Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 4 of 22
Found at i:477511 original size:18 final size:17
Alignment explanation
Indices: 477490--477523 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
477480 TATTTATTAA
477490 ATATATTTTATTTATATC
1 ATATATTTTA-TTATATC
*
477508 ATATTTTTTATTATAT
1 ATATATTTTATTATAT
477524 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATATTTTATTATATC
Found at i:477512 original size:25 final size:25
Alignment explanation
Indices: 477459--477512 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
477449 ATTATCATTT
* * *
477459 TATTTAATATATTATTTTTTATATT
1 TATTAAATATATTATTATTTATATA
477484 TATTAAATATATT-TTATTTATATCA
1 TATTAAATATATTATTATTTATAT-A
477509 TATT
1 TATT
477513 TTTTATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTAAATATATTATTATTTATATA
Found at i:477528 original size:38 final size:39
Alignment explanation
Indices: 477455--477533 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
477445 TTACATTATC
* *
477455 ATTTTATTTAATATATTATTTTTTATATTTATTAAATAT
1 ATTTTATTTAATATATTATTTTTTATATATATTAAAAAT
477494 ATTTTATTT-ATATCA-TATTTTTTAT-TATATTTAAAAAT
1 ATTTTATTTAATAT-ATTATTTTTTATATATA-TTAAAAAT
477532 AT
1 AT
477534 CAAACTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 3 0.08
38 23 0.64
39 10 0.28
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTATTTAATATATTATTTTTTATATATATTAAAAAT
Found at i:478021 original size:23 final size:23
Alignment explanation
Indices: 477974--478110 Score: 65
Period size: 23 Copynumber: 6.0 Consensus size: 23
477964 GATTCGAATA
*
477974 TAAATTTTTATATATTTATAATT
1 TAAATTTATATATATTTATAATT
477997 TAAATTTATAT-TATTT-TAAGTTT
1 TAAATTTATATATATTTATAA--TT
* * * *
478020 TAGA-TAATATTAAATATCATAATT
1 TAAATTTATA-TATAT-TTATAATT
* * **
478044 T-ATTTTATTTATATAGATAA--
1 TAAATTTATATATATTTATAATT
*
478064 TAAATTCATATATATTTA-AATT
1 TAAATTTATATATATTTATAATT
*
478086 TAATATTTATTTATATATT-TAATT
1 TAA-ATTTATATATAT-TTATAATT
478110 T
1 T
478111 TTATTTTATT
Statistics
Matches: 82, Mismatches: 19, Indels: 25
0.65 0.15 0.20
Matches are distributed among these distances:
20 3 0.04
21 14 0.17
22 16 0.20
23 30 0.37
24 15 0.18
25 1 0.01
26 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (23 bp):
TAAATTTATATATATTTATAATT
Found at i:478100 original size:25 final size:24
Alignment explanation
Indices: 478072--478121 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
478062 AATAAATTCA
478072 TATATATTTAAATTTAATATTTATT
1 TATATATTTAAATTTAAT-TTTATT
* *
478097 TATATATTTAATTTTTATTTTATT
1 TATATATTTAAATTTAATTTTATT
478121 T
1 T
478122 TTTGAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATATATTTAAATTTAATTTTATT
Found at i:478107 original size:19 final size:17
Alignment explanation
Indices: 478071--478116 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
478061 TAATAAATTC
*
478071 ATATATATTTAAATTTA
1 ATATTTATTTAAATTTA
478088 ATATTTATTTATATATTTA
1 ATATTTATTTA-A-ATTTA
*
478107 ATTTTTATTT
1 ATATTTATTT
478117 TATTTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 1 0.04
19 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTATTTAAATTTA
Found at i:478110 original size:13 final size:13
Alignment explanation
Indices: 478072--478110 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
478062 AATAAATTCA
478072 TATATATTTAAATT
1 TATATATTT-AATT
478086 TA-ATATTT-ATT
1 TATATATTTAATT
478097 TATATATTTAATT
1 TATATATTTAATT
478110 T
1 T
478111 TTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.22
12 6 0.26
13 10 0.43
14 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATATTTAATT
Found at i:478145 original size:9 final size:9
Alignment explanation
Indices: 478131--478163 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
478121 TTTTGAAAGT
478131 AATTTAATA
1 AATTTAATA
478140 AATTTAA-A
1 AATTTAATA
*
478148 TATTTAATA
1 AATTTAATA
478157 AATTTAA
1 AATTTAA
478164 ATGTTCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTTAATA
Found at i:478154 original size:17 final size:17
Alignment explanation
Indices: 478132--478165 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
478122 TTTGAAAGTA
478132 ATTTAATAAATTTAAAT
1 ATTTAATAAATTTAAAT
478149 ATTTAATAAATTTAAAT
1 ATTTAATAAATTTAAAT
478166 GTTCAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAATAAATTTAAAT
Found at i:478223 original size:17 final size:17
Alignment explanation
Indices: 478199--478236 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
478189 CAGATATGAA
478199 TTTAAATAAT-AAT-A-
1 TTTAAATAATAAATAAT
478213 TTTAAATAATAAATAAT
1 TTTAAATAATAAATAAT
478230 TTTAAAT
1 TTTAAAT
478237 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 3 0.14
16 1 0.05
17 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATAATAAATAAT
Found at i:478640 original size:10 final size:10
Alignment explanation
Indices: 478611--478641 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
478601 ATCTAGTATG
*
478611 ATATATATAT
1 ATATATATAA
478621 ATATATATAA
1 ATATATATAA
478631 ATATATATAA
1 ATATATATAA
478641 A
1 A
478642 ATTAGAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATATATATAA
Found at i:478894 original size:2 final size:2
Alignment explanation
Indices: 478881--478912 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
478871 GTACTTAATC
*
478881 TA TA TA TG 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
478913 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:478917 original size:2 final size:2
Alignment explanation
Indices: 478912--478958 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
478902 ATATATATAT
*
478912 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
478954 AG AG A
1 AG AG A
478959 AGCCATACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:480927 original size:3 final size:3
Alignment explanation
Indices: 480919--480947 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
480909 TGTATACTAT
480919 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
480948 TTTTGAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:487477 original size:2 final size:2
Alignment explanation
Indices: 487470--487500 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
487460 ATTATCATGA
487470 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
487501 TCCTCTGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:488086 original size:17 final size:16
Alignment explanation
Indices: 488067--488097 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
488057 TTTCTTCGTT
488067 TTTTGGAACTTAATCG
1 TTTTGGAACTTAATCG
488083 TTTTGGAACTTAATC
1 TTTTGGAACTTAATC
488098 ACTGCAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (16 bp):
TTTTGGAACTTAATCG
Found at i:489385 original size:2 final size:2
Alignment explanation
Indices: 489378--489411 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
489368 CTTTGTGTTC
489378 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
489412 TCTCATGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:494752 original size:26 final size:26
Alignment explanation
Indices: 494704--494754 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
494694 ATATAGGACC
*
494704 TGTATTAAACAGTGAAACGGCTATAA
1 TGTATTAAACAGTGAAACAGCTATAA
*
494730 TGTATTAAACAGTGAAATAGCTATA
1 TGTATTAAACAGTGAAACAGCTATA
494755 GTGCTACCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (26 bp):
TGTATTAAACAGTGAAACAGCTATAA
Found at i:500976 original size:3 final size:3
Alignment explanation
Indices: 500968--501011 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
500958 TTGTACATTA
500968 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
501012 GTCTCTTGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:506855 original size:15 final size:15
Alignment explanation
Indices: 506784--506855 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
506774 ATTAATAATA
* *
506784 TTAAAAAATTTATTT
1 TTAATAAATTAATTT
506799 TTAATAAATTAATTCT
1 TTAATAAATTAATT-T
*
506815 TGAATTAAATTAA-TT
1 TTAA-TAAATTAATTT
** *
506830 AAAATTTAATTAATTT
1 TTAA-TAAATTAATTT
506846 TTAATAAATT
1 TTAATAAATT
506856 TCAATAAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 28 0.62
16 9 0.20
17 8 0.18
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
TTAATAAATTAATTT
Found at i:508980 original size:31 final size:31
Alignment explanation
Indices: 508918--508981 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
508908 AAGTTATAAG
* * *
508918 AAAATAATTATATTAATTACCTTATCTAAGA
1 AAAAAAATTATATTAATTACCTTAACCAAGA
508949 AAAAAAATTATATTAATTCACC-TAACCAAGA
1 AAAAAAATTATATTAATT-ACCTTAACCAAGA
508980 AA
1 AA
508982 CTCTTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAAAATTATATTAATTACCTTAACCAAGA
Found at i:509305 original size:2 final size:2
Alignment explanation
Indices: 509298--509332 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
509288 GGAATCTATT
509298 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
509333 TTTGTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:509427 original size:9 final size:9
Alignment explanation
Indices: 509400--509484 Score: 51
Period size: 9 Copynumber: 10.0 Consensus size: 9
509390 AAAAATATAA
509400 AAATAATATT
1 AAAT-ATATT
509410 -AAT-TATT
1 AAATATATT
509417 AAATATATT
1 AAATATATT
509426 AAA-AT-TAT
1 AAATATAT-T
509434 AAATATA--
1 AAATATATT
*
509441 ATATATATT
1 AAATATATT
509450 AAATATATT
1 AAATATATT
* *
509459 --TTATTTT
1 AAATATATT
*
509466 AATATTTATT
1 AA-ATATATT
509476 AAATATATT
1 AAATATATT
509485 TTTTTATATA
Statistics
Matches: 57, Mismatches: 8, Indels: 21
0.66 0.09 0.24
Matches are distributed among these distances:
7 16 0.28
8 9 0.16
9 26 0.46
10 6 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AAATATATT
Found at i:509455 original size:33 final size:36
Alignment explanation
Indices: 509389--509458 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
509379 TTTTTAATTA
509389 TAAAAATATAAAAATAATATTAATTATTAAATATAT
1 TAAAAATATAAAAATAATATTAATTATTAAATATAT
* *
509425 TAAAATTATAAATATAATA-T-A-TATTAAATATAT
1 TAAAAATATAAAAATAATATTAATTATTAAATATAT
509458 T
1 T
509459 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 13 0.41
34 1 0.03
35 1 0.03
36 17 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
TAAAAATATAAAAATAATATTAATTATTAAATATAT
Found at i:509832 original size:21 final size:20
Alignment explanation
Indices: 509795--509850 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
509785 TTATATTTAT
*
509795 ATATAATAT-TTTAAATATA
1 ATATAATATATATAAATATA
509814 ATTATAATATATATAAATATA
1 A-TATAATATATATAAATATA
*
509835 ATA-AAAATATATAAAT
1 ATATAATATATATAAAT
509851 TATAGGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
20 10 0.30
21 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATATATATAAATATA
Found at i:510110 original size:16 final size:17
Alignment explanation
Indices: 510089--510125 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
510079 AAAATATAGA
510089 AAAAATAT-AAAATAAT
1 AAAAATATAAAAATAAT
*
510105 AAAAATTTAAAAATAAT
1 AAAAATATAAAAATAAT
510122 AAAA
1 AAAA
510126 TTATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATAAAAATAAT
Found at i:510807 original size:21 final size:21
Alignment explanation
Indices: 510782--510821 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
510772 TAAGTTGATT
510782 TAAAT-TATTATTTATTTAATA
1 TAAATATATT-TTTATTTAATA
510803 TAAATATATTTTTATTTAA
1 TAAATATATTTTTATTTAA
510822 ATTTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATATATTTTTATTTAATA
Found at i:512119 original size:17 final size:16
Alignment explanation
Indices: 512097--512151 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
512087 GTATATGTGT
512097 ATTTTATATTCATATAA
1 ATTTTATATT-ATATAA
512114 ATTTTAATATGT-TA-ATA
1 ATTTT-ATAT-TATATA-A
512131 A-TTTATATTATATAA
1 ATTTTATATTATATAA
512146 ATTTTA
1 ATTTTA
512152 AAATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
14 1 0.03
15 8 0.25
16 9 0.28
17 9 0.28
18 4 0.12
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:512224 original size:18 final size:19
Alignment explanation
Indices: 512203--512238 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
512193 TCATATCAAT
512203 TTTTATATTAT-ATTTTAA
1 TTTTATATTATAATTTTAA
*
512221 TTTTTTATTATAATTTTA
1 TTTTATATTATAATTTTA
512239 TAATATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATATTATAATTTTAA
Found at i:512224 original size:19 final size:19
Alignment explanation
Indices: 512200--512238 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
512190 ATGTCATATC
512200 AATTTTTATATTAT-ATTTT
1 AATTTTT-TATTATAATTTT
512219 AATTTTTTATTATAATTTT
1 AATTTTTTATTATAATTTT
512238 A
1 A
512239 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
AATTTTTTATTATAATTTT
Found at i:512491 original size:16 final size:16
Alignment explanation
Indices: 512470--512503 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
512460 TGTTGAACAA
512470 AATCCTACTCAAAAGT
1 AATCCTACTCAAAAGT
*
512486 AATCCTACTCCAAAGT
1 AATCCTACTCAAAAGT
512502 AA
1 AA
512504 AAGTTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (16 bp):
AATCCTACTCAAAAGT
Found at i:512524 original size:2 final size:2
Alignment explanation
Indices: 512517--512548 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
512507 TTGATAATTC
512517 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
512549 TTTTAGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:512579 original size:34 final size:32
Alignment explanation
Indices: 512541--512618 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 32
512531 ATATATATAT
*
512541 ATATATATTTTTAGATTTTATAATTATATTTAAA
1 ATATATATTTATAGATTTTATAA-TAT-TTTAAA
* *
512575 ATATATATTTATATATTTTTTAATATTTTAATA
1 ATATATATTTATAGATTTTATAATATTTTAA-A
*
512608 ATTTAT-TTTAT
1 ATATATATTTAT
512619 TTAAAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 10 0.26
33 9 0.23
34 20 0.51
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
ATATATATTTATAGATTTTATAATATTTTAAA
Found at i:512588 original size:44 final size:44
Alignment explanation
Indices: 512531--512615 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 44
512521 ATATATATAT
512531 ATATATATATATATATATTTTT-AGATTTT-ATAATTATATTTAAA
1 ATATATATATATATAT-TTTTTAAGATTTTAATAATT-TATTTAAA
* *
512575 ATATATATTTATATATTTTTTAATATTTTAATAATTTATTT
1 ATATATATATATATATTTTTTAAGATTTTAATAATTTATTT
512616 TATTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 5 0.14
44 26 0.70
45 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (44 bp):
ATATATATATATATATTTTTTAAGATTTTAATAATTTATTTAAA
Found at i:512636 original size:17 final size:18
Alignment explanation
Indices: 512577--512658 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 18
512567 TATTTAAAAT
*
512577 ATATATTTATATATTTTTTA
1 ATATATTTA-ATA-ATTTTA
512597 ATAT-TTTAATAA-TTTA
1 ATATATTTAATAATTTTA
* *
512613 TTTTATTTAA-AATTTTA
1 ATATATTTAATAATTTTA
*
512630 ATATATTTATATAA-TTAA
1 ATATATTTA-ATAATTTTA
512648 ATAATATTTAA
1 AT-ATATTTAA
512659 ATTATTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
16 8 0.16
17 16 0.31
18 10 0.20
19 13 0.25
20 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATTTAATAATTTTA
Found at i:512647 original size:25 final size:25
Alignment explanation
Indices: 512594--512648 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
512584 TATATATTTT
* * *
512594 TTAATATTTTAATAATTTATTTTAT
1 TTAAAATTTTAATAATTTATTATAA
512619 TTAAAATTTTAATATATTTA-TATAA
1 TTAAAATTTTAATA-ATTTATTATAA
512644 TTAAA
1 TTAAA
512649 TAATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAAAATTTTAATAATTTATTATAA
Found at i:512661 original size:35 final size:33
Alignment explanation
Indices: 512592--512659 Score: 82
Period size: 36 Copynumber: 2.0 Consensus size: 33
512582 TTTATATATT
* **
512592 TTTTAATATTTTAATAATTTATTTTATTTAAAA
1 TTTTAATATTTTAATAATTAATAATATTTAAAA
512625 TTTTAATATATTTATATAATTAAATAATATTTAAA
1 TTTTAATAT-TTTA-ATAATT-AATAATATTTAAA
512660 TTATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 9 0.31
34 4 0.14
35 6 0.21
36 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTTAATATTTTAATAATTAATAATATTTAAAA
Found at i:512665 original size:19 final size:18
Alignment explanation
Indices: 512616--512665 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
512606 TAATTTATTT
512616 TATTTAAAATT-TT-AATA
1 TATTT-AAATTATTAAATA
* *
512633 TATTTATATAATTAAATAA
1 TATTTAAATTATTAAAT-A
512652 TATTTAAATTATTA
1 TATTTAAATTATTA
512666 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 7 0.27
18 3 0.12
19 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTAAATTATTAAATA
Found at i:514029 original size:14 final size:14
Alignment explanation
Indices: 514010--514038 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
514000 TATAGCATAA
514010 AATATAATATATTT
1 AATATAATATATTT
514024 AATATAATATATTT
1 AATATAATATATTT
514038 A
1 A
514039 TATGTATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATAATATATTT
Found at i:514083 original size:8 final size:9
Alignment explanation
Indices: 514064--514118 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
514054 TATTTAAAGT
514064 TTTAATATA
1 TTTAATATA
514073 TTTAATA-A
1 TTTAATATA
514081 TTT-ATATTA
1 TTTAATA-TA
514090 TTTTAATATA
1 -TTTAATATA
* *
514100 TATATACATA
1 TTTA-ATATA
514110 TTTAATATA
1 TTTAATATA
514119 AATATTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 15 0.41
10 12 0.32
11 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TTTAATATA
Found at i:514084 original size:17 final size:18
Alignment explanation
Indices: 514064--514118 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
514054 TATTTAAAGT
514064 TTTAATATATTTAATA-A
1 TTTAATATATTTAATATA
514081 TTT-ATATTATTTTAATATA
1 TTTAATA-TA-TTTAATATA
* *
514100 TATATACATATTTAATATA
1 TTTA-ATATATTTAATATA
514119 AATATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 7 0.23
19 12 0.39
20 2 0.06
21 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAATATATTTAATATA
Found at i:514113 original size:19 final size:18
Alignment explanation
Indices: 514070--514123 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
514060 AAGTTTTAAT
*
514070 ATATTTAATA-ATTTATA
1 ATATTTAATATATATATA
*
514087 TTATTTTAATATATATATA
1 ATA-TTTAATATATATATA
*
514106 CATATTTAATATAAATAT
1 -ATATTTAATATATATAT
514124 TAAATCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 7 0.23
19 19 0.63
20 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTAATATATATATA
Found at i:514355 original size:3 final size:3
Alignment explanation
Indices: 514347--514379 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
514337 GACGAAAGGA
514347 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
514380 TGTGAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:516561 original size:15 final size:15
Alignment explanation
Indices: 516541--516582 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
516531 AGCGCTTCCC
516541 AAATTTCCCATGCTT
1 AAATTTCCCATGCTT
*
516556 AAATTTCCCATGTTT
1 AAATTTCCCATGCTT
* *
516571 GAATTTTCCATG
1 AAATTTCCCATG
516583 ACCATGGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (15 bp):
AAATTTCCCATGCTT
Found at i:517421 original size:15 final size:15
Alignment explanation
Indices: 517401--517435 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
517391 GCCTTGTGGG
517401 GGATATCCATGAGGA
1 GGATATCCATGAGGA
* *
517416 GGATATCCCTGGGGA
1 GGATATCCATGAGGA
517431 GGATA
1 GGATA
517436 GGATCCATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (15 bp):
GGATATCCATGAGGA
Found at i:519576 original size:3 final size:3
Alignment explanation
Indices: 519568--519601 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
519558 AAAATGGATA
*
519568 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
519602 TTGTGCAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:524431 original size:26 final size:28
Alignment explanation
Indices: 524400--524463 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 28
524390 TATATATATA
*
524400 TATATAAAATACAA-A-TAT-ATTAAAAT
1 TATATAAAATA-AATATTATAAATAAAAT
524426 TATATAAAATAAATATTATAAATAAAAT
1 TATATAAAATAAATATTATAAATAAAAT
524454 TATAATAAAA
1 TAT-ATAAAA
524464 AATAAATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 2 0.06
26 12 0.36
27 3 0.09
28 10 0.30
29 6 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
TATATAAAATAAATATTATAAATAAAAT
Found at i:524431 original size:28 final size:29
Alignment explanation
Indices: 524397--524470 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 29
524387 ATATATATAT
*
524397 ATATATATAAAATACAA-A-TAT-ATTAAA
1 ATATATATAAAATA-AATATTATAAATAAA
524424 AT-TATATAAAATAAATATTATAAATAAA
1 ATATATATAAAATAAATATTATAAATAAA
*
524452 ATTATAATAAAAAATAAAT
1 A-TAT-ATATAAAATAAAT
524471 GTAACCAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 2 0.05
26 12 0.31
27 5 0.13
28 6 0.15
29 1 0.03
30 1 0.03
31 12 0.31
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
ATATATATAAAATAAATATTATAAATAAA
Found at i:524537 original size:42 final size:41
Alignment explanation
Indices: 524490--524613 Score: 96
Period size: 39 Copynumber: 3.1 Consensus size: 41
524480 CCAACCTAAT
*
524490 TTTAAATTTTTTTTTACTTAGGTATCCTCATTTGTTTTATGA
1 TTTAAA-TTTTTTTTACTTAGATATCCTCATTTGTTTTATGA
*** * * * ** * *
524532 TTTAAAATAAATATTATTTAGTTAT-C-C-TTAATTATATTA
1 TTT-AAATTTTTTTTACTTAGATATCCTCATTTGTTTTATGA
524571 -TT-AATTTTTTTTACTTAGATATCCTCATTTGTTTTATGA
1 TTTAAATTTTTTTTACTTAGATATCCTCATTTGTTTTATGA
524610 TTTA
1 TTTA
524614 GTTATCTCTC
Statistics
Matches: 56, Mismatches: 20, Indels: 13
0.63 0.22 0.15
Matches are distributed among these distances:
36 14 0.25
37 1 0.02
38 3 0.05
39 16 0.29
40 3 0.05
41 1 0.02
42 15 0.27
43 3 0.05
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.57
Consensus pattern (41 bp):
TTTAAATTTTTTTTACTTAGATATCCTCATTTGTTTTATGA
Found at i:526323 original size:4 final size:4
Alignment explanation
Indices: 526306--526344 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
526296 AATTATACAC
**
526306 AAAT AAAT TTAT AAAT AAAT AAAT AAAT AAA- AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
526345 TTACTCATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:527066 original size:23 final size:23
Alignment explanation
Indices: 527016--527066 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
527006 TGTTTTAAAT
*
527016 TTATATTTTATTATTTATTATAA
1 TTATAATTTATTATTTATTATAA
* *
527039 ATATAATTT-TTATTTATTTATCA
1 TTATAATTTATTATTTA-TTATAA
527062 TTATA
1 TTATA
527067 TATATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTATAATTTATTATTTATTATAA
Found at i:527073 original size:26 final size:24
Alignment explanation
Indices: 527011--527075 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
527001 TAATATGTTT
* *
527011 TAAATTTATATTTTATTATTTATTA
1 TAAATATAT-TTTTATTATTTATCA
527036 TAAATATAATTTTTATTTATTTATCA
1 TAAATAT-ATTTTTA-TTATTTATCA
*
527062 TTATATATATTTTT
1 -TAAATATATTTTT
527076 TAATTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 11 0.32
26 17 0.50
27 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TAAATATATTTTTATTATTTATCA
Found at i:527087 original size:27 final size:27
Alignment explanation
Indices: 527038--527106 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
527028 ATTTATTATA
* *
527038 AATATAATTTTT-ATTTATTTATCATT
1 AATATATTTTTTAATTTATATATCATT
*
527064 ATATATATTTTTTAATTTA-ATATCTTT
1 A-ATATATTTTTTAATTTATATATCATT
527091 AATAATTATTTTTTAA
1 AAT-A-TATTTTTTAA
527107 AATATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
AATATATTTTTTAATTTATATATCATT
Found at i:528914 original size:24 final size:23
Alignment explanation
Indices: 528875--528919 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
528865 CAATAATTTA
528875 TAAAAAATAATAAAAAAATTTAAG
1 TAAAAAATAAT-AAAAAATTTAAG
* *
528899 TAAAAAATATTTAAAAATTTA
1 TAAAAAATAATAAAAAATTTA
528920 TATAATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAAAAATAATAAAAAATTTAAG
Found at i:529191 original size:15 final size:15
Alignment explanation
Indices: 529171--529200 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
529161 AAAGAGACAA
529171 ATGTATTTATTTATT
1 ATGTATTTATTTATT
529186 ATGTATTTATTTATT
1 ATGTATTTATTTATT
529201 TTACAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
ATGTATTTATTTATT
Found at i:531258 original size:18 final size:18
Alignment explanation
Indices: 531220--531258 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
531210 AATTACTTTA
*
531220 AAATATATTAAAACAACT
1 AAATATATTAAAACAAAT
531238 AAAT-TATTAAAACTAAAT
1 AAATATATTAAAAC-AAAT
531256 AAA
1 AAA
531259 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATATATTAAAACAAAT
Found at i:531633 original size:34 final size:34
Alignment explanation
Indices: 531586--531654 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
531576 CACGTACTTC
* *
531586 TCACGAATGATATATGCGTTAATTTATGATACCT
1 TCACGAATAATATATGCGCTAATTTATGATACCT
*
531620 TCACGAATAATATATGTGCTAATTTATGATACCT
1 TCACGAATAATATATGCGCTAATTTATGATACCT
531654 T
1 T
531655 ATTTTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (34 bp):
TCACGAATAATATATGCGCTAATTTATGATACCT
Found at i:532284 original size:20 final size:21
Alignment explanation
Indices: 532248--532310 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
532238 TATATTTTTA
532248 TAAATTT-ATATAATTAATATT
1 TAAATTTAATA-AATTAATATT
* *
532269 TTAA-TTAATAAATTAATAAT
1 TAAATTTAATAAATTAATATT
532289 TAAATTTAATAATATTACATAT
1 TAAATTTAATAA-ATTA-ATAT
532311 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.41
21 13 0.38
22 4 0.12
23 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTTAATAAATTAATATT
Found at i:540947 original size:5 final size:5
Alignment explanation
Indices: 540931--541002 Score: 65
Period size: 5 Copynumber: 13.8 Consensus size: 5
540921 AAAAATTTTA
* * * *
540931 AATTT AAATT AATTT AATTTT AA-TT AAATT AATAT ATATTT AATTAA
1 AATTT AATTT AATTT AA-TTT AATTT AATTT AATTT A-ATTT AATT-T
540978 AATATT AATTT AATTT AATTT AATT
1 AAT-TT AATTT AATTT AATTT AATT
541003 ATAAATATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.07
5 35 0.64
6 15 0.27
7 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
AATTT
Found at i:540990 original size:28 final size:28
Alignment explanation
Indices: 540953--541019 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
540943 TTTAATTTTA
540953 ATTAAATTAATATATATTTAATTA-AAAT
1 ATTAAATTAATATA-ATTTAATTATAAAT
* *
540981 ATTAATTTAATTTAATTTAATTATAAAT
1 ATTAAATTAATATAATTTAATTATAAAT
*
541009 ATAATAATTAA
1 ATTA-AATTAA
541020 AATTTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 9 0.27
28 19 0.58
29 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTAAATTAATATAATTTAATTATAAAT
Found at i:540996 original size:42 final size:42
Alignment explanation
Indices: 540938--541046 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 42
540928 TTAAATTTAA
* *
540938 ATTAATTTAATTTTAATTAAATTAATATATAT-TTAATTAAAAT
1 ATTAATTTAA-TTTAATT-AATTAATAAATATAATAATTAAAAT
540981 ATTAATTTAATTTAATTTAATT-ATAAATATAATAATTAAAAT
1 ATTAATTTAATTTAA-TTAATTAATAAATATAATAATTAAAAT
* * *
541023 TTTAATATTATTTTAAATAATTAA
1 ATTAAT-TTAATTTAATTAATTAA
541047 GTTTTAAGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
41 7 0.12
42 29 0.51
43 21 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
ATTAATTTAATTTAATTAATTAATAAATATAATAATTAAAAT
Found at i:541030 original size:48 final size:48
Alignment explanation
Indices: 540922--541038 Score: 116
Period size: 48 Copynumber: 2.4 Consensus size: 48
540912 ATTAACTTAA
*
540922 AAAATTTTAA-ATTTAAATTAATTTAATTTTAATTAAATTAATATATAT
1 AAAATTTTAATA-TTAATTTAATTTAATTTTAATTAAATTAATATATAT
** **
540970 TTAATTAAAATATTAATTTAATTTAA-TTTAATTATAAATATAATA-AT-T
1 AAAATTTTAATATTAATTTAATTTAATTTTAA-T-TAAAT-TAATATATAT
*
541018 AAAATTTTAATATTATTTTAA
1 AAAATTTTAATATTAATTTAA
541039 ATAATTAAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
47 5 0.09
48 37 0.67
49 8 0.15
50 5 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (48 bp):
AAAATTTTAATATTAATTTAATTTAATTTTAATTAAATTAATATATAT
Found at i:541409 original size:32 final size:33
Alignment explanation
Indices: 541365--541458 Score: 106
Period size: 33 Copynumber: 2.8 Consensus size: 33
541355 TCATTATAAT
541365 ATTTTTTT-AAATATTACTATTATT-TTTATTA
1 ATTTTTTTAAAATATTACTATTATTATTTATTA
541396 ATTTTTTTAAAATAATATA-TATT-TTATTTATTA
1 ATTTTTTTAAAAT-AT-TACTATTATTATTTATTA
* *
541429 ATTTTATGAAAATATTACGTATCTATTATT
1 ATTTTTTTAAAATATTAC-TAT-TATTATT
541459 CGAATCCACC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
31 10 0.19
32 8 0.15
33 27 0.51
34 3 0.06
35 5 0.09
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (33 bp):
ATTTTTTTAAAATATTACTATTATTATTTATTA
Found at i:541631 original size:23 final size:23
Alignment explanation
Indices: 541604--541666 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 23
541594 TATCCTATCT
541604 AAATAAATTTTTAATTTATATTC
1 AAATAAATTTTTAATTTATATTC
* * *
541627 AAATAATTTTTTTTATTTTATATTT
1 AAATAA--ATTTTTAATTTATATTC
*
541652 AAATAAATATTTAAT
1 AAATAAATTTTTAAT
541667 CTAAATCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
23 12 0.38
25 20 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATAAATTTTTAATTTATATTC
Found at i:541718 original size:21 final size:23
Alignment explanation
Indices: 541676--541721 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
541666 TCTAAATCAA
541676 TATTGTTAATAAAAATTAAAAAT
1 TATTGTTAATAAAAATTAAAAAT
*
541699 TATT-TTAATATAAA-TAAAAAT
1 TATTGTTAATAAAAATTAAAAAT
541720 TA
1 TA
541722 AAATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 9 0.41
23 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TATTGTTAATAAAAATTAAAAAT
Found at i:541744 original size:28 final size:29
Alignment explanation
Indices: 541683--541738 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
541673 CAATATTGTT
* *
541683 AATAAAAATTAAAA-ATTATTTTAATATA
1 AATAAAAATTAAAATTTTATTTAAATATA
541711 AATAAAAATTAAAATTTTATTTAAATAT
1 AATAAAAATTAAAATTTTATTTAAATAT
541739 TCTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AATAAAAATTAAAATTTTATTTAAATATA
Found at i:541893 original size:21 final size:21
Alignment explanation
Indices: 541869--541927 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
541859 TTATTATTAG
541869 ATATAATTTAATTATAAAAAT
1 ATATAATTTAATTATAAAAAT
541890 ATATAAATATTAA-TAT-AAAAT
1 ATAT-AAT-TTAATTATAAAAAT
* *
541911 ATTTAAATTAATT-TAAA
1 ATATAATTTAATTATAAA
541928 TTCGACCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 12 0.38
22 6 0.19
23 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATTTAATTATAAAAAT
Found at i:542111 original size:15 final size:15
Alignment explanation
Indices: 542067--542115 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
542057 AGCCTTTACC
542067 TTTCTATCAATCTCT
1 TTTCTATCAATCTCT
* **
542082 TTTCTCT-TTTCTCT
1 TTTCTATCAATCTCT
542096 TTTCTATCAATCTCT
1 TTTCTATCAATCTCT
542111 TTTCT
1 TTTCT
542116 CTCCTTTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTATCAATCTCT
Found at i:546500 original size:2 final size:2
Alignment explanation
Indices: 546493--546529 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
546483 AAAATACAAT
546493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
546530 TTCATTACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:547863 original size:34 final size:33
Alignment explanation
Indices: 547819--547885 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
547809 AGCTACGCTG
* *
547819 GAGGGGCGAACACAATCGCCATGCTTGGCGACCA
1 GAGGGACGAACACAATCGCC-CGCTTGGCGACCA
**
547853 GAGGGACGAACACGGTCGCCCGCTTGGCGACCA
1 GAGGGACGAACACAATCGCCCGCTTGGCGACCA
547886 AACATGGGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.24, C:0.31, G:0.34, T:0.10
Consensus pattern (33 bp):
GAGGGACGAACACAATCGCCCGCTTGGCGACCA
Found at i:551428 original size:59 final size:58
Alignment explanation
Indices: 551286--551524 Score: 280
Period size: 59 Copynumber: 4.0 Consensus size: 58
551276 TATGGTAATC
551286 TGGGTGACTTGGCATCACTTAGTGTGCGAGTCTTGGTCGCCTTAGTGGCGATCTAAAGTTT
1 TGGGTGACTTGGCATCAC-TAGTGTGCGAGTC-TGGTCGCCTTAGTGGCGATCTAAAG-TT
* * * *
551347 TGGGTGACTTGGCATCACCTAGTGTACGAGTCTGGTCGCCTTGGTGACGATTTAAAGTT
1 TGGGTGACTTGGCATCA-CTAGTGTGCGAGTCTGGTCGCCTTAGTGGCGATCTAAAGTT
* * * *
551406 TGGGTGACTTGGCACCATCTAGTGCGCGAGTCTGGTCGCCTTTGTGGCGATCTAAACTT
1 TGGGTGACTTGGCATCA-CTAGTGTGCGAGTCTGGTCGCCTTAGTGGCGATCTAAAGTT
* * * * * * *
551465 TGGGTGACTTGACGTCACCTAGTGCGCAAGTCTTGGTCGCCCTGGTGGCGATCTTAAGTT
1 TGGGTGACTTGGCATCA-CTAGTGTGCGAGTC-TGGTCGCCTTAGTGGCGATCTAAAGTT
551525 GTAGTGTGAT
Statistics
Matches: 155, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
59 80 0.52
60 45 0.29
61 29 0.19
62 1 0.01
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.32
Consensus pattern (58 bp):
TGGGTGACTTGGCATCACTAGTGTGCGAGTCTGGTCGCCTTAGTGGCGATCTAAAGTT
Found at i:551524 original size:119 final size:120
Alignment explanation
Indices: 551286--551521 Score: 325
Period size: 119 Copynumber: 2.0 Consensus size: 120
551276 TATGGTAATC
* * *
551286 TGGGTGACTTGGCATCACTTAGTGTGCGAGTCTTGGTCGCCTTAGTGGCGATCTAAAGTTTTGGG
1 TGGGTGACTTGGCACCACTTAGTGCGCGAGTCTTGGTCGCCTTAGTGGCGATCTAAAGCTTTGGG
* * * *
551351 TGACTTGGCATCACCTAGTGTACGAGTCTGGTCGCCTTGGTGACGATTTAAAGTT
66 TGACTTGACATCACCTAGTGCACAAGTCTGGTCGCCCTGGTGACGATTTAAAGTT
*
551406 TGGGTGACTTGGCACCA-TCTAGTGCGCGAGTC-TGGTCGCCTTTGTGGCGATCTAAA-CTTTGG
1 TGGGTGACTTGGCACCACT-TAGTGCGCGAGTCTTGGTCGCCTTAGTGGCGATCTAAAGCTTTGG
* * *
551468 GTGACTTGACGTCACCTAGTGCGCAAGTCTTGGTCGCCCTGGTGGCGATCTTAA
65 GTGACTTGACATCACCTAGTGCACAAGTC-TGGTCGCCCTGGTGACGAT-TTAA
551522 GTTGTAGTGT
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
118 29 0.28
119 41 0.40
120 32 0.31
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (120 bp):
TGGGTGACTTGGCACCACTTAGTGCGCGAGTCTTGGTCGCCTTAGTGGCGATCTAAAGCTTTGGG
TGACTTGACATCACCTAGTGCACAAGTCTGGTCGCCCTGGTGACGATTTAAAGTT
Found at i:561823 original size:28 final size:28
Alignment explanation
Indices: 561783--561843 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
561773 GATTCAAGTA
561783 GGTTCAGGTACGGGCTTGTTTAGGTTTG
1 GGTTCAGGTACGGGCTTGTTTAGGTTTG
561811 GGTTCAGGTACGGGCTTGTTTAGGTTTG
1 GGTTCAGGTACGGGCTTGTTTAGGTTTG
*
561839 AGTTC
1 GGTTC
561844 GTTTAAATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.11, C:0.11, G:0.38, T:0.39
Consensus pattern (28 bp):
GGTTCAGGTACGGGCTTGTTTAGGTTTG
Found at i:562306 original size:21 final size:22
Alignment explanation
Indices: 562282--562324 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
562272 AATTGTATTA
562282 ATATTT-TAAAAAATTTAAAAT
1 ATATTTATAAAAAATTTAAAAT
*
562303 ATATTTAGTAAAATATTTAAAA
1 ATATTTA-TAAAAAATTTAAAA
562325 ACTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATTTATAAAAAATTTAAAAT
Found at i:562359 original size:22 final size:23
Alignment explanation
Indices: 562334--562376 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
562324 AACTCATTTA
* *
562334 ATCTTAAC-TAAAAGTTCATGCC
1 ATCTAAACTTAAAAGCTCATGCC
562356 ATCTAAACTTAAAAGCTCATG
1 ATCTAAACTTAAAAGCTCATG
562377 TAAACTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (23 bp):
ATCTAAACTTAAAAGCTCATGCC
Found at i:562691 original size:41 final size:41
Alignment explanation
Indices: 562646--562723 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
562636 TTATCCTTAT
*
562646 TTTTTTATCTTTAAAAAACTATTGAATGTAGTTCTTGTTTC
1 TTTTTTATCCTTAAAAAACTATTGAATGTAGTTCTTGTTTC
*
562687 TTTTTTATCCTTAAAGAACTATTGAATGTAGTTCTTG
1 TTTTTTATCCTTAAAAAACTATTGAATGTAGTTCTTG
562724 AGTGTGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (41 bp):
TTTTTTATCCTTAAAAAACTATTGAATGTAGTTCTTGTTTC
Found at i:563704 original size:25 final size:25
Alignment explanation
Indices: 563661--563709 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
563651 TTAAAAATTA
*
563661 AAAATTTATTTTATTTTTAATATAT
1 AAAATTTATATTATTTTTAATATAT
563686 AAAATTTA-ATTATTATTTAATATA
1 AAAATTTATATTATT-TTTAATATA
563710 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AAAATTTATATTATTTTTAATATAT
Found at i:563812 original size:21 final size:21
Alignment explanation
Indices: 563786--563846 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 21
563776 TATATTTTTA
563786 TAAAATTAAATATAATAAATT
1 TAAAATTAAATATAATAAATT
563807 TAAAA-TAATATATTAA-AAATT
1 TAAAATTAA-ATA-TAATAAATT
* *
563828 TTATATATATAATATAATA
1 TAAAAT-TA-AATATAATA
563847 TAGAAGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
20 3 0.09
21 16 0.50
22 6 0.19
23 6 0.19
24 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATTAAATATAATAAATT
Found at i:564000 original size:22 final size:21
Alignment explanation
Indices: 563966--564006 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
563956 TCAAAAATTG
*
563966 AAAATTTCAGGAAATAAAATA
1 AAAATTTCAGGAAAAAAAATA
*
563987 AAAATTTTAGGGAAAAAAAA
1 AAAATTTCA-GGAAAAAAAA
564007 GAGTTAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAATTTCAGGAAAAAAAATA
Found at i:564558 original size:3 final size:3
Alignment explanation
Indices: 564552--564577 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
564542 GGAAGAAGAA
564552 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
564578 AGAAGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:564603 original size:9 final size:9
Alignment explanation
Indices: 564549--564604 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
564539 AAAGGAAGAA
564549 GAAGATGAT
1 GAAGATGAT
*
564558 GATGATGAT
1 GAAGATGAT
*
564567 GATGATGAT
1 GAAGATGAT
* *
564576 GAAGAAGAA
1 GAAGATGAT
* *
564585 GGAGAAGAT
1 GAAGATGAT
564594 GAAGATGAT
1 GAAGATGAT
564603 GA
1 GA
564605 TGGAAAAGAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.20
Consensus pattern (9 bp):
GAAGATGAT
Found at i:575788 original size:23 final size:22
Alignment explanation
Indices: 575762--575830 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
575752 GGTAACATCC
575762 AATAAGTATAAAATTTGACTTTT
1 AATAAGTATAAAATTTGA-TTTT
** * **
575785 AATATTTTTAAAGAGATGATATTT
1 AATAAGTATAAA-ATTTGAT-TTT
*
575809 AATAAGTATGAAATTTGATTTT
1 AATAAGTATAAAATTTGATTTT
575831 TAACATACGT
Statistics
Matches: 33, Mismatches: 11, Indels: 5
0.67 0.22 0.10
Matches are distributed among these distances:
22 3 0.09
23 15 0.45
24 15 0.45
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (22 bp):
AATAAGTATAAAATTTGATTTT
Found at i:586976 original size:11 final size:12
Alignment explanation
Indices: 586960--586995 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
586950 AATAAAAAAT
586960 ATTTTATT-TAA
1 ATTTTATTATAA
586971 ATTTTATTATAA
1 ATTTTATTATAA
*
586983 ATATTATTATAA
1 ATTTTATTATAA
586995 A
1 A
586996 AATAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTATTATAA
Found at i:587042 original size:32 final size:32
Alignment explanation
Indices: 586980--587069 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
586970 AATTTTATTA
* * *
586980 TAAATATTATTATAAA-AATAATTTTTAATTTT
1 TAAATATTATTTTAAATAATAA-TATAAATTTT
*
587012 TTAATATTATTTTAAATAATAATATAAATTTT
1 TAAATATTATTTTAAATAATAATATAAATTTT
587044 TAAAT-TTA-TTT-AAT-ATAAATATAAAT
1 TAAATATTATTTTAAATAAT-AATATAAAT
587070 AAAAAATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.04
29 12 0.24
30 3 0.06
31 3 0.06
32 26 0.51
33 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAAATATTATTTTAAATAATAATATAAATTTT
Found at i:587377 original size:21 final size:21
Alignment explanation
Indices: 587353--587398 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
587343 ACGTAACGTG
* *
587353 AATAAAATATTAAAAA-ATTTA
1 AATAAAA-AATAAAAATATATA
587374 AATAAAAAATAAAAATATATA
1 AATAAAAAATAAAAATATATA
587395 AATA
1 AATA
587399 TATGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAAAAATAAAAATATATA
Found at i:594287 original size:37 final size:37
Alignment explanation
Indices: 594237--594307 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
594227 CCACCCAAGC
*
594237 ATATACCCTAAACTCAAGTCCTTCATTCTTCTAAAGG
1 ATATACCCTAAACTCAAGTCCTTCATGCTTCTAAAGG
*
594274 ATATACCCTAAACTCAAGTTCTTCATGCTTCTAA
1 ATATACCCTAAACTCAAGTCCTTCATGCTTCTAA
594308 GGTTTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (37 bp):
ATATACCCTAAACTCAAGTCCTTCATGCTTCTAAAGG
Found at i:597396 original size:2 final size:2
Alignment explanation
Indices: 597391--597417 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
597381 GGGGGGGGGG
597391 GA 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 GA G
597418 GGTTGCCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:598034 original size:18 final size:18
Alignment explanation
Indices: 597992--598052 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
597982 TGTCTCAGAA
597992 ATATAATATAATAAAAAAT
1 ATATAATATAA-AAAAAAT
* * *
598011 AAATAATATAACATAAAT
1 ATATAATATAAAAAAAAT
*
598029 ATATAA-ATTAATAAAAAT
1 ATATAATA-TAAAAAAAAT
598047 ATATAA
1 ATATAA
598053 ATTATTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 1 0.03
18 24 0.69
19 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAATATAAAAAAAAT
Found at i:598729 original size:16 final size:15
Alignment explanation
Indices: 598693--598743 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
598683 TTATATAAAT
598693 AAAATATAA-AATATA
1 AAAATA-AATAATATA
*
598708 ATAATAAGATTAA-ATA
1 AAAATAA-A-TAATATA
598724 AAAATAAATAATATA
1 AAAATAAATAATATA
598739 AAAAT
1 AAAAT
598744 TTATATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 15 0.50
16 9 0.30
17 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAATAAATAATATA
Found at i:598753 original size:31 final size:31
Alignment explanation
Indices: 598680--598754 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
598670 TGATCTACAT
*
598680 AATTTATATAAAT-AAAATATAAAATATAAT
1 AATTTATATAAATAAAAATATAAAATATAAA
* *
598710 AA-TAAGATTAAATAAAAATA-AATAATATAAA
1 AATTTATA-TAAATAAAAATATAA-AATATAAA
598741 AATTTATATAAATA
1 AATTTATATAAATA
598755 TATAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
29 3 0.08
30 9 0.25
31 21 0.58
32 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (31 bp):
AATTTATATAAATAAAAATATAAAATATAAA
Found at i:602724 original size:24 final size:24
Alignment explanation
Indices: 602696--602748 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
602686 AATGAGTGGT
602696 ATTTTTTAAAAAAAAAAGTAAG-A
1 ATTTTTTAAAAAAAAAAGTAAGCA
** *
602719 ATTTTTT-AATTAAAAATTAAGCA
1 ATTTTTTAAAAAAAAAAGTAAGCA
602742 ATTTTTT
1 ATTTTTT
602749 TAAGTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
ATTTTTTAAAAAAAAAAGTAAGCA
Found at i:602733 original size:23 final size:24
Alignment explanation
Indices: 602696--602759 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
602686 AATGAGTGGT
*
602696 ATTTTTTAAAAAAAAAAGTAAG-A
1 ATTTTTTAAATAAAAAAGTAAGCA
* *
602719 ATTTTTT-AATTAAAAATTAAGCA
1 ATTTTTTAAATAAAAAAGTAAGCA
*
602742 ATTTTTTTAAGTAAAAAA
1 A-TTTTTTAAATAAAAAA
602760 AACTATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 11 0.33
23 9 0.27
24 6 0.18
25 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (24 bp):
ATTTTTTAAATAAAAAAGTAAGCA
Found at i:602749 original size:24 final size:22
Alignment explanation
Indices: 602708--602758 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
602698 TTTTTAAAAA
*
602708 AAAAAGTAAGAATTTTTTAATT
1 AAAAAGTAAGAATTTTTTAAGT
*
602730 AAAAATTAAGCAATTTTTTTAAGT
1 AAAAAGTAAG-AA-TTTTTTAAGT
602754 AAAAA
1 AAAAA
602759 AAACTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (22 bp):
AAAAAGTAAGAATTTTTTAAGT
Found at i:602808 original size:20 final size:19
Alignment explanation
Indices: 602785--602833 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
602775 GTGAGACTCT
*
602785 TAATTTTATATTTATTTTAA
1 TAATTTTATAGTT-TTTTAA
*
602805 TAATTTATTTAGTTTTTTAA
1 TAATTT-TATAGTTTTTTAA
*
602825 TAAATTTAT
1 TAATTTTAT
602834 TAATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TAATTTTATAGTTTTTTAA
Found at i:602813 original size:17 final size:19
Alignment explanation
Indices: 602793--602834 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
602783 CTTAATTTTA
602793 TATTTA-TTTTAAT-AATT
1 TATTTATTTTTAATAAATT
602810 TATTTAGTTTTTTAATAAATT
1 TATTTA--TTTTTAATAAATT
602831 TATT
1 TATT
602835 AATTATATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTATTTTTAATAAATT
Found at i:604957 original size:19 final size:19
Alignment explanation
Indices: 604905--604962 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
604895 TAATAAAATA
* *
604905 TTTATTTGTTTG-TATTTAA
1 TTTA-TTGTTTGAAATTTAT
* *
604924 TTTATTATTTAAAATTTAT
1 TTTATTGTTTGAAATTTAT
*
604943 TTTATTGTTTGAAATATAT
1 TTTATTGTTTGAAATTTAT
604962 T
1 T
604963 AAAAAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTATTGTTTGAAATTTAT
Found at i:605263 original size:14 final size:14
Alignment explanation
Indices: 605244--605271 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
605234 AATTTTAAAA
605244 AATATTTTTATATT
1 AATATTTTTATATT
605258 AATATTTTTATATT
1 AATATTTTTATATT
605272 TTATAATTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:606120 original size:20 final size:20
Alignment explanation
Indices: 606097--606134 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
606087 TAAACTATGT
606097 GATATATATATATATATAGA
1 GATATATATATATATATAGA
* *
606117 GATATATTTATATTTATA
1 GATATATATATATATATA
606135 TTATTAACTA
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:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
GATATATATATATATATAGA
Found at i:606684 original size:22 final size:21
Alignment explanation
Indices: 606645--606685 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
606635 TTAATTATAA
**
606645 TAAATTATTAAATTAAATATT
1 TAAATTATTAAAAAAAATATT
606666 TAAATTTATTAAAAAAAATA
1 TAAA-TTATTAAAAAAAATA
606686 ATTTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTATTAAAAAAAATATT
Found at i:607921 original size:15 final size:16
Alignment explanation
Indices: 607890--607922 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
607880 AAATAAAATC
607890 ATGAATGAAATTATTT
1 ATGAATGAAATTATTT
*
607906 ATGAATTAAA-TATTT
1 ATGAATGAAATTATTT
607921 AT
1 AT
607923 TTTAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
ATGAATGAAATTATTT
Found at i:608937 original size:21 final size:18
Alignment explanation
Indices: 608913--608956 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
608903 ATGTTTTCTC
608913 TTTTGGTTACTGCATCTCCTG
1 TTTTGGTT--TGCA-CTCCTG
*
608934 TTTTGGTTTGCACTGCTG
1 TTTTGGTTTGCACTCCTG
608952 TTTTG
1 TTTTG
608957 CTTGGTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 4 0.18
21 8 0.36
ACGTcount: A:0.07, C:0.18, G:0.23, T:0.52
Consensus pattern (18 bp):
TTTTGGTTTGCACTCCTG
Found at i:609770 original size:375 final size:370
Alignment explanation
Indices: 609080--610200 Score: 1575
Period size: 375 Copynumber: 3.0 Consensus size: 370
609070 TTATGTTGTT
** *
609080 GAGAGAGATGTTGGTGGTGGTGATTTTGTTATAGAAAGACATGTAAGAAAGAGGTGGGATATAGT
1 GAGAGAGATGTTGGTGGTGACGATTTTGTTATAGAAAGACATGTAGGAAAGAGGTGGGATATAGT
* * * * ** * * ** *
609145 -AGAGAATGCTGATGAGAATGCTAGTTTGGTCGATCGTGAGATTAGTAAAGCCGAGGAAGACGAT
66 CA-AGAATGTTGATGAGAAAGTTAGTTTGGTTGATAATGAGGTTAGTGAAGTTGAGGAAGATGAT
* * * * *
609209 GGTTCAGTTTGTAAGAAGCCGTTAGTTGATGAGGATTTGGATTCTATGGGTACTCATTGTGAGAA
130 GGTTCAGTTCGTTATAAGCTGTTAGTTGATGAGGATTTGGATTCTATGGGTATTCATTGTGAGAA
* * * * ** * **
609274 TGGAGTGATTCATGGGGGGGAGGGAATGTTGAATGATTTGTTACTGGATTATAAGAGGGAAAAAG
195 TGGAGTGATTGA-CGTGGAG-GGGAATGTTGAATGATTTGTT-C-GGAGAAGAAGAGGGAAAATC
* * *
609339 AGGACGAGATGCTGGGGAGTGCATGTGTATTGGGTATGGGGGAGCCTGCGGAGGATCAACATCTT
256 AGGAGGAGATGCTGGGGAGTG-AAGTGTATTGAGTATGGGGGAGCCTGCGGAGGATCAACATCTT
*
609404 TTGGCAGATGAGGTACATGATAGGAATCTTCAAGTAGACAATGGTAAATTC
320 TTGGCAGATGAGGTACATGATAGGAATCTTGAAGTAGACAATGGTAAATTC
* *
609455 GAGAGAGATGTTGGTGGTGACGATTTTGTTTTAGGAAGACATGTAGGAAAGAGGTGGGATATAGT
1 GAGAGAGATGTTGGTGGTGACGATTTTGTTATAGAAAGACATGTAGGAAAGAGGTGGGATATAGT
609520 CAAGAATGTTGATGAGAAAGTTAGTTTGGTTGATAATGAGGTTAGTGAAGTTGAGGAAGATGATG
66 CAAGAATGTTGATGAGAAAGTTAGTTTGGTTGATAATGAGGTTAGTGAAGTTGAGGAAGATGATG
* * *
609585 GTTCAGTTCGTTATAAGCTGTTAGTTGATGAGAATGTGGATTCTATGGGTATTCATTGTGAAAAT
131 GTTCAGTTCGTTATAAGCTGTTAGTTGATGAGGATTTGGATTCTATGGGTATTCATTGTGAGAAT
609650 GGAGTGATTGACGTGATGAGGGGAATGTTGAATGATTTGTTGGCGGAGAAGAAGAGGGAAAATCA
196 GGAGTGATTGACGTG--GAGGGGAATGTTGAATGATTTGTT--CGGAGAAGAAGAGGGAAAATCA
* *
609715 GGAGGAGATGCTGGGGAGTGAAGCTGTATTCAGCATGGGGGAGCCTGCGGAGGATCAACATCTTT
257 GGAGGAGATGCTGGGGAGTGAAG-TGTATTGAGTATGGGGGAGCCTGCGGAGGATCAACATCTTT
* *
609780 TGGCAGATGAGGTACATGGTAGGAATCTTGAAGTGGACAATGGTAAATTC
321 TGGCAGATGAGGTACATGATAGGAATCTTGAAGTAGACAATGGTAAATTC
* * *
609830 AAGAGAGATGTTGGTGGTGACGATTTTGTTGTAGAAAGACGTGTAGGAAAGAGGTGGGATAT-GT
1 GAGAGAGATGTTGGTGGTGACGATTTTGTTATAGAAAGACATGTAGGAAAGAGGTGGGATATAG-
*
609894 TCGAGAATGTTGATGAGAAAGTTAGTTTGGTTGATAATGAGGTTAGTGAAGTTGAGGAAGATGAT
65 TCAAGAATGTTGATGAGAAAGTTAGTTTGGTTGATAATGAGGTTAGTGAAGTTGAGGAAGATGAT
* * * *
609959 GTTTCAGTTCGTTATAAGCTGTTAGTAGATGAGGATTTGGATTCTATGGGTTTTCATCGTGAGAA
130 GGTTCAGTTCGTTATAAGCTGTTAGTTGATGAGGATTTGGATTCTATGGGTATTCATTGTGAGAA
* * *
610024 TGGAGTGATTGATGGCGTGGA-GGGAATGCTGAATGATTTGTT-GGAGAAGAAGAGGGAAATTCT
195 TGGAGTGATTGA---CGTGGAGGGGAATGTTGAATGATTTGTTCGGAGAAGAAGAGGGAAAATCA
610087 GGAGGAGATGCTGGGGAGTGAAGGTGTATTGAGTATGGGGGAGCCTGCGGAGGATCAACATCTTT
257 GGAGGAGATGCTGGGGAGTGAA-GTGTATTGAGTATGGGGGAGCCTGCGGAGGATCAACATCTTT
* **
610152 TGGCAGATGAGGTACATGATAGGAATCTTGAAGCAGATGATGGTAAATT
321 TGGCAGATGAGGTACATGATAGGAATCTTGAAGTAGACAATGGTAAATT
610201 TGCAGCGAAT
Statistics
Matches: 672, Mismatches: 64, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
372 124 0.18
373 1 0.00
374 5 0.01
375 532 0.79
376 6 0.01
378 4 0.01
ACGTcount: A:0.29, C:0.07, G:0.35, T:0.29
Consensus pattern (370 bp):
GAGAGAGATGTTGGTGGTGACGATTTTGTTATAGAAAGACATGTAGGAAAGAGGTGGGATATAGT
CAAGAATGTTGATGAGAAAGTTAGTTTGGTTGATAATGAGGTTAGTGAAGTTGAGGAAGATGATG
GTTCAGTTCGTTATAAGCTGTTAGTTGATGAGGATTTGGATTCTATGGGTATTCATTGTGAGAAT
GGAGTGATTGACGTGGAGGGGAATGTTGAATGATTTGTTCGGAGAAGAAGAGGGAAAATCAGGAG
GAGATGCTGGGGAGTGAAGTGTATTGAGTATGGGGGAGCCTGCGGAGGATCAACATCTTTTGGCA
GATGAGGTACATGATAGGAATCTTGAAGTAGACAATGGTAAATTC
Found at i:611614 original size:156 final size:156
Alignment explanation
Indices: 611328--611622 Score: 362
Period size: 156 Copynumber: 1.9 Consensus size: 156
611318 GAGTCTGTGG
* * * ***
611328 ATGTTGTCCAAGCCGAGAATAGAGATGTTCATCATGATGTGGTTGAGATCACATTGGGAGACAGA
1 ATGTTGACCAAGCCGAAAATAGAGATGTTCATCATGATGTGATTGAGATCACATCAAGAGACAGA
* * * **
611393 GAAAGTCAGCTGGAAATGGAATCAAATTTGTCTGAAGCTGGAGCAGCTACTCATTCAGAGTTCAA
66 GAAAGTCAGCGGGAAATGGAACCAAATTTGTCTGAAGCTGGAGCAACTACTCATTCAGAACTCAA
*
611458 TGCAAGTGATATTGAATCAACTATTC
131 TCCAAGTGATATTGAATCAACTATTC
* ***
611484 ATGTTGACCAAGCTGAAAATAGAGATGTTCATCATGATGTGATT-AGCATCACATCAAGAGGTGG
1 ATGTTGACCAAGCCGAAAATAGAGATGTTCATCATGATGTGATTGAG-ATCACATCAAGAGACAG
* * * *
611548 AGAAATTCAGCGGGAATTGGAACCAGATTTGTCTGAAGCTCGG-GCAACTACTCATAT-GGAACT
65 AGAAAGTCAGCGGGAAATGGAACCAAATTTGTCTGAAGCT-GGAGCAACTACTCAT-TCAGAACT
611611 CAATCCAAGTGA
128 CAATCCAAGTGA
611623 AATTCATCCA
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
155 2 0.02
156 111 0.96
157 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (156 bp):
ATGTTGACCAAGCCGAAAATAGAGATGTTCATCATGATGTGATTGAGATCACATCAAGAGACAGA
GAAAGTCAGCGGGAAATGGAACCAAATTTGTCTGAAGCTGGAGCAACTACTCATTCAGAACTCAA
TCCAAGTGATATTGAATCAACTATTC
Found at i:614259 original size:2 final size:2
Alignment explanation
Indices: 614252--614298 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
614242 TTGACCTTGA
*
614252 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
614295 AT AT
1 AT AT
614299 TTGTAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:616157 original size:2 final size:2
Alignment explanation
Indices: 616150--616177 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
616140 CGGTCAGATT
616150 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
616178 TTACCGTTAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:624835 original size:44 final size:44
Alignment explanation
Indices: 624779--624862 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
624769 CTTTAAAGGA
624779 ATAAATCAAACTTTTTTTATAA-AAATAATCACTATTAAATTACT
1 ATAAATCAAAC-TTTTTTATAAGAAATAATCACTATTAAATTACT
* ** *
624823 ATAAATCTAACTTTTTTATAAGATTTAATTACTATTAAAT
1 ATAAATCAAACTTTTTTATAAGAAATAATCACTATTAAAT
624863 AATAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 10 0.29
44 25 0.71
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (44 bp):
ATAAATCAAACTTTTTTATAAGAAATAATCACTATTAAATTACT
Found at i:631846 original size:6 final size:6
Alignment explanation
Indices: 631835--631877 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
631825 TAGTAACTAC
*
631835 TATAAT TATAAT TGTAAT TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT TATAAT T
631878 CTATTCTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
TATAAT
Found at i:634608 original size:17 final size:18
Alignment explanation
Indices: 634586--634629 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
634576 ATAAAAATTT
634586 TAAAAAAA-ATTATAAAA
1 TAAAAAAATATTATAAAA
634603 TAAAAAAATTGATTATAAAA
1 TAAAAAAA-T-ATTATAAAA
634623 TAAAAAA
1 TAAAAAA
634630 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
20 16 0.67
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
TAAAAAAATATTATAAAA
Found at i:635107 original size:21 final size:22
Alignment explanation
Indices: 635083--635123 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
635073 TTAATATTAA
635083 ATTTTAAAA-TTTTTATTTACT
1 ATTTTAAAATTTTTTATTTACT
635104 ATTTTAAAATTTTTTATTTA
1 ATTTTAAAATTTTTTATTTA
635124 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTAAAATTTTTTATTTACT
Found at i:635129 original size:22 final size:21
Alignment explanation
Indices: 635081--635130 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
635071 ATTTAATATT
635081 AAATTTTAAAATTTTTATTTA
1 AAATTTTAAAATTTTTATTTA
**
635102 CTATTTTAAAATTTTTTATTTA
1 AAATTTTAAAA-TTTTTATTTA
635124 AAATTTT
1 AAATTTT
635131 TTTCTCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
AAATTTTAAAATTTTTATTTA
Found at i:635140 original size:16 final size:14
Alignment explanation
Indices: 635106--635132 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
635096 TATTTACTAT
635106 TTTAAAATTTTTTA
1 TTTAAAATTTTTTA
635120 TTTAAAATTTTTT
1 TTTAAAATTTTTT
635133 TCTCTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAAAATTTTTTA
Found at i:637626 original size:17 final size:17
Alignment explanation
Indices: 637587--637628 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
637577 ATCCACTGGA
637587 GGAAAGCATCTCAAGTT
1 GGAAAGCATCTCAAGTT
* *
637604 GCAAAGCATGTC-AGTTT
1 GGAAAGCATCTCAAG-TT
637621 GGAAAGCA
1 GGAAAGCA
637629 AACAAGGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (17 bp):
GGAAAGCATCTCAAGTT
Found at i:640645 original size:12 final size:12
Alignment explanation
Indices: 640628--640654 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
640618 TAAAAATTAA
640628 AAATTCAAATTC
1 AAATTCAAATTC
640640 AAATTCAAATTC
1 AAATTCAAATTC
640652 AAA
1 AAA
640655 AAATAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTCAAATTC
Found at i:640821 original size:27 final size:26
Alignment explanation
Indices: 640749--640821 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
640739 ATAAAATTAA
* * *
640749 AAAATAAGAGCATGGGAAAAGAAATGG
1 AAAATACG-GCATGGGAAAGGAAATAG
640776 AAAATACGGCATGGGAAAGGAAATAG
1 AAAATACGGCATGGGAAAGGAAATAG
* *
640802 AAAATGCATGCATGGGAAAG
1 AAAATAC-GGCATGGGAAAG
640822 CATAAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 22 0.55
27 18 0.45
ACGTcount: A:0.51, C:0.07, G:0.30, T:0.12
Consensus pattern (26 bp):
AAAATACGGCATGGGAAAGGAAATAG
Found at i:640861 original size:50 final size:51
Alignment explanation
Indices: 640807--640921 Score: 223
Period size: 51 Copynumber: 2.3 Consensus size: 51
640797 AATAGAAAAT
640807 GCATGCATGGGAAAGCAT-AAAAATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAAATTGCAATTGGAGACAAAACATGCAGAG
640857 GCATGCATGGGAAAGCATAAAAAATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAAATTGCAATTGGAGACAAAACATGCAGAG
640908 GCATGCATGGGAAA
1 GCATGCATGGGAAA
640922 TGAAAAAGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 18 0.28
51 46 0.72
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (51 bp):
GCATGCATGGGAAAGCATAAAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:641547 original size:16 final size:18
Alignment explanation
Indices: 641510--641548 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
641500 AGCACGCAAC
641510 AGCAACTCCAGCGAGAGT
1 AGCAACTCCAGCGAGAGT
641528 AGCAACTCCAGC-AG-GT
1 AGCAACTCCAGCGAGAGT
641544 AGCAA
1 AGCAA
641549 TTTAATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 12 0.57
ACGTcount: A:0.36, C:0.28, G:0.26, T:0.10
Consensus pattern (18 bp):
AGCAACTCCAGCGAGAGT
Found at i:642590 original size:79 final size:79
Alignment explanation
Indices: 642455--642962 Score: 827
Period size: 79 Copynumber: 6.4 Consensus size: 79
642445 GTTAAGTTTC
* *
642455 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
642520 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * * *
642534 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTACGAGGGAATATTCCAACCCCGATT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
642599 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * ** *
642613 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTTCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
642678 TTATTTCTAAAACA
66 TTATTTCTAAAACA
642692 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
642757 TTATTTCTAAAACA
66 TTATTTCTAAAACA
* * *
642771 TCAATTTTTCATAATCGGGGATACTCCAACTCCGTTATTTACGAGGGGATATTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
642836 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * *
642850 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
642915 TTGTTTCTAAAACA
66 TTATTTCTAAAACA
*
642929 TCAATTTTTCATAATCGGGGATACTCTAACCCCG
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCG
642963 ATTTTATTTT
Statistics
Matches: 393, Mismatches: 36, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 393 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Found at i:642870 original size:237 final size:237
Alignment explanation
Indices: 642455--642962 Score: 917
Period size: 237 Copynumber: 2.1 Consensus size: 237
642445 GTTAAGTTTC
*
642455 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
642520 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTACGAGGGAATA
66 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTACGAGGGAATA
642585 TTCCAACCCCGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
131 TTCCAACCCCGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
** *
642650 TTTTTGAGGGGATACTTCAACCCCGGTTTTATTTCTAAAACA
196 TTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
*
642692 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
* *
642757 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCGTTATTTACGAGGGGATA
66 TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTACGAGGGAATA
*
642822 TTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
131 TTCCAACCCCGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
* *
642887 TTTCCGAGGGGATACTCCAACCTCGGTTTTGTTTCTAAAACA
196 TTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
*
642929 TCAATTTTTCATAATCGGGGATACTCTAACCCCG
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCG
642963 ATTTTATTTT
Statistics
Matches: 260, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
237 260 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (237 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCT
TTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTACGAGGGAATA
TTCCAACCCCGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
TTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
Found at i:644758 original size:2 final size:2
Alignment explanation
Indices: 644736--644784 Score: 62
Period size: 2 Copynumber: 23.0 Consensus size: 2
644726 CATTGTGCAA
*
644736 AT AT CAT AT CAT AT CAT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT -AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
644779 AT AT AT
1 AT AT AT
644785 GTATCTTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 36 0.86
3 6 0.14
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:648049 original size:11 final size:11
Alignment explanation
Indices: 648035--648075 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
648025 CATTTCATAT
648035 TTTTTTCTTTC
1 TTTTTTCTTTC
648046 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
648059 TTCTTTCTTTC
1 TTTTTTCTTTC
648070 TTTTTT
1 TTTTTT
648076 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Done.