Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold285
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: 926752
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
File 4 of 6
Found at i:487962 original size:13 final size:13
Alignment explanation
Indices: 487944--487968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487934 TTTTTATTTG
487944 AATTATTTTATAA
1 AATTATTTTATAA
487957 AATTATTTTATA
1 AATTATTTTATA
487969 CGATTTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTATTTTATAA
Found at i:488010 original size:35 final size:32
Alignment explanation
Indices: 487971--488043 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
487961 ATTTTATACG
* *
487971 ATTTAATTTATTAATAATAAAAATTTAATAATATA
1 ATTTAATTGATTAAT-AT-AAAAGTTAATAATA-A
*
488006 ATTTAA-TGATTTATATAAAAGTTAATAATAA
1 ATTTAATTGATTAATATAAAAGTTAATAATAA
488037 ATTTAAT
1 ATTTAAT
488044 AAATCAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 7 0.21
32 13 0.38
33 2 0.06
34 6 0.18
35 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
ATTTAATTGATTAATATAAAAGTTAATAATAA
Found at i:495858 original size:30 final size:30
Alignment explanation
Indices: 495803--495859 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
495793 AAGAGACAAG
*
495803 AATTTTACATTGATTGTATATTAAAATATA
1 AATTTTACATTGATTGTACATTAAAATATA
*
495833 AATTTTCCATTGATTGTACCA-TAAAAT
1 AATTTTACATTGATTGTA-CATTAAAAT
495860 TTAATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (30 bp):
AATTTTACATTGATTGTACATTAAAATATA
Found at i:499620 original size:20 final size:20
Alignment explanation
Indices: 499592--499635 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
499582 AAATACTAAT
*
499592 TTAAGTAATAATATATACAG
1 TTAAATAATAATATATACAG
499612 TTAAATAATAATATATACAG
1 TTAAATAATAATATATACAG
499632 TTAA
1 TTAA
499636 TCTAGTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (20 bp):
TTAAATAATAATATATACAG
Found at i:501276 original size:15 final size:16
Alignment explanation
Indices: 501252--501294 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
501242 TAATCACTTT
*
501252 AAATATATAAATTATA
1 AAATATATAAAATATA
501268 AAATA-ATAAAATATA
1 AAATATATAAAATATA
501283 AAAT-TA-AAAATA
1 AAATATATAAAATA
501295 ATTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATATAAAATATA
Found at i:503618 original size:21 final size:21
Alignment explanation
Indices: 503589--503792 Score: 199
Period size: 21 Copynumber: 10.0 Consensus size: 21
503579 AATAGCTCGC
* * *
503589 AATAAAATTTTAGTAACTTTT
1 AATATAATTTTAATAATTTTT
503610 AATATAATTTTAATAATTTTT
1 AATATAATTTTAATAATTTTT
*
503631 TATATAATTTTAATAATTTTT
1 AATATAATTTTAATAATTTTT
* *
503652 AATAAAATTTCAATAA-TTTT
1 AATATAATTTTAATAATTTTT
*
503672 -ATATAATTTTCA-AATTTTT
1 AATATAATTTTAATAATTTTT
* *
503691 AATATAATTTTGA-AATCATTT
1 AATATAATTTTAATAAT-TTTT
*
503712 AATATAATTTCAATAA-TTTT
1 AATATAATTTTAATAATTTTT
503732 -ATATAATTTTAA-AATTTTT
1 AATATAATTTTAATAATTTTT
***
503751 AATATAATTTTGAA-AGCATTT
1 AATATAATTTT-AATAATTTTT
* *
503772 AATATAATTTTGATATTTTTT
1 AATATAATTTTAATAATTTTT
503793 TGTAATTATT
Statistics
Matches: 152, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.03
19 28 0.18
20 32 0.21
21 86 0.57
22 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATAATTTTAATAATTTTT
Found at i:503694 original size:81 final size:81
Alignment explanation
Indices: 503605--503809 Score: 229
Period size: 81 Copynumber: 2.5 Consensus size: 81
503595 ATTTTAGTAA
*
503605 CTTTTAATATAATTTTAATAATTTTTTATATAATTTTAATAATTTTTAATAAAATTTCAATAA-T
1 CTTTTAATATAATTTTGATAATTTTTTATATAATTTTAATAA-TTTT-ATAAAATTTCAA-AATT
503669 TTT-ATATAATTTTCAAA-
63 TTTAATATAATTTTCAAAG
* * * * * *
503686 TTTTTAATATAATTTTGA-AATCATTTAATATAATTTCAATAATTTTATATAATTTTAAAATTTT
1 CTTTTAATATAATTTTGATAAT-TTTTTATATAATTTTAATAATTTTATAAAATTTCAAAATTTT
*
503750 TAATATAATTTTGAAAG
65 TAATATAATTTTCAAAG
* * * *
503767 CATTTAATATAATTTTGATATTTTTTTGTAATTATTTTAATAA
1 CTTTTAATATAATTTTGATAATTTTTTAT-ATAATTTTAATAA
503810 CATTGATATA
Statistics
Matches: 102, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
78 2 0.02
79 14 0.14
80 20 0.20
81 53 0.52
82 13 0.13
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (81 bp):
CTTTTAATATAATTTTGATAATTTTTTATATAATTTTAATAATTTTATAAAATTTCAAAATTTTT
AATATAATTTTCAAAG
Found at i:503749 original size:8 final size:10
Alignment explanation
Indices: 503606--503761 Score: 103
Period size: 10 Copynumber: 15.4 Consensus size: 10
503596 TTTTAGTAAC
503606 TTTTAATATAA
1 TTTT-ATATAA
503617 TTTTA-ATAA
1 TTTTATATAA
503626 TTTTTTATATAA
1 --TTTTATATAA
503638 TTTTA-ATAA
1 TTTTATATAA
*
503647 TTTTTAATAAAA
1 -TTTT-ATATAA
*
503659 TTTCA-ATAA
1 TTTTATATAA
503668 TTTTATATAA
1 TTTTATATAA
*
503678 TTTTCA-A-AT
1 TTTT-ATATAA
503687 TTTTAATATAA
1 TTTT-ATATAA
* *
503698 TTTTGAAATCA
1 TTTT-ATATAA
*
503709 TTTAATATAA
1 TTTTATATAA
*
503719 TTTCA-ATAA
1 TTTTATATAA
503728 TTTTATATAA
1 TTTTATATAA
503738 TTTTA-A-AA
1 TTTTATATAA
503746 TTTTTAATATAA
1 -TTTT-ATATAA
503758 TTTT
1 TTTT
503762 GAAAGCATTT
Statistics
Matches: 115, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.02
9 34 0.30
10 39 0.34
11 31 0.27
12 9 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (10 bp):
TTTTATATAA
Found at i:503773 original size:30 final size:30
Alignment explanation
Indices: 503683--503773 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
503673 TATAATTTTC
503683 AAATTTTTAATATAATTTTGAAATCATTTA
1 AAATTTTTAATATAATTTTGAAATCATTTA
* * * * *
503713 ATATAATTTCA-ATAATTTT-ATATAATTTTA
1 AAAT-TTTTAATATAATTTTGAAATCA-TTTA
*
503743 AAATTTTTAATATAATTTTGAAAGCATTTA
1 AAATTTTTAATATAATTTTGAAATCATTTA
503773 A
1 A
503774 TATAATTTTG
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
29 8 0.17
30 31 0.67
31 7 0.15
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
AAATTTTTAATATAATTTTGAAATCATTTA
Found at i:503799 original size:60 final size:60
Alignment explanation
Indices: 503606--503781 Score: 255
Period size: 60 Copynumber: 2.9 Consensus size: 60
503596 TTTTAGTAAC
* ** *
503606 TTTTAATATAATTTTAATAATTTTTTATATAATTTT-AATAATTTTTAATAAAATTTCAATAA
1 TTTT-ATATAATTTTAA-AATTTTTAATATAATTTTGAA-AACATTTAATATAATTTCAATAA
* *
503668 TTTTATATAATTTTCAAATTTTTAATATAATTTTGAAATCATTTAATATAATTTCAATAA
1 TTTTATATAATTTTAAAATTTTTAATATAATTTTGAAAACATTTAATATAATTTCAATAA
*
503728 TTTTATATAATTTTAAAATTTTTAATATAATTTTGAAAGCATTTAATATAATTT
1 TTTTATATAATTTTAAAATTTTTAATATAATTTTGAAAACATTTAATATAATTT
503782 TGATATTTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
60 88 0.84
61 13 0.12
62 4 0.04
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (60 bp):
TTTTATATAATTTTAAAATTTTTAATATAATTTTGAAAACATTTAATATAATTTCAATAA
Found at i:503992 original size:34 final size:34
Alignment explanation
Indices: 503937--504153 Score: 274
Period size: 34 Copynumber: 6.4 Consensus size: 34
503927 TATTTAAATC
* * *
503937 TGTTGATTAAAT-GGTGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
503970 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
504004 TGTTGACTAAATGAGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
** * *
504038 TGTTGATTAAATAAGAAATTTGATAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
504072 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
504106 TGTTGACTAAATGGGAGATTTGGTAGGTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
504140 TGTTGATTAAATGG
1 TGTTGATTAAATGG
504154 TAGTTTTTAC
Statistics
Matches: 159, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
33 12 0.08
34 147 0.92
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:504129 original size:102 final size:102
Alignment explanation
Indices: 503953--504151 Score: 335
Period size: 102 Copynumber: 2.0 Consensus size: 102
503943 TTAAATGGTG
* * * * *
503953 ATTTGGTAGTTTATCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGA
1 ATTTGATAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGA
504018 GAGATTTGGTAGCTTACCATTGTTGATTAAATAAGAA
66 GAGATTTGGTAGCTTACCATTGTTGATTAAATAAGAA
*
504055 ATTTGATAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGG
1 ATTTGATAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGA
*
504120 GAGATTTGGTAGGTTACCATTGTTGATTAAAT
66 GAGATTTGGTAGCTTACCATTGTTGATTAAAT
504152 GGTAGTTTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (102 bp):
ATTTGATAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGA
GAGATTTGGTAGCTTACCATTGTTGATTAAATAAGAA
Found at i:508625 original size:34 final size:34
Alignment explanation
Indices: 508568--508785 Score: 240
Period size: 34 Copynumber: 6.4 Consensus size: 34
508558 AAGTGGGAGA
* *
508568 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
508601 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
508635 ATTGTTGACTAAATGTGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
508669 ATTGTTAATTAAATGAGAAATTTGGTAGCTTATC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
508703 ATTGTTAATTAAATGGGTGATTTGGTGGCTTATC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
508737 ATTGTTGACTAAATGAGAGATTTGGTAGGTTGCA
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
508771 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
508786 ATGGTTTTTA
Statistics
Matches: 157, Mismatches: 27, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
33 14 0.09
34 143 0.91
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:508714 original size:102 final size:102
Alignment explanation
Indices: 508567--508786 Score: 316
Period size: 102 Copynumber: 2.2 Consensus size: 102
508557 CAAGTGGGAG
** * * *
508567 AATTGTTGATTAAATG-GTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTT
1 AATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTAATTAAATGGGTGATTTGGTGGCT
* *
508631 TGCCATTGTTGACTAAATGTGAGATTTGGTAGCTTAC
66 TACCATTGTTGACTAAATGAGAGATTTGGTAGCTTAC
* * *
508668 CATTGTTAATTAAATGAGAAATTTGGTAGCTTATCATTGTTAATTAAATGGGTGATTTGGTGGCT
1 AATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTAATTAAATGGGTGATTTGGTGGCT
* * *
508733 TATCATTGTTGACTAAATGAGAGATTTGGTAGGTTGC
66 TACCATTGTTGACTAAATGAGAGATTTGGTAGCTTAC
508770 AATTGTTGATTAAATGA
1 AATTGTTGATTAAATGA
508787 TGGTTTTTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
101 14 0.14
102 89 0.86
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.41
Consensus pattern (102 bp):
AATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTAATTAAATGGGTGATTTGGTGGCT
TACCATTGTTGACTAAATGAGAGATTTGGTAGCTTAC
Found at i:511085 original size:16 final size:17
Alignment explanation
Indices: 511054--511088 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
511044 TAAAAATTTA
511054 AAAATATTACATAAAAAT
1 AAAATATTA-ATAAAAAT
511072 AAAATATT-ATAAAAAT
1 AAAATATTAATAAAAAT
511088 A
1 A
511089 TATAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATATTAATAAAAAT
Found at i:511095 original size:20 final size:20
Alignment explanation
Indices: 511043--511114 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 20
511033 TTTTTAATAA
*
511043 ATAAAAATTTA-AAAATATT
1 ATAAAAATATATAAAATATT
* *
511062 ACATAAA-A-ATAAAATATT
1 ATAAAAATATATAAAATATT
* *
511080 ATAAAAATATATAAAAGATA
1 ATAAAAATATATAAAATATT
511100 ATAAATAATTATATA
1 ATAAA-AA-TATATA
511115 TTATATTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
17 1 0.02
18 13 0.32
19 6 0.15
20 13 0.32
21 2 0.05
22 6 0.15
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (20 bp):
ATAAAAATATATAAAATATT
Found at i:511100 original size:27 final size:26
Alignment explanation
Indices: 511041--511105 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
511031 TTTTTTTAAT
511041 AAATAAAAATTTAAAAATATTACATAA
1 AAATAAAAATTTAAAAATATTA-ATAA
511068 AAATAAAATATTATAAAAATA-T-ATAA
1 AAATAAAA-ATT-TAAAAATATTAATAA
511094 AAGATAATAAAT
1 AA-ATAA-AAAT
511106 AATTATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 6 0.18
27 14 0.41
28 6 0.18
29 8 0.24
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAAAAATTTAAAAATATTAATAA
Found at i:511437 original size:21 final size:20
Alignment explanation
Indices: 511413--511458 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
511403 AAAATTAGTT
511413 ATTATAGTAATAAGATTAAAA
1 ATTATAGTAATAAGATT-AAA
* * *
511434 ATTATAGTGATGATATTAAA
1 ATTATAGTAATAAGATTAAA
511454 ATTAT
1 ATTAT
511459 TGGTTGGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
ATTATAGTAATAAGATTAAA
Found at i:511621 original size:11 final size:11
Alignment explanation
Indices: 511595--511628 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
511585 ATAATAATTA
511595 AAAATATATATT
1 AAAAT-TATATT
*
511607 AAAATTATCTT
1 AAAATTATATT
511618 AAAATTATATT
1 AAAATTATATT
511629 TATATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATTATATT
Found at i:516874 original size:18 final size:18
Alignment explanation
Indices: 516842--516891 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
516832 CTATGATTAC
* *
516842 AAAAATCTATAATTCTTA
1 AAAAATCTGTGATTCTTA
* *
516860 GAAAATTTGTGATTCTTA
1 AAAAATCTGTGATTCTTA
516878 AAAAATCTGTGATT
1 AAAAATCTGTGATT
516892 GGTACTAATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (18 bp):
AAAAATCTGTGATTCTTA
Found at i:518539 original size:12 final size:12
Alignment explanation
Indices: 518519--518566 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
518509 TTATACCAAT
*
518519 TAATAAAATTTA
1 TAATTAAATTTA
518531 TAATTAAATTTTTA
1 TAATTAAA--TTTA
* *
518545 TAATCAAATTTT
1 TAATTAAATTTA
518557 TAATTAAATT
1 TAATTAAATT
518567 AATTTGATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 19 0.63
14 11 0.37
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTAAATTTA
Found at i:518546 original size:14 final size:14
Alignment explanation
Indices: 518527--518566 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
518517 ATTAATAAAA
518527 TTTATAATTAAATT
1 TTTATAATTAAATT
*
518541 TTTATAATCAAA-T
1 TTTATAATTAAATT
518554 TTT-TAATTAAATT
1 TTTATAATTAAATT
518567 AATTTGATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 5 0.22
14 11 0.48
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATAATTAAATT
Found at i:522468 original size:21 final size:22
Alignment explanation
Indices: 522430--522475 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
522420 ATCTGTTGAA
* **
522430 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
522451 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
522473 ACT
1 ACT
522476 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:525665 original size:30 final size:30
Alignment explanation
Indices: 525609--525665 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
525599 GTAGATAACG
* * *
525609 TATAAATTTATATAATATTAATATATTAAA
1 TATAAATATAAATAATAATAATATATTAAA
525639 TATAAATATAAATAAATAATAA-ATATT
1 TATAAATATAAAT-AATAATAATATATT
525666 TATGATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
TATAAATATAAATAATAATAATATATTAAA
Found at i:525818 original size:22 final size:22
Alignment explanation
Indices: 525775--525821 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
525765 ATTTAAAAAA
* *
525775 TTATTTTTATATTGATATTTAT
1 TTATTTTTATATTGAAAATTAT
525797 TTATTTTTATCATT-AAAATTAT
1 TTATTTTTAT-ATTGAAAATTAT
525819 TTA
1 TTA
525822 AAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTTTTATATTGAAAATTAT
Found at i:526962 original size:28 final size:30
Alignment explanation
Indices: 526915--526973 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
526905 ATATAGGTTA
*
526915 TAAATTTTTAATAGT-CAAAATT-AATTAT
1 TAAATTTTTAATAGTAAAAAATTAAATTAT
* *
526943 TAAATTTTTATTATTAAAAAATTAAATTAT
1 TAAATTTTTAATAGTAAAAAATTAAATTAT
526973 T
1 T
526974 TAAGTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 6 0.23
30 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
TAAATTTTTAATAGTAAAAAATTAAATTAT
Found at i:528233 original size:34 final size:33
Alignment explanation
Indices: 528179--528397 Score: 240
Period size: 34 Copynumber: 6.5 Consensus size: 33
528169 GTGGTTTTGG
* *
528179 TGTTGATTAAATGGTGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
* * *
528212 TGTTGATTAAATTGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAA-TGGTGATTTGGTAGCTTACCAT
* *
528246 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* ** *
528280 TGTTGATTAGATGAGAAATTTGGTAGCTTATCAT
1 TGTTGATTAAATG-GTGATTTGGTAGCTTACCAT
* *
528314 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCAT
* * * *
528348 TGTTGACTAAATGGTAGATTTGGCAGGTTGCCAT
1 TGTTGATTAAATGGT-GATTTGGTAGCTTACCAT
528382 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
528398 GTTTTTACCA
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
33 17 0.11
34 138 0.88
35 1 0.01
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCAT
Found at i:528382 original size:102 final size:102
Alignment explanation
Indices: 528195--528390 Score: 311
Period size: 102 Copynumber: 1.9 Consensus size: 102
528185 TTAAATGGTG
* * * * *
528195 ATTTGGTAGTTTATCATTGTTGATTAAATTGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGG
1 ATTTGGTAGCTTATCATTATTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGG
*
528260 GAGATTTGGTAGCTTACCATTGTTGATTAGATGAGAA
66 GAGATTTGGCAGCTTACCATTGTTGATTAGATGAGAA
528297 ATTTGGTAGCTTATCATTATTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGG
1 ATTTGGTAGCTTATCATTATTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGG
* * *
528362 TAGATTTGGCAGGTTGCCATTGTTGATTA
66 GAGATTTGGCAGCTTACCATTGTTGATTA
528391 AATGGTGGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (102 bp):
ATTTGGTAGCTTATCATTATTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGG
GAGATTTGGCAGCTTACCATTGTTGATTAGATGAGAA
Found at i:532852 original size:34 final size:34
Alignment explanation
Indices: 532795--533011 Score: 267
Period size: 34 Copynumber: 6.4 Consensus size: 34
532785 AAGTGGGAGA
*
532795 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
532828 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGTC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
532862 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
532896 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
532930 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * **
532964 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
532998 ATTGTTGATTAAAT
1 ATTGTTGATTAAAT
533012 AGTGGTTTTT
Statistics
Matches: 158, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 141 0.89
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:532938 original size:102 final size:101
Alignment explanation
Indices: 532795--533011 Score: 326
Period size: 102 Copynumber: 2.1 Consensus size: 101
532785 AAGTGGGAGA
** * * * *
532795 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
*
532860 TCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
532896 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * **
532961 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGTC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
532998 ATTGTTGATTAAAT
1 ATTGTTGATTAAAT
533012 AGTGGTTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 15 0.14
102 89 0.86
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:542596 original size:39 final size:39
Alignment explanation
Indices: 542523--542599 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
542513 CTGCTTTTAG
* * *
542523 TCAAGCTAAGGCAGAAGACTTAGATTAGTGGCTATAATA
1 TCAAGCTAAGGCAAAAGACTTAAATTAGTAGCTATAATA
*
542562 TCAAGTTAAGGCAAAAGACTTAAATT-GTTAGCTATAAT
1 TCAAGCTAAGGCAAAAGACTTAAATTAG-TAGCTATAAT
542600 TAAGTCATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (39 bp):
TCAAGCTAAGGCAAAAGACTTAAATTAGTAGCTATAATA
Found at i:547301 original size:28 final size:27
Alignment explanation
Indices: 547270--547331 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 27
547260 TTTCTTACAA
547270 ACAAAAATAACCACCATATTTGACAAAT
1 ACAAAAA-AACCACCATATTTGACAAAT
*
547298 ACAAATGAAACCACCATATTTGACAAAT
1 ACAAA-AAAACCACCATATTTGACAAAT
547326 ACAAAA
1 ACAAAA
547332 GTTGGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (27 bp):
ACAAAAAAACCACCATATTTGACAAAT
Found at i:551840 original size:24 final size:25
Alignment explanation
Indices: 551798--551874 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
551788 TTTTCTAATA
* *
551798 AAAATTAGCCACAAATTTTGACAAAT
1 AAAA-TAGCCACCATTTTTGACAAAT
* * *
551824 AACA-AGCCACCATTTTTTACAAACA
1 AAAATAGCCACCATTTTTGACAAA-T
* *
551849 AAAATAACCACCATATTTGACAAAT
1 AAAATAGCCACCATTTTTGACAAAT
551874 A
1 A
551875 CAAAGGAAAC
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
24 16 0.41
25 4 0.10
26 19 0.49
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (25 bp):
AAAATAGCCACCATTTTTGACAAAT
Found at i:551877 original size:28 final size:27
Alignment explanation
Indices: 551830--551907 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
551820 AAATAACAAG
* *
551830 CCACCATTTTTTAC-AA-ACAAAAATAA
1 CCACCATATTTAACAAATACAAAAA-AA
* *
551856 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTAACAAATACAAA-AAAA
*
551884 CCATCATATTTAACAAATACAAAA
1 CCACCATATTTAACAAATACAAAA
551908 GTTGACATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 12 0.28
27 2 0.05
28 28 0.65
29 1 0.02
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.23
Consensus pattern (27 bp):
CCACCATATTTAACAAATACAAAAAAA
Found at i:554870 original size:3 final size:3
Alignment explanation
Indices: 554862--554889 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
554852 AAGGCCATTC
554862 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
554890 TTCACCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:559427 original size:2 final size:2
Alignment explanation
Indices: 559420--559473 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
559410 ATGTCCATAC
* *
559420 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AC 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
559462 AT AT AT AT AT AT
1 AT AT AT AT AT AT
559474 GTCATAGGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:559438 original size:20 final size:20
Alignment explanation
Indices: 559415--559473 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
559405 AGTATATGTC
*
559415 CATACATATATATATATATA
1 CATATATATATATATATATA
559435 CATATATATATATATATATA
1 CATATATATATATATATATA
559455 CATATATATATATATATAT
1 CATATATATATATATATAT
559474 GTCATAGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
CATATATATATATATATATA
Found at i:563011 original size:75 final size:75
Alignment explanation
Indices: 562884--563044 Score: 220
Period size: 75 Copynumber: 2.1 Consensus size: 75
562874 CTTGTTATTC
562884 GAAAGATCAAGTGTTGTAAGATTCTTCAGCTTTGAAAGCACATCTAACTTGATGACACCACTAAA
1 GAAAGATCAAGTGTTGTAAGATTCTTCAGCTTTGAAAGCACATCTAACTTGATGACACCACTAAA
562949 ATTATTTGAT
66 ATTATTTGAT
* * * * **
562959 GAAAGATCGAGTGTT-TCAAGTTTCTGT-AGTTTTGAAAGCATATCTGAA-TTGATGATGCCACT
1 GAAAGATCAAGTGTTGT-AAGATTCT-TCAGCTTTGAAAGCACATCT-AACTTGATGACACCACT
563021 AAAATTATTTGAT
63 AAAATTATTTGAT
563034 GAAAGATCAAG
1 GAAAGATCAAG
563045 ATCGATAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
74 1 0.01
75 72 0.95
76 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (75 bp):
GAAAGATCAAGTGTTGTAAGATTCTTCAGCTTTGAAAGCACATCTAACTTGATGACACCACTAAA
ATTATTTGAT
Found at i:565435 original size:20 final size:20
Alignment explanation
Indices: 565398--565436 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
565388 ACTCTTTTGC
**
565398 TTTTTAATTTTTTTTAATTG
1 TTTTTAATTTTTGATAATTG
*
565418 TTTTTACTTTTTGATAATT
1 TTTTTAATTTTTGATAATT
565437 ATATTATACG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTAATTTTTGATAATTG
Found at i:565689 original size:15 final size:14
Alignment explanation
Indices: 565661--565761 Score: 65
Period size: 12 Copynumber: 7.6 Consensus size: 14
565651 TCTGTGTAAT
565661 ATATATAATATATA
1 ATATATAATATATA
*
565675 ATATCATAATTTATA
1 ATAT-ATAATATATA
* * *
565690 TTTTTTAATCATATA
1 ATATATAAT-ATATA
565705 A-ATATAA-ATATA
1 ATATATAATATATA
565717 A-ATATAA-AT-TA
1 ATATATAATATATA
* *
565728 TTATAT-ATATTTTA
1 ATATATAATA-TATA
565742 A-ATATAA-ATATA
1 ATATATAATATATA
565754 ATATATAA
1 ATATATAA
565762 ATAATATTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.04
12 23 0.34
13 12 0.18
14 15 0.22
15 15 0.22
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATATAATATATA
Found at i:565709 original size:6 final size:6
Alignment explanation
Indices: 565700--565764 Score: 69
Period size: 6 Copynumber: 10.5 Consensus size: 6
565690 TTTTTTAATC
* * *
565700 ATATAA ATATAA ATATAA ATATAA AT-TATT ATATATA TTTTAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATATA-A ATATAA ATATAA
565749 ATATAA TATATAA ATA
1 ATATAA -ATATAA ATA
565765 ATATTAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
5 2 0.04
6 36 0.72
7 12 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATAA
Found at i:565710 original size:43 final size:43
Alignment explanation
Indices: 565663--565782 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
565653 TGTGTAATAT
* *
565663 ATATAATATATAATAT-CATAATT-TATATTTTTTAATCATATAA
1 ATATAATATATAATATAAATAATTATATATATTTTAA--ATATAA
*
565706 ATATAA-ATATAAATATAAATTATTATATATATTTTAAATATAA
1 ATATAATATAT-AATATAAATAATTATATATATTTTAAATATAA
*
565749 ATATAATATATAA-ATAATATTAATTATATTTATT
1 ATATAATATATAATATAA-A-TAATTATATATATT
565783 ACATTACTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
42 8 0.12
43 26 0.39
44 21 0.32
45 11 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (43 bp):
ATATAATATATAATATAAATAATTATATATATTTTAAATATAA
Found at i:574390 original size:14 final size:15
Alignment explanation
Indices: 574363--574392 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
574353 TAATCGCATA
574363 AAATTATATAAATAT
1 AAATTATATAAATAT
574378 AAATTAT-TAAATAT
1 AAATTATATAAATAT
574392 A
1 A
574393 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTATATAAATAT
Found at i:579238 original size:3 final size:3
Alignment explanation
Indices: 579230--579283 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
579220 ATTCAATTTT
579230 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
579278 TTC TTC
1 TTC TTC
579284 ATCCTCTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:582646 original size:28 final size:28
Alignment explanation
Indices: 582615--582670 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
582605 ATAGCTGATT
582615 TAATAGTTGTTCAACATTGTAGGTTTAG
1 TAATAGTTGTTCAACATTGTAGGTTTAG
582643 TAATAGTTGTTCAACATTGTAGGTTTAG
1 TAATAGTTGTTCAACATTGTAGGTTTAG
582671 GGTTGGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (28 bp):
TAATAGTTGTTCAACATTGTAGGTTTAG
Found at i:585488 original size:21 final size:20
Alignment explanation
Indices: 585440--585500 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
585430 TAAATAATAT
* *
585440 ATTTTATTTAA-TTATTAAAA
1 ATTTAATTTAATTTATT-TAA
585460 ATTTAATTTAATTTATTTAA
1 ATTTAATTTAATTTATTTAA
*
585480 ATTTAAATTTATATTTTTTTA
1 ATTT-AATTTA-ATTTATTTA
585501 CAAAACGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.46
21 11 0.31
22 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATTTAATTTATTTAA
Found at i:587328 original size:2 final size:2
Alignment explanation
Indices: 587321--587347 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
587311 TTGTAGAATC
587321 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
587348 AAACAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:589870 original size:2 final size:2
Alignment explanation
Indices: 589853--589903 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
589843 AACATGTTAT
* * *
589853 TA TA -A TA TA TA CA TA TA TA TA TA TA TG CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
589894 TA TA TA TA TA
1 TA TA TA TA TA
589904 ATACATCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:590850 original size:179 final size:178
Alignment explanation
Indices: 590541--590894 Score: 645
Period size: 179 Copynumber: 2.0 Consensus size: 178
590531 ATTATAAAAG
*
590541 GAACCCTAAAGTATTCTATTTTTATTATAATGAGACAGAAAAAAAGTAATGGCATCATAAATTAA
1 GAACCCTAAAGTATTCTATTTTTATTATAACGAGACAGAAAAAAAGTAATGGCATCATAAATTAA
590606 GATTGTTCAATTACAACCATATAAGCAGTCTTCAAAATTCAAGCTTATCACACTTATAGACAACA
66 GATTGTTCAATTACAACCATATAAGCAGTCTTCAAAATTCAAGCTTATCACACTTATAGACAACA
* *
590671 TGCTACAGCTCTCTTCGGATCATTTTTTAATTGCTCTAGAGCCGCATA
131 TGCTACAGCTCTCTCCAGATCATTTTTTAATTGCTCTAGAGCCGCATA
590719 GAACCCTAAAGTATTCTATTTTTATTATAACGAGACAGAAAAAAAAGTAATGGCATCATAAATTA
1 GAACCCTAAAGTATTCTATTTTTATTATAACGAGACAG-AAAAAAAGTAATGGCATCATAAATTA
* * *
590784 AGATTGTTCAATTACAACCATATAAGCAGTCTTCAAAATTCAAGCTTATCTCACTTGTATACAAC
65 AGATTGTTCAATTACAACCATATAAGCAGTCTTCAAAATTCAAGCTTATCACACTTATAGACAAC
590849 ATGCTACAGCTCTCTCCAGATCATTTTTTAATTGCTCTAGAGCCGC
130 ATGCTACAGCTCTCTCCAGATCATTTTTTAATTGCTCTAGAGCCGC
590895 TTAAAACTGT
Statistics
Matches: 169, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
178 37 0.22
179 132 0.78
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (178 bp):
GAACCCTAAAGTATTCTATTTTTATTATAACGAGACAGAAAAAAAGTAATGGCATCATAAATTAA
GATTGTTCAATTACAACCATATAAGCAGTCTTCAAAATTCAAGCTTATCACACTTATAGACAACA
TGCTACAGCTCTCTCCAGATCATTTTTTAATTGCTCTAGAGCCGCATA
Found at i:592669 original size:67 final size:67
Alignment explanation
Indices: 592567--592767 Score: 341
Period size: 67 Copynumber: 3.0 Consensus size: 67
592557 AGACTGGTAT
*
592567 AAACACATTACAAGCCCAAATCCAAGATGATGATATGCCATGTATAGAATGGACAGGTCCAGAGG
1 AAACACATTACAAGCCCAAATCCAAGATGATGATATGCCATGTATAGAATAGACAGGTCCAGAGG
592632 AC
66 AC
* * * *
592634 ATACACATTACAAGCCCCAATCCACA-ATGACGATATGCCATGTATAGAATAGAAAGGTCCAGAG
1 AAACACATTACAAGCCCAAATCCA-AGATGATGATATGCCATGTATAGAATAGACAGGTCCAGAG
592698 GAC
65 GAC
592701 AAACACATTACAAGCCCAAATCCAAGATGATGATATGCCATGTATAGAATAGACAGGTCCAGAGG
1 AAACACATTACAAGCCCAAATCCAAGATGATGATATGCCATGTATAGAATAGACAGGTCCAGAGG
592766 AC
66 AC
592768 TGAATCTCAT
Statistics
Matches: 123, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
66 1 0.01
67 121 0.98
68 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (67 bp):
AAACACATTACAAGCCCAAATCCAAGATGATGATATGCCATGTATAGAATAGACAGGTCCAGAGG
AC
Found at i:593817 original size:14 final size:15
Alignment explanation
Indices: 593782--593819 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
593772 GGACATTTCC
593782 AAAAACTAAGACCCA
1 AAAAACTAAGACCCA
* *
593797 TACAACTAA-ACCCA
1 AAAAACTAAGACCCA
593811 AAAAACTAA
1 AAAAACTAA
593820 TTTTACAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.61, C:0.26, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAACTAAGACCCA
Found at i:595710 original size:19 final size:19
Alignment explanation
Indices: 595682--595721 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
595672 ATTTTAAATC
*
595682 TATTATATTC-AATATATTA
1 TATTAAATTCAAAT-TATTA
595701 TATTAAATTCAAATTATTA
1 TATTAAATTCAAATTATTA
595720 TA
1 TA
595722 ATACTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAAATTCAAATTATTA
Found at i:597672 original size:22 final size:21
Alignment explanation
Indices: 597642--597682 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
597632 TTATATATAT
*
597642 ATATATATATATATGATAAAAA
1 ATATATATAAATAT-ATAAAAA
*
597664 ATATTTATAAATATATAAA
1 ATATATATAAATATATAAA
597683 TATTAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATATATAAATATATAAAAA
Found at i:609503 original size:2 final size:2
Alignment explanation
Indices: 609496--609522 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
609486 TCAACAATAC
609496 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
609523 AGTAAAATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:609843 original size:3 final size:3
Alignment explanation
Indices: 609829--609872 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
609819 TAGAATATAT
*
609829 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
609873 TGATGTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:610053 original size:2 final size:2
Alignment explanation
Indices: 610046--610074 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
610036 AAGTCCAAGT
610046 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 T
610075 GTATGTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:610079 original size:4 final size:4
Alignment explanation
Indices: 610072--610110 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
610062 TATATATATA
610072 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
610111 ATAGTGTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:611914 original size:2 final size:2
Alignment explanation
Indices: 611893--611958 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
611883 TCATACCACC
* * * * *
611893 AT AT AT AC AT AC AT AA AT AT AT AT AT AT AT AT GT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
611935 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
611959 TTCTTAAAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:613170 original size:2 final size:2
Alignment explanation
Indices: 613163--613190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
613153 GCTAAATTGA
613163 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
613191 TTCTCTTGGG
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:619152 original size:23 final size:22
Alignment explanation
Indices: 619126--619175 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
619116 TATTTGTTAT
* * *
619126 TTAAAAATTTTATAATTTTTTTA
1 TTAAAAATTATAT-ATTTTATAA
*
619149 TTAATAATTATATATTTTATAA
1 TTAAAAATTATATATTTTATAA
619171 TTAAA
1 TTAAA
619176 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAAAATTATATATTTTATAA
Found at i:620649 original size:15 final size:14
Alignment explanation
Indices: 620609--620638 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
620599 TTTTACTATA
*
620609 ATTAAAATTAAAAT
1 ATTAAAAATAAAAT
620623 ATTAAAAATAAAAT
1 ATTAAAAATAAAAT
620637 AT
1 AT
620639 ATACAAGTAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAAAATAAAAT
Found at i:620941 original size:26 final size:26
Alignment explanation
Indices: 620910--620966 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
620900 CCTTCACATT
*
620910 ATAATAT-TATATATTTAATAAATTAC
1 ATAATATATATA-AATTAATAAATTAC
* *
620936 ATAATATATATAAATTAATATATTAT
1 ATAATATATATAAATTAATAAATTAC
620962 ATAAT
1 ATAAT
620967 TAAAAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATATATATAAATTAATAAATTAC
Found at i:620963 original size:21 final size:21
Alignment explanation
Indices: 620913--620970 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
620903 TCACATTATA
*
620913 ATATTATATATTTAATAAATT
1 ATATTATATATTAAATAAATT
* * *
620934 ACATAATATATATAAATTAA-T
1 ATATTATATAT-TAAATAAATT
620955 ATATTATATAATTAAA
1 ATATTATAT-ATTAAA
620971 AGATAATCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTATATATTAAATAAATT
Found at i:622731 original size:30 final size:30
Alignment explanation
Indices: 622675--622732 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
622665 GTATCACGAG
* *
622675 TTATTTAAATAAAAAATTCAATTAATAAAA
1 TTATTTAAATAAAAAATTAAAGTAATAAAA
*
622705 TTATTTAAA-AACATAATTAAAGTAATAA
1 TTATTTAAATAA-AAAATTAAAGTAATAA
622733 TATTCGGAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (30 bp):
TTATTTAAATAAAAAATTAAAGTAATAAAA
Found at i:624950 original size:5 final size:5
Alignment explanation
Indices: 624940--625023 Score: 58
Period size: 5 Copynumber: 18.2 Consensus size: 5
624930 TTTAAAATTT
* * *
624940 ATATA ATATA A-ATA AT-TA ATATA TTATA ATATT TTA-A ATA-A ATTATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A-TATA
* *
624987 ATATA ATAAA ATA-A AT-TA AAATA ATATA A-AT- ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
625024 ATTATTAGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
3 1 0.02
4 21 0.34
5 38 0.61
6 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:624984 original size:19 final size:20
Alignment explanation
Indices: 624941--625018 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
624931 TTAAAATTTA
*
624941 TATAATATAAATAATTAATATAT
1 TATAATAT-AATAA--AATAAAT
* *
624964 TATAATAT-TTTAAATAAAT
1 TATAATATAATAAAATAAAT
624983 TATAATATAATAAAATAAAT
1 TATAATATAATAAAATAAAT
625003 TA-AA-ATAATATAAATA
1 TATAATATAATA-AAATA
625019 TATAAATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.12
19 21 0.44
20 11 0.23
21 2 0.04
23 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATAATATAATAAAATAAAT
Found at i:624987 original size:42 final size:44
Alignment explanation
Indices: 624906--625019 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 44
624896 TGTAAAAATC
**
624906 AATAATAAATAAATATATAAATATTTTAAAATTTATATAATATA
1 AATAATAAATAAATATATAAATATTTTAAAAAATATATAATATA
* *
624950 AATAATTAATATAT-TAT-AATATTTTAAATAAAT-TATAATATA
1 AATAATAAATAAATATATAAATATTTTAAA-AAATATATAATATA
*
624992 ATAAAATAAATTAAAATAATATAAATAT
1 A-ATAATAAA-T-AAAT-ATATAAATAT
625020 ATAAATTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
42 21 0.38
43 11 0.20
44 13 0.23
45 3 0.05
47 3 0.05
48 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (44 bp):
AATAATAAATAAATATATAAATATTTTAAAAAATATATAATATA
Found at i:625027 original size:23 final size:23
Alignment explanation
Indices: 624931--625015 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
624921 TATAAATATT
*
624931 TTAAAATTTATATAATATAAAT-AA
1 TTAAAA-TAATATAATA-AAATAAA
* * ***
624955 TTAATATATTATAATATTTTAAA
1 TTAAAATAATATAATAAAATAAA
624978 -TAAATTATAATATAATAAAATAAA
1 TTAAA--ATAATATAATAAAATAAA
625002 TTAAAATAATATAA
1 TTAAAATAATATAA
625016 ATATATAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 4 0.09
23 19 0.41
24 19 0.41
25 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAAATAATATAATAAAATAAA
Found at i:626828 original size:18 final size:17
Alignment explanation
Indices: 626795--626831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
626785 GACATTAGTT
626795 TAATATTAAAATAATTA
1 TAATATTAAAATAATTA
*
626812 TAATATTAGATATAATTA
1 TAATATTA-AAATAATTA
626830 TA
1 TA
626832 TAAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAATATTAAAATAATTA
Found at i:626848 original size:17 final size:17
Alignment explanation
Indices: 626823--626875 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
626813 AATATTAGAT
*
626823 ATAATTATATAAATATA
1 ATAAATATATAAATATA
626840 ATAAATATATAAA-A-A
1 ATAAATATATAAATATA
626855 ATAAA-AT-TATAATATA
1 ATAAATATATA-AATATA
626871 ATAAA
1 ATAAA
626876 ATAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 2 0.06
14 4 0.12
15 7 0.22
16 7 0.22
17 12 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAATATATAAATATA
Found at i:626873 original size:16 final size:16
Alignment explanation
Indices: 626834--626963 Score: 69
Period size: 16 Copynumber: 8.1 Consensus size: 16
626824 TAATTATATA
626834 AATATAAT-AAATATAT
1 AATATAATAAAAT-TAT
*
626850 AA-AAAATAAAATTAT
1 AATATAATAAAATTAT
626865 AATATAATAAAA-TA-
1 AATATAATAAAATTAT
* *
626879 AATATATTTTAAAATTTT
1 AATATA--ATAAAATTAT
*
626897 TATA-ACATCAAAA-T-T
1 AATATA-AT-AAAATTAT
626912 AATATAAATAAAAATTAT
1 AATAT-AAT-AAAATTAT
* * *
626930 -TTTTAATATAATTAT
1 AATATAATAAAATTAT
626945 AATATAATAAAATATAT
1 AATATAATAAAAT-TAT
626962 AA
1 AA
626964 ATATTACGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
14 6 0.07
15 22 0.26
16 39 0.45
17 15 0.17
18 4 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAATAAAATTAT
Found at i:627200 original size:16 final size:16
Alignment explanation
Indices: 627148--627202 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
627138 TGAATATAAA
627148 AATTTAAA-CTAAAAT
1 AATTTAAATCTAAAAT
* **
627163 AATTTAAATTTAATTT
1 AATTTAAATCTAAAAT
627179 AATTTAAATCTAAAAT
1 AATTTAAATCTAAAAT
*
627195 ATTTTAAA
1 AATTTAAA
627203 ATAATGAGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAAATCTAAAAT
Found at i:627315 original size:28 final size:28
Alignment explanation
Indices: 627245--627316 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
627235 ATTTAACATA
627245 TAAAA-ATAAATATTTATATTTATATTT
1 TAAAATATAAATATTTATATTTATATTT
* * * *
627272 TAGAGTTTAAATATTTTTATTTA-ATTT
1 TAAAATATAAATATTTATATTTATATTT
627299 TAAAATATAAATAATTTA
1 TAAAATATAAAT-ATTTA
627317 ACATATTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
TAAAATATAAATATTTATATTTATATTT
Found at i:632684 original size:2 final size:2
Alignment explanation
Indices: 632677--632730 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
632667 TTTTGATTGG
632677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
632719 TA TG TA TA -A TA T
1 TA TA TA TA TA TA T
632731 GTATTATGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:635111 original size:27 final size:25
Alignment explanation
Indices: 635081--635154 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 25
635071 ATTTAAATTT
635081 TATTTTATTATTTAAAATATATTAA
1 TATTTTATTATTTAAAATATATTAA
* * * **
635106 AATATTATATAATTAATTTTATATTAA
1 TATTTTAT-TATTTAA-AATATATTAA
635133 TATTTTATTAAATTTAAAATAT
1 TATTTTATT--ATTTAAAATAT
635155 TTTATTTTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
25 6 0.17
26 7 0.20
27 17 0.49
28 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTTTATTATTTAAAATATATTAA
Found at i:635981 original size:2 final size:2
Alignment explanation
Indices: 635976--636007 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
635966 TATATAATGG
635976 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
636008 GCAATCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:639022 original size:24 final size:23
Alignment explanation
Indices: 638995--639040 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
638985 ATCATTTTTA
638995 AAATCATTATGATA-ATTTAATTAT
1 AAAT-ATT-TGATATATTTAATTAT
639019 AAATATTTGATATTATTTAATT
1 AAATATTTGATA-TATTTAATT
639041 TAGTAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 3 0.15
24 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
AAATATTTGATATATTTAATTAT
Found at i:639600 original size:16 final size:17
Alignment explanation
Indices: 639569--639608 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
639559 ATGTATTTTG
639569 AAATAATTATTTTAAATT
1 AAAT-ATTATTTTAAATT
639587 AAATATTA-TTTAAATT
1 AAATATTATTTTAAATT
*
639603 ACATAT
1 AAATAT
639609 GATTAGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 4 0.19
18 4 0.19
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATTATTTTAAATT
Found at i:641254 original size:6 final size:6
Alignment explanation
Indices: 641245--641272 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
641235 TGAAAATTAT
641245 GGCTCA GGCTCA GGCTCA GGCTCA GGCT
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCT
641273 GCCCATTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (6 bp):
GGCTCA
Found at i:643007 original size:2 final size:2
Alignment explanation
Indices: 643000--643027 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
642990 GTTTGATCAG
643000 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
643028 GTATCAATGT
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):
TA
Found at i:648328 original size:2 final size:2
Alignment explanation
Indices: 648267--648311 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
648257 CTACTCTTTA
*
648267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
648309 AT A
1 AT A
648312 CACACACACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:650119 original size:17 final size:17
Alignment explanation
Indices: 650099--650131 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
650089 AAGAAAATAA
650099 AACATAAACCTTGAATT
1 AACATAAACCTTGAATT
650116 AACATAAACCTTGAAT
1 AACATAAACCTTGAAT
650132 CTTTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (17 bp):
AACATAAACCTTGAATT
Found at i:650841 original size:16 final size:16
Alignment explanation
Indices: 650820--650852 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
650810 ACAGAAATGA
650820 AGATTGAAATTTGCAT
1 AGATTGAAATTTGCAT
650836 AGATTGAAATTTGCAT
1 AGATTGAAATTTGCAT
650852 A
1 A
650853 CGTAGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
AGATTGAAATTTGCAT
Found at i:655497 original size:26 final size:27
Alignment explanation
Indices: 655444--655496 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
655434 ATATTAATTT
**
655444 TTTTATTTATAAAATTTAAATTTAAAA
1 TTTTATTTATAAAAAATAAATTTAAAA
655471 TTTTATTTA-AAAAAATAAATATTAAA
1 TTTTATTTATAAAAAATAAAT-TTAAA
655497 TCACCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTTATTTATAAAAAATAAATTTAAAA
Found at i:656403 original size:27 final size:28
Alignment explanation
Indices: 656356--656416 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
656346 TAAAGCTTAT
*
656356 ATTTAATTAATAAAATTTTATT-TATTTA
1 ATTTAATTAATAAAATATTATTAT-TTTA
656384 ATTTAATT-ATAAAATATTATTATTTTA
1 ATTTAATTAATAAAATATTATTATTTTA
656411 ATTTAA
1 ATTTAA
656417 AAAAAACGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTAATTAATAAAATATTATTATTTTA
Found at i:656873 original size:4 final size:5
Alignment explanation
Indices: 656858--656926 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
656848 TATAAATAAA
* * * *
656858 TATAT TATAT TA-AT TATGT T-TAAA TATAT TATAT AATAT T-TAT TA-AA
1 TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT
656905 TATAT TATATT TATAT TATAT T
1 TATAT TATA-T TATAT TATAT T
656927 TTGTATTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
4 12 0.24
5 32 0.64
6 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:656923 original size:23 final size:23
Alignment explanation
Indices: 656854--656923 Score: 90
Period size: 23 Copynumber: 3.0 Consensus size: 23
656844 ACGATATAAA
656854 TAAATATATTATATTAATTATGT-T
1 TAAATATATTATATTAA-TAT-TAT
656878 TAAATATATTATA-TAATATTTAT
1 TAAATATATTATATTAATA-TTAT
*
656901 TAAATATATTATATTTATATTAT
1 TAAATATATTATATTAATATTAT
656924 ATTTTGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 3 0.07
23 22 0.52
24 17 0.40
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
TAAATATATTATATTAATATTAT
Found at i:656925 original size:18 final size:16
Alignment explanation
Indices: 656882--656925 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
656872 TATGTTTAAA
656882 TATATTATATAATATT
1 TATATTATATAATATT
* *
656898 TATTAAATATATTATATT
1 TA-T-ATTATATAATATT
656916 TATATTATAT
1 TATATTATAT
656926 TTTGTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTATATAATATT
Found at i:657906 original size:17 final size:17
Alignment explanation
Indices: 657886--657920 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
657876 ATATAAATTT
657886 AAAT-AAAAATATTATAA
1 AAATAAAAAATATT-TAA
657903 AAATAAAAAATATTTAA
1 AAATAAAAAATATTTAA
657920 A
1 A
657921 CTGAAACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAAAAAATATTTAA
Found at i:660858 original size:15 final size:16
Alignment explanation
Indices: 660830--660864 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
660820 CAAATAAAAA
660830 TAAATTTAAAATAATT
1 TAAATTTAAAATAATT
660846 TAAATTT-AAATAATT
1 TAAATTTAAAATAATT
660861 TAAA
1 TAAA
660865 ACGACACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:661673 original size:23 final size:24
Alignment explanation
Indices: 661639--661703 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 24
661629 TTTTAATTAT
661639 ATTTTATATATAATATAA-ATAAA
1 ATTTTATATATAATATAATATAAA
* *
661662 ATTTTATTTAT-ATAATAATTTAAA
1 ATTTTATATATAAT-ATAATATAAA
661686 ATTTTATAATATAATATA
1 ATTTTAT-ATATAATATA
661704 TCATTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 14 0.40
24 11 0.31
25 6 0.17
26 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTATATATAATATAATATAAA
Found at i:661698 original size:25 final size:25
Alignment explanation
Indices: 661643--661703 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
661633 AATTATATTT
661643 TATATATAATATAAATAAAATTTTA
1 TATATATAATATAAATAAAATTTTA
* **
661668 TTTATATAATA-ATTTAAAATTTTA
1 TATATATAATATAAATAAAATTTTA
661692 TA-ATATAATATA
1 TATATATAATATA
661704 TCATTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 8 0.26
24 13 0.42
25 10 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATATAATATAAATAAAATTTTA
Found at i:661724 original size:21 final size:20
Alignment explanation
Indices: 661686--661762 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 20
661676 ATAATTTAAA
661686 ATTTTATAATATAATATATC
1 ATTTTATAATATAATATATC
* *
661706 ATTTATATTATATATTATAT-
1 ATTT-TATAATATAATATATC
** *
661726 ATTACATAATATAA-A-ATT
1 ATTTTATAATATAATATATC
*
661744 ATTTTTATATTATAATATA
1 A-TTTTATAATATAATATA
661763 AATAGTTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 17 0.40
20 8 0.19
21 14 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTATAATATAATATATC
Found at i:661751 original size:40 final size:40
Alignment explanation
Indices: 661625--661757 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
661615 TCATTTTATT
* *
661625 TTATTTTTA-ATTATATTTTATATATAATATAA-ATAAAA
1 TTATTTTTATATTATATATTATATATTATATAATATAAAA
* * * *
661663 TT-TTATTTATATAATA-ATT-TAAAATTTTATAATATAATA
1 TTATT-TTTATATTATATATTAT-ATATTATATAATATAAAA
* *
661702 -TATCATTTATATTATATATTATATATTACATAATATAAAA
1 TTAT-TTTTATATTATATATTATATATTATATAATATAAAA
661742 TTATTTTTATATTATA
1 TTATTTTTATATTATA
661758 ATATAAATAG
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
37 3 0.04
38 17 0.23
39 21 0.29
40 28 0.38
41 4 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (40 bp):
TTATTTTTATATTATATATTATATATTATATAATATAAAA
Found at i:664773 original size:15 final size:15
Alignment explanation
Indices: 664748--664789 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
664738 AATATTTTTT
664748 AATTT-ATTTTTAAA
1 AATTTAATTTTTAAA
**
664762 AATTTAATTTTTAGT
1 AATTTAATTTTTAAA
664777 AATTTAATATTTT
1 AATTTAAT-TTTT
664790 TTAGTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:670526 original size:20 final size:21
Alignment explanation
Indices: 670497--670537 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
670487 GATTTGAATT
670497 AAAATAATTTTAAATATTAAA
1 AAAATAATTTTAAATATTAAA
**
670518 AAAAT-ATTTTTCATATTAAA
1 AAAATAATTTTAAATATTAAA
670538 TAAGTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATAATTTTAAATATTAAA
Found at i:685893 original size:15 final size:14
Alignment explanation
Indices: 685861--685904 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
685851 TTATTTTATA
*
685861 TAAATTGAATAATT
1 TAAATTGATTAATT
685875 TAAATTGATTAAGTT
1 TAAATTGATTAA-TT
685890 TAAATT-ATT-ATT
1 TAAATTGATTAATT
685902 TAA
1 TAA
685905 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 5 0.18
13 1 0.04
14 14 0.50
15 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
TAAATTGATTAATT
Found at i:685922 original size:22 final size:24
Alignment explanation
Indices: 685897--685941 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
685887 GTTTAAATTA
685897 TTATTTAATAA-TAAA-AATATAT
1 TTATTTAATAATTAAATAATATAT
*
685919 TTATTTATTAATTAAATAATATA
1 TTATTTAATAATTAAATAATATA
685942 AATATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTTAATAATTAAATAATATAT
Found at i:686177 original size:14 final size:14
Alignment explanation
Indices: 686158--686185 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
686148 ATTAATAATA
686158 AAATATTTATATAT
1 AAATATTTATATAT
686172 AAATATTTATATAT
1 AAATATTTATATAT
686186 TTTATTTTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATATAT
Found at i:686279 original size:16 final size:16
Alignment explanation
Indices: 686253--686285 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
686243 ATTTTCTTTC
686253 TTTATCATATAA-CTT
1 TTTATCATATAAGCTT
686268 TTTATACATATAAGCTT
1 TTTAT-CATATAAGCTT
686285 T
1 T
686286 AAAATTAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTATCATATAAGCTT
Found at i:691273 original size:17 final size:17
Alignment explanation
Indices: 691253--691295 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
691243 ATTTAATAAA
691253 TATATTTATTTTAAAAT
1 TATATTTATTTTAAAAT
*
691270 TATATTAATTTTAAAAT
1 TATATTTATTTTAAAAT
*
691287 TGTATTTAT
1 TATATTTAT
691296 CAAATTACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATATTTATTTTAAAAT
Found at i:692311 original size:23 final size:24
Alignment explanation
Indices: 692285--692356 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 24
692275 TATAGTTTTT
692285 ATAATTATATTTAAATAAAAAT-A
1 ATAATTATATTTAAATAAAAATAA
692308 ATAATTAT-TATTAAATAATAATATAA
1 ATAATTATAT-TTAAATAA-AA-ATAA
692334 ATTAATT-TGATTTAAATTAAAAA
1 A-TAATTAT-ATTTAAA-TAAAAA
692357 ATATTACATC
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
22 1 0.02
23 16 0.39
24 2 0.05
25 2 0.05
26 4 0.10
27 12 0.29
28 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (24 bp):
ATAATTATATTTAAATAAAAATAA
Found at i:692747 original size:22 final size:22
Alignment explanation
Indices: 692722--692764 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
692712 TAATTAATAG
692722 TTTATAT-TTTACTTTTATTCTT
1 TTTATATATTTA-TTTTATTCTT
*
692744 TTTATTTATTTATTTTATTCT
1 TTTATATATTTATTTTATTCT
692765 GATCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATATATTTATTTTATTCTT
Found at i:697428 original size:23 final size:23
Alignment explanation
Indices: 697377--697432 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
697367 ATTATTTGTT
697377 TACTTT-AATATAAAAATAAAAA
1 TACTTTAAATATAAAAATAAAAA
* * *
697399 AAGTTTAAATAT-AAAATAAATCA
1 TACTTTAAATATAAAAATAAA-AA
697422 TACTTTAAATA
1 TACTTTAAATA
697433 GATTAAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (23 bp):
TACTTTAAATATAAAAATAAAAA
Found at i:698412 original size:6 final size:7
Alignment explanation
Indices: 698401--698436 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
698391 CCAAAACATA
698401 AAAAAT-
1 AAAAATC
698407 AAAAATC
1 AAAAATC
698414 AAAAATC
1 AAAAATC
698421 AAAAATC
1 AAAAATC
698428 AAAAA-C
1 AAAAATC
698434 AAA
1 AAA
698437 TATTAAACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:699689 original size:3 final size:3
Alignment explanation
Indices: 699681--699718 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
699671 GTCTCATAAT
699681 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
699719 GTGTTATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:700031 original size:20 final size:20
Alignment explanation
Indices: 700008--700071 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
699998 TATTTAAAAT
700008 ATATTTTTATATTAATATTA
1 ATATTTTTATATTAATATTA
700028 ATA-TTTTATAATT-ATAATTAA
1 ATATTTTTAT-ATTAAT-ATT-A
*
700049 AAATTTTTAT-TTAA-A-TA
1 ATATTTTTATATTAATATTA
700066 ATATTT
1 ATATTT
700072 AAATTATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
17 6 0.16
18 1 0.03
19 9 0.24
20 11 0.30
21 4 0.11
22 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTTTATATTAATATTA
Found at i:704319 original size:2 final size:2
Alignment explanation
Indices: 704312--704340 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
704302 TAACAGCGTG
704312 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 T
704341 TATCAATCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:704599 original size:17 final size:17
Alignment explanation
Indices: 704577--704611 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
704567 GTATTTCTTA
704577 TAGATTCAATTCCTAGC
1 TAGATTCAATTCCTAGC
*
704594 TAGATTCAATTTCTAGC
1 TAGATTCAATTCCTAGC
704611 T
1 T
704612 CATGCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (17 bp):
TAGATTCAATTCCTAGC
Found at i:706202 original size:21 final size:22
Alignment explanation
Indices: 706177--706226 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
706167 CACACTAAAT
**
706177 TTTAATTTTTTTAATTTATA-A
1 TTTAATTTAATTAATTTATATA
706198 TTTAATTTAATTAATTTATATA
1 TTTAATTTAATTAATTTATATA
*
706220 ATTAATT
1 TTTAATT
706227 AATATTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAATTTAATTAATTTATATA
Found at i:711339 original size:21 final size:21
Alignment explanation
Indices: 711286--711344 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
711276 AGTATAATAT
711286 TTTTAA-TAA-TATTT-AAAA
1 TTTTAATTAATTATTTAAAAA
*
711304 TTTTAATATATTTATTTAAAAA
1 TTTTAAT-TAATTATTTAAAAA
*
711326 TTTTAATTAATTATATAAA
1 TTTTAATTAATTATTTAAA
711345 TTTATTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
20 2 0.06
21 15 0.44
22 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTAATTAATTATTTAAAAA
Found at i:711357 original size:17 final size:17
Alignment explanation
Indices: 711312--711363 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
711302 AATTTTAATA
*
711312 TATTTATT-TAAAAATTT
1 TATTTATTATATAAA-TT
*
711329 TAATTAATTATATAAATT
1 T-ATTTATTATATAAATT
711347 TATTTATTATATTAAAT
1 TATTTATTATA-TAAAT
711364 AAATAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.34
18 14 0.48
19 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTATTATATAAATT
Found at i:711857 original size:6 final size:6
Alignment explanation
Indices: 711846--711896 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
711836 GACCCTCTGG
* *
711846 GGGGCT GGGGCT GGAGCT GGAGCT GGGGCT GGGGCT GGGGCT GGGGCT
1 GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT GGGGCT
711894 GGG
1 GGG
711897 CGGTGTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.04, C:0.16, G:0.65, T:0.16
Consensus pattern (6 bp):
GGGGCT
Found at i:713123 original size:21 final size:22
Alignment explanation
Indices: 713099--713144 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
713089 AATAATATTT
* *
713099 ATATTTAAAT-TTAATTATAAA
1 ATATATAAATATTAATTAAAAA
713120 ATATATAAATATTAATTAAAAA
1 ATATATAAATATTAATTAAAAA
713142 ATA
1 ATA
713145 AATTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATAAATATTAATTAAAAA
Found at i:713134 original size:28 final size:28
Alignment explanation
Indices: 713081--713134 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
713071 ATCATTATTA
* *
713081 TTAATTAAAATAATATTTATATTTAAAT
1 TTAATTAAAATAATATATAAATTTAAAT
*
713109 TTAATTATAA-AATATATAAATATTAA
1 TTAATTAAAATAATATATAAAT-TTAA
713135 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAATTAAAATAATATATAAATTTAAAT
Found at i:715263 original size:20 final size:19
Alignment explanation
Indices: 715205--715263 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
715195 ATTATAATTT
715205 TTTTAATAAAATTTATTTAA
1 TTTTAATAAAA-TTATTTAA
*
715225 TTTATAAATAAAAAT-TTTAA
1 TTT-T-AATAAAATTATTTAA
*
715245 TTTTATTAAAAGTTATTTA
1 TTTTAATAAAA-TTATTTA
715264 TTAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.19
19 2 0.06
20 15 0.47
21 2 0.06
22 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAATAAAATTATTTAA
Found at i:724002 original size:151 final size:154
Alignment explanation
Indices: 723694--724002 Score: 331
Period size: 160 Copynumber: 2.0 Consensus size: 154
723684 CCAGCATCGA
* * *
723694 GTCCAAGGAATTTCGAAGCAGTAGCAAGCGTTCATTGATAGAAAAAGGCAGAGAAGCCATTAAAG
1 GTCCAAGCAATTTCGAAGCAGTAGCAAGCGTTCACTGATAGAAAAAGCCAGAGAAGCCATTAAAG
* * *
723759 CCAGCATAGAAAGAAATGGCGGATATCCATTCGAGCCAAAGCGACGACCACTAAGTCCAGGCCGG
66 CCAGCATACAAAGAAATGGCGGAAATCCATGCGAGCCAAA--GACG--CACTAAGTCCAGG-CGG
* * * *
723824 AGGCCTGATCCTCTTCATCACTGATCATT
126 AGACCTGATCCTCTCCATCAATAATCATT
* * * **
723853 GTCCAAGCAATTTCGAAGCAGTAGCAAGCGTTTTACTGATAGAAGAAGCCTGAGAAGCCATTATT
1 GTCCAAGCAATTTCGAAGCAGTAGCAAGCG-TTCACTGATAGAAAAAGCCAGAGAAGCCATTAAA
* * * * * *
723918 GCCAGCATTCAAAGACATGGGGGAAATCCATGCGTGTCGAA-ACG-ACTAAGTCCAGG-GG-GAC
65 GCCAGCATACAAAGAAATGGCGGAAATCCATGCGAGCCAAAGACGCACTAAGTCCAGGCGGAGAC
723979 CTGATCCT-TACCATCAATAATCAT
130 CTGATCCTCT-CCATCAATAATCAT
724003 ACATTTTTAT
Statistics
Matches: 127, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
150 1 0.01
151 21 0.17
152 2 0.02
154 12 0.09
157 3 0.02
159 29 0.23
160 59 0.46
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (154 bp):
GTCCAAGCAATTTCGAAGCAGTAGCAAGCGTTCACTGATAGAAAAAGCCAGAGAAGCCATTAAAG
CCAGCATACAAAGAAATGGCGGAAATCCATGCGAGCCAAAGACGCACTAAGTCCAGGCGGAGACC
TGATCCTCTCCATCAATAATCATT
Found at i:725426 original size:47 final size:44
Alignment explanation
Indices: 725375--725461 Score: 111
Period size: 47 Copynumber: 1.9 Consensus size: 44
725365 TTTACACGAT
* * *
725375 ATTTATATTATTTTTTATATAATATTATATTTAAAGTATTATTTAAA
1 ATTTATATAAATTTTAATAT-AT-TTATA-TTAAAGTATTATTTAAA
*
725422 ATTTATATAAATTTTAATATATTTATATTATAGTATTATT
1 ATTTATATAAATTTTAATATATTTATATTAAAGTATTATT
725462 AATATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 12 0.33
45 5 0.14
46 2 0.06
47 17 0.47
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (44 bp):
ATTTATATAAATTTTAATATATTTATATTAAAGTATTATTTAAA
Found at i:725495 original size:12 final size:12
Alignment explanation
Indices: 725373--725497 Score: 54
Period size: 12 Copynumber: 10.8 Consensus size: 12
725363 TATTTACACG
725373 ATATTTATATTA
1 ATATTTATATTA
* *
725385 TTTTTTATA-TA
1 ATATTTATATTA
725396 ATA-TTATATTTA
1 ATATTTATA-TTA
725408 A-AGTATTAT-TTA
1 ATA-T-TTATATTA
*
725420 AAATTTATA-TA
1 ATATTTATATTA
*
725431 A-ATTT-TAAT-
1 ATATTTATATTA
725440 ATATTTATATT-
1 ATATTTATATTA
*
725451 ATA-GTATTATTA
1 ATATTTA-TATTA
* *
725463 ATATTATAAAAATA
1 ATATT-T-ATATTA
*
725477 ATTTTTATATTA
1 ATATTTATATTA
725489 ATATTTATA
1 ATATTTATA
725498 AATAATTATA
Statistics
Matches: 85, Mismatches: 13, Indels: 30
0.66 0.10 0.23
Matches are distributed among these distances:
9 3 0.04
10 16 0.19
11 21 0.25
12 30 0.35
13 2 0.02
14 12 0.14
15 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
ATATTTATATTA
Found at i:725497 original size:44 final size:44
Alignment explanation
Indices: 725387--725497 Score: 104
Period size: 44 Copynumber: 2.5 Consensus size: 44
725377 TTATATTATT
* *
725387 TTTTATATAATATTATATTTAAAGTATTATTTAAAATTTATATAAA
1 TTTTA-AT-ATATTATATTTATAGTATTATTTAAAATTTATAAAAA
*
725433 TTTTAATATATT-TATATTATAGTATTA-TTAATA-TTATAAAAA
1 TTTTAATATATTATAT-TTATAGTATTATTTAAAATTTATAAAAA
*
725475 TAATTT-TTATATTAATATTTATA
1 T--TTTAATATATT-ATATTTATA
725498 AATAATTATA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
42 9 0.16
43 14 0.25
44 23 0.41
45 5 0.09
46 5 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (44 bp):
TTTTAATATATTATATTTATAGTATTATTTAAAATTTATAAAAA
Done.