTAGGTTATTCCCCTTA
196 TTGTCCATGAAGCATGAAGTTTAGATTGTGATCTGTTTATATTGTGCTCTAGGTTATTCCCCTTA
43682298 TCATTATACTTATTGGATGTCATTACAACTTAGTGCACTGTCCCTTGCATCTTGTGACAAAATTT
261 TCATTATACTTATTGGATGTCATTACAACTTAGTGCACTGTCCCTTGCATCTTGTGACAAAATTT
43682363 GCAAATTTTATGCTCTTGGGTTGTTTTTACATTTAAATCATATGGCATATTATATTTATGGTTTA
326 GCAAATTTTATGCTCTTGGGTTGTTTTTACATTTAAATCATATGGCATATTATATTTATGGTTTA
*
43682428 GGGATACTGCCTTTGAGTCTTCTTTTTTTGGTTTGATATGGCCAGTTCTAGTTGCTGGAGTGCAA
391 GGGATAATGCCTTTGAGTCTTCTTTTTTTGGTTTGATATGGCCAGTTCTAGTTGCTGGAGTGCAA
*
43682493 ATCTGCGCCAGGCTCCATGCCTGATTGTTCTTGCTTATTCTTCATTGTAATGAAATTATAACTGA
456 ACCTGCGCCAGGCTCCATGCCTGATTGTTCTTGCTTATTCTTCATTGTAATGAAATTATAACTGA
43682558 AACTTTAATTGAGGTACAAAGCTATTGGACTAGTTTGAATTATATCTAGTTTGTAAATGAAAAAC
521 AACTTTAATTGAGGTACAAAGCTATTGGACTAGTTTGAATTATATCTAGTTTGTAAATGAAAAAC
43682623 TCGG
586 TCGG
43682627 ATGTAAATCTGGCTTTAGTGGTAATATATATTTCCATATTTCCTTTTATCTGACTTTGCAATTGC
1 ATGTAAATCTGGCTTTAGTGGTAATATATATTTCCATATTTCCTTTTATCTGACTTTGCAATTGC
43682692 ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTTTGTATTTTTCTTGAATGATCTGCT
66 ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTTTGTATTTTTCTTGAATGATCTGCT
43682757 TATATTGTGCTCTGGATTTAAAAAAAAAGAAGCAAATTTACGTGTATTGAAGTTAGCTTTGAAAA
131 TATATTGTGCTCTGGATTTAAAAAAAAAGAAGCAAATTTACGTGTATTGAAGTTAGCTTTGAAAA
43682822 TTGTCCATGAAGCATGAAGTTTAGATTGTGATCTGTTTATATTGTGCTCTAGGTTATTCCCCTTA
196 TTGTCCATGAAGCATGAAGTTTAGATTGTGATCTGTTTATATTGTGCTCTAGGTTATTCCCCTTA
43682887 TCATTATACTTATTGGATGTCATTACAACTTAGTGCACTGTCCCTTGCATCTTGTGACAAAATTT
261 TCATTATACTTATTGGATGTCATTACAACTTAGTGCACTGTCCCTTGCATCTTGTGACAAAATTT
43682952 GCAAATTTTATGCTCTTGGGTTGTTTTTACATTTAAATCATATGGCATATTATATTTATGGTTTA
326 GCAAATTTTATGCTCTTGGGTTGTTTTTACATTTAAATCATATGGCATATTATATTTATGGTTTA
*
43683017 GGGATAATGCCTTTGAGTCTTCTTTTTTTGGTTTGATATGGCCAGTTCTAGTTGCTGGAGTGCAG
391 GGGATAATGCCTTTGAGTCTTCTTTTTTTGGTTTGATATGGCCAGTTCTAGTTGCTGGAGTGCAA
43683082 ACCTGCGCCAGGCTCCATGCCTGATTGTTCTTGCTTATTCTTCATTGTAATGAAATTATAACTGA
456 ACCTGCGCCAGGCTCCATGCCTGATTGTTCTTGCTTATTCTTCATTGTAATGAAATTATAACTGA
*
43683147 AACTTTAATTGAGGTACAAAGCTATTGGACTAGTTTGAATTGTATCTAGTTTGTAAATGAAAAAC
521 AACTTTAATTGAGGTACAAAGCTATTGGACTAGTTTGAATTATATCTAGTTTGTAAATGAAAAAC
43683212 TCGG
586 TCGG
* * *
43683216 ATGTAAATCTAGCTTTAGTGGTAATACATATTTCCATATTTCCTTTTATCTGGCTTTGCAATTGC
1 ATGTAAATCTGGCTTTAGTGGTAATATATATTTCCATATTTCCTTTTATCTGACTTTGCAATTGC
*
43683281 ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTCTGTATTTTTCTTGAA
66 ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTTTGTATTTTTCTTGAA
43683337 AATGGTTTCT
Statistics
Matches: 702, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
589 702 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (589 bp):
ATGTAAATCTGGCTTTAGTGGTAATATATATTTCCATATTTCCTTTTATCTGACTTTGCAATTGC
ATGTAAATCTGTTGTTGAAGTTTTCAATTGAAAATGGTTTTTGTATTTTTCTTGAATGATCTGCT
TATATTGTGCTCTGGATTTAAAAAAAAAGAAGCAAATTTACGTGTATTGAAGTTAGCTTTGAAAA
TTGTCCATGAAGCATGAAGTTTAGATTGTGATCTGTTTATATTGTGCTCTAGGTTATTCCCCTTA
TCATTATACTTATTGGATGTCATTACAACTTAGTGCACTGTCCCTTGCATCTTGTGACAAAATTT
GCAAATTTTATGCTCTTGGGTTGTTTTTACATTTAAATCATATGGCATATTATATTTATGGTTTA
GGGATAATGCCTTTGAGTCTTCTTTTTTTGGTTTGATATGGCCAGTTCTAGTTGCTGGAGTGCAA
ACCTGCGCCAGGCTCCATGCCTGATTGTTCTTGCTTATTCTTCATTGTAATGAAATTATAACTGA
AACTTTAATTGAGGTACAAAGCTATTGGACTAGTTTGAATTATATCTAGTTTGTAAATGAAAAAC
TCGG
Found at i:43683336 original size:24 final size:24
Alignment explanation
Indices: 43683299--43683355 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
43683289 CTGTTGTTGA
43683299 AGTTTTCAATTGAAAATGGTTTCTGT
1 AGTTTTC--TTGAAAATGGTTTCTGT
*
43683325 ATTTTTCTTGAAAATGGTTTCTGT
1 AGTTTTCTTGAAAATGGTTTCTGT
43683349 AGTTTTC
1 AGTTTTC
43683356 AATTTGTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 23 0.79
26 6 0.21
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.51
Consensus pattern (24 bp):
AGTTTTCTTGAAAATGGTTTCTGT
Found at i:43685040 original size:45 final size:44
Alignment explanation
Indices: 43684957--43685043 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
43684947 AATATCATTC
* **
43684957 CATTCAACCAAACACAAGAATACTATTATGCCTCTATTCCATCA
1 CATTCAACCAAACACAAGAATACTATTACGCAACTATTCCATCA
43685001 CATTCAACCAAACA-ATTA-AATTACTATTACGCAACTATTCCAT
1 CATTCAACCAAACACA--AGAA-TACTATTACGCAACTATTCCAT
43685044 TACAGCTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 1 0.03
44 16 0.43
45 20 0.54
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.29
Consensus pattern (44 bp):
CATTCAACCAAACACAAGAATACTATTACGCAACTATTCCATCA
Found at i:43688356 original size:44 final size:43
Alignment explanation
Indices: 43688283--43688481 Score: 156
Period size: 43 Copynumber: 4.6 Consensus size: 43
43688273 TGATTTCATA
* *
43688283 TAAGACCATAGCTGGGCTATGGCACCGATATATGAGACTTTGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATATGAGA-TTTGTG
* * *
43688327 TAAGACCATATCTGGGATATAGCATCGATATAT-ATGATTACGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATATGA-GATT-TGTG
* *
43688371 TAAGACCAT-GTCTGGGACATTGGCATCG-T-TATGTGATTTCGTG
1 TAAGACCATAG-CTGGGATA-TGGCATCGATATATGAGATTT-GTG
* * * * ***
43688414 TAAGACCATAGCTGGGCTATTGACATCGATATGTGATA-ACATG
1 TAAGACCATAGCTGGGATA-TGGCATCGATATATGAGATTTGTG
* *
43688457 TAAGGCCATATCTGGGATATGGCAT
1 TAAGACCATAGCTGGGATATGGCAT
43688482 TGTATGTGTT
Statistics
Matches: 123, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
42 5 0.04
43 54 0.44
44 53 0.43
45 11 0.09
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (43 bp):
TAAGACCATAGCTGGGATATGGCATCGATATATGAGATTTGTG
Found at i:43694335 original size:49 final size:45
Alignment explanation
Indices: 43694247--43694348 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 45
43694237 TTCATATAGA
* * *
43694247 ACTACACTTCTTTTATTTTATTTTAGAATAAGGTTTTTCAACCTT
1 ACTACACTTCATTTATTTTATTTTAGAATAAGATGTTTCAACCTT
*
43694292 ATTACACTTCATTTATTTGATATTGATTAGAATAAGATGTTTCAACCTT
1 ACTACACTTCATTTATTT--TATT--TTAGAATAAGATGTTTCAACCTT
43694341 ACTACACT
1 ACTACACT
43694349 CCTTCTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 16 0.33
47 4 0.08
49 28 0.58
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (45 bp):
ACTACACTTCATTTATTTTATTTTAGAATAAGATGTTTCAACCTT
Found at i:43698841 original size:49 final size:49
Alignment explanation
Indices: 43698742--43698841 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 49
43698732 TTATTTTATT
* * * ** *
43698742 TTAGAATAAGGTTTTTCAACCTTATTATACTTTATCTATTTGATATTGA
1 TTAGAATAAGGTGTTTCAACCTTACTACACCCTATCTATTAGATATTGA
43698791 TTAGAATAAGGTGTTTCAACCTTACTACACCCCT-TCTATTAGA-ATATGA
1 TTAGAATAAGGTGTTTCAACCTTACTACA-CCCTATCTATTAGATAT-TGA
43698840 TT
1 TT
43698842 TTACAAGCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
48 2 0.05
49 39 0.91
50 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (49 bp):
TTAGAATAAGGTGTTTCAACCTTACTACACCCTATCTATTAGATATTGA
Found at i:43705132 original size:12 final size:12
Alignment explanation
Indices: 43705115--43705139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43705105 AGCAACAATG
43705115 ATTTTAGTTTTT
1 ATTTTAGTTTTT
43705127 ATTTTAGTTTTT
1 ATTTTAGTTTTT
43705139 A
1 A
43705140 GTTTCTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
ATTTTAGTTTTT
Found at i:43713433 original size:16 final size:16
Alignment explanation
Indices: 43713412--43713452 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
43713402 AAATATTATT
43713412 ATTAAATTCAAATGAA
1 ATTAAATTCAAATGAA
* *
43713428 ATTAAACTGAAATGAA
1 ATTAAATTCAAATGAA
*
43713444 ATGAAATTC
1 ATTAAATTC
43713453 CAAAGACTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (16 bp):
ATTAAATTCAAATGAA
Found at i:43714196 original size:19 final size:19
Alignment explanation
Indices: 43714172--43714208 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43714162 TGAAACAAGT
*
43714172 TATAATTTTTTTAAAAATA
1 TATAATATTTTTAAAAATA
*
43714191 TATAATATTTTTAGAAAT
1 TATAATATTTTTAAAAAT
43714209 TACTTGCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATAATATTTTTAAAAATA
Found at i:43714703 original size:15 final size:16
Alignment explanation
Indices: 43714681--43714716 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43714671 AGGGTGATGA
* *
43714681 TAAAAAAAATATAAAT
1 TAAAAAAATTAAAAAT
43714697 TAAAAAAATTAAAAAT
1 TAAAAAAATTAAAAAT
43714713 TAAA
1 TAAA
43714717 TAAAGGACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAAAATTAAAAAT
Found at i:43729681 original size:45 final size:45
Alignment explanation
Indices: 43729617--43729705 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
43729607 AATAGATACT
* *
43729617 CGATGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGATGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
* *
43729662 CGATGGAATCAGCACATAGCAACTACCTTACTAATCAATGATGT
1 CGATGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
43729706 TCAGTTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (45 bp):
CGATGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:43729771 original size:51 final size:50
Alignment explanation
Indices: 43729716--43729899 Score: 190
Period size: 51 Copynumber: 3.6 Consensus size: 50
43729706 TCAGTTCACA
* * * *
43729716 TAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATTTGATCCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGATACACG
* * * * * * *
43729767 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTCGATACACG
* * * * *
43729818 TAGTAGCCTGCACATAGTACTACACATGCGGCC-TATCATTCCAGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGA-TACACG
43729868 TAGTAGCCTGCACATAGTACTACACACGTGAC
1 TAGTAGCCTGCACATAGTACTACACACGTGAC
43729900 AATCCCTTTC
Statistics
Matches: 105, Mismatches: 26, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
49 4 0.04
50 34 0.32
51 65 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGATACACG
Found at i:43729892 original size:101 final size:101
Alignment explanation
Indices: 43729714--43729898 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
43729704 GTTCAGTTCA
* * ** *
43729714 CATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATTTGATCCACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATTCCATACACGTAGTAGCCTGCA
43729779 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* *
43729816 CATAGTAGCCTGCACATAGTACTACACATGCGGCC-TATCATTCCAGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCCA-TACACGTAGTAGCCTGCA
43729880 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
43729899 CAATCCCTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 7 0.09
101 36 0.48
102 32 0.43
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCCATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:43730172 original size:30 final size:30
Alignment explanation
Indices: 43730131--43730187 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
43730121 AAAATCATAC
* *
43730131 TTTTGCAAAATTATGTTTTTGCCCCTAAAG
1 TTTTACAAAATTATGATTTTGCCCCTAAAG
43730161 TTTTACAAAATTATGATTTTGCCCCTA
1 TTTTACAAAATTATGATTTTGCCCCTA
43730188 GGCTCGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTTACAAAATTATGATTTTGCCCCTAAAG
Found at i:43731162 original size:19 final size:19
Alignment explanation
Indices: 43731138--43731175 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
43731128 TTGGGTTAGG
43731138 GACTAAATTGTAA-AAACTA
1 GACTAAATTG-AATAAACTA
43731157 GACTAAATTGAATAAACTA
1 GACTAAATTGAATAAACTA
43731176 TGAAGCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
GACTAAATTGAATAAACTA
Found at i:43733474 original size:42 final size:44
Alignment explanation
Indices: 43733422--43733506 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
43733412 TAAACATTAA
*
43733422 AAAATTATTTTAAAAATAAAAAA-AATAAA-AAAAAAT-TATTTT
1 AAAAGTATTTTAAAAATAAAAAATAA-AAATAAAAAATATATTTT
*
43733464 AAAAGTATTTTAAAATTAAAAAATAAAAATAAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAATAAAAAATATATTT
43733507 ATTATATTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 24 0.63
43 9 0.24
44 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (44 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAATAAAAAATATATTTT
Found at i:43734405 original size:6 final size:6
Alignment explanation
Indices: 43734394--43734441 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
43734384 GTCTCCCTGC
* *
43734394 AAAATA AAAATA AAAATA AATAATA AGAAA-A AAAATT AAAATT AAAAT
1 AAAATA AAAATA AAAATA AA-AATA A-AAATA AAAATA AAAATA AAAAT
43734442 GGGTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
5 3 0.08
6 27 0.71
7 7 0.18
8 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:43734416 original size:16 final size:16
Alignment explanation
Indices: 43734395--43734441 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
43734385 TCTCCCTGCA
43734395 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
* *
43734411 AAATAATAAGAAAAA-
1 AAATAAAAATAAAAAT
* *
43734426 AAATTAAAATTAAAAT
1 AAATAAAAATAAAAAT
43734442 GGGTATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:43737029 original size:14 final size:13
Alignment explanation
Indices: 43737000--43737033 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
43736990 GGTAATTTTT
43737000 TAAAAGAAAAAAA
1 TAAAAGAAAAAAA
*
43737013 TAAAATAAAATAAA
1 TAAAAGAAAA-AAA
43737027 TAAAAGA
1 TAAAAGA
43737034 CGATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
TAAAAGAAAAAAA
Found at i:43748861 original size:7 final size:7
Alignment explanation
Indices: 43748849--43748873 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43748839 TTAAAAGAAG
43748849 AAATTCT
1 AAATTCT
43748856 AAATTCT
1 AAATTCT
43748863 AAATTCT
1 AAATTCT
43748870 AAAT
1 AAAT
43748874 CCAAAATCCA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTCT
Found at i:43755745 original size:137 final size:137
Alignment explanation
Indices: 43755515--43755906 Score: 590
Period size: 140 Copynumber: 2.8 Consensus size: 137
43755505 TAGAAAAATG
* * *
43755515 AATTATATTCTTTCC-AAAAGATATTAATTTCCATGCCTTTTATATTTTAACCGAAGTTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAA-TTAATTAA
*
43755579 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC-AATT
65 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
43755643 CATATATT
130 CATATATT
* *
43755651 AATTATATTCTTTCCAAAAAAATAATAATTTCAATGTCTTTTATATTTTGACCGATATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGA-ATTAATTAA
* * *
43755716 TATAACTATTTATATTAATAAATTTGGTAAAATATAAATATAAATAATATTTTGTATGAATCAAA
65 TATAACTATTTATATTAATAAATTCGGTAAAATAT--ATACAATTAATATTTTGTATGAATCAAA
43755781 TTCATATATT
128 TTCATATATT
* * * *
43755791 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATATTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACC-GAATTAATTAA
* *
43755856 TATATCTATTTATATTAATAAATTCGGTAAAATGTATACAATTAATATTTT
65 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTT
43755907 ATATTTTGAT
Statistics
Matches: 230, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
136 15 0.07
137 75 0.33
138 15 0.07
139 23 0.10
140 101 0.44
141 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAATTAATTAAT
ATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:43759334 original size:18 final size:17
Alignment explanation
Indices: 43759282--43759331 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
43759272 GTTGGGCTTG
*
43759282 GCCTTTCCATTGTCCTTA
1 GCCTTTCCTTTG-CCTTA
* *
43759300 GGCTTTGCCTTAGCCTTA
1 GCCTTT-CCTTTGCCTTA
43759318 GCCTTTCCTTTGCC
1 GCCTTTCCTTTGCC
43759332 CTTGTTCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.08, C:0.34, G:0.16, T:0.42
Consensus pattern (17 bp):
GCCTTTCCTTTGCCTTA
Found at i:43763195 original size:27 final size:27
Alignment explanation
Indices: 43763165--43763560 Score: 318
Period size: 27 Copynumber: 14.8 Consensus size: 27
43763155 TCATCTCTTA
**
43763165 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
43763192 GGGGTATTTC-GATCATTTTACCTTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * *
43763219 AGGGTATTTCGGTCATATTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
43763246 AGGATATTTCAGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
43763273 GGGGTATTTCAATCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
** *
43763299 GGGGTATTTTGGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
43763326 GGGGTAGTTT-GGTCATTCTACCCTAAG
1 GGGGTA-TTTCAGTCATTTTACCCTATG
* * * *
43763353 AGGGTATTTCGGTCATCTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
43763380 AGGGTATTTTAGTCATTTTATCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
*** *
43763407 GGGGTATTTTTTTCATTCTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
43763433 AGGGTATTTCAGTCATTTTATCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * * *
43763460 GGGGTATTTCGGTTATTTTATCTTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
43763487 AGGGTATTTCGGTAATTTTACCTTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
** *
43763513 -GGGTATTTTGGTCAGTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* **
43763539 AGGGTATTTTGGTCATTTTACC
1 GGGGTATTTCAGTCATTTTACC
43763561 TATTTTGGGG
Statistics
Matches: 310, Mismatches: 51, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
25 21 0.07
26 46 0.15
27 239 0.77
28 4 0.01
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:43763224 original size:54 final size:54
Alignment explanation
Indices: 43763174--43763560 Score: 379
Period size: 54 Copynumber: 7.2 Consensus size: 54
43763164 AGGGGTATAA
* *
43763174 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATGAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
* * * * * * *
43763228 CGGTCATATTACCCTATGAGGATATTTCAGTCATTCTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
* * * *
43763282 CAATCATTTTACCCTAT-GGGGTATTTTGGTCATTCTACCCTATGGGGGTAGTTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTA-TTT
* * * * * *
43763336 -GGTCATTCTACCCTAAGAGGGTATTTCGGTCATCTTACCCTATAAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
* * * *** *
43763389 TAGTCATTTTATCCTATAGGGGTATTTTTTTCATTCTACCCTAT-AGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
* * * * * *
43763442 CAGTCATTTTATCCTATAGGGGTATTTCGGTTATTTTATCTTATAAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
* * * * *
43763496 CGGTAATTTTACCTTAT--GGGTATTTTGGTCAGTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
**
43763548 TGGTCATTTTACC
1 CAGTCATTTTACC
43763561 TATTTTGGGG
Statistics
Matches: 272, Mismatches: 57, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
52 40 0.15
53 89 0.33
54 143 0.53
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (54 bp):
CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGAGGGTATTT
Found at i:43763360 original size:134 final size:132
Alignment explanation
Indices: 43763174--43763547 Score: 430
Period size: 134 Copynumber: 2.8 Consensus size: 132
43763164 AGGGGTATAA
* *
43763174 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATGAGGGTATTTCGGTCATATTA
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTAAGAGGGTATTTCGGTCATATTA
* * *
43763239 CCCTATGAGGATATTTCAGTCATTCTACCCTATGGGGGTATTTCAATCATTTTACCCTATGGGGT
66 CCCTATGAGG-TATTTTAGTCATT-TACCCTATGGGGGTATTTCAATCATTCTACCCTATAGGGT
43763304 ATTT
129 ATTT
** * * * *
43763308 TGGTCATTCTACCCTATGGGGGTAGTTT-GGTCATTCTACCCTAAGAGGGTATTTCGGTCATCTT
1 CAGTCATTTTACCCTATGGGGGTA-TTTCGGTCATTTTACCTTAAGAGGGTATTTCGGTCATATT
* * * ***
43763372 ACCCTATAAGGGTATTTTAGTCATTTTATCCTATAGGGGTATTTTTTTCATTCTACCCTATAGGG
65 ACCCTATGA-GGTATTTTAGTCA-TTTACCCTATGGGGGTATTTCAATCATTCTACCCTATAGGG
43763437 TATTT
128 TATTT
* * * * * *
43763442 CAGTCATTTTATCCTATAGGGGTATTTCGGTTATTTTATCTTATA-AGGGTATTTCGGTAATTTT
1 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTA-AGAGGGTATTTCGGTCATATT
* * *
43763506 ACCTTATG-GGTATTTTGGTCAGTTTACCCTATGAGGGTATTT
65 ACCCTATGAGGTATTTTAGTCA-TTTACCCTATGGGGGTATTT
43763548 TGGTCATTTT
Statistics
Matches: 200, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
132 29 0.14
133 3 0.01
134 160 0.80
135 8 0.04
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (132 bp):
CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTAAGAGGGTATTTCGGTCATATTA
CCCTATGAGGTATTTTAGTCATTTACCCTATGGGGGTATTTCAATCATTCTACCCTATAGGGTAT
TT
Found at i:43766085 original size:79 final size:82
Alignment explanation
Indices: 43765974--43766158 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
43765964 GCTACTCGTT
* *
43765974 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
43766037 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
43766054 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
43766117 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
43766134 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43766159 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:43766158 original size:40 final size:40
Alignment explanation
Indices: 43765955--43766158 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
43765945 CGGAATTTAA
** *
43765955 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
43765995 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
43766035 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
43766074 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
43766114 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
43766154 CCGGA
1 CCGGA
43766159 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:43774839 original size:6 final size:6
Alignment explanation
Indices: 43774828--43774858 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
43774818 AAAAAGAACA
43774828 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
43774859 GGAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:43779352 original size:20 final size:21
Alignment explanation
Indices: 43779312--43779352 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43779302 ATTTTTTTTT
*
43779312 ATCTTTTAGTCCCAGAATCAA
1 ATCTTTTAGTCCCAAAATCAA
43779333 ATCTTTTAGT-CCAAAATCAA
1 ATCTTTTAGTCCCAAAATCAA
43779353 GCTGTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (21 bp):
ATCTTTTAGTCCCAAAATCAA
Found at i:43784648 original size:13 final size:14
Alignment explanation
Indices: 43784578--43784651 Score: 53
Period size: 14 Copynumber: 5.2 Consensus size: 14
43784568 CTCGCAAGAC
43784578 TTTTCACTTTTTTT
1 TTTTCACTTTTTTT
* *
43784592 TTCTT-TCTTCTTTT
1 TT-TTCACTTTTTTT
* *
43784606 TTTTAACTCGATTTTT
1 TTTTCACT--TTTTTT
* *
43784622 TTGTCACTTCTTTT
1 TTTTCACTTTTTTT
43784636 TTTTC-CTTTTTTT
1 TTTTCACTTTTTTT
43784649 TTT
1 TTT
43784652 GATTTTTTTG
Statistics
Matches: 45, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
13 12 0.27
14 21 0.47
15 2 0.04
16 10 0.22
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTCACTTTTTTT
Found at i:43784659 original size:21 final size:21
Alignment explanation
Indices: 43784633--43784691 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
43784623 TGTCACTTCT
43784633 TTTTTTTCCTTTTTTTTTTGA
1 TTTTTTTCCTTTTTTTTTTGA
***
43784654 TTTTTTTGAATTTTTTTTTGA
1 TTTTTTTCCTTTTTTTTTTGA
* *
43784675 ATTTCTTCTCTTTTTTT
1 TTTTTTTC-CTTTTTTT
43784692 ATATCCAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTTTCCTTTTTTTTTTGA
Found at i:43784669 original size:12 final size:12
Alignment explanation
Indices: 43784643--43784678 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
43784633 TTTTTTTCCT
43784643 TTTTTTTTTG-A
1 TTTTTTTTTGAA
43784654 --TTTTTTTGAA
1 TTTTTTTTTGAA
43784664 TTTTTTTTTGAA
1 TTTTTTTTTGAA
43784676 TTT
1 TTT
43784679 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.36
10 1 0.05
12 13 0.59
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:43797277 original size:140 final size:139
Alignment explanation
Indices: 43797025--43797437 Score: 602
Period size: 140 Copynumber: 3.0 Consensus size: 139
43797015 TAGAAAAATA
* * *
43797025 AATTATATTCTTTCTAAAAGAATATTAATTTGTATATCTTTTATATTTTGACCGAAATTAATTTA
1 AATTATATTCTTTCTAAACGAATATTAATTTCTATGTCTTTTATATTTTGACCGAAATTAATTTA
* * * *
43797090 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACTATTAATATTTTGTATGAATTAAATT
66 TATAACTATTTATATTAATAAATTCGGTAAAATAT-TACAATTAATATTTTGTATGAATCAAATT
43797155 CATATATATT
130 CATATATATT
* * *
43797165 AATTATATTCTTTCCAAACTAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAA-TTA
1 AATTATATTCTTTCTAAACGAATATTAATTTCTATGTCTTTTATATTTTGACCGAAATTAATTTA
*
43797229 GTATAACTTTTTATATTAATAAATTCGGTAAAATATTGACAATTAATATTTTGTATGAATCAAAT
66 -TATAACTATTTATATTAATAAATTCGGTAAAATATT-ACAATTAATATTTTGTATGAATCAAAT
43797294 TC--ATATATT
129 TCATATATATT
* * *
43797303 AATTATATTCTTT-TTAACGGAATATTAATTTCTATGTCTTCTATATCTTGACCGAAATTAATTT
1 AATTATATTCTTTCTAAAC-GAATATTAATTTCTATGTCTTTTATATTTTGACCGAAATTAATTT
* * *
43797367 ATATAACTATTTATATTAATAAATTCGGTAATATA-TATAATTAATATTTTGTATGAATCAAACT
65 ATATAACTATTTATATTAATAAATTCGGTAAAATATTACAATTAATATTTTGTATGAATCAAATT
43797431 CATATAT
130 CATATAT
43797438 TAATTTTATC
Statistics
Matches: 247, Mismatches: 20, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
136 27 0.11
137 4 0.02
138 94 0.38
139 7 0.03
140 115 0.47
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (139 bp):
AATTATATTCTTTCTAAACGAATATTAATTTCTATGTCTTTTATATTTTGACCGAAATTAATTTA
TATAACTATTTATATTAATAAATTCGGTAAAATATTACAATTAATATTTTGTATGAATCAAATTC
ATATATATT
Found at i:43801901 original size:26 final size:26
Alignment explanation
Indices: 43801832--43801902 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
43801822 CGTTCTGACC
* **
43801832 CACAGCTCATGTGAGCAGGCTCATTT
1 CACAGCTCGTGTGAGCATACTCATTT
* *
43801858 CACAGCCCGTGTAAGCATACTCATTT
1 CACAGCTCGTGTGAGCATACTCATTT
*
43801884 CATAGCTCGTGTGAGCATA
1 CACAGCTCGTGTGAGCATA
43801903 TATGTACAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATACTCATTT
Found at i:43808792 original size:15 final size:15
Alignment explanation
Indices: 43808772--43808801 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43808762 ATGTTATAAT
43808772 AATAAATAAAAAGAA
1 AATAAATAAAAAGAA
*
43808787 AATAAATGAAAAGAA
1 AATAAATAAAAAGAA
43808802 TATTAAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AATAAATAAAAAGAA
Found at i:43810116 original size:23 final size:25
Alignment explanation
Indices: 43810069--43810126 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
43810059 GGCTAAGGCT
43810069 ATGTTTGGTATGATAGCTTAGCTTA
1 ATGTTTGGTATGATAGCTTAGCTTA
*
43810094 ATGTTTGGTATG-T-GTTTAGCTTA
1 ATGTTTGGTATGATAGCTTAGCTTA
* *
43810117 AAGCTTGGTA
1 ATGTTTGGTA
43810127 GCCTAAGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 17 0.57
24 1 0.03
25 12 0.40
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.45
Consensus pattern (25 bp):
ATGTTTGGTATGATAGCTTAGCTTA
Found at i:43812701 original size:16 final size:17
Alignment explanation
Indices: 43812654--43812707 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
43812644 TCTGTATTAT
*
43812654 TATTTAA-AAATCAATA
1 TATTTAATAAATAAATA
*
43812670 TATTTAAT-TATAAA-A
1 TATTTAATAAATAAATA
43812685 TATTTTAATAAATAAATA
1 TA-TTTAATAAATAAATA
*
43812703 AATTT
1 TATTT
43812708 GAATTTAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 3 0.10
16 17 0.57
17 8 0.27
18 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTAATAAATAAATA
Found at i:43816760 original size:43 final size:45
Alignment explanation
Indices: 43816716--43816818 Score: 172
Period size: 47 Copynumber: 2.3 Consensus size: 45
43816706 CATTTAATTG
43816716 TTATTTATTTA-CTTAGTTTTAATCAAACTTACATTAGTATTTGT
1 TTATTTATTTATCTTAGTTTTAATCAAACTTACATTAGTATTTGT
*
43816760 TTATTTATTTATTGGTTAGTTTTAATCAAACTTACATTAGTATTTGT
1 TTATTTATTTA-T-CTTAGTTTTAATCAAACTTACATTAGTATTTGT
43816807 TTATTTATTTAT
1 TTATTTATTTAT
43816819 TGGTTTGTTC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
44 11 0.20
46 1 0.02
47 43 0.78
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (45 bp):
TTATTTATTTATCTTAGTTTTAATCAAACTTACATTAGTATTTGT
Found at i:43816785 original size:47 final size:47
Alignment explanation
Indices: 43816728--43816823 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
43816718 ATTTATTTAC
43816728 TTAGTTTTAATCAAACTTACATTAGTATTTGTTTATTTATTTATTGG
1 TTAGTTTTAATCAAACTTACATTAGTATTTGTTTATTTATTTATTGG
43816775 TTAGTTTTAATCAAACTTACATTAGTATTTGTTTATTTATTTATTGG
1 TTAGTTTTAATCAAACTTACATTAGTATTTGTTTATTTATTTATTGG
43816822 TT
1 TT
43816824 TGTTCATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (47 bp):
TTAGTTTTAATCAAACTTACATTAGTATTTGTTTATTTATTTATTGG
Found at i:43817446 original size:107 final size:107
Alignment explanation
Indices: 43817188--43817718 Score: 949
Period size: 107 Copynumber: 5.0 Consensus size: 107
43817178 TAAAGAAAGG
43817188 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * * *
43817253 CAATTTCTCGTTTGA-CCAAATAGCCAAGTATCCTTCTAAAA
66 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
*
43817294 TTTTAAAATAAGGCAATACTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
43817359 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
43817401 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
43817466 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
43817508 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
43817573 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
* *
43817615 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAACGTGCTGGATTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * * *
43817680 CGATTTCTCATTTGA-CCAAATAGCTAAATATCCTCTTAA
66 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAA
43817719 GTTTTAATCC
Statistics
Matches: 412, Mismatches: 12, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
106 99 0.24
107 313 0.76
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (107 bp):
TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
Found at i:43838331 original size:128 final size:128
Alignment explanation
Indices: 43837415--43838300 Score: 1396
Period size: 128 Copynumber: 6.9 Consensus size: 128
43837405 CAAAGAAGCC
* * * * *
43837415 AATCTTATCTCCCTGAATTTACAGTGGAGTGGATTAAAACCACAGATTTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* *
43837480 CAGTAAAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGACGAAAGAAAAG
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
* * *
43837543 AATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * **
43837608 CAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAACC
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
***
43837671 AAT-CTCATCTCCCTGAAGTTGCAGTGGAATAGATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 AATCCT-ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
* * * * *
43837735 ACAGTAGAGCAGATCGCGTCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAAATGAAAGAAAAG
65 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
*
43837799 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* **
43837864 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAATC
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
* * * *
43837927 AATCCCATCTCCCTGAAGTTGCAGTGGAACGAATTAAAACCACAGATATTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * * *
43837992 CAATAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTAGAGGAGACGAAAGAAAAG
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
*
43838055 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * *
43838120 CAGTAGAGCAGGTTGCATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACGAAAGAAAAG
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
*
43838183 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
*
43838248 CATTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGAC
43838301 TAAAACCACA
Statistics
Matches: 690, Mismatches: 66, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
127 2 0.00
128 686 0.99
129 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (128 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAAG
Found at i:43839030 original size:4 final size:4
Alignment explanation
Indices: 43839021--43839063 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
43839011 TTTTTTGATC
* * *
43839021 TATT TATT TATT TGTTT TATT TATT TATT TGTT TATT TTTT TA
1 TATT TATT TATT T-ATT TATT TATT TATT TATT TATT TATT TA
43839064 CGAATCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:43839041 original size:17 final size:16
Alignment explanation
Indices: 43839021--43839063 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
43839011 TTTTTTGATC
43839021 TATTTATTTATTTGTTT
1 TATTTATTTATTTG-TT
43839038 TATTTATTTATTTGTT
1 TATTTATTTATTTGTT
*
43839054 TATTTTTTTA
1 TATTTATTTA
43839064 CGAATCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (16 bp):
TATTTATTTATTTGTT
Found at i:43840042 original size:15 final size:15
Alignment explanation
Indices: 43840024--43840054 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43840014 AAATTTAAAT
43840024 TTATTATTATGGTTG
1 TTATTATTATGGTTG
*
43840039 TTATTATTATTGTTG
1 TTATTATTATGGTTG
43840054 T
1 T
43840055 AATATTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (15 bp):
TTATTATTATGGTTG
Found at i:43840551 original size:108 final size:106
Alignment explanation
Indices: 43840305--43840622 Score: 474
Period size: 108 Copynumber: 3.0 Consensus size: 106
43840295 TAAAGAAAGG
* *
43840305 TTTTAAAATAAGGCAATATTTTACGTTTGGAAATTTGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * *
43840370 CGATTTCTCGTTTGACCAAATAGCCAAGTATCCTTCTAAAA
66 CGATTTCTCATTTGACCAAATAGCCAAATATCCTTTTAAAA
* * *
43840411 TTTTAAAATAAGGTAATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAACGTGTTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * *
43840476 CGATTTCTCTTTTTTACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTC-ATTTGA-CCAAATAGCCAAATATCCTTTTAAAA
* * *
43840519 TTTTAAAATAAGGCAATATTTTGTGTTTGGAAATTCGAGAAAACCTGGCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* *
43840584 CGATTTCTCATTTGACCAAATAGCTAAATATCCTCTTAA
66 CGATTTCTCATTTGACCAAATAGCCAAATATCCTTTTAA
43840623 GTTTTAATCC
Statistics
Matches: 189, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
106 90 0.48
107 8 0.04
108 91 0.48
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (106 bp):
TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCATTTGACCAAATAGCCAAATATCCTTTTAAAA
Found at i:43840648 original size:108 final size:104
Alignment explanation
Indices: 43840318--43840630 Score: 385
Period size: 106 Copynumber: 3.0 Consensus size: 104
43840308 TAAAATAAGG
* * *
43840318 CAATATTTTACGTTTGGAAATTTGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCATTT
* * *
43840383 GACCAAATAGCCAAGTATCCTTCTAAAATTTTAAAATAAGGT
66 GACCAAATAGCCAAATATCC-TCTTAAATTTT--AATAAAGT
* * *
43840425 -AATATTTTGCGTTTGGAAATTCGAGAAAATGTGCCCTAACGTGTTGGGTTTCGATTTCTCTTTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC-ATT
* * * * *
43840489 TTACCCAAATAGCCAAATACCCTTTTAAAATTTTAAAATAAGG
65 TGA-CCAAATAGCCAAATATCCTCTT-AAATTTTAATA-AAGT
* * *
43840532 CAATATTTTGTGTTTGGAAATTCGAGAAAACCTGGCCTAACGTGCTGGGTTTCGATTTCTCATTT
1 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCATTT
* *
43840597 GACCAAATAGCTAAATATCCTCTTAAGTTTTAAT
66 GACCAAATAGCCAAATATCCTCTTAAATTTTAAT
43840631 CCATGTCATT
Statistics
Matches: 176, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
105 8 0.05
106 78 0.44
107 12 0.07
108 78 0.44
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (104 bp):
CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCATTT
GACCAAATAGCCAAATATCCTCTTAAATTTTAATAAAGT
Found at i:43851797 original size:30 final size:30
Alignment explanation
Indices: 43851761--43851819 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
43851751 TATTTTATTG
43851761 TTAATTTTGTTATTATTTTAAAGGCATTTC
1 TTAATTTTGTTATTATTTTAAAGGCATTTC
43851791 TTAATTTTGTTATTATTTTAAAGGCATTT
1 TTAATTTTGTTATTATTTTAAAGGCATTT
43851820 AATTGTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTC
Found at i:43854595 original size:25 final size:25
Alignment explanation
Indices: 43854547--43854605 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
43854537 GATATACATA
43854547 ATATACAAAATAAAAAAATGTAATAT
1 ATATA-AAAATAAAAAAATGTAATAT
*
43854573 ATATAAAAATAGAAGAAAT-TAATAT
1 ATATAAAAATA-AAAAAATGTAATAT
*
43854598 -TAAAAAAA
1 ATATAAAAA
43854606 AGGTCCGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.23
25 12 0.40
26 11 0.37
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (25 bp):
ATATAAAAATAAAAAAATGTAATAT
Found at i:43859082 original size:48 final size:50
Alignment explanation
Indices: 43859030--43859155 Score: 139
Period size: 50 Copynumber: 2.6 Consensus size: 50
43859020 TCACAGTATG
* * * *
43859030 AGTTGATGGAAGTTTGATGGCTGAGATGAT-AAA-ACATTTATCTACACA
1 AGTTGATGGAAGTTTGATGACTGAAATGATGAAACAAATCTATCTACACA
* * * * * *
43859078 AGTTGATGGAAGCTTGATGATTGAAATGATGAAACAAATCTCTTTGCATA
1 AGTTGATGGAAGTTTGATGACTGAAATGATGAAACAAATCTATCTACACA
*
43859128 AGTTGATGGAAGTTTGATGACTAAAATG
1 AGTTGATGGAAGTTTGATGACTGAAATG
43859156 TTAACTAGTC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
48 26 0.41
49 3 0.05
50 34 0.54
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.32
Consensus pattern (50 bp):
AGTTGATGGAAGTTTGATGACTGAAATGATGAAACAAATCTATCTACACA
Found at i:43864472 original size:5 final size:5
Alignment explanation
Indices: 43864462--43864490 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
43864452 GAAAACAAAG
43864462 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
43864491 GTTCTAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:43868620 original size:47 final size:47
Alignment explanation
Indices: 43868530--43868623 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
43868520 TCTGAAAAGT
* * *
43868530 TAGATTTTTAGGACACATTGTTTCGGCAGAAGGCATTATAGTTGATC
1 TAGATTTTTAGGACACATTGTTTCGACAGAAGGCATCAGAGTTGATC
*
43868577 TAGATTTTTAGGACACATTGTTTCGACAGAAGGCATCGGAGTTGATC
1 TAGATTTTTAGGACACATTGTTTCGACAGAAGGCATCAGAGTTGATC
43868624 CAAGCAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (47 bp):
TAGATTTTTAGGACACATTGTTTCGACAGAAGGCATCAGAGTTGATC
Found at i:43869670 original size:31 final size:31
Alignment explanation
Indices: 43869622--43869689 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
43869612 AGTCCCTTAT
*
43869622 AATACAAATAGTCAGATATACAGTATGCAGA
1 AATAGAAATAGTCAGATATACAGTATGCAGA
* *
43869653 AATAGAAATAGTTAGATATACGGTATGCAGA
1 AATAGAAATAGTCAGATATACAGTATGCAGA
43869684 AATAGA
1 AATAGA
43869690 CTAGGCCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.24
Consensus pattern (31 bp):
AATAGAAATAGTCAGATATACAGTATGCAGA
Found at i:43874214 original size:40 final size:40
Alignment explanation
Indices: 43874144--43874481 Score: 416
Period size: 40 Copynumber: 8.5 Consensus size: 40
43874134 AAATCACGTA
* * **
43874144 CCTTCGGAATTTAA-CCGGATATAGCT-ACTCGTTCAAATG
1 CCTTCGGAACTTAACCCGGATTTAG-TAACTCGCACAAATG
* * *
43874183 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATG
1 CCTTCGGAACTTAACCCGGATT-TAGTAACTCGCACAAATG
43874223 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
43874263 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
43874303 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
* *
43874343 CCTTCGGAACTTAACTCGGATTTAGTAACTCGCACCAATG
1 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
* * * *
43874383 CCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCACAAATG
1 CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
* ** * * * *
43874422 CCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
1 CCTTCGGAACTTAACCCGGATTTAGTAAC-TCGCACAAATG
* *
43874462 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGAACTTAACCCGGA
43874482 CATCATTCTT
Statistics
Matches: 264, Mismatches: 29, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
39 45 0.17
40 209 0.79
41 10 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CCTTCGGAACTTAACCCGGATTTAGTAACTCGCACAAATG
Found at i:43886139 original size:23 final size:25
Alignment explanation
Indices: 43886093--43886139 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
43886083 CAACTTCTAA
43886093 AGAAAACTCAAGAGAGAAATTTTGG
1 AGAAAACTCAAGAGAGAAATTTTGG
43886118 AGAAAACTCAA-AGA-AAATTTTG
1 AGAAAACTCAAGAGAGAAATTTTG
43886140 CTCTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 11 0.50
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (25 bp):
AGAAAACTCAAGAGAGAAATTTTGG
Found at i:43894070 original size:20 final size:21
Alignment explanation
Indices: 43894045--43894083 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43894035 TTCGAAAGTG
*
43894045 AAAAG-AAGGAAAATGAGAGC
1 AAAAGAAAAGAAAATGAGAGC
43894065 AAAAGAAAAGAAAATGAGA
1 AAAAGAAAAGAAAATGAGA
43894084 AAAGTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.05
Consensus pattern (21 bp):
AAAAGAAAAGAAAATGAGAGC
Found at i:43902053 original size:23 final size:23
Alignment explanation
Indices: 43902023--43902076 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
43902013 AATAGGAAAC
*
43902023 TTAAATTTCCAATTTTTTTTGTT
1 TTAAATTTCCAATTTGTTTTGTT
43902046 TTAAATTTCCAATTTGTTTTGTT
1 TTAAATTTCCAATTTGTTTTGTT
43902069 TT-AATTTC
1 TTAAATTTC
43902077 AAATAAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.22, C:0.09, G:0.06, T:0.63
Consensus pattern (23 bp):
TTAAATTTCCAATTTGTTTTGTT
Found at i:43906990 original size:20 final size:20
Alignment explanation
Indices: 43906965--43907005 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43906955 ACCCAAAGAA
43906965 CATATTTTTAAGTTTATGTT
1 CATATTTTTAAGTTTATGTT
43906985 CATATTTTTAAGTTTATGTT
1 CATATTTTTAAGTTTATGTT
43907005 C
1 C
43907006 CTGAGCCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (20 bp):
CATATTTTTAAGTTTATGTT
Found at i:43909195 original size:17 final size:18
Alignment explanation
Indices: 43909164--43909197 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43909154 TAGTTAATTC
*
43909164 ATCAAATTAACTAATTTT
1 ATCAAATCAACTAATTTT
43909182 ATCAAATCAA-TAATTT
1 ATCAAATCAACTAATTT
43909198 ATCCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
ATCAAATCAACTAATTTT
Found at i:43911373 original size:20 final size:20
Alignment explanation
Indices: 43911321--43911373 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
43911311 AGTAACCCCT
43911321 AAAATTA-TATAAA-AATAAA
1 AAAATTACT-TAAATAATAAA
* **
43911340 AAAATAACCCAAATAATAAA
1 AAAATTACTTAAATAATAAA
43911360 AAAATTACTTAAAT
1 AAAATTACTTAAAT
43911374 GAAAATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATTACTTAAATAATAAA
Found at i:43912585 original size:20 final size:21
Alignment explanation
Indices: 43912544--43912587 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43912534 CACGCTATCT
*
43912544 AATTTAATTAAATTAGATAAA
1 AATTTAATTAAATTAAATAAA
*
43912565 AATTTATTTAAA-TAAATAAA
1 AATTTAATTAAATTAAATAAA
43912585 AAT
1 AAT
43912588 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTAATTAAATTAAATAAA
Found at i:43912596 original size:17 final size:17
Alignment explanation
Indices: 43912574--43912609 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
43912564 AAATTTATTT
43912574 AAATAAATAAAAATAAA
1 AAATAAATAAAAATAAA
*
43912591 AAATAAATAAAGATAAA
1 AAATAAATAAAAATAAA
43912608 AA
1 AA
43912610 TTAGCACGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (17 bp):
AAATAAATAAAAATAAA
Found at i:43913845 original size:17 final size:16
Alignment explanation
Indices: 43913805--43913846 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
43913795 TTGAATGAGT
*
43913805 AAACAAATAAATTATA
1 AAACAAATAAATAATA
43913821 AAAC--ATAAATAATTA
1 AAACAAATAAATAA-TA
43913836 AAACAAATAAA
1 AAACAAATAAA
43913847 ACTTAGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 4 0.18
17 5 0.23
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACAAATAAATAATA
Found at i:43916830 original size:22 final size:22
Alignment explanation
Indices: 43916803--43916856 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
43916793 GTTTATCGAT
*
43916803 TTATTTCGTTTGTTTATTT-TTC
1 TTATTTC-TTTATTTATTTCTTC
*
43916825 TTATTTCTTTATTTATTTCTTT
1 TTATTTCTTTATTTATTTCTTC
43916847 TTATTTCTTT
1 TTATTTCTTT
43916857 TATTCCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (22 bp):
TTATTTCTTTATTTATTTCTTC
Found at i:43916859 original size:9 final size:9
Alignment explanation
Indices: 43916836--43916877 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
43916826 TATTTCTTTA
43916836 TTTATTTCTT
1 TTTATTTC-T
43916846 TTTATTTCT
1 TTTATTTCT
*
43916855 TTTATTCCT
1 TTTATTTCT
*
43916864 TTTATTTAT
1 TTTATTTCT
43916873 TTTAT
1 TTTAT
43916878 GGTTTATCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTCT
Found at i:43918808 original size:6 final size:6
Alignment explanation
Indices: 43918790--43918821 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
43918780 TGCAAATGGA
43918790 TCATTT CTCATTT TCATTT TCATTT TCATTT T
1 TCATTT -TCATTT TCATTT TCATTT TCATTT T
43918822 TGAGAAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (6 bp):
TCATTT
Found at i:43923505 original size:24 final size:25
Alignment explanation
Indices: 43923478--43923535 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
43923468 GAAAATGAGC
*
43923478 TTAAAATAAGTAATATA-AATTGA-T
1 TTAAAATAAATAATATAGAA-TGATT
* *
43923502 TTAAAGTAAATAGTATAGAATGATT
1 TTAAAATAAATAATATAGAATGATT
43923527 TTAAAATAA
1 TTAAAATAA
43923536 TTATTACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.36
Consensus pattern (25 bp):
TTAAAATAAATAATATAGAATGATT
Found at i:43925389 original size:132 final size:131
Alignment explanation
Indices: 43925228--43925524 Score: 339
Period size: 131 Copynumber: 2.3 Consensus size: 131
43925218 CGCTGCAACT
* * * * * * *
43925228 TCAGGGAGATAAGACTTGTAACTTCAATCTAGTTTCCTACTACCTTGGGAAAATAAGATTCACCA
1 TCAGGGAGATAGGACTGGTGACTTAAATCTACTTCCCTACTACCTTGGGAAAATAAAATTCACCA
* * * * *
43925293 TCTTCGATCTGCTGCACTACTTCTTAGGGAGATA-AG-GTCTACAATA-TTCAACCTACTCCACT
66 TCTTCGATCTAC-CCACTACTGCTTAAGGA-A-ACAGAATCTACAA-ACTTCAACCTACTCCACT
43925355 GCTGC
127 GCTGC
* * * ** *
43925360 TCAGGGAGATAGGACTGGTGGCTTAAATCTTCTTCCCTACTACCTTGGGAAGATAAAATTCGTCG
1 TCAGGGAGATAGGACTGGTGACTTAAATCTACTTCCCTACTACCTTGGGAAAATAAAATTCACCA
*
43925425 TCTTCGATCTACCCACTACTGCTTAAGGAAACAGAATCTACAAACTTCAACTTACTCCACTGCTG
66 TCTTCGATCTACCCACTACTGCTTAAGGAAACAGAATCTACAAACTTCAACCTACTCCACTGCTG
43925490 C
131 C
* **
43925491 TCAGGGAGATAGGACTGGTGTCTTCGATCTACTT
1 TCAGGGAGATAGGACTGGTGACTTAAATCTACTT
43925525 TGATGCTAGT
Statistics
Matches: 139, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
129 1 0.01
130 4 0.03
131 71 0.51
132 63 0.45
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (131 bp):
TCAGGGAGATAGGACTGGTGACTTAAATCTACTTCCCTACTACCTTGGGAAAATAAAATTCACCA
TCTTCGATCTACCCACTACTGCTTAAGGAAACAGAATCTACAAACTTCAACCTACTCCACTGCTG
C
Found at i:43925498 original size:131 final size:132
Alignment explanation
Indices: 43925263--43925510 Score: 342
Period size: 131 Copynumber: 1.9 Consensus size: 132
43925253 AATCTAGTTT
* * * * *
43925263 CCTACTACCTTGGGAAAATAAGATTCACCATCTTCGATCTGCTGCACTACTTCTTAGGGAGATAA
1 CCTACTACCTTGGGAAAATAAAATTCACCATCTTCGATCTACTCCACTACTGCTTAAGGAGATAA
*
43925328 GGTCTACAATATTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTCT
66 GATCTACAATATTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTCT
43925393 TC
131 TC
* ** *
43925395 CCTACTACCTTGGGAAGATAAAATTCGTCGTCTTCGATCTAC-CCACTACTGCTTAAGGA-A-AC
1 CCTACTACCTTGGGAAAATAAAATTCACCATCTTCGATCTACTCCACTACTGCTTAAGGAGATA-
*
43925457 AGAATCTACAA-ACTTCAACTTACTCCACTGCTGCTCAGGGAGATAGGACTGGTG
65 AG-ATCTACAATA-TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTG
43925511 TCTTCGATCT
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
129 1 0.01
130 4 0.04
131 61 0.60
132 36 0.35
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
CCTACTACCTTGGGAAAATAAAATTCACCATCTTCGATCTACTCCACTACTGCTTAAGGAGATAA
GATCTACAATATTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTCT
TC
Found at i:43925577 original size:45 final size:45
Alignment explanation
Indices: 43925511--43926007 Score: 690
Period size: 45 Copynumber: 11.0 Consensus size: 45
43925501 AGGACTGGTG
* * * *
43925511 TCTTCGATCTACTTTGATGCTAGTACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * * *
43925556 TCTTCGATCTACTTTGCTGCTAATACATGAAGACAAGACCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
43925601 TCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
43925646 TCTTCGACCTACTTCACTGCCAATACAGGAAGACAAGAGT-TGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA-TCTGCTA
* *
43925691 TCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
43925736 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
43925781 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAAATATGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* **
43925826 TCTTCGATCTATTTCGCTGCCAATGTAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
43925871 TCTTCGATCTACTTCGCTACCAATACAGGAAGATAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
43925916 TCTTTGATCTACTTCACTGCCAATACAGGAAGACAAGATCCGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* **
43925961 TCTTCGCTCTACTTCGCTGCCAATACAAAAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
43926006 TC
1 TC
43926008 CTTTCTTTTC
Statistics
Matches: 397, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
44 1 0.00
45 395 0.99
46 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
Found at i:43927343 original size:46 final size:46
Alignment explanation
Indices: 43927272--43927364 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
43927262 TCCATTTTTA
* * *
43927272 CTTTTTTTTTGGACTCAAAGCGCCCTTTGTGGCTTTTTACCTTGGT
1 CTTTTTTTTAGGACTCAAAGCGCCCTTTGCGGCTTTTCACCTTGGT
* *
43927318 CTTTTTTTTAGGACTCAAAGTGCCCTTTGCGGGTTTTCACCTTGGT
1 CTTTTTTTTAGGACTCAAAGCGCCCTTTGCGGCTTTTCACCTTGGT
43927364 C
1 C
43927365 CCTTCTCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (46 bp):
CTTTTTTTTAGGACTCAAAGCGCCCTTTGCGGCTTTTCACCTTGGT
Found at i:43928261 original size:5 final size:5
Alignment explanation
Indices: 43928251--43928289 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
43928241 GGCCTCTCCA
43928251 TTTTC TTTTC TTTTC TTTT- TTTTCC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC TTTT
43928290 TCCATCATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:43928280 original size:20 final size:19
Alignment explanation
Indices: 43928251--43928290 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
43928241 GGCCTCTCCA
43928251 TTTTCTTTTCTTTTCTTTT
1 TTTTCTTTTCTTTTCTTTT
43928270 TTTTCCTTTTCTTTTCTTTT
1 TTTT-CTTTTCTTTTCTTTT
43928290 T
1 T
43928291 CCATCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTCTTTTCTTTTCTTTT
Found at i:43932084 original size:24 final size:25
Alignment explanation
Indices: 43932048--43932114 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
43932038 ATATTATACG
** *
43932048 AGAATGAGCTTAAAATAACTAATAT
1 AGAATGATTTTAAAATAAATAATAT
* *
43932073 A-AATTGA-TTTAAAGTAAATAGTAT
1 AGAA-TGATTTTAAAATAAATAATAT
43932097 AGAATGATTTTAAAATAA
1 AGAATGATTTTAAAATAA
43932115 TTATTATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
24 19 0.56
25 15 0.44
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (25 bp):
AGAATGATTTTAAAATAAATAATAT
Found at i:43932330 original size:14 final size:15
Alignment explanation
Indices: 43932296--43932333 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43932286 AATAGTAGCT
*
43932296 TAATAATAACAAGAA
1 TAATATTAACAAGAA
*
43932311 TAATATTAACAA-AC
1 TAATATTAACAAGAA
43932325 TAATATTAA
1 TAATATTAA
43932334 ACTTAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (15 bp):
TAATATTAACAAGAA
Found at i:43933814 original size:72 final size:72
Alignment explanation
Indices: 43933736--43933876 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 72
43933726 TGCTCCTAAT
* * *
43933736 CAATCACTTGTATTTCTATAAGCTCAAGCACATAAAACACAAGAAAAATCAGA-GAAAATGTAAA
1 CAATCACTTGTATTTCTACAAGCTCAAGCACACAAAACAAAAGAAAAATCA-ATGAAAATGTAAA
43933800 AATTTAAC
65 AATTTAAC
*
43933808 CAATCACTTGTATTTCTACAAGCTCAAGCACACAAAAGAAAAGAAAAATCAATGAAAATGTAAAA
1 CAATCACTTGTATTTCTACAAGCTCAAGCACACAAAACAAAAGAAAAATCAATGAAAATGTAAAA
43933873 ATTT
66 ATTT
43933877 GAAGCAAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 1 0.02
72 63 0.98
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.23
Consensus pattern (72 bp):
CAATCACTTGTATTTCTACAAGCTCAAGCACACAAAACAAAAGAAAAATCAATGAAAATGTAAAA
ATTTAAC
Found at i:43939553 original size:128 final size:128
Alignment explanation
Indices: 43939320--43939556 Score: 334
Period size: 128 Copynumber: 1.9 Consensus size: 128
43939310 AAAAATCTCA
*
43939320 ATATCAGAATTTGCAACGTTTCAAAATATTATATCAAGAGGTTTTCTAAGAAAAAGTATCAAATT
1 ATATCAAAATTTGCAACGTTTCAAAATATTATATCAAGAGGTTTTCTAAGAAAAAGTATCAAATT
* * *
43939385 ATTCATATATTTTAGTAAAAGAGCATTCCCATCAGAAAATCTCCATTGAGATGAAGAATTTCG
66 ATTCATATAATTTAGTAAAAGAGAATTCCCACCAGAAAATCTCCATTGAGATGAAGAATTTCG
* * * * * *
43939448 ATATCAAAATTTGTGAA-GTTTTAAAATGTTATA-CTAAGAGGTTTTCTGATAAATAGTATCAAA
1 ATATCAAAATTTG-CAACGTTTCAAAATATTATATC-AAGAGGTTTTCTAAGAAAAAGTATCAAA
* *
43939511 TTATTCATATAATTTCGTAAAAGAGAATTCCCACCAGGAAATCTCC
64 TTATTCATATAATTTAGTAAAAGAGAATTCCCACCAGAAAATCTCC
43939557 TTTAGTTAGT
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
127 1 0.01
128 92 0.97
129 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (128 bp):
ATATCAAAATTTGCAACGTTTCAAAATATTATATCAAGAGGTTTTCTAAGAAAAAGTATCAAATT
ATTCATATAATTTAGTAAAAGAGAATTCCCACCAGAAAATCTCCATTGAGATGAAGAATTTCG
Found at i:43939738 original size:120 final size:120
Alignment explanation
Indices: 43939578--43939818 Score: 401
Period size: 120 Copynumber: 2.0 Consensus size: 120
43939568 GAGATGAAGG
*
43939578 ATTTCATTAAATTAGGCTATAGACTATATTGCAAGAAAATTCAAATTGAGTGGTTAATTGTATAA
1 ATTTCATTAAATTAGGCTATAGACTATATTGCAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
* * *
43939643 AGTATTGATTTTTAGTAAGGAAAGAAGGAAAGGGTTTATGAGGTTATTTTACCCA
66 AGTATTGATTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGAGGTAATTTTACCCA
* * *
43939698 ATTTTATTAAATTAGGCTATGGACTATTTTGCAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
1 ATTTCATTAAATTAGGCTATAGACTATATTGCAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
* *
43939763 AGTATTGGTTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGGGGTAATTTTACCCA
66 AGTATTGATTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGAGGTAATTTTACCCA
43939818 A
1 A
43939819 GGTCTATTGT
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (120 bp):
ATTTCATTAAATTAGGCTATAGACTATATTGCAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
AGTATTGATTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGAGGTAATTTTACCCA
Found at i:43943702 original size:79 final size:81
Alignment explanation
Indices: 43943599--43943783 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
43943589 GCTCCTCGTT
** *
43943599 CAAATGCCTTCGGGACAGAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
* *
43943661 CGGATTTAGTAAC-TCGCA
63 CGGATATAGTAACTTAGCA
**
43943679 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
43943743 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
43943759 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43943784 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 5 0.05
79 52 0.57
80 34 0.37
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:43943783 original size:40 final size:40
Alignment explanation
Indices: 43943599--43943783 Score: 202
Period size: 40 Copynumber: 4.7 Consensus size: 40
43943589 GCTCCTCGTT
** * *
43943599 CAAATGCCTTCGGGACAGAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
43943639 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
43943679 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
43943718 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
43943759 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43943784 CATCATTCAA
Statistics
Matches: 123, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.02
39 30 0.24
40 75 0.61
41 14 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:43952870 original size:79 final size:81
Alignment explanation
Indices: 43952768--43952952 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
43952758 GCTCCTCGTT
* * *
43952768 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
43952831 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
43952848 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
43952912 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
43952928 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43952953 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:43952952 original size:40 final size:40
Alignment explanation
Indices: 43952768--43952952 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
43952758 GCTCCTCGTT
* *
43952768 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
43952808 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
43952848 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
43952887 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
43952928 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43952953 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:43955866 original size:63 final size:63
Alignment explanation
Indices: 43955767--43955896 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
43955757 CATGAGTAAT
43955767 GTATTGTTGTGTTTTGTGCATTACAGGGTTCGGTTGGCTAAGACGTGCTTTACACGTGCCAAA
1 GTATTGTTGTGTTTTGTGCATTACAGGGTTCGGTTGGCTAAGACGTGCTTTACACGTGCCAAA
43955830 GTATTGTTGTGTTTTGTGCATTACAGGGTTCGGTTGGCTAAGACGTGCTTTACACGTGCCAAA
1 GTATTGTTGTGTTTTGTGCATTACAGGGTTCGGTTGGCTAAGACGTGCTTTACACGTGCCAAA
43955893 GTAT
1 GTAT
43955897 CGTTAAACGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.37
Consensus pattern (63 bp):
GTATTGTTGTGTTTTGTGCATTACAGGGTTCGGTTGGCTAAGACGTGCTTTACACGTGCCAAA
Found at i:43958346 original size:13 final size:13
Alignment explanation
Indices: 43958256--43958347 Score: 62
Period size: 13 Copynumber: 7.0 Consensus size: 13
43958246 AAATGTGTGA
*
43958256 ATGAAATGTTTAG
1 ATGAAATGTTTAT
*
43958269 ATGAAATGGTTAT
1 ATGAAATGTTTAT
* *
43958282 ACGAAACGTTTAT
1 ATGAAATGTTTAT
* *
43958295 ATGGACATAG-ATAT
1 AT-GAAAT-GTTTAT
*
43958309 ATGAAACAG-TTAT
1 ATGAAA-TGTTTAT
*
43958322 ATGAAGTGTTTAT
1 ATGAAATGTTTAT
*
43958335 ATGAAATATTTAT
1 ATGAAATGTTTAT
43958348 TGGAATATAG
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
12 1 0.02
13 49 0.83
14 8 0.14
15 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (13 bp):
ATGAAATGTTTAT
Found at i:43960815 original size:22 final size:20
Alignment explanation
Indices: 43960777--43960819 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
43960767 TAATTGACTA
*
43960777 TTAAAATAAAATAAAAAATT
1 TTAAAATAAAAAAAAAAATT
43960797 TTAAAATAAAAAACTAAAAATT
1 TTAAAATAAAAAA--AAAAATT
43960819 T
1 T
43960820 GAATGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TTAAAATAAAAAAAAAAATT
Found at i:43968823 original size:41 final size:41
Alignment explanation
Indices: 43968575--43968812 Score: 395
Period size: 41 Copynumber: 5.8 Consensus size: 41
43968565 TTTATCGTTA
* * * *
43968575 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* *
43968616 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* *
43968657 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
43968698 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
43968739 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
43968780 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
43968813 AAGAGCCGGT
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 192 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:43969083 original size:33 final size:32
Alignment explanation
Indices: 43969027--43969090 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
43969017 ATATATATAT
43969027 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
43969059 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
43969091 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:43969107 original size:33 final size:33
Alignment explanation
Indices: 43969034--43969107 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
43969024 TATATATATA
* * **
43969034 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
43969066 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
43969099 TGTATGTAT
1 TATATGTAT
43969108 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:43976106 original size:2 final size:2
Alignment explanation
Indices: 43976099--43976123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43976089 TGTGTTAAGT
43976099 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43976124 TCGGATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43976600 original size:41 final size:41
Alignment explanation
Indices: 43976311--43976589 Score: 445
Period size: 41 Copynumber: 6.8 Consensus size: 41
43976301 TTTATCGTTA
* * * *
43976311 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
43976352 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* *
43976393 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* *
43976434 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
43976475 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
43976516 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
43976557 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
43976590 AAGAGCCGGT
Statistics
Matches: 227, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 223 0.98
42 1 0.00
43 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:43976860 original size:33 final size:32
Alignment explanation
Indices: 43976804--43976867 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
43976794 ATAGATATGT
43976804 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
43976836 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
43976868 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:43976884 original size:33 final size:33
Alignment explanation
Indices: 43976811--43976884 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
43976801 TGTATATATA
* * **
43976811 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
43976843 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
43976876 TGTATGTAT
1 TATATGTAT
43976885 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:43978090 original size:13 final size:12
Alignment explanation
Indices: 43978068--43978097 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
43978058 ATTTTAAGTT
43978068 ATTTGTGTGAAA
1 ATTTGTGTGAAA
43978080 ATTTCGTGTGAAA
1 ATTT-GTGTGAAA
43978093 ATTTG
1 ATTTG
43978098 ATTGTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.43
Consensus pattern (12 bp):
ATTTGTGTGAAA
Found at i:43979538 original size:76 final size:76
Alignment explanation
Indices: 43979377--43979539 Score: 188
Period size: 76 Copynumber: 2.1 Consensus size: 76
43979367 TAAAGGTATG
* *
43979377 AGGTTCGAATACAAATATGTATGTATATAATCAAGTTATTGAGTTGAGAATTAATGTATGAATTT
1 AGGTTCG-A-ACAAATATGTATGCATATAATCAAGTTATTGAGTTGAGAATTAAAGTATGAATTT
**
43979442 TATAATTATAGGG
64 TATAATTATAGAC
* * * *
43979455 AGATTCGAACATATATGTATGCATTTAATCAAGTTATTGAGTTG-GAAATTAAAGTATG-TTTCT
1 AGGTTCGAACAAATATGTATGCATATAATCAAGTTATTGAGTTGAG-AATTAAAGTATGAATT-T
43979518 TAT-ATTCATAGAC
64 TATAATT-ATAGAC
43979531 AGGTTCGAA
1 AGGTTCGAA
43979540 TATAGAGATT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
75 6 0.08
76 60 0.82
77 1 0.01
78 6 0.08
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (76 bp):
AGGTTCGAACAAATATGTATGCATATAATCAAGTTATTGAGTTGAGAATTAAAGTATGAATTTTA
TAATTATAGAC
Found at i:43979836 original size:41 final size:41
Alignment explanation
Indices: 43979734--43979828 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
43979724 GGCTTTGTGC
*
43979734 CTAGCAGGCTTAACGCCGGTGAAATATTTCGGACTATACGT
1 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
*
43979775 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATATGT
1 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
43979816 CTAGCAGGCTTAA
1 CTAGCAGGCTTAA
43979829 TGTCGGTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
Found at i:43981818 original size:34 final size:34
Alignment explanation
Indices: 43981758--43981836 Score: 81
Period size: 34 Copynumber: 2.3 Consensus size: 34
43981748 TTAAGTTTAC
* *
43981758 ATATATATATATGGGTAGTATTGAATACGT-ACAA
1 ATATATATGTATAGGTAGTATTGAATACGTGA-AA
* * *
43981792 ATATATATGTATAGTTAGT-TTCGAATAGGTGAAT
1 ATATATATGTATAGGTAGTATT-GAATACGTGAAA
43981826 ATATATATGTA
1 ATATATATGTA
43981837 AAATTATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 2 0.05
34 35 0.92
35 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (34 bp):
ATATATATGTATAGGTAGTATTGAATACGTGAAA
Found at i:43982130 original size:41 final size:41
Alignment explanation
Indices: 43982085--43982188 Score: 174
Period size: 41 Copynumber: 2.5 Consensus size: 41
43982075 GACTTTAAGT
*
43982085 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAAC
*
43982126 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
43982167 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
43982189 ATATGTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
Found at i:43982171 original size:82 final size:82
Alignment explanation
Indices: 43982031--43982188 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 82
43982021 ATTGAAATTT
* *
43982031 TCAGGTTTAAAACCTAGCAGGCTTAAGGCCGGTGAAATAATTCAGACTTTAAGTCTAGCAGGCTA
1 TCAGGTTTAAAACCTAGCAGGCTTAAGGCCGGTGAAATAATTCAGACTATAAGCCTAGCAGGCTA
43982096 AGTGCCGGTGATCTGAA
66 AGTGCCGGTGATCTGAA
* *
43982113 TCAGG-TTATAAACCTAGCAGGC-TAAGTGCCGGTG-ATTGGAA-TCAGGCTATAAGCCTAGCAG
1 TCAGGTTTA-AAACCTAGCAGGCTTAAG-GCCGGTGAAAT--AATTCAGACTATAAGCCTAGCAG
43982174 GCTAAGTGCCGGTGA
62 GCTAAGTGCCGGTGA
43982189 ATATGTTAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
81 9 0.13
82 57 0.84
83 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
TCAGGTTTAAAACCTAGCAGGCTTAAGGCCGGTGAAATAATTCAGACTATAAGCCTAGCAGGCTA
AGTGCCGGTGATCTGAA
Done.