Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold321
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: 1029294
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.30
Warning! 84004 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:432148 original size:35 final size:35
Alignment explanation
Indices: 432103--432178 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
432093 TTATGTGACT
*
432103 CAAATTCTAAGAGATTACTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
* *
432138 CAAAATCTAAGAGATTGCTTGCAAGTCAAGTTAGA
1 CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
432173 CAAAAT
1 CAAAAT
432179 ATATTTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (35 bp):
CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
Found at i:433904 original size:20 final size:19
Alignment explanation
Indices: 433879--433932 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
433869 AGTATTTTAT
433879 ATAAAAATCAT-TATAAATC
1 ATAAAAATCATATA-AAATC
*
433898 AATAAAAAATTATATAAAATC
1 -AT-AAAAATCATATAAAATC
433919 ATAAAAAT-ATATAA
1 ATAAAAATCATATAA
433933 TTAATGAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 4 0.13
21 13 0.42
22 2 0.06
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAAATCATATAAAATC
Found at i:437862 original size:9 final size:9
Alignment explanation
Indices: 437848--437881 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
437838 GTTTTCGAAT
437848 TCGAATAAC
1 TCGAATAAC
437857 TCGAATAAC
1 TCGAATAAC
*
437866 TCGAATAAT
1 TCGAATAAC
437875 TCGAATA
1 TCGAATA
437882 TCAAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:438134 original size:26 final size:25
Alignment explanation
Indices: 438097--438145 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
438087 AACTTTTTAT
*
438097 TTTTCTCCAAAATTTTTACTCTCAC
1 TTTTCCCCAAAATTTTTACTCTCAC
438122 TTTTCCCCTAAAATTTTTACTCTC
1 TTTTCCCC-AAAATTTTTACTCTC
438146 TTCCCATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTCCCCAAAATTTTTACTCTCAC
Found at i:445176 original size:19 final size:19
Alignment explanation
Indices: 445152--445188 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
445142 TTTATATTTT
*
445152 AAATATGTTAGCAATGTGA
1 AAATATATTAGCAATGTGA
445171 AAATATATTAGCAATGTG
1 AAATATATTAGCAATGTG
445189 GGATTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
AAATATATTAGCAATGTGA
Found at i:449399 original size:44 final size:44
Alignment explanation
Indices: 449310--449468 Score: 144
Period size: 44 Copynumber: 3.6 Consensus size: 44
449300 GTTTTAATCC
* ** *
449310 GCTCCACTGCAACTTCAGGGAGATAGGATTAT-CAAATTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-TGCTTATTCAGTCT
* *
449354 GCTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTTATTCAGTCT
** * * * *
449398 GC-CCACTGTGACTTCAGGGTGATAAGACTTG-TTTTCTCAGTAT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTTAT-TCAGTCT
** *
449441 ATTCCGCTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
449469 CCCGATGCGA
Statistics
Matches: 93, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 3 0.03
43 31 0.33
44 59 0.63
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTTGCTTATTCAGTCT
Found at i:449719 original size:15 final size:15
Alignment explanation
Indices: 449696--449730 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
449686 CTGTTATCTT
* *
449696 CAACAAGCTTCACTA
1 CAACCAGCTCCACTA
449711 CAACCAGCTCCACTA
1 CAACCAGCTCCACTA
449726 CAACC
1 CAACC
449731 GATGGAGGCA
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:0.37, C:0.43, G:0.06, T:0.14
Consensus pattern (15 bp):
CAACCAGCTCCACTA
Found at i:449749 original size:102 final size:102
Alignment explanation
Indices: 449609--449817 Score: 283
Period size: 102 Copynumber: 2.0 Consensus size: 102
449599 CTGCTATCTT
* * * * **
449609 CAACTAGCTCCAATGCAACCGATGGAGGCAAGACTTTGTTTTCGATCTGCTTCGCTGTTGACGCA
1 CAACCAGCTCCAATACAACCGATGGAGGCAAGACTTTGTTTCCGATCTGCTTCACTGTCAACGCA
* *
449674 GGAAGGCAAGATCTGTTATCTTCAACAAGCTTCACTA
66 GGAAGGCAAGATCTGCTATCTTCAACAAGCTCCACTA
* * * *
449711 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGTA
1 CAACCAGCTCCAATACAACCGATGGAGGCAAGACTTTGTTTCCGATCTGCTTCACTGTCAACGCA
* * *
449776 GGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTG
66 GGAAGGCAAGATCTGCTATCTTCAACAAGCTCCACTA
449813 CAACC
1 CAACC
449818 GATGGAGGTA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (102 bp):
CAACCAGCTCCAATACAACCGATGGAGGCAAGACTTTGTTTCCGATCTGCTTCACTGTCAACGCA
GGAAGGCAAGATCTGCTATCTTCAACAAGCTCCACTA
Found at i:449857 original size:87 final size:87
Alignment explanation
Indices: 449711--450495 Score: 1291
Period size: 87 Copynumber: 9.0 Consensus size: 87
449701 AGCTTCACTA
*
449711 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGTA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
449776 GGAAGGCAAGATCTGCTGTCTT
66 GGAAGGCAAGATCTGCTGTCTT
* * * *
449798 CAACCAGCTCCACTGCAACCGATGGAGGTAAGGCTTTGTTTTCGATCTGCTTCGCTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
449863 GGAAGGCAAGATCTGCTGTCTT
66 GGAAGGCAAGATCTGCTGTCTT
* * *
449885 CAACCAGCTCCACTATAACCGATGGAGGTAAGGCTTTGTTTCTGATCTGCTTCACTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
* * *
449950 AGAAGGCAAGATCTGTTATCTT
66 GGAAGGCAAGATCTGCTGTCTT
* * *
449972 CAACCAGCTCCTCTACAATCGATGGAGGCAAGGCTTTGTTTCTGATCTGCTTCACTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
* *
450037 GGAAGGCAAGATTTGTTGTCTT
66 GGAAGGCAAGATCTGCTGTCTT
* * *
450059 CAACCAGCTCCACTACAACCAATGGAGGCAAGGCTTTGTTTCCGATCTCCTTCACTGTTAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
450124 GGAAGGCAAGATCTGCTGTCTT
66 GGAAGGCAAGATCTGCTGTCTT
*
450146 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATTTGCTTCACTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
450211 GGAAGGCAAGATCTGCTGTCTT
66 GGAAGGCAAGATCTGCTGTCTT
* * *
450233 CAACCAGCTTCACTACAACTGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTTACTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
*
450298 GGAAGGCAAGATCTGCTATCTT
66 GGAAGGCAAGATCTGCTGTCTT
* *
450320 CAACCAGTTCCACTACAACCGATGGAGGCAAGGTTTTGTTTCCGATCTGCTTCACTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
*
450385 GGAAGGCAAGATCTGCTGTTTT
66 GGAAGGCAAGATCTGCTGTCTT
* * *
450407 CAACCATCTCCATTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCGCTGTCAATGCA
1 CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
*
450472 GGAAGGCAAGATCTGCTATCTT
66 GGAAGGCAAGATCTGCTGTCTT
450494 CA
1 CA
450496 CTAATCTGTT
Statistics
Matches: 647, Mismatches: 51, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 647 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (87 bp):
CAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTCCGATCTGCTTCACTGTCAATGCA
GGAAGGCAAGATCTGCTGTCTT
Found at i:451945 original size:6 final size:6
Alignment explanation
Indices: 451923--452032 Score: 79
Period size: 6 Copynumber: 18.8 Consensus size: 6
451913 CTCTTTTCAT
* * *
451923 ATTTT- ATTTTG ACTTTG ATTTTG GTTTTG ATTAATT- -TTTCT- TTTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT--TTG ATTT-TG ATTTTG
* * * * *
451970 CTTTTG ACTTTG ATTTT- -TTTTC TTTTTG TTTTTG ATTTTG ATTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
452016 ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTT
452033 TTTCTCTCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
4 5 0.06
5 7 0.08
6 73 0.84
8 2 0.02
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.70
Consensus pattern (6 bp):
ATTTTG
Found at i:451997 original size:28 final size:29
Alignment explanation
Indices: 451948--452014 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
451938 TGATTTTGGT
*
451948 TTTGATTAATTTTTCTTTTTTGCTTTTGAC
1 TTTGATT-TTTTTTCTTTTTTGCTTTTGAC
* *
451978 TTTGATTTTTTTTC-TTTTTGTTTTTGAT
1 TTTGATTTTTTTTCTTTTTTGCTTTTGAC
452006 TTTGATTTT
1 TTTGATTTT
452015 GATTTTGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 21 0.62
29 6 0.18
30 7 0.21
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.73
Consensus pattern (29 bp):
TTTGATTTTTTTTCTTTTTTGCTTTTGAC
Found at i:452049 original size:15 final size:13
Alignment explanation
Indices: 452029--452063 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
452019 TTGATTTTGA
452029 TTTTTTTCTCTCTT
1 TTTTTTTC-CTCTT
*
452043 TTCTTTTCCTCTT
1 TTTTTTTCCTCTT
452056 TTTTTTTC
1 TTTTTTTC
452064 GAATCGGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTCCTCTT
Found at i:460563 original size:3 final size:3
Alignment explanation
Indices: 460555--460604 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
460545 TAAATGAAGC
460555 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
460603 TT
1 TT
460605 TATTTTATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:461894 original size:125 final size:125
Alignment explanation
Indices: 461672--461923 Score: 486
Period size: 125 Copynumber: 2.0 Consensus size: 125
461662 CAAATCAAGA
*
461672 GGTACATCATCATGTTTCTTTCTAGGCCTAACTATTGAGTTTGTCGAGTATTTTTATTCGAGTCT
1 GGTACATCATCAAGTTTCTTTCTAGGCCTAACTATTGAGTTTGTCGAGTATTTTTATTCGAGTCT
461737 ATGCTTACTGTATATACGGTAGCTATTAATTCCATATTAAACCCAATTTTCCAAGCATTT
66 ATGCTTACTGTATATACGGTAGCTATTAATTCCATATTAAACCCAATTTTCCAAGCATTT
*
461797 GGTACATCATCAAGTTTCTTTCTAGGCCTAACTATTGAGTTTGTCGAGTATTTTTTTTCGAGTCT
1 GGTACATCATCAAGTTTCTTTCTAGGCCTAACTATTGAGTTTGTCGAGTATTTTTATTCGAGTCT
461862 ATGCTTACTGTATATACGGTAGCTATTAATTCCATATTAAACCCAATTTTCCAAGCATTT
66 ATGCTTACTGTATATACGGTAGCTATTAATTCCATATTAAACCCAATTTTCCAAGCATTT
461922 GG
1 GG
461924 GTCCTTCTCT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (125 bp):
GGTACATCATCAAGTTTCTTTCTAGGCCTAACTATTGAGTTTGTCGAGTATTTTTATTCGAGTCT
ATGCTTACTGTATATACGGTAGCTATTAATTCCATATTAAACCCAATTTTCCAAGCATTT
Found at i:475783 original size:39 final size:41
Alignment explanation
Indices: 475720--475809 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
475710 TTAAAAATAT
* *
475720 TTATATTAAAAAAAACTATCATAAATATAACAAATGTTTCA
1 TTATATTAAAAAAAACTATAATAAATATAACAAATATTTCA
* * *
475761 TTATATTAAAAAATA-TA-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAAAACTATAATAAATATAACAAATATTTCA
*
475800 TTGTATTAAA
1 TTATATTAAA
475810 TATAATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 27 0.63
40 2 0.05
41 14 0.33
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAAAACTATAATAAATATAACAAATATTTCA
Found at i:478595 original size:3 final size:3
Alignment explanation
Indices: 478587--478636 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
478577 TAAATGAAGC
478587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
478635 TT
1 TT
478637 TATTTTATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:484006 original size:17 final size:18
Alignment explanation
Indices: 483973--484006 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
483963 TTCACTTTTC
*
483973 AATGTAAACATTTCTCTA
1 AATGTAAACACTTCTCTA
483991 AATGTAAAC-CTTCTCT
1 AATGTAAACACTTCTCT
484007 TCATGAATAA
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:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (18 bp):
AATGTAAACACTTCTCTA
Found at i:484821 original size:35 final size:35
Alignment explanation
Indices: 484777--484846 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
484767 ATTGTCATAT
* * *
484777 TGGTTATCCACGTATCTTGATATATACTAGAATCA
1 TGGTAATCCACGTATCCTGATATAAACTAGAATCA
*
484812 TGGTAATCCATGTATCCTGATATAAACTAGAATCA
1 TGGTAATCCACGTATCCTGATATAAACTAGAATCA
484847 GACAGCAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (35 bp):
TGGTAATCCACGTATCCTGATATAAACTAGAATCA
Found at i:484944 original size:2 final size:2
Alignment explanation
Indices: 484937--484961 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
484927 AGTCTTGGTA
484937 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 A
484962 GCAAAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:487538 original size:14 final size:14
Alignment explanation
Indices: 487500--487538 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
487490 CCAGTCCTCA
487500 ACATTGTATTCTCC
1 ACATTGTATTCTCC
*
487514 AC-TTTTATTCTCC
1 ACATTGTATTCTCC
487527 ACATTGTATTCT
1 ACATTGTATTCT
487539 ATTAGTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (14 bp):
ACATTGTATTCTCC
Found at i:487826 original size:20 final size:21
Alignment explanation
Indices: 487784--487827 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
487774 TTACCCTAAA
* * *
487784 CCCCAAATATTTTTATTTTTT
1 CCCCAAATACTTTTACTTCTT
487805 CCCCAAA-ACTTTTACTTCTT
1 CCCCAAATACTTTTACTTCTT
487825 CCC
1 CCC
487828 ACTTTCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (21 bp):
CCCCAAATACTTTTACTTCTT
Found at i:487961 original size:17 final size:17
Alignment explanation
Indices: 487910--487967 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 17
487900 TTTGAATATT
487910 TTCCCTCCAAAATTTTA-
1 TTCCC-CCAAAATTTTAC
487927 TT-CCCC--AA-TTTAC
1 TTCCCCCAAAATTTTAC
487940 TTCCCCCCAAAATTTTAC
1 TT-CCCCCAAAATTTTAC
487958 -TCCCCCAAAA
1 TTCCCCCAAAA
487968 CCTTCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
12 4 0.11
13 4 0.11
15 6 0.17
16 11 0.31
17 5 0.14
18 5 0.14
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.33
Consensus pattern (17 bp):
TTCCCCCAAAATTTTAC
Found at i:488517 original size:11 final size:11
Alignment explanation
Indices: 488501--488537 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
488491 AAGATAATTG
488501 AAGCAACTGGC
1 AAGCAACTGGC
*
488512 AAGCAA-TTG-
1 AAGCAACTGGC
488521 AAGCAACTGGC
1 AAGCAACTGGC
488532 AAGCAA
1 AAGCAA
488538 AGAAGCTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.27
10 4 0.18
11 12 0.55
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (11 bp):
AAGCAACTGGC
Found at i:488521 original size:20 final size:20
Alignment explanation
Indices: 488496--488537 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
488486 ATCAGAAGAT
488496 AATTGAAGCAACTGGCAAGC
1 AATTGAAGCAACTGGCAAGC
488516 AATTGAAGCAACTGGCAAGC
1 AATTGAAGCAACTGGCAAGC
488536 AA
1 AA
488538 AGAAGCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (20 bp):
AATTGAAGCAACTGGCAAGC
Found at i:489160 original size:12 final size:12
Alignment explanation
Indices: 489143--489167 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
489133 TGTTATTTCG
489143 GGTCGGTTAACC
1 GGTCGGTTAACC
489155 GGTCGGTTAACC
1 GGTCGGTTAACC
489167 G
1 G
489168 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:489886 original size:1 final size:1
Alignment explanation
Indices: 489880--489915 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
489870 TTCTCCTTTC
489880 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
489916 GTTTGCATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:492705 original size:19 final size:19
Alignment explanation
Indices: 492682--492782 Score: 148
Period size: 19 Copynumber: 5.3 Consensus size: 19
492672 TCTATGATAG
492682 CATATCATATCTAAGATTA
1 CATATCATATCTAAGATTA
* *
492701 TATATCATATCTAAGATTG
1 CATATCATATCTAAGATTA
492720 CATATCATATCTAAGATTA
1 CATATCATATCTAAGATTA
* * *
492739 TATATTATATCTAAGATTG
1 CATATCATATCTAAGATTA
*
492758 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTA
492777 CATATC
1 CATATC
492783 CCTGAAGATT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 73 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.40
Consensus pattern (19 bp):
CATATCATATCTAAGATTA
Found at i:492728 original size:38 final size:38
Alignment explanation
Indices: 492672--492775 Score: 181
Period size: 38 Copynumber: 2.7 Consensus size: 38
492662 AATCATATCT
* *
492672 TCTATGATAGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
492710 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
492748 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
492776 GCATATCCCT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:503150 original size:33 final size:33
Alignment explanation
Indices: 503113--503259 Score: 117
Period size: 33 Copynumber: 4.4 Consensus size: 33
503103 CATATAAAGG
**
503113 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
503146 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGGT
1 GGTTGCTAAGTGCTGATTCC-CCG-AT-T--CAT-T---GGT
*
503188 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
**
503215 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
503248 GGTTGCTAAGTG
1 GGTTGCTAAGTG
503260 AGGAATTCAC
Statistics
Matches: 89, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
27 20 0.22
28 2 0.02
31 2 0.02
32 2 0.02
33 29 0.33
34 3 0.03
35 2 0.02
36 1 0.01
38 2 0.02
39 1 0.01
41 2 0.02
42 23 0.26
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:503218 original size:27 final size:28
Alignment explanation
Indices: 503183--503236 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
503173 CTGAAATGTG
503183 AAGGTGGTTGCTAAGTGCTGATTCCCCC
1 AAGGTGGTTGCTAAGTGCTGATTCCCCC
**
503211 AAGG-GGTTGCTGTGTGCTGATTCCCC
1 AAGGTGGTTGCTAAGTGCTGATTCCCC
503237 GATTCATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.15, C:0.24, G:0.31, T:0.30
Consensus pattern (28 bp):
AAGGTGGTTGCTAAGTGCTGATTCCCCC
Found at i:510816 original size:7 final size:7
Alignment explanation
Indices: 510804--510856 Score: 70
Period size: 7 Copynumber: 7.1 Consensus size: 7
510794 AAATACAAGG
510804 CTAAACC
1 CTAAACC
510811 CTAAACC
1 CTAAACC
510818 CTAAAACC
1 CT-AAACC
510826 CTAAAACC
1 CT-AAACC
510834 CTAAACC
1 CTAAACC
*
510841 CTAAAAAC
1 CT-AAACC
510849 CTAAACC
1 CTAAACC
510856 C
1 C
510857 CATGCCTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 21 0.50
8 21 0.50
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
CTAAACC
Found at i:510824 original size:15 final size:15
Alignment explanation
Indices: 510804--510856 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
510794 AAATACAAGG
510804 CTAAACCCT-AAACC
1 CTAAACCCTAAAACC
510818 CTAAAACCCTAAAACC
1 CT-AAACCCTAAAACC
*
510834 CTAAACCCTAAAAAC
1 CTAAACCCTAAAACC
510849 CTAAACCC
1 CTAAACCC
510857 CATGCCTTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
14 2 0.06
15 27 0.75
16 7 0.19
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (15 bp):
CTAAACCCTAAAACC
Found at i:510826 original size:8 final size:8
Alignment explanation
Indices: 510806--510853 Score: 73
Period size: 8 Copynumber: 6.2 Consensus size: 8
510796 ATACAAGGCT
510806 AAACCCT-
1 AAACCCTA
510813 AAACCCTA
1 AAACCCTA
510821 AAACCCTA
1 AAACCCTA
510829 AAACCCT-
1 AAACCCTA
510836 AAACCCTA
1 AAACCCTA
*
510844 AAAACCTA
1 AAACCCTA
510852 AA
1 AA
510854 CCCCATGCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
7 14 0.37
8 24 0.63
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.12
Consensus pattern (8 bp):
AAACCCTA
Found at i:510836 original size:23 final size:23
Alignment explanation
Indices: 510806--510853 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
510796 ATACAAGGCT
*
510806 AAACCCTAAACCCTAAAACCCTA
1 AAACCCTAAACCCTAAAAACCTA
510829 AAACCCTAAACCCTAAAAACCTA
1 AAACCCTAAACCCTAAAAACCTA
510852 AA
1 AA
510854 CCCCATGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.12
Consensus pattern (23 bp):
AAACCCTAAACCCTAAAAACCTA
Found at i:511578 original size:19 final size:19
Alignment explanation
Indices: 511554--511593 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
511544 AGCCGTGTCG
* *
511554 CGTGGCCGTGAGTCACGCA
1 CGTGGCCATGAGTCACACA
*
511573 CGTGGCCATGTGTCACACA
1 CGTGGCCATGAGTCACACA
511592 CG
1 CG
511594 GCTGAGACAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (19 bp):
CGTGGCCATGAGTCACACA
Found at i:513129 original size:36 final size:36
Alignment explanation
Indices: 513080--513166 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
513070 TAGTCCAACC
* **
513080 AAACACACTAGATGCTCACACGAGTTAATCCCTCCA
1 AAACACACCAGATGCTCACACGAGCCAATCCCTCCA
*
513116 AAACGCACCAGATGCTCACACGAGCCAATCCCTCC-
1 AAACACACCAGATGCTCACACGAGCCAATCCCTCCA
513151 -AACACACCA-ATGCTCA
1 AAACACACCAGATGCTCA
513167 TAAGAGCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.15
34 8 0.17
36 31 0.67
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (36 bp):
AAACACACCAGATGCTCACACGAGCCAATCCCTCCA
Found at i:513179 original size:33 final size:33
Alignment explanation
Indices: 513073--513226 Score: 137
Period size: 33 Copynumber: 4.5 Consensus size: 33
513063 ACATCGTTAG
* * *
513073 TCCAACCAAACACACTAGATGCTCACACGAGTTAA
1 TCCAACC-AACACACCA-ATGCTCACAAGAGCTAA
** * * *
513108 TCCCTCCAAAACGCACCAGATGCTCACACGAGCCAA
1 TCCAACC--AACACACCA-ATGCTCACAAGAGCTAA
** *
513144 TCCCTCCAACACACCAATGCTCATAAGAGCTAA
1 TCCAACCAACACACCAATGCTCACAAGAGCTAA
* *
513177 TCCAACCAGCACACCAATGCTCAAAAGAGCTAA
1 TCCAACCAACACACCAATGCTCACAAGAGCTAA
*
513210 TCCAACTAACACACCAA
1 TCCAACCAACACACCAA
513227 ATCGCAAAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
33 58 0.57
34 8 0.08
35 5 0.05
36 31 0.30
ACGTcount: A:0.39, C:0.36, G:0.10, T:0.14
Consensus pattern (33 bp):
TCCAACCAACACACCAATGCTCACAAGAGCTAA
Found at i:518252 original size:13 final size:13
Alignment explanation
Indices: 518213--518263 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
518203 AGTTCTTCAT
518213 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
518226 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
518239 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
518252 TGCTTTTGAAAA
1 TGCTTTTGAAAA
518264 ATTTGAGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 26 0.81
14 3 0.09
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:518252 original size:26 final size:27
Alignment explanation
Indices: 518213--518264 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
518203 AGTTCTTCAT
518213 TGCTTTTGAAAAGTGC-TGTGAAAAAG
1 TGCTTTTGAAAAGTGCTTGTGAAAAAG
* *
518239 TGCTTTTGAGAAGTGCTTTTGAAAAA
1 TGCTTTTGAAAAGTGCTTGTGAAAAA
518265 TTTGAGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (27 bp):
TGCTTTTGAAAAGTGCTTGTGAAAAAG
Found at i:518606 original size:28 final size:28
Alignment explanation
Indices: 518567--518654 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
518557 TATTTTAAAC
518567 ACATTTATTTACAATTTGTTTAACATAA
1 ACATTTATTTACAATTTGTTTAACATAA
* * *
518595 ACATTTATTTACCACTTGTTTAACATAC
1 ACATTTATTTACAATTTGTTTAACATAA
** *
518623 ACATATTAGATACACATTTATTTAACATAA
1 ACAT-TTATTTACA-ATTTGTTTAACATAA
518653 AC
1 AC
518655 CTAACTCTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 29 0.59
29 6 0.12
30 14 0.29
ACGTcount: A:0.40, C:0.16, G:0.03, T:0.41
Consensus pattern (28 bp):
ACATTTATTTACAATTTGTTTAACATAA
Found at i:519141 original size:24 final size:24
Alignment explanation
Indices: 519109--519180 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
519099 TGAAGAATAC
519109 GGTAATCAAGAGCATGCAAGCATT
1 GGTAATCAAGAGCATGCAAGCATT
519133 GGTAATCAAGAGCATGCAAGCATT
1 GGTAATCAAGAGCATGCAAGCATT
519157 GGTAATCAAGAGCATGCAAGCATT
1 GGTAATCAAGAGCATGCAAGCATT
519181 AAAAGAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (24 bp):
GGTAATCAAGAGCATGCAAGCATT
Found at i:520035 original size:19 final size:19
Alignment explanation
Indices: 520011--520049 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
520001 GTGGTGGAGA
520011 AGAGGAACAAA-ACACCAGC
1 AGAGGAACAAAGA-ACCAGC
520030 AGAGGAACAAAGAACCAGC
1 AGAGGAACAAAGAACCAGC
520049 A
1 A
520050 TCAGCAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.54, C:0.23, G:0.23, T:0.00
Consensus pattern (19 bp):
AGAGGAACAAAGAACCAGC
Found at i:520054 original size:25 final size:24
Alignment explanation
Indices: 520026--520142 Score: 118
Period size: 25 Copynumber: 5.0 Consensus size: 24
520016 AACAAAACAC
520026 CAGCAGAGGAACAAAGAACCAGCA
1 CAGCAGAGGAACAAAGAACCAGCA
520050 TCAGCAGAGGAACAAAGAACCAGCA
1 -CAGCAGAGGAACAAAGAACCAGCA
* * *
520075 CAACCAGAAGAACAAAGAACCAACA
1 C-AGCAGAGGAACAAAGAACCAGCA
* *
520100 CCAGTAGAGGATCAAAG-A--AG--
1 -CAGCAGAGGAACAAAGAACCAGCA
*
520120 CAGCAGAGGAACAAATAACCAGC
1 CAGCAGAGGAACAAAGAACCAGC
520143 GATGAGAGAA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
19 13 0.17
20 1 0.01
22 3 0.04
24 2 0.03
25 55 0.73
26 1 0.01
ACGTcount: A:0.50, C:0.24, G:0.22, T:0.03
Consensus pattern (24 bp):
CAGCAGAGGAACAAAGAACCAGCA
Found at i:520093 original size:50 final size:50
Alignment explanation
Indices: 520029--520124 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
520019 AAAACACCAG
* * *
520029 CAGAGGAACAAAGAACCAGCATCAGCAGAGGAACAAAGAACCAGCACAAC
1 CAGAAGAACAAAGAACCAACACCAGCAGAGGAACAAAGAACCAGCACAAC
* * *
520079 CAGAAGAACAAAGAACCAACACCAGTAGAGGATCAAAGAAGCAGCA
1 CAGAAGAACAAAGAACCAACACCAGCAGAGGAACAAAGAACCAGCA
520125 GAGGAACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.51, C:0.24, G:0.22, T:0.03
Consensus pattern (50 bp):
CAGAAGAACAAAGAACCAACACCAGCAGAGGAACAAAGAACCAGCACAAC
Found at i:520142 original size:19 final size:19
Alignment explanation
Indices: 520099--520142 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
520089 AAGAACCAAC
* *
520099 ACCAGTAGAGGATCAAAGA
1 ACCAGCAGAGGAACAAAGA
* *
520118 AGCAGCAGAGGAACAAATA
1 ACCAGCAGAGGAACAAAGA
520137 ACCAGC
1 ACCAGC
520143 GATGAGAGAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.20, G:0.25, T:0.07
Consensus pattern (19 bp):
ACCAGCAGAGGAACAAAGA
Found at i:537789 original size:28 final size:28
Alignment explanation
Indices: 537722--537775 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
537712 AAGCTCGACG
537722 ACTTGAGGAATTTTTTCTTTCCAAGACA
1 ACTTGAGGAATTTTTTCTTTCCAAGACA
537750 ACTTGAGGAATTTTTTCTTTCCAAGA
1 ACTTGAGGAATTTTTTCTTTCCAAGA
537776 TTCAATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (28 bp):
ACTTGAGGAATTTTTTCTTTCCAAGACA
Found at i:568830 original size:26 final size:27
Alignment explanation
Indices: 568789--568846 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
568779 GGGTCGCGAT
*
568789 ACTTGAAACCGGGTATTGCGTGACATG
1 ACTTGAAACCGGGTATCGCGTGACATG
* *
568816 ACTTG-AATCGGGTATCGCGTGACTTG
1 ACTTGAAACCGGGTATCGCGTGACATG
568842 ACTTG
1 ACTTG
568847 GATATCACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (27 bp):
ACTTGAAACCGGGTATCGCGTGACATG
Found at i:575544 original size:33 final size:34
Alignment explanation
Indices: 575506--575570 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
575496 ACAATGTAAG
*
575506 TAAAAATATT-AAAAATAAAATTA-TTTAATTAAC
1 TAAAAA-ATTCAAAAATAAAAATATTTTAATTAAC
575539 TAAAAAATTCAAAAATAAAAATATTTTAATTA
1 TAAAAAATTCAAAAATAAAAATATTTTAATTA
575571 TGTACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 3 0.10
33 18 0.62
34 8 0.28
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (34 bp):
TAAAAAATTCAAAAATAAAAATATTTTAATTAAC
Found at i:575545 original size:34 final size:36
Alignment explanation
Indices: 575507--575587 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 36
575497 CAATGTAAGT
*
575507 AAAAATATTAAAAATAAAATTA-TTTAATTAACTA-
1 AAAAATATTAAAAATAAAAATATTTTAATTAACTAC
* **
575541 AAAAAT-TCAAAAATAAAAATATTTTAATTATGTAC
1 AAAAATATTAAAAATAAAAATATTTTAATTAACTAC
575576 AAAAA-ATTAAAA
1 AAAAATATTAAAA
575588 CATTATCTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 13 0.33
34 16 0.41
35 10 0.26
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (36 bp):
AAAAATATTAAAAATAAAAATATTTTAATTAACTAC
Found at i:576045 original size:20 final size:20
Alignment explanation
Indices: 576020--576057 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
576010 CCTATGATCG
*
576020 ATTAAATACCTAATTATCTA
1 ATTAAATAACTAATTATCTA
*
576040 ATTAAATAATTAATTATC
1 ATTAAATAACTAATTATC
576058 CTCGATTGAG
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:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAATAACTAATTATCTA
Found at i:589793 original size:42 final size:43
Alignment explanation
Indices: 589710--589796 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 43
589700 TTTTATCCTA
* *
589710 GAAAAATAGAATTTAAAAAAAGGAGAAGATAATCTTAGGTTGTT
1 GAAAAATA-AATTTAAAAAAAGGAGAAGATAAACATAGGTTGTT
* *
589754 GAAAAAT-AATTTAAAAAGAGGAGAAGATAAACATGGGTTGTT
1 GAAAAATAAATTTAAAAAAAGGAGAAGATAAACATAGGTTGTT
589796 G
1 G
589797 GATTTACCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 32 0.82
44 7 0.18
ACGTcount: A:0.49, C:0.02, G:0.23, T:0.25
Consensus pattern (43 bp):
GAAAAATAAATTTAAAAAAAGGAGAAGATAAACATAGGTTGTT
Found at i:599186 original size:18 final size:16
Alignment explanation
Indices: 599165--599212 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
599155 TAATTTGCCT
599165 TTTTTAATTTTATTATAA
1 TTTTT-ATTTTATT-TAA
*
599183 TTTTTGTTTTTAGTTTAA
1 TTTTT-ATTTTA-TTTAA
599201 TTTTTATTTTAT
1 TTTTTATTTTAT
599213 ATTCTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 18 0.69
19 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTTATTTTATTTAA
Found at i:601701 original size:10 final size:10
Alignment explanation
Indices: 601686--601733 Score: 73
Period size: 10 Copynumber: 4.9 Consensus size: 10
601676 ATTTTATTTT
601686 TATTCTATTC
1 TATTCTATTC
601696 TATTCTATTC
1 TATTCTATTC
601706 TATTCTATTC
1 TATTCTATTC
601716 TATTCATATT-
1 TATTC-TATTC
601726 TATT-TATT
1 TATTCTATT
601734 ATTTATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 4 0.11
10 29 0.78
11 4 0.11
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTCTATTC
Found at i:601706 original size:15 final size:15
Alignment explanation
Indices: 601686--601733 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
601676 ATTTTATTTT
601686 TATTCTATTCTATTC
1 TATTCTATTCTATTC
601701 TATTCTATTCTATTC
1 TATTCTATTCTATTC
601716 TATTCATATT-TATT-
1 TATTC-TATTCTATTC
601730 TATT
1 TATT
601734 ATTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.12
15 24 0.75
16 4 0.12
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTCTATTCTATTC
Found at i:602011 original size:22 final size:21
Alignment explanation
Indices: 601973--602016 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
601963 ATCAGTTTCA
601973 TATTTTTATTCATTTATTTCTT
1 TATTTTTATTCATTTA-TTCTT
*
601995 TATTTTTTTTC-TATTATTCTT
1 TATTTTTATTCAT-TTATTCTT
602016 T
1 T
602017 TTATTCTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTATTCATTTATTCTT
Found at i:602126 original size:13 final size:14
Alignment explanation
Indices: 602108--602139 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
602098 TTGGTATTTT
602108 ATTATT-TTCATTC
1 ATTATTATTCATTC
602121 ATTATTATTCATTC
1 ATTATTATTCATTC
602135 -TTATT
1 ATTATT
602140 CCCTAGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATTCATTC
Found at i:602186 original size:13 final size:13
Alignment explanation
Indices: 602168--602211 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
602158 TATGAGTTTA
602168 TTATTTTATTGTT
1 TTATTTTATTGTT
602181 TTATTTTATTG-T
1 TTATTTTATTGTT
* *
602193 CTATTATTATTATT
1 TTATT-TTATTGTT
602207 TTATT
1 TTATT
602212 CGTCCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 5 0.19
13 16 0.62
14 5 0.19
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (13 bp):
TTATTTTATTGTT
Found at i:605742 original size:41 final size:41
Alignment explanation
Indices: 605697--605799 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
605687 GGCTTAGCAC
* * * *
605697 CTAGCAGGCTTATTGCCAGTGAAACAATTCAGATTTTATGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATTCAAACTATATGT
* *
605738 CTAGCAGGCTTAATGCCGGTGAAACATTTCAAACTATATGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATTCAAACTATATGT
605779 CTAGCAGGC-TAAGTGCCAGTG
1 CTAGCAGGCTTAA-TGCCAGTG
605800 TATTGAATCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 3 0.06
41 51 0.94
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCAGTGAAACAATTCAAACTATATGT
Found at i:606886 original size:12 final size:12
Alignment explanation
Indices: 606845--606906 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
606835 GGGTGTTATA
*
606845 ATTTTTATTTTT
1 ATTTTTATTGTT
606857 A-TTTTA-TGTTT
1 ATTTTTATTG-TT
**
606868 AAGTTTATTGTT
1 ATTTTTATTGTT
606880 ATTTTTA--GTT
1 ATTTTTATTGTT
*
606890 CTTTTTATTGTT
1 ATTTTTATTGTT
606902 ATTTT
1 ATTTT
606907 CTTAGACTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
10 10 0.26
11 8 0.21
12 19 0.49
13 2 0.05
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.73
Consensus pattern (12 bp):
ATTTTTATTGTT
Found at i:614143 original size:36 final size:37
Alignment explanation
Indices: 614097--614169 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
614087 GTCTCCAATT
* *
614097 TCACATTTCAATTC-AATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
*
614133 TCACAATTCAATTCAAAATTCACTTTTTCATTTTCAA
1 TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
614170 GTCAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 13 0.39
37 20 0.61
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAAAATTCACTTTTTCACTTTCAA
Found at i:620504 original size:130 final size:130
Alignment explanation
Indices: 620271--620636 Score: 376
Period size: 130 Copynumber: 2.8 Consensus size: 130
620261 ACTTATTTTG
* * * * *
620271 TTGTTAAAAATTTTATTAATAATTAACAATGACAAATCGTTTCATTGCTATTAATAAGTAAAAGA
1 TTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTCGTTGCGATTAATAAGTAAAA-A
** * * * ** *
620336 TTAAATTACATAACGACATTTTAAGGTTATTGCTAATATTTTAATGTTTA-ACAGTAACTTGTGT
65 TTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTAGA-AACAACTTATGT
620400 -C
129 GC
* * * *
620401 TTGTTACAAATTTTATTAAGAATTCACAATGACAAATCATGTCGTTGCGATGAATAAGCATAAAA
1 TTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTCGTTGCGATTAATAAGTA-AAAA
* * * * * *
620466 TTAATTTATGCAACAACATTTTAATGTTGCTGTTAATATTTTAACGTTTAGAAACAACTTATTTG
65 TTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTAGAAACAACTTATGTG
*
620531 G
130 C
* * * * * * *
620532 TTGTTACACATTTTATTAATAATTCACAACGACAAATTGTGTTGTTACGGTTAATAGGTAAAAAA
1 TTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTCGTTGCGATTAATAAGT-AAAAA
* * *
620597 TTAAATTATGTAACAACATTTTAAAGTCATTGCTAATATT
65 TTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATT
620637 ATAATATTTA
Statistics
Matches: 190, Mismatches: 42, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
130 100 0.53
131 89 0.47
132 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (130 bp):
TTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTCGTTGCGATTAATAAGTAAAAAT
TAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTAGAAACAACTTATGTGC
Found at i:620597 original size:131 final size:130
Alignment explanation
Indices: 620260--620659 Score: 399
Period size: 131 Copynumber: 3.1 Consensus size: 130
620250 TGTTAATACT
* * * *
620260 AACTTATTTTGTTGTTAAAAATTTTATTAATAATTAACAATGACAAATCGT-TTCATTGCTATTA
1 AACTTA-TTTGTTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTT-GTTGCGATTA
* ** * * *
620324 ATAAGTAAAAGATTAAATTACATAACGACATTTTAAGGTTATTGCTAATATTTTAATGTTTAACA
64 ATAAGTAAAAAATTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTAACA
**
620389 GT
129 AC
* * * * * * *
620391 AACTTGTGTCTTGTTACAAATTTTATTAAGAATTCACAATGACAAATCATGTCGTTGCGATGAAT
1 AACTTATTTGTTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTTGTTGCGATTAAT
* * * * * * *
620456 AAGCATAAAATTAATTTATGCAACAACATTTTAATGTTGCTGTTAATATTTTAACGTTTAGA-AA
66 AAGTAAAAAATTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTA-ACAA
620520 C
130 C
* * * * *
620521 AACTTATTTGGTTGTTACACATTTTATTAATAATTCACAACGACAAATTGTGTTGTTACGGTTAA
1 AACTTATTT-GTTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTTGTTGCGATTAA
* * * * * **
620586 TAGGTAAAAAATTAAATTATGTAACAACATTTTAAAGTCATTGCTAATATTATAATATTTAACAA
65 TAAGTAAAAAATTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTAACAA
620651 C
130 C
*
620652 AATTTATT
1 AACTTATT
620660 GTTACATATA
Statistics
Matches: 213, Mismatches: 52, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
130 103 0.48
131 110 0.52
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (130 bp):
AACTTATTTGTTGTTACAAATTTTATTAATAATTCACAATGACAAATCGTGTTGTTGCGATTAAT
AAGTAAAAAATTAAATTATGTAACAACATTTTAAGGTTACTGCTAATATTTTAACGTTTAACAAC
Found at i:626247 original size:19 final size:19
Alignment explanation
Indices: 626199--626249 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
626189 AACATATATT
626199 TTTAATGTTTATATTATAATA
1 TTTAA-GTTT-TATTATAATA
*
626220 TTTTA-TTTTATTAATAA-A
1 TTTAAGTTTTATT-ATAATA
626238 TTTAAGTTTTAT
1 TTTAAGTTTTAT
626250 GTTATAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.35
19 13 0.50
21 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTAAGTTTTATTATAATA
Found at i:626923 original size:29 final size:30
Alignment explanation
Indices: 626858--626924 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
626848 ATAAATACCA
*
626858 ATATAAACTATAGTTTAATGTGTAATTATGT
1 ATATAAACTATAGTTT-ATGTGTAATTATAT
* * *
626889 ACATAAACTTTAGTTT-TGTGTAATTTTAT
1 ATATAAACTATAGTTTATGTGTAATTATAT
626918 ATATAAA
1 ATATAAA
626925 ATTTTGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 17 0.55
31 14 0.45
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (30 bp):
ATATAAACTATAGTTTATGTGTAATTATAT
Found at i:634336 original size:4 final size:4
Alignment explanation
Indices: 634327--634357 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
634317 CTCCCAGGTG
634327 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATC
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATC
634358 AAGATTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:634988 original size:12 final size:12
Alignment explanation
Indices: 634931--634998 Score: 70
Period size: 12 Copynumber: 5.7 Consensus size: 12
634921 GGAAAAGAGT
634931 GAGAGAGA-G-A
1 GAGAGAGAGGAA
634941 GAGAGAGA-GAGA
1 GAGAGAGAGGA-A
634953 GAGAGAGAGAGAGA
1 GAGAGAGAG-GA-A
634967 GAGAGAGAGGAA
1 GAGAGAGAGGAA
*
634979 GTGAGAGAGGAA
1 GAGAGAGAGGAA
*
634991 GTGAGAGA
1 GAGAGAGA
634999 AGTAACCTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
10 9 0.17
12 29 0.55
13 2 0.04
14 13 0.25
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (12 bp):
GAGAGAGAGGAA
Found at i:634998 original size:2 final size:2
Alignment explanation
Indices: 634926--634987 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
634916 GTGGGGGAAA
*
634926 AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG 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
*
634968 AG AG AG AG -G A- AG TG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
634988 GAAGTGAGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:645427 original size:128 final size:129
Alignment explanation
Indices: 645267--645551 Score: 416
Period size: 129 Copynumber: 2.2 Consensus size: 129
645257 GGGGGAAAGT
* **
645267 GGGA-GGGAGTAAAAGTTTTGGGGGAAATTAAAAAGTTTTGAGGGTTTTTG-GGGAGTAAAATTT
1 GGGAGGGGAGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTGCGAAAGTAAAATTT
* * *
645330 T-GAAGGAAATTAAATAGAGGGAGTAAAATGGGGG-AAATGGGTTTAGGGTAGATGGGGGTGGGA
66 TAG-AGGAAAATAAAT-GAGGGACTAAAATGGGGGTAAATGGGTTTAGGGTAGATAGGGGTGGGA
645393 G
129 G
645394 GGGAGGGGAGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTGCGAAAGTAAAATTT
1 GGGAGGGGAGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTGCGAAAGTAAAATTT
* * *
645459 TAGAGGAAAATAAATGGGGGACTAAAATGGGGGTAAATGGGTTTGGGGTAGATAGGGGTGGGAT
66 TAGAGGAAAATAAATGAGGGACTAAAATGGGGGTAAATGGGTTTAGGGTAGATAGGGGTGGGAG
* * *
645523 GAGAGGGGAGTAAAAGTTTTAGAGGAAAA
1 GGGAGGGGAGTAAAAGTTTTGGGGGAAAA
645552 GTACAAATGT
Statistics
Matches: 142, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
127 4 0.03
128 61 0.43
129 76 0.54
130 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.40, T:0.25
Consensus pattern (129 bp):
GGGAGGGGAGTAAAAGTTTTGGGGGAAAATAAAAAGTTTTGAGGGTTTTTGCGAAAGTAAAATTT
TAGAGGAAAATAAATGAGGGACTAAAATGGGGGTAAATGGGTTTAGGGTAGATAGGGGTGGGAG
Found at i:660112 original size:26 final size:26
Alignment explanation
Indices: 660072--660154 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
660062 CAATAATAAT
* *
660072 AGTATCGCAGGAAAGCTACTAGTAAC
1 AGTATCGCAGCAAAGCTACCAGTAAC
* *
660098 AGTATCGCAGCAAAGCTGCCAGTGAC
1 AGTATCGCAGCAAAGCTACCAGTAAC
* ** *
660124 AGTATCGC-TCAAAAATGCCAGTAAC
1 AGTATCGCAGCAAAGCTACCAGTAAC
660149 AGTATC
1 AGTATC
660155 CCAACCCCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 19 0.39
26 30 0.61
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (26 bp):
AGTATCGCAGCAAAGCTACCAGTAAC
Found at i:660142 original size:25 final size:26
Alignment explanation
Indices: 660092--660154 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 26
660082 GAAAGCTACT
**
660092 AGTAACAGTATCGCAGCAAAGCTGCC
1 AGTAACAGTATCGCAGCAAAAATGCC
* *
660118 AGTGACAGTATCGC-TCAAAAATGCC
1 AGTAACAGTATCGCAGCAAAAATGCC
660143 AGTAACAGTATC
1 AGTAACAGTATC
660155 CCAACCCCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (26 bp):
AGTAACAGTATCGCAGCAAAAATGCC
Found at i:664887 original size:16 final size:16
Alignment explanation
Indices: 664866--664903 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
664856 GATGGCCACT
664866 GGAGCTGCTCCAGGCA
1 GGAGCTGCTCCAGGCA
664882 GGAGCTGCTCCAGGCA
1 GGAGCTGCTCCAGGCA
664898 GGAGCT
1 GGAGCT
664904 CAATACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.13
Consensus pattern (16 bp):
GGAGCTGCTCCAGGCA
Found at i:667211 original size:28 final size:29
Alignment explanation
Indices: 667179--667239 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
667169 GAGCCCTATT
*
667179 CAATAACAGT-GCAGTGTGGGCCTTAGCC
1 CAATAACAGTAACAGTGTGGGCCTTAGCC
* *
667207 TAAT-ATAGTAACAGTGTGGGCCTTAGCC
1 CAATAACAGTAACAGTGTGGGCCTTAGCC
667235 CAATA
1 CAATA
667240 CAATTTCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (29 bp):
CAATAACAGTAACAGTGTGGGCCTTAGCC
Found at i:667254 original size:33 final size:32
Alignment explanation
Indices: 667151--667255 Score: 87
Period size: 33 Copynumber: 3.3 Consensus size: 32
667141 ATACAACAAG
* * *
667151 CAGTAACAGTCTGGGCCTGAGCCCTATTCAATAA
1 CAGTAACAGTGTGGGCCTTAGCCC-A-TCAATAT
*
667185 CAGT-GCAGTGTGGGCCTTAG-CC-T-AATAT
1 CAGTAACAGTGTGGGCCTTAGCCCATCAATAT
*
667213 -AGTAACAGTGTGGGCCTTAGCCCAATACAATTT
1 CAGTAACAGTGTGGGCCTTAGCCC-AT-CAATAT
667246 CAGT-ACAGTG
1 CAGTAACAGTG
667256 CAATAATGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
27 3 0.05
28 19 0.33
29 3 0.05
31 1 0.02
32 2 0.03
33 23 0.40
34 7 0.12
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (32 bp):
CAGTAACAGTGTGGGCCTTAGCCCATCAATAT
Found at i:667418 original size:26 final size:28
Alignment explanation
Indices: 667351--667429 Score: 90
Period size: 26 Copynumber: 2.9 Consensus size: 28
667341 CAACTCACCA
* *
667351 ATATCACAACAAAGTTACCAGTAATAAT
1 ATATCGCAACAAAGTTGCCAGTAATAAT
* *
667379 AGTATCGCAGCAAAGTTGCCAGTAA-CAT
1 A-TATCGCAACAAAGTTGCCAGTAATAAT
*
667407 -TATCGCAACAAAGCTGCCAGTAA
1 ATATCGCAACAAAGTTGCCAGTAA
667430 AAGTTTACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
26 21 0.48
28 3 0.07
29 20 0.45
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (28 bp):
ATATCGCAACAAAGTTGCCAGTAATAAT
Found at i:667647 original size:29 final size:27
Alignment explanation
Indices: 667600--667666 Score: 116
Period size: 29 Copynumber: 2.4 Consensus size: 27
667590 GGGTAAACTA
667600 GTCATTTTACCCTTTAAGGGTATTTTG
1 GTCATTTTACCCTTTAAGGGTATTTTG
667627 GTCATTTACTACCCTTTAAGGGTATTTTG
1 GTCATTT--TACCCTTTAAGGGTATTTTG
667656 GTCATTTTACC
1 GTCATTTTACC
667667 TATTTTGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 11 0.29
29 27 0.71
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.46
Consensus pattern (27 bp):
GTCATTTTACCCTTTAAGGGTATTTTG
Found at i:672337 original size:379 final size:379
Alignment explanation
Indices: 671638--672399 Score: 1359
Period size: 379 Copynumber: 2.0 Consensus size: 379
671628 GATAGCTCAA
671638 CAAAGTTACAATCAAGAATAAATATCCACTACCTCATATTGATGATTTGTTTGATCAATTGAAGG
1 CAAAGTTACAATCAAGAATAAATATCCACTACCTCATATTGATGATTTGTTTGATCAATTGAAGG
* * *
671703 GTGCCATAATGTTTTCAAATATTGATCTCCGTTCTGGTTATTATCAGTTACGAGTGAAAGATTCT
66 GTGCCACAATGTTTTCAAATATTGATATCCATTCTGGTTATTATCAGTTACGAGTGAAAGATTCT
* *
671768 AATATGCCGGAAACAACATTCAGAACCAAGTACAGATATTATGAATTCCTTTTGATGTCGTTTTT
131 AATATACCGGAAACAACATTCAGAACCAAGTACAGATATTATGAATTCCTTGTGATGTCGTTTTT
* *
671833 TAATTAATGCACATGCGGTATTTATGGATTTGATGAATAAAATTTTCAAATCTTATTTGGATAGA
196 TAATTAATGCACATGCAGTATTTATAGATTTGATGAATAAAATTTTCAAATCTTATTTGGATAGA
* *
671898 TTTGTTGTGGTATTTATTGATGATATTCTGGTATATTCCCGAGATGGGACTGAACATGCCGAACA
261 TTTGTTATGGTATTTATTGATGATATTCTGGTATATTCCCGAGATGAGACTGAACATGCCGAACA
671963 TCTGAGAATTGTTCTGCAAAATTTGTGAGAAAAACAACTGTATGCTAAATTTAG
326 TCTGAGAATTGTTCTGCAAAATTTGTGAGAAAAACAACTGTATGCTAAATTTAG
* *
672017 CAAAGTTACAATCAAGAATAAATATCTACTACCTCGTATTGATGATTTGTTTGATCAATTGAAGG
1 CAAAGTTACAATCAAGAATAAATATCCACTACCTCATATTGATGATTTGTTTGATCAATTGAAGG
672082 GTGCCACAATGTTTTCAAATATTGATATCCATTCTGGTTATTATCAGTTACGAGTGAAAGATTCT
66 GTGCCACAATGTTTTCAAATATTGATATCCATTCTGGTTATTATCAGTTACGAGTGAAAGATTCT
*
672147 AATATACCGGAAACAACATTCAGAACCAAGTACGGATATTATGAATTCCTTGTGATG-CTGTTTT
131 AATATACCGGAAACAACATTCAGAACCAAGTACAGATATTATGAATTCCTTGTGATGTC-G-TTT
*
672211 TTTAATTAATGCACATGCAGTATTTATAGATTTGATGAATAGAATTTTCAAAT-TGTATTTGG-T
194 TTTAATTAATGCACATGCAGTATTTATAGATTTGATGAATAAAATTTTCAAATCT-TATTTGGAT
672274 AGATTTGTTATGGTATTTATTGATGATATTCTGGTATATTCCCGAGATGAGACTGAACATGCCGA
258 AGATTTGTTATGGTATTTATTGATGATATTCTGGTATATTCCCGAGATGAGACTGAACATGCCGA
672339 ACATCTGAGAATTGTTCTGCAAAATTTGTGAGAAAAACAACTGTATGCTAAATTTAG
323 ACATCTGAGAATTGTTCTGCAAAATTTGTGAGAAAAACAACTGTATGCTAAATTTAG
672396 CAAA
1 CAAA
672400 TGTGAATTTT
Statistics
Matches: 367, Mismatches: 13, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
378 1 0.00
379 306 0.83
380 60 0.16
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (379 bp):
CAAAGTTACAATCAAGAATAAATATCCACTACCTCATATTGATGATTTGTTTGATCAATTGAAGG
GTGCCACAATGTTTTCAAATATTGATATCCATTCTGGTTATTATCAGTTACGAGTGAAAGATTCT
AATATACCGGAAACAACATTCAGAACCAAGTACAGATATTATGAATTCCTTGTGATGTCGTTTTT
TAATTAATGCACATGCAGTATTTATAGATTTGATGAATAAAATTTTCAAATCTTATTTGGATAGA
TTTGTTATGGTATTTATTGATGATATTCTGGTATATTCCCGAGATGAGACTGAACATGCCGAACA
TCTGAGAATTGTTCTGCAAAATTTGTGAGAAAAACAACTGTATGCTAAATTTAG
Found at i:674642 original size:16 final size:16
Alignment explanation
Indices: 674621--674671 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
674611 GGGGAGAGTT
674621 GTATGATAGAAATATC
1 GTATGATAGAAATATC
674637 GTATGA-AGAAA-AT-
1 GTATGATAGAAATATC
*
674650 TTATGATAGAAATATC
1 GTATGATAGAAATATC
674666 GTATGA
1 GTATGA
674672 AAATTTCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 7 0.23
16 11 0.37
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (16 bp):
GTATGATAGAAATATC
Found at i:676806 original size:25 final size:25
Alignment explanation
Indices: 676778--676826 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
676768 ACAGCTCTTA
*
676778 TGAGCATCCC-AGTATTTGGCTCTCG
1 TGAGCATCCCGA-TACTTGGCTCTCG
*
676803 TGAGCTTCCCGATACTTGGCTCTC
1 TGAGCATCCCGATACTTGGCTCTC
676827 ACAAGCTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (25 bp):
TGAGCATCCCGATACTTGGCTCTCG
Found at i:676868 original size:25 final size:25
Alignment explanation
Indices: 676790--676869 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
676780 AGCATCCCAG
** *
676790 TATTTGGCTCTCGTGAGCTTCCCGA
1 TATTTGGCTCTCACGAGCTTCCTGA
* * *
676815 TACTTGGCTCTCACAAGCTTCCTGT
1 TATTTGGCTCTCACGAGCTTCCTGA
*
676840 TATTTAGCTCTCACGAGCTTCCTGA
1 TATTTGGCTCTCACGAGCTTCCTGA
676865 TATTT
1 TATTT
676870 TGCTTGGAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.16, C:0.28, G:0.17, T:0.39
Consensus pattern (25 bp):
TATTTGGCTCTCACGAGCTTCCTGA
Found at i:679640 original size:20 final size:21
Alignment explanation
Indices: 679607--679646 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
679597 TTAACTTTAT
*
679607 TTCATATTATTTTTGAATTAA
1 TTCATATTAATTTTGAATTAA
*
679628 TTCA-ATTAATTTTTAATTA
1 TTCATATTAATTTTGAATTA
679647 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (21 bp):
TTCATATTAATTTTGAATTAA
Found at i:680708 original size:23 final size:23
Alignment explanation
Indices: 680681--680724 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
680671 TTATATGTAT
*
680681 TTTCC-TTTGTTTTCTTATTATGC
1 TTTCCATTTG-TTTATTATTATGC
680704 TTTCCATTTGTTTATTATTAT
1 TTTCCATTTGTTTATTATTAT
680725 TTTGTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (23 bp):
TTTCCATTTGTTTATTATTATGC
Found at i:680853 original size:16 final size:17
Alignment explanation
Indices: 680823--680856 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
680813 TGATTTATTA
*
680823 TATTCCTTTATTTTTAT
1 TATTCCTTTAGTTTTAT
680840 TATTCC-TTAGTTTTAT
1 TATTCCTTTAGTTTTAT
680856 T
1 T
680857 TTATTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTCCTTTAGTTTTAT
Found at i:684042 original size:30 final size:30
Alignment explanation
Indices: 683998--684062 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
683988 CGCGGCTTGT
* * *
683998 ACACATGCCTATGTGT-TCCACATGAGCTGG
1 ACACAAGCCCATGTGTGT-CACATGAGCTAG
*
684028 ACACAAGCCCATGTGTGTCACATGGGCTAG
1 ACACAAGCCCATGTGTGTCACATGAGCTAG
684058 ACACA
1 ACACA
684063 CGCTCTTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (30 bp):
ACACAAGCCCATGTGTGTCACATGAGCTAG
Found at i:691648 original size:12 final size:12
Alignment explanation
Indices: 691633--691657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
691623 ACGAATGAGT
691633 ACATAGGCTGGG
1 ACATAGGCTGGG
691645 ACATAGGCTGGG
1 ACATAGGCTGGG
691657 A
1 A
691658 GACGGCCGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.40, T:0.16
Consensus pattern (12 bp):
ACATAGGCTGGG
Found at i:698517 original size:263 final size:263
Alignment explanation
Indices: 698050--698581 Score: 965
Period size: 263 Copynumber: 2.0 Consensus size: 263
698040 TTAGGTTAGT
* *
698050 AGACAGAGGATGATTAAGATGTAAAAAGCGGTGTTCGTAAAAAATAACATGGCGAGAAATGAGAA
1 AGACAGAGGATGATTAAGATGTAAAAAGCGGTGTTCATAAAAAATAACATGGCGAGAAATGACAA
* *
698115 TTTTACCGTCTGGTATAAGACACTGATACCCTTTGTGCTGAGAATTATACCCTAAAAATGTGCAT
66 TTTTACCGCCTGGTATAAGACACTGATACCCTTTGTGCTGAGAACTATACCCTAAAAATGTGCAT
* *
698180 GGTTGAGATCGAAATTCCAATTTATGATTGTGAAATGGTCGAAGATAAGGAAAGCAGTAGCATCC
131 GGTTGAGATCGAAATTCCAATTTATGATTGTGAAAGGGTCGAAGATAAGGAAAACAGTAGCATCC
698245 AAACACGCGTAGATGATTATAAGAAGGATCTTCACCATAAAAAGCCATGTATGGAAAGTCGCCCT
196 AAACACGCGTAGATGATTATAAGAAGGATCTTCACCATAAAAAGCCATGTATGGAAAGTCGCCCT
698310 TCA
261 TCA
*
698313 AGACAGAGGATGATTAAGATGTAAAAAGTGGTGTTCATAAAAAATAACATGGCGAGAAATGACAA
1 AGACAGAGGATGATTAAGATGTAAAAAGCGGTGTTCATAAAAAATAACATGGCGAGAAATGACAA
*
698378 TTTTACCGCCTGGTATAAGACACTGATACCCTTTGTGCTGAGAACTATACCCTAAAAATGTGCTT
66 TTTTACCGCCTGGTATAAGACACTGATACCCTTTGTGCTGAGAACTATACCCTAAAAATGTGCAT
*
698443 GGTTGAGATCGAAATTCCAATTTATGATTGTGAAAGGGTCGATGATAAGGAAAACAGTAGCATCC
131 GGTTGAGATCGAAATTCCAATTTATGATTGTGAAAGGGTCGAAGATAAGGAAAACAGTAGCATCC
* *
698508 AAACACGCGTAGATGATTATAAGAAGGATCTTCACCATAAAGAGCCATGTATGGAAAGTTGCCCT
196 AAACACGCGTAGATGATTATAAGAAGGATCTTCACCATAAAAAGCCATGTATGGAAAGTCGCCCT
698573 TCA
261 TCA
698576 AGACAG
1 AGACAG
698582 GGGTGGGAAG
Statistics
Matches: 258, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
263 258 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (263 bp):
AGACAGAGGATGATTAAGATGTAAAAAGCGGTGTTCATAAAAAATAACATGGCGAGAAATGACAA
TTTTACCGCCTGGTATAAGACACTGATACCCTTTGTGCTGAGAACTATACCCTAAAAATGTGCAT
GGTTGAGATCGAAATTCCAATTTATGATTGTGAAAGGGTCGAAGATAAGGAAAACAGTAGCATCC
AAACACGCGTAGATGATTATAAGAAGGATCTTCACCATAAAAAGCCATGTATGGAAAGTCGCCCT
TCA
Found at i:702647 original size:31 final size:31
Alignment explanation
Indices: 702609--702685 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
702599 ATAATGATGC
702609 TCTTGGCCATTAAGGTAAGTGATGTGGGGGT
1 TCTTGGCCATTAAGGTAAGTGATGTGGGGGT
702640 TCTTGGCCATTAAGGTAAGTGATGTGGGGGT
1 TCTTGGCCATTAAGGTAAGTGATGTGGGGGT
*
702671 TCTTGGCCATAAAGG
1 TCTTGGCCATTAAGG
702686 GACTCATATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.21, C:0.12, G:0.36, T:0.31
Consensus pattern (31 bp):
TCTTGGCCATTAAGGTAAGTGATGTGGGGGT
Found at i:716949 original size:19 final size:19
Alignment explanation
Indices: 716925--716962 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
716915 NNNNNNNNNN
716925 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
716944 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
716963 CCTGAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
ATATCTAAGATTGCATATC
Found at i:717524 original size:132 final size:132
Alignment explanation
Indices: 717289--718305 Score: 1696
Period size: 132 Copynumber: 7.7 Consensus size: 132
717279 TTGGACTTAC
* * * * *
717289 AATCTTCAACCTATTCCACTGCTGACTAGGG-AGATATG-ATTACTGTCTTCAATGTACTCCACT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCACT
* * *
717352 GTAACCACAGGGAGGTAAAATCCACCTTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAC
64 ATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT
717417 CTGA
129 CTGA
*
717421 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTATTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* * * * *
717486 AACCACAGGGAGGTAAAATCCGCCATCTTTGATTTGCTCCACTACTGCTTAGGGTGATTAGATCT
66 AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
717551 GA
131 GA
*
717553 AATCTTCAATCTATTCCACTGTTGTTCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
*
717618 AACCATAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
717683 GA
131 GA
* *
717685 AATCTTCAATCTATTCCACTGTTGTCCAAGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
*
717750 AACCATAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
717815 GA
131 GA
*
717817 AATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
*
717882 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
717947 GA
131 GA
* * * *
717949 AATCTTCAATCTATTCCACTGTTGCCCAAGGAAGTAGAATTGCTGGGTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
*
718014 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
718079 GA
131 GA
*
718081 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTAGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* *
718146 AACCATAGGGAGGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
718211 GA
131 GA
* * *
718213 AATCTTCAATCTATTCCACTGTTGCCCAAGGAAGTAGAATTACTAGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
* *
718278 AACCATAGGGAGGTAAAATCTACCATCT
66 AACCACAGGGAGGTAAAATCCACCATCT
718306 CGTCATCTTC
Statistics
Matches: 840, Mismatches: 43, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
131 1 0.00
132 837 1.00
133 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
AACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
GA
Found at i:719861 original size:6 final size:6
Alignment explanation
Indices: 719850--719895 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
719840 CCCTGGTAGA
719850 TTTTGT TTTTGT TTTTGT TTTT-T TTTTGT TTTT-T TGTTT-T TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T-TTTGT TTTTGT
719896 CATCCCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:719875 original size:17 final size:16
Alignment explanation
Indices: 719850--719895 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
719840 CCCTGGTAGA
*
719850 TTTTGTTTTTGTTTTT
1 TTTTTTTTTTGTTTTT
719866 GTTTTTTTTTTGTTTTT
1 -TTTTTTTTTTGTTTTT
719883 TTGTTTTTTTTGT
1 TT-TTTTTTTTGT
719896 CATCCCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 2 0.07
17 25 0.93
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTTGTTTTT
Found at i:719881 original size:8 final size:8
Alignment explanation
Indices: 719855--719892 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
719845 GTAGATTTTG
719855 TTTTTGTT
1 TTTTTGTT
*
719863 TTTGTTTTT
1 TTT-TTGTT
719872 TTTTTGTT
1 TTTTTGTT
719880 TTTTTGTT
1 TTTTTGTT
719888 TTTTT
1 TTTTT
719893 TGTCATCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTGTT
Found at i:724345 original size:19 final size:19
Alignment explanation
Indices: 724321--724358 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
724311 NNNNNNNNNN
724321 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
724340 ATATCTAAGATTGCATATC
1 ATATCTAAGATTGCATATC
724359 CCTGAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
ATATCTAAGATTGCATATC
Found at i:736628 original size:16 final size:16
Alignment explanation
Indices: 736607--736647 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
736597 AGAAAAAAAA
736607 TATAATTAATTTTAAT
1 TATAATTAATTTTAAT
736623 TATAATTAATTTTAAT
1 TATAATTAATTTTAAT
736639 TATAATTAA
1 TATAATTAA
736648 ATAAACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATAATTAATTTTAAT
Found at i:739007 original size:26 final size:26
Alignment explanation
Indices: 738978--739030 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
738968 GTTATAAAAA
738978 AAAGACTATTTATAAGCTAAATTCGT
1 AAAGACTATTTATAAGCTAAATTCGT
739004 AAAGACTATTTATAAGCTAAATTCGT
1 AAAGACTATTTATAAGCTAAATTCGT
739030 A
1 A
739031 GGTCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (26 bp):
AAAGACTATTTATAAGCTAAATTCGT
Found at i:739085 original size:24 final size:24
Alignment explanation
Indices: 739041--739086 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
739031 GGTCAAAAAA
* **
739041 ATTATGCTAATAAATGTTAAATAT
1 ATTATACTAATAAATACTAAATAT
739065 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACTAAAT
739087 CTTCTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATAT
Found at i:741037 original size:24 final size:24
Alignment explanation
Indices: 741009--741061 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
740999 ATTTGTAGGT
* * *
741009 TAAATAAATTGTGCTAATAAATTC
1 TAAATAAATTATACTAATAAATAC
*
741033 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
741057 TAAAT
1 TAAAT
741062 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:742758 original size:20 final size:22
Alignment explanation
Indices: 742733--742772 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
742723 TCTTGACTTT
742733 AAAATTG-A-GTTTTAGTTATG
1 AAAATTGAATGTTTTAGTTATG
742753 AAAATTGAATGTTTTAGTTA
1 AAAATTGAATGTTTTAGTTA
742773 AAACCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (22 bp):
AAAATTGAATGTTTTAGTTATG
Found at i:743515 original size:36 final size:36
Alignment explanation
Indices: 743475--743552 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
743465 ATGATGAATG
* * *
743475 ATGTGAAAGTGAATATGAGGGTGTGTTGTTCATGCC
1 ATGTGAAAGTAAATATGAGGGTATGTTATTCATGCC
* *
743511 ATGTGACAGTAAATATGTGGGTATGTTATTCATGCC
1 ATGTGAAAGTAAATATGAGGGTATGTTATTCATGCC
743547 ATGTGA
1 ATGTGA
743553 TAGTCTTTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.09, G:0.29, T:0.35
Consensus pattern (36 bp):
ATGTGAAAGTAAATATGAGGGTATGTTATTCATGCC
Found at i:749886 original size:6 final size:6
Alignment explanation
Indices: 749871--749911 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
749861 TTGTGTAAAT
*
749871 ATAATA ATAATG ATAATG ATAATG ATAATG ATAATG ATAAT
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAAT
749912 TAGAAATCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (6 bp):
ATAATG
Found at i:760483 original size:27 final size:27
Alignment explanation
Indices: 760444--760496 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
760434 TGGCATCGTA
*
760444 GAATAGTCCAACAGGACATTAAACACG
1 GAATAGTCCAACAGGACAGTAAACACG
* * *
760471 GAATATTCTAACAGGATAGTAAACAC
1 GAATAGTCCAACAGGACAGTAAACAC
760497 AAGGATTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (27 bp):
GAATAGTCCAACAGGACAGTAAACACG
Found at i:774226 original size:29 final size:29
Alignment explanation
Indices: 774193--774252 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
774183 TTCGAAGAGG
*
774193 AACCTGTCCAAATCTTGGAACATGATGTT
1 AACCTGTCCAAATCTTGGAACATGATCTT
* *
774222 AACCTGTCCAGATCTTGTAACATGATCTT
1 AACCTGTCCAAATCTTGGAACATGATCTT
774251 AA
1 AA
774253 GGTACTAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (29 bp):
AACCTGTCCAAATCTTGGAACATGATCTT
Found at i:778060 original size:15 final size:14
Alignment explanation
Indices: 778036--778066 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
778026 ATCGTAATTT
778036 AATAAATAAATTAA
1 AATAAATAAATTAA
778050 AATAAATTAAATTAA
1 AATAAA-TAAATTAA
778065 AA
1 AA
778067 GATGATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAATAAATTAA
Found at i:782362 original size:19 final size:19
Alignment explanation
Indices: 782314--782380 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
782304 CTCTCAACAA
* *
782314 AAAATACAAAATAATTTTC
1 AAAATTCAAAATAATTTTT
782333 AAAAGTTCAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
782353 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
*
782371 AAAATCCAAA
1 AAAATTCAAA
782381 TTTTATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 14 0.33
19 12 0.28
20 17 0.40
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:782385 original size:16 final size:17
Alignment explanation
Indices: 782346--782387 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
782336 AGTTCAAAAT
782346 AATTTT-TAAAATTCAA
1 AATTTTATAAAATTCAA
*
782362 AATATTTATAAAA-TCCA
1 AAT-TTTATAAAATTCAA
782379 AATTTTATA
1 AATTTTATA
782388 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTTATAAAATTCAA
Found at i:784086 original size:44 final size:43
Alignment explanation
Indices: 784037--784140 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
784027 TAAAATTAGA
* * *
784037 ATAACTTTTATTTCATTCTAATTATTTGTAAATGTATTATTACC
1 ATAACTTTTATTTCATTATAATTATGT-TAAATGTATAATTACC
* ** *
784081 ATAACTTCTATTAAATTATAATTATGTTAAATGTATAATTATC
1 ATAACTTTTATTTCATTATAATTATGTTAAATGTATAATTACC
*
784124 ACAACTATTTTATTTCA
1 ATAAC--TTTTATTTCA
784141 ACTTTTTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 18 0.38
44 22 0.47
45 7 0.15
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (43 bp):
ATAACTTTTATTTCATTATAATTATGTTAAATGTATAATTACC
Found at i:784117 original size:17 final size:16
Alignment explanation
Indices: 784091--784122 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
784081 ATAACTTCTA
784091 TTAAATTATAATTATG
1 TTAAATTATAATTATG
784107 TTAAATGTATAATTAT
1 TTAAAT-TATAATTAT
784123 CACAACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAATTATAATTATG
Found at i:787488 original size:24 final size:23
Alignment explanation
Indices: 787455--787501 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
787445 ATAATTTTAA
787455 TTTTTCTTTTCTTTTAACTTTCC
1 TTTTTCTTTTCTTTTAACTTTCC
*
787478 TTTTTCTTTTTCTTTTAGCTTTCC
1 TTTTTC-TTTTCTTTTAACTTTCC
787502 AGAACGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTCTTTTCTTTTAACTTTCC
Found at i:792906 original size:42 final size:42
Alignment explanation
Indices: 792841--792939 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
792831 TACTTCCACG
* * * *
792841 TAAGTGCATCATCAGATGTATCGAAGTAATTATATTGGCACA
1 TAAGTGCATCATCAGATGAATCGAAGCAAATATACTGGCACA
792883 TAAGTGCATCATCAGA-GAAATCGAAGCAAATATACTGGCACA
1 TAAGTGCATCATCAGATG-AATCGAAGCAAATATACTGGCACA
792925 TAAGTGCATCATCAG
1 TAAGTGCATCATCAG
792940 CTATACTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.02
42 51 0.98
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (42 bp):
TAAGTGCATCATCAGATGAATCGAAGCAAATATACTGGCACA
Found at i:793046 original size:8 final size:8
Alignment explanation
Indices: 793033--793062 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
793023 CTCAATTTAA
793033 CATCATTT
1 CATCATTT
793041 CATCATTT
1 CATCATTT
793049 CATCATTT
1 CATCATTT
793057 CATCAT
1 CATCAT
793063 ATAATGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (8 bp):
CATCATTT
Found at i:793984 original size:21 final size:21
Alignment explanation
Indices: 793946--793985 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
793936 GTTTAGTTAA
*
793946 CTTAATTTAATCATATTTTAT
1 CTTAATTTAATCAAATTTTAT
793967 CTTAA-TTAATCACAATTTT
1 CTTAATTTAATCA-AATTTT
793986 TTAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (21 bp):
CTTAATTTAATCAAATTTTAT
Found at i:800348 original size:125 final size:128
Alignment explanation
Indices: 800166--800420 Score: 444
Period size: 125 Copynumber: 2.0 Consensus size: 128
800156 ACATAATTGT
800166 AAAAGATCATATTCAAACATAAGAAAGTTTATAAAATCCTATCTTCAATTCAATTCAAGCATTTG
1 AAAAGATCATATTCAAACATAAGAAAGTTTATAAAATCCTATCTTCAATTCAATTCAAGCATTTG
* *
800231 TAAATTGTATGCGCACACATATATT-CATATATATA-T-CTACTTAACTAAATTTAATACAAA
66 TAAATTGTATGCACACACATATATTACATATATATATTAATACTTAACTAAATTTAATACAAA
* *
800291 AAAAGATCATATTCAAACATAAGAGAGTTTATGAAATCCTATCTTCAATTCAATTCAAGCATTTG
1 AAAAGATCATATTCAAACATAAGAAAGTTTATAAAATCCTATCTTCAATTCAATTCAAGCATTTG
800356 TAAATTGTATGCACACACATATATTCACATATATATATTAATACTTAACTAAATTTAATACAAA
66 TAAATTGTATGCACACACATATATT-ACATATATATATTAATACTTAACTAAATTTAATACAAA
800420 A
1 A
800421 CTTTACATAT
Statistics
Matches: 122, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
125 87 0.71
127 10 0.08
128 1 0.01
129 24 0.20
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (128 bp):
AAAAGATCATATTCAAACATAAGAAAGTTTATAAAATCCTATCTTCAATTCAATTCAAGCATTTG
TAAATTGTATGCACACACATATATTACATATATATATTAATACTTAACTAAATTTAATACAAA
Found at i:802429 original size:134 final size:134
Alignment explanation
Indices: 802188--802481 Score: 360
Period size: 134 Copynumber: 2.2 Consensus size: 134
802178 GTTATAACCA
* * * * * * *
802188 AAATACCTCCATAGGATAAAATAATCGAAATACCCCTATAGGGTAGAATGACTGAAATACCTCCA
1 AAATACCCCCATAGGGTAAAATGACCGAAACA-CCCTATAAGGTAAAATGACTGAAATACCTCCA
* **
802253 TAAGGTAAAATGACCGAAATACCCGCATAAGGTAGAATGACCGAAATACCCTTATAAGATAGAAT
65 TAAGGTAAAATGACCGAAATACCCGCATAAGGTAAAATGACCGAAATACCCCAATAAGATAGAAT
*
802318 GACTG
130 GACCG
* *
802323 AAATACCCCTATAGGGTAGAATGACCGAAACACCCTATAAGGTAAAATGA-TCGAAATACC-CCT
1 AAATACCCCCATAGGGTAAAATGACCGAAACACCCTATAAGGTAAAATGACT-GAAATACCTCC-
** * ** *
802386 ATGGGGTAAAATGACCGAAATACCC-CTATAGGGTAAAATGACCGAAATACCCCAATGGGGTAGA
64 ATAAGGTAAAATGACCGAAATACCCGC-ATAAGGTAAAATGACCGAAATACCCCAATAAGATAGA
802450 ATGACCG
128 ATGACCG
802457 AAATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
802482 TGTTATGGAT
Statistics
Matches: 135, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
133 4 0.03
134 106 0.79
135 25 0.19
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (134 bp):
AAATACCCCCATAGGGTAAAATGACCGAAACACCCTATAAGGTAAAATGACTGAAATACCTCCAT
AAGGTAAAATGACCGAAATACCCGCATAAGGTAAAATGACCGAAATACCCCAATAAGATAGAATG
ACCG
Found at i:802479 original size:27 final size:27
Alignment explanation
Indices: 802188--802481 Score: 335
Period size: 27 Copynumber: 10.9 Consensus size: 27
802178 GTTATAACCA
* * *
802188 AAATACCTCC-ATAGGATAAAATAATCG
1 AAATACC-CCTATAGGGTAAAATGACCG
* *
802215 AAATACCCCTATAGGGTAGAATGACTG
1 AAATACCCCTATAGGGTAAAATGACCG
*
802242 AAATACCTCC-ATAAGGTAAAATGACCG
1 AAATACC-CCTATAGGGTAAAATGACCG
* *
802269 AAATACCCGC-ATAAGGTAGAATGACCG
1 AAATACCC-CTATAGGGTAAAATGACCG
* * * * *
802296 AAATACCCTTATAAGATAGAATGACTG
1 AAATACCCCTATAGGGTAAAATGACCG
*
802323 AAATACCCCTATAGGGTAGAATGACCG
1 AAATACCCCTATAGGGTAAAATGACCG
* * *
802350 AAACA-CCCTATAAGGTAAAATGATCG
1 AAATACCCCTATAGGGTAAAATGACCG
*
802376 AAATACCCCTATGGGGTAAAATGACCG
1 AAATACCCCTATAGGGTAAAATGACCG
802403 AAATACCCCTATAGGGTAAAATGACCG
1 AAATACCCCTATAGGGTAAAATGACCG
* * *
802430 AAATACCCCAATGGGGTAGAATGACCG
1 AAATACCCCTATAGGGTAAAATGACCG
*
802457 AAATACCCCCATAGGGTAAAATGAC
1 AAATACCCCTATAGGGTAAAATGAC
802482 TGTTATGGAT
Statistics
Matches: 231, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
26 25 0.11
27 204 0.88
28 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATACCCCTATAGGGTAAAATGACCG
Found at i:805464 original size:44 final size:45
Alignment explanation
Indices: 805399--805528 Score: 176
Period size: 44 Copynumber: 2.9 Consensus size: 45
805389 ATATTGATAT
*
805399 ATTAGCTCTTCTAGAGCTTTCAACTAATTTTATACTA-CAAAATA
1 ATTAGCTCTTCTAGAGTTTTCAACTAATTTTATACTAGCAAAATA
805443 ATTAGCTCTTCTAGAGTTTTCAACTAATTTTGA-ACTAGC-AAATA
1 ATTAGCTCTTCTAGAGTTTTCAACTAATTTT-ATACTAGCAAAATA
* * * * *
805487 ATTAGCTCTTTTAAAATTTTCAACTAATTTTGTACTATCAAA
1 ATTAGCTCTTCTAGAGTTTTCAACTAATTTTATACTAGCAAA
805529 TATTACATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 72 0.95
45 4 0.05
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (45 bp):
ATTAGCTCTTCTAGAGTTTTCAACTAATTTTATACTAGCAAAATA
Found at i:807148 original size:15 final size:14
Alignment explanation
Indices: 807120--807146 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
807110 TATTATTACC
807120 TTTTTAAATATTTA
1 TTTTTAAATATTTA
807134 TTTTTAAATATTT
1 TTTTTAAATATTT
807147 TACCATACTC
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):
TTTTTAAATATTTA
Found at i:808670 original size:31 final size:30
Alignment explanation
Indices: 808635--808697 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
808625 CTTTGAGTTC
808635 CACCATATATTATTACGTAT-AAGTTTTACTT
1 CACCATATATTATTACGTATGAA-TTTTA-TT
* *
808666 CACCATGTATTATTATGTATGAATTTTATT
1 CACCATATATTATTACGTATGAATTTTATT
808696 CA
1 CA
808698 ATTAATCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 23 0.79
32 2 0.07
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (30 bp):
CACCATATATTATTACGTATGAATTTTATT
Found at i:809129 original size:15 final size:14
Alignment explanation
Indices: 809087--809132 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
809077 TATGATGATA
809087 ATTTTTTTT--ATT
1 ATTTTTTTTGGATT
**
809099 ATTTTTTTTGTTTT
1 ATTTTTTTTGGATT
809113 ATTTTTTATTGGATT
1 ATTTTTT-TTGGATT
809128 ATTTT
1 ATTTT
809133 GCTTCTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 9 0.32
14 9 0.32
15 10 0.36
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
ATTTTTTTTGGATT
Found at i:810352 original size:3 final size:3
Alignment explanation
Indices: 810344--810388 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
810334 ACAAATTTCA
* *
810344 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAAT TAT TAT CAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TA
810389 GTTTTATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:810450 original size:17 final size:16
Alignment explanation
Indices: 810419--810452 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
810409 TATTCGTTAG
*
810419 TTTTGTTTTTTTTTAT
1 TTTTATTTTTTTTTAT
810435 TTTTATTTTTTATTTAT
1 TTTTATTTTTT-TTTAT
810452 T
1 T
810453 CTATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTATTTTTTTTTAT
Found at i:815230 original size:7 final size:8
Alignment explanation
Indices: 815211--815240 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
815201 AGACTCAAAA
815211 AAAAAATC
1 AAAAAATC
815219 AAAAAATC
1 AAAAAATC
815227 AAAAAATC
1 AAAAAATC
815235 AAAAAA
1 AAAAAA
815241 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATC
Done.