Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 23 of 33
Found at i:3756526 original size:17 final size:18
Alignment explanation
Indices: 3756500--3756533 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3756490 TCACATATCC
*
3756500 TTTTATTTTTAATTAATT
1 TTTTATTTTTAAGTAATT
3756518 TTTTA-TTTTAAGTAAT
1 TTTTATTTTTAAGTAAT
3756534 AGATATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATTTTTAAGTAATT
Found at i:3757165 original size:16 final size:15
Alignment explanation
Indices: 3757129--3757166 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3757119 TTTTAATATT
*
3757129 ATAATCATATTTAAA
1 ATAATTATATTTAAA
3757144 AT-ATTATATATTAAA
1 ATAATTATAT-TTAAA
3757159 ATAATTAT
1 ATAATTAT
3757167 CTTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTATATTTAAA
Found at i:3757372 original size:32 final size:33
Alignment explanation
Indices: 3757318--3757398 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
3757308 AATATATAAA
* **
3757318 AATAATT-ATTTTATATTTATTTTAATACA-TT
1 AATAATTCATATTATATAAATTTTAATACATTT
*
3757349 AATAATTCATATTATATAAATTTTAATATATTT
1 AATAATTCATATTATATAAATTTTAATACATTT
*
3757382 ACGT-ATTCATATTATAT
1 A-ATAATTCATATTATAT
3757399 TTATATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 7 0.17
32 18 0.43
33 16 0.38
34 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (33 bp):
AATAATTCATATTATATAAATTTTAATACATTT
Found at i:3758827 original size:2 final size:2
Alignment explanation
Indices: 3758820--3758850 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3758810 GAAACAATTA
3758820 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3758851 AGATATACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3759549 original size:24 final size:24
Alignment explanation
Indices: 3759504--3759549 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3759494 ATTATAATTG
* ** *
3759504 ATAATTATAATATTTAATATATTT
1 ATAATTATAACAAATAAAATATTT
3759528 ATAATTATAACAAATAAAATAT
1 ATAATTATAACAAATAAAATAT
3759550 GATTAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTATAACAAATAAAATATTT
Found at i:3761844 original size:17 final size:18
Alignment explanation
Indices: 3761811--3761860 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3761801 ATATTTTAAA
*
3761811 ATTAATATAATATAAA-TT
1 ATTAATA-AATAAAAATTT
3761829 ATTAATAAATAAAAATTT
1 ATTAATAAATAAAAATTT
3761847 ATATAA-AAATAAAA
1 AT-TAATAAATAAAA
3761861 TAAATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.24
18 19 0.66
19 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAATAAATAAAAATTT
Found at i:3762101 original size:16 final size:16
Alignment explanation
Indices: 3762080--3762111 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3762070 TTATCTAATT
3762080 ATTTTTATACTTTTAA
1 ATTTTTATACTTTTAA
*
3762096 ATTTTTATTCTTTTAA
1 ATTTTTATACTTTTAA
3762112 TAATTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTATACTTTTAA
Found at i:3762344 original size:2 final size:2
Alignment explanation
Indices: 3762339--3762367 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3762329 CAAAAAAAAA
3762339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3762368 AGTTATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3762960 original size:18 final size:18
Alignment explanation
Indices: 3762937--3762978 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3762927 TATATTTGTA
3762937 TATTTTTATCAT-ATATAT
1 TATTTTTAT-ATCATATAT
*
3762955 TATTTTTATATCATATCT
1 TATTTTTATATCATATAT
3762973 TATTTT
1 TATTTT
3762979 AATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTTATATCATATAT
Found at i:3763673 original size:16 final size:15
Alignment explanation
Indices: 3763639--3763671 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3763629 TAAATATAAA
3763639 TAAATATAA-TTTTT
1 TAAATATAATTTTTT
3763653 TAAATATAATTTTTT
1 TAAATATAATTTTTT
3763668 TAAA
1 TAAA
3763672 ATTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATAATTTTTT
Found at i:3763680 original size:16 final size:14
Alignment explanation
Indices: 3763639--3763682 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
3763629 TAAATATAAA
*
3763639 TAAATATAATTTTT
1 TAAATATATTTTTT
3763653 TAAATATAATTTTTT
1 TAAATAT-ATTTTTT
3763668 TAAAATTATATTTTT
1 T-AAA-TATATTTTT
3763683 ATATTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 7 0.27
16 9 0.35
17 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATATATTTTTT
Found at i:3763681 original size:15 final size:16
Alignment explanation
Indices: 3763639--3763682 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
3763629 TAAATATAAA
3763639 TAAATAT-A-ATTTTT
1 TAAATATAATATTTTT
3763653 TAAATATAAT-TTTTT
1 TAAATATAATATTTTT
*
3763668 TAAA-ATTATATTTTT
1 TAAATATAATATTTTT
3763683 ATATTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATATAATATTTTT
Found at i:3763711 original size:23 final size:22
Alignment explanation
Indices: 3763674--3763729 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
3763664 TTTTTAAAAT
3763674 TATATTTTT-ATATTTATATTGAAA
1 TATATTTTTAAT-TTTA-ATT-AAA
3763698 TATATTTTTAATTTTAATTAAA
1 TATATTTTTAATTTTAATTAAA
3763720 -ATATTTTTAA
1 TATATTTTTAA
3763730 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.32
22 3 0.10
23 3 0.10
24 13 0.42
25 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATATTTTTAATTTTAATTAAA
Found at i:3765688 original size:101 final size:101
Alignment explanation
Indices: 3765509--3765792 Score: 417
Period size: 101 Copynumber: 2.8 Consensus size: 101
3765499 AGTTATTATC
* * * * * * * * *
3765509 ATTGTTGACTATCCTTCACCAACCTTTGA-TAATAGAGAAAGGTGGTCGTAATTGTTGATGATTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATTATTGTTGACGATTC
*
3765573 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATT
66 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
*
3765609 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAAAGAGAGGTGGCCATTATTGTTGACGATTC
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATTATTGTTGACGATTC
* *
3765674 TTCACCAACTTTTGACAATAGAGAGAGGTGGCCATA
66 TTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
* * *
3765710 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGGCAATTATTGTTAACGATTC
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATTATTGTTGACGATTC
3765775 TTCACCAACCTTTGACAA
66 TTCACCAACCTTTGACAA
3765793 ATGTGGCCAT
Statistics
Matches: 165, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
100 27 0.16
101 138 0.84
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (101 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATTATTGTTGACGATTC
TTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
Found at i:3765795 original size:51 final size:51
Alignment explanation
Indices: 3765509--3765794 Score: 407
Period size: 50 Copynumber: 5.7 Consensus size: 51
3765499 AGTTATTATC
* * * * * * *
3765509 ATTGTTGACTATCCTTCACCAACCTTTGA-TAATAGAGAAAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
* * *
3765559 ATTGTTGATGATTATTCACCAACCTTTGAC-AATAGAGAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
*
3765609 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAAAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
* *
3765660 ATTGTTGACGATTCTTCACCAACTTTTGAC-AATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
* *
3765710 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGGCAATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
*
3765761 ATTGTTAACGATTCTTCACCAACCTTTGACAAAT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAAAT
3765795 GTGGCCATAA
Statistics
Matches: 212, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
50 115 0.54
51 97 0.46
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (51 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAAATAGAGAGAGGTGGCCATT
Found at i:3770523 original size:51 final size:50
Alignment explanation
Indices: 3770187--3770520 Score: 542
Period size: 50 Copynumber: 6.6 Consensus size: 50
3770177 AGTTGTTGCC
* * * * * *
3770187 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAAAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
* *
3770237 ATTGTTGACAATTCTTTACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
3770287 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
3770337 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
* *
3770387 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGGCTATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATT
* *
3770438 ATTGTTGACGATTCTTCACCAACCTTTGACAAATGGAGAGAGGTGACCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATT
3770489 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
3770521 ATGTGGCCAT
Statistics
Matches: 270, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
50 173 0.64
51 97 0.36
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
Found at i:3778277 original size:18 final size:18
Alignment explanation
Indices: 3778254--3778292 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3778244 GATCTCTCCT
3778254 TCACATTGAGGCTAGCTA
1 TCACATTGAGGCTAGCTA
*
3778272 TCACATTGATGCTAGCTA
1 TCACATTGAGGCTAGCTA
3778290 TCA
1 TCA
3778293 ACTAAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (18 bp):
TCACATTGAGGCTAGCTA
Found at i:3779841 original size:12 final size:13
Alignment explanation
Indices: 3779816--3779844 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3779806 GAAACTACAG
3779816 TTTCTTTCTTCTT
1 TTTCTTTCTTCTT
3779829 TTTCTTT-TTCTT
1 TTTCTTTCTTCTT
3779841 TTTC
1 TTTC
3779845 CATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTCTT
Found at i:3780132 original size:4 final size:4
Alignment explanation
Indices: 3780123--3780243 Score: 61
Period size: 4 Copynumber: 29.2 Consensus size: 4
3780113 TAAATACAAT
* * * *
3780123 ATAC ATAC ATTC ATAT ATAC ATATGT ATAC ATAC --AC ATAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATA--C ATAC ATAC ATAC ATAC ATAC ATAC
* *
3780171 GTATAC ATAC --AC ATAT ATAC ATAC GTATAC ATAC ATAC ACAC ATAC
1 --ATAC ATAC ATAC ATAC ATAC ATAC --ATAC ATAC ATAC ATAC ATAC
* * *
3780217 GTATAC ATAC ATAT ATAT ATAT ATAC A
1 --ATAC ATAC ATAC ATAC ATAC ATAC A
3780244 CACACACACA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
2 4 0.04
4 72 0.79
6 15 0.16
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:3780199 original size:10 final size:10
Alignment explanation
Indices: 3780162--3780231 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
3780152 CATACACATA
3780162 TATACATACG
1 TATACATACG
3780172 TATACATAC-
1 TATACATACG
3780181 ---ACATA--
1 TATACATACG
3780186 TATACATACG
1 TATACATACG
*
3780196 TATACATACA
1 TATACATACG
*
3780206 TACACACATACG
1 T--ATACATACG
*
3780218 TATACATACA
1 TATACATACG
3780228 TATA
1 TATA
3780232 TATATATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
6 5 0.10
8 5 0.10
10 30 0.62
12 8 0.17
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (10 bp):
TATACATACG
Found at i:3780235 original size:14 final size:14
Alignment explanation
Indices: 3780121--3780235 Score: 74
Period size: 14 Copynumber: 8.4 Consensus size: 14
3780111 TGTAAATACA
3780121 ATATACATACAT-T
1 ATATACATACATAT
3780134 CATAT--ATACATAT
1 -ATATACATACATAT
* *
3780147 GTATACATACACAT
1 ATATACATACATAT
*
3780161 ATATACATACGTAT
1 ATATACATACATAT
* * *
3780175 ACATACACATATAT
1 ATATACATACATAT
* * * *
3780189 ACATACGTATACAT
1 ATATACATACATAT
* * *
3780203 ACATACACACATAC
1 ATATACATACATAT
*
3780217 GTATACATACATAT
1 ATATACATACATAT
3780231 ATATA
1 ATATA
3780236 TATATACACA
Statistics
Matches: 76, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
12 9 0.12
13 1 0.01
14 66 0.87
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.31
Consensus pattern (14 bp):
ATATACATACATAT
Found at i:3780257 original size:46 final size:46
Alignment explanation
Indices: 3780127--3780259 Score: 140
Period size: 46 Copynumber: 2.9 Consensus size: 46
3780117 TACAATATAC
* * * * * *
3780127 ATACATTCATATATACATATGTATACATACACATATATACATACGT
1 ATACATACATATATATATATATATACACACACATACACACATACGT
* * ** * *
3780173 ATACATACACATATATACATACGTATACATACATACACACATACGT
1 ATACATACATATATATATATATATACACACACATACACACATACGT
* *
3780219 ATACATACATATATATATATATACACACACACACACACACA
1 ATACATACATATATATATATATATACACACACATACACACA
3780260 CTCGAGTTCG
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (46 bp):
ATACATACATATATATATATATATACACACACATACACACATACGT
Found at i:3795338 original size:64 final size:64
Alignment explanation
Indices: 3795237--3795371 Score: 254
Period size: 64 Copynumber: 2.1 Consensus size: 64
3795227 GAACAATAAC
*
3795237 TGAGTAACCATTTCGCCCTCTTAAAACAAGCAGCAGCTTCTTCCCTTTAATCAAACTAATCAAT
1 TGAGTAACCATTTCGCCCTCTTAAAACAAGCAGCAGCTTCTTCCCTTCAATCAAACTAATCAAT
3795301 TGAGTAACCATTTCGCCCTCTTAAAACAAGCAGCAGCTTCTTCCCTTCAATCAAACTAATCAAT
1 TGAGTAACCATTTCGCCCTCTTAAAACAAGCAGCAGCTTCTTCCCTTCAATCAAACTAATCAAT
3795365 TG-GTAAC
1 TGAGTAAC
3795372 TAACTGGCTG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 5 0.07
64 65 0.93
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (64 bp):
TGAGTAACCATTTCGCCCTCTTAAAACAAGCAGCAGCTTCTTCCCTTCAATCAAACTAATCAAT
Found at i:3807093 original size:60 final size:60
Alignment explanation
Indices: 3807000--3807118 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
3806990 GGTTTATACT
* * *
3807000 TCTAGACTTTGTTCAGCTTAATCTAGCTCTGAATACCTGGTAAGAAATGCGCAAGGTACG
1 TCTAGACTTTGTTCAGCTTAAGCTAGCTCTGAATACCTGATAAGAAACGCGCAAGGTACG
3807060 TCTAGACTTTGGTT-AGCTTAAGCTAGCTCTGAATACCTGATAAGAAACGCGCAAGGTAC
1 TCTAGACTTT-GTTCAGCTTAAGCTAGCTCTGAATACCTGATAAGAAACGCGCAAGGTAC
3807119 AAGTATAGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 52 0.95
61 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (60 bp):
TCTAGACTTTGTTCAGCTTAAGCTAGCTCTGAATACCTGATAAGAAACGCGCAAGGTACG
Found at i:3808445 original size:2 final size:2
Alignment explanation
Indices: 3808438--3808464 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3808428 GACTAGAATT
3808438 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3808465 TATGTTAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3813417 original size:2 final size:2
Alignment explanation
Indices: 3813410--3813446 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3813400 TATTAATACA
*
3813410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3813447 AAAAATGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3818099 original size:15 final size:15
Alignment explanation
Indices: 3818081--3818114 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3818071 GTAAAAAACG
*
3818081 AAAGGATAAAGAGAA
1 AAAGGAAAAAGAGAA
*
3818096 AAAGGAAAAAGTGAA
1 AAAGGAAAAAGAGAA
3818111 AAAG
1 AAAG
3818115 ATTCAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (15 bp):
AAAGGAAAAAGAGAA
Found at i:3820577 original size:3 final size:3
Alignment explanation
Indices: 3820569--3820593 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3820559 ATATTAATTC
3820569 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
3820594 AGAGGAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3820987 original size:2 final size:2
Alignment explanation
Indices: 3820980--3821018 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3820970 TTTTCTTTAC
3820980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3821019 CATACATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3821433 original size:2 final size:2
Alignment explanation
Indices: 3821426--3821453 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3821416 CTACTAATGG
3821426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3821454 GAGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3822711 original size:6 final size:6
Alignment explanation
Indices: 3822700--3822789 Score: 72
Period size: 6 Copynumber: 15.0 Consensus size: 6
3822690 TCCAATGATC
* * * * *
3822700 ACCATG ACCATG ACCATG ACCACG ACCACG ACCACG ACCACG ACCATC
1 ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG
** ** * * *
3822748 ACCACC ACCACC ACCATC ATCATG ACCATG AACATG ACCATG
1 ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG
3822790 GGTAATTATA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.34, C:0.42, G:0.12, T:0.11
Consensus pattern (6 bp):
ACCATG
Found at i:3822726 original size:18 final size:18
Alignment explanation
Indices: 3822700--3822789 Score: 81
Period size: 18 Copynumber: 5.0 Consensus size: 18
3822690 TCCAATGATC
*
3822700 ACCATGACCATGACCATG
1 ACCACGACCATGACCATG
* *
3822718 ACCACGACCACGACCACG
1 ACCACGACCATGACCATG
* **
3822736 ACCACGACCATCACCACC
1 ACCACGACCATGACCATG
* * *
3822754 ACCACCACCATCATCATG
1 ACCACGACCATGACCATG
* *
3822772 ACCATGAACATGACCATG
1 ACCACGACCATGACCATG
3822790 GGTAATTATA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.34, C:0.42, G:0.12, T:0.11
Consensus pattern (18 bp):
ACCACGACCATGACCATG
Found at i:3826484 original size:42 final size:42
Alignment explanation
Indices: 3826422--3826507 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
3826412 GCCCTTGATG
3826422 TTTTTTTAATTTCAAGAAATTGATGGAAACAAGCACAAAAGT
1 TTTTTTTAATTTCAAGAAATTGATGGAAACAAGCACAAAAGT
*
3826464 TTTTTTTAATTTCAATAAATTGATGGAAACAAGCACAAAAGT
1 TTTTTTTAATTTCAAGAAATTGATGGAAACAAGCACAAAAGT
3826506 TT
1 TT
3826508 GAGTGCAGGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (42 bp):
TTTTTTTAATTTCAAGAAATTGATGGAAACAAGCACAAAAGT
Found at i:3842320 original size:27 final size:27
Alignment explanation
Indices: 3842285--3842336 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3842275 ATAAAAATAT
*
3842285 AAATATT-AATATAAAAATAATTTTTAA
1 AAATATTAAAAAT-AAAATAATTTTTAA
*
3842312 AAATTTTAAAAATAAAATAATTTTT
1 AAATATTAAAAATAAAATAATTTTT
3842337 TTAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATATTAAAAATAAAATAATTTTTAA
Found at i:3842867 original size:2 final size:2
Alignment explanation
Indices: 3842862--3842901 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3842852 TAATTTGTCG
3842862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3842902 CAGGTTCGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3843408 original size:2 final size:2
Alignment explanation
Indices: 3843401--3843434 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3843391 GTCGGTTTAA
3843401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3843435 TTATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3848646 original size:58 final size:58
Alignment explanation
Indices: 3848512--3848832 Score: 398
Period size: 58 Copynumber: 5.5 Consensus size: 58
3848502 TCGACGACGG
* * * * *
3848512 TCTAAGTTTGGATGACTTGGCGTCATTTA--ATGTGGTAATTTGGGTCGCCTTGGTAGCGA
1 TCTAAGTTTGGGTGACTTGGCGTCACTTAGCGTGTGG--ATCT-GGTCGCCTTGGTGGCGA
* * ** *
3848571 -CTTAAGTTTGGGGGACTTGGCGTCACCTAATGTGT-GAGTTTGGTCGCCTTGGTGGCGA
1 TC-TAAGTTTGGGTGACTTGGCGTCACTTAGCGTGTGGA-TCTGGTCGCCTTGGTGGCGA
* * *
3848629 TCTAAGTTTGGGTGACTTGTCGTCACTTAGCGCGTGGATCTGGTCACCTTGGTGGCGA
1 TCTAAGTTTGGGTGACTTGGCGTCACTTAGCGTGTGGATCTGGTCGCCTTGGTGGCGA
* * *
3848687 TCTAAGTTTGGGTGACTCGACATCACTTAGCGTGTGGATCTGGTCGCCTTGGTGGCGA
1 TCTAAGTTTGGGTGACTTGGCGTCACTTAGCGTGTGGATCTGGTCGCCTTGGTGGCGA
* *
3848745 TCTAAGTTTGGGTGACTCGGTGTCACTTAGCGTGTGGATCTGGTCGCCTTGGTGGCGA
1 TCTAAGTTTGGGTGACTTGGCGTCACTTAGCGTGTGGATCTGGTCGCCTTGGTGGCGA
*
3848803 TCTGAGTTTGGGTGACTTGGCGTCACTTAG
1 TCTAAGTTTGGGTGACTTGGCGTCACTTAG
3848833 TGTGATAAAA
Statistics
Matches: 231, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
58 198 0.86
59 29 0.13
60 1 0.00
61 3 0.01
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.34
Consensus pattern (58 bp):
TCTAAGTTTGGGTGACTTGGCGTCACTTAGCGTGTGGATCTGGTCGCCTTGGTGGCGA
Found at i:3855369 original size:20 final size:21
Alignment explanation
Indices: 3855330--3855369 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3855320 TGTTTTTAAT
*
3855330 ATTTTGTAAATTTTTAATAAA
1 ATTTTGTAAATTTCTAATAAA
*
3855351 ATTTT-TAACTTTCTAATAA
1 ATTTTGTAAATTTCTAATAA
3855370 TTTTATTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTTGTAAATTTCTAATAAA
Found at i:3859434 original size:23 final size:23
Alignment explanation
Indices: 3859391--3859435 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3859381 TTCGATTATA
* *
3859391 TGTTTATGAATATATTTATTTAG
1 TGTTTATGAATAAATTCATTTAG
*
3859414 TGTTTATGATTAAATTCATTTA
1 TGTTTATGAATAAATTCATTTA
3859436 ATTTAACGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (23 bp):
TGTTTATGAATAAATTCATTTAG
Found at i:3862761 original size:7 final size:7
Alignment explanation
Indices: 3862749--3862781 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3862739 TATTTGAGAA
3862749 TTTAAAT
1 TTTAAAT
3862756 TTTAAAT
1 TTTAAAT
*
3862763 TTTAAAG
1 TTTAAAT
3862770 TTT-AAT
1 TTTAAAT
3862776 TTTAAA
1 TTTAAA
3862782 AGTTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (7 bp):
TTTAAAT
Found at i:3862776 original size:13 final size:14
Alignment explanation
Indices: 3862749--3862792 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3862739 TATTTGAGAA
*
3862749 TTTAAATTTTAAAT
1 TTTAAAGTTTAAAT
3862763 TTTAAAGTTT-AAT
1 TTTAAAGTTTAAAT
3862776 TTTAAAAGTTATAAAT
1 TTT-AAAGTT-TAAAT
3862792 T
1 T
3862793 ATGTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.23
14 15 0.58
15 1 0.04
16 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
TTTAAAGTTTAAAT
Found at i:3864334 original size:2 final size:2
Alignment explanation
Indices: 3864329--3864366 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3864319 GAAAGAGAGC
3864329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3864367 TCTTTTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3865755 original size:2 final size:2
Alignment explanation
Indices: 3865748--3865773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3865738 GAGAAAGAAG
3865748 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3865774 GAATCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3866874 original size:30 final size:29
Alignment explanation
Indices: 3866840--3866899 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
3866830 TAATTATAAA
*
3866840 TATATAAATAAT-AATATTAAAATAATATTT
1 TATAT-AATAATAAATAATAAAATAA-ATTT
* *
3866870 TATATTATTATAAATAATAAAATAAATTT
1 TATATAATAATAAATAATAAAATAAATTT
3866899 T
1 T
3866900 CAGATGATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATATAATAATAAATAATAAAATAAATTT
Found at i:3873055 original size:2 final size:2
Alignment explanation
Indices: 3873048--3873094 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3873038 TAGTAGACAT
3873048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3873090 TA TA T
1 TA TA T
3873095 CCAGGGGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3880762 original size:14 final size:15
Alignment explanation
Indices: 3880732--3880763 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3880722 TCATATTAAT
3880732 AATTTTTATAATATA
1 AATTTTTATAATATA
3880747 AATTTTTA-AATATA
1 AATTTTTATAATATA
3880761 AAT
1 AAT
3880764 ATATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTTTATAATATA
Found at i:3880766 original size:20 final size:21
Alignment explanation
Indices: 3880741--3880784 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
3880731 TAATTTTTAT
3880741 AATATA-AAT-TTTTAAATATA
1 AATATATAATATTTTAAATA-A
3880761 AATATATAATATTTTAAATAA
1 AATATATAATATTTTAAATAA
3880782 AAT
1 AAT
3880785 TACATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATATAATATTTTAAATAA
Found at i:3884719 original size:20 final size:21
Alignment explanation
Indices: 3884677--3884716 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3884667 AATTTGAATT
*
3884677 TTTTTTTATAATTATTATAAA
1 TTTTTTTATAATTATCATAAA
3884698 TTTTTTTA-AATT-TCATAAA
1 TTTTTTTATAATTATCATAAA
3884717 ATTAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTTTATAATTATCATAAA
Found at i:3886884 original size:5 final size:5
Alignment explanation
Indices: 3886834--3886869 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
3886824 TTATTAAATA
*
3886834 TATTT AATTT TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
3886870 TATAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:3887303 original size:2 final size:2
Alignment explanation
Indices: 3887296--3887330 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3887286 TTCCAATTCA
3887296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3887331 ATAACTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3888509 original size:4 final size:4
Alignment explanation
Indices: 3888495--3888526 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
3888485 ACTGGGATTA
3888495 ATTT GATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATT
3888527 AGTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:3892975 original size:17 final size:16
Alignment explanation
Indices: 3892955--3893002 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
3892945 AATAATTAAA
3892955 ATATAATATAAAATAT
1 ATATAATATAAAATAT
3892971 GATATAATAT-AAATAT
1 -ATATAATATAAAATAT
3892987 A-ATAATATATAAATAT
1 ATATAATATA-AAATAT
3893003 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.24
15 1 0.03
16 12 0.41
17 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
ATATAATATAAAATAT
Found at i:3893268 original size:20 final size:19
Alignment explanation
Indices: 3893232--3893275 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3893222 TTTTCCTCCC
* *
3893232 GTTTATTTTTTATATTTTA
1 GTTTATTTTTAAAATTTTA
3893251 GTTTATTTTTCAAAATTTTA
1 GTTTATTTTT-AAAATTTTA
*
3893271 TTTTA
1 GTTTA
3893276 AAATTTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
GTTTATTTTTAAAATTTTA
Found at i:3893322 original size:18 final size:19
Alignment explanation
Indices: 3893295--3893331 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3893285 ATTATTATTT
*
3893295 ATTTTGTATAA-TAAATAA
1 ATTTTATATAATTAAATAA
3893313 ATTTTATATAATTAAATAA
1 ATTTTATATAATTAAATAA
3893332 TGAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTTATATAATTAAATAA
Found at i:3893436 original size:23 final size:24
Alignment explanation
Indices: 3893393--3893451 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
3893383 ATCAGTACTT
* *
3893393 TATAAAA-TAATATTTTAAATATA
1 TATAAAATTAATATTATAAATACA
*
3893416 TATAAAATTAAT-TTATCAATACA
1 TATAAAATTAATATTATAAATACA
*
3893439 TATTTAAATTAAT
1 TA-TAAAATTAAT
3893452 GTGTCTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAAAATTAATATTATAAATACA
Found at i:3896275 original size:32 final size:32
Alignment explanation
Indices: 3896237--3896298 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
3896227 ATGTGTATAC
*
3896237 AAATTTTAATATATTAATA-ATTTATATCATAT
1 AAATTTTAAAAT-TTAATATATTTATATCATAT
*
3896269 AAATTTTAAAATTTTATATATTTATATCAT
1 AAATTTTAAAATTTAATATATTTATATCAT
3896299 GTTTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (32 bp):
AAATTTTAAAATTTAATATATTTATATCATAT
Found at i:3917258 original size:3 final size:3
Alignment explanation
Indices: 3917250--3917283 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3917240 CTACATATAT
3917250 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3917284 ATATATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:3917816 original size:2 final size:2
Alignment explanation
Indices: 3917770--3917797 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3917760 CAAAACAGGA
3917770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3917798 CGATACACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3918127 original size:22 final size:21
Alignment explanation
Indices: 3918102--3918143 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3918092 ATATATATAA
3918102 ATATTATTAT-ATTAATATTTAT
1 ATATT-TTATAATTAA-ATTTAT
3918124 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
3918144 AATAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:3918132 original size:24 final size:24
Alignment explanation
Indices: 3918077--3918143 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
3918067 TTCCTTAATT
*
3918077 TATTTTATTAT-TTAAATATATATA
1 TATTTTATTATATT-AATATTTATA
* *
3918101 AATATTATTATATTAATATTTATA
1 TATTTTATTATATTAATATTTATA
3918125 TATTTTA-TA-ATTAA-ATTTA
1 TATTTTATTATATTAATATTTA
3918144 AATAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.14
22 5 0.14
23 2 0.05
24 23 0.62
25 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTTATTATATTAATATTTATA
Found at i:3918607 original size:2 final size:2
Alignment explanation
Indices: 3918600--3918626 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3918590 ATATCATGTT
3918600 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3918627 TTTAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3918821 original size:21 final size:21
Alignment explanation
Indices: 3918731--3918883 Score: 100
Period size: 21 Copynumber: 7.4 Consensus size: 21
3918721 AATTAAATTT
* * *
3918731 AATTATATGAAA-ATTACTAC
1 AATTATATTAAATATTATTAA
* *
3918751 AATTATATAAAAT-TTATCAA
1 AATTATATTAAATATTATTAA
** *
3918771 AGCTATA-TAAATGTTA-TAA
1 AATTATATTAAATATTATTAA
*
3918790 ATATTACATTAAATATTATTAA
1 A-ATTATATTAAATATTATTAA
* *
3918812 AACTATATTAACA-GTTATTAA
1 AATTATATTAA-ATATTATTAA
* **
3918833 AATTATATTAAAAATTAACAA
1 AATTATATTAAATATTATTAA
* *
3918854 AATCATATCAAATGATTATTAA
1 AATTATATTAAAT-ATTATTAA
3918876 AATTATAT
1 AATTATAT
3918884 CAAAGCTATC
Statistics
Matches: 100, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 7 0.07
20 27 0.27
21 48 0.48
22 18 0.18
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.39
Consensus pattern (21 bp):
AATTATATTAAATATTATTAA
Found at i:3918843 original size:42 final size:42
Alignment explanation
Indices: 3918751--3918969 Score: 141
Period size: 42 Copynumber: 5.2 Consensus size: 42
3918741 AAATTACTAC
* *
3918751 AATTATATAAAAT-TTATCAAAGCTATA-TAAATGTTA-TAA
1 AATTATATTAAATATTATCAAAACTATATTAAATGTTATTAA
* *
3918790 ATATTACATTAAATATTATTAAAACTATATTAACA-GTTATTAA
1 A-ATTATATTAAATATTATCAAAACTATATTAA-ATGTTATTAA
* * *
3918833 AATTATATTAAAAATTAACAAAA-TCATATCAAATGATTATTAA
1 AATTATATTAAATATTATCAAAACT-ATATTAAATG-TTATTAA
* ** *
3918876 AATTATATCAAA-GCTATCAAAACGATATTCAAA-GTTATTAACTCAA
1 AATTATATTAAATATTATCAAAACTATATT-AAATGTTA-T---T-AA
* * * *
3918922 AATTATATCAAATGTTAT-TAAACTAT-TATAAATGTTACTAA
1 AATTATATTAAATATTATCAAAACTATAT-TAAATGTTATTAA
3918963 AATTATA
1 AATTATA
3918970 AAGTTATCAA
Statistics
Matches: 143, Mismatches: 19, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
39 1 0.01
40 10 0.07
41 26 0.18
42 46 0.32
43 26 0.18
45 5 0.03
46 25 0.17
47 4 0.03
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.37
Consensus pattern (42 bp):
AATTATATTAAATATTATCAAAACTATATTAAATGTTATTAA
Found at i:3918877 original size:22 final size:21
Alignment explanation
Indices: 3918703--3918887 Score: 83
Period size: 21 Copynumber: 8.9 Consensus size: 21
3918693 AAATAAAAGA
* *
3918703 TATTCAAATTATATAAAAAAT
1 TATTAAAATTATATCAAAAAT
* *
3918724 TAAATT-TAATTATAT-GAAAAT
1 T--ATTAAAATTATATCAAAAAT
* * *
3918745 TACTACAATTATAT-AAAATT
1 TATTAAAATTATATCAAAAAT
* ** **
3918765 TATCAAAGCTATAT-AAATGT
1 TATTAAAATTATATCAAAAAT
* * *
3918785 TA-TAAATATTACATTAAATAT
1 TATTAAA-ATTATATCAAAAAT
* * * *
3918806 TATTAAAACTATATTAACAGT
1 TATTAAAATTATATCAAAAAT
*
3918827 TATTAAAATTATATTAAAAAT
1 TATTAAAATTATATCAAAAAT
** * *
3918848 TAACAAAATCATATCAAATGAT
1 TATTAAAATTATATCAAA-AAT
3918870 TATTAAAATTATATCAAA
1 TATTAAAATTATATCAAA
3918888 GCTATCAAAA
Statistics
Matches: 123, Mismatches: 34, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.04
20 31 0.25
21 55 0.45
22 29 0.24
23 3 0.02
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (21 bp):
TATTAAAATTATATCAAAAAT
Found at i:3918908 original size:43 final size:43
Alignment explanation
Indices: 3918826--3918933 Score: 103
Period size: 43 Copynumber: 2.4 Consensus size: 43
3918816 ATATTAACAG
* *
3918826 TTATTAAAATTATATTAAAAATTAACAAAATCATATCAAA-TGA
1 TTATTAAAATTATA-TCAAAACTAACAAAATCATATCAAAGTGA
* * *
3918869 TTATTAAAATTATATCAAAGCTATCAAAA-CGATATTCAAAGTTA
1 TTATTAAAATTATATCAAAACTAACAAAATC-ATA-TCAAAGTGA
*
3918913 TTAACTCAAAATTATATCAAA
1 TT-A-TTAAAATTATATCAAA
3918934 TGTTATTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.02
42 14 0.26
43 19 0.35
44 4 0.07
45 1 0.02
46 15 0.28
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (43 bp):
TTATTAAAATTATATCAAAACTAACAAAATCATATCAAAGTGA
Found at i:3918956 original size:20 final size:18
Alignment explanation
Indices: 3918931--3918976 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
3918921 AAATTATATC
3918931 AAATGTTATTAAACTATTAT
1 AAATGTTATTAAA--ATTAT
*
3918951 AAATGTTACTAAAATTAT
1 AAATGTTATTAAAATTAT
3918969 AAA-GTTAT
1 AAATGTTAT
3918977 CAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 8 0.33
20 12 0.50
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (18 bp):
AAATGTTATTAAAATTAT
Found at i:3923692 original size:14 final size:14
Alignment explanation
Indices: 3923670--3923703 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3923660 TAAAGAGTAA
* *
3923670 TTTTGATTTTTTTT
1 TTTTAATTTTTTTG
3923684 TTTTAATTTTTTTG
1 TTTTAATTTTTTTG
3923698 TTTTAA
1 TTTTAA
3923704 GCGAAGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTAATTTTTTTG
Found at i:3924384 original size:8 final size:8
Alignment explanation
Indices: 3924369--3924406 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
3924359 TAATTTACTT
3924369 TCTCTTTC
1 TCTCTTTC
*
3924377 TTTCTTTC
1 TCTCTTTC
*
3924385 TCTCTCTC
1 TCTCTTTC
3924393 TCTCTTTC
1 TCTCTTTC
3924401 TCTCTT
1 TCTCTT
3924407 AATTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (8 bp):
TCTCTTTC
Found at i:3924404 original size:10 final size:10
Alignment explanation
Indices: 3924366--3924405 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3924356 AAGTAATTTA
*
3924366 CTTTCTCTTT
1 CTTTCTCTCT
*
3924376 CTTTCTTTCT
1 CTTTCTCTCT
*
3924386 CTCTCTCTCT
1 CTTTCTCTCT
3924396 CTTTCTCTCT
1 CTTTCTCTCT
3924406 TAATTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
CTTTCTCTCT
Found at i:3924437 original size:3 final size:3
Alignment explanation
Indices: 3924429--3924474 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3924419 AAAAGAAACA
3924429 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3924475 TGTTTGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3925914 original size:3 final size:3
Alignment explanation
Indices: 3925906--3925937 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3925896 ACTAAAACTA
*
3925906 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3925938 GAGTTGGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3928538 original size:198 final size:198
Alignment explanation
Indices: 3928200--3928571 Score: 708
Period size: 198 Copynumber: 1.9 Consensus size: 198
3928190 AGGACTTCCA
3928200 ATTGTATGTCTCCCACAATTTTTTTAACTTCATACTCAAATAGATCTTTCTAATATAAATAAATA
1 ATTGTATGTCTCCCACAATTTTTTTAACTTCATACTCAAATAGATCTTTCTAATATAAATAAATA
3928265 TTTATATGCACACTTTTCCATGCTTCCCAAAGCATAACAAAGGCACACACTTTCAGACAAGTAAA
66 TTTATATGCACACTTTTCCATGCTTCCCAAAGCATAACAAAGGCACACACTTTCAGACAAGTAAA
3928330 TTAAATTCAAACATTTAACAGTCCATTGAAATATCATAAATATATCATAAACATTTAACAAAGGC
131 TTAAATTCAAACATTTAACAGTCCATTGAAATATCATAAATATATCATAAACATTTAACAAAGGC
3928395 AGG
196 AGG
3928398 ATTGTATGTCTCCCACAATTTTTTTAACTTCATACTCAAATAGATCTTTCTAATATAAATAAATA
1 ATTGTATGTCTCCCACAATTTTTTTAACTTCATACTCAAATAGATCTTTCTAATATAAATAAATA
* *
3928463 TTTATATGCACACTTTTCCATGCTTCCCAAAGCATAACAAAGGCAGAGACTTTCAGACAAGTAAA
66 TTTATATGCACACTTTTCCATGCTTCCCAAAGCATAACAAAGGCACACACTTTCAGACAAGTAAA
* *
3928528 TTAAATTCAAACATTTAACAGTCGATTGATATATCATAAATATA
131 TTAAATTCAAACATTTAACAGTCCATTGAAATATCATAAATATA
3928572 GGAAGCAACA
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 170 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (198 bp):
ATTGTATGTCTCCCACAATTTTTTTAACTTCATACTCAAATAGATCTTTCTAATATAAATAAATA
TTTATATGCACACTTTTCCATGCTTCCCAAAGCATAACAAAGGCACACACTTTCAGACAAGTAAA
TTAAATTCAAACATTTAACAGTCCATTGAAATATCATAAATATATCATAAACATTTAACAAAGGC
AGG
Found at i:3930476 original size:6 final size:6
Alignment explanation
Indices: 3930454--3930486 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3930444 CAAACAGCTT
3930454 AAAATA CAAAA-A AAAATA AAAATA AAAATA AAA
1 AAAATA -AAAATA AAAATA AAAATA AAAATA AAA
3930487 TCTTTCCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.16
6 17 0.68
7 4 0.16
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:3930477 original size:18 final size:17
Alignment explanation
Indices: 3930454--3930487 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3930444 CAAACAGCTT
3930454 AAAATACAAAAAAAAATA
1 AAAATA-AAAAAAAAATA
*
3930472 AAAATAAAAATAAAAT
1 AAAATAAAAAAAAAAT
3930488 CTTTCCTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAAAAAATA
Found at i:3937834 original size:16 final size:16
Alignment explanation
Indices: 3937794--3937836 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3937784 TGAATATATA
3937794 AATATATTAAA--ATT
1 AATATATTAAATTATT
* *
3937808 TATATAATAAATTATT
1 AATATATTAAATTATT
3937824 AATATATTAAATT
1 AATATATTAAATT
3937837 TTATATGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 9 0.39
16 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATTAAATTATT
Found at i:3937850 original size:38 final size:37
Alignment explanation
Indices: 3937808--3937927 Score: 115
Period size: 38 Copynumber: 3.2 Consensus size: 37
3937798 TATTAAAATT
*
3937808 TATATAATAAATTATTAATATATTAAATTTTATATGAA
1 TATATAATAAATTATTAATATATTAAA-TTTATATAAA
* ** *
3937846 TATATAAT--ATT-TTAATATAATTATATCAAAACTTAAA
1 TATATAATAAATTATTAATAT-ATTAAATTTATA--TAAA
3937883 TA-AT-ATAAATTATTAATATATTATAATTTATATAAA
1 TATATAATAAATTATTAATATATTA-AATTTATATAAA
3937919 TATATAATA
1 TATATAATA
3937928 CTTAAATATA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
35 12 0.19
36 16 0.25
37 14 0.22
38 22 0.34
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (37 bp):
TATATAATAAATTATTAATATATTAAATTTATATAAA
Found at i:3937897 original size:73 final size:71
Alignment explanation
Indices: 3937789--3937940 Score: 207
Period size: 73 Copynumber: 2.1 Consensus size: 71
3937779 TACTATGAAT
* * * * *
3937789 ATATAAATATATTAAAATTTATATAATAAATTATTAATATATTA-AATTTTATATGAATATATAA
1 ATATAATTATATCAAAACTTAAATAATAAATTATTAATATATTATAA-TTTATATAAATATATAA
* *
3937853 TATTTTA
65 TACTTAA
3937860 ATATAATTATATCAAAACTTAAATAATATAAATTATTAATATATTATAATTTATATAAATATATA
1 ATATAATTATATCAAAACTTAAAT-A-ATAAATTATTAATATATTATAATTTATATAAATATATA
3937925 ATACTTAA
64 ATACTTAA
3937933 ATATAATT
1 ATATAATT
3937941 GTAGCGTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
71 20 0.28
72 1 0.01
73 48 0.68
74 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (71 bp):
ATATAATTATATCAAAACTTAAATAATAAATTATTAATATATTATAATTTATATAAATATATAAT
ACTTAA
Found at i:3941384 original size:2 final size:2
Alignment explanation
Indices: 3941377--3941409 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3941367 ACTGAAGAGA
3941377 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3941410 TAAAAGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3943705 original size:32 final size:32
Alignment explanation
Indices: 3943669--3943751 Score: 157
Period size: 32 Copynumber: 2.6 Consensus size: 32
3943659 GGCACACTCG
3943669 AGAAATCAATAATATAAAGTGTAAAAACATCA
1 AGAAATCAATAATATAAAGTGTAAAAACATCA
3943701 AGAAATCAATAATATAAAGTGTAAAAACATCA
1 AGAAATCAATAATATAAAGTGTAAAAACATCA
*
3943733 AGAAATCAATAAGATAAAG
1 AGAAATCAATAATATAAAG
3943752 CAAAGGGCAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.20
Consensus pattern (32 bp):
AGAAATCAATAATATAAAGTGTAAAAACATCA
Found at i:3944999 original size:16 final size:16
Alignment explanation
Indices: 3944978--3945010 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3944968 TGGGGAAAAT
3944978 GAAAAATTATTCAGAA
1 GAAAAATTATTCAGAA
3944994 GAAAAATTATTCAGAA
1 GAAAAATTATTCAGAA
3945010 G
1 G
3945011 CTAGGAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.24
Consensus pattern (16 bp):
GAAAAATTATTCAGAA
Found at i:3948309 original size:20 final size:18
Alignment explanation
Indices: 3948286--3948336 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
3948276 TATATTTTAA
3948286 AATAAAAATAAAATTAATTT
1 AATAAAAATAAAA-T-ATTT
3948306 AATAAAAATATAAATATTT
1 AATAAAAATA-AAATATTT
*
3948325 AA-AAAATTAAAA
1 AATAAAAATAAAA
3948337 ATGTTACTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 6 0.21
19 6 0.21
20 11 0.38
21 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAAATAAAATATTT
Found at i:3956454 original size:36 final size:37
Alignment explanation
Indices: 3956414--3956490 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
3956404 CAAGTTCACG
3956414 TATGGAACTTA-AGAAATAATTAGCAAAAGTTAAAGC
1 TATGGAACTTAGAGAAATAATTAGCAAAAGTTAAAGC
* * * *
3956450 TATGGAACTTAGAGAGATAATTATCCAAAGTTCAAGC
1 TATGGAACTTAGAGAAATAATTAGCAAAAGTTAAAGC
3956487 TATG
1 TATG
3956491 ATATACAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.27
Consensus pattern (37 bp):
TATGGAACTTAGAGAAATAATTAGCAAAAGTTAAAGC
Found at i:3962434 original size:2 final size:2
Alignment explanation
Indices: 3962427--3962456 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3962417 CATATTTAAC
*
3962427 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3962457 TCAAGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3962729 original size:5 final size:5
Alignment explanation
Indices: 3962721--3962765 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
3962711 AAATTAAATA
* *
3962721 ATTAT ATTAT TTTAT ATT-T ATTAT A-TAT -TTAT ATTGT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
3962766 TAAAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
4 10 0.30
5 23 0.70
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (5 bp):
ATTAT
Found at i:3962737 original size:27 final size:27
Alignment explanation
Indices: 3962701--3962764 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 27
3962691 AAAAAATAAA
*
3962701 TATAATATATAAATTAAATAATTATAT
1 TATATTATATAAATTAAATAATTATAT
* ** * *
3962728 TATTTTATATTTATTATATATTTATAT
1 TATATTATATAAATTAAATAATTATAT
*
3962755 TGTATTATAT
1 TATATTATAT
3962765 TTAAAATTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TATATTATATAAATTAAATAATTATAT
Found at i:3962765 original size:27 final size:27
Alignment explanation
Indices: 3962713--3962767 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3962703 TAATATATAA
*
3962713 ATTAAATAATTATATTATTTTATATTT
1 ATTAAATAATTATATTATATTATATTT
* * *
3962740 ATTATATATTTATATTGTATTATATTT
1 ATTAAATAATTATATTATATTATATTT
3962767 A
1 A
3962768 AAATTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
ATTAAATAATTATATTATATTATATTT
Found at i:3966737 original size:13 final size:12
Alignment explanation
Indices: 3966719--3966751 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3966709 TGACTACATG
3966719 TTTCTTTTTTCTT
1 TTTCTTTTTT-TT
3966732 TTTCTTTTTTTT
1 TTTCTTTTTTTT
3966744 TTT-TTTTT
1 TTTCTTTTT
3966752 GAAAATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 5 0.25
13 10 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:3967297 original size:20 final size:20
Alignment explanation
Indices: 3967274--3967311 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3967264 GCACAATTAA
3967274 TCTCAATTTTTGCCATGTAC
1 TCTCAATTTTTGCCATGTAC
3967294 TCTCAATTTTTGCCATGT
1 TCTCAATTTTTGCCATGT
3967312 CCATAGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (20 bp):
TCTCAATTTTTGCCATGTAC
Found at i:3975810 original size:14 final size:13
Alignment explanation
Indices: 3975778--3975812 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
3975768 TCTCCAGTTA
3975778 ATTATTATTTATT
1 ATTATTATTTATT
3975791 ATTTATTATTTATTT
1 A-TTATTATTTA-TT
3975806 ATTATTA
1 ATTATTA
3975813 AATTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 16 0.80
15 3 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATTATTTATT
Found at i:3975811 original size:7 final size:7
Alignment explanation
Indices: 3975779--3975804 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3975769 CTCCAGTTAA
3975779 TTATTAT
1 TTATTAT
3975786 TTATTAT
1 TTATTAT
3975793 TTATTAT
1 TTATTAT
3975800 TTATT
1 TTATT
3975805 TATTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTAT
Found at i:3976568 original size:16 final size:17
Alignment explanation
Indices: 3976543--3976577 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3976533 ATTATCATTT
3976543 AATTTATA-TTTAAATA
1 AATTTATATTTTAAATA
*
3976559 AATTTTTATTTTAAATA
1 AATTTATATTTTAAATA
3976576 AA
1 AA
3976578 ATATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATATTTTAAATA
Found at i:3976588 original size:17 final size:17
Alignment explanation
Indices: 3976550--3976588 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3976540 TTTAATTTAT
* *
3976550 ATTTAAATAAATTTTTA
1 ATTTAAATAAAATATTA
*
3976567 TTTTAAATAAAATATTA
1 ATTTAAATAAAATATTA
3976584 ATTTA
1 ATTTA
3976589 TATTATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATAAAATATTA
Found at i:3976588 original size:22 final size:21
Alignment explanation
Indices: 3976541--3976599 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
3976531 TTATTATCAT
3976541 TTAATTTATATTTAAAT--AAA
1 TTAATTTAT-TTTAAATAAAAA
3976561 TT--TTTATTTTAAATAAAATA
1 TTAATTTATTTTAAATAAAA-A
* *
3976581 TTAATTTATATTATATAAA
1 TTAATTTATTTTAAATAAA
3976600 TTAGATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 2 0.06
20 5 0.16
22 13 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATTTATTTTAAATAAAAA
Found at i:3976931 original size:30 final size:30
Alignment explanation
Indices: 3976871--3976950 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
3976861 AAAATTAATG
*
3976871 ATTTTATTTAAATATATATTAAATAATAAA
1 ATTTTATTTAAATATAAATTAAATAATAAA
* * *
3976901 ATTTTATTTAACTGTAAATTAAA-AGTTAAA
1 ATTTTATTTAAATATAAATTAAATA-ATAAA
*
3976931 ATTTT-TTCAAATA-AAATTAA
1 ATTTTATTTAAATATAAATTAA
3976951 CGAACTTACC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.17
29 6 0.14
30 29 0.69
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTTTATTTAAATATAAATTAAATAATAAA
Found at i:3983957 original size:13 final size:13
Alignment explanation
Indices: 3983921--3983957 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
3983911 TCTGCCTATA
3983921 TATATATAAAATT
1 TATATATAAAATT
*
3983934 TAT-T-TATAATT
1 TATATATAAAATT
3983945 TATATATAAAATT
1 TATATATAAAATT
3983958 ATGTTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.45
12 2 0.10
13 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATATAAAATT
Found at i:3991294 original size:19 final size:19
Alignment explanation
Indices: 3991272--3991312 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3991262 TATTATTTAA
*
3991272 TTAAATT-TGATTTGAAAAT
1 TTAAATTATCATTT-AAAAT
3991291 TTAAATTATCATTTAAAAT
1 TTAAATTATCATTTAAAAT
3991310 TTA
1 TTA
3991313 TTAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
TTAAATTATCATTTAAAAT
Found at i:3994135 original size:14 final size:15
Alignment explanation
Indices: 3994118--3994147 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3994108 TTAAGCTTAA
3994118 ATTAA-CCTTAATTG
1 ATTAACCCTTAATTG
3994132 ATTAACCCTTAATTG
1 ATTAACCCTTAATTG
3994147 A
1 A
3994148 CGAAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTAACCCTTAATTG
Found at i:3994257 original size:21 final size:21
Alignment explanation
Indices: 3994232--3994271 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3994222 AGATAAATAT
* *
3994232 ATTAAAATTTTTATAATATTA
1 ATTAAAAATATTATAATATTA
3994253 ATTAAAAATATTATAATAT
1 ATTAAAAATATTATAATAT
3994272 ATATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAAAAATATTATAATATTA
Found at i:3996596 original size:2 final size:2
Alignment explanation
Indices: 3996591--3996619 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3996581 TATATGTGAA
3996591 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3996620 ATATATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3999164 original size:8 final size:7
Alignment explanation
Indices: 3999142--3999223 Score: 56
Period size: 6 Copynumber: 12.7 Consensus size: 7
3999132 ATAAATTTAA
3999142 ATATAAT
1 ATATAAT
3999149 AT-TAAT
1 ATATAAT
3999155 ATATACAT
1 ATATA-AT
3999163 ATA-AAT
1 ATATAAT
3999169 ATAT--T
1 ATATAAT
* *
3999174 TTAAAAT
1 ATATAAT
*
3999181 TTAT-AT
1 ATATAAT
3999187 ATATAAT
1 ATATAAT
3999194 ATAT--T
1 ATATAAT
3999199 AT-TAAT
1 ATATAAT
3999205 AT-TAAT
1 ATATAAT
3999211 ATATAAAT
1 ATAT-AAT
3999219 ATATA
1 ATATA
3999224 TCATACAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
4 1 0.02
5 6 0.10
6 25 0.41
7 17 0.28
8 12 0.20
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATAAT
Found at i:3999191 original size:26 final size:26
Alignment explanation
Indices: 3999139--3999222 Score: 95
Period size: 25 Copynumber: 3.3 Consensus size: 26
3999129 TAAATAAATT
* * *
3999139 TAAATATAATATTAATA-TATACATA
1 TAAATATATTATTAAAATTATATATA
3999164 TAAATATATT-TTAAAATT-TATATA
1 TAAATATATTATTAAAATTATATATA
*
3999188 TATAATATATTATTAATATTA-ATATA
1 TA-AATATATTATTAAAATTATATATA
3999214 TAAATATAT
1 TAAATATAT
3999223 ATCATACAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 12 0.24
25 25 0.49
26 14 0.27
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATATATTATTAAAATTATATATA
Found at i:3999817 original size:18 final size:19
Alignment explanation
Indices: 3999777--3999814 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3999767 AATTTTTATT
*
3999777 ATTAATATATTAAAAATAA
1 ATTAATATATAAAAAATAA
3999796 ATTAATATATAAAAAATAA
1 ATTAATATATAAAAAATAA
3999815 TTATTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTAATATATAAAAAATAA
Found at i:3999929 original size:2 final size:2
Alignment explanation
Indices: 3999917--3999955 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3999907 AGGAAGTCTC
3999917 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3999956 AAGAGGAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4000145 original size:28 final size:28
Alignment explanation
Indices: 4000114--4000173 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
4000104 AAGTGATATG
4000114 TATAAATAAATTTTAATA-ATTTAAAATT
1 TATAAAT-AATTTTAATATATTTAAAATT
* * *
4000142 TATATATAATTTTAATATTTTTATAATT
1 TATAAATAATTTTAATATATTTAAAATT
4000170 TATA
1 TATA
4000174 TTATATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATAAATAATTTTAATATATTTAAAATT
Found at i:4000174 original size:28 final size:27
Alignment explanation
Indices: 4000122--4000174 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
4000112 TGTATAAATA
4000122 AATTTTAATAATTTAAAATTTATATAT
1 AATTTTAATAATTTAAAATTTATATAT
* *
4000149 AATTTTAATATTTTTATAATTTATAT
1 AATTTTAATA-ATTTAAAATTTATAT
4000175 TATATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
AATTTTAATAATTTAAAATTTATATAT
Found at i:4000310 original size:16 final size:17
Alignment explanation
Indices: 4000280--4000317 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
4000270 AGGTTTGTTT
*
4000280 TAATATTTTATAAAATA
1 TAATATTTTAAAAAATA
4000297 TAAT-TTTTAAAAAATA
1 TAATATTTTAAAAAATA
4000313 TAATA
1 TAATA
4000318 ATAAGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATTTTAAAAAATA
Found at i:4000905 original size:31 final size:33
Alignment explanation
Indices: 4000870--4000930 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
4000860 ATACATAAAA
*
4000870 ATATT-AAATTTACATAAA-ATAAATTATTAAT
1 ATATTAAAATTTACATAAATATAAAATATTAAT
*
4000901 ATATTAAAATTTATATAAATATAAAATATT
1 ATATTAAAATTTACATAAATATAAAATATT
4000931 TTAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 5 0.19
32 12 0.46
33 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATTAAAATTTACATAAATATAAAATATTAAT
Found at i:4000922 original size:18 final size:16
Alignment explanation
Indices: 4000868--4000925 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
4000858 GAATACATAA
*
4000868 AAATATTAAATTTACAT
1 AAATA-TAAATTTATAT
4000885 AAA-ATAAA-TTAT-T
1 AAATATAAATTTATAT
4000898 AATATATTAAAATTTATAT
1 AA-ATA-T-AAATTTATAT
4000917 AAATATAAA
1 AAATATAAA
4000926 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 5 0.15
16 5 0.15
17 7 0.21
18 7 0.21
19 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAAATTTATAT
Found at i:4000952 original size:26 final size:27
Alignment explanation
Indices: 4000898--4000982 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 27
4000888 ATAAATTATT
4000898 AATATATTAAAATTTATATAAATATAA
1 AATATATTAAAATTTATATAAATATAA
* *
4000925 AATAT-TTTAAATTTATTTATAATA-AA
1 AATATATTAAAATTTATATA-AATATAA
* *
4000951 AA-A-ATTCAAATATAATATTAATATATAA
1 AATATATTAAAAT-TTATA-TAA-ATATAA
4000979 AATA
1 AATA
4000983 AAAAAATTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
25 7 0.15
26 20 0.43
27 14 0.30
28 4 0.09
29 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATATTAAAATTTATATAAATATAA
Found at i:4001243 original size:12 final size:14
Alignment explanation
Indices: 4001226--4001258 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
4001216 AAATTTAATA
4001226 TTTTTAATG-CT-T
1 TTTTTAATGTCTAT
4001238 TTTTTAATGTCTAT
1 TTTTTAATGTCTAT
4001252 TTTTTAA
1 TTTTTAA
4001259 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 2 0.11
14 8 0.42
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (14 bp):
TTTTTAATGTCTAT
Found at i:4001552 original size:17 final size:19
Alignment explanation
Indices: 4001514--4001561 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
4001504 GACATGAATA
*
4001514 AATATATTTAATATATATTT
1 AATA-ATTTAATATACATTT
4001534 AA-AATTTAA-ATACATTT
1 AATAATTTAATATACATTT
4001551 AATAATTTAAT
1 AATAATTTAAT
4001562 TATGATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.36
18 13 0.52
19 1 0.04
20 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTTAATATACATTT
Found at i:4006336 original size:2 final size:2
Alignment explanation
Indices: 4006329--4006363 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4006319 AACTGTCTGC
4006329 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4006364 ATGTAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4010622 original size:19 final size:19
Alignment explanation
Indices: 4010592--4010647 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
4010582 ATTCTTTCTT
4010592 TTTTAAAT-TTTATTTAAA
1 TTTTAAATATTTATTTAAA
**
4010610 TTTTAAATATTTATTTTTA
1 TTTTAAATATTTATTTAAA
*
4010629 TTTTATAA-ATTTTTTTAAA
1 TTTTA-AATATTTATTTAAA
4010648 ATAAATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 8 0.26
19 21 0.68
20 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAATATTTATTTAAA
Found at i:4010705 original size:37 final size:37
Alignment explanation
Indices: 4010664--4010770 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 37
4010654 AATATGTTAA
4010664 TATTTTTTAATTAT-TATTTAATATAAATATAAATATT
1 TATTTTTTAATTATATATTTAATATAAATATAAATA-T
* **
4010701 TATTTTTTAA-TATATATTTTAT-TATTTGATAAATAT
1 TATTTTTTAATTATATATTTAATATAAAT-ATAAATAT
* * *
4010737 AATTTTAATAATT-TATGTTTTAATATAAATATAA
1 TATTTT-TTAATTATAT-ATTTAATATAAATATAA
4010771 TTTTTTAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
36 12 0.22
37 30 0.55
38 10 0.18
39 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (37 bp):
TATTTTTTAATTATATATTTAATATAAATATAAATAT
Found at i:4010726 original size:26 final size:26
Alignment explanation
Indices: 4010663--4010850 Score: 70
Period size: 26 Copynumber: 7.2 Consensus size: 26
4010653 TAATATGTTA
*
4010663 ATATTTT-TTAATTATTATTTAATAT
1 ATATTTTATTATTTATTATTTAATAT
* * * * *
4010688 AAATATAAATATTTATTTTTTAATAT
1 ATATTTTATTATTTATTATTTAATAT
4010714 ATATTTTATTATTTGA-TA---AATAT
1 ATATTTTATTATTT-ATTATTTAATAT
*
4010737 A-ATTTTAATAATTTATGT-TTTAATAT
1 ATATTTT-ATTATTTAT-TATTTAATAT
* * * *
4010763 AAATATAATTTTTTAAATTATTATAA-AT
1 ATATTTTATTATTT--ATTATT-TAATAT
4010791 ATAATTTTACTTATATTTTATTATTTAATAT
1 AT-ATTTTA--T-TA-TTTATTATTTAATAT
* * * * *
4010822 AAATATGATT-TTAATTATTTATTAT
1 ATATTTTATTATTTATTATTTAATAT
4010847 ATAT
1 ATAT
4010851 ATATTAATCA
Statistics
Matches: 118, Mismatches: 26, Indels: 38
0.65 0.14 0.21
Matches are distributed among these distances:
22 6 0.05
23 12 0.10
24 1 0.01
25 20 0.17
26 37 0.31
27 6 0.05
28 8 0.07
29 7 0.06
30 7 0.06
31 10 0.08
32 1 0.01
33 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (26 bp):
ATATTTTATTATTTATTATTTAATAT
Found at i:4010736 original size:19 final size:19
Alignment explanation
Indices: 4010692--4010736 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4010682 TAATATAAAT
*
4010692 ATAAATA-TTTATTTTTTA
1 ATAAATATTTTATTATTTA
* *
4010710 ATATATATTTTATTATTTG
1 ATAAATATTTTATTATTTA
4010729 ATAAATAT
1 ATAAATAT
4010737 AATTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATAAATATTTTATTATTTA
Found at i:4010741 original size:22 final size:20
Alignment explanation
Indices: 4010671--4010743 Score: 60
Period size: 23 Copynumber: 3.4 Consensus size: 20
4010661 TAATATTTTT
*
4010671 TAATTATTATTTAATATAAATA
1 TAATT-TTATTT-TTATAAATA
4010693 TAAATATTTATTTTT-T-AATA
1 T-AAT-TTTATTTTTATAAATA
4010713 TATATTTTATTATTTGATAAATA
1 TA-ATTTTATT-TTT-ATAAATA
4010736 TAATTTTA
1 TAATTTTA
4010744 ATAATTTATG
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
19 7 0.16
20 10 0.23
21 1 0.02
22 9 0.21
23 15 0.35
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (20 bp):
TAATTTTATTTTTATAAATA
Found at i:4010838 original size:56 final size:53
Alignment explanation
Indices: 4010712--4010840 Score: 138
Period size: 56 Copynumber: 2.3 Consensus size: 53
4010702 ATTTTTTAAT
4010712 ATATATTTT-ATTATTTGATAAATATAATTTTAATAATTTATGTTTTAATATAA
1 ATATATTTTAATTA-TTGATAAATATAATTTTAATAATTTATGTTTTAATATAA
*
4010765 ATATAATTTTTTAAATTATT-ATAAATATAATTTTACTTATATTTTAT-TATTTAATATAA
1 ATAT-A--TTTT-AATTATTGATAAATATAATTTTA---ATAATTTATGT-TTTAATATAA
4010824 ATATGATTTTAATTATT
1 ATAT-ATTTTAATTATT
4010841 TATTATATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
53 4 0.06
54 1 0.02
56 26 0.40
57 6 0.09
58 5 0.08
59 23 0.35
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (53 bp):
ATATATTTTAATTATTGATAAATATAATTTTAATAATTTATGTTTTAATATAA
Found at i:4010847 original size:25 final size:24
Alignment explanation
Indices: 4010805--4010852 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
4010795 TTTTACTTAT
4010805 ATTTTATTATTTAATATAAATATG
1 ATTTTATTATTTAATATAAATATG
* *
4010829 ATTTTAATTATTTATTATATATAT
1 ATTTT-ATTATTTAATATAAATAT
4010853 ATTAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTTATTATTTAATATAAATATG
Found at i:4011207 original size:13 final size:13
Alignment explanation
Indices: 4011189--4011213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4011179 AATAACATAG
4011189 TACATATTCTAAA
1 TACATATTCTAAA
4011202 TACATATTCTAA
1 TACATATTCTAA
4011214 TATTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TACATATTCTAAA
Done.