Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 24 of 24
Found at i:3297701 original size:21 final size:22
Alignment explanation
Indices: 3297677--3297718 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
3297667 ATAAAAATTT
3297677 TATTTTTAATAA-ATATTTATA
1 TATTTTTAATAATATATTTATA
*
3297698 TATTTTTTATAATTATATTTA
1 TATTTTTAATAA-TATATTTA
3297719 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTAATAATATATTTATA
Found at i:3302888 original size:30 final size:30
Alignment explanation
Indices: 3302852--3302921 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
3302842 GATCGGGTGA
3302852 GGATTTGGGACGAGAGCGATGGGAGACGGT
1 GGATTTGGGACGAGAGCGATGGGAGACGGT
3302882 GGATTTGGGACGAGAGCGATGGGAGACGGT
1 GGATTTGGGACGAGAGCGATGGGAGACGGT
3302912 GGATTTGGGA
1 GGATTTGGGA
3302922 GGTGAGTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.23, C:0.09, G:0.50, T:0.19
Consensus pattern (30 bp):
GGATTTGGGACGAGAGCGATGGGAGACGGT
Found at i:3308677 original size:2 final size:2
Alignment explanation
Indices: 3308670--3308708 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3308660 TATTCTCACT
3308670 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3308709 TTGTGATCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3313128 original size:15 final size:16
Alignment explanation
Indices: 3313108--3313158 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
3313098 AATTTATATC
3313108 ATATAAATATTTTAT-
1 ATATAAATATTTTATA
*
3313123 ATATAAA-ATATTATA
1 ATATAAATATTTTATA
* *
3313138 ATATAAATATTATAAA
1 ATATAAATATTTTATA
3313154 ATATA
1 ATATA
3313159 TTGAATCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 6 0.20
15 14 0.47
16 10 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAAATATTTTATA
Found at i:3313145 original size:14 final size:14
Alignment explanation
Indices: 3313108--3313152 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
3313098 AATTTATATC
*
3313108 ATATAAATATTTTA
1 ATATAAATATTATA
3313122 TATATAAAATATTATA
1 -ATAT-AAATATTATA
3313138 ATATAAATATTATA
1 ATATAAATATTATA
3313152 A
1 A
3313153 AATATATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 11 0.39
15 8 0.29
16 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAAATATTATA
Found at i:3322663 original size:3 final size:3
Alignment explanation
Indices: 3322651--3322684 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
3322641 TATTTTACTT
3322651 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
3322685 GATTTAGCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3323116 original size:16 final size:18
Alignment explanation
Indices: 3323076--3323117 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3323066 TTTTATGCAT
*
3323076 ATATGTATATATTAATATA
1 ATAT-TATATATTAATACA
3323095 ATATTATAT-TTAATACA
1 ATATTATATATTAATACA
3323112 A-ATTAT
1 ATATTAT
3323118 TTGTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
18 5 0.23
19 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATTATATATTAATACA
Found at i:3324019 original size:18 final size:17
Alignment explanation
Indices: 3323971--3324037 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
3323961 TTAATTGTTA
3323971 ATTAAA-ATA-ATTTTAT
1 ATTAAATATATATTTT-T
*
3323987 ATTTAATATATTATTTTT
1 ATTAAATATA-TATTTTT
3324005 ATTAAATTATATATTTTT
1 ATTAAA-TATATATTTTT
*
3324023 ATAAAATAT-TATTTT
1 ATTAAATATATATTTT
3324038 AATCAAAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
16 11 0.25
17 6 0.14
18 18 0.41
19 9 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTAAATATATATTTTT
Found at i:3324046 original size:17 final size:16
Alignment explanation
Indices: 3323994--3324037 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
3323984 TATATTTAAT
3323994 ATATTATTTTTATTAAA
1 ATATTATTTTTA-TAAA
*
3324011 TTATATATTTTTATAAA
1 ATAT-TATTTTTATAAA
3324028 ATATTATTTT
1 ATATTATTTT
3324038 AATCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 10 0.42
18 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATTTTTATAAA
Found at i:3324639 original size:18 final size:18
Alignment explanation
Indices: 3324597--3324639 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3324587 TATTTTATAA
*
3324597 ATTTAAATATTAAATTTAT
1 ATTT-AATAATAAATTTAT
3324616 -TATTAATAATAAATTTAT
1 AT-TTAATAATAAATTTAT
3324634 ATTTAA
1 ATTTAA
3324640 ATATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAATAATAAATTTAT
Found at i:3324658 original size:14 final size:15
Alignment explanation
Indices: 3324628--3324677 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
3324618 TTAATAATAA
3324628 ATTTA-TATTTAAAT
1 ATTTATTATTTAAAT
*
3324642 ATTTATTATTT-ATT
1 ATTTATTATTTAAAT
* *
3324656 ATTTGTTATCTAAAT
1 ATTTATTATTTAAAT
*
3324671 ATATATT
1 ATTTATT
3324678 TTATTTAGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTTATTATTTAAAT
Found at i:3324820 original size:14 final size:13
Alignment explanation
Indices: 3324798--3324837 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
3324788 TAGATTTTTT
3324798 TTTAAAAATTTAA
1 TTTAAAAATTTAA
*
3324811 TTTAATAAATTCAA
1 TTTAA-AAATTTAA
3324825 TTTAACAAATTTA
1 TTTAA-AAATTTA
3324838 GATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (13 bp):
TTTAAAAATTTAA
Found at i:3333565 original size:2 final size:2
Alignment explanation
Indices: 3333558--3333604 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3333548 GCTGATTACA
3333558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3333600 AT AT A
1 AT AT A
3333605 CACAGAACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3334734 original size:13 final size:13
Alignment explanation
Indices: 3334716--3334742 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3334706 GGGTAATATA
3334716 TATTTAAATTTAT
1 TATTTAAATTTAT
3334729 TATTTAAATTTAT
1 TATTTAAATTTAT
3334742 T
1 T
3334743 TTATTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTAAATTTAT
Found at i:3334761 original size:15 final size:15
Alignment explanation
Indices: 3334711--3334762 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3334701 AATTCGGGTA
3334711 ATATATATTTAAATT-
1 ATAT-TATTTAAATTG
*
3334726 -TATTATTTAAATTT
1 ATATTATTTAAATTG
* *
3334740 ATTTTATTTATATTG
1 ATATTATTTAAATTG
3334755 ATATTATT
1 ATATTATT
3334763 GGATATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 10 0.32
14 3 0.10
15 18 0.58
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
ATATTATTTAAATTG
Found at i:3335277 original size:12 final size:12
Alignment explanation
Indices: 3335262--3335312 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
3335252 TTATTTAAAA
*
3335262 ATTTATTTTATT
1 ATTTATTATATT
3335274 ATTTATTATATT
1 ATTTATTATATT
**
3335286 A-TTAAAATATT
1 ATTTATTATATT
*
3335297 ATTT-TTATAAT
1 ATTTATTATATT
3335308 ATTTA
1 ATTTA
3335313 AATATTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:3335310 original size:22 final size:23
Alignment explanation
Indices: 3335270--3335323 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3335260 AAATTTATTT
*
3335270 TATTATTTATTATATTATTAAAA
1 TATTATTTATTATAATATTAAAA
*
3335293 TATTATTT-TTATAATATTTAAA
1 TATTATTTATTATAATATTAAAA
3335315 TATT-TTTAT
1 TATTATTTAT
3335324 AATTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 17 0.61
23 8 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTTATTATAATATTAAAA
Found at i:3335401 original size:16 final size:16
Alignment explanation
Indices: 3335382--3335412 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3335372 ATTAAATTTA
3335382 ATAAATTTTAATCAAC
1 ATAAATTTTAATCAAC
*
3335398 ATAAATTTTATTCAA
1 ATAAATTTTAATCAA
3335413 AACTTGACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAATTTTAATCAAC
Found at i:3335858 original size:2 final size:2
Alignment explanation
Indices: 3335851--3335883 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3335841 TCCAGAGGAG
3335851 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3335884 TTCCATCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3337584 original size:2 final size:2
Alignment explanation
Indices: 3337577--3337604 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3337567 AATAAAACTC
3337577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3337605 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3338636 original size:3 final size:3
Alignment explanation
Indices: 3338628--3338667 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3338618 ACTTTCTAGG
3338628 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3338668 CTTTTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3339311 original size:29 final size:29
Alignment explanation
Indices: 3339269--3339329 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
3339259 TTTTTGGTCA
* *
3339269 AATTACATCTATATACCTAAGTCTTAACT
1 AATTACATATATATACCTAAATCTTAACT
*
3339298 AATTACATATATATACCTAAATTTTAACT
1 AATTACATATATATACCTAAATCTTAACT
3339327 AAT
1 AAT
3339330 GGCAGTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (29 bp):
AATTACATATATATACCTAAATCTTAACT
Found at i:3339620 original size:2 final size:2
Alignment explanation
Indices: 3339615--3339654 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3339605 ACCAAGACAT
3339615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3339655 GAAGAGATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3339754 original size:23 final size:23
Alignment explanation
Indices: 3339711--3339754 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3339701 TATAAATATT
*
3339711 TTTAAAAATTGATATTTAATAAA
1 TTTAAAAATTGATATTCAATAAA
*
3339734 TTTAAAATTTGA-ATATCAATA
1 TTTAAAAATTGATAT-TCAATA
3339755 TCTATAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTAAAAATTGATATTCAATAAA
Found at i:3340969 original size:2 final size:2
Alignment explanation
Indices: 3340962--3341029 Score: 56
Period size: 2 Copynumber: 36.0 Consensus size: 2
3340952 TCCTCTGATT
* *
3340962 TA TA TA TA TA TA TA TA TA T- TC TA TA TA TA T- TGA TG TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* *
3341002 -A GA T- TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3341030 ATTACTCAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
1 5 0.09
2 49 0.89
3 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3342453 original size:26 final size:26
Alignment explanation
Indices: 3342422--3342477 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
3342412 AATCGGAGAT
* *
3342422 TAATGTTGGTTTGTTGTGATCATTAG
1 TAATGTTGGTGTGTTATGATCATTAG
3342448 TAATGTTGGTGTGTTATGATCATTAG
1 TAATGTTGGTGTGTTATGATCATTAG
3342474 TAAT
1 TAAT
3342478 ACCCCCCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.48
Consensus pattern (26 bp):
TAATGTTGGTGTGTTATGATCATTAG
Found at i:3343385 original size:2 final size:2
Alignment explanation
Indices: 3343378--3343407 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3343368 TATTAACATT
3343378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3343408 AAATAGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3344231 original size:20 final size:20
Alignment explanation
Indices: 3344197--3344237 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3344187 TTATTAAAAT
**
3344197 TTTTTATTTTTAATTTCATA
1 TTTTTATTTAAAATTTCATA
*
3344217 TTTTTATTTAAAATTTTATA
1 TTTTTATTTAAAATTTCATA
3344237 T
1 T
3344238 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATTTAAAATTTCATA
Found at i:3344740 original size:13 final size:14
Alignment explanation
Indices: 3344705--3344742 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3344695 TTAAATTTAA
3344705 TAAAAATAATATAT
1 TAAAAATAATATAT
* *
3344719 TAAATATAAT-TTT
1 TAAAAATAATATAT
3344732 TAAAAATAATA
1 TAAAAATAATA
3344743 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAAATAATATAT
Found at i:3344754 original size:26 final size:27
Alignment explanation
Indices: 3344705--3344761 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3344695 TTAAATTTAA
*
3344705 TAAAAATAATATATTAAATATAATTTT
1 TAAAAATAATATATTAAATATAATATT
*
3344732 TAAAAATAATA-ATTTTAAT-TAATATT
1 TAAAAATAATATA-TTAAATATAATATT
3344758 TAAA
1 TAAA
3344762 TATATGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAAAATAATATATTAAATATAATATT
Found at i:3354382 original size:26 final size:27
Alignment explanation
Indices: 3354347--3354397 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
3354337 TTTTTAATAA
3354347 AATAATAATAATTTTATCATATTTTTT
1 AATAATAATAATTTTATCATATTTTTT
*
3354374 AATAA-AATAATTTTATTATATTTT
1 AATAATAATAATTTTATCATATTTT
3354398 AAATTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
AATAATAATAATTTTATCATATTTTTT
Found at i:3355092 original size:21 final size:22
Alignment explanation
Indices: 3355068--3355109 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3355058 TTTTTTATGC
3355068 TTATTTTAATTTTTAT-TTATT
1 TTATTTTAATTTTTATATTATT
*
3355089 TTATTTTTATTTTTATATTAT
1 TTATTTTAATTTTTATATTAT
3355110 AATTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTTTAATTTTTATATTATT
Found at i:3355096 original size:15 final size:16
Alignment explanation
Indices: 3355068--3355100 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3355058 TTTTTTATGC
3355068 TTATTTTAATTTTTAT
1 TTATTTTAATTTTTAT
3355084 TTATTTT-ATTTTTAT
1 TTATTTTAATTTTTAT
3355099 TT
1 TT
3355101 TTATATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTAATTTTTAT
Found at i:3355198 original size:30 final size:30
Alignment explanation
Indices: 3355097--3355225 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
3355087 TTTTATTTTT
* *
3355097 ATTTTTATATTATAATTATATT-TAAAATATTA
1 ATTTTTATA-TATTATTATATTATATAATA--A
* * * *
3355129 TATATTTATATA-AATTTTAATATATTAA-AA
1 -ATTTTTATATATTATTATATTATA-TAATAA
* *
3355159 ATTTATATATTTATATTATATTA-ATAATAA
1 ATTTTTATATAT-TATTATATTATATAATAA
*
3355189 ATTTTTATATATTATTATATTATATTATAA
1 ATTTTTATATATTATTATATTATATAATAA
3355219 ATATTTT
1 AT-TTTT
3355226 TTTTTTGTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
29 21 0.28
30 22 0.29
31 18 0.24
32 5 0.07
33 10 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTTATATATTATTATATTATATAATAA
Found at i:3355228 original size:34 final size:32
Alignment explanation
Indices: 3355091--3355215 Score: 103
Period size: 34 Copynumber: 3.8 Consensus size: 32
3355081 TATTTATTTT
*
3355091 ATTTTTAT-T-TTTATATTATAATT-ATATTTAA
1 ATTTTTATATATTTATATTAT-ATTAATA-ATAA
* * * *
3355122 AATATTATATATTTATATAAATTTTAATATATTAA
1 ATTTTTATATATTTATAT-TATATTAATA-A-TAA
**
3355157 AAATTTATATATTTATATTATATTAATAATAA
1 ATTTTTATATATTTATATTATATTAATAATAA
3355189 ATTTTTATATATTATTATATTATATTA
1 ATTTTTATATA-T-TTATATTATATTA
3355216 TAAATATTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
31 6 0.08
32 13 0.17
33 11 0.14
34 27 0.36
35 19 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTTTATATATTTATATTATATTAATAATAA
Found at i:3358068 original size:2 final size:2
Alignment explanation
Indices: 3358061--3358090 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3358051 TGCATGGTAC
3358061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3358091 GTAGGTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3360311 original size:19 final size:18
Alignment explanation
Indices: 3360278--3360317 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3360268 AATTATATTT
*
3360278 TTAAAATAATAATTTATA
1 TTAAAATAATAATTTAAA
*
3360296 TTAAATATATTAATTTAAA
1 TTAAA-ATAATAATTTAAA
3360315 TTA
1 TTA
3360318 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATAATAATTTAAA
Found at i:3360335 original size:21 final size:22
Alignment explanation
Indices: 3360294--3360337 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3360284 TAATAATTTA
*
3360294 TATTAAATATATTAATTTAAAT
1 TATTAAAAATATTAATTTAAAT
*
3360316 TATTAAAAAT-TTATTTTAAAT
1 TATTAAAAATATTAATTTAAAT
3360337 T
1 T
3360338 TTACATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTAAAAATATTAATTTAAAT
Found at i:3365522 original size:15 final size:15
Alignment explanation
Indices: 3365502--3365539 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3365492 TTAATTTATT
3365502 TTTAATTTAAATATA-
1 TTTAATTT-AATATAG
*
3365517 TTTAATTTAATTTAG
1 TTTAATTTAATATAG
3365532 TTTAATTT
1 TTTAATTT
3365540 TTAATTCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTAATTTAATATAG
Found at i:3365750 original size:35 final size:34
Alignment explanation
Indices: 3365677--3365750 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 34
3365667 TTTTATTTTA
*
3365677 ATTAATTTAAATTTTTAAAAAATAAAATATTACAC
1 ATTAATTTAAATTTTTAAAAAATAAAATA-TAAAC
* *
3365712 ATTAATTATAATTTTTTAAAAACTAAAATA-AAATC
1 ATTAATT-TAAATTTTTAAAAAATAAAATATAAA-C
3365747 ATTA
1 ATTA
3365751 TCACCTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 2 0.06
35 12 0.35
36 20 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (34 bp):
ATTAATTTAAATTTTTAAAAAATAAAATATAAAC
Found at i:3366775 original size:19 final size:19
Alignment explanation
Indices: 3366753--3366826 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
3366743 TTTATATTAT
3366753 TTAAATTTAAAAATATTTA
1 TTAAATTTAAAAATATTTA
* *
3366772 TTAAATATAAATATATTTTTA
1 TTAAATTTAAA-A-ATATTTA
3366793 GTTAAATTTAATAAA-ATTT-
1 -TTAAATTTAA-AAATATTTA
3366812 TTATATATTTAAAAA
1 TTA-A-ATTTAAAAA
3366827 ATTATATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 3 0.07
19 14 0.31
20 10 0.22
21 7 0.16
22 10 0.22
23 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
TTAAATTTAAAAATATTTA
Found at i:3367418 original size:14 final size:13
Alignment explanation
Indices: 3367400--3367424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3367390 GGTTAAAAAA
3367400 AAAAAAAGGCCAG
1 AAAAAAAGGCCAG
3367413 AAAAAAAGGCCA
1 AAAAAAAGGCCA
3367425 AAGCCATAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGCCAG
Found at i:3368503 original size:48 final size:48
Alignment explanation
Indices: 3368447--3368544 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
3368437 GATCGTGATT
*
3368447 TGTATGTTGCTGGTGATCTTTATGAGAACGATGTTGCTACTCCCGCCA
1 TGTATGTTGCTGGTGATCTTTATGAGAACGATGTTGCTACACCCGCCA
*
3368495 TGTATGTTGCTGGTGATCTTTATGAGAACGATGTTGTTACACCCGCCA
1 TGTATGTTGCTGGTGATCTTTATGAGAACGATGTTGCTACACCCGCCA
3368543 TG
1 TG
3368545 ATCGTTGTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (48 bp):
TGTATGTTGCTGGTGATCTTTATGAGAACGATGTTGCTACACCCGCCA
Found at i:3370492 original size:32 final size:33
Alignment explanation
Indices: 3370429--3370509 Score: 121
Period size: 32 Copynumber: 2.5 Consensus size: 33
3370419 TCATGTTTAA
*
3370429 AATATTTTATATTTATATAAATTTTTAATATATT
1 AATAATTTATA-TTATATAAATTTTTAATATATT
3370463 AATAATTTATATTATATAAA-TTTTAATATATT
1 AATAATTTATATTATATAAATTTTTAATATATT
3370495 AA-ATATTTATATTAT
1 AATA-ATTTATATTAT
3370510 CATGTTATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
31 1 0.02
32 25 0.56
33 9 0.20
34 10 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTATATAAATTTTTAATATATT
Found at i:3373050 original size:32 final size:34
Alignment explanation
Indices: 3372977--3373086 Score: 98
Period size: 32 Copynumber: 3.1 Consensus size: 34
3372967 TAAAAAAATT
*
3372977 AATTTGACATAAACATAAATATATCTAAATATGTATTAA
1 AATTT-ACATAAACATAAATATAT-T-AATA--TATAAA
3373016 AATTTACATAAA-ATAAAT-TATTAATATATAAA
1 AATTTACATAAACATAAATATATTAATATATAAA
* * * *
3373048 AATTTATATAAATATATAATATTTTACATACATAAA
1 AATTTACATAAACATA-AATATATTA-ATATATAAA
3373084 AAT
1 AAT
3373087 AAAACATAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
32 16 0.25
33 3 0.05
34 7 0.11
35 5 0.08
36 14 0.22
37 6 0.10
38 7 0.11
39 5 0.08
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (34 bp):
AATTTACATAAACATAAATATATTAATATATAAA
Found at i:3373298 original size:27 final size:29
Alignment explanation
Indices: 3373260--3373316 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
3373250 AAACGTATTT
*
3373260 TTTTTCTTTTTCC-TTTCTTTCC-TCTTC
1 TTTTTCTCTTTCCTTTTCTTTCCTTCTTC
3373287 TTTTTCTCTTTCCTTTTTCTTTCCTTCTTC
1 TTTTTCTCTTTCC-TTTTCTTTCCTTCTTC
3373317 ATCAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
29 9 0.35
30 5 0.19
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTTCTCTTTCCTTTTCTTTCCTTCTTC
Found at i:3373722 original size:25 final size:26
Alignment explanation
Indices: 3373692--3373749 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
3373682 ATGACATAAT
* *
3373692 TTTTAAAAATTA-TAAA-AAATTTAAG
1 TTTTAAAAATAATTAAATAAA-TTAAA
3373717 TTTTAAAAATAATTAAATAAATTAAA
1 TTTTAAAAATAATTAAATAAATTAAA
3373743 TTTTAAA
1 TTTTAAA
3373750 TTTCACCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 11 0.38
26 15 0.52
27 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TTTTAAAAATAATTAAATAAATTAAA
Found at i:3377983 original size:21 final size:20
Alignment explanation
Indices: 3377953--3377993 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3377943 AAATAACACA
* *
3377953 TTTATTTTATTTGAATAAAT
1 TTTATTTTATATGAAAAAAT
3377973 TTTATTTTTATATGAAAAAAT
1 TTTA-TTTTATATGAAAAAAT
3377994 GATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTATTTTATATGAAAAAAT
Found at i:3377999 original size:21 final size:21
Alignment explanation
Indices: 3377957--3377999 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3377947 AACACATTTA
* * **
3377957 TTTTATTTGAATAAATTTTAT
1 TTTTATATGAAAAAATGATAT
3377978 TTTTATATGAAAAAATGATAT
1 TTTTATATGAAAAAATGATAT
3377999 T
1 T
3378000 AATAATTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTATATGAAAAAATGATAT
Found at i:3381693 original size:14 final size:13
Alignment explanation
Indices: 3381666--3381711 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3381656 AATTTTTATT
3381666 TAAAT-TTAATTA
1 TAAATATTAATTA
3381678 TAAATATTAATATA
1 TAAATATTAAT-TA
3381692 TAAATA-TAATT-
1 TAAATATTAATTA
*
3381703 TTAATATTA
1 TAAATATTA
3381712 TTTTAAATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.17
12 8 0.27
13 9 0.30
14 8 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATTAATTA
Found at i:3383242 original size:16 final size:16
Alignment explanation
Indices: 3383197--3383234 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
3383187 TATTCTTATA
3383197 ATAAATTTT-A-ATTT
1 ATAAATTTTAATATTT
3383211 -TAAATTTTAATATTT
1 ATAAATTTTAATATTT
3383226 ATAAATTTT
1 ATAAATTTT
3383235 TATTTTTACG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 4 0.19
16 8 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAATATTT
Found at i:3385666 original size:2 final size:2
Alignment explanation
Indices: 3385659--3385683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3385649 ATTGAGACCT
3385659 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
3385684 GGGTCAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3386961 original size:16 final size:14
Alignment explanation
Indices: 3386925--3386954 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3386915 TAAATCTATT
*
3386925 TATATTTATAAATG
1 TATAATTATAAATG
3386939 TATAATTATAAATG
1 TATAATTATAAATG
3386953 TA
1 TA
3386955 AATAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
TATAATTATAAATG
Found at i:3388541 original size:3 final size:3
Alignment explanation
Indices: 3388528--3388564 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3388518 TAAAATGTGA
*
3388528 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3388565 CTAAATCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3388966 original size:17 final size:15
Alignment explanation
Indices: 3388942--3388991 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
3388932 ATATTGAATA
3388942 TATTTATTATTATTTT
1 TATTTATT-TTATTTT
*
3388958 TATTTTATTTAAATTTT
1 TA-TTTATTT-TATTTT
3388975 TATTTATTTTTATTTT
1 TATTTA-TTTTATTTT
3388991 T
1 T
3388992 TAAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTATTTTATTTT
Found at i:3388993 original size:17 final size:16
Alignment explanation
Indices: 3388942--3388991 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
3388932 ATATTGAATA
*
3388942 TATTTATTATTATTTT
1 TATTTATTTTTATTTT
**
3388958 TATTTTATTTAAATTTT
1 TA-TTTATTTTTATTTT
3388975 TATTTATTTTTATTTT
1 TATTTATTTTTATTTT
3388991 T
1 T
3388992 TAAATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTATTTTTATTTT
Found at i:3393480 original size:2 final size:2
Alignment explanation
Indices: 3393473--3393502 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3393463 TACGGTCCTC
3393473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3393503 TGTCAGATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3396918 original size:30 final size:31
Alignment explanation
Indices: 3396887--3396956 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
3396877 CTTGAAGGGG
3396887 AATCATTTAGGTTTGGTGTCTACAGTTGGGA
1 AATCATTTAGGTTTGGTGTCTACAGTTGGGA
* *
3396918 AACCATTTAGGTTTGGTGTCTACGGTTGGGA
1 AATCATTTAGGTTTGGTGTCTACAGTTGGGA
3396949 AATCATTT
1 AATCATTT
3396957 GTATGCCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (31 bp):
AATCATTTAGGTTTGGTGTCTACAGTTGGGA
Found at i:3397946 original size:19 final size:19
Alignment explanation
Indices: 3397924--3397960 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3397914 ATTTATTTTG
*
3397924 TTCATTAATCAATATTGTC
1 TTCATTAAGCAATATTGTC
3397943 TTCATTAAGCAATATTGT
1 TTCATTAAGCAATATTGT
3397961 AATTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (19 bp):
TTCATTAAGCAATATTGTC
Found at i:3420798 original size:22 final size:22
Alignment explanation
Indices: 3420773--3420814 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3420763 ATATTAAGAA
3420773 TATATAAAATTTAAAATATTTG
1 TATATAAAATTTAAAATATTTG
***
3420795 TATATTTTATTTAAAATATT
1 TATATAAAATTTAAAATATT
3420815 ATTTATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATAAAATTTAAAATATTTG
Found at i:3421261 original size:24 final size:24
Alignment explanation
Indices: 3421234--3421284 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3421224 TATATTACTT
3421234 TTAATTAATAAAAGAAATAATGTA
1 TTAATTAATAAAAGAAATAATGTA
3421258 TTAATTAATAAAAGAAATAATGTA
1 TTAATTAATAAAAGAAATAATGTA
3421282 TTA
1 TTA
3421285 TACAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TTAATTAATAAAAGAAATAATGTA
Found at i:3423366 original size:24 final size:25
Alignment explanation
Indices: 3423331--3423379 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
3423321 AGTCTCTAAA
3423331 TTTTATCATTTTATT-TAAACAAAT
1 TTTTATCATTTTATTATAAACAAAT
3423355 TTTTAT-ATTTTTATTATAAACAAAT
1 TTTTATCA-TTTTATTATAAACAAAT
3423380 AACTAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.04
24 13 0.57
25 9 0.39
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTATCATTTTATTATAAACAAAT
Found at i:3423903 original size:19 final size:20
Alignment explanation
Indices: 3423879--3423919 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3423869 CAAATCTTTT
3423879 AAGGT-AAAAAGCATAAGCA
1 AAGGTAAAAAAGCATAAGCA
*
3423898 AAGGTAAAAAATCATAAGCA
1 AAGGTAAAAAAGCATAAGCA
3423918 AA
1 AA
3423920 AAGGTAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.61, C:0.10, G:0.17, T:0.12
Consensus pattern (20 bp):
AAGGTAAAAAAGCATAAGCA
Found at i:3434991 original size:17 final size:17
Alignment explanation
Indices: 3434949--3434996 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
3434939 CATATTTAAA
*
3434949 ATATTATATAAATTTTG
1 ATATTATATAAAATTTG
3434966 ATA-TA-ATAATAATTT-
1 ATATTATATAA-AATTTG
3434981 ATATTATATAAAATTT
1 ATATTATATAAAATTT
3434997 TAATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.26
16 13 0.48
17 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATATTATATAAAATTTG
Found at i:3434998 original size:17 final size:17
Alignment explanation
Indices: 3434949--3434998 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
3434939 CATATTTAAA
3434949 ATATTATAT-AAATTTT
1 ATATTATATAAAATTTT
3434965 GATA-TA-ATAATAA-TTT
1 -ATATTATATAA-AATTTT
3434981 ATATTATATAAAATTTT
1 ATATTATATAAAATTTT
3434998 A
1 A
3434999 ATATATTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATATTATATAAAATTTT
Found at i:3435003 original size:15 final size:15
Alignment explanation
Indices: 3434953--3435004 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3434943 TTTAAAATAT
*
3434953 TATAT-AAATTTTGA
1 TATATAAAATTTTAA
*
3434967 TATAATAATAATTTATAT
1 TAT-ATAA-AATTT-TAA
3434985 TATATAAAATTTTAA
1 TATATAAAATTTTAA
3435000 TATAT
1 TATAT
3435005 TTTCATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 6 0.19
17 9 0.29
18 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATAAAATTTTAA
Found at i:3436229 original size:16 final size:17
Alignment explanation
Indices: 3436203--3436237 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3436193 ATATTTATTT
*
3436203 TTAAATAAAATTATATA
1 TTAAATAAAATCATATA
3436220 TTAAAT-AAATCATATA
1 TTAAATAAAATCATATA
3436236 TT
1 TT
3436238 TATATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATAAAATCATATA
Found at i:3436416 original size:3 final size:3
Alignment explanation
Indices: 3436408--3436438 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3436398 TTTCAAGATA
3436408 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3436439 GCTATTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3436978 original size:11 final size:11
Alignment explanation
Indices: 3436956--3437010 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
3436946 ATATATTTTA
3436956 ATATTT-TATT
1 ATATTTATATT
3436966 ATATTTATATT
1 ATATTTATATT
*
3436977 ATTTTTA-ATT
1 ATATTTATATT
*
3436987 -T-TTTATATC
1 ATATTTATATT
3436996 ATATTTATATT
1 ATATTTATATT
3437007 ATAT
1 ATAT
3437011 AAATATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.11
9 3 0.08
10 10 0.26
11 21 0.55
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTTATATT
Found at i:3436988 original size:34 final size:34
Alignment explanation
Indices: 3436909--3436988 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 34
3436899 ATAATTTTAA
* *
3436909 ATTTTAAATTTTAATAATTTATTTTATATAAATT
1 ATTTTTAATTTTAATAATTTATTATATATAAATT
** * * *
3436943 -TTAATATATTTTAATATTTTATTATATTTATATT
1 ATTTTTA-ATTTTAATAATTTATTATATATAAATT
3436977 ATTTTTAATTTT
1 ATTTTTAATTTT
3436989 TTATATCATA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
33 3 0.09
34 28 0.80
35 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (34 bp):
ATTTTTAATTTTAATAATTTATTATATATAAATT
Found at i:3437002 original size:30 final size:30
Alignment explanation
Indices: 3436928--3437010 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 30
3436918 TTTAATAATT
* *
3436928 TATTTTATATAAATTT-TAATATATTTTAA
1 TATTTTATATATATTTATATTATATTTTAA
3436957 TATTTTAT-TATATTTATATTAT-TTTTAA
1 TATTTTATATATATTTATATTATATTTTAA
*
3436985 TTTTTTATATCATATTTATATTATAT
1 TATTTTATAT-ATATTTATATTATAT
3437011 AAATATATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 19 0.40
29 14 0.30
30 13 0.28
31 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTATATATATTTATATTATATTTTAA
Found at i:3437017 original size:24 final size:24
Alignment explanation
Indices: 3436990--3437041 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3436980 TTTAATTTTT
*
3436990 TATATCATATTT-ATATTATATAAA
1 TATATCATATTTAAAATTATA-AAA
**
3437014 TATATTTTATTTAAAATTATAAAA
1 TATATCATATTTAAAATTATAAAA
3437038 TATA
1 TATA
3437042 CCCCTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATCATATTTAAAATTATAAAA
Found at i:3440408 original size:14 final size:14
Alignment explanation
Indices: 3440373--3440417 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
3440363 AGTAAAGATC
*
3440373 AAATGAATA-AAAT
1 AAATAAATATAAAT
3440386 AAAATTAAATATAAAT
1 -AAA-TAAATATAAAT
3440402 AAATAAATATAAAT
1 AAATAAATATAAAT
3440416 AA
1 AA
3440418 TATATTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 16 0.57
15 8 0.29
16 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATAAATATAAAT
Done.