Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 11 of 211
Found at i:3129207 original size:30 final size:30
Alignment explanation
Indices: 3129152--3129209 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3129142 TAATATCAAC
** *
3129152 AATAAATTAAAAATTGGTATGAACAATAAT
1 AATAAATTAAAAATTAATATCAACAATAAT
*
3129182 AATAAATTAAAGATTAATATCAACAATA
1 AATAAATTAAAAATTAATATCAACAATA
3129210 TTTTATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAAATTAAAAATTAATATCAACAATAAT
Found at i:3132189 original size:18 final size:18
Alignment explanation
Indices: 3132168--3132209 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3132158 GAAAATGAAC
* *
3132168 TTTTAAATTTTTTTTATT
1 TTTTAAAGTTTTTATATT
3132186 TTTTAAAGTTTTTATATT
1 TTTTAAAGTTTTTATATT
3132204 TTTTAA
1 TTTTAA
3132210 GAATTAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTAAAGTTTTTATATT
Found at i:3141369 original size:51 final size:52
Alignment explanation
Indices: 3141280--3141378 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 52
3141270 GATAAAAGTT
3141280 CAAATTAATTACTTTTAGTTTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
1 CAAATTAATTACTTTTAG-TTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
** *
3141333 CAAATTAATTGTTTTTAG-TTTAGAAATAAAATTGTAAGTATTGAAA
1 CAAATTAATTACTTTTAGTTTTAGAAATAAAATTGTAAATATTGAAA
3141379 CTTTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 27 0.63
53 16 0.37
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.40
Consensus pattern (52 bp):
CAAATTAATTACTTTTAGTTTTAGAAATAAAATTGTAAATATTGAAAAGGTA
Found at i:3144512 original size:21 final size:22
Alignment explanation
Indices: 3144486--3144532 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3144476 CTCTGCTCAA
*
3144486 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3144507 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3144529 ACTC
1 ACTC
3144533 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3149353 original size:92 final size:91
Alignment explanation
Indices: 3149196--3149405 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 91
3149186 ATTGATTTTA
* * * *
3149196 ATAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTA
1 ATAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTA
* *
3149261 TATTTAAT-ATTAATTATTTTAAATTGT
65 TATGTAATAATT-ATTATTTTAAATTAT
*
3149288 ATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATT
1 ATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATT
3149352 ATATGTAATAATTATTATTTTAAATTAT
64 ATATGTAATAATTATTATTTTAAATTAT
* * * *
3149380 ACAAATTCATAAAATATAATTTATTA
1 ATAAATTCATATAAGAAAATTTATTA
3149406 GTTATAATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 71 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
ATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTAT
Found at i:3149368 original size:24 final size:25
Alignment explanation
Indices: 3149333--3149380 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
3149323 TTATGAAATT
3149333 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
3149357 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
3149381 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:3149582 original size:15 final size:15
Alignment explanation
Indices: 3149547--3149598 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3149537 TAAGAAATTT
*
3149547 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3149561 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3149575 TATTTAATAATAAT-
1 TATTTAATTATAATA
3149589 TATGTTAATT
1 TAT-TTAATT
3149599 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3149702 original size:15 final size:15
Alignment explanation
Indices: 3149667--3149718 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3149657 TTAAGAATTT
*
3149667 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3149681 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3149695 TATTTAATAATAAT-
1 TATTTAATTATAATA
3149709 TATGTTAATT
1 TAT-TTAATT
3149719 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3149705 original size:120 final size:120
Alignment explanation
Indices: 3149421--3149834 Score: 726
Period size: 120 Copynumber: 3.4 Consensus size: 120
3149411 AATTATTTTA
* * * *
3149421 AATTTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-AT
*
3149483 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
3149541 AAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTT
1 -AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTT
3149606 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
3149662 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
3149727 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
3149782 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
3149835 TAAATATGAT
Statistics
Matches: 285, Mismatches: 5, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
120 179 0.63
121 104 0.36
122 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:3149817 original size:16 final size:16
Alignment explanation
Indices: 3149796--3149837 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3149786 TTATTAAATT
*
3149796 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3149812 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
3149827 AT-TATGTTTAA
1 ATATAT-TTTAA
3149838 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3149822 original size:15 final size:15
Alignment explanation
Indices: 3149787--3149828 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3149777 TTAAGAATTT
*
3149787 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3149801 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3149815 TATTTAATAATAAT
1 TATTTAATTATAAT
3149829 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3149948 original size:153 final size:156
Alignment explanation
Indices: 3149771--3150083 Score: 524
Period size: 153 Copynumber: 2.0 Consensus size: 156
3149761 ATAAGAATAT
* * *
3149771 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
* *
3149836 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
3149901 T-A-A-TTACCAAAACAAATTTCTGC
131 TAACATTTACCAAAACAAATTTATGC
* *
3149924 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
3149989 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
3150054 TAATCATTTACCAAAACAAATTTATGC
131 TAA-CATTTACCAAAACAAATTTATGC
3150081 TAA
1 TAA
3150084 GGGTATTCTA
Statistics
Matches: 148, Mismatches: 8, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
153 124 0.84
154 1 0.01
156 1 0.01
157 22 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAACATTTACCAAAACAAATTTATGC
Found at i:3150227 original size:16 final size:16
Alignment explanation
Indices: 3150206--3150257 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
3150196 GATTTGTTAT
3150206 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3150222 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3150238 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
3150254 TACA
1 TACA
3150258 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3151492 original size:29 final size:29
Alignment explanation
Indices: 3151439--3151496 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3151429 ATAACTTTTT
*
3151439 TTTTATTTACCAAAATATTATAAAAAAAA
1 TTTTATTTACCAAAATATTACAAAAAAAA
3151468 TTTTATTTACCAAAATA-TACCAAAAAAAA
1 TTTTATTTACCAAAATATTA-CAAAAAAAA
3151497 AAACCTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (29 bp):
TTTTATTTACCAAAATATTACAAAAAAAA
Found at i:3151558 original size:27 final size:27
Alignment explanation
Indices: 3151519--3151604 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
3151509 GCCTGATCAA
* * *
3151519 GCCAATCACATTGGAGGCACCAAAGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
3151546 GCCAATGAGATTGGAGGCACCAATGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
* *
3151573 GCCAAAGAGATTGGCGGCACCAATGGT
1 GCCAATGAGATTGGAGGCACCAATGGT
3151600 GCCAA
1 GCCAA
3151605 AGGACTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.30, T:0.15
Consensus pattern (27 bp):
GCCAATGAGATTGGAGGCACCAATGGT
Found at i:3151605 original size:27 final size:27
Alignment explanation
Indices: 3151528--3151606 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
3151518 AGCCAATCAC
* *
3151528 ATTGGAGGCACCAAAGGTGCCAATGAG
1 ATTGGAGGCACCAATGGTGCCAAAGAG
3151555 ATTGGAGGCACCAATGGTGCCAAAGAG
1 ATTGGAGGCACCAATGGTGCCAAAGAG
*
3151582 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGAGGCACCAATGGTGCCAAAG
3151607 GACTAAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.15
Consensus pattern (27 bp):
ATTGGAGGCACCAATGGTGCCAAAGAG
Found at i:3152181 original size:18 final size:18
Alignment explanation
Indices: 3152158--3152221 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 18
3152148 TAAGATAGAG
3152158 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* * *
3152176 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATAG-T
*
3152195 TTATTAAATGAGAATTGT
1 TTATTAAATGAGAATAGT
3152213 TTATTAAAT
1 TTATTAAAT
3152222 TAAAATAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 24 0.63
19 14 0.37
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:3152193 original size:37 final size:37
Alignment explanation
Indices: 3152145--3152240 Score: 165
Period size: 37 Copynumber: 2.6 Consensus size: 37
3152135 GTTAAGTGAT
*
3152145 AATTAAGATAGAGTTATTAAATGAGAATAGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
*
3152182 AATTAAAATAGAGTTATTAAATGAGAATTGTTTATTA
1 AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
*
3152219 AATTAAAATAAAGTTATTAAAT
1 AATTAAAATAGAGTTATTAAAT
3152241 AAACTATTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (37 bp):
AATTAAAATAGAGTTATTAAATGAGAATAGTTTATTA
Found at i:3152200 original size:19 final size:19
Alignment explanation
Indices: 3152145--3152240 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 19
3152135 GTTAAGTGAT
*
3152145 AATTAAGATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * *
3152164 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
3152182 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * * *
3152201 AATGAGAATTG-TTTATTA
1 AATTAAAATAGAGTTATTA
*
3152219 AATTAAAATAAAGTTATTA
1 AATTAAAATAGAGTTATTA
3152238 AAT
1 AAT
3152241 AAACTATTCT
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
18 28 0.47
19 31 0.53
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
AATTAAAATAGAGTTATTA
Found at i:3152259 original size:37 final size:37
Alignment explanation
Indices: 3152145--3152260 Score: 121
Period size: 37 Copynumber: 3.1 Consensus size: 37
3152135 GTTAAGTGAT
* * *
3152145 AATTAAGATAGAGTTATTAAATGAGAA-TAGTTTATTA
1 AATTAAAATAAAGTTATTAAATGAGAACTA-TTTATCA
* * * *
3152182 AATTAAAATAGAGTTATTAAATGAGAATTGTTTATTA
1 AATTAAAATAAAGTTATTAAATGAGAACTATTTATCA
3152219 AATTAAAATAAAGTTATTAAAT-A-AACTATTCTCATCA
1 AATTAAAATAAAGTTATTAAATGAGAACTATT-T-ATCA
3152256 AATTA
1 AATTA
3152261 CCAAAATAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
35 5 0.07
36 2 0.03
37 62 0.89
38 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.38
Consensus pattern (37 bp):
AATTAAAATAAAGTTATTAAATGAGAACTATTTATCA
Found at i:3152374 original size:27 final size:27
Alignment explanation
Indices: 3152351--3152412 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
3152341 TTTTTTTTGT
3152351 ATATTTTGATAAATAAAAAATTTTATA
1 ATATTTTGATAAATAAAAAATTTTATA
**
3152378 ATATTTTGATAAATAAAAAAAGTTATA
1 ATATTTTGATAAATAAAAAATTTTATA
3152405 ATATTTTG
1 ATATTTTG
3152413 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAATTTTATA
Found at i:3156685 original size:22 final size:22
Alignment explanation
Indices: 3156660--3156729 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
3156650 TTTATAAGAT
3156660 AATTAGAAACGTTGGTAGATCG
1 AATTAGAAACGTTGGTAGATCG
** **
3156682 AATTAGGGA-GTTTATAAGAT--
1 AATTAGAAACGTTGGT-AGATCG
3156702 AATTAGAAACGTTGGTAGATCG
1 AATTAGAAACGTTGGTAGATCG
3156724 AATTAG
1 AATTAG
3156730 GGGTGTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 17 0.47
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (22 bp):
AATTAGAAACGTTGGTAGATCG
Found at i:3156707 original size:42 final size:42
Alignment explanation
Indices: 3156648--3156731 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3156638 GGGATATGTA
3156648 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
1 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
3156690 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
1 AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
3156732 GTGTATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (42 bp):
AGTTTATAAGATAATTAGAAACGTTGGTAGATCGAATTAGGG
Found at i:3156721 original size:20 final size:20
Alignment explanation
Indices: 3156656--3156721 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
3156646 TAAGTTTATA
3156656 AGATAATTAGAAACGTTGGT
1 AGATAATTAGAAACGTTGGT
** **
3156676 AGATCGAATTAGGGA-GTTTAT
1 AGAT--AATTAGAAACGTTGGT
3156697 AAGATAATTAGAAACGTTGGT
1 -AGATAATTAGAAACGTTGGT
3156718 AGAT
1 AGAT
3156722 CGAATTAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 15 0.44
21 8 0.24
22 11 0.32
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (20 bp):
AGATAATTAGAAACGTTGGT
Found at i:3156794 original size:14 final size:14
Alignment explanation
Indices: 3156775--3156804 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3156765 TGCTCATGCA
3156775 AGCTTAATCAATAG
1 AGCTTAATCAATAG
3156789 AGCTTAATCAATAG
1 AGCTTAATCAATAG
3156803 AG
1 AG
3156805 TTTGAGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (14 bp):
AGCTTAATCAATAG
Found at i:3157594 original size:28 final size:29
Alignment explanation
Indices: 3157544--3157600 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
3157534 TTTCCACACG
*
3157544 GGCTGGACACACAGTCGTGTGTGCCAAACA
1 GGCTGGACACACAGTCG-ATGTGCCAAACA
*
3157574 GGCTGGACACACGGTC-ATGTGCCAAAC
1 GGCTGGACACACAGTCGATGTGCCAAAC
3157601 CATGTCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
30 15 0.60
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (29 bp):
GGCTGGACACACAGTCGATGTGCCAAACA
Found at i:3158993 original size:45 final size:45
Alignment explanation
Indices: 3158924--3159010 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
3158914 GTGTATAACT
3158924 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
1 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
3158969 TATCTCATCTATTGAAT-CTGATAAGTATGATTTATCTTCCTT
1 TATCTCATCTATTGAATCCT-ATAAGTATGATTTATCTTCCTT
3159011 AATAAGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (45 bp):
TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
Found at i:3159590 original size:8 final size:8
Alignment explanation
Indices: 3159544--3159614 Score: 80
Period size: 8 Copynumber: 9.2 Consensus size: 8
3159534 GGCATAAGTG
3159544 TATATATAT
1 TATA-ATAT
3159553 TATAAATAT
1 TAT-AATAT
3159562 T-TAA-AT
1 TATAATAT
*
3159568 T-TAA-AA
1 TATAATAT
3159574 TAT-ATAT
1 TATAATAT
3159581 TATAATAT
1 TATAATAT
3159589 TATAATAT
1 TATAATAT
3159597 TATAATAT
1 TATAATAT
3159605 TATAATAT
1 TATAATAT
3159613 TA
1 TA
3159615 AAACTTAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
6 9 0.16
7 7 0.12
8 31 0.55
9 8 0.14
10 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TATAATAT
Found at i:3159642 original size:51 final size:52
Alignment explanation
Indices: 3159544--3159653 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 52
3159534 GGCATAAGTG
* * * *
3159544 TATATATATTATAAATATTTAAATTTAAAATATATATTATAATATTATAATAT
1 TATA-ATATTATAAATATTAAAACTTAAAATATATAGTATAACATTATAATAT
*
3159597 TATAATATTAT-AATATTAAAACTTAAAAGT-TA-AGTATATACATTATTATAT
1 TATAATATTATAAATATTAAAACTTAAAA-TATATAGTATA-ACATTATAATAT
3159648 TATAAT
1 TATAAT
3159654 GATAAAGTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
50 5 0.10
51 33 0.66
52 8 0.16
53 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (52 bp):
TATAATATTATAAATATTAAAACTTAAAATATATAGTATAACATTATAATAT
Found at i:3159725 original size:17 final size:16
Alignment explanation
Indices: 3159705--3159744 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3159695 AACTACACAG
3159705 AGAAGGAAAGAAAGAAA
1 AGAAGGAAAGAAAG-AA
**
3159722 AGAAAAAAAGAAAGAA
1 AGAAGGAAAGAAAGAA
3159738 AGAAGGA
1 AGAAGGA
3159745 GAAAAATTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAGGAAAGAAAGAA
Found at i:3159734 original size:21 final size:22
Alignment explanation
Indices: 3159710--3159750 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3159700 CACAGAGAAG
3159710 GAAAGAAAGAA-AAGAAAAAAA
1 GAAAGAAAGAAGAAGAAAAAAA
*
3159731 GAAAGAAAGAAGGAGAAAAA
1 GAAAGAAAGAAGAAGAAAAA
3159751 TTAGGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAGAAGAAAAAAA
Found at i:3161493 original size:29 final size:30
Alignment explanation
Indices: 3161461--3161519 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
3161451 TTAAGTTTAC
3161461 AATGTATTATTTTAT-TTAT-ATAT-TTTTTT
1 AATG-ATT-TTTTATCTTATAATATGTTTTTT
3161490 AATGATTTTTTATCTTATAATATGTTTTTT
1 AATGATTTTTTATCTTATAATATGTTTTTT
3161520 TCTAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 6 0.22
28 7 0.26
29 8 0.30
30 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (30 bp):
AATGATTTTTTATCTTATAATATGTTTTTT
Found at i:3161589 original size:17 final size:18
Alignment explanation
Indices: 3161569--3161602 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3161559 TATATGAATA
*
3161569 TATTTTTTATA-ACATAC
1 TATTTTATATATACATAC
3161586 TATTTTATATATACATA
1 TATTTTATATATACATA
3161603 TATAATTTAT
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:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTATATATACATAC
Found at i:3161829 original size:3 final size:3
Alignment explanation
Indices: 3161821--3161875 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
3161811 ATATATTGAT
3161821 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3161869 TTA TTA T
1 TTA TTA T
3161876 CTTGGTGAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3164203 original size:51 final size:51
Alignment explanation
Indices: 3164070--3164265 Score: 229
Period size: 51 Copynumber: 3.9 Consensus size: 51
3164060 AGTGAAAGTG
* * * *
3164070 ATGGTCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
*
3164119 ATGGGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * * * * *
3164170 TTCGATCACGTGTGTAGTACTATGTGCAAGCTACT-TCGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTAT-GTGTACCGGATAGTA
*
3164222 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
3164266 AACATCATTG
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.02
50 41 0.33
51 77 0.63
52 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
Found at i:3164257 original size:102 final size:101
Alignment explanation
Indices: 3164074--3164258 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
3164064 AAAGTGATGG
* *
3164074 TCACGTGTGTAGTACTATGTGCAGGGTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
3164139 TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* *
3164175 TCACGTGTGTAGTACTATGTGCAAGCTACTTCGTGTATCGG-ATGGTAAT-GGTCACATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAAT-G--ATGGGTCACATGTGTAG
3164238 TACTATGTGCAGGCTACTATG
63 TACTATGTGCAGGCTACTATG
3164259 TGAACCGAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 38 0.49
102 35 0.45
103 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGAATGATGGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:3171885 original size:15 final size:15
Alignment explanation
Indices: 3171865--3171895 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3171855 AGTAGTAAAA
3171865 TCTGAAACATTGATG
1 TCTGAAACATTGATG
3171880 TCTGAAACATTGATG
1 TCTGAAACATTGATG
3171895 T
1 T
3171896 AGTAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (15 bp):
TCTGAAACATTGATG
Found at i:3173883 original size:103 final size:103
Alignment explanation
Indices: 3173705--3174073 Score: 510
Period size: 103 Copynumber: 3.6 Consensus size: 103
3173695 TAACCGTTAT
* * * * * * *
3173705 CGGTGGATTCCGCACTTAGCAACCACCAAT-GAATCGAGGAATCAGCACACAGCAACCCATTGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATAG-GTAGGGGAATCAGCACACAGCAACCCCTCGGG
* * *
3173769 GGAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
65 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * **
3173807 CGGTGGAATCAGCACTTAGCAACCACCAA-ATGAGTCGGGGAGTCAGCACTTAGCAACCCCTCGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATA-G-GTAGGGGAATCAGCACACAGCAACCCCTCGG
3173871 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
64 GGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* **
3173911 CGGTGGGATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTCGGGG
3173976 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * *
3174014 TGGTGGGATCAGCACTTAGCAACCACGAATAGGTAGGGGAATCAGCACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCT
3174074 TTATATGCAA
Statistics
Matches: 244, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
102 27 0.11
103 175 0.72
104 41 0.17
105 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACACAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:3182042 original size:45 final size:45
Alignment explanation
Indices: 3181973--3182059 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
3181963 GTGTATAACT
3181973 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
1 TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
3182018 TATCTCATCTATTGAAT-CTGATAAGTATGATTTATCTTCCTT
1 TATCTCATCTATTGAATCCT-ATAAGTATGATTTATCTTCCTT
3182060 AATAAGGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (45 bp):
TATCTCATCTATTGAATCCTATAAGTATGATTTATCTTCCTTGTC
Found at i:3182638 original size:28 final size:31
Alignment explanation
Indices: 3182589--3182645 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
3182579 CGCATAAGTG
3182589 TATATATATTATAAATATTTAAAG-TTAATA
1 TATATATATTATAAATATTTAAAGCTTAATA
3182619 TATATATATTAT-AATA-TTAAAGCTTAA
1 TATATATATTATAAATATTTAAAGCTTAA
3182646 AAGTTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
29 8 0.31
30 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (31 bp):
TATATATATTATAAATATTTAAAGCTTAATA
Found at i:3182736 original size:25 final size:25
Alignment explanation
Indices: 3182702--3182767 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
3182692 AAACAAATGG
* * *
3182702 AAAATGAAGGAGAGAAAGAAACGAA
1 AAAAAGAAGGAAAGAAAGAAAAGAA
*
3182727 ACAAAGAAGGAAAGAAAGAAAAGAA
1 AAAAAGAAGGAAAGAAAGAAAAGAA
*
3182752 AAAAAGAAAGAAAGAA
1 AAAAAGAAGGAAAGAA
3182768 GGAGAATAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.71, C:0.03, G:0.24, T:0.02
Consensus pattern (25 bp):
AAAAAGAAGGAAAGAAAGAAAAGAA
Found at i:3182745 original size:4 final size:4
Alignment explanation
Indices: 3182714--3182767 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
3182704 AATGAAGGAG
* * *
3182714 AGAA AGAA ACGAA ACAA AGAA GGAA AGAA AGAAA AGAA AAAA AGAA AGAA
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA
3182764 AGAA
1 AGAA
3182768 GGAGAATAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3182760 original size:21 final size:21
Alignment explanation
Indices: 3182714--3182767 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3182704 AATGAAGGAG
*
3182714 AGAAAGAAACG-AAACAAAGAA
1 AGAAAGAAA-GAAAACAAAAAA
* *
3182735 GGAAAGAAAGAAAAGAAAAAA
1 AGAAAGAAAGAAAACAAAAAA
3182756 AGAAAGAAAGAA
1 AGAAAGAAAGAA
3182768 GGAGAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAGAAAACAAAAAA
Found at i:3183680 original size:41 final size:40
Alignment explanation
Indices: 3183635--3183745 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 40
3183625 CGACTTCGAG
3183635 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
1 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
* * *
3183675 TTCGATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAA
1 -TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
* * *
3183713 CCGATAAGACACTGGATGTCAATTTATTACTTC
1 TCGATGAGACACTGGGTGTCAATTTATTACTTC
3183746 AAATTATCTA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
37 17 0.29
38 13 0.22
39 2 0.03
40 7 0.12
41 20 0.34
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAA
Found at i:3183736 original size:37 final size:38
Alignment explanation
Indices: 3183636--3183738 Score: 118
Period size: 37 Copynumber: 2.7 Consensus size: 38
3183626 GACTTCGAGT
*
3183636 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAA--T-TTACTTCGGATTAATC
* * *
3183677 CGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTACTTCGGATTAATC
* *
3183714 CGATAAGACACTGGATGTCAATTTA
1 CGATGAGACACTGGGTGTCAATTTA
3183739 TTACTTCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
37 21 0.39
38 13 0.24
39 1 0.02
41 19 0.35
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAATTTACTTCGGATTAATC
Found at i:3192387 original size:27 final size:27
Alignment explanation
Indices: 3192348--3192422 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
3192338 TAGTATTGGC
* *
3192348 GCCTATCTCAGAGGTGCCAATGGTGGT
1 GCCTATCTGAGAGGTGCCAATAGTGGT
*
3192375 GCCTATCTGAGAGGTGCCATTAGTGGT
1 GCCTATCTGAGAGGTGCCAATAGTGGT
* *
3192402 GCC-ATGTTGAGAGGCGCCAAT
1 GCCTAT-CTGAGAGGTGCCAAT
3192423 TGTATTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 39 0.95
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.25
Consensus pattern (27 bp):
GCCTATCTGAGAGGTGCCAATAGTGGT
Found at i:3192510 original size:15 final size:16
Alignment explanation
Indices: 3192490--3192526 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3192480 ACAAAATCAA
3192490 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
3192505 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
3192521 ATAAAA
1 ATAAAA
3192527 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:3192807 original size:27 final size:27
Alignment explanation
Indices: 3192750--3193083 Score: 485
Period size: 27 Copynumber: 12.8 Consensus size: 27
3192740 ATTATAAAAT
3192750 AATTACAATATTCATAC--AA--ACAA
1 AATTACAATATTCATACAAAATTACAA
*
3192773 TATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
3192800 AATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
* *
3192827 AATTACAATATTCATATAAAATTACGA
1 AATTACAATATTCATACAAAATTACAA
3192854 AATTACAATATTCATAC--AA--ACAA
1 AATTACAATATTCATACAAAATTACAA
*
3192877 TATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
3192904 AATTACAATATTCATATAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
3192931 TATTACAATATTCATAC--AA--ACAA
1 AATTACAATATTCATACAAAATTACAA
*
3192954 TATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
3192981 AATTACAATATTCATATAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
* *
3193008 TATTACAATATTCATACAAAATTATAA
1 AATTACAATATTCATACAAAATTACAA
3193035 AATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
*
3193062 AATTACAATATTCTTACAAAAT
1 AATTACAATATTCATACAAAAT
3193084 ACTAATCCAA
Statistics
Matches: 280, Mismatches: 19, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
23 56 0.20
25 10 0.04
27 214 0.76
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (27 bp):
AATTACAATATTCATACAAAATTACAA
Found at i:3192838 original size:77 final size:75
Alignment explanation
Indices: 3192750--3193074 Score: 458
Period size: 77 Copynumber: 4.2 Consensus size: 75
3192740 ATTATAAAAT
*
3192750 AATTACAATATTC-ATACAA-ACAATATTACAATATTCATACAAAATTACAAAATTACAATATTC
1 AATTACAATATTCAATAAAATACAATATTACAATATTCATAC--AA--ACAAAATTACAATATTC
3192813 ATACAAAATTACAA
62 ATACAAAATTACAA
*
3192827 AATTACAATATTCATATAAAATTACGAA-ATTACAATATTCATACAAACAATATTACAATATTCA
1 AATTACAATATTCA-ATAAAA-TAC-AATATTACAATATTCATACAAACAAAATTACAATATTCA
3192891 TACAAAATTACAA
63 TACAAAATTACAA
*
3192904 AATTACAATATTCATATAAAATTACAATATTACAATATTCATACAAACAATATTACAATATTCAT
1 AATTACAATATTCA-ATAAAA-TACAATATTACAATATTCATACAAACAAAATTACAATATTCAT
3192969 ACAAAATTACAA
64 ACAAAATTACAA
*
3192981 AATTACAATATTCATATAAAATTACAATATTACAATATTCATACAAAATTATAAAATTACAATAT
1 AATTACAATATTCA-ATAAAA-TACAATATTACAATATTCATAC--AA--ACAAAATTACAATAT
3193046 TCATACAAAATTACAA
60 TCATACAAAATTACAA
3193062 AATTACAATATTC
1 AATTACAATATTC
3193075 TTACAAAATA
Statistics
Matches: 234, Mismatches: 4, Indels: 16
0.92 0.02 0.06
Matches are distributed among these distances:
76 2 0.01
77 161 0.69
79 9 0.04
81 60 0.26
82 2 0.01
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (75 bp):
AATTACAATATTCAATAAAATACAATATTACAATATTCATACAAACAAAATTACAATATTCATAC
AAAATTACAA
Found at i:3192870 original size:104 final size:103
Alignment explanation
Indices: 3192750--3193081 Score: 492
Period size: 104 Copynumber: 3.2 Consensus size: 103
3192740 ATTATAAAAT
3192750 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
3192815 ACAAAATTACAAAATTACAATATTCATATAAAATTACGA
66 ACAAAATTACAAAATTACAATATTCATATAAAATTAC-A
3192854 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
* * *
3192919 ATAAAATTACAATATTACAATATTC--ATACAA--ACA
66 ACAAAATTACAAAATTACAATATTCATATAAAATTACA
* * *
3192953 ATATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAATTACAATATTACAATA
1 A-ATTACAATATTCATAC--AA--ACAATATTACAATATTCATACAAAATTACAAAATTACAATA
* *
3193018 TTCATACAAAATTATAAAATTACAATATTCATACAAAATTACAA
61 TTCATACAAAATTACAAAATTACAATATTCATATAAAATTAC-A
*
3193062 AATTACAATATTCTTACAAA
1 AATTACAATATTCATACAAA
3193082 ATACTAATCC
Statistics
Matches: 206, Mismatches: 12, Indels: 20
0.87 0.05 0.08
Matches are distributed among these distances:
99 2 0.01
100 18 0.09
102 7 0.03
104 154 0.75
106 6 0.03
108 17 0.08
109 2 0.01
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (103 bp):
AATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAAAATTACAATATTCAT
ACAAAATTACAAAATTACAATATTCATATAAAATTACA
Found at i:3193081 original size:19 final size:19
Alignment explanation
Indices: 3192795--3193031 Score: 108
Period size: 19 Copynumber: 12.5 Consensus size: 19
3192785 CATACAAAAT
3192795 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
3192814 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
* **
3192830 TACAATATT-C-ATATAAAA
1 TACAAAATTACAATAT-TCA
*
3192848 TTACGAAATTACAATATTCA
1 -TACAAAATTACAATATTCA
3192868 TACAAACAATATTACAATATTCA
1 TAC--A-AA-ATTACAATATTCA
*
3192891 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
* **
3192907 TACAATATT-C-ATATAAAA
1 TACAAAATTACAATAT-TCA
*
3192925 TTACAATATTACAATATTCA
1 -TACAAAATTACAATATTCA
3192945 TACAAACAATATTACAATATTCA
1 TAC--A-AA-ATTACAATATTCA
*
3192968 TACAAAATTACAA-AAT--
1 TACAAAATTACAATATTCA
* **
3192984 TACAATATT-C-ATATAAAA
1 TACAAAATTACAATAT-TCA
*
3193002 TTACAATATTACAATATTCA
1 -TACAAAATTACAATATTCA
3193022 TACAAAATTA
1 TACAAAATTA
3193032 TAAAATTACA
Statistics
Matches: 166, Mismatches: 23, Indels: 58
0.67 0.09 0.23
Matches are distributed among these distances:
14 3 0.02
15 6 0.04
16 24 0.14
18 6 0.04
19 67 0.40
20 10 0.06
21 15 0.09
22 3 0.02
23 32 0.19
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:3193132 original size:61 final size:61
Alignment explanation
Indices: 3193062--3193407 Score: 431
Period size: 61 Copynumber: 5.4 Consensus size: 61
3193052 AAAATTACAA
* *
3193062 AATTACAATATTCTTACAAAATACTAATCCAAAACTATAAATAAAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
* *
3193123 AATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
* * * *
3193184 AATTACACTATTCATTCAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACGA
1 AATTACAATATTCATACAAAA-TAC--TA---AT-CAAAA-ACT-AT-AAATAA-A-AAAT---T
3193249 AATTAATTATAAAAT
51 AA-T--T-ATAAAAT
*
3193264 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
*
3193325 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATATAAAATTAATTATAAAAT
1 AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
3193386 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
3193408 TATAATATTC
Statistics
Matches: 250, Mismatches: 16, Indels: 38
0.82 0.05 0.12
Matches are distributed among these distances:
61 165 0.66
62 4 0.02
64 3 0.01
65 2 0.01
67 2 0.01
68 9 0.04
69 4 0.02
70 5 0.02
71 6 0.02
72 4 0.02
73 9 0.04
74 2 0.01
76 2 0.01
77 3 0.01
79 4 0.02
80 26 0.10
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (61 bp):
AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTATAAAAT
Found at i:3193184 original size:80 final size:80
Alignment explanation
Indices: 3193100--3193285 Score: 234
Period size: 80 Copynumber: 2.3 Consensus size: 80
3193090 CCAAAACTAT
* *
3193100 AAATAA-AAAATTAATT-ATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAA
1 AAATAATAAAACT-ATTCATAAAA-AATTACAATATTCATACAAAATACTAATCAAAAAATACAA
3193163 ATACAAAATTAATTATA
64 ATACAAAATTAATTATA
* * ** *
3193180 AAATAATTACACTATTCATTCAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAAT
1 AAATAATAAAACTATTCATAAAAAATTACAATATTCATACAAAATACTAATCAAAAAATACAAAT
*
3193245 ACGAAATTAATTATA
66 ACAAAATTAATTATA
* *
3193260 AAATAATTACAA-TATTCATACAAAAT
1 AAATAA-TAAAACTATTCATAAAAAAT
3193286 ACTAATCAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
80 82 0.90
81 9 0.10
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (80 bp):
AAATAATAAAACTATTCATAAAAAATTACAATATTCATACAAAATACTAATCAAAAAATACAAAT
ACAAAATTAATTATA
Found at i:3193208 original size:19 final size:19
Alignment explanation
Indices: 3193184--3193224 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3193174 ATTATAAAAT
* *
3193184 AATTACACTATTCATTCAA
1 AATTACAATATTCATACAA
3193203 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
3193222 AAT
1 AAT
3193225 ACTAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:3193242 original size:141 final size:141
Alignment explanation
Indices: 3193057--3193514 Score: 529
Period size: 141 Copynumber: 3.2 Consensus size: 141
3193047 CATACAAAAT
* * *
3193057 TACAAAATTACAATATTCTTACAAAATACTAATCCAAAACTATAAATAAAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATAAAAAATTAATTATAAAA
3193122 TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
66 TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
*
3193187 TACACTATTCA
131 TACAATATTCA
* **
3193198 TTCAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACGAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATAAAAAATTAATTATAAAA
*
3193263 TAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAAT
66 TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
3193328 TACAATATTCA
131 TACAATATTCA
* * *
3193339 TACAAAA-TAC--TAATCA-A-AAACTA-TAAAT-ATAAAAT-TAATTATAAAATAATTACAATA
1 TACAAAATTACAATATTCATACAAAATACT-AATCAAAAAATATAA--ATAAAA-AATT---A-A
* * * * ** * *
3193396 TTCATACAA-AATTATAATATTCATATAAAATTACAAAATTACAATATTCATACAAAATTATAAT
58 TT-ATAAAATAATTACAATATTCATACAAAA-TAC-TAA-T-CAA-AAAC-TAC-AAA-TACAAA
3193460 ATTAATTATAAAATAATTACAATATTCA
114 ATTAATTATAAAATAATTACAATATTCA
3193488 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
3193515 TACCCATTGG
Statistics
Matches: 270, Mismatches: 25, Indels: 31
0.83 0.08 0.10
Matches are distributed among these distances:
134 3 0.01
135 7 0.03
136 12 0.04
137 5 0.02
138 5 0.02
140 4 0.01
141 161 0.60
142 8 0.03
143 2 0.01
144 1 0.00
145 3 0.01
146 2 0.01
147 2 0.01
148 3 0.01
149 39 0.14
150 3 0.01
152 5 0.02
153 1 0.00
154 4 0.01
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (141 bp):
TACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATAAAAAATTAATTATAAAA
TAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAAT
TACAATATTCA
Found at i:3193292 original size:202 final size:210
Alignment explanation
Indices: 3192976--3193495 Score: 680
Period size: 202 Copynumber: 2.5 Consensus size: 210
3192966 CATACAAAAT
* * ** * *
3192976 TACAAAATTACAATATTCATATAAAATTACAATATTACAATATTCATACAAAATTATAAAATTAC
1 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTAGAATATT--
* *
3193041 AATATTCATACAAAATTACAAAATTACAATATTCTTACAAAATACTAATCCAAAACTATAAATAA
64 -A-ATT-AT--AAAA-T----AATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAA
3193106 AAAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAA
119 AAAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAA
*
3193171 TTAATTATAAAATAATTACACTATTCA
184 TTAATTATAAAATAATTACAATATTCA
* * *
3193198 TTCAAAATTACAATATTCATACAAAA-TAC-TAA-T-CAA-A-AAATA-TAAA-TACGAA-ATTA
1 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTA-GAATATTA
*
3193254 ATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTA
65 ATTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTA
* *
3193319 TAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATATAAAATTAATTATAAA
130 TAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAA
3193384 ATAATTACAATATTCA
195 ATAATTACAATATTCA
* * ** *
3193400 TACAAAATTATAATATTCATATAAAATTACAAAATTACAATATTCATACAAAATTATAATATTAA
1 TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTAGAATATTAA
3193465 TTATAAAATAATTACAATATTCATACAAAAT
66 TTATAAAATAATTACAATATTCATACAAAAT
3193496 TACAATATTC
Statistics
Matches: 266, Mismatches: 22, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
202 153 0.58
203 3 0.01
204 2 0.01
205 1 0.00
206 4 0.02
207 5 0.02
208 3 0.01
209 7 0.03
210 41 0.15
211 1 0.00
214 5 0.02
215 5 0.02
216 3 0.01
217 1 0.00
218 3 0.01
219 1 0.00
220 1 0.00
221 3 0.01
222 24 0.09
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.32
Consensus pattern (210 bp):
TACAAAATTACAATATTCATACAAAATTACAAAATTACAATATAAATACAAAATTAGAATATTAA
TTATAAAATAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATAAAAAATTAATTAT
AAAATAATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAA
TAATTACAATATTCA
Found at i:3193325 original size:80 final size:79
Alignment explanation
Indices: 3193123--3193293 Score: 247
Period size: 80 Copynumber: 2.2 Consensus size: 79
3193113 ATTATAAAAT
* * *
3193123 AATTACAATATTCATACAAAATACTAATCAAAAACTACAAATACAAAATTAATTATAAAATAATT
1 AATTAC-ATAATCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAATAATT
* *
3193188 ACACTATTCATTCAA
65 ACAATATTCATACAA
* *
3193203 AATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACGAAATTAATTATAAAATAATT
1 AATTAC-ATAATCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAATAATT
3193268 ACAATATTCATACAA
65 ACAATATTCATACAA
3193283 AA-TAC-TAATCA
1 AATTACATAATCA
3193294 AAAACTATAA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
77 5 0.06
79 3 0.04
80 77 0.91
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (79 bp):
AATTACATAATCATACAAAATACTAATCAAAAAATATAAATACAAAATTAATTATAAAATAATTA
CAATATTCATACAA
Found at i:3193342 original size:34 final size:34
Alignment explanation
Indices: 3193304--3193409 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 34
3193294 AAAACTATAA
3193304 ATACAAAATTAATTATAAAATAATTACAATATTC
1 ATACAAAATTAATTATAAAATAATTACAATATTC
* * * * *
3193338 ATACAAAA-TACTAATCAAA-AACTATAA-A-T-
1 ATACAAAATTAATTATAAAATAATTACAATATTC
3193367 AT--AAAATTAATTATAAAATAATTACAATATTC
1 ATACAAAATTAATTATAAAATAATTACAATATTC
3193399 ATACAAAATTA
1 ATACAAAATTA
3193410 TAATATTCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
27 4 0.07
28 8 0.15
29 8 0.15
30 2 0.04
31 2 0.04
32 8 0.15
33 8 0.15
34 15 0.27
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (34 bp):
ATACAAAATTAATTATAAAATAATTACAATATTC
Found at i:3193414 original size:19 final size:19
Alignment explanation
Indices: 3193386--3193517 Score: 120
Period size: 19 Copynumber: 6.3 Consensus size: 19
3193376 ATTATAAAAT
3193386 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
*
3193405 AATTATAATATTCATATAAAATTACAA
1 AATTACAATATTC-------A-TACAA
3193432 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
3193451 AATTATAATATTAATTATAAAA
1 AATTACAATA-T--TCATACAA
3193473 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
3193493 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
3193512 AATTAC
1 AATTAC
3193518 CCATTGGCGC
Statistics
Matches: 93, Mismatches: 8, Indels: 24
0.74 0.06 0.19
Matches are distributed among these distances:
19 51 0.55
20 8 0.09
22 7 0.08
23 9 0.10
26 1 0.01
27 17 0.18
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:3193446 original size:46 final size:44
Alignment explanation
Indices: 3193386--3193517 Score: 189
Period size: 46 Copynumber: 3.0 Consensus size: 44
3193376 ATTATAAAAT
3193386 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
1 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
*
3193430 AAAATTACAATATTCATACAAAATTATAATATTAATTATAAAA-T--
1 --AATTACAATATTCATACAAAATTATAATATTCA-TATAAAATTAC
* *
3193474 AATTACAATATTCATACAAAATTACAATATTCATACAAAATTAC
1 AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
3193518 CCATTGGCGC
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
41 6 0.08
42 32 0.41
46 33 0.42
47 7 0.09
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (44 bp):
AATTACAATATTCATACAAAATTATAATATTCATATAAAATTAC
Found at i:3193463 original size:27 final size:27
Alignment explanation
Indices: 3193400--3193455 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3193390 ACAATATTCA
* *
3193400 TACAAAATTATAATATTCATATAAAAT
1 TACAAAATTACAATATTCATACAAAAT
3193427 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
3193454 TA
1 TA
3193456 TAATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (27 bp):
TACAAAATTACAATATTCATACAAAAT
Found at i:3193491 original size:42 final size:42
Alignment explanation
Indices: 3193366--3193504 Score: 199
Period size: 42 Copynumber: 3.2 Consensus size: 42
3193356 AAACTATAAA
*
3193366 TATAAAATTAATTATAAAATAATTACAATATTCATACAAAAT
1 TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
*
3193408 TATAATATTCA-TATAAAATTACAAAATTACAATATTCATACAAAAT
1 TATAATATTAATTATAAAA-T----AATTACAATATTCATACAAAAT
3193454 TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
1 TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
*
3193496 TACAATATT
1 TATAATATT
3193505 CATACAAAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
41 7 0.08
42 40 0.46
46 33 0.38
47 7 0.08
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.37
Consensus pattern (42 bp):
TATAATATTAATTATAAAATAATTACAATATTCATACAAAAT
Found at i:3193662 original size:27 final size:28
Alignment explanation
Indices: 3193632--3193697 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 28
3193622 TTATTTAAAT
*
3193632 TTTTTTTAAAAATAAAAAATAA-TAATA
1 TTTTTTTAAAAAGAAAAAATAATTAATA
*
3193659 TTTTATTCAAAAAAAGAAAAAATAATTTAATA
1 TTTT-TT--TAAAAAGAAAAAATAA-TTAATA
3193691 TTTTTTT
1 TTTTTTT
3193698 TATTCATTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 4 0.13
28 2 0.06
30 14 0.45
31 2 0.06
32 9 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
TTTTTTTAAAAAGAAAAAATAATTAATA
Found at i:3195594 original size:12 final size:12
Alignment explanation
Indices: 3195577--3195609 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3195567 GTGAAGATGA
*
3195577 TGGTGGTGGAGG
1 TGGTGGGGGAGG
3195589 TGGTGGGGGAGG
1 TGGTGGGGGAGG
3195601 TGGTGGGGG
1 TGGTGGGGG
3195610 CAACTGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.73, T:0.21
Consensus pattern (12 bp):
TGGTGGGGGAGG
Found at i:3197658 original size:20 final size:20
Alignment explanation
Indices: 3197635--3197672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3197625 TCTTAAGATT
*
3197635 TTAAACATATTTTTACACTG
1 TTAAACATATTTTAACACTG
*
3197655 TTAAATATATTTTAACAC
1 TTAAACATATTTTAACAC
3197673 CATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (20 bp):
TTAAACATATTTTAACACTG
Found at i:3202378 original size:27 final size:23
Alignment explanation
Indices: 3202327--3202374 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3202317 TTTTTCAAAG
3202327 AATTTTTTAAATAAATAAGAAAT
1 AATTTTTTAAATAAATAAGAAAT
3202350 AATTTTTTAAATAAATAAGAAAT
1 AATTTTTTAAATAAATAAGAAAT
3202373 AA
1 AA
3202375 ATAAACTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTTTTTAAATAAATAAGAAAT
Found at i:3205766 original size:31 final size:31
Alignment explanation
Indices: 3205731--3205796 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3205721 TTACAATTAG
*
3205731 GTCATTGAAATATTCAAAAATTTTTATTTAA
1 GTCATTGAAATATTCAAAAAATTTTATTTAA
** *
3205762 GTCATTGAGCTATTCAAAAAATTTTATTTGA
1 GTCATTGAAATATTCAAAAAATTTTATTTAA
3205793 GTCA
1 GTCA
3205797 CTGGATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (31 bp):
GTCATTGAAATATTCAAAAAATTTTATTTAA
Found at i:3206679 original size:24 final size:24
Alignment explanation
Indices: 3206639--3206685 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3206629 ACAATCAATT
*
3206639 TATTAATAATACTCACAATTTAAC
1 TATTAATAACACTCACAATTTAAC
*
3206663 TATTAATGAACAC-CACATTTTAA
1 TATTAAT-AACACTCACAATTTAA
3206686 ATCAAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (24 bp):
TATTAATAACACTCACAATTTAAC
Found at i:3207881 original size:103 final size:104
Alignment explanation
Indices: 3207702--3207966 Score: 424
Period size: 103 Copynumber: 2.6 Consensus size: 104
3207692 GACCGTTATT
* * * *
3207702 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
3207767 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
3207805 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
3207870 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
3207909 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACGCAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
3207967 TTATGTACAA
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:3208328 original size:30 final size:29
Alignment explanation
Indices: 3208294--3208358 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3208284 TAATCCACCA
3208294 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
3208324 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
3208354 CCCAA
1 CCCAA
3208359 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:3208332 original size:31 final size:30
Alignment explanation
Indices: 3208301--3208358 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3208291 CCACCCAACT
3208301 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
3208331 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
3208359 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:3215256 original size:26 final size:26
Alignment explanation
Indices: 3215226--3215275 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3215216 CCACTTAATC
*
3215226 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACATAGCAACCCCTT
3215252 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
3215276 CTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTT
Found at i:3215369 original size:102 final size:103
Alignment explanation
Indices: 3215193--3215455 Score: 413
Period size: 102 Copynumber: 2.6 Consensus size: 103
3215183 AACCGTTATT
* * * *
3215193 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTGGGGGAA
** *
3215258 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
3215295 GGTGGATATCGCACTTAGCACCACCAATGAA-CGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT-GGGGGA
3215359 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
3215398 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
3215456 TTATGTACAA
Statistics
Matches: 148, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
101 26 0.18
102 56 0.38
103 42 0.28
104 24 0.16
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (103 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:3215817 original size:30 final size:29
Alignment explanation
Indices: 3215783--3215847 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3215773 TAATCCACCA
3215783 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
3215813 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
3215843 CCCAA
1 CCCAA
3215848 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:3215821 original size:31 final size:30
Alignment explanation
Indices: 3215790--3215847 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3215780 CCACCCAACT
3215790 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
3215820 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
3215848 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:3219941 original size:19 final size:20
Alignment explanation
Indices: 3219901--3219944 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3219891 GTTTCTTTTG
* *
3219901 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
3219920 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
3219939 GCATTA
1 GCATTA
3219945 GACTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:3224187 original size:85 final size:86
Alignment explanation
Indices: 3223990--3224338 Score: 520
Period size: 86 Copynumber: 4.1 Consensus size: 86
3223980 AGTAAAAATT
* * * * * * *
3223990 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTAAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
*
3224055 GTATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
3224076 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
3224141 GCATTGACAGC-AAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
3224161 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
*
3224226 GCACTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* * * *
3224247 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTTCTTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
* * *
3224312 GTATTTGGCAGTGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
3224334 GAAGA
1 GAAGA
3224339 TGGCAATTTT
Statistics
Matches: 242, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
85 84 0.35
86 138 0.57
87 20 0.08
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (86 bp):
GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:3224206 original size:41 final size:41
Alignment explanation
Indices: 3224076--3224206 Score: 106
Period size: 41 Copynumber: 3.1 Consensus size: 41
3224066 GAAGCAGATC
3224076 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTT
* * * * * * * * *
3224117 GAAGATAGCAGATCTTGCC-TTC-CTGCATTGACAGCA-AGCAGATC
1 GAAG--A-CAAACCTTGCCACTCTC-G-TTTG-TAGTAGAGCTGGTT
3224161 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTT
3224202 GAAGA
1 GAAGA
3224207 TAGCAGATCT
Statistics
Matches: 63, Mismatches: 18, Indels: 18
0.64 0.18 0.18
Matches are distributed among these distances:
40 3 0.05
41 26 0.41
42 5 0.08
43 5 0.08
44 21 0.33
45 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.26
Consensus pattern (41 bp):
GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTT
Found at i:3224284 original size:171 final size:173
Alignment explanation
Indices: 3223990--3224338 Score: 522
Period size: 171 Copynumber: 2.0 Consensus size: 173
3223980 AGTAAAAATT
* * * *
3223990 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTAAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGGTCGTAGCAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * *
3224055 GTATTGACAGCGAAGCAGATCGAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAA
66 GCACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAA
3224120 GATAGCAGATCTTGCCTTCCTGCA-TTGACAG-CAAGCAGATC
131 GATAGCAGATCTTGCCTTCCTGCATTTGACAGTCAAGCAGATC
* * * *
3224161 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGGTCGTAGCAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
3224226 GCACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAA
66 GCACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAA
* * * * * *
3224291 GATATCAGATCTTTCTTTCCTGTATTTGGCAGTGAAGCAGATC
131 GATAGCAGATCTTGCCTTCCTGCATTTGACAGTCAAGCAGATC
3224334 GAAGA
1 GAAGA
3224339 TGGCAATTTT
Statistics
Matches: 158, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
171 138 0.87
172 6 0.04
173 14 0.09
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (173 bp):
GAAGACAAACCTTGCCACTCTCGGTCGTAGCAGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
GCACTGACAGCGAAGCAGATCGAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAA
GATAGCAGATCTTGCCTTCCTGCATTTGACAGTCAAGCAGATC
Found at i:3224454 original size:46 final size:46
Alignment explanation
Indices: 3224395--3224707 Score: 223
Period size: 46 Copynumber: 6.9 Consensus size: 46
3224385 AACTCTATCT
* *
3224395 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTC
* * * * * *
3224441 CCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATCTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTACCTC
* * * ** * * *
3224487 CCTGTGA-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTATCTC
1 CCTGT-ATCTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TACCTC
* *
3224531 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTC
* * * * * *
3224577 CCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATCTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTACCTC
* * * * * *
3224623 CCTGTGA-CT-ACAGTGGAGTAGATTGAAG-TCG-ATAACTCTATCTC
1 CCTGT-ATCTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TACCTC
*
3224667 CCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTT
1 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTT
3224708 GTCTTCTCAT
Statistics
Matches: 195, Mismatches: 56, Indels: 32
0.69 0.20 0.11
Matches are distributed among these distances:
43 8 0.04
44 26 0.13
45 60 0.31
46 91 0.47
47 10 0.05
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (46 bp):
CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTACCTC
Found at i:3224567 original size:136 final size:136
Alignment explanation
Indices: 3224286--3224713 Score: 740
Period size: 136 Copynumber: 3.2 Consensus size: 136
3224276 GCAGAGCTGG
* * *
3224286 TTGAAGATAT-CAGATCTTTCTTTCCTGTATTTGGCAGTGAAGCAGATCGAAGATGGCA-ATTTT
1 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
*
3224349 ACCTCCC--TGACAACAGTGGAGTACATTGAAGCCGATAACTCTATCT-CCTGTATCTGGCAGTG
65 ACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTG
3224411 GAATAGA
130 GAATAGA
3224418 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
3224483 CCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
66 CCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
3224548 AATAGA
131 AATAGA
3224554 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
* * *
3224619 CCTCCCTGTGACTACAGTGGAGTAGATTGAAGTCGATAACTCTATCTCCCTGTATTTGGCAGTGG
66 CCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
3224684 AATAGA
131 AATAGA
*
3224690 TTGAAGATTGCAGATCTTGTCTTC
1 TTGAAGATTGCAGATCTTGCCTTC
3224714 TCATATTGGT
Statistics
Matches: 283, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
131 1 0.00
132 53 0.19
133 12 0.04
135 38 0.13
136 179 0.63
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (136 bp):
TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCAGTGG
AATAGA
Found at i:3224696 original size:90 final size:93
Alignment explanation
Indices: 3224309--3224704 Score: 234
Period size: 90 Copynumber: 4.4 Consensus size: 93
3224299 ATCTTTCTTT
* * *
3224309 CCTGTATTTGGCAGT-GAAGCAGATCGAAGATGGCA-ATTTTACCTCCCTG-A-C-AACAGTGGA
1 CCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGA
* * *
3224369 GTACATTGAAG-CCG-ATAACTCTATCT-
65 GTAGATTGAAGATCGCATAACTCTACCTC
* * * * * * * * *
3224395 CCTGTATCTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAG
1 CCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAG
* * * * * *
3224460 CAGATCGAAGATGGCA-GATTTTACCTC
66 TAGATTGAAGATCGCATAACTCTACCTC
* * * * ** ** * * * *
3224487 CCTGTGA-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTATCTCCCTGTATCTGGCAGTGGA
1 CCTGT-ATTTGGCAGTGGAATAGATTGAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGA
* * * * * *
3224549 ATAGATTGAAGATTGCAGATCT-TGCCTT
65 GTAGATTGAAGATCGCATAACTCTACCTC
* * *
3224577 CCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGA-CT-ACAGTGG
1 CCTGTATTTGGCAGTGGAA-TAGATTGAAGATGGCAGATTTTACCTCCCTGT-ATCTGACAGTGG
*
3224639 AGTAGATTGAAG-TCG-ATAACTCTATCTC
64 AGTAGATTGAAGATCGCATAACTCTACCTC
*
3224667 CCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGAT
1 CCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGAT
3224705 CTTGTCTTCT
Statistics
Matches: 220, Mismatches: 73, Indels: 30
0.68 0.23 0.09
Matches are distributed among these distances:
86 27 0.12
87 14 0.06
88 1 0.00
89 5 0.02
90 92 0.42
91 57 0.26
92 22 0.10
93 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (93 bp):
CCTGTATTTGGCAGTGGAATAGATTGAAGATGGCAGATTTTACCTCCCTGTATCTGACAGTGGAG
TAGATTGAAGATCGCATAACTCTACCTC
Found at i:3224791 original size:44 final size:43
Alignment explanation
Indices: 3224682--3225183 Score: 386
Period size: 44 Copynumber: 11.4 Consensus size: 43
3224672 ATTTGGCAGT
* * *
3224682 GGAA-TAGATTGAAGATTGCAGATCTTGTCTT-CTCATATTGGTG
1 GGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCT-ATATTGG-C
* * * * *
3224725 GCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTATTGGC
1 G-GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGC
* * * *
3224769 GTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTA
1 G-GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-C
* * *
3224814 GGAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCAT-TTGGTG
1 GGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-C
* * * *
3224856 GCGAAGTAGATCGTAGAAAGCAGATCTTGTCTTCATGTATTGGC
1 G-GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGC
* ** *
3224900 GTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATTGGTA
1 G-GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-C
* * * *
3224945 GGAAGTGGATCGACGAT-GCAGATCTTGTCTTCCCATATTGGTG
1 GGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-C
* * * *
3224988 GCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
1 G-GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGC
* * * * **
3225032 GTGAAGTAGATCGAATATAGCAGGTCCTATCTTCCTATATTGATA
1 G-GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTG-GC
* * * * *
3225077 GGAAGTGGATCCAAGATA-CAGATCTTGTCTTCCCATACTGGT
1 GGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGC
* * *
3225119 GTTGAAGTAGATCGAAGATTGCAGATCTTGCCTTCCTGTATTTGGC
1 G--GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATA-TTGGC
*
3225165 AGAGAAGCAGATCGAAGAT
1 -G-GAAGTAGATCGAAGAT
3225184 TACAGTCTTA
Statistics
Matches: 359, Mismatches: 84, Indels: 29
0.76 0.18 0.06
Matches are distributed among these distances:
42 7 0.02
43 69 0.19
44 191 0.53
45 72 0.20
46 19 0.05
47 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
GGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGC
Found at i:3225046 original size:132 final size:132
Alignment explanation
Indices: 3224692--3225183 Score: 752
Period size: 132 Copynumber: 3.7 Consensus size: 132
3224682 GGAATAGATT
* *
3224692 GAAGATTGCAGATCTTGTCTTCTCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTATCT
1 GAAGA-TGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCT
* *
3224757 TCATGTATTGGCGTGAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGG
65 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGG
3224822 ATC
130 ATC
*
3224825 GAAGATGCAGATCTTGTCTTCCCAT-TTGGTGGCGAAGTAGATCGTAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTT
**
3224889 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCGGTCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGA
3224954 TC
131 TC
*
3224956 GACGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTT
* *
3225021 CATGTATTGGCGTGAAGTAGATCGAATATAGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGA
3225086 TC
131 TC
* * * ** * ** *
3225088 CAAGATACAGATCTTGTCTTCCCATACTGGTGTTGAAGTAGATCGAAGATTGCAGATCTTGCCTT
1 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTT
* * *
3225153 CCTGTATTTGGCAGAGAAGCAGATCGAAGAT
66 CATGTA-TTGGC-GTGAAGTAGATCGAAGAT
3225184 TACAGTCTTA
Statistics
Matches: 329, Mismatches: 27, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
131 124 0.38
132 180 0.55
133 10 0.03
134 15 0.05
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTT
CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGA
TC
Found at i:3231038 original size:61 final size:61
Alignment explanation
Indices: 3230970--3231280 Score: 232
Period size: 61 Copynumber: 5.2 Consensus size: 61
3230960 CTTTTATAGT
3230970 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
* * ** * * * ** * ** *
3231031 ATCATATATTTTAATTAAAATATATTTAATAATAACTATGTTAA--ATT-A-TCTTTTA-TAGT
1 ATCATATATTATGATTTGAGTA-AATTCATAA-AAGAATATTAATTATTAAGAATTTTATTA-A
*
3231090 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * ** * *
3231151 ATTATATATGT-TAATTAT-AATATATTTAATAATAATTATGTTAA-T-TT-A-TATTTTA-TAG
1 ATCATATAT-TATGATT-TGAGTA-AATTCATAA-AAGAATATTAATTATTAAGAATTTTATTA-
*
3231209 T
61 A
*
3231210 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
*
3231271 ATTATATATT
1 ATCATATATT
3231281 TTAATTATAA
Statistics
Matches: 180, Mismatches: 50, Indels: 40
0.67 0.19 0.15
Matches are distributed among these distances:
57 16 0.09
58 19 0.11
59 48 0.27
60 4 0.02
61 57 0.32
62 20 0.11
63 16 0.09
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (61 bp):
ATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:3231094 original size:59 final size:58
Alignment explanation
Indices: 3231031--3231219 Score: 150
Period size: 59 Copynumber: 3.2 Consensus size: 58
3231021 ATTTTATTAA
*
3231031 ATCATATATTTTAATTAAAATATATTTAATAATAACTATGTTAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAA-TATGTTAAATTATATTTTATAGT
* * ** * * * * * *
3231090 ATCATATATTATGATTTGAGTAAATTCATATAAGAATA--TTAATTATTAAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTA-ATAATAATATGTTAA--ATT-A-TATTTTA-TAGT
* * * *
3231151 ATTATATATGTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAA-TATGTTAAATTATATTTTATAGT
3231210 ATCATATATT
1 ATCATATATT
3231220 ATGATTTGAG
Statistics
Matches: 94, Mismatches: 26, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
57 4 0.04
58 2 0.02
59 40 0.43
60 14 0.15
61 28 0.30
62 2 0.02
63 4 0.04
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATAATAATATGTTAAATTATATTTTATAGT
Found at i:3231156 original size:69 final size:69
Alignment explanation
Indices: 3231083--3231276 Score: 181
Period size: 69 Copynumber: 3.1 Consensus size: 69
3231073 AAATTATCTT
3231083 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
3231148 TAAA
66 TAAA
** * * * * ** *
3231152 TTATA-TATGTTA-ATTAT-A----A-TATATTTA-ATAA-TA-ATT-A-TGTTAA-TT-TATAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
3231202 T---
66 TAAA
3231203 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
3231268 TAAA
66 TAAA
3231272 TTATA
1 TTATA
3231277 TATTTTAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 36
0.62 0.13 0.25
Matches are distributed among these distances:
51 5 0.06
52 5 0.06
53 5 0.06
54 6 0.07
56 5 0.06
57 1 0.01
58 4 0.04
59 7 0.08
60 8 0.09
61 7 0.08
62 4 0.04
63 1 0.01
64 5 0.06
66 6 0.07
67 5 0.06
68 5 0.06
69 10 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (69 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
TAAA
Found at i:3231173 original size:120 final size:120
Alignment explanation
Indices: 3230959--3231317 Score: 637
Period size: 120 Copynumber: 3.0 Consensus size: 120
3230949 TGATCAGTTT
*
3230959 TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATAAAAGAATATTAATTATTAAGAATT
1 TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
* * *
3231024 TTATTAAATCATATATTTTAATTAAAATATATTTAATAATAACTATGTTAAATTA
66 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTA
3231079 TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
1 TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
* *
3231144 TTATTAAATTATATATGTTAATTATAATATATTTAATAATAATTATGTTAATTTA
66 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTA
*
3231199 TATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
1 TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
*
3231264 TTATTAAATTATATATTTTAATTATAATATATTTAATAGTAATTATGTTTAAAT
66 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
3231318 ATGATTAAAT
Statistics
Matches: 228, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
120 223 0.98
121 5 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (120 bp):
TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTA
Found at i:3231185 original size:15 final size:16
Alignment explanation
Indices: 3231154--3231195 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
3231144 TTATTAAATT
*
3231154 ATATATGTTAATTATA
1 ATATATGTTAATAATA
3231170 ATATAT-TTAATAATA
1 ATATATGTTAATAATA
3231185 AT-TATGTTAAT
1 ATATATGTTAAT
3231196 TTATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 3 0.12
15 15 0.62
16 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
ATATATGTTAATAATA
Found at i:3231552 original size:16 final size:16
Alignment explanation
Indices: 3231531--3231598 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
3231521 GATTTGCTAT
3231531 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3231547 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3231563 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
3231579 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3231595 TACA
1 TACA
3231599 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3235732 original size:24 final size:24
Alignment explanation
Indices: 3235704--3235754 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3235694 CTCCCTTCAA
*
3235704 TCGTAGACGTAGCCCTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
* *
3235728 TCGTAGGCGGAGCCGTTCTCCAAT
1 TCGTAGACGGAGCCCTTCTCCAAT
3235752 TCG
1 TCG
3235755 CAGGCCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (24 bp):
TCGTAGACGGAGCCCTTCTCCAAT
Found at i:3235759 original size:24 final size:24
Alignment explanation
Indices: 3235714--3235759 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3235704 TCGTAGACGT
*
3235714 AGCCCTTCTCCAATTCGTAGGCGG
1 AGCCCTTCTCCAATTCGCAGGCGG
*
3235738 AGCCGTTCTCCAATTCGCAGGC
1 AGCCCTTCTCCAATTCGCAGGC
3235760 CTCTTCGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.35, G:0.24, T:0.24
Consensus pattern (24 bp):
AGCCCTTCTCCAATTCGCAGGCGG
Found at i:3238083 original size:18 final size:18
Alignment explanation
Indices: 3238060--3238100 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3238050 ATATTACAAA
*
3238060 ATTTTGATGAT-AAACATG
1 ATTTTGATCATGAAA-ATG
3238078 ATTTTGATCATGAAAATG
1 ATTTTGATCATGAAAATG
3238096 ATTTT
1 ATTTT
3238101 CCAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
ATTTTGATCATGAAAATG
Found at i:3250523 original size:20 final size:20
Alignment explanation
Indices: 3250500--3250540 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3250490 AGGGTTCAAG
*
3250500 GTTTGGGCTTC-AGAGTTTGA
1 GTTTGGGATTCGAG-GTTTGA
3250520 GTTTGGGATTCGAGGTTTGA
1 GTTTGGGATTCGAGGTTTGA
3250540 G
1 G
3250541 GTTTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.15, C:0.07, G:0.39, T:0.39
Consensus pattern (20 bp):
GTTTGGGATTCGAGGTTTGA
Found at i:3250537 original size:34 final size:33
Alignment explanation
Indices: 3250475--3250538 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
3250465 TGGTACAAGA
*
3250475 TTCAGATTTGGGTTTAGGGTTCAAGGTTTGGGC
1 TTCAGATTTGAGTTTAGGGTTCAAGGTTTGGGC
*
3250508 TTCAGAGTTTGAGTTT-GGGATTCGAGGTTTG
1 TTCAGA-TTTGAGTTTAGGG-TTCAAGGTTTG
3250539 AGGTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.41
Consensus pattern (33 bp):
TTCAGATTTGAGTTTAGGGTTCAAGGTTTGGGC
Found at i:3255296 original size:7 final size:7
Alignment explanation
Indices: 3255284--3255309 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3255274 TAATTTTTAA
3255284 AAAATAT
1 AAAATAT
3255291 AAAATAT
1 AAAATAT
3255298 AAAATAT
1 AAAATAT
3255305 AAAAT
1 AAAAT
3255310 TTTATAAATA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATAT
Found at i:3256039 original size:18 final size:18
Alignment explanation
Indices: 3256008--3256042 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3255998 TTAGTAATTA
3256008 TTTTAAGATAAAAATATC
1 TTTTAAGATAAAAATATC
* *
3256026 TTTTATGATTAAAATAT
1 TTTTAAGATAAAAATAT
3256043 GTTAAGGTTT
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:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTTAAGATAAAAATATC
Found at i:3259493 original size:44 final size:45
Alignment explanation
Indices: 3259415--3259499 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 45
3259405 TTATAAAATA
* *
3259415 AAATTAGTAAATGTAAAATTTTCATTTAAGCCCTT-TAAAATTTT
1 AAATTAGTAAATATAAAATTTACATTTAAGCCCTTCTAAAATTTT
*
3259459 AAATTAGTAAATATAAAATTATAC-TTT-GGTCCCTTCTAAAA
1 AAATTAGTAAATATAAAATT-TACATTTAAG-CCCTTCTAAAA
3259500 ATAATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 1 0.03
44 27 0.77
45 7 0.20
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (45 bp):
AAATTAGTAAATATAAAATTTACATTTAAGCCCTTCTAAAATTTT
Found at i:3260654 original size:3 final size:3
Alignment explanation
Indices: 3260646--3260693 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3260636 TTTCTCTCTC
3260646 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3260694 TTTCTCTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3265767 original size:12 final size:13
Alignment explanation
Indices: 3265739--3265769 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3265729 AGTAAGTTAA
3265739 TTTTTTAAAAATG
1 TTTTTTAAAAATG
3265752 TTTTTTAAAAAT-
1 TTTTTTAAAAATG
3265764 TTTTTT
1 TTTTTT
3265770 GAACAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
TTTTTTAAAAATG
Found at i:3283907 original size:153 final size:152
Alignment explanation
Indices: 3283620--3283907 Score: 319
Period size: 153 Copynumber: 1.9 Consensus size: 152
3283610 CTAACAGACA
* *** *
3283620 AACTAACAGAGGTACCAACTTAGGAAAAAAAAGTAGTTTGGGTATTACTTGTGACAAAAAAAAAT
1 AACTAACAGAGGTACCAACTTAGGAAAAAAAAGTAGCTTAAATATTACTTGTGACAAAAAAAAAC
* * * * * * ** * *
3283685 ATTTAGGTATCAAAATGGGAAAAATGCATAGTTTAGGTACCGATTTGTGGGTTAAGCCCTTTTTT
66 ATTTAGATATCAAAATGGAAAAAATACATAATTTAAGTACCAATTTGTGAATTAAACCC--TTTA
3283750 TTTTATAAATAAACTTAACAGTTT
129 TTTTATAAATAAACTTAACAGTTT
* * *
3283774 AACTAACCGATGTACCAACTT-GGGAAAAAAAGTAGCTTAAATATTACTTGTGACAAAAAAAAAC
1 AACTAACAGAGGTACCAACTTAGGAAAAAAAAGTAGCTTAAATATTACTTGTGACAAAAAAAAAC
* * * *
3283838 GTTTAGATATCAAGATGATAAAAAATACATATAATTTAAGTACCAATTTGTGAATTAAATCC-TT
66 ATTTAGATATCAAAATG-GAAAAAATAC--ATAATTTAAGTACCAATTTGTGAATTAAACCCTTT
3283902 ATTTTA
128 ATTTTA
3283908 CAAGTAGAGT
Statistics
Matches: 109, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
153 58 0.53
154 26 0.24
156 25 0.23
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (152 bp):
AACTAACAGAGGTACCAACTTAGGAAAAAAAAGTAGCTTAAATATTACTTGTGACAAAAAAAAAC
ATTTAGATATCAAAATGGAAAAAATACATAATTTAAGTACCAATTTGTGAATTAAACCCTTTATT
TTATAAATAAACTTAACAGTTT
Found at i:3291066 original size:17 final size:17
Alignment explanation
Indices: 3291039--3291091 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
3291029 CAAATTCATA
*
3291039 TATAAACTTTGATTTAG
1 TATAAATTTTGATTTAG
3291056 TATATAA-TTTGA--TA-
1 TATA-AATTTTGATTTAG
3291070 TATAAATTTTGATTTAG
1 TATAAATTTTGATTTAG
3291087 TATAA
1 TATAA
3291092 TATACATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 9 0.29
15 2 0.06
16 2 0.06
17 14 0.45
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (17 bp):
TATAAATTTTGATTTAG
Found at i:3291090 original size:19 final size:18
Alignment explanation
Indices: 3291037--3291090 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 18
3291027 TTCAAATTCA
3291037 TATATAAACTTTGATTTAG
1 TATATAAA-TTTGATTTAG
3291056 TATAT-AATTTGA--TA-
1 TATATAAATTTGATTTAG
*
3291070 TATA-AATTTTGATTTAG
1 TATATAAATTTGATTTAG
3291087 TATA
1 TATA
3291091 ATATACATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
16 2 0.07
17 9 0.30
18 2 0.07
19 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (18 bp):
TATATAAATTTGATTTAG
Found at i:3291396 original size:12 final size:12
Alignment explanation
Indices: 3291379--3291403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3291369 CATAAGACGT
3291379 TATAATATAATA
1 TATAATATAATA
3291391 TATAATATAATA
1 TATAATATAATA
3291403 T
1 T
3291404 CAGATATTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAATATAATA
Found at i:3292340 original size:19 final size:19
Alignment explanation
Indices: 3292300--3292340 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3292290 TTAGTATATG
**
3292300 TATATATATGTTTGTGGTT
1 TATATATATGTTTGTGAAT
3292319 TATATATATGTTTGTGAAT
1 TATATATATGTTTGTGAAT
3292338 TAT
1 TAT
3292341 GAGAGGAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (19 bp):
TATATATATGTTTGTGAAT
Found at i:3294056 original size:18 final size:19
Alignment explanation
Indices: 3294013--3294060 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
3294003 CAATTTTATA
3294013 TAATAATTTTTTTGCAATATT
1 TAATAA-TTTTTT-CAATATT
*
3294034 T-ATAATTTTTT-AATTTT
1 TAATAATTTTTTCAATATT
3294051 TAATAATTTT
1 TAATAATTTT
3294061 ATTCTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.24
18 8 0.32
19 6 0.24
20 4 0.16
21 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TAATAATTTTTTCAATATT
Found at i:3294094 original size:19 final size:18
Alignment explanation
Indices: 3294035--3294096 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
3294025 TGCAATATTT
* *
3294035 ATAATTTTTTAATTTTTA
1 ATAATTTTATATTTTTTA
3294053 ATAATTTTAT-TCTTTTT-
1 ATAATTTTATAT-TTTTTA
**
3294070 GCAATTTTATATTATTTTA
1 ATAATTTTATATT-TTTTA
3294089 ATAATTTT
1 ATAATTTT
3294097 TTCCCATTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 9 0.26
18 19 0.56
19 6 0.18
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (18 bp):
ATAATTTTATATTTTTTA
Found at i:3294208 original size:38 final size:36
Alignment explanation
Indices: 3294140--3294215 Score: 98
Period size: 38 Copynumber: 2.1 Consensus size: 36
3294130 TGAAAATTCT
*
3294140 AATAATTTTCATTATTTTAAAAATTCTAATTTTTAA
1 AATAATTTTCATTATTTTAAAAATTATAATTTTTAA
***
3294176 AATAATTTTCTATTATTTTTAATTTTTATAATTTTTAA
1 AATAATTTTC-ATTA-TTTTAAAAATTATAATTTTTAA
3294214 AA
1 AA
3294216 ACTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 10 0.29
37 4 0.12
38 20 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (36 bp):
AATAATTTTCATTATTTTAAAAATTATAATTTTTAA
Found at i:3294211 original size:16 final size:17
Alignment explanation
Indices: 3294178--3294213 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3294168 ATTTTTAAAA
*
3294178 TAATTTTCTATTATTTT
1 TAATTTTCTATAATTTT
3294195 TAATTTT-TATAATTTT
1 TAATTTTCTATAATTTT
3294211 TAA
1 TAA
3294214 AAACTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTCTATAATTTT
Found at i:3295091 original size:18 final size:19
Alignment explanation
Indices: 3295070--3295112 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3295060 AAATTCTAAA
*
3295070 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
3295088 AATTTTAAAAATTATTTTG
1 AATTTTAAAAATTATTTTG
3295107 AATTTT
1 AATTTT
3295113 TTTTTGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:3301282 original size:20 final size:22
Alignment explanation
Indices: 3301243--3301282 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3301233 ACACTTCTCG
*
3301243 AGGTATCACGATATCCACCTCT
1 AGGTATCACGACATCCACCTCT
3301265 AGGTATC-CGACA-CCACCT
1 AGGTATCACGACATCCACCT
3301283 TCGTCAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (22 bp):
AGGTATCACGACATCCACCTCT
Found at i:3309445 original size:31 final size:31
Alignment explanation
Indices: 3309401--3309466 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3309391 TTAATATAAT
* * *
3309401 ATTTGGTAATTGAATTTGACAATTTTTTTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
* *
3309432 ATTTGATATTTGAACTTGACTATTTTTCTTA
1 ATTTGATAATTGAACTTGACAATTTTTCTTA
3309463 ATTT
1 ATTT
3309467 AGTACTTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (31 bp):
ATTTGATAATTGAACTTGACAATTTTTCTTA
Found at i:3310638 original size:18 final size:18
Alignment explanation
Indices: 3310615--3310657 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3310605 GAATAGGTTT
3310615 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
3310633 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
3310651 TTAATTA
1 TTAATTA
3310658 CACTTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:3326088 original size:19 final size:19
Alignment explanation
Indices: 3326064--3326101 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3326054 GCTTCCTTGC
3326064 CATAGAAAATAAGCCTATT
1 CATAGAAAATAAGCCTATT
3326083 CATAGAAAATAAGCCTATT
1 CATAGAAAATAAGCCTATT
3326102 TCAGCTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CATAGAAAATAAGCCTATT
Found at i:3327217 original size:14 final size:14
Alignment explanation
Indices: 3327198--3327225 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3327188 ACAACCCCAG
3327198 AACAATAGAAGAGT
1 AACAATAGAAGAGT
3327212 AACAATAGAAGAGT
1 AACAATAGAAGAGT
3327226 TAAGTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AACAATAGAAGAGT
Found at i:3334303 original size:20 final size:21
Alignment explanation
Indices: 3334262--3334308 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
3334252 GGCCCGGTCC
3334262 ATTTTTTAATAAAATACTAAAA
1 ATTTTTTAATAAAATAC-AAAA
3334284 ATTTATTTAA-AAAATA-AAAA
1 ATTT-TTTAATAAAATACAAAA
3334304 ATTTT
1 ATTTT
3334309 AAAAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
22 10 0.42
23 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTTTAATAAAATACAAAA
Found at i:3335177 original size:58 final size:57
Alignment explanation
Indices: 3335110--3335225 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 57
3335100 TTTACCATAT
* *
3335110 AAACACTTT-GGTATTGTACTCATAATAATATTTTATAATAATTTCTTTTAAGAATAAA
1 AAACACTTTGGGTATTGTACTCATAAAAATA-TTTATAATAATCT-TTTTAAGAATAAA
* *
3335168 AAACTCTTTGGGTATTTTACTCATAAAAATATTTATAATAATCTTTTTAAGAATAAA
1 AAACACTTTGGGTATTGTACTCATAAAAATATTTATAATAATCTTTTTAAGAATAAA
3335225 A
1 A
3335226 TTAGCATGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 14 0.26
58 20 0.38
59 19 0.36
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (57 bp):
AAACACTTTGGGTATTGTACTCATAAAAATATTTATAATAATCTTTTTAAGAATAAA
Found at i:3335247 original size:56 final size:59
Alignment explanation
Indices: 3335121--3335249 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 59
3335111 AACACTTTGG
* * * * * *
3335121 TATTGTACTCATAATAATATTTTATAATAATTTCTTTTAAGAATAAAAAACTCTTTGGG
1 TATTTTACTCATAAAAATATTTTATAATAATCTCTTTTAAGAATAAAAAACGCTATGGA
*
3335180 TATTTTACTCATAAAAATA-TTTATAATAATCT-TTTTAAGAATAAAATTA-GC-ATGGA
1 TATTTTACTCATAAAAATATTTTATAATAATCTCTTTTAAGAATAAAA-AACGCTATGGA
*
3335236 TGTTTTACTCATAA
1 TATTTTACTCATAA
3335250 GATTTTTACT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 16 0.26
57 15 0.25
58 13 0.21
59 17 0.28
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (59 bp):
TATTTTACTCATAAAAATATTTTATAATAATCTCTTTTAAGAATAAAAAACGCTATGGA
Found at i:3338545 original size:6 final size:6
Alignment explanation
Indices: 3338534--3338558 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3338524 ACCATACGCA
3338534 TGCATC TGCATC TGCATC TGCATC T
1 TGCATC TGCATC TGCATC TGCATC T
3338559 TCAACTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (6 bp):
TGCATC
Found at i:3343233 original size:21 final size:22
Alignment explanation
Indices: 3343204--3343250 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3343194 CAGAAGGAGT
*
3343204 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3343226 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3343247 GAGT
1 GAGT
3343251 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Done.